From 5ed24b330eaac2aea7f35e3071f88ab9543d6c6b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 23 Aug 2020 21:46:18 -0400 Subject: [PATCH 0001/1217] add preliminary support for testing pair styles in the GPU package --- unittest/force-styles/test_pair_style.cpp | 115 +++++++++++++++++++++- 1 file changed, 114 insertions(+), 1 deletion(-) diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index 2cc39f712d..3d45c2075a 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -109,7 +109,6 @@ LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool new } else { command("variable newton_pair index off"); } - command("variable input_dir index " + INPUT_FOLDER); for (auto &pre_command : cfg.pre_commands) { @@ -124,6 +123,8 @@ LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool new for (auto &pair_coeff : cfg.pair_coeff) { command("pair_coeff " + pair_coeff); } + command("pair_modify table 0"); + command("pair_modify table/disp 0"); for (auto &post_command : cfg.post_commands) { command(post_command); @@ -798,6 +799,118 @@ TEST(PairStyle, omp) if (!verbose) ::testing::internal::GetCapturedStdout(); }; +TEST(PairStyle, gpu) +{ + if (!LAMMPS::is_installed_pkg("GPU")) GTEST_SKIP(); + const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf", "gpu"}; + + char **argv = (char **)args; + int argc = sizeof(args) / sizeof(char *); + + ::testing::internal::CaptureStdout(); + LAMMPS *lmp = init_lammps(argc, argv, test_config, false); + + std::string output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + + if (!lmp) { + std::cerr << "One or more prerequisite styles with /gpu suffix\n" + "are not available in this LAMMPS configuration:\n"; + for (auto &prerequisite : test_config.prerequisites) { + std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n"; + } + GTEST_SKIP(); + } + + EXPECT_THAT(output, StartsWith("LAMMPS (")); + EXPECT_THAT(output, HasSubstr("Loop time")); + + // abort if running in parallel and not all atoms are local + const int nlocal = lmp->atom->nlocal; + ASSERT_EQ(lmp->atom->natoms, nlocal); + + // skip over tests using tabulated coulomb + if ((lmp->force->pair->ncoultablebits > 0) || (lmp->force->pair->ndisptablebits > 0)) { + if (!verbose) ::testing::internal::CaptureStdout(); + cleanup_lammps(lmp, test_config); + if (!verbose) ::testing::internal::GetCapturedStdout(); + GTEST_SKIP(); + } + + // relax error a bit for GPU package + double epsilon = 7.5 * test_config.epsilon; + // relax test precision when using pppm and single precision FFTs +#if defined(FFT_SINGLE) + if (lmp->force->kspace && lmp->force->kspace->compute_flag) + if (utils::strmatch(lmp->force->kspace_style, "^pppm")) epsilon *= 2.0e8; +#endif + const std::vector &f_ref = test_config.init_forces; + const std::vector &f_run = test_config.run_forces; + ErrorStats stats; + + auto f = lmp->atom->f; + auto tag = lmp->atom->tag; + stats.reset(); + for (int i = 0; i < nlocal; ++i) { + EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon); + EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon); + EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon); + } + if (print_stats) std::cerr << "init_forces stats, newton off:" << stats << std::endl; + + auto pair = lmp->force->pair; + auto stress = pair->virial; + stats.reset(); + EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, 10 * epsilon); + if (print_stats) std::cerr << "init_stress stats, newton off:" << stats << std::endl; + + stats.reset(); + EXPECT_FP_LE_WITH_EPS(pair->eng_vdwl, test_config.init_vdwl, epsilon); + EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.init_coul, epsilon); + if (print_stats) std::cerr << "init_energy stats, newton off:" << stats << std::endl; + + if (!verbose) ::testing::internal::CaptureStdout(); + run_lammps(lmp); + if (!verbose) ::testing::internal::GetCapturedStdout(); + + f = lmp->atom->f; + tag = lmp->atom->tag; + stats.reset(); + for (int i = 0; i < nlocal; ++i) { + EXPECT_FP_LE_WITH_EPS(f[i][0], f_run[tag[i]].x, 5 * epsilon); + EXPECT_FP_LE_WITH_EPS(f[i][1], f_run[tag[i]].y, 5 * epsilon); + EXPECT_FP_LE_WITH_EPS(f[i][2], f_run[tag[i]].z, 5 * epsilon); + } + if (print_stats) std::cerr << "run_forces stats, newton off:" << stats << std::endl; + + stress = pair->virial; + stats.reset(); + EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, 10 * epsilon); + EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, 10 * epsilon); + if (print_stats) std::cerr << "run_stress stats, newton off:" << stats << std::endl; + + stats.reset(); + auto id = lmp->modify->find_compute("sum"); + auto energy = lmp->modify->compute[id]->compute_scalar(); + EXPECT_FP_LE_WITH_EPS(pair->eng_vdwl, test_config.run_vdwl, epsilon); + EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.run_coul, epsilon); + EXPECT_FP_LE_WITH_EPS((pair->eng_vdwl + pair->eng_coul), energy, epsilon); + if (print_stats) std::cerr << "run_energy stats, newton off:" << stats << std::endl; + + if (!verbose) ::testing::internal::CaptureStdout(); + cleanup_lammps(lmp, test_config); + if (!verbose) ::testing::internal::GetCapturedStdout(); +}; + TEST(PairStyle, intel) { if (!LAMMPS::is_installed_pkg("USER-INTEL")) GTEST_SKIP(); From 13cf665712363469ef4fabab3afb20352bd6bc7e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 23 Aug 2020 21:47:17 -0400 Subject: [PATCH 0002/1217] update pair style unit test input files to be compatible with testing GPU package styles --- unittest/force-styles/tests/atomic-pair-atm.yaml | 2 +- unittest/force-styles/tests/atomic-pair-edip.yaml | 2 +- unittest/force-styles/tests/atomic-pair-meam_c.yaml | 2 +- unittest/force-styles/tests/atomic-pair-meam_spline.yaml | 2 +- unittest/force-styles/tests/atomic-pair-meam_sw_spline.yaml | 2 +- unittest/force-styles/tests/atomic-pair-polymorphic_eam.yaml | 2 +- unittest/force-styles/tests/manybody-pair-airebo.yaml | 2 +- unittest/force-styles/tests/manybody-pair-airebo_00.yaml | 2 +- unittest/force-styles/tests/manybody-pair-airebo_m.yaml | 2 +- unittest/force-styles/tests/manybody-pair-airebo_m00.yaml | 2 +- unittest/force-styles/tests/manybody-pair-bop.yaml | 2 +- unittest/force-styles/tests/manybody-pair-bop_save.yaml | 2 +- unittest/force-styles/tests/manybody-pair-comb.yaml | 2 +- unittest/force-styles/tests/manybody-pair-comb3.yaml | 2 +- unittest/force-styles/tests/manybody-pair-extep.yaml | 2 +- unittest/force-styles/tests/manybody-pair-gw.yaml | 2 +- unittest/force-styles/tests/manybody-pair-gw_zbl.yaml | 2 +- unittest/force-styles/tests/manybody-pair-lcbop.yaml | 2 +- unittest/force-styles/tests/manybody-pair-meam_c.yaml | 2 +- unittest/force-styles/tests/manybody-pair-mliap_snap.yaml | 2 +- .../force-styles/tests/manybody-pair-mliap_snap_chem.yaml | 2 +- unittest/force-styles/tests/manybody-pair-nb3b_harmonic.yaml | 2 +- unittest/force-styles/tests/manybody-pair-polymorphic_sw.yaml | 2 +- .../force-styles/tests/manybody-pair-polymorphic_tersoff.yaml | 2 +- unittest/force-styles/tests/manybody-pair-rebo.yaml | 2 +- unittest/force-styles/tests/manybody-pair-snap.yaml | 2 +- unittest/force-styles/tests/manybody-pair-snap_chem.yaml | 2 +- unittest/force-styles/tests/manybody-pair-sw-multi.yaml | 2 +- unittest/force-styles/tests/manybody-pair-sw.yaml | 2 +- unittest/force-styles/tests/manybody-pair-tersoff.yaml | 2 +- unittest/force-styles/tests/manybody-pair-tersoff_mod.yaml | 2 +- unittest/force-styles/tests/manybody-pair-tersoff_mod_c.yaml | 2 +- unittest/force-styles/tests/manybody-pair-tersoff_table.yaml | 2 +- unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml | 2 +- unittest/force-styles/tests/manybody-pair-vashishta.yaml | 2 +- .../force-styles/tests/manybody-pair-vashishta_table.yaml | 2 +- unittest/force-styles/tests/manybody-pair_edip_multi.yaml | 2 +- unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml | 2 +- unittest/force-styles/tests/mol-pair-buck.yaml | 2 +- unittest/force-styles/tests/mol-pair-buck_coul_long.yaml | 2 +- unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml | 2 +- unittest/force-styles/tests/mol-pair-coul_streitz_long.yaml | 2 +- unittest/force-styles/tests/mol-pair-coul_streitz_wolf.yaml | 2 +- unittest/force-styles/tests/mol-pair-e3b.yaml | 2 +- unittest/force-styles/tests/mol-pair-lj_cubic.yaml | 2 +- unittest/force-styles/tests/mol-pair-lj_cut_tip4p_cut.yaml | 2 +- unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml | 2 +- .../force-styles/tests/mol-pair-lj_cut_tip4p_long_soft.yaml | 2 +- unittest/force-styles/tests/mol-pair-lj_cut_tip4p_table.yaml | 2 +- unittest/force-styles/tests/mol-pair-lj_long_tip4p_long.yaml | 2 +- .../force-styles/tests/mol-pair-lj_table_tip4p_table.yaml | 2 +- unittest/force-styles/tests/mol-pair-tip4p_cut.yaml | 4 ++-- unittest/force-styles/tests/mol-pair-tip4p_long.yaml | 2 +- unittest/force-styles/tests/mol-pair-tip4p_long_soft.yaml | 2 +- unittest/force-styles/tests/mol-pair-tip4p_table.yaml | 2 +- unittest/force-styles/tests/mol-pair-zbl.yaml | 2 +- 56 files changed, 57 insertions(+), 57 deletions(-) diff --git a/unittest/force-styles/tests/atomic-pair-atm.yaml b/unittest/force-styles/tests/atomic-pair-atm.yaml index 3297ae8ba6..dc0db1e37d 100644 --- a/unittest/force-styles/tests/atomic-pair-atm.yaml +++ b/unittest/force-styles/tests/atomic-pair-atm.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair atm pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.metal pair_style: atm 12.0 5.0 diff --git a/unittest/force-styles/tests/atomic-pair-edip.yaml b/unittest/force-styles/tests/atomic-pair-edip.yaml index c46742a30c..f7a16be94d 100644 --- a/unittest/force-styles/tests/atomic-pair-edip.yaml +++ b/unittest/force-styles/tests/atomic-pair-edip.yaml @@ -7,7 +7,7 @@ prerequisites: ! | pre_commands: ! | echo screen variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" atom_modify map array units metal lattice diamond 5.43 diff --git a/unittest/force-styles/tests/atomic-pair-meam_c.yaml b/unittest/force-styles/tests/atomic-pair-meam_c.yaml index 7e5e04f258..a254155a2b 100644 --- a/unittest/force-styles/tests/atomic-pair-meam_c.yaml +++ b/unittest/force-styles/tests/atomic-pair-meam_c.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair meam/c pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.metal pair_style: meam/c diff --git a/unittest/force-styles/tests/atomic-pair-meam_spline.yaml b/unittest/force-styles/tests/atomic-pair-meam_spline.yaml index 26b41e3246..e395d8b1b4 100644 --- a/unittest/force-styles/tests/atomic-pair-meam_spline.yaml +++ b/unittest/force-styles/tests/atomic-pair-meam_spline.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair meam/spline pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.metal pair_style: meam/spline diff --git a/unittest/force-styles/tests/atomic-pair-meam_sw_spline.yaml b/unittest/force-styles/tests/atomic-pair-meam_sw_spline.yaml index 255a424c9e..e8c744851b 100644 --- a/unittest/force-styles/tests/atomic-pair-meam_sw_spline.yaml +++ b/unittest/force-styles/tests/atomic-pair-meam_sw_spline.yaml @@ -7,7 +7,7 @@ prerequisites: ! | pre_commands: ! | echo screen variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" atom_modify map array units metal lattice diamond 5.43 diff --git a/unittest/force-styles/tests/atomic-pair-polymorphic_eam.yaml b/unittest/force-styles/tests/atomic-pair-polymorphic_eam.yaml index 4ac11509e6..635c57742c 100644 --- a/unittest/force-styles/tests/atomic-pair-polymorphic_eam.yaml +++ b/unittest/force-styles/tests/atomic-pair-polymorphic_eam.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair polymorphic pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | change_box all x final 0 18 y final 0 18 z final 0 18 input_file: in.metal diff --git a/unittest/force-styles/tests/manybody-pair-airebo.yaml b/unittest/force-styles/tests/manybody-pair-airebo.yaml index 57c71a6325..1dfecf47f8 100644 --- a/unittest/force-styles/tests/manybody-pair-airebo.yaml +++ b/unittest/force-styles/tests/manybody-pair-airebo.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair airebo pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.airebo pair_style: airebo 3.0 1 1 diff --git a/unittest/force-styles/tests/manybody-pair-airebo_00.yaml b/unittest/force-styles/tests/manybody-pair-airebo_00.yaml index 30fe7fde4e..408ed51ce0 100644 --- a/unittest/force-styles/tests/manybody-pair-airebo_00.yaml +++ b/unittest/force-styles/tests/manybody-pair-airebo_00.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair airebo pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.airebo pair_style: airebo 3.0 0 0 diff --git a/unittest/force-styles/tests/manybody-pair-airebo_m.yaml b/unittest/force-styles/tests/manybody-pair-airebo_m.yaml index e5d4a97ec1..f57e9add95 100644 --- a/unittest/force-styles/tests/manybody-pair-airebo_m.yaml +++ b/unittest/force-styles/tests/manybody-pair-airebo_m.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair airebo/morse pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.airebo pair_style: airebo/morse 3.0 1 1 diff --git a/unittest/force-styles/tests/manybody-pair-airebo_m00.yaml b/unittest/force-styles/tests/manybody-pair-airebo_m00.yaml index 50325ee197..770ee99d98 100644 --- a/unittest/force-styles/tests/manybody-pair-airebo_m00.yaml +++ b/unittest/force-styles/tests/manybody-pair-airebo_m00.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair airebo/morse pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.airebo pair_style: airebo/morse 3.0 0 0 diff --git a/unittest/force-styles/tests/manybody-pair-bop.yaml b/unittest/force-styles/tests/manybody-pair-bop.yaml index 14ed8865a0..b750d77d8c 100644 --- a/unittest/force-styles/tests/manybody-pair-bop.yaml +++ b/unittest/force-styles/tests/manybody-pair-bop.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair bop pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" comm_modify cutoff 14.0 post_commands: ! | change_box all x final 0 14 y final 0 14 z final 0 14 diff --git a/unittest/force-styles/tests/manybody-pair-bop_save.yaml b/unittest/force-styles/tests/manybody-pair-bop_save.yaml index 72a2351f5d..c3102bcdcc 100644 --- a/unittest/force-styles/tests/manybody-pair-bop_save.yaml +++ b/unittest/force-styles/tests/manybody-pair-bop_save.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair bop pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" comm_modify cutoff 14.0 post_commands: ! | change_box all x final 0 14 y final 0 14 z final 0 14 diff --git a/unittest/force-styles/tests/manybody-pair-comb.yaml b/unittest/force-styles/tests/manybody-pair-comb.yaml index 58de3040c3..6a18ab6733 100644 --- a/unittest/force-styles/tests/manybody-pair-comb.yaml +++ b/unittest/force-styles/tests/manybody-pair-comb.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair comb pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody-charge pair_style: comb diff --git a/unittest/force-styles/tests/manybody-pair-comb3.yaml b/unittest/force-styles/tests/manybody-pair-comb3.yaml index 1d44d5e289..4b79f2b5b0 100644 --- a/unittest/force-styles/tests/manybody-pair-comb3.yaml +++ b/unittest/force-styles/tests/manybody-pair-comb3.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair comb3 pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody-charge pair_style: comb3 polar_off diff --git a/unittest/force-styles/tests/manybody-pair-extep.yaml b/unittest/force-styles/tests/manybody-pair-extep.yaml index 2bc3ad35a7..1a490a0120 100644 --- a/unittest/force-styles/tests/manybody-pair-extep.yaml +++ b/unittest/force-styles/tests/manybody-pair-extep.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair extep pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: extep diff --git a/unittest/force-styles/tests/manybody-pair-gw.yaml b/unittest/force-styles/tests/manybody-pair-gw.yaml index b9e284293e..b01e0221f3 100644 --- a/unittest/force-styles/tests/manybody-pair-gw.yaml +++ b/unittest/force-styles/tests/manybody-pair-gw.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair gw pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: gw diff --git a/unittest/force-styles/tests/manybody-pair-gw_zbl.yaml b/unittest/force-styles/tests/manybody-pair-gw_zbl.yaml index 7d9fd2460d..6c5c302770 100644 --- a/unittest/force-styles/tests/manybody-pair-gw_zbl.yaml +++ b/unittest/force-styles/tests/manybody-pair-gw_zbl.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair gw/zbl pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: gw/zbl diff --git a/unittest/force-styles/tests/manybody-pair-lcbop.yaml b/unittest/force-styles/tests/manybody-pair-lcbop.yaml index c666afd3ae..6e07460668 100644 --- a/unittest/force-styles/tests/manybody-pair-lcbop.yaml +++ b/unittest/force-styles/tests/manybody-pair-lcbop.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair lcbop pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: lcbop diff --git a/unittest/force-styles/tests/manybody-pair-meam_c.yaml b/unittest/force-styles/tests/manybody-pair-meam_c.yaml index 2f5051abad..23593c1cca 100644 --- a/unittest/force-styles/tests/manybody-pair-meam_c.yaml +++ b/unittest/force-styles/tests/manybody-pair-meam_c.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair meam/c pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: meam/c diff --git a/unittest/force-styles/tests/manybody-pair-mliap_snap.yaml b/unittest/force-styles/tests/manybody-pair-mliap_snap.yaml index a45d7a8f49..32927b9750 100644 --- a/unittest/force-styles/tests/manybody-pair-mliap_snap.yaml +++ b/unittest/force-styles/tests/manybody-pair-mliap_snap.yaml @@ -7,7 +7,7 @@ prerequisites: ! | pair zbl pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: hybrid/overlay zbl 4.0 4.8 mliap model linear Ta06A.mliap.model descriptor diff --git a/unittest/force-styles/tests/manybody-pair-mliap_snap_chem.yaml b/unittest/force-styles/tests/manybody-pair-mliap_snap_chem.yaml index e4719e6eb5..b5e6ca7b36 100644 --- a/unittest/force-styles/tests/manybody-pair-mliap_snap_chem.yaml +++ b/unittest/force-styles/tests/manybody-pair-mliap_snap_chem.yaml @@ -7,7 +7,7 @@ prerequisites: ! | pair zbl pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" variable zblz1 index 49 variable zblz2 index 15 post_commands: ! "" diff --git a/unittest/force-styles/tests/manybody-pair-nb3b_harmonic.yaml b/unittest/force-styles/tests/manybody-pair-nb3b_harmonic.yaml index bd33af6f16..c449e733ce 100644 --- a/unittest/force-styles/tests/manybody-pair-nb3b_harmonic.yaml +++ b/unittest/force-styles/tests/manybody-pair-nb3b_harmonic.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair nb3b/harmonic pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" variable units delete variable units index real post_commands: ! | diff --git a/unittest/force-styles/tests/manybody-pair-polymorphic_sw.yaml b/unittest/force-styles/tests/manybody-pair-polymorphic_sw.yaml index 2aee0ed5fb..ba10a03e94 100644 --- a/unittest/force-styles/tests/manybody-pair-polymorphic_sw.yaml +++ b/unittest/force-styles/tests/manybody-pair-polymorphic_sw.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair polymorphic pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | change_box all x final 0 9.8 y final 0 9.8 z final 0 9.8 input_file: in.manybody diff --git a/unittest/force-styles/tests/manybody-pair-polymorphic_tersoff.yaml b/unittest/force-styles/tests/manybody-pair-polymorphic_tersoff.yaml index 2025068084..8f8ed15eeb 100644 --- a/unittest/force-styles/tests/manybody-pair-polymorphic_tersoff.yaml +++ b/unittest/force-styles/tests/manybody-pair-polymorphic_tersoff.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair polymorphic pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | change_box all x final 0 9.9 y final 0 9.9 z final 0 9.9 input_file: in.manybody diff --git a/unittest/force-styles/tests/manybody-pair-rebo.yaml b/unittest/force-styles/tests/manybody-pair-rebo.yaml index 6cc14a8259..94c442cc58 100644 --- a/unittest/force-styles/tests/manybody-pair-rebo.yaml +++ b/unittest/force-styles/tests/manybody-pair-rebo.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair rebo pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.airebo pair_style: rebo diff --git a/unittest/force-styles/tests/manybody-pair-snap.yaml b/unittest/force-styles/tests/manybody-pair-snap.yaml index 2dc2b6a568..e1d466f1f0 100644 --- a/unittest/force-styles/tests/manybody-pair-snap.yaml +++ b/unittest/force-styles/tests/manybody-pair-snap.yaml @@ -7,7 +7,7 @@ prerequisites: ! | pair zbl pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: hybrid/overlay zbl 4.0 4.8 snap diff --git a/unittest/force-styles/tests/manybody-pair-snap_chem.yaml b/unittest/force-styles/tests/manybody-pair-snap_chem.yaml index 8e8c2c8f86..10098a64d9 100644 --- a/unittest/force-styles/tests/manybody-pair-snap_chem.yaml +++ b/unittest/force-styles/tests/manybody-pair-snap_chem.yaml @@ -7,7 +7,7 @@ prerequisites: ! | pair zbl pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: hybrid/overlay zbl 4.0 4.2 snap diff --git a/unittest/force-styles/tests/manybody-pair-sw-multi.yaml b/unittest/force-styles/tests/manybody-pair-sw-multi.yaml index 45d912c0c2..5152d63b2a 100644 --- a/unittest/force-styles/tests/manybody-pair-sw-multi.yaml +++ b/unittest/force-styles/tests/manybody-pair-sw-multi.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair sw pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: sw diff --git a/unittest/force-styles/tests/manybody-pair-sw.yaml b/unittest/force-styles/tests/manybody-pair-sw.yaml index 0d18a55a9d..f3744ec031 100644 --- a/unittest/force-styles/tests/manybody-pair-sw.yaml +++ b/unittest/force-styles/tests/manybody-pair-sw.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair sw pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: sw diff --git a/unittest/force-styles/tests/manybody-pair-tersoff.yaml b/unittest/force-styles/tests/manybody-pair-tersoff.yaml index b3f2e22f48..c3c6b39fd8 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair tersoff pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: tersoff diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_mod.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_mod.yaml index 6427c8f9fa..5f6655aeb1 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_mod.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_mod.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair tersoff/mod pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: tersoff/mod diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_mod_c.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_mod_c.yaml index f172c97895..e14866b11c 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_mod_c.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_mod_c.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair tersoff/mod/c pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: tersoff/mod/c diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_table.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_table.yaml index 3cb005cf46..36a30ac27b 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_table.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_table.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair tersoff/table pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: tersoff/table diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml index d11fed80ca..05808d5520 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair tersoff/zbl pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: tersoff/zbl diff --git a/unittest/force-styles/tests/manybody-pair-vashishta.yaml b/unittest/force-styles/tests/manybody-pair-vashishta.yaml index d0f2eb94ad..50baf7d7a0 100644 --- a/unittest/force-styles/tests/manybody-pair-vashishta.yaml +++ b/unittest/force-styles/tests/manybody-pair-vashishta.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair vashishta pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: vashishta diff --git a/unittest/force-styles/tests/manybody-pair-vashishta_table.yaml b/unittest/force-styles/tests/manybody-pair-vashishta_table.yaml index b04f710dac..7bf18c0058 100644 --- a/unittest/force-styles/tests/manybody-pair-vashishta_table.yaml +++ b/unittest/force-styles/tests/manybody-pair-vashishta_table.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair vashishta/table pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: vashishta/table 10000 0.2 diff --git a/unittest/force-styles/tests/manybody-pair_edip_multi.yaml b/unittest/force-styles/tests/manybody-pair_edip_multi.yaml index ae1200100b..5aa31dcc9e 100644 --- a/unittest/force-styles/tests/manybody-pair_edip_multi.yaml +++ b/unittest/force-styles/tests/manybody-pair_edip_multi.yaml @@ -6,7 +6,7 @@ prerequisites: ! | pair edip/multi pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody pair_style: edip/multi diff --git a/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml b/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml index bdb35df831..02bf840ad9 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml @@ -1,7 +1,7 @@ --- lammps_version: 21 Jul 2020 date_generated: Sat Aug 1 16:17:46 202 -epsilon: 5e-14 +epsilon: 7.5e-14 prerequisites: ! | atom full pair born/coul/dsf diff --git a/unittest/force-styles/tests/mol-pair-buck.yaml b/unittest/force-styles/tests/mol-pair-buck.yaml index 947e2e9755..562ff550a5 100644 --- a/unittest/force-styles/tests/mol-pair-buck.yaml +++ b/unittest/force-styles/tests/mol-pair-buck.yaml @@ -1,7 +1,7 @@ --- lammps_version: 21 Jul 2020 date_generated: Fri Jul 31 12:07:29 202 -epsilon: 5e-14 +epsilon: 7.5e-14 prerequisites: ! | atom full pair buck diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_long.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_long.yaml index f93f53861d..ed7db64343 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_long.yaml @@ -1,7 +1,7 @@ --- lammps_version: 21 Jul 2020 date_generated: Sat Aug 1 08:33:03 202 -epsilon: 5e-14 +epsilon: 5e-13 prerequisites: ! | atom full pair buck/coul/long diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml index 8082009c41..30891f3e60 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml @@ -1,7 +1,7 @@ --- lammps_version: 21 Jul 2020 date_generated: Sat Aug 1 08:36:45 202 -epsilon: 5e-14 +epsilon: 2.5e-13 prerequisites: ! | atom full pair buck/coul/msm diff --git a/unittest/force-styles/tests/mol-pair-coul_streitz_long.yaml b/unittest/force-styles/tests/mol-pair-coul_streitz_long.yaml index f37079d9ad..a0e6bbbe90 100644 --- a/unittest/force-styles/tests/mol-pair-coul_streitz_long.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_streitz_long.yaml @@ -8,7 +8,7 @@ prerequisites: ! | pre_commands: ! | variable units index metal variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | pair_modify mix arithmetic velocity all scale 100.0 diff --git a/unittest/force-styles/tests/mol-pair-coul_streitz_wolf.yaml b/unittest/force-styles/tests/mol-pair-coul_streitz_wolf.yaml index fcb8b91122..68f0a9c0a1 100644 --- a/unittest/force-styles/tests/mol-pair-coul_streitz_wolf.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_streitz_wolf.yaml @@ -8,7 +8,7 @@ prerequisites: ! | pre_commands: ! | variable units index metal variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | pair_modify mix arithmetic velocity all scale 100.0 diff --git a/unittest/force-styles/tests/mol-pair-e3b.yaml b/unittest/force-styles/tests/mol-pair-e3b.yaml index 961cd77784..342db5b02b 100644 --- a/unittest/force-styles/tests/mol-pair-e3b.yaml +++ b/unittest/force-styles/tests/mol-pair-e3b.yaml @@ -8,7 +8,7 @@ prerequisites: ! | pair e3b pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | pair_modify mix arithmetic input_file: in.fourmol diff --git a/unittest/force-styles/tests/mol-pair-lj_cubic.yaml b/unittest/force-styles/tests/mol-pair-lj_cubic.yaml index 3850747330..f7ac67a3a9 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cubic.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cubic.yaml @@ -1,7 +1,7 @@ --- lammps_version: 21 Jul 2020 date_generated: Sat Aug 1 13:39:00 202 -epsilon: 5e-14 +epsilon: 7.5e-14 prerequisites: ! | atom full pair lj/cubic diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_cut.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_cut.yaml index 3c550f4a7d..cccc9ba760 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_cut.yaml @@ -7,7 +7,7 @@ prerequisites: ! | pair lj/cut/tip4p/cut pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | pair_modify mix arithmetic input_file: in.fourmol diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml index 7b334554b3..820bef3fc3 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml @@ -8,7 +8,7 @@ prerequisites: ! | kspace pppm/tip4p pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | pair_modify mix arithmetic pair_modify table 0 diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long_soft.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long_soft.yaml index 254b45b510..f9fcfd8a40 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long_soft.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long_soft.yaml @@ -8,7 +8,7 @@ prerequisites: ! | kspace pppm/tip4p pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | pair_modify mix arithmetic pair_modify table 0 diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_table.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_table.yaml index cab2e7c3c1..40a342f24a 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_table.yaml @@ -8,7 +8,7 @@ prerequisites: ! | kspace pppm/tip4p pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | pair_modify mix arithmetic pair_modify table 16 diff --git a/unittest/force-styles/tests/mol-pair-lj_long_tip4p_long.yaml b/unittest/force-styles/tests/mol-pair-lj_long_tip4p_long.yaml index 6e7a91b1d4..b713dbfdd6 100644 --- a/unittest/force-styles/tests/mol-pair-lj_long_tip4p_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_long_tip4p_long.yaml @@ -8,7 +8,7 @@ prerequisites: ! | kspace pppm/disp/tip4p pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | pair_modify mix arithmetic pair_modify table 0 diff --git a/unittest/force-styles/tests/mol-pair-lj_table_tip4p_table.yaml b/unittest/force-styles/tests/mol-pair-lj_table_tip4p_table.yaml index 359f98d281..411716eb84 100644 --- a/unittest/force-styles/tests/mol-pair-lj_table_tip4p_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_table_tip4p_table.yaml @@ -8,7 +8,7 @@ prerequisites: ! | kspace pppm/disp/tip4p pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | pair_modify mix arithmetic pair_modify table 16 diff --git a/unittest/force-styles/tests/mol-pair-tip4p_cut.yaml b/unittest/force-styles/tests/mol-pair-tip4p_cut.yaml index 2d9e3c7666..8bf231754b 100644 --- a/unittest/force-styles/tests/mol-pair-tip4p_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-tip4p_cut.yaml @@ -1,13 +1,13 @@ --- lammps_version: 21 Jul 2020 date_generated: Thu Aug 6 16:52:44 202 -epsilon: 1e-14 +epsilon: 7.5e-13 prerequisites: ! | atom full pair tip4p/cut pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | pair_modify mix arithmetic input_file: in.fourmol diff --git a/unittest/force-styles/tests/mol-pair-tip4p_long.yaml b/unittest/force-styles/tests/mol-pair-tip4p_long.yaml index 9d96a981c2..a81c8caab3 100644 --- a/unittest/force-styles/tests/mol-pair-tip4p_long.yaml +++ b/unittest/force-styles/tests/mol-pair-tip4p_long.yaml @@ -7,7 +7,7 @@ prerequisites: ! | pair tip4p/long pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | pair_modify mix arithmetic pair_modify table 0 diff --git a/unittest/force-styles/tests/mol-pair-tip4p_long_soft.yaml b/unittest/force-styles/tests/mol-pair-tip4p_long_soft.yaml index c55d60adf9..156e60afdd 100644 --- a/unittest/force-styles/tests/mol-pair-tip4p_long_soft.yaml +++ b/unittest/force-styles/tests/mol-pair-tip4p_long_soft.yaml @@ -9,7 +9,7 @@ prerequisites: ! | pair lj/cut pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | pair_modify mix arithmetic pair_modify table 0 diff --git a/unittest/force-styles/tests/mol-pair-tip4p_table.yaml b/unittest/force-styles/tests/mol-pair-tip4p_table.yaml index 6dd612151f..83d7d6d289 100644 --- a/unittest/force-styles/tests/mol-pair-tip4p_table.yaml +++ b/unittest/force-styles/tests/mol-pair-tip4p_table.yaml @@ -7,7 +7,7 @@ prerequisites: ! | pair tip4p/long pre_commands: ! | variable newton_pair delete - variable newton_pair index on + if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! | pair_modify mix arithmetic pair_modify table 16 diff --git a/unittest/force-styles/tests/mol-pair-zbl.yaml b/unittest/force-styles/tests/mol-pair-zbl.yaml index 8aca114255..48046b9584 100644 --- a/unittest/force-styles/tests/mol-pair-zbl.yaml +++ b/unittest/force-styles/tests/mol-pair-zbl.yaml @@ -1,7 +1,7 @@ --- lammps_version: 21 Jul 2020 date_generated: Sat Aug 1 14:40:56 202 -epsilon: 1e-12 +epsilon: 2e-12 prerequisites: ! | atom full pair zbl From 5127071da27955a5e529bfaaf0ffaabc23aef142 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 26 Aug 2020 18:41:32 -0400 Subject: [PATCH 0003/1217] Fixes segfault due to uninitialized pointers --- src/KSPACE/pair_buck_coul_long.cpp | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp index a46424baf7..a63047ea9f 100644 --- a/src/KSPACE/pair_buck_coul_long.cpp +++ b/src/KSPACE/pair_buck_coul_long.cpp @@ -43,7 +43,17 @@ PairBuckCoulLong::PairBuckCoulLong(LAMMPS *lmp) : Pair(lmp) { ewaldflag = pppmflag = 1; writedata = 1; - ftable = NULL; + ftable = nullptr; + cut_lj = nullptr; + cut_ljsq = nullptr; + a = nullptr; + rho = nullptr; + c = nullptr; + rhoinv = nullptr; + buck1 = nullptr; + buck2 = nullptr; + offset = nullptr; + cut_respa = nullptr; } /* ---------------------------------------------------------------------- */ From 9b0c07f79781bfd418f01652b3d0be912f64550f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Aug 2020 19:06:29 -0400 Subject: [PATCH 0004/1217] remove undesired trailing whitespace --- .../force-styles/tests/mol-pair-born.yaml | 28 ++++++++--------- .../tests/mol-pair-born_coul_dsf.yaml | 28 ++++++++--------- .../tests/mol-pair-born_coul_long.yaml | 30 +++++++++---------- .../tests/mol-pair-born_coul_msm.yaml | 30 +++++++++---------- .../tests/mol-pair-born_coul_wolf.yaml | 28 ++++++++--------- .../force-styles/tests/mol-pair-morse.yaml | 30 +++++++++---------- 6 files changed, 87 insertions(+), 87 deletions(-) diff --git a/unittest/force-styles/tests/mol-pair-born.yaml b/unittest/force-styles/tests/mol-pair-born.yaml index ed7b5976b0..2323ddee17 100644 --- a/unittest/force-styles/tests/mol-pair-born.yaml +++ b/unittest/force-styles/tests/mol-pair-born.yaml @@ -10,20 +10,20 @@ post_commands: ! "" input_file: in.fourmol pair_style: born 8.0 pair_coeff: ! | - 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 - 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 - 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 - 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 - 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 - 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 - 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 - 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 - 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 - 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 - 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 - 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 - 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 - 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 + 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 + 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 + 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 + 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 + 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 + 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 + 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 + 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 extract: ! | a 2 diff --git a/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml b/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml index 02bf840ad9..cd6b6abab0 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml @@ -10,20 +10,20 @@ post_commands: ! "" input_file: in.fourmol pair_style: born/coul/dsf 0.25 8.0 pair_coeff: ! | - 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 - 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 - 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 - 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 - 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 - 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 - 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 - 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 - 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 - 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 - 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 - 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 - 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 - 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 + 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 + 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 + 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 + 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 + 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 + 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 + 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 + 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 extract: ! "" natoms: 29 diff --git a/unittest/force-styles/tests/mol-pair-born_coul_long.yaml b/unittest/force-styles/tests/mol-pair-born_coul_long.yaml index e45f7dc6b7..e35b4417d9 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_long.yaml @@ -15,21 +15,21 @@ post_commands: ! | input_file: in.fourmol pair_style: born/coul/long 8.0 pair_coeff: ! | - 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 - 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 - 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 - 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 - 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 - 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 - 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 - 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 - 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 - 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 - 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 - 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 - 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 - 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 - 5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 + 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 + 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 + 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 + 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 + 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 + 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 + 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 + 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 extract: ! | cut_coul 0 natoms: 29 diff --git a/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml index 779a79dd9f..a06da1edc5 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml @@ -16,21 +16,21 @@ post_commands: ! | input_file: in.fourmol pair_style: born/coul/msm 12.0 pair_coeff: ! | - 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 - 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 - 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 - 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 - 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 - 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 - 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 - 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 - 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 - 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 - 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 - 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 - 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 - 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 - 5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 + 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 + 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 + 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 + 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 + 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 + 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 + 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 + 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 extract: ! | cut_coul 0 natoms: 29 diff --git a/unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml b/unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml index 7d419e2da2..afaf63d7c3 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml @@ -10,20 +10,20 @@ post_commands: ! "" input_file: in.fourmol pair_style: born/coul/wolf 0.25 8.0 pair_coeff: ! | - 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 - 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 - 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 - 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 - 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 - 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 - 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 - 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 - 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 - 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 - 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 - 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 - 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 - 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 + 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 + 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 + 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 + 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 + 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 + 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 + 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 + 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 extract: ! "" natoms: 29 diff --git a/unittest/force-styles/tests/mol-pair-morse.yaml b/unittest/force-styles/tests/mol-pair-morse.yaml index 60e5f8736f..aae3f78199 100644 --- a/unittest/force-styles/tests/mol-pair-morse.yaml +++ b/unittest/force-styles/tests/mol-pair-morse.yaml @@ -10,21 +10,21 @@ post_commands: ! "" input_file: in.fourmol pair_style: morse 8.0 pair_coeff: ! | - 1 1 0.0202798941614106 2.78203488021395 2.725417159299 - 1 2 0.0101167811264648 3.9793050302425 1.90749569018897 - 1 3 0.0202934330695928 2.43948720203264 3.10711749999622 - 1 4 0.0175731334238374 2.48316585521317 3.05258880102438 - 1 5 0.0175731334238374 2.48316585521317 3.05258880102438 - 2 2 0.00503064360487288 6.98433077606902 1.08960295117864 - 2 3 0.0101296013842819 3.31380153807866 2.28919067558352 - 2 4 0.00497405122588691 14.0508902925745 0.544416409093563 - 2 5 0.00877114211614446 3.39491256196178 2.23466262511073 - 3 3 0.0203039874239943 2.17204344301477 3.48881895084762 - 3 4 0.0175825321440736 2.20660439192238 3.43428999287994 - 3 5 0.0175825321440736 2.20660439192238 3.43428999287994 - 4 4 0.0152259201379927 2.24227873774009 3.37976131582396 - 4 5 0.0152259201379927 2.24227873774009 3.37976131582396 - 5 5 0.0152259201379927 2.24227873774009 3.37976131582396 + 1 1 0.0202798941614106 2.78203488021395 2.725417159299 + 1 2 0.0101167811264648 3.9793050302425 1.90749569018897 + 1 3 0.0202934330695928 2.43948720203264 3.10711749999622 + 1 4 0.0175731334238374 2.48316585521317 3.05258880102438 + 1 5 0.0175731334238374 2.48316585521317 3.05258880102438 + 2 2 0.00503064360487288 6.98433077606902 1.08960295117864 + 2 3 0.0101296013842819 3.31380153807866 2.28919067558352 + 2 4 0.00497405122588691 14.0508902925745 0.544416409093563 + 2 5 0.00877114211614446 3.39491256196178 2.23466262511073 + 3 3 0.0203039874239943 2.17204344301477 3.48881895084762 + 3 4 0.0175825321440736 2.20660439192238 3.43428999287994 + 3 5 0.0175825321440736 2.20660439192238 3.43428999287994 + 4 4 0.0152259201379927 2.24227873774009 3.37976131582396 + 4 5 0.0152259201379927 2.24227873774009 3.37976131582396 + 5 5 0.0152259201379927 2.24227873774009 3.37976131582396 extract: ! | d0 2 r0 2 From c4579a75025401d0cd0bcc91ec38e1e4467c810b Mon Sep 17 00:00:00 2001 From: julient31 Date: Wed, 30 Sep 2020 11:43:01 -0600 Subject: [PATCH 0005/1217] First commit - added spin/kk style files - modified few necessary files - compiles, but SegFault when running --- src/KOKKOS/Install.sh | 2 + src/KOKKOS/atom_kokkos.cpp | 6 + src/KOKKOS/atom_kokkos.h | 5 + src/KOKKOS/atom_vec_spin_kokkos.cpp | 1308 +++++++++++++++++++++++++++ src/KOKKOS/atom_vec_spin_kokkos.h | 132 +++ src/KOKKOS/kokkos_type.h | 59 ++ src/atom_masks.h | 6 + 7 files changed, 1518 insertions(+) create mode 100644 src/KOKKOS/atom_vec_spin_kokkos.cpp create mode 100644 src/KOKKOS/atom_vec_spin_kokkos.h diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index 03508578ae..4c5c9d7e1d 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -63,6 +63,8 @@ action atom_vec_bond_kokkos.cpp atom_vec_bond.cpp action atom_vec_bond_kokkos.h atom_vec_bond.h action atom_vec_charge_kokkos.cpp action atom_vec_charge_kokkos.h +action atom_vec_spin_kokkos.cpp +action atom_vec_spin_kokkos.h action atom_vec_dpd_kokkos.cpp atom_vec_dpd.cpp action atom_vec_dpd_kokkos.h atom_vec_dpd.h action atom_vec_full_kokkos.cpp atom_vec_full.cpp diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp index a587494d09..b85b063190 100644 --- a/src/KOKKOS/atom_kokkos.cpp +++ b/src/KOKKOS/atom_kokkos.cpp @@ -76,6 +76,12 @@ AtomKokkos::~AtomKokkos() memoryKK->destroy_kokkos(k_improper_atom3, improper_atom3); memoryKK->destroy_kokkos(k_improper_atom4, improper_atom4); + // SPIN package + + memoryKK->destroy_kokkos(k_sp, sp); + memoryKK->destroy_kokkos(k_fm, fm); + memoryKK->destroy_kokkos(k_fm_long, fm_long); + // USER-DPD package memoryKK->destroy_kokkos(k_uCond,uCond); memoryKK->destroy_kokkos(k_uMech,uMech); diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index 6eebbad661..e2c666fea5 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -54,6 +54,11 @@ class AtomKokkos : public Atom { DAT::tdual_float_2d k_dvector; + // SPIN package + + DAT::tdual_sp_array k_sp; + DAT::tdual_fm_array k_fm; + DAT::tdual_fm_long_array k_fm_long; // USER-DPD package DAT::tdual_efloat_1d k_uCond, k_uMech, k_uChem, k_uCG, k_uCGnew, diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp new file mode 100644 index 0000000000..c5c2ffb5be --- /dev/null +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -0,0 +1,1308 @@ +/* ---------------------------------------------------------------------- + + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include "atom_vec_spin_kokkos.h" + +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "comm_kokkos.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "memory_kokkos.h" +#include "modify.h" + +using namespace LAMMPS_NS; + +#define DELTA 10 + +/* ---------------------------------------------------------------------- */ + +AtomVecSpinKokkos::AtomVecSpinKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) +{ + molecular = 0; + mass_type = 1; + forceclearflag = 1; + + comm_x_only = comm_f_only = 0; + size_forward = 7; + size_reverse = 9; + size_border = 10; + size_velocity = 3; + size_data_atom = 9; + size_data_vel = 4; + xcol_data = 4; + + atom->sp_flag = 1; + + k_count = DAT::tdual_int_1d("atom::k_count",1); + atomKK = (AtomKokkos *) atom; + commKK = (CommKokkos *) comm; +} + +/* ---------------------------------------------------------------------- + grow atom arrays + n = 0 grows arrays by a chunk + n > 0 allocates arrays to size n +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::grow(int n) +{ + int step = MAX(DELTA,nmax*0.01); + if (n == 0) nmax += step; + else nmax = n; + atomKK->nmax = nmax; + if (nmax < 0 || nmax > MAXSMALLINT) + error->one(FLERR,"Per-processor system is too big"); + + atomKK->sync(Device,ALL_MASK); + atomKK->modified(Device,ALL_MASK); + + memoryKK->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag"); + memoryKK->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type"); + memoryKK->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask"); + memoryKK->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image"); + + // allocating mech. quantities + + memoryKK->grow_kokkos(atomKK->k_x,atomKK->x,nmax,"atom:x"); + memoryKK->grow_kokkos(atomKK->k_v,atomKK->v,nmax,"atom:v"); + memoryKK->grow_kokkos(atomKK->k_f,atomKK->f,nmax,"atom:f"); + + // allocating mag. quantities + + memoryKK->grow_kokkos(atomKK->k_sp,atomKK->sp,nmax,"atom:sp"); + memoryKK->grow_kokkos(atomKK->k_fm,atomKK->fm,nmax,"atom:fm"); + memoryKK->grow_kokkos(atomKK->k_fm_long,atomKK->fm_long,nmax,"atom:fm_long"); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax); +} + +/* ---------------------------------------------------------------------- + reset local array ptrs +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::grow_reset() +{ + tag = atomKK->tag; + d_tag = atomKK->k_tag.d_view; + h_tag = atomKK->k_tag.h_view; + + type = atomKK->type; + d_type = atomKK->k_type.d_view; + h_type = atomKK->k_type.h_view; + mask = atomKK->mask; + d_mask = atomKK->k_mask.d_view; + h_mask = atomKK->k_mask.h_view; + image = atomKK->image; + d_image = atomKK->k_image.d_view; + h_image = atomKK->k_image.h_view; + + x = atomKK->x; + d_x = atomKK->k_x.d_view; + h_x = atomKK->k_x.h_view; + v = atomKK->v; + d_v = atomKK->k_v.d_view; + h_v = atomKK->k_v.h_view; + f = atomKK->f; + d_f = atomKK->k_f.d_view; + h_f = atomKK->k_f.h_view; + + sp = atomKK->sp; + d_sp = atomKK->k_sp.d_view; + h_sp = atomKK->k_sp.h_view; + fm = atomKK->fm; + d_fm = atomKK->k_fm.d_view; + h_fm = atomKK->k_fm.h_view; + fm_long = atomKK->fm_long; + d_fm_long = atomKK->k_fm_long.d_view; + h_fm_long = atomKK->k_fm_long.h_view; +} + +/* ---------------------------------------------------------------------- + copy atom I info to atom J +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::copy(int i, int j, int delflag) +{ + h_tag[j] = h_tag[i]; + h_type[j] = h_type[i]; + mask[j] = mask[i]; + h_image[j] = h_image[i]; + h_x(j,0) = h_x(i,0); + h_x(j,1) = h_x(i,1); + h_x(j,2) = h_x(i,2); + h_v(j,0) = h_v(i,0); + h_v(j,1) = h_v(i,1); + h_v(j,2) = h_v(i,2); + + h_sp(j,0) = h_sp(i,0); + h_sp(j,1) = h_sp(i,1); + h_sp(j,2) = h_sp(i,2); + h_sp(j,3) = h_sp(i,3); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSpinKokkos_PackComm { + typedef DeviceType device_type; + + typename ArrayTypes::t_x_array_randomread _x; + typename ArrayTypes::t_sp_array_randomread _sp; + typename ArrayTypes::t_xfloat_2d_um _buf; + typename ArrayTypes::t_int_2d_const _list; + const int _iswap; + X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz; + X_FLOAT _pbc[6]; + + AtomVecSpinKokkos_PackComm( + const typename DAT::tdual_x_array &x, + const typename DAT::tdual_sp_array &sp, + const typename DAT::tdual_xfloat_2d &buf, + const typename DAT::tdual_int_2d &list, + const int & iswap, + const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd, + const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc): + _x(x.view()),_sp(sp.view()), + _list(list.view()),_iswap(iswap), + _xprd(xprd),_yprd(yprd),_zprd(zprd), + _xy(xy),_xz(xz),_yz(yz) { + const size_t maxsend = (buf.view().extent(0)*buf.view().extent(1))/3; + // const size_t elements = 3; + const size_t elements = 7; + buffer_view(_buf,buf,maxsend,elements); + _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2]; + _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5]; + }; + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + const int j = _list(_iswap,i); + if (PBC_FLAG == 0) { + _buf(i,0) = _x(j,0); + _buf(i,1) = _x(j,1); + _buf(i,2) = _x(j,2); + _buf(i,3) = _sp(j,0); + _buf(i,4) = _sp(j,1); + _buf(i,5) = _sp(j,2); + _buf(i,6) = _sp(j,3); + } else { + if (TRICLINIC == 0) { + _buf(i,0) = _x(j,0) + _pbc[0]*_xprd; + _buf(i,1) = _x(j,1) + _pbc[1]*_yprd; + _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; + _buf(i,3) = _sp(j,0); + _buf(i,4) = _sp(j,1); + _buf(i,5) = _sp(j,2); + _buf(i,6) = _sp(j,3); + } else { + _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz; + _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz; + _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; + _buf(i,3) = _sp(j,0); + _buf(i,4) = _sp(j,1); + _buf(i,5) = _sp(j,2); + _buf(i,6) = _sp(j,3); + } + } + } +}; + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSpinKokkos_PackBorder { + typedef DeviceType device_type; + + typename ArrayTypes::t_xfloat_2d _buf; + const typename ArrayTypes::t_int_2d_const _list; + const int _iswap; + const typename ArrayTypes::t_x_array_randomread _x; + const typename ArrayTypes::t_tagint_1d _tag; + const typename ArrayTypes::t_int_1d _type; + const typename ArrayTypes::t_int_1d _mask; + const typename ArrayTypes::t_sp_array_randomread _sp; + X_FLOAT _dx,_dy,_dz; + + AtomVecSpinKokkos_PackBorder( + const typename ArrayTypes::t_xfloat_2d &buf, + const typename ArrayTypes::t_int_2d_const &list, + const int & iswap, + const typename ArrayTypes::t_x_array &x, + const typename ArrayTypes::t_tagint_1d &tag, + const typename ArrayTypes::t_int_1d &type, + const typename ArrayTypes::t_int_1d &mask, + const typename ArrayTypes::t_sp_array &sp, + const X_FLOAT &dx, const X_FLOAT &dy, const X_FLOAT &dz): + _buf(buf),_list(list),_iswap(iswap), + _x(x),_tag(tag),_type(type),_mask(mask),_sp(sp), + _dx(dx),_dy(dy),_dz(dz) {} + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + const int j = _list(_iswap,i); + if (PBC_FLAG == 0) { + _buf(i,0) = _x(j,0); + _buf(i,1) = _x(j,1); + _buf(i,2) = _x(j,2); + _buf(i,3) = d_ubuf(_tag(j)).d; + _buf(i,4) = d_ubuf(_type(j)).d; + _buf(i,5) = d_ubuf(_mask(j)).d; + _buf(i,6) = _sp(j,0); + _buf(i,7) = _sp(j,1); + _buf(i,8) = _sp(j,2); + _buf(i,9) = _sp(j,3); + } else { + _buf(i,0) = _x(j,0) + _dx; + _buf(i,1) = _x(j,1) + _dy; + _buf(i,2) = _x(j,2) + _dz; + _buf(i,3) = d_ubuf(_tag(j)).d; + _buf(i,4) = d_ubuf(_type(j)).d; + _buf(i,5) = d_ubuf(_mask(j)).d; + _buf(i,6) = _sp(j,0); + _buf(i,7) = _sp(j,1); + _buf(i,8) = _sp(j,2); + _buf(i,9) = _sp(j,3); + } + } +}; + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, DAT::tdual_xfloat_2d buf,int iswap, + int pbc_flag, int *pbc, ExecutionSpace space) +{ + X_FLOAT dx,dy,dz; + + if (pbc_flag != 0) { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + if(space==Host) { + AtomVecSpinKokkos_PackBorder f( + buf.view(), k_sendlist.view(), + iswap,h_x,h_tag,h_type,h_mask,h_sp,dx,dy,dz); + Kokkos::parallel_for(n,f); + } else { + AtomVecSpinKokkos_PackBorder f( + buf.view(), k_sendlist.view(), + iswap,d_x,d_tag,d_type,d_mask,d_sp,dx,dy,dz); + Kokkos::parallel_for(n,f); + } + + } else { + dx = dy = dz = 0; + if(space==Host) { + AtomVecSpinKokkos_PackBorder f( + buf.view(), k_sendlist.view(), + iswap,h_x,h_tag,h_type,h_mask,h_sp,dx,dy,dz); + Kokkos::parallel_for(n,f); + } else { + AtomVecSpinKokkos_PackBorder f( + buf.view(), k_sendlist.view(), + iswap,d_x,d_tag,d_type,d_mask,d_sp,dx,dy,dz); + Kokkos::parallel_for(n,f); + } + } + return n*size_border; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_border(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0); + buf[m++] = h_x(j,1); + buf[m++] = h_x(j,2); + buf[m++] = ubuf(h_tag(j)).d; + buf[m++] = ubuf(h_type(j)).d; + buf[m++] = ubuf(h_mask(j)).d; + buf[m++] = h_sp(j,0); + buf[m++] = h_sp(j,1); + buf[m++] = h_sp(j,2); + buf[m++] = h_sp(j,3); + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + buf[m++] = ubuf(h_tag(j)).d; + buf[m++] = ubuf(h_type(j)).d; + buf[m++] = ubuf(h_mask(j)).d; + buf[m++] = h_sp(j,0); + buf[m++] = h_sp(j,1); + buf[m++] = h_sp(j,2); + buf[m++] = h_sp(j,3); + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_border_vel(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz,dvx,dvy,dvz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0); + buf[m++] = h_x(j,1); + buf[m++] = h_x(j,2); + buf[m++] = ubuf(h_tag(j)).d; + buf[m++] = ubuf(h_type(j)).d; + buf[m++] = ubuf(h_mask(j)).d; + buf[m++] = h_sp(j,0); + buf[m++] = h_sp(j,1); + buf[m++] = h_sp(j,2); + buf[m++] = h_sp(j,3); + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + buf[m++] = ubuf(h_tag(j)).d; + buf[m++] = ubuf(h_type(j)).d; + buf[m++] = ubuf(h_mask(j)).d; + buf[m++] = h_sp(j,0); + buf[m++] = h_sp(j,1); + buf[m++] = h_sp(j,2); + buf[m++] = h_sp(j,3); + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + buf[m++] = ubuf(h_tag(j)).d; + buf[m++] = ubuf(h_type(j)).d; + buf[m++] = ubuf(h_mask(j)).d; + buf[m++] = h_sp(j,0); + buf[m++] = h_sp(j,1); + buf[m++] = h_sp(j,2); + buf[m++] = h_sp(j,3); + if (mask[i] & deform_groupbit) { + buf[m++] = h_v(j,0) + dvx; + buf[m++] = h_v(j,1) + dvy; + buf[m++] = h_v(j,2) + dvz; + } else { + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + } + } + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_border_hybrid(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_sp(j,0); + buf[m++] = h_sp(j,1); + buf[m++] = h_sp(j,2); + buf[m++] = h_sp(j,3); + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSpinKokkos_UnpackBorder { + typedef DeviceType device_type; + + const typename ArrayTypes::t_xfloat_2d_const _buf; + typename ArrayTypes::t_x_array _x; + typename ArrayTypes::t_tagint_1d _tag; + typename ArrayTypes::t_int_1d _type; + typename ArrayTypes::t_int_1d _mask; + typename ArrayTypes::t_sp_array _sp; + int _first; + + + AtomVecSpinKokkos_UnpackBorder( + const typename ArrayTypes::t_xfloat_2d_const &buf, + typename ArrayTypes::t_x_array &x, + typename ArrayTypes::t_tagint_1d &tag, + typename ArrayTypes::t_int_1d &type, + typename ArrayTypes::t_int_1d &mask, + typename ArrayTypes::t_sp_array &sp, + const int& first): + _buf(buf),_x(x),_tag(tag),_type(type),_mask(mask),_sp(sp),_first(first){ + }; + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + _x(i+_first,0) = _buf(i,0); + _x(i+_first,1) = _buf(i,1); + _x(i+_first,2) = _buf(i,2); + _tag(i+_first) = (tagint) d_ubuf(_buf(i,3)).i; + _type(i+_first) = (int) d_ubuf(_buf(i,4)).i; + _mask(i+_first) = (int) d_ubuf(_buf(i,5)).i; + _sp(i+_first,0) = _buf(i,6); + _sp(i+_first,1) = _buf(i,7); + _sp(i+_first,2) = _buf(i,8); + _sp(i+_first,3) = _buf(i,9); + } +}; + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::unpack_border_kokkos(const int &n, const int &first, + const DAT::tdual_xfloat_2d &buf,ExecutionSpace space) { + if (first+n >= nmax) { + grow(first+n+100); + } + if(space==Host) { + struct AtomVecSpinKokkos_UnpackBorder + f(buf.view(),h_x,h_tag,h_type,h_mask,h_sp,first); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSpinKokkos_UnpackBorder + f(buf.view(),d_x,d_tag,d_type,d_mask,d_sp,first); + Kokkos::parallel_for(n,f); + } + atomKK->modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|SP_MASK); +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::unpack_border(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + + for (i = first; i < last; i++) { + if (i == nmax) { + grow(0); + } + atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|SP_MASK); + h_x(i,0) = buf[m++]; + h_x(i,1) = buf[m++]; + h_x(i,2) = buf[m++]; + h_tag(i) = (tagint) ubuf(buf[m++]).i; + h_type(i) = (int) ubuf(buf[m++]).i; + h_mask(i) = (int) ubuf(buf[m++]).i; + h_sp(i,0) = buf[m++]; + h_sp(i,1) = buf[m++]; + h_sp(i,2) = buf[m++]; + h_sp(i,3) = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::unpack_border_vel(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) grow(0); + atomKK->modified(Host,X_MASK|V_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|SP_MASK); + h_x(i,0) = buf[m++]; + h_x(i,1) = buf[m++]; + h_x(i,2) = buf[m++]; + h_tag(i) = (tagint) ubuf(buf[m++]).i; + h_type(i) = (int) ubuf(buf[m++]).i; + h_mask(i) = (int) ubuf(buf[m++]).i; + h_sp(i,0) = buf[m++]; + h_sp(i,1) = buf[m++]; + h_sp(i,2) = buf[m++]; + h_sp(i,3) = buf[m++]; + h_v(i,0) = buf[m++]; + h_v(i,1) = buf[m++]; + h_v(i,2) = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::unpack_border_hybrid(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) + h_sp(i,0) = buf[m++]; + h_sp(i,1) = buf[m++]; + h_sp(i,2) = buf[m++]; + h_sp(i,3) = buf[m++]; + return m; +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSpinKokkos_PackExchangeFunctor { + typedef DeviceType device_type; + typedef ArrayTypes AT; + typename AT::t_x_array_randomread _x; + typename AT::t_v_array_randomread _v; + typename AT::t_tagint_1d_randomread _tag; + typename AT::t_int_1d_randomread _type; + typename AT::t_int_1d_randomread _mask; + typename AT::t_imageint_1d_randomread _image; + typename AT::t_sp_array_randomread _sp; + typename AT::t_x_array _xw; + typename AT::t_v_array _vw; + typename AT::t_tagint_1d _tagw; + typename AT::t_int_1d _typew; + typename AT::t_int_1d _maskw; + typename AT::t_imageint_1d _imagew; + typename AT::t_sp_array _spw; + + typename AT::t_xfloat_2d_um _buf; + typename AT::t_int_1d_const _sendlist; + typename AT::t_int_1d_const _copylist; + int _nlocal,_dim; + X_FLOAT _lo,_hi; + + AtomVecSpinKokkos_PackExchangeFunctor( + const AtomKokkos* atom, + const typename AT::tdual_xfloat_2d buf, + typename AT::tdual_int_1d sendlist, + typename AT::tdual_int_1d copylist,int nlocal, int dim, + X_FLOAT lo, X_FLOAT hi): + _x(atom->k_x.view()), + _v(atom->k_v.view()), + _tag(atom->k_tag.view()), + _type(atom->k_type.view()), + _mask(atom->k_mask.view()), + _image(atom->k_image.view()), + _sp(atom->k_sp.view()), + _xw(atom->k_x.view()), + _vw(atom->k_v.view()), + _tagw(atom->k_tag.view()), + _typew(atom->k_type.view()), + _maskw(atom->k_mask.view()), + _imagew(atom->k_image.view()), + _spw(atom->k_sp.view()), + _sendlist(sendlist.template view()), + _copylist(copylist.template view()), + _nlocal(nlocal),_dim(dim), + _lo(lo),_hi(hi){ + const size_t elements = 15; + const int maxsendlist = (buf.template view().extent(0)* + buf.template view().extent(1))/elements; + + buffer_view(_buf,buf,maxsendlist,elements); + } + + KOKKOS_INLINE_FUNCTION + void operator() (const int &mysend) const { + const int i = _sendlist(mysend); + _buf(mysend,0) = 15; + _buf(mysend,1) = _x(i,0); + _buf(mysend,2) = _x(i,1); + _buf(mysend,3) = _x(i,2); + _buf(mysend,4) = _v(i,0); + _buf(mysend,5) = _v(i,1); + _buf(mysend,6) = _v(i,2); + _buf(mysend,7) = d_ubuf(_tag[i]).d; + _buf(mysend,8) = d_ubuf(_type[i]).d; + _buf(mysend,9) = d_ubuf(_mask[i]).d; + _buf(mysend,10) = d_ubuf(_image[i]).d; + _buf(mysend,11) = _sp(i,0); + _buf(mysend,12) = _sp(i,1); + _buf(mysend,13) = _sp(i,2); + _buf(mysend,14) = _sp(i,3); + const int j = _copylist(mysend); + + if(j>-1) { + _xw(i,0) = _x(j,0); + _xw(i,1) = _x(j,1); + _xw(i,2) = _x(j,2); + _vw(i,0) = _v(j,0); + _vw(i,1) = _v(j,1); + _vw(i,2) = _v(j,2); + _tagw(i) = _tag(j); + _typew(i) = _type(j); + _maskw(i) = _mask(j); + _imagew(i) = _image(j); + _spw(i,0) = _sp(j,0); + _spw(i,1) = _sp(j,1); + _spw(i,2) = _sp(j,2); + _spw(i,3) = _sp(j,3); + } + } +}; + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &k_buf, + DAT::tdual_int_1d k_sendlist, + DAT::tdual_int_1d k_copylist, + ExecutionSpace space,int dim, + X_FLOAT lo,X_FLOAT hi ) +{ + if(nsend > (int) (k_buf.view().extent(0)*k_buf.view().extent(1))/15) { + int newsize = nsend*15/k_buf.view().extent(1)+1; + k_buf.resize(newsize,k_buf.view().extent(1)); + } + if(space == Host) { + AtomVecSpinKokkos_PackExchangeFunctor + f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi); + Kokkos::parallel_for(nsend,f); + return nsend*15; + } else { + AtomVecSpinKokkos_PackExchangeFunctor + f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi); + Kokkos::parallel_for(nsend,f); + return nsend*15; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_exchange(int i, double *buf) +{ + int m = 1; + buf[m++] = h_x(i,0); + buf[m++] = h_x(i,1); + buf[m++] = h_x(i,2); + buf[m++] = h_v(i,0); + buf[m++] = h_v(i,1); + buf[m++] = h_v(i,2); + buf[m++] = ubuf(h_tag(i)).d; + buf[m++] = ubuf(h_type(i)).d; + buf[m++] = ubuf(h_mask(i)).d; + buf[m++] = ubuf(h_image(i)).d; + buf[m++] = h_sp(i,0); + buf[m++] = h_sp(i,1); + buf[m++] = h_sp(i,2); + buf[m++] = h_sp(i,3); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSpinKokkos_UnpackExchangeFunctor { + typedef DeviceType device_type; + typedef ArrayTypes AT; + typename AT::t_x_array _x; + typename AT::t_v_array _v; + typename AT::t_tagint_1d _tag; + typename AT::t_int_1d _type; + typename AT::t_int_1d _mask; + typename AT::t_imageint_1d _image; + typename AT::t_sp_array _sp; + typename AT::t_xfloat_2d_um _buf; + typename AT::t_int_1d _nlocal; + int _dim; + X_FLOAT _lo,_hi; + + AtomVecSpinKokkos_UnpackExchangeFunctor( + const AtomKokkos* atom, + const typename AT::tdual_xfloat_2d buf, + typename AT::tdual_int_1d nlocal, + int dim, X_FLOAT lo, X_FLOAT hi): + _x(atom->k_x.view()), + _v(atom->k_v.view()), + _tag(atom->k_tag.view()), + _type(atom->k_type.view()), + _mask(atom->k_mask.view()), + _image(atom->k_image.view()), + _sp(atom->k_sp.view()), + _nlocal(nlocal.template view()),_dim(dim), + _lo(lo),_hi(hi){ + const size_t elements = 15; + const int maxsendlist = (buf.template view().extent(0)*buf.template view().extent(1))/elements; + + buffer_view(_buf,buf,maxsendlist,elements); + } + + KOKKOS_INLINE_FUNCTION + void operator() (const int &myrecv) const { + X_FLOAT x = _buf(myrecv,_dim+1); + if (x >= _lo && x < _hi) { + int i = Kokkos::atomic_fetch_add(&_nlocal(0),1); + _x(i,0) = _buf(myrecv,1); + _x(i,1) = _buf(myrecv,2); + _x(i,2) = _buf(myrecv,3); + _v(i,0) = _buf(myrecv,4); + _v(i,1) = _buf(myrecv,5); + _v(i,2) = _buf(myrecv,6); + _tag[i] = (tagint) d_ubuf(_buf(myrecv,7)).i; + _type[i] = (int) d_ubuf(_buf(myrecv,8)).i; + _mask[i] = (int) d_ubuf(_buf(myrecv,9)).i; + _image[i] = (imageint) d_ubuf(_buf(myrecv,10)).i; + _sp(i,0) = _buf(myrecv,11); + _sp(i,1) = _buf(myrecv,12); + _sp(i,2) = _buf(myrecv,13); + _sp(i,3) = _buf(myrecv,14); + } + } +}; + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv, + int nlocal,int dim,X_FLOAT lo,X_FLOAT hi, + ExecutionSpace space) { + if(space == Host) { + k_count.h_view(0) = nlocal; + AtomVecSpinKokkos_UnpackExchangeFunctor f(atomKK,k_buf,k_count,dim,lo,hi); + Kokkos::parallel_for(nrecv/15,f); + return k_count.h_view(0); + } else { + k_count.h_view(0) = nlocal; + k_count.modify(); + k_count.sync(); + AtomVecSpinKokkos_UnpackExchangeFunctor + f(atomKK,k_buf,k_count,dim,lo,hi); + Kokkos::parallel_for(nrecv/15,f); + k_count.modify(); + k_count.sync(); + + return k_count.h_view(0); + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::unpack_exchange(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | + MASK_MASK | IMAGE_MASK | SP_MASK); + + int m = 1; + h_x(nlocal,0) = buf[m++]; + h_x(nlocal,1) = buf[m++]; + h_x(nlocal,2) = buf[m++]; + h_v(nlocal,0) = buf[m++]; + h_v(nlocal,1) = buf[m++]; + h_v(nlocal,2) = buf[m++]; + h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; + h_type(nlocal) = (int) ubuf(buf[m++]).i; + h_mask(nlocal) = (int) ubuf(buf[m++]).i; + h_image(nlocal) = (imageint) ubuf(buf[m++]).i; + h_sp(nlocal,0) = buf[m++]; + h_sp(nlocal,1) = buf[m++]; + h_sp(nlocal,2) = buf[m++]; + h_sp(nlocal,3) = buf[m++]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]-> + unpack_exchange(nlocal,&buf[m]); + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + size of restart data for all atoms owned by this proc + include extra data stored by fixes +------------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::size_restart() +{ + int i; + + int nlocal = atom->nlocal; + int n = 15 * nlocal; + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + for (i = 0; i < nlocal; i++) + n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); + + return n; +} + +/* ---------------------------------------------------------------------- + pack atom I's data for restart file including extra quantities + xyz must be 1st 3 values, so that read_restart can test on them + molecular types may be negative, but write as positive +------------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_restart(int i, double *buf) +{ + atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | + MASK_MASK | IMAGE_MASK | SP_MASK); + + int m = 1; + buf[m++] = h_x(i,0); + buf[m++] = h_x(i,1); + buf[m++] = h_x(i,2); + buf[m++] = ubuf(h_tag(i)).d; + buf[m++] = ubuf(h_type(i)).d; + buf[m++] = ubuf(h_mask(i)).d; + buf[m++] = ubuf(h_image(i)).d; + buf[m++] = h_v(i,0); + buf[m++] = h_v(i,1); + buf[m++] = h_v(i,2); + + buf[m++] = h_sp(i,0); + buf[m++] = h_sp(i,1); + buf[m++] = h_sp(i,2); + buf[m++] = h_sp(i,3); + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- + unpack data for one atom from restart file including extra quantities +------------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::unpack_restart(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) { + grow(0); + if (atom->nextra_store) + memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); + } + + atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | + MASK_MASK | IMAGE_MASK | SP_MASK); + + int m = 1; + h_x(nlocal,0) = buf[m++]; + h_x(nlocal,1) = buf[m++]; + h_x(nlocal,2) = buf[m++]; + h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; + h_type(nlocal) = (int) ubuf(buf[m++]).i; + h_mask(nlocal) = (int) ubuf(buf[m++]).i; + h_image(nlocal) = (imageint) ubuf(buf[m++]).i; + h_v(nlocal,0) = buf[m++]; + h_v(nlocal,1) = buf[m++]; + h_v(nlocal,2) = buf[m++]; + + h_sp(nlocal,0) = buf[m++]; + h_sp(nlocal,1) = buf[m++]; + h_sp(nlocal,2) = buf[m++]; + h_sp(nlocal,3) = buf[m++]; + + double **extra = atom->extra; + if (atom->nextra_store) { + int size = static_cast (buf[0]) - m; + for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; + } + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + create one atom of itype at coord + set other values to defaults +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::create_atom(int itype, double *coord) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) { + atomKK->modified(Host,ALL_MASK); + grow(0); + } + atomKK->sync(Host,ALL_MASK); + atomKK->modified(Host,ALL_MASK); + + tag[nlocal] = 0; + type[nlocal] = itype; + h_x(nlocal,0) = coord[0]; + h_x(nlocal,1) = coord[1]; + h_x(nlocal,2) = coord[2]; + h_mask[nlocal] = 1; + h_image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + h_v(nlocal,0) = 0.0; + h_v(nlocal,1) = 0.0; + h_v(nlocal,2) = 0.0; + + h_sp(nlocal,0) = 0.0; + h_sp(nlocal,1) = 0.0; + h_sp(nlocal,2) = 0.0; + h_sp(nlocal,3) = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack one line from Atoms section of data file + initialize other atom quantities +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::data_atom(double *coord, imageint imagetmp, + char **values) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + h_tag[nlocal] = utils::inumeric(FLERR,values[0],true,lmp); + h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); + if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) + error->one(FLERR,"Invalid atom type in Atoms section of data file"); + + h_sp(nlocal,3) = utils::numeric(FLERR,values[2],true,lmp); + h_sp(nlocal,0) = utils::numeric(FLERR,values[6],true,lmp); + h_sp(nlocal,1) = utils::numeric(FLERR,values[7],true,lmp); + h_sp(nlocal,2) = utils::numeric(FLERR,values[8],true,lmp); + double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] + + sp[nlocal][1]*sp[nlocal][1] + + sp[nlocal][2]*sp[nlocal][2]); + h_sp(nlocal,0) *= inorm; + h_sp(nlocal,1) *= inorm; + h_sp(nlocal,2) *= inorm; + + h_x(nlocal,0) = coord[0]; + h_x(nlocal,1) = coord[1]; + h_x(nlocal,2) = coord[2]; + + h_image[nlocal] = imagetmp; + + h_mask[nlocal] = 1; + h_v(nlocal,0) = 0.0; + h_v(nlocal,1) = 0.0; + h_v(nlocal,2) = 0.0; + + atomKK->modified(Host,ALL_MASK); + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack hybrid quantities from one line in Atoms section of data file + initialize other atom quantities for this sub-style +------------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::data_atom_hybrid(int nlocal, char **values) +{ + h_sp(nlocal,3) = utils::numeric(FLERR,values[0],true,lmp); + h_sp(nlocal,0) = utils::numeric(FLERR,values[1],true,lmp); + h_sp(nlocal,1) = utils::numeric(FLERR,values[2],true,lmp); + h_sp(nlocal,2) = utils::numeric(FLERR,values[3],true,lmp); + double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] + + sp[nlocal][1]*sp[nlocal][1] + + sp[nlocal][2]*sp[nlocal][2]); + sp[nlocal][0] *= inorm; + sp[nlocal][1] *= inorm; + sp[nlocal][2] *= inorm; + + return 4; +} + +/* ---------------------------------------------------------------------- + pack atom info for data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::pack_data(double **buf) +{ + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + buf[i][0] = h_tag[i]; + buf[i][1] = h_type[i]; + buf[i][2] = h_sp(i,0); + buf[i][3] = h_x(i,0); + buf[i][4] = h_x(i,1); + buf[i][5] = h_x(i,2); + buf[i][2] = h_sp(i,1); + buf[i][2] = h_sp(i,2); + buf[i][2] = h_sp(i,3); + buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX; + buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX; + buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX; + } +} + +/* ---------------------------------------------------------------------- + pack hybrid atom info for data file +------------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_data_hybrid(int i, double *buf) +{ + buf[0] = h_sp(i,3); + buf[1] = h_sp(i,0); + buf[2] = h_sp(i,1); + buf[3] = h_sp(i,2); + return 4; +} + +/* ---------------------------------------------------------------------- + write atom info to data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::write_data(FILE *fp, int n, double **buf) +{ + for (int i = 0; i < n; i++) + fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n", + (int) buf[i][0],(int) buf[i][1],buf[i][2],buf[i][3],buf[i][4], + buf[i][5],(int) buf[i][6],(int) buf[i][7],(int) buf[i][8]); +} + +/* ---------------------------------------------------------------------- + write hybrid atom info to data file +------------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::write_data_hybrid(FILE *fp, double *buf) +{ + fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e",buf[0],buf[1],buf[2],buf[3]); + return 4; +} + +/* ---------------------------------------------------------------------- + return # of bytes of allocated memory +------------------------------------------------------------------------- */ + +double AtomVecSpinKokkos::memory_usage() +{ + bigint bytes = 0; + + if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); + if (atom->memcheck("type")) bytes += memory->usage(type,nmax); + if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); + if (atom->memcheck("image")) bytes += memory->usage(image,nmax); + if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); + if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); + if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3); + + if (atom->memcheck("sp")) bytes += memory->usage(sp,nmax,4); + if (atom->memcheck("fm")) bytes += memory->usage(fm,nmax*comm->nthreads,3); + if (atom->memcheck("fm_long")) bytes += memory->usage(fm_long,nmax*comm->nthreads,3); + + return bytes; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::sync(ExecutionSpace space, unsigned int mask) +{ + if (space == Device) { + if (mask & X_MASK) atomKK->k_x.sync(); + if (mask & V_MASK) atomKK->k_v.sync(); + if (mask & F_MASK) atomKK->k_f.sync(); + if (mask & TAG_MASK) atomKK->k_tag.sync(); + if (mask & TYPE_MASK) atomKK->k_type.sync(); + if (mask & MASK_MASK) atomKK->k_mask.sync(); + if (mask & IMAGE_MASK) atomKK->k_image.sync(); + if (mask & SP_MASK) atomKK->k_sp.sync(); + if (mask & FM_MASK) atomKK->k_fm.sync(); + if (mask & FML_MASK) atomKK->k_fm_long.sync(); + } else { + if (mask & X_MASK) atomKK->k_x.sync(); + if (mask & V_MASK) atomKK->k_v.sync(); + if (mask & F_MASK) atomKK->k_f.sync(); + if (mask & TAG_MASK) atomKK->k_tag.sync(); + if (mask & TYPE_MASK) atomKK->k_type.sync(); + if (mask & MASK_MASK) atomKK->k_mask.sync(); + if (mask & IMAGE_MASK) atomKK->k_image.sync(); + if (mask & SP_MASK) atomKK->k_sp.sync(); + if (mask & FM_MASK) atomKK->k_fm.sync(); + if (mask & FML_MASK) atomKK->k_fm_long.sync(); + } +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::modified(ExecutionSpace space, unsigned int mask) +{ + if (space == Device) { + if (mask & X_MASK) atomKK->k_x.modify(); + if (mask & V_MASK) atomKK->k_v.modify(); + if (mask & F_MASK) atomKK->k_f.modify(); + if (mask & TAG_MASK) atomKK->k_tag.modify(); + if (mask & TYPE_MASK) atomKK->k_type.modify(); + if (mask & MASK_MASK) atomKK->k_mask.modify(); + if (mask & IMAGE_MASK) atomKK->k_image.modify(); + if (mask & SP_MASK) atomKK->k_sp.modify(); + if (mask & FM_MASK) atomKK->k_fm.modify(); + if (mask & FML_MASK) atomKK->k_fm_long.modify(); + } else { + if (mask & X_MASK) atomKK->k_x.modify(); + if (mask & V_MASK) atomKK->k_v.modify(); + if (mask & F_MASK) atomKK->k_f.modify(); + if (mask & TAG_MASK) atomKK->k_tag.modify(); + if (mask & TYPE_MASK) atomKK->k_type.modify(); + if (mask & MASK_MASK) atomKK->k_mask.modify(); + if (mask & IMAGE_MASK) atomKK->k_image.modify(); + if (mask & SP_MASK) atomKK->k_sp.modify(); + if (mask & FM_MASK) atomKK->k_fm.modify(); + if (mask & FML_MASK) atomKK->k_fm_long.modify(); + } +} + +void AtomVecSpinKokkos::sync_overlapping_device(ExecutionSpace space, unsigned int mask) +{ + if (space == Device) { + if ((mask & X_MASK) && atomKK->k_x.need_sync()) + perform_async_copy(atomKK->k_x,space); + if ((mask & V_MASK) && atomKK->k_v.need_sync()) + perform_async_copy(atomKK->k_v,space); + if ((mask & F_MASK) && atomKK->k_f.need_sync()) + perform_async_copy(atomKK->k_f,space); + if ((mask & TAG_MASK) && atomKK->k_tag.need_sync()) + perform_async_copy(atomKK->k_tag,space); + if ((mask & TYPE_MASK) && atomKK->k_type.need_sync()) + perform_async_copy(atomKK->k_type,space); + if ((mask & MASK_MASK) && atomKK->k_mask.need_sync()) + perform_async_copy(atomKK->k_mask,space); + if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync()) + perform_async_copy(atomKK->k_image,space); + if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) + perform_async_copy(atomKK->k_sp,space); + if ((mask & FM_MASK) && atomKK->k_sp.need_sync()) + perform_async_copy(atomKK->k_fm,space); + if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) + perform_async_copy(atomKK->k_fm_long,space); + } else { + if ((mask & X_MASK) && atomKK->k_x.need_sync()) + perform_async_copy(atomKK->k_x,space); + if ((mask & V_MASK) && atomKK->k_v.need_sync()) + perform_async_copy(atomKK->k_v,space); + if ((mask & F_MASK) && atomKK->k_f.need_sync()) + perform_async_copy(atomKK->k_f,space); + if ((mask & TAG_MASK) && atomKK->k_tag.need_sync()) + perform_async_copy(atomKK->k_tag,space); + if ((mask & TYPE_MASK) && atomKK->k_type.need_sync()) + perform_async_copy(atomKK->k_type,space); + if ((mask & MASK_MASK) && atomKK->k_mask.need_sync()) + perform_async_copy(atomKK->k_mask,space); + if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync()) + perform_async_copy(atomKK->k_image,space); + if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) + perform_async_copy(atomKK->k_sp,space); + if ((mask & FM_MASK) && atomKK->k_fm.need_sync()) + perform_async_copy(atomKK->k_fm,space); + if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) + perform_async_copy(atomKK->k_fm_long,space); + } +} + +/* ---------------------------------------------------------------------- + clear all forces (mech and mag) +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::force_clear(int /*n*/, size_t nbytes) +{ + memset(&atom->f[0][0],0,3*nbytes); + memset(&atom->fm[0][0],0,3*nbytes); + memset(&atom->fm_long[0][0],0,3*nbytes); +} diff --git a/src/KOKKOS/atom_vec_spin_kokkos.h b/src/KOKKOS/atom_vec_spin_kokkos.h new file mode 100644 index 0000000000..a9f7077a24 --- /dev/null +++ b/src/KOKKOS/atom_vec_spin_kokkos.h @@ -0,0 +1,132 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef ATOM_CLASS + +AtomStyle(spin/kk,AtomVecSpinKokkos) +AtomStyle(spin/kk/device,AtomVecSpinKokkos) +AtomStyle(spin/kk/host,AtomVecSpinKokkos) + +#else + +#ifndef LMP_ATOM_VEC_SPIN_KOKKOS_H +#define LMP_ATOM_VEC_SPIN_KOKKOS_H + +#include "atom_vec_kokkos.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +class AtomVecSpinKokkos : public AtomVecKokkos { + public: + AtomVecSpinKokkos(class LAMMPS *); + void grow(int); + void copy(int, int, int); + int pack_border(int, int *, double *, int, int *); + int pack_border_vel(int, int *, double *, int, int *); + int pack_border_hybrid(int, int *, double *); + void unpack_border(int, int, double *); + void unpack_border_vel(int, int, double *); + int unpack_border_hybrid(int, int, double *); + int pack_exchange(int, double *); + int unpack_exchange(double *); + int size_restart(); + int pack_restart(int, double *); + int unpack_restart(double *); + void create_atom(int, double *); + void data_atom(double *, imageint, char **); + int data_atom_hybrid(int, char **); + void pack_data(double **); + int pack_data_hybrid(int, double *); + void write_data(FILE *, int, double **); + int write_data_hybrid(FILE *, double *); + double memory_usage(); + + // clear magnetic and mechanic forces + + void force_clear(int, size_t); + + void grow_reset(); + // input lists to be checked + int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, + DAT::tdual_xfloat_2d buf,int iswap, + int pbc_flag, int *pbc, ExecutionSpace space); + void unpack_border_kokkos(const int &n, const int &nfirst, + const DAT::tdual_xfloat_2d &buf, + ExecutionSpace space); + int pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &buf, + DAT::tdual_int_1d k_sendlist, + DAT::tdual_int_1d k_copylist, + ExecutionSpace space, int dim, + X_FLOAT lo, X_FLOAT hi); + int unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv, + int nlocal, int dim, X_FLOAT lo, X_FLOAT hi, + ExecutionSpace space); + + void sync(ExecutionSpace space, unsigned int mask); + void modified(ExecutionSpace space, unsigned int mask); + void sync_overlapping_device(ExecutionSpace space, unsigned int mask); + + protected: + tagint *tag; + int *type,*mask; + imageint *image; + double **x,**v,**f; // lattice quantities + + // spin quantities + double **sp; // sp[i][0-2] direction of the spin i + // sp[i][3] atomic magnetic moment of the spin i + double **fm; // fm[i][0-2] direction of magnetic precession + double **fm_long; // storage of long-range spin prec. components + + DAT::t_tagint_1d d_tag; + HAT::t_tagint_1d h_tag; + + DAT::t_int_1d d_type, d_mask; + HAT::t_int_1d h_type, h_mask; + + DAT::t_imageint_1d d_image; + HAT::t_imageint_1d h_image; + + DAT::t_x_array d_x; + DAT::t_v_array d_v; + DAT::t_f_array d_f; + + DAT::t_sp_array d_sp; + DAT::t_fm_array d_fm; + DAT::t_fm_long_array d_fm_long; + + HAT::t_sp_array h_sp; + HAT::t_fm_array h_fm; + HAT::t_fm_long_array h_fm_long; + + DAT::tdual_int_1d k_count; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Per-processor system is too big + +The number of owned atoms plus ghost atoms on a single +processor must fit in 32-bit integer. + +E: Invalid atom type in Atoms section of data file + +Atom types must range from 1 to specified # of types. + +*/ diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index 5930a9e207..b6992602d0 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -758,6 +758,38 @@ typedef tdual_virial_array::t_dev_um t_virial_array_um; typedef tdual_virial_array::t_dev_const_um t_virial_array_const_um; typedef tdual_virial_array::t_dev_const_randomread t_virial_array_randomread; +// Spin Types + +//3d SP_FLOAT array n*4 +#ifdef LMP_KOKKOS_NO_LEGACY +typedef Kokkos::DualView tdual_sp_array; +#else +typedef Kokkos::DualView tdual_sp_array; +#endif +typedef tdual_sp_array::t_dev t_sp_array; +typedef tdual_sp_array::t_dev_const t_sp_array_const; +typedef tdual_sp_array::t_dev_um t_sp_array_um; +typedef tdual_sp_array::t_dev_const_um t_sp_array_const_um; +typedef tdual_sp_array::t_dev_const_randomread t_sp_array_randomread; + +//3d FM_FLOAT array n*3 + +typedef Kokkos::DualView tdual_fm_array; +typedef tdual_fm_array::t_dev t_fm_array; +typedef tdual_fm_array::t_dev_const t_fm_array_const; +typedef tdual_fm_array::t_dev_um t_fm_array_um; +typedef tdual_fm_array::t_dev_const_um t_fm_array_const_um; +typedef tdual_fm_array::t_dev_const_randomread t_fm_array_randomread; + +//3d FML_FLOAT array n*3 + +typedef Kokkos::DualView tdual_fm_long_array; +typedef tdual_fm_long_array::t_dev t_fm_long_array; +typedef tdual_fm_long_array::t_dev_const t_fm_long_array_const; +typedef tdual_fm_long_array::t_dev_um t_fm_long_array_um; +typedef tdual_fm_long_array::t_dev_const_um t_fm_long_array_const_um; +typedef tdual_fm_long_array::t_dev_const_randomread t_fm_long_array_randomread; + //Energy Types //1d E_FLOAT array n @@ -994,6 +1026,33 @@ typedef tdual_virial_array::t_host_um t_virial_array_um; typedef tdual_virial_array::t_host_const_um t_virial_array_const_um; typedef tdual_virial_array::t_host_const_randomread t_virial_array_randomread; +// Spin types + +//2d X_FLOAT array n*3 +typedef Kokkos::DualView tdual_sp_array; +typedef tdual_sp_array::t_host t_sp_array; +typedef tdual_sp_array::t_host_const t_sp_array_const; +typedef tdual_sp_array::t_host_um t_sp_array_um; +typedef tdual_sp_array::t_host_const_um t_sp_array_const_um; +typedef tdual_sp_array::t_host_const_randomread t_sp_array_randomread; + +//2d F_FLOAT array n*3 +typedef Kokkos::DualView tdual_fm_array; +//typedef Kokkos::DualView tdual_f_array; +typedef tdual_fm_array::t_host t_fm_array; +typedef tdual_fm_array::t_host_const t_fm_array_const; +typedef tdual_fm_array::t_host_um t_fm_array_um; +typedef tdual_fm_array::t_host_const_um t_fm_array_const_um; +typedef tdual_fm_array::t_host_const_randomread t_fm_array_randomread; + +//2d F_FLOAT array n*3 +typedef Kokkos::DualView tdual_fm_long_array; +//typedef Kokkos::DualView tdual_f_array; +typedef tdual_fm_long_array::t_host t_fm_long_array; +typedef tdual_fm_long_array::t_host_const t_fm_long_array_const; +typedef tdual_fm_long_array::t_host_um t_fm_long_array_um; +typedef tdual_fm_long_array::t_host_const_um t_fm_long_array_const_um; +typedef tdual_fm_long_array::t_host_const_randomread t_fm_long_array_randomread; //Energy Types diff --git a/src/atom_masks.h b/src/atom_masks.h index 8e29448488..daad323835 100644 --- a/src/atom_masks.h +++ b/src/atom_masks.h @@ -42,6 +42,12 @@ #define ENERGY_MASK 0x00010000 #define VIRIAL_MASK 0x00020000 +// SPIN + +#define SP_MASK 0x00000001 +#define FM_MASK 0x00000002 +#define FML_MASK 0x00000004 + // DPD #define DPDRHO_MASK 0x00040000 From b1b014aed3e15e2d8ca02b68a0cf567edcff67e8 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Fri, 2 Oct 2020 15:09:47 -0600 Subject: [PATCH 0006/1217] Fixing merge conflicts --- src/comm.cpp | 6 + src/comm.h | 1 + src/comm_brick.cpp | 6 + src/nbin.cpp | 9 + src/nbin.h | 14 + src/nbin_bytype.cpp | 466 ++++++++++++++++++++++++ src/nbin_bytype.h | 56 +++ src/nbin_standard.h | 2 +- src/neighbor.cpp | 17 +- src/neighbor.h | 6 +- src/npair_full_bytype.cpp | 144 ++++++++ src/npair_full_bytype.h | 43 +++ src/npair_half_bytype_newton.cpp | 219 +++++++++++ src/npair_half_bytype_newton.h | 43 +++ src/npair_half_size_bytype_newtoff.cpp | 130 +++++++ src/npair_half_size_bytype_newtoff.h | 43 +++ src/npair_half_size_bytype_newton.cpp | 189 ++++++++++ src/npair_half_size_bytype_newton.h | 43 +++ src/nstencil.h | 4 + src/nstencil_full_bytype_3d.cpp | 192 ++++++++++ src/nstencil_full_bytype_3d.h | 53 +++ src/nstencil_half_bytype_2d_newton.cpp | 192 ++++++++++ src/nstencil_half_bytype_2d_newton.h | 52 +++ src/nstencil_half_bytype_3d_newtoff.cpp | 190 ++++++++++ src/nstencil_half_bytype_3d_newtoff.h | 51 +++ src/nstencil_half_bytype_3d_newton.cpp | 194 ++++++++++ src/nstencil_half_bytype_3d_newton.h | 52 +++ 27 files changed, 2413 insertions(+), 4 deletions(-) create mode 100644 src/nbin_bytype.cpp create mode 100644 src/nbin_bytype.h create mode 100644 src/npair_full_bytype.cpp create mode 100644 src/npair_full_bytype.h create mode 100755 src/npair_half_bytype_newton.cpp create mode 100755 src/npair_half_bytype_newton.h create mode 100644 src/npair_half_size_bytype_newtoff.cpp create mode 100644 src/npair_half_size_bytype_newtoff.h create mode 100755 src/npair_half_size_bytype_newton.cpp create mode 100755 src/npair_half_size_bytype_newton.h create mode 100644 src/nstencil_full_bytype_3d.cpp create mode 100644 src/nstencil_full_bytype_3d.h create mode 100644 src/nstencil_half_bytype_2d_newton.cpp create mode 100644 src/nstencil_half_bytype_2d_newton.h create mode 100644 src/nstencil_half_bytype_3d_newtoff.cpp create mode 100644 src/nstencil_half_bytype_3d_newtoff.h create mode 100644 src/nstencil_half_bytype_3d_newton.cpp create mode 100644 src/nstencil_half_bytype_3d_newton.h diff --git a/src/comm.cpp b/src/comm.cpp index 32a4152294..1efe966459 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -76,6 +76,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) grid2proc = nullptr; xsplit = ysplit = zsplit = nullptr; rcbnew = 0; + multi_bytype = 0; // use of OpenMP threads // query OpenMP for number of threads/process set by user at run-time @@ -326,6 +327,11 @@ void Comm::modify_params(int narg, char **arg) for (i=nlo; i<=nhi; ++i) cutusermulti[i] = cut; iarg += 3; + } else if (strcmp(arg[iarg],"cutoff/bytype") == 0) { + if (mode == Comm::SINGLE) + error->all(FLERR,"Use cutoff/bytype in mode multi only"); + multi_bytype = 1; + iarg += 1; } else if (strcmp(arg[iarg],"vel") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command"); if (strcmp(arg[iarg+1],"yes") == 0) ghost_velocity = 1; diff --git a/src/comm.h b/src/comm.h index c8d7add79c..e5fc1bdee4 100644 --- a/src/comm.h +++ b/src/comm.h @@ -161,6 +161,7 @@ class Comm : protected Pointers { int (*)(int, char *, int &, int *&, char *&, void *), int, char *&, int, void *, int); void rendezvous_stats(int, int, int, int, int, int, bigint); + int multi_bytype; // 1 if multi cutoff is intra-type cutoff public: enum{MULTIPLE}; diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 374c394b0b..57703b578c 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -181,6 +181,12 @@ void CommBrick::setup() cutghostmulti[i][0] = MAX(cut,cuttype[i]); cutghostmulti[i][1] = MAX(cut,cuttype[i]); cutghostmulti[i][2] = MAX(cut,cuttype[i]); + if (multi_bytype == 1) { + // Set the BYTYPE cutoff + cutghostmulti[i][0] = sqrt(neighbor->cutneighsq[i][i]); + cutghostmulti[i][1] = sqrt(neighbor->cutneighsq[i][i]); + cutghostmulti[i][2] = sqrt(neighbor->cutneighsq[i][i]); + } } } diff --git a/src/nbin.cpp b/src/nbin.cpp index 1fe011e9f2..64ae7e7b83 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -150,6 +150,15 @@ int NBin::coord2bin(double *x) return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo); } +/* ---------------------------------------------------------------------- + to be overridden by NBinType + ------------------------------------------------------------------------- */ + +int NBin::coord2bin(double * x, int itype) +{ + error->all(FLERR,"coord2bin(x, itype) not available.\n"); + return -1; +} /* ---------------------------------------------------------------------- */ diff --git a/src/nbin.h b/src/nbin.h index 4bfe579514..96cc7eac64 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -37,6 +37,18 @@ class NBin : protected Pointers { double cutoff_custom; // cutoff set by requestor + // Analogues for NBinType + int * nbinx_type, * nbiny_type, * nbinz_type; + int * mbins_type; + int * mbinx_type, * mbiny_type, * mbinz_type; + int * mbinxlo_type, * mbinylo_type, * mbinzlo_type; + double * binsizex_type, * binsizey_type, * binsizez_type; + double * bininvx_type, * bininvy_type, * bininvz_type; + + int ** binhead_type; + int ** bins_type; + int ** atom2bin_type; + NBin(class LAMMPS *); ~NBin(); void post_constructor(class NeighRequest *); @@ -50,6 +62,8 @@ class NBin : protected Pointers { // Kokkos package int kokkos; // 1 if class stores Kokkos data + // For NBinType + virtual int coord2bin(double *, int); protected: diff --git a/src/nbin_bytype.cpp b/src/nbin_bytype.cpp new file mode 100644 index 0000000000..f719ed116f --- /dev/null +++ b/src/nbin_bytype.cpp @@ -0,0 +1,466 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nbin_bytype.h" +#include "neighbor.h" +#include "atom.h" +#include "group.h" +#include "domain.h" +#include "comm.h" +#include "update.h" +#include "error.h" + +#include +#include "memory.h" + +using namespace LAMMPS_NS; + +#define SMALL 1.0e-6 // Duplicated from NBinStandard +#define CUT2BIN_RATIO 100 // Duplicated from NBinStandard + +/* ---------------------------------------------------------------------- */ + +NBinBytype::NBinBytype(LAMMPS *lmp) : NBin(lmp) { + + nbinx_type = NULL; nbiny_type = NULL; nbinz_type = NULL; + mbins_type = NULL; + mbinx_type = NULL; mbiny_type = NULL, mbinz_type = NULL; + mbinxlo_type = NULL; + mbinylo_type = NULL; + mbinzlo_type = NULL; + binsizex_type = NULL; binsizey_type = NULL; binsizez_type = NULL; + bininvx_type = NULL; bininvy_type = NULL; bininvz_type = NULL; + binhead_type = NULL; + bins_type = NULL; + atom2bin_type = NULL; + maxtypes = 0; + maxbins_type = NULL; +} + +NBinBytype::~NBinBytype() { + + memory->destroy(nbinx_type); + memory->destroy(nbiny_type); + memory->destroy(nbinz_type); + memory->destroy(mbins_type); + memory->destroy(mbinx_type); + memory->destroy(mbiny_type); + memory->destroy(mbinz_type); + memory->destroy(mbinxlo_type); + memory->destroy(mbinylo_type); + memory->destroy(mbinzlo_type); + + memory->destroy(binsizex_type); + memory->destroy(binsizey_type); + memory->destroy(binsizez_type); + memory->destroy(bininvx_type); + memory->destroy(bininvy_type); + memory->destroy(bininvz_type); + + for (int n = 1; n <= maxtypes; n++) { + memory->destroy(binhead_type[n]); + memory->destroy(bins_type[n]); + memory->destroy(atom2bin_type[n]); + } + delete [] binhead_type; + delete [] bins_type; + delete [] atom2bin_type; + + memory->destroy(maxbins_type); +} + +/* ---------------------------------------------------------------------- + arrange storage for types + allows ntypes to change, but not currently expected after initialisation + ------------------------------------------------------------------------- */ + +void NBinBytype::setup_types() { + + int n; + + if (atom->ntypes > maxtypes) { + + // Clear any/all memory for existing types + + for (n = 1; n <= maxtypes; n++) { + memory->destroy(atom2bin_type[n]); + memory->destroy(binhead_type[n]); + memory->destroy(bins_type[n]); + } + delete [] atom2bin_type; + delete [] binhead_type; + delete [] bins_type; + + // Realloacte at updated maxtypes + + maxtypes = atom->ntypes; + + atom2bin_type = new int*[maxtypes+1](); + binhead_type = new int*[maxtypes+1](); + bins_type = new int*[maxtypes+1](); + + memory->destroy(nbinx_type); + memory->destroy(nbiny_type); + memory->destroy(nbinz_type); + memory->create(nbinx_type, maxtypes+1, "nBinType:nbinx_type"); + memory->create(nbiny_type, maxtypes+1, "nBinType:nbiny_type"); + memory->create(nbinz_type, maxtypes+1, "nBinType:nbinz_type"); + + memory->destroy(mbins_type); + memory->destroy(mbinx_type); + memory->destroy(mbiny_type); + memory->destroy(mbinz_type); + memory->create(mbins_type, maxtypes+1, "nBinType:mbins_type"); + memory->create(mbinx_type, maxtypes+1, "nBinType:mbinx_type"); + memory->create(mbiny_type, maxtypes+1, "nBinType:mbiny_type"); + memory->create(mbinz_type, maxtypes+1, "nBinType:mbinz_type"); + + memory->destroy(mbinxlo_type); + memory->destroy(mbinylo_type); + memory->destroy(mbinzlo_type); + memory->create(mbinxlo_type, maxtypes+1, "nBinType:mbinxlo_type"); + memory->create(mbinylo_type, maxtypes+1, "nBinType:mbinylo_type"); + memory->create(mbinzlo_type, maxtypes+1, "nBinType:mbinzlo_type"); + + memory->destroy(binsizex_type); + memory->destroy(binsizey_type); + memory->destroy(binsizez_type); + memory->create(binsizex_type, maxtypes+1, "nBinType:binsizex_type"); + memory->create(binsizey_type, maxtypes+1, "nBinType:binsizey_type"); + memory->create(binsizez_type, maxtypes+1, "nBinType:binsizez_type"); + + memory->destroy(bininvx_type); + memory->destroy(bininvy_type); + memory->destroy(bininvz_type); + memory->create(bininvx_type, maxtypes+1, "nBinType:bininvx_type"); + memory->create(bininvy_type, maxtypes+1, "nBinType:bininvy_type"); + memory->create(bininvz_type, maxtypes+1, "nBinType:bininvz_type"); + + memory->destroy(maxbins_type); + memory->create(maxbins_type, maxtypes+1, "nBinType:maxbins_type"); + // make sure reallocation occurs in bin_atoms_setup() + for (n = 1; n <= maxtypes; n++) { + maxbins_type[n] = 0; + } + maxatom = 0; + } + +} + +/* --------------------------------------------------------------------- + identify index of type with smallest cutoff + --------------------------------------------------------------------- */ + +int NBinBytype::itype_min() { + + int itypemin = 1; + double ** cutneighsq; + + cutneighsq = neighbor->cutneighsq; + + for (int n = 1; n <= atom->ntypes; n++) { + if (cutneighsq[n][n] < cutneighsq[itypemin][itypemin]) { + itypemin = n; + } + } + + return itypemin; +} + +/* ---------------------------------------------------------------------- + setup neighbor binning geometry + ---------------------------------------------------------------------- */ + +void NBinBytype::setup_bins(int style) +{ + int n; + int itypemin; + + setup_types(); + itypemin = itype_min(); + + // bbox = size of bbox of entire domain + // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost + // for triclinic: + // bbox bounds all 8 corners of tilted box + // subdomain is in lamda coords + // include dimension-dependent extension via comm->cutghost + // domain->bbox() converts lamda extent to box coords and computes bbox + + double bbox[3],bsubboxlo[3],bsubboxhi[3]; + double *cutghost = comm->cutghost; + + if (triclinic == 0) { + bsubboxlo[0] = domain->sublo[0] - cutghost[0]; + bsubboxlo[1] = domain->sublo[1] - cutghost[1]; + bsubboxlo[2] = domain->sublo[2] - cutghost[2]; + bsubboxhi[0] = domain->subhi[0] + cutghost[0]; + bsubboxhi[1] = domain->subhi[1] + cutghost[1]; + bsubboxhi[2] = domain->subhi[2] + cutghost[2]; + } else { + double lo[3],hi[3]; + lo[0] = domain->sublo_lamda[0] - cutghost[0]; + lo[1] = domain->sublo_lamda[1] - cutghost[1]; + lo[2] = domain->sublo_lamda[2] - cutghost[2]; + hi[0] = domain->subhi_lamda[0] + cutghost[0]; + hi[1] = domain->subhi_lamda[1] + cutghost[1]; + hi[2] = domain->subhi_lamda[2] + cutghost[2]; + domain->bbox(lo,hi,bsubboxlo,bsubboxhi); + } + + bbox[0] = bboxhi[0] - bboxlo[0]; + bbox[1] = bboxhi[1] - bboxlo[1]; + bbox[2] = bboxhi[2] - bboxlo[2]; + + // For each type... + + for (n = 1; n <= atom->ntypes; n++) { + // binsize_user only relates to smallest type + // optimal bin size is roughly 1/2 the type-type cutoff + // special case of all cutoffs = 0.0, binsize = box size + + double binsize_optimal; + if (n == itypemin && binsizeflag) binsize_optimal = binsize_user; + else binsize_optimal = 0.5*sqrt(neighbor->cutneighsq[n][n]); + if (binsize_optimal == 0.0) binsize_optimal = bbox[0]; + double binsizeinv = 1.0/binsize_optimal; + + // test for too many global bins in any dimension due to huge global domain + + if (bbox[0]*binsizeinv > MAXSMALLINT || bbox[1]*binsizeinv > MAXSMALLINT || + bbox[2]*binsizeinv > MAXSMALLINT) + error->all(FLERR,"Domain too large for neighbor bins"); + + // create actual bins + // always have one bin even if cutoff > bbox + // for 2d, nbinz_type[n] = 1 + + nbinx_type[n] = static_cast (bbox[0]*binsizeinv); + nbiny_type[n] = static_cast (bbox[1]*binsizeinv); + if (dimension == 3) nbinz_type[n] = static_cast (bbox[2]*binsizeinv); + else nbinz_type[n] = 1; + + if (nbinx_type[n] == 0) nbinx_type[n] = 1; + if (nbiny_type[n] == 0) nbiny_type[n] = 1; + if (nbinz_type[n] == 0) nbinz_type[n] = 1; + + // compute actual bin size for nbins to fit into box exactly + // error if actual bin size << cutoff, since will create a zillion bins + // this happens when nbin = 1 and box size << cutoff + // typically due to non-periodic, flat system in a particular dim + // in that extreme case, should use NSQ not BIN neighbor style + + binsizex_type[n] = bbox[0]/nbinx_type[n]; + binsizey_type[n] = bbox[1]/nbiny_type[n]; + binsizez_type[n] = bbox[2]/nbinz_type[n]; + + bininvx_type[n] = 1.0 / binsizex_type[n]; + bininvy_type[n] = 1.0 / binsizey_type[n]; + bininvz_type[n] = 1.0 / binsizez_type[n]; + + if (binsize_optimal*bininvx_type[n] > CUT2BIN_RATIO || + binsize_optimal*bininvy_type[n] > CUT2BIN_RATIO || + binsize_optimal*bininvz_type[n] > CUT2BIN_RATIO) + error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); + + // mbinlo/hi = lowest and highest global bins my ghost atoms could be in + // coord = lowest and highest values of coords for my ghost atoms + // static_cast(-1.5) = -1, so subract additional -1 + // add in SMALL for round-off safety + + int mbinxhi,mbinyhi,mbinzhi; + double coord; + + coord = bsubboxlo[0] - SMALL*bbox[0]; + mbinxlo_type[n] = static_cast ((coord-bboxlo[0])*bininvx_type[n]); + if (coord < bboxlo[0]) mbinxlo_type[n] = mbinxlo_type[n] - 1; + coord = bsubboxhi[0] + SMALL*bbox[0]; + mbinxhi = static_cast ((coord-bboxlo[0])*bininvx_type[n]); + + coord = bsubboxlo[1] - SMALL*bbox[1]; + mbinylo_type[n] = static_cast ((coord-bboxlo[1])*bininvy_type[n]); + if (coord < bboxlo[1]) mbinylo_type[n] = mbinylo_type[n] - 1; + coord = bsubboxhi[1] + SMALL*bbox[1]; + mbinyhi = static_cast ((coord-bboxlo[1])*bininvy_type[n]); + + if (dimension == 3) { + coord = bsubboxlo[2] - SMALL*bbox[2]; + mbinzlo_type[n] = static_cast ((coord-bboxlo[2])*bininvz_type[n]); + if (coord < bboxlo[2]) mbinzlo_type[n] = mbinzlo_type[n] - 1; + coord = bsubboxhi[2] + SMALL*bbox[2]; + mbinzhi = static_cast ((coord-bboxlo[2])*bininvz_type[n]); + } + + // extend bins by 1 to insure stencil extent is included + // for 2d, only 1 bin in z + + mbinxlo_type[n] = mbinxlo_type[n] - 1; + mbinxhi = mbinxhi + 1; + mbinx_type[n] = mbinxhi - mbinxlo_type[n] + 1; + + mbinylo_type[n] = mbinylo_type[n] - 1; + mbinyhi = mbinyhi + 1; + mbiny_type[n] = mbinyhi - mbinylo_type[n] + 1; + + if (dimension == 3) { + mbinzlo_type[n] = mbinzlo_type[n] - 1; + mbinzhi = mbinzhi + 1; + } else mbinzlo_type[n] = mbinzhi = 0; + mbinz_type[n] = mbinzhi - mbinzlo_type[n] + 1; + + bigint bbin = ((bigint) mbinx_type[n]) + * ((bigint) mbiny_type[n]) * ((bigint) mbinz_type[n]) + 1; + if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins"); + mbins_type[n] = bbin; + } + +} + +/* ---------------------------------------------------------------------- + bin owned and ghost atoms by type +------------------------------------------------------------------------- */ + +void NBinBytype::bin_atoms() +{ + int i,ibin,n; + + last_bin = update->ntimestep; + for (n = 1; n <= maxtypes; n++) { + for (i = 0; i < mbins_type[n]; i++) binhead_type[n][i] = -1; + } + + // bin in reverse order so linked list will be in forward order + // also puts ghost atoms at end of list, which is necessary + + double **x = atom->x; + int *mask = atom->mask; + int *type = atom->type; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + + if (includegroup) { + int bitmask = group->bitmask[includegroup]; + for (i = nall-1; i >= nlocal; i--) { + if (mask[i] & bitmask) { + n = type[i]; + ibin = coord2bin(x[i], n); + atom2bin_type[n][i] = ibin; + bins_type[n][i] = binhead_type[n][ibin]; + binhead_type[n][ibin] = i; + } + } + for (i = atom->nfirst-1; i >= 0; i--) { + n = type[i]; + ibin = coord2bin(x[i], n); + atom2bin_type[n][i] = ibin; + bins_type[n][i] = binhead_type[n][ibin]; + binhead_type[n][ibin] = i; + } + } else { + for (i = nall-1; i >= 0; i--) { + n = type[i]; + ibin = coord2bin(x[i], n); + atom2bin_type[n][i] = ibin; + bins_type[n][i] = binhead_type[n][ibin]; + binhead_type[n][ibin] = i; + } + } +} + + +/* ---------------------------------------------------------------------- + allocate/reallocate vectors +------------------------------------------------------------------------- */ + +void NBinBytype::bin_atoms_setup(int nall) { + + // all atom2bin, bins must be of length nall + if (nall > maxatom) { + for (int n = 1; n <= maxtypes; n++) { + memory->destroy(bins_type[n]); + memory->destroy(atom2bin_type[n]); + memory->create(bins_type[n], nall, "NBinBytype:bin_type"); + memory->create(atom2bin_type[n], nall, "NBinBytype:atom2bin_type"); + } + maxatom = nall; + } + + for (int n = 1; n <= maxtypes; n++) { + if (mbins_type[n] > maxbins_type[n]) { + maxbins_type[n] = mbins_type[n]; + memory->destroy(binhead_type[n]); + memory->create(binhead_type[n], mbins_type[n], "NBinBytype:mbins_type"); + } + } + +} + + +/* ---------------------------------------------------------------------- + convert atom coords into local bin # for bin type it +------------------------------------------------------------------------- */ + +int NBinBytype::coord2bin(double *x, int it) +{ + int ix,iy,iz; + int ibin; + + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) + error->one(FLERR,"Non-numeric positions - simulation unstable"); + + if (x[0] >= bboxhi[0]) + ix = static_cast ((x[0]-bboxhi[0])*bininvx_type[it]) + nbinx_type[it]; + else if (x[0] >= bboxlo[0]) { + ix = static_cast ((x[0]-bboxlo[0])*bininvx_type[it]); + ix = MIN(ix,nbinx_type[it]-1); + } else + ix = static_cast ((x[0]-bboxlo[0])*bininvx_type[it]) - 1; + + if (x[1] >= bboxhi[1]) + iy = static_cast ((x[1]-bboxhi[1])*bininvy_type[it]) + nbiny_type[it]; + else if (x[1] >= bboxlo[1]) { + iy = static_cast ((x[1]-bboxlo[1])*bininvy_type[it]); + iy = MIN(iy,nbiny_type[it]-1); + } else + iy = static_cast ((x[1]-bboxlo[1])*bininvy_type[it]) - 1; + + if (x[2] >= bboxhi[2]) + iz = static_cast ((x[2]-bboxhi[2])*bininvz_type[it]) + nbinz_type[it]; + else if (x[2] >= bboxlo[2]) { + iz = static_cast ((x[2]-bboxlo[2])*bininvz_type[it]); + iz = MIN(iz,nbinz_type[it]-1); + } else + iz = static_cast ((x[2]-bboxlo[2])*bininvz_type[it]) - 1; + + + ibin = (iz-mbinzlo_type[it])*mbiny_type[it]*mbinx_type[it] + + (iy-mbinylo_type[it])*mbinx_type[it] + + (ix-mbinxlo_type[it]); + return ibin; +} + + +/* ---------------------------------------------------------------------- + tot up for types + ---------------------------------------------------------------------- */ + +bigint NBinBytype::memory_usage() +{ + bigint bytes = 0; + + for (int m = 1; m < maxtypes; m++) { + bytes += 2*maxatom*sizeof(int); + bytes += maxbins_type[m]*sizeof(int); + } + return bytes; +} diff --git a/src/nbin_bytype.h b/src/nbin_bytype.h new file mode 100644 index 0000000000..89e6ca3650 --- /dev/null +++ b/src/nbin_bytype.h @@ -0,0 +1,56 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NBIN_CLASS + +NBinStyle(bytype, + NBinBytype, + NB_BYTYPE) + +#else + +#ifndef LMP_NBIN_BYTYPE_H +#define LMP_NBIN_BYTYPE_H + +#include "nbin.h" + +namespace LAMMPS_NS { + +class NBinBytype : public NBin { + public: + + NBinBytype(class LAMMPS *); + ~NBinBytype(); + void bin_atoms_setup(int); + void setup_bins(int); + void bin_atoms(); + + int coord2bin(double *x, int itype); + bigint memory_usage(); + + private: + int maxtypes; + int * maxbins_type; + + void setup_types(); + int itype_min(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nbin_standard.h b/src/nbin_standard.h index 14b587c24c..06defdb101 100644 --- a/src/nbin_standard.h +++ b/src/nbin_standard.h @@ -15,7 +15,7 @@ NBinStyle(standard, NBinStandard, - 0) + NB_STANDARD) #else diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 58737b815d..6e861b5a2b 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1620,6 +1620,14 @@ int Neighbor::choose_bin(NeighRequest *rq) if (!rq->kokkos_device != !(mask & NB_KOKKOS_DEVICE)) continue; if (!rq->kokkos_host != !(mask & NB_KOKKOS_HOST)) continue; + // neighbor style is BIN or MULTI or BYTYPE and must match + + if (style == Neighbor::BIN || style == Neighbor::MULTI) { + if (!(mask & NB_STANDARD)) continue; + } else if (style == Neighbor::BYTYPE) { + if (!(mask & NB_BYTYPE)) continue; + } + return i+1; } @@ -1690,12 +1698,14 @@ int Neighbor::choose_stencil(NeighRequest *rq) if (!rq->ghost != !(mask & NS_GHOST)) continue; if (!rq->ssa != !(mask & NS_SSA)) continue; - // neighbor style is BIN or MULTI and must match + // neighbor style is one of BIN, MULTI or BYTYPE and must match if (style == Neighbor::BIN) { if (!(mask & NS_BIN)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NS_MULTI)) continue; + } else if (style == Neighbor::BYTYPE) { + if (!(mask & NS_BYTYPE)) continue; } // dimension is 2 or 3 and must match @@ -1825,7 +1835,7 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!rq->halffull != !(mask & NP_HALF_FULL)) continue; if (!rq->off2on != !(mask & NP_OFF2ON)) continue; - // neighbor style is one of NSQ,BIN,MULTI and must match + // neighbor style is one of NSQ,BIN,MULTI or BYTYPE and must match if (style == Neighbor::NSQ) { if (!(mask & NP_NSQ)) continue; @@ -1833,6 +1843,8 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!(mask & NP_BIN)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NP_MULTI)) continue; + } else if (style == Neighbor::BYTYPE) { + if (!(mask & NP_BYTYPE)) continue; } // domain triclinic flag is on or off and must match @@ -2199,6 +2211,7 @@ void Neighbor::set(int narg, char **arg) if (strcmp(arg[1],"nsq") == 0) style = Neighbor::NSQ; else if (strcmp(arg[1],"bin") == 0) style = Neighbor::BIN; else if (strcmp(arg[1],"multi") == 0) style = Neighbor::MULTI; + else if (strcmp(arg[1],"bytype") == 0) style = Neighbor::BYTYPE; else error->all(FLERR,"Illegal neighbor command"); if (style == Neighbor::MULTI && lmp->citeme) lmp->citeme->add(cite_neigh_multi); diff --git a/src/neighbor.h b/src/neighbor.h index 9ee2af9c75..e5b76dd41b 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -20,7 +20,7 @@ namespace LAMMPS_NS { class Neighbor : protected Pointers { public: - enum{NSQ,BIN,MULTI}; + enum{NSQ,BIN,MULTI,BYTYPE}; int style; // 0,1,2 = nsq, bin, multi int every; // build every this many steps int delay; // delay build for this many steps @@ -239,6 +239,8 @@ namespace NeighConst { static const int NB_KOKKOS_DEVICE = 1<<1; static const int NB_KOKKOS_HOST = 1<<2; static const int NB_SSA = 1<<3; + static const int NB_BYTYPE = 1<<4; + static const int NB_STANDARD = 1<<5; static const int NS_BIN = 1<<0; static const int NS_MULTI = 1<<1; @@ -252,6 +254,7 @@ namespace NeighConst { static const int NS_TRI = 1<<9; static const int NS_GHOST = 1<<10; static const int NS_SSA = 1<<11; + static const int NS_BYTYPE = 1<<12; static const int NP_NSQ = 1<<0; static const int NP_BIN = 1<<1; @@ -278,6 +281,7 @@ namespace NeighConst { static const int NP_SKIP = 1<<22; static const int NP_HALF_FULL = 1<<23; static const int NP_OFF2ON = 1<<24; + static const int NP_BYTYPE = 1<<25; } } diff --git a/src/npair_full_bytype.cpp b/src/npair_full_bytype.cpp new file mode 100644 index 0000000000..d244c263ed --- /dev/null +++ b/src/npair_full_bytype.cpp @@ -0,0 +1,144 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "npair_full_bytype.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "domain.h" +#include "my_page.h" +#include "error.h" + +#include "nbin.h" +#include "nstencil.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairFullBytype::NPairFullBytype(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction for all neighbors + multi-type stencil is itype dependent and is distance checked + every neighbor pair appears in list of both atoms i and j + KS ADJUST +------------------------------------------------------------------------- */ + +void NPairFullBytype::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + if (molecular == 2) moltemplate = 1; + else moltemplate = 0; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // loop over all atoms in other bins in stencil, including self + // skip if i,j neighbor cutoff is less than bin distance + // skip i = j + + int kbin; + ibin = nb->atom2bin_type[itype][i]; + for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + if (itype == ktype) { + kbin = ibin; + } + else { + // Locate i in ktype bin + kbin = nb->coord2bin(x[i], ktype); + } + + s = this->ns->stencil_type[itype][ktype]; + ns = this->ns->nstencil_type[itype][ktype]; + for (k = 0; k < ns; k++) { + int js = this->nb->binhead_type[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = this->nb->bins_type[ktype][j]) { + jtype = type[j]; + if (i == j) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; + list->gnum = 0; +} diff --git a/src/npair_full_bytype.h b/src/npair_full_bytype.h new file mode 100644 index 0000000000..9ce221ff22 --- /dev/null +++ b/src/npair_full_bytype.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(full/bytype, + NPairFullBytype, + NP_FULL | NP_BYTYPE | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_FULL_BYTYPE_H +#define LMP_NPAIR_FULL_BYTYPE_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairFullBytype : public NPair { + public: + NPairFullBytype(class LAMMPS *); + ~NPairFullBytype() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/npair_half_bytype_newton.cpp b/src/npair_half_bytype_newton.cpp new file mode 100755 index 0000000000..66899564be --- /dev/null +++ b/src/npair_half_bytype_newton.cpp @@ -0,0 +1,219 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "npair_half_bytype_newton.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "domain.h" +#include "my_page.h" +#include "error.h" + +#include "nbin.h" +#include "nstencil.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfBytypeNewton::NPairHalfBytypeNewton(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + KS REWRTIE + binned neighbor list construction with full Newton's 3rd law + each owned atom i checks its own bin and other bins in Newton stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfBytypeNewton::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + if (molecular == 2) moltemplate = 1; + else moltemplate = 0; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + int js; + int kbin; + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = nb->atom2bin_type[itype][i]; + + for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + + if (itype == ktype) { + + // own bin ... + js = nb->bins_type[itype][i]; + for (j = js; j >= 0; j = nb->bins_type[itype][j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = this->ns->stencil_type[itype][itype]; + ns = this->ns->nstencil_type[itype][itype]; + for (k = 0; k < ns; k++) { + js = nb->binhead_type[itype][ibin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[itype][j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + + } + else { + // smaller -> larger: locate i in the ktype bin structure + + kbin = nb->coord2bin(x[i], ktype); + s = this->ns->stencil_type[itype][ktype]; + ns = this->ns->nstencil_type[itype][ktype]; + + for (k = 0; k < ns; k++) { + js = nb->binhead_type[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[ktype][j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + } + } + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_bytype_newton.h b/src/npair_half_bytype_newton.h new file mode 100755 index 0000000000..8be7292219 --- /dev/null +++ b/src/npair_half_bytype_newton.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/bytype/newton, + NPairHalfBytypeNewton, + NP_HALF | NP_BYTYPE | NP_NEWTON | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_BYTYPE_NEWTON_H +#define LMP_NPAIR_HALF_BYTYPE_NEWTON_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfBytypeNewton : public NPair { + public: + NPairHalfBytypeNewton(class LAMMPS *); + ~NPairHalfBytypeNewton() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/npair_half_size_bytype_newtoff.cpp b/src/npair_half_size_bytype_newtoff.cpp new file mode 100644 index 0000000000..f065c60736 --- /dev/null +++ b/src/npair_half_size_bytype_newtoff.cpp @@ -0,0 +1,130 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +es certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "npair_half_size_bytype_newtoff.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +#include "nbin.h" +#include "nstencil.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeBytypeNewtoff::NPairHalfSizeBytypeNewtoff(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + REWRITE + binned neighbor list construction with partial Newton's 3rd law + each owned atom i checks own bin and other bins in stencil + multi-type stencil is itype dependent and is distance checked + pair stored once if i,j are both owned and i < j + pair stored by me if j is ghost (also stored by proc owning j) +------------------------------------------------------------------------- */ + +void NPairHalfSizeBytypeNewtoff::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // skip if i,j neighbor cutoff is less than bin distance + // stores own/own pairs only once + // stores own/ghost pairs on both procs + + int kbin; + + ibin = nb->atom2bin_type[itype][i]; + for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + if (itype == ktype) { + kbin = ibin; + } + else { + // Locate i in ktype bin + kbin = nb->coord2bin(x[i], ktype); + } + s = this->ns->stencil_type[itype][ktype]; + ns = this->ns->nstencil_type[itype][ktype]; + for (k = 0; k < ns; k++) { + int js = nb->binhead_type[ktype][kbin + s[k]]; + for (j = js; j >=0; j = nb->bins_type[ktype][j]) { + if (j <= i) continue; + jtype = type[j]; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_size_bytype_newtoff.h b/src/npair_half_size_bytype_newtoff.h new file mode 100644 index 0000000000..e131a12f4b --- /dev/null +++ b/src/npair_half_size_bytype_newtoff.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/bytype/newtoff, + NPairHalfSizeBytypeNewtoff, + NP_HALF | NP_SIZE | NP_BYTYPE | NP_NEWTOFF | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTOFF_H +#define LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTOFF_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeBytypeNewtoff : public NPair { + public: + NPairHalfSizeBytypeNewtoff(class LAMMPS *); + ~NPairHalfSizeBytypeNewtoff() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/npair_half_size_bytype_newton.cpp b/src/npair_half_size_bytype_newton.cpp new file mode 100755 index 0000000000..3981635439 --- /dev/null +++ b/src/npair_half_size_bytype_newton.cpp @@ -0,0 +1,189 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "npair_half_size_bytype_newton.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +#include "nbin.h" +#include "nstencil.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeBytypeNewton::NPairHalfSizeBytypeNewton(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + KS REWRTIE + binned neighbor list construction with full Newton's 3rd law + each owned atom i checks its own bin and other bins in Newton stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfSizeBytypeNewton::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + int js; + int kbin; + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = nb->atom2bin_type[itype][i]; + + for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + + if (itype == ktype) { + + // own bin ... + js = nb->bins_type[itype][i]; + for (j = js; j >= 0; j = nb->bins_type[itype][j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = this->ns->stencil_type[itype][itype]; + ns = this->ns->nstencil_type[itype][itype]; + for (k = 0; k < ns; k++) { + js = nb->binhead_type[itype][ibin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[itype][j]) { + jtype = type[j]; + // KS. CHECK ME if (cutsq[jtype] < distsq[k]) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + } + else { + // KS + // smaller -> larger: locate i in the ktype bin structure + kbin = nb->coord2bin(x[i], ktype); + + s = this->ns->stencil_type[itype][ktype]; + ns = this->ns->nstencil_type[itype][ktype]; + for (k = 0; k < ns; k++) { + js = nb->binhead_type[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[ktype][j]) { + + jtype = type[j]; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + } + } + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_size_bytype_newton.h b/src/npair_half_size_bytype_newton.h new file mode 100755 index 0000000000..a6bb7a00a8 --- /dev/null +++ b/src/npair_half_size_bytype_newton.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/bytype/newton, + NPairHalfSizeBytypeNewton, + NP_HALF | NP_SIZE | NP_BYTYPE | NP_NEWTON | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_H +#define LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeBytypeNewton : public NPair { + public: + NPairHalfSizeBytypeNewton(class LAMMPS *); + ~NPairHalfSizeBytypeNewton() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil.h b/src/nstencil.h index 75e678b483..bdd656b937 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -34,6 +34,10 @@ class NStencil : protected Pointers { double cutoff_custom; // cutoff set by requestor + // BYTYPE stencils + int ** nstencil_type; // No. of bins for stencil[itype][jtype] + int *** stencil_type; // Stencil for [itype][jtype] + NStencil(class LAMMPS *); virtual ~NStencil(); void post_constructor(class NeighRequest *); diff --git a/src/nstencil_full_bytype_3d.cpp b/src/nstencil_full_bytype_3d.cpp new file mode 100644 index 0000000000..3936ec2483 --- /dev/null +++ b/src/nstencil_full_bytype_3d.cpp @@ -0,0 +1,192 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nstencil_full_bytype_3d.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilFullBytype3d::NStencilFullBytype3d(LAMMPS *lmp) : + NStencil(lmp) +{ + maxstencil_type = NULL; +} + +NStencilFullBytype3d::~NStencilFullBytype3d() { + + if (maxstencil_type) { + memory->destroy(nstencil_type); + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = 0; j <= atom->ntypes; j++) { + if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); + } + delete [] stencil_type[i]; + } + delete [] stencil_type; + memory->destroy(maxstencil_type); + } +} + +void NStencilFullBytype3d::copy_bin_info_bytype(int itype) { + + mbinx = nb->mbinx_type[itype]; + mbiny = nb->mbiny_type[itype]; + mbinz = nb->mbinz_type[itype]; + binsizex = nb->binsizex_type[itype]; + binsizey = nb->binsizey_type[itype]; + binsizez = nb->binsizez_type[itype]; + bininvx = nb->bininvx_type[itype]; + bininvy = nb->bininvy_type[itype]; + bininvz = nb->bininvz_type[itype]; +} + +int NStencilFullBytype3d::copy_neigh_info_bytype(int itype) { + + cutneighmaxsq = neighbor->cutneighsq[itype][itype]; + cutneighmax = sqrt(cutneighmaxsq); + cuttypesq = neighbor->cuttypesq; + + // sx,sy,sz = max range of stencil in each dim + // smax = max possible size of entire 3d stencil + // stencil will be empty if cutneighmax = 0.0 + + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + return ((2*sx+1) * (2*sy+1) * (2*sz+1)); +} + +void NStencilFullBytype3d::create_setup() +{ + + int itype, jtype; + int maxtypes; + int smax; + + //printf("NStencilFullBytype3d::create_steup()\n"); + maxtypes = atom->ntypes; + + if (maxstencil_type == NULL) { + memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "BAD A"); + memory->create(nstencil_type, maxtypes+1, maxtypes+1, "BAD B"); + stencil_type = new int**[maxtypes+1](); + for (itype = 1; itype <= maxtypes; ++itype) { + stencil_type[itype] = new int*[maxtypes+1](); + for (jtype = 1; jtype <= maxtypes; ++jtype) { + maxstencil_type[itype][jtype] = 0; + } + } + } + + // like -> like => use standard newtoff stencil at bin + + for (itype = 1; itype <= maxtypes; ++itype) { + copy_bin_info_bytype(itype); + smax = copy_neigh_info_bytype(itype); + if (smax > maxstencil_type[itype][itype]) { + maxstencil_type[itype][itype] = smax; + memory->destroy(stencil_type[itype][itype]); + memory->create(stencil_type[itype][itype], smax, + "NStencilFullBytype::create_steup() stencil"); + } + create_newtoff(itype, itype, cutneighmaxsq); + } + + // smaller -> larger => use existing newtoff stencil in larger bin + // larger -> smaller => use multi-like stencil for small-large in smaller bin + // If types are same cutoff, use existing like-like stencil. + + for (itype = 1; itype <= maxtypes; ++itype) { + for (jtype = 1; jtype <= maxtypes; ++jtype) { + if (itype == jtype) continue; + if (cuttypesq[itype] <= cuttypesq[jtype]) { + // Potential destroy/create problem? + nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; + stencil_type[itype][jtype] = stencil_type[jtype][jtype]; + } + else { + copy_bin_info_bytype(jtype); + // smax = copy_neigh_info_bytype(jtype); + + cutneighmaxsq = cuttypesq[jtype]; + cutneighmax = sqrt(cutneighmaxsq); + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + smax = (2*sx+1) * (2*sy+1) * (2*sz+1); + if (smax > maxstencil_type[itype][jtype]) { + maxstencil_type[itype][jtype] = smax; + memory->destroy(stencil_type[itype][jtype]); + memory->create(stencil_type[itype][jtype], smax, "Bad C"); + } + create_newtoff(itype, jtype, cuttypesq[jtype]); + } + } + } + + //for (itype = 1; itype <= maxtypes; itype++) { + // for (jtype = 1; jtype <= maxtypes; jtype++) { + // printf("i j n %d %d %d\n", itype, jtype, nstencil_type[itype][jtype]); + // printf("i j n %d %d %d\n", itype, jtype, maxstencil_type[itype][jtype]); + // } + // } + +} + +void NStencilFullBytype3d::create_newtoff(int itype, int jtype, double cutsq) { + + int i, j, k, ns; + + ns = 0; + + for (k = -sz; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; + + nstencil_type[itype][jtype] = ns; +} + +/* ---------------------------------------------------------------------- + create stencil based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilFullBytype3d::create() +{ + //int i,j,k; + + //nstencil = 0; + + //for (k = -sz; k <= sz; k++) + // for (j = -sy; j <= sy; j++) + // for (i = -sx; i <= sx; i++) + // if (bin_distance(i,j,k) < cutneighmaxsq) + // stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i; +} diff --git a/src/nstencil_full_bytype_3d.h b/src/nstencil_full_bytype_3d.h new file mode 100644 index 0000000000..6e61365d17 --- /dev/null +++ b/src/nstencil_full_bytype_3d.h @@ -0,0 +1,53 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(full/bytype/3d, + NStencilFullBytype3d, + NS_FULL | NS_BYTYPE | NS_3D | + NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_FULL_BYTYPE_3D_H +#define LMP_NSTENCIL_FULL_BYTYPE_3D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilFullBytype3d : public NStencil { + public: + NStencilFullBytype3d(class LAMMPS *); + ~NStencilFullBytype3d(); + void create(); + void create_setup(); + +private: + int ** maxstencil_type; + + void copy_bin_info_bytype(int); + int copy_neigh_info_bytype(int); + void create_newtoff(int, int, double); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_bytype_2d_newton.cpp b/src/nstencil_half_bytype_2d_newton.cpp new file mode 100644 index 0000000000..18ed0972ff --- /dev/null +++ b/src/nstencil_half_bytype_2d_newton.cpp @@ -0,0 +1,192 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nstencil_half_bytype_2d_newton.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfBytype2dNewton::NStencilHalfBytype2dNewton(LAMMPS *lmp) : + NStencil(lmp) +{ + maxstencil_type = NULL; +} + +NStencilHalfBytype2dNewton::~NStencilHalfBytype2dNewton() { + + memory->destroy(nstencil_type); + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = 0; j <= atom->ntypes; j++) { + if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); + } + delete [] stencil_type[i]; + } + delete [] stencil_type; + memory->destroy(maxstencil_type); +} + +// KS To superclass +void NStencilHalfBytype2dNewton::copy_bin_info_bytype(int itype) { + + mbinx = nb->mbinx_type[itype]; + mbiny = nb->mbiny_type[itype]; + mbinz = nb->mbinz_type[itype]; + binsizex = nb->binsizex_type[itype]; + binsizey = nb->binsizey_type[itype]; + binsizez = nb->binsizez_type[itype]; + bininvx = nb->bininvx_type[itype]; + bininvy = nb->bininvy_type[itype]; + bininvz = nb->bininvz_type[itype]; +} + +// KS To superclass? +int NStencilHalfBytype2dNewton::copy_neigh_info_bytype(int itype) { + + cutneighmaxsq = neighbor->cutneighsq[itype][itype]; + cutneighmax = sqrt(cutneighmaxsq); + cuttypesq = neighbor->cuttypesq; + + // sx,sy,sz = max range of stencil in each dim + // smax = max possible size of entire 2d stencil + // stencil will be empty if cutneighmax = 0.0 + + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + return ((2*sx+1) * (2*sy+1) * (2*sz+1)); +} + +void NStencilHalfBytype2dNewton::create_setup() +{ + + int itype, jtype; + int maxtypes; + int smax; + + // maxstencil_type to superclass? + maxtypes = atom->ntypes; + + if (maxstencil_type == NULL) { + memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "maxstencil_type"); + memory->create(nstencil_type, maxtypes+1, maxtypes+1, "nstencil_type"); + stencil_type = new int**[maxtypes+1](); + for (itype = 1; itype <= maxtypes; ++itype) { + stencil_type[itype] = new int*[maxtypes+1](); + for (jtype = 1; jtype <= maxtypes; ++jtype) { + maxstencil_type[itype][jtype] = 0; + nstencil_type[itype][jtype] = 0; + } + } + } + + // like -> like => use standard Newton stencil at bin + + for (itype = 1; itype <= maxtypes; ++itype) { + copy_bin_info_bytype(itype); + smax = copy_neigh_info_bytype(itype); + if (smax > maxstencil_type[itype][itype]) { + maxstencil_type[itype][itype] = smax; + memory->destroy(stencil_type[itype][itype]); + memory->create(stencil_type[itype][itype], smax, + "NStencilHalfBytypeNewton::create_steup() stencil"); + } + create_newton(itype, itype, cutneighmaxsq); + } + + // Cross types: "Newton on" reached by using Newton off stencil and + // looking one way through hierarchy + // smaller -> larger => use Newton off stencil in larger bin + // larger -> smaller => no nstecil required + // If cut offs are same, use existing type-type stencil + + for (itype = 1; itype <= maxtypes; ++itype) { + for (jtype = 1; jtype <= maxtypes; ++jtype) { + if (itype == jtype) continue; + if (cuttypesq[itype] == cuttypesq[jtype]) { + nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; + stencil_type[itype][jtype] = stencil_type[jtype][jtype]; + } + else if (cuttypesq[itype] < cuttypesq[jtype]) { + copy_bin_info_bytype(jtype); + + cutneighmaxsq = cuttypesq[jtype]; + cutneighmax = sqrt(cutneighmaxsq); + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + smax = (2*sx+1) * (2*sy+1) * (2*sz+1); + if (smax > maxstencil_type[itype][jtype]) { + maxstencil_type[itype][jtype] = smax; + memory->destroy(stencil_type[itype][jtype]); + memory->create(stencil_type[itype][jtype], smax, "stencil_type[]"); + } + create_newtoff(itype, jtype, cuttypesq[jtype]); + } + } + } + +} + +void NStencilHalfBytype2dNewton::create_newton(int itype, int jtype, double cutsq) { + + int i, j, ns; + + ns = 0; + + for (j = 0; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (j > 0 || (j == 0 && i > 0)) { + if (bin_distance(i,j,0) < cutsq) + stencil_type[itype][jtype][ns++] = j*mbinx + i; + } + nstencil_type[itype][jtype] = ns; +} + +void NStencilHalfBytype2dNewton::create_newtoff(int itype, int jtype, double cutsq) { + + int i, j, ns; + + ns = 0; + + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,0) < cutsq) + stencil_type[itype][jtype][ns++] = j*mbinx + i; + + nstencil_type[itype][jtype] = ns; +} + +/* ---------------------------------------------------------------------- + create stencil based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfBytype2dNewton::create() +{ + // KS. Move "creation" here. +} diff --git a/src/nstencil_half_bytype_2d_newton.h b/src/nstencil_half_bytype_2d_newton.h new file mode 100644 index 0000000000..4d33c26a71 --- /dev/null +++ b/src/nstencil_half_bytype_2d_newton.h @@ -0,0 +1,52 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/bytype/2d/newton, + NStencilHalfBytype2dNewton, + NS_HALF | NS_BYTYPE | NS_2D | NS_NEWTON | NS_ORTHO) + +#else + +#ifndef LMP_NSTENCIL_HALF_BYTYPE_2D_NEWTON_H +#define LMP_NSTENCIL_HALF_BYTYPE_2D_NEWTON_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfBytype2dNewton : public NStencil { + public: + NStencilHalfBytype2dNewton(class LAMMPS *); + ~NStencilHalfBytype2dNewton(); + void create_setup(); + void create(); + + private: + int ** maxstencil_type; + + void copy_bin_info_bytype(int); + int copy_neigh_info_bytype(int); + void create_newton(int, int, double); + void create_newtoff(int, int, double); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_bytype_3d_newtoff.cpp b/src/nstencil_half_bytype_3d_newtoff.cpp new file mode 100644 index 0000000000..f111715e5d --- /dev/null +++ b/src/nstencil_half_bytype_3d_newtoff.cpp @@ -0,0 +1,190 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nstencil_half_bytype_3d_newtoff.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfBytype3dNewtoff::NStencilHalfBytype3dNewtoff(LAMMPS *lmp) : + NStencil(lmp) +{ + maxstencil_type = NULL; +} + +NStencilHalfBytype3dNewtoff::~NStencilHalfBytype3dNewtoff() { + + memory->destroy(nstencil_type); + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = 0; j <= atom->ntypes; j++) { + if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); + } + delete [] stencil_type[i]; + } + delete [] stencil_type; + memory->destroy(maxstencil_type); +} + +void NStencilHalfBytype3dNewtoff::copy_bin_info_bytype(int itype) { + + mbinx = nb->mbinx_type[itype]; + mbiny = nb->mbiny_type[itype]; + mbinz = nb->mbinz_type[itype]; + binsizex = nb->binsizex_type[itype]; + binsizey = nb->binsizey_type[itype]; + binsizez = nb->binsizez_type[itype]; + bininvx = nb->bininvx_type[itype]; + bininvy = nb->bininvy_type[itype]; + bininvz = nb->bininvz_type[itype]; +} + +int NStencilHalfBytype3dNewtoff::copy_neigh_info_bytype(int itype) { + + cutneighmaxsq = neighbor->cutneighsq[itype][itype]; + cutneighmax = sqrt(cutneighmaxsq); + cuttypesq = neighbor->cuttypesq; + + // sx,sy,sz = max range of stencil in each dim + // smax = max possible size of entire 3d stencil + // stencil will be empty if cutneighmax = 0.0 + + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + return ((2*sx+1) * (2*sy+1) * (2*sz+1)); +} + +void NStencilHalfBytype3dNewtoff::create_setup() +{ + + int itype, jtype; + int maxtypes; + int smax; + + //printf("NStencilHalfBytype3dNewtoff::create_steup()\n"); + maxtypes = atom->ntypes; + + if (maxstencil_type == NULL) { + memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "BAD A"); + memory->create(nstencil_type, maxtypes+1, maxtypes+1, "BAD B"); + stencil_type = new int**[maxtypes+1](); + for (itype = 1; itype <= maxtypes; ++itype) { + stencil_type[itype] = new int*[maxtypes+1](); + for (jtype = 1; jtype <= maxtypes; ++jtype) { + maxstencil_type[itype][jtype] = 0; + } + } + } + + // like -> like => use standard newtoff stencil at bin + + for (itype = 1; itype <= maxtypes; ++itype) { + copy_bin_info_bytype(itype); + smax = copy_neigh_info_bytype(itype); + if (smax > maxstencil_type[itype][itype]) { + maxstencil_type[itype][itype] = smax; + memory->destroy(stencil_type[itype][itype]); + memory->create(stencil_type[itype][itype], smax, + "NStencilHalfBytypeNewtoff::create_steup() stencil"); + } + create_newtoff(itype, itype, cutneighmaxsq); + } + + // smaller -> larger => use existing newtoff stencil in larger bin + // larger -> smaller => use multi-like stencil for small-large in smaller bin + // If types are same cutoff, use existing like-like stencil. + + for (itype = 1; itype <= maxtypes; ++itype) { + for (jtype = 1; jtype <= maxtypes; ++jtype) { + if (itype == jtype) continue; + if (cuttypesq[itype] <= cuttypesq[jtype]) { + // Potential destroy/create problem? + nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; + stencil_type[itype][jtype] = stencil_type[jtype][jtype]; + } + else { + copy_bin_info_bytype(jtype); + // smax = copy_neigh_info_bytype(jtype); + + cutneighmaxsq = cuttypesq[jtype]; + cutneighmax = sqrt(cutneighmaxsq); + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + smax = (2*sx+1) * (2*sy+1) * (2*sz+1); + if (smax > maxstencil_type[itype][jtype]) { + maxstencil_type[itype][jtype] = smax; + memory->destroy(stencil_type[itype][jtype]); + memory->create(stencil_type[itype][jtype], smax, "Bad C"); + } + create_newtoff(itype, jtype, cuttypesq[jtype]); + } + } + } + + //for (itype = 1; itype <= maxtypes; itype++) { + // for (jtype = 1; jtype <= maxtypes; jtype++) { + // printf("i j n %d %d %d\n", itype, jtype, nstencil_type[itype][jtype]); + // printf("i j n %d %d %d\n", itype, jtype, maxstencil_type[itype][jtype]); + // } + // } + +} + +void NStencilHalfBytype3dNewtoff::create_newtoff(int itype, int jtype, double cutsq) { + + int i, j, k, ns; + + ns = 0; + + for (k = -sz; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; + + nstencil_type[itype][jtype] = ns; +} + +/* ---------------------------------------------------------------------- + create stencil based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfBytype3dNewtoff::create() +{ + //int i,j,k; + + //nstencil = 0; + + //for (k = -sz; k <= sz; k++) + // for (j = -sy; j <= sy; j++) + // for (i = -sx; i <= sx; i++) + // if (bin_distance(i,j,k) < cutneighmaxsq) + // stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i; +} diff --git a/src/nstencil_half_bytype_3d_newtoff.h b/src/nstencil_half_bytype_3d_newtoff.h new file mode 100644 index 0000000000..bf83a31e9a --- /dev/null +++ b/src/nstencil_half_bytype_3d_newtoff.h @@ -0,0 +1,51 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/bytype/3d/newtoff, + NStencilHalfBytype3dNewtoff, + NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTOFF | NS_ORTHO | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTOFF_H +#define LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTOFF_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfBytype3dNewtoff : public NStencil { + public: + NStencilHalfBytype3dNewtoff(class LAMMPS *); + ~NStencilHalfBytype3dNewtoff(); + void create_setup(); + void create(); + + private: + int ** maxstencil_type; + + void copy_bin_info_bytype(int); + int copy_neigh_info_bytype(int); + void create_newtoff(int, int, double); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_bytype_3d_newton.cpp b/src/nstencil_half_bytype_3d_newton.cpp new file mode 100644 index 0000000000..94c1ecd94d --- /dev/null +++ b/src/nstencil_half_bytype_3d_newton.cpp @@ -0,0 +1,194 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nstencil_half_bytype_3d_newton.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfBytype3dNewton::NStencilHalfBytype3dNewton(LAMMPS *lmp) : + NStencil(lmp) +{ + maxstencil_type = NULL; +} + +NStencilHalfBytype3dNewton::~NStencilHalfBytype3dNewton() { + + memory->destroy(nstencil_type); + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = 0; j <= atom->ntypes; j++) { + if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); + } + delete [] stencil_type[i]; + } + delete [] stencil_type; + memory->destroy(maxstencil_type); +} + +// KS To superclass +void NStencilHalfBytype3dNewton::copy_bin_info_bytype(int itype) { + + mbinx = nb->mbinx_type[itype]; + mbiny = nb->mbiny_type[itype]; + mbinz = nb->mbinz_type[itype]; + binsizex = nb->binsizex_type[itype]; + binsizey = nb->binsizey_type[itype]; + binsizez = nb->binsizez_type[itype]; + bininvx = nb->bininvx_type[itype]; + bininvy = nb->bininvy_type[itype]; + bininvz = nb->bininvz_type[itype]; +} + +// KS To superclass? +int NStencilHalfBytype3dNewton::copy_neigh_info_bytype(int itype) { + + cutneighmaxsq = neighbor->cutneighsq[itype][itype]; + cutneighmax = sqrt(cutneighmaxsq); + cuttypesq = neighbor->cuttypesq; + + // sx,sy,sz = max range of stencil in each dim + // smax = max possible size of entire 3d stencil + // stencil will be empty if cutneighmax = 0.0 + + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + return ((2*sx+1) * (2*sy+1) * (2*sz+1)); +} + +void NStencilHalfBytype3dNewton::create_setup() +{ + + int itype, jtype; + int maxtypes; + int smax; + + // maxstencil_type to superclass? + maxtypes = atom->ntypes; + + if (maxstencil_type == NULL) { + memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "maxstencil_type"); + memory->create(nstencil_type, maxtypes+1, maxtypes+1, "nstencil_type"); + stencil_type = new int**[maxtypes+1](); + for (itype = 1; itype <= maxtypes; ++itype) { + stencil_type[itype] = new int*[maxtypes+1](); + for (jtype = 1; jtype <= maxtypes; ++jtype) { + maxstencil_type[itype][jtype] = 0; + nstencil_type[itype][jtype] = 0; + } + } + } + + // like -> like => use standard Newton stencil at bin + + for (itype = 1; itype <= maxtypes; ++itype) { + copy_bin_info_bytype(itype); + smax = copy_neigh_info_bytype(itype); + if (smax > maxstencil_type[itype][itype]) { + maxstencil_type[itype][itype] = smax; + memory->destroy(stencil_type[itype][itype]); + memory->create(stencil_type[itype][itype], smax, + "NStencilHalfBytypeNewton::create_steup() stencil"); + } + create_newton(itype, itype, cutneighmaxsq); + } + + // Cross types: "Newton on" reached by using Newton off stencil and + // looking one way through hierarchy + // smaller -> larger => use Newton off stencil in larger bin + // larger -> smaller => no nstecil required + // If cut offs are same, use existing type-type stencil + + for (itype = 1; itype <= maxtypes; ++itype) { + for (jtype = 1; jtype <= maxtypes; ++jtype) { + if (itype == jtype) continue; + if (cuttypesq[itype] == cuttypesq[jtype]) { + nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; + stencil_type[itype][jtype] = stencil_type[jtype][jtype]; + } + else if (cuttypesq[itype] < cuttypesq[jtype]) { + copy_bin_info_bytype(jtype); + + cutneighmaxsq = cuttypesq[jtype]; + cutneighmax = sqrt(cutneighmaxsq); + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + smax = (2*sx+1) * (2*sy+1) * (2*sz+1); + if (smax > maxstencil_type[itype][jtype]) { + maxstencil_type[itype][jtype] = smax; + memory->destroy(stencil_type[itype][jtype]); + memory->create(stencil_type[itype][jtype], smax, "stencil_type[]"); + } + create_newtoff(itype, jtype, cuttypesq[jtype]); + } + } + } + +} + +void NStencilHalfBytype3dNewton::create_newton(int itype, int jtype, double cutsq) { + + int i, j, k, ns; + + ns = 0; + + for (k = 0; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (k > 0 || j > 0 || (j == 0 && i > 0)) { + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; + } + nstencil_type[itype][jtype] = ns; +} + +void NStencilHalfBytype3dNewton::create_newtoff(int itype, int jtype, double cutsq) { + + int i, j, k, ns; + + ns = 0; + + for (k = -sz; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; + + nstencil_type[itype][jtype] = ns; +} + +/* ---------------------------------------------------------------------- + create stencil based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfBytype3dNewton::create() +{ + // KS. Move "creation" here. +} diff --git a/src/nstencil_half_bytype_3d_newton.h b/src/nstencil_half_bytype_3d_newton.h new file mode 100644 index 0000000000..1245e2cd08 --- /dev/null +++ b/src/nstencil_half_bytype_3d_newton.h @@ -0,0 +1,52 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/bytype/3d/newton, + NStencilHalfBytype3dNewton, + NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTON | NS_ORTHO | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H +#define LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfBytype3dNewton : public NStencil { + public: + NStencilHalfBytype3dNewton(class LAMMPS *); + ~NStencilHalfBytype3dNewton(); + void create_setup(); + void create(); + + private: + int ** maxstencil_type; + + void copy_bin_info_bytype(int); + int copy_neigh_info_bytype(int); + void create_newton(int, int, double); + void create_newtoff(int, int, double); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ From e125d464d1977df0cc76a28043cc324e74827fb0 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 5 Oct 2020 16:09:50 -0600 Subject: [PATCH 0007/1217] Replacing molecular enumeration --- src/npair_full_bytype.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/npair_full_bytype.cpp b/src/npair_full_bytype.cpp index d244c263ed..6f13d77672 100644 --- a/src/npair_full_bytype.cpp +++ b/src/npair_full_bytype.cpp @@ -57,7 +57,7 @@ void NPairFullBytype::build(NeighList *list) int *molindex = atom->molindex; int *molatom = atom->molatom; Molecule **onemols = atom->avec->onemols; - if (molecular == 2) moltemplate = 1; + if (molecular == Atom::TEMPLATE) moltemplate = 1; else moltemplate = 0; int *ilist = list->ilist; @@ -113,7 +113,7 @@ void NPairFullBytype::build(NeighList *list) rsq = delx*delx + dely*dely + delz*delz; if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { + if (molecular != Atom::ATOMIC) { if (!moltemplate) which = find_special(special[i],nspecial[i],tag[j]); else if (imol >= 0) From aa1a87687bbaec39252f26afe77dc54931857b04 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 8 Oct 2020 07:32:36 -0600 Subject: [PATCH 0008/1217] Fix minor issues --- src/KOKKOS/atom_vec_spin_kokkos.cpp | 15 +++++++++------ src/KOKKOS/atom_vec_spin_kokkos.h | 2 +- 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp index c5c2ffb5be..188748d655 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.cpp +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -97,6 +97,9 @@ void AtomVecSpinKokkos::grow(int n) memoryKK->grow_kokkos(atomKK->k_fm,atomKK->fm,nmax,"atom:fm"); memoryKK->grow_kokkos(atomKK->k_fm_long,atomKK->fm_long,nmax,"atom:fm_long"); + grow_pointers(); + atomKK->sync(Host,ALL_MASK); + if (atom->nextra_grow) for (int iextra = 0; iextra < atom->nextra_grow; iextra++) modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax); @@ -106,7 +109,7 @@ void AtomVecSpinKokkos::grow(int n) reset local array ptrs ------------------------------------------------------------------------- */ -void AtomVecSpinKokkos::grow_reset() +void AtomVecSpinKokkos::grow_pointers() { tag = atomKK->tag; d_tag = atomKK->k_tag.d_view; @@ -121,7 +124,7 @@ void AtomVecSpinKokkos::grow_reset() image = atomKK->image; d_image = atomKK->k_image.d_view; h_image = atomKK->k_image.h_view; - + x = atomKK->x; d_x = atomKK->k_x.d_view; h_x = atomKK->k_x.h_view; @@ -389,7 +392,7 @@ int AtomVecSpinKokkos::pack_border(int n, int *list, double *buf, buf[m++] = h_sp(j,3); } } - + if (atom->nextra_border) for (int iextra = 0; iextra < atom->nextra_border; iextra++) m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); @@ -478,7 +481,7 @@ int AtomVecSpinKokkos::pack_border_vel(int n, int *list, double *buf, } } } - + if (atom->nextra_border) for (int iextra = 0; iextra < atom->nextra_border; iextra++) m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); @@ -1026,8 +1029,8 @@ void AtomVecSpinKokkos::create_atom(int itype, double *coord) atomKK->sync(Host,ALL_MASK); atomKK->modified(Host,ALL_MASK); - tag[nlocal] = 0; - type[nlocal] = itype; + h_tag[nlocal] = 0; + h_type[nlocal] = itype; h_x(nlocal,0) = coord[0]; h_x(nlocal,1) = coord[1]; h_x(nlocal,2) = coord[2]; diff --git a/src/KOKKOS/atom_vec_spin_kokkos.h b/src/KOKKOS/atom_vec_spin_kokkos.h index a9f7077a24..5dca7b4e13 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.h +++ b/src/KOKKOS/atom_vec_spin_kokkos.h @@ -56,7 +56,7 @@ class AtomVecSpinKokkos : public AtomVecKokkos { void force_clear(int, size_t); - void grow_reset(); + void grow_pointers(); // input lists to be checked int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, DAT::tdual_xfloat_2d buf,int iswap, From e8ebce1b5281ca0d4e8651918c64f24d940d7ec0 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 8 Oct 2020 08:21:55 -0600 Subject: [PATCH 0009/1217] Fix GPU compile error --- src/KOKKOS/kokkos_type.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index b6992602d0..041a6d4771 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -1028,8 +1028,8 @@ typedef tdual_virial_array::t_host_const_randomread t_virial_array_randomread; // Spin types -//2d X_FLOAT array n*3 -typedef Kokkos::DualView tdual_sp_array; +//2d X_FLOAT array n*4 +typedef Kokkos::DualView tdual_sp_array; typedef tdual_sp_array::t_host t_sp_array; typedef tdual_sp_array::t_host_const t_sp_array_const; typedef tdual_sp_array::t_host_um t_sp_array_um; From c85498e98baf752c05ec5f2a8ea7ecaaba9535eb Mon Sep 17 00:00:00 2001 From: julient31 Date: Fri, 9 Oct 2020 09:47:47 -0600 Subject: [PATCH 0010/1217] started to add spin/kk to the doc modified validaion tests for kokkos compatibility --- doc/src/atom_style.rst | 2 +- .../llg_exchange.py | 2 +- .../run-test-exchange.sh | 5 +++-- .../test-spin-precession.in | 12 ++++++++-- .../validation_damped_exchange/two_spins.data | 22 ------------------- .../validation_nve/in.spin.iron-nve | 7 +++++- .../validation_nve/run-test-nve.sh | 5 +++-- 7 files changed, 24 insertions(+), 31 deletions(-) delete mode 100644 examples/SPIN/test_problems/validation_damped_exchange/two_spins.data diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index 4957901676..a59f8d31e0 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -27,7 +27,7 @@ Syntax template-ID = ID of molecule template specified in a separate :doc:`molecule ` command *hybrid* args = list of one or more sub-styles, each with their args -* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk* +* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk* or *spin/kk* Examples """""""" diff --git a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py index 49eecb5b44..dd1c543bb3 100755 --- a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py +++ b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py @@ -65,6 +65,6 @@ for t in range (0,N): # calc. average magnetization Sm = (S1+S2)*0.5 # calc. energy - en = -2.0*J0*(np.dot(S1,S2)) + en = -J0*(np.dot(S1,S2)) # print res. in ps for comparison with LAMMPS print(t*dt/1000.0,Sm[0],Sm[1],Sm[2],en) diff --git a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh index 599730fe7b..ce8a6c3dbf 100755 --- a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh +++ b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh @@ -4,8 +4,9 @@ rm res_*.dat # compute Lammps -./../../../../src/lmp_serial \ - -in test-spin-precession.in +../../../../src/lmp_serial -in test-spin-precession.in +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in test-spin-precession.in in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" diff --git a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in index 0ca49364d2..6eea93224e 100644 --- a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in +++ b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in @@ -2,10 +2,18 @@ units metal atom_style spin -atom_modify map array +# atom_style spin/kk boundary f f f -read_data two_spins.data +atom_modify map array +lattice sc 3.0 +region box block 0 2 0 1 0 1 +create_box 1 box +create_atoms 1 box + +mass 1 55.845 +set atom 1 spin 2.0 1.0 0.0 0.0 +set atom 2 spin 2.0 0.0 1.0 0.0 pair_style spin/exchange 3.1 pair_coeff * * exchange 3.1 11.254 0.0 1.0 diff --git a/examples/SPIN/test_problems/validation_damped_exchange/two_spins.data b/examples/SPIN/test_problems/validation_damped_exchange/two_spins.data deleted file mode 100644 index 013f813751..0000000000 --- a/examples/SPIN/test_problems/validation_damped_exchange/two_spins.data +++ /dev/null @@ -1,22 +0,0 @@ -LAMMPS data file via write_data, version 19 Sep 2019, timestep = 0 - -2 atoms -1 atom types - -0.0 6.0 xlo xhi -0.0 3.0 ylo yhi -0.0 3.0 zlo zhi - -Masses - -1 1 - -Atoms # spin - -1 1 2.0 0.0 0.0 0.0 1.0 0.0 0.0 0 0 0 -2 1 2.0 3.0 0.0 0.0 0.0 1.0 0.0 0 0 0 - -Velocities - -1 0.0 0.0 0.0 -2 0.0 0.0 0.0 diff --git a/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve b/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve index f00fb1ec12..a29d0158cf 100644 --- a/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve +++ b/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve @@ -3,6 +3,7 @@ clear units metal atom_style spin +# atom_style spin/kk dimension 3 boundary p p p @@ -46,4 +47,8 @@ variable tmag equal c_out_mag[6] thermo_style custom step time v_tmag temp v_emag ke pe etotal thermo 200 -run 100000 +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +# run 100000 +run 10000 diff --git a/examples/SPIN/test_problems/validation_nve/run-test-nve.sh b/examples/SPIN/test_problems/validation_nve/run-test-nve.sh index 441e7cf46d..a8eb179b7f 100755 --- a/examples/SPIN/test_problems/validation_nve/run-test-nve.sh +++ b/examples/SPIN/test_problems/validation_nve/run-test-nve.sh @@ -4,8 +4,9 @@ rm res_*.dat # compute Lammps -./../../../../src/lmp_serial \ - -in in.spin.iron-nve +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in in.spin.iron-nve +../../../../src/lmp_serial -in in.spin.iron-nve in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" From 58e27a9c51047efe50770f86bdf21c4bfdd61ea7 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Fri, 9 Oct 2020 13:50:20 -0600 Subject: [PATCH 0011/1217] More edits and documentation --- doc/src/comm_modify.rst | 9 ++++++++- doc/src/neighbor.rst | 16 +++++++++++++++- src/comm.h | 4 ++++ src/comm_tiled.cpp | 6 ++++++ src/nbin_bytype.cpp | 16 +++++++--------- src/nbin_bytype.h | 16 ++++++++++++++++ src/npair_full_bytype.cpp | 6 ++---- src/npair_full_bytype.h | 4 ++++ src/npair_half_size_bytype_newtoff.cpp | 2 -- src/npair_half_size_bytype_newtoff.h | 4 ++++ src/npair_half_size_bytype_newton.cpp | 2 -- src/npair_half_size_bytype_newton.h | 6 +++++- src/nstencil_full_bytype_3d.cpp | 12 ++++++++++-- src/nstencil_half_bytype_2d_newton.cpp | 11 ++++++++++- src/nstencil_half_bytype_3d_newtoff.cpp | 12 ++++++++++-- src/nstencil_half_bytype_3d_newton.cpp | 13 ++++++++++++- 16 files changed, 113 insertions(+), 26 deletions(-) diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 9a2ae60f1e..2940b14283 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -11,7 +11,7 @@ Syntax comm_modify keyword value ... * zero or more keyword/value pairs may be appended -* keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel* +* keyword = *mode* or *cutoff* or *cutoff/multi* or *cutoff/bytype* or *group* or *vel* .. parsed-literal:: @@ -20,6 +20,7 @@ Syntax *cutoff/multi* type value type = atom type or type range (supports asterisk notation) value = Rcut (distance units) = communicate atoms for selected types from this far away + *cutoff/byptype* arg = none = communicate atoms for each type by a distance equal to the largest interaction distance for that type *group* value = group-ID = only communicate atoms in the group *vel* value = *yes* or *no* = do or do not communicate velocity info with ghost atoms @@ -92,6 +93,12 @@ cutoffs are determined per atom type, a type specifier is needed and cutoff for one or multiple types can be extended. Also ranges of types using the usual asterisk notation can be given. +The *cutoff/bytype* option applies to *multi* and automtically sets communication +cutoffs for each particle type based on the largest interaction distance +between two particles of the same type. This method is only compatible +with Newton on and the *bytype* neighbor style. See the :doc:`neighbor bytype ` +command for more information. + These are simulation scenarios in which it may be useful or even necessary to set a ghost cutoff > neighbor cutoff: diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index 1bb591587c..8db9131545 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -11,7 +11,7 @@ Syntax neighbor skin style * skin = extra distance beyond force cutoff (distance units) -* style = *bin* or *nsq* or *multi* +* style = *bin* or *nsq* or *multi* or *bytype* Examples """""""" @@ -60,6 +60,14 @@ This imposes some extra setup overhead, but the searches themselves may be much faster for the short-cutoff cases. See the :doc:`comm_modify mode multi ` command for a communication option that may also be beneficial for simulations of this kind. +The *bytype* style is an extension of the *multi* style that was +presented by Shire, Hanley, and Stratford :ref:`(Shire) `. +For style *bytype*, different bin lists are created for each different +type and separate bin sizes are generated. Whether *bytype* or *multi* +is faster may depend on the specifics of your system. See the +:doc:`comm_modify mode bytype ` command for a compatible +communication option. + The :doc:`neigh_modify ` command has additional options that control how often neighbor lists are built and which pairs are stored in the list. @@ -86,3 +94,9 @@ Default | 0.001 bin for units = si, skin = 0.001 meters = 1.0 mm | 0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm | + +---------- + +.. _bytype-Shire: + +**(Shire)** Shire, Hanley and Stratford, Comp Part Mech, (2020). diff --git a/src/comm.h b/src/comm.h index e5fc1bdee4..3105e09a61 100644 --- a/src/comm.h +++ b/src/comm.h @@ -199,6 +199,10 @@ E: Use cutoff keyword to set cutoff in single mode Mode is single so cutoff/multi keyword cannot be used. +E: Use cutoff/bytype in mode multi only + +Mode is single so cutoff/bytype keyword cannot be used. + E: Cannot set cutoff/multi before simulation box is defined Self-explanatory. diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index dbdc887097..4759639bff 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -183,6 +183,12 @@ void CommTiled::setup() cutghostmulti[i][0] = MAX(cut,cuttype[i]); cutghostmulti[i][1] = MAX(cut,cuttype[i]); cutghostmulti[i][2] = MAX(cut,cuttype[i]); + if (multi_bytype == 1) { + // Set the BYTYPE cutoff + cutghostmulti[i][0] = sqrt(neighbor->cutneighsq[i][i]); + cutghostmulti[i][1] = sqrt(neighbor->cutneighsq[i][i]); + cutghostmulti[i][2] = sqrt(neighbor->cutneighsq[i][i]); + } } } diff --git a/src/nbin_bytype.cpp b/src/nbin_bytype.cpp index f719ed116f..70732a4b97 100644 --- a/src/nbin_bytype.cpp +++ b/src/nbin_bytype.cpp @@ -19,14 +19,12 @@ #include "comm.h" #include "update.h" #include "error.h" - -#include #include "memory.h" using namespace LAMMPS_NS; -#define SMALL 1.0e-6 // Duplicated from NBinStandard -#define CUT2BIN_RATIO 100 // Duplicated from NBinStandard +#define SMALL 1.0e-6 +#define CUT2BIN_RATIO 100 /* ---------------------------------------------------------------------- */ @@ -238,7 +236,7 @@ void NBinBytype::setup_bins(int style) // test for too many global bins in any dimension due to huge global domain if (bbox[0]*binsizeinv > MAXSMALLINT || bbox[1]*binsizeinv > MAXSMALLINT || - bbox[2]*binsizeinv > MAXSMALLINT) + bbox[2]*binsizeinv > MAXSMALLINT) error->all(FLERR,"Domain too large for neighbor bins"); // create actual bins @@ -269,8 +267,8 @@ void NBinBytype::setup_bins(int style) bininvz_type[n] = 1.0 / binsizez_type[n]; if (binsize_optimal*bininvx_type[n] > CUT2BIN_RATIO || - binsize_optimal*bininvy_type[n] > CUT2BIN_RATIO || - binsize_optimal*bininvz_type[n] > CUT2BIN_RATIO) + binsize_optimal*bininvy_type[n] > CUT2BIN_RATIO || + binsize_optimal*bininvz_type[n] > CUT2BIN_RATIO) error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); // mbinlo/hi = lowest and highest global bins my ghost atoms could be in @@ -352,8 +350,8 @@ void NBinBytype::bin_atoms() int bitmask = group->bitmask[includegroup]; for (i = nall-1; i >= nlocal; i--) { if (mask[i] & bitmask) { - n = type[i]; - ibin = coord2bin(x[i], n); + n = type[i]; + ibin = coord2bin(x[i], n); atom2bin_type[n][i] = ibin; bins_type[n][i] = binhead_type[n][ibin]; binhead_type[n][ibin] = i; diff --git a/src/nbin_bytype.h b/src/nbin_bytype.h index 89e6ca3650..ad2b95ef4b 100644 --- a/src/nbin_bytype.h +++ b/src/nbin_bytype.h @@ -53,4 +53,20 @@ class NBinBytype : public NBin { /* ERROR/WARNING messages: +E: Domain too large for neighbor bins + +UNDOCUMENTED + +E: Cannot use neighbor bins - box size << cutoff + +UNDOCUMENTED + +E: Too many neighbor bins + +UNDOCUMENTED + +E Non-numeric positions - simulation unstable + +UNDOCUMENTED + */ diff --git a/src/npair_full_bytype.cpp b/src/npair_full_bytype.cpp index 6f13d77672..3b9a89bb56 100644 --- a/src/npair_full_bytype.cpp +++ b/src/npair_full_bytype.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_bytype.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -20,7 +19,6 @@ #include "domain.h" #include "my_page.h" #include "error.h" - #include "nbin.h" #include "nstencil.h" @@ -102,9 +100,9 @@ void NPairFullBytype::build(NeighList *list) for (k = 0; k < ns; k++) { int js = this->nb->binhead_type[ktype][kbin + s[k]]; for (j = js; j >= 0; j = this->nb->bins_type[ktype][j]) { - jtype = type[j]; if (i == j) continue; - + + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/npair_full_bytype.h b/src/npair_full_bytype.h index 9ce221ff22..fdcd6b5fb1 100644 --- a/src/npair_full_bytype.h +++ b/src/npair_full_bytype.h @@ -40,4 +40,8 @@ class NPairFullBytype : public NPair { /* ERROR/WARNING messages: +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + */ diff --git a/src/npair_half_size_bytype_newtoff.cpp b/src/npair_half_size_bytype_newtoff.cpp index f065c60736..220ae747a7 100644 --- a/src/npair_half_size_bytype_newtoff.cpp +++ b/src/npair_half_size_bytype_newtoff.cpp @@ -13,13 +13,11 @@ es certain rights in this software. This software is distributed under #include #include "npair_half_size_bytype_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "my_page.h" #include "error.h" - #include "nbin.h" #include "nstencil.h" diff --git a/src/npair_half_size_bytype_newtoff.h b/src/npair_half_size_bytype_newtoff.h index e131a12f4b..183bd39fb3 100644 --- a/src/npair_half_size_bytype_newtoff.h +++ b/src/npair_half_size_bytype_newtoff.h @@ -40,4 +40,8 @@ class NPairHalfSizeBytypeNewtoff : public NPair { /* ERROR/WARNING messages: +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + */ diff --git a/src/npair_half_size_bytype_newton.cpp b/src/npair_half_size_bytype_newton.cpp index 3981635439..339c4859a6 100755 --- a/src/npair_half_size_bytype_newton.cpp +++ b/src/npair_half_size_bytype_newton.cpp @@ -13,13 +13,11 @@ #include #include "npair_half_size_bytype_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "my_page.h" #include "error.h" - #include "nbin.h" #include "nstencil.h" diff --git a/src/npair_half_size_bytype_newton.h b/src/npair_half_size_bytype_newton.h index a6bb7a00a8..3cd1ee05d1 100755 --- a/src/npair_half_size_bytype_newton.h +++ b/src/npair_half_size_bytype_newton.h @@ -40,4 +40,8 @@ class NPairHalfSizeBytypeNewton : public NPair { /* ERROR/WARNING messages: -*/ +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + +*/ \ No newline at end of file diff --git a/src/nstencil_full_bytype_3d.cpp b/src/nstencil_full_bytype_3d.cpp index 3936ec2483..cecccdfb14 100644 --- a/src/nstencil_full_bytype_3d.cpp +++ b/src/nstencil_full_bytype_3d.cpp @@ -17,7 +17,6 @@ #include "nbin.h" #include "memory.h" #include "atom.h" - #include using namespace LAMMPS_NS; @@ -30,6 +29,8 @@ NStencilFullBytype3d::NStencilFullBytype3d(LAMMPS *lmp) : maxstencil_type = NULL; } +/* ---------------------------------------------------------------------- */ + NStencilFullBytype3d::~NStencilFullBytype3d() { if (maxstencil_type) { @@ -45,6 +46,8 @@ NStencilFullBytype3d::~NStencilFullBytype3d() { } } +/* ---------------------------------------------------------------------- */ + void NStencilFullBytype3d::copy_bin_info_bytype(int itype) { mbinx = nb->mbinx_type[itype]; @@ -58,6 +61,8 @@ void NStencilFullBytype3d::copy_bin_info_bytype(int itype) { bininvz = nb->bininvz_type[itype]; } +/* ---------------------------------------------------------------------- */ + int NStencilFullBytype3d::copy_neigh_info_bytype(int itype) { cutneighmaxsq = neighbor->cutneighsq[itype][itype]; @@ -78,6 +83,8 @@ int NStencilFullBytype3d::copy_neigh_info_bytype(int itype) { return ((2*sx+1) * (2*sy+1) * (2*sz+1)); } +/* ---------------------------------------------------------------------- */ + void NStencilFullBytype3d::create_setup() { @@ -85,7 +92,6 @@ void NStencilFullBytype3d::create_setup() int maxtypes; int smax; - //printf("NStencilFullBytype3d::create_steup()\n"); maxtypes = atom->ntypes; if (maxstencil_type == NULL) { @@ -159,6 +165,8 @@ void NStencilFullBytype3d::create_setup() } +/* ---------------------------------------------------------------------- */ + void NStencilFullBytype3d::create_newtoff(int itype, int jtype, double cutsq) { int i, j, k, ns; diff --git a/src/nstencil_half_bytype_2d_newton.cpp b/src/nstencil_half_bytype_2d_newton.cpp index 18ed0972ff..66158202bf 100644 --- a/src/nstencil_half_bytype_2d_newton.cpp +++ b/src/nstencil_half_bytype_2d_newton.cpp @@ -17,7 +17,6 @@ #include "nbin.h" #include "memory.h" #include "atom.h" - #include using namespace LAMMPS_NS; @@ -43,6 +42,8 @@ NStencilHalfBytype2dNewton::~NStencilHalfBytype2dNewton() { memory->destroy(maxstencil_type); } +/* ---------------------------------------------------------------------- */ + // KS To superclass void NStencilHalfBytype2dNewton::copy_bin_info_bytype(int itype) { @@ -57,6 +58,8 @@ void NStencilHalfBytype2dNewton::copy_bin_info_bytype(int itype) { bininvz = nb->bininvz_type[itype]; } +/* ---------------------------------------------------------------------- */ + // KS To superclass? int NStencilHalfBytype2dNewton::copy_neigh_info_bytype(int itype) { @@ -78,6 +81,8 @@ int NStencilHalfBytype2dNewton::copy_neigh_info_bytype(int itype) { return ((2*sx+1) * (2*sy+1) * (2*sz+1)); } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype2dNewton::create_setup() { @@ -153,6 +158,8 @@ void NStencilHalfBytype2dNewton::create_setup() } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype2dNewton::create_newton(int itype, int jtype, double cutsq) { int i, j, ns; @@ -168,6 +175,8 @@ void NStencilHalfBytype2dNewton::create_newton(int itype, int jtype, double cuts nstencil_type[itype][jtype] = ns; } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype2dNewton::create_newtoff(int itype, int jtype, double cutsq) { int i, j, ns; diff --git a/src/nstencil_half_bytype_3d_newtoff.cpp b/src/nstencil_half_bytype_3d_newtoff.cpp index f111715e5d..fedc8060ce 100644 --- a/src/nstencil_half_bytype_3d_newtoff.cpp +++ b/src/nstencil_half_bytype_3d_newtoff.cpp @@ -17,7 +17,6 @@ #include "nbin.h" #include "memory.h" #include "atom.h" - #include using namespace LAMMPS_NS; @@ -30,6 +29,8 @@ NStencilHalfBytype3dNewtoff::NStencilHalfBytype3dNewtoff(LAMMPS *lmp) : maxstencil_type = NULL; } +/* ---------------------------------------------------------------------- */ + NStencilHalfBytype3dNewtoff::~NStencilHalfBytype3dNewtoff() { memory->destroy(nstencil_type); @@ -43,6 +44,8 @@ NStencilHalfBytype3dNewtoff::~NStencilHalfBytype3dNewtoff() { memory->destroy(maxstencil_type); } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype3dNewtoff::copy_bin_info_bytype(int itype) { mbinx = nb->mbinx_type[itype]; @@ -56,6 +59,8 @@ void NStencilHalfBytype3dNewtoff::copy_bin_info_bytype(int itype) { bininvz = nb->bininvz_type[itype]; } +/* ---------------------------------------------------------------------- */ + int NStencilHalfBytype3dNewtoff::copy_neigh_info_bytype(int itype) { cutneighmaxsq = neighbor->cutneighsq[itype][itype]; @@ -76,6 +81,8 @@ int NStencilHalfBytype3dNewtoff::copy_neigh_info_bytype(int itype) { return ((2*sx+1) * (2*sy+1) * (2*sz+1)); } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype3dNewtoff::create_setup() { @@ -83,7 +90,6 @@ void NStencilHalfBytype3dNewtoff::create_setup() int maxtypes; int smax; - //printf("NStencilHalfBytype3dNewtoff::create_steup()\n"); maxtypes = atom->ntypes; if (maxstencil_type == NULL) { @@ -157,6 +163,8 @@ void NStencilHalfBytype3dNewtoff::create_setup() } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype3dNewtoff::create_newtoff(int itype, int jtype, double cutsq) { int i, j, k, ns; diff --git a/src/nstencil_half_bytype_3d_newton.cpp b/src/nstencil_half_bytype_3d_newton.cpp index 94c1ecd94d..7fc53fe762 100644 --- a/src/nstencil_half_bytype_3d_newton.cpp +++ b/src/nstencil_half_bytype_3d_newton.cpp @@ -17,7 +17,6 @@ #include "nbin.h" #include "memory.h" #include "atom.h" - #include using namespace LAMMPS_NS; @@ -30,6 +29,8 @@ NStencilHalfBytype3dNewton::NStencilHalfBytype3dNewton(LAMMPS *lmp) : maxstencil_type = NULL; } +/* ---------------------------------------------------------------------- */ + NStencilHalfBytype3dNewton::~NStencilHalfBytype3dNewton() { memory->destroy(nstencil_type); @@ -43,6 +44,8 @@ NStencilHalfBytype3dNewton::~NStencilHalfBytype3dNewton() { memory->destroy(maxstencil_type); } +/* ---------------------------------------------------------------------- */ + // KS To superclass void NStencilHalfBytype3dNewton::copy_bin_info_bytype(int itype) { @@ -57,6 +60,8 @@ void NStencilHalfBytype3dNewton::copy_bin_info_bytype(int itype) { bininvz = nb->bininvz_type[itype]; } +/* ---------------------------------------------------------------------- */ + // KS To superclass? int NStencilHalfBytype3dNewton::copy_neigh_info_bytype(int itype) { @@ -78,6 +83,8 @@ int NStencilHalfBytype3dNewton::copy_neigh_info_bytype(int itype) { return ((2*sx+1) * (2*sy+1) * (2*sz+1)); } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype3dNewton::create_setup() { @@ -153,6 +160,8 @@ void NStencilHalfBytype3dNewton::create_setup() } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype3dNewton::create_newton(int itype, int jtype, double cutsq) { int i, j, k, ns; @@ -169,6 +178,8 @@ void NStencilHalfBytype3dNewton::create_newton(int itype, int jtype, double cuts nstencil_type[itype][jtype] = ns; } +/* ---------------------------------------------------------------------- */ + void NStencilHalfBytype3dNewton::create_newtoff(int itype, int jtype, double cutsq) { int i, j, k, ns; From 557ef57526e7a61bb466f3904a46a8a0c1983113 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Thu, 29 Oct 2020 15:13:28 -0600 Subject: [PATCH 0012/1217] Adding initial support for triclinic boundaries --- src/npair_half_bytype_newton_tri.cpp | 190 +++++++++++++++++++ src/npair_half_bytype_newton_tri.h | 43 +++++ src/npair_half_size_bytype_newton_tri.cpp | 166 +++++++++++++++++ src/npair_half_size_bytype_newton_tri.h | 47 +++++ src/nstencil_half_bytype_3d_newton.h | 2 +- src/nstencil_half_bytype_3d_newton_tri.cpp | 203 +++++++++++++++++++++ src/nstencil_half_bytype_3d_newton_tri.h | 52 ++++++ 7 files changed, 702 insertions(+), 1 deletion(-) create mode 100755 src/npair_half_bytype_newton_tri.cpp create mode 100755 src/npair_half_bytype_newton_tri.h create mode 100755 src/npair_half_size_bytype_newton_tri.cpp create mode 100755 src/npair_half_size_bytype_newton_tri.h create mode 100755 src/nstencil_half_bytype_3d_newton_tri.cpp create mode 100755 src/nstencil_half_bytype_3d_newton_tri.h diff --git a/src/npair_half_bytype_newton_tri.cpp b/src/npair_half_bytype_newton_tri.cpp new file mode 100755 index 0000000000..6b28e76789 --- /dev/null +++ b/src/npair_half_bytype_newton_tri.cpp @@ -0,0 +1,190 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "npair_half_bytype_newton_tri.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "domain.h" +#include "my_page.h" +#include "error.h" + +#include "nbin.h" +#include "nstencil.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfBytypeNewtonTri::NPairHalfBytypeNewtonTri(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + KS REWRTIE + binned neighbor list construction with Newton's 3rd law for triclinic + each owned atom i checks its own bin and other bins in triclinic stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfBytypeNewtonTri::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + if (molecular == 2) moltemplate = 1; + else moltemplate = 0; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + int js; + int kbin; + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = nb->atom2bin_type[itype][i]; + + for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + + if (itype == ktype) { + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = this->ns->stencil_type[itype][itype]; + ns = this->ns->nstencil_type[itype][itype]; + for (k = 0; k < ns; k++) { + js = nb->binhead_type[itype][ibin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[itype][j]) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + + } + else { + // smaller -> larger: locate i in the ktype bin structure + + kbin = nb->coord2bin(x[i], ktype); + s = this->ns->stencil_type[itype][ktype]; + ns = this->ns->nstencil_type[itype][ktype]; + + for (k = 0; k < ns; k++) { + js = nb->binhead_type[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[ktype][j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + } + } + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_bytype_newton_tri.h b/src/npair_half_bytype_newton_tri.h new file mode 100755 index 0000000000..0582801028 --- /dev/null +++ b/src/npair_half_bytype_newton_tri.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/bytype/newton/tri, + NPairHalfBytypeNewtonTri, + NP_HALF | NP_BYTYPE | NP_NEWTON | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_BYTYPE_NEWTON_TRI_H +#define LMP_NPAIR_HALF_BYTYPE_NEWTON_TRI_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfBytypeNewtonTri : public NPair { + public: + NPairHalfBytypeNewtonTri(class LAMMPS *); + ~NPairHalfBytypeNewtonTri() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/npair_half_size_bytype_newton_tri.cpp b/src/npair_half_size_bytype_newton_tri.cpp new file mode 100755 index 0000000000..62d499b10f --- /dev/null +++ b/src/npair_half_size_bytype_newton_tri.cpp @@ -0,0 +1,166 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "npair_half_size_bytype_newton_tri.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" +#include "nbin.h" +#include "nstencil.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeBytypeNewtonTri::NPairHalfSizeBytypeNewtonTri(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + KS REWRTIE + binned neighbor list construction with Newton's 3rd law for triclinic + each owned atom i checks its own bin and other bins in triclinic stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfSizeBytypeNewtonTri::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + int js; + int kbin; + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = nb->atom2bin_type[itype][i]; + + for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + + if (itype == ktype) { + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = this->ns->stencil_type[itype][itype]; + ns = this->ns->nstencil_type[itype][itype]; + for (k = 0; k < ns; k++) { + js = nb->binhead_type[itype][ibin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[itype][j]) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + jtype = type[j]; + // KS. CHECK ME if (cutsq[jtype] < distsq[k]) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + } + else { + // KS + // smaller -> larger: locate i in the ktype bin structure + kbin = nb->coord2bin(x[i], ktype); + + s = this->ns->stencil_type[itype][ktype]; + ns = this->ns->nstencil_type[itype][ktype]; + for (k = 0; k < ns; k++) { + js = nb->binhead_type[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = nb->bins_type[ktype][j]) { + + jtype = type[j]; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + } + } + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_size_bytype_newton_tri.h b/src/npair_half_size_bytype_newton_tri.h new file mode 100755 index 0000000000..0f770e780d --- /dev/null +++ b/src/npair_half_size_bytype_newton_tri.h @@ -0,0 +1,47 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/bytype/newton/tri, + NPairHalfSizeBytypeNewtonTri, + NP_HALF | NP_SIZE | NP_BYTYPE | NP_NEWTON | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_TRI_H +#define LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_TRI_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeBytypeNewtonTri : public NPair { + public: + NPairHalfSizeBytypeNewtonTri(class LAMMPS *); + ~NPairHalfSizeBytypeNewtonTri() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + +*/ \ No newline at end of file diff --git a/src/nstencil_half_bytype_3d_newton.h b/src/nstencil_half_bytype_3d_newton.h index 1245e2cd08..cbb88fcb1d 100644 --- a/src/nstencil_half_bytype_3d_newton.h +++ b/src/nstencil_half_bytype_3d_newton.h @@ -15,7 +15,7 @@ NStencilStyle(half/bytype/3d/newton, NStencilHalfBytype3dNewton, - NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTON | NS_ORTHO | NS_TRI) + NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTON | NS_ORTHO) #else diff --git a/src/nstencil_half_bytype_3d_newton_tri.cpp b/src/nstencil_half_bytype_3d_newton_tri.cpp new file mode 100755 index 0000000000..f1ab713725 --- /dev/null +++ b/src/nstencil_half_bytype_3d_newton_tri.cpp @@ -0,0 +1,203 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nstencil_half_bytype_3d_newton.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfBytype3dNewton::NStencilHalfBytype3dNewton(LAMMPS *lmp) : + NStencil(lmp) +{ + maxstencil_type = NULL; +} + +/* ---------------------------------------------------------------------- */ + +NStencilHalfBytype3dNewton::~NStencilHalfBytype3dNewton() { + + memory->destroy(nstencil_type); + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = 0; j <= atom->ntypes; j++) { + if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); + } + delete [] stencil_type[i]; + } + delete [] stencil_type; + memory->destroy(maxstencil_type); +} + +/* ---------------------------------------------------------------------- */ + +// KS To superclass +void NStencilHalfBytype3dNewton::copy_bin_info_bytype(int itype) { + + mbinx = nb->mbinx_type[itype]; + mbiny = nb->mbiny_type[itype]; + mbinz = nb->mbinz_type[itype]; + binsizex = nb->binsizex_type[itype]; + binsizey = nb->binsizey_type[itype]; + binsizez = nb->binsizez_type[itype]; + bininvx = nb->bininvx_type[itype]; + bininvy = nb->bininvy_type[itype]; + bininvz = nb->bininvz_type[itype]; +} + +/* ---------------------------------------------------------------------- */ + +// KS To superclass? +int NStencilHalfBytype3dNewton::copy_neigh_info_bytype(int itype) { + + cutneighmaxsq = neighbor->cutneighsq[itype][itype]; + cutneighmax = sqrt(cutneighmaxsq); + cuttypesq = neighbor->cuttypesq; + + // sx,sy,sz = max range of stencil in each dim + // smax = max possible size of entire 3d stencil + // stencil will be empty if cutneighmax = 0.0 + + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + return ((2*sx+1) * (2*sy+1) * (2*sz+1)); +} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfBytype3dNewton::create_setup() +{ + + int itype, jtype; + int maxtypes; + int smax; + + // maxstencil_type to superclass? + maxtypes = atom->ntypes; + + if (maxstencil_type == NULL) { + memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "maxstencil_type"); + memory->create(nstencil_type, maxtypes+1, maxtypes+1, "nstencil_type"); + stencil_type = new int**[maxtypes+1](); + for (itype = 1; itype <= maxtypes; ++itype) { + stencil_type[itype] = new int*[maxtypes+1](); + for (jtype = 1; jtype <= maxtypes; ++jtype) { + maxstencil_type[itype][jtype] = 0; + nstencil_type[itype][jtype] = 0; + } + } + } + + // like -> like => use standard Newton stencil at bin + + for (itype = 1; itype <= maxtypes; ++itype) { + copy_bin_info_bytype(itype); + smax = copy_neigh_info_bytype(itype); + if (smax > maxstencil_type[itype][itype]) { + maxstencil_type[itype][itype] = smax; + memory->destroy(stencil_type[itype][itype]); + memory->create(stencil_type[itype][itype], smax, + "NStencilHalfBytypeNewton::create_steup() stencil"); + } + create_newton(itype, itype, cutneighmaxsq); + } + + // Cross types: "Newton on" reached by using Newton off stencil and + // looking one way through hierarchy + // smaller -> larger => use Newton off stencil in larger bin + // larger -> smaller => no nstecil required + // If cut offs are same, use existing type-type stencil + + for (itype = 1; itype <= maxtypes; ++itype) { + for (jtype = 1; jtype <= maxtypes; ++jtype) { + if (itype == jtype) continue; + if (cuttypesq[itype] == cuttypesq[jtype]) { + nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; + stencil_type[itype][jtype] = stencil_type[jtype][jtype]; + } + else if (cuttypesq[itype] < cuttypesq[jtype]) { + copy_bin_info_bytype(jtype); + + cutneighmaxsq = cuttypesq[jtype]; + cutneighmax = sqrt(cutneighmaxsq); + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + + smax = (2*sx+1) * (2*sy+1) * (2*sz+1); + if (smax > maxstencil_type[itype][jtype]) { + maxstencil_type[itype][jtype] = smax; + memory->destroy(stencil_type[itype][jtype]); + memory->create(stencil_type[itype][jtype], smax, "stencil_type[]"); + } + create_newtoff(itype, jtype, cuttypesq[jtype]); + } + } + } + +} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfBytype3dNewton::create_newton(int itype, int jtype, double cutsq) { + + int i, j, k, ns; + + ns = 0; + + for (k = 0; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; + nstencil_type[itype][jtype] = ns; +} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfBytype3dNewton::create_newtoff(int itype, int jtype, double cutsq) { + + int i, j, k, ns; + + ns = 0; + + for (k = -sz; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; + + nstencil_type[itype][jtype] = ns; +} + +/* ---------------------------------------------------------------------- + create stencil based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfBytype3dNewton::create() +{ + // KS. Move "creation" here. +} diff --git a/src/nstencil_half_bytype_3d_newton_tri.h b/src/nstencil_half_bytype_3d_newton_tri.h new file mode 100755 index 0000000000..e419161bb5 --- /dev/null +++ b/src/nstencil_half_bytype_3d_newton_tri.h @@ -0,0 +1,52 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/bytype/3d/newton, + NStencilHalfBytype3dNewton, + NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTON | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H +#define LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfBytype3dNewton : public NStencil { + public: + NStencilHalfBytype3dNewton(class LAMMPS *); + ~NStencilHalfBytype3dNewton(); + void create_setup(); + void create(); + + private: + int ** maxstencil_type; + + void copy_bin_info_bytype(int); + int copy_neigh_info_bytype(int); + void create_newton(int, int, double); + void create_newtoff(int, int, double); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ From 12288630f576273a2848f6a2bd0e272b142b2e29 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 9 Nov 2020 16:32:11 -0700 Subject: [PATCH 0013/1217] Fixing comm and renaming bytype --- src/comm.cpp | 12 ++-- src/comm.h | 6 +- src/comm_brick.cpp | 58 +++++++++++++------ src/comm_tiled.cpp | 33 ++++++----- ...{nbin_bytype.cpp => nbin_multi_tiered.cpp} | 0 src/{nbin_bytype.h => nbin_multi_tiered.h} | 0 src/neighbor.cpp | 20 +++---- src/neighbor.h | 32 +++++----- ...bytype.cpp => npair_full_multi_tiered.cpp} | 0 ...ull_bytype.h => npair_full_multi_tiered.h} | 0 ...cpp => npair_half_multi_tiered_newton.cpp} | 0 ...ton.h => npair_half_multi_tiered_newton.h} | 0 ...=> npair_half_multi_tiered_newton_tri.cpp} | 0 ...h => npair_half_multi_tiered_newton_tri.h} | 0 ... npair_half_size_multi_tiered_newtoff.cpp} | 0 ...=> npair_half_size_multi_tiered_newtoff.h} | 0 ...> npair_half_size_multi_tiered_newton.cpp} | 0 ... => npair_half_size_multi_tiered_newton.h} | 0 ...air_half_size_multi_tiered_newton_tri.cpp} | 0 ...npair_half_size_multi_tiered_newton_tri.h} | 0 ....cpp => nstencil_full_multi_tiered_3d.cpp} | 0 ...e_3d.h => nstencil_full_multi_tiered_3d.h} | 0 ... nstencil_half_multi_tiered_2d_newton.cpp} | 0 ...=> nstencil_half_multi_tiered_2d_newton.h} | 0 ...nstencil_half_multi_tiered_3d_newtoff.cpp} | 0 ...> nstencil_half_multi_tiered_3d_newtoff.h} | 0 ... nstencil_half_multi_tiered_3d_newton.cpp} | 0 ...=> nstencil_half_multi_tiered_3d_newton.h} | 0 ...encil_half_multi_tiered_3d_newton_tri.cpp} | 0 ...stencil_half_multi_tiered_3d_newton_tri.h} | 0 30 files changed, 98 insertions(+), 63 deletions(-) rename src/{nbin_bytype.cpp => nbin_multi_tiered.cpp} (100%) rename src/{nbin_bytype.h => nbin_multi_tiered.h} (100%) rename src/{npair_full_bytype.cpp => npair_full_multi_tiered.cpp} (100%) rename src/{npair_full_bytype.h => npair_full_multi_tiered.h} (100%) rename src/{npair_half_bytype_newton.cpp => npair_half_multi_tiered_newton.cpp} (100%) rename src/{npair_half_bytype_newton.h => npair_half_multi_tiered_newton.h} (100%) rename src/{npair_half_bytype_newton_tri.cpp => npair_half_multi_tiered_newton_tri.cpp} (100%) rename src/{npair_half_bytype_newton_tri.h => npair_half_multi_tiered_newton_tri.h} (100%) rename src/{npair_half_size_bytype_newtoff.cpp => npair_half_size_multi_tiered_newtoff.cpp} (100%) rename src/{npair_half_size_bytype_newtoff.h => npair_half_size_multi_tiered_newtoff.h} (100%) rename src/{npair_half_size_bytype_newton.cpp => npair_half_size_multi_tiered_newton.cpp} (100%) rename src/{npair_half_size_bytype_newton.h => npair_half_size_multi_tiered_newton.h} (100%) rename src/{npair_half_size_bytype_newton_tri.cpp => npair_half_size_multi_tiered_newton_tri.cpp} (100%) rename src/{npair_half_size_bytype_newton_tri.h => npair_half_size_multi_tiered_newton_tri.h} (100%) rename src/{nstencil_full_bytype_3d.cpp => nstencil_full_multi_tiered_3d.cpp} (100%) rename src/{nstencil_full_bytype_3d.h => nstencil_full_multi_tiered_3d.h} (100%) rename src/{nstencil_half_bytype_2d_newton.cpp => nstencil_half_multi_tiered_2d_newton.cpp} (100%) rename src/{nstencil_half_bytype_2d_newton.h => nstencil_half_multi_tiered_2d_newton.h} (100%) rename src/{nstencil_half_bytype_3d_newtoff.cpp => nstencil_half_multi_tiered_3d_newtoff.cpp} (100%) rename src/{nstencil_half_bytype_3d_newtoff.h => nstencil_half_multi_tiered_3d_newtoff.h} (100%) rename src/{nstencil_half_bytype_3d_newton.cpp => nstencil_half_multi_tiered_3d_newton.cpp} (100%) rename src/{nstencil_half_bytype_3d_newton.h => nstencil_half_multi_tiered_3d_newton.h} (100%) rename src/{nstencil_half_bytype_3d_newton_tri.cpp => nstencil_half_multi_tiered_3d_newton_tri.cpp} (100%) rename src/{nstencil_half_bytype_3d_newton_tri.h => nstencil_half_multi_tiered_3d_newton_tri.h} (100%) diff --git a/src/comm.cpp b/src/comm.cpp index 1efe966459..b6f905d9a2 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -76,7 +76,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) grid2proc = nullptr; xsplit = ysplit = zsplit = nullptr; rcbnew = 0; - multi_bytype = 0; + multi_tiered = 0; // use of OpenMP threads // query OpenMP for number of threads/process set by user at run-time @@ -241,6 +241,10 @@ void Comm::init() maxexchange_fix_dynamic = 0; for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; + + // Can't used multi/tiered communication with Newton off + if (force->newton == 0 && multi_tiered) + error->all(FLERR,"Cannot use multi/tiered communication with Newton off"); } /* ---------------------------------------------------------------------- @@ -327,10 +331,10 @@ void Comm::modify_params(int narg, char **arg) for (i=nlo; i<=nhi; ++i) cutusermulti[i] = cut; iarg += 3; - } else if (strcmp(arg[iarg],"cutoff/bytype") == 0) { + } else if (strcmp(arg[iarg],"cutoff/tiered") == 0) { if (mode == Comm::SINGLE) - error->all(FLERR,"Use cutoff/bytype in mode multi only"); - multi_bytype = 1; + error->all(FLERR,"Use cutoff/tiered in mode multi only"); + multi_tiered = 1; iarg += 1; } else if (strcmp(arg[iarg],"vel") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command"); diff --git a/src/comm.h b/src/comm.h index 3105e09a61..037eaab348 100644 --- a/src/comm.h +++ b/src/comm.h @@ -161,7 +161,7 @@ class Comm : protected Pointers { int (*)(int, char *, int &, int *&, char *&, void *), int, char *&, int, void *, int); void rendezvous_stats(int, int, int, int, int, int, bigint); - int multi_bytype; // 1 if multi cutoff is intra-type cutoff + int multi_tiered; // 1 if multi cutoff is intra-type cutoff public: enum{MULTIPLE}; @@ -247,6 +247,10 @@ E: Processor count in z must be 1 for 2d simulation Self-explanatory. +E: Cannot use multi/tiered communication with Newton off + +Self-explanatory. + E: Cannot put data on ring from nullptr pointer W: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 57703b578c..c9fd00e9f5 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -174,18 +174,25 @@ void CommBrick::setup() cutghost[0] = cutghost[1] = cutghost[2] = cut; if (mode == Comm::MULTI) { - double *cuttype = neighbor->cuttype; - for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = MAX(cut,cuttype[i]); - cutghostmulti[i][1] = MAX(cut,cuttype[i]); - cutghostmulti[i][2] = MAX(cut,cuttype[i]); - if (multi_bytype == 1) { - // Set the BYTYPE cutoff - cutghostmulti[i][0] = sqrt(neighbor->cutneighsq[i][i]); - cutghostmulti[i][1] = sqrt(neighbor->cutneighsq[i][i]); - cutghostmulti[i][2] = sqrt(neighbor->cutneighsq[i][i]); + if (multi_tiered) { + // If using tiered binlists, use the itype-itype interaction distance for communication + double **cutneighsq = neighbor->cutneighsq; + for (i = 1; i <= ntypes; i++) { + cut = 0.0; + if (cutusermulti) cut = cutusermulti[i]; + cutghostmulti[i][0] = MAX(cut,sqrt(cutneighsq[i][i])); + cutghostmulti[i][1] = MAX(cut,sqrt(cutneighsq[i][i])); + cutghostmulti[i][2] = MAX(cut,sqrt(cutneighsq[i][i])); + } + } else { + // If using a single binlist, use the max itype-jtype interaction distance for communication + double *cuttype = neighbor->cuttype; + for (i = 1; i <= ntypes; i++) { + cut = 0.0; + if (cutusermulti) cut = cutusermulti[i]; + cutghostmulti[i][0] = MAX(cut,cuttype[i]); + cutghostmulti[i][1] = MAX(cut,cuttype[i]); + cutghostmulti[i][2] = MAX(cut,cuttype[i]); } } } @@ -204,13 +211,26 @@ void CommBrick::setup() cutghost[2] = cut * length2; if (mode == Comm::MULTI) { - double *cuttype = neighbor->cuttype; - for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = length0 * MAX(cut,cuttype[i]); - cutghostmulti[i][1] = length1 * MAX(cut,cuttype[i]); - cutghostmulti[i][2] = length2 * MAX(cut,cuttype[i]); + if (multi_tiered) { + // If using tiered binlists, use the itype-itype interaction distance for communication + double **cutneighsq = neighbor->cutneighsq; + for (i = 1; i <= ntypes; i++) { + cut = 0.0; + if (cutusermulti) cut = cutusermulti[i]; + cutghostmulti[i][0] = length0 * MAX(cut,sqrt(cutneighsq[i][i])); + cutghostmulti[i][1] = length1 * MAX(cut,sqrt(cutneighsq[i][i])); + cutghostmulti[i][2] = length2 * MAX(cut,sqrt(cutneighsq[i][i])); + } + } else { + // If using a single binlist, use the max itype-jtype interaction distance for communication + double *cuttype = neighbor->cuttype; + for (i = 1; i <= ntypes; i++) { + cut = 0.0; + if (cutusermulti) cut = cutusermulti[i]; + cutghostmulti[i][0] = length0 * MAX(cut,cuttype[i]); + cutghostmulti[i][1] = length1 * MAX(cut,cuttype[i]); + cutghostmulti[i][2] = length2 * MAX(cut,cuttype[i]); + } } } } diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 4759639bff..b82d54b3ab 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -175,20 +175,27 @@ void CommTiled::setup() // check that cutoff < any periodic box length if (mode == Comm::MULTI) { - double *cuttype = neighbor->cuttype; double cut; - for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = MAX(cut,cuttype[i]); - cutghostmulti[i][1] = MAX(cut,cuttype[i]); - cutghostmulti[i][2] = MAX(cut,cuttype[i]); - if (multi_bytype == 1) { - // Set the BYTYPE cutoff - cutghostmulti[i][0] = sqrt(neighbor->cutneighsq[i][i]); - cutghostmulti[i][1] = sqrt(neighbor->cutneighsq[i][i]); - cutghostmulti[i][2] = sqrt(neighbor->cutneighsq[i][i]); - } + if (multi_tiered) { + // If using tiered binlists, use the itype-itype interaction distance for communication + double **cutneighsq = neighbor->cutneighsq; + for (i = 1; i <= ntypes; i++) { + cut = 0.0; + if (cutusermulti) cut = cutusermulti[i]; + cutghostmulti[i][0] = MAX(cut,sqrt(cutneighsq[i][i])); + cutghostmulti[i][1] = MAX(cut,sqrt(cutneighsq[i][i])); + cutghostmulti[i][2] = MAX(cut,sqrt(cutneighsq[i][i])); + } + } else { + // If using a single binlist, use the max itype-jtype interaction distance for communication + double *cuttype = neighbor->cuttype; + for (i = 1; i <= ntypes; i++) { + cut = 0.0; + if (cutusermulti) cut = cutusermulti[i]; + cutghostmulti[i][0] = MAX(cut,cuttype[i]); + cutghostmulti[i][1] = MAX(cut,cuttype[i]); + cutghostmulti[i][2] = MAX(cut,cuttype[i]); + } } } diff --git a/src/nbin_bytype.cpp b/src/nbin_multi_tiered.cpp similarity index 100% rename from src/nbin_bytype.cpp rename to src/nbin_multi_tiered.cpp diff --git a/src/nbin_bytype.h b/src/nbin_multi_tiered.h similarity index 100% rename from src/nbin_bytype.h rename to src/nbin_multi_tiered.h diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 6e861b5a2b..740b16b66e 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1620,12 +1620,12 @@ int Neighbor::choose_bin(NeighRequest *rq) if (!rq->kokkos_device != !(mask & NB_KOKKOS_DEVICE)) continue; if (!rq->kokkos_host != !(mask & NB_KOKKOS_HOST)) continue; - // neighbor style is BIN or MULTI or BYTYPE and must match + // neighbor style is BIN or MULTI or MULTI/TIERED and must match if (style == Neighbor::BIN || style == Neighbor::MULTI) { if (!(mask & NB_STANDARD)) continue; - } else if (style == Neighbor::BYTYPE) { - if (!(mask & NB_BYTYPE)) continue; + } else if (style == Neighbor::MULTI_TIERED) { + if (!(mask & NB_MULTI_TIERED)) continue; } return i+1; @@ -1698,14 +1698,14 @@ int Neighbor::choose_stencil(NeighRequest *rq) if (!rq->ghost != !(mask & NS_GHOST)) continue; if (!rq->ssa != !(mask & NS_SSA)) continue; - // neighbor style is one of BIN, MULTI or BYTYPE and must match + // neighbor style is one of BIN, MULTI, or MULT/TIERED and must match if (style == Neighbor::BIN) { if (!(mask & NS_BIN)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NS_MULTI)) continue; - } else if (style == Neighbor::BYTYPE) { - if (!(mask & NS_BYTYPE)) continue; + } else if (style == Neighbor::MULT_TIERED) { + if (!(mask & NS_MULT_TIERED)) continue; } // dimension is 2 or 3 and must match @@ -1835,7 +1835,7 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!rq->halffull != !(mask & NP_HALF_FULL)) continue; if (!rq->off2on != !(mask & NP_OFF2ON)) continue; - // neighbor style is one of NSQ,BIN,MULTI or BYTYPE and must match + // neighbor style is one of NSQ, BIN, MULTI, or MULTI/TIERED and must match if (style == Neighbor::NSQ) { if (!(mask & NP_NSQ)) continue; @@ -1843,8 +1843,8 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!(mask & NP_BIN)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NP_MULTI)) continue; - } else if (style == Neighbor::BYTYPE) { - if (!(mask & NP_BYTYPE)) continue; + } else if (style == Neighbor::MULT_TIERED) { + if (!(mask & NP_MULT_TIERED)) continue; } // domain triclinic flag is on or off and must match @@ -2211,7 +2211,7 @@ void Neighbor::set(int narg, char **arg) if (strcmp(arg[1],"nsq") == 0) style = Neighbor::NSQ; else if (strcmp(arg[1],"bin") == 0) style = Neighbor::BIN; else if (strcmp(arg[1],"multi") == 0) style = Neighbor::MULTI; - else if (strcmp(arg[1],"bytype") == 0) style = Neighbor::BYTYPE; + else if (strcmp(arg[1],"multi/tiered") == 0) style = Neighbor::MULT_TIERED; else error->all(FLERR,"Illegal neighbor command"); if (style == Neighbor::MULTI && lmp->citeme) lmp->citeme->add(cite_neigh_multi); diff --git a/src/neighbor.h b/src/neighbor.h index e5b76dd41b..fd8cc49067 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -20,7 +20,7 @@ namespace LAMMPS_NS { class Neighbor : protected Pointers { public: - enum{NSQ,BIN,MULTI,BYTYPE}; + enum{NSQ,BIN,MULTI,MULTI_TIERED}; int style; // 0,1,2 = nsq, bin, multi int every; // build every this many steps int delay; // delay build for this many steps @@ -239,22 +239,22 @@ namespace NeighConst { static const int NB_KOKKOS_DEVICE = 1<<1; static const int NB_KOKKOS_HOST = 1<<2; static const int NB_SSA = 1<<3; - static const int NB_BYTYPE = 1<<4; + static const int NB_MULTI_TIERED = 1<<4; static const int NB_STANDARD = 1<<5; - static const int NS_BIN = 1<<0; - static const int NS_MULTI = 1<<1; - static const int NS_HALF = 1<<2; - static const int NS_FULL = 1<<3; - static const int NS_2D = 1<<4; - static const int NS_3D = 1<<5; - static const int NS_NEWTON = 1<<6; - static const int NS_NEWTOFF = 1<<7; - static const int NS_ORTHO = 1<<8; - static const int NS_TRI = 1<<9; - static const int NS_GHOST = 1<<10; - static const int NS_SSA = 1<<11; - static const int NS_BYTYPE = 1<<12; + static const int NS_BIN = 1<<0; + static const int NS_MULTI = 1<<1; + static const int NS_HALF = 1<<2; + static const int NS_FULL = 1<<3; + static const int NS_2D = 1<<4; + static const int NS_3D = 1<<5; + static const int NS_NEWTON = 1<<6; + static const int NS_NEWTOFF = 1<<7; + static const int NS_ORTHO = 1<<8; + static const int NS_TRI = 1<<9; + static const int NS_GHOST = 1<<10; + static const int NS_SSA = 1<<11; + static const int NS_MULTI_TIERED = 1<<12; static const int NP_NSQ = 1<<0; static const int NP_BIN = 1<<1; @@ -281,7 +281,7 @@ namespace NeighConst { static const int NP_SKIP = 1<<22; static const int NP_HALF_FULL = 1<<23; static const int NP_OFF2ON = 1<<24; - static const int NP_BYTYPE = 1<<25; + static const int NP_MULTI_TIERED = 1<<25; } } diff --git a/src/npair_full_bytype.cpp b/src/npair_full_multi_tiered.cpp similarity index 100% rename from src/npair_full_bytype.cpp rename to src/npair_full_multi_tiered.cpp diff --git a/src/npair_full_bytype.h b/src/npair_full_multi_tiered.h similarity index 100% rename from src/npair_full_bytype.h rename to src/npair_full_multi_tiered.h diff --git a/src/npair_half_bytype_newton.cpp b/src/npair_half_multi_tiered_newton.cpp similarity index 100% rename from src/npair_half_bytype_newton.cpp rename to src/npair_half_multi_tiered_newton.cpp diff --git a/src/npair_half_bytype_newton.h b/src/npair_half_multi_tiered_newton.h similarity index 100% rename from src/npair_half_bytype_newton.h rename to src/npair_half_multi_tiered_newton.h diff --git a/src/npair_half_bytype_newton_tri.cpp b/src/npair_half_multi_tiered_newton_tri.cpp similarity index 100% rename from src/npair_half_bytype_newton_tri.cpp rename to src/npair_half_multi_tiered_newton_tri.cpp diff --git a/src/npair_half_bytype_newton_tri.h b/src/npair_half_multi_tiered_newton_tri.h similarity index 100% rename from src/npair_half_bytype_newton_tri.h rename to src/npair_half_multi_tiered_newton_tri.h diff --git a/src/npair_half_size_bytype_newtoff.cpp b/src/npair_half_size_multi_tiered_newtoff.cpp similarity index 100% rename from src/npair_half_size_bytype_newtoff.cpp rename to src/npair_half_size_multi_tiered_newtoff.cpp diff --git a/src/npair_half_size_bytype_newtoff.h b/src/npair_half_size_multi_tiered_newtoff.h similarity index 100% rename from src/npair_half_size_bytype_newtoff.h rename to src/npair_half_size_multi_tiered_newtoff.h diff --git a/src/npair_half_size_bytype_newton.cpp b/src/npair_half_size_multi_tiered_newton.cpp similarity index 100% rename from src/npair_half_size_bytype_newton.cpp rename to src/npair_half_size_multi_tiered_newton.cpp diff --git a/src/npair_half_size_bytype_newton.h b/src/npair_half_size_multi_tiered_newton.h similarity index 100% rename from src/npair_half_size_bytype_newton.h rename to src/npair_half_size_multi_tiered_newton.h diff --git a/src/npair_half_size_bytype_newton_tri.cpp b/src/npair_half_size_multi_tiered_newton_tri.cpp similarity index 100% rename from src/npair_half_size_bytype_newton_tri.cpp rename to src/npair_half_size_multi_tiered_newton_tri.cpp diff --git a/src/npair_half_size_bytype_newton_tri.h b/src/npair_half_size_multi_tiered_newton_tri.h similarity index 100% rename from src/npair_half_size_bytype_newton_tri.h rename to src/npair_half_size_multi_tiered_newton_tri.h diff --git a/src/nstencil_full_bytype_3d.cpp b/src/nstencil_full_multi_tiered_3d.cpp similarity index 100% rename from src/nstencil_full_bytype_3d.cpp rename to src/nstencil_full_multi_tiered_3d.cpp diff --git a/src/nstencil_full_bytype_3d.h b/src/nstencil_full_multi_tiered_3d.h similarity index 100% rename from src/nstencil_full_bytype_3d.h rename to src/nstencil_full_multi_tiered_3d.h diff --git a/src/nstencil_half_bytype_2d_newton.cpp b/src/nstencil_half_multi_tiered_2d_newton.cpp similarity index 100% rename from src/nstencil_half_bytype_2d_newton.cpp rename to src/nstencil_half_multi_tiered_2d_newton.cpp diff --git a/src/nstencil_half_bytype_2d_newton.h b/src/nstencil_half_multi_tiered_2d_newton.h similarity index 100% rename from src/nstencil_half_bytype_2d_newton.h rename to src/nstencil_half_multi_tiered_2d_newton.h diff --git a/src/nstencil_half_bytype_3d_newtoff.cpp b/src/nstencil_half_multi_tiered_3d_newtoff.cpp similarity index 100% rename from src/nstencil_half_bytype_3d_newtoff.cpp rename to src/nstencil_half_multi_tiered_3d_newtoff.cpp diff --git a/src/nstencil_half_bytype_3d_newtoff.h b/src/nstencil_half_multi_tiered_3d_newtoff.h similarity index 100% rename from src/nstencil_half_bytype_3d_newtoff.h rename to src/nstencil_half_multi_tiered_3d_newtoff.h diff --git a/src/nstencil_half_bytype_3d_newton.cpp b/src/nstencil_half_multi_tiered_3d_newton.cpp similarity index 100% rename from src/nstencil_half_bytype_3d_newton.cpp rename to src/nstencil_half_multi_tiered_3d_newton.cpp diff --git a/src/nstencil_half_bytype_3d_newton.h b/src/nstencil_half_multi_tiered_3d_newton.h similarity index 100% rename from src/nstencil_half_bytype_3d_newton.h rename to src/nstencil_half_multi_tiered_3d_newton.h diff --git a/src/nstencil_half_bytype_3d_newton_tri.cpp b/src/nstencil_half_multi_tiered_3d_newton_tri.cpp similarity index 100% rename from src/nstencil_half_bytype_3d_newton_tri.cpp rename to src/nstencil_half_multi_tiered_3d_newton_tri.cpp diff --git a/src/nstencil_half_bytype_3d_newton_tri.h b/src/nstencil_half_multi_tiered_3d_newton_tri.h similarity index 100% rename from src/nstencil_half_bytype_3d_newton_tri.h rename to src/nstencil_half_multi_tiered_3d_newton_tri.h From 943a187be722c94cd669a6c80da6b6c85084bb4f Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 10 Nov 2020 16:39:56 -0700 Subject: [PATCH 0014/1217] Renamed to multi2, initial stencil edits --- src/comm.cpp | 14 +- src/comm.h | 2 +- src/comm_brick.cpp | 4 +- src/comm_tiled.cpp | 4 +- src/nbin.cpp | 138 ++---- src/nbin.h | 47 +- src/nbin_multi2.cpp | 414 ++++++++++++++++ src/{nbin_multi_tiered.h => nbin_multi2.h} | 26 +- src/nbin_multi_tiered.cpp | 464 ------------------ src/nbin_standard.cpp | 85 ++++ src/nbin_standard.h | 6 + src/neighbor.cpp | 20 +- src/neighbor.h | 8 +- ...ewton.cpp => npair_half_multi2_newton.cpp} | 0 ...ed_newton.h => npair_half_multi2_newton.h} | 0 ...i.cpp => npair_half_multi2_newton_tri.cpp} | 0 ...n_tri.h => npair_half_multi2_newton_tri.h} | 0 ...cpp => npair_half_size_multi2_newtoff.cpp} | 0 ...off.h => npair_half_size_multi2_newtoff.h} | 0 ....cpp => npair_half_size_multi2_newton.cpp} | 0 ...wton.h => npair_half_size_multi2_newton.h} | 0 ... => npair_half_size_multi2_newton_tri.cpp} | 0 ....h => npair_half_size_multi2_newton_tri.h} | 0 src/nstencil.cpp | 250 +++++++--- src/nstencil.h | 30 +- ...red_3d.cpp => nstencil_full_multi2_3d.cpp} | 24 +- ..._tiered_3d.h => nstencil_full_multi2_3d.h} | 11 +- ...cpp => nstencil_half_multi2_2d_newton.cpp} | 0 ...ton.h => nstencil_half_multi2_2d_newton.h} | 0 ...pp => nstencil_half_multi2_3d_newtoff.cpp} | 0 ...ff.h => nstencil_half_multi2_3d_newtoff.h} | 0 ...cpp => nstencil_half_multi2_3d_newton.cpp} | 0 ...ton.h => nstencil_half_multi2_3d_newton.h} | 0 ...=> nstencil_half_multi2_3d_newton_tri.cpp} | 0 ...h => nstencil_half_multi2_3d_newton_tri.h} | 0 35 files changed, 845 insertions(+), 702 deletions(-) create mode 100644 src/nbin_multi2.cpp rename src/{nbin_multi_tiered.h => nbin_multi2.h} (75%) delete mode 100644 src/nbin_multi_tiered.cpp rename src/{npair_half_multi_tiered_newton.cpp => npair_half_multi2_newton.cpp} (100%) rename src/{npair_half_multi_tiered_newton.h => npair_half_multi2_newton.h} (100%) rename src/{npair_half_multi_tiered_newton_tri.cpp => npair_half_multi2_newton_tri.cpp} (100%) rename src/{npair_half_multi_tiered_newton_tri.h => npair_half_multi2_newton_tri.h} (100%) rename src/{npair_half_size_multi_tiered_newtoff.cpp => npair_half_size_multi2_newtoff.cpp} (100%) rename src/{npair_half_size_multi_tiered_newtoff.h => npair_half_size_multi2_newtoff.h} (100%) rename src/{npair_half_size_multi_tiered_newton.cpp => npair_half_size_multi2_newton.cpp} (100%) rename src/{npair_half_size_multi_tiered_newton.h => npair_half_size_multi2_newton.h} (100%) rename src/{npair_half_size_multi_tiered_newton_tri.cpp => npair_half_size_multi2_newton_tri.cpp} (100%) rename src/{npair_half_size_multi_tiered_newton_tri.h => npair_half_size_multi2_newton_tri.h} (100%) rename src/{nstencil_full_multi_tiered_3d.cpp => nstencil_full_multi2_3d.cpp} (90%) rename src/{nstencil_full_multi_tiered_3d.h => nstencil_full_multi2_3d.h} (83%) rename src/{nstencil_half_multi_tiered_2d_newton.cpp => nstencil_half_multi2_2d_newton.cpp} (100%) rename src/{nstencil_half_multi_tiered_2d_newton.h => nstencil_half_multi2_2d_newton.h} (100%) rename src/{nstencil_half_multi_tiered_3d_newtoff.cpp => nstencil_half_multi2_3d_newtoff.cpp} (100%) rename src/{nstencil_half_multi_tiered_3d_newtoff.h => nstencil_half_multi2_3d_newtoff.h} (100%) rename src/{nstencil_half_multi_tiered_3d_newton.cpp => nstencil_half_multi2_3d_newton.cpp} (100%) rename src/{nstencil_half_multi_tiered_3d_newton.h => nstencil_half_multi2_3d_newton.h} (100%) rename src/{nstencil_half_multi_tiered_3d_newton_tri.cpp => nstencil_half_multi2_3d_newton_tri.cpp} (100%) rename src/{nstencil_half_multi_tiered_3d_newton_tri.h => nstencil_half_multi2_3d_newton_tri.h} (100%) diff --git a/src/comm.cpp b/src/comm.cpp index b6f905d9a2..ad0c836432 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -76,7 +76,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) grid2proc = nullptr; xsplit = ysplit = zsplit = nullptr; rcbnew = 0; - multi_tiered = 0; + multi2 = 0; // use of OpenMP threads // query OpenMP for number of threads/process set by user at run-time @@ -242,9 +242,9 @@ void Comm::init() for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; - // Can't used multi/tiered communication with Newton off - if (force->newton == 0 && multi_tiered) - error->all(FLERR,"Cannot use multi/tiered communication with Newton off"); + // Can't used multi2 communication with Newton off + if (force->newton == 0 && multi2) + error->all(FLERR,"Cannot use multi2 communication with Newton off"); } /* ---------------------------------------------------------------------- @@ -331,10 +331,10 @@ void Comm::modify_params(int narg, char **arg) for (i=nlo; i<=nhi; ++i) cutusermulti[i] = cut; iarg += 3; - } else if (strcmp(arg[iarg],"cutoff/tiered") == 0) { + } else if (strcmp(arg[iarg],"cutoff/multi2") == 0) { if (mode == Comm::SINGLE) - error->all(FLERR,"Use cutoff/tiered in mode multi only"); - multi_tiered = 1; + error->all(FLERR,"Use cutoff/multi2 in mode multi only"); + multi2 = 1; iarg += 1; } else if (strcmp(arg[iarg],"vel") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command"); diff --git a/src/comm.h b/src/comm.h index 037eaab348..d8d842ace5 100644 --- a/src/comm.h +++ b/src/comm.h @@ -161,7 +161,7 @@ class Comm : protected Pointers { int (*)(int, char *, int &, int *&, char *&, void *), int, char *&, int, void *, int); void rendezvous_stats(int, int, int, int, int, int, bigint); - int multi_tiered; // 1 if multi cutoff is intra-type cutoff + int multi2; // 1 if multi cutoff is intra-type cutoff public: enum{MULTIPLE}; diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index c9fd00e9f5..981e86c2a4 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -174,8 +174,8 @@ void CommBrick::setup() cutghost[0] = cutghost[1] = cutghost[2] = cut; if (mode == Comm::MULTI) { - if (multi_tiered) { - // If using tiered binlists, use the itype-itype interaction distance for communication + if (multi2) { + // If using multi2 binlists, use the itype-itype interaction distance for communication double **cutneighsq = neighbor->cutneighsq; for (i = 1; i <= ntypes; i++) { cut = 0.0; diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index b82d54b3ab..16ae86b4a3 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -176,8 +176,8 @@ void CommTiled::setup() if (mode == Comm::MULTI) { double cut; - if (multi_tiered) { - // If using tiered binlists, use the itype-itype interaction distance for communication + if (multi2) { + // If using multi2 binlists, use the itype-itype interaction distance for communication double **cutneighsq = neighbor->cutneighsq; for (i = 1; i <= ntypes; i++) { cut = 0.0; diff --git a/src/nbin.cpp b/src/nbin.cpp index 64ae7e7b83..4ab3270287 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -31,6 +31,21 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp) bins = nullptr; atom2bin = nullptr; + nbinx_tiered = nullptr; nbiny_tiered = nullptr; nbinz_tiered = nullptr; + mbins_tiered = nullptr; + mbinx_tiered = nullptr; mbiny_tiered = nullptr, mbinz_tiered = nullptr; + mbinxlo_tiered = nullptr; + mbinylo_tiered = nullptr; + mbinzlo_tiered = nullptr; + binsizex_tiered = nullptr; binsizey_tiered = nullptr; binsizez_tiered = nullptr; + bininvx_tiered = nullptr; bininvy_tiered = nullptr; bininvz_tiered = nullptr; + binhead_tiered = nullptr; + bins_tiered = nullptr; + atom2bin_tiered = nullptr; + maxbins_tiered = nullptr; + + maxtypes = 0; + neighbor->last_setup_bins = -1; // geometry settings @@ -48,6 +63,37 @@ NBin::~NBin() memory->destroy(binhead); memory->destroy(bins); memory->destroy(atom2bin); + + if (!bins_tiered) return; + + memory->destroy(nbinx_tiered); + memory->destroy(nbiny_tiered); + memory->destroy(nbinz_tiered); + memory->destroy(mbins_tiered); + memory->destroy(mbinx_tiered); + memory->destroy(mbiny_tiered); + memory->destroy(mbinz_tiered); + memory->destroy(mbinxlo_tiered); + memory->destroy(mbinylo_tiered); + memory->destroy(mbinzlo_tiered); + + memory->destroy(binsizex_tiered); + memory->destroy(binsizey_tiered); + memory->destroy(binsizez_tiered); + memory->destroy(bininvx_tiered); + memory->destroy(bininvy_tiered); + memory->destroy(bininvz_tiered); + + for (int n = 1; n <= maxtypes; n++) { + memory->destroy(binhead_tiered[n]); + memory->destroy(bins_tiered[n]); + memory->destroy(atom2bin_tiered[n]); + } + delete [] binhead_tiered; + delete [] bins_tiered; + delete [] atom2bin_tiered; + + memory->destroy(maxbins_tiered); } /* ---------------------------------------------------------------------- */ @@ -77,95 +123,3 @@ void NBin::copy_neighbor_info() if (cutoff_custom > 0.0) cutneighmax = cutoff_custom; } - -/* ---------------------------------------------------------------------- - setup for bin_atoms() -------------------------------------------------------------------------- */ - -void NBin::bin_atoms_setup(int nall) -{ - // binhead = per-bin vector, mbins in length - // add 1 bin for USER-INTEL package - - if (mbins > maxbin) { - maxbin = mbins; - memory->destroy(binhead); - memory->create(binhead,maxbin,"neigh:binhead"); - } - - // bins and atom2bin = per-atom vectors - // for both local and ghost atoms - - if (nall > maxatom) { - maxatom = nall; - memory->destroy(bins); - memory->create(bins,maxatom,"neigh:bins"); - memory->destroy(atom2bin); - memory->create(atom2bin,maxatom,"neigh:atom2bin"); - } -} - -/* ---------------------------------------------------------------------- - convert atom coords into local bin # - for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo - take special care to insure ghosts are in correct bins even w/ roundoff - hi ghost atoms = nbin,nbin+1,etc - owned atoms = 0 to nbin-1 - lo ghost atoms = -1,-2,etc - this is necessary so that both procs on either side of PBC - treat a pair of atoms straddling the PBC in a consistent way - for triclinic, doesn't matter since stencil & neigh list built differently -------------------------------------------------------------------------- */ - -int NBin::coord2bin(double *x) -{ - int ix,iy,iz; - - if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable"); - - if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx) + nbinx; - else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx); - ix = MIN(ix,nbinx-1); - } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx) - 1; - - if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy) + nbiny; - else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy); - iy = MIN(iy,nbiny-1); - } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy) - 1; - - if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz) + nbinz; - else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz); - iz = MIN(iz,nbinz-1); - } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz) - 1; - - return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo); -} -/* ---------------------------------------------------------------------- - to be overridden by NBinType - ------------------------------------------------------------------------- */ - -int NBin::coord2bin(double * x, int itype) -{ - error->all(FLERR,"coord2bin(x, itype) not available.\n"); - return -1; -} - -/* ---------------------------------------------------------------------- */ - -double NBin::memory_usage() -{ - double bytes = 0; - bytes += maxbin*sizeof(int); - bytes += 2*maxatom*sizeof(int); - return bytes; -} diff --git a/src/nbin.h b/src/nbin.h index 96cc7eac64..33b93ef79c 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -22,6 +22,9 @@ class NBin : protected Pointers { public: int istyle; // 1-N index into binnames bigint last_bin; // last timestep atoms were binned + double cutoff_custom; // cutoff set by requestor + + // Variables for NBinStandard int nbinx,nbiny,nbinz; // # of global bins int mbins; // # of local bins and offset on this proc @@ -35,35 +38,32 @@ class NBin : protected Pointers { int *bins; // index of next atom in same bin int *atom2bin; // bin assignment for each atom (local+ghost) - double cutoff_custom; // cutoff set by requestor - - // Analogues for NBinType - int * nbinx_type, * nbiny_type, * nbinz_type; - int * mbins_type; - int * mbinx_type, * mbiny_type, * mbinz_type; - int * mbinxlo_type, * mbinylo_type, * mbinzlo_type; - double * binsizex_type, * binsizey_type, * binsizez_type; - double * bininvx_type, * bininvy_type, * bininvz_type; - - int ** binhead_type; - int ** bins_type; - int ** atom2bin_type; + // Analogues for NBinMultimulti2 + + int *nbinx_multi2, *nbiny_multi2, *nbinz_multi2; + int *mbins_multi2; + int *mbinx_multi2, *mbiny_multi2, *mbinz_multi2; + int *mbinxlo_multi2, *mbinylo_multi2, *mbinzlo_multi2; + double *binsizex_multi2, *binsizey_multi2, *binsizez_multi2; + double *bininvx_multi2, *bininvy_multi2, *bininvz_multi2; + int **binhead_multi2; + int **bins_multi2; + int **atom2bin_multi2; + NBin(class LAMMPS *); ~NBin(); void post_constructor(class NeighRequest *); virtual void copy_neighbor_info(); - virtual void bin_atoms_setup(int); - double memory_usage(); + virtual void bin_atoms_setup(int) = 0; virtual void setup_bins(int) = 0; virtual void bin_atoms() = 0; + virtual double memory_usage() {return 0.0;} // Kokkos package int kokkos; // 1 if class stores Kokkos data - // For NBinType - virtual int coord2bin(double *, int); protected: @@ -81,12 +81,23 @@ class NBin : protected Pointers { int dimension; int triclinic; - int maxbin; // size of binhead array + // data for standard NBin + int maxatom; // size of bins array + // data for standard NBin + + int maxbin; // size of binhead array + + // data for multi/multi2 NBin + + int maxtypes; // size of multi2 arrays + int * maxbins_multi2; // size of 2nd dimension of binhead_multi2 array + // methods int coord2bin(double *); + int coord2bin(double *, int); }; } diff --git a/src/nbin_multi2.cpp b/src/nbin_multi2.cpp new file mode 100644 index 0000000000..7a87ba940c --- /dev/null +++ b/src/nbin_multi2.cpp @@ -0,0 +1,414 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nbin_multi2.h" +#include "neighbor.h" +#include "atom.h" +#include "group.h" +#include "domain.h" +#include "comm.h" +#include "update.h" +#include "error.h" +#include "memory.h" + +using namespace LAMMPS_NS; + +#define SMALL 1.0e-6 +#define CUT2BIN_RATIO 100 + +/* ---------------------------------------------------------------------- */ + +NBinMulti2::NBinMulti2(LAMMPS *lmp) : NBin(lmp) {} + +/* ---------------------------------------------------------------------- + setup for bin_atoms() +------------------------------------------------------------------------- */ + +void NBinMulti2::bin_atoms_setup(int nall) +{ + // binhead_multi2[n] = per-bin vector mbins in length mbins_multi2[n] + + for (int n = 1; n <= maxtypes; n++) { + if (mbins_multi2[n] > maxbins_multi2[n]) { + maxbins_multi2[n] = mbins_multi2[n]; + memory->destroy(binhead_multi2[n]); + memory->create(binhead_multi2[n], mbins_multi2[n], "neigh:mbins_multi2"); + } + } + + // bins_multi2[n] and atom2bin_multi2[n] = per-atom vectors + // for both local and ghost atoms + + if (nall > maxatom) { + maxatom = nall; + for (int n = 1; n <= maxtypes; n++) { + memory->destroy(bins_multi2[n]); + memory->destroy(atom2bin_multi2[n]); + memory->create(bins_multi2[n], maxatom, "neigh:bin_multi2"); + memory->create(atom2bin_multi2[n], maxatom, "neigh:atom2bin_multi2"); + } + } +} + +/* --------------------------------------------------------------------- + Identify index of type with smallest cutoff +------------------------------------------------------------------------ */ + +int NBinMulti2::itype_min() { + + int itypemin = 1; + double ** cutneighsq; + + cutneighsq = neighbor->cutneighsq; + + for (int n = 1; n <= atom->ntypes; n++) { + if (cutneighsq[n][n] < cutneighsq[itypemin][itypemin]) { + itypemin = n; + } + } + + return itypemin; +} + +/* ---------------------------------------------------------------------- + setup neighbor binning geometry + ---------------------------------------------------------------------- */ + +void NBinMulti2::setup_bins(int style) +{ + int n; + int itypemin; + + // Initialize arrays + + if (atom->ntypes > maxtypes) { + + // Clear any/all memory for existing types + + for (n = 1; n <= maxtypes; n++) { + memory->destroy(atom2bin_multi2[n]); + memory->destroy(binhead_multi2[n]); + memory->destroy(bins_multi2[n]); + } + delete [] atom2bin_multi2; + delete [] binhead_multi2; + delete [] bins_multi2; + + // Realloacte at updated maxtypes + + maxtypes = atom->ntypes; + + atom2bin_multi2 = new int*[maxtypes+1](); + binhead_multi2 = new int*[maxtypes+1](); + bins_multi2 = new int*[maxtypes+1](); + + memory->destroy(nbinx_multi2); + memory->destroy(nbiny_multi2); + memory->destroy(nbinz_multi2); + memory->create(nbinx_multi2, maxtypes+1, "neigh:nbinx_multi2"); + memory->create(nbiny_multi2, maxtypes+1, "neigh:nbiny_multi2"); + memory->create(nbinz_multi2, maxtypes+1, "neigh:nbinz_multi2"); + + memory->destroy(mbins_multi2); + memory->destroy(mbinx_multi2); + memory->destroy(mbiny_multi2); + memory->destroy(mbinz_multi2); + memory->create(mbins_multi2, maxtypes+1, "neigh:mbins_multi2"); + memory->create(mbinx_multi2, maxtypes+1, "neigh:mbinx_multi2"); + memory->create(mbiny_multi2, maxtypes+1, "neigh:mbiny_multi2"); + memory->create(mbinz_multi2, maxtypes+1, "neigh:mbinz_multi2"); + + memory->destroy(mbinxlo_multi2); + memory->destroy(mbinylo_multi2); + memory->destroy(mbinzlo_multi2); + memory->create(mbinxlo_multi2, maxtypes+1, "neigh:mbinxlo_multi2"); + memory->create(mbinylo_multi2, maxtypes+1, "neigh:mbinylo_multi2"); + memory->create(mbinzlo_multi2, maxtypes+1, "neigh:mbinzlo_multi2"); + + memory->destroy(binsizex_multi2); + memory->destroy(binsizey_multi2); + memory->destroy(binsizez_multi2); + memory->create(binsizex_multi2, maxtypes+1, "neigh:binsizex_multi2"); + memory->create(binsizey_multi2, maxtypes+1, "neigh:binsizey_multi2"); + memory->create(binsizez_multi2, maxtypes+1, "neigh:binsizez_multi2"); + + memory->destroy(bininvx_multi2); + memory->destroy(bininvy_multi2); + memory->destroy(bininvz_multi2); + memory->create(bininvx_multi2, maxtypes+1, "neigh:bininvx_multi2"); + memory->create(bininvy_multi2, maxtypes+1, "neigh:bininvy_multi2"); + memory->create(bininvz_multi2, maxtypes+1, "neigh:bininvz_multi2"); + + memory->destroy(maxbins_multi2); + memory->create(maxbins_multi2, maxtypes+1, "neigh:maxbins_multi2"); + // make sure reallocation occurs in bin_atoms_setup() + for (n = 1; n <= maxtypes; n++) { + maxbins_multi2[n] = 0; + } + maxatom = 0; + } + + itypemin = itype_min(); + + // bbox = size of bbox of entire domain + // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost + // for triclinic: + // bbox bounds all 8 corners of tilted box + // subdomain is in lamda coords + // include dimension-dependent extension via comm->cutghost + // domain->bbox() converts lamda extent to box coords and computes bbox + + double bbox[3],bsubboxlo[3],bsubboxhi[3]; + double *cutghost = comm->cutghost; + + if (triclinic == 0) { + bsubboxlo[0] = domain->sublo[0] - cutghost[0]; + bsubboxlo[1] = domain->sublo[1] - cutghost[1]; + bsubboxlo[2] = domain->sublo[2] - cutghost[2]; + bsubboxhi[0] = domain->subhi[0] + cutghost[0]; + bsubboxhi[1] = domain->subhi[1] + cutghost[1]; + bsubboxhi[2] = domain->subhi[2] + cutghost[2]; + } else { + double lo[3],hi[3]; + lo[0] = domain->sublo_lamda[0] - cutghost[0]; + lo[1] = domain->sublo_lamda[1] - cutghost[1]; + lo[2] = domain->sublo_lamda[2] - cutghost[2]; + hi[0] = domain->subhi_lamda[0] + cutghost[0]; + hi[1] = domain->subhi_lamda[1] + cutghost[1]; + hi[2] = domain->subhi_lamda[2] + cutghost[2]; + domain->bbox(lo,hi,bsubboxlo,bsubboxhi); + } + + bbox[0] = bboxhi[0] - bboxlo[0]; + bbox[1] = bboxhi[1] - bboxlo[1]; + bbox[2] = bboxhi[2] - bboxlo[2]; + + // For each type... + + for (n = 1; n <= atom->ntypes; n++) { + // binsize_user only relates to smallest type + // optimal bin size is roughly 1/2 the type-type cutoff + // special case of all cutoffs = 0.0, binsize = box size + + double binsize_optimal; + if (n == itypemin && binsizeflag) binsize_optimal = binsize_user; + else binsize_optimal = 0.5*sqrt(neighbor->cutneighsq[n][n]); + if (binsize_optimal == 0.0) binsize_optimal = bbox[0]; + double binsizeinv = 1.0/binsize_optimal; + + // test for too many global bins in any dimension due to huge global domain + + if (bbox[0]*binsizeinv > MAXSMALLINT || bbox[1]*binsizeinv > MAXSMALLINT || + bbox[2]*binsizeinv > MAXSMALLINT) + error->all(FLERR,"Domain too large for neighbor bins"); + + // create actual bins + // always have one bin even if cutoff > bbox + // for 2d, nbinz_multi2[n] = 1 + + nbinx_multi2[n] = static_cast (bbox[0]*binsizeinv); + nbiny_multi2[n] = static_cast (bbox[1]*binsizeinv); + if (dimension == 3) nbinz_multi2[n] = static_cast (bbox[2]*binsizeinv); + else nbinz_multi2[n] = 1; + + if (nbinx_multi2[n] == 0) nbinx_multi2[n] = 1; + if (nbiny_multi2[n] == 0) nbiny_multi2[n] = 1; + if (nbinz_multi2[n] == 0) nbinz_multi2[n] = 1; + + // compute actual bin size for nbins to fit into box exactly + // error if actual bin size << cutoff, since will create a zillion bins + // this happens when nbin = 1 and box size << cutoff + // typically due to non-periodic, flat system in a particular dim + // in that extreme case, should use NSQ not BIN neighbor style + + binsizex_multi2[n] = bbox[0]/nbinx_multi2[n]; + binsizey_multi2[n] = bbox[1]/nbiny_multi2[n]; + binsizez_multi2[n] = bbox[2]/nbinz_multi2[n]; + + bininvx_multi2[n] = 1.0 / binsizex_multi2[n]; + bininvy_multi2[n] = 1.0 / binsizey_multi2[n]; + bininvz_multi2[n] = 1.0 / binsizez_multi2[n]; + + if (binsize_optimal*bininvx_multi2[n] > CUT2BIN_RATIO || + binsize_optimal*bininvy_multi2[n] > CUT2BIN_RATIO || + binsize_optimal*bininvz_multi2[n] > CUT2BIN_RATIO) + error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); + + // mbinlo/hi = lowest and highest global bins my ghost atoms could be in + // coord = lowest and highest values of coords for my ghost atoms + // static_cast(-1.5) = -1, so subract additional -1 + // add in SMALL for round-off safety + + int mbinxhi,mbinyhi,mbinzhi; + double coord; + + coord = bsubboxlo[0] - SMALL*bbox[0]; + mbinxlo_multi2[n] = static_cast ((coord-bboxlo[0])*bininvx_multi2[n]); + if (coord < bboxlo[0]) mbinxlo_multi2[n] = mbinxlo_multi2[n] - 1; + coord = bsubboxhi[0] + SMALL*bbox[0]; + mbinxhi = static_cast ((coord-bboxlo[0])*bininvx_multi2[n]); + + coord = bsubboxlo[1] - SMALL*bbox[1]; + mbinylo_multi2[n] = static_cast ((coord-bboxlo[1])*bininvy_multi2[n]); + if (coord < bboxlo[1]) mbinylo_multi2[n] = mbinylo_multi2[n] - 1; + coord = bsubboxhi[1] + SMALL*bbox[1]; + mbinyhi = static_cast ((coord-bboxlo[1])*bininvy_multi2[n]); + + if (dimension == 3) { + coord = bsubboxlo[2] - SMALL*bbox[2]; + mbinzlo_multi2[n] = static_cast ((coord-bboxlo[2])*bininvz_multi2[n]); + if (coord < bboxlo[2]) mbinzlo_multi2[n] = mbinzlo_multi2[n] - 1; + coord = bsubboxhi[2] + SMALL*bbox[2]; + mbinzhi = static_cast ((coord-bboxlo[2])*bininvz_multi2[n]); + } + + // extend bins by 1 to insure stencil extent is included + // for 2d, only 1 bin in z + + mbinxlo_multi2[n] = mbinxlo_multi2[n] - 1; + mbinxhi = mbinxhi + 1; + mbinx_multi2[n] = mbinxhi - mbinxlo_multi2[n] + 1; + + mbinylo_multi2[n] = mbinylo_multi2[n] - 1; + mbinyhi = mbinyhi + 1; + mbiny_multi2[n] = mbinyhi - mbinylo_multi2[n] + 1; + + if (dimension == 3) { + mbinzlo_multi2[n] = mbinzlo_multi2[n] - 1; + mbinzhi = mbinzhi + 1; + } else mbinzlo_multi2[n] = mbinzhi = 0; + mbinz_multi2[n] = mbinzhi - mbinzlo_multi2[n] + 1; + + bigint bbin = ((bigint) mbinx_multi2[n]) + * ((bigint) mbiny_multi2[n]) * ((bigint) mbinz_multi2[n]) + 1; + if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins"); + mbins_multi2[n] = bbin; + } + +} + +/* ---------------------------------------------------------------------- + bin owned and ghost atoms by type +------------------------------------------------------------------------- */ + +void NBinMulti2::bin_atoms() +{ + int i,ibin,n; + + last_bin = update->ntimestep; + for (n = 1; n <= maxtypes; n++) { + for (i = 0; i < mbins_multi2[n]; i++) binhead_multi2[n][i] = -1; + } + + // bin in reverse order so linked list will be in forward order + // also puts ghost atoms at end of list, which is necessary + + double **x = atom->x; + int *mask = atom->mask; + int *type = atom->type; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + + if (includegroup) { + int bitmask = group->bitmask[includegroup]; + for (i = nall-1; i >= nlocal; i--) { + if (mask[i] & bitmask) { + n = type[i]; + ibin = coord2bin(x[i], n); + atom2bin_multi2[n][i] = ibin; + bins_multi2[n][i] = binhead_multi2[n][ibin]; + binhead_multi2[n][ibin] = i; + } + } + for (i = atom->nfirst-1; i >= 0; i--) { + n = type[i]; + ibin = coord2bin(x[i], n); + atom2bin_multi2[n][i] = ibin; + bins_multi2[n][i] = binhead_multi2[n][ibin]; + binhead_multi2[n][ibin] = i; + } + } else { + for (i = nall-1; i >= 0; i--) { + n = type[i]; + ibin = coord2bin(x[i], n); + atom2bin_multi2[n][i] = ibin; + bins_multi2[n][i] = binhead_multi2[n][ibin]; + binhead_multi2[n][ibin] = i; + } + } +} + +/* ---------------------------------------------------------------------- + convert atom coords into local bin # for a particular type + for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo + take special care to insure ghosts are in correct bins even w/ roundoff + hi ghost atoms = nbin,nbin+1,etc + owned atoms = 0 to nbin-1 + lo ghost atoms = -1,-2,etc + this is necessary so that both procs on either side of PBC + treat a pair of atoms straddling the PBC in a consistent way + for triclinic, doesn't matter since stencil & neigh list built differently +------------------------------------------------------------------------- */ + +int NBinMulti2::coord2bin(double *x, int it) +{ + int ix,iy,iz; + int ibin; + + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) + error->one(FLERR,"Non-numeric positions - simulation unstable"); + + if (x[0] >= bboxhi[0]) + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi2[it]) + nbinx_multi2[it]; + else if (x[0] >= bboxlo[0]) { + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]); + ix = MIN(ix,nbinx_multi2[it]-1); + } else + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]) - 1; + + if (x[1] >= bboxhi[1]) + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi2[it]) + nbiny_multi2[it]; + else if (x[1] >= bboxlo[1]) { + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]); + iy = MIN(iy,nbiny_multi2[it]-1); + } else + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]) - 1; + + if (x[2] >= bboxhi[2]) + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi2[it]) + nbinz_multi2[it]; + else if (x[2] >= bboxlo[2]) { + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]); + iz = MIN(iz,nbinz_multi2[it]-1); + } else + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]) - 1; + + + ibin = (iz-mbinzlo_multi2[it])*mbiny_multi2[it]*mbinx_multi2[it] + + (iy-mbinylo_multi2[it])*mbinx_multi2[it] + + (ix-mbinxlo_multi2[it]); + return ibin; +} + + +/* ---------------------------------------------------------------------- */ + +double NBinMulti2::memory_usage() +{ + double bytes = 0; + + for (int m = 1; m < maxtypes; m++) { + bytes += maxbins_multi2[m]*sizeof(int); + bytes += 2*maxatom*sizeof(int); + } + return bytes; +} diff --git a/src/nbin_multi_tiered.h b/src/nbin_multi2.h similarity index 75% rename from src/nbin_multi_tiered.h rename to src/nbin_multi2.h index ad2b95ef4b..8cca7b1023 100644 --- a/src/nbin_multi_tiered.h +++ b/src/nbin_multi2.h @@ -13,36 +13,32 @@ #ifdef NBIN_CLASS -NBinStyle(bytype, - NBinBytype, - NB_BYTYPE) +NBinStyle(multi2, + NBinMulti2, + NB_MULTI2) #else -#ifndef LMP_NBIN_BYTYPE_H -#define LMP_NBIN_BYTYPE_H +#ifndef LMP_NBIN_MULTI2_H +#define LMP_NBIN_MULTI2_H #include "nbin.h" namespace LAMMPS_NS { -class NBinBytype : public NBin { +class NBinMulti2 : public NBin { public: - NBinBytype(class LAMMPS *); - ~NBinBytype(); + NBinMulti2(class LAMMPS *); + ~NBinMulti2() {} void bin_atoms_setup(int); void setup_bins(int); - void bin_atoms(); - - int coord2bin(double *x, int itype); - bigint memory_usage(); + void bin_atoms(); + double memory_usage(); private: - int maxtypes; - int * maxbins_type; - void setup_types(); + int coord2bin(double *, int); int itype_min(); }; diff --git a/src/nbin_multi_tiered.cpp b/src/nbin_multi_tiered.cpp deleted file mode 100644 index 70732a4b97..0000000000 --- a/src/nbin_multi_tiered.cpp +++ /dev/null @@ -1,464 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nbin_bytype.h" -#include "neighbor.h" -#include "atom.h" -#include "group.h" -#include "domain.h" -#include "comm.h" -#include "update.h" -#include "error.h" -#include "memory.h" - -using namespace LAMMPS_NS; - -#define SMALL 1.0e-6 -#define CUT2BIN_RATIO 100 - -/* ---------------------------------------------------------------------- */ - -NBinBytype::NBinBytype(LAMMPS *lmp) : NBin(lmp) { - - nbinx_type = NULL; nbiny_type = NULL; nbinz_type = NULL; - mbins_type = NULL; - mbinx_type = NULL; mbiny_type = NULL, mbinz_type = NULL; - mbinxlo_type = NULL; - mbinylo_type = NULL; - mbinzlo_type = NULL; - binsizex_type = NULL; binsizey_type = NULL; binsizez_type = NULL; - bininvx_type = NULL; bininvy_type = NULL; bininvz_type = NULL; - binhead_type = NULL; - bins_type = NULL; - atom2bin_type = NULL; - maxtypes = 0; - maxbins_type = NULL; -} - -NBinBytype::~NBinBytype() { - - memory->destroy(nbinx_type); - memory->destroy(nbiny_type); - memory->destroy(nbinz_type); - memory->destroy(mbins_type); - memory->destroy(mbinx_type); - memory->destroy(mbiny_type); - memory->destroy(mbinz_type); - memory->destroy(mbinxlo_type); - memory->destroy(mbinylo_type); - memory->destroy(mbinzlo_type); - - memory->destroy(binsizex_type); - memory->destroy(binsizey_type); - memory->destroy(binsizez_type); - memory->destroy(bininvx_type); - memory->destroy(bininvy_type); - memory->destroy(bininvz_type); - - for (int n = 1; n <= maxtypes; n++) { - memory->destroy(binhead_type[n]); - memory->destroy(bins_type[n]); - memory->destroy(atom2bin_type[n]); - } - delete [] binhead_type; - delete [] bins_type; - delete [] atom2bin_type; - - memory->destroy(maxbins_type); -} - -/* ---------------------------------------------------------------------- - arrange storage for types - allows ntypes to change, but not currently expected after initialisation - ------------------------------------------------------------------------- */ - -void NBinBytype::setup_types() { - - int n; - - if (atom->ntypes > maxtypes) { - - // Clear any/all memory for existing types - - for (n = 1; n <= maxtypes; n++) { - memory->destroy(atom2bin_type[n]); - memory->destroy(binhead_type[n]); - memory->destroy(bins_type[n]); - } - delete [] atom2bin_type; - delete [] binhead_type; - delete [] bins_type; - - // Realloacte at updated maxtypes - - maxtypes = atom->ntypes; - - atom2bin_type = new int*[maxtypes+1](); - binhead_type = new int*[maxtypes+1](); - bins_type = new int*[maxtypes+1](); - - memory->destroy(nbinx_type); - memory->destroy(nbiny_type); - memory->destroy(nbinz_type); - memory->create(nbinx_type, maxtypes+1, "nBinType:nbinx_type"); - memory->create(nbiny_type, maxtypes+1, "nBinType:nbiny_type"); - memory->create(nbinz_type, maxtypes+1, "nBinType:nbinz_type"); - - memory->destroy(mbins_type); - memory->destroy(mbinx_type); - memory->destroy(mbiny_type); - memory->destroy(mbinz_type); - memory->create(mbins_type, maxtypes+1, "nBinType:mbins_type"); - memory->create(mbinx_type, maxtypes+1, "nBinType:mbinx_type"); - memory->create(mbiny_type, maxtypes+1, "nBinType:mbiny_type"); - memory->create(mbinz_type, maxtypes+1, "nBinType:mbinz_type"); - - memory->destroy(mbinxlo_type); - memory->destroy(mbinylo_type); - memory->destroy(mbinzlo_type); - memory->create(mbinxlo_type, maxtypes+1, "nBinType:mbinxlo_type"); - memory->create(mbinylo_type, maxtypes+1, "nBinType:mbinylo_type"); - memory->create(mbinzlo_type, maxtypes+1, "nBinType:mbinzlo_type"); - - memory->destroy(binsizex_type); - memory->destroy(binsizey_type); - memory->destroy(binsizez_type); - memory->create(binsizex_type, maxtypes+1, "nBinType:binsizex_type"); - memory->create(binsizey_type, maxtypes+1, "nBinType:binsizey_type"); - memory->create(binsizez_type, maxtypes+1, "nBinType:binsizez_type"); - - memory->destroy(bininvx_type); - memory->destroy(bininvy_type); - memory->destroy(bininvz_type); - memory->create(bininvx_type, maxtypes+1, "nBinType:bininvx_type"); - memory->create(bininvy_type, maxtypes+1, "nBinType:bininvy_type"); - memory->create(bininvz_type, maxtypes+1, "nBinType:bininvz_type"); - - memory->destroy(maxbins_type); - memory->create(maxbins_type, maxtypes+1, "nBinType:maxbins_type"); - // make sure reallocation occurs in bin_atoms_setup() - for (n = 1; n <= maxtypes; n++) { - maxbins_type[n] = 0; - } - maxatom = 0; - } - -} - -/* --------------------------------------------------------------------- - identify index of type with smallest cutoff - --------------------------------------------------------------------- */ - -int NBinBytype::itype_min() { - - int itypemin = 1; - double ** cutneighsq; - - cutneighsq = neighbor->cutneighsq; - - for (int n = 1; n <= atom->ntypes; n++) { - if (cutneighsq[n][n] < cutneighsq[itypemin][itypemin]) { - itypemin = n; - } - } - - return itypemin; -} - -/* ---------------------------------------------------------------------- - setup neighbor binning geometry - ---------------------------------------------------------------------- */ - -void NBinBytype::setup_bins(int style) -{ - int n; - int itypemin; - - setup_types(); - itypemin = itype_min(); - - // bbox = size of bbox of entire domain - // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost - // for triclinic: - // bbox bounds all 8 corners of tilted box - // subdomain is in lamda coords - // include dimension-dependent extension via comm->cutghost - // domain->bbox() converts lamda extent to box coords and computes bbox - - double bbox[3],bsubboxlo[3],bsubboxhi[3]; - double *cutghost = comm->cutghost; - - if (triclinic == 0) { - bsubboxlo[0] = domain->sublo[0] - cutghost[0]; - bsubboxlo[1] = domain->sublo[1] - cutghost[1]; - bsubboxlo[2] = domain->sublo[2] - cutghost[2]; - bsubboxhi[0] = domain->subhi[0] + cutghost[0]; - bsubboxhi[1] = domain->subhi[1] + cutghost[1]; - bsubboxhi[2] = domain->subhi[2] + cutghost[2]; - } else { - double lo[3],hi[3]; - lo[0] = domain->sublo_lamda[0] - cutghost[0]; - lo[1] = domain->sublo_lamda[1] - cutghost[1]; - lo[2] = domain->sublo_lamda[2] - cutghost[2]; - hi[0] = domain->subhi_lamda[0] + cutghost[0]; - hi[1] = domain->subhi_lamda[1] + cutghost[1]; - hi[2] = domain->subhi_lamda[2] + cutghost[2]; - domain->bbox(lo,hi,bsubboxlo,bsubboxhi); - } - - bbox[0] = bboxhi[0] - bboxlo[0]; - bbox[1] = bboxhi[1] - bboxlo[1]; - bbox[2] = bboxhi[2] - bboxlo[2]; - - // For each type... - - for (n = 1; n <= atom->ntypes; n++) { - // binsize_user only relates to smallest type - // optimal bin size is roughly 1/2 the type-type cutoff - // special case of all cutoffs = 0.0, binsize = box size - - double binsize_optimal; - if (n == itypemin && binsizeflag) binsize_optimal = binsize_user; - else binsize_optimal = 0.5*sqrt(neighbor->cutneighsq[n][n]); - if (binsize_optimal == 0.0) binsize_optimal = bbox[0]; - double binsizeinv = 1.0/binsize_optimal; - - // test for too many global bins in any dimension due to huge global domain - - if (bbox[0]*binsizeinv > MAXSMALLINT || bbox[1]*binsizeinv > MAXSMALLINT || - bbox[2]*binsizeinv > MAXSMALLINT) - error->all(FLERR,"Domain too large for neighbor bins"); - - // create actual bins - // always have one bin even if cutoff > bbox - // for 2d, nbinz_type[n] = 1 - - nbinx_type[n] = static_cast (bbox[0]*binsizeinv); - nbiny_type[n] = static_cast (bbox[1]*binsizeinv); - if (dimension == 3) nbinz_type[n] = static_cast (bbox[2]*binsizeinv); - else nbinz_type[n] = 1; - - if (nbinx_type[n] == 0) nbinx_type[n] = 1; - if (nbiny_type[n] == 0) nbiny_type[n] = 1; - if (nbinz_type[n] == 0) nbinz_type[n] = 1; - - // compute actual bin size for nbins to fit into box exactly - // error if actual bin size << cutoff, since will create a zillion bins - // this happens when nbin = 1 and box size << cutoff - // typically due to non-periodic, flat system in a particular dim - // in that extreme case, should use NSQ not BIN neighbor style - - binsizex_type[n] = bbox[0]/nbinx_type[n]; - binsizey_type[n] = bbox[1]/nbiny_type[n]; - binsizez_type[n] = bbox[2]/nbinz_type[n]; - - bininvx_type[n] = 1.0 / binsizex_type[n]; - bininvy_type[n] = 1.0 / binsizey_type[n]; - bininvz_type[n] = 1.0 / binsizez_type[n]; - - if (binsize_optimal*bininvx_type[n] > CUT2BIN_RATIO || - binsize_optimal*bininvy_type[n] > CUT2BIN_RATIO || - binsize_optimal*bininvz_type[n] > CUT2BIN_RATIO) - error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); - - // mbinlo/hi = lowest and highest global bins my ghost atoms could be in - // coord = lowest and highest values of coords for my ghost atoms - // static_cast(-1.5) = -1, so subract additional -1 - // add in SMALL for round-off safety - - int mbinxhi,mbinyhi,mbinzhi; - double coord; - - coord = bsubboxlo[0] - SMALL*bbox[0]; - mbinxlo_type[n] = static_cast ((coord-bboxlo[0])*bininvx_type[n]); - if (coord < bboxlo[0]) mbinxlo_type[n] = mbinxlo_type[n] - 1; - coord = bsubboxhi[0] + SMALL*bbox[0]; - mbinxhi = static_cast ((coord-bboxlo[0])*bininvx_type[n]); - - coord = bsubboxlo[1] - SMALL*bbox[1]; - mbinylo_type[n] = static_cast ((coord-bboxlo[1])*bininvy_type[n]); - if (coord < bboxlo[1]) mbinylo_type[n] = mbinylo_type[n] - 1; - coord = bsubboxhi[1] + SMALL*bbox[1]; - mbinyhi = static_cast ((coord-bboxlo[1])*bininvy_type[n]); - - if (dimension == 3) { - coord = bsubboxlo[2] - SMALL*bbox[2]; - mbinzlo_type[n] = static_cast ((coord-bboxlo[2])*bininvz_type[n]); - if (coord < bboxlo[2]) mbinzlo_type[n] = mbinzlo_type[n] - 1; - coord = bsubboxhi[2] + SMALL*bbox[2]; - mbinzhi = static_cast ((coord-bboxlo[2])*bininvz_type[n]); - } - - // extend bins by 1 to insure stencil extent is included - // for 2d, only 1 bin in z - - mbinxlo_type[n] = mbinxlo_type[n] - 1; - mbinxhi = mbinxhi + 1; - mbinx_type[n] = mbinxhi - mbinxlo_type[n] + 1; - - mbinylo_type[n] = mbinylo_type[n] - 1; - mbinyhi = mbinyhi + 1; - mbiny_type[n] = mbinyhi - mbinylo_type[n] + 1; - - if (dimension == 3) { - mbinzlo_type[n] = mbinzlo_type[n] - 1; - mbinzhi = mbinzhi + 1; - } else mbinzlo_type[n] = mbinzhi = 0; - mbinz_type[n] = mbinzhi - mbinzlo_type[n] + 1; - - bigint bbin = ((bigint) mbinx_type[n]) - * ((bigint) mbiny_type[n]) * ((bigint) mbinz_type[n]) + 1; - if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins"); - mbins_type[n] = bbin; - } - -} - -/* ---------------------------------------------------------------------- - bin owned and ghost atoms by type -------------------------------------------------------------------------- */ - -void NBinBytype::bin_atoms() -{ - int i,ibin,n; - - last_bin = update->ntimestep; - for (n = 1; n <= maxtypes; n++) { - for (i = 0; i < mbins_type[n]; i++) binhead_type[n][i] = -1; - } - - // bin in reverse order so linked list will be in forward order - // also puts ghost atoms at end of list, which is necessary - - double **x = atom->x; - int *mask = atom->mask; - int *type = atom->type; - int nlocal = atom->nlocal; - int nall = nlocal + atom->nghost; - - if (includegroup) { - int bitmask = group->bitmask[includegroup]; - for (i = nall-1; i >= nlocal; i--) { - if (mask[i] & bitmask) { - n = type[i]; - ibin = coord2bin(x[i], n); - atom2bin_type[n][i] = ibin; - bins_type[n][i] = binhead_type[n][ibin]; - binhead_type[n][ibin] = i; - } - } - for (i = atom->nfirst-1; i >= 0; i--) { - n = type[i]; - ibin = coord2bin(x[i], n); - atom2bin_type[n][i] = ibin; - bins_type[n][i] = binhead_type[n][ibin]; - binhead_type[n][ibin] = i; - } - } else { - for (i = nall-1; i >= 0; i--) { - n = type[i]; - ibin = coord2bin(x[i], n); - atom2bin_type[n][i] = ibin; - bins_type[n][i] = binhead_type[n][ibin]; - binhead_type[n][ibin] = i; - } - } -} - - -/* ---------------------------------------------------------------------- - allocate/reallocate vectors -------------------------------------------------------------------------- */ - -void NBinBytype::bin_atoms_setup(int nall) { - - // all atom2bin, bins must be of length nall - if (nall > maxatom) { - for (int n = 1; n <= maxtypes; n++) { - memory->destroy(bins_type[n]); - memory->destroy(atom2bin_type[n]); - memory->create(bins_type[n], nall, "NBinBytype:bin_type"); - memory->create(atom2bin_type[n], nall, "NBinBytype:atom2bin_type"); - } - maxatom = nall; - } - - for (int n = 1; n <= maxtypes; n++) { - if (mbins_type[n] > maxbins_type[n]) { - maxbins_type[n] = mbins_type[n]; - memory->destroy(binhead_type[n]); - memory->create(binhead_type[n], mbins_type[n], "NBinBytype:mbins_type"); - } - } - -} - - -/* ---------------------------------------------------------------------- - convert atom coords into local bin # for bin type it -------------------------------------------------------------------------- */ - -int NBinBytype::coord2bin(double *x, int it) -{ - int ix,iy,iz; - int ibin; - - if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable"); - - if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_type[it]) + nbinx_type[it]; - else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_type[it]); - ix = MIN(ix,nbinx_type[it]-1); - } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_type[it]) - 1; - - if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_type[it]) + nbiny_type[it]; - else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_type[it]); - iy = MIN(iy,nbiny_type[it]-1); - } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_type[it]) - 1; - - if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_type[it]) + nbinz_type[it]; - else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_type[it]); - iz = MIN(iz,nbinz_type[it]-1); - } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_type[it]) - 1; - - - ibin = (iz-mbinzlo_type[it])*mbiny_type[it]*mbinx_type[it] - + (iy-mbinylo_type[it])*mbinx_type[it] - + (ix-mbinxlo_type[it]); - return ibin; -} - - -/* ---------------------------------------------------------------------- - tot up for types - ---------------------------------------------------------------------- */ - -bigint NBinBytype::memory_usage() -{ - bigint bytes = 0; - - for (int m = 1; m < maxtypes; m++) { - bytes += 2*maxatom*sizeof(int); - bytes += maxbins_type[m]*sizeof(int); - } - return bytes; -} diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp index 9a28121384..e63c8dcd56 100644 --- a/src/nbin_standard.cpp +++ b/src/nbin_standard.cpp @@ -29,6 +29,33 @@ using namespace LAMMPS_NS; NBinStandard::NBinStandard(LAMMPS *lmp) : NBin(lmp) {} +/* ---------------------------------------------------------------------- + setup for bin_atoms() +------------------------------------------------------------------------- */ + +void NBinStandard::bin_atoms_setup(int nall) +{ + // binhead = per-bin vector, mbins in length + // add 1 bin for USER-INTEL package + + if (mbins > maxbin) { + maxbin = mbins; + memory->destroy(binhead); + memory->create(binhead,maxbin,"neigh:binhead"); + } + + // bins and atom2bin = per-atom vectors + // for both local and ghost atoms + + if (nall > maxatom) { + maxatom = nall; + memory->destroy(bins); + memory->create(bins,maxatom,"neigh:bins"); + memory->destroy(atom2bin); + memory->create(atom2bin,maxatom,"neigh:atom2bin"); + } +} + /* ---------------------------------------------------------------------- setup neighbor binning geometry bin numbering in each dimension is global: @@ -230,3 +257,61 @@ void NBinStandard::bin_atoms() } } } + + +/* ---------------------------------------------------------------------- + convert atom coords into local bin # + for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo + take special care to insure ghosts are in correct bins even w/ roundoff + hi ghost atoms = nbin,nbin+1,etc + owned atoms = 0 to nbin-1 + lo ghost atoms = -1,-2,etc + this is necessary so that both procs on either side of PBC + treat a pair of atoms straddling the PBC in a consistent way + for triclinic, doesn't matter since stencil & neigh list built differently +------------------------------------------------------------------------- */ + +int NBinStandard::coord2bin(double *x) +{ + int ix,iy,iz; + + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) + error->one(FLERR,"Non-numeric positions - simulation unstable"); + + if (x[0] >= bboxhi[0]) + ix = static_cast ((x[0]-bboxhi[0])*bininvx) + nbinx; + else if (x[0] >= bboxlo[0]) { + ix = static_cast ((x[0]-bboxlo[0])*bininvx); + ix = MIN(ix,nbinx-1); + } else + ix = static_cast ((x[0]-bboxlo[0])*bininvx) - 1; + + if (x[1] >= bboxhi[1]) + iy = static_cast ((x[1]-bboxhi[1])*bininvy) + nbiny; + else if (x[1] >= bboxlo[1]) { + iy = static_cast ((x[1]-bboxlo[1])*bininvy); + iy = MIN(iy,nbiny-1); + } else + iy = static_cast ((x[1]-bboxlo[1])*bininvy) - 1; + + if (x[2] >= bboxhi[2]) + iz = static_cast ((x[2]-bboxhi[2])*bininvz) + nbinz; + else if (x[2] >= bboxlo[2]) { + iz = static_cast ((x[2]-bboxlo[2])*bininvz); + iz = MIN(iz,nbinz-1); + } else + iz = static_cast ((x[2]-bboxlo[2])*bininvz) - 1; + + return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo); +} + + +/* ---------------------------------------------------------------------- */ + +double NBinStandard::memory_usage() +{ + double bytes = 0; + bytes += maxbin*sizeof(int); + bytes += 2*maxatom*sizeof(int); + return bytes; +} diff --git a/src/nbin_standard.h b/src/nbin_standard.h index 06defdb101..d8ecb435b7 100644 --- a/src/nbin_standard.h +++ b/src/nbin_standard.h @@ -30,8 +30,14 @@ class NBinStandard : public NBin { public: NBinStandard(class LAMMPS *); ~NBinStandard() {} + void bin_atoms_setup(int); void setup_bins(int); void bin_atoms(); + double memory_usage(); + + private: + + int coord2bin(double *); }; } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 740b16b66e..d4a2727662 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1620,12 +1620,12 @@ int Neighbor::choose_bin(NeighRequest *rq) if (!rq->kokkos_device != !(mask & NB_KOKKOS_DEVICE)) continue; if (!rq->kokkos_host != !(mask & NB_KOKKOS_HOST)) continue; - // neighbor style is BIN or MULTI or MULTI/TIERED and must match + // neighbor style is BIN or MULTI or MULTI2 and must match if (style == Neighbor::BIN || style == Neighbor::MULTI) { if (!(mask & NB_STANDARD)) continue; - } else if (style == Neighbor::MULTI_TIERED) { - if (!(mask & NB_MULTI_TIERED)) continue; + } else if (style == Neighbor::MULTI2) { + if (!(mask & NB_MULTI2)) continue; } return i+1; @@ -1698,14 +1698,14 @@ int Neighbor::choose_stencil(NeighRequest *rq) if (!rq->ghost != !(mask & NS_GHOST)) continue; if (!rq->ssa != !(mask & NS_SSA)) continue; - // neighbor style is one of BIN, MULTI, or MULT/TIERED and must match + // neighbor style is one of BIN, MULTI, or MULTI2 and must match if (style == Neighbor::BIN) { if (!(mask & NS_BIN)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NS_MULTI)) continue; - } else if (style == Neighbor::MULT_TIERED) { - if (!(mask & NS_MULT_TIERED)) continue; + } else if (style == Neighbor::MULTI2) { + if (!(mask & NS_MULTI2)) continue; } // dimension is 2 or 3 and must match @@ -1835,7 +1835,7 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!rq->halffull != !(mask & NP_HALF_FULL)) continue; if (!rq->off2on != !(mask & NP_OFF2ON)) continue; - // neighbor style is one of NSQ, BIN, MULTI, or MULTI/TIERED and must match + // neighbor style is one of NSQ, BIN, MULTI, or MULTI2 and must match if (style == Neighbor::NSQ) { if (!(mask & NP_NSQ)) continue; @@ -1843,8 +1843,8 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!(mask & NP_BIN)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NP_MULTI)) continue; - } else if (style == Neighbor::MULT_TIERED) { - if (!(mask & NP_MULT_TIERED)) continue; + } else if (style == Neighbor::MULTI2) { + if (!(mask & NP_MULTI2)) continue; } // domain triclinic flag is on or off and must match @@ -2211,7 +2211,7 @@ void Neighbor::set(int narg, char **arg) if (strcmp(arg[1],"nsq") == 0) style = Neighbor::NSQ; else if (strcmp(arg[1],"bin") == 0) style = Neighbor::BIN; else if (strcmp(arg[1],"multi") == 0) style = Neighbor::MULTI; - else if (strcmp(arg[1],"multi/tiered") == 0) style = Neighbor::MULT_TIERED; + else if (strcmp(arg[1],"multi2") == 0) style = Neighbor::MULTI2; else error->all(FLERR,"Illegal neighbor command"); if (style == Neighbor::MULTI && lmp->citeme) lmp->citeme->add(cite_neigh_multi); diff --git a/src/neighbor.h b/src/neighbor.h index fd8cc49067..0012cb29fa 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -20,7 +20,7 @@ namespace LAMMPS_NS { class Neighbor : protected Pointers { public: - enum{NSQ,BIN,MULTI,MULTI_TIERED}; + enum{NSQ,BIN,MULTI,MULTI2}; int style; // 0,1,2 = nsq, bin, multi int every; // build every this many steps int delay; // delay build for this many steps @@ -239,7 +239,7 @@ namespace NeighConst { static const int NB_KOKKOS_DEVICE = 1<<1; static const int NB_KOKKOS_HOST = 1<<2; static const int NB_SSA = 1<<3; - static const int NB_MULTI_TIERED = 1<<4; + static const int NB_MULTI2 = 1<<4; static const int NB_STANDARD = 1<<5; static const int NS_BIN = 1<<0; @@ -254,7 +254,7 @@ namespace NeighConst { static const int NS_TRI = 1<<9; static const int NS_GHOST = 1<<10; static const int NS_SSA = 1<<11; - static const int NS_MULTI_TIERED = 1<<12; + static const int NS_MULTI2 = 1<<12; static const int NP_NSQ = 1<<0; static const int NP_BIN = 1<<1; @@ -281,7 +281,7 @@ namespace NeighConst { static const int NP_SKIP = 1<<22; static const int NP_HALF_FULL = 1<<23; static const int NP_OFF2ON = 1<<24; - static const int NP_MULTI_TIERED = 1<<25; + static const int NP_MULTI2 = 1<<25; } } diff --git a/src/npair_half_multi_tiered_newton.cpp b/src/npair_half_multi2_newton.cpp similarity index 100% rename from src/npair_half_multi_tiered_newton.cpp rename to src/npair_half_multi2_newton.cpp diff --git a/src/npair_half_multi_tiered_newton.h b/src/npair_half_multi2_newton.h similarity index 100% rename from src/npair_half_multi_tiered_newton.h rename to src/npair_half_multi2_newton.h diff --git a/src/npair_half_multi_tiered_newton_tri.cpp b/src/npair_half_multi2_newton_tri.cpp similarity index 100% rename from src/npair_half_multi_tiered_newton_tri.cpp rename to src/npair_half_multi2_newton_tri.cpp diff --git a/src/npair_half_multi_tiered_newton_tri.h b/src/npair_half_multi2_newton_tri.h similarity index 100% rename from src/npair_half_multi_tiered_newton_tri.h rename to src/npair_half_multi2_newton_tri.h diff --git a/src/npair_half_size_multi_tiered_newtoff.cpp b/src/npair_half_size_multi2_newtoff.cpp similarity index 100% rename from src/npair_half_size_multi_tiered_newtoff.cpp rename to src/npair_half_size_multi2_newtoff.cpp diff --git a/src/npair_half_size_multi_tiered_newtoff.h b/src/npair_half_size_multi2_newtoff.h similarity index 100% rename from src/npair_half_size_multi_tiered_newtoff.h rename to src/npair_half_size_multi2_newtoff.h diff --git a/src/npair_half_size_multi_tiered_newton.cpp b/src/npair_half_size_multi2_newton.cpp similarity index 100% rename from src/npair_half_size_multi_tiered_newton.cpp rename to src/npair_half_size_multi2_newton.cpp diff --git a/src/npair_half_size_multi_tiered_newton.h b/src/npair_half_size_multi2_newton.h similarity index 100% rename from src/npair_half_size_multi_tiered_newton.h rename to src/npair_half_size_multi2_newton.h diff --git a/src/npair_half_size_multi_tiered_newton_tri.cpp b/src/npair_half_size_multi2_newton_tri.cpp similarity index 100% rename from src/npair_half_size_multi_tiered_newton_tri.cpp rename to src/npair_half_size_multi2_newton_tri.cpp diff --git a/src/npair_half_size_multi_tiered_newton_tri.h b/src/npair_half_size_multi2_newton_tri.h similarity index 100% rename from src/npair_half_size_multi_tiered_newton_tri.h rename to src/npair_half_size_multi2_newton_tri.h diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 861fcd537e..3518b7db55 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -51,6 +51,15 @@ using namespace LAMMPS_NS; stencil follows same rules for half/full, newton on/off, triclinic cutoff is not cutneighmaxsq, but max cutoff for that atom type no versions that allow ghost on (any need for it?) + for multi/tiered: + create one stencil for each itype-jtype pairing + stencils do not generally follow the same rules for half/full or newton on/off + whole stencils including all surrounding bins are always used except + for same-type stencils with newton on which uses a split stencil + for orthogonal boxes, a split stencil includes bins to the "upper right" of central bin + for triclinic, a split stencil includes bins in the z (3D) or y (2D) plane of self and above + cutoff is not cutneighmaxsq, but max cutoff for that atom type + no versions that allow ghost on (any need for it?) ------------------------------------------------------------------------- */ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) @@ -64,6 +73,11 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) nstencil_multi = nullptr; stencil_multi = nullptr; distsq_multi = nullptr; + + stencil_split = nullptr; + stencil_skip = nullptr; + stencil_bin_type = nullptr; + stencil_cut = nullptr; dimension = domain->dimension; } @@ -75,16 +89,44 @@ NStencil::~NStencil() memory->destroy(stencil); memory->destroy(stencilxyz); - if (!stencil_multi) return; + if (stencil_multi) { - int n = atom->ntypes; - for (int i = 1; i <= n; i++) { - memory->destroy(stencil_multi[i]); - memory->destroy(distsq_multi[i]); + int n = atom->ntypes; + for (int i = 1; i <= n; i++) { + memory->destroy(stencil_multi[i]); + memory->destroy(distsq_multi[i]); + } + delete [] nstencil_multi; + delete [] stencil_multi; + delete [] distsq_multi; + } + + if (stencil_multi_tiered) { + + int n = atom->ntypes; + memory->destroy(nstencil_multi_tiered); + for (int i = 1; i <= n; i++) { + for (int j = 0; j <= n; j++) { + if (! stencil_skip[i][j]) + memory->destroy(stencil_multi_tiered[i][j]); + } + delete [] stencil_multi_tiered[i]; + } + delete [] stencil_multi_tiered; + memory->destroy(maxstencil_multi_tiered); + memory->destroy(stencil_split); + memory->destroy(stencil_skip); + memory->destroy(stencil_bin_type); + memory->destroy(stencil_cut); + + memory->destroy(sx_multi_tiered); + memory->destroy(sy_multi_tiered); + memory->destroy(sz_multi_tiered); + + memory->destroy(binsizex_multi_tiered); + memory->destroy(binsizey_multi_tiered); + memory->destroy(binsizez_multi_tiered); } - delete [] nstencil_multi; - delete [] stencil_multi; - delete [] distsq_multi; } /* ---------------------------------------------------------------------- */ @@ -105,6 +147,7 @@ void NStencil::copy_neighbor_info() cutneighmax = neighbor->cutneighmax; cutneighmaxsq = neighbor->cutneighmaxsq; cuttypesq = neighbor->cuttypesq; + cutneighsq = neighbor->cutneighsq; // overwrite Neighbor cutoff with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -132,6 +175,23 @@ void NStencil::copy_bin_info() bininvz = nb->bininvz; } +/* ---------------------------------------------------------------------- + copy needed info for a given type from NBin class to this stencil class +------------------------------------------------------------------------- */ + +void NStencil::copy_bin_info_multi_tiered(int type) +{ + mbinx = nb->mbinx_tiered[type]; + mbiny = nb->mbiny_tiered[type]; + mbinz = nb->mbinz_tiered[type]; + binsizex = nb->binsizex_tiered[type]; + binsizey = nb->binsizey_tiered[type]; + binsizez = nb->binsizez_tiered[type]; + bininvx = nb->bininvx_tiered[type]; + bininvy = nb->bininvy_tiered[type]; + bininvz = nb->bininvz_tiered[type]; +} + /* ---------------------------------------------------------------------- insure NBin data is current insure stencils are allocated large enough @@ -139,59 +199,131 @@ void NStencil::copy_bin_info() void NStencil::create_setup() { - if (nb) copy_bin_info(); - last_stencil = update->ntimestep; - - // sx,sy,sz = max range of stencil in each dim - // smax = max possible size of entire 3d stencil - // stencil will be empty if cutneighmax = 0.0 - - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - if (dimension == 2) sz = 0; - - int smax = (2*sx+1) * (2*sy+1) * (2*sz+1); - - // reallocate stencil structs if necessary - // for BIN and MULTI styles - - if (neighstyle == Neighbor::BIN) { - if (smax > maxstencil) { - maxstencil = smax; - memory->destroy(stencil); - memory->create(stencil,maxstencil,"neighstencil:stencil"); - if (xyzflag) { - memory->destroy(stencilxyz); - memory->create(stencilxyz,maxstencil,3,"neighstencil:stencilxyz"); + + if (neighstyle != Neighbor::MULTI_TIERED){ + if (nb) copy_bin_info(); + last_stencil = update->ntimestep; + + // sx,sy,sz = max range of stencil in each dim + // smax = max possible size of entire 3d stencil + // stencil will be empty if cutneighmax = 0.0 + + sx = static_cast (cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast (cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast (cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + if (dimension == 2) sz = 0; + + int smax = (2*sx+1) * (2*sy+1) * (2*sz+1); + + // reallocate stencil structs if necessary + // for BIN and MULTI styles + + if (neighstyle == Neighbor::BIN) { + if (smax > maxstencil) { + maxstencil = smax; + memory->destroy(stencil); + memory->create(stencil,maxstencil,"neighstencil:stencil"); + if (xyzflag) { + memory->destroy(stencilxyz); + memory->create(stencilxyz,maxstencil,3,"neighstencil:stencilxyz"); + } + } + + } else { + int i; + int n = atom->ntypes; + if (maxstencil_multi == 0) { + nstencil_multi = new int[n+1]; + stencil_multi = new int*[n+1]; + distsq_multi = new double*[n+1]; + for (i = 1; i <= n; i++) { + nstencil_multi[i] = 0; + stencil_multi[i] = nullptr; + distsq_multi[i] = nullptr; + } + } + if (smax > maxstencil_multi) { + maxstencil_multi = smax; + for (i = 1; i <= n; i++) { + memory->destroy(stencil_multi[i]); + memory->destroy(distsq_multi[i]); + memory->create(stencil_multi[i],maxstencil_multi, + "neighstencil:stencil_multi"); + memory->create(distsq_multi[i],maxstencil_multi, + "neighstencil:distsq_multi"); + } } } - } else { - int i; + int i, j, bin_type, smax; + double stencil_range; int n = atom->ntypes; - if (maxstencil_multi == 0) { - nstencil_multi = new int[n+1]; - stencil_multi = new int*[n+1]; - distsq_multi = new double*[n+1]; - for (i = 1; i <= n; i++) { - nstencil_multi[i] = 0; - stencil_multi[i] = nullptr; - distsq_multi[i] = nullptr; - } - } - if (smax > maxstencil_multi) { - maxstencil_multi = smax; - for (i = 1; i <= n; i++) { - memory->destroy(stencil_multi[i]); - memory->destroy(distsq_multi[i]); - memory->create(stencil_multi[i],maxstencil_multi, - "neighstencil:stencil_multi"); - memory->create(distsq_multi[i],maxstencil_multi, - "neighstencil:distsq_multi"); + + // Allocate arrays to store stencil information + memory->create(stencil_split, n, n, + "neighstencil:stencil_split");" + memory->create(stencil_skip, n, n, + "neighstencil:stencil_skip");" + memory->create(stencil_bin_type, n, n, + "neighstencil:stencil_bin_type");" + memory->create(stencil_cut, n, n, + "neighstencil:stencil_cut");" + + memory->create(sx_multi_tiered, n, n, + "neighstencil:sx_multi_tiered");" + memory->create(sy_multi_tiered, n, n, + "neighstencil:sy_multi_tiered");" + memory->create(sz_multi_tiered, n, n, + "neighstencil:sz_multi_tiered");" + + memory->create(binsizex_multi_tiered, n, n, + "neighstencil:binsizex_multi_tiered");" + memory->create(binsizey_multi_tiered, n, n, + "neighstencil:binsizey_multi_tiered");" + memory->create(binsizez_multi_tiered, n, n, + "neighstencil:binsizez_multi_tiered");" + + // Determine which stencils need to be built + set_stencil_properties(); + + for (i = 1; i <= n; ++i) { + for (j = 1; j <= n; ++j) { + + // Skip creation of unused stencils + if (stencil_skip[i][j]) continue; + + // Copy bin info for this particular pair of types + bin_type = stencil_bin_type[i][j]; + copy_bin_info_bytype(bin_type); + + binsizex_multi_tiered[i][j] = binsizex; + binsizey_multi_tiered[i][j] = binsizey; + binsizez_multi_tiered[i][j] = binsizez; + + stencil_range = stencil_cut[i][j]; + + sx = static_cast (stencil_range*bininvx); + if (sx*binsizex < stencil_range) sx++; + sy = static_cast (stencil_range*bininvy); + if (sy*binsizey < stencil_range) sy++; + sz = static_cast (stencil_range*bininvz); + if (sz*binsizez < stencil_range) sz++; + + sx_multi_tiered[i][j] = sx; + sy_multi_tiered[i][j] = sy; + sz_multi_tiered[i][j] = sz; + + smax = ((2*sx+1) * (2*sy+1) * (2*sz+1)); + + if (smax > maxstencil_multi_tiered[i][j]) { + maxstencil_multi_tiered[i][j] = smax; + memory->destroy(stencil_multi_tiered[i][j]); + memory->create(stencil_multi_tiered[i][j], smax, + "neighstencil::stencil_multi_tiered"); + } } } } @@ -231,6 +363,10 @@ double NStencil::memory_usage() } else if (neighstyle == Neighbor::MULTI) { bytes += atom->ntypes*maxstencil_multi * sizeof(int); bytes += atom->ntypes*maxstencil_multi * sizeof(double); + } else if (neighstyle == Neighbor::MULTI_TIERED) { + bytes += atom->ntypes*maxstencil_multi * sizeof(int); + bytes += atom->ntypes*maxstencil_multi * sizeof(int); + bytes += atom->ntypes*maxstencil_multi * sizeof(double); } return bytes; } diff --git a/src/nstencil.h b/src/nstencil.h index bdd656b937..58c39ee13c 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -29,14 +29,22 @@ class NStencil : protected Pointers { int **stencilxyz; // bin offsets in xyz dims int *nstencil_multi; // # bins in each type-based multi stencil int **stencil_multi; // list of bin offsets in each stencil + int ** nstencil_multi_tiered; // # bins bins in each itype-jtype tiered multi stencil + int *** stencil_multi_tiered; // list of bin offsets in each tiered multi stencil + int ** maxstencil_type; // max double **distsq_multi; // sq distances to bins in each stencil int sx,sy,sz; // extent of stencil in each dim + int **sx_multi_tiered; // analogs for multi tiered + int **sy_multi_tiered; + int **sz_multi_tiered; - double cutoff_custom; // cutoff set by requestor - - // BYTYPE stencils - int ** nstencil_type; // No. of bins for stencil[itype][jtype] - int *** stencil_type; // Stencil for [itype][jtype] + double cutoff_custom; // cutoff set by requestor + + // Arrays to store options for multi/tiered itype-jtype stencils + bool **stencil_half; // flag creation of a half stencil for itype-jtype + bool **stencil_skip; // skip creation of itype-jtype stencils (for newton on) + int **stencil_bin_type; // what type to use for bin information + double **stencil_cut; // cutoff used for stencil size NStencil(class LAMMPS *); virtual ~NStencil(); @@ -57,12 +65,19 @@ class NStencil : protected Pointers { double cutneighmax; double cutneighmaxsq; double *cuttypesq; + double *cutneighsq; // data from NBin class int mbinx,mbiny,mbinz; double binsizex,binsizey,binsizez; double bininvx,bininvy,bininvz; + + // analogs for multi-tiered + + double **binsizex_multi_tiered; + double **binsizey_multi_tiered; + double **binsizez_multi_tiered; // data common to all NStencil variants @@ -76,6 +91,11 @@ class NStencil : protected Pointers { void copy_bin_info(); // copy info from NBin class double bin_distance(int, int, int); // distance between bin corners + + // methods for multi/tiered NStencil + + void copy_bin_info_multi_tiered(int); // copy mult/tiered info from NBin class + void set_stencil_properties(); // determine which stencils to build and how }; } diff --git a/src/nstencil_full_multi_tiered_3d.cpp b/src/nstencil_full_multi2_3d.cpp similarity index 90% rename from src/nstencil_full_multi_tiered_3d.cpp rename to src/nstencil_full_multi2_3d.cpp index cecccdfb14..099e2adeb8 100644 --- a/src/nstencil_full_multi_tiered_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -46,23 +46,9 @@ NStencilFullBytype3d::~NStencilFullBytype3d() { } } -/* ---------------------------------------------------------------------- */ - -void NStencilFullBytype3d::copy_bin_info_bytype(int itype) { - - mbinx = nb->mbinx_type[itype]; - mbiny = nb->mbiny_type[itype]; - mbinz = nb->mbinz_type[itype]; - binsizex = nb->binsizex_type[itype]; - binsizey = nb->binsizey_type[itype]; - binsizez = nb->binsizez_type[itype]; - bininvx = nb->bininvx_type[itype]; - bininvy = nb->bininvy_type[itype]; - bininvz = nb->bininvz_type[itype]; -} /* ---------------------------------------------------------------------- */ - +INCORPORTE INTO CREATE THEN DELETE, NOTE NAME OF CUTNEIGHMAX ETC int NStencilFullBytype3d::copy_neigh_info_bytype(int itype) { cutneighmaxsq = neighbor->cutneighsq[itype][itype]; @@ -104,13 +90,13 @@ void NStencilFullBytype3d::create_setup() maxstencil_type[itype][jtype] = 0; } } - } + } MOVE TO PARENT CLASS // like -> like => use standard newtoff stencil at bin for (itype = 1; itype <= maxtypes; ++itype) { copy_bin_info_bytype(itype); - smax = copy_neigh_info_bytype(itype); + smax = copy_neigh_info_bytype(itype); uses cutneighsq[itype][itype] to create s's if (smax > maxstencil_type[itype][itype]) { maxstencil_type[itype][itype] = smax; memory->destroy(stencil_type[itype][itype]); @@ -127,7 +113,7 @@ void NStencilFullBytype3d::create_setup() for (itype = 1; itype <= maxtypes; ++itype) { for (jtype = 1; jtype <= maxtypes; ++jtype) { if (itype == jtype) continue; - if (cuttypesq[itype] <= cuttypesq[jtype]) { + if (cuttypesq[itype] <= cuttypesq[jtype]) { This does work to say which prticle is smller // Potential destroy/create problem? nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; stencil_type[itype][jtype] = stencil_type[jtype][jtype]; @@ -136,7 +122,7 @@ void NStencilFullBytype3d::create_setup() copy_bin_info_bytype(jtype); // smax = copy_neigh_info_bytype(jtype); - cutneighmaxsq = cuttypesq[jtype]; + cutneighmaxsq = cuttypesq[jtype]; Does it need to be this big? Can't I use cutneighsq[i][j]? cutneighmax = sqrt(cutneighmaxsq); sx = static_cast (cutneighmax*bininvx); if (sx*binsizex < cutneighmax) sx++; diff --git a/src/nstencil_full_multi_tiered_3d.h b/src/nstencil_full_multi2_3d.h similarity index 83% rename from src/nstencil_full_multi_tiered_3d.h rename to src/nstencil_full_multi2_3d.h index 6e61365d17..b9b835fd24 100644 --- a/src/nstencil_full_multi_tiered_3d.h +++ b/src/nstencil_full_multi2_3d.h @@ -13,15 +13,15 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(full/bytype/3d, - NStencilFullBytype3d, - NS_FULL | NS_BYTYPE | NS_3D | +NStencilStyle(full/multi/tiered/3d, + NStencilFullMultiTiered3d, + NS_FULL | NS_Multi_Tiered | NS_3D | NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) #else -#ifndef LMP_NSTENCIL_FULL_BYTYPE_3D_H -#define LMP_NSTENCIL_FULL_BYTYPE_3D_H +#ifndef LMP_NSTENCIL_FULL_MULTI_TIERED_3D_H +#define LMP_NSTENCIL_FULL_MULTI_TIERED_3D_H #include "nstencil.h" @@ -37,7 +37,6 @@ class NStencilFullBytype3d : public NStencil { private: int ** maxstencil_type; - void copy_bin_info_bytype(int); int copy_neigh_info_bytype(int); void create_newtoff(int, int, double); diff --git a/src/nstencil_half_multi_tiered_2d_newton.cpp b/src/nstencil_half_multi2_2d_newton.cpp similarity index 100% rename from src/nstencil_half_multi_tiered_2d_newton.cpp rename to src/nstencil_half_multi2_2d_newton.cpp diff --git a/src/nstencil_half_multi_tiered_2d_newton.h b/src/nstencil_half_multi2_2d_newton.h similarity index 100% rename from src/nstencil_half_multi_tiered_2d_newton.h rename to src/nstencil_half_multi2_2d_newton.h diff --git a/src/nstencil_half_multi_tiered_3d_newtoff.cpp b/src/nstencil_half_multi2_3d_newtoff.cpp similarity index 100% rename from src/nstencil_half_multi_tiered_3d_newtoff.cpp rename to src/nstencil_half_multi2_3d_newtoff.cpp diff --git a/src/nstencil_half_multi_tiered_3d_newtoff.h b/src/nstencil_half_multi2_3d_newtoff.h similarity index 100% rename from src/nstencil_half_multi_tiered_3d_newtoff.h rename to src/nstencil_half_multi2_3d_newtoff.h diff --git a/src/nstencil_half_multi_tiered_3d_newton.cpp b/src/nstencil_half_multi2_3d_newton.cpp similarity index 100% rename from src/nstencil_half_multi_tiered_3d_newton.cpp rename to src/nstencil_half_multi2_3d_newton.cpp diff --git a/src/nstencil_half_multi_tiered_3d_newton.h b/src/nstencil_half_multi2_3d_newton.h similarity index 100% rename from src/nstencil_half_multi_tiered_3d_newton.h rename to src/nstencil_half_multi2_3d_newton.h diff --git a/src/nstencil_half_multi_tiered_3d_newton_tri.cpp b/src/nstencil_half_multi2_3d_newton_tri.cpp similarity index 100% rename from src/nstencil_half_multi_tiered_3d_newton_tri.cpp rename to src/nstencil_half_multi2_3d_newton_tri.cpp diff --git a/src/nstencil_half_multi_tiered_3d_newton_tri.h b/src/nstencil_half_multi2_3d_newton_tri.h similarity index 100% rename from src/nstencil_half_multi_tiered_3d_newton_tri.h rename to src/nstencil_half_multi2_3d_newton_tri.h From af57879416adc0578f88a1470115075c7a460da0 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 10 Nov 2020 17:15:28 -0700 Subject: [PATCH 0015/1217] Labelling stencils half/full, removing unnecessary newton on/off designation --- src/neighbor.cpp | 29 ++- src/neighbor.h | 12 +- src/nstencil_full_bin_2d.h | 3 +- src/nstencil_full_bin_3d.h | 3 +- src/nstencil_full_ghost_bin_2d.h | 3 +- src/nstencil_full_ghost_bin_3d.h | 3 +- src/nstencil_full_multi2_3d.h | 4 +- src/nstencil_full_multi_2d.h | 3 +- src/nstencil_full_multi_3d.h | 3 +- ...2d_newton.cpp => nstencil_half_bin_2d.cpp} | 6 +- ...bin_3d_newton.h => nstencil_half_bin_2d.h} | 16 +- src/nstencil_half_bin_2d_newtoff.cpp | 37 ---- src/nstencil_half_bin_2d_newtoff.h | 43 ---- src/nstencil_half_bin_2d_newton_tri.h | 43 ---- ...n_tri.cpp => nstencil_half_bin_2d_tri.cpp} | 6 +- ...2d_newton.h => nstencil_half_bin_2d_tri.h} | 16 +- ...3d_newton.cpp => nstencil_half_bin_3d.cpp} | 6 +- ...lti_2d_newton.h => nstencil_half_bin_3d.h} | 16 +- src/nstencil_half_bin_3d_newtoff.cpp | 38 ---- src/nstencil_half_bin_3d_newtoff.h | 43 ---- src/nstencil_half_bin_3d_newton_tri.h | 43 ---- ...n_tri.cpp => nstencil_half_bin_3d_tri.cpp} | 6 +- ...3d_newton.h => nstencil_half_bin_3d_tri.h} | 16 +- src/nstencil_half_ghost_bin_2d_newtoff.cpp | 44 ---- src/nstencil_half_ghost_bin_2d_newtoff.h | 44 ---- src/nstencil_half_ghost_bin_3d_newtoff.cpp | 45 ---- src/nstencil_half_ghost_bin_3d_newtoff.h | 44 ---- src/nstencil_half_multi2_2d_newton.cpp | 201 ------------------ src/nstencil_half_multi2_2d_newton.h | 52 ----- ...newton.cpp => nstencil_half_multi2_3d.cpp} | 0 ...newton_tri.h => nstencil_half_multi2_3d.h} | 9 +- ...> nstencil_half_multi2_3d_delete_noff.cpp} | 0 ... => nstencil_half_multi2_3d_delete_noff.h} | 0 ...ri.cpp => nstencil_half_multi2_3d_tri.cpp} | 0 ...newton.h => nstencil_half_multi2_3d_tri.h} | 9 +- ..._newton.cpp => nstencil_half_multi_2d.cpp} | 8 +- src/nstencil_half_multi_2d.h | 42 ++++ src/nstencil_half_multi_2d_newtoff.cpp | 51 ----- src/nstencil_half_multi_2d_newtoff.h | 43 ---- src/nstencil_half_multi_2d_newton_tri.h | 43 ---- ...tri.cpp => nstencil_half_multi_2d_tri.cpp} | 8 +- src/nstencil_half_multi_2d_tri.h | 42 ++++ ..._newton.cpp => nstencil_half_multi_3d.cpp} | 8 +- src/nstencil_half_multi_3d.h | 42 ++++ src/nstencil_half_multi_3d_newtoff.cpp | 52 ----- src/nstencil_half_multi_3d_newtoff.h | 43 ---- src/nstencil_half_multi_3d_newton_tri.h | 43 ---- ...tri.cpp => nstencil_half_multi_3d_tri.cpp} | 8 +- src/nstencil_half_multi_3d_tri.h | 42 ++++ 49 files changed, 261 insertions(+), 1060 deletions(-) rename src/{nstencil_half_bin_2d_newton.cpp => nstencil_half_bin_2d.cpp} (87%) rename src/{nstencil_half_bin_3d_newton.h => nstencil_half_bin_2d.h} (69%) delete mode 100644 src/nstencil_half_bin_2d_newtoff.cpp delete mode 100644 src/nstencil_half_bin_2d_newtoff.h delete mode 100644 src/nstencil_half_bin_2d_newton_tri.h rename src/{nstencil_half_bin_2d_newton_tri.cpp => nstencil_half_bin_2d_tri.cpp} (87%) rename src/{nstencil_half_bin_2d_newton.h => nstencil_half_bin_2d_tri.h} (69%) rename src/{nstencil_half_bin_3d_newton.cpp => nstencil_half_bin_3d.cpp} (88%) rename src/{nstencil_half_multi_2d_newton.h => nstencil_half_bin_3d.h} (68%) delete mode 100644 src/nstencil_half_bin_3d_newtoff.cpp delete mode 100644 src/nstencil_half_bin_3d_newtoff.h delete mode 100644 src/nstencil_half_bin_3d_newton_tri.h rename src/{nstencil_half_bin_3d_newton_tri.cpp => nstencil_half_bin_3d_tri.cpp} (88%) rename src/{nstencil_half_multi_3d_newton.h => nstencil_half_bin_3d_tri.h} (68%) delete mode 100644 src/nstencil_half_ghost_bin_2d_newtoff.cpp delete mode 100644 src/nstencil_half_ghost_bin_2d_newtoff.h delete mode 100644 src/nstencil_half_ghost_bin_3d_newtoff.cpp delete mode 100644 src/nstencil_half_ghost_bin_3d_newtoff.h delete mode 100644 src/nstencil_half_multi2_2d_newton.cpp delete mode 100644 src/nstencil_half_multi2_2d_newton.h rename src/{nstencil_half_multi2_3d_newton.cpp => nstencil_half_multi2_3d.cpp} (100%) rename src/{nstencil_half_multi2_3d_newton_tri.h => nstencil_half_multi2_3d.h} (82%) mode change 100755 => 100644 rename src/{nstencil_half_multi2_3d_newtoff.cpp => nstencil_half_multi2_3d_delete_noff.cpp} (100%) rename src/{nstencil_half_multi2_3d_newtoff.h => nstencil_half_multi2_3d_delete_noff.h} (100%) rename src/{nstencil_half_multi2_3d_newton_tri.cpp => nstencil_half_multi2_3d_tri.cpp} (100%) rename src/{nstencil_half_multi2_3d_newton.h => nstencil_half_multi2_3d_tri.h} (82%) mode change 100644 => 100755 rename src/{nstencil_half_multi_2d_newton.cpp => nstencil_half_multi_2d.cpp} (89%) create mode 100644 src/nstencil_half_multi_2d.h delete mode 100644 src/nstencil_half_multi_2d_newtoff.cpp delete mode 100644 src/nstencil_half_multi_2d_newtoff.h delete mode 100644 src/nstencil_half_multi_2d_newton_tri.h rename src/{nstencil_half_multi_2d_newton_tri.cpp => nstencil_half_multi_2d_tri.cpp} (88%) create mode 100644 src/nstencil_half_multi_2d_tri.h rename src/{nstencil_half_multi_3d_newton.cpp => nstencil_half_multi_3d.cpp} (90%) create mode 100644 src/nstencil_half_multi_3d.h delete mode 100644 src/nstencil_half_multi_3d_newtoff.cpp delete mode 100644 src/nstencil_half_multi_3d_newtoff.h delete mode 100644 src/nstencil_half_multi_3d_newton_tri.h rename src/{nstencil_half_multi_3d_newton_tri.cpp => nstencil_half_multi_3d_tri.cpp} (89%) create mode 100644 src/nstencil_half_multi_3d_tri.h diff --git a/src/neighbor.cpp b/src/neighbor.cpp index d4a2727662..2b4911958f 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1660,9 +1660,15 @@ int Neighbor::choose_stencil(NeighRequest *rq) else if (rq->newton == 1) newtflag = 1; else if (rq->newton == 2) newtflag = 0; - //printf("STENCIL RQ FLAGS: hff %d %d n %d g %d s %d newtflag %d\n", + // request a full stencil if building full neighbor list or newton is off + + int fullflag = 0; + if (rq->full) fullflag = 1; + if (!newtflag) fullflag = 1; + + //printf("STENCIL RQ FLAGS: hff %d %d n %d g %d s %d newtflag %d fullflag %d\n", // rq->half,rq->full,rq->newton,rq->ghost,rq->ssa, - // newtflag); + // newtflag, fullflag); // use request and system settings to match exactly one NStencil class mask // checks are bitwise using NeighConst bit masks @@ -1672,24 +1678,15 @@ int Neighbor::choose_stencil(NeighRequest *rq) for (int i = 0; i < nsclass; i++) { mask = stencilmasks[i]; - //printf("III %d: half %d full %d newton %d newtoff %d ghost %d ssa %d\n", - // i,mask & NS_HALF,mask & NS_FULL,mask & NS_NEWTON, - // mask & NS_NEWTOFF,mask & NS_GHOST,mask & NS_SSA); + //printf("III %d: half %d full %d ghost %d ssa %d\n", + // i,mask & NS_HALF,mask & NS_FULL,mask & NS_GHOST,mask & NS_SSA); // exactly one of half or full is set and must match - if (rq->half) { - if (!(mask & NS_HALF)) continue; - } else if (rq->full) { + if (fullflag) { if (!(mask & NS_FULL)) continue; - } - - // newtflag is on or off and must match - - if (newtflag) { - if (!(mask & NS_NEWTON)) continue; - } else if (!newtflag) { - if (!(mask & NS_NEWTOFF)) continue; + } else { + if (!(mask & NS_HALF)) continue; } // require match of these request flags and mask bits diff --git a/src/neighbor.h b/src/neighbor.h index 0012cb29fa..b1cc95f5e7 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -248,13 +248,11 @@ namespace NeighConst { static const int NS_FULL = 1<<3; static const int NS_2D = 1<<4; static const int NS_3D = 1<<5; - static const int NS_NEWTON = 1<<6; - static const int NS_NEWTOFF = 1<<7; - static const int NS_ORTHO = 1<<8; - static const int NS_TRI = 1<<9; - static const int NS_GHOST = 1<<10; - static const int NS_SSA = 1<<11; - static const int NS_MULTI2 = 1<<12; + static const int NS_ORTHO = 1<<6; + static const int NS_TRI = 1<<7; + static const int NS_GHOST = 1<<8; + static const int NS_SSA = 1<<9; + static const int NS_MULTI2 = 1<<10; static const int NP_NSQ = 1<<0; static const int NP_BIN = 1<<1; diff --git a/src/nstencil_full_bin_2d.h b/src/nstencil_full_bin_2d.h index d85063596f..0d97cc2634 100644 --- a/src/nstencil_full_bin_2d.h +++ b/src/nstencil_full_bin_2d.h @@ -15,8 +15,7 @@ NStencilStyle(full/bin/2d, NStencilFullBin2d, - NS_FULL | NS_BIN | NS_2D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_BIN | NS_2D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_bin_3d.h b/src/nstencil_full_bin_3d.h index facddd8ead..47f84aebcc 100644 --- a/src/nstencil_full_bin_3d.h +++ b/src/nstencil_full_bin_3d.h @@ -15,8 +15,7 @@ NStencilStyle(full/bin/3d, NStencilFullBin3d, - NS_FULL | NS_BIN | NS_3D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_BIN | NS_3D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_ghost_bin_2d.h b/src/nstencil_full_ghost_bin_2d.h index 531c7d2eb1..db870f9c04 100644 --- a/src/nstencil_full_ghost_bin_2d.h +++ b/src/nstencil_full_ghost_bin_2d.h @@ -15,8 +15,7 @@ NStencilStyle(full/ghost/bin/2d, NStencilFullGhostBin2d, - NS_FULL | NS_GHOST | NS_BIN | NS_2D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_GHOST | NS_BIN | NS_2D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_ghost_bin_3d.h b/src/nstencil_full_ghost_bin_3d.h index ed4ca6c4d6..d99be6d869 100644 --- a/src/nstencil_full_ghost_bin_3d.h +++ b/src/nstencil_full_ghost_bin_3d.h @@ -15,8 +15,7 @@ NStencilStyle(full/ghost/bin/3d, NStencilFullGhostBin3d, - NS_FULL | NS_GHOST | NS_BIN | NS_3D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_GHOST | NS_BIN | NS_3D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_multi2_3d.h b/src/nstencil_full_multi2_3d.h index b9b835fd24..48bdfd2611 100644 --- a/src/nstencil_full_multi2_3d.h +++ b/src/nstencil_full_multi2_3d.h @@ -14,9 +14,7 @@ #ifdef NSTENCIL_CLASS NStencilStyle(full/multi/tiered/3d, - NStencilFullMultiTiered3d, - NS_FULL | NS_Multi_Tiered | NS_3D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NStencilFullMultiTiered3d, NS_FULL | NS_Multi_Tiered | NS_3D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_multi_2d.h b/src/nstencil_full_multi_2d.h index f78eecc55f..2c28bb56bf 100644 --- a/src/nstencil_full_multi_2d.h +++ b/src/nstencil_full_multi_2d.h @@ -15,8 +15,7 @@ NStencilStyle(full/multi/2d, NStencilFullMulti2d, - NS_FULL | NS_MULTI | NS_2D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_MULTI | NS_2D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_multi_3d.h b/src/nstencil_full_multi_3d.h index 9e3696f5d2..b2edfd8b0d 100644 --- a/src/nstencil_full_multi_3d.h +++ b/src/nstencil_full_multi_3d.h @@ -15,8 +15,7 @@ NStencilStyle(full/multi/3d, NStencilFullMulti3d, - NS_FULL | NS_MULTI | NS_3D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_MULTI | NS_3D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_half_bin_2d_newton.cpp b/src/nstencil_half_bin_2d.cpp similarity index 87% rename from src/nstencil_half_bin_2d_newton.cpp rename to src/nstencil_half_bin_2d.cpp index 8fdc8f1aa9..fc7b552118 100644 --- a/src/nstencil_half_bin_2d_newton.cpp +++ b/src/nstencil_half_bin_2d.cpp @@ -11,19 +11,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_2d_newton.h" +#include "nstencil_half_bin_2d.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin2dNewton::NStencilHalfBin2dNewton(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfBin2d::NStencilHalfBin2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfBin2dNewton::create() +void NStencilHalfBin2d::create() { int i,j; diff --git a/src/nstencil_half_bin_3d_newton.h b/src/nstencil_half_bin_2d.h similarity index 69% rename from src/nstencil_half_bin_3d_newton.h rename to src/nstencil_half_bin_2d.h index 96f19adae1..29a8868221 100644 --- a/src/nstencil_half_bin_3d_newton.h +++ b/src/nstencil_half_bin_2d.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bin/3d/newton, - NStencilHalfBin3dNewton, - NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_ORTHO) +NStencilStyle(half/bin/2d, + NStencilHalfBin2d, + NS_HALF | NS_BIN | NS_2D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTON_H -#define LMP_NSTENCIL_HALF_BIN_3D_NEWTON_H +#ifndef LMP_NSTENCIL_HALF_BIN_2D_H +#define LMP_NSTENCIL_HALF_BIN_2D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfBin3dNewton : public NStencil { +class NStencilHalfBin2d : public NStencil { public: - NStencilHalfBin3dNewton(class LAMMPS *); - ~NStencilHalfBin3dNewton() {} + NStencilHalfBin2d(class LAMMPS *); + ~NStencilHalfBin2d() {} void create(); }; diff --git a/src/nstencil_half_bin_2d_newtoff.cpp b/src/nstencil_half_bin_2d_newtoff.cpp deleted file mode 100644 index f3a6c5d08b..0000000000 --- a/src/nstencil_half_bin_2d_newtoff.cpp +++ /dev/null @@ -1,37 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_bin_2d_newtoff.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfBin2dNewtoff::NStencilHalfBin2dNewtoff(LAMMPS *lmp) : - NStencil(lmp) {} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfBin2dNewtoff::create() -{ - int i,j; - - nstencil = 0; - - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutneighmaxsq) - stencil[nstencil++] = j*mbinx + i; -} diff --git a/src/nstencil_half_bin_2d_newtoff.h b/src/nstencil_half_bin_2d_newtoff.h deleted file mode 100644 index 7a350df1bc..0000000000 --- a/src/nstencil_half_bin_2d_newtoff.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/bin/2d/newtoff, - NStencilHalfBin2dNewtoff, - NS_HALF | NS_BIN | NS_2D | NS_NEWTOFF | NS_ORTHO | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTOFF_H -#define LMP_NSTENCIL_HALF_BIN_2D_NEWTOFF_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfBin2dNewtoff : public NStencil { - public: - NStencilHalfBin2dNewtoff(class LAMMPS *); - ~NStencilHalfBin2dNewtoff() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_bin_2d_newton_tri.h b/src/nstencil_half_bin_2d_newton_tri.h deleted file mode 100644 index b9926608d7..0000000000 --- a/src/nstencil_half_bin_2d_newton_tri.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/bin/2d/newton/tri, - NStencilHalfBin2dNewtonTri, - NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_TRI_H -#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_TRI_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfBin2dNewtonTri : public NStencil { - public: - NStencilHalfBin2dNewtonTri(class LAMMPS *); - ~NStencilHalfBin2dNewtonTri() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_bin_2d_newton_tri.cpp b/src/nstencil_half_bin_2d_tri.cpp similarity index 87% rename from src/nstencil_half_bin_2d_newton_tri.cpp rename to src/nstencil_half_bin_2d_tri.cpp index 30d064fb29..0ad5456d62 100644 --- a/src/nstencil_half_bin_2d_newton_tri.cpp +++ b/src/nstencil_half_bin_2d_tri.cpp @@ -11,20 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_2d_newton_tri.h" +#include "nstencil_half_bin_2d_tri.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin2dNewtonTri::NStencilHalfBin2dNewtonTri(LAMMPS *lmp) : +NStencilHalfBin2dTri::NStencilHalfBin2dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfBin2dNewtonTri::create() +void NStencilHalfBin2dTri::create() { int i,j; diff --git a/src/nstencil_half_bin_2d_newton.h b/src/nstencil_half_bin_2d_tri.h similarity index 69% rename from src/nstencil_half_bin_2d_newton.h rename to src/nstencil_half_bin_2d_tri.h index 64bbfc5fe4..4dba9151ba 100644 --- a/src/nstencil_half_bin_2d_newton.h +++ b/src/nstencil_half_bin_2d_tri.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bin/2d/newton, - NStencilHalfBin2dNewton, - NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_ORTHO) +NStencilStyle(half/bin/2d/tri, + NStencilHalfBin2dTri, + NS_HALF | NS_BIN | NS_2D | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_H -#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_H +#ifndef LMP_NSTENCIL_HALF_BIN_2D_TRI_H +#define LMP_NSTENCIL_HALF_BIN_2D_TRI_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfBin2dNewton : public NStencil { +class NStencilHalfBin2dTri : public NStencil { public: - NStencilHalfBin2dNewton(class LAMMPS *); - ~NStencilHalfBin2dNewton() {} + NStencilHalfBin2dTri(class LAMMPS *); + ~NStencilHalfBin2dTri() {} void create(); }; diff --git a/src/nstencil_half_bin_3d_newton.cpp b/src/nstencil_half_bin_3d.cpp similarity index 88% rename from src/nstencil_half_bin_3d_newton.cpp rename to src/nstencil_half_bin_3d.cpp index 998ed28afe..43dcd2b648 100644 --- a/src/nstencil_half_bin_3d_newton.cpp +++ b/src/nstencil_half_bin_3d.cpp @@ -11,19 +11,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_3d_newton.h" +#include "nstencil_half_bin_3d.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin3dNewton::NStencilHalfBin3dNewton(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfBin3d::NStencilHalfBin3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfBin3dNewton::create() +void NStencilHalfBin3d::create() { int i,j,k; diff --git a/src/nstencil_half_multi_2d_newton.h b/src/nstencil_half_bin_3d.h similarity index 68% rename from src/nstencil_half_multi_2d_newton.h rename to src/nstencil_half_bin_3d.h index 9ecac4c696..729dcf9c91 100644 --- a/src/nstencil_half_multi_2d_newton.h +++ b/src/nstencil_half_bin_3d.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/multi/2d/newton, - NStencilHalfMulti2dNewton, - NS_HALF | NS_MULTI | NS_2D | NS_NEWTON | NS_ORTHO) +NStencilStyle(half/bin/3d, + NStencilHalfBin3d, + NS_HALF | NS_BIN | NS_3D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_HALF_MULTI_2D_NEWTON_H -#define LMP_NSTENCIL_HALF_MULTI_2D_NEWTON_H +#ifndef LMP_NSTENCIL_HALF_BIN_3D_H +#define LMP_NSTENCIL_HALF_BIN_3D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfMulti2dNewton : public NStencil { +class NStencilHalfBin3d : public NStencil { public: - NStencilHalfMulti2dNewton(class LAMMPS *); - ~NStencilHalfMulti2dNewton() {} + NStencilHalfBin3d(class LAMMPS *); + ~NStencilHalfBin3d() {} void create(); }; diff --git a/src/nstencil_half_bin_3d_newtoff.cpp b/src/nstencil_half_bin_3d_newtoff.cpp deleted file mode 100644 index e44a93d47d..0000000000 --- a/src/nstencil_half_bin_3d_newtoff.cpp +++ /dev/null @@ -1,38 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_bin_3d_newtoff.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfBin3dNewtoff::NStencilHalfBin3dNewtoff(LAMMPS *lmp) : - NStencil(lmp) {} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfBin3dNewtoff::create() -{ - int i,j,k; - - nstencil = 0; - - for (k = -sz; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutneighmaxsq) - stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i; -} diff --git a/src/nstencil_half_bin_3d_newtoff.h b/src/nstencil_half_bin_3d_newtoff.h deleted file mode 100644 index d1eac666cc..0000000000 --- a/src/nstencil_half_bin_3d_newtoff.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/bin/3d/newtoff, - NStencilHalfBin3dNewtoff, - NS_HALF | NS_BIN | NS_3D | NS_NEWTOFF | NS_ORTHO | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTOFF_H -#define LMP_NSTENCIL_HALF_BIN_3D_NEWTOFF_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfBin3dNewtoff : public NStencil { - public: - NStencilHalfBin3dNewtoff(class LAMMPS *); - ~NStencilHalfBin3dNewtoff() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_bin_3d_newton_tri.h b/src/nstencil_half_bin_3d_newton_tri.h deleted file mode 100644 index 8c265acb46..0000000000 --- a/src/nstencil_half_bin_3d_newton_tri.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/bin/3d/newton/tri, - NStencilHalfBin3dNewtonTri, - NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTON_TRI_H -#define LMP_NSTENCIL_HALF_BIN_3D_NEWTON_TRI_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfBin3dNewtonTri : public NStencil { - public: - NStencilHalfBin3dNewtonTri(class LAMMPS *); - ~NStencilHalfBin3dNewtonTri() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_bin_3d_newton_tri.cpp b/src/nstencil_half_bin_3d_tri.cpp similarity index 88% rename from src/nstencil_half_bin_3d_newton_tri.cpp rename to src/nstencil_half_bin_3d_tri.cpp index 2aae44ceaf..ca016d956a 100644 --- a/src/nstencil_half_bin_3d_newton_tri.cpp +++ b/src/nstencil_half_bin_3d_tri.cpp @@ -11,20 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_3d_newton_tri.h" +#include "nstencil_half_bin_3d_tri.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin3dNewtonTri::NStencilHalfBin3dNewtonTri(LAMMPS *lmp) : +NStencilHalfBin3dTri::NStencilHalfBin3dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfBin3dNewtonTri::create() +void NStencilHalfBin3dTri::create() { int i,j,k; diff --git a/src/nstencil_half_multi_3d_newton.h b/src/nstencil_half_bin_3d_tri.h similarity index 68% rename from src/nstencil_half_multi_3d_newton.h rename to src/nstencil_half_bin_3d_tri.h index bbdc7752c6..33183cd318 100644 --- a/src/nstencil_half_multi_3d_newton.h +++ b/src/nstencil_half_bin_3d_tri.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/multi/3d/newton, - NStencilHalfMulti3dNewton, - NS_HALF | NS_MULTI | NS_3D | NS_NEWTON | NS_ORTHO) +NStencilStyle(half/bin/3d/tri, + NStencilHalfBin3dTri, + NS_HALF | NS_BIN | NS_3D | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_MULTI_3D_NEWTON_H -#define LMP_NSTENCIL_HALF_MULTI_3D_NEWTON_H +#ifndef LMP_NSTENCIL_HALF_BIN_3D_TRI_H +#define LMP_NSTENCIL_HALF_BIN_3D_TRI_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfMulti3dNewton : public NStencil { +class NStencilHalfBin3dTri : public NStencil { public: - NStencilHalfMulti3dNewton(class LAMMPS *); - ~NStencilHalfMulti3dNewton() {} + NStencilHalfBin3dTri(class LAMMPS *); + ~NStencilHalfBin3dTri() {} void create(); }; diff --git a/src/nstencil_half_ghost_bin_2d_newtoff.cpp b/src/nstencil_half_ghost_bin_2d_newtoff.cpp deleted file mode 100644 index 6f9a7585fe..0000000000 --- a/src/nstencil_half_ghost_bin_2d_newtoff.cpp +++ /dev/null @@ -1,44 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_ghost_bin_2d_newtoff.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfGhostBin2dNewtoff:: -NStencilHalfGhostBin2dNewtoff(LAMMPS *lmp) : NStencil(lmp) -{ - xyzflag = 1; -} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfGhostBin2dNewtoff::create() -{ - int i,j; - - nstencil = 0; - - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutneighmaxsq) { - stencilxyz[nstencil][0] = i; - stencilxyz[nstencil][1] = j; - stencilxyz[nstencil][2] = 0; - stencil[nstencil++] = j*mbinx + i; - } -} diff --git a/src/nstencil_half_ghost_bin_2d_newtoff.h b/src/nstencil_half_ghost_bin_2d_newtoff.h deleted file mode 100644 index 3286810c1c..0000000000 --- a/src/nstencil_half_ghost_bin_2d_newtoff.h +++ /dev/null @@ -1,44 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/ghost/bin/2d/newtoff, - NStencilHalfGhostBin2dNewtoff, - NS_HALF | NS_GHOST | NS_BIN | NS_2D | - NS_NEWTOFF | NS_ORTHO | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_GHOST_BIN_2D_NEWTOFF_H -#define LMP_NSTENCIL_HALF_GHOST_BIN_2D_NEWTOFF_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfGhostBin2dNewtoff : public NStencil { - public: - NStencilHalfGhostBin2dNewtoff(class LAMMPS *); - ~NStencilHalfGhostBin2dNewtoff() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_ghost_bin_3d_newtoff.cpp b/src/nstencil_half_ghost_bin_3d_newtoff.cpp deleted file mode 100644 index 6492fe4a4e..0000000000 --- a/src/nstencil_half_ghost_bin_3d_newtoff.cpp +++ /dev/null @@ -1,45 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_ghost_bin_3d_newtoff.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfGhostBin3dNewtoff:: -NStencilHalfGhostBin3dNewtoff(LAMMPS *lmp) : NStencil(lmp) -{ - xyzflag = 1; -} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfGhostBin3dNewtoff::create() -{ - int i,j,k; - - nstencil = 0; - - for (k = -sz; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutneighmaxsq) { - stencilxyz[nstencil][0] = i; - stencilxyz[nstencil][1] = j; - stencilxyz[nstencil][2] = k; - stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i; - } -} diff --git a/src/nstencil_half_ghost_bin_3d_newtoff.h b/src/nstencil_half_ghost_bin_3d_newtoff.h deleted file mode 100644 index ee58c29342..0000000000 --- a/src/nstencil_half_ghost_bin_3d_newtoff.h +++ /dev/null @@ -1,44 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/ghost/bin/3d/newtoff, - NStencilHalfGhostBin3dNewtoff, - NS_HALF | NS_GHOST | NS_BIN | NS_3D | - NS_NEWTOFF | NS_ORTHO | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_GHOST_BIN_3D_NEWTOFF_H -#define LMP_NSTENCIL_HALF_GHOST_BIN_3D_NEWTOFF_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfGhostBin3dNewtoff : public NStencil { - public: - NStencilHalfGhostBin3dNewtoff(class LAMMPS *); - ~NStencilHalfGhostBin3dNewtoff() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi2_2d_newton.cpp b/src/nstencil_half_multi2_2d_newton.cpp deleted file mode 100644 index 66158202bf..0000000000 --- a/src/nstencil_half_multi2_2d_newton.cpp +++ /dev/null @@ -1,201 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_bytype_2d_newton.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "nbin.h" -#include "memory.h" -#include "atom.h" -#include - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfBytype2dNewton::NStencilHalfBytype2dNewton(LAMMPS *lmp) : - NStencil(lmp) -{ - maxstencil_type = NULL; -} - -NStencilHalfBytype2dNewton::~NStencilHalfBytype2dNewton() { - - memory->destroy(nstencil_type); - for (int i = 1; i <= atom->ntypes; i++) { - for (int j = 0; j <= atom->ntypes; j++) { - if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); - } - delete [] stencil_type[i]; - } - delete [] stencil_type; - memory->destroy(maxstencil_type); -} - -/* ---------------------------------------------------------------------- */ - -// KS To superclass -void NStencilHalfBytype2dNewton::copy_bin_info_bytype(int itype) { - - mbinx = nb->mbinx_type[itype]; - mbiny = nb->mbiny_type[itype]; - mbinz = nb->mbinz_type[itype]; - binsizex = nb->binsizex_type[itype]; - binsizey = nb->binsizey_type[itype]; - binsizez = nb->binsizez_type[itype]; - bininvx = nb->bininvx_type[itype]; - bininvy = nb->bininvy_type[itype]; - bininvz = nb->bininvz_type[itype]; -} - -/* ---------------------------------------------------------------------- */ - -// KS To superclass? -int NStencilHalfBytype2dNewton::copy_neigh_info_bytype(int itype) { - - cutneighmaxsq = neighbor->cutneighsq[itype][itype]; - cutneighmax = sqrt(cutneighmaxsq); - cuttypesq = neighbor->cuttypesq; - - // sx,sy,sz = max range of stencil in each dim - // smax = max possible size of entire 2d stencil - // stencil will be empty if cutneighmax = 0.0 - - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - return ((2*sx+1) * (2*sy+1) * (2*sz+1)); -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype2dNewton::create_setup() -{ - - int itype, jtype; - int maxtypes; - int smax; - - // maxstencil_type to superclass? - maxtypes = atom->ntypes; - - if (maxstencil_type == NULL) { - memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "maxstencil_type"); - memory->create(nstencil_type, maxtypes+1, maxtypes+1, "nstencil_type"); - stencil_type = new int**[maxtypes+1](); - for (itype = 1; itype <= maxtypes; ++itype) { - stencil_type[itype] = new int*[maxtypes+1](); - for (jtype = 1; jtype <= maxtypes; ++jtype) { - maxstencil_type[itype][jtype] = 0; - nstencil_type[itype][jtype] = 0; - } - } - } - - // like -> like => use standard Newton stencil at bin - - for (itype = 1; itype <= maxtypes; ++itype) { - copy_bin_info_bytype(itype); - smax = copy_neigh_info_bytype(itype); - if (smax > maxstencil_type[itype][itype]) { - maxstencil_type[itype][itype] = smax; - memory->destroy(stencil_type[itype][itype]); - memory->create(stencil_type[itype][itype], smax, - "NStencilHalfBytypeNewton::create_steup() stencil"); - } - create_newton(itype, itype, cutneighmaxsq); - } - - // Cross types: "Newton on" reached by using Newton off stencil and - // looking one way through hierarchy - // smaller -> larger => use Newton off stencil in larger bin - // larger -> smaller => no nstecil required - // If cut offs are same, use existing type-type stencil - - for (itype = 1; itype <= maxtypes; ++itype) { - for (jtype = 1; jtype <= maxtypes; ++jtype) { - if (itype == jtype) continue; - if (cuttypesq[itype] == cuttypesq[jtype]) { - nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; - stencil_type[itype][jtype] = stencil_type[jtype][jtype]; - } - else if (cuttypesq[itype] < cuttypesq[jtype]) { - copy_bin_info_bytype(jtype); - - cutneighmaxsq = cuttypesq[jtype]; - cutneighmax = sqrt(cutneighmaxsq); - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - smax = (2*sx+1) * (2*sy+1) * (2*sz+1); - if (smax > maxstencil_type[itype][jtype]) { - maxstencil_type[itype][jtype] = smax; - memory->destroy(stencil_type[itype][jtype]); - memory->create(stencil_type[itype][jtype], smax, "stencil_type[]"); - } - create_newtoff(itype, jtype, cuttypesq[jtype]); - } - } - } - -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype2dNewton::create_newton(int itype, int jtype, double cutsq) { - - int i, j, ns; - - ns = 0; - - for (j = 0; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (j > 0 || (j == 0 && i > 0)) { - if (bin_distance(i,j,0) < cutsq) - stencil_type[itype][jtype][ns++] = j*mbinx + i; - } - nstencil_type[itype][jtype] = ns; -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype2dNewton::create_newtoff(int itype, int jtype, double cutsq) { - - int i, j, ns; - - ns = 0; - - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutsq) - stencil_type[itype][jtype][ns++] = j*mbinx + i; - - nstencil_type[itype][jtype] = ns; -} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfBytype2dNewton::create() -{ - // KS. Move "creation" here. -} diff --git a/src/nstencil_half_multi2_2d_newton.h b/src/nstencil_half_multi2_2d_newton.h deleted file mode 100644 index 4d33c26a71..0000000000 --- a/src/nstencil_half_multi2_2d_newton.h +++ /dev/null @@ -1,52 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/bytype/2d/newton, - NStencilHalfBytype2dNewton, - NS_HALF | NS_BYTYPE | NS_2D | NS_NEWTON | NS_ORTHO) - -#else - -#ifndef LMP_NSTENCIL_HALF_BYTYPE_2D_NEWTON_H -#define LMP_NSTENCIL_HALF_BYTYPE_2D_NEWTON_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfBytype2dNewton : public NStencil { - public: - NStencilHalfBytype2dNewton(class LAMMPS *); - ~NStencilHalfBytype2dNewton(); - void create_setup(); - void create(); - - private: - int ** maxstencil_type; - - void copy_bin_info_bytype(int); - int copy_neigh_info_bytype(int); - void create_newton(int, int, double); - void create_newtoff(int, int, double); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi2_3d_newton.cpp b/src/nstencil_half_multi2_3d.cpp similarity index 100% rename from src/nstencil_half_multi2_3d_newton.cpp rename to src/nstencil_half_multi2_3d.cpp diff --git a/src/nstencil_half_multi2_3d_newton_tri.h b/src/nstencil_half_multi2_3d.h old mode 100755 new mode 100644 similarity index 82% rename from src/nstencil_half_multi2_3d_newton_tri.h rename to src/nstencil_half_multi2_3d.h index e419161bb5..e39db1c1e1 --- a/src/nstencil_half_multi2_3d_newton_tri.h +++ b/src/nstencil_half_multi2_3d.h @@ -13,14 +13,13 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bytype/3d/newton, - NStencilHalfBytype3dNewton, - NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTON | NS_TRI) +NStencilStyle(half/bytype/3d, + NStencilHalfBytype3dNewton, NS_HALF | NS_BYTYPE | NS_3D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H -#define LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H +#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_H +#define LMP_NSTENCIL_HALF_BYTYPE_3D_H #include "nstencil.h" diff --git a/src/nstencil_half_multi2_3d_newtoff.cpp b/src/nstencil_half_multi2_3d_delete_noff.cpp similarity index 100% rename from src/nstencil_half_multi2_3d_newtoff.cpp rename to src/nstencil_half_multi2_3d_delete_noff.cpp diff --git a/src/nstencil_half_multi2_3d_newtoff.h b/src/nstencil_half_multi2_3d_delete_noff.h similarity index 100% rename from src/nstencil_half_multi2_3d_newtoff.h rename to src/nstencil_half_multi2_3d_delete_noff.h diff --git a/src/nstencil_half_multi2_3d_newton_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp similarity index 100% rename from src/nstencil_half_multi2_3d_newton_tri.cpp rename to src/nstencil_half_multi2_3d_tri.cpp diff --git a/src/nstencil_half_multi2_3d_newton.h b/src/nstencil_half_multi2_3d_tri.h old mode 100644 new mode 100755 similarity index 82% rename from src/nstencil_half_multi2_3d_newton.h rename to src/nstencil_half_multi2_3d_tri.h index cbb88fcb1d..5424d73f11 --- a/src/nstencil_half_multi2_3d_newton.h +++ b/src/nstencil_half_multi2_3d_tri.h @@ -13,14 +13,13 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bytype/3d/newton, - NStencilHalfBytype3dNewton, - NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTON | NS_ORTHO) +NStencilStyle(half/bytype/3d, + NStencilHalfBytype3d, NS_HALF | NS_BYTYPE | NS_3D | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H -#define LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTON_H +#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_H +#define LMP_NSTENCIL_HALF_BYTYPE_3D_H #include "nstencil.h" diff --git a/src/nstencil_half_multi_2d_newton.cpp b/src/nstencil_half_multi_2d.cpp similarity index 89% rename from src/nstencil_half_multi_2d_newton.cpp rename to src/nstencil_half_multi_2d.cpp index f6f6c488a5..db009030cf 100644 --- a/src/nstencil_half_multi_2d_newton.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_2d_newton.h" +#include "nstencil_half_multi_2d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti2dNewton:: -NStencilHalfMulti2dNewton(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMulti2d:: +NStencilHalfMulti2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti2dNewton::create() +void NStencilHalfMulti2d::create() { int i,j,n; double rsq,typesq; diff --git a/src/nstencil_half_multi_2d.h b/src/nstencil_half_multi_2d.h new file mode 100644 index 0000000000..128d37a2e9 --- /dev/null +++ b/src/nstencil_half_multi_2d.h @@ -0,0 +1,42 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/multi/2d, + NStencilHalfMulti2d, NS_HALF | NS_MULTI | NS_2D | NS_ORTHO) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_2D_H +#define LMP_NSTENCIL_HALF_MULTI_2D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti2d : public NStencil { + public: + NStencilHalfMulti2d(class LAMMPS *); + ~NStencilHalfMulti2d() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi_2d_newtoff.cpp b/src/nstencil_half_multi_2d_newtoff.cpp deleted file mode 100644 index 63cd3fd524..0000000000 --- a/src/nstencil_half_multi_2d_newtoff.cpp +++ /dev/null @@ -1,51 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_multi_2d_newtoff.h" -#include "atom.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfMulti2dNewtoff:: -NStencilHalfMulti2dNewtoff(LAMMPS *lmp) : NStencil(lmp) {} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfMulti2dNewtoff::create() -{ - int i,j,n; - double rsq,typesq; - int *s; - double *distsq; - - int ntypes = atom->ntypes; - for (int itype = 1; itype <= ntypes; itype++) { - typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - n = 0; - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) { - rsq = bin_distance(i,j,0); - if (rsq < typesq) { - distsq[n] = rsq; - s[n++] = j*mbinx + i; - } - } - nstencil_multi[itype] = n; - } -} diff --git a/src/nstencil_half_multi_2d_newtoff.h b/src/nstencil_half_multi_2d_newtoff.h deleted file mode 100644 index 5603f37beb..0000000000 --- a/src/nstencil_half_multi_2d_newtoff.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi/2d/newtoff, - NStencilHalfMulti2dNewtoff, - NS_HALF | NS_MULTI | NS_2D | NS_NEWTOFF | NS_ORTHO | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI_2D_NEWTOFF_H -#define LMP_NSTENCIL_HALF_MULTI_2D_NEWTOFF_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti2dNewtoff : public NStencil { - public: - NStencilHalfMulti2dNewtoff(class LAMMPS *); - ~NStencilHalfMulti2dNewtoff() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi_2d_newton_tri.h b/src/nstencil_half_multi_2d_newton_tri.h deleted file mode 100644 index 62d7dfdebf..0000000000 --- a/src/nstencil_half_multi_2d_newton_tri.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi/2d/newton/tri, - NStencilHalfMulti2dNewtonTri, - NS_HALF | NS_MULTI | NS_2D | NS_NEWTON | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI_2D_NEWTON_TRI_H -#define LMP_NSTENCIL_HALF_MULTI_2D_NEWTON_TRI_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti2dNewtonTri : public NStencil { - public: - NStencilHalfMulti2dNewtonTri(class LAMMPS *); - ~NStencilHalfMulti2dNewtonTri() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi_2d_newton_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp similarity index 88% rename from src/nstencil_half_multi_2d_newton_tri.cpp rename to src/nstencil_half_multi_2d_tri.cpp index b44ab36ea0..fef551f3e0 100644 --- a/src/nstencil_half_multi_2d_newton_tri.cpp +++ b/src/nstencil_half_multi_2d_tri.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_2d_newton_tri.h" +#include "nstencil_half_multi_2d_tri.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti2dNewtonTri:: -NStencilHalfMulti2dNewtonTri(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMulti2dTri:: +NStencilHalfMulti2dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti2dNewtonTri::create() +void NStencilHalfMulti2dTri::create() { int i,j,n; double rsq,typesq; diff --git a/src/nstencil_half_multi_2d_tri.h b/src/nstencil_half_multi_2d_tri.h new file mode 100644 index 0000000000..776c42e96b --- /dev/null +++ b/src/nstencil_half_multi_2d_tri.h @@ -0,0 +1,42 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/multi/2d/tri, + NStencilHalfMulti2dTri, NS_HALF | NS_MULTI | NS_2D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_2D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_2D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti2dTri : public NStencil { + public: + NStencilHalfMulti2dTri(class LAMMPS *); + ~NStencilHalfMulti2dTri() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi_3d_newton.cpp b/src/nstencil_half_multi_3d.cpp similarity index 90% rename from src/nstencil_half_multi_3d_newton.cpp rename to src/nstencil_half_multi_3d.cpp index 5b0c7f9f63..ca1c7f2f02 100644 --- a/src/nstencil_half_multi_3d_newton.cpp +++ b/src/nstencil_half_multi_3d.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_3d_newton.h" +#include "nstencil_half_multi_3d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti3dNewton:: -NStencilHalfMulti3dNewton(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMulti3d:: +NStencilHalfMulti3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti3dNewton::create() +void NStencilHalfMulti3d::create() { int i,j,k,n; double rsq,typesq; diff --git a/src/nstencil_half_multi_3d.h b/src/nstencil_half_multi_3d.h new file mode 100644 index 0000000000..51cf9d5c29 --- /dev/null +++ b/src/nstencil_half_multi_3d.h @@ -0,0 +1,42 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/multi/3d, + NStencilHalfMulti3d, NS_HALF | NS_MULTI | NS_3D | NS_ORTHO) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_3D_H +#define LMP_NSTENCIL_HALF_MULTI_3D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti3d : public NStencil { + public: + NStencilHalfMulti3d(class LAMMPS *); + ~NStencilHalfMulti3d() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi_3d_newtoff.cpp b/src/nstencil_half_multi_3d_newtoff.cpp deleted file mode 100644 index 5a83c4e002..0000000000 --- a/src/nstencil_half_multi_3d_newtoff.cpp +++ /dev/null @@ -1,52 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_multi_3d_newtoff.h" -#include "atom.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfMulti3dNewtoff:: -NStencilHalfMulti3dNewtoff(LAMMPS *lmp) : NStencil(lmp) {} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfMulti3dNewtoff::create() -{ - int i,j,k,n; - double rsq,typesq; - int *s; - double *distsq; - - int ntypes = atom->ntypes; - for (int itype = 1; itype <= ntypes; itype++) { - typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - n = 0; - for (k = -sz; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) { - rsq = bin_distance(i,j,k); - if (rsq < typesq) { - distsq[n] = rsq; - s[n++] = k*mbiny*mbinx + j*mbinx + i; - } - } - nstencil_multi[itype] = n; - } -} diff --git a/src/nstencil_half_multi_3d_newtoff.h b/src/nstencil_half_multi_3d_newtoff.h deleted file mode 100644 index 99428deb6a..0000000000 --- a/src/nstencil_half_multi_3d_newtoff.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi/3d/newtoff, - NStencilHalfMulti3dNewtoff, - NS_HALF | NS_MULTI | NS_3D | NS_NEWTOFF | NS_ORTHO | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI_3D_NEWTOFF_H -#define LMP_NSTENCIL_HALF_MULTI_3D_NEWTOFF_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti3dNewtoff : public NStencil { - public: - NStencilHalfMulti3dNewtoff(class LAMMPS *); - ~NStencilHalfMulti3dNewtoff() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi_3d_newton_tri.h b/src/nstencil_half_multi_3d_newton_tri.h deleted file mode 100644 index f6866489a4..0000000000 --- a/src/nstencil_half_multi_3d_newton_tri.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi/3d/newton/tri, - NStencilHalfMulti3dNewtonTri, - NS_HALF | NS_MULTI | NS_3D | NS_NEWTON | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI_3D_NEWTON_TRI_H -#define LMP_NSTENCIL_HALF_MULTI_3D_NEWTON_TRI_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti3dNewtonTri : public NStencil { - public: - NStencilHalfMulti3dNewtonTri(class LAMMPS *); - ~NStencilHalfMulti3dNewtonTri() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi_3d_newton_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp similarity index 89% rename from src/nstencil_half_multi_3d_newton_tri.cpp rename to src/nstencil_half_multi_3d_tri.cpp index b25a0d0bdb..2970977a1e 100644 --- a/src/nstencil_half_multi_3d_newton_tri.cpp +++ b/src/nstencil_half_multi_3d_tri.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_3d_newton_tri.h" +#include "nstencil_half_multi_3d_tri.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti3dNewtonTri:: -NStencilHalfMulti3dNewtonTri(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMulti3dTri:: +NStencilHalfMulti3dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti3dNewtonTri::create() +void NStencilHalfMulti3dTri::create() { int i,j,k,n; double rsq,typesq; diff --git a/src/nstencil_half_multi_3d_tri.h b/src/nstencil_half_multi_3d_tri.h new file mode 100644 index 0000000000..f33f65cfea --- /dev/null +++ b/src/nstencil_half_multi_3d_tri.h @@ -0,0 +1,42 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/multi/3d/tri, + NStencilHalfMulti3dTri, NS_HALF | NS_MULTI | NS_3D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_3D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_3D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti3dTri : public NStencil { + public: + NStencilHalfMulti3dTri(class LAMMPS *); + ~NStencilHalfMulti3dTri() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ From dd1cce1da5dfd7da50b55e792e64883871c9cd1e Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 10 Nov 2020 20:03:00 -0700 Subject: [PATCH 0016/1217] Finish stencil classes --- src/nstencil.cpp | 173 +++++++------ src/nstencil.h | 23 +- src/nstencil_full_multi2_2d.cpp | 97 +++++++ ...elete_noff.h => nstencil_full_multi2_2d.h} | 23 +- src/nstencil_full_multi2_3d.cpp | 203 +++++---------- src/nstencil_full_multi2_3d.h | 22 +- src/nstencil_half_multi2_2d.cpp | 111 ++++++++ src/nstencil_half_multi2_2d.h | 46 ++++ src/nstencil_half_multi2_2d_tri.cpp | 108 ++++++++ src/nstencil_half_multi2_2d_tri.h | 45 ++++ src/nstencil_half_multi2_3d.cpp | 240 ++++++------------ src/nstencil_half_multi2_3d.h | 23 +- src/nstencil_half_multi2_3d_delete_noff.cpp | 198 --------------- src/nstencil_half_multi2_3d_tri.cpp | 150 ++++++----- src/nstencil_half_multi2_3d_tri.h | 24 +- 15 files changed, 779 insertions(+), 707 deletions(-) create mode 100644 src/nstencil_full_multi2_2d.cpp rename src/{nstencil_half_multi2_3d_delete_noff.h => nstencil_full_multi2_2d.h} (58%) create mode 100644 src/nstencil_half_multi2_2d.cpp create mode 100644 src/nstencil_half_multi2_2d.h create mode 100755 src/nstencil_half_multi2_2d_tri.cpp create mode 100755 src/nstencil_half_multi2_2d_tri.h delete mode 100644 src/nstencil_half_multi2_3d_delete_noff.cpp diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 3518b7db55..525369d573 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -31,33 +31,33 @@ using namespace LAMMPS_NS; sx,sy,sz = bin bounds = furthest the stencil could possibly extend calculated below in create_setup() 3d creates xyz stencil, 2d creates xy stencil - for half list with newton off: + for full list or half list with newton off + use a full stencil stencil is all surrounding bins including self regardless of triclinic - for half list with newton on: + for half list with newton on + use a half stencil stencil is bins to the "upper right" of central bin stencil does not include self no versions that allow ghost on (no callers need it?) for half list with newton on and triclinic: + use a half stencil stencil is all bins in z-plane of self and above, but not below in 2d is all bins in y-plane of self and above, but not below stencil includes self no versions that allow ghost on (no callers need it?) - for full list: - stencil is all surrounding bins including self - regardless of newton on/off or triclinic for multi: create one stencil for each atom type stencil follows same rules for half/full, newton on/off, triclinic cutoff is not cutneighmaxsq, but max cutoff for that atom type no versions that allow ghost on (any need for it?) - for multi/tiered: + for multi2: create one stencil for each itype-jtype pairing stencils do not generally follow the same rules for half/full or newton on/off - whole stencils including all surrounding bins are always used except - for same-type stencils with newton on which uses a split stencil - for orthogonal boxes, a split stencil includes bins to the "upper right" of central bin - for triclinic, a split stencil includes bins in the z (3D) or y (2D) plane of self and above + full stencils including all surrounding bins are always used except + for same-type stencils with newton on which uses a half stencil + for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin + for triclinic, a half stencil includes bins in the z (3D) or y (2D) plane of self and above cutoff is not cutneighmaxsq, but max cutoff for that atom type no versions that allow ghost on (any need for it?) ------------------------------------------------------------------------- */ @@ -74,7 +74,7 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) stencil_multi = nullptr; distsq_multi = nullptr; - stencil_split = nullptr; + stencil_half = nullptr; stencil_skip = nullptr; stencil_bin_type = nullptr; stencil_cut = nullptr; @@ -101,31 +101,31 @@ NStencil::~NStencil() delete [] distsq_multi; } - if (stencil_multi_tiered) { + if (stencil_multi2) { int n = atom->ntypes; - memory->destroy(nstencil_multi_tiered); + memory->destroy(nstencil_multi2); for (int i = 1; i <= n; i++) { for (int j = 0; j <= n; j++) { if (! stencil_skip[i][j]) - memory->destroy(stencil_multi_tiered[i][j]); + memory->destroy(stencil_multi2[i][j]); } - delete [] stencil_multi_tiered[i]; + delete [] stencil_multi2[i]; } - delete [] stencil_multi_tiered; - memory->destroy(maxstencil_multi_tiered); - memory->destroy(stencil_split); + delete [] stencil_multi2; + memory->destroy(maxstencil_multi2); + memory->destroy(stencil_half); memory->destroy(stencil_skip); memory->destroy(stencil_bin_type); memory->destroy(stencil_cut); - memory->destroy(sx_multi_tiered); - memory->destroy(sy_multi_tiered); - memory->destroy(sz_multi_tiered); + memory->destroy(sx_multi2); + memory->destroy(sy_multi2); + memory->destroy(sz_multi2); - memory->destroy(binsizex_multi_tiered); - memory->destroy(binsizey_multi_tiered); - memory->destroy(binsizez_multi_tiered); + memory->destroy(binsizex_multi2); + memory->destroy(binsizey_multi2); + memory->destroy(binsizez_multi2); } } @@ -179,17 +179,17 @@ void NStencil::copy_bin_info() copy needed info for a given type from NBin class to this stencil class ------------------------------------------------------------------------- */ -void NStencil::copy_bin_info_multi_tiered(int type) +void NStencil::copy_bin_info_multi2(int type) { - mbinx = nb->mbinx_tiered[type]; - mbiny = nb->mbiny_tiered[type]; - mbinz = nb->mbinz_tiered[type]; - binsizex = nb->binsizex_tiered[type]; - binsizey = nb->binsizey_tiered[type]; - binsizez = nb->binsizez_tiered[type]; - bininvx = nb->bininvx_tiered[type]; - bininvy = nb->bininvy_tiered[type]; - bininvz = nb->bininvz_tiered[type]; + mbinx = nb->mbinx2[type]; + mbiny = nb->mbiny2[type]; + mbinz = nb->mbinz2[type]; + binsizex = nb->binsizex2[type]; + binsizey = nb->binsizey2[type]; + binsizez = nb->binsizez2[type]; + bininvx = nb->bininvx2[type]; + bininvy = nb->bininvy2[type]; + bininvz = nb->bininvz2[type]; } /* ---------------------------------------------------------------------- @@ -200,7 +200,7 @@ void NStencil::copy_bin_info_multi_tiered(int type) void NStencil::create_setup() { - if (neighstyle != Neighbor::MULTI_TIERED){ + if (neighstyle != Neighbor::MULTI2){ if (nb) copy_bin_info(); last_stencil = update->ntimestep; @@ -263,34 +263,53 @@ void NStencil::create_setup() int n = atom->ntypes; // Allocate arrays to store stencil information - memory->create(stencil_split, n, n, - "neighstencil:stencil_split");" - memory->create(stencil_skip, n, n, - "neighstencil:stencil_skip");" - memory->create(stencil_bin_type, n, n, - "neighstencil:stencil_bin_type");" - memory->create(stencil_cut, n, n, - "neighstencil:stencil_cut");" + memory->create(stencil_half, n+1, n+1, + "neighstencil:stencil_half"); + memory->create(stencil_skip, n+1, n+1, + "neighstencil:stencil_skip"); + memory->create(stencil_bin_type, n+1, n+1, + "neighstencil:stencil_bin_type"); + memory->create(stencil_cut, n+1, n+1, + "neighstencil:stencil_cut"); - memory->create(sx_multi_tiered, n, n, - "neighstencil:sx_multi_tiered");" - memory->create(sy_multi_tiered, n, n, - "neighstencil:sy_multi_tiered");" - memory->create(sz_multi_tiered, n, n, - "neighstencil:sz_multi_tiered");" + memory->create(sx_multi2, n+1, n+1, "neighstencil:sx_multi2"); + memory->create(sy_multi2, n+1, n+1, "neighstencil:sy_multi2"); + memory->create(sz_multi2, n+1, n+1, "neighstencil:sz_multi2"); - memory->create(binsizex_multi_tiered, n, n, - "neighstencil:binsizex_multi_tiered");" - memory->create(binsizey_multi_tiered, n, n, - "neighstencil:binsizey_multi_tiered");" - memory->create(binsizez_multi_tiered, n, n, - "neighstencil:binsizez_multi_tiered");" - + memory->create(binsizex_multi2, n+1, n+1, + "neighstencil:binsizex_multi2"); + memory->create(binsizey_multi2, n+1, n+1, + "neighstencil:binsizey_multi2"); + memory->create(binsizez_multi2, n+1, n+1, + "neighstencil:binsizez_multi2"); + + // Skip all stencils by default, initialize smax + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { + stencil_skip[i][j] = 1; + maxstencil_multi2[i][j] = 0; + } + } + // Determine which stencils need to be built set_stencil_properties(); - for (i = 1; i <= n; ++i) { - for (j = 1; j <= n; ++j) { + // Allocate arrays to store stencils + + if (!maxstencil_multi2) { + memory->create(maxstencil_multi2, n+1, n+1, "neighstencil::stencil_multi2"); + memory->create(nstencil_multi2, n+1, n+1, "neighstencil::nstencil_multi2"); + stencil_multi2 = new int**[n+1](); + for (i = 1; i <= n; ++i) { + stencil_multi2[i] = new int*[n+1](); + for (j = 1; j <= n; ++j) { + maxstencil_multi2[i][j] = 0; + } + } + } + + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { // Skip creation of unused stencils if (stencil_skip[i][j]) continue; @@ -299,9 +318,9 @@ void NStencil::create_setup() bin_type = stencil_bin_type[i][j]; copy_bin_info_bytype(bin_type); - binsizex_multi_tiered[i][j] = binsizex; - binsizey_multi_tiered[i][j] = binsizey; - binsizez_multi_tiered[i][j] = binsizez; + binsizex_multi2[i][j] = binsizex; + binsizey_multi2[i][j] = binsizey; + binsizez_multi2[i][j] = binsizez; stencil_range = stencil_cut[i][j]; @@ -312,17 +331,17 @@ void NStencil::create_setup() sz = static_cast (stencil_range*bininvz); if (sz*binsizez < stencil_range) sz++; - sx_multi_tiered[i][j] = sx; - sy_multi_tiered[i][j] = sy; - sz_multi_tiered[i][j] = sz; + sx_multi2[i][j] = sx; + sy_multi2[i][j] = sy; + sz_multi2[i][j] = sz; smax = ((2*sx+1) * (2*sy+1) * (2*sz+1)); - if (smax > maxstencil_multi_tiered[i][j]) { - maxstencil_multi_tiered[i][j] = smax; - memory->destroy(stencil_multi_tiered[i][j]); - memory->create(stencil_multi_tiered[i][j], smax, - "neighstencil::stencil_multi_tiered"); + if (smax > maxstencil_multi2[i][j]) { + maxstencil_multi2[i][j] = smax; + memory->destroy(stencil_multi2[i][j]); + memory->create(stencil_multi2[i][j], smax, + "neighstencil::stencil_multi2"); } } } @@ -363,10 +382,18 @@ double NStencil::memory_usage() } else if (neighstyle == Neighbor::MULTI) { bytes += atom->ntypes*maxstencil_multi * sizeof(int); bytes += atom->ntypes*maxstencil_multi * sizeof(double); - } else if (neighstyle == Neighbor::MULTI_TIERED) { - bytes += atom->ntypes*maxstencil_multi * sizeof(int); - bytes += atom->ntypes*maxstencil_multi * sizeof(int); - bytes += atom->ntypes*maxstencil_multi * sizeof(double); + } else if (neighstyle == Neighbor::MULTI2) { + int n = atom->ntypes; + for (i = 1; i <= n; ++i) { + for (j = 1; j <= n; ++j) { + bytes += maxstencil_multi2[i][j] * sizeof(int); + bytes += maxstencil_multi2[i][j] * sizeof(int); + bytes += maxstencil_multi2[i][j] * sizeof(double); + } + } + bytes += 2 * n * n * sizeof(bool); + bytes += 6 * n * n * sizeof(int); + bytes += 4 * n * n * sizeof(double); } return bytes; } diff --git a/src/nstencil.h b/src/nstencil.h index 58c39ee13c..7c6a04a56a 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -29,14 +29,17 @@ class NStencil : protected Pointers { int **stencilxyz; // bin offsets in xyz dims int *nstencil_multi; // # bins in each type-based multi stencil int **stencil_multi; // list of bin offsets in each stencil - int ** nstencil_multi_tiered; // # bins bins in each itype-jtype tiered multi stencil - int *** stencil_multi_tiered; // list of bin offsets in each tiered multi stencil - int ** maxstencil_type; // max double **distsq_multi; // sq distances to bins in each stencil + int ** nstencil_multi2; // # bins bins in each itype-jtype multi2 stencil + int *** stencil_multi2; // list of bin offsets in each multi2 stencil + int ** maxstencil_multi2; // max stencil size for each multi2 stencil + + ^do i need a multi 2 analog to distsq_multi? + int sx,sy,sz; // extent of stencil in each dim - int **sx_multi_tiered; // analogs for multi tiered - int **sy_multi_tiered; - int **sz_multi_tiered; + int **sx_multi2; // analogs for multi tiered + int **sy_multi2; + int **sz_multi2; double cutoff_custom; // cutoff set by requestor @@ -75,9 +78,9 @@ class NStencil : protected Pointers { // analogs for multi-tiered - double **binsizex_multi_tiered; - double **binsizey_multi_tiered; - double **binsizez_multi_tiered; + double **binsizex_multi2; + double **binsizey_multi2; + double **binsizez_multi2; // data common to all NStencil variants @@ -94,7 +97,7 @@ class NStencil : protected Pointers { // methods for multi/tiered NStencil - void copy_bin_info_multi_tiered(int); // copy mult/tiered info from NBin class + void copy_bin_info_multi2(int); // copy mult/tiered info from NBin class void set_stencil_properties(); // determine which stencils to build and how }; diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp new file mode 100644 index 0000000000..f62cddb0b5 --- /dev/null +++ b/src/nstencil_full_multi2_2d.cpp @@ -0,0 +1,97 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nstencil_full_multi2_2d.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilFullMulti22d::NStencilFullMulti22d(LAMMPS *lmp) : NStencil(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void NStencilFullMulti22d::set_stencil_properties() +{ + int n = atom->ntypes; + int i, j; + + // like -> like => use half stencil + for (i = 1; i <= n; i++) { + stencil_half[i][i] = 0; + stencil_skip[i][i] = 0; + stencil_bin_type[i][i] = i; + stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + } + + // smaller -> larger => use existing newtoff stencil in larger bin + // larger -> smaller => use multi-like stencil for small-large in smaller bin + // If types are same cutoff, use existing like-like stencil. + + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { + if(i == j) continue; + + stencil_half[i][j] = 0; + stencil_skip[i][j] = 0; + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + + if(cuttypesq[i] <= cuttypesq[j]){ + stencil_bin_type[i][j] = i; + } else { + stencil_bin_type[i][j] = j; + } + } + } +} + +/* ---------------------------------------------------------------------- + create stencils based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilFullMulti22d::create() +{ + int itype, jtype, i, j, k, ns; + int n = atom->ntypes; + double cutsq; + + + for (itype = 1; itype <= n; itype++) { + for (jtype = 1; jtype <= n; jtype++) { + if (stencil_skip[itype][jtype]) continue; + + ns = 0; + + sx = sx_multi2[itype][jtype]; + sy = sy_multi2[itype][jtype]; + + mbinx = mbinx_multi2[itype][jtype]; + mbiny = mbiny_multi2[itype][jtype]; + + cutsq = stencil_cut[itype][jtype]; + + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,0) < cutsq) + stencil_type[itype][jtype][ns++] = j*mbinx + i; + + nstencil_multi2[itype][jtype] = ns; + } + } +} diff --git a/src/nstencil_half_multi2_3d_delete_noff.h b/src/nstencil_full_multi2_2d.h similarity index 58% rename from src/nstencil_half_multi2_3d_delete_noff.h rename to src/nstencil_full_multi2_2d.h index bf83a31e9a..1dfc5ae4d6 100644 --- a/src/nstencil_half_multi2_3d_delete_noff.h +++ b/src/nstencil_full_multi2_2d.h @@ -13,32 +13,27 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bytype/3d/newtoff, - NStencilHalfBytype3dNewtoff, - NS_HALF | NS_BYTYPE | NS_3D | NS_NEWTOFF | NS_ORTHO | NS_TRI) +NStencilStyle(full/multi2/2d, + NStencilFullMulti22d, NS_FULL | NS_Multi2 | NS_2D | NS_ORTHO | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTOFF_H -#define LMP_NSTENCIL_HALF_BYTYPE_3D_NEWTOFF_H +#ifndef LMP_NSTENCIL_FULL_MULTI2_2D_H +#define LMP_NSTENCIL_FULL_MULTI2_2D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfBytype3dNewtoff : public NStencil { +class NStencilFullMulti22d : public NStencil { public: - NStencilHalfBytype3dNewtoff(class LAMMPS *); - ~NStencilHalfBytype3dNewtoff(); - void create_setup(); + NStencilFullMulti22d(class LAMMPS *); + ~NStencilFullMulti22d(); void create(); - private: - int ** maxstencil_type; + protected: + void set_stencil_properties(); - void copy_bin_info_bytype(int); - int copy_neigh_info_bytype(int); - void create_newtoff(int, int, double); }; } diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 099e2adeb8..77ae62738c 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_full_bytype_3d.h" +#include "nstencil_full_multi2_3d.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,164 +23,79 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilFullBytype3d::NStencilFullBytype3d(LAMMPS *lmp) : - NStencil(lmp) +NStencilFullMulti23d::NStencilFullMulti23d(LAMMPS *lmp) : NStencil(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void NStencilFullMulti23d::set_stencil_properties() { - maxstencil_type = NULL; -} - -/* ---------------------------------------------------------------------- */ - -NStencilFullBytype3d::~NStencilFullBytype3d() { - - if (maxstencil_type) { - memory->destroy(nstencil_type); - for (int i = 1; i <= atom->ntypes; i++) { - for (int j = 0; j <= atom->ntypes; j++) { - if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); - } - delete [] stencil_type[i]; - } - delete [] stencil_type; - memory->destroy(maxstencil_type); - } -} - - -/* ---------------------------------------------------------------------- */ -INCORPORTE INTO CREATE THEN DELETE, NOTE NAME OF CUTNEIGHMAX ETC -int NStencilFullBytype3d::copy_neigh_info_bytype(int itype) { - - cutneighmaxsq = neighbor->cutneighsq[itype][itype]; - cutneighmax = sqrt(cutneighmaxsq); - cuttypesq = neighbor->cuttypesq; - - // sx,sy,sz = max range of stencil in each dim - // smax = max possible size of entire 3d stencil - // stencil will be empty if cutneighmax = 0.0 - - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - return ((2*sx+1) * (2*sy+1) * (2*sz+1)); -} - -/* ---------------------------------------------------------------------- */ - -void NStencilFullBytype3d::create_setup() -{ - - int itype, jtype; - int maxtypes; - int smax; - - maxtypes = atom->ntypes; - - if (maxstencil_type == NULL) { - memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "BAD A"); - memory->create(nstencil_type, maxtypes+1, maxtypes+1, "BAD B"); - stencil_type = new int**[maxtypes+1](); - for (itype = 1; itype <= maxtypes; ++itype) { - stencil_type[itype] = new int*[maxtypes+1](); - for (jtype = 1; jtype <= maxtypes; ++jtype) { - maxstencil_type[itype][jtype] = 0; - } - } - } MOVE TO PARENT CLASS - - // like -> like => use standard newtoff stencil at bin - - for (itype = 1; itype <= maxtypes; ++itype) { - copy_bin_info_bytype(itype); - smax = copy_neigh_info_bytype(itype); uses cutneighsq[itype][itype] to create s's - if (smax > maxstencil_type[itype][itype]) { - maxstencil_type[itype][itype] = smax; - memory->destroy(stencil_type[itype][itype]); - memory->create(stencil_type[itype][itype], smax, - "NStencilFullBytype::create_steup() stencil"); - } - create_newtoff(itype, itype, cutneighmaxsq); + int n = atom->ntypes; + int i, j; + + // like -> like => use half stencil + for (i = 1; i <= n; i++) { + stencil_half[i][i] = 0; + stencil_skip[i][i] = 0; + stencil_bin_type[i][i] = i; + stencil_cut[i][i] = sqrt(cutneighsq[i][i]); } // smaller -> larger => use existing newtoff stencil in larger bin // larger -> smaller => use multi-like stencil for small-large in smaller bin // If types are same cutoff, use existing like-like stencil. - for (itype = 1; itype <= maxtypes; ++itype) { - for (jtype = 1; jtype <= maxtypes; ++jtype) { - if (itype == jtype) continue; - if (cuttypesq[itype] <= cuttypesq[jtype]) { This does work to say which prticle is smller - // Potential destroy/create problem? - nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; - stencil_type[itype][jtype] = stencil_type[jtype][jtype]; - } - else { - copy_bin_info_bytype(jtype); - // smax = copy_neigh_info_bytype(jtype); + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { + if(i == j) continue; - cutneighmaxsq = cuttypesq[jtype]; Does it need to be this big? Can't I use cutneighsq[i][j]? - cutneighmax = sqrt(cutneighmaxsq); - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - smax = (2*sx+1) * (2*sy+1) * (2*sz+1); - if (smax > maxstencil_type[itype][jtype]) { - maxstencil_type[itype][jtype] = smax; - memory->destroy(stencil_type[itype][jtype]); - memory->create(stencil_type[itype][jtype], smax, "Bad C"); - } - create_newtoff(itype, jtype, cuttypesq[jtype]); + stencil_half[i][j] = 0; + stencil_skip[i][j] = 0; + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + + if(cuttypesq[i] <= cuttypesq[j]){ + stencil_bin_type[i][j] = i; + } else { + stencil_bin_type[i][j] = j; } } } - - //for (itype = 1; itype <= maxtypes; itype++) { - // for (jtype = 1; jtype <= maxtypes; jtype++) { - // printf("i j n %d %d %d\n", itype, jtype, nstencil_type[itype][jtype]); - // printf("i j n %d %d %d\n", itype, jtype, maxstencil_type[itype][jtype]); - // } - // } - -} - -/* ---------------------------------------------------------------------- */ - -void NStencilFullBytype3d::create_newtoff(int itype, int jtype, double cutsq) { - - int i, j, k, ns; - - ns = 0; - - for (k = -sz; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - - nstencil_type[itype][jtype] = ns; } /* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff + create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilFullBytype3d::create() +void NStencilFullMulti23d::create() { - //int i,j,k; - - //nstencil = 0; - - //for (k = -sz; k <= sz; k++) - // for (j = -sy; j <= sy; j++) - // for (i = -sx; i <= sx; i++) - // if (bin_distance(i,j,k) < cutneighmaxsq) - // stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i; + int itype, jtype, i, j, k, ns; + int n = atom->ntypes; + double cutsq; + + + for (itype = 1; itype <= n; itype++) { + for (jtype = 1; jtype <= n; jtype++) { + if (stencil_skip[itype][jtype]) continue; + + ns = 0; + + sx = sx_multi2[itype][jtype]; + sy = sy_multi2[itype][jtype]; + sz = sz_multi2[itype][jtype]; + + mbinx = mbinx_multi2[itype][jtype]; + mbiny = mbiny_multi2[itype][jtype]; + mbinz = mbinz_multi2[itype][jtype]; + + cutsq = stencil_cut[itype][jtype]; + + for (k = -sz; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = + k*mbiny*mbinx + j*mbinx + i; + + nstencil_multi2[itype][jtype] = ns; + } + } } diff --git a/src/nstencil_full_multi2_3d.h b/src/nstencil_full_multi2_3d.h index 48bdfd2611..f7baefc8e9 100644 --- a/src/nstencil_full_multi2_3d.h +++ b/src/nstencil_full_multi2_3d.h @@ -13,30 +13,26 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(full/multi/tiered/3d, - NStencilFullMultiTiered3d, NS_FULL | NS_Multi_Tiered | NS_3D | NS_ORTHO | NS_TRI) +NStencilStyle(full/multi2/3d, + NStencilFullMulti23d, NS_FULL | NS_Multi2 | NS_3D | NS_ORTHO | NS_TRI) #else -#ifndef LMP_NSTENCIL_FULL_MULTI_TIERED_3D_H -#define LMP_NSTENCIL_FULL_MULTI_TIERED_3D_H +#ifndef LMP_NSTENCIL_FULL_MULTI2_3D_H +#define LMP_NSTENCIL_FULL_MULTI2_3D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilFullBytype3d : public NStencil { +class NStencilFullMulti23d : public NStencil { public: - NStencilFullBytype3d(class LAMMPS *); - ~NStencilFullBytype3d(); + NStencilFullMulti23d(class LAMMPS *); + ~NStencilFullMulti23d(); void create(); - void create_setup(); -private: - int ** maxstencil_type; - - int copy_neigh_info_bytype(int); - void create_newtoff(int, int, double); + protected: + void set_stencil_properties(); }; diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp new file mode 100644 index 0000000000..86da6ea91e --- /dev/null +++ b/src/nstencil_half_multi2_2d.cpp @@ -0,0 +1,111 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nstencil_half_multi2_2d.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfMulti22d::NStencilHalfMulti23d(LAMMPS *lmp) : + NStencil(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfMulti23d::set_stencil_properties() +{ + int n = atom->ntypes; + int i, j; + + // like -> like => use half stencil + for (i = 1; i <= n; i++) { + stencil_half[i][i] = 1; + stencil_skip[i][i] = 0; + stencil_bin_type[i][i] = i; + stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + } + + // Cross types: use full stencil, looking one way through hierarchy + // smaller -> larger => use full stencil in larger bin + // larger -> smaller => no nstecil required + // If cut offs are same, use existing type-type stencil + + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { + if(i == j) continue; + if(cuttypesq[i] > cuttypesq[j]) continue; + + stencil_skip[i][j] = 0; + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + + if(cuttypesq[i] == cuttypesq[j]){ + stencil_half[i][j] = 1; + stencil_bin_type[i][j] = i; + } else { + stencil_half[i][j] = 0; + stencil_bin_type[i][j] = j; + } + } + } +} + +/* ---------------------------------------------------------------------- + create stencils based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfMulti23d::create() +{ + int itype, jtype, i, j, ns; + int n = atom->ntypes; + double cutsq; + + + for (itype = 1; itype <= n; itype++) { + for (jtype = 1; jtype <= n; jtype++) { + if (stencil_skip[itype][jtype]) continue; + + ns = 0; + + sx = sx_multi2[itype][jtype]; + sy = sy_multi2[itype][jtype]; + + mbinx = mbinx_multi2[itype][jtype]; + mbiny = mbiny_multi2[itype][jtype]; + + cutsq = stencil_cut[itype][jtype]; + + if (stencil_half[itype][jtype]) { + for (j = 0; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (j > 0 || (j == 0 && i > 0)) { + if (bin_distance(i,j,0) < cutsq) + stencil_type[itype][jtype][ns++] = j*mbinx + i; + } + } else { + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,0) < cutsq) + stencil_type[itype][jtype][ns++] = j*mbinx + i; + } + + nstencil_multi2[itype][jtype] = ns; + } + } +} + diff --git a/src/nstencil_half_multi2_2d.h b/src/nstencil_half_multi2_2d.h new file mode 100644 index 0000000000..ba3a471833 --- /dev/null +++ b/src/nstencil_half_multi2_2d.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/multi2/2d, + NStencilHalfMulti22d, NS_HALF | NS_MULTI2 | NS_2D | NS_ORTHO) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI2_2D_H +#define LMP_NSTENCIL_HALF_MULTI2_2D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti22d : public NStencil { + public: + NStencilHalfMulti22d(class LAMMPS *); + ~NStencilHalfMulti22d(); + void create(); + + protected: + void set_stencil_properties(); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp new file mode 100755 index 0000000000..46f55300ce --- /dev/null +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -0,0 +1,108 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nstencil_half_multi2_2d_tri.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfMulti22dTri::NStencilHalfMulti22d(LAMMPS *lmp) : + NStencil(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfMulti22d::set_stencil_properties() +{ + int n = atom->ntypes; + int i, j; + + // like -> like => use half stencil + for (i = 1; i <= n; i++) { + stencil_half[i][i] = 1; + stencil_skip[i][i] = 0; + stencil_bin_type[i][i] = i; + stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + } + + // Cross types: use full stencil, looking one way through hierarchy + // smaller -> larger => use full stencil in larger bin + // larger -> smaller => no nstecil required + // If cut offs are same, use existing type-type stencil + + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { + if(i == j) continue; + if(cuttypesq[i] > cuttypesq[j]) continue; + + stencil_skip[i][j] = 0; + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + + if(cuttypesq[i] == cuttypesq[j]){ + stencil_half[i][j] = 1; + stencil_bin_type[i][j] = i; + } else { + stencil_half[i][j] = 0; + stencil_bin_type[i][j] = j; + } + } + } +} + +/* ---------------------------------------------------------------------- + create stencils based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfMulti22d::create() +{ + int itype, jtype, i, j, ns; + int n = atom->ntypes; + double cutsq; + + + for (itype = 1; itype <= n; itype++) { + for (jtype = 1; jtype <= n; jtype++) { + if (stencil_skip[itype][jtype]) continue; + + ns = 0; + + sx = sx_multi2[itype][jtype]; + sy = sy_multi2[itype][jtype]; + + mbinx = mbinx_multi2[itype][jtype]; + mbiny = mbiny_multi2[itype][jtype]; + + cutsq = stencil_cut[itype][jtype]; + + if (stencil_half[itype][jtype]) { + for (j = 0; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,0) < cutsq) + stencil_type[itype][jtype][ns++] = j*mbinx + i; + } else { + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,0) < cutsq) + stencil_type[itype][jtype][ns++] = j*mbinx + i; + } + + nstencil_multi2[itype][jtype] = ns; + } + } +} diff --git a/src/nstencil_half_multi2_2d_tri.h b/src/nstencil_half_multi2_2d_tri.h new file mode 100755 index 0000000000..1d25e56776 --- /dev/null +++ b/src/nstencil_half_multi2_2d_tri.h @@ -0,0 +1,45 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/multi2/2d/tri, + NStencilHalfMulti22dTri, NS_HALF | NS_MULTI2 | NS_2D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI2_2D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI2_2D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti22dTri : public NStencil { + public: + NStencilHalfMulti22dTri(class LAMMPS *); + ~NStencilHalfMulti22dTri(); + void create(); + + protected: + void set_stencil_properties(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index 7fc53fe762..02a65bd3a1 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bytype_3d_newton.h" +#include "nstencil_half_multi2_3d.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,183 +23,95 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBytype3dNewton::NStencilHalfBytype3dNewton(LAMMPS *lmp) : - NStencil(lmp) +NStencilHalfMulti23d::NStencilHalfMulti23d(LAMMPS *lmp) : + NStencil(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfMulti23d::set_stencil_properties() { - maxstencil_type = NULL; -} - -/* ---------------------------------------------------------------------- */ - -NStencilHalfBytype3dNewton::~NStencilHalfBytype3dNewton() { - - memory->destroy(nstencil_type); - for (int i = 1; i <= atom->ntypes; i++) { - for (int j = 0; j <= atom->ntypes; j++) { - if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); - } - delete [] stencil_type[i]; - } - delete [] stencil_type; - memory->destroy(maxstencil_type); -} - -/* ---------------------------------------------------------------------- */ - -// KS To superclass -void NStencilHalfBytype3dNewton::copy_bin_info_bytype(int itype) { - - mbinx = nb->mbinx_type[itype]; - mbiny = nb->mbiny_type[itype]; - mbinz = nb->mbinz_type[itype]; - binsizex = nb->binsizex_type[itype]; - binsizey = nb->binsizey_type[itype]; - binsizez = nb->binsizez_type[itype]; - bininvx = nb->bininvx_type[itype]; - bininvy = nb->bininvy_type[itype]; - bininvz = nb->bininvz_type[itype]; -} - -/* ---------------------------------------------------------------------- */ - -// KS To superclass? -int NStencilHalfBytype3dNewton::copy_neigh_info_bytype(int itype) { - - cutneighmaxsq = neighbor->cutneighsq[itype][itype]; - cutneighmax = sqrt(cutneighmaxsq); - cuttypesq = neighbor->cuttypesq; - - // sx,sy,sz = max range of stencil in each dim - // smax = max possible size of entire 3d stencil - // stencil will be empty if cutneighmax = 0.0 - - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - return ((2*sx+1) * (2*sy+1) * (2*sz+1)); -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewton::create_setup() -{ - - int itype, jtype; - int maxtypes; - int smax; - - // maxstencil_type to superclass? - maxtypes = atom->ntypes; - - if (maxstencil_type == NULL) { - memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "maxstencil_type"); - memory->create(nstencil_type, maxtypes+1, maxtypes+1, "nstencil_type"); - stencil_type = new int**[maxtypes+1](); - for (itype = 1; itype <= maxtypes; ++itype) { - stencil_type[itype] = new int*[maxtypes+1](); - for (jtype = 1; jtype <= maxtypes; ++jtype) { - maxstencil_type[itype][jtype] = 0; - nstencil_type[itype][jtype] = 0; - } - } + int n = atom->ntypes; + int i, j; + + // like -> like => use half stencil + for (i = 1; i <= n; i++) { + stencil_half[i][i] = 1; + stencil_skip[i][i] = 0; + stencil_bin_type[i][i] = i; + stencil_cut[i][i] = sqrt(cutneighsq[i][i]); } - // like -> like => use standard Newton stencil at bin - - for (itype = 1; itype <= maxtypes; ++itype) { - copy_bin_info_bytype(itype); - smax = copy_neigh_info_bytype(itype); - if (smax > maxstencil_type[itype][itype]) { - maxstencil_type[itype][itype] = smax; - memory->destroy(stencil_type[itype][itype]); - memory->create(stencil_type[itype][itype], smax, - "NStencilHalfBytypeNewton::create_steup() stencil"); - } - create_newton(itype, itype, cutneighmaxsq); - } - - // Cross types: "Newton on" reached by using Newton off stencil and - // looking one way through hierarchy - // smaller -> larger => use Newton off stencil in larger bin + // Cross types: use full stencil, looking one way through hierarchy + // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstecil required // If cut offs are same, use existing type-type stencil - for (itype = 1; itype <= maxtypes; ++itype) { - for (jtype = 1; jtype <= maxtypes; ++jtype) { - if (itype == jtype) continue; - if (cuttypesq[itype] == cuttypesq[jtype]) { - nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; - stencil_type[itype][jtype] = stencil_type[jtype][jtype]; - } - else if (cuttypesq[itype] < cuttypesq[jtype]) { - copy_bin_info_bytype(jtype); + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { + if(i == j) continue; + if(cuttypesq[i] > cuttypesq[j]) continue; - cutneighmaxsq = cuttypesq[jtype]; - cutneighmax = sqrt(cutneighmaxsq); - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - smax = (2*sx+1) * (2*sy+1) * (2*sz+1); - if (smax > maxstencil_type[itype][jtype]) { - maxstencil_type[itype][jtype] = smax; - memory->destroy(stencil_type[itype][jtype]); - memory->create(stencil_type[itype][jtype], smax, "stencil_type[]"); - } - create_newtoff(itype, jtype, cuttypesq[jtype]); + stencil_skip[i][j] = 0; + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + + if(cuttypesq[i] == cuttypesq[j]){ + stencil_half[i][j] = 1; + stencil_bin_type[i][j] = i; + } else { + stencil_half[i][j] = 0; + stencil_bin_type[i][j] = j; } } } - -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewton::create_newton(int itype, int jtype, double cutsq) { - - int i, j, k, ns; - - ns = 0; - - for (k = 0; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (k > 0 || j > 0 || (j == 0 && i > 0)) { - if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - } - nstencil_type[itype][jtype] = ns; -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewton::create_newtoff(int itype, int jtype, double cutsq) { - - int i, j, k, ns; - - ns = 0; - - for (k = -sz; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - - nstencil_type[itype][jtype] = ns; } /* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff + create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfBytype3dNewton::create() +void NStencilHalfMulti23d::create() { - // KS. Move "creation" here. + int itype, jtype, i, j, k, ns; + int n = atom->ntypes; + double cutsq; + + + for (itype = 1; itype <= n; itype++) { + for (jtype = 1; jtype <= n; jtype++) { + if (stencil_skip[itype][jtype]) continue; + + ns = 0; + + sx = sx_multi2[itype][jtype]; + sy = sy_multi2[itype][jtype]; + sz = sz_multi2[itype][jtype]; + + mbinx = mbinx_multi2[itype][jtype]; + mbiny = mbiny_multi2[itype][jtype]; + mbinz = mbinz_multi2[itype][jtype]; + + cutsq = stencil_cut[itype][jtype]; + + if (stencil_half[itype][jtype]) { + for (k = 0; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (k > 0 || j > 0 || (j == 0 && i > 0)) { + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = + k*mbiny*mbinx + j*mbinx + i; + } + } else { + for (k = -sz; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = + k*mbiny*mbinx + j*mbinx + i; + } + + nstencil_multi2[itype][jtype] = ns; + } + } } + diff --git a/src/nstencil_half_multi2_3d.h b/src/nstencil_half_multi2_3d.h index e39db1c1e1..9cae8269cb 100644 --- a/src/nstencil_half_multi2_3d.h +++ b/src/nstencil_half_multi2_3d.h @@ -13,32 +13,27 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bytype/3d, - NStencilHalfBytype3dNewton, NS_HALF | NS_BYTYPE | NS_3D | NS_ORTHO) +NStencilStyle(half/multi2/3d, + NStencilHalfMulti23d, NS_HALF | NS_MULTI2 | NS_3D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_H -#define LMP_NSTENCIL_HALF_BYTYPE_3D_H +#ifndef LMP_NSTENCIL_HALF_MULTI2_3D_H +#define LMP_NSTENCIL_HALF_MULTI2_3D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfBytype3dNewton : public NStencil { +class NStencilHalfMulti23d : public NStencil { public: - NStencilHalfBytype3dNewton(class LAMMPS *); - ~NStencilHalfBytype3dNewton(); - void create_setup(); + NStencilHalfMulti23d(class LAMMPS *); + ~NStencilHalfMulti23d(); void create(); - private: - int ** maxstencil_type; + protected: + void set_stencil_properties(); - void copy_bin_info_bytype(int); - int copy_neigh_info_bytype(int); - void create_newton(int, int, double); - void create_newtoff(int, int, double); }; } diff --git a/src/nstencil_half_multi2_3d_delete_noff.cpp b/src/nstencil_half_multi2_3d_delete_noff.cpp deleted file mode 100644 index fedc8060ce..0000000000 --- a/src/nstencil_half_multi2_3d_delete_noff.cpp +++ /dev/null @@ -1,198 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_bytype_3d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "nbin.h" -#include "memory.h" -#include "atom.h" -#include - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfBytype3dNewtoff::NStencilHalfBytype3dNewtoff(LAMMPS *lmp) : - NStencil(lmp) -{ - maxstencil_type = NULL; -} - -/* ---------------------------------------------------------------------- */ - -NStencilHalfBytype3dNewtoff::~NStencilHalfBytype3dNewtoff() { - - memory->destroy(nstencil_type); - for (int i = 1; i <= atom->ntypes; i++) { - for (int j = 0; j <= atom->ntypes; j++) { - if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); - } - delete [] stencil_type[i]; - } - delete [] stencil_type; - memory->destroy(maxstencil_type); -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewtoff::copy_bin_info_bytype(int itype) { - - mbinx = nb->mbinx_type[itype]; - mbiny = nb->mbiny_type[itype]; - mbinz = nb->mbinz_type[itype]; - binsizex = nb->binsizex_type[itype]; - binsizey = nb->binsizey_type[itype]; - binsizez = nb->binsizez_type[itype]; - bininvx = nb->bininvx_type[itype]; - bininvy = nb->bininvy_type[itype]; - bininvz = nb->bininvz_type[itype]; -} - -/* ---------------------------------------------------------------------- */ - -int NStencilHalfBytype3dNewtoff::copy_neigh_info_bytype(int itype) { - - cutneighmaxsq = neighbor->cutneighsq[itype][itype]; - cutneighmax = sqrt(cutneighmaxsq); - cuttypesq = neighbor->cuttypesq; - - // sx,sy,sz = max range of stencil in each dim - // smax = max possible size of entire 3d stencil - // stencil will be empty if cutneighmax = 0.0 - - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - return ((2*sx+1) * (2*sy+1) * (2*sz+1)); -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewtoff::create_setup() -{ - - int itype, jtype; - int maxtypes; - int smax; - - maxtypes = atom->ntypes; - - if (maxstencil_type == NULL) { - memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "BAD A"); - memory->create(nstencil_type, maxtypes+1, maxtypes+1, "BAD B"); - stencil_type = new int**[maxtypes+1](); - for (itype = 1; itype <= maxtypes; ++itype) { - stencil_type[itype] = new int*[maxtypes+1](); - for (jtype = 1; jtype <= maxtypes; ++jtype) { - maxstencil_type[itype][jtype] = 0; - } - } - } - - // like -> like => use standard newtoff stencil at bin - - for (itype = 1; itype <= maxtypes; ++itype) { - copy_bin_info_bytype(itype); - smax = copy_neigh_info_bytype(itype); - if (smax > maxstencil_type[itype][itype]) { - maxstencil_type[itype][itype] = smax; - memory->destroy(stencil_type[itype][itype]); - memory->create(stencil_type[itype][itype], smax, - "NStencilHalfBytypeNewtoff::create_steup() stencil"); - } - create_newtoff(itype, itype, cutneighmaxsq); - } - - // smaller -> larger => use existing newtoff stencil in larger bin - // larger -> smaller => use multi-like stencil for small-large in smaller bin - // If types are same cutoff, use existing like-like stencil. - - for (itype = 1; itype <= maxtypes; ++itype) { - for (jtype = 1; jtype <= maxtypes; ++jtype) { - if (itype == jtype) continue; - if (cuttypesq[itype] <= cuttypesq[jtype]) { - // Potential destroy/create problem? - nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; - stencil_type[itype][jtype] = stencil_type[jtype][jtype]; - } - else { - copy_bin_info_bytype(jtype); - // smax = copy_neigh_info_bytype(jtype); - - cutneighmaxsq = cuttypesq[jtype]; - cutneighmax = sqrt(cutneighmaxsq); - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - smax = (2*sx+1) * (2*sy+1) * (2*sz+1); - if (smax > maxstencil_type[itype][jtype]) { - maxstencil_type[itype][jtype] = smax; - memory->destroy(stencil_type[itype][jtype]); - memory->create(stencil_type[itype][jtype], smax, "Bad C"); - } - create_newtoff(itype, jtype, cuttypesq[jtype]); - } - } - } - - //for (itype = 1; itype <= maxtypes; itype++) { - // for (jtype = 1; jtype <= maxtypes; jtype++) { - // printf("i j n %d %d %d\n", itype, jtype, nstencil_type[itype][jtype]); - // printf("i j n %d %d %d\n", itype, jtype, maxstencil_type[itype][jtype]); - // } - // } - -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewtoff::create_newtoff(int itype, int jtype, double cutsq) { - - int i, j, k, ns; - - ns = 0; - - for (k = -sz; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - - nstencil_type[itype][jtype] = ns; -} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewtoff::create() -{ - //int i,j,k; - - //nstencil = 0; - - //for (k = -sz; k <= sz; k++) - // for (j = -sy; j <= sy; j++) - // for (i = -sx; i <= sx; i++) - // if (bin_distance(i,j,k) < cutneighmaxsq) - // stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i; -} diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index f1ab713725..bcaf22abbd 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bytype_3d_newton.h" +#include "nstencil_half_multi2_3d_tri.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,31 +23,100 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBytype3dNewton::NStencilHalfBytype3dNewton(LAMMPS *lmp) : - NStencil(lmp) -{ - maxstencil_type = NULL; -} +NStencilHalfMulti23dTri::NStencilHalfMulti23d(LAMMPS *lmp) : + NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -NStencilHalfBytype3dNewton::~NStencilHalfBytype3dNewton() { - - memory->destroy(nstencil_type); - for (int i = 1; i <= atom->ntypes; i++) { - for (int j = 0; j <= atom->ntypes; j++) { - if (maxstencil_type[i][j] > 0) memory->destroy(stencil_type[i][j]); - } - delete [] stencil_type[i]; +void NStencilHalfMulti23d::set_stencil_properties() +{ + int n = atom->ntypes; + int i, j; + + // like -> like => use half stencil + for (i = 1; i <= n; i++) { + stencil_half[i][i] = 1; + stencil_skip[i][i] = 0; + stencil_bin_type[i][i] = i; + stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + } + + // Cross types: use full stencil, looking one way through hierarchy + // smaller -> larger => use full stencil in larger bin + // larger -> smaller => no nstecil required + // If cut offs are same, use existing type-type stencil + + for (i = 1; i <= n; i++) { + for (j = 1; j <= n; j++) { + if(i == j) continue; + if(cuttypesq[i] > cuttypesq[j]) continue; + + stencil_skip[i][j] = 0; + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + + if(cuttypesq[i] == cuttypesq[j]){ + stencil_half[i][j] = 1; + stencil_bin_type[i][j] = i; + } else { + stencil_half[i][j] = 0; + stencil_bin_type[i][j] = j; + } + } + } +} + +/* ---------------------------------------------------------------------- + create stencils based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfMulti23d::create() +{ + int itype, jtype, i, j, k, ns; + int n = atom->ntypes; + double cutsq; + + + for (itype = 1; itype <= n; itype++) { + for (jtype = 1; jtype <= n; jtype++) { + if (stencil_skip[itype][jtype]) continue; + + ns = 0; + + sx = sx_multi2[itype][jtype]; + sy = sy_multi2[itype][jtype]; + sz = sz_multi2[itype][jtype]; + + mbinx = mbinx_multi2[itype][jtype]; + mbiny = mbiny_multi2[itype][jtype]; + mbinz = mbinz_multi2[itype][jtype]; + + cutsq = stencil_cut[itype][jtype]; + + if (stencil_half[itype][jtype]) { + for (k = 0; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = + k*mbiny*mbinx + j*mbinx + i; + } else { + for (k = -sz; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,k) < cutsq) + stencil_type[itype][jtype][ns++] = + k*mbiny*mbinx + j*mbinx + i; + } + + nstencil_multi2[itype][jtype] = ns; + } } - delete [] stencil_type; - memory->destroy(maxstencil_type); } /* ---------------------------------------------------------------------- */ // KS To superclass -void NStencilHalfBytype3dNewton::copy_bin_info_bytype(int itype) { +void NStencilHalfMulti23d::copy_bin_info_bytype(int itype) { mbinx = nb->mbinx_type[itype]; mbiny = nb->mbiny_type[itype]; @@ -63,7 +132,7 @@ void NStencilHalfBytype3dNewton::copy_bin_info_bytype(int itype) { /* ---------------------------------------------------------------------- */ // KS To superclass? -int NStencilHalfBytype3dNewton::copy_neigh_info_bytype(int itype) { +int NStencilHalfMulti23d::copy_neigh_info_bytype(int itype) { cutneighmaxsq = neighbor->cutneighsq[itype][itype]; cutneighmax = sqrt(cutneighmaxsq); @@ -85,7 +154,7 @@ int NStencilHalfBytype3dNewton::copy_neigh_info_bytype(int itype) { /* ---------------------------------------------------------------------- */ -void NStencilHalfBytype3dNewton::create_setup() +void NStencilHalfMulti23d::create_setup() { int itype, jtype; @@ -157,47 +226,4 @@ void NStencilHalfBytype3dNewton::create_setup() } } } - -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewton::create_newton(int itype, int jtype, double cutsq) { - - int i, j, k, ns; - - ns = 0; - - for (k = 0; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - nstencil_type[itype][jtype] = ns; -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewton::create_newtoff(int itype, int jtype, double cutsq) { - - int i, j, k, ns; - - ns = 0; - - for (k = -sz; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - - nstencil_type[itype][jtype] = ns; -} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfBytype3dNewton::create() -{ - // KS. Move "creation" here. } diff --git a/src/nstencil_half_multi2_3d_tri.h b/src/nstencil_half_multi2_3d_tri.h index 5424d73f11..f4b37ebebe 100755 --- a/src/nstencil_half_multi2_3d_tri.h +++ b/src/nstencil_half_multi2_3d_tri.h @@ -13,32 +13,26 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bytype/3d, - NStencilHalfBytype3d, NS_HALF | NS_BYTYPE | NS_3D | NS_TRI) +NStencilStyle(half/multi2/3d/tri, + NStencilHalfMulti23dTri, NS_HALF | NS_MULTI2 | NS_3D | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_BYTYPE_3D_H -#define LMP_NSTENCIL_HALF_BYTYPE_3D_H +#ifndef LMP_NSTENCIL_HALF_MULTI2_3D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI2_3D_TRI_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfBytype3dNewton : public NStencil { +class NStencilHalfMulti23dTri : public NStencil { public: - NStencilHalfBytype3dNewton(class LAMMPS *); - ~NStencilHalfBytype3dNewton(); - void create_setup(); + NStencilHalfMulti23dTri(class LAMMPS *); + ~NStencilHalfMulti23dTri(); void create(); - private: - int ** maxstencil_type; - - void copy_bin_info_bytype(int); - int copy_neigh_info_bytype(int); - void create_newton(int, int, double); - void create_newtoff(int, int, double); + protected: + void set_stencil_properties(); }; } From bdc21c87b211f6f08be703471c3d4bee5934bc89 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 10 Nov 2020 20:15:54 -0700 Subject: [PATCH 0017/1217] Clarifying multi2 stencil label --- src/nstencil.cpp | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 525369d573..b7cfe4dc72 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -53,9 +53,10 @@ using namespace LAMMPS_NS; no versions that allow ghost on (any need for it?) for multi2: create one stencil for each itype-jtype pairing - stencils do not generally follow the same rules for half/full or newton on/off - full stencils including all surrounding bins are always used except - for same-type stencils with newton on which uses a half stencil + the full/half stencil label refers to the same-type stencil + a half list with newton on has a half same-type stencil + a full list or half list with newton of has a full same-type stencil + cross type stencils are always full to allow small-to-large lookups for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin for triclinic, a half stencil includes bins in the z (3D) or y (2D) plane of self and above cutoff is not cutneighmaxsq, but max cutoff for that atom type From 061229093cb7c28058fdbdcff2fd13c9226d78de Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 10 Nov 2020 22:44:55 -0700 Subject: [PATCH 0018/1217] Adding npair classes --- src/npair.cpp | 65 +++++ src/npair.h | 14 ++ ...multi_tiered.cpp => npair_full_multi2.cpp} | 83 ++++--- ...ull_multi_tiered.h => npair_full_multi2.h} | 16 +- src/npair_half_multi2_newtoff.cpp | 143 +++++++++++ src/npair_half_multi2_newtoff.h | 47 ++++ src/npair_half_multi2_newton.cpp | 225 +++++++++--------- src/npair_half_multi2_newton.h | 16 +- src/npair_half_multi2_newton_tri.cpp | 172 +++++++------ src/npair_half_multi2_newton_tri.h | 16 +- src/npair_half_size_multi2_newtoff.cpp | 68 +++--- src/npair_half_size_multi2_newtoff.h | 16 +- src/npair_half_size_multi2_newton.cpp | 183 +++++++------- src/npair_half_size_multi2_newton.h | 16 +- src/npair_half_size_multi2_newton_tri.cpp | 145 ++++++----- src/npair_half_size_multi2_newton_tri.h | 16 +- src/nstencil.h | 4 +- 17 files changed, 738 insertions(+), 507 deletions(-) rename src/{npair_full_multi_tiered.cpp => npair_full_multi2.cpp} (63%) rename src/{npair_full_multi_tiered.h => npair_full_multi2.h} (75%) create mode 100755 src/npair_half_multi2_newtoff.cpp create mode 100755 src/npair_half_multi2_newtoff.h diff --git a/src/npair.cpp b/src/npair.cpp index 698ff28067..920728a692 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -134,6 +134,25 @@ void NPair::copy_bin_info() atom2bin = nb->atom2bin; bins = nb->bins; binhead = nb->binhead; + + nbinx_multi2 = nb->nbinx_multi2; + nbiny_multi2 = nb->nbiny_multi2; + nbinz_multi2 = nb->nbinz_multi2; + mbins_multi2 = nb->mbins_multi2; + mbinx_multi2 = nb->mbinx_multi2; + mbiny_multi2 = nb->mbiny_multi2; + mbinz_multi2 = nb->mbinz_multi2; + mbinxlo_multi2 = nb->mbinxlo_multi2; + mbinylo_multi2 = nb->mbinylo_multi2; + mbinzlo_multi2 = nb->mbinzlo_multi2; + + bininvx_multi2 = nb->bininvx_multi2; + bininvy_multi2 = nb->bininvy_multi2; + bininvz_multi2 = nb->bininvz_multi2; + + atom2bin_multi2 = nb->atom2bin_multi2; + bins_multi2 = nb->bins_multi2; + binhead_multi2 = nb->binhead_multi2; } /* ---------------------------------------------------------------------- @@ -148,6 +167,9 @@ void NPair::copy_stencil_info() nstencil_multi = ns->nstencil_multi; stencil_multi = ns->stencil_multi; distsq_multi = ns->distsq_multi; + + nstencil_multi2 = ns->nstencil_multi2; + stencil_multi2 = ns->stencil_multi2; } /* ---------------------------------------------------------------------- @@ -241,3 +263,46 @@ int NPair::coord2bin(double *x, int &ix, int &iy, int &iz) return iz*mbiny*mbinx + iy*mbinx + ix; } + +/* ---------------------------------------------------------------------- + same as coord2bin in NbinMulti2 +------------------------------------------------------------------------- */ + +int NPair::coord2bin(double *x, int it) +{ + int ix,iy,iz; + int ibin; + + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) + error->one(FLERR,"Non-numeric positions - simulation unstable"); + + if (x[0] >= bboxhi[0]) + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi2[it]) + nbinx_multi2[it]; + else if (x[0] >= bboxlo[0]) { + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]); + ix = MIN(ix,nbinx_multi2[it]-1); + } else + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]) - 1; + + if (x[1] >= bboxhi[1]) + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi2[it]) + nbiny_multi2[it]; + else if (x[1] >= bboxlo[1]) { + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]); + iy = MIN(iy,nbiny_multi2[it]-1); + } else + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]) - 1; + + if (x[2] >= bboxhi[2]) + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi2[it]) + nbinz_multi2[it]; + else if (x[2] >= bboxlo[2]) { + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]); + iz = MIN(iz,nbinz_multi2[it]-1); + } else + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]) - 1; + + + ibin = (iz-mbinzlo_multi2[it])*mbiny_multi2[it]*mbinx_multi2[it] + + (iy-mbinylo_multi2[it])*mbinx_multi2[it] + + (ix-mbinxlo_multi2[it]); + return ibin; +} \ No newline at end of file diff --git a/src/npair.h b/src/npair.h index ec75042302..87b2584521 100644 --- a/src/npair.h +++ b/src/npair.h @@ -79,6 +79,14 @@ class NPair : protected Pointers { int *atom2bin,*bins; int *binhead; + int *nbinx_multi2, *nbiny_multi2, *nbinz_multi2; + int *mbins_multi2; + int *mbinx_multi2, *mbiny_multi2, *mbinz_multi2; + int *mbinxlo_multi2, *mbinylo_multi2, *mbinzlo_multi2; + double *bininvx_multi2, *bininvy_multi2, *bininvz_multi2; + int **binhead_multi2,**bins_multi2; + int **atom2bin_multi2; + // data from NStencil class int nstencil; @@ -88,6 +96,9 @@ class NPair : protected Pointers { int **stencil_multi; double **distsq_multi; + int ** nstencil_multi2; + int *** stencil_multi2; + // data common to all NPair variants int molecular; @@ -102,6 +113,9 @@ class NPair : protected Pointers { int coord2bin(double *); // mapping atom coord to a bin int coord2bin(double *, int &, int &, int&); // ditto + int coord2bin(double *, int); // mapping atom coord to type bin + + // find_special: determine if atom j is in special list of atom i // if it is not, return 0 // if it is and special flag is 0 (both coeffs are 0.0), return -1 diff --git a/src/npair_full_multi_tiered.cpp b/src/npair_full_multi2.cpp similarity index 63% rename from src/npair_full_multi_tiered.cpp rename to src/npair_full_multi2.cpp index 3b9a89bb56..4fbdc6148b 100644 --- a/src/npair_full_multi_tiered.cpp +++ b/src/npair_full_multi2.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_full_bytype.h" +#include "npair_full_multi2.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -19,28 +19,27 @@ #include "domain.h" #include "my_page.h" #include "error.h" -#include "nbin.h" -#include "nstencil.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairFullBytype::NPairFullBytype(LAMMPS *lmp) : NPair(lmp) {} +NPairFullMulti2::NPairFullMulti2(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- + REWRITE binned neighbor list construction for all neighbors multi-type stencil is itype dependent and is distance checked every neighbor pair appears in list of both atoms i and j - KS ADJUST ------------------------------------------------------------------------- */ -void NPairFullBytype::build(NeighList *list) +void NPairFullMulti2::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; + int js; double **x = atom->x; int *type = atom->type; @@ -84,48 +83,46 @@ void NPairFullBytype::build(NeighList *list) // skip if i,j neighbor cutoff is less than bin distance // skip i = j - int kbin; - ibin = nb->atom2bin_type[itype][i]; - for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + ibin = atom2bin_multi2[itype][i]; + for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { - kbin = ibin; - } - else { - // Locate i in ktype bin - kbin = nb->coord2bin(x[i], ktype); + kbin = ibin; + } else { + // Locate i in ktype bin + kbin = coord2bin(x[i], ktype); } - s = this->ns->stencil_type[itype][ktype]; - ns = this->ns->nstencil_type[itype][ktype]; + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; for (k = 0; k < ns; k++) { - int js = this->nb->binhead_type[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = this->nb->bins_type[ktype][j]) { - if (i == j) continue; + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if (i == j) continue; - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular != Atom::ATOMIC) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } } } diff --git a/src/npair_full_multi_tiered.h b/src/npair_full_multi2.h similarity index 75% rename from src/npair_full_multi_tiered.h rename to src/npair_full_multi2.h index fdcd6b5fb1..f552e5bf47 100644 --- a/src/npair_full_multi_tiered.h +++ b/src/npair_full_multi2.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(full/bytype, - NPairFullBytype, - NP_FULL | NP_BYTYPE | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) +NPairStyle(full/multi2, + NPairFullMulti2, + NP_FULL | NP_MULTI2 | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_FULL_BYTYPE_H -#define LMP_NPAIR_FULL_BYTYPE_H +#ifndef LMP_NPAIR_FULL_MULTI2_H +#define LMP_NPAIR_FULL_MULTI2_H #include "npair.h" namespace LAMMPS_NS { -class NPairFullBytype : public NPair { +class NPairFullMulti2 : public NPair { public: - NPairFullBytype(class LAMMPS *); - ~NPairFullBytype() {} + NPairFullMulti2(class LAMMPS *); + ~NPairFullMulti2() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi2_newtoff.cpp b/src/npair_half_multi2_newtoff.cpp new file mode 100755 index 0000000000..83a8054247 --- /dev/null +++ b/src/npair_half_multi2_newtoff.cpp @@ -0,0 +1,143 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "npair_half_multi2_newtoff.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "domain.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfMulti2Newtoff::NPairHalfMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + REWRITE + binned neighbor list construction with partial Newton's 3rd law + each owned atom i checks own bin and other bins in stencil + multi-type stencil is itype dependent and is distance checked + pair stored once if i,j are both owned and i < j + pair stored by me if j is ghost (also stored by proc owning j) +------------------------------------------------------------------------- */ + +void NPairHalfMulti2Newtoff::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + int js; + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + if (molecular == Atom::TEMPLATE) moltemplate = 1; + else moltemplate = 0; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // skip if i,j neighbor cutoff is less than bin distance + // stores own/own pairs only once + // stores own/ghost pairs on both procs + + ibin = nb->atom2bin_type[itype][i]; + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + if (itype == ktype) { + kbin = ibin; + } else { + // Locate i in ktype bin + kbin = coord2bin(x[i], ktype); + } + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >=0; j = nb->bins_multi2[ktype][j]) { + if (j <= i) continue; + + jtype = type[j]; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_multi2_newtoff.h b/src/npair_half_multi2_newtoff.h new file mode 100755 index 0000000000..30a6d3164d --- /dev/null +++ b/src/npair_half_multi2_newtoff.h @@ -0,0 +1,47 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/multi2/newtoff, + NPairHalfMulti2Newtoff, + NP_HALF | NP_MULTI2 | NP_NEWTOFF | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI2_NEWTOFF_H +#define LMP_NPAIR_HALF_MULTI2_NEWTOFF_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMulti2Newtoff : public NPair { + public: + NPairHalfMulti2Newtoff(class LAMMPS *); + ~NPairHalfMulti2Newtoff() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + +*/ diff --git a/src/npair_half_multi2_newton.cpp b/src/npair_half_multi2_newton.cpp index 66899564be..58397f645e 100755 --- a/src/npair_half_multi2_newton.cpp +++ b/src/npair_half_multi2_newton.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include "npair_half_bytype_newton.h" -#include "neighbor.h" +#include "npair_half_multi2_newton.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -22,14 +20,11 @@ #include "my_page.h" #include "error.h" -#include "nbin.h" -#include "nstencil.h" - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfBytypeNewton::NPairHalfBytypeNewton(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMulti2Newton::NPairHalfMulti2Newton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- KS REWRTIE @@ -39,12 +34,13 @@ NPairHalfBytypeNewton::NPairHalfBytypeNewton(LAMMPS *lmp) : NPair(lmp) {} every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfBytypeNewton::build(NeighList *list) +void NPairHalfMulti2Newton::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; + int js; double **x = atom->x; int *type = atom->type; @@ -84,129 +80,124 @@ void NPairHalfBytypeNewton::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - int js; - int kbin; - // own type: loop over atoms ahead in bin, including ghosts at end of list // if j is owned atom, store by virtue of being ahead of i in list // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = nb->atom2bin_type[itype][i]; - - for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + ibin = atom2bin_multi2[itype][i]; + for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { - // own bin ... - js = nb->bins_type[itype][i]; - for (j = js; j >= 0; j = nb->bins_type[itype][j]) { - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + // own bin ... + js = bins_multi2[itype][i]; + for (j = js; j >= 0; j = bins_multi2[itype][j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } } - } - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } - - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = this->ns->stencil_type[itype][itype]; - ns = this->ns->nstencil_type[itype][itype]; - for (k = 0; k < ns; k++) { - js = nb->binhead_type[itype][ibin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[itype][j]) { - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } } - } - } - - } - else { + } else { // smaller -> larger: locate i in the ktype bin structure - kbin = nb->coord2bin(x[i], ktype); - s = this->ns->stencil_type[itype][ktype]; - ns = this->ns->nstencil_type[itype][ktype]; - - for (k = 0; k < ns; k++) { - js = nb->binhead_type[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[ktype][j]) { - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; + kbin = coord2bin(x[i], ktype); + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } } - } - } } } + ilist[inum++] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/npair_half_multi2_newton.h b/src/npair_half_multi2_newton.h index 8be7292219..8037d2e172 100755 --- a/src/npair_half_multi2_newton.h +++ b/src/npair_half_multi2_newton.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/bytype/newton, - NPairHalfBytypeNewton, - NP_HALF | NP_BYTYPE | NP_NEWTON | NP_ORTHO) +NPairStyle(half/multi2/newton, + NPairHalfMulti2Newton, + NP_HALF | NP_MULTI2 | NP_NEWTON | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_BYTYPE_NEWTON_H -#define LMP_NPAIR_HALF_BYTYPE_NEWTON_H +#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_H +#define LMP_NPAIR_HALF_MULTI2_NEWTON_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfBytypeNewton : public NPair { +class NPairHalfMulti2Newton : public NPair { public: - NPairHalfBytypeNewton(class LAMMPS *); - ~NPairHalfBytypeNewton() {} + NPairHalfMulti2Newton(class LAMMPS *); + ~NPairHalfMulti2Newton() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi2_newton_tri.cpp b/src/npair_half_multi2_newton_tri.cpp index 6b28e76789..c741a860f1 100755 --- a/src/npair_half_multi2_newton_tri.cpp +++ b/src/npair_half_multi2_newton_tri.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include "npair_half_bytype_newton_tri.h" -#include "neighbor.h" +#include "npair_half_multi2_newton_tri.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -22,14 +20,11 @@ #include "my_page.h" #include "error.h" -#include "nbin.h" -#include "nstencil.h" - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfBytypeNewtonTri::NPairHalfBytypeNewtonTri(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMulti2NewtonTri::NPairHalfMulti2NewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- KS REWRTIE @@ -39,12 +34,13 @@ NPairHalfBytypeNewtonTri::NPairHalfBytypeNewtonTri(LAMMPS *lmp) : NPair(lmp) {} every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfBytypeNewtonTri::build(NeighList *list) +void NPairHalfMulti2NewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; + int js; double **x = atom->x; int *type = atom->type; @@ -83,101 +79,97 @@ void NPairHalfBytypeNewtonTri::build(NeighList *list) iatom = molatom[i]; tagprev = tag[i] - iatom - 1; } - - int js; - int kbin; - + // own type: loop over atoms ahead in bin, including ghosts at end of list // if j is owned atom, store by virtue of being ahead of i in list // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = nb->atom2bin_type[itype][i]; + ibin = atom2bin_multi2[itype][i]; - for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = this->ns->stencil_type[itype][itype]; - ns = this->ns->nstencil_type[itype][itype]; - for (k = 0; k < ns; k++) { - js = nb->binhead_type[itype][ibin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[itype][j]) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp) { - if (x[j][0] < xtmp) continue; - if (x[j][0] == xtmp && j <= i) continue; - } - } - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][j]) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } } - } - } - - } - else { + } else { // smaller -> larger: locate i in the ktype bin structure - kbin = nb->coord2bin(x[i], ktype); - s = this->ns->stencil_type[itype][ktype]; - ns = this->ns->nstencil_type[itype][ktype]; - - for (k = 0; k < ns; k++) { - js = nb->binhead_type[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[ktype][j]) { - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; + kbin = coord2bin(x[i], ktype); + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } } - } - } } } + ilist[inum++] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/npair_half_multi2_newton_tri.h b/src/npair_half_multi2_newton_tri.h index 0582801028..0787860c52 100755 --- a/src/npair_half_multi2_newton_tri.h +++ b/src/npair_half_multi2_newton_tri.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/bytype/newton/tri, - NPairHalfBytypeNewtonTri, - NP_HALF | NP_BYTYPE | NP_NEWTON | NP_TRI) +NPairStyle(half/multi2/newton/tri, + NPairHalfMulti2NewtonTri, + NP_HALF | NP_MULTI2 | NP_NEWTON | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_BYTYPE_NEWTON_TRI_H -#define LMP_NPAIR_HALF_BYTYPE_NEWTON_TRI_H +#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_H +#define LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfBytypeNewtonTri : public NPair { +class NPairHalfMulti2NewtonTri : public NPair { public: - NPairHalfBytypeNewtonTri(class LAMMPS *); - ~NPairHalfBytypeNewtonTri() {} + NPairHalfMulti2NewtonTri(class LAMMPS *); + ~NPairHalfMulti2NewtonTri() {} void build(class NeighList *); }; diff --git a/src/npair_half_size_multi2_newtoff.cpp b/src/npair_half_size_multi2_newtoff.cpp index 220ae747a7..0ea9e493ce 100644 --- a/src/npair_half_size_multi2_newtoff.cpp +++ b/src/npair_half_size_multi2_newtoff.cpp @@ -12,20 +12,18 @@ es certain rights in this software. This software is distributed under ------------------------------------------------------------------------- */ #include -#include "npair_half_size_bytype_newtoff.h" +#include "npair_half_size_multi2_newtoff.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "my_page.h" #include "error.h" -#include "nbin.h" -#include "nstencil.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeBytypeNewtoff::NPairHalfSizeBytypeNewtoff(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMulti2Newtoff::NPairHalfSizeMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- REWRITE @@ -36,12 +34,13 @@ NPairHalfSizeBytypeNewtoff::NPairHalfSizeBytypeNewtoff(LAMMPS *lmp) : NPair(lmp) pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfSizeBytypeNewtoff::build(NeighList *list) +void NPairHalfSizeMulti2Newtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; + int js; double **x = atom->x; double *radius = atom->radius; @@ -78,41 +77,40 @@ void NPairHalfSizeBytypeNewtoff::build(NeighList *list) // stores own/own pairs only once // stores own/ghost pairs on both procs - int kbin; - ibin = nb->atom2bin_type[itype][i]; - for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { - kbin = ibin; + kbin = ibin; + } else { + // Locate i in ktype bin + kbin = coord2bin(x[i], ktype); } - else { - // Locate i in ktype bin - kbin = nb->coord2bin(x[i], ktype); - } - s = this->ns->stencil_type[itype][ktype]; - ns = this->ns->nstencil_type[itype][ktype]; + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; for (k = 0; k < ns; k++) { - int js = nb->binhead_type[ktype][kbin + s[k]]; - for (j = js; j >=0; j = nb->bins_type[ktype][j]) { - if (j <= i) continue; - jtype = type[j]; + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >=0; j = nb->bins_multi2[ktype][j]) { + if (j <= i) continue; + + jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } } } diff --git a/src/npair_half_size_multi2_newtoff.h b/src/npair_half_size_multi2_newtoff.h index 183bd39fb3..15540666c3 100644 --- a/src/npair_half_size_multi2_newtoff.h +++ b/src/npair_half_size_multi2_newtoff.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/size/bytype/newtoff, - NPairHalfSizeBytypeNewtoff, - NP_HALF | NP_SIZE | NP_BYTYPE | NP_NEWTOFF | NP_ORTHO | NP_TRI) +NPairStyle(half/size/multi2/newtoff, + NPairHalfSizeMulti2Newtoff, + NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTOFF_H -#define LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTOFF_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_H +#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfSizeBytypeNewtoff : public NPair { +class NPairHalfSizeMulti2Newtoff : public NPair { public: - NPairHalfSizeBytypeNewtoff(class LAMMPS *); - ~NPairHalfSizeBytypeNewtoff() {} + NPairHalfSizeMulti2Newtoff(class LAMMPS *); + ~NPairHalfSizeMulti2Newtoff() {} void build(class NeighList *); }; diff --git a/src/npair_half_size_multi2_newton.cpp b/src/npair_half_size_multi2_newton.cpp index 339c4859a6..3b89c259ec 100755 --- a/src/npair_half_size_multi2_newton.cpp +++ b/src/npair_half_size_multi2_newton.cpp @@ -11,21 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include "npair_half_size_bytype_newton.h" +#include "npair_half_size_multi2_newton.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "my_page.h" #include "error.h" -#include "nbin.h" -#include "nstencil.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeBytypeNewton::NPairHalfSizeBytypeNewton(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMulti2Newton::NPairHalfSizeMulti2Newton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- KS REWRTIE @@ -35,9 +32,9 @@ NPairHalfSizeBytypeNewton::NPairHalfSizeBytypeNewton(LAMMPS *lmp) : NPair(lmp) { every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeBytypeNewton::build(NeighList *list) +void NPairHalfSizeMulti2Newton::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -71,110 +68,104 @@ void NPairHalfSizeBytypeNewton::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - int js; - int kbin; - // own type: loop over atoms ahead in bin, including ghosts at end of list // if j is owned atom, store by virtue of being ahead of i in list // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = nb->atom2bin_type[itype][i]; + ibin = nb->atom2bin_multi2[itype][i]; - for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { - // own bin ... - js = nb->bins_type[itype][i]; - for (j = js; j >= 0; j = nb->bins_type[itype][j]) { - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + // own bin ... + js = bins_multi2[itype][i]; + for (j = js; j >= 0; j = bins_multi2[itype][j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } } - } - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } - - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = this->ns->stencil_type[itype][itype]; - ns = this->ns->nstencil_type[itype][itype]; - for (k = 0; k < ns; k++) { - js = nb->binhead_type[itype][ibin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[itype][j]) { - jtype = type[j]; - // KS. CHECK ME if (cutsq[jtype] < distsq[k]) continue; - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][j]) { + jtype = type[j]; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } } - } - } - - } - else { - // KS + } else { // smaller -> larger: locate i in the ktype bin structure - kbin = nb->coord2bin(x[i], ktype); - - s = this->ns->stencil_type[itype][ktype]; - ns = this->ns->nstencil_type[itype][ktype]; - for (k = 0; k < ns; k++) { - js = nb->binhead_type[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[ktype][j]) { - - jtype = type[j]; - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + kbin = coord2bin(x[i], ktype); + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + + jtype = type[j]; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } } - } - } } } + ilist[inum++] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/npair_half_size_multi2_newton.h b/src/npair_half_size_multi2_newton.h index 3cd1ee05d1..8c7bc1cc9e 100755 --- a/src/npair_half_size_multi2_newton.h +++ b/src/npair_half_size_multi2_newton.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/size/bytype/newton, - NPairHalfSizeBytypeNewton, - NP_HALF | NP_SIZE | NP_BYTYPE | NP_NEWTON | NP_ORTHO) +NPairStyle(half/size/multi2/newton, + NPairHalfSizeMulti2Newton, + NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_H -#define LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_H +#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfSizeBytypeNewton : public NPair { +class NPairHalfSizeMulti2Newton : public NPair { public: - NPairHalfSizeBytypeNewton(class LAMMPS *); - ~NPairHalfSizeBytypeNewton() {} + NPairHalfSizeMulti2Newton(class LAMMPS *); + ~NPairHalfSizeMulti2Newton() {} void build(class NeighList *); }; diff --git a/src/npair_half_size_multi2_newton_tri.cpp b/src/npair_half_size_multi2_newton_tri.cpp index 62d499b10f..1c0c1d514f 100755 --- a/src/npair_half_size_multi2_newton_tri.cpp +++ b/src/npair_half_size_multi2_newton_tri.cpp @@ -11,21 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include "npair_half_size_bytype_newton_tri.h" +#include "npair_half_size_multi2_newton_tri.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "my_page.h" #include "error.h" -#include "nbin.h" -#include "nstencil.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeBytypeNewtonTri::NPairHalfSizeBytypeNewtonTri(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMulti2NewtonTri::NPairHalfSizeMulti2NewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- KS REWRTIE @@ -35,9 +32,9 @@ NPairHalfSizeBytypeNewtonTri::NPairHalfSizeBytypeNewtonTri(LAMMPS *lmp) : NPair( every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeBytypeNewtonTri::build(NeighList *list) +void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -71,89 +68,83 @@ void NPairHalfSizeBytypeNewtonTri::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - int js; - int kbin; - // own type: loop over atoms ahead in bin, including ghosts at end of list // if j is owned atom, store by virtue of being ahead of i in list // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = nb->atom2bin_type[itype][i]; + ibin = atom2bin_multi2[itype][i]; - for (int ktype = 1; ktype <= atom->ntypes; ktype++) { + for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = this->ns->stencil_type[itype][itype]; - ns = this->ns->nstencil_type[itype][itype]; - for (k = 0; k < ns; k++) { - js = nb->binhead_type[itype][ibin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[itype][j]) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp) { - if (x[j][0] < xtmp) continue; - if (x[j][0] == xtmp && j <= i) continue; - } - } - jtype = type[j]; - // KS. CHECK ME if (cutsq[jtype] < distsq[k]) continue; - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][j]) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + jtype = type[j]; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } } - } - } - - } - else { - // KS + } else { // smaller -> larger: locate i in the ktype bin structure - kbin = nb->coord2bin(x[i], ktype); - - s = this->ns->stencil_type[itype][ktype]; - ns = this->ns->nstencil_type[itype][ktype]; - for (k = 0; k < ns; k++) { - js = nb->binhead_type[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = nb->bins_type[ktype][j]) { - - jtype = type[j]; - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + kbin = coord2bin(x[i], ktype); + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + + jtype = type[j]; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } } - } - } } } + ilist[inum++] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/npair_half_size_multi2_newton_tri.h b/src/npair_half_size_multi2_newton_tri.h index 0f770e780d..6ce4f6d2fb 100755 --- a/src/npair_half_size_multi2_newton_tri.h +++ b/src/npair_half_size_multi2_newton_tri.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/size/bytype/newton/tri, - NPairHalfSizeBytypeNewtonTri, - NP_HALF | NP_SIZE | NP_BYTYPE | NP_NEWTON | NP_TRI) +NPairStyle(half/size/multi2/newton/tri, + NPairHalfSizeMulti2NewtonTri, + NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_TRI_H -#define LMP_NPAIR_HALF_SIZE_BYTYPE_NEWTON_TRI_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_H +#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfSizeBytypeNewtonTri : public NPair { +class NPairHalfSizeMulti2NewtonTri : public NPair { public: - NPairHalfSizeBytypeNewtonTri(class LAMMPS *); - ~NPairHalfSizeBytypeNewtonTri() {} + NPairHalfSizeMulti2NewtonTri(class LAMMPS *); + ~NPairHalfSizeMulti2NewtonTri() {} void build(class NeighList *); }; diff --git a/src/nstencil.h b/src/nstencil.h index 7c6a04a56a..faf4ca0872 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -34,7 +34,9 @@ class NStencil : protected Pointers { int *** stencil_multi2; // list of bin offsets in each multi2 stencil int ** maxstencil_multi2; // max stencil size for each multi2 stencil - ^do i need a multi 2 analog to distsq_multi? + // Note distsq_multi is used in multi to quickly skip bins beyond interaction cutoff + // Not quite sure why bins are beyond this distance? Have to think + // Probably not needed for multi2 since bins are more efficiently chosen int sx,sy,sz; // extent of stencil in each dim int **sx_multi2; // analogs for multi tiered From 9a3ece75f25c9b6d8aa0ab1b6f2af6e8cf9c8875 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 10 Nov 2020 23:30:58 -0700 Subject: [PATCH 0019/1217] Batch 1 of typo/bug fixes --- src/comm_brick.cpp | 4 +- src/nbin.cpp | 72 +++++++------- src/npair_half_size_multi2_newtoff.cpp | 4 +- src/nstencil.cpp | 8 ++ src/nstencil.h | 5 +- src/nstencil_full_multi2_2d.h | 2 +- src/nstencil_full_multi2_3d.cpp | 2 +- src/nstencil_full_multi2_3d.h | 2 +- src/nstencil_half_multi2_2d.cpp | 10 +- src/nstencil_half_multi2_2d_tri.cpp | 10 +- src/nstencil_half_multi2_3d_tri.cpp | 125 +------------------------ 11 files changed, 70 insertions(+), 174 deletions(-) diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 981e86c2a4..e283e08e20 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -211,8 +211,8 @@ void CommBrick::setup() cutghost[2] = cut * length2; if (mode == Comm::MULTI) { - if (multi_tiered) { - // If using tiered binlists, use the itype-itype interaction distance for communication + if (multi2) { + // If using multi2 binlists, use the itype-itype interaction distance for communication double **cutneighsq = neighbor->cutneighsq; for (i = 1; i <= ntypes; i++) { cut = 0.0; diff --git a/src/nbin.cpp b/src/nbin.cpp index 4ab3270287..cf6ef3ddd4 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -31,18 +31,18 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp) bins = nullptr; atom2bin = nullptr; - nbinx_tiered = nullptr; nbiny_tiered = nullptr; nbinz_tiered = nullptr; - mbins_tiered = nullptr; - mbinx_tiered = nullptr; mbiny_tiered = nullptr, mbinz_tiered = nullptr; - mbinxlo_tiered = nullptr; - mbinylo_tiered = nullptr; - mbinzlo_tiered = nullptr; - binsizex_tiered = nullptr; binsizey_tiered = nullptr; binsizez_tiered = nullptr; - bininvx_tiered = nullptr; bininvy_tiered = nullptr; bininvz_tiered = nullptr; - binhead_tiered = nullptr; - bins_tiered = nullptr; - atom2bin_tiered = nullptr; - maxbins_tiered = nullptr; + nbinx_multi2 = nullptr; nbiny_multi2 = nullptr; nbinz_multi2 = nullptr; + mbins_multi2 = nullptr; + mbinx_multi2 = nullptr; mbiny_multi2 = nullptr, mbinz_multi2 = nullptr; + mbinxlo_multi2 = nullptr; + mbinylo_multi2 = nullptr; + mbinzlo_multi2 = nullptr; + binsizex_multi2 = nullptr; binsizey_multi2 = nullptr; binsizez_multi2 = nullptr; + bininvx_multi2 = nullptr; bininvy_multi2 = nullptr; bininvz_multi2 = nullptr; + binhead_multi2 = nullptr; + bins_multi2 = nullptr; + atom2bin_multi2 = nullptr; + maxbins_multi2 = nullptr; maxtypes = 0; @@ -64,36 +64,36 @@ NBin::~NBin() memory->destroy(bins); memory->destroy(atom2bin); - if (!bins_tiered) return; + if (!bins_multi2) return; - memory->destroy(nbinx_tiered); - memory->destroy(nbiny_tiered); - memory->destroy(nbinz_tiered); - memory->destroy(mbins_tiered); - memory->destroy(mbinx_tiered); - memory->destroy(mbiny_tiered); - memory->destroy(mbinz_tiered); - memory->destroy(mbinxlo_tiered); - memory->destroy(mbinylo_tiered); - memory->destroy(mbinzlo_tiered); + memory->destroy(nbinx_multi2); + memory->destroy(nbiny_multi2); + memory->destroy(nbinz_multi2); + memory->destroy(mbins_multi2); + memory->destroy(mbinx_multi2); + memory->destroy(mbiny_multi2); + memory->destroy(mbinz_multi2); + memory->destroy(mbinxlo_multi2); + memory->destroy(mbinylo_multi2); + memory->destroy(mbinzlo_multi2); - memory->destroy(binsizex_tiered); - memory->destroy(binsizey_tiered); - memory->destroy(binsizez_tiered); - memory->destroy(bininvx_tiered); - memory->destroy(bininvy_tiered); - memory->destroy(bininvz_tiered); + memory->destroy(binsizex_multi2); + memory->destroy(binsizey_multi2); + memory->destroy(binsizez_multi2); + memory->destroy(bininvx_multi2); + memory->destroy(bininvy_multi2); + memory->destroy(bininvz_multi2); for (int n = 1; n <= maxtypes; n++) { - memory->destroy(binhead_tiered[n]); - memory->destroy(bins_tiered[n]); - memory->destroy(atom2bin_tiered[n]); + memory->destroy(binhead_multi2[n]); + memory->destroy(bins_multi2[n]); + memory->destroy(atom2bin_multi2[n]); } - delete [] binhead_tiered; - delete [] bins_tiered; - delete [] atom2bin_tiered; + delete [] binhead_multi2; + delete [] bins_multi2; + delete [] atom2bin_multi2; - memory->destroy(maxbins_tiered); + memory->destroy(maxbins_multi2); } /* ---------------------------------------------------------------------- */ diff --git a/src/npair_half_size_multi2_newtoff.cpp b/src/npair_half_size_multi2_newtoff.cpp index 0ea9e493ce..0e0137a77e 100644 --- a/src/npair_half_size_multi2_newtoff.cpp +++ b/src/npair_half_size_multi2_newtoff.cpp @@ -77,7 +77,7 @@ void NPairHalfSizeMulti2Newtoff::build(NeighList *list) // stores own/own pairs only once // stores own/ghost pairs on both procs - ibin = nb->atom2bin_type[itype][i]; + ibin = atom2bin_multi2[itype][i]; for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { kbin = ibin; @@ -90,7 +90,7 @@ void NPairHalfSizeMulti2Newtoff::build(NeighList *list) ns = nstencil_multi2[itype][ktype]; for (k = 0; k < ns; k++) { js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >=0; j = nb->bins_multi2[ktype][j]) { + for (j = js; j >=0; j = bins_multi2[ktype][j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/nstencil.cpp b/src/nstencil.cpp index b7cfe4dc72..bcde1024b3 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -284,6 +284,10 @@ void NStencil::create_setup() memory->create(binsizez_multi2, n+1, n+1, "neighstencil:binsizez_multi2"); + memory->create(mbinx_multi2, n+1, n+1,"neighstencil:mbinx_multi2"); + memory->create(mbiney_multi2, n+1, n+1, "neighstencil:mbiny_multi2"); + memory->create(mbinz_multi2, n+1, n+1, "neighstencil:mbinz_multi2"); + // Skip all stencils by default, initialize smax for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { @@ -323,6 +327,10 @@ void NStencil::create_setup() binsizey_multi2[i][j] = binsizey; binsizez_multi2[i][j] = binsizez; + mbinx_multi2[i][j] = mbinx; + mbiny_multi2[i][j] = mbiny; + mbinz_multi2[i][j] = mbinz; + stencil_range = stencil_cut[i][j]; sx = static_cast (stencil_range*bininvx); diff --git a/src/nstencil.h b/src/nstencil.h index faf4ca0872..158ced07d2 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -70,7 +70,7 @@ class NStencil : protected Pointers { double cutneighmax; double cutneighmaxsq; double *cuttypesq; - double *cutneighsq; + double **cutneighsq; // data from NBin class @@ -80,6 +80,9 @@ class NStencil : protected Pointers { // analogs for multi-tiered + int **mbinx_multi2; + int **mbiny_multi2; + int **mbinz_multi2; double **binsizex_multi2; double **binsizey_multi2; double **binsizez_multi2; diff --git a/src/nstencil_full_multi2_2d.h b/src/nstencil_full_multi2_2d.h index 1dfc5ae4d6..b9f46056c5 100644 --- a/src/nstencil_full_multi2_2d.h +++ b/src/nstencil_full_multi2_2d.h @@ -14,7 +14,7 @@ #ifdef NSTENCIL_CLASS NStencilStyle(full/multi2/2d, - NStencilFullMulti22d, NS_FULL | NS_Multi2 | NS_2D | NS_ORTHO | NS_TRI) + NStencilFullMulti22d, NS_FULL | NS_MULTI2 | NS_2D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 77ae62738c..808c2d334d 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -92,7 +92,7 @@ void NStencilFullMulti23d::create() for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = + stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; nstencil_multi2[itype][jtype] = ns; diff --git a/src/nstencil_full_multi2_3d.h b/src/nstencil_full_multi2_3d.h index f7baefc8e9..102471f2c7 100644 --- a/src/nstencil_full_multi2_3d.h +++ b/src/nstencil_full_multi2_3d.h @@ -14,7 +14,7 @@ #ifdef NSTENCIL_CLASS NStencilStyle(full/multi2/3d, - NStencilFullMulti23d, NS_FULL | NS_Multi2 | NS_3D | NS_ORTHO | NS_TRI) + NStencilFullMulti23d, NS_FULL | NS_MULTI2 | NS_3D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index 86da6ea91e..3daf872fa9 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -23,12 +23,12 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti22d::NStencilHalfMulti23d(LAMMPS *lmp) : +NStencilHalfMulti22d::NStencilHalfMulti22d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilHalfMulti23d::set_stencil_properties() +void NStencilHalfMulti22d::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -69,7 +69,7 @@ void NStencilHalfMulti23d::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti23d::create() +void NStencilHalfMulti22d::create() { int itype, jtype, i, j, ns; int n = atom->ntypes; @@ -95,13 +95,13 @@ void NStencilHalfMulti23d::create() for (i = -sx; i <= sx; i++) if (j > 0 || (j == 0 && i > 0)) { if (bin_distance(i,j,0) < cutsq) - stencil_type[itype][jtype][ns++] = j*mbinx + i; + stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,0) < cutsq) - stencil_type[itype][jtype][ns++] = j*mbinx + i; + stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } nstencil_multi2[itype][jtype] = ns; diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp index 46f55300ce..9e8ae81036 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -23,12 +23,12 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti22dTri::NStencilHalfMulti22d(LAMMPS *lmp) : +NStencilHalfMulti22dTri::NStencilHalfMulti22dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilHalfMulti22d::set_stencil_properties() +void NStencilHalfMulti22dTri::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -69,7 +69,7 @@ void NStencilHalfMulti22d::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti22d::create() +void NStencilHalfMulti22dTri::create() { int itype, jtype, i, j, ns; int n = atom->ntypes; @@ -94,12 +94,12 @@ void NStencilHalfMulti22d::create() for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,0) < cutsq) - stencil_type[itype][jtype][ns++] = j*mbinx + i; + stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,0) < cutsq) - stencil_type[itype][jtype][ns++] = j*mbinx + i; + stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } nstencil_multi2[itype][jtype] = ns; diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index bcaf22abbd..652b1ed60f 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -23,12 +23,12 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti23dTri::NStencilHalfMulti23d(LAMMPS *lmp) : +NStencilHalfMulti23dTri::NStencilHalfMulti23dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilHalfMulti23d::set_stencil_properties() +void NStencilHalfMulti23dTri::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -69,7 +69,7 @@ void NStencilHalfMulti23d::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti23d::create() +void NStencilHalfMulti23dTri::create() { int itype, jtype, i, j, k, ns; int n = atom->ntypes; @@ -97,14 +97,14 @@ void NStencilHalfMulti23d::create() for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = + stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = + stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } @@ -112,118 +112,3 @@ void NStencilHalfMulti23d::create() } } } - -/* ---------------------------------------------------------------------- */ - -// KS To superclass -void NStencilHalfMulti23d::copy_bin_info_bytype(int itype) { - - mbinx = nb->mbinx_type[itype]; - mbiny = nb->mbiny_type[itype]; - mbinz = nb->mbinz_type[itype]; - binsizex = nb->binsizex_type[itype]; - binsizey = nb->binsizey_type[itype]; - binsizez = nb->binsizez_type[itype]; - bininvx = nb->bininvx_type[itype]; - bininvy = nb->bininvy_type[itype]; - bininvz = nb->bininvz_type[itype]; -} - -/* ---------------------------------------------------------------------- */ - -// KS To superclass? -int NStencilHalfMulti23d::copy_neigh_info_bytype(int itype) { - - cutneighmaxsq = neighbor->cutneighsq[itype][itype]; - cutneighmax = sqrt(cutneighmaxsq); - cuttypesq = neighbor->cuttypesq; - - // sx,sy,sz = max range of stencil in each dim - // smax = max possible size of entire 3d stencil - // stencil will be empty if cutneighmax = 0.0 - - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - return ((2*sx+1) * (2*sy+1) * (2*sz+1)); -} - -/* ---------------------------------------------------------------------- */ - -void NStencilHalfMulti23d::create_setup() -{ - - int itype, jtype; - int maxtypes; - int smax; - - // maxstencil_type to superclass? - maxtypes = atom->ntypes; - - if (maxstencil_type == NULL) { - memory->create(maxstencil_type, maxtypes+1, maxtypes+1, "maxstencil_type"); - memory->create(nstencil_type, maxtypes+1, maxtypes+1, "nstencil_type"); - stencil_type = new int**[maxtypes+1](); - for (itype = 1; itype <= maxtypes; ++itype) { - stencil_type[itype] = new int*[maxtypes+1](); - for (jtype = 1; jtype <= maxtypes; ++jtype) { - maxstencil_type[itype][jtype] = 0; - nstencil_type[itype][jtype] = 0; - } - } - } - - // like -> like => use standard Newton stencil at bin - - for (itype = 1; itype <= maxtypes; ++itype) { - copy_bin_info_bytype(itype); - smax = copy_neigh_info_bytype(itype); - if (smax > maxstencil_type[itype][itype]) { - maxstencil_type[itype][itype] = smax; - memory->destroy(stencil_type[itype][itype]); - memory->create(stencil_type[itype][itype], smax, - "NStencilHalfBytypeNewton::create_steup() stencil"); - } - create_newton(itype, itype, cutneighmaxsq); - } - - // Cross types: "Newton on" reached by using Newton off stencil and - // looking one way through hierarchy - // smaller -> larger => use Newton off stencil in larger bin - // larger -> smaller => no nstecil required - // If cut offs are same, use existing type-type stencil - - for (itype = 1; itype <= maxtypes; ++itype) { - for (jtype = 1; jtype <= maxtypes; ++jtype) { - if (itype == jtype) continue; - if (cuttypesq[itype] == cuttypesq[jtype]) { - nstencil_type[itype][jtype] = nstencil_type[jtype][jtype]; - stencil_type[itype][jtype] = stencil_type[jtype][jtype]; - } - else if (cuttypesq[itype] < cuttypesq[jtype]) { - copy_bin_info_bytype(jtype); - - cutneighmaxsq = cuttypesq[jtype]; - cutneighmax = sqrt(cutneighmaxsq); - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - - smax = (2*sx+1) * (2*sy+1) * (2*sz+1); - if (smax > maxstencil_type[itype][jtype]) { - maxstencil_type[itype][jtype] = smax; - memory->destroy(stencil_type[itype][jtype]); - memory->create(stencil_type[itype][jtype], smax, "stencil_type[]"); - } - create_newtoff(itype, jtype, cuttypesq[jtype]); - } - } - } -} From f94c82910d542ea194ec9e959da9f81966e41f03 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Wed, 11 Nov 2020 10:11:49 -0700 Subject: [PATCH 0020/1217] Fixing remaining bugs to compile --- src/nbin_standard.cpp | 1 + src/npair_half_multi2_newtoff.cpp | 4 ++-- src/npair_half_size_multi2_newton.cpp | 2 +- src/nstencil.cpp | 28 +++++++++++++-------------- src/nstencil.h | 4 ++-- src/nstencil_full_multi2_2d.cpp | 2 +- src/nstencil_full_multi2_2d.h | 2 +- src/nstencil_full_multi2_3d.h | 2 +- src/nstencil_half_multi2_2d.h | 2 +- src/nstencil_half_multi2_2d_tri.h | 2 +- src/nstencil_half_multi2_3d.cpp | 4 ++-- src/nstencil_half_multi2_3d.h | 2 +- src/nstencil_half_multi2_3d_tri.h | 2 +- 13 files changed, 29 insertions(+), 28 deletions(-) diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp index e63c8dcd56..07dfd3a6cb 100644 --- a/src/nbin_standard.cpp +++ b/src/nbin_standard.cpp @@ -19,6 +19,7 @@ #include "comm.h" #include "update.h" #include "error.h" +#include "memory.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_multi2_newtoff.cpp b/src/npair_half_multi2_newtoff.cpp index 83a8054247..b44f2bcc62 100755 --- a/src/npair_half_multi2_newtoff.cpp +++ b/src/npair_half_multi2_newtoff.cpp @@ -87,7 +87,7 @@ void NPairHalfMulti2Newtoff::build(NeighList *list) // stores own/own pairs only once // stores own/ghost pairs on both procs - ibin = nb->atom2bin_type[itype][i]; + ibin = atom2bin_multi2[itype][i]; for (ktype = 1; ktype <= atom->ntypes; ktype++) { if (itype == ktype) { kbin = ibin; @@ -100,7 +100,7 @@ void NPairHalfMulti2Newtoff::build(NeighList *list) ns = nstencil_multi2[itype][ktype]; for (k = 0; k < ns; k++) { js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >=0; j = nb->bins_multi2[ktype][j]) { + for (j = js; j >=0; j = bins_multi2[ktype][j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/npair_half_size_multi2_newton.cpp b/src/npair_half_size_multi2_newton.cpp index 3b89c259ec..a1832f6a49 100755 --- a/src/npair_half_size_multi2_newton.cpp +++ b/src/npair_half_size_multi2_newton.cpp @@ -72,7 +72,7 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) // if j is owned atom, store by virtue of being ahead of i in list // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = nb->atom2bin_multi2[itype][i]; + ibin = atom2bin_multi2[itype][i]; for (ktype = 1; ktype <= atom->ntypes; ktype++) { diff --git a/src/nstencil.cpp b/src/nstencil.cpp index bcde1024b3..033d79e279 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -182,15 +182,15 @@ void NStencil::copy_bin_info() void NStencil::copy_bin_info_multi2(int type) { - mbinx = nb->mbinx2[type]; - mbiny = nb->mbiny2[type]; - mbinz = nb->mbinz2[type]; - binsizex = nb->binsizex2[type]; - binsizey = nb->binsizey2[type]; - binsizez = nb->binsizez2[type]; - bininvx = nb->bininvx2[type]; - bininvy = nb->bininvy2[type]; - bininvz = nb->bininvz2[type]; + mbinx = nb->mbinx_multi2[type]; + mbiny = nb->mbiny_multi2[type]; + mbinz = nb->mbinz_multi2[type]; + binsizex = nb->binsizex_multi2[type]; + binsizey = nb->binsizey_multi2[type]; + binsizez = nb->binsizez_multi2[type]; + bininvx = nb->bininvx_multi2[type]; + bininvy = nb->bininvy_multi2[type]; + bininvz = nb->bininvz_multi2[type]; } /* ---------------------------------------------------------------------- @@ -284,8 +284,8 @@ void NStencil::create_setup() memory->create(binsizez_multi2, n+1, n+1, "neighstencil:binsizez_multi2"); - memory->create(mbinx_multi2, n+1, n+1,"neighstencil:mbinx_multi2"); - memory->create(mbiney_multi2, n+1, n+1, "neighstencil:mbiny_multi2"); + memory->create(mbinx_multi2, n+1, n+1, "neighstencil:mbinx_multi2"); + memory->create(mbiny_multi2, n+1, n+1, "neighstencil:mbiny_multi2"); memory->create(mbinz_multi2, n+1, n+1, "neighstencil:mbinz_multi2"); // Skip all stencils by default, initialize smax @@ -321,7 +321,7 @@ void NStencil::create_setup() // Copy bin info for this particular pair of types bin_type = stencil_bin_type[i][j]; - copy_bin_info_bytype(bin_type); + copy_bin_info_multi2(bin_type); binsizex_multi2[i][j] = binsizex; binsizey_multi2[i][j] = binsizey; @@ -393,8 +393,8 @@ double NStencil::memory_usage() bytes += atom->ntypes*maxstencil_multi * sizeof(double); } else if (neighstyle == Neighbor::MULTI2) { int n = atom->ntypes; - for (i = 1; i <= n; ++i) { - for (j = 1; j <= n; ++j) { + for (int i = 1; i <= n; i++) { + for (int j = 1; j <= n; j++) { bytes += maxstencil_multi2[i][j] * sizeof(int); bytes += maxstencil_multi2[i][j] * sizeof(int); bytes += maxstencil_multi2[i][j] * sizeof(double); diff --git a/src/nstencil.h b/src/nstencil.h index 158ced07d2..5f010cb377 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -102,8 +102,8 @@ class NStencil : protected Pointers { // methods for multi/tiered NStencil - void copy_bin_info_multi2(int); // copy mult/tiered info from NBin class - void set_stencil_properties(); // determine which stencils to build and how + void copy_bin_info_multi2(int); // copy mult/tiered info from NBin class + virtual void set_stencil_properties(){} // determine which stencils to build and how }; } diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index f62cddb0b5..ba503fd5f5 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -89,7 +89,7 @@ void NStencilFullMulti22d::create() for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,0) < cutsq) - stencil_type[itype][jtype][ns++] = j*mbinx + i; + stencil_multi2[itype][jtype][ns++] = j*mbinx + i; nstencil_multi2[itype][jtype] = ns; } diff --git a/src/nstencil_full_multi2_2d.h b/src/nstencil_full_multi2_2d.h index b9f46056c5..46e12db039 100644 --- a/src/nstencil_full_multi2_2d.h +++ b/src/nstencil_full_multi2_2d.h @@ -28,7 +28,7 @@ namespace LAMMPS_NS { class NStencilFullMulti22d : public NStencil { public: NStencilFullMulti22d(class LAMMPS *); - ~NStencilFullMulti22d(); + ~NStencilFullMulti22d() {} void create(); protected: diff --git a/src/nstencil_full_multi2_3d.h b/src/nstencil_full_multi2_3d.h index 102471f2c7..fb6a19ec6f 100644 --- a/src/nstencil_full_multi2_3d.h +++ b/src/nstencil_full_multi2_3d.h @@ -28,7 +28,7 @@ namespace LAMMPS_NS { class NStencilFullMulti23d : public NStencil { public: NStencilFullMulti23d(class LAMMPS *); - ~NStencilFullMulti23d(); + ~NStencilFullMulti23d(){} void create(); protected: diff --git a/src/nstencil_half_multi2_2d.h b/src/nstencil_half_multi2_2d.h index ba3a471833..8e79fd0541 100644 --- a/src/nstencil_half_multi2_2d.h +++ b/src/nstencil_half_multi2_2d.h @@ -28,7 +28,7 @@ namespace LAMMPS_NS { class NStencilHalfMulti22d : public NStencil { public: NStencilHalfMulti22d(class LAMMPS *); - ~NStencilHalfMulti22d(); + ~NStencilHalfMulti22d() {} void create(); protected: diff --git a/src/nstencil_half_multi2_2d_tri.h b/src/nstencil_half_multi2_2d_tri.h index 1d25e56776..4072c6d31b 100755 --- a/src/nstencil_half_multi2_2d_tri.h +++ b/src/nstencil_half_multi2_2d_tri.h @@ -28,7 +28,7 @@ namespace LAMMPS_NS { class NStencilHalfMulti22dTri : public NStencil { public: NStencilHalfMulti22dTri(class LAMMPS *); - ~NStencilHalfMulti22dTri(); + ~NStencilHalfMulti22dTri() {} void create(); protected: diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index 02a65bd3a1..a129d6b53b 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -98,7 +98,7 @@ void NStencilHalfMulti23d::create() for (i = -sx; i <= sx; i++) if (k > 0 || j > 0 || (j == 0 && i > 0)) { if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = + stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } } else { @@ -106,7 +106,7 @@ void NStencilHalfMulti23d::create() for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance(i,j,k) < cutsq) - stencil_type[itype][jtype][ns++] = + stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } diff --git a/src/nstencil_half_multi2_3d.h b/src/nstencil_half_multi2_3d.h index 9cae8269cb..6a0d8f90a2 100644 --- a/src/nstencil_half_multi2_3d.h +++ b/src/nstencil_half_multi2_3d.h @@ -28,7 +28,7 @@ namespace LAMMPS_NS { class NStencilHalfMulti23d : public NStencil { public: NStencilHalfMulti23d(class LAMMPS *); - ~NStencilHalfMulti23d(); + ~NStencilHalfMulti23d() {} void create(); protected: diff --git a/src/nstencil_half_multi2_3d_tri.h b/src/nstencil_half_multi2_3d_tri.h index f4b37ebebe..de449ce1d8 100755 --- a/src/nstencil_half_multi2_3d_tri.h +++ b/src/nstencil_half_multi2_3d_tri.h @@ -28,7 +28,7 @@ namespace LAMMPS_NS { class NStencilHalfMulti23dTri : public NStencil { public: NStencilHalfMulti23dTri(class LAMMPS *); - ~NStencilHalfMulti23dTri(); + ~NStencilHalfMulti23dTri() {} void create(); protected: From ac527f4615b8a845c3fea69f66b782fbf2e2df0d Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Wed, 11 Nov 2020 15:39:53 -0700 Subject: [PATCH 0021/1217] Fixing bugs in nstencil --- src/nstencil.cpp | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 033d79e279..c537767d64 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -74,7 +74,11 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) nstencil_multi = nullptr; stencil_multi = nullptr; distsq_multi = nullptr; - + + nstencil_multi2 = nullptr; + stencil_multi2 = nullptr; + maxstencil_multi2 = nullptr; + stencil_half = nullptr; stencil_skip = nullptr; stencil_bin_type = nullptr; @@ -292,7 +296,6 @@ void NStencil::create_setup() for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { stencil_skip[i][j] = 1; - maxstencil_multi2[i][j] = 0; } } From b6dfc28e38c122c0a284a3d0d791e50f2621ad4d Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Wed, 11 Nov 2020 22:50:59 -0700 Subject: [PATCH 0022/1217] Resetting bin sizes in stencils --- src/nstencil_full_multi2_2d.cpp | 5 +++++ src/nstencil_full_multi2_3d.cpp | 5 +++++ src/nstencil_half_multi2_2d.cpp | 5 +++++ src/nstencil_half_multi2_2d_tri.cpp | 5 +++++ src/nstencil_half_multi2_3d.cpp | 5 +++++ src/nstencil_half_multi2_3d_tri.cpp | 5 +++++ 6 files changed, 30 insertions(+) diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index ba503fd5f5..8ff504b48d 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -84,6 +84,11 @@ void NStencilFullMulti22d::create() mbinx = mbinx_multi2[itype][jtype]; mbiny = mbiny_multi2[itype][jtype]; + // Redefine for use in bin_distance() + binsizex = binsizex_multi2[itype][jtype]; + binsizey = binsizey_multi2[itype][jtype]; + binsizez = binsizez_multi2[itype][jtype]; + cutsq = stencil_cut[itype][jtype]; for (j = -sy; j <= sy; j++) diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 808c2d334d..1257650c5e 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -86,6 +86,11 @@ void NStencilFullMulti23d::create() mbiny = mbiny_multi2[itype][jtype]; mbinz = mbinz_multi2[itype][jtype]; + // Redefine for use in bin_distance() + binsizex = binsizex_multi2[itype][jtype]; + binsizey = binsizey_multi2[itype][jtype]; + binsizez = binsizez_multi2[itype][jtype]; + cutsq = stencil_cut[itype][jtype]; for (k = -sz; k <= sz; k++) diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index 3daf872fa9..89d2903f1c 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -88,6 +88,11 @@ void NStencilHalfMulti22d::create() mbinx = mbinx_multi2[itype][jtype]; mbiny = mbiny_multi2[itype][jtype]; + // Redefine for use in bin_distance() + binsizex = binsizex_multi2[itype][jtype]; + binsizey = binsizey_multi2[itype][jtype]; + binsizez = binsizez_multi2[itype][jtype]; + cutsq = stencil_cut[itype][jtype]; if (stencil_half[itype][jtype]) { diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp index 9e8ae81036..4b4019cef2 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -88,6 +88,11 @@ void NStencilHalfMulti22dTri::create() mbinx = mbinx_multi2[itype][jtype]; mbiny = mbiny_multi2[itype][jtype]; + // Redefine for use in bin_distance() + binsizex = binsizex_multi2[itype][jtype]; + binsizey = binsizey_multi2[itype][jtype]; + binsizez = binsizez_multi2[itype][jtype]; + cutsq = stencil_cut[itype][jtype]; if (stencil_half[itype][jtype]) { diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index a129d6b53b..1777e748de 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -90,6 +90,11 @@ void NStencilHalfMulti23d::create() mbiny = mbiny_multi2[itype][jtype]; mbinz = mbinz_multi2[itype][jtype]; + // Redefine for use in bin_distance() + binsizex = binsizex_multi2[itype][jtype]; + binsizey = binsizey_multi2[itype][jtype]; + binsizez = binsizez_multi2[itype][jtype]; + cutsq = stencil_cut[itype][jtype]; if (stencil_half[itype][jtype]) { diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index 652b1ed60f..4a9ba63b20 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -90,6 +90,11 @@ void NStencilHalfMulti23dTri::create() mbiny = mbiny_multi2[itype][jtype]; mbinz = mbinz_multi2[itype][jtype]; + // Redefine for use in bin_distance() + binsizex = binsizex_multi2[itype][jtype]; + binsizey = binsizey_multi2[itype][jtype]; + binsizez = binsizez_multi2[itype][jtype]; + cutsq = stencil_cut[itype][jtype]; if (stencil_half[itype][jtype]) { From 6909839ff0fde523596878d2e7138d6e5e399c1c Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Thu, 12 Nov 2020 15:03:44 -0700 Subject: [PATCH 0023/1217] Fix full multi stencil --- src/nstencil_full_multi2_2d.cpp | 5 +++-- src/nstencil_full_multi2_3d.cpp | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index 8ff504b48d..c59edbe90d 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -50,11 +50,12 @@ void NStencilFullMulti22d::set_stencil_properties() stencil_half[i][j] = 0; stencil_skip[i][j] = 0; - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); if(cuttypesq[i] <= cuttypesq[j]){ - stencil_bin_type[i][j] = i; + stencil_cut[i][j] = sqrt(cutneighsq[j][j]); + stencil_bin_type[i][j] = j; } else { + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); stencil_bin_type[i][j] = j; } } diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 1257650c5e..6021382022 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -50,11 +50,12 @@ void NStencilFullMulti23d::set_stencil_properties() stencil_half[i][j] = 0; stencil_skip[i][j] = 0; - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); if(cuttypesq[i] <= cuttypesq[j]){ - stencil_bin_type[i][j] = i; + stencil_cut[i][j] = sqrt(cutneighsq[j][j]); + stencil_bin_type[i][j] = j; } else { + stencil_cut[i][j] = sqrt(cutneighsq[i][j]); stencil_bin_type[i][j] = j; } } From af11a54a272831e3383b1184871057ab88708928 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Thu, 12 Nov 2020 18:37:53 -0700 Subject: [PATCH 0024/1217] Copying more variables to classes and moving/clarifying definitions --- src/nbin.cpp | 93 ++++++++++++++++++++++ src/nbin.h | 2 +- src/nbin_multi2.cpp | 58 +------------- src/nbin_multi2.h | 1 - src/nbin_standard.cpp | 48 ----------- src/nbin_standard.h | 4 - src/nstencil.cpp | 119 ++++++++++++++++++---------- src/nstencil.h | 47 +++++++---- src/nstencil_full_multi2_2d.cpp | 17 ++-- src/nstencil_full_multi2_3d.cpp | 21 +++-- src/nstencil_half_multi2_2d.cpp | 13 +-- src/nstencil_half_multi2_2d_tri.cpp | 19 ++--- src/nstencil_half_multi2_3d.cpp | 23 +++--- src/nstencil_half_multi2_3d_tri.cpp | 23 +++--- 14 files changed, 252 insertions(+), 236 deletions(-) diff --git a/src/nbin.cpp b/src/nbin.cpp index cf6ef3ddd4..39c7ce6447 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -123,3 +123,96 @@ void NBin::copy_neighbor_info() if (cutoff_custom > 0.0) cutneighmax = cutoff_custom; } + + + +/* ---------------------------------------------------------------------- + convert atom coords into local bin # + for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo + take special care to insure ghosts are in correct bins even w/ roundoff + hi ghost atoms = nbin,nbin+1,etc + owned atoms = 0 to nbin-1 + lo ghost atoms = -1,-2,etc + this is necessary so that both procs on either side of PBC + treat a pair of atoms straddling the PBC in a consistent way + for triclinic, doesn't matter since stencil & neigh list built differently +------------------------------------------------------------------------- */ + +int NBin::coord2bin(double *x) +{ + int ix,iy,iz; + + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) + error->one(FLERR,"Non-numeric positions - simulation unstable"); + + if (x[0] >= bboxhi[0]) + ix = static_cast ((x[0]-bboxhi[0])*bininvx) + nbinx; + else if (x[0] >= bboxlo[0]) { + ix = static_cast ((x[0]-bboxlo[0])*bininvx); + ix = MIN(ix,nbinx-1); + } else + ix = static_cast ((x[0]-bboxlo[0])*bininvx) - 1; + + if (x[1] >= bboxhi[1]) + iy = static_cast ((x[1]-bboxhi[1])*bininvy) + nbiny; + else if (x[1] >= bboxlo[1]) { + iy = static_cast ((x[1]-bboxlo[1])*bininvy); + iy = MIN(iy,nbiny-1); + } else + iy = static_cast ((x[1]-bboxlo[1])*bininvy) - 1; + + if (x[2] >= bboxhi[2]) + iz = static_cast ((x[2]-bboxhi[2])*bininvz) + nbinz; + else if (x[2] >= bboxlo[2]) { + iz = static_cast ((x[2]-bboxlo[2])*bininvz); + iz = MIN(iz,nbinz-1); + } else + iz = static_cast ((x[2]-bboxlo[2])*bininvz) - 1; + + return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo); +} + + +/* ---------------------------------------------------------------------- + convert atom coords into local bin # for a particular type +------------------------------------------------------------------------- */ + +int NBin::coord2bin_multi2(double *x, int it) +{ + int ix,iy,iz; + int ibin; + + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) + error->one(FLERR,"Non-numeric positions - simulation unstable"); + + if (x[0] >= bboxhi[0]) + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi2[it]) + nbinx_multi2[it]; + else if (x[0] >= bboxlo[0]) { + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]); + ix = MIN(ix,nbinx_multi2[it]-1); + } else + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]) - 1; + + if (x[1] >= bboxhi[1]) + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi2[it]) + nbiny_multi2[it]; + else if (x[1] >= bboxlo[1]) { + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]); + iy = MIN(iy,nbiny_multi2[it]-1); + } else + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]) - 1; + + if (x[2] >= bboxhi[2]) + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi2[it]) + nbinz_multi2[it]; + else if (x[2] >= bboxlo[2]) { + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]); + iz = MIN(iz,nbinz_multi2[it]-1); + } else + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]) - 1; + + + ibin = (iz-mbinzlo_multi2[it])*mbiny_multi2[it]*mbinx_multi2[it] + + (iy-mbinylo_multi2[it])*mbinx_multi2[it] + + (ix-mbinxlo_multi2[it]); + return ibin; +} + diff --git a/src/nbin.h b/src/nbin.h index 33b93ef79c..441e4815dd 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -97,7 +97,7 @@ class NBin : protected Pointers { // methods int coord2bin(double *); - int coord2bin(double *, int); + int coord2bin_multi2(double *, int); }; } diff --git a/src/nbin_multi2.cpp b/src/nbin_multi2.cpp index 7a87ba940c..f57558a36c 100644 --- a/src/nbin_multi2.cpp +++ b/src/nbin_multi2.cpp @@ -324,7 +324,7 @@ void NBinMulti2::bin_atoms() for (i = nall-1; i >= nlocal; i--) { if (mask[i] & bitmask) { n = type[i]; - ibin = coord2bin(x[i], n); + ibin = coord2bin_multi2(x[i], n); atom2bin_multi2[n][i] = ibin; bins_multi2[n][i] = binhead_multi2[n][ibin]; binhead_multi2[n][ibin] = i; @@ -332,7 +332,7 @@ void NBinMulti2::bin_atoms() } for (i = atom->nfirst-1; i >= 0; i--) { n = type[i]; - ibin = coord2bin(x[i], n); + ibin = coord2bin_multi2(x[i], n); atom2bin_multi2[n][i] = ibin; bins_multi2[n][i] = binhead_multi2[n][ibin]; binhead_multi2[n][ibin] = i; @@ -340,7 +340,7 @@ void NBinMulti2::bin_atoms() } else { for (i = nall-1; i >= 0; i--) { n = type[i]; - ibin = coord2bin(x[i], n); + ibin = coord2bin_multi2(x[i], n); atom2bin_multi2[n][i] = ibin; bins_multi2[n][i] = binhead_multi2[n][ibin]; binhead_multi2[n][ibin] = i; @@ -348,58 +348,6 @@ void NBinMulti2::bin_atoms() } } -/* ---------------------------------------------------------------------- - convert atom coords into local bin # for a particular type - for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo - take special care to insure ghosts are in correct bins even w/ roundoff - hi ghost atoms = nbin,nbin+1,etc - owned atoms = 0 to nbin-1 - lo ghost atoms = -1,-2,etc - this is necessary so that both procs on either side of PBC - treat a pair of atoms straddling the PBC in a consistent way - for triclinic, doesn't matter since stencil & neigh list built differently -------------------------------------------------------------------------- */ - -int NBinMulti2::coord2bin(double *x, int it) -{ - int ix,iy,iz; - int ibin; - - if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable"); - - if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi2[it]) + nbinx_multi2[it]; - else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]); - ix = MIN(ix,nbinx_multi2[it]-1); - } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]) - 1; - - if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi2[it]) + nbiny_multi2[it]; - else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]); - iy = MIN(iy,nbiny_multi2[it]-1); - } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]) - 1; - - if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi2[it]) + nbinz_multi2[it]; - else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]); - iz = MIN(iz,nbinz_multi2[it]-1); - } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]) - 1; - - - ibin = (iz-mbinzlo_multi2[it])*mbiny_multi2[it]*mbinx_multi2[it] - + (iy-mbinylo_multi2[it])*mbinx_multi2[it] - + (ix-mbinxlo_multi2[it]); - return ibin; -} - - /* ---------------------------------------------------------------------- */ double NBinMulti2::memory_usage() diff --git a/src/nbin_multi2.h b/src/nbin_multi2.h index 8cca7b1023..3094027f64 100644 --- a/src/nbin_multi2.h +++ b/src/nbin_multi2.h @@ -38,7 +38,6 @@ class NBinMulti2 : public NBin { private: - int coord2bin(double *, int); int itype_min(); }; diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp index 07dfd3a6cb..4298a9670c 100644 --- a/src/nbin_standard.cpp +++ b/src/nbin_standard.cpp @@ -259,54 +259,6 @@ void NBinStandard::bin_atoms() } } - -/* ---------------------------------------------------------------------- - convert atom coords into local bin # - for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo - take special care to insure ghosts are in correct bins even w/ roundoff - hi ghost atoms = nbin,nbin+1,etc - owned atoms = 0 to nbin-1 - lo ghost atoms = -1,-2,etc - this is necessary so that both procs on either side of PBC - treat a pair of atoms straddling the PBC in a consistent way - for triclinic, doesn't matter since stencil & neigh list built differently -------------------------------------------------------------------------- */ - -int NBinStandard::coord2bin(double *x) -{ - int ix,iy,iz; - - if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable"); - - if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx) + nbinx; - else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx); - ix = MIN(ix,nbinx-1); - } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx) - 1; - - if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy) + nbiny; - else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy); - iy = MIN(iy,nbiny-1); - } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy) - 1; - - if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz) + nbinz; - else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz); - iz = MIN(iz,nbinz-1); - } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz) - 1; - - return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo); -} - - /* ---------------------------------------------------------------------- */ double NBinStandard::memory_usage() diff --git a/src/nbin_standard.h b/src/nbin_standard.h index d8ecb435b7..89b749c948 100644 --- a/src/nbin_standard.h +++ b/src/nbin_standard.h @@ -34,10 +34,6 @@ class NBinStandard : public NBin { void setup_bins(int); void bin_atoms(); double memory_usage(); - - private: - - int coord2bin(double *); }; } diff --git a/src/nstencil.cpp b/src/nstencil.cpp index c537767d64..2ace1125e8 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -124,13 +124,17 @@ NStencil::~NStencil() memory->destroy(stencil_bin_type); memory->destroy(stencil_cut); - memory->destroy(sx_multi2); - memory->destroy(sy_multi2); - memory->destroy(sz_multi2); + memory->destroy(stencil_sx_multi2); + memory->destroy(stencil_sy_multi2); + memory->destroy(stencil_sz_multi2); + + memory->destroy(stencil_mbinx_multi2); + memory->destroy(stencil_mbiny_multi2); + memory->destroy(stencil_mbinz_multi2); - memory->destroy(binsizex_multi2); - memory->destroy(binsizey_multi2); - memory->destroy(binsizez_multi2); + memory->destroy(stencil_binsizex_multi2); + memory->destroy(stencil_binsizey_multi2); + memory->destroy(stencil_binsizez_multi2); } } @@ -181,20 +185,20 @@ void NStencil::copy_bin_info() } /* ---------------------------------------------------------------------- - copy needed info for a given type from NBin class to this stencil class + copy needed info for multi2 from NBin class to this stencil class ------------------------------------------------------------------------- */ -void NStencil::copy_bin_info_multi2(int type) +void NStencil::copy_bin_info_multi2() { - mbinx = nb->mbinx_multi2[type]; - mbiny = nb->mbiny_multi2[type]; - mbinz = nb->mbinz_multi2[type]; - binsizex = nb->binsizex_multi2[type]; - binsizey = nb->binsizey_multi2[type]; - binsizez = nb->binsizez_multi2[type]; - bininvx = nb->bininvx_multi2[type]; - bininvy = nb->bininvy_multi2[type]; - bininvz = nb->bininvz_multi2[type]; + mbinx_multi2 = nb->mbinx_multi2; + mbiny_multi2 = nb->mbiny_multi2; + mbinz_multi2 = nb->mbinz_multi2; + binsizex_multi2 = nb->binsizex_multi2; + binsizey_multi2 = nb->binsizey_multi2; + binsizez_multi2 = nb->binsizez_multi2; + bininvx_multi2 = nb->bininvx_multi2; + bininvy_multi2 = nb->bininvy_multi2; + bininvz_multi2 = nb->bininvz_multi2; } /* ---------------------------------------------------------------------- @@ -266,6 +270,8 @@ void NStencil::create_setup() int i, j, bin_type, smax; double stencil_range; int n = atom->ntypes; + + if(nb) copy_bin_info_multi2(); // Allocate arrays to store stencil information memory->create(stencil_half, n+1, n+1, @@ -277,20 +283,26 @@ void NStencil::create_setup() memory->create(stencil_cut, n+1, n+1, "neighstencil:stencil_cut"); - memory->create(sx_multi2, n+1, n+1, "neighstencil:sx_multi2"); - memory->create(sy_multi2, n+1, n+1, "neighstencil:sy_multi2"); - memory->create(sz_multi2, n+1, n+1, "neighstencil:sz_multi2"); + memory->create(stencil_sx_multi2, n+1, n+1, + "neighstencil:stencil_sx_multi2"); + memory->create(stencil_sy_multi2, n+1, n+1, + "neighstencil:stencil_sy_multi2"); + memory->create(stencil_sz_multi2, n+1, n+1, + "neighstencil:stencil_sz_multi2"); - memory->create(binsizex_multi2, n+1, n+1, - "neighstencil:binsizex_multi2"); - memory->create(binsizey_multi2, n+1, n+1, - "neighstencil:binsizey_multi2"); - memory->create(binsizez_multi2, n+1, n+1, - "neighstencil:binsizez_multi2"); + memory->create(stencil_binsizex_multi2, n+1, n+1, + "neighstencil:stencil_binsizex_multi2"); + memory->create(stencil_binsizey_multi2, n+1, n+1, + "neighstencil:stencil_binsizey_multi2"); + memory->create(stencil_binsizez_multi2, n+1, n+1, + "neighstencil:stencil_binsizez_multi2"); - memory->create(mbinx_multi2, n+1, n+1, "neighstencil:mbinx_multi2"); - memory->create(mbiny_multi2, n+1, n+1, "neighstencil:mbiny_multi2"); - memory->create(mbinz_multi2, n+1, n+1, "neighstencil:mbinz_multi2"); + memory->create(stencil_mbinx_multi2, n+1, n+1, + "neighstencil:stencil_mbinx_multi2"); + memory->create(stencil_mbiny_multi2, n+1, n+1, + "neighstencil:stencil_mbiny_multi2"); + memory->create(stencil_mbinz_multi2, n+1, n+1, + "neighstencil:stencil_mbinz_multi2"); // Skip all stencils by default, initialize smax for (i = 1; i <= n; i++) { @@ -324,28 +336,27 @@ void NStencil::create_setup() // Copy bin info for this particular pair of types bin_type = stencil_bin_type[i][j]; - copy_bin_info_multi2(bin_type); - binsizex_multi2[i][j] = binsizex; - binsizey_multi2[i][j] = binsizey; - binsizez_multi2[i][j] = binsizez; + stencil_binsizex_multi2[i][j] = binsizex_multi2[bin_type]; + stencil_binsizey_multi2[i][j] = binsizey_multi2[bin_type]; + stencil_binsizez_multi2[i][j] = binsizez_multi2[bin_type]; - mbinx_multi2[i][j] = mbinx; - mbiny_multi2[i][j] = mbiny; - mbinz_multi2[i][j] = mbinz; + stencil_mbinx_multi2[i][j] = mbinx_multi2[bin_type]; + stencil_mbiny_multi2[i][j] = mbiny_multi2[bin_type]; + stencil_mbinz_multi2[i][j] = mbinz_multi2[bin_type]; stencil_range = stencil_cut[i][j]; - sx = static_cast (stencil_range*bininvx); + sx = static_cast (stencil_range*bininvx_multi2[bin_type]); if (sx*binsizex < stencil_range) sx++; - sy = static_cast (stencil_range*bininvy); + sy = static_cast (stencil_range*bininvy_multi2[bin_type]); if (sy*binsizey < stencil_range) sy++; - sz = static_cast (stencil_range*bininvz); + sz = static_cast (stencil_range*bininvz_multi2[bin_type]); if (sz*binsizez < stencil_range) sz++; - sx_multi2[i][j] = sx; - sy_multi2[i][j] = sy; - sz_multi2[i][j] = sz; + stencil_sx_multi2[i][j] = sx; + stencil_sy_multi2[i][j] = sy; + stencil_sz_multi2[i][j] = sz; smax = ((2*sx+1) * (2*sy+1) * (2*sz+1)); @@ -383,6 +394,30 @@ double NStencil::bin_distance(int i, int j, int k) return (delx*delx + dely*dely + delz*delz); } + +/* ---------------------------------------------------------------------- + compute closest distance for a given atom type +------------------------------------------------------------------------- */ + +double NStencil::bin_distance_multi2(int i, int j, int k, int type) +{ + double delx,dely,delz; + + if (i > 0) delx = (i-1)*binsizex_multi2[type]; + else if (i == 0) delx = 0.0; + else delx = (i+1)*binsizex_multi2[type]; + + if (j > 0) dely = (j-1)*binsizey_multi2[type]; + else if (j == 0) dely = 0.0; + else dely = (j+1)*binsizey_multi2[type]; + + if (k > 0) delz = (k-1)*binsizez_multi2[type]; + else if (k == 0) delz = 0.0; + else delz = (k+1)*binsizez_multi2[type]; + + return (delx*delx + dely*dely + delz*delz); +} + /* ---------------------------------------------------------------------- */ double NStencil::memory_usage() diff --git a/src/nstencil.h b/src/nstencil.h index 5f010cb377..68c7702f79 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -39,13 +39,13 @@ class NStencil : protected Pointers { // Probably not needed for multi2 since bins are more efficiently chosen int sx,sy,sz; // extent of stencil in each dim - int **sx_multi2; // analogs for multi tiered - int **sy_multi2; - int **sz_multi2; + int **stencil_sx_multi2; // analogs for each multi2 stencil + int **stencil_sy_multi2; + int **stencil_sz_multi2; double cutoff_custom; // cutoff set by requestor - // Arrays to store options for multi/tiered itype-jtype stencils + // Arrays to store options for multi2 itype-jtype stencils bool **stencil_half; // flag creation of a half stencil for itype-jtype bool **stencil_skip; // skip creation of itype-jtype stencils (for newton on) int **stencil_bin_type; // what type to use for bin information @@ -78,15 +78,27 @@ class NStencil : protected Pointers { double binsizex,binsizey,binsizez; double bininvx,bininvy,bininvz; - // analogs for multi-tiered + // data from NBin class for multi2 + + int *mbinx_multi2; + int *mbiny_multi2; + int *mbinz_multi2; + double *binsizex_multi2; + double *binsizey_multi2; + double *binsizez_multi2; + double *bininvx_multi2; + double *bininvy_multi2; + double *bininvz_multi2; + + // Stored bin information for each stencil + + int **stencil_mbinx_multi2; + int **stencil_mbiny_multi2; + int **stencil_mbinz_multi2; + double **stencil_binsizex_multi2; + double **stencil_binsizey_multi2; + double **stencil_binsizez_multi2; - int **mbinx_multi2; - int **mbiny_multi2; - int **mbinz_multi2; - double **binsizex_multi2; - double **binsizey_multi2; - double **binsizez_multi2; - // data common to all NStencil variants int xyzflag; // 1 if stencilxyz is allocated @@ -95,15 +107,16 @@ class NStencil : protected Pointers { int dimension; - // methods for all NStencil variants + // methods for standard NStencil variants void copy_bin_info(); // copy info from NBin class double bin_distance(int, int, int); // distance between bin corners - // methods for multi/tiered NStencil - - void copy_bin_info_multi2(int); // copy mult/tiered info from NBin class - virtual void set_stencil_properties(){} // determine which stencils to build and how + // methods for multi2 NStencil + + double bin_distance_multi2(int, int, int, int); // distance between bin corners for different types + void copy_bin_info_multi2(); // copy mult2 info from NBin class + virtual void set_stencil_properties(){} // determine which stencils to build and how }; } diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index c59edbe90d..627a1e2f9e 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -68,7 +68,7 @@ void NStencilFullMulti22d::set_stencil_properties() void NStencilFullMulti22d::create() { - int itype, jtype, i, j, k, ns; + int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; double cutsq; @@ -79,22 +79,19 @@ void NStencilFullMulti22d::create() ns = 0; - sx = sx_multi2[itype][jtype]; - sy = sy_multi2[itype][jtype]; + sx = stencil_sx_multi2[itype][jtype]; + sy = stencil_sy_multi2[itype][jtype]; - mbinx = mbinx_multi2[itype][jtype]; - mbiny = mbiny_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi2[itype][jtype]; + mbiny = stencil_mbiny_multi2[itype][jtype]; - // Redefine for use in bin_distance() - binsizex = binsizex_multi2[itype][jtype]; - binsizey = binsizey_multi2[itype][jtype]; - binsizez = binsizez_multi2[itype][jtype]; + bin_type = stencil_bin_type[i][j]; cutsq = stencil_cut[itype][jtype]; for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutsq) + if (bin_distance_multi2(i,j,0,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = j*mbinx + i; nstencil_multi2[itype][jtype] = ns; diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 6021382022..19bf30ec07 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -68,7 +68,7 @@ void NStencilFullMulti23d::set_stencil_properties() void NStencilFullMulti23d::create() { - int itype, jtype, i, j, k, ns; + int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; double cutsq; @@ -79,25 +79,22 @@ void NStencilFullMulti23d::create() ns = 0; - sx = sx_multi2[itype][jtype]; - sy = sy_multi2[itype][jtype]; - sz = sz_multi2[itype][jtype]; + sx = stencil_sx_multi2[itype][jtype]; + sy = stencil_sy_multi2[itype][jtype]; + sz = stencil_sz_multi2[itype][jtype]; - mbinx = mbinx_multi2[itype][jtype]; - mbiny = mbiny_multi2[itype][jtype]; - mbinz = mbinz_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi2[itype][jtype]; + mbiny = stencil_mbiny_multi2[itype][jtype]; + mbinz = stencil_mbinz_multi2[itype][jtype]; - // Redefine for use in bin_distance() - binsizex = binsizex_multi2[itype][jtype]; - binsizey = binsizey_multi2[itype][jtype]; - binsizez = binsizez_multi2[itype][jtype]; + bin_type = stencil_bin_type[i][j]; cutsq = stencil_cut[itype][jtype]; for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutsq) + if (bin_distance_multi2(i,j,k,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index 89d2903f1c..2a3c8da45c 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -82,16 +82,11 @@ void NStencilHalfMulti22d::create() ns = 0; - sx = sx_multi2[itype][jtype]; - sy = sy_multi2[itype][jtype]; + sx = stencil_sx_multi2[itype][jtype]; + sy = stencil_sy_multi2[itype][jtype]; - mbinx = mbinx_multi2[itype][jtype]; - mbiny = mbiny_multi2[itype][jtype]; - - // Redefine for use in bin_distance() - binsizex = binsizex_multi2[itype][jtype]; - binsizey = binsizey_multi2[itype][jtype]; - binsizez = binsizez_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi2[itype][jtype]; + mbiny = stencil_mbiny_multi2[itype][jtype]; cutsq = stencil_cut[itype][jtype]; diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp index 4b4019cef2..08568139ad 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -71,7 +71,7 @@ void NStencilHalfMulti22dTri::set_stencil_properties() void NStencilHalfMulti22dTri::create() { - int itype, jtype, i, j, ns; + int itype, jtype, bin_type, i, j, ns; int n = atom->ntypes; double cutsq; @@ -82,28 +82,25 @@ void NStencilHalfMulti22dTri::create() ns = 0; - sx = sx_multi2[itype][jtype]; - sy = sy_multi2[itype][jtype]; + sx = stencil_sx_multi2[itype][jtype]; + sy = stencil_sy_multi2[itype][jtype]; - mbinx = mbinx_multi2[itype][jtype]; - mbiny = mbiny_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi2[itype][jtype]; + mbiny = stencil_mbiny_multi2[itype][jtype]; - // Redefine for use in bin_distance() - binsizex = binsizex_multi2[itype][jtype]; - binsizey = binsizey_multi2[itype][jtype]; - binsizez = binsizez_multi2[itype][jtype]; + bin_type = stencil_bin_type[i][j]; cutsq = stencil_cut[itype][jtype]; if (stencil_half[itype][jtype]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutsq) + if (bin_distance_multi2(i,j,0,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutsq) + if (bin_distance_multi2(i,j,0,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index 1777e748de..21bd29269a 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -71,7 +71,7 @@ void NStencilHalfMulti23d::set_stencil_properties() void NStencilHalfMulti23d::create() { - int itype, jtype, i, j, k, ns; + int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; double cutsq; @@ -82,18 +82,15 @@ void NStencilHalfMulti23d::create() ns = 0; - sx = sx_multi2[itype][jtype]; - sy = sy_multi2[itype][jtype]; - sz = sz_multi2[itype][jtype]; + sx = stencil_sx_multi2[itype][jtype]; + sy = stencil_sy_multi2[itype][jtype]; + sz = stencil_sz_multi2[itype][jtype]; - mbinx = mbinx_multi2[itype][jtype]; - mbiny = mbiny_multi2[itype][jtype]; - mbinz = mbinz_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi2[itype][jtype]; + mbiny = stencil_mbiny_multi2[itype][jtype]; + mbinz = stencil_mbinz_multi2[itype][jtype]; - // Redefine for use in bin_distance() - binsizex = binsizex_multi2[itype][jtype]; - binsizey = binsizey_multi2[itype][jtype]; - binsizez = binsizez_multi2[itype][jtype]; + bin_type = stencil_bin_type[i][j]; cutsq = stencil_cut[itype][jtype]; @@ -102,7 +99,7 @@ void NStencilHalfMulti23d::create() for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (k > 0 || j > 0 || (j == 0 && i > 0)) { - if (bin_distance(i,j,k) < cutsq) + if (bin_distance_multi2(i,j,k,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } @@ -110,7 +107,7 @@ void NStencilHalfMulti23d::create() for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutsq) + if (bin_distance_multi2(i,j,k,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index 4a9ba63b20..1b71a096e3 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -71,7 +71,7 @@ void NStencilHalfMulti23dTri::set_stencil_properties() void NStencilHalfMulti23dTri::create() { - int itype, jtype, i, j, k, ns; + int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; double cutsq; @@ -82,18 +82,15 @@ void NStencilHalfMulti23dTri::create() ns = 0; - sx = sx_multi2[itype][jtype]; - sy = sy_multi2[itype][jtype]; - sz = sz_multi2[itype][jtype]; + sx = stencil_sx_multi2[itype][jtype]; + sy = stencil_sy_multi2[itype][jtype]; + sz = stencil_sz_multi2[itype][jtype]; - mbinx = mbinx_multi2[itype][jtype]; - mbiny = mbiny_multi2[itype][jtype]; - mbinz = mbinz_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi2[itype][jtype]; + mbiny = stencil_mbiny_multi2[itype][jtype]; + mbinz = stencil_mbinz_multi2[itype][jtype]; - // Redefine for use in bin_distance() - binsizex = binsizex_multi2[itype][jtype]; - binsizey = binsizey_multi2[itype][jtype]; - binsizez = binsizez_multi2[itype][jtype]; + bin_type = stencil_bin_type[i][j]; cutsq = stencil_cut[itype][jtype]; @@ -101,14 +98,14 @@ void NStencilHalfMulti23dTri::create() for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutsq) + if (bin_distance_multi2(i,j,k,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutsq) + if (bin_distance_multi2(i,j,k,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } From 00a74558ff441d39b537de9892542c2d83ae5a47 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 22 Nov 2020 20:01:14 -0700 Subject: [PATCH 0025/1217] Fixing typos --- src/comm_brick.cpp | 46 +++++++++++++++++++++-------- src/comm_tiled.cpp | 27 +++++++++++------ src/nstencil.cpp | 1 + src/nstencil_full_multi2_2d.cpp | 2 +- src/nstencil_full_multi2_3d.cpp | 2 +- src/nstencil_half_multi2_2d.cpp | 8 +++-- src/nstencil_half_multi2_2d_tri.cpp | 2 +- src/nstencil_half_multi2_3d.cpp | 2 +- src/nstencil_half_multi2_3d_tri.cpp | 2 +- 9 files changed, 63 insertions(+), 29 deletions(-) diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index e283e08e20..ad8669d6c1 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -158,7 +158,7 @@ void CommBrick::setup() // for multi: // cutghostmulti = same as cutghost, only for each atom type - int i; + int i,j; int ntypes = atom->ntypes; double *prd,*sublo,*subhi; @@ -175,14 +175,23 @@ void CommBrick::setup() if (mode == Comm::MULTI) { if (multi2) { - // If using multi2 binlists, use the itype-itype interaction distance for communication + // If using multi2 binlists, communicate itype particles a distance + // equal to the max of itype-jtype interaction given smaller jtype particles double **cutneighsq = neighbor->cutneighsq; - for (i = 1; i <= ntypes; i++) { + double *cuttypesq = neighbor->cuttypesq; + for (i = 1; i <= ntypes; i++) { cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = MAX(cut,sqrt(cutneighsq[i][i])); - cutghostmulti[i][1] = MAX(cut,sqrt(cutneighsq[i][i])); - cutghostmulti[i][2] = MAX(cut,sqrt(cutneighsq[i][i])); + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } + for (j = 1; j <= ntypes; j++){ + if(cuttypesq[j] > cuttypesq[i]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); + } } } else { // If using a single binlist, use the max itype-jtype interaction distance for communication @@ -212,14 +221,27 @@ void CommBrick::setup() if (mode == Comm::MULTI) { if (multi2) { - // If using multi2 binlists, use the itype-itype interaction distance for communication + // If using multi2 binlists, communicate itype particles a distance + // equal to the max of itype-jtype interaction given smaller jtype particles double **cutneighsq = neighbor->cutneighsq; + double *cuttypesq = neighbor->cuttypesq; for (i = 1; i <= ntypes; i++) { cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = length0 * MAX(cut,sqrt(cutneighsq[i][i])); - cutghostmulti[i][1] = length1 * MAX(cut,sqrt(cutneighsq[i][i])); - cutghostmulti[i][2] = length2 * MAX(cut,sqrt(cutneighsq[i][i])); + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } + for (j = 1; j <= ntypes; j++){ + if(cuttypesq[j] > cuttypesq[i]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); + } + + cutghostmulti[i][0] *= length0; + cutghostmulti[i][1] *= length1; + cutghostmulti[i][2] *= length2; } } else { // If using a single binlist, use the max itype-jtype interaction distance for communication diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 16ae86b4a3..4835251b77 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -177,15 +177,24 @@ void CommTiled::setup() if (mode == Comm::MULTI) { double cut; if (multi2) { - // If using multi2 binlists, use the itype-itype interaction distance for communication - double **cutneighsq = neighbor->cutneighsq; - for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = MAX(cut,sqrt(cutneighsq[i][i])); - cutghostmulti[i][1] = MAX(cut,sqrt(cutneighsq[i][i])); - cutghostmulti[i][2] = MAX(cut,sqrt(cutneighsq[i][i])); - } + // If using multi2 binlists, communicate itype particles a distance + // equal to the max of itype-jtype interaction given smaller jtype particles + double **cutneighsq = neighbor->cutneighsq; + double *cuttypesq = neighbor->cuttypesq; + for (i = 1; i <= ntypes; i++) { + cut = 0.0; + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } + for (j = 1; j <= ntypes; j++){ + if(cuttypesq[j] > cuttypesq[i]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); + } + } } else { // If using a single binlist, use the max itype-jtype interaction distance for communication double *cuttype = neighbor->cuttype; diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 2ace1125e8..57aff6a71b 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -324,6 +324,7 @@ void NStencil::create_setup() stencil_multi2[i] = new int*[n+1](); for (j = 1; j <= n; ++j) { maxstencil_multi2[i][j] = 0; + nstencil_multi2[i][j] = 0; } } } diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index 627a1e2f9e..2a31f95dad 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -85,7 +85,7 @@ void NStencilFullMulti22d::create() mbinx = stencil_mbinx_multi2[itype][jtype]; mbiny = stencil_mbiny_multi2[itype][jtype]; - bin_type = stencil_bin_type[i][j]; + bin_type = stencil_bin_type[itype][jtype]; cutsq = stencil_cut[itype][jtype]; diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 19bf30ec07..e028e631a8 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -87,7 +87,7 @@ void NStencilFullMulti23d::create() mbiny = stencil_mbiny_multi2[itype][jtype]; mbinz = stencil_mbinz_multi2[itype][jtype]; - bin_type = stencil_bin_type[i][j]; + bin_type = stencil_bin_type[itype][jtype]; cutsq = stencil_cut[itype][jtype]; diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index 2a3c8da45c..70aa24f9f2 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -71,7 +71,7 @@ void NStencilHalfMulti22d::set_stencil_properties() void NStencilHalfMulti22d::create() { - int itype, jtype, i, j, ns; + int itype, jtype, bin_type, i, j, ns; int n = atom->ntypes; double cutsq; @@ -88,19 +88,21 @@ void NStencilHalfMulti22d::create() mbinx = stencil_mbinx_multi2[itype][jtype]; mbiny = stencil_mbiny_multi2[itype][jtype]; + bin_type = stencil_bin_type[itype][jtype]; + cutsq = stencil_cut[itype][jtype]; if (stencil_half[itype][jtype]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) if (j > 0 || (j == 0 && i > 0)) { - if (bin_distance(i,j,0) < cutsq) + if (bin_distance_multi2(i,j,0,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutsq) + if (bin_distance_multi2(i,j,0,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = j*mbinx + i; } diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp index 08568139ad..739803c0db 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -88,7 +88,7 @@ void NStencilHalfMulti22dTri::create() mbinx = stencil_mbinx_multi2[itype][jtype]; mbiny = stencil_mbiny_multi2[itype][jtype]; - bin_type = stencil_bin_type[i][j]; + bin_type = stencil_bin_type[itype][jtype]; cutsq = stencil_cut[itype][jtype]; diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index 21bd29269a..1433273f27 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -90,7 +90,7 @@ void NStencilHalfMulti23d::create() mbiny = stencil_mbiny_multi2[itype][jtype]; mbinz = stencil_mbinz_multi2[itype][jtype]; - bin_type = stencil_bin_type[i][j]; + bin_type = stencil_bin_type[itype][jtype]; cutsq = stencil_cut[itype][jtype]; diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index 1b71a096e3..b62993caa2 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -90,7 +90,7 @@ void NStencilHalfMulti23dTri::create() mbiny = stencil_mbiny_multi2[itype][jtype]; mbinz = stencil_mbinz_multi2[itype][jtype]; - bin_type = stencil_bin_type[i][j]; + bin_type = stencil_bin_type[itype][jtype]; cutsq = stencil_cut[itype][jtype]; From de5df539c9f244f62949efdbf51aa8ec75c68bdf Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 22 Nov 2020 20:40:47 -0700 Subject: [PATCH 0026/1217] Changing particle size metric to neighcutsq --- src/nstencil_full_multi2_2d.cpp | 2 +- src/nstencil_full_multi2_3d.cpp | 2 +- src/nstencil_half_multi2_2d.cpp | 4 ++-- src/nstencil_half_multi2_2d_tri.cpp | 4 ++-- src/nstencil_half_multi2_3d.cpp | 4 ++-- src/nstencil_half_multi2_3d_tri.cpp | 4 ++-- 6 files changed, 10 insertions(+), 10 deletions(-) diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index 2a31f95dad..0170fc5cab 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -51,7 +51,7 @@ void NStencilFullMulti22d::set_stencil_properties() stencil_half[i][j] = 0; stencil_skip[i][j] = 0; - if(cuttypesq[i] <= cuttypesq[j]){ + if(cutneighsq[i][i] <= cutneighsq[j][j]){ stencil_cut[i][j] = sqrt(cutneighsq[j][j]); stencil_bin_type[i][j] = j; } else { diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index e028e631a8..72da5b379f 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -51,7 +51,7 @@ void NStencilFullMulti23d::set_stencil_properties() stencil_half[i][j] = 0; stencil_skip[i][j] = 0; - if(cuttypesq[i] <= cuttypesq[j]){ + if(cutneighsq[i][i] <= cutneighsq[j][j]){ stencil_cut[i][j] = sqrt(cutneighsq[j][j]); stencil_bin_type[i][j] = j; } else { diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index 70aa24f9f2..2a84fc0e34 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -49,12 +49,12 @@ void NStencilHalfMulti22d::set_stencil_properties() for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { if(i == j) continue; - if(cuttypesq[i] > cuttypesq[j]) continue; + if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; stencil_cut[i][j] = sqrt(cutneighsq[i][j]); - if(cuttypesq[i] == cuttypesq[j]){ + if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; stencil_bin_type[i][j] = i; } else { diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp index 739803c0db..f91e0f6524 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -49,12 +49,12 @@ void NStencilHalfMulti22dTri::set_stencil_properties() for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { if(i == j) continue; - if(cuttypesq[i] > cuttypesq[j]) continue; + if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; stencil_cut[i][j] = sqrt(cutneighsq[i][j]); - if(cuttypesq[i] == cuttypesq[j]){ + if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; stencil_bin_type[i][j] = i; } else { diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index 1433273f27..fb6b5d8cd9 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -49,12 +49,12 @@ void NStencilHalfMulti23d::set_stencil_properties() for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { if(i == j) continue; - if(cuttypesq[i] > cuttypesq[j]) continue; + if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; stencil_cut[i][j] = sqrt(cutneighsq[i][j]); - if(cuttypesq[i] == cuttypesq[j]){ + if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; stencil_bin_type[i][j] = i; } else { diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index b62993caa2..013688081e 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -49,12 +49,12 @@ void NStencilHalfMulti23dTri::set_stencil_properties() for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { if(i == j) continue; - if(cuttypesq[i] > cuttypesq[j]) continue; + if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; stencil_cut[i][j] = sqrt(cutneighsq[i][j]); - if(cuttypesq[i] == cuttypesq[j]){ + if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; stencil_bin_type[i][j] = i; } else { From d7047245f412fb969ef0bd120a9d83a0d37eb1d0 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 22 Nov 2020 21:22:29 -0700 Subject: [PATCH 0027/1217] Add cross type self bin check for newton --- src/npair_half_multi2_newton.cpp | 39 +++++++++++++++++++++++ src/npair_half_multi2_newton_tri.cpp | 13 ++++++++ src/npair_half_size_multi2_newton.cpp | 33 +++++++++++++++++++ src/npair_half_size_multi2_newton_tri.cpp | 13 ++++++++ 4 files changed, 98 insertions(+) diff --git a/src/npair_half_multi2_newton.cpp b/src/npair_half_multi2_newton.cpp index 58397f645e..413da06284 100755 --- a/src/npair_half_multi2_newton.cpp +++ b/src/npair_half_multi2_newton.cpp @@ -163,6 +163,45 @@ void NPairHalfMulti2Newton::build(NeighList *list) // smaller -> larger: locate i in the ktype bin structure kbin = coord2bin(x[i], ktype); + + // if same size, use half list so check own bin + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + js = binhead_multi2[ktype][kbin]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + s = stencil_multi2[itype][ktype]; ns = nstencil_multi2[itype][ktype]; diff --git a/src/npair_half_multi2_newton_tri.cpp b/src/npair_half_multi2_newton_tri.cpp index c741a860f1..7970ee94a0 100755 --- a/src/npair_half_multi2_newton_tri.cpp +++ b/src/npair_half_multi2_newton_tri.cpp @@ -143,6 +143,19 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) for (j = js; j >= 0; j = bins_multi2[ktype][j]) { jtype = type[j]; + + // if same size, use half stencil + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + } + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/npair_half_size_multi2_newton.cpp b/src/npair_half_size_multi2_newton.cpp index a1832f6a49..3b34b1a514 100755 --- a/src/npair_half_size_multi2_newton.cpp +++ b/src/npair_half_size_multi2_newton.cpp @@ -138,6 +138,39 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) // smaller -> larger: locate i in the ktype bin structure kbin = coord2bin(x[i], ktype); + // if same size, use half list so check own bin + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + js = binhead_multi2[ktype][kbin]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + // Check other stencils + s = stencil_multi2[itype][ktype]; ns = nstencil_multi2[itype][ktype]; for (k = 0; k < ns; k++) { diff --git a/src/npair_half_size_multi2_newton_tri.cpp b/src/npair_half_size_multi2_newton_tri.cpp index 1c0c1d514f..3a2065c36e 100755 --- a/src/npair_half_size_multi2_newton_tri.cpp +++ b/src/npair_half_size_multi2_newton_tri.cpp @@ -115,6 +115,7 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) } } else { // smaller -> larger: locate i in the ktype bin structure + kbin = coord2bin(x[i], ktype); s = stencil_multi2[itype][ktype]; @@ -124,6 +125,18 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) for (j = js; j >= 0; j = bins_multi2[ktype][j]) { jtype = type[j]; + + // if same size, use half stencil + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + } if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; From 9b9e5022d67dd341c3126e965c6f161a9905049f Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Thu, 26 Nov 2020 14:57:48 -0700 Subject: [PATCH 0028/1217] initializing comm distances, temporarily sorting nlit dumps --- src/comm_brick.cpp | 18 ++++++++++++---- src/comm_tiled.cpp | 9 ++++++-- src/compute_property_local.cpp | 38 +++++++++++++++++++++++++--------- 3 files changed, 49 insertions(+), 16 deletions(-) diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index ad8669d6c1..9daca70233 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -180,14 +180,19 @@ void CommBrick::setup() double **cutneighsq = neighbor->cutneighsq; double *cuttypesq = neighbor->cuttypesq; for (i = 1; i <= ntypes; i++) { - cut = 0.0; + if (cutusermulti) { cutghostmulti[i][0] = cutusermulti[i]; cutghostmulti[i][1] = cutusermulti[i]; cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; } + for (j = 1; j <= ntypes; j++){ - if(cuttypesq[j] > cuttypesq[i]) continue; + if(cutneighsq[j][j] > cutneighsq[i][i]) continue; cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); @@ -226,14 +231,19 @@ void CommBrick::setup() double **cutneighsq = neighbor->cutneighsq; double *cuttypesq = neighbor->cuttypesq; for (i = 1; i <= ntypes; i++) { - cut = 0.0; + if (cutusermulti) { cutghostmulti[i][0] = cutusermulti[i]; cutghostmulti[i][1] = cutusermulti[i]; cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; } + for (j = 1; j <= ntypes; j++){ - if(cuttypesq[j] > cuttypesq[i]) continue; + if(cutneighsq[j][j] > cutneighsq[i][i]) continue; cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 4835251b77..6657977eee 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -182,14 +182,19 @@ void CommTiled::setup() double **cutneighsq = neighbor->cutneighsq; double *cuttypesq = neighbor->cuttypesq; for (i = 1; i <= ntypes; i++) { - cut = 0.0; + if (cutusermulti) { cutghostmulti[i][0] = cutusermulti[i]; cutghostmulti[i][1] = cutusermulti[i]; cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; } + for (j = 1; j <= ntypes; j++){ - if(cuttypesq[j] > cuttypesq[i]) continue; + if(cutneighsq[j][j] > cutneighsq[i][i]) continue; cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp index 36940164aa..fd0391831c 100644 --- a/src/compute_property_local.cpp +++ b/src/compute_property_local.cpp @@ -665,12 +665,16 @@ double ComputePropertyLocal::memory_usage() void ComputePropertyLocal::pack_patom1(int n) { - int i; + int i,j; tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { i = indices[m][0]; - buf[n] = tag[i]; + j = indices[m][1]; + if(tag[i] < tag[j]) + buf[n] = tag[i]; + else + buf[n] = tag[j]; n += nvalues; } } @@ -679,12 +683,16 @@ void ComputePropertyLocal::pack_patom1(int n) void ComputePropertyLocal::pack_patom2(int n) { - int i; + int i,j; tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { - i = indices[m][1]; - buf[n] = tag[i]; + i = indices[m][0]; + j = indices[m][1]; + if(tag[i] > tag[j]) + buf[n] = tag[i]; + else + buf[n] = tag[j]; n += nvalues; } } @@ -693,12 +701,17 @@ void ComputePropertyLocal::pack_patom2(int n) void ComputePropertyLocal::pack_ptype1(int n) { - int i; + int i,j; int *type = atom->type; + tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { i = indices[m][0]; - buf[n] = type[i]; + j = indices[m][1]; + if(tag[i] < tag[j]) + buf[n] = type[i]; + else + buf[n] = type[j]; n += nvalues; } } @@ -707,12 +720,17 @@ void ComputePropertyLocal::pack_ptype1(int n) void ComputePropertyLocal::pack_ptype2(int n) { - int i; + int i,j; int *type = atom->type; + tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { - i = indices[m][1]; - buf[n] = type[i]; + i = indices[m][0]; + j = indices[m][1]; + if(tag[i] > tag[j]) + buf[n] = type[i]; + else + buf[n] = type[j]; n += nvalues; } } From 73a6bb36216f8049ce0ba92162f85a8acae71b52 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Thu, 26 Nov 2020 15:58:05 -0700 Subject: [PATCH 0029/1217] Fixing mistake with stencil cutoffs not being squ squared --- src/nstencil.cpp | 10 +++++----- src/nstencil.h | 2 +- src/nstencil_full_multi2_2d.cpp | 8 ++++---- src/nstencil_full_multi2_3d.cpp | 8 ++++---- src/nstencil_half_multi2_2d.cpp | 6 +++--- src/nstencil_half_multi2_2d_tri.cpp | 6 +++--- src/nstencil_half_multi2_3d.cpp | 6 +++--- src/nstencil_half_multi2_3d_tri.cpp | 6 +++--- 8 files changed, 26 insertions(+), 26 deletions(-) diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 57aff6a71b..e362662dde 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -82,7 +82,7 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) stencil_half = nullptr; stencil_skip = nullptr; stencil_bin_type = nullptr; - stencil_cut = nullptr; + stencil_cutsq = nullptr; dimension = domain->dimension; } @@ -122,7 +122,7 @@ NStencil::~NStencil() memory->destroy(stencil_half); memory->destroy(stencil_skip); memory->destroy(stencil_bin_type); - memory->destroy(stencil_cut); + memory->destroy(stencil_cutsq); memory->destroy(stencil_sx_multi2); memory->destroy(stencil_sy_multi2); @@ -280,8 +280,8 @@ void NStencil::create_setup() "neighstencil:stencil_skip"); memory->create(stencil_bin_type, n+1, n+1, "neighstencil:stencil_bin_type"); - memory->create(stencil_cut, n+1, n+1, - "neighstencil:stencil_cut"); + memory->create(stencil_cutsq, n+1, n+1, + "neighstencil:stencil_cutsq"); memory->create(stencil_sx_multi2, n+1, n+1, "neighstencil:stencil_sx_multi2"); @@ -346,7 +346,7 @@ void NStencil::create_setup() stencil_mbiny_multi2[i][j] = mbiny_multi2[bin_type]; stencil_mbinz_multi2[i][j] = mbinz_multi2[bin_type]; - stencil_range = stencil_cut[i][j]; + stencil_range = sqrt(stencil_cutsq[i][j]); sx = static_cast (stencil_range*bininvx_multi2[bin_type]); if (sx*binsizex < stencil_range) sx++; diff --git a/src/nstencil.h b/src/nstencil.h index 68c7702f79..3c10221603 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -49,7 +49,7 @@ class NStencil : protected Pointers { bool **stencil_half; // flag creation of a half stencil for itype-jtype bool **stencil_skip; // skip creation of itype-jtype stencils (for newton on) int **stencil_bin_type; // what type to use for bin information - double **stencil_cut; // cutoff used for stencil size + double **stencil_cutsq; // cutoff used for stencil size NStencil(class LAMMPS *); virtual ~NStencil(); diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index 0170fc5cab..a10798677d 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -37,7 +37,7 @@ void NStencilFullMulti22d::set_stencil_properties() stencil_half[i][i] = 0; stencil_skip[i][i] = 0; stencil_bin_type[i][i] = i; - stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + stencil_cutsq[i][i] = cutneighsq[i][i]; } // smaller -> larger => use existing newtoff stencil in larger bin @@ -52,10 +52,10 @@ void NStencilFullMulti22d::set_stencil_properties() stencil_skip[i][j] = 0; if(cutneighsq[i][i] <= cutneighsq[j][j]){ - stencil_cut[i][j] = sqrt(cutneighsq[j][j]); + stencil_cutsq[i][j] = cutneighsq[j][j]; stencil_bin_type[i][j] = j; } else { - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + stencil_cutsq[i][j] = cutneighsq[i][j]; stencil_bin_type[i][j] = j; } } @@ -87,7 +87,7 @@ void NStencilFullMulti22d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cut[itype][jtype]; + cutsq = stencil_cutsq[itype][jtype]; for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 72da5b379f..7e224be7ab 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -37,7 +37,7 @@ void NStencilFullMulti23d::set_stencil_properties() stencil_half[i][i] = 0; stencil_skip[i][i] = 0; stencil_bin_type[i][i] = i; - stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + stencil_cutsq[i][i] = cutneighsq[i][i]; } // smaller -> larger => use existing newtoff stencil in larger bin @@ -52,10 +52,10 @@ void NStencilFullMulti23d::set_stencil_properties() stencil_skip[i][j] = 0; if(cutneighsq[i][i] <= cutneighsq[j][j]){ - stencil_cut[i][j] = sqrt(cutneighsq[j][j]); + stencil_cutsq[i][j] = cutneighsq[j][j]; stencil_bin_type[i][j] = j; } else { - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + stencil_cutsq[i][j] = cutneighsq[i][j]; stencil_bin_type[i][j] = j; } } @@ -89,7 +89,7 @@ void NStencilFullMulti23d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cut[itype][jtype]; + cutsq = stencil_cutsq[itype][jtype]; for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index 2a84fc0e34..7ea058e70b 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -38,7 +38,7 @@ void NStencilHalfMulti22d::set_stencil_properties() stencil_half[i][i] = 1; stencil_skip[i][i] = 0; stencil_bin_type[i][i] = i; - stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + stencil_cutsq[i][i] = cutneighsq[i][i]; } // Cross types: use full stencil, looking one way through hierarchy @@ -52,7 +52,7 @@ void NStencilHalfMulti22d::set_stencil_properties() if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -90,7 +90,7 @@ void NStencilHalfMulti22d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cut[itype][jtype]; + cutsq = stencil_cutsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (j = 0; j <= sy; j++) diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp index f91e0f6524..fb974877af 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -38,7 +38,7 @@ void NStencilHalfMulti22dTri::set_stencil_properties() stencil_half[i][i] = 1; stencil_skip[i][i] = 0; stencil_bin_type[i][i] = i; - stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + stencil_cutsq[i][i] = cutneighsq[i][i]; } // Cross types: use full stencil, looking one way through hierarchy @@ -52,7 +52,7 @@ void NStencilHalfMulti22dTri::set_stencil_properties() if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -90,7 +90,7 @@ void NStencilHalfMulti22dTri::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cut[itype][jtype]; + cutsq = stencil_cutsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (j = 0; j <= sy; j++) diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index fb6b5d8cd9..92cdc4e5e6 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -38,7 +38,7 @@ void NStencilHalfMulti23d::set_stencil_properties() stencil_half[i][i] = 1; stencil_skip[i][i] = 0; stencil_bin_type[i][i] = i; - stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + stencil_cutsq[i][i] = cutneighsq[i][i]; } // Cross types: use full stencil, looking one way through hierarchy @@ -52,7 +52,7 @@ void NStencilHalfMulti23d::set_stencil_properties() if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -92,7 +92,7 @@ void NStencilHalfMulti23d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cut[itype][jtype]; + cutsq = stencil_cutsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (k = 0; k <= sz; k++) diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index 013688081e..d114635113 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -38,7 +38,7 @@ void NStencilHalfMulti23dTri::set_stencil_properties() stencil_half[i][i] = 1; stencil_skip[i][i] = 0; stencil_bin_type[i][i] = i; - stencil_cut[i][i] = sqrt(cutneighsq[i][i]); + stencil_cutsq[i][i] = cutneighsq[i][i]; } // Cross types: use full stencil, looking one way through hierarchy @@ -52,7 +52,7 @@ void NStencilHalfMulti23dTri::set_stencil_properties() if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cut[i][j] = sqrt(cutneighsq[i][j]); + stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -92,7 +92,7 @@ void NStencilHalfMulti23dTri::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cut[itype][jtype]; + cutsq = stencil_cutsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (k = 0; k <= sz; k++) From f8d35139c359803938e85eceb1a8f16ab6dfc7eb Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Fri, 27 Nov 2020 17:16:52 -0700 Subject: [PATCH 0030/1217] Adding files for OMP --- src/USER-OMP/npair_full_multi2_omp.cpp | 149 ++++++++++ src/USER-OMP/npair_full_multi2_omp.h | 44 +++ .../npair_half_multi2_newtoff_omp.cpp | 154 +++++++++++ src/USER-OMP/npair_half_multi2_newtoff_omp.h | 43 +++ src/USER-OMP/npair_half_multi2_newton_omp.cpp | 259 ++++++++++++++++++ src/USER-OMP/npair_half_multi2_newton_omp.h | 43 +++ .../npair_half_multi2_newton_tri_omp.cpp | 206 ++++++++++++++ .../npair_half_multi2_newton_tri_omp.h | 43 +++ .../npair_half_size_multi2_newtoff_omp.cpp | 135 +++++++++ .../npair_half_size_multi2_newtoff_omp.h | 43 +++ .../npair_half_size_multi2_newton_omp.cpp | 221 +++++++++++++++ .../npair_half_size_multi2_newton_omp.h | 43 +++ .../npair_half_size_multi2_newton_tri_omp.cpp | 181 ++++++++++++ .../npair_half_size_multi2_newton_tri_omp.h | 43 +++ 14 files changed, 1607 insertions(+) create mode 100755 src/USER-OMP/npair_full_multi2_omp.cpp create mode 100755 src/USER-OMP/npair_full_multi2_omp.h create mode 100755 src/USER-OMP/npair_half_multi2_newtoff_omp.cpp create mode 100755 src/USER-OMP/npair_half_multi2_newtoff_omp.h create mode 100755 src/USER-OMP/npair_half_multi2_newton_omp.cpp create mode 100755 src/USER-OMP/npair_half_multi2_newton_omp.h create mode 100755 src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp create mode 100755 src/USER-OMP/npair_half_multi2_newton_tri_omp.h create mode 100755 src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp create mode 100755 src/USER-OMP/npair_half_size_multi2_newtoff_omp.h create mode 100755 src/USER-OMP/npair_half_size_multi2_newton_omp.cpp create mode 100755 src/USER-OMP/npair_half_size_multi2_newton_omp.h create mode 100755 src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp create mode 100755 src/USER-OMP/npair_half_size_multi2_newton_tri_omp.h diff --git a/src/USER-OMP/npair_full_multi2_omp.cpp b/src/USER-OMP/npair_full_multi2_omp.cpp new file mode 100755 index 0000000000..8e025806c9 --- /dev/null +++ b/src/USER-OMP/npair_full_multi2_omp.cpp @@ -0,0 +1,149 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "omp_compat.h" +#include "npair_full_multi2_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "domain.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairFullMulti2Omp::NPairFullMulti2Omp(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction for all neighbors + multi-type stencil is itype dependent and is distance checked + every neighbor pair appears in list of both atoms i and j +------------------------------------------------------------------------- */ + +void NPairFullMulti2Omp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int molecular = atom->molecular; + const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + int js; + + // loop over each atom, storing neighbors + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + for (i = ifrom; i < ito; i++) { + + n = 0; + neighptr = ipage.vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // loop over all atoms in other bins in stencil, including self + // skip if i,j neighbor cutoff is less than bin distance + // skip i = j + + ibin = atom2bin_multi2[itype][i]; + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + if (itype == ktype) { + kbin = ibin; + } else { + // Locate i in ktype bin + kbin = coord2bin(x[i], ktype); + } + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if (i == j) continue; + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + } + + ilist[i] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + NPAIR_OMP_CLOSE; + list->inum = nlocal; + list->gnum = 0; +} diff --git a/src/USER-OMP/npair_full_multi2_omp.h b/src/USER-OMP/npair_full_multi2_omp.h new file mode 100755 index 0000000000..d2bc478532 --- /dev/null +++ b/src/USER-OMP/npair_full_multi2_omp.h @@ -0,0 +1,44 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(full/multi2/omp, + NPairFullMulti2Omp, + NP_FULL | NP_MULTI2 | NP_OMP | + NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_FULL_MULTI2_OMP_H +#define LMP_NPAIR_FULL_MULTI2_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairFullMulti2Omp : public NPair { + public: + NPairFullMulti2Omp(class LAMMPS *); + ~NPairFullMulti2Omp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp new file mode 100755 index 0000000000..44689e1efc --- /dev/null +++ b/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp @@ -0,0 +1,154 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "omp_compat.h" +#include "npair_half_multi2_newtoff_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "domain.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfMulti2NewtoffOmp::NPairHalfMulti2NewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with partial Newton's 3rd law + each owned atom i checks own bin and other bins in stencil + multi-type stencil is itype dependent and is distance checked + pair stored once if i,j are both owned and i < j + pair stored by me if j is ghost (also stored by proc owning j) +------------------------------------------------------------------------- */ + +void NPairHalfMulti2NewtoffOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int molecular = atom->molecular; + const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + int js; + + // loop over each atom, storing neighbors + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + for (i = ifrom; i < ito; i++) { + + n = 0; + neighptr = ipage.vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // skip if i,j neighbor cutoff is less than bin distance + // stores own/own pairs only once + // stores own/ghost pairs on both procs + + ibin = atom2bin_multi2[itype][i]; + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + if (itype == ktype) { + kbin = ibin; + } else { + // Locate i in ktype bin + kbin = coord2bin(x[i], ktype); + } + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >=0; j = bins_multi2[ktype][j]) { + if (j <= i) continue; + + jtype = type[j]; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + } + + + ilist[i] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + NPAIR_OMP_CLOSE; + list->inum = nlocal; +} diff --git a/src/USER-OMP/npair_half_multi2_newtoff_omp.h b/src/USER-OMP/npair_half_multi2_newtoff_omp.h new file mode 100755 index 0000000000..a9e9a842cb --- /dev/null +++ b/src/USER-OMP/npair_half_multi2_newtoff_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/multi2/newtoff/omp, + NPairHalfMulti2NewtoffOmp, + NP_HALF | NP_MULTI2 | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI2_NEWTOFF_OMP_H +#define LMP_NPAIR_HALF_MULTI2_NEWTOFF_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMulti2NewtoffOmp : public NPair { + public: + NPairHalfMulti2NewtoffOmp(class LAMMPS *); + ~NPairHalfMulti2NewtoffOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_multi2_newton_omp.cpp new file mode 100755 index 0000000000..cc86410fa9 --- /dev/null +++ b/src/USER-OMP/npair_half_multi2_newton_omp.cpp @@ -0,0 +1,259 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "omp_compat.h" +#include "npair_half_multi2_newton_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "domain.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfMulti2NewtonOmp::NPairHalfMulti2NewtonOmp(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with full Newton's 3rd law + each owned atom i checks its own bin and other bins in Newton stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfMulti2NewtonOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int molecular = atom->molecular; + const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + int js; + + // loop over each atom, storing neighbors + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + for (i = ifrom; i < ito; i++) { + + n = 0; + neighptr = ipage.vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = atom2bin_multi2[itype][i]; + + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + if (itype == ktype) { + + // own bin ... + js = bins_multi2[itype][i]; + for (j = js; j >= 0; j = bins_multi2[itype][j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + } else { + // smaller -> larger: locate i in the ktype bin structure + + kbin = coord2bin(x[i], ktype); + + // if same size, use half list so check own bin + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + js = binhead_multi2[ktype][kbin]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + } + } + + ilist[i] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + NPAIR_OMP_CLOSE; + list->inum = nlocal; +} diff --git a/src/USER-OMP/npair_half_multi2_newton_omp.h b/src/USER-OMP/npair_half_multi2_newton_omp.h new file mode 100755 index 0000000000..2ea2bd1ad0 --- /dev/null +++ b/src/USER-OMP/npair_half_multi2_newton_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/multi2/newton/omp, + NPairHalfMulti2NewtonOmp, + NP_HALF | NP_MULTI2 | NP_NEWTON | NP_OMP | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_OMP_H +#define LMP_NPAIR_HALF_MULTI2_NEWTON_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMulti2NewtonOmp : public NPair { + public: + NPairHalfMulti2NewtonOmp(class LAMMPS *); + ~NPairHalfMulti2NewtonOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp new file mode 100755 index 0000000000..707c247607 --- /dev/null +++ b/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp @@ -0,0 +1,206 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "omp_compat.h" +#include "npair_half_multi2_newton_tri_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "domain.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfMulti2NewtonTriOmp::NPairHalfMulti2NewtonTriOmp(LAMMPS *lmp) : + NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with Newton's 3rd law for triclinic + each owned atom i checks its own bin and other bins in triclinic stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int molecular = atom->molecular; + const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + int js; + + // loop over each atom, storing neighbors + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + for (i = ifrom; i < ito; i++) { + + n = 0; + neighptr = ipage.vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = atom2bin_multi2[itype][i]; + + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + + if (itype == ktype) { + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][j]) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + } else { + // smaller -> larger: locate i in the ktype bin structure + + kbin = coord2bin(x[i], ktype); + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + + jtype = type[j]; + + // if same size, use half stencil + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + } + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + } + } + + ilist[i] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + NPAIR_OMP_CLOSE; + list->inum = nlocal; +} diff --git a/src/USER-OMP/npair_half_multi2_newton_tri_omp.h b/src/USER-OMP/npair_half_multi2_newton_tri_omp.h new file mode 100755 index 0000000000..dd9eea6847 --- /dev/null +++ b/src/USER-OMP/npair_half_multi2_newton_tri_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/multi2/newton/tri/omp, + NPairHalfMulti2NewtonTriOmp, + NP_HALF | NP_MULTI2 | NP_NEWTON | NP_TRI | NP_OMP) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_OMP_H +#define LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMulti2NewtonTriOmp : public NPair { + public: + NPairHalfMulti2NewtonTriOmp(class LAMMPS *); + ~NPairHalfMulti2NewtonTriOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp new file mode 100755 index 0000000000..d4578985ed --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp @@ -0,0 +1,135 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "omp_compat.h" +#include "npair_half_size_multi2_newtoff_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMulti2NewtoffOmp::NPairHalfSizeMulti2NewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with partial Newton's 3rd law + each owned atom i checks own bin and other bins in stencil + multi-type stencil is itype dependent and is distance checked + pair stored once if i,j are both owned and i < j + pair stored by me if j is ghost (also stored by proc owning j) +------------------------------------------------------------------------- */ + +void NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int history = list->history; + const int mask_history = 3 << SBBITS; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + int js; + + // loop over each atom, storing neighbors + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + for (i = ifrom; i < ito; i++) { + + n = 0; + neighptr = ipage.vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // skip if i,j neighbor cutoff is less than bin distance + // stores own/own pairs only once + // stores own/ghost pairs on both procs + + ibin = atom2bin_multi2[itype][i]; + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + if (itype == ktype) { + kbin = ibin; + } else { + // Locate i in ktype bin + kbin = coord2bin(x[i], ktype); + } + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >=0; j = bins_multi2[ktype][j]) { + if (j <= i) continue; + + jtype = type[j]; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + } + + + ilist[i] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + NPAIR_OMP_CLOSE; + list->inum = nlocal; +} diff --git a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.h b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.h new file mode 100755 index 0000000000..fd592d839c --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi2/newtoff/omp, + NPairHalfSizeMulti2NewtoffOmp, + NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMulti2NewtoffOmp : public NPair { + public: + NPairHalfSizeMulti2NewtoffOmp(class LAMMPS *); + ~NPairHalfSizeMulti2NewtoffOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp new file mode 100755 index 0000000000..5d8080f913 --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp @@ -0,0 +1,221 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "omp_compat.h" +#include "npair_half_size_multi2_newton_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMulti2NewtonOmp::NPairHalfSizeMulti2NewtonOmp(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with full Newton's 3rd law + each owned atom i checks its own bin and other bins in Newton stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int history = list->history; + const int mask_history = 3 << SBBITS; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + int js; + + // loop over each atom, storing neighbors + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + for (i = ifrom; i < ito; i++) { + + n = 0; + neighptr = ipage.vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = atom2bin_multi2[itype][i]; + + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + + if (itype == ktype) { + + // own bin ... + js = bins_multi2[itype][i]; + for (j = js; j >= 0; j = bins_multi2[itype][j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][j]) { + jtype = type[j]; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + } else { + // smaller -> larger: locate i in the ktype bin structure + kbin = coord2bin(x[i], ktype); + + // if same size, use half list so check own bin + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + js = binhead_multi2[ktype][kbin]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + // Check other stencils + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + + jtype = type[j]; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + } + } + + ilist[i] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + NPAIR_OMP_CLOSE; + list->inum = nlocal; +} diff --git a/src/USER-OMP/npair_half_size_multi2_newton_omp.h b/src/USER-OMP/npair_half_size_multi2_newton_omp.h new file mode 100755 index 0000000000..38b4dde272 --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi2_newton_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi2/newton/omp, + NPairHalfSizeMulti2NewtonOmp, + NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_OMP | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMulti2NewtonOmp : public NPair { + public: + NPairHalfSizeMulti2NewtonOmp(class LAMMPS *); + ~NPairHalfSizeMulti2NewtonOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp new file mode 100755 index 0000000000..12365ff27c --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp @@ -0,0 +1,181 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "omp_compat.h" +#include "npair_half_size_multi2_newton_tri_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMulti2NewtonTriOmp::NPairHalfSizeMulti2NewtonTriOmp(LAMMPS *lmp) : + NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with Newton's 3rd law for triclinic + each owned atom i checks its own bin and other bins in triclinic stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int history = list->history; + const int mask_history = 3 << SBBITS; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + int js; + + // loop over each atom, storing neighbors + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + for (i = ifrom; i < ito; i++) { + + n = 0; + neighptr = ipage.vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + // own type: loop over atoms ahead in bin, including ghosts at end of list + // if j is owned atom, store by virtue of being ahead of i in list + // if j is ghost, store if x[j] "above and to right of" x[i] + + ibin = atom2bin_multi2[itype][i]; + + for (ktype = 1; ktype <= atom->ntypes; ktype++) { + + if (itype == ktype) { + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + s = stencil_multi2[itype][itype]; + ns = nstencil_multi2[itype][itype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[itype][ibin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[itype][j]) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + jtype = type[j]; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + } else { + // smaller -> larger: locate i in the ktype bin structure + + kbin = coord2bin(x[i], ktype); + + s = stencil_multi2[itype][ktype]; + ns = nstencil_multi2[itype][ktype]; + for (k = 0; k < ns; k++) { + js = binhead_multi2[ktype][kbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + + jtype = type[j]; + + // if same size, use half stencil + if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + } + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + } + } + + ilist[i] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + NPAIR_OMP_CLOSE; + list->inum = nlocal; +} diff --git a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.h new file mode 100755 index 0000000000..494a419c8f --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi2/newton/tri/omp, + NPairHalfSizeMulti2NewtonTriOmp, + NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_TRI | NP_OMP) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMulti2NewtonTriOmp : public NPair { + public: + NPairHalfSizeMulti2NewtonTriOmp(class LAMMPS *); + ~NPairHalfSizeMulti2NewtonTriOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ From cea20da5be0d8088468cf301d66cd0f91fb9965e Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 29 Nov 2020 16:07:20 -0700 Subject: [PATCH 0031/1217] Simplifying stencils --- src/nstencil.cpp | 6 +----- src/nstencil.h | 1 - src/nstencil_full_multi2_2d.cpp | 25 +++---------------------- src/nstencil_full_multi2_3d.cpp | 26 ++++---------------------- src/nstencil_half_multi2_2d.cpp | 16 +++------------- src/nstencil_half_multi2_2d_tri.cpp | 16 +++------------- src/nstencil_half_multi2_3d.cpp | 16 +++------------- src/nstencil_half_multi2_3d_tri.cpp | 16 +++------------- 8 files changed, 20 insertions(+), 102 deletions(-) diff --git a/src/nstencil.cpp b/src/nstencil.cpp index e362662dde..1658654e5a 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -82,7 +82,6 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) stencil_half = nullptr; stencil_skip = nullptr; stencil_bin_type = nullptr; - stencil_cutsq = nullptr; dimension = domain->dimension; } @@ -122,7 +121,6 @@ NStencil::~NStencil() memory->destroy(stencil_half); memory->destroy(stencil_skip); memory->destroy(stencil_bin_type); - memory->destroy(stencil_cutsq); memory->destroy(stencil_sx_multi2); memory->destroy(stencil_sy_multi2); @@ -280,8 +278,6 @@ void NStencil::create_setup() "neighstencil:stencil_skip"); memory->create(stencil_bin_type, n+1, n+1, "neighstencil:stencil_bin_type"); - memory->create(stencil_cutsq, n+1, n+1, - "neighstencil:stencil_cutsq"); memory->create(stencil_sx_multi2, n+1, n+1, "neighstencil:stencil_sx_multi2"); @@ -346,7 +342,7 @@ void NStencil::create_setup() stencil_mbiny_multi2[i][j] = mbiny_multi2[bin_type]; stencil_mbinz_multi2[i][j] = mbinz_multi2[bin_type]; - stencil_range = sqrt(stencil_cutsq[i][j]); + stencil_range = sqrt(cutneighsq[i][j]); sx = static_cast (stencil_range*bininvx_multi2[bin_type]); if (sx*binsizex < stencil_range) sx++; diff --git a/src/nstencil.h b/src/nstencil.h index 3c10221603..60e584b2a0 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -49,7 +49,6 @@ class NStencil : protected Pointers { bool **stencil_half; // flag creation of a half stencil for itype-jtype bool **stencil_skip; // skip creation of itype-jtype stencils (for newton on) int **stencil_bin_type; // what type to use for bin information - double **stencil_cutsq; // cutoff used for stencil size NStencil(class LAMMPS *); virtual ~NStencil(); diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi2_2d.cpp index a10798677d..658dba1c28 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi2_2d.cpp @@ -32,32 +32,13 @@ void NStencilFullMulti22d::set_stencil_properties() int n = atom->ntypes; int i, j; - // like -> like => use half stencil - for (i = 1; i <= n; i++) { - stencil_half[i][i] = 0; - stencil_skip[i][i] = 0; - stencil_bin_type[i][i] = i; - stencil_cutsq[i][i] = cutneighsq[i][i]; - } - - // smaller -> larger => use existing newtoff stencil in larger bin - // larger -> smaller => use multi-like stencil for small-large in smaller bin - // If types are same cutoff, use existing like-like stencil. + // Always look up neighbor using full stencil and neighbor's bin for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - if(i == j) continue; - stencil_half[i][j] = 0; stencil_skip[i][j] = 0; - - if(cutneighsq[i][i] <= cutneighsq[j][j]){ - stencil_cutsq[i][j] = cutneighsq[j][j]; - stencil_bin_type[i][j] = j; - } else { - stencil_cutsq[i][j] = cutneighsq[i][j]; - stencil_bin_type[i][j] = j; - } + stencil_bin_type[i][j] = j; } } } @@ -87,7 +68,7 @@ void NStencilFullMulti22d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cutsq[itype][jtype]; + cutsq = cutneighsq[itype][jtype]; for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi2_3d.cpp index 7e224be7ab..7bbe5208f2 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi2_3d.cpp @@ -32,32 +32,14 @@ void NStencilFullMulti23d::set_stencil_properties() int n = atom->ntypes; int i, j; - // like -> like => use half stencil - for (i = 1; i <= n; i++) { - stencil_half[i][i] = 0; - stencil_skip[i][i] = 0; - stencil_bin_type[i][i] = i; - stencil_cutsq[i][i] = cutneighsq[i][i]; - } - - // smaller -> larger => use existing newtoff stencil in larger bin - // larger -> smaller => use multi-like stencil for small-large in smaller bin - // If types are same cutoff, use existing like-like stencil. + // Always look up neighbor using full stencil and neighbor's bin + // Stencil cutoff set by i-j cutoff for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - if(i == j) continue; - stencil_half[i][j] = 0; stencil_skip[i][j] = 0; - - if(cutneighsq[i][i] <= cutneighsq[j][j]){ - stencil_cutsq[i][j] = cutneighsq[j][j]; - stencil_bin_type[i][j] = j; - } else { - stencil_cutsq[i][j] = cutneighsq[i][j]; - stencil_bin_type[i][j] = j; - } + stencil_bin_type[i][j] = j; } } } @@ -89,7 +71,7 @@ void NStencilFullMulti23d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cutsq[itype][jtype]; + cutsq = cutneighsq[itype][jtype]; for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index 7ea058e70b..c2f2127548 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -32,27 +32,17 @@ void NStencilHalfMulti22d::set_stencil_properties() { int n = atom->ntypes; int i, j; - - // like -> like => use half stencil - for (i = 1; i <= n; i++) { - stencil_half[i][i] = 1; - stencil_skip[i][i] = 0; - stencil_bin_type[i][i] = i; - stencil_cutsq[i][i] = cutneighsq[i][i]; - } // Cross types: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin - // larger -> smaller => no nstecil required - // If cut offs are same, use existing type-type stencil + // larger -> smaller => no nstencil required + // If cut offs are same, use half stencil for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - if(i == j) continue; if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -90,7 +80,7 @@ void NStencilHalfMulti22d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cutsq[itype][jtype]; + cutsq = cutneighsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (j = 0; j <= sy; j++) diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi2_2d_tri.cpp index fb974877af..7143378305 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi2_2d_tri.cpp @@ -32,27 +32,17 @@ void NStencilHalfMulti22dTri::set_stencil_properties() { int n = atom->ntypes; int i, j; - - // like -> like => use half stencil - for (i = 1; i <= n; i++) { - stencil_half[i][i] = 1; - stencil_skip[i][i] = 0; - stencil_bin_type[i][i] = i; - stencil_cutsq[i][i] = cutneighsq[i][i]; - } // Cross types: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin - // larger -> smaller => no nstecil required - // If cut offs are same, use existing type-type stencil + // larger -> smaller => no nstencil required + // If cut offs are same, use half stencil for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - if(i == j) continue; if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -90,7 +80,7 @@ void NStencilHalfMulti22dTri::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cutsq[itype][jtype]; + cutsq = cutneighsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (j = 0; j <= sy; j++) diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index 92cdc4e5e6..57702cdb50 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -32,27 +32,17 @@ void NStencilHalfMulti23d::set_stencil_properties() { int n = atom->ntypes; int i, j; - - // like -> like => use half stencil - for (i = 1; i <= n; i++) { - stencil_half[i][i] = 1; - stencil_skip[i][i] = 0; - stencil_bin_type[i][i] = i; - stencil_cutsq[i][i] = cutneighsq[i][i]; - } // Cross types: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin - // larger -> smaller => no nstecil required - // If cut offs are same, use existing type-type stencil + // larger -> smaller => no nstencil required + // If cut offs are same, use half stencil for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - if(i == j) continue; if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -92,7 +82,7 @@ void NStencilHalfMulti23d::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cutsq[itype][jtype]; + cutsq = cutneighsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (k = 0; k <= sz; k++) diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi2_3d_tri.cpp index d114635113..33915d4741 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi2_3d_tri.cpp @@ -33,26 +33,16 @@ void NStencilHalfMulti23dTri::set_stencil_properties() int n = atom->ntypes; int i, j; - // like -> like => use half stencil - for (i = 1; i <= n; i++) { - stencil_half[i][i] = 1; - stencil_skip[i][i] = 0; - stencil_bin_type[i][i] = i; - stencil_cutsq[i][i] = cutneighsq[i][i]; - } - // Cross types: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin - // larger -> smaller => no nstecil required - // If cut offs are same, use existing type-type stencil + // larger -> smaller => no nstencil required + // If cut offs are same, use half stencil for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - if(i == j) continue; if(cutneighsq[i][i] > cutneighsq[j][j]) continue; stencil_skip[i][j] = 0; - stencil_cutsq[i][j] = cutneighsq[i][j]; if(cutneighsq[i][i] == cutneighsq[j][j]){ stencil_half[i][j] = 1; @@ -92,7 +82,7 @@ void NStencilHalfMulti23dTri::create() bin_type = stencil_bin_type[itype][jtype]; - cutsq = stencil_cutsq[itype][jtype]; + cutsq = cutneighsq[itype][jtype]; if (stencil_half[itype][jtype]) { for (k = 0; k <= sz; k++) From 2c79fbebe8ab700c226715c571d06e5fd47ff4a9 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 29 Nov 2020 17:48:43 -0700 Subject: [PATCH 0032/1217] Adding todo note for comm, testing for full nlist --- src/comm.cpp | 2 + src/pair_full_print.cpp | 341 ++++++++++++++++++++++++++++++++++++++++ src/pair_full_print.h | 72 +++++++++ 3 files changed, 415 insertions(+) create mode 100644 src/pair_full_print.cpp create mode 100644 src/pair_full_print.h diff --git a/src/comm.cpp b/src/comm.cpp index ad0c836432..7930b08f87 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -243,6 +243,8 @@ void Comm::init() if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; // Can't used multi2 communication with Newton off + // TODO: need to somehow restrict this option with full neighbor lists + // CANNOT use multi2 communication with full nlist if (force->newton == 0 && multi2) error->all(FLERR,"Cannot use multi2 communication with Newton off"); } diff --git a/src/pair_full_print.cpp b/src/pair_full_print.cpp new file mode 100644 index 0000000000..bf42a81288 --- /dev/null +++ b/src/pair_full_print.cpp @@ -0,0 +1,341 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "pair_full_print.h" + +#include +#include +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairFullPrint::PairFullPrint(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairFullPrint::~PairFullPrint() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(prefactor); + memory->destroy(cut); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairFullPrint::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double r,rsq,arg,factor_lj; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + tagint *tag = atom->tag; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + printf("NLIST %d %d %d %d\n", tag[i], tag[j], type[i], type[j]); + r = sqrt(rsq); + arg = MY_PI*r/cut[itype][jtype]; + if (r > 0.0) fpair = factor_lj * prefactor[itype][jtype] * + sin(arg) * MY_PI/cut[itype][jtype]/r; + else fpair = 0.0; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + + if (eflag) + evdwl = factor_lj * prefactor[itype][jtype] * (1.0+cos(arg)); + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairFullPrint::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(prefactor,n+1,n+1,"pair:prefactor"); + memory->create(cut,n+1,n+1,"pair:cut"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairFullPrint::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + + cut_global = utils::numeric(FLERR,arg[0],false,lmp); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairFullPrint::coeff(int narg, char **arg) +{ + if (narg < 3 || narg > 4) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + + double prefactor_one = utils::numeric(FLERR,arg[2],false,lmp); + + double cut_one = cut_global; + if (narg == 4) cut_one = utils::numeric(FLERR,arg[3],false,lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + prefactor[i][j] = prefactor_one; + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style + ------------------------------------------------------------------------- */ + +void PairFullPrint::init_style() { + // need a full neighbor list + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; +} + + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairFullPrint::init_one(int i, int j) +{ + // always mix prefactors geometrically + + if (setflag[i][j] == 0) { + prefactor[i][j] = sqrt(prefactor[i][i]*prefactor[j][j]); + cut[i][j] = mix_distance(cut[i][i],cut[j][j]); + } + + prefactor[j][i] = prefactor[i][j]; + cut[j][i] = cut[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairFullPrint::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&prefactor[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairFullPrint::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + utils::sfread(FLERR,&prefactor[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + } + MPI_Bcast(&prefactor[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairFullPrint::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairFullPrint::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); + } + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairFullPrint::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g\n",i,prefactor[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairFullPrint::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g\n",i,j,prefactor[i][j],cut[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairFullPrint::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, + double &fforce) +{ + double r,arg,philj; + + r = sqrt(rsq); + arg = MY_PI*r/cut[itype][jtype]; + fforce = factor_lj * prefactor[itype][jtype] * + sin(arg) * MY_PI/cut[itype][jtype]/r; + + philj = prefactor[itype][jtype] * (1.0+cos(arg)); + return factor_lj*philj; +} + +/* ---------------------------------------------------------------------- */ + +void *PairFullPrint::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str,"a") == 0) return (void *) prefactor; + return nullptr; +} diff --git a/src/pair_full_print.h b/src/pair_full_print.h new file mode 100644 index 0000000000..31b51f4e97 --- /dev/null +++ b/src/pair_full_print.h @@ -0,0 +1,72 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(full/print,PairFullPrint) + +#else + +#ifndef LMP_PAIR_FULL_PRINT_H +#define LMP_PAIR_FULL_PRINT_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairFullPrint : public Pair { + friend class Pair; + + public: + PairFullPrint(class LAMMPS *); + virtual ~PairFullPrint(); + void init_style(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + double single(int, int, int, int, double, double, double, double &); + void *extract(const char *, int &); + + protected: + double cut_global; + double **prefactor; + double **cut; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +*/ From 8a0dac90ca1c850a4017410fd0e50d26f713a393 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 29 Nov 2020 19:57:14 -0700 Subject: [PATCH 0033/1217] Removing redundant k variables in npair --- src/USER-OMP/npair_full_multi2_omp.cpp | 21 ++++++------- .../npair_half_multi2_newtoff_omp.cpp | 24 +++++++------- src/USER-OMP/npair_half_multi2_newton_omp.cpp | 28 +++++++---------- .../npair_half_multi2_newton_tri_omp.cpp | 26 +++++++--------- .../npair_half_size_multi2_newtoff_omp.cpp | 24 +++++++------- .../npair_half_size_multi2_newton_omp.cpp | 31 ++++++++----------- .../npair_half_size_multi2_newton_tri_omp.cpp | 25 +++++++-------- src/comm.cpp | 3 ++ src/npair_full_multi2.cpp | 21 ++++++------- src/npair_half_multi2_newton.cpp | 28 +++++++---------- src/npair_half_multi2_newton_tri.cpp | 26 +++++++--------- src/npair_half_size_multi2_newtoff.cpp | 24 +++++++------- src/npair_half_size_multi2_newton.cpp | 31 ++++++++----------- src/npair_half_size_multi2_newton_tri.cpp | 25 +++++++-------- 14 files changed, 152 insertions(+), 185 deletions(-) diff --git a/src/USER-OMP/npair_full_multi2_omp.cpp b/src/USER-OMP/npair_full_multi2_omp.cpp index 8e025806c9..33ac289375 100755 --- a/src/USER-OMP/npair_full_multi2_omp.cpp +++ b/src/USER-OMP/npair_full_multi2_omp.cpp @@ -46,7 +46,7 @@ void NPairFullMulti2Omp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -94,22 +94,21 @@ void NPairFullMulti2Omp::build(NeighList *list) // skip i = j ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { - kbin = ibin; + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + if (itype == jtype) { + jbin = ibin; } else { - // Locate i in ktype bin - kbin = coord2bin(x[i], ktype); + // Locate i in jtype bin + jbin = coord2bin(x[i], jtype); } - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (i == j) continue; - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp index 44689e1efc..f440865bc7 100755 --- a/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp @@ -48,7 +48,7 @@ void NPairHalfMulti2NewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -98,23 +98,21 @@ void NPairHalfMulti2NewtoffOmp::build(NeighList *list) // stores own/ghost pairs on both procs ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { - kbin = ibin; + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + if (itype == jtype) { + jbin = ibin; } else { - // Locate i in ktype bin - kbin = coord2bin(x[i], ktype); + // Locate i in jtype bin + jbin = coord2bin(x[i], jtype); } - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi2[jtype][j]) { if (j <= i) continue; - - jtype = type[j]; - + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_multi2_newton_omp.cpp index cc86410fa9..4035a44a8e 100755 --- a/src/USER-OMP/npair_half_multi2_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi2_newton_omp.cpp @@ -47,7 +47,7 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -96,8 +96,8 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + if (itype == jtype) { // own bin ... js = bins_multi2[itype][i]; @@ -110,7 +110,6 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -144,7 +143,6 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) js = binhead_multi2[itype][ibin + s[k]]; for (j = js; j >= 0; j = bins_multi2[itype][j]) { - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -170,14 +168,14 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure + // smaller -> larger: locate i in the jtype bin structure - kbin = coord2bin(x[i], ktype); + jbin = coord2bin(x[i], jtype); // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ - js = binhead_multi2[ktype][kbin]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -186,7 +184,6 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -212,14 +209,13 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) } } - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp index 707c247607..25f49a5b09 100755 --- a/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp @@ -48,7 +48,7 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -97,9 +97,9 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == ktype) { + if (itype == jtype) { // loop over all atoms in other bins in stencil, store every pair // skip if i,j neighbor cutoff is less than bin distance @@ -117,7 +117,7 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) if (x[j][0] == xtmp && j <= i) continue; } } - jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -143,20 +143,18 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure + // smaller -> larger: locate i in the jtype bin structure - kbin = coord2bin(x[i], ktype); - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + jbin = coord2bin(x[i], jtype); + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { - - jtype = type[j]; - + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp index d4578985ed..8e95b2c5b8 100755 --- a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp @@ -46,7 +46,7 @@ void NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; + int i,j,k,n,itype,jtype,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -86,23 +86,21 @@ void NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) // stores own/ghost pairs on both procs ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { - kbin = ibin; + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + if (itype == jtype) { + jbin = ibin; } else { - // Locate i in ktype bin - kbin = coord2bin(x[i], ktype); + // Locate i in jtype bin + jbin = coord2bin(x[i], jtype); } - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi2[jtype][j]) { if (j <= i) continue; - - jtype = type[j]; - + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp index 5d8080f913..ae490fe837 100755 --- a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp @@ -45,7 +45,7 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; + int i,j,k,n,itype,jtype,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -84,9 +84,9 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == ktype) { + if (itype == jtype) { // own bin ... js = bins_multi2[itype][i]; @@ -99,7 +99,6 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -125,7 +124,6 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi2[itype][ibin + s[k]]; for (j = js; j >= 0; j = bins_multi2[itype][j]) { - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; @@ -145,13 +143,13 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure - kbin = coord2bin(x[i], ktype); + // smaller -> larger: locate i in the jtype bin structure + jbin = coord2bin(x[i], jtype); // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ - js = binhead_multi2[ktype][kbin]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -160,7 +158,6 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -181,14 +178,12 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) // Check other stencils - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { - - jtype = type[j]; - + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp index 12365ff27c..c1dea8ca79 100755 --- a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp @@ -46,7 +46,7 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; + int i,j,k,n,itype,jtype,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -85,9 +85,9 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == ktype) { + if (itype == jtype) { // loop over all atoms in other bins in stencil, store every pair // skip if i,j neighbor cutoff is less than bin distance @@ -105,7 +105,6 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) if (x[j][0] == xtmp && j <= i) continue; } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; @@ -125,20 +124,18 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure + // smaller -> larger: locate i in the jtype bin structure - kbin = coord2bin(x[i], ktype); + jbin = coord2bin(x[i], jtype); - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { - - jtype = type[j]; - + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/comm.cpp b/src/comm.cpp index 7930b08f87..2e1192e150 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -245,6 +245,9 @@ void Comm::init() // Can't used multi2 communication with Newton off // TODO: need to somehow restrict this option with full neighbor lists // CANNOT use multi2 communication with full nlist + // Could remove NP_NEWTON from npair_full_*multi2*, but could be cryptic + // Also could be cases where you want newton off (hybrid) but don't use multi2 comm + // Could add check on neighbor build, if full and comm->multi2 error... if (force->newton == 0 && multi2) error->all(FLERR,"Cannot use multi2 communication with Newton off"); } diff --git a/src/npair_full_multi2.cpp b/src/npair_full_multi2.cpp index 4fbdc6148b..8af77aea22 100644 --- a/src/npair_full_multi2.cpp +++ b/src/npair_full_multi2.cpp @@ -35,7 +35,7 @@ NPairFullMulti2::NPairFullMulti2(LAMMPS *lmp) : NPair(lmp) {} void NPairFullMulti2::build(NeighList *list) { - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -84,22 +84,21 @@ void NPairFullMulti2::build(NeighList *list) // skip i = j ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { - kbin = ibin; + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + if (itype == jtype) { + jbin = ibin; } else { - // Locate i in ktype bin - kbin = coord2bin(x[i], ktype); + // Locate i in jtype bin + jbin = coord2bin(x[i], jtype); } - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (i == j) continue; - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/npair_half_multi2_newton.cpp b/src/npair_half_multi2_newton.cpp index 413da06284..ee3114ec8b 100755 --- a/src/npair_half_multi2_newton.cpp +++ b/src/npair_half_multi2_newton.cpp @@ -36,7 +36,7 @@ NPairHalfMulti2Newton::NPairHalfMulti2Newton(LAMMPS *lmp) : NPair(lmp) {} void NPairHalfMulti2Newton::build(NeighList *list) { - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -86,8 +86,8 @@ void NPairHalfMulti2Newton::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + if (itype == jtype) { // own bin ... js = bins_multi2[itype][i]; @@ -100,7 +100,6 @@ void NPairHalfMulti2Newton::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -134,7 +133,6 @@ void NPairHalfMulti2Newton::build(NeighList *list) js = binhead_multi2[itype][ibin + s[k]]; for (j = js; j >= 0; j = bins_multi2[itype][j]) { - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -160,14 +158,14 @@ void NPairHalfMulti2Newton::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure + // smaller -> larger: locate i in the jtype bin structure - kbin = coord2bin(x[i], ktype); + jbin = coord2bin(x[i], jtype); // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ - js = binhead_multi2[ktype][kbin]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -176,7 +174,6 @@ void NPairHalfMulti2Newton::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -202,14 +199,13 @@ void NPairHalfMulti2Newton::build(NeighList *list) } } - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/npair_half_multi2_newton_tri.cpp b/src/npair_half_multi2_newton_tri.cpp index 7970ee94a0..6c0fc35985 100755 --- a/src/npair_half_multi2_newton_tri.cpp +++ b/src/npair_half_multi2_newton_tri.cpp @@ -36,7 +36,7 @@ NPairHalfMulti2NewtonTri::NPairHalfMulti2NewtonTri(LAMMPS *lmp) : NPair(lmp) {} void NPairHalfMulti2NewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -86,9 +86,9 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == ktype) { + if (itype == jtype) { // loop over all atoms in other bins in stencil, store every pair // skip if i,j neighbor cutoff is less than bin distance @@ -106,7 +106,7 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) if (x[j][0] == xtmp && j <= i) continue; } } - jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -132,20 +132,18 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure + // smaller -> larger: locate i in the jtype bin structure - kbin = coord2bin(x[i], ktype); - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + jbin = coord2bin(x[i], jtype); + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { - - jtype = type[j]; - + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/npair_half_size_multi2_newtoff.cpp b/src/npair_half_size_multi2_newtoff.cpp index 0e0137a77e..efbd8f2fe4 100644 --- a/src/npair_half_size_multi2_newtoff.cpp +++ b/src/npair_half_size_multi2_newtoff.cpp @@ -36,7 +36,7 @@ NPairHalfSizeMulti2Newtoff::NPairHalfSizeMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) void NPairHalfSizeMulti2Newtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns; + int i,j,k,n,itype,jtype,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -78,23 +78,21 @@ void NPairHalfSizeMulti2Newtoff::build(NeighList *list) // stores own/ghost pairs on both procs ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { - kbin = ibin; + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + if (itype == jtype) { + jbin = ibin; } else { - // Locate i in ktype bin - kbin = coord2bin(x[i], ktype); + // Locate i in jtype bin + jbin = coord2bin(x[i], jtype); } - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi2[jtype][j]) { if (j <= i) continue; - - jtype = type[j]; - + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/npair_half_size_multi2_newton.cpp b/src/npair_half_size_multi2_newton.cpp index 3b34b1a514..8a143124fd 100755 --- a/src/npair_half_size_multi2_newton.cpp +++ b/src/npair_half_size_multi2_newton.cpp @@ -34,7 +34,7 @@ NPairHalfSizeMulti2Newton::NPairHalfSizeMulti2Newton(LAMMPS *lmp) : NPair(lmp) { void NPairHalfSizeMulti2Newton::build(NeighList *list) { - int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns,js; + int i,j,k,n,itype,jtype,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -74,9 +74,9 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == ktype) { + if (itype == jtype) { // own bin ... js = bins_multi2[itype][i]; @@ -89,7 +89,6 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -115,7 +114,6 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi2[itype][ibin + s[k]]; for (j = js; j >= 0; j = bins_multi2[itype][j]) { - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; @@ -135,13 +133,13 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure - kbin = coord2bin(x[i], ktype); + // smaller -> larger: locate i in the jtype bin structure + jbin = coord2bin(x[i], jtype); // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ - js = binhead_multi2[ktype][kbin]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -150,7 +148,6 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -171,14 +168,12 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) // Check other stencils - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { - - jtype = type[j]; - + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/npair_half_size_multi2_newton_tri.cpp b/src/npair_half_size_multi2_newton_tri.cpp index 3a2065c36e..e5b3b414ec 100755 --- a/src/npair_half_size_multi2_newton_tri.cpp +++ b/src/npair_half_size_multi2_newton_tri.cpp @@ -34,7 +34,7 @@ NPairHalfSizeMulti2NewtonTri::NPairHalfSizeMulti2NewtonTri(LAMMPS *lmp) : NPair( void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns,js; + int i,j,k,n,itype,jtype,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -74,9 +74,9 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { + for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == ktype) { + if (itype == jtype) { // loop over all atoms in other bins in stencil, store every pair // skip if i,j neighbor cutoff is less than bin distance @@ -94,7 +94,6 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) if (x[j][0] == xtmp && j <= i) continue; } } - jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; @@ -114,20 +113,18 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) } } } else { - // smaller -> larger: locate i in the ktype bin structure + // smaller -> larger: locate i in the jtype bin structure - kbin = coord2bin(x[i], ktype); + jbin = coord2bin(x[i], jtype); - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[ktype][j]) { - - jtype = type[j]; - + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[ktype][ktype]){ + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; From 6c9bb854c017b92b1a1f0f28da4deeda3aa6735a Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 30 Nov 2020 10:51:15 -0700 Subject: [PATCH 0034/1217] Revamping multi2 npair classes, fixed bug if two types had same cut, better comments --- src/USER-OMP/npair_full_multi2_omp.cpp | 23 ++- .../npair_half_multi2_newtoff_omp.cpp | 28 +-- src/USER-OMP/npair_half_multi2_newton_omp.cpp | 192 ++++++++--------- .../npair_half_multi2_newton_tri_omp.cpp | 136 +++++------- .../npair_half_size_multi2_newtoff_omp.cpp | 29 +-- .../npair_half_size_multi2_newton_omp.cpp | 160 +++++++-------- .../npair_half_size_multi2_newton_tri_omp.cpp | 113 ++++------ src/npair_full_multi2.cpp | 24 +-- src/npair_half_multi2_newtoff.cpp | 44 ++-- src/npair_half_multi2_newton.cpp | 193 ++++++++---------- src/npair_half_multi2_newton_tri.cpp | 137 +++++-------- src/npair_half_size_multi2_newtoff.cpp | 29 +-- src/npair_half_size_multi2_newton.cpp | 161 +++++++-------- src/npair_half_size_multi2_newton_tri.cpp | 116 ++++------- 14 files changed, 600 insertions(+), 785 deletions(-) diff --git a/src/USER-OMP/npair_full_multi2_omp.cpp b/src/USER-OMP/npair_full_multi2_omp.cpp index 33ac289375..39f711fe4f 100755 --- a/src/USER-OMP/npair_full_multi2_omp.cpp +++ b/src/USER-OMP/npair_full_multi2_omp.cpp @@ -30,7 +30,7 @@ NPairFullMulti2Omp::NPairFullMulti2Omp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi-type stencil is itype dependent and is distance checked + multi2-type stencil is itype-jtype dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ @@ -89,21 +89,22 @@ void NPairFullMulti2Omp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // loop over all atoms in other bins in stencil, including self - // skip if i,j neighbor cutoff is less than bin distance - // skip i = j - ibin = atom2bin_multi2[itype][i]; + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { - jbin = ibin; - } else { - // Locate i in jtype bin - jbin = coord2bin(x[i], jtype); - } + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + + // loop over all atoms in surrounding bins in stencil including self + // skip i = j + // use full stencil for all type combinations s = stencil_multi2[itype][jtype]; ns = nstencil_multi2[itype][jtype]; + for (k = 0; k < ns; k++) { js = binhead_multi2[jtype][jbin + s[k]]; for (j = js; j >= 0; j = bins_multi2[jtype][j]) { diff --git a/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp index f440865bc7..bfd0d34a6c 100755 --- a/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp @@ -30,8 +30,8 @@ NPairHalfMulti2NewtoffOmp::NPairHalfMulti2NewtoffOmp(LAMMPS *lmp) : NPair(lmp) { /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law + multi2-type stencil is itype-jtype dependent each owned atom i checks own bin and other bins in stencil - multi-type stencil is itype dependent and is distance checked pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ @@ -91,23 +91,24 @@ void NPairHalfMulti2NewtoffOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // loop over all atoms in other bins in stencil including self - // only store pair if i < j - // skip if i,j neighbor cutoff is less than bin distance - // stores own/own pairs only once - // stores own/ghost pairs on both procs - ibin = atom2bin_multi2[itype][i]; + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { - jbin = ibin; - } else { - // Locate i in jtype bin - jbin = coord2bin(x[i], jtype); - } + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // stores own/own pairs only once + // stores own/ghost pairs on both procs + // use full stencil for all type combinations + s = stencil_multi2[itype][jtype]; ns = nstencil_multi2[itype][jtype]; + for (k = 0; k < ns; k++) { js = binhead_multi2[jtype][jbin + s[k]]; for (j = js; j >=0; j = bins_multi2[jtype][j]) { @@ -139,7 +140,6 @@ void NPairHalfMulti2NewtoffOmp::build(NeighList *list) } } - ilist[i] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/USER-OMP/npair_half_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_multi2_newton_omp.cpp index 4035a44a8e..cbdbd69f50 100755 --- a/src/USER-OMP/npair_half_multi2_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi2_newton_omp.cpp @@ -30,8 +30,8 @@ NPairHalfMulti2NewtonOmp::NPairHalfMulti2NewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law + multi2-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in Newton stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -90,91 +90,27 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = atom2bin_multi2[itype][i]; - + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); - // own bin ... - js = bins_multi2[itype][i]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } - } + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + + // if same size: use half stencil + if(itype == jtype){ + + // if same type, implement with: + // loop over rest of atoms in i's bin, ghosts are at end of linked list + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + js = bins_multi2[itype][i]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } - - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } - } - } else { - // smaller -> larger: locate i in the jtype bin structure - - jbin = coord2bin(x[i], jtype); - - // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - js = binhead_multi2[jtype][jbin]; for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -183,7 +119,7 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) if (x[j][1] == ytmp && x[j][0] < xtmp) continue; } } - + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -207,40 +143,88 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) } else neighptr[n++] = j; } } - } - - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + } else { + + // if different types, implement with: + // loop over all atoms in jtype bin + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - + if(j < i) continue; + + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - + if (rsq <= cutneighsq[itype][jtype]) { if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; } + } + } + } + + // for all types, loop over all atoms in other bins in stencil, store every pair + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; } } - } + } } ilist[i] = i; diff --git a/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp index 25f49a5b09..5d0d724b58 100755 --- a/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp @@ -31,8 +31,8 @@ NPairHalfMulti2NewtonTriOmp::NPairHalfMulti2NewtonTriOmp(LAMMPS *lmp) : /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic + multi2-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in triclinic stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -90,25 +90,34 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) iatom = molatom[i]; tagprev = tag[i] - iatom - 1; } - - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] ibin = atom2bin_multi2[itype][i]; - + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + + // loop over all atoms in bins in stencil + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + // if half: pairs for atoms j "below" i are excluded + // below = lower z or (equal z and lower y) or (equal zy and lower x) + // (equal zyx and j <= i) + // latter excludes self-self interaction but allows superposed atoms - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + + // if same size (e.g. same type), use half stencil + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -116,80 +125,33 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) if (x[j][0] < xtmp) continue; if (x[j][0] == xtmp && j <= i) continue; } - } - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } + } + } + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; } } - } else { - // smaller -> larger: locate i in the jtype bin structure - - jbin = coord2bin(x[i], jtype); - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; - - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - - // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp) { - if (x[j][0] < xtmp) continue; - if (x[j][0] == xtmp && j <= i) continue; - } - } - } - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } - } - } + } } ilist[i] = i; diff --git a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp index 8e95b2c5b8..3b1f979a8e 100755 --- a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp @@ -27,9 +27,10 @@ using namespace LAMMPS_NS; NPairHalfSizeMulti2NewtoffOmp::NPairHalfSizeMulti2NewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- + size particles binned neighbor list construction with partial Newton's 3rd law + multi2-type stencil is itype-jtype dependent each owned atom i checks own bin and other bins in stencil - multi-type stencil is itype dependent and is distance checked pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ @@ -79,23 +80,24 @@ void NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - // loop over all atoms in other bins in stencil including self - // only store pair if i < j - // skip if i,j neighbor cutoff is less than bin distance - // stores own/own pairs only once - // stores own/ghost pairs on both procs - ibin = atom2bin_multi2[itype][i]; + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { - jbin = ibin; - } else { - // Locate i in jtype bin - jbin = coord2bin(x[i], jtype); - } + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // stores own/own pairs only once + // stores own/ghost pairs on both procs + // use full stencil for all type combinations + s = stencil_multi2[itype][jtype]; ns = nstencil_multi2[itype][jtype]; + for (k = 0; k < ns; k++) { js = binhead_multi2[jtype][jbin + s[k]]; for (j = js; j >=0; j = bins_multi2[jtype][j]) { @@ -120,7 +122,6 @@ void NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) } } - ilist[i] = i; firstneigh[i] = neighptr; numneigh[i] = n; diff --git a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp index ae490fe837..b7367abd57 100755 --- a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp @@ -27,9 +27,10 @@ using namespace LAMMPS_NS; NPairHalfSizeMulti2NewtonOmp::NPairHalfSizeMulti2NewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- + size particles binned neighbor list construction with full Newton's 3rd law + multi2-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in Newton stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -78,77 +79,27 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = atom2bin_multi2[itype][i]; - + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); - if (itype == jtype) { - - // own bin ... - js = bins_multi2[itype][i]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } - } + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + + // if same size: use half stencil + if(itype == jtype){ + + // if same type, implement with: + // loop over rest of atoms in i's bin, ghosts are at end of linked list + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + js = bins_multi2[itype][i]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } - - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } - } - } else { - // smaller -> larger: locate i in the jtype bin structure - jbin = coord2bin(x[i], jtype); - - // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - js = binhead_multi2[jtype][jbin]; for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -157,41 +108,82 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) if (x[j][1] == ytmp && x[j][0] < xtmp) continue; } } - + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; radsum = radi + radius[j]; cutdistsq = (radsum+skin) * (radsum+skin); - + if (rsq <= cutdistsq) { if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; } - } - } - - // Check other stencils + } + } else { + + // if different types, implement with: + // loop over all atoms in jtype bin + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - + if(j < i) continue; + + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; radsum = radi + radius[j]; cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + } + + // for all types, loop over all atoms in other bins in stencil, store every pair + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); if (rsq <= cutdistsq) { if (history && rsq < radsum*radsum) diff --git a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp index c1dea8ca79..66f9cbce0a 100755 --- a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp @@ -28,9 +28,10 @@ NPairHalfSizeMulti2NewtonTriOmp::NPairHalfSizeMulti2NewtonTriOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- + size particles binned neighbor list construction with Newton's 3rd law for triclinic + multi2-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in triclinic stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -79,24 +80,34 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = atom2bin_multi2[itype][i]; + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { + + // loop over all atoms in bins in stencil + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + // if half: pairs for atoms j "below" i are excluded + // below = lower z or (equal z and lower y) or (equal zy and lower x) + // (equal zyx and j <= i) + // latter excludes self-self interaction but allows superposed atoms + + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + + // if same size (e.g. same type), use half stencil + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -104,66 +115,26 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) if (x[j][0] < xtmp) continue; if (x[j][0] == xtmp && j <= i) continue; } - } + } + } + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; } } - } else { - // smaller -> larger: locate i in the jtype bin structure - - jbin = coord2bin(x[i], jtype); - - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - - // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp) { - if (x[j][0] < xtmp) continue; - if (x[j][0] == xtmp && j <= i) continue; - } - } - } - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } - } - } + } } ilist[i] = i; diff --git a/src/npair_full_multi2.cpp b/src/npair_full_multi2.cpp index 8af77aea22..732c5e581e 100644 --- a/src/npair_full_multi2.cpp +++ b/src/npair_full_multi2.cpp @@ -27,9 +27,8 @@ using namespace LAMMPS_NS; NPairFullMulti2::NPairFullMulti2(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- - REWRITE binned neighbor list construction for all neighbors - multi-type stencil is itype dependent and is distance checked + multi2-type stencil is itype-jtype dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ @@ -79,21 +78,22 @@ void NPairFullMulti2::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // loop over all atoms in other bins in stencil, including self - // skip if i,j neighbor cutoff is less than bin distance - // skip i = j - ibin = atom2bin_multi2[itype][i]; + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { - jbin = ibin; - } else { - // Locate i in jtype bin - jbin = coord2bin(x[i], jtype); - } + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + + // loop over all atoms in surrounding bins in stencil including self + // skip i = j + // use full stencil for all type combinations s = stencil_multi2[itype][jtype]; ns = nstencil_multi2[itype][jtype]; + for (k = 0; k < ns; k++) { js = binhead_multi2[jtype][jbin + s[k]]; for (j = js; j >= 0; j = bins_multi2[jtype][j]) { diff --git a/src/npair_half_multi2_newtoff.cpp b/src/npair_half_multi2_newtoff.cpp index b44f2bcc62..ecd97fe689 100755 --- a/src/npair_half_multi2_newtoff.cpp +++ b/src/npair_half_multi2_newtoff.cpp @@ -27,17 +27,16 @@ using namespace LAMMPS_NS; NPairHalfMulti2Newtoff::NPairHalfMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- - REWRITE binned neighbor list construction with partial Newton's 3rd law + multi2-type stencil is itype-jtype dependent each owned atom i checks own bin and other bins in stencil - multi-type stencil is itype dependent and is distance checked pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ void NPairHalfMulti2Newtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,ktype,ibin,kbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -81,30 +80,29 @@ void NPairHalfMulti2Newtoff::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // loop over all atoms in other bins in stencil including self - // only store pair if i < j - // skip if i,j neighbor cutoff is less than bin distance - // stores own/own pairs only once - // stores own/ghost pairs on both procs - ibin = atom2bin_multi2[itype][i]; - for (ktype = 1; ktype <= atom->ntypes; ktype++) { - if (itype == ktype) { - kbin = ibin; - } else { - // Locate i in ktype bin - kbin = coord2bin(x[i], ktype); - } + + // loop through stencils for all types + for (jtype = 1; jtype <= atom->ntypes; jtype++) { + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // stores own/own pairs only once + // stores own/ghost pairs on both procs + // use full stencil for all type combinations + + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; - s = stencil_multi2[itype][ktype]; - ns = nstencil_multi2[itype][ktype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[ktype][kbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[ktype][j]) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi2[jtype][j]) { if (j <= i) continue; - - jtype = type[j]; - + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/npair_half_multi2_newton.cpp b/src/npair_half_multi2_newton.cpp index ee3114ec8b..6a7f52168a 100755 --- a/src/npair_half_multi2_newton.cpp +++ b/src/npair_half_multi2_newton.cpp @@ -27,10 +27,9 @@ using namespace LAMMPS_NS; NPairHalfMulti2Newton::NPairHalfMulti2Newton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- - KS REWRTIE binned neighbor list construction with full Newton's 3rd law + multi2-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in Newton stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -80,91 +79,27 @@ void NPairHalfMulti2Newton::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = atom2bin_multi2[itype][i]; - + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); - // own bin ... - js = bins_multi2[itype][i]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } - } + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + + // if same size: use half stencil + if(itype == jtype){ + + // if same type, implement with: + // loop over rest of atoms in i's bin, ghosts are at end of linked list + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + js = bins_multi2[itype][i]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } - - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } - } - } else { - // smaller -> larger: locate i in the jtype bin structure - - jbin = coord2bin(x[i], jtype); - - // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - js = binhead_multi2[jtype][jbin]; for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -173,7 +108,7 @@ void NPairHalfMulti2Newton::build(NeighList *list) if (x[j][1] == ytmp && x[j][0] < xtmp) continue; } } - + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -197,40 +132,88 @@ void NPairHalfMulti2Newton::build(NeighList *list) } else neighptr[n++] = j; } } - } - - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + } else { + + // if different types, implement with: + // loop over all atoms in jtype bin + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - + if(j < i) continue; + + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - + if (rsq <= cutneighsq[itype][jtype]) { if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; } + } + } + } + + // for all types, loop over all atoms in other bins in stencil, store every pair + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; } } - } + } } ilist[inum++] = i; diff --git a/src/npair_half_multi2_newton_tri.cpp b/src/npair_half_multi2_newton_tri.cpp index 6c0fc35985..9d0db60d50 100755 --- a/src/npair_half_multi2_newton_tri.cpp +++ b/src/npair_half_multi2_newton_tri.cpp @@ -27,10 +27,9 @@ using namespace LAMMPS_NS; NPairHalfMulti2NewtonTri::NPairHalfMulti2NewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- - KS REWRTIE binned neighbor list construction with Newton's 3rd law for triclinic + multi2-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in triclinic stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -79,25 +78,34 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) iatom = molatom[i]; tagprev = tag[i] - iatom - 1; } - - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] ibin = atom2bin_multi2[itype][i]; - + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + + // loop over all atoms in bins in stencil + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + // if half: pairs for atoms j "below" i are excluded + // below = lower z or (equal z and lower y) or (equal zy and lower x) + // (equal zyx and j <= i) + // latter excludes self-self interaction but allows superposed atoms - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + + // if same size (e.g. same type), use half stencil + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -105,80 +113,33 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) if (x[j][0] < xtmp) continue; if (x[j][0] == xtmp && j <= i) continue; } - } - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } + } + } + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; } } - } else { - // smaller -> larger: locate i in the jtype bin structure - - jbin = coord2bin(x[i], jtype); - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; - - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - - // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp) { - if (x[j][0] < xtmp) continue; - if (x[j][0] == xtmp && j <= i) continue; - } - } - } - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } - } - } + } } ilist[inum++] = i; diff --git a/src/npair_half_size_multi2_newtoff.cpp b/src/npair_half_size_multi2_newtoff.cpp index efbd8f2fe4..b559f83414 100644 --- a/src/npair_half_size_multi2_newtoff.cpp +++ b/src/npair_half_size_multi2_newtoff.cpp @@ -26,10 +26,10 @@ using namespace LAMMPS_NS; NPairHalfSizeMulti2Newtoff::NPairHalfSizeMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- - REWRITE + size particles binned neighbor list construction with partial Newton's 3rd law + multi2-type stencil is itype-jtype dependent each owned atom i checks own bin and other bins in stencil - multi-type stencil is itype dependent and is distance checked pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ @@ -71,23 +71,24 @@ void NPairHalfSizeMulti2Newtoff::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - // loop over all atoms in other bins in stencil including self - // only store pair if i < j - // skip if i,j neighbor cutoff is less than bin distance - // stores own/own pairs only once - // stores own/ghost pairs on both procs - ibin = atom2bin_multi2[itype][i]; + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { - jbin = ibin; - } else { - // Locate i in jtype bin - jbin = coord2bin(x[i], jtype); - } + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // stores own/own pairs only once + // stores own/ghost pairs on both procs + // use full stencil for all type combinations + s = stencil_multi2[itype][jtype]; ns = nstencil_multi2[itype][jtype]; + for (k = 0; k < ns; k++) { js = binhead_multi2[jtype][jbin + s[k]]; for (j = js; j >=0; j = bins_multi2[jtype][j]) { diff --git a/src/npair_half_size_multi2_newton.cpp b/src/npair_half_size_multi2_newton.cpp index 8a143124fd..bd5c6f6146 100755 --- a/src/npair_half_size_multi2_newton.cpp +++ b/src/npair_half_size_multi2_newton.cpp @@ -25,10 +25,10 @@ using namespace LAMMPS_NS; NPairHalfSizeMulti2Newton::NPairHalfSizeMulti2Newton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- - KS REWRTIE + size particles binned neighbor list construction with full Newton's 3rd law + multi2-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in Newton stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -68,77 +68,27 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = atom2bin_multi2[itype][i]; - + + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { + + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); - if (itype == jtype) { - - // own bin ... - js = bins_multi2[itype][i]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } - } + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + + // if same size: use half stencil + if(itype == jtype){ + + // if same type, implement with: + // loop over rest of atoms in i's bin, ghosts are at end of linked list + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + js = bins_multi2[itype][i]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } - - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } - } - } else { - // smaller -> larger: locate i in the jtype bin structure - jbin = coord2bin(x[i], jtype); - - // if same size, use half list so check own bin - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - js = binhead_multi2[jtype][jbin]; for (j = js; j >= 0; j = bins_multi2[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -147,41 +97,82 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) if (x[j][1] == ytmp && x[j][0] < xtmp) continue; } } - + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; radsum = radi + radius[j]; cutdistsq = (radsum+skin) * (radsum+skin); - + if (rsq <= cutdistsq) { if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; } - } - } - - // Check other stencils + } + } else { + + // if different types, implement with: + // loop over all atoms in jtype bin + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; + js = binhead_multi2[jtype][jbin]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - + if(j < i) continue; + + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; radsum = radi + radius[j]; cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + } + + // for all types, loop over all atoms in other bins in stencil, store every pair + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); if (rsq <= cutdistsq) { if (history && rsq < radsum*radsum) diff --git a/src/npair_half_size_multi2_newton_tri.cpp b/src/npair_half_size_multi2_newton_tri.cpp index e5b3b414ec..8cde0cbb36 100755 --- a/src/npair_half_size_multi2_newton_tri.cpp +++ b/src/npair_half_size_multi2_newton_tri.cpp @@ -25,10 +25,10 @@ using namespace LAMMPS_NS; NPairHalfSizeMulti2NewtonTri::NPairHalfSizeMulti2NewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- - KS REWRTIE + size particles binned neighbor list construction with Newton's 3rd law for triclinic + multi2-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in triclinic stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -68,24 +68,34 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - // own type: loop over atoms ahead in bin, including ghosts at end of list - // if j is owned atom, store by virtue of being ahead of i in list - // if j is ghost, store if x[j] "above and to right of" x[i] - ibin = atom2bin_multi2[itype][i]; + // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { - if (itype == jtype) { + // if same type use own bin + if(itype == jtype) jbin = ibin; + else jbin = coord2bin(x[i], jtype); - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - - s = stencil_multi2[itype][itype]; - ns = nstencil_multi2[itype][itype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[itype][ibin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[itype][j]) { + + // loop over all atoms in bins in stencil + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + // if half: pairs for atoms j "below" i are excluded + // below = lower z or (equal z and lower y) or (equal zy and lower x) + // (equal zyx and j <= i) + // latter excludes self-self interaction but allows superposed atoms + + s = stencil_multi2[itype][jtype]; + ns = nstencil_multi2[itype][jtype]; + + for (k = 0; k < ns; k++) { + js = binhead_multi2[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + + // if same size (e.g. same type), use half stencil + if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -93,68 +103,28 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) if (x[j][0] < xtmp) continue; if (x[j][0] == xtmp && j <= i) continue; } - } + } + } + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; } } - } else { - // smaller -> larger: locate i in the jtype bin structure - - jbin = coord2bin(x[i], jtype); - - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; - for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { - - // if same size, use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp) { - if (x[j][0] < xtmp) continue; - if (x[j][0] == xtmp && j <= i) continue; - } - } - } - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } - } - } + } } - + ilist[inum++] = i; firstneigh[i] = neighptr; numneigh[i] = n; From e716abd34aafcdab1e29054475646aabf00fd932 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 30 Nov 2020 11:00:53 -0700 Subject: [PATCH 0035/1217] Fixing bad bracket --- .../npair_half_size_multi2_newton_omp.cpp | 19 +++++++++---------- src/npair_half_size_multi2_newton.cpp | 17 ++++++++--------- 2 files changed, 17 insertions(+), 19 deletions(-) diff --git a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp index b7367abd57..3a3a2fbe74 100755 --- a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp @@ -179,21 +179,20 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; - else + else neighptr[n++] = j; - } } } - } + } } ilist[i] = i; diff --git a/src/npair_half_size_multi2_newton.cpp b/src/npair_half_size_multi2_newton.cpp index bd5c6f6146..bc6116b21c 100755 --- a/src/npair_half_size_multi2_newton.cpp +++ b/src/npair_half_size_multi2_newton.cpp @@ -168,18 +168,17 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) neighptr[n++] = j ^ mask_history; - else + else neighptr[n++] = j; - } } } } From 6308248a44a8dbc4cb07e2c73e94cbc835756726 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 30 Nov 2020 20:55:04 -0700 Subject: [PATCH 0036/1217] Replacing binsizex with multi2 version --- src/comm.cpp | 1 + src/nstencil.cpp | 6 +++--- src/nstencil_half_multi2_2d.cpp | 2 +- src/nstencil_half_multi2_3d.cpp | 2 +- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index 2e1192e150..fdafdbaf17 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -248,6 +248,7 @@ void Comm::init() // Could remove NP_NEWTON from npair_full_*multi2*, but could be cryptic // Also could be cases where you want newton off (hybrid) but don't use multi2 comm // Could add check on neighbor build, if full and comm->multi2 error... + // or just add check on comm setup - is that run before every run? Only if box change... if (force->newton == 0 && multi2) error->all(FLERR,"Cannot use multi2 communication with Newton off"); } diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 1658654e5a..709b48a257 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -345,11 +345,11 @@ void NStencil::create_setup() stencil_range = sqrt(cutneighsq[i][j]); sx = static_cast (stencil_range*bininvx_multi2[bin_type]); - if (sx*binsizex < stencil_range) sx++; + if (sx*binsizex_multi2[bin_type] < stencil_range) sx++; sy = static_cast (stencil_range*bininvy_multi2[bin_type]); - if (sy*binsizey < stencil_range) sy++; + if (sy*binsizey_multi2[bin_type] < stencil_range) sy++; sz = static_cast (stencil_range*bininvz_multi2[bin_type]); - if (sz*binsizez < stencil_range) sz++; + if (sz*binsizez_multi2[bin_type] < stencil_range) sz++; stencil_sx_multi2[i][j] = sx; stencil_sy_multi2[i][j] = sy; diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi2_2d.cpp index c2f2127548..f240d87b54 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi2_2d.cpp @@ -88,7 +88,7 @@ void NStencilHalfMulti22d::create() if (j > 0 || (j == 0 && i > 0)) { if (bin_distance_multi2(i,j,0,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = j*mbinx + i; - } + } } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi2_3d.cpp index 57702cdb50..83ecb24cba 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi2_3d.cpp @@ -92,7 +92,7 @@ void NStencilHalfMulti23d::create() if (bin_distance_multi2(i,j,k,bin_type) < cutsq) stencil_multi2[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - } + } } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) From ca5c9217022b19ebe1cafba818b0e16060e9ac8a Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Thu, 3 Dec 2020 13:00:21 +0000 Subject: [PATCH 0037/1217] added brownian dynamics integrator fix bd/sphere. --- doc/src/fix_bd_sphere.rst | 168 ++++++++++++++++++++++++ src/fix_bd_sphere.cpp | 264 ++++++++++++++++++++++++++++++++++++++ src/fix_bd_sphere.h | 104 +++++++++++++++ src/random_mars.cpp | 16 +++ src/random_mars.h | 2 + 5 files changed, 554 insertions(+) create mode 100644 doc/src/fix_bd_sphere.rst create mode 100644 src/fix_bd_sphere.cpp create mode 100644 src/fix_bd_sphere.h diff --git a/doc/src/fix_bd_sphere.rst b/doc/src/fix_bd_sphere.rst new file mode 100644 index 0000000000..2ab184e4fb --- /dev/null +++ b/doc/src/fix_bd_sphere.rst @@ -0,0 +1,168 @@ +.. index:: fix bd/sphere + +fix bd/sphere command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID bd/sphere gamma_t gamma_r diff_t diff_r seed keyword args + +* ID, group-ID are documented in :doc:`fix ` command +* bd/sphere = style name of this fix command +* gamma_t = translational friction coefficient +* gamma_r = rotational friction coefficient +* diff_t = translational diffusion coefficient +* diff_r = rotational diffusion coefficient +* zero or more keyword/value pairs may be appended +* keyword = *rng* or *rotate_planar* + + .. parsed-literal:: + + *rng* arg = *uniform* or *gaussian* or *none* + uniform = use uniform random number generator + gaussian = use gaussian random number generator + none = turn off noise + *rotate_planar* arg = *yes* or *no* + yes = only allow rotations in 2D plane (2D simulation only) + no = allow for full 3D rotations + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix 1 all bd/sphere 1.0 1.0 1.0 1.0 1294019 + fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rng none + fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rotate_planar yes + fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rotate_planar no rng gaussian + + +Description +""""""""""" + +Perform Brownian Dynamics integration to update position, velocity, +angular velocity, and dipole moment for finite-size spherical particles +in the group each timestep. Brownian Dynamics uses Newton's laws of +motion in the limit that inertial forces are negligible compared to +viscous forces. The stochastic equations of motion are + +.. math:: + + dr = \frac{F}{\gamma_t}dt+\sqrt{2D_t}dW_t, \\ + d\Omega = \frac{T}{\gamma_r}dt + \sqrt{2D_r}dW_r, + +where :math:`d\Omega` is an infinitesimal rotation vector (see e.g. +Chapter 4 of :ref:`(GoldsteinCM) `), :math:`dW_t` and +:math:`dW_r` are Wiener processes (see e.g. :ref:`(GardinerC) `). +The dipole vectors :math:`e_i` are updated using the rotation matrix + +.. math:: + + e_i(t+dt) = e^{\theta_X} e_i(t),\\ + +where :math:`\omega=d\Omega/dt` is the angular velocity, +:math:`\Delta\theta=|\omega|dt` is the rotation angle about +the :math:`\omega` axis, and +:math:`(\theta_X)_{ij}=-\epsilon_{ijk}d\Omega_k` is the +infinitesimal rotation matrix (see e.g. :ref:`(Callegari1) `, +section 7.4). + +IMPORTANT NOTE: This integrator is designed for generic non-equilibrium +simulations with additive noise. There are two important cases which +(conceptually) reduce the number of free parameters in this fix. +(a) In equilibrium simulations +(where fluctuation dissipation theorems are obeyed), one can define +the thermal energy :math:`k_bT=D_t\gamma_t=D_r\gamma_r`. +(b) When a no-slip boundary condition is expected between the spheres and +the surrounding medium, the condition +:math:`\gamma_t=3\gamma_r/\sigma^2` must be explicitly +accounted for (e.g. by setting *gamma_t* to 3 and *gamma_r* to 1) where +:math:`sigma` is the particle diameter. +If both (a) and (b) are true, then one must ensure this explicitly via +the above relationships. + +If the *rng* keyword is used with the *uniform* value, then the noise +is generated from a uniform distribution (see +:ref:`(Dunweg) ` for why this works). This is the same method +of noise generation as used in :doc:`fix_langevin `. + +If the *rng* keyword is used with the *gaussian* value, then the noise +is generated from a gaussian distribution. Typically this added +complexity is unnecessary, and one should be fine using the *uniform* +value for reasons argued in :ref:`(Dunweg) `. + +If the *rng* keyword is used with the *none* value, then the noise +terms are set to zero. + +If the *rotate_planar* keyword is used with the *yes* value, then only +two dimensional rotational diffusion occurs (i.e. only the z-component +of the angular momentum is non-zero). This option is only available to +2D simulations. + +If the *rotate_planar* keyword is used with the *no* value, then three +dimensional rotational diffusion occurs regardless of the simulation +dimension. + +---------- + +.. include:: accel_styles.rst + +---------- + +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. +None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :doc:`output commands `. +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during +:doc:`energy minimization `. + +Restrictions +"""""""""""" + +This fix requires that atoms store torque and angular velocity (omega) +as defined by the :doc:`atom_style sphere ` command. +They must also store a dipole moment as defined by the +:doc:`atom_style dipole ` command. + +All particles in the group must be finite-size spheres. They cannot +be point particles. + +Related commands +"""""""""""""""" + +:doc:`fix langevin `, :doc:`fix nve/sphere `, +:doc:`atom style ` + +Default +""""""" + +The default for *rng* is *uniform* and the default for *rotate_planar* +is *no*. + +---------- + +.. _GoldsteinCM: + +**(GoldsteinCM)** Goldstein, Poole, and Safko, Classical Mechanics, 3rd Ed. (2001). + +.. _GardinerC: + +**(GardinerC)** Gardiner, A Handbook for the Natural and Social Sciences 4th Ed. (2009). + +.. _Callegari1: + +**(Callegari1)** Callegari and Volpe, *Numerical Simulations of Active Brownian +Particles*, Flowing Matter, 211-238 (2019). + +.. _Dunweg1: + +**(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). + + diff --git a/src/fix_bd_sphere.cpp b/src/fix_bd_sphere.cpp new file mode 100644 index 0000000000..a30e8150f6 --- /dev/null +++ b/src/fix_bd_sphere.cpp @@ -0,0 +1,264 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp. + + Contributing author: Sam Cameron (University of Bristol) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "fix_bd_sphere.h" +#include "math_extra.h" +#include "atom.h" +#include "force.h" +#include "update.h" +#include "comm.h" +#include "domain.h" +#include "random_mars.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + time_integrate = 1; + + if (narg != 8 && narg != 10 && narg != 12) + error->all(FLERR,"Illegal fix bd/sphere command."); + + if (!atom->sphere_flag) + error->all(FLERR,"Fix bd/sphere requires atom style sphere"); + if (!atom->mu_flag) + error->all(FLERR,"Fix bd/sphere requires atom attribute mu"); + + gamma_t = force->numeric(FLERR,arg[3]); + if (gamma_t <= 0.0) + error->all(FLERR,"Fix bd/sphere translational viscous drag " + "coefficient must be > 0."); + + gamma_r = force->numeric(FLERR,arg[4]); + if (gamma_t <= 0.0) + error->all(FLERR,"Fix bd/sphere rotational viscous drag " + "coefficient must be > 0."); + + diff_t = force->numeric(FLERR,arg[5]); + if (diff_t <= 0.0) + error->all(FLERR,"Fix bd/sphere translational diffusion " + "coefficient must be > 0."); + + diff_r = force->numeric(FLERR,arg[6]); + if (diff_r <= 0.0) + error->all(FLERR,"Fix bd/sphere rotational diffusion " + "coefficient must be > 0."); + + seed = force->inumeric(FLERR,arg[7]); + if (seed <= 0) error->all(FLERR,"Fix bd/sphere seed must be > 0."); + + noise_flag = 1; + gaussian_noise_flag = 0; + rotate_planar_flag = 0; + + int iarg == 8; + + while (iarg < narg) { + if (strcmp(arg[iarg],"rng") == 0) { + if (strcmp(arg[iarg + 1],"uniform") == 0) { + noise_flag = 1; + } else if (strcmp(arg[iarg + 1],"gaussian") == 0) { + noise_flag = 1; + gaussian_noise_flag = 1; + } else if (strcmp(arg[iarg + 1],"none") == 0) { + noise_flag = 0; + } else { + error->all(FLERR,"Illegal fix/bd/sphere command."); + } + } else if (strcmp(arg[iarg],"rotate_planar") == 0) { + + if (strcmp(arg[iarg + 1],"yes") == 0) { + rotate_planar_flag = 1; + if (domain->dimension != 2) { + error->all(FLERR,"Cannot constrain rotational degrees of freedom " + "to the xy plane if the simulation is in 3D " + "(in fix/bd/sphere)."); + } + } else if (strcmp(arg[iarg + 1],"no") == 0) { + rotate_planar_flag = 0; + } else { + error->all(FLERR,"Illegal fix/bd/sphere command."); + } + } else { + error->all(FLERR,"Illegal fix/bd/sphere command."); + } + iarg = iarg + 2; + } + + + // initialize Marsaglia RNG with processor-unique seed + random = new RanMars(lmp,seed + comm->me); + + +} + +/* ---------------------------------------------------------------------- */ + +int FixBdSphere::setmask() +{ + int mask = 0; + mask |= INITIAL_INTEGRATE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +FixBdSphere::~FixBdSphere() +{ + + delete random; + +} + + +/* ---------------------------------------------------------------------- */ + +void FixBdSphere::init() +{ + + g1 = force->ftm2v/gamma_t; + g3 = force->ftm2v/gamma_r; + if (noise_flag == 0) { + g2 = 0; + g4 = 0; + rng_func = &RanMars::zero_rng; + } else if (gaussian_noise_flag == 1) { + g2 = sqrt(2 * diff_t); + g4 = sqrt(2 * diff_r); + rng_func = &RanMars::gaussian; + } else { + g2 = sqrt( 24 * diff_t); + g4 = sqrt( 24 * diff_r ); + rng_func = &RanMars::uniform_middle; + } + + if (domain->dimension == 2 && rotate_planar_flag == 0) { + error->warning(FLERR,"Using a 2D simulation, but allowing for " + "full (3D) rotation (in fix/bd/sphere)."); + } + + +} + +/* ---------------------------------------------------------------------- */ + +void FixBdSphere::initial_integrate(int /* vflag */) +{ + double **x = atom->x; + double **v = atom->v; + double **mu = atom->mu; + double **f = atom->f; + double **omega = atom->omega; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double dx,dy,dz; + double dtheta; + double mux,muy,muz,mu_tmp,wx,wy,wz; + double prefac_1, prefac_2; + + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + // set timestep here since dt may have changed + dt = update->dt; + sqrtdt = sqrt(dt); + + int d3rot; // whether to compute angular momentum in xy plane + + if (rotate_planar_flag) { + d3rot = 0; + } else { + d3rot = 1; + } + + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + dx = (dt * g1 * f[i][0] + + sqrtdt * g2 * (random->*rng_func)()); + x[i][0] += dx; + v[i][0] = dx/dt; + dy = (dt * g1 * f[i][1] + + sqrtdt * g2 * (random->*rng_func)()); + x[i][1] += dy; + v[i][1] = dy/dt; + + dz = (dt * g1 * f[i][2] + + sqrtdt * g2 * (random->*rng_func)()); + x[i][2] += dz; + v[i][2] = dz/dt; + + + omega[i][0] = d3rot*(g3* torque[i][0] + + g4 * (random->*rng_func)()/sqrtdt); + omega[i][1] = d3rot*(g3* torque[i][1] + + g4 * (random->*rng_func)()/sqrtdt); + omega[i][2] = (g3* torque[i][2] + + g4 * (random->*rng_func)()/sqrtdt); + + dtheta = sqrt((omega[i][0]*dt)**2+(omega[i][1]*dt)**2+(omega[i][2]*dt)**2); + + if (abs(dtheta) < 1e-14) { + prefac_1 = dt; + prefac_2 = 0.5*dt*dt; + } else { + prefac_1 = dt*sin(dtheta)/dtheta; + prefac_2 = dt*dt*(1-cos(dtheta))/(dtheta*dtheta); + } + + mux = mu[i][0]; + muy = mu[i][1]; + muz = mu[i][2]; + + wx = omega[i][0]; + wy = omega[i][1]; + wz = omega[i][2]; + + mu[i][0] = (mux + prefac_1 * ( -wz*muy + wy*muz ) + + prefac_2 * ( -1*( wz*wz + wy*wy ) * mux + + ( wz*muz + wy*muy ) * wx)); + + mu[i][1] = (muy + prefac_1 * ( wz*mux - wx*muz ) + + prefac_2 * ( -1*(wz*wz + wx*wx) * muy + + ( wz*muz + wx*mux ) * wy)); + + mu[i][2] = (muz + prefac_1 * ( -wy*mux + wx*muy ) + + prefac_2 * ( -1*( wx*wx + wy*wy ) * muz + + ( wy*muy + wx*mux ) * wz)); + + mu_tmp = sqrt(mu[i][0]*mu[i][0]+mu[i][1]*mu[i][1]+mu[i][2]*mu[i][2]); + + mu[i][0] = mu[i][0]/mu_tmp; + mu[i][1] = mu[i][1]/mu_tmp; + mu[i][2] = mu[i][2]/mu_tmp; + + } + } + + return; +} diff --git a/src/fix_bd_sphere.h b/src/fix_bd_sphere.h new file mode 100644 index 0000000000..2777427bc8 --- /dev/null +++ b/src/fix_bd_sphere.h @@ -0,0 +1,104 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(bd/sphere,FixBdSphere) + +#else + +#ifndef LMP_FIX_BD_SPHERE_H +#define LMP_FIX_BD_SPHERE_H + +#include "fix_nve.h" + +namespace LAMMPS_NS { + +class FixBdSphere : public Fix { + public: + FixBdSphere(class LAMMPS *, int, char **); + virtual ~FixBdSphere(); + void init(); + void initial_integrate(int); + int setmask(); + + private: + typedef double (RanMars::*rng_member)(); + rng_member rng_func; // placeholder for RNG function + int seed; // RNG seed + + double dt, sqrtdt; // time step interval and its sqrt + + + double gamma_t,gamma_r; // translational and rotational damping params + double diff_t,diff_r; // translational and rotational diffusion coeffs + + double g1,g2, g3, g4; // prefactors in time stepping + int noise_flag; // 0/1 for noise off/on + int gaussian_noise_flag; // 0/1 for uniform/gaussian noise + int rotate_planar_flag; // 0/1 for 2D/3D rotational dof + +protected: + class RanMars *random; + + int activity_flag; +}; + +} +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal fix bd/sphere command. + +Wrong number/type of input arguments. + +E: Compute bd/sphere requires atom style sphere + +Self-explanatory. + +E: Compute bd/sphere requires atom attribute mu + +Self-explanatory. + +E: Fix bd/sphere translational viscous drag coefficient must be > 0. + +Self-explanatory. + +E: Fix bd/sphere rotational viscous drag coefficient must be > 0. + +Self-explanatory. + +E: Fix bd/sphere translational diffusion coefficient must be > 0. + +Self-explanatory. + +E: Fix bd/sphere rotational diffusion coefficient must be > 0. + +Self-explanatory. + +E: Fix bd/sphere seed must be > 0. + +E: Cannot constrain rotational degrees of freedom + to the xy plane if the simulation is in 3D (in fix/bd/sphere). + +Self-explanatory. + +W: Using a 2D simulation, but allowing for full (3D) rotation + (in fix/bd/sphere). + +Self-explanatory. + + +*/ diff --git a/src/random_mars.cpp b/src/random_mars.cpp index 621d7d3008..f31a92624a 100644 --- a/src/random_mars.cpp +++ b/src/random_mars.cpp @@ -94,6 +94,22 @@ double RanMars::uniform() return uni; } +/* ---------------------------------------------------------------------- + uniform RN shifted to be symmetric about zero (for fix bd/sphere). +------------------------------------------------------------------------- */ +double RanMars::uniform_middle() +{ + return uniform()-0.5; +} + +/* ---------------------------------------------------------------------- + Return 0 (for fix/bd/sphere). +------------------------------------------------------------------------- */ +double RanMars::zero_rng() +{ + return 0.0; +} + /* ---------------------------------------------------------------------- gaussian RN ------------------------------------------------------------------------- */ diff --git a/src/random_mars.h b/src/random_mars.h index 1bcd16b051..7028ef54d2 100644 --- a/src/random_mars.h +++ b/src/random_mars.h @@ -23,6 +23,8 @@ class RanMars : protected Pointers { RanMars(class LAMMPS *, int); ~RanMars(); double uniform(); + double uniform_middle(); + double zero_rng(); double gaussian(); double gaussian(double mu, double sigma); double rayleigh(double sigma); From a7d2059d8610b7f259c7efb7f9ea8dc068ac4a3b Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Sat, 5 Dec 2020 09:33:15 +0000 Subject: [PATCH 0038/1217] Fixed some issues after initial testing. --- src/fix_bd_sphere.cpp | 23 +++++++++++++---------- src/fix_bd_sphere.h | 5 ++--- 2 files changed, 15 insertions(+), 13 deletions(-) diff --git a/src/fix_bd_sphere.cpp b/src/fix_bd_sphere.cpp index a30e8150f6..50f6964d6a 100644 --- a/src/fix_bd_sphere.cpp +++ b/src/fix_bd_sphere.cpp @@ -17,10 +17,10 @@ Contributing author: Sam Cameron (University of Bristol) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_bd_sphere.h" + +#include +#include #include "math_extra.h" #include "atom.h" #include "force.h" @@ -49,34 +49,34 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : if (!atom->mu_flag) error->all(FLERR,"Fix bd/sphere requires atom attribute mu"); - gamma_t = force->numeric(FLERR,arg[3]); + gamma_t = utils::numeric(FLERR,arg[3],false,lmp); if (gamma_t <= 0.0) error->all(FLERR,"Fix bd/sphere translational viscous drag " "coefficient must be > 0."); - gamma_r = force->numeric(FLERR,arg[4]); + gamma_r = utils::numeric(FLERR,arg[4],false,lmp); if (gamma_t <= 0.0) error->all(FLERR,"Fix bd/sphere rotational viscous drag " "coefficient must be > 0."); - diff_t = force->numeric(FLERR,arg[5]); + diff_t = utils::numeric(FLERR,arg[5],false,lmp); if (diff_t <= 0.0) error->all(FLERR,"Fix bd/sphere translational diffusion " "coefficient must be > 0."); - diff_r = force->numeric(FLERR,arg[6]); + diff_r = utils::numeric(FLERR,arg[6],false,lmp); if (diff_r <= 0.0) error->all(FLERR,"Fix bd/sphere rotational diffusion " "coefficient must be > 0."); - seed = force->inumeric(FLERR,arg[7]); + seed = utils::inumeric(FLERR,arg[7],false,lmp); if (seed <= 0) error->all(FLERR,"Fix bd/sphere seed must be > 0."); noise_flag = 1; gaussian_noise_flag = 0; rotate_planar_flag = 0; - int iarg == 8; + int iarg = 8; while (iarg < narg) { if (strcmp(arg[iarg],"rng") == 0) { @@ -174,6 +174,7 @@ void FixBdSphere::initial_integrate(int /* vflag */) double **mu = atom->mu; double **f = atom->f; double **omega = atom->omega; + double **torque = atom->torque; int *mask = atom->mask; int nlocal = atom->nlocal; double dx,dy,dz; @@ -221,7 +222,9 @@ void FixBdSphere::initial_integrate(int /* vflag */) omega[i][2] = (g3* torque[i][2] + g4 * (random->*rng_func)()/sqrtdt); - dtheta = sqrt((omega[i][0]*dt)**2+(omega[i][1]*dt)**2+(omega[i][2]*dt)**2); + dtheta = sqrt((omega[i][0]*dt)*(omega[i][0]*dt) + +(omega[i][1]*dt)*(omega[i][1]*dt) + +(omega[i][2]*dt)*(omega[i][2]*dt)); if (abs(dtheta) < 1e-14) { prefac_1 = dt; diff --git a/src/fix_bd_sphere.h b/src/fix_bd_sphere.h index 2777427bc8..2188684db7 100644 --- a/src/fix_bd_sphere.h +++ b/src/fix_bd_sphere.h @@ -33,8 +33,6 @@ class FixBdSphere : public Fix { int setmask(); private: - typedef double (RanMars::*rng_member)(); - rng_member rng_func; // placeholder for RNG function int seed; // RNG seed double dt, sqrtdt; // time step interval and its sqrt @@ -50,8 +48,9 @@ class FixBdSphere : public Fix { protected: class RanMars *random; + typedef double (RanMars::*rng_member)(); + rng_member rng_func; // placeholder for RNG function - int activity_flag; }; } From 3c918029f0d1b1e753702ad82a3faef61e861e51 Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Sun, 6 Dec 2020 19:23:15 +0000 Subject: [PATCH 0039/1217] Added virial flag to fix_bd_sphere. --- doc/src/fix_bd_sphere.rst | 34 +++++------ src/fix_bd_sphere.cpp | 120 +++++++++++++++++++++++++------------- src/fix_bd_sphere.h | 5 +- 3 files changed, 98 insertions(+), 61 deletions(-) diff --git a/doc/src/fix_bd_sphere.rst b/doc/src/fix_bd_sphere.rst index 2ab184e4fb..013d0604bb 100644 --- a/doc/src/fix_bd_sphere.rst +++ b/doc/src/fix_bd_sphere.rst @@ -17,7 +17,7 @@ Syntax * diff_t = translational diffusion coefficient * diff_r = rotational diffusion coefficient * zero or more keyword/value pairs may be appended -* keyword = *rng* or *rotate_planar* +* keyword = *rng* .. parsed-literal:: @@ -25,9 +25,6 @@ Syntax uniform = use uniform random number generator gaussian = use gaussian random number generator none = turn off noise - *rotate_planar* arg = *yes* or *no* - yes = only allow rotations in 2D plane (2D simulation only) - no = allow for full 3D rotations Examples """""""" @@ -36,8 +33,8 @@ Examples fix 1 all bd/sphere 1.0 1.0 1.0 1.0 1294019 fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rng none - fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rotate_planar yes - fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rotate_planar no rng gaussian + fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rng uniform + fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rng gaussian Description @@ -70,6 +67,12 @@ the :math:`\omega` axis, and infinitesimal rotation matrix (see e.g. :ref:`(Callegari1) `, section 7.4). +The :doc:`fix_modify ` *virial* option is supported by this +fix to add the contribution due to the added forces on atoms to the +system's virial as part of :doc:`thermodynamic output `. +The default is *virial no* + + IMPORTANT NOTE: This integrator is designed for generic non-equilibrium simulations with additive noise. There are two important cases which (conceptually) reduce the number of free parameters in this fix. @@ -84,6 +87,13 @@ accounted for (e.g. by setting *gamma_t* to 3 and *gamma_r* to 1) where If both (a) and (b) are true, then one must ensure this explicitly via the above relationships. +IMPORTANT NOTE: The diffusion coefficient :math:`D_t` is measured +in units of (length*length)/time and the diffusion coefficient +:math:`D_r` is measured in units of 1/time, where time and length +are in the units specified on the :doc:`units ` page. Similarly, +:math:`\gamma_t` and :math:`\gamma_r` are measured in +units of mass/time and (mass*length*length)/(time). + If the *rng* keyword is used with the *uniform* value, then the noise is generated from a uniform distribution (see :ref:`(Dunweg) ` for why this works). This is the same method @@ -97,15 +107,6 @@ value for reasons argued in :ref:`(Dunweg) `. If the *rng* keyword is used with the *none* value, then the noise terms are set to zero. -If the *rotate_planar* keyword is used with the *yes* value, then only -two dimensional rotational diffusion occurs (i.e. only the z-component -of the angular momentum is non-zero). This option is only available to -2D simulations. - -If the *rotate_planar* keyword is used with the *no* value, then three -dimensional rotational diffusion occurs regardless of the simulation -dimension. - ---------- .. include:: accel_styles.rst @@ -143,8 +144,7 @@ Related commands Default """"""" -The default for *rng* is *uniform* and the default for *rotate_planar* -is *no*. +The default for *rng* is *uniform*. ---------- diff --git a/src/fix_bd_sphere.cpp b/src/fix_bd_sphere.cpp index 50f6964d6a..3a8a0811b9 100644 --- a/src/fix_bd_sphere.cpp +++ b/src/fix_bd_sphere.cpp @@ -31,6 +31,7 @@ #include "memory.h" #include "error.h" + using namespace LAMMPS_NS; using namespace FixConst; @@ -39,9 +40,11 @@ using namespace FixConst; FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { + virial_flag = 1; + time_integrate = 1; - if (narg != 8 && narg != 10 && narg != 12) + if (narg != 8 && narg != 10) error->all(FLERR,"Illegal fix bd/sphere command."); if (!atom->sphere_flag) @@ -59,6 +62,7 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Fix bd/sphere rotational viscous drag " "coefficient must be > 0."); + // note that diffusion is in units of epsilon**2*tau**3/(m**2*sigma**2) diff_t = utils::numeric(FLERR,arg[5],false,lmp); if (diff_t <= 0.0) error->all(FLERR,"Fix bd/sphere translational diffusion " @@ -74,7 +78,6 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : noise_flag = 1; gaussian_noise_flag = 0; - rotate_planar_flag = 0; int iarg = 8; @@ -90,20 +93,6 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : } else { error->all(FLERR,"Illegal fix/bd/sphere command."); } - } else if (strcmp(arg[iarg],"rotate_planar") == 0) { - - if (strcmp(arg[iarg + 1],"yes") == 0) { - rotate_planar_flag = 1; - if (domain->dimension != 2) { - error->all(FLERR,"Cannot constrain rotational degrees of freedom " - "to the xy plane if the simulation is in 3D " - "(in fix/bd/sphere)."); - } - } else if (strcmp(arg[iarg + 1],"no") == 0) { - rotate_planar_flag = 0; - } else { - error->all(FLERR,"Illegal fix/bd/sphere command."); - } } else { error->all(FLERR,"Illegal fix/bd/sphere command."); } @@ -123,6 +112,7 @@ int FixBdSphere::setmask() { int mask = 0; mask |= INITIAL_INTEGRATE; + mask |= POST_FORCE; return mask; } @@ -136,11 +126,13 @@ FixBdSphere::~FixBdSphere() } + /* ---------------------------------------------------------------------- */ void FixBdSphere::init() { + g1 = force->ftm2v/gamma_t; g3 = force->ftm2v/gamma_r; if (noise_flag == 0) { @@ -148,21 +140,22 @@ void FixBdSphere::init() g4 = 0; rng_func = &RanMars::zero_rng; } else if (gaussian_noise_flag == 1) { - g2 = sqrt(2 * diff_t); - g4 = sqrt(2 * diff_r); + g2 = gamma_t*sqrt(2 * diff_t)/force->ftm2v; + g4 = gamma_r*sqrt(2 * diff_r)/force->ftm2v; rng_func = &RanMars::gaussian; } else { - g2 = sqrt( 24 * diff_t); - g4 = sqrt( 24 * diff_r ); + g2 = gamma_t*sqrt( 24 * diff_t)/force->ftm2v; + g4 = gamma_r*sqrt( 24 * diff_r )/force->ftm2v; rng_func = &RanMars::uniform_middle; } - if (domain->dimension == 2 && rotate_planar_flag == 0) { - error->warning(FLERR,"Using a 2D simulation, but allowing for " - "full (3D) rotation (in fix/bd/sphere)."); - } + dt = update->dt; + sqrtdt = sqrt(dt); +} - +void FixBdSphere::setup(int vflag) +{ + post_force(vflag); } /* ---------------------------------------------------------------------- */ @@ -181,16 +174,15 @@ void FixBdSphere::initial_integrate(int /* vflag */) double dtheta; double mux,muy,muz,mu_tmp,wx,wy,wz; double prefac_1, prefac_2; - + if (igroup == atom->firstgroup) nlocal = atom->nfirst; - // set timestep here since dt may have changed + int d3rot; // whether to compute angular momentum in xy plane + dt = update->dt; sqrtdt = sqrt(dt); - - int d3rot; // whether to compute angular momentum in xy plane - if (rotate_planar_flag) { + if (domain->dimension==2) { d3rot = 0; } else { d3rot = 1; @@ -200,27 +192,22 @@ void FixBdSphere::initial_integrate(int /* vflag */) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { - dx = (dt * g1 * f[i][0] - + sqrtdt * g2 * (random->*rng_func)()); + dx = dt * g1 * f[i][0]; x[i][0] += dx; v[i][0] = dx/dt; - dy = (dt * g1 * f[i][1] - + sqrtdt * g2 * (random->*rng_func)()); + + dy = dt * g1 * f[i][1]; x[i][1] += dy; v[i][1] = dy/dt; - dz = (dt * g1 * f[i][2] - + sqrtdt * g2 * (random->*rng_func)()); + dz = dt * g1 * f[i][2]; x[i][2] += dz; v[i][2] = dz/dt; - omega[i][0] = d3rot*(g3* torque[i][0] - + g4 * (random->*rng_func)()/sqrtdt); - omega[i][1] = d3rot*(g3* torque[i][1] - + g4 * (random->*rng_func)()/sqrtdt); - omega[i][2] = (g3* torque[i][2] - + g4 * (random->*rng_func)()/sqrtdt); + omega[i][0] = d3rot * g3* torque[i][0]; + omega[i][1] = d3rot * g3* torque[i][1]; + omega[i][2] = g3* torque[i][2]; dtheta = sqrt((omega[i][0]*dt)*(omega[i][0]*dt) +(omega[i][1]*dt)*(omega[i][1]*dt) @@ -265,3 +252,52 @@ void FixBdSphere::initial_integrate(int /* vflag */) return; } + +/* ---------------------------------------------------------------------- + apply random force, stolen from MISC/fix_efield.cpp +------------------------------------------------------------------------- */ + +void FixBdSphere::post_force(int vflag) +{ + double **f = atom->f; + double **x = atom->x; + double **torque = atom->torque; + int *mask = atom->mask; + imageint *image = atom->image; + int nlocal = atom->nlocal; + + // virial setup + + if (vflag) v_setup(vflag); + else evflag = 0; + + + + double fx,fy,fz; + double v[6]; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + + fx = g2 * (random->*rng_func)()/sqrtdt; + fy = g2 * (random->*rng_func)()/sqrtdt; + fz = g2 * (random->*rng_func)()/sqrtdt; + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + + torque[i][0] = g4*(random->*rng_func)()/sqrtdt; + torque[i][1] = g4*(random->*rng_func)()/sqrtdt; + torque[i][2] = g4*(random->*rng_func)()/sqrtdt; + + if (evflag) { + v[0] = fx*x[i][0]; + v[1] = fy*x[i][1]; + v[2] = fz*x[i][2]; + v[3] = fx*x[i][1]; + v[4] = fx*x[i][2]; + v[5] = fy*x[i][2]; + v_tally(i, v); + } + } +} diff --git a/src/fix_bd_sphere.h b/src/fix_bd_sphere.h index 2188684db7..873ba9ef2a 100644 --- a/src/fix_bd_sphere.h +++ b/src/fix_bd_sphere.h @@ -20,7 +20,7 @@ FixStyle(bd/sphere,FixBdSphere) #ifndef LMP_FIX_BD_SPHERE_H #define LMP_FIX_BD_SPHERE_H -#include "fix_nve.h" +#include "fix.h" namespace LAMMPS_NS { @@ -30,6 +30,8 @@ class FixBdSphere : public Fix { virtual ~FixBdSphere(); void init(); void initial_integrate(int); + void setup(int); + void post_force(int); int setmask(); private: @@ -44,7 +46,6 @@ class FixBdSphere : public Fix { double g1,g2, g3, g4; // prefactors in time stepping int noise_flag; // 0/1 for noise off/on int gaussian_noise_flag; // 0/1 for uniform/gaussian noise - int rotate_planar_flag; // 0/1 for 2D/3D rotational dof protected: class RanMars *random; From 9848492d93657617efe0caa18afd5bdecac3a5cc Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Tue, 8 Dec 2020 11:16:42 +0000 Subject: [PATCH 0040/1217] Added example input scripts for fix_bd_sphere code. --- examples/bd_sphere/README.txt | 22 ++ examples/bd_sphere/in2d.bd | 76 +++++ examples/bd_sphere/in3d_virial_on.bd | 77 ++++++ .../log_gaussian_4_1_7_13_2d.lammps.log | 259 ++++++++++++++++++ .../log_uniform_10_1_5_15_3d.lammps.log | 259 ++++++++++++++++++ 5 files changed, 693 insertions(+) create mode 100644 examples/bd_sphere/README.txt create mode 100644 examples/bd_sphere/in2d.bd create mode 100644 examples/bd_sphere/in3d_virial_on.bd create mode 100644 examples/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log create mode 100644 examples/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log diff --git a/examples/bd_sphere/README.txt b/examples/bd_sphere/README.txt new file mode 100644 index 0000000000..b044f11edc --- /dev/null +++ b/examples/bd_sphere/README.txt @@ -0,0 +1,22 @@ +The input file in2d.bd demonstrates how to run a 2d simulation +of particles undergoing overdamped brownian motion in both +translational and rotational degrees of freedom. + +The input file in3d_virial_on.bd demonstrates how to run a +similar simulation but in 3d. In this case, the virial +contribution of the brownian dynamics (the sum +sum_i /(3*volume) where W is +a random variable with mean 0 and variance dt) is +calculated via the fix_modify command. For long +enough times, this will be equal to rho*D_t*gamma_t +(the ideal gas term in equilibrium systems). + +To confirm rotational diffusion is working correctly, +run the above simulations with dump files on and +measure \sum_i, and one should +find that this decays as an exponential with +timescale 1/((d-1)*D_r). + +Note that both of the simulations above are not long +enough to get good statistics on e.g. ideal gas +pressure, rotational diffusion, or translational diffusion. diff --git a/examples/bd_sphere/in2d.bd b/examples/bd_sphere/in2d.bd new file mode 100644 index 0000000000..c11381ad5a --- /dev/null +++ b/examples/bd_sphere/in2d.bd @@ -0,0 +1,76 @@ +# 2d overdamped brownian dynamics + +variable rng string gaussian +variable gamma_t equal 4.0 +variable gamma_r equal 1.0 +variable D_t equal 7.0 +variable D_r equal 13.0 +variable seed equal 1974019 + + +variable params string ${rng}_${gamma_t}_${gamma_r}_${D_t}_${D_r} + + +log log_${params}_2d.lammps.log +units lj +atom_style hybrid dipole sphere +dimension 2 +newton off + + +lattice sq 0.4 +region box block -16 16 -16 16 -0.2 0.2 +create_box 1 box +create_atoms 1 box +mass * 1.0 +set type * dipole/random ${seed} 1.0 +velocity all create 1.0 1 loop geom + + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + + +pair_style none + + + +#compute d all property/atom mux muy muz + +fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix 2 all enforce2d + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +reset_timestep 0 + + +#initialisation for the main run + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +# write trajectory and thermo in a log-scale frequency +# uncomment next three lines for dump output +#dump 1 all custom 2000 dump_${params}_2d.lammpstrj id type & +# x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 1000 + +# main run +run 120000 + + diff --git a/examples/bd_sphere/in3d_virial_on.bd b/examples/bd_sphere/in3d_virial_on.bd new file mode 100644 index 0000000000..1ef88930c1 --- /dev/null +++ b/examples/bd_sphere/in3d_virial_on.bd @@ -0,0 +1,77 @@ +# 3d overdamped brownian dynamics + + +variable rng string uniform +variable gamma_t equal 10.0 +variable gamma_r equal 1.0 +variable D_t equal 5.0 +variable D_r equal 15.0 +variable seed equal 553910 + + +variable params string ${rng}_${gamma_t}_${gamma_r}_${D_t}_${D_r} + + +log log_${params}_3d.lammps.log +units lj +atom_style hybrid dipole sphere +dimension 3 +newton off + + +lattice sc 0.4 +region box block -8 8 -8 8 -8 8 +create_box 1 box +create_atoms 1 box +mass * 1.0 +set type * dipole/random ${seed} 1.0 +velocity all create 1.0 1 loop geom + + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + + +pair_style none + + + +#compute d all property/atom mux muy muz + +fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix_modify 1 virial yes + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +reset_timestep 0 + + +#initialisation for the main run + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +# write trajectory and thermo in a log-scale frequency +# uncomment the next three lines for dump file +#dump 1 all custom 10000 dump_${params}_3d.lammpstrj id type & +# x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 1000 + +# main run +run 120000 + + diff --git a/examples/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log b/examples/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log new file mode 100644 index 0000000000..72b90efe0e --- /dev/null +++ b/examples/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log @@ -0,0 +1,259 @@ +units lj +atom_style hybrid dipole sphere +WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (src/atom_vec_hybrid.cpp:157) +dimension 2 +newton off + + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 +region box block -16 16 -16 16 -0.2 0.2 +create_box 1 box +Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 1024 atoms + create_atoms CPU = 0.002 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 1974019 1.0 +Setting atom values ... + 1024 settings made for dipole/random +velocity all create 1.0 1 loop geom + + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + + +pair_style none + + + +#compute d all property/atom mux muy muz + +fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 4 1 7 ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 4 1 7 13 ${seed} rng ${rng} +fix 1 all bd/sphere 4 1 7 13 1974019 rng ${rng} +fix 1 all bd/sphere 4 1 7 13 1974019 rng gaussian +fix 2 all enforce2d + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.289 | 4.289 | 4.289 Mbytes +Step Temp E_pair c_press + 0 1 0 0 + 50000 7.3671759e+10 0 0 +Loop time of 10.2295 on 1 procs for 50000 steps with 1024 atoms + +Performance: 0.042 tau/day, 4887.825 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.033217 | 0.033217 | 0.033217 | 0.0 | 0.32 +Output | 2.1435e-05 | 2.1435e-05 | 2.1435e-05 | 0.0 | 0.00 +Modify | 10.047 | 10.047 | 10.047 | 0.0 | 98.21 +Other | | 0.1497 | | | 1.46 + +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 65.0000 ave 65 max 65 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + + +#initialisation for the main run + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +# write trajectory and thermo in a log-scale frequency +# uncomment next three lines for dump output +#dump 1 all custom 2000 dump_${params}_2d.lammpstrj id type # x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 1000 + +# main run +run 120000 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes +Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 7.3671759e+10 0 0 0 0 0 0 + 1000 710744.42 0 0.1332856 0.13577642 0 0.26906203 0 + 2000 705025.5 0 0.27078701 0.27355073 0 0.54433774 0 + 3000 750845.29 0 0.41036556 0.39710766 0 0.80747321 0 + 4000 752542.47 0 0.53097803 0.53654063 0 1.0675187 0 + 5000 731812.26 0 0.66927129 0.65872533 0 1.3279966 0 + 6000 716119.24 0 0.79097615 0.76825364 0 1.5592298 0 + 7000 726294.28 0 0.93322099 0.91220222 0 1.8454232 0 + 8000 673771.54 0 1.0789689 1.031843 0 2.1108119 0 + 9000 757173.95 0 1.2328252 1.2024778 0 2.435303 0 + 10000 693711.95 0 1.3972184 1.3045575 0 2.7017759 0 + 11000 774897.65 0 1.584036 1.4168797 0 3.0009157 0 + 12000 764910.09 0 1.7344079 1.5751172 0 3.3095251 0 + 13000 752859.5 0 1.8538323 1.7336107 0 3.5874429 0 + 14000 746333.26 0 2.0392353 1.9027299 0 3.9419652 0 + 15000 735704.24 0 2.1714465 2.000952 0 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0 + 53000 741211.89 0 7.2287282 7.2318431 0 14.460571 0 + 54000 723668.97 0 7.3732634 7.3847301 0 14.757994 0 + 55000 751846.88 0 7.5566634 7.4927365 0 15.0494 0 + 56000 762648.27 0 7.7651818 7.5379796 0 15.303161 0 + 57000 710175.2 0 7.9051989 7.6644542 0 15.569653 0 + 58000 740068.94 0 8.0296854 7.8307471 0 15.860433 0 + 59000 728119.43 0 8.1562433 8.039333 0 16.195576 0 + 60000 728768.48 0 8.316192 8.1643843 0 16.480576 0 + 61000 707538.83 0 8.3727565 8.3895027 0 16.762259 0 + 62000 713931.41 0 8.4657927 8.5517529 0 17.017546 0 + 63000 742604.95 0 8.6550684 8.7189851 0 17.374053 0 + 64000 738981.54 0 8.7331005 8.9208616 0 17.653962 0 + 65000 701685.87 0 8.898571 8.977933 0 17.876504 0 + 66000 716151.39 0 9.0229699 9.1292403 0 18.15221 0 + 67000 732641.29 0 9.151611 9.3249179 0 18.476529 0 + 68000 740870.85 0 9.233452 9.4667607 0 18.700213 0 + 69000 733159.17 0 9.1743719 9.5648134 0 18.739185 0 + 70000 693562.75 0 9.3414089 9.7425241 0 19.083933 0 + 71000 748694.53 0 9.5036102 9.8686571 0 19.372267 0 + 72000 721046.02 0 9.7116931 10.0195 0 19.731193 0 + 73000 736631.66 0 9.7095662 10.205306 0 19.914872 0 + 74000 751264.08 0 9.9413234 10.327844 0 20.269167 0 + 75000 729223.27 0 10.211903 10.412516 0 20.624419 0 + 76000 747811 0 10.332266 10.544251 0 20.876517 0 + 77000 717505.01 0 10.521195 10.737774 0 21.258969 0 + 78000 712288.89 0 10.712514 10.874932 0 21.587446 0 + 79000 728912.34 0 10.755227 10.968257 0 21.723484 0 + 80000 743505.67 0 11.026063 11.070234 0 22.096298 0 + 81000 732218.14 0 11.321417 11.31773 0 22.639147 0 + 82000 777186.61 0 11.480074 11.401465 0 22.881539 0 + 83000 734805.95 0 11.7524 11.62552 0 23.37792 0 + 84000 753703.38 0 11.863318 11.833925 0 23.697243 0 + 85000 755730.75 0 12.068564 11.937143 0 24.005707 0 + 86000 725021.19 0 12.258195 12.034586 0 24.292781 0 + 87000 731844.67 0 12.341844 12.331792 0 24.673636 0 + 88000 707368.15 0 12.431452 12.547314 0 24.978766 0 + 89000 784756.28 0 12.405699 12.686021 0 25.09172 0 + 90000 760278.97 0 12.542669 12.851925 0 25.394593 0 + 91000 753765.97 0 12.703534 13.08092 0 25.784454 0 + 92000 705869.22 0 12.971838 13.210092 0 26.18193 0 + 93000 741699.59 0 13.110745 13.383115 0 26.49386 0 + 94000 717372.41 0 13.252109 13.466388 0 26.718497 0 + 95000 721820.49 0 13.373146 13.660605 0 27.033751 0 + 96000 777409.97 0 13.596822 13.886961 0 27.483782 0 + 97000 741480.91 0 13.752545 14.204624 0 27.957169 0 + 98000 725755.72 0 13.918302 14.219292 0 28.137594 0 + 99000 729710.24 0 14.065417 14.213142 0 28.278559 0 + 100000 700366.74 0 14.278054 14.324135 0 28.602189 0 + 101000 722737.18 0 14.398464 14.46904 0 28.867505 0 + 102000 758930.85 0 14.408098 14.637964 0 29.046061 0 + 103000 725233.66 0 14.526482 14.719688 0 29.24617 0 + 104000 752416.52 0 14.641393 14.952087 0 29.59348 0 + 105000 769047.5 0 14.780788 15.182945 0 29.963733 0 + 106000 734849.98 0 14.840982 15.316112 0 30.157094 0 + 107000 720210.74 0 15.010029 15.372792 0 30.382821 0 + 108000 741216.55 0 15.113143 15.488575 0 30.601718 0 + 109000 714158.43 0 15.057499 15.592865 0 30.650364 0 + 110000 743262.25 0 15.381281 15.798368 0 31.179649 0 + 111000 728836.92 0 15.488226 16.034645 0 31.522871 0 + 112000 753490.67 0 15.679979 16.350819 0 32.030799 0 + 113000 730699.5 0 15.82813 16.680136 0 32.508266 0 + 114000 705526.22 0 16.099699 16.920095 0 33.019794 0 + 115000 752408.36 0 16.393466 17.053935 0 33.447401 0 + 116000 713697.16 0 16.634939 17.35349 0 33.98843 0 + 117000 690041.5 0 16.727379 17.457936 0 34.185315 0 + 118000 745594.37 0 16.838659 17.585392 0 34.424052 0 + 119000 714487.42 0 17.064214 17.743478 0 34.807692 0 + 120000 716557.14 0 17.105558 17.845925 0 34.951483 0 +Loop time of 25.2131 on 1 procs for 120000 steps with 1024 atoms + +Performance: 4112.144 tau/day, 4759.427 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0016123 | 0.0016123 | 0.0016123 | 0.0 | 0.01 +Comm | 0.025898 | 0.025898 | 0.025898 | 0.0 | 0.10 +Output | 0.0037882 | 0.0037882 | 0.0037882 | 0.0 | 0.02 +Modify | 24.767 | 24.767 | 24.767 | 0.0 | 98.23 +Other | | 0.4146 | | | 1.64 + +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 1049 +Dangerous builds = 0 + + +Total wall time: 0:00:35 diff --git a/examples/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log b/examples/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log new file mode 100644 index 0000000000..fda48dc71a --- /dev/null +++ b/examples/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log @@ -0,0 +1,259 @@ +units lj +atom_style hybrid dipole sphere +WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (src/atom_vec_hybrid.cpp:157) +dimension 3 +newton off + + +lattice sc 0.4 +Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 +region box block -8 8 -8 8 -8 8 +create_box 1 box +Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4096 atoms + create_atoms CPU = 0.003 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 553910 1.0 +Setting atom values ... + 4096 settings made for dipole/random +velocity all create 1.0 1 loop geom + + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + + +pair_style none + + + +#compute d all property/atom mux muy muz + +fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 10 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 10 1 ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 10 1 5 ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 10 1 5 15 ${seed} rng ${rng} +fix 1 all bd/sphere 10 1 5 15 553910 rng ${rng} +fix 1 all bd/sphere 10 1 5 15 553910 rng uniform +fix_modify 1 virial yes + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.362 | 4.362 | 4.362 Mbytes +Step Temp E_pair c_press + 0 1 0 -32553.271 + 50000 5.2351457e+10 0 -15026.42 +Loop time of 18.6303 on 1 procs for 50000 steps with 4096 atoms + +Performance: 0.023 tau/day, 2683.804 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.31439 | 0.31439 | 0.31439 | 0.0 | 1.69 +Output | 5.5046e-05 | 5.5046e-05 | 5.5046e-05 | 0.0 | 0.00 +Modify | 17.718 | 17.718 | 17.718 | 0.0 | 95.11 +Other | | 0.5974 | | | 3.21 + +Nlocal: 4096.00 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 817.000 ave 817 max 817 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + + +#initialisation for the main run + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +# write trajectory and thermo in a log-scale frequency +# uncomment the next three lines for dump file +#dump 1 all custom 10000 dump_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 1000 + +# main run +run 120000 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.737 | 4.737 | 4.737 Mbytes +Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 5.2351457e+10 0 0 0 0 0 -233.83012 + 1000 522590.88 0 0.10259269 0.10487519 0.10391005 0.31137793 -13.730626 + 2000 521776.08 0 0.20662097 0.2118237 0.20371673 0.62216139 -141.90848 + 3000 529408.9 0 0.30711557 0.3105565 0.30293728 0.92060935 28.335187 + 4000 518069.42 0 0.39918073 0.40643835 0.40168024 1.2072993 -12.262269 + 5000 520487.75 0 0.50222348 0.50854461 0.50304351 1.5138116 303.56775 + 6000 527970.5 0 0.60443861 0.60363711 0.59884932 1.806925 218.55799 + 7000 519424.68 0 0.69529071 0.70025532 0.70347351 2.0990195 -363.51723 + 8000 521925.72 0 0.80545039 0.81520807 0.79930708 2.4199655 510.47732 + 9000 518397.28 0 0.91236827 0.9050426 0.89431985 2.7117307 537.74151 + 10000 525696.47 0 0.99494325 0.99433832 0.98574884 2.9750304 411.56896 + 11000 524505.88 0 1.0863677 1.1232636 1.0810609 3.2906921 32.652569 + 12000 525350.08 0 1.1816136 1.2412674 1.189996 3.612877 45.304061 + 13000 524598.12 0 1.2841566 1.3381915 1.2906249 3.912973 -376.50739 + 14000 525438.09 0 1.3964076 1.4420032 1.3915611 4.2299719 -31.273339 + 15000 523531.08 0 1.4829127 1.5436611 1.4892074 4.5157811 -357.26366 + 16000 532366.43 0 1.5871965 1.6432286 1.6020146 4.8324397 435.10667 + 17000 523629.21 0 1.6968632 1.7574539 1.6967316 5.1510487 280.59816 + 18000 521432.94 0 1.7973983 1.8462477 1.8087416 5.4523876 134.69384 + 19000 530778.78 0 1.888653 1.9328611 1.9268155 5.7483296 -64.346115 + 20000 525623.21 0 1.9718697 2.0048196 2.0068177 5.983507 73.884028 + 21000 524862.26 0 2.0414226 2.0967449 2.0878261 6.2259936 163.95173 + 22000 529123.04 0 2.143889 2.1850282 2.1972491 6.5261662 234.87793 + 23000 519629.76 0 2.2297952 2.2661611 2.2805197 6.776476 57.65702 + 24000 523746.18 0 2.3293654 2.3658544 2.3842082 7.079428 46.291089 + 25000 515851.07 0 2.4177426 2.4559274 2.5029961 7.3766661 -16.353546 + 26000 515592.59 0 2.5352044 2.5438918 2.5657776 7.6448738 -65.259248 + 27000 527764.96 0 2.6498176 2.6423592 2.6715377 7.9637146 324.48367 + 28000 527177.18 0 2.7405087 2.7431537 2.7702133 8.2538757 -47.906223 + 29000 521079.66 0 2.8294642 2.8410515 2.8546167 8.5251323 -135.36173 + 30000 526092.8 0 2.961898 2.9361476 2.9319586 8.8300042 206.28635 + 31000 529595.93 0 3.0638234 3.0128995 3.0434232 9.1201461 -35.946596 + 32000 521173.83 0 3.159344 3.1397814 3.1455147 9.4446401 328.73193 + 33000 522989.77 0 3.2567127 3.2348491 3.2444068 9.7359686 362.33435 + 34000 522930.45 0 3.3489514 3.3433962 3.3391822 10.03153 178.73773 + 35000 530664.64 0 3.4445399 3.4843743 3.4205275 10.349442 146.02898 + 36000 521443.26 0 3.520475 3.6171115 3.5179112 10.655498 244.07172 + 37000 529669.54 0 3.6076942 3.7233869 3.6169718 10.948053 79.46077 + 38000 527521.93 0 3.7093699 3.8275855 3.7451165 11.282072 -91.131074 + 39000 523237.65 0 3.8088585 3.9559041 3.8748751 11.639638 -70.265271 + 40000 522798.75 0 3.89319 4.0420406 3.9196106 11.854841 91.631855 + 41000 524228.77 0 3.9863379 4.1602581 4.0393136 12.18591 113.26515 + 42000 524546.08 0 4.0969366 4.2738786 4.1218115 12.492627 313.83957 + 43000 515948.22 0 4.2161418 4.3700009 4.2178962 12.804039 92.993253 + 44000 527319.42 0 4.3267431 4.4688062 4.3274029 13.122952 -118.91153 + 45000 526222.74 0 4.4289127 4.5531203 4.4604075 13.442441 -474.98113 + 46000 524617.54 0 4.5422968 4.6316235 4.5445894 13.71851 -303.23458 + 47000 524067.07 0 4.6284944 4.6989745 4.5884153 13.915884 -343.41107 + 48000 535659.25 0 4.7221068 4.7505302 4.7212887 14.193926 149.75872 + 49000 527425.65 0 4.8098179 4.8761354 4.8362998 14.522253 -272.18936 + 50000 516588.98 0 4.9077783 4.9950242 4.9826783 14.885481 -52.925733 + 51000 522291.86 0 5.0022325 5.0659091 5.0525647 15.120706 -52.985883 + 52000 530056.07 0 5.123751 5.1470734 5.1603805 15.431205 -231.29334 + 53000 525624.96 0 5.2412036 5.2543541 5.2717587 15.767316 294.19678 + 54000 524407.27 0 5.3530927 5.359043 5.342451 16.054587 -55.282671 + 55000 519989.37 0 5.4458173 5.4781678 5.413865 16.33785 -135.28414 + 56000 524987.68 0 5.5282178 5.5825979 5.5127172 16.623533 84.654044 + 57000 525610.66 0 5.6202713 5.6925409 5.5964466 16.909259 407.16526 + 58000 523097.93 0 5.7390671 5.7830376 5.6921201 17.214225 -271.05243 + 59000 525357.74 0 5.8037507 5.8654514 5.7920744 17.461276 -213.07815 + 60000 522185.96 0 5.9067925 5.9909357 5.903525 17.801253 330.09637 + 61000 527694.33 0 6.0576096 6.0907943 6.0202838 18.168688 310.22884 + 62000 522936.57 0 6.1422565 6.1888677 6.124212 18.455336 -24.591697 + 63000 526642.55 0 6.2261061 6.2832608 6.2023277 18.711695 -130.32823 + 64000 514826.49 0 6.3032614 6.3628539 6.3184362 18.984552 195.43036 + 65000 529338.23 0 6.4152502 6.4482512 6.4241507 19.287652 -77.817059 + 66000 527425.07 0 6.5122194 6.5052947 6.5518104 19.569324 8.0143425 + 67000 525258.85 0 6.6292334 6.6417881 6.6438938 19.914915 152.1905 + 68000 527067.89 0 6.7569918 6.6951219 6.7357134 20.187827 -337.54654 + 69000 522395.33 0 6.8401085 6.7836633 6.8243746 20.448146 34.755329 + 70000 522200.34 0 6.9549662 6.8773008 6.9537894 20.786056 352.30283 + 71000 527550.11 0 7.0441399 6.9837133 7.0860791 21.113932 171.42143 + 72000 529564.22 0 7.1744229 7.0581688 7.1507041 21.383296 269.04569 + 73000 524175.53 0 7.248828 7.1693905 7.2974868 21.715705 -84.993601 + 74000 528604.1 0 7.3358903 7.2983204 7.390523 22.024734 -6.8495991 + 75000 519136.15 0 7.445248 7.4224403 7.4690469 22.336735 250.23521 + 76000 518470.58 0 7.5747768 7.5354904 7.5612252 22.671492 274.53956 + 77000 518459.51 0 7.6660567 7.6557812 7.7020797 23.023918 430.07722 + 78000 516646.23 0 7.7596088 7.7130901 7.7896654 23.262364 536.21298 + 79000 517511.57 0 7.9021784 7.82098 7.8840028 23.607161 193.80468 + 80000 520654.84 0 7.991107 7.8932454 8.0049184 23.889271 -6.0066355 + 81000 522331.74 0 8.0616391 7.9990606 8.0954141 24.156114 47.271954 + 82000 521540.3 0 8.1268306 8.0763829 8.1861513 24.389365 36.265762 + 83000 529154.07 0 8.2537975 8.1854268 8.2745822 24.713807 113.94154 + 84000 525977.29 0 8.2999431 8.26591 8.2970498 24.862903 -72.444836 + 85000 520505.41 0 8.3872349 8.3551374 8.4251458 25.167518 -346.6703 + 86000 516334.67 0 8.4947842 8.4504822 8.5238751 25.469142 -3.8332672 + 87000 524745.34 0 8.5405071 8.5348571 8.6344387 25.709803 -149.22382 + 88000 521384.87 0 8.5798155 8.6260785 8.7133565 25.919251 22.009599 + 89000 519680.71 0 8.6657392 8.6857605 8.8319304 26.18343 -180.94487 + 90000 522482.4 0 8.7310324 8.7844751 8.9636862 26.479194 -102.50361 + 91000 527450.69 0 8.8250902 8.8445728 9.0456076 26.715271 325.68024 + 92000 519060.77 0 8.9054775 8.9412744 9.1259074 26.972659 130.73028 + 93000 518170.14 0 9.0378587 9.0315875 9.2346184 27.304065 -111.68498 + 94000 531639.53 0 9.1268874 9.0952299 9.3437063 27.565824 -26.423328 + 95000 519776.1 0 9.2332576 9.1903006 9.4516001 27.875158 -113.46356 + 96000 527082.72 0 9.2993234 9.2533436 9.534409 28.087076 -46.720611 + 97000 526965.16 0 9.3485677 9.3197496 9.6631942 28.331512 159.18386 + 98000 529790.04 0 9.4759113 9.5177629 9.783846 28.77752 343.32872 + 99000 520964.82 0 9.6488022 9.6573355 9.882432 29.18857 -257.85576 + 100000 520863.58 0 9.7452168 9.7659565 9.9878877 29.499061 -108.52324 + 101000 526760.86 0 9.8073751 9.8508213 10.127532 29.785728 120.22249 + 102000 519249.89 0 9.9315855 9.9767409 10.221605 30.129931 -176.50647 + 103000 525003.9 0 10.023982 10.062451 10.315002 30.401435 422.1401 + 104000 519112.73 0 10.086117 10.136879 10.415222 30.638218 -147.66505 + 105000 517898.24 0 10.180438 10.240942 10.525346 30.946725 158.63054 + 106000 528046.35 0 10.258163 10.41411 10.601663 31.273936 -128.04669 + 107000 527105.8 0 10.364015 10.485036 10.795177 31.644228 183.82165 + 108000 522024.28 0 10.450786 10.544065 10.902961 31.897812 -39.692553 + 109000 519497.83 0 10.556206 10.61633 11.046222 32.218758 173.75988 + 110000 521070.8 0 10.64856 10.745382 11.071387 32.465329 -128.45389 + 111000 525657.64 0 10.830485 10.852954 11.188295 32.871734 -214.60249 + 112000 519426.33 0 10.987769 10.97575 11.26012 33.223639 292.35901 + 113000 526472.45 0 11.029941 11.086376 11.418772 33.535089 189.69245 + 114000 520070.28 0 11.107229 11.183295 11.454757 33.745281 -40.433571 + 115000 525812.59 0 11.153992 11.305378 11.537521 33.99689 -106.38733 + 116000 524464.26 0 11.256779 11.413082 11.633295 34.303156 -159.59643 + 117000 519838.94 0 11.344413 11.480104 11.706366 34.530883 -2.0346135 + 118000 524075.83 0 11.441416 11.597533 11.783056 34.822005 -350.05313 + 119000 533816.71 0 11.52766 11.681986 11.917713 35.127359 -521.58975 + 120000 524509.31 0 11.63865 11.792667 12.080379 35.511696 273.09647 +Loop time of 46.6725 on 1 procs for 120000 steps with 4096 atoms + +Performance: 2221.438 tau/day, 2571.109 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0063169 | 0.0063169 | 0.0063169 | 0.0 | 0.01 +Comm | 0.057082 | 0.057082 | 0.057082 | 0.0 | 0.12 +Output | 0.0068489 | 0.0068489 | 0.0068489 | 0.0 | 0.01 +Modify | 44.98 | 44.98 | 44.98 | 0.0 | 96.37 +Other | | 1.622 | | | 3.48 + +Nlocal: 4096.00 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 992 +Dangerous builds = 0 + + +Total wall time: 0:01:05 From 6b51bf104a3b19adee21ac1305f6ba6882cbfc1f Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Tue, 8 Dec 2020 14:52:28 +0000 Subject: [PATCH 0041/1217] Added unit test for fix bd/sphere. --- unittest/force-styles/tests/data.bdsphere | 86 +++++++++++++++++++ .../tests/fix-timestep-bd_sphere.yaml | 80 +++++++++++++++++ unittest/force-styles/tests/in.bdsphere | 16 ++++ 3 files changed, 182 insertions(+) create mode 100644 unittest/force-styles/tests/data.bdsphere create mode 100644 unittest/force-styles/tests/fix-timestep-bd_sphere.yaml create mode 100644 unittest/force-styles/tests/in.bdsphere diff --git a/unittest/force-styles/tests/data.bdsphere b/unittest/force-styles/tests/data.bdsphere new file mode 100644 index 0000000000..3fbad7d05e --- /dev/null +++ b/unittest/force-styles/tests/data.bdsphere @@ -0,0 +1,86 @@ +LAMMPS data file via write_data, version 30 Nov 2020, timestep = 120000 + +32 atoms +1 atom types + +-2.7144176165949063 2.7144176165949063 xlo xhi +-2.7144176165949063 2.7144176165949063 ylo yhi +-1.3572088082974532 1.3572088082974532 zlo zhi + +Masses + +1 1 + +Pair Coeffs # zero + +1 + +Atoms # hybrid + +1 1 0.8174385639059338 -1.5010271964354949 1.0637924298773633 0 0.6257069940596588 -0.111108944542851 -0.7721046302331049 1 1 -1 0 -1 +2 1 -1.5885878110813303 2.2401728691740113 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--git a/unittest/force-styles/tests/fix-timestep-bd_sphere.yaml b/unittest/force-styles/tests/fix-timestep-bd_sphere.yaml new file mode 100644 index 0000000000..66a65bc3ba --- /dev/null +++ b/unittest/force-styles/tests/fix-timestep-bd_sphere.yaml @@ -0,0 +1,80 @@ +--- +lammps_version: 24 Aug 2020 +date_generated: Tue Dec 08 12:28:40 2020 +epsilon: 1e-12 +prerequisites: ! | + atom hybrid dipole sphere + fix bd_sphere +pre_commands: ! "" +post_commands: ! | + fix test solute bd_sphere 1.0 1.0 1.0 1.0 1049270 + fix_modify test virial yes +input_file: in.bdsphere +natoms: 32 +run_pos: ! |2 +1 0.8198132185477983 -1.5120221815010249 1.069236010215717 +2 -1.583657719347759 2.2448791290372445 0.48185576252150486 +3 -1.1880610036164596 -2.678219122115848 -1.1824396130063375 +4 0.1908794667962731 1.3593710068293134 -1.1524405138570022 +5 -2.502067366922716 -1.6291621715156412 -1.155308629818198 +6 -1.214213515524568 -0.33667539680264325 0.5468489960944642 +7 1.2020658999364164 0.5045561046001554 -0.5265404283266816 +8 1.8138899397447894 1.5212405777462397 0.04943268689972926 +9 -0.547736141448719 2.2385521615789026 0.5146647473679599 +10 -0.38821952892982114 0.7570899758491753 -0.23554333362488367 +11 -0.7101567507222957 1.1587573566149103 0.19674801175715137 +12 1.0217947252204158 0.1732739652383159 0.3064332055619567 +13 -1.43254480550968 -2.4145346257525504 0.22508495277327453 +14 -1.7469141674373843 1.605802890508775 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+15 462.14962458969075 517.8011186395346 582.1970348843957 +16 579.8864331189503 -723.7080269305067 -397.93358494791835 +17 -74.75036331228799 -271.6937286797369 318.88308122021147 +18 -390.80278885093725 -625.5459111419849 -678.090840223804 +19 -598.6933260882906 41.7579655827356 750.013779723682 +20 158.9763823000137 310.0053213378944 226.83667759758563 +21 -578.1763126419472 755.241466585726 -387.1851268613029 +22 -686.649568451259 496.2326396493665 -392.30182210275524 +23 139.72339904857833 686.4901911325059 460.94182891802774 +24 625.6387119562066 -178.79780516572728 194.63377933230842 +25 761.5753760889415 -550.6374632586046 -355.3666363468769 +26 -167.9925585211552 -748.0176849962858 537.6949353742531 +27 -687.973065038564 -637.3675344653028 -231.07938308121751 +28 -480.2313784604401 372.9809695991278 24.972745276651647 +29 67.21410614540838 54.58636231646205 639.3712010004265 +30 -469.9090654062959 715.7242943947524 -386.21519675922724 +31 -380.59017466972404 487.7214660680053 177.24466119039292 +32 138.31144158562722 31.005629253137737 621.8772779588675 +... diff --git a/unittest/force-styles/tests/in.bdsphere b/unittest/force-styles/tests/in.bdsphere new file mode 100644 index 0000000000..1fb583f51d --- /dev/null +++ b/unittest/force-styles/tests/in.bdsphere @@ -0,0 +1,16 @@ +variable newton_pair index on +variable newton_bond index on +variable units index lj +variable input_dir index . +variable data_file index ${input_dir}/data.bdsphere +variable pair_style index 'zero 8.0' + +atom_style hybrid dipole sphere +atom_modify map array +neigh_modify delay 2 every 2 check no +units ${units} +timestep 0.00001 +newton ${newton_pair} ${newton_bond} + +pair_style ${pair_style} +read_data ${data_file} From dab4c7409accde6198c59f4bad28e7cd12c06986 Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Wed, 9 Dec 2020 21:04:23 +0000 Subject: [PATCH 0042/1217] Changes for pull request 2511. --- doc/src/Commands_fix.rst | 1 + doc/src/fix.rst | 1 + doc/src/fix_bd_sphere.rst | 38 ++--- examples/bd_sphere/README.txt | 12 +- examples/bd_sphere/{in2d.bd => in2ddipole.bd} | 2 +- examples/bd_sphere/in3d_virial_on.bd | 12 +- .../log_gaussian_4_1_7_13_2d.lammps.log | 46 +++---- .../log_uniform_10_1_5_15_3d.lammps.log | 50 +++---- src/fix_bd_sphere.cpp | 130 ++++++++++-------- src/fix_bd_sphere.h | 13 +- .../tests/fix-timestep-bd_sphere.yaml | 2 +- 11 files changed, 152 insertions(+), 155 deletions(-) rename examples/bd_sphere/{in2d.bd => in2ddipole.bd} (98%) diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index d1bc20c9ca..1be5348bfe 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -39,6 +39,7 @@ OPT. * :doc:`ave/time ` * :doc:`aveforce ` * :doc:`balance ` + * :doc:`bd/sphere ` * :doc:`bocs ` * :doc:`bond/break ` * :doc:`bond/create ` diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 37ddbbeb3e..0993a885a5 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -181,6 +181,7 @@ accelerated styles exist. * :doc:`ave/histo/weight ` - weighted version of fix ave/histo * :doc:`ave/time ` - compute/output global time-averaged quantities * :doc:`aveforce ` - add an averaged force to each atom +* :doc:`bd/sphere ` - overdamped translational and rotational brownian dynamics * :doc:`balance ` - perform dynamic load-balancing * :doc:`bocs ` - NPT style time integration with pressure correction * :doc:`bond/break ` - break bonds on the fly diff --git a/doc/src/fix_bd_sphere.rst b/doc/src/fix_bd_sphere.rst index 013d0604bb..ee731c47d8 100644 --- a/doc/src/fix_bd_sphere.rst +++ b/doc/src/fix_bd_sphere.rst @@ -17,14 +17,15 @@ Syntax * diff_t = translational diffusion coefficient * diff_r = rotational diffusion coefficient * zero or more keyword/value pairs may be appended -* keyword = *rng* +* keyword = *rng* or *dipole* .. parsed-literal:: - *rng* arg = *uniform* or *gaussian* or *none* - uniform = use uniform random number generator - gaussian = use gaussian random number generator - none = turn off noise + *rng* value = *uniform* or *gaussian* or *none* + *uniform* = use uniform random number generator + *gaussian* = use gaussian random number generator + *none* = turn off noise + *dipole* value = none = update orientation of dipoles during integration Examples """""""" @@ -32,9 +33,9 @@ Examples .. code-block:: LAMMPS fix 1 all bd/sphere 1.0 1.0 1.0 1.0 1294019 - fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rng none + fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rng none dipole fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rng uniform - fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rng gaussian + fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 dipole rng gaussian Description @@ -52,8 +53,8 @@ viscous forces. The stochastic equations of motion are d\Omega = \frac{T}{\gamma_r}dt + \sqrt{2D_r}dW_r, where :math:`d\Omega` is an infinitesimal rotation vector (see e.g. -Chapter 4 of :ref:`(GoldsteinCM) `), :math:`dW_t` and -:math:`dW_r` are Wiener processes (see e.g. :ref:`(GardinerC) `). +Chapter 4 of :ref:`(Goldstein) `), :math:`dW_t` and +:math:`dW_r` are Wiener processes (see e.g. :ref:`(Gardiner) `). The dipole vectors :math:`e_i` are updated using the rotation matrix .. math:: @@ -64,13 +65,13 @@ where :math:`\omega=d\Omega/dt` is the angular velocity, :math:`\Delta\theta=|\omega|dt` is the rotation angle about the :math:`\omega` axis, and :math:`(\theta_X)_{ij}=-\epsilon_{ijk}d\Omega_k` is the -infinitesimal rotation matrix (see e.g. :ref:`(Callegari1) `, +infinitesimal rotation matrix (see e.g. :ref:`(Callegari) `, section 7.4). The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the added forces on atoms to the system's virial as part of :doc:`thermodynamic output `. -The default is *virial no* +The default is *virial no*. IMPORTANT NOTE: This integrator is designed for generic non-equilibrium @@ -96,17 +97,20 @@ units of mass/time and (mass*length*length)/(time). If the *rng* keyword is used with the *uniform* value, then the noise is generated from a uniform distribution (see -:ref:`(Dunweg) ` for why this works). This is the same method +:ref:`(Dunweg) ` for why this works). This is the same method of noise generation as used in :doc:`fix_langevin `. If the *rng* keyword is used with the *gaussian* value, then the noise is generated from a gaussian distribution. Typically this added complexity is unnecessary, and one should be fine using the *uniform* -value for reasons argued in :ref:`(Dunweg) `. +value for reasons argued in :ref:`(Dunweg) `. If the *rng* keyword is used with the *none* value, then the noise terms are set to zero. +If the *dipole* keyword is used, then the dipole moments of the particles +are updated as described above. + ---------- .. include:: accel_styles.rst @@ -150,18 +154,18 @@ The default for *rng* is *uniform*. .. _GoldsteinCM: -**(GoldsteinCM)** Goldstein, Poole, and Safko, Classical Mechanics, 3rd Ed. (2001). +**(Goldstein)** Goldstein, Poole, and Safko, Classical Mechanics, 3rd Ed. (2001). .. _GardinerC: -**(GardinerC)** Gardiner, A Handbook for the Natural and Social Sciences 4th Ed. (2009). +**(Gardiner)** Gardiner, A Handbook for the Natural and Social Sciences 4th Ed. (2009). .. _Callegari1: -**(Callegari1)** Callegari and Volpe, *Numerical Simulations of Active Brownian +**(Callegari)** Callegari and Volpe, *Numerical Simulations of Active Brownian Particles*, Flowing Matter, 211-238 (2019). -.. _Dunweg1: +.. _Dunweg6: **(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). diff --git a/examples/bd_sphere/README.txt b/examples/bd_sphere/README.txt index b044f11edc..2f66504581 100644 --- a/examples/bd_sphere/README.txt +++ b/examples/bd_sphere/README.txt @@ -1,6 +1,8 @@ -The input file in2d.bd demonstrates how to run a 2d simulation +The input file in2ddipole.bd demonstrates how to run a 2d simulation of particles undergoing overdamped brownian motion in both -translational and rotational degrees of freedom. +translational and rotational degrees of freedom. Dipole +updating is turned on, so the package DIPOLE must be built +for this example to work. The input file in3d_virial_on.bd demonstrates how to run a similar simulation but in 3d. In this case, the virial @@ -9,11 +11,13 @@ sum_i /(3*volume) where W is a random variable with mean 0 and variance dt) is calculated via the fix_modify command. For long enough times, this will be equal to rho*D_t*gamma_t -(the ideal gas term in equilibrium systems). +(the ideal gas term in equilibrium systems). Note that +no dipole updating is performed. To confirm rotational diffusion is working correctly, run the above simulations with dump files on and -measure \sum_i, and one should +measure \sum_i where e_i is the +dipole vector of particle i, and one should find that this decays as an exponential with timescale 1/((d-1)*D_r). diff --git a/examples/bd_sphere/in2d.bd b/examples/bd_sphere/in2ddipole.bd similarity index 98% rename from examples/bd_sphere/in2d.bd rename to examples/bd_sphere/in2ddipole.bd index c11381ad5a..1f7898207f 100644 --- a/examples/bd_sphere/in2d.bd +++ b/examples/bd_sphere/in2ddipole.bd @@ -38,7 +38,7 @@ pair_style none #compute d all property/atom mux muy muz -fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole fix 2 all enforce2d compute press all pressure NULL virial diff --git a/examples/bd_sphere/in3d_virial_on.bd b/examples/bd_sphere/in3d_virial_on.bd index 1ef88930c1..0e2f02beb0 100644 --- a/examples/bd_sphere/in3d_virial_on.bd +++ b/examples/bd_sphere/in3d_virial_on.bd @@ -14,7 +14,7 @@ variable params string ${rng}_${gamma_t}_${gamma_r}_${D_t}_${D_r} log log_${params}_3d.lammps.log units lj -atom_style hybrid dipole sphere +atom_style sphere dimension 3 newton off @@ -23,22 +23,16 @@ lattice sc 0.4 region box block -8 8 -8 8 -8 8 create_box 1 box create_atoms 1 box -mass * 1.0 -set type * dipole/random ${seed} 1.0 +#mass * 1.0 velocity all create 1.0 1 loop geom neighbor 1.0 bin neigh_modify every 1 delay 1 check yes - - pair_style none - -#compute d all property/atom mux muy muz - fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} fix_modify 1 virial yes @@ -65,7 +59,7 @@ thermo_style custom step temp epair c_msd[*] c_press # write trajectory and thermo in a log-scale frequency # uncomment the next three lines for dump file #dump 1 all custom 10000 dump_${params}_3d.lammpstrj id type & -# x y xu yu mux muy muz fx fy fz +# x y xu yu fx fy fz #dump_modify 1 first yes sort id timestep 0.00001 diff --git a/examples/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log b/examples/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log index 72b90efe0e..a735ea6baa 100644 --- a/examples/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log +++ b/examples/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log @@ -13,7 +13,7 @@ Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.29 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 1024 atoms - create_atoms CPU = 0.002 seconds + create_atoms CPU = 0.001 seconds mass * 1.0 set type * dipole/random ${seed} 1.0 set type * dipole/random 1974019 1.0 @@ -33,13 +33,13 @@ pair_style none #compute d all property/atom mux muy muz -fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} -fix 1 all bd/sphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} -fix 1 all bd/sphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} -fix 1 all bd/sphere 4 1 7 ${D_r} ${seed} rng ${rng} -fix 1 all bd/sphere 4 1 7 13 ${seed} rng ${rng} -fix 1 all bd/sphere 4 1 7 13 1974019 rng ${rng} -fix 1 all bd/sphere 4 1 7 13 1974019 rng gaussian +fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all bd/sphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all bd/sphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all bd/sphere 4 1 7 ${D_r} ${seed} rng ${rng} dipole +fix 1 all bd/sphere 4 1 7 13 ${seed} rng ${rng} dipole +fix 1 all bd/sphere 4 1 7 13 1974019 rng ${rng} dipole +fix 1 all bd/sphere 4 1 7 13 1974019 rng gaussian dipole fix 2 all enforce2d compute press all pressure NULL virial @@ -56,9 +56,9 @@ Per MPI rank memory allocation (min/avg/max) = 4.289 | 4.289 | 4.289 Mbytes Step Temp E_pair c_press 0 1 0 0 50000 7.3671759e+10 0 0 -Loop time of 10.2295 on 1 procs for 50000 steps with 1024 atoms +Loop time of 11.2219 on 1 procs for 50000 steps with 1024 atoms -Performance: 0.042 tau/day, 4887.825 timesteps/s +Performance: 0.038 tau/day, 4455.573 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: @@ -66,10 +66,10 @@ Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.033217 | 0.033217 | 0.033217 | 0.0 | 0.32 -Output | 2.1435e-05 | 2.1435e-05 | 2.1435e-05 | 0.0 | 0.00 -Modify | 10.047 | 10.047 | 10.047 | 0.0 | 98.21 -Other | | 0.1497 | | | 1.46 +Comm | 0.028513 | 0.028513 | 0.028513 | 0.0 | 0.25 +Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00 +Modify | 11.048 | 11.048 | 11.048 | 0.0 | 98.45 +Other | | 0.1458 | | | 1.30 Nlocal: 1024.00 ave 1024 max 1024 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -228,20 +228,20 @@ Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press 118000 745594.37 0 16.838659 17.585392 0 34.424052 0 119000 714487.42 0 17.064214 17.743478 0 34.807692 0 120000 716557.14 0 17.105558 17.845925 0 34.951483 0 -Loop time of 25.2131 on 1 procs for 120000 steps with 1024 atoms +Loop time of 27.2068 on 1 procs for 120000 steps with 1024 atoms -Performance: 4112.144 tau/day, 4759.427 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 3810.806 tau/day, 4410.656 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0.0016123 | 0.0016123 | 0.0016123 | 0.0 | 0.01 -Comm | 0.025898 | 0.025898 | 0.025898 | 0.0 | 0.10 -Output | 0.0037882 | 0.0037882 | 0.0037882 | 0.0 | 0.02 -Modify | 24.767 | 24.767 | 24.767 | 0.0 | 98.23 -Other | | 0.4146 | | | 1.64 +Neigh | 0.0015633 | 0.0015633 | 0.0015633 | 0.0 | 0.01 +Comm | 0.021682 | 0.021682 | 0.021682 | 0.0 | 0.08 +Output | 0.0032539 | 0.0032539 | 0.0032539 | 0.0 | 0.01 +Modify | 26.802 | 26.802 | 26.802 | 0.0 | 98.51 +Other | | 0.3781 | | | 1.39 Nlocal: 1024.00 ave 1024 max 1024 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -256,4 +256,4 @@ Neighbor list builds = 1049 Dangerous builds = 0 -Total wall time: 0:00:35 +Total wall time: 0:00:38 diff --git a/examples/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log b/examples/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log index fda48dc71a..57f90193ac 100644 --- a/examples/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log +++ b/examples/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log @@ -1,6 +1,5 @@ units lj -atom_style hybrid dipole sphere -WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (src/atom_vec_hybrid.cpp:157) +atom_style sphere dimension 3 newton off @@ -13,26 +12,17 @@ Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4096 atoms - create_atoms CPU = 0.003 seconds -mass * 1.0 -set type * dipole/random ${seed} 1.0 -set type * dipole/random 553910 1.0 -Setting atom values ... - 4096 settings made for dipole/random + create_atoms CPU = 0.001 seconds +#mass * 1.0 velocity all create 1.0 1 loop geom neighbor 1.0 bin neigh_modify every 1 delay 1 check yes - - pair_style none - -#compute d all property/atom mux muy muz - fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} fix 1 all bd/sphere 10 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} fix 1 all bd/sphere 10 1 ${D_t} ${D_r} ${seed} rng ${rng} @@ -52,13 +42,13 @@ thermo 50001 run 50000 WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118) WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) -Per MPI rank memory allocation (min/avg/max) = 4.362 | 4.362 | 4.362 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.581 | 3.581 | 3.581 Mbytes Step Temp E_pair c_press 0 1 0 -32553.271 50000 5.2351457e+10 0 -15026.42 -Loop time of 18.6303 on 1 procs for 50000 steps with 4096 atoms +Loop time of 16.0183 on 1 procs for 50000 steps with 4096 atoms -Performance: 0.023 tau/day, 2683.804 timesteps/s +Performance: 0.027 tau/day, 3121.426 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: @@ -66,10 +56,10 @@ Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.31439 | 0.31439 | 0.31439 | 0.0 | 1.69 -Output | 5.5046e-05 | 5.5046e-05 | 5.5046e-05 | 0.0 | 0.00 -Modify | 17.718 | 17.718 | 17.718 | 0.0 | 95.11 -Other | | 0.5974 | | | 3.21 +Comm | 0.074984 | 0.074984 | 0.074984 | 0.0 | 0.47 +Output | 3.0041e-05 | 3.0041e-05 | 3.0041e-05 | 0.0 | 0.00 +Modify | 15.366 | 15.366 | 15.366 | 0.0 | 95.93 +Other | | 0.5772 | | | 3.60 Nlocal: 4096.00 ave 4096 max 4096 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -96,7 +86,7 @@ thermo_style custom step temp epair c_msd[*] c_press # write trajectory and thermo in a log-scale frequency # uncomment the next three lines for dump file -#dump 1 all custom 10000 dump_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz +#dump 1 all custom 10000 dump_${params}_3d.lammpstrj id type # x y xu yu fx fy fz #dump_modify 1 first yes sort id timestep 0.00001 @@ -105,7 +95,7 @@ thermo 1000 # main run run 120000 WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) -Per MPI rank memory allocation (min/avg/max) = 4.737 | 4.737 | 4.737 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.956 | 3.956 | 3.956 Mbytes Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press 0 5.2351457e+10 0 0 0 0 0 -233.83012 1000 522590.88 0 0.10259269 0.10487519 0.10391005 0.31137793 -13.730626 @@ -228,20 +218,20 @@ Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press 118000 524075.83 0 11.441416 11.597533 11.783056 34.822005 -350.05313 119000 533816.71 0 11.52766 11.681986 11.917713 35.127359 -521.58975 120000 524509.31 0 11.63865 11.792667 12.080379 35.511696 273.09647 -Loop time of 46.6725 on 1 procs for 120000 steps with 4096 atoms +Loop time of 39.6359 on 1 procs for 120000 steps with 4096 atoms -Performance: 2221.438 tau/day, 2571.109 timesteps/s +Performance: 2615.809 tau/day, 3027.557 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0.0063169 | 0.0063169 | 0.0063169 | 0.0 | 0.01 -Comm | 0.057082 | 0.057082 | 0.057082 | 0.0 | 0.12 -Output | 0.0068489 | 0.0068489 | 0.0068489 | 0.0 | 0.01 -Modify | 44.98 | 44.98 | 44.98 | 0.0 | 96.37 -Other | | 1.622 | | | 3.48 +Neigh | 0.0059817 | 0.0059817 | 0.0059817 | 0.0 | 0.02 +Comm | 0.039473 | 0.039473 | 0.039473 | 0.0 | 0.10 +Output | 0.0063653 | 0.0063653 | 0.0063653 | 0.0 | 0.02 +Modify | 38.085 | 38.085 | 38.085 | 0.0 | 96.09 +Other | | 1.499 | | | 3.78 Nlocal: 4096.00 ave 4096 max 4096 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -256,4 +246,4 @@ Neighbor list builds = 992 Dangerous builds = 0 -Total wall time: 0:01:05 +Total wall time: 0:00:55 diff --git a/src/fix_bd_sphere.cpp b/src/fix_bd_sphere.cpp index 3a8a0811b9..ba7cd2a81c 100644 --- a/src/fix_bd_sphere.cpp +++ b/src/fix_bd_sphere.cpp @@ -35,6 +35,10 @@ using namespace LAMMPS_NS; using namespace FixConst; +#define SMALL 1e-14 + +enum{NONE,DIPOLE}; + /* ---------------------------------------------------------------------- */ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : @@ -43,14 +47,14 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : virial_flag = 1; time_integrate = 1; - - if (narg != 8 && narg != 10) + + extra = NONE; + + if (narg > 11 || narg < 8 ) error->all(FLERR,"Illegal fix bd/sphere command."); if (!atom->sphere_flag) error->all(FLERR,"Fix bd/sphere requires atom style sphere"); - if (!atom->mu_flag) - error->all(FLERR,"Fix bd/sphere requires atom attribute mu"); gamma_t = utils::numeric(FLERR,arg[3],false,lmp); if (gamma_t <= 0.0) @@ -62,7 +66,7 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Fix bd/sphere rotational viscous drag " "coefficient must be > 0."); - // note that diffusion is in units of epsilon**2*tau**3/(m**2*sigma**2) + diff_t = utils::numeric(FLERR,arg[5],false,lmp); if (diff_t <= 0.0) error->all(FLERR,"Fix bd/sphere translational diffusion " @@ -83,6 +87,9 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : while (iarg < narg) { if (strcmp(arg[iarg],"rng") == 0) { + if (narg == iarg + 1) { + error->all(FLERR,"Illegal fix/bd/sphere command."); + } if (strcmp(arg[iarg + 1],"uniform") == 0) { noise_flag = 1; } else if (strcmp(arg[iarg + 1],"gaussian") == 0) { @@ -93,17 +100,21 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : } else { error->all(FLERR,"Illegal fix/bd/sphere command."); } + iarg = iarg + 2; + } else if (strcmp(arg[iarg],"dipole") == 0) { + extra = DIPOLE; + iarg = iarg + 1; } else { error->all(FLERR,"Illegal fix/bd/sphere command."); } - iarg = iarg + 2; } - + if (extra == DIPOLE && !atom->mu_flag) + error->all(FLERR,"Fix bd/sphere update dipole requires atom attribute mu"); + // initialize Marsaglia RNG with processor-unique seed random = new RanMars(lmp,seed + comm->me); - } /* ---------------------------------------------------------------------- */ @@ -120,9 +131,7 @@ int FixBdSphere::setmask() FixBdSphere::~FixBdSphere() { - delete random; - } @@ -131,8 +140,7 @@ FixBdSphere::~FixBdSphere() void FixBdSphere::init() { - - + g1 = force->ftm2v/gamma_t; g3 = force->ftm2v/gamma_r; if (noise_flag == 0) { @@ -164,16 +172,12 @@ void FixBdSphere::initial_integrate(int /* vflag */) { double **x = atom->x; double **v = atom->v; - double **mu = atom->mu; double **f = atom->f; double **omega = atom->omega; double **torque = atom->torque; int *mask = atom->mask; int nlocal = atom->nlocal; double dx,dy,dz; - double dtheta; - double mux,muy,muz,mu_tmp,wx,wy,wz; - double prefac_1, prefac_2; if (igroup == atom->firstgroup) nlocal = atom->nfirst; @@ -188,7 +192,6 @@ void FixBdSphere::initial_integrate(int /* vflag */) d3rot = 1; } - for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { @@ -204,49 +207,62 @@ void FixBdSphere::initial_integrate(int /* vflag */) x[i][2] += dz; v[i][2] = dz/dt; - omega[i][0] = d3rot * g3* torque[i][0]; omega[i][1] = d3rot * g3* torque[i][1]; omega[i][2] = g3* torque[i][2]; - - dtheta = sqrt((omega[i][0]*dt)*(omega[i][0]*dt) - +(omega[i][1]*dt)*(omega[i][1]*dt) - +(omega[i][2]*dt)*(omega[i][2]*dt)); - - if (abs(dtheta) < 1e-14) { - prefac_1 = dt; - prefac_2 = 0.5*dt*dt; - } else { - prefac_1 = dt*sin(dtheta)/dtheta; - prefac_2 = dt*dt*(1-cos(dtheta))/(dtheta*dtheta); + + } + } + + if (extra == DIPOLE) { + + double **mu = atom->mu; + double dtheta; + double mux,muy,muz,mu_tmp,wx,wy,wz; + double prefac_1, prefac_2; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + dtheta = sqrt((omega[i][0]*dt)*(omega[i][0]*dt) + +(omega[i][1]*dt)*(omega[i][1]*dt) + +(omega[i][2]*dt)*(omega[i][2]*dt)); + + + if (fabs(dtheta) < SMALL) { + prefac_1 = dt; + prefac_2 = 0.5*dt*dt; + } else { + prefac_1 = dt*sin(dtheta)/dtheta; + prefac_2 = dt*dt*(1-cos(dtheta))/(dtheta*dtheta); + } + + mux = mu[i][0]; + muy = mu[i][1]; + muz = mu[i][2]; + + wx = omega[i][0]; + wy = omega[i][1]; + wz = omega[i][2]; + + mu[i][0] = (mux + prefac_1 * ( -wz*muy + wy*muz ) + + prefac_2 * ( -1*( wz*wz + wy*wy ) * mux + + ( wz*muz + wy*muy ) * wx)); + + mu[i][1] = (muy + prefac_1 * ( wz*mux - wx*muz ) + + prefac_2 * ( -1*(wz*wz + wx*wx) * muy + + ( wz*muz + wx*mux ) * wy)); + + mu[i][2] = (muz + prefac_1 * ( -wy*mux + wx*muy ) + + prefac_2 * ( -1*( wx*wx + wy*wy ) * muz + + ( wy*muy + wx*mux ) * wz)); + + mu_tmp = sqrt(mu[i][0]*mu[i][0]+mu[i][1]*mu[i][1]+mu[i][2]*mu[i][2]); + + mu[i][0] = mu[i][0]/mu_tmp; + mu[i][1] = mu[i][1]/mu_tmp; + mu[i][2] = mu[i][2]/mu_tmp; } - - mux = mu[i][0]; - muy = mu[i][1]; - muz = mu[i][2]; - - wx = omega[i][0]; - wy = omega[i][1]; - wz = omega[i][2]; - - mu[i][0] = (mux + prefac_1 * ( -wz*muy + wy*muz ) - + prefac_2 * ( -1*( wz*wz + wy*wy ) * mux - + ( wz*muz + wy*muy ) * wx)); - - mu[i][1] = (muy + prefac_1 * ( wz*mux - wx*muz ) - + prefac_2 * ( -1*(wz*wz + wx*wx) * muy - + ( wz*muz + wx*mux ) * wy)); - - mu[i][2] = (muz + prefac_1 * ( -wy*mux + wx*muy ) - + prefac_2 * ( -1*( wx*wx + wy*wy ) * muz - + ( wy*muy + wx*mux ) * wz)); - - mu_tmp = sqrt(mu[i][0]*mu[i][0]+mu[i][1]*mu[i][1]+mu[i][2]*mu[i][2]); - - mu[i][0] = mu[i][0]/mu_tmp; - mu[i][1] = mu[i][1]/mu_tmp; - mu[i][2] = mu[i][2]/mu_tmp; - } } @@ -271,8 +287,6 @@ void FixBdSphere::post_force(int vflag) if (vflag) v_setup(vflag); else evflag = 0; - - double fx,fy,fz; double v[6]; diff --git a/src/fix_bd_sphere.h b/src/fix_bd_sphere.h index 873ba9ef2a..245e04274e 100644 --- a/src/fix_bd_sphere.h +++ b/src/fix_bd_sphere.h @@ -36,7 +36,7 @@ class FixBdSphere : public Fix { private: int seed; // RNG seed - + int extra; // set if dipole is used double dt, sqrtdt; // time step interval and its sqrt @@ -90,15 +90,4 @@ Self-explanatory. E: Fix bd/sphere seed must be > 0. -E: Cannot constrain rotational degrees of freedom - to the xy plane if the simulation is in 3D (in fix/bd/sphere). - -Self-explanatory. - -W: Using a 2D simulation, but allowing for full (3D) rotation - (in fix/bd/sphere). - -Self-explanatory. - - */ diff --git a/unittest/force-styles/tests/fix-timestep-bd_sphere.yaml b/unittest/force-styles/tests/fix-timestep-bd_sphere.yaml index 66a65bc3ba..b69f37e206 100644 --- a/unittest/force-styles/tests/fix-timestep-bd_sphere.yaml +++ b/unittest/force-styles/tests/fix-timestep-bd_sphere.yaml @@ -7,7 +7,7 @@ prerequisites: ! | fix bd_sphere pre_commands: ! "" post_commands: ! | - fix test solute bd_sphere 1.0 1.0 1.0 1.0 1049270 + fix test solute bd_sphere 1.0 1.0 1.0 1.0 1049270 dipole fix_modify test virial yes input_file: in.bdsphere natoms: 32 From ee99a2e960b1072e750b6bcd2c1e1f2000a3faa9 Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Thu, 10 Dec 2020 09:12:21 +0000 Subject: [PATCH 0043/1217] Added reset_dt() function. Have not moved files to USER-MISC folder yet (waiting to hear back on some comments). --- src/fix_bd_sphere.cpp | 10 +++++++--- src/fix_bd_sphere.h | 1 + 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/src/fix_bd_sphere.cpp b/src/fix_bd_sphere.cpp index ba7cd2a81c..cc3c788349 100644 --- a/src/fix_bd_sphere.cpp +++ b/src/fix_bd_sphere.cpp @@ -182,9 +182,6 @@ void FixBdSphere::initial_integrate(int /* vflag */) if (igroup == atom->firstgroup) nlocal = atom->nfirst; int d3rot; // whether to compute angular momentum in xy plane - - dt = update->dt; - sqrtdt = sqrt(dt); if (domain->dimension==2) { d3rot = 0; @@ -315,3 +312,10 @@ void FixBdSphere::post_force(int vflag) } } } + +void FixBdSphere::reset_dt() +{ + + dt = update->dt; + sqrtdt = sqrt(dt); +} diff --git a/src/fix_bd_sphere.h b/src/fix_bd_sphere.h index 245e04274e..8a3df214a6 100644 --- a/src/fix_bd_sphere.h +++ b/src/fix_bd_sphere.h @@ -33,6 +33,7 @@ class FixBdSphere : public Fix { void setup(int); void post_force(int); int setmask(); + void reset_dt(); private: int seed; // RNG seed From 4fa48edb815406dec5c162b389c9625a56d5ae8a Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Thu, 10 Dec 2020 11:36:15 -0700 Subject: [PATCH 0044/1217] Adding size/multi npair files --- src/npair_half_size_multi_newtoff.cpp | 117 +++++++++++++++++++ src/npair_half_size_multi_newtoff.h | 46 ++++++++ src/npair_half_size_multi_newton.cpp | 143 +++++++++++++++++++++++ src/npair_half_size_multi_newton.h | 46 ++++++++ src/npair_half_size_multi_newton_tri.cpp | 125 ++++++++++++++++++++ src/npair_half_size_multi_newton_tri.h | 46 ++++++++ 6 files changed, 523 insertions(+) create mode 100644 src/npair_half_size_multi_newtoff.cpp create mode 100644 src/npair_half_size_multi_newtoff.h create mode 100644 src/npair_half_size_multi_newton.cpp create mode 100644 src/npair_half_size_multi_newton.h create mode 100644 src/npair_half_size_multi_newton_tri.cpp create mode 100644 src/npair_half_size_multi_newton_tri.h diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp new file mode 100644 index 0000000000..9dd9c9f38b --- /dev/null +++ b/src/npair_half_size_multi_newtoff.cpp @@ -0,0 +1,117 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "npair_half_size_multi_newtoff.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + size particles + binned neighbor list construction with partial Newton's 3rd law + each owned atom i checks own bin and other bins in stencil + multi-type stencil is itype dependent and is distance checked + pair stored once if i,j are both owned and i < j + pair stored by me if j is ghost (also stored by proc owning j) +------------------------------------------------------------------------- */ + +void NPairHalfSizeMultiNewtoff::build(NeighList *list) +{ + int i,j,k,m,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // skip if i,j neighbor cutoff is less than bin distance + // stores own/own pairs only once + // stores own/ghost pairs on both procs + + ibin = atom2bin[i]; + s = stencil_multi[itype]; + distsq = distsq_multi[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + if (j <= i) continue; + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_size_multi_newtoff.h b/src/npair_half_size_multi_newtoff.h new file mode 100644 index 0000000000..6f88240db6 --- /dev/null +++ b/src/npair_half_size_multi_newtoff.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/newtoff, + NPairHalfSizeMultiNewtoff, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiNewtoff : public NPair { + public: + NPairHalfSizeMultiNewtoff(class LAMMPS *); + ~NPairHalfSizeMultiNewtoff() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp new file mode 100644 index 0000000000..631ba72340 --- /dev/null +++ b/src/npair_half_size_multi_newton.cpp @@ -0,0 +1,143 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "npair_half_size_multi_newton.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + size particles + binned neighbor list construction with full Newton's 3rd law + each owned atom i checks its own bin and other bins in Newton stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfSizeMultiNewton::build(NeighList *list) +{ + int i,j,k,m,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + // loop over rest of atoms in i's bin, ghosts are at end of linked list + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + for (j = bins[i]; j >= 0; j = bins[j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + ibin = atom2bin[i]; + s = stencil_multi[itype]; + distsq = distsq_multi[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_size_multi_newton.h b/src/npair_half_size_multi_newton.h new file mode 100644 index 0000000000..2be10aa3d2 --- /dev/null +++ b/src/npair_half_size_multi_newton.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/newton, + NPairHalfSizeMultiNewton, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiNewton : public NPair { + public: + NPairHalfSizeMultiNewton(class LAMMPS *); + ~NPairHalfSizeMultiNewton() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp new file mode 100644 index 0000000000..49745a87b0 --- /dev/null +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -0,0 +1,125 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "npair_half_size_multi_newton_tri.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with Newton's 3rd law for triclinic + each owned atom i checks its own bin and other bins in triclinic stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfSizeMultiNewtonTri::build(NeighList *list) +{ + int i,j,k,m,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + + // loop over all atoms in bins, including self, in stencil + // skip if i,j neighbor cutoff is less than bin distance + // bins below self are excluded from stencil + // pairs for atoms j "below" i are excluded + // below = lower z or (equal z and lower y) or (equal zy and lower x) + // (equal zyx and j <= i) + // latter excludes self-self interaction but allows superposed atoms + + ibin = atom2bin[i]; + s = stencil_multi[itype]; + distsq = distsq_multi[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_size_multi_newton_tri.h b/src/npair_half_size_multi_newton_tri.h new file mode 100644 index 0000000000..5a24d3437b --- /dev/null +++ b/src/npair_half_size_multi_newton_tri.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/newton/tri, + NPairHalfSizeMultiNewtonTri, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiNewtonTri : public NPair { + public: + NPairHalfSizeMultiNewtonTri(class LAMMPS *); + ~NPairHalfSizeMultiNewtonTri() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ From f81a17abbd922674bb4630610bd5e59feae202fa Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Fri, 11 Dec 2020 12:11:02 +0000 Subject: [PATCH 0045/1217] Moved fix_bd_sphere to src/USER-MISC folder, examples to examples/USER/misc folder, and added one-liner on README file. --- doc/src/fix_bd_sphere.rst | 4 ++++ examples/{ => USER/misc}/bd_sphere/README.txt | 0 examples/{ => USER/misc}/bd_sphere/in2ddipole.bd | 0 examples/{ => USER/misc}/bd_sphere/in3d_virial_on.bd | 0 .../misc}/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log | 0 .../misc}/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log | 0 src/USER-MISC/README | 1 + src/{ => USER-MISC}/fix_bd_sphere.cpp | 0 src/{ => USER-MISC}/fix_bd_sphere.h | 0 9 files changed, 5 insertions(+) rename examples/{ => USER/misc}/bd_sphere/README.txt (100%) rename examples/{ => USER/misc}/bd_sphere/in2ddipole.bd (100%) rename examples/{ => USER/misc}/bd_sphere/in3d_virial_on.bd (100%) rename examples/{ => USER/misc}/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log (100%) rename examples/{ => USER/misc}/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log (100%) rename src/{ => USER-MISC}/fix_bd_sphere.cpp (100%) rename src/{ => USER-MISC}/fix_bd_sphere.h (100%) diff --git a/doc/src/fix_bd_sphere.rst b/doc/src/fix_bd_sphere.rst index ee731c47d8..f1c9756a78 100644 --- a/doc/src/fix_bd_sphere.rst +++ b/doc/src/fix_bd_sphere.rst @@ -136,6 +136,10 @@ as defined by the :doc:`atom_style sphere ` command. They must also store a dipole moment as defined by the :doc:`atom_style dipole ` command. +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` +doc page for more info. + All particles in the group must be finite-size spheres. They cannot be point particles. diff --git a/examples/bd_sphere/README.txt b/examples/USER/misc/bd_sphere/README.txt similarity index 100% rename from examples/bd_sphere/README.txt rename to examples/USER/misc/bd_sphere/README.txt diff --git a/examples/bd_sphere/in2ddipole.bd b/examples/USER/misc/bd_sphere/in2ddipole.bd similarity index 100% rename from examples/bd_sphere/in2ddipole.bd rename to examples/USER/misc/bd_sphere/in2ddipole.bd diff --git a/examples/bd_sphere/in3d_virial_on.bd b/examples/USER/misc/bd_sphere/in3d_virial_on.bd similarity index 100% rename from examples/bd_sphere/in3d_virial_on.bd rename to examples/USER/misc/bd_sphere/in3d_virial_on.bd diff --git a/examples/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log b/examples/USER/misc/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log similarity index 100% rename from examples/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log rename to examples/USER/misc/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log diff --git a/examples/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log b/examples/USER/misc/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log similarity index 100% rename from examples/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log rename to examples/USER/misc/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 538fdb7952..2dd16d23ac 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -53,6 +53,7 @@ dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18 fix accelerate/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 +fix bd/sphere, Sam Cameron (U of Bristol), samuel.j.m.cameron at gmail.com, 10 Dec 2020 fix electron/stopping/fit, James Stewart (SNL), jstewa .at. sandia.gov, 23 Sep 2020 fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019 fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018 diff --git a/src/fix_bd_sphere.cpp b/src/USER-MISC/fix_bd_sphere.cpp similarity index 100% rename from src/fix_bd_sphere.cpp rename to src/USER-MISC/fix_bd_sphere.cpp diff --git a/src/fix_bd_sphere.h b/src/USER-MISC/fix_bd_sphere.h similarity index 100% rename from src/fix_bd_sphere.h rename to src/USER-MISC/fix_bd_sphere.h From 86ebe0a9d38c5cdd0066930ad18f7d2805d6514b Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Sun, 13 Dec 2020 16:56:00 +0000 Subject: [PATCH 0046/1217] Minor change to doc for bd/sphere. --- doc/src/fix_bd_sphere.rst | 63 ++++++++++++++++++++------------------- 1 file changed, 33 insertions(+), 30 deletions(-) diff --git a/doc/src/fix_bd_sphere.rst b/doc/src/fix_bd_sphere.rst index f1c9756a78..177af6e6d7 100644 --- a/doc/src/fix_bd_sphere.rst +++ b/doc/src/fix_bd_sphere.rst @@ -25,7 +25,7 @@ Syntax *uniform* = use uniform random number generator *gaussian* = use gaussian random number generator *none* = turn off noise - *dipole* value = none = update orientation of dipoles during integration + *dipole* value = none = update orientation of dipoles during integration Examples """""""" @@ -68,32 +68,32 @@ the :math:`\omega` axis, and infinitesimal rotation matrix (see e.g. :ref:`(Callegari) `, section 7.4). -The :doc:`fix_modify ` *virial* option is supported by this -fix to add the contribution due to the added forces on atoms to the -system's virial as part of :doc:`thermodynamic output `. -The default is *virial no*. +.. note:: + This integrator is designed for generic non-equilibrium + simulations with additive noise. There are two important cases which + (conceptually) reduce the number of free parameters in this fix. + (a) In equilibrium simulations + (where fluctuation dissipation theorems are obeyed), one can define + the thermal energy :math:`k_bT=D_t\gamma_t=D_r\gamma_r`. + (b) When a no-slip boundary condition is expected between the spheres and + the surrounding medium, the condition + :math:`\gamma_t=3\gamma_r/\sigma^2` must be explicitly + accounted for (e.g. by setting *gamma_t* to 3 and *gamma_r* to 1) where + :math:`sigma` is the particle diameter. + If both (a) and (b) are true, then one must ensure this explicitly via + the above relationships. +--------- -IMPORTANT NOTE: This integrator is designed for generic non-equilibrium -simulations with additive noise. There are two important cases which -(conceptually) reduce the number of free parameters in this fix. -(a) In equilibrium simulations -(where fluctuation dissipation theorems are obeyed), one can define -the thermal energy :math:`k_bT=D_t\gamma_t=D_r\gamma_r`. -(b) When a no-slip boundary condition is expected between the spheres and -the surrounding medium, the condition -:math:`\gamma_t=3\gamma_r/\sigma^2` must be explicitly -accounted for (e.g. by setting *gamma_t* to 3 and *gamma_r* to 1) where -:math:`sigma` is the particle diameter. -If both (a) and (b) are true, then one must ensure this explicitly via -the above relationships. +.. note:: + The diffusion coefficient :math:`D_t` is measured + in units of (length*length)/time and the diffusion coefficient + :math:`D_r` is measured in units of 1/time, where time and length + are in the units specified on the :doc:`units ` page. Similarly, + :math:`\gamma_t` and :math:`\gamma_r` are measured in + units of mass/time and (mass*length*length)/(time). -IMPORTANT NOTE: The diffusion coefficient :math:`D_t` is measured -in units of (length*length)/time and the diffusion coefficient -:math:`D_r` is measured in units of 1/time, where time and length -are in the units specified on the :doc:`units ` page. Similarly, -:math:`\gamma_t` and :math:`\gamma_r` are measured in -units of mass/time and (mass*length*length)/(time). +--------- If the *rng* keyword is used with the *uniform* value, then the noise is generated from a uniform distribution (see @@ -121,9 +121,14 @@ Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. -None of the :doc:`fix_modify ` options -are relevant to this fix. No global or per-atom quantities are stored +No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. + +The :doc:`fix_modify ` *virial* option is supported by this +fix to add the contribution due to the added forces on atoms to the +system's virial as part of :doc:`thermodynamic output `. +The default is *virial no*. + No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. @@ -133,15 +138,13 @@ Restrictions This fix requires that atoms store torque and angular velocity (omega) as defined by the :doc:`atom_style sphere ` command. -They must also store a dipole moment as defined by the -:doc:`atom_style dipole ` command. +If the *dipole* keyword is used, they must also store a dipole moment +as defined by the :doc:`atom_style dipole ` command. This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -All particles in the group must be finite-size spheres. They cannot -be point particles. Related commands """""""""""""""" From f2e7f5263e85e7ea02685d9c420db2d4126737ab Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Wed, 16 Dec 2020 16:14:13 +0000 Subject: [PATCH 0047/1217] Added bd integrator for ellipsoidal particles as well. --- doc/src/Commands_fix.rst | 1 + doc/src/fix.rst | 3 +- doc/src/fix_bd_asphere.rst | 149 +++++++ examples/USER/misc/bd_asphere/README.txt | 2 + examples/USER/misc/bd_asphere/in3d.bd | 71 ++++ .../log_gaussian_4_1_7_13_3d.lammps.log | 154 +++++++ src/USER-MISC/README | 3 +- src/USER-MISC/fix_bd_asphere.cpp | 392 ++++++++++++++++++ src/USER-MISC/fix_bd_asphere.h | 103 +++++ 9 files changed, 876 insertions(+), 2 deletions(-) create mode 100644 doc/src/fix_bd_asphere.rst create mode 100644 examples/USER/misc/bd_asphere/README.txt create mode 100644 examples/USER/misc/bd_asphere/in3d.bd create mode 100644 examples/USER/misc/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log create mode 100644 src/USER-MISC/fix_bd_asphere.cpp create mode 100644 src/USER-MISC/fix_bd_asphere.h diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index 1be5348bfe..8be0908a1a 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -40,6 +40,7 @@ OPT. * :doc:`aveforce ` * :doc:`balance ` * :doc:`bd/sphere ` + * :doc:`bd/asphere ` * :doc:`bocs ` * :doc:`bond/break ` * :doc:`bond/create ` diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 0993a885a5..c395489a58 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -181,8 +181,9 @@ accelerated styles exist. * :doc:`ave/histo/weight ` - weighted version of fix ave/histo * :doc:`ave/time ` - compute/output global time-averaged quantities * :doc:`aveforce ` - add an averaged force to each atom -* :doc:`bd/sphere ` - overdamped translational and rotational brownian dynamics * :doc:`balance ` - perform dynamic load-balancing +* :doc:`bd/asphere ` - integrate positions and orientations in overdamped motion +* :doc:`bd/sphere ` - overdamped translational and rotational brownian dynamics * :doc:`bocs ` - NPT style time integration with pressure correction * :doc:`bond/break ` - break bonds on the fly * :doc:`bond/create ` - create bonds on the fly diff --git a/doc/src/fix_bd_asphere.rst b/doc/src/fix_bd_asphere.rst new file mode 100644 index 0000000000..8c0337cb5e --- /dev/null +++ b/doc/src/fix_bd_asphere.rst @@ -0,0 +1,149 @@ +.. index:: fix bd/asphere + +fix bd/asphere command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID bd/asphere gamma_t gamma_r diff_t diff_r seed keyword args + +* ID, group-ID are documented in :doc:`fix ` command +* bd/asphere = style name of this fix command +* gamma_t = translational friction coefficient +* gamma_r = rotational friction coefficient +* diff_t = translational diffusion coefficient +* diff_r = rotational diffusion coefficient +* zero or more keyword/value pairs may be appended +* keyword = *rng* or *dipole* + + .. parsed-literal:: + + *rng* value = *uniform* or *gaussian* or *none* + *uniform* = use uniform random number generator + *gaussian* = use gaussian random number generator + *none* = turn off noise + *dipole* value = none = update orientation of dipoles during integration + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix 1 all bd/asphere 1.0 1.0 1.0 1.0 1294019 + fix 1 all bd/asphere 1.0 1.0 1.0 1.0 19581092 rng none dipole + fix 1 all bd/asphere 1.0 1.0 1.0 1.0 19581092 rng uniform + fix 1 all bd/asphere 1.0 1.0 1.0 1.0 19581092 dipole rng gaussian + + +Description +""""""""""" + +Perform Brownian Dynamics integration to update position, velocity, +angular velocity, particle orientation, and dipole moment for +finite-size elipsoidal particles in the group each timestep. +Brownian Dynamics uses Newton's laws of +motion in the limit that inertial forces are negligible compared to +viscous forces. The stochastic equations of motion are + +.. math:: + + dr = \frac{F}{\gamma_t}dt+\sqrt{2D_t}dW_t, \\ + d\Omega = \frac{T}{\gamma_r}dt + \sqrt{2D_r}dW_r, + +where :math:`d\Omega` is an infinitesimal rotation vector (see e.g. +Chapter 4 of :ref:`(Goldstein) `), :math:`dW_t` and +:math:`dW_r` are Wiener processes (see e.g. :ref:`(Gardiner) `). +The quaternions :math:`q` of the ellipsoid are updated each timestep from +the angular velocity vector. + +See :doc:`fix bd/sphere ` for discussion on the +values of :math:`\gamma_t`, :math:`\gamma_r`, :math:`D_t`, +and :math:`D_r` when simulating equilibrium systems. + + +If the *rng* keyword is used with the *uniform* value, then the noise +is generated from a uniform distribution (see +:ref:`(Dunweg) ` for why this works). This is the same method +of noise generation as used in :doc:`fix_langevin `. + +If the *rng* keyword is used with the *gaussian* value, then the noise +is generated from a gaussian distribution. Typically this added +complexity is unnecessary, and one should be fine using the *uniform* +value for reasons argued in :ref:`(Dunweg) `. + +If the *rng* keyword is used with the *none* value, then the noise +terms are set to zero. + +If the *dipole* keyword is used, then the dipole moments of the particles +are updated by setting them along the x axis of the ellipsoidal frames of +reference. + +---------- + +.. include:: accel_styles.rst + +---------- + +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. +No global or per-atom quantities are stored +by this fix for access by various :doc:`output commands `. + +The :doc:`fix_modify ` *virial* option is supported by this +fix to add the contribution due to the added forces on atoms to the +system's virial as part of :doc:`thermodynamic output `. +The default is *virial no*. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during +:doc:`energy minimization `. + + +Restrictions +"""""""""""" + +This fix requires that atoms store torque and angular velocity (omega) +as defined by the :doc:`atom_style sphere ` command, as well +as atoms which have a definite orientation as defined by the +:doc:`atom_style ellipsoid ` command. +Optionally, they can also store a dipole moment as defined by the +:doc:`atom_style dipole ` command. + +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` +doc page for more info. + +All particles in the group must be finite-size ellipsoids. They cannot +be point particles. + +Related commands +"""""""""""""""" + +:doc:`fix bd/sphere `, :doc:`fix langevin `, +:doc:`fix nve/asphere `, :doc:`atom style ` + +Default +""""""" + +The default for *rng* is *uniform*. + +---------- + +.. _GoldsteinCM1: + +**(Goldstein)** Goldstein, Poole, and Safko, Classical Mechanics, 3rd Ed. (2001). + +.. _GardinerC1: + +**(Gardiner)** Gardiner, A Handbook for the Natural and Social Sciences 4th Ed. (2009). + +.. _Dunweg7: + +**(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). + + diff --git a/examples/USER/misc/bd_asphere/README.txt b/examples/USER/misc/bd_asphere/README.txt new file mode 100644 index 0000000000..7cb5d2e8e6 --- /dev/null +++ b/examples/USER/misc/bd_asphere/README.txt @@ -0,0 +1,2 @@ +The input file in2d.bd demonstrates how to run a 2d simulation +of ellipsoidal particles undergoing overdamped brownian motion. diff --git a/examples/USER/misc/bd_asphere/in3d.bd b/examples/USER/misc/bd_asphere/in3d.bd new file mode 100644 index 0000000000..6163eb0c58 --- /dev/null +++ b/examples/USER/misc/bd_asphere/in3d.bd @@ -0,0 +1,71 @@ +# 3d overdamped brownian dynamics + +variable rng string gaussian +variable gamma_t equal 4.0 +variable gamma_r equal 1.0 +variable D_t equal 7.0 +variable D_r equal 13.0 +variable seed equal 1974019 + +variable params string ${rng}_${gamma_t}_${gamma_r}_${D_t}_${D_r} + + +log log_${params}_3d.lammps.log +units lj +atom_style hybrid dipole sphere ellipsoid +dimension 3 +newton off + + +lattice sc 0.4 +region box block -4 4 -4 4 -4 4 +create_box 1 box +create_atoms 1 box +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * shape 1 1 1 +set type * quat/random ${seed} +velocity all create 1.0 1 loop geom + + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + + +pair_style none + + +fix 1 all bd/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole + + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50000 +run 50000 +reset_timestep 0 + + +#initialisation for the main run + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +# write trajectory and thermo in a log-scale frequency +#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type & +# x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 10000 + +# main run +run 120000 diff --git a/examples/USER/misc/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log b/examples/USER/misc/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log new file mode 100644 index 0000000000..c6926dbccf --- /dev/null +++ b/examples/USER/misc/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log @@ -0,0 +1,154 @@ +units lj +atom_style hybrid dipole sphere ellipsoid +WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (src/atom_vec_hybrid.cpp:157) +WARNING: Peratom rmass is in multiple sub-styles - must be used consistently (src/atom_vec_hybrid.cpp:219) +dimension 3 +newton off + + +lattice sc 0.4 +Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 +region box block -4 4 -4 4 -4 4 +create_box 1 box +Created orthogonal box = (-5.4288352 -5.4288352 -5.4288352) to (5.4288352 5.4288352 5.4288352) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 512 atoms + create_atoms CPU = 0.001 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 1974019 1.0 +Setting atom values ... + 512 settings made for dipole/random +set type * shape 1 1 1 +Setting atom values ... + 512 settings made for shape +set type * quat/random ${seed} +set type * quat/random 1974019 +Setting atom values ... + 512 settings made for quat/random +velocity all create 1.0 1 loop geom + + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + + +pair_style none + + +fix 1 all bd/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all bd/asphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all bd/asphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all bd/asphere 4 1 7 ${D_r} ${seed} rng ${rng} dipole +fix 1 all bd/asphere 4 1 7 13 ${seed} rng ${rng} dipole +fix 1 all bd/asphere 4 1 7 13 1974019 rng ${rng} dipole +fix 1 all bd/asphere 4 1 7 13 1974019 rng gaussian dipole + + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50000 +run 50000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.379 | 5.379 Mbytes +Step Temp E_pair c_press + 0 1 0 0 + 50000 1.3923773e+11 0 0 +Loop time of 5.68636 on 1 procs for 50000 steps with 512 atoms + +Performance: 0.076 tau/day, 8792.977 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.11589 | 0.11589 | 0.11589 | 0.0 | 2.04 +Output | 2.1155e-05 | 2.1155e-05 | 2.1155e-05 | 0.0 | 0.00 +Modify | 5.4911 | 5.4911 | 5.4911 | 0.0 | 96.57 +Other | | 0.07936 | | | 1.40 + +Nlocal: 512.000 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 217.000 ave 217 max 217 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + + +#initialisation for the main run + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +# write trajectory and thermo in a log-scale frequency +dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type x y xu yu mux muy muz fx fy fz +dump 1 all custom 1000 dump_gaussian_4_1_7_13_2d.lammpstrj id type x y xu yu mux muy muz fx fy fz +dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 10000 + +# main run +run 120000 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 7.103 | 7.103 | 7.103 Mbytes +Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 1.3923773e+11 0 0 0 0 0 0 + 10000 1413805.2 0 1.3943053 1.4055827 1.4346505 4.2345385 0 + 20000 1380788.4 0 2.8560158 2.6537192 2.698195 8.2079299 0 + 30000 1368735.7 0 4.2694087 4.1286924 3.9635117 12.361613 0 + 40000 1349446 0 5.4328386 6.0271243 5.3571941 16.817157 0 + 50000 1366690 0 7.0372792 7.3342977 6.7676981 21.139275 0 + 60000 1413212.4 0 8.6092241 8.3859529 8.3650987 25.360276 0 + 70000 1401310 0 10.085131 9.4972009 9.7949174 29.377249 0 + 80000 1419160.7 0 11.413946 10.964643 11.007284 33.385873 0 + 90000 1298713.5 0 12.556318 12.457196 12.055966 37.06948 0 + 100000 1430838.3 0 14.104796 13.817001 13.596538 41.518335 0 + 110000 1364246.8 0 15.382464 15.09201 15.017312 45.491785 0 + 120000 1389237.6 0 16.632972 16.343173 16.015748 48.991892 0 +Loop time of 13.595 on 1 procs for 120000 steps with 512 atoms + +Performance: 7626.329 tau/day, 8826.770 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.00079148 | 0.00079148 | 0.00079148 | 0.0 | 0.01 +Comm | 0.029132 | 0.029132 | 0.029132 | 0.0 | 0.21 +Output | 0.15178 | 0.15178 | 0.15178 | 0.0 | 1.12 +Modify | 13.222 | 13.222 | 13.222 | 0.0 | 97.25 +Other | | 0.1916 | | | 1.41 + +Nlocal: 512.000 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 1110 +Dangerous builds = 0 +Total wall time: 0:00:19 diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 2dd16d23ac..ac41d60dfd 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -53,7 +53,8 @@ dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18 fix accelerate/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 -fix bd/sphere, Sam Cameron (U of Bristol), samuel.j.m.cameron at gmail.com, 10 Dec 2020 +fix bd/sphere, Sam Cameron (U of Bristol), samuel.j.m.cameron at gmail.com, 13 Dec 2020 +fix bd/asphere, Sam Cameron (U of Bristol), samuel.j.m.cameron at gmail.com, 13 Dec 2020 fix electron/stopping/fit, James Stewart (SNL), jstewa .at. sandia.gov, 23 Sep 2020 fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019 fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018 diff --git a/src/USER-MISC/fix_bd_asphere.cpp b/src/USER-MISC/fix_bd_asphere.cpp new file mode 100644 index 0000000000..88772b9237 --- /dev/null +++ b/src/USER-MISC/fix_bd_asphere.cpp @@ -0,0 +1,392 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp. + + Contributing author: Sam Cameron (University of Bristol) +------------------------------------------------------------------------- */ + +#include "fix_bd_asphere.h" + +#include +#include +#include "math_extra.h" +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "force.h" +#include "update.h" +#include "comm.h" +#include "domain.h" +#include "random_mars.h" +#include "memory.h" +#include "error.h" + + +using namespace LAMMPS_NS; +using namespace FixConst; + +#define SMALL 1e-14 + +enum{NODIPOLE,DIPOLE}; + +/* ---------------------------------------------------------------------- */ + +FixBdAsphere::FixBdAsphere(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + virial_flag = 1; + + time_integrate = 1; + + dipole_flag = NODIPOLE; + + + if (narg > 11 || narg < 8 ) + error->all(FLERR,"Illegal fix bd/asphere command."); + + if (!atom->sphere_flag) + error->all(FLERR,"Fix bd/asphere requires atom style sphere"); + + gamma_t = utils::numeric(FLERR,arg[3],false,lmp); + if (gamma_t <= 0.0) + error->all(FLERR,"Fix bd/asphere translational viscous drag " + "coefficient must be > 0."); + + gamma_r = utils::numeric(FLERR,arg[4],false,lmp); + if (gamma_t <= 0.0) + error->all(FLERR,"Fix bd/asphere rotational viscous drag " + "coefficient must be > 0."); + + + diff_t = utils::numeric(FLERR,arg[5],false,lmp); + if (diff_t <= 0.0) + error->all(FLERR,"Fix bd/asphere translational diffusion " + "coefficient must be > 0."); + + diff_r = utils::numeric(FLERR,arg[6],false,lmp); + if (diff_r <= 0.0) + error->all(FLERR,"Fix bd/asphere rotational diffusion " + "coefficient must be > 0."); + + seed = utils::inumeric(FLERR,arg[7],false,lmp); + if (seed <= 0) error->all(FLERR,"Fix bd/asphere seed must be > 0."); + + noise_flag = 1; + gaussian_noise_flag = 0; + + int iarg = 8; + + while (iarg < narg) { + if (strcmp(arg[iarg],"rng") == 0) { + if (narg == iarg + 1) { + error->all(FLERR,"Illegal fix/bd/asphere command."); + } + if (strcmp(arg[iarg + 1],"uniform") == 0) { + noise_flag = 1; + } else if (strcmp(arg[iarg + 1],"gaussian") == 0) { + noise_flag = 1; + gaussian_noise_flag = 1; + } else if (strcmp(arg[iarg + 1],"none") == 0) { + noise_flag = 0; + } else { + error->all(FLERR,"Illegal fix/bd/asphere command."); + } + iarg = iarg + 2; + } else if (strcmp(arg[iarg],"dipole") == 0) { + dipole_flag = DIPOLE; + iarg = iarg + 1; + } else { + error->all(FLERR,"Illegal fix/bd/asphere command."); + } + } + + if (dipole_flag == DIPOLE && !atom->mu_flag) + error->all(FLERR,"Fix bd/asphere dipole requires atom attribute mu"); + + // initialize Marsaglia RNG with processor-unique seed + random = new RanMars(lmp,seed + comm->me); + +} + +/* ---------------------------------------------------------------------- */ + +int FixBdAsphere::setmask() +{ + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +FixBdAsphere::~FixBdAsphere() +{ + delete random; +} + + + +/* ---------------------------------------------------------------------- */ + +void FixBdAsphere::init() +{ + + + avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); + if (!avec) + error->all(FLERR,"Compute bd/asphere requires " + "atom style ellipsoid"); + + // check that all particles are finite-size ellipsoids + // no point particles allowed, spherical is OK + + int *ellipsoid = atom->ellipsoid; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + if (ellipsoid[i] < 0) + error->one(FLERR,"Fix bd/asphere requires extended particles"); + + + if (dipole_flag == DIPOLE) { + + double f_act[3] = { 1.0, 0.0, 0.0 }; + double f_rot[3]; + double *quat; + int *ellipsoid = atom->ellipsoid; + AtomVecEllipsoid::Bonus *bonus = avec->bonus; + + double Q[3][3]; + + double **mu = atom->mu; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + quat = bonus[ellipsoid[i]].quat; + MathExtra::quat_to_mat( quat, Q ); + MathExtra::matvec( Q, f_act, f_rot ); + + mu[i][0] = f_rot[0]; + mu[i][1] = f_rot[1]; + mu[i][2] = f_rot[2]; + + } + } + } + + g1 = force->ftm2v/gamma_t; + g3 = force->ftm2v/gamma_r; + if (noise_flag == 0) { + g2 = 0; + g4 = 0; + rng_func = &RanMars::zero_rng; + } else if (gaussian_noise_flag == 1) { + g2 = gamma_t*sqrt(2 * diff_t)/force->ftm2v; + g4 = gamma_r*sqrt(2 * diff_r)/force->ftm2v; + rng_func = &RanMars::gaussian; + } else { + g2 = gamma_t*sqrt( 24 * diff_t)/force->ftm2v; + g4 = gamma_r*sqrt( 24 * diff_r )/force->ftm2v; + rng_func = &RanMars::uniform_middle; + } + + dt = update->dt; + sqrtdt = sqrt(dt); +} + +void FixBdAsphere::setup(int vflag) +{ + post_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + + +void FixBdAsphere::initial_integrate(int /* vflag */) +{ + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double **omega = atom->omega; + double **torque = atom->torque; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + int d3rot; // whether to compute angular momentum in xy plane + + if (domain->dimension==2) { + d3rot = 0; + } else { + d3rot = 1; + } + + if (dipole_flag == DIPOLE) { + + // if dipole is being tracked, then update it along with + // quaternions accordingly along with angular velocity + + double wq[4]; + + double *quat; + int *ellipsoid = atom->ellipsoid; + AtomVecEllipsoid::Bonus *bonus = avec->bonus; + + // project dipole along x axis of quat + double f_act[3] = { 1.0, 0.0, 0.0 }; + double f_rot[3]; + + double Q[3][3]; + + double **mu = atom->mu; + + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + update_x_and_omega(x[i],v[i],omega[i],f[i],torque[i],d3rot); + + quat = bonus[ellipsoid[i]].quat; + + MathExtra::vecquat(omega[i],quat,wq); + + quat[0] = quat[0] + 0.5*dt*wq[0]; + quat[1] = quat[1] + 0.5*dt*wq[1]; + quat[2] = quat[2] + 0.5*dt*wq[2]; + quat[3] = quat[3] + 0.5*dt*wq[3]; + MathExtra::qnormalize(quat); + + MathExtra::quat_to_mat( quat, Q ); + MathExtra::matvec( Q, f_act, f_rot ); + + mu[i][0] = f_rot[0]; + mu[i][1] = f_rot[1]; + mu[i][2] = f_rot[2]; + + } + } + } else { + + // if no dipole, just update quaternions and + // angular velocity + + + double wq[4]; + + double *quat; + int *ellipsoid = atom->ellipsoid; + AtomVecEllipsoid::Bonus *bonus = avec->bonus; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + update_x_and_omega(x[i],v[i],omega[i],f[i],torque[i],d3rot); + + quat = bonus[ellipsoid[i]].quat; + + MathExtra::vecquat(omega[i],quat,wq); + + quat[0] = quat[0] + 0.5*dt*wq[0]; + quat[1] = quat[1] + 0.5*dt*wq[1]; + quat[2] = quat[2] + 0.5*dt*wq[2]; + quat[3] = quat[3] + 0.5*dt*wq[3]; + MathExtra::qnormalize(quat); + + } + } + } + return; +} + +void FixBdAsphere::update_x_and_omega(double *x, double *v, double *omega, + double *f, double *torque, int d3rot) +{ + double dx, dy, dz; + + dx = dt * g1 * f[0]; + x[0] += dx; + v[0] = dx/dt; + + dy = dt * g1 * f[1]; + x[1] += dy; + v[1] = dy/dt; + + dz = dt * g1 * f[2]; + x[2] += dz; + v[2] = dz/dt; + + omega[0] = d3rot * g3* torque[0]; + omega[1] = d3rot * g3* torque[1]; + omega[2] = g3* torque[2]; + + return; +} + +/* ---------------------------------------------------------------------- + apply random force, stolen from MISC/fix_efield.cpp +------------------------------------------------------------------------- */ + +void FixBdAsphere::post_force(int vflag) +{ + double **f = atom->f; + double **x = atom->x; + double **torque = atom->torque; + int *mask = atom->mask; + imageint *image = atom->image; + int nlocal = atom->nlocal; + + // virial setup + + if (vflag) v_setup(vflag); + else evflag = 0; + + double fx,fy,fz; + double v[6]; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + + fx = g2 * (random->*rng_func)()/sqrtdt; + fy = g2 * (random->*rng_func)()/sqrtdt; + fz = g2 * (random->*rng_func)()/sqrtdt; + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + + torque[i][0] = g4*(random->*rng_func)()/sqrtdt; + torque[i][1] = g4*(random->*rng_func)()/sqrtdt; + torque[i][2] = g4*(random->*rng_func)()/sqrtdt; + + if (evflag) { + v[0] = fx*x[i][0]; + v[1] = fy*x[i][1]; + v[2] = fz*x[i][2]; + v[3] = fx*x[i][1]; + v[4] = fx*x[i][2]; + v[5] = fy*x[i][2]; + v_tally(i, v); + } + } +} + +void FixBdAsphere::reset_dt() +{ + + dt = update->dt; + sqrtdt = sqrt(dt); +} diff --git a/src/USER-MISC/fix_bd_asphere.h b/src/USER-MISC/fix_bd_asphere.h new file mode 100644 index 0000000000..696b659729 --- /dev/null +++ b/src/USER-MISC/fix_bd_asphere.h @@ -0,0 +1,103 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(bd/asphere,FixBdAsphere) + +#else + +#ifndef LMP_FIX_BD_ASPHERE_H +#define LMP_FIX_BD_ASPHERE_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixBdAsphere : public Fix { + public: + FixBdAsphere(class LAMMPS *, int, char **); + virtual ~FixBdAsphere(); + void init(); + void initial_integrate(int); + void setup(int); + void post_force(int); + int setmask(); + void reset_dt(); + void update_x_and_omega(double *, double *, double *, + double *, double *, int ); + + + private: + int seed; // RNG seed + int dipole_flag; // set if dipole is used + double dt, sqrtdt; // time step interval and its sqrt + + + double gamma_t,gamma_r; // translational and rotational damping params + double diff_t,diff_r; // translational and rotational diffusion coeffs + + double g1,g2, g3, g4; // prefactors in time stepping + int noise_flag; // 0/1 for noise off/on + int gaussian_noise_flag; // 0/1 for uniform/gaussian noise + + class AtomVecEllipsoid *avec; + +protected: + class RanMars *random; + typedef double (RanMars::*rng_member)(); + rng_member rng_func; // placeholder for RNG function + +}; + +} +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal fix bd/asphere command. + +Wrong number/type of input arguments. + +E: Compute bd/asphere requires atom style sphere + +Self-explanatory. + +E: Compute bd/asphere requires atom style ellipsoid + +Self-explanatory. + +E: Compute bd/asphere dipole requires atom attribute mu + +Self-explanatory. + +E: Fix bd/asphere translational viscous drag coefficient must be > 0. + +Self-explanatory. + +E: Fix bd/asphere rotational viscous drag coefficient must be > 0. + +Self-explanatory. + +E: Fix bd/asphere translational diffusion coefficient must be > 0. + +Self-explanatory. + +E: Fix bd/asphere rotational diffusion coefficient must be > 0. + +Self-explanatory. + +E: Fix bd/asphere seed must be > 0. + +*/ From d9440a582c66086fd6c18e78f0f7716a4a969d8a Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Wed, 16 Dec 2020 17:30:28 +0000 Subject: [PATCH 0048/1217] Final touches on docs to discuss temperature in overdamped dynamics. --- doc/src/fix_bd_asphere.rst | 2 +- doc/src/fix_bd_sphere.rst | 14 ++++++++++++++ 2 files changed, 15 insertions(+), 1 deletion(-) diff --git a/doc/src/fix_bd_asphere.rst b/doc/src/fix_bd_asphere.rst index 8c0337cb5e..67d32e2038 100644 --- a/doc/src/fix_bd_asphere.rst +++ b/doc/src/fix_bd_asphere.rst @@ -61,7 +61,7 @@ the angular velocity vector. See :doc:`fix bd/sphere ` for discussion on the values of :math:`\gamma_t`, :math:`\gamma_r`, :math:`D_t`, -and :math:`D_r` when simulating equilibrium systems. +:math:`D_r`, and temperature when simulating equilibrium systems. If the *rng* keyword is used with the *uniform* value, then the noise diff --git a/doc/src/fix_bd_sphere.rst b/doc/src/fix_bd_sphere.rst index 177af6e6d7..eeaaca470c 100644 --- a/doc/src/fix_bd_sphere.rst +++ b/doc/src/fix_bd_sphere.rst @@ -85,6 +85,16 @@ section 7.4). --------- +.. note:: + Temperature computation using the :doc:`compute temp ` + will not correctly compute temperature of these overdamped dynamics + since we are explicitly neglecting inertial effects. + See e.g. chapter 6 of :ref:`(Doi) ` for more details on this. + Temperature is instead defined in terms of the note above (for + equilibrium systems). + +--------- + .. note:: The diffusion coefficient :math:`D_t` is measured in units of (length*length)/time and the diffusion coefficient @@ -172,6 +182,10 @@ The default for *rng* is *uniform*. **(Callegari)** Callegari and Volpe, *Numerical Simulations of Active Brownian Particles*, Flowing Matter, 211-238 (2019). +.. _Doi1: + +**(Doi)** Doi, Soft Matter Physics (2013). + .. _Dunweg6: **(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). From 4c1f44935039a8ec85186fee7635e3cd08405f7e Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Sat, 19 Dec 2020 17:42:47 +0000 Subject: [PATCH 0049/1217] Moved brownian dynamics files to be in USER-BROWNIAN package --- cmake/CMakeLists.txt | 2 +- doc/src/Commands_fix.rst | 4 +- doc/src/fix.rst | 4 +- ...d_asphere.rst => fix_brownian_asphere.rst} | 22 ++++---- ..._bd_sphere.rst => fix_brownian_sphere.rst} | 18 +++---- .../{misc => brownian}/bd_asphere/README.txt | 0 .../bd_asphere/in3d.brownian} | 2 +- .../log_gaussian_4_1_7_13_3d.lammps.log | 49 +++++++++-------- .../{misc => brownian}/bd_sphere/README.txt | 10 ++-- .../bd_sphere/in2ddipole.brownian} | 2 +- .../bd_sphere/in3d_virial_on.brownian} | 2 +- .../log_gaussian_4_1_7_13_2d.lammps.log | 53 ++++++++++--------- .../log_uniform_10_1_5_15_3d.lammps.log | 0 .../fix_brownian_asphere.cpp} | 46 ++++++++-------- .../fix_brownian_asphere.h} | 30 +++++------ .../fix_brownian_sphere.cpp} | 40 +++++++------- .../fix_brownian_sphere.h} | 28 +++++----- src/USER-MISC/README | 2 - .../tests/{data.bdsphere => data.brownian} | 0 ...sphere.yaml => fix-timestep-brownian.yaml} | 6 +-- .../tests/{in.bdsphere => in.brownian} | 2 +- 21 files changed, 160 insertions(+), 162 deletions(-) rename doc/src/{fix_bd_asphere.rst => fix_brownian_asphere.rst} (86%) rename doc/src/{fix_bd_sphere.rst => fix_brownian_sphere.rst} (92%) rename examples/USER/{misc => brownian}/bd_asphere/README.txt (100%) rename examples/USER/{misc/bd_asphere/in3d.bd => brownian/bd_asphere/in3d.brownian} (93%) rename examples/USER/{misc => brownian}/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log (74%) rename examples/USER/{misc => brownian}/bd_sphere/README.txt (73%) rename examples/USER/{misc/bd_sphere/in2ddipole.bd => brownian/bd_sphere/in2ddipole.brownian} (93%) rename examples/USER/{misc/bd_sphere/in3d_virial_on.bd => brownian/bd_sphere/in3d_virial_on.brownian} (93%) rename examples/USER/{misc => brownian}/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log (89%) rename examples/USER/{misc => brownian}/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log (100%) rename src/{USER-MISC/fix_bd_asphere.cpp => USER-BROWNIAN/fix_brownian_asphere.cpp} (85%) rename src/{USER-MISC/fix_bd_asphere.h => USER-BROWNIAN/fix_brownian_asphere.h} (69%) rename src/{USER-MISC/fix_bd_sphere.cpp => USER-BROWNIAN/fix_brownian_sphere.cpp} (85%) rename src/{USER-MISC/fix_bd_sphere.h => USER-BROWNIAN/fix_brownian_sphere.h} (70%) rename unittest/force-styles/tests/{data.bdsphere => data.brownian} (100%) rename unittest/force-styles/tests/{fix-timestep-bd_sphere.yaml => fix-timestep-brownian.yaml} (97%) rename unittest/force-styles/tests/{in.bdsphere => in.brownian} (88%) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 42e6d12ffb..26d86e0a06 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -112,7 +112,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY - USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS) + USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS USER-BROWNIAN) set(SUFFIX_PACKAGES CORESHELL USER-OMP KOKKOS OPT USER-INTEL GPU) foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES}) option(PKG_${PKG} "Build ${PKG} Package" OFF) diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index 8be0908a1a..361ec7e982 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -39,8 +39,8 @@ OPT. * :doc:`ave/time ` * :doc:`aveforce ` * :doc:`balance ` - * :doc:`bd/sphere ` - * :doc:`bd/asphere ` + * :doc:`brownian/asphere ` + * :doc:`brownian/sphere ` * :doc:`bocs ` * :doc:`bond/break ` * :doc:`bond/create ` diff --git a/doc/src/fix.rst b/doc/src/fix.rst index c395489a58..5efe002f31 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -182,8 +182,8 @@ accelerated styles exist. * :doc:`ave/time ` - compute/output global time-averaged quantities * :doc:`aveforce ` - add an averaged force to each atom * :doc:`balance ` - perform dynamic load-balancing -* :doc:`bd/asphere ` - integrate positions and orientations in overdamped motion -* :doc:`bd/sphere ` - overdamped translational and rotational brownian dynamics +* :doc:`brownian/asphere ` - overdamped translational and rotational brownian for ellipsoids +* :doc:`brownian/sphere ` - overdamped translational and rotational brownian for spheres * :doc:`bocs ` - NPT style time integration with pressure correction * :doc:`bond/break ` - break bonds on the fly * :doc:`bond/create ` - create bonds on the fly diff --git a/doc/src/fix_bd_asphere.rst b/doc/src/fix_brownian_asphere.rst similarity index 86% rename from doc/src/fix_bd_asphere.rst rename to doc/src/fix_brownian_asphere.rst index 67d32e2038..58dd453de9 100644 --- a/doc/src/fix_bd_asphere.rst +++ b/doc/src/fix_brownian_asphere.rst @@ -1,17 +1,17 @@ -.. index:: fix bd/asphere +.. index:: fix brownian/asphere -fix bd/asphere command -====================== +fix brownian/asphere command +============================ Syntax """""" .. parsed-literal:: - fix ID group-ID bd/asphere gamma_t gamma_r diff_t diff_r seed keyword args + fix ID group-ID brownian/asphere gamma_t gamma_r diff_t diff_r seed keyword args * ID, group-ID are documented in :doc:`fix ` command -* bd/asphere = style name of this fix command +* brownian/asphere = style name of this fix command * gamma_t = translational friction coefficient * gamma_r = rotational friction coefficient * diff_t = translational diffusion coefficient @@ -32,10 +32,10 @@ Examples .. code-block:: LAMMPS - fix 1 all bd/asphere 1.0 1.0 1.0 1.0 1294019 - fix 1 all bd/asphere 1.0 1.0 1.0 1.0 19581092 rng none dipole - fix 1 all bd/asphere 1.0 1.0 1.0 1.0 19581092 rng uniform - fix 1 all bd/asphere 1.0 1.0 1.0 1.0 19581092 dipole rng gaussian + fix 1 all brownian/asphere 1.0 1.0 1.0 1.0 1294019 + fix 1 all brownian/asphere 1.0 1.0 1.0 1.0 19581092 rng none dipole + fix 1 all brownian/asphere 1.0 1.0 1.0 1.0 19581092 rng uniform + fix 1 all brownian/asphere 1.0 1.0 1.0 1.0 19581092 dipole rng gaussian Description @@ -59,7 +59,7 @@ Chapter 4 of :ref:`(Goldstein) `), :math:`dW_t` and The quaternions :math:`q` of the ellipsoid are updated each timestep from the angular velocity vector. -See :doc:`fix bd/sphere ` for discussion on the +See :doc:`fix brownian/sphere ` for discussion on the values of :math:`\gamma_t`, :math:`\gamma_r`, :math:`D_t`, :math:`D_r`, and temperature when simulating equilibrium systems. @@ -124,7 +124,7 @@ be point particles. Related commands """""""""""""""" -:doc:`fix bd/sphere `, :doc:`fix langevin `, +:doc:`fix brownian/sphere `, :doc:`fix langevin `, :doc:`fix nve/asphere `, :doc:`atom style ` Default diff --git a/doc/src/fix_bd_sphere.rst b/doc/src/fix_brownian_sphere.rst similarity index 92% rename from doc/src/fix_bd_sphere.rst rename to doc/src/fix_brownian_sphere.rst index eeaaca470c..231486dee1 100644 --- a/doc/src/fix_bd_sphere.rst +++ b/doc/src/fix_brownian_sphere.rst @@ -1,17 +1,17 @@ -.. index:: fix bd/sphere +.. index:: fix brownian/sphere -fix bd/sphere command -====================== +fix brownian/sphere command +=========================== Syntax """""" .. parsed-literal:: - fix ID group-ID bd/sphere gamma_t gamma_r diff_t diff_r seed keyword args + fix ID group-ID brownian/sphere gamma_t gamma_r diff_t diff_r seed keyword args * ID, group-ID are documented in :doc:`fix ` command -* bd/sphere = style name of this fix command +* brownian/sphere = style name of this fix command * gamma_t = translational friction coefficient * gamma_r = rotational friction coefficient * diff_t = translational diffusion coefficient @@ -32,10 +32,10 @@ Examples .. code-block:: LAMMPS - fix 1 all bd/sphere 1.0 1.0 1.0 1.0 1294019 - fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rng none dipole - fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rng uniform - fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 dipole rng gaussian + fix 1 all brownian/sphere 1.0 1.0 1.0 1.0 1294019 + fix 1 all brownian/sphere 1.0 1.0 1.0 1.0 19581092 rng none dipole + fix 1 all brownian/sphere 1.0 1.0 1.0 1.0 19581092 rng uniform + fix 1 all brownian/sphere 1.0 1.0 1.0 1.0 19581092 dipole rng gaussian Description diff --git a/examples/USER/misc/bd_asphere/README.txt b/examples/USER/brownian/bd_asphere/README.txt similarity index 100% rename from examples/USER/misc/bd_asphere/README.txt rename to examples/USER/brownian/bd_asphere/README.txt diff --git a/examples/USER/misc/bd_asphere/in3d.bd b/examples/USER/brownian/bd_asphere/in3d.brownian similarity index 93% rename from examples/USER/misc/bd_asphere/in3d.bd rename to examples/USER/brownian/bd_asphere/in3d.brownian index 6163eb0c58..67d95a82b9 100644 --- a/examples/USER/misc/bd_asphere/in3d.bd +++ b/examples/USER/brownian/bd_asphere/in3d.brownian @@ -36,7 +36,7 @@ neigh_modify every 1 delay 1 check yes pair_style none -fix 1 all bd/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole compute press all pressure NULL virial diff --git a/examples/USER/misc/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log b/examples/USER/brownian/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log similarity index 74% rename from examples/USER/misc/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log rename to examples/USER/brownian/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log index c6926dbccf..21bd04f7da 100644 --- a/examples/USER/misc/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log +++ b/examples/USER/brownian/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log @@ -38,13 +38,13 @@ neigh_modify every 1 delay 1 check yes pair_style none -fix 1 all bd/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/asphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/asphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/asphere 4 1 7 ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/asphere 4 1 7 13 ${seed} rng ${rng} dipole -fix 1 all bd/asphere 4 1 7 13 1974019 rng ${rng} dipole -fix 1 all bd/asphere 4 1 7 13 1974019 rng gaussian dipole +fix 1 all brownian/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 4 1 7 ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 4 1 7 13 ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 4 1 7 13 1974019 rng ${rng} dipole +fix 1 all brownian/asphere 4 1 7 13 1974019 rng gaussian dipole compute press all pressure NULL virial @@ -61,9 +61,9 @@ Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.379 | 5.379 Mbytes Step Temp E_pair c_press 0 1 0 0 50000 1.3923773e+11 0 0 -Loop time of 5.68636 on 1 procs for 50000 steps with 512 atoms +Loop time of 5.61345 on 1 procs for 50000 steps with 512 atoms -Performance: 0.076 tau/day, 8792.977 timesteps/s +Performance: 0.077 tau/day, 8907.171 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: @@ -71,10 +71,10 @@ Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.11589 | 0.11589 | 0.11589 | 0.0 | 2.04 -Output | 2.1155e-05 | 2.1155e-05 | 2.1155e-05 | 0.0 | 0.00 -Modify | 5.4911 | 5.4911 | 5.4911 | 0.0 | 96.57 -Other | | 0.07936 | | | 1.40 +Comm | 0.11822 | 0.11822 | 0.11822 | 0.0 | 2.11 +Output | 2.0199e-05 | 2.0199e-05 | 2.0199e-05 | 0.0 | 0.00 +Modify | 5.4135 | 5.4135 | 5.4135 | 0.0 | 96.44 +Other | | 0.0817 | | | 1.46 Nlocal: 512.000 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -100,9 +100,8 @@ thermo_style custom step temp epair c_msd[*] c_press # write trajectory and thermo in a log-scale frequency -dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type x y xu yu mux muy muz fx fy fz -dump 1 all custom 1000 dump_gaussian_4_1_7_13_2d.lammpstrj id type x y xu yu mux muy muz fx fy fz -dump_modify 1 first yes sort id +#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id timestep 0.00001 thermo 10000 @@ -110,7 +109,7 @@ thermo 10000 # main run run 120000 WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) -Per MPI rank memory allocation (min/avg/max) = 7.103 | 7.103 | 7.103 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.754 | 5.754 | 5.754 Mbytes Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press 0 1.3923773e+11 0 0 0 0 0 0 10000 1413805.2 0 1.3943053 1.4055827 1.4346505 4.2345385 0 @@ -125,20 +124,20 @@ Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press 100000 1430838.3 0 14.104796 13.817001 13.596538 41.518335 0 110000 1364246.8 0 15.382464 15.09201 15.017312 45.491785 0 120000 1389237.6 0 16.632972 16.343173 16.015748 48.991892 0 -Loop time of 13.595 on 1 procs for 120000 steps with 512 atoms +Loop time of 13.2439 on 1 procs for 120000 steps with 512 atoms -Performance: 7626.329 tau/day, 8826.770 timesteps/s +Performance: 7828.487 tau/day, 9060.749 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0.00079148 | 0.00079148 | 0.00079148 | 0.0 | 0.01 -Comm | 0.029132 | 0.029132 | 0.029132 | 0.0 | 0.21 -Output | 0.15178 | 0.15178 | 0.15178 | 0.0 | 1.12 -Modify | 13.222 | 13.222 | 13.222 | 0.0 | 97.25 -Other | | 0.1916 | | | 1.41 +Neigh | 0.00075178 | 0.00075178 | 0.00075178 | 0.0 | 0.01 +Comm | 0.0282 | 0.0282 | 0.0282 | 0.0 | 0.21 +Output | 0.00032692 | 0.00032692 | 0.00032692 | 0.0 | 0.00 +Modify | 13.017 | 13.017 | 13.017 | 0.0 | 98.29 +Other | | 0.1976 | | | 1.49 Nlocal: 512.000 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -151,4 +150,4 @@ Total # of neighbors = 0 Ave neighs/atom = 0.0000000 Neighbor list builds = 1110 Dangerous builds = 0 -Total wall time: 0:00:19 +Total wall time: 0:00:18 diff --git a/examples/USER/misc/bd_sphere/README.txt b/examples/USER/brownian/bd_sphere/README.txt similarity index 73% rename from examples/USER/misc/bd_sphere/README.txt rename to examples/USER/brownian/bd_sphere/README.txt index 2f66504581..8987a23601 100644 --- a/examples/USER/misc/bd_sphere/README.txt +++ b/examples/USER/brownian/bd_sphere/README.txt @@ -1,11 +1,11 @@ -The input file in2ddipole.bd demonstrates how to run a 2d simulation -of particles undergoing overdamped brownian motion in both -translational and rotational degrees of freedom. Dipole +The input file in2ddipole.brownian demonstrates how to run a +2d simulation of particles undergoing overdamped brownian motion +in both translational and rotational degrees of freedom. Dipole updating is turned on, so the package DIPOLE must be built for this example to work. -The input file in3d_virial_on.bd demonstrates how to run a -similar simulation but in 3d. In this case, the virial +The input file in3d_virial_on.brownian demonstrates how to run +a similar simulation but in 3d. In this case, the virial contribution of the brownian dynamics (the sum sum_i /(3*volume) where W is a random variable with mean 0 and variance dt) is diff --git a/examples/USER/misc/bd_sphere/in2ddipole.bd b/examples/USER/brownian/bd_sphere/in2ddipole.brownian similarity index 93% rename from examples/USER/misc/bd_sphere/in2ddipole.bd rename to examples/USER/brownian/bd_sphere/in2ddipole.brownian index 1f7898207f..73d90e4ebf 100644 --- a/examples/USER/misc/bd_sphere/in2ddipole.bd +++ b/examples/USER/brownian/bd_sphere/in2ddipole.brownian @@ -38,7 +38,7 @@ pair_style none #compute d all property/atom mux muy muz -fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole fix 2 all enforce2d compute press all pressure NULL virial diff --git a/examples/USER/misc/bd_sphere/in3d_virial_on.bd b/examples/USER/brownian/bd_sphere/in3d_virial_on.brownian similarity index 93% rename from examples/USER/misc/bd_sphere/in3d_virial_on.bd rename to examples/USER/brownian/bd_sphere/in3d_virial_on.brownian index 0e2f02beb0..481d9bc1b4 100644 --- a/examples/USER/misc/bd_sphere/in3d_virial_on.bd +++ b/examples/USER/brownian/bd_sphere/in3d_virial_on.brownian @@ -33,7 +33,7 @@ neigh_modify every 1 delay 1 check yes pair_style none -fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} fix_modify 1 virial yes compute press all pressure NULL virial diff --git a/examples/USER/misc/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log b/examples/USER/brownian/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log similarity index 89% rename from examples/USER/misc/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log rename to examples/USER/brownian/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log index a735ea6baa..b10f77f0cd 100644 --- a/examples/USER/misc/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log +++ b/examples/USER/brownian/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log @@ -13,7 +13,7 @@ Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.29 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 1024 atoms - create_atoms CPU = 0.001 seconds + create_atoms CPU = 0.002 seconds mass * 1.0 set type * dipole/random ${seed} 1.0 set type * dipole/random 1974019 1.0 @@ -33,13 +33,13 @@ pair_style none #compute d all property/atom mux muy muz -fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/sphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/sphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/sphere 4 1 7 ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/sphere 4 1 7 13 ${seed} rng ${rng} dipole -fix 1 all bd/sphere 4 1 7 13 1974019 rng ${rng} dipole -fix 1 all bd/sphere 4 1 7 13 1974019 rng gaussian dipole +fix 1 all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/sphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/sphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/sphere 4 1 7 ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/sphere 4 1 7 13 ${seed} rng ${rng} dipole +fix 1 all brownian/sphere 4 1 7 13 1974019 rng ${rng} dipole +fix 1 all brownian/sphere 4 1 7 13 1974019 rng gaussian dipole fix 2 all enforce2d compute press all pressure NULL virial @@ -56,9 +56,9 @@ Per MPI rank memory allocation (min/avg/max) = 4.289 | 4.289 | 4.289 Mbytes Step Temp E_pair c_press 0 1 0 0 50000 7.3671759e+10 0 0 -Loop time of 11.2219 on 1 procs for 50000 steps with 1024 atoms +Loop time of 11.2532 on 1 procs for 50000 steps with 1024 atoms -Performance: 0.038 tau/day, 4455.573 timesteps/s +Performance: 0.038 tau/day, 4443.198 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: @@ -66,10 +66,10 @@ Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.028513 | 0.028513 | 0.028513 | 0.0 | 0.25 -Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00 -Modify | 11.048 | 11.048 | 11.048 | 0.0 | 98.45 -Other | | 0.1458 | | | 1.30 +Comm | 0.031456 | 0.031456 | 0.031456 | 0.0 | 0.28 +Output | 2.0958e-05 | 2.0958e-05 | 2.0958e-05 | 0.0 | 0.00 +Modify | 11.067 | 11.067 | 11.067 | 0.0 | 98.35 +Other | | 0.1546 | | | 1.37 Nlocal: 1024.00 ave 1024 max 1024 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -96,8 +96,9 @@ thermo_style custom step temp epair c_msd[*] c_press # write trajectory and thermo in a log-scale frequency # uncomment next three lines for dump output -#dump 1 all custom 2000 dump_${params}_2d.lammpstrj id type # x y xu yu mux muy muz fx fy fz -#dump_modify 1 first yes sort id +dump 1 all custom 2000 dump_${params}_2d.lammpstrj id type x y xu yu mux muy muz fx fy fz +dump 1 all custom 2000 dump_gaussian_4_1_7_13_2d.lammpstrj id type x y xu yu mux muy muz fx fy fz +dump_modify 1 first yes sort id timestep 0.00001 thermo 1000 @@ -105,7 +106,7 @@ thermo 1000 # main run run 120000 WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) -Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes +Per MPI rank memory allocation (min/avg/max) = 6.113 | 6.113 | 6.113 Mbytes Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press 0 7.3671759e+10 0 0 0 0 0 0 1000 710744.42 0 0.1332856 0.13577642 0 0.26906203 0 @@ -228,20 +229,20 @@ Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press 118000 745594.37 0 16.838659 17.585392 0 34.424052 0 119000 714487.42 0 17.064214 17.743478 0 34.807692 0 120000 716557.14 0 17.105558 17.845925 0 34.951483 0 -Loop time of 27.2068 on 1 procs for 120000 steps with 1024 atoms +Loop time of 28.1507 on 1 procs for 120000 steps with 1024 atoms -Performance: 3810.806 tau/day, 4410.656 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 3683.037 tau/day, 4262.774 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0.0015633 | 0.0015633 | 0.0015633 | 0.0 | 0.01 -Comm | 0.021682 | 0.021682 | 0.021682 | 0.0 | 0.08 -Output | 0.0032539 | 0.0032539 | 0.0032539 | 0.0 | 0.01 -Modify | 26.802 | 26.802 | 26.802 | 0.0 | 98.51 -Other | | 0.3781 | | | 1.39 +Neigh | 0.0016237 | 0.0016237 | 0.0016237 | 0.0 | 0.01 +Comm | 0.027064 | 0.027064 | 0.027064 | 0.0 | 0.10 +Output | 0.1712 | 0.1712 | 0.1712 | 0.0 | 0.61 +Modify | 27.545 | 27.545 | 27.545 | 0.0 | 97.85 +Other | | 0.4062 | | | 1.44 Nlocal: 1024.00 ave 1024 max 1024 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -256,4 +257,4 @@ Neighbor list builds = 1049 Dangerous builds = 0 -Total wall time: 0:00:38 +Total wall time: 0:00:39 diff --git a/examples/USER/misc/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log b/examples/USER/brownian/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log similarity index 100% rename from examples/USER/misc/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log rename to examples/USER/brownian/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log diff --git a/src/USER-MISC/fix_bd_asphere.cpp b/src/USER-BROWNIAN/fix_brownian_asphere.cpp similarity index 85% rename from src/USER-MISC/fix_bd_asphere.cpp rename to src/USER-BROWNIAN/fix_brownian_asphere.cpp index 88772b9237..123a7a5f5f 100644 --- a/src/USER-MISC/fix_bd_asphere.cpp +++ b/src/USER-BROWNIAN/fix_brownian_asphere.cpp @@ -17,7 +17,7 @@ Contributing author: Sam Cameron (University of Bristol) ------------------------------------------------------------------------- */ -#include "fix_bd_asphere.h" +#include "fix_brownian_asphere.h" #include #include @@ -42,7 +42,7 @@ enum{NODIPOLE,DIPOLE}; /* ---------------------------------------------------------------------- */ -FixBdAsphere::FixBdAsphere(LAMMPS *lmp, int narg, char **arg) : +FixBrownianAsphere::FixBrownianAsphere(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { virial_flag = 1; @@ -53,34 +53,34 @@ FixBdAsphere::FixBdAsphere(LAMMPS *lmp, int narg, char **arg) : if (narg > 11 || narg < 8 ) - error->all(FLERR,"Illegal fix bd/asphere command."); + error->all(FLERR,"Illegal fix brownian/asphere command."); if (!atom->sphere_flag) - error->all(FLERR,"Fix bd/asphere requires atom style sphere"); + error->all(FLERR,"Fix brownian/asphere requires atom style sphere"); gamma_t = utils::numeric(FLERR,arg[3],false,lmp); if (gamma_t <= 0.0) - error->all(FLERR,"Fix bd/asphere translational viscous drag " + error->all(FLERR,"Fix brownian/asphere translational viscous drag " "coefficient must be > 0."); gamma_r = utils::numeric(FLERR,arg[4],false,lmp); if (gamma_t <= 0.0) - error->all(FLERR,"Fix bd/asphere rotational viscous drag " + error->all(FLERR,"Fix brownian/asphere rotational viscous drag " "coefficient must be > 0."); diff_t = utils::numeric(FLERR,arg[5],false,lmp); if (diff_t <= 0.0) - error->all(FLERR,"Fix bd/asphere translational diffusion " + error->all(FLERR,"Fix brownian/asphere translational diffusion " "coefficient must be > 0."); diff_r = utils::numeric(FLERR,arg[6],false,lmp); if (diff_r <= 0.0) - error->all(FLERR,"Fix bd/asphere rotational diffusion " + error->all(FLERR,"Fix brownian/asphere rotational diffusion " "coefficient must be > 0."); seed = utils::inumeric(FLERR,arg[7],false,lmp); - if (seed <= 0) error->all(FLERR,"Fix bd/asphere seed must be > 0."); + if (seed <= 0) error->all(FLERR,"Fix brownian/asphere seed must be > 0."); noise_flag = 1; gaussian_noise_flag = 0; @@ -90,7 +90,7 @@ FixBdAsphere::FixBdAsphere(LAMMPS *lmp, int narg, char **arg) : while (iarg < narg) { if (strcmp(arg[iarg],"rng") == 0) { if (narg == iarg + 1) { - error->all(FLERR,"Illegal fix/bd/asphere command."); + error->all(FLERR,"Illegal fix/brownian/asphere command."); } if (strcmp(arg[iarg + 1],"uniform") == 0) { noise_flag = 1; @@ -100,19 +100,19 @@ FixBdAsphere::FixBdAsphere(LAMMPS *lmp, int narg, char **arg) : } else if (strcmp(arg[iarg + 1],"none") == 0) { noise_flag = 0; } else { - error->all(FLERR,"Illegal fix/bd/asphere command."); + error->all(FLERR,"Illegal fix/brownian/asphere command."); } iarg = iarg + 2; } else if (strcmp(arg[iarg],"dipole") == 0) { dipole_flag = DIPOLE; iarg = iarg + 1; } else { - error->all(FLERR,"Illegal fix/bd/asphere command."); + error->all(FLERR,"Illegal fix/brownian/asphere command."); } } if (dipole_flag == DIPOLE && !atom->mu_flag) - error->all(FLERR,"Fix bd/asphere dipole requires atom attribute mu"); + error->all(FLERR,"Fix brownian/asphere dipole requires atom attribute mu"); // initialize Marsaglia RNG with processor-unique seed random = new RanMars(lmp,seed + comm->me); @@ -121,7 +121,7 @@ FixBdAsphere::FixBdAsphere(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -int FixBdAsphere::setmask() +int FixBrownianAsphere::setmask() { int mask = 0; mask |= INITIAL_INTEGRATE; @@ -131,7 +131,7 @@ int FixBdAsphere::setmask() /* ---------------------------------------------------------------------- */ -FixBdAsphere::~FixBdAsphere() +FixBrownianAsphere::~FixBrownianAsphere() { delete random; } @@ -140,13 +140,13 @@ FixBdAsphere::~FixBdAsphere() /* ---------------------------------------------------------------------- */ -void FixBdAsphere::init() +void FixBrownianAsphere::init() { avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); if (!avec) - error->all(FLERR,"Compute bd/asphere requires " + error->all(FLERR,"Compute brownian/asphere requires " "atom style ellipsoid"); // check that all particles are finite-size ellipsoids @@ -159,7 +159,7 @@ void FixBdAsphere::init() for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) if (ellipsoid[i] < 0) - error->one(FLERR,"Fix bd/asphere requires extended particles"); + error->one(FLERR,"Fix brownian/asphere requires extended particles"); if (dipole_flag == DIPOLE) { @@ -208,7 +208,7 @@ void FixBdAsphere::init() sqrtdt = sqrt(dt); } -void FixBdAsphere::setup(int vflag) +void FixBrownianAsphere::setup(int vflag) { post_force(vflag); } @@ -216,7 +216,7 @@ void FixBdAsphere::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixBdAsphere::initial_integrate(int /* vflag */) +void FixBrownianAsphere::initial_integrate(int /* vflag */) { double **x = atom->x; double **v = atom->v; @@ -313,7 +313,7 @@ void FixBdAsphere::initial_integrate(int /* vflag */) return; } -void FixBdAsphere::update_x_and_omega(double *x, double *v, double *omega, +void FixBrownianAsphere::update_x_and_omega(double *x, double *v, double *omega, double *f, double *torque, int d3rot) { double dx, dy, dz; @@ -341,7 +341,7 @@ void FixBdAsphere::update_x_and_omega(double *x, double *v, double *omega, apply random force, stolen from MISC/fix_efield.cpp ------------------------------------------------------------------------- */ -void FixBdAsphere::post_force(int vflag) +void FixBrownianAsphere::post_force(int vflag) { double **f = atom->f; double **x = atom->x; @@ -384,7 +384,7 @@ void FixBdAsphere::post_force(int vflag) } } -void FixBdAsphere::reset_dt() +void FixBrownianAsphere::reset_dt() { dt = update->dt; diff --git a/src/USER-MISC/fix_bd_asphere.h b/src/USER-BROWNIAN/fix_brownian_asphere.h similarity index 69% rename from src/USER-MISC/fix_bd_asphere.h rename to src/USER-BROWNIAN/fix_brownian_asphere.h index 696b659729..31ccf4fc8b 100644 --- a/src/USER-MISC/fix_bd_asphere.h +++ b/src/USER-BROWNIAN/fix_brownian_asphere.h @@ -13,21 +13,21 @@ #ifdef FIX_CLASS -FixStyle(bd/asphere,FixBdAsphere) +FixStyle(brownian/asphere,FixBrownianAsphere) #else -#ifndef LMP_FIX_BD_ASPHERE_H -#define LMP_FIX_BD_ASPHERE_H +#ifndef LMP_FIX_BROWNIAN_ASPHERE_H +#define LMP_FIX_BROWNIAN_ASPHERE_H #include "fix.h" namespace LAMMPS_NS { -class FixBdAsphere : public Fix { +class FixBrownianAsphere : public Fix { public: - FixBdAsphere(class LAMMPS *, int, char **); - virtual ~FixBdAsphere(); + FixBrownianAsphere(class LAMMPS *, int, char **); + virtual ~FixBrownianAsphere(); void init(); void initial_integrate(int); void setup(int); @@ -66,38 +66,38 @@ protected: /* ERROR/WARNING messages: -E: Illegal fix bd/asphere command. +E: Illegal fix brownian/asphere command. Wrong number/type of input arguments. -E: Compute bd/asphere requires atom style sphere +E: Compute brownian/asphere requires atom style sphere Self-explanatory. -E: Compute bd/asphere requires atom style ellipsoid +E: Compute brownian/asphere requires atom style ellipsoid Self-explanatory. -E: Compute bd/asphere dipole requires atom attribute mu +E: Compute brownian/asphere dipole requires atom attribute mu Self-explanatory. -E: Fix bd/asphere translational viscous drag coefficient must be > 0. +E: Fix brownian/asphere translational viscous drag coefficient must be > 0. Self-explanatory. -E: Fix bd/asphere rotational viscous drag coefficient must be > 0. +E: Fix brownian/asphere rotational viscous drag coefficient must be > 0. Self-explanatory. -E: Fix bd/asphere translational diffusion coefficient must be > 0. +E: Fix brownian/asphere translational diffusion coefficient must be > 0. Self-explanatory. -E: Fix bd/asphere rotational diffusion coefficient must be > 0. +E: Fix brownian/asphere rotational diffusion coefficient must be > 0. Self-explanatory. -E: Fix bd/asphere seed must be > 0. +E: Fix brownian/asphere seed must be > 0. */ diff --git a/src/USER-MISC/fix_bd_sphere.cpp b/src/USER-BROWNIAN/fix_brownian_sphere.cpp similarity index 85% rename from src/USER-MISC/fix_bd_sphere.cpp rename to src/USER-BROWNIAN/fix_brownian_sphere.cpp index cc3c788349..c3e0cd2457 100644 --- a/src/USER-MISC/fix_bd_sphere.cpp +++ b/src/USER-BROWNIAN/fix_brownian_sphere.cpp @@ -17,7 +17,7 @@ Contributing author: Sam Cameron (University of Bristol) ------------------------------------------------------------------------- */ -#include "fix_bd_sphere.h" +#include "fix_brownian_sphere.h" #include #include @@ -41,7 +41,7 @@ enum{NONE,DIPOLE}; /* ---------------------------------------------------------------------- */ -FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : +FixBrownianSphere::FixBrownianSphere(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { virial_flag = 1; @@ -51,34 +51,34 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : extra = NONE; if (narg > 11 || narg < 8 ) - error->all(FLERR,"Illegal fix bd/sphere command."); + error->all(FLERR,"Illegal fix brownian/sphere command."); if (!atom->sphere_flag) - error->all(FLERR,"Fix bd/sphere requires atom style sphere"); + error->all(FLERR,"Fix brownian/sphere requires atom style sphere"); gamma_t = utils::numeric(FLERR,arg[3],false,lmp); if (gamma_t <= 0.0) - error->all(FLERR,"Fix bd/sphere translational viscous drag " + error->all(FLERR,"Fix brownian/sphere translational viscous drag " "coefficient must be > 0."); gamma_r = utils::numeric(FLERR,arg[4],false,lmp); if (gamma_t <= 0.0) - error->all(FLERR,"Fix bd/sphere rotational viscous drag " + error->all(FLERR,"Fix brownian/sphere rotational viscous drag " "coefficient must be > 0."); diff_t = utils::numeric(FLERR,arg[5],false,lmp); if (diff_t <= 0.0) - error->all(FLERR,"Fix bd/sphere translational diffusion " + error->all(FLERR,"Fix brownian/sphere translational diffusion " "coefficient must be > 0."); diff_r = utils::numeric(FLERR,arg[6],false,lmp); if (diff_r <= 0.0) - error->all(FLERR,"Fix bd/sphere rotational diffusion " + error->all(FLERR,"Fix brownian/sphere rotational diffusion " "coefficient must be > 0."); seed = utils::inumeric(FLERR,arg[7],false,lmp); - if (seed <= 0) error->all(FLERR,"Fix bd/sphere seed must be > 0."); + if (seed <= 0) error->all(FLERR,"Fix brownian/sphere seed must be > 0."); noise_flag = 1; gaussian_noise_flag = 0; @@ -88,7 +88,7 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : while (iarg < narg) { if (strcmp(arg[iarg],"rng") == 0) { if (narg == iarg + 1) { - error->all(FLERR,"Illegal fix/bd/sphere command."); + error->all(FLERR,"Illegal fix/brownian/sphere command."); } if (strcmp(arg[iarg + 1],"uniform") == 0) { noise_flag = 1; @@ -98,19 +98,19 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : } else if (strcmp(arg[iarg + 1],"none") == 0) { noise_flag = 0; } else { - error->all(FLERR,"Illegal fix/bd/sphere command."); + error->all(FLERR,"Illegal fix/brownian/sphere command."); } iarg = iarg + 2; } else if (strcmp(arg[iarg],"dipole") == 0) { extra = DIPOLE; iarg = iarg + 1; } else { - error->all(FLERR,"Illegal fix/bd/sphere command."); + error->all(FLERR,"Illegal fix/brownian/sphere command."); } } if (extra == DIPOLE && !atom->mu_flag) - error->all(FLERR,"Fix bd/sphere update dipole requires atom attribute mu"); + error->all(FLERR,"Fix brownian/sphere update dipole requires atom attribute mu"); // initialize Marsaglia RNG with processor-unique seed random = new RanMars(lmp,seed + comm->me); @@ -119,7 +119,7 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -int FixBdSphere::setmask() +int FixBrownianSphere::setmask() { int mask = 0; mask |= INITIAL_INTEGRATE; @@ -129,7 +129,7 @@ int FixBdSphere::setmask() /* ---------------------------------------------------------------------- */ -FixBdSphere::~FixBdSphere() +FixBrownianSphere::~FixBrownianSphere() { delete random; } @@ -138,7 +138,7 @@ FixBdSphere::~FixBdSphere() /* ---------------------------------------------------------------------- */ -void FixBdSphere::init() +void FixBrownianSphere::init() { g1 = force->ftm2v/gamma_t; @@ -161,14 +161,14 @@ void FixBdSphere::init() sqrtdt = sqrt(dt); } -void FixBdSphere::setup(int vflag) +void FixBrownianSphere::setup(int vflag) { post_force(vflag); } /* ---------------------------------------------------------------------- */ -void FixBdSphere::initial_integrate(int /* vflag */) +void FixBrownianSphere::initial_integrate(int /* vflag */) { double **x = atom->x; double **v = atom->v; @@ -270,7 +270,7 @@ void FixBdSphere::initial_integrate(int /* vflag */) apply random force, stolen from MISC/fix_efield.cpp ------------------------------------------------------------------------- */ -void FixBdSphere::post_force(int vflag) +void FixBrownianSphere::post_force(int vflag) { double **f = atom->f; double **x = atom->x; @@ -313,7 +313,7 @@ void FixBdSphere::post_force(int vflag) } } -void FixBdSphere::reset_dt() +void FixBrownianSphere::reset_dt() { dt = update->dt; diff --git a/src/USER-MISC/fix_bd_sphere.h b/src/USER-BROWNIAN/fix_brownian_sphere.h similarity index 70% rename from src/USER-MISC/fix_bd_sphere.h rename to src/USER-BROWNIAN/fix_brownian_sphere.h index 8a3df214a6..8d30001fdd 100644 --- a/src/USER-MISC/fix_bd_sphere.h +++ b/src/USER-BROWNIAN/fix_brownian_sphere.h @@ -13,21 +13,21 @@ #ifdef FIX_CLASS -FixStyle(bd/sphere,FixBdSphere) +FixStyle(brownian/sphere,FixBrownianSphere) #else -#ifndef LMP_FIX_BD_SPHERE_H -#define LMP_FIX_BD_SPHERE_H +#ifndef LMP_FIX_BROWNIAN_SPHERE_H +#define LMP_FIX_BROWNIAN_SPHERE_H #include "fix.h" namespace LAMMPS_NS { -class FixBdSphere : public Fix { +class FixBrownianSphere : public Fix { public: - FixBdSphere(class LAMMPS *, int, char **); - virtual ~FixBdSphere(); + FixBrownianSphere(class LAMMPS *, int, char **); + virtual ~FixBrownianSphere(); void init(); void initial_integrate(int); void setup(int); @@ -61,34 +61,34 @@ protected: /* ERROR/WARNING messages: -E: Illegal fix bd/sphere command. +E: Illegal fix brownian/sphere command. Wrong number/type of input arguments. -E: Compute bd/sphere requires atom style sphere +E: Compute brownian/sphere requires atom style sphere Self-explanatory. -E: Compute bd/sphere requires atom attribute mu +E: Compute brownian/sphere requires atom attribute mu Self-explanatory. -E: Fix bd/sphere translational viscous drag coefficient must be > 0. +E: Fix brownian/sphere translational viscous drag coefficient must be > 0. Self-explanatory. -E: Fix bd/sphere rotational viscous drag coefficient must be > 0. +E: Fix brownian/sphere rotational viscous drag coefficient must be > 0. Self-explanatory. -E: Fix bd/sphere translational diffusion coefficient must be > 0. +E: Fix brownian/sphere translational diffusion coefficient must be > 0. Self-explanatory. -E: Fix bd/sphere rotational diffusion coefficient must be > 0. +E: Fix brownian/sphere rotational diffusion coefficient must be > 0. Self-explanatory. -E: Fix bd/sphere seed must be > 0. +E: Fix brownian/sphere seed must be > 0. */ diff --git a/src/USER-MISC/README b/src/USER-MISC/README index ac41d60dfd..538fdb7952 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -53,8 +53,6 @@ dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18 fix accelerate/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 -fix bd/sphere, Sam Cameron (U of Bristol), samuel.j.m.cameron at gmail.com, 13 Dec 2020 -fix bd/asphere, Sam Cameron (U of Bristol), samuel.j.m.cameron at gmail.com, 13 Dec 2020 fix electron/stopping/fit, James Stewart (SNL), jstewa .at. sandia.gov, 23 Sep 2020 fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019 fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018 diff --git a/unittest/force-styles/tests/data.bdsphere b/unittest/force-styles/tests/data.brownian similarity index 100% rename from unittest/force-styles/tests/data.bdsphere rename to unittest/force-styles/tests/data.brownian diff --git a/unittest/force-styles/tests/fix-timestep-bd_sphere.yaml b/unittest/force-styles/tests/fix-timestep-brownian.yaml similarity index 97% rename from unittest/force-styles/tests/fix-timestep-bd_sphere.yaml rename to unittest/force-styles/tests/fix-timestep-brownian.yaml index b69f37e206..76477d874e 100644 --- a/unittest/force-styles/tests/fix-timestep-bd_sphere.yaml +++ b/unittest/force-styles/tests/fix-timestep-brownian.yaml @@ -4,12 +4,12 @@ date_generated: Tue Dec 08 12:28:40 2020 epsilon: 1e-12 prerequisites: ! | atom hybrid dipole sphere - fix bd_sphere + fix brownian/sphere pre_commands: ! "" post_commands: ! | - fix test solute bd_sphere 1.0 1.0 1.0 1.0 1049270 dipole + fix test solute brownian/sphere 1.0 1.0 1.0 1.0 1049270 dipole fix_modify test virial yes -input_file: in.bdsphere +input_file: in.brownian natoms: 32 run_pos: ! |2 1 0.8198132185477983 -1.5120221815010249 1.069236010215717 diff --git a/unittest/force-styles/tests/in.bdsphere b/unittest/force-styles/tests/in.brownian similarity index 88% rename from unittest/force-styles/tests/in.bdsphere rename to unittest/force-styles/tests/in.brownian index 1fb583f51d..cf85742e59 100644 --- a/unittest/force-styles/tests/in.bdsphere +++ b/unittest/force-styles/tests/in.brownian @@ -2,7 +2,7 @@ variable newton_pair index on variable newton_bond index on variable units index lj variable input_dir index . -variable data_file index ${input_dir}/data.bdsphere +variable data_file index ${input_dir}/data.brownian variable pair_style index 'zero 8.0' atom_style hybrid dipole sphere From a9c6d6f117a72829823b2a3f99ceca8992086a71 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 14:11:46 -0700 Subject: [PATCH 0050/1217] Removing temporary utilities --- src/compute_property_local.cpp | 48 ++--- src/pair_full_print.cpp | 341 --------------------------------- src/pair_full_print.h | 72 ------- 3 files changed, 15 insertions(+), 446 deletions(-) delete mode 100644 src/pair_full_print.cpp delete mode 100644 src/pair_full_print.h diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp index fd0391831c..651e1190b1 100644 --- a/src/compute_property_local.cpp +++ b/src/compute_property_local.cpp @@ -35,7 +35,7 @@ enum{TYPE,RADIUS}; ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), - vlocal(nullptr), alocal(nullptr), indices(nullptr), pack_choice(nullptr) + vlocal(NULL), alocal(NULL), indices(NULL), pack_choice(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute property/local command"); @@ -233,7 +233,7 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) : // error check - if (atom->molecular == Atom::TEMPLATE && (kindflag == BOND || kindflag == ANGLE || + if (atom->molecular == 2 && (kindflag == BOND || kindflag == ANGLE || kindflag == DIHEDRAL || kindflag == IMPROPER)) error->all(FLERR,"Compute property/local does not (yet) work " "with atom_style template"); @@ -254,8 +254,8 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute property/local requires atom attribute radius"); nmax = 0; - vlocal = nullptr; - alocal = nullptr; + vlocal = NULL; + alocal = NULL; } /* ---------------------------------------------------------------------- */ @@ -273,7 +273,7 @@ ComputePropertyLocal::~ComputePropertyLocal() void ComputePropertyLocal::init() { if (kindflag == NEIGH || kindflag == PAIR) { - if (force->pair == nullptr) + if (force->pair == NULL) error->all(FLERR,"No pair style is defined for compute property/local"); if (force->pair->single_enable == 0) error->all(FLERR,"Pair style does not support compute property/local"); @@ -665,16 +665,12 @@ double ComputePropertyLocal::memory_usage() void ComputePropertyLocal::pack_patom1(int n) { - int i,j; + int i; tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { i = indices[m][0]; - j = indices[m][1]; - if(tag[i] < tag[j]) - buf[n] = tag[i]; - else - buf[n] = tag[j]; + buf[n] = tag[i]; n += nvalues; } } @@ -683,16 +679,12 @@ void ComputePropertyLocal::pack_patom1(int n) void ComputePropertyLocal::pack_patom2(int n) { - int i,j; + int i; tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { - i = indices[m][0]; - j = indices[m][1]; - if(tag[i] > tag[j]) - buf[n] = tag[i]; - else - buf[n] = tag[j]; + i = indices[m][1]; + buf[n] = tag[i]; n += nvalues; } } @@ -701,17 +693,12 @@ void ComputePropertyLocal::pack_patom2(int n) void ComputePropertyLocal::pack_ptype1(int n) { - int i,j; + int i; int *type = atom->type; - tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { i = indices[m][0]; - j = indices[m][1]; - if(tag[i] < tag[j]) - buf[n] = type[i]; - else - buf[n] = type[j]; + buf[n] = type[i]; n += nvalues; } } @@ -720,17 +707,12 @@ void ComputePropertyLocal::pack_ptype1(int n) void ComputePropertyLocal::pack_ptype2(int n) { - int i,j; + int i; int *type = atom->type; - tagint *tag = atom->tag; for (int m = 0; m < ncount; m++) { - i = indices[m][0]; - j = indices[m][1]; - if(tag[i] > tag[j]) - buf[n] = type[i]; - else - buf[n] = type[j]; + i = indices[m][1]; + buf[n] = type[i]; n += nvalues; } } diff --git a/src/pair_full_print.cpp b/src/pair_full_print.cpp deleted file mode 100644 index bf42a81288..0000000000 --- a/src/pair_full_print.cpp +++ /dev/null @@ -1,341 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "pair_full_print.h" - -#include -#include -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "neighbor.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" - - -using namespace LAMMPS_NS; -using namespace MathConst; - -/* ---------------------------------------------------------------------- */ - -PairFullPrint::PairFullPrint(LAMMPS *lmp) : Pair(lmp) -{ - writedata = 1; -} - -/* ---------------------------------------------------------------------- */ - -PairFullPrint::~PairFullPrint() -{ - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - - memory->destroy(prefactor); - memory->destroy(cut); - } -} - -/* ---------------------------------------------------------------------- */ - -void PairFullPrint::compute(int eflag, int vflag) -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; - double r,rsq,arg,factor_lj; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = 0.0; - ev_init(eflag,vflag); - - double **x = atom->x; - double **f = atom->f; - tagint *tag = atom->tag; - int *type = atom->type; - int nlocal = atom->nlocal; - double *special_lj = force->special_lj; - int newton_pair = force->newton_pair; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // loop over neighbors of my atoms - - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - factor_lj = special_lj[sbmask(j)]; - j &= NEIGHMASK; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - jtype = type[j]; - - if (rsq < cutsq[itype][jtype]) { - printf("NLIST %d %d %d %d\n", tag[i], tag[j], type[i], type[j]); - r = sqrt(rsq); - arg = MY_PI*r/cut[itype][jtype]; - if (r > 0.0) fpair = factor_lj * prefactor[itype][jtype] * - sin(arg) * MY_PI/cut[itype][jtype]/r; - else fpair = 0.0; - - f[i][0] += delx*fpair; - f[i][1] += dely*fpair; - f[i][2] += delz*fpair; - - if (eflag) - evdwl = factor_lj * prefactor[itype][jtype] * (1.0+cos(arg)); - - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,0.0,fpair,delx,dely,delz); - } - } - } - - if (vflag_fdotr) virial_fdotr_compute(); -} - -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ - -void PairFullPrint::allocate() -{ - allocated = 1; - int n = atom->ntypes; - - memory->create(setflag,n+1,n+1,"pair:setflag"); - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - - memory->create(prefactor,n+1,n+1,"pair:prefactor"); - memory->create(cut,n+1,n+1,"pair:cut"); -} - -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ - -void PairFullPrint::settings(int narg, char **arg) -{ - if (narg != 1) error->all(FLERR,"Illegal pair_style command"); - - cut_global = utils::numeric(FLERR,arg[0],false,lmp); - - // reset cutoffs that have been explicitly set - - if (allocated) { - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) - if (setflag[i][j]) cut[i][j] = cut_global; - } -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairFullPrint::coeff(int narg, char **arg) -{ - if (narg < 3 || narg > 4) - error->all(FLERR,"Incorrect args for pair coefficients"); - if (!allocated) allocate(); - - int ilo,ihi,jlo,jhi; - utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); - utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); - - double prefactor_one = utils::numeric(FLERR,arg[2],false,lmp); - - double cut_one = cut_global; - if (narg == 4) cut_one = utils::numeric(FLERR,arg[3],false,lmp); - - int count = 0; - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - prefactor[i][j] = prefactor_one; - cut[i][j] = cut_one; - setflag[i][j] = 1; - count++; - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - -/* ---------------------------------------------------------------------- - init specific to this pair style - ------------------------------------------------------------------------- */ - -void PairFullPrint::init_style() { - // need a full neighbor list - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; -} - - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairFullPrint::init_one(int i, int j) -{ - // always mix prefactors geometrically - - if (setflag[i][j] == 0) { - prefactor[i][j] = sqrt(prefactor[i][i]*prefactor[j][j]); - cut[i][j] = mix_distance(cut[i][i],cut[j][j]); - } - - prefactor[j][i] = prefactor[i][j]; - cut[j][i] = cut[i][j]; - - return cut[i][j]; -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairFullPrint::write_restart(FILE *fp) -{ - write_restart_settings(fp); - - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) { - fwrite(&setflag[i][j],sizeof(int),1,fp); - if (setflag[i][j]) { - fwrite(&prefactor[i][j],sizeof(double),1,fp); - fwrite(&cut[i][j],sizeof(double),1,fp); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairFullPrint::read_restart(FILE *fp) -{ - read_restart_settings(fp); - - allocate(); - - int i,j; - int me = comm->me; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) { - if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); - if (setflag[i][j]) { - if (me == 0) { - utils::sfread(FLERR,&prefactor[i][j],sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); - } - MPI_Bcast(&prefactor[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairFullPrint::write_restart_settings(FILE *fp) -{ - fwrite(&cut_global,sizeof(double),1,fp); - fwrite(&mix_flag,sizeof(int),1,fp); -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairFullPrint::read_restart_settings(FILE *fp) -{ - if (comm->me == 0) { - utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); - } - MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); - MPI_Bcast(&mix_flag,1,MPI_INT,0,world); -} - -/* ---------------------------------------------------------------------- - proc 0 writes to data file -------------------------------------------------------------------------- */ - -void PairFullPrint::write_data(FILE *fp) -{ - for (int i = 1; i <= atom->ntypes; i++) - fprintf(fp,"%d %g\n",i,prefactor[i][i]); -} - -/* ---------------------------------------------------------------------- - proc 0 writes all pairs to data file -------------------------------------------------------------------------- */ - -void PairFullPrint::write_data_all(FILE *fp) -{ - for (int i = 1; i <= atom->ntypes; i++) - for (int j = i; j <= atom->ntypes; j++) - fprintf(fp,"%d %d %g %g\n",i,j,prefactor[i][j],cut[i][j]); -} - -/* ---------------------------------------------------------------------- */ - -double PairFullPrint::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, - double /*factor_coul*/, double factor_lj, - double &fforce) -{ - double r,arg,philj; - - r = sqrt(rsq); - arg = MY_PI*r/cut[itype][jtype]; - fforce = factor_lj * prefactor[itype][jtype] * - sin(arg) * MY_PI/cut[itype][jtype]/r; - - philj = prefactor[itype][jtype] * (1.0+cos(arg)); - return factor_lj*philj; -} - -/* ---------------------------------------------------------------------- */ - -void *PairFullPrint::extract(const char *str, int &dim) -{ - dim = 2; - if (strcmp(str,"a") == 0) return (void *) prefactor; - return nullptr; -} diff --git a/src/pair_full_print.h b/src/pair_full_print.h deleted file mode 100644 index 31b51f4e97..0000000000 --- a/src/pair_full_print.h +++ /dev/null @@ -1,72 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef PAIR_CLASS - -PairStyle(full/print,PairFullPrint) - -#else - -#ifndef LMP_PAIR_FULL_PRINT_H -#define LMP_PAIR_FULL_PRINT_H - -#include "pair.h" - -namespace LAMMPS_NS { - -class PairFullPrint : public Pair { - friend class Pair; - - public: - PairFullPrint(class LAMMPS *); - virtual ~PairFullPrint(); - void init_style(); - virtual void compute(int, int); - void settings(int, char **); - void coeff(int, char **); - double init_one(int, int); - void write_restart(FILE *); - void read_restart(FILE *); - void write_restart_settings(FILE *); - void read_restart_settings(FILE *); - void write_data(FILE *); - void write_data_all(FILE *); - double single(int, int, int, int, double, double, double, double &); - void *extract(const char *, int &); - - protected: - double cut_global; - double **prefactor; - double **cut; - - void allocate(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Incorrect args for pair coefficients - -Self-explanatory. Check the input script or data file. - -*/ From 0549da668d1556dddcd49c5f031732ff82dda0ca Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 16:06:47 -0700 Subject: [PATCH 0051/1217] Renaming multi->multi/old, updating lmpcite --- ...i_omp.cpp => npair_full_multi_old_omp.cpp} | 6 +-- ...multi_omp.h => npair_full_multi_old_omp.h} | 16 +++---- ...p => npair_half_multi_old_newtoff_omp.cpp} | 6 +-- ...p.h => npair_half_multi_old_newtoff_omp.h} | 16 +++---- ...pp => npair_half_multi_old_newton_omp.cpp} | 6 +-- ...mp.h => npair_half_multi_old_newton_omp.h} | 16 +++---- ...> npair_half_multi_old_newton_tri_omp.cpp} | 6 +-- ... => npair_half_multi_old_newton_tri_omp.h} | 16 +++---- .../npair_half_size_multi_newton_omp.h | 43 ----------------- .../npair_half_size_multi_newton_tri_omp.h | 43 ----------------- ...npair_half_size_multi_old_newtoff_omp.cpp} | 6 +-- ...> npair_half_size_multi_old_newtoff_omp.h} | 16 +++---- ... npair_half_size_multi_old_newton_omp.cpp} | 6 +-- .../npair_half_size_multi_old_newton_omp.h | 43 +++++++++++++++++ ...ir_half_size_multi_old_newton_tri_omp.cpp} | 6 +-- ...npair_half_size_multi_old_newton_tri_omp.h | 43 +++++++++++++++++ src/USER-OMP/npair_halffull_newtoff_omp.h | 4 +- src/USER-OMP/npair_halffull_newton_omp.h | 4 +- src/USER-OMP/npair_skip_omp.h | 12 ++--- src/comm.h | 2 +- src/nbin_standard.cpp | 2 +- src/neighbor.cpp | 41 +++++++++++++---- src/neighbor.h | 10 ++-- ...ull_multi.cpp => npair_full_multi_old.cpp} | 6 +-- ...ir_full_multi.h => npair_full_multi_old.h} | 16 +++---- ...f.cpp => npair_half_multi_old_newtoff.cpp} | 6 +-- ...ewton.h => npair_half_multi_old_newtoff.h} | 16 +++---- ...on.cpp => npair_half_multi_old_newton.cpp} | 6 +-- ...ewtoff.h => npair_half_multi_old_newton.h} | 16 +++---- ...pp => npair_half_multi_old_newton_tri.cpp} | 6 +-- ...ri.h => npair_half_multi_old_newton_tri.h} | 16 +++---- src/npair_half_size_multi_newtoff.h | 46 ------------------- src/npair_half_size_multi_newton.h | 46 ------------------- src/npair_half_size_multi_newton_tri.h | 46 ------------------- ... => npair_half_size_multi_old_newtoff.cpp} | 6 +-- src/npair_half_size_multi_old_newtoff.h | 46 +++++++++++++++++++ ...p => npair_half_size_multi_old_newton.cpp} | 6 +-- src/npair_half_size_multi_old_newton.h | 46 +++++++++++++++++++ ... npair_half_size_multi_old_newton_tri.cpp} | 8 ++-- src/npair_half_size_multi_old_newton_tri.h | 46 +++++++++++++++++++ src/npair_halffull_newtoff.h | 8 ++-- src/npair_halffull_newton.h | 4 +- src/npair_skip.h | 4 +- src/npair_skip_respa.h | 2 +- src/npair_skip_size.h | 2 +- src/npair_skip_size_off2on.h | 2 +- src/npair_skip_size_off2on_oneside.h | 2 +- 47 files changed, 399 insertions(+), 378 deletions(-) rename src/USER-OMP/{npair_full_multi_omp.cpp => npair_full_multi_old_omp.cpp} (96%) rename src/USER-OMP/{npair_full_multi_omp.h => npair_full_multi_old_omp.h} (73%) rename src/USER-OMP/{npair_half_multi_newtoff_omp.cpp => npair_half_multi_old_newtoff_omp.cpp} (95%) rename src/USER-OMP/{npair_half_multi_newton_tri_omp.h => npair_half_multi_old_newtoff_omp.h} (67%) rename src/USER-OMP/{npair_half_multi_newton_omp.cpp => npair_half_multi_old_newton_omp.cpp} (96%) rename src/USER-OMP/{npair_half_multi_newton_omp.h => npair_half_multi_old_newton_omp.h} (68%) rename src/USER-OMP/{npair_half_multi_newton_tri_omp.cpp => npair_half_multi_old_newton_tri_omp.cpp} (96%) rename src/USER-OMP/{npair_half_multi_newtoff_omp.h => npair_half_multi_old_newton_tri_omp.h} (67%) delete mode 100644 src/USER-OMP/npair_half_size_multi_newton_omp.h delete mode 100644 src/USER-OMP/npair_half_size_multi_newton_tri_omp.h rename src/USER-OMP/{npair_half_size_multi_newtoff_omp.cpp => npair_half_size_multi_old_newtoff_omp.cpp} (95%) rename src/USER-OMP/{npair_half_size_multi_newtoff_omp.h => npair_half_size_multi_old_newtoff_omp.h} (67%) rename src/USER-OMP/{npair_half_size_multi_newton_omp.cpp => npair_half_size_multi_old_newton_omp.cpp} (95%) create mode 100644 src/USER-OMP/npair_half_size_multi_old_newton_omp.h rename src/USER-OMP/{npair_half_size_multi_newton_tri_omp.cpp => npair_half_size_multi_old_newton_tri_omp.cpp} (95%) create mode 100644 src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h rename src/{npair_full_multi.cpp => npair_full_multi_old.cpp} (96%) rename src/{npair_full_multi.h => npair_full_multi_old.h} (73%) rename src/{npair_half_multi_newtoff.cpp => npair_half_multi_old_newtoff.cpp} (95%) rename src/{npair_half_multi_newton.h => npair_half_multi_old_newtoff.h} (71%) rename src/{npair_half_multi_newton.cpp => npair_half_multi_old_newton.cpp} (96%) rename src/{npair_half_multi_newtoff.h => npair_half_multi_old_newton.h} (72%) rename src/{npair_half_multi_newton_tri.cpp => npair_half_multi_old_newton_tri.cpp} (96%) rename src/{npair_half_multi_newton_tri.h => npair_half_multi_old_newton_tri.h} (70%) delete mode 100644 src/npair_half_size_multi_newtoff.h delete mode 100644 src/npair_half_size_multi_newton.h delete mode 100644 src/npair_half_size_multi_newton_tri.h rename src/{npair_half_size_multi_newtoff.cpp => npair_half_size_multi_old_newtoff.cpp} (94%) create mode 100644 src/npair_half_size_multi_old_newtoff.h rename src/{npair_half_size_multi_newton.cpp => npair_half_size_multi_old_newton.cpp} (95%) create mode 100644 src/npair_half_size_multi_old_newton.h rename src/{npair_half_size_multi_newton_tri.cpp => npair_half_size_multi_old_newton_tri.cpp} (92%) create mode 100644 src/npair_half_size_multi_old_newton_tri.h diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_old_omp.cpp similarity index 96% rename from src/USER-OMP/npair_full_multi_omp.cpp rename to src/USER-OMP/npair_full_multi_old_omp.cpp index ce17b4a5a9..ef4c4ef5e4 100644 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_old_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_full_multi_omp.h" +#include "npair_full_multi_old_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,7 +26,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {} +NPairFullMultiOldOmp::NPairFullMultiOldOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors @@ -34,7 +34,7 @@ NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {} every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ -void NPairFullMultiOmp::build(NeighList *list) +void NPairFullMultiOldOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; diff --git a/src/USER-OMP/npair_full_multi_omp.h b/src/USER-OMP/npair_full_multi_old_omp.h similarity index 73% rename from src/USER-OMP/npair_full_multi_omp.h rename to src/USER-OMP/npair_full_multi_old_omp.h index 882e649183..2c1711f257 100644 --- a/src/USER-OMP/npair_full_multi_omp.h +++ b/src/USER-OMP/npair_full_multi_old_omp.h @@ -13,24 +13,24 @@ #ifdef NPAIR_CLASS -NPairStyle(full/multi/omp, - NPairFullMultiOmp, - NP_FULL | NP_MULTI | NP_OMP | +NPairStyle(full/multi/old/omp, + NPairFullMultiOldOmp, + NP_FULL | NP_MULTI_OLD | NP_OMP | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_FULL_MULTI_OMP_H -#define LMP_NPAIR_FULL_MULTI_OMP_H +#ifndef LMP_NPAIR_FULL_MULTI_OLD_OMP_H +#define LMP_NPAIR_FULL_MULTI_OLD_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairFullMultiOmp : public NPair { +class NPairFullMultiOldOmp : public NPair { public: - NPairFullMultiOmp(class LAMMPS *); - ~NPairFullMultiOmp() {} + NPairFullMultiOldOmp(class LAMMPS *); + ~NPairFullMultiOldOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp similarity index 95% rename from src/USER-OMP/npair_half_multi_newtoff_omp.cpp rename to src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp index 2bc90838d6..2839ebfa14 100644 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_multi_newtoff_omp.h" +#include "npair_half_multi_old_newtoff_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,7 +26,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMultiNewtoffOmp::NPairHalfMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiOldNewtoffOmp::NPairHalfMultiOldNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law @@ -36,7 +36,7 @@ NPairHalfMultiNewtoffOmp::NPairHalfMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfMultiNewtoffOmp::build(NeighList *list) +void NPairHalfMultiOldNewtoffOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.h b/src/USER-OMP/npair_half_multi_old_newtoff_omp.h similarity index 67% rename from src/USER-OMP/npair_half_multi_newton_tri_omp.h rename to src/USER-OMP/npair_half_multi_old_newtoff_omp.h index 80faf8188f..0487be35ef 100644 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.h +++ b/src/USER-OMP/npair_half_multi_old_newtoff_omp.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi/newton/tri/omp, - NPairHalfMultiNewtonTriOmp, - NP_HALF | NP_MULTI | NP_NEWTON | NP_TRI | NP_OMP) +NPairStyle(half/multi/old/newtoff/omp, + NPairHalfMultiOldNewtoffOmp, + NP_HALF | NP_MULTI_OLD | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_TRI_OMP_H -#define LMP_NPAIR_HALF_MULTI_NEWTON_TRI_OMP_H +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_OMP_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMultiNewtonTriOmp : public NPair { +class NPairHalfMultiOldNewtoffOmp : public NPair { public: - NPairHalfMultiNewtonTriOmp(class LAMMPS *); - ~NPairHalfMultiNewtonTriOmp() {} + NPairHalfMultiOldNewtoffOmp(class LAMMPS *); + ~NPairHalfMultiOldNewtoffOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_old_newton_omp.cpp similarity index 96% rename from src/USER-OMP/npair_half_multi_newton_omp.cpp rename to src/USER-OMP/npair_half_multi_old_newton_omp.cpp index dbaad2adec..bc77cc518b 100644 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_old_newton_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_multi_newton_omp.h" +#include "npair_half_multi_old_newton_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,7 +26,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMultiNewtonOmp::NPairHalfMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiOldNewtonOmp::NPairHalfMultiOldNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law @@ -35,7 +35,7 @@ NPairHalfMultiNewtonOmp::NPairHalfMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMultiNewtonOmp::build(NeighList *list) +void NPairHalfMultiOldNewtonOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; diff --git a/src/USER-OMP/npair_half_multi_newton_omp.h b/src/USER-OMP/npair_half_multi_old_newton_omp.h similarity index 68% rename from src/USER-OMP/npair_half_multi_newton_omp.h rename to src/USER-OMP/npair_half_multi_old_newton_omp.h index 85df36bb09..145ef9d0be 100644 --- a/src/USER-OMP/npair_half_multi_newton_omp.h +++ b/src/USER-OMP/npair_half_multi_old_newton_omp.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi/newton/omp, - NPairHalfMultiNewtonOmp, - NP_HALF | NP_MULTI | NP_NEWTON | NP_OMP | NP_ORTHO) +NPairStyle(half/multi/old/newton/omp, + NPairHalfMultiOldNewtonOmp, + NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_OMP | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_OMP_H -#define LMP_NPAIR_HALF_MULTI_NEWTON_OMP_H +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_OMP_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMultiNewtonOmp : public NPair { +class NPairHalfMultiOldNewtonOmp : public NPair { public: - NPairHalfMultiNewtonOmp(class LAMMPS *); - ~NPairHalfMultiNewtonOmp() {} + NPairHalfMultiOldNewtonOmp(class LAMMPS *); + ~NPairHalfMultiOldNewtonOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp similarity index 96% rename from src/USER-OMP/npair_half_multi_newton_tri_omp.cpp rename to src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp index dd219a616e..3d5a577396 100644 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_multi_newton_tri_omp.h" +#include "npair_half_multi_old_newton_tri_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,7 +26,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMultiNewtonTriOmp::NPairHalfMultiNewtonTriOmp(LAMMPS *lmp) : +NPairHalfMultiOldNewtonTriOmp::NPairHalfMultiOldNewtonTriOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- @@ -36,7 +36,7 @@ NPairHalfMultiNewtonTriOmp::NPairHalfMultiNewtonTriOmp(LAMMPS *lmp) : every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMultiNewtonTriOmp::build(NeighList *list) +void NPairHalfMultiOldNewtonTriOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.h b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.h similarity index 67% rename from src/USER-OMP/npair_half_multi_newtoff_omp.h rename to src/USER-OMP/npair_half_multi_old_newton_tri_omp.h index a7aebf6579..29bb456570 100644 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.h +++ b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi/newtoff/omp, - NPairHalfMultiNewtoffOmp, - NP_HALF | NP_MULTI | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) +NPairStyle(half/multi/old/newton/tri/omp, + NPairHalfMultiOldNewtonTriOmp, + NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_TRI | NP_OMP) #else -#ifndef LMP_NPAIR_HALF_MULTI_NEWTOFF_OMP_H -#define LMP_NPAIR_HALF_MULTI_NEWTOFF_OMP_H +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_OMP_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMultiNewtoffOmp : public NPair { +class NPairHalfMultiOldNewtonTriOmp : public NPair { public: - NPairHalfMultiNewtoffOmp(class LAMMPS *); - ~NPairHalfMultiNewtoffOmp() {} + NPairHalfMultiOldNewtonTriOmp(class LAMMPS *); + ~NPairHalfMultiOldNewtonTriOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.h b/src/USER-OMP/npair_half_size_multi_newton_omp.h deleted file mode 100644 index 03d712145f..0000000000 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi/newton/omp, - NPairHalfSizeMultiNewtonOmp, - NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_OMP | NP_ORTHO) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_OMP_H -#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_OMP_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMultiNewtonOmp : public NPair { - public: - NPairHalfSizeMultiNewtonOmp(class LAMMPS *); - ~NPairHalfSizeMultiNewtonOmp() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h deleted file mode 100644 index 6e936c8da4..0000000000 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi/newton/tri/omp, - NPairHalfSizeMultiNewtonTriOmp, - NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_TRI | NP_OMP) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_OMP_H -#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_OMP_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMultiNewtonTriOmp : public NPair { - public: - NPairHalfSizeMultiNewtonTriOmp(class LAMMPS *); - ~NPairHalfSizeMultiNewtonTriOmp() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp similarity index 95% rename from src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp rename to src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp index 33722eb9d3..e3001185c1 100644 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_size_multi_newtoff_omp.h" +#include "npair_half_size_multi_old_newtoff_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) : +NPairHalfSizeMultiNewtoffOldOmp::NPairHalfSizeMultiNewtoffOldOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- @@ -36,7 +36,7 @@ NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) : pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) +void NPairHalfSizeMultiNewtoffOldOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.h b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.h similarity index 67% rename from src/USER-OMP/npair_half_size_multi_newtoff_omp.h rename to src/USER-OMP/npair_half_size_multi_old_newtoff_omp.h index dd883d7f3c..b7a7d9f4ac 100644 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.h +++ b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.h @@ -13,24 +13,24 @@ #ifdef NPAIR_CLASS -NPairStyle(half/size/multi/newtoff/omp, - NPairHalfSizeMultiNewtoffOmp, - NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_OMP | +NPairStyle(half/size/multi/old/newtoff/omp, + NPairHalfSizeMultiOldNewtoffOmp, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_OMP_H -#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_OMP_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfSizeMultiNewtoffOmp : public NPair { +class NPairHalfSizeMultiOldNewtoffOmp : public NPair { public: - NPairHalfSizeMultiNewtoffOmp(class LAMMPS *); - ~NPairHalfSizeMultiNewtoffOmp() {} + NPairHalfSizeMultiOldNewtoffOmp(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtoffOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp similarity index 95% rename from src/USER-OMP/npair_half_size_multi_newton_omp.cpp rename to src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp index 0be87457e3..ee166a57cf 100644 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_size_multi_newton_omp.h" +#include "npair_half_size_multi_old_newton_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) : +NPairHalfSizeMultiNewtonOldOmp::NPairHalfSizeMultiNewtonOldOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- @@ -35,7 +35,7 @@ NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) : every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) +void NPairHalfSizeMultiNewtonOldOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_omp.h b/src/USER-OMP/npair_half_size_multi_old_newton_omp.h new file mode 100644 index 0000000000..7573b8c89e --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi_old_newton_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/old/newton/omp, + NPairHalfSizeMultiOldNewtonOmp, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTON | NP_OMP | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewtonOmp : public NPair { + public: + NPairHalfSizeMultiOldNewtonOmp(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtonOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp similarity index 95% rename from src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp rename to src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp index ef26a5f2bd..81e896db6c 100644 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_size_multi_newton_tri_omp.h" +#include "npair_half_size_multi_old_newton_tri_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtonTriOmp::NPairHalfSizeMultiNewtonTriOmp(LAMMPS *lmp) : +NPairHalfSizeMultiOldNewtonTriOmp::NPairHalfSizeMultiOldNewtonTriOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- @@ -35,7 +35,7 @@ NPairHalfSizeMultiNewtonTriOmp::NPairHalfSizeMultiNewtonTriOmp(LAMMPS *lmp) : every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) +void NPairHalfSizeMultiOldNewtonTriOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h new file mode 100644 index 0000000000..4cd1c58e6f --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/old/newton/tri/omp, + NPairHalfSizeMultiOldNewtonTriOmp, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTON | NP_TRI | NP_OMP) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_TRI_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_TRI_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewtonTriOmp : public NPair { + public: + NPairHalfSizeMultiOldNewtonTriOmp(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtonTriOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.h b/src/USER-OMP/npair_halffull_newtoff_omp.h index 961544a952..010921d13e 100644 --- a/src/USER-OMP/npair_halffull_newtoff_omp.h +++ b/src/USER-OMP/npair_halffull_newtoff_omp.h @@ -15,12 +15,12 @@ NPairStyle(halffull/newtoff/omp, NPairHalffullNewtoffOmp, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI |NP_OMP) NPairStyle(halffull/newtoff/skip/omp, NPairHalffullNewtoffOmp, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI | NP_SKIP | NP_OMP) #else diff --git a/src/USER-OMP/npair_halffull_newton_omp.h b/src/USER-OMP/npair_halffull_newton_omp.h index ef8be32a74..88dbc3653b 100644 --- a/src/USER-OMP/npair_halffull_newton_omp.h +++ b/src/USER-OMP/npair_halffull_newton_omp.h @@ -15,12 +15,12 @@ NPairStyle(halffull/newton/omp, NPairHalffullNewtonOmp, - NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_ORTHO | NP_TRI| NP_OMP) NPairStyle(halffull/newton/skip/omp, NPairHalffullNewtonOmp, - NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_ORTHO | NP_TRI | NP_SKIP | NP_OMP) #else diff --git a/src/USER-OMP/npair_skip_omp.h b/src/USER-OMP/npair_skip_omp.h index a6ee1930d4..c080296e36 100644 --- a/src/USER-OMP/npair_skip_omp.h +++ b/src/USER-OMP/npair_skip_omp.h @@ -19,36 +19,36 @@ NPairStyle(skip/omp, NPairSkip, NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/half/respa/omp, NPairSkipRespa, NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/half/size/omp, NPairSkipSize, - NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | + NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/size/off2on/omp, NPairSkipSizeOff2on, NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/size/off2on/oneside/omp, NPairSkipSizeOff2onOneside, NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON | NP_NEWTOFF | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/ghost/omp, NPairSkip, NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP | NP_GHOST) #endif diff --git a/src/comm.h b/src/comm.h index d8d842ace5..5cd47bd5cd 100644 --- a/src/comm.h +++ b/src/comm.h @@ -152,6 +152,7 @@ class Comm : protected Pointers { int ncores; // # of cores per node int coregrid[3]; // 3d grid of cores within a node int user_coregrid[3]; // user request for cores in each dim + int multi2; // 1 if multi cutoff is intra-type cutoff void init_exchange(); int rendezvous_irregular(int, char *, int, int, int *, @@ -161,7 +162,6 @@ class Comm : protected Pointers { int (*)(int, char *, int &, int *&, char *&, void *), int, char *&, int, void *, int); void rendezvous_stats(int, int, int, int, int, int, bigint); - int multi2; // 1 if multi cutoff is intra-type cutoff public: enum{MULTIPLE}; diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp index 8295a621fb..ebf7114d94 100644 --- a/src/nbin_standard.cpp +++ b/src/nbin_standard.cpp @@ -115,7 +115,7 @@ void NBinStandard::setup_bins(int style) // optimal bin size is roughly 1/2 the cutoff // for BIN style, binsize = 1/2 of max neighbor cutoff - // for MULTI style, binsize = 1/2 of min neighbor cutoff + // for MULTI_OLD style, binsize = 1/2 of min neighbor cutoff // special case of all cutoffs = 0.0, binsize = box size double binsize_optimal; diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 401bd7298b..0854dee227 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -58,6 +58,19 @@ using namespace NeighConst; enum{NONE,ALL,PARTIAL,TEMPLATE}; +static const char cite_neigh_multi_old[] = + "neighbor multi/old command:\n\n" + "@Article{Intveld08,\n" + " author = {P.{\\,}J.~in{\\,}'t~Veld and S.{\\,}J.~Plimpton" + " and G.{\\,}S.~Grest},\n" + " title = {Accurate and Efficient Methods for Modeling Colloidal\n" + " Mixtures in an Explicit Solvent using Molecular Dynamics},\n" + " journal = {Comp.~Phys.~Comm.},\n" + " year = 2008,\n" + " volume = 179,\n" + " pages = {320--329}\n" + "}\n\n"; + static const char cite_neigh_multi[] = "neighbor multi command:\n\n" "@Article{Intveld08,\n" @@ -69,6 +82,13 @@ static const char cite_neigh_multi[] = " year = 2008,\n" " volume = 179,\n" " pages = {320--329}\n" + "}\n\n" + "@article{Shire2020,\n" + " author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},\n" + " title = {DEM simulations of polydisperse media: efficient contact\n" + " detection applied to investigate the quasi-static limit},\n" + " journal = {Computational Particle Mechanics},\n" + " year = {2020}\n" "}\n\n"; //#define NEIGH_LIST_DEBUG 1 @@ -1622,10 +1642,10 @@ int Neighbor::choose_bin(NeighRequest *rq) // neighbor style is BIN or MULTI or MULTI2 and must match - if (style == Neighbor::BIN || style == Neighbor::MULTI) { + if (style == Neighbor::BIN || style == Neighbor::MULTI_OLD) { if (!(mask & NB_STANDARD)) continue; - } else if (style == Neighbor::MULTI2) { - if (!(mask & NB_MULTI2)) continue; + } else if (style == Neighbor::MULTI) { + if (!(mask & NB_MULTI)) continue; } return i+1; @@ -1695,14 +1715,14 @@ int Neighbor::choose_stencil(NeighRequest *rq) if (!rq->ghost != !(mask & NS_GHOST)) continue; if (!rq->ssa != !(mask & NS_SSA)) continue; - // neighbor style is one of BIN, MULTI, or MULTI2 and must match + // neighbor style is one of BIN, MULTI_OLD, or MULTI and must match if (style == Neighbor::BIN) { if (!(mask & NS_BIN)) continue; + } else if (style == Neighbor::MULTI_OLD) { + if (!(mask & NS_MULTI_OLD)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NS_MULTI)) continue; - } else if (style == Neighbor::MULTI2) { - if (!(mask & NS_MULTI2)) continue; } // dimension is 2 or 3 and must match @@ -1832,16 +1852,16 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!rq->halffull != !(mask & NP_HALF_FULL)) continue; if (!rq->off2on != !(mask & NP_OFF2ON)) continue; - // neighbor style is one of NSQ, BIN, MULTI, or MULTI2 and must match + // neighbor style is one of NSQ, BIN, MULTI_OLD, or MULTI and must match if (style == Neighbor::NSQ) { if (!(mask & NP_NSQ)) continue; } else if (style == Neighbor::BIN) { if (!(mask & NP_BIN)) continue; + } else if (style == Neighbor::MULTI_OLD) { + if (!(mask & NP_MULTI_OLD)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NP_MULTI)) continue; - } else if (style == Neighbor::MULTI2) { - if (!(mask & NP_MULTI2)) continue; } // domain triclinic flag is on or off and must match @@ -2211,9 +2231,10 @@ void Neighbor::set(int narg, char **arg) if (strcmp(arg[1],"nsq") == 0) style = Neighbor::NSQ; else if (strcmp(arg[1],"bin") == 0) style = Neighbor::BIN; else if (strcmp(arg[1],"multi") == 0) style = Neighbor::MULTI; - else if (strcmp(arg[1],"multi2") == 0) style = Neighbor::MULTI2; + else if (strcmp(arg[1],"multi/old") == 0) style = Neighbor::MULTI_OLD; else error->all(FLERR,"Illegal neighbor command"); + if (style == Neighbor::MULTI_OLD && lmp->citeme) lmp->citeme->add(cite_neigh_multi_old); if (style == Neighbor::MULTI && lmp->citeme) lmp->citeme->add(cite_neigh_multi); } diff --git a/src/neighbor.h b/src/neighbor.h index b1cc95f5e7..2943f7e082 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -20,8 +20,8 @@ namespace LAMMPS_NS { class Neighbor : protected Pointers { public: - enum{NSQ,BIN,MULTI,MULTI2}; - int style; // 0,1,2 = nsq, bin, multi + enum{NSQ,BIN,MULTI_OLD,MULTI}; + int style; // 0,1,2 = nsq, bin, multi/old, multi int every; // build every this many steps int delay; // delay build for this many steps int dist_check; // 0 = always build, 1 = only if 1/2 dist @@ -239,7 +239,7 @@ namespace NeighConst { static const int NB_KOKKOS_DEVICE = 1<<1; static const int NB_KOKKOS_HOST = 1<<2; static const int NB_SSA = 1<<3; - static const int NB_MULTI2 = 1<<4; + static const int NB_MULTI = 1<<4; static const int NB_STANDARD = 1<<5; static const int NS_BIN = 1<<0; @@ -252,7 +252,7 @@ namespace NeighConst { static const int NS_TRI = 1<<7; static const int NS_GHOST = 1<<8; static const int NS_SSA = 1<<9; - static const int NS_MULTI2 = 1<<10; + static const int NS_MULTI_OLD = 1<<10; static const int NP_NSQ = 1<<0; static const int NP_BIN = 1<<1; @@ -279,7 +279,7 @@ namespace NeighConst { static const int NP_SKIP = 1<<22; static const int NP_HALF_FULL = 1<<23; static const int NP_OFF2ON = 1<<24; - static const int NP_MULTI2 = 1<<25; + static const int NP_MULTI_OLD = 1<<25; } } diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi_old.cpp similarity index 96% rename from src/npair_full_multi.cpp rename to src/npair_full_multi_old.cpp index 79a9c7cec3..9a800a80b5 100644 --- a/src/npair_full_multi.cpp +++ b/src/npair_full_multi_old.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_full_multi.h" +#include "npair_full_multi_old.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairFullMulti::NPairFullMulti(LAMMPS *lmp) : NPair(lmp) {} +NPairFullMultiOld::NPairFullMultiOld(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors @@ -32,7 +32,7 @@ NPairFullMulti::NPairFullMulti(LAMMPS *lmp) : NPair(lmp) {} every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ -void NPairFullMulti::build(NeighList *list) +void NPairFullMultiOld::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; tagint tagprev; diff --git a/src/npair_full_multi.h b/src/npair_full_multi_old.h similarity index 73% rename from src/npair_full_multi.h rename to src/npair_full_multi_old.h index 481a673060..f53b6451e2 100644 --- a/src/npair_full_multi.h +++ b/src/npair_full_multi_old.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(full/multi, - NPairFullMulti, - NP_FULL | NP_MULTI | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) +NPairStyle(full/multi/old, + NPairFullMultiOld, + NP_FULL | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_FULL_MULTI_H -#define LMP_NPAIR_FULL_MULTI_H +#ifndef LMP_NPAIR_FULL_MULTI_OLD_H +#define LMP_NPAIR_FULL_MULTI_OLD_H #include "npair.h" namespace LAMMPS_NS { -class NPairFullMulti : public NPair { +class NPairFullMultiOld : public NPair { public: - NPairFullMulti(class LAMMPS *); - ~NPairFullMulti() {} + NPairFullMultiOld(class LAMMPS *); + ~NPairFullMultiOld() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_old_newtoff.cpp similarity index 95% rename from src/npair_half_multi_newtoff.cpp rename to src/npair_half_multi_old_newtoff.cpp index 3979e494a9..351fd65c32 100644 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_old_newtoff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_multi_newtoff.h" +#include "npair_half_multi_old_newtoff.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiOldNewtoff::NPairHalfMultiOldNewtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law @@ -34,7 +34,7 @@ NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfMultiNewtoff::build(NeighList *list) +void NPairHalfMultiOldNewtoff::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; tagint tagprev; diff --git a/src/npair_half_multi_newton.h b/src/npair_half_multi_old_newtoff.h similarity index 71% rename from src/npair_half_multi_newton.h rename to src/npair_half_multi_old_newtoff.h index 427b771780..7a3e7b3671 100644 --- a/src/npair_half_multi_newton.h +++ b/src/npair_half_multi_old_newtoff.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi/newton, - NPairHalfMultiNewton, - NP_HALF | NP_MULTI | NP_NEWTON | NP_ORTHO) +NPairStyle(half/multi/old/newtoff, + NPairHalfMultiOldNewtoff, + NP_HALF | NP_MULTI_OLD | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_H -#define LMP_NPAIR_HALF_MULTI_NEWTON_H +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMultiNewton : public NPair { +class NPairHalfMultiOldNewtoff : public NPair { public: - NPairHalfMultiNewton(class LAMMPS *); - ~NPairHalfMultiNewton() {} + NPairHalfMultiOldNewtoff(class LAMMPS *); + ~NPairHalfMultiOldNewtoff() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_old_newton.cpp similarity index 96% rename from src/npair_half_multi_newton.cpp rename to src/npair_half_multi_old_newton.cpp index 7ea58d29ad..5af420017d 100644 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_old_newton.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_multi_newton.h" +#include "npair_half_multi_old_newton.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiOldNewton::NPairHalfMultiOldNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law @@ -33,7 +33,7 @@ NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {} every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMultiNewton::build(NeighList *list) +void NPairHalfMultiOldNewton::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; tagint tagprev; diff --git a/src/npair_half_multi_newtoff.h b/src/npair_half_multi_old_newton.h similarity index 72% rename from src/npair_half_multi_newtoff.h rename to src/npair_half_multi_old_newton.h index 593e2c1d9d..337e54abed 100644 --- a/src/npair_half_multi_newtoff.h +++ b/src/npair_half_multi_old_newton.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi/newtoff, - NPairHalfMultiNewtoff, - NP_HALF | NP_MULTI | NP_NEWTOFF | NP_ORTHO | NP_TRI) +NPairStyle(half/multi/old/newton, + NPairHalfMultiOldNewton, + NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_MULTI_NEWTOFF_H -#define LMP_NPAIR_HALF_MULTI_NEWTOFF_H +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMultiNewtoff : public NPair { +class NPairHalfMultiOldNewton : public NPair { public: - NPairHalfMultiNewtoff(class LAMMPS *); - ~NPairHalfMultiNewtoff() {} + NPairHalfMultiOldNewton(class LAMMPS *); + ~NPairHalfMultiOldNewton() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_old_newton_tri.cpp similarity index 96% rename from src/npair_half_multi_newton_tri.cpp rename to src/npair_half_multi_old_newton_tri.cpp index a1095c3fe2..f22e0fbf4f 100644 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_old_newton_tri.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_multi_newton_tri.h" +#include "npair_half_multi_old_newton_tri.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMultiNewtonTri::NPairHalfMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiOldNewtonTri::NPairHalfMultiOldNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic @@ -33,7 +33,7 @@ NPairHalfMultiNewtonTri::NPairHalfMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMultiNewtonTri::build(NeighList *list) +void NPairHalfMultiOldNewtonTri::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; tagint tagprev; diff --git a/src/npair_half_multi_newton_tri.h b/src/npair_half_multi_old_newton_tri.h similarity index 70% rename from src/npair_half_multi_newton_tri.h rename to src/npair_half_multi_old_newton_tri.h index 6fe7577259..3c9202992a 100644 --- a/src/npair_half_multi_newton_tri.h +++ b/src/npair_half_multi_old_newton_tri.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi/newton/tri, - NPairHalfMultiNewtonTri, - NP_HALF | NP_MULTI | NP_NEWTON | NP_TRI) +NPairStyle(half/multi/old/newton/tri, + NPairHalfMultiOldNewtonTri, + NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_TRI_H -#define LMP_NPAIR_HALF_MULTI_NEWTON_TRI_H +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMultiNewtonTri : public NPair { +class NPairHalfMultiOldNewtonTri : public NPair { public: - NPairHalfMultiNewtonTri(class LAMMPS *); - ~NPairHalfMultiNewtonTri() {} + NPairHalfMultiOldNewtonTri(class LAMMPS *); + ~NPairHalfMultiOldNewtonTri() {} void build(class NeighList *); }; diff --git a/src/npair_half_size_multi_newtoff.h b/src/npair_half_size_multi_newtoff.h deleted file mode 100644 index f255f9a17d..0000000000 --- a/src/npair_half_size_multi_newtoff.h +++ /dev/null @@ -1,46 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi/newtoff, - NPairHalfSizeMultiNewtoff, - NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_ORTHO | NP_TRI) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_H -#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMultiNewtoff : public NPair { - public: - NPairHalfSizeMultiNewtoff(class LAMMPS *); - ~NPairHalfSizeMultiNewtoff() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Neighbor list overflow, boost neigh_modify one - -UNDOCUMENTED -*/ diff --git a/src/npair_half_size_multi_newton.h b/src/npair_half_size_multi_newton.h deleted file mode 100644 index 3e3d6f4180..0000000000 --- a/src/npair_half_size_multi_newton.h +++ /dev/null @@ -1,46 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi/newton, - NPairHalfSizeMultiNewton, - NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_ORTHO) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_H -#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMultiNewton : public NPair { - public: - NPairHalfSizeMultiNewton(class LAMMPS *); - ~NPairHalfSizeMultiNewton() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Neighbor list overflow, boost neigh_modify one - -UNDOCUMENTED -*/ diff --git a/src/npair_half_size_multi_newton_tri.h b/src/npair_half_size_multi_newton_tri.h deleted file mode 100644 index 6afe8201a7..0000000000 --- a/src/npair_half_size_multi_newton_tri.h +++ /dev/null @@ -1,46 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi/newton/tri, - NPairHalfSizeMultiNewtonTri, - NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_TRI) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_H -#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMultiNewtonTri : public NPair { - public: - NPairHalfSizeMultiNewtonTri(class LAMMPS *); - ~NPairHalfSizeMultiNewtonTri() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Neighbor list overflow, boost neigh_modify one - -UNDOCUMENTED -*/ diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_old_newtoff.cpp similarity index 94% rename from src/npair_half_size_multi_newtoff.cpp rename to src/npair_half_size_multi_old_newtoff.cpp index 813a642b96..394ad58981 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_old_newtoff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_size_multi_newtoff.h" +#include "npair_half_size_multi_old_newtoff.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -22,7 +22,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiOldNewtoff::NPairHalfSizeMultiOldNewtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles @@ -33,7 +33,7 @@ NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) { pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewtoff::build(NeighList *list) +void NPairHalfSizeMultiOldNewtoff::build(NeighList *list) { int i,j,k,m,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; diff --git a/src/npair_half_size_multi_old_newtoff.h b/src/npair_half_size_multi_old_newtoff.h new file mode 100644 index 0000000000..ca429d8914 --- /dev/null +++ b/src/npair_half_size_multi_old_newtoff.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/old/newtoff, + NPairHalfSizeMultiOldNewtoff, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTOFF | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewtoff : public NPair { + public: + NPairHalfSizeMultiOldNewtoff(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtoff() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_old_newton.cpp similarity index 95% rename from src/npair_half_size_multi_newton.cpp rename to src/npair_half_size_multi_old_newton.cpp index 0d12924629..65b197a86b 100644 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_old_newton.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_size_multi_newton.h" +#include "npair_half_size_multi_old_newton.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -22,7 +22,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiOldNewton::NPairHalfSizeMultiOldNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles @@ -32,7 +32,7 @@ NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {} every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewton::build(NeighList *list) +void NPairHalfSizeMultiOldNewton::build(NeighList *list) { int i,j,k,m,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; diff --git a/src/npair_half_size_multi_old_newton.h b/src/npair_half_size_multi_old_newton.h new file mode 100644 index 0000000000..e954ee07b1 --- /dev/null +++ b/src/npair_half_size_multi_old_newton.h @@ -0,0 +1,46 @@ +g/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/old/newton, + NPairHalfSizeMultiOldNewton, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTON | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewton : public NPair { + public: + NPairHalfSizeMultiOldNewton(class LAMMPS *); + ~NPairHalfSizeMultiOldNewton() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_old_newton_tri.cpp similarity index 92% rename from src/npair_half_size_multi_newton_tri.cpp rename to src/npair_half_size_multi_old_newton_tri.cpp index adc4c080ec..93d3beeb0a 100644 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_old_newton_tri.cpp @@ -1,4 +1,4 @@ -/* ---------------------------------------------------------------------- +re/* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_size_multi_newton_tri.h" +#include "npair_half_size_multi_old_newton_tri.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -22,7 +22,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiOldNewtonTri::NPairHalfSizeMultiOldNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic @@ -31,7 +31,7 @@ NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lm every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewtonTri::build(NeighList *list) +void NPairHalfSizeMultiOldNewtonTri::build(NeighList *list) { int i,j,k,m,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; diff --git a/src/npair_half_size_multi_old_newton_tri.h b/src/npair_half_size_multi_old_newton_tri.h new file mode 100644 index 0000000000..126735e9c8 --- /dev/null +++ b/src/npair_half_size_multi_old_newton_tri.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/old/newton/tri, + NPairHalfSizeMultiOldNewtonTri, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTON | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_TRI_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_TRI_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewtonTri : public NPair { + public: + NPairHalfSizeMultiOldNewtonTri(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtonTri() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ diff --git a/src/npair_halffull_newtoff.h b/src/npair_halffull_newtoff.h index 2f711629be..307156ef13 100644 --- a/src/npair_halffull_newtoff.h +++ b/src/npair_halffull_newtoff.h @@ -15,22 +15,22 @@ NPairStyle(halffull/newtoff, NPairHalffullNewtoff, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI) NPairStyle(halffull/newtoff/skip, NPairHalffullNewtoff, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI | NP_SKIP) NPairStyle(halffull/newtoff/ghost, NPairHalffullNewtoff, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI | NP_GHOST) NPairStyle(halffull/newtoff/skip/ghost, NPairHalffullNewtoff, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI | NP_SKIP | NP_GHOST) #else diff --git a/src/npair_halffull_newton.h b/src/npair_halffull_newton.h index dc82225216..f5f36b9e8c 100644 --- a/src/npair_halffull_newton.h +++ b/src/npair_halffull_newton.h @@ -15,12 +15,12 @@ NPairStyle(halffull/newton, NPairHalffullNewton, - NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_ORTHO | NP_TRI) NPairStyle(halffull/newton/skip, NPairHalffullNewton, - NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_ORTHO | NP_TRI | NP_SKIP) #else diff --git a/src/npair_skip.h b/src/npair_skip.h index 5fde8e7039..aae8abf6e4 100644 --- a/src/npair_skip.h +++ b/src/npair_skip.h @@ -16,13 +16,13 @@ NPairStyle(skip, NPairSkip, NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) NPairStyle(skip/ghost, NPairSkip, NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_GHOST) #else diff --git a/src/npair_skip_respa.h b/src/npair_skip_respa.h index a309d47124..31bcf0b510 100644 --- a/src/npair_skip_respa.h +++ b/src/npair_skip_respa.h @@ -16,7 +16,7 @@ NPairStyle(skip/half/respa, NPairSkipRespa, NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else diff --git a/src/npair_skip_size.h b/src/npair_skip_size.h index ae3f77d6ed..76f810bdc1 100644 --- a/src/npair_skip_size.h +++ b/src/npair_skip_size.h @@ -15,7 +15,7 @@ NPairStyle(skip/half/size, NPairSkipSize, - NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | + NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else diff --git a/src/npair_skip_size_off2on.h b/src/npair_skip_size_off2on.h index 59fc0878ef..7236e9e993 100644 --- a/src/npair_skip_size_off2on.h +++ b/src/npair_skip_size_off2on.h @@ -16,7 +16,7 @@ NPairStyle(skip/size/off2on, NPairSkipSizeOff2on, NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else diff --git a/src/npair_skip_size_off2on_oneside.h b/src/npair_skip_size_off2on_oneside.h index f7ae2338b7..e8b5977a34 100644 --- a/src/npair_skip_size_off2on_oneside.h +++ b/src/npair_skip_size_off2on_oneside.h @@ -16,7 +16,7 @@ NPairStyle(skip/size/off2on/oneside, NPairSkipSizeOff2onOneside, NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON | NP_NEWTOFF | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else From 42278e87665404fa5df52214ffbee9b3934ffb99 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 17:09:11 -0700 Subject: [PATCH 0052/1217] Renaming multi2->multi npair classes, renaming npair multi variables --- src/USER-OMP/npair_full_multi_old_omp.cpp | 6 +- ...ulti2_omp.cpp => npair_full_multi_omp.cpp} | 18 ++--- ...ll_multi2_omp.h => npair_full_multi_omp.h} | 16 ++--- ...p.cpp => npair_half_multi_newtoff_omp.cpp} | 18 ++--- src/USER-OMP/npair_half_multi_newtoff_omp.h | 43 ++++++++++++ ...mp.cpp => npair_half_multi_newton_omp.cpp} | 26 +++---- ...on_omp.h => npair_half_multi_newton_omp.h} | 16 ++--- ...pp => npair_half_multi_newton_tri_omp.cpp} | 18 ++--- .../npair_half_multi_newton_tri_omp.h | 43 ++++++++++++ .../npair_half_multi_old_newtoff_omp.cpp | 6 +- .../npair_half_multi_old_newton_omp.cpp | 6 +- .../npair_half_multi_old_newton_tri_omp.cpp | 6 +- .../npair_half_size_multi2_newtoff_omp.h | 43 ------------ .../npair_half_size_multi2_newton_omp.h | 43 ------------ .../npair_half_size_multi2_newton_tri_omp.h | 43 ------------ ... => npair_half_size_multi_newtoff_omp.cpp} | 18 ++--- ....h => npair_half_size_multi_newtoff_omp.h} | 16 ++--- ...p => npair_half_size_multi_newton_omp.cpp} | 26 +++---- ...p.h => npair_half_size_multi_newton_omp.h} | 16 ++--- ... npair_half_size_multi_newton_tri_omp.cpp} | 18 ++--- .../npair_half_size_multi_newton_tri_omp.h | 43 ++++++++++++ .../npair_half_size_multi_old_newtoff_omp.cpp | 6 +- .../npair_half_size_multi_old_newton_omp.cpp | 6 +- ...air_half_size_multi_old_newton_tri_omp.cpp | 6 +- src/npair.cpp | 70 +++++++++---------- src/npair.h | 24 +++---- ...r_full_multi2.cpp => npair_full_multi.cpp} | 18 ++--- ...npair_full_multi2.h => npair_full_multi.h} | 16 ++--- src/npair_full_multi_old.cpp | 6 +- ...wtoff.cpp => npair_half_multi_newtoff.cpp} | 18 ++--- ...2_newtoff.h => npair_half_multi_newtoff.h} | 16 ++--- ...newton.cpp => npair_half_multi_newton.cpp} | 26 +++---- ...ti2_newton.h => npair_half_multi_newton.h} | 16 ++--- ...ri.cpp => npair_half_multi_newton_tri.cpp} | 18 ++--- ...on_tri.h => npair_half_multi_newton_tri.h} | 16 ++--- src/npair_half_multi_old_newtoff.cpp | 6 +- src/npair_half_multi_old_newton.cpp | 6 +- src/npair_half_multi_old_newton_tri.cpp | 6 +- src/npair_half_size_multi2_newton_tri.h | 47 ------------- ....cpp => npair_half_size_multi_newtoff.cpp} | 18 ++--- ...toff.h => npair_half_size_multi_newtoff.h} | 16 ++--- ...n.cpp => npair_half_size_multi_newton.cpp} | 26 +++---- ...ewton.h => npair_half_size_multi_newton.h} | 16 ++--- ...p => npair_half_size_multi_newton_tri.cpp} | 18 ++--- src/npair_half_size_multi_newton_tri.h | 47 +++++++++++++ src/npair_half_size_multi_old_newtoff.cpp | 6 +- src/npair_half_size_multi_old_newton.cpp | 6 +- src/npair_half_size_multi_old_newton_tri.cpp | 6 +- 48 files changed, 487 insertions(+), 487 deletions(-) rename src/USER-OMP/{npair_full_multi2_omp.cpp => npair_full_multi_omp.cpp} (90%) rename src/USER-OMP/{npair_full_multi2_omp.h => npair_full_multi_omp.h} (75%) rename src/USER-OMP/{npair_half_multi2_newtoff_omp.cpp => npair_half_multi_newtoff_omp.cpp} (90%) create mode 100755 src/USER-OMP/npair_half_multi_newtoff_omp.h rename src/USER-OMP/{npair_half_multi2_newton_omp.cpp => npair_half_multi_newton_omp.cpp} (91%) rename src/USER-OMP/{npair_half_multi2_newton_omp.h => npair_half_multi_newton_omp.h} (69%) rename src/USER-OMP/{npair_half_multi2_newton_tri_omp.cpp => npair_half_multi_newton_tri_omp.cpp} (91%) create mode 100755 src/USER-OMP/npair_half_multi_newton_tri_omp.h delete mode 100755 src/USER-OMP/npair_half_size_multi2_newtoff_omp.h delete mode 100755 src/USER-OMP/npair_half_size_multi2_newton_omp.h delete mode 100755 src/USER-OMP/npair_half_size_multi2_newton_tri_omp.h rename src/USER-OMP/{npair_half_size_multi2_newtoff_omp.cpp => npair_half_size_multi_newtoff_omp.cpp} (88%) rename src/USER-OMP/{npair_half_multi2_newtoff_omp.h => npair_half_size_multi_newtoff_omp.h} (66%) rename src/USER-OMP/{npair_half_size_multi2_newton_omp.cpp => npair_half_size_multi_newton_omp.cpp} (89%) rename src/USER-OMP/{npair_half_multi2_newton_tri_omp.h => npair_half_size_multi_newton_omp.h} (67%) rename src/USER-OMP/{npair_half_size_multi2_newton_tri_omp.cpp => npair_half_size_multi_newton_tri_omp.cpp} (90%) create mode 100755 src/USER-OMP/npair_half_size_multi_newton_tri_omp.h rename src/{npair_full_multi2.cpp => npair_full_multi.cpp} (90%) rename src/{npair_full_multi2.h => npair_full_multi.h} (74%) rename src/{npair_half_multi2_newtoff.cpp => npair_half_multi_newtoff.cpp} (90%) rename src/{npair_half_multi2_newtoff.h => npair_half_multi_newtoff.h} (72%) rename src/{npair_half_multi2_newton.cpp => npair_half_multi_newton.cpp} (91%) rename src/{npair_half_multi2_newton.h => npair_half_multi_newton.h} (71%) rename src/{npair_half_multi2_newton_tri.cpp => npair_half_multi_newton_tri.cpp} (91%) rename src/{npair_half_multi2_newton_tri.h => npair_half_multi_newton_tri.h} (70%) delete mode 100755 src/npair_half_size_multi2_newton_tri.h rename src/{npair_half_size_multi2_newtoff.cpp => npair_half_size_multi_newtoff.cpp} (87%) rename src/{npair_half_size_multi2_newtoff.h => npair_half_size_multi_newtoff.h} (69%) rename src/{npair_half_size_multi2_newton.cpp => npair_half_size_multi_newton.cpp} (89%) rename src/{npair_half_size_multi2_newton.h => npair_half_size_multi_newton.h} (70%) rename src/{npair_half_size_multi2_newton_tri.cpp => npair_half_size_multi_newton_tri.cpp} (89%) create mode 100755 src/npair_half_size_multi_newton_tri.h diff --git a/src/USER-OMP/npair_full_multi_old_omp.cpp b/src/USER-OMP/npair_full_multi_old_omp.cpp index ef4c4ef5e4..46890f6438 100644 --- a/src/USER-OMP/npair_full_multi_old_omp.cpp +++ b/src/USER-OMP/npair_full_multi_old_omp.cpp @@ -94,10 +94,10 @@ void NPairFullMultiOldOmp::build(NeighList *list) // skip i = j ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/USER-OMP/npair_full_multi2_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp similarity index 90% rename from src/USER-OMP/npair_full_multi2_omp.cpp rename to src/USER-OMP/npair_full_multi_omp.cpp index 39f711fe4f..cf897f9dea 100755 --- a/src/USER-OMP/npair_full_multi2_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_full_multi2_omp.h" +#include "npair_full_multi_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,15 +26,15 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairFullMulti2Omp::NPairFullMulti2Omp(LAMMPS *lmp) : NPair(lmp) {} +NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ -void NPairFullMulti2Omp::build(NeighList *list) +void NPairFullMultiOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -89,7 +89,7 @@ void NPairFullMulti2Omp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -102,12 +102,12 @@ void NPairFullMulti2Omp::build(NeighList *list) // skip i = j // use full stencil for all type combinations - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (i == j) continue; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/USER-OMP/npair_full_multi2_omp.h b/src/USER-OMP/npair_full_multi_omp.h similarity index 75% rename from src/USER-OMP/npair_full_multi2_omp.h rename to src/USER-OMP/npair_full_multi_omp.h index d2bc478532..882e649183 100755 --- a/src/USER-OMP/npair_full_multi2_omp.h +++ b/src/USER-OMP/npair_full_multi_omp.h @@ -13,24 +13,24 @@ #ifdef NPAIR_CLASS -NPairStyle(full/multi2/omp, - NPairFullMulti2Omp, - NP_FULL | NP_MULTI2 | NP_OMP | +NPairStyle(full/multi/omp, + NPairFullMultiOmp, + NP_FULL | NP_MULTI | NP_OMP | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_FULL_MULTI2_OMP_H -#define LMP_NPAIR_FULL_MULTI2_OMP_H +#ifndef LMP_NPAIR_FULL_MULTI_OMP_H +#define LMP_NPAIR_FULL_MULTI_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairFullMulti2Omp : public NPair { +class NPairFullMultiOmp : public NPair { public: - NPairFullMulti2Omp(class LAMMPS *); - ~NPairFullMulti2Omp() {} + NPairFullMultiOmp(class LAMMPS *); + ~NPairFullMultiOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp similarity index 90% rename from src/USER-OMP/npair_half_multi2_newtoff_omp.cpp rename to src/USER-OMP/npair_half_multi_newtoff_omp.cpp index bfd0d34a6c..bf7644f01f 100755 --- a/src/USER-OMP/npair_half_multi2_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_multi2_newtoff_omp.h" +#include "npair_half_multi_newtoff_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,17 +26,17 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMulti2NewtoffOmp::NPairHalfMulti2NewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiNewtoffOmp::NPairHalfMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks own bin and other bins in stencil pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfMulti2NewtoffOmp::build(NeighList *list) +void NPairHalfMultiNewtoffOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -91,7 +91,7 @@ void NPairHalfMulti2NewtoffOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -106,12 +106,12 @@ void NPairHalfMulti2NewtoffOmp::build(NeighList *list) // stores own/ghost pairs on both procs // use full stencil for all type combinations - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jtype][j]) { if (j <= i) continue; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.h b/src/USER-OMP/npair_half_multi_newtoff_omp.h new file mode 100755 index 0000000000..a7aebf6579 --- /dev/null +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/multi/newtoff/omp, + NPairHalfMultiNewtoffOmp, + NP_HALF | NP_MULTI | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI_NEWTOFF_OMP_H +#define LMP_NPAIR_HALF_MULTI_NEWTOFF_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMultiNewtoffOmp : public NPair { + public: + NPairHalfMultiNewtoffOmp(class LAMMPS *); + ~NPairHalfMultiNewtoffOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp similarity index 91% rename from src/USER-OMP/npair_half_multi2_newton_omp.cpp rename to src/USER-OMP/npair_half_multi_newton_omp.cpp index cbdbd69f50..c68a3a150f 100755 --- a/src/USER-OMP/npair_half_multi2_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_multi2_newton_omp.h" +#include "npair_half_multi_newton_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,16 +26,16 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMulti2NewtonOmp::NPairHalfMulti2NewtonOmp(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiNewtonOmp::NPairHalfMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMulti2NewtonOmp::build(NeighList *list) +void NPairHalfMultiNewtonOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -90,7 +90,7 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -109,9 +109,9 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - js = bins_multi2[itype][i]; + js = bins_multi[itype][i]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -150,9 +150,9 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi2[jtype][jbin]; + js = binhead_multi[jtype][jbin]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if(j < i) continue; if (j >= nlocal) { @@ -194,12 +194,12 @@ void NPairHalfMulti2NewtonOmp::build(NeighList *list) // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/USER-OMP/npair_half_multi2_newton_omp.h b/src/USER-OMP/npair_half_multi_newton_omp.h similarity index 69% rename from src/USER-OMP/npair_half_multi2_newton_omp.h rename to src/USER-OMP/npair_half_multi_newton_omp.h index 2ea2bd1ad0..85df36bb09 100755 --- a/src/USER-OMP/npair_half_multi2_newton_omp.h +++ b/src/USER-OMP/npair_half_multi_newton_omp.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi2/newton/omp, - NPairHalfMulti2NewtonOmp, - NP_HALF | NP_MULTI2 | NP_NEWTON | NP_OMP | NP_ORTHO) +NPairStyle(half/multi/newton/omp, + NPairHalfMultiNewtonOmp, + NP_HALF | NP_MULTI | NP_NEWTON | NP_OMP | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_OMP_H -#define LMP_NPAIR_HALF_MULTI2_NEWTON_OMP_H +#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_OMP_H +#define LMP_NPAIR_HALF_MULTI_NEWTON_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMulti2NewtonOmp : public NPair { +class NPairHalfMultiNewtonOmp : public NPair { public: - NPairHalfMulti2NewtonOmp(class LAMMPS *); - ~NPairHalfMulti2NewtonOmp() {} + NPairHalfMultiNewtonOmp(class LAMMPS *); + ~NPairHalfMultiNewtonOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp similarity index 91% rename from src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp rename to src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index 5d0d724b58..3f3ac37b6d 100755 --- a/src/USER-OMP/npair_half_multi2_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_multi2_newton_tri_omp.h" +#include "npair_half_multi_newton_tri_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -26,17 +26,17 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMulti2NewtonTriOmp::NPairHalfMulti2NewtonTriOmp(LAMMPS *lmp) : +NPairHalfMultiNewtonTriOmp::NPairHalfMultiNewtonTriOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) +void NPairHalfMultiNewtonTriOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -91,7 +91,7 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -109,12 +109,12 @@ void NPairHalfMulti2NewtonTriOmp::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { // if same size (e.g. same type), use half stencil if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.h b/src/USER-OMP/npair_half_multi_newton_tri_omp.h new file mode 100755 index 0000000000..80faf8188f --- /dev/null +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/multi/newton/tri/omp, + NPairHalfMultiNewtonTriOmp, + NP_HALF | NP_MULTI | NP_NEWTON | NP_TRI | NP_OMP) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_TRI_OMP_H +#define LMP_NPAIR_HALF_MULTI_NEWTON_TRI_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMultiNewtonTriOmp : public NPair { + public: + NPairHalfMultiNewtonTriOmp(class LAMMPS *); + ~NPairHalfMultiNewtonTriOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp index 2839ebfa14..961bac8fb7 100644 --- a/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp @@ -98,10 +98,10 @@ void NPairHalfMultiOldNewtoffOmp::build(NeighList *list) // stores own/ghost pairs on both procs ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { if (j <= i) continue; diff --git a/src/USER-OMP/npair_half_multi_old_newton_omp.cpp b/src/USER-OMP/npair_half_multi_old_newton_omp.cpp index bc77cc518b..affae74dbd 100644 --- a/src/USER-OMP/npair_half_multi_old_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_old_newton_omp.cpp @@ -132,10 +132,10 @@ void NPairHalfMultiOldNewtonOmp::build(NeighList *list) // skip if i,j neighbor cutoff is less than bin distance ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp index 3d5a577396..c023b08cb7 100644 --- a/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp @@ -100,10 +100,10 @@ void NPairHalfMultiOldNewtonTriOmp::build(NeighList *list) // latter excludes self-self interaction but allows superposed atoms ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.h b/src/USER-OMP/npair_half_size_multi2_newtoff_omp.h deleted file mode 100755 index fd592d839c..0000000000 --- a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi2/newtoff/omp, - NPairHalfSizeMulti2NewtoffOmp, - NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_OMP_H -#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_OMP_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMulti2NewtoffOmp : public NPair { - public: - NPairHalfSizeMulti2NewtoffOmp(class LAMMPS *); - ~NPairHalfSizeMulti2NewtoffOmp() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/USER-OMP/npair_half_size_multi2_newton_omp.h b/src/USER-OMP/npair_half_size_multi2_newton_omp.h deleted file mode 100755 index 38b4dde272..0000000000 --- a/src/USER-OMP/npair_half_size_multi2_newton_omp.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi2/newton/omp, - NPairHalfSizeMulti2NewtonOmp, - NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_OMP | NP_ORTHO) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_OMP_H -#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_OMP_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMulti2NewtonOmp : public NPair { - public: - NPairHalfSizeMulti2NewtonOmp(class LAMMPS *); - ~NPairHalfSizeMulti2NewtonOmp() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.h deleted file mode 100755 index 494a419c8f..0000000000 --- a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi2/newton/tri/omp, - NPairHalfSizeMulti2NewtonTriOmp, - NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_TRI | NP_OMP) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_OMP_H -#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_OMP_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMulti2NewtonTriOmp : public NPair { - public: - NPairHalfSizeMulti2NewtonTriOmp(class LAMMPS *); - ~NPairHalfSizeMulti2NewtonTriOmp() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp similarity index 88% rename from src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp rename to src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp index 3b1f979a8e..8201ba8cb6 100755 --- a/src/USER-OMP/npair_half_size_multi2_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_size_multi2_newtoff_omp.h" +#include "npair_half_size_multi_newtoff_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -24,18 +24,18 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMulti2NewtoffOmp::NPairHalfSizeMulti2NewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks own bin and other bins in stencil pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) +void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; @@ -80,7 +80,7 @@ void NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -95,12 +95,12 @@ void NPairHalfSizeMulti2NewtoffOmp::build(NeighList *list) // stores own/ghost pairs on both procs // use full stencil for all type combinations - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jtype][j]) { if (j <= i) continue; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/USER-OMP/npair_half_multi2_newtoff_omp.h b/src/USER-OMP/npair_half_size_multi_newtoff_omp.h similarity index 66% rename from src/USER-OMP/npair_half_multi2_newtoff_omp.h rename to src/USER-OMP/npair_half_size_multi_newtoff_omp.h index a9e9a842cb..b25a372186 100755 --- a/src/USER-OMP/npair_half_multi2_newtoff_omp.h +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi2/newtoff/omp, - NPairHalfMulti2NewtoffOmp, - NP_HALF | NP_MULTI2 | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) +NPairStyle(half/size/multi/newtoff/omp, + NPairHalfSizeMultiNewtoffOmp, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_MULTI2_NEWTOFF_OMP_H -#define LMP_NPAIR_HALF_MULTI2_NEWTOFF_OMP_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMulti2NewtoffOmp : public NPair { +class NPairHalfSizeMultiNewtoffOmp : public NPair { public: - NPairHalfMulti2NewtoffOmp(class LAMMPS *); - ~NPairHalfMulti2NewtoffOmp() {} + NPairHalfSizeMultiNewtoffOmp(class LAMMPS *); + ~NPairHalfSizeMultiNewtoffOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp similarity index 89% rename from src/USER-OMP/npair_half_size_multi2_newton_omp.cpp rename to src/USER-OMP/npair_half_size_multi_newton_omp.cpp index 3a3a2fbe74..197b41c12e 100755 --- a/src/USER-OMP/npair_half_size_multi2_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_size_multi2_newton_omp.h" +#include "npair_half_size_multi_newton_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -24,17 +24,17 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMulti2NewtonOmp::NPairHalfSizeMulti2NewtonOmp(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with full Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) +void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; @@ -79,7 +79,7 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -98,9 +98,9 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - js = bins_multi2[itype][i]; + js = bins_multi[itype][i]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -132,9 +132,9 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi2[jtype][jbin]; + js = binhead_multi[jtype][jbin]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if(j < i) continue; if (j >= nlocal) { @@ -169,12 +169,12 @@ void NPairHalfSizeMulti2NewtonOmp::build(NeighList *list) // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/USER-OMP/npair_half_multi2_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi_newton_omp.h similarity index 67% rename from src/USER-OMP/npair_half_multi2_newton_tri_omp.h rename to src/USER-OMP/npair_half_size_multi_newton_omp.h index dd9eea6847..03d712145f 100755 --- a/src/USER-OMP/npair_half_multi2_newton_tri_omp.h +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi2/newton/tri/omp, - NPairHalfMulti2NewtonTriOmp, - NP_HALF | NP_MULTI2 | NP_NEWTON | NP_TRI | NP_OMP) +NPairStyle(half/size/multi/newton/omp, + NPairHalfSizeMultiNewtonOmp, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_OMP | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_OMP_H -#define LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_OMP_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_OMP_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMulti2NewtonTriOmp : public NPair { +class NPairHalfSizeMultiNewtonOmp : public NPair { public: - NPairHalfMulti2NewtonTriOmp(class LAMMPS *); - ~NPairHalfMulti2NewtonTriOmp() {} + NPairHalfSizeMultiNewtonOmp(class LAMMPS *); + ~NPairHalfSizeMultiNewtonOmp() {} void build(class NeighList *); }; diff --git a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp similarity index 90% rename from src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp rename to src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp index 66f9cbce0a..cd123202b1 100755 --- a/src/USER-OMP/npair_half_size_multi2_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "npair_half_size_multi2_newton_tri_omp.h" +#include "npair_half_size_multi_newton_tri_omp.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" @@ -24,18 +24,18 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMulti2NewtonTriOmp::NPairHalfSizeMulti2NewtonTriOmp(LAMMPS *lmp) : +NPairHalfSizeMultiNewtonTriOmp::NPairHalfSizeMultiNewtonTriOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) +void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; @@ -80,7 +80,7 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -99,12 +99,12 @@ void NPairHalfSizeMulti2NewtonTriOmp::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { // if same size (e.g. same type), use half stencil if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h new file mode 100755 index 0000000000..6e936c8da4 --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/newton/tri/omp, + NPairHalfSizeMultiNewtonTriOmp, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_TRI | NP_OMP) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiNewtonTriOmp : public NPair { + public: + NPairHalfSizeMultiNewtonTriOmp(class LAMMPS *); + ~NPairHalfSizeMultiNewtonTriOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp index e3001185c1..3ed703586d 100644 --- a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp @@ -86,10 +86,10 @@ void NPairHalfSizeMultiNewtoffOldOmp::build(NeighList *list) // stores own/ghost pairs on both procs ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { if (j <= i) continue; diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp index ee166a57cf..37203c53db 100644 --- a/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp @@ -112,10 +112,10 @@ void NPairHalfSizeMultiNewtonOldOmp::build(NeighList *list) // skip if i,j neighbor cutoff is less than bin distance ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp index 81e896db6c..8352e28643 100644 --- a/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp @@ -87,10 +87,10 @@ void NPairHalfSizeMultiOldNewtonTriOmp::build(NeighList *list) // latter excludes self-self interaction but allows superposed atoms ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/npair.cpp b/src/npair.cpp index 4d86badf76..07e476e1dd 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -135,24 +135,24 @@ void NPair::copy_bin_info() bins = nb->bins; binhead = nb->binhead; - nbinx_multi2 = nb->nbinx_multi2; - nbiny_multi2 = nb->nbiny_multi2; - nbinz_multi2 = nb->nbinz_multi2; - mbins_multi2 = nb->mbins_multi2; - mbinx_multi2 = nb->mbinx_multi2; - mbiny_multi2 = nb->mbiny_multi2; - mbinz_multi2 = nb->mbinz_multi2; - mbinxlo_multi2 = nb->mbinxlo_multi2; - mbinylo_multi2 = nb->mbinylo_multi2; - mbinzlo_multi2 = nb->mbinzlo_multi2; + nbinx_multi = nb->nbinx_multi; + nbiny_multi = nb->nbiny_multi; + nbinz_multi = nb->nbinz_multi; + mbins_multi = nb->mbins_multi; + mbinx_multi = nb->mbinx_multi; + mbiny_multi = nb->mbiny_multi; + mbinz_multi = nb->mbinz_multi; + mbinxlo_multi = nb->mbinxlo_multi; + mbinylo_multi = nb->mbinylo_multi; + mbinzlo_multi = nb->mbinzlo_multi; - bininvx_multi2 = nb->bininvx_multi2; - bininvy_multi2 = nb->bininvy_multi2; - bininvz_multi2 = nb->bininvz_multi2; + bininvx_multi = nb->bininvx_multi; + bininvy_multi = nb->bininvy_multi; + bininvz_multi = nb->bininvz_multi; - atom2bin_multi2 = nb->atom2bin_multi2; - bins_multi2 = nb->bins_multi2; - binhead_multi2 = nb->binhead_multi2; + atom2bin_multi = nb->atom2bin_multi; + bins_multi = nb->bins_multi; + binhead_multi = nb->binhead_multi; } /* ---------------------------------------------------------------------- @@ -164,12 +164,12 @@ void NPair::copy_stencil_info() nstencil = ns->nstencil; stencil = ns->stencil; stencilxyz = ns->stencilxyz; + nstencil_multi_old = ns->nstencil_multi_old; + stencil_multi_old = ns->stencil_multi_old; + distsq_multi_old = ns->distsq_multi_old; + nstencil_multi = ns->nstencil_multi; stencil_multi = ns->stencil_multi; - distsq_multi = ns->distsq_multi; - - nstencil_multi2 = ns->nstencil_multi2; - stencil_multi2 = ns->stencil_multi2; } /* ---------------------------------------------------------------------- @@ -277,32 +277,32 @@ int NPair::coord2bin(double *x, int it) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi2[it]) + nbinx_multi2[it]; + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[it]) + nbinx_multi[it]; else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]); - ix = MIN(ix,nbinx_multi2[it]-1); + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]); + ix = MIN(ix,nbinx_multi[it]-1); } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]) - 1; + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]) - 1; if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi2[it]) + nbiny_multi2[it]; + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[it]) + nbiny_multi[it]; else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]); - iy = MIN(iy,nbiny_multi2[it]-1); + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]); + iy = MIN(iy,nbiny_multi[it]-1); } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]) - 1; + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]) - 1; if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi2[it]) + nbinz_multi2[it]; + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[it]) + nbinz_multi[it]; else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]); - iz = MIN(iz,nbinz_multi2[it]-1); + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]); + iz = MIN(iz,nbinz_multi[it]-1); } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]) - 1; + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]) - 1; - ibin = (iz-mbinzlo_multi2[it])*mbiny_multi2[it]*mbinx_multi2[it] - + (iy-mbinylo_multi2[it])*mbinx_multi2[it] - + (ix-mbinxlo_multi2[it]); + ibin = (iz-mbinzlo_multi[it])*mbiny_multi[it]*mbinx_multi[it] + + (iy-mbinylo_multi[it])*mbinx_multi[it] + + (ix-mbinxlo_multi[it]); return ibin; } \ No newline at end of file diff --git a/src/npair.h b/src/npair.h index 87b2584521..c56c6bdb20 100644 --- a/src/npair.h +++ b/src/npair.h @@ -79,25 +79,25 @@ class NPair : protected Pointers { int *atom2bin,*bins; int *binhead; - int *nbinx_multi2, *nbiny_multi2, *nbinz_multi2; - int *mbins_multi2; - int *mbinx_multi2, *mbiny_multi2, *mbinz_multi2; - int *mbinxlo_multi2, *mbinylo_multi2, *mbinzlo_multi2; - double *bininvx_multi2, *bininvy_multi2, *bininvz_multi2; - int **binhead_multi2,**bins_multi2; - int **atom2bin_multi2; + int *nbinx_multi, *nbiny_multi, *nbinz_multi; + int *mbins_multi; + int *mbinx_multi, *mbiny_multi, *mbinz_multi; + int *mbinxlo_multi, *mbinylo_multi, *mbinzlo_multi; + double *bininvx_multi, *bininvy_multi, *bininvz_multi; + int **binhead_multi,**bins_multi; + int **atom2bin_multi; // data from NStencil class int nstencil; int *stencil; int **stencilxyz; - int *nstencil_multi; - int **stencil_multi; - double **distsq_multi; + int *nstencil_multi_old; + int **stencil_multi_old; + double **distsq_multi_old; - int ** nstencil_multi2; - int *** stencil_multi2; + int ** nstencil_multi; + int *** stencil_multi; // data common to all NPair variants diff --git a/src/npair_full_multi2.cpp b/src/npair_full_multi.cpp similarity index 90% rename from src/npair_full_multi2.cpp rename to src/npair_full_multi.cpp index 732c5e581e..4463964d5f 100644 --- a/src/npair_full_multi2.cpp +++ b/src/npair_full_multi.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_full_multi2.h" +#include "npair_full_multi.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,15 +24,15 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairFullMulti2::NPairFullMulti2(LAMMPS *lmp) : NPair(lmp) {} +NPairFullMulti::NPairFullMulti(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ -void NPairFullMulti2::build(NeighList *list) +void NPairFullMulti::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; @@ -78,7 +78,7 @@ void NPairFullMulti2::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -91,12 +91,12 @@ void NPairFullMulti2::build(NeighList *list) // skip i = j // use full stencil for all type combinations - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (i == j) continue; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/npair_full_multi2.h b/src/npair_full_multi.h similarity index 74% rename from src/npair_full_multi2.h rename to src/npair_full_multi.h index f552e5bf47..481a673060 100644 --- a/src/npair_full_multi2.h +++ b/src/npair_full_multi.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(full/multi2, - NPairFullMulti2, - NP_FULL | NP_MULTI2 | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) +NPairStyle(full/multi, + NPairFullMulti, + NP_FULL | NP_MULTI | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_FULL_MULTI2_H -#define LMP_NPAIR_FULL_MULTI2_H +#ifndef LMP_NPAIR_FULL_MULTI_H +#define LMP_NPAIR_FULL_MULTI_H #include "npair.h" namespace LAMMPS_NS { -class NPairFullMulti2 : public NPair { +class NPairFullMulti : public NPair { public: - NPairFullMulti2(class LAMMPS *); - ~NPairFullMulti2() {} + NPairFullMulti(class LAMMPS *); + ~NPairFullMulti() {} void build(class NeighList *); }; diff --git a/src/npair_full_multi_old.cpp b/src/npair_full_multi_old.cpp index 9a800a80b5..328b3325ab 100644 --- a/src/npair_full_multi_old.cpp +++ b/src/npair_full_multi_old.cpp @@ -83,10 +83,10 @@ void NPairFullMultiOld::build(NeighList *list) // skip i = j ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/npair_half_multi2_newtoff.cpp b/src/npair_half_multi_newtoff.cpp similarity index 90% rename from src/npair_half_multi2_newtoff.cpp rename to src/npair_half_multi_newtoff.cpp index ecd97fe689..c0dcaf0c98 100755 --- a/src/npair_half_multi2_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_multi2_newtoff.h" +#include "npair_half_multi_newtoff.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,17 +24,17 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMulti2Newtoff::NPairHalfMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks own bin and other bins in stencil pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfMulti2Newtoff::build(NeighList *list) +void NPairHalfMultiNewtoff::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; @@ -80,7 +80,7 @@ void NPairHalfMulti2Newtoff::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -95,12 +95,12 @@ void NPairHalfMulti2Newtoff::build(NeighList *list) // stores own/ghost pairs on both procs // use full stencil for all type combinations - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jtype][j]) { if (j <= i) continue; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/npair_half_multi2_newtoff.h b/src/npair_half_multi_newtoff.h similarity index 72% rename from src/npair_half_multi2_newtoff.h rename to src/npair_half_multi_newtoff.h index 30a6d3164d..593e2c1d9d 100755 --- a/src/npair_half_multi2_newtoff.h +++ b/src/npair_half_multi_newtoff.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi2/newtoff, - NPairHalfMulti2Newtoff, - NP_HALF | NP_MULTI2 | NP_NEWTOFF | NP_ORTHO | NP_TRI) +NPairStyle(half/multi/newtoff, + NPairHalfMultiNewtoff, + NP_HALF | NP_MULTI | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_MULTI2_NEWTOFF_H -#define LMP_NPAIR_HALF_MULTI2_NEWTOFF_H +#ifndef LMP_NPAIR_HALF_MULTI_NEWTOFF_H +#define LMP_NPAIR_HALF_MULTI_NEWTOFF_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMulti2Newtoff : public NPair { +class NPairHalfMultiNewtoff : public NPair { public: - NPairHalfMulti2Newtoff(class LAMMPS *); - ~NPairHalfMulti2Newtoff() {} + NPairHalfMultiNewtoff(class LAMMPS *); + ~NPairHalfMultiNewtoff() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi2_newton.cpp b/src/npair_half_multi_newton.cpp similarity index 91% rename from src/npair_half_multi2_newton.cpp rename to src/npair_half_multi_newton.cpp index 6a7f52168a..e097052fe5 100755 --- a/src/npair_half_multi2_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_multi2_newton.h" +#include "npair_half_multi_newton.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,16 +24,16 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMulti2Newton::NPairHalfMulti2Newton(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMulti2Newton::build(NeighList *list) +void NPairHalfMultiNewton::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; @@ -79,7 +79,7 @@ void NPairHalfMulti2Newton::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -98,9 +98,9 @@ void NPairHalfMulti2Newton::build(NeighList *list) // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - js = bins_multi2[itype][i]; + js = bins_multi[itype][i]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -139,9 +139,9 @@ void NPairHalfMulti2Newton::build(NeighList *list) // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi2[jtype][jbin]; + js = binhead_multi[jtype][jbin]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if(j < i) continue; if (j >= nlocal) { @@ -183,12 +183,12 @@ void NPairHalfMulti2Newton::build(NeighList *list) // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/npair_half_multi2_newton.h b/src/npair_half_multi_newton.h similarity index 71% rename from src/npair_half_multi2_newton.h rename to src/npair_half_multi_newton.h index 8037d2e172..64021a9f58 100755 --- a/src/npair_half_multi2_newton.h +++ b/src/npair_half_multi_newton.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi2/newton, - NPairHalfMulti2Newton, - NP_HALF | NP_MULTI2 | NP_NEWTON | NP_ORTHO) +NPairStyle(half/multi/newton, + NPairHalfMultiNewton, + NP_HALF | NP_MULTI | NP_NEWTON | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_H -#define LMP_NPAIR_HALF_MULTI2_NEWTON_H +#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_H +#define LMP_NPAIR_HALF_MULTI_NEWTON_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMulti2Newton : public NPair { +class NPairHalfMultiNewton : public NPair { public: - NPairHalfMulti2Newton(class LAMMPS *); - ~NPairHalfMulti2Newton() {} + NPairHalfMultiNewton(class LAMMPS *); + ~NPairHalfMultiNewton() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi2_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp similarity index 91% rename from src/npair_half_multi2_newton_tri.cpp rename to src/npair_half_multi_newton_tri.cpp index 9d0db60d50..fabaf5f202 100755 --- a/src/npair_half_multi2_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_multi2_newton_tri.h" +#include "npair_half_multi_newton_tri.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,16 +24,16 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfMulti2NewtonTri::NPairHalfMulti2NewtonTri(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfMultiNewtonTri::NPairHalfMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfMulti2NewtonTri::build(NeighList *list) +void NPairHalfMultiNewtonTri::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; @@ -79,7 +79,7 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -97,12 +97,12 @@ void NPairHalfMulti2NewtonTri::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { // if same size (e.g. same type), use half stencil if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ diff --git a/src/npair_half_multi2_newton_tri.h b/src/npair_half_multi_newton_tri.h similarity index 70% rename from src/npair_half_multi2_newton_tri.h rename to src/npair_half_multi_newton_tri.h index 0787860c52..51b720e0c4 100755 --- a/src/npair_half_multi2_newton_tri.h +++ b/src/npair_half_multi_newton_tri.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/multi2/newton/tri, - NPairHalfMulti2NewtonTri, - NP_HALF | NP_MULTI2 | NP_NEWTON | NP_TRI) +NPairStyle(half/multi/newton/tri, + NPairHalfMultiNewtonTri, + NP_HALF | NP_MULTI | NP_NEWTON | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_H -#define LMP_NPAIR_HALF_MULTI2_NEWTON_TRI_H +#ifndef LMP_NPAIR_HALF_MULTI_NEWTON_TRI_H +#define LMP_NPAIR_HALF_MULTI_NEWTON_TRI_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfMulti2NewtonTri : public NPair { +class NPairHalfMultiNewtonTri : public NPair { public: - NPairHalfMulti2NewtonTri(class LAMMPS *); - ~NPairHalfMulti2NewtonTri() {} + NPairHalfMultiNewtonTri(class LAMMPS *); + ~NPairHalfMultiNewtonTri() {} void build(class NeighList *); }; diff --git a/src/npair_half_multi_old_newtoff.cpp b/src/npair_half_multi_old_newtoff.cpp index 351fd65c32..fa9544aa68 100644 --- a/src/npair_half_multi_old_newtoff.cpp +++ b/src/npair_half_multi_old_newtoff.cpp @@ -87,10 +87,10 @@ void NPairHalfMultiOldNewtoff::build(NeighList *list) // stores own/ghost pairs on both procs ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { if (j <= i) continue; diff --git a/src/npair_half_multi_old_newton.cpp b/src/npair_half_multi_old_newton.cpp index 5af420017d..db3a7c015c 100644 --- a/src/npair_half_multi_old_newton.cpp +++ b/src/npair_half_multi_old_newton.cpp @@ -121,10 +121,10 @@ void NPairHalfMultiOldNewton::build(NeighList *list) // skip if i,j neighbor cutoff is less than bin distance ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/npair_half_multi_old_newton_tri.cpp b/src/npair_half_multi_old_newton_tri.cpp index f22e0fbf4f..1b142aa9ab 100644 --- a/src/npair_half_multi_old_newton_tri.cpp +++ b/src/npair_half_multi_old_newton_tri.cpp @@ -88,10 +88,10 @@ void NPairHalfMultiOldNewtonTri::build(NeighList *list) // latter excludes self-self interaction but allows superposed atoms ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/npair_half_size_multi2_newton_tri.h b/src/npair_half_size_multi2_newton_tri.h deleted file mode 100755 index 6ce4f6d2fb..0000000000 --- a/src/npair_half_size_multi2_newton_tri.h +++ /dev/null @@ -1,47 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NPAIR_CLASS - -NPairStyle(half/size/multi2/newton/tri, - NPairHalfSizeMulti2NewtonTri, - NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_TRI) - -#else - -#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_H -#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_TRI_H - -#include "npair.h" - -namespace LAMMPS_NS { - -class NPairHalfSizeMulti2NewtonTri : public NPair { - public: - NPairHalfSizeMulti2NewtonTri(class LAMMPS *); - ~NPairHalfSizeMulti2NewtonTri() {} - void build(class NeighList *); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Neighbor list overflow, boost neigh_modify one - -UNDOCUMENTED - -*/ \ No newline at end of file diff --git a/src/npair_half_size_multi2_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp similarity index 87% rename from src/npair_half_size_multi2_newtoff.cpp rename to src/npair_half_size_multi_newtoff.cpp index b559f83414..65b6b68fb2 100644 --- a/src/npair_half_size_multi2_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -12,7 +12,7 @@ es certain rights in this software. This software is distributed under ------------------------------------------------------------------------- */ #include -#include "npair_half_size_multi2_newtoff.h" +#include "npair_half_size_multi_newtoff.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -23,18 +23,18 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMulti2Newtoff::NPairHalfSizeMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks own bin and other bins in stencil pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfSizeMulti2Newtoff::build(NeighList *list) +void NPairHalfSizeMultiNewtoff::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; @@ -71,7 +71,7 @@ void NPairHalfSizeMulti2Newtoff::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -86,12 +86,12 @@ void NPairHalfSizeMulti2Newtoff::build(NeighList *list) // stores own/ghost pairs on both procs // use full stencil for all type combinations - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jtype][j]) { if (j <= i) continue; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/npair_half_size_multi2_newtoff.h b/src/npair_half_size_multi_newtoff.h similarity index 69% rename from src/npair_half_size_multi2_newtoff.h rename to src/npair_half_size_multi_newtoff.h index 15540666c3..47c922cb7e 100644 --- a/src/npair_half_size_multi2_newtoff.h +++ b/src/npair_half_size_multi_newtoff.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/size/multi2/newtoff, - NPairHalfSizeMulti2Newtoff, - NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTOFF | NP_ORTHO | NP_TRI) +NPairStyle(half/size/multi/newtoff, + NPairHalfSizeMultiNewtoff, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_H -#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTOFF_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTOFF_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfSizeMulti2Newtoff : public NPair { +class NPairHalfSizeMultiNewtoff : public NPair { public: - NPairHalfSizeMulti2Newtoff(class LAMMPS *); - ~NPairHalfSizeMulti2Newtoff() {} + NPairHalfSizeMultiNewtoff(class LAMMPS *); + ~NPairHalfSizeMultiNewtoff() {} void build(class NeighList *); }; diff --git a/src/npair_half_size_multi2_newton.cpp b/src/npair_half_size_multi_newton.cpp similarity index 89% rename from src/npair_half_size_multi2_newton.cpp rename to src/npair_half_size_multi_newton.cpp index bc6116b21c..8fa3b9bc1b 100755 --- a/src/npair_half_size_multi2_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_size_multi2_newton.h" +#include "npair_half_size_multi_newton.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -22,17 +22,17 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMulti2Newton::NPairHalfSizeMulti2Newton(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with full Newton's 3rd law - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMulti2Newton::build(NeighList *list) +void NPairHalfSizeMultiNewton::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; @@ -68,7 +68,7 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -87,9 +87,9 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - js = bins_multi2[itype][i]; + js = bins_multi[itype][i]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -121,9 +121,9 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi2[jtype][jbin]; + js = binhead_multi[jtype][jbin]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if(j < i) continue; if (j >= nlocal) { @@ -158,12 +158,12 @@ void NPairHalfSizeMulti2Newton::build(NeighList *list) // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/npair_half_size_multi2_newton.h b/src/npair_half_size_multi_newton.h similarity index 70% rename from src/npair_half_size_multi2_newton.h rename to src/npair_half_size_multi_newton.h index 8c7bc1cc9e..d31496873d 100755 --- a/src/npair_half_size_multi2_newton.h +++ b/src/npair_half_size_multi_newton.h @@ -13,23 +13,23 @@ #ifdef NPAIR_CLASS -NPairStyle(half/size/multi2/newton, - NPairHalfSizeMulti2Newton, - NP_HALF | NP_SIZE | NP_MULTI2 | NP_NEWTON | NP_ORTHO) +NPairStyle(half/size/multi/newton, + NPairHalfSizeMultiNewton, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_ORTHO) #else -#ifndef LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_H -#define LMP_NPAIR_HALF_SIZE_MULTI2_NEWTON_H +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_H #include "npair.h" namespace LAMMPS_NS { -class NPairHalfSizeMulti2Newton : public NPair { +class NPairHalfSizeMultiNewton : public NPair { public: - NPairHalfSizeMulti2Newton(class LAMMPS *); - ~NPairHalfSizeMulti2Newton() {} + NPairHalfSizeMultiNewton(class LAMMPS *); + ~NPairHalfSizeMultiNewton() {} void build(class NeighList *); }; diff --git a/src/npair_half_size_multi2_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp similarity index 89% rename from src/npair_half_size_multi2_newton_tri.cpp rename to src/npair_half_size_multi_newton_tri.cpp index 8cde0cbb36..780fa95f0b 100755 --- a/src/npair_half_size_multi2_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "npair_half_size_multi2_newton_tri.h" +#include "npair_half_size_multi_newton_tri.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -22,17 +22,17 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMulti2NewtonTri::NPairHalfSizeMulti2NewtonTri(LAMMPS *lmp) : NPair(lmp) {} +NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic - multi2-type stencil is itype-jtype dependent + multi-type stencil is itype-jtype dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) +void NPairHalfSizeMultiNewtonTri::build(NeighList *list) { int i,j,k,n,itype,jtype,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; @@ -68,7 +68,7 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi2[itype][i]; + ibin = atom2bin_multi[itype][i]; // loop through stencils for all types for (jtype = 1; jtype <= atom->ntypes; jtype++) { @@ -87,12 +87,12 @@ void NPairHalfSizeMulti2NewtonTri::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi2[itype][jtype]; - ns = nstencil_multi2[itype][jtype]; + s = stencil_multi[itype][jtype]; + ns = nstencil_multi[itype][jtype]; for (k = 0; k < ns; k++) { - js = binhead_multi2[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi2[jtype][j]) { + js = binhead_multi[jtype][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jtype][j]) { // if same size (e.g. same type), use half stencil if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ diff --git a/src/npair_half_size_multi_newton_tri.h b/src/npair_half_size_multi_newton_tri.h new file mode 100755 index 0000000000..9bc1238e77 --- /dev/null +++ b/src/npair_half_size_multi_newton_tri.h @@ -0,0 +1,47 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/newton/tri, + NPairHalfSizeMultiNewtonTri, + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTON | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_H +#define LMP_NPAIR_HALF_SIZE_MULTI_NEWTON_TRI_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiNewtonTri : public NPair { + public: + NPairHalfSizeMultiNewtonTri(class LAMMPS *); + ~NPairHalfSizeMultiNewtonTri() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + +*/ \ No newline at end of file diff --git a/src/npair_half_size_multi_old_newtoff.cpp b/src/npair_half_size_multi_old_newtoff.cpp index 394ad58981..35095b4856 100644 --- a/src/npair_half_size_multi_old_newtoff.cpp +++ b/src/npair_half_size_multi_old_newtoff.cpp @@ -77,10 +77,10 @@ void NPairHalfSizeMultiOldNewtoff::build(NeighList *list) // stores own/ghost pairs on both procs ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { if (j <= i) continue; diff --git a/src/npair_half_size_multi_old_newton.cpp b/src/npair_half_size_multi_old_newton.cpp index 65b197a86b..0112c0593f 100644 --- a/src/npair_half_size_multi_old_newton.cpp +++ b/src/npair_half_size_multi_old_newton.cpp @@ -104,10 +104,10 @@ void NPairHalfSizeMultiOldNewton::build(NeighList *list) // skip if i,j neighbor cutoff is less than bin distance ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/npair_half_size_multi_old_newton_tri.cpp b/src/npair_half_size_multi_old_newton_tri.cpp index 93d3beeb0a..2b63e116d7 100644 --- a/src/npair_half_size_multi_old_newton_tri.cpp +++ b/src/npair_half_size_multi_old_newton_tri.cpp @@ -78,10 +78,10 @@ void NPairHalfSizeMultiOldNewtonTri::build(NeighList *list) // latter excludes self-self interaction but allows superposed atoms ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; + ns = nstencil_multi_old[itype]; for (k = 0; k < ns; k++) { for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { jtype = type[j]; From 42e5130893a4842a86e4b09db30bb4980318eb10 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 17:18:54 -0700 Subject: [PATCH 0053/1217] Renaming multi->multi2 in nbin files --- src/nbin.cpp | 104 +++++------ src/nbin.h | 28 +-- src/{nbin_multi2.cpp => nbin_multi.cpp} | 222 ++++++++++++------------ src/{nbin_multi2.h => nbin_multi.h} | 16 +- 4 files changed, 185 insertions(+), 185 deletions(-) rename src/{nbin_multi2.cpp => nbin_multi.cpp} (55%) rename src/{nbin_multi2.h => nbin_multi.h} (85%) diff --git a/src/nbin.cpp b/src/nbin.cpp index 26aebd3a3a..084d3bfc4a 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -31,18 +31,18 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp) bins = nullptr; atom2bin = nullptr; - nbinx_multi2 = nullptr; nbiny_multi2 = nullptr; nbinz_multi2 = nullptr; - mbins_multi2 = nullptr; - mbinx_multi2 = nullptr; mbiny_multi2 = nullptr, mbinz_multi2 = nullptr; - mbinxlo_multi2 = nullptr; - mbinylo_multi2 = nullptr; - mbinzlo_multi2 = nullptr; - binsizex_multi2 = nullptr; binsizey_multi2 = nullptr; binsizez_multi2 = nullptr; - bininvx_multi2 = nullptr; bininvy_multi2 = nullptr; bininvz_multi2 = nullptr; - binhead_multi2 = nullptr; - bins_multi2 = nullptr; - atom2bin_multi2 = nullptr; - maxbins_multi2 = nullptr; + nbinx_multi = nullptr; nbiny_multi = nullptr; nbinz_multi = nullptr; + mbins_multi = nullptr; + mbinx_multi = nullptr; mbiny_multi = nullptr, mbinz_multi = nullptr; + mbinxlo_multi = nullptr; + mbinylo_multi = nullptr; + mbinzlo_multi = nullptr; + binsizex_multi = nullptr; binsizey_multi = nullptr; binsizez_multi = nullptr; + bininvx_multi = nullptr; bininvy_multi = nullptr; bininvz_multi = nullptr; + binhead_multi = nullptr; + bins_multi = nullptr; + atom2bin_multi = nullptr; + maxbins_multi = nullptr; maxtypes = 0; @@ -64,36 +64,36 @@ NBin::~NBin() memory->destroy(bins); memory->destroy(atom2bin); - if (!bins_multi2) return; + if (!bins_multi) return; - memory->destroy(nbinx_multi2); - memory->destroy(nbiny_multi2); - memory->destroy(nbinz_multi2); - memory->destroy(mbins_multi2); - memory->destroy(mbinx_multi2); - memory->destroy(mbiny_multi2); - memory->destroy(mbinz_multi2); - memory->destroy(mbinxlo_multi2); - memory->destroy(mbinylo_multi2); - memory->destroy(mbinzlo_multi2); + memory->destroy(nbinx_multi); + memory->destroy(nbiny_multi); + memory->destroy(nbinz_multi); + memory->destroy(mbins_multi); + memory->destroy(mbinx_multi); + memory->destroy(mbiny_multi); + memory->destroy(mbinz_multi); + memory->destroy(mbinxlo_multi); + memory->destroy(mbinylo_multi); + memory->destroy(mbinzlo_multi); - memory->destroy(binsizex_multi2); - memory->destroy(binsizey_multi2); - memory->destroy(binsizez_multi2); - memory->destroy(bininvx_multi2); - memory->destroy(bininvy_multi2); - memory->destroy(bininvz_multi2); + memory->destroy(binsizex_multi); + memory->destroy(binsizey_multi); + memory->destroy(binsizez_multi); + memory->destroy(bininvx_multi); + memory->destroy(bininvy_multi); + memory->destroy(bininvz_multi); for (int n = 1; n <= maxtypes; n++) { - memory->destroy(binhead_multi2[n]); - memory->destroy(bins_multi2[n]); - memory->destroy(atom2bin_multi2[n]); + memory->destroy(binhead_multi[n]); + memory->destroy(bins_multi[n]); + memory->destroy(atom2bin_multi[n]); } - delete [] binhead_multi2; - delete [] bins_multi2; - delete [] atom2bin_multi2; + delete [] binhead_multi; + delete [] bins_multi; + delete [] atom2bin_multi; - memory->destroy(maxbins_multi2); + memory->destroy(maxbins_multi); } /* ---------------------------------------------------------------------- */ @@ -177,7 +177,7 @@ int NBin::coord2bin(double *x) convert atom coords into local bin # for a particular type ------------------------------------------------------------------------- */ -int NBin::coord2bin_multi2(double *x, int it) +int NBin::coord2bin_multi(double *x, int it) { int ix,iy,iz; int ibin; @@ -186,33 +186,33 @@ int NBin::coord2bin_multi2(double *x, int it) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi2[it]) + nbinx_multi2[it]; + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[it]) + nbinx_multi[it]; else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]); - ix = MIN(ix,nbinx_multi2[it]-1); + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]); + ix = MIN(ix,nbinx_multi[it]-1); } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi2[it]) - 1; + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]) - 1; if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi2[it]) + nbiny_multi2[it]; + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[it]) + nbiny_multi[it]; else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]); - iy = MIN(iy,nbiny_multi2[it]-1); + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]); + iy = MIN(iy,nbiny_multi[it]-1); } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi2[it]) - 1; + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]) - 1; if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi2[it]) + nbinz_multi2[it]; + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[it]) + nbinz_multi[it]; else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]); - iz = MIN(iz,nbinz_multi2[it]-1); + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]); + iz = MIN(iz,nbinz_multi[it]-1); } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi2[it]) - 1; + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]) - 1; - ibin = (iz-mbinzlo_multi2[it])*mbiny_multi2[it]*mbinx_multi2[it] - + (iy-mbinylo_multi2[it])*mbinx_multi2[it] - + (ix-mbinxlo_multi2[it]); + ibin = (iz-mbinzlo_multi[it])*mbiny_multi[it]*mbinx_multi[it] + + (iy-mbinylo_multi[it])*mbinx_multi[it] + + (ix-mbinxlo_multi[it]); return ibin; } diff --git a/src/nbin.h b/src/nbin.h index 441e4815dd..8f95ad987e 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -38,18 +38,18 @@ class NBin : protected Pointers { int *bins; // index of next atom in same bin int *atom2bin; // bin assignment for each atom (local+ghost) - // Analogues for NBinMultimulti2 + // Analogues for NBinMultimulti - int *nbinx_multi2, *nbiny_multi2, *nbinz_multi2; - int *mbins_multi2; - int *mbinx_multi2, *mbiny_multi2, *mbinz_multi2; - int *mbinxlo_multi2, *mbinylo_multi2, *mbinzlo_multi2; - double *binsizex_multi2, *binsizey_multi2, *binsizez_multi2; - double *bininvx_multi2, *bininvy_multi2, *bininvz_multi2; + int *nbinx_multi, *nbiny_multi, *nbinz_multi; + int *mbins_multi; + int *mbinx_multi, *mbiny_multi, *mbinz_multi; + int *mbinxlo_multi, *mbinylo_multi, *mbinzlo_multi; + double *binsizex_multi, *binsizey_multi, *binsizez_multi; + double *bininvx_multi, *bininvy_multi, *bininvz_multi; - int **binhead_multi2; - int **bins_multi2; - int **atom2bin_multi2; + int **binhead_multi; + int **bins_multi; + int **atom2bin_multi; NBin(class LAMMPS *); ~NBin(); @@ -89,15 +89,15 @@ class NBin : protected Pointers { int maxbin; // size of binhead array - // data for multi/multi2 NBin + // data for multi/multi NBin - int maxtypes; // size of multi2 arrays - int * maxbins_multi2; // size of 2nd dimension of binhead_multi2 array + int maxtypes; // size of multi arrays + int * maxbins_multi; // size of 2nd dimension of binhead_multi array // methods int coord2bin(double *); - int coord2bin_multi2(double *, int); + int coord2bin_multi(double *, int); }; } diff --git a/src/nbin_multi2.cpp b/src/nbin_multi.cpp similarity index 55% rename from src/nbin_multi2.cpp rename to src/nbin_multi.cpp index f57558a36c..302fe30d88 100644 --- a/src/nbin_multi2.cpp +++ b/src/nbin_multi.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nbin_multi2.h" +#include "nbin_multi.h" #include "neighbor.h" #include "atom.h" #include "group.h" @@ -28,34 +28,34 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NBinMulti2::NBinMulti2(LAMMPS *lmp) : NBin(lmp) {} +NBinMulti::NBinMulti(LAMMPS *lmp) : NBin(lmp) {} /* ---------------------------------------------------------------------- setup for bin_atoms() ------------------------------------------------------------------------- */ -void NBinMulti2::bin_atoms_setup(int nall) +void NBinMulti::bin_atoms_setup(int nall) { - // binhead_multi2[n] = per-bin vector mbins in length mbins_multi2[n] + // binhead_multi[n] = per-bin vector mbins in length mbins_multi[n] for (int n = 1; n <= maxtypes; n++) { - if (mbins_multi2[n] > maxbins_multi2[n]) { - maxbins_multi2[n] = mbins_multi2[n]; - memory->destroy(binhead_multi2[n]); - memory->create(binhead_multi2[n], mbins_multi2[n], "neigh:mbins_multi2"); + if (mbins_multi[n] > maxbins_multi[n]) { + maxbins_multi[n] = mbins_multi[n]; + memory->destroy(binhead_multi[n]); + memory->create(binhead_multi[n], mbins_multi[n], "neigh:mbins_multi"); } } - // bins_multi2[n] and atom2bin_multi2[n] = per-atom vectors + // bins_multi[n] and atom2bin_multi[n] = per-atom vectors // for both local and ghost atoms if (nall > maxatom) { maxatom = nall; for (int n = 1; n <= maxtypes; n++) { - memory->destroy(bins_multi2[n]); - memory->destroy(atom2bin_multi2[n]); - memory->create(bins_multi2[n], maxatom, "neigh:bin_multi2"); - memory->create(atom2bin_multi2[n], maxatom, "neigh:atom2bin_multi2"); + memory->destroy(bins_multi[n]); + memory->destroy(atom2bin_multi[n]); + memory->create(bins_multi[n], maxatom, "neigh:bin_multi"); + memory->create(atom2bin_multi[n], maxatom, "neigh:atom2bin_multi"); } } } @@ -64,7 +64,7 @@ void NBinMulti2::bin_atoms_setup(int nall) Identify index of type with smallest cutoff ------------------------------------------------------------------------ */ -int NBinMulti2::itype_min() { +int NBinMulti::itype_min() { int itypemin = 1; double ** cutneighsq; @@ -84,7 +84,7 @@ int NBinMulti2::itype_min() { setup neighbor binning geometry ---------------------------------------------------------------------- */ -void NBinMulti2::setup_bins(int style) +void NBinMulti::setup_bins(int style) { int n; int itypemin; @@ -96,64 +96,64 @@ void NBinMulti2::setup_bins(int style) // Clear any/all memory for existing types for (n = 1; n <= maxtypes; n++) { - memory->destroy(atom2bin_multi2[n]); - memory->destroy(binhead_multi2[n]); - memory->destroy(bins_multi2[n]); + memory->destroy(atom2bin_multi[n]); + memory->destroy(binhead_multi[n]); + memory->destroy(bins_multi[n]); } - delete [] atom2bin_multi2; - delete [] binhead_multi2; - delete [] bins_multi2; + delete [] atom2bin_multi; + delete [] binhead_multi; + delete [] bins_multi; // Realloacte at updated maxtypes maxtypes = atom->ntypes; - atom2bin_multi2 = new int*[maxtypes+1](); - binhead_multi2 = new int*[maxtypes+1](); - bins_multi2 = new int*[maxtypes+1](); + atom2bin_multi = new int*[maxtypes+1](); + binhead_multi = new int*[maxtypes+1](); + bins_multi = new int*[maxtypes+1](); - memory->destroy(nbinx_multi2); - memory->destroy(nbiny_multi2); - memory->destroy(nbinz_multi2); - memory->create(nbinx_multi2, maxtypes+1, "neigh:nbinx_multi2"); - memory->create(nbiny_multi2, maxtypes+1, "neigh:nbiny_multi2"); - memory->create(nbinz_multi2, maxtypes+1, "neigh:nbinz_multi2"); + memory->destroy(nbinx_multi); + memory->destroy(nbiny_multi); + memory->destroy(nbinz_multi); + memory->create(nbinx_multi, maxtypes+1, "neigh:nbinx_multi"); + memory->create(nbiny_multi, maxtypes+1, "neigh:nbiny_multi"); + memory->create(nbinz_multi, maxtypes+1, "neigh:nbinz_multi"); - memory->destroy(mbins_multi2); - memory->destroy(mbinx_multi2); - memory->destroy(mbiny_multi2); - memory->destroy(mbinz_multi2); - memory->create(mbins_multi2, maxtypes+1, "neigh:mbins_multi2"); - memory->create(mbinx_multi2, maxtypes+1, "neigh:mbinx_multi2"); - memory->create(mbiny_multi2, maxtypes+1, "neigh:mbiny_multi2"); - memory->create(mbinz_multi2, maxtypes+1, "neigh:mbinz_multi2"); + memory->destroy(mbins_multi); + memory->destroy(mbinx_multi); + memory->destroy(mbiny_multi); + memory->destroy(mbinz_multi); + memory->create(mbins_multi, maxtypes+1, "neigh:mbins_multi"); + memory->create(mbinx_multi, maxtypes+1, "neigh:mbinx_multi"); + memory->create(mbiny_multi, maxtypes+1, "neigh:mbiny_multi"); + memory->create(mbinz_multi, maxtypes+1, "neigh:mbinz_multi"); - memory->destroy(mbinxlo_multi2); - memory->destroy(mbinylo_multi2); - memory->destroy(mbinzlo_multi2); - memory->create(mbinxlo_multi2, maxtypes+1, "neigh:mbinxlo_multi2"); - memory->create(mbinylo_multi2, maxtypes+1, "neigh:mbinylo_multi2"); - memory->create(mbinzlo_multi2, maxtypes+1, "neigh:mbinzlo_multi2"); + memory->destroy(mbinxlo_multi); + memory->destroy(mbinylo_multi); + memory->destroy(mbinzlo_multi); + memory->create(mbinxlo_multi, maxtypes+1, "neigh:mbinxlo_multi"); + memory->create(mbinylo_multi, maxtypes+1, "neigh:mbinylo_multi"); + memory->create(mbinzlo_multi, maxtypes+1, "neigh:mbinzlo_multi"); - memory->destroy(binsizex_multi2); - memory->destroy(binsizey_multi2); - memory->destroy(binsizez_multi2); - memory->create(binsizex_multi2, maxtypes+1, "neigh:binsizex_multi2"); - memory->create(binsizey_multi2, maxtypes+1, "neigh:binsizey_multi2"); - memory->create(binsizez_multi2, maxtypes+1, "neigh:binsizez_multi2"); + memory->destroy(binsizex_multi); + memory->destroy(binsizey_multi); + memory->destroy(binsizez_multi); + memory->create(binsizex_multi, maxtypes+1, "neigh:binsizex_multi"); + memory->create(binsizey_multi, maxtypes+1, "neigh:binsizey_multi"); + memory->create(binsizez_multi, maxtypes+1, "neigh:binsizez_multi"); - memory->destroy(bininvx_multi2); - memory->destroy(bininvy_multi2); - memory->destroy(bininvz_multi2); - memory->create(bininvx_multi2, maxtypes+1, "neigh:bininvx_multi2"); - memory->create(bininvy_multi2, maxtypes+1, "neigh:bininvy_multi2"); - memory->create(bininvz_multi2, maxtypes+1, "neigh:bininvz_multi2"); + memory->destroy(bininvx_multi); + memory->destroy(bininvy_multi); + memory->destroy(bininvz_multi); + memory->create(bininvx_multi, maxtypes+1, "neigh:bininvx_multi"); + memory->create(bininvy_multi, maxtypes+1, "neigh:bininvy_multi"); + memory->create(bininvz_multi, maxtypes+1, "neigh:bininvz_multi"); - memory->destroy(maxbins_multi2); - memory->create(maxbins_multi2, maxtypes+1, "neigh:maxbins_multi2"); + memory->destroy(maxbins_multi); + memory->create(maxbins_multi, maxtypes+1, "neigh:maxbins_multi"); // make sure reallocation occurs in bin_atoms_setup() for (n = 1; n <= maxtypes; n++) { - maxbins_multi2[n] = 0; + maxbins_multi[n] = 0; } maxatom = 0; } @@ -214,16 +214,16 @@ void NBinMulti2::setup_bins(int style) // create actual bins // always have one bin even if cutoff > bbox - // for 2d, nbinz_multi2[n] = 1 + // for 2d, nbinz_multi[n] = 1 - nbinx_multi2[n] = static_cast (bbox[0]*binsizeinv); - nbiny_multi2[n] = static_cast (bbox[1]*binsizeinv); - if (dimension == 3) nbinz_multi2[n] = static_cast (bbox[2]*binsizeinv); - else nbinz_multi2[n] = 1; + nbinx_multi[n] = static_cast (bbox[0]*binsizeinv); + nbiny_multi[n] = static_cast (bbox[1]*binsizeinv); + if (dimension == 3) nbinz_multi[n] = static_cast (bbox[2]*binsizeinv); + else nbinz_multi[n] = 1; - if (nbinx_multi2[n] == 0) nbinx_multi2[n] = 1; - if (nbiny_multi2[n] == 0) nbiny_multi2[n] = 1; - if (nbinz_multi2[n] == 0) nbinz_multi2[n] = 1; + if (nbinx_multi[n] == 0) nbinx_multi[n] = 1; + if (nbiny_multi[n] == 0) nbiny_multi[n] = 1; + if (nbinz_multi[n] == 0) nbinz_multi[n] = 1; // compute actual bin size for nbins to fit into box exactly // error if actual bin size << cutoff, since will create a zillion bins @@ -231,17 +231,17 @@ void NBinMulti2::setup_bins(int style) // typically due to non-periodic, flat system in a particular dim // in that extreme case, should use NSQ not BIN neighbor style - binsizex_multi2[n] = bbox[0]/nbinx_multi2[n]; - binsizey_multi2[n] = bbox[1]/nbiny_multi2[n]; - binsizez_multi2[n] = bbox[2]/nbinz_multi2[n]; + binsizex_multi[n] = bbox[0]/nbinx_multi[n]; + binsizey_multi[n] = bbox[1]/nbiny_multi[n]; + binsizez_multi[n] = bbox[2]/nbinz_multi[n]; - bininvx_multi2[n] = 1.0 / binsizex_multi2[n]; - bininvy_multi2[n] = 1.0 / binsizey_multi2[n]; - bininvz_multi2[n] = 1.0 / binsizez_multi2[n]; + bininvx_multi[n] = 1.0 / binsizex_multi[n]; + bininvy_multi[n] = 1.0 / binsizey_multi[n]; + bininvz_multi[n] = 1.0 / binsizez_multi[n]; - if (binsize_optimal*bininvx_multi2[n] > CUT2BIN_RATIO || - binsize_optimal*bininvy_multi2[n] > CUT2BIN_RATIO || - binsize_optimal*bininvz_multi2[n] > CUT2BIN_RATIO) + if (binsize_optimal*bininvx_multi[n] > CUT2BIN_RATIO || + binsize_optimal*bininvy_multi[n] > CUT2BIN_RATIO || + binsize_optimal*bininvz_multi[n] > CUT2BIN_RATIO) error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); // mbinlo/hi = lowest and highest global bins my ghost atoms could be in @@ -253,46 +253,46 @@ void NBinMulti2::setup_bins(int style) double coord; coord = bsubboxlo[0] - SMALL*bbox[0]; - mbinxlo_multi2[n] = static_cast ((coord-bboxlo[0])*bininvx_multi2[n]); - if (coord < bboxlo[0]) mbinxlo_multi2[n] = mbinxlo_multi2[n] - 1; + mbinxlo_multi[n] = static_cast ((coord-bboxlo[0])*bininvx_multi[n]); + if (coord < bboxlo[0]) mbinxlo_multi[n] = mbinxlo_multi[n] - 1; coord = bsubboxhi[0] + SMALL*bbox[0]; - mbinxhi = static_cast ((coord-bboxlo[0])*bininvx_multi2[n]); + mbinxhi = static_cast ((coord-bboxlo[0])*bininvx_multi[n]); coord = bsubboxlo[1] - SMALL*bbox[1]; - mbinylo_multi2[n] = static_cast ((coord-bboxlo[1])*bininvy_multi2[n]); - if (coord < bboxlo[1]) mbinylo_multi2[n] = mbinylo_multi2[n] - 1; + mbinylo_multi[n] = static_cast ((coord-bboxlo[1])*bininvy_multi[n]); + if (coord < bboxlo[1]) mbinylo_multi[n] = mbinylo_multi[n] - 1; coord = bsubboxhi[1] + SMALL*bbox[1]; - mbinyhi = static_cast ((coord-bboxlo[1])*bininvy_multi2[n]); + mbinyhi = static_cast ((coord-bboxlo[1])*bininvy_multi[n]); if (dimension == 3) { coord = bsubboxlo[2] - SMALL*bbox[2]; - mbinzlo_multi2[n] = static_cast ((coord-bboxlo[2])*bininvz_multi2[n]); - if (coord < bboxlo[2]) mbinzlo_multi2[n] = mbinzlo_multi2[n] - 1; + mbinzlo_multi[n] = static_cast ((coord-bboxlo[2])*bininvz_multi[n]); + if (coord < bboxlo[2]) mbinzlo_multi[n] = mbinzlo_multi[n] - 1; coord = bsubboxhi[2] + SMALL*bbox[2]; - mbinzhi = static_cast ((coord-bboxlo[2])*bininvz_multi2[n]); + mbinzhi = static_cast ((coord-bboxlo[2])*bininvz_multi[n]); } // extend bins by 1 to insure stencil extent is included // for 2d, only 1 bin in z - mbinxlo_multi2[n] = mbinxlo_multi2[n] - 1; + mbinxlo_multi[n] = mbinxlo_multi[n] - 1; mbinxhi = mbinxhi + 1; - mbinx_multi2[n] = mbinxhi - mbinxlo_multi2[n] + 1; + mbinx_multi[n] = mbinxhi - mbinxlo_multi[n] + 1; - mbinylo_multi2[n] = mbinylo_multi2[n] - 1; + mbinylo_multi[n] = mbinylo_multi[n] - 1; mbinyhi = mbinyhi + 1; - mbiny_multi2[n] = mbinyhi - mbinylo_multi2[n] + 1; + mbiny_multi[n] = mbinyhi - mbinylo_multi[n] + 1; if (dimension == 3) { - mbinzlo_multi2[n] = mbinzlo_multi2[n] - 1; + mbinzlo_multi[n] = mbinzlo_multi[n] - 1; mbinzhi = mbinzhi + 1; - } else mbinzlo_multi2[n] = mbinzhi = 0; - mbinz_multi2[n] = mbinzhi - mbinzlo_multi2[n] + 1; + } else mbinzlo_multi[n] = mbinzhi = 0; + mbinz_multi[n] = mbinzhi - mbinzlo_multi[n] + 1; - bigint bbin = ((bigint) mbinx_multi2[n]) - * ((bigint) mbiny_multi2[n]) * ((bigint) mbinz_multi2[n]) + 1; + bigint bbin = ((bigint) mbinx_multi[n]) + * ((bigint) mbiny_multi[n]) * ((bigint) mbinz_multi[n]) + 1; if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins"); - mbins_multi2[n] = bbin; + mbins_multi[n] = bbin; } } @@ -301,13 +301,13 @@ void NBinMulti2::setup_bins(int style) bin owned and ghost atoms by type ------------------------------------------------------------------------- */ -void NBinMulti2::bin_atoms() +void NBinMulti::bin_atoms() { int i,ibin,n; last_bin = update->ntimestep; for (n = 1; n <= maxtypes; n++) { - for (i = 0; i < mbins_multi2[n]; i++) binhead_multi2[n][i] = -1; + for (i = 0; i < mbins_multi[n]; i++) binhead_multi[n][i] = -1; } // bin in reverse order so linked list will be in forward order @@ -324,38 +324,38 @@ void NBinMulti2::bin_atoms() for (i = nall-1; i >= nlocal; i--) { if (mask[i] & bitmask) { n = type[i]; - ibin = coord2bin_multi2(x[i], n); - atom2bin_multi2[n][i] = ibin; - bins_multi2[n][i] = binhead_multi2[n][ibin]; - binhead_multi2[n][ibin] = i; + ibin = coord2bin_multi(x[i], n); + atom2bin_multi[n][i] = ibin; + bins_multi[n][i] = binhead_multi[n][ibin]; + binhead_multi[n][ibin] = i; } } for (i = atom->nfirst-1; i >= 0; i--) { n = type[i]; - ibin = coord2bin_multi2(x[i], n); - atom2bin_multi2[n][i] = ibin; - bins_multi2[n][i] = binhead_multi2[n][ibin]; - binhead_multi2[n][ibin] = i; + ibin = coord2bin_multi(x[i], n); + atom2bin_multi[n][i] = ibin; + bins_multi[n][i] = binhead_multi[n][ibin]; + binhead_multi[n][ibin] = i; } } else { for (i = nall-1; i >= 0; i--) { n = type[i]; - ibin = coord2bin_multi2(x[i], n); - atom2bin_multi2[n][i] = ibin; - bins_multi2[n][i] = binhead_multi2[n][ibin]; - binhead_multi2[n][ibin] = i; + ibin = coord2bin_multi(x[i], n); + atom2bin_multi[n][i] = ibin; + bins_multi[n][i] = binhead_multi[n][ibin]; + binhead_multi[n][ibin] = i; } } } /* ---------------------------------------------------------------------- */ -double NBinMulti2::memory_usage() +double NBinMulti::memory_usage() { double bytes = 0; for (int m = 1; m < maxtypes; m++) { - bytes += maxbins_multi2[m]*sizeof(int); + bytes += maxbins_multi[m]*sizeof(int); bytes += 2*maxatom*sizeof(int); } return bytes; diff --git a/src/nbin_multi2.h b/src/nbin_multi.h similarity index 85% rename from src/nbin_multi2.h rename to src/nbin_multi.h index 3094027f64..856f3fa722 100644 --- a/src/nbin_multi2.h +++ b/src/nbin_multi.h @@ -13,24 +13,24 @@ #ifdef NBIN_CLASS -NBinStyle(multi2, - NBinMulti2, - NB_MULTI2) +NBinStyle(multi, + NBinMulti, + NB_MULTI) #else -#ifndef LMP_NBIN_MULTI2_H -#define LMP_NBIN_MULTI2_H +#ifndef LMP_NBIN_MULTI_H +#define LMP_NBIN_MULTI_H #include "nbin.h" namespace LAMMPS_NS { -class NBinMulti2 : public NBin { +class NBinMulti : public NBin { public: - NBinMulti2(class LAMMPS *); - ~NBinMulti2() {} + NBinMulti(class LAMMPS *); + ~NBinMulti() {} void bin_atoms_setup(int); void setup_bins(int); void bin_atoms(); From 4a85afcde21dc63a8b35c5a1b789042bbb43dd07 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 17:22:42 -0700 Subject: [PATCH 0054/1217] Removing redundant stencils --- src/nstencil_half_bin_2d_newtoff.cpp | 37 --------------- src/nstencil_half_bin_3d_newtoff.cpp | 38 ---------------- src/nstencil_half_ghost_bin_2d_newtoff.cpp | 44 ------------------ src/nstencil_half_ghost_bin_3d_newtoff.cpp | 45 ------------------- src/nstencil_half_multi_2d_newtoff.cpp | 51 --------------------- src/nstencil_half_multi_3d_newtoff.cpp | 52 ---------------------- 6 files changed, 267 deletions(-) delete mode 100644 src/nstencil_half_bin_2d_newtoff.cpp delete mode 100644 src/nstencil_half_bin_3d_newtoff.cpp delete mode 100644 src/nstencil_half_ghost_bin_2d_newtoff.cpp delete mode 100644 src/nstencil_half_ghost_bin_3d_newtoff.cpp delete mode 100644 src/nstencil_half_multi_2d_newtoff.cpp delete mode 100644 src/nstencil_half_multi_3d_newtoff.cpp diff --git a/src/nstencil_half_bin_2d_newtoff.cpp b/src/nstencil_half_bin_2d_newtoff.cpp deleted file mode 100644 index 09c74d8b69..0000000000 --- a/src/nstencil_half_bin_2d_newtoff.cpp +++ /dev/null @@ -1,37 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_bin_2d_newtoff.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfBin2dNewtoff::NStencilHalfBin2dNewtoff(LAMMPS *lmp) : - NStencil(lmp) {} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfBin2dNewtoff::create() -{ - int i,j; - - nstencil = 0; - - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutneighmaxsq) - stencil[nstencil++] = j*mbinx + i; -} diff --git a/src/nstencil_half_bin_3d_newtoff.cpp b/src/nstencil_half_bin_3d_newtoff.cpp deleted file mode 100644 index 36b2a11c66..0000000000 --- a/src/nstencil_half_bin_3d_newtoff.cpp +++ /dev/null @@ -1,38 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_bin_3d_newtoff.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfBin3dNewtoff::NStencilHalfBin3dNewtoff(LAMMPS *lmp) : - NStencil(lmp) {} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfBin3dNewtoff::create() -{ - int i,j,k; - - nstencil = 0; - - for (k = -sz; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutneighmaxsq) - stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i; -} diff --git a/src/nstencil_half_ghost_bin_2d_newtoff.cpp b/src/nstencil_half_ghost_bin_2d_newtoff.cpp deleted file mode 100644 index 0aa5202da8..0000000000 --- a/src/nstencil_half_ghost_bin_2d_newtoff.cpp +++ /dev/null @@ -1,44 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_ghost_bin_2d_newtoff.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfGhostBin2dNewtoff:: -NStencilHalfGhostBin2dNewtoff(LAMMPS *lmp) : NStencil(lmp) -{ - xyzflag = 1; -} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfGhostBin2dNewtoff::create() -{ - int i,j; - - nstencil = 0; - - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutneighmaxsq) { - stencilxyz[nstencil][0] = i; - stencilxyz[nstencil][1] = j; - stencilxyz[nstencil][2] = 0; - stencil[nstencil++] = j*mbinx + i; - } -} diff --git a/src/nstencil_half_ghost_bin_3d_newtoff.cpp b/src/nstencil_half_ghost_bin_3d_newtoff.cpp deleted file mode 100644 index 95016108e4..0000000000 --- a/src/nstencil_half_ghost_bin_3d_newtoff.cpp +++ /dev/null @@ -1,45 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_ghost_bin_3d_newtoff.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfGhostBin3dNewtoff:: -NStencilHalfGhostBin3dNewtoff(LAMMPS *lmp) : NStencil(lmp) -{ - xyzflag = 1; -} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfGhostBin3dNewtoff::create() -{ - int i,j,k; - - nstencil = 0; - - for (k = -sz; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutneighmaxsq) { - stencilxyz[nstencil][0] = i; - stencilxyz[nstencil][1] = j; - stencilxyz[nstencil][2] = k; - stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i; - } -} diff --git a/src/nstencil_half_multi_2d_newtoff.cpp b/src/nstencil_half_multi_2d_newtoff.cpp deleted file mode 100644 index 9b6ea08862..0000000000 --- a/src/nstencil_half_multi_2d_newtoff.cpp +++ /dev/null @@ -1,51 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_multi_2d_newtoff.h" -#include "atom.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfMulti2dNewtoff:: -NStencilHalfMulti2dNewtoff(LAMMPS *lmp) : NStencil(lmp) {} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfMulti2dNewtoff::create() -{ - int i,j,n; - double rsq,typesq; - int *s; - double *distsq; - - int ntypes = atom->ntypes; - for (int itype = 1; itype <= ntypes; itype++) { - typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - n = 0; - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) { - rsq = bin_distance(i,j,0); - if (rsq < typesq) { - distsq[n] = rsq; - s[n++] = j*mbinx + i; - } - } - nstencil_multi[itype] = n; - } -} diff --git a/src/nstencil_half_multi_3d_newtoff.cpp b/src/nstencil_half_multi_3d_newtoff.cpp deleted file mode 100644 index 533ba21c3a..0000000000 --- a/src/nstencil_half_multi_3d_newtoff.cpp +++ /dev/null @@ -1,52 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_multi_3d_newtoff.h" -#include "atom.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfMulti3dNewtoff:: -NStencilHalfMulti3dNewtoff(LAMMPS *lmp) : NStencil(lmp) {} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfMulti3dNewtoff::create() -{ - int i,j,k,n; - double rsq,typesq; - int *s; - double *distsq; - - int ntypes = atom->ntypes; - for (int itype = 1; itype <= ntypes; itype++) { - typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - n = 0; - for (k = -sz; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) { - rsq = bin_distance(i,j,k); - if (rsq < typesq) { - distsq[n] = rsq; - s[n++] = k*mbiny*mbinx + j*mbinx + i; - } - } - nstencil_multi[itype] = n; - } -} From 1c52ff15c37df375d8b91b1f1b7c81aefed481da Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 17:39:20 -0700 Subject: [PATCH 0055/1217] Renaming multi nstencils to multi/old --- src/nstencil.cpp | 232 +++++++++--------- src/nstencil.h | 60 +++-- ..._2d.cpp => nstencil_full_multi_old_2d.cpp} | 12 +- src/nstencil_full_multi_old_2d.h | 43 ++++ ..._3d.cpp => nstencil_full_multi_old_3d.cpp} | 12 +- src/nstencil_full_multi_old_3d.h | 43 ++++ src/nstencil_half_multi_3d.h | 42 ---- src/nstencil_half_multi_3d_tri.h | 42 ---- ..._2d.cpp => nstencil_half_multi_old_2d.cpp} | 14 +- ..._2d_tri.h => nstencil_half_multi_old_2d.h} | 14 +- ...cpp => nstencil_half_multi_old_2d_tri.cpp} | 14 +- ..._2d.h => nstencil_half_multi_old_2d_tri.h} | 14 +- ..._3d.cpp => nstencil_half_multi_old_3d.cpp} | 14 +- ...ulti_2d.h => nstencil_half_multi_old_3d.h} | 15 +- ...cpp => nstencil_half_multi_old_3d_tri.cpp} | 14 +- ..._3d.h => nstencil_half_multi_old_3d_tri.h} | 15 +- 16 files changed, 298 insertions(+), 302 deletions(-) rename src/{nstencil_full_multi_2d.cpp => nstencil_full_multi_old_2d.cpp} (83%) create mode 100644 src/nstencil_full_multi_old_2d.h rename src/{nstencil_full_multi_3d.cpp => nstencil_full_multi_old_3d.cpp} (84%) create mode 100644 src/nstencil_full_multi_old_3d.h delete mode 100644 src/nstencil_half_multi_3d.h delete mode 100644 src/nstencil_half_multi_3d_tri.h rename src/{nstencil_half_multi_2d.cpp => nstencil_half_multi_old_2d.cpp} (84%) rename src/{nstencil_half_multi_2d_tri.h => nstencil_half_multi_old_2d.h} (71%) rename src/{nstencil_half_multi_2d_tri.cpp => nstencil_half_multi_old_2d_tri.cpp} (82%) rename src/{nstencil_half_multi_2d.h => nstencil_half_multi_old_2d_tri.h} (69%) rename src/{nstencil_half_multi_3d.cpp => nstencil_half_multi_old_3d.cpp} (84%) rename src/{nstencil_full_multi_2d.h => nstencil_half_multi_old_3d.h} (71%) rename src/{nstencil_half_multi_3d_tri.cpp => nstencil_half_multi_old_3d_tri.cpp} (83%) rename src/{nstencil_full_multi_3d.h => nstencil_half_multi_old_3d_tri.h} (69%) diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 6fece15dcd..42ddbaff30 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -46,12 +46,12 @@ using namespace LAMMPS_NS; in 2d is all bins in y-plane of self and above, but not below stencil includes self no versions that allow ghost on (no callers need it?) - for multi: + for multi/old: create one stencil for each atom type stencil follows same rules for half/full, newton on/off, triclinic cutoff is not cutneighmaxsq, but max cutoff for that atom type no versions that allow ghost on (any need for it?) - for multi2: + for multi: create one stencil for each itype-jtype pairing the full/half stencil label refers to the same-type stencil a half list with newton on has a half same-type stencil @@ -68,16 +68,16 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) last_stencil = -1; xyzflag = 0; - maxstencil = maxstencil_multi = 0; + maxstencil = maxstencil_multi_old = 0; stencil = nullptr; stencilxyz = nullptr; - nstencil_multi = nullptr; - stencil_multi = nullptr; - distsq_multi = nullptr; + nstencil_multi_old = nullptr; + stencil_multi_old = nullptr; + distsq_multi_old = nullptr; - nstencil_multi2 = nullptr; - stencil_multi2 = nullptr; - maxstencil_multi2 = nullptr; + nstencil_multi = nullptr; + stencil_multi = nullptr; + maxstencil_multi = nullptr; stencil_half = nullptr; stencil_skip = nullptr; @@ -93,46 +93,46 @@ NStencil::~NStencil() memory->destroy(stencil); memory->destroy(stencilxyz); - if (stencil_multi) { + if (stencil_multi_old) { int n = atom->ntypes; for (int i = 1; i <= n; i++) { - memory->destroy(stencil_multi[i]); - memory->destroy(distsq_multi[i]); + memory->destroy(stencil_multi_old[i]); + memory->destroy(distsq_multi_old[i]); } - delete [] nstencil_multi; - delete [] stencil_multi; - delete [] distsq_multi; + delete [] nstencil_multi_old; + delete [] stencil_multi_old; + delete [] distsq_multi_old; } - if (stencil_multi2) { + if (stencil_multi) { int n = atom->ntypes; - memory->destroy(nstencil_multi2); + memory->destroy(nstencil_multi); for (int i = 1; i <= n; i++) { for (int j = 0; j <= n; j++) { if (! stencil_skip[i][j]) - memory->destroy(stencil_multi2[i][j]); + memory->destroy(stencil_multi[i][j]); } - delete [] stencil_multi2[i]; + delete [] stencil_multi[i]; } - delete [] stencil_multi2; - memory->destroy(maxstencil_multi2); + delete [] stencil_multi; + memory->destroy(maxstencil_multi); memory->destroy(stencil_half); memory->destroy(stencil_skip); memory->destroy(stencil_bin_type); - memory->destroy(stencil_sx_multi2); - memory->destroy(stencil_sy_multi2); - memory->destroy(stencil_sz_multi2); + memory->destroy(stencil_sx_multi); + memory->destroy(stencil_sy_multi); + memory->destroy(stencil_sz_multi); - memory->destroy(stencil_mbinx_multi2); - memory->destroy(stencil_mbiny_multi2); - memory->destroy(stencil_mbinz_multi2); + memory->destroy(stencil_mbinx_multi); + memory->destroy(stencil_mbiny_multi); + memory->destroy(stencil_mbinz_multi); - memory->destroy(stencil_binsizex_multi2); - memory->destroy(stencil_binsizey_multi2); - memory->destroy(stencil_binsizez_multi2); + memory->destroy(stencil_binsizex_multi); + memory->destroy(stencil_binsizey_multi); + memory->destroy(stencil_binsizez_multi); } } @@ -183,20 +183,20 @@ void NStencil::copy_bin_info() } /* ---------------------------------------------------------------------- - copy needed info for multi2 from NBin class to this stencil class + copy needed info for multi from NBin class to this stencil class ------------------------------------------------------------------------- */ -void NStencil::copy_bin_info_multi2() +void NStencil::copy_bin_info_multi() { - mbinx_multi2 = nb->mbinx_multi2; - mbiny_multi2 = nb->mbiny_multi2; - mbinz_multi2 = nb->mbinz_multi2; - binsizex_multi2 = nb->binsizex_multi2; - binsizey_multi2 = nb->binsizey_multi2; - binsizez_multi2 = nb->binsizez_multi2; - bininvx_multi2 = nb->bininvx_multi2; - bininvy_multi2 = nb->bininvy_multi2; - bininvz_multi2 = nb->bininvz_multi2; + mbinx_multi = nb->mbinx_multi; + mbiny_multi = nb->mbiny_multi; + mbinz_multi = nb->mbinz_multi; + binsizex_multi = nb->binsizex_multi; + binsizey_multi = nb->binsizey_multi; + binsizez_multi = nb->binsizez_multi; + bininvx_multi = nb->bininvx_multi; + bininvy_multi = nb->bininvy_multi; + bininvz_multi = nb->bininvz_multi; } /* ---------------------------------------------------------------------- @@ -207,7 +207,7 @@ void NStencil::copy_bin_info_multi2() void NStencil::create_setup() { - if (neighstyle != Neighbor::MULTI2){ + if (neighstyle != Neighbor::MULTI){ if (nb) copy_bin_info(); last_stencil = update->ntimestep; @@ -242,25 +242,25 @@ void NStencil::create_setup() } else { int i; int n = atom->ntypes; - if (maxstencil_multi == 0) { - nstencil_multi = new int[n+1]; - stencil_multi = new int*[n+1]; - distsq_multi = new double*[n+1]; + if (maxstencil_multi_old == 0) { + nstencil_multi_old = new int[n+1]; + stencil_multi_old = new int*[n+1]; + distsq_multi_old = new double*[n+1]; for (i = 1; i <= n; i++) { - nstencil_multi[i] = 0; - stencil_multi[i] = nullptr; - distsq_multi[i] = nullptr; + nstencil_multi_old[i] = 0; + stencil_multi_old[i] = nullptr; + distsq_multi_old[i] = nullptr; } } - if (smax > maxstencil_multi) { - maxstencil_multi = smax; + if (smax > maxstencil_multi_old) { + maxstencil_multi_old = smax; for (i = 1; i <= n; i++) { - memory->destroy(stencil_multi[i]); - memory->destroy(distsq_multi[i]); - memory->create(stencil_multi[i],maxstencil_multi, - "neighstencil:stencil_multi"); - memory->create(distsq_multi[i],maxstencil_multi, - "neighstencil:distsq_multi"); + memory->destroy(stencil_multi_old[i]); + memory->destroy(distsq_multi_old[i]); + memory->create(stencil_multi_old[i],maxstencil_multi_old, + "neighstencil:stencil_multi_old"); + memory->create(distsq_multi_old[i],maxstencil_multi_old, + "neighstencil:distsq_multi_old"); } } } @@ -269,7 +269,7 @@ void NStencil::create_setup() double stencil_range; int n = atom->ntypes; - if(nb) copy_bin_info_multi2(); + if(nb) copy_bin_info_multi(); // Allocate arrays to store stencil information memory->create(stencil_half, n+1, n+1, @@ -279,26 +279,26 @@ void NStencil::create_setup() memory->create(stencil_bin_type, n+1, n+1, "neighstencil:stencil_bin_type"); - memory->create(stencil_sx_multi2, n+1, n+1, - "neighstencil:stencil_sx_multi2"); - memory->create(stencil_sy_multi2, n+1, n+1, - "neighstencil:stencil_sy_multi2"); - memory->create(stencil_sz_multi2, n+1, n+1, - "neighstencil:stencil_sz_multi2"); + memory->create(stencil_sx_multi, n+1, n+1, + "neighstencil:stencil_sx_multi"); + memory->create(stencil_sy_multi, n+1, n+1, + "neighstencil:stencil_sy_multi"); + memory->create(stencil_sz_multi, n+1, n+1, + "neighstencil:stencil_sz_multi"); - memory->create(stencil_binsizex_multi2, n+1, n+1, - "neighstencil:stencil_binsizex_multi2"); - memory->create(stencil_binsizey_multi2, n+1, n+1, - "neighstencil:stencil_binsizey_multi2"); - memory->create(stencil_binsizez_multi2, n+1, n+1, - "neighstencil:stencil_binsizez_multi2"); + memory->create(stencil_binsizex_multi, n+1, n+1, + "neighstencil:stencil_binsizex_multi"); + memory->create(stencil_binsizey_multi, n+1, n+1, + "neighstencil:stencil_binsizey_multi"); + memory->create(stencil_binsizez_multi, n+1, n+1, + "neighstencil:stencil_binsizez_multi"); - memory->create(stencil_mbinx_multi2, n+1, n+1, - "neighstencil:stencil_mbinx_multi2"); - memory->create(stencil_mbiny_multi2, n+1, n+1, - "neighstencil:stencil_mbiny_multi2"); - memory->create(stencil_mbinz_multi2, n+1, n+1, - "neighstencil:stencil_mbinz_multi2"); + memory->create(stencil_mbinx_multi, n+1, n+1, + "neighstencil:stencil_mbinx_multi"); + memory->create(stencil_mbiny_multi, n+1, n+1, + "neighstencil:stencil_mbiny_multi"); + memory->create(stencil_mbinz_multi, n+1, n+1, + "neighstencil:stencil_mbinz_multi"); // Skip all stencils by default, initialize smax for (i = 1; i <= n; i++) { @@ -312,15 +312,15 @@ void NStencil::create_setup() // Allocate arrays to store stencils - if (!maxstencil_multi2) { - memory->create(maxstencil_multi2, n+1, n+1, "neighstencil::stencil_multi2"); - memory->create(nstencil_multi2, n+1, n+1, "neighstencil::nstencil_multi2"); - stencil_multi2 = new int**[n+1](); + if (!maxstencil_multi) { + memory->create(maxstencil_multi, n+1, n+1, "neighstencil::stencil_multi"); + memory->create(nstencil_multi, n+1, n+1, "neighstencil::nstencil_multi"); + stencil_multi = new int**[n+1](); for (i = 1; i <= n; ++i) { - stencil_multi2[i] = new int*[n+1](); + stencil_multi[i] = new int*[n+1](); for (j = 1; j <= n; ++j) { - maxstencil_multi2[i][j] = 0; - nstencil_multi2[i][j] = 0; + maxstencil_multi[i][j] = 0; + nstencil_multi[i][j] = 0; } } } @@ -334,34 +334,34 @@ void NStencil::create_setup() // Copy bin info for this particular pair of types bin_type = stencil_bin_type[i][j]; - stencil_binsizex_multi2[i][j] = binsizex_multi2[bin_type]; - stencil_binsizey_multi2[i][j] = binsizey_multi2[bin_type]; - stencil_binsizez_multi2[i][j] = binsizez_multi2[bin_type]; + stencil_binsizex_multi[i][j] = binsizex_multi[bin_type]; + stencil_binsizey_multi[i][j] = binsizey_multi[bin_type]; + stencil_binsizez_multi[i][j] = binsizez_multi[bin_type]; - stencil_mbinx_multi2[i][j] = mbinx_multi2[bin_type]; - stencil_mbiny_multi2[i][j] = mbiny_multi2[bin_type]; - stencil_mbinz_multi2[i][j] = mbinz_multi2[bin_type]; + stencil_mbinx_multi[i][j] = mbinx_multi[bin_type]; + stencil_mbiny_multi[i][j] = mbiny_multi[bin_type]; + stencil_mbinz_multi[i][j] = mbinz_multi[bin_type]; stencil_range = sqrt(cutneighsq[i][j]); - sx = static_cast (stencil_range*bininvx_multi2[bin_type]); - if (sx*binsizex_multi2[bin_type] < stencil_range) sx++; - sy = static_cast (stencil_range*bininvy_multi2[bin_type]); - if (sy*binsizey_multi2[bin_type] < stencil_range) sy++; - sz = static_cast (stencil_range*bininvz_multi2[bin_type]); - if (sz*binsizez_multi2[bin_type] < stencil_range) sz++; + sx = static_cast (stencil_range*bininvx_multi[bin_type]); + if (sx*binsizex_multi[bin_type] < stencil_range) sx++; + sy = static_cast (stencil_range*bininvy_multi[bin_type]); + if (sy*binsizey_multi[bin_type] < stencil_range) sy++; + sz = static_cast (stencil_range*bininvz_multi[bin_type]); + if (sz*binsizez_multi[bin_type] < stencil_range) sz++; - stencil_sx_multi2[i][j] = sx; - stencil_sy_multi2[i][j] = sy; - stencil_sz_multi2[i][j] = sz; + stencil_sx_multi[i][j] = sx; + stencil_sy_multi[i][j] = sy; + stencil_sz_multi[i][j] = sz; smax = ((2*sx+1) * (2*sy+1) * (2*sz+1)); - if (smax > maxstencil_multi2[i][j]) { - maxstencil_multi2[i][j] = smax; - memory->destroy(stencil_multi2[i][j]); - memory->create(stencil_multi2[i][j], smax, - "neighstencil::stencil_multi2"); + if (smax > maxstencil_multi[i][j]) { + maxstencil_multi[i][j] = smax; + memory->destroy(stencil_multi[i][j]); + memory->create(stencil_multi[i][j], smax, + "neighstencil::stencil_multi"); } } } @@ -396,21 +396,21 @@ double NStencil::bin_distance(int i, int j, int k) compute closest distance for a given atom type ------------------------------------------------------------------------- */ -double NStencil::bin_distance_multi2(int i, int j, int k, int type) +double NStencil::bin_distance_multi(int i, int j, int k, int type) { double delx,dely,delz; - if (i > 0) delx = (i-1)*binsizex_multi2[type]; + if (i > 0) delx = (i-1)*binsizex_multi[type]; else if (i == 0) delx = 0.0; - else delx = (i+1)*binsizex_multi2[type]; + else delx = (i+1)*binsizex_multi[type]; - if (j > 0) dely = (j-1)*binsizey_multi2[type]; + if (j > 0) dely = (j-1)*binsizey_multi[type]; else if (j == 0) dely = 0.0; - else dely = (j+1)*binsizey_multi2[type]; + else dely = (j+1)*binsizey_multi[type]; - if (k > 0) delz = (k-1)*binsizez_multi2[type]; + if (k > 0) delz = (k-1)*binsizez_multi[type]; else if (k == 0) delz = 0.0; - else delz = (k+1)*binsizez_multi2[type]; + else delz = (k+1)*binsizez_multi[type]; return (delx*delx + dely*dely + delz*delz); } @@ -423,16 +423,16 @@ double NStencil::memory_usage() if (neighstyle == Neighbor::BIN) { bytes += memory->usage(stencil,maxstencil); bytes += memory->usage(stencilxyz,maxstencil,3); + } else if (neighstyle == Neighbor::MULTI_OLD) { + bytes += atom->ntypes*maxstencil_multi_old * sizeof(int); + bytes += atom->ntypes*maxstencil_multi_old * sizeof(double); } else if (neighstyle == Neighbor::MULTI) { - bytes += atom->ntypes*maxstencil_multi * sizeof(int); - bytes += atom->ntypes*maxstencil_multi * sizeof(double); - } else if (neighstyle == Neighbor::MULTI2) { int n = atom->ntypes; for (int i = 1; i <= n; i++) { for (int j = 1; j <= n; j++) { - bytes += maxstencil_multi2[i][j] * sizeof(int); - bytes += maxstencil_multi2[i][j] * sizeof(int); - bytes += maxstencil_multi2[i][j] * sizeof(double); + bytes += maxstencil_multi[i][j] * sizeof(int); + bytes += maxstencil_multi[i][j] * sizeof(int); + bytes += maxstencil_multi[i][j] * sizeof(double); } } bytes += 2 * n * n * sizeof(bool); diff --git a/src/nstencil.h b/src/nstencil.h index 60e584b2a0..28c7fb0ec2 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -27,21 +27,17 @@ class NStencil : protected Pointers { int nstencil; // # of bins in stencil int *stencil; // list of bin offsets int **stencilxyz; // bin offsets in xyz dims - int *nstencil_multi; // # bins in each type-based multi stencil - int **stencil_multi; // list of bin offsets in each stencil - double **distsq_multi; // sq distances to bins in each stencil - int ** nstencil_multi2; // # bins bins in each itype-jtype multi2 stencil - int *** stencil_multi2; // list of bin offsets in each multi2 stencil - int ** maxstencil_multi2; // max stencil size for each multi2 stencil - - // Note distsq_multi is used in multi to quickly skip bins beyond interaction cutoff - // Not quite sure why bins are beyond this distance? Have to think - // Probably not needed for multi2 since bins are more efficiently chosen + int *nstencil_multi_old; // # bins in each type-based old multi stencil + int **stencil_multi_old; // list of bin offsets in each stencil + double **distsq_multi_old; // sq distances to bins in each stencil + int ** nstencil_multi; // # bins bins in each itype-jtype multi stencil + int *** stencil_multi; // list of bin offsets in each multi stencil + int ** maxstencil_multi; // max stencil size for each multi stencil int sx,sy,sz; // extent of stencil in each dim - int **stencil_sx_multi2; // analogs for each multi2 stencil - int **stencil_sy_multi2; - int **stencil_sz_multi2; + int **stencil_sx_multi; // analogs for each multi stencil + int **stencil_sy_multi; + int **stencil_sz_multi; double cutoff_custom; // cutoff set by requestor @@ -77,32 +73,32 @@ class NStencil : protected Pointers { double binsizex,binsizey,binsizez; double bininvx,bininvy,bininvz; - // data from NBin class for multi2 + // data from NBin class for multi - int *mbinx_multi2; - int *mbiny_multi2; - int *mbinz_multi2; - double *binsizex_multi2; - double *binsizey_multi2; - double *binsizez_multi2; - double *bininvx_multi2; - double *bininvy_multi2; - double *bininvz_multi2; + int *mbinx_multi; + int *mbiny_multi; + int *mbinz_multi; + double *binsizex_multi; + double *binsizey_multi; + double *binsizez_multi; + double *bininvx_multi; + double *bininvy_multi; + double *bininvz_multi; // Stored bin information for each stencil - int **stencil_mbinx_multi2; - int **stencil_mbiny_multi2; - int **stencil_mbinz_multi2; - double **stencil_binsizex_multi2; - double **stencil_binsizey_multi2; - double **stencil_binsizez_multi2; + int **stencil_mbinx_multi; + int **stencil_mbiny_multi; + int **stencil_mbinz_multi; + double **stencil_binsizex_multi; + double **stencil_binsizey_multi; + double **stencil_binsizez_multi; // data common to all NStencil variants int xyzflag; // 1 if stencilxyz is allocated int maxstencil; // max size of stencil - int maxstencil_multi; // max sizes of stencils + int maxstencil_multi_old; // max sizes of stencils int dimension; @@ -113,8 +109,8 @@ class NStencil : protected Pointers { // methods for multi2 NStencil - double bin_distance_multi2(int, int, int, int); // distance between bin corners for different types - void copy_bin_info_multi2(); // copy mult2 info from NBin class + double bin_distance_multi(int, int, int, int); // distance between bin corners for different types + void copy_bin_info_multi(); // copy multi info from NBin class virtual void set_stencil_properties(){} // determine which stencils to build and how }; diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_old_2d.cpp similarity index 83% rename from src/nstencil_full_multi_2d.cpp rename to src/nstencil_full_multi_old_2d.cpp index b71ca5e55d..ec2dba322e 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_old_2d.cpp @@ -11,20 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_full_multi_2d.h" +#include "nstencil_full_multi_old_2d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilFullMulti2d::NStencilFullMulti2d(LAMMPS *lmp) : NStencil(lmp) {} +NStencilFullMultiOld2d::NStencilFullMultiOld2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilFullMulti2d::create() +void NStencilFullMultiOld2d::create() { int i,j,n; double rsq,typesq; @@ -34,8 +34,8 @@ void NStencilFullMulti2d::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) { @@ -45,6 +45,6 @@ void NStencilFullMulti2d::create() s[n++] = j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_full_multi_old_2d.h b/src/nstencil_full_multi_old_2d.h new file mode 100644 index 0000000000..d75df8bce7 --- /dev/null +++ b/src/nstencil_full_multi_old_2d.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(full/multi/old/2d, + NStencilFullMultiOld2d, + NS_FULL | NS_MULTI_OLD | NS_2D | NS_ORTHO | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_FULL_MULTI_OLD_2D_H +#define LMP_NSTENCIL_FULL_MULTI_OLD_2D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilFullMultiOld2d : public NStencil { + public: + NStencilFullMultiOld2d(class LAMMPS *); + ~NStencilFullMultiOld2d() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_old_3d.cpp similarity index 84% rename from src/nstencil_full_multi_3d.cpp rename to src/nstencil_full_multi_old_3d.cpp index 2c63476ae6..2bfd962261 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_old_3d.cpp @@ -11,20 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_full_multi_3d.h" +#include "nstencil_full_multi_old_3d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilFullMulti3d::NStencilFullMulti3d(LAMMPS *lmp) : NStencil(lmp) {} +NStencilFullMultiOld3d::NStencilFullMultiOld3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilFullMulti3d::create() +void NStencilFullMultiOld3d::create() { int i,j,k,n; double rsq,typesq; @@ -34,8 +34,8 @@ void NStencilFullMulti3d::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) @@ -46,6 +46,6 @@ void NStencilFullMulti3d::create() s[n++] = k*mbiny*mbinx + j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_full_multi_old_3d.h b/src/nstencil_full_multi_old_3d.h new file mode 100644 index 0000000000..bcc6f551a0 --- /dev/null +++ b/src/nstencil_full_multi_old_3d.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(full/multi/old/3d, + NStencilFullMultiOld3d, + NS_FULL | NS_MULTI_OLD | NS_3D | NS_ORTHO | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_FULL_MULTI_OLD_3D_H +#define LMP_NSTENCIL_FULL_MULTI_OLD_3D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilFullMultiOld3d : public NStencil { + public: + NStencilFullMultiOld3d(class LAMMPS *); + ~NStencilFullMultiOld3d() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi_3d.h b/src/nstencil_half_multi_3d.h deleted file mode 100644 index 51cf9d5c29..0000000000 --- a/src/nstencil_half_multi_3d.h +++ /dev/null @@ -1,42 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi/3d, - NStencilHalfMulti3d, NS_HALF | NS_MULTI | NS_3D | NS_ORTHO) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI_3D_H -#define LMP_NSTENCIL_HALF_MULTI_3D_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti3d : public NStencil { - public: - NStencilHalfMulti3d(class LAMMPS *); - ~NStencilHalfMulti3d() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi_3d_tri.h b/src/nstencil_half_multi_3d_tri.h deleted file mode 100644 index f33f65cfea..0000000000 --- a/src/nstencil_half_multi_3d_tri.h +++ /dev/null @@ -1,42 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi/3d/tri, - NStencilHalfMulti3dTri, NS_HALF | NS_MULTI | NS_3D | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI_3D_TRI_H -#define LMP_NSTENCIL_HALF_MULTI_3D_TRI_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti3dTri : public NStencil { - public: - NStencilHalfMulti3dTri(class LAMMPS *); - ~NStencilHalfMulti3dTri() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi_2d.cpp b/src/nstencil_half_multi_old_2d.cpp similarity index 84% rename from src/nstencil_half_multi_2d.cpp rename to src/nstencil_half_multi_old_2d.cpp index 6642c2decd..18efc14703 100644 --- a/src/nstencil_half_multi_2d.cpp +++ b/src/nstencil_half_multi_old_2d.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_2d.h" +#include "nstencil_half_multi_old_2d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti2d:: -NStencilHalfMulti2d(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMultiOld2d:: +NStencilHalfMultiOld2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti2d::create() +void NStencilHalfMultiOld2d::create() { int i,j,n; double rsq,typesq; @@ -35,8 +35,8 @@ void NStencilHalfMulti2d::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) @@ -47,6 +47,6 @@ void NStencilHalfMulti2d::create() s[n++] = j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_half_multi_2d_tri.h b/src/nstencil_half_multi_old_2d.h similarity index 71% rename from src/nstencil_half_multi_2d_tri.h rename to src/nstencil_half_multi_old_2d.h index 776c42e96b..ef9e127978 100644 --- a/src/nstencil_half_multi_2d_tri.h +++ b/src/nstencil_half_multi_old_2d.h @@ -13,22 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/multi/2d/tri, - NStencilHalfMulti2dTri, NS_HALF | NS_MULTI | NS_2D | NS_TRI) +NStencilStyle(half/multi/old/2d, + NStencilHalfMultiOld2d, NS_HALF | NS_MULTI_OLD | NS_2D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_HALF_MULTI_2D_TRI_H -#define LMP_NSTENCIL_HALF_MULTI_2D_TRI_H +#ifndef LMP_NSTENCIL_HALF_MULTI_OLD_2D_H +#define LMP_NSTENCIL_HALF_MULTI_OLD_2D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfMulti2dTri : public NStencil { +class NStencilHalfMultiOld2d : public NStencil { public: - NStencilHalfMulti2dTri(class LAMMPS *); - ~NStencilHalfMulti2dTri() {} + NStencilHalfMultiOld2d(class LAMMPS *); + ~NStencilHalfMultiOld2d() {} void create(); }; diff --git a/src/nstencil_half_multi_2d_tri.cpp b/src/nstencil_half_multi_old_2d_tri.cpp similarity index 82% rename from src/nstencil_half_multi_2d_tri.cpp rename to src/nstencil_half_multi_old_2d_tri.cpp index f9ed49404c..24056c2ada 100644 --- a/src/nstencil_half_multi_2d_tri.cpp +++ b/src/nstencil_half_multi_old_2d_tri.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_2d_tri.h" +#include "nstencil_half_multi_old_2d_tri.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti2dTri:: -NStencilHalfMulti2dTri(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMultiOld2dTri:: +NStencilHalfMultiOld2dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti2dTri::create() +void NStencilHalfMultiOld2dTri::create() { int i,j,n; double rsq,typesq; @@ -35,8 +35,8 @@ void NStencilHalfMulti2dTri::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) { @@ -46,6 +46,6 @@ void NStencilHalfMulti2dTri::create() s[n++] = j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_half_multi_2d.h b/src/nstencil_half_multi_old_2d_tri.h similarity index 69% rename from src/nstencil_half_multi_2d.h rename to src/nstencil_half_multi_old_2d_tri.h index 128d37a2e9..0c79ae8c96 100644 --- a/src/nstencil_half_multi_2d.h +++ b/src/nstencil_half_multi_old_2d_tri.h @@ -13,22 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/multi/2d, - NStencilHalfMulti2d, NS_HALF | NS_MULTI | NS_2D | NS_ORTHO) +NStencilStyle(half/multi/old/2d/tri, + NStencilHalfMultiOld2dTri, NS_HALF | NS_MULTI_OLD | NS_2D | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_MULTI_2D_H -#define LMP_NSTENCIL_HALF_MULTI_2D_H +#ifndef LMP_NSTENCIL_HALF_MULTI_OLD_2D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_OLD_2D_TRI_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfMulti2d : public NStencil { +class NStencilHalfMultiOld2dTri : public NStencil { public: - NStencilHalfMulti2d(class LAMMPS *); - ~NStencilHalfMulti2d() {} + NStencilHalfMultiOld2dTri(class LAMMPS *); + ~NStencilHalfMultiOld2dTri() {} void create(); }; diff --git a/src/nstencil_half_multi_3d.cpp b/src/nstencil_half_multi_old_3d.cpp similarity index 84% rename from src/nstencil_half_multi_3d.cpp rename to src/nstencil_half_multi_old_3d.cpp index 119398f960..ebdd09674d 100644 --- a/src/nstencil_half_multi_3d.cpp +++ b/src/nstencil_half_multi_old_3d.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_3d.h" +#include "nstencil_half_multi_old_3d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti3d:: -NStencilHalfMulti3d(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMultiOld3d:: +NStencilHalfMultiOld3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti3d::create() +void NStencilHalfMultiOld3d::create() { int i,j,k,n; double rsq,typesq; @@ -35,8 +35,8 @@ void NStencilHalfMulti3d::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) @@ -48,6 +48,6 @@ void NStencilHalfMulti3d::create() s[n++] = k*mbiny*mbinx + j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_full_multi_2d.h b/src/nstencil_half_multi_old_3d.h similarity index 71% rename from src/nstencil_full_multi_2d.h rename to src/nstencil_half_multi_old_3d.h index 2c28bb56bf..b37134b4cc 100644 --- a/src/nstencil_full_multi_2d.h +++ b/src/nstencil_half_multi_old_3d.h @@ -13,23 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(full/multi/2d, - NStencilFullMulti2d, - NS_FULL | NS_MULTI | NS_2D | NS_ORTHO | NS_TRI) +NStencilStyle(half/multi_old/3d, + NStencilHalfMultiOld3d, NS_HALF | NS_MULTI_OLD | NS_3D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_FULL_MULTI_2D_H -#define LMP_NSTENCIL_FULL_MULTI_2D_H +#ifndef LMP_NSTENCIL_HALF_MULTI_OLD_3D_H +#define LMP_NSTENCIL_HALF_MULTI_OLD_3D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilFullMulti2d : public NStencil { +class NStencilHalfMultiOld3d : public NStencil { public: - NStencilFullMulti2d(class LAMMPS *); - ~NStencilFullMulti2d() {} + NStencilHalfMultiOld3d(class LAMMPS *); + ~NStencilHalfMultiOld3d() {} void create(); }; diff --git a/src/nstencil_half_multi_3d_tri.cpp b/src/nstencil_half_multi_old_3d_tri.cpp similarity index 83% rename from src/nstencil_half_multi_3d_tri.cpp rename to src/nstencil_half_multi_old_3d_tri.cpp index ca31a5a073..27dd320c6b 100644 --- a/src/nstencil_half_multi_3d_tri.cpp +++ b/src/nstencil_half_multi_old_3d_tri.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_3d_tri.h" +#include "nstencil_half_multi_old_3d_tri.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti3dTri:: -NStencilHalfMulti3dTri(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMultiOld3dTri:: +NStencilHalfMultiOld3dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti3dTri::create() +void NStencilHalfMultiOld3dTri::create() { int i,j,k,n; double rsq,typesq; @@ -35,8 +35,8 @@ void NStencilHalfMulti3dTri::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) @@ -47,6 +47,6 @@ void NStencilHalfMulti3dTri::create() s[n++] = k*mbiny*mbinx + j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_full_multi_3d.h b/src/nstencil_half_multi_old_3d_tri.h similarity index 69% rename from src/nstencil_full_multi_3d.h rename to src/nstencil_half_multi_old_3d_tri.h index b2edfd8b0d..cbc98a8ba8 100644 --- a/src/nstencil_full_multi_3d.h +++ b/src/nstencil_half_multi_old_3d_tri.h @@ -13,23 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(full/multi/3d, - NStencilFullMulti3d, - NS_FULL | NS_MULTI | NS_3D | NS_ORTHO | NS_TRI) +NStencilStyle(half/multi/old/3d/tri, + NStencilHalfMultiOld3dTri, NS_HALF | NS_MULTI_OLD | NS_3D | NS_TRI) #else -#ifndef LMP_NSTENCIL_FULL_MULTI_3D_H -#define LMP_NSTENCIL_FULL_MULTI_3D_H +#ifndef LMP_NSTENCIL_HALF_MULTI_OLD_3D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_OLD_3D_TRI_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilFullMulti3d : public NStencil { +class NStencilHalfMultiOld3dTri : public NStencil { public: - NStencilFullMulti3d(class LAMMPS *); - ~NStencilFullMulti3d() {} + NStencilHalfMultiOld3dTri(class LAMMPS *); + ~NStencilHalfMultiOld3dTri() {} void create(); }; From 5d097845e78e801dd819670c8fd9af4a06eb529a Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 17:45:46 -0700 Subject: [PATCH 0056/1217] Renaming multi2->multi in nstencil --- src/nstencil.h | 4 +- ...lti2_2d.cpp => nstencil_full_multi_2d.cpp} | 22 ++++----- ...l_multi2_3d.h => nstencil_full_multi_2d.h} | 14 +++--- ...lti2_3d.cpp => nstencil_full_multi_3d.cpp} | 26 +++++------ ...f_multi2_2d.h => nstencil_full_multi_3d.h} | 14 +++--- src/nstencil_half_multi2_2d_tri.h | 45 ------------------- src/nstencil_half_multi2_3d_tri.h | 45 ------------------- ...lti2_2d.cpp => nstencil_half_multi_2d.cpp} | 26 +++++------ ...f_multi2_3d.h => nstencil_half_multi_2d.h} | 14 +++--- ...tri.cpp => nstencil_half_multi_2d_tri.cpp} | 26 +++++------ src/nstencil_half_multi_2d_tri.h | 45 +++++++++++++++++++ ...lti2_3d.cpp => nstencil_half_multi_3d.cpp} | 30 ++++++------- ...l_multi2_2d.h => nstencil_half_multi_3d.h} | 14 +++--- ...tri.cpp => nstencil_half_multi_3d_tri.cpp} | 30 ++++++------- src/nstencil_half_multi_3d_tri.h | 45 +++++++++++++++++++ 15 files changed, 200 insertions(+), 200 deletions(-) rename src/{nstencil_full_multi2_2d.cpp => nstencil_full_multi_2d.cpp} (77%) rename src/{nstencil_full_multi2_3d.h => nstencil_full_multi_2d.h} (73%) rename src/{nstencil_full_multi2_3d.cpp => nstencil_full_multi_3d.cpp} (75%) rename src/{nstencil_half_multi2_2d.h => nstencil_full_multi_3d.h} (73%) delete mode 100755 src/nstencil_half_multi2_2d_tri.h delete mode 100755 src/nstencil_half_multi2_3d_tri.h rename src/{nstencil_half_multi2_2d.cpp => nstencil_half_multi_2d.cpp} (78%) rename src/{nstencil_half_multi2_3d.h => nstencil_half_multi_2d.h} (73%) rename src/{nstencil_half_multi2_2d_tri.cpp => nstencil_half_multi_2d_tri.cpp} (78%) create mode 100755 src/nstencil_half_multi_2d_tri.h rename src/{nstencil_half_multi2_3d.cpp => nstencil_half_multi_3d.cpp} (78%) rename src/{nstencil_full_multi2_2d.h => nstencil_half_multi_3d.h} (73%) rename src/{nstencil_half_multi2_3d_tri.cpp => nstencil_half_multi_3d_tri.cpp} (77%) create mode 100755 src/nstencil_half_multi_3d_tri.h diff --git a/src/nstencil.h b/src/nstencil.h index 28c7fb0ec2..5bff8cbfac 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -41,7 +41,7 @@ class NStencil : protected Pointers { double cutoff_custom; // cutoff set by requestor - // Arrays to store options for multi2 itype-jtype stencils + // Arrays to store options for multi itype-jtype stencils bool **stencil_half; // flag creation of a half stencil for itype-jtype bool **stencil_skip; // skip creation of itype-jtype stencils (for newton on) int **stencil_bin_type; // what type to use for bin information @@ -107,7 +107,7 @@ class NStencil : protected Pointers { void copy_bin_info(); // copy info from NBin class double bin_distance(int, int, int); // distance between bin corners - // methods for multi2 NStencil + // methods for multi NStencil double bin_distance_multi(int, int, int, int); // distance between bin corners for different types void copy_bin_info_multi(); // copy multi info from NBin class diff --git a/src/nstencil_full_multi2_2d.cpp b/src/nstencil_full_multi_2d.cpp similarity index 77% rename from src/nstencil_full_multi2_2d.cpp rename to src/nstencil_full_multi_2d.cpp index 658dba1c28..9712db7ac8 100644 --- a/src/nstencil_full_multi2_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_full_multi2_2d.h" +#include "nstencil_full_multi_2d.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,11 +23,11 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilFullMulti22d::NStencilFullMulti22d(LAMMPS *lmp) : NStencil(lmp) {} +NStencilFullMulti2d::NStencilFullMulti2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilFullMulti22d::set_stencil_properties() +void NStencilFullMulti2d::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -47,7 +47,7 @@ void NStencilFullMulti22d::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilFullMulti22d::create() +void NStencilFullMulti2d::create() { int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; @@ -60,11 +60,11 @@ void NStencilFullMulti22d::create() ns = 0; - sx = stencil_sx_multi2[itype][jtype]; - sy = stencil_sy_multi2[itype][jtype]; + sx = stencil_sx_multi[itype][jtype]; + sy = stencil_sy_multi[itype][jtype]; - mbinx = stencil_mbinx_multi2[itype][jtype]; - mbiny = stencil_mbiny_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi[itype][jtype]; + mbiny = stencil_mbiny_multi[itype][jtype]; bin_type = stencil_bin_type[itype][jtype]; @@ -72,10 +72,10 @@ void NStencilFullMulti22d::create() for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,0,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = j*mbinx + i; - nstencil_multi2[itype][jtype] = ns; + nstencil_multi[itype][jtype] = ns; } } } diff --git a/src/nstencil_full_multi2_3d.h b/src/nstencil_full_multi_2d.h similarity index 73% rename from src/nstencil_full_multi2_3d.h rename to src/nstencil_full_multi_2d.h index fb6a19ec6f..9990716b3a 100644 --- a/src/nstencil_full_multi2_3d.h +++ b/src/nstencil_full_multi_2d.h @@ -13,22 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(full/multi2/3d, - NStencilFullMulti23d, NS_FULL | NS_MULTI2 | NS_3D | NS_ORTHO | NS_TRI) +NStencilStyle(full/multi/2d, + NStencilFullMulti2d, NS_FULL | NS_MULTI | NS_2D | NS_ORTHO | NS_TRI) #else -#ifndef LMP_NSTENCIL_FULL_MULTI2_3D_H -#define LMP_NSTENCIL_FULL_MULTI2_3D_H +#ifndef LMP_NSTENCIL_FULL_MULTI_2D_H +#define LMP_NSTENCIL_FULL_MULTI_2D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilFullMulti23d : public NStencil { +class NStencilFullMulti2d : public NStencil { public: - NStencilFullMulti23d(class LAMMPS *); - ~NStencilFullMulti23d(){} + NStencilFullMulti2d(class LAMMPS *); + ~NStencilFullMulti2d() {} void create(); protected: diff --git a/src/nstencil_full_multi2_3d.cpp b/src/nstencil_full_multi_3d.cpp similarity index 75% rename from src/nstencil_full_multi2_3d.cpp rename to src/nstencil_full_multi_3d.cpp index 7bbe5208f2..b3f8db53b7 100644 --- a/src/nstencil_full_multi2_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_full_multi2_3d.h" +#include "nstencil_full_multi_3d.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,11 +23,11 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilFullMulti23d::NStencilFullMulti23d(LAMMPS *lmp) : NStencil(lmp) {} +NStencilFullMulti3d::NStencilFullMulti3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilFullMulti23d::set_stencil_properties() +void NStencilFullMulti3d::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -48,7 +48,7 @@ void NStencilFullMulti23d::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilFullMulti23d::create() +void NStencilFullMulti3d::create() { int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; @@ -61,13 +61,13 @@ void NStencilFullMulti23d::create() ns = 0; - sx = stencil_sx_multi2[itype][jtype]; - sy = stencil_sy_multi2[itype][jtype]; - sz = stencil_sz_multi2[itype][jtype]; + sx = stencil_sx_multi[itype][jtype]; + sy = stencil_sy_multi[itype][jtype]; + sz = stencil_sz_multi[itype][jtype]; - mbinx = stencil_mbinx_multi2[itype][jtype]; - mbiny = stencil_mbiny_multi2[itype][jtype]; - mbinz = stencil_mbinz_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi[itype][jtype]; + mbiny = stencil_mbiny_multi[itype][jtype]; + mbinz = stencil_mbinz_multi[itype][jtype]; bin_type = stencil_bin_type[itype][jtype]; @@ -76,11 +76,11 @@ void NStencilFullMulti23d::create() for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,k,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; - nstencil_multi2[itype][jtype] = ns; + nstencil_multi[itype][jtype] = ns; } } } diff --git a/src/nstencil_half_multi2_2d.h b/src/nstencil_full_multi_3d.h similarity index 73% rename from src/nstencil_half_multi2_2d.h rename to src/nstencil_full_multi_3d.h index 8e79fd0541..ed3401b2bd 100644 --- a/src/nstencil_half_multi2_2d.h +++ b/src/nstencil_full_multi_3d.h @@ -13,22 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/multi2/2d, - NStencilHalfMulti22d, NS_HALF | NS_MULTI2 | NS_2D | NS_ORTHO) +NStencilStyle(full/multi/3d, + NStencilFullMulti3d, NS_FULL | NS_MULTI | NS_3D | NS_ORTHO | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_MULTI2_2D_H -#define LMP_NSTENCIL_HALF_MULTI2_2D_H +#ifndef LMP_NSTENCIL_FULL_MULTI_3D_H +#define LMP_NSTENCIL_FULL_MULTI_3D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfMulti22d : public NStencil { +class NStencilFullMulti3d : public NStencil { public: - NStencilHalfMulti22d(class LAMMPS *); - ~NStencilHalfMulti22d() {} + NStencilFullMulti3d(class LAMMPS *); + ~NStencilFullMulti3d(){} void create(); protected: diff --git a/src/nstencil_half_multi2_2d_tri.h b/src/nstencil_half_multi2_2d_tri.h deleted file mode 100755 index 4072c6d31b..0000000000 --- a/src/nstencil_half_multi2_2d_tri.h +++ /dev/null @@ -1,45 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi2/2d/tri, - NStencilHalfMulti22dTri, NS_HALF | NS_MULTI2 | NS_2D | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI2_2D_TRI_H -#define LMP_NSTENCIL_HALF_MULTI2_2D_TRI_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti22dTri : public NStencil { - public: - NStencilHalfMulti22dTri(class LAMMPS *); - ~NStencilHalfMulti22dTri() {} - void create(); - - protected: - void set_stencil_properties(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi2_3d_tri.h b/src/nstencil_half_multi2_3d_tri.h deleted file mode 100755 index de449ce1d8..0000000000 --- a/src/nstencil_half_multi2_3d_tri.h +++ /dev/null @@ -1,45 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi2/3d/tri, - NStencilHalfMulti23dTri, NS_HALF | NS_MULTI2 | NS_3D | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI2_3D_TRI_H -#define LMP_NSTENCIL_HALF_MULTI2_3D_TRI_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti23dTri : public NStencil { - public: - NStencilHalfMulti23dTri(class LAMMPS *); - ~NStencilHalfMulti23dTri() {} - void create(); - - protected: - void set_stencil_properties(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi2_2d.cpp b/src/nstencil_half_multi_2d.cpp similarity index 78% rename from src/nstencil_half_multi2_2d.cpp rename to src/nstencil_half_multi_2d.cpp index f240d87b54..0b320394b7 100644 --- a/src/nstencil_half_multi2_2d.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi2_2d.h" +#include "nstencil_half_multi_2d.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,12 +23,12 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti22d::NStencilHalfMulti22d(LAMMPS *lmp) : +NStencilHalfMulti2d::NStencilHalfMulti2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilHalfMulti22d::set_stencil_properties() +void NStencilHalfMulti2d::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -59,7 +59,7 @@ void NStencilHalfMulti22d::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti22d::create() +void NStencilHalfMulti2d::create() { int itype, jtype, bin_type, i, j, ns; int n = atom->ntypes; @@ -72,11 +72,11 @@ void NStencilHalfMulti22d::create() ns = 0; - sx = stencil_sx_multi2[itype][jtype]; - sy = stencil_sy_multi2[itype][jtype]; + sx = stencil_sx_multi[itype][jtype]; + sy = stencil_sy_multi[itype][jtype]; - mbinx = stencil_mbinx_multi2[itype][jtype]; - mbiny = stencil_mbiny_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi[itype][jtype]; + mbiny = stencil_mbiny_multi[itype][jtype]; bin_type = stencil_bin_type[itype][jtype]; @@ -86,17 +86,17 @@ void NStencilHalfMulti22d::create() for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) if (j > 0 || (j == 0 && i > 0)) { - if (bin_distance_multi2(i,j,0,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = j*mbinx + i; } } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,0,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = j*mbinx + i; } - nstencil_multi2[itype][jtype] = ns; + nstencil_multi[itype][jtype] = ns; } } } diff --git a/src/nstencil_half_multi2_3d.h b/src/nstencil_half_multi_2d.h similarity index 73% rename from src/nstencil_half_multi2_3d.h rename to src/nstencil_half_multi_2d.h index 6a0d8f90a2..2c18bb7b07 100644 --- a/src/nstencil_half_multi2_3d.h +++ b/src/nstencil_half_multi_2d.h @@ -13,22 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/multi2/3d, - NStencilHalfMulti23d, NS_HALF | NS_MULTI2 | NS_3D | NS_ORTHO) +NStencilStyle(half/multi/2d, + NStencilHalfMulti2d, NS_HALF | NS_MULTI | NS_2D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_HALF_MULTI2_3D_H -#define LMP_NSTENCIL_HALF_MULTI2_3D_H +#ifndef LMP_NSTENCIL_HALF_MULTI_2D_H +#define LMP_NSTENCIL_HALF_MULTI_2D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfMulti23d : public NStencil { +class NStencilHalfMulti2d : public NStencil { public: - NStencilHalfMulti23d(class LAMMPS *); - ~NStencilHalfMulti23d() {} + NStencilHalfMulti2d(class LAMMPS *); + ~NStencilHalfMulti2d() {} void create(); protected: diff --git a/src/nstencil_half_multi2_2d_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp similarity index 78% rename from src/nstencil_half_multi2_2d_tri.cpp rename to src/nstencil_half_multi_2d_tri.cpp index 7143378305..95b0b483c5 100755 --- a/src/nstencil_half_multi2_2d_tri.cpp +++ b/src/nstencil_half_multi_2d_tri.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi2_2d_tri.h" +#include "nstencil_half_multi_2d_tri.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,12 +23,12 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti22dTri::NStencilHalfMulti22dTri(LAMMPS *lmp) : +NStencilHalfMulti2dTri::NStencilHalfMulti2dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilHalfMulti22dTri::set_stencil_properties() +void NStencilHalfMulti2dTri::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -59,7 +59,7 @@ void NStencilHalfMulti22dTri::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti22dTri::create() +void NStencilHalfMulti2dTri::create() { int itype, jtype, bin_type, i, j, ns; int n = atom->ntypes; @@ -72,11 +72,11 @@ void NStencilHalfMulti22dTri::create() ns = 0; - sx = stencil_sx_multi2[itype][jtype]; - sy = stencil_sy_multi2[itype][jtype]; + sx = stencil_sx_multi[itype][jtype]; + sy = stencil_sy_multi[itype][jtype]; - mbinx = stencil_mbinx_multi2[itype][jtype]; - mbiny = stencil_mbiny_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi[itype][jtype]; + mbiny = stencil_mbiny_multi[itype][jtype]; bin_type = stencil_bin_type[itype][jtype]; @@ -85,16 +85,16 @@ void NStencilHalfMulti22dTri::create() if (stencil_half[itype][jtype]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,0,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = j*mbinx + i; } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,0,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = j*mbinx + i; } - nstencil_multi2[itype][jtype] = ns; + nstencil_multi[itype][jtype] = ns; } } } diff --git a/src/nstencil_half_multi_2d_tri.h b/src/nstencil_half_multi_2d_tri.h new file mode 100755 index 0000000000..3cd49caa9d --- /dev/null +++ b/src/nstencil_half_multi_2d_tri.h @@ -0,0 +1,45 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/multi/2d/tri, + NStencilHalfMulti2dTri, NS_HALF | NS_MULTI | NS_2D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_2D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_2D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti2dTri : public NStencil { + public: + NStencilHalfMulti2dTri(class LAMMPS *); + ~NStencilHalfMulti2dTri() {} + void create(); + + protected: + void set_stencil_properties(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi2_3d.cpp b/src/nstencil_half_multi_3d.cpp similarity index 78% rename from src/nstencil_half_multi2_3d.cpp rename to src/nstencil_half_multi_3d.cpp index 83ecb24cba..1f94fb16cd 100644 --- a/src/nstencil_half_multi2_3d.cpp +++ b/src/nstencil_half_multi_3d.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi2_3d.h" +#include "nstencil_half_multi_3d.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,12 +23,12 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti23d::NStencilHalfMulti23d(LAMMPS *lmp) : +NStencilHalfMulti3d::NStencilHalfMulti3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilHalfMulti23d::set_stencil_properties() +void NStencilHalfMulti3d::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -59,7 +59,7 @@ void NStencilHalfMulti23d::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti23d::create() +void NStencilHalfMulti3d::create() { int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; @@ -72,13 +72,13 @@ void NStencilHalfMulti23d::create() ns = 0; - sx = stencil_sx_multi2[itype][jtype]; - sy = stencil_sy_multi2[itype][jtype]; - sz = stencil_sz_multi2[itype][jtype]; + sx = stencil_sx_multi[itype][jtype]; + sy = stencil_sy_multi[itype][jtype]; + sz = stencil_sz_multi[itype][jtype]; - mbinx = stencil_mbinx_multi2[itype][jtype]; - mbiny = stencil_mbiny_multi2[itype][jtype]; - mbinz = stencil_mbinz_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi[itype][jtype]; + mbiny = stencil_mbiny_multi[itype][jtype]; + mbinz = stencil_mbinz_multi[itype][jtype]; bin_type = stencil_bin_type[itype][jtype]; @@ -89,20 +89,20 @@ void NStencilHalfMulti23d::create() for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (k > 0 || j > 0 || (j == 0 && i > 0)) { - if (bin_distance_multi2(i,j,k,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,k,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } - nstencil_multi2[itype][jtype] = ns; + nstencil_multi[itype][jtype] = ns; } } } diff --git a/src/nstencil_full_multi2_2d.h b/src/nstencil_half_multi_3d.h similarity index 73% rename from src/nstencil_full_multi2_2d.h rename to src/nstencil_half_multi_3d.h index 46e12db039..a020192243 100644 --- a/src/nstencil_full_multi2_2d.h +++ b/src/nstencil_half_multi_3d.h @@ -13,22 +13,22 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(full/multi2/2d, - NStencilFullMulti22d, NS_FULL | NS_MULTI2 | NS_2D | NS_ORTHO | NS_TRI) +NStencilStyle(half/multi/3d, + NStencilHalfMulti3d, NS_HALF | NS_MULTI | NS_3D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_FULL_MULTI2_2D_H -#define LMP_NSTENCIL_FULL_MULTI2_2D_H +#ifndef LMP_NSTENCIL_HALF_MULTI_3D_H +#define LMP_NSTENCIL_HALF_MULTI_3D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilFullMulti22d : public NStencil { +class NStencilHalfMulti3d : public NStencil { public: - NStencilFullMulti22d(class LAMMPS *); - ~NStencilFullMulti22d() {} + NStencilHalfMulti3d(class LAMMPS *); + ~NStencilHalfMulti3d() {} void create(); protected: diff --git a/src/nstencil_half_multi2_3d_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp similarity index 77% rename from src/nstencil_half_multi2_3d_tri.cpp rename to src/nstencil_half_multi_3d_tri.cpp index 33915d4741..30e59e92e8 100755 --- a/src/nstencil_half_multi2_3d_tri.cpp +++ b/src/nstencil_half_multi_3d_tri.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi2_3d_tri.h" +#include "nstencil_half_multi_3d_tri.h" #include "neighbor.h" #include "neigh_list.h" #include "nbin.h" @@ -23,12 +23,12 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti23dTri::NStencilHalfMulti23dTri(LAMMPS *lmp) : +NStencilHalfMulti3dTri::NStencilHalfMulti3dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- */ -void NStencilHalfMulti23dTri::set_stencil_properties() +void NStencilHalfMulti3dTri::set_stencil_properties() { int n = atom->ntypes; int i, j; @@ -59,7 +59,7 @@ void NStencilHalfMulti23dTri::set_stencil_properties() create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti23dTri::create() +void NStencilHalfMulti3dTri::create() { int itype, jtype, bin_type, i, j, k, ns; int n = atom->ntypes; @@ -72,13 +72,13 @@ void NStencilHalfMulti23dTri::create() ns = 0; - sx = stencil_sx_multi2[itype][jtype]; - sy = stencil_sy_multi2[itype][jtype]; - sz = stencil_sz_multi2[itype][jtype]; + sx = stencil_sx_multi[itype][jtype]; + sy = stencil_sy_multi[itype][jtype]; + sz = stencil_sz_multi[itype][jtype]; - mbinx = stencil_mbinx_multi2[itype][jtype]; - mbiny = stencil_mbiny_multi2[itype][jtype]; - mbinz = stencil_mbinz_multi2[itype][jtype]; + mbinx = stencil_mbinx_multi[itype][jtype]; + mbiny = stencil_mbiny_multi[itype][jtype]; + mbinz = stencil_mbinz_multi[itype][jtype]; bin_type = stencil_bin_type[itype][jtype]; @@ -88,19 +88,19 @@ void NStencilHalfMulti23dTri::create() for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,k,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi2(i,j,k,bin_type) < cutsq) - stencil_multi2[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_type) < cutsq) + stencil_multi[itype][jtype][ns++] = k*mbiny*mbinx + j*mbinx + i; } - nstencil_multi2[itype][jtype] = ns; + nstencil_multi[itype][jtype] = ns; } } } diff --git a/src/nstencil_half_multi_3d_tri.h b/src/nstencil_half_multi_3d_tri.h new file mode 100755 index 0000000000..eb76e6fb2c --- /dev/null +++ b/src/nstencil_half_multi_3d_tri.h @@ -0,0 +1,45 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/multi/3d/tri, + NStencilHalfMulti3dTri, NS_HALF | NS_MULTI | NS_3D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_3D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_3D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti3dTri : public NStencil { + public: + NStencilHalfMulti3dTri(class LAMMPS *); + ~NStencilHalfMulti3dTri() {} + void create(); + + protected: + void set_stencil_properties(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ From 0a36baf86d87b5aa1ce403e9c417afd6427d9634 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 17:51:09 -0700 Subject: [PATCH 0057/1217] Updating naming in other classes --- src/comm.cpp | 22 +++++++++++----------- src/comm.h | 2 +- src/comm_brick.cpp | 8 ++++---- src/comm_tiled.cpp | 4 ++-- src/neighbor.cpp | 2 +- 5 files changed, 19 insertions(+), 19 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index f814c804c9..afd4d891ee 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -76,7 +76,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) grid2proc = nullptr; xsplit = ysplit = zsplit = nullptr; rcbnew = 0; - multi2 = 0; + multi_reduce = 0; // use of OpenMP threads // query OpenMP for number of threads/process set by user at run-time @@ -242,15 +242,15 @@ void Comm::init() for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; - // Can't used multi2 communication with Newton off + // Can't used multi_reduce communication with Newton off // TODO: need to somehow restrict this option with full neighbor lists - // CANNOT use multi2 communication with full nlist - // Could remove NP_NEWTON from npair_full_*multi2*, but could be cryptic - // Also could be cases where you want newton off (hybrid) but don't use multi2 comm - // Could add check on neighbor build, if full and comm->multi2 error... + // CANNOT use multi_reduce communication with full nlist + // Could remove NP_NEWTON from npair_full_*multi_reduce*, but could be cryptic + // Also could be cases where you want newton off (hybrid) but don't use multi_reduce comm + // Could add check on neighbor build, if full and comm->multi_reduce error... // or just add check on comm setup - is that run before every run? Only if box change... - if (force->newton == 0 && multi2) - error->all(FLERR,"Cannot use multi2 communication with Newton off"); + if (force->newton == 0 && multi_reduce) + error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); } /* ---------------------------------------------------------------------- @@ -337,10 +337,10 @@ void Comm::modify_params(int narg, char **arg) for (i=nlo; i<=nhi; ++i) cutusermulti[i] = cut; iarg += 3; - } else if (strcmp(arg[iarg],"cutoff/multi2") == 0) { + } else if (strcmp(arg[iarg],"multi/reduce") == 0) { if (mode == Comm::SINGLE) - error->all(FLERR,"Use cutoff/multi2 in mode multi only"); - multi2 = 1; + error->all(FLERR,"Use multi/reduce in mode multi only"); + multi_reduce = 1; iarg += 1; } else if (strcmp(arg[iarg],"vel") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command"); diff --git a/src/comm.h b/src/comm.h index 5cd47bd5cd..4ae4faf7fd 100644 --- a/src/comm.h +++ b/src/comm.h @@ -152,7 +152,7 @@ class Comm : protected Pointers { int ncores; // # of cores per node int coregrid[3]; // 3d grid of cores within a node int user_coregrid[3]; // user request for cores in each dim - int multi2; // 1 if multi cutoff is intra-type cutoff + int multi_reduce; // 1 if multi cutoff is intra-type cutoff void init_exchange(); int rendezvous_irregular(int, char *, int, int, int *, diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index b22c254e3a..7f84d619e4 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -174,8 +174,8 @@ void CommBrick::setup() cutghost[0] = cutghost[1] = cutghost[2] = cut; if (mode == Comm::MULTI) { - if (multi2) { - // If using multi2 binlists, communicate itype particles a distance + if (multi_reduce) { + // If using multi/reduce binlists, communicate itype particles a distance // equal to the max of itype-jtype interaction given smaller jtype particles double **cutneighsq = neighbor->cutneighsq; double *cuttypesq = neighbor->cuttypesq; @@ -225,8 +225,8 @@ void CommBrick::setup() cutghost[2] = cut * length2; if (mode == Comm::MULTI) { - if (multi2) { - // If using multi2 binlists, communicate itype particles a distance + if (multi_reduce) { + // If using multi/reduce binlists, communicate itype particles a distance // equal to the max of itype-jtype interaction given smaller jtype particles double **cutneighsq = neighbor->cutneighsq; double *cuttypesq = neighbor->cuttypesq; diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 4ff4774cd7..ce76fa7442 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -176,8 +176,8 @@ void CommTiled::setup() if (mode == Comm::MULTI) { double cut; - if (multi2) { - // If using multi2 binlists, communicate itype particles a distance + if (multi_reduce) { + // If using multi/reduce binlists, communicate itype particles a distance // equal to the max of itype-jtype interaction given smaller jtype particles double **cutneighsq = neighbor->cutneighsq; double *cuttypesq = neighbor->cuttypesq; diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 0854dee227..fe34e738b0 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1640,7 +1640,7 @@ int Neighbor::choose_bin(NeighRequest *rq) if (!rq->kokkos_device != !(mask & NB_KOKKOS_DEVICE)) continue; if (!rq->kokkos_host != !(mask & NB_KOKKOS_HOST)) continue; - // neighbor style is BIN or MULTI or MULTI2 and must match + // neighbor style is BIN or MULTI or MULTI_OLD and must match if (style == Neighbor::BIN || style == Neighbor::MULTI_OLD) { if (!(mask & NB_STANDARD)) continue; From fee6df1ab69ec546566d941e5cee2a263f2edf2d Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 19 Dec 2020 18:07:10 -0700 Subject: [PATCH 0058/1217] Fixing typos --- src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp | 4 ++-- src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp | 4 ++-- src/npair_half_size_multi_old_newton.h | 2 +- src/npair_half_size_multi_old_newton_tri.cpp | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp index 3ed703586d..204f811ca2 100644 --- a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtoffOldOmp::NPairHalfSizeMultiNewtoffOldOmp(LAMMPS *lmp) : +NPairHalfSizeMultiOldNewtoffOmp::NPairHalfSizeMultiOldNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- @@ -36,7 +36,7 @@ NPairHalfSizeMultiNewtoffOldOmp::NPairHalfSizeMultiNewtoffOldOmp(LAMMPS *lmp) : pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewtoffOldOmp::build(NeighList *list) +void NPairHalfSizeMultiOldNewtoffOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp index 37203c53db..6248004ce6 100644 --- a/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtonOldOmp::NPairHalfSizeMultiNewtonOldOmp(LAMMPS *lmp) : +NPairHalfSizeMultiOldNewtonOmp::NPairHalfSizeMultiOldNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- @@ -35,7 +35,7 @@ NPairHalfSizeMultiNewtonOldOmp::NPairHalfSizeMultiNewtonOldOmp(LAMMPS *lmp) : every pair stored exactly once by some processor ------------------------------------------------------------------------- */ -void NPairHalfSizeMultiNewtonOldOmp::build(NeighList *list) +void NPairHalfSizeMultiOldNewtonOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int history = list->history; diff --git a/src/npair_half_size_multi_old_newton.h b/src/npair_half_size_multi_old_newton.h index e954ee07b1..edd87a72ed 100644 --- a/src/npair_half_size_multi_old_newton.h +++ b/src/npair_half_size_multi_old_newton.h @@ -1,4 +1,4 @@ -g/* -*- c++ -*- ---------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov diff --git a/src/npair_half_size_multi_old_newton_tri.cpp b/src/npair_half_size_multi_old_newton_tri.cpp index 2b63e116d7..f29c323944 100644 --- a/src/npair_half_size_multi_old_newton_tri.cpp +++ b/src/npair_half_size_multi_old_newton_tri.cpp @@ -1,4 +1,4 @@ -re/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov From 05ecf8613423679a8fb065ef5702c0e95884c947 Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Sun, 20 Dec 2020 16:39:04 +0000 Subject: [PATCH 0059/1217] Made changes to propel/self. Kept all features of previous version (and tested they stayed the same), but additionally added dipole option for direction of self-propulsion. Also updated examples. --- doc/src/fix_propel_self.rst | 178 +++++++--- .../{bd_asphere => asphere}/README.txt | 0 .../{bd_asphere => asphere}/in3d.brownian | 0 .../log_gaussian_4_1_7_13_3d.lammps.log | 0 .../brownian/{bd_sphere => sphere}/README.txt | 0 .../{bd_sphere => sphere}/in2ddipole.brownian | 0 .../in3d_virial_on.brownian | 0 .../log_gaussian_4_1_7_13_2d.lammps.log | 0 .../log_uniform_10_1_5_15_3d.lammps.log | 0 .../USER/brownian/spherical_ABP/in.2d_abp | 70 ++++ .../brownian/spherical_ABP/in.3d_ideal_abp | 74 +++++ .../log_WCA_1_1_1_3_4_2d.lammps.log | 163 +++++++++ .../log_ideal_1_1_1_3_4_3d.lammps.log | 150 +++++++++ .../propel_self/2d_velocity/in.2d_langevin | 54 --- .../propel_self/2d_velocity/in.2d_viscous | 37 --- .../3d_quaternion/in.3d_quaternion | 40 --- src/USER-BROWNIAN/fix_propel_self.cpp | 312 ++++++++++++++++++ .../fix_propel_self.h | 51 ++- src/USER-MISC/README | 1 - src/USER-MISC/fix_propel_self.cpp | 258 --------------- 20 files changed, 919 insertions(+), 469 deletions(-) rename examples/USER/brownian/{bd_asphere => asphere}/README.txt (100%) rename examples/USER/brownian/{bd_asphere => asphere}/in3d.brownian (100%) rename examples/USER/brownian/{bd_asphere => asphere}/log_gaussian_4_1_7_13_3d.lammps.log (100%) rename examples/USER/brownian/{bd_sphere => sphere}/README.txt (100%) rename examples/USER/brownian/{bd_sphere => sphere}/in2ddipole.brownian (100%) rename examples/USER/brownian/{bd_sphere => sphere}/in3d_virial_on.brownian (100%) rename examples/USER/brownian/{bd_sphere => sphere}/log_gaussian_4_1_7_13_2d.lammps.log (100%) rename examples/USER/brownian/{bd_sphere => sphere}/log_uniform_10_1_5_15_3d.lammps.log (100%) create mode 100644 examples/USER/brownian/spherical_ABP/in.2d_abp create mode 100644 examples/USER/brownian/spherical_ABP/in.3d_ideal_abp create mode 100644 examples/USER/brownian/spherical_ABP/log_WCA_1_1_1_3_4_2d.lammps.log create mode 100644 examples/USER/brownian/spherical_ABP/log_ideal_1_1_1_3_4_3d.lammps.log delete mode 100644 examples/USER/misc/propel_self/2d_velocity/in.2d_langevin delete mode 100644 examples/USER/misc/propel_self/2d_velocity/in.2d_viscous delete mode 100644 examples/USER/misc/propel_self/3d_quaternion/in.3d_quaternion create mode 100644 src/USER-BROWNIAN/fix_propel_self.cpp rename src/{USER-MISC => USER-BROWNIAN}/fix_propel_self.h (55%) delete mode 100644 src/USER-MISC/fix_propel_self.cpp diff --git a/doc/src/fix_propel_self.rst b/doc/src/fix_propel_self.rst index 3a1bfb3166..6644d97d46 100644 --- a/doc/src/fix_propel_self.rst +++ b/doc/src/fix_propel_self.rst @@ -8,53 +8,117 @@ Syntax .. parsed-literal:: - fix ID group-ID propel/self mode magnitude keyword values ... + fix ID group-ID propel/self magnitude keyword values * ID, group-ID are documented in :doc:`fix ` command * propel/self = style name of this fix command -* mode = velocity or quat -* magnitude = magnitude of the active force -* one or more keyword/value pairs may be appended to args -* keyword = *types* +* magnitude = magnitude of self-propulsion force +* one (and only one) keyword/value pair must be appended to args +* keyword = *dipole* or *velocity* or *quat* + + .. parsed-literal:: + + *dipole* value = none = apply force along dipole direction + *velocity* value = none = apply force along velocity direction + *quat* values = direction vector *sx* and *sy* and *sz* + *sx* = x component of force direction in ellipsoid frame + *sy* = y component of force direction in ellipsoid frame + *sz* = z component of force direction in ellipsoid frame + - *types* values = one or more atom types Examples """""""" .. code-block:: LAMMPS - fix active_group all propel/self velocity 1.0 - fix constant_velocity all viscous 1.0 - - fix active_group all propel/self quat 1.0 - - fix active all propel/self quat 1.0 types 1 2 4 + fix propel/self all 40.0 dipole + fix propel/self all 10.0 velocity + fix propel/self all 15.7 quat 1.0 0.0 0.0 Description """"""""""" -Adds a force of a constant magnitude to each atom in the group. The nature in -which the force is added depends on the mode. +Add a force to each atom in the group due to a self-propulsion force. The +force is given by -For *mode* = *velocity*, the active force acts along the velocity vector of -each atom. This can be interpreted as a velocity-dependent friction, -such as proposed by :ref:`(Erdmann) `. +.. math:: -For *mode* = *quat* the force is applied along the axis obtained -by rotating the x-axis along the atom's quaternion. In other words, the -force is along the x-axis in the atom's body frame. This mode requires -all atoms in the group to have a quaternion, so atom_style should -either be ellipsoid or body. In combination with Langevin thermostat -for translation and rotation in the overdamped regime, the quaternion -mode corresponds to the active Brownian particle model introduced by -:ref:`(Henkes) `, :ref:`(Bialke) ` and :ref:`(Fily) -`. + F_i = f_P e_i -By default, this fix is applied to all atoms in the group. You can -override this behavior by specifying the atom types the fix should work -on through the *types* keyword. +where *i* is the particle the force is being applied to, :math:`f_P` +is the magnitude of the force, and :math:`e_i` is the vector direction +of the force. The specification of :math:`e_i` is based on which of the +three keywords (*dipole* or *velocity* or *quat*) one selects. +For keyword *dipole*, :math:`e_i` is just equal to +the dipole vectors of the atoms in the group. Therefore, if the dipoles +are not unit vectors, the :math:`e_i` will not be unit vectors. + +.. note:: + + If another command changes the magnitude of the dipole, this force will + change accordingly (since :math:`|e_i|` will change, which is physically + equivalent to re-scaling :math:`f_P` while keeping :math:`|e_i|` constant), + and no warning will be provided by LAMMPS. This is almost never what you + want, so ensure you aren't changing dipole magnitudes with another LAMMPS + fix or pair style. Furthermore, self-propulsion forces (almost) always + set :math:`e_i` to be a unit vector for all times, so it's best to set + all the dipole magnitudes to 1.0 unless you have a good reason not to + (see the :doc:`set ` command on how to do this). + +For keyword *velocity*, :math:`e_i` points in the direction +of the current velocity (a unit-vector). This can be interpreted as a +velocity-dependent friction, as proposed by e.g. :ref:`(Erdmann) `. + +For keyword *quat*, :math:`e_i` points in the direction of the unit +vector defined by its arguments *sx*, *sy*, and *sz*, which are +themselves defined within the coordinate frame of the atom's +ellipsoid. For instance, for an ellipsoid with long axis along +its x-direction, if one wanted the self-propulsion force to also +be along this axis, set *sx* equal to 1 and *sy*, *sz* both equal +to zero. For *quat*, :math:`e_i` will always be a unit vector, +so multiplying all three arguments *sx*, *sy*, and *sz* by a +positive scalar will not change the self-propulsion force +(multiplying by a negative scalar will change the sign of the +force). + +Along with adding a force contribution, this fix can also +contribute to the virial (pressure) of the system, defined as +:math:`f_P \sum_i /(d V)`, where :math:`r_i` is the +*unwrapped* coordinate of particle i in the case of periodic +boundary conditions. See :ref:`(Winkler) ` for a +discussion of this active pressure contribution. + +For keywords *dipole* and *quat*, this fix is by default +included in pressure computations. + +For keyword *velocity*, this fix is by default not included +in pressure computations. + + +.. note:: + + In contrast to equilibrium systems, pressure of active systems + in general depends on the geometry of the container. + The active pressure contribution as calculated in this fix + is only valid for certain boundary conditions (spherical + walls, rectangular walls, or periodic boundary conditions). + For other geometries, the pressure must be measured via + explicit calculation of the force per unit area on a wall, + and so one must not calculate it using this fix. + (Use :doc:`fix_modify ` as described below + to turn off the virial contribution of this fix). Again, + see :ref:`(Winkler) ` for discussion of why this + is the case. + + Furthermore, when dealing with active systems, the temperature + is no longer well defined. Therefore, one should ensure that + the *virial* flag is used in the + :doc:`compute pressure ` command (turning + off temperature contributions). + + ---------- Restart, fix_modify, output, run start/stop, minimize info @@ -62,40 +126,48 @@ Restart, fix_modify, output, run start/stop, minimize info No information about this fix is written to :doc:`binary restart files `. -This fix is not imposed during minimization. +The :doc:`fix_modify ` *virial* option is supported by this +fix to add the contribution due to the added forces on atoms to the +system's virial as part of :doc:`thermodynamic output `. +The default is *virial yes* for keywords *dipole* and *quat*. The +default is *virial no* for keyword *velocity*. + + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + Restrictions """""""""""" -In quat mode, this fix makes use of per-atom quaternions to take -into account the fact that the orientation can rotate and hence the -direction of the active force can change. The quat mode -of this fix only works with atom_style ellipsoid. +With keyword *dipole*, this fix only works when the DIPOLE package is enabled. +See the :doc:`Build package ` doc page for more info. + +This fix is part of the USER-BROWNIAN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` +doc page for more info. + Related commands """""""""""""""" -:doc:`fix setforce `, :doc:`fix addforce ` - -.. _Erdmann: - -**(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer, -Eur. Phys. J. B 15, 105-113, 2000. - -.. _Henkes: - -**(Henkes)** Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011. - -.. _Bialke: - -**(Bialke)** J. Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012. - -.. _Fily: - -**(Fily)** Y. Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012. +:doc:`fix efield ` , :doc:`fix setforce `, +:doc:`fix addforce ` Default """"""" -types +none +---------- + + +.. _Erdmann1: + +**(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer, +Eur. Phys. J. B 15, 105-113, 2000. + + +.. _Winkler1: + +**(Winkler)** Winkler, Wysocki, and Gompper, Soft Matter, 11, 6680 (2015). diff --git a/examples/USER/brownian/bd_asphere/README.txt b/examples/USER/brownian/asphere/README.txt similarity index 100% rename from examples/USER/brownian/bd_asphere/README.txt rename to examples/USER/brownian/asphere/README.txt diff --git a/examples/USER/brownian/bd_asphere/in3d.brownian b/examples/USER/brownian/asphere/in3d.brownian similarity index 100% rename from examples/USER/brownian/bd_asphere/in3d.brownian rename to examples/USER/brownian/asphere/in3d.brownian diff --git a/examples/USER/brownian/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log b/examples/USER/brownian/asphere/log_gaussian_4_1_7_13_3d.lammps.log similarity index 100% rename from examples/USER/brownian/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log rename to examples/USER/brownian/asphere/log_gaussian_4_1_7_13_3d.lammps.log diff --git a/examples/USER/brownian/bd_sphere/README.txt b/examples/USER/brownian/sphere/README.txt similarity index 100% rename from examples/USER/brownian/bd_sphere/README.txt rename to examples/USER/brownian/sphere/README.txt diff --git a/examples/USER/brownian/bd_sphere/in2ddipole.brownian b/examples/USER/brownian/sphere/in2ddipole.brownian similarity index 100% rename from examples/USER/brownian/bd_sphere/in2ddipole.brownian rename to examples/USER/brownian/sphere/in2ddipole.brownian diff --git a/examples/USER/brownian/bd_sphere/in3d_virial_on.brownian b/examples/USER/brownian/sphere/in3d_virial_on.brownian similarity index 100% rename from examples/USER/brownian/bd_sphere/in3d_virial_on.brownian rename to examples/USER/brownian/sphere/in3d_virial_on.brownian diff --git a/examples/USER/brownian/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log b/examples/USER/brownian/sphere/log_gaussian_4_1_7_13_2d.lammps.log similarity index 100% rename from examples/USER/brownian/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log rename to examples/USER/brownian/sphere/log_gaussian_4_1_7_13_2d.lammps.log diff --git a/examples/USER/brownian/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log b/examples/USER/brownian/sphere/log_uniform_10_1_5_15_3d.lammps.log similarity index 100% rename from examples/USER/brownian/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log rename to examples/USER/brownian/sphere/log_uniform_10_1_5_15_3d.lammps.log diff --git a/examples/USER/brownian/spherical_ABP/in.2d_abp b/examples/USER/brownian/spherical_ABP/in.2d_abp new file mode 100644 index 0000000000..d626445926 --- /dev/null +++ b/examples/USER/brownian/spherical_ABP/in.2d_abp @@ -0,0 +1,70 @@ +# 2D overdamped active brownian particle dynamics (ABP) +# with WCA potential + +variable gamma_t equal 1.0 +variable gamma_r equal 1.0 +variable D_t equal 1.0 +variable D_r equal 3.0 +variable seed equal 1974019 +variable fp equal 4.0 + +variable params string ${gamma_t}_${gamma_r}_${D_t}_${D_r}_${fp} + + +log log_WCA_${params}_2d.lammps.log +units lj +atom_style hybrid dipole sphere +dimension 2 +newton off + + +lattice sq 0.4 +region box block -16 16 -16 16 -0.2 0.2 +create_box 1 box +create_atoms 1 box +mass * 1.0 +set type * dipole/random ${seed} 1.0 +velocity all create 1.0 1 loop geom + +# more careful with neighbors since higher diffusion in abps +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + +# WCA potential (purely repulsive) +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.1224 +pair_modify shift yes + + + +# overdamped brownian dynamics time-step +fix step all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} dipole +# self-propulsion force along the dipole direction +fix activity all propel/self ${fp} dipole +fix 2 all enforce2d + + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +reset_timestep 0 + + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +timestep 0.00001 +thermo 10000 + +# main run +run 200000 diff --git a/examples/USER/brownian/spherical_ABP/in.3d_ideal_abp b/examples/USER/brownian/spherical_ABP/in.3d_ideal_abp new file mode 100644 index 0000000000..e131d07059 --- /dev/null +++ b/examples/USER/brownian/spherical_ABP/in.3d_ideal_abp @@ -0,0 +1,74 @@ +# 3D overdamped active brownian dynamics with no interactions + +variable gamma_t equal 1.0 +variable gamma_r equal 1.0 +variable D_t equal 1.0 +variable D_r equal 3.0 +variable seed equal 1974019 +variable fp equal 4.0 + +variable params string ${gamma_t}_${gamma_r}_${D_t}_${D_r}_${fp} + + +log log_ideal_${params}_3d.lammps.log +units lj +atom_style hybrid dipole sphere +dimension 3 +newton off + + +lattice sc 0.4 +region box block -8 8 -8 8 -8 8 +create_box 1 box +create_atoms 1 box +mass * 1.0 +set type * dipole/random ${seed} 1.0 +velocity all create 1.0 1 loop geom + +pair_style none + +# overdamped brownian dynamics time-step +fix step all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} dipole +# self-propulsion force along the dipole direction +fix activity all propel/self ${fp} dipole + + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +reset_timestep 0 + + +# MSD to demonstrate expected diffusive behaviour for ideal active +# brownian motion, which is +# +# MSD = (2*d*D_t + 2*fp**2/(gamma_t**2*(d-1)*D_r))*t +# +# with d being simulation dimension +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +timestep 0.00001 +thermo 10000 + +# main run +run 120000 + +# if you want to check that rotational diffusion is behaving as expected, +# uncomment next three lines for dump output and then plot , +# which should decay exponentially with timescale (d-1)*D_r (with d +# being simulation dimension) + +#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type & +# x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +#run 120000 \ No newline at end of file diff --git a/examples/USER/brownian/spherical_ABP/log_WCA_1_1_1_3_4_2d.lammps.log b/examples/USER/brownian/spherical_ABP/log_WCA_1_1_1_3_4_2d.lammps.log new file mode 100644 index 0000000000..0c51314cca --- /dev/null +++ b/examples/USER/brownian/spherical_ABP/log_WCA_1_1_1_3_4_2d.lammps.log @@ -0,0 +1,163 @@ +units lj +atom_style hybrid dipole sphere +WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (src/atom_vec_hybrid.cpp:157) +dimension 2 +newton off + + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 +region box block -16 16 -16 16 -0.2 0.2 +create_box 1 box +Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 1024 atoms + create_atoms CPU = 0.001 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 1974019 1.0 +Setting atom values ... + 1024 settings made for dipole/random +velocity all create 1.0 1 loop geom + +# more careful with neighbors since higher diffusion in abps +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + +# WCA potential (purely repulsive) +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.1224 +pair_modify shift yes + + + +# overdamped brownian dynamics time-step +fix step all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} dipole +fix step all brownian/sphere 1 ${gamma_r} ${D_t} ${D_r} ${seed} dipole +fix step all brownian/sphere 1 1 ${D_t} ${D_r} ${seed} dipole +fix step all brownian/sphere 1 1 1 ${D_r} ${seed} dipole +fix step all brownian/sphere 1 1 1 3 ${seed} dipole +fix step all brownian/sphere 1 1 1 3 1974019 dipole +# self-propulsion force along the dipole direction +fix activity all propel/self ${fp} dipole +fix activity all propel/self 4 dipole +fix 2 all enforce2d + + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +Neighbor list info ... + update every 1 steps, delay 1 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.1224 + ghost atom cutoff = 2.1224 + binsize = 1.0612, bins = 48 48 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/2d/newtoff + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.052 | 5.052 | 5.052 Mbytes +Step Temp E_pair c_press + 0 1 0 -0.53979198 + 50000 1.0371295e+10 0 -0.542818 +Loop time of 2.25396 on 4 procs for 50000 steps with 1024 atoms + +Performance: 0.192 tau/day, 22183.200 timesteps/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.1034 | 0.10382 | 0.10438 | 0.1 | 4.61 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.26698 | 0.26833 | 0.26924 | 0.2 | 11.90 +Output | 2.2284e-05 | 2.4926e-05 | 3.2332e-05 | 0.0 | 0.00 +Modify | 1.7222 | 1.7237 | 1.727 | 0.1 | 76.48 +Other | | 0.1581 | | | 7.01 + +Nlocal: 256.000 ave 256 max 256 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 105.000 ave 105 max 105 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 544.000 ave 544 max 544 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2176 +Ave neighs/atom = 2.1250000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +timestep 0.00001 +thermo 10000 + +# main run +run 200000 +Per MPI rank memory allocation (min/avg/max) = 5.427 | 5.427 | 5.427 Mbytes +Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 1.0371295e+10 0 0 0 0 0 -0.542818 + 10000 107356.09 0.079828495 0.19584264 0.19679822 0 0.39264086 0.00078740793 + 20000 101692.44 0.11317533 0.40847364 0.42097802 0 0.82945167 0.74111888 + 30000 105763.55 0.10261852 0.68303669 0.66125751 0 1.3442942 0.71112533 + 40000 105127.29 0.12371743 0.97990144 0.94005552 0 1.919957 1.0574552 + 50000 101579.58 0.12771813 1.3059069 1.2364468 0 2.5423537 1.059263 + 60000 104914.36 0.12055843 1.6215593 1.525488 0 3.1470473 0.79873537 + 70000 106629.18 0.1278745 1.9639958 1.8682794 0 3.8322752 0.91950208 + 80000 103286.54 0.13927689 2.3201565 2.2373383 0 4.5574948 1.1875034 + 90000 106451.61 0.093479681 2.6287902 2.5753347 0 5.2041249 1.0861163 + 100000 102199.72 0.13269425 2.9127976 2.9369237 0 5.8497214 1.4841998 + 110000 105229.73 0.10594209 3.1798718 3.3495317 0 6.5294035 1.5444784 + 120000 106262.36 0.11902575 3.6267452 3.7188125 0 7.3455578 1.3366518 + 130000 109388.12 0.10562576 3.929973 4.0226942 0 7.9526672 1.324534 + 140000 107697.35 0.13028752 4.231893 4.3780995 0 8.6099925 1.7406167 + 150000 103928.72 0.12278994 4.5826286 4.7578662 0 9.3404948 1.3024003 + 160000 103370.23 0.11391216 4.8767011 5.1181189 0 9.99482 1.4325241 + 170000 103821.53 0.11163256 5.153318 5.3785963 0 10.531914 1.4569115 + 180000 106824.99 0.13225083 5.4080929 5.7399804 0 11.148073 1.334984 + 190000 101794.6 0.10632938 5.7384925 6.080955 0 11.819448 0.81285422 + 200000 102128.67 0.13703498 6.0414673 6.4511058 0 12.492573 0.42904128 +Loop time of 9.60419 on 4 procs for 200000 steps with 1024 atoms + +Performance: 17992.140 tau/day, 20824.236 timesteps/s +100.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.71756 | 0.75121 | 0.79008 | 3.0 | 7.82 +Neigh | 0.018158 | 0.018773 | 0.019357 | 0.3 | 0.20 +Comm | 1.0469 | 1.0597 | 1.0738 | 1.2 | 11.03 +Output | 0.00051435 | 0.00057078 | 0.00070838 | 0.0 | 0.01 +Modify | 6.8012 | 6.9883 | 7.1513 | 4.9 | 72.76 +Other | | 0.7857 | | | 8.18 + +Nlocal: 256.000 ave 265 max 240 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 88.5000 ave 91 max 87 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +Neighs: 678.500 ave 713 max 597 min +Histogram: 1 0 0 0 0 0 0 0 1 2 + +Total # of neighbors = 2714 +Ave neighs/atom = 2.6503906 +Neighbor list builds = 241 +Dangerous builds = 0 +Total wall time: 0:00:11 diff --git a/examples/USER/brownian/spherical_ABP/log_ideal_1_1_1_3_4_3d.lammps.log b/examples/USER/brownian/spherical_ABP/log_ideal_1_1_1_3_4_3d.lammps.log new file mode 100644 index 0000000000..be6c1d5d41 --- /dev/null +++ b/examples/USER/brownian/spherical_ABP/log_ideal_1_1_1_3_4_3d.lammps.log @@ -0,0 +1,150 @@ +units lj +atom_style hybrid dipole sphere +WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (src/atom_vec_hybrid.cpp:157) +dimension 3 +newton off + + +lattice sc 0.4 +Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 +region box block -8 8 -8 8 -8 8 +create_box 1 box +Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670) + 2 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 4096 atoms + create_atoms CPU = 0.002 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 1974019 1.0 +Setting atom values ... + 4096 settings made for dipole/random +velocity all create 1.0 1 loop geom + +pair_style none + +# overdamped brownian dynamics time-step +fix step all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} dipole +fix step all brownian/sphere 1 ${gamma_r} ${D_t} ${D_r} ${seed} dipole +fix step all brownian/sphere 1 1 ${D_t} ${D_r} ${seed} dipole +fix step all brownian/sphere 1 1 1 ${D_r} ${seed} dipole +fix step all brownian/sphere 1 1 1 3 ${seed} dipole +fix step all brownian/sphere 1 1 1 3 1974019 dipole +# self-propulsion force along the dipole direction +fix activity all propel/self ${fp} dipole +fix activity all propel/self 4 dipole + + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.319 | 4.319 | 4.319 Mbytes +Step Temp E_pair c_press + 0 1 0 0.068021726 + 50000 1.046425e+10 0 0.067505633 +Loop time of 7.83903 on 4 procs for 50000 steps with 4096 atoms + +Performance: 0.055 tau/day, 6378.340 timesteps/s +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.50238 | 0.51891 | 0.53617 | 1.7 | 6.62 +Output | 2.6343e-05 | 3.6075e-05 | 4.6997e-05 | 0.0 | 0.00 +Modify | 6.9536 | 6.9732 | 7.0105 | 0.8 | 88.95 +Other | | 0.3469 | | | 4.43 + +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 353.000 ave 353 max 353 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + + +# MSD to demonstrate expected diffusive behaviour for ideal active +# brownian motion, which is +# +# MSD = (2*d*D_t + 2*fp**2/(gamma_t**2*(d-1)*D_r))*t +# +# with d being simulation dimension +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +timestep 0.00001 +thermo 10000 + +# main run +run 120000 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.694 | 4.694 | 4.694 Mbytes +Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 1.046425e+10 0 0 0 0 0 0.067505633 + 10000 106340.56 0 0.2469318 0.23662295 0.2441413 0.72769605 0.19939966 + 20000 104620.27 0 0.55429324 0.5231436 0.54976641 1.6272032 0.26601423 + 30000 106130.45 0 0.87562668 0.84813496 0.89321299 2.6169746 0.30836996 + 40000 105773.31 0 1.2262635 1.1899278 1.2626926 3.6788838 0.35392219 + 50000 103804.88 0 1.5851624 1.5645815 1.6434185 4.7931624 0.33326997 + 60000 105746.45 0 1.9928016 1.9347072 1.9837329 5.9112417 0.2550878 + 70000 104500.3 0 2.3269429 2.2774077 2.3368821 6.9412326 0.25218225 + 80000 105381.46 0 2.7114959 2.6937299 2.7171132 8.122339 0.36940892 + 90000 104542.79 0 3.0828648 3.084417 3.0783207 9.2456025 0.36106481 + 100000 104246.75 0 3.4635513 3.5105066 3.4545226 10.42858 0.3712313 + 110000 103099.55 0 3.8471061 3.9389997 3.8220676 11.608173 0.38466185 + 120000 103098.45 0 4.2014598 4.3456831 4.1888659 12.736009 0.36710217 +Loop time of 22.8893 on 4 procs for 120000 steps with 4096 atoms + +Performance: 4529.619 tau/day, 5242.615 timesteps/s +100.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0049489 | 0.0050479 | 0.0050978 | 0.1 | 0.02 +Comm | 0.082752 | 0.084491 | 0.085332 | 0.4 | 0.37 +Output | 0.00054352 | 0.0006034 | 0.00064793 | 0.0 | 0.00 +Modify | 21.069 | 21.521 | 21.964 | 7.0 | 94.02 +Other | | 1.278 | | | 5.58 + +Nlocal: 1024.00 ave 1050 max 1010 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 2169 +Dangerous builds = 0 + +# if you want to check that rotational diffusion is behaving as expected, +# uncomment next three lines for dump output and then plot , +# which should decay exponentially with timescale (d-1)*D_r (with d +# being simulation dimension) + +#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +#run 120000 +Total wall time: 0:00:30 diff --git a/examples/USER/misc/propel_self/2d_velocity/in.2d_langevin b/examples/USER/misc/propel_self/2d_velocity/in.2d_langevin deleted file mode 100644 index 6a23e0d005..0000000000 --- a/examples/USER/misc/propel_self/2d_velocity/in.2d_langevin +++ /dev/null @@ -1,54 +0,0 @@ -dimension 2 -boundary p p p - -variable L equal 20 -region total block -$L $L -$L $L -0.5 0.5 -lattice hex 0.3 -create_box 2 total -create_atoms 1 box - -# Set random fraction to passive: -set type 1 type/fraction 2 0.5 1337 - -# Purely repulsive particles: -variable rc equal "2^(1.0/6.0)" -pair_style lj/cut ${rc} -pair_coeff * * 1.0 1.0 -pair_modify shift yes - -mass * 1.0 - -fix step all nve -fix temp all langevin 1.0 1.0 1.0 13 -fix twod all enforce2d - -neighbor 0.6 bin - -dump traj all custom 250 2d_active.dump.bin id type x y z - -thermo_style custom time step pe ke etotal temp -thermo 1000 -run 5000 - -group one type 1 -group two type 2 - -compute ke1 one ke -compute ke2 two ke - -thermo_style custom step pe ke etotal temp c_ke1 c_ke2 - -fix active all propel/self velocity 1.0 - -# With active force there is more motion so increase bin size: -neighbor 1.0 bin -run 10000 - -# Only make type 1 active: -fix active all propel/self velocity 1.0 types 1 - -# With active force there is more motion so increase bin size: -neighbor 1.0 bin -run 10000 - - diff --git a/examples/USER/misc/propel_self/2d_velocity/in.2d_viscous b/examples/USER/misc/propel_self/2d_velocity/in.2d_viscous deleted file mode 100644 index 1283a5d574..0000000000 --- a/examples/USER/misc/propel_self/2d_velocity/in.2d_viscous +++ /dev/null @@ -1,37 +0,0 @@ -dimension 2 -boundary p p p - -variable L equal 20 -region total block -$L $L -$L $L -0.5 0.5 -lattice hex 0.3 -create_box 2 total -create_atoms 1 box - -# Set random fraction to passive: -set type 1 type/fraction 2 0.5 1337 - -# Purely repulsive particles: -variable rc equal "2^(1.0/6.0)" -pair_style lj/cut ${rc} -pair_coeff * * 1.0 1.0 -pair_modify shift yes - -mass * 1.0 - -fix step all nve -fix twod all enforce2d - -neighbor 0.6 bin - -dump traj all custom 250 2d_active.dump.bin id type x y z - -thermo_style custom step pe ke etotal temp -thermo 1000 -run 10000 - -fix active all propel/self velocity 1.0 -fix fric all viscous 1.0 - -# With active force there is more motion so increase bin size: -neighbor 1.0 bin -run 10000 diff --git a/examples/USER/misc/propel_self/3d_quaternion/in.3d_quaternion b/examples/USER/misc/propel_self/3d_quaternion/in.3d_quaternion deleted file mode 100644 index d6b6aff7dd..0000000000 --- a/examples/USER/misc/propel_self/3d_quaternion/in.3d_quaternion +++ /dev/null @@ -1,40 +0,0 @@ -dimension 3 -boundary p p p - -atom_style ellipsoid -variable L equal 20 -region total block -$L $L -$L $L -$L $L -lattice sc 0.1 -create_box 2 total -create_atoms 1 box - -# Set random fraction to passive: -set type 1 type/fraction 2 0.5 1337 - -# Purely repulsive particles: -variable rc equal "2^(1.0/6.0)" -pair_style lj/cut ${rc} -pair_coeff * * 1.0 1.0 -pair_modify shift yes - -# mass * 1.0 -set type * shape 1.0 1.0 1.0 -set type * density 1.9098593171027443 -set type * quat 0 0 1 0 - -fix step all nve/asphere -fix temp all langevin 1.0 1.0 1.0 13 angmom 3.333333333 - -neighbor 0.6 bin - -dump traj all custom 100 3d_active.dump.bin id type x y z fx fy fz - -thermo_style custom step pe ke etotal temp -thermo 100 -run 500 - -fix active all propel/self quat 1.0 - -# With active force there is more motion so increase bin size: -neighbor 1.0 bin -run 500 diff --git a/src/USER-BROWNIAN/fix_propel_self.cpp b/src/USER-BROWNIAN/fix_propel_self.cpp new file mode 100644 index 0000000000..1755f59840 --- /dev/null +++ b/src/USER-BROWNIAN/fix_propel_self.cpp @@ -0,0 +1,312 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ----------------------------------------------------------------------- + Contributed by Stefan Paquay @ Brandeis University + + Thanks to Liesbeth Janssen @ Eindhoven University for useful discussions! + + Current maintainer: Sam Cameron @ University of Bristol + +----------------------------------------------------------------------- */ + +#include +#include +#include +#include "fix_propel_self.h" +#include "math_extra.h" +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "force.h" +#include "update.h" +#include "comm.h" +#include "domain.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +enum{DIPOLE,VELOCITY,QUAT}; + +#define TOL 1e-14 + +/* ---------------------------------------------------------------------- */ + +FixPropelSelf::FixPropelSelf(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + + virial_flag = 1; + + if (narg < 5) + error->all(FLERR,"Illegal fix propel/self command"); + + + magnitude = utils::numeric(FLERR,arg[3],false,lmp); + + if (strcmp(arg[4],"velocity") == 0) { + mode = VELOCITY; + thermo_virial = 0; + if (narg != 5) { + error->all(FLERR,"Illegal fix propel/self command"); + } + } else if (strcmp(arg[4],"dipole") == 0) { + mode = DIPOLE; + thermo_virial = 1; + if (narg != 5) { + error->all(FLERR,"Illegal fix propel/self command"); + } + } else if (strcmp(arg[4],"quat") == 0) { + mode = QUAT; + thermo_virial = 1; + if (narg != 8) { + error->all(FLERR,"Illegal fix propel/self command"); + } else { + sx = utils::numeric(FLERR,arg[5],false,lmp); + sy = utils::numeric(FLERR,arg[6],false,lmp); + sz = utils::numeric(FLERR,arg[7],false,lmp); + double qnorm = sqrt(sx*sx + sy*sy + sz*sz); + sx = sx/qnorm; + sy = sy/qnorm; + sz = sz/qnorm; + } + } else { + error->all(FLERR,"Illegal fix propel/self command"); + } + + + + +} + +/* ---------------------------------------------------------------------- */ + +int FixPropelSelf::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +FixPropelSelf::~FixPropelSelf() +{ + +} + + +/* ---------------------------------------------------------------------- */ + +void FixPropelSelf::init() +{ + if (mode == DIPOLE && !atom->mu_flag) + error->all(FLERR,"Fix propel/self requires atom attribute mu " + "with option dipole."); + + if (mode == QUAT) { + avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); + if (!avec) + error->all(FLERR,"Fix propel/self requires " + "atom style ellipsoid with option quat."); + + // check that all particles are finite-size ellipsoids + // no point particles allowed, spherical is OK + + int *ellipsoid = atom->ellipsoid; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + if (ellipsoid[i] < 0) + error->one(FLERR,"Fix propel/self requires extended particles " + "with option quat."); + } + +} + +void FixPropelSelf::setup(int vflag) +{ + post_force(vflag); +} + +void FixPropelSelf::post_force(int vflag) +{ + if (mode == DIPOLE) + post_force_dipole(vflag); + else if (mode == VELOCITY) + post_force_velocity(vflag); + else if (mode == QUAT) + post_force_quaternion(vflag); + +} + + +void FixPropelSelf::post_force_dipole(int vflag) +{ + double **f = atom->f; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double **x = atom->x; + double **mu = atom->mu; + double fx,fy,fz; + + + // energy and virial setup + double vi[6]; + if (vflag) v_setup(vflag); + else evflag = 0; + + // if domain has PBC, need to unwrap for virial + double unwrap[3]; + imageint *image = atom->image; + + // Add the active force to the atom force: + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + + fx = magnitude*mu[i][0]; + fy = magnitude*mu[i][1]; + fz = magnitude*mu[i][2]; + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + + if (evflag) { + domain->unmap(x[i],image[i],unwrap); + vi[0] = fx*unwrap[0]; + vi[1] = fy*unwrap[1]; + vi[2] = fz*unwrap[2]; + vi[3] = fx*unwrap[1]; + vi[4] = fx*unwrap[2]; + vi[5] = fy*unwrap[2]; + v_tally(i, vi); + } + } +} + + +void FixPropelSelf::post_force_velocity(int vflag) +{ + double **f = atom->f; + double **v = atom->v; + double **x = atom->x; + int *mask = atom->mask; + int nlocal = atom->nlocal; + int *type = atom->type; + double nv2,fnorm,fx,fy,fz; + + + // energy and virial setup + double vi[6]; + if (vflag) v_setup(vflag); + else evflag = 0; + + // if domain has PBC, need to unwrap for virial + double unwrap[3]; + imageint *image = atom->image; + + // Add the active force to the atom force: + for(int i = 0; i < nlocal; ++i) { + if( mask[i] & groupbit ){ + + nv2 = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]; + fnorm = 0.0; + + if (nv2 > TOL) { + + // Without this check you can run into numerical + // issues because fnorm will blow up. + + fnorm = magnitude / sqrt(nv2); + } + fx = fnorm * v[i][0]; + fy = fnorm * v[i][1]; + fz = fnorm * v[i][2]; + + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + + if (evflag) { + domain->unmap(x[i],image[i],unwrap); + vi[0] = fx*unwrap[0]; + vi[1] = fy*unwrap[1]; + vi[2] = fz*unwrap[2]; + vi[3] = fx*unwrap[1]; + vi[4] = fx*unwrap[2]; + vi[5] = fy*unwrap[2]; + v_tally(i, vi); + } + } + } +} + +void FixPropelSelf::post_force_quaternion(int vflag) +{ + double **f = atom->f; + double **x = atom->x; + int *mask = atom->mask; + int nlocal = atom->nlocal; + int *type = atom->type; + int* ellipsoid = atom->ellipsoid; + + // ellipsoidal properties + AtomVecEllipsoid::Bonus *bonus = avec->bonus; + double f_act[3] = { sx, sy, sz }; + double f_rot[3]; + double *quat; + double Q[3][3]; + double fx,fy,fz; + + + // energy and virial setup + double vi[6]; + if (vflag) v_setup(vflag); + else evflag = 0; + + // if domain has PBC, need to unwrap for virial + double unwrap[3]; + imageint *image = atom->image; + + // Add the active force to the atom force: + for( int i = 0; i < nlocal; ++i ){ + if( mask[i] & groupbit ){ + + quat = bonus[ellipsoid[i]].quat; + MathExtra::quat_to_mat( quat, Q ); + MathExtra::matvec( Q, f_act, f_rot ); + + fx = magnitude*f_rot[0]; + fy = magnitude*f_rot[1]; + fz = magnitude*f_rot[2]; + + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + + if (evflag) { + domain->unmap(x[i],image[i],unwrap); + vi[0] = fx*unwrap[0]; + vi[1] = fy*unwrap[1]; + vi[2] = fz*unwrap[2]; + vi[3] = fx*unwrap[1]; + vi[4] = fx*unwrap[2]; + vi[5] = fy*unwrap[2]; + v_tally(i, vi); + } + } + } +} diff --git a/src/USER-MISC/fix_propel_self.h b/src/USER-BROWNIAN/fix_propel_self.h similarity index 55% rename from src/USER-MISC/fix_propel_self.h rename to src/USER-BROWNIAN/fix_propel_self.h index 47d1e1255b..a51ffe671b 100644 --- a/src/USER-MISC/fix_propel_self.h +++ b/src/USER-BROWNIAN/fix_propel_self.h @@ -21,51 +21,50 @@ FixStyle(propel/self,FixPropelSelf) #define LMP_FIX_PROPEL_SELF_H #include "fix.h" - namespace LAMMPS_NS { class FixPropelSelf : public Fix { public: - FixPropelSelf(class LAMMPS *, int, char **); virtual ~FixPropelSelf(); - virtual int setmask(); - virtual void post_force(int); + void init(); + void post_force(int); + void setup(int); + int setmask(); - double memory_usage(); - - protected: - enum operation_modes { - VELOCITY = 0, - QUATERNION = 1 - }; - -private: + private: double magnitude; + double sx,sy,sz; int mode; - // If 0, apply fix to everything in group. If > 0, apply only to those - // types i for which i <= n_types_filter _and_ apply_to_type[i] == 1: - int n_types_filter; - int *apply_to_type; //< Specifies, per type, if the fix applies to it or not. + void post_force_dipole(int); + void post_force_velocity(int); + void post_force_quaternion(int); + class AtomVecEllipsoid *avec; - int atoms_have_quaternion(); - - template void post_force_velocity(int); - template void post_force_quaternion(int); }; -} +} #endif #endif /* ERROR/WARNING messages: -E: Illegal ... command +E: Illegal fix propel/self command. -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. +Wrong number/type of input arguments. + +E: Fix propel/self requires atom attribute mu with option dipole. + +Self-explanatory. + +E: Fix propel/self requires atom style ellipsoid with option quat. + +Self-explanatory. + +Fix propel/self requires extended particles with option quat. + +Self-explanatory. */ diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 538fdb7952..b7199906a3 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -68,7 +68,6 @@ fix nvk, Efrem Braun (UC Berkeley), efrem.braun at gmail.com, https://github.com fix orient/eco Adrian A. Schratt and Volker Mohles (Ruhr-Uni Bochum), volker.mohles at rub.de, 6 Jun 2020 fix pafi, Thomas Swinburne (CNRS), swinburne at cinam.univ-mrs.fr, 1st Sep 2020 fix pimd, Yuxing Peng (U Chicago), yuxing at uchicago.edu, 24 Nov 2014 -fix propel/self, Stefan Paquay (Brandeis U), stefanpaquay at gmail.com, 20 Jan 2020 fix rhok, Ulf Pedersen (Roskilde U), ulf at urp.dk, 25 Sep 2017 fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008 fix ti/spring, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013 diff --git a/src/USER-MISC/fix_propel_self.cpp b/src/USER-MISC/fix_propel_self.cpp deleted file mode 100644 index 9299f4d23b..0000000000 --- a/src/USER-MISC/fix_propel_self.cpp +++ /dev/null @@ -1,258 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ----------------------------------------------------------------------- - Contributed by Stefan Paquay @ Brandeis University - - Thanks to Liesbeth Janssen @ Eindhoven University for useful discussions! ------------------------------------------------------------------------ */ - -#include "fix_propel_self.h" - -#include "atom.h" -#include "atom_vec_ellipsoid.h" -#include "error.h" -#include "math_const.h" -#include "math_extra.h" - -#include -#include -#include - -using namespace LAMMPS_NS; -using namespace FixConst; -using namespace MathConst; - -#define PRINT_DEBUG_OUTPUT 0 - -/* ---------------------------------------------------------------------- */ - -FixPropelSelf::FixPropelSelf( LAMMPS *lmp, int narg, char **argv ) - : Fix(lmp, narg, argv), magnitude(0.0), - mode(VELOCITY), n_types_filter(0), apply_to_type(nullptr) -{ - if (narg < 5) error->all(FLERR, "Illegal fix propel/self command"); - - // The fix is to support the following cases: - // 1. Simple atoms, in which case the force points along the velocity - // 2. Aspherical particles with an orientation. - // The first argument (mode) is used to differentiate between these. - - // args: fix ID all propel/self mode magnitude - // Optional args are - - const char *mode_str = argv[3]; - - if (strcmp(mode_str, "velocity") == 0) { - mode = VELOCITY; - - } else if (strcmp(mode_str, "quat") == 0) { - - // This mode should only be supported if the atom style has - // a quaternion (and if all atoms in the group have it) - - if (!atoms_have_quaternion()) { - error->all(FLERR, "All fix atoms need to be extended particles"); - } - mode = QUATERNION; - - } else { - char msg[2048]; - sprintf(msg, "Illegal mode \"%s\" for fix propel/self", mode_str); - error->all(FLERR, msg); - } - - magnitude = utils::numeric( FLERR, argv[4] ,false,lmp); - - // Handle rest of args: - - int iarg = 5; - while (iarg < narg) { - - if (strcmp(argv[iarg],"types") == 0) { - - apply_to_type = new int[atom->ntypes+1]; - memset(apply_to_type, 0, atom->ntypes * sizeof(int)); - - // consume all following numerical arguments as types - - iarg++; - int flag=0; - while (iarg < narg) { - if (isdigit(argv[iarg][0])) { - int thistype = utils::inumeric(FLERR,argv[iarg],false,lmp); - if ((thistype < 1) || (thistype > atom->ntypes)) - error->all(FLERR,"Illegal atom type to types keyword"); - apply_to_type[thistype] = 1; - flag = 1; - iarg++; - } else break; - } - if (!flag) - error->all(FLERR,"'types' keyword requires at least one type"); - else - n_types_filter = 1; - - } else { - error->all(FLERR,"Illegal fix propel/self command."); - } - } -} - -/* ---------------------------------------------------------------------- */ - -FixPropelSelf::~FixPropelSelf() -{ - delete[] apply_to_type; -} -/* ---------------------------------------------------------------------- */ - -int FixPropelSelf::setmask() -{ - int mask = 0; - mask |= POST_FORCE; - - return mask; -} - -/* ---------------------------------------------------------------------- */ - -double FixPropelSelf::memory_usage() -{ - // magnitude + thermostat_orient + mode + n_types_filter + apply_to_type - double bytes = sizeof(double) + 3*sizeof(int) + sizeof(int*); - bytes += sizeof(int)*atom->ntypes*n_types_filter; - - return bytes; -} - -/* ---------------------------------------------------------------------- */ - -void FixPropelSelf::post_force(int vflag ) -{ - switch(mode) { - case QUATERNION: - if (n_types_filter) post_force_quaternion<1>(vflag); - else post_force_quaternion<0>(vflag); - break; - case VELOCITY: - if (n_types_filter) post_force_velocity<1>(vflag); - else post_force_velocity<0>(vflag); - break; - default: - ; - } -} - -/* ---------------------------------------------------------------------- */ - -template -void FixPropelSelf::post_force_quaternion(int /* vflag */ ) -{ - double **f = atom->f; - - int *mask = atom->mask; - int nlocal = atom->nlocal; - int *type = atom->type; - int* ellipsoid = atom->ellipsoid; - - AtomVecEllipsoid *av = static_cast(atom->style_match("ellipsoid")); - AtomVecEllipsoid::Bonus *bonus = av->bonus; - - // Add the active force to the atom force: - - for( int i = 0; i < nlocal; ++i ){ - if( mask[i] & groupbit ){ - if (filter_by_type && !apply_to_type[type[i]]) { - continue; - } - - double f_act[3] = { 1.0, 0.0, 0.0 }; - double f_rot[3]; - - double *quat = bonus[ellipsoid[i]].quat; - - double Q[3][3]; - MathExtra::quat_to_mat( quat, Q ); - MathExtra::matvec( Q, f_act, f_rot ); - - f[i][0] += magnitude * f_rot[0]; - f[i][1] += magnitude * f_rot[1]; - f[i][2] += magnitude * f_rot[2]; - } - } -} - -/* ---------------------------------------------------------------------- */ - -template -void FixPropelSelf::post_force_velocity(int /*vflag*/) -{ - double **f = atom->f; - double **v = atom->v; - int *mask = atom->mask; - int nlocal = atom->nlocal; - int *type = atom->type; - - // Add the active force to the atom force: - - for(int i = 0; i < nlocal; ++i) { - if( mask[i] & groupbit ){ - if (filter_by_type && !apply_to_type[type[i]]) { - continue; - } - - const double *vi = v[i]; - double f_act[3] = { vi[0], vi[1], vi[2] }; - double nv2 = vi[0]*vi[0] + vi[1]*vi[1] + vi[2]*vi[2]; - double fnorm = 0.0; - const double TOL = 1e-14; - - if (nv2 > TOL) { - - // Without this check you can run into numerical - // issues because fnorm will blow up. - - fnorm = magnitude / sqrt(nv2); - } - - f[i][0] += fnorm * f_act[0]; - f[i][1] += fnorm * f_act[1]; - f[i][2] += fnorm * f_act[2]; - } - } -} - -/* ---------------------------------------------------------------------- */ - -int FixPropelSelf::atoms_have_quaternion() -{ - if (!atom->ellipsoid_flag) { - error->all(FLERR, "Mode 'quat' requires atom style ellipsoid"); - return 0; - } - - int *mask = atom->mask; - int flag=0,flagall=0; - - // Make sure all atoms have ellipsoid data: - - for (int i = 0; i < atom->nlocal; ++i) - if (mask[i] & groupbit) - if (atom->ellipsoid[i] < 0) ++flag; - - MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world); - if (flagall > 0) return 0; - - return 1; -} From 129210c7a0e87045ff888bdb28d91936d8536734 Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Sun, 20 Dec 2020 17:38:32 +0000 Subject: [PATCH 0060/1217] Updated examples and docs, and added basic brownian dynamics integrator (no rotational degrees of freedom). --- doc/src/Commands_fix.rst | 1 + doc/src/fix.rst | 5 +- doc/src/fix_brownian.rst | 151 +++++++++++ doc/src/fix_brownian_asphere.rst | 21 +- doc/src/fix_brownian_sphere.rst | 43 ++- doc/src/fix_propel_self.rst | 7 +- .../USER/brownian/2d_velocity/in.2d_velocity | 64 +++++ .../2d_velocity/log_1_1_4_2d.lammps.log | 248 ++++++++++++++++++ examples/USER/brownian/asphere/README.txt | 2 +- examples/USER/brownian/asphere/in3d.brownian | 30 +-- .../log_gaussian_1_0.33_1_3_3d.lammps.log | 141 ++++++++++ .../USER/brownian/sphere/in2ddipole.brownian | 25 +- .../brownian/sphere/in3d_virial_on.brownian | 22 +- .../USER/brownian/translational/in.brownian | 65 +++++ .../brownian/translational/log_1_1.lammps.log | 246 +++++++++++++++++ src/USER-BROWNIAN/fix_brownian.cpp | 217 +++++++++++++++ src/USER-BROWNIAN/fix_brownian.h | 79 ++++++ 17 files changed, 1268 insertions(+), 99 deletions(-) create mode 100644 doc/src/fix_brownian.rst create mode 100644 examples/USER/brownian/2d_velocity/in.2d_velocity create mode 100644 examples/USER/brownian/2d_velocity/log_1_1_4_2d.lammps.log create mode 100644 examples/USER/brownian/asphere/log_gaussian_1_0.33_1_3_3d.lammps.log create mode 100644 examples/USER/brownian/translational/in.brownian create mode 100644 examples/USER/brownian/translational/log_1_1.lammps.log create mode 100644 src/USER-BROWNIAN/fix_brownian.cpp create mode 100644 src/USER-BROWNIAN/fix_brownian.h diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index 361ec7e982..9ee699faea 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -39,6 +39,7 @@ OPT. * :doc:`ave/time ` * :doc:`aveforce ` * :doc:`balance ` + * :doc:`brownian ` * :doc:`brownian/asphere ` * :doc:`brownian/sphere ` * :doc:`bocs ` diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 5efe002f31..373e5ac29f 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -182,8 +182,9 @@ accelerated styles exist. * :doc:`ave/time ` - compute/output global time-averaged quantities * :doc:`aveforce ` - add an averaged force to each atom * :doc:`balance ` - perform dynamic load-balancing -* :doc:`brownian/asphere ` - overdamped translational and rotational brownian for ellipsoids -* :doc:`brownian/sphere ` - overdamped translational and rotational brownian for spheres +* :doc:`brownian ` - overdamped translational brownian motion +* :doc:`brownian/asphere ` - overdamped translational and rotational brownian motion for ellipsoids +* :doc:`brownian/sphere ` - overdamped translational and rotational brownian motion for spheres * :doc:`bocs ` - NPT style time integration with pressure correction * :doc:`bond/break ` - break bonds on the fly * :doc:`bond/create ` - create bonds on the fly diff --git a/doc/src/fix_brownian.rst b/doc/src/fix_brownian.rst new file mode 100644 index 0000000000..e3f3a2679f --- /dev/null +++ b/doc/src/fix_brownian.rst @@ -0,0 +1,151 @@ +.. index:: fix brownian + +fix brownian command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID brownian gamma_t diff_t seed keyword args + +* ID, group-ID are documented in :doc:`fix ` command +* brownian/sphere = style name of this fix command +* gamma_t = translational friction coefficient +* diff_t = translational diffusion coefficient +* zero or more keyword/value pairs may be appended +* keyword = *rng* + + .. parsed-literal:: + + *rng* value = *uniform* or *gaussian* or *none* + *uniform* = use uniform random number generator + *gaussian* = use gaussian random number generator + *none* = turn off noise + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix 1 all brownian 1.0 3.0 1294019 + fix 1 all brownian 1.0 3.0 19581092 rng none + fix 1 all brownian 1.0 3.0 19581092 rng uniform + fix 1 all brownian 1.0 3.0 19581092 rng gaussian + + +Description +""""""""""" + +Perform Brownian Dynamics integration to update position and velocity +of atoms in the group each timestep. Brownian Dynamics uses Newton's laws of +motion in the limit that inertial forces are negligible compared to +viscous forces. The stochastic equation of motion is + +.. math:: + + dr = \frac{F}{\gamma_t}dt+\sqrt{2D_t}dW_t, \\ + +where :math:`dW_t` is a Wiener processes (see e.g. :ref:`(Gardiner) `). + +.. note:: + This integrator is designed for generic non-equilibrium + simulations with additive noise. There are two important cases which + (conceptually) reduce the number of free parameters in this fix. + (a) In equilibrium simulations + (where fluctuation dissipation theorems are obeyed), one can define + the thermal energy :math:`k_bT=D_t\gamma_t`. + +--------- + +.. note:: + Temperature computation using the :doc:`compute temp ` + will not correctly compute temperature of these overdamped dynamics + since we are explicitly neglecting inertial effects. + See e.g. chapter 6 of :ref:`(Doi) ` for more details on this. + Temperature is instead defined in terms of the note above (for + equilibrium systems). + +--------- + +.. note:: + The diffusion coefficient :math:`D_t` is measured + in units of (length*length)/time, where time and length + are in the units specified on the :doc:`units ` page. + Similarly, :math:`\gamma_t` is measured in + units of mass/time. + +--------- + +If the *rng* keyword is used with the *uniform* value, then the noise +is generated from a uniform distribution (see +:ref:`(Dunweg) ` for why this works). This is the same method +of noise generation as used in :doc:`fix_langevin `. + +If the *rng* keyword is used with the *gaussian* value, then the noise +is generated from a gaussian distribution. Typically this added +complexity is unnecessary, and one should be fine using the *uniform* +value for reasons argued in :ref:`(Dunweg) `. + +If the *rng* keyword is used with the *none* value, then the noise +terms are set to zero. + + +---------- + +.. include:: accel_styles.rst + +---------- + +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. +No global or per-atom quantities are stored +by this fix for access by various :doc:`output commands `. + +The :doc:`fix_modify ` *virial* option is supported by this +fix to add the contribution due to the added forces on atoms to the +system's virial as part of :doc:`thermodynamic output `. +The default is *virial no*. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during +:doc:`energy minimization `. + +Restrictions +"""""""""""" + +This fix is part of the USER-BROWNIAN package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` +doc page for more info. + + +Related commands +"""""""""""""""" + +:doc:`fix langevin `, :doc:`fix nve/sphere `, +:doc:`fix brownian/sphere `, +:doc:`fix brownian/asphere ` + +Default +""""""" + +The default for *rng* is *uniform*. + +---------- + +.. _GardinerC1: + +**(Gardiner)** Gardiner, A Handbook for the Natural and Social Sciences 4th Ed. (2009). + +.. _Doi1: + +**(Doi)** Doi, Soft Matter Physics (2013). + +.. _Dunweg6: + +**(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). + + diff --git a/doc/src/fix_brownian_asphere.rst b/doc/src/fix_brownian_asphere.rst index 58dd453de9..c59774ca65 100644 --- a/doc/src/fix_brownian_asphere.rst +++ b/doc/src/fix_brownian_asphere.rst @@ -54,8 +54,8 @@ viscous forces. The stochastic equations of motion are d\Omega = \frac{T}{\gamma_r}dt + \sqrt{2D_r}dW_r, where :math:`d\Omega` is an infinitesimal rotation vector (see e.g. -Chapter 4 of :ref:`(Goldstein) `), :math:`dW_t` and -:math:`dW_r` are Wiener processes (see e.g. :ref:`(Gardiner) `). +Chapter 4 of :ref:`(Goldstein) `), :math:`dW_t` and +:math:`dW_r` are Wiener processes (see e.g. :ref:`(Gardiner) `). The quaternions :math:`q` of the ellipsoid are updated each timestep from the angular velocity vector. @@ -66,13 +66,13 @@ values of :math:`\gamma_t`, :math:`\gamma_r`, :math:`D_t`, If the *rng* keyword is used with the *uniform* value, then the noise is generated from a uniform distribution (see -:ref:`(Dunweg) ` for why this works). This is the same method +:ref:`(Dunweg) ` for why this works). This is the same method of noise generation as used in :doc:`fix_langevin `. If the *rng* keyword is used with the *gaussian* value, then the noise is generated from a gaussian distribution. Typically this added complexity is unnecessary, and one should be fine using the *uniform* -value for reasons argued in :ref:`(Dunweg) `. +value for reasons argued in :ref:`(Dunweg) `. If the *rng* keyword is used with the *none* value, then the noise terms are set to zero. @@ -114,7 +114,7 @@ as atoms which have a definite orientation as defined by the Optionally, they can also store a dipole moment as defined by the :doc:`atom_style dipole ` command. -This fix is part of the USER-MISC package. It is only enabled if +This fix is part of the USER-BROWNIAN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -124,8 +124,9 @@ be point particles. Related commands """""""""""""""" -:doc:`fix brownian/sphere `, :doc:`fix langevin `, -:doc:`fix nve/asphere `, :doc:`atom style ` +:doc:`fix brownian `, :doc:`fix brownian/sphere `, +:doc:`fix propel/self `, :doc:`fix langevin `, +:doc:`fix nve/asphere ` Default """"""" @@ -134,15 +135,15 @@ The default for *rng* is *uniform*. ---------- -.. _GoldsteinCM1: +.. _GoldsteinCM2: **(Goldstein)** Goldstein, Poole, and Safko, Classical Mechanics, 3rd Ed. (2001). -.. _GardinerC1: +.. _GardinerC3: **(Gardiner)** Gardiner, A Handbook for the Natural and Social Sciences 4th Ed. (2009). -.. _Dunweg7: +.. _Dunweg8: **(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). diff --git a/doc/src/fix_brownian_sphere.rst b/doc/src/fix_brownian_sphere.rst index 231486dee1..7e73226e08 100644 --- a/doc/src/fix_brownian_sphere.rst +++ b/doc/src/fix_brownian_sphere.rst @@ -53,8 +53,8 @@ viscous forces. The stochastic equations of motion are d\Omega = \frac{T}{\gamma_r}dt + \sqrt{2D_r}dW_r, where :math:`d\Omega` is an infinitesimal rotation vector (see e.g. -Chapter 4 of :ref:`(Goldstein) `), :math:`dW_t` and -:math:`dW_r` are Wiener processes (see e.g. :ref:`(Gardiner) `). +Chapter 4 of :ref:`(Goldstein) `), :math:`dW_t` and +:math:`dW_r` are Wiener processes (see e.g. :ref:`(Gardiner) `). The dipole vectors :math:`e_i` are updated using the rotation matrix .. math:: @@ -85,35 +85,31 @@ section 7.4). --------- -.. note:: - Temperature computation using the :doc:`compute temp ` - will not correctly compute temperature of these overdamped dynamics - since we are explicitly neglecting inertial effects. - See e.g. chapter 6 of :ref:`(Doi) ` for more details on this. - Temperature is instead defined in terms of the note above (for - equilibrium systems). +See note on the unphysical result of using :doc:`compute temp ` +with this fix in :doc:`fix brownian `. --------- .. note:: - The diffusion coefficient :math:`D_t` is measured - in units of (length*length)/time and the diffusion coefficient - :math:`D_r` is measured in units of 1/time, where time and length - are in the units specified on the :doc:`units ` page. Similarly, - :math:`\gamma_t` and :math:`\gamma_r` are measured in + The diffusion coefficient :math:`D_t` and the translational + drag coefficient :math:`\gamma_t` are discussed in + :doc:`fix brownian `. The diffusion coefficient + :math:`D_r` is measured in units of 1/time, where time is in the + units specified on the :doc:`units ` page. Similarly, + and :math:`\gamma_r` is measured in units of mass/time and (mass*length*length)/(time). --------- If the *rng* keyword is used with the *uniform* value, then the noise is generated from a uniform distribution (see -:ref:`(Dunweg) ` for why this works). This is the same method +:ref:`(Dunweg) ` for why this works). This is the same method of noise generation as used in :doc:`fix_langevin `. If the *rng* keyword is used with the *gaussian* value, then the noise is generated from a gaussian distribution. Typically this added complexity is unnecessary, and one should be fine using the *uniform* -value for reasons argued in :ref:`(Dunweg) `. +value for reasons argued in :ref:`(Dunweg) `. If the *rng* keyword is used with the *none* value, then the noise terms are set to zero. @@ -151,7 +147,7 @@ as defined by the :doc:`atom_style sphere ` command. If the *dipole* keyword is used, they must also store a dipole moment as defined by the :doc:`atom_style dipole ` command. -This fix is part of the USER-MISC package. It is only enabled if +This fix is part of the USER-BROWNIAN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -159,8 +155,9 @@ doc page for more info. Related commands """""""""""""""" +:doc:`fix brownian `, :doc:`fix brownian/asphere `, +:doc:`fix propel/self `, :doc:`fix langevin `, :doc:`fix nve/sphere `, -:doc:`atom style ` Default """"""" @@ -169,11 +166,11 @@ The default for *rng* is *uniform*. ---------- -.. _GoldsteinCM: +.. _GoldsteinCM1: **(Goldstein)** Goldstein, Poole, and Safko, Classical Mechanics, 3rd Ed. (2001). -.. _GardinerC: +.. _GardinerC2: **(Gardiner)** Gardiner, A Handbook for the Natural and Social Sciences 4th Ed. (2009). @@ -182,11 +179,7 @@ The default for *rng* is *uniform*. **(Callegari)** Callegari and Volpe, *Numerical Simulations of Active Brownian Particles*, Flowing Matter, 211-238 (2019). -.. _Doi1: - -**(Doi)** Doi, Soft Matter Physics (2013). - -.. _Dunweg6: +.. _Dunweg7: **(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). diff --git a/doc/src/fix_propel_self.rst b/doc/src/fix_propel_self.rst index 6644d97d46..582d9e4294 100644 --- a/doc/src/fix_propel_self.rst +++ b/doc/src/fix_propel_self.rst @@ -21,10 +21,9 @@ Syntax *dipole* value = none = apply force along dipole direction *velocity* value = none = apply force along velocity direction *quat* values = direction vector *sx* and *sy* and *sz* - *sx* = x component of force direction in ellipsoid frame - *sy* = y component of force direction in ellipsoid frame - *sz* = z component of force direction in ellipsoid frame - + *sx* = x component of force direction in ellipsoid frame + *sy* = y component of force direction in ellipsoid frame + *sz* = z component of force direction in ellipsoid frame Examples diff --git a/examples/USER/brownian/2d_velocity/in.2d_velocity b/examples/USER/brownian/2d_velocity/in.2d_velocity new file mode 100644 index 0000000000..b731f5f477 --- /dev/null +++ b/examples/USER/brownian/2d_velocity/in.2d_velocity @@ -0,0 +1,64 @@ +# 2d overdamped brownian dynamics with self-propulsion +# force in direction of velocity. + +variable gamma_t equal 1.0 +variable D_t equal 1.0 +variable seed equal 1974019 +variable fp equal 4.0 + +variable params string ${gamma_t}_${D_t}_${fp} + + +log log_${params}_2d.lammps.log +units lj +dimension 2 +newton off + + +lattice sq 0.4 +region box block -16 16 -16 16 -0.2 0.2 +create_box 1 box +create_atoms 1 box +mass * 1.0 +velocity all create 1.0 1 loop geom + + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + + +pair_style none + +fix step all brownian ${gamma_t} ${D_t} ${seed} +fix vel all propel/self ${fp} velocity +fix 2 all enforce2d +fix_modify vel virial yes + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +reset_timestep 0 + + +#initialisation for the main run + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +timestep 0.00001 +thermo 1000 + +# main run +run 120000 + + diff --git a/examples/USER/brownian/2d_velocity/log_1_1_4_2d.lammps.log b/examples/USER/brownian/2d_velocity/log_1_1_4_2d.lammps.log new file mode 100644 index 0000000000..f6b234e9ee --- /dev/null +++ b/examples/USER/brownian/2d_velocity/log_1_1_4_2d.lammps.log @@ -0,0 +1,248 @@ +units lj +dimension 2 +newton off + + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 +region box block -16 16 -16 16 -0.2 0.2 +create_box 1 box +Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 1024 atoms + create_atoms CPU = 0.001 seconds +mass * 1.0 +velocity all create 1.0 1 loop geom + + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + + +pair_style none + + + +#compute d all property/atom mux muy muz + +fix step all brownian ${gamma_t} ${D_t} ${seed} +fix step all brownian 1 ${D_t} ${seed} +fix step all brownian 1 1 ${seed} +fix step all brownian 1 1 1974019 +fix vel all propel/self ${fp} velocity +fix vel all propel/self 4 velocity +fix 2 all enforce2d +fix_modify vel virial yes + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 2.289 | 2.289 | 2.289 Mbytes +Step Temp E_pair c_press + 0 1 0 -0.18336111 + 50000 1.9663098e+10 0 -0.75033044 +Loop time of 2.45902 on 1 procs for 50000 steps with 1024 atoms + +Performance: 0.176 tau/day, 20333.276 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0078395 | 0.0078395 | 0.0078395 | 0.0 | 0.32 +Output | 2.2947e-05 | 2.2947e-05 | 2.2947e-05 | 0.0 | 0.00 +Modify | 2.332 | 2.332 | 2.332 | 0.0 | 94.83 +Other | | 0.1192 | | | 4.85 + +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 65.0000 ave 65 max 65 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + + +#initialisation for the main run + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +timestep 0.00001 +thermo 1000 + +# main run +run 120000 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes +Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 1.9663098e+10 0 0 0 0 0 -0.75033044 + 1000 199346.07 0 0.01933096 0.020555579 0 0.039886539 -0.45701943 + 2000 198310 0 0.040165459 0.041283119 0 0.081448577 0.34264096 + 3000 204115.93 0 0.057654441 0.060411193 0 0.11806563 -0.41710363 + 4000 196903.18 0 0.075874071 0.08470884 0 0.16058291 -0.18627889 + 5000 201382.13 0 0.097484871 0.1049401 0 0.20242497 -0.12876225 + 6000 195317.96 0 0.11872475 0.12469358 0 0.24341834 -0.3084651 + 7000 192139.34 0 0.14148561 0.14363452 0 0.28512013 0.0032867364 + 8000 201737.84 0 0.16055109 0.16405717 0 0.32460826 0.36435453 + 9000 199390.58 0 0.17897382 0.18795928 0 0.3669331 0.025659298 + 10000 207807.41 0 0.19680417 0.20733821 0 0.40414239 -0.35368379 + 11000 201936.29 0 0.21666426 0.22702132 0 0.44368558 0.044253449 + 12000 196863.68 0 0.2394452 0.24672678 0 0.48617198 0.059027892 + 13000 199368.34 0 0.26647368 0.2700584 0 0.53653208 0.27090461 + 14000 201246.39 0 0.28799289 0.29823282 0 0.58622571 0.59883778 + 15000 195355.47 0 0.29975278 0.32348787 0 0.62324065 -0.70763643 + 16000 198372.41 0 0.32191014 0.34434864 0 0.66625878 -0.36543908 + 17000 193442.08 0 0.33927003 0.36811239 0 0.70738242 0.28541473 + 18000 197441 0 0.36067818 0.38982011 0 0.75049829 -0.45670227 + 19000 208769.5 0 0.37965583 0.41015661 0 0.78981244 -0.47803396 + 20000 198311.2 0 0.3968078 0.42701175 0 0.82381955 -0.18642397 + 21000 201365.22 0 0.4151043 0.44909345 0 0.86419775 0.86839756 + 22000 198253.24 0 0.4396583 0.46388261 0 0.90354091 -0.19592545 + 23000 204598.51 0 0.45382292 0.49253671 0 0.94635963 -0.24169987 + 24000 211421.88 0 0.46086338 0.51831304 0 0.97917642 0.49751915 + 25000 198690.71 0 0.47110913 0.53640271 0 1.0075118 -0.24475563 + 26000 203981.49 0 0.49265476 0.55310571 0 1.0457605 0.20237224 + 27000 201128.99 0 0.52865208 0.57516064 0 1.1038127 -0.40826104 + 28000 198529.77 0 0.54479087 0.59876678 0 1.1435576 0.41576857 + 29000 205024.27 0 0.56195744 0.61217109 0 1.1741285 -0.79146635 + 30000 201565.62 0 0.58276132 0.63743585 0 1.2201972 -0.065832917 + 31000 197893.43 0 0.61132665 0.66126375 0 1.2725904 0.47907079 + 32000 201395.11 0 0.61904956 0.67520462 0 1.2942542 -0.7408472 + 33000 202064.22 0 0.64760511 0.69087605 0 1.3384812 -0.14601514 + 34000 191227.75 0 0.65698736 0.73857849 0 1.3955659 0.2177548 + 35000 199474.65 0 0.66491543 0.76604575 0 1.4309612 -0.64627039 + 36000 195252.77 0 0.67565581 0.79911139 0 1.4747672 0.0293298 + 37000 198167.14 0 0.68899202 0.81268008 0 1.5016721 -0.0055245918 + 38000 202995.35 0 0.70224976 0.82436547 0 1.5266152 -0.2826768 + 39000 197129.03 0 0.71270072 0.8579444 0 1.5706451 0.063623666 + 40000 199153.69 0 0.73777312 0.88820969 0 1.6259828 -0.26740551 + 41000 205347.31 0 0.75613153 0.9006214 0 1.6567529 0.82415354 + 42000 199423.73 0 0.76864739 0.92457092 0 1.6932183 -0.16636304 + 43000 198052 0 0.79841199 0.93832523 0 1.7367372 -0.016241224 + 44000 205205.39 0 0.81727188 0.96823569 0 1.7855076 -0.10405924 + 45000 199116.46 0 0.83208052 0.99352694 0 1.8256075 0.040835286 + 46000 198759.48 0 0.84291542 1.0038949 0 1.8468104 0.46109436 + 47000 189676.9 0 0.86430719 1.0131299 0 1.8774371 -0.67947102 + 48000 199801.4 0 0.90662572 1.0286589 0 1.9352846 -0.5293946 + 49000 199730.89 0 0.93530132 1.0568273 0 1.9921286 -0.27562311 + 50000 203272.56 0 0.96366375 1.0790026 0 2.0426664 -0.10629234 + 51000 196992.09 0 0.97818106 1.1030549 0 2.0812359 0.31719382 + 52000 204063.62 0 1.0068773 1.1239506 0 2.130828 -7.1998264e-05 + 53000 204349.41 0 1.0277098 1.1546477 0 2.1823575 0.16897786 + 54000 203207.3 0 1.0415673 1.1881409 0 2.2297082 -0.25033492 + 55000 194841.07 0 1.0600954 1.2179033 0 2.2779987 0.0062433629 + 56000 198601.58 0 1.071562 1.2363958 0 2.3079578 -0.13124124 + 57000 196654.6 0 1.0997086 1.2486573 0 2.3483659 -0.46425912 + 58000 197781.48 0 1.112526 1.2706195 0 2.3831455 0.26007922 + 59000 199853.9 0 1.1295132 1.2978402 0 2.4273533 -0.030877018 + 60000 201698.14 0 1.1690892 1.3228782 0 2.4919675 -0.23190043 + 61000 199260.52 0 1.1870513 1.3431945 0 2.5302458 -0.040373885 + 62000 196909.15 0 1.2007194 1.3683525 0 2.5690719 0.21318495 + 63000 203927.79 0 1.2442809 1.3964232 0 2.6407041 0.10156282 + 64000 205322.27 0 1.2721207 1.4159422 0 2.6880629 0.33393307 + 65000 199142.6 0 1.2989685 1.4330729 0 2.7320414 -0.65644005 + 66000 205023.06 0 1.2948208 1.4255094 0 2.7203302 0.22290721 + 67000 209750.01 0 1.3127511 1.4369628 0 2.7497139 -0.40241279 + 68000 200205.19 0 1.3355277 1.4541568 0 2.7896846 0.6665415 + 69000 198653.01 0 1.3500764 1.4962697 0 2.8463461 -0.28396983 + 70000 207485.71 0 1.3825583 1.5095552 0 2.8921135 0.34774599 + 71000 203918.68 0 1.4090995 1.5246756 0 2.9337751 0.071958672 + 72000 199038.47 0 1.4246969 1.5612784 0 2.9859753 -0.42129173 + 73000 197380.7 0 1.445835 1.6025372 0 3.0483722 -0.099854135 + 74000 205006.49 0 1.4703253 1.606784 0 3.0771093 0.137244 + 75000 196040.42 0 1.4897388 1.6297195 0 3.1194583 -0.46715263 + 76000 200022.09 0 1.5178017 1.6560075 0 3.1738092 -0.21504553 + 77000 200766.4 0 1.5184584 1.6673791 0 3.1858374 0.54447858 + 78000 199636.76 0 1.5344452 1.6845098 0 3.2189549 0.021903761 + 79000 204188.86 0 1.5567356 1.7205197 0 3.2772553 0.15356898 + 80000 199862.31 0 1.5669731 1.7265239 0 3.2934969 -0.26342032 + 81000 198557.57 0 1.5735674 1.7468943 0 3.3204617 0.22068216 + 82000 203675.4 0 1.5898596 1.7646027 0 3.3544624 0.51221445 + 83000 203412.56 0 1.6066548 1.7813624 0 3.3880172 0.33512263 + 84000 200896.36 0 1.6112635 1.812552 0 3.4238154 1.1657793 + 85000 198987.17 0 1.652135 1.8336748 0 3.4858098 -0.20419704 + 86000 203027.04 0 1.6728041 1.864244 0 3.5370481 0.61746313 + 87000 203913.8 0 1.6783324 1.8762967 0 3.554629 0.28428076 + 88000 205061.23 0 1.6781682 1.879458 0 3.5576262 0.089285353 + 89000 198210.89 0 1.7017682 1.9029345 0 3.6047027 -0.23977904 + 90000 196170.91 0 1.7291253 1.9258436 0 3.6549689 0.15806438 + 91000 202846.79 0 1.7592339 1.9431644 0 3.7023983 0.17723099 + 92000 198976.91 0 1.762318 1.9742003 0 3.7365183 0.25668658 + 93000 194578.12 0 1.7880716 2.0009816 0 3.7890532 0.20231476 + 94000 200319.82 0 1.7854494 2.020855 0 3.8063044 0.14729427 + 95000 202430.33 0 1.7925005 2.0480213 0 3.8405218 -0.28291245 + 96000 200145.58 0 1.8113602 2.0621043 0 3.8734644 0.05547277 + 97000 194617.53 0 1.8286924 2.0729365 0 3.9016289 -0.59829377 + 98000 200829.37 0 1.8485835 2.077731 0 3.9263145 0.78242718 + 99000 198197.55 0 1.8537119 2.0873455 0 3.9410573 -0.52970118 + 100000 204149.63 0 1.8897394 2.0942927 0 3.9840321 0.58118967 + 101000 198654.59 0 1.9126448 2.1380708 0 4.0507156 -0.61766977 + 102000 201198.05 0 1.9433521 2.143049 0 4.0864011 0.15570108 + 103000 200383.43 0 1.9669578 2.1361518 0 4.1031095 -0.10556532 + 104000 204363.26 0 1.9827272 2.1564095 0 4.1391367 -0.060748593 + 105000 198267.87 0 1.9904164 2.1804141 0 4.1708305 0.40995747 + 106000 202082.12 0 1.993709 2.1925288 0 4.1862378 -0.52458386 + 107000 200209.49 0 2.015427 2.219161 0 4.234588 -0.67350679 + 108000 203112.58 0 2.0467303 2.2405372 0 4.2872675 0.25033168 + 109000 203844.13 0 2.056314 2.2623929 0 4.3187068 0.3384149 + 110000 201740.33 0 2.0706519 2.285547 0 4.3561989 0.35582365 + 111000 202493.05 0 2.0725826 2.308685 0 4.3812676 -0.26487212 + 112000 205404.09 0 2.0969613 2.3252767 0 4.422238 0.58346057 + 113000 201223.54 0 2.0876103 2.3316941 0 4.4193044 0.37747414 + 114000 208649.11 0 2.1095116 2.3488008 0 4.4583124 0.068129648 + 115000 202708.5 0 2.1233837 2.3701129 0 4.4934966 -0.23734073 + 116000 202482.42 0 2.1221907 2.4262516 0 4.5484424 -0.087142119 + 117000 200384.65 0 2.1487723 2.4619437 0 4.6107161 -0.13673271 + 118000 196885.36 0 2.158057 2.4818335 0 4.6398905 0.31912412 + 119000 194064.42 0 2.1821315 2.5032336 0 4.6853651 0.17615749 + 120000 195203.09 0 2.1939678 2.539838 0 4.7338058 0.5106086 +Loop time of 6.05038 on 1 procs for 120000 steps with 1024 atoms + +Performance: 17136.102 tau/day, 19833.451 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.00031301 | 0.00031301 | 0.00031301 | 0.0 | 0.01 +Comm | 0.0072472 | 0.0072472 | 0.0072472 | 0.0 | 0.12 +Output | 0.0036492 | 0.0036492 | 0.0036492 | 0.0 | 0.06 +Modify | 5.7173 | 5.7173 | 5.7173 | 0.0 | 94.50 +Other | | 0.3218 | | | 5.32 + +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 154 +Dangerous builds = 0 + + +Total wall time: 0:00:08 diff --git a/examples/USER/brownian/asphere/README.txt b/examples/USER/brownian/asphere/README.txt index 7cb5d2e8e6..47e79353c6 100644 --- a/examples/USER/brownian/asphere/README.txt +++ b/examples/USER/brownian/asphere/README.txt @@ -1,2 +1,2 @@ -The input file in2d.bd demonstrates how to run a 2d simulation +The input file in3d.brownian demonstrates how to run a 3d simulation of ellipsoidal particles undergoing overdamped brownian motion. diff --git a/examples/USER/brownian/asphere/in3d.brownian b/examples/USER/brownian/asphere/in3d.brownian index 67d95a82b9..19487978ce 100644 --- a/examples/USER/brownian/asphere/in3d.brownian +++ b/examples/USER/brownian/asphere/in3d.brownian @@ -1,10 +1,14 @@ -# 3d overdamped brownian dynamics +# 3d overdamped brownian dynamics for ellipsoids +# with dipole moment also being updated +# choose variables to obey thermal equilibrium +# (fluctuation dissipation theorem) and no-slip +# boundary condition variable rng string gaussian -variable gamma_t equal 4.0 -variable gamma_r equal 1.0 -variable D_t equal 7.0 -variable D_r equal 13.0 +variable gamma_t equal 1.0 +variable gamma_r equal 0.33 +variable D_t equal 1.0 +variable D_r equal 3.0 variable seed equal 1974019 variable params string ${rng}_${gamma_t}_${gamma_r}_${D_t}_${D_r} @@ -27,16 +31,11 @@ set type * shape 1 1 1 set type * quat/random ${seed} velocity all create 1.0 1 loop geom - -neighbor 1.0 bin -neigh_modify every 1 delay 1 check yes - - - pair_style none -fix 1 all brownian/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} & + ${seed} rng ${rng} dipole compute press all pressure NULL virial @@ -50,8 +49,6 @@ run 50000 reset_timestep 0 -#initialisation for the main run - # MSD compute msd all msd @@ -59,11 +56,6 @@ compute msd all msd thermo_style custom step temp epair c_msd[*] c_press -# write trajectory and thermo in a log-scale frequency -#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type & -# x y xu yu mux muy muz fx fy fz -#dump_modify 1 first yes sort id - timestep 0.00001 thermo 10000 diff --git a/examples/USER/brownian/asphere/log_gaussian_1_0.33_1_3_3d.lammps.log b/examples/USER/brownian/asphere/log_gaussian_1_0.33_1_3_3d.lammps.log new file mode 100644 index 0000000000..2ed81ec8ba --- /dev/null +++ b/examples/USER/brownian/asphere/log_gaussian_1_0.33_1_3_3d.lammps.log @@ -0,0 +1,141 @@ +units lj +atom_style hybrid dipole sphere ellipsoid +WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (src/atom_vec_hybrid.cpp:157) +WARNING: Peratom rmass is in multiple sub-styles - must be used consistently (src/atom_vec_hybrid.cpp:219) +dimension 3 +newton off + + +lattice sc 0.4 +Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 +region box block -4 4 -4 4 -4 4 +create_box 1 box +Created orthogonal box = (-5.4288352 -5.4288352 -5.4288352) to (5.4288352 5.4288352 5.4288352) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 512 atoms + create_atoms CPU = 0.002 seconds +mass * 1.0 +set type * dipole/random ${seed} 1.0 +set type * dipole/random 1974019 1.0 +Setting atom values ... + 512 settings made for dipole/random +set type * shape 1 1 1 +Setting atom values ... + 512 settings made for shape +set type * quat/random ${seed} +set type * quat/random 1974019 +Setting atom values ... + 512 settings made for quat/random +velocity all create 1.0 1 loop geom + +pair_style none + + +fix 1 all brownian/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 1 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 1 0.33 ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 1 0.33 1 ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 1 0.33 1 3 ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 1 0.33 1 3 1974019 rng ${rng} dipole +fix 1 all brownian/asphere 1 0.33 1 3 1974019 rng gaussian dipole + + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50000 +run 50000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.379 | 5.379 Mbytes +Step Temp E_pair c_press + 0 1 0 0 + 50000 1.9891104e+10 0 0 +Loop time of 5.53749 on 1 procs for 50000 steps with 512 atoms + +Performance: 0.078 tau/day, 9029.362 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.11711 | 0.11711 | 0.11711 | 0.0 | 2.11 +Output | 2.034e-05 | 2.034e-05 | 2.034e-05 | 0.0 | 0.00 +Modify | 5.3401 | 5.3401 | 5.3401 | 0.0 | 96.44 +Other | | 0.08027 | | | 1.45 + +Nlocal: 512.000 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 217.000 ave 217 max 217 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +timestep 0.00001 +thermo 10000 + +# main run +run 120000 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 5.754 | 5.754 | 5.754 Mbytes +Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 1.9891104e+10 0 0 0 0 0 0 + 10000 201972.17 0 0.19918647 0.20079752 0.20495007 0.60493407 0 + 20000 197255.49 0 0.40800225 0.37910274 0.38545643 1.1725614 0 + 30000 195533.67 0 0.60991554 0.5898132 0.56621596 1.7659447 0 + 40000 192777.99 0 0.7761198 0.86101776 0.76531344 2.402451 0 + 50000 195241.43 0 1.0053256 1.0477568 0.96681401 3.0198964 0 + 60000 201887.49 0 1.2298892 1.1979933 1.1950141 3.6228965 0 + 70000 200187.14 0 1.4407329 1.356743 1.3992739 4.1967498 0 + 80000 202737.24 0 1.6305637 1.5663775 1.5724692 4.7694104 0 + 90000 185530.51 0 1.7937597 1.7795995 1.7222809 5.2956401 0 + 100000 204405.47 0 2.0149709 1.9738573 1.9423625 5.9311907 0 + 110000 194892.4 0 2.1974948 2.1560014 2.1453303 6.4988264 0 + 120000 198462.51 0 2.3761388 2.334739 2.287964 6.9988418 0 +Loop time of 13.0463 on 1 procs for 120000 steps with 512 atoms + +Performance: 7947.110 tau/day, 9198.044 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0011789 | 0.0011789 | 0.0011789 | 0.0 | 0.01 +Comm | 0.030109 | 0.030109 | 0.030109 | 0.0 | 0.23 +Output | 0.00030614 | 0.00030614 | 0.00030614 | 0.0 | 0.00 +Modify | 12.834 | 12.834 | 12.834 | 0.0 | 98.38 +Other | | 0.1803 | | | 1.38 + +Nlocal: 512.000 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 1748 +Dangerous builds = 0 +Total wall time: 0:00:18 diff --git a/examples/USER/brownian/sphere/in2ddipole.brownian b/examples/USER/brownian/sphere/in2ddipole.brownian index 73d90e4ebf..e7a8374984 100644 --- a/examples/USER/brownian/sphere/in2ddipole.brownian +++ b/examples/USER/brownian/sphere/in2ddipole.brownian @@ -1,4 +1,5 @@ -# 2d overdamped brownian dynamics +# 2d overdamped brownian dynamics of a sphere +# with dipole also being updated variable rng string gaussian variable gamma_t equal 4.0 @@ -26,19 +27,10 @@ mass * 1.0 set type * dipole/random ${seed} 1.0 velocity all create 1.0 1 loop geom - -neighbor 1.0 bin -neigh_modify every 1 delay 1 check yes - - - pair_style none - - -#compute d all property/atom mux muy muz - -fix 1 all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} & + ${D_r} ${seed} rng ${rng} dipole fix 2 all enforce2d compute press all pressure NULL virial @@ -51,9 +43,6 @@ thermo 50001 run 50000 reset_timestep 0 - -#initialisation for the main run - # MSD compute msd all msd @@ -61,12 +50,6 @@ compute msd all msd thermo_style custom step temp epair c_msd[*] c_press -# write trajectory and thermo in a log-scale frequency -# uncomment next three lines for dump output -#dump 1 all custom 2000 dump_${params}_2d.lammpstrj id type & -# x y xu yu mux muy muz fx fy fz -#dump_modify 1 first yes sort id - timestep 0.00001 thermo 1000 diff --git a/examples/USER/brownian/sphere/in3d_virial_on.brownian b/examples/USER/brownian/sphere/in3d_virial_on.brownian index 481d9bc1b4..2fb08cbb17 100644 --- a/examples/USER/brownian/sphere/in3d_virial_on.brownian +++ b/examples/USER/brownian/sphere/in3d_virial_on.brownian @@ -1,4 +1,6 @@ -# 3d overdamped brownian dynamics +# 3d overdamped brownian dynamics of sphere, with +# virial contribution (i.e. ideal gas pressure) +# included variable rng string uniform @@ -16,7 +18,6 @@ log log_${params}_3d.lammps.log units lj atom_style sphere dimension 3 -newton off lattice sc 0.4 @@ -26,14 +27,11 @@ create_atoms 1 box #mass * 1.0 velocity all create 1.0 1 loop geom - -neighbor 1.0 bin -neigh_modify every 1 delay 1 check yes - pair_style none -fix 1 all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} & + ${D_r} ${seed} rng ${rng} fix_modify 1 virial yes compute press all pressure NULL virial @@ -46,22 +44,12 @@ thermo 50001 run 50000 reset_timestep 0 - -#initialisation for the main run - # MSD compute msd all msd thermo_style custom step temp epair c_msd[*] c_press - -# write trajectory and thermo in a log-scale frequency -# uncomment the next three lines for dump file -#dump 1 all custom 10000 dump_${params}_3d.lammpstrj id type & -# x y xu yu fx fy fz -#dump_modify 1 first yes sort id - timestep 0.00001 thermo 1000 diff --git a/examples/USER/brownian/translational/in.brownian b/examples/USER/brownian/translational/in.brownian new file mode 100644 index 0000000000..fbf43e68c6 --- /dev/null +++ b/examples/USER/brownian/translational/in.brownian @@ -0,0 +1,65 @@ +# 3d overdamped brownian dynamics + +variable gamma_t equal 1.0 +variable D_t equal 1.0 +variable seed equal 1974019 + +variable params string ${gamma_t}_${D_t} + + +log log_${params}.lammps.log +units lj +dimension 3 +newton off + + +lattice sc 0.4 +region box block -8 8 -8 8 -8 8 +create_box 1 box +create_atoms 1 box +mass * 1.0 +velocity all create 1.0 1 loop geom + + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + + +pair_style none + +# simple overdamped brownian dynamics time-stepper +fix step all brownian ${gamma_t} ${D_t} ${seed} + +# turn on the virial contribution from the noise +# (this is the ideal gas pressure, but it is really noisy +# for small systems) +fix_modify step virial yes + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +reset_timestep 0 + + +#initialisation for the main run + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +timestep 0.00001 +thermo 1000 + +# main run +run 120000 + + diff --git a/examples/USER/brownian/translational/log_1_1.lammps.log b/examples/USER/brownian/translational/log_1_1.lammps.log new file mode 100644 index 0000000000..0fdba989bd --- /dev/null +++ b/examples/USER/brownian/translational/log_1_1.lammps.log @@ -0,0 +1,246 @@ +units lj +dimension 3 +newton off + + +lattice sc 0.4 +Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 +region box block -8 8 -8 8 -8 8 +create_box 1 box +Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4096 atoms + create_atoms CPU = 0.002 seconds +mass * 1.0 +velocity all create 1.0 1 loop geom + + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + + +pair_style none + +# simple overdamped brownian dynamics time-stepper +fix step all brownian ${gamma_t} ${D_t} ${seed} +fix step all brownian 1 ${D_t} ${seed} +fix step all brownian 1 1 ${seed} +fix step all brownian 1 1 1974019 + +# turn on the virial contribution from the noise +# (this is the ideal gas pressure, but it is really noisy +# for small systems) +fix_modify step virial yes + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 2.319 | 2.319 | 2.319 Mbytes +Step Temp E_pair c_press + 0 1 0 1500.0667 + 50000 2.0204192e+10 0 809.28898 +Loop time of 8.36695 on 1 procs for 50000 steps with 4096 atoms + +Performance: 0.052 tau/day, 5975.895 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.081773 | 0.081773 | 0.081773 | 0.0 | 0.98 +Output | 3.0396e-05 | 3.0396e-05 | 3.0396e-05 | 0.0 | 0.00 +Modify | 7.8039 | 7.8039 | 7.8039 | 0.0 | 93.27 +Other | | 0.4812 | | | 5.75 + +Nlocal: 4096.00 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 817.000 ave 817 max 817 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + + +#initialisation for the main run + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +timestep 0.00001 +thermo 1000 + +# main run +run 120000 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 2.694 | 2.694 | 2.694 Mbytes +Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 2.0204192e+10 0 0 0 0 0 3.053092 + 1000 199589.87 0 0.020515986 0.019445659 0.020084014 0.060045658 -10.855191 + 2000 202255.37 0 0.039423387 0.039839097 0.041243768 0.12050625 -7.8484884 + 3000 197932.37 0 0.058057959 0.060232381 0.061205106 0.17949545 14.441358 + 4000 201354.42 0 0.08020915 0.080140903 0.081351793 0.24170185 -2.7088264 + 5000 201599.34 0 0.10065125 0.099423954 0.10004367 0.30011888 10.000367 + 6000 198355.3 0 0.12039302 0.12228165 0.12136204 0.36403671 -7.7331104 + 7000 201842.08 0 0.13901495 0.14401324 0.14070032 0.42372851 1.049759 + 8000 200224.96 0 0.16063188 0.16389028 0.16409878 0.48862093 14.748306 + 9000 198468.62 0 0.18050666 0.18555949 0.18441359 0.55047975 -7.2751841 + 10000 197958.21 0 0.20229316 0.20438608 0.20471694 0.61139618 -8.8169492 + 11000 200852.8 0 0.22244961 0.22388152 0.22417791 0.67050904 -0.56323783 + 12000 200135.84 0 0.24070342 0.23964066 0.24829459 0.72863867 -20.246433 + 13000 199160.33 0 0.26021951 0.2581362 0.27210493 0.79046065 6.2400743 + 14000 200016.58 0 0.28005738 0.27429833 0.29107673 0.84543244 9.8390268 + 15000 200805.25 0 0.30110658 0.29756813 0.31002936 0.90870407 -9.7474978 + 16000 201221.83 0 0.31982855 0.31758368 0.33140494 0.96881716 -11.937757 + 17000 199690.18 0 0.33896659 0.33908504 0.35143307 1.0294847 -11.627541 + 18000 197165.97 0 0.35589324 0.3605585 0.37062404 1.0870758 17.045279 + 19000 202921.66 0 0.36968243 0.3825335 0.38579438 1.1380103 -3.2942099 + 20000 200415.26 0 0.39189833 0.39811842 0.40650662 1.1965234 -0.55679809 + 21000 198882.79 0 0.41394816 0.42495341 0.42660986 1.2655114 0.26572202 + 22000 199352.13 0 0.43200564 0.44555233 0.44842807 1.325986 5.9839474 + 23000 200565.11 0 0.45248704 0.46736174 0.4633773 1.3832261 0.51141727 + 24000 197632.73 0 0.47648878 0.49070755 0.48561349 1.4528098 11.301781 + 25000 203284.74 0 0.50103025 0.5117464 0.50162451 1.5144012 4.0966379 + 26000 200458.42 0 0.52111051 0.53245594 0.52193205 1.5754985 -9.2090189 + 27000 197553.02 0 0.54097922 0.553215 0.5440757 1.6382699 -6.0708365 + 28000 200874.32 0 0.55707209 0.57015852 0.56334199 1.6905726 -17.349073 + 29000 199494.43 0 0.57734934 0.59276209 0.58014344 1.7502549 -7.0407471 + 30000 199898.09 0 0.60161157 0.6156313 0.60516078 1.8224036 -1.3770813 + 31000 200867.7 0 0.62383361 0.64008503 0.6272796 1.8911982 -8.3200079 + 32000 198811.59 0 0.64361889 0.66089102 0.64987533 1.9543852 -0.21133799 + 33000 198224.12 0 0.66695348 0.67669734 0.67749939 2.0211502 0.87075722 + 34000 202553.2 0 0.69470773 0.69930784 0.69600623 2.0900218 1.7428524 + 35000 199227.86 0 0.71973625 0.72255845 0.71991572 2.1622104 2.4381317 + 36000 200719.05 0 0.73772312 0.74086704 0.74438632 2.2229765 -8.8184183 + 37000 198054.45 0 0.75901548 0.76107029 0.76677002 2.2868558 9.0699905 + 38000 198496.92 0 0.77679013 0.78067416 0.78055585 2.3380201 -8.8374756 + 39000 199224.19 0 0.79689891 0.8074183 0.79624042 2.4005576 -2.3099574 + 40000 199514.11 0 0.81493522 0.8271518 0.81729253 2.4593796 8.5411105 + 41000 199926.55 0 0.82918834 0.84950171 0.83531381 2.5140039 -6.8276624 + 42000 201659.21 0 0.84991161 0.87416096 0.86612093 2.5901935 -11.006396 + 43000 201502.51 0 0.87967597 0.89570393 0.88920119 2.6645811 9.4305203 + 44000 194956.27 0 0.9022655 0.91604833 0.90539218 2.723706 1.7636771 + 45000 201853.02 0 0.92302957 0.93661741 0.93225051 2.7918975 9.6483674 + 46000 200572.92 0 0.94062662 0.94933155 0.94953376 2.8394919 1.0882497 + 47000 202008.49 0 0.95397524 0.97655157 0.96534559 2.8958724 -7.9450141 + 48000 199748.89 0 0.97441115 0.99687233 0.98429144 2.9555749 5.0525854 + 49000 203008.7 0 0.99757948 1.0095536 0.99836015 3.0054932 28.410878 + 50000 198810.18 0 1.0182591 1.0287254 1.0110652 3.0580497 22.596989 + 51000 201716 0 1.0414747 1.0448379 1.0361279 3.1224404 -0.3397634 + 52000 200682.63 0 1.0640391 1.0597767 1.0596255 3.1834413 8.9163814 + 53000 201068.23 0 1.0804112 1.0740541 1.077586 3.2320513 8.9631815 + 54000 203379.33 0 1.0965663 1.0832317 1.0981473 3.2779453 -7.8020084 + 55000 197117.81 0 1.1145489 1.1008769 1.1259188 3.3413446 13.723633 + 56000 201100.37 0 1.1420502 1.1311309 1.1425839 3.415765 10.39045 + 57000 199911.61 0 1.1641357 1.1461183 1.1598876 3.4701416 -1.5384143 + 58000 202180.4 0 1.1787793 1.1703422 1.1794284 3.5285498 4.9552552 + 59000 202359.35 0 1.2017068 1.1846051 1.1912556 3.5775675 14.774737 + 60000 196182.35 0 1.2297664 1.2087508 1.2116928 3.65021 12.484104 + 61000 201858.45 0 1.2505094 1.2255583 1.2330327 3.7091004 3.6962199 + 62000 198313.02 0 1.2756755 1.2437434 1.2514738 3.7708927 -6.5600779 + 63000 198423.1 0 1.2998594 1.262369 1.2656961 3.8279245 3.1919497 + 64000 202601.56 0 1.3177969 1.2812961 1.2841642 3.8832572 7.1735962 + 65000 201270.73 0 1.3353533 1.3006911 1.306668 3.9427124 3.7612957 + 66000 199480.32 0 1.3502663 1.3165416 1.3300249 3.9968327 -8.0484056 + 67000 202829.47 0 1.3628924 1.3369328 1.339246 4.0390712 -2.962791 + 68000 200269.53 0 1.3901352 1.3600404 1.3528283 4.1030039 29.395886 + 69000 201514.31 0 1.4135333 1.3834796 1.3719116 4.1689245 9.5358653 + 70000 198898.14 0 1.4323413 1.4056025 1.4015088 4.2394526 13.713608 + 71000 198446.83 0 1.4424061 1.4229225 1.4231698 4.2884984 9.5266069 + 72000 199550.94 0 1.4730822 1.4438093 1.4436864 4.360578 5.4060926 + 73000 201536.57 0 1.4860349 1.4557531 1.4673417 4.4091297 2.7527606 + 74000 201688.68 0 1.5078921 1.4770318 1.4889958 4.4739197 -2.5507167 + 75000 203168.01 0 1.5264946 1.4942757 1.5095341 4.5303045 13.955087 + 76000 198782.86 0 1.5363851 1.5145529 1.5306446 4.5815826 1.6748995 + 77000 199306.04 0 1.55336 1.5308045 1.5501462 4.6343107 1.4463705 + 78000 199420.52 0 1.5679804 1.5445387 1.5765555 4.6890745 -15.926362 + 79000 198711.33 0 1.5818761 1.5651424 1.5966885 4.743707 -23.662716 + 80000 202734.35 0 1.6045976 1.5878467 1.6155179 4.8079623 1.4177771 + 81000 199953.12 0 1.6266918 1.6125491 1.6370893 4.8763302 14.40188 + 82000 201254.27 0 1.6418366 1.6362867 1.6497081 4.9278313 -4.3503 + 83000 200442.35 0 1.6671772 1.6544269 1.6638838 4.9854878 -5.5569751 + 84000 201442.09 0 1.6772029 1.6819435 1.6824211 5.0415676 -17.634517 + 85000 202012.75 0 1.7026782 1.7059915 1.7079961 5.1166659 8.8311485 + 86000 198613.4 0 1.725679 1.7251262 1.7235885 5.1743936 10.070509 + 87000 198650.79 0 1.748013 1.7447674 1.7397963 5.2325767 7.3326989 + 88000 199753.54 0 1.7793864 1.7677848 1.7548586 5.3020298 -3.8460869 + 89000 200851.56 0 1.7992856 1.7843281 1.7671516 5.3507653 10.274664 + 90000 202029.24 0 1.8178051 1.8010651 1.7886511 5.4075213 1.1705818 + 91000 200963.98 0 1.8425785 1.8123748 1.8079693 5.4629226 -8.0390883 + 92000 200443.4 0 1.8743616 1.8355736 1.8340515 5.5439867 -12.186363 + 93000 197974.1 0 1.8911764 1.8440063 1.8442582 5.579441 10.189145 + 94000 201285.41 0 1.9040394 1.8567044 1.8663386 5.6270824 7.8537148 + 95000 198472.81 0 1.9268236 1.8638624 1.8855767 5.6762627 11.556616 + 96000 198171.93 0 1.9378011 1.8811168 1.9024245 5.7213424 -7.3493903 + 97000 200055.5 0 1.9539002 1.9031647 1.9221125 5.7791774 -7.2823252 + 98000 200350.77 0 1.973424 1.9255707 1.9393139 5.8383087 2.3526328 + 99000 198923.17 0 1.9946733 1.9416292 1.9616759 5.8979785 -8.6362233 + 100000 196205.31 0 2.015688 1.967164 1.9801696 5.9630216 1.5261152 + 101000 198842.45 0 2.0402634 1.9858628 1.9939889 6.0201151 6.8070808 + 102000 199060.56 0 2.0583018 2.0040652 2.0225396 6.0849067 5.4626963 + 103000 204892.64 0 2.0788003 2.0245826 2.0405395 6.1439224 -19.988675 + 104000 198709.07 0 2.0990457 2.0519007 2.0571079 6.2080544 -21.365135 + 105000 198916.99 0 2.1089408 2.0758832 2.0899796 6.2748037 4.3696238 + 106000 202191.68 0 2.1172909 2.0923523 2.1208274 6.3304706 8.2072292 + 107000 202428.89 0 2.1387532 2.114944 2.1418816 6.3955788 4.1099611 + 108000 197690.67 0 2.1620575 2.136726 2.1703555 6.469139 5.7183695 + 109000 200098.73 0 2.1814376 2.1464455 2.1828177 6.5107008 7.4366333 + 110000 197901.18 0 2.1955124 2.1764141 2.1994286 6.5713551 -6.4288954 + 111000 199478.54 0 2.2167884 2.1900638 2.2140739 6.6209261 22.379137 + 112000 198391.65 0 2.249996 2.2100316 2.2309406 6.6909682 -20.040892 + 113000 200542.42 0 2.2634106 2.2313768 2.2610988 6.7558862 0.2953844 + 114000 202117.15 0 2.28441 2.2517036 2.2787302 6.8148438 16.75177 + 115000 200004.06 0 2.2957226 2.2730837 2.2901883 6.8589947 -4.3125612 + 116000 200648.11 0 2.3184059 2.2934521 2.3257075 6.9375656 5.7210624 + 117000 198600.57 0 2.3413891 2.3102468 2.3511234 7.0027593 -2.9987639 + 118000 199817.34 0 2.3732051 2.3347741 2.3601752 7.0681544 -3.3658539 + 119000 200556.96 0 2.3873448 2.3595646 2.3774937 7.1244031 20.860601 + 120000 200997.81 0 2.4097258 2.3736031 2.3871081 7.170437 -5.3623487 +Loop time of 20.5037 on 1 procs for 120000 steps with 4096 atoms + +Performance: 5056.640 tau/day, 5852.593 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0012425 | 0.0012425 | 0.0012425 | 0.0 | 0.01 +Comm | 0.015074 | 0.015074 | 0.015074 | 0.0 | 0.07 +Output | 0.006156 | 0.006156 | 0.006156 | 0.0 | 0.03 +Modify | 19.243 | 19.243 | 19.243 | 0.0 | 93.85 +Other | | 1.238 | | | 6.04 + +Nlocal: 4096.00 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 205 +Dangerous builds = 0 + + +Total wall time: 0:00:28 diff --git a/src/USER-BROWNIAN/fix_brownian.cpp b/src/USER-BROWNIAN/fix_brownian.cpp new file mode 100644 index 0000000000..f25f6d6b32 --- /dev/null +++ b/src/USER-BROWNIAN/fix_brownian.cpp @@ -0,0 +1,217 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp. + + Contributing author: Sam Cameron (University of Bristol) +------------------------------------------------------------------------- */ + +#include "fix_brownian.h" + +#include +#include +#include "math_extra.h" +#include "atom.h" +#include "force.h" +#include "update.h" +#include "comm.h" +#include "domain.h" +#include "random_mars.h" +#include "memory.h" +#include "error.h" + + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixBrownian::FixBrownian(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + virial_flag = 1; + + time_integrate = 1; + + if (narg != 6 && narg != 8) + error->all(FLERR,"Illegal fix brownian command."); + + gamma_t = utils::numeric(FLERR,arg[3],false,lmp); + if (gamma_t <= 0.0) + error->all(FLERR,"Fix brownian viscous drag " + "coefficient must be > 0."); + + diff_t = utils::numeric(FLERR,arg[4],false,lmp); + if (diff_t <= 0.0) + error->all(FLERR,"Fix brownian diffusion " + "coefficient must be > 0."); + + seed = utils::inumeric(FLERR,arg[5],false,lmp); + if (seed <= 0) error->all(FLERR,"Fix brownian seed must be > 0."); + + noise_flag = 1; + gaussian_noise_flag = 0; + + if (narg == 8) { + + if (strcmp(arg[6],"rng") == 0) { + if (strcmp(arg[7],"uniform") == 0) { + noise_flag = 1; + } else if (strcmp(arg[7],"gaussian") == 0) { + noise_flag = 1; + gaussian_noise_flag = 1; + } else if (strcmp(arg[7],"none") == 0) { + noise_flag = 0; + } else { + error->all(FLERR,"Illegal fix brownian command."); + } + } else { + error->all(FLERR,"Illegal fix brownian command."); + } + } + + // initialize Marsaglia RNG with processor-unique seed + random = new RanMars(lmp,seed + comm->me); + +} + +/* ---------------------------------------------------------------------- */ + +int FixBrownian::setmask() +{ + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +FixBrownian::~FixBrownian() +{ + delete random; +} + + + +/* ---------------------------------------------------------------------- */ + +void FixBrownian::init() +{ + + g1 = force->ftm2v/gamma_t; + if (noise_flag == 0) { + g2 = 0; + rng_func = &RanMars::zero_rng; + } else if (gaussian_noise_flag == 1) { + g2 = gamma_t*sqrt(2 * diff_t)/force->ftm2v; + rng_func = &RanMars::gaussian; + } else { + g2 = gamma_t*sqrt( 24 * diff_t)/force->ftm2v; + rng_func = &RanMars::uniform_middle; + } + + dt = update->dt; + sqrtdt = sqrt(dt); +} + +void FixBrownian::setup(int vflag) +{ + post_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixBrownian::initial_integrate(int /* vflag */) +{ + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double dx,dy,dz; + + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + dx = dt * g1 * f[i][0]; + x[i][0] += dx; + v[i][0] = dx/dt; + + dy = dt * g1 * f[i][1]; + x[i][1] += dy; + v[i][1] = dy/dt; + + dz = dt * g1 * f[i][2]; + x[i][2] += dz; + v[i][2] = dz/dt; + + } + } + + + return; +} + +/* ---------------------------------------------------------------------- + apply random force, stolen from MISC/fix_efield.cpp +------------------------------------------------------------------------- */ + +void FixBrownian::post_force(int vflag) +{ + double **f = atom->f; + double **x = atom->x; + int *mask = atom->mask; + imageint *image = atom->image; + int nlocal = atom->nlocal; + + // virial setup + + if (vflag) v_setup(vflag); + else evflag = 0; + + double fx,fy,fz; + double v[6]; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + + fx = g2 * (random->*rng_func)()/sqrtdt; + fy = g2 * (random->*rng_func)()/sqrtdt; + fz = g2 * (random->*rng_func)()/sqrtdt; + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + + if (evflag) { + v[0] = fx*x[i][0]; + v[1] = fy*x[i][1]; + v[2] = fz*x[i][2]; + v[3] = fx*x[i][1]; + v[4] = fx*x[i][2]; + v[5] = fy*x[i][2]; + v_tally(i, v); + } + } +} + +void FixBrownian::reset_dt() +{ + + dt = update->dt; + sqrtdt = sqrt(dt); +} diff --git a/src/USER-BROWNIAN/fix_brownian.h b/src/USER-BROWNIAN/fix_brownian.h new file mode 100644 index 0000000000..fb56edb39e --- /dev/null +++ b/src/USER-BROWNIAN/fix_brownian.h @@ -0,0 +1,79 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(brownian,FixBrownian) + +#else + +#ifndef LMP_FIX_BROWNIAN_H +#define LMP_FIX_BROWNIAN_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixBrownian : public Fix { + public: + FixBrownian(class LAMMPS *, int, char **); + virtual ~FixBrownian(); + void init(); + void initial_integrate(int); + void setup(int); + void post_force(int); + int setmask(); + void reset_dt(); + + private: + int seed; // RNG seed + double dt, sqrtdt; // time step interval and its sqrt + + + double gamma_t; // translational damping param + double diff_t; // translational diffusion coeff + + double g1,g2; // prefactors in time stepping + int noise_flag; // 0/1 for noise off/on + int gaussian_noise_flag; // 0/1 for uniform/gaussian noise + +protected: + class RanMars *random; + typedef double (RanMars::*rng_member)(); + rng_member rng_func; // placeholder for RNG function + +}; + +} +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal fix brownian command. + +Wrong number/type of input arguments. + +E: Fix brownian viscous drag coefficient must be > 0. + +Self-explanatory. + +E: Fix brownian diffusion coefficient must be > 0. + +Self-explanatory. + +E: Fix brownian seed must be > 0. + +Self-explanatory. + +*/ From bce37abe8f18a62e42e3d3ba501d03bc14c158cd Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 20 Dec 2020 15:15:19 -0700 Subject: [PATCH 0061/1217] Clarifying variable names --- src/nstencil.cpp | 34 +++++++++++++++--------------- src/nstencil.h | 6 +++--- src/nstencil_full_multi_2d.cpp | 10 ++++----- src/nstencil_full_multi_3d.cpp | 10 ++++----- src/nstencil_half_multi_2d.cpp | 16 +++++++------- src/nstencil_half_multi_2d_tri.cpp | 16 +++++++------- src/nstencil_half_multi_3d.cpp | 16 +++++++------- src/nstencil_half_multi_3d_tri.cpp | 16 +++++++------- 8 files changed, 62 insertions(+), 62 deletions(-) diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 42ddbaff30..f6281a1964 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -79,9 +79,9 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) stencil_multi = nullptr; maxstencil_multi = nullptr; - stencil_half = nullptr; - stencil_skip = nullptr; - stencil_bin_type = nullptr; + flag_half_multi = nullptr; + flag_skip_multi = nullptr; + bin_type_multi = nullptr; dimension = domain->dimension; } @@ -111,16 +111,16 @@ NStencil::~NStencil() memory->destroy(nstencil_multi); for (int i = 1; i <= n; i++) { for (int j = 0; j <= n; j++) { - if (! stencil_skip[i][j]) + if (! flag_skip_multi[i][j]) memory->destroy(stencil_multi[i][j]); } delete [] stencil_multi[i]; } delete [] stencil_multi; memory->destroy(maxstencil_multi); - memory->destroy(stencil_half); - memory->destroy(stencil_skip); - memory->destroy(stencil_bin_type); + memory->destroy(flag_half_multi); + memory->destroy(flag_skip_multi); + memory->destroy(bin_type_multi); memory->destroy(stencil_sx_multi); memory->destroy(stencil_sy_multi); @@ -272,12 +272,12 @@ void NStencil::create_setup() if(nb) copy_bin_info_multi(); // Allocate arrays to store stencil information - memory->create(stencil_half, n+1, n+1, - "neighstencil:stencil_half"); - memory->create(stencil_skip, n+1, n+1, - "neighstencil:stencil_skip"); - memory->create(stencil_bin_type, n+1, n+1, - "neighstencil:stencil_bin_type"); + memory->create(flag_half_multi, n+1, n+1, + "neighstencil:flag_half_multi"); + memory->create(flag_skip_multi, n+1, n+1, + "neighstencil:flag_skip_multi"); + memory->create(bin_type_multi, n+1, n+1, + "neighstencil:bin_type_multi"); memory->create(stencil_sx_multi, n+1, n+1, "neighstencil:stencil_sx_multi"); @@ -303,7 +303,7 @@ void NStencil::create_setup() // Skip all stencils by default, initialize smax for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - stencil_skip[i][j] = 1; + flag_skip_multi[i][j] = 1; } } @@ -329,10 +329,10 @@ void NStencil::create_setup() for (j = 1; j <= n; j++) { // Skip creation of unused stencils - if (stencil_skip[i][j]) continue; + if (flag_skip_multi[i][j]) continue; - // Copy bin info for this particular pair of types - bin_type = stencil_bin_type[i][j]; + // Copy bin info for this pair of atom types + bin_type = bin_type_multi[i][j]; stencil_binsizex_multi[i][j] = binsizex_multi[bin_type]; stencil_binsizey_multi[i][j] = binsizey_multi[bin_type]; diff --git a/src/nstencil.h b/src/nstencil.h index 5bff8cbfac..9ca8bab55d 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -42,9 +42,9 @@ class NStencil : protected Pointers { double cutoff_custom; // cutoff set by requestor // Arrays to store options for multi itype-jtype stencils - bool **stencil_half; // flag creation of a half stencil for itype-jtype - bool **stencil_skip; // skip creation of itype-jtype stencils (for newton on) - int **stencil_bin_type; // what type to use for bin information + bool **flag_half_multi; // flag creation of a half stencil for itype-jtype + bool **flag_skip_multi; // skip creation of itype-jtype stencils (for newton on) + int **bin_type_multi; // what type to use for bin information NStencil(class LAMMPS *); virtual ~NStencil(); diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp index 9712db7ac8..61557f2d00 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -36,9 +36,9 @@ void NStencilFullMulti2d::set_stencil_properties() for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - stencil_half[i][j] = 0; - stencil_skip[i][j] = 0; - stencil_bin_type[i][j] = j; + flag_half_multi[i][j] = 0; + flag_skip_multi[i][j] = 0; + bin_type_multi[i][j] = j; } } } @@ -56,7 +56,7 @@ void NStencilFullMulti2d::create() for (itype = 1; itype <= n; itype++) { for (jtype = 1; jtype <= n; jtype++) { - if (stencil_skip[itype][jtype]) continue; + if (flag_skip_multi[itype][jtype]) continue; ns = 0; @@ -66,7 +66,7 @@ void NStencilFullMulti2d::create() mbinx = stencil_mbinx_multi[itype][jtype]; mbiny = stencil_mbiny_multi[itype][jtype]; - bin_type = stencil_bin_type[itype][jtype]; + bin_type = bin_type_multi[itype][jtype]; cutsq = cutneighsq[itype][jtype]; diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp index b3f8db53b7..f4935b70e0 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -37,9 +37,9 @@ void NStencilFullMulti3d::set_stencil_properties() for (i = 1; i <= n; i++) { for (j = 1; j <= n; j++) { - stencil_half[i][j] = 0; - stencil_skip[i][j] = 0; - stencil_bin_type[i][j] = j; + flag_half_multi[i][j] = 0; + flag_skip_multi[i][j] = 0; + bin_type_multi[i][j] = j; } } } @@ -57,7 +57,7 @@ void NStencilFullMulti3d::create() for (itype = 1; itype <= n; itype++) { for (jtype = 1; jtype <= n; jtype++) { - if (stencil_skip[itype][jtype]) continue; + if (flag_skip_multi[itype][jtype]) continue; ns = 0; @@ -69,7 +69,7 @@ void NStencilFullMulti3d::create() mbiny = stencil_mbiny_multi[itype][jtype]; mbinz = stencil_mbinz_multi[itype][jtype]; - bin_type = stencil_bin_type[itype][jtype]; + bin_type = bin_type_multi[itype][jtype]; cutsq = cutneighsq[itype][jtype]; diff --git a/src/nstencil_half_multi_2d.cpp b/src/nstencil_half_multi_2d.cpp index 0b320394b7..b407746602 100644 --- a/src/nstencil_half_multi_2d.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -42,14 +42,14 @@ void NStencilHalfMulti2d::set_stencil_properties() for (j = 1; j <= n; j++) { if(cutneighsq[i][i] > cutneighsq[j][j]) continue; - stencil_skip[i][j] = 0; + flag_skip_multi[i][j] = 0; if(cutneighsq[i][i] == cutneighsq[j][j]){ - stencil_half[i][j] = 1; - stencil_bin_type[i][j] = i; + flag_half_multi[i][j] = 1; + bin_type_multi[i][j] = i; } else { - stencil_half[i][j] = 0; - stencil_bin_type[i][j] = j; + flag_half_multi[i][j] = 0; + bin_type_multi[i][j] = j; } } } @@ -68,7 +68,7 @@ void NStencilHalfMulti2d::create() for (itype = 1; itype <= n; itype++) { for (jtype = 1; jtype <= n; jtype++) { - if (stencil_skip[itype][jtype]) continue; + if (flag_skip_multi[itype][jtype]) continue; ns = 0; @@ -78,11 +78,11 @@ void NStencilHalfMulti2d::create() mbinx = stencil_mbinx_multi[itype][jtype]; mbiny = stencil_mbiny_multi[itype][jtype]; - bin_type = stencil_bin_type[itype][jtype]; + bin_type = bin_type_multi[itype][jtype]; cutsq = cutneighsq[itype][jtype]; - if (stencil_half[itype][jtype]) { + if (flag_half_multi[itype][jtype]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) if (j > 0 || (j == 0 && i > 0)) { diff --git a/src/nstencil_half_multi_2d_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp index 95b0b483c5..cd9f85da60 100755 --- a/src/nstencil_half_multi_2d_tri.cpp +++ b/src/nstencil_half_multi_2d_tri.cpp @@ -42,14 +42,14 @@ void NStencilHalfMulti2dTri::set_stencil_properties() for (j = 1; j <= n; j++) { if(cutneighsq[i][i] > cutneighsq[j][j]) continue; - stencil_skip[i][j] = 0; + flag_skip_multi[i][j] = 0; if(cutneighsq[i][i] == cutneighsq[j][j]){ - stencil_half[i][j] = 1; - stencil_bin_type[i][j] = i; + flag_half_multi[i][j] = 1; + bin_type_multi[i][j] = i; } else { - stencil_half[i][j] = 0; - stencil_bin_type[i][j] = j; + flag_half_multi[i][j] = 0; + bin_type_multi[i][j] = j; } } } @@ -68,7 +68,7 @@ void NStencilHalfMulti2dTri::create() for (itype = 1; itype <= n; itype++) { for (jtype = 1; jtype <= n; jtype++) { - if (stencil_skip[itype][jtype]) continue; + if (flag_skip_multi[itype][jtype]) continue; ns = 0; @@ -78,11 +78,11 @@ void NStencilHalfMulti2dTri::create() mbinx = stencil_mbinx_multi[itype][jtype]; mbiny = stencil_mbiny_multi[itype][jtype]; - bin_type = stencil_bin_type[itype][jtype]; + bin_type = bin_type_multi[itype][jtype]; cutsq = cutneighsq[itype][jtype]; - if (stencil_half[itype][jtype]) { + if (flag_half_multi[itype][jtype]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) if (bin_distance_multi(i,j,0,bin_type) < cutsq) diff --git a/src/nstencil_half_multi_3d.cpp b/src/nstencil_half_multi_3d.cpp index 1f94fb16cd..d66cfe98b9 100644 --- a/src/nstencil_half_multi_3d.cpp +++ b/src/nstencil_half_multi_3d.cpp @@ -42,14 +42,14 @@ void NStencilHalfMulti3d::set_stencil_properties() for (j = 1; j <= n; j++) { if(cutneighsq[i][i] > cutneighsq[j][j]) continue; - stencil_skip[i][j] = 0; + flag_skip_multi[i][j] = 0; if(cutneighsq[i][i] == cutneighsq[j][j]){ - stencil_half[i][j] = 1; - stencil_bin_type[i][j] = i; + flag_half_multi[i][j] = 1; + bin_type_multi[i][j] = i; } else { - stencil_half[i][j] = 0; - stencil_bin_type[i][j] = j; + flag_half_multi[i][j] = 0; + bin_type_multi[i][j] = j; } } } @@ -68,7 +68,7 @@ void NStencilHalfMulti3d::create() for (itype = 1; itype <= n; itype++) { for (jtype = 1; jtype <= n; jtype++) { - if (stencil_skip[itype][jtype]) continue; + if (flag_skip_multi[itype][jtype]) continue; ns = 0; @@ -80,11 +80,11 @@ void NStencilHalfMulti3d::create() mbiny = stencil_mbiny_multi[itype][jtype]; mbinz = stencil_mbinz_multi[itype][jtype]; - bin_type = stencil_bin_type[itype][jtype]; + bin_type = bin_type_multi[itype][jtype]; cutsq = cutneighsq[itype][jtype]; - if (stencil_half[itype][jtype]) { + if (flag_half_multi[itype][jtype]) { for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) diff --git a/src/nstencil_half_multi_3d_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp index 30e59e92e8..e4a5747ca6 100755 --- a/src/nstencil_half_multi_3d_tri.cpp +++ b/src/nstencil_half_multi_3d_tri.cpp @@ -42,14 +42,14 @@ void NStencilHalfMulti3dTri::set_stencil_properties() for (j = 1; j <= n; j++) { if(cutneighsq[i][i] > cutneighsq[j][j]) continue; - stencil_skip[i][j] = 0; + flag_skip_multi[i][j] = 0; if(cutneighsq[i][i] == cutneighsq[j][j]){ - stencil_half[i][j] = 1; - stencil_bin_type[i][j] = i; + flag_half_multi[i][j] = 1; + bin_type_multi[i][j] = i; } else { - stencil_half[i][j] = 0; - stencil_bin_type[i][j] = j; + flag_half_multi[i][j] = 0; + bin_type_multi[i][j] = j; } } } @@ -68,7 +68,7 @@ void NStencilHalfMulti3dTri::create() for (itype = 1; itype <= n; itype++) { for (jtype = 1; jtype <= n; jtype++) { - if (stencil_skip[itype][jtype]) continue; + if (flag_skip_multi[itype][jtype]) continue; ns = 0; @@ -80,11 +80,11 @@ void NStencilHalfMulti3dTri::create() mbiny = stencil_mbiny_multi[itype][jtype]; mbinz = stencil_mbinz_multi[itype][jtype]; - bin_type = stencil_bin_type[itype][jtype]; + bin_type = bin_type_multi[itype][jtype]; cutsq = cutneighsq[itype][jtype]; - if (stencil_half[itype][jtype]) { + if (flag_half_multi[itype][jtype]) { for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) From 5ae32146eb7069cbe16c14903ca4a9bc66f31fd2 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 20 Dec 2020 17:18:32 -0700 Subject: [PATCH 0062/1217] Adding full neighbor list check for new reduced comm --- src/comm.cpp | 16 +++++++--------- src/neighbor.cpp | 13 +++++++++++++ src/neighbor.h | 1 + 3 files changed, 21 insertions(+), 9 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index afd4d891ee..84e3b9ad65 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -242,15 +242,13 @@ void Comm::init() for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; - // Can't used multi_reduce communication with Newton off - // TODO: need to somehow restrict this option with full neighbor lists - // CANNOT use multi_reduce communication with full nlist - // Could remove NP_NEWTON from npair_full_*multi_reduce*, but could be cryptic - // Also could be cases where you want newton off (hybrid) but don't use multi_reduce comm - // Could add check on neighbor build, if full and comm->multi_reduce error... - // or just add check on comm setup - is that run before every run? Only if box change... - if (force->newton == 0 && multi_reduce) - error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); + // Can't used multi/reduce communication with Newton off or full neighbor lits + if(multi_reduce){ + if (force->newton == 0) + error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); + if (neighbor->any_full()) + error->all(FLERR,"Cannot use multi/reduce communication with a full neighbor list"); + } } /* ---------------------------------------------------------------------- diff --git a/src/neighbor.cpp b/src/neighbor.cpp index fe34e738b0..d130219931 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -2420,6 +2420,19 @@ int Neighbor::exclude_setting() return exclude; } +/* ---------------------------------------------------------------------- + check if any of the old requested neighbor lists are full +------------------------------------------------------------------------- */ + +int Neighbor::any_full() +{ + int any_full = 0; + for(int i = 0; i < old_nrequest; i++) { + if(old_requests[i]->full) any_full = 1; + } + return any_full; +} + /* ---------------------------------------------------------------------- return # of bytes of allocated memory ------------------------------------------------------------------------- */ diff --git a/src/neighbor.h b/src/neighbor.h index 2943f7e082..d1a5cf9112 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -122,6 +122,7 @@ class Neighbor : protected Pointers { void exclusion_group_group_delete(int, int); // rm a group-group exclusion int exclude_setting(); // return exclude value to accelerator pkg class NeighRequest *find_request(void *); // find a neighbor request + int any_full(); // Check if any old requests had full neighbor lists double memory_usage(); From 5a3cb38705ee169fa5da4b96cd17716f3a24bb8c Mon Sep 17 00:00:00 2001 From: Sam Cameron Date: Mon, 21 Dec 2020 10:58:27 +0000 Subject: [PATCH 0063/1217] Made requested changes to fix propel/self. Last thing to change would be to re-introduce the types keyword into this fix if that was deemed to be best. --- doc/src/fix_propel_self.rst | 55 ++++---- .../USER/brownian/2d_velocity/in.2d_velocity | 2 +- .../USER/brownian/spherical_ABP/in.2d_abp | 2 +- .../brownian/spherical_ABP/in.3d_ideal_abp | 2 +- .../log_WCA_1_1_1_3_4_2d.lammps.log | 126 +++++++++--------- .../log_ideal_1_1_1_3_4_3d.lammps.log | 92 ++++++------- src/USER-BROWNIAN/fix_propel_self.cpp | 52 ++++---- 7 files changed, 170 insertions(+), 161 deletions(-) diff --git a/doc/src/fix_propel_self.rst b/doc/src/fix_propel_self.rst index 582d9e4294..ba8c48cf6b 100644 --- a/doc/src/fix_propel_self.rst +++ b/doc/src/fix_propel_self.rst @@ -8,22 +8,19 @@ Syntax .. parsed-literal:: - fix ID group-ID propel/self magnitude keyword values + fix ID group-ID propel/self mode magnitude keyword values * ID, group-ID are documented in :doc:`fix ` command * propel/self = style name of this fix command +* mode = *dipole* or *velocity* or *quat* * magnitude = magnitude of self-propulsion force -* one (and only one) keyword/value pair must be appended to args -* keyword = *dipole* or *velocity* or *quat* +* zero or one keyword/value pairs may be appended +* keyword = *qvector* .. parsed-literal:: - *dipole* value = none = apply force along dipole direction - *velocity* value = none = apply force along velocity direction - *quat* values = direction vector *sx* and *sy* and *sz* - *sx* = x component of force direction in ellipsoid frame - *sy* = y component of force direction in ellipsoid frame - *sz* = z component of force direction in ellipsoid frame + *qvector* value = direction of force in ellipsoid frame + *sx*, *sy*, *sz* = components of *qvector* Examples @@ -31,9 +28,9 @@ Examples .. code-block:: LAMMPS - fix propel/self all 40.0 dipole - fix propel/self all 10.0 velocity - fix propel/self all 15.7 quat 1.0 0.0 0.0 + fix active all propel/self dipole 40.0 + fix active all propel/self velocity 10.0 + fix active all propel/self quat 15.7 qvector 1.0 0.0 0.0 Description """"""""""" @@ -50,7 +47,7 @@ is the magnitude of the force, and :math:`e_i` is the vector direction of the force. The specification of :math:`e_i` is based on which of the three keywords (*dipole* or *velocity* or *quat*) one selects. -For keyword *dipole*, :math:`e_i` is just equal to +For mode *dipole*, :math:`e_i` is just equal to the dipole vectors of the atoms in the group. Therefore, if the dipoles are not unit vectors, the :math:`e_i` will not be unit vectors. @@ -66,21 +63,31 @@ are not unit vectors, the :math:`e_i` will not be unit vectors. all the dipole magnitudes to 1.0 unless you have a good reason not to (see the :doc:`set ` command on how to do this). -For keyword *velocity*, :math:`e_i` points in the direction +For mode *velocity*, :math:`e_i` points in the direction of the current velocity (a unit-vector). This can be interpreted as a velocity-dependent friction, as proposed by e.g. :ref:`(Erdmann) `. -For keyword *quat*, :math:`e_i` points in the direction of the unit -vector defined by its arguments *sx*, *sy*, and *sz*, which are -themselves defined within the coordinate frame of the atom's +For mode *quat*, :math:`e_i` points in the direction of a unit +vector, oriented in the coordinate frame of the ellipsoidal particles, +which defaults to point along the x-direction. This default behaviour +can be changed by via the *quatvec* keyword. + +The optional *quatvec* keyword specifies the direction of self-propulsion +via a unit vector (sx,sy,sz). The arguments *sx*, *sy*, and *sz*, are +defined within the coordinate frame of the atom's ellipsoid. For instance, for an ellipsoid with long axis along its x-direction, if one wanted the self-propulsion force to also be along this axis, set *sx* equal to 1 and *sy*, *sz* both equal -to zero. For *quat*, :math:`e_i` will always be a unit vector, -so multiplying all three arguments *sx*, *sy*, and *sz* by a -positive scalar will not change the self-propulsion force -(multiplying by a negative scalar will change the sign of the -force). +to zero. This keyword may only be specified for mode *quat*. + +.. note:: + + In using keyword *quatvec*, the three arguments *sx*, + *sy*, and *sz* will be automatically normalised to components + of a unit vector internally to avoid users having to explicitly + do so themselves. Therefore, in mode *quat*, the vectors :math:`e_i` + will always be of unit length. + Along with adding a force contribution, this fix can also contribute to the virial (pressure) of the system, defined as @@ -89,10 +96,10 @@ contribute to the virial (pressure) of the system, defined as boundary conditions. See :ref:`(Winkler) ` for a discussion of this active pressure contribution. -For keywords *dipole* and *quat*, this fix is by default +For modes *dipole* and *quat*, this fix is by default included in pressure computations. -For keyword *velocity*, this fix is by default not included +For mode *velocity*, this fix is by default not included in pressure computations. diff --git a/examples/USER/brownian/2d_velocity/in.2d_velocity b/examples/USER/brownian/2d_velocity/in.2d_velocity index b731f5f477..cbd7d543cb 100644 --- a/examples/USER/brownian/2d_velocity/in.2d_velocity +++ b/examples/USER/brownian/2d_velocity/in.2d_velocity @@ -31,7 +31,7 @@ neigh_modify every 1 delay 1 check yes pair_style none fix step all brownian ${gamma_t} ${D_t} ${seed} -fix vel all propel/self ${fp} velocity +fix vel all propel/self velocity ${fp} fix 2 all enforce2d fix_modify vel virial yes diff --git a/examples/USER/brownian/spherical_ABP/in.2d_abp b/examples/USER/brownian/spherical_ABP/in.2d_abp index d626445926..9db5a46cf6 100644 --- a/examples/USER/brownian/spherical_ABP/in.2d_abp +++ b/examples/USER/brownian/spherical_ABP/in.2d_abp @@ -41,7 +41,7 @@ pair_modify shift yes # overdamped brownian dynamics time-step fix step all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} dipole # self-propulsion force along the dipole direction -fix activity all propel/self ${fp} dipole +fix activity all propel/self dipole ${fp} fix 2 all enforce2d diff --git a/examples/USER/brownian/spherical_ABP/in.3d_ideal_abp b/examples/USER/brownian/spherical_ABP/in.3d_ideal_abp index e131d07059..4c3d403f20 100644 --- a/examples/USER/brownian/spherical_ABP/in.3d_ideal_abp +++ b/examples/USER/brownian/spherical_ABP/in.3d_ideal_abp @@ -30,7 +30,7 @@ pair_style none # overdamped brownian dynamics time-step fix step all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} dipole # self-propulsion force along the dipole direction -fix activity all propel/self ${fp} dipole +fix activity all propel/self dipole ${fp} compute press all pressure NULL virial diff --git a/examples/USER/brownian/spherical_ABP/log_WCA_1_1_1_3_4_2d.lammps.log b/examples/USER/brownian/spherical_ABP/log_WCA_1_1_1_3_4_2d.lammps.log index 0c51314cca..8f334c77fb 100644 --- a/examples/USER/brownian/spherical_ABP/log_WCA_1_1_1_3_4_2d.lammps.log +++ b/examples/USER/brownian/spherical_ABP/log_WCA_1_1_1_3_4_2d.lammps.log @@ -10,10 +10,10 @@ Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 region box block -16 16 -16 16 -0.2 0.2 create_box 1 box Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777) - 2 by 2 by 1 MPI processor grid + 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 1024 atoms - create_atoms CPU = 0.001 seconds + create_atoms CPU = 0.002 seconds mass * 1.0 set type * dipole/random ${seed} 1.0 set type * dipole/random 1974019 1.0 @@ -41,8 +41,8 @@ fix step all brownian/sphere 1 1 1 ${D_r} ${seed} dipole fix step all brownian/sphere 1 1 1 3 ${seed} dipole fix step all brownian/sphere 1 1 1 3 1974019 dipole # self-propulsion force along the dipole direction -fix activity all propel/self ${fp} dipole -fix activity all propel/self 4 dipole +fix activity all propel/self dipole ${fp} +fix activity all propel/self dipole 4 fix 2 all enforce2d @@ -66,34 +66,34 @@ Neighbor list info ... pair build: half/bin/newtoff stencil: half/bin/2d/newtoff bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.052 | 5.052 | 5.052 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.066 | 5.066 | 5.066 Mbytes Step Temp E_pair c_press 0 1 0 -0.53979198 - 50000 1.0371295e+10 0 -0.542818 -Loop time of 2.25396 on 4 procs for 50000 steps with 1024 atoms + 50000 1.0902879e+10 0 -0.53710405 +Loop time of 6.3887 on 1 procs for 50000 steps with 1024 atoms -Performance: 0.192 tau/day, 22183.200 timesteps/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 0.068 tau/day, 7826.319 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.1034 | 0.10382 | 0.10438 | 0.1 | 4.61 +Pair | 0.34323 | 0.34323 | 0.34323 | 0.0 | 5.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.26698 | 0.26833 | 0.26924 | 0.2 | 11.90 -Output | 2.2284e-05 | 2.4926e-05 | 3.2332e-05 | 0.0 | 0.00 -Modify | 1.7222 | 1.7237 | 1.727 | 0.1 | 76.48 -Other | | 0.1581 | | | 7.01 +Comm | 0.070232 | 0.070232 | 0.070232 | 0.0 | 1.10 +Output | 2.5077e-05 | 2.5077e-05 | 2.5077e-05 | 0.0 | 0.00 +Modify | 5.8232 | 5.8232 | 5.8232 | 0.0 | 91.15 +Other | | 0.152 | | | 2.38 -Nlocal: 256.000 ave 256 max 256 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 105.000 ave 105 max 105 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 544.000 ave 544 max 544 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 201.000 ave 201 max 201 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2112.00 ave 2112 max 2112 min +Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 2176 -Ave neighs/atom = 2.1250000 +Total # of neighbors = 2112 +Ave neighs/atom = 2.0625000 Neighbor list builds = 0 Dangerous builds = 0 reset_timestep 0 @@ -111,53 +111,53 @@ thermo 10000 # main run run 200000 -Per MPI rank memory allocation (min/avg/max) = 5.427 | 5.427 | 5.427 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.441 | 5.441 | 5.441 Mbytes Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press - 0 1.0371295e+10 0 0 0 0 0 -0.542818 - 10000 107356.09 0.079828495 0.19584264 0.19679822 0 0.39264086 0.00078740793 - 20000 101692.44 0.11317533 0.40847364 0.42097802 0 0.82945167 0.74111888 - 30000 105763.55 0.10261852 0.68303669 0.66125751 0 1.3442942 0.71112533 - 40000 105127.29 0.12371743 0.97990144 0.94005552 0 1.919957 1.0574552 - 50000 101579.58 0.12771813 1.3059069 1.2364468 0 2.5423537 1.059263 - 60000 104914.36 0.12055843 1.6215593 1.525488 0 3.1470473 0.79873537 - 70000 106629.18 0.1278745 1.9639958 1.8682794 0 3.8322752 0.91950208 - 80000 103286.54 0.13927689 2.3201565 2.2373383 0 4.5574948 1.1875034 - 90000 106451.61 0.093479681 2.6287902 2.5753347 0 5.2041249 1.0861163 - 100000 102199.72 0.13269425 2.9127976 2.9369237 0 5.8497214 1.4841998 - 110000 105229.73 0.10594209 3.1798718 3.3495317 0 6.5294035 1.5444784 - 120000 106262.36 0.11902575 3.6267452 3.7188125 0 7.3455578 1.3366518 - 130000 109388.12 0.10562576 3.929973 4.0226942 0 7.9526672 1.324534 - 140000 107697.35 0.13028752 4.231893 4.3780995 0 8.6099925 1.7406167 - 150000 103928.72 0.12278994 4.5826286 4.7578662 0 9.3404948 1.3024003 - 160000 103370.23 0.11391216 4.8767011 5.1181189 0 9.99482 1.4325241 - 170000 103821.53 0.11163256 5.153318 5.3785963 0 10.531914 1.4569115 - 180000 106824.99 0.13225083 5.4080929 5.7399804 0 11.148073 1.334984 - 190000 101794.6 0.10632938 5.7384925 6.080955 0 11.819448 0.81285422 - 200000 102128.67 0.13703498 6.0414673 6.4511058 0 12.492573 0.42904128 -Loop time of 9.60419 on 4 procs for 200000 steps with 1024 atoms + 0 1.0902879e+10 0 0 0 0 0 -0.53710405 + 10000 103498.6 0.087662767 0.18719065 0.2007338 0 0.38792445 0.16080254 + 20000 104785.56 0.12719481 0.4197551 0.40722743 0 0.82698253 0.5007164 + 30000 103183.73 0.1126518 0.67800477 0.67921667 0 1.3572214 0.36634317 + 40000 102912.87 0.092584777 0.96234448 0.97188884 0 1.9342333 0.46170129 + 50000 103516.68 0.12761757 1.2381642 1.3203398 0 2.558504 0.85712805 + 60000 104999.77 0.14482924 1.5437166 1.6177103 0 3.1614269 1.1403162 + 70000 103925.7 0.11302021 1.886 1.9262949 0 3.8122949 1.1056086 + 80000 105000.14 0.14502228 2.205833 2.2668945 0 4.4727275 1.0757792 + 90000 105980.8 0.12089413 2.515801 2.647111 0 5.162912 1.1160525 + 100000 106557.86 0.10934038 2.7977098 2.8965145 0 5.6942242 0.56901933 + 110000 104241.46 0.12719985 3.1612652 3.2283956 0 6.3896608 0.95100999 + 120000 101910.56 0.12002691 3.5844099 3.5366227 0 7.1210326 1.2526653 + 130000 104435.28 0.10695039 3.8328815 3.8286503 0 7.6615318 1.6198184 + 140000 104864.99 0.11226471 4.1822059 4.285915 0 8.4681209 1.5190757 + 150000 103209.43 0.11229036 4.430069 4.5491143 0 8.9791833 1.1568204 + 160000 106692.61 0.11151476 4.7593714 5.0322819 0 9.7916533 1.2337266 + 170000 105232.19 0.12039818 5.0665907 5.3612901 0 10.427881 1.3881139 + 180000 107126.86 0.10793969 5.4129878 5.6391008 0 11.052089 1.6691607 + 190000 103814.36 0.096916503 5.7355093 5.9557837 0 11.691293 1.3863335 + 200000 103976.84 0.10928015 6.1871603 6.3393786 0 12.526539 1.1687077 +Loop time of 27.4513 on 1 procs for 200000 steps with 1024 atoms -Performance: 17992.140 tau/day, 20824.236 timesteps/s -100.0% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 6294.793 tau/day, 7285.640 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.71756 | 0.75121 | 0.79008 | 3.0 | 7.82 -Neigh | 0.018158 | 0.018773 | 0.019357 | 0.3 | 0.20 -Comm | 1.0469 | 1.0597 | 1.0738 | 1.2 | 11.03 -Output | 0.00051435 | 0.00057078 | 0.00070838 | 0.0 | 0.01 -Modify | 6.8012 | 6.9883 | 7.1513 | 4.9 | 72.76 -Other | | 0.7857 | | | 8.18 +Pair | 3.2525 | 3.2525 | 3.2525 | 0.0 | 11.85 +Neigh | 0.054678 | 0.054678 | 0.054678 | 0.0 | 0.20 +Comm | 0.26582 | 0.26582 | 0.26582 | 0.0 | 0.97 +Output | 0.0006103 | 0.0006103 | 0.0006103 | 0.0 | 0.00 +Modify | 23.265 | 23.265 | 23.265 | 0.0 | 84.75 +Other | | 0.6131 | | | 2.23 -Nlocal: 256.000 ave 265 max 240 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 88.5000 ave 91 max 87 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Neighs: 678.500 ave 713 max 597 min -Histogram: 1 0 0 0 0 0 0 0 1 2 +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 166.000 ave 166 max 166 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2634.00 ave 2634 max 2634 min +Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 2714 -Ave neighs/atom = 2.6503906 -Neighbor list builds = 241 +Total # of neighbors = 2634 +Ave neighs/atom = 2.5722656 +Neighbor list builds = 238 Dangerous builds = 0 -Total wall time: 0:00:11 +Total wall time: 0:00:33 diff --git a/examples/USER/brownian/spherical_ABP/log_ideal_1_1_1_3_4_3d.lammps.log b/examples/USER/brownian/spherical_ABP/log_ideal_1_1_1_3_4_3d.lammps.log index be6c1d5d41..c5cbe4936d 100644 --- a/examples/USER/brownian/spherical_ABP/log_ideal_1_1_1_3_4_3d.lammps.log +++ b/examples/USER/brownian/spherical_ABP/log_ideal_1_1_1_3_4_3d.lammps.log @@ -10,10 +10,10 @@ Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 region box block -8 8 -8 8 -8 8 create_box 1 box Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670) - 2 by 1 by 2 MPI processor grid + 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4096 atoms - create_atoms CPU = 0.002 seconds + create_atoms CPU = 0.003 seconds mass * 1.0 set type * dipole/random ${seed} 1.0 set type * dipole/random 1974019 1.0 @@ -31,8 +31,8 @@ fix step all brownian/sphere 1 1 1 ${D_r} ${seed} dipole fix step all brownian/sphere 1 1 1 3 ${seed} dipole fix step all brownian/sphere 1 1 1 3 1974019 dipole # self-propulsion force along the dipole direction -fix activity all propel/self ${fp} dipole -fix activity all propel/self 4 dipole +fix activity all propel/self dipole ${fp} +fix activity all propel/self dipole 4 compute press all pressure NULL virial @@ -45,31 +45,31 @@ thermo 50001 run 50000 WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118) WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) -Per MPI rank memory allocation (min/avg/max) = 4.319 | 4.319 | 4.319 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.362 | 4.362 | 4.362 Mbytes Step Temp E_pair c_press 0 1 0 0.068021726 - 50000 1.046425e+10 0 0.067505633 -Loop time of 7.83903 on 4 procs for 50000 steps with 4096 atoms + 50000 1.0486812e+10 0 0.068203091 +Loop time of 25.3706 on 1 procs for 50000 steps with 4096 atoms -Performance: 0.055 tau/day, 6378.340 timesteps/s -97.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 0.017 tau/day, 1970.786 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.50238 | 0.51891 | 0.53617 | 1.7 | 6.62 -Output | 2.6343e-05 | 3.6075e-05 | 4.6997e-05 | 0.0 | 0.00 -Modify | 6.9536 | 6.9732 | 7.0105 | 0.8 | 88.95 -Other | | 0.3469 | | | 4.43 +Comm | 0.31005 | 0.31005 | 0.31005 | 0.0 | 1.22 +Output | 3.2633e-05 | 3.2633e-05 | 3.2633e-05 | 0.0 | 0.00 +Modify | 24.471 | 24.471 | 24.471 | 0.0 | 96.45 +Other | | 0.5897 | | | 2.32 -Nlocal: 1024.00 ave 1024 max 1024 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 353.000 ave 353 max 353 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Nlocal: 4096.00 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 817.000 ave 817 max 817 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0.0000000 @@ -96,46 +96,46 @@ thermo 10000 # main run run 120000 WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) -Per MPI rank memory allocation (min/avg/max) = 4.694 | 4.694 | 4.694 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.737 | 4.737 | 4.737 Mbytes Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press - 0 1.046425e+10 0 0 0 0 0 0.067505633 - 10000 106340.56 0 0.2469318 0.23662295 0.2441413 0.72769605 0.19939966 - 20000 104620.27 0 0.55429324 0.5231436 0.54976641 1.6272032 0.26601423 - 30000 106130.45 0 0.87562668 0.84813496 0.89321299 2.6169746 0.30836996 - 40000 105773.31 0 1.2262635 1.1899278 1.2626926 3.6788838 0.35392219 - 50000 103804.88 0 1.5851624 1.5645815 1.6434185 4.7931624 0.33326997 - 60000 105746.45 0 1.9928016 1.9347072 1.9837329 5.9112417 0.2550878 - 70000 104500.3 0 2.3269429 2.2774077 2.3368821 6.9412326 0.25218225 - 80000 105381.46 0 2.7114959 2.6937299 2.7171132 8.122339 0.36940892 - 90000 104542.79 0 3.0828648 3.084417 3.0783207 9.2456025 0.36106481 - 100000 104246.75 0 3.4635513 3.5105066 3.4545226 10.42858 0.3712313 - 110000 103099.55 0 3.8471061 3.9389997 3.8220676 11.608173 0.38466185 - 120000 103098.45 0 4.2014598 4.3456831 4.1888659 12.736009 0.36710217 -Loop time of 22.8893 on 4 procs for 120000 steps with 4096 atoms + 0 1.0486812e+10 0 0 0 0 0 0.068203091 + 10000 104209.87 0 0.25428952 0.2512451 0.23617807 0.74171269 0.1910208 + 20000 104433.46 0 0.55611319 0.57499464 0.54362634 1.6747342 0.27977792 + 30000 104615.53 0 0.88377871 0.8933002 0.88683731 2.6639162 0.31709969 + 40000 105930.5 0 1.2301515 1.262995 1.2479624 3.7411089 0.26149988 + 50000 105556.39 0 1.5798848 1.6402779 1.6392277 4.8593905 0.34401188 + 60000 104644.58 0 1.9782384 1.9902061 2.0327974 6.0012419 0.26709167 + 70000 104314.31 0 2.3681872 2.3695505 2.4241916 7.1619294 0.24191407 + 80000 105700 0 2.7109374 2.7434271 2.8309194 8.2852839 0.28355159 + 90000 103411.61 0 3.1023448 3.0881218 3.1599155 9.350382 0.3070844 + 100000 105432.12 0 3.4853878 3.4372177 3.5153198 10.437925 0.28141015 + 110000 105723.04 0 3.8405786 3.7967805 3.8738332 11.511192 0.33248553 + 120000 104734.31 0 4.2454301 4.1714561 4.2234474 12.640334 0.3603781 +Loop time of 63.7803 on 1 procs for 120000 steps with 4096 atoms -Performance: 4529.619 tau/day, 5242.615 timesteps/s -100.0% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 1625.581 tau/day, 1881.459 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0.0049489 | 0.0050479 | 0.0050978 | 0.1 | 0.02 -Comm | 0.082752 | 0.084491 | 0.085332 | 0.4 | 0.37 -Output | 0.00054352 | 0.0006034 | 0.00064793 | 0.0 | 0.00 -Modify | 21.069 | 21.521 | 21.964 | 7.0 | 94.02 -Other | | 1.278 | | | 5.58 +Neigh | 0.013032 | 0.013032 | 0.013032 | 0.0 | 0.02 +Comm | 0.093045 | 0.093045 | 0.093045 | 0.0 | 0.15 +Output | 0.00069845 | 0.00069845 | 0.00069845 | 0.0 | 0.00 +Modify | 62.279 | 62.279 | 62.279 | 0.0 | 97.65 +Other | | 1.394 | | | 2.19 -Nlocal: 1024.00 ave 1050 max 1010 min -Histogram: 2 0 0 1 0 0 0 0 0 1 +Nlocal: 4096.00 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0.00000 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0.0000000 -Neighbor list builds = 2169 +Neighbor list builds = 2174 Dangerous builds = 0 # if you want to check that rotational diffusion is behaving as expected, @@ -147,4 +147,4 @@ Dangerous builds = 0 #dump_modify 1 first yes sort id #run 120000 -Total wall time: 0:00:30 +Total wall time: 0:01:29 diff --git a/src/USER-BROWNIAN/fix_propel_self.cpp b/src/USER-BROWNIAN/fix_propel_self.cpp index 1755f59840..59bb080cc5 100644 --- a/src/USER-BROWNIAN/fix_propel_self.cpp +++ b/src/USER-BROWNIAN/fix_propel_self.cpp @@ -16,8 +16,7 @@ Thanks to Liesbeth Janssen @ Eindhoven University for useful discussions! - Current maintainer: Sam Cameron @ University of Bristol - + Current maintainer: Sam Cameron @ University of Bristol ----------------------------------------------------------------------- */ #include @@ -49,44 +48,47 @@ FixPropelSelf::FixPropelSelf(LAMMPS *lmp, int narg, char **arg) : virial_flag = 1; - if (narg < 5) + if (narg != 5 && narg != 9) error->all(FLERR,"Illegal fix propel/self command"); - - magnitude = utils::numeric(FLERR,arg[3],false,lmp); - if (strcmp(arg[4],"velocity") == 0) { + if (strcmp(arg[3],"velocity") == 0) { mode = VELOCITY; thermo_virial = 0; - if (narg != 5) { - error->all(FLERR,"Illegal fix propel/self command"); - } - } else if (strcmp(arg[4],"dipole") == 0) { + } else if (strcmp(arg[3],"dipole") == 0) { mode = DIPOLE; thermo_virial = 1; - if (narg != 5) { - error->all(FLERR,"Illegal fix propel/self command"); - } - } else if (strcmp(arg[4],"quat") == 0) { + } else if (strcmp(arg[3],"quat") == 0) { mode = QUAT; thermo_virial = 1; - if (narg != 8) { - error->all(FLERR,"Illegal fix propel/self command"); - } else { - sx = utils::numeric(FLERR,arg[5],false,lmp); - sy = utils::numeric(FLERR,arg[6],false,lmp); - sz = utils::numeric(FLERR,arg[7],false,lmp); - double qnorm = sqrt(sx*sx + sy*sy + sz*sz); - sx = sx/qnorm; - sy = sy/qnorm; - sz = sz/qnorm; - } } else { error->all(FLERR,"Illegal fix propel/self command"); } + magnitude = utils::numeric(FLERR,arg[4],false,lmp); + // check for keyword + if (narg == 9) { + if (mode != QUAT) { + error->all(FLERR,"Illegal fix propel/self command"); + } + if (strcmp(arg[5],"qvector") == 0) { + sx = utils::numeric(FLERR,arg[6],false,lmp); + sy = utils::numeric(FLERR,arg[7],false,lmp); + sz = utils::numeric(FLERR,arg[8],false,lmp); + double snorm = sqrt(sx*sx + sy*sy + sz*sz); + sx = sx/snorm; + sy = sy/snorm; + sz = sz/snorm; + } else { + error->all(FLERR,"Illegal fix propel/self command"); + } + } else { + sx = 1.0; + sy = 0.0; + sz = 0.0; + } } From b421c3d67652aa6fd0657542e5914a633c73bf47 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 22 Dec 2020 10:20:06 -0700 Subject: [PATCH 0064/1217] Adding arguments, initialization, and communication for custom groupings --- src/comm_brick.cpp | 44 ++++++++++++----------- src/comm_tiled.cpp | 46 +++++++++++++----------- src/neighbor.cpp | 87 +++++++++++++++++++++++++++++++++++++++++++++- src/neighbor.h | 9 ++++- 4 files changed, 143 insertions(+), 43 deletions(-) diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 7f84d619e4..528456ab7c 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -175,10 +175,11 @@ void CommBrick::setup() if (mode == Comm::MULTI) { if (multi_reduce) { - // If using multi/reduce binlists, communicate itype particles a distance - // equal to the max of itype-jtype interaction given smaller jtype particles - double **cutneighsq = neighbor->cutneighsq; - double *cuttypesq = neighbor->cuttypesq; + // If using multi/reduce, communicate itype particles a distance equal + // to the max of itype-jtype group interaction given smaller jtype group + int igroup, jgroup; + double **cutmultisq = neighbor->cutmultisq; + int *map_type_multi = neighbor->map_type_multi; for (i = 1; i <= ntypes; i++) { if (cutusermulti) { @@ -191,11 +192,14 @@ void CommBrick::setup() cutghostmulti[i][2] = 0.0; } + igroup = map_type_multi[i]; for (j = 1; j <= ntypes; j++){ - if(cutneighsq[j][j] > cutneighsq[i][i]) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); + jgroup = map_type_multi[j]; + + if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); } } } else { @@ -226,10 +230,11 @@ void CommBrick::setup() if (mode == Comm::MULTI) { if (multi_reduce) { - // If using multi/reduce binlists, communicate itype particles a distance - // equal to the max of itype-jtype interaction given smaller jtype particles - double **cutneighsq = neighbor->cutneighsq; - double *cuttypesq = neighbor->cuttypesq; + // If using multi/reduce, communicate itype particles a distance equal + // to the max of itype-jtype group interaction given smaller jtype group + int igroup, jgroup; + double **cutmultisq = neighbor->cutmultisq; + int *map_type_multi = neighbor->map_type_multi; for (i = 1; i <= ntypes; i++) { if (cutusermulti) { @@ -242,16 +247,15 @@ void CommBrick::setup() cutghostmulti[i][2] = 0.0; } + igroup = map_type_multi[i]; for (j = 1; j <= ntypes; j++){ - if(cutneighsq[j][j] > cutneighsq[i][i]) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); + jgroup = map_type_multi[j]; + + if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); } - - cutghostmulti[i][0] *= length0; - cutghostmulti[i][1] *= length1; - cutghostmulti[i][2] *= length2; } } else { // If using a single binlist, use the max itype-jtype interaction distance for communication diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index ce76fa7442..64d1207a64 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -177,29 +177,33 @@ void CommTiled::setup() if (mode == Comm::MULTI) { double cut; if (multi_reduce) { - // If using multi/reduce binlists, communicate itype particles a distance - // equal to the max of itype-jtype interaction given smaller jtype particles - double **cutneighsq = neighbor->cutneighsq; - double *cuttypesq = neighbor->cuttypesq; - for (i = 1; i <= ntypes; i++) { + // If using multi/reduce, communicate itype particles a distance equal + // to the max of itype-jtype group interaction given smaller jtype group + int igroup, jgroup; + double **cutmultisq = neighbor->cutmultisq; + int *map_type_multi = neighbor->map_type_multi; + for (i = 1; i <= ntypes; i++) { - if (cutusermulti) { - cutghostmulti[i][0] = cutusermulti[i]; - cutghostmulti[i][1] = cutusermulti[i]; - cutghostmulti[i][2] = cutusermulti[i]; - } else { - cutghostmulti[i][0] = 0.0; - cutghostmulti[i][1] = 0.0; - cutghostmulti[i][2] = 0.0; - } - - for (j = 1; j <= ntypes; j++){ - if(cutneighsq[j][j] > cutneighsq[i][i]) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutneighsq[i][j])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutneighsq[i][j])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutneighsq[i][j])); - } + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; } + + igroup = map_type_multi[i]; + for (j = 1; j <= ntypes; j++){ + jgroup = map_type_multi[j]; + + if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); + } + } } else { // If using a single binlist, use the max itype-jtype interaction distance for communication double *cuttype = neighbor->cuttype; diff --git a/src/neighbor.cpp b/src/neighbor.cpp index d130219931..b08de6cb02 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -188,6 +188,12 @@ pairclass(nullptr), pairnames(nullptr), pairmasks(nullptr) nex_mol = maxex_mol = 0; ex_mol_group = ex_mol_bit = ex_mol_intra = nullptr; + // Multi data + + map_type_multi = nullptr; + cutmultisq = nullptr; + multi_groups = 0; + // Kokkos setting copymode = 0; @@ -253,6 +259,9 @@ Neighbor::~Neighbor() memory->destroy(ex_mol_group); delete [] ex_mol_bit; memory->destroy(ex_mol_intra); + + memory->destroy(map_type_multi); + memory->destroy(cutmultisq); } /* ---------------------------------------------------------------------- */ @@ -336,6 +345,35 @@ void Neighbor::init() } cutneighmaxsq = cutneighmax * cutneighmax; + // multi cutoffs + if(style == Neighbor::MULTI){ + int igroup, jgroup; + // If not defined, create default mapping + if(not map_type_multi) { + memory->create(map_type_multi,n+1,"neigh:map_type_multi"); + n_multi_groups = n; + for(i = 1; i <= n; i++) + map_type_multi[i] = i-1; + } + + // Define maximum interaction distance for each pair of groups + memory->grow(cutmultisq, n_multi_groups, n_multi_groups, "neigh:cutmultisq"); + for(i = 0; i < n_multi_groups; i++) + for(j = 0; j < n_multi_groups; j++) + cutmultisq[i][j] = 0.0; + + for(i = 1; i <= n; i++){ + igroup = map_type_multi[i]; + for(j = 1; j <= n; j++){ + jgroup = map_type_multi[j]; + if(cutneighsq[i][j] > cutmultisq[igroup][jgroup]) { + cutmultisq[igroup][jgroup] = cutneighsq[i][j]; + cutmultisq[jgroup][igroup] = cutneighsq[i][j]; + } + } + } + } + // rRESPA cutoffs int respa = 0; @@ -1934,6 +1972,7 @@ NPair *Neighbor::pair_creator(LAMMPS *lmp) /* ---------------------------------------------------------------------- setup neighbor binning and neighbor stencils called before run and every reneighbor if box size/shape changes + initialize default settings for multi before run only operates on perpetual lists build_one() operates on occasional lists ------------------------------------------------------------------------- */ @@ -2379,9 +2418,55 @@ void Neighbor::modify_params(int narg, char **arg) } else if (strcmp(arg[iarg+1],"none") == 0) { nex_type = nex_group = nex_mol = 0; iarg += 2; - + } else error->all(FLERR,"Illegal neigh_modify command"); + } else if (strcmp(arg[iarg],"multi/custom") == 0) { + if(style != Neighbor::MULTI) + error->all(FLERR,"Cannot use multi/custom command without multi setting"); + + if(iarg+2 > narg) + error->all(FLERR,"Invalid multi/custom command"); + int nextra = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if(iarg+1+nextra > narg) + error->all(FLERR,"Invalid multi/custom command"); + int ntypes = atom->ntypes; + int n, nlo, nhi, i, j, igroup, jgroup; + + if(not map_type_multi) + memory->create(map_type_multi,ntypes+1,"neigh:map_type_multi"); + + // Erase previous mapping + for(i = 1; i <= ntypes; i++) + map_type_multi[i] = -1; + + // For each custom range, define mapping for types in interval + n_multi_groups = 0; + char *id; + for(i = 0; i < nextra; i++){ + n = strlen(arg[iarg+2+i]) + 1; + id = new char[n]; + strcpy(id,arg[iarg+2+i]); + utils::bounds(FLERR,id,1,ntypes,nlo,nhi,error); + delete [] id; + + for (j = nlo; j <= nhi; j++) { + if(map_type_multi[j] != -1) + error->all(FLERR,"Type specified more than once in multi/custom commnd"); + map_type_multi[j] = n_multi_groups; + } + n_multi_groups += 1; + } + + // Create seprate group for each undefined atom type + for(i = 1; i <= ntypes; i++){ + if(map_type_multi[i] == -1){ + map_type_multi[i] = n_multi_groups; + n_multi_groups += 1; + } + } + + iarg += 2 + nextra; } else error->all(FLERR,"Illegal neigh_modify command"); } } diff --git a/src/neighbor.h b/src/neighbor.h index d1a5cf9112..ad3de851cf 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -21,7 +21,7 @@ namespace LAMMPS_NS { class Neighbor : protected Pointers { public: enum{NSQ,BIN,MULTI_OLD,MULTI}; - int style; // 0,1,2 = nsq, bin, multi/old, multi + int style; // 0,1,2,3 = nsq, bin, multi/old, multi int every; // build every this many steps int delay; // delay build for this many steps int dist_check; // 0 = always build, 1 = only if 1/2 dist @@ -102,6 +102,13 @@ class Neighbor : protected Pointers { int nimproperlist; // list of impropers to compute int **improperlist; + // optional type grouping for multi + + int multi_groups; // 1 if custom groupings are defined for multi + int n_multi_groups; // # of custom groupings + int *map_type_multi; // ntype array mapping types to custom groupings + double **cutmultisq; // cutoffs for each combination of custom groupings + // public methods Neighbor(class LAMMPS *); From 2458eaf4f9bb4e58a5a277f02475b7b1f04ca7c6 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 26 Dec 2020 11:03:29 -0700 Subject: [PATCH 0065/1217] Adding custom grouping option --- src/USER-OMP/npair_full_multi_omp.cpp | 28 ++-- src/USER-OMP/npair_half_multi_newtoff_omp.cpp | 28 ++-- src/USER-OMP/npair_half_multi_newton_omp.cpp | 54 ++++---- .../npair_half_multi_newton_tri_omp.cpp | 30 +++-- .../npair_half_size_multi_newtoff_omp.cpp | 28 ++-- .../npair_half_size_multi_newton_omp.cpp | 48 ++++--- .../npair_half_size_multi_newton_tri_omp.cpp | 30 +++-- src/comm_brick.cpp | 6 +- src/nbin.cpp | 45 ++++--- src/nbin.h | 12 +- src/nbin_multi.cpp | 98 +++++++------- src/nbin_multi.h | 2 +- src/neighbor.cpp | 2 +- src/npair.cpp | 40 +++--- src/npair.h | 5 +- src/npair_full_multi.cpp | 33 ++--- src/npair_half_multi_newtoff.cpp | 31 ++--- src/npair_half_multi_newton.cpp | 57 ++++---- src/npair_half_multi_newton_tri.cpp | 35 ++--- src/npair_half_size_multi_newtoff.cpp | 31 ++--- src/npair_half_size_multi_newton.cpp | 59 ++++---- src/npair_half_size_multi_newton_tri.cpp | 31 ++--- src/nstencil.cpp | 126 +++++++++--------- src/nstencil.h | 7 +- src/nstencil_full_multi_2d.cpp | 36 ++--- src/nstencil_full_multi_3d.cpp | 40 +++--- src/nstencil_half_multi_2d.cpp | 50 +++---- src/nstencil_half_multi_2d_tri.cpp | 50 +++---- src/nstencil_half_multi_3d.cpp | 54 ++++---- src/nstencil_half_multi_3d_tri.cpp | 54 ++++---- 30 files changed, 599 insertions(+), 551 deletions(-) diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp index cf897f9dea..11b8bae196 100755 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -30,7 +30,7 @@ NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ @@ -46,7 +46,7 @@ void NPairFullMultiOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -80,6 +80,7 @@ void NPairFullMultiOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -89,27 +90,28 @@ void NPairFullMultiOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in surrounding bins in stencil including self // skip i = j - // use full stencil for all type combinations + // use full stencil for all group combinations - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if (i == j) continue; + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp index bf7644f01f..e3e03ee8ed 100755 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -30,7 +30,7 @@ NPairHalfMultiNewtoffOmp::NPairHalfMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks own bin and other bins in stencil pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) @@ -48,7 +48,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -82,6 +82,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -91,29 +92,30 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in other bins in stencil including self // only store pair if i < j // stores own/own pairs only once // stores own/ghost pairs on both procs - // use full stencil for all type combinations + // use full stencil for all group combinations - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jgroup][j]) { if (j <= i) continue; + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index c68a3a150f..28db1b3c0d 100755 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -30,7 +30,7 @@ NPairHalfMultiNewtonOmp::NPairHalfMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -47,7 +47,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -81,6 +81,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -90,28 +91,28 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ // if same size: use half stencil - if(itype == jtype){ + if(igroup == jgroup){ - // if same type, implement with: + // if same group, implement with: // loop over rest of atoms in i's bin, ghosts are at end of linked list // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - js = bins_multi[itype][i]; + js = bins_multi[igroup][i]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -120,6 +121,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) } } + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -145,14 +147,14 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) } } else { - // if different types, implement with: - // loop over all atoms in jtype bin + // if different groups, implement with: + // loop over all atoms in jgroup bin // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi[jtype][jbin]; + js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if(j < i) continue; if (j >= nlocal) { @@ -163,8 +165,9 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) } } + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; @@ -189,20 +192,21 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) } } - // for all types, loop over all atoms in other bins in stencil, store every pair + // for all groups, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index 3f3ac37b6d..0289967d30 100755 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -31,7 +31,7 @@ NPairHalfMultiNewtonTriOmp::NPairHalfMultiNewtonTriOmp(LAMMPS *lmp) : /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -48,7 +48,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,ibin,jbin,igroup,jgroup,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -82,6 +82,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -91,14 +92,14 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in bins in stencil // stencil is empty if i larger than j @@ -109,15 +110,15 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { - // if same size (e.g. same type), use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + // if same size (same group), use half stencil + if(cutmultisq[igroup][igroup] == cutmutlisq[jgroup][jgroup]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -128,6 +129,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) } } + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp index 8201ba8cb6..35cfaad5e6 100755 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp @@ -29,7 +29,7 @@ NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) : NPair( /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks own bin and other bins in stencil pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) @@ -47,7 +47,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,ns; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -75,34 +75,36 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in other bins in stencil including self // only store pair if i < j // stores own/own pairs only once // stores own/ghost pairs on both procs - // use full stencil for all type combinations + // use full stencil for all group combinations - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jgroup][j]) { if (j <= i) continue; + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp index 197b41c12e..974b8c5809 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -29,7 +29,7 @@ NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) : NPair(lm /* ---------------------------------------------------------------------- size particles binned neighbor list construction with full Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -46,7 +46,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,ns; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -74,33 +74,34 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_group; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ // if same size: use half stencil - if(itype == jtype){ + if(igroup == jgroup){ - // if same type, implement with: + // if same group, implement with: // loop over rest of atoms in i's bin, ghosts are at end of linked list // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - js = bins_multi[itype][i]; + js = bins_multi[igroup][i]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -109,6 +110,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) } } + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -127,14 +129,14 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) } } else { - // if different types, implement with: - // loop over all atoms in jtype bin + // if different groups, implement with: + // loop over all atoms in jgroup bin // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi[jtype][jbin]; + js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if(j < i) continue; if (j >= nlocal) { @@ -145,6 +147,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) } } + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; @@ -164,18 +167,19 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) } } - // for all types, loop over all atoms in other bins in stencil, store every pair + // for all groups, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp index cd123202b1..d1c5a97498 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp @@ -30,7 +30,7 @@ NPairHalfSizeMultiNewtonTriOmp::NPairHalfSizeMultiNewtonTriOmp(LAMMPS *lmp) : /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -47,7 +47,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,ns; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -75,19 +75,20 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in bins in stencil @@ -99,15 +100,15 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { - // if same size (e.g. same type), use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + // if same size (same group), use half stencil + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -118,6 +119,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) } } + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 528456ab7c..74865476f5 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -252,9 +252,9 @@ void CommBrick::setup() jgroup = map_type_multi[j]; if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][0] = length0 * MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][1] = length1 * MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][2] = length2 * MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); } } } else { diff --git a/src/nbin.cpp b/src/nbin.cpp index 084d3bfc4a..cb10014b36 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -43,8 +43,11 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp) bins_multi = nullptr; atom2bin_multi = nullptr; maxbins_multi = nullptr; + + map_type_multi = nullptr; + cutmultisq = nullptr; - maxtypes = 0; + maxgroups = 0; neighbor->last_setup_bins = -1; @@ -84,7 +87,7 @@ NBin::~NBin() memory->destroy(bininvy_multi); memory->destroy(bininvz_multi); - for (int n = 1; n <= maxtypes; n++) { + for (int n = 0; n < maxgroups; n++) { memory->destroy(binhead_multi[n]); memory->destroy(bins_multi[n]); memory->destroy(atom2bin_multi[n]); @@ -117,6 +120,10 @@ void NBin::copy_neighbor_info() binsize_user = neighbor->binsize_user; bboxlo = neighbor->bboxlo; bboxhi = neighbor->bboxhi; + + n_multi_groups = neighbor->n_multi_groups; + map_type_multi = neighbor->map_type_multi; + cutmultisq = neighbor->cutmultisq; // overwrite Neighbor cutoff with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -174,10 +181,10 @@ int NBin::coord2bin(double *x) /* ---------------------------------------------------------------------- - convert atom coords into local bin # for a particular type + convert atom coords into local bin # for a particular grouping ------------------------------------------------------------------------- */ -int NBin::coord2bin_multi(double *x, int it) +int NBin::coord2bin_multi(double *x, int ig) { int ix,iy,iz; int ibin; @@ -186,33 +193,33 @@ int NBin::coord2bin_multi(double *x, int it) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[it]) + nbinx_multi[it]; + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ig]) + nbinx_multi[ig]; else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]); - ix = MIN(ix,nbinx_multi[it]-1); + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]); + ix = MIN(ix,nbinx_multi[ig]-1); } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]) - 1; + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]) - 1; if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[it]) + nbiny_multi[it]; + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[ig]) + nbiny_multi[ig]; else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]); - iy = MIN(iy,nbiny_multi[it]-1); + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]); + iy = MIN(iy,nbiny_multi[ig]-1); } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]) - 1; + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]) - 1; if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[it]) + nbinz_multi[it]; + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[ig]) + nbinz_multi[ig]; else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]); - iz = MIN(iz,nbinz_multi[it]-1); + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]); + iz = MIN(iz,nbinz_multi[ig]-1); } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]) - 1; + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]) - 1; - ibin = (iz-mbinzlo_multi[it])*mbiny_multi[it]*mbinx_multi[it] - + (iy-mbinylo_multi[it])*mbinx_multi[it] - + (ix-mbinxlo_multi[it]); + ibin = (iz-mbinzlo_multi[ig])*mbiny_multi[ig]*mbinx_multi[ig] + + (iy-mbinylo_multi[ig])*mbinx_multi[ig] + + (ix-mbinxlo_multi[ig]); return ibin; } diff --git a/src/nbin.h b/src/nbin.h index 8f95ad987e..19035d619e 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -75,6 +75,9 @@ class NBin : protected Pointers { int binsizeflag; double binsize_user; double *bboxlo,*bboxhi; + int n_multi_groups; + int *map_type_multi; + double **cutmultisq; // data common to all NBin variants @@ -84,15 +87,12 @@ class NBin : protected Pointers { // data for standard NBin int maxatom; // size of bins array - - // data for standard NBin - int maxbin; // size of binhead array - // data for multi/multi NBin + // data for multi NBin - int maxtypes; // size of multi arrays - int * maxbins_multi; // size of 2nd dimension of binhead_multi array + int maxgroups; // size of multi arrays + int * maxbins_multi; // size of 2nd dimension of binhead_multi array // methods diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index 302fe30d88..b39489c3fe 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -38,7 +38,7 @@ void NBinMulti::bin_atoms_setup(int nall) { // binhead_multi[n] = per-bin vector mbins in length mbins_multi[n] - for (int n = 1; n <= maxtypes; n++) { + for (int n = 0; n < maxgroups; n++) { if (mbins_multi[n] > maxbins_multi[n]) { maxbins_multi[n] = mbins_multi[n]; memory->destroy(binhead_multi[n]); @@ -48,10 +48,12 @@ void NBinMulti::bin_atoms_setup(int nall) // bins_multi[n] and atom2bin_multi[n] = per-atom vectors // for both local and ghost atoms + + // TODO: maxatom should be maxatom per group if (nall > maxatom) { maxatom = nall; - for (int n = 1; n <= maxtypes; n++) { + for (int n = 0; n < maxgroups; n++) { memory->destroy(bins_multi[n]); memory->destroy(atom2bin_multi[n]); memory->create(bins_multi[n], maxatom, "neigh:bin_multi"); @@ -61,23 +63,16 @@ void NBinMulti::bin_atoms_setup(int nall) } /* --------------------------------------------------------------------- - Identify index of type with smallest cutoff + Identify index of group with smallest cutoff ------------------------------------------------------------------------ */ -int NBinMulti::itype_min() { +int NBinMulti::igroup_min() +{ + int imin = 0; + for (int n = 0; n < maxgroups; n++) + if (cutmultisq[n][n] < cutmultisq[imin][imin]) imin = n; - int itypemin = 1; - double ** cutneighsq; - - cutneighsq = neighbor->cutneighsq; - - for (int n = 1; n <= atom->ntypes; n++) { - if (cutneighsq[n][n] < cutneighsq[itypemin][itypemin]) { - itypemin = n; - } - } - - return itypemin; + return imin; } /* ---------------------------------------------------------------------- @@ -87,15 +82,15 @@ int NBinMulti::itype_min() { void NBinMulti::setup_bins(int style) { int n; - int itypemin; + int igroupmin; // Initialize arrays - if (atom->ntypes > maxtypes) { + if (n_multi_groups > maxgroups) { // Clear any/all memory for existing types - for (n = 1; n <= maxtypes; n++) { + for (n = 0; n < maxgroups; n++) { memory->destroy(atom2bin_multi[n]); memory->destroy(binhead_multi[n]); memory->destroy(bins_multi[n]); @@ -106,59 +101,60 @@ void NBinMulti::setup_bins(int style) // Realloacte at updated maxtypes - maxtypes = atom->ntypes; + maxgroups = n_multi_groups; - atom2bin_multi = new int*[maxtypes+1](); - binhead_multi = new int*[maxtypes+1](); - bins_multi = new int*[maxtypes+1](); + atom2bin_multi = new int*[maxgroups](); + binhead_multi = new int*[maxgroups](); + bins_multi = new int*[maxgroups](); memory->destroy(nbinx_multi); memory->destroy(nbiny_multi); memory->destroy(nbinz_multi); - memory->create(nbinx_multi, maxtypes+1, "neigh:nbinx_multi"); - memory->create(nbiny_multi, maxtypes+1, "neigh:nbiny_multi"); - memory->create(nbinz_multi, maxtypes+1, "neigh:nbinz_multi"); + memory->create(nbinx_multi, maxgroups, "neigh:nbinx_multi"); + memory->create(nbiny_multi, maxgroups, "neigh:nbiny_multi"); + memory->create(nbinz_multi, maxgroups, "neigh:nbinz_multi"); memory->destroy(mbins_multi); memory->destroy(mbinx_multi); memory->destroy(mbiny_multi); memory->destroy(mbinz_multi); - memory->create(mbins_multi, maxtypes+1, "neigh:mbins_multi"); - memory->create(mbinx_multi, maxtypes+1, "neigh:mbinx_multi"); - memory->create(mbiny_multi, maxtypes+1, "neigh:mbiny_multi"); - memory->create(mbinz_multi, maxtypes+1, "neigh:mbinz_multi"); + memory->create(mbins_multi, maxgroups, "neigh:mbins_multi"); + memory->create(mbinx_multi, maxgroups, "neigh:mbinx_multi"); + memory->create(mbiny_multi, maxgroups, "neigh:mbiny_multi"); + memory->create(mbinz_multi, maxgroups, "neigh:mbinz_multi"); memory->destroy(mbinxlo_multi); memory->destroy(mbinylo_multi); memory->destroy(mbinzlo_multi); - memory->create(mbinxlo_multi, maxtypes+1, "neigh:mbinxlo_multi"); - memory->create(mbinylo_multi, maxtypes+1, "neigh:mbinylo_multi"); - memory->create(mbinzlo_multi, maxtypes+1, "neigh:mbinzlo_multi"); + memory->create(mbinxlo_multi, maxgroups, "neigh:mbinxlo_multi"); + memory->create(mbinylo_multi, maxgroups, "neigh:mbinylo_multi"); + memory->create(mbinzlo_multi, maxgroups, "neigh:mbinzlo_multi"); memory->destroy(binsizex_multi); memory->destroy(binsizey_multi); memory->destroy(binsizez_multi); - memory->create(binsizex_multi, maxtypes+1, "neigh:binsizex_multi"); - memory->create(binsizey_multi, maxtypes+1, "neigh:binsizey_multi"); - memory->create(binsizez_multi, maxtypes+1, "neigh:binsizez_multi"); + memory->create(binsizex_multi, maxgroups, "neigh:binsizex_multi"); + memory->create(binsizey_multi, maxgroups, "neigh:binsizey_multi"); + memory->create(binsizez_multi, maxgroups, "neigh:binsizez_multi"); memory->destroy(bininvx_multi); memory->destroy(bininvy_multi); memory->destroy(bininvz_multi); - memory->create(bininvx_multi, maxtypes+1, "neigh:bininvx_multi"); - memory->create(bininvy_multi, maxtypes+1, "neigh:bininvy_multi"); - memory->create(bininvz_multi, maxtypes+1, "neigh:bininvz_multi"); + memory->create(bininvx_multi, maxgroups, "neigh:bininvx_multi"); + memory->create(bininvy_multi, maxgroups, "neigh:bininvy_multi"); + memory->create(bininvz_multi, maxgroups, "neigh:bininvz_multi"); memory->destroy(maxbins_multi); - memory->create(maxbins_multi, maxtypes+1, "neigh:maxbins_multi"); + memory->create(maxbins_multi, maxgroups, "neigh:maxbins_multi"); + // make sure reallocation occurs in bin_atoms_setup() - for (n = 1; n <= maxtypes; n++) { + for (n = 0; n < maxgroups; n++) { maxbins_multi[n] = 0; } maxatom = 0; } - itypemin = itype_min(); + igroupmin = igroup_min(); // bbox = size of bbox of entire domain // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost @@ -193,16 +189,16 @@ void NBinMulti::setup_bins(int style) bbox[1] = bboxhi[1] - bboxlo[1]; bbox[2] = bboxhi[2] - bboxlo[2]; - // For each type... + // For each grouping... - for (n = 1; n <= atom->ntypes; n++) { + for (n = 0; n < maxgroups; n++) { // binsize_user only relates to smallest type // optimal bin size is roughly 1/2 the type-type cutoff // special case of all cutoffs = 0.0, binsize = box size double binsize_optimal; - if (n == itypemin && binsizeflag) binsize_optimal = binsize_user; - else binsize_optimal = 0.5*sqrt(neighbor->cutneighsq[n][n]); + if (n == igroupmin && binsizeflag) binsize_optimal = binsize_user; + else binsize_optimal = 0.5*sqrt(cutmultisq[n][n]); if (binsize_optimal == 0.0) binsize_optimal = bbox[0]; double binsizeinv = 1.0/binsize_optimal; @@ -306,7 +302,7 @@ void NBinMulti::bin_atoms() int i,ibin,n; last_bin = update->ntimestep; - for (n = 1; n <= maxtypes; n++) { + for (n = 0; n < maxgroups; n++) { for (i = 0; i < mbins_multi[n]; i++) binhead_multi[n][i] = -1; } @@ -323,7 +319,7 @@ void NBinMulti::bin_atoms() int bitmask = group->bitmask[includegroup]; for (i = nall-1; i >= nlocal; i--) { if (mask[i] & bitmask) { - n = type[i]; + n = map_type_multi[type[i]]; ibin = coord2bin_multi(x[i], n); atom2bin_multi[n][i] = ibin; bins_multi[n][i] = binhead_multi[n][ibin]; @@ -331,7 +327,7 @@ void NBinMulti::bin_atoms() } } for (i = atom->nfirst-1; i >= 0; i--) { - n = type[i]; + n = map_type_multi[type[i]]; ibin = coord2bin_multi(x[i], n); atom2bin_multi[n][i] = ibin; bins_multi[n][i] = binhead_multi[n][ibin]; @@ -339,7 +335,7 @@ void NBinMulti::bin_atoms() } } else { for (i = nall-1; i >= 0; i--) { - n = type[i]; + n = map_type_multi[type[i]]; ibin = coord2bin_multi(x[i], n); atom2bin_multi[n][i] = ibin; bins_multi[n][i] = binhead_multi[n][ibin]; @@ -354,7 +350,7 @@ double NBinMulti::memory_usage() { double bytes = 0; - for (int m = 1; m < maxtypes; m++) { + for (int m = 0; m < maxgroups; m++) { bytes += maxbins_multi[m]*sizeof(int); bytes += 2*maxatom*sizeof(int); } diff --git a/src/nbin_multi.h b/src/nbin_multi.h index 856f3fa722..84ec0348bc 100644 --- a/src/nbin_multi.h +++ b/src/nbin_multi.h @@ -38,7 +38,7 @@ class NBinMulti : public NBin { private: - int itype_min(); + int igroup_min(); }; } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index b08de6cb02..94add1f324 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -350,8 +350,8 @@ void Neighbor::init() int igroup, jgroup; // If not defined, create default mapping if(not map_type_multi) { - memory->create(map_type_multi,n+1,"neigh:map_type_multi"); n_multi_groups = n; + memory->create(map_type_multi,n+1,"neigh:map_type_multi"); for(i = 1; i <= n; i++) map_type_multi[i] = i-1; } diff --git a/src/npair.cpp b/src/npair.cpp index 07e476e1dd..b2ecc953ea 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -95,6 +95,12 @@ void NPair::copy_neighbor_info() special_flag = neighbor->special_flag; + // multi info + + n_multi_groups = neighbor->n_multi_groups; + map_type_multi = neighbor->map_type_multi; + cutmultisq = neighbor->cutmultisq; + // overwrite per-type Neighbor cutoffs with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -265,10 +271,10 @@ int NPair::coord2bin(double *x, int &ix, int &iy, int &iz) /* ---------------------------------------------------------------------- - same as coord2bin in NbinMulti2 + multi version of coord2bin for a given grouping ------------------------------------------------------------------------- */ -int NPair::coord2bin(double *x, int it) +int NPair::coord2bin(double *x, int ig) { int ix,iy,iz; int ibin; @@ -277,32 +283,32 @@ int NPair::coord2bin(double *x, int it) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[it]) + nbinx_multi[it]; + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ig]) + nbinx_multi[ig]; else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]); - ix = MIN(ix,nbinx_multi[it]-1); + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]); + ix = MIN(ix,nbinx_multi[ig]-1); } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[it]) - 1; + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]) - 1; if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[it]) + nbiny_multi[it]; + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[ig]) + nbiny_multi[ig]; else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]); - iy = MIN(iy,nbiny_multi[it]-1); + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]); + iy = MIN(iy,nbiny_multi[ig]-1); } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[it]) - 1; + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]) - 1; if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[it]) + nbinz_multi[it]; + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[ig]) + nbinz_multi[ig]; else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]); - iz = MIN(iz,nbinz_multi[it]-1); + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]); + iz = MIN(iz,nbinz_multi[ig]-1); } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[it]) - 1; + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]) - 1; - ibin = (iz-mbinzlo_multi[it])*mbiny_multi[it]*mbinx_multi[it] - + (iy-mbinylo_multi[it])*mbinx_multi[it] - + (ix-mbinxlo_multi[it]); + ibin = (iz-mbinzlo_multi[ig])*mbiny_multi[ig]*mbinx_multi[ig] + + (iy-mbinylo_multi[ig])*mbinx_multi[ig] + + (ix-mbinxlo_multi[ig]); return ibin; } \ No newline at end of file diff --git a/src/npair.h b/src/npair.h index c56c6bdb20..4d99e3a8e6 100644 --- a/src/npair.h +++ b/src/npair.h @@ -48,7 +48,10 @@ class NPair : protected Pointers { double cut_middle_sq; double cut_middle_inside_sq; double *bboxlo,*bboxhi; - + int n_multi_groups; + int *map_type_multi; + double **cutmultisq; + // exclusion data from Neighbor class int nex_type; // # of entries in type exclusion list diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp index 4463964d5f..f29f04107a 100644 --- a/src/npair_full_multi.cpp +++ b/src/npair_full_multi.cpp @@ -28,13 +28,13 @@ NPairFullMulti::NPairFullMulti(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ void NPairFullMulti::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -67,8 +67,8 @@ void NPairFullMulti::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -78,29 +78,30 @@ void NPairFullMulti::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in surrounding bins in stencil including self // skip i = j - // use full stencil for all type combinations + // use full stencil for all group combinations - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if (i == j) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp index c0dcaf0c98..85832b11b1 100755 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -28,7 +28,7 @@ NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks own bin and other bins in stencil pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) @@ -36,7 +36,7 @@ NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} void NPairHalfMultiNewtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -69,8 +69,8 @@ void NPairHalfMultiNewtoff::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -80,30 +80,31 @@ void NPairHalfMultiNewtoff::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in other bins in stencil including self // only store pair if i < j // stores own/own pairs only once // stores own/ghost pairs on both procs - // use full stencil for all type combinations + // use full stencil for all group combinations - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jgroup][j]) { if (j <= i) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index e097052fe5..d18b009460 100755 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -28,14 +28,14 @@ NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfMultiNewton::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -68,8 +68,8 @@ void NPairHalfMultiNewton::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -79,28 +79,28 @@ void NPairHalfMultiNewton::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ // if same size: use half stencil - if(itype == jtype){ + if(igroup == jgroup){ - // if same type, implement with: + // if same group, implement with: // loop over rest of atoms in i's bin, ghosts are at end of linked list // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - js = bins_multi[itype][i]; + js = bins_multi[igroup][i]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -109,7 +109,8 @@ void NPairHalfMultiNewton::build(NeighList *list) } } - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; @@ -134,14 +135,14 @@ void NPairHalfMultiNewton::build(NeighList *list) } } else { - // if different types, implement with: - // loop over all atoms in jtype bin + // if different groups, implement with: + // loop over all atoms in jgroup bin // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi[jtype][jbin]; + js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if(j < i) continue; if (j >= nlocal) { @@ -152,7 +153,8 @@ void NPairHalfMultiNewton::build(NeighList *list) } } - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; @@ -178,20 +180,21 @@ void NPairHalfMultiNewton::build(NeighList *list) } } - // for all types, loop over all atoms in other bins in stencil, store every pair + // for all groups, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { - - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp index fabaf5f202..ebf871ad99 100755 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -28,14 +28,14 @@ NPairHalfMultiNewtonTri::NPairHalfMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfMultiNewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -68,8 +68,8 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -79,14 +79,14 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in bins in stencil // stencil is empty if i larger than j @@ -97,15 +97,15 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { - // if same size (e.g. same type), use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + // if same size (same group), use half stencil + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -116,8 +116,9 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) } } - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp index 65b6b68fb2..ec4fbad9aa 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -28,7 +28,7 @@ NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) { /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks own bin and other bins in stencil pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) @@ -36,7 +36,7 @@ NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) { void NPairHalfSizeMultiNewtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,jbin,ns; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -64,37 +64,38 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in other bins in stencil including self // only store pair if i < j // stores own/own pairs only once // stores own/ghost pairs on both procs - // use full stencil for all type combinations + // use full stencil for all group combinations - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >=0; j = bins_multi[jgroup][j]) { if (j <= i) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index 8fa3b9bc1b..c3a13f4b81 100755 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -27,14 +27,14 @@ NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with full Newton's 3rd law - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfSizeMultiNewton::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,jbin,ns,js; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -61,35 +61,35 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ // if same size: use half stencil - if(itype == jtype){ + if(igroup == jgroup){ - // if same type, implement with: + // if same group, implement with: // loop over rest of atoms in i's bin, ghosts are at end of linked list // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - js = bins_multi[itype][i]; + js = bins_multi[igroup][i]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -98,7 +98,8 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) } } - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; @@ -116,14 +117,14 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) } } else { - // if different types, implement with: - // loop over all atoms in jtype bin + // if different groups, implement with: + // loop over all atoms in jgroup bin // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi[jtype][jbin]; + js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { if(j < i) continue; if (j >= nlocal) { @@ -134,8 +135,9 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) } } - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; @@ -153,20 +155,21 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) } } - // for all types, loop over all atoms in other bins in stencil, store every pair + // for all groups, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 780fa95f0b..7c792c6a19 100755 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -27,14 +27,14 @@ NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lm /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic - multi-type stencil is itype-jtype dependent + multi stencil is igroup-jgroup dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,jbin,ns,js; + int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -61,21 +61,21 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + igroup = map_type_multi[itype]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[itype][i]; + ibin = atom2bin_multi[igroup][i]; - // loop through stencils for all types - for (jtype = 1; jtype <= atom->ntypes; jtype++) { + // loop through stencils for all groups + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { - // if same type use own bin - if(itype == jtype) jbin = ibin; - else jbin = coord2bin(x[i], jtype); + // if same group use own bin + if(igroup == jgroup) jbin = ibin; + else jbin = coord2bin(x[i], jgroup); // loop over all atoms in bins in stencil @@ -87,15 +87,15 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[itype][jtype]; - ns = nstencil_multi[itype][jtype]; + s = stencil_multi[igroup][jgroup]; + ns = nstencil_multi[igroup][jgroup]; for (k = 0; k < ns; k++) { - js = binhead_multi[jtype][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jtype][j]) { + js = binhead_multi[jgroup][jbin + s[k]]; + for (j = js; j >= 0; j = bins_multi[jgroup][j]) { - // if same size (e.g. same type), use half stencil - if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){ + // if same size (same group), use half stencil + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -106,6 +106,7 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) } } + jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; diff --git a/src/nstencil.cpp b/src/nstencil.cpp index f6281a1964..acd7272245 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -52,14 +52,14 @@ using namespace LAMMPS_NS; cutoff is not cutneighmaxsq, but max cutoff for that atom type no versions that allow ghost on (any need for it?) for multi: - create one stencil for each itype-jtype pairing - the full/half stencil label refers to the same-type stencil - a half list with newton on has a half same-type stencil - a full list or half list with newton of has a full same-type stencil - cross type stencils are always full to allow small-to-large lookups + create one stencil for each igroup-jgroup pairing + the full/half stencil label refers to the same-group stencil + a half list with newton on has a half same-group stencil + a full list or half list with newton of has a full same-group stencil + cross group stencils are always full to allow small-to-large lookups for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin for triclinic, a half stencil includes bins in the z (3D) or y (2D) plane of self and above - cutoff is not cutneighmaxsq, but max cutoff for that atom type + cutoff is not cutneighmaxsq, but max cutoff for that atom group no versions that allow ghost on (any need for it?) ------------------------------------------------------------------------- */ @@ -81,7 +81,7 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) flag_half_multi = nullptr; flag_skip_multi = nullptr; - bin_type_multi = nullptr; + bin_group_multi = nullptr; dimension = domain->dimension; } @@ -107,10 +107,10 @@ NStencil::~NStencil() if (stencil_multi) { - int n = atom->ntypes; + int n = n_multi_groups; memory->destroy(nstencil_multi); - for (int i = 1; i <= n; i++) { - for (int j = 0; j <= n; j++) { + for (int i = 0; i < n; i++) { + for (int j = 0; j < n; j++) { if (! flag_skip_multi[i][j]) memory->destroy(stencil_multi[i][j]); } @@ -120,7 +120,7 @@ NStencil::~NStencil() memory->destroy(maxstencil_multi); memory->destroy(flag_half_multi); memory->destroy(flag_skip_multi); - memory->destroy(bin_type_multi); + memory->destroy(bin_group_multi); memory->destroy(stencil_sx_multi); memory->destroy(stencil_sy_multi); @@ -155,6 +155,10 @@ void NStencil::copy_neighbor_info() cutneighmaxsq = neighbor->cutneighmaxsq; cuttypesq = neighbor->cuttypesq; cutneighsq = neighbor->cutneighsq; + + n_multi_groups = neighbor->n_multi_groups; + map_type_multi = neighbor->map_type_multi; + cutmultisq = neighbor->cutmultisq; // overwrite Neighbor cutoff with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -265,44 +269,44 @@ void NStencil::create_setup() } } } else { - int i, j, bin_type, smax; + int i, j, bin_group, smax; double stencil_range; - int n = atom->ntypes; + int n = n_multi_groups; if(nb) copy_bin_info_multi(); // Allocate arrays to store stencil information - memory->create(flag_half_multi, n+1, n+1, + memory->create(flag_half_multi, n, n, "neighstencil:flag_half_multi"); - memory->create(flag_skip_multi, n+1, n+1, + memory->create(flag_skip_multi, n, n, "neighstencil:flag_skip_multi"); - memory->create(bin_type_multi, n+1, n+1, - "neighstencil:bin_type_multi"); + memory->create(bin_group_multi, n, n, + "neighstencil:bin_group_multi"); - memory->create(stencil_sx_multi, n+1, n+1, + memory->create(stencil_sx_multi, n, n, "neighstencil:stencil_sx_multi"); - memory->create(stencil_sy_multi, n+1, n+1, + memory->create(stencil_sy_multi, n, n, "neighstencil:stencil_sy_multi"); - memory->create(stencil_sz_multi, n+1, n+1, + memory->create(stencil_sz_multi, n, n, "neighstencil:stencil_sz_multi"); - memory->create(stencil_binsizex_multi, n+1, n+1, + memory->create(stencil_binsizex_multi, n, n, "neighstencil:stencil_binsizex_multi"); - memory->create(stencil_binsizey_multi, n+1, n+1, + memory->create(stencil_binsizey_multi, n, n, "neighstencil:stencil_binsizey_multi"); - memory->create(stencil_binsizez_multi, n+1, n+1, + memory->create(stencil_binsizez_multi, n, n, "neighstencil:stencil_binsizez_multi"); - memory->create(stencil_mbinx_multi, n+1, n+1, + memory->create(stencil_mbinx_multi, n, n, "neighstencil:stencil_mbinx_multi"); - memory->create(stencil_mbiny_multi, n+1, n+1, + memory->create(stencil_mbiny_multi, n, n, "neighstencil:stencil_mbiny_multi"); - memory->create(stencil_mbinz_multi, n+1, n+1, + memory->create(stencil_mbinz_multi, n, n, "neighstencil:stencil_mbinz_multi"); // Skip all stencils by default, initialize smax - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { flag_skip_multi[i][j] = 1; } } @@ -313,43 +317,43 @@ void NStencil::create_setup() // Allocate arrays to store stencils if (!maxstencil_multi) { - memory->create(maxstencil_multi, n+1, n+1, "neighstencil::stencil_multi"); - memory->create(nstencil_multi, n+1, n+1, "neighstencil::nstencil_multi"); - stencil_multi = new int**[n+1](); - for (i = 1; i <= n; ++i) { - stencil_multi[i] = new int*[n+1](); - for (j = 1; j <= n; ++j) { + memory->create(maxstencil_multi, n, n, "neighstencil::stencil_multi"); + memory->create(nstencil_multi, n, n, "neighstencil::nstencil_multi"); + stencil_multi = new int**[n](); + for (i = 0; i < n; ++i) { + stencil_multi[i] = new int*[n](); + for (j = 0; j < n; ++j) { maxstencil_multi[i][j] = 0; nstencil_multi[i][j] = 0; } } } - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { // Skip creation of unused stencils if (flag_skip_multi[i][j]) continue; // Copy bin info for this pair of atom types - bin_type = bin_type_multi[i][j]; + bin_group = bin_group_multi[i][j]; - stencil_binsizex_multi[i][j] = binsizex_multi[bin_type]; - stencil_binsizey_multi[i][j] = binsizey_multi[bin_type]; - stencil_binsizez_multi[i][j] = binsizez_multi[bin_type]; + stencil_binsizex_multi[i][j] = binsizex_multi[bin_group]; + stencil_binsizey_multi[i][j] = binsizey_multi[bin_group]; + stencil_binsizez_multi[i][j] = binsizez_multi[bin_group]; - stencil_mbinx_multi[i][j] = mbinx_multi[bin_type]; - stencil_mbiny_multi[i][j] = mbiny_multi[bin_type]; - stencil_mbinz_multi[i][j] = mbinz_multi[bin_type]; + stencil_mbinx_multi[i][j] = mbinx_multi[bin_group]; + stencil_mbiny_multi[i][j] = mbiny_multi[bin_group]; + stencil_mbinz_multi[i][j] = mbinz_multi[bin_group]; - stencil_range = sqrt(cutneighsq[i][j]); + stencil_range = sqrt(cutmultisq[i][j]); - sx = static_cast (stencil_range*bininvx_multi[bin_type]); - if (sx*binsizex_multi[bin_type] < stencil_range) sx++; - sy = static_cast (stencil_range*bininvy_multi[bin_type]); - if (sy*binsizey_multi[bin_type] < stencil_range) sy++; - sz = static_cast (stencil_range*bininvz_multi[bin_type]); - if (sz*binsizez_multi[bin_type] < stencil_range) sz++; + sx = static_cast (stencil_range*bininvx_multi[bin_group]); + if (sx*binsizex_multi[bin_group] < stencil_range) sx++; + sy = static_cast (stencil_range*bininvy_multi[bin_group]); + if (sy*binsizey_multi[bin_group] < stencil_range) sy++; + sz = static_cast (stencil_range*bininvz_multi[bin_group]); + if (sz*binsizez_multi[bin_group] < stencil_range) sz++; stencil_sx_multi[i][j] = sx; stencil_sy_multi[i][j] = sy; @@ -393,24 +397,24 @@ double NStencil::bin_distance(int i, int j, int k) /* ---------------------------------------------------------------------- - compute closest distance for a given atom type + compute closest distance for a given atom grouping ------------------------------------------------------------------------- */ -double NStencil::bin_distance_multi(int i, int j, int k, int type) +double NStencil::bin_distance_multi(int i, int j, int k, int group) { double delx,dely,delz; - if (i > 0) delx = (i-1)*binsizex_multi[type]; + if (i > 0) delx = (i-1)*binsizex_multi[group]; else if (i == 0) delx = 0.0; - else delx = (i+1)*binsizex_multi[type]; + else delx = (i+1)*binsizex_multi[group]; - if (j > 0) dely = (j-1)*binsizey_multi[type]; + if (j > 0) dely = (j-1)*binsizey_multi[group]; else if (j == 0) dely = 0.0; - else dely = (j+1)*binsizey_multi[type]; + else dely = (j+1)*binsizey_multi[group]; - if (k > 0) delz = (k-1)*binsizez_multi[type]; + if (k > 0) delz = (k-1)*binsizez_multi[group]; else if (k == 0) delz = 0.0; - else delz = (k+1)*binsizez_multi[type]; + else delz = (k+1)*binsizez_multi[group]; return (delx*delx + dely*dely + delz*delz); } @@ -427,9 +431,9 @@ double NStencil::memory_usage() bytes += atom->ntypes*maxstencil_multi_old * sizeof(int); bytes += atom->ntypes*maxstencil_multi_old * sizeof(double); } else if (neighstyle == Neighbor::MULTI) { - int n = atom->ntypes; - for (int i = 1; i <= n; i++) { - for (int j = 1; j <= n; j++) { + int n = n_multi_groups; + for (int i = 0; i < n; i++) { + for (int j = 0; j < n; j++) { bytes += maxstencil_multi[i][j] * sizeof(int); bytes += maxstencil_multi[i][j] * sizeof(int); bytes += maxstencil_multi[i][j] * sizeof(double); diff --git a/src/nstencil.h b/src/nstencil.h index 9ca8bab55d..b06f340d6f 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -44,7 +44,7 @@ class NStencil : protected Pointers { // Arrays to store options for multi itype-jtype stencils bool **flag_half_multi; // flag creation of a half stencil for itype-jtype bool **flag_skip_multi; // skip creation of itype-jtype stencils (for newton on) - int **bin_type_multi; // what type to use for bin information + int **bin_group_multi; // what group to use for bin information NStencil(class LAMMPS *); virtual ~NStencil(); @@ -66,7 +66,10 @@ class NStencil : protected Pointers { double cutneighmaxsq; double *cuttypesq; double **cutneighsq; - + double **cutmultisq; + int n_multi_groups; + int *map_type_multi; + // data from NBin class int mbinx,mbiny,mbinz; diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp index 61557f2d00..4c96f41a56 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -29,16 +29,16 @@ NStencilFullMulti2d::NStencilFullMulti2d(LAMMPS *lmp) : NStencil(lmp) {} void NStencilFullMulti2d::set_stencil_properties() { - int n = atom->ntypes; + int n = n_multi_groups; int i, j; // Always look up neighbor using full stencil and neighbor's bin - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { flag_half_multi[i][j] = 0; flag_skip_multi[i][j] = 0; - bin_type_multi[i][j] = j; + bin_group_multi[i][j] = j; } } } @@ -49,33 +49,33 @@ void NStencilFullMulti2d::set_stencil_properties() void NStencilFullMulti2d::create() { - int itype, jtype, bin_type, i, j, k, ns; - int n = atom->ntypes; + int igroup, jgroup, bin_group, i, j, k, ns; + int n = n_multi_groups; double cutsq; - for (itype = 1; itype <= n; itype++) { - for (jtype = 1; jtype <= n; jtype++) { - if (flag_skip_multi[itype][jtype]) continue; + for (igroup = 0; igroup < n; igroup++) { + for (jgroup = 0; jgroup < n; jgroup++) { + if (flag_skip_multi[igroup][jgroup]) continue; ns = 0; - sx = stencil_sx_multi[itype][jtype]; - sy = stencil_sy_multi[itype][jtype]; + sx = stencil_sx_multi[igroup][jgroup]; + sy = stencil_sy_multi[igroup][jgroup]; - mbinx = stencil_mbinx_multi[itype][jtype]; - mbiny = stencil_mbiny_multi[itype][jtype]; + mbinx = stencil_mbinx_multi[igroup][jgroup]; + mbiny = stencil_mbiny_multi[igroup][jgroup]; - bin_type = bin_type_multi[itype][jtype]; + bin_group = bin_group_multi[igroup][jgroup]; - cutsq = cutneighsq[itype][jtype]; + cutsq = cutmultisq[igroup][jgroup]; for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; - nstencil_multi[itype][jtype] = ns; + nstencil_multi[igroup][jgroup] = ns; } } } diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp index f4935b70e0..bc76433723 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -29,17 +29,17 @@ NStencilFullMulti3d::NStencilFullMulti3d(LAMMPS *lmp) : NStencil(lmp) {} void NStencilFullMulti3d::set_stencil_properties() { - int n = atom->ntypes; + int n = n_multi_groups; int i, j; // Always look up neighbor using full stencil and neighbor's bin // Stencil cutoff set by i-j cutoff - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { flag_half_multi[i][j] = 0; flag_skip_multi[i][j] = 0; - bin_type_multi[i][j] = j; + bin_group_multi[i][j] = j; } } } @@ -50,37 +50,37 @@ void NStencilFullMulti3d::set_stencil_properties() void NStencilFullMulti3d::create() { - int itype, jtype, bin_type, i, j, k, ns; - int n = atom->ntypes; + int igroup, jgroup, bin_group, i, j, k, ns; + int n = n_multi_groups; double cutsq; - for (itype = 1; itype <= n; itype++) { - for (jtype = 1; jtype <= n; jtype++) { - if (flag_skip_multi[itype][jtype]) continue; + for (igroup = 0; igroup < n; igroup++) { + for (jgroup = 0; jgroup < n; jgroup++) { + if (flag_skip_multi[igroup][jgroup]) continue; ns = 0; - sx = stencil_sx_multi[itype][jtype]; - sy = stencil_sy_multi[itype][jtype]; - sz = stencil_sz_multi[itype][jtype]; + sx = stencil_sx_multi[igroup][jgroup]; + sy = stencil_sy_multi[igroup][jgroup]; + sz = stencil_sz_multi[igroup][jgroup]; - mbinx = stencil_mbinx_multi[itype][jtype]; - mbiny = stencil_mbiny_multi[itype][jtype]; - mbinz = stencil_mbinz_multi[itype][jtype]; + mbinx = stencil_mbinx_multi[igroup][jgroup]; + mbiny = stencil_mbiny_multi[igroup][jgroup]; + mbinz = stencil_mbinz_multi[igroup][jgroup]; - bin_type = bin_type_multi[itype][jtype]; + bin_group = bin_group_multi[igroup][jgroup]; - cutsq = cutneighsq[itype][jtype]; + cutsq = cutmultisq[igroup][jgroup]; for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = k*mbiny*mbinx + j*mbinx + i; - nstencil_multi[itype][jtype] = ns; + nstencil_multi[igroup][jgroup] = ns; } } } diff --git a/src/nstencil_half_multi_2d.cpp b/src/nstencil_half_multi_2d.cpp index b407746602..8be8a1c151 100644 --- a/src/nstencil_half_multi_2d.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti2d::NStencilHalfMulti2d(LAMMPS *lmp) : void NStencilHalfMulti2d::set_stencil_properties() { - int n = atom->ntypes; + int n = n_multi_groups; int i, j; - // Cross types: use full stencil, looking one way through hierarchy + // Cross groups: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { - if(cutneighsq[i][i] > cutneighsq[j][j]) continue; + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + if(cutmultisq[i][i] > cutmultisq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutneighsq[i][i] == cutneighsq[j][j]){ + if(cutmultisq[i][i] == cutmultisq[j][j]){ flag_half_multi[i][j] = 1; - bin_type_multi[i][j] = i; + bin_group_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_type_multi[i][j] = j; + bin_group_multi[i][j] = j; } } } @@ -61,42 +61,42 @@ void NStencilHalfMulti2d::set_stencil_properties() void NStencilHalfMulti2d::create() { - int itype, jtype, bin_type, i, j, ns; - int n = atom->ntypes; + int igroup, jgroup, bin_group, i, j, ns; + int n = n_multi_groups; double cutsq; - for (itype = 1; itype <= n; itype++) { - for (jtype = 1; jtype <= n; jtype++) { - if (flag_skip_multi[itype][jtype]) continue; + for (igroup = 0; igroup < n; igroup++) { + for (jgroup = 0; jgroup < n; jgroup++) { + if (flag_skip_multi[igroup][jgroup]) continue; ns = 0; - sx = stencil_sx_multi[itype][jtype]; - sy = stencil_sy_multi[itype][jtype]; + sx = stencil_sx_multi[igroup][jgroup]; + sy = stencil_sy_multi[igroup][jgroup]; - mbinx = stencil_mbinx_multi[itype][jtype]; - mbiny = stencil_mbiny_multi[itype][jtype]; + mbinx = stencil_mbinx_multi[igroup][jgroup]; + mbiny = stencil_mbiny_multi[igroup][jgroup]; - bin_type = bin_type_multi[itype][jtype]; + bin_group = bin_group_multi[igroup][jgroup]; - cutsq = cutneighsq[itype][jtype]; + cutsq = cutmultisq[igroup][jgroup]; - if (flag_half_multi[itype][jtype]) { + if (flag_half_multi[igroup][jgroup]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) if (j > 0 || (j == 0 && i > 0)) { - if (bin_distance_multi(i,j,0,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; } } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; } - nstencil_multi[itype][jtype] = ns; + nstencil_multi[igroup][jgroup] = ns; } } } diff --git a/src/nstencil_half_multi_2d_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp index cd9f85da60..4a4e74c4a0 100755 --- a/src/nstencil_half_multi_2d_tri.cpp +++ b/src/nstencil_half_multi_2d_tri.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti2dTri::NStencilHalfMulti2dTri(LAMMPS *lmp) : void NStencilHalfMulti2dTri::set_stencil_properties() { - int n = atom->ntypes; + int n = n_multi_groups; int i, j; - // Cross types: use full stencil, looking one way through hierarchy + // Cross groups: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { - if(cutneighsq[i][i] > cutneighsq[j][j]) continue; + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + if(cutmultisq[i][i] > cutmultisq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutneighsq[i][i] == cutneighsq[j][j]){ + if(cutmultisq[i][i] == cutmultisq[j][j]){ flag_half_multi[i][j] = 1; - bin_type_multi[i][j] = i; + bin_group_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_type_multi[i][j] = j; + bin_group_multi[i][j] = j; } } } @@ -61,40 +61,40 @@ void NStencilHalfMulti2dTri::set_stencil_properties() void NStencilHalfMulti2dTri::create() { - int itype, jtype, bin_type, i, j, ns; - int n = atom->ntypes; + int igroup, jgroup, bin_group, i, j, ns; + int n = n_multi_groups; double cutsq; - for (itype = 1; itype <= n; itype++) { - for (jtype = 1; jtype <= n; jtype++) { - if (flag_skip_multi[itype][jtype]) continue; + for (igroup = 0; igroup < n; igroup++) { + for (jgroup = 0; jgroup < n; jgroup++) { + if (flag_skip_multi[igroup][jgroup]) continue; ns = 0; - sx = stencil_sx_multi[itype][jtype]; - sy = stencil_sy_multi[itype][jtype]; + sx = stencil_sx_multi[igroup][jgroup]; + sy = stencil_sy_multi[igroup][jgroup]; - mbinx = stencil_mbinx_multi[itype][jtype]; - mbiny = stencil_mbiny_multi[itype][jtype]; + mbinx = stencil_mbinx_multi[igroup][jgroup]; + mbiny = stencil_mbiny_multi[igroup][jgroup]; - bin_type = bin_type_multi[itype][jtype]; + bin_group = bin_group_multi[igroup][jgroup]; - cutsq = cutneighsq[itype][jtype]; + cutsq = cutmultisq[igroup][jgroup]; - if (flag_half_multi[itype][jtype]) { + if (flag_half_multi[igroup][jgroup]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; } - nstencil_multi[itype][jtype] = ns; + nstencil_multi[igroup][jgroup] = ns; } } } diff --git a/src/nstencil_half_multi_3d.cpp b/src/nstencil_half_multi_3d.cpp index d66cfe98b9..ad4970603c 100644 --- a/src/nstencil_half_multi_3d.cpp +++ b/src/nstencil_half_multi_3d.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti3d::NStencilHalfMulti3d(LAMMPS *lmp) : void NStencilHalfMulti3d::set_stencil_properties() { - int n = atom->ntypes; + int n = n_multi_groups; int i, j; - // Cross types: use full stencil, looking one way through hierarchy + // Cross groups: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { - if(cutneighsq[i][i] > cutneighsq[j][j]) continue; + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + if(cutmultisq[i][i] > cutmultisq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutneighsq[i][i] == cutneighsq[j][j]){ + if(cutmultisq[i][i] == cutmultisq[j][j]){ flag_half_multi[i][j] = 1; - bin_type_multi[i][j] = i; + bin_group_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_type_multi[i][j] = j; + bin_group_multi[i][j] = j; } } } @@ -61,48 +61,48 @@ void NStencilHalfMulti3d::set_stencil_properties() void NStencilHalfMulti3d::create() { - int itype, jtype, bin_type, i, j, k, ns; - int n = atom->ntypes; + int igroup, jgroup, bin_group, i, j, k, ns; + int n = n_multi_groups; double cutsq; - for (itype = 1; itype <= n; itype++) { - for (jtype = 1; jtype <= n; jtype++) { - if (flag_skip_multi[itype][jtype]) continue; + for (igroup = 0; igroup < n; igroup++) { + for (jgroup = 0; jgroup < n; jgroup++) { + if (flag_skip_multi[igroup][jgroup]) continue; ns = 0; - sx = stencil_sx_multi[itype][jtype]; - sy = stencil_sy_multi[itype][jtype]; - sz = stencil_sz_multi[itype][jtype]; + sx = stencil_sx_multi[igroup][jgroup]; + sy = stencil_sy_multi[igroup][jgroup]; + sz = stencil_sz_multi[igroup][jgroup]; - mbinx = stencil_mbinx_multi[itype][jtype]; - mbiny = stencil_mbiny_multi[itype][jtype]; - mbinz = stencil_mbinz_multi[itype][jtype]; + mbinx = stencil_mbinx_multi[igroup][jgroup]; + mbiny = stencil_mbiny_multi[igroup][jgroup]; + mbinz = stencil_mbinz_multi[igroup][jgroup]; - bin_type = bin_type_multi[itype][jtype]; + bin_group = bin_group_multi[igroup][jgroup]; - cutsq = cutneighsq[itype][jtype]; + cutsq = cutmultisq[igroup][jgroup]; - if (flag_half_multi[itype][jtype]) { + if (flag_half_multi[igroup][jgroup]) { for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (k > 0 || j > 0 || (j == 0 && i > 0)) { - if (bin_distance_multi(i,j,k,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = k*mbiny*mbinx + j*mbinx + i; } } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = k*mbiny*mbinx + j*mbinx + i; } - nstencil_multi[itype][jtype] = ns; + nstencil_multi[igroup][jgroup] = ns; } } } diff --git a/src/nstencil_half_multi_3d_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp index e4a5747ca6..779f0865a5 100755 --- a/src/nstencil_half_multi_3d_tri.cpp +++ b/src/nstencil_half_multi_3d_tri.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti3dTri::NStencilHalfMulti3dTri(LAMMPS *lmp) : void NStencilHalfMulti3dTri::set_stencil_properties() { - int n = atom->ntypes; + int n = n_multi_groups; int i, j; - // Cross types: use full stencil, looking one way through hierarchy + // Cross groups: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil - for (i = 1; i <= n; i++) { - for (j = 1; j <= n; j++) { - if(cutneighsq[i][i] > cutneighsq[j][j]) continue; + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + if(cutmultisq[i][i] > cutmultisq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutneighsq[i][i] == cutneighsq[j][j]){ + if(cutmultisq[i][i] == cutmultisq[j][j]){ flag_half_multi[i][j] = 1; - bin_type_multi[i][j] = i; + bin_group_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_type_multi[i][j] = j; + bin_group_multi[i][j] = j; } } } @@ -61,46 +61,46 @@ void NStencilHalfMulti3dTri::set_stencil_properties() void NStencilHalfMulti3dTri::create() { - int itype, jtype, bin_type, i, j, k, ns; - int n = atom->ntypes; + int igroup, jgroup, bin_group, i, j, k, ns; + int n = n_multi_groups; double cutsq; - for (itype = 1; itype <= n; itype++) { - for (jtype = 1; jtype <= n; jtype++) { - if (flag_skip_multi[itype][jtype]) continue; + for (igroup = 0; igroup < n; igroup++) { + for (jgroup = 0; jgroup < n; jgroup++) { + if (flag_skip_multi[igroup][jgroup]) continue; ns = 0; - sx = stencil_sx_multi[itype][jtype]; - sy = stencil_sy_multi[itype][jtype]; - sz = stencil_sz_multi[itype][jtype]; + sx = stencil_sx_multi[igroup][jgroup]; + sy = stencil_sy_multi[igroup][jgroup]; + sz = stencil_sz_multi[igroup][jgroup]; - mbinx = stencil_mbinx_multi[itype][jtype]; - mbiny = stencil_mbiny_multi[itype][jtype]; - mbinz = stencil_mbinz_multi[itype][jtype]; + mbinx = stencil_mbinx_multi[igroup][jgroup]; + mbiny = stencil_mbiny_multi[igroup][jgroup]; + mbinz = stencil_mbinz_multi[igroup][jgroup]; - bin_type = bin_type_multi[itype][jtype]; + bin_group = bin_group_multi[igroup][jgroup]; - cutsq = cutneighsq[itype][jtype]; + cutsq = cutmultisq[igroup][jgroup]; - if (flag_half_multi[itype][jtype]) { + if (flag_half_multi[igroup][jgroup]) { for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = k*mbiny*mbinx + j*mbinx + i; } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_type) < cutsq) - stencil_multi[itype][jtype][ns++] = + if (bin_distance_multi(i,j,k,bin_group) < cutsq) + stencil_multi[igroup][jgroup][ns++] = k*mbiny*mbinx + j*mbinx + i; } - nstencil_multi[itype][jtype] = ns; + nstencil_multi[igroup][jgroup] = ns; } } } From a88fab75587bfbe6e86fd65a20fe5f081c89538c Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 26 Dec 2020 11:07:48 -0700 Subject: [PATCH 0066/1217] Missed typos in user-omp --- src/USER-OMP/npair_half_multi_newton_tri_omp.cpp | 2 +- src/USER-OMP/npair_half_size_multi_newton_omp.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index 0289967d30..2e4cf0ec19 100755 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -118,7 +118,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) for (j = js; j >= 0; j = bins_multi[jgroup][j]) { // if same size (same group), use half stencil - if(cutmultisq[igroup][igroup] == cutmutlisq[jgroup][jgroup]){ + if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp index 974b8c5809..87b4fa1601 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -83,7 +83,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) ibin = atom2bin_multi[igroup][i]; // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_group; jgroup++) { + for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { // if same group use own bin if(igroup == jgroup) jbin = ibin; From 50be21902ef87bd6a789144f509ac919812861f0 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 26 Dec 2020 16:00:33 -0700 Subject: [PATCH 0067/1217] Reducing memory consumption for multi --- src/USER-OMP/npair_full_multi_omp.cpp | 4 +- src/USER-OMP/npair_half_multi_newtoff_omp.cpp | 4 +- src/USER-OMP/npair_half_multi_newton_omp.cpp | 10 ++--- .../npair_half_multi_newton_tri_omp.cpp | 4 +- .../npair_half_size_multi_newtoff_omp.cpp | 4 +- .../npair_half_size_multi_newton_omp.cpp | 10 ++--- .../npair_half_size_multi_newton_tri_omp.cpp | 4 +- src/nbin.cpp | 8 +--- src/nbin.h | 2 - src/nbin_multi.cpp | 37 +++++++------------ src/npair.cpp | 2 - src/npair.h | 3 +- src/npair_full_multi.cpp | 4 +- src/npair_half_multi_newtoff.cpp | 4 +- src/npair_half_multi_newton.cpp | 10 ++--- src/npair_half_multi_newton_tri.cpp | 4 +- src/npair_half_size_multi_newtoff.cpp | 4 +- src/npair_half_size_multi_newton.cpp | 10 ++--- src/npair_half_size_multi_newton_tri.cpp | 4 +- 19 files changed, 56 insertions(+), 76 deletions(-) diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp index 11b8bae196..4b38e660d4 100755 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -90,7 +90,7 @@ void NPairFullMultiOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -108,7 +108,7 @@ void NPairFullMultiOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if (i == j) continue; jtype = type[j]; diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp index e3e03ee8ed..93d150f445 100755 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -92,7 +92,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -112,7 +112,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jgroup][j]) { + for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index 28db1b3c0d..a7a3e6d6f7 100755 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -91,7 +91,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -110,9 +110,9 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - js = bins_multi[igroup][i]; + js = bins[i]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -154,7 +154,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if(j < i) continue; if (j >= nlocal) { @@ -202,7 +202,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index 2e4cf0ec19..b5882580a8 100755 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -92,7 +92,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -115,7 +115,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { // if same size (same group), use half stencil if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp index 35cfaad5e6..0d588b2f24 100755 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp @@ -81,7 +81,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -101,7 +101,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jgroup][j]) { + for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp index 87b4fa1601..0137873600 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -80,7 +80,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -99,9 +99,9 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - js = bins_multi[igroup][i]; + js = bins[i]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -136,7 +136,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if(j < i) continue; if (j >= nlocal) { @@ -177,7 +177,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp index d1c5a97498..396e870846 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp @@ -81,7 +81,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -105,7 +105,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { // if same size (same group), use half stencil if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ diff --git a/src/nbin.cpp b/src/nbin.cpp index cb10014b36..c28c22882c 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -40,8 +40,6 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp) binsizex_multi = nullptr; binsizey_multi = nullptr; binsizez_multi = nullptr; bininvx_multi = nullptr; bininvy_multi = nullptr; bininvz_multi = nullptr; binhead_multi = nullptr; - bins_multi = nullptr; - atom2bin_multi = nullptr; maxbins_multi = nullptr; map_type_multi = nullptr; @@ -67,7 +65,7 @@ NBin::~NBin() memory->destroy(bins); memory->destroy(atom2bin); - if (!bins_multi) return; + if (!binhead_multi) return; memory->destroy(nbinx_multi); memory->destroy(nbiny_multi); @@ -89,12 +87,8 @@ NBin::~NBin() for (int n = 0; n < maxgroups; n++) { memory->destroy(binhead_multi[n]); - memory->destroy(bins_multi[n]); - memory->destroy(atom2bin_multi[n]); } delete [] binhead_multi; - delete [] bins_multi; - delete [] atom2bin_multi; memory->destroy(maxbins_multi); } diff --git a/src/nbin.h b/src/nbin.h index 19035d619e..e31e5bab99 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -48,8 +48,6 @@ class NBin : protected Pointers { double *bininvx_multi, *bininvy_multi, *bininvz_multi; int **binhead_multi; - int **bins_multi; - int **atom2bin_multi; NBin(class LAMMPS *); ~NBin(); diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index b39489c3fe..b8832bdfea 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -46,19 +46,16 @@ void NBinMulti::bin_atoms_setup(int nall) } } - // bins_multi[n] and atom2bin_multi[n] = per-atom vectors + // bins and atom2bin = per-atom vectors // for both local and ghost atoms - - // TODO: maxatom should be maxatom per group + // for multi, bins and atom2bin correspond to different binlists if (nall > maxatom) { maxatom = nall; - for (int n = 0; n < maxgroups; n++) { - memory->destroy(bins_multi[n]); - memory->destroy(atom2bin_multi[n]); - memory->create(bins_multi[n], maxatom, "neigh:bin_multi"); - memory->create(atom2bin_multi[n], maxatom, "neigh:atom2bin_multi"); - } + memory->destroy(bins); + memory->create(bins,maxatom,"neigh:bins"); + memory->destroy(atom2bin); + memory->create(atom2bin,maxatom,"neigh:atom2bin"); } } @@ -90,22 +87,16 @@ void NBinMulti::setup_bins(int style) // Clear any/all memory for existing types - for (n = 0; n < maxgroups; n++) { - memory->destroy(atom2bin_multi[n]); + for (n = 0; n < maxgroups; n++) memory->destroy(binhead_multi[n]); - memory->destroy(bins_multi[n]); - } - delete [] atom2bin_multi; + delete [] binhead_multi; - delete [] bins_multi; // Realloacte at updated maxtypes maxgroups = n_multi_groups; - atom2bin_multi = new int*[maxgroups](); binhead_multi = new int*[maxgroups](); - bins_multi = new int*[maxgroups](); memory->destroy(nbinx_multi); memory->destroy(nbiny_multi); @@ -321,24 +312,24 @@ void NBinMulti::bin_atoms() if (mask[i] & bitmask) { n = map_type_multi[type[i]]; ibin = coord2bin_multi(x[i], n); - atom2bin_multi[n][i] = ibin; - bins_multi[n][i] = binhead_multi[n][ibin]; + atom2bin[i] = ibin; + bins[i] = binhead_multi[n][ibin]; binhead_multi[n][ibin] = i; } } for (i = atom->nfirst-1; i >= 0; i--) { n = map_type_multi[type[i]]; ibin = coord2bin_multi(x[i], n); - atom2bin_multi[n][i] = ibin; - bins_multi[n][i] = binhead_multi[n][ibin]; + atom2bin[i] = ibin; + bins[i] = binhead_multi[n][ibin]; binhead_multi[n][ibin] = i; } } else { for (i = nall-1; i >= 0; i--) { n = map_type_multi[type[i]]; ibin = coord2bin_multi(x[i], n); - atom2bin_multi[n][i] = ibin; - bins_multi[n][i] = binhead_multi[n][ibin]; + atom2bin[i] = ibin; + bins[i] = binhead_multi[n][ibin]; binhead_multi[n][ibin] = i; } } diff --git a/src/npair.cpp b/src/npair.cpp index b2ecc953ea..facd9086d1 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -156,8 +156,6 @@ void NPair::copy_bin_info() bininvy_multi = nb->bininvy_multi; bininvz_multi = nb->bininvz_multi; - atom2bin_multi = nb->atom2bin_multi; - bins_multi = nb->bins_multi; binhead_multi = nb->binhead_multi; } diff --git a/src/npair.h b/src/npair.h index 4d99e3a8e6..d1fcf2e6b2 100644 --- a/src/npair.h +++ b/src/npair.h @@ -87,8 +87,7 @@ class NPair : protected Pointers { int *mbinx_multi, *mbiny_multi, *mbinz_multi; int *mbinxlo_multi, *mbinylo_multi, *mbinzlo_multi; double *bininvx_multi, *bininvy_multi, *bininvz_multi; - int **binhead_multi,**bins_multi; - int **atom2bin_multi; + int **binhead_multi; // data from NStencil class diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp index f29f04107a..c78f7b2d1d 100644 --- a/src/npair_full_multi.cpp +++ b/src/npair_full_multi.cpp @@ -78,7 +78,7 @@ void NPairFullMulti::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -96,7 +96,7 @@ void NPairFullMulti::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if (i == j) continue; jtype = type[j]; diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp index 85832b11b1..11bab91e6a 100755 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -80,7 +80,7 @@ void NPairHalfMultiNewtoff::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -100,7 +100,7 @@ void NPairHalfMultiNewtoff::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jgroup][j]) { + for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index d18b009460..777aab5826 100755 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -79,7 +79,7 @@ void NPairHalfMultiNewton::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -98,9 +98,9 @@ void NPairHalfMultiNewton::build(NeighList *list) // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - js = bins_multi[igroup][i]; + js = bins[i]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -142,7 +142,7 @@ void NPairHalfMultiNewton::build(NeighList *list) js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if(j < i) continue; if (j >= nlocal) { @@ -190,7 +190,7 @@ void NPairHalfMultiNewton::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp index ebf871ad99..6969c9cfab 100755 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -79,7 +79,7 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -102,7 +102,7 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { // if same size (same group), use half stencil if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp index ec4fbad9aa..e361bbce76 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -71,7 +71,7 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -91,7 +91,7 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >=0; j = bins_multi[jgroup][j]) { + for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index c3a13f4b81..500e06bc35 100755 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -68,7 +68,7 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -87,9 +87,9 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - js = bins_multi[igroup][i]; + js = bins[i]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { @@ -124,7 +124,7 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { if(j < i) continue; if (j >= nlocal) { @@ -165,7 +165,7 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 7c792c6a19..0000f7b4d3 100755 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -68,7 +68,7 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) ztmp = x[i][2]; radi = radius[i]; - ibin = atom2bin_multi[igroup][i]; + ibin = atom2bin[i]; // loop through stencils for all groups for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { @@ -92,7 +92,7 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jgroup][jbin + s[k]]; - for (j = js; j >= 0; j = bins_multi[jgroup][j]) { + for (j = js; j >= 0; j = bins[j]) { // if same size (same group), use half stencil if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ From d5f34f62967070da33a64f9dd800bf93267be9dd Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Fri, 8 Jan 2021 15:27:23 -0700 Subject: [PATCH 0068/1217] Examples and documentation --- doc/src/comm_modify.rst | 16 +- doc/src/neigh_modify.rst | 20 +- doc/src/neighbor.rst | 32 +-- examples/multi/in.colloid | 67 +++++++ examples/multi/in.granular | 58 ++++++ examples/multi/log.30Nov20.colloid.intel.1 | 183 ++++++++++++++++++ examples/multi/log.30Nov20.colloid.intel.4 | 183 ++++++++++++++++++ .../multi/log.30Nov20.colloid.old.intel.1 | 183 ++++++++++++++++++ .../multi/log.30Nov20.colloid.old.intel.4 | 183 ++++++++++++++++++ examples/multi/log.30Nov20.granular.intel.1 | 175 +++++++++++++++++ examples/multi/log.30Nov20.granular.intel.4 | 175 +++++++++++++++++ .../multi/log.30Nov20.granular.old.intel.1 | 175 +++++++++++++++++ .../multi/log.30Nov20.granular.old.intel.4 | 175 +++++++++++++++++ src/comm.cpp | 2 + 14 files changed, 1604 insertions(+), 23 deletions(-) create mode 100644 examples/multi/in.colloid create mode 100644 examples/multi/in.granular create mode 100644 examples/multi/log.30Nov20.colloid.intel.1 create mode 100644 examples/multi/log.30Nov20.colloid.intel.4 create mode 100644 examples/multi/log.30Nov20.colloid.old.intel.1 create mode 100644 examples/multi/log.30Nov20.colloid.old.intel.4 create mode 100644 examples/multi/log.30Nov20.granular.intel.1 create mode 100644 examples/multi/log.30Nov20.granular.intel.4 create mode 100644 examples/multi/log.30Nov20.granular.old.intel.1 create mode 100644 examples/multi/log.30Nov20.granular.old.intel.4 diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 895d3cf4fd..5f084561a1 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -66,9 +66,10 @@ For many systems this is an efficient algorithm, but for systems with widely varying cutoffs for different type pairs, the *multi* mode can be faster. In this case, each atom type is assigned its own distance cutoff for communication purposes, and fewer atoms will be -communicated. See the :doc:`neighbor multi ` command for a +communicated. See the :doc:`neighbor multi ` command for a neighbor list construction option that may also be beneficial for -simulations of this kind. +simulations of this kind. The *multi* mode is compatable with both the +*multi* and *multi/old* neighbor styles. The *cutoff* keyword allows you to extend the ghost cutoff distance for communication mode *single*\ , which is the distance from the borders @@ -95,11 +96,12 @@ using the usual asterisk notation can be given. For granular pair styles, the default cutoff is set to the sum of the current maximum atomic radii for each type. -The *cutoff/bytype* option applies to *multi* and automtically sets communication -cutoffs for each particle type based on the largest interaction distance -between two particles of the same type. This method is only compatible -with Newton on and the *bytype* neighbor style. See the :doc:`neighbor bytype ` -command for more information. +The *multi/reduce* option applies to *multi* and automatically sets communication +cutoffs for different sized particles based on the largest interaction distance +between two particles in the same multi grouping. This reduces the number of +ghost that need to be communicated This method is only compatible with the +*multi* neighbor style and requires only half neighbor lists and Newton on. +See the :doc:`neighbor multi ` command for more information. These are simulation scenarios in which it may be useful or even necessary to set a ghost cutoff > neighbor cutoff: diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index 2618953dd7..33f24af96e 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -14,7 +14,7 @@ Syntax .. parsed-literal:: - keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* + keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *multi/custom* *delay* value = N N = delay building until this many steps since last build *every* value = M @@ -47,6 +47,9 @@ Syntax N = max number of neighbors of one atom *binsize* value = size size = bin size for neighbor list construction (distance units) + *multi/custom* values = N types + N = number of custom groups + types = N separate types or groups of types (see below) Examples """""""" @@ -58,6 +61,7 @@ Examples neigh_modify exclude group frozen frozen check no neigh_modify exclude group residue1 chain3 neigh_modify exclude molecule/intra rigid + neigh_modify multi/custom 2 1*2 3*4 Description """"""""""" @@ -197,6 +201,20 @@ small, the optimal number of atoms is checked, but bin overhead goes up. If you set the binsize to 0.0, LAMMPS will use the default binsize of 1/2 the cutoff. +The *multi/custom* option allows you to define custom groups of atom +types for the *multi* neighbor mode. By grouping atom types with +similar cutoffs, one may be able to improve performance by reducing +overhead. You must first specify the number of custom groups N to be +defined followed by N ranges of types. The range can be specified as a +single numeric value, or a wildcard asterisk can be used to specify a range +of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For +example, if N = the number of atom types, then an asterisk with no numeric +values means all types from 1 to N. A leading asterisk means all types +from 1 to n (inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n (inclusive). +Note that any atom types not included in a custom group will be automatically +placed within a new, separate group. + Restrictions """""""""""" diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index f638160d21..52d59dae75 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -11,7 +11,7 @@ Syntax neighbor skin style * skin = extra distance beyond force cutoff (distance units) -* style = *bin* or *nsq* or *multi* or *bytype* +* style = *bin* or *nsq* or *multi* or *multi/old* Examples """""""" @@ -55,22 +55,24 @@ For the *bin* style, the bin size is set to 1/2 of the largest cutoff distance between any pair of atom types and a single set of bins is defined to search over for all atom types. This can be inefficient if one pair of types has a very long cutoff, but -other type pairs have a much shorter cutoff. For style *multi* the -bin size is set to 1/2 of the shortest cutoff distance and multiple -sets of bins are defined to search over for different atom types. +other type pairs have a much shorter cutoff. The *multi* style uses +different sized bins for groups of different sized particles. Different +sets of bins are then used to construct the neighbor lists as as further +described by Shire, Hanley, and Stratford :ref:`(Shire) `. This imposes some extra setup overhead, but the searches themselves -may be much faster for the short-cutoff cases. -See the :doc:`comm_modify mode multi ` command for a -communication option that may also be beneficial for simulations of -this kind. +may be much faster. By default, separate groups of particles are defined +for each atom type. For systems with two or more types with similar +cutoffs, one can reduce the extra overhead by defining custom groupings +using the :doc:`neigh_modify ` command. See the +:doc:`comm_modify mode bytype ` command for compatible +communication options that may be beneficial for simulations of this kind. -The *bytype* style is an extension of the *multi* style that was -presented by Shire, Hanley, and Stratford :ref:`(Shire) `. -For style *bytype*, different bin lists are created for each different -type and separate bin sizes are generated. Whether *bytype* or *multi* -is faster may depend on the specifics of your system. See the -:doc:`comm_modify mode bytype ` command for a compatible -communication option. +An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest +cutoff distance and multiple sets of bins are defined to search over for +different atom types. This algorithm used to be the default *multi* +algorithm in LAMMPS but was found to be significantly slower than the new +approach. Although, there may be instances where the *multi/old* style +could outperform the new style. The :doc:`neigh_modify ` command has additional options that control how often neighbor lists are built and which pairs are diff --git a/examples/multi/in.colloid b/examples/multi/in.colloid new file mode 100644 index 0000000000..b332560777 --- /dev/null +++ b/examples/multi/in.colloid @@ -0,0 +1,67 @@ +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +create_atoms 1 box + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +set group all type/fraction 3 0.333 43684 +set group all type/fraction 4 0.250 87811 + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +delete_atoms region sphere2 +create_atoms 5 single 60.0 60.0 0.0 units box +create_atoms 5 single 130.0 130.0 0.0 units box + +set type 1 mass 400 +set type 2 mass 1 + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 multi/custom 2 1*4 5 +comm_modify mode multi multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 & + mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +#dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 diff --git a/examples/multi/in.granular b/examples/multi/in.granular new file mode 100644 index 0000000000..00dd4ad2bb --- /dev/null +++ b/examples/multi/in.granular @@ -0,0 +1,58 @@ +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +create_atoms 1 box +change_box all triclinic + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +delete_atoms region sphere2 +create_atoms 2 single 20.0 20.0 0.0 units box +create_atoms 2 single 60.0 60.0 0.0 units box + +set type 2 mass 400 +set type 1 mass 1 +set type 2 diameter 20 +set type 1 diameter 1 + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 +comm_modify mode multi vel yes multi/reduce + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +#dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 diff --git a/examples/multi/log.30Nov20.colloid.intel.1 b/examples/multi/log.30Nov20.colloid.intel.1 new file mode 100644 index 0000000000..2bc82eaab0 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.intel.1 @@ -0,0 +1,183 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #/old +neigh_modify delay 0 multi/custom 2 1*4 5 +comm_modify mode multi multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/2d + bin: multi +Per MPI rank memory allocation (min/avg/max) = 5.538 | 5.538 | 5.538 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69 + 3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12 + 4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299 + 5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92 + 6000 2.0797015 -0.086800285 1.992214 0.082095164 78182.702 + 7000 2.0867886 -0.10960963 1.9764893 0.10103655 63990.386 + 8000 2.0803886 -0.12736298 1.9523381 0.12561727 52648.372 + 9000 2.0605661 -0.14572043 1.9141648 0.15154081 44589.764 + 10000 2.0636909 -0.18556771 1.8774412 0.1604707 38996.941 + 11000 2.0498344 -0.20303461 1.8461224 0.18295046 34927.993 + 12000 2.0466611 -0.2217963 1.8241884 0.23031182 31760.363 + 13000 2.0441824 -0.24716826 1.7963386 0.22167931 29178.226 + 14000 2.047513 -0.26988172 1.7769547 0.24070752 26991.372 + 15000 2.0154283 -0.26144354 1.7533187 0.27587713 25247.715 + 16000 2.0160849 -0.28106984 1.7343488 0.32297139 23703.607 + 17000 2.0184729 -0.31071368 1.7070922 0.29815613 22300.6 + 18000 2.0237288 -0.33944941 1.6836106 0.3262795 21098.856 + 19000 2.0329827 -0.35438937 1.6779215 0.33691952 19989.867 + 20000 2.021113 -0.37316841 1.6472766 0.39687648 18978.666 + 21000 2.0352439 -0.40857976 1.6259915 0.38632613 18146.277 + 22000 2.0158566 -0.41271329 1.6024771 0.41480502 17409.593 + 23000 2.0170409 -0.42611776 1.5902566 0.40446612 16748.968 + 24000 2.0108878 -0.43899286 1.5712304 0.42075035 16086.941 + 25000 2.0218394 -0.47012156 1.5510497 0.46655183 15460.154 + 26000 2.0100713 -0.47985916 1.5295479 0.45575323 15013.774 + 27000 2.0251738 -0.5016665 1.5228381 0.50151992 14591.521 + 28000 2.0062966 -0.50284394 1.5027897 0.5462034 14135.093 + 29000 2.0146666 -0.53126035 1.4827405 0.60379062 13725.945 + 30000 2.0036455 -0.53246643 1.4705169 0.56784088 13417.305 + 31000 2.0127662 -0.54487777 1.4672233 0.6427741 13139.392 + 32000 2.0221816 -0.5625554 1.4589579 0.60695012 12779.609 + 33000 2.024983 -0.59515221 1.4291616 0.60005385 12584.572 + 34000 2.0184045 -0.59033569 1.4274018 0.62519753 12355.49 + 35000 2.0155635 -0.61190466 1.4029927 0.71044196 12106.819 + 36000 2.0252503 -0.61581601 1.408765 0.68805882 11728.608 + 37000 2.0112487 -0.64540754 1.3651765 0.66981639 11475.772 + 38000 2.0147475 -0.64161981 1.3724619 0.71130901 11285.511 + 39000 2.0213092 -0.67174661 1.3488946 0.6969697 11044.647 + 40000 2.0178739 -0.67924699 1.3379601 0.77309897 10824.198 + 41000 1.9952353 -0.67490899 1.3196669 0.76592358 10646.649 + 42000 2.002415 -0.70533555 1.2964178 0.81084741 10519.804 + 43000 2.0211625 -0.71370366 1.3067909 0.77355048 10434.893 + 44000 2.0252106 -0.72635544 1.2981859 0.83770143 10132.262 + 45000 2.0126446 -0.75197714 1.2600024 0.88927993 9946.7842 + 46000 2.0431159 -0.78445975 1.257981 0.84492327 9869.8151 + 47000 2.0199724 -0.76967899 1.2496259 0.90977181 9653.4334 + 48000 2.0109636 -0.78968551 1.2206135 0.89458323 9496.7246 + 49000 2.0131059 -0.79687252 1.2155681 0.91239613 9418.3093 + 50000 2.0073361 -0.79981468 1.206858 0.98524334 9289.4715 +Loop time of 20.4651 on 1 procs for 50000 steps with 3026 atoms + +Performance: 1055453.279 tau/day, 2443.179 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.099 | 11.099 | 11.099 | 0.0 | 54.23 +Neigh | 2.7536 | 2.7536 | 2.7536 | 0.0 | 13.46 +Comm | 0.53353 | 0.53353 | 0.53353 | 0.0 | 2.61 +Output | 0.11209 | 0.11209 | 0.11209 | 0.0 | 0.55 +Modify | 5.1627 | 5.1627 | 5.1627 | 0.0 | 25.23 +Other | | 0.8046 | | | 3.93 + +Nlocal: 3026.00 ave 3026 max 3026 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 584.000 ave 584 max 584 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 25892.0 ave 25892 max 25892 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 25892 +Ave neighs/atom = 8.5565102 +Neighbor list builds = 4330 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:20 diff --git a/examples/multi/log.30Nov20.colloid.intel.4 b/examples/multi/log.30Nov20.colloid.intel.4 new file mode 100644 index 0000000000..48a5846a09 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.intel.4 @@ -0,0 +1,183 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #/old +neigh_modify delay 0 multi/custom 2 1*4 5 +comm_modify mode multi multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/2d + bin: multi +Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.382 | 5.384 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688 + 3000 1.8956738 -0.090814176 1.8042332 0.075557943 77825.289 + 4000 1.9570462 -0.072505537 1.8838939 0.072824365 90931.708 + 5000 2.0376745 -0.083247829 1.9537533 0.068496975 90055.295 + 6000 2.0744887 -0.085395371 1.9884077 0.0821927 78070.648 + 7000 2.1002183 -0.11654617 1.9829781 0.10523249 63934.448 + 8000 2.0818325 -0.13271654 1.948428 0.11909162 52636.484 + 9000 2.0693987 -0.16404154 1.9046733 0.14702552 44539.609 + 10000 2.0667772 -0.19779488 1.8682993 0.17245383 38822.542 + 11000 2.0640582 -0.22114917 1.842227 0.18083079 34788.927 + 12000 2.0308462 -0.20353105 1.8266441 0.20640739 31706.009 + 13000 2.0395895 -0.24217765 1.7967378 0.21832952 29152.654 + 14000 2.030848 -0.2586169 1.77156 0.26577748 27068.89 + 15000 2.0222966 -0.27554585 1.7460825 0.2777169 25272.786 + 16000 2.0398867 -0.31547563 1.723737 0.27763622 23666.792 + 17000 2.03026 -0.32453791 1.7050512 0.28099246 22272.809 + 18000 2.0345512 -0.35026242 1.6836164 0.36600779 21023.172 + 19000 2.0242864 -0.35813231 1.6654851 0.33415432 19941.244 + 20000 2.0132465 -0.36563904 1.6469422 0.403365 18979.884 + 21000 2.0280384 -0.4075867 1.6197815 0.37205362 18152.487 + 22000 2.0206494 -0.40600336 1.6139782 0.42704594 17370.812 + 23000 2.0395761 -0.45083258 1.5880695 0.40276343 16700.427 + 24000 2.017203 -0.44930293 1.5672335 0.43867313 16161.79 + 25000 2.0191846 -0.4672218 1.5512955 0.47031215 15622.756 + 26000 2.0131624 -0.46436088 1.5481363 0.51717944 15141.645 + 27000 2.0322461 -0.50659994 1.5249745 0.49218933 14627.657 + 28000 2.0169304 -0.50555565 1.5107082 0.55547935 14186.079 + 29000 2.024656 -0.52258414 1.5014028 0.59125812 13759.99 + 30000 2.0153725 -0.53585947 1.478847 0.57235811 13384.355 + 31000 2.0163261 -0.56383766 1.4518221 0.58232057 13098.196 + 32000 2.0109673 -0.56784395 1.4424588 0.58282178 12831.934 + 33000 2.0099169 -0.57625621 1.4329964 0.65139601 12479.442 + 34000 2.0238152 -0.60189607 1.4212503 0.62659152 12210.628 + 35000 2.0359989 -0.62654733 1.4087787 0.67574446 11972.725 + 36000 2.0222689 -0.62880837 1.3927923 0.66602146 11690.049 + 37000 1.9982569 -0.62746376 1.3701328 0.71326589 11433.825 + 38000 1.9969836 -0.63975181 1.3565719 0.72799891 11285.497 + 39000 2.0071087 -0.65781805 1.3486274 0.79121297 11107.469 + 40000 2.0243046 -0.6881221 1.3355135 0.77519099 10943.846 + 41000 2.0351657 -0.70309175 1.3314014 0.68815156 10742.515 + 42000 2.0224788 -0.70975664 1.3120538 0.80484619 10505.657 + 43000 2.0123135 -0.70818545 1.3034631 0.84204556 10353.024 + 44000 1.999883 -0.70981202 1.2894101 0.94070546 10212.224 + 45000 2.0127291 -0.73338075 1.2786832 0.82095205 10109.959 + 46000 2.0109037 -0.75130029 1.2589389 0.88538358 9953.4822 + 47000 1.9879175 -0.73152019 1.2557404 0.92089629 9832.892 + 48000 2.0108204 -0.76655178 1.2436041 0.95379465 9633.6453 + 49000 1.9868193 -0.76613798 1.2200247 0.88790224 9504.2918 + 50000 2.0141467 -0.80029827 1.2131829 1.0064263 9346.3268 +Loop time of 7.28248 on 4 procs for 50000 steps with 3026 atoms + +Performance: 2966022.789 tau/day, 6865.793 timesteps/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.1624 | 2.5918 | 2.9227 | 17.4 | 35.59 +Neigh | 0.62508 | 0.7436 | 0.83321 | 9.2 | 10.21 +Comm | 1.1035 | 1.5265 | 2.0746 | 29.3 | 20.96 +Output | 0.050094 | 0.050233 | 0.05062 | 0.1 | 0.69 +Modify | 1.8164 | 1.8966 | 1.9583 | 4.2 | 26.04 +Other | | 0.4737 | | | 6.50 + +Nlocal: 756.500 ave 839 max 673 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Nghost: 292.500 ave 307 max 282 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 6435.25 ave 7367 max 5493 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 25741 +Ave neighs/atom = 8.5066094 +Neighbor list builds = 4335 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:07 diff --git a/examples/multi/log.30Nov20.colloid.old.intel.1 b/examples/multi/log.30Nov20.colloid.old.intel.1 new file mode 100644 index 0000000000..291e8f89df --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.old.intel.1 @@ -0,0 +1,183 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old +neigh_modify delay 0 #multi/custom 2 1*4 5 +comm_modify mode multi #multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/old/newton + stencil: half/multi/old/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.611 | 5.611 | 5.611 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69 + 3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12 + 4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299 + 5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92 + 6000 2.0797015 -0.086800284 1.992214 0.082095164 78182.702 + 7000 2.086794 -0.10961479 1.9764895 0.10103993 63990.387 + 8000 2.082863 -0.12779588 1.9543788 0.12672452 52629.802 + 9000 2.0718275 -0.15189022 1.9192526 0.14728063 44541.722 + 10000 2.0603856 -0.18054161 1.8791631 0.16715133 38940.135 + 11000 2.046791 -0.20458359 1.841531 0.19532742 34907.116 + 12000 2.0406846 -0.2252868 1.8147234 0.2036178 31740.208 + 13000 2.0369763 -0.23721632 1.7990869 0.25542564 29079.901 + 14000 2.0376121 -0.26282517 1.7741135 0.24722118 26947.344 + 15000 2.0312772 -0.2851101 1.7454959 0.2801199 25180.963 + 16000 2.0080448 -0.28992973 1.7174515 0.30099318 23723.043 + 17000 2.0234993 -0.30440169 1.7184289 0.3193226 22342.977 + 18000 2.0216103 -0.32036933 1.7005729 0.3460322 21068.99 + 19000 2.0493952 -0.37711533 1.6716026 0.33804972 20013.325 + 20000 2.0307894 -0.38462795 1.6454903 0.37041981 19092.745 + 21000 2.0328577 -0.39442652 1.6377594 0.36327057 18260.298 + 22000 2.0325613 -0.40481002 1.6270796 0.42756691 17447.199 + 23000 2.0199358 -0.42175719 1.5975111 0.40948041 16768.71 + 24000 2.0149952 -0.43618764 1.5781417 0.45406069 16187.334 + 25000 2.0153221 -0.45884172 1.5558143 0.52717203 15605.577 + 26000 2.0099026 -0.47080566 1.5384327 0.49181459 15088.041 + 27000 2.0128537 -0.49799999 1.5141885 0.53907465 14590.392 + 28000 2.0287266 -0.53112525 1.4969309 0.59750714 14208.419 + 29000 2.0143609 -0.53175704 1.4819381 0.56118773 13840.642 + 30000 2.0235262 -0.53923416 1.4836234 0.52579997 13500.15 + 31000 2.0390444 -0.57976823 1.4586023 0.5760349 13082.091 + 32000 2.018046 -0.57797686 1.4394022 0.59127933 12761.726 + 33000 2.0059068 -0.57185148 1.4333925 0.58992758 12473.866 + 34000 1.9828456 -0.57147221 1.4107181 0.77593228 12208.869 + 35000 1.9900097 -0.58349168 1.4058604 0.681968 11937.285 + 36000 2.0271405 -0.64374859 1.382722 0.63152587 11675.264 + 37000 2.0032809 -0.63520712 1.3674117 0.71639384 11440.274 + 38000 2.0000566 -0.63941617 1.3599795 0.74099652 11235.252 + 39000 1.9872705 -0.64765522 1.3389586 0.7575743 11080.857 + 40000 2.0224403 -0.6795645 1.3422075 0.82918546 10861.905 + 41000 2.0137595 -0.69863075 1.3144633 0.80397759 10712.981 + 42000 1.9950915 -0.68892531 1.3055069 0.77631365 10632.931 + 43000 2.0080851 -0.70534369 1.3020778 0.82408436 10408.82 + 44000 2.0239806 -0.73189482 1.2914169 0.83228695 10227.18 + 45000 2.0019542 -0.72613202 1.2751606 0.9145618 10044.013 + 46000 2.0173095 -0.75370218 1.2629407 0.99791312 9837.9611 + 47000 1.9921201 -0.75875076 1.232711 1.0047839 9711.2083 + 48000 2.0283587 -0.79063641 1.237052 0.83617499 9610.9933 + 49000 2.0051919 -0.79078067 1.2137485 0.95651813 9411.7165 + 50000 2.0140985 -0.81796958 1.1954634 0.93791038 9296.069 +Loop time of 29.8066 on 1 procs for 50000 steps with 3026 atoms + +Performance: 724671.093 tau/day, 1677.479 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.698 | 11.698 | 11.698 | 0.0 | 39.25 +Neigh | 10.292 | 10.292 | 10.292 | 0.0 | 34.53 +Comm | 1.405 | 1.405 | 1.405 | 0.0 | 4.71 +Output | 0.11474 | 0.11474 | 0.11474 | 0.0 | 0.38 +Modify | 5.3019 | 5.3019 | 5.3019 | 0.0 | 17.79 +Other | | 0.9947 | | | 3.34 + +Nlocal: 3026.00 ave 3026 max 3026 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2292.00 ave 2292 max 2292 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 25767.0 ave 25767 max 25767 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 25767 +Ave neighs/atom = 8.5152016 +Neighbor list builds = 4332 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:29 diff --git a/examples/multi/log.30Nov20.colloid.old.intel.4 b/examples/multi/log.30Nov20.colloid.old.intel.4 new file mode 100644 index 0000000000..0eae8cc8e7 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.old.intel.4 @@ -0,0 +1,183 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old +neigh_modify delay 0 #multi/custom 2 1*4 5 +comm_modify mode multi #multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/old/newton + stencil: half/multi/old/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.438 | 5.441 | 5.444 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688 + 3000 1.8956738 -0.090814168 1.8042332 0.075557943 77825.289 + 4000 1.9567884 -0.072243657 1.8838981 0.072836007 90931.521 + 5000 2.0386455 -0.084279096 1.9536927 0.06867562 90054.581 + 6000 2.0816461 -0.093158646 1.9877995 0.082802397 78084.994 + 7000 2.0854943 -0.10553618 1.979269 0.10230351 63886.068 + 8000 2.0923948 -0.14072173 1.9509816 0.11775174 52590.899 + 9000 2.0687841 -0.15957251 1.9085279 0.14963059 44575.69 + 10000 2.0607467 -0.18970216 1.8703636 0.17210861 39016.271 + 11000 2.0538523 -0.20866031 1.8445133 0.18554787 34992.223 + 12000 2.0408745 -0.22276635 1.8174337 0.21228473 31794.869 + 13000 2.0366678 -0.24217764 1.7938171 0.22999314 29186.441 + 14000 2.0470314 -0.26923854 1.7771164 0.2576977 26941.432 + 15000 2.0262458 -0.27296827 1.7526079 0.25960813 25184.491 + 16000 2.0410096 -0.30940081 1.7309343 0.27842776 23619.633 + 17000 2.027379 -0.32411477 1.7025943 0.32102949 22231.582 + 18000 2.0338405 -0.34468182 1.6884866 0.3306203 21028.933 + 19000 2.032206 -0.36558904 1.6659454 0.33926726 19958.945 + 20000 2.0347643 -0.3915229 1.642569 0.33718716 19054.271 + 21000 2.0242901 -0.38913219 1.634489 0.38062225 18190.934 + 22000 2.0207557 -0.41078199 1.6093059 0.40143768 17422.03 + 23000 2.0069068 -0.42062708 1.5856165 0.40146954 16717.999 + 24000 2.0300595 -0.4536262 1.5757624 0.49229743 16097.323 + 25000 2.0347548 -0.47655047 1.5575319 0.46787969 15564.848 + 26000 2.0180789 -0.46537586 1.5520362 0.48541997 15072.597 + 27000 2.0150506 -0.4886202 1.5257645 0.53829749 14621.24 + 28000 2.0175464 -0.50951413 1.5073655 0.50140171 14253.441 + 29000 2.0186127 -0.53911975 1.4788258 0.52955802 13930.266 + 30000 2.0006844 -0.52621334 1.4738099 0.60130639 13650.051 + 31000 2.0179614 -0.54573939 1.4715551 0.58747508 13285.903 + 32000 2.0333208 -0.57431851 1.4583303 0.62631039 12894.077 + 33000 2.0017273 -0.57778326 1.4232825 0.61159622 12595.987 + 34000 2.0063025 -0.58192939 1.4237101 0.66174764 12316.964 + 35000 2.0174782 -0.60591394 1.4108976 0.63571024 12063.433 + 36000 2.025112 -0.64319133 1.3812514 0.62829458 11930.246 + 37000 2.0431268 -0.64342323 1.3990283 0.68038546 11651.664 + 38000 2.0064271 -0.63716263 1.3686014 0.72167175 11345.421 + 39000 2.0284014 -0.67236471 1.3553663 0.68693225 11062.293 + 40000 2.0181711 -0.6962559 1.3212483 0.76033095 10864.176 + 41000 1.9908152 -0.66607906 1.3240783 0.90250403 10812.599 + 42000 2.0007084 -0.68853623 1.311511 0.88096905 10627.922 + 43000 1.998883 -0.69053805 1.3076844 0.81765345 10469.928 + 44000 2.0197069 -0.72507021 1.2939693 0.87004916 10194.954 + 45000 2.0112835 -0.72638581 1.284233 0.99236207 9968.2662 + 46000 2.0195002 -0.75152677 1.2673061 0.92706763 9751.1162 + 47000 1.983694 -0.75006702 1.2329714 0.8945741 9652.1453 + 48000 1.9977505 -0.77207122 1.225019 0.92107083 9647.1543 + 49000 2.0000901 -0.76254934 1.2368798 1.0320945 9536.2823 + 50000 2.0150929 -0.80463979 1.2097872 0.99556424 9324.0277 +Loop time of 11.239 on 4 procs for 50000 steps with 3026 atoms + +Performance: 1921872.705 tau/day, 4448.779 timesteps/s +98.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.3936 | 2.7411 | 3.1078 | 16.7 | 24.39 +Neigh | 2.2948 | 2.6755 | 3.1013 | 18.5 | 23.81 +Comm | 2.522 | 3.3135 | 4.0361 | 31.7 | 29.48 +Output | 0.040863 | 0.041031 | 0.041456 | 0.1 | 0.37 +Modify | 1.844 | 1.9014 | 1.9701 | 3.4 | 16.92 +Other | | 0.5666 | | | 5.04 + +Nlocal: 756.500 ave 838 max 693 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1282.50 ave 1333 max 1216 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Neighs: 6426.25 ave 7350 max 5786 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 25705 +Ave neighs/atom = 8.4947125 +Neighbor list builds = 4326 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:11 diff --git a/examples/multi/log.30Nov20.granular.intel.1 b/examples/multi/log.30Nov20.granular.intel.1 new file mode 100644 index 0000000000..2e313231ca --- /dev/null +++ b/examples/multi/log.30Nov20.granular.intel.1 @@ -0,0 +1,175 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #/old +neigh_modify delay 0 +comm_modify mode multi vel yes + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/newton/tri + stencil: half/multi/2d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 11.78 | 11.78 | 11.78 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 + 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 + 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 + 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 + 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 + 6000 0.025856 0 0.025848141 0.021241317 7603.5534 + 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 + 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 + 9000 0.016370159 0 0.016365184 0.020261904 6515.3445 + 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 + 11000 0.014156551 0 0.014152248 0.021324815 5815.4665 + 12000 0.013725406 0 0.013721235 0.021159958 5483.6304 + 13000 0.013215746 0 0.013211729 0.021685712 5165.4758 + 14000 0.012398153 0 0.012394384 0.024155434 4862.8657 + 15000 0.011842796 0 0.011839196 0.028503991 4577.9008 + 16000 0.011433182 0 0.011429706 0.033564839 4309.8792 + 17000 0.011166574 0 0.01116318 0.040592677 4058.9964 + 18000 0.01100067 0 0.010997326 0.04899206 3825.155 + 19000 0.010224474 0 0.010221366 0.063670337 3607.6577 + 20000 0.0091360559 0 0.0091332789 0.088230111 3408.5658 + 21000 0.007733647 0 0.0077312964 0.11769368 3227.7002 + 22000 0.0060202358 0 0.0060184059 0.15272491 3064.3986 + 23000 0.004670574 0 0.0046691543 0.19450724 2918.0014 + 24000 0.0040248313 0 0.004023608 0.24161742 2788.4113 + 25000 0.0032075275 0 0.0032065526 0.2897693 2674.5604 + 26000 0.0021358024 0 0.0021351532 0.33635617 2574.9564 + 27000 0.0016902752 0 0.0016897614 0.37624266 2487.2379 + 28000 0.0014038218 0 0.0014033951 0.41492104 2409.2461 + 29000 0.00090262506 0 0.0009023507 0.45392905 2340.0308 + 30000 0.00049466342 0 0.00049451306 0.49295072 2279.2316 + 31000 0.00056998139 0 0.00056980815 0.53299515 2226.5683 + 32000 0.00057326945 0 0.0005730952 0.56856537 2181.7092 + 33000 0.00044845112 0 0.00044831481 0.59623471 2142.7573 + 34000 0.00059840183 0 0.00059821994 0.61758983 2107.1253 + 35000 0.00075310993 0 0.00075288103 0.63756827 2072.7217 + 36000 0.00053774066 0 0.00053757721 0.66026064 2039.1655 + 37000 0.00030440106 0 0.00030430853 0.69059102 2007.7903 + 38000 0.00034436264 0 0.00034425797 0.72166344 1980.7137 + 39000 0.00039693498 0 0.00039681433 0.74680327 1957.9531 + 40000 0.00035425567 0 0.000354148 0.76604186 1937.3834 + 41000 0.0003094733 0 0.00030937924 0.78323163 1916.7027 + 42000 0.00027259246 0 0.0002725096 0.80315535 1895.0714 + 43000 0.00020659817 0 0.00020653538 0.8274603 1873.5407 + 44000 0.00016023333 0 0.00016018463 0.85418969 1853.8674 + 45000 0.00016111931 0 0.00016107034 0.87913944 1837.1141 + 46000 0.00016130888 0 0.00016125985 0.89921705 1822.7354 + 47000 0.00015755049 0 0.0001575026 0.91653538 1809.0285 + 48000 0.00017794781 0 0.00017789372 0.93582908 1794.7041 + 49000 0.00018878437 0 0.00018872699 0.95775203 1780.032 + 50000 0.0001778042 0 0.00017775016 0.97893714 1765.9439 +Loop time of 77.4487 on 1 procs for 50000 steps with 3290 atoms + +Performance: 278894.354 tau/day, 645.589 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 60.017 | 60.017 | 60.017 | 0.0 | 77.49 +Neigh | 0.47 | 0.47 | 0.47 | 0.0 | 0.61 +Comm | 6.6765 | 6.6765 | 6.6765 | 0.0 | 8.62 +Output | 0.24799 | 0.24799 | 0.24799 | 0.0 | 0.32 +Modify | 8.8677 | 8.8677 | 8.8677 | 0.0 | 11.45 +Other | | 1.17 | | | 1.51 + +Nlocal: 3290.00 ave 3290 max 3290 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 6295.00 ave 6295 max 6295 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 53729.0 ave 53729 max 53729 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 53729 +Ave neighs/atom = 16.331003 +Neighbor list builds = 348 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:17 diff --git a/examples/multi/log.30Nov20.granular.intel.4 b/examples/multi/log.30Nov20.granular.intel.4 new file mode 100644 index 0000000000..d53684c596 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.intel.4 @@ -0,0 +1,175 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 +comm_modify mode multi vel yes multi/reduce + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/newton/tri + stencil: half/multi/2d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 11.33 | 11.33 | 11.33 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 + 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 + 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 + 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 + 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 + 6000 0.025856 0 0.025848141 0.021241317 7603.5534 + 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 + 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 + 9000 0.01637016 0 0.016365184 0.020261904 6515.3445 + 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 + 11000 0.014156553 0 0.01415225 0.021324818 5815.4665 + 12000 0.013725412 0 0.01372124 0.021159958 5483.6304 + 13000 0.013215733 0 0.013211716 0.021685624 5165.4758 + 14000 0.012398179 0 0.012394411 0.024155572 4862.8657 + 15000 0.01184269 0 0.01183909 0.028504106 4577.901 + 16000 0.01143291 0 0.011429435 0.033564204 4309.88 + 17000 0.011166204 0 0.01116281 0.040588854 4058.9972 + 18000 0.011000875 0 0.010997532 0.048998904 3825.1569 + 19000 0.010225905 0 0.010222797 0.063669586 3607.6622 + 20000 0.0091390249 0 0.0091362471 0.088165396 3408.567 + 21000 0.0077382016 0 0.0077358496 0.11770473 3227.6936 + 22000 0.0060173113 0 0.0060154823 0.15261992 3064.3873 + 23000 0.0046667554 0 0.004665337 0.19453813 2917.9782 + 24000 0.0040425764 0 0.0040413476 0.24145834 2788.3897 + 25000 0.0031933187 0 0.0031923481 0.28989732 2674.5164 + 26000 0.0021139018 0 0.0021132592 0.33598721 2574.9313 + 27000 0.0017005052 0 0.0016999884 0.37665029 2487.1628 + 28000 0.001443434 0 0.0014429952 0.41572112 2409.3271 + 29000 0.00089885805 0 0.00089858484 0.45343123 2340.2314 + 30000 0.00048558336 0 0.00048543577 0.49175966 2279.2156 + 31000 0.00058132898 0 0.00058115228 0.53236819 2226.2347 + 32000 0.00057751441 0 0.00057733887 0.56915062 2181.2736 + 33000 0.00044720497 0 0.00044706904 0.59696122 2142.5709 + 34000 0.00060927898 0 0.00060909379 0.61734988 2107.128 + 35000 0.00077422577 0 0.00077399045 0.63696024 2072.6004 + 36000 0.00055753008 0 0.00055736062 0.65981839 2038.8237 + 37000 0.0003140158 0 0.00031392035 0.69018918 2007.323 + 38000 0.00034970199 0 0.0003495957 0.72155094 1980.1702 + 39000 0.00041435514 0 0.00041422919 0.7468053 1957.3837 + 40000 0.00037229543 0 0.00037218227 0.76581519 1936.8032 + 41000 0.00031027679 0 0.00031018248 0.78321128 1916.1103 + 42000 0.00026621832 0 0.00026613741 0.80267694 1894.4646 + 43000 0.00020544063 0 0.00020537818 0.82714181 1872.768 + 44000 0.00015635243 0 0.00015630491 0.85496512 1853.0303 + 45000 0.00014985611 0 0.00014981056 0.87924561 1836.4779 + 46000 0.00015645346 0 0.00015640591 0.89896131 1822.2004 + 47000 0.00016007816 0 0.00016002951 0.91662026 1808.4601 + 48000 0.00017439363 0 0.00017434063 0.93565314 1794.1244 + 49000 0.00018647711 0 0.00018642043 0.95733125 1779.401 + 50000 0.00018463414 0 0.00018457802 0.96449755 1765.1506 +Loop time of 22.3987 on 4 procs for 50000 steps with 3290 atoms + +Performance: 964340.770 tau/day, 2232.270 timesteps/s +99.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.5158 | 12.318 | 15.836 | 92.1 | 54.99 +Neigh | 0.092527 | 0.11392 | 0.13595 | 5.6 | 0.51 +Comm | 2.7127 | 6.2337 | 10.096 | 131.0 | 27.83 +Output | 0.088027 | 0.088284 | 0.088812 | 0.1 | 0.39 +Modify | 2.8544 | 3.0435 | 3.2034 | 9.2 | 13.59 +Other | | 0.6017 | | | 2.69 + +Nlocal: 822.500 ave 859 max 785 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 395.750 ave 424 max 368 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 13439.5 ave 14346 max 12017 min +Histogram: 1 0 0 0 0 1 0 0 0 2 + +Total # of neighbors = 53758 +Ave neighs/atom = 16.339818 +Neighbor list builds = 348 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:22 diff --git a/examples/multi/log.30Nov20.granular.old.intel.1 b/examples/multi/log.30Nov20.granular.old.intel.1 new file mode 100644 index 0000000000..ad827423c5 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.old.intel.1 @@ -0,0 +1,175 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old +neigh_modify delay 0 +comm_modify mode multi vel yes + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/old/newton/tri + stencil: half/multi/old/2d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.75 | 11.75 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 + 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 + 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 + 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 + 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 + 6000 0.025856 0 0.025848141 0.021241317 7603.5534 + 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 + 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 + 9000 0.016370159 0 0.016365184 0.020261904 6515.3445 + 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 + 11000 0.014156551 0 0.014152248 0.021324815 5815.4665 + 12000 0.013725406 0 0.013721235 0.021159958 5483.6304 + 13000 0.013215746 0 0.013211729 0.021685712 5165.4758 + 14000 0.012398153 0 0.012394384 0.024155434 4862.8657 + 15000 0.011842796 0 0.011839196 0.028503991 4577.9008 + 16000 0.011433182 0 0.011429706 0.033564839 4309.8792 + 17000 0.011166574 0 0.01116318 0.040592677 4058.9964 + 18000 0.01100067 0 0.010997326 0.04899206 3825.155 + 19000 0.010224474 0 0.010221366 0.063670337 3607.6577 + 20000 0.0091360558 0 0.0091332789 0.088230111 3408.5658 + 21000 0.0077336471 0 0.0077312964 0.11769368 3227.7002 + 22000 0.0060202357 0 0.0060184059 0.15272492 3064.3986 + 23000 0.0046705738 0 0.0046691542 0.19450723 2918.0014 + 24000 0.0040248311 0 0.0040236078 0.24161743 2788.4113 + 25000 0.0032075267 0 0.0032065518 0.28976925 2674.5604 + 26000 0.0021358008 0 0.0021351516 0.33635615 2574.9564 + 27000 0.0016902771 0 0.0016897633 0.37624261 2487.2379 + 28000 0.0014038216 0 0.0014033949 0.41492061 2409.2461 + 29000 0.00090262588 0 0.00090235152 0.45392924 2340.0308 + 30000 0.00049466445 0 0.0004945141 0.49295063 2279.2316 + 31000 0.00056998139 0 0.00056980814 0.53299532 2226.5683 + 32000 0.00057327032 0 0.00057309607 0.56856551 2181.7093 + 33000 0.00044845449 0 0.00044831818 0.59623461 2142.7574 + 34000 0.00059840346 0 0.00059822157 0.61758978 2107.1254 + 35000 0.00075311121 0 0.0007528823 0.63756791 2072.7217 + 36000 0.00053773653 0 0.00053757309 0.66026022 2039.1654 + 37000 0.00030439696 0 0.00030430444 0.69059127 2007.7901 + 38000 0.00034435616 0 0.00034425149 0.72166346 1980.7136 + 39000 0.00039692535 0 0.0003968047 0.7468036 1957.9531 + 40000 0.0003542502 0 0.00035414252 0.76604173 1937.3834 + 41000 0.0003094667 0 0.00030937263 0.78323183 1916.7027 + 42000 0.00027258976 0 0.0002725069 0.80315572 1895.0714 + 43000 0.00020659987 0 0.00020653707 0.82746098 1873.5408 + 44000 0.00016023865 0 0.00016018994 0.85418945 1853.8677 + 45000 0.00016112731 0 0.00016107833 0.87913874 1837.1144 + 46000 0.00016131366 0 0.00016126463 0.89921653 1822.7355 + 47000 0.00015754747 0 0.00015749958 0.91653641 1809.0285 + 48000 0.00017794764 0 0.00017789356 0.93582953 1794.7043 + 49000 0.00018879338 0 0.000188736 0.95775166 1780.0323 + 50000 0.00017781117 0 0.00017775712 0.97893641 1765.9442 +Loop time of 80.8597 on 1 procs for 50000 steps with 3290 atoms + +Performance: 267129.375 tau/day, 618.355 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 61.524 | 61.524 | 61.524 | 0.0 | 76.09 +Neigh | 2.2021 | 2.2021 | 2.2021 | 0.0 | 2.72 +Comm | 6.748 | 6.748 | 6.748 | 0.0 | 8.35 +Output | 0.25904 | 0.25904 | 0.25904 | 0.0 | 0.32 +Modify | 8.9408 | 8.9408 | 8.9408 | 0.0 | 11.06 +Other | | 1.186 | | | 1.47 + +Nlocal: 3290.00 ave 3290 max 3290 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 6295.00 ave 6295 max 6295 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 53729.0 ave 53729 max 53729 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 53729 +Ave neighs/atom = 16.331003 +Neighbor list builds = 348 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:20 diff --git a/examples/multi/log.30Nov20.granular.old.intel.4 b/examples/multi/log.30Nov20.granular.old.intel.4 new file mode 100644 index 0000000000..e41741b536 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.old.intel.4 @@ -0,0 +1,175 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old +neigh_modify delay 0 +comm_modify mode multi vel yes #multi/reduce + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/old/newton/tri + stencil: half/multi/old/2d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.48 | 11.48 | 11.49 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 + 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 + 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 + 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 + 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 + 6000 0.025856 0 0.025848141 0.021241317 7603.5534 + 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 + 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 + 9000 0.01637016 0 0.016365184 0.020261904 6515.3445 + 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 + 11000 0.014156553 0 0.01415225 0.021324818 5815.4665 + 12000 0.013725412 0 0.01372124 0.021159958 5483.6304 + 13000 0.013215733 0 0.013211716 0.021685624 5165.4758 + 14000 0.012398179 0 0.012394411 0.024155572 4862.8657 + 15000 0.01184269 0 0.01183909 0.028504106 4577.901 + 16000 0.01143291 0 0.011429435 0.033564204 4309.88 + 17000 0.011166204 0 0.01116281 0.040588854 4058.9972 + 18000 0.011000875 0 0.010997532 0.048998904 3825.1569 + 19000 0.010225905 0 0.010222797 0.063669588 3607.6622 + 20000 0.0091390255 0 0.0091362477 0.088165402 3408.567 + 21000 0.0077382041 0 0.0077358521 0.11770474 3227.6936 + 22000 0.00601731 0 0.0060154811 0.15261994 3064.3873 + 23000 0.0046667591 0 0.0046653407 0.19453819 2917.9782 + 24000 0.0040425749 0 0.0040413461 0.24145833 2788.3897 + 25000 0.0031933217 0 0.0031923511 0.28989713 2674.5164 + 26000 0.0021138997 0 0.0021132571 0.33598673 2574.9312 + 27000 0.001700508 0 0.0016999912 0.37665013 2487.1626 + 28000 0.0014434246 0 0.0014429859 0.41572163 2409.327 + 29000 0.00089885063 0 0.00089857742 0.453431 2340.2313 + 30000 0.00048556478 0 0.00048541719 0.49176025 2279.2155 + 31000 0.00058130972 0 0.00058113303 0.53236818 2226.2349 + 32000 0.00057749847 0 0.00057732294 0.5691506 2181.2738 + 33000 0.00044719326 0 0.00044705733 0.59696179 2142.571 + 34000 0.00060924828 0 0.0006090631 0.61735036 2107.1282 + 35000 0.00077419805 0 0.00077396273 0.63696098 2072.6008 + 36000 0.00055752003 0 0.00055735057 0.65981842 2038.8242 + 37000 0.00031402452 0 0.00031392907 0.69018949 2007.3235 + 38000 0.00034969879 0 0.0003495925 0.72155053 1980.1706 + 39000 0.00041434197 0 0.00041421603 0.74680715 1957.3838 + 40000 0.00037229243 0 0.00037217927 0.76581686 1936.8034 + 41000 0.00031028842 0 0.00031019411 0.78321059 1916.1108 + 42000 0.00026623668 0 0.00026615575 0.80267329 1894.4649 + 43000 0.00020543723 0 0.00020537479 0.82714001 1872.7672 + 44000 0.0001563321 0 0.00015628458 0.85496396 1853.0284 + 45000 0.00014981713 0 0.00014977159 0.87924842 1836.4755 + 46000 0.00015641585 0 0.00015636831 0.89896936 1822.1989 + 47000 0.00016004701 0 0.00015999837 0.91661933 1808.4606 + 48000 0.00017437702 0 0.00017432402 0.93565475 1794.1258 + 49000 0.00018645903 0 0.00018640235 0.95733183 1779.4032 + 50000 0.00018469122 0 0.00018463508 0.96446925 1765.1534 +Loop time of 30.9351 on 4 procs for 50000 steps with 3290 atoms + +Performance: 698235.574 tau/day, 1616.286 timesteps/s +89.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.3702 | 12.796 | 16.045 | 84.3 | 41.36 +Neigh | 0.43499 | 0.55158 | 0.64861 | 12.8 | 1.78 +Comm | 10.183 | 13.476 | 16.961 | 83.7 | 43.56 +Output | 0.088474 | 0.088715 | 0.089272 | 0.1 | 0.29 +Modify | 3.0446 | 3.1809 | 3.3227 | 7.4 | 10.28 +Other | | 0.8418 | | | 2.72 + +Nlocal: 822.500 ave 859 max 785 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 3049.75 ave 3089 max 2999 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 13440.5 ave 14459 max 11964 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 53762 +Ave neighs/atom = 16.341033 +Neighbor list builds = 348 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:30 diff --git a/src/comm.cpp b/src/comm.cpp index 84e3b9ad65..542ddfdf10 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -248,6 +248,8 @@ void Comm::init() error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); if (neighbor->any_full()) error->all(FLERR,"Cannot use multi/reduce communication with a full neighbor list"); + if (neighbor->style != Neighbor::MULTI) + error->all(FLERR,"Cannot use multi/reduce communication without multi-style neighbor lists"); } } From a25c77e512762a6eee146e20baa477143b83ef6f Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 12 Jan 2021 23:04:14 -0700 Subject: [PATCH 0069/1217] Misc comments, typos, and cleanups --- doc/src/comm_modify.rst | 8 +- doc/src/neigh_modify.rst | 12 +- examples/multi/in.granular | 2 +- src/USER-OMP/npair_half_multi_newton_omp.cpp | 125 ++++++----------- .../npair_half_size_multi_newton_omp.cpp | 100 +++++-------- src/comm.cpp | 1 - src/comm_brick.cpp | 132 +++++++----------- src/comm_tiled.cpp | 16 +-- src/nbin_multi.cpp | 69 ++++----- src/nbin_multi.h | 4 - src/neighbor.cpp | 21 +-- src/npair.cpp | 10 +- src/npair.h | 2 +- src/npair_half_multi_newton.cpp | 123 ++++++---------- src/npair_half_size_multi_newton.cpp | 100 +++++-------- src/npair_half_size_multi_newton_tri.cpp | 1 - src/nstencil.cpp | 29 ++-- src/nstencil.h | 6 +- 18 files changed, 285 insertions(+), 476 deletions(-) diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 5f084561a1..a3f7dba4eb 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -11,7 +11,7 @@ Syntax comm_modify keyword value ... * zero or more keyword/value pairs may be appended -* keyword = *mode* or *cutoff* or *cutoff/multi* or *cutoff/bytype* or *group* or *vel* +* keyword = *mode* or *cutoff* or *cutoff/multi* or *multi/reduce* or *group* or *vel* .. parsed-literal:: @@ -20,7 +20,7 @@ Syntax *cutoff/multi* type value type = atom type or type range (supports asterisk notation) value = Rcut (distance units) = communicate atoms for selected types from this far away - *cutoff/byptype* arg = none = communicate atoms for each type by a distance equal to the largest interaction distance for that type + *multi/reduce* arg = none = reduce number of communicated ghost atoms for multi style *group* value = group-ID = only communicate atoms in the group *vel* value = *yes* or *no* = do or do not communicate velocity info with ghost atoms @@ -96,10 +96,10 @@ using the usual asterisk notation can be given. For granular pair styles, the default cutoff is set to the sum of the current maximum atomic radii for each type. -The *multi/reduce* option applies to *multi* and automatically sets communication +The *multi/reduce* option applies to *multi* and sets communication cutoffs for different sized particles based on the largest interaction distance between two particles in the same multi grouping. This reduces the number of -ghost that need to be communicated This method is only compatible with the +ghost atoms that need to be communicated. This method is only compatible with the *multi* neighbor style and requires only half neighbor lists and Newton on. See the :doc:`neighbor multi ` command for more information. diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index 33f24af96e..c6f573ef08 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -47,9 +47,9 @@ Syntax N = max number of neighbors of one atom *binsize* value = size size = bin size for neighbor list construction (distance units) - *multi/custom* values = N types + *multi/custom* values = N arg1 ... argN N = number of custom groups - types = N separate types or groups of types (see below) + arg = N separate types or ranges of types (see below) Examples """""""" @@ -208,12 +208,12 @@ overhead. You must first specify the number of custom groups N to be defined followed by N ranges of types. The range can be specified as a single numeric value, or a wildcard asterisk can be used to specify a range of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For -example, if N = the number of atom types, then an asterisk with no numeric -values means all types from 1 to N. A leading asterisk means all types -from 1 to n (inclusive). A trailing asterisk means all types from n to N +example, if M = the number of atom types, then an asterisk with no numeric +values means all types from 1 to M. A leading asterisk means all types +from 1 to n (inclusive). A trailing asterisk means all types from n to M (inclusive). A middle asterisk means all types from m to n (inclusive). Note that any atom types not included in a custom group will be automatically -placed within a new, separate group. +placed within a separate group. Restrictions """""""""""" diff --git a/examples/multi/in.granular b/examples/multi/in.granular index 00dd4ad2bb..8f1743f90d 100644 --- a/examples/multi/in.granular +++ b/examples/multi/in.granular @@ -1,4 +1,4 @@ -# Big colloid particles and small LJ particles +# Bidisperse set of grains units lj atom_style sphere diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index a7a3e6d6f7..11a84a3040 100755 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -100,96 +100,55 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) if(igroup == jgroup) jbin = ibin; else jbin = coord2bin(x[i], jgroup); + // if same size: uses half stencil so check central bin if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ - // if same size: use half stencil - if(igroup == jgroup){ - - // if same group, implement with: - // loop over rest of atoms in i's bin, ghosts are at end of linked list - // if j is owned atom, store it, since j is beyond i in linked list - // if j is ghost, only store if j coords are "above and to the right" of i - - js = bins[i]; + if(igroup == jgroup) js = bins[i]; + else js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins[j]) { - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } - } - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } - } else { - - // if different groups, implement with: - // loop over all atoms in jgroup bin - // if j is owned atom, store it if j > i - // if j is ghost, only store if j coords are "above and to the right" of i + // if same group, + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi[jgroup][jbin]; + // if different groups, + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - for (j = js; j >= 0; j = bins[j]) { - if(j < i) continue; + for (j = js; j >= 0; j = bins[j]) { + if(igroup != jgroup and j < i) continue; - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; } - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } - } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } } // for all groups, loop over all atoms in other bins in stencil, store every pair diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp index 0137873600..cec3edd02b 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -89,80 +89,46 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) if(igroup == jgroup) jbin = ibin; else jbin = coord2bin(x[i], jgroup); + // if same size: uses half stencil so check central bin if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ - - // if same size: use half stencil - if(igroup == jgroup){ - - // if same group, implement with: - // loop over rest of atoms in i's bin, ghosts are at end of linked list - // if j is owned atom, store it, since j is beyond i in linked list - // if j is ghost, only store if j coords are "above and to the right" of i - - js = bins[i]; - - for (j = js; j >= 0; j = bins[j]) { - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } - } - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); + if(igroup == jgroup) js = bins[i]; + else js = binhead_multi[jgroup][jbin]; + + // if same group, + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + // if different groups, + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + for (j = js; j >= 0; j = bins[j]) { + if(igroup != jgroup and j < i) continue; + + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; } } - } else { - - // if different groups, implement with: - // loop over all atoms in jgroup bin - // if j is owned atom, store it if j > i - // if j is ghost, only store if j coords are "above and to the right" of i + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - js = binhead_multi[jgroup][jbin]; + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); - for (j = js; j >= 0; j = bins[j]) { - if(j < i) continue; - - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } - } - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; } } } diff --git a/src/comm.cpp b/src/comm.cpp index 542ddfdf10..867eab6256 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -242,7 +242,6 @@ void Comm::init() for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; - // Can't used multi/reduce communication with Newton off or full neighbor lits if(multi_reduce){ if (force->newton == 0) error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 74865476f5..939669fb75 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -167,54 +167,55 @@ void CommBrick::setup() error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms " "will be generated. Atoms may get lost."); + + if (mode == Comm::MULTI) { + if (multi_reduce) { + // If using multi/reduce, communicate itype particles a distance equal + // to the max of itype-jtype group interaction + // only consider smaller jtype groups + int igroup, jgroup; + double **cutmultisq = neighbor->cutmultisq; + int *map_type_multi = neighbor->map_type_multi; + for (i = 1; i <= ntypes; i++) { + + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; + } + + igroup = map_type_multi[i]; + for (j = 1; j <= ntypes; j++){ + jgroup = map_type_multi[j]; + + if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); + } + } + } else { + // otherwise, communicate a distance equal to the maximum interaction distance for each type + double *cuttype = neighbor->cuttype; + for (i = 1; i <= ntypes; i++) { + double tmp = 0.0; + if (cutusermulti) tmp = cutusermulti[i]; + cutghostmulti[i][0] = MAX(tmp,cuttype[i]); + cutghostmulti[i][1] = MAX(tmp,cuttype[i]); + cutghostmulti[i][2] = MAX(tmp,cuttype[i]); + } + } + } + if (triclinic == 0) { prd = domain->prd; sublo = domain->sublo; subhi = domain->subhi; cutghost[0] = cutghost[1] = cutghost[2] = cut; - - if (mode == Comm::MULTI) { - if (multi_reduce) { - // If using multi/reduce, communicate itype particles a distance equal - // to the max of itype-jtype group interaction given smaller jtype group - int igroup, jgroup; - double **cutmultisq = neighbor->cutmultisq; - int *map_type_multi = neighbor->map_type_multi; - for (i = 1; i <= ntypes; i++) { - - if (cutusermulti) { - cutghostmulti[i][0] = cutusermulti[i]; - cutghostmulti[i][1] = cutusermulti[i]; - cutghostmulti[i][2] = cutusermulti[i]; - } else { - cutghostmulti[i][0] = 0.0; - cutghostmulti[i][1] = 0.0; - cutghostmulti[i][2] = 0.0; - } - - igroup = map_type_multi[i]; - for (j = 1; j <= ntypes; j++){ - jgroup = map_type_multi[j]; - - if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); - } - } - } else { - // If using a single binlist, use the max itype-jtype interaction distance for communication - double *cuttype = neighbor->cuttype; - for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = MAX(cut,cuttype[i]); - cutghostmulti[i][1] = MAX(cut,cuttype[i]); - cutghostmulti[i][2] = MAX(cut,cuttype[i]); - } - } - } - } else { prd = domain->prd_lamda; sublo = domain->sublo_lamda; @@ -227,46 +228,11 @@ void CommBrick::setup() cutghost[1] = cut * length1; length2 = h_inv[2]; cutghost[2] = cut * length2; - - if (mode == Comm::MULTI) { - if (multi_reduce) { - // If using multi/reduce, communicate itype particles a distance equal - // to the max of itype-jtype group interaction given smaller jtype group - int igroup, jgroup; - double **cutmultisq = neighbor->cutmultisq; - int *map_type_multi = neighbor->map_type_multi; - for (i = 1; i <= ntypes; i++) { - - if (cutusermulti) { - cutghostmulti[i][0] = cutusermulti[i]; - cutghostmulti[i][1] = cutusermulti[i]; - cutghostmulti[i][2] = cutusermulti[i]; - } else { - cutghostmulti[i][0] = 0.0; - cutghostmulti[i][1] = 0.0; - cutghostmulti[i][2] = 0.0; - } - - igroup = map_type_multi[i]; - for (j = 1; j <= ntypes; j++){ - jgroup = map_type_multi[j]; - - if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; - cutghostmulti[i][0] = length0 * MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][1] = length1 * MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][2] = length2 * MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); - } - } - } else { - // If using a single binlist, use the max itype-jtype interaction distance for communication - double *cuttype = neighbor->cuttype; - for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = length0 * MAX(cut,cuttype[i]); - cutghostmulti[i][1] = length1 * MAX(cut,cuttype[i]); - cutghostmulti[i][2] = length2 * MAX(cut,cuttype[i]); - } + if (mode == Comm::MULTI){ + for (i = 1; i <= ntypes; i++) { + cutghostmulti[i][0] *= length0; + cutghostmulti[i][1] *= length1; + cutghostmulti[i][2] *= length2; } } } diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 64d1207a64..06edbf7416 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -175,10 +175,10 @@ void CommTiled::setup() // check that cutoff < any periodic box length if (mode == Comm::MULTI) { - double cut; if (multi_reduce) { // If using multi/reduce, communicate itype particles a distance equal - // to the max of itype-jtype group interaction given smaller jtype group + // to the max of itype-jtype group interaction + // only consider smaller jtype groups int igroup, jgroup; double **cutmultisq = neighbor->cutmultisq; int *map_type_multi = neighbor->map_type_multi; @@ -205,14 +205,14 @@ void CommTiled::setup() } } } else { - // If using a single binlist, use the max itype-jtype interaction distance for communication + // otherwise, communicate a distance equal to the maximum interaction distance for each type double *cuttype = neighbor->cuttype; for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = MAX(cut,cuttype[i]); - cutghostmulti[i][1] = MAX(cut,cuttype[i]); - cutghostmulti[i][2] = MAX(cut,cuttype[i]); + double tmp = 0.0; + if (cutusermulti) tmp = cutusermulti[i]; + cutghostmulti[i][0] = MAX(tmp,cuttype[i]); + cutghostmulti[i][1] = MAX(tmp,cuttype[i]); + cutghostmulti[i][2] = MAX(tmp,cuttype[i]); } } } diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index b8832bdfea..04756ff803 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -59,41 +59,41 @@ void NBinMulti::bin_atoms_setup(int nall) } } -/* --------------------------------------------------------------------- - Identify index of group with smallest cutoff ------------------------------------------------------------------------- */ - -int NBinMulti::igroup_min() -{ - int imin = 0; - for (int n = 0; n < maxgroups; n++) - if (cutmultisq[n][n] < cutmultisq[imin][imin]) imin = n; - - return imin; -} - /* ---------------------------------------------------------------------- setup neighbor binning geometry - ---------------------------------------------------------------------- */ + bin numbering in each dimension is global: + 0 = 0.0 to binsize, 1 = binsize to 2*binsize, etc + nbin-1,nbin,etc = bbox-binsize to bbox, bbox to bbox+binsize, etc + -1,-2,etc = -binsize to 0.0, -2*binsize to -binsize, etc + code will work for any binsize + since next(xyz) and stencil extend as far as necessary + binsize = 1/2 of cutoff is roughly optimal + for orthogonal boxes: + a dim must be filled exactly by integer # of bins + in periodic, procs on both sides of PBC must see same bin boundary + in non-periodic, coord2bin() still assumes this by use of nbin xyz + for triclinic boxes: + tilted simulation box cannot contain integer # of bins + stencil & neigh list built differently to account for this + mbinlo_multi = lowest global bin any of my ghost atoms could fall into for each grouping + mbinhi_multi = highest global bin any of my ghost atoms could fall into for each grouping + mbin_multi = number of bins I need in a dimension for each grouping +------------------------------------------------------------------------- */ void NBinMulti::setup_bins(int style) { int n; - int igroupmin; // Initialize arrays - if (n_multi_groups > maxgroups) { - // Clear any/all memory for existing types - + // Clear any/all memory for existing groupings for (n = 0; n < maxgroups; n++) memory->destroy(binhead_multi[n]); delete [] binhead_multi; - // Realloacte at updated maxtypes - + // Realloacte at updated maxgroups maxgroups = n_multi_groups; binhead_multi = new int*[maxgroups](); @@ -138,14 +138,18 @@ void NBinMulti::setup_bins(int style) memory->destroy(maxbins_multi); memory->create(maxbins_multi, maxgroups, "neigh:maxbins_multi"); - // make sure reallocation occurs in bin_atoms_setup() + // ensure reallocation occurs in bin_atoms_setup() for (n = 0; n < maxgroups; n++) { maxbins_multi[n] = 0; } maxatom = 0; } - igroupmin = igroup_min(); + // Identify smallest group + int igroupmin = 0; + for (n = 0; n < maxgroups; n++) + if (cutmultisq[n][n] < cutmultisq[igroupmin][igroupmin]) + igroupmin = n; // bbox = size of bbox of entire domain // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost @@ -182,16 +186,18 @@ void NBinMulti::setup_bins(int style) // For each grouping... + double binsize_optimal, binsizeinv, coord; + int mbinxhi,mbinyhi,mbinzhi; + for (n = 0; n < maxgroups; n++) { - // binsize_user only relates to smallest type - // optimal bin size is roughly 1/2 the type-type cutoff + // binsize_user only relates to smallest group + // optimal bin size is roughly 1/2 the group-group cutoff // special case of all cutoffs = 0.0, binsize = box size - double binsize_optimal; if (n == igroupmin && binsizeflag) binsize_optimal = binsize_user; else binsize_optimal = 0.5*sqrt(cutmultisq[n][n]); if (binsize_optimal == 0.0) binsize_optimal = bbox[0]; - double binsizeinv = 1.0/binsize_optimal; + binsizeinv = 1.0/binsize_optimal; // test for too many global bins in any dimension due to huge global domain @@ -216,7 +222,7 @@ void NBinMulti::setup_bins(int style) // error if actual bin size << cutoff, since will create a zillion bins // this happens when nbin = 1 and box size << cutoff // typically due to non-periodic, flat system in a particular dim - // in that extreme case, should use NSQ not BIN neighbor style + // in that extreme case, cannot use multi, should use NSQ not BIN neighbor style binsizex_multi[n] = bbox[0]/nbinx_multi[n]; binsizey_multi[n] = bbox[1]/nbiny_multi[n]; @@ -236,9 +242,6 @@ void NBinMulti::setup_bins(int style) // static_cast(-1.5) = -1, so subract additional -1 // add in SMALL for round-off safety - int mbinxhi,mbinyhi,mbinzhi; - double coord; - coord = bsubboxlo[0] - SMALL*bbox[0]; mbinxlo_multi[n] = static_cast ((coord-bboxlo[0])*bininvx_multi[n]); if (coord < bboxlo[0]) mbinxlo_multi[n] = mbinxlo_multi[n] - 1; @@ -340,10 +343,8 @@ void NBinMulti::bin_atoms() double NBinMulti::memory_usage() { double bytes = 0; - - for (int m = 0; m < maxgroups; m++) { + for (int m = 0; m < maxgroups; m++) bytes += maxbins_multi[m]*sizeof(int); - bytes += 2*maxatom*sizeof(int); - } + bytes += 2*maxatom*sizeof(int); return bytes; } diff --git a/src/nbin_multi.h b/src/nbin_multi.h index 84ec0348bc..490af10dbb 100644 --- a/src/nbin_multi.h +++ b/src/nbin_multi.h @@ -35,10 +35,6 @@ class NBinMulti : public NBin { void setup_bins(int); void bin_atoms(); double memory_usage(); - - private: - - int igroup_min(); }; } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 94add1f324..5c8d8ec594 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -83,6 +83,11 @@ static const char cite_neigh_multi[] = " volume = 179,\n" " pages = {320--329}\n" "}\n\n" + "@article{Stratford2018,\n" + " author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin},\n" + " title = {Implementation of multi-level contact detection in LAMMPS},\n" + " year = {2018}\n" + "}\n\n" "@article{Shire2020,\n" " author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},\n" " title = {DEM simulations of polydisperse media: efficient contact\n" @@ -348,7 +353,8 @@ void Neighbor::init() // multi cutoffs if(style == Neighbor::MULTI){ int igroup, jgroup; - // If not defined, create default mapping + + // If not defined from custom grouping, create default map if(not map_type_multi) { n_multi_groups = n; memory->create(map_type_multi,n+1,"neigh:map_type_multi"); @@ -1678,12 +1684,11 @@ int Neighbor::choose_bin(NeighRequest *rq) if (!rq->kokkos_device != !(mask & NB_KOKKOS_DEVICE)) continue; if (!rq->kokkos_host != !(mask & NB_KOKKOS_HOST)) continue; - // neighbor style is BIN or MULTI or MULTI_OLD and must match - - if (style == Neighbor::BIN || style == Neighbor::MULTI_OLD) { - if (!(mask & NB_STANDARD)) continue; - } else if (style == Neighbor::MULTI) { + // multi neighbor style require multi bin style + if (style == Neighbor::MULTI) { if (!(mask & NB_MULTI)) continue; + } else { + if (!(mask & NB_STANDARD)) continue; } return i+1; @@ -1719,7 +1724,6 @@ int Neighbor::choose_stencil(NeighRequest *rq) else if (rq->newton == 2) newtflag = 0; // request a full stencil if building full neighbor list or newton is off - int fullflag = 0; if (rq->full) fullflag = 1; if (!newtflag) fullflag = 1; @@ -1972,7 +1976,6 @@ NPair *Neighbor::pair_creator(LAMMPS *lmp) /* ---------------------------------------------------------------------- setup neighbor binning and neighbor stencils called before run and every reneighbor if box size/shape changes - initialize default settings for multi before run only operates on perpetual lists build_one() operates on occasional lists ------------------------------------------------------------------------- */ @@ -2458,7 +2461,7 @@ void Neighbor::modify_params(int narg, char **arg) n_multi_groups += 1; } - // Create seprate group for each undefined atom type + // Create separate group for each undefined atom type for(i = 1; i <= ntypes; i++){ if(map_type_multi[i] == -1){ map_type_multi[i] = n_multi_groups; diff --git a/src/npair.cpp b/src/npair.cpp index facd9086d1..95a61fbefa 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -304,9 +304,9 @@ int NPair::coord2bin(double *x, int ig) } else iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]) - 1; - - ibin = (iz-mbinzlo_multi[ig])*mbiny_multi[ig]*mbinx_multi[ig] - + (iy-mbinylo_multi[ig])*mbinx_multi[ig] - + (ix-mbinxlo_multi[ig]); + ix -= mbinxlo_multi[ig]; + iy -= mbinylo_multi[ig]; + iz -= mbinzlo_multi[ig]; + ibin = iz*mbiny_multi[ig]*mbinx_multi[ig] + iy*mbinx_multi[ig] + ix; return ibin; -} \ No newline at end of file +} diff --git a/src/npair.h b/src/npair.h index d1fcf2e6b2..c857ec0924 100644 --- a/src/npair.h +++ b/src/npair.h @@ -115,7 +115,7 @@ class NPair : protected Pointers { int coord2bin(double *); // mapping atom coord to a bin int coord2bin(double *, int &, int &, int&); // ditto - int coord2bin(double *, int); // mapping atom coord to type bin + int coord2bin(double *, int); // mapping atom coord to group bin // find_special: determine if atom j is in special list of atom i diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index 777aab5826..aa8f606242 100755 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -88,96 +88,55 @@ void NPairHalfMultiNewton::build(NeighList *list) if(igroup == jgroup) jbin = ibin; else jbin = coord2bin(x[i], jgroup); + // if same size: uses half stencil so check central bin if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ - // if same size: use half stencil - if(igroup == jgroup){ - - // if same group, implement with: - // loop over rest of atoms in i's bin, ghosts are at end of linked list - // if j is owned atom, store it, since j is beyond i in linked list - // if j is ghost, only store if j coords are "above and to the right" of i - - js = bins[i]; + if(igroup == jgroup) js = bins[i]; + else js = binhead_multi[jgroup][jbin]; - for (j = js; j >= 0; j = bins[j]) { - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } - } - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } - } else { - - // if different groups, implement with: - // loop over all atoms in jgroup bin - // if j is owned atom, store it if j > i - // if j is ghost, only store if j coords are "above and to the right" of i + // if same group, + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i - js = binhead_multi[jgroup][jbin]; + // if different groups, + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - for (j = js; j >= 0; j = bins[j]) { - if(j < i) continue; + for (j = js; j >= 0; j = bins[j]) { + if(igroup != jgroup and j < i) continue; - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; } - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + } - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } - } + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } } // for all groups, loop over all atoms in other bins in stencil, store every pair diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index 500e06bc35..84571a3b02 100755 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -77,80 +77,46 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) if(igroup == jgroup) jbin = ibin; else jbin = coord2bin(x[i], jgroup); + // if same size: uses half stencil so check central bin if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ - - // if same size: use half stencil - if(igroup == jgroup){ - - // if same group, implement with: - // loop over rest of atoms in i's bin, ghosts are at end of linked list - // if j is owned atom, store it, since j is beyond i in linked list - // if j is ghost, only store if j coords are "above and to the right" of i - - js = bins[i]; - - for (j = js; j >= 0; j = bins[j]) { - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } - } - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); + if(igroup == jgroup) js = bins[i]; + else js = binhead_multi[jgroup][jbin]; + + // if same group, + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + // if different groups, + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + for (j = js; j >= 0; j = bins[j]) { + if(igroup != jgroup and j < i) continue; + + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; } } - } else { - - // if different groups, implement with: - // loop over all atoms in jgroup bin - // if j is owned atom, store it if j > i - // if j is ghost, only store if j coords are "above and to the right" of i + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - js = binhead_multi[jgroup][jbin]; + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); - for (j = js; j >= 0; j = bins[j]) { - if(j < i) continue; - - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } - } - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; } } } diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 0000f7b4d3..2000927c63 100755 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -77,7 +77,6 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) if(igroup == jgroup) jbin = ibin; else jbin = coord2bin(x[i], jgroup); - // loop over all atoms in bins in stencil // stencil is empty if i larger than j // stencil is half if i same size as j diff --git a/src/nstencil.cpp b/src/nstencil.cpp index acd7272245..3d86b57b9e 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -55,7 +55,7 @@ using namespace LAMMPS_NS; create one stencil for each igroup-jgroup pairing the full/half stencil label refers to the same-group stencil a half list with newton on has a half same-group stencil - a full list or half list with newton of has a full same-group stencil + a full list or half list with newton off has a full same-group stencil cross group stencils are always full to allow small-to-large lookups for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin for triclinic, a half stencil includes bins in the z (3D) or y (2D) plane of self and above @@ -76,7 +76,7 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) distsq_multi_old = nullptr; nstencil_multi = nullptr; - stencil_multi = nullptr; + stencil_multi = nullptr; maxstencil_multi = nullptr; flag_half_multi = nullptr; @@ -230,7 +230,7 @@ void NStencil::create_setup() int smax = (2*sx+1) * (2*sy+1) * (2*sz+1); // reallocate stencil structs if necessary - // for BIN and MULTI styles + // for BIN and MULTI_OLD styles if (neighstyle == Neighbor::BIN) { if (smax > maxstencil) { @@ -315,9 +315,8 @@ void NStencil::create_setup() set_stencil_properties(); // Allocate arrays to store stencils - if (!maxstencil_multi) { - memory->create(maxstencil_multi, n, n, "neighstencil::stencil_multi"); + memory->create(maxstencil_multi, n, n, "neighstencil::maxstencil_multi"); memory->create(nstencil_multi, n, n, "neighstencil::nstencil_multi"); stencil_multi = new int**[n](); for (i = 0; i < n; ++i) { @@ -325,6 +324,7 @@ void NStencil::create_setup() for (j = 0; j < n; ++j) { maxstencil_multi[i][j] = 0; nstencil_multi[i][j] = 0; + stencil_multi[i][j] = nullptr; } } } @@ -400,21 +400,21 @@ double NStencil::bin_distance(int i, int j, int k) compute closest distance for a given atom grouping ------------------------------------------------------------------------- */ -double NStencil::bin_distance_multi(int i, int j, int k, int group) +double NStencil::bin_distance_multi(int i, int j, int k, int ig) { double delx,dely,delz; - if (i > 0) delx = (i-1)*binsizex_multi[group]; + if (i > 0) delx = (i-1)*binsizex_multi[ig]; else if (i == 0) delx = 0.0; - else delx = (i+1)*binsizex_multi[group]; + else delx = (i+1)*binsizex_multi[ig]; - if (j > 0) dely = (j-1)*binsizey_multi[group]; + if (j > 0) dely = (j-1)*binsizey_multi[ig]; else if (j == 0) dely = 0.0; - else dely = (j+1)*binsizey_multi[group]; + else dely = (j+1)*binsizey_multi[ig]; - if (k > 0) delz = (k-1)*binsizez_multi[group]; + if (k > 0) delz = (k-1)*binsizez_multi[ig]; else if (k == 0) delz = 0.0; - else delz = (k+1)*binsizez_multi[group]; + else delz = (k+1)*binsizez_multi[ig]; return (delx*delx + dely*dely + delz*delz); } @@ -435,13 +435,8 @@ double NStencil::memory_usage() for (int i = 0; i < n; i++) { for (int j = 0; j < n; j++) { bytes += maxstencil_multi[i][j] * sizeof(int); - bytes += maxstencil_multi[i][j] * sizeof(int); - bytes += maxstencil_multi[i][j] * sizeof(double); } } - bytes += 2 * n * n * sizeof(bool); - bytes += 6 * n * n * sizeof(int); - bytes += 4 * n * n * sizeof(double); } return bytes; } diff --git a/src/nstencil.h b/src/nstencil.h index b06f340d6f..b38276b45f 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -30,7 +30,7 @@ class NStencil : protected Pointers { int *nstencil_multi_old; // # bins in each type-based old multi stencil int **stencil_multi_old; // list of bin offsets in each stencil double **distsq_multi_old; // sq distances to bins in each stencil - int ** nstencil_multi; // # bins bins in each itype-jtype multi stencil + int ** nstencil_multi; // # bins bins in each igroup-jgroup multi stencil int *** stencil_multi; // list of bin offsets in each multi stencil int ** maxstencil_multi; // max stencil size for each multi stencil @@ -42,8 +42,8 @@ class NStencil : protected Pointers { double cutoff_custom; // cutoff set by requestor // Arrays to store options for multi itype-jtype stencils - bool **flag_half_multi; // flag creation of a half stencil for itype-jtype - bool **flag_skip_multi; // skip creation of itype-jtype stencils (for newton on) + bool **flag_half_multi; // flag creation of a half stencil for igroup-jgroup + bool **flag_skip_multi; // skip creation of igroup-jgroup stencils (for newton on) int **bin_group_multi; // what group to use for bin information NStencil(class LAMMPS *); From 3e639fe97957a9398642d63a56389f54824bd8c9 Mon Sep 17 00:00:00 2001 From: kipbarrett Date: Mon, 25 Jan 2021 16:41:35 -0600 Subject: [PATCH 0070/1217] Initial inclusion of rann potential --- src/activation.cpp | 44 + src/activation.h | 39 + src/activation_linear.cpp | 42 + src/activation_linear.h | 42 + src/activation_sigI.cpp | 41 + src/activation_sigI.h | 42 + src/fingerprint.cpp | 106 ++ src/fingerprint.h | 58 + src/fingerprint_bond.cpp | 912 +++++++++ src/fingerprint_bond.h | 67 + src/fingerprint_bondscreened.cpp | 946 +++++++++ src/fingerprint_bondscreened.h | 67 + src/fingerprint_bondscreenedspin.cpp | 1019 ++++++++++ src/fingerprint_bondscreenedspin.h | 67 + src/fingerprint_bondspin.cpp | 1015 ++++++++++ src/fingerprint_bondspin.h | 67 + src/fingerprint_radial.cpp | 253 +++ src/fingerprint_radial.h | 56 + src/fingerprint_radialscreened.cpp | 266 +++ src/fingerprint_radialscreened.h | 59 + src/fingerprint_radialscreenedspin.cpp | 279 +++ src/fingerprint_radialscreenedspin.h | 59 + src/fingerprint_radialspin.cpp | 265 +++ src/fingerprint_radialspin.h | 56 + src/pair_rann.cpp | 2423 ++++++++++++++++++++++++ src/pair_rann.h | 153 ++ src/style_activation.h | 2 + src/style_fingerprint.h | 8 + 28 files changed, 8453 insertions(+) create mode 100644 src/activation.cpp create mode 100644 src/activation.h create mode 100644 src/activation_linear.cpp create mode 100644 src/activation_linear.h create mode 100644 src/activation_sigI.cpp create mode 100644 src/activation_sigI.h create mode 100644 src/fingerprint.cpp create mode 100644 src/fingerprint.h create mode 100644 src/fingerprint_bond.cpp create mode 100644 src/fingerprint_bond.h create mode 100644 src/fingerprint_bondscreened.cpp create mode 100644 src/fingerprint_bondscreened.h create mode 100644 src/fingerprint_bondscreenedspin.cpp create mode 100644 src/fingerprint_bondscreenedspin.h create mode 100644 src/fingerprint_bondspin.cpp create mode 100644 src/fingerprint_bondspin.h create mode 100644 src/fingerprint_radial.cpp create mode 100644 src/fingerprint_radial.h create mode 100644 src/fingerprint_radialscreened.cpp create mode 100644 src/fingerprint_radialscreened.h create mode 100644 src/fingerprint_radialscreenedspin.cpp create mode 100644 src/fingerprint_radialscreenedspin.h create mode 100644 src/fingerprint_radialspin.cpp create mode 100644 src/fingerprint_radialspin.h create mode 100644 src/pair_rann.cpp create mode 100644 src/pair_rann.h create mode 100644 src/style_activation.h create mode 100644 src/style_fingerprint.h diff --git a/src/activation.cpp b/src/activation.cpp new file mode 100644 index 0000000000..aaa409c4b0 --- /dev/null +++ b/src/activation.cpp @@ -0,0 +1,44 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + ----------------------------------------------------------------------*/ + + +#include "activation.h" + + +using namespace LAMMPS_NS; + +Activation::Activation(PairRANN *pair) { + empty = true; + style = "empty"; +} + +Activation::~Activation(){ + +} + +//default is linear activation (no change). +double Activation::activation_function(double A){ + return A; +} + +double Activation::dactivation_function(double A){ + return 1.0; +} + +double Activation::ddactivation_function(double A){ + return 0.0; +} diff --git a/src/activation.h b/src/activation.h new file mode 100644 index 0000000000..3fba49723d --- /dev/null +++ b/src/activation.h @@ -0,0 +1,39 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + ----------------------------------------------------------------------*/ + +#ifndef ACTIVATION_H_ +#define ACTIVATION_H_ + +#include "pair_rann.h" + +namespace LAMMPS_NS { + + class Activation { + public: + Activation(class PairRANN *); + virtual ~Activation(); + virtual double activation_function(double); + virtual double dactivation_function(double); + virtual double ddactivation_function(double); + bool empty; + const char *style; + }; +} + + + +#endif /* ACTIVATION_H_ */ diff --git a/src/activation_linear.cpp b/src/activation_linear.cpp new file mode 100644 index 0000000000..2ad9594be1 --- /dev/null +++ b/src/activation_linear.cpp @@ -0,0 +1,42 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + ----------------------------------------------------------------------*/ + +#include +#include "activation_linear.h" +#include "activation.h" + + +using namespace LAMMPS_NS; + +Activation_linear::Activation_linear(PairRANN *pair) : Activation(pair){ + empty = false; + style = "linear"; +} + +double Activation_linear::activation_function(double A) +{ + return A; +} + +double Activation_linear::dactivation_function(double A) +{ + return 1.0; +} + +double Activation_linear::ddactivation_function(double){ + return 0.0; +} diff --git a/src/activation_linear.h b/src/activation_linear.h new file mode 100644 index 0000000000..ba39436f03 --- /dev/null +++ b/src/activation_linear.h @@ -0,0 +1,42 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu +*/ + +#ifdef ACTIVATION_CLASS + +ActivationStyle(linear,Activation_linear) + +#else + +#ifndef ACTIVATION_LINEAR_H_ +#define ACTIVATION_LINEAR_H_ + +#include "activation.h" + +namespace LAMMPS_NS { + +class Activation_linear : public Activation { +public: + Activation_linear(class PairRANN *); + double activation_function(double); + double dactivation_function(double); + double ddactivation_function(double); +}; + +} + +#endif +#endif /* ACTIVATION_LINEAR_H_ */ diff --git a/src/activation_sigI.cpp b/src/activation_sigI.cpp new file mode 100644 index 0000000000..cdf82982da --- /dev/null +++ b/src/activation_sigI.cpp @@ -0,0 +1,41 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + ----------------------------------------------------------------------*/ + +#include +#include "activation_sigI.h" + +using namespace LAMMPS_NS; + +Activation_sigI::Activation_sigI(PairRANN *pair) : Activation(pair){ + empty = false; + style = "sigI"; +} + +double Activation_sigI::activation_function(double in){ + if (in>34)return in; + return 0.1*in + 0.9*log(exp(in) + 1); +} + +double Activation_sigI::dactivation_function(double in){ + if (in>34)return 1; + return 0.1 + 0.9/(exp(in)+1)*exp(in); +} + +double Activation_sigI::ddactivation_function(double in){ + if (in>34)return 0; + return 0.9*exp(in)/(exp(in)+1)/(exp(in)+1);; +} diff --git a/src/activation_sigI.h b/src/activation_sigI.h new file mode 100644 index 0000000000..b47433a336 --- /dev/null +++ b/src/activation_sigI.h @@ -0,0 +1,42 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu +*/ + +#ifdef ACTIVATION_CLASS + +ActivationStyle(sigI,Activation_sigI) + +#else + +#ifndef ACTIVATION_SIGI_H_ +#define ACTIVATION_SIGI_H_ + +#include "activation.h" + +namespace LAMMPS_NS { + + class Activation_sigI : public Activation { + public: + Activation_sigI(class PairRANN *); + double activation_function(double); + double dactivation_function(double); + double ddactivation_function(double); + }; +} + + +#endif +#endif /* ACTIVATION_SIGI_H_ */ diff --git a/src/fingerprint.cpp b/src/fingerprint.cpp new file mode 100644 index 0000000000..cdcb5855bd --- /dev/null +++ b/src/fingerprint.cpp @@ -0,0 +1,106 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + ----------------------------------------------------------------------*/ + +#include "fingerprint.h" +#include +#include +#include +#include +#include +#include + + +using namespace LAMMPS_NS; + +Fingerprint::Fingerprint(PairRANN *pair) +{ + spin = false; + screen = false; + empty = true; + fullydefined = false; + n_body_type = 0; + style = "empty"; + this->pair = pair; +} + +Fingerprint::~Fingerprint(){ + +} + +bool Fingerprint::parse_values(char *word,char *line1){ + return false; +} + +void Fingerprint::init(int *i,int id){ + +} + +void Fingerprint::allocate(){ + +} + +void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ + +} + +void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ + +} + +void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz,double *sx, double *sy, double *sz, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ + +} + +void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz,double *sx, double *sy, double *sz, double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ + +} + +void Fingerprint::write_values(FILE *fid){ + +} + +int Fingerprint::get_length(){ + return 0; +} + +//Smooth cutoff, goes from 1 to zero over the interval rc-dr to rc. Same as MEAM uses. Used by generateradialtable and generatexpcuttable. +double Fingerprint::cutofffunction(double r,double rc, double dr){ + double out; + if (r < (rc -dr))out=1; + else if (r>rc)out=0; + else { + out = pow(1-pow(1-(rc-r)/dr,4.0),2.0); + } + return out; +} + +void Fingerprint::generate_rinvssqrttable(){ + int buf = 5; + int m; + double r1; + double cutmax = pair->cutmax; + int res = pair->res; + rinvsqrttable = new double[res+buf]; + for (m=0;m<(res+buf);m++){ + r1 = cutmax*cutmax*(double)(m)/(double)(res); + rinvsqrttable[m] = 1/sqrt(r1); + } +} + + + + diff --git a/src/fingerprint.h b/src/fingerprint.h new file mode 100644 index 0000000000..1bef4c0ab8 --- /dev/null +++ b/src/fingerprint.h @@ -0,0 +1,58 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + ----------------------------------------------------------------------*/ + +#ifndef FINGERPRINT_H_ +#define FINGERPRINT_H_ + +#include "pair_rann.h" + +namespace LAMMPS_NS { + + class Fingerprint { + public: + Fingerprint(PairRANN *); + virtual ~Fingerprint(); + virtual bool parse_values(char*,char*); + virtual void write_values(FILE *); + virtual void init(int*,int); + virtual void allocate(); + void init_screen(int); + virtual void compute_fingerprint(double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*);//no screen,no spin + virtual void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*);//screen + virtual void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*);//spin + virtual void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*);//spin,screen + virtual int get_length(); + virtual double cutofffunction(double,double, double); + virtual void generate_rinvssqrttable(); + bool spin; + bool screen; + int n_body_type;//i-j vs. i-j-k vs. i-j-k-l, etc. + bool empty; + bool fullydefined; + int startingneuron; + int id;//based on ordering of fingerprints listed for i-j in potential file + const char *style; + int* atomtypes; + double *rinvsqrttable; + double rc; + PairRANN *pair; + }; + +} + + +#endif /* FINGERPRINT_H_ */ diff --git a/src/fingerprint_bond.cpp b/src/fingerprint_bond.cpp new file mode 100644 index 0000000000..7fdece310c --- /dev/null +++ b/src/fingerprint_bond.cpp @@ -0,0 +1,912 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@cavs.msstate.edu + ----------------------------------------------------------------------*/ + + +#include "fingerprint_bond.h" +#include "fingerprint.h" +#include +#include +#include +#include +#include +#include + +using namespace LAMMPS_NS; + +Fingerprint_bond::Fingerprint_bond(PairRANN *pair) : Fingerprint(pair) +{ + n_body_type = 3; + dr = 0; + re = 0; + rc = 0; + alpha_k = new double [1]; + alpha_k[0] = -1; + k = 0; + m = 0; + id = -1; + style = "bond"; + atomtypes = new int [n_body_type]; + empty = true; + pair->allscreen = false; +} + +Fingerprint_bond::~Fingerprint_bond(){ + delete [] alpha_k; + delete [] atomtypes; + delete [] expcuttable; + delete [] dfctable; + for (int i=0;i<(m*(m+1))>>1;i++){ + delete [] coeff[i]; + delete [] coeffx[i]; + delete [] coeffy[i]; + delete [] coeffz[i]; + delete [] Mf[i]; + } + delete [] coeff; + delete [] coeffx; + delete [] coeffy; + delete [] coeffz; + delete [] Mf; + delete [] rinvsqrttable; +} + +bool Fingerprint_bond::parse_values(char * constant, char * line1){ + char **words=new char *[MAXLINE]; + int nwords,l; + nwords=0; + words[nwords++] = strtok(line1,": ,\t\n"); + while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; + nwords -= 1; + if (strcmp(constant,"re")==0){ + re = strtod(words[0],NULL); + } + else if (strcmp(constant,"rc")==0){ + rc = strtod(words[0],NULL); + } + else if (strcmp(constant,"alphak")==0){ + delete [] alpha_k; + alpha_k = new double [nwords]; + for (l=0;lerrorf("Undefined value for bond power"); + delete [] words; + if (re!=0.0 && rc!=0.0 && alpha_k[0]!=-1 && dr!=0.0 && m!=0 && k!=0)return true; + return false; +} + +void Fingerprint_bond::write_values(FILE *fid){ + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alphak:\n",style,id); + for (i=0;ielementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:k:\n",style,id); + fprintf(fid,"%d\n",k); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:m:\n",style,id); + fprintf(fid,"%d\n",m); +} + +void Fingerprint_bond::init(int *i,int id){ + for (int j=0;jk = 0; + alpha_k = new double [1]; + alpha_k[0]=-1; + empty = false; + this->id = id; +} + +//number of neurons defined by this fingerprint +int Fingerprint_bond::get_length(){ + return m*k; +} + +void Fingerprint_bond::allocate(){ + generate_exp_cut_table(); + generate_coefficients(); + generate_rinvssqrttable(); +} + +//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop and do3bodyfeatureset_doubleneighborloop. +void Fingerprint_bond::generate_exp_cut_table(){ + int m,n; + double r1; + int buf = 5; + int res = pair->res; + double cutmax = pair->cutmax; + expcuttable = new double [(res+buf)*(this->k)]; + dfctable = new double [res+buf]; + for (m=0;m<(res+buf);m++){ + r1 = cutmax*cutmax*(double)(m)/(double)(res); + for (n=0;n<(this->k);n++){ + expcuttable[n+m*(this->k)] = exp(-alpha_k[n]/re*sqrt(r1))*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ + dfctable[m]=0; + } + else{ + dfctable[m]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } +} + +//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop. +void Fingerprint_bond::generate_coefficients(){ //calculates multinomial coefficient for each term + int p,mb,mc; + int n,p1,i1; + mb = this->m; + mc=(mb*(mb+1))>>1; + coeff = new int *[mc]; + coeffx = new int *[mc]; + coeffy = new int *[mc]; + coeffz = new int *[mc]; + for (p=0;pm+1]; + for (p=0;pm+1;p++){ + M[p]=0; + } + for (p1=0;p1sims[sid]; + ilist = sim->ilist; + numneigh = sim->numneigh; + i = ilist[ii]; +// jnum = numneigh[i]; + //select the more efficient algorithm for this particular potential and environment. + if (jnum*2>(m+1)*m*20){ + do3bodyfeatureset_singleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,sid,xn,yn,zn,tn,jnum,jl); + } + else{ + do3bodyfeatureset_doubleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,sid,xn,yn,zn,tn,jnum,jl); + + } +} + +//Called by do3bodyfeatureset. Algorithm for high neighbor numbers and small series of bond angle powers +void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ + int i,j,jj,itype,jtype,kk,m,n,mcount,a,a1,a2,ai; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + int count=0; + PairRANN::Simulation *sim = &pair->sims[sid]; +// double **x = sim->x; + int *type = sim->type; + double cutmax = pair->cutmax; + int res = pair->res; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; +// numneigh = sim->numneigh; +// firstneigh = sim->firstneigh; + int nelements=pair->nelements; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; +// xtmp = x[i][0]; +// ytmp = x[i][1]; +// ztmp = x[i][2]; +// jlist = firstneigh[i]; +// jnum = numneigh[i]; + double expr[jnum][this->k+12]; + int p = this->k; + int countmb=((this->m)*(this->m+1))>>1; + // calculate interpolation expr, rinvs and dfc, for each neighbor + for (jj = 0; jj < jnum; jj++) { +// j = jlist[jj]; +// j &= NEIGHMASK; +// jtype = pair->map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype && atomtypes[2] != nelements && atomtypes[2] != jtype){ + expr[jj][0]=0; + continue; + } +// delx = xtmp - x[j][0]; +// dely = ytmp - x[j][1]; +// delz = ztmp - x[j][2]; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc){ + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*this->k]; + double *p1 = &expcuttable[m1*this->k]; + double *p2 = &expcuttable[(m1+1)*this->k]; + double *p3 = &expcuttable[(m1+2)*this->k]; + for (kk=0;kkk;kk++){ + expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); + } + double* q = &dfctable[m1-1]; + double* ri = &rinvsqrttable[m1-1]; + double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + double rinvs = ri[1] + 0.5 * r1*(ri[2] - ri[0] + r1*(2.0*ri[0] - 5.0*ri[1] + 4.0*ri[2] - ri[3] + r1*(3.0*(ri[1] - ri[2]) + ri[3] - ri[0]))); + + expr[jj][p]=delx*rinvs; + expr[jj][p+1]=dely*rinvs; + expr[jj][p+2]=delz*rinvs; + //Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy. + if (expr[jj][p]*expr[jj][p]<0.000000000001){ + expr[jj][p] = 0.000001; + } + if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001){ + expr[jj][p+1] = 0.000001; + } + if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001){ + expr[jj][p+2] = 0.000001; + } + expr[jj][p+3] = -dfc*expr[jj][p]; + expr[jj][p+4] = rinvs/expr[jj][p]; + expr[jj][p+5] = rinvs*expr[jj][p]; + expr[jj][p+6] = -dfc*expr[jj][p+1]; + expr[jj][p+7] = rinvs/expr[jj][p+1]; + expr[jj][p+8] = rinvs*expr[jj][p+1]; + expr[jj][p+9] = -dfc*expr[jj][p+2]; + expr[jj][p+10] = rinvs/expr[jj][p+2]; + expr[jj][p+11] = rinvs*expr[jj][p+2]; + } + + int kb = this->k; + int mb = this->m; + count = startingneuron; + double Bb[mb]; + double dBbx; + double dBby; + double dBbz; +// double dBbx1[mb]; +// double dBby1[mb]; +// double dBbz1[mb]; + double yprod; + for (mcount=0;mcountcoeffx[mcount]; + int *coeffy = this->coeffy[mcount]; + int *coeffz = this->coeffz[mcount]; + int *coeff = this->coeff[mcount]; + a = mb+1; + for (a1=0;a1map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype){ + continue; + } + double yprod = expr[jj][ai]; + double *y4 = &expr[jj][p]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[2] != nelements && atomtypes[2] != jtype){ + continue; + } + double yprod = expr[jj][ai]; + double *y4 = &expr[jj][p]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[2] != nelements && atomtypes[2] != jtype){ + continue; + } + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype){ + continue; + } + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype){ + continue; + } + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2sims[sid]; + double **x = sim->x; + int *type = sim->type; + int nelements = pair->nelements; + int res = pair->res; + double cutmax = pair->cutmax; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; +// numneigh = sim->numneigh; +// firstneigh = sim->firstneigh; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; +// xtmp = x[i][0]; +// ytmp = x[i][1]; +// ztmp = x[i][2]; +// jlist = firstneigh[i]; +// jnum = numneigh[i]; + double expr[jnum][this->k]; + double y[jnum][3]; + double ri[jnum]; + double dfc[jnum]; + int kb = this->k; + int mb = this->m; + double c41[this->k]; + double c51[this->k]; + double c61[this->k]; + double ct[this->k]; + for (jj = 0; jj < jnum; jj++) { +// j = jlist[jj]; +// j &= NEIGHMASK; +// jtype = pair->map[type[j]]; + jtype = tn[jj]; + if (jtypes != nelements && jtypes != jtype && ktypes != nelements && ktypes != jtype){ + expr[jj][0]=0; + continue; + } +// delx = xtmp - x[j][0]; +// dely = ytmp - x[j][1]; +// delz = ztmp - x[j][2]; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc){ + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (!(m1>=1 && m1 <= res))pair->errorf("Neighbor list is invalid.");//usually results from nan somewhere. + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*this->k]; + double *p1 = &expcuttable[m1*this->k]; + double *p2 = &expcuttable[(m1+1)*this->k]; + double *p3 = &expcuttable[(m1+2)*this->k]; + for (kk=0;kkk;kk++){ + expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); + } + double* q = &dfctable[m1-1]; + double* r2 = &rinvsqrttable[m1-1]; + dfc[jj] = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + ri[jj] = r2[1] + 0.5 * r1*(r2[2] - r2[0] + r1*(2.0*r2[0] - 5.0*r2[1] + 4.0*r2[2] - r2[3] + r1*(3.0*(r2[1] - r2[2]) + r2[3] - r2[0]))); + y[jj][0]=delx*ri[jj]; + y[jj][1]=dely*ri[jj]; + y[jj][2]=delz*ri[jj]; + } +// if (i==5){ +// for (jj=0;jjmap[type[j]]; + jtype = tn[jj]; + if (jtypes != nelements && jtypes != jtype){ + continue; + } + for (n = 0;nk;n++){ + ct[n] = 2*alpha_k[n]/re; + c41[n]=(-ct[n]+2*dfc[jj])*y[jj][0]; + c51[n]=(-ct[n]+2*dfc[jj])*y[jj][1]; + c61[n]= (-ct[n]+2*dfc[jj])*y[jj][2]; + } + if (jtypes==ktypes){ + for (kk=jj+1;kk< jnum; kk++){ + if (expr[kk][0]==0)continue; +// int k1 = jlist[kk]; +// k1 &= NEIGHMASK; +// ktype = pair->map[type[k1]]; + ktype = tn[kk]; + if (ktypes != nelements && ktypes != ktype){ + continue; + } + count = startingneuron; + double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); + double c1 = 2*ri[jj]*(y[kk][0]-dot*y[jj][0]); + double c2 = 2*ri[jj]*(y[kk][1]-dot*y[jj][1]); + double c3 = 2*ri[jj]*(y[kk][2]-dot*y[jj][2]); + double c10 = 2*ri[kk]*(y[jj][0]-dot*y[kk][0]); + double c11 = 2*ri[kk]*(y[jj][1]-dot*y[kk][1]); + double c12 = 2*ri[kk]*(y[jj][2]-dot*y[kk][2]); +// double c1 = 2*ri[jj]*y[kk][0]*(1-y[jj][0]*y[jj][0]); +// double c2 = 2*ri[jj]*y[kk][1]*(1-y[jj][1]*y[jj][1]); +// double c3 = 2*ri[jj]*y[kk][2]*(1-y[jj][2]*y[jj][2]); +// double c10 = 2*ri[kk]*y[jj][0]*(1-y[kk][0]*y[kk][0]); +// double c11 = 2*ri[kk]*y[jj][1]*(1-y[kk][1]*y[kk][1]); +// double c12 = 2*ri[kk]*y[jj][2]*(1-y[kk][2]*y[kk][2]); + for (n=0;nmap[type[k1]]; + ktype = tn[kk]; + if (ktypes != nelements && ktypes != ktype){ + continue; + } + count = startingneuron; + double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); + double c1 = ri[jj]*(y[kk][0]-dot*y[jj][0]); + double c2 = ri[jj]*(y[kk][1]-dot*y[jj][1]); + double c3 = ri[jj]*(y[kk][2]-dot*y[jj][2]); + double c10 = ri[kk]*(y[jj][0]-dot*y[kk][0]); + double c11 = ri[kk]*(y[jj][1]-dot*y[kk][1]); + double c12 = ri[kk]*(y[jj][2]-dot*y[kk][2]); +// double c1 = 2*ri[jj]*y[kk][0]*(1-y[jj][0]*y[jj][0]); +// double c2 = 2*ri[jj]*y[kk][1]*(1-y[jj][1]*y[jj][1]); +// double c3 = 2*ri[jj]*y[kk][2]*(1-y[jj][2]*y[jj][2]); +// double c10 = 2*ri[kk]*y[jj][0]*(1-y[kk][0]*y[kk][0]); +// double c11 = 2*ri[kk]*y[jj][1]*(1-y[kk][1]*y[kk][1]); +// double c12 = 2*ri[kk]*y[jj][2]*(1-y[kk][2]*y[kk][2]); + for (n=0;n +#include +#include +#include +#include +#include + +using namespace LAMMPS_NS; + +Fingerprint_bondscreened::Fingerprint_bondscreened(PairRANN *pair) : Fingerprint(pair) +{ + n_body_type = 3; + dr = 0; + re = 0; + rc = 0; + alpha_k = new double [1]; + alpha_k[0] = -1; + k = 0; + m = 0; + id = -1; + style = "bondscreened"; + atomtypes = new int [n_body_type]; + empty = true; + pair->doscreen = true; + screen = true; +} + +Fingerprint_bondscreened::~Fingerprint_bondscreened(){ + delete [] alpha_k; + delete [] atomtypes; + delete [] expcuttable; + delete [] dfctable; + for (int i=0;i<(m*(m+1))>>1;i++){ + delete [] coeff[i]; + delete [] coeffx[i]; + delete [] coeffy[i]; + delete [] coeffz[i]; + delete [] Mf[i]; + } + delete [] coeff; + delete [] coeffx; + delete [] coeffy; + delete [] coeffz; + delete [] Mf; + delete [] rinvsqrttable; +} + +bool Fingerprint_bondscreened::parse_values(char * constant, char * line1){ + char **words=new char *[MAXLINE]; + int nwords,l; + nwords=0; + words[nwords++] = strtok(line1,": ,\t\n"); + while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; + nwords -= 1; + if (strcmp(constant,"re")==0){ + re = strtod(words[0],NULL); + } + else if (strcmp(constant,"rc")==0){ + rc = strtod(words[0],NULL); + } + else if (strcmp(constant,"alphak")==0){ + delete [] alpha_k; + alpha_k = new double [nwords]; + for (l=0;lerrorf("Undefined value for bond power"); + delete [] words; + if (re!=0.0 && rc!=0.0 && alpha_k[0]!=-1 && dr!=0.0 && m!=0 && k!=0)return true; + return false; +} + +void Fingerprint_bondscreened::write_values(FILE *fid){ + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alphak:\n",style,id); + for (i=0;ielementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:k:\n",style,id); + fprintf(fid,"%d\n",k); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:m:\n",style,id); + fprintf(fid,"%d\n",m); +} + +void Fingerprint_bondscreened::init(int *i,int id){ + for (int j=0;jk = 0; + alpha_k = new double [1]; + alpha_k[0]=-1; + empty = false; + this->id = id; +} + +//number of neurons defined by this fingerprint +int Fingerprint_bondscreened::get_length(){ + return m*k; +} + +void Fingerprint_bondscreened::allocate(){ + generate_exp_cut_table(); + generate_coefficients(); + generate_rinvssqrttable(); +} + +//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop and do3bodyfeatureset_doubleneighborloop. +void Fingerprint_bondscreened::generate_exp_cut_table(){ + int m,n; + double r1; + int buf = 5; + int res = pair->res; + double cutmax = pair->cutmax; + expcuttable = new double [(res+buf)*(this->k)]; + dfctable = new double [res+buf]; + for (m=0;m<(res+buf);m++){ + r1 = cutmax*cutmax*(double)(m)/(double)(res); + for (n=0;n<(this->k);n++){ + expcuttable[n+m*(this->k)] = exp(-alpha_k[n]/re*sqrt(r1))*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ + dfctable[m]=0; + } + else{ + dfctable[m]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } +} + + +//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop. +void Fingerprint_bondscreened::generate_coefficients(){ //calculates multinomial coefficient for each term + int p,mb,mc; + int n,p1,i1; + mb = this->m; + mc=(mb*(mb+1))>>1; + coeff = new int *[mc]; + coeffx = new int *[mc]; + coeffy = new int *[mc]; + coeffz = new int *[mc]; + for (p=0;pm+1]; + for (p=0;pm+1;p++){ + M[p]=0; + } + for (p1=0;p1sims[sid]; +// ilist = sim->ilist; +// numneigh = sim->numneigh; +// i = ilist[ii]; +// jnum = numneigh[i]; + //select the more efficient algorithm for this particular potential and environment. + if (jnum*2>(m+1)*m*20){ + do3bodyfeatureset_singleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,sid,xn,yn,zn,tn,jnum,jl); + } + else{ + do3bodyfeatureset_doubleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,sid,xn,yn,zn,tn,jnum,jl); + + } +} + +//Called by do3bodyfeatureset. Algorithm for high neighbor numbers and small series of bond angle powers +void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ + int i,j,jj,itype,jtype,kk,m,n,mcount,a,a1,a2,ai; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + int count=0; + PairRANN::Simulation *sim = &pair->sims[sid]; +// double **x = sim->x; + //double **f = atom->f; + int *type = sim->type; + double cutmax = pair->cutmax; + int res = pair->res; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; +// numneigh = sim->numneigh; +// firstneigh = sim->firstneigh; + int nelements=pair->nelements; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; +// xtmp = x[i][0]; +// ytmp = x[i][1]; +// ztmp = x[i][2]; +// jlist = firstneigh[i]; +// jnum = numneigh[i]; + double expr[jnum][this->k+12]; + int p = this->k; + int countmb=((this->m)*(this->m+1))>>1; + // calculate interpolation expr, rinvs and dfc, for each neighbor + for (jj = 0; jj < jnum; jj++) { + if (Bij[jj]==false){continue;} +// j = jlist[jj]; +// j &= NEIGHMASK; +// jtype = pair->map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype && atomtypes[2] != nelements && atomtypes[2] != jtype){ + expr[jj][0]=0; + continue; + } +// delx = xtmp - x[j][0]; +// dely = ytmp - x[j][1]; +// delz = ztmp - x[j][2]; + delx=xn[jj]; + dely=yn[jj]; + delz=zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc){ + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*this->k]; + double *p1 = &expcuttable[m1*this->k]; + double *p2 = &expcuttable[(m1+1)*this->k]; + double *p3 = &expcuttable[(m1+2)*this->k]; + for (kk=0;kkk;kk++){ + expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); + expr[jj][kk] *= Sik[jj]; + } + double* q = &dfctable[m1-1]; + double* ri = &rinvsqrttable[m1-1]; + double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + double rinvs = ri[1] + 0.5 * r1*(ri[2] - ri[0] + r1*(2.0*ri[0] - 5.0*ri[1] + 4.0*ri[2] - ri[3] + r1*(3.0*(ri[1] - ri[2]) + ri[3] - ri[0]))); + + expr[jj][p]=delx*rinvs; + expr[jj][p+1]=dely*rinvs; + expr[jj][p+2]=delz*rinvs; + //Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy. + if (expr[jj][p]*expr[jj][p]<0.000000000001){ + expr[jj][p] = 0.000001; + } + if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001){ + expr[jj][p+1] = 0.000001; + } + if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001){ + expr[jj][p+2] = 0.000001; + } + expr[jj][p+3] = -dfc*expr[jj][p]-dSikx[jj]; + expr[jj][p+4] = rinvs/expr[jj][p]; + expr[jj][p+5] = rinvs*expr[jj][p]; + expr[jj][p+6] = -dfc*expr[jj][p+1]-dSiky[jj]; + expr[jj][p+7] = rinvs/expr[jj][p+1]; + expr[jj][p+8] = rinvs*expr[jj][p+1]; + expr[jj][p+9] = -dfc*expr[jj][p+2]-dSikz[jj]; + expr[jj][p+10] = rinvs/expr[jj][p+2]; + expr[jj][p+11] = rinvs*expr[jj][p+2]; + } + + int kb = this->k; + int mb = this->m; +// int ind = kb+mb*kb; + count = startingneuron; + double Bb[mb]; + double dBbx; + double dBby; + double dBbz; + double dBbx1[mb]; + double dBby1[mb]; + double dBbz1[mb]; + double yprod; + for (mcount=0;mcountcoeffx[mcount]; + int *coeffy = this->coeffy[mcount]; + int *coeffz = this->coeffz[mcount]; + int *coeff = this->coeff[mcount]; + a = mb+1; + for (a1=0;a1map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype){ + continue; + } + double yprod = expr[jj][ai]; + double *y4 = &expr[jj][p]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[2] != nelements && atomtypes[2] != jtype){ + continue; + } + double yprod = expr[jj][ai]; + double *y4 = &expr[jj][p]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[2] != nelements && atomtypes[2] != jtype){ + continue; + } + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype){ + continue; + } + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype){ + continue; + } + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2sims[sid]; +// double **x = sim->x; + int *type = sim->type; + int nelements = pair->nelements; + int res = pair->res; + double cutmax = pair->cutmax; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; +// numneigh = sim->numneigh; +// firstneigh = sim->firstneigh; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; +// xtmp = x[i][0]; +// ytmp = x[i][1]; +// ztmp = x[i][2]; +// jlist = firstneigh[i]; +// jnum = numneigh[i]; + double expr[jnum][this->k]; + double y[jnum][3]; + double ri[jnum]; + double dfc[jnum]; + int kb = this->k; + int mb = this->m; + double Bijk[kb][mb]; + double c41[this->k]; + double c51[this->k]; + double c61[this->k]; + double ct[this->k]; + for (jj = 0; jj < jnum; jj++) { + if (Bij[jj]==false){continue;} +// j = jlist[jj]; +// j &= NEIGHMASK; +// jtype = pair->map[type[j]]; + jtype = tn[jj]; + if (jtypes != nelements && jtypes != jtype && ktypes != nelements && ktypes != jtype){ + expr[jj][0]=0; + continue; + } +// delx = xtmp - x[j][0]; +// dely = ytmp - x[j][1]; +// delz = ztmp - x[j][2]; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc){ + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (!(m1>=1 && m1 <= res))pair->errorf("Neighbor list is invalid.");//usually results from nan somewhere. + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*this->k]; + double *p1 = &expcuttable[m1*this->k]; + double *p2 = &expcuttable[(m1+1)*this->k]; + double *p3 = &expcuttable[(m1+2)*this->k]; + for (kk=0;kkk;kk++){ + expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); + expr[jj][kk] *= Sik[jj]; + } + double* q = &dfctable[m1-1]; + double* r2 = &rinvsqrttable[m1-1]; + dfc[jj] = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + ri[jj] = r2[1] + 0.5 * r1*(r2[2] - r2[0] + r1*(2.0*r2[0] - 5.0*r2[1] + 4.0*r2[2] - r2[3] + r1*(3.0*(r2[1] - r2[2]) + r2[3] - r2[0]))); + y[jj][0]=delx*ri[jj]; + y[jj][1]=dely*ri[jj]; + y[jj][2]=delz*ri[jj]; + } + for (jj = 0; jj < jnum; jj++) { + if (Bij[jj]==false){continue;} + if (expr[jj][0]==0)continue; +// j = jlist[jj]; +// j &= NEIGHMASK; +// jtype = pair->map[type[j]]; + jtype =tn[jj]; + if (jtypes != nelements && jtypes != jtype){ + continue; + } + for (n = 0;nk;n++){ + ct[n] = alpha_k[n]/re; + c41[n]=(-ct[n]+dfc[jj])*y[jj][0]+dSikx[jj]; + c51[n]=(-ct[n]+dfc[jj])*y[jj][1]+dSiky[jj]; + c61[n]=(-ct[n]+dfc[jj])*y[jj][2]+dSikz[jj]; + } + for (n=0;nmap[type[k1]]; + ktype = tn[kk]; + if (ktypes != nelements && ktypes != ktype){ + continue; + } + count = startingneuron; + double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); + double c1 = ri[jj]*(y[kk][0]-dot*y[jj][0]); + double c2 = ri[jj]*(y[kk][1]-dot*y[jj][1]); + double c3 = ri[jj]*(y[kk][2]-dot*y[jj][2]); + double c10 = ri[kk]*(y[jj][0]-dot*y[kk][0]); + double c11 = ri[kk]*(y[jj][1]-dot*y[kk][1]); + double c12 = ri[kk]*(y[jj][2]-dot*y[kk][2]); + for (n=0;nSik[kk]*pair->Sik[jj]; +// double c4 = c41[n]+4*pair->dSikx[kk]; +// double c5 = c51[n]+4*pair->dSiky[kk]; +// double c6 = c61[n]+4*pair->dSikz[kk]; +// //m=0 +// features[count]+=dot1; +// Bijk[n][0]+=dot1; +// dfeaturesx[jj*f+count]+=dot1*c4; +// dfeaturesy[jj*f+count]+=dot1*c5; +// dfeaturesz[jj*f+count]+=dot1*c6; +// c4*=dot; +// c5*=dot; +// c6*=dot; +// count++; +// for (m=1;mmap[type[k1]]; + ktype = tn[kk]; + if (ktypes != nelements && ktypes != ktype){ + continue; + } + count = startingneuron; + for (n=0;nBij[kk]==false){continue;} +// if (expr[kk][0]==0)continue; +// int k1 = jlist[kk]; +// k1 &= NEIGHMASK; +// ktype = pair->map[type[k1]]; +// if (ktypes != nelements && ktypes != ktype){ +// continue; +// } +// count = startingneuron; +// double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); +// double c1 = ri[jj]*(y[kk][0]-dot*y[jj][0]); +// double c2 = ri[jj]*(y[kk][1]-dot*y[jj][1]); +// double c3 = ri[jj]*(y[kk][2]-dot*y[jj][2]); +// double c10 = ri[kk]*(y[jj][0]-dot*y[kk][0]); +// double c11 = ri[kk]*(y[jj][1]-dot*y[kk][1]); +// double c12 = ri[kk]*(y[jj][2]-dot*y[kk][2]); +// for (n=0;nSik[kk]*pair->Sik[jj]; +// double c4 = c41[n]/2; +// double c5 = c51[n]/2; +// double c6 = c61[n]/2; +// double ct2 = -ct[n]/2+dfc[kk]; +// double c42 = ct2*y[kk][0]+pair->dSikx[kk]; +// double c52 = ct2*y[kk][1]+pair->dSiky[kk]; +// double c62 = ct2*y[kk][2]+pair->dSikz[kk]; +// //m=0 +// features[count]+=dot1; +// dfeaturesx[jj*f+count]+=dot1*c4; +// dfeaturesy[jj*f+count]+=dot1*c5; +// dfeaturesz[jj*f+count]+=dot1*c6; +// dfeaturesx[kk*f+count]+=dot1*c42; +// dfeaturesy[kk*f+count]+=dot1*c52; +// dfeaturesz[kk*f+count]+=dot1*c62; +// c4*=dot; +// c5*=dot; +// c6*=dot; +// c42*=dot; +// c52*=dot; +// c62*=dot; +// count++; +// for (m=1;m +#include +#include +#include +#include +#include + +using namespace LAMMPS_NS; + +Fingerprint_bondscreenedspin::Fingerprint_bondscreenedspin(PairRANN *pair) : Fingerprint(pair) +{ + n_body_type = 3; + dr = 0; + re = 0; + rc = 0; + alpha_k = new double [1]; + alpha_k[0] = -1; + k = 0; + m = 0; + id = -1; + style = "bondscreenedspin"; + atomtypes = new int [n_body_type]; + empty = true; + pair->doscreen = true; + screen = true; + pair->dospin = true; + spin = true; +} + +Fingerprint_bondscreenedspin::~Fingerprint_bondscreenedspin(){ + delete [] alpha_k; + delete [] atomtypes; + delete [] expcuttable; + delete [] dfctable; + for (int i=0;i<(m*(m+1))>>1;i++){ + delete [] coeff[i]; + delete [] coeffx[i]; + delete [] coeffy[i]; + delete [] coeffz[i]; + delete [] Mf[i]; + } + delete [] coeff; + delete [] coeffx; + delete [] coeffy; + delete [] coeffz; + delete [] Mf; + delete [] rinvsqrttable; +} + +bool Fingerprint_bondscreenedspin::parse_values(char * constant, char * line1){ + char **words=new char *[MAXLINE]; + int nwords,l; + nwords=0; + words[nwords++] = strtok(line1,": ,\t\n"); + while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; + nwords -= 1; + if (strcmp(constant,"re")==0){ + re = strtod(words[0],NULL); + } + else if (strcmp(constant,"rc")==0){ + rc = strtod(words[0],NULL); + } + else if (strcmp(constant,"alphak")==0){ + delete [] alpha_k; + alpha_k = new double [nwords]; + for (l=0;lerrorf("Undefined value for bond power"); + delete [] words; + if (re!=0.0 && rc!=0.0 && alpha_k[0]!=-1 && dr!=0.0 && m!=0 && k!=0)return true; + return false; +} + +void Fingerprint_bondscreenedspin::write_values(FILE *fid){ + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alphak:\n",style,id); + for (i=0;ielementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:k:\n",style,id); + fprintf(fid,"%d\n",k); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:m:\n",style,id); + fprintf(fid,"%d\n",m); +} + +void Fingerprint_bondscreenedspin::init(int *i,int id){ + for (int j=0;jk = 0; + alpha_k = new double [1]; + alpha_k[0]=-1; + empty = false; + this->id = id; +} + +//number of neurons defined by this fingerprint +int Fingerprint_bondscreenedspin::get_length(){ + return m*k; +} + +void Fingerprint_bondscreenedspin::allocate(){ + generate_exp_cut_table(); + generate_coefficients(); + generate_rinvssqrttable(); +} + +//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop and do3bodyfeatureset_doubleneighborloop. +void Fingerprint_bondscreenedspin::generate_exp_cut_table(){ + int m,n; + double r1; + int buf = 5; + int res = pair->res; + double cutmax = pair->cutmax; + expcuttable = new double [(res+buf)*(this->k)]; + dfctable = new double [res+buf]; + for (m=0;m<(res+buf);m++){ + r1 = cutmax*cutmax*(double)(m)/(double)(res); + for (n=0;n<(this->k);n++){ + expcuttable[n+m*(this->k)] = exp(-alpha_k[n]/re*sqrt(r1))*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ + dfctable[m]=0; + } + else{ + dfctable[m]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } +} + + +//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop. +void Fingerprint_bondscreenedspin::generate_coefficients(){ //calculates multinomial coefficient for each term + int p,mb,mc; + int n,p1,i1; + mb = this->m; + mc=(mb*(mb+1))>>1; + coeff = new int *[mc]; + coeffx = new int *[mc]; + coeffy = new int *[mc]; + coeffz = new int *[mc]; + for (p=0;pm+1]; + for (p=0;pm+1;p++){ + M[p]=0; + } + for (p1=0;p1sims[sid]; +// ilist = sim->ilist; +// numneigh = sim->numneigh; +// i = ilist[ii]; +// jnum = numneigh[i]; + //select the more efficient algorithm for this particular potential and environment. + if (jnum*2>(m+1)*m*20){ + do3bodyfeatureset_singleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,dspinx,dspiny,dspinz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,sid,xn,yn,zn,tn,jnum,jl); + } + else{ + do3bodyfeatureset_doubleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,dspinx,dspiny,dspinz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,sid,xn,yn,zn,tn,jnum,jl); + + } +} + +//Called by do3bodyfeatureset. Algorithm for high neighbor numbers and small series of bond angle powers +void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz, double *dspinx, double *dspiny, double *dspinz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ + int i,j,jj,itype,jtype,kk,m,n,mcount,a,a1,a2,ai; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + int count=0; + PairRANN::Simulation *sim = &pair->sims[sid]; +// double **x = sim->x; + //double **f = atom->f; + int *type = sim->type; + double cutmax = pair->cutmax; + int res = pair->res; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; +// numneigh = sim->numneigh; +// firstneigh = sim->firstneigh; + int nelements=pair->nelements; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; +// xtmp = x[i][0]; +// ytmp = x[i][1]; +// ztmp = x[i][2]; +// jlist = firstneigh[i]; +// jnum = numneigh[i]; + double expr[jnum][this->k+12]; + int p = this->k; + int countmb=((this->m)*(this->m+1))>>1; + double *si = sim->s[i]; + // calculate interpolation expr, rinvs and dfc, for each neighbor + for (jj = 0; jj < jnum; jj++) { + if (Bij[jj]==false){continue;} +// j = jlist[jj]; +// j &= NEIGHMASK; +// jtype = pair->map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype && atomtypes[2] != nelements && atomtypes[2] != jtype){ + expr[jj][0]=0; + continue; + } +// delx = xtmp - x[j][0]; +// dely = ytmp - x[j][1]; +// delz = ztmp - x[j][2]; + delx=xn[jj]; + dely=yn[jj]; + delz=zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc){ + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*this->k]; + double *p1 = &expcuttable[m1*this->k]; + double *p2 = &expcuttable[(m1+1)*this->k]; + double *p3 = &expcuttable[(m1+2)*this->k]; + for (kk=0;kkk;kk++){ + expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); + expr[jj][kk] *= Sik[jj]; + } + double* q = &dfctable[m1-1]; + double* ri = &rinvsqrttable[m1-1]; + double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + double rinvs = ri[1] + 0.5 * r1*(ri[2] - ri[0] + r1*(2.0*ri[0] - 5.0*ri[1] + 4.0*ri[2] - ri[3] + r1*(3.0*(ri[1] - ri[2]) + ri[3] - ri[0]))); + + expr[jj][p]=delx*rinvs; + expr[jj][p+1]=dely*rinvs; + expr[jj][p+2]=delz*rinvs; + //Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy. + if (expr[jj][p]*expr[jj][p]<0.000000000001){ + expr[jj][p] = 0.000001; + } + if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001){ + expr[jj][p+1] = 0.000001; + } + if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001){ + expr[jj][p+2] = 0.000001; + } + expr[jj][p+3] = -dfc*expr[jj][p]-dSikx[jj]; + expr[jj][p+4] = rinvs/expr[jj][p]; + expr[jj][p+5] = rinvs*expr[jj][p]; + expr[jj][p+6] = -dfc*expr[jj][p+1]-dSiky[jj]; + expr[jj][p+7] = rinvs/expr[jj][p+1]; + expr[jj][p+8] = rinvs*expr[jj][p+1]; + expr[jj][p+9] = -dfc*expr[jj][p+2]-dSikz[jj]; + expr[jj][p+10] = rinvs/expr[jj][p+2]; + expr[jj][p+11] = rinvs*expr[jj][p+2]; + } + + int kb = this->k; + int mb = this->m; +// int ind = kb+mb*kb; + count = startingneuron; + double Bb[mb]; + double Bbs[mb]; + double dBbx; + double dBby; + double dBbz; +// double dBbx1[mb]; +// double dBby1[mb]; +// double dBbz1[mb]; + double yprod; + for (mcount=0;mcountcoeffx[mcount]; + int *coeffy = this->coeffy[mcount]; + int *coeffz = this->coeffz[mcount]; + int *coeff = this->coeff[mcount]; + a = mb+1; + for (a1=0;a1map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype){ + continue; + } + j = jl[jj]; + double *sj = sim->s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double yprod = expr[jj][ai]; + double *y4 = &expr[jj][p]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[2] != nelements && atomtypes[2] != jtype){ + continue; + } + j = jl[jj]; + double *sj = sim->s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double yprod = expr[jj][ai]; + double *y4 = &expr[jj][p]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[2] != nelements && atomtypes[2] != jtype){ + continue; + } + j = jl[jj]; + double *sj = sim->s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype){ + continue; + } + j = jl[jj]; + double *sj = sim->s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype){ + continue; + } + j = jl[jj]; + double *sj = sim->s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2sims[sid]; +// double **x = sim->x; + int *type = sim->type; + int nelements = pair->nelements; + int res = pair->res; + double cutmax = pair->cutmax; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; +// numneigh = sim->numneigh; +// firstneigh = sim->firstneigh; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; +// xtmp = x[i][0]; +// ytmp = x[i][1]; +// ztmp = x[i][2]; +// jlist = firstneigh[i]; +// jnum = numneigh[i]; + double expr[jnum][this->k]; + double y[jnum][3]; + double ri[jnum]; + double dfc[jnum]; + int kb = this->k; + int mb = this->m; + double Bijk[kb][mb]; + double c41[this->k]; + double c51[this->k]; + double c61[this->k]; + double ct[this->k]; + double *si = sim->s[i]; + for (jj = 0; jj < jnum; jj++) { + if (Bij[jj]==false){continue;} +// j = jlist[jj]; +// j &= NEIGHMASK; +// jtype = pair->map[type[j]]; + jtype = tn[jj]; + if (jtypes != nelements && jtypes != jtype && ktypes != nelements && ktypes != jtype){ + expr[jj][0]=0; + continue; + } +// delx = xtmp - x[j][0]; +// dely = ytmp - x[j][1]; +// delz = ztmp - x[j][2]; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc){ + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (!(m1>=1 && m1 <= res))pair->errorf("Neighbor list is invalid.");//usually results from nan somewhere. + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*this->k]; + double *p1 = &expcuttable[m1*this->k]; + double *p2 = &expcuttable[(m1+1)*this->k]; + double *p3 = &expcuttable[(m1+2)*this->k]; + for (kk=0;kkk;kk++){ + expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); + expr[jj][kk] *= Sik[jj]; + } + double* q = &dfctable[m1-1]; + double* r2 = &rinvsqrttable[m1-1]; + dfc[jj] = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + ri[jj] = r2[1] + 0.5 * r1*(r2[2] - r2[0] + r1*(2.0*r2[0] - 5.0*r2[1] + 4.0*r2[2] - r2[3] + r1*(3.0*(r2[1] - r2[2]) + r2[3] - r2[0]))); + y[jj][0]=delx*ri[jj]; + y[jj][1]=dely*ri[jj]; + y[jj][2]=delz*ri[jj]; + } + for (jj = 0; jj < jnum; jj++) { + if (Bij[jj]==false){continue;} + if (expr[jj][0]==0)continue; +// j = jlist[jj]; +// j &= NEIGHMASK; +// jtype = pair->map[type[j]]; + jtype =tn[jj]; + if (jtypes != nelements && jtypes != jtype){ + continue; + } + j = jl[jj]; + double *sj = sim->s[j]; + double spj = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + for (n = 0;nk;n++){ + ct[n] = alpha_k[n]/re; + c41[n]=(-ct[n]+dfc[jj])*y[jj][0]+dSikx[jj]; + c51[n]=(-ct[n]+dfc[jj])*y[jj][1]+dSiky[jj]; + c61[n]=(-ct[n]+dfc[jj])*y[jj][2]+dSikz[jj]; + } + for (n=0;nmap[type[k1]]; + ktype = tn[kk]; + if (ktypes != nelements && ktypes != ktype){ + continue; + } + j = jl[kk]; + double *sk = sim->s[j]; + double spk = si[0]*sk[0]+si[1]*sk[1]+si[2]*sk[2]; + count = startingneuron; + double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); + double c1 = ri[jj]*(y[kk][0]-dot*y[jj][0]); + double c2 = ri[jj]*(y[kk][1]-dot*y[jj][1]); + double c3 = ri[jj]*(y[kk][2]-dot*y[jj][2]); + double c10 = ri[kk]*(y[jj][0]-dot*y[kk][0]); + double c11 = ri[kk]*(y[jj][1]-dot*y[kk][1]); + double c12 = ri[kk]*(y[jj][2]-dot*y[kk][2]); + for (n=0;nSik[kk]*pair->Sik[jj]; +// double c4 = c41[n]+4*pair->dSikx[kk]; +// double c5 = c51[n]+4*pair->dSiky[kk]; +// double c6 = c61[n]+4*pair->dSikz[kk]; +// //m=0 +// features[count]+=dot1; +// Bijk[n][0]+=dot1; +// dfeaturesx[jj*f+count]+=dot1*c4; +// dfeaturesy[jj*f+count]+=dot1*c5; +// dfeaturesz[jj*f+count]+=dot1*c6; +// c4*=dot; +// c5*=dot; +// c6*=dot; +// count++; +// for (m=1;mmap[type[k1]]; + ktype = tn[kk]; + if (ktypes != nelements && ktypes != ktype){ + continue; + } + count = startingneuron; + for (n=0;nBij[kk]==false){continue;} +// if (expr[kk][0]==0)continue; +// int k1 = jlist[kk]; +// k1 &= NEIGHMASK; +// ktype = pair->map[type[k1]]; +// if (ktypes != nelements && ktypes != ktype){ +// continue; +// } +// count = startingneuron; +// double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); +// double c1 = ri[jj]*(y[kk][0]-dot*y[jj][0]); +// double c2 = ri[jj]*(y[kk][1]-dot*y[jj][1]); +// double c3 = ri[jj]*(y[kk][2]-dot*y[jj][2]); +// double c10 = ri[kk]*(y[jj][0]-dot*y[kk][0]); +// double c11 = ri[kk]*(y[jj][1]-dot*y[kk][1]); +// double c12 = ri[kk]*(y[jj][2]-dot*y[kk][2]); +// for (n=0;nSik[kk]*pair->Sik[jj]; +// double c4 = c41[n]/2; +// double c5 = c51[n]/2; +// double c6 = c61[n]/2; +// double ct2 = -ct[n]/2+dfc[kk]; +// double c42 = ct2*y[kk][0]+pair->dSikx[kk]; +// double c52 = ct2*y[kk][1]+pair->dSiky[kk]; +// double c62 = ct2*y[kk][2]+pair->dSikz[kk]; +// //m=0 +// features[count]+=dot1; +// dfeaturesx[jj*f+count]+=dot1*c4; +// dfeaturesy[jj*f+count]+=dot1*c5; +// dfeaturesz[jj*f+count]+=dot1*c6; +// dfeaturesx[kk*f+count]+=dot1*c42; +// dfeaturesy[kk*f+count]+=dot1*c52; +// dfeaturesz[kk*f+count]+=dot1*c62; +// c4*=dot; +// c5*=dot; +// c6*=dot; +// c42*=dot; +// c52*=dot; +// c62*=dot; +// count++; +// for (m=1;m +#include +#include +#include +#include +#include + +using namespace LAMMPS_NS; + +Fingerprint_bondspin::Fingerprint_bondspin(PairRANN *pair) : Fingerprint(pair) +{ + n_body_type = 3; + dr = 0; + re = 0; + rc = 0; + alpha_k = new double [1]; + alpha_k[0] = -1; + k = 0; + m = 0; + id = -1; + style = "bondspin"; + atomtypes = new int [n_body_type]; + empty = true; + pair->allscreen = false; + pair->dospin = true; + spin = true; +} + +Fingerprint_bondspin::~Fingerprint_bondspin(){ + delete [] alpha_k; + delete [] atomtypes; + delete [] expcuttable; + delete [] dfctable; + for (int i=0;i<(m*(m+1))>>1;i++){ + delete [] coeff[i]; + delete [] coeffx[i]; + delete [] coeffy[i]; + delete [] coeffz[i]; + delete [] Mf[i]; + } + delete [] coeff; + delete [] coeffx; + delete [] coeffy; + delete [] coeffz; + delete [] Mf; + delete [] rinvsqrttable; +} + +bool Fingerprint_bondspin::parse_values(char * constant, char * line1){ + char **words=new char *[MAXLINE]; + int nwords,l; + nwords=0; + words[nwords++] = strtok(line1,": ,\t\n"); + while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; + nwords -= 1; + if (strcmp(constant,"re")==0){ + re = strtod(words[0],NULL); + } + else if (strcmp(constant,"rc")==0){ + rc = strtod(words[0],NULL); + } + else if (strcmp(constant,"alphak")==0){ + delete [] alpha_k; + alpha_k = new double [nwords]; + for (l=0;lerrorf("Undefined value for bond power"); + delete [] words; + if (re!=0.0 && rc!=0.0 && alpha_k[0]!=-1 && dr!=0.0 && m!=0 && k!=0)return true; + return false; +} + +void Fingerprint_bondspin::write_values(FILE *fid){ + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alphak:\n",style,id); + for (i=0;ielementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:k:\n",style,id); + fprintf(fid,"%d\n",k); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:m:\n",style,id); + fprintf(fid,"%d\n",m); +} + +void Fingerprint_bondspin::init(int *i,int id){ + for (int j=0;jk = 0; + alpha_k = new double [1]; + alpha_k[0]=-1; + empty = false; + this->id = id; +} + +//number of neurons defined by this fingerprint +int Fingerprint_bondspin::get_length(){ + return m*k; +} + +void Fingerprint_bondspin::allocate(){ + generate_exp_cut_table(); + generate_coefficients(); + generate_rinvssqrttable(); +} + +//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop and do3bodyfeatureset_doubleneighborloop. +void Fingerprint_bondspin::generate_exp_cut_table(){ + int m,n; + double r1; + int buf = 5; + int res = pair->res; + double cutmax = pair->cutmax; + expcuttable = new double [(res+buf)*(this->k)]; + dfctable = new double [res+buf]; + for (m=0;m<(res+buf);m++){ + r1 = cutmax*cutmax*(double)(m)/(double)(res); + for (n=0;n<(this->k);n++){ + expcuttable[n+m*(this->k)] = exp(-alpha_k[n]/re*sqrt(r1))*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ + dfctable[m]=0; + } + else{ + dfctable[m]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } +} + +//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop. +void Fingerprint_bondspin::generate_coefficients(){ //calculates multinomial coefficient for each term + int p,mb,mc; + int n,p1,i1; + mb = this->m; + mc=(mb*(mb+1))>>1; + coeff = new int *[mc]; + coeffx = new int *[mc]; + coeffy = new int *[mc]; + coeffz = new int *[mc]; + for (p=0;pm+1]; + for (p=0;pm+1;p++){ + M[p]=0; + } + for (p1=0;p1sims[sid]; + ilist = sim->ilist; + numneigh = sim->numneigh; + i = ilist[ii]; +// jnum = numneigh[i]; + //select the more efficient algorithm for this particular potential and environment. + + if (jnum*2>(m+1)*m*20){ + do3bodyfeatureset_singleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,dspinx,dspiny,dspinz,ii,sid,xn,yn,zn,tn,jnum,jl); + } + else{ + do3bodyfeatureset_doubleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,dspinx,dspiny,dspinz,ii,sid,xn,yn,zn,tn,jnum,jl); + } +} + +//Called by do3bodyfeatureset. Algorithm for high neighbor numbers and small series of bond angle powers +void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,double * dspinx,double *dspiny,double *dspinz,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ + int i,j,jj,itype,jtype,kk,m,n,mcount,a,a1,a2,ai; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + int count=0; + PairRANN::Simulation *sim = &pair->sims[sid]; +// double **x = sim->x; + int *type = sim->type; + double cutmax = pair->cutmax; + int res = pair->res; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; +// numneigh = sim->numneigh; +// firstneigh = sim->firstneigh; + int nelements=pair->nelements; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; +// xtmp = x[i][0]; +// ytmp = x[i][1]; +// ztmp = x[i][2]; +// jlist = firstneigh[i]; +// jnum = numneigh[i]; + double expr[jnum][this->k+12]; + int p = this->k; + int countmb=((this->m)*(this->m+1))>>1; + double *si = sim->s[i]; + // calculate interpolation expr, rinvs and dfc, for each neighbor + for (jj = 0; jj < jnum; jj++) { +// j = jlist[jj]; +// j &= NEIGHMASK; +// jtype = pair->map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype && atomtypes[2] != nelements && atomtypes[2] != jtype){ + expr[jj][0]=0; + continue; + } +// delx = xtmp - x[j][0]; +// dely = ytmp - x[j][1]; +// delz = ztmp - x[j][2]; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc){ + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*this->k]; + double *p1 = &expcuttable[m1*this->k]; + double *p2 = &expcuttable[(m1+1)*this->k]; + double *p3 = &expcuttable[(m1+2)*this->k]; + for (kk=0;kkk;kk++){ + expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); + } + double* q = &dfctable[m1-1]; + double* ri = &rinvsqrttable[m1-1]; + double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + double rinvs = ri[1] + 0.5 * r1*(ri[2] - ri[0] + r1*(2.0*ri[0] - 5.0*ri[1] + 4.0*ri[2] - ri[3] + r1*(3.0*(ri[1] - ri[2]) + ri[3] - ri[0]))); + + expr[jj][p]=delx*rinvs; + expr[jj][p+1]=dely*rinvs; + expr[jj][p+2]=delz*rinvs; + //Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy. + if (expr[jj][p]*expr[jj][p]<0.000000000001){ + expr[jj][p] = 0.000001; + } + if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001){ + expr[jj][p+1] = 0.000001; + } + if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001){ + expr[jj][p+2] = 0.000001; + } + expr[jj][p+3] = -dfc*expr[jj][p]; + expr[jj][p+4] = rinvs/expr[jj][p]; + expr[jj][p+5] = rinvs*expr[jj][p]; + expr[jj][p+6] = -dfc*expr[jj][p+1]; + expr[jj][p+7] = rinvs/expr[jj][p+1]; + expr[jj][p+8] = rinvs*expr[jj][p+1]; + expr[jj][p+9] = -dfc*expr[jj][p+2]; + expr[jj][p+10] = rinvs/expr[jj][p+2]; + expr[jj][p+11] = rinvs*expr[jj][p+2]; + } + + int kb = this->k; + int mb = this->m; + count = startingneuron; + double Bb[mb]; + double Bbs[mb]; + double dBbx; + double dBby; + double dBbz; +// double dBbx1[mb]; +// double dBby1[mb]; +// double dBbz1[mb]; + double yprod; + for (mcount=0;mcountcoeffx[mcount]; + int *coeffy = this->coeffy[mcount]; + int *coeffz = this->coeffz[mcount]; + int *coeff = this->coeff[mcount]; + a = mb+1; + for (a1=0;a1map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype){ + continue; + } + j = jl[jj]; + double *sj = sim->s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double yprod = expr[jj][ai]; + double *y4 = &expr[jj][p]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[2] != nelements && atomtypes[2] != jtype){ + continue; + } + j = jl[jj]; + double *sj = sim->s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double yprod = expr[jj][ai]; + double *y4 = &expr[jj][p]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[2] != nelements && atomtypes[2] != jtype){ + continue; + } + j = jl[jj]; + double *sj = sim->s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype){ + continue; + } + j = jl[jj]; + double *sj = sim->s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2map[type[j]]; + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype){ + continue; + } + j = jl[jj]; + double *sj = sim->s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2sims[sid]; + double **x = sim->x; + int *type = sim->type; + int nelements = pair->nelements; + int res = pair->res; + double cutmax = pair->cutmax; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; +// numneigh = sim->numneigh; +// firstneigh = sim->firstneigh; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; +// xtmp = x[i][0]; +// ytmp = x[i][1]; +// ztmp = x[i][2]; +// jlist = firstneigh[i]; +// jnum = numneigh[i]; + double expr[jnum][this->k]; + double y[jnum][3]; + double ri[jnum]; + double dfc[jnum]; + int kb = this->k; + int mb = this->m; + double c41[this->k]; + double c51[this->k]; + double c61[this->k]; + double ct[this->k]; + double *si = sim->s[i]; + for (jj = 0; jj < jnum; jj++) { +// j = jlist[jj]; +// j &= NEIGHMASK; +// jtype = pair->map[type[j]]; + jtype = tn[jj]; + if (jtypes != nelements && jtypes != jtype && ktypes != nelements && ktypes != jtype){ + expr[jj][0]=0; + continue; + } +// delx = xtmp - x[j][0]; +// dely = ytmp - x[j][1]; +// delz = ztmp - x[j][2]; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc){ + expr[jj][0]=0; + continue; + } +// j = jl[jj]; +// double *sj = sim->s[j]; +// double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (!(m1>=1 && m1 <= res))pair->errorf("Neighbor list is invalid.");//usually results from nan somewhere. + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*this->k]; + double *p1 = &expcuttable[m1*this->k]; + double *p2 = &expcuttable[(m1+1)*this->k]; + double *p3 = &expcuttable[(m1+2)*this->k]; + for (kk=0;kkk;kk++){ + expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); +// expr[jj][kk]*= sp; + } + double* q = &dfctable[m1-1]; + double* r2 = &rinvsqrttable[m1-1]; + dfc[jj] = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + ri[jj] = r2[1] + 0.5 * r1*(r2[2] - r2[0] + r1*(2.0*r2[0] - 5.0*r2[1] + 4.0*r2[2] - r2[3] + r1*(3.0*(r2[1] - r2[2]) + r2[3] - r2[0]))); + y[jj][0]=delx*ri[jj]; + y[jj][1]=dely*ri[jj]; + y[jj][2]=delz*ri[jj]; + } +// if (i==5){ +// for (jj=0;jjmap[type[j]]; + jtype = tn[jj]; + if (jtypes != nelements && jtypes != jtype){ + continue; + } + j = jl[jj]; + double *sj = sim->s[j]; + double spj = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + for (n = 0;nk;n++){ + ct[n] = 2*alpha_k[n]/re; + c41[n]=(-ct[n]+2*dfc[jj])*y[jj][0]; + c51[n]=(-ct[n]+2*dfc[jj])*y[jj][1]; + c61[n]= (-ct[n]+2*dfc[jj])*y[jj][2]; + } + if (jtypes==ktypes){ + for (kk=jj+1;kk< jnum; kk++){ + if (expr[kk][0]==0)continue; +// int k1 = jlist[kk]; +// k1 &= NEIGHMASK; +// ktype = pair->map[type[k1]]; + ktype = tn[kk]; + if (ktypes != nelements && ktypes != ktype){ + continue; + } + j = jl[kk]; + double *sk = sim->s[j]; + double spk = si[0]*sk[0]+si[1]*sk[1]+si[2]*sk[2]; + count = startingneuron; + double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); + double c1 = 2*ri[jj]*(y[kk][0]-dot*y[jj][0]); + double c2 = 2*ri[jj]*(y[kk][1]-dot*y[jj][1]); + double c3 = 2*ri[jj]*(y[kk][2]-dot*y[jj][2]); + double c10 = 2*ri[kk]*(y[jj][0]-dot*y[kk][0]); + double c11 = 2*ri[kk]*(y[jj][1]-dot*y[kk][1]); + double c12 = 2*ri[kk]*(y[jj][2]-dot*y[kk][2]); +// double c1 = 2*ri[jj]*y[kk][0]*(1-y[jj][0]*y[jj][0]); +// double c2 = 2*ri[jj]*y[kk][1]*(1-y[jj][1]*y[jj][1]); +// double c3 = 2*ri[jj]*y[kk][2]*(1-y[jj][2]*y[jj][2]); +// double c10 = 2*ri[kk]*y[jj][0]*(1-y[kk][0]*y[kk][0]); +// double c11 = 2*ri[kk]*y[jj][1]*(1-y[kk][1]*y[kk][1]); +// double c12 = 2*ri[kk]*y[jj][2]*(1-y[kk][2]*y[kk][2]); + for (n=0;nmap[type[k1]]; + ktype = tn[kk]; + if (ktypes != nelements && ktypes != ktype){ + continue; + } + j = jl[kk]; + double *sk = sim->s[j]; + double spk = si[0]*sk[0]+si[1]*sk[1]+si[2]*sk[2]; + count = startingneuron; + double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); + double c1 = ri[jj]*(y[kk][0]-dot*y[jj][0]); + double c2 = ri[jj]*(y[kk][1]-dot*y[jj][1]); + double c3 = ri[jj]*(y[kk][2]-dot*y[jj][2]); + double c10 = ri[kk]*(y[jj][0]-dot*y[kk][0]); + double c11 = ri[kk]*(y[jj][1]-dot*y[kk][1]); + double c12 = ri[kk]*(y[jj][2]-dot*y[kk][2]); +// double c1 = 2*ri[jj]*y[kk][0]*(1-y[jj][0]*y[jj][0]); +// double c2 = 2*ri[jj]*y[kk][1]*(1-y[jj][1]*y[jj][1]); +// double c3 = 2*ri[jj]*y[kk][2]*(1-y[jj][2]*y[jj][2]); +// double c10 = 2*ri[kk]*y[jj][0]*(1-y[kk][0]*y[kk][0]); +// double c11 = 2*ri[kk]*y[jj][1]*(1-y[kk][1]*y[kk][1]); +// double c12 = 2*ri[kk]*y[jj][2]*(1-y[kk][2]*y[kk][2]); + for (n=0;n +#include +#include +#include +#include +#include + + +using namespace LAMMPS_NS; + +Fingerprint_radial::Fingerprint_radial(PairRANN *pair) : Fingerprint(pair) +{ + n_body_type = 2; + dr = 0; + re = 0; + rc = 0; + alpha = new double [1]; + alpha[0] = -1; + n = 0; + o = 0; + id = -1; + style = "radial"; + atomtypes = new int [n_body_type]; + empty = true; + fullydefined = false; + pair->allscreen = false; +} + +Fingerprint_radial::~Fingerprint_radial() +{ + delete [] atomtypes; + delete [] radialtable; + delete [] alpha; + delete [] dfctable; + delete [] rinvsqrttable; +} + +bool Fingerprint_radial::parse_values(char* constant,char * line1){ + int l; + char **words=new char *[MAXLINE]; + int nwords; + nwords=0; + words[nwords++] = strtok(line1,": ,\t\n"); + while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; + nwords -= 1; + if (strcmp(constant,"re")==0){ + re = strtod(line1,NULL); + } + else if (strcmp(constant,"rc")==0){ + rc = strtod(line1,NULL); + } + else if (strcmp(constant,"alpha")==0){ + delete [] alpha; + alpha = new double [nwords]; + for (l=0;lerrorf("Undefined value for radial power"); + //code will run with default o=0 if o is never specified. All other values must be defined in potential file. + delete [] words; + if (re!=0 && rc!=0 && alpha!=0 && dr!=0 && n!=0)return true; + return false; +} + +void Fingerprint_radial::write_values(FILE *fid){ + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alpha:\n",style,id); + for (i=0;i<(n-o+1);i++){ + fprintf(fid,"%f ",alpha[i]); + } + fprintf(fid,"\n"); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:o:\n",style,id); + fprintf(fid,"%d\n",o); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:n:\n",style,id); + fprintf(fid,"%d\n",n); +} + +//called after fingerprint is fully defined and tables can be computed. +void Fingerprint_radial::allocate() +{ + int k,m; + double r1; + int buf = 5; + int res = pair->res; + double cutmax = pair->cutmax; + radialtable = new double [(res+buf)*get_length()]; + dfctable = new double [res+buf]; + for (k=0;k<(res+buf);k++){ + r1 = cutmax*cutmax*(double)(k)/(double)(res); + for (m=0;m<=(n-o);m++){ + radialtable[k*(n-o+1)+m]=pow(sqrt(r1)/re,m+o)*exp(-alpha[m]*sqrt(r1)/re)*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ + dfctable[k]=0; + } + else{ + dfctable[k]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } + generate_rinvssqrttable(); +} + +//called after fingerprint is declared for i-j type, but before its parameters are read. +void Fingerprint_radial::init(int *i,int id) +{ + empty = false; + for (int j=0;jid = id; +} + +void Fingerprint_radial::compute_fingerprint(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) +{ + int nelements = pair->nelements; + int res = pair->res; + int i,j,jj,itype,jtype,l; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + // + PairRANN::Simulation *sim = &pair->sims[sid]; + int count=0; +// double **x = sim->x; + int *type = sim->type; + ilist = sim->ilist; + double cutmax = pair->cutmax; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double cutinv2 = 1/cutmax/cutmax; +// numneigh = sim->numneigh; +// firstneigh = sim->firstneigh; +// xtmp = x[i][0]; +// ytmp = x[i][1]; +// ztmp = x[i][2]; +// jlist = firstneigh[i]; +// jnum = numneigh[i]; + //loop over neighbors + for (jj = 0; jj < jnum; jj++) { +// j = jlist[jj]; +// j &= NEIGHMASK; +// jtype = pair->map[type[j]]; + jtype =tn[jj]; + if (this->atomtypes[1] != nelements && this->atomtypes[1] != jtype)continue; +// delx = xtmp - x[j][0]; +// dely = ytmp - x[j][1]; +// delz = ztmp - x[j][2]; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq > rc*rc)continue; + count = startingneuron; + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (m1>res || m1<1){pair->errorf("invalid neighbor radius!");} + if (radialtable[m1]==0){continue;} + //cubic interpolation from tables + double *p1 = &radialtable[m1*(n-o+1)]; + double *p2 = &radialtable[(m1+1)*(n-o+1)]; + double *p3 = &radialtable[(m1+2)*(n-o+1)]; + double *p0 = &radialtable[(m1-1)*(n-o+1)]; + double *q = &dfctable[m1-1]; + double *rinvs = &rinvsqrttable[m1-1]; + r1 = r1-trunc(r1); + double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + double ri = rinvs[1] + 0.5 * r1*(rinvs[2] - rinvs[0] + r1*(2.0*rinvs[0] - 5.0*rinvs[1] + 4.0*rinvs[2] - rinvs[3] + r1*(3.0*(rinvs[1] - rinvs[2]) + rinvs[3] - rinvs[0]))); + for (l=0;l<=(n-o);l++){ + double rt = p1[l]+0.5*r1*(p2[l]-p0[l]+r1*(2.0*p0[l]-5.0*p1[l]+4.0*p2[l]-p3[l]+r1*(3.0*(p1[l]-p2[l])+p3[l]-p0[l]))); + features[count]+=rt; + rt *= (l+o)/rsq+(-alpha[l]/re+dfc)*ri; + //update neighbor's features + dfeaturesx[jj*f+count]+=rt*delx; + dfeaturesy[jj*f+count]+=rt*dely; + dfeaturesz[jj*f+count]+=rt*delz; + //update atom's features + dfeaturesx[jnum*f+count]-=rt*delx; + dfeaturesy[jnum*f+count]-=rt*dely; + dfeaturesz[jnum*f+count]-=rt*delz; + count++; + } + } + +} + +int Fingerprint_radial::get_length() +{ + return n-o+1; +} diff --git a/src/fingerprint_radial.h b/src/fingerprint_radial.h new file mode 100644 index 0000000000..e828aa2c41 --- /dev/null +++ b/src/fingerprint_radial.h @@ -0,0 +1,56 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + ----------------------------------------------------------------------*/ + +#ifdef FINGERPRINT_CLASS + +FingerprintStyle(radial,Fingerprint_radial) + +#else + +#ifndef FINGERPRINT_RADIAL_H_ +#define FINGERPRINT_RADIAL_H_ + +#include "fingerprint.h" + +namespace LAMMPS_NS { + +class Fingerprint_radial : public Fingerprint { + public: + Fingerprint_radial(PairRANN *); + ~Fingerprint_radial(); + bool parse_values(char*,char*); + void write_values(FILE *); + void init(int*,int); + void allocate(); + void compute_fingerprint(double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*); + int get_length(); + + double *radialtable; + double *dfctable; + double dr; + double *alpha; + double re; + int n;//highest term + int o;//lowest term + +}; + + +} + +#endif +#endif /* FINGERPRINT_RADIAL_H_ */ diff --git a/src/fingerprint_radialscreened.cpp b/src/fingerprint_radialscreened.cpp new file mode 100644 index 0000000000..003c7abbc3 --- /dev/null +++ b/src/fingerprint_radialscreened.cpp @@ -0,0 +1,266 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + ----------------------------------------------------------------------*/ + + +#include "fingerprint_radialscreened.h" +#include +#include +#include +#include +#include +#include + + +using namespace LAMMPS_NS; + +Fingerprint_radialscreened::Fingerprint_radialscreened(PairRANN *pair) : Fingerprint(pair) +{ + n_body_type = 2; + dr = 0; + re = 0; + rc = 0; + alpha = new double [1]; + alpha[0] = -1; + n = 0; + o = 0; + id = -1; + style = "radialscreened"; + atomtypes = new int [n_body_type]; + empty = true; + fullydefined = false; + pair->doscreen = true; + screen = true; +} + +Fingerprint_radialscreened::~Fingerprint_radialscreened() +{ + delete [] atomtypes; + delete [] radialtable; + delete [] alpha; + delete [] dfctable; + delete [] rinvsqrttable; +} + +bool Fingerprint_radialscreened::parse_values(char* constant,char * line1){ + int l; + char **words=new char *[MAXLINE]; + int nwords; + nwords=0; + words[nwords++] = strtok(line1,": ,\t\n"); + while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; + nwords -= 1; + if (strcmp(constant,"re")==0){ + re = strtod(line1,NULL); + } + else if (strcmp(constant,"rc")==0){ + rc = strtod(line1,NULL); + } + else if (strcmp(constant,"alpha")==0){ + delete [] alpha; + alpha = new double [nwords]; + for (l=0;lerrorf("Undefined value for radial power"); + //code will run with default o=0 if o is never specified. All other values must be defined in potential file. + delete [] words; + if (re!=0 && rc!=0 && alpha!=0 && dr!=0 && n!=0)return true; + return false; +} + +void Fingerprint_radialscreened::write_values(FILE *fid){ + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alpha:\n",style,id); + for (i=0;i<(n-o+1);i++){ + fprintf(fid,"%f ",alpha[i]); + } + fprintf(fid,"\n"); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:o:\n",style,id); + fprintf(fid,"%d\n",o); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:n:\n",style,id); + fprintf(fid,"%d\n",n); +} + +//called after fingerprint is fully defined and tables can be computed. +void Fingerprint_radialscreened::allocate() +{ + int k,m; + double r1; + int buf = 5; + int res = pair->res; + double cutmax = pair->cutmax; + radialtable = new double [(res+buf)*get_length()]; + dfctable = new double [res+buf]; + for (k=0;k<(res+buf);k++){ + r1 = cutmax*cutmax*(double)(k)/(double)(res); + for (m=0;m<=(n-o);m++){ + radialtable[k*(n-o+1)+m]=pow(sqrt(r1)/re,m+o)*exp(-alpha[m]*sqrt(r1)/re)*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ + dfctable[k]=0; + } + else{ + dfctable[k]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } + generate_rinvssqrttable(); +} + +//called after fingerprint is declared for i-j type, but before its parameters are read. +void Fingerprint_radialscreened::init(int *i,int id) +{ + empty = false; + for (int j=0;jid = id; +} + +void Fingerprint_radialscreened::compute_fingerprint(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) +{ + int nelements = pair->nelements; + int res = pair->res; + int i,j,jj,itype,jtype,l,kk; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + // + PairRANN::Simulation *sim = &pair->sims[sid]; + int count=0; + double **x = sim->x; + int *type = sim->type; + ilist = sim->ilist; + double cutmax = pair->cutmax; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double cutinv2 = 1/cutmax/cutmax; +// numneigh = sim->numneigh; +// firstneigh = sim->firstneigh; +// xtmp = x[i][0]; +// ytmp = x[i][1]; +// ztmp = x[i][2]; +// jlist = firstneigh[i]; +// jnum = numneigh[i]; + //loop over neighbors + for (jj = 0; jj < jnum; jj++) { + if (Bij[jj]==false){continue;} +// j = jlist[jj]; +// j &= NEIGHMASK; +// jtype = pair->map[type[j]]; + jtype = tn[jj]; + if (this->atomtypes[1] != nelements && this->atomtypes[1] != jtype)continue; +// delx = xtmp - x[j][0]; +// dely = ytmp - x[j][1]; +// delz = ztmp - x[j][2]; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq > rc*rc)continue; + count = startingneuron; + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (m1>res || m1<1){pair->errorf("invalid neighbor radius!");} + if (radialtable[m1]==0){continue;} + //cubic interpolation from tables + double *p1 = &radialtable[m1*(n-o+1)]; + double *p2 = &radialtable[(m1+1)*(n-o+1)]; + double *p3 = &radialtable[(m1+2)*(n-o+1)]; + double *p0 = &radialtable[(m1-1)*(n-o+1)]; + double *q = &dfctable[m1-1]; + double *rinvs = &rinvsqrttable[m1-1]; + r1 = r1-trunc(r1); + double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + double ri = rinvs[1] + 0.5 * r1*(rinvs[2] - rinvs[0] + r1*(2.0*rinvs[0] - 5.0*rinvs[1] + 4.0*rinvs[2] - rinvs[3] + r1*(3.0*(rinvs[1] - rinvs[2]) + rinvs[3] - rinvs[0]))); + for (l=0;l<=(n-o);l++){ + double rt = Sik[jj]*(p1[l]+0.5*r1*(p2[l]-p0[l]+r1*(2.0*p0[l]-5.0*p1[l]+4.0*p2[l]-p3[l]+r1*(3.0*(p1[l]-p2[l])+p3[l]-p0[l])))); + features[count]+=rt; + double rt1 = rt*((l+o)/rsq+(-alpha[l]/re+dfc)*ri); + //update neighbor's features + dfeaturesx[jj*f+count]+=rt1*delx+rt*dSikx[jj]; + dfeaturesy[jj*f+count]+=rt1*dely+rt*dSiky[jj]; + dfeaturesz[jj*f+count]+=rt1*delz+rt*dSikz[jj]; + for (kk=0;kk +#include +#include +#include +#include +#include + + +using namespace LAMMPS_NS; + +Fingerprint_radialscreenedspin::Fingerprint_radialscreenedspin(PairRANN *pair) : Fingerprint(pair) +{ + n_body_type = 2; + dr = 0; + re = 0; + rc = 0; + alpha = new double [1]; + alpha[0] = -1; + n = 0; + o = 0; + id = -1; + style = "radialscreenedspin"; + atomtypes = new int [n_body_type]; + empty = true; + fullydefined = false; + pair->doscreen = true; + screen = true; + pair->dospin = true; + spin = true; +} + +Fingerprint_radialscreenedspin::~Fingerprint_radialscreenedspin() +{ + delete [] atomtypes; + delete [] radialtable; + delete [] alpha; + delete [] dfctable; + delete [] rinvsqrttable; +} + +bool Fingerprint_radialscreenedspin::parse_values(char* constant,char * line1){ + int l; + char **words=new char *[MAXLINE]; + int nwords; + nwords=0; + words[nwords++] = strtok(line1,": ,\t\n"); + while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; + nwords -= 1; + if (strcmp(constant,"re")==0){ + re = strtod(line1,NULL); + } + else if (strcmp(constant,"rc")==0){ + rc = strtod(line1,NULL); + } + else if (strcmp(constant,"alpha")==0){ + delete [] alpha; + alpha = new double [nwords]; + for (l=0;lerrorf("Undefined value for radial power"); + //code will run with default o=0 if o is never specified. All other values must be defined in potential file. + delete [] words; + if (re!=0 && rc!=0 && alpha!=0 && dr!=0 && n!=0)return true; + return false; +} + +void Fingerprint_radialscreenedspin::write_values(FILE *fid){ + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alpha:\n",style,id); + for (i=0;i<(n-o+1);i++){ + fprintf(fid,"%f ",alpha[i]); + } + fprintf(fid,"\n"); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:o:\n",style,id); + fprintf(fid,"%d\n",o); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:n:\n",style,id); + fprintf(fid,"%d\n",n); +} + +//called after fingerprint is fully defined and tables can be computed. +void Fingerprint_radialscreenedspin::allocate() +{ + int k,m; + double r1; + int buf = 5; + int res = pair->res; + double cutmax = pair->cutmax; + radialtable = new double [(res+buf)*get_length()]; + dfctable = new double [res+buf]; + for (k=0;k<(res+buf);k++){ + r1 = cutmax*cutmax*(double)(k)/(double)(res); + for (m=0;m<=(n-o);m++){ + radialtable[k*(n-o+1)+m]=pow(sqrt(r1)/re,m+o)*exp(-alpha[m]*sqrt(r1)/re)*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ + dfctable[k]=0; + } + else{ + dfctable[k]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } + generate_rinvssqrttable(); +} + +//called after fingerprint is declared for i-j type, but before its parameters are read. +void Fingerprint_radialscreenedspin::init(int *i,int id) +{ + empty = false; + for (int j=0;jid = id; +} + +void Fingerprint_radialscreenedspin::compute_fingerprint(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,double * dspinx,double *dspiny,double *dspinz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) +{ + int nelements = pair->nelements; + int res = pair->res; + int i,j,jj,itype,jtype,l,kk; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + // + PairRANN::Simulation *sim = &pair->sims[sid]; + int count=0; + double **x = sim->x; + int *type = sim->type; + ilist = sim->ilist; + double cutmax = pair->cutmax; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double cutinv2 = 1/cutmax/cutmax; + double *si = sim->s[i]; +// numneigh = sim->numneigh; +// firstneigh = sim->firstneigh; +// xtmp = x[i][0]; +// ytmp = x[i][1]; +// ztmp = x[i][2]; +// jlist = firstneigh[i]; +// jnum = numneigh[i]; + //loop over neighbors + for (jj = 0; jj < jnum; jj++) { + if (Bij[jj]==false){continue;} +// j = jlist[jj]; +// j &= NEIGHMASK; +// jtype = pair->map[type[j]]; + jtype = tn[jj]; + if (this->atomtypes[1] != nelements && this->atomtypes[1] != jtype)continue; +// delx = xtmp - x[j][0]; +// dely = ytmp - x[j][1]; +// delz = ztmp - x[j][2]; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq > rc*rc)continue; + count = startingneuron; + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (m1>res || m1<1){pair->errorf("invalid neighbor radius!");} + if (radialtable[m1]==0){continue;} + j=jl[jj]; + double *sj = sim->s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + //cubic interpolation from tables + double *p1 = &radialtable[m1*(n-o+1)]; + double *p2 = &radialtable[(m1+1)*(n-o+1)]; + double *p3 = &radialtable[(m1+2)*(n-o+1)]; + double *p0 = &radialtable[(m1-1)*(n-o+1)]; + double *q = &dfctable[m1-1]; + double *rinvs = &rinvsqrttable[m1-1]; + r1 = r1-trunc(r1); + double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + double ri = rinvs[1] + 0.5 * r1*(rinvs[2] - rinvs[0] + r1*(2.0*rinvs[0] - 5.0*rinvs[1] + 4.0*rinvs[2] - rinvs[3] + r1*(3.0*(rinvs[1] - rinvs[2]) + rinvs[3] - rinvs[0]))); + for (l=0;l<=(n-o);l++){ + double rt = Sik[jj]*(p1[l]+0.5*r1*(p2[l]-p0[l]+r1*(2.0*p0[l]-5.0*p1[l]+4.0*p2[l]-p3[l]+r1*(3.0*(p1[l]-p2[l])+p3[l]-p0[l])))); + //update neighbor's features + dspinx[jj*f+count]+=rt*si[0]; + dspiny[jj*f+count]+=rt*si[1]; + dspinz[jj*f+count]+=rt*si[2]; + dspinx[jnum*f+count]+=rt*sj[0]; + dspiny[jnum*f+count]+=rt*sj[1]; + dspinz[jnum*f+count]+=rt*sj[2]; + rt *= sp; + features[count]+=rt; + double rt1 = rt*((l+o)/rsq+(-alpha[l]/re+dfc)*ri); + dfeaturesx[jj*f+count]+=rt1*delx+rt*dSikx[jj]; + dfeaturesy[jj*f+count]+=rt1*dely+rt*dSiky[jj]; + dfeaturesz[jj*f+count]+=rt1*delz+rt*dSikz[jj]; + for (kk=0;kk +#include +#include +#include +#include +#include + + +using namespace LAMMPS_NS; + +Fingerprint_radialspin::Fingerprint_radialspin(PairRANN *pair) : Fingerprint(pair) +{ + n_body_type = 2; + dr = 0; + re = 0; + rc = 0; + alpha = new double [1]; + alpha[0] = -1; + n = 0; + o = 0; + id = -1; + style = "radialspin"; + atomtypes = new int [n_body_type]; + empty = true; + fullydefined = false; + pair->allscreen = false; + pair->dospin = true; + spin = true; +} + +Fingerprint_radialspin::~Fingerprint_radialspin() +{ + delete [] atomtypes; + delete [] radialtable; + delete [] alpha; + delete [] dfctable; + delete [] rinvsqrttable; +} + +bool Fingerprint_radialspin::parse_values(char* constant,char * line1){ + int l; + char **words=new char *[MAXLINE]; + int nwords; + nwords=0; + words[nwords++] = strtok(line1,": ,\t\n"); + while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; + nwords -= 1; + if (strcmp(constant,"re")==0){ + re = strtod(line1,NULL); + } + else if (strcmp(constant,"rc")==0){ + rc = strtod(line1,NULL); + } + else if (strcmp(constant,"alpha")==0){ + delete [] alpha; + alpha = new double [nwords]; + for (l=0;lerrorf("Undefined value for radial power"); + //code will run with default o=0 if o is never specified. All other values must be defined in potential file. + delete [] words; + if (re!=0 && rc!=0 && alpha!=0 && dr!=0 && n!=0)return true; + return false; +} + +void Fingerprint_radialspin::write_values(FILE *fid){ + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alpha:\n",style,id); + for (i=0;i<(n-o+1);i++){ + fprintf(fid,"%f ",alpha[i]); + } + fprintf(fid,"\n"); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:o:\n",style,id); + fprintf(fid,"%d\n",o); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:n:\n",style,id); + fprintf(fid,"%d\n",n); +} + +//called after fingerprint is fully defined and tables can be computed. +void Fingerprint_radialspin::allocate() +{ + int k,m; + double r1; + int buf = 5; + int res = pair->res; + double cutmax = pair->cutmax; + radialtable = new double [(res+buf)*get_length()]; + dfctable = new double [res+buf]; + for (k=0;k<(res+buf);k++){ + r1 = cutmax*cutmax*(double)(k)/(double)(res); + for (m=0;m<=(n-o);m++){ + radialtable[k*(n-o+1)+m]=pow(sqrt(r1)/re,m+o)*exp(-alpha[m]*sqrt(r1)/re)*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ + dfctable[k]=0; + } + else{ + dfctable[k]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } + generate_rinvssqrttable(); +} + +//called after fingerprint is declared for i-j type, but before its parameters are read. +void Fingerprint_radialspin::init(int *i,int id) +{ + empty = false; + for (int j=0;jid = id; +} + +void Fingerprint_radialspin::compute_fingerprint(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,double * dspinx,double *dspiny,double *dspinz,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) +{ + int nelements = pair->nelements; + int res = pair->res; + int i,j,jj,itype,jtype,l; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + // + PairRANN::Simulation *sim = &pair->sims[sid]; + int count=0; +// double **x = sim->x; + int *type = sim->type; + ilist = sim->ilist; + double cutmax = pair->cutmax; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double cutinv2 = 1/cutmax/cutmax; + double *si = sim->s[i]; +// numneigh = sim->numneigh; + firstneigh = sim->firstneigh; +// xtmp = x[i][0]; +// ytmp = x[i][1]; +// ztmp = x[i][2]; + jlist = firstneigh[i]; +// jnum = numneigh[i]; + //loop over neighbors + for (jj = 0; jj < jnum; jj++) { + j = jl[jj]; + // jtype = pair->map[type[j]]; + jtype =tn[jj]; + if (this->atomtypes[1] != nelements && this->atomtypes[1] != jtype)continue; + // delx = xtmp - x[j][0]; + // dely = ytmp - x[j][1]; + // delz = ztmp - x[j][2]; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq > rc*rc)continue; + count = startingneuron; + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (m1>res || m1<1){pair->errorf("invalid neighbor radius!");} + if (radialtable[m1]==0){continue;} + double *sj = sim->s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + //cubic interpolation from tables + double *p1 = &radialtable[m1*(n-o+1)]; + double *p2 = &radialtable[(m1+1)*(n-o+1)]; + double *p3 = &radialtable[(m1+2)*(n-o+1)]; + double *p0 = &radialtable[(m1-1)*(n-o+1)]; + double *q = &dfctable[m1-1]; + double *rinvs = &rinvsqrttable[m1-1]; + r1 = r1-trunc(r1); + double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + double ri = rinvs[1] + 0.5 * r1*(rinvs[2] - rinvs[0] + r1*(2.0*rinvs[0] - 5.0*rinvs[1] + 4.0*rinvs[2] - rinvs[3] + r1*(3.0*(rinvs[1] - rinvs[2]) + rinvs[3] - rinvs[0]))); + for (l=0;l<=(n-o);l++){ + double rt = p1[l]+0.5*r1*(p2[l]-p0[l]+r1*(2.0*p0[l]-5.0*p1[l]+4.0*p2[l]-p3[l]+r1*(3.0*(p1[l]-p2[l])+p3[l]-p0[l]))); + dspinx[jj*f+count]+=rt*si[0]; + dspiny[jj*f+count]+=rt*si[1]; + dspinz[jj*f+count]+=rt*si[2]; + dspinx[jnum*f+count]+=rt*sj[0]; + dspiny[jnum*f+count]+=rt*sj[1]; + dspinz[jnum*f+count]+=rt*sj[2]; + rt *= sp; + features[count]+=rt; + rt *= (l+o)/rsq+(-alpha[l]/re+dfc)*ri; + //update neighbor's features + dfeaturesx[jj*f+count]+=rt*delx; + dfeaturesy[jj*f+count]+=rt*dely; + dfeaturesz[jj*f+count]+=rt*delz; + //update atom's features + dfeaturesx[jnum*f+count]-=rt*delx; + dfeaturesy[jnum*f+count]-=rt*dely; + dfeaturesz[jnum*f+count]-=rt*delz; + count++; + } + } + +} + +int Fingerprint_radialspin::get_length() +{ + return n-o+1; +} diff --git a/src/fingerprint_radialspin.h b/src/fingerprint_radialspin.h new file mode 100644 index 0000000000..c42b904d61 --- /dev/null +++ b/src/fingerprint_radialspin.h @@ -0,0 +1,56 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + ----------------------------------------------------------------------*/ + +#ifdef FINGERPRINT_CLASS + +FingerprintStyle(radialspin,Fingerprint_radialspin) + +#else + +#ifndef FINGERPRINT_RADIALspin_H_ +#define FINGERPRINT_RADIALspin_H_ + +#include "fingerprint.h" + +namespace LAMMPS_NS { + +class Fingerprint_radialspin : public Fingerprint { + public: + Fingerprint_radialspin(PairRANN *); + ~Fingerprint_radialspin(); + bool parse_values(char*,char*); + void write_values(FILE *); + void init(int*,int); + void allocate(); + void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*); + int get_length(); + + double *radialtable; + double *dfctable; + double dr; + double *alpha; + double re; + int n;//highest term + int o;//lowest term + +}; + + +} + +#endif +#endif /* FINGERPRINT_RADIAL_H_ */ diff --git a/src/pair_rann.cpp b/src/pair_rann.cpp new file mode 100644 index 0000000000..84333d7710 --- /dev/null +++ b/src/pair_rann.cpp @@ -0,0 +1,2423 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@cavs.msstate.edu + ----------------------------------------------------------------------*/ + +#include +#include +#include +#include +#include +#include +#include "atom.h" +#include "style_fingerprint.h" +#include "style_activation.h" +#include "force.h" +#include "comm.h" +#include "memory.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "memory.h" +#include "error.h" +#include "update.h" +#include "pair_rann.h" + + + +using namespace LAMMPS_NS; + +PairRANN::PairRANN(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 0; + restartinfo = 0; + one_coeff = 1; + manybody_flag = 1; + + allocated = 0; + + nelements = -1; + elements = NULL; + mass = NULL; + + // set comm size needed by this Pair + // comm unused for now. + + comm_forward = 38; + comm_reverse = 30; + res = 10000; + cutmax = 0; + //at least one of the following will change during fingerprint definition: + doscreen = false; + allscreen = true; + dospin = false; + + fingerprint_map = new FingerprintCreatorMap(); + + #define FINGERPRINT_CLASS + #define FingerprintStyle(key,Class) \ + (*fingerprint_map)[#key] = &fingerprint_creator; + #include "style_fingerprint.h" + #undef FingerprintStyle + #undef FINGERPRINT_CLASS + + activation_map = new ActivationCreatorMap(); + + #define ACTIVATION_CLASS + #define ActivationStyle(key,Class) \ + (*activation_map)[#key] = &activation_creator; + #include "style_activation.h" + #undef ActivationStyle + #undef ACTIVATION_CLASS +} + +PairRANN::~PairRANN() +{ + //clear memory + delete [] mass; + for (int i=0;i0){ + for (int j=0;j0){ + delete [] fingerprints[i]; + delete [] activation[i]; + } + } + delete [] fingerprints; + delete [] activation; + delete [] fingerprintcount; + delete [] fingerprintperelement; + delete [] fingerprintlength; + delete [] screening_min; + delete [] screening_max; +} + + + +void PairRANN::allocate(char **elementword) +{ + int i,j,k,l,n; + n = atom->ntypes; + memory->create(setflag,n+1,n+1,"pair:setflag"); + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + cutmax = 0; + nelementsp=nelements+1; + //initialize arrays + elements = new char *[nelements]; + elementsp = new char *[nelementsp];//elements + 'all' + mass = new double[nelements]; + net = new NNarchitecture[nelementsp]; + weightdefined = new bool*[nelementsp]; + biasdefined = new bool *[nelementsp]; + activation = new Activation**[nelementsp]; + fingerprints = new Fingerprint**[nelementsp]; + fingerprintlength = new int[nelementsp]; + fingerprintperelement = new int [nelementsp]; + fingerprintcount = new int[nelementsp]; + screening_min = new double [nelements*nelements*nelements]; + screening_max = new double [nelements*nelements*nelements]; + for (i=0;i 0) error->all(FLERR,"Illegal pair_style command"); +} + +void PairRANN::coeff(int narg, char **arg) +{ + int i,j; + map = new int [atom->ntypes+1]; + + + if (narg != 3 + atom->ntypes) + error->all(FLERR,"Incorrect args for pair coefficients"); + + + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); + nelements = -1; + read_file(arg[2]); + + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if NULL + + for (i = 3; i < narg; i++) { + if (strcmp(arg[i],"NULL") == 0) { + map[i-2] = -1; + continue; + } + for (j = 0; j < nelements; j++) + { + if (strcmp(arg[i],elements[j]) == 0) break; + } + if (j < nelements) map[i-2] = j; + else error->all(FLERR,"No matching element in NN potential file"); + } + // clear setflag since coeff() called once with I,J = * * + + int n = atom->ntypes; + for (i = 1; i <= n; i++) + for (j = i; j <= n; j++) + setflag[i][j] = 0; + + // set setflag i,j for type pairs where both are mapped to elements + // set mass of atom type if i = j + + int count = 0; + for (i = 1; i <= n; i++) { + for (j = i; j <= n; j++) { + if (map[i] >= 0 && map[j] >= 0) { + setflag[i][j] = 1; + if (i == j) atom->set_mass(FLERR,i,mass[map[i]]); + count++; + } + } + } + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + for (i=0;iallocate(); + } + } + allocated=1; +} + +void PairRANN::read_file(char *filename) +{ + FILE *fp; + int eof = 0,i,j,k,l; + int n,nwords; + char line [MAXLINE],line1[MAXLINE]; + + char *ptr; + bool comment; + char str[128]; + fp = force->open_potential(filename); + if (fp == NULL) { + sprintf(str,"Cannot open NN potential file %s",filename); + error->one(FLERR,str); + } + while (eof == 0){ + ptr = fgets(line,MAXLINE,fp); + if (ptr == NULL) { + if (check_potential()) {//looks to see if everything needed appears to be defined + error->one(FLERR,"Invalid syntax in potential file, values are inconsistent or missing"); + } + else{ + update_stack_size(); + fclose(fp); + eof = 1; + break; + } + } + else n = strlen(line) + 1; + // strip comment, skip line if blank + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = count_words(line); + char **words = new char* [strlen(line)]; + if (nwords == 0) continue; + comment = true; + while (comment==true){ + ptr = fgets(line1,MAXLINE,fp); + if (ptr==NULL)error->one(FLERR,"Unexpected end of file"); + if ((ptr = strchr(line1,'#'))) *ptr = '\0'; + nwords = count_words(line1); + if (nwords == 0) continue; + comment = false; + } + nwords = 0; + words[nwords++] = strtok(line,": ,\t_\n"); + while ((words[nwords++] = strtok(NULL,": ,\t_\n"))) continue; + if (strcmp(words[0],"atomtypes")==0)read_atom_types(words,line1); + else if (strcmp(words[0],"mass")==0)read_mass(words,line1); + else if (strcmp(words[0],"fingerprintsperelement")==0)read_fpe(words,line1); + else if (strcmp(words[0],"fingerprints")==0)read_fingerprints(words,nwords-1,line1); + else if (strcmp(words[0],"fingerprintconstants")==0)read_fingerprint_constants(words,nwords-1,line1); + else if (strcmp(words[0],"networklayers")==0)read_network_layers(words,line1); + else if (strcmp(words[0],"layersize")==0)read_layer_size(words,line1); + else if (strcmp(words[0],"weight")==0)read_weight(words,line1,fp); + else if (strcmp(words[0],"bias")==0)read_bias(words,line1,fp); + else if (strcmp(words[0],"activationfunctions")==0)read_activation_functions(words,line1); + else if (strcmp(words[0],"calibrationparameters")==0)continue;//information on how the network was trained + else if (strcmp(words[0],"screening")==0)read_screening(words,nwords-1,line1); + else error->one(FLERR,"Could not understand file syntax: unknown keyword"); + delete [] words; + } +} + +void PairRANN::read_atom_types(char **words,char * line1){ + int nwords = 0; + int t = count_words(line1)+1; + char **elementword = new char *[t]; + elementword[nwords++] = strtok(line1," ,\t:_\n"); + while ((elementword[nwords++] = strtok(NULL," ,\t:_\n"))) continue; + if (nwords < 1) errorf("Incorrect syntax for atom types"); + elementword[nwords-1] = new char [strlen("all")+1]; + char elt [] = "all"; + strcpy(elementword[nwords-1],elt); + nelements = nwords-1; + allocate(elementword); +} + +void PairRANN::read_mass(char **words,char * line1){ + if (nelements == -1)error->one(FLERR,"atom types must be defined before mass in potential file."); + int nwords = 0,i; + for (i=0;ione(FLERR,"mass element not found in atom types."); +} + +void PairRANN::read_fpe(char **words,char * line1){ + int i,j; + if (nelements == -1)error->one(FLERR,"atom types must be defined before fingerprints per element in potential file."); + for (i=0;ione(FLERR,"fingerprint-per-element element not found in atom types"); +} + +void PairRANN::read_fingerprints(char **words,int nwords,char * line1){ + int nwords1=0,i,j,k,l,m,i1; + bool found; + char str[MAXLINE]; + char **words1 = new char * [count_words(line1)+1]; + words1[nwords1++] = strtok(line1," ,\t:_\n"); + while ((words1[nwords1++] = strtok(NULL," ,\t:_\n"))) continue; + nwords1 -= 1; + if (nelements == -1)error->one(FLERR,"atom types must be defined before fingerprints in potential file."); + int atomtypes[nwords-1]; + for (i=1;ione(FLERR,"fingerprint element not found in atom types");} + } + i = atomtypes[0]; + k = 0; + if (fingerprintperelement[i]==-1){error->one(FLERR,"fingerprint per element must be defined before fingerprints");} + while (kn_body_type); + std::cout<n_body_type!=nwords-1){error->one(FLERR,"invalid fingerprint for element combination");} + k++; + fingerprints[i][i1]->init(atomtypes,strtol(words1[k++],NULL,10)); + fingerprintcount[i]++; + } + delete [] words1; +} + + +void PairRANN::read_fingerprint_constants(char **words,int nwords,char * line1){ + int i,j,k,l,m,i1; + bool found; + char str [128]; + if (nelements == -1)error->one(FLERR,"atom types must be defined before fingerprints in potential file."); + int n_body_type = nwords-4; + int atomtypes[n_body_type]; + for (i=1;i<=n_body_type;i++){ + found = false; + for (j=0;jone(FLERR,"fingerprint element not found in atom types");} + } + i = atomtypes[0]; + found = false; + for (k=0;kempty){continue;} + if (n_body_type!=fingerprints[i][k]->n_body_type){continue;} + for (j=0;jatomtypes[j]!=atomtypes[j]){break;} + if (j==n_body_type-1){ + if (strcmp(words[nwords-3],fingerprints[i][k]->style)==0 && strtol(words[nwords-2],NULL,10)==fingerprints[i][k]->id){ + found=true; + i1 = k; + break; + } + } + } + if (found){break;} + } + if (!found){error->one(FLERR,"cannot define constants for unknown fingerprint");} + fingerprints[i][i1]->fullydefined=fingerprints[i][i1]->parse_values(words[nwords-1],line1); +} + +void PairRANN::read_network_layers(char **words,char *line1){ + int i,j; + if (nelements == -1)error->one(FLERR,"atom types must be defined before network layers in potential file."); + for (i=0;ione(FLERR,"invalid number of network layers"); + delete [] net[i].dimensions; + net[i].dimensions = new int [net[i].layers]; + weightdefined[i] = new bool [net[i].layers]; + biasdefined[i] = new bool [net[i].layers]; + net[i].Weights = new double * [net[i].layers-1]; + net[i].Biases = new double * [net[i].layers-1]; + for (j=0;jone(FLERR,"network layers element not found in atom types"); +} + +void PairRANN::read_layer_size(char **words,char* line1){ + int i; + for (i=0;ione(FLERR,"networklayers for each atom type must be defined before the corresponding layer sizes."); + int j = strtol(words[2],NULL,10); + if (j>=net[i].layers || j<0){errorf("invalid layer in layer size definition");}; + net[i].dimensions[j]= strtol(line1,NULL,10); +// net[i].Weights[j] = new double [1]; +// net[i].Weights[j][0]=0; +// net[i].Biases[j] = new double [1]; +// net[i].Biases[j][0] = 0; + return; + } + } + error->one(FLERR,"layer size element not found in atom types"); +} + +void PairRANN::read_weight(char **words,char* line1,FILE* fp){ + int i,j,k,l,nwords; + char *ptr; + char **words1; + for (l=0;lone(FLERR,"networklayers must be defined before weights."); + i=strtol(words[2],NULL,10); + if (i>=net[l].layers || i<0)error->one(FLERR,"invalid weight layer"); + if (net[l].dimensions[i]==0 || net[l].dimensions[i+1]==0) error->one(FLERR,"network layer sizes must be defined before corresponding weight"); +// delete [] net[l].Weights[i]; + net[l].Weights[i] = new double [net[l].dimensions[i]*net[l].dimensions[i+1]]; + weightdefined[l][i] = true; + int n = count_words(line1)+1; + words1 = new char* [n]; + nwords=0; + words1[nwords++] = strtok(line1," ,\t:_\n"); + while ((words1[nwords++] = strtok(NULL," ,\t:_\n"))) continue; + nwords -= 1; + if (nwords != net[l].dimensions[i])error->one(FLERR,"invalid weights per line"); + for (k=0;kone(FLERR,"invalid weights per line"); + for (k=0;kone(FLERR,"weight element not found in atom types"); +} + +void PairRANN::read_bias(char **words,char* line1,FILE* fp){ + int i,j,l,nwords; + char *ptr; + for (l=0;lone(FLERR,"networklayers must be defined before biases."); + i=strtol(words[2],NULL,10); + if (i>=net[l].layers || i<0)error->one(FLERR,"invalid bias layer"); + if (net[l].dimensions[i]==0) error->one(FLERR,"network layer sizes must be defined before corresponding bias"); +// delete [] net[l].Biases[i]; + biasdefined[l][i] = true; + net[l].Biases[i] = new double [net[l].dimensions[i+1]]; + words[0] = strtok(line1," ,\t:_\n"); + net[l].Biases[i][0] = strtod(words[0],NULL); + for (j=1;jone(FLERR,"bias element not found in atom types"); +} + +void PairRANN::read_activation_functions(char** words,char * line1){ + int i,j,l,nwords; + int *ptr; + for (l=0;lone(FLERR,"networklayers must be defined before activation functions."); + i = strtol(words[2],NULL,10); + if (i>=net[l].layers || i<0)error->one(FLERR,"invalid activation layer"); + nwords=0; + words[nwords++] = strtok(line1," ,\t:_\n"); + delete activation[l][i]; + activation[l][i]=create_activation(line1); + return; + } + } + error->one(FLERR,"activation function element not found in atom types"); +} + +void PairRANN::read_screening(char** words,int nwords,char *line1){ + int i,j,k; + bool found; +// char str[MAXLINE]; +// sprintf(str,"%d\n",nwords); +// for (i=0;inet[i].maxlayer)net[i].maxlayer = net[i].dimensions[j]; + } + if (net[i].dimensions[net[i].layers-1]!=1)return true;//output layer must have single neuron (the energy) + for (j=0;jempty)return true;//undefined activations + for (k=0;kfullydefined==false)return true; + fingerprints[i][j]->startingneuron = fingerprintlength[i]; + fingerprintlength[i] +=fingerprints[i][j]->get_length(); + if (fingerprints[i][j]->rc>cutmax){cutmax = fingerprints[i][j]->rc;} + } + if (net[i].dimensions[0]!=fingerprintlength[i])return true; + } + return false;//everything looks good +} + +void PairRANN::compute(int eflag, int vflag) +{ + //perform force/energy computation_ + if (dospin){ + if (strcmp(update->unit_style,"metal") != 0) + error->all(FLERR,"Spin pair styles require metal units"); + if (!atom->sp_flag) + error->all(FLERR,"Spin pair styles requires atom/spin style"); + } + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = vflag_atom = 0; + int ii,i,j; + int nn = 0; + sims = new Simulation[1]; + sims->inum = listfull->inum; + sims->ilist=listfull->ilist; + sims->id = listfull->ilist; + sims->type = atom->type; + sims->x = atom->x; + sims->numneigh = listfull->numneigh; + sims->firstneigh = listfull->firstneigh; + if (dospin){ + sims->s = atom->sp; + } + int itype,f,jnum,len; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + if (eflag_global){eng_vdwl=0;eng_coul=0;} + double energy=0; + double **force = atom->f; + double **fm = atom->fm; + double **virial = vatom; + char str[MAXLINE]; + //loop over atoms + for (ii=0;iiinum;ii++){ + i = sims->ilist[ii]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + double xn[jnum]; + double yn[jnum]; + double zn[jnum]; + int tn[jnum]; + int jl[jnum]; + cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); + double features [f]; + double dfeaturesx[f*jnum]; + double dfeaturesy[f*jnum]; + double dfeaturesz[f*jnum]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + itype = nelements; + //do fingerprints for type "all" + len = fingerprintperelement[itype]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + clock_t t3 = clock(); + //run fingerprints through network + if (dospin){ + propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&energy,force,fm,virial,ii,jnum,jl); + } + else { + propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&energy,force,virial,ii,jnum,jl); + } + //testdfeatures(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii); + clock_t t4 = clock(); + double ts = (double) (t2-t1) / CLOCKS_PER_SEC * 1000.0; + double tf = (double) (t3-t2) / CLOCKS_PER_SEC * 1000.0; + double tp = (double) (t4-t3) / CLOCKS_PER_SEC * 1000.0; + sprintf(str,"screen time: %f, fingerprint time: %f, propagation time: %f\n",ts,tf,tp); +// std::cout<cutmax*cutmax){ + continue; + } + xn[count]=delx; + yn[count]=dely; + zn[count]=delz; + tn[count]=jtype; + jl[count]=j; + count++; + } + jnum[0]=count+1; +} + +void PairRANN::screen_neighbor_list(double *xn,double *yn, double *zn,int *tn, int* jnum,int *jl,int i,int sn,bool *Bij,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz){ + double xnc[jnum[0]],ync[jnum[0]],znc[jnum[0]]; + double Sikc[jnum[0]]; + double dSikxc[jnum[0]]; + double dSikyc[jnum[0]]; + double dSikzc[jnum[0]]; + double dSijkxc[jnum[0]][jnum[0]]; + double dSijkyc[jnum[0]][jnum[0]]; + double dSijkzc[jnum[0]][jnum[0]]; + int jj,kk,count,count1,tnc[jnum[0]],jlc[jnum[0]]; + count = 0; + for (jj=0;jjtype; + inum = sims->inum; + ilist = sims->ilist; + int f = net[itype].dimensions[0]; + double cutinv2 = 1/cutmax/cutmax; + i = sims->ilist[ii]; + numneigh = sims->numneigh; + firstneigh = sims->firstneigh; + jlist = firstneigh[i]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + double xn[jnum]; + double yn[jnum]; + double zn[jnum]; + int tn[jnum]; + int jl[jnum]; + double features1x [f]; + double features2x [f]; + double features1y [f]; + double features2y [f]; + double features1z [f]; + double features2z [f]; + double features1sx [f]; + double features2sx [f]; + double features1sy [f]; + double features2sy [f]; + double features1sz [f]; + double features2sz [f]; + double dfeaturesx1[f*jnum]; + double dfeaturesy1[f*jnum]; + double dfeaturesz1[f*jnum]; + double dspinx1[f*jnum]; + double dspiny1[f*jnum]; + double dspinz1[f*jnum]; + double dfxtest[f*jnum]; + double dfytest[f*jnum]; + double dfztest[f*jnum]; + double dfstestx[f*jnum]; + double dfstesty[f*jnum]; + double dfstestz[f*jnum]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1x,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1x,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1x,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1x,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + xn[jj] = xn[jj]-2*del; + if (doscreen){ + screen(Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,0,xn,yn,zn,tn,jnum-1); + } + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2x,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2x,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2x,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2x,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + for (k=0;kspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1y,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1y,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1y,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1y,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + yn[jj] = yn[jj]-2*del; + if (doscreen){ + screen(Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,0,xn,yn,zn,tn,jnum-1); + } + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2y,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2y,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2y,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2y,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + for (k=0;kspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1z,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1z,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1z,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1z,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + zn[jj] = zn[jj]-2*del; + if (doscreen){ + screen(Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,0,xn,yn,zn,tn,jnum-1); + } + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2z,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2z,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2z,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2z,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + for (k=0;ks[jj1][0]+=del; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + sims->s[jj1][0]-=2*del; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + for (k=0;ks[jj1][0]+=del; + sims->s[jj1][1]+=del; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + sims->s[jj1][1]-=2*del; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + for (k=0;ks[jj1][1]+=del; + sims->s[jj1][2]+=del; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + sims->s[jj1][2]-=2*del; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + for (k=0;ks[jj1][2]+=del; + for (k=0;kone(FLERR,"terminate"); + } +} + +void PairRANN::testdenergy(){ + double **force = atom->f; + double **fm = atom->fm; + double del = 0.00002; + int ii,i,j; + int nn = 0; + double ex1,ex2,ey1,ey2,ez1,ez2,esx1,esx2,esy1,esy2,esz1,esz2; + ex1=ex2=ey1=ey2=ez1=ez2=esx1=esx2=esy1=esy2=esz1=esz2=0.0; + double **force1 = new double *[listfull->maxatom]; + double **fm1 = new double *[listfull->maxatom]; + double **force1n = new double *[listfull->maxatom]; + double **fm1n = new double *[listfull->maxatom]; + for (i=0;imaxatom;i++){ + force1[i]=new double [3]; + fm1[i] = new double [3]; + force1n[i]=new double [3]; + fm1n[i] = new double [3]; + } + for (int n=0;ninum;n++){ + int itype,f,jnum,len; + double **virial = vatom; + char str[MAXLINE]; + eng_vdwl=0; + //loop over atoms + sims->x[n][0]+=del; + for (ii=0;iiinum;ii++){ + i = sims->ilist[ii]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + double xn[jnum]; + double yn[jnum]; + double zn[jnum]; + int tn[jnum]; + int jl[jnum]; + cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); + double features [f]; + double dfeaturesx[f*jnum]; + double dfeaturesy[f*jnum]; + double dfeaturesz[f*jnum]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + itype = nelements; + //do fingerprints for type "all" + len = fingerprintperelement[itype]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + //run fingerprints through network + if (dospin){ + propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&ex1,force1,fm1,virial,ii,jnum,jl); + } + else { + propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&ex1,force1,virial,ii,jnum,jl); + } + ex1=eng_vdwl; + } + eng_vdwl=0; + //loop over atoms + sims->x[n][0]-=2*del; + for (ii=0;iiinum;ii++){ + i = sims->ilist[ii]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + double xn[jnum]; + double yn[jnum]; + double zn[jnum]; + int tn[jnum]; + int jl[jnum]; + cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); + double features [f]; + double dfeaturesx[f*jnum]; + double dfeaturesy[f*jnum]; + double dfeaturesz[f*jnum]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + itype = nelements; + //do fingerprints for type "all" + len = fingerprintperelement[itype]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + //run fingerprints through network + if (dospin){ + propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&ex2,force1,fm1,virial,ii,jnum,jl); + } + else { + propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&ex2,force1,virial,ii,jnum,jl); + } + ex2=eng_vdwl; + } + force1n[n][0]=(ex1-ex2)/2/del; + eng_vdwl=0; + //loop over atoms + sims->x[n][0]+=del; + sims->x[n][1]+=del; + for (ii=0;iiinum;ii++){ + i = sims->ilist[ii]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + double xn[jnum]; + double yn[jnum]; + double zn[jnum]; + int tn[jnum]; + int jl[jnum]; + cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); + double features [f]; + double dfeaturesx[f*jnum]; + double dfeaturesy[f*jnum]; + double dfeaturesz[f*jnum]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + itype = nelements; + //do fingerprints for type "all" + len = fingerprintperelement[itype]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + //run fingerprints through network + if (dospin){ + propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&ey1,force1,fm1,virial,ii,jnum,jl); + } + else { + propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&ey1,force1,virial,ii,jnum,jl); + } + ey1=eng_vdwl; + } + eng_vdwl=0; + //loop over atoms + sims->x[n][1]-=2*del; + for (ii=0;iiinum;ii++){ + i = sims->ilist[ii]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + double xn[jnum]; + double yn[jnum]; + double zn[jnum]; + int tn[jnum]; + int jl[jnum]; + cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); + double features [f]; + double dfeaturesx[f*jnum]; + double dfeaturesy[f*jnum]; + double dfeaturesz[f*jnum]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + itype = nelements; + //do fingerprints for type "all" + len = fingerprintperelement[itype]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + //run fingerprints through network + if (dospin){ + propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&ey2,force1,fm1,virial,ii,jnum,jl); + } + else { + propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&ey2,force1,virial,ii,jnum,jl); + } + ey2=eng_vdwl; + } + eng_vdwl=0; + force1n[n][1]=(ey1-ey2)/2/del; + //loop over atoms + sims->x[n][1]+=del; + sims->x[n][2]+=del; + for (ii=0;iiinum;ii++){ + i = sims->ilist[ii]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + double xn[jnum]; + double yn[jnum]; + double zn[jnum]; + int tn[jnum]; + int jl[jnum]; + cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); + double features [f]; + double dfeaturesx[f*jnum]; + double dfeaturesy[f*jnum]; + double dfeaturesz[f*jnum]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + itype = nelements; + //do fingerprints for type "all" + len = fingerprintperelement[itype]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + //run fingerprints through network + if (dospin){ + propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&ez1,force1,fm1,virial,ii,jnum,jl); + } + else { + propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&ez1,force1,virial,ii,jnum,jl); + } + ez1=eng_vdwl; + } + eng_vdwl=0; + //loop over atoms + sims->x[n][2]-=2*del; + for (ii=0;iiinum;ii++){ + i = sims->ilist[ii]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + double xn[jnum]; + double yn[jnum]; + double zn[jnum]; + int tn[jnum]; + int jl[jnum]; + cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); + double features [f]; + double dfeaturesx[f*jnum]; + double dfeaturesy[f*jnum]; + double dfeaturesz[f*jnum]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + itype = nelements; + //do fingerprints for type "all" + len = fingerprintperelement[itype]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + //run fingerprints through network + if (dospin){ + propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&ez2,force1,fm1,virial,ii,jnum,jl); + } + else { + propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&ez2,force1,virial,ii,jnum,jl); + } + ez2=eng_vdwl; + } + eng_vdwl=0; + sims->x[n][2]+=del; + force1n[n][2]=(ez1-ez2)/2/del; + + //loop over atoms + sims->s[n][0]+=del; + for (ii=0;iiinum;ii++){ + i = sims->ilist[ii]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + double xn[jnum]; + double yn[jnum]; + double zn[jnum]; + int tn[jnum]; + int jl[jnum]; + cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); + double features [f]; + double dfeaturesx[f*jnum]; + double dfeaturesy[f*jnum]; + double dfeaturesz[f*jnum]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + itype = nelements; + //do fingerprints for type "all" + len = fingerprintperelement[itype]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + //run fingerprints through network + if (dospin){ + propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&esx1,force1,fm1,virial,ii,jnum,jl); + } + else { + propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&esx1,force1,virial,ii,jnum,jl); + } + esx1=eng_vdwl; + } + eng_vdwl=0; + //loop over atoms + sims->s[n][0]-=2*del; + for (ii=0;iiinum;ii++){ + i = sims->ilist[ii]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + double xn[jnum]; + double yn[jnum]; + double zn[jnum]; + int tn[jnum]; + int jl[jnum]; + cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); + double features [f]; + double dfeaturesx[f*jnum]; + double dfeaturesy[f*jnum]; + double dfeaturesz[f*jnum]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + itype = nelements; + //do fingerprints for type "all" + len = fingerprintperelement[itype]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + //run fingerprints through network + if (dospin){ + propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&esx2,force1,fm1,virial,ii,jnum,jl); + } + else { + propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&esx2,force1,virial,ii,jnum,jl); + } + esx2=eng_vdwl; + } + eng_vdwl=0; + fm1n[n][0]=(esx1-esx2)/2/del; + //loop over atoms + sims->s[n][0]+=del; + sims->s[n][1]+=del; + for (ii=0;iiinum;ii++){ + i = sims->ilist[ii]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + double xn[jnum]; + double yn[jnum]; + double zn[jnum]; + int tn[jnum]; + int jl[jnum]; + cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); + double features [f]; + double dfeaturesx[f*jnum]; + double dfeaturesy[f*jnum]; + double dfeaturesz[f*jnum]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + itype = nelements; + //do fingerprints for type "all" + len = fingerprintperelement[itype]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + //run fingerprints through network + if (dospin){ + propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&esy1,force1,fm1,virial,ii,jnum,jl); + } + else { + propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&esy1,force1,virial,ii,jnum,jl); + } + esy1=eng_vdwl; + } + eng_vdwl=0; + //loop over atoms + sims->s[n][1]-=2*del; + for (ii=0;iiinum;ii++){ + i = sims->ilist[ii]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + double xn[jnum]; + double yn[jnum]; + double zn[jnum]; + int tn[jnum]; + int jl[jnum]; + cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); + double features [f]; + double dfeaturesx[f*jnum]; + double dfeaturesy[f*jnum]; + double dfeaturesz[f*jnum]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + itype = nelements; + //do fingerprints for type "all" + len = fingerprintperelement[itype]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + //run fingerprints through network + if (dospin){ + propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&esy2,force1,fm1,virial,ii,jnum,jl); + } + else { + propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&esy2,force1,virial,ii,jnum,jl); + } + esy2=eng_vdwl; + } + eng_vdwl=0; + fm1n[n][1]=(esy1-esy2)/2/del; + //loop over atoms + sims->x[n][1]+=del; + sims->x[n][2]+=del; + for (ii=0;iiinum;ii++){ + i = sims->ilist[ii]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + double xn[jnum]; + double yn[jnum]; + double zn[jnum]; + int tn[jnum]; + int jl[jnum]; + cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); + double features [f]; + double dfeaturesx[f*jnum]; + double dfeaturesy[f*jnum]; + double dfeaturesz[f*jnum]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + itype = nelements; + //do fingerprints for type "all" + len = fingerprintperelement[itype]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + //run fingerprints through network + if (dospin){ + propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&esz1,force1,fm1,virial,ii,jnum,jl); + } + else { + propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&esz1,force1,virial,ii,jnum,jl); + } + esz1=eng_vdwl; + } + eng_vdwl=0; + //loop over atoms + sims->s[n][2]-=2*del; + for (ii=0;iiinum;ii++){ + i = sims->ilist[ii]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + double xn[jnum]; + double yn[jnum]; + double zn[jnum]; + int tn[jnum]; + int jl[jnum]; + cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); + double features [f]; + double dfeaturesx[f*jnum]; + double dfeaturesy[f*jnum]; + double dfeaturesz[f*jnum]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + itype = nelements; + //do fingerprints for type "all" + len = fingerprintperelement[itype]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + //run fingerprints through network + if (dospin){ + propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&esz2,force1,fm1,virial,ii,jnum,jl); + } + else { + propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&esz2,force1,virial,ii,jnum,jl); + } + esz2=eng_vdwl; + } + eng_vdwl=0; + sims->s[n][2]+=del; + fm1n[n][2]=(esz1-esz2)/2/del; + sprintf(str,"atom: %d fx: %f fxn: %f fy: %f fyn: %f fz: %f fzn: %f fmx: %f fmxn: %f fmy: %f fmyn: %f fmz: %f fmzn: %f\n",n,force[n][0],force1n[n][0],force[n][1],force1n[n][1],force[n][2],force1n[n][2],fm[n][0],fm1n[n][0],fm[n][1],fm1n[n][1],fm[n][2],fm1n[n][2]); + std::cout<x; + double xtmp,ytmp,ztmp,delx,dely,delz,rij,delx2,dely2,delz2,rik,delx3,dely3,delz3,rjk; + i = sim->ilist[ii]; + itype = map[sim->type[i]]; +// jnum = sim->numneigh[i]; +// jlist = sim->firstneigh[i]; +// xtmp = x[i][0]; +// ytmp = x[i][1]; +// ztmp = x[i][2]; + for (int jj=0;jjtype[k]]; + ktype = tn[kk]; +// delx2 = xtmp - x[k][0]; +// dely2 = ytmp - x[k][1]; +// delz2 = ztmp - x[k][2]; + delx2 = xn[kk]; + dely2 = yn[kk]; + delz2 = zn[kk]; + rik = delx2*delx2+dely2*dely2+delz2*delz2; + if (rik>cutmax*cutmax){ + Bij[kk]= false; + continue; + } + for (jj=0;jjtype[j]]; +// delx = xtmp - x[j][0]; +// dely = ytmp - x[j][1]; +// delz = ztmp - x[j][2]; + jtype = tn[jj]; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rij = delx*delx+dely*dely+delz*delz; + if (rij>cutmax*cutmax){ + Bij[jj] = false; + continue; + } +// delx3 = x[j][0]-x[k][0]; +// dely3 = x[j][1]-x[k][1]; +// delz3 = x[j][2]-x[k][2]; + delx3 = delx2-delx; + dely3 = dely2-dely; + delz3 = delz2-delz; + rjk = delx3*delx3+dely3*dely3+delz3*delz3; + if (rik+rjk<=rij){continue;}//bond angle > 90 degrees + if (rik+rij<=rjk){continue;}//bond angle > 90 degrees + double Cmax = screening_max[itype*nelements*nelements+jtype*nelements+ktype]; + double Cmin = screening_min[itype*nelements*nelements+jtype*nelements+ktype]; + double temp1 = rij-rik+rjk; + Cn = temp1*temp1-4*rij*rjk; + //Cn = (rij-rik+rjk)*(rij-rik+rjk)-4*rij*rjk; + temp1 = rij-rjk; + Cd = temp1*temp1-rik*rik; + //Cd = (rij-rjk)*(rij-rjk)-rik*rik; + Cijk = Cn/Cd; + //Cijk = 1+2*(rik*rij+rik*rjk-rik*rik)/(rik*rik-(rij-rjk)*(rij-rjk)); + C = (Cijk-Cmin)/(Cmax-Cmin); + if (C>=1){continue;} + else if (C<=0){ + Bij[kk]=false; + break; + } + dC = Cmax-Cmin; + dC *= dC; + dC *= dC; + temp1 = 1-C; + temp1 *= temp1; + temp1 *= temp1; + Sijk = 1-temp1; + Sijk *= Sijk; + Dij = 4*rik*(Cn+4*rjk*(rij+rik-rjk))/Cd/Cd; + Dik = -4*(rij*Cn+rjk*Cn+8*rij*rik*rjk)/Cd/Cd; + Djk = 4*rik*(Cn+4*rij*(rik-rij+rjk))/Cd/Cd; + temp1 = Cijk-Cmax; + double temp2 = temp1*temp1; + dfc = 8*temp1*temp2/(temp2*temp2-dC); + Sik[kk] *= Sijk; + dSijkx[kk*jnum+jj] = dfc*(delx*Dij-delx3*Djk); + dSikx[kk] += dfc*(delx2*Dik+delx3*Djk); + dSijky[kk*jnum+jj] = dfc*(dely*Dij-dely3*Djk); + dSiky[kk] += dfc*(dely2*Dik+dely3*Djk); + dSijkz[kk*jnum+jj] = dfc*(delz*Dij-delz3*Djk); + dSikz[kk] += dfc*(delz2*Dik+delz3*Djk); + } + } +} + + +//Called by getproperties. Propagate features and dfeatures through network. Updates force and energy +void PairRANN::propagateforward(double *features,double *dfeaturesx,double *dfeaturesy,double *dfeaturesz, double * energy,double **force,double **virial, int ii,int jnum,int *jl){ + int i,j,k,jj,j1,itype,i1; + int *ilist,*numneigh; + ilist = listfull->ilist; + int inum = listfull->inum; + int *type = atom->type; + i1=ilist[ii]; + itype = map[type[i1]]; + NNarchitecture net1 = net[itype]; +// numneigh = listfull->numneigh; +// jnum = numneigh[ilist[ii]]+1;//extra value on the end of the array is the self term. +// firstneigh = listfull->firstneigh; +// jlist = firstneigh[i1]; + int L = net1.layers-1; + double layer[net1.maxlayer]; + double sum[net1.maxlayer]; + double sum1[net1.maxlayer]; + double dlayerx[jnum][net1.maxlayer]; + double dlayersumx[jnum][net1.maxlayer]; + double dlayery[jnum][net1.maxlayer]; + double dlayersumy[jnum][net1.maxlayer]; + double dlayerz[jnum][net1.maxlayer]; + double dlayersumz[jnum][net1.maxlayer]; + //energy output with forces from analytical derivatives + double dsum1; + int f = net1.dimensions[0]; + for (i=0;idactivation_function(sum[j]); + sum[j] = activation[itype][i]->activation_function(sum[j]); + if (i==L-1){ + energy[j] = sum[j]; + if (eflag_atom)eatom[i1]=sum[j]; + if (eflag_global){eng_vdwl +=sum[j];} + } + //force propagation + for (jj=0;jjilist; + int inum = listfull->inum; + int *type = atom->type; + i1=ilist[ii]; + itype = map[type[i1]]; + NNarchitecture net1 = net[itype]; +// numneigh = listfull->numneigh; +// jnum = numneigh[ilist[ii]]+1;//extra value on the end of the array is the self term. +// firstneigh = listfull->firstneigh; +// jlist = firstneigh[i1]; + int L = net1.layers-1; + double layer[net1.maxlayer]; + double sum[net1.maxlayer]; + double sum1[net1.maxlayer]; + double dlayerx[jnum][net1.maxlayer]; + double dlayersumx[jnum][net1.maxlayer]; + double dlayery[jnum][net1.maxlayer]; + double dlayersumy[jnum][net1.maxlayer]; + double dlayerz[jnum][net1.maxlayer]; + double dlayersumz[jnum][net1.maxlayer]; + double dsx[jnum][net1.maxlayer]; + double dssumx[jnum][net1.maxlayer]; + double dsy[jnum][net1.maxlayer]; + double dssumy[jnum][net1.maxlayer]; + double dsz[jnum][net1.maxlayer]; + double dssumz[jnum][net1.maxlayer]; + //energy output with forces from analytical derivatives + double dsum1; + int f = net1.dimensions[0]; + for (i=0;idactivation_function(sum[j]); + sum[j] = activation[itype][i]->activation_function(sum[j]); + if (i==L-1){ + energy[j] = sum[j]; + if (eflag_atom)eatom[i1]=sum[j]; + if (eflag_global){eng_vdwl +=sum[j];} + } + //force propagation + for (jj=0;jjrequest(this,instance_me); + neighbor->requests[irequest_full]->id = 1; + neighbor->requests[irequest_full]->half = 0; + neighbor->requests[irequest_full]->full = 1; +} + + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairRANN::init_one(int i, int j) +{ + return cutmax; +} + +void PairRANN::errorf(char * message){ + this->error->all(FLERR,message); +} + +template +Fingerprint *PairRANN::fingerprint_creator(PairRANN* pair) +{ + return new T(pair); +} + +Fingerprint *PairRANN::create_fingerprint(const char *style) +{ + if (fingerprint_map->find(style) != fingerprint_map->end()) { + FingerprintCreator fingerprint_creator = (*fingerprint_map)[style]; + return fingerprint_creator(this); + } + char str[128]; + sprintf(str,"Unknown fingerprint style %s",style); + error->all(FLERR,str); + return NULL; +} + +template +Activation *PairRANN::activation_creator(PairRANN* pair) +{ + return new T(pair); +} + +Activation *PairRANN::create_activation(const char *style) +{ + if (activation_map->find(style) != activation_map->end()) { + ActivationCreator activation_creator = (*activation_map)[style]; + return activation_creator(this); + } + char str[128]; + sprintf(str,"Unknown activation style %s",style); + error->all(FLERR,str); + return NULL; +} + diff --git a/src/pair_rann.h b/src/pair_rann.h new file mode 100644 index 0000000000..d2746954d2 --- /dev/null +++ b/src/pair_rann.h @@ -0,0 +1,153 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@cavs.msstate.edu + ----------------------------------------------------------------------*/ + + +#ifdef PAIR_CLASS + +PairStyle(rann,PairRANN) + +#else + +#ifndef LMP_PAIR_RANN +#define LMP_PAIR_RANN + +#define MAXLINE 4096 + +#include "neigh_list.h" +#include "pair.h" +#include +#include +#include +#include + +namespace LAMMPS_NS { + +class PairRANN : public Pair { + public: + + //inherited functions + PairRANN(class LAMMPS *); + ~PairRANN(); + void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void init_list(int , NeighList *); + void errorf(char*); + int count_words(char *); + //black magic for modular fingerprints and activations + class Activation ***activation; + class Fingerprint ***fingerprints; + typedef Fingerprint *(*FingerprintCreator)(PairRANN *); + typedef Activation *(*ActivationCreator)(PairRANN *); + typedef std::map FingerprintCreatorMap; + typedef std::map ActivationCreatorMap; + FingerprintCreatorMap *fingerprint_map; + ActivationCreatorMap *activation_map; + Fingerprint * create_fingerprint(const char *); + Activation * create_activation(const char *); + + //global variables + int nelements; // # of elements (distinct from LAMMPS atom types since multiple atom types can be mapped to one element) + int nelementsp; // nelements+1 + char **elements; // names of elements + char **elementsp; // names of elements with "all" appended as the last "element" + double *mass; // mass of each element + double cutmax; // max radial distance for neighbor lists + int *map; // mapping from atom types to elements + int *fingerprintcount; // static variable used in initialization + int *fingerprintlength; // # of input neurons defined by fingerprints of each element. + int *fingerprintperelement; // # of fingerprints for each element + bool doscreen;//screening is calculated if any defined fingerprint uses it + bool allscreen;//all fingerprints use screening so screened neighbors can be completely ignored + bool dospin; + int res;//Resolution of function tables for cubic interpolation. + int memguess; +// double *Sik,*dSikx,*dSiky,*dSikz,*dSijkx,*dSijky,*dSijkz; +// bool *Bij; + double *screening_min; + double *screening_max; + bool **weightdefined; + bool **biasdefined; + + struct Simulation{ + int *id; + bool forces; + bool spins; + double **x; + double **f; + double **s; + double box[3][3]; + double origin[3]; + double **features; + double **dfx; + double **dfy; + double **dfz; + double **dsx; + double **dsy; + double **dsz; + int *ilist,*numneigh,**firstneigh,*type,inum,gnum; + }; + Simulation *sims; + + struct NNarchitecture{ + int layers; + int *dimensions;//vector of length layers with entries for neurons per layer + double **Weights; + double **Biases; + int *activations;//unused + int maxlayer;//longest layer (for memory allocation) + }; + NNarchitecture *net;//array of networks, 1 for each element. + + private: + template static Fingerprint *fingerprint_creator(PairRANN *); + template static Activation *activation_creator(PairRANN *); + //new functions + void allocate(char **);//called after reading element list, but before reading the rest of the potential + void read_file(char *);//read potential file + void read_atom_types(char **,char *); + void read_mass(char **,char *); + void read_fpe(char**,char *);//fingerprints per element. Count total fingerprints defined for each 1st element in element combinations + void read_fingerprints(char **,int,char *); + void read_fingerprint_constants(char **,int,char *); + void read_network_layers(char**,char*);//include input and output layer (hidden layers + 2) + void read_layer_size(char**,char*); + void read_weight(char**,char*,FILE*);//weights should be formatted as properly shaped matrices + void read_bias(char**,char*,FILE*);//biases should be formatted as properly shaped vectors + void read_activation_functions(char**,char*); + void read_screening(char**,int, char*); + bool check_potential();//after finishing reading potential file + void propagateforward(double *,double *,double *,double *,double *,double **,double **,int,int,int*);//called by compute to get force and energy + void propagateforwardspin(double *,double *,double *,double *,double *,double *,double *,double *,double **,double **,double**,int,int,int*);//called by compute to get force and energy + void screen(double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int *,int); + void testdfeatures(double *,double *, double *, double *,double *,double *, double *,int); + void testdenergy(); + void cull_neighbor_list(double *,double *,double *,int *,int *,int *,int,int); + void screen_neighbor_list(double *,double *,double *,int *,int *,int *,int,int,bool*,double*,double*,double*,double*,double*,double*,double*); + void update_stack_size(); +}; + +} + +#endif +#endif + + + diff --git a/src/style_activation.h b/src/style_activation.h new file mode 100644 index 0000000000..4cdd4ff031 --- /dev/null +++ b/src/style_activation.h @@ -0,0 +1,2 @@ +#include "activation_linear.h" +#include "activation_sigI.h" diff --git a/src/style_fingerprint.h b/src/style_fingerprint.h new file mode 100644 index 0000000000..2647d31274 --- /dev/null +++ b/src/style_fingerprint.h @@ -0,0 +1,8 @@ +#include "fingerprint_bond.h" +#include "fingerprint_bondscreened.h" +#include "fingerprint_bondscreenedspin.h" +#include "fingerprint_bondspin.h" +#include "fingerprint_radial.h" +#include "fingerprint_radialscreened.h" +#include "fingerprint_radialscreenedspin.h" +#include "fingerprint_radialspin.h" From ec82a4602d2dcf0a03deecca2cc5d437a8c081a1 Mon Sep 17 00:00:00 2001 From: kipbarrett Date: Fri, 29 Jan 2021 17:08:24 -0600 Subject: [PATCH 0071/1217] should be all ready --- doc/src/pair_rann.rst | 393 +++++++++++++++++++++++++++++++++++++++ potentials/Mg.rann | 91 +++++++++ potentials/MgAl.rann | 420 ++++++++++++++++++++++++++++++++++++++++++ potentials/Ti.rann | 125 +++++++++++++ potentials/Zn.rann | 124 +++++++++++++ potentials/Zr.rann | 124 +++++++++++++ 6 files changed, 1277 insertions(+) create mode 100644 doc/src/pair_rann.rst create mode 100644 potentials/Mg.rann create mode 100644 potentials/MgAl.rann create mode 100644 potentials/Ti.rann create mode 100644 potentials/Zn.rann create mode 100644 potentials/Zr.rann diff --git a/doc/src/pair_rann.rst b/doc/src/pair_rann.rst new file mode 100644 index 0000000000..72f1768364 --- /dev/null +++ b/doc/src/pair_rann.rst @@ -0,0 +1,393 @@ +.. index:: pair_style rann + +pair_style rann command +======================= + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style rann + pair_coeff file Type1_element Type2_element Type3_element... + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style rann + pair_coeff ** Mg.rann Mg + pair_coeff ** MgAlalloy.rann Mg Mg Al Mg + +Description +""""""""""" + +Style *rann* computes pairwise interactions for a variety of materials +using rapid atomistic neural network (RANN) potentials (:ref:`Dickel ` , :ref:`Nitol `). +Neural network potentials work by first generating a series of symmetry functions +i.e. structural fingerprints from the neighbor list and then using these values +as the input layer of a neural network. There is a single output neuron in the +final layer which is the energy. Atomic forces are found by analytical +derivatives computed via backpropagation. For alloy systems, each element has a unique +network. + +Potential file syntax +""""""""""""""""""""" + +The RANN potential is defined by a single text file which contains all the fitting parameters for the alloy system. +The potential file also defines the active fingerprints, network architecture, activation functions, etc. +The potential file is divided into several sections which are identified by one of the following keywords: + +* atomtypes + +* mass + +* fingerprintsperelement + +* fingerprints + +* fingerprintconstants + +* screening (optional) + +* networklayers + +* layersize + +* weight + +* bias + +* activationfunctions + +* calibrationparameters (ignored) + +# is treated as a comment marker, similar to LAMMPS input scripts. Sections are not required to follow a rigid +ordering, but do require previous definition of prerequisite information. E.g., fingerprintconstants for a +particular fingerprint must follow the fingerprints definition; layersize for a particular layer must follow +the declaration of network layers. + +*atomtypes* are defined as follows using element keywords separated by spaces. + +.. code-block:: + + atomtypes: + Fe Mg Al etc. + +*mass* must be specified for each element keyword as follows: + +.. code-block:: + + mass:Mg: + 24.305 + mass:Fe: + 55.847 + mass:Al: + 26.982 + +*fingerprintsperelement* specifies how many fingerprints are active for computing the energy of a given atom. +This number must be specified for each element keyword. Active elements for each fingerprint depend upon the +type of the central atom and the neighboring atoms. Pairwise fingerprints may be defined for a Mg atom based +exclusively on its Al neighbors, for example. Bond fingerprints may use two neighborlists of different +element types. In computing fingerprintsperelement from all defined fingerprints, only the fingerprints +defined for atoms of a particular element should be considered, regardless of the elements used in its +neighbor list. In the following code, for example, some fingerprints may compute pairwise fingerprints summing +contributions about Fe atoms based on a neighbor list of exclusively Al atoms, but if there are no fingerprints +summing contributions of all neighbors about a central Al atom, then fingerprintsperelement of Al is zero: + +.. code-block:: + + fingerprintsperelement:Mg: + 5 + fingerprintsperelement:Fe: + 2 + fingerprintsperelement:Al: + 0 + +*fingerprints* specifies the active fingerprints for a certain element combination. Pair fingerprints are +specified for two elements, while bond fingerprints are specified for three elements. Only one fingerprints +header should be used for an individual combination of elements. The ordering of the fingerprints in the +network input layer is determined by the order of element combinations specified by subsequent *fingerprints* +lines, and the order of the fingerprints defined for each element combination. Multiple fingerprints of the same style or +different ones may be specified. If the same style and element combination is used for multiple fingerprints, +they should have different id numbers. The first element specifies the atoms for which this fingerprint is +computed while the other(s) specify which atoms to use in the neighbor lists for the computation. Switching +the second and third element type in bond fingerprints has no effect on the computation: + +.. code-block:: + + fingerprints:Mg_Mg: + radial_0 radialscreened_0 radial_1 + fingerprints:Mg_Al_Fe: + bond_0 bondspin_0 + fingerprints:Mg_Al: + radial_0 radialscreened_0 + +The following fingerprint styles are currently defined. See the :ref:`formulation section ` below for their definitions: + +* radial + +* radialscreened + +* radialspin + +* radialscreenedspin + +* bond + +* bondscreened + +* bondspin + +* bondscreenedspin + +*fingerprintconstants* specifies the metaparameters for a defined fingerprint. For all radial styles, re, rc, +alpha, dr, o, and n must be specified. re should usually be the stable interatomic distance, rc is the cutoff +radius, dr is the cutoff smoothing distance, o is the lowest radial power term (which may be negative), and n +is the highest power term. The total length of the fingerprint vector is (n-o+1). alpha is a list of decay parameters +used for exponential decay of radial contributions. It may be set proportionally to the bulk modulus similarly +to MEAM potentials, but other values may provided better fitting in special cases. Bond style fingerprints require +specification of re, rc, alphak, dr, k, and m. Here m is the power of the bond cosines and k is the number of +decay parameters. Cosine powers go from 0 to m-1 and are each computed for all values of alphak. Thus the total +length of the fingerprint vector is m*k. + +.. code-block:: + + fingerprintconstants:Mg_Mg:radialscreened_0:re: + 3.193592 + fingerprintconstants:Mg_Mg:radialscreened_0:rc: + 6.000000 + fingerprintconstants:Mg_Mg:radialscreened_0:alpha: + 5.520000 5.520000 5.520000 5.520000 5.520000 + fingerprintconstants:Mg_Mg:radialscreened_0:dr: + 2.806408 + fingerprintconstants:Mg_Mg:radialscreened_0:o: + -1 + fingerprintconstants:Mg_Mg:radialscreened_0:n: + 3 + +*screening* specifies the Cmax and Cmin values used in the screening fingerprints. Neighbors' contribution to the +fingerprint are ommitted if they are blocked by a closer neighbor, and reduced if they are partially blocked. +Larger values of Cmin correspond to neighbors being blocked more easily. Cmax cannot be greater than 3, and +Cmin cannot be greater than Cmax or less than zero. Screening may be ommitted in which case the default values +Cmax = 2.8, Cmin = 0.8 are used. Since screening is a bond computation, it is specified separately for each +combination of three elements in which the latter two may be interchanged with no effect. + +.. code-block:: + + screening:Mg_Mg_Mg:Cmax: + 2.700000 + screening:Mg_Mg_Mg:Cmin: + 0.400000 + +*networklayers* species the size of the neural network for each atom. It counts both the input and output layer +and so is 2+hiddenlayers. + +.. code-block:: + + networklayers:Mg: + 3 + +*layersize* specifies the length of each layer, including the input layer and output layer. The input layer is +layer 0. The size of the input layer size must match the summed length of all the fingerprints for that element, +and the output layer size must be 1: + +.. code-block:: + + layersize:Mg:0: + 14 + layersize:Mg:1: + 20 + layersize:Mg:2: + 1 + +*weight* specifies the weight for a given element and layer. Weight cannot be specified for the output layer. +The weight of layer i is a mxn matrix where m is the layer size of i and n is the layer size of i+1: + +.. code-block:: + + weight:Mg:0: + w11 w12 w13 ... + w21 w22 w23 ... + ... + +*bias* specifies the bias for a given element and layer. Bias cannot be specified for the output layer. +The bias of layer i is a nx1 vector where n is the layer size of i+1: + +.. code-block:: + + bias:Mg:0: + b1 + b2 + b3 + ... + +*activationfunctions* specifies the activation function for a given element and layer. Activation functions +cannot be specified for the output layer: + +.. code-block:: + + activationfunctions:Mg:0: + sigI + activationfunctions:Mg:1: + linear + +The following activation styles are currently specified. See the :ref:`formulation section ` below for their definitions. + +* sigI + +* linear + +*calibrationparameters* specifies a number of parameters used to calibrate the potential. These are ignored +by LAMMPS. + +Formulation +""""""""""" + +In the RANN formulation, the total energy of a system of atoms +is given by: + +.. math:: + + E = \sum_{\alpha} E^{\alpha}\\\\ + E^{\alpha} = {}^{N}\!A^{\alpha}\\\\ + {}^{n+1}\!A_i^{\alpha} = {}^{n}\!F\left({}^{n}\!W_{ij}{\;}^{n}\!A_j^{\alpha}+{}^{n}\!B_i\right)\\\\ + {}^{0}\!A_i^{\alpha} = \left[\begin{array} S{}^1\!S\!f^\alpha\\ {}^2\!S\!f^\alpha \\...\\\end{array}\right] + +Here :math:`E^\alpha` is the energy of atom :math:`\alpha`, :math:`{}^n\!F()`, :math:`{}^n\!W_{ij}` and :math:`{}^n\!B_i` are +the activation function, weight matrix and bias vector of the n-th layer respectively. The +inputs to the first layer are a collection of structural fingerprints which are collected and reshaped into a single long vector. +The individual fingerprints may be defined in any order and have various shapes and sizes. Multiple fingerprints of the same +type and varying parameters may also be defined in the input layer. + +Eight types of structural fingerprints are currently defined. In the following, :math:`\beta` and :math:`\gamma` span the +full neighborlist of atom :math:`\alpha`. :math:`\delta_i` are decay metaparameters, and :math:`r_e` is a metaparameter +roughly proportional to the first neighbor distance. :math:`r_c` and :math:`dr` are the neighbor cutoff distance and +cutoff smoothing distance respectively. :math:`S^{\alpha\beta}` is the MEAM screening function +:ref:`(Baskes) `, :math:`s_i^\alpha` and :math:`s_i^\beta` are the atom spin vectors :ref:`(Tranchida) `. +:math:`r^{\alpha\beta}` is the distance from atom :math:`\alpha` to atom :math:`\beta`, and :math:`\theta^{\alpha\beta\gamma}` +is the bond angle: + +.. math :: + + cos\left(\theta^{\alpha\beta\gamma}\right)=\frac{\mathbf{r}^{\alpha\beta} \cdot \mathbf{r}^{\alpha\gamma}}{r^{\alpha\beta}r^{\alpha\gamma}} + +:math:`S^{\alpha\beta}` is defined as :ref:`(Baskes) `: + +.. math:: + + X^{\gamma\beta} = \left(\frac{r^{\gamma\beta}}{r^{\alpha\beta}}\right)^2\\ + \\ + X^{\alpha\gamma} = \left(\frac{r^{\alpha\gamma}}{r^{\alpha\beta}}\right)^2\\ + \\ + C = \frac{2\left(X^{\alpha\gamma}+X^{\gamma\beta}\right)-\left(X^{\alpha\gamma}-X^{\gamma\beta}\right)^2-1}{1-\left(X^{\alpha\gamma}-X^{\gamma\beta}\right)^2}\\ + \\ + f_c(x) = \left[\begin{array} 11 \; x \geq 1\\ \left(1-\left(1-x\right)^4\right)^2 \; 0 Date: Fri, 29 Jan 2021 17:09:40 -0600 Subject: [PATCH 0072/1217] maybe the last one --- doc/src/Commands_pair.rst | 1 + doc/src/pair_rann.rst | 4 +- doc/src/pair_style.rst | 1 + potentials/Mg.rann | 91 -- src/activation.cpp | 17 +- src/activation.h | 17 +- src/activation_linear.cpp | 20 +- src/activation_linear.h | 18 +- src/activation_sigI.cpp | 17 +- src/activation_sigI.h | 19 +- src/fingerprint.cpp | 21 +- src/fingerprint.h | 18 +- src/fingerprint_bond.cpp | 23 +- src/fingerprint_bond.h | 17 +- src/fingerprint_bondscreened.cpp | 22 +- src/fingerprint_bondscreened.h | 16 +- src/fingerprint_bondscreenedspin.cpp | 24 +- src/fingerprint_bondscreenedspin.h | 16 +- src/fingerprint_bondspin.cpp | 24 +- src/fingerprint_bondspin.h | 16 +- src/fingerprint_radial.cpp | 24 +- src/fingerprint_radial.h | 16 +- src/fingerprint_radialscreened.cpp | 23 +- src/fingerprint_radialscreened.h | 16 +- src/fingerprint_radialscreenedspin.cpp | 24 +- src/fingerprint_radialscreenedspin.h | 16 +- src/fingerprint_radialspin.cpp | 24 +- src/fingerprint_radialspin.h | 17 +- src/pair_rann.cpp | 1354 ++---------------------- src/pair_rann.h | 40 +- 30 files changed, 471 insertions(+), 1485 deletions(-) delete mode 100644 potentials/Mg.rann diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 2ca0e88729..8d28bb7bb6 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -221,6 +221,7 @@ OPT. * :doc:`polymorphic ` * :doc:`python ` * :doc:`quip ` + * :doc:`rann ` * :doc:`reax/c (ko) ` * :doc:`rebo (io) ` * :doc:`resquared (go) ` diff --git a/doc/src/pair_rann.rst b/doc/src/pair_rann.rst index 72f1768364..af9b90de14 100644 --- a/doc/src/pair_rann.rst +++ b/doc/src/pair_rann.rst @@ -253,7 +253,7 @@ is given by: E = \sum_{\alpha} E^{\alpha}\\\\ E^{\alpha} = {}^{N}\!A^{\alpha}\\\\ {}^{n+1}\!A_i^{\alpha} = {}^{n}\!F\left({}^{n}\!W_{ij}{\;}^{n}\!A_j^{\alpha}+{}^{n}\!B_i\right)\\\\ - {}^{0}\!A_i^{\alpha} = \left[\begin{array} S{}^1\!S\!f^\alpha\\ {}^2\!S\!f^\alpha \\...\\\end{array}\right] + {}^{0}\!A_i^{\alpha} = \left[\begin{array}{c} {}^1\!S\!f^\alpha\\ {}^2\!S\!f^\alpha \\...\\\end{array}\right] Here :math:`E^\alpha` is the energy of atom :math:`\alpha`, :math:`{}^n\!F()`, :math:`{}^n\!W_{ij}` and :math:`{}^n\!B_i` are the activation function, weight matrix and bias vector of the n-th layer respectively. The @@ -283,7 +283,7 @@ is the bond angle: \\ C = \frac{2\left(X^{\alpha\gamma}+X^{\gamma\beta}\right)-\left(X^{\alpha\gamma}-X^{\gamma\beta}\right)^2-1}{1-\left(X^{\alpha\gamma}-X^{\gamma\beta}\right)^2}\\ \\ - f_c(x) = \left[\begin{array} 11 \; x \geq 1\\ \left(1-\left(1-x\right)^4\right)^2 \; 0` - polymorphic 3-body potential * :doc:`python ` - * :doc:`quip ` - +* :doc:`rann ` - * :doc:`reax/c ` - ReaxFF potential in C * :doc:`rebo ` - second generation REBO potential of Brenner * :doc:`resquared ` - Everaers RE-Squared ellipsoidal potential diff --git a/potentials/Mg.rann b/potentials/Mg.rann deleted file mode 100644 index 23ce143f2e..0000000000 --- a/potentials/Mg.rann +++ /dev/null @@ -1,91 +0,0 @@ -# Neural Network Potential file created by MATLAB -atomtypes: -Mg -mass:Mg: -24.305 -fingerprints:Mg_Mg: - radialpower_0 -fingerprints:Mg_Mg_Mg: - bondpower_0 -fingerprintconstants:Mg_Mg:radialpower_0:re: -3.1936 -fingerprintconstants:Mg_Mg:radialpower_0:rc: -6 -fingerprintconstants:Mg_Mg:radialpower_0:dr: -2.8064 -fingerprintconstants:Mg_Mg:radialpower_0:n: -3 -fingerprintconstants:Mg_Mg:radialpower_0:o: --1 -fingerprintconstants:Mg_Mg:radialpower_0:alpha: -5.52 5.52 5.52 5.52 5.52 -fingerprintconstants:Mg_Mg_Mg:bondpower_0:re: -3.1936 -fingerprintconstants:Mg_Mg_Mg:bondpower_0:rc: -6 -fingerprintconstants:Mg_Mg_Mg:bondpower_0:dr: -2.8064 -fingerprintconstants:Mg_Mg_Mg:bondpower_0:m: -8 -fingerprintconstants:Mg_Mg_Mg:bondpower_0:alphak: -1 2 6 9 -fingerprintconstants:Mg_Mg_Mg:bondpower_0:k: -4 -networklayers:Mg: -3 -layersize:Mg:0: -37 -layersize:Mg:1: -20 -layersize:Mg:2: -1 -weight:Mg:0: - 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-6.854080311751575 -3.366413846641228 -13.072799595088947 -1.947514492844213 13.713838929601375 -0.019406446538777 8.473917855409606 1.004610551903908 9.093996565522684 3.207103662168222 3.901439651670244 2.983318187189680 -2.524579939084030 3.252784494652512 2.950876646744284 3.372023470643452 -0.464237673645948 3.755696203886226 3.808960469764337 2.339907193946746 5.146170730857166 17.834156726071658 0.035731510216900 6.005254664256362 -1.999420765454485 4.690139638769533 -9.977721762987899 7.426200989135139 1.184394487193257 -0.046748770059314 0.150461492361159 1.259105030698577 0.036602097122206 1.061204719522792 -0.582916554758782 1.475480676393535 -0.874188624044419 - -0.091871803641423 0.155712039736981 -1.736705516334532 -3.235473587990033 -7.662082879932669 0.592839860436439 -7.068870826737258 -0.399637343479208 -6.149104660398526 -2.063383569534510 7.873997147178776 -3.605791816207420 20.150381452293846 -3.351880740983101 -0.863899319401915 -4.018547645815094 -0.784923284019245 -4.442513682373789 0.250780859062035 -5.184517276334443 0.558648923127730 1.885233769145124 0.001521615587180 0.634399323585855 -0.213531910461594 0.494460218427058 -1.058719613823579 0.784528439330135 0.124197877420478 -0.004983773553378 0.015924450492573 0.133399802571537 0.003863441417922 0.112429943824441 -0.061782783107639 0.156329122431333 -0.092647205069654 - 0.482137277570261 0.655431110773911 0.092243100481870 0.244841673165367 0.207743962910201 -0.645933694930810 -0.982792443155817 -0.909615692956593 0.313478029717837 -0.555365598226454 4.163468659783327 -0.412159823135017 6.862260499419868 -3.302281380717564 1.482065536636173 -2.407385962358501 1.098207258186840 -1.807106215233626 1.383175114366523 -1.461187579432369 1.404195771393285 0.800616887078038 0.003684546162640 0.269069405372722 -0.087549656335027 0.209484975310045 -0.442918898899253 0.331272282874469 0.053885366476729 -0.002067807910823 0.006698932859304 0.056045887718202 0.001629610981992 0.047234045216482 -0.025947665446354 0.065674182157580 -0.038913439761760 - 12.149148826917946 4.657579636724005 1.764736473860053 0.870668138244216 6.223017368077887 -1.046145904487804 0.953308100141891 -1.978615490874998 -3.417207462372495 -2.506835762341485 -3.697370786082169 -0.450785302259934 -3.125213455592869 -1.637693139214092 -1.348769649727682 -1.994082907081566 2.283115627163778 -2.635964849784550 -3.318422800479618 -3.639669251682635 -0.145614294451353 -1.483837070228372 0.212891384076277 -0.324023869431791 0.362382513657968 -0.276474277638942 1.166715100587859 -0.608385924126500 -0.008353550840676 0.006659952284272 -0.013796269604796 -0.130275245160746 -0.002411584088968 -0.109852596493500 0.062271293211841 -0.153386893869237 0.092727416429870 -bias:Mg:0: - -5.812840455195256 - 15.010638582099496 - 29.624659288791705 - 6.089482003604780 - -20.183942564953359 - -19.131750622870765 - 25.425690046060971 - 27.624111929794111 - 0.740297410586282 - -4.844537022087861 - 20.211971127789965 - -3.950026427133535 - 28.926886494246766 - 25.304822365917076 - 27.383284316546206 - -14.878350779530585 - -13.726815004417979 - 0.300936029014161 - -1.610552372672948 - 17.876279610284211 -weight:Mg:1: - 8.393525190816597 -9.799005074799757 -7.735480085336927 -8.104124576752014 12.240026012539039 5.213425998776577 -3.945232488424331 -5.429176982828405 -99.914578185849578 3.921063641589451 -12.243519026057772 3.482819561249847 -6.785425943665748 -4.818862897620001 -5.773098229238692 5.383347312306200 8.019798211775075 8.499369933136281 3.569846715528147 -8.397559798533649 -bias:Mg:1: -1713.7664607023298 -activationfunctions:Mg:0: -sigI -activationfunctions:Mg:1: -linear diff --git a/src/activation.cpp b/src/activation.cpp index aaa409c4b0..5286eb4730 100644 --- a/src/activation.cpp +++ b/src/activation.cpp @@ -10,10 +10,23 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #include "activation.h" diff --git a/src/activation.h b/src/activation.h index 3fba49723d..0188f80bff 100644 --- a/src/activation.h +++ b/src/activation.h @@ -10,10 +10,23 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #ifndef ACTIVATION_H_ #define ACTIVATION_H_ diff --git a/src/activation_linear.cpp b/src/activation_linear.cpp index 2ad9594be1..ddb9ae54c9 100644 --- a/src/activation_linear.cpp +++ b/src/activation_linear.cpp @@ -10,14 +10,26 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ -#include #include "activation_linear.h" -#include "activation.h" + using namespace LAMMPS_NS; diff --git a/src/activation_linear.h b/src/activation_linear.h index ba39436f03..2ea0f55729 100644 --- a/src/activation_linear.h +++ b/src/activation_linear.h @@ -10,11 +10,23 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu -*/ + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #ifdef ACTIVATION_CLASS ActivationStyle(linear,Activation_linear) diff --git a/src/activation_sigI.cpp b/src/activation_sigI.cpp index cdf82982da..b14f1c503d 100644 --- a/src/activation_sigI.cpp +++ b/src/activation_sigI.cpp @@ -10,12 +10,23 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” -#include +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #include "activation_sigI.h" using namespace LAMMPS_NS; diff --git a/src/activation_sigI.h b/src/activation_sigI.h index b47433a336..404af35cfd 100644 --- a/src/activation_sigI.h +++ b/src/activation_sigI.h @@ -10,10 +10,23 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu -*/ + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #ifdef ACTIVATION_CLASS diff --git a/src/fingerprint.cpp b/src/fingerprint.cpp index cdcb5855bd..89786b632a 100644 --- a/src/fingerprint.cpp +++ b/src/fingerprint.cpp @@ -10,18 +10,25 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #include "fingerprint.h" -#include -#include -#include -#include -#include -#include using namespace LAMMPS_NS; diff --git a/src/fingerprint.h b/src/fingerprint.h index 1bef4c0ab8..35645742f4 100644 --- a/src/fingerprint.h +++ b/src/fingerprint.h @@ -10,10 +10,24 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + +----------------*/ #ifndef FINGERPRINT_H_ #define FINGERPRINT_H_ diff --git a/src/fingerprint_bond.cpp b/src/fingerprint_bond.cpp index 7fdece310c..1f8630ccb2 100644 --- a/src/fingerprint_bond.cpp +++ b/src/fingerprint_bond.cpp @@ -10,21 +10,26 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@cavs.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #include "fingerprint_bond.h" -#include "fingerprint.h" -#include -#include -#include -#include -#include -#include + using namespace LAMMPS_NS; diff --git a/src/fingerprint_bond.h b/src/fingerprint_bond.h index 1d07d34f3b..42d5cb03c6 100644 --- a/src/fingerprint_bond.h +++ b/src/fingerprint_bond.h @@ -10,10 +10,23 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #ifdef FINGERPRINT_CLASS diff --git a/src/fingerprint_bondscreened.cpp b/src/fingerprint_bondscreened.cpp index 54659581a7..c573f6aedb 100644 --- a/src/fingerprint_bondscreened.cpp +++ b/src/fingerprint_bondscreened.cpp @@ -10,21 +10,25 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@cavs.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #include "fingerprint_bondscreened.h" -#include "fingerprint.h" -#include -#include -#include -#include -#include -#include using namespace LAMMPS_NS; diff --git a/src/fingerprint_bondscreened.h b/src/fingerprint_bondscreened.h index 912cd1f84f..945e1615fc 100644 --- a/src/fingerprint_bondscreened.h +++ b/src/fingerprint_bondscreened.h @@ -10,11 +10,23 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #ifdef FINGERPRINT_CLASS FingerprintStyle(bondscreened,Fingerprint_bondscreened) diff --git a/src/fingerprint_bondscreenedspin.cpp b/src/fingerprint_bondscreenedspin.cpp index cf1812b700..ce7e7c9e51 100644 --- a/src/fingerprint_bondscreenedspin.cpp +++ b/src/fingerprint_bondscreenedspin.cpp @@ -10,21 +10,25 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@cavs.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” - +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #include "fingerprint_bondscreenedspin.h" -#include "fingerprint.h" -#include -#include -#include -#include -#include -#include + using namespace LAMMPS_NS; diff --git a/src/fingerprint_bondscreenedspin.h b/src/fingerprint_bondscreenedspin.h index 8a081305ff..e560c16ddb 100644 --- a/src/fingerprint_bondscreenedspin.h +++ b/src/fingerprint_bondscreenedspin.h @@ -10,11 +10,23 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #ifdef FINGERPRINT_CLASS FingerprintStyle(bondscreenedspin,Fingerprint_bondscreenedspin) diff --git a/src/fingerprint_bondspin.cpp b/src/fingerprint_bondspin.cpp index 69e214c77a..78a0bdd815 100644 --- a/src/fingerprint_bondspin.cpp +++ b/src/fingerprint_bondspin.cpp @@ -10,21 +10,25 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@cavs.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” - +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #include "fingerprint_bondspin.h" -#include "fingerprint.h" -#include -#include -#include -#include -#include -#include + using namespace LAMMPS_NS; diff --git a/src/fingerprint_bondspin.h b/src/fingerprint_bondspin.h index 5190af7107..56c540b508 100644 --- a/src/fingerprint_bondspin.h +++ b/src/fingerprint_bondspin.h @@ -10,11 +10,23 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #ifdef FINGERPRINT_CLASS FingerprintStyle(bondspin,Fingerprint_bondspin) diff --git a/src/fingerprint_radial.cpp b/src/fingerprint_radial.cpp index f42dfc8cef..71dbcd9ad8 100644 --- a/src/fingerprint_radial.cpp +++ b/src/fingerprint_radial.cpp @@ -10,20 +10,26 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #include "fingerprint_radial.h" -#include "fingerprint.h" -#include -#include -#include -#include -#include -#include + using namespace LAMMPS_NS; diff --git a/src/fingerprint_radial.h b/src/fingerprint_radial.h index e828aa2c41..aeb1c2eca3 100644 --- a/src/fingerprint_radial.h +++ b/src/fingerprint_radial.h @@ -10,11 +10,23 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #ifdef FINGERPRINT_CLASS FingerprintStyle(radial,Fingerprint_radial) diff --git a/src/fingerprint_radialscreened.cpp b/src/fingerprint_radialscreened.cpp index 003c7abbc3..3101ca0ab0 100644 --- a/src/fingerprint_radialscreened.cpp +++ b/src/fingerprint_radialscreened.cpp @@ -10,19 +10,26 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #include "fingerprint_radialscreened.h" -#include -#include -#include -#include -#include -#include + using namespace LAMMPS_NS; diff --git a/src/fingerprint_radialscreened.h b/src/fingerprint_radialscreened.h index 1a2cc518ab..7f9b729222 100644 --- a/src/fingerprint_radialscreened.h +++ b/src/fingerprint_radialscreened.h @@ -10,11 +10,23 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #ifdef FINGERPRINT_CLASS FingerprintStyle(radialscreened,Fingerprint_radialscreened) diff --git a/src/fingerprint_radialscreenedspin.cpp b/src/fingerprint_radialscreenedspin.cpp index 906715109c..48ad061489 100644 --- a/src/fingerprint_radialscreenedspin.cpp +++ b/src/fingerprint_radialscreenedspin.cpp @@ -10,19 +10,25 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” - +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #include "fingerprint_radialscreenedspin.h" -#include -#include -#include -#include -#include -#include + using namespace LAMMPS_NS; diff --git a/src/fingerprint_radialscreenedspin.h b/src/fingerprint_radialscreenedspin.h index f5a835111d..76c4eae50a 100644 --- a/src/fingerprint_radialscreenedspin.h +++ b/src/fingerprint_radialscreenedspin.h @@ -10,11 +10,23 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #ifdef FINGERPRINT_CLASS FingerprintStyle(radialscreenedspin,Fingerprint_radialscreenedspin) diff --git a/src/fingerprint_radialspin.cpp b/src/fingerprint_radialspin.cpp index 36b74488b6..67ff6982c5 100644 --- a/src/fingerprint_radialspin.cpp +++ b/src/fingerprint_radialspin.cpp @@ -10,21 +10,25 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” - +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #include "fingerprint_radialspin.h" -#include "fingerprint.h" -#include -#include -#include -#include -#include -#include using namespace LAMMPS_NS; diff --git a/src/fingerprint_radialspin.h b/src/fingerprint_radialspin.h index c42b904d61..428c0e74e4 100644 --- a/src/fingerprint_radialspin.h +++ b/src/fingerprint_radialspin.h @@ -10,10 +10,23 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- - Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #ifdef FINGERPRINT_CLASS diff --git a/src/pair_rann.cpp b/src/pair_rann.cpp index 84333d7710..3507c931dc 100644 --- a/src/pair_rann.cpp +++ b/src/pair_rann.cpp @@ -10,36 +10,42 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@cavs.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ -#include -#include -#include -#include -#include -#include -#include "atom.h" #include "style_fingerprint.h" #include "style_activation.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" -#include "error.h" -#include "update.h" + #include "pair_rann.h" - - using namespace LAMMPS_NS; +static const char cite_user_rann_package[] = + "USER-RANN package:\n\n" + "@Article{Nitol2021,\n" + " author = {Nitol, Mashroor S and Dickel, Doyl E and Barrett, Christopher D},\n" + " title = {Artificial neural network potential for pure zinc},\n" + " journal = {Computational Materials Science},\n" + " year = 2021,\n" + " volume = 188,\n" + " pages = {110207}\n" + "}\n\n"; + PairRANN::PairRANN(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; @@ -241,44 +247,43 @@ void PairRANN::read_file(char *filename) FILE *fp; int eof = 0,i,j,k,l; int n,nwords; - char line [MAXLINE],line1[MAXLINE]; - + int longline = 4096; + char line [longline],line1[longline]; char *ptr; bool comment; char str[128]; - fp = force->open_potential(filename); + fp = utils::open_potential(filename,lmp,nullptr); if (fp == NULL) { - sprintf(str,"Cannot open NN potential file %s",filename); + sprintf(str,"Cannot open rann potential file %s",filename); error->one(FLERR,str); } while (eof == 0){ - ptr = fgets(line,MAXLINE,fp); + ptr = fgets(line,longline,fp); if (ptr == NULL) { if (check_potential()) {//looks to see if everything needed appears to be defined error->one(FLERR,"Invalid syntax in potential file, values are inconsistent or missing"); } else{ - update_stack_size(); fclose(fp); eof = 1; break; } } else n = strlen(line) + 1; - // strip comment, skip line if blank - if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nwords = count_words(line); - char **words = new char* [strlen(line)]; - if (nwords == 0) continue; + if ((ptr = strchr(line,'#'))) *ptr = '\0';//strip comments from end of lines + if (count_words(line)==0){continue;}//skip comment line comment = true; while (comment==true){ - ptr = fgets(line1,MAXLINE,fp); - if (ptr==NULL)error->one(FLERR,"Unexpected end of file"); + ptr = fgets(line1,longline,fp); + if (ptr==NULL)errorf("Unexpected end of parameter file (keyword given with no value)"); if ((ptr = strchr(line1,'#'))) *ptr = '\0'; nwords = count_words(line1); if (nwords == 0) continue; comment = false; } + line1[strlen(line1)-1] = '\0';//replace \n with \0 + nwords = count_words(line); + char **words=new char *[nwords+1]; nwords = 0; words[nwords++] = strtok(line,": ,\t_\n"); while ((words[nwords++] = strtok(NULL,": ,\t_\n"))) continue; @@ -369,8 +374,6 @@ void PairRANN::read_fingerprints(char **words,int nwords,char * line1){ i1 = fingerprintcount[i]; delete fingerprints[i][i1]; fingerprints[i][i1] = create_fingerprint(words1[k]); - sprintf(str,"%d %d\n",nwords-1,fingerprints[i][i1]->n_body_type); - std::cout<n_body_type!=nwords-1){error->one(FLERR,"invalid fingerprint for element combination");} k++; fingerprints[i][i1]->init(atomtypes,strtol(words1[k++],NULL,10)); @@ -425,15 +428,17 @@ void PairRANN::read_network_layers(char **words,char *line1){ for (i=0;ione(FLERR,"invalid number of network layers"); + if (net[i].layers < 1)errorf("invalid number of network layers"); delete [] net[i].dimensions; - net[i].dimensions = new int [net[i].layers]; weightdefined[i] = new bool [net[i].layers]; biasdefined[i] = new bool [net[i].layers]; + net[i].dimensions = new int [net[i].layers]; net[i].Weights = new double * [net[i].layers-1]; net[i].Biases = new double * [net[i].layers-1]; + net[i].activations = new int [net[i].layers-1]; for (j=0;jone(FLERR,"networklayers for each atom type must be defined before the corresponding layer sizes."); int j = strtol(words[2],NULL,10); - if (j>=net[i].layers || j<0){errorf("invalid layer in layer size definition");}; + if (j>=net[i].layers || j<0){error->one(FLERR,"invalid layer in layer size definition");}; net[i].dimensions[j]= strtol(line1,NULL,10); -// net[i].Weights[j] = new double [1]; -// net[i].Weights[j][0]=0; -// net[i].Biases[j] = new double [1]; -// net[i].Biases[j][0] = 0; return; } } - error->one(FLERR,"layer size element not found in atom types"); + errorf("layer size element not found in atom types"); } void PairRANN::read_weight(char **words,char* line1,FILE* fp){ int i,j,k,l,nwords; char *ptr; + int longline = 4096; char **words1; for (l=0;lone(FLERR,"networklayers must be defined before weights."); + if (net[l].layers==0)errorf("networklayers must be defined before weights."); i=strtol(words[2],NULL,10); if (i>=net[l].layers || i<0)error->one(FLERR,"invalid weight layer"); - if (net[l].dimensions[i]==0 || net[l].dimensions[i+1]==0) error->one(FLERR,"network layer sizes must be defined before corresponding weight"); -// delete [] net[l].Weights[i]; + if (net[l].dimensions[i]==0 || net[l].dimensions[i+1]==0) errorf("network layer sizes must be defined before corresponding weight"); net[l].Weights[i] = new double [net[l].dimensions[i]*net[l].dimensions[i+1]]; weightdefined[l][i] = true; int n = count_words(line1)+1; @@ -489,7 +490,8 @@ void PairRANN::read_weight(char **words,char* line1,FILE* fp){ net[l].Weights[i][k] = strtod(words1[k],NULL); } for (j=1;jone(FLERR,"weight element not found in atom types"); + errorf("weight element not found in atom types"); } void PairRANN::read_bias(char **words,char* line1,FILE* fp){ @@ -552,13 +554,6 @@ void PairRANN::read_activation_functions(char** words,char * line1){ void PairRANN::read_screening(char** words,int nwords,char *line1){ int i,j,k; bool found; -// char str[MAXLINE]; -// sprintf(str,"%d\n",nwords); -// for (i=0;itype[i]]; f = net[itype].dimensions[0]; jnum = sims->numneigh[i]; - double xn[jnum]; - double yn[jnum]; - double zn[jnum]; - int tn[jnum]; - int jl[jnum]; + double *xn = new double[jnum]; + double *yn = new double[jnum]; + double *zn = new double[jnum]; + int *tn = new int[jnum]; + int *jl = new int[jnum]; cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); double features [f]; - double dfeaturesx[f*jnum]; - double dfeaturesy[f*jnum]; - double dfeaturesz[f*jnum]; + double *dfeaturesx = new double[f*jnum]; + double *dfeaturesy = new double[f*jnum]; + double *dfeaturesz = new double[f*jnum]; for (j=0;jspin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); } - clock_t t3 = clock(); //run fingerprints through network if (dospin){ propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&energy,force,fm,virial,ii,jnum,jl); @@ -733,15 +725,26 @@ void PairRANN::compute(int eflag, int vflag) else { propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&energy,force,virial,ii,jnum,jl); } - //testdfeatures(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii); - clock_t t4 = clock(); - double ts = (double) (t2-t1) / CLOCKS_PER_SEC * 1000.0; - double tf = (double) (t3-t2) / CLOCKS_PER_SEC * 1000.0; - double tp = (double) (t4-t3) / CLOCKS_PER_SEC * 1000.0; - sprintf(str,"screen time: %f, fingerprint time: %f, propagation time: %f\n",ts,tf,tp); -// std::cout<type; - inum = sims->inum; - ilist = sims->ilist; - int f = net[itype].dimensions[0]; - double cutinv2 = 1/cutmax/cutmax; - i = sims->ilist[ii]; - numneigh = sims->numneigh; - firstneigh = sims->firstneigh; - jlist = firstneigh[i]; - itype = map[sims->type[i]]; - f = net[itype].dimensions[0]; - jnum = sims->numneigh[i]; - double xn[jnum]; - double yn[jnum]; - double zn[jnum]; - int tn[jnum]; - int jl[jnum]; - double features1x [f]; - double features2x [f]; - double features1y [f]; - double features2y [f]; - double features1z [f]; - double features2z [f]; - double features1sx [f]; - double features2sx [f]; - double features1sy [f]; - double features2sy [f]; - double features1sz [f]; - double features2sz [f]; - double dfeaturesx1[f*jnum]; - double dfeaturesy1[f*jnum]; - double dfeaturesz1[f*jnum]; - double dspinx1[f*jnum]; - double dspiny1[f*jnum]; - double dspinz1[f*jnum]; - double dfxtest[f*jnum]; - double dfytest[f*jnum]; - double dfztest[f*jnum]; - double dfstestx[f*jnum]; - double dfstesty[f*jnum]; - double dfstestz[f*jnum]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1x,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1x,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1x,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1x,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - xn[jj] = xn[jj]-2*del; - if (doscreen){ - screen(Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,0,xn,yn,zn,tn,jnum-1); - } - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2x,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2x,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2x,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2x,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - for (k=0;kspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1y,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1y,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1y,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1y,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - yn[jj] = yn[jj]-2*del; - if (doscreen){ - screen(Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,0,xn,yn,zn,tn,jnum-1); - } - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2y,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2y,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2y,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2y,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - for (k=0;kspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1z,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1z,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1z,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1z,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - zn[jj] = zn[jj]-2*del; - if (doscreen){ - screen(Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,0,xn,yn,zn,tn,jnum-1); - } - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2z,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2z,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2z,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2z,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - for (k=0;ks[jj1][0]+=del; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - sims->s[jj1][0]-=2*del; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2sx,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - for (k=0;ks[jj1][0]+=del; - sims->s[jj1][1]+=del; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - sims->s[jj1][1]-=2*del; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2sy,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - for (k=0;ks[jj1][1]+=del; - sims->s[jj1][2]+=del; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features1sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features1sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - sims->s[jj1][2]-=2*del; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features2sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features2sz,dfeaturesx1,dfeaturesy1,dfeaturesz1,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - for (k=0;ks[jj1][2]+=del; - for (k=0;kone(FLERR,"terminate"); - } -} - -void PairRANN::testdenergy(){ - double **force = atom->f; - double **fm = atom->fm; - double del = 0.00002; - int ii,i,j; - int nn = 0; - double ex1,ex2,ey1,ey2,ez1,ez2,esx1,esx2,esy1,esy2,esz1,esz2; - ex1=ex2=ey1=ey2=ez1=ez2=esx1=esx2=esy1=esy2=esz1=esz2=0.0; - double **force1 = new double *[listfull->maxatom]; - double **fm1 = new double *[listfull->maxatom]; - double **force1n = new double *[listfull->maxatom]; - double **fm1n = new double *[listfull->maxatom]; - for (i=0;imaxatom;i++){ - force1[i]=new double [3]; - fm1[i] = new double [3]; - force1n[i]=new double [3]; - fm1n[i] = new double [3]; - } - for (int n=0;ninum;n++){ - int itype,f,jnum,len; - double **virial = vatom; - char str[MAXLINE]; - eng_vdwl=0; - //loop over atoms - sims->x[n][0]+=del; - for (ii=0;iiinum;ii++){ - i = sims->ilist[ii]; - itype = map[sims->type[i]]; - f = net[itype].dimensions[0]; - jnum = sims->numneigh[i]; - double xn[jnum]; - double yn[jnum]; - double zn[jnum]; - int tn[jnum]; - int jl[jnum]; - cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); - double features [f]; - double dfeaturesx[f*jnum]; - double dfeaturesy[f*jnum]; - double dfeaturesz[f*jnum]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - itype = nelements; - //do fingerprints for type "all" - len = fingerprintperelement[itype]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - //run fingerprints through network - if (dospin){ - propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&ex1,force1,fm1,virial,ii,jnum,jl); - } - else { - propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&ex1,force1,virial,ii,jnum,jl); - } - ex1=eng_vdwl; - } - eng_vdwl=0; - //loop over atoms - sims->x[n][0]-=2*del; - for (ii=0;iiinum;ii++){ - i = sims->ilist[ii]; - itype = map[sims->type[i]]; - f = net[itype].dimensions[0]; - jnum = sims->numneigh[i]; - double xn[jnum]; - double yn[jnum]; - double zn[jnum]; - int tn[jnum]; - int jl[jnum]; - cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); - double features [f]; - double dfeaturesx[f*jnum]; - double dfeaturesy[f*jnum]; - double dfeaturesz[f*jnum]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - itype = nelements; - //do fingerprints for type "all" - len = fingerprintperelement[itype]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - //run fingerprints through network - if (dospin){ - propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&ex2,force1,fm1,virial,ii,jnum,jl); - } - else { - propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&ex2,force1,virial,ii,jnum,jl); - } - ex2=eng_vdwl; - } - force1n[n][0]=(ex1-ex2)/2/del; - eng_vdwl=0; - //loop over atoms - sims->x[n][0]+=del; - sims->x[n][1]+=del; - for (ii=0;iiinum;ii++){ - i = sims->ilist[ii]; - itype = map[sims->type[i]]; - f = net[itype].dimensions[0]; - jnum = sims->numneigh[i]; - double xn[jnum]; - double yn[jnum]; - double zn[jnum]; - int tn[jnum]; - int jl[jnum]; - cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); - double features [f]; - double dfeaturesx[f*jnum]; - double dfeaturesy[f*jnum]; - double dfeaturesz[f*jnum]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - itype = nelements; - //do fingerprints for type "all" - len = fingerprintperelement[itype]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - //run fingerprints through network - if (dospin){ - propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&ey1,force1,fm1,virial,ii,jnum,jl); - } - else { - propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&ey1,force1,virial,ii,jnum,jl); - } - ey1=eng_vdwl; - } - eng_vdwl=0; - //loop over atoms - sims->x[n][1]-=2*del; - for (ii=0;iiinum;ii++){ - i = sims->ilist[ii]; - itype = map[sims->type[i]]; - f = net[itype].dimensions[0]; - jnum = sims->numneigh[i]; - double xn[jnum]; - double yn[jnum]; - double zn[jnum]; - int tn[jnum]; - int jl[jnum]; - cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); - double features [f]; - double dfeaturesx[f*jnum]; - double dfeaturesy[f*jnum]; - double dfeaturesz[f*jnum]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - itype = nelements; - //do fingerprints for type "all" - len = fingerprintperelement[itype]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - //run fingerprints through network - if (dospin){ - propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&ey2,force1,fm1,virial,ii,jnum,jl); - } - else { - propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&ey2,force1,virial,ii,jnum,jl); - } - ey2=eng_vdwl; - } - eng_vdwl=0; - force1n[n][1]=(ey1-ey2)/2/del; - //loop over atoms - sims->x[n][1]+=del; - sims->x[n][2]+=del; - for (ii=0;iiinum;ii++){ - i = sims->ilist[ii]; - itype = map[sims->type[i]]; - f = net[itype].dimensions[0]; - jnum = sims->numneigh[i]; - double xn[jnum]; - double yn[jnum]; - double zn[jnum]; - int tn[jnum]; - int jl[jnum]; - cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); - double features [f]; - double dfeaturesx[f*jnum]; - double dfeaturesy[f*jnum]; - double dfeaturesz[f*jnum]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - itype = nelements; - //do fingerprints for type "all" - len = fingerprintperelement[itype]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - //run fingerprints through network - if (dospin){ - propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&ez1,force1,fm1,virial,ii,jnum,jl); - } - else { - propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&ez1,force1,virial,ii,jnum,jl); - } - ez1=eng_vdwl; - } - eng_vdwl=0; - //loop over atoms - sims->x[n][2]-=2*del; - for (ii=0;iiinum;ii++){ - i = sims->ilist[ii]; - itype = map[sims->type[i]]; - f = net[itype].dimensions[0]; - jnum = sims->numneigh[i]; - double xn[jnum]; - double yn[jnum]; - double zn[jnum]; - int tn[jnum]; - int jl[jnum]; - cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); - double features [f]; - double dfeaturesx[f*jnum]; - double dfeaturesy[f*jnum]; - double dfeaturesz[f*jnum]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - itype = nelements; - //do fingerprints for type "all" - len = fingerprintperelement[itype]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - //run fingerprints through network - if (dospin){ - propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&ez2,force1,fm1,virial,ii,jnum,jl); - } - else { - propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&ez2,force1,virial,ii,jnum,jl); - } - ez2=eng_vdwl; - } - eng_vdwl=0; - sims->x[n][2]+=del; - force1n[n][2]=(ez1-ez2)/2/del; - - //loop over atoms - sims->s[n][0]+=del; - for (ii=0;iiinum;ii++){ - i = sims->ilist[ii]; - itype = map[sims->type[i]]; - f = net[itype].dimensions[0]; - jnum = sims->numneigh[i]; - double xn[jnum]; - double yn[jnum]; - double zn[jnum]; - int tn[jnum]; - int jl[jnum]; - cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); - double features [f]; - double dfeaturesx[f*jnum]; - double dfeaturesy[f*jnum]; - double dfeaturesz[f*jnum]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - itype = nelements; - //do fingerprints for type "all" - len = fingerprintperelement[itype]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - //run fingerprints through network - if (dospin){ - propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&esx1,force1,fm1,virial,ii,jnum,jl); - } - else { - propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&esx1,force1,virial,ii,jnum,jl); - } - esx1=eng_vdwl; - } - eng_vdwl=0; - //loop over atoms - sims->s[n][0]-=2*del; - for (ii=0;iiinum;ii++){ - i = sims->ilist[ii]; - itype = map[sims->type[i]]; - f = net[itype].dimensions[0]; - jnum = sims->numneigh[i]; - double xn[jnum]; - double yn[jnum]; - double zn[jnum]; - int tn[jnum]; - int jl[jnum]; - cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); - double features [f]; - double dfeaturesx[f*jnum]; - double dfeaturesy[f*jnum]; - double dfeaturesz[f*jnum]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - itype = nelements; - //do fingerprints for type "all" - len = fingerprintperelement[itype]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - //run fingerprints through network - if (dospin){ - propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&esx2,force1,fm1,virial,ii,jnum,jl); - } - else { - propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&esx2,force1,virial,ii,jnum,jl); - } - esx2=eng_vdwl; - } - eng_vdwl=0; - fm1n[n][0]=(esx1-esx2)/2/del; - //loop over atoms - sims->s[n][0]+=del; - sims->s[n][1]+=del; - for (ii=0;iiinum;ii++){ - i = sims->ilist[ii]; - itype = map[sims->type[i]]; - f = net[itype].dimensions[0]; - jnum = sims->numneigh[i]; - double xn[jnum]; - double yn[jnum]; - double zn[jnum]; - int tn[jnum]; - int jl[jnum]; - cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); - double features [f]; - double dfeaturesx[f*jnum]; - double dfeaturesy[f*jnum]; - double dfeaturesz[f*jnum]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - itype = nelements; - //do fingerprints for type "all" - len = fingerprintperelement[itype]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - //run fingerprints through network - if (dospin){ - propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&esy1,force1,fm1,virial,ii,jnum,jl); - } - else { - propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&esy1,force1,virial,ii,jnum,jl); - } - esy1=eng_vdwl; - } - eng_vdwl=0; - //loop over atoms - sims->s[n][1]-=2*del; - for (ii=0;iiinum;ii++){ - i = sims->ilist[ii]; - itype = map[sims->type[i]]; - f = net[itype].dimensions[0]; - jnum = sims->numneigh[i]; - double xn[jnum]; - double yn[jnum]; - double zn[jnum]; - int tn[jnum]; - int jl[jnum]; - cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); - double features [f]; - double dfeaturesx[f*jnum]; - double dfeaturesy[f*jnum]; - double dfeaturesz[f*jnum]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - itype = nelements; - //do fingerprints for type "all" - len = fingerprintperelement[itype]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - //run fingerprints through network - if (dospin){ - propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&esy2,force1,fm1,virial,ii,jnum,jl); - } - else { - propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&esy2,force1,virial,ii,jnum,jl); - } - esy2=eng_vdwl; - } - eng_vdwl=0; - fm1n[n][1]=(esy1-esy2)/2/del; - //loop over atoms - sims->x[n][1]+=del; - sims->x[n][2]+=del; - for (ii=0;iiinum;ii++){ - i = sims->ilist[ii]; - itype = map[sims->type[i]]; - f = net[itype].dimensions[0]; - jnum = sims->numneigh[i]; - double xn[jnum]; - double yn[jnum]; - double zn[jnum]; - int tn[jnum]; - int jl[jnum]; - cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); - double features [f]; - double dfeaturesx[f*jnum]; - double dfeaturesy[f*jnum]; - double dfeaturesz[f*jnum]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - itype = nelements; - //do fingerprints for type "all" - len = fingerprintperelement[itype]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - //run fingerprints through network - if (dospin){ - propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&esz1,force1,fm1,virial,ii,jnum,jl); - } - else { - propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&esz1,force1,virial,ii,jnum,jl); - } - esz1=eng_vdwl; - } - eng_vdwl=0; - //loop over atoms - sims->s[n][2]-=2*del; - for (ii=0;iiinum;ii++){ - i = sims->ilist[ii]; - itype = map[sims->type[i]]; - f = net[itype].dimensions[0]; - jnum = sims->numneigh[i]; - double xn[jnum]; - double yn[jnum]; - double zn[jnum]; - int tn[jnum]; - int jl[jnum]; - cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); - double features [f]; - double dfeaturesx[f*jnum]; - double dfeaturesy[f*jnum]; - double dfeaturesz[f*jnum]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - itype = nelements; - //do fingerprints for type "all" - len = fingerprintperelement[itype]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - //run fingerprints through network - if (dospin){ - propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&esz2,force1,fm1,virial,ii,jnum,jl); - } - else { - propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&esz2,force1,virial,ii,jnum,jl); - } - esz2=eng_vdwl; - } - eng_vdwl=0; - sims->s[n][2]+=del; - fm1n[n][2]=(esz1-esz2)/2/del; - sprintf(str,"atom: %d fx: %f fxn: %f fy: %f fyn: %f fz: %f fzn: %f fmx: %f fmxn: %f fmy: %f fmyn: %f fmz: %f fmzn: %f\n",n,force[n][0],force1n[n][0],force[n][1],force1n[n][1],force[n][2],force1n[n][2],fm[n][0],fm1n[n][0],fm[n][1],fm1n[n][1],fm[n][2],fm1n[n][2]); - std::cout<error->all(FLERR,message); } diff --git a/src/pair_rann.h b/src/pair_rann.h index d2746954d2..1358c67fb0 100644 --- a/src/pair_rann.h +++ b/src/pair_rann.h @@ -10,12 +10,23 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@cavs.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ #ifdef PAIR_CLASS @@ -26,14 +37,26 @@ PairStyle(rann,PairRANN) #ifndef LMP_PAIR_RANN #define LMP_PAIR_RANN -#define MAXLINE 4096 +#define MAXLINE 1024 +#include +#include +#include +#include +#include +#include "atom.h" +#include "force.h" +#include "comm.h" +#include "memory.h" +#include "neighbor.h" #include "neigh_list.h" +#include "neigh_request.h" +#include "memory.h" +#include "error.h" +#include "update.h" #include "pair.h" #include -#include #include -#include namespace LAMMPS_NS { @@ -49,7 +72,7 @@ class PairRANN : public Pair { void init_style(); double init_one(int, int); void init_list(int , NeighList *); - void errorf(char*); + void errorf(const char*); int count_words(char *); //black magic for modular fingerprints and activations class Activation ***activation; @@ -79,8 +102,6 @@ class PairRANN : public Pair { bool dospin; int res;//Resolution of function tables for cubic interpolation. int memguess; -// double *Sik,*dSikx,*dSiky,*dSikz,*dSijkx,*dSijky,*dSijkz; -// bool *Bij; double *screening_min; double *screening_max; bool **weightdefined; @@ -137,11 +158,8 @@ class PairRANN : public Pair { void propagateforward(double *,double *,double *,double *,double *,double **,double **,int,int,int*);//called by compute to get force and energy void propagateforwardspin(double *,double *,double *,double *,double *,double *,double *,double *,double **,double **,double**,int,int,int*);//called by compute to get force and energy void screen(double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int *,int); - void testdfeatures(double *,double *, double *, double *,double *,double *, double *,int); - void testdenergy(); void cull_neighbor_list(double *,double *,double *,int *,int *,int *,int,int); void screen_neighbor_list(double *,double *,double *,int *,int *,int *,int,int,bool*,double*,double*,double*,double*,double*,double*,double*); - void update_stack_size(); }; } From d79a2c3a02b295dd1d8c1cb636546d8de6c16015 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 2 Feb 2021 09:39:13 -0700 Subject: [PATCH 0073/1217] Adding collection array, new user arguments, and multi communication --- src/GRANULAR/pair_gran_hooke_history.cpp | 21 + src/GRANULAR/pair_gran_hooke_history.h | 2 + src/GRANULAR/pair_granular.cpp | 48 ++ src/GRANULAR/pair_granular.h | 2 + ...n_ssa.cpp => nstencil_half_bin_2d_ssa.cpp} | 6 +- ...ewton_ssa.h => nstencil_half_bin_2d_ssa.h} | 16 +- ...n_ssa.cpp => nstencil_half_bin_3d_ssa.cpp} | 6 +- ...ewton_ssa.h => nstencil_half_bin_3d_ssa.h} | 16 +- src/USER-OMP/npair_full_multi_omp.cpp | 26 +- src/USER-OMP/npair_half_multi_newtoff_omp.cpp | 26 +- src/USER-OMP/npair_half_multi_newton_omp.cpp | 38 +- .../npair_half_multi_newton_tri_omp.cpp | 28 +- .../npair_half_size_multi_newtoff_omp.cpp | 26 +- .../npair_half_size_multi_newton_omp.cpp | 38 +- .../npair_half_size_multi_newton_tri_omp.cpp | 28 +- src/comm.cpp | 70 +- src/comm.h | 11 +- src/comm_brick.cpp | 219 +++-- src/comm_brick.h | 10 +- src/comm_tiled.cpp | 294 +++++-- src/comm_tiled.h | 10 +- src/init | 789 ++++++++++++++++++ src/nbin.cpp | 46 +- src/nbin.h | 7 +- src/nbin_multi.cpp | 90 +- src/neighbor.cpp | 255 ++++-- src/neighbor.h | 16 +- src/npair.cpp | 44 +- src/npair.h | 5 +- src/npair_full_multi.cpp | 26 +- src/npair_half_multi_newtoff.cpp | 26 +- src/npair_half_multi_newton.cpp | 38 +- src/npair_half_multi_newton_tri.cpp | 30 +- src/npair_half_size_multi_newtoff.cpp | 26 +- src/npair_half_size_multi_newton.cpp | 38 +- src/npair_half_size_multi_newton_tri.cpp | 28 +- src/npair_half_size_multi_old_newtoff.cpp | 2 +- src/npair_half_size_multi_old_newton.cpp | 2 +- src/npair_half_size_multi_old_newton_tri.cpp | 2 +- src/nstencil.cpp | 80 +- src/nstencil.h | 12 +- src/nstencil_full_multi_2d.cpp | 32 +- src/nstencil_full_multi_3d.cpp | 36 +- src/nstencil_half_multi_2d.cpp | 46 +- src/nstencil_half_multi_2d_tri.cpp | 46 +- src/nstencil_half_multi_3d.cpp | 50 +- src/nstencil_half_multi_3d_tri.cpp | 50 +- src/pair.cpp | 1 + src/pair.h | 3 + src/pair_hybrid.cpp | 37 + src/pair_hybrid.h | 2 + 51 files changed, 2109 insertions(+), 697 deletions(-) rename src/USER-DPD/{nstencil_half_bin_2d_newton_ssa.cpp => nstencil_half_bin_2d_ssa.cpp} (95%) rename src/USER-DPD/{nstencil_half_bin_2d_newton_ssa.h => nstencil_half_bin_2d_ssa.h} (66%) rename src/USER-DPD/{nstencil_half_bin_3d_newton_ssa.cpp => nstencil_half_bin_3d_ssa.cpp} (97%) rename src/USER-DPD/{nstencil_half_bin_3d_newton_ssa.h => nstencil_half_bin_3d_ssa.h} (66%) create mode 100644 src/init diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 7b7586d355..46b41126aa 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -43,6 +43,7 @@ PairGranHookeHistory::PairGranHookeHistory(LAMMPS *lmp) : Pair(lmp) single_enable = 1; no_virial_fdotr_compute = 1; centroidstressflag = CENTROID_NOTAVAIL; + finitecutflag = 1; history = 1; size_history = 3; @@ -796,3 +797,23 @@ double PairGranHookeHistory::memory_usage() double bytes = nmax * sizeof(double); return bytes; } + +/* ---------------------------------------------------------------------- + self-interaction range of particle +------------------------------------------------------------------------- */ + +double PairGranHookeHistory::atom2cut(int i) +{ + double cut = atom->radius[i]*2; + return cut; +} + +/* ---------------------------------------------------------------------- + maximum interaction range for two finite particles +------------------------------------------------------------------------- */ + +double PairGranHookeHistory::radii2cut(double r1, double r2) +{ + double cut = r1+r2; + return cut; +} \ No newline at end of file diff --git a/src/GRANULAR/pair_gran_hooke_history.h b/src/GRANULAR/pair_gran_hooke_history.h index c27ce8a9af..9575c49d0c 100644 --- a/src/GRANULAR/pair_gran_hooke_history.h +++ b/src/GRANULAR/pair_gran_hooke_history.h @@ -42,6 +42,8 @@ class PairGranHookeHistory : public Pair { int pack_forward_comm(int, int *, double *, int, int *); void unpack_forward_comm(int, int, double *); double memory_usage(); + double atom2cut(int); + double radii2cut(double,double); protected: double kn,kt,gamman,gammat,xmu; diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 215926e23e..0f1fbd49f3 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -67,6 +67,7 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp) single_enable = 1; no_virial_fdotr_compute = 1; centroidstressflag = CENTROID_NOTAVAIL; + finitecutflag = 1; single_extra = 12; svector = new double[single_extra]; @@ -1819,3 +1820,50 @@ void PairGranular::transfer_history(double* source, double* target) for (int i = 0; i < size_history; i++) target[i] = history_transfer_factors[i]*source[i]; } + +/* ---------------------------------------------------------------------- + self-interaction range of particle +------------------------------------------------------------------------- */ + +double PairGranular::atom2cut(int i) +{ + double cut; + + cut = atom->radius[i]*2; + if(beyond_contact) { + int itype = atom->type[i] + if(normal_model[itype][itype] == JKR) { + cut += pulloffdistance(cut, cut, itype, itype); + } + } + + return cut; +} + +/* ---------------------------------------------------------------------- + maximum interaction range for two finite particles +------------------------------------------------------------------------- */ + +double PairGranular::radii2cut(double r1, double r2) +{ + double cut = 0.0; + + if(beyond_contact) { + int n = atom->ntypes; + double temp; + + // Check all combinations of i and j to find theoretical maximum pull off distance + for(int i = 0; i < n; i++){ + for(int j = 0; j < n; j++){ + if(normal_model[i][j] == JKR) { + temp = pulloffdistance(r1, r2, i, j); + if(temp > cut) cut = temp; + } + } + } + } + + cut += r1 + r2; + + return cut; +} diff --git a/src/GRANULAR/pair_granular.h b/src/GRANULAR/pair_granular.h index 7ef4f2af98..7fe47b3275 100644 --- a/src/GRANULAR/pair_granular.h +++ b/src/GRANULAR/pair_granular.h @@ -40,6 +40,8 @@ class PairGranular : public Pair { int pack_forward_comm(int, int *, double *, int, int *); void unpack_forward_comm(int, int, double *); double memory_usage(); + double atom2cut(int); + double radii2cut(double,double); protected: double dt; diff --git a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_2d_ssa.cpp similarity index 95% rename from src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp rename to src/USER-DPD/nstencil_half_bin_2d_ssa.cpp index 803a80f3e3..aca7b9df09 100644 --- a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp +++ b/src/USER-DPD/nstencil_half_bin_2d_ssa.cpp @@ -16,13 +16,13 @@ James Larentzos and Timothy I. Mattox (Engility Corporation) ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_2d_newton_ssa.h" +#include "nstencil_half_bin_2d_ssa.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) : +NStencilHalfBin2dSSA::NStencilHalfBin2dSSA(LAMMPS *lmp) : NStencilSSA(lmp) {} /* ---------------------------------------------------------------------- @@ -37,7 +37,7 @@ NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) : to locate all the Active Interaction Region (AIR) ghosts for SSA ------------------------------------------------------------------------- */ -void NStencilHalfBin2dNewtonSSA::create() +void NStencilHalfBin2dSSA::create() { int i,j,pos = 0; nstencil_ssa[0] = 0; // redundant info, but saves a conditional diff --git a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h b/src/USER-DPD/nstencil_half_bin_2d_ssa.h similarity index 66% rename from src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h rename to src/USER-DPD/nstencil_half_bin_2d_ssa.h index 1d5cc3f6b2..a50c852670 100644 --- a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h +++ b/src/USER-DPD/nstencil_half_bin_2d_ssa.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bin/2d/newton/ssa, - NStencilHalfBin2dNewtonSSA, - NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_SSA | NS_ORTHO | NS_GHOST) +NStencilStyle(half/bin/2d/ssa, + NStencilHalfBin2dSSA, + NS_HALF | NS_BIN | NS_2D | NS_SSA | NS_ORTHO | NS_GHOST) #else -#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_SSA_H -#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_SSA_H +#ifndef LMP_NSTENCIL_HALF_BIN_2D_SSA_H +#define LMP_NSTENCIL_HALF_BIN_2D_SSA_H #include "nstencil_ssa.h" namespace LAMMPS_NS { -class NStencilHalfBin2dNewtonSSA : public NStencilSSA { +class NStencilHalfBin2dSSA : public NStencilSSA { public: - NStencilHalfBin2dNewtonSSA(class LAMMPS *); - ~NStencilHalfBin2dNewtonSSA() {} + NStencilHalfBin2dSSA(class LAMMPS *); + ~NStencilHalfBin2dSSA() {} void create(); }; diff --git a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_3d_ssa.cpp similarity index 97% rename from src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp rename to src/USER-DPD/nstencil_half_bin_3d_ssa.cpp index c20dabe28f..8e33f5414f 100644 --- a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp +++ b/src/USER-DPD/nstencil_half_bin_3d_ssa.cpp @@ -16,13 +16,13 @@ James Larentzos and Timothy I. Mattox (Engility Corporation) ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_3d_newton_ssa.h" +#include "nstencil_half_bin_3d_ssa.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) : +NStencilHalfBin3dSSA::NStencilHalfBin3dSSA(LAMMPS *lmp) : NStencilSSA(lmp) {} /* ---------------------------------------------------------------------- @@ -37,7 +37,7 @@ NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) : to locate all the Active Interaction Region (AIR) ghosts for SSA ------------------------------------------------------------------------- */ -void NStencilHalfBin3dNewtonSSA::create() +void NStencilHalfBin3dSSA::create() { int i,j,k,pos = 0; nstencil_ssa[0] = 0; // redundant info, but saves a conditional diff --git a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h b/src/USER-DPD/nstencil_half_bin_3d_ssa.h similarity index 66% rename from src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h rename to src/USER-DPD/nstencil_half_bin_3d_ssa.h index 450a696e46..94f8fb4142 100644 --- a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h +++ b/src/USER-DPD/nstencil_half_bin_3d_ssa.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bin/3d/newton/ssa, - NStencilHalfBin3dNewtonSSA, - NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_SSA | NS_ORTHO | NS_GHOST) +NStencilStyle(half/bin/3d/ssa, + NStencilHalfBin3dSSA, + NS_HALF | NS_BIN | NS_3D | NS_SSA | NS_ORTHO | NS_GHOST) #else -#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTON_SSA_H -#define LMP_NSTENCIL_HALF_BIN_3D_NEWTON_SSA_H +#ifndef LMP_NSTENCIL_HALF_BIN_3D_SSA_H +#define LMP_NSTENCIL_HALF_BIN_3D_SSA_H #include "nstencil_ssa.h" namespace LAMMPS_NS { -class NStencilHalfBin3dNewtonSSA : public NStencilSSA { +class NStencilHalfBin3dSSA : public NStencilSSA { public: - NStencilHalfBin3dNewtonSSA(class LAMMPS *); - ~NStencilHalfBin3dNewtonSSA() {} + NStencilHalfBin3dSSA(class LAMMPS *); + ~NStencilHalfBin3dSSA() {} void create(); }; diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp index 4b38e660d4..4fc6fb4a68 100755 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_full_multi_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -30,7 +31,7 @@ NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ @@ -46,7 +47,7 @@ void NPairFullMultiOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -54,6 +55,7 @@ void NPairFullMultiOmp::build(NeighList *list) // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -80,7 +82,7 @@ void NPairFullMultiOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -92,22 +94,22 @@ void NPairFullMultiOmp::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in surrounding bins in stencil including self // skip i = j - // use full stencil for all group combinations + // use full stencil for all collection combinations - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { if (i == j) continue; diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp index 93d150f445..ed0e770b2f 100755 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_half_multi_newtoff_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -30,7 +31,7 @@ NPairHalfMultiNewtoffOmp::NPairHalfMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks own bin and other bins in stencil pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) @@ -48,7 +49,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -56,6 +57,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -82,7 +84,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -94,24 +96,24 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in other bins in stencil including self // only store pair if i < j // stores own/own pairs only once // stores own/ghost pairs on both procs - // use full stencil for all group combinations + // use full stencil for all collection combinations - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index 11a84a3040..13d286ab5b 100755 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_half_multi_newton_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -30,7 +31,7 @@ NPairHalfMultiNewtonOmp::NPairHalfMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -47,7 +48,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -55,6 +56,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -81,7 +83,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -93,29 +95,29 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // if same size: uses half stencil so check central bin - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - if(igroup == jgroup) js = bins[i]; - else js = binhead_multi[jgroup][jbin]; + if(icollection == jcollection) js = bins[i]; + else js = binhead_multi[jcollection][jbin]; - // if same group, + // if same collection, // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - // if different groups, + // if different collections, // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i for (j = js; j >= 0; j = bins[j]) { - if(igroup != jgroup and j < i) continue; + if(icollection != jcollection and j < i) continue; if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -151,16 +153,16 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) } } - // for all groups, loop over all atoms in other bins in stencil, store every pair + // for all collections, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index b5882580a8..cb758673d4 100755 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_half_multi_newton_tri_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -31,7 +32,7 @@ NPairHalfMultiNewtonTriOmp::NPairHalfMultiNewtonTriOmp(LAMMPS *lmp) : /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -48,7 +49,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,jbin,igroup,jgroup,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,ibin,jbin,icollection,jcollection,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; @@ -56,6 +57,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -82,7 +84,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -94,12 +96,12 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in bins in stencil // stencil is empty if i larger than j @@ -110,15 +112,15 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { - // if same size (same group), use half stencil - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + // if same size (same collection), use half stencil + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp index 0d588b2f24..0efb4f067a 100755 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_half_size_multi_newtoff_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -29,7 +30,7 @@ NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) : NPair( /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks own bin and other bins in stencil pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) @@ -47,7 +48,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -55,6 +56,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -75,7 +77,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -83,24 +85,24 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in other bins in stencil including self // only store pair if i < j // stores own/own pairs only once // stores own/ghost pairs on both procs - // use full stencil for all group combinations + // use full stencil for all collection combinations - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp index cec3edd02b..68885fb453 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_half_size_multi_newton_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -29,7 +30,7 @@ NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) : NPair(lm /* ---------------------------------------------------------------------- size particles binned neighbor list construction with full Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -46,7 +47,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -54,6 +55,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -74,7 +76,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -82,29 +84,29 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // if same size: uses half stencil so check central bin - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - if(igroup == jgroup) js = bins[i]; - else js = binhead_multi[jgroup][jbin]; + if(icollection == jcollection) js = bins[i]; + else js = binhead_multi[jcollection][jbin]; - // if same group, + // if same collection, // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - // if different groups, + // if different collections, // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i for (j = js; j >= 0; j = bins[j]) { - if(igroup != jgroup and j < i) continue; + if(icollection != jcollection and j < i) continue; if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -133,16 +135,16 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) } } - // for all groups, loop over all atoms in other bins in stencil, store every pair + // for all collections, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp index 396e870846..76f61b8792 100755 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_half_size_multi_newton_tri_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -30,7 +31,7 @@ NPairHalfSizeMultiNewtonTriOmp::NPairHalfSizeMultiNewtonTriOmp(LAMMPS *lmp) : /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -47,7 +48,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; @@ -55,6 +56,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -75,7 +77,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -83,12 +85,12 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in bins in stencil @@ -100,15 +102,15 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { - // if same size (same group), use half stencil - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + // if same size (same collection), use half stencil + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/comm.cpp b/src/comm.cpp index 867eab6256..3f2d4ecde6 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -58,6 +58,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) bordergroup = 0; cutghostuser = 0.0; cutusermulti = nullptr; + cutusermultiold = nullptr; ghost_velocity = 0; user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0; @@ -118,6 +119,7 @@ Comm::~Comm() memory->destroy(ysplit); memory->destroy(zsplit); memory->destroy(cutusermulti); + memory->destroy(cutusermultiold); delete [] customfile; delete [] outfile; } @@ -146,8 +148,13 @@ void Comm::copy_arrays(Comm *oldcomm) } if (oldcomm->cutusermulti) { - memory->create(cutusermulti,atom->ntypes+1,"comm:cutusermulti"); - memcpy(cutusermulti,oldcomm->cutusermulti,atom->ntypes+1); + memory->create(cutusermulti,ncollections,"comm:cutusermulti"); + memcpy(cutusermulti,oldcomm->cutusermulti,ncollections); + } + + if (oldcomm->cutusermultiold) { + memory->create(cutusermultiold,atom->ntypes+1,"comm:cutusermultiold"); + memcpy(cutusermultiold,oldcomm->cutusermultiold,atom->ntypes+1); } if (customfile) { @@ -242,13 +249,16 @@ void Comm::init() for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; + if(mode == Comm::MULTI and neighbor->style != Neighbor::MULTI) + error->all(FLERR,"Cannot use comm mode multi without multi-style neighbor lists"); + if(multi_reduce){ if (force->newton == 0) error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); if (neighbor->any_full()) error->all(FLERR,"Cannot use multi/reduce communication with a full neighbor list"); - if (neighbor->style != Neighbor::MULTI) - error->all(FLERR,"Cannot use multi/reduce communication without multi-style neighbor lists"); + if(mode != Comm::MULTI) + error->all(FLERR,"Cannot use multi/reduce communication without mode multi"); } } @@ -285,13 +295,20 @@ void Comm::modify_params(int narg, char **arg) if (strcmp(arg[iarg+1],"single") == 0) { // need to reset cutghostuser when switching comm mode if (mode == Comm::MULTI) cutghostuser = 0.0; + if (mode == Comm::MULTIOLD) cutghostuser = 0.0; memory->destroy(cutusermulti); cutusermulti = nullptr; mode = Comm::SINGLE; } else if (strcmp(arg[iarg+1],"multi") == 0) { // need to reset cutghostuser when switching comm mode if (mode == Comm::SINGLE) cutghostuser = 0.0; + if (mode == Comm::MULTIOLD) cutghostuser = 0.0; mode = Comm::MULTI; + } else if (strcmp(arg[iarg+1],"multi/old") == 0) { + // need to reset cutghostuser when switching comm mode + if (mode == Comm::SINGLE) cutghostuser = 0.0; + if (mode == Comm::MULTI) cutghostuser = 0.0; + mode = Comm::MULTIOLD; } else error->all(FLERR,"Illegal comm_modify command"); iarg += 2; } else if (strcmp(arg[iarg],"group") == 0) { @@ -308,6 +325,9 @@ void Comm::modify_params(int narg, char **arg) if (mode == Comm::MULTI) error->all(FLERR, "Use cutoff/multi keyword to set cutoff in multi mode"); + if (mode == Comm::MULTIOLD) + error->all(FLERR, + "Use cutoff/multi/old keyword to set cutoff in multi mode"); cutghostuser = utils::numeric(FLERR,arg[iarg+1],false,lmp); if (cutghostuser < 0.0) error->all(FLERR,"Invalid cutoff in comm_modify command"); @@ -317,18 +337,20 @@ void Comm::modify_params(int narg, char **arg) double cut; if (mode == Comm::SINGLE) error->all(FLERR,"Use cutoff keyword to set cutoff in single mode"); - if (domain->box_exist == 0) + if (mode == Comm::MULTIOLD) + error->all(FLERR,"Use cutoff/multi/old keyword to set cutoff in multi/old mode"); + if (domain->box_exist == 0) error->all(FLERR, "Cannot set cutoff/multi before simulation box is defined"); - const int ntypes = atom->ntypes; + ncollections = neighbor->ncollections; if (iarg+3 > narg) error->all(FLERR,"Illegal comm_modify command"); if (cutusermulti == nullptr) { - memory->create(cutusermulti,ntypes+1,"comm:cutusermulti"); - for (i=0; i < ntypes+1; ++i) + memory->create(cutusermulti,ncollections,"comm:cutusermulti"); + for (i=0; i < ncollections; ++i) cutusermulti[i] = -1.0; } - utils::bounds(FLERR,arg[iarg+1],1,ntypes,nlo,nhi,error); + utils::bounds(FLERR,arg[iarg+1],1,ncollections,nlo,nhi,error); cut = utils::numeric(FLERR,arg[iarg+2],false,lmp); cutghostuser = MAX(cutghostuser,cut); if (cut < 0.0) @@ -336,9 +358,35 @@ void Comm::modify_params(int narg, char **arg) for (i=nlo; i<=nhi; ++i) cutusermulti[i] = cut; iarg += 3; - } else if (strcmp(arg[iarg],"multi/reduce") == 0) { + } else if (strcmp(arg[iarg],"cutoff/multi/old") == 0) { + int i,nlo,nhi; + double cut; if (mode == Comm::SINGLE) - error->all(FLERR,"Use multi/reduce in mode multi only"); + error->all(FLERR,"Use cutoff keyword to set cutoff in single mode"); + if (mode == Comm::MULTI) + error->all(FLERR,"Use cutoff/multi keyword to set cutoff in multi mode"); + if (domain->box_exist == 0) + error->all(FLERR, + "Cannot set cutoff/multi before simulation box is defined"); + const int ntypes = atom->ntypes; + if (iarg+3 > narg) + error->all(FLERR,"Illegal comm_modify command"); + if (cutusermultiold == nullptr) { + memory->create(cutusermultiold,ntypes+1,"comm:cutusermultiold"); + for (i=0; i < ntypes+1; ++i) + cutusermultiold[i] = -1.0; + } + utils::bounds(FLERR,arg[iarg+1],1,ntypes,nlo,nhi,error); + cut = utils::numeric(FLERR,arg[iarg+2],false,lmp); + cutghostuser = MAX(cutghostuser,cut); + if (cut < 0.0) + error->all(FLERR,"Invalid cutoff in comm_modify command"); + for (i=nlo; i<=nhi; ++i) + cutusermultiold[i] = cut; + iarg += 3; + } else if (strcmp(arg[iarg],"reduce/multi") == 0) { + if (mode == Comm::SINGLE) + error->all(FLERR,"Use reduce/multi in mode multi only"); multi_reduce = 1; iarg += 1; } else if (strcmp(arg[iarg],"vel") == 0) { diff --git a/src/comm.h b/src/comm.h index 4ae4faf7fd..877941523c 100644 --- a/src/comm.h +++ b/src/comm.h @@ -25,14 +25,15 @@ class Comm : protected Pointers { // LAYOUT_NONUNIFORM = logical bricks, but diff sizes via LB // LAYOUT_TILED = general tiling, due to RCB LB enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; - int mode; // 0 = single cutoff, 1 = multi-type cutoff - enum{SINGLE,MULTI}; + int mode; // 0 = single cutoff, 1 = multi-collection cutoff, 2 = multiold-type cutoff + enum{SINGLE,MULTI,MULTIOLD}; int me,nprocs; // proc info int ghost_velocity; // 1 if ghost atoms have velocity, 0 if not double cutghost[3]; // cutoffs used for acquiring ghost atoms double cutghostuser; // user-specified ghost cutoff (mode == 0) - double *cutusermulti; // per type user ghost cutoff (mode == 1) + double *cutusermulti; // per collection user ghost cutoff (mode == 1) + double *cutusermultiold; // per type user ghost cutoff (mode == 2) int recv_from_partition; // recv proc layout from this partition int send_to_partition; // send my proc layout to this partition // -1 if no recv or send @@ -152,7 +153,9 @@ class Comm : protected Pointers { int ncores; // # of cores per node int coregrid[3]; // 3d grid of cores within a node int user_coregrid[3]; // user request for cores in each dim - int multi_reduce; // 1 if multi cutoff is intra-type cutoff + int multi_reduce; // 1 if multi cutoff is intra-collection cutoff + int ncollections; // number of collection cutoffs defined for multi + int ncollections_prior; // value of ncollections at last setup void init_exchange(); int rendezvous_irregular(int, char *, int, int, int *, diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 939669fb75..ca0fea8757 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -46,6 +46,7 @@ CommBrick::CommBrick(LAMMPS *lmp) : size_reverse_send(nullptr), size_reverse_recv(nullptr), slablo(nullptr), slabhi(nullptr), multilo(nullptr), multihi(nullptr), cutghostmulti(nullptr), pbc_flag(nullptr), pbc(nullptr), firstrecv(nullptr), + multioldlo(nullptr), multioldhi(nullptr), cutghostmultiold(nullptr), sendlist(nullptr), localsendlist(nullptr), maxsendlist(nullptr), buf_send(nullptr), buf_recv(nullptr) { @@ -65,6 +66,11 @@ CommBrick::~CommBrick() memory->destroy(cutghostmulti); } + if (mode == Comm::MULTIOLD) { + free_multiold(); + memory->destroy(cutghostmultiold); + } + if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]); if (localsendlist) memory->destroy(localsendlist); memory->sfree(sendlist); @@ -101,6 +107,9 @@ void CommBrick::init_buffers() multilo = multihi = nullptr; cutghostmulti = nullptr; + multioldlo = multioldhi = nullptr; + cutghostmultiold = nullptr; + buf_send = buf_recv = nullptr; maxsend = maxrecv = BUFMIN; grow_send(maxsend,2); @@ -128,23 +137,37 @@ void CommBrick::init() init_exchange(); if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2); - // memory for multi-style communication + // memory for multi style communication + // allocate in setup if (mode == Comm::MULTI && multilo == nullptr) { allocate_multi(maxswap); - memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti"); - } - if (mode == Comm::SINGLE && multilo) { + memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); + ncollections_prior = ncollections; + } + if ((mode == Comm::SINGLE or mode == Comm::MULTIOLD) && multilo) { free_multi(); memory->destroy(cutghostmulti); } + + // memory for multi/old-style communication + + if (mode == Comm::MULTIOLD && multioldlo == nullptr) { + allocate_multiold(maxswap); + memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold"); + } + if ((mode == Comm::SINGLE or mode == Comm::MULTI) && multioldlo) { + free_multiold(); + memory->destroy(cutghostmultiold); + } } /* ---------------------------------------------------------------------- setup spatial-decomposition communication patterns function of neighbor cutoff(s) & cutghostuser & current box size single mode sets slab boundaries (slablo,slabhi) based on max cutoff - multi mode sets type-dependent slab boundaries (multilo,multihi) + multi mode sets collection-dependent slab boundaries (multilo,multihi) + multi/old mode sets type-dependent slab boundaries (multioldlo,multioldhi) ------------------------------------------------------------------------- */ void CommBrick::setup() @@ -156,8 +179,10 @@ void CommBrick::setup() // neigh->cutghost = distance between tilted planes in box coords // cutghost is in lamda coords = distance between those planes // for multi: - // cutghostmulti = same as cutghost, only for each atom type - + // cutghostmulti = same as cutghost, only for each atom collection + // for multi/old: + // cutghostmultiold = same as cutghost, only for each atom type + int i,j; int ntypes = atom->ntypes; double *prd,*sublo,*subhi; @@ -167,49 +192,58 @@ void CommBrick::setup() error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms " "will be generated. Atoms may get lost."); - if (mode == Comm::MULTI) { - if (multi_reduce) { - // If using multi/reduce, communicate itype particles a distance equal - // to the max of itype-jtype group interaction - // only consider smaller jtype groups - int igroup, jgroup; - double **cutmultisq = neighbor->cutmultisq; - int *map_type_multi = neighbor->map_type_multi; - for (i = 1; i <= ntypes; i++) { - - if (cutusermulti) { - cutghostmulti[i][0] = cutusermulti[i]; - cutghostmulti[i][1] = cutusermulti[i]; - cutghostmulti[i][2] = cutusermulti[i]; - } else { - cutghostmulti[i][0] = 0.0; - cutghostmulti[i][1] = 0.0; - cutghostmulti[i][2] = 0.0; - } - - igroup = map_type_multi[i]; - for (j = 1; j <= ntypes; j++){ - jgroup = map_type_multi[j]; - - if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); - } + // build initial collection array + neighbor->build_collection(0); + + if(cutusermulti and ncollections != neighbor->ncollections) + error->all(FLERR, "Cannot change number of collections after defining comm_modify multi/cutoff"); + else ncollections = neighbor->ncollections; + + // reallocate memory for multi-style communication at setup if ncollections change + if(ncollections_prior != ncollections){ + if(multilo) free_multi(); + if(cutghostmulti) memory->destroy(cutghostmulti); + + allocate_multi(maxswap); + memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); + ncollections_prior = ncollections; + } + + double **cutcollectionsq = neighbor->cutcollectionsq; + // If using multi/reduce, communicate particles a distance equal + // to the max cutoff with equally sized or smaller collections + // If not, communicate the maximum cutoff of the entire collection + for (i = 0; i < ncollections; i++) { + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; } - } else { - // otherwise, communicate a distance equal to the maximum interaction distance for each type - double *cuttype = neighbor->cuttype; - for (i = 1; i <= ntypes; i++) { - double tmp = 0.0; - if (cutusermulti) tmp = cutusermulti[i]; - cutghostmulti[i][0] = MAX(tmp,cuttype[i]); - cutghostmulti[i][1] = MAX(tmp,cuttype[i]); - cutghostmulti[i][2] = MAX(tmp,cuttype[i]); + + for (j = 0; j < ncollections; j++){ + if(multi_reduce and cutcollectionsq[j][j] > cutcollectionsq[i][i]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j])); } } } + + if (mode == Comm::MULTIOLD) { + double *cuttype = neighbor->cuttype; + for (i = 1; i <= ntypes; i++) { + double tmp = 0.0; + if (cutusermultiold) tmp = cutusermultiold[i]; + cutghostmultiold[i][0] = MAX(tmp,cuttype[i]); + cutghostmultiold[i][1] = MAX(tmp,cuttype[i]); + cutghostmultiold[i][2] = MAX(tmp,cuttype[i]); + } + } if (triclinic == 0) { prd = domain->prd; @@ -228,13 +262,21 @@ void CommBrick::setup() cutghost[1] = cut * length1; length2 = h_inv[2]; cutghost[2] = cut * length2; - if (mode == Comm::MULTI){ - for (i = 1; i <= ntypes; i++) { + if (mode == Comm::MULTI) { + for (i = 0; i < ncollections; i++) { cutghostmulti[i][0] *= length0; cutghostmulti[i][1] *= length1; cutghostmulti[i][2] *= length2; } } + + if (mode == Comm::MULTIOLD) { + for (i = 1; i <= ntypes; i++) { + cutghostmultiold[i][0] *= length0; + cutghostmultiold[i][1] *= length1; + cutghostmultiold[i][2] *= length2; + } + } } // recvneed[idim][0/1] = # of procs away I recv atoms from, within cutghost @@ -378,12 +420,18 @@ void CommBrick::setup() if (ineed < 2) slablo[iswap] = -BIG; else slablo[iswap] = 0.5 * (sublo[dim] + subhi[dim]); slabhi[iswap] = sublo[dim] + cutghost[dim]; - } else { - for (i = 1; i <= ntypes; i++) { + } else if (mode == Comm::MULTI) { + for (i = 0; i < ncollections; i++) { if (ineed < 2) multilo[iswap][i] = -BIG; else multilo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); multihi[iswap][i] = sublo[dim] + cutghostmulti[i][dim]; } + } else { + for (i = 1; i <= ntypes; i++) { + if (ineed < 2) multioldlo[iswap][i] = -BIG; + else multioldlo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); + multioldhi[iswap][i] = sublo[dim] + cutghostmultiold[i][dim]; + } } if (myloc[dim] == 0) { pbc_flag[iswap] = 1; @@ -401,12 +449,18 @@ void CommBrick::setup() slablo[iswap] = subhi[dim] - cutghost[dim]; if (ineed < 2) slabhi[iswap] = BIG; else slabhi[iswap] = 0.5 * (sublo[dim] + subhi[dim]); - } else { - for (i = 1; i <= ntypes; i++) { + } else if (mode == Comm::MULTI) { + for (i = 0; i < ncollections; i++) { multilo[iswap][i] = subhi[dim] - cutghostmulti[i][dim]; if (ineed < 2) multihi[iswap][i] = BIG; else multihi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); } + } else { + for (i = 1; i <= ntypes; i++) { + multioldlo[iswap][i] = subhi[dim] - cutghostmultiold[i][dim]; + if (ineed < 2) multioldhi[iswap][i] = BIG; + else multioldhi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); + } } if (myloc[dim] == procgrid[dim]-1) { pbc_flag[iswap] = 1; @@ -727,15 +781,19 @@ void CommBrick::exchange() void CommBrick::borders() { - int i,n,itype,iswap,dim,ineed,twoneed; - int nsend,nrecv,sendflag,nfirst,nlast,ngroup; + int i,n,itype,icollection,iswap,dim,ineed,twoneed; + int nsend,nrecv,sendflag,nfirst,nlast,ngroup,nprior; double lo,hi; int *type; + int *collection; double **x; double *buf,*mlo,*mhi; MPI_Request request; AtomVec *avec = atom->avec; + // After exchanging/sorting, need to reconstruct collection array for border communication + if(mode == Comm::MULTI) neighbor->build_collection(0); + // do swaps over all 3 dimensions iswap = 0; @@ -756,10 +814,14 @@ void CommBrick::borders() if (mode == Comm::SINGLE) { lo = slablo[iswap]; hi = slabhi[iswap]; - } else { - type = atom->type; + } else if (mode == Comm::MULTI) { + collection = neighbor->collection; mlo = multilo[iswap]; mhi = multihi[iswap]; + } else { + type = atom->type; + mlo = multioldlo[iswap]; + mhi = multioldhi[iswap]; } if (ineed % 2 == 0) { nfirst = nlast; @@ -788,6 +850,14 @@ void CommBrick::borders() if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); sendlist[iswap][nsend++] = i; } + } else if (mode == Comm::MULTI) { + for (i = nfirst; i < nlast; i++) { + icollection = collection[i]; + if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) { + if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); + sendlist[iswap][nsend++] = i; + } + } } else { for (i = nfirst; i < nlast; i++) { itype = type[i]; @@ -878,7 +948,10 @@ void CommBrick::borders() size_reverse_send[iswap] = nrecv*size_reverse; size_reverse_recv[iswap] = nsend*size_reverse; firstrecv[iswap] = atom->nlocal + atom->nghost; + nprior = atom->nlocal + atom->nghost; atom->nghost += nrecv; + if(neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); + iswap++; } } @@ -1431,6 +1504,12 @@ void CommBrick::grow_swap(int n) allocate_multi(n); } + if (mode == Comm::MULTIOLD) { + free_multiold(); + allocate_multiold(n); + } + + sendlist = (int **) memory->srealloc(sendlist,n*sizeof(int *),"comm:sendlist"); memory->grow(maxsendlist,n,"comm:maxsendlist"); @@ -1462,15 +1541,26 @@ void CommBrick::allocate_swap(int n) } /* ---------------------------------------------------------------------- - allocation of multi-type swap info + allocation of multi-collection swap info ------------------------------------------------------------------------- */ void CommBrick::allocate_multi(int n) { - multilo = memory->create(multilo,n,atom->ntypes+1,"comm:multilo"); - multihi = memory->create(multihi,n,atom->ntypes+1,"comm:multihi"); + multilo = memory->create(multilo,n,ncollections,"comm:multilo"); + multihi = memory->create(multihi,n,ncollections,"comm:multihi"); } +/* ---------------------------------------------------------------------- + allocation of multi/old-type swap info +------------------------------------------------------------------------- */ + +void CommBrick::allocate_multiold(int n) +{ + multioldlo = memory->create(multioldlo,n,atom->ntypes+1,"comm:multioldlo"); + multioldhi = memory->create(multioldhi,n,atom->ntypes+1,"comm:multioldhi"); +} + + /* ---------------------------------------------------------------------- free memory for swaps ------------------------------------------------------------------------- */ @@ -1492,7 +1582,7 @@ void CommBrick::free_swap() } /* ---------------------------------------------------------------------- - free memory for multi-type swaps + free memory for multi-collection swaps ------------------------------------------------------------------------- */ void CommBrick::free_multi() @@ -1502,6 +1592,17 @@ void CommBrick::free_multi() multilo = multihi = nullptr; } +/* ---------------------------------------------------------------------- + free memory for multi/old-type swaps +------------------------------------------------------------------------- */ + +void CommBrick::free_multiold() +{ + memory->destroy(multioldlo); + memory->destroy(multioldhi); + multioldlo = multioldhi = nullptr; +} + /* ---------------------------------------------------------------------- extract data potentially useful to other classes ------------------------------------------------------------------------- */ diff --git a/src/comm_brick.h b/src/comm_brick.h index 6165f54de5..a1794fdb7b 100644 --- a/src/comm_brick.h +++ b/src/comm_brick.h @@ -61,8 +61,10 @@ class CommBrick : public Comm { int *size_reverse_send; // # to send in each reverse comm int *size_reverse_recv; // # to recv in each reverse comm double *slablo,*slabhi; // bounds of slab to send at each swap - double **multilo,**multihi; // bounds of slabs for multi-type swap - double **cutghostmulti; // cutghost on a per-type basis + double **multilo,**multihi; // bounds of slabs for multi-collection swap + double **multioldlo,**multioldhi; // bounds of slabs for multi-type swap + double **cutghostmulti; // cutghost on a per-collection basis + double **cutghostmultiold; // cutghost on a per-type basis int *pbc_flag; // general flag for sending atoms thru PBC int **pbc; // dimension flags for PBC adjustments @@ -84,11 +86,13 @@ class CommBrick : public Comm { virtual void grow_send(int, int); // reallocate send buffer virtual void grow_recv(int); // free/allocate recv buffer virtual void grow_list(int, int); // reallocate one sendlist - virtual void grow_swap(int); // grow swap and multi arrays + virtual void grow_swap(int); // grow swap, multi, and multi/old arrays virtual void allocate_swap(int); // allocate swap arrays virtual void allocate_multi(int); // allocate multi arrays + virtual void allocate_multiold(int); // allocate multi/old arrays virtual void free_swap(); // free swap arrays virtual void free_multi(); // free multi arrays + virtual void free_multiold(); // free multi/old arrays }; } diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 2e916e7e1e..accdbf7b04 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -53,6 +53,7 @@ CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp) overlap = nullptr; rcbinfo = nullptr; cutghostmulti = nullptr; + cutghostmultiold = nullptr; init_buffers(); } @@ -81,6 +82,7 @@ CommTiled::~CommTiled() deallocate_swap(maxswap); memory->sfree(rcbinfo); memory->destroy(cutghostmulti); + memory->destroy(cutghostmultiold); } /* ---------------------------------------------------------------------- @@ -98,7 +100,9 @@ void CommTiled::init_buffers() overlap = nullptr; rcbinfo = nullptr; cutghostmulti = nullptr; + cutghostmultiold = nullptr; sendbox_multi = nullptr; + sendbox_multiold = nullptr; maxswap = 6; allocate_swap(maxswap); @@ -115,9 +119,10 @@ void CommTiled::init() nswap = 2*domain->dimension; - memory->destroy(cutghostmulti); - if (mode == Comm::MULTI) - memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti"); + memory->destroy(cutghostmultiold); + if (mode == Comm::MULTIOLD) + memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold"); + int bufextra_old = bufextra; init_exchange(); @@ -173,49 +178,62 @@ void CommTiled::setup() // set cutoff for comm forward and comm reverse // check that cutoff < any periodic box length - + if (mode == Comm::MULTI) { - if (multi_reduce) { - // If using multi/reduce, communicate itype particles a distance equal - // to the max of itype-jtype group interaction - // only consider smaller jtype groups - int igroup, jgroup; - double **cutmultisq = neighbor->cutmultisq; - int *map_type_multi = neighbor->map_type_multi; - for (i = 1; i <= ntypes; i++) { - - if (cutusermulti) { - cutghostmulti[i][0] = cutusermulti[i]; - cutghostmulti[i][1] = cutusermulti[i]; - cutghostmulti[i][2] = cutusermulti[i]; - } else { - cutghostmulti[i][0] = 0.0; - cutghostmulti[i][1] = 0.0; - cutghostmulti[i][2] = 0.0; - } + // build collection from scratch as it is needed for atom exchange + neighbor->build_collection(0); + + if(cutusermulti and ncollections != neighbor->ncollections) + error->all(FLERR, "Cannot change number of collections after defining comm_modify multi/cutoff"); + + ncollections = neighbor->ncollections; + + // allocate memory for multi-style communication at setup as ncollections can change + if(ncollections_prior != ncollections){ + memory->destroy(cutghostmulti); + if (mode == Comm::MULTI) + memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); - igroup = map_type_multi[i]; - for (j = 1; j <= ntypes; j++){ - jgroup = map_type_multi[j]; - - if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup])); - } + for(i = 0; i < maxswap; i ++) + grow_swap_send_multi(i,DELTA_PROCS); + + ncollections_prior = ncollections; + } + + double **cutcollectionsq = neighbor->cutcollectionsq; + // If using multi/reduce, communicate particles a distance equal + // to the max cutoff with equally sized or smaller collections + // If not, communicate the maximum cutoff of the entire collection + for (i = 0; i < ncollections; i++) { + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; } - } else { - // otherwise, communicate a distance equal to the maximum interaction distance for each type - double *cuttype = neighbor->cuttype; - for (i = 1; i <= ntypes; i++) { - double tmp = 0.0; - if (cutusermulti) tmp = cutusermulti[i]; - cutghostmulti[i][0] = MAX(tmp,cuttype[i]); - cutghostmulti[i][1] = MAX(tmp,cuttype[i]); - cutghostmulti[i][2] = MAX(tmp,cuttype[i]); + + for (j = 0; j < ncollections; j++){ + if(multi_reduce and cutcollectionsq[j][j] > cutcollectionsq[i][i]) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j])); } } } + + if (mode == Comm::MULTIOLD) { + double *cuttype = neighbor->cuttype; + for (i = 1; i <= ntypes; i++) { + double tmp = 0.0; + if (cutusermultiold) tmp = cutusermultiold[i]; + cutghostmultiold[i][0] = MAX(tmp,cuttype[i]); + cutghostmultiold[i][1] = MAX(tmp,cuttype[i]); + cutghostmultiold[i][2] = MAX(tmp,cuttype[i]); + } + } double cut = get_comm_cutoff(); if ((cut == 0.0) && (me == 0)) @@ -233,12 +251,20 @@ void CommTiled::setup() length2 = h_inv[2]; cutghost[2] = cut * length2; if (mode == Comm::MULTI) { - for (i = 1; i <= ntypes; i++) { + for (i = 0; i < ncollections; i++) { cutghostmulti[i][0] *= length0; cutghostmulti[i][1] *= length1; cutghostmulti[i][2] *= length2; } } + + if (mode == Comm::MULTIOLD) { + for (i = 1; i <= ntypes; i++) { + cutghostmultiold[i][0] *= length0; + cutghostmultiold[i][1] *= length1; + cutghostmultiold[i][2] *= length2; + } + } } if ((periodicity[0] && cutghost[0] > prd[0]) || @@ -376,7 +402,7 @@ void CommTiled::setup() // extend sbox in those lower dims to include ghost atoms // single mode and multi mode - double oboxlo[3],oboxhi[3],sbox[6],sbox_multi[6]; + double oboxlo[3],oboxhi[3],sbox[6],sbox_multi[6],sbox_multiold[6]; if (mode == Comm::SINGLE) { for (i = 0; i < noverlap; i++) { @@ -465,7 +491,7 @@ void CommTiled::setup() sbox[5] = MIN(oboxhi[2],hi2[2]); } - for (int itype = 1; itype <= atom->ntypes; itype++) { + for (int icollection = 0; icollection < ncollections; icollection++) { sbox_multi[0] = sbox[0]; sbox_multi[1] = sbox[1]; sbox_multi[2] = sbox[2]; @@ -476,36 +502,112 @@ void CommTiled::setup() sbox_multi[idim] = sublo[idim]; if (i < noverlap1) sbox_multi[3+idim] = - MIN(sbox_multi[3+idim]+cutghostmulti[itype][idim],subhi[idim]); + MIN(sbox_multi[3+idim]+cutghostmulti[icollection][idim],subhi[idim]); else sbox_multi[3+idim] = - MIN(sbox_multi[3+idim]-prd[idim]+cutghostmulti[itype][idim], + MIN(sbox_multi[3+idim]-prd[idim]+cutghostmulti[icollection][idim], subhi[idim]); } else { if (i < noverlap1) sbox_multi[idim] = - MAX(sbox_multi[idim]-cutghostmulti[itype][idim],sublo[idim]); + MAX(sbox_multi[idim]-cutghostmulti[icollection][idim],sublo[idim]); else sbox_multi[idim] = - MAX(sbox_multi[idim]+prd[idim]-cutghostmulti[itype][idim], + MAX(sbox_multi[idim]+prd[idim]-cutghostmulti[icollection][idim], sublo[idim]); sbox_multi[3+idim] = subhi[idim]; } if (idim >= 1) { if (sbox_multi[0] == oboxlo[0]) - sbox_multi[0] -= cutghostmulti[itype][idim]; + sbox_multi[0] -= cutghostmulti[icollection][idim]; if (sbox_multi[3] == oboxhi[0]) - sbox_multi[3] += cutghostmulti[itype][idim]; + sbox_multi[3] += cutghostmulti[icollection][idim]; } if (idim == 2) { if (sbox_multi[1] == oboxlo[1]) - sbox_multi[1] -= cutghostmulti[itype][idim]; + sbox_multi[1] -= cutghostmulti[icollection][idim]; if (sbox_multi[4] == oboxhi[1]) - sbox_multi[4] += cutghostmulti[itype][idim]; + sbox_multi[4] += cutghostmulti[icollection][idim]; } - memcpy(sendbox_multi[iswap][i][itype],sbox_multi,6*sizeof(double)); + memcpy(sendbox_multi[iswap][i][icollection],sbox_multi,6*sizeof(double)); + } + } + } + + if (mode == Comm::MULTIOLD) { + for (i = 0; i < noverlap; i++) { + pbc_flag[iswap][i] = 0; + pbc[iswap][i][0] = pbc[iswap][i][1] = pbc[iswap][i][2] = + pbc[iswap][i][3] = pbc[iswap][i][4] = pbc[iswap][i][5] = 0; + + (this->*box_other)(idim,idir,overlap[i],oboxlo,oboxhi); + + if (i < noverlap1) { + sbox[0] = MAX(oboxlo[0],lo1[0]); + sbox[1] = MAX(oboxlo[1],lo1[1]); + sbox[2] = MAX(oboxlo[2],lo1[2]); + sbox[3] = MIN(oboxhi[0],hi1[0]); + sbox[4] = MIN(oboxhi[1],hi1[1]); + sbox[5] = MIN(oboxhi[2],hi1[2]); + } else { + pbc_flag[iswap][i] = 1; + if (idir == 0) pbc[iswap][i][idim] = 1; + else pbc[iswap][i][idim] = -1; + if (triclinic) { + if (idim == 1) pbc[iswap][i][5] = pbc[iswap][i][idim]; + if (idim == 2) pbc[iswap][i][4] = pbc[iswap][i][3] = pbc[iswap][i][idim]; + } + sbox[0] = MAX(oboxlo[0],lo2[0]); + sbox[1] = MAX(oboxlo[1],lo2[1]); + sbox[2] = MAX(oboxlo[2],lo2[2]); + sbox[3] = MIN(oboxhi[0],hi2[0]); + sbox[4] = MIN(oboxhi[1],hi2[1]); + sbox[5] = MIN(oboxhi[2],hi2[2]); + } + + for (int itype = 1; itype <= atom->ntypes; itype++) { + sbox_multiold[0] = sbox[0]; + sbox_multiold[1] = sbox[1]; + sbox_multiold[2] = sbox[2]; + sbox_multiold[3] = sbox[3]; + sbox_multiold[4] = sbox[4]; + sbox_multiold[5] = sbox[5]; + if (idir == 0) { + sbox_multiold[idim] = sublo[idim]; + if (i < noverlap1) + sbox_multiold[3+idim] = + MIN(sbox_multiold[3+idim]+cutghostmultiold[itype][idim],subhi[idim]); + else + sbox_multiold[3+idim] = + MIN(sbox_multiold[3+idim]-prd[idim]+cutghostmultiold[itype][idim], + subhi[idim]); + } else { + if (i < noverlap1) + sbox_multiold[idim] = + MAX(sbox_multiold[idim]-cutghostmultiold[itype][idim],sublo[idim]); + else + sbox_multiold[idim] = + MAX(sbox_multiold[idim]+prd[idim]-cutghostmultiold[itype][idim], + sublo[idim]); + sbox_multiold[3+idim] = subhi[idim]; + } + + if (idim >= 1) { + if (sbox_multiold[0] == oboxlo[0]) + sbox_multiold[0] -= cutghostmultiold[itype][idim]; + if (sbox_multiold[3] == oboxhi[0]) + sbox_multiold[3] += cutghostmultiold[itype][idim]; + } + if (idim == 2) { + if (sbox_multiold[1] == oboxlo[1]) + sbox_multiold[1] -= cutghostmultiold[itype][idim]; + if (sbox_multiold[4] == oboxhi[1]) + sbox_multiold[4] += cutghostmultiold[itype][idim]; + } + + memcpy(sendbox_multiold[iswap][i][itype],sbox_multiold,6*sizeof(double)); } } } @@ -937,11 +1039,14 @@ void CommTiled::exchange() void CommTiled::borders() { - int i,m,n,nlast,nsend,nrecv,ngroup,ncount,ncountall; + int i,m,n,nlast,nsend,nrecv,ngroup,nprior,ncount,ncountall; double xlo,xhi,ylo,yhi,zlo,zhi; double *bbox; double **x; AtomVec *avec = atom->avec; + + // After exchanging, need to reconstruct collection array for border communication + if(mode == Comm::MULTI) neighbor->build_collection(0); // send/recv max one = max # of atoms in single send/recv for any swap // send/recv max all = max # of atoms in all sends/recvs within any swap @@ -1008,6 +1113,56 @@ void CommTiled::borders() smaxone = MAX(smaxone,ncount); ncountall += ncount; + } else if (mode == Comm::MULTI) { + + int* collection=neighbor->collection; + int icollection; + ncount = 0; + + if (!bordergroup) { + for (i = 0; i < nlast; i++) { + icollection=collection[i]; + bbox = sendbox_multi[iswap][m][icollection]; + xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; + xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; + if (x[i][0] >= xlo && x[i][0] < xhi && + x[i][1] >= ylo && x[i][1] < yhi && + x[i][2] >= zlo && x[i][2] < zhi) { + if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount); + sendlist[iswap][m][ncount++] = i; + } + } + } else { + ngroup = atom->nfirst; + for (i = 0; i < ngroup; i++) { + icollection=collection[i]; + bbox = sendbox_multi[iswap][m][icollection]; + xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; + xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; + if (x[i][0] >= xlo && x[i][0] < xhi && + x[i][1] >= ylo && x[i][1] < yhi && + x[i][2] >= zlo && x[i][2] < zhi) { + if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount); + sendlist[iswap][m][ncount++] = i; + } + } + for (i = atom->nlocal; i < nlast; i++) { + icollection=collection[i]; + bbox = sendbox_multi[iswap][m][icollection]; + xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; + xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; + if (x[i][0] >= xlo && x[i][0] < xhi && + x[i][1] >= ylo && x[i][1] < yhi && + x[i][2] >= zlo && x[i][2] < zhi) { + if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount); + sendlist[iswap][m][ncount++] = i; + } + } + } + + sendnum[iswap][m] = ncount; + smaxone = MAX(smaxone,ncount); + ncountall += ncount; } else { int* type=atom->type; @@ -1017,7 +1172,7 @@ void CommTiled::borders() if (!bordergroup) { for (i = 0; i < nlast; i++) { itype=type[i]; - bbox = sendbox_multi[iswap][m][itype]; + bbox = sendbox_multiold[iswap][m][itype]; xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; if (x[i][0] >= xlo && x[i][0] < xhi && @@ -1031,7 +1186,7 @@ void CommTiled::borders() ngroup = atom->nfirst; for (i = 0; i < ngroup; i++) { itype=type[i]; - bbox = sendbox_multi[iswap][m][itype]; + bbox = sendbox_multiold[iswap][m][itype]; xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; if (x[i][0] >= xlo && x[i][0] < xhi && @@ -1043,7 +1198,7 @@ void CommTiled::borders() } for (i = atom->nlocal; i < nlast; i++) { itype=type[i]; - bbox = sendbox_multi[iswap][m][itype]; + bbox = sendbox_multiold[iswap][m][itype]; xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; if (x[i][0] >= xlo && x[i][0] < xhi && @@ -1179,8 +1334,11 @@ void CommTiled::borders() // increment ghost atoms n = nrecvproc[iswap]; - if (n) + if (n) { + nprior = atom->nghost + atom->nlocal; atom->nghost += forward_recv_offset[iswap][n-1] + recvnum[iswap][n-1]; + if(neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); + } } // For molecular systems we lose some bits for local atom indices due @@ -2120,6 +2278,7 @@ void CommTiled::allocate_swap(int n) pbc = new int**[n]; sendbox = new double**[n]; sendbox_multi = new double***[n]; + sendbox_multiold = new double***[n]; maxsendlist = new int*[n]; sendlist = new int**[n]; @@ -2134,6 +2293,7 @@ void CommTiled::allocate_swap(int n) pbc[i] = nullptr; sendbox[i] = nullptr; sendbox_multi[i] = nullptr; + sendbox_multiold[i] = nullptr; maxsendlist[i] = nullptr; sendlist[i] = nullptr; } @@ -2182,8 +2342,9 @@ void CommTiled::grow_swap_send(int i, int n, int nold) memory->create(pbc[i],n,6,"comm:pbc_flag"); memory->destroy(sendbox[i]); memory->create(sendbox[i],n,6,"comm:sendbox"); - memory->destroy(sendbox_multi[i]); - memory->create(sendbox_multi[i],n,atom->ntypes+1,6,"comm:sendbox_multi"); + grow_swap_send_multi(i,n); + memory->destroy(sendbox_multiold[i]); + memory->create(sendbox_multiold[i],n,atom->ntypes+1,6,"comm:sendbox_multiold"); delete [] maxsendlist[i]; maxsendlist[i] = new int[n]; @@ -2215,6 +2376,19 @@ void CommTiled::grow_swap_recv(int i, int n) size_reverse_send[i] = new int[n]; } + +/* ---------------------------------------------------------------------- + grow info for swap I for multi as ncollections can change +------------------------------------------------------------------------- */ + +void CommTiled::grow_swap_send_multi(int i, int n) +{ + memory->destroy(sendbox_multi[i]); + + if(ncollections > 0) + memory->create(sendbox_multi[i],n,ncollections,6,"comm:sendbox_multi"); +} + /* ---------------------------------------------------------------------- deallocate swap info ------------------------------------------------------------------------- */ @@ -2243,6 +2417,7 @@ void CommTiled::deallocate_swap(int n) memory->destroy(pbc[i]); memory->destroy(sendbox[i]); memory->destroy(sendbox_multi[i]); + memory->destroy(sendbox_multiold[i]); delete [] maxsendlist[i]; @@ -2265,6 +2440,7 @@ void CommTiled::deallocate_swap(int n) delete [] pbc; delete [] sendbox; delete [] sendbox_multi; + delete [] sendbox_multiold; delete [] maxsendlist; delete [] sendlist; diff --git a/src/comm_tiled.h b/src/comm_tiled.h index fa2c76e6e9..fdb175117e 100644 --- a/src/comm_tiled.h +++ b/src/comm_tiled.h @@ -77,9 +77,12 @@ class CommTiled : public Comm { double ***sendbox; // bounding box of atoms to send per swap/proc - double **cutghostmulti; // cutghost on a per-type basis + double **cutghostmulti; // cutghost on a per-collection basis + double **cutghostmultiold; // cutghost on a per-type basis double ****sendbox_multi; // bounding box of atoms to send // per swap/proc for multi comm + double ****sendbox_multiold; // bounding box of atoms to send + // per swap/proc for multi/old comm // exchange comm info, proc lists do not include self @@ -148,6 +151,7 @@ class CommTiled : public Comm { void grow_list(int, int, int); // reallocate sendlist for one swap/proc void allocate_swap(int); // allocate swap arrays void grow_swap_send(int, int, int); // grow swap arrays for send and recv + void grow_swap_send_multi(int, int); // grow multi swap arrays for send and recv void grow_swap_recv(int, int); void deallocate_swap(int); // deallocate swap arrays @@ -163,10 +167,6 @@ E: Cannot yet use comm_style tiled with triclinic box Self-explanatory. -E: Cannot yet use comm_style tiled with multi-mode comm - -Self-explanatory. - E: Communication cutoff for comm_style tiled cannot exceed periodic box length Self-explanatory. diff --git a/src/init b/src/init new file mode 100644 index 0000000000..617c9effa3 --- /dev/null +++ b/src/init @@ -0,0 +1,789 @@ +angle_charmm.cpp: if (comm->me == 0) { +angle_cosine.cpp: if (comm->me == 0) utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,nullptr,error); +angle_cosine_periodic.cpp: if (comm->me == 0) { +angle_cosine_squared.cpp: if (comm->me == 0) { +angle.cpp: memory->create(eatom,comm->nthreads*maxeatom,"angle:eatom"); +angle.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"angle:vatom"); +angle.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"angle:cvatom"); +angle.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); +angle.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); +angle.cpp: bytes += comm->nthreads*maxcvatom*9 * sizeof(double); +angle_deprecated.cpp: if (lmp->comm->me == 0) +angle_harmonic.cpp: if (comm->me == 0) { +angle_hybrid.cpp: const int nthreads = comm->nthreads; +angle_hybrid.cpp: if (comm->nthreads > 1) { +angle_hybrid.cpp: int me = comm->me; +angle_table.cpp: if (comm->me == 0) { +angle_zero.cpp: if (comm->me == 0) { +atom.cpp: if (comm->layout != Comm::LAYOUT_TILED) { +atom.cpp: if (comm->myloc[0] == 0) sublo[0] -= epsilon[0]; +atom.cpp: if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += epsilon[0]; +atom.cpp: if (comm->myloc[1] == 0) sublo[1] -= epsilon[1]; +atom.cpp: if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += epsilon[1]; +atom.cpp: if (comm->myloc[2] == 0) sublo[2] -= epsilon[2]; +atom.cpp: if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += epsilon[2]; +atom.cpp: if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0]; +atom.cpp: if (comm->mysplit[0][1] == 1.0) subhi[0] += epsilon[0]; +atom.cpp: if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1]; +atom.cpp: if (comm->mysplit[1][1] == 1.0) subhi[1] += epsilon[1]; +atom.cpp: if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2]; +atom.cpp: if (comm->mysplit[2][1] == 1.0) subhi[2] += epsilon[2]; +atom.cpp: if (comm->me == 0) { +atom.cpp: called by comm->exchange() if atom_modify first group is set +atom.cpp: always called between comm->exchange() and comm->borders() +atom.cpp: if (comm->me == 0) +atom_map.cpp: int nper = static_cast (natoms/comm->nprocs); +atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); +atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); +atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); +atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); +atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); +atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); +atom_vec.cpp: f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f"); +atom_vec.cpp: const int nthreads = threads[i] ? comm->nthreads : 1; +atom_vec.cpp: bytes += memory->usage(f,nmax*comm->nthreads,3); +atom_vec.cpp: const int nthreads = threads[i] ? comm->nthreads : 1; +atom_vec_hybrid.cpp: if (mass_pertype && mass_peratom && comm->me == 0) +atom_vec_hybrid.cpp: if ((ptr && strstr(ptr+1,dup)) && (comm->me == 0)) +atom_vec_line.cpp: //if (comm->me == 1 && update->ntimestep == 873) +atom_vec_line.cpp: printf("BAD vecline ptrs: %s: %d %d: %d\n",str,comm->me, +atom_vec_line.cpp: str,comm->me,update->ntimestep,count,nlocal_bonus); +balance.cpp: int *procgrid = comm->procgrid; +balance.cpp: if (style == BISECTION && comm->style == 0) +balance.cpp: // init entire system since comm->setup is done +balance.cpp: comm->setup(); +balance.cpp: comm->exchange(); +balance.cpp: if (comm->layout == Comm::LAYOUT_TILED && style != BISECTION) { +balance.cpp: if (comm->layout == Comm::LAYOUT_UNIFORM) { +balance.cpp: comm->layout = Comm::LAYOUT_NONUNIFORM; +balance.cpp: } else if (comm->layout == Comm::LAYOUT_NONUNIFORM) { +balance.cpp: comm->layout = Comm::LAYOUT_UNIFORM; +balance.cpp: } else if (comm->layout == Comm::LAYOUT_TILED) { +balance.cpp: comm->layout = Comm::LAYOUT_UNIFORM; +balance.cpp: else comm->layout = Comm::LAYOUT_NONUNIFORM; +balance.cpp: comm->xsplit[i] = i * 1.0/procgrid[0]; +balance.cpp: comm->xsplit[procgrid[0]] = 1.0; +balance.cpp: for (int i = 0; i <= procgrid[0]; i++) comm->xsplit[i] = user_xsplit[i]; +balance.cpp: comm->ysplit[i] = i * 1.0/procgrid[1]; +balance.cpp: comm->ysplit[procgrid[1]] = 1.0; +balance.cpp: for (int i = 0; i <= procgrid[1]; i++) comm->ysplit[i] = user_ysplit[i]; +balance.cpp: comm->zsplit[i] = i * 1.0/procgrid[2]; +balance.cpp: comm->zsplit[procgrid[2]] = 1.0; +balance.cpp: for (int i = 0; i <= procgrid[2]; i++) comm->zsplit[i] = user_zsplit[i]; +balance.cpp: comm->layout = Comm::LAYOUT_NONUNIFORM; +balance.cpp: comm->layout = Comm::LAYOUT_TILED; +balance.cpp: for (int i = 0; i <= comm->procgrid[0]; i++) +balance.cpp: mesg += fmt::format(" {:.8}",comm->xsplit[i]); +balance.cpp: for (int i = 0; i <= comm->procgrid[1]; i++) +balance.cpp: mesg += fmt::format(" {:.8}",comm->ysplit[i]); +balance.cpp: for (int i = 0; i <= comm->procgrid[2]; i++) +balance.cpp: mesg += fmt::format(" {:.8}",comm->zsplit[i]); +balance.cpp: if (outflag && comm->me == 0) { +balance.cpp: comm->rcbnew = 1; +balance.cpp: if (idim >= 0) comm->rcbcutfrac = (rcb->cut - boxlo[idim]) / prd[idim]; +balance.cpp: else comm->rcbcutfrac = 0.0; +balance.cpp: comm->rcbcutdim = idim; +balance.cpp: double (*mysplit)[2] = comm->mysplit; +balance.cpp: int max = MAX(comm->procgrid[0],comm->procgrid[1]); +balance.cpp: max = MAX(max,comm->procgrid[2]); +balance.cpp: if (comm->layout == Comm::LAYOUT_TILED) { +balance.cpp: int *procgrid = comm->procgrid; +balance.cpp: double *xsplit = comm->xsplit; +balance.cpp: double *ysplit = comm->ysplit; +balance.cpp: double *zsplit = comm->zsplit; +balance.cpp: int *procgrid = comm->procgrid; +balance.cpp: split = comm->xsplit; +balance.cpp: split = comm->ysplit; +balance.cpp: split = comm->zsplit; +balance.cpp: double *xsplit = comm->xsplit; +balance.cpp: double *ysplit = comm->ysplit; +balance.cpp: double *zsplit = comm->zsplit; +balance.cpp: int nx = comm->procgrid[0]; +balance.cpp: int ny = comm->procgrid[1]; +balance.cpp: int nz = comm->procgrid[2]; +bond.cpp: memory->create(eatom,comm->nthreads*maxeatom,"bond:eatom"); +bond.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"bond:vatom"); +bond.cpp: if (comm->me == 0) { +bond.cpp: if (comm->me == 0) { +bond.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); +bond.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); +bond_deprecated.cpp: if (lmp->comm->me == 0) +bond_fene.cpp: if (comm->me == 0) +bond_fene.cpp: if (comm->me == 0) { +bond_fene_expand.cpp: if (comm->me == 0) +bond_fene_expand.cpp: if (comm->me == 0) { +bond_gromos.cpp: if (comm->me == 0) { +bond_harmonic.cpp: if (comm->me == 0) { +bond_hybrid.cpp: const int nthreads = comm->nthreads; +bond_hybrid.cpp: int me = comm->me; +bond_morse.cpp: if (comm->me == 0) { +bond_nonlinear.cpp: if (comm->me == 0) { +bond_quartic.cpp: if (comm->me == 0) { +bond_table.cpp: if (comm->me == 0) { +bond_zero.cpp: if (comm->me == 0) { +change_box.cpp: if (comm->me == 0) utils::logmesg(lmp,"Changing box ...\n"); +change_box.cpp: if (natoms != atom->natoms && comm->me == 0) +comm_brick.cpp: if (oldcomm->layout == Comm::LAYOUT_TILED) +comm_brick.cpp: layout = oldcomm->layout; +comm.cpp: if (oldcomm->grid2proc) { +comm.cpp: memcpy(&grid2proc[0][0][0],&oldcomm->grid2proc[0][0][0], +comm.cpp: memcpy(xsplit,oldcomm->xsplit,(procgrid[0]+1)*sizeof(double)); +comm.cpp: memcpy(ysplit,oldcomm->ysplit,(procgrid[1]+1)*sizeof(double)); +comm.cpp: memcpy(zsplit,oldcomm->zsplit,(procgrid[2]+1)*sizeof(double)); +comm.cpp: if (oldcomm->cutusermulti) { +comm.cpp: memcpy(cutusermulti,oldcomm->cutusermulti,ncollections); +comm.cpp: if (oldcomm->cutusermultiold) { +comm.cpp: memcpy(cutusermultiold,oldcomm->cutusermultiold,atom->ntypes+1); +comm.cpp: int n = strlen(oldcomm->customfile) + 1; +comm.cpp: strcpy(customfile,oldcomm->customfile); +comm.cpp: int n = strlen(oldcomm->outfile) + 1; +comm.cpp: strcpy(outfile,oldcomm->outfile); +comm_tiled.cpp: layout = oldcomm->layout; +compute_adf.cpp: if (mycutneigh > comm->cutghostuser) +compute_aggregate_atom.cpp: if (count > 1 && comm->me == 0) +compute_aggregate_atom.cpp: comm->forward_comm_compute(this); +compute_aggregate_atom.cpp: comm->forward_comm_compute(this); +compute_aggregate_atom.cpp: comm->reverse_comm_compute(this); +compute_bond_local.cpp: if (velflag && !comm->ghost_velocity) ghostvelflag = 1; +compute_bond_local.cpp: if (ghostvelflag && !initflag) comm->forward_comm_compute(this); +compute_centro_atom.cpp: if (count > 1 && comm->me == 0) +compute_centroid_stress_atom.cpp: comm->reverse_comm_compute(this); +compute_chunk_atom.cpp: int nprocs = comm->nprocs; +compute_chunk_atom.cpp: comm->ring(n,sizeof(int),list,1,idring,nullptr,(void *)this,0); +compute_chunk_atom.cpp: callback from comm->ring() +compute_chunk_atom.cpp: if (flagall && comm->me == 0) +compute_cluster_atom.cpp: if (count > 1 && comm->me == 0) +compute_cluster_atom.cpp: comm->forward_comm_compute(this); +compute_cluster_atom.cpp: comm->forward_comm_compute(this); +compute_cluster_atom.cpp: comm->forward_comm_compute(this); +compute_cna_atom.cpp: comm->me == 0) +compute_cna_atom.cpp: if (count > 1 && comm->me == 0) +compute_cna_atom.cpp: if (nerrorall && comm->me == 0) +compute_cna_atom.cpp: if (nerrorall && comm->me == 0) +compute_contact_atom.cpp: if (count > 1 && comm->me == 0) +compute_contact_atom.cpp: if (force->newton_pair) comm->reverse_comm_compute(this); +compute_coord_atom.cpp: comm->forward_comm_compute(this); +compute_deprecated.cpp: if (lmp->comm->me == 0) +compute_erotate_sphere_atom.cpp: if (count > 1 && comm->me == 0) +compute_fragment_atom.cpp: if (count > 1 && comm->me == 0) +compute_fragment_atom.cpp: comm->forward_comm_compute(this); +compute_fragment_atom.cpp: comm->forward_comm_compute(this); +compute_group_group.cpp: if ((fabs(e_correction) > SMALL) && (comm->me == 0)) +compute_hexorder_atom.cpp: if (count > 1 && comm->me == 0) +compute_ke_atom.cpp: if (count > 1 && comm->me == 0) +compute_orientorder_atom.cpp: if (count > 1 && comm->me == 0) +compute_pe_atom.cpp: comm->reverse_comm_compute(this); +compute_property_atom.cpp: int me = comm->me; +compute_rdf.cpp: cutghost = MAX(force->pair->cutforce+skin,comm->cutghostuser); +compute_rdf.cpp: cutghost = comm->cutghostuser; +compute_rdf.cpp: if (comm->me == 0) +compute_stress_atom.cpp: comm->reverse_comm_compute(this); +compute_temp_deform.cpp: comm->me == 0) +compute_temp_deform.cpp: if (i == modify->nfix && comm->me == 0) +create_atoms.cpp: if (comm->layout != Comm::LAYOUT_TILED) { +create_atoms.cpp: if (comm->myloc[0] == 0) sublo[0] -= epsilon[0]; +create_atoms.cpp: if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*epsilon[0]; +create_atoms.cpp: if (comm->myloc[1] == 0) sublo[1] -= epsilon[1]; +create_atoms.cpp: if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= 2.0*epsilon[1]; +create_atoms.cpp: if (comm->myloc[2] == 0) sublo[2] -= epsilon[2]; +create_atoms.cpp: if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= 2.0*epsilon[2]; +create_atoms.cpp: if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0]; +create_atoms.cpp: if (comm->mysplit[0][1] == 1.0) subhi[0] -= 2.0*epsilon[0]; +create_atoms.cpp: if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1]; +create_atoms.cpp: if (comm->mysplit[1][1] == 1.0) subhi[1] -= 2.0*epsilon[1]; +create_atoms.cpp: if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2]; +create_atoms.cpp: if (comm->mysplit[2][1] == 1.0) subhi[2] -= 2.0*epsilon[2]; +create_bonds.cpp: // init entire system since comm->borders and neighbor->build is done +create_bonds.cpp: if (rmax > neighbor->cutneighmin && comm->me == 0) +create_bonds.cpp: comm->setup(); +create_bonds.cpp: comm->exchange(); +create_bonds.cpp: comm->borders(); +create_bonds.cpp: if (comm->me == 0) +create_box.cpp: comm->set_proc_grid(); +delete_atoms.cpp: } else if (comm->me == 0) +delete_atoms.cpp: if (comm->me == 0) { +delete_atoms.cpp: if (comm->me == 0) utils::logmesg(lmp,"System init for delete_atoms ...\n"); +delete_atoms.cpp: // init entire system since comm->borders and neighbor->build is done +delete_atoms.cpp: if (cut > neighbor->cutneighmin && comm->me == 0) +delete_atoms.cpp: comm->setup(); +delete_atoms.cpp: comm->exchange(); +delete_atoms.cpp: comm->borders(); +delete_atoms.cpp: RanMars *random = new RanMars(lmp,seed + comm->me); +delete_atoms.cpp: // pass list to all other procs via comm->ring() +delete_atoms.cpp: comm->ring(n,sizeof(tagint),list,1,bondring,nullptr,(void *)this); +delete_atoms.cpp: // pass list to all other procs via comm->ring() +delete_atoms.cpp: comm->ring(n,sizeof(tagint),list,1,molring,nullptr,(void *)this); +delete_atoms.cpp: callback from comm->ring() in delete_bond() +delete_atoms.cpp: callback from comm->ring() in delete_molecule() +delete_bonds.cpp: // init entire system since comm->borders is done +delete_bonds.cpp: if (comm->me == 0) utils::logmesg(lmp,"System init for delete_bonds ...\n"); +delete_bonds.cpp: if (comm->me == 0) utils::logmesg(lmp,"Deleting bonds ...\n"); +delete_bonds.cpp: comm->setup(); +delete_bonds.cpp: comm->exchange(); +delete_bonds.cpp: comm->borders(); +delete_bonds.cpp: if (comm->me == 0) { +deprecated.cpp: if (lmp->comm->me == 0) +deprecated.cpp: if (lmp->comm->me == 0) +dihedral_charmm.cpp: if (comm->me == 0) { +dihedral_charmmfsw.cpp: if (comm->me == 0) { +dihedral.cpp: memory->create(eatom,comm->nthreads*maxeatom,"dihedral:eatom"); +dihedral.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"dihedral:vatom"); +dihedral.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"dihedral:cvatom"); +dihedral.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); +dihedral.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); +dihedral.cpp: bytes += comm->nthreads*maxcvatom*9 * sizeof(double); +dihedral_deprecated.cpp: if (lmp->comm->me == 0) +dihedral_harmonic.cpp: if (comm->me == 0) { +dihedral_helix.cpp: if (comm->me == 0) { +dihedral_hybrid.cpp: int me = comm->me; +dihedral_multi_harmonic.cpp: if (comm->me == 0) { +dihedral_opls.cpp: if (comm->me == 0) { +displace_atoms.cpp: if (comm->me == 0) utils::logmesg(lmp,"Displacing atoms ...\n"); +displace_atoms.cpp: if (natoms != atom->natoms && comm->me == 0) +domain.cpp: else if (comm->me == 0) +domain.cpp: uses comm->xyz_split or comm->mysplit +domain.cpp: if (comm->layout != Comm::LAYOUT_TILED) { +domain.cpp: int *myloc = comm->myloc; +domain.cpp: double *xsplit = comm->xsplit; +domain.cpp: double *ysplit = comm->ysplit; +domain.cpp: double *zsplit = comm->zsplit; +domain.cpp: double (*mysplit)[2] = comm->mysplit; +domain.cpp: uses comm->xyz_split or comm->mysplit +domain.cpp: if (comm->layout != Comm::LAYOUT_TILED) { +domain.cpp: int *myloc = comm->myloc; +domain.cpp: int *procgrid = comm->procgrid; +domain.cpp: double *xsplit = comm->xsplit; +domain.cpp: double *ysplit = comm->ysplit; +domain.cpp: double *zsplit = comm->zsplit; +domain.cpp: double (*mysplit)[2] = comm->mysplit; +domain.cpp: comm->forward_comm_array(3,unwrap); +domain.cpp: if (flagall && comm->me == 0) +domain.cpp: if (all && comm->me == 0) +domain.cpp: if (all && comm->me == 0) +domain.cpp: if (flagall && comm->me == 0) +domain.cpp: since may lead to lost atoms in comm->exchange() +domain.cpp: if (flagall && comm->me == 0) +domain.cpp: if ((flag_all > 0) && (comm->me == 0)) +domain.cpp: if (comm->me == 0) { +dump_deprecated.cpp: if (lmp->comm->me == 0) +dump_image.cpp: comm->forward_comm_dump(this); +dump_movie.cpp: if ((comm->me == 0) && (fp == nullptr)) { +finish.cpp: const int nthreads = comm->nthreads; +fix_balance.cpp: if (lbstyle == BISECTION && comm->style == 0) +fix_balance.cpp: compute final imbalance factor based on nlocal after comm->exchange() +fix_balance.cpp: // invoke balancer and reset comm->uniform flag +fix_balance.cpp: comm->layout = Comm::LAYOUT_NONUNIFORM; +fix_balance.cpp: comm->layout = Comm::LAYOUT_TILED; +fix_balance.cpp: // since may lead to lost atoms in comm->exchange() +fix_balance.cpp: // else allow caller's comm->exchange() to do it +fix_balance.cpp: // b/c atoms may migrate again in comm->exchange() +fix_balance.cpp: // can only be done after atoms migrate in comm->exchange() +fix_box_relax.cpp: if (temperature->igroup != 0 && comm->me == 0) +fix_cmap.cpp: if (comm->me == 0) { +fix_cmap.cpp: if (comm->me == 0) +fix_cmap.cpp: if (comm->me == 0) fclose(fp); +fix_cmap.cpp: if (comm->me == 0) { +fix_deform.cpp: if (comm->me == 0) { +fix_deprecated.cpp: if (lmp->comm->me == 0) +fix_deprecated.cpp: if (lmp->comm->me == 0) +fix_dt_reset.cpp: strcmp(output->dump[i]->style,"xtc") == 0) && comm->me == 0) +fix_group.cpp: if (warn && comm->me == 0) +fix_halt.cpp: if (comm->me == 0 && msgflag == YESMSG) error->message(FLERR,message); +fix_langevin.cpp: random = new RanMars(lmp,seed + comm->me); +fix_langevin.cpp: if (temperature->igroup != igroup && comm->me == 0) +fix_move.cpp: if (comm->me == 0) { +fix_neigh_history.cpp: int nmypage = comm->nthreads; +fix_neigh_history.cpp: comm->reverse_comm_fix(this,0); +fix_neigh_history.cpp: comm->reverse_comm_fix_variable(this); +fix_neigh_history.cpp: int nmypage = comm->nthreads; +fix_neigh_history.cpp: if (comm->me == 0) { +fix_nh.cpp: if (comm->me == 0) { +fix_nh.cpp: if (temperature->igroup != 0 && comm->me == 0) +fix_nve_limit.cpp: if (comm->me == 0) +fix_pour.cpp: if (comm->layout != Comm::LAYOUT_TILED) { +fix_pour.cpp: if (comm->myloc[2] == comm->procgrid[2]-1 && +fix_pour.cpp: if (comm->mysplit[2][1] == 1.0 && +fix_pour.cpp: if (comm->layout != Comm::LAYOUT_TILED) { +fix_pour.cpp: if (comm->myloc[1] == comm->procgrid[1]-1 && +fix_pour.cpp: if (comm->mysplit[1][1] == 1.0 && +fix_press_berendsen.cpp: if (temperature->igroup != 0 && comm->me == 0) +fix_property_atom.cpp: if (flag && comm->me == 0) +fix_recenter.cpp: if (flag && comm->me == 0) +fix_restrain.cpp: comm->me,update->ntimestep)); +fix_restrain.cpp: comm->me,update->ntimestep)); +fix_restrain.cpp: comm->me,update->ntimestep)); +fix_restrain.cpp: comm->me,update->ntimestep)); +fix_restrain.cpp: ids[m][2],comm->me,update->ntimestep)); +fix_restrain.cpp: ids[m][2],comm->me,update->ntimestep)); +fix_restrain.cpp: ids[m][2],ids[m][3],comm->me, +fix_restrain.cpp: ids[m][2],ids[m][3],comm->me, +fix_restrain.cpp: comm->me,x[i1][0],x[i1][1],x[i1][2], +fix_restrain.cpp: comm->me,x[i2][0],x[i2][1],x[i2][2], +fix_restrain.cpp: comm->me,x[i3][0],x[i3][1],x[i3][2], +fix_restrain.cpp: comm->me,x[i4][0],x[i4][1],x[i4][2]); +fix_spring_chunk.cpp: if (comm->me == 0) { +fix_spring_chunk.cpp: if (comm->me == 0) +fix_spring_rg.cpp: if (comm->me == 0) { +fix_store.cpp: // PERATOM may be comm->exchanged before filled by caller +fix_store.cpp: if (comm->me == 0) { +fix_temp_berendsen.cpp: if (temperature->igroup != igroup && comm->me == 0) +fix_temp_berendsen.cpp: if (comm->me == 0) { +fix_temp_csld.cpp: random = new RanMars(lmp,seed + comm->me); +fix_temp_csld.cpp: if (temperature->igroup != igroup && comm->me == 0) +fix_temp_csld.cpp: int nsize = PRNGSIZE*comm->nprocs+2; // pRNG state per proc + nprocs + energy +fix_temp_csld.cpp: if (comm->me == 0) { +fix_temp_csld.cpp: list[1] = comm->nprocs; +fix_temp_csld.cpp: if (comm->me == 0) { +fix_temp_csld.cpp: if (nprocs != comm->nprocs) { +fix_temp_csld.cpp: if (comm->me == 0) +fix_temp_csld.cpp: } else random->set_state(list+2+comm->me*103); +fix_temp_csvr.cpp: random = new RanMars(lmp,seed + comm->me); +fix_temp_csvr.cpp: if (comm->me == 0) { +fix_temp_csvr.cpp: if (temperature->igroup != igroup && comm->me == 0) +fix_temp_csvr.cpp: int nsize = PRNGSIZE*comm->nprocs+2; // pRNG state per proc + nprocs + energy +fix_temp_csvr.cpp: if (comm->me == 0) { +fix_temp_csvr.cpp: list[1] = comm->nprocs; +fix_temp_csvr.cpp: if (comm->me == 0) { +fix_temp_csvr.cpp: if (nprocs != comm->nprocs) { +fix_temp_csvr.cpp: if (comm->me == 0) +fix_temp_csvr.cpp: } else random->set_state(list+2+comm->me*103); +fix_temp_rescale.cpp: if (temperature->igroup != igroup && comm->me == 0) +fix_temp_rescale.cpp: if (comm->me == 0) { +fix_wall_gran_region.cpp: if (comm->me) return; +fix_wall_reflect.cpp: if (nrigid && comm->me == 0) +force.cpp: if (comm->me == 0) { +group.cpp: // pass list to all other procs via comm->ring() +group.cpp: comm->ring(n,sizeof(tagint),list,1,molring,nullptr,(void *)this); +group.cpp: callback from comm->ring() +imbalance_neigh.cpp: if (comm->me == 0 && !did_warn) +improper.cpp: memory->create(eatom,comm->nthreads*maxeatom,"improper:eatom"); +improper.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"improper:vatom"); +improper.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"improper:cvatom"); +improper.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); +improper.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); +improper_cvff.cpp: if (comm->me == 0) { +improper_deprecated.cpp: if (lmp->comm->me == 0) +improper_harmonic.cpp: if (comm->me == 0) { +improper_hybrid.cpp: int me = comm->me; +improper_umbrella.cpp: if (comm->me == 0) { +info.cpp: if (comm->me != 0) return; +info.cpp: commstyles[comm->style], commlayout[comm->layout], +info.cpp: comm->ghost_velocity ? "yes" : "no"); +info.cpp: if (comm->mode == 0) +info.cpp: comm->get_comm_cutoff()); +info.cpp: if (comm->mode == 1) { +info.cpp: if (comm->cutusermulti) cut = MAX(cut,comm->cutusermulti[i]); +info.cpp: fmt::print(out,"Nprocs = {}, Nthreads = {}\n",comm->nprocs,comm->nthreads); +info.cpp: fmt::print(out,"Processor grid = {} x {} x {}\n",comm->procgrid[0], +info.cpp: comm->procgrid[1], comm->procgrid[2]); +info.cpp: style = commstyles[comm->style]; +info.cpp: bytes += comm->memory_usage(); +input.cpp: comm->modify_params(narg,arg); +input.cpp: if (comm->style == 0) return; +input.cpp: if (comm->style == 1) return; +input.cpp: comm->set_processors(narg,arg); +irregular.cpp: can be used in place of comm->exchange() +irregular.cpp: if (!preassign) comm->coord2proc_setup(); +irregular.cpp: mproclist[nsendatom] = comm->coord2proc(x[i],igx,igy,igz); +irregular.cpp: if not, caller can decide to use comm->exchange() instead +irregular.cpp: if (comm->layout == Comm::LAYOUT_TILED) return 1; +irregular.cpp: // cannot check via comm->procneigh since it ignores PBC +irregular.cpp: int *myloc = comm->myloc; +irregular.cpp: int *procgrid = comm->procgrid; +irregular.cpp: comm->coord2proc(x[i],igx,igy,igz); +kspace.cpp: if ((qsqsum == 0.0) && (comm->me == 0) && warn_nocharge && warning_flag) { +kspace.cpp: if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message); +kspace.cpp: if (comm->me == 0) { +kspace.cpp: if ((table_accuracy > spr) && (comm->me == 0)) +kspace.cpp: if (slab_volfactor < 2.0 && comm->me == 0) +kspace_deprecated.cpp: if (lmp->comm->me == 0) +lammps.cpp: const int me = comm->me; +lammps.cpp: comm->init(); // comm must come after force, modify, neighbor, atom +lattice.cpp: if (comm->me == 0) +library.cpp: && (lmp->comm->me == 0)) { +library.cpp: && (lmp->comm->me == 0)) { +library.cpp: lmp->comm->set_proc_grid(); +library.cpp: if (strcmp(keyword,"world_rank") == 0) return lmp->comm->me; +library.cpp: if (strcmp(keyword,"world_size") == 0) return lmp->comm->nprocs; +library.cpp: if (strcmp(keyword,"nthreads") == 0) return lmp->comm->nthreads; +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: int nprocs = lmp->comm->nprocs; +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: int nprocs = lmp->comm->nprocs; +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) +library.cpp: if (lmp->comm->me == 0) lmp->error->warning(FLERR,msg); +min.cpp: if (comm->me == 0) +min.cpp: if (comm->me == 0 && screen) { +min.cpp: if (comm->me == 0 && screen) +min.cpp: comm->setup(); +min.cpp: comm->exchange(); +min.cpp: comm->borders(); +min.cpp: // atoms may have migrated in comm->exchange() +min.cpp: if (force->newton) comm->reverse_comm(); +min.cpp: comm->setup(); +min.cpp: comm->exchange(); +min.cpp: comm->borders(); +min.cpp: // atoms may have migrated in comm->exchange() +min.cpp: if (force->newton) comm->reverse_comm(); +min.cpp: comm->forward_comm(); +min.cpp: comm->setup(); +min.cpp: comm->exchange(); +min.cpp: comm->borders(); +min.cpp: comm->reverse_comm(); +min_fire.cpp: if (comm->me == 0 && logfile) { +modify.cpp: if (comm->me == 0 && checkall) +modify.cpp: if (fix[ifix]->igroup != igroup && comm->me == 0) +modify.cpp: if (comm->me == 0) +modify.cpp: if (comm->me == 0) +modify.cpp: int me = comm->me; +modify.cpp: int me = comm->me; +modify.cpp: if (flag && comm->me == 0) { +modify.cpp: if (flag && comm->me == 0) { +molecule.cpp: me = comm->me; +nbin_multi.cpp: // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost +nbin_multi.cpp: // include dimension-dependent extension via comm->cutghost +nbin_multi.cpp: double *cutghost = comm->cutghost; +nbin_standard.cpp: // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost +nbin_standard.cpp: // include dimension-dependent extension via comm->cutghost +nbin_standard.cpp: double *cutghost = comm->cutghost; +neighbor.cpp: if (!same && comm->me == 0) print_pairwise_info(); +neighbor.cpp: if (comm->me == 0) printf("SAME flag %d\n",same); +neighbor.cpp: const double cutghost = MAX(cutneighmax,comm->cutghostuser); +neigh_list.cpp: int nmypage = comm->nthreads; +neigh_list.cpp: if (comm->me != 0) return; +neigh_list.cpp: int nmypage = comm->nthreads; +ntopo.cpp: me = comm->me; +ntopo.cpp: nprocs = comm->nprocs; +output.cpp: if (thermo->modified && comm->me == 0) +output.cpp: if (strchr(arg[1],'%')) multiproc = comm->nprocs; +output.cpp: mbavg /= comm->nprocs; +output.cpp: if (comm->me == 0) +pair_beck.cpp: int me = comm->me; +pair_beck.cpp: int me = comm->me; +pair_born_coul_dsf.cpp: int me = comm->me; +pair_born_coul_dsf.cpp: if (comm->me == 0) { +pair_born_coul_wolf.cpp: int me = comm->me; +pair_born_coul_wolf.cpp: if (comm->me == 0) { +pair_born.cpp: int me = comm->me; +pair_born.cpp: if (comm->me == 0) { +pair_brownian.cpp: random = new RanMars(lmp,seed + comm->me); +pair_brownian.cpp: if (force->newton_pair == 0 && comm->me == 0) +pair_brownian.cpp: int me = comm->me; +pair_brownian.cpp: int me = comm->me; +pair_brownian.cpp: random = new RanMars(lmp,seed + comm->me); +pair_buck_coul_cut.cpp: int me = comm->me; +pair_buck_coul_cut.cpp: if (comm->me == 0) { +pair_buck.cpp: int me = comm->me; +pair_buck.cpp: if (comm->me == 0) { +pair_colloid.cpp: if (comm->me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); +pair_colloid.cpp: if (comm->me == 0) { +pair_colloid.cpp: int me = comm->me; +pair_coul_cut.cpp: int me = comm->me; +pair_coul_cut.cpp: if (comm->me == 0) { +pair_coul_debye.cpp: if (comm->me == 0) { +pair_coul_dsf.cpp: int me = comm->me; +pair_coul_dsf.cpp: if (comm->me == 0) { +pair_coul_streitz.cpp: if (comm->me == 0) { +pair_coul_streitz.cpp: if (comm->me != 0) { +pair_coul_wolf.cpp: int me = comm->me; +pair_coul_wolf.cpp: if (comm->me == 0) { +pair.cpp: if (tail_flag && domain->nonperiodic && comm->me == 0) +pair.cpp: if (!compute_flag && tail_flag && comm->me == 0) +pair.cpp: if (!compute_flag && offset_flag && comm->me == 0) +pair.cpp: if (flag && comm->me == 0) +pair.cpp: if (comm->me == 0) +pair.cpp: if (comm->me == 0) +pair.cpp: memory->create(eatom,comm->nthreads*maxeatom,"pair:eatom"); +pair.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"pair:vatom"); +pair.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"pair:cvatom"); +pair.cpp: if (comm->me == 0) { +pair.cpp: if ((comm->me == 0) && (epair)) +pair.cpp: if (comm->me == 0) +pair.cpp: if (comm->me == 0) fprintf(fp,"%d %.15g %.15g %.15g\n",i+1,r,e,f); +pair.cpp: if (comm->me == 0) fclose(fp); +pair.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); +pair.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); +pair.cpp: bytes += comm->nthreads*maxcvatom*9 * sizeof(double); +pair_deprecated.cpp: if (lmp->comm->me == 0) +pair_deprecated.cpp: if (lmp->comm->me == 0) +pair_dpd.cpp: random = new RanMars(lmp,seed + comm->me); +pair_dpd.cpp: if (comm->ghost_velocity == 0) +pair_dpd.cpp: if (force->newton_pair == 0 && comm->me == 0) error->warning(FLERR, +pair_dpd.cpp: int me = comm->me; +pair_dpd.cpp: if (comm->me == 0) { +pair_dpd.cpp: random = new RanMars(lmp,seed + comm->me); +pair_dpd_tstat.cpp: random = new RanMars(lmp,seed + comm->me); +pair_dpd_tstat.cpp: int me = comm->me; +pair_dpd_tstat.cpp: if (comm->me == 0) { +pair_dpd_tstat.cpp: random = new RanMars(lmp,seed + comm->me); +pair_gauss.cpp: int me = comm->me; +pair_gauss.cpp: if (comm->me == 0) { +pair_gran_hertz_history.cpp: comm->forward_comm_pair(this); +pair_gran_hooke.cpp: comm->forward_comm_pair(this); +pair_gran_hooke_history.cpp: comm->forward_comm_pair(this); +pair_gran_hooke_history.cpp: if (comm->ghost_velocity == 0) +pair_gran_hooke_history.cpp: int me = comm->me; +pair_gran_hooke_history.cpp: if (comm->me == 0) { +pair_granular.cpp: comm->forward_comm_pair(this); +pair_granular.cpp: if (comm->ghost_velocity == 0) +pair_granular.cpp: int me = comm->me; +pair_hybrid.cpp: int me = comm->me; +pair_lj96_cut.cpp: int me = comm->me; +pair_lj96_cut.cpp: int me = comm->me; +pair_lj_charmm_coul_charmm.cpp: int me = comm->me; +pair_lj_charmm_coul_charmm.cpp: if (comm->me == 0) { +pair_lj_charmmfsw_coul_charmmfsh.cpp: if ((comm->me == 0) && (force->qqr2e != force->qqr2e_charmm_real)) +pair_lj_charmmfsw_coul_charmmfsh.cpp: if ((comm->me == 0) && (force->qqr2e == force->qqr2e_charmm_real)) +pair_lj_charmmfsw_coul_charmmfsh.cpp: int me = comm->me; +pair_lj_charmmfsw_coul_charmmfsh.cpp: if (comm->me == 0) { +pair_lj_cubic.cpp: int me = comm->me; +pair_lj_cubic.cpp: int me = comm->me; +pair_lj_cut_coul_cut.cpp: int me = comm->me; +pair_lj_cut_coul_cut.cpp: if (comm->me == 0) { +pair_lj_cut_coul_debye.cpp: if (comm->me == 0) { +pair_lj_cut_coul_dsf.cpp: int me = comm->me; +pair_lj_cut_coul_dsf.cpp: if (comm->me == 0) { +pair_lj_cut_coul_wolf.cpp: int me = comm->me; +pair_lj_cut_coul_wolf.cpp: int me = comm->me; +pair_lj_cut.cpp: int me = comm->me; +pair_lj_cut.cpp: int me = comm->me; +pair_lj_cut_tip4p_cut.cpp: int me = comm->me; +pair_lj_cut_tip4p_cut.cpp: if (comm->me == 0) { +pair_lj_expand.cpp: int me = comm->me; +pair_lj_expand.cpp: if (comm->me == 0) { +pair_lj_gromacs_coul_gromacs.cpp: int me = comm->me; +pair_lj_gromacs_coul_gromacs.cpp: if (comm->me == 0) { +pair_lj_gromacs.cpp: int me = comm->me; +pair_lj_gromacs.cpp: int me = comm->me; +pair_lj_smooth.cpp: int me = comm->me; +pair_lj_smooth.cpp: int me = comm->me; +pair_lj_smooth_linear.cpp: int me = comm->me; +pair_lj_smooth_linear.cpp: int me = comm->me; +pair_lubricate.cpp: // no need to do this if not shearing since comm->ghost_velocity is set +pair_lubricate.cpp: comm->forward_comm_pair(this); +pair_lubricate.cpp: if (comm->ghost_velocity == 0) +pair_lubricate.cpp: int me = comm->me; +pair_lubricate.cpp: int me = comm->me; +pair_lubricate_poly.cpp: // no need to do this if not shearing since comm->ghost_velocity is set +pair_lubricate_poly.cpp: comm->forward_comm_pair(this); +pair_lubricate_poly.cpp: if (comm->ghost_velocity == 0) +pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU.cpp: comm->forward_comm_pair(this); +pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU.cpp: comm->forward_comm_pair(this); +pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU.cpp: comm->forward_comm_pair(this); +pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU.cpp: comm->forward_comm_pair(this); +pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU.cpp: comm->forward_comm_pair(this); +pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU.cpp: comm->forward_comm_pair(this); +pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); // not really needed +pair_lubricateU.cpp: if (comm->ghost_velocity == 0) +pair_lubricateU.cpp: int me = comm->me; +pair_lubricateU.cpp: int me = comm->me; +pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU_poly.cpp: comm->forward_comm_pair(this); +pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU_poly.cpp: comm->forward_comm_pair(this); +pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); +pair_lubricateU_poly.cpp: comm->forward_comm_pair(this); +pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); // not really needed +pair_lubricateU_poly.cpp: if (comm->ghost_velocity == 0) +pair_lubricateU_poly.cpp: if (!comm->me) { +pair_mie_cut.cpp: int me = comm->me; +pair_mie_cut.cpp: int me = comm->me; +pair_morse.cpp: int me = comm->me; +pair_morse.cpp: if (comm->me == 0) { +pair_soft.cpp: int me = comm->me; +pair_soft.cpp: if (comm->me == 0) { +pair_table.cpp: if (comm->me == 0) { +pair_tip4p_cut.cpp: int me = comm->me; +pair_tip4p_cut.cpp: if (comm->me == 0) { +pair_ufm.cpp: int me = comm->me; +pair_ufm.cpp: int me = comm->me; +pair_yukawa.cpp: int me = comm->me; +pair_yukawa.cpp: if (comm->me == 0) { +pair_zbl.cpp: int me = comm->me; +pair_zbl.cpp: int me = comm->me; +pair_zero.cpp: int me = comm->me; +pair_zero.cpp: int me = comm->me; +potential_file_reader.cpp: if (comm->me != 0) { +random_mars.cpp: //if (comm->me == 0) printf("%d %ld %ld %g %ld\n", +read_data.cpp: if (comm->nprocs == 1) n = static_cast (atom->natoms); +read_data.cpp: else n = static_cast (LB_FACTOR * atom->natoms / comm->nprocs); +read_data.cpp: comm->set_proc_grid(); +read_data.cpp: comm->set_proc_grid(); +read_data.cpp: // do comm->init() but not comm->setup() b/c pair/neigh cutoffs not yet set +read_data.cpp: // need call to map_set() b/c comm->exchange clears atom map +read_data.cpp: if (comm->me == 0) +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_data.cpp: int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf); +read_data.cpp: int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf); +read_data.cpp: int eof = comm->read_lines_from_file(fp,nsq,MAXLINE,buf); +read_data.cpp: int eof = comm->read_lines_from_file(fp,nbondtypes,MAXLINE,buf); +read_data.cpp: int eof = comm->read_lines_from_file(fp,nangletypes,MAXLINE,buf); +read_data.cpp: int eof = comm->read_lines_from_file(fp,ndihedraltypes,MAXLINE,buf); +read_data.cpp: int eof = comm->read_lines_from_file(fp,nimpropertypes,MAXLINE,buf); +read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); +read_dump.cpp: comm->set_proc_grid(0); +read_restart.cpp: comm->set_proc_grid(); +read_restart.cpp: if (comm->me == 0) +read_restart.cpp: if (nprocs_file != comm->nprocs && me == 0) +read_restart.cpp: comm->nprocs)); +read_restart.cpp: if (comm->user_procgrid[0] != 0 && +read_restart.cpp: procgrid[0] != comm->user_procgrid[0]) flag = 1; +read_restart.cpp: if (comm->user_procgrid[1] != 0 && +read_restart.cpp: procgrid[1] != comm->user_procgrid[1]) flag = 1; +read_restart.cpp: if (comm->user_procgrid[2] != 0 && +read_restart.cpp: procgrid[2] != comm->user_procgrid[2]) flag = 1; +read_restart.cpp: if (comm->me ==0) +read_restart.cpp: comm->mode = read_int(); +read_restart.cpp: comm->cutghostuser = read_double(); +read_restart.cpp: comm->ghost_velocity = read_int(); +read_restart.cpp: if (comm->me ==0) +read_restart.cpp: if (comm->me ==0) +read_restart.cpp: if (comm->me ==0) +read_restart.cpp: if (comm->me ==0) +read_restart.cpp: if (comm->me ==0) +read_restart.cpp: if (comm->me ==0) +region_deprecated.cpp: if (lmp->comm->me == 0) +replicate.cpp: int me = comm->me; +replicate.cpp: int nprocs = comm->nprocs; +replicate.cpp: if (comm->me == 0) +replicate.cpp: comm->set_proc_grid(); +replicate.cpp: if (comm->layout != Comm::LAYOUT_TILED) { +replicate.cpp: if (comm->myloc[0] == 0) sublo[0] -= epsilon[0]; +replicate.cpp: if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += epsilon[0]; +replicate.cpp: if (comm->myloc[1] == 0) sublo[1] -= epsilon[1]; +replicate.cpp: if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += epsilon[1]; +replicate.cpp: if (comm->myloc[2] == 0) sublo[2] -= epsilon[2]; +replicate.cpp: if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += epsilon[2]; +replicate.cpp: if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0]; +replicate.cpp: if (comm->mysplit[0][1] == 1.0) subhi[0] += epsilon[0]; +replicate.cpp: if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1]; +replicate.cpp: if (comm->mysplit[1][1] == 1.0) subhi[1] += epsilon[1]; +replicate.cpp: if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2]; +replicate.cpp: if (comm->mysplit[2][1] == 1.0) subhi[2] += epsilon[2]; +reset_atom_ids.cpp: if (comm->me == 0) utils::logmesg(lmp,"Resetting atom IDs ...\n"); +reset_atom_ids.cpp: // initialize system since comm->borders() will be invoked +reset_atom_ids.cpp: comm->setup(); +reset_atom_ids.cpp: comm->exchange(); +reset_atom_ids.cpp: comm->borders(); +reset_atom_ids.cpp: comm->forward_comm_array(1,newIDs); +reset_atom_ids.cpp: int me = comm->me; +reset_atom_ids.cpp: int nprocs = comm->nprocs; +reset_atom_ids.cpp: int nreturn = comm->rendezvous(1,nlocal,(char *) atombuf,sizeof(AtomRvous), +reset_atom_ids.cpp: // rptr->comm->me,i,n,in[i].ibin,binlo,binhi); +reset_atom_ids.cpp: // pass outbuf of IDRvous datums back to comm->rendezvous +reset_mol_ids.cpp: if (comm->me == 0) utils::logmesg(lmp,"Resetting molecule IDs ...\n"); +reset_mol_ids.cpp: // initialize system since comm->borders() will be invoked +reset_mol_ids.cpp: comm->setup(); +reset_mol_ids.cpp: comm->exchange(); +reset_mol_ids.cpp: comm->borders(); +reset_mol_ids.cpp: if (comm->me == 0) { +respa.cpp: if (comm->me == 0) { +respa.cpp: if (flag && comm->me == 0) +respa.cpp: if (modify->nfix == 0 && comm->me == 0) +respa.cpp: if (comm->me == 0 && screen) { +respa.cpp: comm->setup(); +respa.cpp: comm->exchange(); +respa.cpp: comm->borders(); +respa.cpp: if (newton[ilevel]) comm->reverse_comm(); +respa.cpp: comm->setup(); +respa.cpp: comm->exchange(); +respa.cpp: comm->borders(); +respa.cpp: if (newton[ilevel]) comm->reverse_comm(); +respa.cpp: comm->setup(); +respa.cpp: comm->exchange(); +respa.cpp: comm->borders(); +respa.cpp: comm->forward_comm(); +respa.cpp: comm->forward_comm(); +respa.cpp: comm->reverse_comm(); +set.cpp: if (comm->me == 0) utils::logmesg(lmp,"Setting atom values ...\n"); +set.cpp: if (comm->me == 0) { +set.cpp: RanMars *ranmars = new RanMars(lmp,seed + comm->me); +set.cpp: // init entire system since comm->exchange is done +set.cpp: if (comm->me == 0) utils::logmesg(lmp," system init for set ...\n"); +set.cpp: comm->setup(); +set.cpp: comm->exchange(); +set.cpp: comm->borders(); +special.cpp: comm->rendezvous(RVOUS,nlocal,(char *) idbuf,sizeof(IDRvous),0,proclist, +special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), +special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), +special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), +special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), +special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), +special.cpp: if (comm->me == 0) diff --git a/src/nbin.cpp b/src/nbin.cpp index c28c22882c..1323a9042a 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -41,11 +41,8 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp) bininvx_multi = nullptr; bininvy_multi = nullptr; bininvz_multi = nullptr; binhead_multi = nullptr; maxbins_multi = nullptr; - - map_type_multi = nullptr; - cutmultisq = nullptr; - maxgroups = 0; + maxcollections = 0; neighbor->last_setup_bins = -1; @@ -85,7 +82,7 @@ NBin::~NBin() memory->destroy(bininvy_multi); memory->destroy(bininvz_multi); - for (int n = 0; n < maxgroups; n++) { + for (int n = 0; n < maxcollections; n++) { memory->destroy(binhead_multi[n]); } delete [] binhead_multi; @@ -115,9 +112,8 @@ void NBin::copy_neighbor_info() bboxlo = neighbor->bboxlo; bboxhi = neighbor->bboxhi; - n_multi_groups = neighbor->n_multi_groups; - map_type_multi = neighbor->map_type_multi; - cutmultisq = neighbor->cutmultisq; + ncollections = neighbor->ncollections; + cutcollectionsq = neighbor->cutcollectionsq; // overwrite Neighbor cutoff with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -175,10 +171,10 @@ int NBin::coord2bin(double *x) /* ---------------------------------------------------------------------- - convert atom coords into local bin # for a particular grouping + convert atom coords into local bin # for a particular collection ------------------------------------------------------------------------- */ -int NBin::coord2bin_multi(double *x, int ig) +int NBin::coord2bin_multi(double *x, int ic) { int ix,iy,iz; int ibin; @@ -187,33 +183,33 @@ int NBin::coord2bin_multi(double *x, int ig) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ig]) + nbinx_multi[ig]; + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ic]) + nbinx_multi[ic]; else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]); - ix = MIN(ix,nbinx_multi[ig]-1); + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ic]); + ix = MIN(ix,nbinx_multi[ic]-1); } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]) - 1; + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ic]) - 1; if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[ig]) + nbiny_multi[ig]; + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[ic]) + nbiny_multi[ic]; else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]); - iy = MIN(iy,nbiny_multi[ig]-1); + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ic]); + iy = MIN(iy,nbiny_multi[ic]-1); } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]) - 1; + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ic]) - 1; if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[ig]) + nbinz_multi[ig]; + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[ic]) + nbinz_multi[ic]; else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]); - iz = MIN(iz,nbinz_multi[ig]-1); + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ic]); + iz = MIN(iz,nbinz_multi[ic]-1); } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]) - 1; + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ic]) - 1; - ibin = (iz-mbinzlo_multi[ig])*mbiny_multi[ig]*mbinx_multi[ig] - + (iy-mbinylo_multi[ig])*mbinx_multi[ig] - + (ix-mbinxlo_multi[ig]); + ibin = (iz-mbinzlo_multi[ic])*mbiny_multi[ic]*mbinx_multi[ic] + + (iy-mbinylo_multi[ic])*mbinx_multi[ic] + + (ix-mbinxlo_multi[ic]); return ibin; } diff --git a/src/nbin.h b/src/nbin.h index e31e5bab99..97299398fa 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -73,9 +73,8 @@ class NBin : protected Pointers { int binsizeflag; double binsize_user; double *bboxlo,*bboxhi; - int n_multi_groups; - int *map_type_multi; - double **cutmultisq; + int ncollections; + double **cutcollectionsq; // data common to all NBin variants @@ -89,7 +88,7 @@ class NBin : protected Pointers { // data for multi NBin - int maxgroups; // size of multi arrays + int maxcollections; // size of multi arrays int * maxbins_multi; // size of 2nd dimension of binhead_multi array // methods diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index 04756ff803..db1e8d5682 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -38,7 +38,7 @@ void NBinMulti::bin_atoms_setup(int nall) { // binhead_multi[n] = per-bin vector mbins in length mbins_multi[n] - for (int n = 0; n < maxgroups; n++) { + for (int n = 0; n < maxcollections; n++) { if (mbins_multi[n] > maxbins_multi[n]) { maxbins_multi[n] = mbins_multi[n]; memory->destroy(binhead_multi[n]); @@ -75,81 +75,80 @@ void NBinMulti::bin_atoms_setup(int nall) for triclinic boxes: tilted simulation box cannot contain integer # of bins stencil & neigh list built differently to account for this - mbinlo_multi = lowest global bin any of my ghost atoms could fall into for each grouping - mbinhi_multi = highest global bin any of my ghost atoms could fall into for each grouping - mbin_multi = number of bins I need in a dimension for each grouping + mbinlo_multi = lowest global bin any of my ghost atoms could fall into for each collection + mbinhi_multi = highest global bin any of my ghost atoms could fall into for each collection + mbin_multi = number of bins I need in a dimension for each collection ------------------------------------------------------------------------- */ -void NBinMulti::setup_bins(int style) +void NBinMulti::setup_bins(int /*style*/) { int n; // Initialize arrays - if (n_multi_groups > maxgroups) { + if (ncollections > maxcollections) { // Clear any/all memory for existing groupings - for (n = 0; n < maxgroups; n++) + for (n = 0; n < maxcollections; n++) memory->destroy(binhead_multi[n]); delete [] binhead_multi; - // Realloacte at updated maxgroups - maxgroups = n_multi_groups; + maxcollections = ncollections; - binhead_multi = new int*[maxgroups](); + binhead_multi = new int*[maxcollections](); memory->destroy(nbinx_multi); memory->destroy(nbiny_multi); memory->destroy(nbinz_multi); - memory->create(nbinx_multi, maxgroups, "neigh:nbinx_multi"); - memory->create(nbiny_multi, maxgroups, "neigh:nbiny_multi"); - memory->create(nbinz_multi, maxgroups, "neigh:nbinz_multi"); + memory->create(nbinx_multi, maxcollections, "neigh:nbinx_multi"); + memory->create(nbiny_multi, maxcollections, "neigh:nbiny_multi"); + memory->create(nbinz_multi, maxcollections, "neigh:nbinz_multi"); memory->destroy(mbins_multi); memory->destroy(mbinx_multi); memory->destroy(mbiny_multi); memory->destroy(mbinz_multi); - memory->create(mbins_multi, maxgroups, "neigh:mbins_multi"); - memory->create(mbinx_multi, maxgroups, "neigh:mbinx_multi"); - memory->create(mbiny_multi, maxgroups, "neigh:mbiny_multi"); - memory->create(mbinz_multi, maxgroups, "neigh:mbinz_multi"); + memory->create(mbins_multi, maxcollections, "neigh:mbins_multi"); + memory->create(mbinx_multi, maxcollections, "neigh:mbinx_multi"); + memory->create(mbiny_multi, maxcollections, "neigh:mbiny_multi"); + memory->create(mbinz_multi, maxcollections, "neigh:mbinz_multi"); memory->destroy(mbinxlo_multi); memory->destroy(mbinylo_multi); memory->destroy(mbinzlo_multi); - memory->create(mbinxlo_multi, maxgroups, "neigh:mbinxlo_multi"); - memory->create(mbinylo_multi, maxgroups, "neigh:mbinylo_multi"); - memory->create(mbinzlo_multi, maxgroups, "neigh:mbinzlo_multi"); + memory->create(mbinxlo_multi, maxcollections, "neigh:mbinxlo_multi"); + memory->create(mbinylo_multi, maxcollections, "neigh:mbinylo_multi"); + memory->create(mbinzlo_multi, maxcollections, "neigh:mbinzlo_multi"); memory->destroy(binsizex_multi); memory->destroy(binsizey_multi); memory->destroy(binsizez_multi); - memory->create(binsizex_multi, maxgroups, "neigh:binsizex_multi"); - memory->create(binsizey_multi, maxgroups, "neigh:binsizey_multi"); - memory->create(binsizez_multi, maxgroups, "neigh:binsizez_multi"); + memory->create(binsizex_multi, maxcollections, "neigh:binsizex_multi"); + memory->create(binsizey_multi, maxcollections, "neigh:binsizey_multi"); + memory->create(binsizez_multi, maxcollections, "neigh:binsizez_multi"); memory->destroy(bininvx_multi); memory->destroy(bininvy_multi); memory->destroy(bininvz_multi); - memory->create(bininvx_multi, maxgroups, "neigh:bininvx_multi"); - memory->create(bininvy_multi, maxgroups, "neigh:bininvy_multi"); - memory->create(bininvz_multi, maxgroups, "neigh:bininvz_multi"); + memory->create(bininvx_multi, maxcollections, "neigh:bininvx_multi"); + memory->create(bininvy_multi, maxcollections, "neigh:bininvy_multi"); + memory->create(bininvz_multi, maxcollections, "neigh:bininvz_multi"); memory->destroy(maxbins_multi); - memory->create(maxbins_multi, maxgroups, "neigh:maxbins_multi"); + memory->create(maxbins_multi, maxcollections, "neigh:maxbins_multi"); // ensure reallocation occurs in bin_atoms_setup() - for (n = 0; n < maxgroups; n++) { + for (n = 0; n < maxcollections; n++) { maxbins_multi[n] = 0; } maxatom = 0; } - // Identify smallest group - int igroupmin = 0; - for (n = 0; n < maxgroups; n++) - if (cutmultisq[n][n] < cutmultisq[igroupmin][igroupmin]) - igroupmin = n; + // Identify smallest collection + int icollectionmin = 0; + for (n = 0; n < maxcollections; n++) + if (cutcollectionsq[n][n] < cutcollectionsq[icollectionmin][icollectionmin]) + icollectionmin = n; // bbox = size of bbox of entire domain // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost @@ -189,13 +188,13 @@ void NBinMulti::setup_bins(int style) double binsize_optimal, binsizeinv, coord; int mbinxhi,mbinyhi,mbinzhi; - for (n = 0; n < maxgroups; n++) { - // binsize_user only relates to smallest group - // optimal bin size is roughly 1/2 the group-group cutoff + for (n = 0; n < maxcollections; n++) { + // binsize_user only relates to smallest collection + // optimal bin size is roughly 1/2 the collection-collection cutoff // special case of all cutoffs = 0.0, binsize = box size - if (n == igroupmin && binsizeflag) binsize_optimal = binsize_user; - else binsize_optimal = 0.5*sqrt(cutmultisq[n][n]); + if (n == icollectionmin && binsizeflag) binsize_optimal = binsize_user; + else binsize_optimal = 0.5*sqrt(cutcollectionsq[n][n]); if (binsize_optimal == 0.0) binsize_optimal = bbox[0]; binsizeinv = 1.0/binsize_optimal; @@ -296,16 +295,15 @@ void NBinMulti::bin_atoms() int i,ibin,n; last_bin = update->ntimestep; - for (n = 0; n < maxgroups; n++) { + for (n = 0; n < maxcollections; n++) { for (i = 0; i < mbins_multi[n]; i++) binhead_multi[n][i] = -1; } - // bin in reverse order so linked list will be in forward order // also puts ghost atoms at end of list, which is necessary + int *collection = neighbor->collection; double **x = atom->x; int *mask = atom->mask; - int *type = atom->type; int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; @@ -313,7 +311,7 @@ void NBinMulti::bin_atoms() int bitmask = group->bitmask[includegroup]; for (i = nall-1; i >= nlocal; i--) { if (mask[i] & bitmask) { - n = map_type_multi[type[i]]; + n = collection[i]; ibin = coord2bin_multi(x[i], n); atom2bin[i] = ibin; bins[i] = binhead_multi[n][ibin]; @@ -321,15 +319,15 @@ void NBinMulti::bin_atoms() } } for (i = atom->nfirst-1; i >= 0; i--) { - n = map_type_multi[type[i]]; + n = collection[i]; ibin = coord2bin_multi(x[i], n); atom2bin[i] = ibin; bins[i] = binhead_multi[n][ibin]; binhead_multi[n][ibin] = i; } } else { - for (i = nall-1; i >= 0; i--) { - n = map_type_multi[type[i]]; + for (i = nall-1; i >= 0; i--) { + n = collection[i]; ibin = coord2bin_multi(x[i], n); atom2bin[i] = ibin; bins[i] = binhead_multi[n][ibin]; @@ -343,7 +341,7 @@ void NBinMulti::bin_atoms() double NBinMulti::memory_usage() { double bytes = 0; - for (int m = 0; m < maxgroups; m++) + for (int m = 0; m < maxcollections; m++) bytes += maxbins_multi[m]*sizeof(int); bytes += 2*maxatom*sizeof(int); return bytes; diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 5a1255edbe..16aca434f1 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -43,6 +43,7 @@ #include "style_npair.h" #include "style_nstencil.h" #include "style_ntopo.h" +#include "tokenizer.h" #include "update.h" #include @@ -53,6 +54,7 @@ using namespace NeighConst; #define RQDELTA 1 #define EXDELTA 1 +#define DELTA_PERATOM 64 #define BIG 1.0e20 @@ -195,9 +197,13 @@ pairclass(nullptr), pairnames(nullptr), pairmasks(nullptr) // Multi data - map_type_multi = nullptr; - cutmultisq = nullptr; - multi_groups = 0; + type2collection = nullptr; + collection2cut = nullptr; + collection = nullptr; + cutcollectionsq = nullptr; + custom_collection_flag = 0; + interval_collection_flag = 0; + nmax_collection = 0; // Kokkos setting @@ -265,8 +271,10 @@ Neighbor::~Neighbor() delete [] ex_mol_bit; memory->destroy(ex_mol_intra); - memory->destroy(map_type_multi); - memory->destroy(cutmultisq); + memory->destroy(type2collection); + memory->destroy(collection2cut); + memory->destroy(collection); + memory->destroy(cutcollectionsq); } /* ---------------------------------------------------------------------- */ @@ -350,33 +358,96 @@ void Neighbor::init() } cutneighmaxsq = cutneighmax * cutneighmax; - // multi cutoffs + // Define cutoffs for multi if(style == Neighbor::MULTI){ - int igroup, jgroup; + int icollection, jcollection; - // If not defined from custom grouping, create default map - if(not map_type_multi) { - n_multi_groups = n; - memory->create(map_type_multi,n+1,"neigh:map_type_multi"); + // If collections not yet defined, create default map using types + if(not custom_collection_flag) { + ncollections = n; + interval_collection_flag = 0; + memory->create(type2collection,n+1,"neigh:type2collection"); for(i = 1; i <= n; i++) - map_type_multi[i] = i-1; + type2collection[i] = i-1; } - // Define maximum interaction distance for each pair of groups - memory->grow(cutmultisq, n_multi_groups, n_multi_groups, "neigh:cutmultisq"); - for(i = 0; i < n_multi_groups; i++) - for(j = 0; j < n_multi_groups; j++) - cutmultisq[i][j] = 0.0; + memory->grow(cutcollectionsq, ncollections, ncollections, "neigh:cutcollectionsq"); - for(i = 1; i <= n; i++){ - igroup = map_type_multi[i]; - for(j = 1; j <= n; j++){ - jgroup = map_type_multi[j]; - if(cutneighsq[i][j] > cutmultisq[igroup][jgroup]) { - cutmultisq[igroup][jgroup] = cutneighsq[i][j]; - cutmultisq[jgroup][igroup] = cutneighsq[i][j]; + // 3 possible ways of defining collections + // 1) Types are used to define collections + // Each collection loops through its owned types, and uses cutneighsq to calculate its cutoff + // 2) Collections are defined by intervals, point particles + // Types are first sorted into collections based on cutneighsq[i][i] + // Each collection loops through its owned types, and uses cutneighsq to calculate its cutoff + // 3) Collections are defined by intervals, finite particles + // + + // Define collection cutoffs + for(i = 0; i < ncollections; i++) + for(j = 0; j < ncollections; j++) + cutcollectionsq[i][j] = 0.0; + + if(not interval_collection_flag){ + finite_cut_flag = 0; + for(i = 1; i <= n; i++){ + icollection = type2collection[i]; + for(j = 1; j <= n; j++){ + jcollection = type2collection[j]; + if(cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) { + cutcollectionsq[icollection][jcollection] = cutneighsq[i][j]; + cutcollectionsq[jcollection][icollection] = cutneighsq[i][j]; + } } } + } else { + if(force->pair->finitecutflag){ + finite_cut_flag = 1; + // If cutoffs depend on finite atom sizes, use radii of intervals to find cutoffs + double ri, rj, tmp; + for(i = 0; i < ncollections; i++){ + ri = collection2cut[i]*0.5; + for(j = 0; j < ncollections; j++){ + rj = collection2cut[j]*0.5; + tmp = force->pair->radii2cut(ri, rj); + cutcollectionsq[i][j] = tmp*tmp; + } + } + } else { + finite_cut_flag = 0; + + // Map types to collections + if(not type2collection) + memory->create(type2collection,n+1,"neigh:type2collection"); + + for(i = 1; i <= n; i++) + type2collection[i] = -1; + + double cuttmp; + for(i = 1; i <= n; i++){ + cuttmp = sqrt(cutneighsq[i][i]); + for(icollection = 0; icollection < ncollections; icollection ++){ + if(collection2cut[icollection] > cuttmp) { + type2collection[i] = icollection; + break; + } + } + + if(type2collection[i] == -1) + error->all(FLERR, "Pair cutoff exceeds interval cutoffs for multi"); + } + + // Define cutoffs + for(i = 1; i <= n; i++){ + icollection = type2collection[i]; + for(j = 1; j <= n; j++){ + jcollection = type2collection[j]; + if(cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) { + cutcollectionsq[icollection][jcollection] = cutneighsq[i][j]; + cutcollectionsq[jcollection][icollection] = cutneighsq[i][j]; + } + } + } + } } } @@ -2100,6 +2171,8 @@ void Neighbor::build(int topoflag) int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; + // rebuild collection array from scratch + if(style == Neighbor::MULTI) build_collection(0); // check that using special bond flags will not overflow neigh lists @@ -2140,7 +2213,7 @@ void Neighbor::build(int topoflag) } } } - + // bin atoms for all NBin instances // not just NBin associated with perpetual lists, also occasional lists // b/c cannot wait to bin occasional lists in build_one() call @@ -2423,53 +2496,91 @@ void Neighbor::modify_params(int narg, char **arg) iarg += 2; } else error->all(FLERR,"Illegal neigh_modify command"); - } else if (strcmp(arg[iarg],"multi/custom") == 0) { + } else if (strcmp(arg[iarg],"collection/interval") == 0) { if(style != Neighbor::MULTI) - error->all(FLERR,"Cannot use multi/custom command without multi setting"); + error->all(FLERR,"Cannot use collection/interval command without multi setting"); if(iarg+2 > narg) - error->all(FLERR,"Invalid multi/custom command"); - int nextra = utils::inumeric(FLERR,arg[iarg+1],false,lmp); - if(iarg+1+nextra > narg) - error->all(FLERR,"Invalid multi/custom command"); + error->all(FLERR,"Invalid collection/interval command"); + ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if(iarg+1+ncollections > narg) + error->all(FLERR,"Invalid collection/interval command"); int ntypes = atom->ntypes; - int n, nlo, nhi, i, j, igroup, jgroup; + int n, nlo, nhi, i, j; + + interval_collection_flag = 1; + custom_collection_flag = 1; + if(not collection2cut) + memory->create(collection2cut,ncollections,"neigh:collection2cut"); - if(not map_type_multi) - memory->create(map_type_multi,ntypes+1,"neigh:map_type_multi"); + // Set upper cutoff for each collection + char *id; + double cut_interval; + for(i = 0; i < ncollections; i++){ + cut_interval = utils::numeric(FLERR,arg[iarg+2+i],false,lmp); + collection2cut[i] = cut_interval; + + if(i != 0) + if(collection2cut[i-1] >= collection2cut[i]) + error->all(FLERR,"Nonsequential interval cutoffs in collection/interval setting"); + } + + iarg += 2 + ncollections; + } else if (strcmp(arg[iarg],"collection/type") == 0) { + if(style != Neighbor::MULTI) + error->all(FLERR,"Cannot use collection/type command without multi setting"); + + if(iarg+2 > narg) + error->all(FLERR,"Invalid collection/type command"); + ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if(iarg+1+ncollections > narg) + error->all(FLERR,"Invalid collection/type command"); + + int ntypes = atom->ntypes; + int n, nlo, nhi, i, j, k; + + interval_collection_flag = 0; + custom_collection_flag = 1; + if(not type2collection) + memory->create(type2collection,ntypes+1,"neigh:type2collection"); // Erase previous mapping for(i = 1; i <= ntypes; i++) - map_type_multi[i] = -1; + type2collection[i] = -1; // For each custom range, define mapping for types in interval - n_multi_groups = 0; - char *id; - for(i = 0; i < nextra; i++){ + int nfield; + char *str; + for(i = 0; i < ncollections; i++){ n = strlen(arg[iarg+2+i]) + 1; - id = new char[n]; - strcpy(id,arg[iarg+2+i]); - utils::bounds(FLERR,id,1,ntypes,nlo,nhi,error); - delete [] id; + str = new char[n]; + strcpy(str,arg[iarg+2+i]); + std::vector words = Tokenizer(str, ",").as_vector(); + nfield = words.size(); + + for (j = 0; j < nfield; j++) { + const char * field = words[j].c_str(); + utils::bounds(FLERR,field,1,ntypes,nlo,nhi,error); - for (j = nlo; j <= nhi; j++) { - if(map_type_multi[j] != -1) - error->all(FLERR,"Type specified more than once in multi/custom commnd"); - map_type_multi[j] = n_multi_groups; + for (k = nlo; k <= nhi; k++) { + if(type2collection[k] != -1) + error->all(FLERR,"Type specified more than once in collection/type commnd"); + type2collection[k] = i; + } } - n_multi_groups += 1; + + delete [] str; } - // Create separate group for each undefined atom type + // Check for undefined atom type for(i = 1; i <= ntypes; i++){ - if(map_type_multi[i] == -1){ - map_type_multi[i] = n_multi_groups; - n_multi_groups += 1; + if(type2collection[i] == -1){ + error->all(FLERR,"Type missing in collection/type commnd"); } } - iarg += 2 + nextra; + iarg += 2 + ncollections; } else error->all(FLERR,"Illegal neigh_modify command"); } } @@ -2521,6 +2632,46 @@ int Neighbor::any_full() return any_full; } +/* ---------------------------------------------------------------------- + populate collection array for multi starting at the index istart +------------------------------------------------------------------------- */ + +void Neighbor::build_collection(int istart) +{ + if (style != Neighbor::MULTI) + error->all(FLERR, "Cannot define atom collections without neighbor style multi"); + + int nmax = atom->nlocal+atom->nghost; + if(nmax > nmax_collection){ + nmax_collection = nmax+DELTA_PERATOM; + memory->grow(collection, nmax_collection, "neigh:collection"); + } + + if(finite_cut_flag){ + double cut; + int icollection; + for(int i = istart; i < nmax; i++){ + cut = force->pair->atom2cut(i); + collection[i] = -1; + + for(icollection = 0; icollection < ncollections; icollection++){ + if(collection2cut[icollection] > cut) { + collection[i] = icollection; + break; + } + } + + if(collection[i] == -1) + error->one(FLERR, "Atom cutoff exceeds interval cutoffs for multi"); + } + } else { + int *type = atom->type; + for(int i = istart; i < nmax; i++){ + collection[i] = type2collection[type[i]]; + } + } +} + /* ---------------------------------------------------------------------- return # of bytes of allocated memory ------------------------------------------------------------------------- */ diff --git a/src/neighbor.h b/src/neighbor.h index b8e1189b35..7b6246dec7 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -104,11 +104,16 @@ class Neighbor : protected Pointers { // optional type grouping for multi - int multi_groups; // 1 if custom groupings are defined for multi - int n_multi_groups; // # of custom groupings - int *map_type_multi; // ntype array mapping types to custom groupings - double **cutmultisq; // cutoffs for each combination of custom groupings - + int custom_collection_flag; // 1 if custom collections are defined for multi + int interval_collection_flag; // 1 if custom collections use intervals + int finite_cut_flag; // 1 if multi considers finite atom size + int ncollections; // # of custom collections + int nmax_collection; // maximum atoms stored in collection array + int *type2collection; // ntype array mapping types to custom collections + double *collection2cut; // ncollection array with upper bounds on cutoff intervals + double **cutcollectionsq; // cutoffs for each combination of collections + int *collection; // local per-atom array to store collection id + // public methods Neighbor(class LAMMPS *); @@ -130,6 +135,7 @@ class Neighbor : protected Pointers { int exclude_setting(); // return exclude value to accelerator pkg class NeighRequest *find_request(void *); // find a neighbor request int any_full(); // Check if any old requests had full neighbor lists + void build_collection(int); // build peratom collection array starting at the given index double memory_usage(); diff --git a/src/npair.cpp b/src/npair.cpp index 95a61fbefa..eee8610958 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -97,9 +97,8 @@ void NPair::copy_neighbor_info() // multi info - n_multi_groups = neighbor->n_multi_groups; - map_type_multi = neighbor->map_type_multi; - cutmultisq = neighbor->cutmultisq; + ncollections = neighbor->ncollections; + cutcollectionsq = neighbor->cutcollectionsq; // overwrite per-type Neighbor cutoffs with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -184,9 +183,8 @@ void NPair::build_setup() { if (nb) copy_bin_info(); if (ns) copy_stencil_info(); - + // set here, since build_setup() always called before build() - last_build = update->ntimestep; } @@ -269,10 +267,10 @@ int NPair::coord2bin(double *x, int &ix, int &iy, int &iz) /* ---------------------------------------------------------------------- - multi version of coord2bin for a given grouping + multi version of coord2bin for a given collection ------------------------------------------------------------------------- */ -int NPair::coord2bin(double *x, int ig) +int NPair::coord2bin(double *x, int ic) { int ix,iy,iz; int ibin; @@ -281,32 +279,32 @@ int NPair::coord2bin(double *x, int ig) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) - ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ig]) + nbinx_multi[ig]; + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ic]) + nbinx_multi[ic]; else if (x[0] >= bboxlo[0]) { - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]); - ix = MIN(ix,nbinx_multi[ig]-1); + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ic]); + ix = MIN(ix,nbinx_multi[ic]-1); } else - ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ig]) - 1; + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ic]) - 1; if (x[1] >= bboxhi[1]) - iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[ig]) + nbiny_multi[ig]; + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[ic]) + nbiny_multi[ic]; else if (x[1] >= bboxlo[1]) { - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]); - iy = MIN(iy,nbiny_multi[ig]-1); + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ic]); + iy = MIN(iy,nbiny_multi[ic]-1); } else - iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ig]) - 1; + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ic]) - 1; if (x[2] >= bboxhi[2]) - iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[ig]) + nbinz_multi[ig]; + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[ic]) + nbinz_multi[ic]; else if (x[2] >= bboxlo[2]) { - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]); - iz = MIN(iz,nbinz_multi[ig]-1); + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ic]); + iz = MIN(iz,nbinz_multi[ic]-1); } else - iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ig]) - 1; + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ic]) - 1; - ix -= mbinxlo_multi[ig]; - iy -= mbinylo_multi[ig]; - iz -= mbinzlo_multi[ig]; - ibin = iz*mbiny_multi[ig]*mbinx_multi[ig] + iy*mbinx_multi[ig] + ix; + ix -= mbinxlo_multi[ic]; + iy -= mbinylo_multi[ic]; + iz -= mbinzlo_multi[ic]; + ibin = iz*mbiny_multi[ic]*mbinx_multi[ic] + iy*mbinx_multi[ic] + ix; return ibin; } diff --git a/src/npair.h b/src/npair.h index c857ec0924..b8416208ca 100644 --- a/src/npair.h +++ b/src/npair.h @@ -48,9 +48,8 @@ class NPair : protected Pointers { double cut_middle_sq; double cut_middle_inside_sq; double *bboxlo,*bboxhi; - int n_multi_groups; - int *map_type_multi; - double **cutmultisq; + int ncollections; + double **cutcollectionsq; // exclusion data from Neighbor class diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp index c78f7b2d1d..0ce717f722 100644 --- a/src/npair_full_multi.cpp +++ b/src/npair_full_multi.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_full_multi.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -28,18 +29,19 @@ NPairFullMulti::NPairFullMulti(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ void NPairFullMulti::build(NeighList *list) { - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; int js; + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -68,7 +70,7 @@ void NPairFullMulti::build(NeighList *list) n = 0; neighptr = ipage->vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -80,22 +82,22 @@ void NPairFullMulti::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in surrounding bins in stencil including self // skip i = j - // use full stencil for all group combinations + // use full stencil for all collection combinations - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { if (i == j) continue; diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp index 11bab91e6a..5f050429ac 100755 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newtoff.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -28,7 +29,7 @@ NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks own bin and other bins in stencil pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) @@ -36,12 +37,13 @@ NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} void NPairHalfMultiNewtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; int js; + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -70,7 +72,7 @@ void NPairHalfMultiNewtoff::build(NeighList *list) n = 0; neighptr = ipage->vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -82,24 +84,24 @@ void NPairHalfMultiNewtoff::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in other bins in stencil including self // only store pair if i < j // stores own/own pairs only once // stores own/ghost pairs on both procs - // use full stencil for all group combinations + // use full stencil for all collection combinations - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index aa8f606242..18e66d4adb 100755 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newton.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -28,19 +29,20 @@ NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfMultiNewton::build(NeighList *list) { - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; int js; + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -69,7 +71,7 @@ void NPairHalfMultiNewton::build(NeighList *list) n = 0; neighptr = ipage->vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -81,29 +83,29 @@ void NPairHalfMultiNewton::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // if same size: uses half stencil so check central bin - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - if(igroup == jgroup) js = bins[i]; - else js = binhead_multi[jgroup][jbin]; + if(icollection == jcollection) js = bins[i]; + else js = binhead_multi[jcollection][jbin]; - // if same group, + // if same collection, // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - // if different groups, + // if different collections, // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i for (j = js; j >= 0; j = bins[j]) { - if(igroup != jgroup and j < i) continue; + if(icollection != jcollection and j < i) continue; if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -139,16 +141,16 @@ void NPairHalfMultiNewton::build(NeighList *list) } } - // for all groups, loop over all atoms in other bins in stencil, store every pair + // for all collections, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp index 6969c9cfab..90c6cf714d 100755 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newton_tri.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -28,19 +29,20 @@ NPairHalfMultiNewtonTri::NPairHalfMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfMultiNewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; int js; - + + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -69,7 +71,7 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) n = 0; neighptr = ipage->vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -81,12 +83,12 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in bins in stencil // stencil is empty if i larger than j @@ -97,15 +99,15 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { - // if same size (same group), use half stencil - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + // if same size (same collection), use half stencil + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp index e361bbce76..77aa4f746b 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -13,6 +13,7 @@ es certain rights in this software. This software is distributed under #include #include "npair_half_size_multi_newtoff.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -28,7 +29,7 @@ NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) { /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks own bin and other bins in stencil pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) @@ -36,12 +37,13 @@ NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) { void NPairHalfSizeMultiNewtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; int js; + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -65,7 +67,7 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) n = 0; neighptr = ipage->vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -73,24 +75,24 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in other bins in stencil including self // only store pair if i < j // stores own/own pairs only once // stores own/ghost pairs on both procs - // use full stencil for all group combinations + // use full stencil for all collection combinations - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >=0; j = bins[j]) { if (j <= i) continue; diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index 84571a3b02..67715ebe68 100755 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_multi_newton.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -27,18 +28,19 @@ NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with full Newton's 3rd law - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfSizeMultiNewton::build(NeighList *list) { - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns,js; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -62,7 +64,7 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) n = 0; neighptr = ipage->vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -70,29 +72,29 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // if same size: uses half stencil so check central bin - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - if(igroup == jgroup) js = bins[i]; - else js = binhead_multi[jgroup][jbin]; + if(icollection == jcollection) js = bins[i]; + else js = binhead_multi[jcollection][jbin]; - // if same group, + // if same collection, // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i - // if different groups, + // if different collections, // if j is owned atom, store it if j > i // if j is ghost, only store if j coords are "above and to the right" of i for (j = js; j >= 0; j = bins[j]) { - if(igroup != jgroup and j < i) continue; + if(icollection != jcollection and j < i) continue; if (j >= nlocal) { if (x[j][2] < ztmp) continue; @@ -121,16 +123,16 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) } } - // for all groups, loop over all atoms in other bins in stencil, store every pair + // for all collections, loop over all atoms in other bins in stencil, store every pair // stencil is empty if i larger than j // stencil is half if i same size as j // stencil is full if i smaller than j - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { jtype = type[j]; diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 2000927c63..2bf033781e 100755 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_multi_newton_tri.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -27,18 +28,19 @@ NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lm /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic - multi stencil is igroup-jgroup dependent + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,ns,js; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -62,7 +64,7 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) n = 0; neighptr = ipage->vget(); itype = type[i]; - igroup = map_type_multi[itype]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -70,12 +72,12 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) ibin = atom2bin[i]; - // loop through stencils for all groups - for (jgroup = 0; jgroup < n_multi_groups; jgroup++) { + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - // if same group use own bin - if(igroup == jgroup) jbin = ibin; - else jbin = coord2bin(x[i], jgroup); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); // loop over all atoms in bins in stencil // stencil is empty if i larger than j @@ -86,15 +88,15 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms - s = stencil_multi[igroup][jgroup]; - ns = nstencil_multi[igroup][jgroup]; + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; for (k = 0; k < ns; k++) { - js = binhead_multi[jgroup][jbin + s[k]]; + js = binhead_multi[jcollection][jbin + s[k]]; for (j = js; j >= 0; j = bins[j]) { - // if same size (same group), use half stencil - if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){ + // if same size (same collection), use half stencil + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/npair_half_size_multi_old_newtoff.cpp b/src/npair_half_size_multi_old_newtoff.cpp index 35095b4856..fd22412f00 100644 --- a/src/npair_half_size_multi_old_newtoff.cpp +++ b/src/npair_half_size_multi_old_newtoff.cpp @@ -35,7 +35,7 @@ NPairHalfSizeMultiOldNewtoff::NPairHalfSizeMultiOldNewtoff(LAMMPS *lmp) : NPair( void NPairHalfSizeMultiOldNewtoff::build(NeighList *list) { - int i,j,k,m,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; diff --git a/src/npair_half_size_multi_old_newton.cpp b/src/npair_half_size_multi_old_newton.cpp index 0112c0593f..1f6918625b 100644 --- a/src/npair_half_size_multi_old_newton.cpp +++ b/src/npair_half_size_multi_old_newton.cpp @@ -34,7 +34,7 @@ NPairHalfSizeMultiOldNewton::NPairHalfSizeMultiOldNewton(LAMMPS *lmp) : NPair(lm void NPairHalfSizeMultiOldNewton::build(NeighList *list) { - int i,j,k,m,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; diff --git a/src/npair_half_size_multi_old_newton_tri.cpp b/src/npair_half_size_multi_old_newton_tri.cpp index f29c323944..e7477fada4 100644 --- a/src/npair_half_size_multi_old_newton_tri.cpp +++ b/src/npair_half_size_multi_old_newton_tri.cpp @@ -33,7 +33,7 @@ NPairHalfSizeMultiOldNewtonTri::NPairHalfSizeMultiOldNewtonTri(LAMMPS *lmp) : NP void NPairHalfSizeMultiOldNewtonTri::build(NeighList *list) { - int i,j,k,m,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,ibin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 3d86b57b9e..c6ed76b6eb 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -52,14 +52,14 @@ using namespace LAMMPS_NS; cutoff is not cutneighmaxsq, but max cutoff for that atom type no versions that allow ghost on (any need for it?) for multi: - create one stencil for each igroup-jgroup pairing - the full/half stencil label refers to the same-group stencil - a half list with newton on has a half same-group stencil - a full list or half list with newton off has a full same-group stencil - cross group stencils are always full to allow small-to-large lookups + create one stencil for each icollection-jcollection pairing + the full/half stencil label refers to the same-collection stencil + a half list with newton on has a half same-collection stencil + a full list or half list with newton off has a full same-collection stencil + cross collection stencils are always full to allow small-to-large lookups for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin for triclinic, a half stencil includes bins in the z (3D) or y (2D) plane of self and above - cutoff is not cutneighmaxsq, but max cutoff for that atom group + cutoff is not cutneighmaxsq, but max cutoff for that atom collection no versions that allow ghost on (any need for it?) ------------------------------------------------------------------------- */ @@ -81,7 +81,7 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) flag_half_multi = nullptr; flag_skip_multi = nullptr; - bin_group_multi = nullptr; + bin_collection_multi = nullptr; dimension = domain->dimension; } @@ -107,7 +107,7 @@ NStencil::~NStencil() if (stencil_multi) { - int n = n_multi_groups; + int n = ncollections; memory->destroy(nstencil_multi); for (int i = 0; i < n; i++) { for (int j = 0; j < n; j++) { @@ -120,7 +120,7 @@ NStencil::~NStencil() memory->destroy(maxstencil_multi); memory->destroy(flag_half_multi); memory->destroy(flag_skip_multi); - memory->destroy(bin_group_multi); + memory->destroy(bin_collection_multi); memory->destroy(stencil_sx_multi); memory->destroy(stencil_sy_multi); @@ -156,9 +156,9 @@ void NStencil::copy_neighbor_info() cuttypesq = neighbor->cuttypesq; cutneighsq = neighbor->cutneighsq; - n_multi_groups = neighbor->n_multi_groups; - map_type_multi = neighbor->map_type_multi; - cutmultisq = neighbor->cutmultisq; + ncollections = neighbor->ncollections; + collection = neighbor->collection; + cutcollectionsq = neighbor->cutcollectionsq; // overwrite Neighbor cutoff with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -269,9 +269,9 @@ void NStencil::create_setup() } } } else { - int i, j, bin_group, smax; + int i, j, bin_collection, smax; double stencil_range; - int n = n_multi_groups; + int n = ncollections; if(nb) copy_bin_info_multi(); @@ -280,8 +280,8 @@ void NStencil::create_setup() "neighstencil:flag_half_multi"); memory->create(flag_skip_multi, n, n, "neighstencil:flag_skip_multi"); - memory->create(bin_group_multi, n, n, - "neighstencil:bin_group_multi"); + memory->create(bin_collection_multi, n, n, + "neighstencil:bin_collection_multi"); memory->create(stencil_sx_multi, n, n, "neighstencil:stencil_sx_multi"); @@ -335,25 +335,25 @@ void NStencil::create_setup() // Skip creation of unused stencils if (flag_skip_multi[i][j]) continue; - // Copy bin info for this pair of atom types - bin_group = bin_group_multi[i][j]; + // Copy bin info for this pair of atom collections + bin_collection = bin_collection_multi[i][j]; - stencil_binsizex_multi[i][j] = binsizex_multi[bin_group]; - stencil_binsizey_multi[i][j] = binsizey_multi[bin_group]; - stencil_binsizez_multi[i][j] = binsizez_multi[bin_group]; + stencil_binsizex_multi[i][j] = binsizex_multi[bin_collection]; + stencil_binsizey_multi[i][j] = binsizey_multi[bin_collection]; + stencil_binsizez_multi[i][j] = binsizez_multi[bin_collection]; - stencil_mbinx_multi[i][j] = mbinx_multi[bin_group]; - stencil_mbiny_multi[i][j] = mbiny_multi[bin_group]; - stencil_mbinz_multi[i][j] = mbinz_multi[bin_group]; + stencil_mbinx_multi[i][j] = mbinx_multi[bin_collection]; + stencil_mbiny_multi[i][j] = mbiny_multi[bin_collection]; + stencil_mbinz_multi[i][j] = mbinz_multi[bin_collection]; - stencil_range = sqrt(cutmultisq[i][j]); + stencil_range = sqrt(cutcollectionsq[i][j]); - sx = static_cast (stencil_range*bininvx_multi[bin_group]); - if (sx*binsizex_multi[bin_group] < stencil_range) sx++; - sy = static_cast (stencil_range*bininvy_multi[bin_group]); - if (sy*binsizey_multi[bin_group] < stencil_range) sy++; - sz = static_cast (stencil_range*bininvz_multi[bin_group]); - if (sz*binsizez_multi[bin_group] < stencil_range) sz++; + sx = static_cast (stencil_range*bininvx_multi[bin_collection]); + if (sx*binsizex_multi[bin_collection] < stencil_range) sx++; + sy = static_cast (stencil_range*bininvy_multi[bin_collection]); + if (sy*binsizey_multi[bin_collection] < stencil_range) sy++; + sz = static_cast (stencil_range*bininvz_multi[bin_collection]); + if (sz*binsizez_multi[bin_collection] < stencil_range) sz++; stencil_sx_multi[i][j] = sx; stencil_sy_multi[i][j] = sy; @@ -397,24 +397,24 @@ double NStencil::bin_distance(int i, int j, int k) /* ---------------------------------------------------------------------- - compute closest distance for a given atom grouping + compute closest distance for a given atom collection ------------------------------------------------------------------------- */ -double NStencil::bin_distance_multi(int i, int j, int k, int ig) +double NStencil::bin_distance_multi(int i, int j, int k, int ic) { double delx,dely,delz; - if (i > 0) delx = (i-1)*binsizex_multi[ig]; + if (i > 0) delx = (i-1)*binsizex_multi[ic]; else if (i == 0) delx = 0.0; - else delx = (i+1)*binsizex_multi[ig]; + else delx = (i+1)*binsizex_multi[ic]; - if (j > 0) dely = (j-1)*binsizey_multi[ig]; + if (j > 0) dely = (j-1)*binsizey_multi[ic]; else if (j == 0) dely = 0.0; - else dely = (j+1)*binsizey_multi[ig]; + else dely = (j+1)*binsizey_multi[ic]; - if (k > 0) delz = (k-1)*binsizez_multi[ig]; + if (k > 0) delz = (k-1)*binsizez_multi[ic]; else if (k == 0) delz = 0.0; - else delz = (k+1)*binsizez_multi[ig]; + else delz = (k+1)*binsizez_multi[ic]; return (delx*delx + dely*dely + delz*delz); } @@ -431,7 +431,7 @@ double NStencil::memory_usage() bytes += atom->ntypes*maxstencil_multi_old * sizeof(int); bytes += atom->ntypes*maxstencil_multi_old * sizeof(double); } else if (neighstyle == Neighbor::MULTI) { - int n = n_multi_groups; + int n = ncollections; for (int i = 0; i < n; i++) { for (int j = 0; j < n; j++) { bytes += maxstencil_multi[i][j] * sizeof(int); diff --git a/src/nstencil.h b/src/nstencil.h index b38276b45f..37cedec045 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -43,8 +43,8 @@ class NStencil : protected Pointers { // Arrays to store options for multi itype-jtype stencils bool **flag_half_multi; // flag creation of a half stencil for igroup-jgroup - bool **flag_skip_multi; // skip creation of igroup-jgroup stencils (for newton on) - int **bin_group_multi; // what group to use for bin information + bool **flag_skip_multi; // skip creation of icollection-jcollection stencils (for newton on) + int **bin_collection_multi; // what collection to use for bin information NStencil(class LAMMPS *); virtual ~NStencil(); @@ -66,9 +66,9 @@ class NStencil : protected Pointers { double cutneighmaxsq; double *cuttypesq; double **cutneighsq; - double **cutmultisq; - int n_multi_groups; - int *map_type_multi; + double **cutcollectionsq; + int ncollections; + int *collection; // data from NBin class @@ -112,7 +112,7 @@ class NStencil : protected Pointers { // methods for multi NStencil - double bin_distance_multi(int, int, int, int); // distance between bin corners for different types + double bin_distance_multi(int, int, int, int); // distance between bin corners for different collections void copy_bin_info_multi(); // copy multi info from NBin class virtual void set_stencil_properties(){} // determine which stencils to build and how }; diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp index 4c96f41a56..b27e3c2a9c 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -29,7 +29,7 @@ NStencilFullMulti2d::NStencilFullMulti2d(LAMMPS *lmp) : NStencil(lmp) {} void NStencilFullMulti2d::set_stencil_properties() { - int n = n_multi_groups; + int n = ncollections; int i, j; // Always look up neighbor using full stencil and neighbor's bin @@ -38,7 +38,7 @@ void NStencilFullMulti2d::set_stencil_properties() for (j = 0; j < n; j++) { flag_half_multi[i][j] = 0; flag_skip_multi[i][j] = 0; - bin_group_multi[i][j] = j; + bin_collection_multi[i][j] = j; } } } @@ -49,33 +49,33 @@ void NStencilFullMulti2d::set_stencil_properties() void NStencilFullMulti2d::create() { - int igroup, jgroup, bin_group, i, j, k, ns; - int n = n_multi_groups; + int icollection, jcollection, bin_collection, i, j, k, ns; + int n = ncollections; double cutsq; - for (igroup = 0; igroup < n; igroup++) { - for (jgroup = 0; jgroup < n; jgroup++) { - if (flag_skip_multi[igroup][jgroup]) continue; + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) continue; ns = 0; - sx = stencil_sx_multi[igroup][jgroup]; - sy = stencil_sy_multi[igroup][jgroup]; + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; - mbinx = stencil_mbinx_multi[igroup][jgroup]; - mbiny = stencil_mbiny_multi[igroup][jgroup]; + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; - bin_group = bin_group_multi[igroup][jgroup]; + bin_collection = bin_collection_multi[icollection][jcollection]; - cutsq = cutmultisq[igroup][jgroup]; + cutsq = cutcollectionsq[icollection][jcollection]; for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; - nstencil_multi[igroup][jgroup] = ns; + nstencil_multi[icollection][jcollection] = ns; } } } diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp index bc76433723..3d97bc10ad 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -29,7 +29,7 @@ NStencilFullMulti3d::NStencilFullMulti3d(LAMMPS *lmp) : NStencil(lmp) {} void NStencilFullMulti3d::set_stencil_properties() { - int n = n_multi_groups; + int n = ncollections; int i, j; // Always look up neighbor using full stencil and neighbor's bin @@ -39,7 +39,7 @@ void NStencilFullMulti3d::set_stencil_properties() for (j = 0; j < n; j++) { flag_half_multi[i][j] = 0; flag_skip_multi[i][j] = 0; - bin_group_multi[i][j] = j; + bin_collection_multi[i][j] = j; } } } @@ -50,37 +50,37 @@ void NStencilFullMulti3d::set_stencil_properties() void NStencilFullMulti3d::create() { - int igroup, jgroup, bin_group, i, j, k, ns; - int n = n_multi_groups; + int icollection, jcollection, bin_collection, i, j, k, ns; + int n = ncollections; double cutsq; - for (igroup = 0; igroup < n; igroup++) { - for (jgroup = 0; jgroup < n; jgroup++) { - if (flag_skip_multi[igroup][jgroup]) continue; + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) continue; ns = 0; - sx = stencil_sx_multi[igroup][jgroup]; - sy = stencil_sy_multi[igroup][jgroup]; - sz = stencil_sz_multi[igroup][jgroup]; + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; + sz = stencil_sz_multi[icollection][jcollection]; - mbinx = stencil_mbinx_multi[igroup][jgroup]; - mbiny = stencil_mbiny_multi[igroup][jgroup]; - mbinz = stencil_mbinz_multi[igroup][jgroup]; + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; + mbinz = stencil_mbinz_multi[icollection][jcollection]; - bin_group = bin_group_multi[igroup][jgroup]; + bin_collection = bin_collection_multi[icollection][jcollection]; - cutsq = cutmultisq[igroup][jgroup]; + cutsq = cutcollectionsq[icollection][jcollection]; for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; - nstencil_multi[igroup][jgroup] = ns; + nstencil_multi[icollection][jcollection] = ns; } } } diff --git a/src/nstencil_half_multi_2d.cpp b/src/nstencil_half_multi_2d.cpp index 8be8a1c151..57352c7c6f 100644 --- a/src/nstencil_half_multi_2d.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti2d::NStencilHalfMulti2d(LAMMPS *lmp) : void NStencilHalfMulti2d::set_stencil_properties() { - int n = n_multi_groups; + int n = ncollections; int i, j; - // Cross groups: use full stencil, looking one way through hierarchy + // Cross collections: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil for (i = 0; i < n; i++) { for (j = 0; j < n; j++) { - if(cutmultisq[i][i] > cutmultisq[j][j]) continue; + if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutmultisq[i][i] == cutmultisq[j][j]){ + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ flag_half_multi[i][j] = 1; - bin_group_multi[i][j] = i; + bin_collection_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_group_multi[i][j] = j; + bin_collection_multi[i][j] = j; } } } @@ -61,42 +61,42 @@ void NStencilHalfMulti2d::set_stencil_properties() void NStencilHalfMulti2d::create() { - int igroup, jgroup, bin_group, i, j, ns; - int n = n_multi_groups; + int icollection, jcollection, bin_collection, i, j, ns; + int n = ncollections; double cutsq; - for (igroup = 0; igroup < n; igroup++) { - for (jgroup = 0; jgroup < n; jgroup++) { - if (flag_skip_multi[igroup][jgroup]) continue; + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) continue; ns = 0; - sx = stencil_sx_multi[igroup][jgroup]; - sy = stencil_sy_multi[igroup][jgroup]; + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; - mbinx = stencil_mbinx_multi[igroup][jgroup]; - mbiny = stencil_mbiny_multi[igroup][jgroup]; + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; - bin_group = bin_group_multi[igroup][jgroup]; + bin_collection = bin_collection_multi[icollection][jcollection]; - cutsq = cutmultisq[igroup][jgroup]; + cutsq = cutcollectionsq[icollection][jcollection]; - if (flag_half_multi[igroup][jgroup]) { + if (flag_half_multi[icollection][jcollection]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) if (j > 0 || (j == 0 && i > 0)) { - if (bin_distance_multi(i,j,0,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; } } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; } - nstencil_multi[igroup][jgroup] = ns; + nstencil_multi[icollection][jcollection] = ns; } } } diff --git a/src/nstencil_half_multi_2d_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp index 4a4e74c4a0..6588248109 100755 --- a/src/nstencil_half_multi_2d_tri.cpp +++ b/src/nstencil_half_multi_2d_tri.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti2dTri::NStencilHalfMulti2dTri(LAMMPS *lmp) : void NStencilHalfMulti2dTri::set_stencil_properties() { - int n = n_multi_groups; + int n = ncollections; int i, j; - // Cross groups: use full stencil, looking one way through hierarchy + // Cross collections: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil for (i = 0; i < n; i++) { for (j = 0; j < n; j++) { - if(cutmultisq[i][i] > cutmultisq[j][j]) continue; + if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutmultisq[i][i] == cutmultisq[j][j]){ + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ flag_half_multi[i][j] = 1; - bin_group_multi[i][j] = i; + bin_collection_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_group_multi[i][j] = j; + bin_collection_multi[i][j] = j; } } } @@ -61,40 +61,40 @@ void NStencilHalfMulti2dTri::set_stencil_properties() void NStencilHalfMulti2dTri::create() { - int igroup, jgroup, bin_group, i, j, ns; - int n = n_multi_groups; + int icollection, jcollection, bin_collection, i, j, ns; + int n = ncollections; double cutsq; - for (igroup = 0; igroup < n; igroup++) { - for (jgroup = 0; jgroup < n; jgroup++) { - if (flag_skip_multi[igroup][jgroup]) continue; + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) continue; ns = 0; - sx = stencil_sx_multi[igroup][jgroup]; - sy = stencil_sy_multi[igroup][jgroup]; + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; - mbinx = stencil_mbinx_multi[igroup][jgroup]; - mbiny = stencil_mbiny_multi[igroup][jgroup]; + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; - bin_group = bin_group_multi[igroup][jgroup]; + bin_collection = bin_collection_multi[icollection][jcollection]; - cutsq = cutmultisq[igroup][jgroup]; + cutsq = cutcollectionsq[icollection][jcollection]; - if (flag_half_multi[igroup][jgroup]) { + if (flag_half_multi[icollection][jcollection]) { for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; } else { for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,0,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = j*mbinx + i; + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; } - nstencil_multi[igroup][jgroup] = ns; + nstencil_multi[icollection][jcollection] = ns; } } } diff --git a/src/nstencil_half_multi_3d.cpp b/src/nstencil_half_multi_3d.cpp index ad4970603c..19cd051392 100644 --- a/src/nstencil_half_multi_3d.cpp +++ b/src/nstencil_half_multi_3d.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti3d::NStencilHalfMulti3d(LAMMPS *lmp) : void NStencilHalfMulti3d::set_stencil_properties() { - int n = n_multi_groups; + int n = ncollections; int i, j; - // Cross groups: use full stencil, looking one way through hierarchy + // Cross collections: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil for (i = 0; i < n; i++) { for (j = 0; j < n; j++) { - if(cutmultisq[i][i] > cutmultisq[j][j]) continue; + if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutmultisq[i][i] == cutmultisq[j][j]){ + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ flag_half_multi[i][j] = 1; - bin_group_multi[i][j] = i; + bin_collection_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_group_multi[i][j] = j; + bin_collection_multi[i][j] = j; } } } @@ -61,48 +61,48 @@ void NStencilHalfMulti3d::set_stencil_properties() void NStencilHalfMulti3d::create() { - int igroup, jgroup, bin_group, i, j, k, ns; - int n = n_multi_groups; + int icollection, jcollection, bin_collection, i, j, k, ns; + int n = ncollections; double cutsq; - for (igroup = 0; igroup < n; igroup++) { - for (jgroup = 0; jgroup < n; jgroup++) { - if (flag_skip_multi[igroup][jgroup]) continue; + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) continue; ns = 0; - sx = stencil_sx_multi[igroup][jgroup]; - sy = stencil_sy_multi[igroup][jgroup]; - sz = stencil_sz_multi[igroup][jgroup]; + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; + sz = stencil_sz_multi[icollection][jcollection]; - mbinx = stencil_mbinx_multi[igroup][jgroup]; - mbiny = stencil_mbiny_multi[igroup][jgroup]; - mbinz = stencil_mbinz_multi[igroup][jgroup]; + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; + mbinz = stencil_mbinz_multi[icollection][jcollection]; - bin_group = bin_group_multi[igroup][jgroup]; + bin_collection = bin_collection_multi[icollection][jcollection]; - cutsq = cutmultisq[igroup][jgroup]; + cutsq = cutcollectionsq[icollection][jcollection]; - if (flag_half_multi[igroup][jgroup]) { + if (flag_half_multi[icollection][jcollection]) { for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) if (k > 0 || j > 0 || (j == 0 && i > 0)) { - if (bin_distance_multi(i,j,k,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; } } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; } - nstencil_multi[igroup][jgroup] = ns; + nstencil_multi[icollection][jcollection] = ns; } } } diff --git a/src/nstencil_half_multi_3d_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp index 779f0865a5..3c5efac463 100755 --- a/src/nstencil_half_multi_3d_tri.cpp +++ b/src/nstencil_half_multi_3d_tri.cpp @@ -30,26 +30,26 @@ NStencilHalfMulti3dTri::NStencilHalfMulti3dTri(LAMMPS *lmp) : void NStencilHalfMulti3dTri::set_stencil_properties() { - int n = n_multi_groups; + int n = ncollections; int i, j; - // Cross groups: use full stencil, looking one way through hierarchy + // Cross collections: use full stencil, looking one way through hierarchy // smaller -> larger => use full stencil in larger bin // larger -> smaller => no nstencil required // If cut offs are same, use half stencil for (i = 0; i < n; i++) { for (j = 0; j < n; j++) { - if(cutmultisq[i][i] > cutmultisq[j][j]) continue; + if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; flag_skip_multi[i][j] = 0; - if(cutmultisq[i][i] == cutmultisq[j][j]){ + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ flag_half_multi[i][j] = 1; - bin_group_multi[i][j] = i; + bin_collection_multi[i][j] = i; } else { flag_half_multi[i][j] = 0; - bin_group_multi[i][j] = j; + bin_collection_multi[i][j] = j; } } } @@ -61,46 +61,46 @@ void NStencilHalfMulti3dTri::set_stencil_properties() void NStencilHalfMulti3dTri::create() { - int igroup, jgroup, bin_group, i, j, k, ns; - int n = n_multi_groups; + int icollection, jcollection, bin_collection, i, j, k, ns; + int n = ncollections; double cutsq; - for (igroup = 0; igroup < n; igroup++) { - for (jgroup = 0; jgroup < n; jgroup++) { - if (flag_skip_multi[igroup][jgroup]) continue; + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) continue; ns = 0; - sx = stencil_sx_multi[igroup][jgroup]; - sy = stencil_sy_multi[igroup][jgroup]; - sz = stencil_sz_multi[igroup][jgroup]; + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; + sz = stencil_sz_multi[icollection][jcollection]; - mbinx = stencil_mbinx_multi[igroup][jgroup]; - mbiny = stencil_mbiny_multi[igroup][jgroup]; - mbinz = stencil_mbinz_multi[igroup][jgroup]; + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; + mbinz = stencil_mbinz_multi[icollection][jcollection]; - bin_group = bin_group_multi[igroup][jgroup]; + bin_collection = bin_collection_multi[icollection][jcollection]; - cutsq = cutmultisq[igroup][jgroup]; + cutsq = cutcollectionsq[icollection][jcollection]; - if (flag_half_multi[igroup][jgroup]) { + if (flag_half_multi[icollection][jcollection]) { for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; } else { for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) - if (bin_distance_multi(i,j,k,bin_group) < cutsq) - stencil_multi[igroup][jgroup][ns++] = + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = k*mbiny*mbinx + j*mbinx + i; } - nstencil_multi[igroup][jgroup] = ns; + nstencil_multi[icollection][jcollection] = ns; } } } diff --git a/src/pair.cpp b/src/pair.cpp index afc5eb2785..04aafbe863 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -63,6 +63,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp) one_coeff = 0; no_virial_fdotr_compute = 0; writedata = 0; + finitecutflag = 0; ghostneigh = 0; unit_convert_flag = utils::NOCONVERT; diff --git a/src/pair.h b/src/pair.h index 5801941458..3c6710229e 100644 --- a/src/pair.h +++ b/src/pair.h @@ -56,6 +56,7 @@ class Pair : protected Pointers { int unit_convert_flag; // value != 0 indicates support for unit conversion. int no_virial_fdotr_compute; // 1 if does not invoke virial_fdotr_compute() int writedata; // 1 if writes coeffs to data file + int finitecutflag; // 1 if cut depends on finite atom size int ghostneigh; // 1 if pair style needs neighbors of ghosts double **cutghost; // cutoff for each ghost pair @@ -205,6 +206,8 @@ class Pair : protected Pointers { virtual void min_xf_get(int) {} virtual void min_x_set(int) {} virtual void transfer_history(double *, double*) {} + virtual double atom2cut(int) {return 0.0;} + virtual double radii2cut(double,double) {return 0.0;} // management of callbacks to be run from ev_tally() diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 3026c9c741..e559e81f84 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -401,6 +401,7 @@ void PairHybrid::flags() if (styles[m]->dispersionflag) dispersionflag = 1; if (styles[m]->tip4pflag) tip4pflag = 1; if (styles[m]->compute_flag) compute_flag = 1; + if (styles[m]->finitecutflag) finitecutflag = 1; } single_enable = (single_enable == nstyles) ? 1 : 0; respa_enable = (respa_enable == nstyles) ? 1 : 0; @@ -1072,6 +1073,42 @@ int PairHybrid::check_ijtype(int itype, int jtype, char *substyle) return 0; } +/* ---------------------------------------------------------------------- + check if substyles calculate self-interaction range of particle +------------------------------------------------------------------------- */ + +double PairHybrid::atom2cut(int i) +{ + double temp, cut; + + cut = 0.0; + for (int m = 0; m < nstyles; m++) { + if (styles[m]->finitecutflag){ + temp = styles[m]->atom2cut(i); + if(temp > cut) cut = temp; + } + } + return cut; +} + +/* ---------------------------------------------------------------------- + check if substyles calculate maximum interaction range for two finite particles +------------------------------------------------------------------------- */ + +double PairHybrid::radii2cut(double r1, double r2) +{ + double temp, cut; + + cut = 0.0; + for (int m = 0; m < nstyles; m++) { + if (styles[m]->finitecutflag){ + temp = styles[m]->radii2cut(r1,r2); + if(temp > cut) cut = temp; + } + } + return cut; +} + /* ---------------------------------------------------------------------- memory usage of each sub-style ------------------------------------------------------------------------- */ diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index 7717d1fd51..9d10e91684 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -58,6 +58,8 @@ class PairHybrid : public Pair { virtual void add_tally_callback(class Compute *); virtual void del_tally_callback(class Compute *); + double atom2cut(int); + double radii2cut(double,double); protected: int nstyles; // # of sub-styles From 0676c953c033a8be591cbc22e7d30e8f9d0ea7d7 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 2 Feb 2021 09:41:50 -0700 Subject: [PATCH 0074/1217] Removing stray file --- src/init | 789 ------------------------------------------------------- 1 file changed, 789 deletions(-) delete mode 100644 src/init diff --git a/src/init b/src/init deleted file mode 100644 index 617c9effa3..0000000000 --- a/src/init +++ /dev/null @@ -1,789 +0,0 @@ -angle_charmm.cpp: if (comm->me == 0) { -angle_cosine.cpp: if (comm->me == 0) utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,nullptr,error); -angle_cosine_periodic.cpp: if (comm->me == 0) { -angle_cosine_squared.cpp: if (comm->me == 0) { -angle.cpp: memory->create(eatom,comm->nthreads*maxeatom,"angle:eatom"); -angle.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"angle:vatom"); -angle.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"angle:cvatom"); -angle.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); -angle.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); -angle.cpp: bytes += comm->nthreads*maxcvatom*9 * sizeof(double); -angle_deprecated.cpp: if (lmp->comm->me == 0) -angle_harmonic.cpp: if (comm->me == 0) { -angle_hybrid.cpp: const int nthreads = comm->nthreads; -angle_hybrid.cpp: if (comm->nthreads > 1) { -angle_hybrid.cpp: int me = comm->me; -angle_table.cpp: if (comm->me == 0) { -angle_zero.cpp: if (comm->me == 0) { -atom.cpp: if (comm->layout != Comm::LAYOUT_TILED) { -atom.cpp: if (comm->myloc[0] == 0) sublo[0] -= epsilon[0]; -atom.cpp: if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += epsilon[0]; -atom.cpp: if (comm->myloc[1] == 0) sublo[1] -= epsilon[1]; -atom.cpp: if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += epsilon[1]; -atom.cpp: if (comm->myloc[2] == 0) sublo[2] -= epsilon[2]; -atom.cpp: if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += epsilon[2]; -atom.cpp: if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0]; -atom.cpp: if (comm->mysplit[0][1] == 1.0) subhi[0] += epsilon[0]; -atom.cpp: if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1]; -atom.cpp: if (comm->mysplit[1][1] == 1.0) subhi[1] += epsilon[1]; -atom.cpp: if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2]; -atom.cpp: if (comm->mysplit[2][1] == 1.0) subhi[2] += epsilon[2]; -atom.cpp: if (comm->me == 0) { -atom.cpp: called by comm->exchange() if atom_modify first group is set -atom.cpp: always called between comm->exchange() and comm->borders() -atom.cpp: if (comm->me == 0) -atom_map.cpp: int nper = static_cast (natoms/comm->nprocs); -atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); -atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); -atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); -atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); -atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); -atom_vec_body.cpp: printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag); -atom_vec.cpp: f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f"); -atom_vec.cpp: const int nthreads = threads[i] ? comm->nthreads : 1; -atom_vec.cpp: bytes += memory->usage(f,nmax*comm->nthreads,3); -atom_vec.cpp: const int nthreads = threads[i] ? comm->nthreads : 1; -atom_vec_hybrid.cpp: if (mass_pertype && mass_peratom && comm->me == 0) -atom_vec_hybrid.cpp: if ((ptr && strstr(ptr+1,dup)) && (comm->me == 0)) -atom_vec_line.cpp: //if (comm->me == 1 && update->ntimestep == 873) -atom_vec_line.cpp: printf("BAD vecline ptrs: %s: %d %d: %d\n",str,comm->me, -atom_vec_line.cpp: str,comm->me,update->ntimestep,count,nlocal_bonus); -balance.cpp: int *procgrid = comm->procgrid; -balance.cpp: if (style == BISECTION && comm->style == 0) -balance.cpp: // init entire system since comm->setup is done -balance.cpp: comm->setup(); -balance.cpp: comm->exchange(); -balance.cpp: if (comm->layout == Comm::LAYOUT_TILED && style != BISECTION) { -balance.cpp: if (comm->layout == Comm::LAYOUT_UNIFORM) { -balance.cpp: comm->layout = Comm::LAYOUT_NONUNIFORM; -balance.cpp: } else if (comm->layout == Comm::LAYOUT_NONUNIFORM) { -balance.cpp: comm->layout = Comm::LAYOUT_UNIFORM; -balance.cpp: } else if (comm->layout == Comm::LAYOUT_TILED) { -balance.cpp: comm->layout = Comm::LAYOUT_UNIFORM; -balance.cpp: else comm->layout = Comm::LAYOUT_NONUNIFORM; -balance.cpp: comm->xsplit[i] = i * 1.0/procgrid[0]; -balance.cpp: comm->xsplit[procgrid[0]] = 1.0; -balance.cpp: for (int i = 0; i <= procgrid[0]; i++) comm->xsplit[i] = user_xsplit[i]; -balance.cpp: comm->ysplit[i] = i * 1.0/procgrid[1]; -balance.cpp: comm->ysplit[procgrid[1]] = 1.0; -balance.cpp: for (int i = 0; i <= procgrid[1]; i++) comm->ysplit[i] = user_ysplit[i]; -balance.cpp: comm->zsplit[i] = i * 1.0/procgrid[2]; -balance.cpp: comm->zsplit[procgrid[2]] = 1.0; -balance.cpp: for (int i = 0; i <= procgrid[2]; i++) comm->zsplit[i] = user_zsplit[i]; -balance.cpp: comm->layout = Comm::LAYOUT_NONUNIFORM; -balance.cpp: comm->layout = Comm::LAYOUT_TILED; -balance.cpp: for (int i = 0; i <= comm->procgrid[0]; i++) -balance.cpp: mesg += fmt::format(" {:.8}",comm->xsplit[i]); -balance.cpp: for (int i = 0; i <= comm->procgrid[1]; i++) -balance.cpp: mesg += fmt::format(" {:.8}",comm->ysplit[i]); -balance.cpp: for (int i = 0; i <= comm->procgrid[2]; i++) -balance.cpp: mesg += fmt::format(" {:.8}",comm->zsplit[i]); -balance.cpp: if (outflag && comm->me == 0) { -balance.cpp: comm->rcbnew = 1; -balance.cpp: if (idim >= 0) comm->rcbcutfrac = (rcb->cut - boxlo[idim]) / prd[idim]; -balance.cpp: else comm->rcbcutfrac = 0.0; -balance.cpp: comm->rcbcutdim = idim; -balance.cpp: double (*mysplit)[2] = comm->mysplit; -balance.cpp: int max = MAX(comm->procgrid[0],comm->procgrid[1]); -balance.cpp: max = MAX(max,comm->procgrid[2]); -balance.cpp: if (comm->layout == Comm::LAYOUT_TILED) { -balance.cpp: int *procgrid = comm->procgrid; -balance.cpp: double *xsplit = comm->xsplit; -balance.cpp: double *ysplit = comm->ysplit; -balance.cpp: double *zsplit = comm->zsplit; -balance.cpp: int *procgrid = comm->procgrid; -balance.cpp: split = comm->xsplit; -balance.cpp: split = comm->ysplit; -balance.cpp: split = comm->zsplit; -balance.cpp: double *xsplit = comm->xsplit; -balance.cpp: double *ysplit = comm->ysplit; -balance.cpp: double *zsplit = comm->zsplit; -balance.cpp: int nx = comm->procgrid[0]; -balance.cpp: int ny = comm->procgrid[1]; -balance.cpp: int nz = comm->procgrid[2]; -bond.cpp: memory->create(eatom,comm->nthreads*maxeatom,"bond:eatom"); -bond.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"bond:vatom"); -bond.cpp: if (comm->me == 0) { -bond.cpp: if (comm->me == 0) { -bond.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); -bond.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); -bond_deprecated.cpp: if (lmp->comm->me == 0) -bond_fene.cpp: if (comm->me == 0) -bond_fene.cpp: if (comm->me == 0) { -bond_fene_expand.cpp: if (comm->me == 0) -bond_fene_expand.cpp: if (comm->me == 0) { -bond_gromos.cpp: if (comm->me == 0) { -bond_harmonic.cpp: if (comm->me == 0) { -bond_hybrid.cpp: const int nthreads = comm->nthreads; -bond_hybrid.cpp: int me = comm->me; -bond_morse.cpp: if (comm->me == 0) { -bond_nonlinear.cpp: if (comm->me == 0) { -bond_quartic.cpp: if (comm->me == 0) { -bond_table.cpp: if (comm->me == 0) { -bond_zero.cpp: if (comm->me == 0) { -change_box.cpp: if (comm->me == 0) utils::logmesg(lmp,"Changing box ...\n"); -change_box.cpp: if (natoms != atom->natoms && comm->me == 0) -comm_brick.cpp: if (oldcomm->layout == Comm::LAYOUT_TILED) -comm_brick.cpp: layout = oldcomm->layout; -comm.cpp: if (oldcomm->grid2proc) { -comm.cpp: memcpy(&grid2proc[0][0][0],&oldcomm->grid2proc[0][0][0], -comm.cpp: memcpy(xsplit,oldcomm->xsplit,(procgrid[0]+1)*sizeof(double)); -comm.cpp: memcpy(ysplit,oldcomm->ysplit,(procgrid[1]+1)*sizeof(double)); -comm.cpp: memcpy(zsplit,oldcomm->zsplit,(procgrid[2]+1)*sizeof(double)); -comm.cpp: if (oldcomm->cutusermulti) { -comm.cpp: memcpy(cutusermulti,oldcomm->cutusermulti,ncollections); -comm.cpp: if (oldcomm->cutusermultiold) { -comm.cpp: memcpy(cutusermultiold,oldcomm->cutusermultiold,atom->ntypes+1); -comm.cpp: int n = strlen(oldcomm->customfile) + 1; -comm.cpp: strcpy(customfile,oldcomm->customfile); -comm.cpp: int n = strlen(oldcomm->outfile) + 1; -comm.cpp: strcpy(outfile,oldcomm->outfile); -comm_tiled.cpp: layout = oldcomm->layout; -compute_adf.cpp: if (mycutneigh > comm->cutghostuser) -compute_aggregate_atom.cpp: if (count > 1 && comm->me == 0) -compute_aggregate_atom.cpp: comm->forward_comm_compute(this); -compute_aggregate_atom.cpp: comm->forward_comm_compute(this); -compute_aggregate_atom.cpp: comm->reverse_comm_compute(this); -compute_bond_local.cpp: if (velflag && !comm->ghost_velocity) ghostvelflag = 1; -compute_bond_local.cpp: if (ghostvelflag && !initflag) comm->forward_comm_compute(this); -compute_centro_atom.cpp: if (count > 1 && comm->me == 0) -compute_centroid_stress_atom.cpp: comm->reverse_comm_compute(this); -compute_chunk_atom.cpp: int nprocs = comm->nprocs; -compute_chunk_atom.cpp: comm->ring(n,sizeof(int),list,1,idring,nullptr,(void *)this,0); -compute_chunk_atom.cpp: callback from comm->ring() -compute_chunk_atom.cpp: if (flagall && comm->me == 0) -compute_cluster_atom.cpp: if (count > 1 && comm->me == 0) -compute_cluster_atom.cpp: comm->forward_comm_compute(this); -compute_cluster_atom.cpp: comm->forward_comm_compute(this); -compute_cluster_atom.cpp: comm->forward_comm_compute(this); -compute_cna_atom.cpp: comm->me == 0) -compute_cna_atom.cpp: if (count > 1 && comm->me == 0) -compute_cna_atom.cpp: if (nerrorall && comm->me == 0) -compute_cna_atom.cpp: if (nerrorall && comm->me == 0) -compute_contact_atom.cpp: if (count > 1 && comm->me == 0) -compute_contact_atom.cpp: if (force->newton_pair) comm->reverse_comm_compute(this); -compute_coord_atom.cpp: comm->forward_comm_compute(this); -compute_deprecated.cpp: if (lmp->comm->me == 0) -compute_erotate_sphere_atom.cpp: if (count > 1 && comm->me == 0) -compute_fragment_atom.cpp: if (count > 1 && comm->me == 0) -compute_fragment_atom.cpp: comm->forward_comm_compute(this); -compute_fragment_atom.cpp: comm->forward_comm_compute(this); -compute_group_group.cpp: if ((fabs(e_correction) > SMALL) && (comm->me == 0)) -compute_hexorder_atom.cpp: if (count > 1 && comm->me == 0) -compute_ke_atom.cpp: if (count > 1 && comm->me == 0) -compute_orientorder_atom.cpp: if (count > 1 && comm->me == 0) -compute_pe_atom.cpp: comm->reverse_comm_compute(this); -compute_property_atom.cpp: int me = comm->me; -compute_rdf.cpp: cutghost = MAX(force->pair->cutforce+skin,comm->cutghostuser); -compute_rdf.cpp: cutghost = comm->cutghostuser; -compute_rdf.cpp: if (comm->me == 0) -compute_stress_atom.cpp: comm->reverse_comm_compute(this); -compute_temp_deform.cpp: comm->me == 0) -compute_temp_deform.cpp: if (i == modify->nfix && comm->me == 0) -create_atoms.cpp: if (comm->layout != Comm::LAYOUT_TILED) { -create_atoms.cpp: if (comm->myloc[0] == 0) sublo[0] -= epsilon[0]; -create_atoms.cpp: if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*epsilon[0]; -create_atoms.cpp: if (comm->myloc[1] == 0) sublo[1] -= epsilon[1]; -create_atoms.cpp: if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= 2.0*epsilon[1]; -create_atoms.cpp: if (comm->myloc[2] == 0) sublo[2] -= epsilon[2]; -create_atoms.cpp: if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= 2.0*epsilon[2]; -create_atoms.cpp: if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0]; -create_atoms.cpp: if (comm->mysplit[0][1] == 1.0) subhi[0] -= 2.0*epsilon[0]; -create_atoms.cpp: if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1]; -create_atoms.cpp: if (comm->mysplit[1][1] == 1.0) subhi[1] -= 2.0*epsilon[1]; -create_atoms.cpp: if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2]; -create_atoms.cpp: if (comm->mysplit[2][1] == 1.0) subhi[2] -= 2.0*epsilon[2]; -create_bonds.cpp: // init entire system since comm->borders and neighbor->build is done -create_bonds.cpp: if (rmax > neighbor->cutneighmin && comm->me == 0) -create_bonds.cpp: comm->setup(); -create_bonds.cpp: comm->exchange(); -create_bonds.cpp: comm->borders(); -create_bonds.cpp: if (comm->me == 0) -create_box.cpp: comm->set_proc_grid(); -delete_atoms.cpp: } else if (comm->me == 0) -delete_atoms.cpp: if (comm->me == 0) { -delete_atoms.cpp: if (comm->me == 0) utils::logmesg(lmp,"System init for delete_atoms ...\n"); -delete_atoms.cpp: // init entire system since comm->borders and neighbor->build is done -delete_atoms.cpp: if (cut > neighbor->cutneighmin && comm->me == 0) -delete_atoms.cpp: comm->setup(); -delete_atoms.cpp: comm->exchange(); -delete_atoms.cpp: comm->borders(); -delete_atoms.cpp: RanMars *random = new RanMars(lmp,seed + comm->me); -delete_atoms.cpp: // pass list to all other procs via comm->ring() -delete_atoms.cpp: comm->ring(n,sizeof(tagint),list,1,bondring,nullptr,(void *)this); -delete_atoms.cpp: // pass list to all other procs via comm->ring() -delete_atoms.cpp: comm->ring(n,sizeof(tagint),list,1,molring,nullptr,(void *)this); -delete_atoms.cpp: callback from comm->ring() in delete_bond() -delete_atoms.cpp: callback from comm->ring() in delete_molecule() -delete_bonds.cpp: // init entire system since comm->borders is done -delete_bonds.cpp: if (comm->me == 0) utils::logmesg(lmp,"System init for delete_bonds ...\n"); -delete_bonds.cpp: if (comm->me == 0) utils::logmesg(lmp,"Deleting bonds ...\n"); -delete_bonds.cpp: comm->setup(); -delete_bonds.cpp: comm->exchange(); -delete_bonds.cpp: comm->borders(); -delete_bonds.cpp: if (comm->me == 0) { -deprecated.cpp: if (lmp->comm->me == 0) -deprecated.cpp: if (lmp->comm->me == 0) -dihedral_charmm.cpp: if (comm->me == 0) { -dihedral_charmmfsw.cpp: if (comm->me == 0) { -dihedral.cpp: memory->create(eatom,comm->nthreads*maxeatom,"dihedral:eatom"); -dihedral.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"dihedral:vatom"); -dihedral.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"dihedral:cvatom"); -dihedral.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); -dihedral.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); -dihedral.cpp: bytes += comm->nthreads*maxcvatom*9 * sizeof(double); -dihedral_deprecated.cpp: if (lmp->comm->me == 0) -dihedral_harmonic.cpp: if (comm->me == 0) { -dihedral_helix.cpp: if (comm->me == 0) { -dihedral_hybrid.cpp: int me = comm->me; -dihedral_multi_harmonic.cpp: if (comm->me == 0) { -dihedral_opls.cpp: if (comm->me == 0) { -displace_atoms.cpp: if (comm->me == 0) utils::logmesg(lmp,"Displacing atoms ...\n"); -displace_atoms.cpp: if (natoms != atom->natoms && comm->me == 0) -domain.cpp: else if (comm->me == 0) -domain.cpp: uses comm->xyz_split or comm->mysplit -domain.cpp: if (comm->layout != Comm::LAYOUT_TILED) { -domain.cpp: int *myloc = comm->myloc; -domain.cpp: double *xsplit = comm->xsplit; -domain.cpp: double *ysplit = comm->ysplit; -domain.cpp: double *zsplit = comm->zsplit; -domain.cpp: double (*mysplit)[2] = comm->mysplit; -domain.cpp: uses comm->xyz_split or comm->mysplit -domain.cpp: if (comm->layout != Comm::LAYOUT_TILED) { -domain.cpp: int *myloc = comm->myloc; -domain.cpp: int *procgrid = comm->procgrid; -domain.cpp: double *xsplit = comm->xsplit; -domain.cpp: double *ysplit = comm->ysplit; -domain.cpp: double *zsplit = comm->zsplit; -domain.cpp: double (*mysplit)[2] = comm->mysplit; -domain.cpp: comm->forward_comm_array(3,unwrap); -domain.cpp: if (flagall && comm->me == 0) -domain.cpp: if (all && comm->me == 0) -domain.cpp: if (all && comm->me == 0) -domain.cpp: if (flagall && comm->me == 0) -domain.cpp: since may lead to lost atoms in comm->exchange() -domain.cpp: if (flagall && comm->me == 0) -domain.cpp: if ((flag_all > 0) && (comm->me == 0)) -domain.cpp: if (comm->me == 0) { -dump_deprecated.cpp: if (lmp->comm->me == 0) -dump_image.cpp: comm->forward_comm_dump(this); -dump_movie.cpp: if ((comm->me == 0) && (fp == nullptr)) { -finish.cpp: const int nthreads = comm->nthreads; -fix_balance.cpp: if (lbstyle == BISECTION && comm->style == 0) -fix_balance.cpp: compute final imbalance factor based on nlocal after comm->exchange() -fix_balance.cpp: // invoke balancer and reset comm->uniform flag -fix_balance.cpp: comm->layout = Comm::LAYOUT_NONUNIFORM; -fix_balance.cpp: comm->layout = Comm::LAYOUT_TILED; -fix_balance.cpp: // since may lead to lost atoms in comm->exchange() -fix_balance.cpp: // else allow caller's comm->exchange() to do it -fix_balance.cpp: // b/c atoms may migrate again in comm->exchange() -fix_balance.cpp: // can only be done after atoms migrate in comm->exchange() -fix_box_relax.cpp: if (temperature->igroup != 0 && comm->me == 0) -fix_cmap.cpp: if (comm->me == 0) { -fix_cmap.cpp: if (comm->me == 0) -fix_cmap.cpp: if (comm->me == 0) fclose(fp); -fix_cmap.cpp: if (comm->me == 0) { -fix_deform.cpp: if (comm->me == 0) { -fix_deprecated.cpp: if (lmp->comm->me == 0) -fix_deprecated.cpp: if (lmp->comm->me == 0) -fix_dt_reset.cpp: strcmp(output->dump[i]->style,"xtc") == 0) && comm->me == 0) -fix_group.cpp: if (warn && comm->me == 0) -fix_halt.cpp: if (comm->me == 0 && msgflag == YESMSG) error->message(FLERR,message); -fix_langevin.cpp: random = new RanMars(lmp,seed + comm->me); -fix_langevin.cpp: if (temperature->igroup != igroup && comm->me == 0) -fix_move.cpp: if (comm->me == 0) { -fix_neigh_history.cpp: int nmypage = comm->nthreads; -fix_neigh_history.cpp: comm->reverse_comm_fix(this,0); -fix_neigh_history.cpp: comm->reverse_comm_fix_variable(this); -fix_neigh_history.cpp: int nmypage = comm->nthreads; -fix_neigh_history.cpp: if (comm->me == 0) { -fix_nh.cpp: if (comm->me == 0) { -fix_nh.cpp: if (temperature->igroup != 0 && comm->me == 0) -fix_nve_limit.cpp: if (comm->me == 0) -fix_pour.cpp: if (comm->layout != Comm::LAYOUT_TILED) { -fix_pour.cpp: if (comm->myloc[2] == comm->procgrid[2]-1 && -fix_pour.cpp: if (comm->mysplit[2][1] == 1.0 && -fix_pour.cpp: if (comm->layout != Comm::LAYOUT_TILED) { -fix_pour.cpp: if (comm->myloc[1] == comm->procgrid[1]-1 && -fix_pour.cpp: if (comm->mysplit[1][1] == 1.0 && -fix_press_berendsen.cpp: if (temperature->igroup != 0 && comm->me == 0) -fix_property_atom.cpp: if (flag && comm->me == 0) -fix_recenter.cpp: if (flag && comm->me == 0) -fix_restrain.cpp: comm->me,update->ntimestep)); -fix_restrain.cpp: comm->me,update->ntimestep)); -fix_restrain.cpp: comm->me,update->ntimestep)); -fix_restrain.cpp: comm->me,update->ntimestep)); -fix_restrain.cpp: ids[m][2],comm->me,update->ntimestep)); -fix_restrain.cpp: ids[m][2],comm->me,update->ntimestep)); -fix_restrain.cpp: ids[m][2],ids[m][3],comm->me, -fix_restrain.cpp: ids[m][2],ids[m][3],comm->me, -fix_restrain.cpp: comm->me,x[i1][0],x[i1][1],x[i1][2], -fix_restrain.cpp: comm->me,x[i2][0],x[i2][1],x[i2][2], -fix_restrain.cpp: comm->me,x[i3][0],x[i3][1],x[i3][2], -fix_restrain.cpp: comm->me,x[i4][0],x[i4][1],x[i4][2]); -fix_spring_chunk.cpp: if (comm->me == 0) { -fix_spring_chunk.cpp: if (comm->me == 0) -fix_spring_rg.cpp: if (comm->me == 0) { -fix_store.cpp: // PERATOM may be comm->exchanged before filled by caller -fix_store.cpp: if (comm->me == 0) { -fix_temp_berendsen.cpp: if (temperature->igroup != igroup && comm->me == 0) -fix_temp_berendsen.cpp: if (comm->me == 0) { -fix_temp_csld.cpp: random = new RanMars(lmp,seed + comm->me); -fix_temp_csld.cpp: if (temperature->igroup != igroup && comm->me == 0) -fix_temp_csld.cpp: int nsize = PRNGSIZE*comm->nprocs+2; // pRNG state per proc + nprocs + energy -fix_temp_csld.cpp: if (comm->me == 0) { -fix_temp_csld.cpp: list[1] = comm->nprocs; -fix_temp_csld.cpp: if (comm->me == 0) { -fix_temp_csld.cpp: if (nprocs != comm->nprocs) { -fix_temp_csld.cpp: if (comm->me == 0) -fix_temp_csld.cpp: } else random->set_state(list+2+comm->me*103); -fix_temp_csvr.cpp: random = new RanMars(lmp,seed + comm->me); -fix_temp_csvr.cpp: if (comm->me == 0) { -fix_temp_csvr.cpp: if (temperature->igroup != igroup && comm->me == 0) -fix_temp_csvr.cpp: int nsize = PRNGSIZE*comm->nprocs+2; // pRNG state per proc + nprocs + energy -fix_temp_csvr.cpp: if (comm->me == 0) { -fix_temp_csvr.cpp: list[1] = comm->nprocs; -fix_temp_csvr.cpp: if (comm->me == 0) { -fix_temp_csvr.cpp: if (nprocs != comm->nprocs) { -fix_temp_csvr.cpp: if (comm->me == 0) -fix_temp_csvr.cpp: } else random->set_state(list+2+comm->me*103); -fix_temp_rescale.cpp: if (temperature->igroup != igroup && comm->me == 0) -fix_temp_rescale.cpp: if (comm->me == 0) { -fix_wall_gran_region.cpp: if (comm->me) return; -fix_wall_reflect.cpp: if (nrigid && comm->me == 0) -force.cpp: if (comm->me == 0) { -group.cpp: // pass list to all other procs via comm->ring() -group.cpp: comm->ring(n,sizeof(tagint),list,1,molring,nullptr,(void *)this); -group.cpp: callback from comm->ring() -imbalance_neigh.cpp: if (comm->me == 0 && !did_warn) -improper.cpp: memory->create(eatom,comm->nthreads*maxeatom,"improper:eatom"); -improper.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"improper:vatom"); -improper.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"improper:cvatom"); -improper.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); -improper.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); -improper_cvff.cpp: if (comm->me == 0) { -improper_deprecated.cpp: if (lmp->comm->me == 0) -improper_harmonic.cpp: if (comm->me == 0) { -improper_hybrid.cpp: int me = comm->me; -improper_umbrella.cpp: if (comm->me == 0) { -info.cpp: if (comm->me != 0) return; -info.cpp: commstyles[comm->style], commlayout[comm->layout], -info.cpp: comm->ghost_velocity ? "yes" : "no"); -info.cpp: if (comm->mode == 0) -info.cpp: comm->get_comm_cutoff()); -info.cpp: if (comm->mode == 1) { -info.cpp: if (comm->cutusermulti) cut = MAX(cut,comm->cutusermulti[i]); -info.cpp: fmt::print(out,"Nprocs = {}, Nthreads = {}\n",comm->nprocs,comm->nthreads); -info.cpp: fmt::print(out,"Processor grid = {} x {} x {}\n",comm->procgrid[0], -info.cpp: comm->procgrid[1], comm->procgrid[2]); -info.cpp: style = commstyles[comm->style]; -info.cpp: bytes += comm->memory_usage(); -input.cpp: comm->modify_params(narg,arg); -input.cpp: if (comm->style == 0) return; -input.cpp: if (comm->style == 1) return; -input.cpp: comm->set_processors(narg,arg); -irregular.cpp: can be used in place of comm->exchange() -irregular.cpp: if (!preassign) comm->coord2proc_setup(); -irregular.cpp: mproclist[nsendatom] = comm->coord2proc(x[i],igx,igy,igz); -irregular.cpp: if not, caller can decide to use comm->exchange() instead -irregular.cpp: if (comm->layout == Comm::LAYOUT_TILED) return 1; -irregular.cpp: // cannot check via comm->procneigh since it ignores PBC -irregular.cpp: int *myloc = comm->myloc; -irregular.cpp: int *procgrid = comm->procgrid; -irregular.cpp: comm->coord2proc(x[i],igx,igy,igz); -kspace.cpp: if ((qsqsum == 0.0) && (comm->me == 0) && warn_nocharge && warning_flag) { -kspace.cpp: if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message); -kspace.cpp: if (comm->me == 0) { -kspace.cpp: if ((table_accuracy > spr) && (comm->me == 0)) -kspace.cpp: if (slab_volfactor < 2.0 && comm->me == 0) -kspace_deprecated.cpp: if (lmp->comm->me == 0) -lammps.cpp: const int me = comm->me; -lammps.cpp: comm->init(); // comm must come after force, modify, neighbor, atom -lattice.cpp: if (comm->me == 0) -library.cpp: && (lmp->comm->me == 0)) { -library.cpp: && (lmp->comm->me == 0)) { -library.cpp: lmp->comm->set_proc_grid(); -library.cpp: if (strcmp(keyword,"world_rank") == 0) return lmp->comm->me; -library.cpp: if (strcmp(keyword,"world_size") == 0) return lmp->comm->nprocs; -library.cpp: if (strcmp(keyword,"nthreads") == 0) return lmp->comm->nthreads; -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: int nprocs = lmp->comm->nprocs; -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: int nprocs = lmp->comm->nprocs; -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) -library.cpp: if (lmp->comm->me == 0) lmp->error->warning(FLERR,msg); -min.cpp: if (comm->me == 0) -min.cpp: if (comm->me == 0 && screen) { -min.cpp: if (comm->me == 0 && screen) -min.cpp: comm->setup(); -min.cpp: comm->exchange(); -min.cpp: comm->borders(); -min.cpp: // atoms may have migrated in comm->exchange() -min.cpp: if (force->newton) comm->reverse_comm(); -min.cpp: comm->setup(); -min.cpp: comm->exchange(); -min.cpp: comm->borders(); -min.cpp: // atoms may have migrated in comm->exchange() -min.cpp: if (force->newton) comm->reverse_comm(); -min.cpp: comm->forward_comm(); -min.cpp: comm->setup(); -min.cpp: comm->exchange(); -min.cpp: comm->borders(); -min.cpp: comm->reverse_comm(); -min_fire.cpp: if (comm->me == 0 && logfile) { -modify.cpp: if (comm->me == 0 && checkall) -modify.cpp: if (fix[ifix]->igroup != igroup && comm->me == 0) -modify.cpp: if (comm->me == 0) -modify.cpp: if (comm->me == 0) -modify.cpp: int me = comm->me; -modify.cpp: int me = comm->me; -modify.cpp: if (flag && comm->me == 0) { -modify.cpp: if (flag && comm->me == 0) { -molecule.cpp: me = comm->me; -nbin_multi.cpp: // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost -nbin_multi.cpp: // include dimension-dependent extension via comm->cutghost -nbin_multi.cpp: double *cutghost = comm->cutghost; -nbin_standard.cpp: // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost -nbin_standard.cpp: // include dimension-dependent extension via comm->cutghost -nbin_standard.cpp: double *cutghost = comm->cutghost; -neighbor.cpp: if (!same && comm->me == 0) print_pairwise_info(); -neighbor.cpp: if (comm->me == 0) printf("SAME flag %d\n",same); -neighbor.cpp: const double cutghost = MAX(cutneighmax,comm->cutghostuser); -neigh_list.cpp: int nmypage = comm->nthreads; -neigh_list.cpp: if (comm->me != 0) return; -neigh_list.cpp: int nmypage = comm->nthreads; -ntopo.cpp: me = comm->me; -ntopo.cpp: nprocs = comm->nprocs; -output.cpp: if (thermo->modified && comm->me == 0) -output.cpp: if (strchr(arg[1],'%')) multiproc = comm->nprocs; -output.cpp: mbavg /= comm->nprocs; -output.cpp: if (comm->me == 0) -pair_beck.cpp: int me = comm->me; -pair_beck.cpp: int me = comm->me; -pair_born_coul_dsf.cpp: int me = comm->me; -pair_born_coul_dsf.cpp: if (comm->me == 0) { -pair_born_coul_wolf.cpp: int me = comm->me; -pair_born_coul_wolf.cpp: if (comm->me == 0) { -pair_born.cpp: int me = comm->me; -pair_born.cpp: if (comm->me == 0) { -pair_brownian.cpp: random = new RanMars(lmp,seed + comm->me); -pair_brownian.cpp: if (force->newton_pair == 0 && comm->me == 0) -pair_brownian.cpp: int me = comm->me; -pair_brownian.cpp: int me = comm->me; -pair_brownian.cpp: random = new RanMars(lmp,seed + comm->me); -pair_buck_coul_cut.cpp: int me = comm->me; -pair_buck_coul_cut.cpp: if (comm->me == 0) { -pair_buck.cpp: int me = comm->me; -pair_buck.cpp: if (comm->me == 0) { -pair_colloid.cpp: if (comm->me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); -pair_colloid.cpp: if (comm->me == 0) { -pair_colloid.cpp: int me = comm->me; -pair_coul_cut.cpp: int me = comm->me; -pair_coul_cut.cpp: if (comm->me == 0) { -pair_coul_debye.cpp: if (comm->me == 0) { -pair_coul_dsf.cpp: int me = comm->me; -pair_coul_dsf.cpp: if (comm->me == 0) { -pair_coul_streitz.cpp: if (comm->me == 0) { -pair_coul_streitz.cpp: if (comm->me != 0) { -pair_coul_wolf.cpp: int me = comm->me; -pair_coul_wolf.cpp: if (comm->me == 0) { -pair.cpp: if (tail_flag && domain->nonperiodic && comm->me == 0) -pair.cpp: if (!compute_flag && tail_flag && comm->me == 0) -pair.cpp: if (!compute_flag && offset_flag && comm->me == 0) -pair.cpp: if (flag && comm->me == 0) -pair.cpp: if (comm->me == 0) -pair.cpp: if (comm->me == 0) -pair.cpp: memory->create(eatom,comm->nthreads*maxeatom,"pair:eatom"); -pair.cpp: memory->create(vatom,comm->nthreads*maxvatom,6,"pair:vatom"); -pair.cpp: memory->create(cvatom,comm->nthreads*maxcvatom,9,"pair:cvatom"); -pair.cpp: if (comm->me == 0) { -pair.cpp: if ((comm->me == 0) && (epair)) -pair.cpp: if (comm->me == 0) -pair.cpp: if (comm->me == 0) fprintf(fp,"%d %.15g %.15g %.15g\n",i+1,r,e,f); -pair.cpp: if (comm->me == 0) fclose(fp); -pair.cpp: double bytes = comm->nthreads*maxeatom * sizeof(double); -pair.cpp: bytes += comm->nthreads*maxvatom*6 * sizeof(double); -pair.cpp: bytes += comm->nthreads*maxcvatom*9 * sizeof(double); -pair_deprecated.cpp: if (lmp->comm->me == 0) -pair_deprecated.cpp: if (lmp->comm->me == 0) -pair_dpd.cpp: random = new RanMars(lmp,seed + comm->me); -pair_dpd.cpp: if (comm->ghost_velocity == 0) -pair_dpd.cpp: if (force->newton_pair == 0 && comm->me == 0) error->warning(FLERR, -pair_dpd.cpp: int me = comm->me; -pair_dpd.cpp: if (comm->me == 0) { -pair_dpd.cpp: random = new RanMars(lmp,seed + comm->me); -pair_dpd_tstat.cpp: random = new RanMars(lmp,seed + comm->me); -pair_dpd_tstat.cpp: int me = comm->me; -pair_dpd_tstat.cpp: if (comm->me == 0) { -pair_dpd_tstat.cpp: random = new RanMars(lmp,seed + comm->me); -pair_gauss.cpp: int me = comm->me; -pair_gauss.cpp: if (comm->me == 0) { -pair_gran_hertz_history.cpp: comm->forward_comm_pair(this); -pair_gran_hooke.cpp: comm->forward_comm_pair(this); -pair_gran_hooke_history.cpp: comm->forward_comm_pair(this); -pair_gran_hooke_history.cpp: if (comm->ghost_velocity == 0) -pair_gran_hooke_history.cpp: int me = comm->me; -pair_gran_hooke_history.cpp: if (comm->me == 0) { -pair_granular.cpp: comm->forward_comm_pair(this); -pair_granular.cpp: if (comm->ghost_velocity == 0) -pair_granular.cpp: int me = comm->me; -pair_hybrid.cpp: int me = comm->me; -pair_lj96_cut.cpp: int me = comm->me; -pair_lj96_cut.cpp: int me = comm->me; -pair_lj_charmm_coul_charmm.cpp: int me = comm->me; -pair_lj_charmm_coul_charmm.cpp: if (comm->me == 0) { -pair_lj_charmmfsw_coul_charmmfsh.cpp: if ((comm->me == 0) && (force->qqr2e != force->qqr2e_charmm_real)) -pair_lj_charmmfsw_coul_charmmfsh.cpp: if ((comm->me == 0) && (force->qqr2e == force->qqr2e_charmm_real)) -pair_lj_charmmfsw_coul_charmmfsh.cpp: int me = comm->me; -pair_lj_charmmfsw_coul_charmmfsh.cpp: if (comm->me == 0) { -pair_lj_cubic.cpp: int me = comm->me; -pair_lj_cubic.cpp: int me = comm->me; -pair_lj_cut_coul_cut.cpp: int me = comm->me; -pair_lj_cut_coul_cut.cpp: if (comm->me == 0) { -pair_lj_cut_coul_debye.cpp: if (comm->me == 0) { -pair_lj_cut_coul_dsf.cpp: int me = comm->me; -pair_lj_cut_coul_dsf.cpp: if (comm->me == 0) { -pair_lj_cut_coul_wolf.cpp: int me = comm->me; -pair_lj_cut_coul_wolf.cpp: int me = comm->me; -pair_lj_cut.cpp: int me = comm->me; -pair_lj_cut.cpp: int me = comm->me; -pair_lj_cut_tip4p_cut.cpp: int me = comm->me; -pair_lj_cut_tip4p_cut.cpp: if (comm->me == 0) { -pair_lj_expand.cpp: int me = comm->me; -pair_lj_expand.cpp: if (comm->me == 0) { -pair_lj_gromacs_coul_gromacs.cpp: int me = comm->me; -pair_lj_gromacs_coul_gromacs.cpp: if (comm->me == 0) { -pair_lj_gromacs.cpp: int me = comm->me; -pair_lj_gromacs.cpp: int me = comm->me; -pair_lj_smooth.cpp: int me = comm->me; -pair_lj_smooth.cpp: int me = comm->me; -pair_lj_smooth_linear.cpp: int me = comm->me; -pair_lj_smooth_linear.cpp: int me = comm->me; -pair_lubricate.cpp: // no need to do this if not shearing since comm->ghost_velocity is set -pair_lubricate.cpp: comm->forward_comm_pair(this); -pair_lubricate.cpp: if (comm->ghost_velocity == 0) -pair_lubricate.cpp: int me = comm->me; -pair_lubricate.cpp: int me = comm->me; -pair_lubricate_poly.cpp: // no need to do this if not shearing since comm->ghost_velocity is set -pair_lubricate_poly.cpp: comm->forward_comm_pair(this); -pair_lubricate_poly.cpp: if (comm->ghost_velocity == 0) -pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU.cpp: comm->forward_comm_pair(this); -pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU.cpp: comm->forward_comm_pair(this); -pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU.cpp: comm->forward_comm_pair(this); -pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU.cpp: comm->forward_comm_pair(this); -pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU.cpp: comm->forward_comm_pair(this); -pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU.cpp: comm->forward_comm_pair(this); -pair_lubricateU.cpp: if (newton_pair) comm->reverse_comm(); // not really needed -pair_lubricateU.cpp: if (comm->ghost_velocity == 0) -pair_lubricateU.cpp: int me = comm->me; -pair_lubricateU.cpp: int me = comm->me; -pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU_poly.cpp: comm->forward_comm_pair(this); -pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU_poly.cpp: comm->forward_comm_pair(this); -pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); -pair_lubricateU_poly.cpp: comm->forward_comm_pair(this); -pair_lubricateU_poly.cpp: if (newton_pair) comm->reverse_comm(); // not really needed -pair_lubricateU_poly.cpp: if (comm->ghost_velocity == 0) -pair_lubricateU_poly.cpp: if (!comm->me) { -pair_mie_cut.cpp: int me = comm->me; -pair_mie_cut.cpp: int me = comm->me; -pair_morse.cpp: int me = comm->me; -pair_morse.cpp: if (comm->me == 0) { -pair_soft.cpp: int me = comm->me; -pair_soft.cpp: if (comm->me == 0) { -pair_table.cpp: if (comm->me == 0) { -pair_tip4p_cut.cpp: int me = comm->me; -pair_tip4p_cut.cpp: if (comm->me == 0) { -pair_ufm.cpp: int me = comm->me; -pair_ufm.cpp: int me = comm->me; -pair_yukawa.cpp: int me = comm->me; -pair_yukawa.cpp: if (comm->me == 0) { -pair_zbl.cpp: int me = comm->me; -pair_zbl.cpp: int me = comm->me; -pair_zero.cpp: int me = comm->me; -pair_zero.cpp: int me = comm->me; -potential_file_reader.cpp: if (comm->me != 0) { -random_mars.cpp: //if (comm->me == 0) printf("%d %ld %ld %g %ld\n", -read_data.cpp: if (comm->nprocs == 1) n = static_cast (atom->natoms); -read_data.cpp: else n = static_cast (LB_FACTOR * atom->natoms / comm->nprocs); -read_data.cpp: comm->set_proc_grid(); -read_data.cpp: comm->set_proc_grid(); -read_data.cpp: // do comm->init() but not comm->setup() b/c pair/neigh cutoffs not yet set -read_data.cpp: // need call to map_set() b/c comm->exchange clears atom map -read_data.cpp: if (comm->me == 0) -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_data.cpp: int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf); -read_data.cpp: int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf); -read_data.cpp: int eof = comm->read_lines_from_file(fp,nsq,MAXLINE,buf); -read_data.cpp: int eof = comm->read_lines_from_file(fp,nbondtypes,MAXLINE,buf); -read_data.cpp: int eof = comm->read_lines_from_file(fp,nangletypes,MAXLINE,buf); -read_data.cpp: int eof = comm->read_lines_from_file(fp,ndihedraltypes,MAXLINE,buf); -read_data.cpp: int eof = comm->read_lines_from_file(fp,nimpropertypes,MAXLINE,buf); -read_data.cpp: eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); -read_dump.cpp: comm->set_proc_grid(0); -read_restart.cpp: comm->set_proc_grid(); -read_restart.cpp: if (comm->me == 0) -read_restart.cpp: if (nprocs_file != comm->nprocs && me == 0) -read_restart.cpp: comm->nprocs)); -read_restart.cpp: if (comm->user_procgrid[0] != 0 && -read_restart.cpp: procgrid[0] != comm->user_procgrid[0]) flag = 1; -read_restart.cpp: if (comm->user_procgrid[1] != 0 && -read_restart.cpp: procgrid[1] != comm->user_procgrid[1]) flag = 1; -read_restart.cpp: if (comm->user_procgrid[2] != 0 && -read_restart.cpp: procgrid[2] != comm->user_procgrid[2]) flag = 1; -read_restart.cpp: if (comm->me ==0) -read_restart.cpp: comm->mode = read_int(); -read_restart.cpp: comm->cutghostuser = read_double(); -read_restart.cpp: comm->ghost_velocity = read_int(); -read_restart.cpp: if (comm->me ==0) -read_restart.cpp: if (comm->me ==0) -read_restart.cpp: if (comm->me ==0) -read_restart.cpp: if (comm->me ==0) -read_restart.cpp: if (comm->me ==0) -read_restart.cpp: if (comm->me ==0) -region_deprecated.cpp: if (lmp->comm->me == 0) -replicate.cpp: int me = comm->me; -replicate.cpp: int nprocs = comm->nprocs; -replicate.cpp: if (comm->me == 0) -replicate.cpp: comm->set_proc_grid(); -replicate.cpp: if (comm->layout != Comm::LAYOUT_TILED) { -replicate.cpp: if (comm->myloc[0] == 0) sublo[0] -= epsilon[0]; -replicate.cpp: if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += epsilon[0]; -replicate.cpp: if (comm->myloc[1] == 0) sublo[1] -= epsilon[1]; -replicate.cpp: if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += epsilon[1]; -replicate.cpp: if (comm->myloc[2] == 0) sublo[2] -= epsilon[2]; -replicate.cpp: if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += epsilon[2]; -replicate.cpp: if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0]; -replicate.cpp: if (comm->mysplit[0][1] == 1.0) subhi[0] += epsilon[0]; -replicate.cpp: if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1]; -replicate.cpp: if (comm->mysplit[1][1] == 1.0) subhi[1] += epsilon[1]; -replicate.cpp: if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2]; -replicate.cpp: if (comm->mysplit[2][1] == 1.0) subhi[2] += epsilon[2]; -reset_atom_ids.cpp: if (comm->me == 0) utils::logmesg(lmp,"Resetting atom IDs ...\n"); -reset_atom_ids.cpp: // initialize system since comm->borders() will be invoked -reset_atom_ids.cpp: comm->setup(); -reset_atom_ids.cpp: comm->exchange(); -reset_atom_ids.cpp: comm->borders(); -reset_atom_ids.cpp: comm->forward_comm_array(1,newIDs); -reset_atom_ids.cpp: int me = comm->me; -reset_atom_ids.cpp: int nprocs = comm->nprocs; -reset_atom_ids.cpp: int nreturn = comm->rendezvous(1,nlocal,(char *) atombuf,sizeof(AtomRvous), -reset_atom_ids.cpp: // rptr->comm->me,i,n,in[i].ibin,binlo,binhi); -reset_atom_ids.cpp: // pass outbuf of IDRvous datums back to comm->rendezvous -reset_mol_ids.cpp: if (comm->me == 0) utils::logmesg(lmp,"Resetting molecule IDs ...\n"); -reset_mol_ids.cpp: // initialize system since comm->borders() will be invoked -reset_mol_ids.cpp: comm->setup(); -reset_mol_ids.cpp: comm->exchange(); -reset_mol_ids.cpp: comm->borders(); -reset_mol_ids.cpp: if (comm->me == 0) { -respa.cpp: if (comm->me == 0) { -respa.cpp: if (flag && comm->me == 0) -respa.cpp: if (modify->nfix == 0 && comm->me == 0) -respa.cpp: if (comm->me == 0 && screen) { -respa.cpp: comm->setup(); -respa.cpp: comm->exchange(); -respa.cpp: comm->borders(); -respa.cpp: if (newton[ilevel]) comm->reverse_comm(); -respa.cpp: comm->setup(); -respa.cpp: comm->exchange(); -respa.cpp: comm->borders(); -respa.cpp: if (newton[ilevel]) comm->reverse_comm(); -respa.cpp: comm->setup(); -respa.cpp: comm->exchange(); -respa.cpp: comm->borders(); -respa.cpp: comm->forward_comm(); -respa.cpp: comm->forward_comm(); -respa.cpp: comm->reverse_comm(); -set.cpp: if (comm->me == 0) utils::logmesg(lmp,"Setting atom values ...\n"); -set.cpp: if (comm->me == 0) { -set.cpp: RanMars *ranmars = new RanMars(lmp,seed + comm->me); -set.cpp: // init entire system since comm->exchange is done -set.cpp: if (comm->me == 0) utils::logmesg(lmp," system init for set ...\n"); -set.cpp: comm->setup(); -set.cpp: comm->exchange(); -set.cpp: comm->borders(); -special.cpp: comm->rendezvous(RVOUS,nlocal,(char *) idbuf,sizeof(IDRvous),0,proclist, -special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), -special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), -special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), -special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), -special.cpp: int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous), -special.cpp: if (comm->me == 0) From 852e4efc6f5f9e3601d67b9742ebdab90cef983e Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 2 Feb 2021 14:50:30 -0700 Subject: [PATCH 0075/1217] Updating documentation/examples, patching comm_modify cutoff/multi command --- doc/src/comm_modify.rst | 54 ++++++++++++++++++++++++-------------- doc/src/neigh_modify.rst | 38 ++++++++++++++++++--------- doc/src/neighbor.rst | 6 ++--- examples/multi/in.colloid | 4 +-- examples/multi/in.granular | 2 +- src/comm.cpp | 20 +++++--------- src/comm.h | 2 ++ src/comm_brick.cpp | 26 +++++++++++++----- src/comm_tiled.cpp | 23 ++++++++++++---- 9 files changed, 113 insertions(+), 62 deletions(-) diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index a3f7dba4eb..489ab407ee 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -15,12 +15,15 @@ Syntax .. parsed-literal:: - *mode* value = *single* or *multi* = communicate atoms within a single or multiple distances + *mode* value = *single*, *multi*, or *multi/old* = communicate atoms within a single or multiple distances *cutoff* value = Rcut (distance units) = communicate atoms from this far away - *cutoff/multi* type value + *cutoff/multi* collection value + collection = atom collection or collection range (supports asterisk notation) + value = Rcut (distance units) = communicate atoms for selected types from this far away + *reduce/multi* arg = none = reduce number of communicated ghost atoms for multi style + *cutoff/multi/old* type value type = atom type or type range (supports asterisk notation) value = Rcut (distance units) = communicate atoms for selected types from this far away - *multi/reduce* arg = none = reduce number of communicated ghost atoms for multi style *group* value = group-ID = only communicate atoms in the group *vel* value = *yes* or *no* = do or do not communicate velocity info with ghost atoms @@ -29,7 +32,7 @@ Examples .. code-block:: LAMMPS - comm_modify mode multi + comm_modify mode multi reduce/multi comm_modify mode multi group solvent comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0 comm_modify vel yes @@ -63,13 +66,18 @@ sub-domain. The distance is by default the maximum of the neighbor cutoff across all atom type pairs. For many systems this is an efficient algorithm, but for systems with -widely varying cutoffs for different type pairs, the *multi* mode can -be faster. In this case, each atom type is assigned its own distance +widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can +be faster. In *multi*, each atom is assigned to a collection which should +correspond to a set of atoms with similar interaction cutoffs. +In this case, each atom collection is assigned its own distance cutoff for communication purposes, and fewer atoms will be -communicated. See the :doc:`neighbor multi ` command for a -neighbor list construction option that may also be beneficial for -simulations of this kind. The *multi* mode is compatable with both the -*multi* and *multi/old* neighbor styles. +communicated. in *multi/old*, a similar technique is used but atoms +are grouped by atom type. See the :doc:`neighbor multi ` and +:doc:`neighbor multi/old ` commands for +neighbor list construction options that may also be beneficial for +simulations of this kind. The *multi* communiction mode is only compatable +with the *multi* neighbor style. The *multi/old* communication mode is compatble +with both the *multi* and *multi/old* neighbor styles. The *cutoff* keyword allows you to extend the ghost cutoff distance for communication mode *single*\ , which is the distance from the borders @@ -89,18 +97,24 @@ warning is printed, if this bond based estimate is larger than the communication cutoff used. The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to -communication mode *multi* instead. Since in this case the communication -cutoffs are determined per atom type, a type specifier is needed and -cutoff for one or multiple types can be extended. Also ranges of types -using the usual asterisk notation can be given. For granular pair styles, -the default cutoff is set to the sum of the current maximum atomic radii -for each type. +communication mode *multi* instead. Since the communication +cutoffs are determined per atom collections, a collection specifier is needed and +cutoff for one or multiple collections can be extended. Also ranges of collections +using the usual asterisk notation can be given. +Note that the arguments for *cutoff/multi* are parsed right before each +simulation to account for potential changes in the number of collections. +Custom cutoffs are preserved between runs but if collections are redefined, +one may want to respecify communication cutoffs. +For granular pair styles,the default cutoff is set to the sum of the +current maximum atomic radii for each collection. +The *cutoff/multi/old* option is similar to *cutoff/multi* except it +operates on atom types as opposed to collections. -The *multi/reduce* option applies to *multi* and sets communication -cutoffs for different sized particles based on the largest interaction distance -between two particles in the same multi grouping. This reduces the number of +The *reduce/multi* option applies to *multi* and sets the communication +cutoff for a particle equal to the maximum interaction distance between particles +in the same collection. This reduces the number of ghost atoms that need to be communicated. This method is only compatible with the -*multi* neighbor style and requires only half neighbor lists and Newton on. +*multi* neighbor style and requires a half neighbor list and Newton on. See the :doc:`neighbor multi ` command for more information. These are simulation scenarios in which it may be useful or even diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index c6f573ef08..6ee21d7419 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -14,7 +14,7 @@ Syntax .. parsed-literal:: - keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *multi/custom* + keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *collection/type* or *collection/interval* *delay* value = N N = delay building until this many steps since last build *every* value = M @@ -47,9 +47,12 @@ Syntax N = max number of neighbors of one atom *binsize* value = size size = bin size for neighbor list construction (distance units) - *multi/custom* values = N arg1 ... argN - N = number of custom groups - arg = N separate types or ranges of types (see below) + *collection/type* values = N arg1 ... argN + N = number of custom collections + arg = N separate lists of types (see below) + *collection/interval* values = N arg1 ... argN + N = number of custom collections + arg = N separate cutoffs for intervals (see below) Examples """""""" @@ -61,7 +64,8 @@ Examples neigh_modify exclude group frozen frozen check no neigh_modify exclude group residue1 chain3 neigh_modify exclude molecule/intra rigid - neigh_modify multi/custom 2 1*2 3*4 + neigh_modify collection/type 2 1*2,5 3*4 + neigh_modify collection/interval 2 1.0 10.0 Description """"""""""" @@ -192,8 +196,9 @@ atom can have. The *binsize* option allows you to specify what size of bins will be used in neighbor list construction to sort and find neighboring atoms. By default, for :doc:`neighbor style bin `, LAMMPS uses bins -that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi `, the bins are 1/2 the size of the minimum pair -cutoff. Typically these are good values for minimizing the time for +that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi `, +the bins are 1/2 the size of the collection interaction cutoff. +Typically these are good values for minimizing the time for neighbor list construction. This setting overrides the default. If you make it too big, there is little overhead due to looping over bins, but more atoms are checked. If you make it too @@ -201,19 +206,28 @@ small, the optimal number of atoms is checked, but bin overhead goes up. If you set the binsize to 0.0, LAMMPS will use the default binsize of 1/2 the cutoff. -The *multi/custom* option allows you to define custom groups of atom +The *collection/type* option allows you to define custom collections of atom types for the *multi* neighbor mode. By grouping atom types with similar cutoffs, one may be able to improve performance by reducing -overhead. You must first specify the number of custom groups N to be -defined followed by N ranges of types. The range can be specified as a +overhead. You must first specify the number of custom collections N to be +defined followed by N lists of types. Each list consists of a series of type +ranges separated by commas. The range can be specified as a single numeric value, or a wildcard asterisk can be used to specify a range of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For example, if M = the number of atom types, then an asterisk with no numeric values means all types from 1 to M. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to M (inclusive). A middle asterisk means all types from m to n (inclusive). -Note that any atom types not included in a custom group will be automatically -placed within a separate group. +Note that all atom types must be included in a custom collection. + +The *collection/interval* option provides a similar capability. +This command allows a user to define custom collections by specifying a +series of cutoff intervals. LAMMPS will automatically sort atoms into these intervals +based on their type-dependent cutoffs or their finite size. +You must first specify the number of custom collections N to be +defined followed by N values representing the upper cutoff of each interval. +This command is particularly useful for granular pairstyles where the interaction distance +of particles depends on their radius and may not depend on their atom type. Restrictions """""""""""" diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index 52d59dae75..bd58f7045d 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -56,13 +56,13 @@ the largest cutoff distance between any pair of atom types and a single set of bins is defined to search over for all atom types. This can be inefficient if one pair of types has a very long cutoff, but other type pairs have a much shorter cutoff. The *multi* style uses -different sized bins for groups of different sized particles. Different +different sized bins for collections of different sized particles. Different sets of bins are then used to construct the neighbor lists as as further described by Shire, Hanley, and Stratford :ref:`(Shire) `. This imposes some extra setup overhead, but the searches themselves -may be much faster. By default, separate groups of particles are defined +may be much faster. By default, separate collections of particles are defined for each atom type. For systems with two or more types with similar -cutoffs, one can reduce the extra overhead by defining custom groupings +cutoffs, one can reduce the extra overhead by defining custom collections using the :doc:`neigh_modify ` command. See the :doc:`comm_modify mode bytype ` command for compatible communication options that may be beneficial for simulations of this kind. diff --git a/examples/multi/in.colloid b/examples/multi/in.colloid index b332560777..835032f2e2 100644 --- a/examples/multi/in.colloid +++ b/examples/multi/in.colloid @@ -30,8 +30,8 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency neighbor 1 multi #multi/old -neigh_modify delay 0 multi/custom 2 1*4 5 -comm_modify mode multi multi/reduce +neigh_modify delay 0 collection/type 2 1*4 5 +comm_modify mode multi reduce/multi # colloid potential diff --git a/examples/multi/in.granular b/examples/multi/in.granular index 8f1743f90d..f43e9505e4 100644 --- a/examples/multi/in.granular +++ b/examples/multi/in.granular @@ -29,7 +29,7 @@ velocity all create 1.44 87287 loop geom neighbor 1 multi #multi/old neigh_modify delay 0 -comm_modify mode multi vel yes multi/reduce +comm_modify mode multi vel yes reduce/multi # colloid potential diff --git a/src/comm.cpp b/src/comm.cpp index 3f2d4ecde6..c84f0249ef 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -35,7 +35,7 @@ #include "update.h" #include - +#include #ifdef _OPENMP #include #endif @@ -59,6 +59,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) cutghostuser = 0.0; cutusermulti = nullptr; cutusermultiold = nullptr; + ncollections_prior = 0; ghost_velocity = 0; user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0; @@ -339,24 +340,17 @@ void Comm::modify_params(int narg, char **arg) error->all(FLERR,"Use cutoff keyword to set cutoff in single mode"); if (mode == Comm::MULTIOLD) error->all(FLERR,"Use cutoff/multi/old keyword to set cutoff in multi/old mode"); - if (domain->box_exist == 0) + if (domain->box_exist == 0) error->all(FLERR, "Cannot set cutoff/multi before simulation box is defined"); - ncollections = neighbor->ncollections; - if (iarg+3 > narg) - error->all(FLERR,"Illegal comm_modify command"); - if (cutusermulti == nullptr) { - memory->create(cutusermulti,ncollections,"comm:cutusermulti"); - for (i=0; i < ncollections; ++i) - cutusermulti[i] = -1.0; - } - utils::bounds(FLERR,arg[iarg+1],1,ncollections,nlo,nhi,error); + + // save arguments so they can be parsed in comm->setup() + // ncollections can be changed by neigh_modify commands cut = utils::numeric(FLERR,arg[iarg+2],false,lmp); cutghostuser = MAX(cutghostuser,cut); if (cut < 0.0) error->all(FLERR,"Invalid cutoff in comm_modify command"); - for (i=nlo; i<=nhi; ++i) - cutusermulti[i] = cut; + usermultiargs.emplace_back(arg[iarg+1], cut); iarg += 3; } else if (strcmp(arg[iarg],"cutoff/multi/old") == 0) { int i,nlo,nhi; diff --git a/src/comm.h b/src/comm.h index 877941523c..2afdfd8765 100644 --- a/src/comm.h +++ b/src/comm.h @@ -33,6 +33,8 @@ class Comm : protected Pointers { double cutghost[3]; // cutoffs used for acquiring ghost atoms double cutghostuser; // user-specified ghost cutoff (mode == 0) double *cutusermulti; // per collection user ghost cutoff (mode == 1) + std::vector> usermultiargs; + // collection args for custom ghost cutoffs double *cutusermultiold; // per type user ghost cutoff (mode == 2) int recv_from_partition; // recv proc layout from this partition int send_to_partition; // send my proc layout to this partition diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index ca0fea8757..3cb841d20f 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -30,6 +30,7 @@ #include #include +#include using namespace LAMMPS_NS; @@ -194,12 +195,9 @@ void CommBrick::setup() if (mode == Comm::MULTI) { // build initial collection array - neighbor->build_collection(0); - - if(cutusermulti and ncollections != neighbor->ncollections) - error->all(FLERR, "Cannot change number of collections after defining comm_modify multi/cutoff"); - else ncollections = neighbor->ncollections; - + neighbor->build_collection(0); + ncollections = neighbor->ncollections; + // reallocate memory for multi-style communication at setup if ncollections change if(ncollections_prior != ncollections){ if(multilo) free_multi(); @@ -207,8 +205,24 @@ void CommBrick::setup() allocate_multi(maxswap); memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); + memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); + for(i = ncollections_prior; i < ncollections; i++) + cutusermulti[i] = -1.0; + ncollections_prior = ncollections; } + + // parse any cutoff/multi commands + int nhi, nlo; + for(auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { + utils::bounds(FLERR,it->first,1,ncollections,nlo,nhi,error); + if(nhi >= ncollections) + error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command"); + for (j=nlo; j<=nhi; ++j) + cutusermulti[j] = it->second; + } + usermultiargs.clear(); + double **cutcollectionsq = neighbor->cutcollectionsq; // If using multi/reduce, communicate particles a distance equal diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index accdbf7b04..c06ad52d6c 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -31,6 +31,7 @@ #include #include +#include using namespace LAMMPS_NS; @@ -182,12 +183,8 @@ void CommTiled::setup() if (mode == Comm::MULTI) { // build collection from scratch as it is needed for atom exchange neighbor->build_collection(0); - - if(cutusermulti and ncollections != neighbor->ncollections) - error->all(FLERR, "Cannot change number of collections after defining comm_modify multi/cutoff"); - ncollections = neighbor->ncollections; - + // allocate memory for multi-style communication at setup as ncollections can change if(ncollections_prior != ncollections){ memory->destroy(cutghostmulti); @@ -197,8 +194,24 @@ void CommTiled::setup() for(i = 0; i < maxswap; i ++) grow_swap_send_multi(i,DELTA_PROCS); + memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); + for(i = ncollections_prior; i < ncollections; i++) + cutusermulti[i] = -1.0; + ncollections_prior = ncollections; + } + + // parse any cutoff/multi commands + int nhi, nlo; + for(auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { + utils::bounds(FLERR,it->first,1,ncollections,nlo,nhi,error); + if(nhi >= ncollections) + error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command"); + + for (j=nlo; j<=nhi; ++j) + cutusermulti[j] = it->second; } + usermultiargs.clear(); double **cutcollectionsq = neighbor->cutcollectionsq; // If using multi/reduce, communicate particles a distance equal From 56841ba9123635e2da4302f4afb8ee7390231d39 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 2 Feb 2021 18:05:19 -0700 Subject: [PATCH 0076/1217] Fixing typo in pair gran, fixing bugs in communication and neighbor --- src/GRANULAR/pair_granular.cpp | 6 +++--- src/comm.cpp | 7 +++++++ src/neighbor.cpp | 2 +- src/nstencil.cpp | 1 + 4 files changed, 12 insertions(+), 4 deletions(-) diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 0f1fbd49f3..e9da16c760 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -1831,9 +1831,9 @@ double PairGranular::atom2cut(int i) cut = atom->radius[i]*2; if(beyond_contact) { - int itype = atom->type[i] + int itype = atom->type[i]; if(normal_model[itype][itype] == JKR) { - cut += pulloffdistance(cut, cut, itype, itype); + cut += pulloff_distance(cut, cut, itype, itype); } } @@ -1856,7 +1856,7 @@ double PairGranular::radii2cut(double r1, double r2) for(int i = 0; i < n; i++){ for(int j = 0; j < n; j++){ if(normal_model[i][j] == JKR) { - temp = pulloffdistance(r1, r2, i, j); + temp = pulloff_distance(r1, r2, i, j); if(temp > cut) cut = temp; } } diff --git a/src/comm.cpp b/src/comm.cpp index c84f0249ef..33e4b894d5 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -735,6 +735,13 @@ double Comm::get_comm_cutoff() maxcommcutoff)); } + // Check maximum interval size for neighbor multi + if(neighbor->interval_collection_flag){ + for(int i = 0; i < neighbor->ncollections; i++){ + maxcommcutoff = MAX(maxcommcutoff, neighbor->collection2cut[i]); + } + } + return maxcommcutoff; } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 16aca434f1..2671553a07 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -2655,7 +2655,7 @@ void Neighbor::build_collection(int istart) collection[i] = -1; for(icollection = 0; icollection < ncollections; icollection++){ - if(collection2cut[icollection] > cut) { + if(collection2cut[icollection] >= cut) { collection[i] = icollection; break; } diff --git a/src/nstencil.cpp b/src/nstencil.cpp index c6ed76b6eb..ca8c3156e3 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -354,6 +354,7 @@ void NStencil::create_setup() if (sy*binsizey_multi[bin_collection] < stencil_range) sy++; sz = static_cast (stencil_range*bininvz_multi[bin_collection]); if (sz*binsizez_multi[bin_collection] < stencil_range) sz++; + if (dimension == 2) sz = 0; stencil_sx_multi[i][j] = sx; stencil_sy_multi[i][j] = sy; From 606b33ea03e824ef9061c5d2f7aa87d0df793c8e Mon Sep 17 00:00:00 2001 From: tc387 Date: Fri, 5 Feb 2021 16:05:37 -0600 Subject: [PATCH 0077/1217] Added fix_charge_regulation source code and documentation. --- doc/src/fix_charge_regulation.rst | 184 +++ examples/USER/misc/charge_regulation/README | 7 + .../misc/charge_regulation/data_acid.chreg | 235 +++ .../misc/charge_regulation/data_polymer.chreg | 264 ++++ .../USER/misc/charge_regulation/in_acid.chreg | 40 + .../misc/charge_regulation/in_polymer.chreg | 35 + .../misc/charge_regulation/log_acid.lammps | 163 ++ .../misc/charge_regulation/log_polymer.lammps | 181 +++ src/USER-MISC/README | 1 + src/USER-MISC/fix_charge_regulation.cpp | 1335 +++++++++++++++++ src/USER-MISC/fix_charge_regulation.h | 117 ++ 11 files changed, 2562 insertions(+) create mode 100644 doc/src/fix_charge_regulation.rst create mode 100644 examples/USER/misc/charge_regulation/README create mode 100644 examples/USER/misc/charge_regulation/data_acid.chreg create mode 100644 examples/USER/misc/charge_regulation/data_polymer.chreg create mode 100644 examples/USER/misc/charge_regulation/in_acid.chreg create mode 100644 examples/USER/misc/charge_regulation/in_polymer.chreg create mode 100644 examples/USER/misc/charge_regulation/log_acid.lammps create mode 100644 examples/USER/misc/charge_regulation/log_polymer.lammps create mode 100644 src/USER-MISC/fix_charge_regulation.cpp create mode 100644 src/USER-MISC/fix_charge_regulation.h diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst new file mode 100644 index 0000000000..585761e8a9 --- /dev/null +++ b/doc/src/fix_charge_regulation.rst @@ -0,0 +1,184 @@ + +.. Yuan documentation master file, created by + sphinx-quickstart on Sat Jan 30 14:06:22 2021. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + tc387: Multiple text additions/changes, Feb 2 2021 +.. index:: fix fix_charge_regulation + +fix_charge_regulation command +============================= +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID charge_regulation cation_type anion_type keyword value(s) + +* ID, group-ID are documented in fix command +* charge_regulation = style name of this fix command +* cation_type = atom type of free cations +* anion_type = atom type of free anions + +* zero or more keyword/value pairs may be appended + + .. parsed-literal:: + + keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves* + *pH* value = pH of the solution + *pKa* value = acid dissociation constant + *pKb* value = base dissociation constant + *pIp* value = chemical potential of free cations + *pIm* value = chemical potential of free anions + *pKs* value = solution self-dissociation constant + *acid_type* = atom type of acid groups + *base_type* = atom type of base groups + *lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers) + *temp* value = temperature + *tempfixid* value = fix ID of temperature thermostat + *nevery* value = invoke this fix every nevery steps + *nmc* value = number of charge regulation MC moves to attempt every nevery steps + *xrd* value = cutoff distance for acid/base reaction + *seed* value = random # seed (positive integer) + *tag* value = yes or no (yes: The code assign unique tags to inserted ions; no: The tag of all inserted ions is "0") + *group* value = group-ID, inserted ions are assigned to group group-ID. Can be used multiple times to assign inserted ions to multiple groups. + *onlysalt* values = flag charge_cation charge_anion. + flag = yes or no (yes: the fix performs only ion insertion/deletion, no: perform acid/base dissociation and ion insertion/deletion) + charge_cation, charge_anion = value of cation/anion charge, must be an integer (only specify if flag = yes) + *pmcmoves* values = pmcA pmcB pmcI - MC move fractions for acid ionization (pmcA), base ionization (pmcB) and free ion exchange (pmcI) + +Examples +"""""""" +.. code-block:: LAMMPS + + fix chareg all charge_regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT + + fix chareg all charge_regulation 1 2 pIp 3 pIm 3 tempfixid fT tag yes onlysalt yes 2 -1 + +Description +""""""""""" +This fix performs Monte Carlo (MC) sampling of charge regulation and exchange of ions with a reservoir as discussed in :ref:`(Curk1) ` and :ref:`(Curk2) `. +The implemented method is largely analogous to the grand-reaction ensemble method in :ref:`(Landsgesell) `. +The implementation is parallelized, compatible with existing LAMMPS functionalities, and applicable to any system utilizing discreet, ionizable groups or surface sites. + + +Specifically, the fix implements the following three types of MC moves, which discretely change the charge state of individual particles and insert ions into the systems: :math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{X}^+`, :math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{X}^-`, +and :math:`\emptyset \rightleftharpoons Z^-\mathrm{X}^{Z^+}+Z^+\mathrm{X}^{-Z^-}`. +In the former two types of reactions, Monte Carlo moves alter the charge value of specific atoms (:math:`\mathrm{A}`, :math:`\mathrm{B}`) and simultaneously insert a counterion to preserve the charge neutrality of the system, modeling the dissociation/association process. +The last type of reaction performs grand canonical MC exchange of ion pairs with a (fictitious) reservoir. + +In our implementation "acid" refers to particles that can attain charge :math:`q=\{0,-1\}` and "base" to particles with :math:`q=\{0,1\}`, +whereas the MC exchange of free ions allows any integer charge values of :math:`{Z^+}` and :math:`{Z^-}`. + +Here we provide several practical examples for modeling charge regulation effects in solvated systems. +An acid ionization reaction (:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{H}^+`) can be defined via a single line in the input file + +.. code-block:: LAMMPS + + fix acid_reaction all charge_regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 7.0 pIm 7.0 + +where the fix attempts to charge :math:`\mathrm{A}` (discharge :math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and insert (delete) a proton (atom type 2). Besides, the fix implements self-ionization reaction of water :math:`\emptyset \rightleftharpoons \mathrm{H}^++\mathrm{OH}^-`. +However, this approach is highly inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of both protons and hydroxyl ions is low, resulting in a relatively low acceptance rate of MC moves. + +A more efficient way is to allow salt ions to +participate in ionization reactions, which can be easily achieved via + +.. code-block:: LAMMPS + + fix acid_reaction all charge_regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0 + +where particles of atom type 4 and 5 are the salt cations and anions, both at chemical potential pI=2.0, see :ref:`(Curk1) ` and :ref:`(Landsgesell) ` for more details. + + + Similarly, we could have simultanously added a base ionization reaction (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`) + +.. code-block:: LAMMPS + + fix base_reaction all charge_regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0 + +where the fix will attempt to charge :math:`\mathrm{B}` (discharge :math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. +If neither the acid or the base type is specified, for example, + +.. code-block:: LAMMPS + + fix salt_reaction all charge_regulation 4 5 pIp 2.0 pIm 2.0 + +the fix simply inserts or deletes an ion pair of a free cation (atom type 4) and a free anion (atom type 5) as done in a conventional grand-canonical MC simulation. + + +The fix is compatible with LAMMPS sub-packages such as *molecule* or *rigid*. That said, the acid and base particles can be part of larger molecules or rigid bodies. Free ions that are inserted to or deleted from the system must be defined as single particles (no bonded interactions allowed) and cannot be part of larger molecules or rigid bodies. If *molecule* package is used, all inserted ions have a molecule ID equal to zero. + +Note that LAMMPS implicitly assumes a constant number of particles (degrees of freedom). Since using this fix alters the total number of particles during the simulation, any thermostat used by LAMMPS, such as NVT or Langevin, must use a dynamic calculation of system temperature. This can be achieved by specifying a dynamic temperature compute (e.g. dtemp) and using it with the desired thermostat, e.g. a Langevin thermostat: + +.. code-block:: LAMMPS + + compute dtemp all temp + compute_modify dtemp dynamic yes + fix fT all langevin 1.0 1.0 1.0 123 + fix_modify fT temp dtemp + +The chemical potential units (e.g. pH) are in the standard log10 representation assuming reference concentration :math:`\rho_0 = \mathrm{mol}/\mathrm{l}`. +Therefore, to perform the internal unit conversion, the length (in nanometers) of the LAMMPS unit length +must be specified via *lunit_nm* (default is set to the Bjerrum length in water at room temprature *lunit_nm* = 0.72nm). For example, in the dilute ideal solution limit, the concentration of free ions +will be :math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. + +The temperature used in MC acceptance probability is set by *temp*. This temperature should be the same as the temperature set by the molecular dynamics thermostat. For most purposes, it is probably best to use *tempfixid* keyword which dynamically sets the temperature equal to the chosen MD thermostat temperature, in the example above we assumed the thermostat fix-ID is *fT*. The inserted particles attain a random velocity corresponding to the specified temperature. Using *tempfixid* overrides any fixed temperature set by *temp*. + +The *xrd* keyword can be used to restrict the inserted/deleted counterions to a specific radial distance from an acid or base particle that is currently participating in a reaction. This can be used to simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* / 2, where *L* is the smallest box dimension, the radial restriction is automatically turned off and free ion can be inserted or deleted anywhere in the simulation box. + +If the *tag yes* is used, every inserted atom gets a unique tag ID, otherwise, the tag of every inserted atom is set to 0. *tag yes* might cause an integer overflow in very long simulations since the tags are unique to every particle and thus increase with every successful particle insertion. + +The *pmcmoves* keyword sets the relative probability of attempting the three types of MC moves (reactions): acid charging, base charging, and ion pair exchange. +The fix only attempts to perform particle charging MC moves if *acid_type* or *base_type* is defined. Otherwise fix only performs free ion insertion/deletion. For example, if *acid_type* is not defined, *pmcA* is automatically set to 0. The vector *pmcmoves* is automatically normalized, for example, if set to *pmcmoves* 0 0.33 0.33, the vector would be normalized to [0,0.5,0.5]. + +The *only_salt* option can be used to perform multivalent grand-canonical ion-exchange moves. If *only_salt yes* is used, no charge exchange is performed, only ion insertion/deletion (*pmcmoves* is set to [0,0,1]), but ions can be multivalent. In the example above, an MC move would consist of three ion insertion/deletion to preserve the charge neutrality of the system. + +The *group* keyword can be used to add inserted particles to a specific group-ID. All inserted particles are automatically added to group *all*. + + +Output +"""""" +This fix computes a global vector of length 8, which can be accessed by various output commands. The vector values are the following global cumulative quantities: + +* 1 = cumulative MC attempts +* 2 = cumulative MC successes +* 3 = current # of neutral acid atoms +* 4 = current # of -1 charged acid atoms +* 5 = current # of neutral base atoms +* 6 = current # of +1 charged acid atoms +* 7 = current # of free cations +* 8 = current # of free anions + + +Restrictions +"""""""""""" +This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. +See the :doc:`Build package ` doc page for more info. + +The :doc:`atom_style `, used must contain the charge property, for example, the style could be *charge* or *full*. Only usable for 3D simulations. Atoms specified as free ions cannot be part of rigid bodies or molecules and cannot have bonding interactions. The scheme is limited to integer charges, any atoms with non-integer charges will not be considered by the fix. + +Note: Region restrictions are not yet implemented. + +Related commands +"""""""""""""""" + +:doc:`fix gcmc `, +:doc:`fix atom/swap ` + +Default +""""""" +pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs=14.0; acid_type = -1; base_type = -1; lunit_nm = 0.72; temp = 1.0; nevery = 100; nmc = 100; xrd = 0; seed = 2345; tag = no; onlysalt = no, pmcmoves = 0.33 0.33 0.33, group-ID = all + +---------- + +.. _Curk1: + +**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Coarse-grained simulation of charge regulation using LAMMPS", preprint (2021). + +.. _Curk2: + +**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL (2021) + +.. _Landsgesell: + +**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, “Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning,” Macromolecules 53, 3007–3020 (2020). diff --git a/examples/USER/misc/charge_regulation/README b/examples/USER/misc/charge_regulation/README new file mode 100644 index 0000000000..e0be86d7e4 --- /dev/null +++ b/examples/USER/misc/charge_regulation/README @@ -0,0 +1,7 @@ +This directory has two input scripts that illustrates how to use fix charge_regulation in LAMMPS to perform coarse-grained molecular dynamics (MD) simulations with incorporation of charge regulation effects. The charge regulation is implemented via Monte Carlo (MC) sampling following the reaction ensemble MC approach, producing a MC/MD hybrid tool for modeling charge regulation in solvated systems. + +The script `in_acid.chreg` sets up a simple weak acid electrolyte (pH=7,pKa=6,pI=3). Four different types of MC moves are implemented: acid protonation & de-protonation, and monovalent ion pair insertion and deletion. Note here we have grouped all free monovalent ions into a single type, a physically natural choice on the level of coarse-grained primitive electrolyte models, which increases the calculation performance but has no effects on thermodynamic observables. The variables such as pH, pKa, pI, and lb at the top of the input script can be adjusted to play with various simulation parameters. The cumulative MC attempted moves and cumulative number of accepted moves, as well as, current number of neutral and charged acid particles, neutral and charged base particles (in this example always 0), and the current number of free cations and anions in the system are printed in the `log_acid.lammps`. + +The script `in_polymer.chreg` sets up a weak polyelectrolyte chain of N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7 and salt pI=3. In this example, we choose to treat salt ions, protons, and hydroxyl ions separately, which results in 5 types of MC moves: acid [type 1] protonation & de-protonation (with protons [type 4] insertion & deletion), acid [type 1] protonation & de-protonation (with salt cation [type 2] insertion & deletion), water self-ionization (insertion and deletion of proton [type4] and hydroxyl ion [type 5] pair), insertion and deletion of monovalent salt pair [type 2 and type 3] , insertion and deletion +Of a proton [type4] and salt anion [type 3]. The current number of neutral and charged acid particles, the current number of free salt cations and anions, and the current number of protons and hydroxyl ions are printed in the `log_polymer.lammps`. + diff --git a/examples/USER/misc/charge_regulation/data_acid.chreg b/examples/USER/misc/charge_regulation/data_acid.chreg new file mode 100644 index 0000000000..edc7082ad0 --- /dev/null +++ b/examples/USER/misc/charge_regulation/data_acid.chreg @@ -0,0 +1,235 @@ +LAMMPS data file generated by get_input.py + +219 atoms +3 atom types +-2.5000000000000000e+01 2.5000000000000000e+01 xlo xhi +-2.5000000000000000e+01 2.5000000000000000e+01 ylo yhi +-2.5000000000000000e+01 2.5000000000000000e+01 zlo zhi + +Masses + +1 1 +2 1 +3 1 + +Atoms + +1 1 0 2.5983275747497636 -8.368052973860795 20.001288664343484 +2 1 -1 -18.182868728594865 -8.079792367885453 8.253737231981816 +3 1 -1 -17.437350808966414 8.120411567445771 10.747650340639332 +4 1 -1 6.502476583291578 -23.497326620756837 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6.272776670877239 10.035821052072265 22.22030412319301 +216 3 -1 14.689947575936934 -7.785907120217196 0.5033983092114553 +217 3 -1 23.173937996535116 -21.041572031861037 -21.057283440516468 +218 3 -1 -6.015120142466472 6.3962924962024985 21.58241945230285 +219 3 -1 -0.77667042466472 0.3962848125024985 1.582473830285 \ No newline at end of file diff --git a/examples/USER/misc/charge_regulation/data_polymer.chreg b/examples/USER/misc/charge_regulation/data_polymer.chreg new file mode 100644 index 0000000000..2c5bd3e1ed --- /dev/null +++ b/examples/USER/misc/charge_regulation/data_polymer.chreg @@ -0,0 +1,264 @@ +##A Weak PE Chain of N=80 + +160 atoms +79 bonds + +5 atom types +1 bond types + +-50 50 xlo xhi +-50 50 ylo yhi +-50 50 zlo zhi + +Masses + +1 1.0 +2 1.0 +3 1.0 +4 1.0 +5 1.0 + +Atoms +# atom_id molecule_id atom_type charge x y z +1 1 1 -1 0 0 -48.37753795169063 +2 1 1 -1 0 0 -47.255075903381254 +3 1 1 -1 0 0 -46.13261385507188 +4 1 1 -1 0 0 -45.01015180676251 +5 1 1 -1 0 0 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-6.273374390373085 +117 0 2 1 13.909148568042937 4.921040289518388 12.111069913598996 +118 0 2 1 6.728324076730296 -48.44092815223126 -35.92436883370601 +119 0 2 1 -18.121173967321912 -15.76903395165283 2.2495451015454933 +120 0 2 1 -11.75253233489407 -45.82569982175387 -12.477142440015896 +121 0 2 1 1.9713864197144133 17.961034900064007 32.97992150691711 +122 0 2 1 -3.993384770632943 -47.63120435620297 27.75490859098018 +123 0 2 1 -0.32208279553454844 -47.30616152402566 -22.751109302380367 +124 0 2 1 -0.135777029397957 23.88599790464609 -31.87440560354473 +125 0 2 1 -6.123924906817393 -2.038519565120424 45.4809181974626 +126 0 2 1 -29.622588299895046 42.40404115712096 6.640479709229595 +127 0 2 1 -11.694512971272673 19.983258641775762 -38.152427411711145 +128 0 2 1 -20.93721440637313 39.46397829322392 -45.52708262202337 +129 0 2 1 34.13340147809369 36.14268504987945 -23.978137043267044 +130 0 2 1 -37.422309952611485 29.181841318883087 27.55677757161692 +131 0 2 1 30.11314373799594 18.721794400471353 1.5553303682670574 +132 0 2 1 -7.3563467211571805 46.84253369205935 -39.84708490437832 +133 0 2 1 -3.695927445484358 2.494403998274727 -7.634369981832755 +134 0 2 1 44.09701173592077 17.717328437831043 31.54108326477207 +135 0 2 1 48.070189931616795 10.601166369398662 -28.28574863896286 +136 0 2 1 -7.044858382811761 -42.080663380241766 -1.4369925734636553 +137 0 2 1 -12.485032488076918 23.87106169116919 6.178803347562642 +138 0 2 1 -15.613232443702309 10.103630885941392 -20.447182948810916 +139 0 2 1 28.610332347774147 37.08335835592116 -19.90280831362493 +140 0 2 1 25.853920233242505 -27.768648181803655 24.971357611943475 +141 0 2 1 9.256159541363296 -23.562096053197934 -4.722701100419371 +142 0 2 1 39.96929397877305 -11.88228547846326 -28.70638149104603 +143 0 2 1 -37.98545134633291 -23.50528193202669 -10.939982626098441 +144 0 2 1 25.40017763114089 -47.49220127581256 15.1783064865064 +145 0 2 1 28.073596076651768 3.6631266774864386 31.54355751177208 +146 0 2 1 -19.596457173068703 46.79824882013442 -12.302655772327597 +147 0 2 1 -36.46192411958321 -2.785830672302666 -25.1901381125736 +148 0 2 1 -27.377389198969894 11.295792272951147 39.32842550184691 +149 0 2 1 32.24967019136358 -20.517755791016402 31.20590722085157 +150 0 2 1 47.70698618147787 9.75462874031868 -28.267447889542563 +151 0 2 1 17.157803106328345 -27.48141290657965 7.7670687016760525 +152 0 2 1 15.089833959419678 5.342811012118396 27.35336620165029 +153 0 2 1 9.836963929211372 -11.047378229392443 -20.960811370690678 +154 0 2 1 44.66600586278604 14.949733274456321 -29.328965994323575 +155 0 2 1 -21.006260382140685 8.492712712433658 -46.31580169190271 +156 0 2 1 -29.970979487850748 -36.46250489415931 26.914372830947457 +157 0 2 1 -1.0821372755756329 -8.453379951300242 -19.95665062432509 +158 0 2 1 -24.033653425909772 -39.51330620205049 20.067656167683793 +159 0 2 1 27.747287624384626 -21.904990435351312 -10.819345241055956 +160 0 2 1 -40.86737066410612 -25.609300376714796 -21.128139356809783 + +Bonds + # bond_id bond_type atom1_id atom2_id +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 5 6 +6 1 6 7 +7 1 7 8 +8 1 8 9 +9 1 9 10 +10 1 10 11 +11 1 11 12 +12 1 12 13 +13 1 13 14 +14 1 14 15 +15 1 15 16 +16 1 16 17 +17 1 17 18 +18 1 18 19 +19 1 19 20 +20 1 20 21 +21 1 21 22 +22 1 22 23 +23 1 23 24 +24 1 24 25 +25 1 25 26 +26 1 26 27 +27 1 27 28 +28 1 28 29 +29 1 29 30 +30 1 30 31 +31 1 31 32 +32 1 32 33 +33 1 33 34 +34 1 34 35 +35 1 35 36 +36 1 36 37 +37 1 37 38 +38 1 38 39 +39 1 39 40 +40 1 40 41 +41 1 41 42 +42 1 42 43 +43 1 43 44 +44 1 44 45 +45 1 45 46 +46 1 46 47 +47 1 47 48 +48 1 48 49 +49 1 49 50 +50 1 50 51 +51 1 51 52 +52 1 52 53 +53 1 53 54 +54 1 54 55 +55 1 55 56 +56 1 56 57 +57 1 57 58 +58 1 58 59 +59 1 59 60 +60 1 60 61 +61 1 61 62 +62 1 62 63 +63 1 63 64 +64 1 64 65 +65 1 65 66 +66 1 66 67 +67 1 67 68 +68 1 68 69 +69 1 69 70 +70 1 70 71 +71 1 71 72 +72 1 72 73 +73 1 73 74 +74 1 74 75 +75 1 75 76 +76 1 76 77 +77 1 77 78 +78 1 78 79 +79 1 79 80 diff --git a/examples/USER/misc/charge_regulation/in_acid.chreg b/examples/USER/misc/charge_regulation/in_acid.chreg new file mode 100644 index 0000000000..32beeda732 --- /dev/null +++ b/examples/USER/misc/charge_regulation/in_acid.chreg @@ -0,0 +1,40 @@ +# Charge regulation lammps for simple weak electrolyte + +units lj +atom_style charge +dimension 3 +boundary p p p +processors * * * +neighbor 3.0 bin +read_data data_acid.chreg + +variable cut_long equal 12.5 +variable nevery equal 100 +variable nmc equal 100 +variable pH equal 7.0 +variable pKa equal 6.0 +variable pIm equal 3.0 +variable pIp equal 3.0 + +variable cut_lj equal 2^(1.0/6.0) +variable lunit_nm equal 0.72 # in the units of nm +velocity all create 1.0 8008 loop geom + +pair_style lj/cut/coul/long ${cut_lj} ${cut_long} +pair_coeff * * 1.0 1.0 ${cut_lj} # charges +kspace_style ewald 1.0e-3 +dielectric 1.0 +pair_modify shift no + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 +fix_modify fT temp dtemp + +fix chareg all charge_regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +thermo 100 +thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] +timestep 0.005 +run 10000 diff --git a/examples/USER/misc/charge_regulation/in_polymer.chreg b/examples/USER/misc/charge_regulation/in_polymer.chreg new file mode 100644 index 0000000000..4dc72a8156 --- /dev/null +++ b/examples/USER/misc/charge_regulation/in_polymer.chreg @@ -0,0 +1,35 @@ +# Charge regulation lammps for a polymer chain +units lj +atom_style full +dimension 3 +boundary p p p +processors * * * +neighbor 3.0 bin +read_data data_polymer.chreg + +bond_style harmonic +bond_coeff 1 100 1.122462 # K R0 +velocity all create 1.0 8008 loop geom + +pair_style lj/cut/coul/long 1.122462 20 +pair_coeff * * 1.0 1.0 1.122462 # charges +kspace_style pppm 1.0e-3 +pair_modify shift no +dielectric 1.0 + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 +fix_modify fT temp dtemp + +fix chareg1 all charge_regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 +fix chareg2 all charge_regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 +fix chareg3 all charge_regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 + +thermo 100 +# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions +thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] +timestep 0.005 +run 10000 diff --git a/examples/USER/misc/charge_regulation/log_acid.lammps b/examples/USER/misc/charge_regulation/log_acid.lammps new file mode 100644 index 0000000000..cbc3661eb1 --- /dev/null +++ b/examples/USER/misc/charge_regulation/log_acid.lammps @@ -0,0 +1,163 @@ +LAMMPS (24 Dec 2020) +Reading data file ... + orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 219 atoms + read_data CPU = 0.001 seconds +Ewald initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:339) + G vector (1/distance) = 0.14221027 + estimated absolute RMS force accuracy = 0.0010128126 + estimated relative force accuracy = 0.0010128126 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +0 atoms in group Fix_CR:exclusion_group:chareg +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 15.5 + ghost atom cutoff = 15.5 + binsize = 7.75, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : lj + Current step : 0 + Time step : 0.005 +Per MPI rank memory allocation (min/avg/max) = 11.91 | 11.91 | 11.91 Mbytes +Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] + 0 -0.054228269 1 0 0 1 99 0 0 109 10 + 100 -0.058672881 0.99159291 100 71 16 84 0 0 92 8 + 200 -0.05399313 0.92006523 200 154 26 74 0 0 85 11 + 300 -0.047035343 0.92728143 300 240 22 78 0 0 85 7 + 400 -0.049597809 1.0617937 400 319 16 84 0 0 92 8 + 500 -0.052409835 1.0006148 500 404 12 88 0 0 97 9 + 600 -0.056012172 0.98059344 600 481 15 85 0 0 92 7 + 700 -0.053639989 0.99572709 700 561 16 84 0 0 94 10 + 800 -0.060026132 0.95764632 800 639 22 78 0 0 84 6 + 900 -0.050785422 0.98399084 900 719 28 72 0 0 82 10 + 1000 -0.062294743 0.97200068 1000 797 26 74 0 0 82 8 + 1100 -0.051269402 1.0064376 1100 877 25 75 0 0 84 9 + 1200 -0.077744839 1.0159098 1200 955 23 77 0 0 88 11 + 1300 -0.084889696 1.1230485 1300 1037 20 80 0 0 90 10 + 1400 -0.059361445 0.96735845 1400 1120 18 82 0 0 93 11 + 1500 -0.052926174 0.95579188 1500 1199 24 76 0 0 86 10 + 1600 -0.052376649 0.99376378 1600 1284 22 78 0 0 89 11 + 1700 -0.052480188 0.96085964 1700 1361 27 73 0 0 84 11 + 1800 -0.065884306 0.96747971 1800 1441 21 79 0 0 84 5 + 1900 -0.054315859 0.95873145 1900 1521 23 77 0 0 84 7 + 2000 -0.037161802 0.93562039 2000 1604 27 73 0 0 79 6 + 2100 -0.034977265 0.97177103 2100 1684 26 74 0 0 85 11 + 2200 -0.047434868 0.97897613 2200 1762 17 83 0 0 93 10 + 2300 -0.047392634 0.96570672 2300 1837 18 82 0 0 92 10 + 2400 -0.044879306 0.98620033 2400 1910 19 81 0 0 89 8 + 2500 -0.069690496 1.0690505 2500 1988 16 84 0 0 91 7 + 2600 -0.081588407 0.97711054 2600 2067 17 83 0 0 92 9 + 2700 -0.06341681 1.0386711 2700 2146 20 80 0 0 85 5 + 2800 -0.045290012 1.0402055 2800 2230 18 82 0 0 91 9 + 2900 -0.046875012 1.0609775 2900 2317 24 76 0 0 86 10 + 3000 -0.031258722 0.93861202 3000 2400 24 76 0 0 85 9 + 3100 -0.04673342 0.90800583 3100 2485 25 75 0 0 90 15 + 3200 -0.054354227 0.94493881 3200 2567 16 84 0 0 94 10 + 3300 -0.053647746 0.92321446 3300 2641 17 83 0 0 94 11 + 3400 -0.031751732 0.93735127 3400 2725 22 78 0 0 92 14 + 3500 -0.053806113 0.98798136 3500 2795 28 72 0 0 84 12 + 3600 -0.040751349 0.84291639 3600 2873 28 72 0 0 84 12 + 3700 -0.051747138 1.072448 3700 2951 24 76 0 0 92 16 + 3800 -0.043420594 1.0076309 3800 3030 26 74 0 0 79 5 + 3900 -0.050845848 1.0250023 3900 3103 29 71 0 0 76 5 + 4000 -0.039837847 1.064111 4000 3182 29 71 0 0 83 12 + 4100 -0.045638995 1.1249685 4100 3262 28 72 0 0 81 9 + 4200 -0.047956491 0.92255907 4200 3348 26 74 0 0 87 13 + 4300 -0.054052822 1.006239 4300 3423 19 81 0 0 90 9 + 4400 -0.053148034 1.0028887 4400 3506 24 76 0 0 83 7 + 4500 -0.062132076 1.0317847 4500 3587 23 77 0 0 82 5 + 4600 -0.04616043 0.99066453 4600 3673 28 72 0 0 82 10 + 4700 -0.066990889 1.0242064 4700 3755 18 82 0 0 90 8 + 4800 -0.0564736 0.91765628 4800 3832 22 78 0 0 91 13 + 4900 -0.052301294 0.95348659 4900 3912 28 72 0 0 81 9 + 5000 -0.062630677 1.0336579 5000 3989 18 82 0 0 92 10 + 5100 -0.053645908 1.0314613 5100 4062 20 80 0 0 85 5 + 5200 -0.062189568 1.0504732 5200 4133 23 77 0 0 84 7 + 5300 -0.049092746 1.0310832 5300 4217 24 76 0 0 82 6 + 5400 -0.051859257 0.99600428 5400 4299 27 73 0 0 80 7 + 5500 -0.065540815 0.98012128 5500 4381 19 81 0 0 92 11 + 5600 -0.071018582 0.9252814 5600 4455 23 77 0 0 84 7 + 5700 -0.066954185 1.0325214 5700 4535 26 74 0 0 82 8 + 5800 -0.064847249 1.0313536 5800 4617 21 79 0 0 90 11 + 5900 -0.063173056 0.95455853 5900 4703 18 82 0 0 92 10 + 6000 -0.064807837 0.97182222 6000 4790 21 79 0 0 91 12 + 6100 -0.07067683 0.91775921 6100 4875 16 84 0 0 94 10 + 6200 -0.071400842 1.0162225 6200 4952 17 83 0 0 87 4 + 6300 -0.078479449 1.0106706 6300 5033 21 79 0 0 84 5 + 6400 -0.083167651 1.0246584 6400 5111 18 82 0 0 90 8 + 6500 -0.092611537 1.0766467 6500 5195 20 80 0 0 88 8 + 6600 -0.096710071 1.0246648 6600 5274 15 85 0 0 91 6 + 6700 -0.073399857 0.94939392 6700 5351 17 83 0 0 92 9 + 6800 -0.062479375 0.9393967 6800 5434 18 82 0 0 93 11 + 6900 -0.065391043 0.93475954 6900 5514 22 78 0 0 89 11 + 7000 -0.045655499 0.98688239 7000 5601 21 79 0 0 90 11 + 7100 -0.061186309 1.0309063 7100 5684 22 78 0 0 87 9 + 7200 -0.074737514 1.0516593 7200 5769 25 75 0 0 80 5 + 7300 -0.075228979 1.0167704 7300 5847 21 79 0 0 86 7 + 7400 -0.06660147 1.0947107 7400 5930 25 75 0 0 87 12 + 7500 -0.071915247 1.10542 7500 6009 24 76 0 0 84 8 + 7600 -0.029974303 0.99202697 7600 6095 28 72 0 0 80 8 + 7700 -0.029024004 1.0390995 7700 6182 28 72 0 0 83 11 + 7800 -0.056250746 0.96393961 7800 6260 18 82 0 0 91 9 + 7900 -0.072178944 0.9833919 7900 6339 21 79 0 0 86 7 + 8000 -0.070377248 1.021342 8000 6419 23 77 0 0 88 11 + 8100 -0.07753283 0.96194312 8100 6493 26 74 0 0 86 12 + 8200 -0.075617309 0.9715344 8200 6576 25 75 0 0 89 14 + 8300 -0.077480013 0.99106705 8300 6662 20 80 0 0 91 11 + 8400 -0.079901928 0.89855112 8400 6744 23 77 0 0 91 14 + 8500 -0.069192745 1.0606791 8500 6822 19 81 0 0 91 10 + 8600 -0.058657202 1.1270217 8600 6898 15 85 0 0 95 10 + 8700 -0.044985397 1.0367419 8700 6979 27 73 0 0 84 11 + 8800 -0.064266376 0.91557003 8800 7060 21 79 0 0 89 10 + 8900 -0.068680533 0.95963643 8900 7133 19 81 0 0 88 7 + 9000 -0.051736144 1.0398547 9000 7213 13 87 0 0 94 7 + 9100 -0.058381436 0.98047663 9100 7290 17 83 0 0 89 6 + 9200 -0.05531014 0.92541631 9200 7368 22 78 0 0 85 7 + 9300 -0.04386907 0.9339658 9300 7454 22 78 0 0 89 11 + 9400 -0.052293168 0.94314034 9400 7539 22 78 0 0 86 8 + 9500 -0.050362046 1.0489028 9500 7617 18 82 0 0 90 8 + 9600 -0.054272227 1.0879161 9600 7697 11 89 0 0 96 7 + 9700 -0.042514179 1.0051505 9700 7771 22 78 0 0 84 6 + 9800 -0.045365018 0.95363669 9800 7850 25 75 0 0 77 2 + 9900 -0.064287274 0.91994667 9900 7928 27 73 0 0 81 8 + 10000 -0.05689162 0.99963208 10000 8011 22 78 0 0 84 6 +Loop time of 19.4452 on 1 procs for 10000 steps with 190 atoms + +Performance: 222162.510 tau/day, 514.265 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.68864 | 0.68864 | 0.68864 | 0.0 | 3.54 +Kspace | 6.7893 | 6.7893 | 6.7893 | 0.0 | 34.92 +Neigh | 0.060782 | 0.060782 | 0.060782 | 0.0 | 0.31 +Comm | 0.047035 | 0.047035 | 0.047035 | 0.0 | 0.24 +Output | 0.0027227 | 0.0027227 | 0.0027227 | 0.0 | 0.01 +Modify | 11.838 | 11.838 | 11.838 | 0.0 | 60.88 +Other | | 0.01878 | | | 0.10 + +Nlocal: 190.000 ave 190 max 190 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 592.000 ave 592 max 592 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2194.00 ave 2194 max 2194 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2194 +Ave neighs/atom = 11.547368 +Neighbor list builds = 10287 +Dangerous builds = 0 +Total wall time: 0:00:19 \ No newline at end of file diff --git a/examples/USER/misc/charge_regulation/log_polymer.lammps b/examples/USER/misc/charge_regulation/log_polymer.lammps new file mode 100644 index 0000000000..87cab63a6c --- /dev/null +++ b/examples/USER/misc/charge_regulation/log_polymer.lammps @@ -0,0 +1,181 @@ +LAMMPS (24 Dec 2020) +Reading data file ... + orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 160 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 79 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:339) + G vector (1/distance) = 0.077106934 + grid = 8 8 8 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00074388331 + estimated relative force accuracy = 0.00074388331 + using double precision KISS FFT + 3d grid and FFT values/proc = 2197 512 +0 atoms in group Fix_CR:exclusion_group:chareg1 +0 atoms in group Fix_CR:exclusion_group:chareg2 +0 atoms in group Fix_CR:exclusion_group:chareg3 +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 23 + ghost atom cutoff = 23 + binsize = 11.5, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : lj + Current step : 0 + Time step : 0.005 +Per MPI rank memory allocation (min/avg/max) = 6.962 | 6.962 | 6.962 Mbytes +Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] + 0 0.49903297 1 0 80 80 0 0 0 + 100 0.63380666 0.87307225 8 72 77 6 1 0 + 200 0.5865464 1.0048645 16 64 81 16 0 1 + 300 0.55802913 1.0499142 19 61 91 29 0 1 + 400 0.44734087 1.0838048 24 56 98 41 0 1 + 500 0.47010775 1.005226 23 57 106 48 0 1 + 600 0.3452105 0.97814306 28 52 109 56 0 1 + 700 0.29208955 0.99766419 32 48 115 67 0 0 + 800 0.27821915 1.0091641 31 49 128 80 1 0 + 900 0.28943788 0.93619239 26 54 145 91 0 0 + 1000 0.22963142 1.0162138 27 53 150 97 0 0 + 1100 0.24238916 0.99146577 31 49 149 100 0 0 + 1200 0.17029095 1.0406453 38 42 144 102 0 0 + 1300 0.15830969 0.94661447 34 46 155 109 0 0 + 1400 0.16698712 1.0116563 35 45 159 114 0 0 + 1500 0.15432936 0.95600941 36 44 162 118 0 0 + 1600 0.16973501 0.98326602 31 49 171 122 0 0 + 1700 0.19725116 0.9915273 33 47 175 128 0 0 + 1800 0.15278999 1.0304873 29 51 193 142 0 0 + 1900 0.17418479 0.99490216 30 50 194 144 0 0 + 2000 0.14238391 0.9638301 32 48 189 141 0 0 + 2100 0.13054378 0.97164976 32 48 192 144 0 0 + 2200 0.092083069 1.0112059 40 40 191 151 0 0 + 2300 0.085175091 1.0070667 39 41 200 159 0 0 + 2400 0.083367076 0.9934796 35 45 208 163 0 0 + 2500 0.11494744 0.97650855 31 49 220 172 1 0 + 2600 0.10796032 0.97047046 34 46 221 175 0 0 + 2700 0.11080141 0.93570013 36 44 223 179 0 0 + 2800 0.096699277 0.97702627 35 45 223 178 0 0 + 2900 0.079403783 1.0870961 32 48 229 181 0 0 + 3000 0.08288836 1.0642515 35 45 231 186 0 0 + 3100 0.094000833 1.0241111 38 42 229 187 0 0 + 3200 0.10011052 1.043594 34 46 235 189 0 0 + 3300 0.096782103 0.99549134 34 46 234 188 0 0 + 3400 0.057703946 1.00292 34 46 236 190 0 0 + 3500 0.074345642 0.95064523 36 44 234 190 0 0 + 3600 0.085872341 0.9759514 35 45 238 192 0 1 + 3700 0.086427565 0.99843063 35 45 240 194 0 1 + 3800 0.076091357 0.98516844 32 48 252 203 0 1 + 3900 0.047187813 1.0063336 37 43 247 204 0 0 + 4000 0.068269223 1.0390369 35 45 248 203 0 0 + 4100 0.074209582 0.99912762 36 44 249 205 0 0 + 4200 0.087016078 1.050265 36 44 246 202 0 0 + 4300 0.081325479 1.0417103 35 45 245 200 0 0 + 4400 0.047345973 0.96517298 39 41 243 202 0 0 + 4500 0.041856955 0.94569673 38 42 245 203 0 0 + 4600 0.049588267 0.99046371 42 38 249 211 0 0 + 4700 0.043079897 1.0098538 43 37 245 208 0 0 + 4800 0.049122913 1.0229995 41 39 247 208 0 0 + 4900 0.059151797 1.0236679 36 44 249 205 0 0 + 5000 0.053806841 1.0308397 42 38 243 205 0 0 + 5100 0.053623833 1.0638841 39 41 246 205 0 0 + 5200 0.086215806 1.0027613 37 43 243 200 0 0 + 5300 0.031422797 1.0338154 38 42 245 203 0 0 + 5400 0.051341116 0.92205149 34 46 246 200 0 0 + 5500 0.039292708 0.97530704 32 48 251 203 0 0 + 5600 0.035215415 1.023123 33 47 246 199 0 0 + 5700 0.054553598 0.95833063 30 50 253 203 0 0 + 5800 0.035699456 1.0721613 37 43 248 205 0 0 + 5900 0.062426908 1.0612245 38 42 252 210 0 0 + 6000 0.056362902 1.0002968 36 44 248 204 0 0 + 6100 0.061550208 0.97270904 38 42 245 203 0 0 + 6200 0.051825485 0.98187623 36 44 253 209 0 0 + 6300 0.052137885 0.98906723 36 44 253 210 1 0 + 6400 0.068218075 1.0511584 36 44 256 212 0 0 + 6500 0.080167413 0.97270144 36 44 252 208 0 0 + 6600 0.052169204 1.0160108 41 39 249 210 0 0 + 6700 0.057313326 0.98033894 38 42 251 209 0 0 + 6800 0.073008094 0.96239565 35 45 256 211 0 0 + 6900 0.060159599 1.0063892 37 43 264 221 0 0 + 7000 0.061738744 1.0031443 39 41 259 218 0 0 + 7100 0.043263424 1.0425248 44 36 255 219 0 0 + 7200 0.052179167 0.99512151 39 41 261 220 0 0 + 7300 0.053258707 1.0171204 43 37 256 219 0 0 + 7400 0.026037532 0.93786837 45 35 259 224 0 0 + 7500 0.029731213 1.0172281 46 34 250 216 0 0 + 7600 0.023118288 0.95628439 42 38 262 224 0 0 + 7700 0.037021854 0.99991854 42 38 263 225 0 0 + 7800 0.050404736 1.0130826 40 40 260 220 0 0 + 7900 0.035658921 0.95772506 40 40 259 219 0 0 + 8000 0.034426806 1.0028052 40 40 254 214 0 0 + 8100 0.041427611 1.0347682 40 40 256 216 0 0 + 8200 0.05986843 0.9804614 38 42 262 220 0 0 + 8300 0.041419023 1.0613186 37 43 264 221 0 0 + 8400 0.065701758 1.0511531 40 40 256 216 0 0 + 8500 0.091954526 0.97190676 37 43 257 214 0 0 + 8600 0.056982532 1.017813 35 45 252 207 0 0 + 8700 0.075615111 1.0148527 29 51 263 212 0 0 + 8800 0.066070082 1.0259454 33 47 260 213 0 0 + 8900 0.055054194 1.0183535 37 43 247 204 0 0 + 9000 0.063070816 1.0266115 39 41 244 203 0 0 + 9100 0.10174156 0.99457684 34 46 246 200 0 0 + 9200 0.071667261 1.033159 33 47 249 202 0 0 + 9300 0.05520096 0.99821492 38 42 243 201 0 0 + 9400 0.050355422 0.99148522 37 43 243 200 0 0 + 9500 0.062314961 1.0042937 36 44 252 208 0 0 + 9600 0.061148899 1.0052132 37 43 254 211 0 0 + 9700 0.078695273 1.0175164 37 43 252 209 0 0 + 9800 0.067487202 1.0110138 35 45 258 213 0 0 + 9900 0.070340779 0.99640142 31 49 263 214 0 0 + 10000 0.037252172 0.99863894 32 48 259 211 0 0 +Loop time of 23.0419 on 1 procs for 10000 steps with 550 atoms + +Performance: 187484.206 tau/day, 433.991 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5444 | 2.5444 | 2.5444 | 0.0 | 11.04 +Bond | 0.025075 | 0.025075 | 0.025075 | 0.0 | 0.11 +Kspace | 4.7385 | 4.7385 | 4.7385 | 0.0 | 20.56 +Neigh | 0.2058 | 0.2058 | 0.2058 | 0.0 | 0.89 +Comm | 0.073087 | 0.073087 | 0.073087 | 0.0 | 0.32 +Output | 0.003464 | 0.003464 | 0.003464 | 0.0 | 0.02 +Modify | 15.417 | 15.417 | 15.417 | 0.0 | 66.91 +Other | | 0.03479 | | | 0.15 + +Nlocal: 550.000 ave 550 max 550 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1023.00 ave 1023 max 1023 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 9644.00 ave 9644 max 9644 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9644 +Ave neighs/atom = 17.534545 +Ave special neighs/atom = 0.85090909 +Neighbor list builds = 7576 +Dangerous builds = 0 +Total wall time: 0:00:23 \ No newline at end of file diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 314fe6146e..ef25a0c116 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -53,6 +53,7 @@ dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18 fix accelerate/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 +fix charge_regulation, Tine Curk and Jiaxing Yuan, tcurk5@gmail.com, 02 Feb 2021 fix electron/stopping/fit, James Stewart (SNL), jstewa .at. sandia.gov, 23 Sep 2020 fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019 fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018 diff --git a/src/USER-MISC/fix_charge_regulation.cpp b/src/USER-MISC/fix_charge_regulation.cpp new file mode 100644 index 0000000000..3bb9de1b27 --- /dev/null +++ b/src/USER-MISC/fix_charge_regulation.cpp @@ -0,0 +1,1335 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Tine Curk (tcurk5@gmail.com) and Jiaxing Yuan (yuanjiaxing123@hotmail.com) +------------------------------------------------------------------------- */ +#include "fix_charge_regulation.h" +#include +#include +#include +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "update.h" +#include "modify.h" +#include "fix.h" +#include "comm.h" +#include "compute.h" +#include "group.h" +#include "domain.h" +#include "region.h" +#include "random_park.h" +#include "force.h" +#include "pair.h" +#include "bond.h" +#include "angle.h" +#include "dihedral.h" +#include "improper.h" +#include "kspace.h" +#include "math_extra.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" +#include "neighbor.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; + +// large energy value used to signal overlap +#define MAXENERGYSIGNAL 1.0e100 +#define MAXENERGYTEST 1.0e50 +#define small 0.0000001 +#define PI 3.1415926 + +/* ---------------------------------------------------------------------- */ +Fix_charge_regulation::Fix_charge_regulation(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), + ngroups(0), groupstrings(NULL), + random_equal(NULL), random_unequal(NULL), + idftemp(NULL), ptype_ID(NULL) { + + // Region restrictions not yet implemented .. + + vector_flag = 1; + size_vector = 8; + global_freq = 1; + extvector = 0; + restart_global = 1; + time_depend = 1; + cr_nmax = 0; + overlap_flag = 0; + energy_stored = 0; + + // necessary to specify the free ion types + cation_type = utils::inumeric(FLERR, arg[3], false, lmp); + anion_type = utils::inumeric(FLERR, arg[4], false, lmp); + + // set defaults and read optional arguments + options(narg - 5, &arg[5]); + + if (nevery <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (nmc < 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (llength_unit_in_nm < 0.0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (*target_temperature_tcp < 0.0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (seed <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (cation_type <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (anion_type <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (reaction_distance < 0.0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (salt_charge[0] <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (salt_charge[1] >= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if ((salt_charge[1] % salt_charge[0] != 0) && (salt_charge[0] % salt_charge[1] != 0)) + error->all(FLERR, + "Illegal fix charge_regulation command, multivalent cation/anion charges are allowed, " + "but must be divisible, e.g. (3,-1) is fine, but (3,-2) is not implemented"); + + if (pmcmoves[0] < 0 || pmcmoves[1] < 0 || pmcmoves[2] < 0) + error->all(FLERR, "Illegal fix charge_regulation command"); + if (acid_type < 0) pmcmoves[0] = 0; + if (base_type < 0) pmcmoves[1] = 0; + // normalize + double psum = pmcmoves[0] + pmcmoves[1] + pmcmoves[2]; + if (psum <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + pmcmoves[0] /= psum; + pmcmoves[1] /= psum; + pmcmoves[2] /= psum; + + force_reneighbor = 1; + next_reneighbor = update->ntimestep + 1; + random_equal = new RanPark(lmp, seed); + random_unequal = new RanPark(lmp, seed); + nacid_attempts = 0; + nacid_successes = 0; + nbase_attempts = 0; + nbase_successes = 0; + nsalt_attempts = 0; + nsalt_successes = 0; +} + +Fix_charge_regulation::~Fix_charge_regulation() { + + memory->destroy(ptype_ID); + + delete random_equal; + delete random_unequal; + + if (group) { + int igroupall = group->find("all"); + neighbor->exclusion_group_group_delete(exclusion_group, igroupall); + } +} + +int Fix_charge_regulation::setmask() { + int mask = 0; + mask |= PRE_EXCHANGE; + return mask; +} + +void Fix_charge_regulation::init() { + + triclinic = domain->triclinic; + + char *id_pe = (char *) "thermo_pe"; + int ipe = modify->find_compute(id_pe); + c_pe = modify->compute[ipe]; + + if (atom->molecule_flag) { + + int flag = 0; + for (int i = 0; i < atom->nlocal; i++) + if (atom->type[i] == cation_type || atom->type[i] == anion_type) + if (atom->molecule[i]) flag = 1; + int flagall = flag; + + MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, world); + if (flagall && comm->me == 0) + error->all(FLERR, "Fix charge regulation cannot exchange individual atoms (ions) belonging to a molecule"); + } + + if (domain->dimension == 2) + error->all(FLERR, "Cannot use fix charge regulation in a 2d simulation"); + + // create a new group for interaction exclusions + // used for attempted atom deletions + // skip if already exists from previous init() + + if (!exclusion_group_bit) { + char **group_arg = new char *[4]; + + // create unique group name for atoms to be excluded + int len = strlen(id) + 30; + group_arg[0] = new char[len]; + sprintf(group_arg[0], "Fix_CR:exclusion_group:%s", id); + group_arg[1] = (char *) "subtract"; + group_arg[2] = (char *) "all"; + group_arg[3] = (char *) "all"; + group->assign(4, group_arg); + exclusion_group = group->find(group_arg[0]); + if (exclusion_group == -1) + error->all(FLERR, "Could not find fix CR exclusion group ID"); + exclusion_group_bit = group->bitmask[exclusion_group]; + + // neighbor list exclusion setup + // turn off interactions between group all and the exclusion group + + int narg = 4; + char **arg = new char *[narg];; + arg[0] = (char *) "exclude"; + arg[1] = (char *) "group"; + arg[2] = group_arg[0]; + arg[3] = (char *) "all"; + neighbor->modify_params(narg, arg); + delete[] group_arg[0]; + delete[] group_arg; + delete[] arg; + } + + // check that no deletable atoms are in atom->firstgroup + // deleting such an atom would not leave firstgroup atoms first + + if (atom->firstgroup >= 0) { + int *mask = atom->mask; + int firstgroupbit = group->bitmask[atom->firstgroup]; + + int flag = 0; + for (int i = 0; i < atom->nlocal; i++) + if ((mask[i] == groupbit) && (mask[i] && firstgroupbit)) flag = 1; + + int flagall; + MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, world); + + if (flagall) + error->all(FLERR, "Cannot do Fix charge regulation on atoms in atom_modify first group"); + } + + // construct group bitmask for all new atoms + // aggregated over all group keywords + + groupbitall = 1 | groupbit; + + for (int igroup = 0; igroup < ngroups; igroup++) { + int jgroup = group->find(groupstrings[igroup]); + if (jgroup == -1) + error->all(FLERR, "Could not find specified fix charge regulation group ID"); + groupbitall |= group->bitmask[jgroup]; + } +} + +void Fix_charge_regulation::pre_exchange() { + + if (next_reneighbor != update->ntimestep) return; + xlo = domain->boxlo[0]; + xhi = domain->boxhi[0]; + ylo = domain->boxlo[1]; + yhi = domain->boxhi[1]; + zlo = domain->boxlo[2]; + zhi = domain->boxhi[2]; + + if (triclinic) { + sublo = domain->sublo_lamda; + subhi = domain->subhi_lamda; + } else { + sublo = domain->sublo; + subhi = domain->subhi; + } + volume = domain->xprd * domain->yprd * domain->zprd; + if (triclinic) domain->x2lamda(atom->nlocal); + domain->pbc(); + comm->exchange(); + atom->nghost = 0; + comm->borders(); + + if (triclinic) domain->lamda2x(atom->nlocal + atom->nghost); + energy_stored = energy_full(); + if (energy_stored > MAXENERGYTEST) + error->warning(FLERR, "Energy of old configuration in fix charge_regulation is > MAXENERGYTEST."); + + if ((reaction_distance > fabs(domain->boxhi[0] - domain->boxlo[0]) / 2) || + (reaction_distance > fabs(domain->boxhi[1] - domain->boxlo[1]) / 2) || + (reaction_distance > fabs(domain->boxhi[2] - domain->boxlo[2]) / 2)) { + error->warning(FLERR, + "reaction distance (rxd) is larger than half the box dimension, resetting default: xrd = 0."); + reaction_distance = 0; + } + // volume in units of (N_A * mol / liter) + volume_rx = (xhi - xlo) * (yhi - ylo) * (zhi - zlo) * pow(llength_unit_in_nm, 3) * 0.602214; + if (reaction_distance < small) { + vlocal_xrd = volume_rx; + } else { + vlocal_xrd = 4.0 * PI * pow(reaction_distance, 3) / 3.0 * pow(llength_unit_in_nm, 3) * 0.602214; + } + beta = 1.0 / (force->boltz * *target_temperature_tcp); + + // reinitialize counters + nacid_neutral = particle_number(acid_type, 0); + nacid_charged = particle_number(acid_type, -1); + nbase_neutral = particle_number(base_type, 0); + nbase_charged = particle_number(base_type, 1); + ncation = particle_number(cation_type, salt_charge[0]); + nanion = particle_number(anion_type, salt_charge[1]); + + + // Attempt exchanges + if (!only_salt_flag) { + + // Do charge regulation + for (int i = 0; i < nmc; i++) { + double rand_number = random_equal->uniform(); + if (rand_number < pmcmoves[0] / 2) { + forward_acid(); + nacid_attempts++; + } else if (rand_number < pmcmoves[0]) { + backward_acid(); + nacid_attempts++; + } else if (rand_number < pmcmoves[0] + pmcmoves[1] / 2) { + forward_base(); + nbase_attempts++; + } else if (rand_number < pmcmoves[0] + pmcmoves[1]) { + backward_base(); + nbase_attempts++; + } else if (rand_number < pmcmoves[0] + pmcmoves[1] + pmcmoves[2] / 2) { + forward_ions(); + nsalt_attempts++; + } else { + backward_ions(); + nsalt_attempts++; + } + } + } else { + // do only ion insertion, multivalent cation/anions are implemented + if (salt_charge[0] >= -salt_charge[1]) { + salt_charge_ratio = -salt_charge[0] / salt_charge[1]; + } else { + salt_charge_ratio = -salt_charge[1] / salt_charge[0]; + } + for (int i = 0; i < nmc; i++) { + double rand_number = random_equal->uniform(); + if (rand_number < 0.5) { + forward_ions_multival(); + nsalt_attempts++; + } else { + backward_ions_multival(); + nsalt_attempts++; + } + } + } + + // assign unique tags to newly inserted ions + if (add_tags_flag && atom->tag_enable) assign_tags(); + + if (triclinic) domain->x2lamda(atom->nlocal); + domain->pbc(); + comm->exchange(); + atom->nghost = 0; + comm->borders(); + if (triclinic) domain->lamda2x(atom->nlocal + atom->nghost); + next_reneighbor = update->ntimestep + nevery; +} + +void Fix_charge_regulation::forward_acid() { + + double energy_before = energy_stored; + double factor; + double *dummyp; + double pos[3]; + pos[0] = 0; + pos[1] = 0; + pos[2] = 0; // acid/base particle position + double pos_all[3]; + int m1 = -1, m2 = -1; + + m1 = get_random_particle(acid_type, 0, 0, dummyp); + if (npart_xrd != nacid_neutral) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + + if (nacid_neutral > 0) { + if (m1 >= 0) { + atom->q[m1] = -1; // assign negative charge to acid + pos[0] = atom->x[m1][0]; + pos[1] = atom->x[m1][1]; + pos[2] = atom->x[m1][2]; + } + npart_xrd2 = ncation; + if (reaction_distance >= small) { + pos_all[0] = pos[0]; + pos_all[1] = pos[1]; + pos_all[2] = pos[2]; + MPI_Allreduce(pos, pos_all, 3, MPI_DOUBLE, MPI_SUM, world); + npart_xrd2 = particle_number_xrd(cation_type, 1, reaction_distance, pos_all); + } + m2 = insert_particle(cation_type, 1, reaction_distance, pos_all); + factor = nacid_neutral * vlocal_xrd * pow(10, -pKa) + * (1 + pow(10, pH - pI_plus)) / ((1 + nacid_charged) * (1 + npart_xrd2)); + + double energy_after = energy_full(); + + if (energy_after < MAXENERGYTEST && + random_equal->uniform() < factor * exp(beta * (energy_before - energy_after))) { + energy_stored = energy_after; + nacid_successes += 1; + ncation++; + nacid_charged++; + nacid_neutral--; + } else { + energy_stored = energy_before; + atom->natoms--; + if (m2 >= 0) { + atom->nlocal--; + } + if (m1 >= 0) { + atom->q[m1] = 0; + } + if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); + } + } +} + +void Fix_charge_regulation::backward_acid() { + + double energy_before = energy_stored; + double factor; + int mask_tmp; + double *dummyp; + double pos[3]; + pos[0] = 0; + pos[1] = 0; + pos[2] = 0; // acid/base particle position + double pos_all[3]; + int m1 = -1, m1_all = -1, m2 = -1, m2_all = -1; + + m1 = get_random_particle(acid_type, -1, 0, dummyp); + if (npart_xrd != nacid_charged) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + + if (nacid_charged > 0) { + if (m1 >= 0) { + atom->q[m1] = 0; + pos[0] = atom->x[m1][0]; + pos[1] = atom->x[m1][1]; + pos[2] = atom->x[m1][2]; + } + if (reaction_distance >= small) { + pos_all[0] = pos[0]; + pos_all[1] = pos[1]; + pos_all[2] = pos[2]; + MPI_Allreduce(pos, pos_all, 3, MPI_DOUBLE, MPI_SUM, world); + } + m2 = get_random_particle(cation_type, 1, reaction_distance, pos_all); + // note: npart_xrd changes everytime get_random_particle is called. + + if (npart_xrd > 0) { + if (m2 >= 0) { + atom->q[m2] = 0; + mask_tmp = atom->mask[m2]; // remember group bits. + atom->mask[m2] = exclusion_group_bit; + } + factor = (1 + nacid_neutral) * vlocal_xrd * pow(10, -pKa) + * (1 + pow(10, pH - pI_plus)) / (nacid_charged * npart_xrd); + + double energy_after = energy_full(); + + if (energy_after < MAXENERGYTEST && + random_equal->uniform() < (1.0 / factor) * exp(beta * (energy_before - energy_after))) { + nacid_successes += 1; + atom->natoms--; + energy_stored = energy_after; + nacid_charged--; + nacid_neutral++; + ncation--; + if (m2 >= 0) { + atom->avec->copy(atom->nlocal - 1, m2, 1); + atom->nlocal--; + } + } else { + energy_stored = energy_before; + if (m1 >= 0) { + atom->q[m1] = -1; + } + if (m2 >= 0) { + atom->q[m2] = 1; + atom->mask[m2] = mask_tmp; + } + } + } else { + if (m1 >= 0) { + atom->q[m1] = -1; + } + } + } +} + +void Fix_charge_regulation::forward_base() { + + double energy_before = energy_stored; + double factor; + double *dummyp; + double pos[3]; + pos[0] = 0; + pos[1] = 0; + pos[2] = 0; // acid/base particle position + double pos_all[3]; + int m1 = -1, m1_all = -1, m2 = -1, m2_all = -1; + + m1 = get_random_particle(base_type, 0, 0, dummyp); + if (npart_xrd != nbase_neutral) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + + if (nbase_neutral > 0) { + if (m1 >= 0) { + atom->q[m1] = 1; // assign negative charge to acid + pos[0] = atom->x[m1][0]; + pos[1] = atom->x[m1][1]; + pos[2] = atom->x[m1][2]; + } + npart_xrd2 = nanion; + if (reaction_distance >= small) { + pos_all[0] = pos[0]; + pos_all[1] = pos[1]; + pos_all[2] = pos[2]; + MPI_Allreduce(pos, pos_all, 3, MPI_DOUBLE, MPI_SUM, world); + npart_xrd2 = particle_number_xrd(anion_type, -1, reaction_distance, pos_all); + } + factor = nbase_neutral * vlocal_xrd * pow(10, -pKb) + * (1 + pow(10, pKs - pH - pI_minus)) / + ((1 + nbase_charged) * (1 + npart_xrd2)); + m2 = insert_particle(anion_type, -1, reaction_distance, pos_all); + + double energy_after = energy_full(); + if (energy_after < MAXENERGYTEST && + random_equal->uniform() < factor * exp(beta * (energy_before - energy_after))) { + energy_stored = energy_after; + nbase_successes += 1; + nbase_charged++; + nbase_neutral--; + nanion++; + } else { + energy_stored = energy_before; + atom->natoms--; + if (m2 >= 0) { + atom->nlocal--; + } + if (m1 >= 0) { + atom->q[m1] = 0; + } + if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); + } + } +} + +void Fix_charge_regulation::backward_base() { + + double energy_before = energy_stored; + double factor; + double *dummyp; + int mask_tmp; + double pos[3]; + pos[0] = 0; + pos[1] = 0; + pos[2] = 0; // acid/base particle position + double pos_all[3]; + int m1 = -1, m1_all = -1, m2 = -1, m2_all = -1; + + m1 = get_random_particle(base_type, 1, 0, dummyp); + if (npart_xrd != nbase_charged) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + + if (nbase_charged > 0) { + if (m1 >= 0) { + atom->q[m1] = 0; + pos[0] = atom->x[m1][0]; + pos[1] = atom->x[m1][1]; + pos[2] = atom->x[m1][2]; + } + if (reaction_distance >= small) { + pos_all[0] = pos[0]; + pos_all[1] = pos[1]; + pos_all[2] = pos[2]; + MPI_Allreduce(pos, pos_all, 3, MPI_DOUBLE, MPI_SUM, world); + } + m2 = get_random_particle(anion_type, -1, reaction_distance, pos_all); + + if (npart_xrd > 0) { + if (m2 >= 0) { + atom->q[m2] = 0; + mask_tmp = atom->mask[m2]; // remember group bits. + atom->mask[m2] = exclusion_group_bit; + } + factor = (1 + nbase_neutral) * vlocal_xrd * pow(10, -pKb) + * (1 + pow(10, pKs - pH - pI_minus)) / (nbase_charged * npart_xrd); + + double energy_after = energy_full(); + + if (energy_after < MAXENERGYTEST && + random_equal->uniform() < (1.0 / factor) * exp(beta * (energy_before - energy_after))) { + nbase_successes += 1; + atom->natoms--; + energy_stored = energy_after; + nbase_charged--; + nbase_neutral++; + nanion--; + if (m2 >= 0) { + atom->avec->copy(atom->nlocal - 1, m2, 1); + atom->nlocal--; + } + } else { + energy_stored = energy_before; + if (m1 >= 0) { + atom->q[m1] = 1; + } + if (m2 >= 0) { + atom->q[m2] = -1; + atom->mask[m2] = mask_tmp; + } + } + } else { + if (m1 >= 0) { + atom->q[m1] = 1; + } + } + } +} + +void Fix_charge_regulation::forward_ions() { + + double energy_before = energy_stored; + double factor; + double *dummyp; + int m1 = -1, m2 = -1; + factor = volume_rx * volume_rx * (pow(10, -pH) + pow(10, -pI_plus)) + * (pow(10, -pKs + pH) + pow(10, -pI_minus)) / + ((1 + ncation) * (1 + nanion)); + + m1 = insert_particle(cation_type, +1, 0, dummyp); + m2 = insert_particle(anion_type, -1, 0, dummyp); + double energy_after = energy_full(); + if (energy_after < MAXENERGYTEST && random_equal->uniform() < factor * exp(beta * (energy_before - energy_after))) { + energy_stored = energy_after; + nsalt_successes += 1; + ncation++; + nanion++; + } else { + energy_stored = energy_before; + atom->natoms--; + if (m1 >= 0) { + atom->nlocal--; + } + atom->natoms--; + if (m2 >= 0) { + atom->nlocal--; + } + if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); + } +} + + +void Fix_charge_regulation::backward_ions() { + + double energy_before = energy_stored; + double factor; + int mask1_tmp, mask2_tmp; + double *dummyp; // dummy pointer + int m1 = -1, m2 = -1; + + m1 = get_random_particle(cation_type, +1, 0, dummyp); + if (npart_xrd != ncation) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (ncation > 0) { + m2 = get_random_particle(anion_type, -1, 0, dummyp); + if (npart_xrd != nanion) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (nanion > 0) { + + // attempt deletion + + if (m1 >= 0) { + atom->q[m1] = 0; + mask1_tmp = atom->mask[m1]; + atom->mask[m1] = exclusion_group_bit; + } + if (m2 >= 0) { + atom->q[m2] = 0; + mask2_tmp = atom->mask[m2]; + atom->mask[m2] = exclusion_group_bit; + } + factor = (volume_rx * volume_rx * (pow(10, -pH) + pow(10, -pI_plus)) * + (pow(10, -pKs + pH) + pow(10, -pI_minus))) / (ncation * nanion); + + double energy_after = energy_full(); + if (energy_after < MAXENERGYTEST && + random_equal->uniform() < (1.0 / factor) * exp(beta * (energy_before - energy_after))) { + energy_stored = energy_after; + nsalt_successes += 1; + ncation--; + nanion--; + + // ions must be deleted in order, otherwise index m could change upon the first deletion + atom->natoms -= 2; + if (m1 > m2) { + if (m1 >= 0) { + atom->avec->copy(atom->nlocal - 1, m1, 1); + atom->nlocal--; + } + if (m2 >= 0) { + atom->avec->copy(atom->nlocal - 1, m2, 1); + atom->nlocal--; + } + } else { + if (m2 >= 0) { + atom->avec->copy(atom->nlocal - 1, m2, 1); + atom->nlocal--; + } + if (m1 >= 0) { + atom->avec->copy(atom->nlocal - 1, m1, 1); + atom->nlocal--; + } + } + if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); + + } else { + energy_stored = energy_before; + + // reassign original charge and mask + if (m1 >= 0) { + atom->q[m1] = 1; + atom->mask[m1] = mask1_tmp; + } + if (m2 >= 0) { + atom->q[m2] = -1; + atom->mask[m2] = mask2_tmp; + } + } + } else { + // reassign original charge and mask + if (m1 >= 0) { + atom->q[m1] = 1; + atom->mask[m1] = mask1_tmp; + } + } + } +} + +void Fix_charge_regulation::forward_ions_multival() { + + double energy_before = energy_stored; + double factor = 1; + double *dummyp; + int mm[salt_charge_ratio + 1];// particle ID array for all ions to be inserted + + if (salt_charge[0] <= -salt_charge[1]) { + // insert one anion and (salt_charge_ratio) cations + + mm[0] = insert_particle(anion_type, salt_charge[1], 0, dummyp); + factor *= volume_rx * pow(10, -pI_minus) / (1 + nanion); + for (int i = 0; i < salt_charge_ratio; i++) { + mm[i + 1] = insert_particle(cation_type, salt_charge[0], 0, dummyp); + factor *= volume_rx * pow(10, -pI_plus) / (1 + ncation + i); + } + } else { + // insert one cation and (salt_charge_ratio) anions + + mm[0] = insert_particle(cation_type, salt_charge[0], 0, dummyp); + factor *= volume_rx * pow(10, -pI_plus) / (1 + ncation); + for (int i = 0; i < salt_charge_ratio; i++) { + mm[i + 1] = insert_particle(anion_type, salt_charge[1], 0, dummyp); + factor *= volume_rx * pow(10, -pI_minus) / (1 + nanion + i); + } + } + + double energy_after = energy_full(); + if (energy_after < MAXENERGYTEST && random_equal->uniform() < factor * exp(beta * (energy_before - energy_after))) { + energy_stored = energy_after; + nsalt_successes += 1; + + if (salt_charge[0] <= -salt_charge[1]) { + ncation += salt_charge_ratio; + nanion++; + } else { + nanion += salt_charge_ratio; + ncation++; + } + } else { + energy_stored = energy_before; + + // delete inserted ions + for (int i = 0; i < salt_charge_ratio + 1; i++) { + atom->natoms--; + if (mm[i] >= 0) { + atom->nlocal--; + } + } + if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); + } +} + +void Fix_charge_regulation::backward_ions_multival() { + + double energy_before = energy_stored; + double factor = 1; + double *dummyp; // dummy pointer + int mm[salt_charge_ratio + 1]; // particle ID array for all deleted ions + double qq[salt_charge_ratio + 1]; // charge array for all deleted ions + int mask_tmp[salt_charge_ratio + 1]; // temporary mask array + + if (salt_charge[0] <= -salt_charge[1]) { + // delete one anion and (salt_charge_ratio) cations + if (ncation < salt_charge_ratio || nanion < 1) return; + + mm[0] = get_random_particle(anion_type, salt_charge[1], 0, dummyp); + if (npart_xrd != nanion) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + factor *= volume_rx * pow(10, -pI_minus) / (nanion); + if (mm[0] >= 0) { + qq[0] = atom->q[mm[0]]; + atom->q[mm[0]] = 0; + mask_tmp[0] = atom->mask[mm[0]]; + atom->mask[mm[0]] = exclusion_group_bit; + } + for (int i = 0; i < salt_charge_ratio; i++) { + mm[i + 1] = get_random_particle(cation_type, salt_charge[0], 0, dummyp); + if (npart_xrd != ncation - i) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + factor *= volume_rx * pow(10, -pI_plus) / (ncation - i); + if (mm[i + 1] >= 0) { + qq[i + 1] = atom->q[mm[i + 1]]; + atom->q[mm[i + 1]] = 0; + mask_tmp[i + 1] = atom->mask[mm[i + 1]]; + atom->mask[mm[i + 1]] = exclusion_group_bit; + } + } + } else { + // delete one cation and (salt_charge_ratio) anions + + if (nanion < salt_charge_ratio || ncation < 1) return; + mm[0] = get_random_particle(cation_type, salt_charge[0], 0, dummyp); + if (npart_xrd != ncation) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + factor *= volume_rx * pow(10, -pI_plus) / (ncation); + if (mm[0] >= 0) { + qq[0] = atom->q[mm[0]]; + atom->q[mm[0]] = 0; + mask_tmp[0] = atom->mask[mm[0]]; + atom->mask[mm[0]] = exclusion_group_bit; + } + for (int i = 0; i < salt_charge_ratio; i++) { + mm[i + 1] = get_random_particle(anion_type, salt_charge[1], 0, dummyp); + if (npart_xrd != nanion - i) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (mm[i + 1] >= 0) { + qq[i + 1] = atom->q[mm[i + 1]]; + atom->q[mm[i + 1]] = 0; + mask_tmp[i + 1] = atom->mask[mm[i + 1]]; + atom->mask[mm[i + 1]] = exclusion_group_bit; + } + factor *= volume_rx * pow(10, -pI_minus) / (nanion - i); + } + } + + // attempt deletion + + double energy_after = energy_full(); + if (energy_after < MAXENERGYTEST && + random_equal->uniform() < (1.0 / factor) * exp(beta * (energy_before - energy_after))) { + energy_stored = energy_after; + + atom->natoms -= 1 + salt_charge_ratio; + // ions must be deleted in order, otherwise index m could change upon the first deletion + for (int i = 0; i < salt_charge_ratio + 1; i++) { + // get max mm value, poor N^2 scaling, but charge ratio is a small number (2 or 3). + int maxmm = -1, jmaxm = -1; + for (int j = 0; j < salt_charge_ratio + 1; j++) { + if (mm[j] > maxmm) { + maxmm = mm[j]; + jmaxm = j; + } + } + if (maxmm < 0) { + break; // already deleted all particles in this thread + } else { + // delete particle maxmm + atom->avec->copy(atom->nlocal - 1, maxmm, 1); + atom->nlocal--; + mm[jmaxm] = -1; + } + } + + // update indices + nsalt_successes += 1; + if (salt_charge[0] <= -salt_charge[1]) { + ncation -= salt_charge_ratio; + nanion--; + } else { + nanion -= salt_charge_ratio; + ncation--; + } + if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); + + } else { + energy_stored = energy_before; + + // reassign original charge and mask + for (int i = 0; i < salt_charge_ratio + 1; i++) { + if (mm[i] >= 0) { + atom->q[mm[i]] = qq[i]; + atom->mask[mm[i]] = mask_tmp[i]; + } + } + } +} + +int Fix_charge_regulation::insert_particle(int ptype, double charge, double rd, double *target) { + + // insert a particle of type (ptype) with charge (charge) within distance (rd) of (target) + + double coord[3]; + int m = -1; + if (rd < small) { + coord[0] = xlo + random_equal->uniform() * (xhi - xlo); + coord[1] = ylo + random_equal->uniform() * (yhi - ylo); + coord[2] = zlo + random_equal->uniform() * (zhi - zlo); + } else { + double radius = reaction_distance * random_equal->uniform(); + double theta = random_equal->uniform() * PI; + double phi = random_equal->uniform() * 2 * PI; + coord[0] = target[0] + radius * sin(theta) * cos(phi); + coord[1] = target[1] + radius * sin(theta) * sin(phi); + coord[2] = target[2] + radius * cos(theta); + coord[0] = coord[0] - floor(1.0 * (coord[0] - xlo) / (xhi - xlo)) * (xhi - xlo); + coord[1] = coord[1] - floor(1.0 * (coord[1] - ylo) / (yhi - ylo)) * (yhi - ylo); + coord[2] = coord[2] - floor(1.0 * (coord[2] - zlo) / (zhi - zlo)) * (zhi - zlo); + } + + if (coord[0] >= sublo[0] && coord[0] < subhi[0] && + coord[1] >= sublo[1] && coord[1] < subhi[1] && + coord[2] >= sublo[2] && coord[2] < subhi[2]) { + atom->avec->create_atom(ptype, coord); + m = atom->nlocal - 1; + atom->mask[m] = groupbitall; + + sigma = sqrt(force->boltz * *target_temperature_tcp / atom->mass[ptype] / force->mvv2e); + atom->v[m][0] = random_unequal->gaussian() * sigma; + atom->v[m][1] = random_unequal->gaussian() * sigma; + atom->v[m][2] = random_unequal->gaussian() * sigma; + atom->q[m] = charge; + modify->create_attribute(m); + + } + atom->nghost = 0; + comm->borders(); + atom->natoms++; + return m; +} + +int Fix_charge_regulation::get_random_particle(int ptype, double charge, double rd, double *target) { + + // returns a randomly chosen particle of type (ptype) with charge (charge) + // chosen among particles within distance (rd) of (target) + + int nlocal = atom->nlocal; + + // expand memory, if necessary + if (atom->nmax > cr_nmax) { + memory->sfree(ptype_ID); + cr_nmax = atom->nmax; + ptype_ID = (int *) memory->smalloc(cr_nmax * sizeof(int), + "CR: local_atom_list"); + } + + int count_local, count_global, count_before; + int m = -1; + count_local = 0; + count_global = 0; + count_before = 0; + + if (rd < small) { //reaction_distance < small: No geometry constraint on random particle choice + for (int i = 0; i < nlocal; i++) { + if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < small && + atom->mask[i] != exclusion_group_bit) { + ptype_ID[count_local] = i; + count_local++; + } + } + } else { + double dx, dy, dz, distance_check; + for (int i = 0; i < nlocal; i++) { + dx = fabs(atom->x[i][0] - target[0]); + dx -= static_cast(1.0 * dx / (xhi - xlo) + 0.5) * (xhi - xlo); + dy = fabs(atom->x[i][1] - target[1]); + dy -= static_cast(1.0 * dy / (yhi - ylo) + 0.5) * (yhi - ylo); + dz = fabs(atom->x[i][2] - target[2]); + dz -= static_cast(1.0 * dz / (zhi - zlo) + 0.5) * (zhi - zlo); + distance_check = dx * dx + dy * dy + dz * dz; + if ((distance_check < rd * rd) && atom->type[i] == ptype && + fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) { + ptype_ID[count_local] = i; + count_local++; + } + } + } + count_global = count_local; + count_before = count_local; + MPI_Allreduce(&count_local, &count_global, 1, MPI_INT, MPI_SUM, world); + MPI_Scan(&count_local, &count_before, 1, MPI_INT, MPI_SUM, world); + count_before -= count_local; + + npart_xrd = count_global; // save the number of particles, for use in MC acceptance ratio + if (count_global > 0) { + const int ID_global = floor(random_equal->uniform() * count_global); + if ((ID_global >= count_before) && (ID_global < (count_before + count_local))) { + const int ID_local = ID_global - count_before; + m = ptype_ID[ID_local]; // local ID of the chosen particle + return m; + } + } + return -1; +} + +double Fix_charge_regulation::energy_full() { + int imolecule; + if (triclinic) domain->x2lamda(atom->nlocal); + domain->pbc(); + comm->exchange(); + atom->nghost = 0; + comm->borders(); + if (triclinic) domain->lamda2x(atom->nlocal + atom->nghost); + if (modify->n_pre_neighbor) modify->pre_neighbor(); + neighbor->build(1); + int eflag = 1; + int vflag = 0; + if (overlap_flag) { + int overlaptestall; + int overlaptest = 0; + double delx, dely, delz, rsq; + double **x = atom->x; + tagint *molecule = atom->molecule; + int nall = atom->nlocal + atom->nghost; + for (int i = 0; i < atom->nlocal; i++) { + for (int j = i + 1; j < nall; j++) { + delx = x[i][0] - x[j][0]; + dely = x[i][1] - x[j][1]; + delz = x[i][2] - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + if (rsq < overlap_cutoffsq) { + overlaptest = 1; + break; + } + } + if (overlaptest) break; + } + overlaptestall = overlaptest; + MPI_Allreduce(&overlaptest, &overlaptestall, 1, + MPI_INT, MPI_MAX, world); + if (overlaptestall) return MAXENERGYSIGNAL; + } + size_t nbytes = sizeof(double) * (atom->nlocal + atom->nghost); + if (nbytes) memset(&atom->f[0][0], 0, 3 * nbytes); + + if (modify->n_pre_force) modify->pre_force(vflag); + + if (force->pair) force->pair->compute(eflag, vflag); + + if (atom->molecular) { + if (force->bond) force->bond->compute(eflag, vflag); + if (force->angle) force->angle->compute(eflag, vflag); + if (force->dihedral) force->dihedral->compute(eflag, vflag); + if (force->improper) force->improper->compute(eflag, vflag); + } + + if (force->kspace) force->kspace->compute(eflag, vflag); + + if (modify->n_post_force) modify->post_force(vflag); + if (modify->n_end_of_step) modify->end_of_step(); + update->eflag_global = update->ntimestep; + double total_energy = c_pe->compute_scalar(); + return total_energy; +} + +int Fix_charge_regulation::particle_number_xrd(int ptype, double charge, double rd, double *target) { + + int count = 0; + if (rd < small) { + for (int i = 0; i < atom->nlocal; i++) { + if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) + count++; + } + } else { + double dx, dy, dz, distance_check; + for (int i = 0; i < atom->nlocal; i++) { + dx = fabs(atom->x[i][0] - target[0]); + dx -= static_cast(1.0 * dx / (xhi - xlo) + 0.5) * (xhi - xlo); + dy = fabs(atom->x[i][1] - target[1]); + dy -= static_cast(1.0 * dy / (yhi - ylo) + 0.5) * (yhi - ylo); + dz = fabs(atom->x[i][2] - target[2]); + dz -= static_cast(1.0 * dz / (zhi - zlo) + 0.5) * (zhi - zlo); + distance_check = dx * dx + dy * dy + dz * dz; + if ((distance_check < rd * rd) && atom->type[i] == ptype && + fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) { + count++; + } + } + } + int count_sum = count; + MPI_Allreduce(&count, &count_sum, 1, MPI_INT, MPI_SUM, world); + return count_sum; +} + +int Fix_charge_regulation::particle_number(int ptype, double charge) { + + int count = 0; + for (int i = 0; i < atom->nlocal; i++) { + if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) + count = count + 1; + } + int count_sum = count; + MPI_Allreduce(&count, &count_sum, 1, MPI_INT, MPI_SUM, world); + return count_sum; +} + +double Fix_charge_regulation::compute_vector(int n) { + double count_temp = 0; + if (n == 0) { + return nacid_attempts + nbase_attempts + nsalt_attempts; + } else if (n == 1) { + return nacid_successes + nbase_successes + nsalt_successes; + } else if (n == 2) { + return particle_number(acid_type, 0); + } else if (n == 3) { + return particle_number(acid_type, -1); + } else if (n == 4) { + return particle_number(base_type, 0); + } else if (n == 5) { + return particle_number(base_type, 1); + } else if (n == 6) { + return particle_number(cation_type, salt_charge[0]); + } else if (n == 7) { + return particle_number(anion_type, salt_charge[1]); + } + return 0.0; +} + +void Fix_charge_regulation::setThermoTemperaturePointer() { + int ifix = -1; + ifix = modify->find_fix(idftemp); + if (ifix == -1) { + error->all(FLERR, + "Fix charge regulation regulation could not find a temperature fix id provided by tempfixid\n"); + } + Fix *temperature_fix = modify->fix[ifix]; + int dim; + target_temperature_tcp = (double *) temperature_fix->extract("t_target", dim); + +} + +void Fix_charge_regulation::assign_tags() { + // Assign tags to ions with zero tags + if (atom->tag_enable) { + tagint *tag = atom->tag; + tagint maxtag_all = 0; + tagint maxtag = 0; + for (int i = 0; i < atom->nlocal; i++) maxtag = MAX(maxtag, tag[i]); + maxtag_all = maxtag; + MPI_Allreduce(&maxtag, &maxtag_all, 1, MPI_LMP_TAGINT, MPI_MAX, world); + if (maxtag_all >= MAXTAGINT) + error->all(FLERR, "New atom IDs exceed maximum allowed ID"); + + tagint notag = 0; + tagint notag_all; + for (int i = 0; i < atom->nlocal; i++) + if (tag[i] == 0 && (atom->type[i] == cation_type || atom->type[i] == anion_type))notag++; + notag_all = notag; + MPI_Allreduce(¬ag, ¬ag_all, 1, MPI_LMP_TAGINT, MPI_SUM, world); + if (notag_all >= MAXTAGINT) + error->all(FLERR, "New atom IDs exceed maximum allowed ID"); + + tagint notag_sum = notag; + MPI_Scan(¬ag, ¬ag_sum, 1, MPI_LMP_TAGINT, MPI_SUM, world); + // itag = 1st new tag that my untagged atoms should use + + tagint itag = maxtag_all + notag_sum - notag + 1; + for (int i = 0; i < atom->nlocal; i++) { + if (tag[i] == 0 && (atom->type[i] == cation_type || atom->type[i] == anion_type)) { + tag[i] = itag++; + } + } + if (atom->map_style) atom->map_init(); + atom->nghost = 0; + comm->borders(); + } +} + +/* ---------------------------------------------------------------------- + parse input options +------------------------------------------------------------------------- */ + +void Fix_charge_regulation::options(int narg, char **arg) { + if (narg < 0) error->all(FLERR, "Illegal fix charge regulation command"); + + // defaults + + pH = 7.0; + pI_plus = 100; + pI_minus = 100; + acid_type = -1; + base_type = -1; + pKa = 100; + pKb = 100; + pKs = 14.0; + nevery = 100; + nmc = 100; + pmcmoves[0] = pmcmoves[1] = pmcmoves[2] = 0.33; + llength_unit_in_nm= 0.72; + + reservoir_temperature = 1.0; + reaction_distance = 0; + seed = 12345; + target_temperature_tcp = &reservoir_temperature; + add_tags_flag = false; + only_salt_flag = false; + salt_charge[0] = 1; // cation charge + salt_charge[1] = -1; // anion charge + + exclusion_group = 0; + exclusion_group_bit = 0; + ngroups = 0; + int ngroupsmax = 0; + groupstrings = NULL; + + int iarg = 0; + while (iarg < narg) { + + if (strcmp(arg[iarg], "lunit_nm") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + llength_unit_in_nm = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "acid_type") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + acid_type = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "base_type") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + base_type = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "pH") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + pH = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "pIp") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + pI_plus = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "pIm") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + pI_minus = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "pKa") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + pKa = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "pKb") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + pKb = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + + } else if (strcmp(arg[iarg], "temp") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + reservoir_temperature = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "pKs") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + pKs = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "tempfixid") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + int n = strlen(arg[iarg + 1]) + 1; + delete[] idftemp; + idftemp = new char[n]; + strcpy(idftemp, arg[iarg + 1]); + setThermoTemperaturePointer(); + iarg += 2; + } else if (strcmp(arg[iarg], "rxd") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + reaction_distance = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + if ((reaction_distance > fabs(domain->boxhi[0] - domain->boxlo[0]) / 2) || + (reaction_distance > fabs(domain->boxhi[1] - domain->boxlo[1]) / 2) || + (reaction_distance > fabs(domain->boxhi[2] - domain->boxlo[2]) / 2)) { + error->warning(FLERR, + "reaction distance (rxd) is larger than half the box dimension, resetting default: xrd = 0."); + reaction_distance = 0; + } + iarg += 2; + } else if (strcmp(arg[iarg], "nevery") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + nevery = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "nmc") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + nmc = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "pmcmoves") == 0) { + if (iarg + 4 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + pmcmoves[0] = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + pmcmoves[1] = utils::numeric(FLERR, arg[iarg + 2], false, lmp); + pmcmoves[2] = utils::numeric(FLERR, arg[iarg + 3], false, lmp); + iarg += 4; + } else if (strcmp(arg[iarg], "seed") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + seed = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "tag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (strcmp(arg[iarg + 1], "yes") == 0) { + add_tags_flag = true; + } else if (strcmp(arg[iarg + 1], "no") == 0) { + add_tags_flag = false; + } else { error->all(FLERR, "Illegal fix charge regulation command"); } + iarg += 2; + } else if (strcmp(arg[iarg], "onlysalt") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (strcmp(arg[iarg + 1], "yes") == 0) { + only_salt_flag = true; + // need to specify salt charge + if (iarg + 4 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + salt_charge[0] = utils::numeric(FLERR, arg[iarg + 2], false, lmp); + salt_charge[1] = utils::numeric(FLERR, arg[iarg + 3], false, lmp); + if (fabs(salt_charge[0] - utils::inumeric(FLERR, arg[iarg + 2], false, lmp)) > small) + error->all(FLERR, "Illegal fix charge regulation command, cation charge must be an integer"); + if (fabs(salt_charge[1] - utils::inumeric(FLERR, arg[iarg + 3], false, lmp)) > small) + error->all(FLERR, "Illegal fix charge regulation command, anion charge must be an integer"); + iarg += 4; + } else if (strcmp(arg[iarg + 1], "no") == 0) { + only_salt_flag = false; + iarg += 2; + } else { error->all(FLERR, "Illegal fix charge regulation command"); } + + } else if (strcmp(arg[iarg], "group") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix fix charge regulation command"); + if (ngroups >= ngroupsmax) { + ngroupsmax = ngroups + 1; + groupstrings = (char **) + memory->srealloc(groupstrings, + ngroupsmax * sizeof(char *), + "fix_charge_regulation:groupstrings"); + } + int n = strlen(arg[iarg + 1]) + 1; + groupstrings[ngroups] = new char[n]; + strcpy(groupstrings[ngroups], arg[iarg + 1]); + ngroups++; + iarg += 2; + } else { error->all(FLERR, "Illegal fix charge regulation command"); } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based arrays +------------------------------------------------------------------------- */ + +double Fix_charge_regulation::memory_usage() { + double bytes = cr_nmax * sizeof(int); + return bytes; +} diff --git a/src/USER-MISC/fix_charge_regulation.h b/src/USER-MISC/fix_charge_regulation.h new file mode 100644 index 0000000000..280a6c0d49 --- /dev/null +++ b/src/USER-MISC/fix_charge_regulation.h @@ -0,0 +1,117 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Tine Curk (curk@northwestern.edu) and Jiaxing Yuan (yuanjiaxing123@hotmail.com) +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(charge_regulation,Fix_charge_regulation) + +#else + +#ifndef LMP_FIX_charge_regulation_H +#define LMP_FIX_charge_regulation_H + +#include "fix.h" + +namespace LAMMPS_NS { + + class Fix_charge_regulation : public Fix { + public: + Fix_charge_regulation(class LAMMPS *, int, char **); + ~Fix_charge_regulation(); + int setmask(); + void init(); + void pre_exchange(); + void forward_acid(); + void backward_acid(); + void forward_base(); + void backward_base(); + void forward_ions(); + void forward_ions_multival(); + void backward_ions(); + void backward_ions_multival(); + int get_random_particle(int, double, double, double *); + int insert_particle(int, double, double, double *); + double energy_full(); + int particle_number(int, double); + int particle_number_xrd(int, double, double, double *); + double compute_vector(int n); + void assign_tags(); + void options(int, char **); + void setThermoTemperaturePointer(); + double memory_usage(); + + private: + int exclusion_group, exclusion_group_bit; + int ngcmc_type, nevery, seed; + int nmc; // mc moves per cycle + double llength_unit_in_nm ; // LAMMPS unit of length in nm, needed since chemical potentials are in units of mol/l + double pH, pKa, pKb, pKs, pI_plus, pI_minus; // chemical potentials + double pmcmoves[3]; // mc move attempt probability, acid, base, salt; and comulative + double pmcc; // mc move cumulative attempt probability + int npart_xrd; // # of particles (ions) within xrd + int npart_xrd2; // # of particles (ions) within xrd + double vlocal_xrd; // # local volume within xrd + bool only_salt_flag; // true if performing only salt insertion/deletion, no acid/base dissociation. + bool add_tags_flag; // true if each inserted atom gets its unique atom tag + int groupbitall; // group bitmask for inserted atoms + int ngroups; // number of group-ids for inserted atoms + char **groupstrings; // list of group-ids for inserted atoms + // counters + unsigned long int nacid_attempts, nacid_successes, nbase_attempts, nbase_successes, nsalt_attempts, nsalt_successes; + int nacid_neutral, nacid_charged, nbase_neutral, nbase_charged, ncation, nanion; // particle type counts + int cr_nmax; // max number of local particles + double reservoir_temperature; + double beta, sigma, volume, volume_rx; // inverse temperature, speed, total volume, reacting volume + int salt_charge[2]; // charge of salt ions: [0] - cation, [1] - anion + int salt_charge_ratio; + double xlo, xhi, ylo, yhi, zlo, zhi; // box size + double energy_stored; // full energy of old/current configuration + int triclinic; // 0 = orthog box, 1 = triclinic + double *sublo, *subhi; // triclinic size + int *ptype_ID; // particle ID array + double overlap_cutoffsq; // square distance cutoff for overlap + int overlap_flag; + int acid_type, cation_type, base_type, anion_type; // reacting atom types + int reaction_distance_flag; + double reaction_distance; // max radial distance for atom insertion + + + class Pair *pair; + class Compute *c_pe; // energy compute pointer + class RanPark *random_equal; // random number generator + class RanPark *random_unequal; // random number generator + char *idftemp; // pointer to the temperature fix + + double *target_temperature_tcp; // current temperature of the thermostat + + }; +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +Self-explanatory. + +*/ From 6d862569ea8ab8f44e68207bd41adfe8a28a5e2b Mon Sep 17 00:00:00 2001 From: tc387 Date: Fri, 5 Feb 2021 16:24:55 -0600 Subject: [PATCH 0078/1217] Updated emails --- src/USER-MISC/fix_charge_regulation.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-MISC/fix_charge_regulation.h b/src/USER-MISC/fix_charge_regulation.h index 280a6c0d49..f0151390e6 100644 --- a/src/USER-MISC/fix_charge_regulation.h +++ b/src/USER-MISC/fix_charge_regulation.h @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Tine Curk (curk@northwestern.edu) and Jiaxing Yuan (yuanjiaxing123@hotmail.com) + Contributing author: Tine Curk (tcurk5@gmail.com) and Jiaxing Yuan (yuanjiaxing123@hotmail.com) ------------------------------------------------------------------------- */ #ifdef FIX_CLASS From d62ba49f1a431b920cb29e0dce8f23b4a9815f26 Mon Sep 17 00:00:00 2001 From: tc387 Date: Fri, 5 Feb 2021 16:57:00 -0600 Subject: [PATCH 0079/1217] added minor comments --- src/USER-MISC/fix_charge_regulation.h | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/USER-MISC/fix_charge_regulation.h b/src/USER-MISC/fix_charge_regulation.h index f0151390e6..e64ea6b63f 100644 --- a/src/USER-MISC/fix_charge_regulation.h +++ b/src/USER-MISC/fix_charge_regulation.h @@ -60,7 +60,7 @@ namespace LAMMPS_NS { int nmc; // mc moves per cycle double llength_unit_in_nm ; // LAMMPS unit of length in nm, needed since chemical potentials are in units of mol/l double pH, pKa, pKb, pKs, pI_plus, pI_minus; // chemical potentials - double pmcmoves[3]; // mc move attempt probability, acid, base, salt; and comulative + double pmcmoves[3]; // mc move attempt probability: acid, base, ion pair exchange double pmcc; // mc move cumulative attempt probability int npart_xrd; // # of particles (ions) within xrd int npart_xrd2; // # of particles (ions) within xrd @@ -70,6 +70,7 @@ namespace LAMMPS_NS { int groupbitall; // group bitmask for inserted atoms int ngroups; // number of group-ids for inserted atoms char **groupstrings; // list of group-ids for inserted atoms + // counters unsigned long int nacid_attempts, nacid_successes, nbase_attempts, nbase_successes, nsalt_attempts, nsalt_successes; int nacid_neutral, nacid_charged, nbase_neutral, nbase_charged, ncation, nanion; // particle type counts @@ -77,7 +78,7 @@ namespace LAMMPS_NS { double reservoir_temperature; double beta, sigma, volume, volume_rx; // inverse temperature, speed, total volume, reacting volume int salt_charge[2]; // charge of salt ions: [0] - cation, [1] - anion - int salt_charge_ratio; + int salt_charge_ratio; // charge ration when using multivalent ion exchange double xlo, xhi, ylo, yhi, zlo, zhi; // box size double energy_stored; // full energy of old/current configuration int triclinic; // 0 = orthog box, 1 = triclinic @@ -86,16 +87,15 @@ namespace LAMMPS_NS { double overlap_cutoffsq; // square distance cutoff for overlap int overlap_flag; int acid_type, cation_type, base_type, anion_type; // reacting atom types - int reaction_distance_flag; - double reaction_distance; // max radial distance for atom insertion + int reaction_distance_flag; // radial reaction restriction flag + double reaction_distance; // max radial distance from acid/base for ion insertion class Pair *pair; - class Compute *c_pe; // energy compute pointer + class Compute *c_pe; // energy compute pointer class RanPark *random_equal; // random number generator class RanPark *random_unequal; // random number generator - char *idftemp; // pointer to the temperature fix - + char *idftemp; // pointer to the temperature fix double *target_temperature_tcp; // current temperature of the thermostat }; From 0bc31fad0922d3f3f76ec5fdd894714112a75826 Mon Sep 17 00:00:00 2001 From: tc387 Date: Fri, 5 Feb 2021 17:03:15 -0600 Subject: [PATCH 0080/1217] header file minor cleanup --- src/USER-MISC/fix_charge_regulation.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/USER-MISC/fix_charge_regulation.h b/src/USER-MISC/fix_charge_regulation.h index e64ea6b63f..d698bd6bb7 100644 --- a/src/USER-MISC/fix_charge_regulation.h +++ b/src/USER-MISC/fix_charge_regulation.h @@ -56,8 +56,8 @@ namespace LAMMPS_NS { private: int exclusion_group, exclusion_group_bit; - int ngcmc_type, nevery, seed; - int nmc; // mc moves per cycle + int nevery, seed; // begin MC cycle every nevery MD timesteps, random seed + int nmc; // MC move attempts per cycle double llength_unit_in_nm ; // LAMMPS unit of length in nm, needed since chemical potentials are in units of mol/l double pH, pKa, pKb, pKs, pI_plus, pI_minus; // chemical potentials double pmcmoves[3]; // mc move attempt probability: acid, base, ion pair exchange From c94a740b4e5c3c800c0c30a6a26279c7cc0390c9 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Fri, 5 Feb 2021 16:43:52 -0700 Subject: [PATCH 0081/1217] Updating examples --- doc/src/Examples.rst | 2 + examples/multi/data.powerlaw | 20015 ++++++++++++++++ examples/multi/in.colloid | 2 +- examples/multi/in.granular | 16 +- examples/multi/in.powerlaw | 33 + examples/multi/log.30Nov20.colloid.intel.1 | 32 +- examples/multi/log.30Nov20.colloid.intel.4 | 30 +- .../multi/log.30Nov20.colloid.old.intel.1 | 30 +- .../multi/log.30Nov20.colloid.old.intel.4 | 32 +- examples/multi/log.30Nov20.granular.intel.1 | 142 +- examples/multi/log.30Nov20.granular.intel.4 | 150 +- .../multi/log.30Nov20.granular.old.intel.1 | 32 +- .../multi/log.30Nov20.granular.old.intel.4 | 34 +- examples/multi/log.30Nov20.powerlaw.intel.1 | 191 + examples/multi/log.30Nov20.powerlaw.intel.4 | 191 + src/nbin_multi.cpp | 5 +- 16 files changed, 20681 insertions(+), 256 deletions(-) create mode 100755 examples/multi/data.powerlaw create mode 100755 examples/multi/in.powerlaw create mode 100644 examples/multi/log.30Nov20.powerlaw.intel.1 create mode 100644 examples/multi/log.30Nov20.powerlaw.intel.4 diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 8a76dca66e..8bfc4ad573 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -108,6 +108,8 @@ Lowercase directories +-------------+------------------------------------------------------------------+ | msst | MSST shock dynamics | +-------------+------------------------------------------------------------------+ +| multi | multi neighboring for systems with large interaction disparities | ++-------------+------------------------------------------------------------------+ | nb3b | use of non-bonded 3-body harmonic pair style | +-------------+------------------------------------------------------------------+ | neb | nudged elastic band (NEB) calculation for barrier finding | diff --git a/examples/multi/data.powerlaw 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-2.7873678456129014e-05 0 0 0 -2.235247321317359e-05 +6603 0.0008315340095250634 -0.0003647525758271505 0 0 0 -7.409182200572651e-05 +4384 0.0007845204963803677 -0.00032119299272343095 0 0 0 -3.5417627423652716e-05 +2220 0.00024746217175723706 5.5562932257161795e-05 0 0 0 1.3754074416042432e-06 +9090 0.00048762069322560563 0.00010568130527693934 0 0 0 -1.8490288620338333e-05 +1315 0.0008578951521183869 -0.00026381216498998 0 0 0 -5.03280754689511e-05 +6594 3.541600478028999e-05 0.00013547007123118596 0 0 0 -0.0005440206202373246 +5164 0.0007813044528566372 -0.0003219984117909091 0 0 0 3.985531377462861e-05 +1286 0.0008502244522568076 -0.00027721234365183874 0 0 0 2.6088694641268207e-05 +4761 0.0006975854370649275 -0.0003050392917545538 0 0 0 0.0005961378980490035 +9377 0.0004929246925413406 5.611051096270155e-05 0 0 0 1.318406506838938e-05 +6573 0.0004456813005752615 3.10647368142668e-05 0 0 0 -4.13492665300345e-05 +433 0.0006836880362626396 5.024995567001619e-06 0 0 0 -3.0467620168779193e-05 +9094 0.000744625343311001 -0.00031967382357756246 0 0 0 2.526728571228735e-05 +2199 0.00042321437699091 2.592987440383578e-05 0 0 0 -8.18072673517025e-06 +1655 0.0007916395866808383 -0.00035457576070874246 0 0 0 -2.377735842840034e-05 +7207 0.0007452629981695557 -0.00015036527011953076 0 0 0 -0.00010872542216077849 +7875 0.0006585619246582422 3.7484154374812544e-05 0 0 0 0.00016718166745976926 +645 0.0006822356766865151 -0.00030148060339422317 0 0 0 9.296688489967334e-05 +9972 0.00036547266030541705 0.00014472173048552157 0 0 0 -3.0834187318466155e-05 +2113 0.0007081949702739137 -0.0007224063339711531 0 0 0 -3.8479080361991125e-05 +1412 -1.2039149567225154e-05 0.00010147738508380671 0 0 0 -0.00014286610388043424 +5701 0.0004761925580242084 5.147696238223329e-05 0 0 0 -0.00015663562454425414 +5800 0.0008450331921778463 -0.00033908595153051745 0 0 0 -3.0708573661039805e-05 diff --git a/examples/multi/in.colloid b/examples/multi/in.colloid index 835032f2e2..71987acbd6 100644 --- a/examples/multi/in.colloid +++ b/examples/multi/in.colloid @@ -31,7 +31,7 @@ velocity all create 1.44 87287 loop geom neighbor 1 multi #multi/old neigh_modify delay 0 collection/type 2 1*4 5 -comm_modify mode multi reduce/multi +comm_modify mode multi reduce/multi #multi/old # colloid potential diff --git a/examples/multi/in.granular b/examples/multi/in.granular index f43e9505e4..99e9ddfb33 100644 --- a/examples/multi/in.granular +++ b/examples/multi/in.granular @@ -1,4 +1,4 @@ -# Bidisperse set of grains +# Big colloid particles and small LJ particles units lj atom_style sphere @@ -28,10 +28,10 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency neighbor 1 multi #multi/old -neigh_modify delay 0 -comm_modify mode multi vel yes reduce/multi +neigh_modify delay 0 collection/interval 2 1 20 +comm_modify mode multi vel yes reduce/multi #multi/old -# colloid potential +# granular potential pair_style granular pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity @@ -42,14 +42,6 @@ fix 3 all deform 1 xy erate 1e-3 #dump 1 all custom 1000 dump.granular id x y z radius -#dump 2 all image 1000 image.*.jpg type type & -# zoom 1.5 center d 0.5 0.5 0.5 -#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 - -#dump 3 all movie 1000 movie.mpg type type & -# zoom 1.5 center d 0.5 0.5 0.5 -#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 - thermo_style custom step temp epair etotal press vol thermo 1000 diff --git a/examples/multi/in.powerlaw b/examples/multi/in.powerlaw new file mode 100755 index 0000000000..90fc7aae3c --- /dev/null +++ b/examples/multi/in.powerlaw @@ -0,0 +1,33 @@ +# Shear power-law distributed granular particles + +units lj +atom_style sphere +dimension 2 +read_data data.powerlaw +change_box all triclinic + +# multi neighbor and comm for efficiency + +neighbor 1 multi +neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200 +comm_modify mode multi vel yes reduce/multi + +# granular potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +# fixes + +fix 1 all nve/sphere +fix 2 all enforce2d +fix 3 all deform 1 xy erate 2e-4 + +# dump 1 all custom 2000 dump.granular id x y z radius + +thermo_style custom step temp epair etotal press vol pxy +thermo 1000 + +timestep 0.005 + +run 100000 diff --git a/examples/multi/log.30Nov20.colloid.intel.1 b/examples/multi/log.30Nov20.colloid.intel.1 index 2bc82eaab0..5dcb8c3bf1 100644 --- a/examples/multi/log.30Nov20.colloid.intel.1 +++ b/examples/multi/log.30Nov20.colloid.intel.1 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -53,9 +53,9 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi #/old -neigh_modify delay 0 multi/custom 2 1*4 5 -comm_modify mode multi multi/reduce +neighbor 1 multi #multi/old +neigh_modify delay 0 collection/type 2 1*4 5 +comm_modify mode multi reduce/multi #multi/old # colloid potential @@ -72,7 +72,7 @@ pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 fix 2 all enforce2d -dump 1 all atom 1000 dump.colloid +#dump 1 all atom 1000 dump.colloid #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -98,7 +98,7 @@ Neighbor list info ... pair build: half/multi/newton stencil: half/multi/2d bin: multi -Per MPI rank memory allocation (min/avg/max) = 5.538 | 5.538 | 5.538 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.385 | 4.385 | 4.385 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395241 0.121 36000 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 @@ -151,20 +151,20 @@ Step Temp E_pair TotEng Press Volume 48000 2.0109636 -0.78968551 1.2206135 0.89458323 9496.7246 49000 2.0131059 -0.79687252 1.2155681 0.91239613 9418.3093 50000 2.0073361 -0.79981468 1.206858 0.98524334 9289.4715 -Loop time of 20.4651 on 1 procs for 50000 steps with 3026 atoms +Loop time of 19.7532 on 1 procs for 50000 steps with 3026 atoms -Performance: 1055453.279 tau/day, 2443.179 timesteps/s +Performance: 1093493.133 tau/day, 2531.234 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 11.099 | 11.099 | 11.099 | 0.0 | 54.23 -Neigh | 2.7536 | 2.7536 | 2.7536 | 0.0 | 13.46 -Comm | 0.53353 | 0.53353 | 0.53353 | 0.0 | 2.61 -Output | 0.11209 | 0.11209 | 0.11209 | 0.0 | 0.55 -Modify | 5.1627 | 5.1627 | 5.1627 | 0.0 | 25.23 -Other | | 0.8046 | | | 3.93 +Pair | 10.789 | 10.789 | 10.789 | 0.0 | 54.62 +Neigh | 2.6848 | 2.6848 | 2.6848 | 0.0 | 13.59 +Comm | 0.53244 | 0.53244 | 0.53244 | 0.0 | 2.70 +Output | 0.0010482 | 0.0010482 | 0.0010482 | 0.0 | 0.01 +Modify | 4.9599 | 4.9599 | 4.9599 | 0.0 | 25.11 +Other | | 0.7856 | | | 3.98 Nlocal: 3026.00 ave 3026 max 3026 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -180,4 +180,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:20 +Total wall time: 0:00:19 diff --git a/examples/multi/log.30Nov20.colloid.intel.4 b/examples/multi/log.30Nov20.colloid.intel.4 index 48a5846a09..906400df66 100644 --- a/examples/multi/log.30Nov20.colloid.intel.4 +++ b/examples/multi/log.30Nov20.colloid.intel.4 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -53,9 +53,9 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi #/old -neigh_modify delay 0 multi/custom 2 1*4 5 -comm_modify mode multi multi/reduce +neighbor 1 multi #multi/old +neigh_modify delay 0 collection/type 2 1*4 5 +comm_modify mode multi reduce/multi #multi/old # colloid potential @@ -72,7 +72,7 @@ pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 fix 2 all enforce2d -dump 1 all atom 1000 dump.colloid +#dump 1 all atom 1000 dump.colloid #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -98,7 +98,7 @@ Neighbor list info ... pair build: half/multi/newton stencil: half/multi/2d bin: multi -Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.382 | 5.384 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.327 | 4.329 | 4.330 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395241 0.121 36000 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 @@ -151,20 +151,20 @@ Step Temp E_pair TotEng Press Volume 48000 2.0108204 -0.76655178 1.2436041 0.95379465 9633.6453 49000 1.9868193 -0.76613798 1.2200247 0.88790224 9504.2918 50000 2.0141467 -0.80029827 1.2131829 1.0064263 9346.3268 -Loop time of 7.28248 on 4 procs for 50000 steps with 3026 atoms +Loop time of 6.98615 on 4 procs for 50000 steps with 3026 atoms -Performance: 2966022.789 tau/day, 6865.793 timesteps/s +Performance: 3091831.080 tau/day, 7157.016 timesteps/s 99.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.1624 | 2.5918 | 2.9227 | 17.4 | 35.59 -Neigh | 0.62508 | 0.7436 | 0.83321 | 9.2 | 10.21 -Comm | 1.1035 | 1.5265 | 2.0746 | 29.3 | 20.96 -Output | 0.050094 | 0.050233 | 0.05062 | 0.1 | 0.69 -Modify | 1.8164 | 1.8966 | 1.9583 | 4.2 | 26.04 -Other | | 0.4737 | | | 6.50 +Pair | 2.2795 | 2.5856 | 2.9414 | 17.4 | 37.01 +Neigh | 0.62273 | 0.70156 | 0.76736 | 7.4 | 10.04 +Comm | 1.0765 | 1.4945 | 1.8884 | 28.6 | 21.39 +Output | 0.00076496 | 0.0008953 | 0.0012832 | 0.0 | 0.01 +Modify | 1.718 | 1.7755 | 1.827 | 3.7 | 25.41 +Other | | 0.4281 | | | 6.13 Nlocal: 756.500 ave 839 max 673 min Histogram: 1 0 1 0 0 0 0 1 0 1 diff --git a/examples/multi/log.30Nov20.colloid.old.intel.1 b/examples/multi/log.30Nov20.colloid.old.intel.1 index 291e8f89df..70c7db2afd 100644 --- a/examples/multi/log.30Nov20.colloid.old.intel.1 +++ b/examples/multi/log.30Nov20.colloid.old.intel.1 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -53,9 +53,9 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi/old +neighbor 1 multi/old #multi neigh_modify delay 0 #multi/custom 2 1*4 5 -comm_modify mode multi #multi/reduce +comm_modify mode multi/old #multi multi/reduce # colloid potential @@ -72,7 +72,7 @@ pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 fix 2 all enforce2d -dump 1 all atom 1000 dump.colloid +#dump 1 all atom 1000 dump.colloid #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -98,7 +98,7 @@ Neighbor list info ... pair build: half/multi/old/newton stencil: half/multi/old/2d bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.611 | 5.611 | 5.611 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.496 | 4.496 | 4.496 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395241 0.121 36000 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 @@ -151,20 +151,20 @@ Step Temp E_pair TotEng Press Volume 48000 2.0283587 -0.79063641 1.237052 0.83617499 9610.9933 49000 2.0051919 -0.79078067 1.2137485 0.95651813 9411.7165 50000 2.0140985 -0.81796958 1.1954634 0.93791038 9296.069 -Loop time of 29.8066 on 1 procs for 50000 steps with 3026 atoms +Loop time of 28.5339 on 1 procs for 50000 steps with 3026 atoms -Performance: 724671.093 tau/day, 1677.479 timesteps/s +Performance: 756994.490 tau/day, 1752.302 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 11.698 | 11.698 | 11.698 | 0.0 | 39.25 -Neigh | 10.292 | 10.292 | 10.292 | 0.0 | 34.53 -Comm | 1.405 | 1.405 | 1.405 | 0.0 | 4.71 -Output | 0.11474 | 0.11474 | 0.11474 | 0.0 | 0.38 -Modify | 5.3019 | 5.3019 | 5.3019 | 0.0 | 17.79 -Other | | 0.9947 | | | 3.34 +Pair | 10.918 | 10.918 | 10.918 | 0.0 | 38.26 +Neigh | 10.375 | 10.375 | 10.375 | 0.0 | 36.36 +Comm | 1.2856 | 1.2856 | 1.2856 | 0.0 | 4.51 +Output | 0.0010955 | 0.0010955 | 0.0010955 | 0.0 | 0.00 +Modify | 5.0132 | 5.0132 | 5.0132 | 0.0 | 17.57 +Other | | 0.9412 | | | 3.30 Nlocal: 3026.00 ave 3026 max 3026 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -180,4 +180,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:29 +Total wall time: 0:00:28 diff --git a/examples/multi/log.30Nov20.colloid.old.intel.4 b/examples/multi/log.30Nov20.colloid.old.intel.4 index 0eae8cc8e7..6d159d9405 100644 --- a/examples/multi/log.30Nov20.colloid.old.intel.4 +++ b/examples/multi/log.30Nov20.colloid.old.intel.4 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -53,9 +53,9 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi/old +neighbor 1 multi/old #multi neigh_modify delay 0 #multi/custom 2 1*4 5 -comm_modify mode multi #multi/reduce +comm_modify mode multi/old #multi multi/reduce # colloid potential @@ -72,7 +72,7 @@ pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 fix 2 all enforce2d -dump 1 all atom 1000 dump.colloid +#dump 1 all atom 1000 dump.colloid #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -98,7 +98,7 @@ Neighbor list info ... pair build: half/multi/old/newton stencil: half/multi/old/2d bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.438 | 5.441 | 5.444 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.404 | 4.406 | 4.410 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395241 0.121 36000 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 @@ -151,20 +151,20 @@ Step Temp E_pair TotEng Press Volume 48000 1.9977505 -0.77207122 1.225019 0.92107083 9647.1543 49000 2.0000901 -0.76254934 1.2368798 1.0320945 9536.2823 50000 2.0150929 -0.80463979 1.2097872 0.99556424 9324.0277 -Loop time of 11.239 on 4 procs for 50000 steps with 3026 atoms +Loop time of 10.7578 on 4 procs for 50000 steps with 3026 atoms -Performance: 1921872.705 tau/day, 4448.779 timesteps/s -98.0% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 2007847.166 tau/day, 4647.794 timesteps/s +98.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.3936 | 2.7411 | 3.1078 | 16.7 | 24.39 -Neigh | 2.2948 | 2.6755 | 3.1013 | 18.5 | 23.81 -Comm | 2.522 | 3.3135 | 4.0361 | 31.7 | 29.48 -Output | 0.040863 | 0.041031 | 0.041456 | 0.1 | 0.37 -Modify | 1.844 | 1.9014 | 1.9701 | 3.4 | 16.92 -Other | | 0.5666 | | | 5.04 +Pair | 2.3814 | 2.6878 | 2.9507 | 15.2 | 24.98 +Neigh | 2.3959 | 2.6615 | 2.9677 | 16.2 | 24.74 +Comm | 2.4113 | 2.9894 | 3.5621 | 29.6 | 27.79 +Output | 0.00077024 | 0.00091029 | 0.0012971 | 0.0 | 0.01 +Modify | 1.7966 | 1.8497 | 1.907 | 3.8 | 17.19 +Other | | 0.5686 | | | 5.29 Nlocal: 756.500 ave 838 max 693 min Histogram: 2 0 0 0 0 0 0 1 0 1 @@ -180,4 +180,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:11 +Total wall time: 0:00:10 diff --git a/examples/multi/log.30Nov20.granular.intel.1 b/examples/multi/log.30Nov20.granular.intel.1 index 2e313231ca..06d02b8531 100644 --- a/examples/multi/log.30Nov20.granular.intel.1 +++ b/examples/multi/log.30Nov20.granular.intel.1 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -51,9 +51,9 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi #/old -neigh_modify delay 0 -comm_modify mode multi vel yes +neighbor 1 multi #multi/old +neigh_modify delay 0 collection/interval 2 1 20 +comm_modify mode multi vel yes reduce/multi #multi/old # colloid potential @@ -64,7 +64,7 @@ fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 fix 2 all enforce2d fix 3 all deform 1 xy erate 1e-3 -dump 1 all custom 1000 dump.granular id x y z radius +#dump 1 all custom 1000 dump.granular id x y z radius #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -90,86 +90,86 @@ Neighbor list info ... pair build: half/size/multi/newton/tri stencil: half/multi/2d/tri bin: multi -Per MPI rank memory allocation (min/avg/max) = 11.78 | 11.78 | 11.78 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.29 | 10.29 | 10.29 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395623 0.66837658 7200 - 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 - 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 - 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 - 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 - 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 - 6000 0.025856 0 0.025848141 0.021241317 7603.5534 - 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 - 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 - 9000 0.016370159 0 0.016365184 0.020261904 6515.3445 - 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 - 11000 0.014156551 0 0.014152248 0.021324815 5815.4665 - 12000 0.013725406 0 0.013721235 0.021159958 5483.6304 - 13000 0.013215746 0 0.013211729 0.021685712 5165.4758 - 14000 0.012398153 0 0.012394384 0.024155434 4862.8657 - 15000 0.011842796 0 0.011839196 0.028503991 4577.9008 - 16000 0.011433182 0 0.011429706 0.033564839 4309.8792 - 17000 0.011166574 0 0.01116318 0.040592677 4058.9964 - 18000 0.01100067 0 0.010997326 0.04899206 3825.155 - 19000 0.010224474 0 0.010221366 0.063670337 3607.6577 - 20000 0.0091360559 0 0.0091332789 0.088230111 3408.5658 - 21000 0.007733647 0 0.0077312964 0.11769368 3227.7002 - 22000 0.0060202358 0 0.0060184059 0.15272491 3064.3986 - 23000 0.004670574 0 0.0046691543 0.19450724 2918.0014 - 24000 0.0040248313 0 0.004023608 0.24161742 2788.4113 - 25000 0.0032075275 0 0.0032065526 0.2897693 2674.5604 - 26000 0.0021358024 0 0.0021351532 0.33635617 2574.9564 - 27000 0.0016902752 0 0.0016897614 0.37624266 2487.2379 - 28000 0.0014038218 0 0.0014033951 0.41492104 2409.2461 - 29000 0.00090262506 0 0.0009023507 0.45392905 2340.0308 - 30000 0.00049466342 0 0.00049451306 0.49295072 2279.2316 - 31000 0.00056998139 0 0.00056980815 0.53299515 2226.5683 - 32000 0.00057326945 0 0.0005730952 0.56856537 2181.7092 - 33000 0.00044845112 0 0.00044831481 0.59623471 2142.7573 - 34000 0.00059840183 0 0.00059821994 0.61758983 2107.1253 - 35000 0.00075310993 0 0.00075288103 0.63756827 2072.7217 - 36000 0.00053774066 0 0.00053757721 0.66026064 2039.1655 - 37000 0.00030440106 0 0.00030430853 0.69059102 2007.7903 - 38000 0.00034436264 0 0.00034425797 0.72166344 1980.7137 - 39000 0.00039693498 0 0.00039681433 0.74680327 1957.9531 - 40000 0.00035425567 0 0.000354148 0.76604186 1937.3834 - 41000 0.0003094733 0 0.00030937924 0.78323163 1916.7027 - 42000 0.00027259246 0 0.0002725096 0.80315535 1895.0714 - 43000 0.00020659817 0 0.00020653538 0.8274603 1873.5407 - 44000 0.00016023333 0 0.00016018463 0.85418969 1853.8674 - 45000 0.00016111931 0 0.00016107034 0.87913944 1837.1141 - 46000 0.00016130888 0 0.00016125985 0.89921705 1822.7354 - 47000 0.00015755049 0 0.0001575026 0.91653538 1809.0285 - 48000 0.00017794781 0 0.00017789372 0.93582908 1794.7041 - 49000 0.00018878437 0 0.00018872699 0.95775203 1780.032 - 50000 0.0001778042 0 0.00017775016 0.97893714 1765.9439 -Loop time of 77.4487 on 1 procs for 50000 steps with 3290 atoms + 1000 0.32604952 0 0.32595042 0.17341597 7862.5013 + 2000 0.12631038 0 0.12627198 0.069126477 8216.6956 + 3000 0.069351715 0 0.069330635 0.040799593 8344.1931 + 4000 0.045023755 0 0.04501007 0.029184795 8239.1832 + 5000 0.032735149 0 0.0327252 0.025640841 7943.5691 + 6000 0.026205227 0 0.026197262 0.021206924 7617.6672 + 7000 0.02165475 0 0.021648168 0.018789365 7255.2897 + 8000 0.018299317 0 0.018293755 0.019272158 6887.3386 + 9000 0.016283763 0 0.016278813 0.020434892 6524.0274 + 10000 0.015148918 0 0.015144313 0.021650465 6168.4941 + 11000 0.014180465 0 0.014176155 0.022320009 5823.98 + 12000 0.013505744 0 0.013501639 0.023978674 5492.4853 + 13000 0.013009585 0 0.01300563 0.024391329 5175.7455 + 14000 0.012494373 0 0.012490576 0.027331543 4874.3212 + 15000 0.012057669 0 0.012054004 0.030561239 4589.518 + 16000 0.011510988 0 0.01150749 0.034613772 4321.1694 + 17000 0.011198594 0 0.01119519 0.042263536 4070.0115 + 18000 0.010978603 0 0.010975266 0.053637275 3836.0304 + 19000 0.010768789 0 0.010765516 0.069472547 3619.75 + 20000 0.0102256 0 0.010222492 0.085332898 3420.2738 + 21000 0.0089630315 0 0.0089603072 0.11199196 3236.9821 + 22000 0.006565581 0 0.0065635854 0.14807426 3071.3012 + 23000 0.0050916998 0 0.0050901522 0.1903446 2923.4162 + 24000 0.0040345997 0 0.0040333734 0.237983 2792.2658 + 25000 0.0032995328 0 0.0032985299 0.29120001 2677.7475 + 26000 0.0024157863 0 0.002415052 0.33851944 2578.4972 + 27000 0.0020664445 0 0.0020658164 0.37561848 2491.0264 + 28000 0.0017843883 0 0.0017838459 0.41119961 2412.3871 + 29000 0.0011813262 0 0.0011809672 0.44749341 2341.7208 + 30000 0.00063084711 0 0.00063065536 0.4879202 2279.0452 + 31000 0.00056027405 0 0.00056010376 0.52932126 2224.9456 + 32000 0.00053304715 0 0.00053288513 0.56822504 2179.1224 + 33000 0.00052245707 0 0.00052229826 0.60025509 2140.5345 + 34000 0.00073726189 0 0.0007370378 0.62001489 2106.3045 + 35000 0.00075804791 0 0.0007578175 0.6359631 2072.525 + 36000 0.00052579203 0 0.00052563222 0.65678516 2038.1907 + 37000 0.00036977909 0 0.0003696667 0.68784389 2005.5831 + 38000 0.00036252798 0 0.00036241779 0.72116044 1977.7441 + 39000 0.00036254566 0 0.00036243547 0.74720837 1954.9127 + 40000 0.00036237175 0 0.00036226161 0.76605408 1934.6006 + 41000 0.00032453104 0 0.00032443239 0.78424188 1914.1939 + 42000 0.00025394755 0 0.00025387036 0.80529272 1893.064 + 43000 0.00021067821 0 0.00021061418 0.82962095 1872.365 + 44000 0.00017927684 0 0.00017922235 0.85522899 1853.531 + 45000 0.0001464225 0 0.000146378 0.87925998 1837.2423 + 46000 0.00012922979 0 0.00012919051 0.8986549 1822.9227 + 47000 0.0001643557 0 0.00016430575 0.91743602 1809.0605 + 48000 0.00020154753 0 0.00020148627 0.93686779 1794.9227 + 49000 0.00017742528 0 0.00017737135 0.94988773 1780.3811 + 50000 0.00015150521 0 0.00015145916 0.97929588 1764.7507 +Loop time of 54.9135 on 1 procs for 50000 steps with 3290 atoms -Performance: 278894.354 tau/day, 645.589 timesteps/s +Performance: 393345.914 tau/day, 910.523 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 60.017 | 60.017 | 60.017 | 0.0 | 77.49 -Neigh | 0.47 | 0.47 | 0.47 | 0.0 | 0.61 -Comm | 6.6765 | 6.6765 | 6.6765 | 0.0 | 8.62 -Output | 0.24799 | 0.24799 | 0.24799 | 0.0 | 0.32 -Modify | 8.8677 | 8.8677 | 8.8677 | 0.0 | 11.45 -Other | | 1.17 | | | 1.51 +Pair | 44.691 | 44.691 | 44.691 | 0.0 | 81.38 +Neigh | 0.21653 | 0.21653 | 0.21653 | 0.0 | 0.39 +Comm | 0.75388 | 0.75388 | 0.75388 | 0.0 | 1.37 +Output | 0.0011999 | 0.0011999 | 0.0011999 | 0.0 | 0.00 +Modify | 8.4718 | 8.4718 | 8.4718 | 0.0 | 15.43 +Other | | 0.7794 | | | 1.42 Nlocal: 3290.00 ave 3290 max 3290 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 6295.00 ave 6295 max 6295 min +Nghost: 525.000 ave 525 max 525 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 53729.0 ave 53729 max 53729 min +Neighs: 26732.0 ave 26732 max 26732 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 53729 -Ave neighs/atom = 16.331003 -Neighbor list builds = 348 +Total # of neighbors = 26732 +Ave neighs/atom = 8.1252280 +Neighbor list builds = 342 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:01:17 +Total wall time: 0:00:54 diff --git a/examples/multi/log.30Nov20.granular.intel.4 b/examples/multi/log.30Nov20.granular.intel.4 index d53684c596..3aa05d79c7 100644 --- a/examples/multi/log.30Nov20.granular.intel.4 +++ b/examples/multi/log.30Nov20.granular.intel.4 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -52,8 +52,8 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency neighbor 1 multi #multi/old -neigh_modify delay 0 -comm_modify mode multi vel yes multi/reduce +neigh_modify delay 0 collection/interval 2 1 20 +comm_modify mode multi vel yes reduce/multi #multi/old # colloid potential @@ -64,7 +64,7 @@ fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 fix 2 all enforce2d fix 3 all deform 1 xy erate 1e-3 -dump 1 all custom 1000 dump.granular id x y z radius +#dump 1 all custom 1000 dump.granular id x y z radius #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -90,86 +90,86 @@ Neighbor list info ... pair build: half/size/multi/newton/tri stencil: half/multi/2d/tri bin: multi -Per MPI rank memory allocation (min/avg/max) = 11.33 | 11.33 | 11.33 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.09 | 10.10 | 10.10 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395623 0.66837658 7200 - 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 - 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 - 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 - 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 - 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 - 6000 0.025856 0 0.025848141 0.021241317 7603.5534 - 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 - 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 - 9000 0.01637016 0 0.016365184 0.020261904 6515.3445 - 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 - 11000 0.014156553 0 0.01415225 0.021324818 5815.4665 - 12000 0.013725412 0 0.01372124 0.021159958 5483.6304 - 13000 0.013215733 0 0.013211716 0.021685624 5165.4758 - 14000 0.012398179 0 0.012394411 0.024155572 4862.8657 - 15000 0.01184269 0 0.01183909 0.028504106 4577.901 - 16000 0.01143291 0 0.011429435 0.033564204 4309.88 - 17000 0.011166204 0 0.01116281 0.040588854 4058.9972 - 18000 0.011000875 0 0.010997532 0.048998904 3825.1569 - 19000 0.010225905 0 0.010222797 0.063669586 3607.6622 - 20000 0.0091390249 0 0.0091362471 0.088165396 3408.567 - 21000 0.0077382016 0 0.0077358496 0.11770473 3227.6936 - 22000 0.0060173113 0 0.0060154823 0.15261992 3064.3873 - 23000 0.0046667554 0 0.004665337 0.19453813 2917.9782 - 24000 0.0040425764 0 0.0040413476 0.24145834 2788.3897 - 25000 0.0031933187 0 0.0031923481 0.28989732 2674.5164 - 26000 0.0021139018 0 0.0021132592 0.33598721 2574.9313 - 27000 0.0017005052 0 0.0016999884 0.37665029 2487.1628 - 28000 0.001443434 0 0.0014429952 0.41572112 2409.3271 - 29000 0.00089885805 0 0.00089858484 0.45343123 2340.2314 - 30000 0.00048558336 0 0.00048543577 0.49175966 2279.2156 - 31000 0.00058132898 0 0.00058115228 0.53236819 2226.2347 - 32000 0.00057751441 0 0.00057733887 0.56915062 2181.2736 - 33000 0.00044720497 0 0.00044706904 0.59696122 2142.5709 - 34000 0.00060927898 0 0.00060909379 0.61734988 2107.128 - 35000 0.00077422577 0 0.00077399045 0.63696024 2072.6004 - 36000 0.00055753008 0 0.00055736062 0.65981839 2038.8237 - 37000 0.0003140158 0 0.00031392035 0.69018918 2007.323 - 38000 0.00034970199 0 0.0003495957 0.72155094 1980.1702 - 39000 0.00041435514 0 0.00041422919 0.7468053 1957.3837 - 40000 0.00037229543 0 0.00037218227 0.76581519 1936.8032 - 41000 0.00031027679 0 0.00031018248 0.78321128 1916.1103 - 42000 0.00026621832 0 0.00026613741 0.80267694 1894.4646 - 43000 0.00020544063 0 0.00020537818 0.82714181 1872.768 - 44000 0.00015635243 0 0.00015630491 0.85496512 1853.0303 - 45000 0.00014985611 0 0.00014981056 0.87924561 1836.4779 - 46000 0.00015645346 0 0.00015640591 0.89896131 1822.2004 - 47000 0.00016007816 0 0.00016002951 0.91662026 1808.4601 - 48000 0.00017439363 0 0.00017434063 0.93565314 1794.1244 - 49000 0.00018647711 0 0.00018642043 0.95733125 1779.401 - 50000 0.00018463414 0 0.00018457802 0.96449755 1765.1506 -Loop time of 22.3987 on 4 procs for 50000 steps with 3290 atoms + 1000 0.32605303 0 0.32595393 0.17341558 7862.5037 + 2000 0.12631567 0 0.12627728 0.069188881 8216.7174 + 3000 0.069373812 0 0.069352726 0.040740832 8344.2982 + 4000 0.045084633 0 0.045070929 0.029328609 8239.3656 + 5000 0.032681746 0 0.032671813 0.025416741 7943.7831 + 6000 0.026301239 0 0.026293245 0.021418793 7617.8426 + 7000 0.021666723 0 0.021660138 0.018961011 7255.9338 + 8000 0.018141337 0 0.018135823 0.019306113 6887.4963 + 9000 0.015922309 0 0.015917469 0.020033398 6524.016 + 10000 0.014744547 0 0.014740066 0.020959503 6168.1945 + 11000 0.013872852 0 0.013868636 0.021708943 5823.3153 + 12000 0.013321594 0 0.013317545 0.02332141 5491.4979 + 13000 0.01269964 0 0.012695779 0.024796428 5174.6263 + 14000 0.01227055 0 0.012266821 0.027785072 4873.4516 + 15000 0.012120508 0 0.012116824 0.029656636 4588.8603 + 16000 0.011612027 0 0.011608498 0.034695109 4320.4674 + 17000 0.011216697 0 0.011213288 0.042746966 4069.4275 + 18000 0.010950166 0 0.010946838 0.053528994 3835.5439 + 19000 0.010887635 0 0.010884325 0.069684492 3619.562 + 20000 0.010563449 0 0.010560238 0.08654561 3420.2636 + 21000 0.0092336323 0 0.0092308257 0.11286068 3237.1408 + 22000 0.006929086 0 0.0069269799 0.15018917 3072.0438 + 23000 0.0052239156 0 0.0052223277 0.19067193 2924.441 + 24000 0.0044210081 0 0.0044196644 0.23908686 2793.2426 + 25000 0.0034916086 0 0.0034905473 0.29112824 2678.7912 + 26000 0.002549072 0 0.0025482972 0.33567824 2579.3738 + 27000 0.0020890726 0 0.0020884377 0.37328514 2491.0502 + 28000 0.001772982 0 0.0017724431 0.41079958 2411.9111 + 29000 0.001127719 0 0.0011273762 0.44752241 2341.1888 + 30000 0.00053266563 0 0.00053250373 0.48791815 2278.5611 + 31000 0.00050278646 0 0.00050263364 0.52896525 2224.5328 + 32000 0.00051880956 0 0.00051865187 0.56884574 2178.6674 + 33000 0.00054908167 0 0.00054891477 0.6016387 2140.3696 + 34000 0.00075213884 0 0.00075191023 0.62070188 2106.6504 + 35000 0.00081295162 0 0.00081270452 0.63492031 2073.0077 + 36000 0.00056699821 0 0.00056682587 0.65608409 2038.3251 + 37000 0.0003540723 0 0.00035396468 0.68803919 2005.497 + 38000 0.00031139738 0 0.00031130273 0.72103717 1977.7345 + 39000 0.00034087822 0 0.00034077461 0.74697975 1954.8979 + 40000 0.00035452426 0 0.0003544165 0.76682035 1934.5695 + 41000 0.00030882258 0 0.00030872871 0.78390763 1914.3326 + 42000 0.00025492799 0 0.00025485051 0.80439795 1893.1474 + 43000 0.00021545017 0 0.00021538468 0.82803644 1872.073 + 44000 0.00017293257 0 0.00017288 0.85436769 1852.6548 + 45000 0.00014097725 0 0.0001409344 0.8796181 1836.0087 + 46000 0.0001139199 0 0.00011388527 0.90006173 1821.7977 + 47000 0.00012678598 0 0.00012674745 0.90876359 1808.4913 + 48000 0.00013796773 0 0.00013792579 0.93661523 1793.8082 + 49000 0.00014723144 0 0.00014718669 0.95869417 1779.1875 + 50000 0.00013610653 0 0.00013606516 0.97777198 1765.3247 +Loop time of 17.7405 on 4 procs for 50000 steps with 3290 atoms -Performance: 964340.770 tau/day, 2232.270 timesteps/s -99.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 1217551.996 tau/day, 2818.407 timesteps/s +100.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 8.5158 | 12.318 | 15.836 | 92.1 | 54.99 -Neigh | 0.092527 | 0.11392 | 0.13595 | 5.6 | 0.51 -Comm | 2.7127 | 6.2337 | 10.096 | 131.0 | 27.83 -Output | 0.088027 | 0.088284 | 0.088812 | 0.1 | 0.39 -Modify | 2.8544 | 3.0435 | 3.2034 | 9.2 | 13.59 -Other | | 0.6017 | | | 2.69 +Pair | 6.6629 | 9.6168 | 12.444 | 76.6 | 54.21 +Neigh | 0.049771 | 0.055182 | 0.06133 | 2.0 | 0.31 +Comm | 1.7883 | 4.6306 | 7.6179 | 111.5 | 26.10 +Output | 0.00085342 | 0.0010606 | 0.0015425 | 0.9 | 0.01 +Modify | 2.7244 | 2.895 | 3.0436 | 8.2 | 16.32 +Other | | 0.5419 | | | 3.05 -Nlocal: 822.500 ave 859 max 785 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Nghost: 395.750 ave 424 max 368 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Neighs: 13439.5 ave 14346 max 12017 min -Histogram: 1 0 0 0 0 1 0 0 0 2 +Nlocal: 822.500 ave 897 max 779 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 190.500 ave 211 max 179 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Neighs: 6665.75 ave 7329 max 6104 min +Histogram: 1 0 0 1 1 0 0 0 0 1 -Total # of neighbors = 53758 -Ave neighs/atom = 16.339818 -Neighbor list builds = 348 +Total # of neighbors = 26663 +Ave neighs/atom = 8.1042553 +Neighbor list builds = 342 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:22 +Total wall time: 0:00:17 diff --git a/examples/multi/log.30Nov20.granular.old.intel.1 b/examples/multi/log.30Nov20.granular.old.intel.1 index ad827423c5..f928621824 100644 --- a/examples/multi/log.30Nov20.granular.old.intel.1 +++ b/examples/multi/log.30Nov20.granular.old.intel.1 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -51,9 +51,9 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi/old -neigh_modify delay 0 -comm_modify mode multi vel yes +neighbor 1 multi/old #multi +neigh_modify delay 0 #collection/interval 2 1 20 +comm_modify mode multi/old vel yes #reduce/multi # colloid potential @@ -64,7 +64,7 @@ fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 fix 2 all enforce2d fix 3 all deform 1 xy erate 1e-3 -dump 1 all custom 1000 dump.granular id x y z radius +#dump 1 all custom 1000 dump.granular id x y z radius #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -90,7 +90,7 @@ Neighbor list info ... pair build: half/size/multi/old/newton/tri stencil: half/multi/old/2d/tri bin: standard -Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.75 | 11.75 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.38 | 10.38 | 10.38 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395623 0.66837658 7200 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 @@ -143,20 +143,20 @@ Step Temp E_pair TotEng Press Volume 48000 0.00017794764 0 0.00017789356 0.93582953 1794.7043 49000 0.00018879338 0 0.000188736 0.95775166 1780.0323 50000 0.00017781117 0 0.00017775712 0.97893641 1765.9442 -Loop time of 80.8597 on 1 procs for 50000 steps with 3290 atoms +Loop time of 74.6636 on 1 procs for 50000 steps with 3290 atoms -Performance: 267129.375 tau/day, 618.355 timesteps/s +Performance: 289297.713 tau/day, 669.671 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 61.524 | 61.524 | 61.524 | 0.0 | 76.09 -Neigh | 2.2021 | 2.2021 | 2.2021 | 0.0 | 2.72 -Comm | 6.748 | 6.748 | 6.748 | 0.0 | 8.35 -Output | 0.25904 | 0.25904 | 0.25904 | 0.0 | 0.32 -Modify | 8.9408 | 8.9408 | 8.9408 | 0.0 | 11.06 -Other | | 1.186 | | | 1.47 +Pair | 56.696 | 56.696 | 56.696 | 0.0 | 75.93 +Neigh | 2.2232 | 2.2232 | 2.2232 | 0.0 | 2.98 +Comm | 6.1867 | 6.1867 | 6.1867 | 0.0 | 8.29 +Output | 0.0012016 | 0.0012016 | 0.0012016 | 0.0 | 0.00 +Modify | 8.432 | 8.432 | 8.432 | 0.0 | 11.29 +Other | | 1.125 | | | 1.51 Nlocal: 3290.00 ave 3290 max 3290 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -172,4 +172,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:01:20 +Total wall time: 0:01:14 diff --git a/examples/multi/log.30Nov20.granular.old.intel.4 b/examples/multi/log.30Nov20.granular.old.intel.4 index e41741b536..507de22119 100644 --- a/examples/multi/log.30Nov20.granular.old.intel.4 +++ b/examples/multi/log.30Nov20.granular.old.intel.4 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles @@ -15,7 +15,7 @@ Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.8528 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 3600 atoms - create_atoms CPU = 0.001 seconds + create_atoms CPU = 0.063 seconds change_box all triclinic Changing box ... triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) @@ -51,9 +51,9 @@ velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency -neighbor 1 multi/old -neigh_modify delay 0 -comm_modify mode multi vel yes #multi/reduce +neighbor 1 multi/old #multi +neigh_modify delay 0 #collection/interval 2 1 20 +comm_modify mode multi/old vel yes #reduce/multi # colloid potential @@ -64,7 +64,7 @@ fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 fix 2 all enforce2d fix 3 all deform 1 xy erate 1e-3 -dump 1 all custom 1000 dump.granular id x y z radius +#dump 1 all custom 1000 dump.granular id x y z radius #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 @@ -90,7 +90,7 @@ Neighbor list info ... pair build: half/size/multi/old/newton/tri stencil: half/multi/old/2d/tri bin: standard -Per MPI rank memory allocation (min/avg/max) = 11.48 | 11.48 | 11.49 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.20 | 10.20 | 10.20 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395623 0.66837658 7200 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 @@ -143,20 +143,20 @@ Step Temp E_pair TotEng Press Volume 48000 0.00017437702 0 0.00017432402 0.93565475 1794.1258 49000 0.00018645903 0 0.00018640235 0.95733183 1779.4032 50000 0.00018469122 0 0.00018463508 0.96446925 1765.1534 -Loop time of 30.9351 on 4 procs for 50000 steps with 3290 atoms +Loop time of 30.1448 on 4 procs for 50000 steps with 3290 atoms -Performance: 698235.574 tau/day, 1616.286 timesteps/s -89.8% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 716540.413 tau/day, 1658.658 timesteps/s +90.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 9.3702 | 12.796 | 16.045 | 84.3 | 41.36 -Neigh | 0.43499 | 0.55158 | 0.64861 | 12.8 | 1.78 -Comm | 10.183 | 13.476 | 16.961 | 83.7 | 43.56 -Output | 0.088474 | 0.088715 | 0.089272 | 0.1 | 0.29 -Modify | 3.0446 | 3.1809 | 3.3227 | 7.4 | 10.28 -Other | | 0.8418 | | | 2.72 +Pair | 8.7565 | 12.704 | 16.036 | 89.8 | 42.14 +Neigh | 0.4494 | 0.56436 | 0.66263 | 11.8 | 1.87 +Comm | 9.5962 | 12.989 | 17.006 | 90.8 | 43.09 +Output | 0.00088467 | 0.0011022 | 0.0015811 | 0.9 | 0.00 +Modify | 2.9732 | 3.0944 | 3.2463 | 7.0 | 10.27 +Other | | 0.7918 | | | 2.63 Nlocal: 822.500 ave 859 max 785 min Histogram: 1 0 1 0 0 0 0 0 1 1 diff --git a/examples/multi/log.30Nov20.powerlaw.intel.1 b/examples/multi/log.30Nov20.powerlaw.intel.1 new file mode 100644 index 0000000000..81b116ddd4 --- /dev/null +++ b/examples/multi/log.30Nov20.powerlaw.intel.1 @@ -0,0 +1,191 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 +read_data data +Reading data file ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10000 atoms + reading velocities ... + 10000 velocities + read_data CPU = 0.027 seconds +change_box all triclinic +Changing box ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + +# multi neighbor and comm for efficiency + +neighbor 1 multi +neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200 +comm_modify mode multi vel yes reduce/multi + +# granular potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +# fixes + +fix 1 all nve/sphere +fix 2 all enforce2d +fix 3 all deform 1 xy erate 2e-4 + +# dump 1 all custom 2000 dump.granular id x y z radius + +thermo_style custom step temp epair etotal press vol pxy +thermo 1000 + +timestep 0.005 + +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 164.7888 + ghost atom cutoff = 164.7888 + binsize = 82.3944, bins = 4 4 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/newton/tri + stencil: half/multi/2d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 14.76 | 14.76 | 14.76 Mbytes +Step Temp E_pair TotEng Press Volume Pxy + 0 0.00014649953 0 0.00014648488 0.027643657 103595.49 -0.0014952693 + 1000 0.00014726802 0 0.00014725329 0.029388139 103595.49 -0.00172238 + 2000 0.00014880425 0 0.00014878937 0.029608995 103595.49 -0.0023614491 + 3000 0.00015154766 0 0.0001515325 0.029668747 103595.49 -0.0029243775 + 4000 0.00015547813 0 0.00015546258 0.029662951 103595.49 -0.0034433688 + 5000 0.00015919808 0 0.00015918216 0.02988062 103595.49 -0.0037443111 + 6000 0.00016272902 0 0.00016271275 0.029776943 103595.49 -0.0042445445 + 7000 0.00016666322 0 0.00016664655 0.029919286 103595.49 -0.0045231987 + 8000 0.00017137531 0 0.00017135817 0.029849078 103595.49 -0.0049023441 + 9000 0.00017774522 0 0.00017772744 0.029925275 103595.49 -0.0051437804 + 10000 0.00018294048 0 0.00018292219 0.030166956 103595.49 -0.0052769381 + 11000 0.00019030719 0 0.00019028816 0.02988594 103595.49 -0.0058095975 + 12000 0.00019806568 0 0.00019804587 0.029852302 103595.49 -0.0060925449 + 13000 0.00020800749 0 0.00020798669 0.029927995 103595.49 -0.0062667347 + 14000 0.00021854888 0 0.00021852703 0.029984135 103595.49 -0.0064949797 + 15000 0.00022975749 0 0.00022973451 0.030063358 103595.49 -0.0065788835 + 16000 0.00024074076 0 0.00024071668 0.03006058 103595.49 -0.006757928 + 17000 0.00025363768 0 0.00025361232 0.030138053 103595.49 -0.0068153904 + 18000 0.00026618156 0 0.00026615494 0.030621109 103595.49 -0.0067026865 + 19000 0.00028000661 0 0.00027997861 0.030520699 103595.49 -0.0067126187 + 20000 0.00029472369 0 0.00029469422 0.030182866 103595.49 -0.0071232374 + 21000 0.00031065822 0 0.00031062716 0.030417926 103595.49 -0.0070815254 + 22000 0.00032789694 0 0.00032786415 0.030434044 103595.49 -0.007044194 + 23000 0.00034491703 0 0.00034488253 0.031195478 103595.49 -0.006895101 + 24000 0.00036262497 0 0.00036258871 0.030348688 103595.49 -0.0073503964 + 25000 0.00038232332 0 0.00038228509 0.030429549 103595.49 -0.0073043833 + 26000 0.00040292952 0 0.00040288922 0.030277517 103595.49 -0.0074475354 + 27000 0.00042260162 0 0.00042255936 0.030270875 103595.49 -0.0074037511 + 28000 0.00044296255 0 0.00044291826 0.030568983 103595.49 -0.0070827585 + 29000 0.00046164594 0 0.00046159978 0.030392129 103595.49 -0.0070495682 + 30000 0.00048018966 0 0.00048014164 0.03027035 103595.49 -0.0071339757 + 31000 0.00049904958 0 0.00049899968 0.030278024 103595.49 -0.0070690708 + 32000 0.00051586592 0 0.00051581433 0.030105498 103595.49 -0.007134143 + 33000 0.000533257 0 0.00053320367 0.029788452 103595.49 -0.0072245811 + 34000 0.00054849405 0 0.0005484392 0.029873916 103595.49 -0.0069597013 + 35000 0.00056356221 0 0.00056350586 0.029706011 103595.49 -0.00704387 + 36000 0.00057701153 0 0.00057695383 0.029584377 103595.49 -0.006959137 + 37000 0.00058975804 0 0.00058969906 0.029510998 103595.49 -0.0069205813 + 38000 0.00060106815 0 0.00060100804 0.029866588 103595.49 -0.006493655 + 39000 0.00061178223 0 0.00061172105 0.0294686 103595.49 -0.0066809721 + 40000 0.00062087616 0 0.00062081407 0.029305512 103595.49 -0.0067040127 + 41000 0.00062938061 0 0.00062931767 0.029313523 103595.49 -0.0065943738 + 42000 0.0006366437 0 0.00063658004 0.029294719 103595.49 -0.0065039414 + 43000 0.00064403805 0 0.00064397364 0.029169615 103595.49 -0.0065453715 + 44000 0.00064990286 0 0.00064983787 0.029173689 103595.49 -0.0064757302 + 45000 0.00065485285 0 0.00065478736 0.02911295 103595.49 -0.0065336599 + 46000 0.00065918851 0 0.00065912259 0.029664657 103595.49 -0.0060618092 + 47000 0.00066143867 0 0.00066137253 0.029672077 103595.49 -0.0061605571 + 48000 0.00066260774 0 0.00066254148 0.029356515 103595.49 -0.0063944326 + 49000 0.0006641111 0 0.00066404469 0.029771162 103595.49 -0.0061440485 + 50000 0.00066562386 0 0.0006655573 0.02944773 103595.49 -0.0063912951 + 51000 0.00066744319 0 0.00066737645 0.029507067 103595.49 -0.00636767 + 52000 0.00066927675 0 0.00066920982 0.029773443 103595.49 -0.0062192673 + 53000 0.00066999455 0 0.00066992755 0.029626747 103595.49 -0.0062819185 + 54000 0.00067204697 0 0.00067197976 0.029608834 103595.49 -0.0063047897 + 55000 0.00067089926 0 0.00067083217 0.029778336 103595.49 -0.006198876 + 56000 0.00067044673 0 0.00067037969 0.029707087 103595.49 -0.0062920606 + 57000 0.00066987451 0 0.00066980752 0.029751879 103595.49 -0.0062887511 + 58000 0.00066781462 0 0.00066774784 0.029673932 103595.49 -0.0063301658 + 59000 0.00065347402 0 0.00065340867 0.029540521 103595.49 -0.0064527808 + 60000 0.00065304518 0 0.00065297988 0.029801357 103595.49 -0.0062633754 + 61000 0.00065183192 0 0.00065176673 0.029786145 103595.49 -0.0063152956 + 62000 0.00065242331 0 0.00065235807 0.030461931 103595.49 -0.0060591261 + 63000 0.00065491938 0 0.00065485389 0.029715839 103595.49 -0.0065344894 + 64000 0.00065769719 0 0.00065763142 0.02977148 103595.49 -0.0065105553 + 65000 0.00066125407 0 0.00066118795 0.029534462 103595.49 -0.0066901883 + 66000 0.00066433913 0 0.0006642727 0.029949304 103595.49 -0.0064367129 + 67000 0.00066819344 0 0.00066812662 0.029629692 103595.49 -0.0067136218 + 68000 0.00067300953 0 0.00067294223 0.029793673 103595.49 -0.0065898421 + 69000 0.00067875538 0 0.0006786875 0.029651968 103595.49 -0.0067198512 + 70000 0.00068416104 0 0.00068409262 0.030125821 103595.49 -0.0063225262 + 71000 0.00068728347 0 0.00068721475 0.02958142 103595.49 -0.0066417995 + 72000 0.00068926082 0 0.00068919189 0.02976018 103595.49 -0.0063898599 + 73000 0.00068953168 0 0.00068946272 0.029574927 103595.49 -0.0065193167 + 74000 0.00069104787 0 0.00069097876 0.030209247 103595.49 -0.0060666707 + 75000 0.00069606779 0 0.00069599818 0.029636657 103595.49 -0.006387635 + 76000 0.00070399158 0 0.00070392118 0.029585803 103595.49 -0.0063291939 + 77000 0.00070284473 0 0.00070277445 0.029936591 103595.49 -0.0060359763 + 78000 0.00070619015 0 0.00070611953 0.029554333 103595.49 -0.0062453302 + 79000 0.00070892936 0 0.00070885847 0.029853506 103595.49 -0.0060833753 + 80000 0.00071125368 0 0.00071118255 0.029625268 103595.49 -0.0062046031 + 81000 0.00070944317 0 0.00070937223 0.029629542 103595.49 -0.0062343125 + 82000 0.00070892851 0 0.00070885762 0.029664456 103595.49 -0.006250692 + 83000 0.00070946812 0 0.00070939718 0.029964177 103595.49 -0.006159583 + 84000 0.00071198659 0 0.00071191539 0.029813631 103595.49 -0.0062607732 + 85000 0.00071266579 0 0.00071259453 0.029645729 103595.49 -0.0064004319 + 86000 0.00071461592 0 0.00071454446 0.029700002 103595.49 -0.0063398759 + 87000 0.00071781454 0 0.00071774276 0.029748726 103595.49 -0.0063600357 + 88000 0.00072016268 0 0.00072009067 0.029772487 103595.49 -0.0063655529 + 89000 0.00072272254 0 0.00072265027 0.030006837 103595.49 -0.0063122612 + 90000 0.00072122914 0 0.00072115701 0.029982109 103595.49 -0.006439831 + 91000 0.00072443479 0 0.00072436235 0.029830121 103595.49 -0.0065202831 + 92000 0.00072738733 0 0.00072731459 0.030194727 103595.49 -0.0062808688 + 93000 0.00072899838 0 0.00072892548 0.030175295 103595.49 -0.0062914883 + 94000 0.00072984304 0 0.00072977006 0.029844017 103595.49 -0.0064737335 + 95000 0.00073206475 0 0.00073199154 0.029798899 103595.49 -0.0064644006 + 96000 0.00073374806 0 0.00073367468 0.030226823 103595.49 -0.0061626549 + 97000 0.00073388886 0 0.00073381547 0.029993629 103595.49 -0.0063710254 + 98000 0.00073534207 0 0.00073526854 0.030245848 103595.49 -0.0063407392 + 99000 0.00073805531 0 0.0007379815 0.030287955 103595.49 -0.0063646707 + 100000 0.0007385798 0 0.00073850594 0.030172948 103595.49 -0.0064654963 +Loop time of 233.709 on 1 procs for 100000 steps with 10000 atoms + +Performance: 184845.371 tau/day, 427.883 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 193.18 | 193.18 | 193.18 | 0.0 | 82.66 +Neigh | 1.1138 | 1.1138 | 1.1138 | 0.0 | 0.48 +Comm | 2.3652 | 2.3652 | 2.3652 | 0.0 | 1.01 +Output | 0.0092981 | 0.0092981 | 0.0092981 | 0.0 | 0.00 +Modify | 32.407 | 32.407 | 32.407 | 0.0 | 13.87 +Other | | 4.628 | | | 1.98 + +Nlocal: 10000.0 ave 10000 max 10000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 446.000 ave 446 max 446 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 34464.0 ave 34464 max 34464 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 34464 +Ave neighs/atom = 3.4464000 +Neighbor list builds = 153 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:03:53 diff --git a/examples/multi/log.30Nov20.powerlaw.intel.4 b/examples/multi/log.30Nov20.powerlaw.intel.4 new file mode 100644 index 0000000000..34d3b85c1b --- /dev/null +++ b/examples/multi/log.30Nov20.powerlaw.intel.4 @@ -0,0 +1,191 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 +read_data data +Reading data file ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 10000 atoms + reading velocities ... + 10000 velocities + read_data CPU = 0.024 seconds +change_box all triclinic +Changing box ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + +# multi neighbor and comm for efficiency + +neighbor 1 multi +neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200 +comm_modify mode multi vel yes reduce/multi + +# granular potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +# fixes + +fix 1 all nve/sphere +fix 2 all enforce2d +fix 3 all deform 1 xy erate 2e-4 + +# dump 1 all custom 2000 dump.granular id x y z radius + +thermo_style custom step temp epair etotal press vol pxy +thermo 1000 + +timestep 0.005 + +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 164.7888 + ghost atom cutoff = 164.7888 + binsize = 82.3944, bins = 4 4 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/newton/tri + stencil: half/multi/2d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.67 | 12.68 Mbytes +Step Temp E_pair TotEng Press Volume Pxy + 0 0.00014649953 0 0.00014648488 0.027643657 103595.49 -0.0014952693 + 1000 0.00014726802 0 0.00014725329 0.029388139 103595.49 -0.00172238 + 2000 0.00014880425 0 0.00014878937 0.029608995 103595.49 -0.0023614491 + 3000 0.00015154766 0 0.0001515325 0.029668747 103595.49 -0.0029243775 + 4000 0.00015547813 0 0.00015546258 0.029662951 103595.49 -0.0034433688 + 5000 0.00015919808 0 0.00015918216 0.02988062 103595.49 -0.0037443111 + 6000 0.00016272902 0 0.00016271275 0.029776943 103595.49 -0.0042445445 + 7000 0.00016666322 0 0.00016664655 0.029919286 103595.49 -0.0045231987 + 8000 0.00017137531 0 0.00017135817 0.029849078 103595.49 -0.0049023441 + 9000 0.00017774522 0 0.00017772744 0.029925275 103595.49 -0.0051437804 + 10000 0.00018294048 0 0.00018292219 0.030166956 103595.49 -0.0052769381 + 11000 0.00019030719 0 0.00019028816 0.02988594 103595.49 -0.0058095975 + 12000 0.00019806568 0 0.00019804587 0.029852302 103595.49 -0.0060925449 + 13000 0.00020800749 0 0.00020798669 0.029927995 103595.49 -0.0062667347 + 14000 0.00021854888 0 0.00021852703 0.029984135 103595.49 -0.0064949797 + 15000 0.00022975749 0 0.00022973451 0.030063358 103595.49 -0.0065788835 + 16000 0.00024074076 0 0.00024071668 0.03006058 103595.49 -0.006757928 + 17000 0.00025363768 0 0.00025361232 0.030138053 103595.49 -0.0068153904 + 18000 0.00026618156 0 0.00026615494 0.030621109 103595.49 -0.0067026865 + 19000 0.00028000661 0 0.00027997861 0.030520699 103595.49 -0.0067126187 + 20000 0.00029472369 0 0.00029469422 0.030182866 103595.49 -0.0071232374 + 21000 0.00031065822 0 0.00031062716 0.030417926 103595.49 -0.0070815254 + 22000 0.00032789694 0 0.00032786415 0.030434044 103595.49 -0.007044194 + 23000 0.00034491703 0 0.00034488253 0.031195478 103595.49 -0.006895101 + 24000 0.00036262497 0 0.00036258871 0.030348688 103595.49 -0.0073503964 + 25000 0.00038232332 0 0.00038228509 0.030429549 103595.49 -0.0073043833 + 26000 0.00040292952 0 0.00040288922 0.030277517 103595.49 -0.0074475354 + 27000 0.00042260162 0 0.00042255936 0.030270875 103595.49 -0.0074037511 + 28000 0.00044296255 0 0.00044291826 0.030568983 103595.49 -0.0070827585 + 29000 0.00046164594 0 0.00046159978 0.030392129 103595.49 -0.0070495682 + 30000 0.00048018966 0 0.00048014164 0.03027035 103595.49 -0.0071339757 + 31000 0.00049904958 0 0.00049899968 0.030278024 103595.49 -0.0070690709 + 32000 0.00051586592 0 0.00051581433 0.030105498 103595.49 -0.007134143 + 33000 0.000533257 0 0.00053320367 0.029788452 103595.49 -0.0072245811 + 34000 0.00054849405 0 0.0005484392 0.029873916 103595.49 -0.0069597013 + 35000 0.00056356221 0 0.00056350586 0.029706011 103595.49 -0.00704387 + 36000 0.00057701153 0 0.00057695383 0.029584377 103595.49 -0.006959137 + 37000 0.00058975804 0 0.00058969906 0.029510998 103595.49 -0.0069205813 + 38000 0.00060106815 0 0.00060100804 0.029866588 103595.49 -0.006493655 + 39000 0.0006117822 0 0.00061172102 0.029468049 103595.49 -0.0066810094 + 40000 0.00062087615 0 0.00062081406 0.02930398 103595.49 -0.0067044715 + 41000 0.00062938044 0 0.0006293175 0.029314381 103595.49 -0.0065941361 + 42000 0.00063664289 0 0.00063657923 0.029294787 103595.49 -0.0065039202 + 43000 0.00064404027 0 0.00064397587 0.029224232 103595.49 -0.0065035306 + 44000 0.00064990723 0 0.00064984224 0.029142324 103595.49 -0.0065034116 + 45000 0.00065485343 0 0.00065478795 0.029121173 103595.49 -0.0065214973 + 46000 0.00065918796 0 0.00065912204 0.029651005 103595.49 -0.0060509446 + 47000 0.00066144517 0 0.00066137903 0.029234729 103595.49 -0.0064672274 + 48000 0.00066261185 0 0.00066254559 0.029229845 103595.49 -0.0065053596 + 49000 0.00066414215 0 0.00066407574 0.029562705 103595.49 -0.0062441985 + 50000 0.0006656453 0 0.00066557874 0.029728174 103595.49 -0.0062147051 + 51000 0.00066738973 0 0.00066732299 0.029928822 103595.49 -0.0060118516 + 52000 0.00066929756 0 0.00066923063 0.029886551 103595.49 -0.0061374389 + 53000 0.00067003172 0 0.00066996472 0.029567015 103595.49 -0.0063482821 + 54000 0.00067198511 0 0.00067191791 0.029833698 103595.49 -0.0061879264 + 55000 0.00067091193 0 0.00067084484 0.029711467 103595.49 -0.006233379 + 56000 0.00067046578 0 0.00067039873 0.030035238 103595.49 -0.0060959401 + 57000 0.00066988234 0 0.00066981535 0.030055225 103595.49 -0.0060935858 + 58000 0.00066786916 0 0.00066780238 0.029282172 103595.49 -0.0066021495 + 59000 0.00065350543 0 0.00065344008 0.029343567 103595.49 -0.0065364678 + 60000 0.0006530936 0 0.0006530283 0.02940862 103595.49 -0.0065558353 + 61000 0.00065187483 0 0.00065180964 0.02929946 103595.49 -0.0066840857 + 62000 0.00065245428 0 0.00065238904 0.030084765 103595.49 -0.0063065368 + 63000 0.0006549311 0 0.00065486561 0.029725525 103595.49 -0.0065305296 + 64000 0.00065774123 0 0.00065767546 0.029562667 103595.49 -0.0066194535 + 65000 0.00066126698 0 0.00066120085 0.029524987 103595.49 -0.0067008104 + 66000 0.0006643846 0 0.00066431816 0.029589813 103595.49 -0.0066689844 + 67000 0.00066823073 0 0.00066816391 0.029613668 103595.49 -0.0067372273 + 68000 0.00067301835 0 0.00067295104 0.029568568 103595.49 -0.0067808311 + 69000 0.00067876831 0 0.00067870043 0.029948152 103595.49 -0.0065107568 + 70000 0.00068419902 0 0.0006841306 0.029572996 103595.49 -0.0067066975 + 71000 0.00068730343 0 0.0006872347 0.029970497 103595.49 -0.0063646358 + 72000 0.00068930016 0 0.00068923123 0.029602044 103595.49 -0.0064953597 + 73000 0.00068953092 0 0.00068946197 0.029671751 103595.49 -0.0064422021 + 74000 0.00069106659 0 0.00069099748 0.029918321 103595.49 -0.0062634576 + 75000 0.00069609345 0 0.00069602384 0.029666179 103595.49 -0.0063552778 + 76000 0.00070399534 0 0.00070392494 0.029599912 103595.49 -0.0063251165 + 77000 0.00070284669 0 0.00070277641 0.029658992 103595.49 -0.0061988379 + 78000 0.00070619715 0 0.00070612653 0.029578035 103595.49 -0.0062153063 + 79000 0.00070895477 0 0.00070888388 0.029617734 103595.49 -0.0062090554 + 80000 0.00071127424 0 0.00071120311 0.029539347 103595.49 -0.0062883775 + 81000 0.00070945256 0 0.00070938162 0.029515493 103595.49 -0.0063350852 + 82000 0.00070895167 0 0.00070888078 0.029537389 103595.49 -0.0063819074 + 83000 0.00070948858 0 0.00070941763 0.02998589 103595.49 -0.0061284544 + 84000 0.00071197606 0 0.00071190486 0.030005566 103595.49 -0.0061829926 + 85000 0.00071266684 0 0.00071259557 0.029675137 103595.49 -0.0063804963 + 86000 0.00071465352 0 0.00071458205 0.029762675 103595.49 -0.0062924985 + 87000 0.00071779428 0 0.0007177225 0.029712831 103595.49 -0.0063812951 + 88000 0.00072016431 0 0.0007200923 0.029932619 103595.49 -0.0063145709 + 89000 0.00072271727 0 0.000722645 0.029818327 103595.49 -0.0064025621 + 90000 0.00072122834 0 0.00072115622 0.029829495 103595.49 -0.0065870713 + 91000 0.00072441206 0 0.00072433962 0.029939415 103595.49 -0.0064224045 + 92000 0.00072735846 0 0.00072728572 0.02991447 103595.49 -0.0064256019 + 93000 0.00072898882 0 0.00072891592 0.030230938 103595.49 -0.0061929729 + 94000 0.00072985209 0 0.00072977911 0.030145973 103595.49 -0.0062797016 + 95000 0.0007320685 0 0.0007319953 0.030113809 103595.49 -0.0062765142 + 96000 0.0007337917 0 0.00073371832 0.029919191 103595.49 -0.0063350801 + 97000 0.00073385417 0 0.00073378078 0.030184207 103595.49 -0.0062855982 + 98000 0.00073531629 0 0.00073524276 0.029974905 103595.49 -0.0064826333 + 99000 0.0007380024 0 0.0007379286 0.030678507 103595.49 -0.0060867823 + 100000 0.00073858055 0 0.00073850669 0.030048209 103595.49 -0.0065772058 +Loop time of 77.8133 on 4 procs for 100000 steps with 10000 atoms + +Performance: 555175.163 tau/day, 1285.128 timesteps/s +100.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 28.939 | 48.992 | 61.808 | 189.4 | 62.96 +Neigh | 0.22765 | 0.31872 | 0.38751 | 10.9 | 0.41 +Comm | 3.53 | 16.362 | 36.515 | 328.8 | 21.03 +Output | 0.0046275 | 0.0064601 | 0.008626 | 1.8 | 0.01 +Modify | 5.0862 | 8.3128 | 10.255 | 74.1 | 10.68 +Other | | 3.821 | | | 4.91 + +Nlocal: 2500.00 ave 3016 max 1605 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 221.500 ave 273 max 176 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Neighs: 8616.00 ave 10377 max 5447 min +Histogram: 1 0 0 0 0 1 0 0 0 2 + +Total # of neighbors = 34464 +Ave neighs/atom = 3.4464000 +Neighbor list builds = 153 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:17 diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index db1e8d5682..46829a2720 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -232,8 +232,9 @@ void NBinMulti::setup_bins(int /*style*/) bininvz_multi[n] = 1.0 / binsizez_multi[n]; if (binsize_optimal*bininvx_multi[n] > CUT2BIN_RATIO || - binsize_optimal*bininvy_multi[n] > CUT2BIN_RATIO || - binsize_optimal*bininvz_multi[n] > CUT2BIN_RATIO) + binsize_optimal*bininvy_multi[n] > CUT2BIN_RATIO) + error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); + if(dimension == 3 and binsize_optimal*bininvz_multi[n] > CUT2BIN_RATIO) error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); // mbinlo/hi = lowest and highest global bins my ghost atoms could be in From 2f5588733bf752bef213e0ea47e6c04cc9516df1 Mon Sep 17 00:00:00 2001 From: tc387 Date: Fri, 5 Feb 2021 18:47:04 -0600 Subject: [PATCH 0082/1217] fixed doc Latex error --- doc/src/fix_charge_regulation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index 585761e8a9..d2384fdc13 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/doc/src/fix_charge_regulation.rst @@ -70,7 +70,7 @@ The last type of reaction performs grand canonical MC exchange of ion pairs with In our implementation "acid" refers to particles that can attain charge :math:`q=\{0,-1\}` and "base" to particles with :math:`q=\{0,1\}`, whereas the MC exchange of free ions allows any integer charge values of :math:`{Z^+}` and :math:`{Z^-}`. -Here we provide several practical examples for modeling charge regulation effects in solvated systems. +Here we provide several practical examples for modeling charge regulation effects in solvated systems. An acid ionization reaction (:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{H}^+`) can be defined via a single line in the input file .. code-block:: LAMMPS From 4421843604c090ef8e776ca32bdab2a6da74f33b Mon Sep 17 00:00:00 2001 From: tc387 Date: Fri, 5 Feb 2021 19:00:33 -0600 Subject: [PATCH 0083/1217] fixed Latex doc error #2 --- doc/src/fix_charge_regulation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index d2384fdc13..a98288eb51 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/doc/src/fix_charge_regulation.rst @@ -106,7 +106,7 @@ If neither the acid or the base type is specified, for example, the fix simply inserts or deletes an ion pair of a free cation (atom type 4) and a free anion (atom type 5) as done in a conventional grand-canonical MC simulation. -The fix is compatible with LAMMPS sub-packages such as *molecule* or *rigid*. That said, the acid and base particles can be part of larger molecules or rigid bodies. Free ions that are inserted to or deleted from the system must be defined as single particles (no bonded interactions allowed) and cannot be part of larger molecules or rigid bodies. If *molecule* package is used, all inserted ions have a molecule ID equal to zero. +The fix is compatible with LAMMPS sub-packages such as *molecule* or *rigid*. That said, the acid and base particles can be part of larger molecules or rigid bodies. Free ions that are inserted to or deleted from the system must be defined as single particles (no bonded interactions allowed) and cannot be part of larger molecules or rigid bodies. If *molecule* package is used, all inserted ions have a molecule ID equal to zero. Note that LAMMPS implicitly assumes a constant number of particles (degrees of freedom). Since using this fix alters the total number of particles during the simulation, any thermostat used by LAMMPS, such as NVT or Langevin, must use a dynamic calculation of system temperature. This can be achieved by specifying a dynamic temperature compute (e.g. dtemp) and using it with the desired thermostat, e.g. a Langevin thermostat: From 65a82bb5858080214b77ecede4ab93ddc021de30 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sat, 6 Feb 2021 12:57:19 -0700 Subject: [PATCH 0084/1217] Adding new example --- examples/multi/data.powerlaw | 40000 +++++++++--------- examples/multi/in.powerlaw | 8 +- examples/multi/log.30Nov20.powerlaw.intel.1 | 344 +- examples/multi/log.30Nov20.powerlaw.intel.4 | 348 +- 4 files changed, 20450 insertions(+), 20250 deletions(-) diff --git a/examples/multi/data.powerlaw b/examples/multi/data.powerlaw index 8d1239f18b..2ce54cf4a6 100755 --- a/examples/multi/data.powerlaw +++ b/examples/multi/data.powerlaw @@ -10,20006 +10,20006 @@ LAMMPS data file via write_data, version 24 Dec 2020, timestep = 400000 Atoms # sphere -5 1 53.3452 1 24.11983771564243 68.3864105656564 0 0 0 0 -16 1 27.0148 1 44.452300814629524 34.553717084559324 0 0 0 0 -17 1 25.5929 1 68.38354504971392 54.06475170935992 0 0 0 0 -37 1 16.0333 1 21.245215917793043 25.77572727368242 0 0 0 0 -8263 1 1.097 1 11.708192742157616 17.87628382394025 0 1 0 0 -3384 1 1.72 1 50.90886093789832 62.30285871322583 0 0 0 0 -1246 1 2.857 1 48.42720785177107 19.125614604813737 0 0 1 0 -163 1 7.4543 1 52.92059018138831 11.758077886663509 0 0 0 0 -166 1 7.4036 1 52.22842193013173 57.14032835838031 0 0 0 0 -168 1 7.3782 1 67.8997369874434 37.71308832601801 0 0 0 0 -6557 1 1.2369 1 11.295799175061966 44.30117186186906 0 1 0 0 -208 1 6.6527 1 61.1259176496811 36.19196224734089 0 0 0 0 -336 1 5.417 1 65.06953771853591 21.29750437142649 0 0 0 0 -346 1 5.3618 1 22.215439365950207 37.0147208031179 0 0 0 0 -5513 1 1.3496 1 57.12033179181392 10.64220332754185 0 0 0 0 -412 1 4.8776 1 17.672010595684508 40.11493119326499 0 0 0 0 -439 1 4.6882 1 71.11713930089661 21.10972952271469 0 0 0 0 -511 1 4.3207 1 61.99786200551653 15.7285378811011 0 0 0 0 -527 1 4.2767 1 51.578706654445845 20.727968822288982 0 0 0 0 -4272 1 1.5377 1 57.071595881584244 19.179812412376158 0 0 1 0 -543 1 4.2317 1 27.26359333718018 39.94157599264931 0 0 0 0 -562 1 4.1677 1 59.81433643375789 66.07528891967839 0 0 0 0 -567 1 4.1383 1 16.49975368111738 34.647919218460544 0 0 0 0 -569 1 4.1329 1 29.01334056124924 32.03678406685905 0 0 0 0 -600 1 4.0221 1 54.27815300580397 62.3600853316132 0 0 0 0 -5108 1 1.4029 1 73.73125627225376 19.677797581451607 0 0 0 0 -617 1 3.975 1 55.98574134419896 67.02182364027037 0 0 0 0 -629 1 3.9339 1 70.33990954744172 31.235263322465816 0 0 0 0 -632 1 3.927 1 59.10259779677181 20.90661579877451 0 0 0 0 -675 1 3.8345 1 67.43217050972282 25.075831741614678 0 0 0 0 -7224 1 1.1762 1 60.56971642466663 73.63795194238719 0 0 0 0 -781 1 3.6204 1 65.88843570308798 16.951378069907122 0 0 0 0 -816 1 3.5492 1 29.47255639818249 36.989781506165265 0 0 0 0 -818 1 3.5444 1 71.07247296695553 25.216862431845435 0 0 0 0 -826 1 3.5256 1 56.16977635130581 23.054438891951555 0 0 0 0 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b/examples/multi/in.powerlaw index 90fc7aae3c..213aa3544e 100755 --- a/examples/multi/in.powerlaw +++ b/examples/multi/in.powerlaw @@ -15,19 +15,19 @@ comm_modify mode multi vel yes reduce/multi # granular potential pair_style granular -pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity +pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity # fixes fix 1 all nve/sphere fix 2 all enforce2d -fix 3 all deform 1 xy erate 2e-4 +fix 3 all deform 1 xy erate 1e-4 -# dump 1 all custom 2000 dump.granular id x y z radius +# dump 1 all custom 20000 dump.granular id x y z radius thermo_style custom step temp epair etotal press vol pxy thermo 1000 timestep 0.005 -run 100000 +run 200000 diff --git a/examples/multi/log.30Nov20.powerlaw.intel.1 b/examples/multi/log.30Nov20.powerlaw.intel.1 index 81b116ddd4..d0ed6e2685 100644 --- a/examples/multi/log.30Nov20.powerlaw.intel.1 +++ b/examples/multi/log.30Nov20.powerlaw.intel.1 @@ -1,12 +1,12 @@ LAMMPS (24 Dec 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task -# Big colloid particles and small LJ particles +# Shear power-law distributed granular particles units lj atom_style sphere dimension 2 -read_data data +read_data data.powerlaw Reading data file ... triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) 1 by 1 by 1 MPI processor grid @@ -28,22 +28,22 @@ comm_modify mode multi vel yes reduce/multi # granular potential pair_style granular -pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity +pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity # fixes fix 1 all nve/sphere fix 2 all enforce2d -fix 3 all deform 1 xy erate 2e-4 +fix 3 all deform 1 xy erate 1e-4 -# dump 1 all custom 2000 dump.granular id x y z radius +# dump 1 all custom 20000 dump.granular id x y z radius thermo_style custom step temp epair etotal press vol pxy thermo 1000 timestep 0.005 -run 100000 +run 200000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -56,136 +56,236 @@ Neighbor list info ... pair build: half/size/multi/newton/tri stencil: half/multi/2d/tri bin: multi -Per MPI rank memory allocation (min/avg/max) = 14.76 | 14.76 | 14.76 Mbytes +Per MPI rank memory allocation (min/avg/max) = 14.77 | 14.77 | 14.77 Mbytes Step Temp E_pair TotEng Press Volume Pxy - 0 0.00014649953 0 0.00014648488 0.027643657 103595.49 -0.0014952693 - 1000 0.00014726802 0 0.00014725329 0.029388139 103595.49 -0.00172238 - 2000 0.00014880425 0 0.00014878937 0.029608995 103595.49 -0.0023614491 - 3000 0.00015154766 0 0.0001515325 0.029668747 103595.49 -0.0029243775 - 4000 0.00015547813 0 0.00015546258 0.029662951 103595.49 -0.0034433688 - 5000 0.00015919808 0 0.00015918216 0.02988062 103595.49 -0.0037443111 - 6000 0.00016272902 0 0.00016271275 0.029776943 103595.49 -0.0042445445 - 7000 0.00016666322 0 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103595.49 -0.090238994 + 139000 0.00069748073 0 0.00069741098 0.55734587 103595.49 -0.090118549 + 140000 0.00071065284 0 0.00071058177 0.55711669 103595.49 -0.090336074 + 141000 0.00070994204 0 0.00070987104 0.55638115 103595.49 -0.089917062 + 142000 0.00071514386 0 0.00071507235 0.55614391 103595.49 -0.090392071 + 143000 0.00071334667 0 0.00071327533 0.55640687 103595.49 -0.091256718 + 144000 0.00069553102 0 0.00069546147 0.55705702 103595.49 -0.091761396 + 145000 0.00068849503 0 0.00068842618 0.55692035 103595.49 -0.091895738 + 146000 0.00068407816 0 0.00068400975 0.55660026 103595.49 -0.092191588 + 147000 0.00069521557 0 0.00069514605 0.55556456 103595.49 -0.092354739 + 148000 0.00068349281 0 0.00068342446 0.55537498 103595.49 -0.092914636 + 149000 0.00067959644 0 0.00067952848 0.55537695 103595.49 -0.093738463 + 150000 0.00067100566 0 0.00067093856 0.55544851 103595.49 -0.094104003 + 151000 0.00068044722 0 0.00068037917 0.5554655 103595.49 -0.094943239 + 152000 0.00068109012 0 0.00068102201 0.55585405 103595.49 -0.095355111 + 153000 0.00068666181 0 0.00068659314 0.55501583 103595.49 -0.095234652 + 154000 0.00068283406 0 0.00068276578 0.55644996 103595.49 -0.095902623 + 155000 0.00069836346 0 0.00069829363 0.55747472 103595.49 -0.096978444 + 156000 0.00072807264 0 0.00072799984 0.55807332 103595.49 -0.097415305 + 157000 0.00077300609 0 0.00077292879 0.55871196 103595.49 -0.098034508 + 158000 0.00081631408 0 0.00081623245 0.558479 103595.49 -0.09825722 + 159000 0.00079291984 0 0.00079284054 0.55784788 103595.49 -0.097758094 + 160000 0.0008203256 0 0.00082024357 0.55700259 103595.49 -0.097519328 + 161000 0.00081471235 0 0.00081463087 0.556622 103595.49 -0.097787992 + 162000 0.00080692462 0 0.00080684393 0.5566795 103595.49 -0.097210216 + 163000 0.00081149678 0 0.00081141564 0.55596697 103595.49 -0.097517476 + 164000 0.00081577795 0 0.00081569637 0.55569684 103595.49 -0.096908869 + 165000 0.00084604988 0 0.00084596528 0.55492052 103595.49 -0.095481627 + 166000 0.00082198923 0 0.00082190703 0.5552628 103595.49 -0.09477531 + 167000 0.00084903108 0 0.00084894618 0.55477991 103595.49 -0.094758799 + 168000 0.00081613582 0 0.00081605421 0.55508416 103595.49 -0.094804088 + 169000 0.00083341061 0 0.00083332727 0.55476794 103595.49 -0.094519882 + 170000 0.00077835092 0 0.00077827308 0.55516626 103595.49 -0.094843673 + 171000 0.00074843733 0 0.00074836249 0.55417469 103595.49 -0.094731356 + 172000 0.0007425125 0 0.00074243825 0.55431854 103595.49 -0.095174333 + 173000 0.00074144093 0 0.00074136678 0.55429464 103595.49 -0.094982598 + 174000 0.00072375323 0 0.00072368086 0.55421045 103595.49 -0.09489531 + 175000 0.0007270779 0 0.00072700519 0.55413607 103595.49 -0.094197685 + 176000 0.00071114682 0 0.00071107571 0.55342226 103595.49 -0.093083865 + 177000 0.00069325125 0 0.00069318193 0.55441386 103595.49 -0.093289572 + 178000 0.00067686202 0 0.00067679434 0.55504892 103595.49 -0.093512587 + 179000 0.00068326039 0 0.00068319206 0.55519365 103595.49 -0.093974329 + 180000 0.00075070045 0 0.00075062538 0.55415541 103595.49 -0.09327459 + 181000 0.00077670344 0 0.00077662577 0.55328725 103595.49 -0.092373689 + 182000 0.00077422781 0 0.00077415038 0.553131 103595.49 -0.092353979 + 183000 0.00080250542 0 0.00080242517 0.5519122 103595.49 -0.091897169 + 184000 0.00081235214 0 0.00081227091 0.55172769 103595.49 -0.091906209 + 185000 0.00078879443 0 0.00078871555 0.55145488 103595.49 -0.091198506 + 186000 0.00078497746 0 0.00078489896 0.55202944 103595.49 -0.091674987 + 187000 0.00079483049 0 0.000794751 0.55278073 103595.49 -0.092508295 + 188000 0.00079056756 0 0.0007904885 0.55362903 103595.49 -0.092801369 + 189000 0.00079162262 0 0.00079154346 0.55429061 103595.49 -0.092964781 + 190000 0.00078121133 0 0.00078113321 0.55386716 103595.49 -0.092689851 + 191000 0.00076574893 0 0.00076567235 0.5546533 103595.49 -0.093414672 + 192000 0.00076215201 0 0.0007620758 0.55503049 103595.49 -0.093986391 + 193000 0.00075652635 0 0.0007564507 0.55477696 103595.49 -0.094417347 + 194000 0.00075725781 0 0.00075718208 0.55457687 103595.49 -0.094241721 + 195000 0.0007434693 0 0.00074339496 0.55471575 103595.49 -0.094102015 + 196000 0.00073792493 0 0.00073785114 0.55463671 103595.49 -0.094452279 + 197000 0.00074673445 0 0.00074665978 0.55459327 103595.49 -0.09463863 + 198000 0.00072734835 0 0.00072727561 0.55514628 103595.49 -0.094622434 + 199000 0.00071846919 0 0.00071839734 0.55501969 103595.49 -0.094414887 + 200000 0.00072384651 0 0.00072377412 0.55533335 103595.49 -0.094159469 +Loop time of 443.321 on 1 procs for 200000 steps with 10000 atoms -Performance: 184845.371 tau/day, 427.883 timesteps/s +Performance: 194892.839 tau/day, 451.141 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 193.18 | 193.18 | 193.18 | 0.0 | 82.66 -Neigh | 1.1138 | 1.1138 | 1.1138 | 0.0 | 0.48 -Comm | 2.3652 | 2.3652 | 2.3652 | 0.0 | 1.01 -Output | 0.0092981 | 0.0092981 | 0.0092981 | 0.0 | 0.00 -Modify | 32.407 | 32.407 | 32.407 | 0.0 | 13.87 -Other | | 4.628 | | | 1.98 +Pair | 362.28 | 362.28 | 362.28 | 0.0 | 81.72 +Neigh | 1.737 | 1.737 | 1.737 | 0.0 | 0.39 +Comm | 5.0082 | 5.0082 | 5.0082 | 0.0 | 1.13 +Output | 0.01774 | 0.01774 | 0.01774 | 0.0 | 0.00 +Modify | 64.992 | 64.992 | 64.992 | 0.0 | 14.66 +Other | | 9.286 | | | 2.09 Nlocal: 10000.0 ave 10000 max 10000 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 446.000 ave 446 max 446 min +Nghost: 487.000 ave 487 max 487 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 34464.0 ave 34464 max 34464 min +Neighs: 34427.0 ave 34427 max 34427 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 34464 -Ave neighs/atom = 3.4464000 -Neighbor list builds = 153 +Total # of neighbors = 34427 +Ave neighs/atom = 3.4427000 +Neighbor list builds = 244 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:03:53 +Total wall time: 0:07:23 diff --git a/examples/multi/log.30Nov20.powerlaw.intel.4 b/examples/multi/log.30Nov20.powerlaw.intel.4 index 34d3b85c1b..109b4582db 100644 --- a/examples/multi/log.30Nov20.powerlaw.intel.4 +++ b/examples/multi/log.30Nov20.powerlaw.intel.4 @@ -1,12 +1,12 @@ LAMMPS (24 Dec 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task -# Big colloid particles and small LJ particles +# Shear power-law distributed granular particles units lj atom_style sphere dimension 2 -read_data data +read_data data.powerlaw Reading data file ... triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) 2 by 2 by 1 MPI processor grid @@ -14,7 +14,7 @@ Reading data file ... 10000 atoms reading velocities ... 10000 velocities - read_data CPU = 0.024 seconds + read_data CPU = 0.114 seconds change_box all triclinic Changing box ... triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) @@ -28,22 +28,22 @@ comm_modify mode multi vel yes reduce/multi # granular potential pair_style granular -pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity +pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity # fixes fix 1 all nve/sphere fix 2 all enforce2d -fix 3 all deform 1 xy erate 2e-4 +fix 3 all deform 1 xy erate 1e-4 -# dump 1 all custom 2000 dump.granular id x y z radius +# dump 1 all custom 20000 dump.granular id x y z radius thermo_style custom step temp epair etotal press vol pxy thermo 1000 timestep 0.005 -run 100000 +run 200000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -58,134 +58,234 @@ Neighbor list info ... bin: multi Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.67 | 12.68 Mbytes Step Temp E_pair TotEng Press Volume Pxy - 0 0.00014649953 0 0.00014648488 0.027643657 103595.49 -0.0014952693 - 1000 0.00014726802 0 0.00014725329 0.029388139 103595.49 -0.00172238 - 2000 0.00014880425 0 0.00014878937 0.029608995 103595.49 -0.0023614491 - 3000 0.00015154766 0 0.0001515325 0.029668747 103595.49 -0.0029243775 - 4000 0.00015547813 0 0.00015546258 0.029662951 103595.49 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0.55282781 103595.49 -0.093282587 + 178000 0.00073688566 0 0.00073681197 0.55223248 103595.49 -0.092190554 + 179000 0.00072455886 0 0.0007244864 0.55244288 103595.49 -0.09182393 + 180000 0.00071894558 0 0.00071887369 0.55281517 103595.49 -0.092177032 + 181000 0.00071752475 0 0.000717453 0.55297293 103595.49 -0.09230934 + 182000 0.00072247421 0 0.00072240196 0.55287294 103595.49 -0.092465908 + 183000 0.00070596821 0 0.00070589761 0.5526242 103595.49 -0.092013313 + 184000 0.00072460909 0 0.00072453663 0.55230817 103595.49 -0.092211243 + 185000 0.00072499917 0 0.00072492667 0.55273387 103595.49 -0.092920761 + 186000 0.00072852698 0 0.00072845413 0.55358929 103595.49 -0.093428623 + 187000 0.00072515668 0 0.00072508417 0.55336733 103595.49 -0.093440126 + 188000 0.00071355728 0 0.00071348593 0.55408468 103595.49 -0.094819333 + 189000 0.00071703212 0 0.00071696042 0.55424355 103595.49 -0.096198144 + 190000 0.00071808849 0 0.00071801668 0.55504118 103595.49 -0.097199842 + 191000 0.00072458142 0 0.00072450896 0.55493515 103595.49 -0.097564772 + 192000 0.00071472504 0 0.00071465357 0.55572657 103595.49 -0.097663072 + 193000 0.00070803966 0 0.00070796886 0.55546116 103595.49 -0.097306162 + 194000 0.00068236077 0 0.00068229254 0.55581155 103595.49 -0.097141594 + 195000 0.00067304613 0 0.00067297882 0.55559507 103595.49 -0.096646489 + 196000 0.00066680808 0 0.0006667414 0.55512029 103595.49 -0.096241456 + 197000 0.00065829161 0 0.00065822578 0.55545375 103595.49 -0.095808778 + 198000 0.0006617611 0 0.00066169492 0.55551074 103595.49 -0.095423531 + 199000 0.00066805655 0 0.00066798975 0.55581298 103595.49 -0.095287337 + 200000 0.00067263902 0 0.00067257175 0.55601669 103595.49 -0.095551006 +Loop time of 145.127 on 4 procs for 200000 steps with 10000 atoms -Performance: 555175.163 tau/day, 1285.128 timesteps/s +Performance: 595339.507 tau/day, 1378.101 timesteps/s 100.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 28.939 | 48.992 | 61.808 | 189.4 | 62.96 -Neigh | 0.22765 | 0.31872 | 0.38751 | 10.9 | 0.41 -Comm | 3.53 | 16.362 | 36.515 | 328.8 | 21.03 -Output | 0.0046275 | 0.0064601 | 0.008626 | 1.8 | 0.01 -Modify | 5.0862 | 8.3128 | 10.255 | 74.1 | 10.68 -Other | | 3.821 | | | 4.91 +Pair | 57.89 | 91.946 | 113.82 | 229.7 | 63.36 +Neigh | 0.34276 | 0.48607 | 0.56708 | 13.1 | 0.33 +Comm | 6.569 | 28.916 | 63.505 | 417.0 | 19.92 +Output | 0.0087178 | 0.011935 | 0.01563 | 2.3 | 0.01 +Modify | 10.432 | 16.495 | 20.378 | 97.7 | 11.37 +Other | | 7.272 | | | 5.01 -Nlocal: 2500.00 ave 3016 max 1605 min +Nlocal: 2500.00 ave 2990 max 1652 min Histogram: 1 0 0 0 0 1 0 0 0 2 -Nghost: 221.500 ave 273 max 176 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Neighs: 8616.00 ave 10377 max 5447 min +Nghost: 228.000 ave 254 max 198 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 8611.25 ave 10364 max 5676 min Histogram: 1 0 0 0 0 1 0 0 0 2 -Total # of neighbors = 34464 -Ave neighs/atom = 3.4464000 -Neighbor list builds = 153 +Total # of neighbors = 34445 +Ave neighs/atom = 3.4445000 +Neighbor list builds = 241 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:01:17 +Total wall time: 0:02:25 From 880b40e10465d7292d4987302b7a49ab86042a64 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 7 Feb 2021 10:44:51 -0700 Subject: [PATCH 0085/1217] Adding setup_bins() method to nbin_intel.cpp --- src/USER-INTEL/nbin_intel.cpp | 161 ++++++++++++++++++++++++++++++++++ src/USER-INTEL/nbin_intel.h | 1 + 2 files changed, 162 insertions(+) diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp index 31b53e3462..848ac6edd8 100644 --- a/src/USER-INTEL/nbin_intel.cpp +++ b/src/USER-INTEL/nbin_intel.cpp @@ -21,11 +21,15 @@ #include "comm.h" #include "error.h" #include "group.h" +#include "domain.h" #include "modify.h" #include "update.h" using namespace LAMMPS_NS; +#define SMALL 1.0e-6 +#define CUT2BIN_RATIO 100 + /* ---------------------------------------------------------------------- */ NBinIntel::NBinIntel(LAMMPS *lmp) : NBinStandard(lmp) { @@ -132,6 +136,163 @@ void NBinIntel::bin_atoms_setup(int nall) } } + +/* ---------------------------------------------------------------------- + setup neighbor binning geometry + bin numbering in each dimension is global: + 0 = 0.0 to binsize, 1 = binsize to 2*binsize, etc + nbin-1,nbin,etc = bbox-binsize to bbox, bbox to bbox+binsize, etc + -1,-2,etc = -binsize to 0.0, -2*binsize to -binsize, etc + code will work for any binsize + since next(xyz) and stencil extend as far as necessary + binsize = 1/2 of cutoff is roughly optimal + for orthogonal boxes: + a dim must be filled exactly by integer # of bins + in periodic, procs on both sides of PBC must see same bin boundary + in non-periodic, coord2bin() still assumes this by use of nbin xyz + for triclinic boxes: + tilted simulation box cannot contain integer # of bins + stencil & neigh list built differently to account for this + mbinlo = lowest global bin any of my ghost atoms could fall into + mbinhi = highest global bin any of my ghost atoms could fall into + mbin = number of bins I need in a dimension +------------------------------------------------------------------------- */ + +void NBinIntel::setup_bins(int style) +{ + // bbox = size of bbox of entire domain + // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost + // for triclinic: + // bbox bounds all 8 corners of tilted box + // subdomain is in lamda coords + // include dimension-dependent extension via comm->cutghost + // domain->bbox() converts lamda extent to box coords and computes bbox + + double bbox[3],bsubboxlo[3],bsubboxhi[3]; + double *cutghost = comm->cutghost; + + if (triclinic == 0) { + bsubboxlo[0] = domain->sublo[0] - cutghost[0]; + bsubboxlo[1] = domain->sublo[1] - cutghost[1]; + bsubboxlo[2] = domain->sublo[2] - cutghost[2]; + bsubboxhi[0] = domain->subhi[0] + cutghost[0]; + bsubboxhi[1] = domain->subhi[1] + cutghost[1]; + bsubboxhi[2] = domain->subhi[2] + cutghost[2]; + } else { + double lo[3],hi[3]; + lo[0] = domain->sublo_lamda[0] - cutghost[0]; + lo[1] = domain->sublo_lamda[1] - cutghost[1]; + lo[2] = domain->sublo_lamda[2] - cutghost[2]; + hi[0] = domain->subhi_lamda[0] + cutghost[0]; + hi[1] = domain->subhi_lamda[1] + cutghost[1]; + hi[2] = domain->subhi_lamda[2] + cutghost[2]; + domain->bbox(lo,hi,bsubboxlo,bsubboxhi); + } + + bbox[0] = bboxhi[0] - bboxlo[0]; + bbox[1] = bboxhi[1] - bboxlo[1]; + bbox[2] = bboxhi[2] - bboxlo[2]; + + // optimal bin size is roughly 1/2 the cutoff + // for BIN style, binsize = 1/2 of max neighbor cutoff + // for MULTI_OLD style, binsize = 1/2 of min neighbor cutoff + // special case of all cutoffs = 0.0, binsize = box size + + double binsize_optimal; + if (binsizeflag) binsize_optimal = binsize_user; + else if (style == Neighbor::BIN) binsize_optimal = 0.5*cutneighmax; + else binsize_optimal = 0.5*cutneighmin; + if (binsize_optimal == 0.0) binsize_optimal = bbox[0]; + double binsizeinv = 1.0/binsize_optimal; + + // test for too many global bins in any dimension due to huge global domain + + if (bbox[0]*binsizeinv > MAXSMALLINT || bbox[1]*binsizeinv > MAXSMALLINT || + bbox[2]*binsizeinv > MAXSMALLINT) + error->all(FLERR,"Domain too large for neighbor bins"); + + // create actual bins + // always have one bin even if cutoff > bbox + // for 2d, nbinz = 1 + + nbinx = static_cast (bbox[0]*binsizeinv); + nbiny = static_cast (bbox[1]*binsizeinv); + if (dimension == 3) nbinz = static_cast (bbox[2]*binsizeinv); + else nbinz = 1; + + if (nbinx == 0) nbinx = 1; + if (nbiny == 0) nbiny = 1; + if (nbinz == 0) nbinz = 1; + + // compute actual bin size for nbins to fit into box exactly + // error if actual bin size << cutoff, since will create a zillion bins + // this happens when nbin = 1 and box size << cutoff + // typically due to non-periodic, flat system in a particular dim + // in that extreme case, should use NSQ not BIN neighbor style + + binsizex = bbox[0]/nbinx; + binsizey = bbox[1]/nbiny; + binsizez = bbox[2]/nbinz; + + bininvx = 1.0 / binsizex; + bininvy = 1.0 / binsizey; + bininvz = 1.0 / binsizez; + + if (binsize_optimal*bininvx > CUT2BIN_RATIO || + binsize_optimal*bininvy > CUT2BIN_RATIO || + binsize_optimal*bininvz > CUT2BIN_RATIO) + error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); + + // mbinlo/hi = lowest and highest global bins my ghost atoms could be in + // coord = lowest and highest values of coords for my ghost atoms + // static_cast(-1.5) = -1, so subract additional -1 + // add in SMALL for round-off safety + + int mbinxhi,mbinyhi,mbinzhi; + double coord; + + coord = bsubboxlo[0] - SMALL*bbox[0]; + mbinxlo = static_cast ((coord-bboxlo[0])*bininvx); + if (coord < bboxlo[0]) mbinxlo = mbinxlo - 1; + coord = bsubboxhi[0] + SMALL*bbox[0]; + mbinxhi = static_cast ((coord-bboxlo[0])*bininvx); + + coord = bsubboxlo[1] - SMALL*bbox[1]; + mbinylo = static_cast ((coord-bboxlo[1])*bininvy); + if (coord < bboxlo[1]) mbinylo = mbinylo - 1; + coord = bsubboxhi[1] + SMALL*bbox[1]; + mbinyhi = static_cast ((coord-bboxlo[1])*bininvy); + + if (dimension == 3) { + coord = bsubboxlo[2] - SMALL*bbox[2]; + mbinzlo = static_cast ((coord-bboxlo[2])*bininvz); + if (coord < bboxlo[2]) mbinzlo = mbinzlo - 1; + coord = bsubboxhi[2] + SMALL*bbox[2]; + mbinzhi = static_cast ((coord-bboxlo[2])*bininvz); + } + + // extend bins by 1 to insure stencil extent is included + // for 2d, only 1 bin in z + + mbinxlo = mbinxlo - 1; + mbinxhi = mbinxhi + 1; + mbinx = mbinxhi - mbinxlo + 1; + + mbinylo = mbinylo - 1; + mbinyhi = mbinyhi + 1; + mbiny = mbinyhi - mbinylo + 1; + + if (dimension == 3) { + mbinzlo = mbinzlo - 1; + mbinzhi = mbinzhi + 1; + } else mbinzlo = mbinzhi = 0; + mbinz = mbinzhi - mbinzlo + 1; + + bigint bbin = ((bigint) mbinx) * ((bigint) mbiny) * ((bigint) mbinz) + 1; + if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins"); + mbins = bbin; +} + /* ---------------------------------------------------------------------- bin owned and ghost atoms ------------------------------------------------------------------------- */ diff --git a/src/USER-INTEL/nbin_intel.h b/src/USER-INTEL/nbin_intel.h index a7a28010ba..e49f332392 100644 --- a/src/USER-INTEL/nbin_intel.h +++ b/src/USER-INTEL/nbin_intel.h @@ -33,6 +33,7 @@ class NBinIntel : public NBinStandard { NBinIntel(class LAMMPS *); ~NBinIntel(); void bin_atoms_setup(int); + void setup_bins(int); void bin_atoms(); int * get_binpacked() { return _binpacked; } From 05f02fbc32230222900853b675be015fd77de018 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 7 Feb 2021 12:40:59 -0700 Subject: [PATCH 0086/1217] Removing setup method and adding correct nbin bitmask --- src/USER-INTEL/nbin_intel.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-INTEL/nbin_intel.h b/src/USER-INTEL/nbin_intel.h index e49f332392..b2b3d5d0ca 100644 --- a/src/USER-INTEL/nbin_intel.h +++ b/src/USER-INTEL/nbin_intel.h @@ -15,7 +15,7 @@ NBinStyle(intel, NBinIntel, - NB_INTEL) + NB_STANDARD | NB_INTEL) #else From 5a4c45f2ea98867af95ac1dc90a600f48ee2c2d6 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 7 Feb 2021 13:02:45 -0700 Subject: [PATCH 0087/1217] Fixing bitmasks and removing method again --- src/USER-INTEL/nbin_intel.cpp | 161 ---------------------------------- src/USER-INTEL/nbin_intel.h | 1 - 2 files changed, 162 deletions(-) diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp index 848ac6edd8..31b53e3462 100644 --- a/src/USER-INTEL/nbin_intel.cpp +++ b/src/USER-INTEL/nbin_intel.cpp @@ -21,15 +21,11 @@ #include "comm.h" #include "error.h" #include "group.h" -#include "domain.h" #include "modify.h" #include "update.h" using namespace LAMMPS_NS; -#define SMALL 1.0e-6 -#define CUT2BIN_RATIO 100 - /* ---------------------------------------------------------------------- */ NBinIntel::NBinIntel(LAMMPS *lmp) : NBinStandard(lmp) { @@ -136,163 +132,6 @@ void NBinIntel::bin_atoms_setup(int nall) } } - -/* ---------------------------------------------------------------------- - setup neighbor binning geometry - bin numbering in each dimension is global: - 0 = 0.0 to binsize, 1 = binsize to 2*binsize, etc - nbin-1,nbin,etc = bbox-binsize to bbox, bbox to bbox+binsize, etc - -1,-2,etc = -binsize to 0.0, -2*binsize to -binsize, etc - code will work for any binsize - since next(xyz) and stencil extend as far as necessary - binsize = 1/2 of cutoff is roughly optimal - for orthogonal boxes: - a dim must be filled exactly by integer # of bins - in periodic, procs on both sides of PBC must see same bin boundary - in non-periodic, coord2bin() still assumes this by use of nbin xyz - for triclinic boxes: - tilted simulation box cannot contain integer # of bins - stencil & neigh list built differently to account for this - mbinlo = lowest global bin any of my ghost atoms could fall into - mbinhi = highest global bin any of my ghost atoms could fall into - mbin = number of bins I need in a dimension -------------------------------------------------------------------------- */ - -void NBinIntel::setup_bins(int style) -{ - // bbox = size of bbox of entire domain - // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost - // for triclinic: - // bbox bounds all 8 corners of tilted box - // subdomain is in lamda coords - // include dimension-dependent extension via comm->cutghost - // domain->bbox() converts lamda extent to box coords and computes bbox - - double bbox[3],bsubboxlo[3],bsubboxhi[3]; - double *cutghost = comm->cutghost; - - if (triclinic == 0) { - bsubboxlo[0] = domain->sublo[0] - cutghost[0]; - bsubboxlo[1] = domain->sublo[1] - cutghost[1]; - bsubboxlo[2] = domain->sublo[2] - cutghost[2]; - bsubboxhi[0] = domain->subhi[0] + cutghost[0]; - bsubboxhi[1] = domain->subhi[1] + cutghost[1]; - bsubboxhi[2] = domain->subhi[2] + cutghost[2]; - } else { - double lo[3],hi[3]; - lo[0] = domain->sublo_lamda[0] - cutghost[0]; - lo[1] = domain->sublo_lamda[1] - cutghost[1]; - lo[2] = domain->sublo_lamda[2] - cutghost[2]; - hi[0] = domain->subhi_lamda[0] + cutghost[0]; - hi[1] = domain->subhi_lamda[1] + cutghost[1]; - hi[2] = domain->subhi_lamda[2] + cutghost[2]; - domain->bbox(lo,hi,bsubboxlo,bsubboxhi); - } - - bbox[0] = bboxhi[0] - bboxlo[0]; - bbox[1] = bboxhi[1] - bboxlo[1]; - bbox[2] = bboxhi[2] - bboxlo[2]; - - // optimal bin size is roughly 1/2 the cutoff - // for BIN style, binsize = 1/2 of max neighbor cutoff - // for MULTI_OLD style, binsize = 1/2 of min neighbor cutoff - // special case of all cutoffs = 0.0, binsize = box size - - double binsize_optimal; - if (binsizeflag) binsize_optimal = binsize_user; - else if (style == Neighbor::BIN) binsize_optimal = 0.5*cutneighmax; - else binsize_optimal = 0.5*cutneighmin; - if (binsize_optimal == 0.0) binsize_optimal = bbox[0]; - double binsizeinv = 1.0/binsize_optimal; - - // test for too many global bins in any dimension due to huge global domain - - if (bbox[0]*binsizeinv > MAXSMALLINT || bbox[1]*binsizeinv > MAXSMALLINT || - bbox[2]*binsizeinv > MAXSMALLINT) - error->all(FLERR,"Domain too large for neighbor bins"); - - // create actual bins - // always have one bin even if cutoff > bbox - // for 2d, nbinz = 1 - - nbinx = static_cast (bbox[0]*binsizeinv); - nbiny = static_cast (bbox[1]*binsizeinv); - if (dimension == 3) nbinz = static_cast (bbox[2]*binsizeinv); - else nbinz = 1; - - if (nbinx == 0) nbinx = 1; - if (nbiny == 0) nbiny = 1; - if (nbinz == 0) nbinz = 1; - - // compute actual bin size for nbins to fit into box exactly - // error if actual bin size << cutoff, since will create a zillion bins - // this happens when nbin = 1 and box size << cutoff - // typically due to non-periodic, flat system in a particular dim - // in that extreme case, should use NSQ not BIN neighbor style - - binsizex = bbox[0]/nbinx; - binsizey = bbox[1]/nbiny; - binsizez = bbox[2]/nbinz; - - bininvx = 1.0 / binsizex; - bininvy = 1.0 / binsizey; - bininvz = 1.0 / binsizez; - - if (binsize_optimal*bininvx > CUT2BIN_RATIO || - binsize_optimal*bininvy > CUT2BIN_RATIO || - binsize_optimal*bininvz > CUT2BIN_RATIO) - error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); - - // mbinlo/hi = lowest and highest global bins my ghost atoms could be in - // coord = lowest and highest values of coords for my ghost atoms - // static_cast(-1.5) = -1, so subract additional -1 - // add in SMALL for round-off safety - - int mbinxhi,mbinyhi,mbinzhi; - double coord; - - coord = bsubboxlo[0] - SMALL*bbox[0]; - mbinxlo = static_cast ((coord-bboxlo[0])*bininvx); - if (coord < bboxlo[0]) mbinxlo = mbinxlo - 1; - coord = bsubboxhi[0] + SMALL*bbox[0]; - mbinxhi = static_cast ((coord-bboxlo[0])*bininvx); - - coord = bsubboxlo[1] - SMALL*bbox[1]; - mbinylo = static_cast ((coord-bboxlo[1])*bininvy); - if (coord < bboxlo[1]) mbinylo = mbinylo - 1; - coord = bsubboxhi[1] + SMALL*bbox[1]; - mbinyhi = static_cast ((coord-bboxlo[1])*bininvy); - - if (dimension == 3) { - coord = bsubboxlo[2] - SMALL*bbox[2]; - mbinzlo = static_cast ((coord-bboxlo[2])*bininvz); - if (coord < bboxlo[2]) mbinzlo = mbinzlo - 1; - coord = bsubboxhi[2] + SMALL*bbox[2]; - mbinzhi = static_cast ((coord-bboxlo[2])*bininvz); - } - - // extend bins by 1 to insure stencil extent is included - // for 2d, only 1 bin in z - - mbinxlo = mbinxlo - 1; - mbinxhi = mbinxhi + 1; - mbinx = mbinxhi - mbinxlo + 1; - - mbinylo = mbinylo - 1; - mbinyhi = mbinyhi + 1; - mbiny = mbinyhi - mbinylo + 1; - - if (dimension == 3) { - mbinzlo = mbinzlo - 1; - mbinzhi = mbinzhi + 1; - } else mbinzlo = mbinzhi = 0; - mbinz = mbinzhi - mbinzlo + 1; - - bigint bbin = ((bigint) mbinx) * ((bigint) mbiny) * ((bigint) mbinz) + 1; - if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins"); - mbins = bbin; -} - /* ---------------------------------------------------------------------- bin owned and ghost atoms ------------------------------------------------------------------------- */ diff --git a/src/USER-INTEL/nbin_intel.h b/src/USER-INTEL/nbin_intel.h index b2b3d5d0ca..fef1bf0f26 100644 --- a/src/USER-INTEL/nbin_intel.h +++ b/src/USER-INTEL/nbin_intel.h @@ -33,7 +33,6 @@ class NBinIntel : public NBinStandard { NBinIntel(class LAMMPS *); ~NBinIntel(); void bin_atoms_setup(int); - void setup_bins(int); void bin_atoms(); int * get_binpacked() { return _binpacked; } From 952216033ee551769611e0d31cfe059856405baf Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 7 Feb 2021 13:33:11 -0700 Subject: [PATCH 0088/1217] Adding correct masks to kokks/user-dpd nbin classes --- src/KOKKOS/nbin_kokkos.h | 4 ++-- src/KOKKOS/nbin_ssa_kokkos.h | 4 ++-- src/USER-DPD/nbin_ssa.h | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/KOKKOS/nbin_kokkos.h b/src/KOKKOS/nbin_kokkos.h index bf2ccc5908..7297489d4a 100644 --- a/src/KOKKOS/nbin_kokkos.h +++ b/src/KOKKOS/nbin_kokkos.h @@ -15,11 +15,11 @@ NBinStyle(kk/host, NBinKokkos, - NB_KOKKOS_HOST) + NB_STANDARD | NB_KOKKOS_HOST) NBinStyle(kk/device, NBinKokkos, - NB_KOKKOS_DEVICE) + NB_STANDARD | NB_KOKKOS_DEVICE) #else diff --git a/src/KOKKOS/nbin_ssa_kokkos.h b/src/KOKKOS/nbin_ssa_kokkos.h index c9a389bed4..b094bf8ae6 100644 --- a/src/KOKKOS/nbin_ssa_kokkos.h +++ b/src/KOKKOS/nbin_ssa_kokkos.h @@ -15,11 +15,11 @@ NBinStyle(ssa/kk/host, NBinSSAKokkos, - NB_SSA | NB_KOKKOS_HOST) + NB_STANDARD | NB_SSA | NB_KOKKOS_HOST) NBinStyle(ssa/kk/device, NBinSSAKokkos, - NB_SSA | NB_KOKKOS_DEVICE) + NB_STANDARD | NB_SSA | NB_KOKKOS_DEVICE) #else diff --git a/src/USER-DPD/nbin_ssa.h b/src/USER-DPD/nbin_ssa.h index eb4b2db24c..7c6bf4325b 100644 --- a/src/USER-DPD/nbin_ssa.h +++ b/src/USER-DPD/nbin_ssa.h @@ -15,7 +15,7 @@ NBinStyle(ssa, NBinSSA, - NB_SSA) + NB_STANDARD | NB_SSA) #else From de1205c5a9e3aa80e6958135169902d22f9afbac Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Sun, 7 Feb 2021 20:38:24 -0700 Subject: [PATCH 0089/1217] Fixing misc valgrind issues, particularly with resizing ncollections --- src/comm.cpp | 2 + src/comm.h | 1 + src/comm_brick.cpp | 11 +-- src/comm_tiled.cpp | 15 ++-- src/nbin_multi.cpp | 6 +- src/neighbor.cpp | 9 ++- src/nstencil.cpp | 121 ++++++++++++++++++++------------- src/nstencil.h | 3 +- src/nstencil_half_multi_2d.cpp | 2 +- 9 files changed, 105 insertions(+), 65 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index 33e4b894d5..d729545dba 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -58,6 +58,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) bordergroup = 0; cutghostuser = 0.0; cutusermulti = nullptr; + cutusermultiflag = 0; cutusermultiold = nullptr; ncollections_prior = 0; ghost_velocity = 0; @@ -348,6 +349,7 @@ void Comm::modify_params(int narg, char **arg) // ncollections can be changed by neigh_modify commands cut = utils::numeric(FLERR,arg[iarg+2],false,lmp); cutghostuser = MAX(cutghostuser,cut); + cutusermultiflag = 1; if (cut < 0.0) error->all(FLERR,"Invalid cutoff in comm_modify command"); usermultiargs.emplace_back(arg[iarg+1], cut); diff --git a/src/comm.h b/src/comm.h index 2afdfd8765..418983b6e6 100644 --- a/src/comm.h +++ b/src/comm.h @@ -33,6 +33,7 @@ class Comm : protected Pointers { double cutghost[3]; // cutoffs used for acquiring ghost atoms double cutghostuser; // user-specified ghost cutoff (mode == 0) double *cutusermulti; // per collection user ghost cutoff (mode == 1) + int cutusermultiflag; std::vector> usermultiargs; // collection args for custom ghost cutoffs double *cutusermultiold; // per type user ghost cutoff (mode == 2) diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 58c6a65837..160ecf2c3d 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -142,6 +142,7 @@ void CommBrick::init() // allocate in setup if (mode == Comm::MULTI && multilo == nullptr) { + ncollections = neighbor->ncollections; allocate_multi(maxswap); memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); ncollections_prior = ncollections; @@ -205,10 +206,12 @@ void CommBrick::setup() allocate_multi(maxswap); memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); - memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); - for(i = ncollections_prior; i < ncollections; i++) - cutusermulti[i] = -1.0; - + if(cutusermultiflag) { + memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); + for(i = ncollections_prior; i < ncollections; i++) + cutusermulti[i] = -1.0; + } + ncollections_prior = ncollections; } diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index c06ad52d6c..0a09dc830d 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -104,6 +104,11 @@ void CommTiled::init_buffers() cutghostmultiold = nullptr; sendbox_multi = nullptr; sendbox_multiold = nullptr; + + // initialize ncollections so grow_swap_send_multi() will not + // construct arrays in init() but will wait for setup() + ncollections = 0; + ncollections_prior = 0; maxswap = 6; allocate_swap(maxswap); @@ -194,10 +199,12 @@ void CommTiled::setup() for(i = 0; i < maxswap; i ++) grow_swap_send_multi(i,DELTA_PROCS); - memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); - for(i = ncollections_prior; i < ncollections; i++) - cutusermulti[i] = -1.0; - + if(cutusermultiflag){ + memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); + for(i = ncollections_prior; i < ncollections; i++) + cutusermulti[i] = -1.0; + } + ncollections_prior = ncollections; } diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index bbc69dc2d6..a39f10d074 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -146,7 +146,7 @@ void NBinMulti::setup_bins(int /*style*/) // Identify smallest collection int icollectionmin = 0; - for (n = 0; n < maxcollections; n++) + for (n = 0; n < ncollections; n++) if (cutcollectionsq[n][n] < cutcollectionsq[icollectionmin][icollectionmin]) icollectionmin = n; @@ -188,7 +188,7 @@ void NBinMulti::setup_bins(int /*style*/) double binsize_optimal, binsizeinv, coord; int mbinxhi,mbinyhi,mbinzhi; - for (n = 0; n < maxcollections; n++) { + for (n = 0; n < ncollections; n++) { // binsize_user only relates to smallest collection // optimal bin size is roughly 1/2 the collection-collection cutoff // special case of all cutoffs = 0.0, binsize = box size @@ -296,7 +296,7 @@ void NBinMulti::bin_atoms() int i,ibin,n; last_bin = update->ntimestep; - for (n = 0; n < maxcollections; n++) { + for (n = 0; n < ncollections; n++) { for (i = 0; i < mbins_multi[n]; i++) binhead_multi[n][i] = -1; } // bin in reverse order so linked list will be in forward order diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 2671553a07..e8f9798df8 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -426,7 +426,7 @@ void Neighbor::init() for(i = 1; i <= n; i++){ cuttmp = sqrt(cutneighsq[i][i]); for(icollection = 0; icollection < ncollections; icollection ++){ - if(collection2cut[icollection] > cuttmp) { + if(collection2cut[icollection] >= cuttmp) { type2collection[i] = icollection; break; } @@ -2503,6 +2503,8 @@ void Neighbor::modify_params(int narg, char **arg) if(iarg+2 > narg) error->all(FLERR,"Invalid collection/interval command"); ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if(ncollections < 1) + error->all(FLERR,"Invalid collection/interval command"); if(iarg+1+ncollections > narg) error->all(FLERR,"Invalid collection/interval command"); @@ -2511,8 +2513,7 @@ void Neighbor::modify_params(int narg, char **arg) interval_collection_flag = 1; custom_collection_flag = 1; - if(not collection2cut) - memory->create(collection2cut,ncollections,"neigh:collection2cut"); + memory->grow(collection2cut,ncollections,"neigh:collection2cut"); // Set upper cutoff for each collection char *id; @@ -2534,6 +2535,8 @@ void Neighbor::modify_params(int narg, char **arg) if(iarg+2 > narg) error->all(FLERR,"Invalid collection/type command"); ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if(ncollections < 1) + error->all(FLERR,"Invalid collection/interval command"); if(iarg+1+ncollections > narg) error->all(FLERR,"Invalid collection/type command"); diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 3cf75d8d68..ba7259a9fc 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -82,6 +82,8 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) flag_half_multi = nullptr; flag_skip_multi = nullptr; bin_collection_multi = nullptr; + + maxcollections = 0; dimension = domain->dimension; } @@ -105,15 +107,12 @@ NStencil::~NStencil() delete [] distsq_multi_old; } - if (stencil_multi) { + if (maxstencil_multi) { - int n = ncollections; memory->destroy(nstencil_multi); - for (int i = 0; i < n; i++) { - for (int j = 0; j < n; j++) { - if (! flag_skip_multi[i][j]) - memory->destroy(stencil_multi[i][j]); - } + for (int i = 0; i < maxcollections; i++) { + for (int j = 0; j < maxcollections; j++) + memory->destroy(stencil_multi[i][j]); delete [] stencil_multi[i]; } delete [] stencil_multi; @@ -275,47 +274,60 @@ void NStencil::create_setup() if(nb) copy_bin_info_multi(); - // Allocate arrays to store stencil information - memory->create(flag_half_multi, n, n, - "neighstencil:flag_half_multi"); - memory->create(flag_skip_multi, n, n, - "neighstencil:flag_skip_multi"); - memory->create(bin_collection_multi, n, n, - "neighstencil:bin_collection_multi"); - - memory->create(stencil_sx_multi, n, n, - "neighstencil:stencil_sx_multi"); - memory->create(stencil_sy_multi, n, n, - "neighstencil:stencil_sy_multi"); - memory->create(stencil_sz_multi, n, n, - "neighstencil:stencil_sz_multi"); - - memory->create(stencil_binsizex_multi, n, n, - "neighstencil:stencil_binsizex_multi"); - memory->create(stencil_binsizey_multi, n, n, - "neighstencil:stencil_binsizey_multi"); - memory->create(stencil_binsizez_multi, n, n, - "neighstencil:stencil_binsizez_multi"); - - memory->create(stencil_mbinx_multi, n, n, - "neighstencil:stencil_mbinx_multi"); - memory->create(stencil_mbiny_multi, n, n, - "neighstencil:stencil_mbiny_multi"); - memory->create(stencil_mbinz_multi, n, n, - "neighstencil:stencil_mbinz_multi"); - - // Skip all stencils by default, initialize smax - for (i = 0; i < n; i++) { - for (j = 0; j < n; j++) { - flag_skip_multi[i][j] = 1; + // Deallocate arrays if previously allocated + if(n > maxcollections and stencil_multi){ + memory->destroy(nstencil_multi); + for (i = 0; i < maxcollections; i++) { + for (j = 0; j < maxcollections; j++) + memory->destroy(stencil_multi[i][j]); + delete [] stencil_multi[i]; } - } + delete [] stencil_multi; + memory->destroy(maxstencil_multi); + memory->destroy(flag_half_multi); + memory->destroy(flag_skip_multi); + memory->destroy(bin_collection_multi); + memory->destroy(stencil_sx_multi); + memory->destroy(stencil_sy_multi); + memory->destroy(stencil_sz_multi); + memory->destroy(stencil_binsizex_multi); + memory->destroy(stencil_binsizey_multi); + memory->destroy(stencil_binsizez_multi); + memory->destroy(stencil_mbinx_multi); + memory->destroy(stencil_mbiny_multi); + memory->destroy(stencil_mbinz_multi); + } - // Determine which stencils need to be built - set_stencil_properties(); - - // Allocate arrays to store stencils - if (!maxstencil_multi) { + // Allocate arrays + if(!maxstencil_multi) { + memory->create(flag_half_multi, n, n, + "neighstencil:flag_half_multi"); + memory->create(flag_skip_multi, n, n, + "neighstencil:flag_skip_multi"); + memory->create(bin_collection_multi, n, n, + "neighstencil:bin_collection_multi"); + + memory->create(stencil_sx_multi, n, n, + "neighstencil:stencil_sx_multi"); + memory->create(stencil_sy_multi, n, n, + "neighstencil:stencil_sy_multi"); + memory->create(stencil_sz_multi, n, n, + "neighstencil:stencil_sz_multi"); + + memory->create(stencil_binsizex_multi, n, n, + "neighstencil:stencil_binsizex_multi"); + memory->create(stencil_binsizey_multi, n, n, + "neighstencil:stencil_binsizey_multi"); + memory->create(stencil_binsizez_multi, n, n, + "neighstencil:stencil_binsizez_multi"); + + memory->create(stencil_mbinx_multi, n, n, + "neighstencil:stencil_mbinx_multi"); + memory->create(stencil_mbiny_multi, n, n, + "neighstencil:stencil_mbiny_multi"); + memory->create(stencil_mbinz_multi, n, n, + "neighstencil:stencil_mbinz_multi"); + memory->create(maxstencil_multi, n, n, "neighstencil::maxstencil_multi"); memory->create(nstencil_multi, n, n, "neighstencil::nstencil_multi"); stencil_multi = new int**[n](); @@ -326,12 +338,22 @@ void NStencil::create_setup() nstencil_multi[i][j] = 0; stencil_multi[i][j] = nullptr; } + } + maxcollections = n; + } + + // Skip all stencils by default, initialize smax + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + flag_skip_multi[i][j] = 1; } - } + } + + // Determine which stencils need to be built + set_stencil_properties(); for (i = 0; i < n; i++) { for (j = 0; j < n; j++) { - // Skip creation of unused stencils if (flag_skip_multi[i][j]) continue; @@ -364,7 +386,8 @@ void NStencil::create_setup() if (smax > maxstencil_multi[i][j]) { maxstencil_multi[i][j] = smax; - memory->destroy(stencil_multi[i][j]); + if(stencil_multi[i][j]) + memory->destroy(stencil_multi[i][j]); memory->create(stencil_multi[i][j], smax, "neighstencil::stencil_multi"); } diff --git a/src/nstencil.h b/src/nstencil.h index 37cedec045..6e8c2da97c 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -33,6 +33,7 @@ class NStencil : protected Pointers { int ** nstencil_multi; // # bins bins in each igroup-jgroup multi stencil int *** stencil_multi; // list of bin offsets in each multi stencil int ** maxstencil_multi; // max stencil size for each multi stencil + int maxcollections; // size of multi arrays int sx,sy,sz; // extent of stencil in each dim int **stencil_sx_multi; // analogs for each multi stencil @@ -42,7 +43,7 @@ class NStencil : protected Pointers { double cutoff_custom; // cutoff set by requestor // Arrays to store options for multi itype-jtype stencils - bool **flag_half_multi; // flag creation of a half stencil for igroup-jgroup + bool **flag_half_multi; // flag creation of a half stencil for icollection-jcollection bool **flag_skip_multi; // skip creation of icollection-jcollection stencils (for newton on) int **bin_collection_multi; // what collection to use for bin information diff --git a/src/nstencil_half_multi_2d.cpp b/src/nstencil_half_multi_2d.cpp index 57352c7c6f..32ee0297ff 100644 --- a/src/nstencil_half_multi_2d.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -71,7 +71,7 @@ void NStencilHalfMulti2d::create() if (flag_skip_multi[icollection][jcollection]) continue; ns = 0; - + sx = stencil_sx_multi[icollection][jcollection]; sy = stencil_sy_multi[icollection][jcollection]; From 58e4938b0f5e6c1006404f0bf9c8718bb87ce371 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 8 Feb 2021 10:50:57 -0700 Subject: [PATCH 0090/1217] Updating examples, updating multi in info, fixing memory issues in comm/neighbor --- src/comm.cpp | 18 ++++++++++++++++-- src/comm_brick.cpp | 24 +++++++++++++++++++++++- src/comm_tiled.cpp | 6 +++--- src/info.cpp | 17 ++++++++++++++++- src/neighbor.cpp | 3 ++- 5 files changed, 60 insertions(+), 8 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index d729545dba..f41f046e63 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -298,18 +298,32 @@ void Comm::modify_params(int narg, char **arg) // need to reset cutghostuser when switching comm mode if (mode == Comm::MULTI) cutghostuser = 0.0; if (mode == Comm::MULTIOLD) cutghostuser = 0.0; - memory->destroy(cutusermulti); - cutusermulti = nullptr; + if(cutusermulti){ + memory->destroy(cutusermulti); + cutusermulti = nullptr; + } + if(cutusermultiold){ + memory->destroy(cutusermultiold); + cutusermultiold = nullptr; + } mode = Comm::SINGLE; } else if (strcmp(arg[iarg+1],"multi") == 0) { // need to reset cutghostuser when switching comm mode if (mode == Comm::SINGLE) cutghostuser = 0.0; if (mode == Comm::MULTIOLD) cutghostuser = 0.0; + if(cutusermultiold){ + memory->destroy(cutusermultiold); + cutusermultiold = nullptr; + } mode = Comm::MULTI; } else if (strcmp(arg[iarg+1],"multi/old") == 0) { // need to reset cutghostuser when switching comm mode if (mode == Comm::SINGLE) cutghostuser = 0.0; if (mode == Comm::MULTI) cutghostuser = 0.0; + if(cutusermulti){ + memory->destroy(cutusermulti); + cutusermulti = nullptr; + } mode = Comm::MULTIOLD; } else error->all(FLERR,"Illegal comm_modify command"); iarg += 2; diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 160ecf2c3d..50c18e5fe7 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -145,6 +145,12 @@ void CommBrick::init() ncollections = neighbor->ncollections; allocate_multi(maxswap); memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); + if(cutusermultiflag) { + memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); + for(int i = ncollections_prior; i < ncollections; i++) + cutusermulti[i] = -1.0; + } + ncollections_prior = ncollections; } if ((mode == Comm::SINGLE or mode == Comm::MULTIOLD) && multilo) { @@ -218,7 +224,7 @@ void CommBrick::setup() // parse any cutoff/multi commands int nhi, nlo; for(auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { - utils::bounds(FLERR,it->first,1,ncollections,nlo,nhi,error); + utils::bounds(FLERR,it->first,0,ncollections,nlo,nhi,error); if(nhi >= ncollections) error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command"); for (j=nlo; j<=nhi; ++j) @@ -898,6 +904,22 @@ void CommBrick::borders() if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); sendlist[iswap][nsend++] = i; } + } else if (mode == Comm::MULTI) { + ngroup = atom->nfirst; + for (i = 0; i < ngroup; i++) { + icollection = collection[i]; + if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) { + if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); + sendlist[iswap][nsend++] = i; + } + } + for (i = atom->nlocal; i < nlast; i++) { + icollection = collection[i]; + if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) { + if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); + sendlist[iswap][nsend++] = i; + } + } } else { ngroup = atom->nfirst; for (i = 0; i < ngroup; i++) { diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 0a09dc830d..27f630f720 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -198,7 +198,6 @@ void CommTiled::setup() for(i = 0; i < maxswap; i ++) grow_swap_send_multi(i,DELTA_PROCS); - if(cutusermultiflag){ memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); for(i = ncollections_prior; i < ncollections; i++) @@ -211,10 +210,10 @@ void CommTiled::setup() // parse any cutoff/multi commands int nhi, nlo; for(auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { - utils::bounds(FLERR,it->first,1,ncollections,nlo,nhi,error); + utils::bounds(FLERR,it->first,0,ncollections,nlo,nhi,error); if(nhi >= ncollections) error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command"); - + for (j=nlo; j<=nhi; ++j) cutusermulti[j] = it->second; } @@ -224,6 +223,7 @@ void CommTiled::setup() // If using multi/reduce, communicate particles a distance equal // to the max cutoff with equally sized or smaller collections // If not, communicate the maximum cutoff of the entire collection + for (i = 0; i < ncollections; i++) { if (cutusermulti) { cutghostmulti[i][0] = cutusermulti[i]; diff --git a/src/info.cpp b/src/info.cpp index bf6f14a48a..0d3c47efa8 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -414,9 +414,24 @@ void Info::command(int narg, char **arg) if (comm->mode == 1) { fputs("Communication mode = multi\n",out); double cut; + for (int i=0; i < neighbor->ncollections; ++i) { + if (comm->cutusermulti) cut = comm->cutusermulti[i]; + else cut = 0.0; + for (int j=0; j < neighbor->ncollections; ++j) { + cut = MAX(cut,sqrt(neighbor->cutcollectionsq[i][j])); + } + + if (comm->cutusermulti) cut = MAX(cut,comm->cutusermulti[i]); + fmt::print(out,"Communication cutoff for collection {} = {:.8}\n", i, cut); + } + } + + if (comm->mode == 2) { + fputs("Communication mode = multi/old\n",out); + double cut; for (int i=1; i <= atom->ntypes && neighbor->cuttype; ++i) { cut = neighbor->cuttype[i]; - if (comm->cutusermulti) cut = MAX(cut,comm->cutusermulti[i]); + if (comm->cutusermultiold) cut = MAX(cut,comm->cutusermultiold[i]); fmt::print(out,"Communication cutoff for type {} = {:.8}\n", i, cut); } } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index e8f9798df8..c33345f88d 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -366,7 +366,8 @@ void Neighbor::init() if(not custom_collection_flag) { ncollections = n; interval_collection_flag = 0; - memory->create(type2collection,n+1,"neigh:type2collection"); + if(not type2collection) + memory->create(type2collection,n+1,"neigh:type2collection"); for(i = 1; i <= n; i++) type2collection[i] = i-1; } From 60113a6ddf92566d4eee3ba03dc960795f1471c5 Mon Sep 17 00:00:00 2001 From: tc387 Date: Wed, 10 Feb 2021 13:24:30 -0600 Subject: [PATCH 0091/1217] Applied edits/optimizations suggested by Axel. Further simplifified/fixed MC acceptance equations, few clarifications to documentation. --- doc/src/fix_charge_regulation.rst | 38 ++- examples/USER/misc/charge_regulation/README | 5 +- .../USER/misc/charge_regulation/in_acid.chreg | 7 +- .../misc/charge_regulation/in_polymer.chreg | 12 +- src/USER-MISC/fix_charge_regulation.cpp | 282 ++++++++++-------- src/USER-MISC/fix_charge_regulation.h | 17 +- 6 files changed, 193 insertions(+), 168 deletions(-) diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index a98288eb51..cb9f55c7cd 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/doc/src/fix_charge_regulation.rst @@ -1,22 +1,18 @@ -.. Yuan documentation master file, created by - sphinx-quickstart on Sat Jan 30 14:06:22 2021. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - tc387: Multiple text additions/changes, Feb 2 2021 -.. index:: fix fix_charge_regulation +.. index:: fix charge/regulation -fix_charge_regulation command +fix charge/regulation command ============================= + Syntax """""" .. parsed-literal:: - fix ID group-ID charge_regulation cation_type anion_type keyword value(s) + fix ID group-ID charge/regulation cation_type anion_type keyword value(s) * ID, group-ID are documented in fix command -* charge_regulation = style name of this fix command +* charge/regulation = style name of this fix command * cation_type = atom type of free cations * anion_type = atom type of free anions @@ -51,9 +47,9 @@ Examples """""""" .. code-block:: LAMMPS - fix chareg all charge_regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT + fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT - fix chareg all charge_regulation 1 2 pIp 3 pIm 3 tempfixid fT tag yes onlysalt yes 2 -1 + fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0 Description """"""""""" @@ -75,7 +71,7 @@ An acid ionization reaction (:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\ .. code-block:: LAMMPS - fix acid_reaction all charge_regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 7.0 pIm 7.0 + fix acid_reaction all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 7.0 pIm 7.0 where the fix attempts to charge :math:`\mathrm{A}` (discharge :math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and insert (delete) a proton (atom type 2). Besides, the fix implements self-ionization reaction of water :math:`\emptyset \rightleftharpoons \mathrm{H}^++\mathrm{OH}^-`. However, this approach is highly inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of both protons and hydroxyl ions is low, resulting in a relatively low acceptance rate of MC moves. @@ -85,7 +81,7 @@ participate in ionization reactions, which can be easily achieved via .. code-block:: LAMMPS - fix acid_reaction all charge_regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0 + fix acid_reaction all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0 where particles of atom type 4 and 5 are the salt cations and anions, both at chemical potential pI=2.0, see :ref:`(Curk1) ` and :ref:`(Landsgesell) ` for more details. @@ -94,14 +90,14 @@ where particles of atom type 4 and 5 are the salt cations and anions, both at ch .. code-block:: LAMMPS - fix base_reaction all charge_regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0 + fix base_reaction all charge/regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0 where the fix will attempt to charge :math:`\mathrm{B}` (discharge :math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. If neither the acid or the base type is specified, for example, .. code-block:: LAMMPS - fix salt_reaction all charge_regulation 4 5 pIp 2.0 pIm 2.0 + fix salt_reaction all charge/regulation 4 5 pIp 2.0 pIm 2.0 the fix simply inserts or deletes an ion pair of a free cation (atom type 4) and a free anion (atom type 5) as done in a conventional grand-canonical MC simulation. @@ -119,7 +115,7 @@ Note that LAMMPS implicitly assumes a constant number of particles (degrees of f The chemical potential units (e.g. pH) are in the standard log10 representation assuming reference concentration :math:`\rho_0 = \mathrm{mol}/\mathrm{l}`. Therefore, to perform the internal unit conversion, the length (in nanometers) of the LAMMPS unit length -must be specified via *lunit_nm* (default is set to the Bjerrum length in water at room temprature *lunit_nm* = 0.72nm). For example, in the dilute ideal solution limit, the concentration of free ions +must be specified via *lunit_nm* (default is set to the Bjerrum length in water at room temprature *lunit_nm* = 0.71nm). For example, in the dilute ideal solution limit, the concentration of free ions will be :math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. The temperature used in MC acceptance probability is set by *temp*. This temperature should be the same as the temperature set by the molecular dynamics thermostat. For most purposes, it is probably best to use *tempfixid* keyword which dynamically sets the temperature equal to the chosen MD thermostat temperature, in the example above we assumed the thermostat fix-ID is *fT*. The inserted particles attain a random velocity corresponding to the specified temperature. Using *tempfixid* overrides any fixed temperature set by *temp*. @@ -138,14 +134,14 @@ The *group* keyword can be used to add inserted particles to a specific group-ID Output """""" -This fix computes a global vector of length 8, which can be accessed by various output commands. The vector values are the following global cumulative quantities: +This fix computes a global vector of length 8, which can be accessed by various output commands. The vector values are the following global quantities: * 1 = cumulative MC attempts * 2 = cumulative MC successes * 3 = current # of neutral acid atoms * 4 = current # of -1 charged acid atoms * 5 = current # of neutral base atoms -* 6 = current # of +1 charged acid atoms +* 6 = current # of +1 charged base atoms * 7 = current # of free cations * 8 = current # of free anions @@ -157,6 +153,8 @@ See the :doc:`Build package ` doc page for more info. The :doc:`atom_style `, used must contain the charge property, for example, the style could be *charge* or *full*. Only usable for 3D simulations. Atoms specified as free ions cannot be part of rigid bodies or molecules and cannot have bonding interactions. The scheme is limited to integer charges, any atoms with non-integer charges will not be considered by the fix. +All interaction potentials used must be continuous, otherwise the MD integration and the particle exchange MC moves do not correspond to the same equilibrium ensemble. For example, if an lj/cut pair style is used, the LJ potential must be shifted so that it vanishes at the cutoff. This can be easily achieved using the :doc:`pair_modify ` command, i.e., by using: *pair_modify shift yes*. + Note: Region restrictions are not yet implemented. Related commands @@ -167,7 +165,7 @@ Related commands Default """"""" -pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs=14.0; acid_type = -1; base_type = -1; lunit_nm = 0.72; temp = 1.0; nevery = 100; nmc = 100; xrd = 0; seed = 2345; tag = no; onlysalt = no, pmcmoves = 0.33 0.33 0.33, group-ID = all +pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0; acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery = 100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves = [1/3, 1/3, 1/3], group-ID = all ---------- @@ -181,4 +179,4 @@ pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs=14.0; acid_type = .. _Landsgesell: -**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, “Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning,” Macromolecules 53, 3007–3020 (2020). +**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, "Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning", Macromolecules 53, 3007–3020 (2020). diff --git a/examples/USER/misc/charge_regulation/README b/examples/USER/misc/charge_regulation/README index e0be86d7e4..5666d6d025 100644 --- a/examples/USER/misc/charge_regulation/README +++ b/examples/USER/misc/charge_regulation/README @@ -2,6 +2,7 @@ This directory has two input scripts that illustrates how to use fix charge_regu The script `in_acid.chreg` sets up a simple weak acid electrolyte (pH=7,pKa=6,pI=3). Four different types of MC moves are implemented: acid protonation & de-protonation, and monovalent ion pair insertion and deletion. Note here we have grouped all free monovalent ions into a single type, a physically natural choice on the level of coarse-grained primitive electrolyte models, which increases the calculation performance but has no effects on thermodynamic observables. The variables such as pH, pKa, pI, and lb at the top of the input script can be adjusted to play with various simulation parameters. The cumulative MC attempted moves and cumulative number of accepted moves, as well as, current number of neutral and charged acid particles, neutral and charged base particles (in this example always 0), and the current number of free cations and anions in the system are printed in the `log_acid.lammps`. -The script `in_polymer.chreg` sets up a weak polyelectrolyte chain of N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7 and salt pI=3. In this example, we choose to treat salt ions, protons, and hydroxyl ions separately, which results in 5 types of MC moves: acid [type 1] protonation & de-protonation (with protons [type 4] insertion & deletion), acid [type 1] protonation & de-protonation (with salt cation [type 2] insertion & deletion), water self-ionization (insertion and deletion of proton [type4] and hydroxyl ion [type 5] pair), insertion and deletion of monovalent salt pair [type 2 and type 3] , insertion and deletion -Of a proton [type4] and salt anion [type 3]. The current number of neutral and charged acid particles, the current number of free salt cations and anions, and the current number of protons and hydroxyl ions are printed in the `log_polymer.lammps`. +The script `in_polymer.chreg` sets up a weak polyelectrolyte chain of N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7 and monovalent salt chemical potential pI=3. In this example, we choose to treat salt ions, protons, and hydroxyl ions separately, which results in 5 types of MC moves: acid [type 1] protonation & de-protonation (with protons [type 4] insertion & deletion), acid [type 1] protonation & de-protonation (with salt cation [type 2] insertion & deletion), water self-ionization (insertion and deletion of proton [type4] and hydroxyl ion [type 5] pair), insertion and deletion of monovalent salt pair [type 2 and type 3] , insertion and deletion +Of a proton [type4] and salt anion [type 3]. +The current number of neutral and charged acid particles, the current number of free salt cations and anions, and the current number of protons and hydroxyl ions are printed in the `log_polymer.lammps`. diff --git a/examples/USER/misc/charge_regulation/in_acid.chreg b/examples/USER/misc/charge_regulation/in_acid.chreg index 32beeda732..73a40f7389 100644 --- a/examples/USER/misc/charge_regulation/in_acid.chreg +++ b/examples/USER/misc/charge_regulation/in_acid.chreg @@ -24,7 +24,7 @@ pair_style lj/cut/coul/long ${cut_lj} ${cut_long} pair_coeff * * 1.0 1.0 ${cut_lj} # charges kspace_style ewald 1.0e-3 dielectric 1.0 -pair_modify shift no +pair_modify shift yes ######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### fix fnve all nve @@ -33,8 +33,9 @@ compute_modify dtemp dynamic yes fix fT all langevin 1.0 1.0 1.0 123 fix_modify fT temp dtemp -fix chareg all charge_regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT thermo 100 thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] +log log_acid.lammps timestep 0.005 -run 10000 +run 20000 diff --git a/examples/USER/misc/charge_regulation/in_polymer.chreg b/examples/USER/misc/charge_regulation/in_polymer.chreg index 4dc72a8156..e35ba28661 100644 --- a/examples/USER/misc/charge_regulation/in_polymer.chreg +++ b/examples/USER/misc/charge_regulation/in_polymer.chreg @@ -14,7 +14,7 @@ velocity all create 1.0 8008 loop geom pair_style lj/cut/coul/long 1.122462 20 pair_coeff * * 1.0 1.0 1.122462 # charges kspace_style pppm 1.0e-3 -pair_modify shift no +pair_modify shift yes dielectric 1.0 ######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### @@ -24,12 +24,14 @@ compute_modify dtemp dynamic yes fix fT all langevin 1.0 1.0 1.0 123 fix_modify fT temp dtemp -fix chareg1 all charge_regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 -fix chareg2 all charge_regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 -fix chareg3 all charge_regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 +fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345 +fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345 +fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345 thermo 100 # print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] +log log_polymer.lammps + timestep 0.005 -run 10000 +run 20000 diff --git a/src/USER-MISC/fix_charge_regulation.cpp b/src/USER-MISC/fix_charge_regulation.cpp index 3bb9de1b27..c43a509f61 100644 --- a/src/USER-MISC/fix_charge_regulation.cpp +++ b/src/USER-MISC/fix_charge_regulation.cpp @@ -15,50 +15,56 @@ Contributing author: Tine Curk (tcurk5@gmail.com) and Jiaxing Yuan (yuanjiaxing123@hotmail.com) ------------------------------------------------------------------------- */ #include "fix_charge_regulation.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "update.h" -#include "modify.h" -#include "fix.h" +#include "bond.h" #include "comm.h" #include "compute.h" -#include "group.h" -#include "domain.h" -#include "region.h" -#include "random_park.h" -#include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "group.h" #include "improper.h" #include "kspace.h" -#include "math_extra.h" #include "math_const.h" +#include "math_extra.h" +#include "math_special.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "molecule.h" #include "neighbor.h" +#include "pair.h" +#include "random_park.h" +#include "region.h" +#include "update.h" + +#include +#include + using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; +using namespace MathSpecial; // large energy value used to signal overlap #define MAXENERGYSIGNAL 1.0e100 #define MAXENERGYTEST 1.0e50 -#define small 0.0000001 -#define PI 3.1415926 +#define SMALL 0.0000001 +#define NA_RHO0 0.602214 // Avogadro's constant times reference concentration (N_A * mol / liter) [nm^-3] /* ---------------------------------------------------------------------- */ -Fix_charge_regulation::Fix_charge_regulation(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), - ngroups(0), groupstrings(NULL), - random_equal(NULL), random_unequal(NULL), - idftemp(NULL), ptype_ID(NULL) { + +FixChargeRegulation::FixChargeRegulation(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), + ngroups(0), groupstrings(NULL), + random_equal(NULL), random_unequal(NULL), + idftemp(NULL), ptype_ID(NULL) + { // Region restrictions not yet implemented .. @@ -79,28 +85,28 @@ Fix_charge_regulation::Fix_charge_regulation(LAMMPS *lmp, int narg, char **arg) // set defaults and read optional arguments options(narg - 5, &arg[5]); - if (nevery <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (nmc < 0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (llength_unit_in_nm < 0.0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (*target_temperature_tcp < 0.0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (seed <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (cation_type <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (anion_type <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (reaction_distance < 0.0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (salt_charge[0] <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (salt_charge[1] >= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (nevery <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (nmc < 0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (llength_unit_in_nm < 0.0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (*target_temperature_tcp < 0.0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (seed <= 0) error->all(FLERR, "Illegal fix charge/regulation command: Seed value (positive integer) must be provided "); + if (cation_type <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (anion_type <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (reaction_distance < 0.0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (salt_charge[0] <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (salt_charge[1] >= 0) error->all(FLERR, "Illegal fix charge/regulation command"); if ((salt_charge[1] % salt_charge[0] != 0) && (salt_charge[0] % salt_charge[1] != 0)) error->all(FLERR, - "Illegal fix charge_regulation command, multivalent cation/anion charges are allowed, " + "Illegal fix charge/regulation command, multivalent cation/anion charges are allowed, " "but must be divisible, e.g. (3,-1) is fine, but (3,-2) is not implemented"); if (pmcmoves[0] < 0 || pmcmoves[1] < 0 || pmcmoves[2] < 0) - error->all(FLERR, "Illegal fix charge_regulation command"); + error->all(FLERR, "Illegal fix charge/regulation command"); if (acid_type < 0) pmcmoves[0] = 0; if (base_type < 0) pmcmoves[1] = 0; // normalize double psum = pmcmoves[0] + pmcmoves[1] + pmcmoves[2]; - if (psum <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (psum <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); pmcmoves[0] /= psum; pmcmoves[1] /= psum; pmcmoves[2] /= psum; @@ -117,7 +123,7 @@ Fix_charge_regulation::Fix_charge_regulation(LAMMPS *lmp, int narg, char **arg) nsalt_successes = 0; } -Fix_charge_regulation::~Fix_charge_regulation() { +FixChargeRegulation::~FixChargeRegulation() { memory->destroy(ptype_ID); @@ -130,18 +136,16 @@ Fix_charge_regulation::~Fix_charge_regulation() { } } -int Fix_charge_regulation::setmask() { +int FixChargeRegulation::setmask() { int mask = 0; mask |= PRE_EXCHANGE; return mask; } -void Fix_charge_regulation::init() { +void FixChargeRegulation::init() { - triclinic = domain->triclinic; - - char *id_pe = (char *) "thermo_pe"; - int ipe = modify->find_compute(id_pe); + triclinic = domain->triclinic; + int ipe = modify->find_compute("thermo_pe"); c_pe = modify->compute[ipe]; if (atom->molecule_flag) { @@ -165,34 +169,27 @@ void Fix_charge_regulation::init() { // skip if already exists from previous init() if (!exclusion_group_bit) { - char **group_arg = new char *[4]; // create unique group name for atoms to be excluded - int len = strlen(id) + 30; - group_arg[0] = new char[len]; - sprintf(group_arg[0], "Fix_CR:exclusion_group:%s", id); - group_arg[1] = (char *) "subtract"; - group_arg[2] = (char *) "all"; - group_arg[3] = (char *) "all"; - group->assign(4, group_arg); - exclusion_group = group->find(group_arg[0]); + + auto group_id = std::string("FixChargeRegulation:CR_exclusion_group:") + id; + group->assign(group_id + " subtract all all"); + exclusion_group = group->find(group_id); if (exclusion_group == -1) - error->all(FLERR, "Could not find fix CR exclusion group ID"); + error->all(FLERR,"Could not find fix charge/regulation exclusion group ID"); exclusion_group_bit = group->bitmask[exclusion_group]; // neighbor list exclusion setup // turn off interactions between group all and the exclusion group int narg = 4; - char **arg = new char *[narg];; + char **arg = new char*[narg];; arg[0] = (char *) "exclude"; arg[1] = (char *) "group"; - arg[2] = group_arg[0]; + arg[2] = (char *) group_id.c_str(); arg[3] = (char *) "all"; - neighbor->modify_params(narg, arg); - delete[] group_arg[0]; - delete[] group_arg; - delete[] arg; + neighbor->modify_params(narg,arg); + delete [] arg; } // check that no deletable atoms are in atom->firstgroup @@ -226,7 +223,7 @@ void Fix_charge_regulation::init() { } } -void Fix_charge_regulation::pre_exchange() { +void FixChargeRegulation::pre_exchange() { if (next_reneighbor != update->ntimestep) return; xlo = domain->boxlo[0]; @@ -263,14 +260,22 @@ void Fix_charge_regulation::pre_exchange() { reaction_distance = 0; } // volume in units of (N_A * mol / liter) - volume_rx = (xhi - xlo) * (yhi - ylo) * (zhi - zlo) * pow(llength_unit_in_nm, 3) * 0.602214; - if (reaction_distance < small) { + volume_rx = (xhi - xlo) * (yhi - ylo) * (zhi - zlo) * cube(llength_unit_in_nm) * NA_RHO0; + if (reaction_distance < SMALL) { vlocal_xrd = volume_rx; } else { - vlocal_xrd = 4.0 * PI * pow(reaction_distance, 3) / 3.0 * pow(llength_unit_in_nm, 3) * 0.602214; + vlocal_xrd = 4.0 * MY_PI * cube(reaction_distance) / 3.0 * cube(llength_unit_in_nm) * NA_RHO0; } beta = 1.0 / (force->boltz * *target_temperature_tcp); + // pre-compute powers + c10pH = pow(10.0,-pH); // dissociated ion (H+) activity + c10pKa = pow(10.0,-pKa); // acid dissociation constant + c10pKb = pow(10.0,-pKb); // base dissociation constant + c10pOH = pow(10.0,-pKs + pH); // dissociated anion (OH-) activity + c10pI_plus = pow(10.0,-pI_plus); // free cation activity + c10pI_minus = pow(10.0,-pI_minus); // free anion activity + // reinitialize counters nacid_neutral = particle_number(acid_type, 0); nacid_charged = particle_number(acid_type, -1); @@ -337,7 +342,7 @@ void Fix_charge_regulation::pre_exchange() { next_reneighbor = update->ntimestep + nevery; } -void Fix_charge_regulation::forward_acid() { +void FixChargeRegulation::forward_acid() { double energy_before = energy_stored; double factor; @@ -360,7 +365,7 @@ void Fix_charge_regulation::forward_acid() { pos[2] = atom->x[m1][2]; } npart_xrd2 = ncation; - if (reaction_distance >= small) { + if (reaction_distance >= SMALL) { pos_all[0] = pos[0]; pos_all[1] = pos[1]; pos_all[2] = pos[2]; @@ -368,8 +373,8 @@ void Fix_charge_regulation::forward_acid() { npart_xrd2 = particle_number_xrd(cation_type, 1, reaction_distance, pos_all); } m2 = insert_particle(cation_type, 1, reaction_distance, pos_all); - factor = nacid_neutral * vlocal_xrd * pow(10, -pKa) - * (1 + pow(10, pH - pI_plus)) / ((1 + nacid_charged) * (1 + npart_xrd2)); + factor = nacid_neutral * vlocal_xrd * c10pKa * c10pI_plus / + (c10pH * (1 + nacid_charged) * (1 + npart_xrd2)); double energy_after = energy_full(); @@ -395,7 +400,7 @@ void Fix_charge_regulation::forward_acid() { } } -void Fix_charge_regulation::backward_acid() { +void FixChargeRegulation::backward_acid() { double energy_before = energy_stored; double factor; @@ -418,7 +423,7 @@ void Fix_charge_regulation::backward_acid() { pos[1] = atom->x[m1][1]; pos[2] = atom->x[m1][2]; } - if (reaction_distance >= small) { + if (reaction_distance >= SMALL) { pos_all[0] = pos[0]; pos_all[1] = pos[1]; pos_all[2] = pos[2]; @@ -433,8 +438,8 @@ void Fix_charge_regulation::backward_acid() { mask_tmp = atom->mask[m2]; // remember group bits. atom->mask[m2] = exclusion_group_bit; } - factor = (1 + nacid_neutral) * vlocal_xrd * pow(10, -pKa) - * (1 + pow(10, pH - pI_plus)) / (nacid_charged * npart_xrd); + factor = (1 + nacid_neutral) * vlocal_xrd * c10pKa * c10pI_plus / + (c10pH * nacid_charged * npart_xrd); double energy_after = energy_full(); @@ -468,7 +473,7 @@ void Fix_charge_regulation::backward_acid() { } } -void Fix_charge_regulation::forward_base() { +void FixChargeRegulation::forward_base() { double energy_before = energy_stored; double factor; @@ -491,16 +496,15 @@ void Fix_charge_regulation::forward_base() { pos[2] = atom->x[m1][2]; } npart_xrd2 = nanion; - if (reaction_distance >= small) { + if (reaction_distance >= SMALL) { pos_all[0] = pos[0]; pos_all[1] = pos[1]; pos_all[2] = pos[2]; MPI_Allreduce(pos, pos_all, 3, MPI_DOUBLE, MPI_SUM, world); npart_xrd2 = particle_number_xrd(anion_type, -1, reaction_distance, pos_all); } - factor = nbase_neutral * vlocal_xrd * pow(10, -pKb) - * (1 + pow(10, pKs - pH - pI_minus)) / - ((1 + nbase_charged) * (1 + npart_xrd2)); + factor = nbase_neutral * vlocal_xrd * c10pKb * c10pI_minus / + (c10pOH * (1 + nbase_charged) * (1 + npart_xrd2)); m2 = insert_particle(anion_type, -1, reaction_distance, pos_all); double energy_after = energy_full(); @@ -526,7 +530,7 @@ void Fix_charge_regulation::forward_base() { } } -void Fix_charge_regulation::backward_base() { +void FixChargeRegulation::backward_base() { double energy_before = energy_stored; double factor; @@ -549,7 +553,7 @@ void Fix_charge_regulation::backward_base() { pos[1] = atom->x[m1][1]; pos[2] = atom->x[m1][2]; } - if (reaction_distance >= small) { + if (reaction_distance >= SMALL) { pos_all[0] = pos[0]; pos_all[1] = pos[1]; pos_all[2] = pos[2]; @@ -563,8 +567,8 @@ void Fix_charge_regulation::backward_base() { mask_tmp = atom->mask[m2]; // remember group bits. atom->mask[m2] = exclusion_group_bit; } - factor = (1 + nbase_neutral) * vlocal_xrd * pow(10, -pKb) - * (1 + pow(10, pKs - pH - pI_minus)) / (nbase_charged * npart_xrd); + factor = (1 + nbase_neutral) * vlocal_xrd * c10pKb * c10pI_minus / + (c10pOH * nbase_charged * npart_xrd); double energy_after = energy_full(); @@ -598,20 +602,20 @@ void Fix_charge_regulation::backward_base() { } } -void Fix_charge_regulation::forward_ions() { +void FixChargeRegulation::forward_ions() { double energy_before = energy_stored; double factor; double *dummyp; int m1 = -1, m2 = -1; - factor = volume_rx * volume_rx * (pow(10, -pH) + pow(10, -pI_plus)) - * (pow(10, -pKs + pH) + pow(10, -pI_minus)) / + factor = volume_rx * volume_rx * c10pI_plus * c10pI_minus / ((1 + ncation) * (1 + nanion)); m1 = insert_particle(cation_type, +1, 0, dummyp); m2 = insert_particle(anion_type, -1, 0, dummyp); double energy_after = energy_full(); - if (energy_after < MAXENERGYTEST && random_equal->uniform() < factor * exp(beta * (energy_before - energy_after))) { + if (energy_after < MAXENERGYTEST && + random_equal->uniform() < factor * exp(beta * (energy_before - energy_after))) { energy_stored = energy_after; nsalt_successes += 1; ncation++; @@ -632,7 +636,7 @@ void Fix_charge_regulation::forward_ions() { } -void Fix_charge_regulation::backward_ions() { +void FixChargeRegulation::backward_ions() { double energy_before = energy_stored; double factor; @@ -659,8 +663,7 @@ void Fix_charge_regulation::backward_ions() { mask2_tmp = atom->mask[m2]; atom->mask[m2] = exclusion_group_bit; } - factor = (volume_rx * volume_rx * (pow(10, -pH) + pow(10, -pI_plus)) * - (pow(10, -pKs + pH) + pow(10, -pI_minus))) / (ncation * nanion); + factor = volume_rx * volume_rx * c10pI_plus * c10pI_minus / (ncation * nanion); double energy_after = energy_full(); if (energy_after < MAXENERGYTEST && @@ -717,7 +720,7 @@ void Fix_charge_regulation::backward_ions() { } } -void Fix_charge_regulation::forward_ions_multival() { +void FixChargeRegulation::forward_ions_multival() { double energy_before = energy_stored; double factor = 1; @@ -728,19 +731,19 @@ void Fix_charge_regulation::forward_ions_multival() { // insert one anion and (salt_charge_ratio) cations mm[0] = insert_particle(anion_type, salt_charge[1], 0, dummyp); - factor *= volume_rx * pow(10, -pI_minus) / (1 + nanion); + factor *= volume_rx * c10pI_minus / (1 + nanion); for (int i = 0; i < salt_charge_ratio; i++) { mm[i + 1] = insert_particle(cation_type, salt_charge[0], 0, dummyp); - factor *= volume_rx * pow(10, -pI_plus) / (1 + ncation + i); + factor *= volume_rx *c10pI_plus / (1 + ncation + i); } } else { // insert one cation and (salt_charge_ratio) anions mm[0] = insert_particle(cation_type, salt_charge[0], 0, dummyp); - factor *= volume_rx * pow(10, -pI_plus) / (1 + ncation); + factor *= volume_rx * c10pI_plus / (1 + ncation); for (int i = 0; i < salt_charge_ratio; i++) { mm[i + 1] = insert_particle(anion_type, salt_charge[1], 0, dummyp); - factor *= volume_rx * pow(10, -pI_minus) / (1 + nanion + i); + factor *= volume_rx * c10pI_minus / (1 + nanion + i); } } @@ -771,7 +774,7 @@ void Fix_charge_regulation::forward_ions_multival() { } } -void Fix_charge_regulation::backward_ions_multival() { +void FixChargeRegulation::backward_ions_multival() { double energy_before = energy_stored; double factor = 1; @@ -786,7 +789,7 @@ void Fix_charge_regulation::backward_ions_multival() { mm[0] = get_random_particle(anion_type, salt_charge[1], 0, dummyp); if (npart_xrd != nanion) error->all(FLERR, "Fix charge regulation salt count inconsistent"); - factor *= volume_rx * pow(10, -pI_minus) / (nanion); + factor *= volume_rx * c10pI_minus / (nanion); if (mm[0] >= 0) { qq[0] = atom->q[mm[0]]; atom->q[mm[0]] = 0; @@ -796,7 +799,7 @@ void Fix_charge_regulation::backward_ions_multival() { for (int i = 0; i < salt_charge_ratio; i++) { mm[i + 1] = get_random_particle(cation_type, salt_charge[0], 0, dummyp); if (npart_xrd != ncation - i) error->all(FLERR, "Fix charge regulation salt count inconsistent"); - factor *= volume_rx * pow(10, -pI_plus) / (ncation - i); + factor *= volume_rx * c10pI_plus / (ncation - i); if (mm[i + 1] >= 0) { qq[i + 1] = atom->q[mm[i + 1]]; atom->q[mm[i + 1]] = 0; @@ -810,7 +813,7 @@ void Fix_charge_regulation::backward_ions_multival() { if (nanion < salt_charge_ratio || ncation < 1) return; mm[0] = get_random_particle(cation_type, salt_charge[0], 0, dummyp); if (npart_xrd != ncation) error->all(FLERR, "Fix charge regulation salt count inconsistent"); - factor *= volume_rx * pow(10, -pI_plus) / (ncation); + factor *= volume_rx * c10pI_plus / (ncation); if (mm[0] >= 0) { qq[0] = atom->q[mm[0]]; atom->q[mm[0]] = 0; @@ -826,7 +829,7 @@ void Fix_charge_regulation::backward_ions_multival() { mask_tmp[i + 1] = atom->mask[mm[i + 1]]; atom->mask[mm[i + 1]] = exclusion_group_bit; } - factor *= volume_rx * pow(10, -pI_minus) / (nanion - i); + factor *= volume_rx * c10pI_minus / (nanion - i); } } @@ -840,7 +843,7 @@ void Fix_charge_regulation::backward_ions_multival() { atom->natoms -= 1 + salt_charge_ratio; // ions must be deleted in order, otherwise index m could change upon the first deletion for (int i = 0; i < salt_charge_ratio + 1; i++) { - // get max mm value, poor N^2 scaling, but charge ratio is a small number (2 or 3). + // get max mm value, poor N^2 scaling, but charge ratio is a SMALL number (2 or 3). int maxmm = -1, jmaxm = -1; for (int j = 0; j < salt_charge_ratio + 1; j++) { if (mm[j] > maxmm) { @@ -883,23 +886,42 @@ void Fix_charge_regulation::backward_ions_multival() { } } -int Fix_charge_regulation::insert_particle(int ptype, double charge, double rd, double *target) { +int FixChargeRegulation::insert_particle(int ptype, double charge, double rd, double *target) { // insert a particle of type (ptype) with charge (charge) within distance (rd) of (target) double coord[3]; int m = -1; - if (rd < small) { + if (rd < SMALL) { coord[0] = xlo + random_equal->uniform() * (xhi - xlo); coord[1] = ylo + random_equal->uniform() * (yhi - ylo); coord[2] = zlo + random_equal->uniform() * (zhi - zlo); } else { - double radius = reaction_distance * random_equal->uniform(); - double theta = random_equal->uniform() * PI; - double phi = random_equal->uniform() * 2 * PI; - coord[0] = target[0] + radius * sin(theta) * cos(phi); - coord[1] = target[1] + radius * sin(theta) * sin(phi); - coord[2] = target[2] + radius * cos(theta); + // get a random point inside a sphere with radius rd + // simple rejection sampling, probably the fastest method + double dxx=1,dyy=1,dzz=1; + while (dxx * dxx + dyy * dyy + dzz * dzz > 1.0) { + dxx = 2 * random_equal->uniform() - 1.0; + dyy = 2 * random_equal->uniform() - 1.0; + dzz = 2 * random_equal->uniform() - 1.0; + } + coord[0] = target[0] + rd * dxx; + coord[1] = target[1] + rd * dyy; + coord[2] = target[2] + rd * dzz; + + // Alternative way, but likely somewhat less efficient + /* + double radius = rd * pow(random_equal->uniform(), THIRD); + double theta = acos(2 * random_equal->uniform() - 1); + double phi = random_equal->uniform() * 2 * MY_PI; + double sinphi = sin(phi); + double cosphi = cos(phi); + double sintheta = sin(theta); + double costheta = cos(theta); + coord[0] = target[0] + radius * sintheta * cosphi; + coord[1] = target[1] + radius * sintheta * sinphi; + coord[2] = target[2] + radius * costheta; + */ coord[0] = coord[0] - floor(1.0 * (coord[0] - xlo) / (xhi - xlo)) * (xhi - xlo); coord[1] = coord[1] - floor(1.0 * (coord[1] - ylo) / (yhi - ylo)) * (yhi - ylo); coord[2] = coord[2] - floor(1.0 * (coord[2] - zlo) / (zhi - zlo)) * (zhi - zlo); @@ -926,7 +948,7 @@ int Fix_charge_regulation::insert_particle(int ptype, double charge, double rd, return m; } -int Fix_charge_regulation::get_random_particle(int ptype, double charge, double rd, double *target) { +int FixChargeRegulation::get_random_particle(int ptype, double charge, double rd, double *target) { // returns a randomly chosen particle of type (ptype) with charge (charge) // chosen among particles within distance (rd) of (target) @@ -947,9 +969,9 @@ int Fix_charge_regulation::get_random_particle(int ptype, double charge, double count_global = 0; count_before = 0; - if (rd < small) { //reaction_distance < small: No geometry constraint on random particle choice + if (rd < SMALL) { //reaction_distance < SMALL: No constraint on random particle choice for (int i = 0; i < nlocal; i++) { - if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < small && + if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < SMALL && atom->mask[i] != exclusion_group_bit) { ptype_ID[count_local] = i; count_local++; @@ -966,7 +988,7 @@ int Fix_charge_regulation::get_random_particle(int ptype, double charge, double dz -= static_cast(1.0 * dz / (zhi - zlo) + 0.5) * (zhi - zlo); distance_check = dx * dx + dy * dy + dz * dz; if ((distance_check < rd * rd) && atom->type[i] == ptype && - fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) { + fabs(atom->q[i] - charge) < SMALL && atom->mask[i] != exclusion_group_bit) { ptype_ID[count_local] = i; count_local++; } @@ -990,7 +1012,7 @@ int Fix_charge_regulation::get_random_particle(int ptype, double charge, double return -1; } -double Fix_charge_regulation::energy_full() { +double FixChargeRegulation::energy_full() { int imolecule; if (triclinic) domain->x2lamda(atom->nlocal); domain->pbc(); @@ -1050,12 +1072,12 @@ double Fix_charge_regulation::energy_full() { return total_energy; } -int Fix_charge_regulation::particle_number_xrd(int ptype, double charge, double rd, double *target) { +int FixChargeRegulation::particle_number_xrd(int ptype, double charge, double rd, double *target) { int count = 0; - if (rd < small) { + if (rd < SMALL) { for (int i = 0; i < atom->nlocal; i++) { - if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) + if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < SMALL && atom->mask[i] != exclusion_group_bit) count++; } } else { @@ -1069,7 +1091,7 @@ int Fix_charge_regulation::particle_number_xrd(int ptype, double charge, double dz -= static_cast(1.0 * dz / (zhi - zlo) + 0.5) * (zhi - zlo); distance_check = dx * dx + dy * dy + dz * dz; if ((distance_check < rd * rd) && atom->type[i] == ptype && - fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) { + fabs(atom->q[i] - charge) < SMALL && atom->mask[i] != exclusion_group_bit) { count++; } } @@ -1079,11 +1101,11 @@ int Fix_charge_regulation::particle_number_xrd(int ptype, double charge, double return count_sum; } -int Fix_charge_regulation::particle_number(int ptype, double charge) { +int FixChargeRegulation::particle_number(int ptype, double charge) { int count = 0; for (int i = 0; i < atom->nlocal; i++) { - if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) + if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < SMALL && atom->mask[i] != exclusion_group_bit) count = count + 1; } int count_sum = count; @@ -1091,7 +1113,7 @@ int Fix_charge_regulation::particle_number(int ptype, double charge) { return count_sum; } -double Fix_charge_regulation::compute_vector(int n) { +double FixChargeRegulation::compute_vector(int n) { double count_temp = 0; if (n == 0) { return nacid_attempts + nbase_attempts + nsalt_attempts; @@ -1113,7 +1135,7 @@ double Fix_charge_regulation::compute_vector(int n) { return 0.0; } -void Fix_charge_regulation::setThermoTemperaturePointer() { +void FixChargeRegulation::setThermoTemperaturePointer() { int ifix = -1; ifix = modify->find_fix(idftemp); if (ifix == -1) { @@ -1126,7 +1148,7 @@ void Fix_charge_regulation::setThermoTemperaturePointer() { } -void Fix_charge_regulation::assign_tags() { +void FixChargeRegulation::assign_tags() { // Assign tags to ions with zero tags if (atom->tag_enable) { tagint *tag = atom->tag; @@ -1167,14 +1189,14 @@ void Fix_charge_regulation::assign_tags() { parse input options ------------------------------------------------------------------------- */ -void Fix_charge_regulation::options(int narg, char **arg) { +void FixChargeRegulation::options(int narg, char **arg) { if (narg < 0) error->all(FLERR, "Illegal fix charge regulation command"); // defaults pH = 7.0; - pI_plus = 100; - pI_minus = 100; + pI_plus = 5; + pI_minus = 5; acid_type = -1; base_type = -1; pKa = 100; @@ -1182,12 +1204,12 @@ void Fix_charge_regulation::options(int narg, char **arg) { pKs = 14.0; nevery = 100; nmc = 100; - pmcmoves[0] = pmcmoves[1] = pmcmoves[2] = 0.33; - llength_unit_in_nm= 0.72; + pmcmoves[0] = pmcmoves[1] = pmcmoves[2] = THIRD; + llength_unit_in_nm= 0.71; // Default set to Bjerrum length in water at 20 degrees C [nm] reservoir_temperature = 1.0; reaction_distance = 0; - seed = 12345; + seed = 0; target_temperature_tcp = &reservoir_temperature; add_tags_flag = false; only_salt_flag = false; @@ -1297,9 +1319,9 @@ void Fix_charge_regulation::options(int narg, char **arg) { if (iarg + 4 > narg) error->all(FLERR, "Illegal fix charge regulation command"); salt_charge[0] = utils::numeric(FLERR, arg[iarg + 2], false, lmp); salt_charge[1] = utils::numeric(FLERR, arg[iarg + 3], false, lmp); - if (fabs(salt_charge[0] - utils::inumeric(FLERR, arg[iarg + 2], false, lmp)) > small) + if (fabs(salt_charge[0] - utils::inumeric(FLERR, arg[iarg + 2], false, lmp)) > SMALL) error->all(FLERR, "Illegal fix charge regulation command, cation charge must be an integer"); - if (fabs(salt_charge[1] - utils::inumeric(FLERR, arg[iarg + 3], false, lmp)) > small) + if (fabs(salt_charge[1] - utils::inumeric(FLERR, arg[iarg + 3], false, lmp)) > SMALL) error->all(FLERR, "Illegal fix charge regulation command, anion charge must be an integer"); iarg += 4; } else if (strcmp(arg[iarg + 1], "no") == 0) { @@ -1329,7 +1351,7 @@ void Fix_charge_regulation::options(int narg, char **arg) { memory usage of local atom-based arrays ------------------------------------------------------------------------- */ -double Fix_charge_regulation::memory_usage() { +double FixChargeRegulation::memory_usage() { double bytes = cr_nmax * sizeof(int); return bytes; } diff --git a/src/USER-MISC/fix_charge_regulation.h b/src/USER-MISC/fix_charge_regulation.h index d698bd6bb7..3afaffddb7 100644 --- a/src/USER-MISC/fix_charge_regulation.h +++ b/src/USER-MISC/fix_charge_regulation.h @@ -17,21 +17,21 @@ #ifdef FIX_CLASS -FixStyle(charge_regulation,Fix_charge_regulation) +FixStyle(charge/regulation,FixChargeRegulation) #else -#ifndef LMP_FIX_charge_regulation_H -#define LMP_FIX_charge_regulation_H +#ifndef LMP_FIX_CHARGE_REGULATION_H +#define LMP_FIX_CHARGE_REGULATION_H #include "fix.h" namespace LAMMPS_NS { - class Fix_charge_regulation : public Fix { + class FixChargeRegulation : public Fix { public: - Fix_charge_regulation(class LAMMPS *, int, char **); - ~Fix_charge_regulation(); + FixChargeRegulation(class LAMMPS *, int, char **); + ~FixChargeRegulation(); int setmask(); void init(); void pre_exchange(); @@ -59,7 +59,8 @@ namespace LAMMPS_NS { int nevery, seed; // begin MC cycle every nevery MD timesteps, random seed int nmc; // MC move attempts per cycle double llength_unit_in_nm ; // LAMMPS unit of length in nm, needed since chemical potentials are in units of mol/l - double pH, pKa, pKb, pKs, pI_plus, pI_minus; // chemical potentials + double pH, pKa, pKb, pKs, pI_plus, pI_minus; // chemical potentials and equilibrium constant in log10 base + double c10pH, c10pKa, c10pKb, c10pOH, c10pI_plus, c10pI_minus; // 10 raised to chemical potential value, in units of concentration [mol/liter] double pmcmoves[3]; // mc move attempt probability: acid, base, ion pair exchange double pmcc; // mc move cumulative attempt probability int npart_xrd; // # of particles (ions) within xrd @@ -78,7 +79,7 @@ namespace LAMMPS_NS { double reservoir_temperature; double beta, sigma, volume, volume_rx; // inverse temperature, speed, total volume, reacting volume int salt_charge[2]; // charge of salt ions: [0] - cation, [1] - anion - int salt_charge_ratio; // charge ration when using multivalent ion exchange + int salt_charge_ratio; // charge ratio when using multivalent ion exchange double xlo, xhi, ylo, yhi, zlo, zhi; // box size double energy_stored; // full energy of old/current configuration int triclinic; // 0 = orthog box, 1 = triclinic From faa2407aa46805bea4caf9e90c768b5bd187a8ed Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Feb 2021 07:04:19 -0500 Subject: [PATCH 0092/1217] plug memory leak --- src/USER-MISC/fix_charge_regulation.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/USER-MISC/fix_charge_regulation.cpp b/src/USER-MISC/fix_charge_regulation.cpp index c43a509f61..0a9619096e 100644 --- a/src/USER-MISC/fix_charge_regulation.cpp +++ b/src/USER-MISC/fix_charge_regulation.cpp @@ -129,6 +129,7 @@ FixChargeRegulation::~FixChargeRegulation() { delete random_equal; delete random_unequal; + delete idftemp; if (group) { int igroupall = group->find("all"); From 8ee693204a7b7f3fb5071770dae1713b34dd8270 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Feb 2021 07:05:07 -0500 Subject: [PATCH 0093/1217] use nullptr instead of NULL to initialize pointers --- src/USER-MISC/fix_charge_regulation.cpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/USER-MISC/fix_charge_regulation.cpp b/src/USER-MISC/fix_charge_regulation.cpp index 0a9619096e..7608849190 100644 --- a/src/USER-MISC/fix_charge_regulation.cpp +++ b/src/USER-MISC/fix_charge_regulation.cpp @@ -61,10 +61,10 @@ using namespace MathSpecial; FixChargeRegulation::FixChargeRegulation(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), - ngroups(0), groupstrings(NULL), - random_equal(NULL), random_unequal(NULL), - idftemp(NULL), ptype_ID(NULL) - { + ngroups(0), groupstrings(nullptr), ptype_ID(nullptr), + random_equal(nullptr), random_unequal(nullptr), + idftemp(nullptr) +{ // Region restrictions not yet implemented .. @@ -1221,7 +1221,7 @@ void FixChargeRegulation::options(int narg, char **arg) { exclusion_group_bit = 0; ngroups = 0; int ngroupsmax = 0; - groupstrings = NULL; + groupstrings = nullptr; int iarg = 0; while (iarg < narg) { From 9671ba79003171d7d50e8bc3c385c99d78d05774 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Feb 2021 07:05:28 -0500 Subject: [PATCH 0094/1217] silence compiler warnings --- src/USER-MISC/fix_charge_regulation.cpp | 21 +++++++++------------ 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/src/USER-MISC/fix_charge_regulation.cpp b/src/USER-MISC/fix_charge_regulation.cpp index 7608849190..8a6530ef2b 100644 --- a/src/USER-MISC/fix_charge_regulation.cpp +++ b/src/USER-MISC/fix_charge_regulation.cpp @@ -347,7 +347,7 @@ void FixChargeRegulation::forward_acid() { double energy_before = energy_stored; double factor; - double *dummyp; + double *dummyp = nullptr; double pos[3]; pos[0] = 0; pos[1] = 0; @@ -406,13 +406,13 @@ void FixChargeRegulation::backward_acid() { double energy_before = energy_stored; double factor; int mask_tmp; - double *dummyp; + double *dummyp = nullptr; double pos[3]; pos[0] = 0; pos[1] = 0; pos[2] = 0; // acid/base particle position double pos_all[3]; - int m1 = -1, m1_all = -1, m2 = -1, m2_all = -1; + int m1 = -1, m2 = -1; m1 = get_random_particle(acid_type, -1, 0, dummyp); if (npart_xrd != nacid_charged) error->all(FLERR, "Fix charge regulation acid count inconsistent"); @@ -478,13 +478,13 @@ void FixChargeRegulation::forward_base() { double energy_before = energy_stored; double factor; - double *dummyp; + double *dummyp = nullptr; double pos[3]; pos[0] = 0; pos[1] = 0; pos[2] = 0; // acid/base particle position double pos_all[3]; - int m1 = -1, m1_all = -1, m2 = -1, m2_all = -1; + int m1 = -1, m2 = -1; m1 = get_random_particle(base_type, 0, 0, dummyp); if (npart_xrd != nbase_neutral) error->all(FLERR, "Fix charge regulation acid count inconsistent"); @@ -535,14 +535,14 @@ void FixChargeRegulation::backward_base() { double energy_before = energy_stored; double factor; - double *dummyp; + double *dummyp = nullptr; int mask_tmp; double pos[3]; pos[0] = 0; pos[1] = 0; pos[2] = 0; // acid/base particle position double pos_all[3]; - int m1 = -1, m1_all = -1, m2 = -1, m2_all = -1; + int m1 = -1, m2 = -1; m1 = get_random_particle(base_type, 1, 0, dummyp); if (npart_xrd != nbase_charged) error->all(FLERR, "Fix charge regulation acid count inconsistent"); @@ -607,7 +607,7 @@ void FixChargeRegulation::forward_ions() { double energy_before = energy_stored; double factor; - double *dummyp; + double *dummyp = nullptr; int m1 = -1, m2 = -1; factor = volume_rx * volume_rx * c10pI_plus * c10pI_minus / ((1 + ncation) * (1 + nanion)); @@ -642,7 +642,7 @@ void FixChargeRegulation::backward_ions() { double energy_before = energy_stored; double factor; int mask1_tmp, mask2_tmp; - double *dummyp; // dummy pointer + double *dummyp = nullptr; int m1 = -1, m2 = -1; m1 = get_random_particle(cation_type, +1, 0, dummyp); @@ -1014,7 +1014,6 @@ int FixChargeRegulation::get_random_particle(int ptype, double charge, double rd } double FixChargeRegulation::energy_full() { - int imolecule; if (triclinic) domain->x2lamda(atom->nlocal); domain->pbc(); comm->exchange(); @@ -1030,7 +1029,6 @@ double FixChargeRegulation::energy_full() { int overlaptest = 0; double delx, dely, delz, rsq; double **x = atom->x; - tagint *molecule = atom->molecule; int nall = atom->nlocal + atom->nghost; for (int i = 0; i < atom->nlocal; i++) { for (int j = i + 1; j < nall; j++) { @@ -1115,7 +1113,6 @@ int FixChargeRegulation::particle_number(int ptype, double charge) { } double FixChargeRegulation::compute_vector(int n) { - double count_temp = 0; if (n == 0) { return nacid_attempts + nbase_attempts + nsalt_attempts; } else if (n == 1) { From 676191f3303751c39ce4a36bcb964f7d079d527d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Feb 2021 07:28:15 -0500 Subject: [PATCH 0095/1217] various cosmetic changes - print warnings only on MPI rank 0 - use the fix name charge/regulation consistently - use domain->prd_half for half box length instead of computing it - use utils::inumeric() to guarantee integer charge input - LAMMPS coding style adjustments --- src/USER-MISC/fix_charge_regulation.cpp | 194 ++++++++++++++---------- 1 file changed, 114 insertions(+), 80 deletions(-) diff --git a/src/USER-MISC/fix_charge_regulation.cpp b/src/USER-MISC/fix_charge_regulation.cpp index 8a6530ef2b..5479082158 100644 --- a/src/USER-MISC/fix_charge_regulation.cpp +++ b/src/USER-MISC/fix_charge_regulation.cpp @@ -85,25 +85,27 @@ FixChargeRegulation::FixChargeRegulation(LAMMPS *lmp, int narg, char **arg) : // set defaults and read optional arguments options(narg - 5, &arg[5]); - if (nevery <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (nmc < 0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (llength_unit_in_nm < 0.0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (*target_temperature_tcp < 0.0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (seed <= 0) error->all(FLERR, "Illegal fix charge/regulation command: Seed value (positive integer) must be provided "); - if (cation_type <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (anion_type <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (reaction_distance < 0.0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (salt_charge[0] <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (salt_charge[1] >= 0) error->all(FLERR, "Illegal fix charge/regulation command"); - if ((salt_charge[1] % salt_charge[0] != 0) && (salt_charge[0] % salt_charge[1] != 0)) - error->all(FLERR, - "Illegal fix charge/regulation command, multivalent cation/anion charges are allowed, " - "but must be divisible, e.g. (3,-1) is fine, but (3,-2) is not implemented"); + if ((nevery <= 0) || (nmc < 0) || (llength_unit_in_nm < 0.0) + || (*target_temperature_tcp < 0.0) || (cation_type <= 0) + || (anion_type <= 0) || (reaction_distance < 0.0) + || (salt_charge[0] <= 0) || (salt_charge[1] >= 0)) + error->all(FLERR, "Illegal fix charge/regulation command"); + + if (seed <= 0) + error->all(FLERR, "Illegal fix charge/regulation command: " + "Seed value (positive integer) must be provided "); + if ((salt_charge[1] % salt_charge[0] != 0) + && (salt_charge[0] % salt_charge[1] != 0)) + error->all(FLERR,"Illegal fix charge/regulation command, " + "multivalent cation/anion charges are allowed, " + "but must be divisible, e.g. (3,-1) is fine, " + "but (3,-2) is not implemented"); if (pmcmoves[0] < 0 || pmcmoves[1] < 0 || pmcmoves[2] < 0) error->all(FLERR, "Illegal fix charge/regulation command"); if (acid_type < 0) pmcmoves[0] = 0; if (base_type < 0) pmcmoves[1] = 0; + // normalize double psum = pmcmoves[0] + pmcmoves[1] + pmcmoves[2]; if (psum <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); @@ -159,11 +161,12 @@ void FixChargeRegulation::init() { MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, world); if (flagall && comm->me == 0) - error->all(FLERR, "Fix charge regulation cannot exchange individual atoms (ions) belonging to a molecule"); + error->all(FLERR, "fix charge/regulation cannot exchange " + "individual atoms (ions) belonging to a molecule"); } if (domain->dimension == 2) - error->all(FLERR, "Cannot use fix charge regulation in a 2d simulation"); + error->all(FLERR, "Cannot use fix charge/regulation in a 2d simulation"); // create a new group for interaction exclusions // used for attempted atom deletions @@ -173,11 +176,12 @@ void FixChargeRegulation::init() { // create unique group name for atoms to be excluded - auto group_id = std::string("FixChargeRegulation:CR_exclusion_group:") + id; + auto group_id = fmt::format("FixChargeRegulation:exclusion_group:{}",id); group->assign(group_id + " subtract all all"); exclusion_group = group->find(group_id); if (exclusion_group == -1) - error->all(FLERR,"Could not find fix charge/regulation exclusion group ID"); + error->all(FLERR,"Could not find fix charge/regulation exclusion " + "group ID"); exclusion_group_bit = group->bitmask[exclusion_group]; // neighbor list exclusion setup @@ -208,7 +212,8 @@ void FixChargeRegulation::init() { MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, world); if (flagall) - error->all(FLERR, "Cannot do Fix charge regulation on atoms in atom_modify first group"); + error->all(FLERR, "Cannot use fix charge/regulation on atoms " + "in atom_modify first group"); } // construct group bitmask for all new atoms @@ -219,7 +224,7 @@ void FixChargeRegulation::init() { for (int igroup = 0; igroup < ngroups; igroup++) { int jgroup = group->find(groupstrings[igroup]); if (jgroup == -1) - error->all(FLERR, "Could not find specified fix charge regulation group ID"); + error->all(FLERR, "Could not find fix charge/regulation group ID"); groupbitall |= group->bitmask[jgroup]; } } @@ -250,22 +255,26 @@ void FixChargeRegulation::pre_exchange() { if (triclinic) domain->lamda2x(atom->nlocal + atom->nghost); energy_stored = energy_full(); - if (energy_stored > MAXENERGYTEST) - error->warning(FLERR, "Energy of old configuration in fix charge_regulation is > MAXENERGYTEST."); + if ((energy_stored > MAXENERGYTEST) && (comm->me == 0)) + error->warning(FLERR, "Energy of old configuration in fix " + "charge/regulation is > MAXENERGYTEST."); - if ((reaction_distance > fabs(domain->boxhi[0] - domain->boxlo[0]) / 2) || - (reaction_distance > fabs(domain->boxhi[1] - domain->boxlo[1]) / 2) || - (reaction_distance > fabs(domain->boxhi[2] - domain->boxlo[2]) / 2)) { - error->warning(FLERR, - "reaction distance (rxd) is larger than half the box dimension, resetting default: xrd = 0."); + if ((reaction_distance > domain->prd_half[0]) || + (reaction_distance > domain->prd_half[1]) || + (reaction_distance > domain->prd_half[2])) { + if (comm->me == 0) + error->warning(FLERR,"reaction distance (rxd) is larger than " + "half the box dimension, resetting default: xrd = 0."); reaction_distance = 0; } // volume in units of (N_A * mol / liter) - volume_rx = (xhi - xlo) * (yhi - ylo) * (zhi - zlo) * cube(llength_unit_in_nm) * NA_RHO0; + volume_rx = (xhi - xlo) * (yhi - ylo) * (zhi - zlo) + * cube(llength_unit_in_nm) * NA_RHO0; if (reaction_distance < SMALL) { vlocal_xrd = volume_rx; } else { - vlocal_xrd = 4.0 * MY_PI * cube(reaction_distance) / 3.0 * cube(llength_unit_in_nm) * NA_RHO0; + vlocal_xrd = 4.0 * MY_PI * cube(reaction_distance) + / 3.0 * cube(llength_unit_in_nm) * NA_RHO0; } beta = 1.0 / (force->boltz * *target_temperature_tcp); @@ -356,7 +365,7 @@ void FixChargeRegulation::forward_acid() { int m1 = -1, m2 = -1; m1 = get_random_particle(acid_type, 0, 0, dummyp); - if (npart_xrd != nacid_neutral) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + if (npart_xrd != nacid_neutral) error->all(FLERR, "fix charge/regulation acid count inconsistent"); if (nacid_neutral > 0) { if (m1 >= 0) { @@ -415,7 +424,8 @@ void FixChargeRegulation::backward_acid() { int m1 = -1, m2 = -1; m1 = get_random_particle(acid_type, -1, 0, dummyp); - if (npart_xrd != nacid_charged) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + if (npart_xrd != nacid_charged) + error->all(FLERR, "fix charge/regulation acid count inconsistent"); if (nacid_charged > 0) { if (m1 >= 0) { @@ -487,7 +497,8 @@ void FixChargeRegulation::forward_base() { int m1 = -1, m2 = -1; m1 = get_random_particle(base_type, 0, 0, dummyp); - if (npart_xrd != nbase_neutral) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + if (npart_xrd != nbase_neutral) + error->all(FLERR, "fix charge/regulation acid count inconsistent"); if (nbase_neutral > 0) { if (m1 >= 0) { @@ -545,7 +556,8 @@ void FixChargeRegulation::backward_base() { int m1 = -1, m2 = -1; m1 = get_random_particle(base_type, 1, 0, dummyp); - if (npart_xrd != nbase_charged) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + if (npart_xrd != nbase_charged) + error->all(FLERR, "fix charge/regulation acid count inconsistent"); if (nbase_charged > 0) { if (m1 >= 0) { @@ -646,10 +658,12 @@ void FixChargeRegulation::backward_ions() { int m1 = -1, m2 = -1; m1 = get_random_particle(cation_type, +1, 0, dummyp); - if (npart_xrd != ncation) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (npart_xrd != ncation) + error->all(FLERR, "fix charge/regulation salt count inconsistent"); if (ncation > 0) { m2 = get_random_particle(anion_type, -1, 0, dummyp); - if (npart_xrd != nanion) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (npart_xrd != nanion) + error->all(FLERR, "fix charge/regulation salt count inconsistent"); if (nanion > 0) { // attempt deletion @@ -789,7 +803,8 @@ void FixChargeRegulation::backward_ions_multival() { if (ncation < salt_charge_ratio || nanion < 1) return; mm[0] = get_random_particle(anion_type, salt_charge[1], 0, dummyp); - if (npart_xrd != nanion) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (npart_xrd != nanion) + error->all(FLERR, "fix charge/regulation salt count inconsistent"); factor *= volume_rx * c10pI_minus / (nanion); if (mm[0] >= 0) { qq[0] = atom->q[mm[0]]; @@ -799,7 +814,8 @@ void FixChargeRegulation::backward_ions_multival() { } for (int i = 0; i < salt_charge_ratio; i++) { mm[i + 1] = get_random_particle(cation_type, salt_charge[0], 0, dummyp); - if (npart_xrd != ncation - i) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (npart_xrd != ncation - i) + error->all(FLERR, "fix charge/regulation salt count inconsistent"); factor *= volume_rx * c10pI_plus / (ncation - i); if (mm[i + 1] >= 0) { qq[i + 1] = atom->q[mm[i + 1]]; @@ -813,7 +829,8 @@ void FixChargeRegulation::backward_ions_multival() { if (nanion < salt_charge_ratio || ncation < 1) return; mm[0] = get_random_particle(cation_type, salt_charge[0], 0, dummyp); - if (npart_xrd != ncation) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (npart_xrd != ncation) + error->all(FLERR, "fix charge/regulation salt count inconsistent"); factor *= volume_rx * c10pI_plus / (ncation); if (mm[0] >= 0) { qq[0] = atom->q[mm[0]]; @@ -823,7 +840,8 @@ void FixChargeRegulation::backward_ions_multival() { } for (int i = 0; i < salt_charge_ratio; i++) { mm[i + 1] = get_random_particle(anion_type, salt_charge[1], 0, dummyp); - if (npart_xrd != nanion - i) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (npart_xrd != nanion - i) + error->all(FLERR, "fix charge/regulation salt count inconsistent"); if (mm[i + 1] >= 0) { qq[i + 1] = atom->q[mm[i + 1]]; atom->q[mm[i + 1]] = 0; @@ -1138,7 +1156,7 @@ void FixChargeRegulation::setThermoTemperaturePointer() { ifix = modify->find_fix(idftemp); if (ifix == -1) { error->all(FLERR, - "Fix charge regulation regulation could not find a temperature fix id provided by tempfixid\n"); + "fix charge/regulation regulation could not find a temperature fix id provided by tempfixid\n"); } Fix *temperature_fix = modify->fix[ifix]; int dim; @@ -1188,7 +1206,7 @@ void FixChargeRegulation::assign_tags() { ------------------------------------------------------------------------- */ void FixChargeRegulation::options(int narg, char **arg) { - if (narg < 0) error->all(FLERR, "Illegal fix charge regulation command"); + if (narg < 0) error->all(FLERR, "Illegal fix charge/regulation command"); // defaults @@ -1224,48 +1242,59 @@ void FixChargeRegulation::options(int narg, char **arg) { while (iarg < narg) { if (strcmp(arg[iarg], "lunit_nm") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); llength_unit_in_nm = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "acid_type") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); acid_type = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "base_type") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); base_type = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pH") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); pH = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pIp") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); pI_plus = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pIm") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); pI_minus = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pKa") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); pKa = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pKb") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); pKb = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "temp") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); reservoir_temperature = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pKs") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); pKs = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "tempfixid") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); int n = strlen(arg[iarg + 1]) + 1; delete[] idftemp; idftemp = new char[n]; @@ -1273,75 +1302,81 @@ void FixChargeRegulation::options(int narg, char **arg) { setThermoTemperaturePointer(); iarg += 2; } else if (strcmp(arg[iarg], "rxd") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); reaction_distance = utils::numeric(FLERR, arg[iarg + 1], false, lmp); - if ((reaction_distance > fabs(domain->boxhi[0] - domain->boxlo[0]) / 2) || - (reaction_distance > fabs(domain->boxhi[1] - domain->boxlo[1]) / 2) || - (reaction_distance > fabs(domain->boxhi[2] - domain->boxlo[2]) / 2)) { - error->warning(FLERR, - "reaction distance (rxd) is larger than half the box dimension, resetting default: xrd = 0."); + if ((reaction_distance > domain->prd_half[0]) || + (reaction_distance > domain->prd_half[1]) || + (reaction_distance > domain->prd_half[2])) { + if (comm->me == 0) + error->warning(FLERR,"reaction distance (rxd) is larger than half " + "the box dimension, resetting default: xrd = 0."); reaction_distance = 0; } iarg += 2; } else if (strcmp(arg[iarg], "nevery") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); nevery = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "nmc") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); nmc = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pmcmoves") == 0) { - if (iarg + 4 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 4 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); pmcmoves[0] = utils::numeric(FLERR, arg[iarg + 1], false, lmp); pmcmoves[1] = utils::numeric(FLERR, arg[iarg + 2], false, lmp); pmcmoves[2] = utils::numeric(FLERR, arg[iarg + 3], false, lmp); iarg += 4; } else if (strcmp(arg[iarg], "seed") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); seed = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "tag") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); if (strcmp(arg[iarg + 1], "yes") == 0) { add_tags_flag = true; } else if (strcmp(arg[iarg + 1], "no") == 0) { add_tags_flag = false; - } else { error->all(FLERR, "Illegal fix charge regulation command"); } + } else error->all(FLERR, "Illegal fix charge/regulation command"); iarg += 2; } else if (strcmp(arg[iarg], "onlysalt") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); if (strcmp(arg[iarg + 1], "yes") == 0) { only_salt_flag = true; // need to specify salt charge - if (iarg + 4 > narg) error->all(FLERR, "Illegal fix charge regulation command"); - salt_charge[0] = utils::numeric(FLERR, arg[iarg + 2], false, lmp); - salt_charge[1] = utils::numeric(FLERR, arg[iarg + 3], false, lmp); - if (fabs(salt_charge[0] - utils::inumeric(FLERR, arg[iarg + 2], false, lmp)) > SMALL) - error->all(FLERR, "Illegal fix charge regulation command, cation charge must be an integer"); - if (fabs(salt_charge[1] - utils::inumeric(FLERR, arg[iarg + 3], false, lmp)) > SMALL) - error->all(FLERR, "Illegal fix charge regulation command, anion charge must be an integer"); + if (iarg + 4 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); + salt_charge[0] = utils::inumeric(FLERR, arg[iarg + 2], false, lmp); + salt_charge[1] = utils::inumeric(FLERR, arg[iarg + 3], false, lmp); iarg += 4; } else if (strcmp(arg[iarg + 1], "no") == 0) { only_salt_flag = false; iarg += 2; - } else { error->all(FLERR, "Illegal fix charge regulation command"); } + } else error->all(FLERR, "Illegal fix charge/regulation command"); } else if (strcmp(arg[iarg], "group") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix fix charge/regulation command"); if (ngroups >= ngroupsmax) { ngroupsmax = ngroups + 1; groupstrings = (char **) - memory->srealloc(groupstrings, - ngroupsmax * sizeof(char *), - "fix_charge_regulation:groupstrings"); + memory->srealloc(groupstrings, + ngroupsmax * sizeof(char *), + "fix_charge_regulation:groupstrings"); } int n = strlen(arg[iarg + 1]) + 1; groupstrings[ngroups] = new char[n]; strcpy(groupstrings[ngroups], arg[iarg + 1]); ngroups++; iarg += 2; - } else { error->all(FLERR, "Illegal fix charge regulation command"); } + } else error->all(FLERR, "Illegal fix charge/regulation command"); } } @@ -1350,6 +1385,5 @@ void FixChargeRegulation::options(int narg, char **arg) { ------------------------------------------------------------------------- */ double FixChargeRegulation::memory_usage() { - double bytes = cr_nmax * sizeof(int); - return bytes; + return (double)cr_nmax * sizeof(int); } From 6c2abf4739a2ba78dc35d122d0697b826405ab9b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Feb 2021 07:53:19 -0500 Subject: [PATCH 0096/1217] update fix charge/regulation input example to follow LAMMPS conventions closer --- examples/USER/misc/charge_regulation/README | 38 +++- .../{data_acid.chreg => data.chreg-acid} | 0 ...{data_polymer.chreg => data.chreg-polymer} | 0 .../{in_acid.chreg => in.chreg-acid} | 41 ++--- .../misc/charge_regulation/in.chreg-polymer | 33 ++++ .../misc/charge_regulation/in_polymer.chreg | 37 ---- .../misc/charge_regulation/log_acid.lammps | 163 ------------------ 7 files changed, 84 insertions(+), 228 deletions(-) rename examples/USER/misc/charge_regulation/{data_acid.chreg => data.chreg-acid} (100%) rename examples/USER/misc/charge_regulation/{data_polymer.chreg => data.chreg-polymer} (100%) rename examples/USER/misc/charge_regulation/{in_acid.chreg => in.chreg-acid} (52%) create mode 100644 examples/USER/misc/charge_regulation/in.chreg-polymer delete mode 100644 examples/USER/misc/charge_regulation/in_polymer.chreg delete mode 100644 examples/USER/misc/charge_regulation/log_acid.lammps diff --git a/examples/USER/misc/charge_regulation/README b/examples/USER/misc/charge_regulation/README index 5666d6d025..c704b67dea 100644 --- a/examples/USER/misc/charge_regulation/README +++ b/examples/USER/misc/charge_regulation/README @@ -1,8 +1,36 @@ -This directory has two input scripts that illustrates how to use fix charge_regulation in LAMMPS to perform coarse-grained molecular dynamics (MD) simulations with incorporation of charge regulation effects. The charge regulation is implemented via Monte Carlo (MC) sampling following the reaction ensemble MC approach, producing a MC/MD hybrid tool for modeling charge regulation in solvated systems. +This directory has two input scripts that illustrates how to use fix +charge_regulation in LAMMPS to perform coarse-grained molecular dynamics +(MD) simulations with incorporation of charge regulation effects. The +charge regulation is implemented via Monte Carlo (MC) sampling following +the reaction ensemble MC approach, producing a MC/MD hybrid tool for +modeling charge regulation in solvated systems. -The script `in_acid.chreg` sets up a simple weak acid electrolyte (pH=7,pKa=6,pI=3). Four different types of MC moves are implemented: acid protonation & de-protonation, and monovalent ion pair insertion and deletion. Note here we have grouped all free monovalent ions into a single type, a physically natural choice on the level of coarse-grained primitive electrolyte models, which increases the calculation performance but has no effects on thermodynamic observables. The variables such as pH, pKa, pI, and lb at the top of the input script can be adjusted to play with various simulation parameters. The cumulative MC attempted moves and cumulative number of accepted moves, as well as, current number of neutral and charged acid particles, neutral and charged base particles (in this example always 0), and the current number of free cations and anions in the system are printed in the `log_acid.lammps`. +The script `in.chreg-acid` sets up a simple weak acid electrolyte +(pH=7,pKa=6,pI=3). Four different types of MC moves are implemented: +acid protonation & de-protonation, and monovalent ion pair insertion and +deletion. Note here we have grouped all free monovalent ions into a +single type, a physically natural choice on the level of coarse-grained +primitive electrolyte models, which increases the calculation +performance but has no effects on thermodynamic observables. The +variables such as pH, pKa, pI, and lb at the top of the input script can +be adjusted to play with various simulation parameters. The cumulative +MC attempted moves and cumulative number of accepted moves, as well as, +current number of neutral and charged acid particles, neutral and +charged base particles (in this example always 0), and the current +number of free cations and anions in the system are printed in the +output. -The script `in_polymer.chreg` sets up a weak polyelectrolyte chain of N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7 and monovalent salt chemical potential pI=3. In this example, we choose to treat salt ions, protons, and hydroxyl ions separately, which results in 5 types of MC moves: acid [type 1] protonation & de-protonation (with protons [type 4] insertion & deletion), acid [type 1] protonation & de-protonation (with salt cation [type 2] insertion & deletion), water self-ionization (insertion and deletion of proton [type4] and hydroxyl ion [type 5] pair), insertion and deletion of monovalent salt pair [type 2 and type 3] , insertion and deletion -Of a proton [type4] and salt anion [type 3]. -The current number of neutral and charged acid particles, the current number of free salt cations and anions, and the current number of protons and hydroxyl ions are printed in the `log_polymer.lammps`. +The script `in.chreg-polymer` sets up a weak poly-electrolyte chain of +N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7 +and monovalent salt chemical potential pI=3. In this example, we choose +to treat salt ions, protons, and hydroxyl ions separately, which results +in 5 types of MC moves: acid [type 1] protonation & de-protonation (with +protons [type 4] insertion & deletion), acid [type 1] protonation & +de-protonation (with salt cation [type 2] insertion & deletion), water +self-ionization (insertion and deletion of proton [type4] and hydroxyl +ion [type 5] pair), insertion and deletion of monovalent salt pair [type +2 and type 3] , insertion and deletion of a proton [type4] and salt +anion [type 3]. The current number of neutral and charged acid +particles, the current number of free salt cations and anions, and the +current number of protons and hydroxyl ions are printed in the output. diff --git a/examples/USER/misc/charge_regulation/data_acid.chreg b/examples/USER/misc/charge_regulation/data.chreg-acid similarity index 100% rename from examples/USER/misc/charge_regulation/data_acid.chreg rename to examples/USER/misc/charge_regulation/data.chreg-acid diff --git a/examples/USER/misc/charge_regulation/data_polymer.chreg b/examples/USER/misc/charge_regulation/data.chreg-polymer similarity index 100% rename from examples/USER/misc/charge_regulation/data_polymer.chreg rename to examples/USER/misc/charge_regulation/data.chreg-polymer diff --git a/examples/USER/misc/charge_regulation/in_acid.chreg b/examples/USER/misc/charge_regulation/in.chreg-acid similarity index 52% rename from examples/USER/misc/charge_regulation/in_acid.chreg rename to examples/USER/misc/charge_regulation/in.chreg-acid index 73a40f7389..68ef5e1b7c 100644 --- a/examples/USER/misc/charge_regulation/in_acid.chreg +++ b/examples/USER/misc/charge_regulation/in.chreg-acid @@ -1,12 +1,9 @@ # Charge regulation lammps for simple weak electrolyte -units lj -atom_style charge -dimension 3 -boundary p p p -processors * * * -neighbor 3.0 bin -read_data data_acid.chreg +units lj +atom_style charge +neighbor 3.0 bin +read_data data.chreg-acid variable cut_long equal 12.5 variable nevery equal 100 @@ -16,26 +13,24 @@ variable pKa equal 6.0 variable pIm equal 3.0 variable pIp equal 3.0 -variable cut_lj equal 2^(1.0/6.0) -variable lunit_nm equal 0.72 # in the units of nm -velocity all create 1.0 8008 loop geom +variable cut_lj equal 2^(1.0/6.0) +variable lunit_nm equal 0.72 # in the units of nm +velocity all create 1.0 8008 loop geom -pair_style lj/cut/coul/long ${cut_lj} ${cut_long} -pair_coeff * * 1.0 1.0 ${cut_lj} # charges -kspace_style ewald 1.0e-3 -dielectric 1.0 -pair_modify shift yes +pair_style lj/cut/coul/long ${cut_lj} ${cut_long} +pair_coeff * * 1.0 1.0 +kspace_style ewald 1.0e-3 +pair_modify shift yes ######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### -fix fnve all nve -compute dtemp all temp -compute_modify dtemp dynamic yes -fix fT all langevin 1.0 1.0 1.0 123 +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 fix_modify fT temp dtemp fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT -thermo 100 +thermo 100 thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] -log log_acid.lammps -timestep 0.005 -run 20000 +timestep 0.005 +run 2000 diff --git a/examples/USER/misc/charge_regulation/in.chreg-polymer b/examples/USER/misc/charge_regulation/in.chreg-polymer new file mode 100644 index 0000000000..0adab9b5e7 --- /dev/null +++ b/examples/USER/misc/charge_regulation/in.chreg-polymer @@ -0,0 +1,33 @@ +# Charge regulation lammps for a polymer chain +units lj +atom_style full +neighbor 3.0 bin +read_data data.chreg-polymer + +bond_style harmonic +bond_coeff 1 100 1.122462 # K R0 +velocity all create 1.0 8008 loop geom + +pair_style lj/cut/coul/long 1.122462 20 +pair_coeff * * 1.0 1.0 1.122462 # charges +kspace_style pppm 1.0e-3 +pair_modify shift yes +dielectric 1.0 + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 +fix_modify fT temp dtemp + +fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345 +fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345 +fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345 + +thermo 100 +# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions +thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] + +timestep 0.005 +run 2000 diff --git a/examples/USER/misc/charge_regulation/in_polymer.chreg b/examples/USER/misc/charge_regulation/in_polymer.chreg deleted file mode 100644 index e35ba28661..0000000000 --- a/examples/USER/misc/charge_regulation/in_polymer.chreg +++ /dev/null @@ -1,37 +0,0 @@ -# Charge regulation lammps for a polymer chain -units lj -atom_style full -dimension 3 -boundary p p p -processors * * * -neighbor 3.0 bin -read_data data_polymer.chreg - -bond_style harmonic -bond_coeff 1 100 1.122462 # K R0 -velocity all create 1.0 8008 loop geom - -pair_style lj/cut/coul/long 1.122462 20 -pair_coeff * * 1.0 1.0 1.122462 # charges -kspace_style pppm 1.0e-3 -pair_modify shift yes -dielectric 1.0 - -######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### -fix fnve all nve -compute dtemp all temp -compute_modify dtemp dynamic yes -fix fT all langevin 1.0 1.0 1.0 123 -fix_modify fT temp dtemp - -fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345 -fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345 -fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345 - -thermo 100 -# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions -thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] -log log_polymer.lammps - -timestep 0.005 -run 20000 diff --git a/examples/USER/misc/charge_regulation/log_acid.lammps b/examples/USER/misc/charge_regulation/log_acid.lammps deleted file mode 100644 index cbc3661eb1..0000000000 --- a/examples/USER/misc/charge_regulation/log_acid.lammps +++ /dev/null @@ -1,163 +0,0 @@ -LAMMPS (24 Dec 2020) -Reading data file ... - orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 219 atoms - read_data CPU = 0.001 seconds -Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:339) - G vector (1/distance) = 0.14221027 - estimated absolute RMS force accuracy = 0.0010128126 - estimated relative force accuracy = 0.0010128126 - KSpace vectors: actual max1d max3d = 257 5 665 - kxmax kymax kzmax = 5 5 5 -0 atoms in group Fix_CR:exclusion_group:chareg -WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 15.5 - ghost atom cutoff = 15.5 - binsize = 7.75, bins = 7 7 7 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Setting up Verlet run ... - Unit style : lj - Current step : 0 - Time step : 0.005 -Per MPI rank memory allocation (min/avg/max) = 11.91 | 11.91 | 11.91 Mbytes -Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] - 0 -0.054228269 1 0 0 1 99 0 0 109 10 - 100 -0.058672881 0.99159291 100 71 16 84 0 0 92 8 - 200 -0.05399313 0.92006523 200 154 26 74 0 0 85 11 - 300 -0.047035343 0.92728143 300 240 22 78 0 0 85 7 - 400 -0.049597809 1.0617937 400 319 16 84 0 0 92 8 - 500 -0.052409835 1.0006148 500 404 12 88 0 0 97 9 - 600 -0.056012172 0.98059344 600 481 15 85 0 0 92 7 - 700 -0.053639989 0.99572709 700 561 16 84 0 0 94 10 - 800 -0.060026132 0.95764632 800 639 22 78 0 0 84 6 - 900 -0.050785422 0.98399084 900 719 28 72 0 0 82 10 - 1000 -0.062294743 0.97200068 1000 797 26 74 0 0 82 8 - 1100 -0.051269402 1.0064376 1100 877 25 75 0 0 84 9 - 1200 -0.077744839 1.0159098 1200 955 23 77 0 0 88 11 - 1300 -0.084889696 1.1230485 1300 1037 20 80 0 0 90 10 - 1400 -0.059361445 0.96735845 1400 1120 18 82 0 0 93 11 - 1500 -0.052926174 0.95579188 1500 1199 24 76 0 0 86 10 - 1600 -0.052376649 0.99376378 1600 1284 22 78 0 0 89 11 - 1700 -0.052480188 0.96085964 1700 1361 27 73 0 0 84 11 - 1800 -0.065884306 0.96747971 1800 1441 21 79 0 0 84 5 - 1900 -0.054315859 0.95873145 1900 1521 23 77 0 0 84 7 - 2000 -0.037161802 0.93562039 2000 1604 27 73 0 0 79 6 - 2100 -0.034977265 0.97177103 2100 1684 26 74 0 0 85 11 - 2200 -0.047434868 0.97897613 2200 1762 17 83 0 0 93 10 - 2300 -0.047392634 0.96570672 2300 1837 18 82 0 0 92 10 - 2400 -0.044879306 0.98620033 2400 1910 19 81 0 0 89 8 - 2500 -0.069690496 1.0690505 2500 1988 16 84 0 0 91 7 - 2600 -0.081588407 0.97711054 2600 2067 17 83 0 0 92 9 - 2700 -0.06341681 1.0386711 2700 2146 20 80 0 0 85 5 - 2800 -0.045290012 1.0402055 2800 2230 18 82 0 0 91 9 - 2900 -0.046875012 1.0609775 2900 2317 24 76 0 0 86 10 - 3000 -0.031258722 0.93861202 3000 2400 24 76 0 0 85 9 - 3100 -0.04673342 0.90800583 3100 2485 25 75 0 0 90 15 - 3200 -0.054354227 0.94493881 3200 2567 16 84 0 0 94 10 - 3300 -0.053647746 0.92321446 3300 2641 17 83 0 0 94 11 - 3400 -0.031751732 0.93735127 3400 2725 22 78 0 0 92 14 - 3500 -0.053806113 0.98798136 3500 2795 28 72 0 0 84 12 - 3600 -0.040751349 0.84291639 3600 2873 28 72 0 0 84 12 - 3700 -0.051747138 1.072448 3700 2951 24 76 0 0 92 16 - 3800 -0.043420594 1.0076309 3800 3030 26 74 0 0 79 5 - 3900 -0.050845848 1.0250023 3900 3103 29 71 0 0 76 5 - 4000 -0.039837847 1.064111 4000 3182 29 71 0 0 83 12 - 4100 -0.045638995 1.1249685 4100 3262 28 72 0 0 81 9 - 4200 -0.047956491 0.92255907 4200 3348 26 74 0 0 87 13 - 4300 -0.054052822 1.006239 4300 3423 19 81 0 0 90 9 - 4400 -0.053148034 1.0028887 4400 3506 24 76 0 0 83 7 - 4500 -0.062132076 1.0317847 4500 3587 23 77 0 0 82 5 - 4600 -0.04616043 0.99066453 4600 3673 28 72 0 0 82 10 - 4700 -0.066990889 1.0242064 4700 3755 18 82 0 0 90 8 - 4800 -0.0564736 0.91765628 4800 3832 22 78 0 0 91 13 - 4900 -0.052301294 0.95348659 4900 3912 28 72 0 0 81 9 - 5000 -0.062630677 1.0336579 5000 3989 18 82 0 0 92 10 - 5100 -0.053645908 1.0314613 5100 4062 20 80 0 0 85 5 - 5200 -0.062189568 1.0504732 5200 4133 23 77 0 0 84 7 - 5300 -0.049092746 1.0310832 5300 4217 24 76 0 0 82 6 - 5400 -0.051859257 0.99600428 5400 4299 27 73 0 0 80 7 - 5500 -0.065540815 0.98012128 5500 4381 19 81 0 0 92 11 - 5600 -0.071018582 0.9252814 5600 4455 23 77 0 0 84 7 - 5700 -0.066954185 1.0325214 5700 4535 26 74 0 0 82 8 - 5800 -0.064847249 1.0313536 5800 4617 21 79 0 0 90 11 - 5900 -0.063173056 0.95455853 5900 4703 18 82 0 0 92 10 - 6000 -0.064807837 0.97182222 6000 4790 21 79 0 0 91 12 - 6100 -0.07067683 0.91775921 6100 4875 16 84 0 0 94 10 - 6200 -0.071400842 1.0162225 6200 4952 17 83 0 0 87 4 - 6300 -0.078479449 1.0106706 6300 5033 21 79 0 0 84 5 - 6400 -0.083167651 1.0246584 6400 5111 18 82 0 0 90 8 - 6500 -0.092611537 1.0766467 6500 5195 20 80 0 0 88 8 - 6600 -0.096710071 1.0246648 6600 5274 15 85 0 0 91 6 - 6700 -0.073399857 0.94939392 6700 5351 17 83 0 0 92 9 - 6800 -0.062479375 0.9393967 6800 5434 18 82 0 0 93 11 - 6900 -0.065391043 0.93475954 6900 5514 22 78 0 0 89 11 - 7000 -0.045655499 0.98688239 7000 5601 21 79 0 0 90 11 - 7100 -0.061186309 1.0309063 7100 5684 22 78 0 0 87 9 - 7200 -0.074737514 1.0516593 7200 5769 25 75 0 0 80 5 - 7300 -0.075228979 1.0167704 7300 5847 21 79 0 0 86 7 - 7400 -0.06660147 1.0947107 7400 5930 25 75 0 0 87 12 - 7500 -0.071915247 1.10542 7500 6009 24 76 0 0 84 8 - 7600 -0.029974303 0.99202697 7600 6095 28 72 0 0 80 8 - 7700 -0.029024004 1.0390995 7700 6182 28 72 0 0 83 11 - 7800 -0.056250746 0.96393961 7800 6260 18 82 0 0 91 9 - 7900 -0.072178944 0.9833919 7900 6339 21 79 0 0 86 7 - 8000 -0.070377248 1.021342 8000 6419 23 77 0 0 88 11 - 8100 -0.07753283 0.96194312 8100 6493 26 74 0 0 86 12 - 8200 -0.075617309 0.9715344 8200 6576 25 75 0 0 89 14 - 8300 -0.077480013 0.99106705 8300 6662 20 80 0 0 91 11 - 8400 -0.079901928 0.89855112 8400 6744 23 77 0 0 91 14 - 8500 -0.069192745 1.0606791 8500 6822 19 81 0 0 91 10 - 8600 -0.058657202 1.1270217 8600 6898 15 85 0 0 95 10 - 8700 -0.044985397 1.0367419 8700 6979 27 73 0 0 84 11 - 8800 -0.064266376 0.91557003 8800 7060 21 79 0 0 89 10 - 8900 -0.068680533 0.95963643 8900 7133 19 81 0 0 88 7 - 9000 -0.051736144 1.0398547 9000 7213 13 87 0 0 94 7 - 9100 -0.058381436 0.98047663 9100 7290 17 83 0 0 89 6 - 9200 -0.05531014 0.92541631 9200 7368 22 78 0 0 85 7 - 9300 -0.04386907 0.9339658 9300 7454 22 78 0 0 89 11 - 9400 -0.052293168 0.94314034 9400 7539 22 78 0 0 86 8 - 9500 -0.050362046 1.0489028 9500 7617 18 82 0 0 90 8 - 9600 -0.054272227 1.0879161 9600 7697 11 89 0 0 96 7 - 9700 -0.042514179 1.0051505 9700 7771 22 78 0 0 84 6 - 9800 -0.045365018 0.95363669 9800 7850 25 75 0 0 77 2 - 9900 -0.064287274 0.91994667 9900 7928 27 73 0 0 81 8 - 10000 -0.05689162 0.99963208 10000 8011 22 78 0 0 84 6 -Loop time of 19.4452 on 1 procs for 10000 steps with 190 atoms - -Performance: 222162.510 tau/day, 514.265 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.68864 | 0.68864 | 0.68864 | 0.0 | 3.54 -Kspace | 6.7893 | 6.7893 | 6.7893 | 0.0 | 34.92 -Neigh | 0.060782 | 0.060782 | 0.060782 | 0.0 | 0.31 -Comm | 0.047035 | 0.047035 | 0.047035 | 0.0 | 0.24 -Output | 0.0027227 | 0.0027227 | 0.0027227 | 0.0 | 0.01 -Modify | 11.838 | 11.838 | 11.838 | 0.0 | 60.88 -Other | | 0.01878 | | | 0.10 - -Nlocal: 190.000 ave 190 max 190 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 592.000 ave 592 max 592 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2194.00 ave 2194 max 2194 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2194 -Ave neighs/atom = 11.547368 -Neighbor list builds = 10287 -Dangerous builds = 0 -Total wall time: 0:00:19 \ No newline at end of file From 7f8e8c635c10f0c99343c0f31565b91ac2de951b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Feb 2021 08:00:59 -0500 Subject: [PATCH 0097/1217] create new reference log files --- .../log.10Feb21.chreg-acid.g++.1 | 125 ++++++++++++ .../log.10Feb21.chreg-acid.g++.4 | 125 ++++++++++++ .../log.10Feb21.chreg-polymer.g++.1 | 131 +++++++++++++ .../log.10Feb21.chreg-polymer.g++.4 | 131 +++++++++++++ .../misc/charge_regulation/log_polymer.lammps | 181 ------------------ 5 files changed, 512 insertions(+), 181 deletions(-) create mode 100644 examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1 create mode 100644 examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4 create mode 100644 examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1 create mode 100644 examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4 delete mode 100644 examples/USER/misc/charge_regulation/log_polymer.lammps diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1 b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1 new file mode 100644 index 0000000000..627281217b --- /dev/null +++ b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1 @@ -0,0 +1,125 @@ +LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task +# Charge regulation lammps for simple weak electrolyte + +units lj +atom_style charge +neighbor 3.0 bin +read_data data.chreg-acid +Reading data file ... + orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 219 atoms + read_data CPU = 0.003 seconds + +variable cut_long equal 12.5 +variable nevery equal 100 +variable nmc equal 100 +variable pH equal 7.0 +variable pKa equal 6.0 +variable pIm equal 3.0 +variable pIp equal 3.0 + +variable cut_lj equal 2^(1.0/6.0) +variable lunit_nm equal 0.72 # in the units of nm +velocity all create 1.0 8008 loop geom + +pair_style lj/cut/coul/long ${cut_lj} ${cut_long} +pair_style lj/cut/coul/long 1.12246204830937 ${cut_long} +pair_style lj/cut/coul/long 1.12246204830937 12.5 +pair_coeff * * 1.0 1.0 +kspace_style ewald 1.0e-3 +pair_modify shift yes + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 +fix_modify fT temp dtemp + +fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc 100 seed 2345 tempfixid fT +thermo 100 +thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] +timestep 0.005 +run 2000 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.14221027 + estimated absolute RMS force accuracy = 0.0010128126 + estimated relative force accuracy = 0.0010128126 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +0 atoms in group FixChargeRegulation:exclusion_group:chareg +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 15.5 + ghost atom cutoff = 15.5 + binsize = 7.75, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.91 | 11.91 | 11.91 Mbytes +Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] + 0 -0.049662059 1 0 0 1 99 0 0 109 10 + 100 -0.053672881 0.99159291 100 71 16 84 0 0 92 8 + 200 -0.053383027 0.90935145 200 156 26 74 0 0 85 11 + 300 -0.040471335 0.97937429 300 240 21 79 0 0 87 8 + 400 -0.036188123 1.0837424 400 319 14 86 0 0 92 6 + 500 -0.057294925 1.0507526 500 407 10 90 0 0 98 8 + 600 -0.056009748 1.0669354 600 487 15 85 0 0 92 7 + 700 -0.069686562 0.99202496 700 567 14 86 0 0 96 10 + 800 -0.054695624 1.0592933 800 647 25 75 0 0 82 7 + 900 -0.058693653 0.97870458 900 728 27 73 0 0 83 10 + 1000 -0.062352957 1.0008923 1000 805 24 76 0 0 84 8 + 1100 -0.065011926 0.91691048 1100 886 22 78 0 0 87 9 + 1200 -0.080463686 0.98879304 1200 963 23 77 0 0 88 11 + 1300 -0.062146141 1.0566033 1300 1047 21 79 0 0 88 9 + 1400 -0.046980246 1.0847512 1400 1129 17 83 0 0 94 11 + 1500 -0.042935292 1.0075805 1500 1203 24 76 0 0 86 10 + 1600 -0.056075891 0.94173489 1600 1277 23 77 0 0 90 13 + 1700 -0.042279161 1.1126317 1700 1355 28 72 0 0 82 10 + 1800 -0.036842528 1.0255327 1800 1436 24 76 0 0 83 7 + 1900 -0.038816022 0.93883373 1900 1511 23 77 0 0 86 9 + 2000 -0.047008287 0.98904085 2000 1592 26 74 0 0 81 7 +Loop time of 11.6365 on 1 procs for 2000 steps with 188 atoms + +Performance: 74249.079 tau/day, 171.873 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.24337 | 0.24337 | 0.24337 | 0.0 | 2.09 +Kspace | 4.6009 | 4.6009 | 4.6009 | 0.0 | 39.54 +Neigh | 0.023451 | 0.023451 | 0.023451 | 0.0 | 0.20 +Comm | 0.027729 | 0.027729 | 0.027729 | 0.0 | 0.24 +Output | 0.0007813 | 0.0007813 | 0.0007813 | 0.0 | 0.01 +Modify | 6.7345 | 6.7345 | 6.7345 | 0.0 | 57.87 +Other | | 0.005713 | | | 0.05 + +Nlocal: 188.000 ave 188 max 188 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 597.000 ave 597 max 597 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2196.00 ave 2196 max 2196 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2196 +Ave neighs/atom = 11.680851 +Neighbor list builds = 2059 +Dangerous builds = 0 +Total wall time: 0:00:11 diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4 b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4 new file mode 100644 index 0000000000..465dcbdb4e --- /dev/null +++ b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4 @@ -0,0 +1,125 @@ +LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task +# Charge regulation lammps for simple weak electrolyte + +units lj +atom_style charge +neighbor 3.0 bin +read_data data.chreg-acid +Reading data file ... + orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 219 atoms + read_data CPU = 0.003 seconds + +variable cut_long equal 12.5 +variable nevery equal 100 +variable nmc equal 100 +variable pH equal 7.0 +variable pKa equal 6.0 +variable pIm equal 3.0 +variable pIp equal 3.0 + +variable cut_lj equal 2^(1.0/6.0) +variable lunit_nm equal 0.72 # in the units of nm +velocity all create 1.0 8008 loop geom + +pair_style lj/cut/coul/long ${cut_lj} ${cut_long} +pair_style lj/cut/coul/long 1.12246204830937 ${cut_long} +pair_style lj/cut/coul/long 1.12246204830937 12.5 +pair_coeff * * 1.0 1.0 +kspace_style ewald 1.0e-3 +pair_modify shift yes + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 +fix_modify fT temp dtemp + +fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc 100 seed 2345 tempfixid fT +thermo 100 +thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] +timestep 0.005 +run 2000 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.14221027 + estimated absolute RMS force accuracy = 0.0010128126 + estimated relative force accuracy = 0.0010128126 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +0 atoms in group FixChargeRegulation:exclusion_group:chareg +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 15.5 + ghost atom cutoff = 15.5 + binsize = 7.75, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.89 | 11.89 | 11.89 Mbytes +Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] + 0 -0.049662059 1 0 0 1 99 0 0 109 10 + 100 -0.06196414 1.0156327 100 72 15 85 0 0 93 8 + 200 -0.053901683 0.95128403 200 160 24 76 0 0 87 11 + 300 -0.043852423 0.98035058 300 246 22 78 0 0 85 7 + 400 -0.048370798 1.0909844 400 324 16 84 0 0 91 7 + 500 -0.042546472 1.026849 500 410 13 87 0 0 95 8 + 600 -0.06133022 0.97805065 600 494 14 86 0 0 93 7 + 700 -0.053815853 1.0641005 700 572 17 83 0 0 91 8 + 800 -0.059974814 1.0192348 800 650 23 77 0 0 83 6 + 900 -0.051808132 1.0773288 900 728 25 75 0 0 85 10 + 1000 -0.050390995 1.0236954 1000 804 28 72 0 0 81 9 + 1100 -0.069766444 1.030965 1100 890 25 75 0 0 85 10 + 1200 -0.074580231 1.0490058 1200 963 21 79 0 0 88 9 + 1300 -0.060169443 0.93456607 1300 1043 22 78 0 0 86 8 + 1400 -0.05120764 1.0374062 1400 1127 19 81 0 0 92 11 + 1500 -0.027644416 0.99804782 1500 1204 24 76 0 0 85 9 + 1600 -0.038599195 0.99015524 1600 1283 22 78 0 0 90 12 + 1700 -0.050222686 1.1444379 1700 1365 27 73 0 0 84 11 + 1800 -0.049338003 1.1188048 1800 1449 22 78 0 0 84 6 + 1900 -0.04533154 0.99894341 1900 1527 22 78 0 0 86 8 + 2000 -0.058837311 0.95302017 2000 1608 26 74 0 0 81 7 +Loop time of 3.98119 on 4 procs for 2000 steps with 188 atoms + +Performance: 217020.495 tau/day, 502.362 timesteps/s +96.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.050626 | 0.061127 | 0.071318 | 3.4 | 1.54 +Kspace | 1.1987 | 1.2504 | 1.288 | 3.1 | 31.41 +Neigh | 0.0056982 | 0.0063858 | 0.0069821 | 0.7 | 0.16 +Comm | 0.068302 | 0.11638 | 0.17922 | 12.8 | 2.92 +Output | 0.00055408 | 0.00092399 | 0.0020106 | 0.0 | 0.02 +Modify | 2.5399 | 2.5406 | 2.5417 | 0.0 | 63.81 +Other | | 0.005394 | | | 0.14 + +Nlocal: 47.0000 ave 55 max 42 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Nghost: 328.250 ave 335 max 317 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 547.000 ave 659 max 466 min +Histogram: 2 0 0 0 0 0 1 0 0 1 + +Total # of neighbors = 2188 +Ave neighs/atom = 11.638298 +Neighbor list builds = 2057 +Dangerous builds = 0 +Total wall time: 0:00:04 diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1 b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1 new file mode 100644 index 0000000000..c386b2bed9 --- /dev/null +++ b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1 @@ -0,0 +1,131 @@ +LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task +# Charge regulation lammps for a polymer chain +units lj +atom_style full +neighbor 3.0 bin +read_data data.chreg-polymer +Reading data file ... + orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 160 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 79 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.009 seconds + +bond_style harmonic +bond_coeff 1 100 1.122462 # K R0 +velocity all create 1.0 8008 loop geom + +pair_style lj/cut/coul/long 1.122462 20 +pair_coeff * * 1.0 1.0 1.122462 # charges +kspace_style pppm 1.0e-3 +pair_modify shift yes +dielectric 1.0 + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 +fix_modify fT temp dtemp + +fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345 +fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345 +fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345 + +thermo 100 +# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions +thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] + +timestep 0.005 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.077106934 + grid = 8 8 8 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00074388331 + estimated relative force accuracy = 0.00074388331 + using double precision FFTW3 + 3d grid and FFT values/proc = 2197 512 +0 atoms in group FixChargeRegulation:exclusion_group:chareg1 +0 atoms in group FixChargeRegulation:exclusion_group:chareg2 +0 atoms in group FixChargeRegulation:exclusion_group:chareg3 +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 23 + ghost atom cutoff = 23 + binsize = 11.5, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.962 | 6.962 | 6.962 Mbytes +Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] + 0 0.50528297 1 0 80 80 0 0 0 + 100 0.61185377 0.95892928 13 67 74 7 0 0 + 200 0.54355177 1.1282424 19 61 76 15 0 0 + 300 0.4519957 1.0764688 20 60 85 26 1 0 + 400 0.41479389 0.99212685 24 56 92 36 0 0 + 500 0.37382446 0.99776674 28 52 98 46 0 0 + 600 0.34785337 1.1115081 28 52 109 57 0 0 + 700 0.34637618 1.0332262 28 52 120 68 0 0 + 800 0.21020932 1.1264036 29 51 125 74 0 0 + 900 0.21246108 1.1168609 30 50 131 81 0 0 + 1000 0.20997475 1.1201478 32 48 132 84 0 0 + 1100 0.1984165 1.0209092 31 49 144 95 0 0 + 1200 0.2061932 0.95880059 35 45 151 106 0 0 + 1300 0.17220376 0.980077 36 44 156 112 0 0 + 1400 0.15671143 0.93535342 37 43 161 118 0 0 + 1500 0.16174665 0.9495928 36 44 168 124 0 0 + 1600 0.11062965 0.94072924 40 40 164 124 0 0 + 1700 0.13002563 0.95010828 38 42 167 125 0 0 + 1800 0.14527814 0.93555342 37 43 172 129 0 0 + 1900 0.17627465 0.96682495 32 48 176 128 0 0 + 2000 0.16497265 0.95226954 33 47 180 133 0 0 +Loop time of 7.45499 on 1 procs for 2000 steps with 393 atoms + +Performance: 115895.577 tau/day, 268.277 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.45607 | 0.45607 | 0.45607 | 0.0 | 6.12 +Bond | 0.0062385 | 0.0062385 | 0.0062385 | 0.0 | 0.08 +Kspace | 2.3257 | 2.3257 | 2.3257 | 0.0 | 31.20 +Neigh | 0.067103 | 0.067103 | 0.067103 | 0.0 | 0.90 +Comm | 0.02577 | 0.02577 | 0.02577 | 0.0 | 0.35 +Output | 0.00087047 | 0.00087047 | 0.00087047 | 0.0 | 0.01 +Modify | 4.5664 | 4.5664 | 4.5664 | 0.0 | 61.25 +Other | | 0.006848 | | | 0.09 + +Nlocal: 393.000 ave 393 max 393 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 749.000 ave 749 max 749 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5359.00 ave 5359 max 5359 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5359 +Ave neighs/atom = 13.636132 +Ave special neighs/atom = 1.1908397 +Neighbor list builds = 1489 +Dangerous builds = 0 +Total wall time: 0:00:07 diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4 b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4 new file mode 100644 index 0000000000..c623d3048b --- /dev/null +++ b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4 @@ -0,0 +1,131 @@ +LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task +# Charge regulation lammps for a polymer chain +units lj +atom_style full +neighbor 3.0 bin +read_data data.chreg-polymer +Reading data file ... + orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 160 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 79 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.016 seconds + +bond_style harmonic +bond_coeff 1 100 1.122462 # K R0 +velocity all create 1.0 8008 loop geom + +pair_style lj/cut/coul/long 1.122462 20 +pair_coeff * * 1.0 1.0 1.122462 # charges +kspace_style pppm 1.0e-3 +pair_modify shift yes +dielectric 1.0 + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 +fix_modify fT temp dtemp + +fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345 +fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345 +fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345 + +thermo 100 +# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions +thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] + +timestep 0.005 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.077106934 + grid = 8 8 8 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00074388331 + estimated relative force accuracy = 0.00074388331 + using double precision FFTW3 + 3d grid and FFT values/proc = 1053 128 +0 atoms in group FixChargeRegulation:exclusion_group:chareg1 +0 atoms in group FixChargeRegulation:exclusion_group:chareg2 +0 atoms in group FixChargeRegulation:exclusion_group:chareg3 +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 23 + ghost atom cutoff = 23 + binsize = 11.5, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.878 | 6.935 | 6.992 Mbytes +Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] + 0 0.50528297 1 0 80 80 0 0 0 + 100 0.60223729 0.89547569 13 67 75 8 0 0 + 200 0.65253636 0.87662399 18 62 78 16 0 0 + 300 0.51550501 1.0542131 22 58 84 27 1 0 + 400 0.43566766 0.94557633 26 54 90 36 0 0 + 500 0.36269507 1.0386276 31 49 94 45 0 0 + 600 0.32430641 0.99903033 27 53 111 58 0 0 + 700 0.30255299 0.91225991 28 52 121 69 0 0 + 800 0.27189951 0.9747089 28 52 127 75 0 0 + 900 0.25495247 1.0747821 28 52 135 83 0 0 + 1000 0.25950416 0.95256449 32 48 134 86 0 0 + 1100 0.22561248 1.0102255 32 48 147 99 0 0 + 1200 0.1734754 0.99475154 33 47 157 110 0 0 + 1300 0.20081084 0.99873599 36 44 160 116 0 0 + 1400 0.14240417 0.99442152 36 44 164 121 1 0 + 1500 0.15314186 0.94559876 39 41 167 126 0 0 + 1600 0.13574107 1.0484195 43 37 164 127 0 0 + 1700 0.14477789 1.0105172 42 38 166 128 0 0 + 1800 0.13493107 1.0349667 41 39 171 132 0 0 + 1900 0.14849779 0.9994329 33 47 178 131 0 0 + 2000 0.14485171 0.99739608 34 46 183 137 0 0 +Loop time of 3.18871 on 4 procs for 2000 steps with 400 atoms + +Performance: 270955.695 tau/day, 627.212 timesteps/s +94.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.086456 | 0.11738 | 0.18562 | 11.8 | 3.68 +Bond | 0.00099182 | 0.0018544 | 0.0030079 | 1.8 | 0.06 +Kspace | 0.77406 | 0.79354 | 0.80895 | 1.5 | 24.89 +Neigh | 0.017894 | 0.017948 | 0.018002 | 0.0 | 0.56 +Comm | 0.029044 | 0.07885 | 0.11432 | 11.3 | 2.47 +Output | 0.00054932 | 0.0009656 | 0.0021319 | 0.0 | 0.03 +Modify | 2.1676 | 2.1706 | 2.1733 | 0.2 | 68.07 +Other | | 0.007591 | | | 0.24 + +Nlocal: 100.000 ave 110 max 89 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 415.000 ave 418 max 411 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 1360.75 ave 1872 max 1018 min +Histogram: 1 1 0 0 1 0 0 0 0 1 + +Total # of neighbors = 5443 +Ave neighs/atom = 13.607500 +Ave special neighs/atom = 1.1700000 +Neighbor list builds = 1492 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/USER/misc/charge_regulation/log_polymer.lammps b/examples/USER/misc/charge_regulation/log_polymer.lammps deleted file mode 100644 index 87cab63a6c..0000000000 --- a/examples/USER/misc/charge_regulation/log_polymer.lammps +++ /dev/null @@ -1,181 +0,0 @@ -LAMMPS (24 Dec 2020) -Reading data file ... - orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 160 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 79 bonds -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.004 seconds -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:339) - G vector (1/distance) = 0.077106934 - grid = 8 8 8 - stencil order = 5 - estimated absolute RMS force accuracy = 0.00074388331 - estimated relative force accuracy = 0.00074388331 - using double precision KISS FFT - 3d grid and FFT values/proc = 2197 512 -0 atoms in group Fix_CR:exclusion_group:chareg1 -0 atoms in group Fix_CR:exclusion_group:chareg2 -0 atoms in group Fix_CR:exclusion_group:chareg3 -WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 23 - ghost atom cutoff = 23 - binsize = 11.5, bins = 9 9 9 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Setting up Verlet run ... - Unit style : lj - Current step : 0 - Time step : 0.005 -Per MPI rank memory allocation (min/avg/max) = 6.962 | 6.962 | 6.962 Mbytes -Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] - 0 0.49903297 1 0 80 80 0 0 0 - 100 0.63380666 0.87307225 8 72 77 6 1 0 - 200 0.5865464 1.0048645 16 64 81 16 0 1 - 300 0.55802913 1.0499142 19 61 91 29 0 1 - 400 0.44734087 1.0838048 24 56 98 41 0 1 - 500 0.47010775 1.005226 23 57 106 48 0 1 - 600 0.3452105 0.97814306 28 52 109 56 0 1 - 700 0.29208955 0.99766419 32 48 115 67 0 0 - 800 0.27821915 1.0091641 31 49 128 80 1 0 - 900 0.28943788 0.93619239 26 54 145 91 0 0 - 1000 0.22963142 1.0162138 27 53 150 97 0 0 - 1100 0.24238916 0.99146577 31 49 149 100 0 0 - 1200 0.17029095 1.0406453 38 42 144 102 0 0 - 1300 0.15830969 0.94661447 34 46 155 109 0 0 - 1400 0.16698712 1.0116563 35 45 159 114 0 0 - 1500 0.15432936 0.95600941 36 44 162 118 0 0 - 1600 0.16973501 0.98326602 31 49 171 122 0 0 - 1700 0.19725116 0.9915273 33 47 175 128 0 0 - 1800 0.15278999 1.0304873 29 51 193 142 0 0 - 1900 0.17418479 0.99490216 30 50 194 144 0 0 - 2000 0.14238391 0.9638301 32 48 189 141 0 0 - 2100 0.13054378 0.97164976 32 48 192 144 0 0 - 2200 0.092083069 1.0112059 40 40 191 151 0 0 - 2300 0.085175091 1.0070667 39 41 200 159 0 0 - 2400 0.083367076 0.9934796 35 45 208 163 0 0 - 2500 0.11494744 0.97650855 31 49 220 172 1 0 - 2600 0.10796032 0.97047046 34 46 221 175 0 0 - 2700 0.11080141 0.93570013 36 44 223 179 0 0 - 2800 0.096699277 0.97702627 35 45 223 178 0 0 - 2900 0.079403783 1.0870961 32 48 229 181 0 0 - 3000 0.08288836 1.0642515 35 45 231 186 0 0 - 3100 0.094000833 1.0241111 38 42 229 187 0 0 - 3200 0.10011052 1.043594 34 46 235 189 0 0 - 3300 0.096782103 0.99549134 34 46 234 188 0 0 - 3400 0.057703946 1.00292 34 46 236 190 0 0 - 3500 0.074345642 0.95064523 36 44 234 190 0 0 - 3600 0.085872341 0.9759514 35 45 238 192 0 1 - 3700 0.086427565 0.99843063 35 45 240 194 0 1 - 3800 0.076091357 0.98516844 32 48 252 203 0 1 - 3900 0.047187813 1.0063336 37 43 247 204 0 0 - 4000 0.068269223 1.0390369 35 45 248 203 0 0 - 4100 0.074209582 0.99912762 36 44 249 205 0 0 - 4200 0.087016078 1.050265 36 44 246 202 0 0 - 4300 0.081325479 1.0417103 35 45 245 200 0 0 - 4400 0.047345973 0.96517298 39 41 243 202 0 0 - 4500 0.041856955 0.94569673 38 42 245 203 0 0 - 4600 0.049588267 0.99046371 42 38 249 211 0 0 - 4700 0.043079897 1.0098538 43 37 245 208 0 0 - 4800 0.049122913 1.0229995 41 39 247 208 0 0 - 4900 0.059151797 1.0236679 36 44 249 205 0 0 - 5000 0.053806841 1.0308397 42 38 243 205 0 0 - 5100 0.053623833 1.0638841 39 41 246 205 0 0 - 5200 0.086215806 1.0027613 37 43 243 200 0 0 - 5300 0.031422797 1.0338154 38 42 245 203 0 0 - 5400 0.051341116 0.92205149 34 46 246 200 0 0 - 5500 0.039292708 0.97530704 32 48 251 203 0 0 - 5600 0.035215415 1.023123 33 47 246 199 0 0 - 5700 0.054553598 0.95833063 30 50 253 203 0 0 - 5800 0.035699456 1.0721613 37 43 248 205 0 0 - 5900 0.062426908 1.0612245 38 42 252 210 0 0 - 6000 0.056362902 1.0002968 36 44 248 204 0 0 - 6100 0.061550208 0.97270904 38 42 245 203 0 0 - 6200 0.051825485 0.98187623 36 44 253 209 0 0 - 6300 0.052137885 0.98906723 36 44 253 210 1 0 - 6400 0.068218075 1.0511584 36 44 256 212 0 0 - 6500 0.080167413 0.97270144 36 44 252 208 0 0 - 6600 0.052169204 1.0160108 41 39 249 210 0 0 - 6700 0.057313326 0.98033894 38 42 251 209 0 0 - 6800 0.073008094 0.96239565 35 45 256 211 0 0 - 6900 0.060159599 1.0063892 37 43 264 221 0 0 - 7000 0.061738744 1.0031443 39 41 259 218 0 0 - 7100 0.043263424 1.0425248 44 36 255 219 0 0 - 7200 0.052179167 0.99512151 39 41 261 220 0 0 - 7300 0.053258707 1.0171204 43 37 256 219 0 0 - 7400 0.026037532 0.93786837 45 35 259 224 0 0 - 7500 0.029731213 1.0172281 46 34 250 216 0 0 - 7600 0.023118288 0.95628439 42 38 262 224 0 0 - 7700 0.037021854 0.99991854 42 38 263 225 0 0 - 7800 0.050404736 1.0130826 40 40 260 220 0 0 - 7900 0.035658921 0.95772506 40 40 259 219 0 0 - 8000 0.034426806 1.0028052 40 40 254 214 0 0 - 8100 0.041427611 1.0347682 40 40 256 216 0 0 - 8200 0.05986843 0.9804614 38 42 262 220 0 0 - 8300 0.041419023 1.0613186 37 43 264 221 0 0 - 8400 0.065701758 1.0511531 40 40 256 216 0 0 - 8500 0.091954526 0.97190676 37 43 257 214 0 0 - 8600 0.056982532 1.017813 35 45 252 207 0 0 - 8700 0.075615111 1.0148527 29 51 263 212 0 0 - 8800 0.066070082 1.0259454 33 47 260 213 0 0 - 8900 0.055054194 1.0183535 37 43 247 204 0 0 - 9000 0.063070816 1.0266115 39 41 244 203 0 0 - 9100 0.10174156 0.99457684 34 46 246 200 0 0 - 9200 0.071667261 1.033159 33 47 249 202 0 0 - 9300 0.05520096 0.99821492 38 42 243 201 0 0 - 9400 0.050355422 0.99148522 37 43 243 200 0 0 - 9500 0.062314961 1.0042937 36 44 252 208 0 0 - 9600 0.061148899 1.0052132 37 43 254 211 0 0 - 9700 0.078695273 1.0175164 37 43 252 209 0 0 - 9800 0.067487202 1.0110138 35 45 258 213 0 0 - 9900 0.070340779 0.99640142 31 49 263 214 0 0 - 10000 0.037252172 0.99863894 32 48 259 211 0 0 -Loop time of 23.0419 on 1 procs for 10000 steps with 550 atoms - -Performance: 187484.206 tau/day, 433.991 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.5444 | 2.5444 | 2.5444 | 0.0 | 11.04 -Bond | 0.025075 | 0.025075 | 0.025075 | 0.0 | 0.11 -Kspace | 4.7385 | 4.7385 | 4.7385 | 0.0 | 20.56 -Neigh | 0.2058 | 0.2058 | 0.2058 | 0.0 | 0.89 -Comm | 0.073087 | 0.073087 | 0.073087 | 0.0 | 0.32 -Output | 0.003464 | 0.003464 | 0.003464 | 0.0 | 0.02 -Modify | 15.417 | 15.417 | 15.417 | 0.0 | 66.91 -Other | | 0.03479 | | | 0.15 - -Nlocal: 550.000 ave 550 max 550 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1023.00 ave 1023 max 1023 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 9644.00 ave 9644 max 9644 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 9644 -Ave neighs/atom = 17.534545 -Ave special neighs/atom = 0.85090909 -Neighbor list builds = 7576 -Dangerous builds = 0 -Total wall time: 0:00:23 \ No newline at end of file From f705d49d4557014e6af45a45fff89606799ac61e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Feb 2021 09:17:14 -0500 Subject: [PATCH 0098/1217] reformat docs, correct spelling errors, and update false positives list --- doc/src/fix_charge_regulation.rst | 202 ++++++++++++++------ doc/utils/sphinx-config/false_positives.txt | 28 ++- 2 files changed, 172 insertions(+), 58 deletions(-) diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index cb9f55c7cd..fb63c8d7a5 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/doc/src/fix_charge_regulation.rst @@ -8,21 +8,21 @@ Syntax """""" .. parsed-literal:: - + fix ID group-ID charge/regulation cation_type anion_type keyword value(s) * ID, group-ID are documented in fix command * charge/regulation = style name of this fix command * cation_type = atom type of free cations * anion_type = atom type of free anions - + * zero or more keyword/value pairs may be appended .. parsed-literal:: - - keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves* + + keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves* *pH* value = pH of the solution - *pKa* value = acid dissociation constant + *pKa* value = acid dissociation constant *pKb* value = base dissociation constant *pIp* value = chemical potential of free cations *pIm* value = chemical potential of free anions @@ -30,7 +30,7 @@ Syntax *acid_type* = atom type of acid groups *base_type* = atom type of base groups *lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers) - *temp* value = temperature + *temp* value = temperature *tempfixid* value = fix ID of temperature thermostat *nevery* value = invoke this fix every nevery steps *nmc* value = number of charge regulation MC moves to attempt every nevery steps @@ -38,124 +38,212 @@ Syntax *seed* value = random # seed (positive integer) *tag* value = yes or no (yes: The code assign unique tags to inserted ions; no: The tag of all inserted ions is "0") *group* value = group-ID, inserted ions are assigned to group group-ID. Can be used multiple times to assign inserted ions to multiple groups. - *onlysalt* values = flag charge_cation charge_anion. + *onlysalt* values = flag charge_cation charge_anion. flag = yes or no (yes: the fix performs only ion insertion/deletion, no: perform acid/base dissociation and ion insertion/deletion) charge_cation, charge_anion = value of cation/anion charge, must be an integer (only specify if flag = yes) - *pmcmoves* values = pmcA pmcB pmcI - MC move fractions for acid ionization (pmcA), base ionization (pmcB) and free ion exchange (pmcI) + *pmcmoves* values = pmcA pmcB pmcI - MC move fractions for acid ionization (pmcA), base ionization (pmcB) and free ion exchange (pmcI) Examples """""""" .. code-block:: LAMMPS - fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT + fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0 Description """"""""""" -This fix performs Monte Carlo (MC) sampling of charge regulation and exchange of ions with a reservoir as discussed in :ref:`(Curk1) ` and :ref:`(Curk2) `. -The implemented method is largely analogous to the grand-reaction ensemble method in :ref:`(Landsgesell) `. -The implementation is parallelized, compatible with existing LAMMPS functionalities, and applicable to any system utilizing discreet, ionizable groups or surface sites. +This fix performs Monte Carlo (MC) sampling of charge regulation and +exchange of ions with a reservoir as discussed in :ref:`(Curk1) ` +and :ref:`(Curk2) `. The implemented method is largely analogous +to the grand-reaction ensemble method in :ref:`(Landsgesell) +`. The implementation is parallelized, compatible with +existing LAMMPS functionalities, and applicable to any system utilizing +discrete, ionizable groups or surface sites. -Specifically, the fix implements the following three types of MC moves, which discretely change the charge state of individual particles and insert ions into the systems: :math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{X}^+`, :math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{X}^-`, -and :math:`\emptyset \rightleftharpoons Z^-\mathrm{X}^{Z^+}+Z^+\mathrm{X}^{-Z^-}`. -In the former two types of reactions, Monte Carlo moves alter the charge value of specific atoms (:math:`\mathrm{A}`, :math:`\mathrm{B}`) and simultaneously insert a counterion to preserve the charge neutrality of the system, modeling the dissociation/association process. -The last type of reaction performs grand canonical MC exchange of ion pairs with a (fictitious) reservoir. +Specifically, the fix implements the following three types of MC moves, +which discretely change the charge state of individual particles and +insert ions into the systems: :math:`\mathrm{A} \rightleftharpoons +\mathrm{A}^-+\mathrm{X}^+`, :math:`\mathrm{B} \rightleftharpoons +\mathrm{B}^++\mathrm{X}^-`, and :math:`\emptyset \rightleftharpoons +Z^-\mathrm{X}^{Z^+}+Z^+\mathrm{X}^{-Z^-}`. In the former two types of +reactions, Monte Carlo moves alter the charge value of specific atoms +(:math:`\mathrm{A}`, :math:`\mathrm{B}`) and simultaneously insert a +counterion to preserve the charge neutrality of the system, modeling the +dissociation/association process. The last type of reaction performs +grand canonical MC exchange of ion pairs with a (fictitious) reservoir. -In our implementation "acid" refers to particles that can attain charge :math:`q=\{0,-1\}` and "base" to particles with :math:`q=\{0,1\}`, -whereas the MC exchange of free ions allows any integer charge values of :math:`{Z^+}` and :math:`{Z^-}`. +In our implementation "acid" refers to particles that can attain charge +:math:`q=\{0,-1\}` and "base" to particles with :math:`q=\{0,1\}`, +whereas the MC exchange of free ions allows any integer charge values of +:math:`{Z^+}` and :math:`{Z^-}`. -Here we provide several practical examples for modeling charge regulation effects in solvated systems. -An acid ionization reaction (:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{H}^+`) can be defined via a single line in the input file +Here we provide several practical examples for modeling charge +regulation effects in solvated systems. An acid ionization reaction +(:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{H}^+`) can be +defined via a single line in the input file .. code-block:: LAMMPS fix acid_reaction all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 7.0 pIm 7.0 -where the fix attempts to charge :math:`\mathrm{A}` (discharge :math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and insert (delete) a proton (atom type 2). Besides, the fix implements self-ionization reaction of water :math:`\emptyset \rightleftharpoons \mathrm{H}^++\mathrm{OH}^-`. -However, this approach is highly inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of both protons and hydroxyl ions is low, resulting in a relatively low acceptance rate of MC moves. +where the fix attempts to charge :math:`\mathrm{A}` (discharge +:math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and +insert (delete) a proton (atom type 2). Besides, the fix implements +self-ionization reaction of water :math:`\emptyset \rightleftharpoons +\mathrm{H}^++\mathrm{OH}^-`. However, this approach is highly +inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of +both protons and hydroxyl ions is low, resulting in a relatively low +acceptance rate of MC moves. -A more efficient way is to allow salt ions to -participate in ionization reactions, which can be easily achieved via +A more efficient way is to allow salt ions to participate in ionization +reactions, which can be easily achieved via .. code-block:: LAMMPS fix acid_reaction all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0 -where particles of atom type 4 and 5 are the salt cations and anions, both at chemical potential pI=2.0, see :ref:`(Curk1) ` and :ref:`(Landsgesell) ` for more details. +where particles of atom type 4 and 5 are the salt cations and anions, +both at chemical potential pI=2.0, see :ref:`(Curk1) ` and +:ref:`(Landsgesell) ` for more details. - Similarly, we could have simultanously added a base ionization reaction (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`) + Similarly, we could have simultaneously added a base ionization reaction + (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`) .. code-block:: LAMMPS fix base_reaction all charge/regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0 - -where the fix will attempt to charge :math:`\mathrm{B}` (discharge :math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. -If neither the acid or the base type is specified, for example, + +where the fix will attempt to charge :math:`\mathrm{B}` (discharge +:math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and +insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. If +neither the acid or the base type is specified, for example, .. code-block:: LAMMPS fix salt_reaction all charge/regulation 4 5 pIp 2.0 pIm 2.0 - -the fix simply inserts or deletes an ion pair of a free cation (atom type 4) and a free anion (atom type 5) as done in a conventional grand-canonical MC simulation. + +the fix simply inserts or deletes an ion pair of a free cation (atom +type 4) and a free anion (atom type 5) as done in a conventional +grand-canonical MC simulation. -The fix is compatible with LAMMPS sub-packages such as *molecule* or *rigid*. That said, the acid and base particles can be part of larger molecules or rigid bodies. Free ions that are inserted to or deleted from the system must be defined as single particles (no bonded interactions allowed) and cannot be part of larger molecules or rigid bodies. If *molecule* package is used, all inserted ions have a molecule ID equal to zero. +The fix is compatible with LAMMPS sub-packages such as *molecule* or +*rigid*. That said, the acid and base particles can be part of larger +molecules or rigid bodies. Free ions that are inserted to or deleted +from the system must be defined as single particles (no bonded +interactions allowed) and cannot be part of larger molecules or rigid +bodies. If *molecule* package is used, all inserted ions have a molecule +ID equal to zero. -Note that LAMMPS implicitly assumes a constant number of particles (degrees of freedom). Since using this fix alters the total number of particles during the simulation, any thermostat used by LAMMPS, such as NVT or Langevin, must use a dynamic calculation of system temperature. This can be achieved by specifying a dynamic temperature compute (e.g. dtemp) and using it with the desired thermostat, e.g. a Langevin thermostat: +Note that LAMMPS implicitly assumes a constant number of particles +(degrees of freedom). Since using this fix alters the total number of +particles during the simulation, any thermostat used by LAMMPS, such as +NVT or Langevin, must use a dynamic calculation of system +temperature. This can be achieved by specifying a dynamic temperature +compute (e.g. dtemp) and using it with the desired thermostat, e.g. a +Langevin thermostat: .. code-block:: LAMMPS compute dtemp all temp - compute_modify dtemp dynamic yes - fix fT all langevin 1.0 1.0 1.0 123 + compute_modify dtemp dynamic yes + fix fT all langevin 1.0 1.0 1.0 123 fix_modify fT temp dtemp -The chemical potential units (e.g. pH) are in the standard log10 representation assuming reference concentration :math:`\rho_0 = \mathrm{mol}/\mathrm{l}`. -Therefore, to perform the internal unit conversion, the length (in nanometers) of the LAMMPS unit length -must be specified via *lunit_nm* (default is set to the Bjerrum length in water at room temprature *lunit_nm* = 0.71nm). For example, in the dilute ideal solution limit, the concentration of free ions -will be :math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. +The chemical potential units (e.g. pH) are in the standard log10 +representation assuming reference concentration :math:`\rho_0 = +\mathrm{mol}/\mathrm{l}`. Therefore, to perform the internal unit +conversion, the length (in nanometers) of the LAMMPS unit length must be +specified via *lunit_nm* (default is set to the Bjerrum length in water +at room temperature *lunit_nm* = 0.71nm). For example, in the dilute +ideal solution limit, the concentration of free ions will be +:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. -The temperature used in MC acceptance probability is set by *temp*. This temperature should be the same as the temperature set by the molecular dynamics thermostat. For most purposes, it is probably best to use *tempfixid* keyword which dynamically sets the temperature equal to the chosen MD thermostat temperature, in the example above we assumed the thermostat fix-ID is *fT*. The inserted particles attain a random velocity corresponding to the specified temperature. Using *tempfixid* overrides any fixed temperature set by *temp*. +The temperature used in MC acceptance probability is set by *temp*. This +temperature should be the same as the temperature set by the molecular +dynamics thermostat. For most purposes, it is probably best to use +*tempfixid* keyword which dynamically sets the temperature equal to the +chosen MD thermostat temperature, in the example above we assumed the +thermostat fix-ID is *fT*. The inserted particles attain a random +velocity corresponding to the specified temperature. Using *tempfixid* +overrides any fixed temperature set by *temp*. -The *xrd* keyword can be used to restrict the inserted/deleted counterions to a specific radial distance from an acid or base particle that is currently participating in a reaction. This can be used to simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* / 2, where *L* is the smallest box dimension, the radial restriction is automatically turned off and free ion can be inserted or deleted anywhere in the simulation box. +The *xrd* keyword can be used to restrict the inserted/deleted +counterions to a specific radial distance from an acid or base particle +that is currently participating in a reaction. This can be used to +simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* / +2, where *L* is the smallest box dimension, the radial restriction is +automatically turned off and free ion can be inserted or deleted +anywhere in the simulation box. -If the *tag yes* is used, every inserted atom gets a unique tag ID, otherwise, the tag of every inserted atom is set to 0. *tag yes* might cause an integer overflow in very long simulations since the tags are unique to every particle and thus increase with every successful particle insertion. +If the *tag yes* is used, every inserted atom gets a unique tag ID, +otherwise, the tag of every inserted atom is set to 0. *tag yes* might +cause an integer overflow in very long simulations since the tags are +unique to every particle and thus increase with every successful +particle insertion. -The *pmcmoves* keyword sets the relative probability of attempting the three types of MC moves (reactions): acid charging, base charging, and ion pair exchange. -The fix only attempts to perform particle charging MC moves if *acid_type* or *base_type* is defined. Otherwise fix only performs free ion insertion/deletion. For example, if *acid_type* is not defined, *pmcA* is automatically set to 0. The vector *pmcmoves* is automatically normalized, for example, if set to *pmcmoves* 0 0.33 0.33, the vector would be normalized to [0,0.5,0.5]. +The *pmcmoves* keyword sets the relative probability of attempting the +three types of MC moves (reactions): acid charging, base charging, and +ion pair exchange. The fix only attempts to perform particle charging +MC moves if *acid_type* or *base_type* is defined. Otherwise fix only +performs free ion insertion/deletion. For example, if *acid_type* is not +defined, *pmcA* is automatically set to 0. The vector *pmcmoves* is +automatically normalized, for example, if set to *pmcmoves* 0 0.33 0.33, +the vector would be normalized to [0,0.5,0.5]. -The *only_salt* option can be used to perform multivalent grand-canonical ion-exchange moves. If *only_salt yes* is used, no charge exchange is performed, only ion insertion/deletion (*pmcmoves* is set to [0,0,1]), but ions can be multivalent. In the example above, an MC move would consist of three ion insertion/deletion to preserve the charge neutrality of the system. +The *only_salt* option can be used to perform multivalent +grand-canonical ion-exchange moves. If *only_salt yes* is used, no +charge exchange is performed, only ion insertion/deletion (*pmcmoves* is +set to [0,0,1]), but ions can be multivalent. In the example above, an +MC move would consist of three ion insertion/deletion to preserve the +charge neutrality of the system. -The *group* keyword can be used to add inserted particles to a specific group-ID. All inserted particles are automatically added to group *all*. +The *group* keyword can be used to add inserted particles to a specific +group-ID. All inserted particles are automatically added to group *all*. Output """""" -This fix computes a global vector of length 8, which can be accessed by various output commands. The vector values are the following global quantities: + +This fix computes a global vector of length 8, which can be accessed by +various output commands. The vector values are the following global +quantities: * 1 = cumulative MC attempts * 2 = cumulative MC successes -* 3 = current # of neutral acid atoms -* 4 = current # of -1 charged acid atoms -* 5 = current # of neutral base atoms -* 6 = current # of +1 charged base atoms -* 7 = current # of free cations +* 3 = current # of neutral acid atoms +* 4 = current # of -1 charged acid atoms +* 5 = current # of neutral base atoms +* 6 = current # of +1 charged base atoms +* 7 = current # of free cations * 8 = current # of free anions Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. -The :doc:`atom_style `, used must contain the charge property, for example, the style could be *charge* or *full*. Only usable for 3D simulations. Atoms specified as free ions cannot be part of rigid bodies or molecules and cannot have bonding interactions. The scheme is limited to integer charges, any atoms with non-integer charges will not be considered by the fix. +This fix is part of the USER-MISC package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package +` doc page for more info. -All interaction potentials used must be continuous, otherwise the MD integration and the particle exchange MC moves do not correspond to the same equilibrium ensemble. For example, if an lj/cut pair style is used, the LJ potential must be shifted so that it vanishes at the cutoff. This can be easily achieved using the :doc:`pair_modify ` command, i.e., by using: *pair_modify shift yes*. +The :doc:`atom_style `, used must contain the charge +property, for example, the style could be *charge* or *full*. Only +usable for 3D simulations. Atoms specified as free ions cannot be part +of rigid bodies or molecules and cannot have bonding interactions. The +scheme is limited to integer charges, any atoms with non-integer charges +will not be considered by the fix. -Note: Region restrictions are not yet implemented. +All interaction potentials used must be continuous, otherwise the MD +integration and the particle exchange MC moves do not correspond to the +same equilibrium ensemble. For example, if an lj/cut pair style is used, +the LJ potential must be shifted so that it vanishes at the cutoff. This +can be easily achieved using the :doc:`pair_modify ` +command, i.e., by using: *pair_modify shift yes*. + +Note: Region restrictions are not yet implemented. Related commands """""""""""""""" diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 9937a98850..3a3729eefa 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -260,6 +260,7 @@ bitmask bitrate bitrates Bitzek +Bjerrum Blaise blanchedalmond blocksize @@ -500,6 +501,8 @@ coulgauss coulombic Coulombic Coulombics +counterion +counterions Courant covalent covalently @@ -728,6 +731,7 @@ DRUDE dsf dsmc dt +dtemp dtgrow dtheta dtshrink @@ -876,6 +880,7 @@ equilibrates equilibrating equilibration Equilibria +equilibria equilization equipartitioning Ercolessi @@ -1210,6 +1215,7 @@ hbnewflag hbond hcp heatconduction +Hebbeker Hebenstreit Hecht Heenen @@ -1277,6 +1283,7 @@ hy hydrophobicity hydrostatic hydrostatically +hydroxyl Hynninen Hyoungki hyperdynamics @@ -1367,6 +1374,7 @@ ints inv invariants inversed +ionizable ionocovalent iostreams iparam @@ -1546,6 +1554,7 @@ Koning Kooser Korn Koskinen +Kosovan Koster Kosztin Kp @@ -1591,6 +1600,7 @@ Lamoureux Lanczos Lande Landron +Landsgesell langevin Langevin Langston @@ -1728,10 +1738,13 @@ lpsapi lrt lsfftw ltbbmalloc +Lua lubricateU lucy -Lua Luding +Luijten +lunit +Lunkad Lussetti Lustig lval @@ -2015,6 +2028,7 @@ multiscale multisectioning multithreading Multithreading +multivalent Mundy Murdick Murtola @@ -2060,6 +2074,7 @@ Nanoletters nanomechanics nanometer nanometers +nanoparticle nanoparticles Nanotube nanotube @@ -2167,6 +2182,7 @@ nm Nm Nmax nmax +nmc Nmin nmin Nmols @@ -2299,6 +2315,7 @@ omp OMP onelevel oneway +onlysalt onn ons OO @@ -2380,6 +2397,8 @@ pbc pc pchain Pchain +pcmoves +pmcmoves Pdamp pdb pdf @@ -2424,6 +2443,7 @@ phosphide Phs Physica physik +pI Piaggi picocoulomb picocoulombs @@ -2435,7 +2455,9 @@ pid piecewise Pieniazek Pieter +pIm pimd +pIp Piola Pisarev Pishevar @@ -2450,6 +2472,9 @@ ploop PloS plt plumedfile +pKa +pKb +pKs pmb Pmolrotate Pmoltrans @@ -2768,6 +2793,7 @@ rst rstyle Rubensson Rubia +Rud Rudd Rudra Rudranarayan From 417e92bc2db164283e13fe068dbd9d7ea23d9e3a Mon Sep 17 00:00:00 2001 From: kipbarrett Date: Thu, 11 Feb 2021 08:43:04 -0600 Subject: [PATCH 0099/1217] Axels requested revisions --- cmake/CMakeLists.txt | 2 +- src/Makefile | 2 +- src/USER-RANN/pair_rann.cpp | 1261 +++++++++++++++++ src/USER-RANN/pair_rann.h | 174 +++ src/USER-RANN/rann_activation.h | 73 + src/USER-RANN/rann_activation_linear.h | 77 + src/USER-RANN/rann_activation_sig_i.h | 77 + src/USER-RANN/rann_fingerprint.cpp | 116 ++ src/USER-RANN/rann_fingerprint.h | 72 + src/USER-RANN/rann_fingerprint_bond.cpp | 808 +++++++++++ src/USER-RANN/rann_fingerprint_bond.h | 80 ++ .../rann_fingerprint_bondscreened.cpp | 762 ++++++++++ src/USER-RANN/rann_fingerprint_bondscreened.h | 80 ++ .../rann_fingerprint_bondscreenedspin.cpp | 814 +++++++++++ .../rann_fingerprint_bondscreenedspin.h | 80 ++ src/USER-RANN/rann_fingerprint_bondspin.cpp | 887 ++++++++++++ src/USER-RANN/rann_fingerprint_bondspin.h | 79 ++ src/USER-RANN/rann_fingerprint_radial.cpp | 239 ++++ src/USER-RANN/rann_fingerprint_radial.h | 70 + .../rann_fingerprint_radialscreened.cpp | 253 ++++ .../rann_fingerprint_radialscreened.h | 72 + .../rann_fingerprint_radialscreenedspin.cpp | 264 ++++ .../rann_fingerprint_radialscreenedspin.h | 72 + src/USER-RANN/rann_fingerprint_radialspin.cpp | 252 ++++ src/USER-RANN/rann_fingerprint_radialspin.h | 69 + src/USER-RANN/rann_list_activation.h | 2 + src/USER-RANN/rann_list_fingerprint.h | 8 + 27 files changed, 6743 insertions(+), 2 deletions(-) create mode 100644 src/USER-RANN/pair_rann.cpp create mode 100644 src/USER-RANN/pair_rann.h create mode 100644 src/USER-RANN/rann_activation.h create mode 100644 src/USER-RANN/rann_activation_linear.h create mode 100644 src/USER-RANN/rann_activation_sig_i.h create mode 100644 src/USER-RANN/rann_fingerprint.cpp create mode 100644 src/USER-RANN/rann_fingerprint.h create mode 100644 src/USER-RANN/rann_fingerprint_bond.cpp create mode 100644 src/USER-RANN/rann_fingerprint_bond.h create mode 100644 src/USER-RANN/rann_fingerprint_bondscreened.cpp create mode 100644 src/USER-RANN/rann_fingerprint_bondscreened.h create mode 100644 src/USER-RANN/rann_fingerprint_bondscreenedspin.cpp create mode 100644 src/USER-RANN/rann_fingerprint_bondscreenedspin.h create mode 100644 src/USER-RANN/rann_fingerprint_bondspin.cpp create mode 100644 src/USER-RANN/rann_fingerprint_bondspin.h create mode 100644 src/USER-RANN/rann_fingerprint_radial.cpp create mode 100644 src/USER-RANN/rann_fingerprint_radial.h create mode 100644 src/USER-RANN/rann_fingerprint_radialscreened.cpp create mode 100644 src/USER-RANN/rann_fingerprint_radialscreened.h create mode 100644 src/USER-RANN/rann_fingerprint_radialscreenedspin.cpp create mode 100644 src/USER-RANN/rann_fingerprint_radialscreenedspin.h create mode 100644 src/USER-RANN/rann_fingerprint_radialspin.cpp create mode 100644 src/USER-RANN/rann_fingerprint_radialspin.h create mode 100644 src/USER-RANN/rann_list_activation.h create mode 100644 src/USER-RANN/rann_list_fingerprint.h diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index c29fba5957..b125556c73 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -110,7 +110,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE - USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION + USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS) set(SUFFIX_PACKAGES CORESHELL USER-OMP KOKKOS OPT USER-INTEL GPU) diff --git a/src/Makefile b/src/Makefile index 7a5e1aa728..f77e127264 100644 --- a/src/Makefile +++ b/src/Makefile @@ -56,7 +56,7 @@ PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-c user-intel user-lb user-manifold user-meamc user-mesodpd user-mesont \ user-mgpt user-misc user-mofff user-molfile \ user-netcdf user-omp user-phonon user-plumed user-ptm user-qmmm \ - user-qtb user-quip user-reaction user-reaxc user-scafacos user-smd user-smtbq \ + user-qtb user-quip user-rann user-reaction user-reaxc user-scafacos user-smd user-smtbq \ user-sdpd user-sph user-tally user-uef user-vtk user-yaff PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \ diff --git a/src/USER-RANN/pair_rann.cpp b/src/USER-RANN/pair_rann.cpp new file mode 100644 index 0000000000..3207b76934 --- /dev/null +++ b/src/USER-RANN/pair_rann.cpp @@ -0,0 +1,1261 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ +#define MAXLINE 1024 +#include "pair_rann.h" +#include "rann_list_activation.h" +#include "rann_list_fingerprint.h" +#include "tokenizer.h" +#include +#include +#include +#include +#include "atom.h" +#include "force.h" +#include "comm.h" +#include "memory.h" +#include "neigh_request.h" +#include "memory.h" +#include "error.h" +#include "update.h" +#include "math_special.h" + +using namespace LAMMPS_NS; + +static const char cite_user_rann_package[] = + "USER-RANN package:\n\n" + "@Article{Nitol2021,\n" + " author = {Nitol, Mashroor S and Dickel, Doyl E and Barrett, Christopher D},\n" + " title = {Artificial neural network potential for pure zinc},\n" + " journal = {Computational Materials Science},\n" + " year = 2021,\n" + " volume = 188,\n" + " pages = {110207}\n" + "}\n\n"; + + +PairRANN::PairRANN(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 0; + restartinfo = 0; + one_coeff = 1; + manybody_flag = 1; + allocated = 0; + nelements = -1; + elements = NULL; + mass = NULL; + + // set comm size needed by this Pair + // comm unused for now. + + comm_forward = 38; + comm_reverse = 30; + res = 10000; + cutmax = 0; + //at least one of the following will change during fingerprint definition: + doscreen = false; + allscreen = true; + + dospin = false; + fingerprint_map = new FingerprintCreatorMap(); + #define FINGERPRINT_CLASS + #define FingerprintStyle(key,Class) \ + (*fingerprint_map)[#key] = &fingerprint_creator; + + #include "rann_list_fingerprint.h" + #undef FingerprintStyle + #undef FINGERPRINT_CLASS + activation_map = new ActivationCreatorMap(); + #define ACTIVATION_CLASS + #define ActivationStyle(key,Class) \ + (*activation_map)[#key] = &activation_creator; + + #include "rann_list_activation.h" + #undef ActivationStyle + #undef ACTIVATION_CLASS +} + +PairRANN::~PairRANN() +{ + //clear memory + delete [] mass; + for (int i=0;i0) { + for (int j=0;j0) { + delete [] fingerprints[i]; + delete [] activation[i]; + } + } + delete [] fingerprints; + delete [] activation; + delete [] fingerprintcount; + delete [] fingerprintperelement; + delete [] fingerprintlength; + delete [] screening_min; + delete [] screening_max; + memory->destroy(xn); + memory->destroy(yn); + memory->destroy(zn); + memory->destroy(tn); + memory->destroy(jl); + memory->destroy(features); + memory->destroy(dfeaturesx); + memory->destroy(dfeaturesy); + memory->destroy(dfeaturesz); + memory->destroy(layer); + memory->destroy(sum); + memory->destroy(sum1); + memory->destroy(dlayerx); + memory->destroy(dlayery); + memory->destroy(dlayerz); + memory->destroy(dlayersumx); + memory->destroy(dlayersumy); + memory->destroy(dlayersumz); + if (doscreen) { + memory->destroy(Sik); + memory->destroy(Bij); + memory->destroy(dSikx); + memory->destroy(dSiky); + memory->destroy(dSikz); + memory->destroy(dSijkx); + memory->destroy(dSijky); + memory->destroy(dSijkz); + memory->destroy(dSijkxc); + memory->destroy(dSijkyc); + memory->destroy(dSijkzc); + } + if (dospin) { + memory->destroy(sx); + memory->destroy(sy); + memory->destroy(sz); + memory->destroy(dlayerx); + memory->destroy(dlayery); + memory->destroy(dlayerz); + memory->destroy(dlayersumx); + memory->destroy(dlayersumy); + memory->destroy(dlayersumz); + } +} + + + +void PairRANN::allocate(std::vector elementwords) +{ + int i,j,k,l,n; + n = atom->ntypes; + memory->create(setflag,n+1,n+1,"pair:setflag"); + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + cutmax = 0; + nmax1 = 100; + nmax2 = 20; + fmax = 0; + fnmax = 0; + nelementsp=nelements+1; + //initialize arrays + elements = new char *[nelements]; + elementsp = new char *[nelementsp];//elements + 'all' + mass = new double[nelements]; + net = new NNarchitecture[nelementsp]; + weightdefined = new bool*[nelementsp]; + biasdefined = new bool *[nelementsp]; + activation = new RANN::Activation**[nelementsp]; + fingerprints = new RANN::Fingerprint**[nelementsp]; + fingerprintlength = new int[nelementsp]; + fingerprintperelement = new int [nelementsp]; + fingerprintcount = new int[nelementsp]; + screening_min = new double [nelements*nelements*nelements]; + screening_max = new double [nelements*nelements*nelements]; + for (i=0;i 0) error->one(FLERR,"Illegal pair_style command"); +} + +void PairRANN::coeff(int narg, char **arg) +{ + int i,j; + map = new int [atom->ntypes+1]; + if (narg != 3 + atom->ntypes) error->one(FLERR,"Incorrect args for pair coefficients"); + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) error->one(FLERR,"Incorrect args for pair coefficients"); + nelements = -1; + read_file(arg[2]); + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if NULL + for (i = 3; i < narg; i++) { + if (strcmp(arg[i],"NULL") == 0) { + map[i-2] = -1; + continue; + } + for (j = 0; j < nelements; j++) { + if (strcmp(arg[i],elements[j]) == 0) break; + } + if (j < nelements) map[i-2] = j; + else error->one(FLERR,"No matching element in NN potential file"); + } + // clear setflag since coeff() called once with I,J = * * + int n = atom->ntypes; + for (i = 1; i <= n; i++) { + for (j = i; j <= n; j++) { + setflag[i][j] = 0; + } + } + // set setflag i,j for type pairs where both are mapped to elements + // set mass of atom type if i = j + int count = 0; + for (i = 1; i <= n; i++) { + for (j = i; j <= n; j++) { + if (map[i] >= 0 && map[j] >= 0) { + setflag[i][j] = 1; + if (i == j) atom->set_mass(FLERR,i,mass[map[i]]); + count++; + } + } + } + if (count == 0) error->one(FLERR,"Incorrect args for pair coefficients"); + for (i=0;iallocate(); + } + } + allocated=1; +} + +void PairRANN::read_file(char *filename) +{ + FILE *fp; + int eof = 0,i,j,k,l; + int n,nwords; + std::string line,line1; + int longline = 4096; + char linetemp[longline]; + char *ptr; + bool comment; + char str[128]; + std::vector linev,line1v; + fp = utils::open_potential(filename,lmp,nullptr); + if (fp == nullptr) {error->one(FLERR,"Cannot open RANN potential file");} + ptr=fgets(linetemp,longline,fp); + strip_comments(linetemp,fp); + line=linetemp; + while (eof == 0) { + ptr=fgets(linetemp,longline,fp); + if (ptr == NULL) { + if (check_potential()) { + error->one(FLERR,"Invalid syntax in potential file, values are inconsistent or missing"); + } + else { + eof = 1; + break; + } + } + strip_comments(linetemp,fp); + line1=linetemp; + Tokenizer values = Tokenizer(line,": ,\t_\n"); + Tokenizer values1 = Tokenizer(line1,": ,\t_\n"); + linev = values.as_vector(); + line1v = values1.as_vector(); + if (linev[0].compare("atomtypes")==0)read_atom_types(linev,line1v); + else if (linev[0].compare("mass")==0)read_mass(linev,line1v); + else if (linev[0].compare("fingerprintsperelement")==0)read_fpe(linev,line1v); + else if (linev[0].compare("fingerprints")==0)read_fingerprints(linev,line1v); + else if (linev[0].compare("fingerprintconstants")==0)read_fingerprint_constants(linev,line1v); + else if (linev[0].compare("networklayers")==0)read_network_layers(linev,line1v); + else if (linev[0].compare("layersize")==0)read_layer_size(linev,line1v); + else if (linev[0].compare("weight")==0)read_weight(linev,line1v,fp); + else if (linev[0].compare("bias")==0)read_bias(linev,line1v,fp); + else if (linev[0].compare("activationfunctions")==0)read_activation_functions(linev,line1v); + else if (linev[0].compare("calibrationparameters")==0)continue;//information on how the network was trained + else if (linev[0].compare("screening")==0)read_screening(linev,line1v); + else error->one(FLERR,"Could not understand file syntax: unknown keyword"); + ptr=fgets(linetemp,longline,fp); + strip_comments(linetemp,fp); + if (ptr == NULL) { + if (check_potential()) { + error->one(FLERR,"Invalid syntax in potential file, values are inconsistent or missing"); + } + else { + eof = 1; + break; + } + } + line=linetemp; + } +} + +void PairRANN::strip_comments(char * line,FILE* fp) { + char *ptr; + bool comment; + utils::trim_comment(line); + if (strlen(line)==0) { + comment = true; + while (comment==true) { + ptr = fgets(line,4096,fp); + if (ptr==NULL) error->one(FLERR,"Unexpected end of RANN file"); + utils::trim_comment(line); + if (strlen(line) == 0) continue; + comment = false; + } + } +} + +void PairRANN::read_atom_types(std::vector line,std::vector line1) { + int nwords = line1.size(); + if (nwords < 1) error->one(FLERR,"Incorrect syntax for atom types"); + nelements = nwords; + line1.resize(nwords+1); + line1[nwords] = "all"; + allocate(line1); +} + +void PairRANN::read_mass(std::vector line,std::vector line1) { + if (nelements == -1)error->one(FLERR,"atom types must be defined before mass in potential file."); + int nwords = 0,i; + for (i=0;ione(FLERR,"mass element not found in atom types."); +} + +void PairRANN::read_fpe(std::vector line,std::vector line1) { + int i,j; + if (nelements == -1)error->one(FLERR,"atom types must be defined before fingerprints per element in potential file."); + for (i=0;ione(FLERR,"fingerprint-per-element element not found in atom types"); +} + +void PairRANN::read_fingerprints(std::vector line,std::vector line1) { + int nwords1,nwords,i,j,k,l,m,i1; + bool found; + char str[MAXLINE]; + nwords1 = line1.size(); + nwords = line.size(); + if (nelements == -1)error->one(FLERR,"atom types must be defined before fingerprints in potential file."); + int atomtypes[nwords-1]; + for (i=1;ione(FLERR,"fingerprint element not found in atom types");} + } + i = atomtypes[0]; + k = 0; + if (fingerprintperelement[i]==-1) {error->one(FLERR,"fingerprint per element must be defined before fingerprints");} + while (kn_body_type!=nwords-1) {error->one(FLERR,"invalid fingerprint for element combination");} + k++; + fingerprints[i][i1]->init(atomtypes,strtol(line1[k++].c_str(),NULL,10)); + fingerprintcount[i]++; + } +} + + +void PairRANN::read_fingerprint_constants(std::vector line,std::vector line1) { + int i,j,k,l,m,i1; + bool found; + char str [128]; + int nwords = line.size(); + if (nelements == -1)error->one(FLERR,"atom types must be defined before fingerprints in potential file."); + int n_body_type = nwords-4; + int atomtypes[n_body_type]; + for (i=1;i<=n_body_type;i++) { + found = false; + for (j=0;jone(FLERR,"fingerprint element not found in atom types");} + } + i = atomtypes[0]; + found = false; + for (k=0;kempty) {continue;} + if (n_body_type!=fingerprints[i][k]->n_body_type) {continue;} + for (j=0;jatomtypes[j]!=atomtypes[j]) {break;} + if (j==n_body_type-1) { + if (line[nwords-3].compare(fingerprints[i][k]->style)==0 && strtol(line[nwords-2].c_str(),NULL,10)==fingerprints[i][k]->id) { + found=true; + i1 = k; + break; + } + } + } + if (found) {break;} + } + if (!found) {error->one(FLERR,"cannot define constants for unknown fingerprint");} + fingerprints[i][i1]->fullydefined=fingerprints[i][i1]->parse_values(line[nwords-1],line1); +} + +void PairRANN::read_network_layers(std::vector line,std::vector line1) { + int i,j; + if (nelements == -1)error->one(FLERR,"atom types must be defined before network layers in potential file."); + for (i=0;ione(FLERR,"invalid number of network layers"); + delete [] net[i].dimensions; + weightdefined[i] = new bool [net[i].layers]; + biasdefined[i] = new bool [net[i].layers]; + net[i].dimensions = new int [net[i].layers]; + net[i].Weights = new double * [net[i].layers-1]; + net[i].Biases = new double * [net[i].layers-1]; + net[i].activations = new int [net[i].layers-1]; + for (j=0;jone(FLERR,"network layers element not found in atom types"); +} + +void PairRANN::read_layer_size(std::vector line,std::vector line1) { + int i; + for (i=0;ione(FLERR,"networklayers for each atom type must be defined before the corresponding layer sizes."); + int j = strtol(line[2].c_str(),NULL,10); + if (j>=net[i].layers || j<0) {error->one(FLERR,"invalid layer in layer size definition");}; + net[i].dimensions[j]= strtol(line1[0].c_str(),NULL,10); + return; + } + } + error->one(FLERR,"layer size element not found in atom types"); +} + +void PairRANN::read_weight(std::vector line,std::vector line1,FILE* fp) { + int i,j,k,l,nwords; + char *ptr; + int longline = 4096; + char linetemp [longline]; + for (l=0;lone(FLERR,"networklayers must be defined before weights."); + i=strtol(line[2].c_str(),NULL,10); + if (i>=net[l].layers || i<0)error->one(FLERR,"invalid weight layer"); + if (net[l].dimensions[i]==0 || net[l].dimensions[i+1]==0) error->one(FLERR,"network layer sizes must be defined before corresponding weight"); + net[l].Weights[i] = new double [net[l].dimensions[i]*net[l].dimensions[i+1]]; + weightdefined[l][i] = true; + nwords = line1.size(); + if (nwords != net[l].dimensions[i])error->one(FLERR,"invalid weights per line"); + for (k=0;kone(FLERR,"unexpected end of potential file!"); + nwords = line1.size(); + if (nwords != net[l].dimensions[i])error->one(FLERR,"invalid weights per line"); + for (k=0;kone(FLERR,"weight element not found in atom types"); +} + +void PairRANN::read_bias(std::vector line,std::vector line1,FILE* fp) { + int i,j,l,nwords; + char *ptr; + char linetemp[MAXLINE]; + for (l=0;lone(FLERR,"networklayers must be defined before biases."); + i=strtol(line[2].c_str(),NULL,10); + if (i>=net[l].layers || i<0)error->one(FLERR,"invalid bias layer"); + if (net[l].dimensions[i]==0) error->one(FLERR,"network layer sizes must be defined before corresponding bias"); + biasdefined[l][i] = true; + net[l].Biases[i] = new double [net[l].dimensions[i+1]]; + net[l].Biases[i][0] = strtod(line1[0].c_str(),NULL); + for (j=1;jone(FLERR,"bias element not found in atom types"); +} + +void PairRANN::read_activation_functions(std::vector line,std::vector line1) { + int i,j,l,nwords; + int *ptr; + for (l=0;lone(FLERR,"networklayers must be defined before activation functions."); + i = strtol(line[2].c_str(),NULL,10); + if (i>=net[l].layers || i<0)error->one(FLERR,"invalid activation layer"); + delete activation[l][i]; + activation[l][i]=create_activation(line1[0].c_str()); + return; + } + } + error->one(FLERR,"activation function element not found in atom types"); +} + +void PairRANN::read_screening(std::vector line,std::vector line1) { + int i,j,k; + bool found; + int nwords = line.size(); + if (nelements == -1)error->one(FLERR,"atom types must be defined before fingerprints in potential file."); + if (nwords!=5)error->one(FLERR,"invalid screening command"); + int n_body_type = 3; + int atomtypes[n_body_type]; + for (i=1;i<=n_body_type;i++) { + found = false; + for (j=0;jone(FLERR,"fingerprint element not found in atom types");} + } + i = atomtypes[0]; + j = atomtypes[1]; + k = atomtypes[2]; + int index = i*nelements*nelements+j*nelements+k; + int index1 = i*nelements*nelements+k*nelements+j; + if (line[4].compare("Cmin")==0) { + screening_min[index] = strtod(line1[0].c_str(),NULL); + screening_min[index1] = screening_min[index]; + } + else if (line[4].compare("Cmax")==0) { + screening_max[index] = strtod(line1[0].c_str(),NULL); + screening_max[index1] = screening_max[index]; + } + else error->one(FLERR,"unrecognized screening keyword"); +} + +//Called after finishing reading the potential file to make sure it is complete. True is bad. +//also does the rest of the memory allocation. +bool PairRANN::check_potential() { + int i,j,k,l; + if (nelements==-1) {return true;} + for (i=0;i<=nelements;i++) { + if (inet[i].maxlayer)net[i].maxlayer = net[i].dimensions[j]; + } + if (net[i].maxlayer>fnmax) {fnmax = net[i].maxlayer;} + if (net[i].dimensions[net[i].layers-1]!=1)return true;//output layer must have single neuron (the energy) + if (net[i].dimensions[0]>fmax)fmax=net[i].dimensions[0]; + for (j=0;jempty)return true;//undefined activations + for (k=0;kfullydefined==false)return true; + fingerprints[i][j]->startingneuron = fingerprintlength[i]; + fingerprintlength[i] +=fingerprints[i][j]->get_length(); + if (fingerprints[i][j]->rc>cutmax) {cutmax = fingerprints[i][j]->rc;} + } + if (net[i].dimensions[0]!=fingerprintlength[i])return true; + } + memory->create(xn,nmax1,"pair:xn"); + memory->create(yn,nmax1,"pair:yn"); + memory->create(zn,nmax1,"pair:zn"); + memory->create(tn,nmax1,"pair:tn"); + memory->create(jl,nmax1,"pair:jl"); + memory->create(features,fmax,"pair:features"); + memory->create(dfeaturesx,fmax*nmax2,"pair:dfeaturesx"); + memory->create(dfeaturesy,fmax*nmax2,"pair:dfeaturesy"); + memory->create(dfeaturesz,fmax*nmax2,"pair:dfeaturesz"); + memory->create(layer,fnmax,"pair:layer"); + memory->create(sum,fnmax,"pair:sum"); + memory->create(sum1,fnmax,"pair:sum1"); + memory->create(dlayerx,nmax2,fnmax,"pair:dlayerx"); + memory->create(dlayery,nmax2,fnmax,"pair:dlayery"); + memory->create(dlayerz,nmax2,fnmax,"pair:dlayerz"); + memory->create(dlayersumx,nmax2,fnmax,"pair:dlayersumx"); + memory->create(dlayersumy,nmax2,fnmax,"pair:dlayersumy"); + memory->create(dlayersumz,nmax2,fnmax,"pair:dlayersumz"); + if (doscreen) { + memory->create(Sik,nmax2,"pair:Sik"); + memory->create(Bij,nmax2,"pair:Bij"); + memory->create(dSikx,nmax2,"pair:dSikx"); + memory->create(dSiky,nmax2,"pair:dSiky"); + memory->create(dSikz,nmax2,"pair:dSikz"); + memory->create(dSijkx,nmax2*nmax2,"pair:dSijkx"); + memory->create(dSijky,nmax2*nmax2,"pair:dSijky"); + memory->create(dSijkz,nmax2*nmax2,"pair:dSijkz"); + memory->create(dSijkxc,nmax2,nmax2,"pair:dSijkxc"); + memory->create(dSijkyc,nmax2,nmax2,"pair:dSijkyc"); + memory->create(dSijkzc,nmax2,nmax2,"pair:dSijkzc"); + } + if (dospin) { + memory->create(sx,fmax*nmax2,"pair:sx"); + memory->create(sy,fmax*nmax2,"pair:sy"); + memory->create(sz,fmax*nmax2,"pair:sz"); + memory->create(dlayerx,nmax2,fnmax,"pair:dsx"); + memory->create(dlayery,nmax2,fnmax,"pair:dsy"); + memory->create(dlayerz,nmax2,fnmax,"pair:dsz"); + memory->create(dlayersumx,nmax2,fnmax,"pair:dssumx"); + memory->create(dlayersumy,nmax2,fnmax,"pair:dssumy"); + memory->create(dlayersumz,nmax2,fnmax,"pair:dssumz"); + } + return false;//everything looks good +} + +void PairRANN::compute(int eflag, int vflag) +{ + //perform force/energy computation_ + if (dospin) { + if (strcmp(update->unit_style,"metal") != 0) + error->one(FLERR,"Spin pair styles require metal units"); + if (!atom->sp_flag) + error->one(FLERR,"Spin pair styles requires atom/spin style"); + } + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = vflag_atom = 0; + int ii,i,j; + int nn = 0; + sims = new Simulation[1]; + sims->inum = listfull->inum; + sims->ilist=listfull->ilist; + sims->id = listfull->ilist; + sims->type = atom->type; + sims->x = atom->x; + sims->numneigh = listfull->numneigh; + sims->firstneigh = listfull->firstneigh; + if (dospin) { + sims->s = atom->sp; + } + int itype,f,jnum,len; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + if (eflag_global) {eng_vdwl=0;eng_coul=0;} + double energy=0; + double **force = atom->f; + double **fm = atom->fm; + double **virial = vatom; + //loop over atoms + for (ii=0;iiinum;ii++) { + i = sims->ilist[ii]; + itype = map[sims->type[i]]; + f = net[itype].dimensions[0]; + jnum = sims->numneigh[i]; + if (jnum>nmax1) { + nmax1 = jnum; + memory->grow(xn,nmax1,"pair:xn"); + memory->grow(yn,nmax1,"pair:yn"); + memory->grow(zn,nmax1,"pair:zn"); + memory->grow(tn,nmax1,"pair:tn"); + memory->grow(jl,nmax1,"pair:jl"); + } + cull_neighbor_list(&jnum,i,0); + if (jnum>nmax2) { + nmax2=jnum; + memory->grow(dfeaturesx,fmax*nmax2,"pair:dfeaturesx"); + memory->grow(dfeaturesy,fmax*nmax2,"pair:dfeaturesy"); + memory->grow(dfeaturesz,fmax*nmax2,"pair:dfeaturesz"); + memory->grow(layer,fnmax,"pair:layer"); + memory->grow(sum,fnmax,"pair:sum"); + memory->grow(sum1,fnmax,"pair:sum1"); + memory->grow(dlayerx,nmax2,fnmax,"pair:dlayerx"); + memory->grow(dlayery,nmax2,fnmax,"pair:dlayery"); + memory->grow(dlayerz,nmax2,fnmax,"pair:dlayerz"); + memory->grow(dlayersumx,nmax2,fnmax,"pair:dlayersumx"); + memory->grow(dlayersumy,nmax2,fnmax,"pair:dlayersumy"); + memory->grow(dlayersumz,nmax2,fnmax,"pair:dlayersumz"); + if (doscreen) { + memory->grow(Sik,nmax2,"pair:Sik"); + memory->grow(Bij,nmax2,"pair:Bij"); + memory->grow(dSikx,nmax2,"pair:dSikx"); + memory->grow(dSiky,nmax2,"pair:dSiky"); + memory->grow(dSikz,nmax2,"pair:dSikz"); + memory->grow(dSijkx,nmax2*nmax2,"pair:dSijkx"); + memory->grow(dSijky,nmax2*nmax2,"pair:dSijky"); + memory->grow(dSijkz,nmax2*nmax2,"pair:dSijkz"); + memory->destroy(dSijkxc); + memory->destroy(dSijkyc); + memory->destroy(dSijkzc); + memory->create(dSijkxc,nmax2,nmax2,"pair:dSijkxc"); + memory->create(dSijkyc,nmax2,nmax2,"pair:dSijkyc"); + memory->create(dSijkzc,nmax2,nmax2,"pair:dSijkzc"); + } + if (dospin) { + memory->grow(sx,fmax*nmax2,"pair:sx"); + memory->grow(sy,fmax*nmax2,"pair:sy"); + memory->grow(sz,fmax*nmax2,"pair:sz"); + memory->grow(dsx,nmax2,fnmax,"pair:dsx"); + memory->grow(dsy,nmax2,fnmax,"pair:dsy"); + memory->grow(dsz,nmax2,fnmax,"pair:dsz"); + memory->grow(dssumx,nmax2,fnmax,"pair:dssumx"); + memory->grow(dssumy,nmax2,fnmax,"pair:dssumy"); + memory->grow(dssumz,nmax2,fnmax,"pair:dssumz"); + } + } + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + itype = nelements; + //do fingerprints for type "all" + len = fingerprintperelement[itype]; + for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); + else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); + } + //run fingerprints through network + if (dospin) { + propagateforwardspin(&energy,force,fm,virial,ii,jnum); + } + else { + propagateforward(&energy,force,virial,ii,jnum); + } + } + if (vflag_fdotr) virial_fdotr_compute(); +} + +void PairRANN::cull_neighbor_list(int* jnum,int i,int sn) { + int *jlist,j,count,jj,*type,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double **x = sims[sn].x; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + type = sims[sn].type; + jlist = sims[sn].firstneigh[i]; + count = 0; + for (jj=0;jjcutmax*cutmax) { + continue; + } + xn[count]=delx; + yn[count]=dely; + zn[count]=delz; + tn[count]=jtype; + jl[count]=j; + count++; + } + jnum[0]=count+1; +} + +void PairRANN::screen_neighbor_list(int *jnum, int i,int sn) { + int jj,kk,count,count1; + count = 0; + for (jj=0;jjilist[ii]; + itype = map[sim->type[i]]; + for (int jj=0;jjcutmax*cutmax) { + Bij[kk]= false; + continue; + } + for (jj=0;jjcutmax*cutmax) { + Bij[jj] = false; + continue; + } + delx3 = delx2-delx; + dely3 = dely2-dely; + delz3 = delz2-delz; + rjk = delx3*delx3+dely3*dely3+delz3*delz3; + if (rik+rjk<=rij) {continue;}//bond angle > 90 degrees + if (rik+rij<=rjk) {continue;}//bond angle > 90 degrees + double Cmax = screening_max[itype*nelements*nelements+jtype*nelements+ktype]; + double Cmin = screening_min[itype*nelements*nelements+jtype*nelements+ktype]; + double temp1 = rij-rik+rjk; + Cn = temp1*temp1-4*rij*rjk; + //a few expanded computations provided for clarity: + //Cn = (rij-rik+rjk)*(rij-rik+rjk)-4*rij*rjk; + //Cd = (rij-rjk)*(rij-rjk)-rik*rik; + //Cijk = 1+2*(rik*rij+rik*rjk-rik*rik)/(rik*rik-(rij-rjk)*(rij-rjk)); + temp1 = rij-rjk; + Cd = temp1*temp1-rik*rik; + Cijk = Cn/Cd; + C = (Cijk-Cmin)/(Cmax-Cmin); + if (C>=1) {continue;} + else if (C<=0) { + Bij[kk]=false; + break; + } + dC = Cmax-Cmin; + dC *= dC; + dC *= dC; + temp1 = 1-C; + temp1 *= temp1; + temp1 *= temp1; + Sijk = 1-temp1; + Sijk *= Sijk; + Dij = 4*rik*(Cn+4*rjk*(rij+rik-rjk))/Cd/Cd; + Dik = -4*(rij*Cn+rjk*Cn+8*rij*rik*rjk)/Cd/Cd; + Djk = 4*rik*(Cn+4*rij*(rik-rij+rjk))/Cd/Cd; + temp1 = Cijk-Cmax; + double temp2 = temp1*temp1; + dfc = 8*temp1*temp2/(temp2*temp2-dC); + Sik[kk] *= Sijk; + dSijkx[kk*jnum+jj] = dfc*(delx*Dij-delx3*Djk); + dSikx[kk] += dfc*(delx2*Dik+delx3*Djk); + dSijky[kk*jnum+jj] = dfc*(dely*Dij-dely3*Djk); + dSiky[kk] += dfc*(dely2*Dik+dely3*Djk); + dSijkz[kk*jnum+jj] = dfc*(delz*Dij-delz3*Djk); + dSikz[kk] += dfc*(delz2*Dik+delz3*Djk); + } + } +} + + +//Called by getproperties. Propagate features and dfeatures through network. Updates force and energy +void PairRANN::propagateforward(double * energy,double **force,double **virial, int ii,int jnum) { + int i,j,k,jj,j1,itype,i1; + int *ilist,*numneigh; + ilist = listfull->ilist; + int inum = listfull->inum; + int *type = atom->type; + i1=ilist[ii]; + itype = map[type[i1]]; + NNarchitecture net1 = net[itype]; + int L = net1.layers-1; + //energy output with forces from analytical derivatives + double dsum1; + int f = net1.dimensions[0]; + for (i=0;idactivation_function(sum[j]); + sum[j] = activation[itype][i]->activation_function(sum[j]); + if (i==L-1) { + energy[j] = sum[j]; + if (eflag_atom)eatom[i1]=sum[j]; + if (eflag_global) {eng_vdwl +=sum[j];} + } + //force propagation + for (jj=0;jjilist; + int inum = listfull->inum; + int *type = atom->type; + i1=ilist[ii]; + itype = map[type[i1]]; + NNarchitecture net1 = net[itype]; + int L = net1.layers-1; + //energy output with forces from analytical derivatives + double dsum1; + int f = net1.dimensions[0]; + for (i=0;idactivation_function(sum[j]); + sum[j] = activation[itype][i]->activation_function(sum[j]); + if (i==L-1) { + energy[j] = sum[j]; + if (eflag_atom)eatom[i1]=sum[j]; + if (eflag_global) {eng_vdwl +=sum[j];} + } + //force propagation + for (jj=0;jjrequest(this,instance_me); + neighbor->requests[irequest_full]->id = 1; + neighbor->requests[irequest_full]->half = 0; + neighbor->requests[irequest_full]->full = 1; +} + + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairRANN::init_one(int i, int j) +{ + return cutmax; +} + +void PairRANN::errorf(const char *file, int line, const char * message) { + error->one(file,line,message); +} + +int PairRANN::factorial(int n) { + return round(MathSpecial::factorial(n)); +} + +template +RANN::Fingerprint *PairRANN::fingerprint_creator(PairRANN* pair) +{ + return new T(pair); +} + +RANN::Fingerprint *PairRANN::create_fingerprint(const char *style) +{ + if (fingerprint_map->find(style) != fingerprint_map->end()) { + FingerprintCreator fingerprint_creator = (*fingerprint_map)[style]; + return fingerprint_creator(this); + } + char str[128]; + sprintf(str,"Unknown fingerprint style %s",style); + error->one(FLERR,str); + return NULL; +} + +template +RANN::Activation *PairRANN::activation_creator(PairRANN* pair) +{ + return new T(pair); +} + +RANN::Activation *PairRANN::create_activation(const char *style) +{ + if (activation_map->find(style) != activation_map->end()) { + ActivationCreator activation_creator = (*activation_map)[style]; + return activation_creator(this); + } + char str[128]; + sprintf(str,"Unknown activation style %s",style); + error->one(FLERR,str); + return NULL; +} + diff --git a/src/USER-RANN/pair_rann.h b/src/USER-RANN/pair_rann.h new file mode 100644 index 0000000000..9f1dbe9212 --- /dev/null +++ b/src/USER-RANN/pair_rann.h @@ -0,0 +1,174 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ + +#ifdef PAIR_CLASS + +PairStyle(rann,PairRANN) + +#else + +#ifndef LMP_PAIR_RANN +#define LMP_PAIR_RANN + + +#include "neighbor.h" +#include "neigh_list.h" +#include "pair.h" +#include + + +namespace LAMMPS_NS { + + namespace RANN { + //forward declarations + class Activation; + class Fingerprint; + } + + class PairRANN : public Pair { + public: + //inherited functions + PairRANN(class LAMMPS *); + ~PairRANN(); + void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void init_list(int , NeighList *); + void errorf(const char*,int,const char*); + int factorial(int); + //black magic for modular fingerprints and activations + class RANN::Activation ***activation; + class RANN::Fingerprint ***fingerprints; + typedef RANN::Fingerprint *(*FingerprintCreator)(PairRANN *); + typedef RANN::Activation *(*ActivationCreator)(PairRANN *); + typedef std::map FingerprintCreatorMap; + typedef std::map ActivationCreatorMap; + FingerprintCreatorMap *fingerprint_map; + ActivationCreatorMap *activation_map; + RANN::Fingerprint * create_fingerprint(const char *); + RANN::Activation * create_activation(const char *); + + //global variables + int nelements; // # of elements (distinct from LAMMPS atom types since multiple atom types can be mapped to one element) + int nelementsp; // nelements+1 + char **elements; // names of elements + char **elementsp; // names of elements with "all" appended as the last "element" + double *mass; // mass of each element + double cutmax; // max radial distance for neighbor lists + int *map; // mapping from atom types to elements + int *fingerprintcount; // static variable used in initialization + int *fingerprintlength; // # of input neurons defined by fingerprints of each element. + int *fingerprintperelement; // # of fingerprints for each element + bool doscreen;//screening is calculated if any defined fingerprint uses it + bool allscreen;//all fingerprints use screening so screened neighbors can be completely ignored + bool dospin; + int res;//Resolution of function tables for cubic interpolation. + int memguess; + double *screening_min; + double *screening_max; + bool **weightdefined; + bool **biasdefined; + int nmax1; + int nmax2; + int fmax; + int fnmax; + //memory actively written to during each compute: + double *xn,*yn,*zn,*Sik,*dSikx,*dSiky,*dSikz,*dSijkx,*dSijky,*dSijkz,*sx,*sy,*sz,**dSijkxc,**dSijkyc,**dSijkzc,*dfeaturesx,*dfeaturesy,*dfeaturesz,*features; + double *layer,*sum,*sum1,**dlayerx,**dlayery,**dlayerz,**dlayersumx,**dlayersumy,**dlayersumz; + double **dsx,**dsy,**dsz,**dssumx,**dssumy,**dssumz; + int *tn,*jl; + bool *Bij; + + struct Simulation{ + int *id; + bool forces; + bool spins; + double **x; + double **f; + double **s; + double box[3][3]; + double origin[3]; + double **features; + double **dfx; + double **dfy; + double **dfz; + double **dsx; + double **dsy; + double **dsz; + int *ilist,*numneigh,**firstneigh,*type,inum,gnum; + }; + + struct NNarchitecture{ + int layers; + int *dimensions;//vector of length layers with entries for neurons per layer + double **Weights; + double **Biases; + int *activations;//unused + int maxlayer;//longest layer (for memory allocation) + }; + + Simulation *sims; + NNarchitecture *net;//array of networks, 1 for each element. + + private: + template static RANN::Fingerprint *fingerprint_creator(PairRANN *); + template static RANN::Activation *activation_creator(PairRANN *); + //new functions + void allocate(std::vector);//called after reading element list, but before reading the rest of the potential + void read_file(char *);//read potential file + void strip_comments(char *,FILE *fp); + void read_atom_types(std::vector,std::vector); + void read_mass(std::vector,std::vector); + void read_fpe(std::vector,std::vector);//fingerprints per element. Count total fingerprints defined for each 1st element in element combinations + void read_fingerprints(std::vector,std::vector); + void read_fingerprint_constants(std::vector,std::vector); + void read_network_layers(std::vector,std::vector);//include input and output layer (hidden layers + 2) + void read_layer_size(std::vector,std::vector); + void read_weight(std::vector,std::vector,FILE*);//weights should be formatted as properly shaped matrices + void read_bias(std::vector,std::vector,FILE*);//biases should be formatted as properly shaped vectors + void read_activation_functions(std::vector,std::vector); + void read_screening(std::vector,std::vector); + bool check_potential();//after finishing reading potential file + void propagateforward(double *,double **,double **,int,int);//called by compute to get force and energy + void propagateforwardspin(double *,double **,double **,double**,int,int);//called by compute to get force and energy + void screen(int,int,int); + void cull_neighbor_list(int *,int,int); + void screen_neighbor_list(int *,int,int); + }; + +} + +#endif +#endif + + + diff --git a/src/USER-RANN/rann_activation.h b/src/USER-RANN/rann_activation.h new file mode 100644 index 0000000000..d8d2940228 --- /dev/null +++ b/src/USER-RANN/rann_activation.h @@ -0,0 +1,73 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ + +#ifndef LMP_RANN_ACTIVATION_H +#define LMP_RANN_ACTIVATION_H + + +namespace LAMMPS_NS { + namespace RANN { + class Activation { + public: + Activation(class PairRANN *); + virtual ~Activation(); + virtual double activation_function(double); + virtual double dactivation_function(double); + virtual double ddactivation_function(double); + bool empty; + const char *style; + }; + + Activation::Activation(PairRANN *_pair) { + empty = true; + style = "empty"; + } + + Activation::~Activation() { + + } + + //default is linear activation (no change). + double Activation::activation_function(double A) { + return A; + } + + double Activation::dactivation_function(double A) { + return 1.0; + } + + double Activation::ddactivation_function(double A) { + return 0.0; + } + } +} + + +#endif /* RANN_ACTIVATION_H_ */ diff --git a/src/USER-RANN/rann_activation_linear.h b/src/USER-RANN/rann_activation_linear.h new file mode 100644 index 0000000000..812c570d3a --- /dev/null +++ b/src/USER-RANN/rann_activation_linear.h @@ -0,0 +1,77 @@ + +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ +#ifdef ACTIVATION_CLASS + +ActivationStyle(linear,Activation_linear) + +#else + +#ifndef LMP_RANN_ACTIVATION_LINEAR_H +#define LMP_RANN_ACTIVATION_LINEAR_H + +#include "rann_activation.h" + +namespace LAMMPS_NS { + namespace RANN { + + class Activation_linear : public Activation { + public: + Activation_linear(class PairRANN *); + double activation_function(double); + double dactivation_function(double); + double ddactivation_function(double); + }; + + Activation_linear::Activation_linear(PairRANN *_pair) : Activation(_pair) { + empty = false; + style = "linear"; + } + + double Activation_linear::activation_function(double A) + { + return A; + } + + double Activation_linear::dactivation_function(double A) + { + return 1.0; + } + + double Activation_linear::ddactivation_function(double) { + return 0.0; + } + + + } +} + +#endif +#endif /* ACTIVATION_LINEAR_H_ */ diff --git a/src/USER-RANN/rann_activation_sig_i.h b/src/USER-RANN/rann_activation_sig_i.h new file mode 100644 index 0000000000..9ca9c55d3d --- /dev/null +++ b/src/USER-RANN/rann_activation_sig_i.h @@ -0,0 +1,77 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ + +#ifdef ACTIVATION_CLASS + +ActivationStyle(sigI,Activation_sigI) + +#else + +#ifndef LMP_RANN_ACTIVATION_SIGI_H +#define LMP_RANN_ACTIVATION_SIGI_H + +#include "rann_activation.h" + +namespace LAMMPS_NS { + namespace RANN { + + class Activation_sigI : public Activation { + public: + Activation_sigI(class PairRANN *); + double activation_function(double); + double dactivation_function(double); + double ddactivation_function(double); + }; + + Activation_sigI::Activation_sigI(PairRANN *_pair) : Activation(_pair) { + empty = false; + style = "sigI"; + } + + double Activation_sigI::activation_function(double in) { + if (in>34)return in; + return 0.1*in + 0.9*log(exp(in) + 1); + } + + double Activation_sigI::dactivation_function(double in) { + if (in>34)return 1; + return 0.1 + 0.9/(exp(in)+1)*exp(in); + } + + double Activation_sigI::ddactivation_function(double in) { + if (in>34)return 0; + return 0.9*exp(in)/(exp(in)+1)/(exp(in)+1);; + } + + } +} + +#endif +#endif /* ACTIVATION_SIGI_H_ */ diff --git a/src/USER-RANN/rann_fingerprint.cpp b/src/USER-RANN/rann_fingerprint.cpp new file mode 100644 index 0000000000..f0bf62ed62 --- /dev/null +++ b/src/USER-RANN/rann_fingerprint.cpp @@ -0,0 +1,116 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ + +#include "rann_fingerprint.h" + +using namespace LAMMPS_NS::RANN; + +Fingerprint::Fingerprint(PairRANN *_pair) +{ + spin = false; + screen = false; + empty = true; + fullydefined = false; + n_body_type = 0; + style = "empty"; + pair = _pair; +} + +Fingerprint::~Fingerprint() { + +} + +bool Fingerprint::parse_values(std::string line,std::vector line1) { + return false; +} + +void Fingerprint::init(int *i,int id) { + +} + +void Fingerprint::allocate() { + +} + +void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) { + +} + +void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) { + +} + +void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz,double *sx, double *sy, double *sz, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) { + +} + +void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz,double *sx, double *sy, double *sz, double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) { + +} + +void Fingerprint::write_values(FILE *fid) { + +} + +int Fingerprint::get_length() { + return 0; +} + +//Smooth cutoff, goes from 1 to zero over the interval rc-dr to rc. Same as MEAM uses. Used by generateradialtable and generatexpcuttable. +double Fingerprint::cutofffunction(double r,double rc, double dr) { + double out; + if (r < (rc -dr))out=1; + else if (r>rc)out=0; + else { + out = 1-(rc-r)/dr; + out *= out; + out *= out; + out = 1-out; + out *= out; + } + return out; +} + +void Fingerprint::generate_rinvssqrttable() { + int buf = 5; + int m; + double r1; + double cutmax = pair->cutmax; + int res = pair->res; + rinvsqrttable = new double[res+buf]; + for (m=0;m<(res+buf);m++) { + r1 = cutmax*cutmax*(double)(m)/(double)(res); + rinvsqrttable[m] = 1/sqrt(r1); + } +} + + + + diff --git a/src/USER-RANN/rann_fingerprint.h b/src/USER-RANN/rann_fingerprint.h new file mode 100644 index 0000000000..8b777ce398 --- /dev/null +++ b/src/USER-RANN/rann_fingerprint.h @@ -0,0 +1,72 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + +----------------*/ + +#ifndef LMP_RANN_FINGERPRINT_H +#define LMP_RANN_FINGERPRINT_H + +#include "pair_rann.h" + +namespace LAMMPS_NS { + namespace RANN { + class Fingerprint { + public: + Fingerprint(PairRANN *); + virtual ~Fingerprint(); + virtual bool parse_values(std::string,std::vector); + virtual void write_values(FILE *); + virtual void init(int*,int); + virtual void allocate(); + void init_screen(int); + virtual void compute_fingerprint(double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*);//no screen,no spin + virtual void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*);//screen + virtual void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*);//spin + virtual void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*);//spin,screen + virtual int get_length(); + virtual double cutofffunction(double,double, double); + virtual void generate_rinvssqrttable(); + bool spin; + bool screen; + int n_body_type;//i-j vs. i-j-k vs. i-j-k-l, etc. + bool empty; + bool fullydefined; + int startingneuron; + int id;//based on ordering of fingerprints listed for i-j in potential file + const char *style; + int* atomtypes; + double *rinvsqrttable; + double rc; + PairRANN *pair; + }; + } +} + + +#endif /* RANN_FINGERPRINT_H_ */ diff --git a/src/USER-RANN/rann_fingerprint_bond.cpp b/src/USER-RANN/rann_fingerprint_bond.cpp new file mode 100644 index 0000000000..672cea718d --- /dev/null +++ b/src/USER-RANN/rann_fingerprint_bond.cpp @@ -0,0 +1,808 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ + +#include "rann_fingerprint_bond.h" + + +using namespace LAMMPS_NS::RANN; + +Fingerprint_bond::Fingerprint_bond(PairRANN *_pair) : Fingerprint(_pair) +{ + n_body_type = 3; + dr = 0; + re = 0; + rc = 0; + alpha_k = new double [1]; + alpha_k[0] = -1; + kmax = 0; + mlength = 0; + id = -1; + style = "bond"; + atomtypes = new int [n_body_type]; + empty = true; + _pair->allscreen = false; +} + +Fingerprint_bond::~Fingerprint_bond() { + delete [] alpha_k; + delete [] atomtypes; + delete [] expcuttable; + delete [] dfctable; + for (int i=0;i<(mlength*(mlength+1))>>1;i++) { + delete [] coeff[i]; + delete [] coeffx[i]; + delete [] coeffy[i]; + delete [] coeffz[i]; + delete [] Mf[i]; + } + delete [] coeff; + delete [] coeffx; + delete [] coeffy; + delete [] coeffz; + delete [] Mf; + delete [] rinvsqrttable; +} + +bool Fingerprint_bond::parse_values(std::string constant,std::vector line1) { + int nwords,l; + nwords=line1.size(); + if (constant.compare("re")==0) { + re = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("rc")==0) { + rc = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("alphak")==0) { + delete [] alpha_k; + alpha_k = new double [nwords]; + for (l=0;lerrorf(FLERR,"Undefined value for bond power"); + if (re!=0.0 && rc!=0.0 && alpha_k[0]!=-1 && dr!=0.0 && mlength!=0 && kmax!=0)return true; + return false; +} + +void Fingerprint_bond::write_values(FILE *fid) { + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alphak:\n",style,id); + for (i=0;ielementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:k:\n",style,id); + fprintf(fid,"%d\n",kmax); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:m:\n",style,id); + fprintf(fid,"%d\n",mlength); +} + +void Fingerprint_bond::init(int *i,int _id) { + for (int j=0;jres; + double cutmax = pair->cutmax; + expcuttable = new double [(res+buf)*(kmax)]; + dfctable = new double [res+buf]; + for (m=0;m<(res+buf);m++) { + r1 = cutmax*cutmax*(double)(m)/(double)(res); + for (n=0;n<(kmax);n++) { + expcuttable[n+m*(kmax)] = exp(-alpha_k[n]/re*sqrt(r1))*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)) { + dfctable[m]=0; + } + else{ + dfctable[m]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } +} + +//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop. +void Fingerprint_bond::generate_coefficients() { //calculates multinomial coefficient for each term + int p,mb,mc; + int n,p1,i1; + mb = mlength; + mc=(mb*(mb+1))>>1; + coeff = new int *[mc]; + coeffx = new int *[mc]; + coeffy = new int *[mc]; + coeffz = new int *[mc]; + for (p=0;pfactorial(p)/pair->factorial(coeffx[p1][p])/pair->factorial(coeffy[p1][p])/pair->factorial(coeffz[p1][p]); + } + } +} + + +//Called by getproperties. Gets 3-body features and dfeatures +void Fingerprint_bond::compute_fingerprint(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) { + int i; + int *ilist,*numneigh; + PairRANN::Simulation *sim = &pair->sims[sid]; + ilist = sim->ilist; + numneigh = sim->numneigh; + i = ilist[ii]; + //select the more efficient algorithm for this particular potential and environment. + if (jnum*2>(mlength+1)*mlength*20) { + do3bodyfeatureset_singleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,sid,xn,yn,zn,tn,jnum,jl); + } + else{ + do3bodyfeatureset_doubleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,sid,xn,yn,zn,tn,jnum,jl); + + } +} + +//Called by do3bodyfeatureset. Algorithm for high neighbor numbers and small series of bond angle powers +void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) { + int i,j,jj,itype,jtype,kk,m,n,mcount,a,a1,a2,ai; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + int count=0; + PairRANN::Simulation *sim = &pair->sims[sid]; + int *type = sim->type; + double cutmax = pair->cutmax; + int res = pair->res; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; + int nelements=pair->nelements; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double expr[jnum][kmax+12]; + int p = kmax; + int countmb=((mlength)*(mlength+1))>>1; + // calculate interpolation expr, rinvs and dfc, for each neighbor + for (jj = 0; jj < jnum; jj++) { + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype && atomtypes[2] != nelements && atomtypes[2] != jtype) { + expr[jj][0]=0; + continue; + } + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc) { + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*kmax]; + double *p1 = &expcuttable[m1*kmax]; + double *p2 = &expcuttable[(m1+1)*kmax]; + double *p3 = &expcuttable[(m1+2)*kmax]; + for (kk=0;kksims[sid]; + double **x = sim->x; + int *type = sim->type; + int nelements = pair->nelements; + int res = pair->res; + double cutmax = pair->cutmax; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double expr[jnum][kmax]; + double y[jnum][3]; + double ri[jnum]; + double dfc[jnum]; + int kb = kmax; + int mb = mlength; + double c41[kmax]; + double c51[kmax]; + double c61[kmax]; + double ct[kmax]; + for (jj = 0; jj < jnum; jj++) { + jtype = tn[jj]; + if (jtypes != nelements && jtypes != jtype && ktypes != nelements && ktypes != jtype) { + expr[jj][0]=0; + continue; + } + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc) { + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (!(m1>=1 && m1 <= res))pair->errorf(FLERR,"Neighbor list is invalid.");//usually results from nan somewhere. + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*kmax]; + double *p1 = &expcuttable[m1*kmax]; + double *p2 = &expcuttable[(m1+1)*kmax]; + double *p3 = &expcuttable[(m1+2)*kmax]; + for (kk=0;kk); + void write_values(FILE *); + void init(int*,int); + void allocate(); + void compute_fingerprint(double*,double*,double*,double*,int,int,double *,double *,double *,int *,int,int *); + void do3bodyfeatureset_doubleneighborloop(double *,double *,double *,double *,int,int,double *,double *,double *,int *,int,int *); + void do3bodyfeatureset_singleneighborloop(double *,double *,double *,double *,int,int,double *,double *,double *,int *,int,int *); + void generate_exp_cut_table(); + void generate_coefficients(); + int get_length(); + + double *expcuttable; + double *dfctable; + double dr; + double *alpha_k; + double re; + int **coeff; + int **coeffx; + int **coeffy; + int **coeffz; + int kmax; + int mlength; + int **Mf; + + }; + + } +} + + +#endif +#endif /* FINGERPRINT_BOND_H_ */ diff --git a/src/USER-RANN/rann_fingerprint_bondscreened.cpp b/src/USER-RANN/rann_fingerprint_bondscreened.cpp new file mode 100644 index 0000000000..5a9a9b7a4c --- /dev/null +++ b/src/USER-RANN/rann_fingerprint_bondscreened.cpp @@ -0,0 +1,762 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ + +#include "rann_fingerprint_bondscreened.h" + +using namespace LAMMPS_NS::RANN; + +Fingerprint_bondscreened::Fingerprint_bondscreened(PairRANN *_pair) : Fingerprint(_pair) +{ + n_body_type = 3; + dr = 0; + re = 0; + rc = 0; + alpha_k = new double [1]; + alpha_k[0] = -1; + kmax = 0; + mlength = 0; + id = -1; + style = "bondscreened"; + atomtypes = new int [n_body_type]; + empty = true; + _pair->doscreen = true; + screen = true; +} + +Fingerprint_bondscreened::~Fingerprint_bondscreened() { + delete [] alpha_k; + delete [] atomtypes; + delete [] expcuttable; + delete [] dfctable; + for (int i=0;i<(mlength*(mlength+1))>>1;i++) { + delete [] coeff[i]; + delete [] coeffx[i]; + delete [] coeffy[i]; + delete [] coeffz[i]; + delete [] Mf[i]; + } + delete [] coeff; + delete [] coeffx; + delete [] coeffy; + delete [] coeffz; + delete [] Mf; + delete [] rinvsqrttable; +} + +bool Fingerprint_bondscreened::parse_values(std::string constant,std::vector line1) { + int nwords,l; + nwords=line1.size(); + if (constant.compare("re")==0) { + re = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("rc")==0) { + rc = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("alphak")==0) { + delete [] alpha_k; + alpha_k = new double [nwords]; + for (l=0;lerrorf(FLERR,"Undefined value for bond power"); + if (re!=0.0 && rc!=0.0 && alpha_k[0]!=-1 && dr!=0.0 && mlength!=0 && kmax!=0)return true; + return false; +} + +void Fingerprint_bondscreened::write_values(FILE *fid) { + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alphak:\n",style,id); + for (i=0;ielementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:k:\n",style,id); + fprintf(fid,"%d\n",kmax); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:m:\n",style,id); + fprintf(fid,"%d\n",mlength); +} + +void Fingerprint_bondscreened::init(int *i,int _id) { + for (int j=0;jres; + double cutmax = pair->cutmax; + expcuttable = new double [(res+buf)*(kmax)]; + dfctable = new double [res+buf]; + for (m=0;m<(res+buf);m++) { + r1 = cutmax*cutmax*(double)(m)/(double)(res); + for (n=0;n<(kmax);n++) { + expcuttable[n+m*(kmax)] = exp(-alpha_k[n]/re*sqrt(r1))*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)) { + dfctable[m]=0; + } + else{ + dfctable[m]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } +} + + +//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop. +void Fingerprint_bondscreened::generate_coefficients() { //calculates multinomial coefficient for each term + int p,mb,mc; + int n,p1,i1; + mb = mlength; + mc=(mb*(mb+1))>>1; + coeff = new int *[mc]; + coeffx = new int *[mc]; + coeffy = new int *[mc]; + coeffz = new int *[mc]; + for (p=0;pfactorial(p)/pair->factorial(coeffx[p1][p])/pair->factorial(coeffy[p1][p])/pair->factorial(coeffz[p1][p]); + } + } +} + + +//Called by getproperties. Gets 3-body features and dfeatures +void Fingerprint_bondscreened::compute_fingerprint(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) { + int i; + //select the more efficient algorithm for this particular potential and environment. + if (jnum*2>(mlength+1)*mlength*20) { + do3bodyfeatureset_singleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,sid,xn,yn,zn,tn,jnum,jl); + } + else{ + do3bodyfeatureset_doubleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,sid,xn,yn,zn,tn,jnum,jl); + + } +} + +//Called by do3bodyfeatureset. Algorithm for high neighbor numbers and small series of bond angle powers +void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) { + int i,j,jj,itype,jtype,kk,m,n,mcount,a,a1,a2,ai; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + int count=0; + PairRANN::Simulation *sim = &pair->sims[sid]; + int *type = sim->type; + double cutmax = pair->cutmax; + int res = pair->res; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; + int nelements=pair->nelements; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double expr[jnum][kmax+12]; + int p = kmax; + int countmb=((mlength)*(mlength+1))>>1; + // calculate interpolation expr, rinvs and dfc, for each neighbor + for (jj = 0; jj < jnum; jj++) { + if (Bij[jj]==false) {continue;} + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype && atomtypes[2] != nelements && atomtypes[2] != jtype) { + expr[jj][0]=0; + continue; + } + delx=xn[jj]; + dely=yn[jj]; + delz=zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc) { + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*kmax]; + double *p1 = &expcuttable[m1*kmax]; + double *p2 = &expcuttable[(m1+1)*kmax]; + double *p3 = &expcuttable[(m1+2)*kmax]; + for (kk=0;kksims[sid]; + int *type = sim->type; + int nelements = pair->nelements; + int res = pair->res; + double cutmax = pair->cutmax; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double expr[jnum][kmax]; + double y[jnum][3]; + double ri[jnum]; + double dfc[jnum]; + int kb = kmax; + int mb = mlength; + double Bijk[kb][mb]; + double c41[kmax]; + double c51[kmax]; + double c61[kmax]; + double ct[kmax]; + for (jj = 0; jj < jnum; jj++) { + if (Bij[jj]==false) {continue;} + jtype = tn[jj]; + if (jtypes != nelements && jtypes != jtype && ktypes != nelements && ktypes != jtype) { + expr[jj][0]=0; + continue; + } + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc) { + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (!(m1>=1 && m1 <= res))pair->errorf(FLERR,"Neighbor list is invalid.");//usually results from nan somewhere. + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*kmax]; + double *p1 = &expcuttable[m1*kmax]; + double *p2 = &expcuttable[(m1+1)*kmax]; + double *p3 = &expcuttable[(m1+2)*kmax]; + for (kk=0;kk); + void write_values(FILE *); + void init(int*,int); + void allocate(); + void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*); + void do3bodyfeatureset_doubleneighborloop(double *,double *,double *,double *,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*); + void do3bodyfeatureset_singleneighborloop(double *,double *,double *,double *,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*); + void generate_exp_cut_table(); + void generate_coefficients(); + int get_length(); + + double *expcuttable; + double *dfctable; + double dr; + double *alpha_k; + double re; + int **coeff; + int **coeffx; + int **coeffy; + int **coeffz; + int kmax; + int mlength; + int **Mf; + + }; + } + +} + + +#endif +#endif /* FINGERPRINT_BOND_H_ */ diff --git a/src/USER-RANN/rann_fingerprint_bondscreenedspin.cpp b/src/USER-RANN/rann_fingerprint_bondscreenedspin.cpp new file mode 100644 index 0000000000..f41dde883d --- /dev/null +++ b/src/USER-RANN/rann_fingerprint_bondscreenedspin.cpp @@ -0,0 +1,814 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ +#include "rann_fingerprint_bondscreenedspin.h" + + +using namespace LAMMPS_NS::RANN; + +Fingerprint_bondscreenedspin::Fingerprint_bondscreenedspin(PairRANN *_pair) : Fingerprint(_pair) +{ + n_body_type = 3; + dr = 0; + re = 0; + rc = 0; + alpha_k = new double [1]; + alpha_k[0] = -1; + kmax = 0; + mlength = 0; + id = -1; + style = "bondscreenedspin"; + atomtypes = new int [n_body_type]; + empty = true; + _pair->doscreen = true; + screen = true; + _pair->dospin = true; + spin = true; +} + +Fingerprint_bondscreenedspin::~Fingerprint_bondscreenedspin() { + delete [] alpha_k; + delete [] atomtypes; + delete [] expcuttable; + delete [] dfctable; + for (int i=0;i<(mlength*(mlength+1))>>1;i++) { + delete [] coeff[i]; + delete [] coeffx[i]; + delete [] coeffy[i]; + delete [] coeffz[i]; + delete [] Mf[i]; + } + delete [] coeff; + delete [] coeffx; + delete [] coeffy; + delete [] coeffz; + delete [] Mf; + delete [] rinvsqrttable; +} + +bool Fingerprint_bondscreenedspin::parse_values(std::string constant,std::vector line1) { + int nwords,l; + nwords=line1.size(); + if (constant.compare("re")==0) { + re = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("rc")==0) { + rc = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("alphak")==0) { + delete [] alpha_k; + alpha_k = new double [nwords]; + for (l=0;lerrorf(FLERR,"Undefined value for bond power"); + if (re!=0.0 && rc!=0.0 && alpha_k[0]!=-1 && dr!=0.0 && mlength!=0 && kmax!=0)return true; + return false; +} + +void Fingerprint_bondscreenedspin::write_values(FILE *fid) { + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alphak:\n",style,id); + for (i=0;ielementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:k:\n",style,id); + fprintf(fid,"%d\n",kmax); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:m:\n",style,id); + fprintf(fid,"%d\n",mlength); +} + +void Fingerprint_bondscreenedspin::init(int *i,int _id) { + for (int j=0;jres; + double cutmax = pair->cutmax; + expcuttable = new double [(res+buf)*(kmax)]; + dfctable = new double [res+buf]; + for (m=0;m<(res+buf);m++) { + r1 = cutmax*cutmax*(double)(m)/(double)(res); + for (n=0;n<(kmax);n++) { + expcuttable[n+m*(kmax)] = exp(-alpha_k[n]/re*sqrt(r1))*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)) { + dfctable[m]=0; + } + else{ + dfctable[m]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } +} + + +//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop. +void Fingerprint_bondscreenedspin::generate_coefficients() { //calculates multinomial coefficient for each term + int p,mb,mc; + int n,p1,i1; + mb = mlength; + mc=(mb*(mb+1))>>1; + coeff = new int *[mc]; + coeffx = new int *[mc]; + coeffy = new int *[mc]; + coeffz = new int *[mc]; + for (p=0;pfactorial(p)/pair->factorial(coeffx[p1][p])/pair->factorial(coeffy[p1][p])/pair->factorial(coeffz[p1][p]); + } + } +} + + +//Called by getproperties. Gets 3-body features and dfeatures +void Fingerprint_bondscreenedspin::compute_fingerprint(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz, double *dspinx, double *dspiny, double *dspinz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) { + int i; + //select the more efficient algorithm for this particular potential and environment. + if (jnum*2>(mlength+1)*mlength*20) { + do3bodyfeatureset_singleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,dspinx,dspiny,dspinz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,sid,xn,yn,zn,tn,jnum,jl); + } + else{ + do3bodyfeatureset_doubleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,dspinx,dspiny,dspinz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,sid,xn,yn,zn,tn,jnum,jl); + + } +} + +//Called by do3bodyfeatureset. Algorithm for high neighbor numbers and small series of bond angle powers +void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz, double *dspinx, double *dspiny, double *dspinz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) { + int i,j,jj,itype,jtype,kk,m,n,mcount,a,a1,a2,ai; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + int count=0; + PairRANN::Simulation *sim = &pair->sims[sid]; + int *type = sim->type; + double cutmax = pair->cutmax; + int res = pair->res; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; + int nelements=pair->nelements; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double expr[jnum][kmax+12]; + int p = kmax; + int countmb=((mlength)*(mlength+1))>>1; + double *si = sim->s[i]; + // calculate interpolation expr, rinvs and dfc, for each neighbor + for (jj = 0; jj < jnum; jj++) { + if (Bij[jj]==false) {continue;} + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype && atomtypes[2] != nelements && atomtypes[2] != jtype) { + expr[jj][0]=0; + continue; + } + delx=xn[jj]; + dely=yn[jj]; + delz=zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc) { + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*kmax]; + double *p1 = &expcuttable[m1*kmax]; + double *p2 = &expcuttable[(m1+1)*kmax]; + double *p3 = &expcuttable[(m1+2)*kmax]; + for (kk=0;kks[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double yprod = expr[jj][ai]; + double *y4 = &expr[jj][p]; + for (a2=0;a2s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double yprod = expr[jj][ai]; + double *y4 = &expr[jj][p]; + for (a2=0;a2s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2sims[sid]; + int *type = sim->type; + int nelements = pair->nelements; + int res = pair->res; + double cutmax = pair->cutmax; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double expr[jnum][kmax]; + double y[jnum][3]; + double ri[jnum]; + double dfc[jnum]; + int kb = kmax; + int mb = mlength; + double Bijk[kb][mb]; + double c41[kmax]; + double c51[kmax]; + double c61[kmax]; + double ct[kmax]; + double *si = sim->s[i]; + for (jj = 0; jj < jnum; jj++) { + if (Bij[jj]==false) {continue;} + jtype = tn[jj]; + if (jtypes != nelements && jtypes != jtype && ktypes != nelements && ktypes != jtype) { + expr[jj][0]=0; + continue; + } + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc) { + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (!(m1>=1 && m1 <= res))pair->errorf(FLERR,"Neighbor list is invalid.");//usually results from nan somewhere. + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*kmax]; + double *p1 = &expcuttable[m1*kmax]; + double *p2 = &expcuttable[(m1+1)*kmax]; + double *p3 = &expcuttable[(m1+2)*kmax]; + for (kk=0;kks[j]; + double spj = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + for (n = 0;ns[j]; + double spk = si[0]*sk[0]+si[1]*sk[1]+si[2]*sk[2]; + count = startingneuron; + double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); + double c1 = ri[jj]*(y[kk][0]-dot*y[jj][0]); + double c2 = ri[jj]*(y[kk][1]-dot*y[jj][1]); + double c3 = ri[jj]*(y[kk][2]-dot*y[jj][2]); + double c10 = ri[kk]*(y[jj][0]-dot*y[kk][0]); + double c11 = ri[kk]*(y[jj][1]-dot*y[kk][1]); + double c12 = ri[kk]*(y[jj][2]-dot*y[kk][2]); + for (n=0;n); + void write_values(FILE *); + void init(int*,int); + void allocate(); + void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*); + void do3bodyfeatureset_doubleneighborloop(double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int *); + void do3bodyfeatureset_singleneighborloop(double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*); + void generate_exp_cut_table(); + void generate_coefficients(); + int get_length(); + + double *expcuttable; + double *dfctable; + double dr; + double *alpha_k; + double re; + int **coeff; + int **coeffx; + int **coeffy; + int **coeffz; + int kmax; + int mlength; + int **Mf; + + }; + + } +} + + +#endif +#endif /* FINGERPRINT_BOND_H_ */ diff --git a/src/USER-RANN/rann_fingerprint_bondspin.cpp b/src/USER-RANN/rann_fingerprint_bondspin.cpp new file mode 100644 index 0000000000..6aadbada86 --- /dev/null +++ b/src/USER-RANN/rann_fingerprint_bondspin.cpp @@ -0,0 +1,887 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ +#include "rann_fingerprint_bondspin.h" + + +using namespace LAMMPS_NS::RANN; + +Fingerprint_bondspin::Fingerprint_bondspin(PairRANN *_pair) : Fingerprint(_pair) +{ + n_body_type = 3; + dr = 0; + re = 0; + rc = 0; + alpha_k = new double [1]; + alpha_k[0] = -1; + kmax = 0; + mlength = 0; + id = -1; + style = "bondspin"; + atomtypes = new int [n_body_type]; + empty = true; + _pair->allscreen = false; + _pair->dospin = true; + spin = true; +} + +Fingerprint_bondspin::~Fingerprint_bondspin() { + delete [] alpha_k; + delete [] atomtypes; + delete [] expcuttable; + delete [] dfctable; + for (int i=0;i<(mlength*(mlength+1))>>1;i++) { + delete [] coeff[i]; + delete [] coeffx[i]; + delete [] coeffy[i]; + delete [] coeffz[i]; + delete [] Mf[i]; + } + delete [] coeff; + delete [] coeffx; + delete [] coeffy; + delete [] coeffz; + delete [] Mf; + delete [] rinvsqrttable; +} + +bool Fingerprint_bondspin::parse_values(std::string constant,std::vector line1) { + int nwords,l; + nwords=line1.size(); + if (constant.compare("re")==0) { + re = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("rc")==0) { + rc = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("alphak")==0) { + delete [] alpha_k; + alpha_k = new double [nwords]; + for (l=0;lerrorf(FLERR,"Undefined value for bond power"); + if (re!=0.0 && rc!=0.0 && alpha_k[0]!=-1 && dr!=0.0 && mlength!=0 && kmax!=0)return true; + return false; +} + +void Fingerprint_bondspin::write_values(FILE *fid) { + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alphak:\n",style,id); + for (i=0;ielementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:k:\n",style,id); + fprintf(fid,"%d\n",kmax); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:m:\n",style,id); + fprintf(fid,"%d\n",mlength); +} + +void Fingerprint_bondspin::init(int *i,int _id) { + for (int j=0;jres; + double cutmax = pair->cutmax; + expcuttable = new double [(res+buf)*(kmax)]; + dfctable = new double [res+buf]; + for (m=0;m<(res+buf);m++) { + r1 = cutmax*cutmax*(double)(m)/(double)(res); + for (n=0;n<(kmax);n++) { + expcuttable[n+m*(kmax)] = exp(-alpha_k[n]/re*sqrt(r1))*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)) { + dfctable[m]=0; + } + else{ + dfctable[m]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } +} + +//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop. +void Fingerprint_bondspin::generate_coefficients() { //calculates multinomial coefficient for each term + int p,mb,mc; + int n,p1,i1; + mb = mlength; + mc=(mb*(mb+1))>>1; + coeff = new int *[mc]; + coeffx = new int *[mc]; + coeffy = new int *[mc]; + coeffz = new int *[mc]; + for (p=0;pfactorial(p)/pair->factorial(coeffx[p1][p])/pair->factorial(coeffy[p1][p])/pair->factorial(coeffz[p1][p]); + } + } +} + + +//Called by getproperties. Gets 3-body features and dfeatures +void Fingerprint_bondspin::compute_fingerprint(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,double * dspinx,double *dspiny,double *dspinz,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) { + int i; + int *ilist,*numneigh; + PairRANN::Simulation *sim = &pair->sims[sid]; + ilist = sim->ilist; + numneigh = sim->numneigh; + i = ilist[ii]; + //select the more efficient algorithm for this particular potential and environment. + if (jnum*2>(mlength+1)*mlength*20) { + do3bodyfeatureset_singleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,dspinx,dspiny,dspinz,ii,sid,xn,yn,zn,tn,jnum,jl); + } + else{ + do3bodyfeatureset_doubleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,dspinx,dspiny,dspinz,ii,sid,xn,yn,zn,tn,jnum,jl); + } +} + +//Called by do3bodyfeatureset. Algorithm for high neighbor numbers and small series of bond angle powers +void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,double * dspinx,double *dspiny,double *dspinz,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) { + int i,j,jj,itype,jtype,kk,m,n,mcount,a,a1,a2,ai; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + int count=0; + PairRANN::Simulation *sim = &pair->sims[sid]; + int *type = sim->type; + double cutmax = pair->cutmax; + int res = pair->res; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; + int nelements=pair->nelements; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double expr[jnum][kmax+12]; + int p = kmax; + int countmb=((mlength)*(mlength+1))>>1; + double *si = sim->s[i]; + // calculate interpolation expr, rinvs and dfc, for each neighbor + for (jj = 0; jj < jnum; jj++) { + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype && atomtypes[2] != nelements && atomtypes[2] != jtype) { + expr[jj][0]=0; + continue; + } + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc) { + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*kmax]; + double *p1 = &expcuttable[m1*kmax]; + double *p2 = &expcuttable[(m1+1)*kmax]; + double *p3 = &expcuttable[(m1+2)*kmax]; + for (kk=0;kks[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double yprod = expr[jj][ai]; + double *y4 = &expr[jj][p]; + for (a2=0;a2s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double yprod = expr[jj][ai]; + double *y4 = &expr[jj][p]; + for (a2=0;a2s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + double *y3 = &expr[jj][p+3]; + double *y4 = &expr[jj][p]; + ai = n; + yprod = expr[jj][ai]; + for (a2=0;a2sims[sid]; + double **x = sim->x; + int *type = sim->type; + int nelements = pair->nelements; + int res = pair->res; + double cutmax = pair->cutmax; + double cutinv2 = 1/cutmax/cutmax; + ilist = sim->ilist; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double expr[jnum][kmax]; + double y[jnum][3]; + double ri[jnum]; + double dfc[jnum]; + int kb = kmax; + int mb = mlength; + double c41[kmax]; + double c51[kmax]; + double c61[kmax]; + double ct[kmax]; + double *si = sim->s[i]; + for (jj = 0; jj < jnum; jj++) { + jtype = tn[jj]; + if (jtypes != nelements && jtypes != jtype && ktypes != nelements && ktypes != jtype) { + expr[jj][0]=0; + continue; + } + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq>rc*rc) { + expr[jj][0]=0; + continue; + } + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (!(m1>=1 && m1 <= res))pair->errorf(FLERR,"Neighbor list is invalid.");//usually results from nan somewhere. + r1 = r1-trunc(r1); + double *p0 = &expcuttable[(m1-1)*kmax]; + double *p1 = &expcuttable[m1*kmax]; + double *p2 = &expcuttable[(m1+1)*kmax]; + double *p3 = &expcuttable[(m1+2)*kmax]; + for (kk=0;kks[j]; + double spj = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + for (n = 0;ns[j]; + double spk = si[0]*sk[0]+si[1]*sk[1]+si[2]*sk[2]; + count = startingneuron; + double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); + double c1 = 2*ri[jj]*(y[kk][0]-dot*y[jj][0]); + double c2 = 2*ri[jj]*(y[kk][1]-dot*y[jj][1]); + double c3 = 2*ri[jj]*(y[kk][2]-dot*y[jj][2]); + double c10 = 2*ri[kk]*(y[jj][0]-dot*y[kk][0]); + double c11 = 2*ri[kk]*(y[jj][1]-dot*y[kk][1]); + double c12 = 2*ri[kk]*(y[jj][2]-dot*y[kk][2]); + for (n=0;ns[j]; + double spk = si[0]*sk[0]+si[1]*sk[1]+si[2]*sk[2]; + count = startingneuron; + double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); + double c1 = ri[jj]*(y[kk][0]-dot*y[jj][0]); + double c2 = ri[jj]*(y[kk][1]-dot*y[jj][1]); + double c3 = ri[jj]*(y[kk][2]-dot*y[jj][2]); + double c10 = ri[kk]*(y[jj][0]-dot*y[kk][0]); + double c11 = ri[kk]*(y[jj][1]-dot*y[kk][1]); + double c12 = ri[kk]*(y[jj][2]-dot*y[kk][2]); + for (n=0;n); + void write_values(FILE *); + void init(int*,int); + void allocate(); + virtual void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*);//spin + void do3bodyfeatureset_doubleneighborloop(double*,double*,double*,double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*); + void do3bodyfeatureset_singleneighborloop(double*,double*,double*,double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*); + void generate_exp_cut_table(); + void generate_coefficients(); + int get_length(); + + double *expcuttable; + double *dfctable; + double dr; + double *alpha_k; + double re; + int **coeff; + int **coeffx; + int **coeffy; + int **coeffz; + int kmax; + int mlength; + int **Mf; + + }; + + } +} + + +#endif +#endif /* FINGERPRINT_BOND_H_ */ diff --git a/src/USER-RANN/rann_fingerprint_radial.cpp b/src/USER-RANN/rann_fingerprint_radial.cpp new file mode 100644 index 0000000000..5df13aa094 --- /dev/null +++ b/src/USER-RANN/rann_fingerprint_radial.cpp @@ -0,0 +1,239 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ + +#include "rann_fingerprint_radial.h" + + + +using namespace LAMMPS_NS::RANN; + +Fingerprint_radial::Fingerprint_radial(PairRANN *_pair) : Fingerprint(_pair) +{ + n_body_type = 2; + dr = 0; + re = 0; + rc = 0; + alpha = new double [1]; + alpha[0] = -1; + nmax = 0; + omin = 0; + id = -1; + style = "radial"; + atomtypes = new int [n_body_type]; + empty = true; + fullydefined = false; + _pair->allscreen = false; +} + +Fingerprint_radial::~Fingerprint_radial() +{ + delete [] atomtypes; + delete [] radialtable; + delete [] alpha; + delete [] dfctable; + delete [] rinvsqrttable; +} + +bool Fingerprint_radial::parse_values(std::string constant,std::vector line1) { + int l; + int nwords=line1.size(); + if (constant.compare("re")==0) { + re = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("rc")==0) { + rc = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("alpha")==0) { + delete [] alpha; + alpha = new double [nwords]; + for (l=0;lerrorf(FLERR,"Undefined value for radial power"); + //code will run with default o=0 if o is never specified. All other values must be defined in potential file. + if (re!=0 && rc!=0 && alpha!=0 && dr!=0 && nmax!=0)return true; + return false; +} + +void Fingerprint_radial::write_values(FILE *fid) { + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alpha:\n",style,id); + for (i=0;i<(nmax-omin+1);i++) { + fprintf(fid,"%f ",alpha[i]); + } + fprintf(fid,"\n"); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:o:\n",style,id); + fprintf(fid,"%d\n",omin); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:n:\n",style,id); + fprintf(fid,"%d\n",nmax); +} + +//called after fingerprint is fully defined and tables can be computed. +void Fingerprint_radial::allocate() +{ + int k,m; + double r1; + int buf = 5; + int res = pair->res; + double cutmax = pair->cutmax; + radialtable = new double [(res+buf)*get_length()]; + dfctable = new double [res+buf]; + for (k=0;k<(res+buf);k++) { + r1 = cutmax*cutmax*(double)(k)/(double)(res); + for (m=0;m<=(nmax-omin);m++) { + radialtable[k*(nmax-omin+1)+m]=pow(sqrt(r1)/re,m+omin)*exp(-alpha[m]*sqrt(r1)/re)*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)) { + dfctable[k]=0; + } + else{ + dfctable[k]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } + generate_rinvssqrttable(); +} + +//called after fingerprint is declared for i-j type, but before its parameters are read. +void Fingerprint_radial::init(int *i,int _id) +{ + empty = false; + for (int j=0;jnelements; + int res = pair->res; + int i,j,jj,itype,jtype,l; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + // + PairRANN::Simulation *sim = &pair->sims[sid]; + int count=0; +// double **x = sim->x; + int *type = sim->type; + ilist = sim->ilist; + double cutmax = pair->cutmax; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double cutinv2 = 1/cutmax/cutmax; + //loop over neighbors + for (jj = 0; jj < jnum; jj++) { + jtype =tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype)continue; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq > rc*rc)continue; + count = startingneuron; + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (m1>res || m1<1) {pair->errorf(FLERR,"invalid neighbor radius!");} + if (radialtable[m1]==0) {continue;} + //cubic interpolation from tables + double *p1 = &radialtable[m1*(nmax-omin+1)]; + double *p2 = &radialtable[(m1+1)*(nmax-omin+1)]; + double *p3 = &radialtable[(m1+2)*(nmax-omin+1)]; + double *p0 = &radialtable[(m1-1)*(nmax-omin+1)]; + double *q = &dfctable[m1-1]; + double *rinvs = &rinvsqrttable[m1-1]; + r1 = r1-trunc(r1); + double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + double ri = rinvs[1] + 0.5 * r1*(rinvs[2] - rinvs[0] + r1*(2.0*rinvs[0] - 5.0*rinvs[1] + 4.0*rinvs[2] - rinvs[3] + r1*(3.0*(rinvs[1] - rinvs[2]) + rinvs[3] - rinvs[0]))); + for (l=0;l<=(nmax-omin);l++) { + double rt = p1[l]+0.5*r1*(p2[l]-p0[l]+r1*(2.0*p0[l]-5.0*p1[l]+4.0*p2[l]-p3[l]+r1*(3.0*(p1[l]-p2[l])+p3[l]-p0[l]))); + features[count]+=rt; + rt *= (l+omin)/rsq+(-alpha[l]/re+dfc)*ri; + //update neighbor's features + dfeaturesx[jj*f+count]+=rt*delx; + dfeaturesy[jj*f+count]+=rt*dely; + dfeaturesz[jj*f+count]+=rt*delz; + //update atom's features + dfeaturesx[jnum*f+count]-=rt*delx; + dfeaturesy[jnum*f+count]-=rt*dely; + dfeaturesz[jnum*f+count]-=rt*delz; + count++; + } + } +} + +int Fingerprint_radial::get_length() +{ + return nmax-omin+1; +} diff --git a/src/USER-RANN/rann_fingerprint_radial.h b/src/USER-RANN/rann_fingerprint_radial.h new file mode 100644 index 0000000000..5f9876f493 --- /dev/null +++ b/src/USER-RANN/rann_fingerprint_radial.h @@ -0,0 +1,70 @@ + +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ +#ifdef FINGERPRINT_CLASS + +FingerprintStyle(radial,Fingerprint_radial) + +#else + +#ifndef LMP_RANN_FINGERPRINT_RADIAL_H +#define LMP_RANN_FINGERPRINT_RADIAL_H + +#include "rann_fingerprint.h" + +namespace LAMMPS_NS { + namespace RANN { + + class Fingerprint_radial : public Fingerprint { + public: + Fingerprint_radial(PairRANN *); + ~Fingerprint_radial(); + bool parse_values(std::string,std::vector); + void write_values(FILE *); + void init(int*,int); + void allocate(); + void compute_fingerprint(double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*); + int get_length(); + + double *radialtable; + double *dfctable; + double dr; + double *alpha; + double re; + int nmax;//highest term + int omin;//lowest term + + }; + + } +} + +#endif +#endif /* FINGERPRINT_RADIAL_H_ */ diff --git a/src/USER-RANN/rann_fingerprint_radialscreened.cpp b/src/USER-RANN/rann_fingerprint_radialscreened.cpp new file mode 100644 index 0000000000..79333a4e3a --- /dev/null +++ b/src/USER-RANN/rann_fingerprint_radialscreened.cpp @@ -0,0 +1,253 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ + +#include "rann_fingerprint_radialscreened.h" + + + +using namespace LAMMPS_NS::RANN; + +Fingerprint_radialscreened::Fingerprint_radialscreened(PairRANN *_pair) : Fingerprint(_pair) +{ + n_body_type = 2; + dr = 0; + re = 0; + rc = 0; + alpha = new double [1]; + alpha[0] = -1; + nmax = 0; + omin = 0; + id = -1; + style = "radialscreened"; + atomtypes = new int [n_body_type]; + empty = true; + fullydefined = false; + _pair->doscreen = true; + screen = true; +} + +Fingerprint_radialscreened::~Fingerprint_radialscreened() +{ + delete [] atomtypes; + delete [] radialtable; + delete [] alpha; + delete [] dfctable; + delete [] rinvsqrttable; +} + +bool Fingerprint_radialscreened::parse_values(std::string constant,std::vector line1) { + int l; + int nwords=line1.size(); + if (constant.compare("re")==0) { + re = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("rc")==0) { + rc = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("alpha")==0) { + delete [] alpha; + alpha = new double [nwords]; + for (l=0;lerrorf(FLERR,"Undefined value for radial power"); + //code will run with default o=0 if o is never specified. All other values must be defined in potential file. + if (re!=0 && rc!=0 && alpha!=0 && dr!=0 && nmax!=0)return true; + return false; +} + +void Fingerprint_radialscreened::write_values(FILE *fid) { + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alpha:\n",style,id); + for (i=0;i<(nmax-omin+1);i++) { + fprintf(fid,"%f ",alpha[i]); + } + fprintf(fid,"\n"); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:o:\n",style,id); + fprintf(fid,"%d\n",omin); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:n:\n",style,id); + fprintf(fid,"%d\n",nmax); +} + +//called after fingerprint is fully defined and tables can be computed. +void Fingerprint_radialscreened::allocate() +{ + int k,m; + double r1; + int buf = 5; + int res = pair->res; + double cutmax = pair->cutmax; + radialtable = new double [(res+buf)*get_length()]; + dfctable = new double [res+buf]; + for (k=0;k<(res+buf);k++) { + r1 = cutmax*cutmax*(double)(k)/(double)(res); + for (m=0;m<=(nmax-omin);m++) { + radialtable[k*(nmax-omin+1)+m]=pow(sqrt(r1)/re,m+omin)*exp(-alpha[m]*sqrt(r1)/re)*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)) { + dfctable[k]=0; + } + else{ + dfctable[k]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } + generate_rinvssqrttable(); +} + +//called after fingerprint is declared for i-j type, but before its parameters are read. +void Fingerprint_radialscreened::init(int *i,int _id) +{ + empty = false; + for (int j=0;jnelements; + int res = pair->res; + int i,j,jj,itype,jtype,l,kk; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + // + PairRANN::Simulation *sim = &pair->sims[sid]; + int count=0; + double **x = sim->x; + int *type = sim->type; + ilist = sim->ilist; + double cutmax = pair->cutmax; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double cutinv2 = 1/cutmax/cutmax; + //loop over neighbors + for (jj = 0; jj < jnum; jj++) { + if (Bij[jj]==false) {continue;} + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype)continue; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq > rc*rc)continue; + count = startingneuron; + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (m1>res || m1<1) {pair->errorf(FLERR,"invalid neighbor radius!");} + if (radialtable[m1]==0) {continue;} + //cubic interpolation from tables + double *p1 = &radialtable[m1*(nmax-omin+1)]; + double *p2 = &radialtable[(m1+1)*(nmax-omin+1)]; + double *p3 = &radialtable[(m1+2)*(nmax-omin+1)]; + double *p0 = &radialtable[(m1-1)*(nmax-omin+1)]; + double *q = &dfctable[m1-1]; + double *rinvs = &rinvsqrttable[m1-1]; + r1 = r1-trunc(r1); + double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + double ri = rinvs[1] + 0.5 * r1*(rinvs[2] - rinvs[0] + r1*(2.0*rinvs[0] - 5.0*rinvs[1] + 4.0*rinvs[2] - rinvs[3] + r1*(3.0*(rinvs[1] - rinvs[2]) + rinvs[3] - rinvs[0]))); + for (l=0;l<=(nmax-omin);l++) { + double rt = Sik[jj]*(p1[l]+0.5*r1*(p2[l]-p0[l]+r1*(2.0*p0[l]-5.0*p1[l]+4.0*p2[l]-p3[l]+r1*(3.0*(p1[l]-p2[l])+p3[l]-p0[l])))); + features[count]+=rt; + double rt1 = rt*((l+omin)/rsq+(-alpha[l]/re+dfc)*ri); + //update neighbor's features + dfeaturesx[jj*f+count]+=rt1*delx+rt*dSikx[jj]; + dfeaturesy[jj*f+count]+=rt1*dely+rt*dSiky[jj]; + dfeaturesz[jj*f+count]+=rt1*delz+rt*dSikz[jj]; + for (kk=0;kk); + void write_values(FILE *); + void init(int*,int); + void allocate(); + void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*); + int get_length(); + + double *radialtable; + double *dfctable; + double dr; + double *alpha; + double re; + int nmax;//highest term + int omin;//lowest term + + }; +} + +} + +#endif + + + +#endif /* FINGERPRINT_RADIALSCREENED_H_ */ diff --git a/src/USER-RANN/rann_fingerprint_radialscreenedspin.cpp b/src/USER-RANN/rann_fingerprint_radialscreenedspin.cpp new file mode 100644 index 0000000000..f594e92077 --- /dev/null +++ b/src/USER-RANN/rann_fingerprint_radialscreenedspin.cpp @@ -0,0 +1,264 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ +#include "rann_fingerprint_radialscreenedspin.h" + + + +using namespace LAMMPS_NS::RANN; + +Fingerprint_radialscreenedspin::Fingerprint_radialscreenedspin(PairRANN *_pair) : Fingerprint(_pair) +{ + n_body_type = 2; + dr = 0; + re = 0; + rc = 0; + alpha = new double [1]; + alpha[0] = -1; + nmax = 0; + omin = 0; + id = -1; + style = "radialscreenedspin"; + atomtypes = new int [n_body_type]; + empty = true; + fullydefined = false; + _pair->doscreen = true; + screen = true; + _pair->dospin = true; + spin = true; +} + +Fingerprint_radialscreenedspin::~Fingerprint_radialscreenedspin() +{ + delete [] atomtypes; + delete [] radialtable; + delete [] alpha; + delete [] dfctable; + delete [] rinvsqrttable; +} + +bool Fingerprint_radialscreenedspin::parse_values(std::string constant,std::vector line1) { + int l; + int nwords=line1.size(); + if (constant.compare("re")==0) { + re = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("rc")==0) { + rc = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("alpha")==0) { + delete [] alpha; + alpha = new double [nwords]; + for (l=0;lerrorf(FLERR,"Undefined value for radial power"); + //code will run with default o=0 if o is never specified. All other values must be defined in potential file. + if (re!=0 && rc!=0 && alpha!=0 && dr!=0 && nmax!=0)return true; + return false; +} + +void Fingerprint_radialscreenedspin::write_values(FILE *fid) { + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alpha:\n",style,id); + for (i=0;i<(nmax-omin+1);i++) { + fprintf(fid,"%f ",alpha[i]); + } + fprintf(fid,"\n"); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:o:\n",style,id); + fprintf(fid,"%d\n",omin); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:n:\n",style,id); + fprintf(fid,"%d\n",nmax); +} + +//called after fingerprint is fully defined and tables can be computed. +void Fingerprint_radialscreenedspin::allocate() +{ + int k,m; + double r1; + int buf = 5; + int res = pair->res; + double cutmax = pair->cutmax; + radialtable = new double [(res+buf)*get_length()]; + dfctable = new double [res+buf]; + for (k=0;k<(res+buf);k++) { + r1 = cutmax*cutmax*(double)(k)/(double)(res); + for (m=0;m<=(nmax-omin);m++) { + radialtable[k*(nmax-omin+1)+m]=pow(sqrt(r1)/re,m+omin)*exp(-alpha[m]*sqrt(r1)/re)*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)) { + dfctable[k]=0; + } + else{ + dfctable[k]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } + generate_rinvssqrttable(); +} + +//called after fingerprint is declared for i-j type, but before its parameters are read. +void Fingerprint_radialscreenedspin::init(int *i,int _id) +{ + empty = false; + for (int j=0;jnelements; + int res = pair->res; + int i,j,jj,itype,jtype,l,kk; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + PairRANN::Simulation *sim = &pair->sims[sid]; + int count=0; + double **x = sim->x; + int *type = sim->type; + ilist = sim->ilist; + double cutmax = pair->cutmax; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double cutinv2 = 1/cutmax/cutmax; + double *si = sim->s[i]; + //loop over neighbors + for (jj = 0; jj < jnum; jj++) { + if (Bij[jj]==false) {continue;} + jtype = tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype)continue; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq > rc*rc)continue; + count = startingneuron; + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (m1>res || m1<1) {pair->errorf(FLERR,"invalid neighbor radius!");} + if (radialtable[m1]==0) {continue;} + j=jl[jj]; + double *sj = sim->s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + //cubic interpolation from tables + double *p1 = &radialtable[m1*(nmax-omin+1)]; + double *p2 = &radialtable[(m1+1)*(nmax-omin+1)]; + double *p3 = &radialtable[(m1+2)*(nmax-omin+1)]; + double *p0 = &radialtable[(m1-1)*(nmax-omin+1)]; + double *q = &dfctable[m1-1]; + double *rinvs = &rinvsqrttable[m1-1]; + r1 = r1-trunc(r1); + double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + double ri = rinvs[1] + 0.5 * r1*(rinvs[2] - rinvs[0] + r1*(2.0*rinvs[0] - 5.0*rinvs[1] + 4.0*rinvs[2] - rinvs[3] + r1*(3.0*(rinvs[1] - rinvs[2]) + rinvs[3] - rinvs[0]))); + for (l=0;l<=(nmax-omin);l++) { + double rt = Sik[jj]*(p1[l]+0.5*r1*(p2[l]-p0[l]+r1*(2.0*p0[l]-5.0*p1[l]+4.0*p2[l]-p3[l]+r1*(3.0*(p1[l]-p2[l])+p3[l]-p0[l])))); + //update neighbor's features + dspinx[jj*f+count]+=rt*si[0]; + dspiny[jj*f+count]+=rt*si[1]; + dspinz[jj*f+count]+=rt*si[2]; + dspinx[jnum*f+count]+=rt*sj[0]; + dspiny[jnum*f+count]+=rt*sj[1]; + dspinz[jnum*f+count]+=rt*sj[2]; + rt *= sp; + features[count]+=rt; + double rt1 = rt*((l+omin)/rsq+(-alpha[l]/re+dfc)*ri); + dfeaturesx[jj*f+count]+=rt1*delx+rt*dSikx[jj]; + dfeaturesy[jj*f+count]+=rt1*dely+rt*dSiky[jj]; + dfeaturesz[jj*f+count]+=rt1*delz+rt*dSikz[jj]; + for (kk=0;kk); + void write_values(FILE *); + void init(int*,int); + void allocate(); + virtual void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*);//spin,screen + int get_length(); + + double *radialtable; + double *dfctable; + double dr; + double *alpha; + double re; + int nmax;//highest term + int omin;//lowest term + + }; + } + +} + +#endif + + + +#endif /* FINGERPRINT_RADIALSCREENED_H_ */ diff --git a/src/USER-RANN/rann_fingerprint_radialspin.cpp b/src/USER-RANN/rann_fingerprint_radialspin.cpp new file mode 100644 index 0000000000..9d61fc08ed --- /dev/null +++ b/src/USER-RANN/rann_fingerprint_radialspin.cpp @@ -0,0 +1,252 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ +#include "rann_fingerprint_radialspin.h" + + + +using namespace LAMMPS_NS::RANN; + +Fingerprint_radialspin::Fingerprint_radialspin(PairRANN *_pair) : Fingerprint(_pair) +{ + n_body_type = 2; + dr = 0; + re = 0; + rc = 0; + alpha = new double [1]; + alpha[0] = -1; + nmax = 0; + omin = 0; + id = -1; + style = "radialspin"; + atomtypes = new int [n_body_type]; + empty = true; + fullydefined = false; + _pair->allscreen = false; + _pair->dospin = true; + spin = true; +} + +Fingerprint_radialspin::~Fingerprint_radialspin() +{ + delete [] atomtypes; + delete [] radialtable; + delete [] alpha; + delete [] dfctable; + delete [] rinvsqrttable; +} + +bool Fingerprint_radialspin::parse_values(std::string constant,std::vector line1) { + int l; + int nwords=line1.size(); + if (constant.compare("re")==0) { + re = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("rc")==0) { + rc = strtod(line1[0].c_str(),NULL); + } + else if (constant.compare("alpha")==0) { + delete [] alpha; + alpha = new double [nwords]; + for (l=0;lerrorf(FLERR,"Undefined value for radial power"); + //code will run with default o=0 if o is never specified. All other values must be defined in potential file. + if (re!=0 && rc!=0 && alpha!=0 && dr!=0 && nmax!=0)return true; + return false; +} + +void Fingerprint_radialspin::write_values(FILE *fid) { + int i; + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:re:\n",style,id); + fprintf(fid,"%f\n",re); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:rc:\n",style,id); + fprintf(fid,"%f\n",rc); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:alpha:\n",style,id); + for (i=0;i<(nmax-omin+1);i++) { + fprintf(fid,"%f ",alpha[i]); + } + fprintf(fid,"\n"); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:dr:\n",style,id); + fprintf(fid,"%f\n",dr); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:o:\n",style,id); + fprintf(fid,"%d\n",omin); + fprintf(fid,"fingerprintconstants:"); + fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); + for (i=1;ielementsp[atomtypes[i]]); + } + fprintf(fid,":%s_%d:n:\n",style,id); + fprintf(fid,"%d\n",nmax); +} + +//called after fingerprint is fully defined and tables can be computed. +void Fingerprint_radialspin::allocate() +{ + int k,m; + double r1; + int buf = 5; + int res = pair->res; + double cutmax = pair->cutmax; + radialtable = new double [(res+buf)*get_length()]; + dfctable = new double [res+buf]; + for (k=0;k<(res+buf);k++) { + r1 = cutmax*cutmax*(double)(k)/(double)(res); + for (m=0;m<=(nmax-omin);m++) { + radialtable[k*(nmax-omin+1)+m]=pow(sqrt(r1)/re,m+omin)*exp(-alpha[m]*sqrt(r1)/re)*cutofffunction(sqrt(r1),rc,dr); + } + if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)) { + dfctable[k]=0; + } + else{ + dfctable[k]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); + } + } + generate_rinvssqrttable(); +} + +//called after fingerprint is declared for i-j type, but before its parameters are read. +void Fingerprint_radialspin::init(int *i,int _id) +{ + empty = false; + for (int j=0;jnelements; + int res = pair->res; + int i,j,jj,itype,jtype,l; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + // + PairRANN::Simulation *sim = &pair->sims[sid]; + int count=0; + int *type = sim->type; + ilist = sim->ilist; + double cutmax = pair->cutmax; + i = ilist[ii]; + itype = pair->map[type[i]]; + int f = pair->net[itype].dimensions[0]; + double cutinv2 = 1/cutmax/cutmax; + double *si = sim->s[i]; + firstneigh = sim->firstneigh; + jlist = firstneigh[i]; + //loop over neighbors + for (jj = 0; jj < jnum; jj++) { + j = jl[jj]; + jtype =tn[jj]; + if (atomtypes[1] != nelements && atomtypes[1] != jtype)continue; + delx = xn[jj]; + dely = yn[jj]; + delz = zn[jj]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq > rc*rc)continue; + count = startingneuron; + double r1 = (rsq*((double)res)*cutinv2); + int m1 = (int)r1; + if (m1>res || m1<1) {pair->errorf(FLERR,"invalid neighbor radius!");} + if (radialtable[m1]==0) {continue;} + double *sj = sim->s[j]; + double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; + //cubic interpolation from tables + double *p1 = &radialtable[m1*(nmax-omin+1)]; + double *p2 = &radialtable[(m1+1)*(nmax-omin+1)]; + double *p3 = &radialtable[(m1+2)*(nmax-omin+1)]; + double *p0 = &radialtable[(m1-1)*(nmax-omin+1)]; + double *q = &dfctable[m1-1]; + double *rinvs = &rinvsqrttable[m1-1]; + r1 = r1-trunc(r1); + double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); + double ri = rinvs[1] + 0.5 * r1*(rinvs[2] - rinvs[0] + r1*(2.0*rinvs[0] - 5.0*rinvs[1] + 4.0*rinvs[2] - rinvs[3] + r1*(3.0*(rinvs[1] - rinvs[2]) + rinvs[3] - rinvs[0]))); + for (l=0;l<=(nmax-omin);l++) { + double rt = p1[l]+0.5*r1*(p2[l]-p0[l]+r1*(2.0*p0[l]-5.0*p1[l]+4.0*p2[l]-p3[l]+r1*(3.0*(p1[l]-p2[l])+p3[l]-p0[l]))); + dspinx[jj*f+count]+=rt*si[0]; + dspiny[jj*f+count]+=rt*si[1]; + dspinz[jj*f+count]+=rt*si[2]; + dspinx[jnum*f+count]+=rt*sj[0]; + dspiny[jnum*f+count]+=rt*sj[1]; + dspinz[jnum*f+count]+=rt*sj[2]; + rt *= sp; + features[count]+=rt; + rt *= (l+omin)/rsq+(-alpha[l]/re+dfc)*ri; + //update neighbor's features + dfeaturesx[jj*f+count]+=rt*delx; + dfeaturesy[jj*f+count]+=rt*dely; + dfeaturesz[jj*f+count]+=rt*delz; + //update atom's features + dfeaturesx[jnum*f+count]-=rt*delx; + dfeaturesy[jnum*f+count]-=rt*dely; + dfeaturesz[jnum*f+count]-=rt*delz; + count++; + } + } +} + +int Fingerprint_radialspin::get_length() +{ + return nmax-omin+1; +} diff --git a/src/USER-RANN/rann_fingerprint_radialspin.h b/src/USER-RANN/rann_fingerprint_radialspin.h new file mode 100644 index 0000000000..6abddd910d --- /dev/null +++ b/src/USER-RANN/rann_fingerprint_radialspin.h @@ -0,0 +1,69 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu + Doyl Dickel (MSU) doyl@me.msstate.edu + ----------------------------------------------------------------------*/ +/* +“The research described and the resulting data presented herein, unless +otherwise noted, was funded under PE 0602784A, Project T53 "Military +Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, +managed by the U.S. Army Combat Capabilities Development Command (CCDC) and +the Engineer Research and Development Center (ERDC). The work described in +this document was conducted at CAVS, MSU. Permission was granted by ERDC +to publish this information. Any opinions, findings and conclusions or +recommendations expressed in this material are those of the author(s) and +do not necessarily reflect the views of the United States Army.​” + +DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 + */ + +#ifdef FINGERPRINT_CLASS + +FingerprintStyle(radialspin,Fingerprint_radialspin) + +#else + +#ifndef LMP_RANN_FINGERPRINT_RADIALSPIN_H +#define LMP_RANN_FINGERPRINT_RADIALSPIN_H + +#include "rann_fingerprint.h" + +namespace LAMMPS_NS { + namespace RANN { + class Fingerprint_radialspin : public Fingerprint { + public: + Fingerprint_radialspin(PairRANN *); + ~Fingerprint_radialspin(); + bool parse_values(std::string,std::vector); + void write_values(FILE *); + void init(int*,int); + void allocate(); + void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*); + int get_length(); + + double *radialtable; + double *dfctable; + double dr; + double *alpha; + double re; + int nmax;//highest term + int omin;//lowest term + + }; + } + +} + +#endif +#endif /* FINGERPRINT_RADIAL_H_ */ diff --git a/src/USER-RANN/rann_list_activation.h b/src/USER-RANN/rann_list_activation.h new file mode 100644 index 0000000000..a140b92c65 --- /dev/null +++ b/src/USER-RANN/rann_list_activation.h @@ -0,0 +1,2 @@ +#include "rann_activation_linear.h" +#include "rann_activation_sig_i.h" diff --git a/src/USER-RANN/rann_list_fingerprint.h b/src/USER-RANN/rann_list_fingerprint.h new file mode 100644 index 0000000000..005c7f1b04 --- /dev/null +++ b/src/USER-RANN/rann_list_fingerprint.h @@ -0,0 +1,8 @@ +#include "rann_fingerprint_bond.h" +#include "rann_fingerprint_bondscreened.h" +#include "rann_fingerprint_bondscreenedspin.h" +#include "rann_fingerprint_bondspin.h" +#include "rann_fingerprint_radial.h" +#include "rann_fingerprint_radialscreened.h" +#include "rann_fingerprint_radialscreenedspin.h" +#include "rann_fingerprint_radialspin.h" From f165fdb61deac367ea8a81dd3e9a67a3c3caea94 Mon Sep 17 00:00:00 2001 From: kipbarrett Date: Thu, 11 Feb 2021 08:48:00 -0600 Subject: [PATCH 0100/1217] remove all files from src that are in src/USER-RANN --- src/activation.cpp | 57 -- src/activation.h | 52 - src/activation_linear.cpp | 54 - src/activation_linear.h | 54 - src/activation_sigI.cpp | 52 - src/activation_sigI.h | 55 -- src/fingerprint.cpp | 113 --- src/fingerprint.h | 72 -- src/fingerprint_bond.cpp | 917 ----------------- src/fingerprint_bond.h | 80 -- src/fingerprint_bondscreened.cpp | 950 ------------------ src/fingerprint_bondscreened.h | 79 -- src/fingerprint_bondscreenedspin.cpp | 1023 ------------------- src/fingerprint_bondscreenedspin.h | 79 -- src/fingerprint_bondspin.cpp | 1019 ------------------- src/fingerprint_bondspin.h | 79 -- src/fingerprint_radial.cpp | 259 ----- src/fingerprint_radial.h | 68 -- src/fingerprint_radialscreened.cpp | 273 ------ src/fingerprint_radialscreened.h | 71 -- src/fingerprint_radialscreenedspin.cpp | 285 ------ src/fingerprint_radialscreenedspin.h | 71 -- src/fingerprint_radialspin.cpp | 269 ----- src/fingerprint_radialspin.h | 69 -- src/pair_rann.cpp | 1247 ------------------------ src/pair_rann.h | 171 ---- 26 files changed, 7518 deletions(-) delete mode 100644 src/activation.cpp delete mode 100644 src/activation.h delete mode 100644 src/activation_linear.cpp delete mode 100644 src/activation_linear.h delete mode 100644 src/activation_sigI.cpp delete mode 100644 src/activation_sigI.h delete mode 100644 src/fingerprint.cpp delete mode 100644 src/fingerprint.h delete mode 100644 src/fingerprint_bond.cpp delete mode 100644 src/fingerprint_bond.h delete mode 100644 src/fingerprint_bondscreened.cpp delete mode 100644 src/fingerprint_bondscreened.h delete mode 100644 src/fingerprint_bondscreenedspin.cpp delete mode 100644 src/fingerprint_bondscreenedspin.h delete mode 100644 src/fingerprint_bondspin.cpp delete mode 100644 src/fingerprint_bondspin.h delete mode 100644 src/fingerprint_radial.cpp delete mode 100644 src/fingerprint_radial.h delete mode 100644 src/fingerprint_radialscreened.cpp delete mode 100644 src/fingerprint_radialscreened.h delete mode 100644 src/fingerprint_radialscreenedspin.cpp delete mode 100644 src/fingerprint_radialscreenedspin.h delete mode 100644 src/fingerprint_radialspin.cpp delete mode 100644 src/fingerprint_radialspin.h delete mode 100644 src/pair_rann.cpp delete mode 100644 src/pair_rann.h diff --git a/src/activation.cpp b/src/activation.cpp deleted file mode 100644 index 5286eb4730..0000000000 --- a/src/activation.cpp +++ /dev/null @@ -1,57 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@me.msstate.edu - ----------------------------------------------------------------------*/ -/* -“The research described and the resulting data presented herein, unless -otherwise noted, was funded under PE 0602784A, Project T53 "Military -Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, -managed by the U.S. Army Combat Capabilities Development Command (CCDC) and -the Engineer Research and Development Center (ERDC). The work described in -this document was conducted at CAVS, MSU. Permission was granted by ERDC -to publish this information. Any opinions, findings and conclusions or -recommendations expressed in this material are those of the author(s) and -do not necessarily reflect the views of the United States Army.​” - -DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 - */ - - -#include "activation.h" - - -using namespace LAMMPS_NS; - -Activation::Activation(PairRANN *pair) { - empty = true; - style = "empty"; -} - -Activation::~Activation(){ - -} - -//default is linear activation (no change). -double Activation::activation_function(double A){ - return A; -} - -double Activation::dactivation_function(double A){ - return 1.0; -} - -double Activation::ddactivation_function(double A){ - return 0.0; -} diff --git a/src/activation.h b/src/activation.h deleted file mode 100644 index 0188f80bff..0000000000 --- a/src/activation.h +++ /dev/null @@ -1,52 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@me.msstate.edu - ----------------------------------------------------------------------*/ -/* -“The research described and the resulting data presented herein, unless -otherwise noted, was funded under PE 0602784A, Project T53 "Military -Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, -managed by the U.S. Army Combat Capabilities Development Command (CCDC) and -the Engineer Research and Development Center (ERDC). The work described in -this document was conducted at CAVS, MSU. Permission was granted by ERDC -to publish this information. Any opinions, findings and conclusions or -recommendations expressed in this material are those of the author(s) and -do not necessarily reflect the views of the United States Army.​” - -DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 - */ - -#ifndef ACTIVATION_H_ -#define ACTIVATION_H_ - -#include "pair_rann.h" - -namespace LAMMPS_NS { - - class Activation { - public: - Activation(class PairRANN *); - virtual ~Activation(); - virtual double activation_function(double); - virtual double dactivation_function(double); - virtual double ddactivation_function(double); - bool empty; - const char *style; - }; -} - - - -#endif /* ACTIVATION_H_ */ diff --git a/src/activation_linear.cpp b/src/activation_linear.cpp deleted file mode 100644 index ddb9ae54c9..0000000000 --- a/src/activation_linear.cpp +++ /dev/null @@ -1,54 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@me.msstate.edu - ----------------------------------------------------------------------*/ -/* -“The research described and the resulting data presented herein, unless -otherwise noted, was funded under PE 0602784A, Project T53 "Military -Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, -managed by the U.S. Army Combat Capabilities Development Command (CCDC) and -the Engineer Research and Development Center (ERDC). The work described in -this document was conducted at CAVS, MSU. Permission was granted by ERDC -to publish this information. Any opinions, findings and conclusions or -recommendations expressed in this material are those of the author(s) and -do not necessarily reflect the views of the United States Army.​” - -DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 - */ - -#include "activation_linear.h" - - - -using namespace LAMMPS_NS; - -Activation_linear::Activation_linear(PairRANN *pair) : Activation(pair){ - empty = false; - style = "linear"; -} - -double Activation_linear::activation_function(double A) -{ - return A; -} - -double Activation_linear::dactivation_function(double A) -{ - return 1.0; -} - -double Activation_linear::ddactivation_function(double){ - return 0.0; -} diff --git a/src/activation_linear.h b/src/activation_linear.h deleted file mode 100644 index 2ea0f55729..0000000000 --- a/src/activation_linear.h +++ /dev/null @@ -1,54 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@me.msstate.edu - ----------------------------------------------------------------------*/ -/* -“The research described and the resulting data presented herein, unless -otherwise noted, was funded under PE 0602784A, Project T53 "Military -Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, -managed by the U.S. Army Combat Capabilities Development Command (CCDC) and -the Engineer Research and Development Center (ERDC). The work described in -this document was conducted at CAVS, MSU. Permission was granted by ERDC -to publish this information. Any opinions, findings and conclusions or -recommendations expressed in this material are those of the author(s) and -do not necessarily reflect the views of the United States Army.​” - -DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 - */ -#ifdef ACTIVATION_CLASS - -ActivationStyle(linear,Activation_linear) - -#else - -#ifndef ACTIVATION_LINEAR_H_ -#define ACTIVATION_LINEAR_H_ - -#include "activation.h" - -namespace LAMMPS_NS { - -class Activation_linear : public Activation { -public: - Activation_linear(class PairRANN *); - double activation_function(double); - double dactivation_function(double); - double ddactivation_function(double); -}; - -} - -#endif -#endif /* ACTIVATION_LINEAR_H_ */ diff --git a/src/activation_sigI.cpp b/src/activation_sigI.cpp deleted file mode 100644 index b14f1c503d..0000000000 --- a/src/activation_sigI.cpp +++ /dev/null @@ -1,52 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@me.msstate.edu - ----------------------------------------------------------------------*/ -/* -“The research described and the resulting data presented herein, unless -otherwise noted, was funded under PE 0602784A, Project T53 "Military -Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, -managed by the U.S. Army Combat Capabilities Development Command (CCDC) and -the Engineer Research and Development Center (ERDC). The work described in -this document was conducted at CAVS, MSU. Permission was granted by ERDC -to publish this information. Any opinions, findings and conclusions or -recommendations expressed in this material are those of the author(s) and -do not necessarily reflect the views of the United States Army.​” - -DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 - */ -#include "activation_sigI.h" - -using namespace LAMMPS_NS; - -Activation_sigI::Activation_sigI(PairRANN *pair) : Activation(pair){ - empty = false; - style = "sigI"; -} - -double Activation_sigI::activation_function(double in){ - if (in>34)return in; - return 0.1*in + 0.9*log(exp(in) + 1); -} - -double Activation_sigI::dactivation_function(double in){ - if (in>34)return 1; - return 0.1 + 0.9/(exp(in)+1)*exp(in); -} - -double Activation_sigI::ddactivation_function(double in){ - if (in>34)return 0; - return 0.9*exp(in)/(exp(in)+1)/(exp(in)+1);; -} diff --git a/src/activation_sigI.h b/src/activation_sigI.h deleted file mode 100644 index 404af35cfd..0000000000 --- a/src/activation_sigI.h +++ /dev/null @@ -1,55 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@me.msstate.edu - ----------------------------------------------------------------------*/ -/* -“The research described and the resulting data presented herein, unless -otherwise noted, was funded under PE 0602784A, Project T53 "Military -Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, -managed by the U.S. Army Combat Capabilities Development Command (CCDC) and -the Engineer Research and Development Center (ERDC). The work described in -this document was conducted at CAVS, MSU. Permission was granted by ERDC -to publish this information. Any opinions, findings and conclusions or -recommendations expressed in this material are those of the author(s) and -do not necessarily reflect the views of the United States Army.​” - -DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 - */ - -#ifdef ACTIVATION_CLASS - -ActivationStyle(sigI,Activation_sigI) - -#else - -#ifndef ACTIVATION_SIGI_H_ -#define ACTIVATION_SIGI_H_ - -#include "activation.h" - -namespace LAMMPS_NS { - - class Activation_sigI : public Activation { - public: - Activation_sigI(class PairRANN *); - double activation_function(double); - double dactivation_function(double); - double ddactivation_function(double); - }; -} - - -#endif -#endif /* ACTIVATION_SIGI_H_ */ diff --git a/src/fingerprint.cpp b/src/fingerprint.cpp deleted file mode 100644 index 89786b632a..0000000000 --- a/src/fingerprint.cpp +++ /dev/null @@ -1,113 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@me.msstate.edu - ----------------------------------------------------------------------*/ -/* -“The research described and the resulting data presented herein, unless -otherwise noted, was funded under PE 0602784A, Project T53 "Military -Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, -managed by the U.S. Army Combat Capabilities Development Command (CCDC) and -the Engineer Research and Development Center (ERDC). The work described in -this document was conducted at CAVS, MSU. Permission was granted by ERDC -to publish this information. Any opinions, findings and conclusions or -recommendations expressed in this material are those of the author(s) and -do not necessarily reflect the views of the United States Army.​” - -DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 - */ - -#include "fingerprint.h" - - -using namespace LAMMPS_NS; - -Fingerprint::Fingerprint(PairRANN *pair) -{ - spin = false; - screen = false; - empty = true; - fullydefined = false; - n_body_type = 0; - style = "empty"; - this->pair = pair; -} - -Fingerprint::~Fingerprint(){ - -} - -bool Fingerprint::parse_values(char *word,char *line1){ - return false; -} - -void Fingerprint::init(int *i,int id){ - -} - -void Fingerprint::allocate(){ - -} - -void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ - -} - -void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ - -} - -void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz,double *sx, double *sy, double *sz, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ - -} - -void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz,double *sx, double *sy, double *sz, double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ - -} - -void Fingerprint::write_values(FILE *fid){ - -} - -int Fingerprint::get_length(){ - return 0; -} - -//Smooth cutoff, goes from 1 to zero over the interval rc-dr to rc. Same as MEAM uses. Used by generateradialtable and generatexpcuttable. -double Fingerprint::cutofffunction(double r,double rc, double dr){ - double out; - if (r < (rc -dr))out=1; - else if (r>rc)out=0; - else { - out = pow(1-pow(1-(rc-r)/dr,4.0),2.0); - } - return out; -} - -void Fingerprint::generate_rinvssqrttable(){ - int buf = 5; - int m; - double r1; - double cutmax = pair->cutmax; - int res = pair->res; - rinvsqrttable = new double[res+buf]; - for (m=0;m<(res+buf);m++){ - r1 = cutmax*cutmax*(double)(m)/(double)(res); - rinvsqrttable[m] = 1/sqrt(r1); - } -} - - - - diff --git a/src/fingerprint.h b/src/fingerprint.h deleted file mode 100644 index 35645742f4..0000000000 --- a/src/fingerprint.h +++ /dev/null @@ -1,72 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@me.msstate.edu - ----------------------------------------------------------------------*/ -/* -“The research described and the resulting data presented herein, unless -otherwise noted, was funded under PE 0602784A, Project T53 "Military -Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, -managed by the U.S. Army Combat Capabilities Development Command (CCDC) and -the Engineer Research and Development Center (ERDC). The work described in -this document was conducted at CAVS, MSU. Permission was granted by ERDC -to publish this information. Any opinions, findings and conclusions or -recommendations expressed in this material are those of the author(s) and -do not necessarily reflect the views of the United States Army.​” - -DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 - -----------------*/ - -#ifndef FINGERPRINT_H_ -#define FINGERPRINT_H_ - -#include "pair_rann.h" - -namespace LAMMPS_NS { - - class Fingerprint { - public: - Fingerprint(PairRANN *); - virtual ~Fingerprint(); - virtual bool parse_values(char*,char*); - virtual void write_values(FILE *); - virtual void init(int*,int); - virtual void allocate(); - void init_screen(int); - virtual void compute_fingerprint(double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*);//no screen,no spin - virtual void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*);//screen - virtual void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*);//spin - virtual void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*);//spin,screen - virtual int get_length(); - virtual double cutofffunction(double,double, double); - virtual void generate_rinvssqrttable(); - bool spin; - bool screen; - int n_body_type;//i-j vs. i-j-k vs. i-j-k-l, etc. - bool empty; - bool fullydefined; - int startingneuron; - int id;//based on ordering of fingerprints listed for i-j in potential file - const char *style; - int* atomtypes; - double *rinvsqrttable; - double rc; - PairRANN *pair; - }; - -} - - -#endif /* FINGERPRINT_H_ */ diff --git a/src/fingerprint_bond.cpp b/src/fingerprint_bond.cpp deleted file mode 100644 index 1f8630ccb2..0000000000 --- a/src/fingerprint_bond.cpp +++ /dev/null @@ -1,917 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@me.msstate.edu - ----------------------------------------------------------------------*/ -/* -“The research described and the resulting data presented herein, unless -otherwise noted, was funded under PE 0602784A, Project T53 "Military -Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, -managed by the U.S. Army Combat Capabilities Development Command (CCDC) and -the Engineer Research and Development Center (ERDC). The work described in -this document was conducted at CAVS, MSU. Permission was granted by ERDC -to publish this information. Any opinions, findings and conclusions or -recommendations expressed in this material are those of the author(s) and -do not necessarily reflect the views of the United States Army.​” - -DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 - */ - -#include "fingerprint_bond.h" - - -using namespace LAMMPS_NS; - -Fingerprint_bond::Fingerprint_bond(PairRANN *pair) : Fingerprint(pair) -{ - n_body_type = 3; - dr = 0; - re = 0; - rc = 0; - alpha_k = new double [1]; - alpha_k[0] = -1; - k = 0; - m = 0; - id = -1; - style = "bond"; - atomtypes = new int [n_body_type]; - empty = true; - pair->allscreen = false; -} - -Fingerprint_bond::~Fingerprint_bond(){ - delete [] alpha_k; - delete [] atomtypes; - delete [] expcuttable; - delete [] dfctable; - for (int i=0;i<(m*(m+1))>>1;i++){ - delete [] coeff[i]; - delete [] coeffx[i]; - delete [] coeffy[i]; - delete [] coeffz[i]; - delete [] Mf[i]; - } - delete [] coeff; - delete [] coeffx; - delete [] coeffy; - delete [] coeffz; - delete [] Mf; - delete [] rinvsqrttable; -} - -bool Fingerprint_bond::parse_values(char * constant, char * line1){ - char **words=new char *[MAXLINE]; - int nwords,l; - nwords=0; - words[nwords++] = strtok(line1,": ,\t\n"); - while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; - nwords -= 1; - if (strcmp(constant,"re")==0){ - re = strtod(words[0],NULL); - } - else if (strcmp(constant,"rc")==0){ - rc = strtod(words[0],NULL); - } - else if (strcmp(constant,"alphak")==0){ - delete [] alpha_k; - alpha_k = new double [nwords]; - for (l=0;lerrorf("Undefined value for bond power"); - delete [] words; - if (re!=0.0 && rc!=0.0 && alpha_k[0]!=-1 && dr!=0.0 && m!=0 && k!=0)return true; - return false; -} - -void Fingerprint_bond::write_values(FILE *fid){ - int i; - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:re:\n",style,id); - fprintf(fid,"%f\n",re); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:rc:\n",style,id); - fprintf(fid,"%f\n",rc); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:alphak:\n",style,id); - for (i=0;ielementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:dr:\n",style,id); - fprintf(fid,"%f\n",dr); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:k:\n",style,id); - fprintf(fid,"%d\n",k); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:m:\n",style,id); - fprintf(fid,"%d\n",m); -} - -void Fingerprint_bond::init(int *i,int id){ - for (int j=0;jk = 0; - alpha_k = new double [1]; - alpha_k[0]=-1; - empty = false; - this->id = id; -} - -//number of neurons defined by this fingerprint -int Fingerprint_bond::get_length(){ - return m*k; -} - -void Fingerprint_bond::allocate(){ - generate_exp_cut_table(); - generate_coefficients(); - generate_rinvssqrttable(); -} - -//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop and do3bodyfeatureset_doubleneighborloop. -void Fingerprint_bond::generate_exp_cut_table(){ - int m,n; - double r1; - int buf = 5; - int res = pair->res; - double cutmax = pair->cutmax; - expcuttable = new double [(res+buf)*(this->k)]; - dfctable = new double [res+buf]; - for (m=0;m<(res+buf);m++){ - r1 = cutmax*cutmax*(double)(m)/(double)(res); - for (n=0;n<(this->k);n++){ - expcuttable[n+m*(this->k)] = exp(-alpha_k[n]/re*sqrt(r1))*cutofffunction(sqrt(r1),rc,dr); - } - if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ - dfctable[m]=0; - } - else{ - dfctable[m]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); - } - } -} - -//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop. -void Fingerprint_bond::generate_coefficients(){ //calculates multinomial coefficient for each term - int p,mb,mc; - int n,p1,i1; - mb = this->m; - mc=(mb*(mb+1))>>1; - coeff = new int *[mc]; - coeffx = new int *[mc]; - coeffy = new int *[mc]; - coeffz = new int *[mc]; - for (p=0;pm+1]; - for (p=0;pm+1;p++){ - M[p]=0; - } - for (p1=0;p1sims[sid]; - ilist = sim->ilist; - numneigh = sim->numneigh; - i = ilist[ii]; -// jnum = numneigh[i]; - //select the more efficient algorithm for this particular potential and environment. - if (jnum*2>(m+1)*m*20){ - do3bodyfeatureset_singleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,sid,xn,yn,zn,tn,jnum,jl); - } - else{ - do3bodyfeatureset_doubleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,sid,xn,yn,zn,tn,jnum,jl); - - } -} - -//Called by do3bodyfeatureset. Algorithm for high neighbor numbers and small series of bond angle powers -void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ - int i,j,jj,itype,jtype,kk,m,n,mcount,a,a1,a2,ai; - double xtmp,ytmp,ztmp,delx,dely,delz,rsq; - int *ilist,*jlist,*numneigh,**firstneigh; - int count=0; - PairRANN::Simulation *sim = &pair->sims[sid]; -// double **x = sim->x; - int *type = sim->type; - double cutmax = pair->cutmax; - int res = pair->res; - double cutinv2 = 1/cutmax/cutmax; - ilist = sim->ilist; -// numneigh = sim->numneigh; -// firstneigh = sim->firstneigh; - int nelements=pair->nelements; - i = ilist[ii]; - itype = pair->map[type[i]]; - int f = pair->net[itype].dimensions[0]; -// xtmp = x[i][0]; -// ytmp = x[i][1]; -// ztmp = x[i][2]; -// jlist = firstneigh[i]; -// jnum = numneigh[i]; - double expr[jnum][this->k+12]; - int p = this->k; - int countmb=((this->m)*(this->m+1))>>1; - // calculate interpolation expr, rinvs and dfc, for each neighbor - for (jj = 0; jj < jnum; jj++) { -// j = jlist[jj]; -// j &= NEIGHMASK; -// jtype = pair->map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype && atomtypes[2] != nelements && atomtypes[2] != jtype){ - expr[jj][0]=0; - continue; - } -// delx = xtmp - x[j][0]; -// dely = ytmp - x[j][1]; -// delz = ztmp - x[j][2]; - delx = xn[jj]; - dely = yn[jj]; - delz = zn[jj]; - rsq = delx*delx + dely*dely + delz*delz; - if (rsq>rc*rc){ - expr[jj][0]=0; - continue; - } - double r1 = (rsq*((double)res)*cutinv2); - int m1 = (int)r1; - r1 = r1-trunc(r1); - double *p0 = &expcuttable[(m1-1)*this->k]; - double *p1 = &expcuttable[m1*this->k]; - double *p2 = &expcuttable[(m1+1)*this->k]; - double *p3 = &expcuttable[(m1+2)*this->k]; - for (kk=0;kkk;kk++){ - expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); - } - double* q = &dfctable[m1-1]; - double* ri = &rinvsqrttable[m1-1]; - double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); - double rinvs = ri[1] + 0.5 * r1*(ri[2] - ri[0] + r1*(2.0*ri[0] - 5.0*ri[1] + 4.0*ri[2] - ri[3] + r1*(3.0*(ri[1] - ri[2]) + ri[3] - ri[0]))); - - expr[jj][p]=delx*rinvs; - expr[jj][p+1]=dely*rinvs; - expr[jj][p+2]=delz*rinvs; - //Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy. - if (expr[jj][p]*expr[jj][p]<0.000000000001){ - expr[jj][p] = 0.000001; - } - if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001){ - expr[jj][p+1] = 0.000001; - } - if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001){ - expr[jj][p+2] = 0.000001; - } - expr[jj][p+3] = -dfc*expr[jj][p]; - expr[jj][p+4] = rinvs/expr[jj][p]; - expr[jj][p+5] = rinvs*expr[jj][p]; - expr[jj][p+6] = -dfc*expr[jj][p+1]; - expr[jj][p+7] = rinvs/expr[jj][p+1]; - expr[jj][p+8] = rinvs*expr[jj][p+1]; - expr[jj][p+9] = -dfc*expr[jj][p+2]; - expr[jj][p+10] = rinvs/expr[jj][p+2]; - expr[jj][p+11] = rinvs*expr[jj][p+2]; - } - - int kb = this->k; - int mb = this->m; - count = startingneuron; - double Bb[mb]; - double dBbx; - double dBby; - double dBbz; -// double dBbx1[mb]; -// double dBby1[mb]; -// double dBbz1[mb]; - double yprod; - for (mcount=0;mcountcoeffx[mcount]; - int *coeffy = this->coeffy[mcount]; - int *coeffz = this->coeffz[mcount]; - int *coeff = this->coeff[mcount]; - a = mb+1; - for (a1=0;a1map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype){ - continue; - } - double yprod = expr[jj][ai]; - double *y4 = &expr[jj][p]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[2] != nelements && atomtypes[2] != jtype){ - continue; - } - double yprod = expr[jj][ai]; - double *y4 = &expr[jj][p]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[2] != nelements && atomtypes[2] != jtype){ - continue; - } - double *y3 = &expr[jj][p+3]; - double *y4 = &expr[jj][p]; - ai = n; - yprod = expr[jj][ai]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype){ - continue; - } - double *y3 = &expr[jj][p+3]; - double *y4 = &expr[jj][p]; - ai = n; - yprod = expr[jj][ai]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype){ - continue; - } - double *y3 = &expr[jj][p+3]; - double *y4 = &expr[jj][p]; - ai = n; - yprod = expr[jj][ai]; - for (a2=0;a2sims[sid]; - double **x = sim->x; - int *type = sim->type; - int nelements = pair->nelements; - int res = pair->res; - double cutmax = pair->cutmax; - double cutinv2 = 1/cutmax/cutmax; - ilist = sim->ilist; -// numneigh = sim->numneigh; -// firstneigh = sim->firstneigh; - i = ilist[ii]; - itype = pair->map[type[i]]; - int f = pair->net[itype].dimensions[0]; -// xtmp = x[i][0]; -// ytmp = x[i][1]; -// ztmp = x[i][2]; -// jlist = firstneigh[i]; -// jnum = numneigh[i]; - double expr[jnum][this->k]; - double y[jnum][3]; - double ri[jnum]; - double dfc[jnum]; - int kb = this->k; - int mb = this->m; - double c41[this->k]; - double c51[this->k]; - double c61[this->k]; - double ct[this->k]; - for (jj = 0; jj < jnum; jj++) { -// j = jlist[jj]; -// j &= NEIGHMASK; -// jtype = pair->map[type[j]]; - jtype = tn[jj]; - if (jtypes != nelements && jtypes != jtype && ktypes != nelements && ktypes != jtype){ - expr[jj][0]=0; - continue; - } -// delx = xtmp - x[j][0]; -// dely = ytmp - x[j][1]; -// delz = ztmp - x[j][2]; - delx = xn[jj]; - dely = yn[jj]; - delz = zn[jj]; - rsq = delx*delx + dely*dely + delz*delz; - if (rsq>rc*rc){ - expr[jj][0]=0; - continue; - } - double r1 = (rsq*((double)res)*cutinv2); - int m1 = (int)r1; - if (!(m1>=1 && m1 <= res))pair->errorf("Neighbor list is invalid.");//usually results from nan somewhere. - r1 = r1-trunc(r1); - double *p0 = &expcuttable[(m1-1)*this->k]; - double *p1 = &expcuttable[m1*this->k]; - double *p2 = &expcuttable[(m1+1)*this->k]; - double *p3 = &expcuttable[(m1+2)*this->k]; - for (kk=0;kkk;kk++){ - expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); - } - double* q = &dfctable[m1-1]; - double* r2 = &rinvsqrttable[m1-1]; - dfc[jj] = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); - ri[jj] = r2[1] + 0.5 * r1*(r2[2] - r2[0] + r1*(2.0*r2[0] - 5.0*r2[1] + 4.0*r2[2] - r2[3] + r1*(3.0*(r2[1] - r2[2]) + r2[3] - r2[0]))); - y[jj][0]=delx*ri[jj]; - y[jj][1]=dely*ri[jj]; - y[jj][2]=delz*ri[jj]; - } -// if (i==5){ -// for (jj=0;jjmap[type[j]]; - jtype = tn[jj]; - if (jtypes != nelements && jtypes != jtype){ - continue; - } - for (n = 0;nk;n++){ - ct[n] = 2*alpha_k[n]/re; - c41[n]=(-ct[n]+2*dfc[jj])*y[jj][0]; - c51[n]=(-ct[n]+2*dfc[jj])*y[jj][1]; - c61[n]= (-ct[n]+2*dfc[jj])*y[jj][2]; - } - if (jtypes==ktypes){ - for (kk=jj+1;kk< jnum; kk++){ - if (expr[kk][0]==0)continue; -// int k1 = jlist[kk]; -// k1 &= NEIGHMASK; -// ktype = pair->map[type[k1]]; - ktype = tn[kk]; - if (ktypes != nelements && ktypes != ktype){ - continue; - } - count = startingneuron; - double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); - double c1 = 2*ri[jj]*(y[kk][0]-dot*y[jj][0]); - double c2 = 2*ri[jj]*(y[kk][1]-dot*y[jj][1]); - double c3 = 2*ri[jj]*(y[kk][2]-dot*y[jj][2]); - double c10 = 2*ri[kk]*(y[jj][0]-dot*y[kk][0]); - double c11 = 2*ri[kk]*(y[jj][1]-dot*y[kk][1]); - double c12 = 2*ri[kk]*(y[jj][2]-dot*y[kk][2]); -// double c1 = 2*ri[jj]*y[kk][0]*(1-y[jj][0]*y[jj][0]); -// double c2 = 2*ri[jj]*y[kk][1]*(1-y[jj][1]*y[jj][1]); -// double c3 = 2*ri[jj]*y[kk][2]*(1-y[jj][2]*y[jj][2]); -// double c10 = 2*ri[kk]*y[jj][0]*(1-y[kk][0]*y[kk][0]); -// double c11 = 2*ri[kk]*y[jj][1]*(1-y[kk][1]*y[kk][1]); -// double c12 = 2*ri[kk]*y[jj][2]*(1-y[kk][2]*y[kk][2]); - for (n=0;nmap[type[k1]]; - ktype = tn[kk]; - if (ktypes != nelements && ktypes != ktype){ - continue; - } - count = startingneuron; - double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); - double c1 = ri[jj]*(y[kk][0]-dot*y[jj][0]); - double c2 = ri[jj]*(y[kk][1]-dot*y[jj][1]); - double c3 = ri[jj]*(y[kk][2]-dot*y[jj][2]); - double c10 = ri[kk]*(y[jj][0]-dot*y[kk][0]); - double c11 = ri[kk]*(y[jj][1]-dot*y[kk][1]); - double c12 = ri[kk]*(y[jj][2]-dot*y[kk][2]); -// double c1 = 2*ri[jj]*y[kk][0]*(1-y[jj][0]*y[jj][0]); -// double c2 = 2*ri[jj]*y[kk][1]*(1-y[jj][1]*y[jj][1]); -// double c3 = 2*ri[jj]*y[kk][2]*(1-y[jj][2]*y[jj][2]); -// double c10 = 2*ri[kk]*y[jj][0]*(1-y[kk][0]*y[kk][0]); -// double c11 = 2*ri[kk]*y[jj][1]*(1-y[kk][1]*y[kk][1]); -// double c12 = 2*ri[kk]*y[jj][2]*(1-y[kk][2]*y[kk][2]); - for (n=0;ndoscreen = true; - screen = true; -} - -Fingerprint_bondscreened::~Fingerprint_bondscreened(){ - delete [] alpha_k; - delete [] atomtypes; - delete [] expcuttable; - delete [] dfctable; - for (int i=0;i<(m*(m+1))>>1;i++){ - delete [] coeff[i]; - delete [] coeffx[i]; - delete [] coeffy[i]; - delete [] coeffz[i]; - delete [] Mf[i]; - } - delete [] coeff; - delete [] coeffx; - delete [] coeffy; - delete [] coeffz; - delete [] Mf; - delete [] rinvsqrttable; -} - -bool Fingerprint_bondscreened::parse_values(char * constant, char * line1){ - char **words=new char *[MAXLINE]; - int nwords,l; - nwords=0; - words[nwords++] = strtok(line1,": ,\t\n"); - while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; - nwords -= 1; - if (strcmp(constant,"re")==0){ - re = strtod(words[0],NULL); - } - else if (strcmp(constant,"rc")==0){ - rc = strtod(words[0],NULL); - } - else if (strcmp(constant,"alphak")==0){ - delete [] alpha_k; - alpha_k = new double [nwords]; - for (l=0;lerrorf("Undefined value for bond power"); - delete [] words; - if (re!=0.0 && rc!=0.0 && alpha_k[0]!=-1 && dr!=0.0 && m!=0 && k!=0)return true; - return false; -} - -void Fingerprint_bondscreened::write_values(FILE *fid){ - int i; - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:re:\n",style,id); - fprintf(fid,"%f\n",re); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:rc:\n",style,id); - fprintf(fid,"%f\n",rc); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:alphak:\n",style,id); - for (i=0;ielementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:dr:\n",style,id); - fprintf(fid,"%f\n",dr); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:k:\n",style,id); - fprintf(fid,"%d\n",k); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:m:\n",style,id); - fprintf(fid,"%d\n",m); -} - -void Fingerprint_bondscreened::init(int *i,int id){ - for (int j=0;jk = 0; - alpha_k = new double [1]; - alpha_k[0]=-1; - empty = false; - this->id = id; -} - -//number of neurons defined by this fingerprint -int Fingerprint_bondscreened::get_length(){ - return m*k; -} - -void Fingerprint_bondscreened::allocate(){ - generate_exp_cut_table(); - generate_coefficients(); - generate_rinvssqrttable(); -} - -//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop and do3bodyfeatureset_doubleneighborloop. -void Fingerprint_bondscreened::generate_exp_cut_table(){ - int m,n; - double r1; - int buf = 5; - int res = pair->res; - double cutmax = pair->cutmax; - expcuttable = new double [(res+buf)*(this->k)]; - dfctable = new double [res+buf]; - for (m=0;m<(res+buf);m++){ - r1 = cutmax*cutmax*(double)(m)/(double)(res); - for (n=0;n<(this->k);n++){ - expcuttable[n+m*(this->k)] = exp(-alpha_k[n]/re*sqrt(r1))*cutofffunction(sqrt(r1),rc,dr); - } - if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ - dfctable[m]=0; - } - else{ - dfctable[m]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); - } - } -} - - -//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop. -void Fingerprint_bondscreened::generate_coefficients(){ //calculates multinomial coefficient for each term - int p,mb,mc; - int n,p1,i1; - mb = this->m; - mc=(mb*(mb+1))>>1; - coeff = new int *[mc]; - coeffx = new int *[mc]; - coeffy = new int *[mc]; - coeffz = new int *[mc]; - for (p=0;pm+1]; - for (p=0;pm+1;p++){ - M[p]=0; - } - for (p1=0;p1sims[sid]; -// ilist = sim->ilist; -// numneigh = sim->numneigh; -// i = ilist[ii]; -// jnum = numneigh[i]; - //select the more efficient algorithm for this particular potential and environment. - if (jnum*2>(m+1)*m*20){ - do3bodyfeatureset_singleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,sid,xn,yn,zn,tn,jnum,jl); - } - else{ - do3bodyfeatureset_doubleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,sid,xn,yn,zn,tn,jnum,jl); - - } -} - -//Called by do3bodyfeatureset. Algorithm for high neighbor numbers and small series of bond angle powers -void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ - int i,j,jj,itype,jtype,kk,m,n,mcount,a,a1,a2,ai; - double xtmp,ytmp,ztmp,delx,dely,delz,rsq; - int *ilist,*jlist,*numneigh,**firstneigh; - int count=0; - PairRANN::Simulation *sim = &pair->sims[sid]; -// double **x = sim->x; - //double **f = atom->f; - int *type = sim->type; - double cutmax = pair->cutmax; - int res = pair->res; - double cutinv2 = 1/cutmax/cutmax; - ilist = sim->ilist; -// numneigh = sim->numneigh; -// firstneigh = sim->firstneigh; - int nelements=pair->nelements; - i = ilist[ii]; - itype = pair->map[type[i]]; - int f = pair->net[itype].dimensions[0]; -// xtmp = x[i][0]; -// ytmp = x[i][1]; -// ztmp = x[i][2]; -// jlist = firstneigh[i]; -// jnum = numneigh[i]; - double expr[jnum][this->k+12]; - int p = this->k; - int countmb=((this->m)*(this->m+1))>>1; - // calculate interpolation expr, rinvs and dfc, for each neighbor - for (jj = 0; jj < jnum; jj++) { - if (Bij[jj]==false){continue;} -// j = jlist[jj]; -// j &= NEIGHMASK; -// jtype = pair->map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype && atomtypes[2] != nelements && atomtypes[2] != jtype){ - expr[jj][0]=0; - continue; - } -// delx = xtmp - x[j][0]; -// dely = ytmp - x[j][1]; -// delz = ztmp - x[j][2]; - delx=xn[jj]; - dely=yn[jj]; - delz=zn[jj]; - rsq = delx*delx + dely*dely + delz*delz; - if (rsq>rc*rc){ - expr[jj][0]=0; - continue; - } - double r1 = (rsq*((double)res)*cutinv2); - int m1 = (int)r1; - r1 = r1-trunc(r1); - double *p0 = &expcuttable[(m1-1)*this->k]; - double *p1 = &expcuttable[m1*this->k]; - double *p2 = &expcuttable[(m1+1)*this->k]; - double *p3 = &expcuttable[(m1+2)*this->k]; - for (kk=0;kkk;kk++){ - expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); - expr[jj][kk] *= Sik[jj]; - } - double* q = &dfctable[m1-1]; - double* ri = &rinvsqrttable[m1-1]; - double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); - double rinvs = ri[1] + 0.5 * r1*(ri[2] - ri[0] + r1*(2.0*ri[0] - 5.0*ri[1] + 4.0*ri[2] - ri[3] + r1*(3.0*(ri[1] - ri[2]) + ri[3] - ri[0]))); - - expr[jj][p]=delx*rinvs; - expr[jj][p+1]=dely*rinvs; - expr[jj][p+2]=delz*rinvs; - //Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy. - if (expr[jj][p]*expr[jj][p]<0.000000000001){ - expr[jj][p] = 0.000001; - } - if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001){ - expr[jj][p+1] = 0.000001; - } - if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001){ - expr[jj][p+2] = 0.000001; - } - expr[jj][p+3] = -dfc*expr[jj][p]-dSikx[jj]; - expr[jj][p+4] = rinvs/expr[jj][p]; - expr[jj][p+5] = rinvs*expr[jj][p]; - expr[jj][p+6] = -dfc*expr[jj][p+1]-dSiky[jj]; - expr[jj][p+7] = rinvs/expr[jj][p+1]; - expr[jj][p+8] = rinvs*expr[jj][p+1]; - expr[jj][p+9] = -dfc*expr[jj][p+2]-dSikz[jj]; - expr[jj][p+10] = rinvs/expr[jj][p+2]; - expr[jj][p+11] = rinvs*expr[jj][p+2]; - } - - int kb = this->k; - int mb = this->m; -// int ind = kb+mb*kb; - count = startingneuron; - double Bb[mb]; - double dBbx; - double dBby; - double dBbz; - double dBbx1[mb]; - double dBby1[mb]; - double dBbz1[mb]; - double yprod; - for (mcount=0;mcountcoeffx[mcount]; - int *coeffy = this->coeffy[mcount]; - int *coeffz = this->coeffz[mcount]; - int *coeff = this->coeff[mcount]; - a = mb+1; - for (a1=0;a1map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype){ - continue; - } - double yprod = expr[jj][ai]; - double *y4 = &expr[jj][p]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[2] != nelements && atomtypes[2] != jtype){ - continue; - } - double yprod = expr[jj][ai]; - double *y4 = &expr[jj][p]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[2] != nelements && atomtypes[2] != jtype){ - continue; - } - double *y3 = &expr[jj][p+3]; - double *y4 = &expr[jj][p]; - ai = n; - yprod = expr[jj][ai]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype){ - continue; - } - double *y3 = &expr[jj][p+3]; - double *y4 = &expr[jj][p]; - ai = n; - yprod = expr[jj][ai]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype){ - continue; - } - double *y3 = &expr[jj][p+3]; - double *y4 = &expr[jj][p]; - ai = n; - yprod = expr[jj][ai]; - for (a2=0;a2sims[sid]; -// double **x = sim->x; - int *type = sim->type; - int nelements = pair->nelements; - int res = pair->res; - double cutmax = pair->cutmax; - double cutinv2 = 1/cutmax/cutmax; - ilist = sim->ilist; -// numneigh = sim->numneigh; -// firstneigh = sim->firstneigh; - i = ilist[ii]; - itype = pair->map[type[i]]; - int f = pair->net[itype].dimensions[0]; -// xtmp = x[i][0]; -// ytmp = x[i][1]; -// ztmp = x[i][2]; -// jlist = firstneigh[i]; -// jnum = numneigh[i]; - double expr[jnum][this->k]; - double y[jnum][3]; - double ri[jnum]; - double dfc[jnum]; - int kb = this->k; - int mb = this->m; - double Bijk[kb][mb]; - double c41[this->k]; - double c51[this->k]; - double c61[this->k]; - double ct[this->k]; - for (jj = 0; jj < jnum; jj++) { - if (Bij[jj]==false){continue;} -// j = jlist[jj]; -// j &= NEIGHMASK; -// jtype = pair->map[type[j]]; - jtype = tn[jj]; - if (jtypes != nelements && jtypes != jtype && ktypes != nelements && ktypes != jtype){ - expr[jj][0]=0; - continue; - } -// delx = xtmp - x[j][0]; -// dely = ytmp - x[j][1]; -// delz = ztmp - x[j][2]; - delx = xn[jj]; - dely = yn[jj]; - delz = zn[jj]; - rsq = delx*delx + dely*dely + delz*delz; - if (rsq>rc*rc){ - expr[jj][0]=0; - continue; - } - double r1 = (rsq*((double)res)*cutinv2); - int m1 = (int)r1; - if (!(m1>=1 && m1 <= res))pair->errorf("Neighbor list is invalid.");//usually results from nan somewhere. - r1 = r1-trunc(r1); - double *p0 = &expcuttable[(m1-1)*this->k]; - double *p1 = &expcuttable[m1*this->k]; - double *p2 = &expcuttable[(m1+1)*this->k]; - double *p3 = &expcuttable[(m1+2)*this->k]; - for (kk=0;kkk;kk++){ - expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); - expr[jj][kk] *= Sik[jj]; - } - double* q = &dfctable[m1-1]; - double* r2 = &rinvsqrttable[m1-1]; - dfc[jj] = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); - ri[jj] = r2[1] + 0.5 * r1*(r2[2] - r2[0] + r1*(2.0*r2[0] - 5.0*r2[1] + 4.0*r2[2] - r2[3] + r1*(3.0*(r2[1] - r2[2]) + r2[3] - r2[0]))); - y[jj][0]=delx*ri[jj]; - y[jj][1]=dely*ri[jj]; - y[jj][2]=delz*ri[jj]; - } - for (jj = 0; jj < jnum; jj++) { - if (Bij[jj]==false){continue;} - if (expr[jj][0]==0)continue; -// j = jlist[jj]; -// j &= NEIGHMASK; -// jtype = pair->map[type[j]]; - jtype =tn[jj]; - if (jtypes != nelements && jtypes != jtype){ - continue; - } - for (n = 0;nk;n++){ - ct[n] = alpha_k[n]/re; - c41[n]=(-ct[n]+dfc[jj])*y[jj][0]+dSikx[jj]; - c51[n]=(-ct[n]+dfc[jj])*y[jj][1]+dSiky[jj]; - c61[n]=(-ct[n]+dfc[jj])*y[jj][2]+dSikz[jj]; - } - for (n=0;nmap[type[k1]]; - ktype = tn[kk]; - if (ktypes != nelements && ktypes != ktype){ - continue; - } - count = startingneuron; - double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); - double c1 = ri[jj]*(y[kk][0]-dot*y[jj][0]); - double c2 = ri[jj]*(y[kk][1]-dot*y[jj][1]); - double c3 = ri[jj]*(y[kk][2]-dot*y[jj][2]); - double c10 = ri[kk]*(y[jj][0]-dot*y[kk][0]); - double c11 = ri[kk]*(y[jj][1]-dot*y[kk][1]); - double c12 = ri[kk]*(y[jj][2]-dot*y[kk][2]); - for (n=0;nSik[kk]*pair->Sik[jj]; -// double c4 = c41[n]+4*pair->dSikx[kk]; -// double c5 = c51[n]+4*pair->dSiky[kk]; -// double c6 = c61[n]+4*pair->dSikz[kk]; -// //m=0 -// features[count]+=dot1; -// Bijk[n][0]+=dot1; -// dfeaturesx[jj*f+count]+=dot1*c4; -// dfeaturesy[jj*f+count]+=dot1*c5; -// dfeaturesz[jj*f+count]+=dot1*c6; -// c4*=dot; -// c5*=dot; -// c6*=dot; -// count++; -// for (m=1;mmap[type[k1]]; - ktype = tn[kk]; - if (ktypes != nelements && ktypes != ktype){ - continue; - } - count = startingneuron; - for (n=0;nBij[kk]==false){continue;} -// if (expr[kk][0]==0)continue; -// int k1 = jlist[kk]; -// k1 &= NEIGHMASK; -// ktype = pair->map[type[k1]]; -// if (ktypes != nelements && ktypes != ktype){ -// continue; -// } -// count = startingneuron; -// double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); -// double c1 = ri[jj]*(y[kk][0]-dot*y[jj][0]); -// double c2 = ri[jj]*(y[kk][1]-dot*y[jj][1]); -// double c3 = ri[jj]*(y[kk][2]-dot*y[jj][2]); -// double c10 = ri[kk]*(y[jj][0]-dot*y[kk][0]); -// double c11 = ri[kk]*(y[jj][1]-dot*y[kk][1]); -// double c12 = ri[kk]*(y[jj][2]-dot*y[kk][2]); -// for (n=0;nSik[kk]*pair->Sik[jj]; -// double c4 = c41[n]/2; -// double c5 = c51[n]/2; -// double c6 = c61[n]/2; -// double ct2 = -ct[n]/2+dfc[kk]; -// double c42 = ct2*y[kk][0]+pair->dSikx[kk]; -// double c52 = ct2*y[kk][1]+pair->dSiky[kk]; -// double c62 = ct2*y[kk][2]+pair->dSikz[kk]; -// //m=0 -// features[count]+=dot1; -// dfeaturesx[jj*f+count]+=dot1*c4; -// dfeaturesy[jj*f+count]+=dot1*c5; -// dfeaturesz[jj*f+count]+=dot1*c6; -// dfeaturesx[kk*f+count]+=dot1*c42; -// dfeaturesy[kk*f+count]+=dot1*c52; -// dfeaturesz[kk*f+count]+=dot1*c62; -// c4*=dot; -// c5*=dot; -// c6*=dot; -// c42*=dot; -// c52*=dot; -// c62*=dot; -// count++; -// for (m=1;mdoscreen = true; - screen = true; - pair->dospin = true; - spin = true; -} - -Fingerprint_bondscreenedspin::~Fingerprint_bondscreenedspin(){ - delete [] alpha_k; - delete [] atomtypes; - delete [] expcuttable; - delete [] dfctable; - for (int i=0;i<(m*(m+1))>>1;i++){ - delete [] coeff[i]; - delete [] coeffx[i]; - delete [] coeffy[i]; - delete [] coeffz[i]; - delete [] Mf[i]; - } - delete [] coeff; - delete [] coeffx; - delete [] coeffy; - delete [] coeffz; - delete [] Mf; - delete [] rinvsqrttable; -} - -bool Fingerprint_bondscreenedspin::parse_values(char * constant, char * line1){ - char **words=new char *[MAXLINE]; - int nwords,l; - nwords=0; - words[nwords++] = strtok(line1,": ,\t\n"); - while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; - nwords -= 1; - if (strcmp(constant,"re")==0){ - re = strtod(words[0],NULL); - } - else if (strcmp(constant,"rc")==0){ - rc = strtod(words[0],NULL); - } - else if (strcmp(constant,"alphak")==0){ - delete [] alpha_k; - alpha_k = new double [nwords]; - for (l=0;lerrorf("Undefined value for bond power"); - delete [] words; - if (re!=0.0 && rc!=0.0 && alpha_k[0]!=-1 && dr!=0.0 && m!=0 && k!=0)return true; - return false; -} - -void Fingerprint_bondscreenedspin::write_values(FILE *fid){ - int i; - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:re:\n",style,id); - fprintf(fid,"%f\n",re); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:rc:\n",style,id); - fprintf(fid,"%f\n",rc); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:alphak:\n",style,id); - for (i=0;ielementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:dr:\n",style,id); - fprintf(fid,"%f\n",dr); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:k:\n",style,id); - fprintf(fid,"%d\n",k); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:m:\n",style,id); - fprintf(fid,"%d\n",m); -} - -void Fingerprint_bondscreenedspin::init(int *i,int id){ - for (int j=0;jk = 0; - alpha_k = new double [1]; - alpha_k[0]=-1; - empty = false; - this->id = id; -} - -//number of neurons defined by this fingerprint -int Fingerprint_bondscreenedspin::get_length(){ - return m*k; -} - -void Fingerprint_bondscreenedspin::allocate(){ - generate_exp_cut_table(); - generate_coefficients(); - generate_rinvssqrttable(); -} - -//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop and do3bodyfeatureset_doubleneighborloop. -void Fingerprint_bondscreenedspin::generate_exp_cut_table(){ - int m,n; - double r1; - int buf = 5; - int res = pair->res; - double cutmax = pair->cutmax; - expcuttable = new double [(res+buf)*(this->k)]; - dfctable = new double [res+buf]; - for (m=0;m<(res+buf);m++){ - r1 = cutmax*cutmax*(double)(m)/(double)(res); - for (n=0;n<(this->k);n++){ - expcuttable[n+m*(this->k)] = exp(-alpha_k[n]/re*sqrt(r1))*cutofffunction(sqrt(r1),rc,dr); - } - if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ - dfctable[m]=0; - } - else{ - dfctable[m]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); - } - } -} - - -//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop. -void Fingerprint_bondscreenedspin::generate_coefficients(){ //calculates multinomial coefficient for each term - int p,mb,mc; - int n,p1,i1; - mb = this->m; - mc=(mb*(mb+1))>>1; - coeff = new int *[mc]; - coeffx = new int *[mc]; - coeffy = new int *[mc]; - coeffz = new int *[mc]; - for (p=0;pm+1]; - for (p=0;pm+1;p++){ - M[p]=0; - } - for (p1=0;p1sims[sid]; -// ilist = sim->ilist; -// numneigh = sim->numneigh; -// i = ilist[ii]; -// jnum = numneigh[i]; - //select the more efficient algorithm for this particular potential and environment. - if (jnum*2>(m+1)*m*20){ - do3bodyfeatureset_singleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,dspinx,dspiny,dspinz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,sid,xn,yn,zn,tn,jnum,jl); - } - else{ - do3bodyfeatureset_doubleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,dspinx,dspiny,dspinz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,sid,xn,yn,zn,tn,jnum,jl); - - } -} - -//Called by do3bodyfeatureset. Algorithm for high neighbor numbers and small series of bond angle powers -void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz, double *dspinx, double *dspiny, double *dspinz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ - int i,j,jj,itype,jtype,kk,m,n,mcount,a,a1,a2,ai; - double xtmp,ytmp,ztmp,delx,dely,delz,rsq; - int *ilist,*jlist,*numneigh,**firstneigh; - int count=0; - PairRANN::Simulation *sim = &pair->sims[sid]; -// double **x = sim->x; - //double **f = atom->f; - int *type = sim->type; - double cutmax = pair->cutmax; - int res = pair->res; - double cutinv2 = 1/cutmax/cutmax; - ilist = sim->ilist; -// numneigh = sim->numneigh; -// firstneigh = sim->firstneigh; - int nelements=pair->nelements; - i = ilist[ii]; - itype = pair->map[type[i]]; - int f = pair->net[itype].dimensions[0]; -// xtmp = x[i][0]; -// ytmp = x[i][1]; -// ztmp = x[i][2]; -// jlist = firstneigh[i]; -// jnum = numneigh[i]; - double expr[jnum][this->k+12]; - int p = this->k; - int countmb=((this->m)*(this->m+1))>>1; - double *si = sim->s[i]; - // calculate interpolation expr, rinvs and dfc, for each neighbor - for (jj = 0; jj < jnum; jj++) { - if (Bij[jj]==false){continue;} -// j = jlist[jj]; -// j &= NEIGHMASK; -// jtype = pair->map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype && atomtypes[2] != nelements && atomtypes[2] != jtype){ - expr[jj][0]=0; - continue; - } -// delx = xtmp - x[j][0]; -// dely = ytmp - x[j][1]; -// delz = ztmp - x[j][2]; - delx=xn[jj]; - dely=yn[jj]; - delz=zn[jj]; - rsq = delx*delx + dely*dely + delz*delz; - if (rsq>rc*rc){ - expr[jj][0]=0; - continue; - } - double r1 = (rsq*((double)res)*cutinv2); - int m1 = (int)r1; - r1 = r1-trunc(r1); - double *p0 = &expcuttable[(m1-1)*this->k]; - double *p1 = &expcuttable[m1*this->k]; - double *p2 = &expcuttable[(m1+1)*this->k]; - double *p3 = &expcuttable[(m1+2)*this->k]; - for (kk=0;kkk;kk++){ - expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); - expr[jj][kk] *= Sik[jj]; - } - double* q = &dfctable[m1-1]; - double* ri = &rinvsqrttable[m1-1]; - double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); - double rinvs = ri[1] + 0.5 * r1*(ri[2] - ri[0] + r1*(2.0*ri[0] - 5.0*ri[1] + 4.0*ri[2] - ri[3] + r1*(3.0*(ri[1] - ri[2]) + ri[3] - ri[0]))); - - expr[jj][p]=delx*rinvs; - expr[jj][p+1]=dely*rinvs; - expr[jj][p+2]=delz*rinvs; - //Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy. - if (expr[jj][p]*expr[jj][p]<0.000000000001){ - expr[jj][p] = 0.000001; - } - if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001){ - expr[jj][p+1] = 0.000001; - } - if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001){ - expr[jj][p+2] = 0.000001; - } - expr[jj][p+3] = -dfc*expr[jj][p]-dSikx[jj]; - expr[jj][p+4] = rinvs/expr[jj][p]; - expr[jj][p+5] = rinvs*expr[jj][p]; - expr[jj][p+6] = -dfc*expr[jj][p+1]-dSiky[jj]; - expr[jj][p+7] = rinvs/expr[jj][p+1]; - expr[jj][p+8] = rinvs*expr[jj][p+1]; - expr[jj][p+9] = -dfc*expr[jj][p+2]-dSikz[jj]; - expr[jj][p+10] = rinvs/expr[jj][p+2]; - expr[jj][p+11] = rinvs*expr[jj][p+2]; - } - - int kb = this->k; - int mb = this->m; -// int ind = kb+mb*kb; - count = startingneuron; - double Bb[mb]; - double Bbs[mb]; - double dBbx; - double dBby; - double dBbz; -// double dBbx1[mb]; -// double dBby1[mb]; -// double dBbz1[mb]; - double yprod; - for (mcount=0;mcountcoeffx[mcount]; - int *coeffy = this->coeffy[mcount]; - int *coeffz = this->coeffz[mcount]; - int *coeff = this->coeff[mcount]; - a = mb+1; - for (a1=0;a1map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype){ - continue; - } - j = jl[jj]; - double *sj = sim->s[j]; - double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - double yprod = expr[jj][ai]; - double *y4 = &expr[jj][p]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[2] != nelements && atomtypes[2] != jtype){ - continue; - } - j = jl[jj]; - double *sj = sim->s[j]; - double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - double yprod = expr[jj][ai]; - double *y4 = &expr[jj][p]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[2] != nelements && atomtypes[2] != jtype){ - continue; - } - j = jl[jj]; - double *sj = sim->s[j]; - double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - double *y3 = &expr[jj][p+3]; - double *y4 = &expr[jj][p]; - ai = n; - yprod = expr[jj][ai]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype){ - continue; - } - j = jl[jj]; - double *sj = sim->s[j]; - double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - double *y3 = &expr[jj][p+3]; - double *y4 = &expr[jj][p]; - ai = n; - yprod = expr[jj][ai]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype){ - continue; - } - j = jl[jj]; - double *sj = sim->s[j]; - double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - double *y3 = &expr[jj][p+3]; - double *y4 = &expr[jj][p]; - ai = n; - yprod = expr[jj][ai]; - for (a2=0;a2sims[sid]; -// double **x = sim->x; - int *type = sim->type; - int nelements = pair->nelements; - int res = pair->res; - double cutmax = pair->cutmax; - double cutinv2 = 1/cutmax/cutmax; - ilist = sim->ilist; -// numneigh = sim->numneigh; -// firstneigh = sim->firstneigh; - i = ilist[ii]; - itype = pair->map[type[i]]; - int f = pair->net[itype].dimensions[0]; -// xtmp = x[i][0]; -// ytmp = x[i][1]; -// ztmp = x[i][2]; -// jlist = firstneigh[i]; -// jnum = numneigh[i]; - double expr[jnum][this->k]; - double y[jnum][3]; - double ri[jnum]; - double dfc[jnum]; - int kb = this->k; - int mb = this->m; - double Bijk[kb][mb]; - double c41[this->k]; - double c51[this->k]; - double c61[this->k]; - double ct[this->k]; - double *si = sim->s[i]; - for (jj = 0; jj < jnum; jj++) { - if (Bij[jj]==false){continue;} -// j = jlist[jj]; -// j &= NEIGHMASK; -// jtype = pair->map[type[j]]; - jtype = tn[jj]; - if (jtypes != nelements && jtypes != jtype && ktypes != nelements && ktypes != jtype){ - expr[jj][0]=0; - continue; - } -// delx = xtmp - x[j][0]; -// dely = ytmp - x[j][1]; -// delz = ztmp - x[j][2]; - delx = xn[jj]; - dely = yn[jj]; - delz = zn[jj]; - rsq = delx*delx + dely*dely + delz*delz; - if (rsq>rc*rc){ - expr[jj][0]=0; - continue; - } - double r1 = (rsq*((double)res)*cutinv2); - int m1 = (int)r1; - if (!(m1>=1 && m1 <= res))pair->errorf("Neighbor list is invalid.");//usually results from nan somewhere. - r1 = r1-trunc(r1); - double *p0 = &expcuttable[(m1-1)*this->k]; - double *p1 = &expcuttable[m1*this->k]; - double *p2 = &expcuttable[(m1+1)*this->k]; - double *p3 = &expcuttable[(m1+2)*this->k]; - for (kk=0;kkk;kk++){ - expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); - expr[jj][kk] *= Sik[jj]; - } - double* q = &dfctable[m1-1]; - double* r2 = &rinvsqrttable[m1-1]; - dfc[jj] = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); - ri[jj] = r2[1] + 0.5 * r1*(r2[2] - r2[0] + r1*(2.0*r2[0] - 5.0*r2[1] + 4.0*r2[2] - r2[3] + r1*(3.0*(r2[1] - r2[2]) + r2[3] - r2[0]))); - y[jj][0]=delx*ri[jj]; - y[jj][1]=dely*ri[jj]; - y[jj][2]=delz*ri[jj]; - } - for (jj = 0; jj < jnum; jj++) { - if (Bij[jj]==false){continue;} - if (expr[jj][0]==0)continue; -// j = jlist[jj]; -// j &= NEIGHMASK; -// jtype = pair->map[type[j]]; - jtype =tn[jj]; - if (jtypes != nelements && jtypes != jtype){ - continue; - } - j = jl[jj]; - double *sj = sim->s[j]; - double spj = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - for (n = 0;nk;n++){ - ct[n] = alpha_k[n]/re; - c41[n]=(-ct[n]+dfc[jj])*y[jj][0]+dSikx[jj]; - c51[n]=(-ct[n]+dfc[jj])*y[jj][1]+dSiky[jj]; - c61[n]=(-ct[n]+dfc[jj])*y[jj][2]+dSikz[jj]; - } - for (n=0;nmap[type[k1]]; - ktype = tn[kk]; - if (ktypes != nelements && ktypes != ktype){ - continue; - } - j = jl[kk]; - double *sk = sim->s[j]; - double spk = si[0]*sk[0]+si[1]*sk[1]+si[2]*sk[2]; - count = startingneuron; - double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); - double c1 = ri[jj]*(y[kk][0]-dot*y[jj][0]); - double c2 = ri[jj]*(y[kk][1]-dot*y[jj][1]); - double c3 = ri[jj]*(y[kk][2]-dot*y[jj][2]); - double c10 = ri[kk]*(y[jj][0]-dot*y[kk][0]); - double c11 = ri[kk]*(y[jj][1]-dot*y[kk][1]); - double c12 = ri[kk]*(y[jj][2]-dot*y[kk][2]); - for (n=0;nSik[kk]*pair->Sik[jj]; -// double c4 = c41[n]+4*pair->dSikx[kk]; -// double c5 = c51[n]+4*pair->dSiky[kk]; -// double c6 = c61[n]+4*pair->dSikz[kk]; -// //m=0 -// features[count]+=dot1; -// Bijk[n][0]+=dot1; -// dfeaturesx[jj*f+count]+=dot1*c4; -// dfeaturesy[jj*f+count]+=dot1*c5; -// dfeaturesz[jj*f+count]+=dot1*c6; -// c4*=dot; -// c5*=dot; -// c6*=dot; -// count++; -// for (m=1;mmap[type[k1]]; - ktype = tn[kk]; - if (ktypes != nelements && ktypes != ktype){ - continue; - } - count = startingneuron; - for (n=0;nBij[kk]==false){continue;} -// if (expr[kk][0]==0)continue; -// int k1 = jlist[kk]; -// k1 &= NEIGHMASK; -// ktype = pair->map[type[k1]]; -// if (ktypes != nelements && ktypes != ktype){ -// continue; -// } -// count = startingneuron; -// double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); -// double c1 = ri[jj]*(y[kk][0]-dot*y[jj][0]); -// double c2 = ri[jj]*(y[kk][1]-dot*y[jj][1]); -// double c3 = ri[jj]*(y[kk][2]-dot*y[jj][2]); -// double c10 = ri[kk]*(y[jj][0]-dot*y[kk][0]); -// double c11 = ri[kk]*(y[jj][1]-dot*y[kk][1]); -// double c12 = ri[kk]*(y[jj][2]-dot*y[kk][2]); -// for (n=0;nSik[kk]*pair->Sik[jj]; -// double c4 = c41[n]/2; -// double c5 = c51[n]/2; -// double c6 = c61[n]/2; -// double ct2 = -ct[n]/2+dfc[kk]; -// double c42 = ct2*y[kk][0]+pair->dSikx[kk]; -// double c52 = ct2*y[kk][1]+pair->dSiky[kk]; -// double c62 = ct2*y[kk][2]+pair->dSikz[kk]; -// //m=0 -// features[count]+=dot1; -// dfeaturesx[jj*f+count]+=dot1*c4; -// dfeaturesy[jj*f+count]+=dot1*c5; -// dfeaturesz[jj*f+count]+=dot1*c6; -// dfeaturesx[kk*f+count]+=dot1*c42; -// dfeaturesy[kk*f+count]+=dot1*c52; -// dfeaturesz[kk*f+count]+=dot1*c62; -// c4*=dot; -// c5*=dot; -// c6*=dot; -// c42*=dot; -// c52*=dot; -// c62*=dot; -// count++; -// for (m=1;mallscreen = false; - pair->dospin = true; - spin = true; -} - -Fingerprint_bondspin::~Fingerprint_bondspin(){ - delete [] alpha_k; - delete [] atomtypes; - delete [] expcuttable; - delete [] dfctable; - for (int i=0;i<(m*(m+1))>>1;i++){ - delete [] coeff[i]; - delete [] coeffx[i]; - delete [] coeffy[i]; - delete [] coeffz[i]; - delete [] Mf[i]; - } - delete [] coeff; - delete [] coeffx; - delete [] coeffy; - delete [] coeffz; - delete [] Mf; - delete [] rinvsqrttable; -} - -bool Fingerprint_bondspin::parse_values(char * constant, char * line1){ - char **words=new char *[MAXLINE]; - int nwords,l; - nwords=0; - words[nwords++] = strtok(line1,": ,\t\n"); - while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; - nwords -= 1; - if (strcmp(constant,"re")==0){ - re = strtod(words[0],NULL); - } - else if (strcmp(constant,"rc")==0){ - rc = strtod(words[0],NULL); - } - else if (strcmp(constant,"alphak")==0){ - delete [] alpha_k; - alpha_k = new double [nwords]; - for (l=0;lerrorf("Undefined value for bond power"); - delete [] words; - if (re!=0.0 && rc!=0.0 && alpha_k[0]!=-1 && dr!=0.0 && m!=0 && k!=0)return true; - return false; -} - -void Fingerprint_bondspin::write_values(FILE *fid){ - int i; - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:re:\n",style,id); - fprintf(fid,"%f\n",re); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:rc:\n",style,id); - fprintf(fid,"%f\n",rc); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:alphak:\n",style,id); - for (i=0;ielementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:dr:\n",style,id); - fprintf(fid,"%f\n",dr); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:k:\n",style,id); - fprintf(fid,"%d\n",k); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:m:\n",style,id); - fprintf(fid,"%d\n",m); -} - -void Fingerprint_bondspin::init(int *i,int id){ - for (int j=0;jk = 0; - alpha_k = new double [1]; - alpha_k[0]=-1; - empty = false; - this->id = id; -} - -//number of neurons defined by this fingerprint -int Fingerprint_bondspin::get_length(){ - return m*k; -} - -void Fingerprint_bondspin::allocate(){ - generate_exp_cut_table(); - generate_coefficients(); - generate_rinvssqrttable(); -} - -//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop and do3bodyfeatureset_doubleneighborloop. -void Fingerprint_bondspin::generate_exp_cut_table(){ - int m,n; - double r1; - int buf = 5; - int res = pair->res; - double cutmax = pair->cutmax; - expcuttable = new double [(res+buf)*(this->k)]; - dfctable = new double [res+buf]; - for (m=0;m<(res+buf);m++){ - r1 = cutmax*cutmax*(double)(m)/(double)(res); - for (n=0;n<(this->k);n++){ - expcuttable[n+m*(this->k)] = exp(-alpha_k[n]/re*sqrt(r1))*cutofffunction(sqrt(r1),rc,dr); - } - if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ - dfctable[m]=0; - } - else{ - dfctable[m]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); - } - } -} - -//Generate table of complex functions for quick reference during compute. Used by do3bodyfeatureset_singleneighborloop. -void Fingerprint_bondspin::generate_coefficients(){ //calculates multinomial coefficient for each term - int p,mb,mc; - int n,p1,i1; - mb = this->m; - mc=(mb*(mb+1))>>1; - coeff = new int *[mc]; - coeffx = new int *[mc]; - coeffy = new int *[mc]; - coeffz = new int *[mc]; - for (p=0;pm+1]; - for (p=0;pm+1;p++){ - M[p]=0; - } - for (p1=0;p1sims[sid]; - ilist = sim->ilist; - numneigh = sim->numneigh; - i = ilist[ii]; -// jnum = numneigh[i]; - //select the more efficient algorithm for this particular potential and environment. - - if (jnum*2>(m+1)*m*20){ - do3bodyfeatureset_singleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,dspinx,dspiny,dspinz,ii,sid,xn,yn,zn,tn,jnum,jl); - } - else{ - do3bodyfeatureset_doubleneighborloop(features,dfeaturesx,dfeaturesy,dfeaturesz,dspinx,dspiny,dspinz,ii,sid,xn,yn,zn,tn,jnum,jl); - } -} - -//Called by do3bodyfeatureset. Algorithm for high neighbor numbers and small series of bond angle powers -void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,double * dspinx,double *dspiny,double *dspinz,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl){ - int i,j,jj,itype,jtype,kk,m,n,mcount,a,a1,a2,ai; - double xtmp,ytmp,ztmp,delx,dely,delz,rsq; - int *ilist,*jlist,*numneigh,**firstneigh; - int count=0; - PairRANN::Simulation *sim = &pair->sims[sid]; -// double **x = sim->x; - int *type = sim->type; - double cutmax = pair->cutmax; - int res = pair->res; - double cutinv2 = 1/cutmax/cutmax; - ilist = sim->ilist; -// numneigh = sim->numneigh; -// firstneigh = sim->firstneigh; - int nelements=pair->nelements; - i = ilist[ii]; - itype = pair->map[type[i]]; - int f = pair->net[itype].dimensions[0]; -// xtmp = x[i][0]; -// ytmp = x[i][1]; -// ztmp = x[i][2]; -// jlist = firstneigh[i]; -// jnum = numneigh[i]; - double expr[jnum][this->k+12]; - int p = this->k; - int countmb=((this->m)*(this->m+1))>>1; - double *si = sim->s[i]; - // calculate interpolation expr, rinvs and dfc, for each neighbor - for (jj = 0; jj < jnum; jj++) { -// j = jlist[jj]; -// j &= NEIGHMASK; -// jtype = pair->map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype && atomtypes[2] != nelements && atomtypes[2] != jtype){ - expr[jj][0]=0; - continue; - } -// delx = xtmp - x[j][0]; -// dely = ytmp - x[j][1]; -// delz = ztmp - x[j][2]; - delx = xn[jj]; - dely = yn[jj]; - delz = zn[jj]; - rsq = delx*delx + dely*dely + delz*delz; - if (rsq>rc*rc){ - expr[jj][0]=0; - continue; - } - double r1 = (rsq*((double)res)*cutinv2); - int m1 = (int)r1; - r1 = r1-trunc(r1); - double *p0 = &expcuttable[(m1-1)*this->k]; - double *p1 = &expcuttable[m1*this->k]; - double *p2 = &expcuttable[(m1+1)*this->k]; - double *p3 = &expcuttable[(m1+2)*this->k]; - for (kk=0;kkk;kk++){ - expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); - } - double* q = &dfctable[m1-1]; - double* ri = &rinvsqrttable[m1-1]; - double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); - double rinvs = ri[1] + 0.5 * r1*(ri[2] - ri[0] + r1*(2.0*ri[0] - 5.0*ri[1] + 4.0*ri[2] - ri[3] + r1*(3.0*(ri[1] - ri[2]) + ri[3] - ri[0]))); - - expr[jj][p]=delx*rinvs; - expr[jj][p+1]=dely*rinvs; - expr[jj][p+2]=delz*rinvs; - //Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy. - if (expr[jj][p]*expr[jj][p]<0.000000000001){ - expr[jj][p] = 0.000001; - } - if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001){ - expr[jj][p+1] = 0.000001; - } - if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001){ - expr[jj][p+2] = 0.000001; - } - expr[jj][p+3] = -dfc*expr[jj][p]; - expr[jj][p+4] = rinvs/expr[jj][p]; - expr[jj][p+5] = rinvs*expr[jj][p]; - expr[jj][p+6] = -dfc*expr[jj][p+1]; - expr[jj][p+7] = rinvs/expr[jj][p+1]; - expr[jj][p+8] = rinvs*expr[jj][p+1]; - expr[jj][p+9] = -dfc*expr[jj][p+2]; - expr[jj][p+10] = rinvs/expr[jj][p+2]; - expr[jj][p+11] = rinvs*expr[jj][p+2]; - } - - int kb = this->k; - int mb = this->m; - count = startingneuron; - double Bb[mb]; - double Bbs[mb]; - double dBbx; - double dBby; - double dBbz; -// double dBbx1[mb]; -// double dBby1[mb]; -// double dBbz1[mb]; - double yprod; - for (mcount=0;mcountcoeffx[mcount]; - int *coeffy = this->coeffy[mcount]; - int *coeffz = this->coeffz[mcount]; - int *coeff = this->coeff[mcount]; - a = mb+1; - for (a1=0;a1map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype){ - continue; - } - j = jl[jj]; - double *sj = sim->s[j]; - double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - double yprod = expr[jj][ai]; - double *y4 = &expr[jj][p]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[2] != nelements && atomtypes[2] != jtype){ - continue; - } - j = jl[jj]; - double *sj = sim->s[j]; - double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - double yprod = expr[jj][ai]; - double *y4 = &expr[jj][p]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[2] != nelements && atomtypes[2] != jtype){ - continue; - } - j = jl[jj]; - double *sj = sim->s[j]; - double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - double *y3 = &expr[jj][p+3]; - double *y4 = &expr[jj][p]; - ai = n; - yprod = expr[jj][ai]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype){ - continue; - } - j = jl[jj]; - double *sj = sim->s[j]; - double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - double *y3 = &expr[jj][p+3]; - double *y4 = &expr[jj][p]; - ai = n; - yprod = expr[jj][ai]; - for (a2=0;a2map[type[j]]; - jtype = tn[jj]; - if (atomtypes[1] != nelements && atomtypes[1] != jtype){ - continue; - } - j = jl[jj]; - double *sj = sim->s[j]; - double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - double *y3 = &expr[jj][p+3]; - double *y4 = &expr[jj][p]; - ai = n; - yprod = expr[jj][ai]; - for (a2=0;a2sims[sid]; - double **x = sim->x; - int *type = sim->type; - int nelements = pair->nelements; - int res = pair->res; - double cutmax = pair->cutmax; - double cutinv2 = 1/cutmax/cutmax; - ilist = sim->ilist; -// numneigh = sim->numneigh; -// firstneigh = sim->firstneigh; - i = ilist[ii]; - itype = pair->map[type[i]]; - int f = pair->net[itype].dimensions[0]; -// xtmp = x[i][0]; -// ytmp = x[i][1]; -// ztmp = x[i][2]; -// jlist = firstneigh[i]; -// jnum = numneigh[i]; - double expr[jnum][this->k]; - double y[jnum][3]; - double ri[jnum]; - double dfc[jnum]; - int kb = this->k; - int mb = this->m; - double c41[this->k]; - double c51[this->k]; - double c61[this->k]; - double ct[this->k]; - double *si = sim->s[i]; - for (jj = 0; jj < jnum; jj++) { -// j = jlist[jj]; -// j &= NEIGHMASK; -// jtype = pair->map[type[j]]; - jtype = tn[jj]; - if (jtypes != nelements && jtypes != jtype && ktypes != nelements && ktypes != jtype){ - expr[jj][0]=0; - continue; - } -// delx = xtmp - x[j][0]; -// dely = ytmp - x[j][1]; -// delz = ztmp - x[j][2]; - delx = xn[jj]; - dely = yn[jj]; - delz = zn[jj]; - rsq = delx*delx + dely*dely + delz*delz; - if (rsq>rc*rc){ - expr[jj][0]=0; - continue; - } -// j = jl[jj]; -// double *sj = sim->s[j]; -// double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - double r1 = (rsq*((double)res)*cutinv2); - int m1 = (int)r1; - if (!(m1>=1 && m1 <= res))pair->errorf("Neighbor list is invalid.");//usually results from nan somewhere. - r1 = r1-trunc(r1); - double *p0 = &expcuttable[(m1-1)*this->k]; - double *p1 = &expcuttable[m1*this->k]; - double *p2 = &expcuttable[(m1+1)*this->k]; - double *p3 = &expcuttable[(m1+2)*this->k]; - for (kk=0;kkk;kk++){ - expr[jj][kk] = p1[kk]+0.5*r1*(p2[kk]-p0[kk]+r1*(2.0*p0[kk]-5.0*p1[kk]+4.0*p2[kk]-p3[kk]+r1*(3.0*(p1[kk]-p2[kk])+p3[kk]-p0[kk]))); -// expr[jj][kk]*= sp; - } - double* q = &dfctable[m1-1]; - double* r2 = &rinvsqrttable[m1-1]; - dfc[jj] = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); - ri[jj] = r2[1] + 0.5 * r1*(r2[2] - r2[0] + r1*(2.0*r2[0] - 5.0*r2[1] + 4.0*r2[2] - r2[3] + r1*(3.0*(r2[1] - r2[2]) + r2[3] - r2[0]))); - y[jj][0]=delx*ri[jj]; - y[jj][1]=dely*ri[jj]; - y[jj][2]=delz*ri[jj]; - } -// if (i==5){ -// for (jj=0;jjmap[type[j]]; - jtype = tn[jj]; - if (jtypes != nelements && jtypes != jtype){ - continue; - } - j = jl[jj]; - double *sj = sim->s[j]; - double spj = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - for (n = 0;nk;n++){ - ct[n] = 2*alpha_k[n]/re; - c41[n]=(-ct[n]+2*dfc[jj])*y[jj][0]; - c51[n]=(-ct[n]+2*dfc[jj])*y[jj][1]; - c61[n]= (-ct[n]+2*dfc[jj])*y[jj][2]; - } - if (jtypes==ktypes){ - for (kk=jj+1;kk< jnum; kk++){ - if (expr[kk][0]==0)continue; -// int k1 = jlist[kk]; -// k1 &= NEIGHMASK; -// ktype = pair->map[type[k1]]; - ktype = tn[kk]; - if (ktypes != nelements && ktypes != ktype){ - continue; - } - j = jl[kk]; - double *sk = sim->s[j]; - double spk = si[0]*sk[0]+si[1]*sk[1]+si[2]*sk[2]; - count = startingneuron; - double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); - double c1 = 2*ri[jj]*(y[kk][0]-dot*y[jj][0]); - double c2 = 2*ri[jj]*(y[kk][1]-dot*y[jj][1]); - double c3 = 2*ri[jj]*(y[kk][2]-dot*y[jj][2]); - double c10 = 2*ri[kk]*(y[jj][0]-dot*y[kk][0]); - double c11 = 2*ri[kk]*(y[jj][1]-dot*y[kk][1]); - double c12 = 2*ri[kk]*(y[jj][2]-dot*y[kk][2]); -// double c1 = 2*ri[jj]*y[kk][0]*(1-y[jj][0]*y[jj][0]); -// double c2 = 2*ri[jj]*y[kk][1]*(1-y[jj][1]*y[jj][1]); -// double c3 = 2*ri[jj]*y[kk][2]*(1-y[jj][2]*y[jj][2]); -// double c10 = 2*ri[kk]*y[jj][0]*(1-y[kk][0]*y[kk][0]); -// double c11 = 2*ri[kk]*y[jj][1]*(1-y[kk][1]*y[kk][1]); -// double c12 = 2*ri[kk]*y[jj][2]*(1-y[kk][2]*y[kk][2]); - for (n=0;nmap[type[k1]]; - ktype = tn[kk]; - if (ktypes != nelements && ktypes != ktype){ - continue; - } - j = jl[kk]; - double *sk = sim->s[j]; - double spk = si[0]*sk[0]+si[1]*sk[1]+si[2]*sk[2]; - count = startingneuron; - double dot = (y[jj][0]*y[kk][0]+y[jj][1]*y[kk][1]+y[jj][2]*y[kk][2]); - double c1 = ri[jj]*(y[kk][0]-dot*y[jj][0]); - double c2 = ri[jj]*(y[kk][1]-dot*y[jj][1]); - double c3 = ri[jj]*(y[kk][2]-dot*y[jj][2]); - double c10 = ri[kk]*(y[jj][0]-dot*y[kk][0]); - double c11 = ri[kk]*(y[jj][1]-dot*y[kk][1]); - double c12 = ri[kk]*(y[jj][2]-dot*y[kk][2]); -// double c1 = 2*ri[jj]*y[kk][0]*(1-y[jj][0]*y[jj][0]); -// double c2 = 2*ri[jj]*y[kk][1]*(1-y[jj][1]*y[jj][1]); -// double c3 = 2*ri[jj]*y[kk][2]*(1-y[jj][2]*y[jj][2]); -// double c10 = 2*ri[kk]*y[jj][0]*(1-y[kk][0]*y[kk][0]); -// double c11 = 2*ri[kk]*y[jj][1]*(1-y[kk][1]*y[kk][1]); -// double c12 = 2*ri[kk]*y[jj][2]*(1-y[kk][2]*y[kk][2]); - for (n=0;nallscreen = false; -} - -Fingerprint_radial::~Fingerprint_radial() -{ - delete [] atomtypes; - delete [] radialtable; - delete [] alpha; - delete [] dfctable; - delete [] rinvsqrttable; -} - -bool Fingerprint_radial::parse_values(char* constant,char * line1){ - int l; - char **words=new char *[MAXLINE]; - int nwords; - nwords=0; - words[nwords++] = strtok(line1,": ,\t\n"); - while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; - nwords -= 1; - if (strcmp(constant,"re")==0){ - re = strtod(line1,NULL); - } - else if (strcmp(constant,"rc")==0){ - rc = strtod(line1,NULL); - } - else if (strcmp(constant,"alpha")==0){ - delete [] alpha; - alpha = new double [nwords]; - for (l=0;lerrorf("Undefined value for radial power"); - //code will run with default o=0 if o is never specified. All other values must be defined in potential file. - delete [] words; - if (re!=0 && rc!=0 && alpha!=0 && dr!=0 && n!=0)return true; - return false; -} - -void Fingerprint_radial::write_values(FILE *fid){ - int i; - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:re:\n",style,id); - fprintf(fid,"%f\n",re); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:rc:\n",style,id); - fprintf(fid,"%f\n",rc); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:alpha:\n",style,id); - for (i=0;i<(n-o+1);i++){ - fprintf(fid,"%f ",alpha[i]); - } - fprintf(fid,"\n"); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:dr:\n",style,id); - fprintf(fid,"%f\n",dr); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:o:\n",style,id); - fprintf(fid,"%d\n",o); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:n:\n",style,id); - fprintf(fid,"%d\n",n); -} - -//called after fingerprint is fully defined and tables can be computed. -void Fingerprint_radial::allocate() -{ - int k,m; - double r1; - int buf = 5; - int res = pair->res; - double cutmax = pair->cutmax; - radialtable = new double [(res+buf)*get_length()]; - dfctable = new double [res+buf]; - for (k=0;k<(res+buf);k++){ - r1 = cutmax*cutmax*(double)(k)/(double)(res); - for (m=0;m<=(n-o);m++){ - radialtable[k*(n-o+1)+m]=pow(sqrt(r1)/re,m+o)*exp(-alpha[m]*sqrt(r1)/re)*cutofffunction(sqrt(r1),rc,dr); - } - if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ - dfctable[k]=0; - } - else{ - dfctable[k]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); - } - } - generate_rinvssqrttable(); -} - -//called after fingerprint is declared for i-j type, but before its parameters are read. -void Fingerprint_radial::init(int *i,int id) -{ - empty = false; - for (int j=0;jid = id; -} - -void Fingerprint_radial::compute_fingerprint(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) -{ - int nelements = pair->nelements; - int res = pair->res; - int i,j,jj,itype,jtype,l; - double xtmp,ytmp,ztmp,delx,dely,delz,rsq; - int *ilist,*jlist,*numneigh,**firstneigh; - // - PairRANN::Simulation *sim = &pair->sims[sid]; - int count=0; -// double **x = sim->x; - int *type = sim->type; - ilist = sim->ilist; - double cutmax = pair->cutmax; - i = ilist[ii]; - itype = pair->map[type[i]]; - int f = pair->net[itype].dimensions[0]; - double cutinv2 = 1/cutmax/cutmax; -// numneigh = sim->numneigh; -// firstneigh = sim->firstneigh; -// xtmp = x[i][0]; -// ytmp = x[i][1]; -// ztmp = x[i][2]; -// jlist = firstneigh[i]; -// jnum = numneigh[i]; - //loop over neighbors - for (jj = 0; jj < jnum; jj++) { -// j = jlist[jj]; -// j &= NEIGHMASK; -// jtype = pair->map[type[j]]; - jtype =tn[jj]; - if (this->atomtypes[1] != nelements && this->atomtypes[1] != jtype)continue; -// delx = xtmp - x[j][0]; -// dely = ytmp - x[j][1]; -// delz = ztmp - x[j][2]; - delx = xn[jj]; - dely = yn[jj]; - delz = zn[jj]; - rsq = delx*delx + dely*dely + delz*delz; - if (rsq > rc*rc)continue; - count = startingneuron; - double r1 = (rsq*((double)res)*cutinv2); - int m1 = (int)r1; - if (m1>res || m1<1){pair->errorf("invalid neighbor radius!");} - if (radialtable[m1]==0){continue;} - //cubic interpolation from tables - double *p1 = &radialtable[m1*(n-o+1)]; - double *p2 = &radialtable[(m1+1)*(n-o+1)]; - double *p3 = &radialtable[(m1+2)*(n-o+1)]; - double *p0 = &radialtable[(m1-1)*(n-o+1)]; - double *q = &dfctable[m1-1]; - double *rinvs = &rinvsqrttable[m1-1]; - r1 = r1-trunc(r1); - double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); - double ri = rinvs[1] + 0.5 * r1*(rinvs[2] - rinvs[0] + r1*(2.0*rinvs[0] - 5.0*rinvs[1] + 4.0*rinvs[2] - rinvs[3] + r1*(3.0*(rinvs[1] - rinvs[2]) + rinvs[3] - rinvs[0]))); - for (l=0;l<=(n-o);l++){ - double rt = p1[l]+0.5*r1*(p2[l]-p0[l]+r1*(2.0*p0[l]-5.0*p1[l]+4.0*p2[l]-p3[l]+r1*(3.0*(p1[l]-p2[l])+p3[l]-p0[l]))); - features[count]+=rt; - rt *= (l+o)/rsq+(-alpha[l]/re+dfc)*ri; - //update neighbor's features - dfeaturesx[jj*f+count]+=rt*delx; - dfeaturesy[jj*f+count]+=rt*dely; - dfeaturesz[jj*f+count]+=rt*delz; - //update atom's features - dfeaturesx[jnum*f+count]-=rt*delx; - dfeaturesy[jnum*f+count]-=rt*dely; - dfeaturesz[jnum*f+count]-=rt*delz; - count++; - } - } - -} - -int Fingerprint_radial::get_length() -{ - return n-o+1; -} diff --git a/src/fingerprint_radial.h b/src/fingerprint_radial.h deleted file mode 100644 index aeb1c2eca3..0000000000 --- a/src/fingerprint_radial.h +++ /dev/null @@ -1,68 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@me.msstate.edu - ----------------------------------------------------------------------*/ -/* -“The research described and the resulting data presented herein, unless -otherwise noted, was funded under PE 0602784A, Project T53 "Military -Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, -managed by the U.S. Army Combat Capabilities Development Command (CCDC) and -the Engineer Research and Development Center (ERDC). The work described in -this document was conducted at CAVS, MSU. Permission was granted by ERDC -to publish this information. Any opinions, findings and conclusions or -recommendations expressed in this material are those of the author(s) and -do not necessarily reflect the views of the United States Army.​” - -DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 - */ -#ifdef FINGERPRINT_CLASS - -FingerprintStyle(radial,Fingerprint_radial) - -#else - -#ifndef FINGERPRINT_RADIAL_H_ -#define FINGERPRINT_RADIAL_H_ - -#include "fingerprint.h" - -namespace LAMMPS_NS { - -class Fingerprint_radial : public Fingerprint { - public: - Fingerprint_radial(PairRANN *); - ~Fingerprint_radial(); - bool parse_values(char*,char*); - void write_values(FILE *); - void init(int*,int); - void allocate(); - void compute_fingerprint(double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*); - int get_length(); - - double *radialtable; - double *dfctable; - double dr; - double *alpha; - double re; - int n;//highest term - int o;//lowest term - -}; - - -} - -#endif -#endif /* FINGERPRINT_RADIAL_H_ */ diff --git a/src/fingerprint_radialscreened.cpp b/src/fingerprint_radialscreened.cpp deleted file mode 100644 index 3101ca0ab0..0000000000 --- a/src/fingerprint_radialscreened.cpp +++ /dev/null @@ -1,273 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@me.msstate.edu - ----------------------------------------------------------------------*/ -/* -“The research described and the resulting data presented herein, unless -otherwise noted, was funded under PE 0602784A, Project T53 "Military -Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, -managed by the U.S. Army Combat Capabilities Development Command (CCDC) and -the Engineer Research and Development Center (ERDC). The work described in -this document was conducted at CAVS, MSU. Permission was granted by ERDC -to publish this information. Any opinions, findings and conclusions or -recommendations expressed in this material are those of the author(s) and -do not necessarily reflect the views of the United States Army.​” - -DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 - */ - -#include "fingerprint_radialscreened.h" - - - -using namespace LAMMPS_NS; - -Fingerprint_radialscreened::Fingerprint_radialscreened(PairRANN *pair) : Fingerprint(pair) -{ - n_body_type = 2; - dr = 0; - re = 0; - rc = 0; - alpha = new double [1]; - alpha[0] = -1; - n = 0; - o = 0; - id = -1; - style = "radialscreened"; - atomtypes = new int [n_body_type]; - empty = true; - fullydefined = false; - pair->doscreen = true; - screen = true; -} - -Fingerprint_radialscreened::~Fingerprint_radialscreened() -{ - delete [] atomtypes; - delete [] radialtable; - delete [] alpha; - delete [] dfctable; - delete [] rinvsqrttable; -} - -bool Fingerprint_radialscreened::parse_values(char* constant,char * line1){ - int l; - char **words=new char *[MAXLINE]; - int nwords; - nwords=0; - words[nwords++] = strtok(line1,": ,\t\n"); - while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; - nwords -= 1; - if (strcmp(constant,"re")==0){ - re = strtod(line1,NULL); - } - else if (strcmp(constant,"rc")==0){ - rc = strtod(line1,NULL); - } - else if (strcmp(constant,"alpha")==0){ - delete [] alpha; - alpha = new double [nwords]; - for (l=0;lerrorf("Undefined value for radial power"); - //code will run with default o=0 if o is never specified. All other values must be defined in potential file. - delete [] words; - if (re!=0 && rc!=0 && alpha!=0 && dr!=0 && n!=0)return true; - return false; -} - -void Fingerprint_radialscreened::write_values(FILE *fid){ - int i; - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:re:\n",style,id); - fprintf(fid,"%f\n",re); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:rc:\n",style,id); - fprintf(fid,"%f\n",rc); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:alpha:\n",style,id); - for (i=0;i<(n-o+1);i++){ - fprintf(fid,"%f ",alpha[i]); - } - fprintf(fid,"\n"); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:dr:\n",style,id); - fprintf(fid,"%f\n",dr); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:o:\n",style,id); - fprintf(fid,"%d\n",o); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:n:\n",style,id); - fprintf(fid,"%d\n",n); -} - -//called after fingerprint is fully defined and tables can be computed. -void Fingerprint_radialscreened::allocate() -{ - int k,m; - double r1; - int buf = 5; - int res = pair->res; - double cutmax = pair->cutmax; - radialtable = new double [(res+buf)*get_length()]; - dfctable = new double [res+buf]; - for (k=0;k<(res+buf);k++){ - r1 = cutmax*cutmax*(double)(k)/(double)(res); - for (m=0;m<=(n-o);m++){ - radialtable[k*(n-o+1)+m]=pow(sqrt(r1)/re,m+o)*exp(-alpha[m]*sqrt(r1)/re)*cutofffunction(sqrt(r1),rc,dr); - } - if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ - dfctable[k]=0; - } - else{ - dfctable[k]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); - } - } - generate_rinvssqrttable(); -} - -//called after fingerprint is declared for i-j type, but before its parameters are read. -void Fingerprint_radialscreened::init(int *i,int id) -{ - empty = false; - for (int j=0;jid = id; -} - -void Fingerprint_radialscreened::compute_fingerprint(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) -{ - int nelements = pair->nelements; - int res = pair->res; - int i,j,jj,itype,jtype,l,kk; - double xtmp,ytmp,ztmp,delx,dely,delz,rsq; - int *ilist,*jlist,*numneigh,**firstneigh; - // - PairRANN::Simulation *sim = &pair->sims[sid]; - int count=0; - double **x = sim->x; - int *type = sim->type; - ilist = sim->ilist; - double cutmax = pair->cutmax; - i = ilist[ii]; - itype = pair->map[type[i]]; - int f = pair->net[itype].dimensions[0]; - double cutinv2 = 1/cutmax/cutmax; -// numneigh = sim->numneigh; -// firstneigh = sim->firstneigh; -// xtmp = x[i][0]; -// ytmp = x[i][1]; -// ztmp = x[i][2]; -// jlist = firstneigh[i]; -// jnum = numneigh[i]; - //loop over neighbors - for (jj = 0; jj < jnum; jj++) { - if (Bij[jj]==false){continue;} -// j = jlist[jj]; -// j &= NEIGHMASK; -// jtype = pair->map[type[j]]; - jtype = tn[jj]; - if (this->atomtypes[1] != nelements && this->atomtypes[1] != jtype)continue; -// delx = xtmp - x[j][0]; -// dely = ytmp - x[j][1]; -// delz = ztmp - x[j][2]; - delx = xn[jj]; - dely = yn[jj]; - delz = zn[jj]; - rsq = delx*delx + dely*dely + delz*delz; - if (rsq > rc*rc)continue; - count = startingneuron; - double r1 = (rsq*((double)res)*cutinv2); - int m1 = (int)r1; - if (m1>res || m1<1){pair->errorf("invalid neighbor radius!");} - if (radialtable[m1]==0){continue;} - //cubic interpolation from tables - double *p1 = &radialtable[m1*(n-o+1)]; - double *p2 = &radialtable[(m1+1)*(n-o+1)]; - double *p3 = &radialtable[(m1+2)*(n-o+1)]; - double *p0 = &radialtable[(m1-1)*(n-o+1)]; - double *q = &dfctable[m1-1]; - double *rinvs = &rinvsqrttable[m1-1]; - r1 = r1-trunc(r1); - double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); - double ri = rinvs[1] + 0.5 * r1*(rinvs[2] - rinvs[0] + r1*(2.0*rinvs[0] - 5.0*rinvs[1] + 4.0*rinvs[2] - rinvs[3] + r1*(3.0*(rinvs[1] - rinvs[2]) + rinvs[3] - rinvs[0]))); - for (l=0;l<=(n-o);l++){ - double rt = Sik[jj]*(p1[l]+0.5*r1*(p2[l]-p0[l]+r1*(2.0*p0[l]-5.0*p1[l]+4.0*p2[l]-p3[l]+r1*(3.0*(p1[l]-p2[l])+p3[l]-p0[l])))); - features[count]+=rt; - double rt1 = rt*((l+o)/rsq+(-alpha[l]/re+dfc)*ri); - //update neighbor's features - dfeaturesx[jj*f+count]+=rt1*delx+rt*dSikx[jj]; - dfeaturesy[jj*f+count]+=rt1*dely+rt*dSiky[jj]; - dfeaturesz[jj*f+count]+=rt1*delz+rt*dSikz[jj]; - for (kk=0;kkdoscreen = true; - screen = true; - pair->dospin = true; - spin = true; -} - -Fingerprint_radialscreenedspin::~Fingerprint_radialscreenedspin() -{ - delete [] atomtypes; - delete [] radialtable; - delete [] alpha; - delete [] dfctable; - delete [] rinvsqrttable; -} - -bool Fingerprint_radialscreenedspin::parse_values(char* constant,char * line1){ - int l; - char **words=new char *[MAXLINE]; - int nwords; - nwords=0; - words[nwords++] = strtok(line1,": ,\t\n"); - while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; - nwords -= 1; - if (strcmp(constant,"re")==0){ - re = strtod(line1,NULL); - } - else if (strcmp(constant,"rc")==0){ - rc = strtod(line1,NULL); - } - else if (strcmp(constant,"alpha")==0){ - delete [] alpha; - alpha = new double [nwords]; - for (l=0;lerrorf("Undefined value for radial power"); - //code will run with default o=0 if o is never specified. All other values must be defined in potential file. - delete [] words; - if (re!=0 && rc!=0 && alpha!=0 && dr!=0 && n!=0)return true; - return false; -} - -void Fingerprint_radialscreenedspin::write_values(FILE *fid){ - int i; - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:re:\n",style,id); - fprintf(fid,"%f\n",re); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:rc:\n",style,id); - fprintf(fid,"%f\n",rc); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:alpha:\n",style,id); - for (i=0;i<(n-o+1);i++){ - fprintf(fid,"%f ",alpha[i]); - } - fprintf(fid,"\n"); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:dr:\n",style,id); - fprintf(fid,"%f\n",dr); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:o:\n",style,id); - fprintf(fid,"%d\n",o); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:n:\n",style,id); - fprintf(fid,"%d\n",n); -} - -//called after fingerprint is fully defined and tables can be computed. -void Fingerprint_radialscreenedspin::allocate() -{ - int k,m; - double r1; - int buf = 5; - int res = pair->res; - double cutmax = pair->cutmax; - radialtable = new double [(res+buf)*get_length()]; - dfctable = new double [res+buf]; - for (k=0;k<(res+buf);k++){ - r1 = cutmax*cutmax*(double)(k)/(double)(res); - for (m=0;m<=(n-o);m++){ - radialtable[k*(n-o+1)+m]=pow(sqrt(r1)/re,m+o)*exp(-alpha[m]*sqrt(r1)/re)*cutofffunction(sqrt(r1),rc,dr); - } - if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ - dfctable[k]=0; - } - else{ - dfctable[k]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); - } - } - generate_rinvssqrttable(); -} - -//called after fingerprint is declared for i-j type, but before its parameters are read. -void Fingerprint_radialscreenedspin::init(int *i,int id) -{ - empty = false; - for (int j=0;jid = id; -} - -void Fingerprint_radialscreenedspin::compute_fingerprint(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,double * dspinx,double *dspiny,double *dspinz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) -{ - int nelements = pair->nelements; - int res = pair->res; - int i,j,jj,itype,jtype,l,kk; - double xtmp,ytmp,ztmp,delx,dely,delz,rsq; - int *ilist,*jlist,*numneigh,**firstneigh; - // - PairRANN::Simulation *sim = &pair->sims[sid]; - int count=0; - double **x = sim->x; - int *type = sim->type; - ilist = sim->ilist; - double cutmax = pair->cutmax; - i = ilist[ii]; - itype = pair->map[type[i]]; - int f = pair->net[itype].dimensions[0]; - double cutinv2 = 1/cutmax/cutmax; - double *si = sim->s[i]; -// numneigh = sim->numneigh; -// firstneigh = sim->firstneigh; -// xtmp = x[i][0]; -// ytmp = x[i][1]; -// ztmp = x[i][2]; -// jlist = firstneigh[i]; -// jnum = numneigh[i]; - //loop over neighbors - for (jj = 0; jj < jnum; jj++) { - if (Bij[jj]==false){continue;} -// j = jlist[jj]; -// j &= NEIGHMASK; -// jtype = pair->map[type[j]]; - jtype = tn[jj]; - if (this->atomtypes[1] != nelements && this->atomtypes[1] != jtype)continue; -// delx = xtmp - x[j][0]; -// dely = ytmp - x[j][1]; -// delz = ztmp - x[j][2]; - delx = xn[jj]; - dely = yn[jj]; - delz = zn[jj]; - rsq = delx*delx + dely*dely + delz*delz; - if (rsq > rc*rc)continue; - count = startingneuron; - double r1 = (rsq*((double)res)*cutinv2); - int m1 = (int)r1; - if (m1>res || m1<1){pair->errorf("invalid neighbor radius!");} - if (radialtable[m1]==0){continue;} - j=jl[jj]; - double *sj = sim->s[j]; - double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - //cubic interpolation from tables - double *p1 = &radialtable[m1*(n-o+1)]; - double *p2 = &radialtable[(m1+1)*(n-o+1)]; - double *p3 = &radialtable[(m1+2)*(n-o+1)]; - double *p0 = &radialtable[(m1-1)*(n-o+1)]; - double *q = &dfctable[m1-1]; - double *rinvs = &rinvsqrttable[m1-1]; - r1 = r1-trunc(r1); - double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); - double ri = rinvs[1] + 0.5 * r1*(rinvs[2] - rinvs[0] + r1*(2.0*rinvs[0] - 5.0*rinvs[1] + 4.0*rinvs[2] - rinvs[3] + r1*(3.0*(rinvs[1] - rinvs[2]) + rinvs[3] - rinvs[0]))); - for (l=0;l<=(n-o);l++){ - double rt = Sik[jj]*(p1[l]+0.5*r1*(p2[l]-p0[l]+r1*(2.0*p0[l]-5.0*p1[l]+4.0*p2[l]-p3[l]+r1*(3.0*(p1[l]-p2[l])+p3[l]-p0[l])))); - //update neighbor's features - dspinx[jj*f+count]+=rt*si[0]; - dspiny[jj*f+count]+=rt*si[1]; - dspinz[jj*f+count]+=rt*si[2]; - dspinx[jnum*f+count]+=rt*sj[0]; - dspiny[jnum*f+count]+=rt*sj[1]; - dspinz[jnum*f+count]+=rt*sj[2]; - rt *= sp; - features[count]+=rt; - double rt1 = rt*((l+o)/rsq+(-alpha[l]/re+dfc)*ri); - dfeaturesx[jj*f+count]+=rt1*delx+rt*dSikx[jj]; - dfeaturesy[jj*f+count]+=rt1*dely+rt*dSiky[jj]; - dfeaturesz[jj*f+count]+=rt1*delz+rt*dSikz[jj]; - for (kk=0;kkallscreen = false; - pair->dospin = true; - spin = true; -} - -Fingerprint_radialspin::~Fingerprint_radialspin() -{ - delete [] atomtypes; - delete [] radialtable; - delete [] alpha; - delete [] dfctable; - delete [] rinvsqrttable; -} - -bool Fingerprint_radialspin::parse_values(char* constant,char * line1){ - int l; - char **words=new char *[MAXLINE]; - int nwords; - nwords=0; - words[nwords++] = strtok(line1,": ,\t\n"); - while ((words[nwords++] = strtok(NULL,": ,\t\n"))) continue; - nwords -= 1; - if (strcmp(constant,"re")==0){ - re = strtod(line1,NULL); - } - else if (strcmp(constant,"rc")==0){ - rc = strtod(line1,NULL); - } - else if (strcmp(constant,"alpha")==0){ - delete [] alpha; - alpha = new double [nwords]; - for (l=0;lerrorf("Undefined value for radial power"); - //code will run with default o=0 if o is never specified. All other values must be defined in potential file. - delete [] words; - if (re!=0 && rc!=0 && alpha!=0 && dr!=0 && n!=0)return true; - return false; -} - -void Fingerprint_radialspin::write_values(FILE *fid){ - int i; - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:re:\n",style,id); - fprintf(fid,"%f\n",re); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:rc:\n",style,id); - fprintf(fid,"%f\n",rc); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:alpha:\n",style,id); - for (i=0;i<(n-o+1);i++){ - fprintf(fid,"%f ",alpha[i]); - } - fprintf(fid,"\n"); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:dr:\n",style,id); - fprintf(fid,"%f\n",dr); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:o:\n",style,id); - fprintf(fid,"%d\n",o); - fprintf(fid,"fingerprintconstants:"); - fprintf(fid,"%s",pair->elementsp[atomtypes[0]]); - for (i=1;ielementsp[atomtypes[i]]); - } - fprintf(fid,":%s_%d:n:\n",style,id); - fprintf(fid,"%d\n",n); -} - -//called after fingerprint is fully defined and tables can be computed. -void Fingerprint_radialspin::allocate() -{ - int k,m; - double r1; - int buf = 5; - int res = pair->res; - double cutmax = pair->cutmax; - radialtable = new double [(res+buf)*get_length()]; - dfctable = new double [res+buf]; - for (k=0;k<(res+buf);k++){ - r1 = cutmax*cutmax*(double)(k)/(double)(res); - for (m=0;m<=(n-o);m++){ - radialtable[k*(n-o+1)+m]=pow(sqrt(r1)/re,m+o)*exp(-alpha[m]*sqrt(r1)/re)*cutofffunction(sqrt(r1),rc,dr); - } - if (sqrt(r1)>=rc || sqrt(r1) <= (rc-dr)){ - dfctable[k]=0; - } - else{ - dfctable[k]=-8*pow(1-(rc-sqrt(r1))/dr,3)/dr/(1-pow(1-(rc-sqrt(r1))/dr,4)); - } - } - generate_rinvssqrttable(); -} - -//called after fingerprint is declared for i-j type, but before its parameters are read. -void Fingerprint_radialspin::init(int *i,int id) -{ - empty = false; - for (int j=0;jid = id; -} - -void Fingerprint_radialspin::compute_fingerprint(double * features,double * dfeaturesx,double *dfeaturesy,double *dfeaturesz,double * dspinx,double *dspiny,double *dspinz,int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) -{ - int nelements = pair->nelements; - int res = pair->res; - int i,j,jj,itype,jtype,l; - double xtmp,ytmp,ztmp,delx,dely,delz,rsq; - int *ilist,*jlist,*numneigh,**firstneigh; - // - PairRANN::Simulation *sim = &pair->sims[sid]; - int count=0; -// double **x = sim->x; - int *type = sim->type; - ilist = sim->ilist; - double cutmax = pair->cutmax; - i = ilist[ii]; - itype = pair->map[type[i]]; - int f = pair->net[itype].dimensions[0]; - double cutinv2 = 1/cutmax/cutmax; - double *si = sim->s[i]; -// numneigh = sim->numneigh; - firstneigh = sim->firstneigh; -// xtmp = x[i][0]; -// ytmp = x[i][1]; -// ztmp = x[i][2]; - jlist = firstneigh[i]; -// jnum = numneigh[i]; - //loop over neighbors - for (jj = 0; jj < jnum; jj++) { - j = jl[jj]; - // jtype = pair->map[type[j]]; - jtype =tn[jj]; - if (this->atomtypes[1] != nelements && this->atomtypes[1] != jtype)continue; - // delx = xtmp - x[j][0]; - // dely = ytmp - x[j][1]; - // delz = ztmp - x[j][2]; - delx = xn[jj]; - dely = yn[jj]; - delz = zn[jj]; - rsq = delx*delx + dely*dely + delz*delz; - if (rsq > rc*rc)continue; - count = startingneuron; - double r1 = (rsq*((double)res)*cutinv2); - int m1 = (int)r1; - if (m1>res || m1<1){pair->errorf("invalid neighbor radius!");} - if (radialtable[m1]==0){continue;} - double *sj = sim->s[j]; - double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2]; - //cubic interpolation from tables - double *p1 = &radialtable[m1*(n-o+1)]; - double *p2 = &radialtable[(m1+1)*(n-o+1)]; - double *p3 = &radialtable[(m1+2)*(n-o+1)]; - double *p0 = &radialtable[(m1-1)*(n-o+1)]; - double *q = &dfctable[m1-1]; - double *rinvs = &rinvsqrttable[m1-1]; - r1 = r1-trunc(r1); - double dfc = q[1] + 0.5 * r1*(q[2] - q[0] + r1*(2.0*q[0] - 5.0*q[1] + 4.0*q[2] - q[3] + r1*(3.0*(q[1] - q[2]) + q[3] - q[0]))); - double ri = rinvs[1] + 0.5 * r1*(rinvs[2] - rinvs[0] + r1*(2.0*rinvs[0] - 5.0*rinvs[1] + 4.0*rinvs[2] - rinvs[3] + r1*(3.0*(rinvs[1] - rinvs[2]) + rinvs[3] - rinvs[0]))); - for (l=0;l<=(n-o);l++){ - double rt = p1[l]+0.5*r1*(p2[l]-p0[l]+r1*(2.0*p0[l]-5.0*p1[l]+4.0*p2[l]-p3[l]+r1*(3.0*(p1[l]-p2[l])+p3[l]-p0[l]))); - dspinx[jj*f+count]+=rt*si[0]; - dspiny[jj*f+count]+=rt*si[1]; - dspinz[jj*f+count]+=rt*si[2]; - dspinx[jnum*f+count]+=rt*sj[0]; - dspiny[jnum*f+count]+=rt*sj[1]; - dspinz[jnum*f+count]+=rt*sj[2]; - rt *= sp; - features[count]+=rt; - rt *= (l+o)/rsq+(-alpha[l]/re+dfc)*ri; - //update neighbor's features - dfeaturesx[jj*f+count]+=rt*delx; - dfeaturesy[jj*f+count]+=rt*dely; - dfeaturesz[jj*f+count]+=rt*delz; - //update atom's features - dfeaturesx[jnum*f+count]-=rt*delx; - dfeaturesy[jnum*f+count]-=rt*dely; - dfeaturesz[jnum*f+count]-=rt*delz; - count++; - } - } - -} - -int Fingerprint_radialspin::get_length() -{ - return n-o+1; -} diff --git a/src/fingerprint_radialspin.h b/src/fingerprint_radialspin.h deleted file mode 100644 index 428c0e74e4..0000000000 --- a/src/fingerprint_radialspin.h +++ /dev/null @@ -1,69 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@me.msstate.edu - ----------------------------------------------------------------------*/ -/* -“The research described and the resulting data presented herein, unless -otherwise noted, was funded under PE 0602784A, Project T53 "Military -Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, -managed by the U.S. Army Combat Capabilities Development Command (CCDC) and -the Engineer Research and Development Center (ERDC). The work described in -this document was conducted at CAVS, MSU. Permission was granted by ERDC -to publish this information. Any opinions, findings and conclusions or -recommendations expressed in this material are those of the author(s) and -do not necessarily reflect the views of the United States Army.​” - -DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 - */ - -#ifdef FINGERPRINT_CLASS - -FingerprintStyle(radialspin,Fingerprint_radialspin) - -#else - -#ifndef FINGERPRINT_RADIALspin_H_ -#define FINGERPRINT_RADIALspin_H_ - -#include "fingerprint.h" - -namespace LAMMPS_NS { - -class Fingerprint_radialspin : public Fingerprint { - public: - Fingerprint_radialspin(PairRANN *); - ~Fingerprint_radialspin(); - bool parse_values(char*,char*); - void write_values(FILE *); - void init(int*,int); - void allocate(); - void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*); - int get_length(); - - double *radialtable; - double *dfctable; - double dr; - double *alpha; - double re; - int n;//highest term - int o;//lowest term - -}; - - -} - -#endif -#endif /* FINGERPRINT_RADIAL_H_ */ diff --git a/src/pair_rann.cpp b/src/pair_rann.cpp deleted file mode 100644 index 3507c931dc..0000000000 --- a/src/pair_rann.cpp +++ /dev/null @@ -1,1247 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@me.msstate.edu - ----------------------------------------------------------------------*/ -/* -“The research described and the resulting data presented herein, unless -otherwise noted, was funded under PE 0602784A, Project T53 "Military -Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, -managed by the U.S. Army Combat Capabilities Development Command (CCDC) and -the Engineer Research and Development Center (ERDC). The work described in -this document was conducted at CAVS, MSU. Permission was granted by ERDC -to publish this information. Any opinions, findings and conclusions or -recommendations expressed in this material are those of the author(s) and -do not necessarily reflect the views of the United States Army.​” - -DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 - */ - -#include "style_fingerprint.h" -#include "style_activation.h" - -#include "pair_rann.h" - -using namespace LAMMPS_NS; - -static const char cite_user_rann_package[] = - "USER-RANN package:\n\n" - "@Article{Nitol2021,\n" - " author = {Nitol, Mashroor S and Dickel, Doyl E and Barrett, Christopher D},\n" - " title = {Artificial neural network potential for pure zinc},\n" - " journal = {Computational Materials Science},\n" - " year = 2021,\n" - " volume = 188,\n" - " pages = {110207}\n" - "}\n\n"; - -PairRANN::PairRANN(LAMMPS *lmp) : Pair(lmp) -{ - single_enable = 0; - restartinfo = 0; - one_coeff = 1; - manybody_flag = 1; - - allocated = 0; - - nelements = -1; - elements = NULL; - mass = NULL; - - // set comm size needed by this Pair - // comm unused for now. - - comm_forward = 38; - comm_reverse = 30; - res = 10000; - cutmax = 0; - //at least one of the following will change during fingerprint definition: - doscreen = false; - allscreen = true; - dospin = false; - - fingerprint_map = new FingerprintCreatorMap(); - - #define FINGERPRINT_CLASS - #define FingerprintStyle(key,Class) \ - (*fingerprint_map)[#key] = &fingerprint_creator; - #include "style_fingerprint.h" - #undef FingerprintStyle - #undef FINGERPRINT_CLASS - - activation_map = new ActivationCreatorMap(); - - #define ACTIVATION_CLASS - #define ActivationStyle(key,Class) \ - (*activation_map)[#key] = &activation_creator; - #include "style_activation.h" - #undef ActivationStyle - #undef ACTIVATION_CLASS -} - -PairRANN::~PairRANN() -{ - //clear memory - delete [] mass; - for (int i=0;i0){ - for (int j=0;j0){ - delete [] fingerprints[i]; - delete [] activation[i]; - } - } - delete [] fingerprints; - delete [] activation; - delete [] fingerprintcount; - delete [] fingerprintperelement; - delete [] fingerprintlength; - delete [] screening_min; - delete [] screening_max; -} - - - -void PairRANN::allocate(char **elementword) -{ - int i,j,k,l,n; - n = atom->ntypes; - memory->create(setflag,n+1,n+1,"pair:setflag"); - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - cutmax = 0; - nelementsp=nelements+1; - //initialize arrays - elements = new char *[nelements]; - elementsp = new char *[nelementsp];//elements + 'all' - mass = new double[nelements]; - net = new NNarchitecture[nelementsp]; - weightdefined = new bool*[nelementsp]; - biasdefined = new bool *[nelementsp]; - activation = new Activation**[nelementsp]; - fingerprints = new Fingerprint**[nelementsp]; - fingerprintlength = new int[nelementsp]; - fingerprintperelement = new int [nelementsp]; - fingerprintcount = new int[nelementsp]; - screening_min = new double [nelements*nelements*nelements]; - screening_max = new double [nelements*nelements*nelements]; - for (i=0;i 0) error->all(FLERR,"Illegal pair_style command"); -} - -void PairRANN::coeff(int narg, char **arg) -{ - int i,j; - map = new int [atom->ntypes+1]; - - - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - nelements = -1; - read_file(arg[2]); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if NULL - - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - { - if (strcmp(arg[i],elements[j]) == 0) break; - } - if (j < nelements) map[i-2] = j; - else error->all(FLERR,"No matching element in NN potential file"); - } - // clear setflag since coeff() called once with I,J = * * - - int n = atom->ntypes; - for (i = 1; i <= n; i++) - for (j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - // set mass of atom type if i = j - - int count = 0; - for (i = 1; i <= n; i++) { - for (j = i; j <= n; j++) { - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - if (i == j) atom->set_mass(FLERR,i,mass[map[i]]); - count++; - } - } - } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); - for (i=0;iallocate(); - } - } - allocated=1; -} - -void PairRANN::read_file(char *filename) -{ - FILE *fp; - int eof = 0,i,j,k,l; - int n,nwords; - int longline = 4096; - char line [longline],line1[longline]; - char *ptr; - bool comment; - char str[128]; - fp = utils::open_potential(filename,lmp,nullptr); - if (fp == NULL) { - sprintf(str,"Cannot open rann potential file %s",filename); - error->one(FLERR,str); - } - while (eof == 0){ - ptr = fgets(line,longline,fp); - if (ptr == NULL) { - if (check_potential()) {//looks to see if everything needed appears to be defined - error->one(FLERR,"Invalid syntax in potential file, values are inconsistent or missing"); - } - else{ - fclose(fp); - eof = 1; - break; - } - } - else n = strlen(line) + 1; - if ((ptr = strchr(line,'#'))) *ptr = '\0';//strip comments from end of lines - if (count_words(line)==0){continue;}//skip comment line - comment = true; - while (comment==true){ - ptr = fgets(line1,longline,fp); - if (ptr==NULL)errorf("Unexpected end of parameter file (keyword given with no value)"); - if ((ptr = strchr(line1,'#'))) *ptr = '\0'; - nwords = count_words(line1); - if (nwords == 0) continue; - comment = false; - } - line1[strlen(line1)-1] = '\0';//replace \n with \0 - nwords = count_words(line); - char **words=new char *[nwords+1]; - nwords = 0; - words[nwords++] = strtok(line,": ,\t_\n"); - while ((words[nwords++] = strtok(NULL,": ,\t_\n"))) continue; - if (strcmp(words[0],"atomtypes")==0)read_atom_types(words,line1); - else if (strcmp(words[0],"mass")==0)read_mass(words,line1); - else if (strcmp(words[0],"fingerprintsperelement")==0)read_fpe(words,line1); - else if (strcmp(words[0],"fingerprints")==0)read_fingerprints(words,nwords-1,line1); - else if (strcmp(words[0],"fingerprintconstants")==0)read_fingerprint_constants(words,nwords-1,line1); - else if (strcmp(words[0],"networklayers")==0)read_network_layers(words,line1); - else if (strcmp(words[0],"layersize")==0)read_layer_size(words,line1); - else if (strcmp(words[0],"weight")==0)read_weight(words,line1,fp); - else if (strcmp(words[0],"bias")==0)read_bias(words,line1,fp); - else if (strcmp(words[0],"activationfunctions")==0)read_activation_functions(words,line1); - else if (strcmp(words[0],"calibrationparameters")==0)continue;//information on how the network was trained - else if (strcmp(words[0],"screening")==0)read_screening(words,nwords-1,line1); - else error->one(FLERR,"Could not understand file syntax: unknown keyword"); - delete [] words; - } -} - -void PairRANN::read_atom_types(char **words,char * line1){ - int nwords = 0; - int t = count_words(line1)+1; - char **elementword = new char *[t]; - elementword[nwords++] = strtok(line1," ,\t:_\n"); - while ((elementword[nwords++] = strtok(NULL," ,\t:_\n"))) continue; - if (nwords < 1) errorf("Incorrect syntax for atom types"); - elementword[nwords-1] = new char [strlen("all")+1]; - char elt [] = "all"; - strcpy(elementword[nwords-1],elt); - nelements = nwords-1; - allocate(elementword); -} - -void PairRANN::read_mass(char **words,char * line1){ - if (nelements == -1)error->one(FLERR,"atom types must be defined before mass in potential file."); - int nwords = 0,i; - for (i=0;ione(FLERR,"mass element not found in atom types."); -} - -void PairRANN::read_fpe(char **words,char * line1){ - int i,j; - if (nelements == -1)error->one(FLERR,"atom types must be defined before fingerprints per element in potential file."); - for (i=0;ione(FLERR,"fingerprint-per-element element not found in atom types"); -} - -void PairRANN::read_fingerprints(char **words,int nwords,char * line1){ - int nwords1=0,i,j,k,l,m,i1; - bool found; - char str[MAXLINE]; - char **words1 = new char * [count_words(line1)+1]; - words1[nwords1++] = strtok(line1," ,\t:_\n"); - while ((words1[nwords1++] = strtok(NULL," ,\t:_\n"))) continue; - nwords1 -= 1; - if (nelements == -1)error->one(FLERR,"atom types must be defined before fingerprints in potential file."); - int atomtypes[nwords-1]; - for (i=1;ione(FLERR,"fingerprint element not found in atom types");} - } - i = atomtypes[0]; - k = 0; - if (fingerprintperelement[i]==-1){error->one(FLERR,"fingerprint per element must be defined before fingerprints");} - while (kn_body_type!=nwords-1){error->one(FLERR,"invalid fingerprint for element combination");} - k++; - fingerprints[i][i1]->init(atomtypes,strtol(words1[k++],NULL,10)); - fingerprintcount[i]++; - } - delete [] words1; -} - - -void PairRANN::read_fingerprint_constants(char **words,int nwords,char * line1){ - int i,j,k,l,m,i1; - bool found; - char str [128]; - if (nelements == -1)error->one(FLERR,"atom types must be defined before fingerprints in potential file."); - int n_body_type = nwords-4; - int atomtypes[n_body_type]; - for (i=1;i<=n_body_type;i++){ - found = false; - for (j=0;jone(FLERR,"fingerprint element not found in atom types");} - } - i = atomtypes[0]; - found = false; - for (k=0;kempty){continue;} - if (n_body_type!=fingerprints[i][k]->n_body_type){continue;} - for (j=0;jatomtypes[j]!=atomtypes[j]){break;} - if (j==n_body_type-1){ - if (strcmp(words[nwords-3],fingerprints[i][k]->style)==0 && strtol(words[nwords-2],NULL,10)==fingerprints[i][k]->id){ - found=true; - i1 = k; - break; - } - } - } - if (found){break;} - } - if (!found){error->one(FLERR,"cannot define constants for unknown fingerprint");} - fingerprints[i][i1]->fullydefined=fingerprints[i][i1]->parse_values(words[nwords-1],line1); -} - -void PairRANN::read_network_layers(char **words,char *line1){ - int i,j; - if (nelements == -1)error->one(FLERR,"atom types must be defined before network layers in potential file."); - for (i=0;ione(FLERR,"network layers element not found in atom types"); -} - -void PairRANN::read_layer_size(char **words,char* line1){ - int i; - for (i=0;ione(FLERR,"networklayers for each atom type must be defined before the corresponding layer sizes."); - int j = strtol(words[2],NULL,10); - if (j>=net[i].layers || j<0){error->one(FLERR,"invalid layer in layer size definition");}; - net[i].dimensions[j]= strtol(line1,NULL,10); - return; - } - } - errorf("layer size element not found in atom types"); -} - -void PairRANN::read_weight(char **words,char* line1,FILE* fp){ - int i,j,k,l,nwords; - char *ptr; - int longline = 4096; - char **words1; - for (l=0;l=net[l].layers || i<0)error->one(FLERR,"invalid weight layer"); - if (net[l].dimensions[i]==0 || net[l].dimensions[i+1]==0) errorf("network layer sizes must be defined before corresponding weight"); - net[l].Weights[i] = new double [net[l].dimensions[i]*net[l].dimensions[i+1]]; - weightdefined[l][i] = true; - int n = count_words(line1)+1; - words1 = new char* [n]; - nwords=0; - words1[nwords++] = strtok(line1," ,\t:_\n"); - while ((words1[nwords++] = strtok(NULL," ,\t:_\n"))) continue; - nwords -= 1; - if (nwords != net[l].dimensions[i])error->one(FLERR,"invalid weights per line"); - for (k=0;kone(FLERR,"invalid weights per line"); - for (k=0;kone(FLERR,"networklayers must be defined before biases."); - i=strtol(words[2],NULL,10); - if (i>=net[l].layers || i<0)error->one(FLERR,"invalid bias layer"); - if (net[l].dimensions[i]==0) error->one(FLERR,"network layer sizes must be defined before corresponding bias"); -// delete [] net[l].Biases[i]; - biasdefined[l][i] = true; - net[l].Biases[i] = new double [net[l].dimensions[i+1]]; - words[0] = strtok(line1," ,\t:_\n"); - net[l].Biases[i][0] = strtod(words[0],NULL); - for (j=1;jone(FLERR,"bias element not found in atom types"); -} - -void PairRANN::read_activation_functions(char** words,char * line1){ - int i,j,l,nwords; - int *ptr; - for (l=0;lone(FLERR,"networklayers must be defined before activation functions."); - i = strtol(words[2],NULL,10); - if (i>=net[l].layers || i<0)error->one(FLERR,"invalid activation layer"); - nwords=0; - words[nwords++] = strtok(line1," ,\t:_\n"); - delete activation[l][i]; - activation[l][i]=create_activation(line1); - return; - } - } - error->one(FLERR,"activation function element not found in atom types"); -} - -void PairRANN::read_screening(char** words,int nwords,char *line1){ - int i,j,k; - bool found; - if (nelements == -1)errorf("atom types must be defined before fingerprints in potential file."); - if (nwords!=5)errorf("invalid screening command"); - int n_body_type = 3; - int atomtypes[n_body_type]; - for (i=1;i<=n_body_type;i++){ - found = false; - for (j=0;jnet[i].maxlayer)net[i].maxlayer = net[i].dimensions[j]; - } - if (net[i].dimensions[net[i].layers-1]!=1)return true;//output layer must have single neuron (the energy) - for (j=0;jempty)return true;//undefined activations - for (k=0;kfullydefined==false)return true; - fingerprints[i][j]->startingneuron = fingerprintlength[i]; - fingerprintlength[i] +=fingerprints[i][j]->get_length(); - if (fingerprints[i][j]->rc>cutmax){cutmax = fingerprints[i][j]->rc;} - } - if (net[i].dimensions[0]!=fingerprintlength[i])return true; - } - return false;//everything looks good -} - -void PairRANN::compute(int eflag, int vflag) -{ - //perform force/energy computation_ - if (dospin){ - if (strcmp(update->unit_style,"metal") != 0) - error->all(FLERR,"Spin pair styles require metal units"); - if (!atom->sp_flag) - error->all(FLERR,"Spin pair styles requires atom/spin style"); - } - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = vflag_atom = 0; - int ii,i,j; - int nn = 0; - sims = new Simulation[1]; - sims->inum = listfull->inum; - sims->ilist=listfull->ilist; - sims->id = listfull->ilist; - sims->type = atom->type; - sims->x = atom->x; - sims->numneigh = listfull->numneigh; - sims->firstneigh = listfull->firstneigh; - if (dospin){ - sims->s = atom->sp; - } - int itype,f,jnum,len; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; - if (eflag_global){eng_vdwl=0;eng_coul=0;} - double energy=0; - double **force = atom->f; - double **fm = atom->fm; - double **virial = vatom; - char str[MAXLINE]; - //loop over atoms - for (ii=0;iiinum;ii++){ - i = sims->ilist[ii]; - itype = map[sims->type[i]]; - f = net[itype].dimensions[0]; - jnum = sims->numneigh[i]; - double *xn = new double[jnum]; - double *yn = new double[jnum]; - double *zn = new double[jnum]; - int *tn = new int[jnum]; - int *jl = new int[jnum]; - cull_neighbor_list(xn,yn,zn,tn,&jnum,jl,i,0); - double features [f]; - double *dfeaturesx = new double[f*jnum]; - double *dfeaturesy = new double[f*jnum]; - double *dfeaturesz = new double[f*jnum]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - itype = nelements; - //do fingerprints for type "all" - len = fingerprintperelement[itype]; - for (j=0;jspin==false && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==false && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==false)fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,ii,nn,xn,yn,zn,tn,jnum-1,jl); - else if (fingerprints[itype][j]->spin==true && fingerprints[itype][j]->screen==true) fingerprints[itype][j]->compute_fingerprint(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,Sik,dSikx,dSiky,dSikz,dSijkx,dSijky,dSijkz,Bij,ii,nn,xn,yn,zn,tn,jnum-1,jl); - } - //run fingerprints through network - if (dospin){ - propagateforwardspin(features,dfeaturesx,dfeaturesy,dfeaturesz,sx,sy,sz,&energy,force,fm,virial,ii,jnum,jl); - } - else { - propagateforward(features,dfeaturesx,dfeaturesy,dfeaturesz,&energy,force,virial,ii,jnum,jl); - } - delete [] xn; - delete [] yn; - delete [] zn; - delete [] tn; - delete [] jl; - delete [] dfeaturesx; - delete [] dfeaturesy; - delete [] dfeaturesz; - delete [] Sik; - delete [] dSikx; - delete [] dSiky; - delete [] dSikz; - delete [] dSijkx; - delete [] dSijky; - delete [] dSijkz; - delete [] Bij; - delete [] sx; - delete [] sy; - delete [] sz; - } - if (vflag_fdotr) virial_fdotr_compute(); -} - -void PairRANN::cull_neighbor_list(double *xn,double *yn, double *zn,int *tn, int* jnum,int *jl,int i,int sn){ - int *jlist,j,count,jj,*type,jtype; - double xtmp,ytmp,ztmp,delx,dely,delz,rsq; - double **x = sims[sn].x; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - type = sims[sn].type; - jlist = sims[sn].firstneigh[i]; - count = 0; - for (jj=0;jjcutmax*cutmax){ - continue; - } - xn[count]=delx; - yn[count]=dely; - zn[count]=delz; - tn[count]=jtype; - jl[count]=j; - count++; - } - jnum[0]=count+1; -} - -void PairRANN::screen_neighbor_list(double *xn,double *yn, double *zn,int *tn, int* jnum,int *jl,int i,int sn,bool *Bij,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz){ - double xnc[jnum[0]],ync[jnum[0]],znc[jnum[0]]; - double Sikc[jnum[0]]; - double dSikxc[jnum[0]]; - double dSikyc[jnum[0]]; - double dSikzc[jnum[0]]; - double dSijkxc[jnum[0]][jnum[0]]; - double dSijkyc[jnum[0]][jnum[0]]; - double dSijkzc[jnum[0]][jnum[0]]; - int jj,kk,count,count1,tnc[jnum[0]],jlc[jnum[0]]; - count = 0; - for (jj=0;jjx; - double xtmp,ytmp,ztmp,delx,dely,delz,rij,delx2,dely2,delz2,rik,delx3,dely3,delz3,rjk; - i = sim->ilist[ii]; - itype = map[sim->type[i]]; -// jnum = sim->numneigh[i]; -// jlist = sim->firstneigh[i]; -// xtmp = x[i][0]; -// ytmp = x[i][1]; -// ztmp = x[i][2]; - for (int jj=0;jjtype[k]]; - ktype = tn[kk]; -// delx2 = xtmp - x[k][0]; -// dely2 = ytmp - x[k][1]; -// delz2 = ztmp - x[k][2]; - delx2 = xn[kk]; - dely2 = yn[kk]; - delz2 = zn[kk]; - rik = delx2*delx2+dely2*dely2+delz2*delz2; - if (rik>cutmax*cutmax){ - Bij[kk]= false; - continue; - } - for (jj=0;jjtype[j]]; -// delx = xtmp - x[j][0]; -// dely = ytmp - x[j][1]; -// delz = ztmp - x[j][2]; - jtype = tn[jj]; - delx = xn[jj]; - dely = yn[jj]; - delz = zn[jj]; - rij = delx*delx+dely*dely+delz*delz; - if (rij>cutmax*cutmax){ - Bij[jj] = false; - continue; - } -// delx3 = x[j][0]-x[k][0]; -// dely3 = x[j][1]-x[k][1]; -// delz3 = x[j][2]-x[k][2]; - delx3 = delx2-delx; - dely3 = dely2-dely; - delz3 = delz2-delz; - rjk = delx3*delx3+dely3*dely3+delz3*delz3; - if (rik+rjk<=rij){continue;}//bond angle > 90 degrees - if (rik+rij<=rjk){continue;}//bond angle > 90 degrees - double Cmax = screening_max[itype*nelements*nelements+jtype*nelements+ktype]; - double Cmin = screening_min[itype*nelements*nelements+jtype*nelements+ktype]; - double temp1 = rij-rik+rjk; - Cn = temp1*temp1-4*rij*rjk; - //Cn = (rij-rik+rjk)*(rij-rik+rjk)-4*rij*rjk; - temp1 = rij-rjk; - Cd = temp1*temp1-rik*rik; - //Cd = (rij-rjk)*(rij-rjk)-rik*rik; - Cijk = Cn/Cd; - //Cijk = 1+2*(rik*rij+rik*rjk-rik*rik)/(rik*rik-(rij-rjk)*(rij-rjk)); - C = (Cijk-Cmin)/(Cmax-Cmin); - if (C>=1){continue;} - else if (C<=0){ - Bij[kk]=false; - break; - } - dC = Cmax-Cmin; - dC *= dC; - dC *= dC; - temp1 = 1-C; - temp1 *= temp1; - temp1 *= temp1; - Sijk = 1-temp1; - Sijk *= Sijk; - Dij = 4*rik*(Cn+4*rjk*(rij+rik-rjk))/Cd/Cd; - Dik = -4*(rij*Cn+rjk*Cn+8*rij*rik*rjk)/Cd/Cd; - Djk = 4*rik*(Cn+4*rij*(rik-rij+rjk))/Cd/Cd; - temp1 = Cijk-Cmax; - double temp2 = temp1*temp1; - dfc = 8*temp1*temp2/(temp2*temp2-dC); - Sik[kk] *= Sijk; - dSijkx[kk*jnum+jj] = dfc*(delx*Dij-delx3*Djk); - dSikx[kk] += dfc*(delx2*Dik+delx3*Djk); - dSijky[kk*jnum+jj] = dfc*(dely*Dij-dely3*Djk); - dSiky[kk] += dfc*(dely2*Dik+dely3*Djk); - dSijkz[kk*jnum+jj] = dfc*(delz*Dij-delz3*Djk); - dSikz[kk] += dfc*(delz2*Dik+delz3*Djk); - } - } -} - - -//Called by getproperties. Propagate features and dfeatures through network. Updates force and energy -void PairRANN::propagateforward(double *features,double *dfeaturesx,double *dfeaturesy,double *dfeaturesz, double * energy,double **force,double **virial, int ii,int jnum,int *jl){ - int i,j,k,jj,j1,itype,i1; - int *ilist,*numneigh; - ilist = listfull->ilist; - int inum = listfull->inum; - int *type = atom->type; - i1=ilist[ii]; - itype = map[type[i1]]; - NNarchitecture net1 = net[itype]; -// numneigh = listfull->numneigh; -// jnum = numneigh[ilist[ii]]+1;//extra value on the end of the array is the self term. -// firstneigh = listfull->firstneigh; -// jlist = firstneigh[i1]; - int L = net1.layers-1; - double layer[net1.maxlayer]; - double sum[net1.maxlayer]; - double sum1[net1.maxlayer]; - double dlayerx[jnum][net1.maxlayer]; - double dlayersumx[jnum][net1.maxlayer]; - double dlayery[jnum][net1.maxlayer]; - double dlayersumy[jnum][net1.maxlayer]; - double dlayerz[jnum][net1.maxlayer]; - double dlayersumz[jnum][net1.maxlayer]; - //energy output with forces from analytical derivatives - double dsum1; - int f = net1.dimensions[0]; - for (i=0;idactivation_function(sum[j]); - sum[j] = activation[itype][i]->activation_function(sum[j]); - if (i==L-1){ - energy[j] = sum[j]; - if (eflag_atom)eatom[i1]=sum[j]; - if (eflag_global){eng_vdwl +=sum[j];} - } - //force propagation - for (jj=0;jjilist; - int inum = listfull->inum; - int *type = atom->type; - i1=ilist[ii]; - itype = map[type[i1]]; - NNarchitecture net1 = net[itype]; -// numneigh = listfull->numneigh; -// jnum = numneigh[ilist[ii]]+1;//extra value on the end of the array is the self term. -// firstneigh = listfull->firstneigh; -// jlist = firstneigh[i1]; - int L = net1.layers-1; - double layer[net1.maxlayer]; - double sum[net1.maxlayer]; - double sum1[net1.maxlayer]; - double dlayerx[jnum][net1.maxlayer]; - double dlayersumx[jnum][net1.maxlayer]; - double dlayery[jnum][net1.maxlayer]; - double dlayersumy[jnum][net1.maxlayer]; - double dlayerz[jnum][net1.maxlayer]; - double dlayersumz[jnum][net1.maxlayer]; - double dsx[jnum][net1.maxlayer]; - double dssumx[jnum][net1.maxlayer]; - double dsy[jnum][net1.maxlayer]; - double dssumy[jnum][net1.maxlayer]; - double dsz[jnum][net1.maxlayer]; - double dssumz[jnum][net1.maxlayer]; - //energy output with forces from analytical derivatives - double dsum1; - int f = net1.dimensions[0]; - for (i=0;idactivation_function(sum[j]); - sum[j] = activation[itype][i]->activation_function(sum[j]); - if (i==L-1){ - energy[j] = sum[j]; - if (eflag_atom)eatom[i1]=sum[j]; - if (eflag_global){eng_vdwl +=sum[j];} - } - //force propagation - for (jj=0;jjrequest(this,instance_me); - neighbor->requests[irequest_full]->id = 1; - neighbor->requests[irequest_full]->half = 0; - neighbor->requests[irequest_full]->full = 1; -} - - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairRANN::init_one(int i, int j) -{ - return cutmax; -} - -void PairRANN::errorf(const char * message){ - this->error->all(FLERR,message); -} - -template -Fingerprint *PairRANN::fingerprint_creator(PairRANN* pair) -{ - return new T(pair); -} - -Fingerprint *PairRANN::create_fingerprint(const char *style) -{ - if (fingerprint_map->find(style) != fingerprint_map->end()) { - FingerprintCreator fingerprint_creator = (*fingerprint_map)[style]; - return fingerprint_creator(this); - } - char str[128]; - sprintf(str,"Unknown fingerprint style %s",style); - error->all(FLERR,str); - return NULL; -} - -template -Activation *PairRANN::activation_creator(PairRANN* pair) -{ - return new T(pair); -} - -Activation *PairRANN::create_activation(const char *style) -{ - if (activation_map->find(style) != activation_map->end()) { - ActivationCreator activation_creator = (*activation_map)[style]; - return activation_creator(this); - } - char str[128]; - sprintf(str,"Unknown activation style %s",style); - error->all(FLERR,str); - return NULL; -} - diff --git a/src/pair_rann.h b/src/pair_rann.h deleted file mode 100644 index 1358c67fb0..0000000000 --- a/src/pair_rann.h +++ /dev/null @@ -1,171 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu - Doyl Dickel (MSU) doyl@me.msstate.edu - ----------------------------------------------------------------------*/ -/* -“The research described and the resulting data presented herein, unless -otherwise noted, was funded under PE 0602784A, Project T53 "Military -Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095, -managed by the U.S. Army Combat Capabilities Development Command (CCDC) and -the Engineer Research and Development Center (ERDC). The work described in -this document was conducted at CAVS, MSU. Permission was granted by ERDC -to publish this information. Any opinions, findings and conclusions or -recommendations expressed in this material are those of the author(s) and -do not necessarily reflect the views of the United States Army.​” - -DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 - */ - -#ifdef PAIR_CLASS - -PairStyle(rann,PairRANN) - -#else - -#ifndef LMP_PAIR_RANN -#define LMP_PAIR_RANN - -#define MAXLINE 1024 - -#include -#include -#include -#include -#include -#include "atom.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" -#include "error.h" -#include "update.h" -#include "pair.h" -#include -#include - -namespace LAMMPS_NS { - -class PairRANN : public Pair { - public: - - //inherited functions - PairRANN(class LAMMPS *); - ~PairRANN(); - void compute(int, int); - void settings(int, char **); - void coeff(int, char **); - void init_style(); - double init_one(int, int); - void init_list(int , NeighList *); - void errorf(const char*); - int count_words(char *); - //black magic for modular fingerprints and activations - class Activation ***activation; - class Fingerprint ***fingerprints; - typedef Fingerprint *(*FingerprintCreator)(PairRANN *); - typedef Activation *(*ActivationCreator)(PairRANN *); - typedef std::map FingerprintCreatorMap; - typedef std::map ActivationCreatorMap; - FingerprintCreatorMap *fingerprint_map; - ActivationCreatorMap *activation_map; - Fingerprint * create_fingerprint(const char *); - Activation * create_activation(const char *); - - //global variables - int nelements; // # of elements (distinct from LAMMPS atom types since multiple atom types can be mapped to one element) - int nelementsp; // nelements+1 - char **elements; // names of elements - char **elementsp; // names of elements with "all" appended as the last "element" - double *mass; // mass of each element - double cutmax; // max radial distance for neighbor lists - int *map; // mapping from atom types to elements - int *fingerprintcount; // static variable used in initialization - int *fingerprintlength; // # of input neurons defined by fingerprints of each element. - int *fingerprintperelement; // # of fingerprints for each element - bool doscreen;//screening is calculated if any defined fingerprint uses it - bool allscreen;//all fingerprints use screening so screened neighbors can be completely ignored - bool dospin; - int res;//Resolution of function tables for cubic interpolation. - int memguess; - double *screening_min; - double *screening_max; - bool **weightdefined; - bool **biasdefined; - - struct Simulation{ - int *id; - bool forces; - bool spins; - double **x; - double **f; - double **s; - double box[3][3]; - double origin[3]; - double **features; - double **dfx; - double **dfy; - double **dfz; - double **dsx; - double **dsy; - double **dsz; - int *ilist,*numneigh,**firstneigh,*type,inum,gnum; - }; - Simulation *sims; - - struct NNarchitecture{ - int layers; - int *dimensions;//vector of length layers with entries for neurons per layer - double **Weights; - double **Biases; - int *activations;//unused - int maxlayer;//longest layer (for memory allocation) - }; - NNarchitecture *net;//array of networks, 1 for each element. - - private: - template static Fingerprint *fingerprint_creator(PairRANN *); - template static Activation *activation_creator(PairRANN *); - //new functions - void allocate(char **);//called after reading element list, but before reading the rest of the potential - void read_file(char *);//read potential file - void read_atom_types(char **,char *); - void read_mass(char **,char *); - void read_fpe(char**,char *);//fingerprints per element. Count total fingerprints defined for each 1st element in element combinations - void read_fingerprints(char **,int,char *); - void read_fingerprint_constants(char **,int,char *); - void read_network_layers(char**,char*);//include input and output layer (hidden layers + 2) - void read_layer_size(char**,char*); - void read_weight(char**,char*,FILE*);//weights should be formatted as properly shaped matrices - void read_bias(char**,char*,FILE*);//biases should be formatted as properly shaped vectors - void read_activation_functions(char**,char*); - void read_screening(char**,int, char*); - bool check_potential();//after finishing reading potential file - void propagateforward(double *,double *,double *,double *,double *,double **,double **,int,int,int*);//called by compute to get force and energy - void propagateforwardspin(double *,double *,double *,double *,double *,double *,double *,double *,double **,double **,double**,int,int,int*);//called by compute to get force and energy - void screen(double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int *,int); - void cull_neighbor_list(double *,double *,double *,int *,int *,int *,int,int); - void screen_neighbor_list(double *,double *,double *,int *,int *,int *,int,int,bool*,double*,double*,double*,double*,double*,double*,double*); -}; - -} - -#endif -#endif - - - From 8dee6cee8d0535de6ea897554d2c115d13c3a756 Mon Sep 17 00:00:00 2001 From: kipbarrett Date: Thu, 11 Feb 2021 09:25:42 -0600 Subject: [PATCH 0101/1217] remove style files from src --- src/style_activation.h | 2 -- src/style_fingerprint.h | 8 -------- 2 files changed, 10 deletions(-) delete mode 100644 src/style_activation.h delete mode 100644 src/style_fingerprint.h diff --git a/src/style_activation.h b/src/style_activation.h deleted file mode 100644 index 4cdd4ff031..0000000000 --- a/src/style_activation.h +++ /dev/null @@ -1,2 +0,0 @@ -#include "activation_linear.h" -#include "activation_sigI.h" diff --git a/src/style_fingerprint.h b/src/style_fingerprint.h deleted file mode 100644 index 2647d31274..0000000000 --- a/src/style_fingerprint.h +++ /dev/null @@ -1,8 +0,0 @@ -#include "fingerprint_bond.h" -#include "fingerprint_bondscreened.h" -#include "fingerprint_bondscreenedspin.h" -#include "fingerprint_bondspin.h" -#include "fingerprint_radial.h" -#include "fingerprint_radialscreened.h" -#include "fingerprint_radialscreenedspin.h" -#include "fingerprint_radialspin.h" From 039ed4c7503858bd93ecb091f83e804597d2c9b6 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 16 Feb 2021 10:24:15 -0700 Subject: [PATCH 0102/1217] Fixing example input scripts with mode multi --- doc/src/comm_modify.rst | 3 ++- examples/granregion/in.granregion.funnel | 2 +- examples/granregion/in.granregion.mixer | 2 +- examples/srd/in.srd.mixture | 2 +- 4 files changed, 5 insertions(+), 4 deletions(-) diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 489ab407ee..06087bd9a2 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -34,7 +34,7 @@ Examples comm_modify mode multi reduce/multi comm_modify mode multi group solvent - comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0 + comm_modift mode multi cutoff/multi 0 10.0 cutoff/multi 2*4 15.0 comm_modify vel yes comm_modify mode single cutoff 5.0 vel yes comm_modify cutoff/multi * 0.0 @@ -101,6 +101,7 @@ communication mode *multi* instead. Since the communication cutoffs are determined per atom collections, a collection specifier is needed and cutoff for one or multiple collections can be extended. Also ranges of collections using the usual asterisk notation can be given. +Collections are indexed from 0 to N-1 where N is the total number of collections. Note that the arguments for *cutoff/multi* are parsed right before each simulation to account for potential changes in the number of collections. Custom cutoffs are preserved between runs but if collections are redefined, diff --git a/examples/granregion/in.granregion.funnel b/examples/granregion/in.granregion.funnel index 63e79a7114..ef74ce5109 100644 --- a/examples/granregion/in.granregion.funnel +++ b/examples/granregion/in.granregion.funnel @@ -86,7 +86,7 @@ pair_style gran/hertz/history & ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 pair_coeff * * -neighbor ${skin} bin +neighbor ${skin} multi thermo ${logfreq} comm_style brick diff --git a/examples/granregion/in.granregion.mixer b/examples/granregion/in.granregion.mixer index f9a9d04cbe..383f51f074 100644 --- a/examples/granregion/in.granregion.mixer +++ b/examples/granregion/in.granregion.mixer @@ -49,7 +49,7 @@ pair_style gran/hertz/history & ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 pair_coeff * * -neighbor ${skin} bin +neighbor ${skin} multi thermo ${logfreq} comm_style brick diff --git a/examples/srd/in.srd.mixture b/examples/srd/in.srd.mixture index ff6e6f5b72..6a0100d800 100644 --- a/examples/srd/in.srd.mixture +++ b/examples/srd/in.srd.mixture @@ -62,7 +62,7 @@ delete_atoms overlap 0.5 small big reset_timestep 0 -neighbor 0.3 bin +neighbor 0.3 multi neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes From 0a06b90b53ed4a5a10df7e873fed845c344ad006 Mon Sep 17 00:00:00 2001 From: Gurgen Date: Wed, 17 Feb 2021 15:33:28 +0300 Subject: [PATCH 0103/1217] template for smooth/spu --- src/GPU/Install.sh | 2 + src/GPU/pair_lj_smooth_gpu.cpp | 255 +++++++++++++++++++++++++++++++++ src/GPU/pair_lj_smooth_gpu.h | 60 ++++++++ 3 files changed, 317 insertions(+) create mode 100644 src/GPU/pair_lj_smooth_gpu.cpp create mode 100644 src/GPU/pair_lj_smooth_gpu.h diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh index 1fefb01d42..536d687e18 100755 --- a/src/GPU/Install.sh +++ b/src/GPU/Install.sh @@ -101,6 +101,8 @@ action pair_lj_cut_coul_msm_gpu.cpp pair_lj_cut_coul_msm.cpp action pair_lj_cut_coul_msm_gpu.h pair_lj_cut_coul_msm.h action pair_lj_cut_gpu.cpp action pair_lj_cut_gpu.h +action pair_lj_smooth_gpu.cpp +action pair_lj_smooth_gpu.h action pair_lj_expand_gpu.cpp action pair_lj_expand_gpu.h action pair_lj_expand_coul_long_gpu.cpp pair_lj_expand_coul_long.cpp diff --git a/src/GPU/pair_lj_smooth_gpu.cpp b/src/GPU/pair_lj_smooth_gpu.cpp new file mode 100644 index 0000000000..4ea5cce92e --- /dev/null +++ b/src/GPU/pair_lj_smooth_gpu.cpp @@ -0,0 +1,255 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Mike Brown (SNL) +------------------------------------------------------------------------- */ + +#include "pair_lj_smooth_gpu.h" +#include +#include + +#include +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "integrate.h" +#include "memory.h" +#include "error.h" +#include "neigh_request.h" +#include "universe.h" +#include "update.h" +#include "domain.h" +#include "gpu_extra.h" +#include "suffix.h" + +using namespace LAMMPS_NS; + +// External functions from cuda library for atom decomposition + +int ljl_gpu_init(const int ntypes, double **cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, double **host_lj4, + double **offset, double *special_lj, const int nlocal, + const int nall, const int max_nbors, const int maxspecial, + const double cell_size, int &gpu_mode, FILE *screen); + +void ljl_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, double **host_lj4, + double **offset); + +void ljl_gpu_clear(); +int ** ljl_gpu_compute_n(const int ago, const int inum, + const int nall, double **host_x, int *host_type, + double *sublo, double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, + const double cpu_time, bool &success); +void ljl_gpu_compute(const int ago, const int inum, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success); +double ljl_gpu_bytes(); + +/* ---------------------------------------------------------------------- */ + +PairLJSmoothGPU::PairLJSmoothGPU(LAMMPS *lmp) : PairLJCut(lmp), gpu_mode(GPU_FORCE) +{ + respa_enable = 0; + cpu_time = 0.0; + suffix_flag |= Suffix::GPU; + GPU_EXTRA::gpu_ready(lmp->modify, lmp->error); +} + +/* ---------------------------------------------------------------------- + free all arrays +------------------------------------------------------------------------- */ + +PairLJSmoothGPU::~PairLJSmoothGPU() +{ + ljl_gpu_clear(); +} + +/* ---------------------------------------------------------------------- */ + +void PairLJSmoothGPU::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); + + int nall = atom->nlocal + atom->nghost; + int inum, host_start; + + bool success = true; + int *ilist, *numneigh, **firstneigh; + if (gpu_mode != GPU_FORCE) { + double sublo[3],subhi[3]; + if (domain->triclinic == 0) { + sublo[0] = domain->sublo[0]; + sublo[1] = domain->sublo[1]; + sublo[2] = domain->sublo[2]; + subhi[0] = domain->subhi[0]; + subhi[1] = domain->subhi[1]; + subhi[2] = domain->subhi[2]; + } else { + domain->bbox(domain->sublo_lamda,domain->subhi_lamda,sublo,subhi); + } + inum = atom->nlocal; + firstneigh = ljl_gpu_compute_n(neighbor->ago, inum, nall, + atom->x, atom->type, sublo, + subhi, atom->tag, atom->nspecial, + atom->special, eflag, vflag, eflag_atom, + vflag_atom, host_start, + &ilist, &numneigh, cpu_time, success); + } else { + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + ljl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, + ilist, numneigh, firstneigh, eflag, vflag, eflag_atom, + vflag_atom, host_start, cpu_time, success); + } + if (!success) + error->one(FLERR,"Insufficient memory on accelerator"); + + if (host_startnewton_pair) + error->all(FLERR,"Cannot use newton pair with lj/cut/gpu pair style"); + + // Repeat cutsq calculation because done after call to init_style + double maxcut = -1.0; + double cut; + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = i; j <= atom->ntypes; j++) { + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + cut = init_one(i,j); + cut *= cut; + if (cut > maxcut) + maxcut = cut; + cutsq[i][j] = cutsq[j][i] = cut; + } else + cutsq[i][j] = cutsq[j][i] = 0.0; + } + } + double cell_size = sqrt(maxcut) + neighbor->skin; + + int maxspecial=0; + if (atom->molecular) + maxspecial=atom->maxspecial; + int success = ljl_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4, + offset, force->special_lj, atom->nlocal, + atom->nlocal+atom->nghost, 300, maxspecial, + cell_size, gpu_mode, screen); + GPU_EXTRA::check_flag(success,error,world); + + if (gpu_mode == GPU_FORCE) { + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJSmoothGPU::reinit() +{ + Pair::reinit(); + + ljl_gpu_reinit(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4, offset); +} + +/* ---------------------------------------------------------------------- */ + +double PairLJSmoothGPU::memory_usage() +{ + double bytes = Pair::memory_usage(); + return bytes + ljl_gpu_bytes(); +} + +/* ---------------------------------------------------------------------- */ + +void PairLJSmoothGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, + int *ilist, int *numneigh, int **firstneigh) { + int i,j,ii,jj,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,r2inv,r6inv,forcelj,factor_lj; + int *jlist; + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + double *special_lj = force->special_lj; + + // loop over neighbors of my atoms + + for (ii = start; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r2inv = 1.0/rsq; + r6inv = r2inv*r2inv*r2inv; + forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + fpair = factor_lj*forcelj*r2inv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + + if (eflag) { + evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) - + offset[itype][jtype]; + evdwl *= factor_lj; + } + + if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz); + } + } + } +} + diff --git a/src/GPU/pair_lj_smooth_gpu.h b/src/GPU/pair_lj_smooth_gpu.h new file mode 100644 index 0000000000..fc245918d0 --- /dev/null +++ b/src/GPU/pair_lj_smooth_gpu.h @@ -0,0 +1,60 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(lj/smooth/gpu,PairLJSmoothGPU) + +#else + +#ifndef LMP_PAIR_LJ_SMOOTH_GPU_H +#define LMP_PAIR_LJ_SMOOTH_GPU_H + +#include "pair_lj_cut.h" + +namespace LAMMPS_NS { + +class PairLJSmoothGPU : public PairLJCut { + public: + PairLJSmoothGPU(LAMMPS *lmp); + ~PairLJSmoothGPU(); + void cpu_compute(int, int, int, int, int *, int *, int **); + void compute(int, int); + void init_style(); + void reinit(); + double memory_usage(); + + enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH }; + + private: + int gpu_mode; + double cpu_time; +}; + +} +#endif +#endif + +/* ERROR/WARNING messages: + +E: Insufficient memory on accelerator + +There is insufficient memory on one of the devices specified for the gpu +package + +E: Cannot use newton pair with lj/cut/gpu pair style + +Self-explanatory. + +*/ + From 4442f38bed112ccf8dabe31428021b8b998a363a Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Sat, 20 Feb 2021 23:04:13 +0100 Subject: [PATCH 0104/1217] Inclusion of n2p2 interface files - github.com/CompPhysVienna/n2p2 commit 2f05836 - example modified (less atoms) --- examples/USER/nnp/data.H2O-360mol | 1096 ++++++++++++++ examples/USER/nnp/in.nnp | 47 + examples/USER/nnp/nnp-data/input.nn | 120 ++ examples/USER/nnp/nnp-data/scaling.data | 72 + examples/USER/nnp/nnp-data/weights.001.data | 1392 ++++++++++++++++++ examples/USER/nnp/nnp-data/weights.008.data | 1467 +++++++++++++++++++ src/USER-NNP/Install.sh | 68 + src/USER-NNP/README | 0 src/USER-NNP/pair_nnp.cpp | 419 ++++++ src/USER-NNP/pair_nnp.h | 70 + 10 files changed, 4751 insertions(+) create mode 100644 examples/USER/nnp/data.H2O-360mol create mode 100644 examples/USER/nnp/in.nnp create mode 100644 examples/USER/nnp/nnp-data/input.nn create mode 100644 examples/USER/nnp/nnp-data/scaling.data create mode 100644 examples/USER/nnp/nnp-data/weights.001.data create mode 100644 examples/USER/nnp/nnp-data/weights.008.data create mode 100644 src/USER-NNP/Install.sh create mode 100644 src/USER-NNP/README create mode 100644 src/USER-NNP/pair_nnp.cpp create mode 100644 src/USER-NNP/pair_nnp.h diff --git a/examples/USER/nnp/data.H2O-360mol b/examples/USER/nnp/data.H2O-360mol new file mode 100644 index 0000000000..3791f07585 --- /dev/null +++ b/examples/USER/nnp/data.H2O-360mol @@ -0,0 +1,1096 @@ +LAMMPS data file, 360 water molecules + +1080 atoms +2 atom types + +0.0 2.2695686722465727E+01 xlo xhi +0.0 2.3586033624598713E+01 ylo yhi +0.0 2.2237130028217017E+01 zlo zhi + +Masses + +1 1.00794 +2 15.9994 + +Atoms # atomic + +1 2 1.7548118361224624E+01 7.3699168122955889E+00 5.5591101411055377E-01 +2 1 1.7052018361224619E+01 7.5604368122955892E+00 1.3882600141105546E+00 +3 1 1.8473918361224619E+01 7.4162968122955890E+00 8.4111101411055411E-01 +4 2 9.1706683612246138E+00 1.2915816812295594E+01 2.5107200141105555E+00 +5 1 9.7830883612246140E+00 1.2151816812295593E+01 2.3347500141105550E+00 +6 1 9.1892283612246164E+00 1.3443216812295594E+01 1.6591000141105545E+00 +7 2 1.8399218361224623E+01 1.7424016812295601E+01 6.5473300141105586E+00 +8 1 1.8345918361224623E+01 1.8268716812295594E+01 7.0339200141105591E+00 +9 1 1.9026818361224624E+01 1.6834816812295600E+01 7.0045500141105599E+00 +10 2 5.7216883612246123E+00 1.6305516812295600E+01 1.0104620014110562E+01 +11 1 6.2668083612246122E+00 1.5517116812295598E+01 9.8182400141105628E+00 +12 1 6.2385083612246124E+00 1.6937316812295599E+01 1.0608050014110562E+01 +13 2 1.1317118361224615E+01 1.1227616812295592E+01 1.5996300141105546E+00 +14 1 1.1296018361224618E+01 1.0203716812295591E+01 1.7394500141105549E+00 +15 1 1.1304118361224615E+01 1.1323916812295593E+01 6.1680301411055383E-01 +16 2 7.8280183612246139E+00 2.2671316812295601E+01 4.2759600141105567E+00 +17 1 7.1177183612246129E+00 2.2216116812295603E+01 3.7208400141105566E+00 +18 1 8.3989583612246133E+00 2.2791416812295601E+01 3.4672900141105565E+00 +19 2 4.3278983612246105E+00 8.5704868122955897E+00 1.9742050014110571E+01 +20 1 5.3082183612246112E+00 8.2615268122955889E+00 1.9662550014110568E+01 +21 1 4.0620583612246106E+00 8.0321368122955903E+00 2.0571250014110571E+01 +22 2 1.7732618361224624E+01 1.5933416812295597E+01 1.9881550014110569E+01 +23 1 1.8279418361224621E+01 1.5600716812295596E+01 2.0596350014110573E+01 +24 1 1.6762718361224621E+01 1.5919016812295597E+01 2.0129250014110571E+01 +25 2 8.8204883612246157E+00 2.0042116812295600E+01 1.5762450014110566E+01 +26 1 7.9101683612246143E+00 1.9947516812295600E+01 1.6194150014110569E+01 +27 1 9.2758283612246135E+00 1.9487716812295599E+01 1.6447350014110569E+01 +28 2 1.1361918361224616E+01 1.2958816812295595E+01 1.5721550014110568E+01 +29 1 1.0710518361224615E+01 1.3138916812295594E+01 1.6487150014110568E+01 +30 1 1.1182418361224618E+01 1.2046616812295593E+01 1.5544250014110565E+01 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1.7778818361224623E+01 1.1435816812295593E+01 3.3615700141105558E+00 +969 1 1.8888418361224623E+01 1.1052616812295591E+01 4.4177400141105574E+00 +970 2 3.3331683612246099E+00 2.1413516812295605E+01 4.4091100141105581E+00 +971 1 4.0140083612246107E+00 2.1587916812295603E+01 3.7370700141105564E+00 +972 1 2.8152483612246098E+00 2.0647116812295604E+01 4.0949500141105570E+00 +973 2 2.1485418361224628E+01 1.3439616812295593E+01 1.8515050014110574E+01 +974 1 2.1232118361224625E+01 1.4409816812295595E+01 1.8622950014110568E+01 +975 1 2.1260918361224622E+01 1.2943316812295594E+01 1.9423250014110568E+01 +976 2 1.5327218361224622E+01 1.1235016812295594E+01 6.0592500141105585E+00 +977 1 1.5020018361224619E+01 1.1987616812295592E+01 6.6193700141105598E+00 +978 1 1.4456518361224619E+01 1.0828416812295591E+01 5.8021100141105579E+00 +979 2 5.3565983612246111E+00 1.2563016812295594E+01 1.0383550014110563E+01 +980 1 4.9874383612246111E+00 1.2201516812295594E+01 1.1265250014110562E+01 +981 1 4.7115983612246106E+00 1.3306916812295594E+01 1.0272250014110563E+01 +982 2 1.3327818361224619E+01 1.2646816812295594E+01 1.7977550014110570E+01 +983 1 1.2756818361224619E+01 1.2533216812295594E+01 1.7175350014110570E+01 +984 1 1.3294018361224618E+01 1.3648916812295596E+01 1.8078250014110566E+01 +985 2 1.5733518361224622E+01 2.1126216812295603E+01 1.1279650014110564E+01 +986 1 1.6342018361224618E+01 2.1831616812295604E+01 1.1643150014110564E+01 +987 1 1.6056418361224623E+01 2.0797916812295600E+01 1.0400750014110562E+01 +988 2 2.1141518361224623E+01 8.9665468122955918E+00 1.0216150014110562E+01 +989 1 2.2048618361224623E+01 9.3445468122955901E+00 1.0211250014110561E+01 +990 1 2.1131918361224624E+01 7.9982568122955895E+00 1.0070990014110562E+01 +991 2 1.6952918361224619E+01 4.4809168122955869E+00 1.3603400141105544E+00 +992 1 1.5977218361224621E+01 4.3960468122955865E+00 1.5795100141105547E+00 +993 1 1.7075618361224620E+01 5.3891468122955875E+00 9.8821101411055423E-01 +994 2 2.8147983612246090E+00 1.8335016812295603E+01 1.6687450014110567E+01 +995 1 3.7292383612246098E+00 1.8106316812295599E+01 1.6439150014110567E+01 +996 1 2.7120783612246098E+00 1.8060816812295599E+01 1.7634450014110573E+01 +997 2 1.3160118361224619E+01 2.1854116812295597E+01 1.6869250014110570E+01 +998 1 1.2921818361224620E+01 2.1262016812295606E+01 1.7604050014110570E+01 +999 1 1.2290218361224618E+01 2.2004216812295599E+01 1.6409850014110567E+01 +1000 2 1.6654118361224619E+01 3.4356068122955858E+00 5.3268000141105585E+00 +1001 1 1.6763518361224619E+01 4.2442668122955860E+00 5.8470000141105576E+00 +1002 1 1.7299318361224621E+01 3.4167768122955859E+00 4.6252900141105568E+00 +1003 2 1.5613183612246082E+00 1.2986316812295593E+01 2.9923100141105561E+00 +1004 1 2.1672183612246085E+00 1.3322516812295593E+01 2.3411500141105552E+00 +1005 1 1.5863483612246085E+00 1.3709516812295595E+01 3.6513500141105570E+00 +1006 2 6.4849083612246119E+00 2.5271168122955849E+00 1.8568450014110571E+01 +1007 1 7.2879383612246134E+00 2.2592968122955850E+00 1.8045950014110566E+01 +1008 1 5.7505583612246109E+00 1.9684868122955843E+00 1.8264250014110566E+01 +1009 2 9.5758483612246152E+00 4.7315968122955869E+00 2.9483000141105560E+00 +1010 1 9.8447783612246162E+00 5.4277568122955868E+00 3.6224300141105563E+00 +1011 1 9.3913583612246132E+00 5.2471068122955877E+00 2.0968400141105548E+00 +1012 2 1.7459518361224628E+01 1.7394616812295595E+01 1.4136050014110564E+01 +1013 1 1.6997518361224621E+01 1.7001616812295595E+01 1.4929850014110565E+01 +1014 1 1.8159518361224624E+01 1.7939816812295597E+01 1.4466550014110565E+01 +1015 2 1.6523918361224624E+01 8.6581968122955892E+00 3.4612500141105564E+00 +1016 1 1.7039518361224623E+01 9.3233368122955920E+00 3.9480000141105562E+00 +1017 1 1.6204518361224622E+01 8.0607768122955896E+00 4.1706000141105566E+00 +1018 2 1.4959218361224620E+01 1.7963316812295599E+01 1.8420150014110572E+01 +1019 1 1.5072318361224621E+01 1.7841916812295597E+01 1.7480050014110571E+01 +1020 1 1.5863718361224620E+01 1.8256416812295598E+01 1.8736850014110569E+01 +1021 2 5.9458283612246126E+00 1.7655468122955842E+00 8.9552400141105615E+00 +1022 1 5.9930583612246124E+00 1.3992668122955838E+00 8.0434000141105599E+00 +1023 1 6.3955783612246124E+00 2.6705268122955848E+00 8.9781900141105631E+00 +1024 2 7.9905683612246134E+00 6.3206668122955882E+00 5.7878000141105588E+00 +1025 1 7.0232783612246132E+00 6.5650168122955890E+00 5.6352000141105574E+00 +1026 1 8.2871683612246141E+00 6.2234468122955882E+00 4.8348300141105574E+00 +1027 2 2.2485118361224625E+01 4.6162468122955866E+00 1.4926050014110565E+01 +1028 1 3.6750636122460728E-01 4.0303968122955869E+00 1.5442850014110565E+01 +1029 1 2.2359918361224626E+01 5.3321768122955868E+00 1.5558650014110567E+01 +1030 2 1.6688383612246085E+00 1.4309368122955839E+00 2.0618750014110571E+01 +1031 1 2.2194783612246085E+00 1.2521468122955839E+00 1.9815950014110573E+01 +1032 1 2.0103483612246089E+00 9.2743081229558355E-01 2.1390350014110570E+01 +1033 2 1.0209818361224615E+01 1.7122116812295598E+01 3.8888100141105570E+00 +1034 1 9.3379483612246137E+00 1.7204816812295597E+01 3.4425700141105562E+00 +1035 1 1.0487818361224615E+01 1.6168916812295599E+01 4.0591700141105562E+00 +1036 2 1.7009718361224621E+01 1.1077816812295593E+01 1.3982750014110566E+01 +1037 1 1.7416618361224621E+01 1.1915716812295594E+01 1.4114250014110565E+01 +1038 1 1.6152518361224622E+01 1.1296216812295594E+01 1.3498650014110565E+01 +1039 2 1.5292118361224619E+01 2.2286916812295601E+01 2.0549250014110573E+01 +1040 1 1.5719918361224620E+01 2.1812016812295600E+01 2.1274150014110575E+01 +1041 1 1.5371618361224622E+01 2.3218716812295604E+01 2.0712450014110569E+01 +1042 2 7.0554283612246129E+00 1.6077516812295599E+01 1.7628950014110565E+01 +1043 1 6.9981783612246131E+00 1.6403416812295596E+01 1.6704450014110570E+01 +1044 1 7.7722083612246129E+00 1.5403516812295596E+01 1.7707550014110570E+01 +1045 2 9.1948983612246149E+00 1.0623516812295591E+01 9.8707000141105627E+00 +1046 1 8.5664583612246137E+00 1.0414716812295591E+01 9.1563400141105618E+00 +1047 1 8.9125783612246146E+00 1.1463416812295593E+01 1.0255350014110562E+01 +1048 2 3.4275083612246098E+00 1.4718216812295594E+01 1.7487000141105546E+00 +1049 1 2.7882983612246091E+00 1.5297516812295596E+01 1.3626300141105543E+00 +1050 1 3.7876783612246099E+00 1.5291116812295597E+01 2.4465400141105555E+00 +1051 2 1.3184418361224617E+01 1.6254416812295595E+01 1.6217400141105547E+00 +1052 1 1.2358318361224617E+01 1.5655016812295598E+01 1.4601300141105547E+00 +1053 1 1.3636118361224620E+01 1.6118716812295595E+01 7.4275201411055392E-01 +1054 2 2.1478318361224627E+01 9.3499668122955910E+00 1.3041450014110564E+01 +1055 1 2.0571518361224623E+01 9.4989368122955913E+00 1.3473650014110564E+01 +1056 1 2.1367718361224625E+01 9.0415068122955891E+00 1.2126950014110564E+01 +1057 2 1.3240818361224617E+01 2.1513516812295602E+01 7.6613400141105599E+00 +1058 1 1.3173218361224619E+01 2.0794016812295602E+01 8.3871300141105607E+00 +1059 1 1.2721018361224617E+01 2.1148516812295600E+01 6.8687800141105599E+00 +1060 2 1.0706218361224616E+01 9.0730668122955915E+00 1.2194050014110564E+01 +1061 1 1.0209918361224616E+01 9.5840168122955909E+00 1.1511850014110562E+01 +1062 1 1.0127718361224616E+01 8.2990868122955899E+00 1.2386250014110566E+01 +1063 2 9.8246936122460771E-01 9.5211468122955907E+00 1.0116250014110562E+01 +1064 1 1.2453883612246077E+00 1.0440616812295591E+01 1.0422250014110562E+01 +1065 1 1.6324283612246082E+00 8.8711068122955901E+00 1.0428050014110564E+01 +1066 2 2.1805418361224621E+01 1.8063116812295597E+01 1.9102050014110567E+01 +1067 1 2.1618318361224627E+01 1.8993216812295604E+01 1.8788850014110569E+01 +1068 1 8.4032061224607005E-02 1.8152616812295598E+01 1.9376750014110570E+01 +1069 2 4.9490783612246112E+00 4.5899568122955863E+00 4.0229100141105567E+00 +1070 1 4.9939883612246110E+00 5.4655868122955873E+00 4.4890400141105573E+00 +1071 1 4.2701383612246104E+00 4.0452668122955862E+00 4.5228100141105569E+00 +1072 2 1.8242218361224626E+01 2.9008968122955854E+00 1.5903950014110567E+01 +1073 1 1.8887118361224626E+01 2.5084568122955848E+00 1.5204150014110565E+01 +1074 1 1.8162418361224624E+01 2.1789868122955851E+00 1.6617050014110568E+01 +1075 2 3.9899383612246102E+00 1.9364416812295598E+01 1.3871050014110565E+01 +1076 1 4.3833283612246108E+00 2.0252516812295600E+01 1.3695350014110566E+01 +1077 1 3.1540783612246095E+00 1.9562116812295599E+01 1.4347050014110566E+01 +1078 2 7.0537683612246127E+00 1.4620616812295594E+01 6.4024900141105583E+00 +1079 1 7.6585583612246131E+00 1.3942216812295593E+01 6.0279100141105584E+00 +1080 1 6.2108683612246125E+00 1.4238816812295596E+01 6.6619400141105594E+00 diff --git a/examples/USER/nnp/in.nnp b/examples/USER/nnp/in.nnp new file mode 100644 index 0000000000..d4664d1c83 --- /dev/null +++ b/examples/USER/nnp/in.nnp @@ -0,0 +1,47 @@ +############################################################################### +# MD simulation for NN water +############################################################################### + +############################################################################### +# VARIABLES +############################################################################### +clear +# Configuration files +variable cfgFile string "data.H2O-360mol" +# Timesteps +variable numSteps equal 10 +variable dt equal 0.0005 +# NN +variable nnpCutoff equal 6.36 +variable nnpDir string "nnp-data" + +############################################################################### +# GENERAL SETUP +############################################################################### +units metal +boundary p p p +atom_style atomic +read_data ${cfgFile} +timestep ${dt} +thermo 1 + +############################################################################### +# NN +############################################################################### +pair_style nnp dir ${nnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254 emap "1:H,2:O" +pair_coeff * * ${nnpCutoff} + +############################################################################### +# INTEGRATOR +############################################################################### +fix INT all nve + +############################################################################### +# OUTPUT +############################################################################### +dump 1 all atom 1 dump.nnp + +############################################################################### +# SIMULATION +############################################################################### +run ${numSteps} diff --git a/examples/USER/nnp/nnp-data/input.nn b/examples/USER/nnp/nnp-data/input.nn new file mode 100644 index 0000000000..885ec0ec70 --- /dev/null +++ b/examples/USER/nnp/nnp-data/input.nn @@ -0,0 +1,120 @@ +############################################################################### +# HDNNP for water H2O +############################################################################### +# Length unit : Bohr +# Energy unit : Ha +# Reference method: RPBE-D3 +############################################################################### + +############################################################################### +# DATA SET NORMALIZATION +############################################################################### +# This section was automatically added by nnp-norm. +mean_energy -2.5521343547039809E+01 +conv_energy 2.4265748255366972E+02 +conv_length 5.8038448995319847E+00 +############################################################################### + +############################################################################### +# GENERAL NNP SETTINGS +############################################################################### +# These keywords are (almost) always required. +number_of_elements 2 # Number of elements. +elements H O # Specification of elements. +#atom_energy H -0.45890771 # Free atom reference energy (H). +#atom_energy O -74.94518524 # Free atom reference energy (O). +cutoff_type 2 # Cutoff type. +scale_symmetry_functions # Scale all symmetry functions with min/max values. +#scale_symmetry_functions_sigma # Scale all symmetry functions with sigma. +scale_min_short 0.0 # Minimum value for scaling. +scale_max_short 1.0 # Maximum value for scaling. +center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value. +global_hidden_layers_short 2 # Number of hidden layers. +global_nodes_short 25 25 # Number of nodes in each hidden layer. +global_activation_short t t l # Activation function for each hidden layer and output layer. +#normalize_nodes # Normalize input of nodes. + +############################################################################### +# SYMMETRY FUNCTIONS +############################################################################### + +# Radial symmetry function (type 2): +#symfunction_short 2 + +# Narrow Angular symmetry function (type 3): +#symfunction_short 3 + +# Wide Angular symmetry function (type 9): +#symfunction_short 9 + +# radial H H +symfunction_short H 2 H 0.001 0.0 12.00 +symfunction_short H 2 H 0.01 0.0 12.00 +symfunction_short H 2 H 0.03 0.0 12.00 +symfunction_short H 2 H 0.06 0.0 12.00 +symfunction_short H 2 H 0.15 1.9 12.00 +symfunction_short H 2 H 0.30 1.9 12.00 +symfunction_short H 2 H 0.60 1.9 12.00 +symfunction_short H 2 H 1.50 1.9 12.00 + +# radial H O / O H +symfunction_short H 2 O 0.001 0.0 12.00 +symfunction_short H 2 O 0.01 0.0 12.00 +symfunction_short H 2 O 0.03 0.0 12.00 +symfunction_short H 2 O 0.06 0.0 12.00 +symfunction_short H 2 O 0.15 0.9 12.00 +symfunction_short H 2 O 0.30 0.9 12.00 +symfunction_short H 2 O 0.60 0.9 12.00 +symfunction_short H 2 O 1.50 0.9 12.00 + +symfunction_short O 2 H 0.001 0.0 12.00 +symfunction_short O 2 H 0.01 0.0 12.00 +symfunction_short O 2 H 0.03 0.0 12.00 +symfunction_short O 2 H 0.06 0.0 12.00 +symfunction_short O 2 H 0.15 0.9 12.00 +symfunction_short O 2 H 0.30 0.9 12.00 +symfunction_short O 2 H 0.60 0.9 12.00 +symfunction_short O 2 H 1.50 0.9 12.00 + +# radial O O +symfunction_short O 2 O 0.001 0.0 12.00 +symfunction_short O 2 O 0.01 0.0 12.00 +symfunction_short O 2 O 0.03 0.0 12.00 +symfunction_short O 2 O 0.06 0.0 12.00 +symfunction_short O 2 O 0.15 4.0 12.00 +symfunction_short O 2 O 0.30 4.0 12.00 +symfunction_short O 2 O 0.60 4.0 12.00 +symfunction_short O 2 O 1.50 4.0 12.00 + +# angular +symfunction_short H 3 O H 0.2 1.0 1.0 12.00000 + +symfunction_short O 3 H H 0.07 1.0 1.0 12.00000 +symfunction_short H 3 O H 0.07 1.0 1.0 12.00000 +symfunction_short O 3 H H 0.07 -1.0 1.0 12.00000 +symfunction_short H 3 O H 0.07 -1.0 1.0 12.00000 + +symfunction_short O 3 H H 0.03 1.0 1.0 12.00000 +symfunction_short H 3 O H 0.03 1.0 1.0 12.00000 +symfunction_short O 3 H H 0.03 -1.0 1.0 12.00000 +symfunction_short H 3 O H 0.03 -1.0 1.0 12.00000 + +symfunction_short O 3 H H 0.01 1.0 4.0 12.00000 +symfunction_short H 3 O H 0.01 1.0 4.0 12.00000 +symfunction_short O 3 H H 0.01 -1.0 4.0 12.00000 +symfunction_short H 3 O H 0.01 -1.0 4.0 12.00000 + +symfunction_short O 3 O H 0.03 1.0 1.0 12.00000 +symfunction_short O 3 O H 0.03 -1.0 1.0 12.00000 +symfunction_short O 3 O H 0.001 1.0 4.0 12.00000 +symfunction_short O 3 O H 0.001 -1.0 4.0 12.00000 + +symfunction_short H 3 O O 0.03 1.0 1.0 12.00000 +symfunction_short H 3 O O 0.03 -1.0 1.0 12.00000 +symfunction_short H 3 O O 0.001 1.0 4.0 12.00000 +symfunction_short H 3 O O 0.001 -1.0 4.0 12.00000 + +symfunction_short O 3 O O 0.03 1.0 1.0 12.00000 +symfunction_short O 3 O O 0.03 -1.0 1.0 12.00000 +symfunction_short O 3 O O 0.001 1.0 4.0 12.00000 +symfunction_short O 3 O O 0.001 -1.0 4.0 12.00000 diff --git a/examples/USER/nnp/nnp-data/scaling.data b/examples/USER/nnp/nnp-data/scaling.data new file mode 100644 index 0000000000..2a9e0ad7a6 --- /dev/null +++ b/examples/USER/nnp/nnp-data/scaling.data @@ -0,0 +1,72 @@ +################################################################################ +# Symmetry function scaling data. +################################################################################ +# Col Name Description +################################################################################ +# 1 e_index Element index. +# 2 sf_index Symmetry function index. +# 3 sf_min Symmetry function minimum. +# 4 sf_max Symmetry function maximum. +# 5 sf_mean Symmetry function mean. +# 6 sf_sigma Symmetry function sigma. +######################################################################################################################### +# 1 2 3 4 5 6 +# e_index sf_index sf_min sf_max sf_mean sf_sigma +######################################################################################################################### + 1 1 1.0882016636170764E+00 9.6166419119419064E+00 2.2691752247542194E+00 6.7883526611658462E-01 + 1 2 7.3274438904180561E-01 5.0028559321574191E+00 1.3272332317543580E+00 3.3936750181780473E-01 + 1 3 7.6010783783215696E-01 7.1427942966219815E+00 1.6470726712825305E+00 5.0771115927383836E-01 + 1 4 5.4842285884800812E-01 3.7661771168267726E+00 1.0163698211361718E+00 2.5362958053787776E-01 + 1 5 4.0080665126604625E-01 4.1469832401668629E+00 9.0925040981537897E-01 2.9758019277508319E-01 + 1 6 3.6209352253798227E-01 2.2678239402766054E+00 6.4931154122889623E-01 1.4835420345383032E-01 + 1 7 1.8919103878435897E-01 2.2292652677252804E+00 4.5693857051003817E-01 1.5976079618578123E-01 + 1 8 2.6704178695764313E-01 1.3208742362468955E+00 4.2395636902644862E-01 8.0492394978461931E-02 + 1 9 2.4513099752055156E-01 9.4751160662053002E-01 3.6244199023263673E-01 5.2993540556109331E-02 + 1 10 2.2248910067848982E-01 2.7596216013647377E+00 5.3891576898130766E-01 2.0137334230483950E-01 + 1 11 1.4743601726548086E-01 5.5599270746969276E-01 2.6773972195910817E-01 2.6188094566404998E-02 + 1 12 9.9110926426029380E-02 1.7265405335201480E+00 2.9553976311554875E-01 1.1619768775752932E-01 + 1 13 6.5093699123904267E-02 3.4521757733971170E-01 1.8521249136783141E-01 1.9741155185936318E-02 + 1 14 3.1653527247865069E-02 9.1293170125596168E-01 1.5025164684953513E-01 5.3480187368038674E-02 + 1 15 2.9202821602466694E-03 2.6453981776124141E-01 7.6525296616004684E-02 1.8780956137549487E-02 + 1 16 3.2145385719803329E-04 2.8696425565429240E-01 4.5792284631233672E-02 2.3263495133568998E-02 + 1 17 2.4693757528509622E-04 1.3848731138266304E-01 1.7693289653297604E-02 9.7460303038080908E-03 + 1 18 5.0992836797990751E-03 5.8319173651547385E-01 2.3851656540978389E-02 3.7790771891778152E-02 + 1 19 3.2282960174310170E-04 2.1613962298381925E-01 1.7072560754702336E-02 1.4026518665786077E-02 + 1 20 4.9647513277769700E-02 1.6851617426880194E+00 1.4541325969622534E-01 1.0954306125703028E-01 + 1 21 3.4073471604482227E-03 3.1637071808861689E-01 1.8422597685566724E-02 2.0125274191649719E-02 + 1 22 1.3121382132811807E-04 1.0258348935693713E-01 6.3684016949344113E-03 6.6071626858835051E-03 + 1 23 3.3813162813665906E-02 9.1618560879938926E-01 8.1266384503339575E-02 5.7918502576695730E-02 + 1 24 4.1708500446352870E-04 1.5785966980407021E-01 4.6646981268568697E-03 9.8630700614506465E-03 + 1 25 7.3528900917695290E-04 5.9225627251013026E-02 3.7042174075139758E-03 3.3118079036492621E-03 + 1 26 8.9828333062972592E-03 1.9426085555380754E-01 2.4093377110646338E-02 1.0980657457661532E-02 + 1 27 2.1228022180417653E-04 8.7777813240869640E-03 2.0550705761547970E-03 5.8802103858137246E-04 + 2 1 1.5142595331454245E+00 1.0005711988559998E+01 2.6544664635087183E+00 6.7806617585688911E-01 + 2 2 4.4366445360926199E-01 4.6195409357987076E+00 9.6587051599896101E-01 3.3688559575009042E-01 + 2 3 1.1907810568758714E+00 7.5323544094345003E+00 2.0327396422723472E+00 5.0607867531004169E-01 + 2 4 2.7576036468694687E-01 3.3862131032504492E+00 6.5929732667024776E-01 2.5004687333979903E-01 + 2 5 8.0580777590695674E-01 4.5356481255168557E+00 1.2986230824577940E+00 2.9449908325462404E-01 + 2 6 1.0517053799863604E-01 1.8909877539194515E+00 3.0673921331641835E-01 1.4198497108573313E-01 + 2 7 5.6949141690859706E-01 2.6154328621607852E+00 8.4791273805289546E-01 1.5714071578589769E-01 + 2 8 2.3251646720171416E-02 9.3641034200657891E-01 1.1140979781150941E-01 6.9796654369842781E-02 + 2 9 5.1354161698115419E-01 1.8545341781448565E+00 7.2488398046527269E-01 9.8011511620611044E-02 + 2 10 1.1057465545812291E-01 2.9121456897811342E+00 4.7474421797982730E-01 2.3441807910092233E-01 + 2 11 3.5269317308496489E-01 1.0714592032613128E+00 5.3547944391821678E-01 4.5179661104166338E-02 + 2 12 3.0424313539726355E-02 2.5277642768509305E+00 3.1652845366685045E-01 2.1026891409654727E-01 + 2 13 1.5980022688828247E-01 6.6348817066386512E-01 3.7042498273566293E-01 3.0753700953611234E-02 + 2 14 2.7781847150922931E-03 2.3030057819082539E+00 1.7737800292869690E-01 1.8600239464755819E-01 + 2 15 9.5641036809349829E-03 3.9085233064570807E-01 1.5305059323200970E-01 2.7862233984302390E-02 + 2 16 3.7500170432292374E-06 2.0367068825281995E+00 5.4144316535640342E-02 1.4305857218443538E-01 + 2 17 2.4726232100491033E-03 3.4335400617385042E-01 1.6684597803376652E-02 2.1902951351570905E-02 + 2 18 1.7405672406959600E-05 5.6319316766205302E-02 9.5478184601751693E-04 3.3588039002222358E-03 + 2 19 5.4785372164647961E-02 3.0182597583971442E+00 2.0392031625072374E-01 2.0088721011517138E-01 + 2 20 1.3795234987637416E-03 4.9878800454061323E-01 1.2788265359933434E-02 3.1829452602194934E-02 + 2 21 6.6852772684814245E-03 2.6739582842775905E-01 3.0851859894574358E-02 1.7089886758420030E-02 + 2 22 1.7021399438214336E-02 1.4167796508898451E+00 7.6274174813506748E-02 9.2852504206357669E-02 + 2 23 1.9759831791959857E-02 4.0756378297923890E-01 4.8843503112397949E-02 2.5474332458885439E-02 + 2 24 5.2768632746659245E-04 2.3324050667069166E-01 7.2057238727819412E-03 1.4495435261027742E-02 + 2 25 1.1144879740881719E-05 3.5285772934088612E-02 4.2545240948261025E-04 2.0471375111485984E-03 + 2 26 1.6013752685265073E-02 8.2245409953473059E-01 5.0845479076508403E-02 5.2802834522172923E-02 + 2 27 3.9898424495541764E-03 7.8557031440100300E-01 3.6926675414383096E-02 5.0474458307624794E-02 + 2 28 4.0523818189746699E-05 9.8448068666705968E-02 1.2119235889230262E-03 5.7945700128174639E-03 + 2 29 6.0374649986214514E-03 9.9251766407842473E-02 1.6156539248049700E-02 5.5245068674135743E-03 + 2 30 2.9595491075765732E-03 1.5478537567691833E-01 1.1641055270110553E-02 8.9415193910804703E-03 diff --git a/examples/USER/nnp/nnp-data/weights.001.data b/examples/USER/nnp/nnp-data/weights.001.data new file mode 100644 index 0000000000..deb5012acb --- /dev/null +++ b/examples/USER/nnp/nnp-data/weights.001.data @@ -0,0 +1,1392 @@ +################################################################################ +# Neural network connection values (weights and biases). +################################################################################ +# Col Name Description +################################################################################ +# 1 connection Neural network connection value. +# 2 t Connection type (a = weight, b = bias). +# 3 index Index enumerating weights. +# 4 l_s Starting point layer (end point layer for biases). +# 5 n_s Starting point neuron in starting layer (end point neuron for biases). +# 6 l_e End point layer. +# 7 n_e End point neuron in end layer. +################################################################################ +# 1 2 3 4 5 6 7 +# connection t index l_s n_s l_e n_e +############################################################ + 1.2539155865352127E+00 a 1 0 1 1 1 + 2.2490365890661286E+00 a 2 0 1 1 2 + 4.9361851928374572E+00 a 3 0 1 1 3 + -2.3971991574908125E+00 a 4 0 1 1 4 + -1.8596992303156465E+00 a 5 0 1 1 5 + 3.8287764168815897E+00 a 6 0 1 1 6 + 7.4523181738636106E+00 a 7 0 1 1 7 + 6.0971861116881998E+00 a 8 0 1 1 8 + -8.7239359226117639E+00 a 9 0 1 1 9 + -1.8255232070184267E+01 a 10 0 1 1 10 + -7.8065643887610179E+00 a 11 0 1 1 11 + 1.4247237398130265E+01 a 12 0 1 1 12 + -3.2217879518334338E+00 a 13 0 1 1 13 + -5.7395252086520712E+00 a 14 0 1 1 14 + 2.0353040522911576E+00 a 15 0 1 1 15 + 7.7520578160630560E+00 a 16 0 1 1 16 + 2.9357257867412252E+00 a 17 0 1 1 17 + -2.9719860930100790E+00 a 18 0 1 1 18 + 8.9245382590288980E+00 a 19 0 1 1 19 + 6.6848134049442169E+00 a 20 0 1 1 20 + -2.2992719903495891E+00 a 21 0 1 1 21 + -1.4401533482181721E+01 a 22 0 1 1 22 + -2.0574070545285186E+00 a 23 0 1 1 23 + -6.3544667277888678E+00 a 24 0 1 1 24 + 3.9668360525851707E+00 a 25 0 1 1 25 + 1.0930597297534963E+01 a 26 0 2 1 1 + 3.0058866618169424E+00 a 27 0 2 1 2 + -4.9950943102999927E+00 a 28 0 2 1 3 + -1.9930957240687266E+00 a 29 0 2 1 4 + 1.6790893133342006E+00 a 30 0 2 1 5 + -4.5254006136507128E+00 a 31 0 2 1 6 + -9.6165021729265252E+00 a 32 0 2 1 7 + -8.7465722730176285E+00 a 33 0 2 1 8 + 1.5506950040431201E+01 a 34 0 2 1 9 + 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2 21 3 1 + -7.2018714033119180E-01 a 1372 2 22 3 1 + 5.9870832883780798E+00 a 1373 2 23 3 1 + -6.0589155387470683E-01 a 1374 2 24 3 1 + 5.0177609140285355E+00 a 1375 2 25 3 1 + 9.7386086372975722E+00 b 1376 3 1 diff --git a/examples/USER/nnp/nnp-data/weights.008.data b/examples/USER/nnp/nnp-data/weights.008.data new file mode 100644 index 0000000000..fbdbaa1411 --- /dev/null +++ b/examples/USER/nnp/nnp-data/weights.008.data @@ -0,0 +1,1467 @@ +################################################################################ +# Neural network connection values (weights and biases). +################################################################################ +# Col Name Description +################################################################################ +# 1 connection Neural network connection value. +# 2 t Connection type (a = weight, b = bias). +# 3 index Index enumerating weights. +# 4 l_s Starting point layer (end point layer for biases). +# 5 n_s Starting point neuron in starting layer (end point neuron for biases). +# 6 l_e End point layer. +# 7 n_e End point neuron in end layer. +################################################################################ +# 1 2 3 4 5 6 7 +# connection t index l_s n_s l_e n_e +############################################################ + -4.2252995889643252E-01 a 1 0 1 1 1 + -6.0555645962054347E+00 a 2 0 1 1 2 + 1.4040722027928377E+01 a 3 0 1 1 3 + -2.7041370011942618E+00 a 4 0 1 1 4 + -3.8202743208058858E+00 a 5 0 1 1 5 + -3.3612643261393358E+00 a 6 0 1 1 6 + -2.0418101025905258E+00 a 7 0 1 1 7 + 7.5707237340996727E+00 a 8 0 1 1 8 + -5.8098755815926548E+00 a 9 0 1 1 9 + -6.0966886893925210E-01 a 10 0 1 1 10 + 5.8061564015115206E+00 a 11 0 1 1 11 + -1.5509339733099867E+00 a 12 0 1 1 12 + 1.9747395485200818E+00 a 13 0 1 1 13 + 4.5260782279680539E-01 a 14 0 1 1 14 + 9.9210415760283279E+00 a 15 0 1 1 15 + -6.5078831481547121E+00 a 16 0 1 1 16 + -3.4768832871318085E+00 a 17 0 1 1 17 + -1.9463994340943838E+00 a 18 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-2.6481374255863193E+00 a 1449 2 24 3 1 + 5.2166795947347921E-01 a 1450 2 25 3 1 + 4.8693043186011655E+00 b 1451 3 1 diff --git a/src/USER-NNP/Install.sh b/src/USER-NNP/Install.sh new file mode 100644 index 0000000000..e17603df76 --- /dev/null +++ b/src/USER-NNP/Install.sh @@ -0,0 +1,68 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# all package files with no dependencies + +for file in *.cpp *.h; do + test -f ${file} && action $file +done + +# edit 2 Makefile.package files to include/exclude package info + +if (test $1 = 1) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*nnp[^ \t]* //g' ../Makefile.package + sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/nnp\/include |' ../Makefile.package + sed -i -e 's|^PKG_PATH =[ \t]*|&-L..\/..\/lib\/nnp\/lib |' ../Makefile.package + sed -i -e 's|^PKG_LIB =[ \t]*|&-lnnpif -lnnp |' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(nnp_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(nnp_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(nnp_SYSPATH) |' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*nnp.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ +include ..\/..\/lib\/nnp\/src\/libnnpif\/LAMMPS\/Makefile.lammps +' ../Makefile.package.settings + + fi + +elif (test $1 = 0) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*nnp[^ \t]* //g' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*nnp.*$/d' ../Makefile.package.settings + fi + +fi diff --git a/src/USER-NNP/README b/src/USER-NNP/README new file mode 100644 index 0000000000..e69de29bb2 diff --git a/src/USER-NNP/pair_nnp.cpp b/src/USER-NNP/pair_nnp.cpp new file mode 100644 index 0000000000..2ccde4418d --- /dev/null +++ b/src/USER-NNP/pair_nnp.cpp @@ -0,0 +1,419 @@ +// n2p2 - A neural network potential package +// Copyright (C) 2018 Andreas Singraber (University of Vienna) +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + +#include +#include +#include "pair_nnp.h" +#include "atom.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "memory.h" +#include "error.h" +#include "update.h" +#include "utils.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairNNP::PairNNP(LAMMPS *lmp) : Pair(lmp) +{ +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete +------------------------------------------------------------------------- */ + +PairNNP::~PairNNP() +{ +} + +/* ---------------------------------------------------------------------- */ + +void PairNNP::compute(int eflag, int vflag) +{ + if(eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + + // Set number of local atoms and add index and element. + interface.setLocalAtoms(atom->nlocal,atom->tag,atom->type); + + // Transfer local neighbor list to NNP interface. + transferNeighborList(); + + // Compute symmetry functions, atomic neural networks and add up energy. + interface.process(); + + // Do all stuff related to extrapolation warnings. + if(showew == true || showewsum > 0 || maxew >= 0) { + handleExtrapolationWarnings(); + } + + // Calculate forces of local and ghost atoms. + interface.getForces(atom->f); + + // Add energy contribution to total energy. + if (eflag_global) + ev_tally(0,0,atom->nlocal,1,interface.getEnergy(),0.0,0.0,0.0,0.0,0.0); + + // Add atomic energy if requested (CAUTION: no physical meaning!). + if (eflag_atom) + for (int i = 0; i < atom->nlocal; ++i) + eatom[i] = interface.getAtomicEnergy(i); + + // If virial needed calculate via F dot r. + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairNNP::settings(int narg, char **arg) +{ + int iarg = 0; + + if (narg == 0) error->all(FLERR,"Illegal pair_style command"); + + // default settings + int len = strlen("nnp/") + 1; + directory = new char[len]; + strcpy(directory,"nnp/"); + showew = true; + showewsum = 0; + maxew = 0; + resetew = false; + cflength = 1.0; + cfenergy = 1.0; + len = strlen("") + 1; + emap = new char[len]; + strcpy(emap,""); + numExtrapolationWarningsTotal = 0; + numExtrapolationWarningsSummary = 0; + + while(iarg < narg) { + // set NNP directory + if (strcmp(arg[iarg],"dir") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + delete[] directory; + len = strlen(arg[iarg+1]) + 2; + directory = new char[len]; + sprintf(directory, "%s/", arg[iarg+1]); + iarg += 2; + // element mapping + } else if (strcmp(arg[iarg],"emap") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + delete[] emap; + len = strlen(arg[iarg+1]) + 1; + emap = new char[len]; + sprintf(emap, "%s", arg[iarg+1]); + iarg += 2; + // show extrapolation warnings + } else if (strcmp(arg[iarg],"showew") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + if (strcmp(arg[iarg+1],"yes") == 0) + showew = true; + else if (strcmp(arg[iarg+1],"no") == 0) + showew = false; + else + error->all(FLERR,"Illegal pair_style command"); + iarg += 2; + // show extrapolation warning summary + } else if (strcmp(arg[iarg],"showewsum") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + showewsum = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + // maximum allowed extrapolation warnings + } else if (strcmp(arg[iarg],"maxew") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + maxew = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + // reset extrapolation warning counter + } else if (strcmp(arg[iarg],"resetew") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + if (strcmp(arg[iarg+1],"yes") == 0) + resetew = true; + else if (strcmp(arg[iarg+1],"no") == 0) + resetew = false; + else + error->all(FLERR,"Illegal pair_style command"); + iarg += 2; + // length unit conversion factor + } else if (strcmp(arg[iarg],"cflength") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + cflength = utils::numeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + // energy unit conversion factor + } else if (strcmp(arg[iarg],"cfenergy") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + cfenergy = utils::numeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + } else error->all(FLERR,"Illegal pair_style command"); + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairNNP::coeff(int narg, char **arg) +{ + if (!allocated) allocate(); + + if (narg != 3) error->all(FLERR,"Incorrect args for pair coefficients"); + + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + + maxCutoffRadius = utils::numeric(FLERR,arg[2],false,lmp); + + // TODO: Check how this flag is set. + int count = 0; + for(int i=ilo; i<=ihi; i++) { + for(int j=MAX(jlo,i); j<=jhi; j++) { + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairNNP::init_style() +{ + int irequest = neighbor->request((void *) this); + neighbor->requests[irequest]->pair = 1; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + + // Return immediately if NNP setup is already completed. + if (interface.isInitialized()) return; + + // Activate screen and logfile output only for rank 0. + if (comm->me == 0) { + if (lmp->screen != NULL) + interface.log.registerCFilePointer(&(lmp->screen)); + if (lmp->logfile != NULL) + interface.log.registerCFilePointer(&(lmp->logfile)); + } + + // Initialize interface on all processors. + interface.initialize(directory, + emap, + showew, + resetew, + showewsum, + maxew, + cflength, + cfenergy, + maxCutoffRadius, + atom->ntypes, + comm->me); + + // LAMMPS cutoff radius (given via pair_coeff) should not be smaller than + // maximum symmetry function cutoff radius. + if (maxCutoffRadius < interface.getMaxCutoffRadius()) + error->all(FLERR,"Inconsistent cutoff radius"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairNNP::init_one(int i, int j) +{ + // TODO: Check how this actually works for different cutoffs. + return maxCutoffRadius; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairNNP::write_restart(FILE *fp) +{ + return; +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairNNP::read_restart(FILE *fp) +{ + return; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairNNP::write_restart_settings(FILE *fp) +{ + return; +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairNNP::read_restart_settings(FILE *fp) +{ + return; +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairNNP::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); +} + +void PairNNP::transferNeighborList() +{ + // Transfer neighbor list to NNP. + double rc2 = maxCutoffRadius * maxCutoffRadius; + for (int ii = 0; ii < list->inum; ++ii) { + int i = list->ilist[ii]; + for (int jj = 0; jj < list->numneigh[i]; ++jj) { + int j = list->firstneigh[i][jj]; + j &= NEIGHMASK; + double dx = atom->x[i][0] - atom->x[j][0]; + double dy = atom->x[i][1] - atom->x[j][1]; + double dz = atom->x[i][2] - atom->x[j][2]; + double d2 = dx * dx + dy * dy + dz * dz; + if (d2 <= rc2) { + interface.addNeighbor(i,j,atom->tag[j],atom->type[j],dx,dy,dz,d2); + } + } + } +} + +void PairNNP::handleExtrapolationWarnings() +{ + // Get number of extrapolation warnings for local atoms. + // TODO: Is the conversion from std::size_t to long ok? + long numCurrentEW = (long)interface.getNumExtrapolationWarnings(); + + // Update (or set, resetew == true) total warnings counter. + if (resetew) numExtrapolationWarningsTotal = numCurrentEW; + else numExtrapolationWarningsTotal += numCurrentEW; + + // Update warnings summary counter. + if(showewsum > 0) { + numExtrapolationWarningsSummary += numCurrentEW; + } + + // If requested write extrapolation warnings. + // Requires communication of all symmetry functions statistics entries to + // rank 0. + if(showew > 0) { + // First collect an overview of extrapolation warnings per process. + long* numEWPerProc = NULL; + if(comm->me == 0) numEWPerProc = new long[comm->nprocs]; + MPI_Gather(&numCurrentEW, 1, MPI_LONG, numEWPerProc, 1, MPI_LONG, 0, world); + + if(comm->me == 0) { + for(int i=1;inprocs;i++) { + if(numEWPerProc[i] > 0) { + long bs = 0; + MPI_Status ms; + // Get buffer size. + MPI_Recv(&bs, 1, MPI_LONG, i, 0, world, &ms); + char* buf = new char[bs]; + // Receive buffer. + MPI_Recv(buf, bs, MPI_BYTE, i, 0, world, &ms); + interface.extractEWBuffer(buf, bs); + delete[] buf; + } + } + interface.writeExtrapolationWarnings(); + } + else if(numCurrentEW > 0) { + // Get desired buffer length for all extrapolation warning entries. + long bs = interface.getEWBufferSize(); + // Allocate and fill buffer. + char* buf = new char[bs]; + interface.fillEWBuffer(buf, bs); + // Send buffer size and buffer. + MPI_Send(&bs, 1, MPI_LONG, 0, 0, world); + MPI_Send(buf, bs, MPI_BYTE, 0, 0, world); + delete[] buf; + } + + if(comm->me == 0) delete[] numEWPerProc; + } + + // If requested gather number of warnings to display summary. + if(showewsum > 0 && update->ntimestep % showewsum == 0) { + long globalEW = 0; + // Communicate the sum over all processors to proc 0. + MPI_Reduce(&numExtrapolationWarningsSummary, + &globalEW, 1, MPI_LONG, MPI_SUM, 0, world); + // Write to screen or logfile. + if(comm->me == 0) { + if(screen) { + fprintf(screen, + "### NNP EW SUMMARY ### TS: %10ld EW %10ld EWPERSTEP %10.3E\n", + update->ntimestep, + globalEW, + double(globalEW) / showewsum); + } + if(logfile) { + fprintf(logfile, + "### NNP EW SUMMARY ### TS: %10ld EW %10ld EWPERSTEP %10.3E\n", + update->ntimestep, + globalEW, + double(globalEW) / showewsum); + } + } + // Reset summary counter. + numExtrapolationWarningsSummary = 0; + } + + // Stop if maximum number of extrapolation warnings is exceeded. + if (numExtrapolationWarningsTotal > maxew) { + error->one(FLERR,"Too many extrapolation warnings"); + } + + // Reset internal extrapolation warnings counters. + interface.clearExtrapolationWarnings(); +} diff --git a/src/USER-NNP/pair_nnp.h b/src/USER-NNP/pair_nnp.h new file mode 100644 index 0000000000..c067118131 --- /dev/null +++ b/src/USER-NNP/pair_nnp.h @@ -0,0 +1,70 @@ +// n2p2 - A neural network potential package +// Copyright (C) 2018 Andreas Singraber (University of Vienna) +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + +#ifdef PAIR_CLASS + +PairStyle(nnp,PairNNP) + +#else + +#ifndef LMP_PAIR_NNP_H +#define LMP_PAIR_NNP_H + +#include "pair.h" +#include "InterfaceLammps.h" + +namespace LAMMPS_NS { + +class PairNNP : public Pair { + + public: + + PairNNP(class LAMMPS *); + virtual ~PairNNP(); + virtual void compute(int, int); + virtual void settings(int, char **); + virtual void coeff(int, char **); + virtual void init_style(); + virtual double init_one(int, int); + virtual void write_restart(FILE *); + virtual void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + + protected: + + virtual void allocate(); + void transferNeighborList(); + void handleExtrapolationWarnings(); + + bool showew; + bool resetew; + int showewsum; + int maxew; + long numExtrapolationWarningsTotal; + long numExtrapolationWarningsSummary; + double cflength; + double cfenergy; + double maxCutoffRadius; + char* directory; + char* emap; + nnp::InterfaceLammps interface; +}; + +} + +#endif +#endif From 28207f15b83a0acda9e583ce0300d0ea336cef7d Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Sun, 21 Feb 2021 00:13:52 +0100 Subject: [PATCH 0105/1217] Switch to forward declaration in header pair_nnp.h --- src/USER-NNP/pair_nnp.cpp | 63 ++++++++++++++++++++------------------- src/USER-NNP/pair_nnp.h | 7 +++-- 2 files changed, 38 insertions(+), 32 deletions(-) diff --git a/src/USER-NNP/pair_nnp.cpp b/src/USER-NNP/pair_nnp.cpp index 2ccde4418d..64043a78bb 100644 --- a/src/USER-NNP/pair_nnp.cpp +++ b/src/USER-NNP/pair_nnp.cpp @@ -26,6 +26,7 @@ #include "error.h" #include "update.h" #include "utils.h" +#include "InterfaceLammps.h" using namespace LAMMPS_NS; @@ -33,6 +34,7 @@ using namespace LAMMPS_NS; PairNNP::PairNNP(LAMMPS *lmp) : Pair(lmp) { + interface = new nnp::InterfaceLammps(); } /* ---------------------------------------------------------------------- @@ -41,6 +43,7 @@ PairNNP::PairNNP(LAMMPS *lmp) : Pair(lmp) PairNNP::~PairNNP() { + delete interface; } /* ---------------------------------------------------------------------- */ @@ -51,13 +54,13 @@ void PairNNP::compute(int eflag, int vflag) else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; // Set number of local atoms and add index and element. - interface.setLocalAtoms(atom->nlocal,atom->tag,atom->type); + interface->setLocalAtoms(atom->nlocal,atom->tag,atom->type); // Transfer local neighbor list to NNP interface. transferNeighborList(); // Compute symmetry functions, atomic neural networks and add up energy. - interface.process(); + interface->process(); // Do all stuff related to extrapolation warnings. if(showew == true || showewsum > 0 || maxew >= 0) { @@ -65,16 +68,16 @@ void PairNNP::compute(int eflag, int vflag) } // Calculate forces of local and ghost atoms. - interface.getForces(atom->f); + interface->getForces(atom->f); // Add energy contribution to total energy. if (eflag_global) - ev_tally(0,0,atom->nlocal,1,interface.getEnergy(),0.0,0.0,0.0,0.0,0.0); + ev_tally(0,0,atom->nlocal,1,interface->getEnergy(),0.0,0.0,0.0,0.0,0.0); // Add atomic energy if requested (CAUTION: no physical meaning!). if (eflag_atom) for (int i = 0; i < atom->nlocal; ++i) - eatom[i] = interface.getAtomicEnergy(i); + eatom[i] = interface->getAtomicEnergy(i); // If virial needed calculate via F dot r. if (vflag_fdotr) virial_fdotr_compute(); @@ -215,32 +218,32 @@ void PairNNP::init_style() neighbor->requests[irequest]->full = 1; // Return immediately if NNP setup is already completed. - if (interface.isInitialized()) return; + if (interface->isInitialized()) return; // Activate screen and logfile output only for rank 0. if (comm->me == 0) { - if (lmp->screen != NULL) - interface.log.registerCFilePointer(&(lmp->screen)); - if (lmp->logfile != NULL) - interface.log.registerCFilePointer(&(lmp->logfile)); + if (lmp->screen != nullptr) + interface->log.registerCFilePointer(&(lmp->screen)); + if (lmp->logfile != nullptr) + interface->log.registerCFilePointer(&(lmp->logfile)); } // Initialize interface on all processors. - interface.initialize(directory, - emap, - showew, - resetew, - showewsum, - maxew, - cflength, - cfenergy, - maxCutoffRadius, - atom->ntypes, - comm->me); + interface->initialize(directory, + emap, + showew, + resetew, + showewsum, + maxew, + cflength, + cfenergy, + maxCutoffRadius, + atom->ntypes, + comm->me); // LAMMPS cutoff radius (given via pair_coeff) should not be smaller than // maximum symmetry function cutoff radius. - if (maxCutoffRadius < interface.getMaxCutoffRadius()) + if (maxCutoffRadius < interface->getMaxCutoffRadius()) error->all(FLERR,"Inconsistent cutoff radius"); } @@ -321,7 +324,7 @@ void PairNNP::transferNeighborList() double dz = atom->x[i][2] - atom->x[j][2]; double d2 = dx * dx + dy * dy + dz * dz; if (d2 <= rc2) { - interface.addNeighbor(i,j,atom->tag[j],atom->type[j],dx,dy,dz,d2); + interface->addNeighbor(i,j,atom->tag[j],atom->type[j],dx,dy,dz,d2); } } } @@ -331,7 +334,7 @@ void PairNNP::handleExtrapolationWarnings() { // Get number of extrapolation warnings for local atoms. // TODO: Is the conversion from std::size_t to long ok? - long numCurrentEW = (long)interface.getNumExtrapolationWarnings(); + long numCurrentEW = (long)interface->getNumExtrapolationWarnings(); // Update (or set, resetew == true) total warnings counter. if (resetew) numExtrapolationWarningsTotal = numCurrentEW; @@ -347,7 +350,7 @@ void PairNNP::handleExtrapolationWarnings() // rank 0. if(showew > 0) { // First collect an overview of extrapolation warnings per process. - long* numEWPerProc = NULL; + long* numEWPerProc = nullptr; if(comm->me == 0) numEWPerProc = new long[comm->nprocs]; MPI_Gather(&numCurrentEW, 1, MPI_LONG, numEWPerProc, 1, MPI_LONG, 0, world); @@ -361,18 +364,18 @@ void PairNNP::handleExtrapolationWarnings() char* buf = new char[bs]; // Receive buffer. MPI_Recv(buf, bs, MPI_BYTE, i, 0, world, &ms); - interface.extractEWBuffer(buf, bs); + interface->extractEWBuffer(buf, bs); delete[] buf; } } - interface.writeExtrapolationWarnings(); + interface->writeExtrapolationWarnings(); } else if(numCurrentEW > 0) { // Get desired buffer length for all extrapolation warning entries. - long bs = interface.getEWBufferSize(); + long bs = interface->getEWBufferSize(); // Allocate and fill buffer. char* buf = new char[bs]; - interface.fillEWBuffer(buf, bs); + interface->fillEWBuffer(buf, bs); // Send buffer size and buffer. MPI_Send(&bs, 1, MPI_LONG, 0, 0, world); MPI_Send(buf, bs, MPI_BYTE, 0, 0, world); @@ -415,5 +418,5 @@ void PairNNP::handleExtrapolationWarnings() } // Reset internal extrapolation warnings counters. - interface.clearExtrapolationWarnings(); + interface->clearExtrapolationWarnings(); } diff --git a/src/USER-NNP/pair_nnp.h b/src/USER-NNP/pair_nnp.h index c067118131..ab86abbc0e 100644 --- a/src/USER-NNP/pair_nnp.h +++ b/src/USER-NNP/pair_nnp.h @@ -24,7 +24,10 @@ PairStyle(nnp,PairNNP) #define LMP_PAIR_NNP_H #include "pair.h" -#include "InterfaceLammps.h" + +namespace nnp { + class InterfaceLammps; +} namespace LAMMPS_NS { @@ -61,7 +64,7 @@ class PairNNP : public Pair { double maxCutoffRadius; char* directory; char* emap; - nnp::InterfaceLammps interface; + nnp::InterfaceLammps* interface; }; } From af974c2aba3d9d110e2b5d4f8fc15168e67660aa Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Mon, 22 Feb 2021 00:29:10 +0100 Subject: [PATCH 0106/1217] Added pair_nnp documentation --- doc/src/Build_extras.rst | 20 ++++ doc/src/Commands_pair.rst | 1 + doc/src/Packages_details.rst | 30 +++++ doc/src/Packages_user.rst | 2 + doc/src/pair_nnp.rst | 222 +++++++++++++++++++++++++++++++++++ doc/src/pair_style.rst | 1 + 6 files changed, 276 insertions(+) create mode 100644 doc/src/pair_nnp.rst diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index cf15de74bd..99aaf69f8f 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -52,6 +52,7 @@ This is the list of packages that may require additional steps. * :ref:`USER-MESONT ` * :ref:`USER-MOLFILE ` * :ref:`USER-NETCDF ` + * :ref:`USER-NNP ` * :ref:`USER-PLUMED ` * :ref:`USER-OMP ` * :ref:`USER-QMMM ` @@ -1586,6 +1587,25 @@ on your system. ---------- +.. _user-nnp: + +USER-NNP package +--------------------------------- + +.. tabs:: + + .. tab:: CMake build + + .. code-block:: bash + + ADD STUFF HERE + + .. tab:: Traditional make + + ADD STUFF HERE + +---------- + .. _user-omp: USER-OMP package diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index e7277e2bbb..7aa27860b1 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -197,6 +197,7 @@ OPT. * :doc:`nm/cut (o) ` * :doc:`nm/cut/coul/cut (o) ` * :doc:`nm/cut/coul/long (o) ` + * :doc:`nnp ` * :doc:`oxdna/coaxstk ` * :doc:`oxdna/excv ` * :doc:`oxdna/hbond ` diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 455df083e4..ea27bd3abf 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -88,6 +88,7 @@ page gives those details. * :ref:`USER-MOFFF ` * :ref:`USER-MOLFILE ` * :ref:`USER-NETCDF ` + * :ref:`USER-NNP ` * :ref:`USER-OMP ` * :ref:`USER-PHONON ` * :ref:`USER-PLUMED ` @@ -1921,6 +1922,35 @@ This package has :ref:`specific installation instructions ` on the ---------- +.. _PKG-USER-NNP: + +USER-NNP package +---------------- + +**Contents:** + +:doc:`pair_style nnp ` command + +.. _n2p2: https://github.com/CompPhysVienna/n2p2 + +To use this package you must have the n2p2 core and interface library +(``libnnp``, ``libnnpif``) available on your system. + +**Author:** Andreas Singraber + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/USER-NNP: filenames -> commands +* src/USER-NNP/README +* :doc:`pair_style nnp ` +* examples/USER/nnp + +---------- + .. _PKG-USER-OMP: USER-OMP package diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index a3efaf15c8..8f7e955924 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -79,6 +79,8 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-NETCDF ` | dump output via NetCDF | :doc:`dump netcdf ` | n/a | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-NNP ` | High-dimensional neural network potenials | :doc:`pair_style nnp ` | USER/nnp | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-OMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-PHONON ` | phonon dynamical matrix | :doc:`fix phonon ` | USER/phonon | no | diff --git a/doc/src/pair_nnp.rst b/doc/src/pair_nnp.rst new file mode 100644 index 0000000000..56ea8bf575 --- /dev/null +++ b/doc/src/pair_nnp.rst @@ -0,0 +1,222 @@ +.. index:: pair_style nnp + +pair_style nnp command +====================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style nnp keyword value ... + +* zero or more keyword/value pairs may be appended +* keyword = *dir* or *showew* or *showewsum* or *maxew* or *resetew* or *cflength* or *cfenergy* +* value depends on the preceding keyword: + +.. parsed-literal:: + + *emap* value = mapping + mapping = Element mapping from LAMMPS atom types to n2p2 elements + *dir* value = directory + directory = Path to NNP configuration files + *showew* value = *yes* or *no* + *showewsum* value = summary + summary = Write EW summary every this many timesteps (*0* turns summary off) + *maxew* value = threshold + threshold = Maximum number of EWs allowed + *resetew* value = *yes* or *no* + *cflength* value = length + length = Length unit conversion factor + *cfenergy* value = energy + energy = Energy unit conversion factor + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style nnp showew yes showewsum 100 maxew 1000 resetew yes cflength 1.8897261328 cfenergy 0.0367493254 emap "1:H,2:O" + pair_coeff * * 6.35 + + pair_style nnp dir "./" showewsum 10000 + pair_coeff * * 6.01 + +Description +""""""""""" + +This pair style adds an interaction based on the high-dimensional neural network +potential method [1]_. These potentials must be carefully trained to reproduce +the potential energy surface in the desired phase-space region prior to their +usage in an MD simulation. This pair style uses an interface to the NNP library +[2]_ [3]_, see the documentation there for more information. + +The maximum cutoff radius of all symmetry functions is the only argument of the +*pair_coeff* command which should be invoked with asterisk wild-cards only: + +.. code-block:: LAMMPS + + pair_coeff * * cutoff + +.. note:: + + The cutoff must be given in LAMMPS length units, even if the neural network + potential has been trained using a different unit system (see remarks about the + *cflength* and *cfenergy* keywords below for details). + +The numeric value may be slightly larger than the actual maximum symmetry +function cutoff radius (to account for rounding errors when converting units), +but must not be smaller. + +---- + +If provided, the keyword *emap* determines the mapping from LAMMPS atom types to +n2p2 elements. The format is a comma-separated list of ``atom type:element`` +pairs, e.g. ``"1:Cu,2:Zn"`` will map atom types 1 and 2 to elements Cu and Zn, +respectively. Atom types not present in the list will be completely ignored by +the NNP. The keyword *emap* is mandatory in a "hybrid" setup (see +:doc:`pair_hybrid `) with "extra" atom types in the simulation +which are not handled by the NNP. + +.. warning:: + + Without an explicit mapping it is by default assumed that the atom type + specifications in LAMMPS configuration files are consistent with the ordering + of elements in the NNP library. Thus, without the *emap* keyword present + atom types must be sorted in order of ascending atomic number, e.g. the only + correct mapping for a configuration containing hydrogen, oxygen and zinc + atoms would be: + + +---------+---------------+-------------+ + | Element | Atomic number | LAMMPS type | + +=========+===============+=============+ + | H | 1 | 1 | + +---------+---------------+-------------+ + | O | 8 | 2 | + +---------+---------------+-------------+ + | Zn | 30 | 3 | + +---------+---------------+-------------+ + +Use the *dir* keyword to specify the directory containing the NNP configuration +files. The directory must contain ``input.nn`` with neural network and symmetry +function setup, ``scaling.data`` with symmetry function scaling data and +``weights.???.data`` with weight parameters for each element. + +The keyword *showew* can be used to turn on/off the display of extrapolation +warnings (EWs) which are issued whenever a symmetry function value is out of +bounds defined by minimum/maximum values in "scaling.data". An extrapolation +warning may look like this: + +.. code-block:: LAMMPS + + ### NNP EXTRAPOLATION WARNING ### STRUCTURE: 0 ATOM: 119 ELEMENT: Cu SYMFUNC: 32 TYPE: 3 VALUE: 2.166E-02 MIN: 2.003E-05 MAX: 1.756E-02 + +stating that the value 2.166E-02 of symmetry function 32 of type 3 (angular +narrow), element Cu (see the log file for a symmetry function listing) was out +of bounds (maximum in ``scaling.data`` is 1.756E-02) for atom 119. Here, the +atom index refers to the LAMMPS tag (global index) and the structure index is +used to print out the MPI rank the atom belongs to. + +.. note:: + + The *showew* keyword should only be set to *yes* for debugging purposes. + Extrapolation warnings may add lots of overhead as they are communicated each + timestep. Also, if the simulation is run in a region where the NNP was not + correctly trained, lots of extrapolation warnings may clog log files and the + console. In a production run use *showewsum* instead. + +The keyword *showewsum* can be used to get an overview of extrapolation warnings +occurring during an MD simulation. The argument specifies the interval at which +extrapolation warning summaries are displayed and logged. An EW summary may look +like this: + +.. code-block:: LAMMPS + + ### NNP EW SUMMARY ### TS: 100 EW 11 EWPERSTEP 1.100E-01 + +Here, at timestep 100 the occurrence of 11 extrapolation warnings since the last +summary is reported, which corresponds to an EW rate of 0.11 per timestep. +Setting *showewsum* to 0 deactivates the EW summaries. + +A maximum number of allowed extrapolation warnings can be specified with the +*maxew* keyword. If the number of EWs exceeds the *maxew* argument the +simulation is stopped. Note however that this is merely an approximate threshold +since the check is only performed at the end of each timestep and each MPI +process counts individually to minimize communication overhead. + +The keyword *resetew* alters the behavior of the above mentioned *maxew* +threshold. If *resetew* is set to *yes* the threshold is applied on a +per-timestep basis and the internal EW counters are reset at the beginning of +each timestep. With *resetew* set to *no* the counters accumulate EWs along the +whole trajectory. + +If the training of a neural network potential has been performed with different +physical units for length and energy than those set in LAMMPS, it is still +possible to use the potential when the unit conversion factors are provided via +the *cflength* and *cfenergy* keywords. If for example, the NNP was +parameterized with Bohr and Hartree training data and symmetry function +parameters (i.e. distances and energies in "input.nn" are given in Bohr and +Hartree) but LAMMPS is set to use *metal* units (Angstrom and eV) the correct +conversion factors are: + +.. code-block:: LAMMPS + + cflength 1.8897261328 + + cfenergy 0.0367493254 + +Thus, arguments of *cflength* and *cfenergy* are the multiplicative factors +required to convert lengths and energies given in LAMMPS units to respective +quantities in native NNP units (1 Angstrom = 1.8897261328 Bohr, 1 eV = +0.0367493254 Hartree). + +---- + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This style does not support mixing. The :doc:`pair_coeff ` command +should only be invoked with asterisk wild cards (see above). + +This style does not support the :doc:`pair_modify ` +shift, table, and tail options. + +This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. + +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , +*middle*\ , *outer* keywords. + +Restrictions +"""""""""""" + +This pair style is part of the USER-NNP package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. + +Please report bugs and feature requests to the `n2p2 GitHub issue page +`__. + +Related commands +^^^^^^^^^^^^^^^^ + +:doc:`pair_coeff `, :doc:`pair_hybrid `, :doc:`units ` + +Default +^^^^^^^ + +The default options are *dir* = "nnp/", *showew* = yes, *showewsum* = 0, *maxew* += 0, *resetew* = no, *cflength* = 1.0, *cfenergy* = 1.0. The default atom type +mapping is determined automatically according to ascending atomic number of +present elements (see above). + +---- + +.. [1] Behler, J.; Parrinello, M. Generalized Neural-Network Representation of + High-Dimensional Potential-Energy Surfaces. Phys. Rev. Lett. 2007, 98 (14), + 146401. https://doi.org/10.1103/PhysRevLett.98.146401 + +.. [2] https://github.com/CompPhysVienna/n2p2 + +.. [3] Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C. Parallel + Multistream Training of High-Dimensional Neural Network Potentials. J. Chem. + Theory Comput. 2019, 15 (5), 3075–3092. https://doi.org/10.1021/acs.jctc.8b01092 diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 524581d2c4..b164e9f828 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -260,6 +260,7 @@ accelerated styles exist. * :doc:`nm/cut ` - N-M potential * :doc:`nm/cut/coul/cut ` - N-M potential with cutoff Coulomb * :doc:`nm/cut/coul/long ` - N-M potential with long-range Coulomb +* :doc:`nnp ` - High-dimensional neural network potential * :doc:`oxdna/coaxstk ` - * :doc:`oxdna/excv ` - * :doc:`oxdna/hbond ` - From 6dbb0230c23ef75673fb5bab552274c08f71df7d Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Mon, 22 Feb 2021 22:57:45 +0100 Subject: [PATCH 0107/1217] Updated documentation, cleaned source --- cmake/CMakeLists.txt | 2 +- cmake/presets/all_off.cmake | 4 ++-- cmake/presets/all_on.cmake | 4 ++-- cmake/presets/nolib.cmake | 4 ++-- doc/src/Build_package.rst | 22 ++++++++++----------- doc/src/pair_nnp.rst | 38 ++++++++++++++++++++++++------------- src/USER-NNP/pair_nnp.cpp | 38 ------------------------------------- src/USER-NNP/pair_nnp.h | 4 ---- 8 files changed, 43 insertions(+), 73 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index aefa9cd597..850d32714e 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -110,7 +110,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF - USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB + USER-MOLFILE USER-NETCDF USER-NNP USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF) diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index bd94b9dbe5..d567b141bf 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -8,8 +8,8 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD - USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP - USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP + USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-NNP + USER-OMP USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 438c119c4c..2b879e9ecf 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -10,8 +10,8 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD - USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP - USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP + USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-NNP + USER-OMP USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index 0245b58cc7..c0236347cb 100644 --- a/cmake/presets/nolib.cmake +++ b/cmake/presets/nolib.cmake @@ -3,8 +3,8 @@ set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB - USER-MOLFILE USER-MESONT USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP - USER-SCAFACOS USER-SMD USER-VTK) + USER-MOLFILE USER-MESONT USER-NETCDF USER-NNP USER-PLUMED USER-QMMM + USER-QUIP USER-SCAFACOS USER-SMD USER-VTK) foreach(PKG ${PACKAGES_WITH_LIB}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index f9fc52f8db..36a7bce482 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -30,17 +30,17 @@ steps, as explained on the :doc:`Build extras ` page. These links take you to the extra instructions for those select packages: -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`COMPRESS ` | :ref:`GPU ` | :ref:`KIM ` | :ref:`KOKKOS ` | :ref:`LATTE ` | :ref:`MESSAGE ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`MSCG ` | :ref:`OPT ` | :ref:`POEMS ` | :ref:`PYTHON ` | :ref:`VORONOI ` | :ref:`USER-ADIOS ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`USER-INTEL ` | :ref:`USER-MOLFILE ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-NETCDF ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | :ref:`USER-QUIP ` | :ref:`USER-SCAFACOS ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | | | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ ++--------------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`COMPRESS ` | :ref:`GPU ` | :ref:`KIM ` | :ref:`KOKKOS ` | :ref:`LATTE ` | :ref:`MESSAGE ` | ++--------------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`MSCG ` | :ref:`OPT ` | :ref:`POEMS ` | :ref:`PYTHON ` | :ref:`VORONOI ` | :ref:`USER-ADIOS ` | ++--------------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`USER-INTEL ` | :ref:`USER-MOLFILE ` | ++--------------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`USER-NETCDF ` | :ref:`USER-NNP ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | :ref:`USER-QUIP ` | ++--------------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`USER-SCAFACOS ` | :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | | ++--------------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ The mechanism for including packages is simple but different for CMake versus make. diff --git a/doc/src/pair_nnp.rst b/doc/src/pair_nnp.rst index 56ea8bf575..78fa635c1f 100644 --- a/doc/src/pair_nnp.rst +++ b/doc/src/pair_nnp.rst @@ -46,13 +46,21 @@ Description """"""""""" This pair style adds an interaction based on the high-dimensional neural network -potential method [1]_. These potentials must be carefully trained to reproduce -the potential energy surface in the desired phase-space region prior to their -usage in an MD simulation. This pair style uses an interface to the NNP library -[2]_ [3]_, see the documentation there for more information. +potential (HDNNP) method as presented in :ref:`(Behler and Parrinello 2007) +`. HDNNPs are machine learning potentials which require +careful training of neural networks prior to application in MD simulations. The +pair style uses an interface to the *n2p2* library :ref:`(Singraber et al 2019) +` which is available on Github `here +`__. Please see the *n2p2* +`documentation `__ for further details. +*n2p2* (and hence this pair style) is compatible with neural network potentials +trained with its own tools and with `RuNNer +`__. However, at this point only +short-range HDNNPs are supported. -The maximum cutoff radius of all symmetry functions is the only argument of the -*pair_coeff* command which should be invoked with asterisk wild-cards only: +The maximum cutoff radius of all symmetry functions (the atomic environment +descriptors of HDNNPs) is the only argument of the *pair_coeff* command which +should be invoked with asterisk wild-cards only: .. code-block:: LAMMPS @@ -211,12 +219,16 @@ present elements (see above). ---- -.. [1] Behler, J.; Parrinello, M. Generalized Neural-Network Representation of - High-Dimensional Potential-Energy Surfaces. Phys. Rev. Lett. 2007, 98 (14), - 146401. https://doi.org/10.1103/PhysRevLett.98.146401 +.. _Behler_Parrinello_2007: -.. [2] https://github.com/CompPhysVienna/n2p2 +**(Behler and Parrinello 2007)** Behler, J.; Parrinello, M. Generalized +Neural-Network Representation of High-Dimensional Potential-Energy Surfaces. +Phys. Rev. Lett. 2007, 98 (14), 146401. +https://doi.org/10.1103/PhysRevLett.98.146401 -.. [3] Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C. Parallel - Multistream Training of High-Dimensional Neural Network Potentials. J. Chem. - Theory Comput. 2019, 15 (5), 3075–3092. https://doi.org/10.1021/acs.jctc.8b01092 +.. _Singraber_et_al_2019: + +**(Singraber et al 2019)** Singraber, A.; Behler, J.; Dellago, C. Library-Based +LAMMPS Implementation of High-Dimensional Neural Network Potentials. J. Chem. +Theory Comput. 2019, 15 (3), 1827–1840. +https://doi.org/10.1021/acs.jctc.8b00770. diff --git a/src/USER-NNP/pair_nnp.cpp b/src/USER-NNP/pair_nnp.cpp index 64043a78bb..c7ac600e45 100644 --- a/src/USER-NNP/pair_nnp.cpp +++ b/src/USER-NNP/pair_nnp.cpp @@ -253,46 +253,9 @@ void PairNNP::init_style() double PairNNP::init_one(int i, int j) { - // TODO: Check how this actually works for different cutoffs. return maxCutoffRadius; } -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairNNP::write_restart(FILE *fp) -{ - return; -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairNNP::read_restart(FILE *fp) -{ - return; -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairNNP::write_restart_settings(FILE *fp) -{ - return; -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairNNP::read_restart_settings(FILE *fp) -{ - return; -} - /* ---------------------------------------------------------------------- allocate all arrays ------------------------------------------------------------------------- */ @@ -333,7 +296,6 @@ void PairNNP::transferNeighborList() void PairNNP::handleExtrapolationWarnings() { // Get number of extrapolation warnings for local atoms. - // TODO: Is the conversion from std::size_t to long ok? long numCurrentEW = (long)interface->getNumExtrapolationWarnings(); // Update (or set, resetew == true) total warnings counter. diff --git a/src/USER-NNP/pair_nnp.h b/src/USER-NNP/pair_nnp.h index ab86abbc0e..0b76739d77 100644 --- a/src/USER-NNP/pair_nnp.h +++ b/src/USER-NNP/pair_nnp.h @@ -42,10 +42,6 @@ class PairNNP : public Pair { virtual void coeff(int, char **); virtual void init_style(); virtual double init_one(int, int); - virtual void write_restart(FILE *); - virtual void read_restart(FILE *); - virtual void write_restart_settings(FILE *); - virtual void read_restart_settings(FILE *); protected: From 7e411f2b1251eadc6f59b6a25bd350574c7a2ac2 Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Tue, 23 Feb 2021 14:05:06 +0100 Subject: [PATCH 0108/1217] New makefile in lib/nnp/ dir, updated Install.sh --- lib/nnp/README | 1 + src/USER-NNP/Install.sh | 5 +---- 2 files changed, 2 insertions(+), 4 deletions(-) create mode 100644 lib/nnp/README diff --git a/lib/nnp/README b/lib/nnp/README new file mode 100644 index 0000000000..a5cfd5cd23 --- /dev/null +++ b/lib/nnp/README @@ -0,0 +1 @@ +WRITE STUFF HERE diff --git a/src/USER-NNP/Install.sh b/src/USER-NNP/Install.sh index e17603df76..cd60ba1598 100644 --- a/src/USER-NNP/Install.sh +++ b/src/USER-NNP/Install.sh @@ -38,9 +38,6 @@ if (test $1 = 1) then if (test -e ../Makefile.package) then sed -i -e 's/[^ \t]*nnp[^ \t]* //g' ../Makefile.package - sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/nnp\/include |' ../Makefile.package - sed -i -e 's|^PKG_PATH =[ \t]*|&-L..\/..\/lib\/nnp\/lib |' ../Makefile.package - sed -i -e 's|^PKG_LIB =[ \t]*|&-lnnpif -lnnp |' ../Makefile.package sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(nnp_SYSINC) |' ../Makefile.package sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(nnp_SYSLIB) |' ../Makefile.package sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(nnp_SYSPATH) |' ../Makefile.package @@ -50,7 +47,7 @@ if (test $1 = 1) then sed -i -e '/^include.*nnp.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ -include ..\/..\/lib\/nnp\/src\/libnnpif\/LAMMPS\/Makefile.lammps +include ..\/..\/lib\/nnp\/Makefile.lammps\ ' ../Makefile.package.settings fi From c56f665c5baab0acd6c0291b580da1918688d3a1 Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Tue, 23 Feb 2021 23:35:18 +0100 Subject: [PATCH 0109/1217] CMake files for finding n2p2 --- cmake/CMakeLists.txt | 3 ++- cmake/Modules/FindN2P2.cmake | 25 +++++++++++++++++++++++++ cmake/Modules/Packages/USER-NNP.cmake | 3 +++ src/Makefile | 8 ++++---- 4 files changed, 34 insertions(+), 5 deletions(-) create mode 100644 cmake/Modules/FindN2P2.cmake create mode 100644 cmake/Modules/Packages/USER-NNP.cmake diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 850d32714e..bb982085e7 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -374,7 +374,8 @@ else() set(CUDA_REQUEST_PIC) endif() -foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM +foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE + USER-NETCDF USER-NNP USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS) if(PKG_${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL}) diff --git a/cmake/Modules/FindN2P2.cmake b/cmake/Modules/FindN2P2.cmake new file mode 100644 index 0000000000..f1a9058f33 --- /dev/null +++ b/cmake/Modules/FindN2P2.cmake @@ -0,0 +1,25 @@ +include(FindPackageHandleStandardArgs) + +if (DEFINED ENV{N2P2_DIR}) + set(N2P2_DIR "${N2P2_DIR}") +endif() +message(STATUS "N2P2_DIR=${N2P2_DIR}") + +find_path(N2P2_INCLUDE_DIR InterfaceLammps.h PATHS "${N2P2_DIR}/include") +find_library(N2P2_LIBNNP NAMES nnp PATHS "${N2P2_DIR}/lib") +find_library(N2P2_LIBNNPIF NAMES nnpif PATHS "${N2P2_DIR}/lib") + +find_package_handle_standard_args(N2P2 DEFAULT_MSG N2P2_INCLUDE_DIR N2P2_LIBNNP) + +if(N2P2_FOUND) + set(N2P2_INCLUDE_DIRS ${N2P2_INCLUDE_DIR}) + set(N2P2_LIBRARIES ${N2P2_LIBNNPIF} ${N2P2_LIBNNP}) + + mark_as_advanced( + N2P2_DIR + N2P2_INCLUDE_DIR + N2P2_LIBNNP + N2P2_LIBNNPIF + ) +endif() + diff --git a/cmake/Modules/Packages/USER-NNP.cmake b/cmake/Modules/Packages/USER-NNP.cmake new file mode 100644 index 0000000000..57eae791d2 --- /dev/null +++ b/cmake/Modules/Packages/USER-NNP.cmake @@ -0,0 +1,3 @@ +find_package(N2P2 REQUIRED) +target_include_directories(lammps PRIVATE ${N2P2_INCLUDE_DIRS}) +target_link_libraries(lammps PRIVATE ${N2P2_LIBRARIES}) diff --git a/src/Makefile b/src/Makefile index 679cbe7b97..3afe821db7 100644 --- a/src/Makefile +++ b/src/Makefile @@ -55,14 +55,14 @@ PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-c user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ user-intel user-lb user-manifold user-meamc user-mesodpd user-mesont \ user-mgpt user-misc user-mofff user-molfile \ - user-netcdf user-omp user-phonon user-plumed user-ptm user-qmmm \ + user-netcdf user-nnp user-omp user-phonon user-plumed user-ptm user-qmmm \ user-qtb user-quip user-reaction user-reaxc user-scafacos user-smd user-smtbq \ user-sdpd user-sph user-tally user-uef user-vtk user-yaff PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \ python voronoi \ user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ - user-netcdf user-plumed user-qmmm user-quip user-scafacos \ + user-netcdf user-nnp user-plumed user-qmmm user-quip user-scafacos \ user-smd user-vtk user-mesont PACKSYS = compress mpiio python user-lb @@ -70,8 +70,8 @@ PACKSYS = compress mpiio python user-lb PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont PACKEXT = kim latte mscg voronoi \ - user-adios user-h5md user-molfile user-netcdf user-plumed user-qmmm user-quip \ - user-smd user-vtk + user-adios user-h5md user-molfile user-netcdf user-nnp user-plumed user-qmmm \ + user-quip user-smd user-vtk PACKALL = $(PACKAGE) $(PACKUSER) From e713a931d3563788db369100662a3a2a01fa5f4f Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Wed, 24 Feb 2021 17:57:24 +0100 Subject: [PATCH 0110/1217] Added lots of docs, finished CMake script --- cmake/Modules/FindN2P2.cmake | 28 ++++++- cmake/Modules/Packages/USER-NNP.cmake | 1 + doc/src/Build_extras.rst | 25 +++++- doc/src/Packages_user.rst | 2 +- doc/src/pair_nnp.rst | 12 +-- doc/utils/sphinx-config/false_positives.txt | 2 + lib/README | 2 + lib/nnp/README | 91 ++++++++++++++++++++- src/.gitignore | 2 + src/USER-NNP/README | 26 ++++++ src/USER-NNP/pair_nnp.cpp | 61 ++++++++------ src/USER-NNP/pair_nnp.h | 40 +++++---- 12 files changed, 238 insertions(+), 54 deletions(-) diff --git a/cmake/Modules/FindN2P2.cmake b/cmake/Modules/FindN2P2.cmake index f1a9058f33..a06850f07f 100644 --- a/cmake/Modules/FindN2P2.cmake +++ b/cmake/Modules/FindN2P2.cmake @@ -1,25 +1,47 @@ include(FindPackageHandleStandardArgs) +# Check if N2P2_DIR is set manually. if (DEFINED ENV{N2P2_DIR}) set(N2P2_DIR "${N2P2_DIR}") +# If not, try if directory "lib/nnp/n2p2" exists. +else() + get_filename_component(_fullpath "${LAMMPS_LIB_SOURCE_DIR}/nnp/n2p2" REALPATH) + if (EXISTS ${_fullpath}) + set(N2P2_DIR "${_fullpath}") + endif() endif() -message(STATUS "N2P2_DIR=${N2P2_DIR}") +# Set path to include directory. find_path(N2P2_INCLUDE_DIR InterfaceLammps.h PATHS "${N2P2_DIR}/include") +# Two libraries need to be linked: libnnp and libnnpif. find_library(N2P2_LIBNNP NAMES nnp PATHS "${N2P2_DIR}/lib") find_library(N2P2_LIBNNPIF NAMES nnpif PATHS "${N2P2_DIR}/lib") +# Users could compile n2p2 with extra flags which are then also required for +# pair_nnp.cpp compilation. To forward them to the LAMMPS build process n2p2 +# writes a file with cmake commands, e.g. +# +# target_compile_definitions(lammps PRIVATE -DNNP_NO_SF_GROUPS) +# +# to "lib/lammps-extra.cmake" which is then included by USER-NNP.cmake. +find_file(N2P2_CMAKE_EXTRA NAMES lammps-extra.cmake PATHS "${N2P2_DIR}/lib") -find_package_handle_standard_args(N2P2 DEFAULT_MSG N2P2_INCLUDE_DIR N2P2_LIBNNP) +find_package_handle_standard_args(N2P2 DEFAULT_MSG + N2P2_DIR + N2P2_INCLUDE_DIR + N2P2_LIBNNP + N2P2_LIBNNPIF + N2P2_CMAKE_EXTRA) if(N2P2_FOUND) set(N2P2_INCLUDE_DIRS ${N2P2_INCLUDE_DIR}) set(N2P2_LIBRARIES ${N2P2_LIBNNPIF} ${N2P2_LIBNNP}) + set(N2P2_CMAKE_EXTRAS ${N2P2_CMAKE_EXTRA}) mark_as_advanced( N2P2_DIR N2P2_INCLUDE_DIR N2P2_LIBNNP N2P2_LIBNNPIF + N2P2_CMAKE_EXTRA ) endif() - diff --git a/cmake/Modules/Packages/USER-NNP.cmake b/cmake/Modules/Packages/USER-NNP.cmake index 57eae791d2..2ebc1f6e36 100644 --- a/cmake/Modules/Packages/USER-NNP.cmake +++ b/cmake/Modules/Packages/USER-NNP.cmake @@ -1,3 +1,4 @@ find_package(N2P2 REQUIRED) target_include_directories(lammps PRIVATE ${N2P2_INCLUDE_DIRS}) target_link_libraries(lammps PRIVATE ${N2P2_LIBRARIES}) +include(${N2P2_CMAKE_EXTRAS}) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 99aaf69f8f..f40972b544 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -1592,17 +1592,38 @@ on your system. USER-NNP package --------------------------------- +To build with the USER-NNP package it is required to download and build the +external `n2p2 `__ library ``v2.2.0`` +(or higher) before starting the LAMMPS build process. More specifically, only +the *n2p2* core library ``libnnp`` and interface library ``libnnpif`` are +actually needed: when using GCC it should suffice to execute ``make libnnpif`` +in the *n2p2* ``src`` directory. For more details please see the `n2p2 build +documentation `__. If +*n2p2* is downloaded and compiled in the LAMMPS directory ``lib/nnp/n2p2`` no +special flags need to be set besides the usual package activation. If you prefer +to install *n2p2* somewhere else on your system you must specify the path via +the ``N2P2_DIR`` variable. + .. tabs:: .. tab:: CMake build + There is one additional setting besides ``-D PKG_USER-NNP=yes`` in case + *n2p2* is not installed in the ``lib/nnp/n2p2`` directory: + .. code-block:: bash - ADD STUFF HERE + -D N2P2_DIR=path # path ... n2p2 installation path .. tab:: Traditional make - ADD STUFF HERE + There is one additional variable that needs to be set besides ``make + yes-user-nnp`` in case *n2p2* is not installed in the ``lib/nnp/n2p2`` + directory: + + .. code-block:: bash + + make N2P2_DIR=path ... ---------- diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index 8f7e955924..77bf13cde6 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -79,7 +79,7 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-NETCDF ` | dump output via NetCDF | :doc:`dump netcdf ` | n/a | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-NNP ` | High-dimensional neural network potenials | :doc:`pair_style nnp ` | USER/nnp | ext | +| :ref:`USER-NNP ` | High-dimensional neural network potentials | :doc:`pair_style nnp ` | USER/nnp | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-OMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ diff --git a/doc/src/pair_nnp.rst b/doc/src/pair_nnp.rst index 78fa635c1f..fe60ef175e 100644 --- a/doc/src/pair_nnp.rst +++ b/doc/src/pair_nnp.rst @@ -112,7 +112,7 @@ function setup, ``scaling.data`` with symmetry function scaling data and The keyword *showew* can be used to turn on/off the display of extrapolation warnings (EWs) which are issued whenever a symmetry function value is out of -bounds defined by minimum/maximum values in "scaling.data". An extrapolation +bounds defined by minimum/maximum values in ``scaling.data``. An extrapolation warning may look like this: .. code-block:: LAMMPS @@ -221,14 +221,14 @@ present elements (see above). .. _Behler_Parrinello_2007: -**(Behler and Parrinello 2007)** Behler, J.; Parrinello, M. Generalized +**(Behler and Parrinello 2007)** `Behler, J.; Parrinello, M. Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces. Phys. Rev. Lett. 2007, 98 (14), 146401. -https://doi.org/10.1103/PhysRevLett.98.146401 +`__ .. _Singraber_et_al_2019: -**(Singraber et al 2019)** Singraber, A.; Behler, J.; Dellago, C. Library-Based +**(Singraber et al 2019)** `Singraber, A.; Behler, J.; Dellago, C. Library-Based LAMMPS Implementation of High-Dimensional Neural Network Potentials. J. Chem. -Theory Comput. 2019, 15 (3), 1827–1840. -https://doi.org/10.1021/acs.jctc.8b00770. +Theory Comput. 2019, 15 (3), 1827-1840 +`__ diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 982e1fde2a..60eb142e20 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2171,6 +2171,8 @@ Nmin nmin Nmols nn +nnp +NNP Nocedal nocite nocoeff diff --git a/lib/README b/lib/README index d89490e202..535f2b228e 100644 --- a/lib/README +++ b/lib/README @@ -41,6 +41,8 @@ mscg hooks to the MSCG library, used by fix_mscg command from Jacob Wagner and Greg Voth group (U Chicago) netcdf hooks to a NetCDF library installed on your system from Lars Pastewka (Karlsruhe Institute of Technology) +nnp hooks to n2p2, neural network potential package, used by USER-NNP + from Andreas Singraber poems POEMS rigid-body integration package, POEMS package from Rudranarayan Mukherjee (RPI) python hooks to the system Python library, used by the PYTHON package diff --git a/lib/nnp/README b/lib/nnp/README index a5cfd5cd23..9aba16606c 100644 --- a/lib/nnp/README +++ b/lib/nnp/README @@ -1 +1,90 @@ -WRITE STUFF HERE +The USER-NNP package requires access to pre-compiled libraries of the n2p2 +package (https://github.com/CompPhysVienna/n2p2). More precisely, the n2p2 core +library ("libnnp"), the interface library ("libnnpif"), some headers and extra +build helper files are needed. These files will be created automatically during +the n2p2 build process. + +Basic build instructions for n2p2 +================================= + +The n2p2 software package comes with lots of useful tools for creating and +applying neural network potentials (NNPs). In order to use n2p2 together with +LAMMPS only a portion of the n2p2 code needs to be compiled. As an example, +everything related to NNP training is not required and would only add unwanted +library dependencies. Hence, the build infrastructure of n2p2 is designed to allow +a separate build of the LAMMPS interface. + +After downloading n2p2, change to the "src" directory and simply execute + + make libnnpif + +which should create the following files needed by the USER-NNP package: + + * "n2p2/lib/libnnp.a" + * "n2p2/lib/libnnpif.a" + * "n2p2/lib/lammps-extra.cmake" + * "n2p2/lib/Makefile.lammps-extra" + * "n2p2/include/InterfaceLammps.h" and many other header files. + +If you prefer dynamically linked libraries use + + make MODE=shared libnnpif + +instead (by default MODE=static) which will create *.so versions of the +libraries. By default, n2p2 uses the GNU C++ compiler and the corresponding +settings can be found in "n2p2/src/makefile.gnu". Other makefile presets are +also available (e.g. "makefile.intel") and can be activated by supplying the +"COMP" argument: + + make COMP=intel libnnpif + +Please make sure that your compiler settings for n2p2 and LAMMPS are compatible +(avoid mixing different compilers). For more information about the n2p2 build +process please visit https://compphysvienna.github.io/n2p2/topics/build.html or +ask questions on the Github issue page +(https://github.com/CompPhysVienna/n2p2/issues). + +Installation directory of n2p2 +============================== + +You can install n2p2 either in this folder (1) or somewhere else on your system (2): + +(1) If n2p2 is installed here, please make sure that the directory is also named + "n2p2", i.e. within "lib/nnp/n2p2" you can see the n2p2 folder structure, in + particular "lib" and "include": + + lib + | + nnp + | + n2p2 + | + ------------------ ... + | | | + include lib src ... + + In this case LAMMPS will automatically find n2p2 during the build process + and you only need to enable the USER-NNP package via CMake (-D + PKG_USER-NNP=yes) or the traditional makefile approach (make yes-user-nnp). + It is also valid to create a link here named "n2p2" which points to the n2p2 + installation directory. + +(2) If n2p2 is installed somewhere else the path must be given as an additional + setting (variable N2P2_DIR) to the build tool. For example, with CMake use + + cmake -D PKG_USER-NNP=yes -D N2P2_DIR= ../cmake/ + + and for the traditional makefiles use + + make yes-user-nnp + make N2P2_DIR= mpi + +Testing a successful build of LAMMPS with USER-NNP +================================================== + +An example is provided in the LAMMPS directory "examples/USER/nnp" which runs +10 timesteps with 360 water molecules. The neural network potential is defined +via files in the "nnp-data" subdirectory. Use the "in.nnp" LAMMPS script file +to run the simulation. You should see a large output of the n2p2 library when +the pair style "nnp" is initialized, followed by the LAMMPS per-timestep +output. diff --git a/src/.gitignore b/src/.gitignore index 45ec71e485..9e37dc316c 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -1079,6 +1079,8 @@ /pair_nm_cut_coul_cut.h /pair_nm_cut_coul_long.cpp /pair_nm_cut_coul_long.h +/pair_nnp.cpp +/pair_nnp.h /pair_oxdna_*.cpp /pair_oxdna_*.h /pair_oxdna2_*.cpp diff --git a/src/USER-NNP/README b/src/USER-NNP/README index e69de29bb2..811498f448 100644 --- a/src/USER-NNP/README +++ b/src/USER-NNP/README @@ -0,0 +1,26 @@ +This package implements the "pair_style nnp" command which can be used in a +LAMMPS input script. This pair style allows to use pre-trained high-dimensional +neural network potentials[1] via an interface to the n2p2 library +(https://github.com/CompPhysVienna/n2p2)[2]. + +Please see the main documentation for the "pair_style nnp" command for further +details on how the pair style is used. An example is provided in the +"examples/USER/nnp" directory of LAMMPS. + +The USER-NNP package requires the external library n2p2 which must be +downloaded and compiled before starting the build process of LAMMPS. A rough +guideline on how to build n2p2 is presented in "lib/nnp/README". This package +supports the LAMMPS build process via CMake and traditional makefiles, please +see the LAMMPS manual section on building with external libraries for more +details. + +This package was created by Andreas Singraber, please ask questions/report bugs +on the n2p2 Github issues page (https://github.com/CompPhysVienna/n2p2/issues). + +[1] Behler, J.; Parrinello, M. Generalized Neural-Network Representation of +High-Dimensional Potential-Energy Surfaces. Phys. Rev. Lett. 2007, 98 (14), +146401. https://doi.org/10.1103/PhysRevLett.98.146401 + +[2] Singraber, A.; Behler, J.; Dellago, C. Library-Based +LAMMPS Implementation of High-Dimensional Neural Network Potentials. J. Chem. +Theory Comput. 2019, 15 (3), 1827-1840. https://doi.org/10.1021/acs.jctc.8b00770 diff --git a/src/USER-NNP/pair_nnp.cpp b/src/USER-NNP/pair_nnp.cpp index c7ac600e45..39217c605d 100644 --- a/src/USER-NNP/pair_nnp.cpp +++ b/src/USER-NNP/pair_nnp.cpp @@ -1,32 +1,35 @@ -// n2p2 - A neural network potential package -// Copyright (C) 2018 Andreas Singraber (University of Vienna) -// -// This program is free software: you can redistribute it and/or modify -// it under the terms of the GNU General Public License as published by -// the Free Software Foundation, either version 3 of the License, or -// (at your option) any later version. -// -// This program is distributed in the hope that it will be useful, -// but WITHOUT ANY WARRANTY; without even the implied warranty of -// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -// GNU General Public License for more details. -// -// You should have received a copy of the GNU General Public License -// along with this program. If not, see . +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + This file initially came from n2p2 (https://github.com/CompPhysVienna/n2p2) + Copyright (2018) Andreas Singraber (University of Vienna) + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Andreas Singraber +------------------------------------------------------------------------- */ -#include -#include #include "pair_nnp.h" +#include #include "atom.h" #include "comm.h" +#include "error.h" +#include "memory.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" #include "update.h" #include "utils.h" -#include "InterfaceLammps.h" +#include "InterfaceLammps.h" // n2p2 interface header using namespace LAMMPS_NS; @@ -89,6 +92,18 @@ void PairNNP::compute(int eflag, int vflag) void PairNNP::settings(int narg, char **arg) { + single_enable = 0; // 1 if single() routine exists + single_hessian_enable = 0; // 1 if single_hessian() routine exists + restartinfo = 0; // 1 if pair style writes restart info + respa_enable = 0; // 1 if inner/middle/outer rRESPA routines + one_coeff = 1; // 1 if allows only one coeff * * call + manybody_flag = 1; // 1 if a manybody potential + unit_convert_flag = 0; // value != 0 indicates support for unit conversion. + no_virial_fdotr_compute = 0; // 1 if does not invoke virial_fdotr_compute() + writedata = 0; // 1 if writes coeffs to data file + ghostneigh = 0; // 1 if pair style needs neighbors of ghosts + reinitflag = 0; // 1 if compatible with fix adapt and alike + int iarg = 0; if (narg == 0) error->all(FLERR,"Illegal pair_style command"); @@ -312,7 +327,7 @@ void PairNNP::handleExtrapolationWarnings() // rank 0. if(showew > 0) { // First collect an overview of extrapolation warnings per process. - long* numEWPerProc = nullptr; + long *numEWPerProc = nullptr; if(comm->me == 0) numEWPerProc = new long[comm->nprocs]; MPI_Gather(&numCurrentEW, 1, MPI_LONG, numEWPerProc, 1, MPI_LONG, 0, world); @@ -323,7 +338,7 @@ void PairNNP::handleExtrapolationWarnings() MPI_Status ms; // Get buffer size. MPI_Recv(&bs, 1, MPI_LONG, i, 0, world, &ms); - char* buf = new char[bs]; + char *buf = new char[bs]; // Receive buffer. MPI_Recv(buf, bs, MPI_BYTE, i, 0, world, &ms); interface->extractEWBuffer(buf, bs); @@ -336,7 +351,7 @@ void PairNNP::handleExtrapolationWarnings() // Get desired buffer length for all extrapolation warning entries. long bs = interface->getEWBufferSize(); // Allocate and fill buffer. - char* buf = new char[bs]; + char *buf = new char[bs]; interface->fillEWBuffer(buf, bs); // Send buffer size and buffer. MPI_Send(&bs, 1, MPI_LONG, 0, 0, world); diff --git a/src/USER-NNP/pair_nnp.h b/src/USER-NNP/pair_nnp.h index 0b76739d77..8a41d1a5d6 100644 --- a/src/USER-NNP/pair_nnp.h +++ b/src/USER-NNP/pair_nnp.h @@ -1,18 +1,22 @@ -// n2p2 - A neural network potential package -// Copyright (C) 2018 Andreas Singraber (University of Vienna) -// -// This program is free software: you can redistribute it and/or modify -// it under the terms of the GNU General Public License as published by -// the Free Software Foundation, either version 3 of the License, or -// (at your option) any later version. -// -// This program is distributed in the hope that it will be useful, -// but WITHOUT ANY WARRANTY; without even the implied warranty of -// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -// GNU General Public License for more details. -// -// You should have received a copy of the GNU General Public License -// along with this program. If not, see . +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + This file initially came from n2p2 (https://github.com/CompPhysVienna/n2p2) + Copyright (2018) Andreas Singraber (University of Vienna) + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Andreas Singraber +------------------------------------------------------------------------- */ #ifdef PAIR_CLASS @@ -58,9 +62,9 @@ class PairNNP : public Pair { double cflength; double cfenergy; double maxCutoffRadius; - char* directory; - char* emap; - nnp::InterfaceLammps* interface; + char *directory; + char *emap; + nnp::InterfaceLammps *interface; }; } From 037441b502b8cd5e6877e37c765303844873d899 Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Wed, 24 Feb 2021 23:35:21 +0100 Subject: [PATCH 0111/1217] More documentation, added citation in source --- doc/src/Build_extras.rst | 13 ++++++------ doc/src/Packages_details.rst | 10 ++++++--- doc/src/pair_nnp.rst | 41 ++++++++++++++++++++++-------------- lib/nnp/README | 33 +++++++++++++++++++++-------- src/USER-NNP/README | 2 +- src/USER-NNP/pair_nnp.cpp | 25 +++++++++++++++++----- 6 files changed, 84 insertions(+), 40 deletions(-) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index f40972b544..6451de9ea5 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -1597,12 +1597,13 @@ external `n2p2 `__ library ``v2.2.0`` (or higher) before starting the LAMMPS build process. More specifically, only the *n2p2* core library ``libnnp`` and interface library ``libnnpif`` are actually needed: when using GCC it should suffice to execute ``make libnnpif`` -in the *n2p2* ``src`` directory. For more details please see the `n2p2 build -documentation `__. If -*n2p2* is downloaded and compiled in the LAMMPS directory ``lib/nnp/n2p2`` no -special flags need to be set besides the usual package activation. If you prefer -to install *n2p2* somewhere else on your system you must specify the path via -the ``N2P2_DIR`` variable. +in the *n2p2* ``src`` directory. For more details please see ``lib/nnp/README`` +and the `n2p2 build documentation +`__. If *n2p2* is +downloaded and compiled in the LAMMPS directory ``lib/nnp/n2p2`` no special +flags need to be set besides the usual package activation. If you prefer to +install *n2p2* somewhere else on your system you must specify the path via the +``N2P2_DIR`` variable. .. tabs:: diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index ea27bd3abf..d1bb18a405 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -1929,12 +1929,15 @@ USER-NNP package **Contents:** -:doc:`pair_style nnp ` command +A :doc:`pair_style nnp ` command which allows to use high-dimensional +neural network potentials (HDNNPs), a form of machine learning potentials. +HDNNPs must be carefully trained prior to their application in a molecular +dynamics simulation. .. _n2p2: https://github.com/CompPhysVienna/n2p2 -To use this package you must have the n2p2 core and interface library -(``libnnp``, ``libnnpif``) available on your system. +To use this package you must have the `n2p2 `_ library installed and +compiled on your system. **Author:** Andreas Singraber @@ -1946,6 +1949,7 @@ This package has :ref:`specific installation instructions ` on the :do * src/USER-NNP: filenames -> commands * src/USER-NNP/README +* lib/nnp/README * :doc:`pair_style nnp ` * examples/USER/nnp diff --git a/doc/src/pair_nnp.rst b/doc/src/pair_nnp.rst index fe60ef175e..3141dce317 100644 --- a/doc/src/pair_nnp.rst +++ b/doc/src/pair_nnp.rst @@ -49,14 +49,13 @@ This pair style adds an interaction based on the high-dimensional neural network potential (HDNNP) method as presented in :ref:`(Behler and Parrinello 2007) `. HDNNPs are machine learning potentials which require careful training of neural networks prior to application in MD simulations. The -pair style uses an interface to the *n2p2* library :ref:`(Singraber et al 2019) -` which is available on Github `here -`__. Please see the *n2p2* +pair style uses an interface to the *n2p2* library :ref:`(Singraber, Behler and +Dellago 2019) ` which is available on Github +`here `__. Please see the *n2p2* `documentation `__ for further details. *n2p2* (and hence this pair style) is compatible with neural network potentials -trained with its own tools and with `RuNNer -`__. However, at this point only -short-range HDNNPs are supported. +trained with its own tools :ref:`(Singraber et al 2019) ` +and with `RuNNer `__. The maximum cutoff radius of all symmetry functions (the atomic environment descriptors of HDNNPs) is the only argument of the *pair_coeff* command which @@ -189,17 +188,20 @@ should only be invoked with asterisk wild cards (see above). This style does not support the :doc:`pair_modify ` shift, table, and tail options. -This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. +This style does not write information to :doc:`binary restart files `. +Thus, you need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , -*middle*\ , *outer* keywords. +This style can only be used via the *pair* keyword of the :doc:`run_style respa +` command. It does not support the *inner*\ , *middle*\ , *outer* +keywords. Restrictions """""""""""" -This pair style is part of the USER-NNP package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This pair style is part of the USER-NNP package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` doc +page for more info. Please report bugs and feature requests to the `n2p2 GitHub issue page `__. @@ -226,9 +228,16 @@ Neural-Network Representation of High-Dimensional Potential-Energy Surfaces. Phys. Rev. Lett. 2007, 98 (14), 146401. `__ +.. _Singraber_Behler_Dellago_2019: + +**(Singraber, Behler and Dellago 2019)** `Singraber, A.; Behler, J.; Dellago, C. +Library-Based LAMMPS Implementation of High-Dimensional Neural Network +Potentials. J. Chem. Theory Comput. 2019, 15 (3), 1827-1840 +`__ + .. _Singraber_et_al_2019: -**(Singraber et al 2019)** `Singraber, A.; Behler, J.; Dellago, C. Library-Based -LAMMPS Implementation of High-Dimensional Neural Network Potentials. J. Chem. -Theory Comput. 2019, 15 (3), 1827-1840 -`__ +**(Singraber et al 2019)** `Singraber, A.; Morawietz, T.; Behler, J.; Dellago, +C. Parallel Multistream Training of High-Dimensional Neural Network Potentials. +J. Chem. Theory Comput. 2019, 15 (5), 3075-3092. +`__ diff --git a/lib/nnp/README b/lib/nnp/README index 9aba16606c..3d6d1cacbd 100644 --- a/lib/nnp/README +++ b/lib/nnp/README @@ -4,12 +4,14 @@ library ("libnnp"), the interface library ("libnnpif"), some headers and extra build helper files are needed. These files will be created automatically during the n2p2 build process. +IMPORTANT: The n2p2 version must be "v2.2.0" or higher. + Basic build instructions for n2p2 ================================= The n2p2 software package comes with lots of useful tools for creating and applying neural network potentials (NNPs). In order to use n2p2 together with -LAMMPS only a portion of the n2p2 code needs to be compiled. As an example, +LAMMPS only some parts of the n2p2 code need to be compiled. As an example, everything related to NNP training is not required and would only add unwanted library dependencies. Hence, the build infrastructure of n2p2 is designed to allow a separate build of the LAMMPS interface. @@ -39,10 +41,23 @@ also available (e.g. "makefile.intel") and can be activated by supplying the make COMP=intel libnnpif Please make sure that your compiler settings for n2p2 and LAMMPS are compatible -(avoid mixing different compilers). For more information about the n2p2 build -process please visit https://compphysvienna.github.io/n2p2/topics/build.html or -ask questions on the Github issue page -(https://github.com/CompPhysVienna/n2p2/issues). +(avoid mixing different compilers). + +If you want to build a serial version of LAMMPS with USER-NNP package n2p2 must +also be built without MPI enabled. This can be achieved with a preprocessor +flag (-DN2P2_NO_MPI) which is (among others) prepared, but commented out, in +the provided compiler-specific settings makefiles. For example, if you use the +GNU compiler simply remove the comment character '#' in front of the +corresponding line in "makefile.gnu". It should then look like this: + + PROJECT_OPTIONS+= -DN2P2_NO_MPI + +After compiling n2p2 with this flag turned on you can build a serial LAMMPS +version with "-D BUILD_MPI=off" (CMake) or "make serial" (traditional). + +For more information about the n2p2 build process please visit +https://compphysvienna.github.io/n2p2/topics/build.html or ask questions on the +Github issue page (https://github.com/CompPhysVienna/n2p2/issues). Installation directory of n2p2 ============================== @@ -64,10 +79,10 @@ You can install n2p2 either in this folder (1) or somewhere else on your system include lib src ... In this case LAMMPS will automatically find n2p2 during the build process - and you only need to enable the USER-NNP package via CMake (-D - PKG_USER-NNP=yes) or the traditional makefile approach (make yes-user-nnp). - It is also valid to create a link here named "n2p2" which points to the n2p2 - installation directory. + and you only need to enable the USER-NNP package via CMake (-D PKG_USER-NNP=yes) + or the traditional makefile approach (make yes-user-nnp). It is also valid to + create a link here named "n2p2" which points to the n2p2 installation + directory. (2) If n2p2 is installed somewhere else the path must be given as an additional setting (variable N2P2_DIR) to the build tool. For example, with CMake use diff --git a/src/USER-NNP/README b/src/USER-NNP/README index 811498f448..a8eae3d865 100644 --- a/src/USER-NNP/README +++ b/src/USER-NNP/README @@ -8,7 +8,7 @@ details on how the pair style is used. An example is provided in the "examples/USER/nnp" directory of LAMMPS. The USER-NNP package requires the external library n2p2 which must be -downloaded and compiled before starting the build process of LAMMPS. A rough +downloaded and compiled before starting the build process of LAMMPS. A guideline on how to build n2p2 is presented in "lib/nnp/README". This package supports the LAMMPS build process via CMake and traditional makefiles, please see the LAMMPS manual section on building with external libraries for more diff --git a/src/USER-NNP/pair_nnp.cpp b/src/USER-NNP/pair_nnp.cpp index 39217c605d..a6b06fb66c 100644 --- a/src/USER-NNP/pair_nnp.cpp +++ b/src/USER-NNP/pair_nnp.cpp @@ -21,6 +21,7 @@ #include "pair_nnp.h" #include #include "atom.h" +#include "citeme.h" #include "comm.h" #include "error.h" #include "memory.h" @@ -33,20 +34,34 @@ using namespace LAMMPS_NS; +static const char cite_user_nnp_package[] = + "USER-NNP package:\n\n" + "@Article{Singraber19,\n" + " author = {Singraber, Andreas and Behler, J{\"o}rg and Dellago, Christoph},\n" + " title = {Library-{{Based LAMMPS Implementation}} of {{High}}-{{Dimensional Neural Network Potentials}}},\n" + " year = {2019},\n" + " month = mar,\n" + " volume = {15},\n" + " pages = {1827--1840},\n" + " doi = {10.1021/acs.jctc.8b00770},\n" + " journal = {J.~Chem.~Theory~Comput.},\n" + " number = {3}\n" + "}\n\n"; + /* ---------------------------------------------------------------------- */ PairNNP::PairNNP(LAMMPS *lmp) : Pair(lmp) { - interface = new nnp::InterfaceLammps(); + if (lmp->citeme) lmp->citeme->add(cite_user_nnp_package); + + interface = new nnp::InterfaceLammps(); } -/* ---------------------------------------------------------------------- - check if allocated, since class can be destructed when incomplete -------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- */ PairNNP::~PairNNP() { - delete interface; + delete interface; } /* ---------------------------------------------------------------------- */ From 0c583fff7dd8fdcb657fdf7c9f5ca1c356681516 Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Thu, 25 Feb 2021 11:54:37 +0100 Subject: [PATCH 0112/1217] Allow for -DLAMMPS_BIGBIG compilation --- lib/nnp/README | 10 +++++----- src/USER-NNP/pair_nnp.cpp | 8 ++++++-- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/lib/nnp/README b/lib/nnp/README index 3d6d1cacbd..004d60df0b 100644 --- a/lib/nnp/README +++ b/lib/nnp/README @@ -44,11 +44,11 @@ Please make sure that your compiler settings for n2p2 and LAMMPS are compatible (avoid mixing different compilers). If you want to build a serial version of LAMMPS with USER-NNP package n2p2 must -also be built without MPI enabled. This can be achieved with a preprocessor -flag (-DN2P2_NO_MPI) which is (among others) prepared, but commented out, in -the provided compiler-specific settings makefiles. For example, if you use the -GNU compiler simply remove the comment character '#' in front of the -corresponding line in "makefile.gnu". It should then look like this: +also be built with MPI disabled. This can be achieved with a preprocessor flag +(-DN2P2_NO_MPI) which is (among others) prepared, but commented out, in the +provided compiler-specific settings makefiles. For example, if you use the GNU +compiler simply remove the comment character '#' in front of the corresponding +line (around line 49) in "makefile.gnu". It should then look like this: PROJECT_OPTIONS+= -DN2P2_NO_MPI diff --git a/src/USER-NNP/pair_nnp.cpp b/src/USER-NNP/pair_nnp.cpp index a6b06fb66c..b2dae5a969 100644 --- a/src/USER-NNP/pair_nnp.cpp +++ b/src/USER-NNP/pair_nnp.cpp @@ -71,8 +71,12 @@ void PairNNP::compute(int eflag, int vflag) if(eflag || vflag) ev_setup(eflag,vflag); else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; - // Set number of local atoms and add index and element. - interface->setLocalAtoms(atom->nlocal,atom->tag,atom->type); + // Set number of local atoms and add element. + interface->setLocalAtoms(atom->nlocal,atom->type); + // Transfer tags separately. Interface::setLocalTags is overloaded internally + // to work with both -DLAMMPS_SMALLBIG (tagint = int) and -DLAMMPS_BIGBIG + // (tagint = int64_t) + interface->setLocalTags(atom->tag); // Transfer local neighbor list to NNP interface. transferNeighborList(); From ed53e2bbff2465dd05ba015a05843b2bb328360c Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Thu, 25 Feb 2021 14:02:00 +0100 Subject: [PATCH 0113/1217] Add ignored Makefile.lammps in lib/nnp --- lib/nnp/Makefile.lammps | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 lib/nnp/Makefile.lammps diff --git a/lib/nnp/Makefile.lammps b/lib/nnp/Makefile.lammps new file mode 100644 index 0000000000..fb5b939541 --- /dev/null +++ b/lib/nnp/Makefile.lammps @@ -0,0 +1,24 @@ +# Settings that the LAMMPS build will import when this package library is used +# Normally, you do NOT need to edit this file! + +# Check out if n2p2 or a link is right here. +N2P2_LOCALDIR=$(realpath ../../lib/nnp/n2p2) +ifeq ($(N2P2_DIR),) + N2P2_DIR=$(shell test -d $(N2P2_LOCALDIR) && echo $(N2P2_LOCALDIR)) +else +# If n2p2 is not found in this directory then use environment variable or set manually here: +# N2P2_DIR= +endif + +# Give up if n2p2 not found yet. +ifeq ($(N2P2_DIR),) +$(error Cannot find library for USER-NNP package, please set environment or make variable N2P2_DIR manually.) +endif + +# Read extra NNP_ compilation flags from makefile provided by n2p2: +include $(N2P2_DIR)/lib/Makefile.lammps-extra + +# Next, add general info to include/lib/path variables. +nnp_SYSINC += -I$(N2P2_DIR)/include +nnp_SYSLIB += -L$(N2P2_DIR)/lib -lnnpif -lnnp +nnp_SYSPATH += From 19311d408db82bab339c84090c4cbd451b5b5d77 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 26 Feb 2021 23:10:43 -0500 Subject: [PATCH 0114/1217] use utils::trim() to remove extra whitespace from ctime() output. --- unittest/force-styles/test_angle_style.cpp | 3 +-- unittest/force-styles/test_bond_style.cpp | 3 +-- unittest/force-styles/test_dihedral_style.cpp | 3 +-- unittest/force-styles/test_fix_timestep.cpp | 3 +-- unittest/force-styles/test_improper_style.cpp | 3 +-- unittest/force-styles/test_pair_style.cpp | 3 +-- 6 files changed, 6 insertions(+), 12 deletions(-) diff --git a/unittest/force-styles/test_angle_style.cpp b/unittest/force-styles/test_angle_style.cpp index 833aa69174..bf5cb34e7f 100644 --- a/unittest/force-styles/test_angle_style.cpp +++ b/unittest/force-styles/test_angle_style.cpp @@ -240,8 +240,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // date_generated std::time_t now = time(NULL); - block = ctime(&now); - block = block.substr(0, block.find("\n") - 1); + block = utils::trim(ctime(&now)); writer.emit("date_generated", block); // epsilon diff --git a/unittest/force-styles/test_bond_style.cpp b/unittest/force-styles/test_bond_style.cpp index 0d20a0bb62..d6a6e9c82d 100644 --- a/unittest/force-styles/test_bond_style.cpp +++ b/unittest/force-styles/test_bond_style.cpp @@ -240,8 +240,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // date_generated std::time_t now = time(NULL); - block = ctime(&now); - block = block.substr(0, block.find("\n") - 1); + block = utils::trim(ctime(&now)); writer.emit("date_generated", block); // epsilon diff --git a/unittest/force-styles/test_dihedral_style.cpp b/unittest/force-styles/test_dihedral_style.cpp index e60968bb0a..a27c50afb7 100644 --- a/unittest/force-styles/test_dihedral_style.cpp +++ b/unittest/force-styles/test_dihedral_style.cpp @@ -249,8 +249,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // date_generated std::time_t now = time(NULL); - block = ctime(&now); - block = block.substr(0, block.find("\n") - 1); + block = utils::trim(ctime(&now)); writer.emit("date_generated", block); // epsilon diff --git a/unittest/force-styles/test_fix_timestep.cpp b/unittest/force-styles/test_fix_timestep.cpp index e4b0fa6e02..2680367c88 100644 --- a/unittest/force-styles/test_fix_timestep.cpp +++ b/unittest/force-styles/test_fix_timestep.cpp @@ -198,8 +198,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // date_generated std::time_t now = time(NULL); - block = ctime(&now); - block = block.substr(0, block.find("\n") - 1); + block = utils::trim(ctime(&now)); writer.emit("date_generated", block); // epsilon diff --git a/unittest/force-styles/test_improper_style.cpp b/unittest/force-styles/test_improper_style.cpp index 858db0fb65..b13b571546 100644 --- a/unittest/force-styles/test_improper_style.cpp +++ b/unittest/force-styles/test_improper_style.cpp @@ -240,8 +240,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // date_generated std::time_t now = time(NULL); - block = ctime(&now); - block = block.substr(0, block.find("\n") - 1); + block = utils::trim(ctime(&now)); writer.emit("date_generated", block); // epsilon diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index aa0edfa2ad..4e1ad8d0e3 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -244,8 +244,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // date_generated std::time_t now = time(NULL); - block = ctime(&now); - block = block.substr(0, block.find("\n") - 1); + block = utils::trim(ctime(&now)); writer.emit("date_generated", block); // epsilon From 981ed019837051167a99303dc38d538e6d9f1a18 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 26 Feb 2021 23:16:51 -0500 Subject: [PATCH 0115/1217] recreate all yaml files with updated timestamps --- unittest/force-styles/tests/angle-charmm.yaml | 4 +- unittest/force-styles/tests/angle-class2.yaml | 4 +- .../force-styles/tests/angle-class2_p6.yaml | 4 +- unittest/force-styles/tests/angle-cosine.yaml | 4 +- .../tests/angle-cosine_delta.yaml | 4 +- .../tests/angle-cosine_periodic.yaml | 4 +- .../tests/angle-cosine_shift.yaml | 4 +- .../tests/angle-cosine_shift_exp.yaml | 4 +- .../tests/angle-cosine_squared.yaml | 4 +- unittest/force-styles/tests/angle-cross.yaml | 4 +- .../force-styles/tests/angle-fourier.yaml | 4 +- .../tests/angle-fourier_simple.yaml | 4 +- .../force-styles/tests/angle-gaussian.yaml | 4 +- .../force-styles/tests/angle-harmonic.yaml | 4 +- unittest/force-styles/tests/angle-hybrid.yaml | 4 +- unittest/force-styles/tests/angle-mm3.yaml | 4 +- .../force-styles/tests/angle-quartic.yaml | 4 +- .../tests/angle-table_linear.yaml | 4 +- .../tests/angle-table_spline.yaml | 4 +- unittest/force-styles/tests/angle-zero.yaml | 4 +- .../force-styles/tests/atomic-pair-adp.yaml | 4 +- .../force-styles/tests/atomic-pair-atm.yaml | 4 +- .../force-styles/tests/atomic-pair-beck.yaml | 4 +- .../force-styles/tests/atomic-pair-born.yaml | 4 +- .../tests/atomic-pair-colloid.yaml | 4 +- .../tests/atomic-pair-colloid_multi.yaml | 4 +- .../tests/atomic-pair-colloid_multi_tri.yaml | 4 +- .../tests/atomic-pair-colloid_tiled.yaml | 4 +- .../tests/atomic-pair-colloid_tiled_tri.yaml | 4 +- .../force-styles/tests/atomic-pair-eam.yaml | 4 +- .../tests/atomic-pair-eam_alloy.yaml | 4 +- .../tests/atomic-pair-eam_alloy_real.yaml | 4 +- .../tests/atomic-pair-eam_cd.yaml | 4 +- .../tests/atomic-pair-eam_cd_old.yaml | 4 +- .../tests/atomic-pair-eam_cd_real.yaml | 4 +- .../tests/atomic-pair-eam_fs.yaml | 4 +- .../tests/atomic-pair-eam_fs_real.yaml | 4 +- .../tests/atomic-pair-eam_he.yaml | 4 +- .../tests/atomic-pair-eam_he_real.yaml | 4 +- .../tests/atomic-pair-eam_real.yaml | 4 +- .../force-styles/tests/atomic-pair-edip.yaml | 4 +- .../force-styles/tests/atomic-pair-eim.yaml | 4 +- .../force-styles/tests/atomic-pair-gauss.yaml | 4 +- .../tests/atomic-pair-hybrid-eam.yaml | 4 +- .../tests/atomic-pair-hybrid-eam_fs.yaml | 4 +- .../tests/atomic-pair-kim_lj.yaml | 4 +- .../tests/atomic-pair-meam_c.yaml | 4 +- .../tests/atomic-pair-meam_spline.yaml | 4 +- .../tests/atomic-pair-meam_sw_spline.yaml | 4 +- .../force-styles/tests/atomic-pair-momb.yaml | 4 +- .../tests/atomic-pair-polymorphic_eam.yaml | 4 +- .../tests/atomic-pair-reax_c.yaml | 4 +- .../tests/atomic-pair-reax_c_lgvdw.yaml | 4 +- .../tests/atomic-pair-reax_c_noqeq.yaml | 4 +- .../tests/atomic-pair-table_bitmap.yaml | 4 +- .../tests/atomic-pair-table_linear.yaml | 4 +- .../tests/atomic-pair-table_lookup.yaml | 4 +- .../tests/atomic-pair-table_spline.yaml | 4 +- .../tests/atomic-pair-yukawa_colloid.yaml | 4 +- unittest/force-styles/tests/bond-class2.yaml | 4 +- unittest/force-styles/tests/bond-fene.yaml | 4 +- .../force-styles/tests/bond-fene_expand.yaml | 4 +- .../force-styles/tests/bond-gaussian.yaml | 4 +- unittest/force-styles/tests/bond-gromos.yaml | 6 +- .../force-styles/tests/bond-harmonic.yaml | 6 +- .../tests/bond-harmonic_shift.yaml | 6 +- .../tests/bond-harmonic_shift_cut.yaml | 6 +- unittest/force-styles/tests/bond-hybrid.yaml | 6 +- unittest/force-styles/tests/bond-mm3.yaml | 6 +- unittest/force-styles/tests/bond-morse.yaml | 6 +- .../force-styles/tests/bond-nonlinear.yaml | 6 +- unittest/force-styles/tests/bond-quartic.yaml | 4 +- .../force-styles/tests/bond-table_linear.yaml | 6 +- .../force-styles/tests/bond-table_spline.yaml | 6 +- unittest/force-styles/tests/bond-zero.yaml | 6 +- .../force-styles/tests/dihedral-charmm.yaml | 2 +- .../tests/dihedral-charmmfsw.yaml | 2 +- .../force-styles/tests/dihedral-class2.yaml | 2 +- .../tests/dihedral-cosine_shift_exp.yaml | 2 +- .../force-styles/tests/dihedral-fourier.yaml | 2 +- .../force-styles/tests/dihedral-harmonic.yaml | 2 +- .../force-styles/tests/dihedral-helix.yaml | 2 +- .../force-styles/tests/dihedral-hybrid.yaml | 2 +- .../tests/dihedral-multi_harmonic.yaml | 2 +- .../tests/dihedral-nharmonic.yaml | 2 +- .../force-styles/tests/dihedral-opls.yaml | 2 +- .../tests/dihedral-quadratic.yaml | 2 +- .../force-styles/tests/dihedral-zero.yaml | 2 +- .../tests/fix-timestep-addforce_const.yaml | 4 +- .../tests/fix-timestep-addforce_variable.yaml | 4 +- .../tests/fix-timestep-aveforce_const.yaml | 4 +- .../tests/fix-timestep-aveforce_variable.yaml | 4 +- .../force-styles/tests/fix-timestep-drag.yaml | 4 +- .../tests/fix-timestep-efield_const.yaml | 6 +- .../tests/fix-timestep-efield_region.yaml | 4 +- .../tests/fix-timestep-efield_variable.yaml | 6 +- .../force-styles/tests/fix-timestep-heat.yaml | 4 +- .../tests/fix-timestep-heat_region.yaml | 4 +- .../tests/fix-timestep-lineforce.yaml | 4 +- .../tests/fix-timestep-momentum.yaml | 4 +- .../tests/fix-timestep-momentum_chunk.yaml | 4 +- .../force-styles/tests/fix-timestep-nph.yaml | 4 +- .../tests/fix-timestep-npt_aniso.yaml | 4 +- .../tests/fix-timestep-npt_iso.yaml | 4 +- .../tests/fix-timestep-npt_tri.yaml | 6 +- .../force-styles/tests/fix-timestep-nve.yaml | 4 +- .../tests/fix-timestep-nve_limit.yaml | 4 +- .../tests/fix-timestep-nve_noforce.yaml | 4 +- .../force-styles/tests/fix-timestep-nvt.yaml | 4 +- .../tests/fix-timestep-oneway.yaml | 4 +- .../tests/fix-timestep-planeforce.yaml | 4 +- .../fix-timestep-press_berendsen_iso.yaml | 4 +- .../tests/fix-timestep-rattle_angle.yaml | 4 +- .../tests/fix-timestep-rattle_bond.yaml | 4 +- .../tests/fix-timestep-restrain.yaml | 6 +- .../tests/fix-timestep-rigid_group.yaml | 4 +- .../tests/fix-timestep-rigid_molecule.yaml | 4 +- .../fix-timestep-rigid_molecule_tri.yaml | 26 +-- .../tests/fix-timestep-rigid_nph.yaml | 4 +- .../tests/fix-timestep-rigid_nph_small.yaml | 4 +- .../tests/fix-timestep-rigid_npt.yaml | 4 +- .../tests/fix-timestep-rigid_npt_small.yaml | 4 +- .../tests/fix-timestep-rigid_nve_group.yaml | 4 +- .../fix-timestep-rigid_nve_molecule.yaml | 4 +- .../tests/fix-timestep-rigid_nve_single.yaml | 4 +- .../tests/fix-timestep-rigid_nve_small.yaml | 4 +- .../tests/fix-timestep-rigid_nvt.yaml | 4 +- .../tests/fix-timestep-rigid_nvt_small.yaml | 4 +- .../tests/fix-timestep-rigid_single.yaml | 4 +- .../tests/fix-timestep-rigid_small.yaml | 4 +- .../tests/fix-timestep-setforce_const.yaml | 4 +- .../tests/fix-timestep-setforce_region.yaml | 4 +- .../tests/fix-timestep-setforce_variable.yaml | 4 +- .../tests/fix-timestep-shake_angle.yaml | 4 +- .../tests/fix-timestep-shake_bond.yaml | 4 +- .../tests/fix-timestep-smd_couple.yaml | 4 +- .../tests/fix-timestep-smd_tether.yaml | 6 +- .../tests/fix-timestep-spring_chunk.yaml | 4 +- .../tests/fix-timestep-spring_couple.yaml | 4 +- .../tests/fix-timestep-spring_rg.yaml | 4 +- .../tests/fix-timestep-spring_self.yaml | 4 +- .../tests/fix-timestep-spring_tether.yaml | 4 +- .../tests/fix-timestep-temp_berendsen.yaml | 4 +- .../tests/fix-timestep-temp_csld.yaml | 4 +- .../tests/fix-timestep-temp_csvr.yaml | 4 +- .../tests/fix-timestep-temp_rescale.yaml | 4 +- .../fix-timestep-wall_harmonic_const.yaml | 6 +- .../tests/fix-timestep-wall_lj1043_const.yaml | 6 +- .../tests/fix-timestep-wall_lj126_const.yaml | 6 +- .../tests/fix-timestep-wall_lj93_const.yaml | 6 +- .../tests/fix-timestep-wall_morse_const.yaml | 6 +- .../force-styles/tests/improper-class2.yaml | 2 +- .../force-styles/tests/improper-cossq.yaml | 2 +- .../force-styles/tests/improper-cvff.yaml | 2 +- .../force-styles/tests/improper-distance.yaml | 2 +- .../force-styles/tests/improper-distharm.yaml | 2 +- .../force-styles/tests/improper-fourier.yaml | 2 +- .../force-styles/tests/improper-harmonic.yaml | 2 +- .../force-styles/tests/improper-hybrid.yaml | 2 +- .../tests/improper-inversion_harmonic.yaml | 2 +- .../force-styles/tests/improper-ring.yaml | 2 +- .../tests/improper-sqdistharm.yaml | 2 +- .../force-styles/tests/improper-umbrella.yaml | 2 +- .../force-styles/tests/improper-zero.yaml | 2 +- unittest/force-styles/tests/kspace-ewald.yaml | 4 +- .../force-styles/tests/kspace-ewald_disp.yaml | 54 ++--- .../tests/kspace-ewald_nozforce.yaml | 4 +- .../force-styles/tests/kspace-ewald_slab.yaml | 4 +- .../force-styles/tests/kspace-ewald_tri.yaml | 4 +- unittest/force-styles/tests/kspace-msm.yaml | 4 +- .../force-styles/tests/kspace-msm_cg.yaml | 4 +- .../force-styles/tests/kspace-msm_nopbc.yaml | 4 +- unittest/force-styles/tests/kspace-pppm.yaml | 4 +- .../force-styles/tests/kspace-pppm_ad.yaml | 4 +- .../force-styles/tests/kspace-pppm_cg.yaml | 4 +- .../force-styles/tests/kspace-pppm_cg_ad.yaml | 4 +- .../tests/kspace-pppm_cg_tiled.yaml | 4 +- .../force-styles/tests/kspace-pppm_disp.yaml | 4 +- .../tests/kspace-pppm_disp_ad.yaml | 4 +- .../tests/kspace-pppm_disp_ad_only.yaml | 4 +- .../tests/kspace-pppm_disp_only.yaml | 4 +- .../tests/kspace-pppm_disp_tip4p.yaml | 4 +- .../tests/kspace-pppm_nozforce.yaml | 4 +- .../force-styles/tests/kspace-pppm_slab.yaml | 4 +- .../tests/kspace-pppm_stagger.yaml | 104 ++++----- .../tests/kspace-pppm_stagger_tiled.yaml | 104 ++++----- .../force-styles/tests/kspace-pppm_tiled.yaml | 4 +- .../force-styles/tests/kspace-pppm_tip4p.yaml | 4 +- .../tests/kspace-pppm_tip4p_ad.yaml | 4 +- .../tests/kspace-pppm_tip4p_nozforce.yaml | 4 +- .../tests/kspace-pppm_tip4p_slab.yaml | 4 +- .../force-styles/tests/kspace-pppm_tri.yaml | 4 +- .../tests/manybody-pair-airebo.yaml | 4 +- .../tests/manybody-pair-airebo_00.yaml | 4 +- .../tests/manybody-pair-airebo_m.yaml | 4 +- .../tests/manybody-pair-airebo_m00.yaml | 4 +- .../force-styles/tests/manybody-pair-bop.yaml | 4 +- .../tests/manybody-pair-bop_save.yaml | 4 +- .../tests/manybody-pair-comb.yaml | 4 +- .../tests/manybody-pair-comb3.yaml | 4 +- .../tests/manybody-pair-edip_multi.yaml | 4 +- .../tests/manybody-pair-extep.yaml | 4 +- .../force-styles/tests/manybody-pair-gw.yaml | 4 +- .../tests/manybody-pair-gw_zbl.yaml | 4 +- .../tests/manybody-pair-lcbop.yaml | 4 +- .../tests/manybody-pair-meam_c.yaml | 4 +- .../tests/manybody-pair-mliap_snap.yaml | 12 +- .../tests/manybody-pair-mliap_snap_chem.yaml | 8 +- .../tests/manybody-pair-nb3b_harmonic.yaml | 4 +- .../tests/manybody-pair-polymorphic_sw.yaml | 4 +- .../manybody-pair-polymorphic_tersoff.yaml | 4 +- .../tests/manybody-pair-rebo.yaml | 4 +- .../tests/manybody-pair-snap.yaml | 12 +- .../tests/manybody-pair-snap_chem.yaml | 8 +- .../tests/manybody-pair-sw-multi.yaml | 4 +- .../force-styles/tests/manybody-pair-sw.yaml | 4 +- .../tests/manybody-pair-tersoff.yaml | 158 ++++++------- .../tests/manybody-pair-tersoff_mod.yaml | 210 +++++++++--------- .../tests/manybody-pair-tersoff_mod_c.yaml | 210 +++++++++--------- .../manybody-pair-tersoff_mod_c_shift.yaml | 4 +- .../manybody-pair-tersoff_mod_shift.yaml | 4 +- .../tests/manybody-pair-tersoff_shift.yaml | 4 +- .../tests/manybody-pair-tersoff_table.yaml | 4 +- .../tests/manybody-pair-tersoff_zbl.yaml | 188 ++++++++-------- .../manybody-pair-tersoff_zbl_shift.yaml | 4 +- .../tests/manybody-pair-vashishta.yaml | 4 +- .../tests/manybody-pair-vashishta_table.yaml | 4 +- .../force-styles/tests/mol-pair-beck.yaml | 4 +- .../force-styles/tests/mol-pair-born.yaml | 4 +- .../tests/mol-pair-born_coul_dsf.yaml | 4 +- .../tests/mol-pair-born_coul_dsf_cs.yaml | 4 +- .../tests/mol-pair-born_coul_long.yaml | 4 +- .../tests/mol-pair-born_coul_long_cs.yaml | 4 +- .../tests/mol-pair-born_coul_msm.yaml | 4 +- .../tests/mol-pair-born_coul_msm_table.yaml | 4 +- .../tests/mol-pair-born_coul_table_cs.yaml | 4 +- .../tests/mol-pair-born_coul_wolf.yaml | 4 +- .../tests/mol-pair-born_coul_wolf_cs.yaml | 4 +- .../force-styles/tests/mol-pair-buck.yaml | 4 +- .../tests/mol-pair-buck_coul_cut.yaml | 4 +- .../tests/mol-pair-buck_coul_long.yaml | 4 +- .../tests/mol-pair-buck_coul_long_cs.yaml | 4 +- .../tests/mol-pair-buck_coul_msm.yaml | 4 +- .../tests/mol-pair-buck_coul_msm_table.yaml | 4 +- .../tests/mol-pair-buck_coul_table.yaml | 4 +- .../tests/mol-pair-buck_coul_table_cs.yaml | 4 +- .../tests/mol-pair-buck_long_coul_long.yaml | 130 +++++------ .../tests/mol-pair-buck_long_coul_off.yaml | 4 +- .../mol-pair-buck_long_cut_coul_long.yaml | 4 +- .../force-styles/tests/mol-pair-buck_mdf.yaml | 4 +- .../tests/mol-pair-buck_table_coul_long.yaml | 4 +- .../tests/mol-pair-buck_table_coul_off.yaml | 4 +- .../tests/mol-pair-buck_table_coul_table.yaml | 130 +++++------ .../tests/mol-pair-cosine_squared.yaml | 4 +- .../force-styles/tests/mol-pair-coul_cut.yaml | 4 +- .../tests/mol-pair-coul_cut_soft.yaml | 4 +- .../tests/mol-pair-coul_debye.yaml | 4 +- .../tests/mol-pair-coul_diel.yaml | 4 +- .../force-styles/tests/mol-pair-coul_dsf.yaml | 4 +- .../tests/mol-pair-coul_long.yaml | 4 +- .../tests/mol-pair-coul_long_cs.yaml | 4 +- .../tests/mol-pair-coul_long_soft.yaml | 4 +- .../force-styles/tests/mol-pair-coul_msm.yaml | 4 +- .../tests/mol-pair-coul_msm_table.yaml | 4 +- .../tests/mol-pair-coul_shield.yaml | 4 +- .../tests/mol-pair-coul_slater_cut.yaml | 4 +- .../tests/mol-pair-coul_slater_long.yaml | 4 +- .../tests/mol-pair-coul_streitz_long.yaml | 4 +- .../tests/mol-pair-coul_streitz_wolf.yaml | 4 +- .../tests/mol-pair-coul_table.yaml | 4 +- .../tests/mol-pair-coul_table_cs.yaml | 4 +- .../tests/mol-pair-coul_wolf.yaml | 4 +- .../tests/mol-pair-coul_wolf_cs.yaml | 4 +- unittest/force-styles/tests/mol-pair-dpd.yaml | 4 +- .../tests/mol-pair-dpd_tstat.yaml | 4 +- unittest/force-styles/tests/mol-pair-e3b.yaml | 4 +- .../force-styles/tests/mol-pair-gauss.yaml | 4 +- .../tests/mol-pair-gauss_cut.yaml | 4 +- .../tests/mol-pair-hybrid-overlay.yaml | 4 +- .../force-styles/tests/mol-pair-hybrid.yaml | 4 +- .../tests/mol-pair-lennard_mdf.yaml | 4 +- .../force-styles/tests/mol-pair-lj96_cut.yaml | 4 +- .../tests/mol-pair-lj_charmm_coul_charmm.yaml | 4 +- ...l-pair-lj_charmm_coul_charmm_implicit.yaml | 4 +- .../tests/mol-pair-lj_charmm_coul_long.yaml | 4 +- .../mol-pair-lj_charmm_coul_long_soft.yaml | 4 +- .../tests/mol-pair-lj_charmm_coul_msm.yaml | 4 +- .../mol-pair-lj_charmm_coul_msm_table.yaml | 4 +- .../tests/mol-pair-lj_charmm_coul_table.yaml | 4 +- .../mol-pair-lj_charmmfsw_coul_charmmfsw.yaml | 4 +- .../mol-pair-lj_charmmfsw_coul_long.yaml | 4 +- .../mol-pair-lj_charmmfsw_coul_table.yaml | 4 +- .../tests/mol-pair-lj_class2.yaml | 4 +- .../tests/mol-pair-lj_class2_coul_cut.yaml | 4 +- .../mol-pair-lj_class2_coul_cut_soft.yaml | 4 +- .../tests/mol-pair-lj_class2_coul_long.yaml | 4 +- .../mol-pair-lj_class2_coul_long_cs.yaml | 4 +- .../mol-pair-lj_class2_coul_long_soft.yaml | 4 +- .../tests/mol-pair-lj_class2_coul_table.yaml | 4 +- .../mol-pair-lj_class2_coul_table_cs.yaml | 4 +- .../tests/mol-pair-lj_class2_soft.yaml | 4 +- .../force-styles/tests/mol-pair-lj_cubic.yaml | 4 +- .../force-styles/tests/mol-pair-lj_cut.yaml | 4 +- .../tests/mol-pair-lj_cut_coul_cut.yaml | 4 +- .../tests/mol-pair-lj_cut_coul_cut_soft.yaml | 4 +- .../tests/mol-pair-lj_cut_coul_debye.yaml | 4 +- .../tests/mol-pair-lj_cut_coul_dsf.yaml | 4 +- .../tests/mol-pair-lj_cut_coul_long.yaml | 4 +- .../tests/mol-pair-lj_cut_coul_long_cs.yaml | 4 +- .../tests/mol-pair-lj_cut_coul_long_soft.yaml | 4 +- .../tests/mol-pair-lj_cut_coul_msm.yaml | 4 +- .../tests/mol-pair-lj_cut_coul_msm_table.yaml | 4 +- .../tests/mol-pair-lj_cut_coul_table.yaml | 4 +- .../tests/mol-pair-lj_cut_coul_table_cs.yaml | 4 +- .../tests/mol-pair-lj_cut_coul_wolf.yaml | 4 +- .../tests/mol-pair-lj_cut_soft.yaml | 4 +- .../tests/mol-pair-lj_cut_tip4p_cut.yaml | 4 +- .../tests/mol-pair-lj_cut_tip4p_long.yaml | 4 +- .../mol-pair-lj_cut_tip4p_long_soft.yaml | 4 +- .../tests/mol-pair-lj_cut_tip4p_table.yaml | 4 +- .../tests/mol-pair-lj_expand.yaml | 4 +- .../tests/mol-pair-lj_expand_coul_long.yaml | 4 +- .../tests/mol-pair-lj_expand_coul_table.yaml | 4 +- .../tests/mol-pair-lj_gromacs.yaml | 4 +- .../mol-pair-lj_gromacs_coul_gromacs.yaml | 4 +- .../tests/mol-pair-lj_long_coul_long.yaml | 130 +++++------ .../tests/mol-pair-lj_long_coul_off.yaml | 4 +- .../tests/mol-pair-lj_long_cut_coul_long.yaml | 4 +- .../mol-pair-lj_long_cut_tip4p_long.yaml | 4 +- .../tests/mol-pair-lj_long_tip4p_long.yaml | 98 ++++---- .../force-styles/tests/mol-pair-lj_mdf.yaml | 4 +- .../force-styles/tests/mol-pair-lj_sdk.yaml | 4 +- .../tests/mol-pair-lj_sdk_coul_long.yaml | 4 +- .../tests/mol-pair-lj_sdk_coul_msm.yaml | 4 +- .../tests/mol-pair-lj_sdk_coul_msm_table.yaml | 4 +- .../tests/mol-pair-lj_sdk_coul_table.yaml | 4 +- .../tests/mol-pair-lj_smooth.yaml | 4 +- .../tests/mol-pair-lj_smooth_linear.yaml | 4 +- .../tests/mol-pair-lj_table_coul_long.yaml | 4 +- .../tests/mol-pair-lj_table_coul_off.yaml | 4 +- .../tests/mol-pair-lj_table_coul_table.yaml | 4 +- .../tests/mol-pair-lj_table_tip4p_long.yaml | 4 +- .../tests/mol-pair-lj_table_tip4p_table.yaml | 4 +- .../force-styles/tests/mol-pair-mie_cut.yaml | 4 +- .../force-styles/tests/mol-pair-morse.yaml | 4 +- .../tests/mol-pair-morse_smooth_linear.yaml | 4 +- .../tests/mol-pair-morse_soft.yaml | 4 +- .../force-styles/tests/mol-pair-nm_cut.yaml | 4 +- .../tests/mol-pair-nm_cut_coul_cut.yaml | 4 +- .../tests/mol-pair-nm_cut_coul_long.yaml | 4 +- .../tests/mol-pair-nm_cut_coul_table.yaml | 4 +- .../tests/mol-pair-python_hybrid.yaml | 4 +- .../tests/mol-pair-python_lj.yaml | 4 +- .../force-styles/tests/mol-pair-soft.yaml | 4 +- .../force-styles/tests/mol-pair-table.yaml | 4 +- .../tests/mol-pair-tip4p_cut.yaml | 4 +- .../tests/mol-pair-tip4p_long.yaml | 4 +- .../tests/mol-pair-tip4p_long_soft.yaml | 4 +- .../tests/mol-pair-tip4p_table.yaml | 4 +- unittest/force-styles/tests/mol-pair-ufm.yaml | 4 +- .../force-styles/tests/mol-pair-wf_cut.yaml | 4 +- .../force-styles/tests/mol-pair-yukawa.yaml | 4 +- unittest/force-styles/tests/mol-pair-zbl.yaml | 4 +- .../force-styles/tests/mol-pair-zero.yaml | 4 +- 364 files changed, 1482 insertions(+), 1482 deletions(-) diff --git a/unittest/force-styles/tests/angle-charmm.yaml b/unittest/force-styles/tests/angle-charmm.yaml index 3d0dc17371..83c9609995 100644 --- a/unittest/force-styles/tests/angle-charmm.yaml +++ b/unittest/force-styles/tests/angle-charmm.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:23 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-class2.yaml b/unittest/force-styles/tests/angle-class2.yaml index a82e2f66b3..ffd48d7727 100644 --- a/unittest/force-styles/tests/angle-class2.yaml +++ b/unittest/force-styles/tests/angle-class2.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:23 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-class2_p6.yaml b/unittest/force-styles/tests/angle-class2_p6.yaml index f8b3982573..72ee6626c8 100644 --- a/unittest/force-styles/tests/angle-class2_p6.yaml +++ b/unittest/force-styles/tests/angle-class2_p6.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:23 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-cosine.yaml b/unittest/force-styles/tests/angle-cosine.yaml index 69d3c7439d..3b80dfe647 100644 --- a/unittest/force-styles/tests/angle-cosine.yaml +++ b/unittest/force-styles/tests/angle-cosine.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:23 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-cosine_delta.yaml b/unittest/force-styles/tests/angle-cosine_delta.yaml index 131e91789f..e59eda767f 100644 --- a/unittest/force-styles/tests/angle-cosine_delta.yaml +++ b/unittest/force-styles/tests/angle-cosine_delta.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:23 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-cosine_periodic.yaml b/unittest/force-styles/tests/angle-cosine_periodic.yaml index 814c837dcd..55beb13fdd 100644 --- a/unittest/force-styles/tests/angle-cosine_periodic.yaml +++ b/unittest/force-styles/tests/angle-cosine_periodic.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:23 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-cosine_shift.yaml b/unittest/force-styles/tests/angle-cosine_shift.yaml index 3ea5e257e0..0518db6d83 100644 --- a/unittest/force-styles/tests/angle-cosine_shift.yaml +++ b/unittest/force-styles/tests/angle-cosine_shift.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:23 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-cosine_shift_exp.yaml b/unittest/force-styles/tests/angle-cosine_shift_exp.yaml index cf19a26b1f..f237af9bb2 100644 --- a/unittest/force-styles/tests/angle-cosine_shift_exp.yaml +++ b/unittest/force-styles/tests/angle-cosine_shift_exp.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:24 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-cosine_squared.yaml b/unittest/force-styles/tests/angle-cosine_squared.yaml index c9ab2e5448..ad00a9e357 100644 --- a/unittest/force-styles/tests/angle-cosine_squared.yaml +++ b/unittest/force-styles/tests/angle-cosine_squared.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:24 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-cross.yaml b/unittest/force-styles/tests/angle-cross.yaml index ccaf5f3be6..5e5db1d8cb 100644 --- a/unittest/force-styles/tests/angle-cross.yaml +++ b/unittest/force-styles/tests/angle-cross.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:24 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-fourier.yaml b/unittest/force-styles/tests/angle-fourier.yaml index d36d2cefd7..487458bf60 100644 --- a/unittest/force-styles/tests/angle-fourier.yaml +++ b/unittest/force-styles/tests/angle-fourier.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:24 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-fourier_simple.yaml b/unittest/force-styles/tests/angle-fourier_simple.yaml index abd9218c7f..ee318b013f 100644 --- a/unittest/force-styles/tests/angle-fourier_simple.yaml +++ b/unittest/force-styles/tests/angle-fourier_simple.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:24 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-gaussian.yaml b/unittest/force-styles/tests/angle-gaussian.yaml index 0103811913..dd11d73b1f 100644 --- a/unittest/force-styles/tests/angle-gaussian.yaml +++ b/unittest/force-styles/tests/angle-gaussian.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 29 Oct 2020 -date_generated: Sat Nov 14 17:18:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:24 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-harmonic.yaml b/unittest/force-styles/tests/angle-harmonic.yaml index 6d9cf67210..7490bf6764 100644 --- a/unittest/force-styles/tests/angle-harmonic.yaml +++ b/unittest/force-styles/tests/angle-harmonic.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:24 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-hybrid.yaml b/unittest/force-styles/tests/angle-hybrid.yaml index f68d23e790..a46c6c69e4 100644 --- a/unittest/force-styles/tests/angle-hybrid.yaml +++ b/unittest/force-styles/tests/angle-hybrid.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:24 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-mm3.yaml b/unittest/force-styles/tests/angle-mm3.yaml index d4bf2b8cb5..cf857f86d5 100644 --- a/unittest/force-styles/tests/angle-mm3.yaml +++ b/unittest/force-styles/tests/angle-mm3.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:35 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:24 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-quartic.yaml b/unittest/force-styles/tests/angle-quartic.yaml index 912825d3a2..3fd927ac4a 100644 --- a/unittest/force-styles/tests/angle-quartic.yaml +++ b/unittest/force-styles/tests/angle-quartic.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:35 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:25 2021 epsilon: 4e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-table_linear.yaml b/unittest/force-styles/tests/angle-table_linear.yaml index 7dc66d9edf..979750b11c 100644 --- a/unittest/force-styles/tests/angle-table_linear.yaml +++ b/unittest/force-styles/tests/angle-table_linear.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:35 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:25 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-table_spline.yaml b/unittest/force-styles/tests/angle-table_spline.yaml index 10edec26fd..7adb7240ec 100644 --- a/unittest/force-styles/tests/angle-table_spline.yaml +++ b/unittest/force-styles/tests/angle-table_spline.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:35 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:25 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/angle-zero.yaml b/unittest/force-styles/tests/angle-zero.yaml index 71f4451d72..b2f1a0ec90 100644 --- a/unittest/force-styles/tests/angle-zero.yaml +++ b/unittest/force-styles/tests/angle-zero.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:35 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:25 2021 epsilon: 1e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/atomic-pair-adp.yaml b/unittest/force-styles/tests/atomic-pair-adp.yaml index c8eb06a3be..8d8a707bff 100644 --- a/unittest/force-styles/tests/atomic-pair-adp.yaml +++ b/unittest/force-styles/tests/atomic-pair-adp.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:21 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:58 2021 epsilon: 5e-13 prerequisites: ! | pair adp diff --git a/unittest/force-styles/tests/atomic-pair-atm.yaml b/unittest/force-styles/tests/atomic-pair-atm.yaml index 525cfdcd5f..0fc90345a3 100644 --- a/unittest/force-styles/tests/atomic-pair-atm.yaml +++ b/unittest/force-styles/tests/atomic-pair-atm.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:21 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:58 2021 epsilon: 5e-12 prerequisites: ! | pair atm diff --git a/unittest/force-styles/tests/atomic-pair-beck.yaml b/unittest/force-styles/tests/atomic-pair-beck.yaml index e2398914a2..3faebc561b 100644 --- a/unittest/force-styles/tests/atomic-pair-beck.yaml +++ b/unittest/force-styles/tests/atomic-pair-beck.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:21 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:59 2021 epsilon: 5e-13 prerequisites: ! | pair beck diff --git a/unittest/force-styles/tests/atomic-pair-born.yaml b/unittest/force-styles/tests/atomic-pair-born.yaml index 4769fc729c..52fcbef141 100644 --- a/unittest/force-styles/tests/atomic-pair-born.yaml +++ b/unittest/force-styles/tests/atomic-pair-born.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:21 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:59 2021 epsilon: 5e-13 prerequisites: ! | pair born diff --git a/unittest/force-styles/tests/atomic-pair-colloid.yaml b/unittest/force-styles/tests/atomic-pair-colloid.yaml index 9ac3710674..537ac447b5 100644 --- a/unittest/force-styles/tests/atomic-pair-colloid.yaml +++ b/unittest/force-styles/tests/atomic-pair-colloid.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:21 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:59 2021 epsilon: 5e-14 prerequisites: ! | pair colloid diff --git a/unittest/force-styles/tests/atomic-pair-colloid_multi.yaml b/unittest/force-styles/tests/atomic-pair-colloid_multi.yaml index 7923d672eb..025a7faa05 100644 --- a/unittest/force-styles/tests/atomic-pair-colloid_multi.yaml +++ b/unittest/force-styles/tests/atomic-pair-colloid_multi.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:21 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:59 2021 epsilon: 5e-14 prerequisites: ! | pair colloid diff --git a/unittest/force-styles/tests/atomic-pair-colloid_multi_tri.yaml b/unittest/force-styles/tests/atomic-pair-colloid_multi_tri.yaml index 38d51f3566..9ead662a06 100644 --- a/unittest/force-styles/tests/atomic-pair-colloid_multi_tri.yaml +++ b/unittest/force-styles/tests/atomic-pair-colloid_multi_tri.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:21 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:59 2021 epsilon: 5e-13 prerequisites: ! | pair colloid diff --git a/unittest/force-styles/tests/atomic-pair-colloid_tiled.yaml b/unittest/force-styles/tests/atomic-pair-colloid_tiled.yaml index 516395e3c2..be3ba744d0 100644 --- a/unittest/force-styles/tests/atomic-pair-colloid_tiled.yaml +++ b/unittest/force-styles/tests/atomic-pair-colloid_tiled.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:21 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:59 2021 epsilon: 5e-14 prerequisites: ! | pair colloid diff --git a/unittest/force-styles/tests/atomic-pair-colloid_tiled_tri.yaml b/unittest/force-styles/tests/atomic-pair-colloid_tiled_tri.yaml index b52ad6fe37..cd6c7595e8 100644 --- a/unittest/force-styles/tests/atomic-pair-colloid_tiled_tri.yaml +++ b/unittest/force-styles/tests/atomic-pair-colloid_tiled_tri.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:21 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:59 2021 epsilon: 5e-13 prerequisites: ! | pair colloid diff --git a/unittest/force-styles/tests/atomic-pair-eam.yaml b/unittest/force-styles/tests/atomic-pair-eam.yaml index 455f932258..c606813d56 100644 --- a/unittest/force-styles/tests/atomic-pair-eam.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:21 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:00 2021 epsilon: 6e-12 prerequisites: ! | pair eam diff --git a/unittest/force-styles/tests/atomic-pair-eam_alloy.yaml b/unittest/force-styles/tests/atomic-pair-eam_alloy.yaml index a2d39bdd7c..072a0a97c0 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_alloy.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_alloy.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:22 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:00 2021 epsilon: 5e-12 prerequisites: ! | pair eam/alloy diff --git a/unittest/force-styles/tests/atomic-pair-eam_alloy_real.yaml b/unittest/force-styles/tests/atomic-pair-eam_alloy_real.yaml index 4684951547..033c341f08 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_alloy_real.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_alloy_real.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:22 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:00 2021 epsilon: 7.5e-12 prerequisites: ! | pair eam/alloy diff --git a/unittest/force-styles/tests/atomic-pair-eam_cd.yaml b/unittest/force-styles/tests/atomic-pair-eam_cd.yaml index c1d189e1d8..bda14a9e5a 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_cd.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_cd.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:22 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:00 2021 epsilon: 5e-12 prerequisites: ! | pair eam/cd diff --git a/unittest/force-styles/tests/atomic-pair-eam_cd_old.yaml b/unittest/force-styles/tests/atomic-pair-eam_cd_old.yaml index 6dd89be146..4f6891bae6 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_cd_old.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_cd_old.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:22 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:00 2021 epsilon: 5e-12 prerequisites: ! | pair eam/cd/old diff --git a/unittest/force-styles/tests/atomic-pair-eam_cd_real.yaml b/unittest/force-styles/tests/atomic-pair-eam_cd_real.yaml index bf5269b8cb..e2ac5f0cae 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_cd_real.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_cd_real.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:22 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:00 2021 epsilon: 5e-12 prerequisites: ! | pair eam/cd diff --git a/unittest/force-styles/tests/atomic-pair-eam_fs.yaml b/unittest/force-styles/tests/atomic-pair-eam_fs.yaml index f978b7d444..89ad740424 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_fs.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_fs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:22 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:01 2021 epsilon: 5e-12 prerequisites: ! | pair eam/fs diff --git a/unittest/force-styles/tests/atomic-pair-eam_fs_real.yaml b/unittest/force-styles/tests/atomic-pair-eam_fs_real.yaml index eae925a38d..bf7f4f338b 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_fs_real.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_fs_real.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:22 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:01 2021 epsilon: 7.5e-12 prerequisites: ! | pair eam/fs diff --git a/unittest/force-styles/tests/atomic-pair-eam_he.yaml b/unittest/force-styles/tests/atomic-pair-eam_he.yaml index f82b4182b3..001301fe1a 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_he.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_he.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Dec 2020 -date_generated: Wed Jan 13 22:16:02 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:01 2021 epsilon: 5e-12 prerequisites: ! | pair eam/he diff --git a/unittest/force-styles/tests/atomic-pair-eam_he_real.yaml b/unittest/force-styles/tests/atomic-pair-eam_he_real.yaml index 62324447a3..236b9538a7 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_he_real.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_he_real.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Dec 2020 -date_generated: Wed Jan 13 22:16:02 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:02 2021 epsilon: 7.5e-12 prerequisites: ! | pair eam/he diff --git a/unittest/force-styles/tests/atomic-pair-eam_real.yaml b/unittest/force-styles/tests/atomic-pair-eam_real.yaml index a9df9364a0..89e7c1ce0b 100644 --- a/unittest/force-styles/tests/atomic-pair-eam_real.yaml +++ b/unittest/force-styles/tests/atomic-pair-eam_real.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:22 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:02 2021 epsilon: 5e-12 prerequisites: ! | pair eam diff --git a/unittest/force-styles/tests/atomic-pair-edip.yaml b/unittest/force-styles/tests/atomic-pair-edip.yaml index 3d9f4a00fa..91b7fd8db4 100644 --- a/unittest/force-styles/tests/atomic-pair-edip.yaml +++ b/unittest/force-styles/tests/atomic-pair-edip.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:22 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:02 2021 epsilon: 7.5e-13 prerequisites: ! | pair edip diff --git a/unittest/force-styles/tests/atomic-pair-eim.yaml b/unittest/force-styles/tests/atomic-pair-eim.yaml index 8e9b4ee2c0..4814029a3c 100644 --- a/unittest/force-styles/tests/atomic-pair-eim.yaml +++ b/unittest/force-styles/tests/atomic-pair-eim.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:22 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:02 2021 epsilon: 1e-11 prerequisites: ! | pair eim diff --git a/unittest/force-styles/tests/atomic-pair-gauss.yaml b/unittest/force-styles/tests/atomic-pair-gauss.yaml index a6db06e019..7d4c2029db 100644 --- a/unittest/force-styles/tests/atomic-pair-gauss.yaml +++ b/unittest/force-styles/tests/atomic-pair-gauss.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:22 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:02 2021 epsilon: 5e-12 prerequisites: ! | pair gauss diff --git a/unittest/force-styles/tests/atomic-pair-hybrid-eam.yaml b/unittest/force-styles/tests/atomic-pair-hybrid-eam.yaml index b3569a7e74..a681657b65 100644 --- a/unittest/force-styles/tests/atomic-pair-hybrid-eam.yaml +++ b/unittest/force-styles/tests/atomic-pair-hybrid-eam.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:23 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:02 2021 epsilon: 1e-11 prerequisites: ! | pair eam/fs diff --git a/unittest/force-styles/tests/atomic-pair-hybrid-eam_fs.yaml b/unittest/force-styles/tests/atomic-pair-hybrid-eam_fs.yaml index 2098f90e13..d2f511b3ea 100644 --- a/unittest/force-styles/tests/atomic-pair-hybrid-eam_fs.yaml +++ b/unittest/force-styles/tests/atomic-pair-hybrid-eam_fs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:23 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:03 2021 epsilon: 5e-12 prerequisites: ! | pair eam/fs diff --git a/unittest/force-styles/tests/atomic-pair-kim_lj.yaml b/unittest/force-styles/tests/atomic-pair-kim_lj.yaml index 87d7994740..84bf844350 100644 --- a/unittest/force-styles/tests/atomic-pair-kim_lj.yaml +++ b/unittest/force-styles/tests/atomic-pair-kim_lj.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:23 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:03 2021 epsilon: 5e-13 prerequisites: ! | pair kim diff --git a/unittest/force-styles/tests/atomic-pair-meam_c.yaml b/unittest/force-styles/tests/atomic-pair-meam_c.yaml index 0d369326cc..7d93a698e0 100644 --- a/unittest/force-styles/tests/atomic-pair-meam_c.yaml +++ b/unittest/force-styles/tests/atomic-pair-meam_c.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:23 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:03 2021 epsilon: 5e-13 prerequisites: ! | pair meam/c diff --git a/unittest/force-styles/tests/atomic-pair-meam_spline.yaml b/unittest/force-styles/tests/atomic-pair-meam_spline.yaml index 43db461160..7fd61ac2aa 100644 --- a/unittest/force-styles/tests/atomic-pair-meam_spline.yaml +++ b/unittest/force-styles/tests/atomic-pair-meam_spline.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:23 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:03 2021 epsilon: 1e-14 prerequisites: ! | pair meam/spline diff --git a/unittest/force-styles/tests/atomic-pair-meam_sw_spline.yaml b/unittest/force-styles/tests/atomic-pair-meam_sw_spline.yaml index ca9bad14f5..b9f330e6de 100644 --- a/unittest/force-styles/tests/atomic-pair-meam_sw_spline.yaml +++ b/unittest/force-styles/tests/atomic-pair-meam_sw_spline.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:23 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:03 2021 epsilon: 1e-14 prerequisites: ! | pair meam/sw/spline diff --git a/unittest/force-styles/tests/atomic-pair-momb.yaml b/unittest/force-styles/tests/atomic-pair-momb.yaml index 525198b071..2ee1c80ff0 100644 --- a/unittest/force-styles/tests/atomic-pair-momb.yaml +++ b/unittest/force-styles/tests/atomic-pair-momb.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:23 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:03 2021 epsilon: 2.5e-12 prerequisites: ! | pair momb diff --git a/unittest/force-styles/tests/atomic-pair-polymorphic_eam.yaml b/unittest/force-styles/tests/atomic-pair-polymorphic_eam.yaml index dcc041f6e0..57f0812bca 100644 --- a/unittest/force-styles/tests/atomic-pair-polymorphic_eam.yaml +++ b/unittest/force-styles/tests/atomic-pair-polymorphic_eam.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:23 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:04 2021 epsilon: 1e-12 prerequisites: ! | pair polymorphic diff --git a/unittest/force-styles/tests/atomic-pair-reax_c.yaml b/unittest/force-styles/tests/atomic-pair-reax_c.yaml index b88eb7235b..fe6c93db05 100644 --- a/unittest/force-styles/tests/atomic-pair-reax_c.yaml +++ b/unittest/force-styles/tests/atomic-pair-reax_c.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:24 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:04 2021 epsilon: 2.5e-11 prerequisites: ! | pair reax/c diff --git a/unittest/force-styles/tests/atomic-pair-reax_c_lgvdw.yaml b/unittest/force-styles/tests/atomic-pair-reax_c_lgvdw.yaml index db4bb284fa..567bddf5ce 100644 --- a/unittest/force-styles/tests/atomic-pair-reax_c_lgvdw.yaml +++ b/unittest/force-styles/tests/atomic-pair-reax_c_lgvdw.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:25 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:06 2021 epsilon: 2e-10 prerequisites: ! | pair reax/c diff --git a/unittest/force-styles/tests/atomic-pair-reax_c_noqeq.yaml b/unittest/force-styles/tests/atomic-pair-reax_c_noqeq.yaml index 32a75749b1..efdf3ff5de 100644 --- a/unittest/force-styles/tests/atomic-pair-reax_c_noqeq.yaml +++ b/unittest/force-styles/tests/atomic-pair-reax_c_noqeq.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:26 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:08 2021 epsilon: 5e-13 prerequisites: ! | pair reax/c diff --git a/unittest/force-styles/tests/atomic-pair-table_bitmap.yaml b/unittest/force-styles/tests/atomic-pair-table_bitmap.yaml index d4401d6895..c67ff58bf8 100644 --- a/unittest/force-styles/tests/atomic-pair-table_bitmap.yaml +++ b/unittest/force-styles/tests/atomic-pair-table_bitmap.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:27 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:09 2021 epsilon: 5e-13 prerequisites: ! | pair table diff --git a/unittest/force-styles/tests/atomic-pair-table_linear.yaml b/unittest/force-styles/tests/atomic-pair-table_linear.yaml index 14dd697e49..bb7f3959e0 100644 --- a/unittest/force-styles/tests/atomic-pair-table_linear.yaml +++ b/unittest/force-styles/tests/atomic-pair-table_linear.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:27 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:10 2021 epsilon: 5e-13 prerequisites: ! | pair table diff --git a/unittest/force-styles/tests/atomic-pair-table_lookup.yaml b/unittest/force-styles/tests/atomic-pair-table_lookup.yaml index 769d94b350..8752fa49a8 100644 --- a/unittest/force-styles/tests/atomic-pair-table_lookup.yaml +++ b/unittest/force-styles/tests/atomic-pair-table_lookup.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:27 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:10 2021 epsilon: 5e-13 prerequisites: ! | pair table diff --git a/unittest/force-styles/tests/atomic-pair-table_spline.yaml b/unittest/force-styles/tests/atomic-pair-table_spline.yaml index a4dce1338b..276dae27c2 100644 --- a/unittest/force-styles/tests/atomic-pair-table_spline.yaml +++ b/unittest/force-styles/tests/atomic-pair-table_spline.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:27 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:10 2021 epsilon: 5e-13 prerequisites: ! | pair table diff --git a/unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml b/unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml index 4011d89240..1529cf51b9 100644 --- a/unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml +++ b/unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:27 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:10 2021 epsilon: 5e-14 prerequisites: ! | atom sphere diff --git a/unittest/force-styles/tests/bond-class2.yaml b/unittest/force-styles/tests/bond-class2.yaml index 13c2493d88..19647a56ed 100644 --- a/unittest/force-styles/tests/bond-class2.yaml +++ b/unittest/force-styles/tests/bond-class2.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:21 2021 epsilon: 1e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/bond-fene.yaml b/unittest/force-styles/tests/bond-fene.yaml index dffbcf6f8b..00b66e2466 100644 --- a/unittest/force-styles/tests/bond-fene.yaml +++ b/unittest/force-styles/tests/bond-fene.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:21 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/bond-fene_expand.yaml b/unittest/force-styles/tests/bond-fene_expand.yaml index 8b3513737f..f29213e126 100644 --- a/unittest/force-styles/tests/bond-fene_expand.yaml +++ b/unittest/force-styles/tests/bond-fene_expand.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:21 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/bond-gaussian.yaml b/unittest/force-styles/tests/bond-gaussian.yaml index 92157d7155..b5553fb053 100644 --- a/unittest/force-styles/tests/bond-gaussian.yaml +++ b/unittest/force-styles/tests/bond-gaussian.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 29 Oct 2020 -date_generated: Sat Nov 14 16:49:01 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:21 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/bond-gromos.yaml b/unittest/force-styles/tests/bond-gromos.yaml index 14fc81b49c..13ad366fed 100644 --- a/unittest/force-styles/tests/bond-gromos.yaml +++ b/unittest/force-styles/tests/bond-gromos.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:21 2021 epsilon: 5e-13 prerequisites: ! | atom full @@ -15,7 +15,7 @@ bond_coeff: ! | 3 350.0 1.3 4 650.0 1.2 5 450.0 1.0 -equilibrium: 5 1.5 1.1 1.3 1.2 1.0 +equilibrium: 5 1.5 1.1 1.3 1.2 1 extract: ! | kappa 1 r0 1 diff --git a/unittest/force-styles/tests/bond-harmonic.yaml b/unittest/force-styles/tests/bond-harmonic.yaml index 0bbe86c3c2..a277586a2e 100644 --- a/unittest/force-styles/tests/bond-harmonic.yaml +++ b/unittest/force-styles/tests/bond-harmonic.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:21 2021 epsilon: 2.5e-13 prerequisites: ! | atom full @@ -15,7 +15,7 @@ bond_coeff: ! | 3 350.0 1.3 4 650.0 1.2 5 450.0 1.0 -equilibrium: 5 1.5 1.1 1.3 1.2 1.0 +equilibrium: 5 1.5 1.1 1.3 1.2 1 extract: ! | kappa 1 r0 1 diff --git a/unittest/force-styles/tests/bond-harmonic_shift.yaml b/unittest/force-styles/tests/bond-harmonic_shift.yaml index bc8fa72d85..9726574bee 100644 --- a/unittest/force-styles/tests/bond-harmonic_shift.yaml +++ b/unittest/force-styles/tests/bond-harmonic_shift.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:22 2021 epsilon: 2.5e-13 prerequisites: ! | atom full @@ -15,7 +15,7 @@ bond_coeff: ! | 3 350.0 1.3 0.3 4 650.0 1.2 0.2 5 450.0 1.0 0.0 -equilibrium: 5 1.5 1.1 1.3 1.2 1.0 +equilibrium: 5 1.5 1.1 1.3 1.2 1 extract: ! "" natoms: 29 init_energy: -9395.51998238922 diff --git a/unittest/force-styles/tests/bond-harmonic_shift_cut.yaml b/unittest/force-styles/tests/bond-harmonic_shift_cut.yaml index 9fe6db9b1f..9406206497 100644 --- a/unittest/force-styles/tests/bond-harmonic_shift_cut.yaml +++ b/unittest/force-styles/tests/bond-harmonic_shift_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:22 2021 epsilon: 2.5e-13 prerequisites: ! | atom full @@ -15,7 +15,7 @@ bond_coeff: ! | 3 350.0 1.3 0.3 4 650.0 1.2 0.2 5 450.0 1.0 0.0 -equilibrium: 5 1.5 1.1 1.3 1.2 1.0 +equilibrium: 5 1.5 1.1 1.3 1.2 1 extract: ! "" natoms: 29 init_energy: 0 diff --git a/unittest/force-styles/tests/bond-hybrid.yaml b/unittest/force-styles/tests/bond-hybrid.yaml index 9e2d6f9be7..44d4579aa2 100644 --- a/unittest/force-styles/tests/bond-hybrid.yaml +++ b/unittest/force-styles/tests/bond-hybrid.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:22 2021 epsilon: 2.5e-13 prerequisites: ! | atom full @@ -16,7 +16,7 @@ bond_coeff: ! | 3 morse 7000.0 0.2 1.3 4 harmonic 650.0 1.2 5 harmonic 450.0 1.0 -equilibrium: 5 1.5 1.1 1.3 1.2 1.0 +equilibrium: 5 1.5 1.1 1.3 1.2 1 extract: ! "" natoms: 29 init_energy: 4.63957309438403 diff --git a/unittest/force-styles/tests/bond-mm3.yaml b/unittest/force-styles/tests/bond-mm3.yaml index f93ee4ace3..4e4c2c19d3 100644 --- a/unittest/force-styles/tests/bond-mm3.yaml +++ b/unittest/force-styles/tests/bond-mm3.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:22 2021 epsilon: 2.5e-13 prerequisites: ! | atom full @@ -15,7 +15,7 @@ bond_coeff: ! | 3 350.0 1.3 4 650.0 1.2 5 450.0 1.0 -equilibrium: 5 1.5 1.1 1.3 1.2 1.0 +equilibrium: 5 1.5 1.1 1.3 1.2 1 extract: ! "" natoms: 29 init_energy: 4.24726500827314 diff --git a/unittest/force-styles/tests/bond-morse.yaml b/unittest/force-styles/tests/bond-morse.yaml index fea8739e5e..ba76e2f153 100644 --- a/unittest/force-styles/tests/bond-morse.yaml +++ b/unittest/force-styles/tests/bond-morse.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:22 2021 epsilon: 2.5e-13 prerequisites: ! | atom full @@ -15,7 +15,7 @@ bond_coeff: ! | 3 7000.0 0.2 1.3 4 7500.0 0.4 1.2 5 7000.0 0.3 1.0 -equilibrium: 5 1.5 1.1 1.3 1.2 1.0 +equilibrium: 5 1.5 1.1 1.3 1.2 1 extract: ! | r0 1 natoms: 29 diff --git a/unittest/force-styles/tests/bond-nonlinear.yaml b/unittest/force-styles/tests/bond-nonlinear.yaml index cb3e10d14f..ef4f59df5b 100644 --- a/unittest/force-styles/tests/bond-nonlinear.yaml +++ b/unittest/force-styles/tests/bond-nonlinear.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:22 2021 epsilon: 5e-13 prerequisites: ! | atom full @@ -15,7 +15,7 @@ bond_coeff: ! | 3 350.0 1.3 2.0 4 650.0 1.2 1.4 5 450.0 1.0 1.1 -equilibrium: 5 1.5 1.1 1.3 1.2 1.0 +equilibrium: 5 1.5 1.1 1.3 1.2 1 extract: ! "" natoms: 29 init_energy: 1.94517280328209 diff --git a/unittest/force-styles/tests/bond-quartic.yaml b/unittest/force-styles/tests/bond-quartic.yaml index b7248b64cf..9d49991d5a 100644 --- a/unittest/force-styles/tests/bond-quartic.yaml +++ b/unittest/force-styles/tests/bond-quartic.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 10:06:36 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:22 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/bond-table_linear.yaml b/unittest/force-styles/tests/bond-table_linear.yaml index 307c9ef9bd..b2ffe6360a 100644 --- a/unittest/force-styles/tests/bond-table_linear.yaml +++ b/unittest/force-styles/tests/bond-table_linear.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:22 2021 epsilon: 2.5e-13 prerequisites: ! | atom full @@ -15,7 +15,7 @@ bond_coeff: ! | 3 ${input_dir}/bond_table.txt harmonic_3 4 ${input_dir}/bond_table.txt harmonic_4 5 ${input_dir}/bond_table.txt harmonic_5 -equilibrium: 5 1.5 1.1 1.3 1.2 1.0 +equilibrium: 5 1.5 1.1 1.3 1.2 1 extract: ! "" natoms: 29 init_energy: 4.83475893645922 diff --git a/unittest/force-styles/tests/bond-table_spline.yaml b/unittest/force-styles/tests/bond-table_spline.yaml index 23ee0426da..3b4ffe462e 100644 --- a/unittest/force-styles/tests/bond-table_spline.yaml +++ b/unittest/force-styles/tests/bond-table_spline.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:23 2021 epsilon: 2.5e-13 prerequisites: ! | atom full @@ -15,7 +15,7 @@ bond_coeff: ! | 3 ${input_dir}/bond_table.txt harmonic_3 4 ${input_dir}/bond_table.txt harmonic_4 5 ${input_dir}/bond_table.txt harmonic_5 -equilibrium: 5 1.5 1.1 1.3 1.2 1.0 +equilibrium: 5 1.5 1.1 1.3 1.2 1 extract: ! "" natoms: 29 init_energy: 4.78937402460163 diff --git a/unittest/force-styles/tests/bond-zero.yaml b/unittest/force-styles/tests/bond-zero.yaml index 9c87712465..e3458f7d50 100644 --- a/unittest/force-styles/tests/bond-zero.yaml +++ b/unittest/force-styles/tests/bond-zero.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:23 2021 epsilon: 1e-14 prerequisites: ! | atom full @@ -15,7 +15,7 @@ bond_coeff: ! | 3 1.3 4 1.2 5 1.0 -equilibrium: 5 1.5 1.1 1.3 1.2 1.0 +equilibrium: 5 1.5 1.1 1.3 1.2 1 extract: ! | r0 1 natoms: 29 diff --git a/unittest/force-styles/tests/dihedral-charmm.yaml b/unittest/force-styles/tests/dihedral-charmm.yaml index 18df3bcd0f..471e85de89 100644 --- a/unittest/force-styles/tests/dihedral-charmm.yaml +++ b/unittest/force-styles/tests/dihedral-charmm.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 19:32:00 202 +date_generated: Fri Feb 26 23:09:34 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/dihedral-charmmfsw.yaml b/unittest/force-styles/tests/dihedral-charmmfsw.yaml index f1aa53eb63..0f0a76c8de 100644 --- a/unittest/force-styles/tests/dihedral-charmmfsw.yaml +++ b/unittest/force-styles/tests/dihedral-charmmfsw.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 19:32:07 202 +date_generated: Fri Feb 26 23:09:34 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/dihedral-class2.yaml b/unittest/force-styles/tests/dihedral-class2.yaml index 9ba2319072..9dfcc918a5 100644 --- a/unittest/force-styles/tests/dihedral-class2.yaml +++ b/unittest/force-styles/tests/dihedral-class2.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 18:38:38 202 +date_generated: Fri Feb 26 23:09:34 2021 epsilon: 8e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/dihedral-cosine_shift_exp.yaml b/unittest/force-styles/tests/dihedral-cosine_shift_exp.yaml index 69735c90a7..806a65bd8a 100644 --- a/unittest/force-styles/tests/dihedral-cosine_shift_exp.yaml +++ b/unittest/force-styles/tests/dihedral-cosine_shift_exp.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 18:38:38 202 +date_generated: Fri Feb 26 23:09:34 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/dihedral-fourier.yaml b/unittest/force-styles/tests/dihedral-fourier.yaml index b2e9dffad2..84b5d8f920 100644 --- a/unittest/force-styles/tests/dihedral-fourier.yaml +++ b/unittest/force-styles/tests/dihedral-fourier.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 18:38:38 202 +date_generated: Fri Feb 26 23:09:35 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/dihedral-harmonic.yaml b/unittest/force-styles/tests/dihedral-harmonic.yaml index 4e8fa89118..6c54a96142 100644 --- a/unittest/force-styles/tests/dihedral-harmonic.yaml +++ b/unittest/force-styles/tests/dihedral-harmonic.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 18:38:38 202 +date_generated: Fri Feb 26 23:09:35 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/dihedral-helix.yaml b/unittest/force-styles/tests/dihedral-helix.yaml index 992916d8ab..f775cd2164 100644 --- a/unittest/force-styles/tests/dihedral-helix.yaml +++ b/unittest/force-styles/tests/dihedral-helix.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 18:38:38 202 +date_generated: Fri Feb 26 23:09:35 2021 epsilon: 4e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/dihedral-hybrid.yaml b/unittest/force-styles/tests/dihedral-hybrid.yaml index 4826754536..4747958fab 100644 --- a/unittest/force-styles/tests/dihedral-hybrid.yaml +++ b/unittest/force-styles/tests/dihedral-hybrid.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 20:43:34 202 +date_generated: Fri Feb 26 23:09:35 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/dihedral-multi_harmonic.yaml b/unittest/force-styles/tests/dihedral-multi_harmonic.yaml index 60ce4d574f..1694ed2e66 100644 --- a/unittest/force-styles/tests/dihedral-multi_harmonic.yaml +++ b/unittest/force-styles/tests/dihedral-multi_harmonic.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 18:38:38 202 +date_generated: Fri Feb 26 23:09:35 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/dihedral-nharmonic.yaml b/unittest/force-styles/tests/dihedral-nharmonic.yaml index b3101ff379..564864a636 100644 --- a/unittest/force-styles/tests/dihedral-nharmonic.yaml +++ b/unittest/force-styles/tests/dihedral-nharmonic.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 18:38:38 202 +date_generated: Fri Feb 26 23:09:35 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/dihedral-opls.yaml b/unittest/force-styles/tests/dihedral-opls.yaml index 3b0c897d68..03164e2c36 100644 --- a/unittest/force-styles/tests/dihedral-opls.yaml +++ b/unittest/force-styles/tests/dihedral-opls.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 18:38:38 202 +date_generated: Fri Feb 26 23:09:35 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/dihedral-quadratic.yaml b/unittest/force-styles/tests/dihedral-quadratic.yaml index c03382dc22..ed230b7c23 100644 --- a/unittest/force-styles/tests/dihedral-quadratic.yaml +++ b/unittest/force-styles/tests/dihedral-quadratic.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 18:38:38 202 +date_generated: Fri Feb 26 23:09:35 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/dihedral-zero.yaml b/unittest/force-styles/tests/dihedral-zero.yaml index 2573cf7501..04652cbfc6 100644 --- a/unittest/force-styles/tests/dihedral-zero.yaml +++ b/unittest/force-styles/tests/dihedral-zero.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 18:38:39 202 +date_generated: Fri Feb 26 23:09:36 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-addforce_const.yaml b/unittest/force-styles/tests/fix-timestep-addforce_const.yaml index 39bbfcf280..47786b33fe 100644 --- a/unittest/force-styles/tests/fix-timestep-addforce_const.yaml +++ b/unittest/force-styles/tests/fix-timestep-addforce_const.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:39 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:53 2021 epsilon: 9e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-addforce_variable.yaml b/unittest/force-styles/tests/fix-timestep-addforce_variable.yaml index 421051601a..78f260bd39 100644 --- a/unittest/force-styles/tests/fix-timestep-addforce_variable.yaml +++ b/unittest/force-styles/tests/fix-timestep-addforce_variable.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:39 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:53 2021 epsilon: 2e-11 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-aveforce_const.yaml b/unittest/force-styles/tests/fix-timestep-aveforce_const.yaml index 18dd4cf4b2..34c6afbbf5 100644 --- a/unittest/force-styles/tests/fix-timestep-aveforce_const.yaml +++ b/unittest/force-styles/tests/fix-timestep-aveforce_const.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:53 2021 epsilon: 2e-11 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-aveforce_variable.yaml b/unittest/force-styles/tests/fix-timestep-aveforce_variable.yaml index 41299b2ec8..6b52979777 100644 --- a/unittest/force-styles/tests/fix-timestep-aveforce_variable.yaml +++ b/unittest/force-styles/tests/fix-timestep-aveforce_variable.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:53 2021 epsilon: 2.5e-11 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-drag.yaml b/unittest/force-styles/tests/fix-timestep-drag.yaml index bb4908f55e..fbcee25721 100644 --- a/unittest/force-styles/tests/fix-timestep-drag.yaml +++ b/unittest/force-styles/tests/fix-timestep-drag.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:53 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-efield_const.yaml b/unittest/force-styles/tests/fix-timestep-efield_const.yaml index 394af87faa..cd0fe2b7d4 100644 --- a/unittest/force-styles/tests/fix-timestep-efield_const.yaml +++ b/unittest/force-styles/tests/fix-timestep-efield_const.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:53 2021 epsilon: 2e-13 prerequisites: ! | atom full @@ -13,7 +13,7 @@ input_file: in.fourmol natoms: 29 global_scalar: -0.0309186331146529 global_vector: ! |- - 3 0.0 -2.220446049250313e-16 2.220446049250313e-16 + 3 0 -2.220446049250313e-16 2.220446049250313e-16 run_pos: ! |2 1 -2.7045797446143222e-01 2.4912780824342802e+00 -1.6702148063946790e-01 2 3.1004707684044314e-01 2.9610914097014920e+00 -8.5452223796947857e-01 diff --git a/unittest/force-styles/tests/fix-timestep-efield_region.yaml b/unittest/force-styles/tests/fix-timestep-efield_region.yaml index f45b6c05c9..6312ce5d52 100644 --- a/unittest/force-styles/tests/fix-timestep-efield_region.yaml +++ b/unittest/force-styles/tests/fix-timestep-efield_region.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:53 2021 epsilon: 2e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-efield_variable.yaml b/unittest/force-styles/tests/fix-timestep-efield_variable.yaml index 94137f59b8..13d43663a2 100644 --- a/unittest/force-styles/tests/fix-timestep-efield_variable.yaml +++ b/unittest/force-styles/tests/fix-timestep-efield_variable.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:53 2021 epsilon: 2e-13 prerequisites: ! | atom full @@ -18,7 +18,7 @@ input_file: in.fourmol natoms: 29 global_scalar: 0 global_vector: ! |- - 3 10.275935322301738 0.0 -1.1102230246251565e-16 + 3 10.275935322301738 0 -1.1102230246251565e-16 run_pos: ! |2 1 -2.7027400245078581e-01 2.4912153249078419e+00 -1.6697700443575972e-01 2 3.1048749486212474e-01 2.9612319277095587e+00 -8.5462053704633356e-01 diff --git a/unittest/force-styles/tests/fix-timestep-heat.yaml b/unittest/force-styles/tests/fix-timestep-heat.yaml index a7197528f5..a93468f7e8 100644 --- a/unittest/force-styles/tests/fix-timestep-heat.yaml +++ b/unittest/force-styles/tests/fix-timestep-heat.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:54 2021 epsilon: 2e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-heat_region.yaml b/unittest/force-styles/tests/fix-timestep-heat_region.yaml index 1439af67ad..9c8f740456 100644 --- a/unittest/force-styles/tests/fix-timestep-heat_region.yaml +++ b/unittest/force-styles/tests/fix-timestep-heat_region.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:54 2021 epsilon: 2e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-lineforce.yaml b/unittest/force-styles/tests/fix-timestep-lineforce.yaml index 8acfe82ce3..fbb3a4f16f 100644 --- a/unittest/force-styles/tests/fix-timestep-lineforce.yaml +++ b/unittest/force-styles/tests/fix-timestep-lineforce.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:54 2021 epsilon: 5e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-momentum.yaml b/unittest/force-styles/tests/fix-timestep-momentum.yaml index 96a3e9d4bb..4ae3b928bf 100644 --- a/unittest/force-styles/tests/fix-timestep-momentum.yaml +++ b/unittest/force-styles/tests/fix-timestep-momentum.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:54 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-momentum_chunk.yaml b/unittest/force-styles/tests/fix-timestep-momentum_chunk.yaml index 454d9c632c..89e6518c7b 100644 --- a/unittest/force-styles/tests/fix-timestep-momentum_chunk.yaml +++ b/unittest/force-styles/tests/fix-timestep-momentum_chunk.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:54 2021 epsilon: 2e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-nph.yaml b/unittest/force-styles/tests/fix-timestep-nph.yaml index 0eb8716aaf..a21fe19fa8 100644 --- a/unittest/force-styles/tests/fix-timestep-nph.yaml +++ b/unittest/force-styles/tests/fix-timestep-nph.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:54 2021 epsilon: 2e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-npt_aniso.yaml b/unittest/force-styles/tests/fix-timestep-npt_aniso.yaml index b086a1b95e..b7d7a2a32e 100644 --- a/unittest/force-styles/tests/fix-timestep-npt_aniso.yaml +++ b/unittest/force-styles/tests/fix-timestep-npt_aniso.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:54 2021 epsilon: 4e-11 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-npt_iso.yaml b/unittest/force-styles/tests/fix-timestep-npt_iso.yaml index 8dec2a1bec..1a47662b76 100644 --- a/unittest/force-styles/tests/fix-timestep-npt_iso.yaml +++ b/unittest/force-styles/tests/fix-timestep-npt_iso.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:54 2021 epsilon: 2e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-npt_tri.yaml b/unittest/force-styles/tests/fix-timestep-npt_tri.yaml index b4093b7a3d..c2a4da9695 100644 --- a/unittest/force-styles/tests/fix-timestep-npt_tri.yaml +++ b/unittest/force-styles/tests/fix-timestep-npt_tri.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:54 2021 epsilon: 5e-12 prerequisites: ! | atom full @@ -13,7 +13,7 @@ input_file: in.fourmol natoms: 29 global_scalar: 354.174797856098 global_vector: ! |- - 48 1.3901404465408471 5.463126417846173 27.522868094744837 0.6808509272696268 1.432899560678195 24.73621155835892 0.059175794171946315 0.058864829843401814 0.12700748296200176 0.02134537927441898 -0.006866713927713234 -0.03517153788806217 0.03214843910942283 0.03135716661218002 0.05847613666451851 0.010015733944968137 -0.004026286211139594 -0.020364872327366976 0.32458573874717506 0.03420953094338522 0.00010301961702814269 0.40071682483624077 0.09021935542363528 0.0016272628807846479 23.20496983817849 1.0856361420490914 5.469362788109317 3.86897924261614 0.20400675418492722 60.79661790199697 0.004555933286932949 0.004555933286932949 0.004555933286932949 0.0 0.0 0.0 23.105498800354294 21.982100664555755 76.44567329133054 2.242648057096569 0.36241390540377744 9.27169098501188 0.06450189547628359 0.006798140909455242 2.0472127318975922e-05 119.66012864844495 6.065599766319885 0.0019732846899264155 + 48 1.3901404465408471 5.463126417846173 27.522868094744837 0.6808509272696268 1.432899560678195 24.73621155835892 0.059175794171946315 0.058864829843401814 0.12700748296200176 0.02134537927441898 -0.006866713927713234 -0.03517153788806217 0.03214843910942283 0.03135716661218002 0.05847613666451851 0.010015733944968137 -0.004026286211139594 -0.020364872327366976 0.32458573874717506 0.03420953094338522 0.00010301961702814269 0.40071682483624077 0.09021935542363528 0.0016272628807846479 23.20496983817849 1.0856361420490914 5.469362788109317 3.86897924261614 0.20400675418492722 60.79661790199697 0.004555933286932949 0.004555933286932949 0.004555933286932949 0 0 0 23.105498800354294 21.982100664555755 76.44567329133054 2.242648057096569 0.36241390540377744 9.27169098501188 0.06450189547628359 0.006798140909455242 2.0472127318975922e-05 119.66012864844495 6.065599766319885 0.0019732846899264155 run_pos: ! |2 1 -8.2271095985417642e-01 2.8289040859356991e+00 -1.1444756137720979e-01 2 -2.2035635832079414e-01 3.3160751622563218e+00 -8.8905665482321261e-01 diff --git a/unittest/force-styles/tests/fix-timestep-nve.yaml b/unittest/force-styles/tests/fix-timestep-nve.yaml index 5d2efa1373..09d1efe402 100644 --- a/unittest/force-styles/tests/fix-timestep-nve.yaml +++ b/unittest/force-styles/tests/fix-timestep-nve.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:40 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:55 2021 epsilon: 2e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-nve_limit.yaml b/unittest/force-styles/tests/fix-timestep-nve_limit.yaml index bc6a16704f..1efd576e57 100644 --- a/unittest/force-styles/tests/fix-timestep-nve_limit.yaml +++ b/unittest/force-styles/tests/fix-timestep-nve_limit.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:41 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:55 2021 epsilon: 2e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-nve_noforce.yaml b/unittest/force-styles/tests/fix-timestep-nve_noforce.yaml index 17e9923d45..33b5295a53 100644 --- a/unittest/force-styles/tests/fix-timestep-nve_noforce.yaml +++ b/unittest/force-styles/tests/fix-timestep-nve_noforce.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:41 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:55 2021 epsilon: 2e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-nvt.yaml b/unittest/force-styles/tests/fix-timestep-nvt.yaml index 6a4ead99c1..298b506ab2 100644 --- a/unittest/force-styles/tests/fix-timestep-nvt.yaml +++ b/unittest/force-styles/tests/fix-timestep-nvt.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:41 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:55 2021 epsilon: 2e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-oneway.yaml b/unittest/force-styles/tests/fix-timestep-oneway.yaml index 01131a3803..413902e1ff 100644 --- a/unittest/force-styles/tests/fix-timestep-oneway.yaml +++ b/unittest/force-styles/tests/fix-timestep-oneway.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:41 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:55 2021 epsilon: 4e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-planeforce.yaml b/unittest/force-styles/tests/fix-timestep-planeforce.yaml index e4ad9f124e..ba1b93f9f2 100644 --- a/unittest/force-styles/tests/fix-timestep-planeforce.yaml +++ b/unittest/force-styles/tests/fix-timestep-planeforce.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:41 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:55 2021 epsilon: 5e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-press_berendsen_iso.yaml b/unittest/force-styles/tests/fix-timestep-press_berendsen_iso.yaml index 5bbf178dc3..c5bed62746 100644 --- a/unittest/force-styles/tests/fix-timestep-press_berendsen_iso.yaml +++ b/unittest/force-styles/tests/fix-timestep-press_berendsen_iso.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:41 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:55 2021 epsilon: 2e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rattle_angle.yaml b/unittest/force-styles/tests/fix-timestep-rattle_angle.yaml index 03ba9a64b9..92ac0b5cab 100644 --- a/unittest/force-styles/tests/fix-timestep-rattle_angle.yaml +++ b/unittest/force-styles/tests/fix-timestep-rattle_angle.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:41 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:55 2021 epsilon: 3e-10 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rattle_bond.yaml b/unittest/force-styles/tests/fix-timestep-rattle_bond.yaml index cad83187c6..2a4b6d9cb6 100644 --- a/unittest/force-styles/tests/fix-timestep-rattle_bond.yaml +++ b/unittest/force-styles/tests/fix-timestep-rattle_bond.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:41 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:55 2021 epsilon: 1e-10 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-restrain.yaml b/unittest/force-styles/tests/fix-timestep-restrain.yaml index b504554484..c6806c3176 100644 --- a/unittest/force-styles/tests/fix-timestep-restrain.yaml +++ b/unittest/force-styles/tests/fix-timestep-restrain.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:41 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:56 2021 epsilon: 2e-13 prerequisites: ! | atom full @@ -13,7 +13,7 @@ input_file: in.fourmol natoms: 29 global_scalar: 114.558406487374 global_vector: ! |- - 3 0.15090319643872077 29.7021302625337 0.0 + 3 0.15090319643872077 29.7021302625337 0 run_pos: ! |2 1 -2.7049081044736850e-01 2.4911173559795530e+00 -1.6698991821614786e-01 2 3.0937052624736794e-01 2.9607167765013171e+00 -8.5481885843536709e-01 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_group.yaml b/unittest/force-styles/tests/fix-timestep-rigid_group.yaml index 00201c36b5..9646f73313 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_group.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_group.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:36:53 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:56 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml b/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml index 418614b035..bf27b25c5d 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:36:54 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:56 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml b/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml index f23297ece8..3a3f0cd59a 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:36:54 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:56 2021 epsilon: 5e-12 prerequisites: ! | atom full @@ -14,7 +14,7 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200116134789241e+01 -2.6907707565985238e+01 -6.0080860422273377e+00 -2.5620423972099417e+01 -1.3450224059984127e+01 -1.4947288486998911e+00 + -4.9200116134788829e+01 -2.6907707565985422e+01 -6.0080860422273261e+00 -2.5620423972099612e+01 -1.3450224059983762e+01 -1.4947288487001149e+00 global_scalar: 18.3405601674143 run_pos: ! |2 1 -2.7993683669226854e-01 2.4726588069312836e+00 -1.7200860244148508e-01 @@ -41,7 +41,7 @@ run_pos: ! |2 22 4.3655322291888483e+00 -4.2084949965552569e+00 -4.4622011117402334e+00 23 5.7380414793463101e+00 -3.5841969195032686e+00 -3.8827839830470232e+00 24 2.0701314765323913e+00 3.1499370533342308e+00 3.1565324852522920e+00 - 25 1.3030170721374779e+00 3.2711173927682236e+00 2.5081940917429755e+00 + 25 1.3030170721374770e+00 3.2711173927682236e+00 2.5081940917429755e+00 26 2.5776230782480054e+00 4.0127347068243875e+00 3.2182355138709262e+00 27 -1.9613581876744357e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678509e+00 @@ -64,15 +64,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625095704480e-04 -3.1032459262907435e-04 8.1043030117346128e-04 - 19 8.5103884665346124e-04 -1.4572280596788089e-03 1.0163621287634045e-03 - 20 -6.5204659278589121e-04 4.3989037444288817e-04 4.9909839028508280e-04 - 21 -1.3888125881903863e-03 -3.1978049143082245e-04 1.1455681499836596e-03 - 22 -1.6084223477729515e-03 -1.5355394240820991e-03 1.4772010826232349e-03 - 23 2.6392672378804170e-04 -3.9375414431174621e-03 -3.6991583139727824e-04 - 24 8.6062827067889477e-04 -9.4179873474469237e-04 5.5396395550012714e-04 - 25 1.5933645477487534e-03 -2.2139156625681600e-03 -5.5078029695647803e-04 - 26 -1.5679561743998831e-03 3.5146224354725699e-04 2.4446924193334539e-03 + 18 3.6149625095704670e-04 -3.1032459262907857e-04 8.1043030117346052e-04 + 19 8.5103884665345799e-04 -1.4572280596788108e-03 1.0163621287634071e-03 + 20 -6.5204659278590292e-04 4.3989037444289630e-04 4.9909839028508204e-04 + 21 -1.3888125881903854e-03 -3.1978049143082060e-04 1.1455681499836594e-03 + 22 -1.6084223477729519e-03 -1.5355394240820970e-03 1.4772010826232353e-03 + 23 2.6392672378803975e-04 -3.9375414431174552e-03 -3.6991583139727889e-04 + 24 8.6062827067889835e-04 -9.4179873474469346e-04 5.5396395550012497e-04 + 25 1.5933645477487516e-03 -2.2139156625681669e-03 -5.5078029695647564e-04 + 26 -1.5679561743998831e-03 3.5146224354726187e-04 2.4446924193334495e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml index 4e5c3cf1bc..4b4f53b240 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:36:55 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:56 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml index 11d6870a42..6a7fa3c8a5 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:36:55 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:56 2021 epsilon: 6.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml b/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml index f85f2119b5..2b1fbc73b5 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:36:56 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:56 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml index 4b5a717e25..008499c206 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:36:56 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:56 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml index ee40036bf9..a78dd6c421 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:36:57 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:56 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml index d422c3d56e..32a3f6af71 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:36:57 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:57 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml index d72a0ff3b7..85aa11e3e0 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:36:58 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:57 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml index 74121559aa..87655f456b 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:36:58 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:57 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml index 8a3a1d9c31..be224eb6ad 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:36:59 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:57 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml index 654b85416a..b0e0040070 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:36:59 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:57 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rigid_single.yaml b/unittest/force-styles/tests/fix-timestep-rigid_single.yaml index e419416c7e..61957af75d 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_single.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_single.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:37:00 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:57 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-rigid_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_small.yaml index 2c5fa3a2c0..837363d059 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_small.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 22:37:00 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:57 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-setforce_const.yaml b/unittest/force-styles/tests/fix-timestep-setforce_const.yaml index 4ff222aff6..05ea1b2adb 100644 --- a/unittest/force-styles/tests/fix-timestep-setforce_const.yaml +++ b/unittest/force-styles/tests/fix-timestep-setforce_const.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:42 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:57 2021 epsilon: 2e-11 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-setforce_region.yaml b/unittest/force-styles/tests/fix-timestep-setforce_region.yaml index bf1d08df34..50eafa8f6a 100644 --- a/unittest/force-styles/tests/fix-timestep-setforce_region.yaml +++ b/unittest/force-styles/tests/fix-timestep-setforce_region.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:42 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:57 2021 epsilon: 5e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-setforce_variable.yaml b/unittest/force-styles/tests/fix-timestep-setforce_variable.yaml index 960368a081..00a1b270f9 100644 --- a/unittest/force-styles/tests/fix-timestep-setforce_variable.yaml +++ b/unittest/force-styles/tests/fix-timestep-setforce_variable.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:42 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:58 2021 epsilon: 1e-11 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-shake_angle.yaml b/unittest/force-styles/tests/fix-timestep-shake_angle.yaml index 1cc3dfe429..3317f7a187 100644 --- a/unittest/force-styles/tests/fix-timestep-shake_angle.yaml +++ b/unittest/force-styles/tests/fix-timestep-shake_angle.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:42 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:58 2021 epsilon: 3e-10 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-shake_bond.yaml b/unittest/force-styles/tests/fix-timestep-shake_bond.yaml index afbba6c6d7..41b3e8c1f9 100644 --- a/unittest/force-styles/tests/fix-timestep-shake_bond.yaml +++ b/unittest/force-styles/tests/fix-timestep-shake_bond.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:42 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:58 2021 epsilon: 3.5e-11 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-smd_couple.yaml b/unittest/force-styles/tests/fix-timestep-smd_couple.yaml index 3b2858ba00..7207392b84 100644 --- a/unittest/force-styles/tests/fix-timestep-smd_couple.yaml +++ b/unittest/force-styles/tests/fix-timestep-smd_couple.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:42 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:58 2021 epsilon: 2e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-smd_tether.yaml b/unittest/force-styles/tests/fix-timestep-smd_tether.yaml index f25b7b0334..c6627219d7 100644 --- a/unittest/force-styles/tests/fix-timestep-smd_tether.yaml +++ b/unittest/force-styles/tests/fix-timestep-smd_tether.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:42 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:58 2021 epsilon: 2e-14 prerequisites: ! | atom full @@ -12,7 +12,7 @@ post_commands: ! | input_file: in.fourmol natoms: 29 global_vector: ! |- - 7 3.468936708094085 -3.4952703851457807 -0.8657730938070575 5.0 1.1439828473945521 1.1439828473945521 0.0 + 7 3.468936708094085 -3.4952703851457807 -0.8657730938070575 5 1.1439828473945521 1.1439828473945521 0 run_pos: ! |2 1 -2.7043651355831022e-01 2.4911967678686477e+00 -1.6696328159792090e-01 2 3.1005937993458582e-01 2.9612162404086972e+00 -8.5466839405216255e-01 diff --git a/unittest/force-styles/tests/fix-timestep-spring_chunk.yaml b/unittest/force-styles/tests/fix-timestep-spring_chunk.yaml index 66a9ff9449..266d88dc85 100644 --- a/unittest/force-styles/tests/fix-timestep-spring_chunk.yaml +++ b/unittest/force-styles/tests/fix-timestep-spring_chunk.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:42 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:58 2021 epsilon: 1e-11 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-spring_couple.yaml b/unittest/force-styles/tests/fix-timestep-spring_couple.yaml index 66588fefaf..496f903c1a 100644 --- a/unittest/force-styles/tests/fix-timestep-spring_couple.yaml +++ b/unittest/force-styles/tests/fix-timestep-spring_couple.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:43 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:58 2021 epsilon: 2e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-spring_rg.yaml b/unittest/force-styles/tests/fix-timestep-spring_rg.yaml index fbd7e9d879..bcb672321e 100644 --- a/unittest/force-styles/tests/fix-timestep-spring_rg.yaml +++ b/unittest/force-styles/tests/fix-timestep-spring_rg.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:43 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:58 2021 epsilon: 2e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-spring_self.yaml b/unittest/force-styles/tests/fix-timestep-spring_self.yaml index 96755572bf..cf303b8757 100644 --- a/unittest/force-styles/tests/fix-timestep-spring_self.yaml +++ b/unittest/force-styles/tests/fix-timestep-spring_self.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:43 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:58 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-spring_tether.yaml b/unittest/force-styles/tests/fix-timestep-spring_tether.yaml index bdb2cad1d4..d7172d3811 100644 --- a/unittest/force-styles/tests/fix-timestep-spring_tether.yaml +++ b/unittest/force-styles/tests/fix-timestep-spring_tether.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:43 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:59 2021 epsilon: 2e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-temp_berendsen.yaml b/unittest/force-styles/tests/fix-timestep-temp_berendsen.yaml index 7975b61a13..8b2d946782 100644 --- a/unittest/force-styles/tests/fix-timestep-temp_berendsen.yaml +++ b/unittest/force-styles/tests/fix-timestep-temp_berendsen.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:43 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:59 2021 epsilon: 2e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-temp_csld.yaml b/unittest/force-styles/tests/fix-timestep-temp_csld.yaml index ef6535888d..a25a54e733 100644 --- a/unittest/force-styles/tests/fix-timestep-temp_csld.yaml +++ b/unittest/force-styles/tests/fix-timestep-temp_csld.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:43 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:59 2021 epsilon: 2e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-temp_csvr.yaml b/unittest/force-styles/tests/fix-timestep-temp_csvr.yaml index 8716de39de..c66a1f2f59 100644 --- a/unittest/force-styles/tests/fix-timestep-temp_csvr.yaml +++ b/unittest/force-styles/tests/fix-timestep-temp_csvr.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:43 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:59 2021 epsilon: 3e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-temp_rescale.yaml b/unittest/force-styles/tests/fix-timestep-temp_rescale.yaml index 6c53252d14..9cb1a096e5 100644 --- a/unittest/force-styles/tests/fix-timestep-temp_rescale.yaml +++ b/unittest/force-styles/tests/fix-timestep-temp_rescale.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:43 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:59 2021 epsilon: 2e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/fix-timestep-wall_harmonic_const.yaml b/unittest/force-styles/tests/fix-timestep-wall_harmonic_const.yaml index e1de14d018..779d1b30c3 100644 --- a/unittest/force-styles/tests/fix-timestep-wall_harmonic_const.yaml +++ b/unittest/force-styles/tests/fix-timestep-wall_harmonic_const.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:43 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:59 2021 epsilon: 3e-14 prerequisites: ! | atom full @@ -17,7 +17,7 @@ run_stress: ! |2- 0.0000000000000000e+00 7.2422093200265749e+02 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 global_scalar: 42.6997744353244 global_vector: ! |- - 2 0.0 161.92409617466126 + 2 0 161.92409617466126 run_pos: ! |2 1 -2.7051715090682593e-01 2.4891718422041942e+00 -1.6687343912524535e-01 2 3.1037661579862175e-01 2.9347166386691113e+00 -8.5496435221221156e-01 diff --git a/unittest/force-styles/tests/fix-timestep-wall_lj1043_const.yaml b/unittest/force-styles/tests/fix-timestep-wall_lj1043_const.yaml index e8be8b41a2..1bf3d793fb 100644 --- a/unittest/force-styles/tests/fix-timestep-wall_lj1043_const.yaml +++ b/unittest/force-styles/tests/fix-timestep-wall_lj1043_const.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:43 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:59 2021 epsilon: 5e-14 prerequisites: ! | atom full @@ -17,7 +17,7 @@ run_stress: ! |2- 0.0000000000000000e+00 -2.6193298572154652e+02 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 global_scalar: -21.0862098649006 global_vector: ! |- - 2 0.0 -57.92496787419014 + 2 0 -57.92496787419014 run_pos: ! |2 1 -2.7044985531646820e-01 2.4925110873587433e+00 -1.6698786670029320e-01 2 3.0995988119031520e-01 2.9684930337266713e+00 -8.5459207531887627e-01 diff --git a/unittest/force-styles/tests/fix-timestep-wall_lj126_const.yaml b/unittest/force-styles/tests/fix-timestep-wall_lj126_const.yaml index e65b582c09..9db35c4e80 100644 --- a/unittest/force-styles/tests/fix-timestep-wall_lj126_const.yaml +++ b/unittest/force-styles/tests/fix-timestep-wall_lj126_const.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:43 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:59 2021 epsilon: 2e-14 prerequisites: ! | atom full @@ -17,7 +17,7 @@ run_stress: ! |2- 0.0000000000000000e+00 -3.4585143439781433e+01 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 global_scalar: -2.5475438051924 global_vector: ! |- - 2 0.0 -7.685735804480931 + 2 0 -7.685735804480931 run_pos: ! |2 1 -2.7045416679061030e-01 2.4913627730949424e+00 -1.6696242213969814e-01 2 3.1002806235873631e-01 2.9622866518897246e+00 -8.5465272505609957e-01 diff --git a/unittest/force-styles/tests/fix-timestep-wall_lj93_const.yaml b/unittest/force-styles/tests/fix-timestep-wall_lj93_const.yaml index d1c27927a2..451ce34c0b 100644 --- a/unittest/force-styles/tests/fix-timestep-wall_lj93_const.yaml +++ b/unittest/force-styles/tests/fix-timestep-wall_lj93_const.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:43 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:59 2021 epsilon: 2e-14 prerequisites: ! | atom full @@ -17,7 +17,7 @@ run_stress: ! |2- 0.0000000000000000e+00 -5.0602303343219951e+01 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 global_scalar: -4.10898799728224 global_vector: ! |- - 2 0.0 -11.164431050504302 + 2 0 -11.164431050504302 run_pos: ! |2 1 -2.7045470054680359e-01 2.4914748797509958e+00 -1.6696421170224640e-01 2 3.1002519717316468e-01 2.9626113274873114e+00 -8.5465020014164161e-01 diff --git a/unittest/force-styles/tests/fix-timestep-wall_morse_const.yaml b/unittest/force-styles/tests/fix-timestep-wall_morse_const.yaml index 2b935dbf14..60261f9bfc 100644 --- a/unittest/force-styles/tests/fix-timestep-wall_morse_const.yaml +++ b/unittest/force-styles/tests/fix-timestep-wall_morse_const.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:43 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:10:00 2021 epsilon: 4e-14 prerequisites: ! | atom full @@ -17,7 +17,7 @@ run_stress: ! |2- 0.0000000000000000e+00 -1.6447328969000660e+03 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 global_scalar: -715.415406257395 global_vector: ! |- - 2 0.0 -362.76807567062644 + 2 0 -362.76807567062644 run_pos: ! |2 1 -2.7045893790409276e-01 2.5008322800634093e+00 -1.6714018607090517e-01 2 3.0963184116147618e-01 3.0014595399936281e+00 -8.5430140686816214e-01 diff --git a/unittest/force-styles/tests/improper-class2.yaml b/unittest/force-styles/tests/improper-class2.yaml index a02d8276ad..2ee0feaa6b 100644 --- a/unittest/force-styles/tests/improper-class2.yaml +++ b/unittest/force-styles/tests/improper-class2.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 19:35:14 202 +date_generated: Fri Feb 26 23:09:36 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/improper-cossq.yaml b/unittest/force-styles/tests/improper-cossq.yaml index a4043011a3..facb268a94 100644 --- a/unittest/force-styles/tests/improper-cossq.yaml +++ b/unittest/force-styles/tests/improper-cossq.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 19:38:24 202 +date_generated: Fri Feb 26 23:09:36 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/improper-cvff.yaml b/unittest/force-styles/tests/improper-cvff.yaml index 462b7e4427..1c432a683b 100644 --- a/unittest/force-styles/tests/improper-cvff.yaml +++ b/unittest/force-styles/tests/improper-cvff.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 19:35:14 202 +date_generated: Fri Feb 26 23:09:36 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/improper-distance.yaml b/unittest/force-styles/tests/improper-distance.yaml index 2de3d21c73..7401dc3f42 100644 --- a/unittest/force-styles/tests/improper-distance.yaml +++ b/unittest/force-styles/tests/improper-distance.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 19:35:14 202 +date_generated: Fri Feb 26 23:09:36 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/improper-distharm.yaml b/unittest/force-styles/tests/improper-distharm.yaml index e07d02aace..6d2bedcb9e 100644 --- a/unittest/force-styles/tests/improper-distharm.yaml +++ b/unittest/force-styles/tests/improper-distharm.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 19:35:14 202 +date_generated: Fri Feb 26 23:09:36 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/improper-fourier.yaml b/unittest/force-styles/tests/improper-fourier.yaml index 0a1b801656..4c3fa1ff7e 100644 --- a/unittest/force-styles/tests/improper-fourier.yaml +++ b/unittest/force-styles/tests/improper-fourier.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 19:35:15 202 +date_generated: Fri Feb 26 23:09:36 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/improper-harmonic.yaml b/unittest/force-styles/tests/improper-harmonic.yaml index 5daaa0c509..e10307e3a2 100644 --- a/unittest/force-styles/tests/improper-harmonic.yaml +++ b/unittest/force-styles/tests/improper-harmonic.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 19:35:15 202 +date_generated: Fri Feb 26 23:09:36 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/improper-hybrid.yaml b/unittest/force-styles/tests/improper-hybrid.yaml index 0f00d56909..5351cb86d4 100644 --- a/unittest/force-styles/tests/improper-hybrid.yaml +++ b/unittest/force-styles/tests/improper-hybrid.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 20:50:39 202 +date_generated: Fri Feb 26 23:09:36 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/improper-inversion_harmonic.yaml b/unittest/force-styles/tests/improper-inversion_harmonic.yaml index 3cabd4c74a..e1fc0499a8 100644 --- a/unittest/force-styles/tests/improper-inversion_harmonic.yaml +++ b/unittest/force-styles/tests/improper-inversion_harmonic.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 19:35:15 202 +date_generated: Fri Feb 26 23:09:37 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/improper-ring.yaml b/unittest/force-styles/tests/improper-ring.yaml index fb2750e36c..355a2ff170 100644 --- a/unittest/force-styles/tests/improper-ring.yaml +++ b/unittest/force-styles/tests/improper-ring.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 19:35:15 202 +date_generated: Fri Feb 26 23:09:37 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/improper-sqdistharm.yaml b/unittest/force-styles/tests/improper-sqdistharm.yaml index ed40f1340f..e16dbde61d 100644 --- a/unittest/force-styles/tests/improper-sqdistharm.yaml +++ b/unittest/force-styles/tests/improper-sqdistharm.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 19:35:15 202 +date_generated: Fri Feb 26 23:09:37 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/improper-umbrella.yaml b/unittest/force-styles/tests/improper-umbrella.yaml index 85fa142b49..f049680409 100644 --- a/unittest/force-styles/tests/improper-umbrella.yaml +++ b/unittest/force-styles/tests/improper-umbrella.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 19:35:15 202 +date_generated: Fri Feb 26 23:09:37 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/improper-zero.yaml b/unittest/force-styles/tests/improper-zero.yaml index 9497e184e2..e082e11908 100644 --- a/unittest/force-styles/tests/improper-zero.yaml +++ b/unittest/force-styles/tests/improper-zero.yaml @@ -1,6 +1,6 @@ --- lammps_version: 10 Feb 2021 -date_generated: Wed Feb 24 19:37:56 202 +date_generated: Fri Feb 26 23:09:37 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-ewald.yaml b/unittest/force-styles/tests/kspace-ewald.yaml index b0c9e46000..f03b236aac 100644 --- a/unittest/force-styles/tests/kspace-ewald.yaml +++ b/unittest/force-styles/tests/kspace-ewald.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:35 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:25 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-ewald_disp.yaml b/unittest/force-styles/tests/kspace-ewald_disp.yaml index 0bf3fb8280..e20bdc149a 100644 --- a/unittest/force-styles/tests/kspace-ewald_disp.yaml +++ b/unittest/force-styles/tests/kspace-ewald_disp.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:35 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:25 2021 epsilon: 5e-12 prerequisites: ! | atom full @@ -61,33 +61,33 @@ run_coul: 0 run_stress: ! |2- 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 run_forces: ! |2 - 1 -1.5321369646512287e-01 3.1811336640254428e-02 -7.5291966466499854e-02 - 2 4.1718499667107591e-02 -6.0993280056077008e-02 7.1251624481841025e-02 - 3 -9.5279894353951251e-03 -1.4941462712424192e-03 -2.3308420217005594e-03 - 4 5.2578632823907109e-02 7.1842522102449641e-03 8.4623035788519083e-03 - 5 5.1098021938378535e-02 9.7285355839204727e-03 1.0253349643675837e-02 - 6 1.1944881653432865e-01 7.6133381161564387e-02 8.1359427537698162e-02 - 7 -6.3591857746436040e-02 -8.6414432169993630e-02 -7.9109433076114163e-02 - 8 -3.7433525775956008e-03 -1.0990369365284677e-01 -1.1224509664376907e-01 - 9 3.4723473525535330e-03 5.8483564454419018e-02 7.3945790434835998e-02 + 1 -1.5321369646512289e-01 3.1811336640254428e-02 -7.5291966466499868e-02 + 2 4.1718499667107597e-02 -6.0993280056077008e-02 7.1251624481841025e-02 + 3 -9.5279894353951268e-03 -1.4941462712424198e-03 -2.3308420217005594e-03 + 4 5.2578632823907102e-02 7.1842522102449641e-03 8.4623035788519083e-03 + 5 5.1098021938378528e-02 9.7285355839204779e-03 1.0253349643675840e-02 + 6 1.1944881653432862e-01 7.6133381161564415e-02 8.1359427537698162e-02 + 7 -6.3591857746436053e-02 -8.6414432169993630e-02 -7.9109433076114136e-02 + 8 -3.7433525775956017e-03 -1.0990369365284679e-01 -1.1224509664376904e-01 + 9 3.4723473525535304e-03 5.8483564454419046e-02 7.3945790434835998e-02 10 -1.9931615263391753e-02 2.3230336652331492e-02 2.2930261922462034e-02 - 11 -2.7043515997570565e-02 3.3096788353233382e-02 2.7833272909244686e-02 - 12 1.4733114619496521e-01 -7.4907012571817977e-02 -9.9310508068793157e-02 - 13 -6.0568451603864093e-02 2.6904500638990563e-02 3.7502952815534972e-02 - 14 -4.7602620526011358e-02 2.4118387991499554e-02 2.8503007637066029e-02 + 11 -2.7043515997570568e-02 3.3096788353233382e-02 2.7833272909244679e-02 + 12 1.4733114619496521e-01 -7.4907012571817991e-02 -9.9310508068793130e-02 + 13 -6.0568451603864079e-02 2.6904500638990563e-02 3.7502952815534972e-02 + 14 -4.7602620526011344e-02 2.4118387991499554e-02 2.8503007637066029e-02 15 -4.5640946475327245e-02 1.1215448404197493e-02 3.2219246480274404e-02 - 16 -2.0008038374075984e-01 1.6245819219836355e-01 1.8812371878208675e-01 - 17 1.3640979614708312e-01 -1.4877360903977560e-01 -1.3970849833566271e-01 + 16 -2.0008038374075982e-01 1.6245819219836355e-01 1.8812371878208675e-01 + 17 1.3640979614708318e-01 -1.4877360903977557e-01 -1.3970849833566271e-01 18 3.1313062271288683e-01 3.0970376465951444e-01 -2.9690888050690195e-01 - 19 -1.2278633817042253e-01 -1.5053154281354220e-01 1.1083205911757414e-01 - 20 -1.7800087923017122e-01 -1.7031941581576107e-01 1.4510467117661957e-01 + 19 -1.2278633817042250e-01 -1.5053154281354220e-01 1.1083205911757414e-01 + 20 -1.7800087923017119e-01 -1.7031941581576107e-01 1.4510467117661957e-01 21 3.5089545735563610e-01 -9.5838434134800643e-02 -2.8233685525513896e-01 - 22 -1.9415564585497339e-01 7.5645499568197841e-02 9.1631181795561512e-02 - 23 -1.4017971783984279e-01 3.7892211453094168e-02 1.1299558998235543e-01 - 24 1.7884203136981469e-01 3.1247703983741304e-01 1.4068927063619113e-01 - 25 -2.7624350380010359e-02 -1.2477864845951722e-01 -2.6147141449362275e-02 - 26 -1.3999328961714030e-01 -1.7823800630539485e-01 -8.7261723908124589e-02 - 27 -3.3286289860045476e-01 1.7647878511351975e-01 -1.8733303262234685e-01 - 28 2.1399771535404677e-01 -1.1748172155357729e-01 1.2097428314785649e-01 - 29 1.5762446207378214e-01 -5.6888082076411807e-02 8.3371966274683518e-02 + 22 -1.9415564585497344e-01 7.5645499568197813e-02 9.1631181795561525e-02 + 23 -1.4017971783984279e-01 3.7892211453094155e-02 1.1299558998235543e-01 + 24 1.7884203136981472e-01 3.1247703983741310e-01 1.4068927063619110e-01 + 25 -2.7624350380010373e-02 -1.2477864845951719e-01 -2.6147141449362272e-02 + 26 -1.3999328961714033e-01 -1.7823800630539485e-01 -8.7261723908124589e-02 + 27 -3.3286289860045476e-01 1.7647878511351969e-01 -1.8733303262234691e-01 + 28 2.1399771535404671e-01 -1.1748172155357726e-01 1.2097428314785651e-01 + 29 1.5762446207378211e-01 -5.6888082076411807e-02 8.3371966274683545e-02 ... diff --git a/unittest/force-styles/tests/kspace-ewald_nozforce.yaml b/unittest/force-styles/tests/kspace-ewald_nozforce.yaml index d18f965aba..f6c3060d3d 100644 --- a/unittest/force-styles/tests/kspace-ewald_nozforce.yaml +++ b/unittest/force-styles/tests/kspace-ewald_nozforce.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:35 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:25 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-ewald_slab.yaml b/unittest/force-styles/tests/kspace-ewald_slab.yaml index 6b133a663c..0df035667a 100644 --- a/unittest/force-styles/tests/kspace-ewald_slab.yaml +++ b/unittest/force-styles/tests/kspace-ewald_slab.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:35 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:25 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-ewald_tri.yaml b/unittest/force-styles/tests/kspace-ewald_tri.yaml index 4141dd0cd1..dddfe7018a 100644 --- a/unittest/force-styles/tests/kspace-ewald_tri.yaml +++ b/unittest/force-styles/tests/kspace-ewald_tri.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:35 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:25 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-msm.yaml b/unittest/force-styles/tests/kspace-msm.yaml index ce503e0d01..f3cbb4604d 100644 --- a/unittest/force-styles/tests/kspace-msm.yaml +++ b/unittest/force-styles/tests/kspace-msm.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:35 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:26 2021 epsilon: 5e-11 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-msm_cg.yaml b/unittest/force-styles/tests/kspace-msm_cg.yaml index 835b6dfe25..25892a4528 100644 --- a/unittest/force-styles/tests/kspace-msm_cg.yaml +++ b/unittest/force-styles/tests/kspace-msm_cg.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:36 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:26 2021 epsilon: 5e-11 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-msm_nopbc.yaml b/unittest/force-styles/tests/kspace-msm_nopbc.yaml index 4d3080bcc9..ce5e3cd0e3 100644 --- a/unittest/force-styles/tests/kspace-msm_nopbc.yaml +++ b/unittest/force-styles/tests/kspace-msm_nopbc.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Wed Sep 16 23:34:54 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:27 2021 epsilon: 5e-11 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm.yaml b/unittest/force-styles/tests/kspace-pppm.yaml index 302f51280b..5282084567 100644 --- a/unittest/force-styles/tests/kspace-pppm.yaml +++ b/unittest/force-styles/tests/kspace-pppm.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:36 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:29 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_ad.yaml b/unittest/force-styles/tests/kspace-pppm_ad.yaml index bdeacc50a9..3f77eb99c5 100644 --- a/unittest/force-styles/tests/kspace-pppm_ad.yaml +++ b/unittest/force-styles/tests/kspace-pppm_ad.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:36 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:29 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_cg.yaml b/unittest/force-styles/tests/kspace-pppm_cg.yaml index fd892d044e..e6bb6c78f3 100644 --- a/unittest/force-styles/tests/kspace-pppm_cg.yaml +++ b/unittest/force-styles/tests/kspace-pppm_cg.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:36 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:29 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_cg_ad.yaml b/unittest/force-styles/tests/kspace-pppm_cg_ad.yaml index a8c1b364e7..a8d9efc1fa 100644 --- a/unittest/force-styles/tests/kspace-pppm_cg_ad.yaml +++ b/unittest/force-styles/tests/kspace-pppm_cg_ad.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:36 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:29 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_cg_tiled.yaml b/unittest/force-styles/tests/kspace-pppm_cg_tiled.yaml index 9477bcba77..270ee0418c 100644 --- a/unittest/force-styles/tests/kspace-pppm_cg_tiled.yaml +++ b/unittest/force-styles/tests/kspace-pppm_cg_tiled.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:36 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:29 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_disp.yaml b/unittest/force-styles/tests/kspace-pppm_disp.yaml index 55243a9a68..8c528baf76 100644 --- a/unittest/force-styles/tests/kspace-pppm_disp.yaml +++ b/unittest/force-styles/tests/kspace-pppm_disp.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:37 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:30 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_disp_ad.yaml b/unittest/force-styles/tests/kspace-pppm_disp_ad.yaml index 02f36588bc..4ef71d7333 100644 --- a/unittest/force-styles/tests/kspace-pppm_disp_ad.yaml +++ b/unittest/force-styles/tests/kspace-pppm_disp_ad.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:37 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:31 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_disp_ad_only.yaml b/unittest/force-styles/tests/kspace-pppm_disp_ad_only.yaml index 6c441a3df8..203eceb209 100644 --- a/unittest/force-styles/tests/kspace-pppm_disp_ad_only.yaml +++ b/unittest/force-styles/tests/kspace-pppm_disp_ad_only.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:38 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:31 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_disp_only.yaml b/unittest/force-styles/tests/kspace-pppm_disp_only.yaml index bd7fe74594..f0243c8da1 100644 --- a/unittest/force-styles/tests/kspace-pppm_disp_only.yaml +++ b/unittest/force-styles/tests/kspace-pppm_disp_only.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:38 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:31 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_disp_tip4p.yaml b/unittest/force-styles/tests/kspace-pppm_disp_tip4p.yaml index d713c813e9..79951aab2f 100644 --- a/unittest/force-styles/tests/kspace-pppm_disp_tip4p.yaml +++ b/unittest/force-styles/tests/kspace-pppm_disp_tip4p.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:38 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:32 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_nozforce.yaml b/unittest/force-styles/tests/kspace-pppm_nozforce.yaml index 57bb160873..7442e862e9 100644 --- a/unittest/force-styles/tests/kspace-pppm_nozforce.yaml +++ b/unittest/force-styles/tests/kspace-pppm_nozforce.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:38 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:32 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_slab.yaml b/unittest/force-styles/tests/kspace-pppm_slab.yaml index 8aa1adbfd7..aa1566aab5 100644 --- a/unittest/force-styles/tests/kspace-pppm_slab.yaml +++ b/unittest/force-styles/tests/kspace-pppm_slab.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:38 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:32 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_stagger.yaml b/unittest/force-styles/tests/kspace-pppm_stagger.yaml index 0e4c9631e2..ea24b6cfd3 100644 --- a/unittest/force-styles/tests/kspace-pppm_stagger.yaml +++ b/unittest/force-styles/tests/kspace-pppm_stagger.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:38 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:33 2021 epsilon: 7.5e-14 prerequisites: ! | atom full @@ -22,67 +22,67 @@ init_coul: 0 init_stress: ! |2- 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 init_forces: ! |2 - 1 -5.2227715900845750e-01 8.1950519891037896e-02 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+ 26 -2.2247931035350965e-01 -9.7223221992333508e-01 7.3515699476410554e-02 + 27 -8.6026914570906943e-01 1.6503940402012782e+00 -9.3240873788746348e-01 + 28 5.7146552243716164e-01 -9.1711088161406340e-01 5.3820268912067859e-01 + 29 4.1232210756742671e-01 -8.0561147447049097e-01 4.4052298379611776e-01 ... diff --git a/unittest/force-styles/tests/kspace-pppm_stagger_tiled.yaml b/unittest/force-styles/tests/kspace-pppm_stagger_tiled.yaml index c38767f900..cb8ba3813e 100644 --- a/unittest/force-styles/tests/kspace-pppm_stagger_tiled.yaml +++ b/unittest/force-styles/tests/kspace-pppm_stagger_tiled.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:39 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:33 2021 epsilon: 7.5e-14 prerequisites: ! | atom full @@ -24,67 +24,67 @@ init_coul: 0 init_stress: ! |2- 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 init_forces: ! |2 - 1 -5.2227715900845750e-01 8.1950519891037896e-02 2.1568864750376832e-01 + 1 -5.2227715900845739e-01 8.1950519891037882e-02 2.1568864750376829e-01 2 2.1709329984201631e-01 -2.7910826043908610e-01 -1.3501796562404628e-01 - 3 -3.4431410110235108e-02 -9.3026609475793179e-03 1.9970153652663108e-02 - 4 1.6294612553322482e-01 2.8820208915782589e-02 -7.8041537992552090e-02 - 5 1.6018614143950777e-01 7.5432356753115826e-02 -3.7722588054429150e-02 + 3 -3.4431410110235101e-02 -9.3026609475793179e-03 1.9970153652663108e-02 + 4 1.6294612553322479e-01 2.8820208915782589e-02 -7.8041537992552104e-02 + 5 1.6018614143950774e-01 7.5432356753115812e-02 -3.7722588054429143e-02 6 5.6492988309033354e-01 4.1696814706534630e-01 -6.7673476362799612e-01 - 7 -3.4216205471660566e-01 -4.0009165524095192e-01 3.9325085501474977e-01 - 8 -1.4121658810415072e-01 -6.1694926607232958e-01 3.3967088097622000e-01 + 7 -3.4216205471660560e-01 -4.0009165524095192e-01 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4.1187460365847078e-01 -8.0559715142821631e-01 4.4313023169089372e-01 run_vdwl: 0 run_coul: 0 run_stress: ! |2- 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 run_forces: ! |2 - 1 -5.2110389443047966e-01 8.2174837617142615e-02 2.1808851100884483e-01 - 2 2.1575362837922490e-01 -2.7985507607146648e-01 -1.3635384720562826e-01 + 1 -5.2110389443047966e-01 8.2174837617142657e-02 2.1808851100884480e-01 + 2 2.1575362837922490e-01 -2.7985507607146654e-01 -1.3635384720562826e-01 3 -3.4412499347272141e-02 -9.2851595240179864e-03 2.0082401999342678e-02 - 4 1.6309295424664277e-01 2.8699106597915747e-02 -7.8424598315124466e-02 - 5 1.6000485976650286e-01 7.5419186199252142e-02 -3.8271532199610915e-02 - 6 5.6452922927167792e-01 4.1651437288870052e-01 -6.8002099522971760e-01 - 7 -3.4234246122559975e-01 -4.0055178531012858e-01 3.9535126657784059e-01 - 8 -1.4009341296531477e-01 -6.1677431194167931e-01 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-2.6071651353161379e-01 -7.7650154707748176e-01 7.6978890572474756e-01 20 -3.9638127767834741e-01 -7.0644000153250031e-01 7.2935384554137617e-01 - 21 5.1893256827191392e-01 5.3441769782139692e-01 -1.1580900287803464e+00 - 22 -2.9449738462629443e-01 -1.1887047311705630e-01 5.8095962163225279e-01 + 21 5.1893256827191392e-01 5.3441769782139703e-01 -1.1580900287803464e+00 + 22 -2.9449738462629454e-01 -1.1887047311705637e-01 5.8095962163225279e-01 23 -2.8790115407696282e-01 -2.8923985224095883e-01 5.5380720899811053e-01 - 24 6.4191177940294664e-02 1.7394984516077767e+00 -2.7670608704288824e-01 - 25 1.2835128052019390e-01 -7.0221042172703485e-01 2.2447137762053931e-01 - 26 -2.2247931035350960e-01 -9.7223221992333508e-01 7.3515699476410554e-02 - 27 -8.6026914570906921e-01 1.6503940402012782e+00 -9.3240873788746348e-01 - 28 5.7146552243716164e-01 -9.1711088161406329e-01 5.3820268912067859e-01 - 29 4.1232210756742665e-01 -8.0561147447049097e-01 4.4052298379611776e-01 + 24 6.4191177940294691e-02 1.7394984516077767e+00 -2.7670608704288829e-01 + 25 1.2835128052019393e-01 -7.0221042172703474e-01 2.2447137762053931e-01 + 26 -2.2247931035350965e-01 -9.7223221992333508e-01 7.3515699476410554e-02 + 27 -8.6026914570906943e-01 1.6503940402012782e+00 -9.3240873788746348e-01 + 28 5.7146552243716164e-01 -9.1711088161406340e-01 5.3820268912067859e-01 + 29 4.1232210756742671e-01 -8.0561147447049097e-01 4.4052298379611776e-01 ... diff --git a/unittest/force-styles/tests/kspace-pppm_tiled.yaml b/unittest/force-styles/tests/kspace-pppm_tiled.yaml index 769826d7c6..d1b95c8ca9 100644 --- a/unittest/force-styles/tests/kspace-pppm_tiled.yaml +++ b/unittest/force-styles/tests/kspace-pppm_tiled.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:39 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:33 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_tip4p.yaml b/unittest/force-styles/tests/kspace-pppm_tip4p.yaml index 8efbeef010..f5785b54d7 100644 --- a/unittest/force-styles/tests/kspace-pppm_tip4p.yaml +++ b/unittest/force-styles/tests/kspace-pppm_tip4p.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:39 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:33 2021 epsilon: 2e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_tip4p_ad.yaml b/unittest/force-styles/tests/kspace-pppm_tip4p_ad.yaml index e2a644a7b2..66404f39b5 100644 --- a/unittest/force-styles/tests/kspace-pppm_tip4p_ad.yaml +++ b/unittest/force-styles/tests/kspace-pppm_tip4p_ad.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:39 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:34 2021 epsilon: 3e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_tip4p_nozforce.yaml b/unittest/force-styles/tests/kspace-pppm_tip4p_nozforce.yaml index f214cd1644..846e1a8605 100644 --- a/unittest/force-styles/tests/kspace-pppm_tip4p_nozforce.yaml +++ b/unittest/force-styles/tests/kspace-pppm_tip4p_nozforce.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:39 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:34 2021 epsilon: 2e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_tip4p_slab.yaml b/unittest/force-styles/tests/kspace-pppm_tip4p_slab.yaml index b64d7db0f6..35a8ef56f5 100644 --- a/unittest/force-styles/tests/kspace-pppm_tip4p_slab.yaml +++ b/unittest/force-styles/tests/kspace-pppm_tip4p_slab.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:39 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:34 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/kspace-pppm_tri.yaml b/unittest/force-styles/tests/kspace-pppm_tri.yaml index effcc73b4c..dbcbe44e52 100644 --- a/unittest/force-styles/tests/kspace-pppm_tri.yaml +++ b/unittest/force-styles/tests/kspace-pppm_tri.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:39 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:34 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/manybody-pair-airebo.yaml b/unittest/force-styles/tests/manybody-pair-airebo.yaml index f78643e7d0..58c81fb093 100644 --- a/unittest/force-styles/tests/manybody-pair-airebo.yaml +++ b/unittest/force-styles/tests/manybody-pair-airebo.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:27 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:10 2021 epsilon: 5e-06 prerequisites: ! | pair airebo diff --git a/unittest/force-styles/tests/manybody-pair-airebo_00.yaml b/unittest/force-styles/tests/manybody-pair-airebo_00.yaml index 1444fed8a2..aa9aea8ca9 100644 --- a/unittest/force-styles/tests/manybody-pair-airebo_00.yaml +++ b/unittest/force-styles/tests/manybody-pair-airebo_00.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:27 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:11 2021 epsilon: 1e-07 prerequisites: ! | pair airebo diff --git a/unittest/force-styles/tests/manybody-pair-airebo_m.yaml b/unittest/force-styles/tests/manybody-pair-airebo_m.yaml index 84df99a6a8..ae1e670cea 100644 --- a/unittest/force-styles/tests/manybody-pair-airebo_m.yaml +++ b/unittest/force-styles/tests/manybody-pair-airebo_m.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:28 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:11 2021 epsilon: 1e-07 prerequisites: ! | pair airebo/morse diff --git a/unittest/force-styles/tests/manybody-pair-airebo_m00.yaml b/unittest/force-styles/tests/manybody-pair-airebo_m00.yaml index e1a365c5bd..eecfd2a08e 100644 --- a/unittest/force-styles/tests/manybody-pair-airebo_m00.yaml +++ b/unittest/force-styles/tests/manybody-pair-airebo_m00.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:28 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:11 2021 epsilon: 1e-07 prerequisites: ! | pair airebo/morse diff --git a/unittest/force-styles/tests/manybody-pair-bop.yaml b/unittest/force-styles/tests/manybody-pair-bop.yaml index 40ca463a5e..0ce8d31d46 100644 --- a/unittest/force-styles/tests/manybody-pair-bop.yaml +++ b/unittest/force-styles/tests/manybody-pair-bop.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:28 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:12 2021 epsilon: 1e-12 prerequisites: ! | pair bop diff --git a/unittest/force-styles/tests/manybody-pair-bop_save.yaml b/unittest/force-styles/tests/manybody-pair-bop_save.yaml index 957476f4eb..1b1d1274a5 100644 --- a/unittest/force-styles/tests/manybody-pair-bop_save.yaml +++ b/unittest/force-styles/tests/manybody-pair-bop_save.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:29 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:13 2021 epsilon: 1e-12 prerequisites: ! | pair bop diff --git a/unittest/force-styles/tests/manybody-pair-comb.yaml b/unittest/force-styles/tests/manybody-pair-comb.yaml index 1b2e0b5c0c..d41aa476db 100644 --- a/unittest/force-styles/tests/manybody-pair-comb.yaml +++ b/unittest/force-styles/tests/manybody-pair-comb.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:29 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:14 2021 epsilon: 1e-12 prerequisites: ! | pair comb diff --git a/unittest/force-styles/tests/manybody-pair-comb3.yaml b/unittest/force-styles/tests/manybody-pair-comb3.yaml index 49e07069dc..2238108055 100644 --- a/unittest/force-styles/tests/manybody-pair-comb3.yaml +++ b/unittest/force-styles/tests/manybody-pair-comb3.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:29 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:14 2021 epsilon: 1e-13 prerequisites: ! | pair comb3 diff --git a/unittest/force-styles/tests/manybody-pair-edip_multi.yaml b/unittest/force-styles/tests/manybody-pair-edip_multi.yaml index 1f12c9955a..ad2dc9018e 100644 --- a/unittest/force-styles/tests/manybody-pair-edip_multi.yaml +++ b/unittest/force-styles/tests/manybody-pair-edip_multi.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:29 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:15 2021 epsilon: 5e-14 prerequisites: ! | pair edip/multi diff --git a/unittest/force-styles/tests/manybody-pair-extep.yaml b/unittest/force-styles/tests/manybody-pair-extep.yaml index 21c02745ab..ec69217b4a 100644 --- a/unittest/force-styles/tests/manybody-pair-extep.yaml +++ b/unittest/force-styles/tests/manybody-pair-extep.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:29 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:15 2021 epsilon: 5e-13 prerequisites: ! | pair extep diff --git a/unittest/force-styles/tests/manybody-pair-gw.yaml b/unittest/force-styles/tests/manybody-pair-gw.yaml index d3455dac5b..94a2db51a4 100644 --- a/unittest/force-styles/tests/manybody-pair-gw.yaml +++ b/unittest/force-styles/tests/manybody-pair-gw.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:30 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:15 2021 epsilon: 5e-13 prerequisites: ! | pair gw diff --git a/unittest/force-styles/tests/manybody-pair-gw_zbl.yaml b/unittest/force-styles/tests/manybody-pair-gw_zbl.yaml index 1d4fc81229..bdda7df922 100644 --- a/unittest/force-styles/tests/manybody-pair-gw_zbl.yaml +++ b/unittest/force-styles/tests/manybody-pair-gw_zbl.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:30 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:15 2021 epsilon: 5e-13 prerequisites: ! | pair gw/zbl diff --git a/unittest/force-styles/tests/manybody-pair-lcbop.yaml b/unittest/force-styles/tests/manybody-pair-lcbop.yaml index be2f18a176..5c406b2315 100644 --- a/unittest/force-styles/tests/manybody-pair-lcbop.yaml +++ b/unittest/force-styles/tests/manybody-pair-lcbop.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:30 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:15 2021 epsilon: 7.5e-12 prerequisites: ! | pair lcbop diff --git a/unittest/force-styles/tests/manybody-pair-meam_c.yaml b/unittest/force-styles/tests/manybody-pair-meam_c.yaml index b1cb051fa7..e2867c4dd6 100644 --- a/unittest/force-styles/tests/manybody-pair-meam_c.yaml +++ b/unittest/force-styles/tests/manybody-pair-meam_c.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:30 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:15 2021 epsilon: 7.5e-12 prerequisites: ! | pair meam/c diff --git a/unittest/force-styles/tests/manybody-pair-mliap_snap.yaml b/unittest/force-styles/tests/manybody-pair-mliap_snap.yaml index e6bef38ab6..3650405db1 100644 --- a/unittest/force-styles/tests/manybody-pair-mliap_snap.yaml +++ b/unittest/force-styles/tests/manybody-pair-mliap_snap.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:30 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:15 2021 epsilon: 5e-13 prerequisites: ! | pair mliap @@ -20,7 +20,7 @@ natoms: 64 init_vdwl: -473.569864629026 init_coul: 0 init_stress: ! |2- - 3.9989504688551500e+02 4.0778136516736993e+02 4.3596322435184845e+02 -2.5242497284339720e+01 1.2811620806363655e+02 2.8644673361821793e+00 + 3.9989504688551500e+02 4.0778136516736993e+02 4.3596322435184823e+02 -2.5242497284339720e+01 1.2811620806363655e+02 2.8644673361821793e+00 init_forces: ! |2 1 -3.7538180163781538e+00 8.8612947043788708e+00 6.7712977816732263e+00 2 -7.6696525239232596e+00 -3.7674335682223203e-01 -5.7958054718422760e+00 @@ -28,7 +28,7 @@ init_forces: ! |2 4 -4.7103509354198474e+00 9.2783458784125941e+00 4.3108702582741429e+00 5 -2.0331946400488916e+00 -2.9593716047756180e+00 -1.6136351145373196e+00 6 1.8086748683348572e+00 4.6479727629048675e+00 3.0425695895915184e-01 - 7 -3.0573043543220644e+00 -4.0575899915120281e+00 1.5283788878527900e+00 + 7 -3.0573043543220644e+00 -4.0575899915120264e+00 1.5283788878527900e+00 8 2.7148403621334427e-01 1.3063473238306007e+00 -1.1268098385676173e+00 9 5.2043326273129953e-01 -2.9340446386399996e+00 -7.6461969078455834e+00 10 -6.2786875145099508e-01 5.6606570005199308e-02 -5.3746300485699576e+00 @@ -64,11 +64,11 @@ init_forces: ! |2 40 9.5193696695210637e+00 -7.0213638399035432e+00 -1.5692669012530696e+00 41 2.4000089474497699e-01 1.0045144396502914e+00 -2.3032449685213630e+00 42 -9.4741999244791426e+00 -6.3134658287662750e+00 -3.6928028439517893e+00 - 43 2.7218639962411773e-01 -1.3813634477251096e+01 5.5147832931992202e-01 + 43 2.7218639962411728e-01 -1.3813634477251096e+01 5.5147832931992291e-01 44 8.0196107396135208e+00 -8.1793730426384545e+00 3.5131695854462590e+00 45 -1.8910274064701343e-01 3.9137627573846219e+00 -7.4450993876429399e+00 46 -3.5282857552811575e+00 -5.1713579630178099e+00 1.2477491203990510e+01 - 47 5.1131478665605341e+00 2.3800985688973468e+00 5.1348001359881987e+00 + 47 5.1131478665605341e+00 2.3800985688973459e+00 5.1348001359881970e+00 48 2.1755560727357057e+00 2.9996491762493216e+00 -9.9575511910097214e-01 49 -2.3978299788760209e+00 -1.2283692236805253e+01 -8.3755937565454435e+00 50 3.6161933080447888e+00 5.6291551969069182e+00 -6.9709721613230968e-01 diff --git a/unittest/force-styles/tests/manybody-pair-mliap_snap_chem.yaml b/unittest/force-styles/tests/manybody-pair-mliap_snap_chem.yaml index 7429d09b91..99f36d8c65 100644 --- a/unittest/force-styles/tests/manybody-pair-mliap_snap_chem.yaml +++ b/unittest/force-styles/tests/manybody-pair-mliap_snap_chem.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:30 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:16 2021 epsilon: 5e-13 prerequisites: ! | pair mliap @@ -31,7 +31,7 @@ init_forces: ! |2 3 6.2372158338858297e-01 2.7149161557212836e-01 -4.8035793806964550e-01 4 -2.0337936615474277e+00 2.9491894607511560e+00 9.8066478014365177e-01 5 -1.9807302026626274e+00 -4.1921845197039964e-01 -3.9514999290884223e-01 - 6 -1.0256636650332082e-01 2.3662295416638282e+00 9.0816298775387960e-01 + 6 -1.0256636650332038e-01 2.3662295416638282e+00 9.0816298775387960e-01 7 -6.0657120592984892e-01 -8.0634286798072863e-01 2.1759740426498744e+00 8 6.0627276316787593e-01 1.0677577347039506e+00 -1.2887262448970753e+00 9 -3.0674852805673963e-01 -2.0605633540913679e+00 -2.5500662803249239e+00 @@ -56,7 +56,7 @@ init_forces: ! |2 28 2.5221087546187970e-01 1.4370172575472946e+00 4.1039332214108297e+00 29 -2.7893073887365909e+00 7.8106446652879402e-01 -8.2039261846997913e-01 30 -1.8694503114341463e+00 7.0812686858707219e-01 -9.1751940639239238e-01 - 31 -7.0985766256762606e-01 8.6963471463259756e-01 -7.5188557225015407e-01 + 31 -7.0985766256762606e-01 8.6963471463259845e-01 -7.5188557225015407e-01 32 -2.4089849337056686e+00 4.0992982351371343e-01 -1.1381600041412354e-01 33 4.3597028481189950e+00 -2.6773596435480469e+00 3.1791467867699659e+00 34 5.1607419486495609e-01 1.3141798772668656e-01 8.7023229642897881e-02 diff --git a/unittest/force-styles/tests/manybody-pair-nb3b_harmonic.yaml b/unittest/force-styles/tests/manybody-pair-nb3b_harmonic.yaml index 06ee4441bb..1eef3f085b 100644 --- a/unittest/force-styles/tests/manybody-pair-nb3b_harmonic.yaml +++ b/unittest/force-styles/tests/manybody-pair-nb3b_harmonic.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:31 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:17 2021 epsilon: 1e-12 prerequisites: ! | pair nb3b/harmonic diff --git a/unittest/force-styles/tests/manybody-pair-polymorphic_sw.yaml b/unittest/force-styles/tests/manybody-pair-polymorphic_sw.yaml index 9f06a83959..c06d51d907 100644 --- a/unittest/force-styles/tests/manybody-pair-polymorphic_sw.yaml +++ b/unittest/force-styles/tests/manybody-pair-polymorphic_sw.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:31 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:17 2021 epsilon: 4e-12 prerequisites: ! | pair polymorphic diff --git a/unittest/force-styles/tests/manybody-pair-polymorphic_tersoff.yaml b/unittest/force-styles/tests/manybody-pair-polymorphic_tersoff.yaml index 568363e7dd..b45c0e4295 100644 --- a/unittest/force-styles/tests/manybody-pair-polymorphic_tersoff.yaml +++ b/unittest/force-styles/tests/manybody-pair-polymorphic_tersoff.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:31 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:17 2021 epsilon: 1e-11 prerequisites: ! | pair polymorphic diff --git a/unittest/force-styles/tests/manybody-pair-rebo.yaml b/unittest/force-styles/tests/manybody-pair-rebo.yaml index 0d8a7fa11a..cba66272c3 100644 --- a/unittest/force-styles/tests/manybody-pair-rebo.yaml +++ b/unittest/force-styles/tests/manybody-pair-rebo.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:31 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:18 2021 epsilon: 1e-07 prerequisites: ! | pair rebo diff --git a/unittest/force-styles/tests/manybody-pair-snap.yaml b/unittest/force-styles/tests/manybody-pair-snap.yaml index 3624630ae8..139d1b94d0 100644 --- a/unittest/force-styles/tests/manybody-pair-snap.yaml +++ b/unittest/force-styles/tests/manybody-pair-snap.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:31 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:18 2021 epsilon: 5e-13 prerequisites: ! | pair snap @@ -19,7 +19,7 @@ natoms: 64 init_vdwl: -473.569864629026 init_coul: 0 init_stress: ! |2- - 3.9989504688551500e+02 4.0778136516736993e+02 4.3596322435184845e+02 -2.5242497284339720e+01 1.2811620806363655e+02 2.8644673361821793e+00 + 3.9989504688551500e+02 4.0778136516736993e+02 4.3596322435184823e+02 -2.5242497284339720e+01 1.2811620806363655e+02 2.8644673361821793e+00 init_forces: ! |2 1 -3.7538180163781538e+00 8.8612947043788708e+00 6.7712977816732263e+00 2 -7.6696525239232596e+00 -3.7674335682223203e-01 -5.7958054718422760e+00 @@ -27,7 +27,7 @@ init_forces: ! |2 4 -4.7103509354198474e+00 9.2783458784125941e+00 4.3108702582741429e+00 5 -2.0331946400488916e+00 -2.9593716047756180e+00 -1.6136351145373196e+00 6 1.8086748683348572e+00 4.6479727629048675e+00 3.0425695895915184e-01 - 7 -3.0573043543220644e+00 -4.0575899915120281e+00 1.5283788878527900e+00 + 7 -3.0573043543220644e+00 -4.0575899915120264e+00 1.5283788878527900e+00 8 2.7148403621334427e-01 1.3063473238306007e+00 -1.1268098385676173e+00 9 5.2043326273129953e-01 -2.9340446386399996e+00 -7.6461969078455834e+00 10 -6.2786875145099508e-01 5.6606570005199308e-02 -5.3746300485699576e+00 @@ -63,11 +63,11 @@ init_forces: ! |2 40 9.5193696695210637e+00 -7.0213638399035432e+00 -1.5692669012530696e+00 41 2.4000089474497699e-01 1.0045144396502914e+00 -2.3032449685213630e+00 42 -9.4741999244791426e+00 -6.3134658287662750e+00 -3.6928028439517893e+00 - 43 2.7218639962411773e-01 -1.3813634477251096e+01 5.5147832931992202e-01 + 43 2.7218639962411728e-01 -1.3813634477251096e+01 5.5147832931992291e-01 44 8.0196107396135208e+00 -8.1793730426384545e+00 3.5131695854462590e+00 45 -1.8910274064701343e-01 3.9137627573846219e+00 -7.4450993876429399e+00 46 -3.5282857552811575e+00 -5.1713579630178099e+00 1.2477491203990510e+01 - 47 5.1131478665605341e+00 2.3800985688973468e+00 5.1348001359881987e+00 + 47 5.1131478665605341e+00 2.3800985688973459e+00 5.1348001359881970e+00 48 2.1755560727357057e+00 2.9996491762493216e+00 -9.9575511910097214e-01 49 -2.3978299788760209e+00 -1.2283692236805253e+01 -8.3755937565454435e+00 50 3.6161933080447888e+00 5.6291551969069182e+00 -6.9709721613230968e-01 diff --git a/unittest/force-styles/tests/manybody-pair-snap_chem.yaml b/unittest/force-styles/tests/manybody-pair-snap_chem.yaml index f441535138..39d2abd804 100644 --- a/unittest/force-styles/tests/manybody-pair-snap_chem.yaml +++ b/unittest/force-styles/tests/manybody-pair-snap_chem.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:32 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:18 2021 epsilon: 5e-13 prerequisites: ! | pair snap @@ -28,7 +28,7 @@ init_forces: ! |2 3 6.2372158338858297e-01 2.7149161557212836e-01 -4.8035793806964550e-01 4 -2.0337936615474277e+00 2.9491894607511560e+00 9.8066478014365177e-01 5 -1.9807302026626274e+00 -4.1921845197039964e-01 -3.9514999290884223e-01 - 6 -1.0256636650332082e-01 2.3662295416638282e+00 9.0816298775387960e-01 + 6 -1.0256636650332038e-01 2.3662295416638282e+00 9.0816298775387960e-01 7 -6.0657120592984892e-01 -8.0634286798072863e-01 2.1759740426498744e+00 8 6.0627276316787593e-01 1.0677577347039506e+00 -1.2887262448970753e+00 9 -3.0674852805673963e-01 -2.0605633540913679e+00 -2.5500662803249239e+00 @@ -53,7 +53,7 @@ init_forces: ! |2 28 2.5221087546187970e-01 1.4370172575472946e+00 4.1039332214108297e+00 29 -2.7893073887365909e+00 7.8106446652879402e-01 -8.2039261846997913e-01 30 -1.8694503114341463e+00 7.0812686858707219e-01 -9.1751940639239238e-01 - 31 -7.0985766256762606e-01 8.6963471463259756e-01 -7.5188557225015407e-01 + 31 -7.0985766256762606e-01 8.6963471463259845e-01 -7.5188557225015407e-01 32 -2.4089849337056686e+00 4.0992982351371343e-01 -1.1381600041412354e-01 33 4.3597028481189950e+00 -2.6773596435480469e+00 3.1791467867699659e+00 34 5.1607419486495609e-01 1.3141798772668656e-01 8.7023229642897881e-02 diff --git a/unittest/force-styles/tests/manybody-pair-sw-multi.yaml b/unittest/force-styles/tests/manybody-pair-sw-multi.yaml index 3816e43dd0..a1be280af9 100644 --- a/unittest/force-styles/tests/manybody-pair-sw-multi.yaml +++ b/unittest/force-styles/tests/manybody-pair-sw-multi.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:32 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:19 2021 epsilon: 2e-08 prerequisites: ! | pair sw diff --git a/unittest/force-styles/tests/manybody-pair-sw.yaml b/unittest/force-styles/tests/manybody-pair-sw.yaml index 8a5bb3bf1a..92ac300c40 100644 --- a/unittest/force-styles/tests/manybody-pair-sw.yaml +++ b/unittest/force-styles/tests/manybody-pair-sw.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:32 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:19 2021 epsilon: 1e-10 prerequisites: ! | pair sw diff --git a/unittest/force-styles/tests/manybody-pair-tersoff.yaml b/unittest/force-styles/tests/manybody-pair-tersoff.yaml index 1b8af70661..366810b84e 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:32 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:20 2021 epsilon: 5e-13 prerequisites: ! | pair tersoff @@ -17,139 +17,139 @@ natoms: 64 init_vdwl: -163.150573313048 init_coul: 0 init_stress: ! |- - -5.4897530176832697e+02 -5.4663450719170669e+02 -5.6139257517016426e+02 -1.4199304590474418e+01 -1.3994570965097115e+01 5.4389605871425246e+01 + -5.4897530176832686e+02 -5.4663450719170669e+02 -5.6139257517016438e+02 -1.4199304590474304e+01 -1.3994570965097115e+01 5.4389605871425204e+01 init_forces: ! |2 - 1 -8.1912892931149894e+00 7.5887354282236608e-01 -1.2625078865710950e+00 + 1 -8.1912892931149894e+00 7.5887354282236519e-01 -1.2625078865710941e+00 2 2.9602498712671452e+00 -1.0588320544842651e+01 1.1519772530615358e+00 - 3 1.9949098978773105e-01 3.3201790603073089e+00 -1.2360541799328186e+00 - 4 7.6414578298653435e-01 4.0213523942979013e-01 9.4797175075936373e+00 + 3 1.9949098978772928e-01 3.3201790603073089e+00 -1.2360541799328195e+00 + 4 7.6414578298653524e-01 4.0213523942979190e-01 9.4797175075936355e+00 5 4.1945116087801502e+00 4.0211675202040693e+00 6.4807220477828054e+00 - 6 6.6450126498528483e+00 -3.3655099236048991e+00 2.4183675473801021e+00 - 7 -4.5091473605325696e+00 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b/unittest/force-styles/tests/manybody-pair-tersoff_mod.yaml index 8a9632b88f..92fc41d7e6 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_mod.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_mod.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:32 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:20 2021 epsilon: 5e-11 prerequisites: ! | pair tersoff/mod @@ -17,139 +17,139 @@ natoms: 64 init_vdwl: -271.724273648021 init_coul: 0 init_stress: ! |2- - 4.5327307609410205e+01 4.8520624491107604e+01 4.9902937603449253e+01 -9.5506101395831298e+00 3.2604807162960689e+01 3.7958926469664576e+00 + 4.5327307609410205e+01 4.8520624491107647e+01 4.9902937603449239e+01 -9.5506101395831298e+00 3.2604807162960675e+01 3.7958926469664611e+00 init_forces: ! |2 - 1 -1.1892795399502762e+00 3.4257359265649283e+00 1.7874368716815203e+00 - 2 -2.0954555386253175e+00 -1.7654085262330996e+00 -1.8532577270904687e+00 - 3 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Fri Feb 26 23:09:20 2021 epsilon: 1e-12 prerequisites: ! | pair tersoff/mod/c @@ -17,139 +17,139 @@ natoms: 64 init_vdwl: -270.221167046491 init_coul: 0 init_stress: ! |2- - 3.7721371080158519e+01 4.0406255097836009e+01 4.5487367411373484e+01 -4.8266606949369901e+00 4.8727889805432568e+01 1.1408515692636302e+01 + 3.7721371080158455e+01 4.0406255097835910e+01 4.5487367411373455e+01 -4.8266606949370061e+00 4.8727889805432582e+01 1.1408515692636255e+01 init_forces: ! |2 - 1 -1.1121702900549253e+00 3.2962355779814700e+00 1.7214327613339293e+00 - 2 -2.6231172245796350e+00 -1.1364993928076723e+00 -2.3817153144708119e+00 + 1 -1.1121702900549244e+00 3.2962355779814692e+00 1.7214327613339284e+00 + 2 -2.6231172245796350e+00 -1.1364993928076714e+00 -2.3817153144708110e+00 3 1.2454687790439651e+00 -2.0768859787664962e-02 -9.0044014975037079e-01 - 4 -2.9108777089667255e+00 3.4825750603217136e+00 1.2609281774155390e+00 - 5 -2.1612651325906471e+00 -4.9869587691769302e-01 1.7250163832481702e-01 + 4 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-2.6385037834899929e+00 - 63 3.8910892690837837e+00 -6.7270549290274504e+00 6.5341336803071237e-01 + 63 3.8910892690837824e+00 -6.7270549290274504e+00 6.5341336803071326e-01 64 5.3129893707953428e+00 6.1163287510784619e+00 1.0836913217935809e+01 ... diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml index 795272a848..eec7384351 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Dec 2020 -date_generated: Mon Jan 11 03:57:49 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:20 2021 epsilon: 1e-12 prerequisites: ! | pair tersoff/mod/c diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_mod_shift.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_mod_shift.yaml index 4cc8e84cba..e40ac3548b 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_mod_shift.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_mod_shift.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Dec 2020 -date_generated: Mon Jan 11 03:57:49 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:20 2021 epsilon: 5e-11 prerequisites: ! | pair tersoff/mod diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_shift.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_shift.yaml index 2558fbc9f2..9676fe954b 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_shift.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_shift.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Dec 2020 -date_generated: Mon Jan 11 03:57:49 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:20 2021 epsilon: 5e-13 prerequisites: ! | pair tersoff diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_table.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_table.yaml index 1a2152a24a..036acc25d1 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_table.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:20 2021 epsilon: 5e-11 prerequisites: ! | pair tersoff/table diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml index 9f946558ac..a503b6e912 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:20 2021 epsilon: 5e-11 prerequisites: ! | pair tersoff/zbl @@ -17,139 +17,139 @@ natoms: 64 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5.1136204143684516e+00 -6.0232742119880056e+00 + 46 -7.1909991859724345e+00 6.5930493717367815e+00 5.4969832160946615e+00 + 47 2.1930190183556797e+00 3.3770787280802104e+00 8.3827321095950467e+00 + 48 -8.4316741550207048e+00 -7.2589166508188434e+00 5.6757900084705000e+00 + 49 -5.2787919951503230e+00 6.9617894250151364e+00 -5.1118372569041028e+00 + 50 6.7549914755953626e+00 -1.9686939048679011e+00 -1.5763956001832342e+00 51 -1.1722835834823451e+01 -4.6090445788619194e-01 -3.5458019581496889e+00 - 52 -2.9146420150158925e-01 1.0390697544380689e+00 3.8461064397951099e+00 - 53 4.9994022968781895e+00 1.1625746423885346e+00 1.0131719546021975e+01 - 54 1.9501032708877051e+00 2.1828284989853479e+00 -1.0229107175251080e+01 - 55 1.1017951893515445e+01 4.0696912545743419e-01 -2.0395244626507556e+00 - 56 -7.9765871790228693e-01 4.0562421889191471e+00 6.1126701396247074e-01 - 57 -3.9071992996955269e+00 9.4745522825635540e+00 3.5315639655021500e+00 + 52 -2.9146420150158747e-01 1.0390697544380672e+00 3.8461064397951104e+00 + 53 4.9994022968781850e+00 1.1625746423885328e+00 1.0131719546021973e+01 + 54 1.9501032708877042e+00 2.1828284989853461e+00 -1.0229107175251080e+01 + 55 1.1017951893515447e+01 4.0696912545743330e-01 -2.0395244626507560e+00 + 56 -7.9765871790228826e-01 4.0562421889191462e+00 6.1126701396247074e-01 + 57 -3.9071992996955269e+00 9.4745522825635557e+00 3.5315639655021500e+00 58 -9.7049015797211631e+00 -2.9167333408943041e+00 5.4251373767880153e+00 - 59 6.2022134360845467e+00 6.8057985261686955e+00 -8.1728610238859503e+00 - 60 -5.4918491605506929e+00 7.8759347682481566e+00 -4.6821853616106752e+00 + 59 6.2022134360845458e+00 6.8057985261686946e+00 -8.1728610238859503e+00 + 60 -5.4918491605506929e+00 7.8759347682481584e+00 -4.6821853616106788e+00 61 -2.4999011490572789e+00 -1.2787139053923346e+01 -2.1638212824307607e-01 - 62 2.6906159661430955e+00 1.3928009268586639e-01 2.0167150507734921e-01 - 63 -5.8283969248223002e+00 -5.9257942363533367e+00 -5.0040717151583411e+00 + 62 2.6906159661430942e+00 1.3928009268586861e-01 2.0167150507734788e-01 + 63 -5.8283969248223002e+00 -5.9257942363533367e+00 -5.0040717151583429e+00 64 5.2440455790444869e+00 5.4539376835505564e+00 -7.4979555890288445e+00 ... diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_zbl_shift.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_zbl_shift.yaml index 75dafe7449..7dda923362 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_zbl_shift.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_zbl_shift.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Dec 2020 -date_generated: Mon Jan 11 03:57:49 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:21 2021 epsilon: 5e-11 prerequisites: ! | pair tersoff/zbl diff --git a/unittest/force-styles/tests/manybody-pair-vashishta.yaml b/unittest/force-styles/tests/manybody-pair-vashishta.yaml index 113d7ae840..8f5e6373eb 100644 --- a/unittest/force-styles/tests/manybody-pair-vashishta.yaml +++ b/unittest/force-styles/tests/manybody-pair-vashishta.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:21 2021 epsilon: 5e-13 prerequisites: ! | pair vashishta diff --git a/unittest/force-styles/tests/manybody-pair-vashishta_table.yaml b/unittest/force-styles/tests/manybody-pair-vashishta_table.yaml index bab37d5c14..466e9ff412 100644 --- a/unittest/force-styles/tests/manybody-pair-vashishta_table.yaml +++ b/unittest/force-styles/tests/manybody-pair-vashishta_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:33 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:09:21 2021 epsilon: 1e-12 prerequisites: ! | pair vashishta/table diff --git a/unittest/force-styles/tests/mol-pair-beck.yaml b/unittest/force-styles/tests/mol-pair-beck.yaml index 160ed57874..ca74372e4c 100644 --- a/unittest/force-styles/tests/mol-pair-beck.yaml +++ b/unittest/force-styles/tests/mol-pair-beck.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:10 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:38 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-born.yaml b/unittest/force-styles/tests/mol-pair-born.yaml index b6bd2c0484..11011100d1 100644 --- a/unittest/force-styles/tests/mol-pair-born.yaml +++ b/unittest/force-styles/tests/mol-pair-born.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 21 Jul 2020 -date_generated: Fri Jul 31 11:30:59 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:38 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml b/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml index 7ced560d68..6280c9a9f3 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 21 Jul 2020 -date_generated: Sat Aug 1 16:17:46 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:38 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-born_coul_dsf_cs.yaml b/unittest/force-styles/tests/mol-pair-born_coul_dsf_cs.yaml index 5389455593..fa49c094f3 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_dsf_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_dsf_cs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:10 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:39 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-born_coul_long.yaml b/unittest/force-styles/tests/mol-pair-born_coul_long.yaml index f61926e37a..d46525ad6c 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:10 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:39 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-born_coul_long_cs.yaml b/unittest/force-styles/tests/mol-pair-born_coul_long_cs.yaml index 0b60d5f627..56de63afb8 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_long_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_long_cs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:10 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:39 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml index 991dd0ef77..c4c907a1e0 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:10 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:39 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml index fe6a0faf84..ee9f18f27c 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:10 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:39 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-born_coul_table_cs.yaml b/unittest/force-styles/tests/mol-pair-born_coul_table_cs.yaml index 79dd45154b..32a2b44328 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_table_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_table_cs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:10 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:39 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml b/unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml index 234e9993c6..797cec95a1 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:11 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:39 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-born_coul_wolf_cs.yaml b/unittest/force-styles/tests/mol-pair-born_coul_wolf_cs.yaml index ab13302868..33323ccdd6 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_wolf_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_wolf_cs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:11 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:40 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-buck.yaml b/unittest/force-styles/tests/mol-pair-buck.yaml index 6600c63b4f..6f4cd2474b 100644 --- a/unittest/force-styles/tests/mol-pair-buck.yaml +++ b/unittest/force-styles/tests/mol-pair-buck.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:11 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:40 2021 epsilon: 6e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_cut.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_cut.yaml index 928473176d..d7d72a1dfe 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:11 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:40 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_long.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_long.yaml index 07606715b8..2791961f69 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:11 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:40 2021 epsilon: 4e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_long_cs.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_long_cs.yaml index f4ee478ef8..4667f63a75 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_long_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_long_cs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:11 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:40 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml index 444f02236d..a3816a6451 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 21 Jul 2020 -date_generated: Sat Aug 1 08:36:45 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:40 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml index 24a23bb444..52536b14d4 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:11 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:40 2021 epsilon: 2e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_table.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_table.yaml index 5e89b1ddf7..ecdbc8478c 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:11 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:40 2021 epsilon: 5e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_table_cs.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_table_cs.yaml index 800e9fe8c4..fed44214d8 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_table_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_table_cs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:11 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:41 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-buck_long_coul_long.yaml b/unittest/force-styles/tests/mol-pair-buck_long_coul_long.yaml index 0cf95ba93b..14624b04e5 100644 --- a/unittest/force-styles/tests/mol-pair-buck_long_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_long_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:11 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:41 2021 epsilon: 2e-09 prerequisites: ! | atom full @@ -32,72 +32,72 @@ pair_coeff: ! | 5 5 127198.698386798 0.207005479340455 37.2289658745028 extract: ! "" natoms: 29 -init_vdwl: 143.844961202964 +init_vdwl: 143.844978614334 init_coul: 225.821815126925 init_stress: ! |2- - 2.6272111873723196e+02 2.4458742404218080e+02 4.2242967619246474e+02 -4.9851077637716458e+01 2.3789370276650072e+01 5.6295168409689467e+01 + 2.6272115366310851e+02 2.4458745276042501e+02 4.2242971713439869e+02 -4.9851077224341211e+01 2.3789370660435189e+01 5.6295145580816097e+01 init_forces: ! |2 - 1 -1.4505624410494478e+00 3.8004146845640946e+01 4.9065031053880901e+01 - 2 2.3385004323266994e+01 1.6548373003634683e+01 -2.9130977751412878e+01 - 3 -1.9512019437951746e+01 -5.0838222458975778e+01 -2.0151694098876884e+01 - 4 -4.2904209818932246e+00 1.1246498890619860e+00 -3.2387274210462231e+00 - 5 -1.8674709846410773e+00 -1.5566490773014534e+00 6.0082552497191397e+00 - 6 -6.9625355347470915e+01 7.3169400283632356e+01 6.3503698624949230e+01 - 7 2.2872748139782947e-02 -2.0565225036292986e+01 -1.2607142869450965e+02 - 8 1.1996695065424641e+00 -1.8715100009380692e+00 3.7423138153540876e+01 - 9 1.2011042893923937e+01 5.3887310332750928e+00 4.7397823880093092e+01 - 10 4.8241827191543997e+01 -6.2511416543000180e+01 -1.8155085286183130e+01 - 11 -2.0864825271762375e+00 -1.9912622313285950e+00 -5.4830247539805992e+00 - 12 1.1616718033393738e+01 3.5495575455578630e+00 -2.2659927233488144e+00 - 13 4.3604500704930667e+00 -1.7673671146127139e+00 -2.5819544454075111e-01 - 14 -2.8754771443668155e+00 7.2404586566233820e-01 -4.7880073941201999e+00 - 15 2.4933061678330612e-01 4.4129067076138435e+00 6.2372609624633168e-01 - 16 4.0308368847826046e+01 -3.2807263621689664e+01 -8.8340531400600753e+01 - 17 -3.8534551365139798e+01 3.0771085961339129e+01 9.2205187827301017e+01 - 18 3.5576850500834917e-01 4.7710862431354206e+00 -7.8576979196455978e+00 - 19 1.9901900021180869e+00 -7.2120494406854874e-01 5.5217488469162515e+00 - 20 -2.9133095976939076e+00 -3.9873825539762580e+00 4.1252912728686368e+00 - 21 -8.8829720545896826e+00 -8.3744024680716311e+00 2.7526234064504237e+01 - 22 -1.5742514391100176e+01 -4.8231234667069982e+00 -2.1626154413397067e+01 - 23 2.4211676287893816e+01 1.3610504586141577e+01 -5.3979045461797428e+00 - 24 5.3565422099278761e+00 -2.4298981889237417e+01 1.3585253788291306e+01 - 25 -2.1457575285633951e+01 1.0104637714343605e+00 -1.7195902085341874e+01 - 26 1.5538242805947316e+01 2.3034633528199404e+01 2.9964006765042197e+00 - 27 4.6260665161027301e+00 -2.6306305085064849e+01 9.9386139884880809e+00 - 28 -2.3342848199176302e+01 7.6603913259359970e+00 -1.5178322120241885e+01 - 29 1.9107789198971762e+01 1.8640339901000139e+01 5.2192425301227203e+00 -run_vdwl: 143.664033848008 -run_coul: 225.788771362758 + 1 -1.4505626034745036e+00 3.8004147184195531e+01 4.9065031148995793e+01 + 2 2.3385004350396244e+01 1.6548373059368291e+01 -2.9130977758085685e+01 + 3 -1.9512020703537843e+01 -5.0838221276192705e+01 -2.0151693376982845e+01 + 4 -4.2904209888378588e+00 1.1246498928035378e+00 -3.2387274227466589e+00 + 5 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4.2108843574777688e+02 -4.9575317711225544e+01 2.3909358907758179e+01 5.6450588933021592e+01 + 2.6298255053149916e+02 2.4459393805653841e+02 4.2108847711322130e+02 -4.9575323006225169e+01 2.3909358002752519e+01 5.6450569769884474e+01 run_forces: ! |2 - 1 -1.3652720446656716e+00 3.7954572140886413e+01 4.8884538610219984e+01 - 2 2.3313139975676521e+01 1.6527407427439215e+01 -2.8962850556748574e+01 - 3 -1.9564712492477259e+01 -5.0756725254438585e+01 -2.0129969655577696e+01 - 4 -4.2684079132961532e+00 1.1154799200799748e+00 -3.2315050710172626e+00 - 5 -1.8626808257808209e+00 -1.5514191365901677e+00 5.9922525317567326e+00 - 6 -6.9327725793824527e+01 7.2910029709312454e+01 6.2943842478017125e+01 - 7 3.2729296511785085e-02 -2.0499844250721825e+01 -1.2523227297784275e+02 - 8 9.0645129380789513e-01 -1.5931691793865552e+00 3.7347008229957787e+01 - 9 1.1981987334884325e+01 5.2954472303848910e+00 4.7222348781695430e+01 - 10 4.8288299691503205e+01 -6.2566569339379377e+01 -1.8224017564064091e+01 - 11 -2.0738715074249523e+00 -1.9563279663018796e+00 -5.4254319559511295e+00 - 12 1.1610862764961743e+01 3.5316918655662044e+00 -2.3173751221395720e+00 - 13 4.3429255708311079e+00 -1.7528672352564680e+00 -2.5697582206668895e-01 - 14 -2.8597049731416870e+00 7.1516577588292751e-01 -4.7422665041230756e+00 - 15 2.4141777805199607e-01 4.4181497005137018e+00 6.3284863696190541e-01 - 16 4.0232203794586695e+01 -3.2797821300800962e+01 -8.8231810120087630e+01 - 17 -3.8475340336751799e+01 3.0789552016439433e+01 9.2071434975793437e+01 - 18 3.0444737165682245e-01 4.7206637253266726e+00 -7.8186561033362132e+00 - 19 2.0279176824528000e+00 -6.9153978261739135e-01 5.5370947284278174e+00 - 20 -2.8995246410850308e+00 -3.9661906680569294e+00 4.0718950075472362e+00 - 21 -8.9482093919054275e+00 -8.3621998308864107e+00 2.7577075884535351e+01 - 22 -1.5805953773942205e+01 -4.8572145959519402e+00 -2.1662217002199810e+01 - 23 2.4340519096091096e+01 1.3631551507334764e+01 -5.4129063248356344e+00 - 24 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-1.5931711516900440e+00 3.7347017369470542e+01 + 9 1.1981987319613346e+01 5.2954473123148720e+00 4.7222348956569590e+01 + 10 4.8288281212283742e+01 -6.2566570322889454e+01 -1.8224021907990483e+01 + 11 -2.0738715105412719e+00 -1.9563279903586321e+00 -5.4254319984735320e+00 + 12 1.1610878367908992e+01 3.5317032256430076e+00 -2.3173846571471395e+00 + 13 4.3429256472591025e+00 -1.7528672157398184e+00 -2.5697584881970975e-01 + 14 -2.8597049514773167e+00 7.1516578275653253e-01 -4.7422665431420148e+00 + 15 2.4141798790025348e-01 4.4181498659013112e+00 6.3284857350558965e-01 + 16 4.0232210797970701e+01 -3.2797832127730494e+01 -8.8231799256317260e+01 + 17 -3.8475339975415856e+01 3.0789551133759257e+01 9.2071437068448233e+01 + 18 3.0444744501753151e-01 4.7206638357915631e+00 -7.8186562242979116e+00 + 19 2.0279176776152252e+00 -6.9153978564093010e-01 5.5370947240235608e+00 + 20 -2.8995246349425892e+00 -3.9661906625562011e+00 4.0718950082869085e+00 + 21 -8.9482093741669626e+00 -8.3621998525228864e+00 2.7577075866251551e+01 + 22 -1.5805953774649829e+01 -4.8572145967141411e+00 -2.1662217002957558e+01 + 23 2.4340519097230196e+01 1.3631551507602921e+01 -5.4129063246281666e+00 + 24 5.5331809763522193e+00 -2.4561349908059270e+01 1.3801516566834152e+01 + 25 -2.1784339528699515e+01 1.0179046212252338e+00 -1.7474990048927918e+01 + 26 1.5689568160812019e+01 2.3291559486515375e+01 3.0620904858297013e+00 + 27 4.7026950277510515e+00 -2.6383838683693700e+01 9.9362504040370077e+00 + 28 -2.3442655457776933e+01 7.6899620159252651e+00 -1.5219891624415277e+01 + 29 1.9130052900332021e+01 1.8687939997809593e+01 5.2629392179006302e+00 ... diff --git a/unittest/force-styles/tests/mol-pair-buck_long_coul_off.yaml b/unittest/force-styles/tests/mol-pair-buck_long_coul_off.yaml index 1c8ab223e0..475e588687 100644 --- a/unittest/force-styles/tests/mol-pair-buck_long_coul_off.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_long_coul_off.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:11 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:41 2021 epsilon: 2e-09 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-buck_long_cut_coul_long.yaml b/unittest/force-styles/tests/mol-pair-buck_long_cut_coul_long.yaml index 4c54416a19..d51ff36d84 100644 --- a/unittest/force-styles/tests/mol-pair-buck_long_cut_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_long_cut_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:11 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:41 2021 epsilon: 2e-09 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-buck_mdf.yaml b/unittest/force-styles/tests/mol-pair-buck_mdf.yaml index 3eb30c04fb..8f284c910c 100644 --- a/unittest/force-styles/tests/mol-pair-buck_mdf.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_mdf.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:11 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:41 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-buck_table_coul_long.yaml b/unittest/force-styles/tests/mol-pair-buck_table_coul_long.yaml index d2a027b202..ff11010ebd 100644 --- a/unittest/force-styles/tests/mol-pair-buck_table_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_table_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:41 2021 epsilon: 2e-09 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-buck_table_coul_off.yaml b/unittest/force-styles/tests/mol-pair-buck_table_coul_off.yaml index 75ea5e64f9..0c4d543e7a 100644 --- a/unittest/force-styles/tests/mol-pair-buck_table_coul_off.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_table_coul_off.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:41 2021 epsilon: 2e-08 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml b/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml index 6618461c9a..c204dd600f 100644 --- a/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:41 2021 epsilon: 2e-09 prerequisites: ! | atom full @@ -32,72 +32,72 @@ pair_coeff: ! | 5 5 127198.698386798 0.207005479340455 37.2289658745028 extract: ! "" natoms: 29 -init_vdwl: 143.844961202964 +init_vdwl: 143.844978614334 init_coul: 225.821848735651 init_stress: ! |2- - 2.6272113814088459e+02 2.4458742749392664e+02 4.2242968800359819e+02 -4.9851073478676085e+01 2.3789377934310345e+01 5.6295172388862447e+01 + 2.6272117306676120e+02 2.4458745621217102e+02 4.2242972894553253e+02 -4.9851073065300838e+01 2.3789378318095498e+01 5.6295149559988992e+01 init_forces: ! |2 - 1 -1.4505640619389681e+00 3.8004146585790465e+01 4.9065029691291613e+01 - 2 2.3385003661429913e+01 1.6548372213986102e+01 -2.9130976125306312e+01 - 3 -1.9512019324113055e+01 -5.0838222586853490e+01 -2.0151694230673115e+01 - 4 -4.2904209431208518e+00 1.1246503634939833e+00 -3.2387272414004546e+00 - 5 -1.8674707369894010e+00 -1.5566480505693736e+00 6.0082554357882367e+00 - 6 -6.9625355684493741e+01 7.3169400746899186e+01 6.3503696978944937e+01 - 7 2.2872248567361957e-02 -2.0565224930504840e+01 -1.2607143020067289e+02 - 8 1.1996689487155892e+00 -1.8715105185863312e+00 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4.7710862380293300e+00 -7.8576991961411933e+00 + 19 1.9901880274797432e+00 -7.2120628273974552e-01 5.5217485914027300e+00 + 20 -2.9133077306028037e+00 -3.9873812666657433e+00 4.1252922615364644e+00 + 21 -8.8829724897811690e+00 -8.3744018546727830e+00 2.7526234698248395e+01 + 22 -1.5742517627293919e+01 -4.8231253819043038e+00 -2.1626156255255044e+01 + 23 2.4211679999720808e+01 1.3610506006400097e+01 -5.3979034247521342e+00 + 24 5.3565423691472525e+00 -2.4298981609236485e+01 1.3585253150887608e+01 + 25 -2.1457576768629711e+01 1.0104626755769854e+00 -1.7195902771340254e+01 + 26 1.5538244608279541e+01 2.3034634695339562e+01 2.9964020489618552e+00 + 27 4.6260663692619683e+00 -2.6306304932222957e+01 9.9386138025705169e+00 + 28 -2.3342851187576169e+01 7.6603903375650901e+00 -1.5178323537982580e+01 + 29 1.9107792107619538e+01 1.8640340506123994e+01 5.2192442277069402e+00 +run_vdwl: 143.664052385482 +run_coul: 225.788807113984 run_stress: ! |2- - 2.6298253730875990e+02 2.4459390608852283e+02 4.2108844885702558e+02 -4.9575312662970951e+01 2.3909364645213543e+01 5.6450595032795320e+01 + 2.6298257278765311e+02 2.4459394060869445e+02 4.2108849022194408e+02 -4.9575317957752254e+01 2.3909363739954845e+01 5.6450575869687796e+01 run_forces: ! |2 - 1 -1.3652735543008816e+00 3.7954571133178902e+01 4.8884537377309172e+01 - 2 2.3313139309989094e+01 1.6527406547056287e+01 -2.8962849270283392e+01 - 3 -1.9564712384032376e+01 -5.0756725329741236e+01 -2.0129969747702308e+01 - 4 -4.2684080200768406e+00 1.1154804510128165e+00 -3.2315048619404054e+00 - 5 -1.8626805980022214e+00 -1.5514180174720389e+00 5.9922526428223755e+00 - 6 -6.9327726613063405e+01 7.2910030587436125e+01 6.2943841090264428e+01 - 7 3.2729124302063782e-02 -2.0499844044312820e+01 -1.2523227476685206e+02 - 8 9.0645037724821509e-01 -1.5931699446420091e+00 3.7347010853073435e+01 - 9 1.1981988562945483e+01 5.2954468151255067e+00 4.7222350357045890e+01 - 10 4.8288299835295966e+01 -6.2566569083557049e+01 -1.8224018086894844e+01 - 11 -2.0738716050222630e+00 -1.9563271603792205e+00 -5.4254318756542368e+00 - 12 1.1610864028639977e+01 3.5316916580070092e+00 -2.3173763560781429e+00 - 13 4.3429257276773807e+00 -1.7528673949822231e+00 -2.5697563580528093e-01 - 14 -2.8597051905279471e+00 7.1516550165881965e-01 -4.7422662564667295e+00 - 15 2.4141775499873258e-01 4.4181494329616786e+00 6.3284916283478820e-01 - 16 4.0232204451083376e+01 -3.2797821752234313e+01 -8.8231810184066035e+01 - 17 -3.8475340125721864e+01 3.0789552823136074e+01 9.2071434225822074e+01 - 18 3.0444797968268300e-01 4.7206637648615688e+00 -7.8186573872028138e+00 - 19 2.0279150125912517e+00 -6.9154201326913600e-01 5.5370944385616223e+00 - 20 -2.8995220719101922e+00 -3.9661888702042210e+00 4.0718961555885951e+00 - 21 -8.9482098879923537e+00 -8.3621991830172071e+00 2.7577076547654709e+01 - 22 -1.5805955548410763e+01 -4.8572159943051245e+00 -2.1662218351727955e+01 - 23 2.4340521395832020e+01 1.3631552339738477e+01 -5.4129057423025664e+00 - 24 5.5331810643516564e+00 -2.4561349600827779e+01 1.3801515937783783e+01 - 25 -2.1784341755480526e+01 1.0179032133762751e+00 -1.7474990741497301e+01 - 26 1.5689570822659292e+01 2.3291561154430479e+01 3.0620923138000120e+00 - 27 4.7026946479168608e+00 -2.6383838593099334e+01 9.9362502379539066e+00 - 28 -2.3442657625683115e+01 7.6899612511865811e+00 -1.5219892618907782e+01 - 29 1.9130054885010718e+01 1.8687940308877128e+01 5.2629405428671072e+00 + 1 -1.3652735930906894e+00 3.7954572425088600e+01 4.8884537536228251e+01 + 2 2.3313139334678663e+01 1.6527406600491211e+01 -2.8962849276354000e+01 + 3 -1.9564718562282973e+01 -5.0756719062921292e+01 -2.0129965576839844e+01 + 4 -4.2684081469531368e+00 1.1154804222099293e+00 -3.2315049292955824e+00 + 5 -1.8626808414826610e+00 -1.5514185255808333e+00 5.9922528781941766e+00 + 6 -6.9327721229262110e+01 7.2910024635730380e+01 6.2943837085648937e+01 + 7 3.2725222830676137e-02 -2.0499842211560001e+01 -1.2523228341650837e+02 + 8 9.0645055137852115e-01 -1.5931719167310145e+00 3.7347019992128743e+01 + 9 1.1981988547677094e+01 5.2954468970124511e+00 4.7222350531971742e+01 + 10 4.8288281356087531e+01 -6.2566570067320434e+01 -1.8224022430624395e+01 + 11 -2.0738716081392377e+00 -1.9563271844965389e+00 -5.4254319181514443e+00 + 12 1.1610879631578506e+01 3.5317030183327125e+00 -2.3173858911656642e+00 + 13 4.3429258040952297e+00 -1.7528673754740225e+00 -2.5697566254992021e-01 + 14 -2.8597051688567952e+00 7.1516550852642913e-01 -4.7422662954861217e+00 + 15 2.4141796485202816e-01 4.4181495983415076e+00 6.3284909937970446e-01 + 16 4.0232211454356282e+01 -3.2797832579156953e+01 -8.8231799320354028e+01 + 17 -3.8475339764361301e+01 3.0789551940448018e+01 9.2071436318485866e+01 + 18 3.0444805304334399e-01 4.7206638753263892e+00 -7.8186575081644856e+00 + 19 2.0279150077542512e+00 -6.9154201629216772e-01 5.5370944341575088e+00 + 20 -2.8995220657682923e+00 -3.9661888647039816e+00 4.0718961563281235e+00 + 21 -8.9482098702532671e+00 -8.3621992046533951e+00 2.7577076529370782e+01 + 22 -1.5805955549117563e+01 -4.8572159950668672e+00 -2.1662218352485397e+01 + 23 2.4340521396969667e+01 1.3631552340005888e+01 -5.4129057420952673e+00 + 24 5.5331811069800025e+00 -2.4561349584081412e+01 1.3801516002278914e+01 + 25 -2.1784341752404423e+01 1.0179032153888428e+00 -1.7474990731263802e+01 + 26 1.5689570827295116e+01 2.3291561157244697e+01 3.0620923168469263e+00 + 27 4.7026946335578899e+00 -2.6383838605477855e+01 9.9362502458408990e+00 + 28 -2.3442657629509469e+01 7.6899612499018408e+00 -1.5219892620516704e+01 + 29 1.9130054888347100e+01 1.8687940309467866e+01 5.2629405449944144e+00 ... diff --git a/unittest/force-styles/tests/mol-pair-cosine_squared.yaml b/unittest/force-styles/tests/mol-pair-cosine_squared.yaml index b1d44726c9..ee6faf6235 100644 --- a/unittest/force-styles/tests/mol-pair-cosine_squared.yaml +++ b/unittest/force-styles/tests/mol-pair-cosine_squared.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:42 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_cut.yaml b/unittest/force-styles/tests/mol-pair-coul_cut.yaml index 6f5c85343b..921e682a9a 100644 --- a/unittest/force-styles/tests/mol-pair-coul_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:42 2021 epsilon: 1e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_cut_soft.yaml b/unittest/force-styles/tests/mol-pair-coul_cut_soft.yaml index 25dfcf21bb..20b467b728 100644 --- a/unittest/force-styles/tests/mol-pair-coul_cut_soft.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_cut_soft.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:42 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_debye.yaml b/unittest/force-styles/tests/mol-pair-coul_debye.yaml index 064ea744c6..a7902442d1 100644 --- a/unittest/force-styles/tests/mol-pair-coul_debye.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_debye.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:42 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_diel.yaml b/unittest/force-styles/tests/mol-pair-coul_diel.yaml index 565cd5f7b2..a417ee09bf 100644 --- a/unittest/force-styles/tests/mol-pair-coul_diel.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_diel.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:42 2021 epsilon: 1e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_dsf.yaml b/unittest/force-styles/tests/mol-pair-coul_dsf.yaml index b586a73bb6..9bc59e4431 100644 --- a/unittest/force-styles/tests/mol-pair-coul_dsf.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_dsf.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:42 2021 epsilon: 1e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_long.yaml b/unittest/force-styles/tests/mol-pair-coul_long.yaml index 884599ba7e..9c3c933100 100644 --- a/unittest/force-styles/tests/mol-pair-coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:42 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_long_cs.yaml b/unittest/force-styles/tests/mol-pair-coul_long_cs.yaml index 164acce939..02426dbdc3 100644 --- a/unittest/force-styles/tests/mol-pair-coul_long_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_long_cs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:42 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_long_soft.yaml b/unittest/force-styles/tests/mol-pair-coul_long_soft.yaml index c1a6832713..b769aabf93 100644 --- a/unittest/force-styles/tests/mol-pair-coul_long_soft.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_long_soft.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:42 2021 epsilon: 3e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_msm.yaml b/unittest/force-styles/tests/mol-pair-coul_msm.yaml index 83e633d42f..83b8550101 100644 --- a/unittest/force-styles/tests/mol-pair-coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_msm.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:43 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml index 05418a2f75..289a3e0e38 100644 --- a/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:12 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:43 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_shield.yaml b/unittest/force-styles/tests/mol-pair-coul_shield.yaml index 58e75ad6d1..fa64e7d0cb 100644 --- a/unittest/force-styles/tests/mol-pair-coul_shield.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_shield.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:43 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_slater_cut.yaml b/unittest/force-styles/tests/mol-pair-coul_slater_cut.yaml index 85a3343367..d08bbf4c86 100644 --- a/unittest/force-styles/tests/mol-pair-coul_slater_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_slater_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:43 2021 epsilon: 1e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_slater_long.yaml b/unittest/force-styles/tests/mol-pair-coul_slater_long.yaml index 9000f80d0d..b731508901 100644 --- a/unittest/force-styles/tests/mol-pair-coul_slater_long.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_slater_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:43 2021 epsilon: 2e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_streitz_long.yaml b/unittest/force-styles/tests/mol-pair-coul_streitz_long.yaml index b2b3509149..5c3c637193 100644 --- a/unittest/force-styles/tests/mol-pair-coul_streitz_long.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_streitz_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:43 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_streitz_wolf.yaml b/unittest/force-styles/tests/mol-pair-coul_streitz_wolf.yaml index ad7aa1ccc1..ec3b354df4 100644 --- a/unittest/force-styles/tests/mol-pair-coul_streitz_wolf.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_streitz_wolf.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:43 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_table.yaml b/unittest/force-styles/tests/mol-pair-coul_table.yaml index aa9ab54062..54baba354c 100644 --- a/unittest/force-styles/tests/mol-pair-coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:44 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_table_cs.yaml b/unittest/force-styles/tests/mol-pair-coul_table_cs.yaml index 2691280d70..d5ed5fab83 100644 --- a/unittest/force-styles/tests/mol-pair-coul_table_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_table_cs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:44 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_wolf.yaml b/unittest/force-styles/tests/mol-pair-coul_wolf.yaml index 4918adc093..a48fa7f565 100644 --- a/unittest/force-styles/tests/mol-pair-coul_wolf.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_wolf.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:44 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-coul_wolf_cs.yaml b/unittest/force-styles/tests/mol-pair-coul_wolf_cs.yaml index 50447386bf..32068ba458 100644 --- a/unittest/force-styles/tests/mol-pair-coul_wolf_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_wolf_cs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:44 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-dpd.yaml b/unittest/force-styles/tests/mol-pair-dpd.yaml index 5f747fa0b2..13e9c1b776 100644 --- a/unittest/force-styles/tests/mol-pair-dpd.yaml +++ b/unittest/force-styles/tests/mol-pair-dpd.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:44 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-dpd_tstat.yaml b/unittest/force-styles/tests/mol-pair-dpd_tstat.yaml index 43f5136973..d43ac13ba0 100644 --- a/unittest/force-styles/tests/mol-pair-dpd_tstat.yaml +++ b/unittest/force-styles/tests/mol-pair-dpd_tstat.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:44 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-e3b.yaml b/unittest/force-styles/tests/mol-pair-e3b.yaml index 416f76db20..03d74c2069 100644 --- a/unittest/force-styles/tests/mol-pair-e3b.yaml +++ b/unittest/force-styles/tests/mol-pair-e3b.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:44 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-gauss.yaml b/unittest/force-styles/tests/mol-pair-gauss.yaml index c83d82f39f..642f2417c8 100644 --- a/unittest/force-styles/tests/mol-pair-gauss.yaml +++ b/unittest/force-styles/tests/mol-pair-gauss.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:44 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-gauss_cut.yaml b/unittest/force-styles/tests/mol-pair-gauss_cut.yaml index ff11a0e41b..c440fc0f1c 100644 --- a/unittest/force-styles/tests/mol-pair-gauss_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-gauss_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:44 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml b/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml index ce962d5a3b..a264411788 100644 --- a/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml +++ b/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:45 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-hybrid.yaml b/unittest/force-styles/tests/mol-pair-hybrid.yaml index 3630d4bdd6..4f55c09d25 100644 --- a/unittest/force-styles/tests/mol-pair-hybrid.yaml +++ b/unittest/force-styles/tests/mol-pair-hybrid.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:13 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:45 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lennard_mdf.yaml b/unittest/force-styles/tests/mol-pair-lennard_mdf.yaml index 6ba6c42bb5..4ba3045057 100644 --- a/unittest/force-styles/tests/mol-pair-lennard_mdf.yaml +++ b/unittest/force-styles/tests/mol-pair-lennard_mdf.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:14 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:45 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj96_cut.yaml b/unittest/force-styles/tests/mol-pair-lj96_cut.yaml index 85191fe5ed..94e19d6663 100644 --- a/unittest/force-styles/tests/mol-pair-lj96_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-lj96_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:14 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:45 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm.yaml index d20b8e2e87..452a1b58d6 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:14 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:45 2021 epsilon: 7e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm_implicit.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm_implicit.yaml index a8333d8d91..91a73b31e3 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm_implicit.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm_implicit.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:14 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:45 2021 epsilon: 2e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_long.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_long.yaml index 7e377ec89c..c58a4849da 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:14 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:45 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_long_soft.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_long_soft.yaml index aa9509679c..0d956e0d3e 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_long_soft.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_long_soft.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:14 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:45 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm.yaml index 93677fc67e..b3884c3b11 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:14 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:46 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml index 0c0bc86099..adf0f0b71b 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:14 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:46 2021 epsilon: 1e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_table.yaml index 31eea37ef8..7d64a7c692 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:14 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:46 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_charmmfsw.yaml b/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_charmmfsw.yaml index 5348900e55..4ed8721c7e 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_charmmfsw.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_charmmfsw.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:14 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:46 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_long.yaml b/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_long.yaml index 898a0759a6..0b95c6c4d0 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:14 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:46 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_table.yaml index 2e578773a8..2af3de8273 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:14 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:46 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_class2.yaml b/unittest/force-styles/tests/mol-pair-lj_class2.yaml index dfded52103..ba4989e6e2 100644 --- a/unittest/force-styles/tests/mol-pair-lj_class2.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_class2.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:14 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:46 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_class2_coul_cut.yaml b/unittest/force-styles/tests/mol-pair-lj_class2_coul_cut.yaml index 719e42f49d..7855313829 100644 --- a/unittest/force-styles/tests/mol-pair-lj_class2_coul_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_class2_coul_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:46 2021 epsilon: 5e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_class2_coul_cut_soft.yaml b/unittest/force-styles/tests/mol-pair-lj_class2_coul_cut_soft.yaml index 0ba6aa7608..8ac23b3583 100644 --- a/unittest/force-styles/tests/mol-pair-lj_class2_coul_cut_soft.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_class2_coul_cut_soft.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:47 2021 epsilon: 5e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_class2_coul_long.yaml b/unittest/force-styles/tests/mol-pair-lj_class2_coul_long.yaml index 0fdcc79f5e..0bae674a35 100644 --- a/unittest/force-styles/tests/mol-pair-lj_class2_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_class2_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:47 2021 epsilon: 5e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_class2_coul_long_cs.yaml b/unittest/force-styles/tests/mol-pair-lj_class2_coul_long_cs.yaml index a8a65171f5..7f88407d20 100644 --- a/unittest/force-styles/tests/mol-pair-lj_class2_coul_long_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_class2_coul_long_cs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:47 2021 epsilon: 5e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_class2_coul_long_soft.yaml b/unittest/force-styles/tests/mol-pair-lj_class2_coul_long_soft.yaml index b18417ceba..673fb46800 100644 --- a/unittest/force-styles/tests/mol-pair-lj_class2_coul_long_soft.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_class2_coul_long_soft.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:47 2021 epsilon: 5e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_class2_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_class2_coul_table.yaml index 3c31c1bde6..39a9299b25 100644 --- a/unittest/force-styles/tests/mol-pair-lj_class2_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_class2_coul_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:47 2021 epsilon: 5e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_class2_coul_table_cs.yaml b/unittest/force-styles/tests/mol-pair-lj_class2_coul_table_cs.yaml index 6d4064039e..8d3537b6c2 100644 --- a/unittest/force-styles/tests/mol-pair-lj_class2_coul_table_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_class2_coul_table_cs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:47 2021 epsilon: 5e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_class2_soft.yaml b/unittest/force-styles/tests/mol-pair-lj_class2_soft.yaml index 55368adbb9..75bf587fe9 100644 --- a/unittest/force-styles/tests/mol-pair-lj_class2_soft.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_class2_soft.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:47 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cubic.yaml b/unittest/force-styles/tests/mol-pair-lj_cubic.yaml index 6d23998ad5..1d9b911db5 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cubic.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cubic.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 30 Nov 2020 -date_generated: Fri Dec 18 22:30:42 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:47 2021 epsilon: 1e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut.yaml b/unittest/force-styles/tests/mol-pair-lj_cut.yaml index 1a45b3d448..4aff257f62 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:48 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_cut.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_cut.yaml index d34748446f..23ee5a4b93 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:48 2021 epsilon: 1e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_cut_soft.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_cut_soft.yaml index bfd5a20a36..2c37fbefe9 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_cut_soft.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_cut_soft.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:48 2021 epsilon: 2e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_debye.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_debye.yaml index b460307579..04e9f26025 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_debye.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_debye.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:48 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_dsf.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_dsf.yaml index e830d17236..109e347449 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_dsf.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_dsf.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:48 2021 epsilon: 8e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_long.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_long.yaml index b4981269c5..e16d0ac162 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:48 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_long_cs.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_long_cs.yaml index 0cd8d0ce00..863b41f597 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_long_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_long_cs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:15 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:48 2021 epsilon: 7.5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_long_soft.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_long_soft.yaml index c3a97c2f2f..acd3ea4ce0 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_long_soft.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_long_soft.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:16 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:48 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml index a861ce9a34..937c115a9a 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:16 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:48 2021 epsilon: 7e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml index 1c53c025f9..de1ab82c24 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:16 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:49 2021 epsilon: 1e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_table.yaml index 2da0d85562..d5eb9d35a1 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:16 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:49 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_table_cs.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_table_cs.yaml index eddedd29da..179900a1f2 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_table_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_table_cs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:16 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:49 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_wolf.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_wolf.yaml index 47c261986a..28b6525f19 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_wolf.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_wolf.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:16 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:49 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_soft.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_soft.yaml index 266af00296..77567c0a76 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_soft.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_soft.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:16 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:49 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_cut.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_cut.yaml index 36e89e8cfa..d57e1df73a 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:16 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:49 2021 epsilon: 1e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml index c3097aee6d..d1bed9430b 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:16 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:49 2021 epsilon: 1e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long_soft.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long_soft.yaml index 08f12b6476..027c91970e 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long_soft.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long_soft.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:16 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:50 2021 epsilon: 1e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_table.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_table.yaml index 22eef49478..77a7f00ad8 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:16 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:50 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_expand.yaml b/unittest/force-styles/tests/mol-pair-lj_expand.yaml index cc94bc7213..7f7a73df55 100644 --- a/unittest/force-styles/tests/mol-pair-lj_expand.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_expand.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:16 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:50 2021 epsilon: 1e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_expand_coul_long.yaml b/unittest/force-styles/tests/mol-pair-lj_expand_coul_long.yaml index e177df874b..9f4b5fa97c 100644 --- a/unittest/force-styles/tests/mol-pair-lj_expand_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_expand_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:16 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:50 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_expand_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_expand_coul_table.yaml index 2ca2d354a7..27ceae8a05 100644 --- a/unittest/force-styles/tests/mol-pair-lj_expand_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_expand_coul_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:17 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:50 2021 epsilon: 2e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_gromacs.yaml b/unittest/force-styles/tests/mol-pair-lj_gromacs.yaml index ecf6b8f0f8..174c94829d 100644 --- a/unittest/force-styles/tests/mol-pair-lj_gromacs.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_gromacs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:17 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:50 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_gromacs_coul_gromacs.yaml b/unittest/force-styles/tests/mol-pair-lj_gromacs_coul_gromacs.yaml index 75d1943339..c1a87514f1 100644 --- a/unittest/force-styles/tests/mol-pair-lj_gromacs_coul_gromacs.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_gromacs_coul_gromacs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:17 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:50 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_long_coul_long.yaml b/unittest/force-styles/tests/mol-pair-lj_long_coul_long.yaml index caa7d765b5..483d54a326 100644 --- a/unittest/force-styles/tests/mol-pair-lj_long_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_long_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:17 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:50 2021 epsilon: 2.5e-09 prerequisites: ! | atom full @@ -27,72 +27,72 @@ extract: ! | sigma 2 cut_coul 0 natoms: 29 -init_vdwl: 749.373775521848 +init_vdwl: 749.373800441949 init_coul: 225.821815126925 init_stress: ! |2- - 2.1566619777740902e+03 2.1561339369037219e+03 4.6267173221155736e+03 -7.5508635166800991e+02 1.8219495486319847e+01 6.7619475900149655e+02 + 2.1566620277629813e+03 2.1561339780157969e+03 4.6267173807038052e+03 -7.5508635107101691e+02 1.8219496027762062e+01 6.7619472632626719e+02 init_forces: ! |2 - 1 -2.0622981429393807e+01 2.6956534558011725e+02 3.3304204925517143e+02 - 2 1.5804318302709490e+02 1.2736090910218131e+02 -1.8761883353245216e+02 - 3 -1.3527896432508211e+02 -3.8712541491749789e+02 -1.4567430834698106e+02 - 4 -7.9525168436030773e+00 2.1530554166296176e+00 -5.8369678142768118e+00 - 5 -3.0584210326688970e+00 -3.3883621918483655e+00 1.2083104660267935e+01 - 6 -8.3040950136399044e+02 9.6005842246557552e+02 1.1483426903619145e+03 - 7 5.8117176187526780e+01 -3.3519934567641707e+02 -1.7141478166388797e+03 - 8 1.4294493171390297e+02 -1.0474128177423346e+02 4.0227521160525629e+02 - 9 8.0782715664878268e+01 7.9461644781068358e+01 3.5173834803878833e+02 - 10 5.3094739039340072e+02 -6.1005894329030184e+02 -1.8379453583600960e+02 - 11 -3.2540352897717737e+00 -4.8803819809385027e+00 -1.0223100643333725e+01 - 12 2.0391732170892919e+01 1.0150596216961747e+01 -6.4978637469860816e+00 - 13 8.0251516080555430e+00 -3.2176927494765719e+00 -3.2683209992541434e-01 - 14 -4.4396727557663969e+00 1.0430005884558371e+00 -8.8469672403790529e+00 - 15 1.4998024458760750e-01 8.2845477274856112e+00 2.0021371706680275e+00 - 16 4.6253004030953110e+02 -3.3139195670429746e+02 -1.1873816589319622e+03 - 17 -4.5576220588835747e+02 3.2170885473451676e+02 1.1992075674372097e+03 - 18 3.5638625258145490e-01 4.7708005940782092e+00 -7.8562962420657412e+00 - 19 1.9902577614639423e+00 -7.2127770268183056e-01 5.5221988819092536e+00 - 20 -2.9135477975119137e+00 -3.9876270289423439e+00 4.1253800349019452e+00 - 21 -6.9663077752668514e+01 -7.7247842870041893e+01 2.1698923839494989e+02 - 22 -1.0627534004387260e+02 -2.6762806431184490e+01 -1.6366217211268523e+02 - 23 1.7552279743617564e+02 1.0442576746894673e+02 -5.2822891559610461e+01 - 24 3.5025338162767611e+01 -2.0265091634797420e+02 1.0716856771722603e+02 - 25 -1.4546282924538690e+02 2.0973208751614084e+01 -1.2144531001524807e+02 - 26 1.0987377305379422e+02 1.8142227933955789e+02 1.3660221686848063e+01 - 27 4.9787264851761520e+01 -2.1702378491087205e+02 8.7171908546104049e+01 - 28 -1.7608392919959783e+02 7.3301696261828440e+01 -1.1852448703320457e+02 - 29 1.2668890412925685e+02 1.4371750554769054e+02 3.1331418002784233e+01 -run_vdwl: 719.707445870818 -run_coul: 225.904237287787 + 1 -2.0622981661660933e+01 2.6956534606458871e+02 3.3304204939116363e+02 + 2 1.5804318306601883e+02 1.2736090918213843e+02 -1.8761883354202345e+02 + 3 -1.3527896613660067e+02 -3.8712541322474209e+02 -1.4567430731367753e+02 + 4 -7.9525168535595512e+00 2.1530554219898832e+00 -5.8369678167150498e+00 + 5 -3.0584211548599773e+00 -3.3883622409374414e+00 1.2083104792629799e+01 + 6 -8.3040950098401379e+02 9.6005842177261275e+02 1.1483426894944605e+03 + 7 5.8117169924759708e+01 -3.3519934246802160e+02 -1.7141478301179534e+03 + 8 1.4294492975961728e+02 -1.0474128441953674e+02 4.0227522786700177e+02 + 9 8.0782715620485192e+01 7.9461644907945399e+01 3.5173834826976304e+02 + 10 5.3094736334968877e+02 -6.1005894723647111e+02 -1.8379453981847473e+02 + 11 -3.2540351174731903e+00 -4.8803826086618827e+00 -1.0223101185000280e+01 + 12 2.0391758367278634e+01 1.0150613828433194e+01 -6.4978796273378174e+00 + 13 8.0251517295680532e+00 -3.2176927284900541e+00 -3.2683214420263229e-01 + 14 -4.4396726967568014e+00 1.0430006507669409e+00 -8.8469673769189328e+00 + 15 1.4998058602555447e-01 8.2845479683942465e+00 2.0021370654547277e+00 + 16 4.6253004977709497e+02 -3.3139197130445098e+02 -1.1873816442531520e+03 + 17 -4.5576220537745553e+02 3.2170885360525574e+02 1.1992075701133558e+03 + 18 3.5638637100685411e-01 4.7708007696323129e+00 -7.8562964240005906e+00 + 19 1.9902577541873943e+00 -7.2127770801066615e-01 5.5221988759400071e+00 + 20 -2.9135477887099177e+00 -3.9876270213526297e+00 4.1253800364116655e+00 + 21 -6.9663077725625229e+01 -7.7247842899394058e+01 2.1698923836747846e+02 + 22 -1.0627534004508448e+02 -2.6762806432167704e+01 -1.6366217211367643e+02 + 23 1.7552279743788071e+02 1.0442576746938796e+02 -5.2822891559245299e+01 + 24 3.5025338224251065e+01 -2.0265091632381331e+02 1.0716856781097904e+02 + 25 -1.4546282924824158e+02 2.0973208750647458e+01 -1.2144531001161199e+02 + 26 1.0987377306154728e+02 1.8142227934422800e+02 1.3660221691842844e+01 + 27 4.9787264831917881e+01 -2.1702378492861621e+02 8.7171908557180572e+01 + 28 -1.7608392920071728e+02 7.3301696261204825e+01 -1.1852448703331862e+02 + 29 1.2668890412943080e+02 1.4371750554744025e+02 3.1331418003647308e+01 +run_vdwl: 719.707466157291 +run_coul: 225.904237287566 run_stress: ! |2- - 2.1107536793307468e+03 2.1122379201857452e+03 4.3599324498565293e+03 -7.3409238214538516e+02 3.5359613445860141e+01 6.3752279062951925e+02 + 2.1107537188662236e+03 2.1122379542510184e+03 4.3599324983027345e+03 -7.3409237546545421e+02 3.5359612031240225e+01 6.3752276727918104e+02 run_forces: ! |2 - 1 -1.7610671323869674e+01 2.6644632319809125e+02 3.2393635185737048e+02 - 2 1.5276958689054419e+02 1.2310601845342437e+02 -1.8097797853205338e+02 - 3 -1.3352437924496681e+02 -3.7931520927920576e+02 -1.4290253280020417e+02 - 4 -7.9210454699422739e+00 2.1479068853687990e+00 -5.8262866027728446e+00 - 5 -3.0436142186020652e+00 -3.3598700412150313e+00 1.2037071546308955e+01 - 6 -8.0541518106738181e+02 9.1789632182348248e+02 1.0248061101238054e+03 - 7 5.5711025014807248e+01 -3.1035014369487737e+02 -1.5712639984017087e+03 - 8 1.3310087453577813e+02 -9.6225162152811720e+01 3.9090026703160601e+02 - 9 7.8393574070627366e+01 7.6654576853511799e+01 3.4092264679070774e+02 - 10 5.2097956066949666e+02 -5.9878732018277447e+02 -1.8147991237770523e+02 - 11 -3.2607667066270936e+00 -4.8312582714797552e+00 -1.0171800769012659e+01 - 12 2.0370356353863581e+01 1.0143689941206798e+01 -6.6267466555479961e+00 - 13 7.9794514497078781e+00 -3.1830746501709997e+00 -3.2644127587370575e-01 - 14 -4.4037331584323880e+00 1.0233682011991643e+00 -8.7298909905895190e+00 - 15 1.3154168744955988e-01 8.2984798374513744e+00 2.0213779317532383e+00 - 16 4.3411491239178514e+02 -3.1229545621436057e+02 -1.1118126613117161e+03 - 17 -4.2721103677584034e+02 3.0241089748456909e+02 1.1238250106811154e+03 - 18 3.0045457761221517e-01 4.7293875917389530e+00 -7.8044958131791784e+00 - 19 2.0270210763586318e+00 -7.0015059579377714e-01 5.5349995515760559e+00 - 20 -2.8986405349039099e+00 -3.9674896299813454e+00 4.0696696823518108e+00 - 21 -6.8658022402852936e+01 -7.5474151287218916e+01 2.1302465879802361e+02 - 22 -1.0464809690544206e+02 -2.6524463281118258e+01 -1.6069148016249562e+02 - 23 1.7288793881586659e+02 1.0241548772353890e+02 -5.1825425141802349e+01 - 24 3.6621512242007107e+01 -2.0125837141004371e+02 1.0765962820446694e+02 - 25 -1.4622310926571268e+02 2.0851692216922846e+01 -1.2215078336950006e+02 - 26 1.0903616825360248e+02 1.8015275208029206e+02 1.3874388664482883e+01 - 27 4.8836594023392919e+01 -2.1313610883088290e+02 8.5044672096502211e+01 - 28 -1.7278645223316221e+02 7.1874824697301463e+01 -1.1608941518893110e+02 - 29 1.2434417725483669e+02 1.4125650253383503e+02 3.1022996433022094e+01 + 1 -1.7610671215147516e+01 2.6644632521711065e+02 3.2393635216495608e+02 + 2 1.5276958690674471e+02 1.2310601849305402e+02 -1.8097797853684457e+02 + 3 -1.3352438109375441e+02 -3.7931520752883262e+02 -1.4290253169413955e+02 + 4 -7.9210457144807673e+00 2.1479067658962112e+00 -5.8262867707772656e+00 + 5 -3.0436146111746609e+00 -3.3598708486321578e+00 1.2037071927910159e+01 + 6 -8.0541518022246134e+02 9.1789632032195846e+02 1.0248061088552281e+03 + 7 5.5711018458020682e+01 -3.1035014038624917e+02 -1.5712640121585557e+03 + 8 1.3310087649542288e+02 -9.6225164941492508e+01 3.9090028139588929e+02 + 9 7.8393574096452653e+01 7.6654576917241798e+01 3.4092264700067278e+02 + 10 5.2097953975583994e+02 -5.9878733321714390e+02 -1.8147990705795451e+02 + 11 -3.2607666278858591e+00 -4.8312585741314322e+00 -1.0171801101420801e+01 + 12 2.0370378822259379e+01 1.0143707538480376e+01 -6.6267605135464889e+00 + 13 7.9794514942654207e+00 -3.1830746441047428e+00 -3.2644128910532161e-01 + 14 -4.4037331178676657e+00 1.0233682060578044e+00 -8.7298910570923951e+00 + 15 1.3154197296741404e-01 8.2984800089639776e+00 2.0213778453832680e+00 + 16 4.3411491585315781e+02 -3.1229546158366014e+02 -1.1118126563874712e+03 + 17 -4.2721103632201573e+02 3.0241089632715619e+02 1.1238250137043428e+03 + 18 3.0045467379022872e-01 4.7293877280888514e+00 -7.8044959748020570e+00 + 19 2.0270210691150932e+00 -7.0015060136201190e-01 5.5349995459560830e+00 + 20 -2.8986405261351393e+00 -3.9674896221724638e+00 4.0696696835467474e+00 + 21 -6.8658022376548189e+01 -7.5474151318419402e+01 2.1302465876840716e+02 + 22 -1.0464809690829846e+02 -2.6524463283005797e+01 -1.6069148016429543e+02 + 23 1.7288793881938844e+02 1.0241548772466190e+02 -5.1825425140716725e+01 + 24 3.6621512295722965e+01 -2.0125837138502857e+02 1.0765962828843737e+02 + 25 -1.4622310926187339e+02 2.0851692219024567e+01 -1.2215078335595025e+02 + 26 1.0903616826048172e+02 1.8015275208444928e+02 1.3874388668825373e+01 + 27 4.8836594003434030e+01 -2.1313610884810515e+02 8.5044672108300603e+01 + 28 -1.7278645223634851e+02 7.1874824696100561e+01 -1.1608941518998317e+02 + 29 1.2434417725692825e+02 1.4125650253409549e+02 3.1022996434798799e+01 ... diff --git a/unittest/force-styles/tests/mol-pair-lj_long_coul_off.yaml b/unittest/force-styles/tests/mol-pair-lj_long_coul_off.yaml index 25043b3ff8..b120893757 100644 --- a/unittest/force-styles/tests/mol-pair-lj_long_coul_off.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_long_coul_off.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:17 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:50 2021 epsilon: 2.5e-09 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_long_cut_coul_long.yaml b/unittest/force-styles/tests/mol-pair-lj_long_cut_coul_long.yaml index 64af0de1a7..ff512d3e09 100644 --- a/unittest/force-styles/tests/mol-pair-lj_long_cut_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_long_cut_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:17 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:51 2021 epsilon: 2.5e-09 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_long_cut_tip4p_long.yaml b/unittest/force-styles/tests/mol-pair-lj_long_cut_tip4p_long.yaml index 123706c3dc..9227228855 100644 --- a/unittest/force-styles/tests/mol-pair-lj_long_cut_tip4p_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_long_cut_tip4p_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:17 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:51 2021 epsilon: 2.5e-09 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_long_tip4p_long.yaml b/unittest/force-styles/tests/mol-pair-lj_long_tip4p_long.yaml index f4920d8699..a6572ed66c 100644 --- a/unittest/force-styles/tests/mol-pair-lj_long_tip4p_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_long_tip4p_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:17 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:51 2021 epsilon: 2.5e-09 prerequisites: ! | atom full @@ -35,72 +35,72 @@ extract: ! | typeA 0 typeB 0 natoms: 29 -init_vdwl: 584.670359070893 +init_vdwl: 584.670383161636 init_coul: 220.904555359383 init_stress: ! |2- - 1.4179907518567816e+03 1.6981521081440758e+03 3.8247897795492727e+03 -1.0685165979600738e+03 -2.2301723603317933e+02 7.0678975460957838e+02 + 1.4179908002675882e+03 1.6981521472771331e+03 3.8247898365498668e+03 -1.0685165973996445e+03 -2.2301723469314501e+02 7.0678972133134016e+02 init_forces: ! |2 - 1 1.3731384454971254e+02 3.9920027816333527e+02 1.4671535385944733e+02 + 1 1.3731384428493124e+02 3.9920027854840805e+02 1.4671535403601737e+02 2 -1.9557407939667784e-01 -2.8434279090485344e+00 -1.2037666274486341e+00 - 3 -1.4543663227279740e+02 -3.8854700219617757e+02 -1.3922266560344775e+02 + 3 -1.4543663403399540e+02 -3.8854700044105419e+02 -1.3922266457674954e+02 4 -7.9314978889013857e-02 1.6212643266693107e-02 -2.3663785465653561e-01 5 -5.4637120859630939e-01 6.5600989679059629e-01 -6.8980117595427104e-02 - 6 -8.3044669735263210e+02 9.6003930511175383e+02 1.1483694862004249e+03 - 7 5.8135902001138916e+01 -3.3519692557212892e+02 -1.7141558244033672e+03 - 8 2.2222306113041898e+02 -1.9487724475012371e+01 7.5254097093507573e+02 + 6 -8.3044669697571760e+02 9.6003930443804529e+02 1.1483694854778580e+03 + 7 5.8135895738828381e+01 -3.3519692236360072e+02 -1.7141558378818368e+03 + 8 2.2222305975187425e+02 -1.9487727502660320e+01 7.5254098660516138e+02 9 1.5618105874324246e+00 -5.8578891996706437e+00 1.3701350515471384e+00 - 10 5.2854811448198768e+02 -6.1591055679501983e+02 -1.9340281827813200e+02 + 10 5.2854808750532732e+02 -6.1591056046926769e+02 -1.9340282225226667e+02 11 -9.3766462457826905e-01 1.0563563299185068e+00 -5.5775022539970631e-01 - 12 2.4920320953166684e+01 1.6044685842922149e+01 -1.2382365264982791e+01 + 12 2.4920347090319872e+01 1.6044703403776545e+01 -1.2382381138510288e+01 13 -7.5720425159299595e-02 3.8772041103398963e-02 -1.8346431648817585e-01 14 -1.0557020156519512e+00 3.6717714938726143e-01 -1.0728817695848940e-01 15 3.5162907632314466e-01 -1.9165325094615621e-01 -1.0148660141104417e+00 - 16 4.6235899435670046e+02 -3.3129450503702833e+02 -1.1872104992473003e+03 - 17 -4.5562419635435378e+02 3.2174933490465634e+02 1.1991777262209341e+03 - 18 3.5327026427352259e-01 4.7616025960598627e+00 -7.8715619141435136e+00 + 16 4.6235900379292781e+02 -3.3129451959604160e+02 -1.1872104846434017e+03 + 17 -4.5562419584375363e+02 3.2174933377566850e+02 1.1991777288967187e+03 + 18 3.5327038190601634e-01 4.7616027705645072e+00 -7.8715620952516669e+00 19 1.9911596893384120e+00 -7.2195675725850206e-01 5.5334689749229105e+00 20 -2.9127135301570397e+00 -4.0021946638596519e+00 4.1375019377447915e+00 - 21 1.5193591883077349e+00 3.2144199030879488e+00 -6.7582252414360386e+00 + 21 1.5193592132463749e+00 3.2144198763444218e+00 -6.7582252673322518e+00 22 4.4657588078956723e+00 1.0585032152255676e+00 5.8268290139589860e+00 23 -6.2938601634201303e+00 -3.9616631352879410e+00 1.3192732707154482e+00 - 24 -1.0905447870604845e+00 6.8024490469623906e+00 -3.6841666676664224e+00 + 24 -1.0905447268336337e+00 6.8024490705444629e+00 -3.6841665762708744e+00 25 4.9746167445264264e+00 -5.2361422570157790e-01 3.9262159421100877e+00 26 -4.3769290854851999e+00 -6.4816134554785325e+00 -8.1534775153570904e-01 - 27 -1.5292288622987564e+00 7.3670370982215285e+00 -2.7248017460341405e+00 + 27 -1.5292288824966420e+00 7.3670370809055621e+00 -2.7248017347638211e+00 28 6.4035032875423159e+00 -2.1779017025677483e+00 4.1727109672631357e+00 29 -4.5201953782892055e+00 -5.1735155675050022e+00 -1.4886429234413563e+00 -run_vdwl: 557.056017138723 -run_coul: 220.913884393424 +run_vdwl: 557.056030477029 +run_coul: 220.91388439321 run_stress: ! |2- - 1.3775223471877366e+03 1.6566887898319319e+03 3.5747571933396416e+03 -1.0386782468208169e+03 -2.0694914366906673e+02 6.6732653084085644e+02 + 1.3775223750599193e+03 1.6566888200245039e+03 3.5747572154246241e+03 -1.0386782389667430e+03 -2.0694915325068987e+02 6.6732651501863484e+02 run_forces: ! |2 - 1 1.3484812659843513e+02 3.9092060800918989e+02 1.4373313137859998e+02 - 2 -2.0271633707648873e-01 -2.8298288761987318e+00 -1.1989313018491383e+00 - 3 -1.4342324899553293e+02 -3.7982436667370501e+02 -1.3597762688785588e+02 - 4 -8.2852639177138657e-02 1.8300393504026149e-02 -2.3762389449071866e-01 - 5 -5.4791673482209124e-01 6.5614563469546494e-01 -6.3941396753216292e-02 - 6 -8.0227486127425436e+02 9.1496525291694797e+02 1.0264249576311956e+03 - 7 5.5771543379925383e+01 -3.1037336716922317e+02 -1.5711704568990347e+03 - 8 2.0819248601410811e+02 -1.2101254710546570e+01 7.2875382950845608e+02 - 9 1.5634160487619546e+00 -5.8771942139639481e+00 1.3776856877372210e+00 - 10 5.1715704548744839e+02 -6.0329365711832054e+02 -1.9113877357061190e+02 - 11 -9.4002639920539743e-01 1.0582108303494102e+00 -5.6167252694801739e-01 - 12 2.4863919762583155e+01 1.6062852620618131e+01 -1.2360597545829215e+01 - 13 -7.5840697095099607e-02 4.0077788679094964e-02 -1.8559573885370806e-01 - 14 -1.0625298052267247e+00 3.6955553581650585e-01 -1.0916767712595477e-01 - 15 3.5311739865286279e-01 -1.9448880340077307e-01 -1.0191647907359309e+00 - 16 4.3394626492285823e+02 -3.1219926534478418e+02 -1.1116473917803178e+03 - 17 -4.2707030325761536e+02 3.0243865908364359e+02 1.1237993806924117e+03 - 18 3.0368395429039413e-01 4.7171895570379352e+00 -7.8295029342293025e+00 - 19 2.0270801847492161e+00 -6.9918333164961344e-01 5.5492247587141375e+00 - 20 -2.8995874776604742e+00 -3.9821844731531963e+00 4.0840163265138711e+00 - 21 1.5208456305724503e+00 3.1993262189952332e+00 -6.7421856947959524e+00 - 22 4.4874876087857585e+00 1.0719243021957119e+00 5.8233438927252603e+00 - 23 -6.3183698445588599e+00 -3.9593735948248070e+00 1.3084674471345548e+00 - 24 -1.1079755165485650e+00 6.8112748041127560e+00 -3.6957336981034130e+00 - 25 5.0093760593232943e+00 -5.0836369921098123e-01 3.9583976051674381e+00 - 26 -4.3931344945010125e+00 -6.5025659801859046e+00 -8.3304413261264720e-01 - 27 -1.5441431471578715e+00 7.3753658554767467e+00 -2.7159697179439259e+00 - 28 6.4199810218638094e+00 -2.1795392395617279e+00 4.1762085294330520e+00 - 29 -4.5208674519252963e+00 -5.1801103225337508e+00 -1.5012632699978348e+00 + 1 1.3484812617575406e+02 3.9092060908116656e+02 1.4373313186999439e+02 + 2 -2.0271633709568476e-01 -2.8298288761956423e+00 -1.1989313018422760e+00 + 3 -1.4342325174055713e+02 -3.7982436396313489e+02 -1.3597762518906373e+02 + 4 -8.2852639170312839e-02 1.8300393499842461e-02 -2.3762389449286375e-01 + 5 -5.4791673481254732e-01 6.5614563468856779e-01 -6.3941396758903993e-02 + 6 -8.0227485954791541e+02 9.1496525050525736e+02 1.0264249558300917e+03 + 7 5.5771542735465069e+01 -3.1037336726230455e+02 -1.5711704577668092e+03 + 8 2.0819248556765424e+02 -1.2101254281688147e+01 7.2875382923317329e+02 + 9 1.5634160486512318e+00 -5.8771942140939055e+00 1.3776856876345804e+00 + 10 5.1715702524063988e+02 -6.0329367024604721e+02 -1.9113876792726958e+02 + 11 -9.4002639917994568e-01 1.0582108302448794e+00 -5.6167252695046399e-01 + 12 2.4863938867166016e+01 1.6062869875084793e+01 -1.2360609625898560e+01 + 13 -7.5840697146929953e-02 4.0077788713113287e-02 -1.8559573885665315e-01 + 14 -1.0625298051164564e+00 3.6955553582007694e-01 -1.0916767715816915e-01 + 15 3.5311739874004949e-01 -1.9448880341844976e-01 -1.0191647907497523e+00 + 16 4.3394626801693568e+02 -3.1219927017642323e+02 -1.1116473874381600e+03 + 17 -4.2707030283376542e+02 3.0243865797177557e+02 1.1237993836385187e+03 + 18 3.0368404844222568e-01 4.7171896888581095e+00 -7.8295030918480828e+00 + 19 2.0270801847430087e+00 -6.9918333167659397e-01 5.5492247587169610e+00 + 20 -2.8995874776653414e+00 -3.9821844731834624e+00 4.0840163265257070e+00 + 21 1.5208456586487951e+00 3.1993261879629271e+00 -6.7421857269435987e+00 + 22 4.4874876087889790e+00 1.0719243022009861e+00 5.8233438927261929e+00 + 23 -6.3183698445659342e+00 -3.9593735948101023e+00 1.3084674471388333e+00 + 24 -1.1079754642593542e+00 6.8112748289396237e+00 -3.6957336164134316e+00 + 25 5.0093760593140946e+00 -5.0836369922018387e-01 3.9583976051551146e+00 + 26 -4.3931344945026183e+00 -6.5025659801902629e+00 -8.3304413261248733e-01 + 27 -1.5441431651250583e+00 7.3753658402581390e+00 -2.7159697072843967e+00 + 28 6.4199810218643059e+00 -2.1795392395603654e+00 4.1762085294336435e+00 + 29 -4.5208674519292567e+00 -5.1801103225235723e+00 -1.5012632699970143e+00 ... diff --git a/unittest/force-styles/tests/mol-pair-lj_mdf.yaml b/unittest/force-styles/tests/mol-pair-lj_mdf.yaml index 47f8b5ca0c..3dc4b08e81 100644 --- a/unittest/force-styles/tests/mol-pair-lj_mdf.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_mdf.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:17 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:52 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk.yaml b/unittest/force-styles/tests/mol-pair-lj_sdk.yaml index dbaf863ae4..6a705107fe 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_sdk.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:17 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:52 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_long.yaml b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_long.yaml index 53097bb236..52871422b1 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:17 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:52 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml index 8c3a199e3a..4df3f42891 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:18 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:52 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml index 6c97aa9d81..f9e55e3fea 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:18 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:52 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_table.yaml index 24ffccc296..914cd9077e 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:18 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:52 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_smooth.yaml b/unittest/force-styles/tests/mol-pair-lj_smooth.yaml index 0171513b43..ea17c7d5b0 100644 --- a/unittest/force-styles/tests/mol-pair-lj_smooth.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_smooth.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:18 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:52 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_smooth_linear.yaml b/unittest/force-styles/tests/mol-pair-lj_smooth_linear.yaml index ccd05990b4..1726804d29 100644 --- a/unittest/force-styles/tests/mol-pair-lj_smooth_linear.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_smooth_linear.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:18 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:53 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_table_coul_long.yaml b/unittest/force-styles/tests/mol-pair-lj_table_coul_long.yaml index a7be6a954d..9b2e520fb5 100644 --- a/unittest/force-styles/tests/mol-pair-lj_table_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_table_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:18 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:53 2021 epsilon: 2.5e-09 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_table_coul_off.yaml b/unittest/force-styles/tests/mol-pair-lj_table_coul_off.yaml index 22af7a5357..4f21995ed5 100644 --- a/unittest/force-styles/tests/mol-pair-lj_table_coul_off.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_table_coul_off.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:18 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:53 2021 epsilon: 2e-08 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_table_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_table_coul_table.yaml index d3cfee2672..d9c02422cb 100644 --- a/unittest/force-styles/tests/mol-pair-lj_table_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_table_coul_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:18 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:53 2021 epsilon: 2.5e-09 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_table_tip4p_long.yaml b/unittest/force-styles/tests/mol-pair-lj_table_tip4p_long.yaml index 8dc5a53716..7eab70a542 100644 --- a/unittest/force-styles/tests/mol-pair-lj_table_tip4p_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_table_tip4p_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:19 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:54 2021 epsilon: 2.5e-09 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-lj_table_tip4p_table.yaml b/unittest/force-styles/tests/mol-pair-lj_table_tip4p_table.yaml index 9ba1ea7802..8274c80cdc 100644 --- a/unittest/force-styles/tests/mol-pair-lj_table_tip4p_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_table_tip4p_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:19 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:54 2021 epsilon: 2.5e-09 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-mie_cut.yaml b/unittest/force-styles/tests/mol-pair-mie_cut.yaml index 286d201e38..ec36aa2349 100644 --- a/unittest/force-styles/tests/mol-pair-mie_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-mie_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:19 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:55 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-morse.yaml b/unittest/force-styles/tests/mol-pair-morse.yaml index 06449cec6d..12a2ab2132 100644 --- a/unittest/force-styles/tests/mol-pair-morse.yaml +++ b/unittest/force-styles/tests/mol-pair-morse.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:19 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:55 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-morse_smooth_linear.yaml b/unittest/force-styles/tests/mol-pair-morse_smooth_linear.yaml index e933b47a0b..a4264cef44 100644 --- a/unittest/force-styles/tests/mol-pair-morse_smooth_linear.yaml +++ b/unittest/force-styles/tests/mol-pair-morse_smooth_linear.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:19 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:55 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-morse_soft.yaml b/unittest/force-styles/tests/mol-pair-morse_soft.yaml index d57e3a155f..2c385f7a80 100644 --- a/unittest/force-styles/tests/mol-pair-morse_soft.yaml +++ b/unittest/force-styles/tests/mol-pair-morse_soft.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:19 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:55 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-nm_cut.yaml b/unittest/force-styles/tests/mol-pair-nm_cut.yaml index b05678514d..861a92dbdd 100644 --- a/unittest/force-styles/tests/mol-pair-nm_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-nm_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:19 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:55 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-nm_cut_coul_cut.yaml b/unittest/force-styles/tests/mol-pair-nm_cut_coul_cut.yaml index 0161426c61..1e8330ec06 100644 --- a/unittest/force-styles/tests/mol-pair-nm_cut_coul_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-nm_cut_coul_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:19 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:55 2021 epsilon: 5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-nm_cut_coul_long.yaml b/unittest/force-styles/tests/mol-pair-nm_cut_coul_long.yaml index e8739a7340..fc190d1aea 100644 --- a/unittest/force-styles/tests/mol-pair-nm_cut_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-nm_cut_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:19 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:55 2021 epsilon: 7.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-nm_cut_coul_table.yaml b/unittest/force-styles/tests/mol-pair-nm_cut_coul_table.yaml index 128309d349..adaa3904a2 100644 --- a/unittest/force-styles/tests/mol-pair-nm_cut_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-nm_cut_coul_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:20 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:56 2021 epsilon: 5e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-python_hybrid.yaml b/unittest/force-styles/tests/mol-pair-python_hybrid.yaml index 189a321fe9..663e3efa2d 100644 --- a/unittest/force-styles/tests/mol-pair-python_hybrid.yaml +++ b/unittest/force-styles/tests/mol-pair-python_hybrid.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:20 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:56 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-python_lj.yaml b/unittest/force-styles/tests/mol-pair-python_lj.yaml index 614741a0a2..ac4fcd9207 100644 --- a/unittest/force-styles/tests/mol-pair-python_lj.yaml +++ b/unittest/force-styles/tests/mol-pair-python_lj.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:20 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:56 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-soft.yaml b/unittest/force-styles/tests/mol-pair-soft.yaml index 7a8a5322ee..b9c049cc18 100644 --- a/unittest/force-styles/tests/mol-pair-soft.yaml +++ b/unittest/force-styles/tests/mol-pair-soft.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:20 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:56 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-table.yaml b/unittest/force-styles/tests/mol-pair-table.yaml index 8d70bac4ab..2d0ff80bd3 100644 --- a/unittest/force-styles/tests/mol-pair-table.yaml +++ b/unittest/force-styles/tests/mol-pair-table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:20 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:56 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-tip4p_cut.yaml b/unittest/force-styles/tests/mol-pair-tip4p_cut.yaml index 0394b0b363..8174c5b905 100644 --- a/unittest/force-styles/tests/mol-pair-tip4p_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-tip4p_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 21 Jul 2020 -date_generated: Thu Aug 6 16:52:44 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:57 2021 epsilon: 7.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-tip4p_long.yaml b/unittest/force-styles/tests/mol-pair-tip4p_long.yaml index 9ee6b51077..d09ccd2a68 100644 --- a/unittest/force-styles/tests/mol-pair-tip4p_long.yaml +++ b/unittest/force-styles/tests/mol-pair-tip4p_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:20 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:57 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-tip4p_long_soft.yaml b/unittest/force-styles/tests/mol-pair-tip4p_long_soft.yaml index 704294440f..88a80c7e19 100644 --- a/unittest/force-styles/tests/mol-pair-tip4p_long_soft.yaml +++ b/unittest/force-styles/tests/mol-pair-tip4p_long_soft.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:20 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:57 2021 epsilon: 1e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-tip4p_table.yaml b/unittest/force-styles/tests/mol-pair-tip4p_table.yaml index 24376bc9b3..1417873385 100644 --- a/unittest/force-styles/tests/mol-pair-tip4p_table.yaml +++ b/unittest/force-styles/tests/mol-pair-tip4p_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:20 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:57 2021 epsilon: 2.5e-13 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-ufm.yaml b/unittest/force-styles/tests/mol-pair-ufm.yaml index 494f1cb5b7..e94703032c 100644 --- a/unittest/force-styles/tests/mol-pair-ufm.yaml +++ b/unittest/force-styles/tests/mol-pair-ufm.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:20 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:57 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-wf_cut.yaml b/unittest/force-styles/tests/mol-pair-wf_cut.yaml index 359c6d7006..0b689fd219 100644 --- a/unittest/force-styles/tests/mol-pair-wf_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-wf_cut.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Dec 2020 -date_generated: Thu Jan 28 03:47:32 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:57 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-yukawa.yaml b/unittest/force-styles/tests/mol-pair-yukawa.yaml index 209afc79bd..9a0882a1ce 100644 --- a/unittest/force-styles/tests/mol-pair-yukawa.yaml +++ b/unittest/force-styles/tests/mol-pair-yukawa.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:20 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:57 2021 epsilon: 5e-14 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-zbl.yaml b/unittest/force-styles/tests/mol-pair-zbl.yaml index 465ae3059e..113072816e 100644 --- a/unittest/force-styles/tests/mol-pair-zbl.yaml +++ b/unittest/force-styles/tests/mol-pair-zbl.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:20 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:57 2021 epsilon: 1e-12 prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/mol-pair-zero.yaml b/unittest/force-styles/tests/mol-pair-zero.yaml index d243cab958..04bffa3b05 100644 --- a/unittest/force-styles/tests/mol-pair-zero.yaml +++ b/unittest/force-styles/tests/mol-pair-zero.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:21 202 +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:57 2021 epsilon: 1e-14 prerequisites: ! | atom full From f797d9cb2e4619167e354d2f0cce15e35fd479d5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 27 Feb 2021 10:36:38 -0500 Subject: [PATCH 0116/1217] must always set pair_modify table (and table/disp) explicitly for long-range styles --- unittest/force-styles/tests/mol-pair-buck_long_coul_long.yaml | 1 + unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml | 1 + unittest/force-styles/tests/mol-pair-lj_long_coul_long.yaml | 1 + unittest/force-styles/tests/mol-pair-lj_long_tip4p_long.yaml | 1 + 4 files changed, 4 insertions(+) diff --git a/unittest/force-styles/tests/mol-pair-buck_long_coul_long.yaml b/unittest/force-styles/tests/mol-pair-buck_long_coul_long.yaml index 14624b04e5..df11a0547c 100644 --- a/unittest/force-styles/tests/mol-pair-buck_long_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_long_coul_long.yaml @@ -9,6 +9,7 @@ prerequisites: ! | pre_commands: ! "" post_commands: ! | pair_modify table 0 + pair_modify table/disp 0 kspace_style ewald/disp 1.0e-6 kspace_modify gewald 0.3 kspace_modify compute no diff --git a/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml b/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml index c204dd600f..39fae48cb4 100644 --- a/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml @@ -9,6 +9,7 @@ prerequisites: ! | pre_commands: ! "" post_commands: ! | pair_modify table 16 + pair_modify table/disp 16 kspace_style ewald/disp 1.0e-6 kspace_modify gewald 0.3 kspace_modify compute no diff --git a/unittest/force-styles/tests/mol-pair-lj_long_coul_long.yaml b/unittest/force-styles/tests/mol-pair-lj_long_coul_long.yaml index 483d54a326..5c083caeac 100644 --- a/unittest/force-styles/tests/mol-pair-lj_long_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_long_coul_long.yaml @@ -10,6 +10,7 @@ pre_commands: ! "" post_commands: ! | pair_modify mix arithmetic pair_modify table 0 + pair_modify table/disp 0 kspace_style ewald/disp 1.0e-6 kspace_modify gewald 0.3 kspace_modify compute no diff --git a/unittest/force-styles/tests/mol-pair-lj_long_tip4p_long.yaml b/unittest/force-styles/tests/mol-pair-lj_long_tip4p_long.yaml index a6572ed66c..25ac675244 100644 --- a/unittest/force-styles/tests/mol-pair-lj_long_tip4p_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_long_tip4p_long.yaml @@ -12,6 +12,7 @@ pre_commands: ! | post_commands: ! | pair_modify mix arithmetic pair_modify table 0 + pair_modify table/disp 0 kspace_style pppm/disp/tip4p 1.0e-5 kspace_modify gewald 0.3 kspace_modify force/disp/real 0.001 From a6f32e472dbc97c01a534c081f2662fbb95f7f4b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 27 Feb 2021 10:39:03 -0500 Subject: [PATCH 0117/1217] add explanation why we set pair_modify table only in the lammps_init() --- unittest/force-styles/test_pair_style.cpp | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index 4e1ad8d0e3..f25923a01b 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -123,6 +123,11 @@ LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool new for (auto &pair_coeff : cfg.pair_coeff) { command("pair_coeff " + pair_coeff); } + + // set this here explicitly to a setting different + // from the default, so we can spot YAML files for + // long-range interactions that do not include these + // settings. they will fail after restart or read data. command("pair_modify table 0"); command("pair_modify table/disp 0"); From 121774dde33924fcf8c3350d4ba8359d770fe980 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 27 Feb 2021 10:58:04 -0500 Subject: [PATCH 0118/1217] adjust epsilon for one test --- unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml b/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml index 39fae48cb4..643786eb0d 100644 --- a/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:41 2021 -epsilon: 2e-09 +epsilon: 8e-07 prerequisites: ! | atom full pair buck/long/coul/long From dfeee1f19be3c6ac3d86401acead974d1beafb9c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 27 Feb 2021 15:42:32 -0500 Subject: [PATCH 0119/1217] run neighbor list on CPU for hybrid pair styles --- unittest/force-styles/test_pair_style.cpp | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index f25923a01b..61815ec5f4 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -814,10 +814,17 @@ TEST(PairStyle, omp) TEST(PairStyle, gpu) { if (!LAMMPS::is_installed_pkg("GPU")) GTEST_SKIP(); - const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf", "gpu"}; + const char *args_neigh[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf", "gpu"}; + const char *args_noneigh[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf", "gpu", "-pk", "gpu", "0", "neigh", "no"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); + char **argv = (char **)args_neigh; + int argc = sizeof(args_neigh) / sizeof(char *); + + // cannot use GPU neighbor list with hybrid pair style (yet) + if (test_config.pair_style.substr(0, 6) == "hybrid") { + argv = (char **)args_noneigh; + argc = sizeof(args_noneigh) / sizeof(char *); + } ::testing::internal::CaptureStdout(); LAMMPS *lmp = init_lammps(argc, argv, test_config, false); From 74713be4a26ab2123f6e79f4fd27989c6c0a9161 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Mar 2021 18:44:30 -0500 Subject: [PATCH 0120/1217] add new key to YAML files: skip_tests --- unittest/force-styles/test_angle_style.cpp | 14 ++++++++++++ unittest/force-styles/test_bond_style.cpp | 16 ++++++++++++++ unittest/force-styles/test_config.h | 3 +++ unittest/force-styles/test_config_reader.cpp | 11 ++++++++++ unittest/force-styles/test_config_reader.h | 1 + unittest/force-styles/test_dihedral_style.cpp | 4 ++++ unittest/force-styles/test_fix_timestep.cpp | 12 ++++++++++ unittest/force-styles/test_improper_style.cpp | 12 ++++++++++ unittest/force-styles/test_pair_style.cpp | 22 +++++++++++++++++++ 9 files changed, 95 insertions(+) diff --git a/unittest/force-styles/test_angle_style.cpp b/unittest/force-styles/test_angle_style.cpp index bf5cb34e7f..ff391127bd 100644 --- a/unittest/force-styles/test_angle_style.cpp +++ b/unittest/force-styles/test_angle_style.cpp @@ -246,6 +246,14 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // epsilon writer.emit("epsilon", config.epsilon); + // skip tests + block.clear(); + for (auto &skip_tests : config.skip_tests) { + if (block.empty()) block = skip_tests; + else block += " " + skip_tests; + } + writer.emit("skip_tests", block); + // prerequisites block.clear(); for (auto &prerequisite : config.prerequisites) { @@ -341,6 +349,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) TEST(AngleStyle, plain) { + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; @@ -567,6 +577,8 @@ TEST(AngleStyle, plain) TEST(AngleStyle, omp) { if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite", "-pk", "omp", "4", "-sf", "omp"}; @@ -740,6 +752,8 @@ TEST(AngleStyle, omp) TEST(AngleStyle, single) { + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; diff --git a/unittest/force-styles/test_bond_style.cpp b/unittest/force-styles/test_bond_style.cpp index d6a6e9c82d..94d2344c03 100644 --- a/unittest/force-styles/test_bond_style.cpp +++ b/unittest/force-styles/test_bond_style.cpp @@ -246,6 +246,14 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // epsilon writer.emit("epsilon", config.epsilon); + // skip tests + block.clear(); + for (auto &skip_tests : config.skip_tests) { + if (block.empty()) block = skip_tests; + else block += " " + skip_tests; + } + writer.emit("skip_tests", block); + // prerequisites block.clear(); for (auto &prerequisite : config.prerequisites) { @@ -341,6 +349,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) TEST(BondStyle, plain) { + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; @@ -567,6 +577,8 @@ TEST(BondStyle, plain) TEST(BondStyle, omp) { if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite", "-pk", "omp", "4", "-sf", "omp"}; @@ -739,6 +751,8 @@ TEST(BondStyle, omp) TEST(BondStyle, single) { + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; @@ -995,6 +1009,8 @@ TEST(BondStyle, single) TEST(BondStyle, extract) { + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; diff --git a/unittest/force-styles/test_config.h b/unittest/force-styles/test_config.h index baf3a5f29a..0417b306cb 100644 --- a/unittest/force-styles/test_config.h +++ b/unittest/force-styles/test_config.h @@ -14,6 +14,7 @@ #ifndef TEST_CONFIG_H #define TEST_CONFIG_H +#include #include #include #include @@ -32,6 +33,7 @@ public: std::string date_generated; std::string basename; double epsilon; + std::set skip_tests; std::vector> prerequisites; std::vector pre_commands; std::vector post_commands; @@ -74,6 +76,7 @@ public: init_vdwl(0), run_vdwl(0), init_coul(0), run_coul(0), init_stress({0, 0, 0, 0, 0, 0}), run_stress({0, 0, 0, 0, 0, 0}), global_scalar(0) { + skip_tests.clear(); prerequisites.clear(); pre_commands.clear(); post_commands.clear(); diff --git a/unittest/force-styles/test_config_reader.cpp b/unittest/force-styles/test_config_reader.cpp index 4ef3692f56..ed7ddf50a1 100644 --- a/unittest/force-styles/test_config_reader.cpp +++ b/unittest/force-styles/test_config_reader.cpp @@ -15,6 +15,7 @@ #include "test_config.h" #include "yaml.h" #include "yaml_reader.h" +#include "utils.h" #include #include @@ -25,11 +26,14 @@ #include #include +using LAMMPS_NS::utils::split_words; + TestConfigReader::TestConfigReader(TestConfig &config) : YamlReader(), config(config) { consumers["lammps_version"] = &TestConfigReader::lammps_version; consumers["date_generated"] = &TestConfigReader::date_generated; consumers["epsilon"] = &TestConfigReader::epsilon; + consumers["skip_tests"] = &TestConfigReader::skip_tests; consumers["prerequisites"] = &TestConfigReader::prerequisites; consumers["pre_commands"] = &TestConfigReader::pre_commands; consumers["post_commands"] = &TestConfigReader::post_commands; @@ -66,6 +70,13 @@ TestConfigReader::TestConfigReader(TestConfig &config) : YamlReader(), config(co consumers["equilibrium"] = &TestConfigReader::equilibrium; } +void TestConfigReader::skip_tests(const yaml_event_t &event) +{ + config.skip_tests.clear(); + for (auto &word : split_words((char *)event.data.scalar.value)) + config.skip_tests.insert(word); +} + void TestConfigReader::prerequisites(const yaml_event_t &event) { config.prerequisites.clear(); diff --git a/unittest/force-styles/test_config_reader.h b/unittest/force-styles/test_config_reader.h index 840228da3a..f82a2b7a15 100644 --- a/unittest/force-styles/test_config_reader.h +++ b/unittest/force-styles/test_config_reader.h @@ -23,6 +23,7 @@ class TestConfigReader : public YamlReader { public: TestConfigReader(TestConfig &config); + void skip_tests(const yaml_event_t &event); void prerequisites(const yaml_event_t &event); void pre_commands(const yaml_event_t &event); void post_commands(const yaml_event_t &event); diff --git a/unittest/force-styles/test_dihedral_style.cpp b/unittest/force-styles/test_dihedral_style.cpp index a27c50afb7..f8ad0a60eb 100644 --- a/unittest/force-styles/test_dihedral_style.cpp +++ b/unittest/force-styles/test_dihedral_style.cpp @@ -344,6 +344,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) TEST(DihedralStyle, plain) { + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"DihedralStyle", "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; @@ -570,6 +572,8 @@ TEST(DihedralStyle, plain) TEST(DihedralStyle, omp) { if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"DihedralStyle", "-log", "none", "-echo", "screen", "-nocite", "-pk", "omp", "4", "-sf", "omp"}; diff --git a/unittest/force-styles/test_fix_timestep.cpp b/unittest/force-styles/test_fix_timestep.cpp index 2680367c88..3fa2e78813 100644 --- a/unittest/force-styles/test_fix_timestep.cpp +++ b/unittest/force-styles/test_fix_timestep.cpp @@ -204,6 +204,14 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // epsilon writer.emit("epsilon", config.epsilon); + // skip tests + block.clear(); + for (auto &skip_tests : config.skip_tests) { + if (block.empty()) block = skip_tests; + else block += " " + skip_tests; + } + writer.emit("skip_tests", block); + // prerequisites block.clear(); for (auto &prerequisite : config.prerequisites) { @@ -287,6 +295,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) TEST(FixTimestep, plain) { if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"FixTimestep", "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; @@ -729,6 +739,8 @@ TEST(FixTimestep, omp) { if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"FixTimestep", "-log", "none", "-echo", "screen", "-nocite", "-pk", "omp", "4", "-sf", "omp"}; diff --git a/unittest/force-styles/test_improper_style.cpp b/unittest/force-styles/test_improper_style.cpp index b13b571546..9e38c03cd1 100644 --- a/unittest/force-styles/test_improper_style.cpp +++ b/unittest/force-styles/test_improper_style.cpp @@ -246,6 +246,14 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // epsilon writer.emit("epsilon", config.epsilon); + // skip tests + block.clear(); + for (auto &skip_tests : config.skip_tests) { + if (block.empty()) block = skip_tests; + else block += " " + skip_tests; + } + writer.emit("skip_tests", block); + // prerequisites block.clear(); for (auto &prerequisite : config.prerequisites) { @@ -335,6 +343,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) TEST(ImproperStyle, plain) { + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"ImproperStyle", "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; @@ -561,6 +571,8 @@ TEST(ImproperStyle, plain) TEST(ImproperStyle, omp) { if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"ImproperStyle", "-log", "none", "-echo", "screen", "-nocite", "-pk", "omp", "4", "-sf", "omp"}; diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index 61815ec5f4..0e61bacfbd 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -255,6 +255,14 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // epsilon writer.emit("epsilon", config.epsilon); + // skip tests + block.clear(); + for (auto &skip_tests : config.skip_tests) { + if (block.empty()) block = skip_tests; + else block += " " + skip_tests; + } + writer.emit("skip_tests", block); + // prerequisites block.clear(); for (auto &prerequisite : config.prerequisites) { @@ -350,6 +358,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) TEST(PairStyle, plain) { + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; @@ -632,6 +642,8 @@ TEST(PairStyle, plain) TEST(PairStyle, omp) { if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-pk", "omp", "4", "-sf", "omp"}; @@ -814,6 +826,8 @@ TEST(PairStyle, omp) TEST(PairStyle, gpu) { if (!LAMMPS::is_installed_pkg("GPU")) GTEST_SKIP(); + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args_neigh[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf", "gpu"}; const char *args_noneigh[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf", "gpu", "-pk", "gpu", "0", "neigh", "no"}; @@ -933,6 +947,8 @@ TEST(PairStyle, gpu) TEST(PairStyle, intel) { if (!LAMMPS::is_installed_pkg("USER-INTEL")) GTEST_SKIP(); + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-pk", "intel", "0", "mode", "double", "omp", "4", "lrt", "no", "-sf", "intel"}; @@ -1073,6 +1089,8 @@ TEST(PairStyle, intel) TEST(PairStyle, opt) { if (!LAMMPS::is_installed_pkg("OPT")) GTEST_SKIP(); + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf", "opt"}; char **argv = (char **)args; @@ -1178,6 +1196,8 @@ TEST(PairStyle, opt) TEST(PairStyle, single) { + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; @@ -1435,6 +1455,8 @@ TEST(PairStyle, single) TEST(PairStyle, extract) { + if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); + const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; From 205b45423c205f76399036bd3e695d21432d8d5e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Mar 2021 20:07:19 -0500 Subject: [PATCH 0121/1217] combine repetitive code into convenience function --- unittest/force-styles/test_angle_style.cpp | 45 +--------------- unittest/force-styles/test_bond_style.cpp | 45 +--------------- unittest/force-styles/test_dihedral_style.cpp | 37 +------------ unittest/force-styles/test_fix_timestep.cpp | 45 +--------------- unittest/force-styles/test_improper_style.cpp | 45 +--------------- unittest/force-styles/test_main.cpp | 52 +++++++++++++++++++ unittest/force-styles/test_main.h | 9 +++- unittest/force-styles/test_pair_style.cpp | 45 +--------------- 8 files changed, 71 insertions(+), 252 deletions(-) diff --git a/unittest/force-styles/test_angle_style.cpp b/unittest/force-styles/test_angle_style.cpp index ff391127bd..05646a93a9 100644 --- a/unittest/force-styles/test_angle_style.cpp +++ b/unittest/force-styles/test_angle_style.cpp @@ -38,7 +38,6 @@ #include #include #include -#include #include #include @@ -235,48 +234,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) YamlWriter writer(outfile); - // lammps_version - writer.emit("lammps_version", lmp->version); - - // date_generated - std::time_t now = time(NULL); - block = utils::trim(ctime(&now)); - writer.emit("date_generated", block); - - // epsilon - writer.emit("epsilon", config.epsilon); - - // skip tests - block.clear(); - for (auto &skip_tests : config.skip_tests) { - if (block.empty()) block = skip_tests; - else block += " " + skip_tests; - } - writer.emit("skip_tests", block); - - // prerequisites - block.clear(); - for (auto &prerequisite : config.prerequisites) { - block += prerequisite.first + " " + prerequisite.second + "\n"; - } - writer.emit_block("prerequisites", block); - - // pre_commands - block.clear(); - for (auto &command : config.pre_commands) { - block += command + "\n"; - } - writer.emit_block("pre_commands", block); - - // post_commands - block.clear(); - for (auto &command : config.post_commands) { - block += command + "\n"; - } - writer.emit_block("post_commands", block); - - // input_file - writer.emit("input_file", config.input_file); + // write yaml header + write_yaml_header(&writer, &test_config, lmp->version); // angle_style writer.emit("angle_style", config.angle_style); diff --git a/unittest/force-styles/test_bond_style.cpp b/unittest/force-styles/test_bond_style.cpp index 94d2344c03..f3aab53b12 100644 --- a/unittest/force-styles/test_bond_style.cpp +++ b/unittest/force-styles/test_bond_style.cpp @@ -38,7 +38,6 @@ #include #include #include -#include #include #include @@ -235,48 +234,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) YamlWriter writer(outfile); - // lammps_version - writer.emit("lammps_version", lmp->version); - - // date_generated - std::time_t now = time(NULL); - block = utils::trim(ctime(&now)); - writer.emit("date_generated", block); - - // epsilon - writer.emit("epsilon", config.epsilon); - - // skip tests - block.clear(); - for (auto &skip_tests : config.skip_tests) { - if (block.empty()) block = skip_tests; - else block += " " + skip_tests; - } - writer.emit("skip_tests", block); - - // prerequisites - block.clear(); - for (auto &prerequisite : config.prerequisites) { - block += prerequisite.first + " " + prerequisite.second + "\n"; - } - writer.emit_block("prerequisites", block); - - // pre_commands - block.clear(); - for (auto &command : config.pre_commands) { - block += command + "\n"; - } - writer.emit_block("pre_commands", block); - - // post_commands - block.clear(); - for (auto &command : config.post_commands) { - block += command + "\n"; - } - writer.emit_block("post_commands", block); - - // input_file - writer.emit("input_file", config.input_file); + // write yaml header + write_yaml_header(&writer, &test_config, lmp->version); // bond_style writer.emit("bond_style", config.bond_style); diff --git a/unittest/force-styles/test_dihedral_style.cpp b/unittest/force-styles/test_dihedral_style.cpp index f8ad0a60eb..95f64d7896 100644 --- a/unittest/force-styles/test_dihedral_style.cpp +++ b/unittest/force-styles/test_dihedral_style.cpp @@ -38,7 +38,6 @@ #include #include #include -#include #include #include @@ -244,40 +243,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) YamlWriter writer(outfile); - // lammps_version - writer.emit("lammps_version", lmp->version); - - // date_generated - std::time_t now = time(NULL); - block = utils::trim(ctime(&now)); - writer.emit("date_generated", block); - - // epsilon - writer.emit("epsilon", config.epsilon); - - // prerequisites - block.clear(); - for (auto &prerequisite : config.prerequisites) { - block += prerequisite.first + " " + prerequisite.second + "\n"; - } - writer.emit_block("prerequisites", block); - - // pre_commands - block.clear(); - for (auto &command : config.pre_commands) { - block += command + "\n"; - } - writer.emit_block("pre_commands", block); - - // post_commands - block.clear(); - for (auto &command : config.post_commands) { - block += command + "\n"; - } - writer.emit_block("post_commands", block); - - // input_file - writer.emit("input_file", config.input_file); + // write yaml header + write_yaml_header(&writer, &test_config, lmp->version); // dihedral_style writer.emit("dihedral_style", config.dihedral_style); diff --git a/unittest/force-styles/test_fix_timestep.cpp b/unittest/force-styles/test_fix_timestep.cpp index 3fa2e78813..6ba3f7f6d7 100644 --- a/unittest/force-styles/test_fix_timestep.cpp +++ b/unittest/force-styles/test_fix_timestep.cpp @@ -42,7 +42,6 @@ #include #include #include -#include #include #include @@ -193,48 +192,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) std::string block(""); YamlWriter writer(outfile); - // lammps_version - writer.emit("lammps_version", lmp->version); - - // date_generated - std::time_t now = time(NULL); - block = utils::trim(ctime(&now)); - writer.emit("date_generated", block); - - // epsilon - writer.emit("epsilon", config.epsilon); - - // skip tests - block.clear(); - for (auto &skip_tests : config.skip_tests) { - if (block.empty()) block = skip_tests; - else block += " " + skip_tests; - } - writer.emit("skip_tests", block); - - // prerequisites - block.clear(); - for (auto &prerequisite : config.prerequisites) { - block += prerequisite.first + " " + prerequisite.second + "\n"; - } - writer.emit_block("prerequisites", block); - - // pre_commands - block.clear(); - for (auto &command : config.pre_commands) { - block += command + "\n"; - } - writer.emit_block("pre_commands", block); - - // post_commands - block.clear(); - for (auto &command : config.post_commands) { - block += command + "\n"; - } - writer.emit_block("post_commands", block); - - // input_file - writer.emit("input_file", config.input_file); + // write yaml header + write_yaml_header(&writer, &test_config, lmp->version); // natoms writer.emit("natoms", natoms); diff --git a/unittest/force-styles/test_improper_style.cpp b/unittest/force-styles/test_improper_style.cpp index 9e38c03cd1..2e61a1e0cb 100644 --- a/unittest/force-styles/test_improper_style.cpp +++ b/unittest/force-styles/test_improper_style.cpp @@ -38,7 +38,6 @@ #include #include #include -#include #include #include @@ -235,48 +234,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) YamlWriter writer(outfile); - // lammps_version - writer.emit("lammps_version", lmp->version); - - // date_generated - std::time_t now = time(NULL); - block = utils::trim(ctime(&now)); - writer.emit("date_generated", block); - - // epsilon - writer.emit("epsilon", config.epsilon); - - // skip tests - block.clear(); - for (auto &skip_tests : config.skip_tests) { - if (block.empty()) block = skip_tests; - else block += " " + skip_tests; - } - writer.emit("skip_tests", block); - - // prerequisites - block.clear(); - for (auto &prerequisite : config.prerequisites) { - block += prerequisite.first + " " + prerequisite.second + "\n"; - } - writer.emit_block("prerequisites", block); - - // pre_commands - block.clear(); - for (auto &command : config.pre_commands) { - block += command + "\n"; - } - writer.emit_block("pre_commands", block); - - // post_commands - block.clear(); - for (auto &command : config.post_commands) { - block += command + "\n"; - } - writer.emit_block("post_commands", block); - - // input_file - writer.emit("input_file", config.input_file); + // write yaml header + write_yaml_header(&writer, &test_config, lmp->version); // improper_style writer.emit("improper_style", config.improper_style); diff --git a/unittest/force-styles/test_main.cpp b/unittest/force-styles/test_main.cpp index 69a2b96822..e26eb6a8fb 100644 --- a/unittest/force-styles/test_main.cpp +++ b/unittest/force-styles/test_main.cpp @@ -16,16 +16,19 @@ #include "test_config.h" #include "test_config_reader.h" #include "utils.h" +#include "yaml_writer.h" #include "gmock/gmock.h" #include "gtest/gtest.h" #include #include +#include #include #include #include using LAMMPS_NS::utils::split_words; +using LAMMPS_NS::utils::trim; // common read_yaml_file function bool read_yaml_file(const char *infile, TestConfig &config) @@ -37,6 +40,55 @@ bool read_yaml_file(const char *infile, TestConfig &config) return true; } +// write out common header items for yaml files +void write_yaml_header(YamlWriter *writer, + TestConfig *cfg, + const char *version) +{ + // lammps_version + writer->emit("lammps_version", version); + + // date_generated + std::time_t now = time(NULL); + std::string block = trim(ctime(&now)); + writer->emit("date_generated", block); + + // epsilon + writer->emit("epsilon", cfg->epsilon); + + // skip tests + block.clear(); + for (auto &skip : cfg->skip_tests) { + if (block.empty()) block = skip; + else block += " " + skip; + } + writer->emit("skip_tests", block); + + // prerequisites + block.clear(); + for (auto &prerequisite : cfg->prerequisites) { + block += prerequisite.first + " " + prerequisite.second + "\n"; + } + writer->emit_block("prerequisites", block); + + // pre_commands + block.clear(); + for (auto &command : cfg->pre_commands) { + block += command + "\n"; + } + writer->emit_block("pre_commands", block); + + // post_commands + block.clear(); + for (auto &command : cfg->post_commands) { + block += command + "\n"; + } + writer->emit_block("post_commands", block); + + // input_file + writer->emit("input_file", cfg->input_file); +} + // need to be defined in unit test body extern void generate_yaml_file(const char *, const TestConfig &); diff --git a/unittest/force-styles/test_main.h b/unittest/force-styles/test_main.h index ee0be2a637..0f30467f6b 100644 --- a/unittest/force-styles/test_main.h +++ b/unittest/force-styles/test_main.h @@ -22,6 +22,10 @@ extern bool print_stats; extern bool verbose; extern std::string INPUT_FOLDER; +// convenience method to write out common entries +void write_yaml_header(class YamlWriter *writer, TestConfig *cfg, + const char *version); + #define EXPECT_FP_LE_WITH_EPS(val1, val2, eps) \ do { \ const double diff = fabs(val1 - val2); \ @@ -31,10 +35,11 @@ extern std::string INPUT_FOLDER; EXPECT_PRED_FORMAT2(::testing::DoubleLE, err, eps); \ } while (0); -#endif - #if defined _WIN32 static const char PATH_SEP = '\\'; #else static const char PATH_SEP = '/'; #endif + +#endif + diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index 0e61bacfbd..6a99fb72cd 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -40,7 +40,6 @@ #include #include #include -#include #include #include @@ -244,48 +243,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) YamlWriter writer(outfile); - // lammps_version - writer.emit("lammps_version", lmp->version); - - // date_generated - std::time_t now = time(NULL); - block = utils::trim(ctime(&now)); - writer.emit("date_generated", block); - - // epsilon - writer.emit("epsilon", config.epsilon); - - // skip tests - block.clear(); - for (auto &skip_tests : config.skip_tests) { - if (block.empty()) block = skip_tests; - else block += " " + skip_tests; - } - writer.emit("skip_tests", block); - - // prerequisites - block.clear(); - for (auto &prerequisite : config.prerequisites) { - block += prerequisite.first + " " + prerequisite.second + "\n"; - } - writer.emit_block("prerequisites", block); - - // pre_commands - block.clear(); - for (auto &command : config.pre_commands) { - block += command + "\n"; - } - writer.emit_block("pre_commands", block); - - // post_commands - block.clear(); - for (auto &command : config.post_commands) { - block += command + "\n"; - } - writer.emit_block("post_commands", block); - - // input_file - writer.emit("input_file", config.input_file); + // write yaml header + write_yaml_header(&writer, &test_config, lmp->version); // pair_style writer.emit("pair_style", config.pair_style); From 5629947d89065b2ac4015457e9a3c6d271a8f81b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Mar 2021 21:43:38 -0500 Subject: [PATCH 0122/1217] add skip test entries for tests failing to run for GPU or USER-INTEL --- unittest/force-styles/tests/kspace-pppm_ad.yaml | 1 + unittest/force-styles/tests/kspace-pppm_disp.yaml | 1 + unittest/force-styles/tests/kspace-pppm_disp_ad.yaml | 1 + unittest/force-styles/tests/kspace-pppm_disp_ad_only.yaml | 1 + unittest/force-styles/tests/kspace-pppm_disp_only.yaml | 1 + unittest/force-styles/tests/kspace-pppm_disp_tip4p.yaml | 1 + unittest/force-styles/tests/manybody-pair-rebo.yaml | 1 + .../force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml | 1 + unittest/force-styles/tests/manybody-pair-tersoff_mod_shift.yaml | 1 + unittest/force-styles/tests/manybody-pair-tersoff_shift.yaml | 1 + unittest/force-styles/tests/manybody-pair-tersoff_zbl_shift.yaml | 1 + unittest/force-styles/tests/mol-pair-dpd.yaml | 1 + unittest/force-styles/tests/mol-pair-dpd_tstat.yaml | 1 + unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml | 1 + unittest/force-styles/tests/mol-pair-hybrid.yaml | 1 + unittest/force-styles/tests/mol-pair-lj_class2.yaml | 1 + 16 files changed, 16 insertions(+) diff --git a/unittest/force-styles/tests/kspace-pppm_ad.yaml b/unittest/force-styles/tests/kspace-pppm_ad.yaml index 3f77eb99c5..5eb711c089 100644 --- a/unittest/force-styles/tests/kspace-pppm_ad.yaml +++ b/unittest/force-styles/tests/kspace-pppm_ad.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:29 2021 epsilon: 7.5e-14 +skip_tests: gpu prerequisites: ! | atom full pair coul/long diff --git a/unittest/force-styles/tests/kspace-pppm_disp.yaml b/unittest/force-styles/tests/kspace-pppm_disp.yaml index 8c528baf76..e7693c8980 100644 --- a/unittest/force-styles/tests/kspace-pppm_disp.yaml +++ b/unittest/force-styles/tests/kspace-pppm_disp.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:30 2021 epsilon: 2.5e-13 +skip_tests: intel prerequisites: ! | atom full pair lj/long/coul/long diff --git a/unittest/force-styles/tests/kspace-pppm_disp_ad.yaml b/unittest/force-styles/tests/kspace-pppm_disp_ad.yaml index 4ef71d7333..11285b1a23 100644 --- a/unittest/force-styles/tests/kspace-pppm_disp_ad.yaml +++ b/unittest/force-styles/tests/kspace-pppm_disp_ad.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:31 2021 epsilon: 2.5e-13 +skip_tests: intel prerequisites: ! | atom full pair lj/long/coul/long diff --git a/unittest/force-styles/tests/kspace-pppm_disp_ad_only.yaml b/unittest/force-styles/tests/kspace-pppm_disp_ad_only.yaml index 203eceb209..81380966d8 100644 --- a/unittest/force-styles/tests/kspace-pppm_disp_ad_only.yaml +++ b/unittest/force-styles/tests/kspace-pppm_disp_ad_only.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:31 2021 epsilon: 2.5e-13 +skip_tests: intel prerequisites: ! | atom full pair lj/long/coul/long diff --git a/unittest/force-styles/tests/kspace-pppm_disp_only.yaml b/unittest/force-styles/tests/kspace-pppm_disp_only.yaml index f0243c8da1..3450805f27 100644 --- a/unittest/force-styles/tests/kspace-pppm_disp_only.yaml +++ b/unittest/force-styles/tests/kspace-pppm_disp_only.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:31 2021 epsilon: 2.5e-13 +skip_tests: intel prerequisites: ! | atom full pair lj/long/coul/long diff --git a/unittest/force-styles/tests/kspace-pppm_disp_tip4p.yaml b/unittest/force-styles/tests/kspace-pppm_disp_tip4p.yaml index 79951aab2f..047a623995 100644 --- a/unittest/force-styles/tests/kspace-pppm_disp_tip4p.yaml +++ b/unittest/force-styles/tests/kspace-pppm_disp_tip4p.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:32 2021 epsilon: 2.5e-13 +skip_tests: intel prerequisites: ! | atom full pair lj/long/tip4p/long diff --git a/unittest/force-styles/tests/manybody-pair-rebo.yaml b/unittest/force-styles/tests/manybody-pair-rebo.yaml index cba66272c3..2e07aad8d6 100644 --- a/unittest/force-styles/tests/manybody-pair-rebo.yaml +++ b/unittest/force-styles/tests/manybody-pair-rebo.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:18 2021 epsilon: 1e-07 +skip_tests: intel prerequisites: ! | pair rebo pre_commands: ! | diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml index eec7384351..a630f67ef8 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:20 2021 epsilon: 1e-12 +skip_tests: intel prerequisites: ! | pair tersoff/mod/c pre_commands: ! | diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_mod_shift.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_mod_shift.yaml index e40ac3548b..a9390a4fd3 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_mod_shift.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_mod_shift.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:20 2021 epsilon: 5e-11 +skip_tests: gpu intel prerequisites: ! | pair tersoff/mod pre_commands: ! | diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_shift.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_shift.yaml index 9676fe954b..9808d348a7 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_shift.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_shift.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:20 2021 epsilon: 5e-13 +skip_tests: gpu intel prerequisites: ! | pair tersoff pre_commands: ! | diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_zbl_shift.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_zbl_shift.yaml index 7dda923362..69b63cf259 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_zbl_shift.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_zbl_shift.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:21 2021 epsilon: 5e-11 +skip_tests: gpu intel prerequisites: ! | pair tersoff/zbl pre_commands: ! | diff --git a/unittest/force-styles/tests/mol-pair-dpd.yaml b/unittest/force-styles/tests/mol-pair-dpd.yaml index 13e9c1b776..4964a74e2a 100644 --- a/unittest/force-styles/tests/mol-pair-dpd.yaml +++ b/unittest/force-styles/tests/mol-pair-dpd.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:44 2021 epsilon: 5e-14 +skip_tests: gpu intel prerequisites: ! | atom full pair dpd diff --git a/unittest/force-styles/tests/mol-pair-dpd_tstat.yaml b/unittest/force-styles/tests/mol-pair-dpd_tstat.yaml index d43ac13ba0..0348c0d601 100644 --- a/unittest/force-styles/tests/mol-pair-dpd_tstat.yaml +++ b/unittest/force-styles/tests/mol-pair-dpd_tstat.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:44 2021 epsilon: 5e-14 +skip_tests: gpu intel prerequisites: ! | atom full pair dpd/tstat diff --git a/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml b/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml index a264411788..0967d5727b 100644 --- a/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml +++ b/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:45 2021 epsilon: 5e-14 +skip_tests: gpu prerequisites: ! | atom full pair lj/cut diff --git a/unittest/force-styles/tests/mol-pair-hybrid.yaml b/unittest/force-styles/tests/mol-pair-hybrid.yaml index 4f55c09d25..95bec97279 100644 --- a/unittest/force-styles/tests/mol-pair-hybrid.yaml +++ b/unittest/force-styles/tests/mol-pair-hybrid.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:45 2021 epsilon: 5e-14 +skip_tests: gpu prerequisites: ! | atom full pair lj/cut diff --git a/unittest/force-styles/tests/mol-pair-lj_class2.yaml b/unittest/force-styles/tests/mol-pair-lj_class2.yaml index ba4989e6e2..779bb4def2 100644 --- a/unittest/force-styles/tests/mol-pair-lj_class2.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_class2.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:46 2021 epsilon: 5e-14 +skip_tests: gpu prerequisites: ! | atom full pair lj/class2 From 6fa3e6d23e8632478ae93b4b01ee4d1d07132ed0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Mar 2021 21:44:41 -0500 Subject: [PATCH 0123/1217] remove hardcoded checks for incompatible styles. use skip_tests keyword instead --- unittest/force-styles/test_pair_style.cpp | 26 ----------------------- 1 file changed, 26 deletions(-) diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index 6a99fb72cd..79f832c0ef 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -627,14 +627,6 @@ TEST(PairStyle, omp) EXPECT_THAT(output, StartsWith("LAMMPS (")); EXPECT_THAT(output, HasSubstr("Loop time")); - if (utils::strmatch(test_config.pair_style, "^dpd")) { - std::cerr << "Skipping pair style " << lmp->force->pair_style << "\n"; - if (!verbose) ::testing::internal::CaptureStdout(); - cleanup_lammps(lmp, test_config); - if (!verbose) ::testing::internal::GetCapturedStdout(); - GTEST_SKIP(); - } - // abort if running in parallel and not all atoms are local const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); @@ -930,24 +922,6 @@ TEST(PairStyle, intel) GTEST_SKIP(); } - if ((test_config.pair_style == "rebo") - || utils::strmatch(test_config.pair_style, "^dpd") - || utils::strmatch(test_config.pair_style, "^tersoff.* shift ")) { - std::cerr << "Skipping pair style " << lmp->force->pair_style << "\n"; - if (!verbose) ::testing::internal::CaptureStdout(); - cleanup_lammps(lmp, test_config); - if (!verbose) ::testing::internal::GetCapturedStdout(); - GTEST_SKIP(); - } - - if (lmp->force->kspace && utils::strmatch(lmp->force->kspace_style, "^pppm/disp/intel")) { - if (!verbose) ::testing::internal::CaptureStdout(); - cleanup_lammps(lmp, test_config); - if (!verbose) ::testing::internal::GetCapturedStdout(); - std::cerr << "Skipping kspace style pppm/disp/intel\n"; - GTEST_SKIP(); - } - // relax error a bit for USER-INTEL package double epsilon = 7.5 * test_config.epsilon; // relax test precision when using pppm and single precision FFTs From fb57d86364a1d5d5eac1456f9a90ae6e13e8e1fa Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Mar 2021 21:45:36 -0500 Subject: [PATCH 0124/1217] dpd and dpd/tsat may only run with 1 thread due to use of per-thread pRNG --- unittest/force-styles/test_pair_style.cpp | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index 79f832c0ef..56dee46ad2 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -606,6 +606,9 @@ TEST(PairStyle, omp) const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-pk", "omp", "4", "-sf", "omp"}; + // cannot run dpd styles with more than 1 thread due to using multiple pRNGs + if (utils::strmatch(test_config.pair_style, "^dpd")) args[8] = "1"; + char **argv = (char **)args; int argc = sizeof(args) / sizeof(char *); @@ -904,6 +907,9 @@ TEST(PairStyle, intel) "-pk", "intel", "0", "mode", "double", "omp", "4", "lrt", "no", "-sf", "intel"}; + // cannot use more than 1 thread for dpd styles due to pRNG + if (utils::strmatch(test_config.pair_style, "^dpd")) args[12] = "1"; + char **argv = (char **)args; int argc = sizeof(args) / sizeof(char *); From e02ad44b8bf49e661e8a27130ec3a3ddc9b34c95 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Mar 2021 22:04:55 -0500 Subject: [PATCH 0125/1217] GPU package does not support tabulated long-range coulomb --- unittest/force-styles/test_pair_style.cpp | 8 ----- .../tests/mol-pair-born_coul_msm_table.yaml | 33 ++++++++++--------- .../tests/mol-pair-buck_coul_msm_table.yaml | 1 + .../tests/mol-pair-buck_coul_table.yaml | 1 + .../tests/mol-pair-buck_table_coul_table.yaml | 1 + .../tests/mol-pair-coul_msm_table.yaml | 1 + .../tests/mol-pair-coul_table.yaml | 1 + .../mol-pair-lj_charmm_coul_msm_table.yaml | 1 + .../tests/mol-pair-lj_charmm_coul_table.yaml | 1 + .../mol-pair-lj_charmmfsw_coul_table.yaml | 1 + .../tests/mol-pair-lj_class2_coul_table.yaml | 1 + .../tests/mol-pair-lj_cut_coul_msm.yaml | 1 + .../tests/mol-pair-lj_cut_coul_msm_table.yaml | 1 + .../tests/mol-pair-lj_cut_coul_table.yaml | 1 + .../tests/mol-pair-lj_expand_coul_table.yaml | 1 + .../tests/mol-pair-lj_sdk_coul_msm_table.yaml | 1 + .../tests/mol-pair-lj_sdk_coul_table.yaml | 1 + .../tests/mol-pair-lj_table_coul_table.yaml | 1 + .../tests/mol-pair-nm_cut_coul_table.yaml | 1 + 19 files changed, 34 insertions(+), 24 deletions(-) diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index 56dee46ad2..38a1e015a6 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -816,14 +816,6 @@ TEST(PairStyle, gpu) const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); - // skip over tests using tabulated coulomb - if ((lmp->force->pair->ncoultablebits > 0) || (lmp->force->pair->ndisptablebits > 0)) { - if (!verbose) ::testing::internal::CaptureStdout(); - cleanup_lammps(lmp, test_config); - if (!verbose) ::testing::internal::GetCapturedStdout(); - GTEST_SKIP(); - } - // relax error a bit for GPU package double epsilon = 7.5 * test_config.epsilon; // relax test precision when using pppm and single precision FFTs diff --git a/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml index ee9f18f27c..ecbcdea3ee 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:39 2021 epsilon: 5e-14 +skip_tests: gpu prerequisites: ! | atom full pair born/coul/msm @@ -15,22 +16,22 @@ post_commands: ! | kspace_modify pressure/scalar no # required for USER-OMP with msm input_file: in.fourmol pair_style: born/coul/msm 12.0 -pair_coeff: ! "1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 - 141.547923828784 \n1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 - 4.09225030876458 \n1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 - 403.51858739517 \n1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 - 303.336540547726 \n1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 - 303.336540547726 \n2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 - 0.177172207445923 \n2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 - 17.5662073921955 \n2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 - 0.000703093129207124 \n2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 - 12.548008396489 \n3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 - 1019.38354056979 \n3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 - 778.254162800904 \n3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 - 778.254162800904 \n4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n" +pair_coeff: ! | + 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 + 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 + 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 + 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 + 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 + 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 + 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 + 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 + 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 extract: ! | cut_coul 0 natoms: 29 diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml index 52536b14d4..06e7a38c18 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:40 2021 epsilon: 2e-13 +skip_tests: gpu prerequisites: ! | atom full pair buck/coul/msm diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_table.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_table.yaml index ecdbc8478c..1875a657f4 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:40 2021 epsilon: 5e-12 +skip_tests: gpu prerequisites: ! | atom full pair buck/coul/long diff --git a/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml b/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml index 643786eb0d..49ddaab6d9 100644 --- a/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_table_coul_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:41 2021 epsilon: 8e-07 +skip_tests: gpu prerequisites: ! | atom full pair buck/long/coul/long diff --git a/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml index 289a3e0e38..e07fd6e639 100644 --- a/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:43 2021 epsilon: 5e-14 +skip_tests: gpu prerequisites: ! | atom full pair coul/msm diff --git a/unittest/force-styles/tests/mol-pair-coul_table.yaml b/unittest/force-styles/tests/mol-pair-coul_table.yaml index 54baba354c..6f1077f19b 100644 --- a/unittest/force-styles/tests/mol-pair-coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:44 2021 epsilon: 7.5e-14 +skip_tests: gpu prerequisites: ! | atom full pair coul/long diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml index adf0f0b71b..0755c7e3a6 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:46 2021 epsilon: 1e-13 +skip_tests: gpu prerequisites: ! | atom full pair lj/charmm/coul/msm diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_table.yaml index 7d64a7c692..17a06d99f3 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:46 2021 epsilon: 5e-13 +skip_tests: gpu prerequisites: ! | atom full pair lj/charmm/coul/long diff --git a/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_table.yaml index 2af3de8273..b0dbfacfd9 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmmfsw_coul_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:46 2021 epsilon: 5e-13 +skip_tests: gpu prerequisites: ! | atom full pair lj/charmmfsw/coul/long diff --git a/unittest/force-styles/tests/mol-pair-lj_class2_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_class2_coul_table.yaml index 39a9299b25..9c442b3ac5 100644 --- a/unittest/force-styles/tests/mol-pair-lj_class2_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_class2_coul_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:47 2021 epsilon: 5e-12 +skip_tests: gpu prerequisites: ! | atom full pair lj/class2/coul/long diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml index 937c115a9a..2bb831e66b 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:48 2021 epsilon: 7e-14 +skip_tests: gpu prerequisites: ! | atom full pair lj/cut/coul/msm diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml index de1ab82c24..ccb0da249f 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:49 2021 epsilon: 1e-13 +skip_tests: gpu prerequisites: ! | atom full pair lj/cut/coul/msm diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_table.yaml index d5eb9d35a1..fe0bd28d96 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:49 2021 epsilon: 5e-13 +skip_tests: gpu prerequisites: ! | atom full pair lj/cut/coul/long diff --git a/unittest/force-styles/tests/mol-pair-lj_expand_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_expand_coul_table.yaml index 27ceae8a05..e5f31de755 100644 --- a/unittest/force-styles/tests/mol-pair-lj_expand_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_expand_coul_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:50 2021 epsilon: 2e-13 +skip_tests: gpu prerequisites: ! | atom full pair lj/expand/coul/long diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml index f9e55e3fea..4f95ee2e34 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:52 2021 epsilon: 5e-14 +skip_tests: gpu prerequisites: ! | atom full pair lj/sdk/coul/long diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_table.yaml index 914cd9077e..09bb65a0cf 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:52 2021 epsilon: 5e-14 +skip_tests: gpu prerequisites: ! | atom full pair lj/sdk/coul/long diff --git a/unittest/force-styles/tests/mol-pair-lj_table_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_table_coul_table.yaml index d9c02422cb..c02f9a31dd 100644 --- a/unittest/force-styles/tests/mol-pair-lj_table_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_table_coul_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:53 2021 epsilon: 2.5e-09 +skip_tests: gpu prerequisites: ! | atom full pair lj/long/coul/long diff --git a/unittest/force-styles/tests/mol-pair-nm_cut_coul_table.yaml b/unittest/force-styles/tests/mol-pair-nm_cut_coul_table.yaml index adaa3904a2..1c796c067a 100644 --- a/unittest/force-styles/tests/mol-pair-nm_cut_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-nm_cut_coul_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:56 2021 epsilon: 5e-12 +skip_tests: gpu prerequisites: ! | atom full pair nm/cut/coul/long From 6c7de1cbd0924b2d14750ce05c7e351500002ba1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Mar 2021 22:14:35 -0500 Subject: [PATCH 0126/1217] no support for pppm on GPU (yet) with nozforce or triclinic cell --- unittest/force-styles/tests/kspace-pppm_nozforce.yaml | 1 + unittest/force-styles/tests/kspace-pppm_tri.yaml | 1 + 2 files changed, 2 insertions(+) diff --git a/unittest/force-styles/tests/kspace-pppm_nozforce.yaml b/unittest/force-styles/tests/kspace-pppm_nozforce.yaml index 7442e862e9..32bd592a3c 100644 --- a/unittest/force-styles/tests/kspace-pppm_nozforce.yaml +++ b/unittest/force-styles/tests/kspace-pppm_nozforce.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:32 2021 epsilon: 7.5e-14 +skip_tests: gpu prerequisites: ! | atom full pair coul/long diff --git a/unittest/force-styles/tests/kspace-pppm_tri.yaml b/unittest/force-styles/tests/kspace-pppm_tri.yaml index dbcbe44e52..60099f24ee 100644 --- a/unittest/force-styles/tests/kspace-pppm_tri.yaml +++ b/unittest/force-styles/tests/kspace-pppm_tri.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:34 2021 epsilon: 7.5e-14 +skip_tests: gpu prerequisites: ! | atom full pair coul/long From 7b49b39a935ed521c3a97693723e37d799c30a25 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Mar 2021 22:28:23 -0500 Subject: [PATCH 0127/1217] fix typo --- unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml index ecbcdea3ee..d7461e8c9e 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml @@ -19,7 +19,7 @@ pair_style: born/coul/msm 12.0 pair_coeff: ! | 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 - 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 + 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 From 92dd89f9e6ec2d1e668f96788e96b4da777d9456 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Mar 2021 22:41:13 -0500 Subject: [PATCH 0128/1217] skip a few more tests that crash with the GPU package (/w OpenCL) --- unittest/force-styles/tests/manybody-pair-tersoff.yaml | 1 + unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml | 1 + unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm.yaml | 1 + unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml | 1 + unittest/force-styles/tests/mol-pair-lj_cut_tip4p_table.yaml | 1 + 5 files changed, 5 insertions(+) diff --git a/unittest/force-styles/tests/manybody-pair-tersoff.yaml b/unittest/force-styles/tests/manybody-pair-tersoff.yaml index 366810b84e..7626e4e5de 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:20 2021 epsilon: 5e-13 +skip_tests: gpu prerequisites: ! | pair tersoff pre_commands: ! | diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml index a503b6e912..a8d668ac3b 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:20 2021 epsilon: 5e-11 +skip_tests: gpu prerequisites: ! | pair tersoff/zbl pre_commands: ! | diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm.yaml index 452a1b58d6..db8265a6b2 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:45 2021 epsilon: 7e-14 +skip_tests: gpu prerequisites: ! | atom full pair lj/charmm/coul/charmm diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml index d1bed9430b..2e76bdcb57 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:49 2021 epsilon: 1e-13 +skip_tests: gpu prerequisites: ! | atom full pair lj/cut/tip4p/long diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_table.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_table.yaml index 77a7f00ad8..f8c3e70c6f 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_table.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:50 2021 epsilon: 5e-13 +skip_tests: gpu prerequisites: ! | atom full pair lj/cut/tip4p/long From cf5614e7d755df64c9585e9d6d845212e4d4de49 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Mar 2021 22:44:24 -0500 Subject: [PATCH 0129/1217] change precision handling so we can on the GPU also run with mixed and single precision --- unittest/force-styles/test_pair_style.cpp | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index 38a1e015a6..274f8f251f 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -816,11 +816,16 @@ TEST(PairStyle, gpu) const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); - // relax error a bit for GPU package - double epsilon = 7.5 * test_config.epsilon; - // relax test precision when using pppm and single precision FFTs + // relax error for GPU package depending on precision setting + double epsilon = test_config.epsilon; + if (Info::has_accelerator_feature("GPU","precision","double")) + epsilon *= 7.5; + else if (Info::has_accelerator_feature("GPU","precision","mixed")) + epsilon *= 5.0e8; + else epsilon *= 1.0e10; + // relax test precision when using pppm and single precision FFTs, but only when also running with double precision #if defined(FFT_SINGLE) - if (lmp->force->kspace && lmp->force->kspace->compute_flag) + if (lmp->force->kspace && lmp->force->kspace->compute_flag && Info::has_accelerator_feature("GPU","precision","double")) if (utils::strmatch(lmp->force->kspace_style, "^pppm")) epsilon *= 2.0e8; #endif const std::vector &f_ref = test_config.init_forces; From 73de926f09fa7c3024fae4d325a4bb9d26ade34c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 27 Feb 2021 15:50:58 -0500 Subject: [PATCH 0130/1217] safer detection and load of lammps shared library --- python/lammps/core.py | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/python/lammps/core.py b/python/lammps/core.py index e13bf9585b..eaf78dfa0c 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -121,18 +121,16 @@ class lammps(object): lib_ext = ".so" if not self.lib: - try: - if not name: - self.lib = CDLL(join(modpath,"liblammps" + lib_ext),RTLD_GLOBAL) + if name: + libpath = join(modpath,"liblammps_%s" % name + lib_ext) + else: + libpath = join(modpath,"liblammps" + lib_ext) + if not os.path.isfile(libpath): + if name: + libpath = "liblammps_%s" % name + lib_ext else: - self.lib = CDLL(join(modpath,"liblammps_%s" % name + lib_ext), - RTLD_GLOBAL) - except: - if not name: - self.lib = CDLL("liblammps" + lib_ext,RTLD_GLOBAL) - else: - self.lib = CDLL("liblammps_%s" % name + lib_ext,RTLD_GLOBAL) - + libpath = "liblammps" + lib_ext + self.lib = CDLL(libpath,RTLD_GLOBAL) # declare all argument and return types for all library methods here. # exceptions are where the arguments depend on certain conditions and From d5c3e1786adfb046e55f5bc0d3d27f195f3a5725 Mon Sep 17 00:00:00 2001 From: Trung Nguyen Date: Tue, 2 Mar 2021 12:57:32 -0600 Subject: [PATCH 0131/1217] Fixing bugs on eam*/gpu for pair hybrid with neigh yes, where the gpu pair style eam is used for only a subset of the pair types. eam being the first substyle works correctly, but otherwise will give incorrect forces --- lib/gpu/lal_eam.cpp | 20 ++++++++++++++------ lib/gpu/lal_eam.cu | 13 ++++++++++--- lib/gpu/lal_eam.h | 6 ++++-- lib/gpu/lal_eam_alloy_ext.cpp | 6 +++--- lib/gpu/lal_eam_ext.cpp | 6 +++--- lib/gpu/lal_eam_fs_ext.cpp | 6 +++--- src/GPU/pair_eam_alloy_gpu.cpp | 4 ++-- src/GPU/pair_eam_fs_gpu.cpp | 4 ++-- src/GPU/pair_eam_gpu.cpp | 4 ++-- 9 files changed, 43 insertions(+), 26 deletions(-) diff --git a/lib/gpu/lal_eam.cpp b/lib/gpu/lal_eam.cpp index cdafe72898..2c0d63f7bf 100644 --- a/lib/gpu/lal_eam.cpp +++ b/lib/gpu/lal_eam.cpp @@ -46,7 +46,7 @@ template int EAMT::init(const int ntypes, double host_cutforcesq, int **host_type2rhor, int **host_type2z2r, int *host_type2frho, double ***host_rhor_spline, double ***host_z2r_spline, - double ***host_frho_spline, double rdr, double rdrho, + double ***host_frho_spline, double** host_cutsq, double rdr, double rdrho, double rhomax, int nrhor, int nrho, int nz2r, int nfrho, int nr, const int nlocal, const int nall, const int max_nbors, const int maxspecial, const double cell_size, @@ -243,6 +243,12 @@ int EAMT::init(const int ntypes, double host_cutforcesq, int **host_type2rhor, z2r_spline2_tex.get_texture(*(this->pair_program),"z2r_sp2_tex"); z2r_spline2_tex.bind_float(z2r_spline2,4); + UCL_H_Vec host_write(lj_types*lj_types,*(this->ucl_device), + UCL_WRITE_ONLY); + host_write.zero(); + cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack1(ntypes,lj_types,cutsq,host_write,host_cutsq); + _allocated=true; this->_max_bytes=type2rhor_z2r.row_bytes() + type2frho.row_bytes() @@ -252,6 +258,7 @@ int EAMT::init(const int ntypes, double host_cutforcesq, int **host_type2rhor, + frho_spline2.row_bytes() + z2r_spline1.row_bytes() + z2r_spline2.row_bytes() + + cutsq.row_bytes() + _fp.device.row_bytes(); return 0; } @@ -270,6 +277,7 @@ void EAMT::clear() { frho_spline2.clear(); z2r_spline1.clear(); z2r_spline2.clear(); + cutsq.clear(); _fp.clear(); @@ -477,7 +485,7 @@ void EAMT::compute2(int *ilist, const bool eflag, const bool vflag, } // --------------------------------------------------------------------------- -// Calculate per-atom energies and forces +// Calculate per-atom fp // --------------------------------------------------------------------------- template int EAMT::loop(const int eflag, const int vflag) { @@ -498,7 +506,7 @@ int EAMT::loop(const int eflag, const int vflag) { k_energy_sel->set_size(GX,BX); k_energy_sel->run(&this->atom->x, &type2rhor_z2r, &type2frho, - &rhor_spline2, &frho_spline1,&frho_spline2, + &rhor_spline2, &frho_spline1, &frho_spline2, &cutsq, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &_fp, &this->ans->engv, &eflag, &ainum, &nbor_pitch, &_ntypes, &_cutforcesq, &_rdr, &_rdrho, @@ -506,7 +514,7 @@ int EAMT::loop(const int eflag, const int vflag) { } else { this->k_energy.set_size(GX,BX); this->k_energy.run(&this->atom->x, &type2rhor_z2r, &type2frho, - &rhor_spline2, &frho_spline1, &frho_spline2, + &rhor_spline2, &frho_spline1, &frho_spline2, &cutsq, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &_fp, &this->ans->engv,&eflag, &ainum, &nbor_pitch, &_ntypes, &_cutforcesq, &_rdr, &_rdrho, &_rhomax, &_nrho, @@ -545,7 +553,7 @@ void EAMT::loop2(const bool _eflag, const bool _vflag) { if (shared_types) { this->k_pair_sel->set_size(GX,BX); this->k_pair_sel->run(&this->atom->x, &_fp, &type2rhor_z2r, - &rhor_spline1, &z2r_spline1, &z2r_spline2, + &rhor_spline1, &z2r_spline1, &z2r_spline2, &cutsq, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &_cutforcesq, &_rdr, @@ -553,7 +561,7 @@ void EAMT::loop2(const bool _eflag, const bool _vflag) { } else { this->k_pair.set_size(GX,BX); this->k_pair.run(&this->atom->x, &_fp, &type2rhor_z2r, &rhor_spline1, - &z2r_spline1, &z2r_spline2, &this->nbor->dev_nbor, + &z2r_spline1, &z2r_spline2, &cutsq, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &_ntypes, &_cutforcesq, &_rdr, &_nr, diff --git a/lib/gpu/lal_eam.cu b/lib/gpu/lal_eam.cu index 3955f3cc8a..4c6aa2f6b2 100644 --- a/lib/gpu/lal_eam.cu +++ b/lib/gpu/lal_eam.cu @@ -216,6 +216,7 @@ __kernel void k_energy(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict rhor_spline2, const __global numtyp4 *restrict frho_spline1, const __global numtyp4 *restrict frho_spline2, + const __global numtyp *restrict cutsq, const __global int *dev_nbor, const __global int *dev_packed, __global numtyp *restrict fp_, @@ -256,7 +257,8 @@ __kernel void k_energy(const __global numtyp4 *restrict x_, numtyp delz = ix.z-jx.z; numtyp rsq = delx*delx+dely*dely+delz*delz; - if (rsq(numtyp)0) { numtyp p = ucl_sqrt(rsq)*rdr + (numtyp)1.0; int m=p; m = MIN(m,nr-1); @@ -281,6 +283,7 @@ __kernel void k_energy_fast(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict rhor_spline2, const __global numtyp4 *restrict frho_spline1, const __global numtyp4 *restrict frho_spline2, + const __global numtyp *restrict cutsq, const __global int *dev_nbor, const __global int *dev_packed, __global numtyp *restrict fp_, @@ -371,6 +374,7 @@ __kernel void k_eam(const __global numtyp4 *restrict x_, const __global numtyp4 *rhor_spline1, const __global numtyp4 *z2r_spline1, const __global numtyp4 *z2r_spline2, + const __global numtyp *cutsq, const __global int *dev_nbor, const __global int *dev_packed, __global acctyp4 *ans, @@ -416,7 +420,8 @@ __kernel void k_eam(const __global numtyp4 *restrict x_, numtyp delz = ix.z-jx.z; numtyp rsq = delx*delx+dely*dely+delz*delz; - if (rsq(numtyp)0) { numtyp r = ucl_sqrt(rsq); numtyp p = r*rdr + (numtyp)1.0; int m=p; @@ -480,6 +485,7 @@ __kernel void k_eam_fast(const __global numtyp4 *x_, const __global numtyp4 *rhor_spline1, const __global numtyp4 *z2r_spline1, const __global numtyp4 *z2r_spline2, + const __global numtyp *cutsq, const __global int *dev_nbor, const __global int *dev_packed, __global acctyp4 *ans, @@ -542,7 +548,8 @@ __kernel void k_eam_fast(const __global numtyp4 *x_, numtyp delz = ix.z-jx.z; numtyp rsq = delx*delx+dely*dely+delz*delz; - if (rsq(numtyp)0) { numtyp r = ucl_sqrt(rsq); numtyp p = r*rdr + (numtyp)1.0; int m=p; diff --git a/lib/gpu/lal_eam.h b/lib/gpu/lal_eam.h index 3cbaeac0b8..efc38537d6 100644 --- a/lib/gpu/lal_eam.h +++ b/lib/gpu/lal_eam.h @@ -40,8 +40,8 @@ class EAM : public BaseAtomic { * - -5 Double precision is not supported on card **/ int init(const int ntypes, double host_cutforcesq, int **host_type2rhor, int **host_type2z2r, int *host_type2frho, double ***host_rhor_spline, - double ***host_z2r_spline, double ***host_frho_spline, double rdr, - double rdrho, double rhomax, int nrhor, int nrho, int nz2r, + double ***host_z2r_spline, double ***host_frho_spline, double** host_cutsq, + double rdr, double rdrho, double rhomax, int nrhor, int nrho, int nz2r, int nfrho, int nr, const int nlocal, const int nall, const int max_nbors, const int maxspecial, const double cell_size, const double gpu_split, FILE *_screen); @@ -112,6 +112,8 @@ class EAM : public BaseAtomic { UCL_D_Vec frho_spline1, frho_spline2; UCL_D_Vec rhor_spline1, rhor_spline2; + UCL_D_Vec cutsq; + numtyp _cutforcesq,_rdr,_rdrho, _rhomax; int _nfrho,_nrhor,_nrho,_nz2r,_nr; diff --git a/lib/gpu/lal_eam_alloy_ext.cpp b/lib/gpu/lal_eam_alloy_ext.cpp index f7c4986e68..5a3dfb9d6d 100644 --- a/lib/gpu/lal_eam_alloy_ext.cpp +++ b/lib/gpu/lal_eam_alloy_ext.cpp @@ -30,7 +30,7 @@ static EAM EAMALMF; int eam_alloy_gpu_init(const int ntypes, double host_cutforcesq, int **host_type2rhor, int **host_type2z2r, int *host_type2frho, double ***host_rhor_spline, double ***host_z2r_spline, - double ***host_frho_spline, + double ***host_frho_spline, double** host_cutsq, double rdr, double rdrho, double rhomax, int nrhor, int nrho, int nz2r, int nfrho, int nr, const int nlocal, const int nall, const int max_nbors, @@ -66,7 +66,7 @@ int eam_alloy_gpu_init(const int ntypes, double host_cutforcesq, if (world_me==0) init_ok=EAMALMF.init(ntypes, host_cutforcesq, host_type2rhor, host_type2z2r, host_type2frho, host_rhor_spline, host_z2r_spline, - host_frho_spline, rdr, rdrho, rhomax, nrhor, nrho, nz2r, + host_frho_spline, host_cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, nlocal, nall, max_nbors, maxspecial, cell_size, gpu_split, screen); @@ -86,7 +86,7 @@ int eam_alloy_gpu_init(const int ntypes, double host_cutforcesq, if (gpu_rank==i && world_me!=0) init_ok=EAMALMF.init(ntypes, host_cutforcesq, host_type2rhor, host_type2z2r, host_type2frho, host_rhor_spline, host_z2r_spline, - host_frho_spline, rdr, rdrho, rhomax, nrhor, nrho, + host_frho_spline, host_cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, nlocal, nall, max_nbors, maxspecial, cell_size, gpu_split, screen); diff --git a/lib/gpu/lal_eam_ext.cpp b/lib/gpu/lal_eam_ext.cpp index 3010e0ea7f..a884335bd9 100644 --- a/lib/gpu/lal_eam_ext.cpp +++ b/lib/gpu/lal_eam_ext.cpp @@ -30,7 +30,7 @@ static EAM EAMMF; int eam_gpu_init(const int ntypes, double host_cutforcesq, int **host_type2rhor, int **host_type2z2r, int *host_type2frho, double ***host_rhor_spline, double ***host_z2r_spline, - double ***host_frho_spline, + double ***host_frho_spline, double** host_cutsq, double rdr, double rdrho, double rhomax, int nrhor, int nrho, int nz2r, int nfrho, int nr, const int nlocal, const int nall, const int max_nbors, @@ -66,7 +66,7 @@ int eam_gpu_init(const int ntypes, double host_cutforcesq, if (world_me==0) init_ok=EAMMF.init(ntypes, host_cutforcesq, host_type2rhor, host_type2z2r, host_type2frho, host_rhor_spline, host_z2r_spline, - host_frho_spline, rdr, rdrho, rhomax, nrhor, nrho, nz2r, + host_frho_spline, host_cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, nlocal, nall, max_nbors, maxspecial, cell_size, gpu_split, screen); @@ -86,7 +86,7 @@ int eam_gpu_init(const int ntypes, double host_cutforcesq, if (gpu_rank==i && world_me!=0) init_ok=EAMMF.init(ntypes, host_cutforcesq, host_type2rhor, host_type2z2r, host_type2frho, host_rhor_spline, host_z2r_spline, - host_frho_spline, rdr, rdrho, rhomax, nrhor, nrho, + host_frho_spline, host_cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, nlocal, nall, max_nbors, maxspecial, cell_size, gpu_split, screen); diff --git a/lib/gpu/lal_eam_fs_ext.cpp b/lib/gpu/lal_eam_fs_ext.cpp index 205b601562..5aad871237 100644 --- a/lib/gpu/lal_eam_fs_ext.cpp +++ b/lib/gpu/lal_eam_fs_ext.cpp @@ -30,7 +30,7 @@ static EAM EAMFSMF; int eam_fs_gpu_init(const int ntypes, double host_cutforcesq, int **host_type2rhor, int **host_type2z2r, int *host_type2frho, double ***host_rhor_spline, double ***host_z2r_spline, - double ***host_frho_spline, + double ***host_frho_spline, double** host_cutsq, double rdr, double rdrho, double rhomax, int nrhor, int nrho, int nz2r, int nfrho, int nr, const int nlocal, const int nall, const int max_nbors, @@ -66,7 +66,7 @@ int eam_fs_gpu_init(const int ntypes, double host_cutforcesq, if (world_me==0) init_ok=EAMFSMF.init(ntypes, host_cutforcesq, host_type2rhor, host_type2z2r, host_type2frho, host_rhor_spline, host_z2r_spline, - host_frho_spline, rdr, rdrho, rhomax, nrhor, nrho, nz2r, + host_frho_spline, host_cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, nlocal, nall, max_nbors, maxspecial, cell_size, gpu_split, screen); @@ -86,7 +86,7 @@ int eam_fs_gpu_init(const int ntypes, double host_cutforcesq, if (gpu_rank==i && world_me!=0) init_ok=EAMFSMF.init(ntypes, host_cutforcesq, host_type2rhor, host_type2z2r, host_type2frho, host_rhor_spline, host_z2r_spline, - host_frho_spline, rdr, rdrho, rhomax, nrhor, nrho, + host_frho_spline, host_cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, nlocal, nall, max_nbors, maxspecial, cell_size, gpu_split, screen); diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index 4678a6f669..56ca8c6f69 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -42,7 +42,7 @@ int eam_alloy_gpu_init(const int ntypes, double host_cutforcesq, int **host_type2rhor, int **host_type2z2r, int *host_type2frho, double ***host_rhor_spline, double ***host_z2r_spline, double ***host_frho_spline, - double rdr, double rdrho, double rhomax, + double** host_cutsq, double rdr, double rdrho, double rhomax, int nrhor, int nrho, int nz2r, int nfrho, int nr, const int nlocal, const int nall, const int max_nbors, const int maxspecial, const double cell_size, @@ -187,7 +187,7 @@ void PairEAMAlloyGPU::init_style() int mnf = 5e-2 * neighbor->oneatom; int success = eam_alloy_gpu_init(atom->ntypes+1, cutforcesq, type2rhor, type2z2r, type2frho, rhor_spline, z2r_spline, frho_spline, - rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, + cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, atom->nlocal, atom->nlocal+atom->nghost, mnf, maxspecial, cell_size, gpu_mode, screen, fp_size); GPU_EXTRA::check_flag(success,error,world); diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index 390bb93987..5cf5c9180a 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -42,7 +42,7 @@ int eam_fs_gpu_init(const int ntypes, double host_cutforcesq, int **host_type2rhor, int **host_type2z2r, int *host_type2frho, double ***host_rhor_spline, double ***host_z2r_spline, double ***host_frho_spline, - double rdr, double rdrho, double rhomax, + double** host_cutsq, double rdr, double rdrho, double rhomax, int nrhor, int nrho, int nz2r, int nfrho, int nr, const int nlocal, const int nall, const int max_nbors, const int maxspecial, const double cell_size, int &gpu_mode, @@ -186,7 +186,7 @@ void PairEAMFSGPU::init_style() int mnf = 5e-2 * neighbor->oneatom; int success = eam_fs_gpu_init(atom->ntypes+1, cutforcesq, type2rhor, type2z2r, type2frho, rhor_spline, z2r_spline, frho_spline, - rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, + cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, atom->nlocal, atom->nlocal+atom->nghost, mnf, maxspecial, cell_size, gpu_mode, screen, fp_size); GPU_EXTRA::check_flag(success,error,world); diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp index e458ea2020..724f71b312 100644 --- a/src/GPU/pair_eam_gpu.cpp +++ b/src/GPU/pair_eam_gpu.cpp @@ -42,7 +42,7 @@ int eam_gpu_init(const int ntypes, double host_cutforcesq, int **host_type2rhor, int **host_type2z2r, int *host_type2frho, double ***host_rhor_spline, double ***host_z2r_spline, double ***host_frho_spline, - double rdr, double rdrho, double rhomax, + double** host_cutsq, double rdr, double rdrho, double rhomax, int nrhor, int nrho, int nz2r, int nfrho, int nr, const int nlocal, const int nall, const int max_nbors, const int maxspecial, const double cell_size, int &gpu_mode, @@ -188,7 +188,7 @@ void PairEAMGPU::init_style() int mnf = 5e-2 * neighbor->oneatom; int success = eam_gpu_init(atom->ntypes+1, cutforcesq, type2rhor, type2z2r, type2frho, rhor_spline, z2r_spline, frho_spline, - rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, + cutsq, rdr, rdrho, rhomax, nrhor, nrho, nz2r, nfrho, nr, atom->nlocal, atom->nlocal+atom->nghost, mnf, maxspecial, cell_size, gpu_mode, screen, fp_size); GPU_EXTRA::check_flag(success,error,world); From e3a892ccd71fb6e452ab9023c047d01bab0220ff Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 4 Mar 2021 10:10:58 -0500 Subject: [PATCH 0132/1217] Start unittests for MPI load balancing --- unittest/commands/CMakeLists.txt | 7 + unittest/commands/test_mpi_load_balancing.cpp | 134 ++++++++++++++++++ 2 files changed, 141 insertions(+) create mode 100644 unittest/commands/test_mpi_load_balancing.cpp diff --git a/unittest/commands/CMakeLists.txt b/unittest/commands/CMakeLists.txt index 7a804820cb..62b3354a9e 100644 --- a/unittest/commands/CMakeLists.txt +++ b/unittest/commands/CMakeLists.txt @@ -22,3 +22,10 @@ add_executable(test_reset_ids test_reset_ids.cpp) target_compile_definitions(test_reset_ids PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR}) target_link_libraries(test_reset_ids PRIVATE lammps GTest::GMock GTest::GTest) add_test(NAME ResetIDs COMMAND test_reset_ids WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + +if(BUILD_MPI) + add_executable(test_mpi_load_balancing test_mpi_load_balancing.cpp) + target_link_libraries(test_mpi_load_balancing PRIVATE lammps GTest::GTest GTest::GMock) + target_compile_definitions(test_mpi_load_balancing PRIVATE ${TEST_CONFIG_DEFS}) + add_mpi_test(NAME MPILoadBalancing NUM_PROCS 4 COMMAND $) +endif() diff --git a/unittest/commands/test_mpi_load_balancing.cpp b/unittest/commands/test_mpi_load_balancing.cpp new file mode 100644 index 0000000000..0288933f8e --- /dev/null +++ b/unittest/commands/test_mpi_load_balancing.cpp @@ -0,0 +1,134 @@ +// unit tests for checking LAMMPS MPI load balancing + +#define LAMMPS_LIB_MPI 1 +#include "lammps.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "input.h" +#include "timer.h" +#include + +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include "../testing/test_mpi_main.h" + +using ::testing::ExitedWithCode; +using ::testing::HasSubstr; +using ::testing::StartsWith; +using ::testing::StrEq; + +namespace LAMMPS_NS +{ + +class MPILoadBalanceTest : public ::testing::Test { +public: + void command(const std::string &line) { lmp->input->one(line); } + +protected: + const char *testbinary = "LAMMPSTest"; + LAMMPS *lmp; + + void SetUp() override + { + const char *args[] = {testbinary, "-log", "none", "-echo", "screen", "-nocite"}; + char **argv = (char **)args; + int argc = sizeof(args) / sizeof(char *); + if (!verbose) ::testing::internal::CaptureStdout(); + lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); + InitSystem(); + if (!verbose) ::testing::internal::GetCapturedStdout(); + } + + virtual void InitSystem() + { + command("units lj"); + command("atom_style atomic"); + command("atom_modify map yes"); + + command("region box block 0 2 0 2 0 2"); + command("create_box 1 box"); + command("mass 1 1.0"); + + + command("pair_style lj/cut 2.5"); + command("pair_coeff 1 1 1.0 1.0 2.5"); + + command("neighbor 0.3 bin"); + command("neigh_modify every 20 delay 0 check no"); + } + + void TearDown() override + { + if (!verbose) ::testing::internal::CaptureStdout(); + delete lmp; + lmp = nullptr; + if (!verbose) ::testing::internal::GetCapturedStdout(); + } +}; + +TEST_F(MPILoadBalanceTest, grid_yz) +{ + command("create_atoms 1 single 0 0 0"); + command("create_atoms 1 single 0 0 0.5"); + command("create_atoms 1 single 0 0.5 0"); + command("create_atoms 1 single 0 0.5 0.5"); + command("create_atoms 1 single 0.5 0 0"); + command("create_atoms 1 single 0.5 0 0.5"); + command("create_atoms 1 single 0.5 0.5 0"); + command("create_atoms 1 single 0.5 0.5 0.5"); + ASSERT_EQ(lmp->atom->natoms, 8); + ASSERT_EQ(lmp->comm->nprocs, 4); + + switch(lmp->comm->me) { + case 0: + ASSERT_EQ(lmp->atom->nlocal, 8); + break; + case 1: + ASSERT_EQ(lmp->atom->nlocal, 0); + break; + case 2: + ASSERT_EQ(lmp->atom->nlocal, 0); + break; + case 3: + ASSERT_EQ(lmp->atom->nlocal, 0); + break; + } + + command("balance 1 x uniform y 0.25 z uniform"); + + switch(lmp->comm->me) { + case 0: + ASSERT_EQ(lmp->atom->nlocal, 4); + break; + case 1: + ASSERT_EQ(lmp->atom->nlocal, 0); + break; + case 2: + ASSERT_EQ(lmp->atom->nlocal, 4); + break; + case 3: + ASSERT_EQ(lmp->atom->nlocal, 0); + break; + } + + command("balance 1 x uniform y 0.25 z 0.25"); + + switch(lmp->comm->me) { + case 0: + ASSERT_EQ(lmp->atom->nlocal, 2); + break; + case 1: + ASSERT_EQ(lmp->atom->nlocal, 2); + break; + case 2: + ASSERT_EQ(lmp->atom->nlocal, 2); + break; + case 3: + ASSERT_EQ(lmp->atom->nlocal, 2); + break; + } +} + +} From 0b9675807b4323335c1f53317aa14120ffc73220 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 4 Mar 2021 17:48:44 -0500 Subject: [PATCH 0133/1217] Fix typos --- doc/src/balance.rst | 4 ++-- doc/src/fix_balance.rst | 2 +- doc/utils/sphinx-config/false_positives.txt | 1 - 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/doc/src/balance.rst b/doc/src/balance.rst index 07ea82eeba..5d42fabb21 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -257,7 +257,7 @@ factor, similar to how the :doc:`fix balance shift ` command operates. The *dimstr* argument is a string of characters, each of which must be -an "x" or "y" or "z". Eacn character can appear zero or one time, +an "x" or "y" or "z". Each character can appear zero or one time, since there is no advantage to balancing on a dimension more than once. You should normally only list dimensions where you expect there to be a density variation in the particles. @@ -285,7 +285,7 @@ plane gets closer to the target value. After the balanced plane positions are determined, if any pair of adjacent planes are closer together than the neighbor skin distance -(as specified by the :doc`neigh_modify ` command), then +(as specified by the :doc:`neigh_modify ` command), then the plane positions are shifted to separate them by at least this amount. This is to prevent particles being lost when dynamics are run with processor sub-domains that are too narrow in one or more diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 1875ab744f..8bab8ebefc 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -216,7 +216,7 @@ above. It changes the positions of cutting planes between processors in an iterative fashion, seeking to reduce the imbalance factor. The *dimstr* argument is a string of characters, each of which must be -an "x" or "y" or "z". Eacn character can appear zero or one time, +an "x" or "y" or "z". Each character can appear zero or one time, since there is no advantage to balancing on a dimension more than once. You should normally only list dimensions where you expect there to be a density variation in the particles. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index d1ffc2eaf3..56c2bdbe73 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -756,7 +756,6 @@ Dyre Dzyaloshinskii Eaa Eaat -Eacn eam eangle earg From 0857bccc105dcc594fb333200f4feac0ce122500 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 4 Mar 2021 18:31:10 -0500 Subject: [PATCH 0134/1217] Add RCB tests --- unittest/commands/test_mpi_load_balancing.cpp | 129 ++++++++++++++++-- 1 file changed, 119 insertions(+), 10 deletions(-) diff --git a/unittest/commands/test_mpi_load_balancing.cpp b/unittest/commands/test_mpi_load_balancing.cpp index 0288933f8e..886df1c31d 100644 --- a/unittest/commands/test_mpi_load_balancing.cpp +++ b/unittest/commands/test_mpi_load_balancing.cpp @@ -5,8 +5,10 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "neighbor.h" #include "input.h" #include "timer.h" +#include "info.h" #include #include "gmock/gmock.h" @@ -43,11 +45,12 @@ protected: virtual void InitSystem() { + command("boundary f f f"); command("units lj"); command("atom_style atomic"); command("atom_modify map yes"); - command("region box block 0 2 0 2 0 2"); + command("region box block 0 20 0 20 0 20"); command("create_box 1 box"); command("mass 1 1.0"); @@ -71,13 +74,13 @@ protected: TEST_F(MPILoadBalanceTest, grid_yz) { command("create_atoms 1 single 0 0 0"); - command("create_atoms 1 single 0 0 0.5"); - command("create_atoms 1 single 0 0.5 0"); - command("create_atoms 1 single 0 0.5 0.5"); - command("create_atoms 1 single 0.5 0 0"); - command("create_atoms 1 single 0.5 0 0.5"); - command("create_atoms 1 single 0.5 0.5 0"); - command("create_atoms 1 single 0.5 0.5 0.5"); + command("create_atoms 1 single 0 0 5"); + command("create_atoms 1 single 0 5 0"); + command("create_atoms 1 single 0 5 5"); + command("create_atoms 1 single 5 0 0"); + command("create_atoms 1 single 5 0 5"); + command("create_atoms 1 single 5 5 0"); + command("create_atoms 1 single 5 5 5"); ASSERT_EQ(lmp->atom->natoms, 8); ASSERT_EQ(lmp->comm->nprocs, 4); @@ -96,7 +99,7 @@ TEST_F(MPILoadBalanceTest, grid_yz) break; } - command("balance 1 x uniform y 0.25 z uniform"); + command("balance 1 x uniform y 0.125 z uniform"); switch(lmp->comm->me) { case 0: @@ -113,7 +116,7 @@ TEST_F(MPILoadBalanceTest, grid_yz) break; } - command("balance 1 x uniform y 0.25 z 0.25"); + command("balance 1 x uniform y 0.125 z 0.125"); switch(lmp->comm->me) { case 0: @@ -131,4 +134,110 @@ TEST_F(MPILoadBalanceTest, grid_yz) } } +TEST_F(MPILoadBalanceTest, rcb) +{ + command("comm_style tiled"); + command("create_atoms 1 single 0 0 0"); + command("create_atoms 1 single 0 0 5"); + command("create_atoms 1 single 0 5 0"); + command("create_atoms 1 single 0 5 5"); + command("create_atoms 1 single 5 0 0"); + command("create_atoms 1 single 5 0 5"); + command("create_atoms 1 single 5 5 0"); + command("create_atoms 1 single 5 5 5"); + + switch(lmp->comm->me) { + case 0: + ASSERT_EQ(lmp->atom->nlocal, 8); + break; + case 1: + ASSERT_EQ(lmp->atom->nlocal, 0); + break; + case 2: + ASSERT_EQ(lmp->atom->nlocal, 0); + break; + case 3: + ASSERT_EQ(lmp->atom->nlocal, 0); + break; + } + + command("balance 1 rcb"); + + switch(lmp->comm->me) { + case 0: + ASSERT_EQ(lmp->atom->nlocal, 2); + break; + case 1: + ASSERT_EQ(lmp->atom->nlocal, 2); + break; + case 2: + ASSERT_EQ(lmp->atom->nlocal, 2); + break; + case 3: + ASSERT_EQ(lmp->atom->nlocal, 2); + break; + } + + double dx = lmp->domain->subhi[0] - lmp->domain->sublo[0]; + double dy = lmp->domain->subhi[1] - lmp->domain->sublo[1]; + double dz = lmp->domain->subhi[2] - lmp->domain->sublo[2]; + + ASSERT_GT(dx, lmp->neighbor->skin); + ASSERT_GT(dy, lmp->neighbor->skin); + ASSERT_GT(dz, lmp->neighbor->skin); +} + +TEST_F(MPILoadBalanceTest, rcb_min_size) +{ + command("comm_style tiled"); + command("create_atoms 1 single 0 0 0"); + command("create_atoms 1 single 0 0 0.25"); + command("create_atoms 1 single 0 0.25 0"); + command("create_atoms 1 single 0 0.25 0.25"); + command("create_atoms 1 single 0.25 0 0"); + command("create_atoms 1 single 0.25 0 0.25"); + command("create_atoms 1 single 0.25 0.25 0"); + command("create_atoms 1 single 0.25 0.25 0.25"); + + switch(lmp->comm->me) { + case 0: + ASSERT_EQ(lmp->atom->nlocal, 8); + break; + case 1: + ASSERT_EQ(lmp->atom->nlocal, 0); + break; + case 2: + ASSERT_EQ(lmp->atom->nlocal, 0); + break; + case 3: + ASSERT_EQ(lmp->atom->nlocal, 0); + break; + } + + command("balance 1 rcb"); + + switch(lmp->comm->me) { + case 0: + ASSERT_EQ(lmp->atom->nlocal, 8); + break; + case 1: + ASSERT_EQ(lmp->atom->nlocal, 0); + break; + case 2: + ASSERT_EQ(lmp->atom->nlocal, 0); + break; + case 3: + ASSERT_EQ(lmp->atom->nlocal, 0); + break; + } + + double dx = lmp->domain->subhi[0] - lmp->domain->sublo[0]; + double dy = lmp->domain->subhi[1] - lmp->domain->sublo[1]; + double dz = lmp->domain->subhi[2] - lmp->domain->sublo[2]; + + ASSERT_GT(dx, lmp->neighbor->skin); + ASSERT_GT(dy, lmp->neighbor->skin); + ASSERT_GT(dz, lmp->neighbor->skin); +} + } From debb0ef63d8aa752f181d373b1618fd107601502 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 5 Mar 2021 10:59:52 -0500 Subject: [PATCH 0135/1217] Add comments for review --- unittest/commands/test_mpi_load_balancing.cpp | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/unittest/commands/test_mpi_load_balancing.cpp b/unittest/commands/test_mpi_load_balancing.cpp index 886df1c31d..cbdea26981 100644 --- a/unittest/commands/test_mpi_load_balancing.cpp +++ b/unittest/commands/test_mpi_load_balancing.cpp @@ -84,6 +84,7 @@ TEST_F(MPILoadBalanceTest, grid_yz) ASSERT_EQ(lmp->atom->natoms, 8); ASSERT_EQ(lmp->comm->nprocs, 4); + // initial state switch(lmp->comm->me) { case 0: ASSERT_EQ(lmp->atom->nlocal, 8); @@ -101,6 +102,7 @@ TEST_F(MPILoadBalanceTest, grid_yz) command("balance 1 x uniform y 0.125 z uniform"); + // state after balance command switch(lmp->comm->me) { case 0: ASSERT_EQ(lmp->atom->nlocal, 4); @@ -118,6 +120,7 @@ TEST_F(MPILoadBalanceTest, grid_yz) command("balance 1 x uniform y 0.125 z 0.125"); + // state after second balance command switch(lmp->comm->me) { case 0: ASSERT_EQ(lmp->atom->nlocal, 2); @@ -146,6 +149,7 @@ TEST_F(MPILoadBalanceTest, rcb) command("create_atoms 1 single 5 5 0"); command("create_atoms 1 single 5 5 5"); + // initial state switch(lmp->comm->me) { case 0: ASSERT_EQ(lmp->atom->nlocal, 8); @@ -163,6 +167,7 @@ TEST_F(MPILoadBalanceTest, rcb) command("balance 1 rcb"); + // state after balance command switch(lmp->comm->me) { case 0: ASSERT_EQ(lmp->atom->nlocal, 2); @@ -178,6 +183,7 @@ TEST_F(MPILoadBalanceTest, rcb) break; } + // box dimensions should have minimal size double dx = lmp->domain->subhi[0] - lmp->domain->sublo[0]; double dy = lmp->domain->subhi[1] - lmp->domain->sublo[1]; double dz = lmp->domain->subhi[2] - lmp->domain->sublo[2]; @@ -199,6 +205,7 @@ TEST_F(MPILoadBalanceTest, rcb_min_size) command("create_atoms 1 single 0.25 0.25 0"); command("create_atoms 1 single 0.25 0.25 0.25"); + // initial state switch(lmp->comm->me) { case 0: ASSERT_EQ(lmp->atom->nlocal, 8); @@ -214,8 +221,11 @@ TEST_F(MPILoadBalanceTest, rcb_min_size) break; } + // this should fail and not change the boxes + // or keep them at a minimum size command("balance 1 rcb"); + // state after balance command switch(lmp->comm->me) { case 0: ASSERT_EQ(lmp->atom->nlocal, 8); @@ -231,6 +241,7 @@ TEST_F(MPILoadBalanceTest, rcb_min_size) break; } + // box dimensions should have minimal size double dx = lmp->domain->subhi[0] - lmp->domain->sublo[0]; double dy = lmp->domain->subhi[1] - lmp->domain->sublo[1]; double dz = lmp->domain->subhi[2] - lmp->domain->sublo[2]; From b5e1851e5da47f0dc1ab57cf16c7aec357491f2b Mon Sep 17 00:00:00 2001 From: kipbarrett Date: Fri, 5 Mar 2021 16:47:13 -0600 Subject: [PATCH 0136/1217] removed factory creation --- src/USER-RANN/rann_list_activation.h | 2 -- src/USER-RANN/rann_list_fingerprint.h | 8 -------- 2 files changed, 10 deletions(-) delete mode 100644 src/USER-RANN/rann_list_activation.h delete mode 100644 src/USER-RANN/rann_list_fingerprint.h diff --git a/src/USER-RANN/rann_list_activation.h b/src/USER-RANN/rann_list_activation.h deleted file mode 100644 index a140b92c65..0000000000 --- a/src/USER-RANN/rann_list_activation.h +++ /dev/null @@ -1,2 +0,0 @@ -#include "rann_activation_linear.h" -#include "rann_activation_sig_i.h" diff --git a/src/USER-RANN/rann_list_fingerprint.h b/src/USER-RANN/rann_list_fingerprint.h deleted file mode 100644 index 005c7f1b04..0000000000 --- a/src/USER-RANN/rann_list_fingerprint.h +++ /dev/null @@ -1,8 +0,0 @@ -#include "rann_fingerprint_bond.h" -#include "rann_fingerprint_bondscreened.h" -#include "rann_fingerprint_bondscreenedspin.h" -#include "rann_fingerprint_bondspin.h" -#include "rann_fingerprint_radial.h" -#include "rann_fingerprint_radialscreened.h" -#include "rann_fingerprint_radialscreenedspin.h" -#include "rann_fingerprint_radialspin.h" From 02021eb3302654c0851e5c5250575a1e5ddbc768 Mon Sep 17 00:00:00 2001 From: kipbarrett Date: Fri, 5 Mar 2021 16:49:04 -0600 Subject: [PATCH 0137/1217] removed factory creation --- src/USER-RANN/pair_rann.cpp | 274 +++++++++++++++++++----------------- src/USER-RANN/pair_rann.h | 90 ++++++------ 2 files changed, 186 insertions(+), 178 deletions(-) diff --git a/src/USER-RANN/pair_rann.cpp b/src/USER-RANN/pair_rann.cpp index 3207b76934..0dcf3740a6 100644 --- a/src/USER-RANN/pair_rann.cpp +++ b/src/USER-RANN/pair_rann.cpp @@ -29,8 +29,6 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 */ #define MAXLINE 1024 #include "pair_rann.h" -#include "rann_list_activation.h" -#include "rann_list_fingerprint.h" #include "tokenizer.h" #include #include @@ -45,6 +43,17 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 #include "error.h" #include "update.h" #include "math_special.h" +#include "rann_fingerprint_bond.h" +#include "rann_fingerprint_bondscreened.h" +#include "rann_fingerprint_bondscreenedspin.h" +#include "rann_fingerprint_bondspin.h" +#include "rann_fingerprint_radial.h" +#include "rann_fingerprint_radialscreened.h" +#include "rann_fingerprint_radialscreenedspin.h" +#include "rann_fingerprint_radialspin.h" +#include "rann_activation_linear.h" +#include "rann_activation_sig_i.h" + using namespace LAMMPS_NS; @@ -83,22 +92,7 @@ PairRANN::PairRANN(LAMMPS *lmp) : Pair(lmp) allscreen = true; dospin = false; - fingerprint_map = new FingerprintCreatorMap(); - #define FINGERPRINT_CLASS - #define FingerprintStyle(key,Class) \ - (*fingerprint_map)[#key] = &fingerprint_creator; - #include "rann_list_fingerprint.h" - #undef FingerprintStyle - #undef FINGERPRINT_CLASS - activation_map = new ActivationCreatorMap(); - #define ACTIVATION_CLASS - #define ActivationStyle(key,Class) \ - (*activation_map)[#key] = &activation_creator; - - #include "rann_list_activation.h" - #undef ActivationStyle - #undef ACTIVATION_CLASS } PairRANN::~PairRANN() @@ -181,7 +175,7 @@ PairRANN::~PairRANN() -void PairRANN::allocate(std::vector elementwords) +void PairRANN::allocate(const std::vector elementwords) { int i,j,k,l,n; n = atom->ntypes; @@ -295,7 +289,9 @@ void PairRANN::read_file(char *filename) int n,nwords; std::string line,line1; int longline = 4096; + int linenum; char linetemp[longline]; + std::string strtemp; char *ptr; bool comment; char str[128]; @@ -303,10 +299,17 @@ void PairRANN::read_file(char *filename) fp = utils::open_potential(filename,lmp,nullptr); if (fp == nullptr) {error->one(FLERR,"Cannot open RANN potential file");} ptr=fgets(linetemp,longline,fp); - strip_comments(linetemp,fp); - line=linetemp; + linenum++; + strtemp=utils::trim_comment(linetemp); + while (strtemp.empty()) { + ptr=fgets(linetemp,longline,fp); + strtemp=utils::trim_comment(linetemp); + linenum++; + } + line=strtemp; while (eof == 0) { ptr=fgets(linetemp,longline,fp); + linenum++; if (ptr == NULL) { if (check_potential()) { error->one(FLERR,"Invalid syntax in potential file, values are inconsistent or missing"); @@ -316,27 +319,38 @@ void PairRANN::read_file(char *filename) break; } } - strip_comments(linetemp,fp); + strtemp=utils::trim_comment(linetemp); + while (strtemp.empty()) { + ptr=fgets(linetemp,longline,fp); + strtemp=utils::trim_comment(linetemp); + linenum++; + } line1=linetemp; Tokenizer values = Tokenizer(line,": ,\t_\n"); Tokenizer values1 = Tokenizer(line1,": ,\t_\n"); linev = values.as_vector(); line1v = values1.as_vector(); - if (linev[0].compare("atomtypes")==0)read_atom_types(linev,line1v); - else if (linev[0].compare("mass")==0)read_mass(linev,line1v); - else if (linev[0].compare("fingerprintsperelement")==0)read_fpe(linev,line1v); - else if (linev[0].compare("fingerprints")==0)read_fingerprints(linev,line1v); - else if (linev[0].compare("fingerprintconstants")==0)read_fingerprint_constants(linev,line1v); - else if (linev[0].compare("networklayers")==0)read_network_layers(linev,line1v); - else if (linev[0].compare("layersize")==0)read_layer_size(linev,line1v); - else if (linev[0].compare("weight")==0)read_weight(linev,line1v,fp); - else if (linev[0].compare("bias")==0)read_bias(linev,line1v,fp); - else if (linev[0].compare("activationfunctions")==0)read_activation_functions(linev,line1v); - else if (linev[0].compare("calibrationparameters")==0)continue;//information on how the network was trained - else if (linev[0].compare("screening")==0)read_screening(linev,line1v); + if (linev[0]=="atomtypes") read_atom_types(linev,line1v,filename,linenum); + else if (linev[0]=="mass") read_mass(linev,line1v,filename,linenum); + else if (linev[0]=="fingerprintsperelement") read_fpe(linev,line1v,filename,linenum); + else if (linev[0]=="fingerprints") read_fingerprints(linev,line1v,filename,linenum); + else if (linev[0]=="fingerprintconstants") read_fingerprint_constants(linev,line1v,filename,linenum); + else if (linev[0]=="networklayers") read_network_layers(linev,line1v,filename,linenum); + else if (linev[0]=="layersize") read_layer_size(linev,line1v,filename,linenum); + else if (linev[0]=="weight") read_weight(linev,line1v,fp,filename,&linenum); + else if (linev[0]=="bias") read_bias(linev,line1v,fp,filename,&linenum); + else if (linev[0]=="activationfunctions") read_activation_functions(linev,line1v,filename,linenum); + else if (linev[0]=="screening") read_screening(linev,line1v,filename,linenum); + else if (linev[0]=="calibrationparameters") continue;//information on how the network was trained else error->one(FLERR,"Could not understand file syntax: unknown keyword"); ptr=fgets(linetemp,longline,fp); - strip_comments(linetemp,fp); + linenum++; + strtemp=utils::trim_comment(linetemp); + while (strtemp.empty()) { + ptr=fgets(linetemp,longline,fp); + strtemp=utils::trim_comment(linetemp); + linenum++; + } if (ptr == NULL) { if (check_potential()) { error->one(FLERR,"Invalid syntax in potential file, values are inconsistent or missing"); @@ -350,49 +364,32 @@ void PairRANN::read_file(char *filename) } } -void PairRANN::strip_comments(char * line,FILE* fp) { - char *ptr; - bool comment; - utils::trim_comment(line); - if (strlen(line)==0) { - comment = true; - while (comment==true) { - ptr = fgets(line,4096,fp); - if (ptr==NULL) error->one(FLERR,"Unexpected end of RANN file"); - utils::trim_comment(line); - if (strlen(line) == 0) continue; - comment = false; - } - } -} - -void PairRANN::read_atom_types(std::vector line,std::vector line1) { +void PairRANN::read_atom_types(std::vector line,std::vector line1,char *filename,int linenum) { int nwords = line1.size(); - if (nwords < 1) error->one(FLERR,"Incorrect syntax for atom types"); + if (nwords < 1) error->one(filename,linenum,"Incorrect syntax for atom types"); nelements = nwords; - line1.resize(nwords+1); - line1[nwords] = "all"; + line1.push_back("all"); allocate(line1); } -void PairRANN::read_mass(std::vector line,std::vector line1) { - if (nelements == -1)error->one(FLERR,"atom types must be defined before mass in potential file."); +void PairRANN::read_mass(std::vector line,std::vector line1,char *filename,int linenum) { + if (nelements == -1)error->one(filename,linenum-1,"atom types must be defined before mass in potential file."); int nwords = 0,i; for (i=0;ione(FLERR,"mass element not found in atom types."); + error->one(filename,linenum-1,"mass element not found in atom types."); } -void PairRANN::read_fpe(std::vector line,std::vector line1) { +void PairRANN::read_fpe(std::vector line,std::vector line1,char *filename,int linenum) { int i,j; - if (nelements == -1)error->one(FLERR,"atom types must be defined before fingerprints per element in potential file."); + if (nelements == -1)error->one(filename,linenum-1,"atom types must be defined before fingerprints per element in potential file."); for (i=0;i line,std::vector l return; } } - error->one(FLERR,"fingerprint-per-element element not found in atom types"); + error->one(filename,linenum-1,"fingerprint-per-element element not found in atom types"); } -void PairRANN::read_fingerprints(std::vector line,std::vector line1) { +void PairRANN::read_fingerprints(std::vector line,std::vector line1,char *filename,int linenum) { int nwords1,nwords,i,j,k,l,m,i1; bool found; char str[MAXLINE]; nwords1 = line1.size(); nwords = line.size(); - if (nelements == -1)error->one(FLERR,"atom types must be defined before fingerprints in potential file."); + if (nelements == -1)error->one(filename,linenum-1,"atom types must be defined before fingerprints in potential file."); int atomtypes[nwords-1]; for (i=1;i line,std::vectorone(FLERR,"fingerprint element not found in atom types");} + if (!found) {error->one(filename,linenum-1,"fingerprint element not found in atom types");} } i = atomtypes[0]; k = 0; - if (fingerprintperelement[i]==-1) {error->one(FLERR,"fingerprint per element must be defined before fingerprints");} + if (fingerprintperelement[i]==-1) {error->one(filename,linenum-1,"fingerprint per element must be defined before fingerprints");} while (k=fingerprintperelement[i]) {error->one(filename,linenum,"more fingerprints defined than fingerprint per element");} delete fingerprints[i][i1]; fingerprints[i][i1] = create_fingerprint(line1[k].c_str()); - if (fingerprints[i][i1]->n_body_type!=nwords-1) {error->one(FLERR,"invalid fingerprint for element combination");} + if (fingerprints[i][i1]->n_body_type!=nwords-1) {error->one(filename,linenum,"invalid fingerprint for element combination");} k++; - fingerprints[i][i1]->init(atomtypes,strtol(line1[k++].c_str(),NULL,10)); + fingerprints[i][i1]->init(atomtypes,utils::inumeric(filename,linenum,line1[k++].c_str(),1,lmp)); fingerprintcount[i]++; } } - -void PairRANN::read_fingerprint_constants(std::vector line,std::vector line1) { +void PairRANN::read_fingerprint_constants(std::vector line,std::vector line1,char *filename,int linenum) { int i,j,k,l,m,i1; bool found; char str [128]; int nwords = line.size(); - if (nelements == -1)error->one(FLERR,"atom types must be defined before fingerprints in potential file."); + if (nelements == -1)error->one(filename,linenum-1,"atom types must be defined before fingerprints in potential file."); int n_body_type = nwords-4; int atomtypes[n_body_type]; for (i=1;i<=n_body_type;i++) { @@ -454,7 +451,7 @@ void PairRANN::read_fingerprint_constants(std::vector line,std::vec break; } } - if (!found) {error->one(FLERR,"fingerprint element not found in atom types");} + if (!found) {error->one(filename,linenum-1,"fingerprint element not found in atom types");} } i = atomtypes[0]; found = false; @@ -464,7 +461,7 @@ void PairRANN::read_fingerprint_constants(std::vector line,std::vec for (j=0;jatomtypes[j]!=atomtypes[j]) {break;} if (j==n_body_type-1) { - if (line[nwords-3].compare(fingerprints[i][k]->style)==0 && strtol(line[nwords-2].c_str(),NULL,10)==fingerprints[i][k]->id) { + if (line[nwords-3].compare(fingerprints[i][k]->style)==0 && utils::inumeric(filename,linenum,line[nwords-2].c_str(),1,lmp)==fingerprints[i][k]->id) { found=true; i1 = k; break; @@ -473,17 +470,17 @@ void PairRANN::read_fingerprint_constants(std::vector line,std::vec } if (found) {break;} } - if (!found) {error->one(FLERR,"cannot define constants for unknown fingerprint");} + if (!found) {error->one(filename,linenum-1,"cannot define constants for unknown fingerprint");} fingerprints[i][i1]->fullydefined=fingerprints[i][i1]->parse_values(line[nwords-1],line1); } -void PairRANN::read_network_layers(std::vector line,std::vector line1) { +void PairRANN::read_network_layers(std::vector line,std::vector line1,char *filename,int linenum) { int i,j; - if (nelements == -1)error->one(FLERR,"atom types must be defined before network layers in potential file."); + if (nelements == -1)error->one(filename,linenum-1,"atom types must be defined before network layers in potential file."); for (i=0;ione(FLERR,"invalid number of network layers"); + net[i].layers = utils::inumeric(filename,linenum,line1[0].c_str(),1,lmp); + if (net[i].layers < 1)error->one(filename,linenum,"invalid number of network layers"); delete [] net[i].dimensions; weightdefined[i] = new bool [net[i].layers]; biasdefined[i] = new bool [net[i].layers]; @@ -504,105 +501,107 @@ void PairRANN::read_network_layers(std::vector line,std::vectorone(FLERR,"network layers element not found in atom types"); + error->one(filename,linenum-1,"network layers element not found in atom types"); } -void PairRANN::read_layer_size(std::vector line,std::vector line1) { +void PairRANN::read_layer_size(std::vector line,std::vector line1,char *filename,int linenum) { int i; for (i=0;ione(FLERR,"networklayers for each atom type must be defined before the corresponding layer sizes."); - int j = strtol(line[2].c_str(),NULL,10); - if (j>=net[i].layers || j<0) {error->one(FLERR,"invalid layer in layer size definition");}; - net[i].dimensions[j]= strtol(line1[0].c_str(),NULL,10); + if (net[i].layers==0)error->one(filename,linenum-1,"networklayers for each atom type must be defined before the corresponding layer sizes."); + int j = utils::inumeric(filename,linenum,line[2].c_str(),1,lmp); + if (j>=net[i].layers || j<0) {error->one(filename,linenum,"invalid layer in layer size definition");}; + net[i].dimensions[j]= utils::inumeric(filename,linenum,line1[0].c_str(),1,lmp); return; } } - error->one(FLERR,"layer size element not found in atom types"); + error->one(filename,linenum-1,"layer size element not found in atom types"); } -void PairRANN::read_weight(std::vector line,std::vector line1,FILE* fp) { +void PairRANN::read_weight(std::vector line,std::vector line1,FILE* fp,char *filename,int *linenum) { int i,j,k,l,nwords; char *ptr; int longline = 4096; char linetemp [longline]; for (l=0;lone(FLERR,"networklayers must be defined before weights."); - i=strtol(line[2].c_str(),NULL,10); - if (i>=net[l].layers || i<0)error->one(FLERR,"invalid weight layer"); - if (net[l].dimensions[i]==0 || net[l].dimensions[i+1]==0) error->one(FLERR,"network layer sizes must be defined before corresponding weight"); + if (net[l].layers==0)error->one(filename,*linenum-1,"networklayers must be defined before weights."); + i=utils::inumeric(filename,*linenum,line[2].c_str(),1,lmp); + if (i>=net[l].layers || i<0)error->one(filename,*linenum-1,"invalid weight layer"); + if (net[l].dimensions[i]==0 || net[l].dimensions[i+1]==0) error->one(filename,*linenum-1,"network layer sizes must be defined before corresponding weight"); net[l].Weights[i] = new double [net[l].dimensions[i]*net[l].dimensions[i+1]]; weightdefined[l][i] = true; nwords = line1.size(); - if (nwords != net[l].dimensions[i])error->one(FLERR,"invalid weights per line"); + if (nwords != net[l].dimensions[i])error->one(filename,*linenum,"invalid weights per line"); for (k=0;kone(FLERR,"unexpected end of potential file!"); + if (ptr==NULL)error->one(filename,*linenum,"unexpected end of potential file!"); nwords = line1.size(); - if (nwords != net[l].dimensions[i])error->one(FLERR,"invalid weights per line"); + if (nwords != net[l].dimensions[i])error->one(filename,*linenum,"invalid weights per line"); for (k=0;kone(FLERR,"weight element not found in atom types"); + error->one(filename,*linenum-1,"weight element not found in atom types"); } -void PairRANN::read_bias(std::vector line,std::vector line1,FILE* fp) { +void PairRANN::read_bias(std::vector line,std::vector line1,FILE* fp,char *filename,int *linenum) { int i,j,l,nwords; char *ptr; char linetemp[MAXLINE]; for (l=0;lone(FLERR,"networklayers must be defined before biases."); - i=strtol(line[2].c_str(),NULL,10); - if (i>=net[l].layers || i<0)error->one(FLERR,"invalid bias layer"); - if (net[l].dimensions[i]==0) error->one(FLERR,"network layer sizes must be defined before corresponding bias"); + if (net[l].layers==0)error->one(filename,*linenum-1,"networklayers must be defined before biases."); + i=utils::inumeric(filename,*linenum,line[2].c_str(),1,lmp); + if (i>=net[l].layers || i<0)error->one(filename,*linenum-1,"invalid bias layer"); + if (net[l].dimensions[i]==0) error->one(filename,*linenum-1,"network layer sizes must be defined before corresponding bias"); biasdefined[l][i] = true; net[l].Biases[i] = new double [net[l].dimensions[i+1]]; - net[l].Biases[i][0] = strtod(line1[0].c_str(),NULL); + net[l].Biases[i][0] = utils::numeric(filename,*linenum,line1[0].c_str(),1,lmp); for (j=1;jone(FLERR,"bias element not found in atom types"); + error->one(filename,*linenum-1,"bias element not found in atom types"); } -void PairRANN::read_activation_functions(std::vector line,std::vector line1) { +void PairRANN::read_activation_functions(std::vector line,std::vector line1,char *filename,int linenum) { int i,j,l,nwords; int *ptr; for (l=0;lone(FLERR,"networklayers must be defined before activation functions."); + if (net[l].layers==0)error->one(filename,linenum-1,"networklayers must be defined before activation functions."); i = strtol(line[2].c_str(),NULL,10); - if (i>=net[l].layers || i<0)error->one(FLERR,"invalid activation layer"); + if (i>=net[l].layers || i<0)error->one(filename,linenum-1,"invalid activation layer"); delete activation[l][i]; activation[l][i]=create_activation(line1[0].c_str()); return; } } - error->one(FLERR,"activation function element not found in atom types"); + error->one(filename,linenum-1,"activation function element not found in atom types"); } -void PairRANN::read_screening(std::vector line,std::vector line1) { +void PairRANN::read_screening(std::vector line,std::vector line1,char *filename,int linenum) { int i,j,k; bool found; int nwords = line.size(); - if (nelements == -1)error->one(FLERR,"atom types must be defined before fingerprints in potential file."); - if (nwords!=5)error->one(FLERR,"invalid screening command"); + if (nelements == -1)error->one(filename,linenum-1,"atom types must be defined before fingerprints in potential file."); + if (nwords!=5)error->one(filename,linenum-1,"invalid screening command"); int n_body_type = 3; int atomtypes[n_body_type]; for (i=1;i<=n_body_type;i++) { @@ -614,7 +613,7 @@ void PairRANN::read_screening(std::vector line,std::vectorone(FLERR,"fingerprint element not found in atom types");} + if (!found) {error->one(filename,linenum-1,"fingerprint element not found in atom types");} } i = atomtypes[0]; j = atomtypes[1]; @@ -622,14 +621,14 @@ void PairRANN::read_screening(std::vector line,std::vectorone(FLERR,"unrecognized screening keyword"); + else error->one(filename,linenum-1,"unrecognized screening keyword"); } //Called after finishing reading the potential file to make sure it is complete. True is bad. @@ -1223,17 +1222,31 @@ int PairRANN::factorial(int n) { return round(MathSpecial::factorial(n)); } -template -RANN::Fingerprint *PairRANN::fingerprint_creator(PairRANN* pair) -{ - return new T(pair); -} - RANN::Fingerprint *PairRANN::create_fingerprint(const char *style) { - if (fingerprint_map->find(style) != fingerprint_map->end()) { - FingerprintCreator fingerprint_creator = (*fingerprint_map)[style]; - return fingerprint_creator(this); + if (strcmp(style,"radial")==0) { + return new RANN::Fingerprint_radial(this); + } + else if (strcmp(style,"radialscreened")==0) { + return new RANN::Fingerprint_radialscreened(this); + } + else if (strcmp(style,"radialscreenedspin")==0) { + return new RANN::Fingerprint_radialscreenedspin(this); + } + else if (strcmp(style,"radialspin")==0) { + return new RANN::Fingerprint_radialspin(this); + } + else if (strcmp(style,"bond")==0) { + return new RANN::Fingerprint_bond(this); + } + else if (strcmp(style,"bondscreened")==0) { + return new RANN::Fingerprint_bondscreened(this); + } + else if (strcmp(style,"bondscreenedspin")==0) { + return new RANN::Fingerprint_bondscreenedspin(this); + } + else if (strcmp(style,"bondspin")==0) { + return new RANN::Fingerprint_bondspin(this); } char str[128]; sprintf(str,"Unknown fingerprint style %s",style); @@ -1241,17 +1254,14 @@ RANN::Fingerprint *PairRANN::create_fingerprint(const char *style) return NULL; } -template -RANN::Activation *PairRANN::activation_creator(PairRANN* pair) -{ - return new T(pair); -} RANN::Activation *PairRANN::create_activation(const char *style) { - if (activation_map->find(style) != activation_map->end()) { - ActivationCreator activation_creator = (*activation_map)[style]; - return activation_creator(this); + if (strcmp(style,"linear")==0) { + return new RANN::Activation_linear(this); + } + else if (strcmp(style,"sigI")==0) { + return new RANN::Activation_sigI(this); } char str[128]; sprintf(str,"Unknown activation style %s",style); diff --git a/src/USER-RANN/pair_rann.h b/src/USER-RANN/pair_rann.h index 9f1dbe9212..a50a46f8a2 100644 --- a/src/USER-RANN/pair_rann.h +++ b/src/USER-RANN/pair_rann.h @@ -41,7 +41,6 @@ PairStyle(rann,PairRANN) #include "neighbor.h" #include "neigh_list.h" #include "pair.h" -#include namespace LAMMPS_NS { @@ -65,15 +64,13 @@ namespace LAMMPS_NS { void init_list(int , NeighList *); void errorf(const char*,int,const char*); int factorial(int); - //black magic for modular fingerprints and activations - class RANN::Activation ***activation; - class RANN::Fingerprint ***fingerprints; - typedef RANN::Fingerprint *(*FingerprintCreator)(PairRANN *); - typedef RANN::Activation *(*ActivationCreator)(PairRANN *); - typedef std::map FingerprintCreatorMap; - typedef std::map ActivationCreatorMap; - FingerprintCreatorMap *fingerprint_map; - ActivationCreatorMap *activation_map; + +// typedef RANN::Fingerprint *(*FingerprintCreator)(PairRANN *); +// typedef RANN::Activation *(*ActivationCreator)(PairRANN *); +// typedef std::map FingerprintCreatorMap; +// typedef std::map ActivationCreatorMap; +// FingerprintCreatorMap *fingerprint_map; +// ActivationCreatorMap *activation_map; RANN::Fingerprint * create_fingerprint(const char *); RANN::Activation * create_activation(const char *); @@ -110,53 +107,54 @@ namespace LAMMPS_NS { struct Simulation{ int *id; - bool forces; - bool spins; - double **x; - double **f; - double **s; - double box[3][3]; - double origin[3]; - double **features; - double **dfx; - double **dfy; - double **dfz; - double **dsx; - double **dsy; - double **dsz; - int *ilist,*numneigh,**firstneigh,*type,inum,gnum; + bool forces; + bool spins; + double **x; + double **f; + double **s; + double box[3][3]; + double origin[3]; + double **features; + double **dfx; + double **dfy; + double **dfz; + double **dsx; + double **dsy; + double **dsz; + int *ilist,*numneigh,**firstneigh,*type,inum,gnum; }; struct NNarchitecture{ - int layers; - int *dimensions;//vector of length layers with entries for neurons per layer - double **Weights; - double **Biases; - int *activations;//unused - int maxlayer;//longest layer (for memory allocation) + int layers; + int *dimensions;//vector of length layers with entries for neurons per layer + double **Weights; + double **Biases; + int *activations;//unused + int maxlayer;//longest layer (for memory allocation) }; Simulation *sims; NNarchitecture *net;//array of networks, 1 for each element. + protected: + RANN::Activation ***activation; + RANN::Fingerprint ***fingerprints; + private: - template static RANN::Fingerprint *fingerprint_creator(PairRANN *); - template static RANN::Activation *activation_creator(PairRANN *); //new functions - void allocate(std::vector);//called after reading element list, but before reading the rest of the potential + void allocate(const std::vector);//called after reading element list, but before reading the rest of the potential void read_file(char *);//read potential file - void strip_comments(char *,FILE *fp); - void read_atom_types(std::vector,std::vector); - void read_mass(std::vector,std::vector); - void read_fpe(std::vector,std::vector);//fingerprints per element. Count total fingerprints defined for each 1st element in element combinations - void read_fingerprints(std::vector,std::vector); - void read_fingerprint_constants(std::vector,std::vector); - void read_network_layers(std::vector,std::vector);//include input and output layer (hidden layers + 2) - void read_layer_size(std::vector,std::vector); - void read_weight(std::vector,std::vector,FILE*);//weights should be formatted as properly shaped matrices - void read_bias(std::vector,std::vector,FILE*);//biases should be formatted as properly shaped vectors - void read_activation_functions(std::vector,std::vector); - void read_screening(std::vector,std::vector); + void read_atom_types(std::vector,std::vector,char*,int); + void read_mass(std::vector,std::vector,char*,int); + void read_fpe(std::vector,std::vector,char*,int);//fingerprints per element. Count total fingerprints defined for each 1st element in element combinations + void read_fingerprints(std::vector,std::vector,char*,int); + void read_fingerprint_constants(std::vector,std::vector,char*,int); + void read_network_layers(std::vector,std::vector,char*,int);//include input and output layer (hidden layers + 2) + void read_layer_size(std::vector,std::vector,char*,int); + void read_weight(std::vector,std::vector,FILE*,char*,int*);//weights should be formatted as properly shaped matrices + void read_bias(std::vector,std::vector,FILE*,char*,int*);//biases should be formatted as properly shaped vectors + void read_activation_functions(std::vector,std::vector,char*,int); + void read_screening(std::vector,std::vector,char*,int); bool check_potential();//after finishing reading potential file void propagateforward(double *,double **,double **,int,int);//called by compute to get force and energy void propagateforwardspin(double *,double **,double **,double**,int,int);//called by compute to get force and energy From fdf06e48b2cfc0b8ec6264c73c3dfafbb05261ec Mon Sep 17 00:00:00 2001 From: kipbarrett Date: Fri, 5 Mar 2021 16:53:49 -0600 Subject: [PATCH 0138/1217] removed factory creation --- src/USER-RANN/pair_rann.h | 6 ------ 1 file changed, 6 deletions(-) diff --git a/src/USER-RANN/pair_rann.h b/src/USER-RANN/pair_rann.h index a50a46f8a2..23bea7a800 100644 --- a/src/USER-RANN/pair_rann.h +++ b/src/USER-RANN/pair_rann.h @@ -65,12 +65,6 @@ namespace LAMMPS_NS { void errorf(const char*,int,const char*); int factorial(int); -// typedef RANN::Fingerprint *(*FingerprintCreator)(PairRANN *); -// typedef RANN::Activation *(*ActivationCreator)(PairRANN *); -// typedef std::map FingerprintCreatorMap; -// typedef std::map ActivationCreatorMap; -// FingerprintCreatorMap *fingerprint_map; -// ActivationCreatorMap *activation_map; RANN::Fingerprint * create_fingerprint(const char *); RANN::Activation * create_activation(const char *); From 4960aeb3c825b831e4bad060a848cb0e7c8d4dfc Mon Sep 17 00:00:00 2001 From: Gurgen Date: Sat, 6 Mar 2021 23:39:37 +0300 Subject: [PATCH 0139/1217] error on line 194 --- lib/gpu/lal_lj_smooth.cu | 233 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 233 insertions(+) create mode 100644 lib/gpu/lal_lj_smooth.cu diff --git a/lib/gpu/lal_lj_smooth.cu b/lib/gpu/lal_lj_smooth.cu new file mode 100644 index 0000000000..b69f8b9388 --- /dev/null +++ b/lib/gpu/lal_lj_smooth.cu @@ -0,0 +1,233 @@ +// ************************************************************************** +// lj_smooth.cu +// ------------------- +// W. Michael Brown (ORNL) +// +// Device code for acceleration of the lj/smooth pair style +// +// __________________________________________________________________________ +// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) +// __________________________________________________________________________ +// +// begin : +// email : brownw@ornl.gov +// *************************************************************************** + +#if defined(NV_KERNEL) || defined(USE_HIP) +#include "lal_aux_fun1.h" +#ifndef _DOUBLE_DOUBLE +_texture( pos_tex,float4); +#else +_texture_2d( pos_tex,int4); +#endif +#else +#define pos_tex x_ +#endif + +__kernel void k_lj_smooth(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict lj1, + const __global numtyp4 *restrict lj3, + const __global numtyp4 *restrict ljsw, + const int lj_types, + const __global numtyp *restrict sp_lj, + const __global int * dev_nbor, + const __global int * dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + acctyp energy=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + if (ii0) { + numtyp e; + if (rsq < lj1[mtype].w) + e = r6inv * (lj3[mtype].x*r6inv - lj3[mtype].y) - lj3[mtype].z; + else + e = ljsw[mtype].x - ljsw[mtype].x*t - + ljsw[mtype].y*tsq/2.0 - ljsw[mtype].z*tsq*t/3.0 - + ljsw[mtype].z*tsq*tsq/4.0 - lj3[mtype].z; + + //numtyp e=r6inv*(lj3[mtype].x*r6inv-lj3[mtype].y); + energy+=factor_lj*e; + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, + ans,engv); + } // if ii +} + +__kernel void k_lj_smooth_fast(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict lj1_in, + const __global numtyp4 *restrict lj3_in, + const __global numtyp4 *restrict ljsw, + const __global numtyp *restrict sp_lj_in, + const __global int * dev_nbor, + const __global int * dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp4 lj1[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp4 lj3[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp sp_lj[4]; + if (tid<4) + sp_lj[tid]=sp_lj_in[tid]; + if (tid0) + lj3[tid]=lj3_in[tid]; + } + + acctyp energy=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + __syncthreads(); + + if (ii0) { + numtyp e; + if (rsq < lj1[mtype].w) + e = r6inv * (lj3[mtype].x*r6inv - lj3[mtype].y) - lj3[mtype].z; + else + e = ljsw[mtype].x - ljsw[mtype].x*t - + ljsw[mtype].y*tsq/2.0 - ljsw[mtype].z*tsq*t/3.0 - + ljsw[mtype].z*tsq*tsq/4.0 - lj3[mtype].z; //??? + + //numtyp e=r6inv*(lj3[mtype].x*r6inv-lj3[mtype].y); + energy+=factor_lj*e; + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, + ans,engv); + } // if ii +} + From e32d059d268bb019dfad141f61a2a72e41d87c73 Mon Sep 17 00:00:00 2001 From: Gurgen Date: Sat, 6 Mar 2021 23:43:25 +0300 Subject: [PATCH 0140/1217] lj/smooth/gpu --- lib/gpu/lal_lj_smooth.cpp | 184 +++++++++++++++++++++++++++++++++ lib/gpu/lal_lj_smooth.h | 92 +++++++++++++++++ lib/gpu/lal_lj_smooth_ext.cpp | 146 ++++++++++++++++++++++++++ src/GPU/pair_lj_smooth_gpu.cpp | 67 ++++++++---- src/GPU/pair_lj_smooth_gpu.h | 6 +- 5 files changed, 470 insertions(+), 25 deletions(-) create mode 100644 lib/gpu/lal_lj_smooth.cpp create mode 100644 lib/gpu/lal_lj_smooth.h create mode 100644 lib/gpu/lal_lj_smooth_ext.cpp diff --git a/lib/gpu/lal_lj_smooth.cpp b/lib/gpu/lal_lj_smooth.cpp new file mode 100644 index 0000000000..5c75539660 --- /dev/null +++ b/lib/gpu/lal_lj_smooth.cpp @@ -0,0 +1,184 @@ +/*************************************************************************** + lj_smooth.cpp + ------------------- + W. Michael Brown (ORNL) + + Class for acceleration of the lj/smooth pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : brownw@ornl.gov + ***************************************************************************/ + +#if defined(USE_OPENCL) +#include "lj_smooth_cl.h" +#elif defined(USE_CUDART) +const char *lj=0; +#else +#include "lj_smooth_cubin.h" +#endif + +#include "lal_lj_smooth.h" +#include +namespace LAMMPS_AL { +#define LJSMOOTHT LJSMOOTH + +extern Device device; + +template +LJSMOOTHT::LJSMOOTH() : BaseAtomic(), _allocated(false) { +} + +template +LJSMOOTHT::~LJSMOOTH() { + clear(); +} + +template +int LJSMOOTHT::bytes_per_atom(const int max_nbors) const { + return this->bytes_per_atom_atomic(max_nbors); +} + +template +int LJSMOOTHT::init(const int ntypes, + double **host_cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, + double **host_lj4, double **host_offset, + double *host_special_lj, const int nlocal, + const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *_screen, + double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw4, + double **cut_inner, double **cut_inner_sq) { + int success; + success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, + _screen,lj_smooth,"k_lj_smooth"); + if (success!=0) + return success; + + // If atom type constants fit in shared memory use fast kernel + int lj_types=ntypes; + shared_types=false; + int max_shared_types=this->device->max_shared_types(); + if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) { + lj_types=max_shared_types; + shared_types=true; + } + _lj_types=lj_types; + + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write(lj_types*lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; iucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,lj1,host_write,host_lj1,host_lj2, + host_cutsq, cut_inner_sq); + + lj3.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,lj3,host_write,host_lj3,host_lj4, + host_offset, cut_inner); + + ljsw.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,ljsw,host_write,host_ljsw1,host_ljsw2, + host_ljsw3,host_ljsw4); + + UCL_H_Vec dview; + sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY); + dview.view(host_special_lj,4,*(this->ucl_device)); + ucl_copy(sp_lj,dview,false); + + _allocated=true; + this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+ljsw.row_bytes()+sp_lj.row_bytes(); + return 0; +} + +template +void LJSMOOTHT::reinit(const int ntypes, double **host_cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, + double **host_lj4, double **host_offset, + double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw4, + double **cut_inner, double **cut_inner_sq) { + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write(_lj_types*_lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; i<_lj_types*_lj_types; i++) + host_write[i]=0.0; + + this->atom->type_pack4(ntypes,_lj_types,lj1,host_write,host_lj1,host_lj2, + host_cutsq, cut_inner_sq); + this->atom->type_pack4(ntypes,_lj_types,lj3,host_write,host_lj3,host_lj4, + host_offset, cut_inner); + this->atom->type_pack4(ntypes,_lj_types,ljsw,host_write,host_ljsw1,host_ljsw2, + host_ljsw3,host_ljsw4); +} + +template +void LJSMOOTHT::clear() { + if (!_allocated) + return; + _allocated=false; + + lj1.clear(); + lj3.clear(); + ljsw.clear(); + sp_lj.clear(); + this->clear_atomic(); +} + +template +double LJSMOOTHT::host_memory_usage() const { + return this->host_memory_usage_atomic()+sizeof(LJSMOOTH); +} + +// --------------------------------------------------------------------------- +// Calculate energies, forces, and torques +// --------------------------------------------------------------------------- +template +void LJSMOOTHT::loop(const bool _eflag, const bool _vflag) { + // Compute the block size and grid size to keep all cores busy + const int BX=this->block_size(); + int eflag, vflag; + if (_eflag) + eflag=1; + else + eflag=0; + + if (_vflag) + vflag=1; + else + vflag=0; + + int GX=static_cast(ceil(static_cast(this->ans->inum())/ + (BX/this->_threads_per_atom))); + + int ainum=this->ans->inum(); + int nbor_pitch=this->nbor->nbor_pitch(); + this->time_pair.start(); + if (shared_types) { + this->k_pair_fast.set_size(GX,BX); + this->k_pair_fast.run(&this->atom->x, &lj1, &lj3, &ljsw, &sp_lj, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->ans->force, &this->ans->engv, &eflag, + &vflag, &ainum, &nbor_pitch, + &this->_threads_per_atom); + } else { + this->k_pair.set_size(GX,BX); + this->k_pair.run(&this->atom->x, &lj1, &lj3, &ljsw, &_lj_types, &sp_lj, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->ans->force, &this->ans->engv, &eflag, &vflag, + &ainum, &nbor_pitch, &this->_threads_per_atom); + } + this->time_pair.stop(); +} + +template class LJSMOOTH; +} diff --git a/lib/gpu/lal_lj_smooth.h b/lib/gpu/lal_lj_smooth.h new file mode 100644 index 0000000000..98dbad87b7 --- /dev/null +++ b/lib/gpu/lal_lj_smooth.h @@ -0,0 +1,92 @@ +/*************************************************************************** + lj_smooth.h + ------------------- + W. Michael Brown (ORNL) + + Class for acceleration of the lj/smooth pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : brownw@ornl.gov + ***************************************************************************/ + +#ifndef LAL_LJ_SMOOTH_H +#define LAL_LJ_SMOOTH_H + +#include "lal_base_atomic.h" + +namespace LAMMPS_AL { + +template +class LJSMOOTH : public BaseAtomic { + public: + LJSMOOTH(); + ~LJSMOOTH(); + + /// Clear any previous data and set up for a new LAMMPS run + /** \param max_nbors initial number of rows in the neighbor matrix + * \param cell_size cutoff + skin + * \param gpu_split fraction of particles handled by device + * + * Returns: + * - 0 if successful + * - -1 if fix gpu not found + * - -3 if there is an out of memory error + * - -4 if the GPU library was not compiled for GPU + * - -5 Double precision is not supported on card **/ + int init(const int ntypes, double **host_cutsq, + double **host_lj1, double **host_lj2, double **host_lj3, + double **host_lj4, double **host_offset, double *host_special_lj, + const int nlocal, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *screen, + double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw4, + double **cut_inner, double **cut_inner_sq); + + /// Send updated coeffs from host to device (to be compatible with fix adapt) + void reinit(const int ntypes, double **host_cutsq, + double **host_lj1, double **host_lj2, double **host_lj3, + double **host_lj4, double **host_offset, + double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw4, + double **cut_inner, double **cut_inner_sq); + + /// Clear all host and device data + /** \note This is called at the beginning of the init() routine **/ + void clear(); + + /// Returns memory usage on device per atom + int bytes_per_atom(const int max_nbors) const; + + /// Total host memory used by library for pair style + double host_memory_usage() const; + + // --------------------------- TYPE DATA -------------------------- + + /// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq, lj1.w = cut_inner_sq + UCL_D_Vec lj1; + /// lj3.x = lj3, lj3.y = lj4, lj3.z = offset, lj3.w = cut_inner + UCL_D_Vec lj3; + /// ljsw.x = ljsw1, ljsw.y = ljsw2, ljsw.z = ljsw3, ljsw.w = ljsw4 + UCL_D_Vec ljsw; + /// Special LJ values + UCL_D_Vec sp_lj; + + /// If atom type constants fit in shared memory, use fast kernels + bool shared_types; + + /// Number of atom types + int _lj_types; + + private: + bool _allocated; + void loop(const bool _eflag, const bool _vflag); +}; + +} + +#endif diff --git a/lib/gpu/lal_lj_smooth_ext.cpp b/lib/gpu/lal_lj_smooth_ext.cpp new file mode 100644 index 0000000000..92624bf7fa --- /dev/null +++ b/lib/gpu/lal_lj_smooth_ext.cpp @@ -0,0 +1,146 @@ +/*************************************************************************** + lj_smooth_ext.cpp + ------------------- + W. Michael Brown (ORNL) + + Functions for LAMMPS access to lj/smooth acceleration routines. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : brownw@ornl.gov + ***************************************************************************/ + +#include +#include +#include + +#include "lal_lj_smooth.h" + +using namespace std; +using namespace LAMMPS_AL; + +static LJSMOOTH LJSMTMF; + +// --------------------------------------------------------------------------- +// Allocate memory on host and device and copy constants to device +// --------------------------------------------------------------------------- +int ljsmt_gpu_init(const int ntypes, double **cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, double **host_lj4, + double **offset, double *special_lj, const int inum, + const int nall, const int max_nbors, const int maxspecial, + const double cell_size, int &gpu_mode, FILE *screen, + double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw4, double **cut_inner, double **cut_inner_sq) { + LJSMTMF.clear(); + gpu_mode=LJSMTMF.device->gpu_mode(); + double gpu_split=LJSMTMF.device->particle_split(); + int first_gpu=LJSMTMF.device->first_device(); + int last_gpu=LJSMTMF.device->last_device(); + int world_me=LJSMTMF.device->world_me(); + int gpu_rank=LJSMTMF.device->gpu_rank(); + int procs_per_gpu=LJSMTMF.device->procs_per_gpu(); + + LJSMTMF.device->init_message(screen,"lj/smooth",first_gpu,last_gpu); + + bool message=false; + if (LJSMTMF.device->replica_me()==0 && screen) + message=true; + + if (message) { + fprintf(screen,"Initializing Device and compiling on process 0..."); + fflush(screen); + } + + int init_ok=0; + if (world_me==0) + init_ok=LJSMTMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, + host_lj4, offset, special_lj, inum, nall, 300, + maxspecial, cell_size, gpu_split, screen, + host_ljsw1, host_ljsw2, host_ljsw3, host_ljsw4, cut_inner, cut_inner_sq); + + LJSMTMF.device->world_barrier(); + if (message) + fprintf(screen,"Done.\n"); + + for (int i=0; igpu_barrier(); + if (message) + fprintf(screen,"Done.\n"); + } + if (message) + fprintf(screen,"\n"); + + if (init_ok==0) + LJSMTMF.estimate_gpu_overhead(); + return init_ok; +} + +// --------------------------------------------------------------------------- +// Copy updated coeffs from host to device +// --------------------------------------------------------------------------- +void ljsmt_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, double **host_lj4, + double **offset, double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw4, double **cut_inner, double **cut_inner_sq) { + int world_me=LJSMTMF.device->world_me(); + int gpu_rank=LJSMTMF.device->gpu_rank(); + int procs_per_gpu=LJSMTMF.device->procs_per_gpu(); + + if (world_me==0) + LJSMTMF.reinit(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4, offset, host_ljsw1, host_ljsw2, host_ljsw3, host_ljsw4, cut_inner, cut_inner_sq); + LJSMTMF.device->world_barrier(); + + for (int i=0; igpu_barrier(); + } +} + +void ljsmt_gpu_clear() { + LJSMTMF.clear(); +} + +int ** ljsmt_gpu_compute_n(const int ago, const int inum_full, + const int nall, double **host_x, int *host_type, + double *sublo, double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success) { + return LJSMTMF.compute(ago, inum_full, nall, host_x, host_type, sublo, + subhi, tag, nspecial, special, eflag, vflag, eatom, + vatom, host_start, ilist, jnum, cpu_time, success); +} + +void ljsmt_gpu_compute(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success) { + LJSMTMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj, + firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success); +} + +double ljsmt_gpu_bytes() { + return LJSMTMF.host_memory_usage(); +} + + diff --git a/src/GPU/pair_lj_smooth_gpu.cpp b/src/GPU/pair_lj_smooth_gpu.cpp index 4ea5cce92e..882055e84d 100644 --- a/src/GPU/pair_lj_smooth_gpu.cpp +++ b/src/GPU/pair_lj_smooth_gpu.cpp @@ -40,34 +40,40 @@ using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition -int ljl_gpu_init(const int ntypes, double **cutsq, double **host_lj1, +int ljsmt_gpu_init(const int ntypes, double **cutsq, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, double **offset, double *special_lj, const int nlocal, const int nall, const int max_nbors, const int maxspecial, - const double cell_size, int &gpu_mode, FILE *screen); + const double cell_size, int &gpu_mode, FILE *screen, + double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw4, + double **cut_inner, double **cut_innersq); -void ljl_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1, +void ljsmt_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, - double **offset); + double **offset, + double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw4, + double **cut_inner, double **cut_innersq); -void ljl_gpu_clear(); -int ** ljl_gpu_compute_n(const int ago, const int inum, +void ljsmt_gpu_clear(); +int ** ljsmt_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x, int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial, tagint **special, const bool eflag, const bool vflag, const bool eatom, const bool vatom, int &host_start, int **ilist, int **jnum, const double cpu_time, bool &success); -void ljl_gpu_compute(const int ago, const int inum, const int nall, +void ljsmt_gpu_compute(const int ago, const int inum, const int nall, double **host_x, int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag, const bool vflag, const bool eatom, const bool vatom, int &host_start, const double cpu_time, bool &success); -double ljl_gpu_bytes(); +double ljsmt_gpu_bytes(); /* ---------------------------------------------------------------------- */ -PairLJSmoothGPU::PairLJSmoothGPU(LAMMPS *lmp) : PairLJCut(lmp), gpu_mode(GPU_FORCE) +PairLJSmoothGPU::PairLJSmoothGPU(LAMMPS *lmp) : PairLJSmooth(lmp), gpu_mode(GPU_FORCE) { respa_enable = 0; cpu_time = 0.0; @@ -81,7 +87,7 @@ PairLJSmoothGPU::PairLJSmoothGPU(LAMMPS *lmp) : PairLJCut(lmp), gpu_mode(GPU_FOR PairLJSmoothGPU::~PairLJSmoothGPU() { - ljl_gpu_clear(); + ljsmt_gpu_clear(); } /* ---------------------------------------------------------------------- */ @@ -108,7 +114,7 @@ void PairLJSmoothGPU::compute(int eflag, int vflag) domain->bbox(domain->sublo_lamda,domain->subhi_lamda,sublo,subhi); } inum = atom->nlocal; - firstneigh = ljl_gpu_compute_n(neighbor->ago, inum, nall, + firstneigh = ljsmt_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag, atom->nspecial, atom->special, eflag, vflag, eflag_atom, @@ -119,7 +125,7 @@ void PairLJSmoothGPU::compute(int eflag, int vflag) ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; - ljl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, + ljsmt_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh, eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success); } @@ -140,10 +146,10 @@ void PairLJSmoothGPU::compute(int eflag, int vflag) void PairLJSmoothGPU::init_style() { - cut_respa = nullptr; + //cut_respa = nullptr; if (force->newton_pair) - error->all(FLERR,"Cannot use newton pair with lj/cut/gpu pair style"); + error->all(FLERR,"Cannot use newton pair with lj/smooth/gpu pair style"); // Repeat cutsq calculation because done after call to init_style double maxcut = -1.0; @@ -165,10 +171,11 @@ void PairLJSmoothGPU::init_style() int maxspecial=0; if (atom->molecular) maxspecial=atom->maxspecial; - int success = ljl_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4, + int success = ljsmt_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4, offset, force->special_lj, atom->nlocal, atom->nlocal+atom->nghost, 300, maxspecial, - cell_size, gpu_mode, screen); + cell_size, gpu_mode, screen, ljsw1, ljsw2, + ljsw3, ljsw4, cut_inner, cut_inner_sq); GPU_EXTRA::check_flag(success,error,world); if (gpu_mode == GPU_FORCE) { @@ -184,7 +191,7 @@ void PairLJSmoothGPU::reinit() { Pair::reinit(); - ljl_gpu_reinit(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4, offset); + ljsmt_gpu_reinit(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4, offset, ljsw1, ljsw2, ljsw3, ljsw4, cut_inner, cut_inner_sq); } /* ---------------------------------------------------------------------- */ @@ -192,7 +199,7 @@ void PairLJSmoothGPU::reinit() double PairLJSmoothGPU::memory_usage() { double bytes = Pair::memory_usage(); - return bytes + ljl_gpu_bytes(); + return bytes + ljsmt_gpu_bytes(); } /* ---------------------------------------------------------------------- */ @@ -202,6 +209,7 @@ void PairLJSmoothGPU::cpu_compute(int start, int inum, int eflag, int /* vflag * int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double rsq,r2inv,r6inv,forcelj,factor_lj; + double r,t,tsq,fskin; int *jlist; double **x = atom->x; @@ -233,8 +241,18 @@ void PairLJSmoothGPU::cpu_compute(int start, int inum, int eflag, int /* vflag * if (rsq < cutsq[itype][jtype]) { r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + if (rsq < cut_inner_sq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + forcelj = r6inv * (lj1[itype][jtype]*r6inv-lj2[itype][jtype]); + } else { + r = sqrt(rsq); + t = r - cut_inner[itype][jtype]; + tsq = t*t; + fskin = ljsw1[itype][jtype] + ljsw2[itype][jtype]*t + + ljsw3[itype][jtype]*tsq + ljsw4[itype][jtype]*tsq*t; + forcelj = fskin*r; + } + fpair = factor_lj*forcelj*r2inv; f[i][0] += delx*fpair; @@ -242,8 +260,13 @@ void PairLJSmoothGPU::cpu_compute(int start, int inum, int eflag, int /* vflag * f[i][2] += delz*fpair; if (eflag) { - evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) - - offset[itype][jtype]; + if (rsq < cut_inner_sq[itype][jtype]) + evdwl = r6inv * (lj3[itype][jtype]*r6inv - + lj4[itype][jtype]) - offset[itype][jtype]; + else + evdwl = ljsw0[itype][jtype] - ljsw1[itype][jtype]*t - + ljsw2[itype][jtype]*tsq/2.0 - ljsw3[itype][jtype]*tsq*t/3.0 - + ljsw4[itype][jtype]*tsq*tsq/4.0 - offset[itype][jtype]; evdwl *= factor_lj; } diff --git a/src/GPU/pair_lj_smooth_gpu.h b/src/GPU/pair_lj_smooth_gpu.h index fc245918d0..414ce4c2d2 100644 --- a/src/GPU/pair_lj_smooth_gpu.h +++ b/src/GPU/pair_lj_smooth_gpu.h @@ -20,11 +20,11 @@ PairStyle(lj/smooth/gpu,PairLJSmoothGPU) #ifndef LMP_PAIR_LJ_SMOOTH_GPU_H #define LMP_PAIR_LJ_SMOOTH_GPU_H -#include "pair_lj_cut.h" +#include "pair_lj_smooth.h" namespace LAMMPS_NS { -class PairLJSmoothGPU : public PairLJCut { +class PairLJSmoothGPU : public PairLJSmooth { public: PairLJSmoothGPU(LAMMPS *lmp); ~PairLJSmoothGPU(); @@ -52,7 +52,7 @@ E: Insufficient memory on accelerator There is insufficient memory on one of the devices specified for the gpu package -E: Cannot use newton pair with lj/cut/gpu pair style +E: Cannot use newton pair with lj/smooth/gpu pair style Self-explanatory. From 27a81ffc867bbbd198c81276d405bd729e27e645 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 9 Mar 2021 15:34:48 -0500 Subject: [PATCH 0141/1217] add initial version of a plugin loader interface (for pair styles) --- src/input.cpp | 10 ++++++ src/input.h | 1 + src/lammpsplugin.cpp | 76 ++++++++++++++++++++++++++++++++++++++++++++ src/lammpsplugin.h | 44 +++++++++++++++++++++++++ 4 files changed, 131 insertions(+) create mode 100644 src/lammpsplugin.cpp create mode 100644 src/lammpsplugin.h diff --git a/src/input.cpp b/src/input.cpp index df5cf0efbe..57ce64815d 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -29,6 +29,7 @@ #include "group.h" #include "improper.h" #include "kspace.h" +#include "lammpsplugin.h" #include "memory.h" #include "min.h" #include "modify.h" @@ -714,6 +715,7 @@ int Input::execute_command() else if (!strcmp(command,"include")) include(); else if (!strcmp(command,"jump")) jump(); else if (!strcmp(command,"label")) label(); + else if (!strcmp(command,"load_plugin")) load_plugin(); else if (!strcmp(command,"log")) log(); else if (!strcmp(command,"next")) next_command(); else if (!strcmp(command,"partition")) partition(); @@ -1029,6 +1031,14 @@ void Input::label() /* ---------------------------------------------------------------------- */ +void Input::load_plugin() +{ + if (narg != 1) error->all(FLERR,"Illegal load_plugin command"); + lammpsplugin_load(arg[0],lmp); +} + +/* ---------------------------------------------------------------------- */ + void Input::log() { if ((narg < 1) || (narg > 2)) error->all(FLERR,"Illegal log command"); diff --git a/src/input.h b/src/input.h index a86b10a686..3b7b6d79c7 100644 --- a/src/input.h +++ b/src/input.h @@ -79,6 +79,7 @@ class Input : protected Pointers { void include(); void jump(); void label(); + void load_plugin(); void log(); void next_command(); void partition(); diff --git a/src/lammpsplugin.cpp b/src/lammpsplugin.cpp new file mode 100644 index 0000000000..d3d409de41 --- /dev/null +++ b/src/lammpsplugin.cpp @@ -0,0 +1,76 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "lammpsplugin.h" + +#include "error.h" +#include "force.h" +#include "lammps.h" +#include "modify.h" + + +#ifdef _WIN32 +#include +#else +#include +#endif + +namespace LAMMPS_NS +{ + + void lammpsplugin_load(const char *file, void *ptr) + { + LAMMPS *lmp = (LAMMPS *)ptr; +#if defined(WIN32) + utils::logmsg(lmp,"Loading of plugins not supported on Windows yet\n"); +#else + void *dso = dlopen(file,RTLD_NOW); + if (dso == nullptr) { + utils::logmesg(lmp,fmt::format("Loading of plugin from file {} failed: " + "{}", file, utils::getsyserror())); + return; + } + + void *initfunc = dlsym(dso,"lammpsplugin_init"); + if (initfunc == nullptr) { + dlclose(dso); + utils::logmesg(lmp,fmt::format("Symbol lookup failure in file {}",file)); + return; + } + ((lammpsplugin_initfunc)(initfunc))(ptr); +#endif + } + + void lammpsplugin_register(lammpsplugin_t *plugin, void *ptr) + { + LAMMPS *lmp = (LAMMPS *)ptr; + + if (plugin == nullptr) return; + if (plugin->version) + utils::logmesg(lmp,fmt::format("Loading: {}\n compiled for LAMMPS " + "version {} loaded into LAMMPS " + "version {}\n", plugin->info, + plugin->version, lmp->version)); + std::string pstyle = plugin->style; + if (pstyle == "pair") { + (*(lmp->force->pair_map))[plugin->name] = + (LAMMPS_NS::Force::PairCreator)plugin->creator; + } else { + utils::logmesg(lmp,fmt::format("Loading plugin for {} styles not " + "yet implemented\n", pstyle)); + } + } +} + + + diff --git a/src/lammpsplugin.h b/src/lammpsplugin.h new file mode 100644 index 0000000000..9784c456ee --- /dev/null +++ b/src/lammpsplugin.h @@ -0,0 +1,44 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_LAMMPSPLUGIN_H +#define LMP_LAMMPSPLUGIN_H + +#ifdef __cplusplus +extern "C" { +#endif + + typedef void *(lammpsplugin_factory)(void *); + typedef void (*lammpsplugin_initfunc)(void *); + + typedef struct { + const char *version; + const char *style; + const char *name; + const char *info; + lammpsplugin_factory *creator; + } lammpsplugin_t; + + void lammpsplugin_init(void *); + +#ifdef __cplusplus +} +#endif + +namespace LAMMPS_NS +{ + extern void lammpsplugin_load(const char *, void *); + extern void lammpsplugin_register(lammpsplugin_t *, void *); +} + +#endif From f0381b48ca95068b6c4ee222240607c4bf14f036 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 9 Mar 2021 15:50:27 -0500 Subject: [PATCH 0142/1217] add example for loading a pair style --- examples/plugins/Makefile | 17 ++ examples/plugins/morse2plugin.cpp | 29 +++ examples/plugins/pair_morse2.cpp | 359 ++++++++++++++++++++++++++++++ examples/plugins/pair_morse2.h | 70 ++++++ 4 files changed, 475 insertions(+) create mode 100644 examples/plugins/Makefile create mode 100644 examples/plugins/morse2plugin.cpp create mode 100644 examples/plugins/pair_morse2.cpp create mode 100644 examples/plugins/pair_morse2.h diff --git a/examples/plugins/Makefile b/examples/plugins/Makefile new file mode 100644 index 0000000000..0c4365dfd8 --- /dev/null +++ b/examples/plugins/Makefile @@ -0,0 +1,17 @@ +CXX=mpicxx +CXXFLAGS=-I../../src -Wall -O3 -fPIC +LD=$(CXX) -shared -rdynamic + +morse2plugin.so: morse2plugin.o pair_morse2.o + $(LD) -o $@ $^ + +.cpp.o: + $(CXX) -o $@ $(CXXFLAGS) -c $< + +pair_morse2.o: pair_morse2.cpp pair_morse2.h +morse2plugin.o: morse2plugin.cpp pair_morse2.h + +clean: + rm -f *~ *.so *.o log.lammps + + diff --git a/examples/plugins/morse2plugin.cpp b/examples/plugins/morse2plugin.cpp new file mode 100644 index 0000000000..bb21f3da95 --- /dev/null +++ b/examples/plugins/morse2plugin.cpp @@ -0,0 +1,29 @@ + +#include "lammpsplugin.h" + +#include "lammps.h" +#include "version.h" + +#include + +#include "pair_morse2.h" + +using namespace LAMMPS_NS; + +static Pair *morse2creator(LAMMPS *lmp) +{ + return new PairMorse2(lmp); +} + +static lammpsplugin_t plugin; +void lammpsplugin_init(void *lmp) +{ + memset(&plugin,0,sizeof(lammpsplugin_t)); + plugin.version = LAMMPS_VERSION; + plugin.style = "pair"; + plugin.name = "morse2"; + plugin.info = "Morse2 variant pair style v1.0 by Axel Kohlmeyer"; + plugin.creator = (lammpsplugin_factory *) &morse2creator; + + lammpsplugin_register(&plugin, (LAMMPS *)lmp); +} diff --git a/examples/plugins/pair_morse2.cpp b/examples/plugins/pair_morse2.cpp new file mode 100644 index 0000000000..a235ad297c --- /dev/null +++ b/examples/plugins/pair_morse2.cpp @@ -0,0 +1,359 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "pair_morse2.h" + +#include +#include +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairMorse2::PairMorse2(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairMorse2::~PairMorse2() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(d0); + memory->destroy(alpha); + memory->destroy(r0); + memory->destroy(morse1); + memory->destroy(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairMorse2::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,r,dr,dexp,factor_lj; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + dr = r - r0[itype][jtype]; + dexp = exp(-alpha[itype][jtype] * dr); + fpair = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - + offset[itype][jtype]; + evdwl *= factor_lj; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairMorse2::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(d0,n+1,n+1,"pair:d0"); + memory->create(alpha,n+1,n+1,"pair:alpha"); + memory->create(r0,n+1,n+1,"pair:r0"); + memory->create(morse1,n+1,n+1,"pair:morse1"); + memory->create(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairMorse2::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + + cut_global = utils::numeric(FLERR,arg[0],false,lmp); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairMorse2::coeff(int narg, char **arg) +{ + if (narg < 5 || narg > 6) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + + double d0_one = utils::numeric(FLERR,arg[2],false,lmp); + double alpha_one = utils::numeric(FLERR,arg[3],false,lmp); + double r0_one = utils::numeric(FLERR,arg[4],false,lmp); + + double cut_one = cut_global; + if (narg == 6) cut_one = utils::numeric(FLERR,arg[5],false,lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + d0[i][j] = d0_one; + alpha[i][j] = alpha_one; + r0[i][j] = r0_one; + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairMorse2::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + morse1[i][j] = 2.0*d0[i][j]*alpha[i][j]; + + if (offset_flag) { + double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]); + offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr)); + } else offset[i][j] = 0.0; + + d0[j][i] = d0[i][j]; + alpha[j][i] = alpha[i][j]; + r0[j][i] = r0[i][j]; + morse1[j][i] = morse1[i][j]; + offset[j][i] = offset[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairMorse2::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&d0[i][j],sizeof(double),1,fp); + fwrite(&alpha[i][j],sizeof(double),1,fp); + fwrite(&r0[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairMorse2::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + utils::sfread(FLERR,&d0[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + } + MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairMorse2::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairMorse2::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); + } + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairMorse2::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g\n",i,d0[i][i],alpha[i][i],r0[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairMorse2::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g %g\n", + i,j,d0[i][j],alpha[i][j],r0[i][j],cut[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairMorse2::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, + double &fforce) +{ + double r,dr,dexp,phi; + + r = sqrt(rsq); + dr = r - r0[itype][jtype]; + dexp = exp(-alpha[itype][jtype] * dr); + fforce = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r; + + phi = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - offset[itype][jtype]; + return factor_lj*phi; +} + +/* ---------------------------------------------------------------------- */ + +void *PairMorse2::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str,"d0") == 0) return (void *) d0; + if (strcmp(str,"r0") == 0) return (void *) r0; + if (strcmp(str,"alpha") == 0) return (void *) alpha; + return nullptr; +} diff --git a/examples/plugins/pair_morse2.h b/examples/plugins/pair_morse2.h new file mode 100644 index 0000000000..c20f381c63 --- /dev/null +++ b/examples/plugins/pair_morse2.h @@ -0,0 +1,70 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_PAIR_MORSE2_H +#define LMP_PAIR_MORSE2_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairMorse2 : public Pair { + public: + PairMorse2(class LAMMPS *); + virtual ~PairMorse2(); + virtual void compute(int, int); + + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + double single(int, int, int, int, double, double, double, double &); + void *extract(const char *, int &); + + protected: + double cut_global; + double **cut; + double **d0,**alpha,**r0; + double **morse1; + double **offset; + + virtual void allocate(); +}; + +} + +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +*/ From fb39ceaaeb3fbfa6ed9c84a8974bf4fb466e5fe2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 9 Mar 2021 16:00:14 -0500 Subject: [PATCH 0143/1217] fix whitespace and typo --- src/lammpsplugin.cpp | 7 ++----- src/lammpsplugin.h | 2 +- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/src/lammpsplugin.cpp b/src/lammpsplugin.cpp index d3d409de41..744203cd5e 100644 --- a/src/lammpsplugin.cpp +++ b/src/lammpsplugin.cpp @@ -27,12 +27,12 @@ namespace LAMMPS_NS { - + void lammpsplugin_load(const char *file, void *ptr) { LAMMPS *lmp = (LAMMPS *)ptr; #if defined(WIN32) - utils::logmsg(lmp,"Loading of plugins not supported on Windows yet\n"); + utils::logmesg(lmp,"Loading of plugins not supported on Windows yet\n"); #else void *dso = dlopen(file,RTLD_NOW); if (dso == nullptr) { @@ -71,6 +71,3 @@ namespace LAMMPS_NS } } } - - - diff --git a/src/lammpsplugin.h b/src/lammpsplugin.h index 9784c456ee..13076cc86f 100644 --- a/src/lammpsplugin.h +++ b/src/lammpsplugin.h @@ -18,7 +18,7 @@ extern "C" { #endif - typedef void *(lammpsplugin_factory)(void *); + typedef void *(lammpsplugin_factory)(void *); typedef void (*lammpsplugin_initfunc)(void *); typedef struct { From f68a7094ad5fe72c8e6caa18ce6276d76d4cdda1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 9 Mar 2021 18:44:51 -0500 Subject: [PATCH 0144/1217] include /omp variant into plugin example --- examples/plugins/Makefile | 9 +- examples/plugins/morse2plugin.cpp | 13 ++- examples/plugins/pair_morse2_omp.cpp | 160 +++++++++++++++++++++++++++ examples/plugins/pair_morse2_omp.h | 41 +++++++ 4 files changed, 218 insertions(+), 5 deletions(-) create mode 100644 examples/plugins/pair_morse2_omp.cpp create mode 100644 examples/plugins/pair_morse2_omp.h diff --git a/examples/plugins/Makefile b/examples/plugins/Makefile index 0c4365dfd8..2f563f924e 100644 --- a/examples/plugins/Makefile +++ b/examples/plugins/Makefile @@ -1,15 +1,16 @@ CXX=mpicxx -CXXFLAGS=-I../../src -Wall -O3 -fPIC -LD=$(CXX) -shared -rdynamic +CXXFLAGS=-I../../src -Wall -O3 -fPIC -I../../src/USER-OMP -fopenmp +LD=$(CXX) -shared -rdynamic -fopenmp -morse2plugin.so: morse2plugin.o pair_morse2.o +morse2plugin.so: morse2plugin.o pair_morse2.o pair_morse2_omp.o $(LD) -o $@ $^ .cpp.o: $(CXX) -o $@ $(CXXFLAGS) -c $< pair_morse2.o: pair_morse2.cpp pair_morse2.h -morse2plugin.o: morse2plugin.cpp pair_morse2.h +pair_morse2_omp.o: pair_morse2_omp.cpp pair_morse2_omp.h pair_morse2.h +morse2plugin.o: morse2plugin.cpp pair_morse2.h pair_morse2_omp.h clean: rm -f *~ *.so *.o log.lammps diff --git a/examples/plugins/morse2plugin.cpp b/examples/plugins/morse2plugin.cpp index bb21f3da95..fbb0882a92 100644 --- a/examples/plugins/morse2plugin.cpp +++ b/examples/plugins/morse2plugin.cpp @@ -7,6 +7,7 @@ #include #include "pair_morse2.h" +#include "pair_morse2_omp.h" using namespace LAMMPS_NS; @@ -15,6 +16,11 @@ static Pair *morse2creator(LAMMPS *lmp) return new PairMorse2(lmp); } +static Pair *morse2ompcreator(LAMMPS *lmp) +{ + return new PairMorse2OMP(lmp); +} + static lammpsplugin_t plugin; void lammpsplugin_init(void *lmp) { @@ -24,6 +30,11 @@ void lammpsplugin_init(void *lmp) plugin.name = "morse2"; plugin.info = "Morse2 variant pair style v1.0 by Axel Kohlmeyer"; plugin.creator = (lammpsplugin_factory *) &morse2creator; - + lammpsplugin_register(&plugin, (LAMMPS *)lmp); + + plugin.style = "pair"; + plugin.name = "morse2/omp"; + plugin.info = "Morse2 variant pair style for OpenMP v1.0 by Axel Kohlmeyer"; + plugin.creator = (lammpsplugin_factory *) &morse2ompcreator; lammpsplugin_register(&plugin, (LAMMPS *)lmp); } diff --git a/examples/plugins/pair_morse2_omp.cpp b/examples/plugins/pair_morse2_omp.cpp new file mode 100644 index 0000000000..14438c764b --- /dev/null +++ b/examples/plugins/pair_morse2_omp.cpp @@ -0,0 +1,160 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + This software is distributed under the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include "pair_morse2_omp.h" + +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "suffix.h" + +#include + +#include "omp_compat.h" +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairMorse2OMP::PairMorse2OMP(LAMMPS *lmp) : + PairMorse2(lmp), ThrOMP(lmp, THR_PAIR) +{ + suffix_flag |= Suffix::OMP; + respa_enable = 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairMorse2OMP::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); + + const int nall = atom->nlocal + atom->nghost; + const int nthreads = comm->nthreads; + const int inum = list->inum; + +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag) +#endif + { + int ifrom, ito, tid; + + loop_setup_thr(ifrom, ito, tid, inum, nthreads); + ThrData *thr = fix->get_thr(tid); + thr->timer(Timer::START); + ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr); + + if (evflag) { + if (eflag) { + if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr); + else eval<1,1,0>(ifrom, ito, thr); + } else { + if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr); + else eval<1,0,0>(ifrom, ito, thr); + } + } else { + if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr); + else eval<0,0,0>(ifrom, ito, thr); + } + + thr->timer(Timer::PAIR); + reduce_thr(this, eflag, vflag, thr); + } // end of omp parallel region +} + +template +void PairMorse2OMP::eval(int iifrom, int iito, ThrData * const thr) +{ + int i,j,ii,jj,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,r,dr,dexp,factor_lj; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + + const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; + dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0]; + const int * _noalias const type = atom->type; + const int nlocal = atom->nlocal; + const double * _noalias const special_lj = force->special_lj; + double fxtmp,fytmp,fztmp; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = iifrom; ii < iito; ++ii) { + + i = ilist[ii]; + xtmp = x[i].x; + ytmp = x[i].y; + ztmp = x[i].z; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + fxtmp=fytmp=fztmp=0.0; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j].x; + dely = ytmp - x[j].y; + delz = ztmp - x[j].z; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + dr = r - r0[itype][jtype]; + dexp = exp(-alpha[itype][jtype] * dr); + fpair = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r; + + fxtmp += delx*fpair; + fytmp += dely*fpair; + fztmp += delz*fpair; + if (NEWTON_PAIR || j < nlocal) { + f[j].x -= delx*fpair; + f[j].y -= dely*fpair; + f[j].z -= delz*fpair; + } + + if (EFLAG) { + evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - + offset[itype][jtype]; + evdwl *= factor_lj; + } + + if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR, + evdwl,0.0,fpair,delx,dely,delz,thr); + } + } + f[i].x += fxtmp; + f[i].y += fytmp; + f[i].z += fztmp; + } +} + +/* ---------------------------------------------------------------------- */ + +double PairMorse2OMP::memory_usage() +{ + double bytes = memory_usage_thr(); + bytes += PairMorse2::memory_usage(); + + return bytes; +} diff --git a/examples/plugins/pair_morse2_omp.h b/examples/plugins/pair_morse2_omp.h new file mode 100644 index 0000000000..c5ed7b5765 --- /dev/null +++ b/examples/plugins/pair_morse2_omp.h @@ -0,0 +1,41 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#ifndef LMP_PAIR_MORSE2_OMP_H +#define LMP_PAIR_MORSE2_OMP_H + +#include "pair_morse2.h" +#include "thr_omp.h" + +namespace LAMMPS_NS { + +class PairMorse2OMP : public PairMorse2, public ThrOMP { + + public: + PairMorse2OMP(class LAMMPS *); + + virtual void compute(int, int); + virtual double memory_usage(); + + private: + template + void eval(int ifrom, int ito, ThrData * const thr); +}; + +} + +#endif From 592490be4ed469afc3b752edd5a684a80f195d10 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 10 Mar 2021 09:50:28 -0500 Subject: [PATCH 0145/1217] add unload/list commands --- src/input.cpp | 36 +++++++++++++++++++++++++--------- src/input.h | 2 +- src/lammpsplugin.cpp | 46 +++++++++++++++++++++++++++++++++++++++++++- src/lammpsplugin.h | 24 ++++++++++++++++------- 4 files changed, 90 insertions(+), 18 deletions(-) diff --git a/src/input.cpp b/src/input.cpp index 57ce64815d..07e3c417f6 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -715,10 +715,10 @@ int Input::execute_command() else if (!strcmp(command,"include")) include(); else if (!strcmp(command,"jump")) jump(); else if (!strcmp(command,"label")) label(); - else if (!strcmp(command,"load_plugin")) load_plugin(); else if (!strcmp(command,"log")) log(); else if (!strcmp(command,"next")) next_command(); else if (!strcmp(command,"partition")) partition(); + else if (!strcmp(command,"plugin")) plugin(); else if (!strcmp(command,"print")) print(); else if (!strcmp(command,"python")) python(); else if (!strcmp(command,"quit")) quit(); @@ -1031,14 +1031,6 @@ void Input::label() /* ---------------------------------------------------------------------- */ -void Input::load_plugin() -{ - if (narg != 1) error->all(FLERR,"Illegal load_plugin command"); - lammpsplugin_load(arg[0],lmp); -} - -/* ---------------------------------------------------------------------- */ - void Input::log() { if ((narg < 1) || (narg > 2)) error->all(FLERR,"Illegal log command"); @@ -1107,6 +1099,32 @@ void Input::partition() /* ---------------------------------------------------------------------- */ +void Input::plugin() +{ + if (narg < 1) error->all(FLERR,"Illegal plugin command"); + std::string cmd = arg[0]; + if (cmd == "load") { + if (narg < 2) error->all(FLERR,"Illegal plugin load command"); + for (int i=1; i < narg; ++i) + lammpsplugin_load(arg[i],lmp); + } else if (cmd == "unload") { + if (narg != 3) error->all(FLERR,"Illegal plugin unload command"); + lammpsplugin_unload(arg[1],arg[2],lmp); + } else if (cmd == "list") { + if (comm->me == 0) { + int num = lammpsplugin_get_num_plugins(); + utils::logmesg(lmp,"Currently loaded plugins\n"); + for (int i=0; i < num; ++i) { + auto entry = lammpsplugin_info(i); + utils::logmesg(lmp,fmt::format("{:4}: {} style plugin {}\n", + i+1,entry->style,entry->name)); + } + } + } else error->all(FLERR,"Illegal plugin command"); +} + +/* ---------------------------------------------------------------------- */ + void Input::print() { if (narg < 1) error->all(FLERR,"Illegal print command"); diff --git a/src/input.h b/src/input.h index 3b7b6d79c7..809a7a5f94 100644 --- a/src/input.h +++ b/src/input.h @@ -79,10 +79,10 @@ class Input : protected Pointers { void include(); void jump(); void label(); - void load_plugin(); void log(); void next_command(); void partition(); + void plugin(); void print(); void python(); void quit(); diff --git a/src/lammpsplugin.cpp b/src/lammpsplugin.cpp index 744203cd5e..3086b829c0 100644 --- a/src/lammpsplugin.cpp +++ b/src/lammpsplugin.cpp @@ -18,6 +18,7 @@ #include "lammps.h" #include "modify.h" +#include #ifdef _WIN32 #include @@ -27,6 +28,7 @@ namespace LAMMPS_NS { + static std::vector pluginlist; void lammpsplugin_load(const char *file, void *ptr) { @@ -34,7 +36,7 @@ namespace LAMMPS_NS #if defined(WIN32) utils::logmesg(lmp,"Loading of plugins not supported on Windows yet\n"); #else - void *dso = dlopen(file,RTLD_NOW); + void *dso = dlopen(file,RTLD_NOW|RTLD_GLOBAL); if (dso == nullptr) { utils::logmesg(lmp,fmt::format("Loading of plugin from file {} failed: " "{}", file, utils::getsyserror())); @@ -48,6 +50,7 @@ namespace LAMMPS_NS return; } ((lammpsplugin_initfunc)(initfunc))(ptr); +// dlclose(dso); #endif } @@ -61,6 +64,12 @@ namespace LAMMPS_NS "version {} loaded into LAMMPS " "version {}\n", plugin->info, plugin->version, lmp->version)); + lammpsplugin_entry_t entry; + entry.style = plugin->style; + entry.name = plugin->name; + entry.handle = nullptr; + pluginlist.push_back(entry); + std::string pstyle = plugin->style; if (pstyle == "pair") { (*(lmp->force->pair_map))[plugin->name] = @@ -68,6 +77,41 @@ namespace LAMMPS_NS } else { utils::logmesg(lmp,fmt::format("Loading plugin for {} styles not " "yet implemented\n", pstyle)); + pluginlist.pop_back(); + } + } + + int lammpsplugin_get_num_plugins() + { + return pluginlist.size(); + } + + const lammpsplugin_entry_t *lammpsplugin_info(int idx) + { + if ((idx < 0) || idx >= pluginlist.size()) return nullptr; + + return &pluginlist[idx]; + } + + int lammpsplugin_find(const char *style, const char *name) + { + for (int i=0; i < pluginlist.size(); ++i) { + if ((strcmp(style,pluginlist[i].style) == 0) + && (strcmp(name,pluginlist[i].name) == 0)) + return i; + } + return -1; + } + + void lammpsplugin_unload(const char *style, const char *name, void *ptr) + { + LAMMPS *lmp = (LAMMPS *)ptr; + std::string pstyle = style; + if (pstyle == "pair") { + auto found = lmp->force->pair_map->find(name); + if (found != lmp->force->pair_map->end()) { + lmp->force->pair_map->erase(found); + } } } } diff --git a/src/lammpsplugin.h b/src/lammpsplugin.h index 13076cc86f..36c442aa5e 100644 --- a/src/lammpsplugin.h +++ b/src/lammpsplugin.h @@ -14,9 +14,9 @@ #ifndef LMP_LAMMPSPLUGIN_H #define LMP_LAMMPSPLUGIN_H -#ifdef __cplusplus +// C style API and data structures required for dynamic loading + extern "C" { -#endif typedef void *(lammpsplugin_factory)(void *); typedef void (*lammpsplugin_initfunc)(void *); @@ -29,16 +29,26 @@ extern "C" { lammpsplugin_factory *creator; } lammpsplugin_t; - void lammpsplugin_init(void *); + typedef struct { + const char *style; + const char *name; + const void *handle; + } lammpsplugin_entry_t; -#ifdef __cplusplus + // prototype for initializer function required + // to load a plugin; uses C bindings + + void lammpsplugin_init(void *); } -#endif namespace LAMMPS_NS { - extern void lammpsplugin_load(const char *, void *); - extern void lammpsplugin_register(lammpsplugin_t *, void *); + extern void lammpsplugin_load(const char *, void *); + extern void lammpsplugin_register(lammpsplugin_t *, void *); + extern int lammpsplugin_get_num_plugins(); + extern const lammpsplugin_entry_t *lammpsplugin_info(int); + extern int lammpsplugin_find(const char *, const char *); + extern void lammpsplugin_unload(const char *, const char *, void *); } #endif From a548ea3bca516006a5ba2d1151ad89e57dc01e95 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 10 Mar 2021 13:40:10 -0500 Subject: [PATCH 0146/1217] Add more tests for dump atom/gz --- unittest/formats/test_dump_atom_gz.cpp | 177 ++++++++++++++++++++++++- unittest/testing/utils.h | 3 + 2 files changed, 177 insertions(+), 3 deletions(-) diff --git a/unittest/formats/test_dump_atom_gz.cpp b/unittest/formats/test_dump_atom_gz.cpp index c8f2eb500c..614910fcf2 100644 --- a/unittest/formats/test_dump_atom_gz.cpp +++ b/unittest/formats/test_dump_atom_gz.cpp @@ -52,14 +52,25 @@ public: void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, std::string compression_style, std::string dump_modify_options, int ntimesteps) + { + generate_text_and_compressed_dump(text_file, compressed_file, compression_style, + dump_modify_options, dump_modify_options, ntimesteps); + } + + void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, + std::string compression_style, + std::string text_options, std::string compressed_options, int ntimesteps) { if (!verbose) ::testing::internal::CaptureStdout(); command(fmt::format("dump id0 all {} 1 {}", dump_style, text_file)); command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_file)); - if (!dump_modify_options.empty()) { - command(fmt::format("dump_modify id0 {}", dump_modify_options)); - command(fmt::format("dump_modify id1 {}", dump_modify_options)); + if (!text_options.empty()) { + command(fmt::format("dump_modify id0 {}", text_options)); + } + + if (!compressed_options.empty()) { + command(fmt::format("dump_modify id1 {}", compressed_options)); } command(fmt::format("run {}", ntimesteps)); @@ -106,6 +117,124 @@ TEST_F(DumpAtomGZTest, compressed_run0) delete_file(converted_file); } +TEST_F(DumpAtomGZTest, compressed_multi_file_run1) +{ + if (!GZIP_BINARY) GTEST_SKIP(); + + auto text_file = "dump_gz_text_multi_file_run1_*.melt"; + auto compressed_file = "dump_gz_compressed_multi_file_run1_*.melt.gz"; + auto text_file_0 = "dump_gz_text_multi_file_run1_0.melt"; + auto text_file_1 = "dump_gz_text_multi_file_run1_1.melt"; + auto compressed_file_0 = "dump_gz_compressed_multi_file_run1_0.melt.gz"; + auto compressed_file_1 = "dump_gz_compressed_multi_file_run1_1.melt.gz"; + + generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "", 1); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(text_file_1); + ASSERT_FILE_EXISTS(compressed_file_0); + ASSERT_FILE_EXISTS(compressed_file_1); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + + ASSERT_THAT(converted_file_0, Eq("dump_gz_compressed_multi_file_run1_0.melt")); + ASSERT_THAT(converted_file_1, Eq("dump_gz_compressed_multi_file_run1_1.melt")); + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + + delete_file(text_file_0); + delete_file(text_file_1); + delete_file(compressed_file_0); + delete_file(compressed_file_1); + delete_file(converted_file_0); + delete_file(converted_file_1); +} + +TEST_F(DumpAtomGZTest, compressed_multi_file_with_pad_run1) +{ + if (!GZIP_BINARY) GTEST_SKIP(); + + auto text_file = "dump_gz_text_multi_file_pad_run1_*.melt"; + auto compressed_file = "dump_gz_compressed_multi_file_pad_run1_*.melt.gz"; + auto text_file_0 = "dump_gz_text_multi_file_pad_run1_000.melt"; + auto text_file_1 = "dump_gz_text_multi_file_pad_run1_001.melt"; + auto compressed_file_0 = "dump_gz_compressed_multi_file_pad_run1_000.melt.gz"; + auto compressed_file_1 = "dump_gz_compressed_multi_file_pad_run1_001.melt.gz"; + + generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "pad 3", 1); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(text_file_1); + ASSERT_FILE_EXISTS(compressed_file_0); + ASSERT_FILE_EXISTS(compressed_file_1); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + + ASSERT_THAT(converted_file_0, Eq("dump_gz_compressed_multi_file_pad_run1_000.melt")); + ASSERT_THAT(converted_file_1, Eq("dump_gz_compressed_multi_file_pad_run1_001.melt")); + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + + delete_file(text_file_0); + delete_file(text_file_1); + delete_file(compressed_file_0); + delete_file(compressed_file_1); + delete_file(converted_file_0); + delete_file(converted_file_1); +} + +TEST_F(DumpAtomGZTest, compressed_multi_file_with_maxfiles_run1) +{ + if (!GZIP_BINARY) GTEST_SKIP(); + + auto text_file = "dump_gz_text_multi_file_run1_*.melt"; + auto compressed_file = "dump_gz_compressed_multi_file_run1_*.melt.gz"; + auto text_file_0 = "dump_gz_text_multi_file_run1_0.melt"; + auto text_file_1 = "dump_gz_text_multi_file_run1_1.melt"; + auto text_file_2 = "dump_gz_text_multi_file_run1_2.melt"; + auto compressed_file_0 = "dump_gz_compressed_multi_file_run1_0.melt.gz"; + auto compressed_file_1 = "dump_gz_compressed_multi_file_run1_1.melt.gz"; + auto compressed_file_2 = "dump_gz_compressed_multi_file_run1_2.melt.gz"; + + generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "maxfiles 2", 2); + + TearDown(); + + ASSERT_FILE_NOT_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(text_file_1); + ASSERT_FILE_EXISTS(text_file_2); + ASSERT_FILE_NOT_EXISTS(compressed_file_0); + ASSERT_FILE_EXISTS(compressed_file_1); + ASSERT_FILE_EXISTS(compressed_file_2); + + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + auto converted_file_2 = convert_compressed_to_text(compressed_file_2); + + ASSERT_THAT(converted_file_1, Eq("dump_gz_compressed_multi_file_run1_1.melt")); + ASSERT_THAT(converted_file_2, Eq("dump_gz_compressed_multi_file_run1_2.melt")); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EXISTS(converted_file_2); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + ASSERT_FILE_EQUAL(text_file_2, converted_file_2); + + delete_file(text_file_1); + delete_file(text_file_2); + delete_file(compressed_file_1); + delete_file(compressed_file_2); + delete_file(converted_file_1); + delete_file(converted_file_2); +} + TEST_F(DumpAtomGZTest, compressed_with_units_run0) { if (!GZIP_BINARY) GTEST_SKIP(); @@ -252,6 +381,48 @@ TEST_F(DumpAtomGZTest, compressed_triclinic_with_image_run0) delete_file(converted_file); } +TEST_F(DumpAtomGZTest, compressed_modify_bad_param) +{ + command("dump id1 all atom/gz 1 dump_gz_text_modify_bad_param_run0_*.melt.gz"); + + TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + command("dump_modify id1 compression_level 12"); + ); +} + +TEST_F(DumpAtomGZTest, compressed_modify_multi_bad_param) +{ + command("dump id1 all atom/gz 1 dump_gz_text_modify_bad_param_run0_*.melt.gz"); + + TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + command("dump_modify id1 pad 3 compression_level 12"); + ); +} + +TEST_F(DumpAtomGZTest, compressed_modify_clevel_run0) +{ + if (!GZIP_BINARY) GTEST_SKIP(); + + auto text_file = "dump_gz_text_modify_clevel_run0.melt"; + auto compressed_file = "dump_gz_compressed_modify_clevel_run0.melt.gz"; + + generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "", "compression_level 3", 0); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file); + ASSERT_FILE_EXISTS(compressed_file); + + auto converted_file = convert_compressed_to_text(compressed_file); + + ASSERT_THAT(converted_file, Eq("dump_gz_compressed_modify_clevel_run0.melt")); + ASSERT_FILE_EXISTS(converted_file); + ASSERT_FILE_EQUAL(text_file, converted_file); + delete_file(text_file); + delete_file(compressed_file); + delete_file(converted_file); +} + int main(int argc, char **argv) { MPI_Init(&argc, &argv); diff --git a/unittest/testing/utils.h b/unittest/testing/utils.h index 39a11a3e12..c76b37872a 100644 --- a/unittest/testing/utils.h +++ b/unittest/testing/utils.h @@ -70,6 +70,9 @@ static bool file_exists(const std::string &filename) } #define ASSERT_FILE_EXISTS(NAME) ASSERT_TRUE(file_exists(NAME)) +#define ASSERT_FILE_NOT_EXISTS(NAME) ASSERT_FALSE(file_exists(NAME)) #define ASSERT_FILE_EQUAL(FILE_A, FILE_B) ASSERT_TRUE(equal_lines(FILE_A, FILE_B)) + + #endif From aa625eaf656ec6ab5b54779c9f9d01add4ae11a5 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 10 Mar 2021 15:48:20 -0500 Subject: [PATCH 0147/1217] Unify dump atom/gz and atom/zstd tests --- unittest/formats/CMakeLists.txt | 17 +- ...m_gz.cpp => test_dump_atom_compressed.cpp} | 245 +++++++++------ unittest/formats/test_dump_atom_zstd.cpp | 284 ------------------ 3 files changed, 154 insertions(+), 392 deletions(-) rename unittest/formats/{test_dump_atom_gz.cpp => test_dump_atom_compressed.cpp} (58%) delete mode 100644 unittest/formats/test_dump_atom_zstd.cpp diff --git a/unittest/formats/CMakeLists.txt b/unittest/formats/CMakeLists.txt index 7b96cf2d32..7b19bfde46 100644 --- a/unittest/formats/CMakeLists.txt +++ b/unittest/formats/CMakeLists.txt @@ -40,11 +40,11 @@ set_tests_properties(DumpAtom PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS if(PKG_COMPRESS) find_program(GZIP_BINARY NAMES gzip REQUIRED) - add_executable(test_dump_atom_gz test_dump_atom_gz.cpp) - target_link_libraries(test_dump_atom_gz PRIVATE lammps GTest::GMock GTest::GTest) - add_test(NAME DumpAtomGZ COMMAND test_dump_atom_gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) - set_tests_properties(DumpAtomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") - set_tests_properties(DumpAtomGZ PROPERTIES ENVIRONMENT "GZIP_BINARY=${GZIP_BINARY}") + add_executable(test_dump_atom_compressed test_dump_atom_compressed.cpp) + target_link_libraries(test_dump_atom_compressed PRIVATE lammps GTest::GMock GTest::GTest) + + add_test(NAME DumpAtomGZ COMMAND test_dump_atom_compressed gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + set_tests_properties(DumpAtomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}") add_executable(test_dump_custom_gz test_dump_custom_gz.cpp) target_link_libraries(test_dump_custom_gz PRIVATE lammps GTest::GMock GTest::GTest) @@ -75,11 +75,8 @@ if(PKG_COMPRESS) find_program(ZSTD_BINARY NAMES zstd) if(Zstd_FOUND AND ZSTD_BINARY) - add_executable(test_dump_atom_zstd test_dump_atom_zstd.cpp) - target_link_libraries(test_dump_atom_zstd PRIVATE lammps GTest::GMock GTest::GTest) - add_test(NAME DumpAtomZstd COMMAND test_dump_atom_zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) - set_tests_properties(DumpAtomZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") - set_tests_properties(DumpAtomZstd PROPERTIES ENVIRONMENT "ZSTD_BINARY=${ZSTD_BINARY}") + add_test(NAME DumpAtomZstd COMMAND test_dump_atom_compressed zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + set_tests_properties(DumpAtomZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${ZSTD_BINARY}") add_executable(test_dump_custom_zstd test_dump_custom_zstd.cpp) target_link_libraries(test_dump_custom_zstd PRIVATE lammps GTest::GMock GTest::GTest) diff --git a/unittest/formats/test_dump_atom_gz.cpp b/unittest/formats/test_dump_atom_compressed.cpp similarity index 58% rename from unittest/formats/test_dump_atom_gz.cpp rename to unittest/formats/test_dump_atom_compressed.cpp index 614910fcf2..2f3f609744 100644 --- a/unittest/formats/test_dump_atom_gz.cpp +++ b/unittest/formats/test_dump_atom_compressed.cpp @@ -21,14 +21,36 @@ #include -char *GZIP_BINARY = nullptr; +const char * COMPRESS_SUFFIX = nullptr; +const char * COMPRESS_EXTENSION = nullptr; +char * COMPRESS_BINARY = nullptr; using ::testing::Eq; -class DumpAtomGZTest : public MeltTest { +class DumpAtomCompressTest : public MeltTest { +protected: std::string dump_style = "atom"; + std::string compression_style = ""; public: + void SetUp() override + { + MeltTest::SetUp(); + compression_style = fmt::format("{}/{}", dump_style, COMPRESS_SUFFIX); + } + + std::string text_dump_filename(std::string ident) { + return fmt::format("dump_{}_text_{}", COMPRESS_SUFFIX, ident); + } + + std::string compressed_dump_filename(std::string ident) { + return fmt::format("dump_{}_compressed_{}.{}", COMPRESS_SUFFIX, ident, COMPRESS_EXTENSION); + } + + std::string converted_dump_filename(std::string ident) { + return fmt::format("dump_{}_compressed_{}", COMPRESS_SUFFIX, ident); + } + void enable_triclinic() { if (!verbose) ::testing::internal::CaptureStdout(); @@ -50,15 +72,13 @@ public: } void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string compression_style, std::string dump_modify_options, int ntimesteps) { - generate_text_and_compressed_dump(text_file, compressed_file, compression_style, + generate_text_and_compressed_dump(text_file, compressed_file, dump_modify_options, dump_modify_options, ntimesteps); } void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string compression_style, std::string text_options, std::string compressed_options, int ntimesteps) { if (!verbose) ::testing::internal::CaptureStdout(); @@ -82,7 +102,7 @@ public: if (!verbose) ::testing::internal::CaptureStdout(); std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.')); std::string cmdline = - fmt::format("{} -d -c {} > {}", GZIP_BINARY, compressed_file, converted_file); + fmt::format("{} -d -c {} > {}", COMPRESS_BINARY, compressed_file, converted_file); system(cmdline.c_str()); if (!verbose) ::testing::internal::GetCapturedStdout(); return converted_file; @@ -90,17 +110,17 @@ public: }; //------------------------------------------------------------------------------------------------- -// GZ compressed files +// compressed files //------------------------------------------------------------------------------------------------- -TEST_F(DumpAtomGZTest, compressed_run0) +TEST_F(DumpAtomCompressTest, compressed_run0) { - if (!GZIP_BINARY) GTEST_SKIP(); + if (!COMPRESS_BINARY) GTEST_SKIP(); - auto text_file = "dump_gz_text_run0.melt"; - auto compressed_file = "dump_gz_compressed_run0.melt.gz"; + auto text_file = text_dump_filename("run0.melt"); + auto compressed_file = compressed_dump_filename("run0.melt"); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "", 0); + generate_text_and_compressed_dump(text_file, compressed_file, "", 0); TearDown(); @@ -109,7 +129,7 @@ TEST_F(DumpAtomGZTest, compressed_run0) auto converted_file = convert_compressed_to_text(compressed_file); - ASSERT_THAT(converted_file, Eq("dump_gz_compressed_run0.melt")); + ASSERT_THAT(converted_file, Eq(converted_dump_filename("run0.melt"))); ASSERT_FILE_EXISTS(converted_file); ASSERT_FILE_EQUAL(text_file, converted_file); delete_file(text_file); @@ -117,31 +137,29 @@ TEST_F(DumpAtomGZTest, compressed_run0) delete_file(converted_file); } -TEST_F(DumpAtomGZTest, compressed_multi_file_run1) +TEST_F(DumpAtomCompressTest, compressed_multi_file_run1) { - if (!GZIP_BINARY) GTEST_SKIP(); + if (!COMPRESS_BINARY) GTEST_SKIP(); - auto text_file = "dump_gz_text_multi_file_run1_*.melt"; - auto compressed_file = "dump_gz_compressed_multi_file_run1_*.melt.gz"; - auto text_file_0 = "dump_gz_text_multi_file_run1_0.melt"; - auto text_file_1 = "dump_gz_text_multi_file_run1_1.melt"; - auto compressed_file_0 = "dump_gz_compressed_multi_file_run1_0.melt.gz"; - auto compressed_file_1 = "dump_gz_compressed_multi_file_run1_1.melt.gz"; + auto base_name = "multi_file_run1_*.melt"; + auto base_name_0 = "multi_file_run1_0.melt"; + auto base_name_1 = "multi_file_run1_1.melt"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "", 1); + generate_text_and_compressed_dump(text_file, compressed_file, "", 1); TearDown(); - ASSERT_FILE_EXISTS(text_file_0); - ASSERT_FILE_EXISTS(text_file_1); - ASSERT_FILE_EXISTS(compressed_file_0); - ASSERT_FILE_EXISTS(compressed_file_1); - auto converted_file_0 = convert_compressed_to_text(compressed_file_0); auto converted_file_1 = convert_compressed_to_text(compressed_file_1); - ASSERT_THAT(converted_file_0, Eq("dump_gz_compressed_multi_file_run1_0.melt")); - ASSERT_THAT(converted_file_1, Eq("dump_gz_compressed_multi_file_run1_1.melt")); + ASSERT_THAT(converted_file_0, Eq(converted_dump_filename(base_name_0))); + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); ASSERT_FILE_EXISTS(converted_file_0); ASSERT_FILE_EXISTS(converted_file_1); ASSERT_FILE_EQUAL(text_file_0, converted_file_0); @@ -155,18 +173,21 @@ TEST_F(DumpAtomGZTest, compressed_multi_file_run1) delete_file(converted_file_1); } -TEST_F(DumpAtomGZTest, compressed_multi_file_with_pad_run1) +TEST_F(DumpAtomCompressTest, compressed_multi_file_with_pad_run1) { - if (!GZIP_BINARY) GTEST_SKIP(); + if (!COMPRESS_BINARY) GTEST_SKIP(); - auto text_file = "dump_gz_text_multi_file_pad_run1_*.melt"; - auto compressed_file = "dump_gz_compressed_multi_file_pad_run1_*.melt.gz"; - auto text_file_0 = "dump_gz_text_multi_file_pad_run1_000.melt"; - auto text_file_1 = "dump_gz_text_multi_file_pad_run1_001.melt"; - auto compressed_file_0 = "dump_gz_compressed_multi_file_pad_run1_000.melt.gz"; - auto compressed_file_1 = "dump_gz_compressed_multi_file_pad_run1_001.melt.gz"; + auto base_name = "multi_file_pad_run1_*.melt"; + auto base_name_0 = "multi_file_pad_run1_000.melt"; + auto base_name_1 = "multi_file_pad_run1_001.melt"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "pad 3", 1); + generate_text_and_compressed_dump(text_file, compressed_file, "pad 3", 1); TearDown(); @@ -178,8 +199,8 @@ TEST_F(DumpAtomGZTest, compressed_multi_file_with_pad_run1) auto converted_file_0 = convert_compressed_to_text(compressed_file_0); auto converted_file_1 = convert_compressed_to_text(compressed_file_1); - ASSERT_THAT(converted_file_0, Eq("dump_gz_compressed_multi_file_pad_run1_000.melt")); - ASSERT_THAT(converted_file_1, Eq("dump_gz_compressed_multi_file_pad_run1_001.melt")); + ASSERT_THAT(converted_file_0, Eq(converted_dump_filename(base_name_0))); + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); ASSERT_FILE_EXISTS(converted_file_0); ASSERT_FILE_EXISTS(converted_file_1); ASSERT_FILE_EQUAL(text_file_0, converted_file_0); @@ -193,20 +214,24 @@ TEST_F(DumpAtomGZTest, compressed_multi_file_with_pad_run1) delete_file(converted_file_1); } -TEST_F(DumpAtomGZTest, compressed_multi_file_with_maxfiles_run1) +TEST_F(DumpAtomCompressTest, compressed_multi_file_with_maxfiles_run1) { - if (!GZIP_BINARY) GTEST_SKIP(); + if (!COMPRESS_BINARY) GTEST_SKIP(); - auto text_file = "dump_gz_text_multi_file_run1_*.melt"; - auto compressed_file = "dump_gz_compressed_multi_file_run1_*.melt.gz"; - auto text_file_0 = "dump_gz_text_multi_file_run1_0.melt"; - auto text_file_1 = "dump_gz_text_multi_file_run1_1.melt"; - auto text_file_2 = "dump_gz_text_multi_file_run1_2.melt"; - auto compressed_file_0 = "dump_gz_compressed_multi_file_run1_0.melt.gz"; - auto compressed_file_1 = "dump_gz_compressed_multi_file_run1_1.melt.gz"; - auto compressed_file_2 = "dump_gz_compressed_multi_file_run1_2.melt.gz"; + auto base_name = "multi_file_maxfiles_run1_*.melt"; + auto base_name_0 = "multi_file_maxfiles_run1_0.melt"; + auto base_name_1 = "multi_file_maxfiles_run1_1.melt"; + auto base_name_2 = "multi_file_maxfiles_run1_2.melt"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto text_file_2 = text_dump_filename(base_name_2); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); + auto compressed_file_2 = compressed_dump_filename(base_name_2); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "maxfiles 2", 2); + generate_text_and_compressed_dump(text_file, compressed_file, "maxfiles 2", 2); TearDown(); @@ -220,8 +245,8 @@ TEST_F(DumpAtomGZTest, compressed_multi_file_with_maxfiles_run1) auto converted_file_1 = convert_compressed_to_text(compressed_file_1); auto converted_file_2 = convert_compressed_to_text(compressed_file_2); - ASSERT_THAT(converted_file_1, Eq("dump_gz_compressed_multi_file_run1_1.melt")); - ASSERT_THAT(converted_file_2, Eq("dump_gz_compressed_multi_file_run1_2.melt")); + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); + ASSERT_THAT(converted_file_2, Eq(converted_dump_filename(base_name_2))); ASSERT_FILE_EXISTS(converted_file_1); ASSERT_FILE_EXISTS(converted_file_2); ASSERT_FILE_EQUAL(text_file_1, converted_file_1); @@ -235,14 +260,15 @@ TEST_F(DumpAtomGZTest, compressed_multi_file_with_maxfiles_run1) delete_file(converted_file_2); } -TEST_F(DumpAtomGZTest, compressed_with_units_run0) +TEST_F(DumpAtomCompressTest, compressed_with_units_run0) { - if (!GZIP_BINARY) GTEST_SKIP(); + if (!COMPRESS_BINARY) GTEST_SKIP(); - auto text_file = "dump_gz_text_with_units_run0.melt"; - auto compressed_file = "dump_gz_compressed_with_units_run0.melt.gz"; + auto base_name = "with_units_run0.melt"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "scale no units yes", + generate_text_and_compressed_dump(text_file, compressed_file, "scale no units yes", 0); TearDown(); @@ -259,15 +285,15 @@ TEST_F(DumpAtomGZTest, compressed_with_units_run0) delete_file(converted_file); } -TEST_F(DumpAtomGZTest, compressed_with_time_run0) +TEST_F(DumpAtomCompressTest, compressed_with_time_run0) { - if (!GZIP_BINARY) GTEST_SKIP(); + if (!COMPRESS_BINARY) GTEST_SKIP(); - auto text_file = "dump_gz_text_with_time_run0.melt"; - auto compressed_file = "dump_gz_compressed_with_time_run0.melt.gz"; + auto base_name = "with_time_run0.melt"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "scale no time yes", - 0); + generate_text_and_compressed_dump(text_file, compressed_file, "scale no time yes", 0); TearDown(); @@ -283,15 +309,16 @@ TEST_F(DumpAtomGZTest, compressed_with_time_run0) delete_file(converted_file); } -TEST_F(DumpAtomGZTest, compressed_triclinic_run0) +TEST_F(DumpAtomCompressTest, compressed_triclinic_run0) { - if (!GZIP_BINARY) GTEST_SKIP(); + if (!COMPRESS_BINARY) GTEST_SKIP(); - auto text_file = "dump_gz_text_tri_run0.melt"; - auto compressed_file = "dump_gz_compressed_tri_run0.melt.gz"; + auto base_name = "tri_run0.melt"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); enable_triclinic(); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "", 0); + generate_text_and_compressed_dump(text_file, compressed_file, "", 0); TearDown(); @@ -307,16 +334,16 @@ TEST_F(DumpAtomGZTest, compressed_triclinic_run0) delete_file(converted_file); } -TEST_F(DumpAtomGZTest, compressed_triclinic_with_units_run0) +TEST_F(DumpAtomCompressTest, compressed_triclinic_with_units_run0) { - if (!GZIP_BINARY) GTEST_SKIP(); + if (!COMPRESS_BINARY) GTEST_SKIP(); - auto text_file = "dump_gz_text_tri_with_units_run0.melt"; - auto compressed_file = "dump_gz_compressed_tri_with_units_run0.melt.gz"; + auto base_name = "tri_with_units_run0.melt"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); enable_triclinic(); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "scale no units yes", - 0); + generate_text_and_compressed_dump(text_file, compressed_file, "scale no units yes", 0); TearDown(); @@ -332,16 +359,16 @@ TEST_F(DumpAtomGZTest, compressed_triclinic_with_units_run0) delete_file(converted_file); } -TEST_F(DumpAtomGZTest, compressed_triclinic_with_time_run0) +TEST_F(DumpAtomCompressTest, compressed_triclinic_with_time_run0) { - if (!GZIP_BINARY) GTEST_SKIP(); + if (!COMPRESS_BINARY) GTEST_SKIP(); - auto text_file = "dump_gz_text_tri_with_time_run0.melt"; - auto compressed_file = "dump_gz_compressed_tri_with_time_run0.melt.gz"; + auto base_name = "tri_with_time_run0.melt"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); enable_triclinic(); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "scale no time yes", - 0); + generate_text_and_compressed_dump(text_file, compressed_file, "scale no time yes", 0); TearDown(); @@ -357,15 +384,16 @@ TEST_F(DumpAtomGZTest, compressed_triclinic_with_time_run0) delete_file(converted_file); } -TEST_F(DumpAtomGZTest, compressed_triclinic_with_image_run0) +TEST_F(DumpAtomCompressTest, compressed_triclinic_with_image_run0) { - if (!GZIP_BINARY) GTEST_SKIP(); + if (!COMPRESS_BINARY) GTEST_SKIP(); - auto text_file = "dump_gz_text_tri_with_image_run0.melt"; - auto compressed_file = "dump_gz_compressed_tri_with_image_run0.melt.gz"; + auto base_name = "tri_with_image_run0.melt"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); enable_triclinic(); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "image yes", 0); + generate_text_and_compressed_dump(text_file, compressed_file, "image yes", 0); TearDown(); @@ -381,32 +409,37 @@ TEST_F(DumpAtomGZTest, compressed_triclinic_with_image_run0) delete_file(converted_file); } -TEST_F(DumpAtomGZTest, compressed_modify_bad_param) +TEST_F(DumpAtomCompressTest, compressed_modify_bad_param) { - command("dump id1 all atom/gz 1 dump_gz_text_modify_bad_param_run0_*.melt.gz"); + if (compression_style != "atom/gz") GTEST_SKIP(); + + command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt"))); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 compression_level 12"); ); } -TEST_F(DumpAtomGZTest, compressed_modify_multi_bad_param) +TEST_F(DumpAtomCompressTest, compressed_modify_multi_bad_param) { - command("dump id1 all atom/gz 1 dump_gz_text_modify_bad_param_run0_*.melt.gz"); + if (compression_style != "atom/gz") GTEST_SKIP(); + + command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt"))); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); ); } -TEST_F(DumpAtomGZTest, compressed_modify_clevel_run0) +TEST_F(DumpAtomCompressTest, compressed_modify_clevel_run0) { - if (!GZIP_BINARY) GTEST_SKIP(); + if (!COMPRESS_BINARY) GTEST_SKIP(); - auto text_file = "dump_gz_text_modify_clevel_run0.melt"; - auto compressed_file = "dump_gz_compressed_modify_clevel_run0.melt.gz"; + auto base_name = "modify_clevel_run0.melt"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/gz", "", "compression_level 3", 0); + generate_text_and_compressed_dump(text_file, compressed_file, "", "compression_level 3", 0); TearDown(); @@ -415,7 +448,7 @@ TEST_F(DumpAtomGZTest, compressed_modify_clevel_run0) auto converted_file = convert_compressed_to_text(compressed_file); - ASSERT_THAT(converted_file, Eq("dump_gz_compressed_modify_clevel_run0.melt")); + ASSERT_THAT(converted_file, Eq(converted_dump_filename(base_name))); ASSERT_FILE_EXISTS(converted_file); ASSERT_FILE_EQUAL(text_file, converted_file); delete_file(text_file); @@ -428,6 +461,24 @@ int main(int argc, char **argv) MPI_Init(&argc, &argv); ::testing::InitGoogleMock(&argc, argv); + if (argc < 2) { + std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; + return 1; + } + + if(strcmp(argv[1], "gz") == 0) { + COMPRESS_SUFFIX = "gz"; + COMPRESS_EXTENSION = "gz"; + } else if(strcmp(argv[1], "zstd") == 0) { + COMPRESS_SUFFIX = "zstd"; + COMPRESS_EXTENSION = "zst"; + } else { + std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; + return 1; + } + + COMPRESS_BINARY = getenv("COMPRESS_BINARY"); + // handle arguments passed via environment variable if (const char *var = getenv("TEST_ARGS")) { std::vector env = utils::split_words(var); @@ -438,8 +489,6 @@ int main(int argc, char **argv) } } - GZIP_BINARY = getenv("GZIP_BINARY"); - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; int rv = RUN_ALL_TESTS(); diff --git a/unittest/formats/test_dump_atom_zstd.cpp b/unittest/formats/test_dump_atom_zstd.cpp deleted file mode 100644 index 41c2fd3c79..0000000000 --- a/unittest/formats/test_dump_atom_zstd.cpp +++ /dev/null @@ -1,284 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "../testing/core.h" -#include "../testing/systems/melt.h" -#include "../testing/utils.h" -#include "fmt/format.h" -#include "utils.h" -#include "gmock/gmock.h" -#include "gtest/gtest.h" - -#include - -char *ZSTD_BINARY = nullptr; - -using ::testing::Eq; - -class DumpAtomZSTDTest : public MeltTest { - std::string dump_style = "atom"; - -public: - void enable_triclinic() - { - if (!verbose) ::testing::internal::CaptureStdout(); - command("change_box all triclinic"); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void generate_dump(std::string dump_file, std::string dump_modify_options, int ntimesteps) - { - if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id all {} 1 {}", dump_style, dump_file)); - - if (!dump_modify_options.empty()) { - command(fmt::format("dump_modify id {}", dump_modify_options)); - } - - command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string compression_style, - std::string dump_modify_options, int ntimesteps) - { - if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id0 all {} 1 {}", dump_style, text_file)); - command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_file)); - - if (!dump_modify_options.empty()) { - command(fmt::format("dump_modify id0 {}", dump_modify_options)); - command(fmt::format("dump_modify id1 {}", dump_modify_options)); - } - - command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - std::string convert_compressed_to_text(std::string compressed_file) - { - if (!verbose) ::testing::internal::CaptureStdout(); - std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.')); - std::string cmdline = - fmt::format("{} -d -c {} > {}", ZSTD_BINARY, compressed_file, converted_file); - system(cmdline.c_str()); - if (!verbose) ::testing::internal::GetCapturedStdout(); - return converted_file; - } -}; - -//------------------------------------------------------------------------------------------------- -// ZSTD compressed files -//------------------------------------------------------------------------------------------------- - -TEST_F(DumpAtomZSTDTest, compressed_run0) -{ - if (!ZSTD_BINARY) GTEST_SKIP(); - - auto text_file = "dump_zstd_text_run0.melt"; - auto compressed_file = "dump_zstd_compressed_run0.melt.zst"; - - generate_text_and_compressed_dump(text_file, compressed_file, "atom/zstd", "", 0); - - // make sure file is closed - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_THAT(converted_file, Eq("dump_zstd_compressed_run0.melt")); - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -TEST_F(DumpAtomZSTDTest, compressed_with_units_run0) -{ - if (!ZSTD_BINARY) GTEST_SKIP(); - - auto text_file = "dump_zstd_text_with_units_run0.melt"; - auto compressed_file = "dump_zstd_compressed_with_units_run0.melt.zst"; - - generate_text_and_compressed_dump(text_file, compressed_file, "atom/zstd", "scale no units yes", - 0); - - // make sure file is closed - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -TEST_F(DumpAtomZSTDTest, compressed_with_time_run0) -{ - if (!ZSTD_BINARY) GTEST_SKIP(); - - auto text_file = "dump_zstd_text_with_time_run0.melt"; - auto compressed_file = "dump_zstd_compressed_with_time_run0.melt.zst"; - - generate_text_and_compressed_dump(text_file, compressed_file, "atom/zstd", "scale no time yes", - 0); - - // make sure file is closed - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -TEST_F(DumpAtomZSTDTest, compressed_triclinic_run0) -{ - if (!ZSTD_BINARY) GTEST_SKIP(); - - auto text_file = "dump_zstd_text_tri_run0.melt"; - auto compressed_file = "dump_zstd_compressed_tri_run0.melt.zst"; - - enable_triclinic(); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/zstd", "", 0); - - // make sure file is closed - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -TEST_F(DumpAtomZSTDTest, compressed_triclinic_with_units_run0) -{ - if (!ZSTD_BINARY) GTEST_SKIP(); - - auto text_file = "dump_zstd_text_tri_with_units_run0.melt"; - auto compressed_file = "dump_zstd_compressed_tri_with_units_run0.melt.zst"; - - enable_triclinic(); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/zstd", "scale no units yes", - 0); - - // make sure file is closed - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -TEST_F(DumpAtomZSTDTest, compressed_triclinic_with_time_run0) -{ - if (!ZSTD_BINARY) GTEST_SKIP(); - - auto text_file = "dump_zstd_text_tri_with_time_run0.melt"; - auto compressed_file = "dump_zstd_compressed_tri_with_time_run0.melt.zst"; - - enable_triclinic(); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/zstd", "scale no time yes", - 0); - - // make sure file is closed - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -TEST_F(DumpAtomZSTDTest, compressed_triclinic_with_image_run0) -{ - if (!ZSTD_BINARY) GTEST_SKIP(); - - auto text_file = "dump_zstd_text_tri_with_image_run0.melt"; - auto compressed_file = "dump_zstd_compressed_tri_with_image_run0.melt.zst"; - - enable_triclinic(); - generate_text_and_compressed_dump(text_file, compressed_file, "atom/zstd", "image yes", 0); - - // make sure file is closed - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -int main(int argc, char **argv) -{ - MPI_Init(&argc, &argv); - ::testing::InitGoogleMock(&argc, argv); - - // handle arguments passed via environment variable - if (const char *var = getenv("TEST_ARGS")) { - std::vector env = utils::split_words(var); - for (auto arg : env) { - if (arg == "-v") { - verbose = true; - } - } - } - - ZSTD_BINARY = getenv("ZSTD_BINARY"); - - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; - - int rv = RUN_ALL_TESTS(); - MPI_Finalize(); - return rv; -} From 20a546c824ece52221b75513906ef98cb1bdc889 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 10 Mar 2021 16:08:51 -0500 Subject: [PATCH 0148/1217] Move testcase in its own file --- unittest/formats/compressed_dump_test.h | 104 ++++++++++++++++++ .../formats/test_dump_atom_compressed.cpp | 86 +-------------- 2 files changed, 107 insertions(+), 83 deletions(-) create mode 100644 unittest/formats/compressed_dump_test.h diff --git a/unittest/formats/compressed_dump_test.h b/unittest/formats/compressed_dump_test.h new file mode 100644 index 0000000000..80b8550060 --- /dev/null +++ b/unittest/formats/compressed_dump_test.h @@ -0,0 +1,104 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +#ifndef TESTCASE_COMPRESSED_DUMP__H +#define TESTCASE_COMPRESSED_DUMP__H + +#include "../testing/core.h" +#include "../testing/systems/melt.h" +#include + +const char * COMPRESS_SUFFIX = nullptr; +const char * COMPRESS_EXTENSION = nullptr; +char * COMPRESS_BINARY = nullptr; + +class CompressedDumpTest : public MeltTest { +protected: + std::string dump_style; + std::string compression_style; + +public: + CompressedDumpTest(const std::string & dump_style) : MeltTest(), dump_style(dump_style) { + compression_style = fmt::format("{}/{}", dump_style, COMPRESS_SUFFIX); + } + + std::string text_dump_filename(std::string ident) { + return fmt::format("dump_{}_text_{}", COMPRESS_SUFFIX, ident); + } + + std::string compressed_dump_filename(std::string ident) { + return fmt::format("dump_{}_compressed_{}.{}", COMPRESS_SUFFIX, ident, COMPRESS_EXTENSION); + } + + std::string converted_dump_filename(std::string ident) { + return fmt::format("dump_{}_compressed_{}", COMPRESS_SUFFIX, ident); + } + + void enable_triclinic() + { + if (!verbose) ::testing::internal::CaptureStdout(); + command("change_box all triclinic"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + } + + void generate_dump(std::string dump_file, std::string dump_modify_options, int ntimesteps) + { + if (!verbose) ::testing::internal::CaptureStdout(); + command(fmt::format("dump id all {} 1 {}", dump_style, dump_file)); + + if (!dump_modify_options.empty()) { + command(fmt::format("dump_modify id {}", dump_modify_options)); + } + + command(fmt::format("run {}", ntimesteps)); + if (!verbose) ::testing::internal::GetCapturedStdout(); + } + + void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, + std::string dump_modify_options, int ntimesteps) + { + generate_text_and_compressed_dump(text_file, compressed_file, + dump_modify_options, dump_modify_options, ntimesteps); + } + + void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, + std::string text_options, std::string compressed_options, int ntimesteps) + { + if (!verbose) ::testing::internal::CaptureStdout(); + command(fmt::format("dump id0 all {} 1 {}", dump_style, text_file)); + command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_file)); + + if (!text_options.empty()) { + command(fmt::format("dump_modify id0 {}", text_options)); + } + + if (!compressed_options.empty()) { + command(fmt::format("dump_modify id1 {}", compressed_options)); + } + + command(fmt::format("run {}", ntimesteps)); + if (!verbose) ::testing::internal::GetCapturedStdout(); + } + + std::string convert_compressed_to_text(std::string compressed_file) + { + if (!verbose) ::testing::internal::CaptureStdout(); + std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.')); + std::string cmdline = + fmt::format("{} -d -c {} > {}", COMPRESS_BINARY, compressed_file, converted_file); + system(cmdline.c_str()); + if (!verbose) ::testing::internal::GetCapturedStdout(); + return converted_file; + } +}; + +#endif diff --git a/unittest/formats/test_dump_atom_compressed.cpp b/unittest/formats/test_dump_atom_compressed.cpp index 2f3f609744..e33366801e 100644 --- a/unittest/formats/test_dump_atom_compressed.cpp +++ b/unittest/formats/test_dump_atom_compressed.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "../testing/core.h" -#include "../testing/systems/melt.h" #include "../testing/utils.h" +#include "compressed_dump_test.h" #include "fmt/format.h" #include "utils.h" #include "gmock/gmock.h" @@ -21,91 +20,12 @@ #include -const char * COMPRESS_SUFFIX = nullptr; -const char * COMPRESS_EXTENSION = nullptr; -char * COMPRESS_BINARY = nullptr; using ::testing::Eq; -class DumpAtomCompressTest : public MeltTest { -protected: - std::string dump_style = "atom"; - std::string compression_style = ""; - +class DumpAtomCompressTest : public CompressedDumpTest { public: - void SetUp() override - { - MeltTest::SetUp(); - compression_style = fmt::format("{}/{}", dump_style, COMPRESS_SUFFIX); - } - - std::string text_dump_filename(std::string ident) { - return fmt::format("dump_{}_text_{}", COMPRESS_SUFFIX, ident); - } - - std::string compressed_dump_filename(std::string ident) { - return fmt::format("dump_{}_compressed_{}.{}", COMPRESS_SUFFIX, ident, COMPRESS_EXTENSION); - } - - std::string converted_dump_filename(std::string ident) { - return fmt::format("dump_{}_compressed_{}", COMPRESS_SUFFIX, ident); - } - - void enable_triclinic() - { - if (!verbose) ::testing::internal::CaptureStdout(); - command("change_box all triclinic"); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void generate_dump(std::string dump_file, std::string dump_modify_options, int ntimesteps) - { - if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id all {} 1 {}", dump_style, dump_file)); - - if (!dump_modify_options.empty()) { - command(fmt::format("dump_modify id {}", dump_modify_options)); - } - - command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string dump_modify_options, int ntimesteps) - { - generate_text_and_compressed_dump(text_file, compressed_file, - dump_modify_options, dump_modify_options, ntimesteps); - } - - void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string text_options, std::string compressed_options, int ntimesteps) - { - if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id0 all {} 1 {}", dump_style, text_file)); - command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_file)); - - if (!text_options.empty()) { - command(fmt::format("dump_modify id0 {}", text_options)); - } - - if (!compressed_options.empty()) { - command(fmt::format("dump_modify id1 {}", compressed_options)); - } - - command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - std::string convert_compressed_to_text(std::string compressed_file) - { - if (!verbose) ::testing::internal::CaptureStdout(); - std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.')); - std::string cmdline = - fmt::format("{} -d -c {} > {}", COMPRESS_BINARY, compressed_file, converted_file); - system(cmdline.c_str()); - if (!verbose) ::testing::internal::GetCapturedStdout(); - return converted_file; + DumpAtomCompressTest() : CompressedDumpTest("atom") { } }; From 8e1ccb6123e4d1800ad0f4eac27ec22aa1ce870d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 07:26:57 -0500 Subject: [PATCH 0149/1217] next iteration: rename functions/files, split header, store dso handle --- examples/plugins/morse2plugin.cpp | 12 +++++++----- src/input.cpp | 10 +++++----- src/lammpsplugin.h | 24 ++++++----------------- src/{lammpsplugin.cpp => plugin.cpp} | 27 ++++++++++++-------------- src/plugin.h | 29 ++++++++++++++++++++++++++++ 5 files changed, 59 insertions(+), 43 deletions(-) rename src/{lammpsplugin.cpp => plugin.cpp} (81%) create mode 100644 src/plugin.h diff --git a/examples/plugins/morse2plugin.cpp b/examples/plugins/morse2plugin.cpp index fbb0882a92..d7290edfb0 100644 --- a/examples/plugins/morse2plugin.cpp +++ b/examples/plugins/morse2plugin.cpp @@ -22,19 +22,21 @@ static Pair *morse2ompcreator(LAMMPS *lmp) } static lammpsplugin_t plugin; -void lammpsplugin_init(void *lmp) +extern "C" void lammpsplugin_init(void *lmp, void *handle, lammpsplugin_regfunc register_plugin) { memset(&plugin,0,sizeof(lammpsplugin_t)); plugin.version = LAMMPS_VERSION; plugin.style = "pair"; plugin.name = "morse2"; - plugin.info = "Morse2 variant pair style v1.0 by Axel Kohlmeyer"; + plugin.info = "Morse2 variant pair style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; plugin.creator = (lammpsplugin_factory *) &morse2creator; - lammpsplugin_register(&plugin, (LAMMPS *)lmp); + plugin.handle = handle; + register_plugin(&plugin,lmp); plugin.style = "pair"; plugin.name = "morse2/omp"; - plugin.info = "Morse2 variant pair style for OpenMP v1.0 by Axel Kohlmeyer"; + plugin.info = "Morse2 variant pair style for OpenMP v1.0"; plugin.creator = (lammpsplugin_factory *) &morse2ompcreator; - lammpsplugin_register(&plugin, (LAMMPS *)lmp); + register_plugin(&plugin,lmp); } diff --git a/src/input.cpp b/src/input.cpp index 07e3c417f6..73a73cd369 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -29,13 +29,13 @@ #include "group.h" #include "improper.h" #include "kspace.h" -#include "lammpsplugin.h" #include "memory.h" #include "min.h" #include "modify.h" #include "neighbor.h" #include "output.h" #include "pair.h" +#include "plugin.h" #include "special.h" #include "style_command.h" #include "thermo.h" @@ -1106,16 +1106,16 @@ void Input::plugin() if (cmd == "load") { if (narg < 2) error->all(FLERR,"Illegal plugin load command"); for (int i=1; i < narg; ++i) - lammpsplugin_load(arg[i],lmp); + plugin_load(arg[i],lmp); } else if (cmd == "unload") { if (narg != 3) error->all(FLERR,"Illegal plugin unload command"); - lammpsplugin_unload(arg[1],arg[2],lmp); + plugin_unload(arg[1],arg[2],lmp); } else if (cmd == "list") { if (comm->me == 0) { - int num = lammpsplugin_get_num_plugins(); + int num = plugin_get_num_plugins(); utils::logmesg(lmp,"Currently loaded plugins\n"); for (int i=0; i < num; ++i) { - auto entry = lammpsplugin_info(i); + auto entry = plugin_info(i); utils::logmesg(lmp,fmt::format("{:4}: {} style plugin {}\n", i+1,entry->style,entry->name)); } diff --git a/src/lammpsplugin.h b/src/lammpsplugin.h index 36c442aa5e..6cdf67e09b 100644 --- a/src/lammpsplugin.h +++ b/src/lammpsplugin.h @@ -14,41 +14,29 @@ #ifndef LMP_LAMMPSPLUGIN_H #define LMP_LAMMPSPLUGIN_H -// C style API and data structures required for dynamic loading +// C style API and data structure required for dynamic loading extern "C" { typedef void *(lammpsplugin_factory)(void *); - typedef void (*lammpsplugin_initfunc)(void *); typedef struct { const char *version; const char *style; const char *name; const char *info; + const char *author; lammpsplugin_factory *creator; + void *handle; } lammpsplugin_t; - typedef struct { - const char *style; - const char *name; - const void *handle; - } lammpsplugin_entry_t; + typedef void (*lammpsplugin_regfunc)(lammpsplugin_t *, void *); + typedef void (*lammpsplugin_initfunc)(void *, void *, lammpsplugin_regfunc); // prototype for initializer function required // to load a plugin; uses C bindings - void lammpsplugin_init(void *); -} - -namespace LAMMPS_NS -{ - extern void lammpsplugin_load(const char *, void *); - extern void lammpsplugin_register(lammpsplugin_t *, void *); - extern int lammpsplugin_get_num_plugins(); - extern const lammpsplugin_entry_t *lammpsplugin_info(int); - extern int lammpsplugin_find(const char *, const char *); - extern void lammpsplugin_unload(const char *, const char *, void *); + void lammpsplugin_init(void *, void *, lammpsplugin_regfunc); } #endif diff --git a/src/lammpsplugin.cpp b/src/plugin.cpp similarity index 81% rename from src/lammpsplugin.cpp rename to src/plugin.cpp index 3086b829c0..f81c453afb 100644 --- a/src/lammpsplugin.cpp +++ b/src/plugin.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "lammpsplugin.h" +#include "plugin.h" #include "error.h" #include "force.h" @@ -28,9 +28,9 @@ namespace LAMMPS_NS { - static std::vector pluginlist; + static std::vector pluginlist; - void lammpsplugin_load(const char *file, void *ptr) + void plugin_load(const char *file, void *ptr) { LAMMPS *lmp = (LAMMPS *)ptr; #if defined(WIN32) @@ -46,15 +46,15 @@ namespace LAMMPS_NS void *initfunc = dlsym(dso,"lammpsplugin_init"); if (initfunc == nullptr) { dlclose(dso); - utils::logmesg(lmp,fmt::format("Symbol lookup failure in file {}",file)); + utils::logmesg(lmp,fmt::format("Symbol lookup failure in file {}\n",file)); return; } - ((lammpsplugin_initfunc)(initfunc))(ptr); + ((lammpsplugin_initfunc)(initfunc))(ptr,dso,&plugin_register); // dlclose(dso); #endif } - void lammpsplugin_register(lammpsplugin_t *plugin, void *ptr) + void plugin_register(lammpsplugin_t *plugin, void *ptr) { LAMMPS *lmp = (LAMMPS *)ptr; @@ -64,11 +64,8 @@ namespace LAMMPS_NS "version {} loaded into LAMMPS " "version {}\n", plugin->info, plugin->version, lmp->version)); - lammpsplugin_entry_t entry; - entry.style = plugin->style; - entry.name = plugin->name; - entry.handle = nullptr; - pluginlist.push_back(entry); + + pluginlist.push_back(*plugin); std::string pstyle = plugin->style; if (pstyle == "pair") { @@ -81,19 +78,19 @@ namespace LAMMPS_NS } } - int lammpsplugin_get_num_plugins() + int plugin_get_num_plugins() { return pluginlist.size(); } - const lammpsplugin_entry_t *lammpsplugin_info(int idx) + const lammpsplugin_t *plugin_info(int idx) { if ((idx < 0) || idx >= pluginlist.size()) return nullptr; return &pluginlist[idx]; } - int lammpsplugin_find(const char *style, const char *name) + int plugin_find(const char *style, const char *name) { for (int i=0; i < pluginlist.size(); ++i) { if ((strcmp(style,pluginlist[i].style) == 0) @@ -103,7 +100,7 @@ namespace LAMMPS_NS return -1; } - void lammpsplugin_unload(const char *style, const char *name, void *ptr) + void plugin_unload(const char *style, const char *name, void *ptr) { LAMMPS *lmp = (LAMMPS *)ptr; std::string pstyle = style; diff --git a/src/plugin.h b/src/plugin.h new file mode 100644 index 0000000000..546ab2a644 --- /dev/null +++ b/src/plugin.h @@ -0,0 +1,29 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_PLUGIN_H +#define LMP_PLUGIN_H + +#include "lammpsplugin.h" + +namespace LAMMPS_NS +{ + void plugin_load(const char *, void *); + void plugin_register(lammpsplugin_t *, void *); + int plugin_get_num_plugins(); + const lammpsplugin_t *plugin_info(int); + int plugin_find(const char *, const char *); + void plugin_unload(const char *, const char *, void *); +} + +#endif From aed8608c7c008f5ae91e6c1a31803d5368df2e45 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 11 Mar 2021 11:59:49 -0500 Subject: [PATCH 0150/1217] Unify dump cfg/gz and cfg/zstd tests --- unittest/formats/CMakeLists.txt | 16 +-- unittest/formats/compressed_dump_test.h | 19 +-- .../formats/test_dump_atom_compressed.cpp | 23 ++- unittest/formats/test_dump_cfg_compressed.cpp | 132 +++++++++++++++++ unittest/formats/test_dump_cfg_gz.cpp | 133 ------------------ unittest/formats/test_dump_cfg_zstd.cpp | 133 ------------------ 6 files changed, 160 insertions(+), 296 deletions(-) create mode 100644 unittest/formats/test_dump_cfg_compressed.cpp delete mode 100644 unittest/formats/test_dump_cfg_gz.cpp delete mode 100644 unittest/formats/test_dump_cfg_zstd.cpp diff --git a/unittest/formats/CMakeLists.txt b/unittest/formats/CMakeLists.txt index 7b19bfde46..cd02aed6b0 100644 --- a/unittest/formats/CMakeLists.txt +++ b/unittest/formats/CMakeLists.txt @@ -52,11 +52,10 @@ if(PKG_COMPRESS) set_tests_properties(DumpCustomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") set_tests_properties(DumpCustomGZ PROPERTIES ENVIRONMENT "GZIP_BINARY=${GZIP_BINARY}") - add_executable(test_dump_cfg_gz test_dump_cfg_gz.cpp) - target_link_libraries(test_dump_cfg_gz PRIVATE lammps GTest::GMock GTest::GTest) - add_test(NAME DumpCfgGZ COMMAND test_dump_cfg_gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) - set_tests_properties(DumpCfgGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") - set_tests_properties(DumpCfgGZ PROPERTIES ENVIRONMENT "GZIP_BINARY=${GZIP_BINARY}") + add_executable(test_dump_cfg_compressed test_dump_cfg_compressed.cpp) + target_link_libraries(test_dump_cfg_compressed PRIVATE lammps GTest::GMock GTest::GTest) + add_test(NAME DumpCfgGZ COMMAND test_dump_cfg_compressed gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + set_tests_properties(DumpCfgGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}") add_executable(test_dump_xyz_gz test_dump_xyz_gz.cpp) target_link_libraries(test_dump_xyz_gz PRIVATE lammps GTest::GMock GTest::GTest) @@ -84,11 +83,8 @@ if(PKG_COMPRESS) set_tests_properties(DumpCustomZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") set_tests_properties(DumpCustomZstd PROPERTIES ENVIRONMENT "ZSTD_BINARY=${ZSTD_BINARY}") - add_executable(test_dump_cfg_zstd test_dump_cfg_zstd.cpp) - target_link_libraries(test_dump_cfg_zstd PRIVATE lammps GTest::GMock GTest::GTest) - add_test(NAME DumpCfgZstd COMMAND test_dump_cfg_zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) - set_tests_properties(DumpCfgZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") - set_tests_properties(DumpCfgZstd PROPERTIES ENVIRONMENT "ZSTD_BINARY=${ZSTD_BINARY}") + add_test(NAME DumpCfgZstd COMMAND test_dump_cfg_compressed zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + set_tests_properties(DumpCfgZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${ZSTD_BINARY}") add_executable(test_dump_xyz_zstd test_dump_xyz_zstd.cpp) target_link_libraries(test_dump_xyz_zstd PRIVATE lammps GTest::GMock GTest::GTest) diff --git a/unittest/formats/compressed_dump_test.h b/unittest/formats/compressed_dump_test.h index 80b8550060..c731a3b1b9 100644 --- a/unittest/formats/compressed_dump_test.h +++ b/unittest/formats/compressed_dump_test.h @@ -64,25 +64,28 @@ public: } void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string dump_modify_options, int ntimesteps) + std::string dump_options, std::string dump_modify_options, int ntimesteps) { generate_text_and_compressed_dump(text_file, compressed_file, + dump_options, dump_options, dump_modify_options, dump_modify_options, ntimesteps); } void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string text_options, std::string compressed_options, int ntimesteps) + std::string text_options, std::string compressed_options, + std::string text_modify_options, std::string compressed_modify_options, + int ntimesteps) { if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id0 all {} 1 {}", dump_style, text_file)); - command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_file)); + command(fmt::format("dump id0 all {} 1 {} {}", dump_style, text_file, text_options)); + command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_file, compressed_options)); - if (!text_options.empty()) { - command(fmt::format("dump_modify id0 {}", text_options)); + if (!text_modify_options.empty()) { + command(fmt::format("dump_modify id0 {}", text_modify_options)); } - if (!compressed_options.empty()) { - command(fmt::format("dump_modify id1 {}", compressed_options)); + if (!compressed_modify_options.empty()) { + command(fmt::format("dump_modify id1 {}", compressed_modify_options)); } command(fmt::format("run {}", ntimesteps)); diff --git a/unittest/formats/test_dump_atom_compressed.cpp b/unittest/formats/test_dump_atom_compressed.cpp index e33366801e..3360872f9e 100644 --- a/unittest/formats/test_dump_atom_compressed.cpp +++ b/unittest/formats/test_dump_atom_compressed.cpp @@ -40,7 +40,7 @@ TEST_F(DumpAtomCompressTest, compressed_run0) auto text_file = text_dump_filename("run0.melt"); auto compressed_file = compressed_dump_filename("run0.melt"); - generate_text_and_compressed_dump(text_file, compressed_file, "", 0); + generate_text_and_compressed_dump(text_file, compressed_file, "", "", 0); TearDown(); @@ -71,7 +71,7 @@ TEST_F(DumpAtomCompressTest, compressed_multi_file_run1) auto compressed_file_0 = compressed_dump_filename(base_name_0); auto compressed_file_1 = compressed_dump_filename(base_name_1); - generate_text_and_compressed_dump(text_file, compressed_file, "", 1); + generate_text_and_compressed_dump(text_file, compressed_file, "", "", 1); TearDown(); @@ -107,7 +107,7 @@ TEST_F(DumpAtomCompressTest, compressed_multi_file_with_pad_run1) auto compressed_file_0 = compressed_dump_filename(base_name_0); auto compressed_file_1 = compressed_dump_filename(base_name_1); - generate_text_and_compressed_dump(text_file, compressed_file, "pad 3", 1); + generate_text_and_compressed_dump(text_file, compressed_file, "", "pad 3", 1); TearDown(); @@ -151,7 +151,7 @@ TEST_F(DumpAtomCompressTest, compressed_multi_file_with_maxfiles_run1) auto compressed_file_1 = compressed_dump_filename(base_name_1); auto compressed_file_2 = compressed_dump_filename(base_name_2); - generate_text_and_compressed_dump(text_file, compressed_file, "maxfiles 2", 2); + generate_text_and_compressed_dump(text_file, compressed_file, "", "maxfiles 2", 2); TearDown(); @@ -188,8 +188,7 @@ TEST_F(DumpAtomCompressTest, compressed_with_units_run0) auto text_file = text_dump_filename(base_name); auto compressed_file = compressed_dump_filename(base_name); - generate_text_and_compressed_dump(text_file, compressed_file, "scale no units yes", - 0); + generate_text_and_compressed_dump(text_file, compressed_file, "", "scale no units yes", 0); TearDown(); @@ -213,7 +212,7 @@ TEST_F(DumpAtomCompressTest, compressed_with_time_run0) auto text_file = text_dump_filename(base_name); auto compressed_file = compressed_dump_filename(base_name); - generate_text_and_compressed_dump(text_file, compressed_file, "scale no time yes", 0); + generate_text_and_compressed_dump(text_file, compressed_file, "", "scale no time yes", 0); TearDown(); @@ -238,7 +237,7 @@ TEST_F(DumpAtomCompressTest, compressed_triclinic_run0) auto compressed_file = compressed_dump_filename(base_name); enable_triclinic(); - generate_text_and_compressed_dump(text_file, compressed_file, "", 0); + generate_text_and_compressed_dump(text_file, compressed_file, "", "", 0); TearDown(); @@ -263,7 +262,7 @@ TEST_F(DumpAtomCompressTest, compressed_triclinic_with_units_run0) auto compressed_file = compressed_dump_filename(base_name); enable_triclinic(); - generate_text_and_compressed_dump(text_file, compressed_file, "scale no units yes", 0); + generate_text_and_compressed_dump(text_file, compressed_file, "", "scale no units yes", 0); TearDown(); @@ -288,7 +287,7 @@ TEST_F(DumpAtomCompressTest, compressed_triclinic_with_time_run0) auto compressed_file = compressed_dump_filename(base_name); enable_triclinic(); - generate_text_and_compressed_dump(text_file, compressed_file, "scale no time yes", 0); + generate_text_and_compressed_dump(text_file, compressed_file, "", "scale no time yes", 0); TearDown(); @@ -313,7 +312,7 @@ TEST_F(DumpAtomCompressTest, compressed_triclinic_with_image_run0) auto compressed_file = compressed_dump_filename(base_name); enable_triclinic(); - generate_text_and_compressed_dump(text_file, compressed_file, "image yes", 0); + generate_text_and_compressed_dump(text_file, compressed_file, "", "image yes", 0); TearDown(); @@ -359,7 +358,7 @@ TEST_F(DumpAtomCompressTest, compressed_modify_clevel_run0) auto text_file = text_dump_filename(base_name); auto compressed_file = compressed_dump_filename(base_name); - generate_text_and_compressed_dump(text_file, compressed_file, "", "compression_level 3", 0); + generate_text_and_compressed_dump(text_file, compressed_file, "", "", "", "compression_level 3", 0); TearDown(); diff --git a/unittest/formats/test_dump_cfg_compressed.cpp b/unittest/formats/test_dump_cfg_compressed.cpp new file mode 100644 index 0000000000..d06eabe57b --- /dev/null +++ b/unittest/formats/test_dump_cfg_compressed.cpp @@ -0,0 +1,132 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "../testing/utils.h" +#include "compressed_dump_test.h" +#include "fmt/format.h" +#include "utils.h" +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include + + +using ::testing::Eq; + +class DumpCfgCompressTest : public CompressedDumpTest { +public: + DumpCfgCompressTest() : CompressedDumpTest("cfg") { + } +}; + +//------------------------------------------------------------------------------------------------- +// compressed files +//------------------------------------------------------------------------------------------------- + +TEST_F(DumpCfgCompressTest, compressed_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "run*.melt.cfg"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + + auto base_name_0 = "run0.melt.cfg"; + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; + + generate_text_and_compressed_dump(text_files, compressed_files, fields, "", 0); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + +TEST_F(DumpCfgCompressTest, compressed_unwrap_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "unwrap_run*.melt.cfg"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + + auto base_name_0 = "unwrap_run0.melt.cfg"; + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "mass type xsu ysu zsu id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; + + generate_text_and_compressed_dump(text_files, compressed_files, fields, "", 0); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + +int main(int argc, char **argv) +{ + MPI_Init(&argc, &argv); + ::testing::InitGoogleMock(&argc, argv); + + if (argc < 2) { + std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; + return 1; + } + + if(strcmp(argv[1], "gz") == 0) { + COMPRESS_SUFFIX = "gz"; + COMPRESS_EXTENSION = "gz"; + } else if(strcmp(argv[1], "zstd") == 0) { + COMPRESS_SUFFIX = "zstd"; + COMPRESS_EXTENSION = "zst"; + } else { + std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; + return 1; + } + + COMPRESS_BINARY = getenv("COMPRESS_BINARY"); + + // handle arguments passed via environment variable + if (const char *var = getenv("TEST_ARGS")) { + std::vector env = utils::split_words(var); + for (auto arg : env) { + if (arg == "-v") { + verbose = true; + } + } + } + + if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; + + int rv = RUN_ALL_TESTS(); + MPI_Finalize(); + return rv; +} diff --git a/unittest/formats/test_dump_cfg_gz.cpp b/unittest/formats/test_dump_cfg_gz.cpp deleted file mode 100644 index ced307dc0a..0000000000 --- a/unittest/formats/test_dump_cfg_gz.cpp +++ /dev/null @@ -1,133 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "../testing/core.h" -#include "../testing/systems/melt.h" -#include "../testing/utils.h" -#include "fmt/format.h" -#include "utils.h" -#include "gmock/gmock.h" -#include "gtest/gtest.h" - -char *GZIP_BINARY = nullptr; - -using ::testing::Eq; - -class DumpCfgGZTest : public MeltTest { - std::string dump_style = "cfg"; - -public: - void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string compression_style, std::string fields, - std::string dump_modify_options, int ntimesteps) - { - if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id0 all {} 1 {} {}", dump_style, text_file, fields)); - command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_file, fields)); - - if (!dump_modify_options.empty()) { - command(fmt::format("dump_modify id0 {}", dump_modify_options)); - command(fmt::format("dump_modify id1 {}", dump_modify_options)); - } - - command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - std::string convert_compressed_to_text(std::string compressed_file) - { - if (!verbose) ::testing::internal::CaptureStdout(); - std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.')); - std::string cmdline = - fmt::format("{} -d -c {} > {}", GZIP_BINARY, compressed_file, converted_file); - system(cmdline.c_str()); - if (!verbose) ::testing::internal::GetCapturedStdout(); - return converted_file; - } -}; - -TEST_F(DumpCfgGZTest, compressed_run0) -{ - if (!GZIP_BINARY) GTEST_SKIP(); - - auto text_files = "dump_cfg_gz_text_run*.melt.cfg"; - auto compressed_files = "dump_cfg_gz_compressed_run*.melt.cfg.gz"; - auto text_file = "dump_cfg_gz_text_run0.melt.cfg"; - auto compressed_file = "dump_cfg_gz_compressed_run0.melt.cfg.gz"; - auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; - - generate_text_and_compressed_dump(text_files, compressed_files, "cfg/gz", fields, "", 0); - - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -TEST_F(DumpCfgGZTest, compressed_unwrap_run0) -{ - if (!GZIP_BINARY) GTEST_SKIP(); - - auto text_files = "dump_cfg_unwrap_gz_text_run*.melt.cfg"; - auto compressed_files = "dump_cfg_unwrap_gz_compressed_run*.melt.cfg.gz"; - auto text_file = "dump_cfg_unwrap_gz_text_run0.melt.cfg"; - auto compressed_file = "dump_cfg_unwrap_gz_compressed_run0.melt.cfg.gz"; - auto fields = "mass type xsu ysu zsu id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; - - generate_text_and_compressed_dump(text_files, compressed_files, "cfg/gz", fields, "", 0); - - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -int main(int argc, char **argv) -{ - MPI_Init(&argc, &argv); - ::testing::InitGoogleMock(&argc, argv); - - // handle arguments passed via environment variable - if (const char *var = getenv("TEST_ARGS")) { - std::vector env = utils::split_words(var); - for (auto arg : env) { - if (arg == "-v") { - verbose = true; - } - } - } - - GZIP_BINARY = getenv("GZIP_BINARY"); - - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; - - int rv = RUN_ALL_TESTS(); - MPI_Finalize(); - return rv; -} diff --git a/unittest/formats/test_dump_cfg_zstd.cpp b/unittest/formats/test_dump_cfg_zstd.cpp deleted file mode 100644 index c13a3d5eaf..0000000000 --- a/unittest/formats/test_dump_cfg_zstd.cpp +++ /dev/null @@ -1,133 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "../testing/core.h" -#include "../testing/systems/melt.h" -#include "../testing/utils.h" -#include "fmt/format.h" -#include "utils.h" -#include "gmock/gmock.h" -#include "gtest/gtest.h" - -char *ZSTD_BINARY = nullptr; - -using ::testing::Eq; - -class DumpCfgZstdTest : public MeltTest { - std::string dump_style = "cfg"; - -public: - void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string compression_style, std::string fields, - std::string dump_modify_options, int ntimesteps) - { - if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id0 all {} 1 {} {}", dump_style, text_file, fields)); - command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_file, fields)); - - if (!dump_modify_options.empty()) { - command(fmt::format("dump_modify id0 {}", dump_modify_options)); - command(fmt::format("dump_modify id1 {}", dump_modify_options)); - } - - command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - std::string convert_compressed_to_text(std::string compressed_file) - { - if (!verbose) ::testing::internal::CaptureStdout(); - std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.')); - std::string cmdline = - fmt::format("{} -d -c {} > {}", ZSTD_BINARY, compressed_file, converted_file); - system(cmdline.c_str()); - if (!verbose) ::testing::internal::GetCapturedStdout(); - return converted_file; - } -}; - -TEST_F(DumpCfgZstdTest, compressed_run0) -{ - if (!ZSTD_BINARY) GTEST_SKIP(); - - auto text_files = "dump_cfg_zstd_text_run*.melt.cfg"; - auto compressed_files = "dump_cfg_zstd_compressed_run*.melt.cfg.zst"; - auto text_file = "dump_cfg_zstd_text_run0.melt.cfg"; - auto compressed_file = "dump_cfg_zstd_compressed_run0.melt.cfg.zst"; - auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; - - generate_text_and_compressed_dump(text_files, compressed_files, "cfg/zstd", fields, "", 0); - - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -TEST_F(DumpCfgZstdTest, compressed_unwrap_run0) -{ - if (!ZSTD_BINARY) GTEST_SKIP(); - - auto text_files = "dump_cfg_unwrap_zstd_text_run*.melt.cfg"; - auto compressed_files = "dump_cfg_unwrap_zstd_compressed_run*.melt.cfg.zst"; - auto text_file = "dump_cfg_unwrap_zstd_text_run0.melt.cfg"; - auto compressed_file = "dump_cfg_unwrap_zstd_compressed_run0.melt.cfg.zst"; - auto fields = "mass type xsu ysu zsu id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; - - generate_text_and_compressed_dump(text_files, compressed_files, "cfg/zstd", fields, "", 0); - - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -int main(int argc, char **argv) -{ - MPI_Init(&argc, &argv); - ::testing::InitGoogleMock(&argc, argv); - - // handle arguments passed via environment variable - if (const char *var = getenv("TEST_ARGS")) { - std::vector env = utils::split_words(var); - for (auto arg : env) { - if (arg == "-v") { - verbose = true; - } - } - } - - ZSTD_BINARY = getenv("ZSTD_BINARY"); - - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; - - int rv = RUN_ALL_TESTS(); - MPI_Finalize(); - return rv; -} From 116ffd62dec936da768d31410c6db873fa3f354d Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 11 Mar 2021 12:11:23 -0500 Subject: [PATCH 0151/1217] Unify dump custom/gz and custom/zstd tests --- unittest/formats/CMakeLists.txt | 24 ++- .../formats/test_dump_custom_compressed.cpp | 122 ++++++++++++++ unittest/formats/test_dump_custom_gz.cpp | 154 ------------------ unittest/formats/test_dump_custom_zstd.cpp | 154 ------------------ 4 files changed, 133 insertions(+), 321 deletions(-) create mode 100644 unittest/formats/test_dump_custom_compressed.cpp delete mode 100644 unittest/formats/test_dump_custom_gz.cpp delete mode 100644 unittest/formats/test_dump_custom_zstd.cpp diff --git a/unittest/formats/CMakeLists.txt b/unittest/formats/CMakeLists.txt index cd02aed6b0..7932c037fa 100644 --- a/unittest/formats/CMakeLists.txt +++ b/unittest/formats/CMakeLists.txt @@ -43,17 +43,18 @@ if(PKG_COMPRESS) add_executable(test_dump_atom_compressed test_dump_atom_compressed.cpp) target_link_libraries(test_dump_atom_compressed PRIVATE lammps GTest::GMock GTest::GTest) - add_test(NAME DumpAtomGZ COMMAND test_dump_atom_compressed gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) - set_tests_properties(DumpAtomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}") - - add_executable(test_dump_custom_gz test_dump_custom_gz.cpp) - target_link_libraries(test_dump_custom_gz PRIVATE lammps GTest::GMock GTest::GTest) - add_test(NAME DumpCustomGZ COMMAND test_dump_custom_gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) - set_tests_properties(DumpCustomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") - set_tests_properties(DumpCustomGZ PROPERTIES ENVIRONMENT "GZIP_BINARY=${GZIP_BINARY}") + add_executable(test_dump_custom_compressed test_dump_custom_compressed.cpp) + target_link_libraries(test_dump_custom_compressed PRIVATE lammps GTest::GMock GTest::GTest) add_executable(test_dump_cfg_compressed test_dump_cfg_compressed.cpp) target_link_libraries(test_dump_cfg_compressed PRIVATE lammps GTest::GMock GTest::GTest) + + add_test(NAME DumpAtomGZ COMMAND test_dump_atom_compressed gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + set_tests_properties(DumpAtomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}") + + add_test(NAME DumpCustomGZ COMMAND test_dump_custom_compressed gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + set_tests_properties(DumpCustomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}") + add_test(NAME DumpCfgGZ COMMAND test_dump_cfg_compressed gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(DumpCfgGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}") @@ -77,11 +78,8 @@ if(PKG_COMPRESS) add_test(NAME DumpAtomZstd COMMAND test_dump_atom_compressed zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(DumpAtomZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${ZSTD_BINARY}") - add_executable(test_dump_custom_zstd test_dump_custom_zstd.cpp) - target_link_libraries(test_dump_custom_zstd PRIVATE lammps GTest::GMock GTest::GTest) - add_test(NAME DumpCustomZstd COMMAND test_dump_custom_zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) - set_tests_properties(DumpCustomZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") - set_tests_properties(DumpCustomZstd PROPERTIES ENVIRONMENT "ZSTD_BINARY=${ZSTD_BINARY}") + add_test(NAME DumpCustomZstd COMMAND test_dump_custom_compressed zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + set_tests_properties(DumpCustomZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${ZSTD_BINARY}") add_test(NAME DumpCfgZstd COMMAND test_dump_cfg_compressed zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(DumpCfgZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${ZSTD_BINARY}") diff --git a/unittest/formats/test_dump_custom_compressed.cpp b/unittest/formats/test_dump_custom_compressed.cpp new file mode 100644 index 0000000000..0afad264fb --- /dev/null +++ b/unittest/formats/test_dump_custom_compressed.cpp @@ -0,0 +1,122 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "../testing/utils.h" +#include "compressed_dump_test.h" +#include "fmt/format.h" +#include "utils.h" +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include + + +using ::testing::Eq; + +class DumpCustomCompressTest : public CompressedDumpTest { +public: + DumpCustomCompressTest() : CompressedDumpTest("custom") { + } +}; + +TEST_F(DumpCustomCompressTest, compressed_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "custom_run1.melt"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); + auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; + + generate_text_and_compressed_dump(text_file, compressed_file, fields, "units yes", 1); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file); + ASSERT_FILE_EXISTS(compressed_file); + + auto converted_file = convert_compressed_to_text(compressed_file); + + ASSERT_FILE_EXISTS(converted_file); + ASSERT_FILE_EQUAL(text_file, converted_file); + delete_file(text_file); + delete_file(compressed_file); + delete_file(converted_file); +} + +TEST_F(DumpCustomCompressTest, compressed_triclinic_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "custom_tri_run1.melt"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); + auto fields = "id type proc x y z xs ys zs xsu ysu zsu vx vy vz fx fy fz"; + + enable_triclinic(); + + generate_text_and_compressed_dump(text_file, compressed_file, fields, "units yes", 1); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file); + ASSERT_FILE_EXISTS(compressed_file); + + auto converted_file = convert_compressed_to_text(compressed_file); + + ASSERT_FILE_EXISTS(converted_file); + ASSERT_FILE_EQUAL(text_file, converted_file); + delete_file(text_file); + delete_file(compressed_file); + delete_file(converted_file); +} + +int main(int argc, char **argv) +{ + MPI_Init(&argc, &argv); + ::testing::InitGoogleMock(&argc, argv); + + if (argc < 2) { + std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; + return 1; + } + + if(strcmp(argv[1], "gz") == 0) { + COMPRESS_SUFFIX = "gz"; + COMPRESS_EXTENSION = "gz"; + } else if(strcmp(argv[1], "zstd") == 0) { + COMPRESS_SUFFIX = "zstd"; + COMPRESS_EXTENSION = "zst"; + } else { + std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; + return 1; + } + + COMPRESS_BINARY = getenv("COMPRESS_BINARY"); + + // handle arguments passed via environment variable + if (const char *var = getenv("TEST_ARGS")) { + std::vector env = utils::split_words(var); + for (auto arg : env) { + if (arg == "-v") { + verbose = true; + } + } + } + + if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; + + int rv = RUN_ALL_TESTS(); + MPI_Finalize(); + return rv; +} diff --git a/unittest/formats/test_dump_custom_gz.cpp b/unittest/formats/test_dump_custom_gz.cpp deleted file mode 100644 index 67c9b535aa..0000000000 --- a/unittest/formats/test_dump_custom_gz.cpp +++ /dev/null @@ -1,154 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "../testing/core.h" -#include "../testing/systems/melt.h" -#include "../testing/utils.h" -#include "fmt/format.h" -#include "utils.h" -#include "gmock/gmock.h" -#include "gtest/gtest.h" - -using ::testing::Eq; - -char *GZIP_BINARY = nullptr; - -class DumpCustomGZTest : public MeltTest { - std::string dump_style = "custom"; - -public: - void enable_triclinic() - { - if (!verbose) ::testing::internal::CaptureStdout(); - command("change_box all triclinic"); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void generate_dump(std::string dump_file, std::string fields, std::string dump_modify_options, - int ntimesteps) - { - if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id all {} 1 {} {}", dump_style, dump_file, fields)); - - if (!dump_modify_options.empty()) { - command(fmt::format("dump_modify id {}", dump_modify_options)); - } - - command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string compression_style, std::string fields, - std::string dump_modify_options, int ntimesteps) - { - if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id0 all {} 1 {} {}", dump_style, text_file, fields)); - command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_file, fields)); - - if (!dump_modify_options.empty()) { - command(fmt::format("dump_modify id0 {}", dump_modify_options)); - command(fmt::format("dump_modify id1 {}", dump_modify_options)); - } - - command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - std::string convert_compressed_to_text(std::string compressed_file) - { - if (!verbose) ::testing::internal::CaptureStdout(); - std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.')); - std::string cmdline = - fmt::format("{} -d -c {} > {}", GZIP_BINARY, compressed_file, converted_file); - system(cmdline.c_str()); - if (!verbose) ::testing::internal::GetCapturedStdout(); - return converted_file; - } -}; - -TEST_F(DumpCustomGZTest, compressed_run1) -{ - if (!GZIP_BINARY) GTEST_SKIP(); - - auto text_file = "dump_custom_gz_text_run1.melt"; - auto compressed_file = "dump_custom_gz_compressed_run1.melt.gz"; - auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; - - generate_text_and_compressed_dump(text_file, compressed_file, "custom/gz", fields, "units yes", - 1); - - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -TEST_F(DumpCustomGZTest, compressed_triclinic_run1) -{ - if (!GZIP_BINARY) GTEST_SKIP(); - - auto text_file = "dump_custom_gz_tri_text_run1.melt"; - auto compressed_file = "dump_custom_gz_tri_compressed_run1.melt.gz"; - auto fields = "id type proc x y z xs ys zs xsu ysu zsu vx vy vz fx fy fz"; - - enable_triclinic(); - - generate_text_and_compressed_dump(text_file, compressed_file, "custom/gz", fields, "units yes", - 1); - - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -int main(int argc, char **argv) -{ - MPI_Init(&argc, &argv); - ::testing::InitGoogleMock(&argc, argv); - - // handle arguments passed via environment variable - if (const char *var = getenv("TEST_ARGS")) { - std::vector env = utils::split_words(var); - for (auto arg : env) { - if (arg == "-v") { - verbose = true; - } - } - } - - GZIP_BINARY = getenv("GZIP_BINARY"); - - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; - - int rv = RUN_ALL_TESTS(); - MPI_Finalize(); - return rv; -} diff --git a/unittest/formats/test_dump_custom_zstd.cpp b/unittest/formats/test_dump_custom_zstd.cpp deleted file mode 100644 index 40328d5592..0000000000 --- a/unittest/formats/test_dump_custom_zstd.cpp +++ /dev/null @@ -1,154 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "../testing/core.h" -#include "../testing/systems/melt.h" -#include "../testing/utils.h" -#include "fmt/format.h" -#include "utils.h" -#include "gmock/gmock.h" -#include "gtest/gtest.h" - -using ::testing::Eq; - -char *ZSTD_BINARY = nullptr; - -class DumpCustomZstdTest : public MeltTest { - std::string dump_style = "custom"; - -public: - void enable_triclinic() - { - if (!verbose) ::testing::internal::CaptureStdout(); - command("change_box all triclinic"); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void generate_dump(std::string dump_file, std::string fields, std::string dump_modify_options, - int ntimesteps) - { - if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id all {} 1 {} {}", dump_style, dump_file, fields)); - - if (!dump_modify_options.empty()) { - command(fmt::format("dump_modify id {}", dump_modify_options)); - } - - command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string compression_style, std::string fields, - std::string dump_modify_options, int ntimesteps) - { - if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id0 all {} 1 {} {}", dump_style, text_file, fields)); - command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_file, fields)); - - if (!dump_modify_options.empty()) { - command(fmt::format("dump_modify id0 {}", dump_modify_options)); - command(fmt::format("dump_modify id1 {}", dump_modify_options)); - } - - command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - std::string convert_compressed_to_text(std::string compressed_file) - { - if (!verbose) ::testing::internal::CaptureStdout(); - std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.')); - std::string cmdline = - fmt::format("{} -d -c {} > {}", ZSTD_BINARY, compressed_file, converted_file); - system(cmdline.c_str()); - if (!verbose) ::testing::internal::GetCapturedStdout(); - return converted_file; - } -}; - -TEST_F(DumpCustomZstdTest, compressed_run1) -{ - if (!ZSTD_BINARY) GTEST_SKIP(); - - auto text_file = "dump_custom_zstd_text_run1.melt"; - auto compressed_file = "dump_custom_zstd_compressed_run1.melt.zst"; - auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; - - generate_text_and_compressed_dump(text_file, compressed_file, "custom/zstd", fields, - "units yes", 1); - - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -TEST_F(DumpCustomZstdTest, compressed_triclinic_run1) -{ - if (!ZSTD_BINARY) GTEST_SKIP(); - - auto text_file = "dump_custom_zstd_tri_text_run1.melt"; - auto compressed_file = "dump_custom_zstd_tri_compressed_run1.melt.zst"; - auto fields = "id type proc x y z xs ys zs xsu ysu zsu vx vy vz fx fy fz"; - - enable_triclinic(); - - generate_text_and_compressed_dump(text_file, compressed_file, "custom/zstd", fields, - "units yes", 1); - - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -int main(int argc, char **argv) -{ - MPI_Init(&argc, &argv); - ::testing::InitGoogleMock(&argc, argv); - - // handle arguments passed via environment variable - if (const char *var = getenv("TEST_ARGS")) { - std::vector env = utils::split_words(var); - for (auto arg : env) { - if (arg == "-v") { - verbose = true; - } - } - } - - ZSTD_BINARY = getenv("ZSTD_BINARY"); - - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; - - int rv = RUN_ALL_TESTS(); - MPI_Finalize(); - return rv; -} From fca6d6bf8f6cda4226471bc0d9625a528a06bf4b Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 11 Mar 2021 12:20:25 -0500 Subject: [PATCH 0152/1217] Unify dump local/gz and local/zstd tests --- unittest/formats/CMakeLists.txt | 21 ++-- .../formats/test_dump_local_compressed.cpp | 102 ++++++++++++++++ unittest/formats/test_dump_local_gz.cpp | 111 ------------------ unittest/formats/test_dump_local_zstd.cpp | 111 ------------------ 4 files changed, 111 insertions(+), 234 deletions(-) create mode 100644 unittest/formats/test_dump_local_compressed.cpp delete mode 100644 unittest/formats/test_dump_local_gz.cpp delete mode 100644 unittest/formats/test_dump_local_zstd.cpp diff --git a/unittest/formats/CMakeLists.txt b/unittest/formats/CMakeLists.txt index 7932c037fa..731e387fc2 100644 --- a/unittest/formats/CMakeLists.txt +++ b/unittest/formats/CMakeLists.txt @@ -49,6 +49,9 @@ if(PKG_COMPRESS) add_executable(test_dump_cfg_compressed test_dump_cfg_compressed.cpp) target_link_libraries(test_dump_cfg_compressed PRIVATE lammps GTest::GMock GTest::GTest) + add_executable(test_dump_local_compressed test_dump_local_compressed.cpp) + target_link_libraries(test_dump_local_compressed PRIVATE lammps GTest::GMock GTest::GTest) + add_test(NAME DumpAtomGZ COMMAND test_dump_atom_compressed gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(DumpAtomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}") @@ -58,18 +61,15 @@ if(PKG_COMPRESS) add_test(NAME DumpCfgGZ COMMAND test_dump_cfg_compressed gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(DumpCfgGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}") + add_test(NAME DumpLocalGZ COMMAND test_dump_local_compressed gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + set_tests_properties(DumpLocalGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}") + add_executable(test_dump_xyz_gz test_dump_xyz_gz.cpp) target_link_libraries(test_dump_xyz_gz PRIVATE lammps GTest::GMock GTest::GTest) add_test(NAME DumpXYZGZ COMMAND test_dump_xyz_gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(DumpXYZGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") set_tests_properties(DumpXYZGZ PROPERTIES ENVIRONMENT "GZIP_BINARY=${GZIP_BINARY}") - add_executable(test_dump_local_gz test_dump_local_gz.cpp) - target_link_libraries(test_dump_local_gz PRIVATE lammps GTest::GMock GTest::GTest) - add_test(NAME DumpLocalGZ COMMAND test_dump_local_gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) - set_tests_properties(DumpLocalGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") - set_tests_properties(DumpLocalGZ PROPERTIES ENVIRONMENT "GZIP_BINARY=${GZIP_BINARY}") - find_package(PkgConfig REQUIRED) pkg_check_modules(Zstd IMPORTED_TARGET libzstd>=1.4) find_program(ZSTD_BINARY NAMES zstd) @@ -84,17 +84,14 @@ if(PKG_COMPRESS) add_test(NAME DumpCfgZstd COMMAND test_dump_cfg_compressed zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(DumpCfgZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${ZSTD_BINARY}") + add_test(NAME DumpLocalZstd COMMAND test_dump_local_compressed zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + set_tests_properties(DumpLocalZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${ZSTD_BINARY}") + add_executable(test_dump_xyz_zstd test_dump_xyz_zstd.cpp) target_link_libraries(test_dump_xyz_zstd PRIVATE lammps GTest::GMock GTest::GTest) add_test(NAME DumpXYZZstd COMMAND test_dump_xyz_zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(DumpXYZZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") set_tests_properties(DumpXYZZstd PROPERTIES ENVIRONMENT "ZSTD_BINARY=${ZSTD_BINARY}") - - add_executable(test_dump_local_zstd test_dump_local_zstd.cpp) - target_link_libraries(test_dump_local_zstd PRIVATE lammps GTest::GMock GTest::GTest) - add_test(NAME DumpLocalZstd COMMAND test_dump_local_zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) - set_tests_properties(DumpLocalZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") - set_tests_properties(DumpLocalZstd PROPERTIES ENVIRONMENT "ZSTD_BINARY=${ZSTD_BINARY}") endif() endif() diff --git a/unittest/formats/test_dump_local_compressed.cpp b/unittest/formats/test_dump_local_compressed.cpp new file mode 100644 index 0000000000..048053fb9a --- /dev/null +++ b/unittest/formats/test_dump_local_compressed.cpp @@ -0,0 +1,102 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "../testing/utils.h" +#include "compressed_dump_test.h" +#include "fmt/format.h" +#include "utils.h" +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include + + +using ::testing::Eq; + +class DumpLocalCompressTest : public CompressedDumpTest { +public: + DumpLocalCompressTest() : CompressedDumpTest("local") { + } +}; + +TEST_F(DumpLocalCompressTest, compressed_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + if (!verbose) ::testing::internal::CaptureStdout(); + command("compute comp all pair/local dist eng"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + + auto base_name = "run*.melt.local"; + auto base_name_0 = "run0.melt.local"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "index c_comp[1]"; + + generate_text_and_compressed_dump(text_files, compressed_files, fields, "", 0); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + +int main(int argc, char **argv) +{ + MPI_Init(&argc, &argv); + ::testing::InitGoogleMock(&argc, argv); + + if (argc < 2) { + std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; + return 1; + } + + if(strcmp(argv[1], "gz") == 0) { + COMPRESS_SUFFIX = "gz"; + COMPRESS_EXTENSION = "gz"; + } else if(strcmp(argv[1], "zstd") == 0) { + COMPRESS_SUFFIX = "zstd"; + COMPRESS_EXTENSION = "zst"; + } else { + std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; + return 1; + } + + COMPRESS_BINARY = getenv("COMPRESS_BINARY"); + + // handle arguments passed via environment variable + if (const char *var = getenv("TEST_ARGS")) { + std::vector env = utils::split_words(var); + for (auto arg : env) { + if (arg == "-v") { + verbose = true; + } + } + } + + if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; + + int rv = RUN_ALL_TESTS(); + MPI_Finalize(); + return rv; +} diff --git a/unittest/formats/test_dump_local_gz.cpp b/unittest/formats/test_dump_local_gz.cpp deleted file mode 100644 index 6ae25ae33d..0000000000 --- a/unittest/formats/test_dump_local_gz.cpp +++ /dev/null @@ -1,111 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "../testing/core.h" -#include "../testing/systems/melt.h" -#include "../testing/utils.h" -#include "fmt/format.h" -#include "utils.h" -#include "gmock/gmock.h" -#include "gtest/gtest.h" - -char *GZIP_BINARY = nullptr; - -using ::testing::Eq; - -class DumpLocalGZTest : public MeltTest { - std::string dump_style = "local"; - -public: - void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string compression_style, std::string fields, - std::string dump_modify_options, int ntimesteps) - { - if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id0 all {} 1 {} {}", dump_style, text_file, fields)); - command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_file, fields)); - - if (!dump_modify_options.empty()) { - command(fmt::format("dump_modify id0 {}", dump_modify_options)); - command(fmt::format("dump_modify id1 {}", dump_modify_options)); - } - - command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - std::string convert_compressed_to_text(std::string compressed_file) - { - if (!verbose) ::testing::internal::CaptureStdout(); - std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.')); - std::string cmdline = - fmt::format("{} -d -c {} > {}", GZIP_BINARY, compressed_file, converted_file); - system(cmdline.c_str()); - if (!verbose) ::testing::internal::GetCapturedStdout(); - return converted_file; - } -}; - -TEST_F(DumpLocalGZTest, compressed_run0) -{ - if (!GZIP_BINARY) GTEST_SKIP(); - - if (!verbose) ::testing::internal::CaptureStdout(); - command("compute comp all pair/local dist eng"); - if (!verbose) ::testing::internal::GetCapturedStdout(); - - auto text_files = "dump_local_gz_text_run*.melt.local"; - auto compressed_files = "dump_local_gz_compressed_run*.melt.local.gz"; - auto text_file = "dump_local_gz_text_run0.melt.local"; - auto compressed_file = "dump_local_gz_compressed_run0.melt.local.gz"; - auto fields = "index c_comp[1]"; - - generate_text_and_compressed_dump(text_files, compressed_files, "local/gz", fields, "", 0); - - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -int main(int argc, char **argv) -{ - MPI_Init(&argc, &argv); - ::testing::InitGoogleMock(&argc, argv); - - // handle arguments passed via environment variable - if (const char *var = getenv("TEST_ARGS")) { - std::vector env = utils::split_words(var); - for (auto arg : env) { - if (arg == "-v") { - verbose = true; - } - } - } - - GZIP_BINARY = getenv("GZIP_BINARY"); - - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; - - int rv = RUN_ALL_TESTS(); - MPI_Finalize(); - return rv; -} diff --git a/unittest/formats/test_dump_local_zstd.cpp b/unittest/formats/test_dump_local_zstd.cpp deleted file mode 100644 index 4a15baf4ca..0000000000 --- a/unittest/formats/test_dump_local_zstd.cpp +++ /dev/null @@ -1,111 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "../testing/core.h" -#include "../testing/systems/melt.h" -#include "../testing/utils.h" -#include "fmt/format.h" -#include "utils.h" -#include "gmock/gmock.h" -#include "gtest/gtest.h" - -char *ZSTD_BINARY = nullptr; - -using ::testing::Eq; - -class DumpLocalGZTest : public MeltTest { - std::string dump_style = "local"; - -public: - void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string compression_style, std::string fields, - std::string dump_modify_options, int ntimesteps) - { - if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id0 all {} 1 {} {}", dump_style, text_file, fields)); - command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_file, fields)); - - if (!dump_modify_options.empty()) { - command(fmt::format("dump_modify id0 {}", dump_modify_options)); - command(fmt::format("dump_modify id1 {}", dump_modify_options)); - } - - command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - std::string convert_compressed_to_text(std::string compressed_file) - { - if (!verbose) ::testing::internal::CaptureStdout(); - std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.')); - std::string cmdline = - fmt::format("{} -d -c {} > {}", ZSTD_BINARY, compressed_file, converted_file); - system(cmdline.c_str()); - if (!verbose) ::testing::internal::GetCapturedStdout(); - return converted_file; - } -}; - -TEST_F(DumpLocalGZTest, compressed_run0) -{ - if (!ZSTD_BINARY) GTEST_SKIP(); - - if (!verbose) ::testing::internal::CaptureStdout(); - command("compute comp all pair/local dist eng"); - if (!verbose) ::testing::internal::GetCapturedStdout(); - - auto text_files = "dump_local_zstd_text_run*.melt.local"; - auto compressed_files = "dump_local_zstd_compressed_run*.melt.local.zst"; - auto text_file = "dump_local_zstd_text_run0.melt.local"; - auto compressed_file = "dump_local_zstd_compressed_run0.melt.local.zst"; - auto fields = "index c_comp[1]"; - - generate_text_and_compressed_dump(text_files, compressed_files, "local/zstd", fields, "", 0); - - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -int main(int argc, char **argv) -{ - MPI_Init(&argc, &argv); - ::testing::InitGoogleMock(&argc, argv); - - // handle arguments passed via environment variable - if (const char *var = getenv("TEST_ARGS")) { - std::vector env = utils::split_words(var); - for (auto arg : env) { - if (arg == "-v") { - verbose = true; - } - } - } - - ZSTD_BINARY = getenv("ZSTD_BINARY"); - - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; - - int rv = RUN_ALL_TESTS(); - MPI_Finalize(); - return rv; -} From 3ebc7823b0b52615d89408256c3b5ae4d100b557 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 11 Mar 2021 12:28:56 -0500 Subject: [PATCH 0153/1217] Unify dump xyz/gz and xyz/zstd tests --- unittest/formats/CMakeLists.txt | 17 ++- unittest/formats/test_dump_xyz_compressed.cpp | 97 ++++++++++++++++ unittest/formats/test_dump_xyz_gz.cpp | 106 ------------------ unittest/formats/test_dump_xyz_zstd.cpp | 106 ------------------ 4 files changed, 104 insertions(+), 222 deletions(-) create mode 100644 unittest/formats/test_dump_xyz_compressed.cpp delete mode 100644 unittest/formats/test_dump_xyz_gz.cpp delete mode 100644 unittest/formats/test_dump_xyz_zstd.cpp diff --git a/unittest/formats/CMakeLists.txt b/unittest/formats/CMakeLists.txt index 731e387fc2..63c7759005 100644 --- a/unittest/formats/CMakeLists.txt +++ b/unittest/formats/CMakeLists.txt @@ -52,6 +52,9 @@ if(PKG_COMPRESS) add_executable(test_dump_local_compressed test_dump_local_compressed.cpp) target_link_libraries(test_dump_local_compressed PRIVATE lammps GTest::GMock GTest::GTest) + add_executable(test_dump_xyz_compressed test_dump_xyz_compressed.cpp) + target_link_libraries(test_dump_xyz_compressed PRIVATE lammps GTest::GMock GTest::GTest) + add_test(NAME DumpAtomGZ COMMAND test_dump_atom_compressed gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(DumpAtomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}") @@ -64,11 +67,8 @@ if(PKG_COMPRESS) add_test(NAME DumpLocalGZ COMMAND test_dump_local_compressed gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(DumpLocalGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}") - add_executable(test_dump_xyz_gz test_dump_xyz_gz.cpp) - target_link_libraries(test_dump_xyz_gz PRIVATE lammps GTest::GMock GTest::GTest) - add_test(NAME DumpXYZGZ COMMAND test_dump_xyz_gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) - set_tests_properties(DumpXYZGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") - set_tests_properties(DumpXYZGZ PROPERTIES ENVIRONMENT "GZIP_BINARY=${GZIP_BINARY}") + add_test(NAME DumpXYZGZ COMMAND test_dump_xyz_compressed gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + set_tests_properties(DumpXYZGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}") find_package(PkgConfig REQUIRED) pkg_check_modules(Zstd IMPORTED_TARGET libzstd>=1.4) @@ -87,11 +87,8 @@ if(PKG_COMPRESS) add_test(NAME DumpLocalZstd COMMAND test_dump_local_compressed zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(DumpLocalZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${ZSTD_BINARY}") - add_executable(test_dump_xyz_zstd test_dump_xyz_zstd.cpp) - target_link_libraries(test_dump_xyz_zstd PRIVATE lammps GTest::GMock GTest::GTest) - add_test(NAME DumpXYZZstd COMMAND test_dump_xyz_zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) - set_tests_properties(DumpXYZZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") - set_tests_properties(DumpXYZZstd PROPERTIES ENVIRONMENT "ZSTD_BINARY=${ZSTD_BINARY}") + add_test(NAME DumpXYZZstd COMMAND test_dump_xyz_compressed zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + set_tests_properties(DumpXYZZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${ZSTD_BINARY}") endif() endif() diff --git a/unittest/formats/test_dump_xyz_compressed.cpp b/unittest/formats/test_dump_xyz_compressed.cpp new file mode 100644 index 0000000000..8f82ccebe2 --- /dev/null +++ b/unittest/formats/test_dump_xyz_compressed.cpp @@ -0,0 +1,97 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "../testing/utils.h" +#include "compressed_dump_test.h" +#include "fmt/format.h" +#include "utils.h" +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include + + +using ::testing::Eq; + +class DumpXYZCompressTest : public CompressedDumpTest { +public: + DumpXYZCompressTest() : CompressedDumpTest("xyz") { + } +}; + +TEST_F(DumpXYZCompressTest, compressed_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "run*.melt.xyz"; + auto base_name_0 = "run0.melt.xyz"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + + generate_text_and_compressed_dump(text_files, compressed_files, "", "", 0); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + +int main(int argc, char **argv) +{ + MPI_Init(&argc, &argv); + ::testing::InitGoogleMock(&argc, argv); + + if (argc < 2) { + std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; + return 1; + } + + if(strcmp(argv[1], "gz") == 0) { + COMPRESS_SUFFIX = "gz"; + COMPRESS_EXTENSION = "gz"; + } else if(strcmp(argv[1], "zstd") == 0) { + COMPRESS_SUFFIX = "zstd"; + COMPRESS_EXTENSION = "zst"; + } else { + std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; + return 1; + } + + COMPRESS_BINARY = getenv("COMPRESS_BINARY"); + + // handle arguments passed via environment variable + if (const char *var = getenv("TEST_ARGS")) { + std::vector env = utils::split_words(var); + for (auto arg : env) { + if (arg == "-v") { + verbose = true; + } + } + } + + if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; + + int rv = RUN_ALL_TESTS(); + MPI_Finalize(); + return rv; +} diff --git a/unittest/formats/test_dump_xyz_gz.cpp b/unittest/formats/test_dump_xyz_gz.cpp deleted file mode 100644 index aef54b4820..0000000000 --- a/unittest/formats/test_dump_xyz_gz.cpp +++ /dev/null @@ -1,106 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "../testing/core.h" -#include "../testing/systems/melt.h" -#include "../testing/utils.h" -#include "fmt/format.h" -#include "utils.h" -#include "gmock/gmock.h" -#include "gtest/gtest.h" - -char *GZIP_BINARY = nullptr; - -using ::testing::Eq; - -class DumpXYZGZTest : public MeltTest { - std::string dump_style = "xyz"; - -public: - void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string compression_style, - std::string dump_modify_options, int ntimesteps) - { - if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id0 all {} 1 {}", dump_style, text_file)); - command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_file)); - - if (!dump_modify_options.empty()) { - command(fmt::format("dump_modify id0 {}", dump_modify_options)); - command(fmt::format("dump_modify id1 {}", dump_modify_options)); - } - - command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - std::string convert_compressed_to_text(std::string compressed_file) - { - if (!verbose) ::testing::internal::CaptureStdout(); - std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.')); - std::string cmdline = - fmt::format("{} -d -c {} > {}", GZIP_BINARY, compressed_file, converted_file); - system(cmdline.c_str()); - if (!verbose) ::testing::internal::GetCapturedStdout(); - return converted_file; - } -}; - -TEST_F(DumpXYZGZTest, compressed_run0) -{ - if (!GZIP_BINARY) GTEST_SKIP(); - - auto text_files = "dump_xyz_gz_text_run*.melt.xyz"; - auto compressed_files = "dump_xyz_gz_compressed_run*.melt.xyz.gz"; - auto text_file = "dump_xyz_gz_text_run0.melt.xyz"; - auto compressed_file = "dump_xyz_gz_compressed_run0.melt.xyz.gz"; - - generate_text_and_compressed_dump(text_files, compressed_files, "xyz/gz", "", 0); - - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -int main(int argc, char **argv) -{ - MPI_Init(&argc, &argv); - ::testing::InitGoogleMock(&argc, argv); - - // handle arguments passed via environment variable - if (const char *var = getenv("TEST_ARGS")) { - std::vector env = utils::split_words(var); - for (auto arg : env) { - if (arg == "-v") { - verbose = true; - } - } - } - - GZIP_BINARY = getenv("GZIP_BINARY"); - - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; - - int rv = RUN_ALL_TESTS(); - MPI_Finalize(); - return rv; -} diff --git a/unittest/formats/test_dump_xyz_zstd.cpp b/unittest/formats/test_dump_xyz_zstd.cpp deleted file mode 100644 index ce0b4ed143..0000000000 --- a/unittest/formats/test_dump_xyz_zstd.cpp +++ /dev/null @@ -1,106 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "../testing/core.h" -#include "../testing/systems/melt.h" -#include "../testing/utils.h" -#include "fmt/format.h" -#include "utils.h" -#include "gmock/gmock.h" -#include "gtest/gtest.h" - -char *ZSTD_BINARY = nullptr; - -using ::testing::Eq; - -class DumpXYZGZTest : public MeltTest { - std::string dump_style = "xyz"; - -public: - void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, - std::string compression_style, - std::string dump_modify_options, int ntimesteps) - { - if (!verbose) ::testing::internal::CaptureStdout(); - command(fmt::format("dump id0 all {} 1 {}", dump_style, text_file)); - command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_file)); - - if (!dump_modify_options.empty()) { - command(fmt::format("dump_modify id0 {}", dump_modify_options)); - command(fmt::format("dump_modify id1 {}", dump_modify_options)); - } - - command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - std::string convert_compressed_to_text(std::string compressed_file) - { - if (!verbose) ::testing::internal::CaptureStdout(); - std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.')); - std::string cmdline = - fmt::format("{} -d -c {} > {}", ZSTD_BINARY, compressed_file, converted_file); - system(cmdline.c_str()); - if (!verbose) ::testing::internal::GetCapturedStdout(); - return converted_file; - } -}; - -TEST_F(DumpXYZGZTest, compressed_run0) -{ - if (!ZSTD_BINARY) GTEST_SKIP(); - - auto text_files = "dump_xyz_zstd_text_run*.melt.xyz"; - auto compressed_files = "dump_xyz_zstd_compressed_run*.melt.xyz.zst"; - auto text_file = "dump_xyz_zstd_text_run0.melt.xyz"; - auto compressed_file = "dump_xyz_zstd_compressed_run0.melt.xyz.zst"; - - generate_text_and_compressed_dump(text_files, compressed_files, "xyz/zstd", "", 0); - - TearDown(); - - ASSERT_FILE_EXISTS(text_file); - ASSERT_FILE_EXISTS(compressed_file); - - auto converted_file = convert_compressed_to_text(compressed_file); - - ASSERT_FILE_EXISTS(converted_file); - ASSERT_FILE_EQUAL(text_file, converted_file); - delete_file(text_file); - delete_file(compressed_file); - delete_file(converted_file); -} - -int main(int argc, char **argv) -{ - MPI_Init(&argc, &argv); - ::testing::InitGoogleMock(&argc, argv); - - // handle arguments passed via environment variable - if (const char *var = getenv("TEST_ARGS")) { - std::vector env = utils::split_words(var); - for (auto arg : env) { - if (arg == "-v") { - verbose = true; - } - } - } - - ZSTD_BINARY = getenv("ZSTD_BINARY"); - - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; - - int rv = RUN_ALL_TESTS(); - MPI_Finalize(); - return rv; -} From c5cb294506c478ea0f01c431a162626d4dff5fc3 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 11 Mar 2021 12:42:19 -0500 Subject: [PATCH 0154/1217] Add other compression tests to xyz tests --- unittest/formats/test_dump_xyz_compressed.cpp | 170 ++++++++++++++++++ 1 file changed, 170 insertions(+) diff --git a/unittest/formats/test_dump_xyz_compressed.cpp b/unittest/formats/test_dump_xyz_compressed.cpp index 8f82ccebe2..b0ab846ba3 100644 --- a/unittest/formats/test_dump_xyz_compressed.cpp +++ b/unittest/formats/test_dump_xyz_compressed.cpp @@ -56,6 +56,176 @@ TEST_F(DumpXYZCompressTest, compressed_run0) delete_file(converted_file_0); } +TEST_F(DumpXYZCompressTest, compressed_multi_file_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "multi_file_run1_*.melt.xyz"; + auto base_name_0 = "multi_file_run1_0.melt.xyz"; + auto base_name_1 = "multi_file_run1_1.melt.xyz"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); + + generate_text_and_compressed_dump(text_file, compressed_file, "", "", 1); + + TearDown(); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + + ASSERT_THAT(converted_file_0, Eq(converted_dump_filename(base_name_0))); + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + + delete_file(text_file_0); + delete_file(text_file_1); + delete_file(compressed_file_0); + delete_file(compressed_file_1); + delete_file(converted_file_0); + delete_file(converted_file_1); +} + +TEST_F(DumpXYZCompressTest, compressed_multi_file_with_pad_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "multi_file_pad_run1_*.melt.xyz"; + auto base_name_0 = "multi_file_pad_run1_000.melt.xyz"; + auto base_name_1 = "multi_file_pad_run1_001.melt.xyz"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); + + generate_text_and_compressed_dump(text_file, compressed_file, "", "pad 3", 1); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(text_file_1); + ASSERT_FILE_EXISTS(compressed_file_0); + ASSERT_FILE_EXISTS(compressed_file_1); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + + ASSERT_THAT(converted_file_0, Eq(converted_dump_filename(base_name_0))); + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + + delete_file(text_file_0); + delete_file(text_file_1); + delete_file(compressed_file_0); + delete_file(compressed_file_1); + delete_file(converted_file_0); + delete_file(converted_file_1); +} + +TEST_F(DumpXYZCompressTest, compressed_multi_file_with_maxfiles_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "multi_file_maxfiles_run1_*.melt.xyz"; + auto base_name_0 = "multi_file_maxfiles_run1_0.melt.xyz"; + auto base_name_1 = "multi_file_maxfiles_run1_1.melt.xyz"; + auto base_name_2 = "multi_file_maxfiles_run1_2.melt.xyz"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto text_file_2 = text_dump_filename(base_name_2); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); + auto compressed_file_2 = compressed_dump_filename(base_name_2); + + generate_text_and_compressed_dump(text_file, compressed_file, "", "maxfiles 2", 2); + + TearDown(); + + ASSERT_FILE_NOT_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(text_file_1); + ASSERT_FILE_EXISTS(text_file_2); + ASSERT_FILE_NOT_EXISTS(compressed_file_0); + ASSERT_FILE_EXISTS(compressed_file_1); + ASSERT_FILE_EXISTS(compressed_file_2); + + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + auto converted_file_2 = convert_compressed_to_text(compressed_file_2); + + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); + ASSERT_THAT(converted_file_2, Eq(converted_dump_filename(base_name_2))); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EXISTS(converted_file_2); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + ASSERT_FILE_EQUAL(text_file_2, converted_file_2); + + delete_file(text_file_1); + delete_file(text_file_2); + delete_file(compressed_file_1); + delete_file(compressed_file_2); + delete_file(converted_file_1); + delete_file(converted_file_2); +} + +TEST_F(DumpXYZCompressTest, compressed_modify_bad_param) +{ + if (compression_style != "xyz/gz") GTEST_SKIP(); + + command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.xyz"))); + + TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + command("dump_modify id1 compression_level 12"); + ); +} + +TEST_F(DumpXYZCompressTest, compressed_modify_multi_bad_param) +{ + if (compression_style != "xyz/gz") GTEST_SKIP(); + + command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.xyz"))); + + TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + command("dump_modify id1 pad 3 compression_level 12"); + ); +} + +TEST_F(DumpXYZCompressTest, compressed_modify_clevel_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "modify_clevel_run0.melt.xyz"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); + + generate_text_and_compressed_dump(text_file, compressed_file, "", "", "", "compression_level 3", 0); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file); + ASSERT_FILE_EXISTS(compressed_file); + + auto converted_file = convert_compressed_to_text(compressed_file); + + ASSERT_THAT(converted_file, Eq(converted_dump_filename(base_name))); + ASSERT_FILE_EXISTS(converted_file); + ASSERT_FILE_EQUAL(text_file, converted_file); + delete_file(text_file); + delete_file(compressed_file); + delete_file(converted_file); +} + int main(int argc, char **argv) { MPI_Init(&argc, &argv); From 7e3d1923ab181b1d6bf8114d608b6db824c7bf0e Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 11 Mar 2021 13:02:18 -0500 Subject: [PATCH 0155/1217] Add more compression tests for dump cfg --- unittest/formats/test_dump_cfg_compressed.cpp | 179 ++++++++++++++++++ 1 file changed, 179 insertions(+) diff --git a/unittest/formats/test_dump_cfg_compressed.cpp b/unittest/formats/test_dump_cfg_compressed.cpp index d06eabe57b..b1eaaeee38 100644 --- a/unittest/formats/test_dump_cfg_compressed.cpp +++ b/unittest/formats/test_dump_cfg_compressed.cpp @@ -91,6 +91,185 @@ TEST_F(DumpCfgCompressTest, compressed_unwrap_run0) delete_file(converted_file_0); } +TEST_F(DumpCfgCompressTest, compressed_multi_file_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "multi_file_run1_*.melt.cfg"; + auto base_name_0 = "multi_file_run1_0.melt.cfg"; + auto base_name_1 = "multi_file_run1_1.melt.cfg"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); + auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; + + generate_text_and_compressed_dump(text_file, compressed_file, fields, "", 1); + + TearDown(); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + + ASSERT_THAT(converted_file_0, Eq(converted_dump_filename(base_name_0))); + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + + delete_file(text_file_0); + delete_file(text_file_1); + delete_file(compressed_file_0); + delete_file(compressed_file_1); + delete_file(converted_file_0); + delete_file(converted_file_1); +} + +TEST_F(DumpCfgCompressTest, compressed_multi_file_with_pad_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "multi_file_pad_run1_*.melt.cfg"; + auto base_name_0 = "multi_file_pad_run1_000.melt.cfg"; + auto base_name_1 = "multi_file_pad_run1_001.melt.cfg"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); + auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; + + generate_text_and_compressed_dump(text_file, compressed_file, fields, "pad 3", 1); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(text_file_1); + ASSERT_FILE_EXISTS(compressed_file_0); + ASSERT_FILE_EXISTS(compressed_file_1); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + + ASSERT_THAT(converted_file_0, Eq(converted_dump_filename(base_name_0))); + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + + delete_file(text_file_0); + delete_file(text_file_1); + delete_file(compressed_file_0); + delete_file(compressed_file_1); + delete_file(converted_file_0); + delete_file(converted_file_1); +} + +TEST_F(DumpCfgCompressTest, compressed_multi_file_with_maxfiles_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "multi_file_maxfiles_run1_*.melt.cfg"; + auto base_name_0 = "multi_file_maxfiles_run1_0.melt.cfg"; + auto base_name_1 = "multi_file_maxfiles_run1_1.melt.cfg"; + auto base_name_2 = "multi_file_maxfiles_run1_2.melt.cfg"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto text_file_2 = text_dump_filename(base_name_2); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); + auto compressed_file_2 = compressed_dump_filename(base_name_2); + auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; + + generate_text_and_compressed_dump(text_file, compressed_file, fields, "maxfiles 2", 2); + + TearDown(); + + ASSERT_FILE_NOT_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(text_file_1); + ASSERT_FILE_EXISTS(text_file_2); + ASSERT_FILE_NOT_EXISTS(compressed_file_0); + ASSERT_FILE_EXISTS(compressed_file_1); + ASSERT_FILE_EXISTS(compressed_file_2); + + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + auto converted_file_2 = convert_compressed_to_text(compressed_file_2); + + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); + ASSERT_THAT(converted_file_2, Eq(converted_dump_filename(base_name_2))); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EXISTS(converted_file_2); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + ASSERT_FILE_EQUAL(text_file_2, converted_file_2); + + delete_file(text_file_1); + delete_file(text_file_2); + delete_file(compressed_file_1); + delete_file(compressed_file_2); + delete_file(converted_file_1); + delete_file(converted_file_2); +} + +TEST_F(DumpCfgCompressTest, compressed_modify_bad_param) +{ + if (compression_style != "cfg/gz") GTEST_SKIP(); + + auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; + command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.cfg"), fields)); + + TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + command("dump_modify id1 compression_level 12"); + ); +} + +TEST_F(DumpCfgCompressTest, compressed_modify_multi_bad_param) +{ + if (compression_style != "cfg/gz") GTEST_SKIP(); + + auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; + command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.cfg"), fields)); + + TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + command("dump_modify id1 pad 3 compression_level 12"); + ); +} + +TEST_F(DumpCfgCompressTest, compressed_modify_clevel_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "modify_clevel_run*.melt.cfg"; + auto base_name_0 = "modify_clevel_run0.melt.cfg"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; + + generate_text_and_compressed_dump(text_file, compressed_file, fields, fields, "", "compression_level 3", 0); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file); + + ASSERT_THAT(converted_file_0, Eq(converted_dump_filename(base_name))); + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + int main(int argc, char **argv) { MPI_Init(&argc, &argv); From f53fcf05456768ea1720fbfb05b19d6d5a5705f2 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 11 Mar 2021 13:12:43 -0500 Subject: [PATCH 0156/1217] Add more compression tests for dump custom --- .../formats/test_dump_atom_compressed.cpp | 4 + unittest/formats/test_dump_cfg_compressed.cpp | 4 + .../formats/test_dump_custom_compressed.cpp | 176 ++++++++++++++++++ unittest/formats/test_dump_xyz_compressed.cpp | 4 + 4 files changed, 188 insertions(+) diff --git a/unittest/formats/test_dump_atom_compressed.cpp b/unittest/formats/test_dump_atom_compressed.cpp index 3360872f9e..c0d1f3bdb6 100644 --- a/unittest/formats/test_dump_atom_compressed.cpp +++ b/unittest/formats/test_dump_atom_compressed.cpp @@ -332,7 +332,9 @@ TEST_F(DumpAtomCompressTest, compressed_modify_bad_param) { if (compression_style != "atom/gz") GTEST_SKIP(); + if (!verbose) ::testing::internal::CaptureStdout(); command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt"))); + if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 compression_level 12"); @@ -343,7 +345,9 @@ TEST_F(DumpAtomCompressTest, compressed_modify_multi_bad_param) { if (compression_style != "atom/gz") GTEST_SKIP(); + if (!verbose) ::testing::internal::CaptureStdout(); command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt"))); + if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); diff --git a/unittest/formats/test_dump_cfg_compressed.cpp b/unittest/formats/test_dump_cfg_compressed.cpp index b1eaaeee38..66ab6921d5 100644 --- a/unittest/formats/test_dump_cfg_compressed.cpp +++ b/unittest/formats/test_dump_cfg_compressed.cpp @@ -222,7 +222,9 @@ TEST_F(DumpCfgCompressTest, compressed_modify_bad_param) if (compression_style != "cfg/gz") GTEST_SKIP(); auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; + if (!verbose) ::testing::internal::CaptureStdout(); command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.cfg"), fields)); + if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 compression_level 12"); @@ -234,7 +236,9 @@ TEST_F(DumpCfgCompressTest, compressed_modify_multi_bad_param) if (compression_style != "cfg/gz") GTEST_SKIP(); auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; + if (!verbose) ::testing::internal::CaptureStdout(); command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.cfg"), fields)); + if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); diff --git a/unittest/formats/test_dump_custom_compressed.cpp b/unittest/formats/test_dump_custom_compressed.cpp index 0afad264fb..8118442dbd 100644 --- a/unittest/formats/test_dump_custom_compressed.cpp +++ b/unittest/formats/test_dump_custom_compressed.cpp @@ -81,6 +81,182 @@ TEST_F(DumpCustomCompressTest, compressed_triclinic_run1) delete_file(converted_file); } +TEST_F(DumpCustomCompressTest, compressed_multi_file_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "multi_file_run1_*.melt.custom"; + auto base_name_0 = "multi_file_run1_0.melt.custom"; + auto base_name_1 = "multi_file_run1_1.melt.custom"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); + auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; + + generate_text_and_compressed_dump(text_file, compressed_file, fields, "", 1); + + TearDown(); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + + ASSERT_THAT(converted_file_0, Eq(converted_dump_filename(base_name_0))); + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + + delete_file(text_file_0); + delete_file(text_file_1); + delete_file(compressed_file_0); + delete_file(compressed_file_1); + delete_file(converted_file_0); + delete_file(converted_file_1); +} + +TEST_F(DumpCustomCompressTest, compressed_multi_file_with_pad_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "multi_file_pad_run1_*.melt.custom"; + auto base_name_0 = "multi_file_pad_run1_000.melt.custom"; + auto base_name_1 = "multi_file_pad_run1_001.melt.custom"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); + auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; + + generate_text_and_compressed_dump(text_file, compressed_file, fields, "pad 3", 1); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(text_file_1); + ASSERT_FILE_EXISTS(compressed_file_0); + ASSERT_FILE_EXISTS(compressed_file_1); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + + ASSERT_THAT(converted_file_0, Eq(converted_dump_filename(base_name_0))); + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + + delete_file(text_file_0); + delete_file(text_file_1); + delete_file(compressed_file_0); + delete_file(compressed_file_1); + delete_file(converted_file_0); + delete_file(converted_file_1); +} + +TEST_F(DumpCustomCompressTest, compressed_multi_file_with_maxfiles_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "multi_file_maxfiles_run1_*.melt.custom"; + auto base_name_0 = "multi_file_maxfiles_run1_0.melt.custom"; + auto base_name_1 = "multi_file_maxfiles_run1_1.melt.custom"; + auto base_name_2 = "multi_file_maxfiles_run1_2.melt.custom"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto text_file_2 = text_dump_filename(base_name_2); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); + auto compressed_file_2 = compressed_dump_filename(base_name_2); + auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; + + generate_text_and_compressed_dump(text_file, compressed_file, fields, "maxfiles 2", 2); + + TearDown(); + + ASSERT_FILE_NOT_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(text_file_1); + ASSERT_FILE_EXISTS(text_file_2); + ASSERT_FILE_NOT_EXISTS(compressed_file_0); + ASSERT_FILE_EXISTS(compressed_file_1); + ASSERT_FILE_EXISTS(compressed_file_2); + + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + auto converted_file_2 = convert_compressed_to_text(compressed_file_2); + + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); + ASSERT_THAT(converted_file_2, Eq(converted_dump_filename(base_name_2))); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EXISTS(converted_file_2); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + ASSERT_FILE_EQUAL(text_file_2, converted_file_2); + + delete_file(text_file_1); + delete_file(text_file_2); + delete_file(compressed_file_1); + delete_file(compressed_file_2); + delete_file(converted_file_1); + delete_file(converted_file_2); +} + +TEST_F(DumpCustomCompressTest, compressed_modify_bad_param) +{ + if (compression_style != "custom/gz") GTEST_SKIP(); + + auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; + command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.custom"), fields)); + + TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + command("dump_modify id1 compression_level 12"); + ); +} + +TEST_F(DumpCustomCompressTest, compressed_modify_multi_bad_param) +{ + if (compression_style != "custom/gz") GTEST_SKIP(); + + auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; + command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.custom"), fields)); + + TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + command("dump_modify id1 pad 3 compression_level 12"); + ); +} + +TEST_F(DumpCustomCompressTest, compressed_modify_clevel_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "modify_clevel_run0.melt.custom"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); + + auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; + generate_text_and_compressed_dump(text_file, compressed_file, fields, fields, "", "compression_level 3", 0); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file); + ASSERT_FILE_EXISTS(compressed_file); + + auto converted_file = convert_compressed_to_text(compressed_file); + + ASSERT_THAT(converted_file, Eq(converted_dump_filename(base_name))); + ASSERT_FILE_EXISTS(converted_file); + ASSERT_FILE_EQUAL(text_file, converted_file); + delete_file(text_file); + delete_file(compressed_file); + delete_file(converted_file); +} + int main(int argc, char **argv) { MPI_Init(&argc, &argv); diff --git a/unittest/formats/test_dump_xyz_compressed.cpp b/unittest/formats/test_dump_xyz_compressed.cpp index b0ab846ba3..9a61c746a0 100644 --- a/unittest/formats/test_dump_xyz_compressed.cpp +++ b/unittest/formats/test_dump_xyz_compressed.cpp @@ -183,7 +183,9 @@ TEST_F(DumpXYZCompressTest, compressed_modify_bad_param) { if (compression_style != "xyz/gz") GTEST_SKIP(); + if (!verbose) ::testing::internal::CaptureStdout(); command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.xyz"))); + if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 compression_level 12"); @@ -194,7 +196,9 @@ TEST_F(DumpXYZCompressTest, compressed_modify_multi_bad_param) { if (compression_style != "xyz/gz") GTEST_SKIP(); + if (!verbose) ::testing::internal::CaptureStdout(); command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.xyz"))); + if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); From 14da94d1893601894f39b86e252ead0eb2f3ec6a Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 11 Mar 2021 13:27:54 -0500 Subject: [PATCH 0157/1217] Add more compression tests for dump local --- .../formats/test_dump_local_compressed.cpp | 194 +++++++++++++++++- 1 file changed, 190 insertions(+), 4 deletions(-) diff --git a/unittest/formats/test_dump_local_compressed.cpp b/unittest/formats/test_dump_local_compressed.cpp index 048053fb9a..b3c96b6edc 100644 --- a/unittest/formats/test_dump_local_compressed.cpp +++ b/unittest/formats/test_dump_local_compressed.cpp @@ -27,16 +27,20 @@ class DumpLocalCompressTest : public CompressedDumpTest { public: DumpLocalCompressTest() : CompressedDumpTest("local") { } + + void SetUp() override { + CompressedDumpTest::SetUp(); + + if (!verbose) ::testing::internal::CaptureStdout(); + command("compute comp all pair/local dist eng"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + } }; TEST_F(DumpLocalCompressTest, compressed_run0) { if (!COMPRESS_BINARY) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); - command("compute comp all pair/local dist eng"); - if (!verbose) ::testing::internal::GetCapturedStdout(); - auto base_name = "run*.melt.local"; auto base_name_0 = "run0.melt.local"; auto text_files = text_dump_filename(base_name); @@ -61,6 +65,188 @@ TEST_F(DumpLocalCompressTest, compressed_run0) delete_file(converted_file_0); } +TEST_F(DumpLocalCompressTest, compressed_multi_file_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "multi_file_run1_*.melt.local"; + auto base_name_0 = "multi_file_run1_0.melt.local"; + auto base_name_1 = "multi_file_run1_1.melt.local"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); + auto fields = "index c_comp[1]"; + + generate_text_and_compressed_dump(text_file, compressed_file, fields, "", 1); + + TearDown(); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + + ASSERT_THAT(converted_file_0, Eq(converted_dump_filename(base_name_0))); + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + + delete_file(text_file_0); + delete_file(text_file_1); + delete_file(compressed_file_0); + delete_file(compressed_file_1); + delete_file(converted_file_0); + delete_file(converted_file_1); +} + +TEST_F(DumpLocalCompressTest, compressed_multi_file_with_pad_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "multi_file_pad_run1_*.melt.local"; + auto base_name_0 = "multi_file_pad_run1_000.melt.local"; + auto base_name_1 = "multi_file_pad_run1_001.melt.local"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); + auto fields = "index c_comp[1]"; + + generate_text_and_compressed_dump(text_file, compressed_file, fields, "pad 3", 1); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(text_file_1); + ASSERT_FILE_EXISTS(compressed_file_0); + ASSERT_FILE_EXISTS(compressed_file_1); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + + ASSERT_THAT(converted_file_0, Eq(converted_dump_filename(base_name_0))); + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + + delete_file(text_file_0); + delete_file(text_file_1); + delete_file(compressed_file_0); + delete_file(compressed_file_1); + delete_file(converted_file_0); + delete_file(converted_file_1); +} + +TEST_F(DumpLocalCompressTest, compressed_multi_file_with_maxfiles_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "multi_file_maxfiles_run1_*.melt.local"; + auto base_name_0 = "multi_file_maxfiles_run1_0.melt.local"; + auto base_name_1 = "multi_file_maxfiles_run1_1.melt.local"; + auto base_name_2 = "multi_file_maxfiles_run1_2.melt.local"; + auto text_file = text_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto text_file_1 = text_dump_filename(base_name_1); + auto text_file_2 = text_dump_filename(base_name_2); + auto compressed_file = compressed_dump_filename(base_name); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto compressed_file_1 = compressed_dump_filename(base_name_1); + auto compressed_file_2 = compressed_dump_filename(base_name_2); + auto fields = "index c_comp[1]"; + + generate_text_and_compressed_dump(text_file, compressed_file, fields, "maxfiles 2", 2); + + TearDown(); + + ASSERT_FILE_NOT_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(text_file_1); + ASSERT_FILE_EXISTS(text_file_2); + ASSERT_FILE_NOT_EXISTS(compressed_file_0); + ASSERT_FILE_EXISTS(compressed_file_1); + ASSERT_FILE_EXISTS(compressed_file_2); + + auto converted_file_1 = convert_compressed_to_text(compressed_file_1); + auto converted_file_2 = convert_compressed_to_text(compressed_file_2); + + ASSERT_THAT(converted_file_1, Eq(converted_dump_filename(base_name_1))); + ASSERT_THAT(converted_file_2, Eq(converted_dump_filename(base_name_2))); + ASSERT_FILE_EXISTS(converted_file_1); + ASSERT_FILE_EXISTS(converted_file_2); + ASSERT_FILE_EQUAL(text_file_1, converted_file_1); + ASSERT_FILE_EQUAL(text_file_2, converted_file_2); + + delete_file(text_file_1); + delete_file(text_file_2); + delete_file(compressed_file_1); + delete_file(compressed_file_2); + delete_file(converted_file_1); + delete_file(converted_file_2); +} + +TEST_F(DumpLocalCompressTest, compressed_modify_bad_param) +{ + if (compression_style != "local/gz") GTEST_SKIP(); + + auto fields = "index c_comp[1]"; + + if (!verbose) ::testing::internal::CaptureStdout(); + command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.local"), fields)); + if (!verbose) ::testing::internal::GetCapturedStdout(); + + TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + command("dump_modify id1 compression_level 12"); + ); +} + +TEST_F(DumpLocalCompressTest, compressed_modify_multi_bad_param) +{ + if (compression_style != "local/gz") GTEST_SKIP(); + + auto fields = "index c_comp[1]"; + + if (!verbose) ::testing::internal::CaptureStdout(); + command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.local"), fields)); + if (!verbose) ::testing::internal::GetCapturedStdout(); + + TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + command("dump_modify id1 pad 3 compression_level 12"); + ); +} + +TEST_F(DumpLocalCompressTest, compressed_modify_clevel_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "modify_clevel_run0.melt.local"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); + auto fields = "index c_comp[1]"; + + generate_text_and_compressed_dump(text_file, compressed_file, fields, fields, "", "compression_level 3", 0); + + TearDown(); + + ASSERT_FILE_EXISTS(text_file); + ASSERT_FILE_EXISTS(compressed_file); + + auto converted_file = convert_compressed_to_text(compressed_file); + + ASSERT_THAT(converted_file, Eq(converted_dump_filename(base_name))); + ASSERT_FILE_EXISTS(converted_file); + ASSERT_FILE_EQUAL(text_file, converted_file); + delete_file(text_file); + delete_file(compressed_file); + delete_file(converted_file); +} + int main(int argc, char **argv) { MPI_Init(&argc, &argv); From ffda7fcc04f926821ccd87dbe7cd7a51ad5f13a7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 14:02:21 -0500 Subject: [PATCH 0158/1217] simpler interfaces --- examples/plugins/morse2plugin.cpp | 32 ++++++++++++++++--------------- src/lammpsplugin.h | 4 ++-- src/plugin.cpp | 27 +++++++++++++++++++------- src/plugin.h | 5 +++-- 4 files changed, 42 insertions(+), 26 deletions(-) diff --git a/examples/plugins/morse2plugin.cpp b/examples/plugins/morse2plugin.cpp index d7290edfb0..cfb6689cae 100644 --- a/examples/plugins/morse2plugin.cpp +++ b/examples/plugins/morse2plugin.cpp @@ -22,21 +22,23 @@ static Pair *morse2ompcreator(LAMMPS *lmp) } static lammpsplugin_t plugin; -extern "C" void lammpsplugin_init(void *lmp, void *handle, lammpsplugin_regfunc register_plugin) +extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) { - memset(&plugin,0,sizeof(lammpsplugin_t)); - plugin.version = LAMMPS_VERSION; - plugin.style = "pair"; - plugin.name = "morse2"; - plugin.info = "Morse2 variant pair style v1.0"; - plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; - plugin.creator = (lammpsplugin_factory *) &morse2creator; - plugin.handle = handle; - register_plugin(&plugin,lmp); + // register plain morse2 pair style + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + memset(&plugin,0,sizeof(lammpsplugin_t)); + plugin.version = LAMMPS_VERSION; + plugin.style = "pair"; + plugin.name = "morse2"; + plugin.info = "Morse2 variant pair style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator = (lammpsplugin_factory *) &morse2creator; + plugin.handle = handle; + register_plugin(&plugin,lmp); - plugin.style = "pair"; - plugin.name = "morse2/omp"; - plugin.info = "Morse2 variant pair style for OpenMP v1.0"; - plugin.creator = (lammpsplugin_factory *) &morse2ompcreator; - register_plugin(&plugin,lmp); + // also register morse2/omp pair style. only need to update changed fields + plugin.name = "morse2/omp"; + plugin.info = "Morse2 variant pair style for OpenMP v1.0"; + plugin.creator = (lammpsplugin_factory *) &morse2ompcreator; + register_plugin(&plugin,lmp); } diff --git a/src/lammpsplugin.h b/src/lammpsplugin.h index 6cdf67e09b..34a0b60811 100644 --- a/src/lammpsplugin.h +++ b/src/lammpsplugin.h @@ -31,12 +31,12 @@ extern "C" { } lammpsplugin_t; typedef void (*lammpsplugin_regfunc)(lammpsplugin_t *, void *); - typedef void (*lammpsplugin_initfunc)(void *, void *, lammpsplugin_regfunc); + typedef void (*lammpsplugin_initfunc)(void *, void *, void *); // prototype for initializer function required // to load a plugin; uses C bindings - void lammpsplugin_init(void *, void *, lammpsplugin_regfunc); + void lammpsplugin_init(void *, void *, void *); } #endif diff --git a/src/plugin.cpp b/src/plugin.cpp index f81c453afb..e978d90059 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -18,6 +18,7 @@ #include "lammps.h" #include "modify.h" +#include #include #ifdef _WIN32 @@ -28,14 +29,20 @@ namespace LAMMPS_NS { + // store list of plugin information data for loaded styles static std::vector pluginlist; + // map of dso handles + static std::map dso_refcounter; - void plugin_load(const char *file, void *ptr) + // load DSO and call included registration function + void plugin_load(const char *file, LAMMPS *lmp) { - LAMMPS *lmp = (LAMMPS *)ptr; #if defined(WIN32) utils::logmesg(lmp,"Loading of plugins not supported on Windows yet\n"); #else + + // open DSO from given path + void *dso = dlopen(file,RTLD_NOW|RTLD_GLOBAL); if (dso == nullptr) { utils::logmesg(lmp,fmt::format("Loading of plugin from file {} failed: " @@ -43,17 +50,23 @@ namespace LAMMPS_NS return; } + // look up lammpsplugin_init() function in DSO. must have C bindings. + void *initfunc = dlsym(dso,"lammpsplugin_init"); if (initfunc == nullptr) { dlclose(dso); utils::logmesg(lmp,fmt::format("Symbol lookup failure in file {}\n",file)); return; } - ((lammpsplugin_initfunc)(initfunc))(ptr,dso,&plugin_register); -// dlclose(dso); + + // call initializer function loaded from DSO and pass pointer to LAMMPS instance, + // the DSO handle (for reference counting) and plugin registration function pointer + + ((lammpsplugin_initfunc)(initfunc))((void *)lmp, dso, (void *)&plugin_register); #endif } + // register new style from plugin with LAMMPS void plugin_register(lammpsplugin_t *plugin, void *ptr) { LAMMPS *lmp = (LAMMPS *)ptr; @@ -99,10 +112,10 @@ namespace LAMMPS_NS } return -1; } - - void plugin_unload(const char *style, const char *name, void *ptr) + + // remove plugin from given style table + void plugin_unload(const char *style, const char *name, LAMMPS *lmp) { - LAMMPS *lmp = (LAMMPS *)ptr; std::string pstyle = style; if (pstyle == "pair") { auto found = lmp->force->pair_map->find(name); diff --git a/src/plugin.h b/src/plugin.h index 546ab2a644..051382ac27 100644 --- a/src/plugin.h +++ b/src/plugin.h @@ -18,12 +18,13 @@ namespace LAMMPS_NS { - void plugin_load(const char *, void *); + class LAMMPS; + void plugin_load(const char *, LAMMPS *); void plugin_register(lammpsplugin_t *, void *); int plugin_get_num_plugins(); const lammpsplugin_t *plugin_info(int); int plugin_find(const char *, const char *); - void plugin_unload(const char *, const char *, void *); + void plugin_unload(const char *, const char *, LAMMPS *); } #endif From 76d857e42888300efb128d201dbdf7fb0be72945 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 11 Mar 2021 14:21:16 -0500 Subject: [PATCH 0159/1217] Add more tests for COMPRESS package --- unittest/formats/CMakeLists.txt | 10 +-- unittest/formats/compressed_dump_test.h | 6 +- .../formats/compressed_dump_test_main.cpp | 66 +++++++++++++++++++ unittest/formats/test_dump_atom.cpp | 1 + .../formats/test_dump_atom_compressed.cpp | 52 +++------------ unittest/formats/test_dump_cfg.cpp | 2 + unittest/formats/test_dump_cfg_compressed.cpp | 52 +++------------ unittest/formats/test_dump_custom.cpp | 1 + .../formats/test_dump_custom_compressed.cpp | 52 +++------------ .../formats/test_dump_local_compressed.cpp | 52 +++------------ unittest/formats/test_dump_xyz_compressed.cpp | 52 +++------------ unittest/testing/core.h | 2 +- 12 files changed, 129 insertions(+), 219 deletions(-) create mode 100644 unittest/formats/compressed_dump_test_main.cpp diff --git a/unittest/formats/CMakeLists.txt b/unittest/formats/CMakeLists.txt index 63c7759005..be0d14c47d 100644 --- a/unittest/formats/CMakeLists.txt +++ b/unittest/formats/CMakeLists.txt @@ -40,19 +40,19 @@ set_tests_properties(DumpAtom PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS if(PKG_COMPRESS) find_program(GZIP_BINARY NAMES gzip REQUIRED) - add_executable(test_dump_atom_compressed test_dump_atom_compressed.cpp) + add_executable(test_dump_atom_compressed test_dump_atom_compressed.cpp compressed_dump_test_main.cpp) target_link_libraries(test_dump_atom_compressed PRIVATE lammps GTest::GMock GTest::GTest) - add_executable(test_dump_custom_compressed test_dump_custom_compressed.cpp) + add_executable(test_dump_custom_compressed test_dump_custom_compressed.cpp compressed_dump_test_main.cpp) target_link_libraries(test_dump_custom_compressed PRIVATE lammps GTest::GMock GTest::GTest) - add_executable(test_dump_cfg_compressed test_dump_cfg_compressed.cpp) + add_executable(test_dump_cfg_compressed test_dump_cfg_compressed.cpp compressed_dump_test_main.cpp) target_link_libraries(test_dump_cfg_compressed PRIVATE lammps GTest::GMock GTest::GTest) - add_executable(test_dump_local_compressed test_dump_local_compressed.cpp) + add_executable(test_dump_local_compressed test_dump_local_compressed.cpp compressed_dump_test_main.cpp) target_link_libraries(test_dump_local_compressed PRIVATE lammps GTest::GMock GTest::GTest) - add_executable(test_dump_xyz_compressed test_dump_xyz_compressed.cpp) + add_executable(test_dump_xyz_compressed test_dump_xyz_compressed.cpp compressed_dump_test_main.cpp) target_link_libraries(test_dump_xyz_compressed PRIVATE lammps GTest::GMock GTest::GTest) add_test(NAME DumpAtomGZ COMMAND test_dump_atom_compressed gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) diff --git a/unittest/formats/compressed_dump_test.h b/unittest/formats/compressed_dump_test.h index c731a3b1b9..c8afb2aac3 100644 --- a/unittest/formats/compressed_dump_test.h +++ b/unittest/formats/compressed_dump_test.h @@ -17,9 +17,9 @@ #include "../testing/systems/melt.h" #include -const char * COMPRESS_SUFFIX = nullptr; -const char * COMPRESS_EXTENSION = nullptr; -char * COMPRESS_BINARY = nullptr; +extern const char * COMPRESS_SUFFIX; +extern const char * COMPRESS_EXTENSION; +extern char * COMPRESS_BINARY; class CompressedDumpTest : public MeltTest { protected: diff --git a/unittest/formats/compressed_dump_test_main.cpp b/unittest/formats/compressed_dump_test_main.cpp new file mode 100644 index 0000000000..e1334f1b9b --- /dev/null +++ b/unittest/formats/compressed_dump_test_main.cpp @@ -0,0 +1,66 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "compressed_dump_test.h" +#include "../testing/utils.h" +#include "fmt/format.h" +#include "utils.h" +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include + +const char * COMPRESS_SUFFIX = nullptr; +const char * COMPRESS_EXTENSION = nullptr; +char * COMPRESS_BINARY = nullptr; +bool verbose = false; + +int main(int argc, char **argv) +{ + MPI_Init(&argc, &argv); + ::testing::InitGoogleMock(&argc, argv); + + if (argc < 2) { + std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; + return 1; + } + + if(strcmp(argv[1], "gz") == 0) { + COMPRESS_SUFFIX = "gz"; + COMPRESS_EXTENSION = "gz"; + } else if(strcmp(argv[1], "zstd") == 0) { + COMPRESS_SUFFIX = "zstd"; + COMPRESS_EXTENSION = "zst"; + } else { + std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; + return 1; + } + + COMPRESS_BINARY = getenv("COMPRESS_BINARY"); + + // handle arguments passed via environment variable + if (const char *var = getenv("TEST_ARGS")) { + std::vector env = utils::split_words(var); + for (auto arg : env) { + if (arg == "-v") { + verbose = true; + } + } + } + + if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; + + int rv = RUN_ALL_TESTS(); + MPI_Finalize(); + return rv; +} diff --git a/unittest/formats/test_dump_atom.cpp b/unittest/formats/test_dump_atom.cpp index 2472aabf2d..39cefdccea 100644 --- a/unittest/formats/test_dump_atom.cpp +++ b/unittest/formats/test_dump_atom.cpp @@ -24,6 +24,7 @@ using ::testing::Eq; char *BINARY2TXT_BINARY = nullptr; +bool verbose = false; class DumpAtomTest : public MeltTest { std::string dump_style = "atom"; diff --git a/unittest/formats/test_dump_atom_compressed.cpp b/unittest/formats/test_dump_atom_compressed.cpp index c0d1f3bdb6..ed591184c3 100644 --- a/unittest/formats/test_dump_atom_compressed.cpp +++ b/unittest/formats/test_dump_atom_compressed.cpp @@ -40,7 +40,11 @@ TEST_F(DumpAtomCompressTest, compressed_run0) auto text_file = text_dump_filename("run0.melt"); auto compressed_file = compressed_dump_filename("run0.melt"); - generate_text_and_compressed_dump(text_file, compressed_file, "", "", 0); + if(compression_style == "atom/zstd") { + generate_text_and_compressed_dump(text_file, compressed_file, "", "", "", "checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_file, compressed_file, "", "", 0); + } TearDown(); @@ -71,7 +75,11 @@ TEST_F(DumpAtomCompressTest, compressed_multi_file_run1) auto compressed_file_0 = compressed_dump_filename(base_name_0); auto compressed_file_1 = compressed_dump_filename(base_name_1); - generate_text_and_compressed_dump(text_file, compressed_file, "", "", 1); + if(compression_style == "atom/zstd") { + generate_text_and_compressed_dump(text_file, compressed_file, "", "", "", "checksum no", 1); + } else { + generate_text_and_compressed_dump(text_file, compressed_file, "", "", 1); + } TearDown(); @@ -378,43 +386,3 @@ TEST_F(DumpAtomCompressTest, compressed_modify_clevel_run0) delete_file(compressed_file); delete_file(converted_file); } - -int main(int argc, char **argv) -{ - MPI_Init(&argc, &argv); - ::testing::InitGoogleMock(&argc, argv); - - if (argc < 2) { - std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; - return 1; - } - - if(strcmp(argv[1], "gz") == 0) { - COMPRESS_SUFFIX = "gz"; - COMPRESS_EXTENSION = "gz"; - } else if(strcmp(argv[1], "zstd") == 0) { - COMPRESS_SUFFIX = "zstd"; - COMPRESS_EXTENSION = "zst"; - } else { - std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; - return 1; - } - - COMPRESS_BINARY = getenv("COMPRESS_BINARY"); - - // handle arguments passed via environment variable - if (const char *var = getenv("TEST_ARGS")) { - std::vector env = utils::split_words(var); - for (auto arg : env) { - if (arg == "-v") { - verbose = true; - } - } - } - - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; - - int rv = RUN_ALL_TESTS(); - MPI_Finalize(); - return rv; -} diff --git a/unittest/formats/test_dump_cfg.cpp b/unittest/formats/test_dump_cfg.cpp index a7f331a0d0..327a9caca7 100644 --- a/unittest/formats/test_dump_cfg.cpp +++ b/unittest/formats/test_dump_cfg.cpp @@ -21,6 +21,8 @@ using ::testing::Eq; +bool verbose = false; + class DumpCfgTest : public MeltTest { std::string dump_style = "cfg"; diff --git a/unittest/formats/test_dump_cfg_compressed.cpp b/unittest/formats/test_dump_cfg_compressed.cpp index 66ab6921d5..834a71db70 100644 --- a/unittest/formats/test_dump_cfg_compressed.cpp +++ b/unittest/formats/test_dump_cfg_compressed.cpp @@ -46,7 +46,11 @@ TEST_F(DumpCfgCompressTest, compressed_run0) auto compressed_file_0 = compressed_dump_filename(base_name_0); auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; - generate_text_and_compressed_dump(text_files, compressed_files, fields, "", 0); + if(compression_style == "cfg/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "", "checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "", 0); + } TearDown(); @@ -106,7 +110,11 @@ TEST_F(DumpCfgCompressTest, compressed_multi_file_run1) auto compressed_file_1 = compressed_dump_filename(base_name_1); auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; - generate_text_and_compressed_dump(text_file, compressed_file, fields, "", 1); + if(compression_style == "cfg/zstd") { + generate_text_and_compressed_dump(text_file, compressed_file, fields, fields, "", "checksum no", 1); + } else { + generate_text_and_compressed_dump(text_file, compressed_file, fields, "", 1); + } TearDown(); @@ -273,43 +281,3 @@ TEST_F(DumpCfgCompressTest, compressed_modify_clevel_run0) delete_file(compressed_file_0); delete_file(converted_file_0); } - -int main(int argc, char **argv) -{ - MPI_Init(&argc, &argv); - ::testing::InitGoogleMock(&argc, argv); - - if (argc < 2) { - std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; - return 1; - } - - if(strcmp(argv[1], "gz") == 0) { - COMPRESS_SUFFIX = "gz"; - COMPRESS_EXTENSION = "gz"; - } else if(strcmp(argv[1], "zstd") == 0) { - COMPRESS_SUFFIX = "zstd"; - COMPRESS_EXTENSION = "zst"; - } else { - std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; - return 1; - } - - COMPRESS_BINARY = getenv("COMPRESS_BINARY"); - - // handle arguments passed via environment variable - if (const char *var = getenv("TEST_ARGS")) { - std::vector env = utils::split_words(var); - for (auto arg : env) { - if (arg == "-v") { - verbose = true; - } - } - } - - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; - - int rv = RUN_ALL_TESTS(); - MPI_Finalize(); - return rv; -} diff --git a/unittest/formats/test_dump_custom.cpp b/unittest/formats/test_dump_custom.cpp index dee27d9f0d..f2d7935426 100644 --- a/unittest/formats/test_dump_custom.cpp +++ b/unittest/formats/test_dump_custom.cpp @@ -22,6 +22,7 @@ using ::testing::Eq; char *BINARY2TXT_BINARY = nullptr; +bool verbose = false; class DumpCustomTest : public MeltTest { std::string dump_style = "custom"; diff --git a/unittest/formats/test_dump_custom_compressed.cpp b/unittest/formats/test_dump_custom_compressed.cpp index 8118442dbd..fb70206590 100644 --- a/unittest/formats/test_dump_custom_compressed.cpp +++ b/unittest/formats/test_dump_custom_compressed.cpp @@ -38,7 +38,11 @@ TEST_F(DumpCustomCompressTest, compressed_run1) auto compressed_file = compressed_dump_filename(base_name); auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; - generate_text_and_compressed_dump(text_file, compressed_file, fields, "units yes", 1); + if(compression_style == "custom/zstd") { + generate_text_and_compressed_dump(text_file, compressed_file, fields, fields, "units yes", "units yes checksum yes", 1); + } else { + generate_text_and_compressed_dump(text_file, compressed_file, fields, "units yes", 1); + } TearDown(); @@ -96,7 +100,11 @@ TEST_F(DumpCustomCompressTest, compressed_multi_file_run1) auto compressed_file_1 = compressed_dump_filename(base_name_1); auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; - generate_text_and_compressed_dump(text_file, compressed_file, fields, "", 1); + if(compression_style == "custom/zstd") { + generate_text_and_compressed_dump(text_file, compressed_file, fields, fields, "", "checksum no", 1); + } else { + generate_text_and_compressed_dump(text_file, compressed_file, fields, "", 1); + } TearDown(); @@ -256,43 +264,3 @@ TEST_F(DumpCustomCompressTest, compressed_modify_clevel_run0) delete_file(compressed_file); delete_file(converted_file); } - -int main(int argc, char **argv) -{ - MPI_Init(&argc, &argv); - ::testing::InitGoogleMock(&argc, argv); - - if (argc < 2) { - std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; - return 1; - } - - if(strcmp(argv[1], "gz") == 0) { - COMPRESS_SUFFIX = "gz"; - COMPRESS_EXTENSION = "gz"; - } else if(strcmp(argv[1], "zstd") == 0) { - COMPRESS_SUFFIX = "zstd"; - COMPRESS_EXTENSION = "zst"; - } else { - std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; - return 1; - } - - COMPRESS_BINARY = getenv("COMPRESS_BINARY"); - - // handle arguments passed via environment variable - if (const char *var = getenv("TEST_ARGS")) { - std::vector env = utils::split_words(var); - for (auto arg : env) { - if (arg == "-v") { - verbose = true; - } - } - } - - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; - - int rv = RUN_ALL_TESTS(); - MPI_Finalize(); - return rv; -} diff --git a/unittest/formats/test_dump_local_compressed.cpp b/unittest/formats/test_dump_local_compressed.cpp index b3c96b6edc..20f90984a1 100644 --- a/unittest/formats/test_dump_local_compressed.cpp +++ b/unittest/formats/test_dump_local_compressed.cpp @@ -49,7 +49,11 @@ TEST_F(DumpLocalCompressTest, compressed_run0) auto compressed_file_0 = compressed_dump_filename(base_name_0); auto fields = "index c_comp[1]"; - generate_text_and_compressed_dump(text_files, compressed_files, fields, "", 0); + if(compression_style == "local/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "", "checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "", 0); + } TearDown(); @@ -80,7 +84,11 @@ TEST_F(DumpLocalCompressTest, compressed_multi_file_run1) auto compressed_file_1 = compressed_dump_filename(base_name_1); auto fields = "index c_comp[1]"; - generate_text_and_compressed_dump(text_file, compressed_file, fields, "", 1); + if(compression_style == "local/zstd") { + generate_text_and_compressed_dump(text_file, compressed_file, fields, fields, "", "checksum no", 1); + } else { + generate_text_and_compressed_dump(text_file, compressed_file, fields, "", 1); + } TearDown(); @@ -246,43 +254,3 @@ TEST_F(DumpLocalCompressTest, compressed_modify_clevel_run0) delete_file(compressed_file); delete_file(converted_file); } - -int main(int argc, char **argv) -{ - MPI_Init(&argc, &argv); - ::testing::InitGoogleMock(&argc, argv); - - if (argc < 2) { - std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; - return 1; - } - - if(strcmp(argv[1], "gz") == 0) { - COMPRESS_SUFFIX = "gz"; - COMPRESS_EXTENSION = "gz"; - } else if(strcmp(argv[1], "zstd") == 0) { - COMPRESS_SUFFIX = "zstd"; - COMPRESS_EXTENSION = "zst"; - } else { - std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; - return 1; - } - - COMPRESS_BINARY = getenv("COMPRESS_BINARY"); - - // handle arguments passed via environment variable - if (const char *var = getenv("TEST_ARGS")) { - std::vector env = utils::split_words(var); - for (auto arg : env) { - if (arg == "-v") { - verbose = true; - } - } - } - - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; - - int rv = RUN_ALL_TESTS(); - MPI_Finalize(); - return rv; -} diff --git a/unittest/formats/test_dump_xyz_compressed.cpp b/unittest/formats/test_dump_xyz_compressed.cpp index 9a61c746a0..f80201872c 100644 --- a/unittest/formats/test_dump_xyz_compressed.cpp +++ b/unittest/formats/test_dump_xyz_compressed.cpp @@ -40,7 +40,11 @@ TEST_F(DumpXYZCompressTest, compressed_run0) auto text_file_0 = text_dump_filename(base_name_0); auto compressed_file_0 = compressed_dump_filename(base_name_0); - generate_text_and_compressed_dump(text_files, compressed_files, "", "", 0); + if(compression_style == "xyz/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, "", "", "", "checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, "", "", 0); + } TearDown(); @@ -70,7 +74,11 @@ TEST_F(DumpXYZCompressTest, compressed_multi_file_run1) auto compressed_file_0 = compressed_dump_filename(base_name_0); auto compressed_file_1 = compressed_dump_filename(base_name_1); - generate_text_and_compressed_dump(text_file, compressed_file, "", "", 1); + if(compression_style == "xyz/zstd") { + generate_text_and_compressed_dump(text_file, compressed_file, "", "", "", "checksum no", 1); + } else { + generate_text_and_compressed_dump(text_file, compressed_file, "", "", 1); + } TearDown(); @@ -229,43 +237,3 @@ TEST_F(DumpXYZCompressTest, compressed_modify_clevel_run0) delete_file(compressed_file); delete_file(converted_file); } - -int main(int argc, char **argv) -{ - MPI_Init(&argc, &argv); - ::testing::InitGoogleMock(&argc, argv); - - if (argc < 2) { - std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; - return 1; - } - - if(strcmp(argv[1], "gz") == 0) { - COMPRESS_SUFFIX = "gz"; - COMPRESS_EXTENSION = "gz"; - } else if(strcmp(argv[1], "zstd") == 0) { - COMPRESS_SUFFIX = "zstd"; - COMPRESS_EXTENSION = "zst"; - } else { - std::cerr << "usage: " << argv[0] << " (gz|zstd)\n\n" << std::endl; - return 1; - } - - COMPRESS_BINARY = getenv("COMPRESS_BINARY"); - - // handle arguments passed via environment variable - if (const char *var = getenv("TEST_ARGS")) { - std::vector env = utils::split_words(var); - for (auto arg : env) { - if (arg == "-v") { - verbose = true; - } - } - } - - if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; - - int rv = RUN_ALL_TESTS(); - MPI_Finalize(); - return rv; -} diff --git a/unittest/testing/core.h b/unittest/testing/core.h index 5852f7fd06..6243eb219e 100644 --- a/unittest/testing/core.h +++ b/unittest/testing/core.h @@ -39,7 +39,7 @@ using ::testing::MatchesRegex; } // whether to print verbose output (i.e. not capturing LAMMPS screen output). -bool verbose = false; +extern bool verbose; class LAMMPSTest : public ::testing::Test { public: From c78ddb29ddf72dc148e1615c02a6af1c30f0ac9d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 16:57:37 -0500 Subject: [PATCH 0160/1217] implement reference counting and means to close unused DSO. Must delete pair style when plugin version is in use --- src/input.cpp | 2 +- src/plugin.cpp | 80 ++++++++++++++++++++++++++++++++++++++++---------- src/plugin.h | 3 +- 3 files changed, 68 insertions(+), 17 deletions(-) diff --git a/src/input.cpp b/src/input.cpp index 73a73cd369..6d1564ecb6 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -1115,7 +1115,7 @@ void Input::plugin() int num = plugin_get_num_plugins(); utils::logmesg(lmp,"Currently loaded plugins\n"); for (int i=0; i < num; ++i) { - auto entry = plugin_info(i); + auto entry = plugin_get_info(i); utils::logmesg(lmp,fmt::format("{:4}: {} style plugin {}\n", i+1,entry->style,entry->name)); } diff --git a/src/plugin.cpp b/src/plugin.cpp index e978d90059..a3126b8acd 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -17,9 +17,10 @@ #include "force.h" #include "lammps.h" #include "modify.h" +#include "pair.h" #include -#include +#include #ifdef _WIN32 #include @@ -30,7 +31,7 @@ namespace LAMMPS_NS { // store list of plugin information data for loaded styles - static std::vector pluginlist; + static std::list pluginlist; // map of dso handles static std::map dso_refcounter; @@ -72,13 +73,18 @@ namespace LAMMPS_NS LAMMPS *lmp = (LAMMPS *)ptr; if (plugin == nullptr) return; - if (plugin->version) - utils::logmesg(lmp,fmt::format("Loading: {}\n compiled for LAMMPS " - "version {} loaded into LAMMPS " - "version {}\n", plugin->info, + utils::logmesg(lmp,fmt::format("Loading plugin: {} by {}\n", + plugin->info, plugin->author)); + if ((plugin->version) && (strcmp(plugin->version,lmp->version) != 0)) + utils::logmesg(lmp,fmt::format(" compiled for LAMMPS version {} " + "loaded into LAMMPS version {}\n", plugin->version, lmp->version)); - pluginlist.push_back(*plugin); + if (dso_refcounter.find(plugin->handle) != dso_refcounter.end()) { + ++ dso_refcounter[plugin->handle]; + } else { + dso_refcounter[plugin->handle] = 1; + } std::string pstyle = plugin->style; if (pstyle == "pair") { @@ -96,32 +102,76 @@ namespace LAMMPS_NS return pluginlist.size(); } - const lammpsplugin_t *plugin_info(int idx) + const lammpsplugin_t *plugin_get_info(int idx) { - if ((idx < 0) || idx >= pluginlist.size()) return nullptr; - - return &pluginlist[idx]; + int i=0; + for (auto p=pluginlist.begin(); p != pluginlist.end(); ++p) { + if (i == idx) return &(*p); + ++i; + } + return nullptr; } int plugin_find(const char *style, const char *name) { - for (int i=0; i < pluginlist.size(); ++i) { - if ((strcmp(style,pluginlist[i].style) == 0) - && (strcmp(name,pluginlist[i].name) == 0)) + int i=0; + for (auto entry : pluginlist) { + if ((strcmp(style,entry.style) == 0) + && (strcmp(name,entry.name) == 0)) return i; + ++i; } return -1; } - // remove plugin from given style table + void plugin_erase(const char *style, const char *name) + { + fmt::print("Erasing {} style {} from list with {} plugins\n", + style, name, pluginlist.size()); + for (auto p=pluginlist.begin(); p != pluginlist.end(); ++p) { + if ((strcmp(style,p->style) == 0) + && (strcmp(name,p->name) == 0)) { + pluginlist.erase(p); + return; + } + } + } + + // remove plugin from given style table and plugin list. + // close dso handle if this is the last plugin from that dso. void plugin_unload(const char *style, const char *name, LAMMPS *lmp) { + int idx = plugin_find(style,name); + if (idx < 0) + lmp->error->all(FLERR,fmt::format("{} style {} is not loaded from " + "a plugin", style, name)); + auto plugin = plugin_get_info(idx); + void *handle = plugin->handle; + utils::logmesg(lmp,fmt::format("Unloading {} style {}\n",style,name)); + plugin_erase(style,name); + std::string pstyle = style; if (pstyle == "pair") { auto found = lmp->force->pair_map->find(name); if (found != lmp->force->pair_map->end()) { lmp->force->pair_map->erase(found); } + + // must delete pair style instance if in use + if (lmp->force->pair_style) { + if (utils::strmatch(lmp->force->pair_style,"^hybrid")) { + if (lmp->force->pair_match(name,1,1) != nullptr) + lmp->force->create_pair("none",0); + } else { + if (strcmp(lmp->force->pair_style,name) == 0) + lmp->force->create_pair("none",0); + } + } + } + + -- dso_refcounter[handle]; + if (dso_refcounter[handle] == 0) { + dlclose(handle); } } } diff --git a/src/plugin.h b/src/plugin.h index 051382ac27..172b2f0c37 100644 --- a/src/plugin.h +++ b/src/plugin.h @@ -22,8 +22,9 @@ namespace LAMMPS_NS void plugin_load(const char *, LAMMPS *); void plugin_register(lammpsplugin_t *, void *); int plugin_get_num_plugins(); - const lammpsplugin_t *plugin_info(int); + const lammpsplugin_t *plugin_get_info(int); int plugin_find(const char *, const char *); + void plugin_erase(const char *, const char *); void plugin_unload(const char *, const char *, LAMMPS *); } From ca88f97a4bf6eec438c8719751aca705c131819c Mon Sep 17 00:00:00 2001 From: Gurgen Date: Fri, 12 Mar 2021 01:40:52 +0300 Subject: [PATCH 0161/1217] added acceleration of lj/smooth on gpu --- lib/gpu/lal_lj_smooth.cpp | 19 +++++++++++++------ lib/gpu/lal_lj_smooth.cu | 10 ++++++---- lib/gpu/lal_lj_smooth.h | 10 ++++++---- lib/gpu/lal_lj_smooth_ext.cpp | 12 ++++++------ src/GPU/pair_lj_smooth_gpu.cpp | 12 ++++++------ 5 files changed, 37 insertions(+), 26 deletions(-) diff --git a/lib/gpu/lal_lj_smooth.cpp b/lib/gpu/lal_lj_smooth.cpp index 5c75539660..d2ab63549d 100644 --- a/lib/gpu/lal_lj_smooth.cpp +++ b/lib/gpu/lal_lj_smooth.cpp @@ -16,7 +16,7 @@ #if defined(USE_OPENCL) #include "lj_smooth_cl.h" #elif defined(USE_CUDART) -const char *lj=0; +const char *lj_smooth=0; #else #include "lj_smooth_cubin.h" #endif @@ -51,7 +51,7 @@ int LJSMOOTHT::init(const int ntypes, const int nall, const int max_nbors, const int maxspecial, const double cell_size, const double gpu_split, FILE *_screen, - double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, double **host_ljsw4, double **cut_inner, double **cut_inner_sq) { int success; @@ -88,6 +88,10 @@ int LJSMOOTHT::init(const int ntypes, ljsw.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); this->atom->type_pack4(ntypes,lj_types,ljsw,host_write,host_ljsw1,host_ljsw2, host_ljsw3,host_ljsw4); + + ljsw0.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,ljsw0,host_write,host_ljsw0,cut_inner,host_ljsw2, + host_ljsw3); UCL_H_Vec dview; sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY); @@ -95,7 +99,7 @@ int LJSMOOTHT::init(const int ntypes, ucl_copy(sp_lj,dview,false); _allocated=true; - this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+ljsw.row_bytes()+sp_lj.row_bytes(); + this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+ljsw.row_bytes()+ljsw0.row_bytes()+sp_lj.row_bytes(); return 0; } @@ -103,7 +107,7 @@ template void LJSMOOTHT::reinit(const int ntypes, double **host_cutsq, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, double **host_offset, - double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, double **host_ljsw4, double **cut_inner, double **cut_inner_sq) { // Allocate a host write buffer for data initialization @@ -119,6 +123,8 @@ void LJSMOOTHT::reinit(const int ntypes, double **host_cutsq, double **host_lj1, host_offset, cut_inner); this->atom->type_pack4(ntypes,_lj_types,ljsw,host_write,host_ljsw1,host_ljsw2, host_ljsw3,host_ljsw4); + this->atom->type_pack4(ntypes,_lj_types,ljsw0,host_write,host_ljsw0, cut_inner, host_ljsw2, + host_ljsw3); } template @@ -130,6 +136,7 @@ void LJSMOOTHT::clear() { lj1.clear(); lj3.clear(); ljsw.clear(); + ljsw0.clear(); sp_lj.clear(); this->clear_atomic(); } @@ -165,14 +172,14 @@ void LJSMOOTHT::loop(const bool _eflag, const bool _vflag) { this->time_pair.start(); if (shared_types) { this->k_pair_fast.set_size(GX,BX); - this->k_pair_fast.run(&this->atom->x, &lj1, &lj3, &ljsw, &sp_lj, + this->k_pair_fast.run(&this->atom->x, &lj1, &lj3, &ljsw, &ljsw0, &sp_lj, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom); } else { this->k_pair.set_size(GX,BX); - this->k_pair.run(&this->atom->x, &lj1, &lj3, &ljsw, &_lj_types, &sp_lj, + this->k_pair.run(&this->atom->x, &lj1, &lj3, &ljsw, &ljsw0, &_lj_types, &sp_lj, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom); diff --git a/lib/gpu/lal_lj_smooth.cu b/lib/gpu/lal_lj_smooth.cu index b69f8b9388..345da1c702 100644 --- a/lib/gpu/lal_lj_smooth.cu +++ b/lib/gpu/lal_lj_smooth.cu @@ -28,6 +28,7 @@ __kernel void k_lj_smooth(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict lj1, const __global numtyp4 *restrict lj3, const __global numtyp4 *restrict ljsw, + const __global numtyp4 *restrict ljsw0, const int lj_types, const __global numtyp *restrict sp_lj, const __global int * dev_nbor, @@ -82,7 +83,7 @@ __kernel void k_lj_smooth(const __global numtyp4 *restrict x_, } else { r = sqrt(rsq); - t = r - lj3[mtype].w; + t = r - ljsw0[mtype].y; tsq = t*t; fskin = ljsw[mtype].x + ljsw[mtype].y*t + ljsw[mtype].z*tsq + ljsw[mtype].w*tsq*t; @@ -98,7 +99,7 @@ __kernel void k_lj_smooth(const __global numtyp4 *restrict x_, if (rsq < lj1[mtype].w) e = r6inv * (lj3[mtype].x*r6inv - lj3[mtype].y) - lj3[mtype].z; else - e = ljsw[mtype].x - ljsw[mtype].x*t - + e = ljsw0[mtype].x - ljsw[mtype].x*t - ljsw[mtype].y*tsq/2.0 - ljsw[mtype].z*tsq*t/3.0 - ljsw[mtype].z*tsq*tsq/4.0 - lj3[mtype].z; @@ -125,6 +126,7 @@ __kernel void k_lj_smooth_fast(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict lj1_in, const __global numtyp4 *restrict lj3_in, const __global numtyp4 *restrict ljsw, + const __global numtyp4 *restrict ljsw0, const __global numtyp *restrict sp_lj_in, const __global int * dev_nbor, const __global int * dev_packed, @@ -191,7 +193,7 @@ __kernel void k_lj_smooth_fast(const __global numtyp4 *restrict x_, } else { r = sqrt(rsq); - t = r - lj3[mtype].w; + t = r - ljsw0[mtype].y; //? //printf("%f\n", r - lj3[mtype].w); tsq = t*t; fskin = ljsw[mtype].x + ljsw[mtype].y*t + @@ -208,7 +210,7 @@ __kernel void k_lj_smooth_fast(const __global numtyp4 *restrict x_, if (rsq < lj1[mtype].w) e = r6inv * (lj3[mtype].x*r6inv - lj3[mtype].y) - lj3[mtype].z; else - e = ljsw[mtype].x - ljsw[mtype].x*t - + e = ljsw0[mtype].x - ljsw[mtype].x*t - ljsw[mtype].y*tsq/2.0 - ljsw[mtype].z*tsq*t/3.0 - ljsw[mtype].z*tsq*tsq/4.0 - lj3[mtype].z; //??? diff --git a/lib/gpu/lal_lj_smooth.h b/lib/gpu/lal_lj_smooth.h index 98dbad87b7..0a4cdf78eb 100644 --- a/lib/gpu/lal_lj_smooth.h +++ b/lib/gpu/lal_lj_smooth.h @@ -43,16 +43,16 @@ class LJSMOOTH : public BaseAtomic { const int nlocal, const int nall, const int max_nbors, const int maxspecial, const double cell_size, const double gpu_split, FILE *screen, - double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, - double **host_ljsw4, + double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, + double **host_ljsw3, double **host_ljsw4, double **cut_inner, double **cut_inner_sq); /// Send updated coeffs from host to device (to be compatible with fix adapt) void reinit(const int ntypes, double **host_cutsq, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, double **host_offset, - double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, - double **host_ljsw4, + double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, + double **host_ljsw3, double **host_ljsw4, double **cut_inner, double **cut_inner_sq); /// Clear all host and device data @@ -73,6 +73,8 @@ class LJSMOOTH : public BaseAtomic { UCL_D_Vec lj3; /// ljsw.x = ljsw1, ljsw.y = ljsw2, ljsw.z = ljsw3, ljsw.w = ljsw4 UCL_D_Vec ljsw; + /// ljsw0 + UCL_D_Vec ljsw0; /// Special LJ values UCL_D_Vec sp_lj; diff --git a/lib/gpu/lal_lj_smooth_ext.cpp b/lib/gpu/lal_lj_smooth_ext.cpp index 92624bf7fa..fd4dfd46be 100644 --- a/lib/gpu/lal_lj_smooth_ext.cpp +++ b/lib/gpu/lal_lj_smooth_ext.cpp @@ -32,7 +32,7 @@ int ljsmt_gpu_init(const int ntypes, double **cutsq, double **host_lj1, double **offset, double *special_lj, const int inum, const int nall, const int max_nbors, const int maxspecial, const double cell_size, int &gpu_mode, FILE *screen, - double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, double **host_ljsw4, double **cut_inner, double **cut_inner_sq) { LJSMTMF.clear(); gpu_mode=LJSMTMF.device->gpu_mode(); @@ -59,7 +59,7 @@ int ljsmt_gpu_init(const int ntypes, double **cutsq, double **host_lj1, init_ok=LJSMTMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4, offset, special_lj, inum, nall, 300, maxspecial, cell_size, gpu_split, screen, - host_ljsw1, host_ljsw2, host_ljsw3, host_ljsw4, cut_inner, cut_inner_sq); + host_ljsw0, host_ljsw1, host_ljsw2, host_ljsw3, host_ljsw4, cut_inner, cut_inner_sq); LJSMTMF.device->world_barrier(); if (message) @@ -77,7 +77,7 @@ int ljsmt_gpu_init(const int ntypes, double **cutsq, double **host_lj1, if (gpu_rank==i && world_me!=0) init_ok=LJSMTMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4, offset, special_lj, inum, nall, 300, maxspecial, - cell_size, gpu_split, screen, host_ljsw1, host_ljsw2, host_ljsw3, + cell_size, gpu_split, screen, host_ljsw0, host_ljsw1, host_ljsw2, host_ljsw3, host_ljsw4, cut_inner, cut_inner_sq); LJSMTMF.device->gpu_barrier(); @@ -97,19 +97,19 @@ int ljsmt_gpu_init(const int ntypes, double **cutsq, double **host_lj1, // --------------------------------------------------------------------------- void ljsmt_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, - double **offset, double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, + double **offset, double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, double **host_ljsw4, double **cut_inner, double **cut_inner_sq) { int world_me=LJSMTMF.device->world_me(); int gpu_rank=LJSMTMF.device->gpu_rank(); int procs_per_gpu=LJSMTMF.device->procs_per_gpu(); if (world_me==0) - LJSMTMF.reinit(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4, offset, host_ljsw1, host_ljsw2, host_ljsw3, host_ljsw4, cut_inner, cut_inner_sq); + LJSMTMF.reinit(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4, offset, host_ljsw0, host_ljsw1, host_ljsw2, host_ljsw3, host_ljsw4, cut_inner, cut_inner_sq); LJSMTMF.device->world_barrier(); for (int i=0; igpu_barrier(); } } diff --git a/src/GPU/pair_lj_smooth_gpu.cpp b/src/GPU/pair_lj_smooth_gpu.cpp index 882055e84d..0203350507 100644 --- a/src/GPU/pair_lj_smooth_gpu.cpp +++ b/src/GPU/pair_lj_smooth_gpu.cpp @@ -45,15 +45,15 @@ int ljsmt_gpu_init(const int ntypes, double **cutsq, double **host_lj1, double **offset, double *special_lj, const int nlocal, const int nall, const int max_nbors, const int maxspecial, const double cell_size, int &gpu_mode, FILE *screen, - double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, - double **host_ljsw4, + double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, + double **host_ljsw3, double **host_ljsw4, double **cut_inner, double **cut_innersq); void ljsmt_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, double **offset, - double **host_ljsw1, double **host_ljsw2, double **host_ljsw3, - double **host_ljsw4, + double **host_ljsw0, double **host_ljsw1, double **host_ljsw2, + double **host_ljsw3, double **host_ljsw4, double **cut_inner, double **cut_innersq); void ljsmt_gpu_clear(); @@ -174,7 +174,7 @@ void PairLJSmoothGPU::init_style() int success = ljsmt_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4, offset, force->special_lj, atom->nlocal, atom->nlocal+atom->nghost, 300, maxspecial, - cell_size, gpu_mode, screen, ljsw1, ljsw2, + cell_size, gpu_mode, screen, ljsw0, ljsw1, ljsw2, ljsw3, ljsw4, cut_inner, cut_inner_sq); GPU_EXTRA::check_flag(success,error,world); @@ -191,7 +191,7 @@ void PairLJSmoothGPU::reinit() { Pair::reinit(); - ljsmt_gpu_reinit(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4, offset, ljsw1, ljsw2, ljsw3, ljsw4, cut_inner, cut_inner_sq); + ljsmt_gpu_reinit(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4, offset, ljsw0, ljsw1, ljsw2, ljsw3, ljsw4, cut_inner, cut_inner_sq); } /* ---------------------------------------------------------------------- */ From b8ae2f5c6f3a4f4e53e19695733c696eb1e631d1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 17:41:08 -0500 Subject: [PATCH 0162/1217] add comments, extra checks, have output only on MPI rank 0 --- src/plugin.cpp | 123 ++++++++++++++++++++++++++++++++++--------------- 1 file changed, 86 insertions(+), 37 deletions(-) diff --git a/src/plugin.cpp b/src/plugin.cpp index a3126b8acd..1b9db01780 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -13,6 +13,7 @@ #include "plugin.h" +#include "comm.h" #include "error.h" #include "force.h" #include "lammps.h" @@ -38,16 +39,18 @@ namespace LAMMPS_NS // load DSO and call included registration function void plugin_load(const char *file, LAMMPS *lmp) { + int me = lmp->comm->me; #if defined(WIN32) - utils::logmesg(lmp,"Loading of plugins not supported on Windows yet\n"); + lmp->error->all(FLERR,"Loading of plugins on Windows not yet supported\n"); #else - // open DSO from given path + // open DSO file from given path load symbols globally void *dso = dlopen(file,RTLD_NOW|RTLD_GLOBAL); if (dso == nullptr) { - utils::logmesg(lmp,fmt::format("Loading of plugin from file {} failed: " - "{}", file, utils::getsyserror())); + if (me == 0) + utils::logmesg(lmp,fmt::format("Open of plugin file {} failed: {}", + file,utils::getsyserror())); return; } @@ -56,30 +59,44 @@ namespace LAMMPS_NS void *initfunc = dlsym(dso,"lammpsplugin_init"); if (initfunc == nullptr) { dlclose(dso); - utils::logmesg(lmp,fmt::format("Symbol lookup failure in file {}\n",file)); + if (me == 0) + utils::logmesg(lmp,fmt::format("Plugin symbol lookup failure in " + "file {}\n",file)); return; } - // call initializer function loaded from DSO and pass pointer to LAMMPS instance, - // the DSO handle (for reference counting) and plugin registration function pointer + // call initializer function loaded from DSO and pass a pointer + // to the LAMMPS instance, the DSO handle (for reference counting) + // and plugin registration function pointer - ((lammpsplugin_initfunc)(initfunc))((void *)lmp, dso, (void *)&plugin_register); + ((lammpsplugin_initfunc)(initfunc))((void *)lmp, dso, + (void *)&plugin_register); #endif } - // register new style from plugin with LAMMPS + // register a new style from a plugin with LAMMPS + // this is the callback function that is called from within + // the plugin initializer function. all plugin information + // is taken from the lammpsplugin_t struct. + void plugin_register(lammpsplugin_t *plugin, void *ptr) { LAMMPS *lmp = (LAMMPS *)ptr; + int me = lmp->comm->me; if (plugin == nullptr) return; - utils::logmesg(lmp,fmt::format("Loading plugin: {} by {}\n", - plugin->info, plugin->author)); - if ((plugin->version) && (strcmp(plugin->version,lmp->version) != 0)) - utils::logmesg(lmp,fmt::format(" compiled for LAMMPS version {} " - "loaded into LAMMPS version {}\n", - plugin->version, lmp->version)); + if (me == 0) { + utils::logmesg(lmp,fmt::format("Loading plugin: {} by {}\n", + plugin->info, plugin->author)); + // print version info only if the versions of host and plugin don't match + if ((plugin->version) && (strcmp(plugin->version,lmp->version) != 0)) + utils::logmesg(lmp,fmt::format(" compiled for LAMMPS version {} " + "loaded into LAMMPS version {}\n", + plugin->version, lmp->version)); + } + pluginlist.push_back(*plugin); + if (dso_refcounter.find(plugin->handle) != dso_refcounter.end()) { ++ dso_refcounter[plugin->handle]; } else { @@ -88,8 +105,15 @@ namespace LAMMPS_NS std::string pstyle = plugin->style; if (pstyle == "pair") { - (*(lmp->force->pair_map))[plugin->name] = - (LAMMPS_NS::Force::PairCreator)plugin->creator; + auto pair_map = lmp->force->pair_map; + if (pair_map->find(plugin->name) != pair_map->end()) { + if (lmp->comm->me == 0) + lmp->error->warning(FLERR,fmt::format("Overriding built-in pair " + "style {} from plugin", + plugin->name)); + } + + (*pair_map)[plugin->name] = (Force::PairCreator)plugin->creator; } else { utils::logmesg(lmp,fmt::format("Loading plugin for {} styles not " "yet implemented\n", pstyle)); @@ -97,20 +121,14 @@ namespace LAMMPS_NS } } + // number of styles loaded from plugin files + int plugin_get_num_plugins() { return pluginlist.size(); } - const lammpsplugin_t *plugin_get_info(int idx) - { - int i=0; - for (auto p=pluginlist.begin(); p != pluginlist.end(); ++p) { - if (i == idx) return &(*p); - ++i; - } - return nullptr; - } + // return position index in list of given plugin of given style int plugin_find(const char *style, const char *name) { @@ -124,10 +142,22 @@ namespace LAMMPS_NS return -1; } + // get pointer to plugin initializer struct at position idx + + const lammpsplugin_t *plugin_get_info(int idx) + { + int i=0; + for (auto p=pluginlist.begin(); p != pluginlist.end(); ++p) { + if (i == idx) return &(*p); + ++i; + } + return nullptr; + } + + // remove plugin of given name and style from internal lists + void plugin_erase(const char *style, const char *name) { - fmt::print("Erasing {} style {} from list with {} plugins\n", - style, name, pluginlist.size()); for (auto p=pluginlist.begin(); p != pluginlist.end(); ++p) { if ((strcmp(style,p->style) == 0) && (strcmp(name,p->name) == 0)) { @@ -138,26 +168,43 @@ namespace LAMMPS_NS } // remove plugin from given style table and plugin list. - // close dso handle if this is the last plugin from that dso. + // optionally close the DSO handle if last plugin from that DSO + // must delete style instance if style is currently active. + void plugin_unload(const char *style, const char *name, LAMMPS *lmp) { + int me = lmp->comm->me; + + // ignore unload request if not loaded from a plugin int idx = plugin_find(style,name); - if (idx < 0) - lmp->error->all(FLERR,fmt::format("{} style {} is not loaded from " - "a plugin", style, name)); - auto plugin = plugin_get_info(idx); - void *handle = plugin->handle; - utils::logmesg(lmp,fmt::format("Unloading {} style {}\n",style,name)); + if (idx < 0) { + if (me == 0) + utils::logmesg(lmp,fmt::format("Ignoring unload of {} style {}: not " + "loaded from a plugin", style, name)); + return; + } + + // copy of DSO handle for later + void *handle = plugin_get_info(idx)->handle; + + // remove selected plugin from list of plugins + + if (me == 0) + utils::logmesg(lmp,fmt::format("Unloading {} style {}\n",style,name)); plugin_erase(style,name); + // remove style of given name from corresponding map + // must delete style instance if currently active so + // we can close the DSO handle if the last reference is gone. + std::string pstyle = style; if (pstyle == "pair") { auto found = lmp->force->pair_map->find(name); - if (found != lmp->force->pair_map->end()) { + if (found != lmp->force->pair_map->end()) lmp->force->pair_map->erase(found); - } // must delete pair style instance if in use + if (lmp->force->pair_style) { if (utils::strmatch(lmp->force->pair_style,"^hybrid")) { if (lmp->force->pair_match(name,1,1) != nullptr) @@ -169,6 +216,8 @@ namespace LAMMPS_NS } } + // if reference count is down to zero, close DSO handle. + -- dso_refcounter[handle]; if (dso_refcounter[handle] == 0) { dlclose(handle); From ee8246f590979e561562fdc621d9598d7004bd53 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 17:44:05 -0500 Subject: [PATCH 0163/1217] recover compilation on windows --- src/plugin.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/plugin.cpp b/src/plugin.cpp index 1b9db01780..19a5c1b754 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -58,7 +58,9 @@ namespace LAMMPS_NS void *initfunc = dlsym(dso,"lammpsplugin_init"); if (initfunc == nullptr) { +#ifndef WIN32 dlclose(dso); +#endif if (me == 0) utils::logmesg(lmp,fmt::format("Plugin symbol lookup failure in " "file {}\n",file)); From 3ec9f2fd5e0b72a942a91ca7ad78807c51b04279 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 17:44:11 -0500 Subject: [PATCH 0164/1217] whitespace --- src/plugin.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/plugin.cpp b/src/plugin.cpp index 19a5c1b754..7e7bd6e86f 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -33,7 +33,7 @@ namespace LAMMPS_NS { // store list of plugin information data for loaded styles static std::list pluginlist; - // map of dso handles + // map of dso handles static std::map dso_refcounter; // load DSO and call included registration function @@ -45,7 +45,7 @@ namespace LAMMPS_NS #else // open DSO file from given path load symbols globally - + void *dso = dlopen(file,RTLD_NOW|RTLD_GLOBAL); if (dso == nullptr) { if (me == 0) @@ -125,7 +125,7 @@ namespace LAMMPS_NS // number of styles loaded from plugin files - int plugin_get_num_plugins() + int plugin_get_num_plugins() { return pluginlist.size(); } @@ -210,7 +210,7 @@ namespace LAMMPS_NS if (lmp->force->pair_style) { if (utils::strmatch(lmp->force->pair_style,"^hybrid")) { if (lmp->force->pair_match(name,1,1) != nullptr) - lmp->force->create_pair("none",0); + lmp->force->create_pair("none",0); } else { if (strcmp(lmp->force->pair_style,name) == 0) lmp->force->create_pair("none",0); From c61de8740c65c8f9555cc08ac6d23fc281a52d4e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 19:33:07 -0500 Subject: [PATCH 0165/1217] add preliminary documentation for plugin command and about how to write plugins --- doc/src/Commands_all.rst | 1 + doc/src/Developer.rst | 1 + doc/src/Developer_plugins.rst | 98 +++++++++++++++++++++++++++++++++++ doc/src/commands_list.rst | 1 + 4 files changed, 101 insertions(+) create mode 100644 doc/src/Developer_plugins.rst diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst index 132425948e..b43fd0ed56 100644 --- a/doc/src/Commands_all.rst +++ b/doc/src/Commands_all.rst @@ -86,6 +86,7 @@ An alphabetic list of all general LAMMPS commands. * :doc:`pair_style ` * :doc:`pair_write ` * :doc:`partition ` + * :doc:`plugin ` * :doc:`prd ` * :doc:`print ` * :doc:`processors ` diff --git a/doc/src/Developer.rst b/doc/src/Developer.rst index 3a0c03b7ea..f54bc4152f 100644 --- a/doc/src/Developer.rst +++ b/doc/src/Developer.rst @@ -14,6 +14,7 @@ of time and requests from the LAMMPS user community. Developer_flow Developer_write Developer_notes + Developer_plugins Developer_unittest Classes Developer_utils diff --git a/doc/src/Developer_plugins.rst b/doc/src/Developer_plugins.rst new file mode 100644 index 0000000000..ffbcf8a667 --- /dev/null +++ b/doc/src/Developer_plugins.rst @@ -0,0 +1,98 @@ +Writing plugins +--------------- + +Plugins provide a mechanism to add functionality to a LAMMPS executable +without recompiling LAMMPS. This uses the operating system's +capability to load dynamic shared object (DSO) files in a way similar +shared libraries and then references specific functions those DSOs. +Any DSO file with plugins has to include an initialization function +with a specific name that has to follow specific rules. When loading +the DSO, this function is called and will then register the contained +plugin(s) with LAMMPS. + +From the programmer perspective this can work because of the object +oriented design where all pair style commands are derived from the class +Pair, all fix style commands from the class Fix and so on and only +functions from those base classes are called directly. When a +:doc:`pair_style` command or :doc:`fix` command is issued a new +instance of such a derived class is created. This is done by a +so-called factory function which is mapped to the style name. Thus +when, for example, the LAMMPS processes the command +``pair_style lj/cut 2.5``, LAMMPS will look up the factory function +for creating the ``PairLJCut`` class and then execute it. The return +value of that function is a ``Pair *`` pointer and the pointer will +be assigned to the location for the currently active pair style. + +A plugin thus has to implement such a factory function and register it +with LAMMPS so that it gets added to the map of available styles of +the given category. To register a plugin with LAMMPS an initialization +function has to be called that follows specific rules explained below. + + +As an example, for a hypothetical pair style "morse2" implemented in a +class ``PairMorse2`` in the files ``pair_morse2.h`` and +``pair_morse2.cpp`` the file with the factory function and initialization +function would look like this: + +.. code-block:: C++ + + #include "lammpsplugin.h" + #include "version.h" + #include "pair_morse2.h" + + using namespace LAMMPS_NS; + + static Pair *morse2creator(LAMMPS *lmp) + { + return new PairMorse2(lmp); + } + + extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) + { + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + lammpsplugin_t plugin; + + plugin.version = LAMMPS_VERSION; + plugin.style = "pair"; + plugin.name = "morse2"; + plugin.info = "Morse2 variant pair style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator = (lammpsplugin_factory *) &morse2creator; + plugin.handle = handle; + (*register_plugin)(&plugin,lmp); + } + +The factory function in this example is called ``morse2creator()``. It +receives a pointer to the LAMMPS class as argument and returns a +pointer to the allocated class instance derived from the ``Pair`` class. +This function may be declared static to avoid clashes with other plugins. +The name of the derived class, ``PairMorse2``, must be unique inside +the entire LAMMPS executable. + +The initialization function **must** be called ``lammpsplugin_init``, it +**must** have C bindings and it takes three void pointers as arguments. +The first is a pointer to the LAMMPS class that calls it and it needs to +be passed to the registration function. The second argument is a +pointer to the internal handle of the DSO file, this needs to added to +the plugin info struct, so that the DSO can be close and unloaded when +all its contained plugins are unloaded. The third argument is a +function pointer to the registration function and needs to be stored +in a variable of ``lammpsplugin_regfunc`` type. + +To register a plugin a struct of the ``lammpsplugin_t`` needs to be filled +with relevant info: current LAMMPS version string, kind of style, name of +style, info string, author string, pointer to factory function, DSO handle. +The the registration function is called with a pointer to the address of +this struct and the pointer of the LAMMPS class. The registration function +will then add the factory function of the plugin style to the respective +style map under the provided name. It will also make a copy of the struct +in a list of all loaded plugins and update the reference counter for loaded +plugins from this specific DSO file. + +The pair style itself (i.e. the PairMorse2 class in this example) can be +written just like any other pair style that is included in LAMMPS. For +a plugin, the use of the ``PairStyle`` macro in the section encapsulated +by ``#ifdef PAIR_CLASS`` is not needed, since the mapping of the class +name to the style name is done by the plugin registration function with +the information from the ``lammpsplugin_t`` struct. It may be included +in case the new code is intended to be later included in LAMMPS directly. diff --git a/doc/src/commands_list.rst b/doc/src/commands_list.rst index 2ec20ac220..e30d5c52dc 100644 --- a/doc/src/commands_list.rst +++ b/doc/src/commands_list.rst @@ -77,6 +77,7 @@ Commands pair_style pair_write partition + plugin prd print processors From dfe4f7a49d353a22c1c9cd56f2027e0b3a9d9ef3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 19:33:50 -0500 Subject: [PATCH 0166/1217] small tweaks and simplify --- examples/plugins/morse2plugin.cpp | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/examples/plugins/morse2plugin.cpp b/examples/plugins/morse2plugin.cpp index cfb6689cae..286aa30c35 100644 --- a/examples/plugins/morse2plugin.cpp +++ b/examples/plugins/morse2plugin.cpp @@ -1,7 +1,6 @@ #include "lammpsplugin.h" -#include "lammps.h" #include "version.h" #include @@ -21,12 +20,12 @@ static Pair *morse2ompcreator(LAMMPS *lmp) return new PairMorse2OMP(lmp); } -static lammpsplugin_t plugin; extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) { - // register plain morse2 pair style + lammpsplugin_t plugin; lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; - memset(&plugin,0,sizeof(lammpsplugin_t)); + + // register plain morse2 pair style plugin.version = LAMMPS_VERSION; plugin.style = "pair"; plugin.name = "morse2"; @@ -34,11 +33,11 @@ extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; plugin.creator = (lammpsplugin_factory *) &morse2creator; plugin.handle = handle; - register_plugin(&plugin,lmp); + (*register_plugin)(&plugin,lmp); // also register morse2/omp pair style. only need to update changed fields plugin.name = "morse2/omp"; plugin.info = "Morse2 variant pair style for OpenMP v1.0"; plugin.creator = (lammpsplugin_factory *) &morse2ompcreator; - register_plugin(&plugin,lmp); + (*register_plugin)(&plugin,lmp); } From b252946fba664c51e92a508b49a96ffd0ace0717 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 19:34:13 -0500 Subject: [PATCH 0167/1217] now fix windows compile for real --- src/plugin.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/plugin.cpp b/src/plugin.cpp index 7e7bd6e86f..07e3c60dd0 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -222,7 +222,9 @@ namespace LAMMPS_NS -- dso_refcounter[handle]; if (dso_refcounter[handle] == 0) { +#ifndef WIN32 dlclose(handle); +#endif } } } From f982d98574269cd4e04db9616664f1758b1cb83d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 19:34:28 -0500 Subject: [PATCH 0168/1217] small tweaks --- examples/plugins/Makefile | 2 +- src/plugin.cpp | 5 ++--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/examples/plugins/Makefile b/examples/plugins/Makefile index 2f563f924e..5d60ae8651 100644 --- a/examples/plugins/Makefile +++ b/examples/plugins/Makefile @@ -1,5 +1,5 @@ CXX=mpicxx -CXXFLAGS=-I../../src -Wall -O3 -fPIC -I../../src/USER-OMP -fopenmp +CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp LD=$(CXX) -shared -rdynamic -fopenmp morse2plugin.so: morse2plugin.o pair_morse2.o pair_morse2_omp.o diff --git a/src/plugin.cpp b/src/plugin.cpp index 07e3c60dd0..f2499e6528 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -58,9 +58,8 @@ namespace LAMMPS_NS void *initfunc = dlsym(dso,"lammpsplugin_init"); if (initfunc == nullptr) { -#ifndef WIN32 dlclose(dso); -#endif + if (me == 0) utils::logmesg(lmp,fmt::format("Plugin symbol lookup failure in " "file {}\n",file)); @@ -182,7 +181,7 @@ namespace LAMMPS_NS if (idx < 0) { if (me == 0) utils::logmesg(lmp,fmt::format("Ignoring unload of {} style {}: not " - "loaded from a plugin", style, name)); + "loaded from a plugin\n", style, name)); return; } From 9209cbba92a9a271b8642a86b766b4e507f9d2ee Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 21:19:04 -0500 Subject: [PATCH 0169/1217] add support for loading plugins for fixes --- doc/src/Developer_plugins.rst | 41 ++++++- examples/plugins/Makefile | 8 ++ examples/plugins/fix_nve2.cpp | 171 ++++++++++++++++++++++++++++++ examples/plugins/fix_nve2.h | 58 ++++++++++ examples/plugins/morse2plugin.cpp | 5 +- examples/plugins/nve2plugin.cpp | 30 ++++++ src/lammpsplugin.h | 6 +- src/plugin.cpp | 14 ++- 8 files changed, 325 insertions(+), 8 deletions(-) create mode 100644 examples/plugins/fix_nve2.cpp create mode 100644 examples/plugins/fix_nve2.h create mode 100644 examples/plugins/nve2plugin.cpp diff --git a/doc/src/Developer_plugins.rst b/doc/src/Developer_plugins.rst index ffbcf8a667..59402165d1 100644 --- a/doc/src/Developer_plugins.rst +++ b/doc/src/Developer_plugins.rst @@ -57,17 +57,54 @@ function would look like this: plugin.name = "morse2"; plugin.info = "Morse2 variant pair style v1.0"; plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; - plugin.creator = (lammpsplugin_factory *) &morse2creator; + plugin.creator1 = (lammpsplugin_factory1 *) &morse2creator; + plugin.creator2 = nullptr; plugin.handle = handle; (*register_plugin)(&plugin,lmp); } The factory function in this example is called ``morse2creator()``. It -receives a pointer to the LAMMPS class as argument and returns a +receives a pointer to the LAMMPS class as only argument and thus has to +be assigned to the *creator1* member of the plugin struct and cast to the +``lammpsplugin_factory1`` pointer type. It returns a pointer to the allocated class instance derived from the ``Pair`` class. This function may be declared static to avoid clashes with other plugins. The name of the derived class, ``PairMorse2``, must be unique inside the entire LAMMPS executable. +If the factory function would be for a fix or compute, which take three +arguments (a pointer to the LAMMPS class, the number of arguments and the +list of argument strings), then the pointer type is ``lammpsplugin_factory2`` +and it must be assigned to the *creator2* member of the plugin struct. +Below is an example for that: + +.. code-block:: C++ + + #include "lammpsplugin.h" + #include "version.h" + #include "fix_nve2.h" + + using namespace LAMMPS_NS; + + static Fix *nve2creator(LAMMPS *lmp, int argc, char **argv) + { + return new FixNVE2(lmp,argc,argv); + } + + extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) + { + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + lammpsplugin_t plugin; + + plugin.version = LAMMPS_VERSION; + plugin.style = "fix"; + plugin.name = "nve2"; + plugin.info = "NVE2 variant fix style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator1 = nullptr; + plugin.creator2 = (lammpsplugin_factory2 *) &nve2creator; + plugin.handle = handle; + (*register_plugin)(&plugin,lmp); + } The initialization function **must** be called ``lammpsplugin_init``, it **must** have C bindings and it takes three void pointers as arguments. diff --git a/examples/plugins/Makefile b/examples/plugins/Makefile index 5d60ae8651..c8ec554d5d 100644 --- a/examples/plugins/Makefile +++ b/examples/plugins/Makefile @@ -2,9 +2,14 @@ CXX=mpicxx CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp LD=$(CXX) -shared -rdynamic -fopenmp +default: morse2plugin.so nve2plugin.so + morse2plugin.so: morse2plugin.o pair_morse2.o pair_morse2_omp.o $(LD) -o $@ $^ +nve2plugin.so: nve2plugin.o fix_nve2.o + $(LD) -o $@ $^ + .cpp.o: $(CXX) -o $@ $(CXXFLAGS) -c $< @@ -12,6 +17,9 @@ pair_morse2.o: pair_morse2.cpp pair_morse2.h pair_morse2_omp.o: pair_morse2_omp.cpp pair_morse2_omp.h pair_morse2.h morse2plugin.o: morse2plugin.cpp pair_morse2.h pair_morse2_omp.h +fix_nve2.o: fix_nve2.cpp fix_nve2.h +nve2plugin.o: nve2plugin.cpp fix_nve2.h + clean: rm -f *~ *.so *.o log.lammps diff --git a/examples/plugins/fix_nve2.cpp b/examples/plugins/fix_nve2.cpp new file mode 100644 index 0000000000..bb6f53b810 --- /dev/null +++ b/examples/plugins/fix_nve2.cpp @@ -0,0 +1,171 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_nve2.h" +#include +#include "atom.h" +#include "force.h" +#include "update.h" +#include "respa.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixNVE2::FixNVE2(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (strcmp(style,"nve/sphere") != 0 && narg < 3) + error->all(FLERR,"Illegal fix nve command"); + + dynamic_group_allow = 1; + time_integrate = 1; +} + +/* ---------------------------------------------------------------------- */ + +int FixNVE2::setmask() +{ + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= FINAL_INTEGRATE; + mask |= INITIAL_INTEGRATE_RESPA; + mask |= FINAL_INTEGRATE_RESPA; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixNVE2::init() +{ + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; + + if (strstr(update->integrate_style,"respa")) + step_respa = ((Respa *) update->integrate)->step; +} + +/* ---------------------------------------------------------------------- + allow for both per-type and per-atom mass +------------------------------------------------------------------------- */ + +void FixNVE2::initial_integrate(int /*vflag*/) +{ + double dtfm; + + // update v and x of atoms in group + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + if (rmass) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = dtf / rmass[i]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixNVE2::final_integrate() +{ + double dtfm; + + // update v of atoms in group + + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + if (rmass) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = dtf / rmass[i]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixNVE2::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) +{ + dtv = step_respa[ilevel]; + dtf = 0.5 * step_respa[ilevel] * force->ftm2v; + + // innermost level - NVE update of v and x + // all other levels - NVE update of v + + if (ilevel == 0) initial_integrate(vflag); + else final_integrate(); +} + +/* ---------------------------------------------------------------------- */ + +void FixNVE2::final_integrate_respa(int ilevel, int /*iloop*/) +{ + dtf = 0.5 * step_respa[ilevel] * force->ftm2v; + final_integrate(); +} + +/* ---------------------------------------------------------------------- */ + +void FixNVE2::reset_dt() +{ + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; +} diff --git a/examples/plugins/fix_nve2.h b/examples/plugins/fix_nve2.h new file mode 100644 index 0000000000..f1b2244128 --- /dev/null +++ b/examples/plugins/fix_nve2.h @@ -0,0 +1,58 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(nve2,FixNVE2) + +#else + +#ifndef LMP_FIX_NVE2_H +#define LMP_FIX_NVE2_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixNVE2 : public Fix { + public: + FixNVE2(class LAMMPS *, int, char **); + virtual ~FixNVE2() {} + int setmask(); + virtual void init(); + virtual void initial_integrate(int); + virtual void final_integrate(); + virtual void initial_integrate_respa(int, int, int); + virtual void final_integrate_respa(int, int); + virtual void reset_dt(); + + protected: + double dtv,dtf; + double *step_respa; + int mass_require; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ diff --git a/examples/plugins/morse2plugin.cpp b/examples/plugins/morse2plugin.cpp index 286aa30c35..7151e35cd2 100644 --- a/examples/plugins/morse2plugin.cpp +++ b/examples/plugins/morse2plugin.cpp @@ -31,13 +31,14 @@ extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) plugin.name = "morse2"; plugin.info = "Morse2 variant pair style v1.0"; plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; - plugin.creator = (lammpsplugin_factory *) &morse2creator; + plugin.creator1 = (lammpsplugin_factory1 *) &morse2creator; + plugin.creator2 = nullptr; plugin.handle = handle; (*register_plugin)(&plugin,lmp); // also register morse2/omp pair style. only need to update changed fields plugin.name = "morse2/omp"; plugin.info = "Morse2 variant pair style for OpenMP v1.0"; - plugin.creator = (lammpsplugin_factory *) &morse2ompcreator; + plugin.creator1 = (lammpsplugin_factory1 *) &morse2ompcreator; (*register_plugin)(&plugin,lmp); } diff --git a/examples/plugins/nve2plugin.cpp b/examples/plugins/nve2plugin.cpp new file mode 100644 index 0000000000..9c9ce3d8d2 --- /dev/null +++ b/examples/plugins/nve2plugin.cpp @@ -0,0 +1,30 @@ + +#include "lammpsplugin.h" + +#include "version.h" + +#include + +#include "fix_nve2.h" + +using namespace LAMMPS_NS; + +static Fix *nve2creator(LAMMPS *lmp, int argc, char **argv) +{ + return new FixNVE2(lmp, argc, argv); +} + +extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) +{ + lammpsplugin_t plugin; + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + + plugin.version = LAMMPS_VERSION; + plugin.style = "fix"; + plugin.name = "nve2"; + plugin.info = "NVE2 variant fix style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator2 = (lammpsplugin_factory2 *) &nve2creator; + plugin.handle = handle; + (*register_plugin)(&plugin,lmp); +} diff --git a/src/lammpsplugin.h b/src/lammpsplugin.h index 34a0b60811..958235fdaa 100644 --- a/src/lammpsplugin.h +++ b/src/lammpsplugin.h @@ -18,7 +18,8 @@ extern "C" { - typedef void *(lammpsplugin_factory)(void *); + typedef void *(lammpsplugin_factory1)(void *); + typedef void *(lammpsplugin_factory2)(void *, int, char **); typedef struct { const char *version; @@ -26,7 +27,8 @@ extern "C" { const char *name; const char *info; const char *author; - lammpsplugin_factory *creator; + lammpsplugin_factory1 *creator1; + lammpsplugin_factory2 *creator2; void *handle; } lammpsplugin_t; diff --git a/src/plugin.cpp b/src/plugin.cpp index f2499e6528..7a42734bd9 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -114,10 +114,20 @@ namespace LAMMPS_NS plugin->name)); } - (*pair_map)[plugin->name] = (Force::PairCreator)plugin->creator; + (*pair_map)[plugin->name] = (Force::PairCreator)plugin->creator1; + } else if (pstyle == "fix") { + auto fix_map = lmp->modify->fix_map; + if (fix_map->find(plugin->name) != fix_map->end()) { + if (lmp->comm->me == 0) + lmp->error->warning(FLERR,fmt::format("Overriding built-in fix " + "style {} from plugin", + plugin->name)); + } + + (*fix_map)[plugin->name] = (Modify::FixCreator)plugin->creator2; } else { utils::logmesg(lmp,fmt::format("Loading plugin for {} styles not " - "yet implemented\n", pstyle)); + "yet implemented\n",pstyle)); pluginlist.pop_back(); } } From 3d1c6b30af02a2e375be66de98180d6609bf6fab Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 21:19:29 -0500 Subject: [PATCH 0170/1217] refuse to load a plugin over an existing plugin for the same style --- src/plugin.cpp | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/src/plugin.cpp b/src/plugin.cpp index 7a42734bd9..d2ea0943ad 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -86,14 +86,25 @@ namespace LAMMPS_NS int me = lmp->comm->me; if (plugin == nullptr) return; + + // ignore load request if same plugin already loaded + int idx = plugin_find(plugin->style,plugin->name); + if (idx >= 0) { + if (me == 0) + utils::logmesg(lmp,fmt::format("Ignoring load of {} style {}: must " + "unload existing {} plugin first\n", + plugin->style,plugin->name,plugin->name)); + return; + } + if (me == 0) { utils::logmesg(lmp,fmt::format("Loading plugin: {} by {}\n", - plugin->info, plugin->author)); + plugin->info,plugin->author)); // print version info only if the versions of host and plugin don't match if ((plugin->version) && (strcmp(plugin->version,lmp->version) != 0)) utils::logmesg(lmp,fmt::format(" compiled for LAMMPS version {} " "loaded into LAMMPS version {}\n", - plugin->version, lmp->version)); + plugin->version,lmp->version)); } pluginlist.push_back(*plugin); @@ -191,7 +202,7 @@ namespace LAMMPS_NS if (idx < 0) { if (me == 0) utils::logmesg(lmp,fmt::format("Ignoring unload of {} style {}: not " - "loaded from a plugin\n", style, name)); + "loaded from a plugin\n",style,name)); return; } From 620dd09509b9ec7cbecbe1c0acc971e242617f19 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 21:36:14 -0500 Subject: [PATCH 0171/1217] delete active fixes when unloading fix style plugin --- src/plugin.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/plugin.cpp b/src/plugin.cpp index d2ea0943ad..0eece6793e 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -236,6 +236,10 @@ namespace LAMMPS_NS lmp->force->create_pair("none",0); } } + } else if (pstyle == "fix") { + for (int ifix = lmp->modify->find_fix_by_style(name); + ifix >= 0; ifix = lmp->modify->find_fix_by_style(name)) + lmp->modify->delete_fix(ifix); } // if reference count is down to zero, close DSO handle. From 347db1458daa89f5ec9ef743d32c625f2b3aaf1e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 22:34:23 -0500 Subject: [PATCH 0172/1217] always link with libdl.so/.a or equivalent except on windows --- cmake/CMakeLists.txt | 5 +++++ cmake/Modules/Packages/USER-MOLFILE.cmake | 4 ---- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 06600d02c4..7081d6aa80 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -240,6 +240,11 @@ if(BUILD_OMP) target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX) endif() +# link with -ldl or equivalent for plugin loading; except on Windows +if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS}) +endif() + # Compiler specific features for testing if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF) diff --git a/cmake/Modules/Packages/USER-MOLFILE.cmake b/cmake/Modules/Packages/USER-MOLFILE.cmake index 4d414acead..427f0ed6fa 100644 --- a/cmake/Modules/Packages/USER-MOLFILE.cmake +++ b/cmake/Modules/Packages/USER-MOLFILE.cmake @@ -2,8 +2,4 @@ set(MOLFILE_INCLUDE_DIR "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to set(MOLFILE_INCLUDE_DIRS "${MOLFILE_INCLUDE_DIR}") add_library(molfile INTERFACE) target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS}) -# no need to link with -ldl on windows -if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") - target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS}) -endif() target_link_libraries(lammps PRIVATE molfile) From 256c478a6bae76c044efb7c262e858b547f3c286 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 22:34:47 -0500 Subject: [PATCH 0173/1217] reorder functions and make header and implemention order consistent --- src/plugin.cpp | 132 +++++++++++++++++++++++++++---------------------- src/plugin.h | 11 +++-- 2 files changed, 80 insertions(+), 63 deletions(-) diff --git a/src/plugin.cpp b/src/plugin.cpp index 0eece6793e..85870952e9 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -31,9 +31,10 @@ namespace LAMMPS_NS { - // store list of plugin information data for loaded styles + // list of plugin information data for loaded styles static std::list pluginlist; - // map of dso handles + + // map for counting references to dso handles static std::map dso_refcounter; // load DSO and call included registration function @@ -44,7 +45,7 @@ namespace LAMMPS_NS lmp->error->all(FLERR,"Loading of plugins on Windows not yet supported\n"); #else - // open DSO file from given path load symbols globally + // open DSO file from given path; load symbols globally void *dso = dlopen(file,RTLD_NOW|RTLD_GLOBAL); if (dso == nullptr) { @@ -54,7 +55,8 @@ namespace LAMMPS_NS return; } - // look up lammpsplugin_init() function in DSO. must have C bindings. + // look up lammpsplugin_init() function in DSO + // function must have C bindings so there is no name mangling void *initfunc = dlsym(dso,"lammpsplugin_init"); if (initfunc == nullptr) { @@ -70,15 +72,17 @@ namespace LAMMPS_NS // to the LAMMPS instance, the DSO handle (for reference counting) // and plugin registration function pointer - ((lammpsplugin_initfunc)(initfunc))((void *)lmp, dso, - (void *)&plugin_register); + (*(lammpsplugin_initfunc)(initfunc))((void *)lmp, dso, + (void *)&plugin_register); #endif } - // register a new style from a plugin with LAMMPS - // this is the callback function that is called from within - // the plugin initializer function. all plugin information - // is taken from the lammpsplugin_t struct. + /* -------------------------------------------------------------------- + register a new style from a plugin with LAMMPS + this is the callback function that is called from within + the plugin initializer function. all plugin information + is taken from the lammpsplugin_t struct. + -------------------------------------------------------------------- */ void plugin_register(lammpsplugin_t *plugin, void *ptr) { @@ -143,55 +147,11 @@ namespace LAMMPS_NS } } - // number of styles loaded from plugin files - - int plugin_get_num_plugins() - { - return pluginlist.size(); - } - - // return position index in list of given plugin of given style - - int plugin_find(const char *style, const char *name) - { - int i=0; - for (auto entry : pluginlist) { - if ((strcmp(style,entry.style) == 0) - && (strcmp(name,entry.name) == 0)) - return i; - ++i; - } - return -1; - } - - // get pointer to plugin initializer struct at position idx - - const lammpsplugin_t *plugin_get_info(int idx) - { - int i=0; - for (auto p=pluginlist.begin(); p != pluginlist.end(); ++p) { - if (i == idx) return &(*p); - ++i; - } - return nullptr; - } - - // remove plugin of given name and style from internal lists - - void plugin_erase(const char *style, const char *name) - { - for (auto p=pluginlist.begin(); p != pluginlist.end(); ++p) { - if ((strcmp(style,p->style) == 0) - && (strcmp(name,p->name) == 0)) { - pluginlist.erase(p); - return; - } - } - } - - // remove plugin from given style table and plugin list. - // optionally close the DSO handle if last plugin from that DSO - // must delete style instance if style is currently active. + /* -------------------------------------------------------------------- + remove plugin from given style table and plugin list + optionally close the DSO handle if it is the last plugin from that DSO + must also delete style instances if style is currently active + -------------------------------------------------------------------- */ void plugin_unload(const char *style, const char *name, LAMMPS *lmp) { @@ -251,4 +211,58 @@ namespace LAMMPS_NS #endif } } + + /* -------------------------------------------------------------------- + remove plugin of given name and style from internal lists + -------------------------------------------------------------------- */ + + void plugin_erase(const char *style, const char *name) + { + for (auto p=pluginlist.begin(); p != pluginlist.end(); ++p) { + if ((strcmp(style,p->style) == 0) + && (strcmp(name,p->name) == 0)) { + pluginlist.erase(p); + return; + } + } + } + + /* -------------------------------------------------------------------- + number of styles loaded from plugin files + -------------------------------------------------------------------- */ + + int plugin_get_num_plugins() + { + return pluginlist.size(); + } + + /* -------------------------------------------------------------------- + return position index in list of given plugin of given style + -------------------------------------------------------------------- */ + + int plugin_find(const char *style, const char *name) + { + int i=0; + for (auto entry : pluginlist) { + if ((strcmp(style,entry.style) == 0) + && (strcmp(name,entry.name) == 0)) + return i; + ++i; + } + return -1; + } + + /* -------------------------------------------------------------------- + get pointer to plugin initializer struct at position idx + -------------------------------------------------------------------- */ + + const lammpsplugin_t *plugin_get_info(int idx) + { + int i=0; + for (auto p=pluginlist.begin(); p != pluginlist.end(); ++p) { + if (i == idx) return &(*p); + ++i; + } + return nullptr; + } } diff --git a/src/plugin.h b/src/plugin.h index 172b2f0c37..32a5a280a1 100644 --- a/src/plugin.h +++ b/src/plugin.h @@ -19,13 +19,16 @@ namespace LAMMPS_NS { class LAMMPS; + void plugin_load(const char *, LAMMPS *); void plugin_register(lammpsplugin_t *, void *); - int plugin_get_num_plugins(); - const lammpsplugin_t *plugin_get_info(int); - int plugin_find(const char *, const char *); - void plugin_erase(const char *, const char *); + void plugin_unload(const char *, const char *, LAMMPS *); + void plugin_erase(const char *, const char *); + + int plugin_get_num_plugins(); + int plugin_find(const char *, const char *); + const lammpsplugin_t *plugin_get_info(int); } #endif From 83583c465eb6f2b88d7eb12befb8b65e5065e508 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 22:58:22 -0500 Subject: [PATCH 0174/1217] add support for command plugins with example --- examples/plugins/Makefile | 8 +++-- examples/plugins/helloplugin.cpp | 49 +++++++++++++++++++++++++++++++ examples/plugins/morse2plugin.cpp | 1 + examples/plugins/nve2plugin.cpp | 2 ++ src/lammpsplugin.h | 2 ++ src/plugin.cpp | 15 ++++++++-- 6 files changed, 73 insertions(+), 4 deletions(-) create mode 100644 examples/plugins/helloplugin.cpp diff --git a/examples/plugins/Makefile b/examples/plugins/Makefile index c8ec554d5d..bf6bc804be 100644 --- a/examples/plugins/Makefile +++ b/examples/plugins/Makefile @@ -2,7 +2,10 @@ CXX=mpicxx CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp LD=$(CXX) -shared -rdynamic -fopenmp -default: morse2plugin.so nve2plugin.so +default: morse2plugin.so nve2plugin.so helloplugin.so + +helloplugin.so: helloplugin.o + $(LD) -o $@ $^ morse2plugin.so: morse2plugin.o pair_morse2.o pair_morse2_omp.o $(LD) -o $@ $^ @@ -13,6 +16,8 @@ nve2plugin.so: nve2plugin.o fix_nve2.o .cpp.o: $(CXX) -o $@ $(CXXFLAGS) -c $< +helloplugin.o: helloplugin.cpp + pair_morse2.o: pair_morse2.cpp pair_morse2.h pair_morse2_omp.o: pair_morse2_omp.cpp pair_morse2_omp.h pair_morse2.h morse2plugin.o: morse2plugin.cpp pair_morse2.h pair_morse2_omp.h @@ -23,4 +28,3 @@ nve2plugin.o: nve2plugin.cpp fix_nve2.h clean: rm -f *~ *.so *.o log.lammps - diff --git a/examples/plugins/helloplugin.cpp b/examples/plugins/helloplugin.cpp new file mode 100644 index 0000000000..1c9d0c2779 --- /dev/null +++ b/examples/plugins/helloplugin.cpp @@ -0,0 +1,49 @@ + +#include "lammpsplugin.h" + +#include "comm.h" +#include "error.h" +#include "pointers.h" +#include "version.h" + +#include + +namespace LAMMPS_NS { + class Hello : protected Pointers { + public: + Hello(class LAMMPS *lmp) : Pointers(lmp) {}; + void command(int, char **); + }; +} + +using namespace LAMMPS_NS; + +void Hello::command(int argc, char **argv) +{ + if (argc != 1) error->all(FLERR,"Illegal hello command"); + if (comm->me == 0) + utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0])); +} + +static void hellocreator(LAMMPS *lmp, int argc, char **argv) +{ + Hello hello(lmp); + hello.command(argc,argv); +} + +extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) +{ + lammpsplugin_t plugin; + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + + plugin.version = LAMMPS_VERSION; + plugin.style = "command"; + plugin.name = "hello"; + plugin.info = "Hello world command v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator1 = nullptr; + plugin.creator2 = nullptr; + plugin.creator3 = (lammpsplugin_factory3 *) &hellocreator; + plugin.handle = handle; + (*register_plugin)(&plugin,lmp); +} diff --git a/examples/plugins/morse2plugin.cpp b/examples/plugins/morse2plugin.cpp index 7151e35cd2..dfc341e0c0 100644 --- a/examples/plugins/morse2plugin.cpp +++ b/examples/plugins/morse2plugin.cpp @@ -33,6 +33,7 @@ extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; plugin.creator1 = (lammpsplugin_factory1 *) &morse2creator; plugin.creator2 = nullptr; + plugin.creator3 = nullptr; plugin.handle = handle; (*register_plugin)(&plugin,lmp); diff --git a/examples/plugins/nve2plugin.cpp b/examples/plugins/nve2plugin.cpp index 9c9ce3d8d2..785ec8dbe1 100644 --- a/examples/plugins/nve2plugin.cpp +++ b/examples/plugins/nve2plugin.cpp @@ -24,7 +24,9 @@ extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) plugin.name = "nve2"; plugin.info = "NVE2 variant fix style v1.0"; plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator1 = nullptr; plugin.creator2 = (lammpsplugin_factory2 *) &nve2creator; + plugin.creator3 = nullptr; plugin.handle = handle; (*register_plugin)(&plugin,lmp); } diff --git a/src/lammpsplugin.h b/src/lammpsplugin.h index 958235fdaa..3de2bcdcdf 100644 --- a/src/lammpsplugin.h +++ b/src/lammpsplugin.h @@ -20,6 +20,7 @@ extern "C" { typedef void *(lammpsplugin_factory1)(void *); typedef void *(lammpsplugin_factory2)(void *, int, char **); + typedef void (lammpsplugin_factory3)(void *, int, char **); typedef struct { const char *version; @@ -29,6 +30,7 @@ extern "C" { const char *author; lammpsplugin_factory1 *creator1; lammpsplugin_factory2 *creator2; + lammpsplugin_factory3 *creator3; void *handle; } lammpsplugin_t; diff --git a/src/plugin.cpp b/src/plugin.cpp index 85870952e9..ea1c46b705 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -15,6 +15,7 @@ #include "comm.h" #include "error.h" +#include "input.h" #include "force.h" #include "lammps.h" #include "modify.h" @@ -128,8 +129,8 @@ namespace LAMMPS_NS "style {} from plugin", plugin->name)); } - (*pair_map)[plugin->name] = (Force::PairCreator)plugin->creator1; + } else if (pstyle == "fix") { auto fix_map = lmp->modify->fix_map; if (fix_map->find(plugin->name) != fix_map->end()) { @@ -138,8 +139,18 @@ namespace LAMMPS_NS "style {} from plugin", plugin->name)); } - (*fix_map)[plugin->name] = (Modify::FixCreator)plugin->creator2; + + } else if (pstyle == "command") { + auto command_map = lmp->input->command_map; + if (command_map->find(plugin->name) != command_map->end()) { + if (lmp->comm->me == 0) + lmp->error->warning(FLERR,fmt::format("Overriding built-in fix " + "style {} from plugin", + plugin->name)); + } + (*command_map)[plugin->name] = (Input::CommandCreator)plugin->creator3; + } else { utils::logmesg(lmp,fmt::format("Loading plugin for {} styles not " "yet implemented\n",pstyle)); From dde00ab344340ffbf29fb5eb34462f1a8439319e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 23:10:26 -0500 Subject: [PATCH 0175/1217] add plugin command documentation --- doc/src/plugin.rst | 76 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 doc/src/plugin.rst diff --git a/doc/src/plugin.rst b/doc/src/plugin.rst new file mode 100644 index 0000000000..42d53aabe3 --- /dev/null +++ b/doc/src/plugin.rst @@ -0,0 +1,76 @@ +.. index:: plugin + +plugin command +============== + +Syntax +"""""" + +.. parsed-literal:: + + plugin command args + +* command = *load* or *unload* or *list* +* args = list of arguments for a particular plugin command + + .. parsed-literal:: + + *load* file = load plugin(s) from shared object in *file* + *unload* style name = unload plugin *name* of style *style* + *list* = print a list of currently loaded plugins + +Examples +"""""""" + +.. code-block:: LAMMPS + + plugin load morse2plugin.so + plugin unload pair morse2/omp + plugin list + +Description +""""""""""" + +The plugin command allows to load (and unload) additional styles and +commands into a LAMMPS binary from so-called dynamic shared object (DSO) +files. This enables to add new functionality to an existing LAMMPS +binary without having to recompile and link the entire executable. + +The *load* command will load and initialize all plugins contained in the +plugin DSO with the given filename. A message with information the +plugin style and name and more will be printed. Individual DSO files +may contain multiple plugins. More details about how to write and +compile the plugin DSO is given in programmer's guide part of the manual +under :doc:`Developer_plugins`. + +The *unload* command will remove the given style or the given name from +the list of available styles. If the plugin style is currently in use, +that style instance will be deleted. + +The *list* command will print a list of the loaded plugins and their +styles and names. + + +Restrictions +"""""""""""" + +Plugins are currently not available on Windows. + +Plugins are dependent on the LAMMPS binary interface (ABI) +and particularly the MPI library used. So they are not guaranteed +to work when the plugin was compiled with a different MPI library +or different compilation settings or a different LAMMPS version. +If there is a mismatch the *plugin* command may fail to load the +plugin(s) or data corruption or crashes may happen. + + +Related commands +"""""""""""""""" + +none + + +Default +""""""" + +none From 524c62994eba5be3c1786ffaab32fc8d3edf9226 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 23:12:00 -0500 Subject: [PATCH 0176/1217] update docs --- doc/src/plugin.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/src/plugin.rst b/doc/src/plugin.rst index 42d53aabe3..25a55565b9 100644 --- a/doc/src/plugin.rst +++ b/doc/src/plugin.rst @@ -17,6 +17,7 @@ Syntax *load* file = load plugin(s) from shared object in *file* *unload* style name = unload plugin *name* of style *style* + *style* = *pair* or *fix* or *command* *list* = print a list of currently loaded plugins Examples @@ -26,6 +27,7 @@ Examples plugin load morse2plugin.so plugin unload pair morse2/omp + plugin unload command hello plugin list Description From d95d5f19547a88dc595922f5254c4b308ec643ac Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 23:52:35 -0500 Subject: [PATCH 0177/1217] store different factory variants in a union --- examples/plugins/helloplugin.cpp | 4 +--- examples/plugins/morse2plugin.cpp | 6 ++---- examples/plugins/nve2plugin.cpp | 4 +--- src/lammpsplugin.h | 8 +++++--- src/plugin.cpp | 6 +++--- 5 files changed, 12 insertions(+), 16 deletions(-) diff --git a/examples/plugins/helloplugin.cpp b/examples/plugins/helloplugin.cpp index 1c9d0c2779..11f2cfb891 100644 --- a/examples/plugins/helloplugin.cpp +++ b/examples/plugins/helloplugin.cpp @@ -41,9 +41,7 @@ extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) plugin.name = "hello"; plugin.info = "Hello world command v1.0"; plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; - plugin.creator1 = nullptr; - plugin.creator2 = nullptr; - plugin.creator3 = (lammpsplugin_factory3 *) &hellocreator; + plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator; plugin.handle = handle; (*register_plugin)(&plugin,lmp); } diff --git a/examples/plugins/morse2plugin.cpp b/examples/plugins/morse2plugin.cpp index dfc341e0c0..a4151dcc3d 100644 --- a/examples/plugins/morse2plugin.cpp +++ b/examples/plugins/morse2plugin.cpp @@ -31,15 +31,13 @@ extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) plugin.name = "morse2"; plugin.info = "Morse2 variant pair style v1.0"; plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; - plugin.creator1 = (lammpsplugin_factory1 *) &morse2creator; - plugin.creator2 = nullptr; - plugin.creator3 = nullptr; + plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2creator; plugin.handle = handle; (*register_plugin)(&plugin,lmp); // also register morse2/omp pair style. only need to update changed fields plugin.name = "morse2/omp"; plugin.info = "Morse2 variant pair style for OpenMP v1.0"; - plugin.creator1 = (lammpsplugin_factory1 *) &morse2ompcreator; + plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2ompcreator; (*register_plugin)(&plugin,lmp); } diff --git a/examples/plugins/nve2plugin.cpp b/examples/plugins/nve2plugin.cpp index 785ec8dbe1..d17db1dfc7 100644 --- a/examples/plugins/nve2plugin.cpp +++ b/examples/plugins/nve2plugin.cpp @@ -24,9 +24,7 @@ extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) plugin.name = "nve2"; plugin.info = "NVE2 variant fix style v1.0"; plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; - plugin.creator1 = nullptr; - plugin.creator2 = (lammpsplugin_factory2 *) &nve2creator; - plugin.creator3 = nullptr; + plugin.creator.v2 = (lammpsplugin_factory2 *) &nve2creator; plugin.handle = handle; (*register_plugin)(&plugin,lmp); } diff --git a/src/lammpsplugin.h b/src/lammpsplugin.h index 3de2bcdcdf..1baed9799d 100644 --- a/src/lammpsplugin.h +++ b/src/lammpsplugin.h @@ -28,9 +28,11 @@ extern "C" { const char *name; const char *info; const char *author; - lammpsplugin_factory1 *creator1; - lammpsplugin_factory2 *creator2; - lammpsplugin_factory3 *creator3; + union { + lammpsplugin_factory1 *v1; + lammpsplugin_factory2 *v2; + lammpsplugin_factory3 *v3; + } creator; void *handle; } lammpsplugin_t; diff --git a/src/plugin.cpp b/src/plugin.cpp index ea1c46b705..a95fde5b73 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -129,7 +129,7 @@ namespace LAMMPS_NS "style {} from plugin", plugin->name)); } - (*pair_map)[plugin->name] = (Force::PairCreator)plugin->creator1; + (*pair_map)[plugin->name] = (Force::PairCreator)plugin->creator.v1; } else if (pstyle == "fix") { auto fix_map = lmp->modify->fix_map; @@ -139,7 +139,7 @@ namespace LAMMPS_NS "style {} from plugin", plugin->name)); } - (*fix_map)[plugin->name] = (Modify::FixCreator)plugin->creator2; + (*fix_map)[plugin->name] = (Modify::FixCreator)plugin->creator.v2; } else if (pstyle == "command") { auto command_map = lmp->input->command_map; @@ -149,7 +149,7 @@ namespace LAMMPS_NS "style {} from plugin", plugin->name)); } - (*command_map)[plugin->name] = (Input::CommandCreator)plugin->creator3; + (*command_map)[plugin->name] = (Input::CommandCreator)plugin->creator.v3; } else { utils::logmesg(lmp,fmt::format("Loading plugin for {} styles not " From 930c0fca30fc24a3180d0ded815b8716063e5af4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Mar 2021 23:59:23 -0500 Subject: [PATCH 0178/1217] must link with -ldl --- src/MAKE/Makefile.mpi | 2 +- src/MAKE/Makefile.serial | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/MAKE/Makefile.mpi b/src/MAKE/Makefile.mpi index db134de68a..c66e66c217 100644 --- a/src/MAKE/Makefile.mpi +++ b/src/MAKE/Makefile.mpi @@ -13,7 +13,7 @@ DEPFLAGS = -M LINK = mpicxx LINKFLAGS = -g -O3 -LIB = +LIB = -ldl SIZE = size ARCHIVE = ar diff --git a/src/MAKE/Makefile.serial b/src/MAKE/Makefile.serial index a0b2959c4b..daf04cc5b0 100644 --- a/src/MAKE/Makefile.serial +++ b/src/MAKE/Makefile.serial @@ -13,7 +13,7 @@ DEPFLAGS = -M LINK = g++ LINKFLAGS = -g -O -LIB = +LIB = -ldl SIZE = size ARCHIVE = ar From a2bcd7fe68f0501733da98c9f941bae9f514b4f5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Mar 2021 00:07:52 -0500 Subject: [PATCH 0179/1217] programmer documentation update --- doc/src/Developer_plugins.rst | 64 +++++++++++++++++++++++++++++++---- 1 file changed, 58 insertions(+), 6 deletions(-) diff --git a/doc/src/Developer_plugins.rst b/doc/src/Developer_plugins.rst index 59402165d1..192c57ccbb 100644 --- a/doc/src/Developer_plugins.rst +++ b/doc/src/Developer_plugins.rst @@ -57,15 +57,14 @@ function would look like this: plugin.name = "morse2"; plugin.info = "Morse2 variant pair style v1.0"; plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; - plugin.creator1 = (lammpsplugin_factory1 *) &morse2creator; - plugin.creator2 = nullptr; + plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2creator; plugin.handle = handle; (*register_plugin)(&plugin,lmp); } The factory function in this example is called ``morse2creator()``. It receives a pointer to the LAMMPS class as only argument and thus has to -be assigned to the *creator1* member of the plugin struct and cast to the +be assigned to the *creator.v1* member of the plugin struct and cast to the ``lammpsplugin_factory1`` pointer type. It returns a pointer to the allocated class instance derived from the ``Pair`` class. This function may be declared static to avoid clashes with other plugins. @@ -74,7 +73,7 @@ the entire LAMMPS executable. If the factory function would be for a fix or compute, which take three arguments (a pointer to the LAMMPS class, the number of arguments and the list of argument strings), then the pointer type is ``lammpsplugin_factory2`` -and it must be assigned to the *creator2* member of the plugin struct. +and it must be assigned to the *creator.v2* member of the plugin struct. Below is an example for that: .. code-block:: C++ @@ -100,12 +99,65 @@ Below is an example for that: plugin.name = "nve2"; plugin.info = "NVE2 variant fix style v1.0"; plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; - plugin.creator1 = nullptr; - plugin.creator2 = (lammpsplugin_factory2 *) &nve2creator; + plugin.creator.v2 = (lammpsplugin_factory2 *) &nve2creator; plugin.handle = handle; (*register_plugin)(&plugin,lmp); } +For command styles there is a third variant of factory function as +demonstrated in the following example, which also shows that the +implementation of the plugin class may also be within the same +file as the plugin interface code: + +.. code-block:: C++ + + #include "lammpsplugin.h" + + #include "comm.h" + #include "error.h" + #include "pointers.h" + #include "version.h" + + #include + + namespace LAMMPS_NS { + class Hello : protected Pointers { + public: + Hello(class LAMMPS *lmp) : Pointers(lmp) {}; + void command(int, char **); + }; + } + + using namespace LAMMPS_NS; + + void Hello::command(int argc, char **argv) + { + if (argc != 1) error->all(FLERR,"Illegal hello command"); + if (comm->me == 0) + utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0])); + } + + static void hellocreator(LAMMPS *lmp, int argc, char **argv) + { + Hello hello(lmp); + hello.command(argc,argv); + } + + extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) + { + lammpsplugin_t plugin; + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + + plugin.version = LAMMPS_VERSION; + plugin.style = "command"; + plugin.name = "hello"; + plugin.info = "Hello world command v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator; + plugin.handle = handle; + (*register_plugin)(&plugin,lmp); + } + The initialization function **must** be called ``lammpsplugin_init``, it **must** have C bindings and it takes three void pointers as arguments. The first is a pointer to the LAMMPS class that calls it and it needs to From c3f6fb914ff9ff287482f805e97663c6a356e2df Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Mar 2021 11:43:37 -0500 Subject: [PATCH 0180/1217] add CMake build environment demo for plugins --- examples/plugins/CMakeLists.txt | 56 +++++++++++++++ examples/plugins/LAMMPSInterfaceCXX.cmake | 86 +++++++++++++++++++++++ 2 files changed, 142 insertions(+) create mode 100644 examples/plugins/CMakeLists.txt create mode 100644 examples/plugins/LAMMPSInterfaceCXX.cmake diff --git a/examples/plugins/CMakeLists.txt b/examples/plugins/CMakeLists.txt new file mode 100644 index 0000000000..2fb8ca746f --- /dev/null +++ b/examples/plugins/CMakeLists.txt @@ -0,0 +1,56 @@ +########################################## +# CMake build system for plugin examples. +# The is meant to be used as a template for plugins that are +# distributed independent from the LAMMPS package. +########################################## + +cmake_minimum_required(VERSION 3.10) + +# enforce out-of-source build +if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR}) + message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. " + "Please remove CMakeCache.txt and CMakeFiles first.") +endif() + +project(plugins VERSION 1.0 LANGUAGES CXX) + +# NOTE: the next line should be commented out when used outside of the LAMMPS package +get_filename_component(LAMMPS_SOURCE_DIR ${PROJECT_SOURCE_DIR}/../../src ABSOLUTE) +set(LAMMPS_HEADER_DIR ${LAMMPS_SOURCE_DIR} CACHE PATH "Location of LAMMPS headers") +if(NOT LAMMPS_HEADER_DIR) + message(FATAL_ERROR "Must set LAMMPS_HEADER_DIR") +endif() + +# by default, install into $HOME/.local (not /usr/local), +# so that no root access (and sudo) is needed +if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) + set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE) +endif() + +# C++11 is required +set(CMAKE_CXX_STANDARD 11) +set(CMAKE_CXX_STANDARD_REQUIRED ON) + +# bail out on windows +if(CMAKE_SYSTEM_NAME STREQUAL Windows) + message(FATAL_ERROR "LAMMPS plugins are currently not supported on Windows") +endif() + +set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}) +include(CheckIncludeFileCXX) +include(LAMMPSInterfaceCXX) + +########################## +# building the plugins + +add_library(morse2plugin MODULE morse2plugin.cpp pair_morse2.cpp pair_morse2_omp.cpp) +target_include_directories(morse2plugin PRIVATE "${LAMMPS_HEADER_DIR}/USER-OMP") +target_link_libraries(morse2plugin PRIVATE lammps) + +add_library(nve2plugin MODULE nve2plugin.cpp fix_nve2.cpp) +target_link_libraries(nve2plugin PRIVATE lammps) + +add_library(helloplugin MODULE helloplugin.cpp) +target_link_libraries(helloplugin PRIVATE lammps) + +set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES PREFIX "") diff --git a/examples/plugins/LAMMPSInterfaceCXX.cmake b/examples/plugins/LAMMPSInterfaceCXX.cmake new file mode 100644 index 0000000000..02f9159319 --- /dev/null +++ b/examples/plugins/LAMMPSInterfaceCXX.cmake @@ -0,0 +1,86 @@ +# Cmake script code to define the LAMMPS C++ interface +# settings required for building LAMMPS plugins + +################################################################################ +# helper function +function(validate_option name values) + string(TOLOWER ${${name}} needle_lower) + string(TOUPPER ${${name}} needle_upper) + list(FIND ${values} ${needle_lower} IDX_LOWER) + list(FIND ${values} ${needle_upper} IDX_UPPER) + if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0) + list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}}) + message(FATAL_ERROR "\n########################################################################\n" + "Invalid value '${${name}}' for option ${name}\n" + "\n" + "Possible values are:\n" + "${POSSIBLE_VALUE_LIST}" + "########################################################################") + endif() +endfunction(validate_option) + +################################################################################# +# LAMMPS C++ interface. We only need the header related parts. +add_library(lammps INTERFACE) +target_include_directories(lammps INTERFACE ${LAMMPS_HEADER_DIR}) + +################################################################################ +# MPI configuration +if(NOT CMAKE_CROSSCOMPILING) + set(MPI_CXX_SKIP_MPICXX TRUE) + find_package(MPI QUIET) + option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) +else() + option(BUILD_MPI "Build MPI version" OFF) +endif() + +if(BUILD_MPI) + find_package(MPI REQUIRED) + option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF) + if(LAMMPS_LONGLONG_TO_LONG) + target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG) + endif() + target_link_libraries(lammps INTERFACE MPI::MPI_CXX) +else() + target_include_directories(lammps INTERFACE "${LAMMPS_SOURCE_DIR}/STUBS") +endif() + +set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)") +set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall) +set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES}) +validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES) +string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES) +target_compile_definitions(lammps INTERFACE -DLAMMPS_${LAMMPS_SIZES}) + +################################################################################ +# detect if we may enable OpenMP support by default +set(BUILD_OMP_DEFAULT OFF) +find_package(OpenMP QUIET) +if(OpenMP_FOUND) + check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE) + if(HAVE_OMP_H_INCLUDE) + set(BUILD_OMP_DEFAULT ON) + endif() +endif() + +option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT}) + +if(BUILD_OMP) + find_package(OpenMP REQUIRED) + check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE) + if(NOT HAVE_OMP_H_INCLUDE) + message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support") + endif() + + if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR + (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR + ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR + ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0))) + # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts. + # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe. + target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=4) + else() + target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=3) + endif() + target_link_libraries(lammps INTERFACE OpenMP::OpenMP_CXX) +endif() From 7b4e14317685278c5e62217aaffddd5bdb2773cb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Mar 2021 14:29:40 -0500 Subject: [PATCH 0181/1217] support building plugins on MacOS (tested on version 11.0 aka Big Sur) --- examples/plugins/CMakeLists.txt | 10 +++++++++- examples/plugins/Makefile | 2 +- examples/plugins/Makefile.macos | 30 ++++++++++++++++++++++++++++++ 3 files changed, 40 insertions(+), 2 deletions(-) create mode 100644 examples/plugins/Makefile.macos diff --git a/examples/plugins/CMakeLists.txt b/examples/plugins/CMakeLists.txt index 2fb8ca746f..74a1cd4e3b 100644 --- a/examples/plugins/CMakeLists.txt +++ b/examples/plugins/CMakeLists.txt @@ -53,4 +53,12 @@ target_link_libraries(nve2plugin PRIVATE lammps) add_library(helloplugin MODULE helloplugin.cpp) target_link_libraries(helloplugin PRIVATE lammps) -set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES PREFIX "") +set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES + PREFIX "" + LINK_FLAGS "-rdynamic") + +# MacOS seems to need this +if(CMAKE_SYSTEM_NAME STREQUAL Darwin) + set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES + LINK_FLAGS "-Wl,-undefined,dynamic_lookup") +endif() diff --git a/examples/plugins/Makefile b/examples/plugins/Makefile index bf6bc804be..dbb0023991 100644 --- a/examples/plugins/Makefile +++ b/examples/plugins/Makefile @@ -26,5 +26,5 @@ fix_nve2.o: fix_nve2.cpp fix_nve2.h nve2plugin.o: nve2plugin.cpp fix_nve2.h clean: - rm -f *~ *.so *.o log.lammps + rm -rf *~ *.so *.dylib *.o log.lammps CMakeCache.txt CMakeFiles diff --git a/examples/plugins/Makefile.macos b/examples/plugins/Makefile.macos new file mode 100644 index 0000000000..2490418a09 --- /dev/null +++ b/examples/plugins/Makefile.macos @@ -0,0 +1,30 @@ +CXX=mpicxx +CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP +LD=$(CXX) -bundle -rdynamic -Wl,-undefined,dynamic_lookup + +default: morse2plugin.dylib nve2plugin.dylib helloplugin.dylib + +helloplugin.dylib: helloplugin.o + $(LD) -o $@ $^ + +morse2plugin.dylib: morse2plugin.o pair_morse2.o pair_morse2_omp.o + $(LD) -o $@ $^ + +nve2plugin.dylib: nve2plugin.o fix_nve2.o + $(LD) -o $@ $^ + +.cpp.o: + $(CXX) -o $@ $(CXXFLAGS) -c $< + +helloplugin.o: helloplugin.cpp + +pair_morse2.o: pair_morse2.cpp pair_morse2.h +pair_morse2_omp.o: pair_morse2_omp.cpp pair_morse2_omp.h pair_morse2.h +morse2plugin.o: morse2plugin.cpp pair_morse2.h pair_morse2_omp.h + +fix_nve2.o: fix_nve2.cpp fix_nve2.h +nve2plugin.o: nve2plugin.cpp fix_nve2.h + +clean: + rm -rf *~ *.dylib *.dylib *.o log.lammps CMakeCache.txt CMakeFiles + From 4b1924fad10322d5173d982115bcdb42252a9477 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Mar 2021 14:29:59 -0500 Subject: [PATCH 0182/1217] add missing check --- src/plugin.cpp | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/plugin.cpp b/src/plugin.cpp index a95fde5b73..68b9978353 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -207,10 +207,16 @@ namespace LAMMPS_NS lmp->force->create_pair("none",0); } } + } else if (pstyle == "fix") { for (int ifix = lmp->modify->find_fix_by_style(name); ifix >= 0; ifix = lmp->modify->find_fix_by_style(name)) lmp->modify->delete_fix(ifix); + + } else if (pstyle == "command") { + auto command_map = lmp->input->command_map; + auto cmd = command_map->find(name); + if (cmd != command_map->end()) command_map->erase(name); } // if reference count is down to zero, close DSO handle. From 1c222286e22e699068a0021221d9c8b1090681e2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Mar 2021 14:30:08 -0500 Subject: [PATCH 0183/1217] correct output --- src/plugin.cpp | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/plugin.cpp b/src/plugin.cpp index 68b9978353..f9bd36f875 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -51,8 +51,7 @@ namespace LAMMPS_NS void *dso = dlopen(file,RTLD_NOW|RTLD_GLOBAL); if (dso == nullptr) { if (me == 0) - utils::logmesg(lmp,fmt::format("Open of plugin file {} failed: {}", - file,utils::getsyserror())); + utils::logmesg(lmp,fmt::format("Open of file {} failed\n",file)); return; } @@ -145,7 +144,7 @@ namespace LAMMPS_NS auto command_map = lmp->input->command_map; if (command_map->find(plugin->name) != command_map->end()) { if (lmp->comm->me == 0) - lmp->error->warning(FLERR,fmt::format("Overriding built-in fix " + lmp->error->warning(FLERR,fmt::format("Overriding built-in command " "style {} from plugin", plugin->name)); } From 98013a1528ab55d9209eff6de4d604574d7bd57e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Mar 2021 15:32:50 -0500 Subject: [PATCH 0184/1217] add draft version of unit test (will have to be improved for MacOS) --- unittest/commands/CMakeLists.txt | 19 +++++++++++++++++++ unittest/commands/test_simple_commands.cpp | 9 +++++++++ 2 files changed, 28 insertions(+) diff --git a/unittest/commands/CMakeLists.txt b/unittest/commands/CMakeLists.txt index 7a804820cb..0fb0c8088e 100644 --- a/unittest/commands/CMakeLists.txt +++ b/unittest/commands/CMakeLists.txt @@ -1,5 +1,24 @@ +# build LAMMPS plugins, but not on Windows +if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + ExternalProject_Add(plugins + SOURCE_DIR "${LAMMPS_DIR}/examples/plugins" + BINARY_DIR "${CMAKE_BINARY_DIR}/plugins" + CMAKE_ARGS ${CMAKE_REQUEST_PIC} + -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} + -DCMAKE_INSTALL_PREFIX= + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} + -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE} + BUILD_BYPRODUCTS /morse2plugin${CMAKE_STATIC_LIBRARY_SUFFIX} + /nve2plugin${CMAKE_STATIC_LIBRARY_SUFFIX} + /helloplugin${CMAKE_STATIC_LIBRARY_SUFFIX} + INSTALL_COMMAND "" + TEST_COMMAND "") +endif() + add_executable(test_simple_commands test_simple_commands.cpp) +add_dependencies(test_simple_commands plugins) target_link_libraries(test_simple_commands PRIVATE lammps GTest::GMock GTest::GTest) add_test(NAME SimpleCommands COMMAND test_simple_commands WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) diff --git a/unittest/commands/test_simple_commands.cpp b/unittest/commands/test_simple_commands.cpp index 4fce58c668..09f81b8f71 100644 --- a/unittest/commands/test_simple_commands.cpp +++ b/unittest/commands/test_simple_commands.cpp @@ -344,6 +344,15 @@ TEST_F(SimpleCommandsTest, Units) TEST_FAILURE(".*ERROR: Illegal units command.*", lmp->input->one("units unknown");); } +TEST_F(SimpleCommandsTest, Plugin) +{ + ::testing::internal::CaptureStdout(); + lmp->input->one("plugin load plugins/helloplugin.so"); + auto text = ::testing::internal::GetCapturedStdout(); + + ASSERT_THAT(text, MatchesRegex(".*Loading plugin: Hello world command.*")); +} + TEST_F(SimpleCommandsTest, Shell) { if (!verbose) ::testing::internal::CaptureStdout(); From 93bbaef5473b3ad126b28865e50b8081c7245aeb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Mar 2021 17:28:22 -0500 Subject: [PATCH 0185/1217] add unit tests for plugin command --- unittest/commands/test_simple_commands.cpp | 66 +++++++++++++++++++++- 1 file changed, 64 insertions(+), 2 deletions(-) diff --git a/unittest/commands/test_simple_commands.cpp b/unittest/commands/test_simple_commands.cpp index 09f81b8f71..08fe53a6b9 100644 --- a/unittest/commands/test_simple_commands.cpp +++ b/unittest/commands/test_simple_commands.cpp @@ -346,11 +346,73 @@ TEST_F(SimpleCommandsTest, Units) TEST_F(SimpleCommandsTest, Plugin) { +#if defined(__APPLE__) + std::string loadfmt("plugin load plugins/{}plugin.dylib"); +#else + std::string loadfmt("plugin load plugins/{}plugin.so"); +#endif ::testing::internal::CaptureStdout(); - lmp->input->one("plugin load plugins/helloplugin.so"); + lmp->input->one(fmt::format(loadfmt, "hello")); auto text = ::testing::internal::GetCapturedStdout(); - + if (verbose) std::cout << text; ASSERT_THAT(text, MatchesRegex(".*Loading plugin: Hello world command.*")); + + ::testing::internal::CaptureStdout(); + lmp->input->one(fmt::format(loadfmt, "xxx")); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*Open of file plugins/xxx.* failed.*")); + + ::testing::internal::CaptureStdout(); + lmp->input->one(fmt::format(loadfmt, "nve2")); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*Loading plugin: NVE2 variant fix style.*")); + ::testing::internal::CaptureStdout(); + lmp->input->one("plugin list"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*1: command style plugin hello" + ".*2: fix style plugin nve2.*")); + + ::testing::internal::CaptureStdout(); + lmp->input->one(fmt::format(loadfmt, "hello")); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*Ignoring load of command style hello: " + "must unload existing hello plugin.*")); + + ::testing::internal::CaptureStdout(); + lmp->input->one("plugin unload command hello"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*Unloading command style hello.*")); + + ::testing::internal::CaptureStdout(); + lmp->input->one("plugin unload pair nve2"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*Ignoring unload of pair style nve2: " + "not loaded from a plugin.*")); + + ::testing::internal::CaptureStdout(); + lmp->input->one("plugin unload fix nve2"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*Unloading fix style nve2.*")); + + ::testing::internal::CaptureStdout(); + lmp->input->one("plugin unload fix nve"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*Ignoring unload of fix style nve: " + "not loaded from a plugin.*")); + + ::testing::internal::CaptureStdout(); + lmp->input->one("plugin list"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*Currently loaded plugins.*")); } TEST_F(SimpleCommandsTest, Shell) From b2085f56d6478552110fcdcc5f16921b30a885b4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Mar 2021 18:35:39 -0500 Subject: [PATCH 0186/1217] install compiled plugins into the current working directory of the tester --- unittest/commands/CMakeLists.txt | 15 ++++++++++----- unittest/commands/test_simple_commands.cpp | 6 +++--- 2 files changed, 13 insertions(+), 8 deletions(-) diff --git a/unittest/commands/CMakeLists.txt b/unittest/commands/CMakeLists.txt index 0fb0c8088e..6c68bfb274 100644 --- a/unittest/commands/CMakeLists.txt +++ b/unittest/commands/CMakeLists.txt @@ -3,17 +3,22 @@ if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") ExternalProject_Add(plugins SOURCE_DIR "${LAMMPS_DIR}/examples/plugins" - BINARY_DIR "${CMAKE_BINARY_DIR}/plugins" + BINARY_DIR ${CMAKE_BINARY_DIR}/build-plugins + INSTALL_DIR ${CMAKE_BINARY_DIR} CMAKE_ARGS ${CMAKE_REQUEST_PIC} -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -DCMAKE_INSTALL_PREFIX= -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE} - BUILD_BYPRODUCTS /morse2plugin${CMAKE_STATIC_LIBRARY_SUFFIX} - /nve2plugin${CMAKE_STATIC_LIBRARY_SUFFIX} - /helloplugin${CMAKE_STATIC_LIBRARY_SUFFIX} - INSTALL_COMMAND "" + BUILD_BYPRODUCTS /morse2plugin${CMAKE_SHARED_LIBRARY_SUFFIX} + /nve2plugin${CMAKE_SHARED_LIBRARY_SUFFIX} + /helloplugin${CMAKE_SHARED_LIBRARY_SUFFIX} + INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_if_different + /morse2plugin${CMAKE_SHARED_LIBRARY_SUFFIX} + /nve2plugin${CMAKE_SHARED_LIBRARY_SUFFIX} + /helloplugin${CMAKE_SHARED_LIBRARY_SUFFIX} + ${CMAKE_CURRENT_BINARY_DIR} TEST_COMMAND "") endif() diff --git a/unittest/commands/test_simple_commands.cpp b/unittest/commands/test_simple_commands.cpp index 08fe53a6b9..0e26734dfb 100644 --- a/unittest/commands/test_simple_commands.cpp +++ b/unittest/commands/test_simple_commands.cpp @@ -347,9 +347,9 @@ TEST_F(SimpleCommandsTest, Units) TEST_F(SimpleCommandsTest, Plugin) { #if defined(__APPLE__) - std::string loadfmt("plugin load plugins/{}plugin.dylib"); + std::string loadfmt("plugin load {}plugin.dylib"); #else - std::string loadfmt("plugin load plugins/{}plugin.so"); + std::string loadfmt("plugin load {}plugin.so"); #endif ::testing::internal::CaptureStdout(); lmp->input->one(fmt::format(loadfmt, "hello")); @@ -361,7 +361,7 @@ TEST_F(SimpleCommandsTest, Plugin) lmp->input->one(fmt::format(loadfmt, "xxx")); text = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << text; - ASSERT_THAT(text, MatchesRegex(".*Open of file plugins/xxx.* failed.*")); + ASSERT_THAT(text, MatchesRegex(".*Open of file xxx.* failed.*")); ::testing::internal::CaptureStdout(); lmp->input->one(fmt::format(loadfmt, "nve2")); From 3e90b1971a9f9890be584c47db12c2d922de5b37 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Mar 2021 22:21:11 -0500 Subject: [PATCH 0187/1217] add preliminary support for compiling/loading plugins on windows --- doc/src/plugin.rst | 3 ++ examples/plugins/CMakeLists.txt | 14 +++----- examples/plugins/Makefile.serial | 30 ++++++++++++++++ src/MAKE/Makefile.mpi | 2 +- src/MAKE/Makefile.serial | 2 +- src/plugin.cpp | 59 ++++++++++++++++++++++++-------- 6 files changed, 85 insertions(+), 25 deletions(-) create mode 100644 examples/plugins/Makefile.serial diff --git a/doc/src/plugin.rst b/doc/src/plugin.rst index 25a55565b9..a75e39ccae 100644 --- a/doc/src/plugin.rst +++ b/doc/src/plugin.rst @@ -58,6 +58,9 @@ Restrictions Plugins are currently not available on Windows. +For the loading of plugins to work, the LAMMPS library must be +:ref:`compiled as a shared library `. + Plugins are dependent on the LAMMPS binary interface (ABI) and particularly the MPI library used. So they are not guaranteed to work when the plugin was compiled with a different MPI library diff --git a/examples/plugins/CMakeLists.txt b/examples/plugins/CMakeLists.txt index 74a1cd4e3b..2db2c041fd 100644 --- a/examples/plugins/CMakeLists.txt +++ b/examples/plugins/CMakeLists.txt @@ -31,11 +31,6 @@ endif() set(CMAKE_CXX_STANDARD 11) set(CMAKE_CXX_STANDARD_REQUIRED ON) -# bail out on windows -if(CMAKE_SYSTEM_NAME STREQUAL Windows) - message(FATAL_ERROR "LAMMPS plugins are currently not supported on Windows") -endif() - set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}) include(CheckIncludeFileCXX) include(LAMMPSInterfaceCXX) @@ -53,12 +48,13 @@ target_link_libraries(nve2plugin PRIVATE lammps) add_library(helloplugin MODULE helloplugin.cpp) target_link_libraries(helloplugin PRIVATE lammps) -set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES - PREFIX "" - LINK_FLAGS "-rdynamic") +set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES PREFIX "") -# MacOS seems to need this if(CMAKE_SYSTEM_NAME STREQUAL Darwin) set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup") +elseif(CMAKE_SYSTEM_NAME STREQUAL Windows) + set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES LINK_FLAGS "-Wl,--undefined") +else() + set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES LINK_FLAGS "-rdynamic") endif() diff --git a/examples/plugins/Makefile.serial b/examples/plugins/Makefile.serial new file mode 100644 index 0000000000..feb58bd9b3 --- /dev/null +++ b/examples/plugins/Makefile.serial @@ -0,0 +1,30 @@ +CXX=g++ +CXXFLAGS=-I../../src -I../../src/STUBS -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp +LD=$(CXX) -shared -rdynamic -fopenmp + +default: morse2plugin.so nve2plugin.so helloplugin.so + +helloplugin.so: helloplugin.o + $(LD) -o $@ $^ + +morse2plugin.so: morse2plugin.o pair_morse2.o pair_morse2_omp.o + $(LD) -o $@ $^ + +nve2plugin.so: nve2plugin.o fix_nve2.o + $(LD) -o $@ $^ + +.cpp.o: + $(CXX) -o $@ $(CXXFLAGS) -c $< + +helloplugin.o: helloplugin.cpp + +pair_morse2.o: pair_morse2.cpp pair_morse2.h +pair_morse2_omp.o: pair_morse2_omp.cpp pair_morse2_omp.h pair_morse2.h +morse2plugin.o: morse2plugin.cpp pair_morse2.h pair_morse2_omp.h + +fix_nve2.o: fix_nve2.cpp fix_nve2.h +nve2plugin.o: nve2plugin.cpp fix_nve2.h + +clean: + rm -rf *~ *.so *.dylib *.o log.lammps CMakeCache.txt CMakeFiles + diff --git a/src/MAKE/Makefile.mpi b/src/MAKE/Makefile.mpi index c66e66c217..68e79e9e8e 100644 --- a/src/MAKE/Makefile.mpi +++ b/src/MAKE/Makefile.mpi @@ -18,7 +18,7 @@ SIZE = size ARCHIVE = ar ARFLAGS = -rc -SHLIBFLAGS = -shared +SHLIBFLAGS = -shared -rdynamic # --------------------------------------------------------------------- # LAMMPS-specific settings, all OPTIONAL diff --git a/src/MAKE/Makefile.serial b/src/MAKE/Makefile.serial index daf04cc5b0..8b4e2e5982 100644 --- a/src/MAKE/Makefile.serial +++ b/src/MAKE/Makefile.serial @@ -18,7 +18,7 @@ SIZE = size ARCHIVE = ar ARFLAGS = -rc -SHLIBFLAGS = -shared +SHLIBFLAGS = -shared -rdynamic # --------------------------------------------------------------------- # LAMMPS-specific settings, all OPTIONAL diff --git a/src/plugin.cpp b/src/plugin.cpp index f9bd36f875..2c4f2da396 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -24,12 +24,49 @@ #include #include -#ifdef _WIN32 +#if defined(_WIN32) #include #else #include #endif +#if defined(_WIN32) + +// open a shared object file +static void *my_dlopen(const char *fname) { + return (void *)LoadLibrary(fname); +} + +// resolve a symbol in shared object +static void *my_dlsym(void *h, const char *sym) { + return (void *)GetProcAddress((HINSTANCE)h, sym); +} + +// close a shared object +static int my_dlclose(void *h) { + /* FreeLibrary returns nonzero on success */ + return !FreeLibrary((HINSTANCE)h); +} + +#else + +// open a shared object file +static void *my_dlopen(const char *fname) { + return dlopen(fname, RTLD_NOW|RTLD_GLOBAL); +} + +// resolve a symbol in shared object +static void *my_dlsym(void *h, const char *sym) { + return dlsym(h, sym); +} + +// close a shared object +static int my_dlclose(void *h) { + return dlclose(h); +} + +#endif + namespace LAMMPS_NS { // list of plugin information data for loaded styles @@ -42,13 +79,11 @@ namespace LAMMPS_NS void plugin_load(const char *file, LAMMPS *lmp) { int me = lmp->comm->me; -#if defined(WIN32) - lmp->error->all(FLERR,"Loading of plugins on Windows not yet supported\n"); -#else // open DSO file from given path; load symbols globally - - void *dso = dlopen(file,RTLD_NOW|RTLD_GLOBAL); + + void *dso = my_dlopen(file); + if (dso == nullptr) { if (me == 0) utils::logmesg(lmp,fmt::format("Open of file {} failed\n",file)); @@ -58,9 +93,10 @@ namespace LAMMPS_NS // look up lammpsplugin_init() function in DSO // function must have C bindings so there is no name mangling - void *initfunc = dlsym(dso,"lammpsplugin_init"); + void *initfunc = my_dlsym(dso,"lammpsplugin_init"); + if (initfunc == nullptr) { - dlclose(dso); + my_dlclose(dso); if (me == 0) utils::logmesg(lmp,fmt::format("Plugin symbol lookup failure in " @@ -74,7 +110,6 @@ namespace LAMMPS_NS (*(lammpsplugin_initfunc)(initfunc))((void *)lmp, dso, (void *)&plugin_register); -#endif } /* -------------------------------------------------------------------- @@ -221,11 +256,7 @@ namespace LAMMPS_NS // if reference count is down to zero, close DSO handle. -- dso_refcounter[handle]; - if (dso_refcounter[handle] == 0) { -#ifndef WIN32 - dlclose(handle); -#endif - } + if (dso_refcounter[handle] == 0) my_dlclose(handle); } /* -------------------------------------------------------------------- From d05137455c660e2c801ebffddc36ca9eaf51b8d2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Mar 2021 22:21:24 -0500 Subject: [PATCH 0188/1217] ignore build folders --- examples/plugins/.gitignore | 1 + 1 file changed, 1 insertion(+) create mode 100644 examples/plugins/.gitignore diff --git a/examples/plugins/.gitignore b/examples/plugins/.gitignore new file mode 100644 index 0000000000..0ec9e7f982 --- /dev/null +++ b/examples/plugins/.gitignore @@ -0,0 +1 @@ +/build* From 4ae7f84c2ac0552c3f123e6e9f02911b526ed6b9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Mar 2021 22:27:38 -0500 Subject: [PATCH 0189/1217] whitespace --- src/plugin.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/plugin.cpp b/src/plugin.cpp index 2c4f2da396..73fcfd947e 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -81,9 +81,9 @@ namespace LAMMPS_NS int me = lmp->comm->me; // open DSO file from given path; load symbols globally - + void *dso = my_dlopen(file); - + if (dso == nullptr) { if (me == 0) utils::logmesg(lmp,fmt::format("Open of file {} failed\n",file)); From e3d9c3126b12c081598b3ac36e5497edca8f12bd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 13 Mar 2021 10:25:44 -0500 Subject: [PATCH 0190/1217] revert back to not supporting loading plugins on windows --- examples/plugins/CMakeLists.txt | 14 +++++--- src/plugin.cpp | 57 ++++++++------------------------- 2 files changed, 22 insertions(+), 49 deletions(-) diff --git a/examples/plugins/CMakeLists.txt b/examples/plugins/CMakeLists.txt index 2db2c041fd..74a1cd4e3b 100644 --- a/examples/plugins/CMakeLists.txt +++ b/examples/plugins/CMakeLists.txt @@ -31,6 +31,11 @@ endif() set(CMAKE_CXX_STANDARD 11) set(CMAKE_CXX_STANDARD_REQUIRED ON) +# bail out on windows +if(CMAKE_SYSTEM_NAME STREQUAL Windows) + message(FATAL_ERROR "LAMMPS plugins are currently not supported on Windows") +endif() + set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}) include(CheckIncludeFileCXX) include(LAMMPSInterfaceCXX) @@ -48,13 +53,12 @@ target_link_libraries(nve2plugin PRIVATE lammps) add_library(helloplugin MODULE helloplugin.cpp) target_link_libraries(helloplugin PRIVATE lammps) -set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES PREFIX "") +set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES + PREFIX "" + LINK_FLAGS "-rdynamic") +# MacOS seems to need this if(CMAKE_SYSTEM_NAME STREQUAL Darwin) set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup") -elseif(CMAKE_SYSTEM_NAME STREQUAL Windows) - set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES LINK_FLAGS "-Wl,--undefined") -else() - set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES LINK_FLAGS "-rdynamic") endif() diff --git a/src/plugin.cpp b/src/plugin.cpp index 73fcfd947e..d654535f56 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -24,49 +24,12 @@ #include #include -#if defined(_WIN32) +#ifdef _WIN32 #include #else #include #endif -#if defined(_WIN32) - -// open a shared object file -static void *my_dlopen(const char *fname) { - return (void *)LoadLibrary(fname); -} - -// resolve a symbol in shared object -static void *my_dlsym(void *h, const char *sym) { - return (void *)GetProcAddress((HINSTANCE)h, sym); -} - -// close a shared object -static int my_dlclose(void *h) { - /* FreeLibrary returns nonzero on success */ - return !FreeLibrary((HINSTANCE)h); -} - -#else - -// open a shared object file -static void *my_dlopen(const char *fname) { - return dlopen(fname, RTLD_NOW|RTLD_GLOBAL); -} - -// resolve a symbol in shared object -static void *my_dlsym(void *h, const char *sym) { - return dlsym(h, sym); -} - -// close a shared object -static int my_dlclose(void *h) { - return dlclose(h); -} - -#endif - namespace LAMMPS_NS { // list of plugin information data for loaded styles @@ -79,11 +42,13 @@ namespace LAMMPS_NS void plugin_load(const char *file, LAMMPS *lmp) { int me = lmp->comm->me; +#if defined(WIN32) + lmp->error->all(FLERR,"Loading of plugins on Windows is not supported\n"); +#else // open DSO file from given path; load symbols globally - void *dso = my_dlopen(file); - + void *dso = dlopen(file,RTLD_NOW|RTLD_GLOBAL); if (dso == nullptr) { if (me == 0) utils::logmesg(lmp,fmt::format("Open of file {} failed\n",file)); @@ -93,10 +58,9 @@ namespace LAMMPS_NS // look up lammpsplugin_init() function in DSO // function must have C bindings so there is no name mangling - void *initfunc = my_dlsym(dso,"lammpsplugin_init"); - + void *initfunc = dlsym(dso,"lammpsplugin_init"); if (initfunc == nullptr) { - my_dlclose(dso); + dlclose(dso); if (me == 0) utils::logmesg(lmp,fmt::format("Plugin symbol lookup failure in " @@ -110,6 +74,7 @@ namespace LAMMPS_NS (*(lammpsplugin_initfunc)(initfunc))((void *)lmp, dso, (void *)&plugin_register); +#endif } /* -------------------------------------------------------------------- @@ -256,7 +221,11 @@ namespace LAMMPS_NS // if reference count is down to zero, close DSO handle. -- dso_refcounter[handle]; - if (dso_refcounter[handle] == 0) my_dlclose(handle); + if (dso_refcounter[handle] == 0) { +#ifndef WIN32 + dlclose(handle); +#endif + } } /* -------------------------------------------------------------------- From 76cff1ed1ec1ce562ed58d4c3f2e0aa483d18444 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 13 Mar 2021 12:17:20 -0500 Subject: [PATCH 0191/1217] add library interface for introspection of loaded plugins --- src/library.cpp | 54 +++++++++++++++++++++++++++++++++++++++++++++++++ src/library.h | 3 +++ 2 files changed, 57 insertions(+) diff --git a/src/library.cpp b/src/library.cpp index 2a7bbf07b3..ae3212d6f3 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -38,6 +38,7 @@ #include "neighbor.h" #include "region.h" #include "output.h" +#include "plugin.h" #include "thermo.h" #include "timer.h" #include "universe.h" @@ -4581,6 +4582,59 @@ int lammps_id_name(void *handle, const char *category, int idx, return 0; } +/* ---------------------------------------------------------------------- */ + +/** Count the number of loaded plugins + * +\verbatim embed:rst +This function counts how many plugins are currently loaded. + +.. versionadded:: 10Mar2021 + +\endverbatim + * + * \return number of loaded plugins + */ +int lammps_plugin_count() +{ + return plugin_get_num_plugins(); +} + +/* ---------------------------------------------------------------------- */ + +/** Look up the info of a loaded plugin by its index in the list of plugins + * +\verbatim embed:rst +This function copies the name of the *style* plugin with the index +*idx* into the provided C-style string buffer. The length of the buffer +must be provided as *buf_size* argument. If the name of the style +exceeds the length of the buffer, it will be truncated accordingly. +If the index is out of range, the function returns 0 and *buffer* is +set to an empty string, otherwise 1. + +.. versionadded:: 10Mar2021 + +\endverbatim + * + * \param idx index of the plugin in the list all or *style* plugins + * \param stylebuf string buffer to copy the style of the plugin to + * \param namebuf string buffer to copy the name of the plugin to + * \param buf_size size of the provided string buffers + * \return 1 if successful, otherwise 0 + */ +int lammps_plugin_name(int idx, char *stylebuf, char *namebuf, int buf_size) +{ + stylebuf[0] = namebuf[0] = '\0'; + + const lammpsplugin_t *plugin = plugin_get_info(idx); + if (plugin) { + strncpy(stylebuf,plugin->style,buf_size); + strncpy(namebuf,plugin->name,buf_size); + return 1; + } + return 0; +} + // ---------------------------------------------------------------------- // utility functions // ---------------------------------------------------------------------- diff --git a/src/library.h b/src/library.h index d98bf426b3..11cd72388a 100644 --- a/src/library.h +++ b/src/library.h @@ -205,6 +205,9 @@ int lammps_has_id(void *, const char *, const char *); int lammps_id_count(void *, const char *); int lammps_id_name(void *, const char *, int, char *, int); +int lammps_plugin_count(); +int lammps_plugin_name(int, char *, char *, int); + /* ---------------------------------------------------------------------- * Utility functions * ---------------------------------------------------------------------- */ From dd94bac0c8b3b61cb1805d703f189b78958a2f3d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 13 Mar 2021 12:17:45 -0500 Subject: [PATCH 0192/1217] better error message when trying to unload an unsupported plugin style --- src/plugin.cpp | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/plugin.cpp b/src/plugin.cpp index d654535f56..fb3186c69e 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -167,6 +167,16 @@ namespace LAMMPS_NS { int me = lmp->comm->me; + // ignore unload request from unsupported style categories + if ((strcmp(style,"pair") != 0) + && (strcmp(style,"fix") != 0) + && (strcmp(style,"command") != 0)) { + if (me == 0) + utils::logmesg(lmp,fmt::format("Ignoring unload: {} is not a " + "supported plugin style\n",style)); + return; + } + // ignore unload request if not loaded from a plugin int idx = plugin_find(style,name); if (idx < 0) { From 79d438e090e9b72ac6db2d04403005bad3086645 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 13 Mar 2021 12:18:07 -0500 Subject: [PATCH 0193/1217] add support for plugin command to LAMMPS shell --- tools/lammps-shell/lammps-shell.cpp | 66 ++++++++++++++++++++++++++++- 1 file changed, 65 insertions(+), 1 deletion(-) diff --git a/tools/lammps-shell/lammps-shell.cpp b/tools/lammps-shell/lammps-shell.cpp index 7ace6d6819..8153c1bcfa 100644 --- a/tools/lammps-shell/lammps-shell.cpp +++ b/tools/lammps-shell/lammps-shell.cpp @@ -128,6 +128,7 @@ const char *cmdlist[] = {"clear", "pair_modify", "pair_style", "pair_write", + "plugin", "processors", "region", "reset_timestep", @@ -347,6 +348,59 @@ static char *variable_expand_generator(const char *text, int state) return nullptr; } +static char *plugin_generator(const char *text, int state) +{ + const char *subcmd[] = {"load", "unload", "list", NULL}; + const char *sub; + static std::size_t idx, len; + if (!state) idx = 0; + len = strlen(text); + + while ((sub = subcmd[idx]) != NULL) { + ++idx; + if (strncmp(text,sub,len) == 0) + return dupstring(sub); + } + return nullptr; +} + +static char *plugin_style_generator(const char *text, int state) +{ + const char *styles[] = {"pair", "fix", "command", NULL}; + const char *s; + static std::size_t idx, len; + if (!state) idx = 0; + len = strlen(text); + while ((s = styles[idx]) != NULL) { + ++idx; + if (strncmp(text,s,len) == 0) + return dupstring(s); + } + return nullptr; +} + +static char *plugin_name_generator(const char *text, int state) +{ + auto words = utils::split_words(text); + if (words.size() < 4) return nullptr; + + static std::size_t idx, len; + if (!state) idx = 0; + len = words[3].size(); + int nmax = lammps_plugin_count(); + + while (idx < nmax) { + char style[buflen], name[buflen]; + lammps_plugin_name(idx, style, name, buflen); + ++idx; + if (words[2] == style) { + if (strncmp(name, words[3].c_str(), len) == 0) + return dupstring(name); + } + } + return nullptr; +} + static char *atom_generator(const char *text, int state) { return style_generator(text, state); @@ -477,14 +531,21 @@ static char **cmd_completion(const char *text, int start, int) matches = rl_completion_matches(text, dump_id_generator); } else if (words[0] == "fix_modify") { matches = rl_completion_matches(text, fix_id_generator); + } else if (words[0] == "plugin") { + matches = rl_completion_matches(text, plugin_generator); } } else if (words.size() == 2) { // expand third word // these commands have a group name as 3rd word - if ((words[0] == "fix") || (words[0] == "compute") || (words[0] == "dump")) { + if ((words[0] == "fix") + || (words[0] == "compute") + || (words[0] == "dump")) { matches = rl_completion_matches(text, group_generator); } else if (words[0] == "region") { matches = rl_completion_matches(text, region_generator); + // plugin style is the third word + } else if ((words[0] == "plugin") && (words[1] == "unload")) { + matches = rl_completion_matches(text, plugin_style_generator); } } else if (words.size() == 3) { // expand fourth word @@ -495,6 +556,9 @@ static char **cmd_completion(const char *text, int start, int) matches = rl_completion_matches(text, compute_generator); } else if (words[0] == "dump") { matches = rl_completion_matches(text, dump_generator); + // plugin name is the fourth word + } else if ((words[0] == "plugin") && (words[1] == "unload")) { + matches = rl_completion_matches(rl_line_buffer, plugin_name_generator); } } } From 88760fa648a69352bd333e6b06c412acb17eec08 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 13 Mar 2021 12:40:04 -0500 Subject: [PATCH 0194/1217] add plugin clear command to unload all loaded plugins --- doc/src/plugin.rst | 18 ++++++++++++------ src/input.cpp | 2 ++ src/plugin.cpp | 12 ++++++++++++ src/plugin.h | 1 + tools/lammps-shell/lammps-shell.cpp | 2 +- 5 files changed, 28 insertions(+), 7 deletions(-) diff --git a/doc/src/plugin.rst b/doc/src/plugin.rst index a75e39ccae..e8a5f67e3c 100644 --- a/doc/src/plugin.rst +++ b/doc/src/plugin.rst @@ -10,7 +10,7 @@ Syntax plugin command args -* command = *load* or *unload* or *list* +* command = *load* or *unload* or *list* or *clear* * args = list of arguments for a particular plugin command .. parsed-literal:: @@ -19,6 +19,7 @@ Syntax *unload* style name = unload plugin *name* of style *style* *style* = *pair* or *fix* or *command* *list* = print a list of currently loaded plugins + *clear* = unload all currently loaded plugins Examples """""""" @@ -29,6 +30,7 @@ Examples plugin unload pair morse2/omp plugin unload command hello plugin list + plugin clear Description """"""""""" @@ -52,21 +54,25 @@ that style instance will be deleted. The *list* command will print a list of the loaded plugins and their styles and names. +The *clear* command will unload all currently loaded plugins. + Restrictions """""""""""" -Plugins are currently not available on Windows. +Plugins are not available on Windows. -For the loading of plugins to work, the LAMMPS library must be -:ref:`compiled as a shared library `. +For the loading of plugins to work the LAMMPS library must be +:ref:`compiled as a shared library `. If plugins +access functions or classes from a package, LAMMPS must have +been compiled with that package included. Plugins are dependent on the LAMMPS binary interface (ABI) and particularly the MPI library used. So they are not guaranteed to work when the plugin was compiled with a different MPI library or different compilation settings or a different LAMMPS version. -If there is a mismatch the *plugin* command may fail to load the -plugin(s) or data corruption or crashes may happen. +There are no checks, so if there is a mismatch the plugin object +will either not load or data corruption and crashes may happen. Related commands diff --git a/src/input.cpp b/src/input.cpp index 6d1564ecb6..1df60f5298 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -1110,6 +1110,8 @@ void Input::plugin() } else if (cmd == "unload") { if (narg != 3) error->all(FLERR,"Illegal plugin unload command"); plugin_unload(arg[1],arg[2],lmp); + } else if (cmd == "clear") { + plugin_clear(lmp); } else if (cmd == "list") { if (comm->me == 0) { int num = plugin_get_num_plugins(); diff --git a/src/plugin.cpp b/src/plugin.cpp index fb3186c69e..99b1b086c5 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -238,6 +238,18 @@ namespace LAMMPS_NS } } + /* -------------------------------------------------------------------- + unload all loaded plugins + -------------------------------------------------------------------- */ + + void plugin_clear(LAMMPS *lmp) + { + while (pluginlist.size() > 0) { + auto p = pluginlist.begin(); + plugin_unload(p->style,p->name,lmp); + } + } + /* -------------------------------------------------------------------- remove plugin of given name and style from internal lists -------------------------------------------------------------------- */ diff --git a/src/plugin.h b/src/plugin.h index 32a5a280a1..90952224a6 100644 --- a/src/plugin.h +++ b/src/plugin.h @@ -25,6 +25,7 @@ namespace LAMMPS_NS void plugin_unload(const char *, const char *, LAMMPS *); void plugin_erase(const char *, const char *); + void plugin_clear(LAMMPS *); int plugin_get_num_plugins(); int plugin_find(const char *, const char *); diff --git a/tools/lammps-shell/lammps-shell.cpp b/tools/lammps-shell/lammps-shell.cpp index 8153c1bcfa..6c8873093f 100644 --- a/tools/lammps-shell/lammps-shell.cpp +++ b/tools/lammps-shell/lammps-shell.cpp @@ -350,7 +350,7 @@ static char *variable_expand_generator(const char *text, int state) static char *plugin_generator(const char *text, int state) { - const char *subcmd[] = {"load", "unload", "list", NULL}; + const char *subcmd[] = {"load", "unload", "list", "clear", NULL}; const char *sub; static std::size_t idx, len; if (!state) idx = 0; From 10189760c68799d957e29c389c06ceb6242e5822 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 13 Mar 2021 12:40:49 -0500 Subject: [PATCH 0195/1217] fix issue of not removing unloaded plugins from fix map --- src/plugin.cpp | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/src/plugin.cpp b/src/plugin.cpp index 99b1b086c5..2d18da64ce 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -186,7 +186,7 @@ namespace LAMMPS_NS return; } - // copy of DSO handle for later + // make copy of DSO handle for later use void *handle = plugin_get_info(idx)->handle; // remove selected plugin from list of plugins @@ -201,6 +201,7 @@ namespace LAMMPS_NS std::string pstyle = style; if (pstyle == "pair") { + auto found = lmp->force->pair_map->find(name); if (found != lmp->force->pair_map->end()) lmp->force->pair_map->erase(found); @@ -218,14 +219,20 @@ namespace LAMMPS_NS } } else if (pstyle == "fix") { + + auto fix_map = lmp->modify->fix_map; + auto found = fix_map->find(name); + if (found != fix_map->end()) fix_map->erase(name); + for (int ifix = lmp->modify->find_fix_by_style(name); ifix >= 0; ifix = lmp->modify->find_fix_by_style(name)) lmp->modify->delete_fix(ifix); } else if (pstyle == "command") { + auto command_map = lmp->input->command_map; - auto cmd = command_map->find(name); - if (cmd != command_map->end()) command_map->erase(name); + auto found = command_map->find(name); + if (found != command_map->end()) command_map->erase(name); } // if reference count is down to zero, close DSO handle. From 98fa3661f382c423748f296e246417f5b4d0698e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 13 Mar 2021 12:41:01 -0500 Subject: [PATCH 0196/1217] silence compiler warning --- src/library.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/library.cpp b/src/library.cpp index ae3212d6f3..3fed6ba8cd 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -988,12 +988,12 @@ to then decide how to cast the (void*) pointer and access the data. \endverbatim * - * \param handle pointer to a previously created LAMMPS instance + * \param handle pointer to a previously created LAMMPS instance (unused) * \param name string with the name of the extracted property * \return integer constant encoding the data type of the property * or -1 if not found. */ -int lammps_extract_global_datatype(void *handle, const char *name) +int lammps_extract_global_datatype(void * /*handle*/, const char *name) { if (strcmp(name,"dt") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"ntimestep") == 0) return LAMMPS_BIGINT; From 15e30ed44da6d9147f08fedc44e5770df4c93da8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 13 Mar 2021 18:41:36 -0500 Subject: [PATCH 0197/1217] report dynamic linker error messages on failures --- src/plugin.cpp | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/plugin.cpp b/src/plugin.cpp index 2d18da64ce..e252ce67e1 100644 --- a/src/plugin.cpp +++ b/src/plugin.cpp @@ -48,23 +48,26 @@ namespace LAMMPS_NS // open DSO file from given path; load symbols globally + dlerror(); void *dso = dlopen(file,RTLD_NOW|RTLD_GLOBAL); if (dso == nullptr) { if (me == 0) - utils::logmesg(lmp,fmt::format("Open of file {} failed\n",file)); + utils::logmesg(lmp,fmt::format("Open of file {} failed: {}\n", + file,dlerror())); return; } // look up lammpsplugin_init() function in DSO // function must have C bindings so there is no name mangling + dlerror(); void *initfunc = dlsym(dso,"lammpsplugin_init"); if (initfunc == nullptr) { dlclose(dso); if (me == 0) utils::logmesg(lmp,fmt::format("Plugin symbol lookup failure in " - "file {}\n",file)); + "file {}: {}\n",file,dlerror())); return; } From 11d2b488c1ae18d3d2aaf83ed49025c4b4a0f174 Mon Sep 17 00:00:00 2001 From: Stephen Sanderson Date: Tue, 16 Mar 2021 16:51:10 +1000 Subject: [PATCH 0198/1217] Fixed incorrect scaling of cdof for 'norm all' --- src/fix_ave_chunk.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index 3b612aeb73..359e3ba588 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -881,7 +881,7 @@ void FixAveChunk::end_of_step() if (count_sum[m] > 0.0) for (j = 0; j < nvalues; j++) { if (which[j] == ArgInfo::TEMPERATURE) { - values_sum[m][j] *= mvv2e / ((cdof + adof*count_sum[m]) * boltz); + values_sum[m][j] *= mvv2e/((repeat*cdof + adof*count_sum[m])*boltz); } else if (which[j] == ArgInfo::DENSITY_NUMBER) { if (volflag == SCALAR) values_sum[m][j] /= chunk_volume_scalar; else values_sum[m][j] /= chunk_volume_vec[m]; From 22fdfa27b57fbcdbc9d8e6045df7567491eb3d5e Mon Sep 17 00:00:00 2001 From: Stephen Sanderson Date: Wed, 17 Mar 2021 09:01:35 +1000 Subject: [PATCH 0199/1217] Updated documentation to clarify the treatment of temperature using norm all --- doc/src/fix_ave_chunk.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index d2dbaa320a..ce7fcd1fca 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -307,7 +307,9 @@ atoms in the chunk. The averaged output value for the chunk on the average over atoms across the entire *Nfreq* timescale. For the *density/number* and *density/mass* values, the volume (bin volume or system volume) used in the final normalization will be the volume at -the final *Nfreq* timestep. +the final *Nfreq* timestep. For the *temp* values, degrees of freedom and +kinetic energy are summed separately across the entire *Nfreq* timescale, and +the output value is calculated by dividing those two sums. If the *norm* setting is *sample*\ , the chunk value is summed over atoms for each sample, as is the count, and an "average sample value" From 11894f83b9b705eb152a0525e7bd5c04834aac7d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 16 Mar 2021 19:50:45 -0400 Subject: [PATCH 0200/1217] clarify and fix grammar issues --- doc/src/Developer_plugins.rst | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/doc/src/Developer_plugins.rst b/doc/src/Developer_plugins.rst index 192c57ccbb..7275c12605 100644 --- a/doc/src/Developer_plugins.rst +++ b/doc/src/Developer_plugins.rst @@ -162,17 +162,20 @@ The initialization function **must** be called ``lammpsplugin_init``, it **must** have C bindings and it takes three void pointers as arguments. The first is a pointer to the LAMMPS class that calls it and it needs to be passed to the registration function. The second argument is a -pointer to the internal handle of the DSO file, this needs to added to -the plugin info struct, so that the DSO can be close and unloaded when -all its contained plugins are unloaded. The third argument is a +pointer to the internal handle of the DSO file, this needs to be added +to the plugin info struct, so that the DSO can be closed and unloaded +when all its contained plugins are unloaded. The third argument is a function pointer to the registration function and needs to be stored -in a variable of ``lammpsplugin_regfunc`` type. +in a variable of ``lammpsplugin_regfunc`` type and then called with a +pointer to the ``lammpsplugin_`` struct and the pointer to the LAMMPS +instance as arguments to register a single plugin. There may be multiple +calls to multiple plugins in the same initialization function. To register a plugin a struct of the ``lammpsplugin_t`` needs to be filled with relevant info: current LAMMPS version string, kind of style, name of -style, info string, author string, pointer to factory function, DSO handle. -The the registration function is called with a pointer to the address of -this struct and the pointer of the LAMMPS class. The registration function +style, info string, author string, pointer to factory function, and the +DSO handle. The registration function is called with a pointer to the address +of this struct and the pointer of the LAMMPS class. The registration function will then add the factory function of the plugin style to the respective style map under the provided name. It will also make a copy of the struct in a list of all loaded plugins and update the reference counter for loaded From 125ae33ccfa4aa97212607bab3487fb4193d015e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 16 Mar 2021 22:43:13 -0400 Subject: [PATCH 0201/1217] convert plugin functionality into a package --- cmake/CMakeLists.txt | 19 +++++-- cmake/presets/most.cmake | 2 +- lib/README | 20 ++++--- lib/plugin/README | 16 ++++++ src/.gitignore | 4 ++ src/MAKE/Makefile.mpi | 2 +- src/MAKE/Makefile.serial | 2 +- src/Makefile | 2 +- src/PLUGIN/Install.sh | 64 ++++++++++++++++++++++ src/PLUGIN/README | 12 ++++ src/{ => PLUGIN}/plugin.cpp | 49 +++++++++++++++++ src/{ => PLUGIN}/plugin.h | 15 ++++- src/input.cpp | 30 ---------- src/library.cpp | 8 +++ unittest/commands/CMakeLists.txt | 2 +- unittest/commands/test_simple_commands.cpp | 2 + 16 files changed, 198 insertions(+), 51 deletions(-) create mode 100644 lib/plugin/README create mode 100755 src/PLUGIN/Install.sh create mode 100644 src/PLUGIN/README rename src/{ => PLUGIN}/plugin.cpp (87%) rename src/{ => PLUGIN}/plugin.h (84%) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 7081d6aa80..f05c7f97eb 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -113,7 +113,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF) set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS - QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI + PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF @@ -240,11 +240,6 @@ if(BUILD_OMP) target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX) endif() -# link with -ldl or equivalent for plugin loading; except on Windows -if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") - target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS}) -endif() - # Compiler specific features for testing if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF) @@ -538,6 +533,18 @@ foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU endif() endforeach() +if(PKG_PLUGIN) + if(BUILD_SHARED_LIBS) + target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN) + else() + message(WARNING "Plugin loading will not work unless BUILD_SHARED_LIBS is enabled") + endif() + # link with -ldl or equivalent for plugin loading; except on Windows + if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS}) + endif() +endif() + ###################################################################### # the windows version of LAMMPS requires a couple extra libraries # and the MPI library - if use - has to be linked right before those diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index bddefc077b..5dc58b735b 100644 --- a/cmake/presets/most.cmake +++ b/cmake/presets/most.cmake @@ -4,7 +4,7 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI - POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI + PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION diff --git a/lib/README b/lib/README index d89490e202..26c3fad9e0 100644 --- a/lib/README +++ b/lib/README @@ -19,12 +19,12 @@ atc atomistic-to-continuum methods, USER-ATC package from Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia) awpmd antisymmetrized wave packet molecular dynamics, AWPMD package from Ilya Valuev (JIHT RAS) -colvars collective variable module (Metadynamics, ABF and more) +colvars collective variable module (Metadynamics, ABF and more) from Giacomo Fiorin and Jerome Henin (ICMS, Temple U) compress hook to system lib for performing I/O compression, COMPRESS pkg - from Axel Kohlmeyer (Temple U) -gpu general GPU routines, GPU package - from Mike Brown (ORNL) + from Axel Kohlmeyer (Temple U) +gpu general GPU routines, GPU package + from Mike Brown (ORNL) h5md ch5md library for output of MD data in HDF5 format from Pierre de Buyl (KU Leuven) kim hooks to the KIM library, used by KIM package @@ -32,26 +32,28 @@ kim hooks to the KIM library, used by KIM package kokkos Kokkos package for GPU and many-core acceleration from Kokkos development team (Sandia) linalg set of BLAS and LAPACK routines needed by USER-ATC package - from Axel Kohlmeyer (Temple U) + from Axel Kohlmeyer (Temple U) message client/server communication library via MPI, sockets, files - from Steve Plimpton (Sandia) + from Steve Plimpton (Sandia) molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package from Axel Kohlmeyer (Temple U) and the VMD development team mscg hooks to the MSCG library, used by fix_mscg command from Jacob Wagner and Greg Voth group (U Chicago) netcdf hooks to a NetCDF library installed on your system from Lars Pastewka (Karlsruhe Institute of Technology) -poems POEMS rigid-body integration package, POEMS package +plugin settings to load styles into LAMMPS from plugins + from Axel Kohlmeyer (Temple U) +poems POEMS rigid-body integration package, POEMS package from Rudranarayan Mukherjee (RPI) python hooks to the system Python library, used by the PYTHON package from the LAMMPS development team -qmmm quantum mechanics/molecular mechanics coupling interface +qmmm quantum mechanics/molecular mechanics coupling interface from Axel Kohlmeyer (Temple U) quip interface to QUIP/libAtoms framework, USER-QUIP package from Albert Bartok-Partay and Gabor Csanyi (U Cambridge) smd hooks to Eigen library, used by USER-SMD package from Georg Ganzenmueller (Ernst Mach Institute, Germany) voronoi hooks to the Voro++ library, used by compute voronoi/atom command - from Daniel Schwen (LANL) + from Daniel Schwen (LANL) vtk hooks to the VTK library, used by dump custom/vtk command from Richard Berger (JKU) diff --git a/lib/plugin/README b/lib/plugin/README new file mode 100644 index 0000000000..15abea011d --- /dev/null +++ b/lib/plugin/README @@ -0,0 +1,16 @@ +This directory has a Makefile.lammps file with settings that allows +LAMMPS to dynamically link LAMMPS plugins. More details about this +are in the manual. + +In order to be able to dynamically load and execute the plugins from +inside LAMMPS, you need to link with a system library containing functions +like dlopen(), dlsym() and so on for dynamic linking of executable code +into an executable. This library is defined by setting the plugin_SYSLIB +variable in the Makefile.lammps file in this dir. For this mechanism +to work, LAMMPS must be built as a shared library (i.e. with mode=shared). + +For Linux and most current unix-like operating systems, this can be +kept at the default setting of "-ldl" (on some platforms this library +is called "-ldld"). The Windows platform is currently not supported. + +See the header of Makefile.lammps for more info. diff --git a/src/.gitignore b/src/.gitignore index 45ec71e485..6fa3aef513 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -172,6 +172,10 @@ /pair_lj_charmmfsw_coul_long.cpp /pair_lj_charmmfsw_coul_long.h +/plugin.cpp +/plugin.h +/lammpsplugin.h + /atom_vec_spin.cpp /atom_vec_spin.h /compute_spin.cpp diff --git a/src/MAKE/Makefile.mpi b/src/MAKE/Makefile.mpi index 68e79e9e8e..9776b0153e 100644 --- a/src/MAKE/Makefile.mpi +++ b/src/MAKE/Makefile.mpi @@ -13,7 +13,7 @@ DEPFLAGS = -M LINK = mpicxx LINKFLAGS = -g -O3 -LIB = -ldl +LIB = SIZE = size ARCHIVE = ar diff --git a/src/MAKE/Makefile.serial b/src/MAKE/Makefile.serial index 8b4e2e5982..0f5952f317 100644 --- a/src/MAKE/Makefile.serial +++ b/src/MAKE/Makefile.serial @@ -13,7 +13,7 @@ DEPFLAGS = -M LINK = g++ LINKFLAGS = -g -O -LIB = -ldl +LIB = SIZE = size ARCHIVE = ar diff --git a/src/Makefile b/src/Makefile index 679cbe7b97..a63c49e344 100644 --- a/src/Makefile +++ b/src/Makefile @@ -48,7 +48,7 @@ endif PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ granular kim kokkos kspace latte manybody mc message misc \ - mliap molecule mpiio mscg opt peri poems \ + mliap molecule mpiio mscg opt peri plugin poems \ python qeq replica rigid shock snap spin srd voronoi PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ diff --git a/src/PLUGIN/Install.sh b/src/PLUGIN/Install.sh new file mode 100755 index 0000000000..0df642193e --- /dev/null +++ b/src/PLUGIN/Install.sh @@ -0,0 +1,64 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# all package files with no dependencies + +for file in *.cpp *.h; do + test -f ${file} && action $file +done + +# edit 2 Makefile.package files to include/exclude package info + +if (test $1 = 1) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*plugin[^ \t]* //' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(plugin_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(plugin_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(plugin_SYSPATH) |' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*plugin.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ +include ..\/..\/lib\/plugin\/Makefile.lammps +' ../Makefile.package.settings + fi + +elif (test $1 = 0) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*plugin[^ \t]* //' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*plugin.*$/d' ../Makefile.package.settings + fi + +fi diff --git a/src/PLUGIN/README b/src/PLUGIN/README new file mode 100644 index 0000000000..4515428e35 --- /dev/null +++ b/src/PLUGIN/README @@ -0,0 +1,12 @@ +This package provides a plugin command that can load LAMMPS +styles linked into shared object files into a LAMMPS binary +at run time without having to recompile and relink LAMMPS. +For more details please see the LAMMPS manual. + +To be able to dynamically load and execute the plugins from inside +LAMMPS, you need to link with an appropriate system library, which +is done using the settings in lib/plugin/Makefile.lammps. See +that file and the lib/plugin/README file for more details. + +The person who created this package is Axel Kohlmeyer at Temple U +(akohlmey at gmail.com). Contact him directly if you have questions. diff --git a/src/plugin.cpp b/src/PLUGIN/plugin.cpp similarity index 87% rename from src/plugin.cpp rename to src/PLUGIN/plugin.cpp index e252ce67e1..1449d0d90f 100644 --- a/src/plugin.cpp +++ b/src/PLUGIN/plugin.cpp @@ -38,9 +38,53 @@ namespace LAMMPS_NS // map for counting references to dso handles static std::map dso_refcounter; + +/* ---------------------------------------------------------------------- */ + + Plugin::Plugin(LAMMPS *lmp) : Pointers(lmp) {} + +/* ---------------------------------------------------------------------- */ + + void Plugin::command(int narg, char **arg) + { + if (narg < 1) error->all(FLERR,"Illegal plugin command"); + +#if defined(LMP_PLUGIN) + std::string cmd = arg[0]; + if (cmd == "load") { + if (narg < 2) error->all(FLERR,"Illegal plugin load command"); + for (int i=1; i < narg; ++i) + plugin_load(arg[i],lmp); + + } else if (cmd == "unload") { + if (narg != 3) error->all(FLERR,"Illegal plugin unload command"); + plugin_unload(arg[1],arg[2],lmp); + + } else if (cmd == "clear") { + plugin_clear(lmp); + + } else if (cmd == "list") { + if (comm->me == 0) { + int num = plugin_get_num_plugins(); + utils::logmesg(lmp,"Currently loaded plugins\n"); + for (int i=0; i < num; ++i) { + auto entry = plugin_get_info(i); + utils::logmesg(lmp,fmt::format("{:4}: {} style plugin {}\n", + i+1,entry->style,entry->name)); + } + } + } else error->all(FLERR,"Illegal plugin command"); +#else + if (comm->me == 0) + error->warning(FLERR,"Ignoring plugin command. LAMMPS must be built as " + "a shared library for it to work."); +#endif + } + // load DSO and call included registration function void plugin_load(const char *file, LAMMPS *lmp) { +#if defined(LMP_PLUGIN) int me = lmp->comm->me; #if defined(WIN32) lmp->error->all(FLERR,"Loading of plugins on Windows is not supported\n"); @@ -77,6 +121,7 @@ namespace LAMMPS_NS (*(lammpsplugin_initfunc)(initfunc))((void *)lmp, dso, (void *)&plugin_register); +#endif #endif } @@ -89,6 +134,7 @@ namespace LAMMPS_NS void plugin_register(lammpsplugin_t *plugin, void *ptr) { +#if defined(LMP_PLUGIN) LAMMPS *lmp = (LAMMPS *)ptr; int me = lmp->comm->me; @@ -158,6 +204,7 @@ namespace LAMMPS_NS "yet implemented\n",pstyle)); pluginlist.pop_back(); } +#endif } /* -------------------------------------------------------------------- @@ -168,6 +215,7 @@ namespace LAMMPS_NS void plugin_unload(const char *style, const char *name, LAMMPS *lmp) { +#if defined(LMP_PLUGIN) int me = lmp->comm->me; // ignore unload request from unsupported style categories @@ -246,6 +294,7 @@ namespace LAMMPS_NS dlclose(handle); #endif } +#endif } /* -------------------------------------------------------------------- diff --git a/src/plugin.h b/src/PLUGIN/plugin.h similarity index 84% rename from src/plugin.h rename to src/PLUGIN/plugin.h index 90952224a6..946b08db1a 100644 --- a/src/plugin.h +++ b/src/PLUGIN/plugin.h @@ -11,14 +11,26 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#ifdef COMMAND_CLASS + +CommandStyle(plugin,Plugin) + +#else + #ifndef LMP_PLUGIN_H #define LMP_PLUGIN_H #include "lammpsplugin.h" +#include "pointers.h" namespace LAMMPS_NS { - class LAMMPS; + + class Plugin : protected Pointers { + public: + Plugin(class LAMMPS *); + void command(int, char **); + }; void plugin_load(const char *, LAMMPS *); void plugin_register(lammpsplugin_t *, void *); @@ -33,3 +45,4 @@ namespace LAMMPS_NS } #endif +#endif diff --git a/src/input.cpp b/src/input.cpp index 9979bb7705..eeb211a6d1 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -35,7 +35,6 @@ #include "neighbor.h" #include "output.h" #include "pair.h" -#include "plugin.h" #include "special.h" #include "style_command.h" #include "thermo.h" @@ -718,7 +717,6 @@ int Input::execute_command() else if (!strcmp(command,"log")) log(); else if (!strcmp(command,"next")) next_command(); else if (!strcmp(command,"partition")) partition(); - else if (!strcmp(command,"plugin")) plugin(); else if (!strcmp(command,"print")) print(); else if (!strcmp(command,"python")) python(); else if (!strcmp(command,"quit")) quit(); @@ -1097,34 +1095,6 @@ void Input::partition() /* ---------------------------------------------------------------------- */ -void Input::plugin() -{ - if (narg < 1) error->all(FLERR,"Illegal plugin command"); - std::string cmd = arg[0]; - if (cmd == "load") { - if (narg < 2) error->all(FLERR,"Illegal plugin load command"); - for (int i=1; i < narg; ++i) - plugin_load(arg[i],lmp); - } else if (cmd == "unload") { - if (narg != 3) error->all(FLERR,"Illegal plugin unload command"); - plugin_unload(arg[1],arg[2],lmp); - } else if (cmd == "clear") { - plugin_clear(lmp); - } else if (cmd == "list") { - if (comm->me == 0) { - int num = plugin_get_num_plugins(); - utils::logmesg(lmp,"Currently loaded plugins\n"); - for (int i=0; i < num; ++i) { - auto entry = plugin_get_info(i); - utils::logmesg(lmp,fmt::format("{:4}: {} style plugin {}\n", - i+1,entry->style,entry->name)); - } - } - } else error->all(FLERR,"Illegal plugin command"); -} - -/* ---------------------------------------------------------------------- */ - void Input::print() { if (narg < 1) error->all(FLERR,"Illegal print command"); diff --git a/src/library.cpp b/src/library.cpp index 68ce180107..414d0f9f3a 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -38,7 +38,9 @@ #include "neighbor.h" #include "region.h" #include "output.h" +#if defined(LMP_PLUGIN) #include "plugin.h" +#endif #include "thermo.h" #include "timer.h" #include "universe.h" @@ -4590,7 +4592,11 @@ This function counts how many plugins are currently loaded. */ int lammps_plugin_count() { +#if defined(LMP_PLUGIN) return plugin_get_num_plugins(); +#else + return 0; +#endif } /* ---------------------------------------------------------------------- */ @@ -4617,6 +4623,7 @@ set to an empty string, otherwise 1. */ int lammps_plugin_name(int idx, char *stylebuf, char *namebuf, int buf_size) { +#if defined(LMP_PLUGIN) stylebuf[0] = namebuf[0] = '\0'; const lammpsplugin_t *plugin = plugin_get_info(idx); @@ -4625,6 +4632,7 @@ int lammps_plugin_name(int idx, char *stylebuf, char *namebuf, int buf_size) strncpy(namebuf,plugin->name,buf_size); return 1; } +#endif return 0; } diff --git a/unittest/commands/CMakeLists.txt b/unittest/commands/CMakeLists.txt index 50f85475d3..6fae0c2463 100644 --- a/unittest/commands/CMakeLists.txt +++ b/unittest/commands/CMakeLists.txt @@ -1,6 +1,6 @@ # build LAMMPS plugins, but not on Windows -if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") +if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows" AND PKG_PLUGIN) ExternalProject_Add(plugins SOURCE_DIR "${LAMMPS_DIR}/examples/plugins" BINARY_DIR ${CMAKE_BINARY_DIR}/build-plugins diff --git a/unittest/commands/test_simple_commands.cpp b/unittest/commands/test_simple_commands.cpp index 448224f730..d98146d4f3 100644 --- a/unittest/commands/test_simple_commands.cpp +++ b/unittest/commands/test_simple_commands.cpp @@ -367,6 +367,7 @@ TEST_F(SimpleCommandsTest, Units) TEST_FAILURE(".*ERROR: Illegal units command.*", lmp->input->one("units unknown");); } +#if defined(LMP_PLUGIN) TEST_F(SimpleCommandsTest, Plugin) { #if defined(__APPLE__) @@ -437,6 +438,7 @@ TEST_F(SimpleCommandsTest, Plugin) if (verbose) std::cout << text; ASSERT_THAT(text, MatchesRegex(".*Currently loaded plugins.*")); } +#endif TEST_F(SimpleCommandsTest, Shell) { From 28e986c266580f87d1f100f22e309ea7f2d60c1e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 16 Mar 2021 23:25:46 -0400 Subject: [PATCH 0202/1217] add python module support for plugins --- python/lammps/core.py | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/python/lammps/core.py b/python/lammps/core.py index eaf78dfa0c..e75647fe44 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -264,6 +264,9 @@ class lammps(object): self.lib.lammps_id_name.argtypes = [c_void_p, c_char_p, c_int, c_char_p, c_int] + self.lib.lammps_plugin_count.argtypes = [ ] + self.lib.lammps_plugin_name.argtypes = [c_int, c_char_p, c_char_p, c_int] + self.lib.lammps_version.argtypes = [c_void_p] self.lib.lammps_get_os_info.argtypes = [c_char_p, c_int] @@ -1594,6 +1597,29 @@ class lammps(object): # ------------------------------------------------------------------------- + def available_plugins(self, category): + """Returns a list of plugins available for a given category + + This is a wrapper around the functions :cpp:func:`lammps_plugin_count()` + and :cpp:func:`lammps_plugin_name()` of the library interface. + + .. versionadded:: 10Mar2021 + + :return: list of style/name pairs of loaded plugins + :rtype: list + """ + + available_plugins = [] + num = self.lib.lammps_plugin_count(self.lmp) + sty = create_string_buffer(100) + nam = create_string_buffer(100) + for idx in range(num): + self.lib.lammps_plugin_name(idx, sty, nam, 100) + available_plugins.append([sty.value.decode(), nam.value.decode()]) + return available_plugins + + # ------------------------------------------------------------------------- + def set_fix_external_callback(self, fix_name, callback, caller=None): import numpy as np From 78126c5eb3f9f9cd961901301f435c0fdef7fed7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 16 Mar 2021 23:32:08 -0400 Subject: [PATCH 0203/1217] fix cmake unit test issue --- unittest/commands/CMakeLists.txt | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/unittest/commands/CMakeLists.txt b/unittest/commands/CMakeLists.txt index 6fae0c2463..a658c8a25d 100644 --- a/unittest/commands/CMakeLists.txt +++ b/unittest/commands/CMakeLists.txt @@ -23,7 +23,9 @@ if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows" AND PKG_PLUGIN) endif() add_executable(test_simple_commands test_simple_commands.cpp) -add_dependencies(test_simple_commands plugins) +if(PKG_PLUGIN) + add_dependencies(test_simple_commands plugins) +endif() target_link_libraries(test_simple_commands PRIVATE lammps GTest::GMock GTest::GTest) add_test(NAME SimpleCommands COMMAND test_simple_commands WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) From 2a6fcee5e00b70dafa49b5992507a1eaa721f797 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 16 Mar 2021 23:42:06 -0400 Subject: [PATCH 0204/1217] add missing file (was ignored by default) --- lib/plugin/Makefile.lammps | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 lib/plugin/Makefile.lammps diff --git a/lib/plugin/Makefile.lammps b/lib/plugin/Makefile.lammps new file mode 100644 index 0000000000..87f4f8a771 --- /dev/null +++ b/lib/plugin/Makefile.lammps @@ -0,0 +1,16 @@ +# This file contains the hooks to build and link LAMMPS so it can load plugins +# +# The plugin_SYSINC and plugin_SYSPATH variables do not typically need +# to be set. If the dl library is not in a place the linker can find +# it, specify its directory via the plugin_SYSPATH variable, e.g. +# -Ldir. + +# ----------------------------------------------------------- + +# Settings that the LAMMPS build will import when this package is installed + +ifeq ($(mode),shared) +plugin_SYSINC = -DLMP_PLUGIN +endif +plugin_SYSLIB = -ldl +plugin_SYSPATH = From ddc77be911e2f61967a1db4685be1c405015d32e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 16 Mar 2021 23:52:44 -0400 Subject: [PATCH 0205/1217] update docs for converting the plugin feature to a package --- doc/src/Packages_details.rst | 23 +++++++++++++++++++++++ doc/src/plugin.rst | 5 ++++- 2 files changed, 27 insertions(+), 1 deletion(-) diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index e858593c4c..301e6bfd4a 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -50,6 +50,7 @@ page gives those details. * :ref:`MSCG ` * :ref:`OPT ` * :ref:`PERI ` + * :ref:`PLUGIN ` * :ref:`POEMS ` * :ref:`PYTHON ` * :ref:`QEQ ` @@ -843,6 +844,28 @@ Foster (UTSA). ---------- +.. _PKG-PLUGIN: + +PLUGIN package +-------------- + +**Contents:** + +A :doc:`plugin ` command that can load and unload several +kind of styles in LAMMPS from shared object files at runtime without +having to recompile and relink LAMMPS. + +**Authors:** Axel Kohlmeyer (Temple U) + +**Supporting info:** + +* src/PLUGIN: filenames -> commands +* :doc:`plugin command ` +* :doc:`Information on writing plugins ` +* examples/plugin + +---------- + .. _PKG-POEMS: POEMS package diff --git a/doc/src/plugin.rst b/doc/src/plugin.rst index e8a5f67e3c..48638bf97a 100644 --- a/doc/src/plugin.rst +++ b/doc/src/plugin.rst @@ -60,7 +60,10 @@ The *clear* command will unload all currently loaded plugins. Restrictions """""""""""" -Plugins are not available on Windows. +The *plugin* command is part of the PLUGIN package. It is +only enabled if LAMMPS was built with that package. +See the :doc:`Build package ` doc page for +more info. Plugins are not available on Windows. For the loading of plugins to work the LAMMPS library must be :ref:`compiled as a shared library `. If plugins From 8d18051232ecde32e3abc0679086aa26e7a42e0f Mon Sep 17 00:00:00 2001 From: Gurgen Date: Thu, 18 Mar 2021 20:48:57 +0300 Subject: [PATCH 0206/1217] acceleration for pair_style lj/smooth --- lib/gpu/lal_lj_smooth.cpp | 17 ++++++----------- lib/gpu/lal_lj_smooth.cu | 32 ++++++++++++++++---------------- lib/gpu/lal_lj_smooth.h | 11 ++++------- 3 files changed, 26 insertions(+), 34 deletions(-) diff --git a/lib/gpu/lal_lj_smooth.cpp b/lib/gpu/lal_lj_smooth.cpp index d2ab63549d..5e4785230b 100644 --- a/lib/gpu/lal_lj_smooth.cpp +++ b/lib/gpu/lal_lj_smooth.cpp @@ -2,13 +2,10 @@ lj_smooth.cpp ------------------- W. Michael Brown (ORNL) - Class for acceleration of the lj/smooth pair style. - __________________________________________________________________________ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) __________________________________________________________________________ - begin : email : brownw@ornl.gov ***************************************************************************/ @@ -83,15 +80,14 @@ int LJSMOOTHT::init(const int ntypes, lj3.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); this->atom->type_pack4(ntypes,lj_types,lj3,host_write,host_lj3,host_lj4, - host_offset, cut_inner); + host_offset); ljsw.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); this->atom->type_pack4(ntypes,lj_types,ljsw,host_write,host_ljsw1,host_ljsw2, host_ljsw3,host_ljsw4); ljsw0.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); - this->atom->type_pack4(ntypes,lj_types,ljsw0,host_write,host_ljsw0,cut_inner,host_ljsw2, - host_ljsw3); + this->atom->type_pack2(ntypes,lj_types,ljsw0,host_write,host_ljsw0,cut_inner); UCL_H_Vec dview; sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY); @@ -118,13 +114,12 @@ void LJSMOOTHT::reinit(const int ntypes, double **host_cutsq, double **host_lj1, host_write[i]=0.0; this->atom->type_pack4(ntypes,_lj_types,lj1,host_write,host_lj1,host_lj2, - host_cutsq, cut_inner_sq); + host_cutsq,cut_inner_sq); this->atom->type_pack4(ntypes,_lj_types,lj3,host_write,host_lj3,host_lj4, - host_offset, cut_inner); + host_offset); this->atom->type_pack4(ntypes,_lj_types,ljsw,host_write,host_ljsw1,host_ljsw2, host_ljsw3,host_ljsw4); - this->atom->type_pack4(ntypes,_lj_types,ljsw0,host_write,host_ljsw0, cut_inner, host_ljsw2, - host_ljsw3); + this->atom->type_pack2(ntypes,_lj_types,ljsw0,host_write,host_ljsw0,cut_inner); } template @@ -188,4 +183,4 @@ void LJSMOOTHT::loop(const bool _eflag, const bool _vflag) { } template class LJSMOOTH; -} +} \ No newline at end of file diff --git a/lib/gpu/lal_lj_smooth.cu b/lib/gpu/lal_lj_smooth.cu index 345da1c702..c02e1b5ae0 100644 --- a/lib/gpu/lal_lj_smooth.cu +++ b/lib/gpu/lal_lj_smooth.cu @@ -28,7 +28,7 @@ __kernel void k_lj_smooth(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict lj1, const __global numtyp4 *restrict lj3, const __global numtyp4 *restrict ljsw, - const __global numtyp4 *restrict ljsw0, + const __global numtyp2 *restrict ljsw0, const int lj_types, const __global numtyp *restrict sp_lj, const __global int * dev_nbor, @@ -56,8 +56,9 @@ __kernel void k_lj_smooth(const __global numtyp4 *restrict x_, numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i]; int itype=ix.w; - numtyp factor_lj; + numtyp force, r6inv, factor_lj, forcelj; numtyp r, t, tsq, fskin; + for ( ; nbor0) { @@ -231,5 +232,4 @@ __kernel void k_lj_smooth_fast(const __global numtyp4 *restrict x_, store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, ans,engv); } // if ii -} - +} \ No newline at end of file diff --git a/lib/gpu/lal_lj_smooth.h b/lib/gpu/lal_lj_smooth.h index 0a4cdf78eb..f869977c58 100644 --- a/lib/gpu/lal_lj_smooth.h +++ b/lib/gpu/lal_lj_smooth.h @@ -2,13 +2,10 @@ lj_smooth.h ------------------- W. Michael Brown (ORNL) - Class for acceleration of the lj/smooth pair style. - __________________________________________________________________________ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) __________________________________________________________________________ - begin : email : brownw@ornl.gov ***************************************************************************/ @@ -69,12 +66,12 @@ class LJSMOOTH : public BaseAtomic { /// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq, lj1.w = cut_inner_sq UCL_D_Vec lj1; - /// lj3.x = lj3, lj3.y = lj4, lj3.z = offset, lj3.w = cut_inner + /// lj3.x = lj3, lj3.y = lj4, lj3.z = offset UCL_D_Vec lj3; /// ljsw.x = ljsw1, ljsw.y = ljsw2, ljsw.z = ljsw3, ljsw.w = ljsw4 UCL_D_Vec ljsw; - /// ljsw0 - UCL_D_Vec ljsw0; + /// ljsw0.x = ljsw0 ljsw0.y = cut_inner + UCL_D_Vec ljsw0; /// Special LJ values UCL_D_Vec sp_lj; @@ -91,4 +88,4 @@ class LJSMOOTH : public BaseAtomic { } -#endif +#endif \ No newline at end of file From 9b29b1594bd35f32a1d728e6c8d32a355c324665 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 18 Mar 2021 14:40:41 -0400 Subject: [PATCH 0207/1217] add support for bond/angle/dihedral/improper plugins --- examples/plugins/CMakeLists.txt | 8 +- examples/plugins/Makefile | 28 +--- examples/plugins/Makefile.common | 36 ++++ examples/plugins/Makefile.macos | 30 +--- examples/plugins/Makefile.serial | 28 +--- examples/plugins/angle_zero2.cpp | 152 +++++++++++++++++ examples/plugins/angle_zero2.h | 57 +++++++ examples/plugins/bond_zero2.cpp | 161 ++++++++++++++++++ examples/plugins/bond_zero2.h | 58 +++++++ examples/plugins/dihedral_zero2.cpp | 121 ++++++++++++++ examples/plugins/dihedral_zero2.h | 57 +++++++ examples/plugins/improper_zero2.cpp | 122 ++++++++++++++ examples/plugins/improper_zero2.h | 53 ++++++ examples/plugins/pair_zero2.cpp | 247 ++++++++++++++++++++++++++++ examples/plugins/pair_zero2.h | 77 +++++++++ examples/plugins/zero2plugin.cpp | 78 +++++++++ src/PLUGIN/plugin.cpp | 94 ++++++++++- 17 files changed, 1323 insertions(+), 84 deletions(-) create mode 100644 examples/plugins/Makefile.common create mode 100644 examples/plugins/angle_zero2.cpp create mode 100644 examples/plugins/angle_zero2.h create mode 100644 examples/plugins/bond_zero2.cpp create mode 100644 examples/plugins/bond_zero2.h create mode 100644 examples/plugins/dihedral_zero2.cpp create mode 100644 examples/plugins/dihedral_zero2.h create mode 100644 examples/plugins/improper_zero2.cpp create mode 100644 examples/plugins/improper_zero2.h create mode 100644 examples/plugins/pair_zero2.cpp create mode 100644 examples/plugins/pair_zero2.h create mode 100644 examples/plugins/zero2plugin.cpp diff --git a/examples/plugins/CMakeLists.txt b/examples/plugins/CMakeLists.txt index 74a1cd4e3b..6e29676530 100644 --- a/examples/plugins/CMakeLists.txt +++ b/examples/plugins/CMakeLists.txt @@ -53,12 +53,16 @@ target_link_libraries(nve2plugin PRIVATE lammps) add_library(helloplugin MODULE helloplugin.cpp) target_link_libraries(helloplugin PRIVATE lammps) -set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES +add_library(zero2plugin MODULE zero2plugin.cpp pair_zero2.cpp bond_zero2.cpp + angle_zero2.cpp dihedral_zero2.cpp improper_zero2.cpp) +target_link_libraries(zero2plugin PRIVATE lammps) + +set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES PREFIX "" LINK_FLAGS "-rdynamic") # MacOS seems to need this if(CMAKE_SYSTEM_NAME STREQUAL Darwin) - set_target_properties(morse2plugin nve2plugin helloplugin PROPERTIES + set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup") endif() diff --git a/examples/plugins/Makefile b/examples/plugins/Makefile index dbb0023991..f4d8b41086 100644 --- a/examples/plugins/Makefile +++ b/examples/plugins/Makefile @@ -1,30 +1,6 @@ CXX=mpicxx CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp LD=$(CXX) -shared -rdynamic -fopenmp +DSOEXT=.so -default: morse2plugin.so nve2plugin.so helloplugin.so - -helloplugin.so: helloplugin.o - $(LD) -o $@ $^ - -morse2plugin.so: morse2plugin.o pair_morse2.o pair_morse2_omp.o - $(LD) -o $@ $^ - -nve2plugin.so: nve2plugin.o fix_nve2.o - $(LD) -o $@ $^ - -.cpp.o: - $(CXX) -o $@ $(CXXFLAGS) -c $< - -helloplugin.o: helloplugin.cpp - -pair_morse2.o: pair_morse2.cpp pair_morse2.h -pair_morse2_omp.o: pair_morse2_omp.cpp pair_morse2_omp.h pair_morse2.h -morse2plugin.o: morse2plugin.cpp pair_morse2.h pair_morse2_omp.h - -fix_nve2.o: fix_nve2.cpp fix_nve2.h -nve2plugin.o: nve2plugin.cpp fix_nve2.h - -clean: - rm -rf *~ *.so *.dylib *.o log.lammps CMakeCache.txt CMakeFiles - +include Makefile.common diff --git a/examples/plugins/Makefile.common b/examples/plugins/Makefile.common new file mode 100644 index 0000000000..e78fa13feb --- /dev/null +++ b/examples/plugins/Makefile.common @@ -0,0 +1,36 @@ +default: morse2plugin$(DSOEXT) nve2plugin$(DSOEXT) helloplugin$(DSOEXT) zero2plugin$(DSOEXT) + +helloplugin$(DSOEXT): helloplugin.o + $(LD) -o $@ $^ + +morse2plugin$(DSOEXT): morse2plugin.o pair_morse2.o pair_morse2_omp.o + $(LD) -o $@ $^ + +nve2plugin$(DSOEXT): nve2plugin.o fix_nve2.o + $(LD) -o $@ $^ + +zero2plugin$(DSOEXT): zero2plugin.o pair_zero2.o bond_zero2.o angle_zero2.o dihedral_zero2.o improper_zero2.o + $(LD) -o $@ $^ + +.cpp.o: + $(CXX) -o $@ $(CXXFLAGS) -c $< + +helloplugin.o: helloplugin.cpp + +pair_morse2.o: pair_morse2.cpp pair_morse2.h +pair_morse2_omp.o: pair_morse2_omp.cpp pair_morse2_omp.h pair_morse2.h +morse2plugin.o: morse2plugin.cpp pair_morse2.h pair_morse2_omp.h + +fix_nve2.o: fix_nve2.cpp fix_nve2.h +nve2plugin.o: nve2plugin.cpp fix_nve2.h + +pair_zero2.o: pair_zero2.cpp pair_zero2.h +bond_zero2.o: bond_zero2.cpp bond_zero2.h +angle_zero2.o: angle_zero2.cpp angle_zero2.h +dihedral_zero2.o: dihedral_zero2.cpp dihedral_zero2.h +improper_zero2.o: improper_zero2.cpp improper_zero2.h +zero2plugin.o: zero2plugin.cpp pair_zero2.h bond_zero2.h angle_zero2.h dihedral_zero2.h + +clean: + rm -rf *~ *.so *.dylib *.o log.lammps CMakeCache.txt CMakeFiles + diff --git a/examples/plugins/Makefile.macos b/examples/plugins/Makefile.macos index 2490418a09..a7c20ff90f 100644 --- a/examples/plugins/Makefile.macos +++ b/examples/plugins/Makefile.macos @@ -1,30 +1,6 @@ CXX=mpicxx -CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP +CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP LD=$(CXX) -bundle -rdynamic -Wl,-undefined,dynamic_lookup +DSOEXT=.dylib -default: morse2plugin.dylib nve2plugin.dylib helloplugin.dylib - -helloplugin.dylib: helloplugin.o - $(LD) -o $@ $^ - -morse2plugin.dylib: morse2plugin.o pair_morse2.o pair_morse2_omp.o - $(LD) -o $@ $^ - -nve2plugin.dylib: nve2plugin.o fix_nve2.o - $(LD) -o $@ $^ - -.cpp.o: - $(CXX) -o $@ $(CXXFLAGS) -c $< - -helloplugin.o: helloplugin.cpp - -pair_morse2.o: pair_morse2.cpp pair_morse2.h -pair_morse2_omp.o: pair_morse2_omp.cpp pair_morse2_omp.h pair_morse2.h -morse2plugin.o: morse2plugin.cpp pair_morse2.h pair_morse2_omp.h - -fix_nve2.o: fix_nve2.cpp fix_nve2.h -nve2plugin.o: nve2plugin.cpp fix_nve2.h - -clean: - rm -rf *~ *.dylib *.dylib *.o log.lammps CMakeCache.txt CMakeFiles - +include Makefile.common diff --git a/examples/plugins/Makefile.serial b/examples/plugins/Makefile.serial index feb58bd9b3..ecc7631a05 100644 --- a/examples/plugins/Makefile.serial +++ b/examples/plugins/Makefile.serial @@ -1,30 +1,6 @@ CXX=g++ CXXFLAGS=-I../../src -I../../src/STUBS -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp LD=$(CXX) -shared -rdynamic -fopenmp +DSOEXT=.so -default: morse2plugin.so nve2plugin.so helloplugin.so - -helloplugin.so: helloplugin.o - $(LD) -o $@ $^ - -morse2plugin.so: morse2plugin.o pair_morse2.o pair_morse2_omp.o - $(LD) -o $@ $^ - -nve2plugin.so: nve2plugin.o fix_nve2.o - $(LD) -o $@ $^ - -.cpp.o: - $(CXX) -o $@ $(CXXFLAGS) -c $< - -helloplugin.o: helloplugin.cpp - -pair_morse2.o: pair_morse2.cpp pair_morse2.h -pair_morse2_omp.o: pair_morse2_omp.cpp pair_morse2_omp.h pair_morse2.h -morse2plugin.o: morse2plugin.cpp pair_morse2.h pair_morse2_omp.h - -fix_nve2.o: fix_nve2.cpp fix_nve2.h -nve2plugin.o: nve2plugin.cpp fix_nve2.h - -clean: - rm -rf *~ *.so *.dylib *.o log.lammps CMakeCache.txt CMakeFiles - +include Makefile.common diff --git a/examples/plugins/angle_zero2.cpp b/examples/plugins/angle_zero2.cpp new file mode 100644 index 0000000000..c0d01f14a5 --- /dev/null +++ b/examples/plugins/angle_zero2.cpp @@ -0,0 +1,152 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Carsten Svaneborg (SDU) +------------------------------------------------------------------------- */ + +#include "angle_zero2.h" + +#include "atom.h" +#include "comm.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +#include + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +AngleZero2::AngleZero2(LAMMPS *lmp) : Angle(lmp), coeffflag(1) {} + +/* ---------------------------------------------------------------------- */ + +AngleZero2::~AngleZero2() +{ + if (allocated && !copymode) { + memory->destroy(setflag); + memory->destroy(theta0); + } +} + +/* ---------------------------------------------------------------------- */ + +void AngleZero2::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); +} + +/* ---------------------------------------------------------------------- */ + +void AngleZero2::settings(int narg, char **arg) +{ + if ((narg != 0) && (narg != 1)) + error->all(FLERR,"Illegal angle_style command"); + + if (narg == 1) { + if (strcmp("nocoeff",arg[0]) == 0) coeffflag=0; + else error->all(FLERR,"Illegal angle_style command"); + } +} + +/* ---------------------------------------------------------------------- */ + +void AngleZero2::allocate() +{ + allocated = 1; + int n = atom->nangletypes; + + memory->create(theta0,n+1,"angle:theta0"); + memory->create(setflag,n+1,"angle:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +void AngleZero2::coeff(int narg, char **arg) +{ + if ((narg < 1) || (coeffflag && narg > 2)) + error->all(FLERR,"Incorrect args for angle coefficients"); + + if (!allocated) allocate(); + + int ilo,ihi; + utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error); + + double theta0_one = 0.0; + if (coeffflag && (narg == 2)) + theta0_one = utils::numeric(FLERR,arg[1],false,lmp); + + // convert theta0 from degrees to radians + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + setflag[i] = 1; + theta0[i] = theta0_one/180.0 * MY_PI; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); +} + +/* ---------------------------------------------------------------------- */ + +double AngleZero2::equilibrium_angle(int i) +{ + return theta0[i]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void AngleZero2::write_restart(FILE *fp) { + fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void AngleZero2::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,nullptr,error); + } + MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world); + + for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1; +} +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void AngleZero2::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nangletypes; i++) + fprintf(fp,"%d %g\n",i,theta0[i]/MY_PI*180.0); +} + +/* ---------------------------------------------------------------------- */ + +double AngleZero2::single(int /*type*/, int /*i1*/, int /*i2*/, int /*i3*/) +{ + return 0.0; +} diff --git a/examples/plugins/angle_zero2.h b/examples/plugins/angle_zero2.h new file mode 100644 index 0000000000..15a16b197f --- /dev/null +++ b/examples/plugins/angle_zero2.h @@ -0,0 +1,57 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_ANGLE_ZERO2_H +#define LMP_ANGLE_ZERO2_H + +#include "angle.h" + +namespace LAMMPS_NS { + +class AngleZero2 : public Angle { + public: + AngleZero2(class LAMMPS *); + virtual ~AngleZero2(); + virtual void compute(int, int); + virtual void coeff(int, char **); + virtual void settings(int, char **); + + double equilibrium_angle(int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_data(FILE *); + + double single(int, int, int, int); + + protected: + double *theta0; + int coeffflag; + + void allocate(); +}; + +} + +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +UNDOCUMENTED + +E: Incorrect args for angle coefficients + +Self-explanatory. Check the input script or data file. + +*/ diff --git a/examples/plugins/bond_zero2.cpp b/examples/plugins/bond_zero2.cpp new file mode 100644 index 0000000000..b015a60ed3 --- /dev/null +++ b/examples/plugins/bond_zero2.cpp @@ -0,0 +1,161 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Carsten Svaneborg (SDU) +------------------------------------------------------------------------- */ + +#include "bond_zero2.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "memory.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +BondZero2::BondZero2(LAMMPS *lmp) : Bond(lmp), coeffflag(1) {} + +/* ---------------------------------------------------------------------- */ + +BondZero2::~BondZero2() +{ + if (allocated && !copymode) { + memory->destroy(setflag); + memory->destroy(r0); + } +} + +/* ---------------------------------------------------------------------- */ + +void BondZero2::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); +} + +/* ---------------------------------------------------------------------- */ + +void BondZero2::settings(int narg, char **arg) +{ + if ((narg != 0) && (narg != 1)) + error->all(FLERR,"Illegal bond_style command"); + + if (narg == 1) { + if (strcmp("nocoeff",arg[0]) == 0) coeffflag=0; + else error->all(FLERR,"Illegal bond_style command"); + } +} + +/* ---------------------------------------------------------------------- */ + +void BondZero2::allocate() +{ + allocated = 1; + int n = atom->nbondtypes; + + memory->create(r0,n+1,"bond:r0"); + memory->create(setflag,n+1,"bond:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +void BondZero2::coeff(int narg, char **arg) +{ + if ((narg < 1) || (coeffflag && narg > 2)) + error->all(FLERR,"Incorrect args for bond coefficients"); + + if (!allocated) allocate(); + + int ilo,ihi; + utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error); + + double r0_one = 0.0; + if (coeffflag && (narg == 2)) + r0_one = utils::numeric(FLERR,arg[1],false,lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + setflag[i] = 1; + r0[i] = r0_one; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients"); +} + +/* ---------------------------------------------------------------------- + return an equilbrium bond length +------------------------------------------------------------------------- */ + +double BondZero2::equilibrium_distance(int i) +{ + return r0[i]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void BondZero2::write_restart(FILE *fp) { + fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void BondZero2::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); + } + MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); + + for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void BondZero2::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nbondtypes; i++) + fprintf(fp,"%d %g\n",i,r0[i]); +} + +/* ---------------------------------------------------------------------- */ + +double BondZero2::single(int /*type*/, double /*rsq*/, int /*i*/, int /*j*/, + double & /*fforce*/) +{ + return 0.0; +} + +/* ---------------------------------------------------------------------- */ + +void *BondZero2::extract(const char *str, int &dim) +{ + dim = 1; + if (strcmp(str,"r0")==0) return (void*) r0; + return nullptr; +} diff --git a/examples/plugins/bond_zero2.h b/examples/plugins/bond_zero2.h new file mode 100644 index 0000000000..37609561a7 --- /dev/null +++ b/examples/plugins/bond_zero2.h @@ -0,0 +1,58 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_BOND_ZERO2_H +#define LMP_BOND_ZERO2_H + +#include "bond.h" + +namespace LAMMPS_NS { + +class BondZero2 : public Bond { + public: + BondZero2(class LAMMPS *); + virtual ~BondZero2(); + virtual void compute(int, int); + virtual void settings(int, char **); + + void coeff(int, char **); + double equilibrium_distance(int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_data(FILE *); + + double single(int, double, int, int, double &); + virtual void *extract(const char *, int &); + + protected: + double *r0; + int coeffflag; + + virtual void allocate(); +}; + +} + +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +UNDOCUMENTED + +E: Incorrect args for bond coefficients + +Self-explanatory. Check the input script or data file. + +*/ diff --git a/examples/plugins/dihedral_zero2.cpp b/examples/plugins/dihedral_zero2.cpp new file mode 100644 index 0000000000..00d9817c96 --- /dev/null +++ b/examples/plugins/dihedral_zero2.cpp @@ -0,0 +1,121 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Carsten Svaneborg (SDU) +------------------------------------------------------------------------- */ + +#include "dihedral_zero2.h" + +#include "atom.h" +#include "error.h" +#include "memory.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +DihedralZero2::DihedralZero2(LAMMPS *lmp) : Dihedral(lmp), coeffflag(1) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +DihedralZero2::~DihedralZero2() +{ + if (allocated && !copymode) { + memory->destroy(setflag); + } +} + +/* ---------------------------------------------------------------------- */ + +void DihedralZero2::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); +} + +/* ---------------------------------------------------------------------- */ + +void DihedralZero2::settings(int narg, char **arg) +{ + if ((narg != 0) && (narg != 1)) + error->all(FLERR,"Illegal dihedral_style command"); + + if (narg == 1) { + if (strcmp("nocoeff",arg[0]) == 0) coeffflag=0; + else error->all(FLERR,"Illegal dihedral_style command"); + } +} + +/* ---------------------------------------------------------------------- */ + +void DihedralZero2::allocate() +{ + allocated = 1; + int n = atom->ndihedraltypes; + + memory->create(setflag,n+1,"dihedral:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +void DihedralZero2::coeff(int narg, char **arg) +{ + if ((narg < 1) || (coeffflag && narg > 1)) + error->all(FLERR,"Incorrect args for dihedral coefficients"); + + if (!allocated) allocate(); + + int ilo,ihi; + utils::bounds(FLERR,arg[0],1,atom->ndihedraltypes,ilo,ihi,error); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + setflag[i] = 1; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients"); +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void DihedralZero2::write_restart(FILE * /*fp*/) {} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void DihedralZero2::read_restart(FILE * /*fp*/) +{ + allocate(); + for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void DihedralZero2::write_data(FILE *fp) { + for (int i = 1; i <= atom->ndihedraltypes; i++) + fprintf(fp,"%d\n",i); +} diff --git a/examples/plugins/dihedral_zero2.h b/examples/plugins/dihedral_zero2.h new file mode 100644 index 0000000000..510e384340 --- /dev/null +++ b/examples/plugins/dihedral_zero2.h @@ -0,0 +1,57 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + + Identical to dihedral harmonic, except if all k's are zero the + force loop is skipped. + +------------------------------------------------------------------------- */ + +#ifndef LMP_DIHEDRAL_ZERO2_H +#define LMP_DIHEDRAL_ZERO2_H + +#include "dihedral.h" + +namespace LAMMPS_NS { + +class DihedralZero2 : public Dihedral { + public: + DihedralZero2(class LAMMPS *); + virtual ~DihedralZero2(); + virtual void compute(int, int); + virtual void coeff(int, char **); + virtual void settings(int, char **); + + void write_restart(FILE *); + void read_restart(FILE *); + void write_data(FILE *); + + protected: + int coeffflag; + + virtual void allocate(); +}; + +} + +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +UNDOCUMENTED + +E: Incorrect args for dihedral coefficients + +UNDOCUMENTED + +*/ diff --git a/examples/plugins/improper_zero2.cpp b/examples/plugins/improper_zero2.cpp new file mode 100644 index 0000000000..2370b32a02 --- /dev/null +++ b/examples/plugins/improper_zero2.cpp @@ -0,0 +1,122 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Carsten Svaneborg (SDU) +------------------------------------------------------------------------- */ + +#include "improper_zero2.h" + +#include "atom.h" +#include "error.h" +#include "memory.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ImproperZero2::ImproperZero2(LAMMPS *lmp) : Improper(lmp), coeffflag(1) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +ImproperZero2::~ImproperZero2() +{ + if (allocated && !copymode) { + memory->destroy(setflag); + } +} + +/* ---------------------------------------------------------------------- */ + +void ImproperZero2::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); +} + +/* ---------------------------------------------------------------------- */ + +void ImproperZero2::settings(int narg, char **arg) +{ + if ((narg != 0) && (narg != 1)) + error->all(FLERR,"Illegal improper_style command"); + + if (narg == 1) { + if (strcmp("nocoeff",arg[0]) == 0) coeffflag=0; + else error->all(FLERR,"Illegal improper_style command"); + } +} + +/* ---------------------------------------------------------------------- */ + +void ImproperZero2::allocate() +{ + allocated = 1; + int n = atom->nimpropertypes; + + memory->create(setflag,n+1,"improper:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +void ImproperZero2::coeff(int narg, char **arg) +{ + if ((narg < 1) || (coeffflag && narg > 1)) + error->all(FLERR,"Incorrect args for improper coefficients"); + + if (!allocated) allocate(); + + int ilo,ihi; + utils::bounds(FLERR,arg[0],1,atom->nimpropertypes,ilo,ihi,error); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + setflag[i] = 1; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients"); +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void ImproperZero2::write_restart(FILE * /*fp*/) {} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void ImproperZero2::read_restart(FILE * /*fp*/) +{ + allocate(); + for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void ImproperZero2::write_data(FILE *fp) { + for (int i = 1; i <= atom->nimpropertypes; i++) + fprintf(fp,"%d\n",i); +} + diff --git a/examples/plugins/improper_zero2.h b/examples/plugins/improper_zero2.h new file mode 100644 index 0000000000..64dd94920a --- /dev/null +++ b/examples/plugins/improper_zero2.h @@ -0,0 +1,53 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_IMPROPER_ZERO2_H +#define LMP_IMPROPER_ZERO2_H + +#include "improper.h" + +namespace LAMMPS_NS { + +class ImproperZero2 : public Improper { + public: + ImproperZero2(class LAMMPS *); + virtual ~ImproperZero2(); + virtual void compute(int, int); + virtual void coeff(int, char **); + virtual void settings(int, char **); + + void write_restart(FILE *); + void read_restart(FILE *); + void write_data(FILE *); + + protected: + int coeffflag; + + virtual void allocate(); +}; + +} + +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +UNDOCUMENTED + +E: Incorrect args for improper coefficients + +Self-explanatory. Check the input script or data file. + +*/ diff --git a/examples/plugins/pair_zero2.cpp b/examples/plugins/pair_zero2.cpp new file mode 100644 index 0000000000..d8e23c902d --- /dev/null +++ b/examples/plugins/pair_zero2.cpp @@ -0,0 +1,247 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Carsten Svaneborg (SDU) +------------------------------------------------------------------------- */ + +#include "pair_zero2.h" + +#include "atom.h" +#include "comm.h" +#include "memory.h" +#include "error.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairZero2::PairZero2(LAMMPS *lmp) : Pair(lmp) { + coeffflag=1; + writedata=1; + single_enable=1; + respa_enable=1; +} + +/* ---------------------------------------------------------------------- */ + +PairZero2::~PairZero2() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(cut); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairZero2::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- */ + +void PairZero2::compute_outer(int eflag, int vflag) +{ + ev_init(eflag,vflag); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairZero2::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cut,n+1,n+1,"pair:cut"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairZero2::settings(int narg, char **arg) +{ + if ((narg != 1) && (narg != 2)) + error->all(FLERR,"Illegal pair_style command"); + + cut_global = utils::numeric(FLERR,arg[0],false,lmp); + if (narg == 2) { + if (strcmp("nocoeff",arg[1]) == 0) coeffflag=0; + else error->all(FLERR,"Illegal pair_style command"); + } + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairZero2::coeff(int narg, char **arg) +{ + if ((narg < 2) || (coeffflag && narg > 3)) + error->all(FLERR,"Incorrect args for pair coefficients"); + + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + + double cut_one = cut_global; + if (coeffflag && (narg == 3)) cut_one = utils::numeric(FLERR,arg[2],false,lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairZero2::init_one(int i, int j) +{ + if (setflag[i][j] == 0) { + cut[i][j] = mix_distance(cut[i][i],cut[j][j]); + } + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairZero2::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairZero2::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + } + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairZero2::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&coeffflag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairZero2::read_restart_settings(FILE *fp) +{ + int me = comm->me; + if (me == 0) { + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&coeffflag,sizeof(int),1,fp,nullptr,error); + } + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&coeffflag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairZero2::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d\n",i); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairZero2::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g\n",i,j,cut[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairZero2::single(int /*i*/, int /*j*/, int /* itype */, int /* jtype */, + double /* rsq */, double /*factor_coul*/, + double /* factor_lj */, double &fforce) +{ + fforce = 0.0; + return 0.0; +} + diff --git a/examples/plugins/pair_zero2.h b/examples/plugins/pair_zero2.h new file mode 100644 index 0000000000..39aa160913 --- /dev/null +++ b/examples/plugins/pair_zero2.h @@ -0,0 +1,77 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + + Pair zero is a dummy pair interaction useful for requiring a + force cutoff distance in the absence of pair-interactions or + with hybrid/overlay if a larger force cutoff distance is required. + + This can be used in conjunction with bond/create to create bonds + that are longer than the cutoff of a given force field, or to + calculate radial distribution functions for models without + pair interactions. + +------------------------------------------------------------------------- */ + +#ifndef LMP_PAIR_ZERO2_H +#define LMP_PAIR_ZERO2_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairZero2 : public Pair { + public: + PairZero2(class LAMMPS *); + virtual ~PairZero2(); + virtual void compute(int, int); + virtual void compute_outer(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + double single(int, int, int, int, double, double, double, double &); + + protected: + double cut_global; + double **cut; + int coeffflag; + + virtual void allocate(); +}; + +} + +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +U: Pair cutoff < Respa interior cutoff + +One or more pairwise cutoffs are too short to use with the specified +rRESPA cutoffs. + +*/ diff --git a/examples/plugins/zero2plugin.cpp b/examples/plugins/zero2plugin.cpp new file mode 100644 index 0000000000..f181eae781 --- /dev/null +++ b/examples/plugins/zero2plugin.cpp @@ -0,0 +1,78 @@ + +#include "lammpsplugin.h" +#include "version.h" + +#include + +#include "pair_zero2.h" +#include "bond_zero2.h" +#include "angle_zero2.h" +#include "dihedral_zero2.h" +#include "improper_zero2.h" + +using namespace LAMMPS_NS; + +static Pair *pairzerocreator(LAMMPS *lmp) +{ + return new PairZero2(lmp); +} + +static Bond *bondzerocreator(LAMMPS *lmp) +{ + return new BondZero2(lmp); +} + +static Angle *anglezerocreator(LAMMPS *lmp) +{ + return new AngleZero2(lmp); +} + +static Dihedral *dihedralzerocreator(LAMMPS *lmp) +{ + return new DihedralZero2(lmp); +} + +static Improper *improperzerocreator(LAMMPS *lmp) +{ + return new ImproperZero2(lmp); +} + +extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) +{ + lammpsplugin_t plugin; + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + + // register zero2 pair style + plugin.version = LAMMPS_VERSION; + plugin.style = "pair"; + plugin.name = "zero2"; + plugin.info = "Zero2 variant pair style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &pairzerocreator; + plugin.handle = handle; + (*register_plugin)(&plugin,lmp); + + // register zero2 bond style + plugin.style = "bond"; + plugin.info = "Zero2 variant bond style v1.0"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &bondzerocreator; + (*register_plugin)(&plugin,lmp); + + // register zero2 angle style + plugin.style = "angle"; + plugin.info = "Zero2 variant angle style v1.0"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &anglezerocreator; + (*register_plugin)(&plugin,lmp); + + // register zero2 dihedral style + plugin.style = "dihedral"; + plugin.info = "Zero2 variant dihedral style v1.0"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &dihedralzerocreator; + (*register_plugin)(&plugin,lmp); + + // register zero2 improper style + plugin.style = "improper"; + plugin.info = "Zero2 variant improper style v1.0"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &improperzerocreator; + (*register_plugin)(&plugin,lmp); +} diff --git a/src/PLUGIN/plugin.cpp b/src/PLUGIN/plugin.cpp index 1449d0d90f..91d22b2897 100644 --- a/src/PLUGIN/plugin.cpp +++ b/src/PLUGIN/plugin.cpp @@ -19,7 +19,6 @@ #include "force.h" #include "lammps.h" #include "modify.h" -#include "pair.h" #include #include @@ -179,6 +178,46 @@ namespace LAMMPS_NS } (*pair_map)[plugin->name] = (Force::PairCreator)plugin->creator.v1; + } else if (pstyle == "bond") { + auto bond_map = lmp->force->bond_map; + if (bond_map->find(plugin->name) != bond_map->end()) { + if (lmp->comm->me == 0) + lmp->error->warning(FLERR,fmt::format("Overriding built-in bond " + "style {} from plugin", + plugin->name)); + } + (*bond_map)[plugin->name] = (Force::BondCreator)plugin->creator.v1; + + } else if (pstyle == "angle") { + auto angle_map = lmp->force->angle_map; + if (angle_map->find(plugin->name) != angle_map->end()) { + if (lmp->comm->me == 0) + lmp->error->warning(FLERR,fmt::format("Overriding built-in angle " + "style {} from plugin", + plugin->name)); + } + (*angle_map)[plugin->name] = (Force::AngleCreator)plugin->creator.v1; + + } else if (pstyle == "dihedral") { + auto dihedral_map = lmp->force->dihedral_map; + if (dihedral_map->find(plugin->name) != dihedral_map->end()) { + if (lmp->comm->me == 0) + lmp->error->warning(FLERR,fmt::format("Overriding built-in dihedral " + "style {} from plugin", + plugin->name)); + } + (*dihedral_map)[plugin->name] = (Force::DihedralCreator)plugin->creator.v1; + + } else if (pstyle == "improper") { + auto improper_map = lmp->force->improper_map; + if (improper_map->find(plugin->name) != improper_map->end()) { + if (lmp->comm->me == 0) + lmp->error->warning(FLERR,fmt::format("Overriding built-in improper " + "style {} from plugin", + plugin->name)); + } + (*improper_map)[plugin->name] = (Force::ImproperCreator)plugin->creator.v1; + } else if (pstyle == "fix") { auto fix_map = lmp->modify->fix_map; if (fix_map->find(plugin->name) != fix_map->end()) { @@ -219,8 +258,9 @@ namespace LAMMPS_NS int me = lmp->comm->me; // ignore unload request from unsupported style categories - if ((strcmp(style,"pair") != 0) - && (strcmp(style,"fix") != 0) + if ((strcmp(style,"pair") != 0) && (strcmp(style,"bond") != 0) + && (strcmp(style,"angle") != 0) && (strcmp(style,"dihedral") != 0) + && (strcmp(style,"improper") != 0) && (strcmp(style,"fix") != 0) && (strcmp(style,"command") != 0)) { if (me == 0) utils::logmesg(lmp,fmt::format("Ignoring unload: {} is not a " @@ -269,6 +309,54 @@ namespace LAMMPS_NS } } + } else if (pstyle == "bond") { + + auto found = lmp->force->bond_map->find(name); + if (found != lmp->force->bond_map->end()) + lmp->force->bond_map->erase(found); + + // must delete bond style instance if in use + + if ((lmp->force->bond_style != nullptr) + && (lmp->force->bond_match(name) != nullptr)) + lmp->force->create_bond("none",0); + + } else if (pstyle == "angle") { + + auto found = lmp->force->angle_map->find(name); + if (found != lmp->force->angle_map->end()) + lmp->force->angle_map->erase(found); + + // must delete angle style instance if in use + + if ((lmp->force->angle_style != nullptr) + && (lmp->force->angle_match(name) != nullptr)) + lmp->force->create_angle("none",0); + + } else if (pstyle == "dihedral") { + + auto found = lmp->force->dihedral_map->find(name); + if (found != lmp->force->dihedral_map->end()) + lmp->force->dihedral_map->erase(found); + + // must delete dihedral style instance if in use + + if ((lmp->force->dihedral_style) + && (lmp->force->dihedral_match(name) != nullptr)) + lmp->force->create_dihedral("none",0); + + } else if (pstyle == "improper") { + + auto found = lmp->force->improper_map->find(name); + if (found != lmp->force->improper_map->end()) + lmp->force->improper_map->erase(found); + + // must delete improper style instance if in use + + if ((lmp->force->improper_style != nullptr) + && (lmp->force->improper_match(name) != nullptr)) + lmp->force->create_improper("none",0); + } else if (pstyle == "fix") { auto fix_map = lmp->modify->fix_map; From fbb3bb14af47b7c893ede7cb4dd39f33826946be Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 18 Mar 2021 17:08:49 -0400 Subject: [PATCH 0208/1217] synchronize interface to managing computes in Modify with that of fixes - add find_compute_by_style() - add delete_compute(int) --- src/modify.cpp | 21 ++++++++++++++++++++- src/modify.h | 11 +++++++---- 2 files changed, 27 insertions(+), 5 deletions(-) diff --git a/src/modify.cpp b/src/modify.cpp index 2c0fd434d6..9cb90fc36f 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -1326,7 +1326,12 @@ void Modify::delete_compute(const std::string &id) { int icompute = find_compute(id); if (icompute < 0) error->all(FLERR,"Could not find compute ID to delete"); - delete compute[icompute]; + delete_compute(icompute); +} + +void Modify::delete_compute(int icompute) +{ + if (compute[icompute]) delete compute[icompute]; // move other Computes down in list one slot @@ -1347,6 +1352,20 @@ int Modify::find_compute(const std::string &id) return -1; } +/* ---------------------------------------------------------------------- + find a compute by style + return index of compute or -1 if not found +------------------------------------------------------------------------- */ + +int Modify::find_compute_by_style(const char *style) +{ + int icompute; + for (icompute = 0; icompute < ncompute; icompute++) + if (utils::strmatch(compute[icompute]->style,style)) break; + if (icompute == ncompute) return -1; + return icompute; +} + /* ---------------------------------------------------------------------- clear invoked flag of all computes called everywhere that computes are used, before computes are invoked diff --git a/src/modify.h b/src/modify.h index ba8efd6525..0f4f7e32d2 100644 --- a/src/modify.h +++ b/src/modify.h @@ -109,21 +109,24 @@ class Modify : protected Pointers { void delete_fix(int); int find_fix(const std::string &); int find_fix_by_style(const char *); - int check_package(const char *); - int check_rigid_group_overlap(int); - int check_rigid_region_overlap(int, class Region *); - int check_rigid_list_overlap(int *); void add_compute(int, char **, int trysuffix=1); void add_compute(const std::string &, int trysuffix=1); void modify_compute(int, char **); void delete_compute(const std::string &); + void delete_compute(int); int find_compute(const std::string &); + int find_compute_by_style(const char *); void clearstep_compute(); void addstep_compute(bigint); void addstep_compute_all(bigint); + int check_package(const char *); + int check_rigid_group_overlap(int); + int check_rigid_region_overlap(int, class Region *); + int check_rigid_list_overlap(int *); + void write_restart(FILE *); int read_restart(FILE *); void restart_deallocate(int); From b2309f624606a56682282ab48b9b81a154e51eb4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 18 Mar 2021 17:09:08 -0400 Subject: [PATCH 0209/1217] add support for computes --- src/PLUGIN/plugin.cpp | 23 ++++++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) diff --git a/src/PLUGIN/plugin.cpp b/src/PLUGIN/plugin.cpp index 91d22b2897..255202b86b 100644 --- a/src/PLUGIN/plugin.cpp +++ b/src/PLUGIN/plugin.cpp @@ -218,6 +218,16 @@ namespace LAMMPS_NS } (*improper_map)[plugin->name] = (Force::ImproperCreator)plugin->creator.v1; + } else if (pstyle == "compute") { + auto compute_map = lmp->modify->compute_map; + if (compute_map->find(plugin->name) != compute_map->end()) { + if (lmp->comm->me == 0) + lmp->error->warning(FLERR,fmt::format("Overriding built-in compute " + "style {} from plugin", + plugin->name)); + } + (*compute_map)[plugin->name] = (Modify::ComputeCreator)plugin->creator.v2; + } else if (pstyle == "fix") { auto fix_map = lmp->modify->fix_map; if (fix_map->find(plugin->name) != fix_map->end()) { @@ -260,7 +270,8 @@ namespace LAMMPS_NS // ignore unload request from unsupported style categories if ((strcmp(style,"pair") != 0) && (strcmp(style,"bond") != 0) && (strcmp(style,"angle") != 0) && (strcmp(style,"dihedral") != 0) - && (strcmp(style,"improper") != 0) && (strcmp(style,"fix") != 0) + && (strcmp(style,"improper") != 0) && (strcmp(style,"compute") != 0) + && (strcmp(style,"fix") != 0) && (strcmp(style,"command") != 0)) { if (me == 0) utils::logmesg(lmp,fmt::format("Ignoring unload: {} is not a " @@ -357,6 +368,16 @@ namespace LAMMPS_NS && (lmp->force->improper_match(name) != nullptr)) lmp->force->create_improper("none",0); + } else if (pstyle == "compute") { + + auto compute_map = lmp->modify->compute_map; + auto found = compute_map->find(name); + if (found != compute_map->end()) compute_map->erase(name); + + for (int icompute = lmp->modify->find_compute_by_style(name); + icompute >= 0; icompute = lmp->modify->find_compute_by_style(name)) + lmp->modify->delete_compute(icompute); + } else if (pstyle == "fix") { auto fix_map = lmp->modify->fix_map; From 03793d5e4dba32bcce433f32c585dc916e7c4147 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 18 Mar 2021 17:23:25 -0400 Subject: [PATCH 0210/1217] simplify --- src/modify.cpp | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/src/modify.cpp b/src/modify.cpp index 9cb90fc36f..80cf2667fe 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -1099,11 +1099,9 @@ int Modify::find_fix(const std::string &id) int Modify::find_fix_by_style(const char *style) { - int ifix; - for (ifix = 0; ifix < nfix; ifix++) - if (utils::strmatch(fix[ifix]->style,style)) break; - if (ifix == nfix) return -1; - return ifix; + for (int ifix = 0; ifix < nfix; ifix++) + if (utils::strmatch(fix[ifix]->style,style)) return ifix; + return -1; } /* ---------------------------------------------------------------------- @@ -1359,11 +1357,9 @@ int Modify::find_compute(const std::string &id) int Modify::find_compute_by_style(const char *style) { - int icompute; - for (icompute = 0; icompute < ncompute; icompute++) - if (utils::strmatch(compute[icompute]->style,style)) break; - if (icompute == ncompute) return -1; - return icompute; + for (int icompute = 0; icompute < ncompute; icompute++) + if (utils::strmatch(compute[icompute]->style,style)) return icompute; + return -1; } /* ---------------------------------------------------------------------- From 023d42b5bb90a289c16fbcfefba9dd42063f7635 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 18 Mar 2021 18:03:12 -0400 Subject: [PATCH 0211/1217] add support for region style plugins --- src/PLUGIN/plugin.cpp | 23 ++++++++++++++++++++++- src/domain.cpp | 24 +++++++++++++++++++++++- src/domain.h | 2 ++ 3 files changed, 47 insertions(+), 2 deletions(-) diff --git a/src/PLUGIN/plugin.cpp b/src/PLUGIN/plugin.cpp index 255202b86b..b52e1a1959 100644 --- a/src/PLUGIN/plugin.cpp +++ b/src/PLUGIN/plugin.cpp @@ -14,6 +14,7 @@ #include "plugin.h" #include "comm.h" +#include "domain.h" #include "error.h" #include "input.h" #include "force.h" @@ -238,6 +239,16 @@ namespace LAMMPS_NS } (*fix_map)[plugin->name] = (Modify::FixCreator)plugin->creator.v2; + } else if (pstyle == "region") { + auto region_map = lmp->domain->region_map; + if (region_map->find(plugin->name) != region_map->end()) { + if (lmp->comm->me == 0) + lmp->error->warning(FLERR,fmt::format("Overriding built-in region " + "style {} from plugin", + plugin->name)); + } + (*region_map)[plugin->name] = (Domain::RegionCreator)plugin->creator.v2; + } else if (pstyle == "command") { auto command_map = lmp->input->command_map; if (command_map->find(plugin->name) != command_map->end()) { @@ -271,7 +282,7 @@ namespace LAMMPS_NS if ((strcmp(style,"pair") != 0) && (strcmp(style,"bond") != 0) && (strcmp(style,"angle") != 0) && (strcmp(style,"dihedral") != 0) && (strcmp(style,"improper") != 0) && (strcmp(style,"compute") != 0) - && (strcmp(style,"fix") != 0) + && (strcmp(style,"fix") != 0) && (strcmp(style,"region") != 0) && (strcmp(style,"command") != 0)) { if (me == 0) utils::logmesg(lmp,fmt::format("Ignoring unload: {} is not a " @@ -388,6 +399,16 @@ namespace LAMMPS_NS ifix >= 0; ifix = lmp->modify->find_fix_by_style(name)) lmp->modify->delete_fix(ifix); + } else if (pstyle == "region") { + + auto region_map = lmp->domain->region_map; + auto found = region_map->find(name); + if (found != region_map->end()) region_map->erase(name); + + for (int iregion = lmp->domain->find_region_by_style(name); + iregion >= 0; iregion = lmp->domain->find_region_by_style(name)) + lmp->domain->delete_region(iregion); + } else if (pstyle == "command") { auto command_map = lmp->input->command_map; diff --git a/src/domain.cpp b/src/domain.cpp index c6dee63221..abf0d70079 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -1816,8 +1816,18 @@ void Domain::delete_region(int narg, char **arg) int iregion = find_region(arg[0]); if (iregion == -1) error->all(FLERR,"Delete region ID does not exist"); + delete_region(iregion); +} + +void Domain::delete_region(int iregion) +{ + if ((iregion < 0) || (iregion >= nregion)) return; + + // delete and move other Regions down in list one slot + delete regions[iregion]; - regions[iregion] = regions[nregion-1]; + for (int i = iregion+1; iregion < nregion; ++i) + regions[i-1] = regions[i]; nregion--; } @@ -1833,6 +1843,18 @@ int Domain::find_region(const std::string &name) return -1; } +/* ---------------------------------------------------------------------- + return region index if name matches existing region style + return -1 if no such region +------------------------------------------------------------------------- */ + +int Domain::find_region_by_style(const std::string &name) +{ + for (int iregion = 0; iregion < nregion; iregion++) + if (name == regions[iregion]->style) return iregion; + return -1; +} + /* ---------------------------------------------------------------------- (re)set boundary settings flag = 0, called from the input script diff --git a/src/domain.h b/src/domain.h index 99349edb5d..5009a67d28 100644 --- a/src/domain.h +++ b/src/domain.h @@ -130,7 +130,9 @@ class Domain : protected Pointers { void set_lattice(int, char **); void add_region(int, char **); void delete_region(int, char **); + void delete_region(int); int find_region(const std::string &); + int find_region_by_style(const std::string &); void set_boundary(int, char **, int); void set_box(int, char **); void print_box(const std::string &); From a5ce7c1ac9e6758c0d3606913f4d54c71d635f09 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 18 Mar 2021 18:03:26 -0400 Subject: [PATCH 0212/1217] better checks for valid data --- src/modify.cpp | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/src/modify.cpp b/src/modify.cpp index 80cf2667fe..79a0ecd41f 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -1069,10 +1069,12 @@ void Modify::delete_fix(const std::string &id) void Modify::delete_fix(int ifix) { - if (fix[ifix]) delete fix[ifix]; - atom->update_callback(ifix); + if ((ifix < 0) || (ifix >= nfix)) return; - // move other Fixes and fmask down in list one slot + // delete instance and move other Fixes and fmask down in list one slot + + delete fix[ifix]; + atom->update_callback(ifix); for (int i = ifix+1; i < nfix; i++) fix[i-1] = fix[i]; for (int i = ifix+1; i < nfix; i++) fmask[i-1] = fmask[i]; @@ -1329,10 +1331,11 @@ void Modify::delete_compute(const std::string &id) void Modify::delete_compute(int icompute) { - if (compute[icompute]) delete compute[icompute]; + if ((icompute < 0) || (icompute >= ncompute)) return; - // move other Computes down in list one slot + // delete and move other Computes down in list one slot + delete compute[icompute]; for (int i = icompute+1; i < ncompute; i++) compute[i-1] = compute[i]; ncompute--; } From 024a9600b15df903b614978bf655f56c06e63a26 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 18 Mar 2021 18:04:13 -0400 Subject: [PATCH 0213/1217] update docs --- doc/src/Developer_plugins.rst | 120 +++++++++++++++----- doc/src/plugin.rst | 2 +- doc/utils/sphinx-config/false_positives.txt | 1 + 3 files changed, 96 insertions(+), 27 deletions(-) diff --git a/doc/src/Developer_plugins.rst b/doc/src/Developer_plugins.rst index 7275c12605..68f1f1387c 100644 --- a/doc/src/Developer_plugins.rst +++ b/doc/src/Developer_plugins.rst @@ -2,36 +2,95 @@ Writing plugins --------------- Plugins provide a mechanism to add functionality to a LAMMPS executable -without recompiling LAMMPS. This uses the operating system's -capability to load dynamic shared object (DSO) files in a way similar -shared libraries and then references specific functions those DSOs. -Any DSO file with plugins has to include an initialization function -with a specific name that has to follow specific rules. When loading -the DSO, this function is called and will then register the contained -plugin(s) with LAMMPS. +without recompiling LAMMPS. The functionality for this and the +:doc:`plugin command ` are implemented in the +:ref:`PLUGIN package ` which must be installed to use plugins. + +Plugins use the operating system's capability to load dynamic shared +object (DSO) files in a way similar shared libraries and then reference +specific functions in those DSOs. Any DSO file with plugins has to include +an initialization function with a specific name, "lammpsplugin_init", that +has to follow specific rules described below. When loading the DSO with +the "plugin" command, this function is looked up and called and will then +register the contained plugin(s) with LAMMPS. From the programmer perspective this can work because of the object -oriented design where all pair style commands are derived from the class -Pair, all fix style commands from the class Fix and so on and only -functions from those base classes are called directly. When a -:doc:`pair_style` command or :doc:`fix` command is issued a new -instance of such a derived class is created. This is done by a -so-called factory function which is mapped to the style name. Thus -when, for example, the LAMMPS processes the command -``pair_style lj/cut 2.5``, LAMMPS will look up the factory function -for creating the ``PairLJCut`` class and then execute it. The return -value of that function is a ``Pair *`` pointer and the pointer will -be assigned to the location for the currently active pair style. +oriented design of LAMMPS where all pair style commands are derived from +the class Pair, all fix style commands from the class Fix and so on and +usually only functions present in those base classes are called +directly. When a :doc:`pair_style` command or :doc:`fix` command is +issued a new instance of such a derived class is created. This is done +by a so-called factory function which is mapped to the style name. Thus +when, for example, the LAMMPS processes the command ``pair_style lj/cut +2.5``, LAMMPS will look up the factory function for creating the +``PairLJCut`` class and then execute it. The return value of that +function is a ``Pair *`` pointer and the pointer will be assigned to the +location for the currently active pair style. -A plugin thus has to implement such a factory function and register it -with LAMMPS so that it gets added to the map of available styles of -the given category. To register a plugin with LAMMPS an initialization -function has to be called that follows specific rules explained below. +A DSO file with a plugin thus has to implement such a factory function +and register it with LAMMPS so that it gets added to the map of available +styles of the given category. To register a plugin with LAMMPS an +initialization function has to be present in the DSO file called +``lammpsplugin_init`` which is called with three ``void *`` arguments: +a pointer to the current LAMMPS instance, a pointer to the opened DSO +handle, and a pointer to the registration function. The registration +function takes two arguments: a pointer to a ``lammpsplugin_t`` struct +with information about the plugin and a pointer to the current LAMMPS +instance. Please see below for an example of how the registration is +done. +Members of ``lammpsplugin_t`` +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -As an example, for a hypothetical pair style "morse2" implemented in a -class ``PairMorse2`` in the files ``pair_morse2.h`` and -``pair_morse2.cpp`` the file with the factory function and initialization +.. list-table:: + :header-rows: 1 + :widths: auto + + * - Member + - Description + * - version + - LAMMPS Version string the plugin was compiled for + * - style + - Style of the plugin (pair, bond, fix, command, etc.) + * - name + - Name of the plugin style + * - info + - String with information about the plugin + * - author + - String with the name and email of the author + * - creator.v1 + - Pointer to factory function for pair, bond, angle, dihedral, or improper styles + * - creator.v2 + - Pointer to factory function for compute, fix, or region styles + * - creator.v3 + - Pointer to factory function for command styles + * - handle + - Pointer to the open DSO file handle + +Only one of the three alternate creator entries can be used at a time +and which of those is determined by the style of plugin. The "creator.v1" +element is for factory functions of supported styles computing forces (i.e. +pair, bond, angle, dihedral, or improper styles) and the function takes +as single argument the pointer to the LAMMPS instance. The factory function +is cast to the ``lammpsplugin_factory1`` type before assignment. The +"creator.v2" element is for factory functions creating an instance of +a fix, compute, or region style and takes three arguments: a pointer to +the LAMMPS instance, an integer with the length of the argument list and +a ``char **`` pointer to the list of arguments. The factory function pointer +needs to be cast to the ``lammpsplugin_factory2`` type before assignment. +The "creator.v3" element takes the same arguments as "creator.v3" but is +specific to creating command styles: the factory function has to instantiate +the command style locally passing the LAMMPS pointer as argument and then +call its "command" member function with the number and list of arguments. +The factory function pointer needs to be cast to the +``lammpsplugin_factory3`` type before assignment. + +Pair style example +^^^^^^^^^^^^^^^^^^ + +As an example, a hypothetical pair style plugin "morse2" implemented in +a class ``PairMorse2`` in the files ``pair_morse2.h`` and +``pair_morse2.cpp`` with the factory function and initialization function would look like this: .. code-block:: C++ @@ -70,6 +129,10 @@ pointer to the allocated class instance derived from the ``Pair`` class. This function may be declared static to avoid clashes with other plugins. The name of the derived class, ``PairMorse2``, must be unique inside the entire LAMMPS executable. + +Fix style example +^^^^^^^^^^^^^^^^^ + If the factory function would be for a fix or compute, which take three arguments (a pointer to the LAMMPS class, the number of arguments and the list of argument strings), then the pointer type is ``lammpsplugin_factory2`` @@ -104,6 +167,8 @@ Below is an example for that: (*register_plugin)(&plugin,lmp); } +Command style example +^^^^^^^^^^^^^^^^^^^^^ For command styles there is a third variant of factory function as demonstrated in the following example, which also shows that the implementation of the plugin class may also be within the same @@ -158,6 +223,9 @@ file as the plugin interface code: (*register_plugin)(&plugin,lmp); } +Additional Details +^^^^^^^^^^^^^^^^^^ + The initialization function **must** be called ``lammpsplugin_init``, it **must** have C bindings and it takes three void pointers as arguments. The first is a pointer to the LAMMPS class that calls it and it needs to @@ -167,7 +235,7 @@ to the plugin info struct, so that the DSO can be closed and unloaded when all its contained plugins are unloaded. The third argument is a function pointer to the registration function and needs to be stored in a variable of ``lammpsplugin_regfunc`` type and then called with a -pointer to the ``lammpsplugin_`` struct and the pointer to the LAMMPS +pointer to the ``lammpsplugin_t`` struct and the pointer to the LAMMPS instance as arguments to register a single plugin. There may be multiple calls to multiple plugins in the same initialization function. diff --git a/doc/src/plugin.rst b/doc/src/plugin.rst index 48638bf97a..02228636bc 100644 --- a/doc/src/plugin.rst +++ b/doc/src/plugin.rst @@ -17,7 +17,7 @@ Syntax *load* file = load plugin(s) from shared object in *file* *unload* style name = unload plugin *name* of style *style* - *style* = *pair* or *fix* or *command* + *style* = *pair* or *bond* or *angle* or *dihedral* or *improper* or *compute* or *fix* or *region* or *command* *list* = print a list of currently loaded plugins *clear* = unload all currently loaded plugins diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 1d66028621..38a6971f4c 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1588,6 +1588,7 @@ lammps Lammps LAMMPS lammpsplot +lammpsplugin Lampis Lamoureux Lanczos From d9d5d3a36a175a492c4c617a4d67a4fa5b7ab68a Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Fri, 19 Mar 2021 09:29:47 -0600 Subject: [PATCH 0214/1217] Correcting skin distance calculation for collection/interval --- src/neighbor.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/neighbor.cpp b/src/neighbor.cpp index c33345f88d..13f5c9f958 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -409,7 +409,7 @@ void Neighbor::init() ri = collection2cut[i]*0.5; for(j = 0; j < ncollections; j++){ rj = collection2cut[j]*0.5; - tmp = force->pair->radii2cut(ri, rj); + tmp = force->pair->radii2cut(ri, rj) + skin; cutcollectionsq[i][j] = tmp*tmp; } } @@ -425,7 +425,8 @@ void Neighbor::init() double cuttmp; for(i = 1; i <= n; i++){ - cuttmp = sqrt(cutneighsq[i][i]); + // Remove skin added to cutneighsq + cuttmp = sqrt(cutneighsq[i][i]) - skin; for(icollection = 0; icollection < ncollections; icollection ++){ if(collection2cut[icollection] >= cuttmp) { type2collection[i] = icollection; From 4269eeeef7fadc8e9f53dd4efd58afb793778356 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 19 Mar 2021 17:22:40 -0400 Subject: [PATCH 0215/1217] Optimize quadratic Kokkos SNAP, pointed out by @weinbe2 --- src/KOKKOS/pair_snap_kokkos.h | 4 +++ src/KOKKOS/pair_snap_kokkos_impl.h | 31 ++++++++++++----- src/KOKKOS/sna_kokkos.h | 3 ++ src/KOKKOS/sna_kokkos_impl.h | 53 ++++++++++++++++++++++++++++++ 4 files changed, 83 insertions(+), 8 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h index 9acf3011ce..b792b85e2b 100644 --- a/src/KOKKOS/pair_snap_kokkos.h +++ b/src/KOKKOS/pair_snap_kokkos.h @@ -50,6 +50,7 @@ struct TagPairSNAPBeta{}; struct TagPairSNAPComputeBi{}; struct TagPairSNAPTransformBi{}; // re-order blist from AoSoA to AoS struct TagPairSNAPComputeYi{}; +struct TagPairSNAPComputeYiWithZlist{}; template struct TagPairSNAPComputeFusedDeidrj{}; @@ -161,6 +162,9 @@ public: KOKKOS_INLINE_FUNCTION void operator() (TagPairSNAPComputeYi,const int iatom_mod, const int idxz, const int iatom_div) const; + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPComputeYiWithZlist,const int iatom_mod, const int idxz, const int iatom_div) const; + template KOKKOS_INLINE_FUNCTION void operator() (TagPairSNAPComputeFusedDeidrj,const typename Kokkos::TeamPolicy >::member_type& team) const; diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 2578f3d47c..3ccc5cec36 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -373,16 +373,18 @@ void PairSNAPKokkos::compute(int eflag_in, //Compute beta = dE_i/dB_i for all i in list typename Kokkos::RangePolicy policy_beta(0,chunk_size); Kokkos::parallel_for("ComputeBeta",policy_beta,*this); - - //ComputeYi - // team_size_compute_yi is defined in `pair_snap_kokkos.h` const int idxz_max = snaKK.idxz_max; - Snap3DRangePolicy - policy_compute_yi({0,0,0},{vector_length,idxz_max,chunk_size_div},{vector_length,tile_size_compute_yi,1}); - Kokkos::parallel_for("ComputeYi",policy_compute_yi,*this); - + if (quadraticflag || eflag) { + Snap3DRangePolicy + policy_compute_yi({0,0,0},{vector_length,idxz_max,chunk_size_div},{vector_length,tile_size_compute_yi,1}); + Kokkos::parallel_for("ComputeYiWithZlist",policy_compute_yi,*this); + } else { + Snap3DRangePolicy + policy_compute_yi({0,0,0},{vector_length,idxz_max,chunk_size_div},{vector_length,tile_size_compute_yi,1}); + Kokkos::parallel_for("ComputeYi",policy_compute_yi,*this); + } } - + // Fused ComputeDuidrj, ComputeDeidrj { // team_size_compute_fused_deidrj is defined in `pair_snap_kokkos.h` @@ -796,6 +798,19 @@ void PairSNAPKokkos::operator() (TagPairSN my_sna.compute_yi(iatom_mod,jjz,iatom_div,d_beta_pack); } +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPComputeYiWithZlist,const int iatom_mod, const int jjz, const int iatom_div) const { + SNAKokkos my_sna = snaKK; + + const int iatom = iatom_mod + iatom_div * vector_length; + if (iatom >= chunk_size) return; + + if (jjz >= my_sna.idxz_max) return; + + my_sna.compute_yi_with_zlist(iatom_mod,jjz,iatom_div,d_beta_pack); +} + template KOKKOS_INLINE_FUNCTION void PairSNAPKokkos::operator() (TagPairSNAPComputeZi,const int iatom_mod, const int jjz, const int iatom_div) const { diff --git a/src/KOKKOS/sna_kokkos.h b/src/KOKKOS/sna_kokkos.h index 55983f2a90..33ef37ca98 100644 --- a/src/KOKKOS/sna_kokkos.h +++ b/src/KOKKOS/sna_kokkos.h @@ -125,6 +125,9 @@ inline void compute_yi(int,int,int, const Kokkos::View &beta_pack); // ForceSNAP KOKKOS_INLINE_FUNCTION + void compute_yi_with_zlist(int,int,int, + const Kokkos::View &beta_pack); // ForceSNAP + KOKKOS_INLINE_FUNCTION void compute_bi(const int&, const int&, const int&); // ForceSNAP // functions for bispectrum coefficients, CPU only diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index 2a44f943d3..2b55f97c30 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -880,6 +880,59 @@ void SNAKokkos::compute_yi(int iatom_mod, } // end loop over elem1 } +/* ---------------------------------------------------------------------- + compute Yi from Ui without storing Zi, looping over zlist indices. + AoSoA data layout to take advantage of coalescing, avoiding warp + divergence. GPU version. +------------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void SNAKokkos::compute_yi_with_zlist(int iatom_mod, int jjz, int iatom_div, + const Kokkos::View &beta_pack) +{ + real_type betaj; + const int j1 = idxz(jjz, 0); + const int j2 = idxz(jjz, 1); + const int j = idxz(jjz, 2); + const int jju_half = idxz(jjz, 9); + int idouble = 0; + for (int elem1 = 0; elem1 < nelements; elem1++) { + for (int elem2 = 0; elem2 < nelements; elem2++) { + auto ztmp = zlist_pack(iatom_mod,jjz,idouble,iatom_div); + // apply to z(j1,j2,j,ma,mb) to unique element of y(j) + // find right y_list[jju] and beta(iatom,jjb) entries + // multiply and divide by j+1 factors + // account for multiplicity of 1, 2, or 3 + // pick out right beta value + for (int elem3 = 0; elem3 < nelements; elem3++) { + if (j >= j1) { + const int jjb = idxb_block(j1, j2, j); + const auto itriple = ((elem1 * nelements + elem2) * nelements + elem3) * idxb_max + jjb; + if (j1 == j) { + if (j2 == j) betaj = 3 * beta_pack(iatom_mod, itriple, iatom_div); + else betaj = 2 * beta_pack(iatom_mod, itriple, iatom_div); + } else betaj = beta_pack(iatom_mod, itriple, iatom_div); + } else if (j >= j2) { + const int jjb = idxb_block(j, j2, j1); + const auto itriple = ((elem3 * nelements + elem2) * nelements + elem1) * idxb_max + jjb; + if (j2 == j) betaj = 2 * beta_pack(iatom_mod, itriple, iatom_div); + else betaj = beta_pack(iatom_mod, itriple, iatom_div); + } else { + const int jjb = idxb_block(j2, j, j1); + const auto itriple = ((elem2 * nelements + elem3) * nelements + elem1) * idxb_max + jjb; + betaj = beta_pack(iatom_mod, itriple, iatom_div); + } + if (!bnorm_flag && j1 > j) + betaj *= (j1 + 1) / (j + 1.0); + Kokkos::atomic_add(&(ylist_pack_re(iatom_mod, jju_half, elem3, iatom_div)), betaj*ztmp.re); + Kokkos::atomic_add(&(ylist_pack_im(iatom_mod, jju_half, elem3, iatom_div)), betaj*ztmp.im); + } // end loop over elem3 + idouble++; + } // end loop over elem2 + } // end loop over elem1 +} + /* ---------------------------------------------------------------------- Fused calculation of the derivative of Ui w.r.t. atom j and accumulation into dEidRj. GPU only. From 012cdf3763f5687bf3044070214942daa126537d Mon Sep 17 00:00:00 2001 From: jrgissing Date: Sat, 20 Mar 2021 16:20:57 -0400 Subject: [PATCH 0216/1217] performance improvement bugfix --- src/USER-REACTION/fix_bond_react.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 91354506d1..46c55f4199 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -2566,6 +2566,7 @@ void FixBondReact::unlimit_bond() } // really should only communicate this per-atom property, not entire reneighboring + MPI_Allreduce(MPI_IN_PLACE,&unlimitflag,1,MPI_INT,MPI_MAX,world); if (unlimitflag) next_reneighbor = update->ntimestep; } From b3f465babe387fe8299d50b5bf003e6baf1adbf9 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Sat, 20 Mar 2021 16:34:55 -0400 Subject: [PATCH 0217/1217] decrease foward_comm nsize due to new placement of probability evaluation --- src/USER-REACTION/fix_bond_react.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 46c55f4199..94d1a596f8 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -965,7 +965,7 @@ void FixBondReact::post_integrate() // forward comm of partner, so ghosts have it commflag = 2; - comm->forward_comm_fix(this,2); + comm->forward_comm_fix(this,1); // consider for reaction: // only if both atoms list each other as winning bond partner From 2bab4808b62b366a6478cf88a8a8679f8db414b5 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Mon, 22 Mar 2021 08:28:43 -0600 Subject: [PATCH 0218/1217] Improve memory coalescing in Kokkos snap force computation, pointed out by @weinbe2 --- src/KOKKOS/pair_snap_kokkos.h | 4 +- src/KOKKOS/pair_snap_kokkos_impl.h | 130 ++++++++++++----------------- 2 files changed, 56 insertions(+), 78 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h index b792b85e2b..b7208a577c 100644 --- a/src/KOKKOS/pair_snap_kokkos.h +++ b/src/KOKKOS/pair_snap_kokkos.h @@ -122,11 +122,11 @@ public: template KOKKOS_INLINE_FUNCTION - void operator() (TagPairSNAPComputeForce,const typename Kokkos::TeamPolicy >::member_type& team) const; + void operator() (TagPairSNAPComputeForce,const int& ii) const; template KOKKOS_INLINE_FUNCTION - void operator() (TagPairSNAPComputeForce,const typename Kokkos::TeamPolicy >::member_type& team, EV_FLOAT&) const; + void operator() (TagPairSNAPComputeForce,const int& ii, EV_FLOAT&) const; KOKKOS_INLINE_FUNCTION void operator() (TagPairSNAPBetaCPU,const int& ii) const; diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 3ccc5cec36..f624131377 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -384,7 +384,7 @@ void PairSNAPKokkos::compute(int eflag_in, Kokkos::parallel_for("ComputeYi",policy_compute_yi,*this); } } - + // Fused ComputeDuidrj, ComputeDeidrj { // team_size_compute_fused_deidrj is defined in `pair_snap_kokkos.h` @@ -420,30 +420,21 @@ void PairSNAPKokkos::compute(int eflag_in, //ComputeForce { - int team_size = team_size_default; if (evflag) { if (neighflag == HALF) { - check_team_size_reduce >(chunk_size,team_size); - typename Kokkos::TeamPolicy > policy_force(chunk_size,team_size,vector_length); - Kokkos::parallel_reduce(policy_force - ,*this,ev_tmp); + typename Kokkos::RangePolicy > policy_force(0,chunk_size); + Kokkos::parallel_reduce(policy_force, *this, ev_tmp); } else if (neighflag == HALFTHREAD) { - check_team_size_reduce >(chunk_size,team_size); - typename Kokkos::TeamPolicy > policy_force(chunk_size,team_size,vector_length); - Kokkos::parallel_reduce(policy_force - ,*this,ev_tmp); + typename Kokkos::RangePolicy > policy_force(0,chunk_size); + Kokkos::parallel_reduce(policy_force, *this, ev_tmp); } } else { if (neighflag == HALF) { - check_team_size_for >(chunk_size,team_size); - typename Kokkos::TeamPolicy > policy_force(chunk_size,team_size,vector_length); - Kokkos::parallel_for(policy_force - ,*this); + typename Kokkos::RangePolicy > policy_force(0,chunk_size); + Kokkos::parallel_for(policy_force, *this); } else if (neighflag == HALFTHREAD) { - check_team_size_for >(chunk_size,team_size); - typename Kokkos::TeamPolicy > policy_force(chunk_size,team_size,vector_length); - Kokkos::parallel_for(policy_force - ,*this); + typename Kokkos::RangePolicy > policy_force(0,chunk_size); + Kokkos::parallel_for(policy_force, *this); } } } @@ -1152,20 +1143,19 @@ void PairSNAPKokkos::operator() (TagPairSN template template KOKKOS_INLINE_FUNCTION -void PairSNAPKokkos::operator() (TagPairSNAPComputeForce,const typename Kokkos::TeamPolicy >::member_type& team, EV_FLOAT& ev) const { +void PairSNAPKokkos::operator() (TagPairSNAPComputeForce, const int& ii, EV_FLOAT& ev) const { // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); auto a_f = v_f.template access::value>(); - int ii = team.league_rank(); const int i = d_ilist[ii + chunk_offset]; + SNAKokkos my_sna = snaKK; + const int ninside = d_ninside(ii); - Kokkos::parallel_for (Kokkos::TeamThreadRange(team,ninside), - [&] (const int jj) { + for (int jj = 0; jj < ninside; jj++) { int j = my_sna.inside(ii,jj); F_FLOAT fij[3]; @@ -1173,28 +1163,23 @@ void PairSNAPKokkos::operator() (TagPairSN fij[1] = my_sna.dedr(ii,jj,1); fij[2] = my_sna.dedr(ii,jj,2); - Kokkos::single(Kokkos::PerThread(team), [&] () { - a_f(i,0) += fij[0]; - a_f(i,1) += fij[1]; - a_f(i,2) += fij[2]; - a_f(j,0) -= fij[0]; - a_f(j,1) -= fij[1]; - a_f(j,2) -= fij[2]; - - // tally global and per-atom virial contribution - - if (EVFLAG) { - if (vflag_either) { - v_tally_xyz(ev,i,j, - fij[0],fij[1],fij[2], - -my_sna.rij(ii,jj,0),-my_sna.rij(ii,jj,1), - -my_sna.rij(ii,jj,2)); - } + a_f(i,0) += fij[0]; + a_f(i,1) += fij[1]; + a_f(i,2) += fij[2]; + a_f(j,0) -= fij[0]; + a_f(j,1) -= fij[1]; + a_f(j,2) -= fij[2]; + // tally global and per-atom virial contribution + if (EVFLAG) { + if (vflag_either) { + v_tally_xyz(ev,i,j, + fij[0],fij[1],fij[2], + -my_sna.rij(ii,jj,0),-my_sna.rij(ii,jj,1), + -my_sna.rij(ii,jj,2)); } + } - }); - }); - + } // tally energy contribution if (EVFLAG) { @@ -1204,48 +1189,41 @@ void PairSNAPKokkos::operator() (TagPairSN const int ielem = d_map[itype]; auto d_coeffi = Kokkos::subview(d_coeffelem, ielem, Kokkos::ALL); - Kokkos::single(Kokkos::PerTeam(team), [&] () { + // evdwl = energy of atom I, sum over coeffs_k * Bi_k - // evdwl = energy of atom I, sum over coeffs_k * Bi_k + auto evdwl = d_coeffi[0]; - auto evdwl = d_coeffi[0]; + // E = beta.B + 0.5*B^t.alpha.B - // E = beta.B + 0.5*B^t.alpha.B + const auto idxb_max = snaKK.idxb_max; - const auto idxb_max = snaKK.idxb_max; + // linear contributions - // linear contributions + for (int icoeff = 0; icoeff < ncoeff; icoeff++) { + const auto idxb = icoeff % idxb_max; + const auto idx_chem = icoeff / idxb_max; + evdwl += d_coeffi[icoeff+1]*my_sna.blist(idxb,idx_chem,ii); + } + // quadratic contributions + if (quadraticflag) { + int k = ncoeff+1; for (int icoeff = 0; icoeff < ncoeff; icoeff++) { const auto idxb = icoeff % idxb_max; const auto idx_chem = icoeff / idxb_max; - evdwl += d_coeffi[icoeff+1]*my_sna.blist(idxb,idx_chem,ii); - } - - // quadratic contributions - - if (quadraticflag) { - int k = ncoeff+1; - for (int icoeff = 0; icoeff < ncoeff; icoeff++) { - const auto idxb = icoeff % idxb_max; - const auto idx_chem = icoeff / idxb_max; - auto bveci = my_sna.blist(idxb,idx_chem,ii); - - evdwl += 0.5*d_coeffi[k++]*bveci*bveci; - for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) { - auto jdxb = jcoeff % idxb_max; - auto jdx_chem = jcoeff / idxb_max; - auto bvecj = my_sna.blist(jdxb,jdx_chem,ii); - - evdwl += d_coeffi[k++]*bveci*bvecj; - } + auto bveci = my_sna.blist(idxb,idx_chem,ii); + evdwl += 0.5*d_coeffi[k++]*bveci*bveci; + for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) { + auto jdxb = jcoeff % idxb_max; + auto jdx_chem = jcoeff / idxb_max; + auto bvecj = my_sna.blist(jdxb,jdx_chem,ii); + evdwl += d_coeffi[k++]*bveci*bvecj; } } - - //ev_tally_full(i,2.0*evdwl,0.0,0.0,0.0,0.0,0.0); - if (eflag_global) ev.evdwl += evdwl; - if (eflag_atom) d_eatom[i] += evdwl; - }); + } + //ev_tally_full(i,2.0*evdwl,0.0,0.0,0.0,0.0,0.0); + if (eflag_global) ev.evdwl += evdwl; + if (eflag_atom) d_eatom[i] += evdwl; } } } @@ -1253,9 +1231,9 @@ void PairSNAPKokkos::operator() (TagPairSN template template KOKKOS_INLINE_FUNCTION -void PairSNAPKokkos::operator() (TagPairSNAPComputeForce,const typename Kokkos::TeamPolicy >::member_type& team) const { +void PairSNAPKokkos::operator() (TagPairSNAPComputeForce,const int& ii) const { EV_FLOAT ev; - this->template operator()(TagPairSNAPComputeForce(), team, ev); + this->template operator()(TagPairSNAPComputeForce(), ii, ev); } /* ---------------------------------------------------------------------- */ From b8f606357842967f84e7dad3c10b871d3fc66e42 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 22 Mar 2021 10:47:49 -0400 Subject: [PATCH 0219/1217] correct documentation of angle style cosine/periodic --- doc/src/angle_cosine_periodic.rst | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index 71c2caa3f0..61b6407eb9 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -32,7 +32,7 @@ center: .. math:: - E = C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right] + E = 2.0*C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right] where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type. @@ -47,10 +47,9 @@ or :doc:`read_restart ` commands: * :math:`B` = 1 or -1 * :math:`n` = 1, 2, 3, 4, 5 or 6 for periodicity -Note that the prefactor :math:`C` is specified and not the overall force +Note that the prefactor :math:`C` is specified as coefficient and not the overall force constant :math:`K = \frac{C}{n^2}`. When :math:`B = 1`, it leads to a minimum for the -linear geometry. When :math:`B = -1`, it leads to a maximum for the linear -geometry. +linear geometry. When :math:`B = -1`, it leads to a maximum for the linear geometry. ---------- From e8c8ceaf81a0bc7621a6f033545ddcfd1d41bb80 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 22 Mar 2021 11:28:22 -0400 Subject: [PATCH 0220/1217] correct attribution of angle style cosine/squared with DREIDING --- doc/src/Howto_bioFF.rst | 1 + doc/src/angle_cosine_periodic.rst | 7 ++----- doc/src/angle_cosine_squared.rst | 14 ++++++++++++-- 3 files changed, 15 insertions(+), 7 deletions(-) diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst index bac1b566e1..9bffe5d4c9 100644 --- a/doc/src/Howto_bioFF.rst +++ b/doc/src/Howto_bioFF.rst @@ -91,6 +91,7 @@ documentation for the formula it computes. * :doc:`bond_style ` harmonic * :doc:`bond_style ` morse +* :doc:`angle_style ` cosine/squared * :doc:`angle_style ` harmonic * :doc:`angle_style ` cosine * :doc:`angle_style ` cosine/periodic diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index 61b6407eb9..ec2426154d 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -24,9 +24,8 @@ Examples Description """"""""""" -The *cosine/periodic* angle style uses the following potential, which -is commonly used in the :doc:`DREIDING ` force field, -particularly for organometallic systems where :math:`n` = 4 might be used +The *cosine/periodic* angle style uses the following potential, which may be +particularly used for organometallic systems where :math:`n` = 4 might be used for an octahedral complex and :math:`n` = 3 might be used for a trigonal center: @@ -36,8 +35,6 @@ center: where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type. -See :ref:`(Mayo) ` for a description of the DREIDING force field - The following coefficients must be defined for each angle type via the :doc:`angle_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read_data ` diff --git a/doc/src/angle_cosine_squared.rst b/doc/src/angle_cosine_squared.rst index 4a6a1debe9..d674eb61d8 100644 --- a/doc/src/angle_cosine_squared.rst +++ b/doc/src/angle_cosine_squared.rst @@ -30,8 +30,11 @@ The *cosine/squared* angle style uses the potential E = K [\cos(\theta) - \cos(\theta_0)]^2 -where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a -prefactor. Note that the usual 1/2 factor is included in :math:`K`. +, which is commonly used in the :doc:`DREIDING ` force field, +where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` +is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. + +See :ref:`(Mayo) ` for a description of the DREIDING force field. The following coefficients must be defined for each angle type via the :doc:`angle_coeff ` command as in the example above, or in @@ -66,3 +69,10 @@ Default """"""" none + +---------- + +.. _cosine-Mayo: + +**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 +(1990). From aabfe40ad3341d0676a875ccbee3c2443748126b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 22 Mar 2021 15:10:45 -0400 Subject: [PATCH 0221/1217] add missing 1/n**2 term to pair style cosine/periodic energy function --- doc/src/angle_cosine_periodic.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index ec2426154d..5e13c98cfc 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -31,7 +31,7 @@ center: .. math:: - E = 2.0*C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right] + E = \frac{2.0}{n^2} * C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right] where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type. From 58744f0a4926a0d9a1991da4718837eb48dff463 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 22 Mar 2021 15:32:24 -0400 Subject: [PATCH 0222/1217] correct expression for K --- doc/src/angle_cosine_periodic.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index 5e13c98cfc..8c60ac1ebb 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -45,7 +45,7 @@ or :doc:`read_restart ` commands: * :math:`n` = 1, 2, 3, 4, 5 or 6 for periodicity Note that the prefactor :math:`C` is specified as coefficient and not the overall force -constant :math:`K = \frac{C}{n^2}`. When :math:`B = 1`, it leads to a minimum for the +constant :math:`K = \frac{2 C}{n^2}`. When :math:`B = 1`, it leads to a minimum for the linear geometry. When :math:`B = -1`, it leads to a maximum for the linear geometry. ---------- From 56121a524c97ca1606be03ac9243e4b47026412d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 22 Mar 2021 16:26:50 -0400 Subject: [PATCH 0223/1217] correct equilibrium angle computation for angle style cosine/periodic if b < 0 --- src/MOLECULE/angle_cosine_periodic.cpp | 4 ++-- unittest/force-styles/tests/angle-cosine_periodic.yaml | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp index f72a196b41..0df103c333 100644 --- a/src/MOLECULE/angle_cosine_periodic.cpp +++ b/src/MOLECULE/angle_cosine_periodic.cpp @@ -222,9 +222,9 @@ void AngleCosinePeriodic::coeff(int narg, char **arg) /* ---------------------------------------------------------------------- */ -double AngleCosinePeriodic::equilibrium_angle(int /*i*/) +double AngleCosinePeriodic::equilibrium_angle(int i) { - return MY_PI; + return MY_PI*(1.0 - (b[i]>0)?0.0:1.0/static_cast(multiplicity[i])); } /* ---------------------------------------------------------------------- diff --git a/unittest/force-styles/tests/angle-cosine_periodic.yaml b/unittest/force-styles/tests/angle-cosine_periodic.yaml index 814c837dcd..d8fba5c6ee 100644 --- a/unittest/force-styles/tests/angle-cosine_periodic.yaml +++ b/unittest/force-styles/tests/angle-cosine_periodic.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:34 202 +lammps_version: 10 Mar 2021 +date_generated: Mon Mar 22 16:25:49 202 epsilon: 2.5e-13 prerequisites: ! | atom full @@ -14,7 +14,7 @@ angle_coeff: ! | 2 45.0 1 2 3 50.0 -1 3 4 100.0 -1 4 -equilibrium: 4 3.141592653589793 3.141592653589793 3.141592653589793 3.141592653589793 +equilibrium: 4 1.5707963267948966 1.5707963267948966 0 0 extract: ! "" natoms: 29 init_energy: 946.676664091363 From ca1496e02848265aa0930002479f996fa4c8f3e1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 22 Mar 2021 21:36:25 -0400 Subject: [PATCH 0224/1217] simplify --- src/KIM/pair_kim.cpp | 49 ++++++++----------- src/USER-MANIFOLD/fix_manifoldforce.cpp | 18 +++---- src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp | 20 +++----- src/USER-MISC/dihedral_table.cpp | 6 +-- 4 files changed, 34 insertions(+), 59 deletions(-) diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 1b709a65c2..cf6374ab2d 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -477,12 +477,10 @@ void PairKIM::coeff(int narg, char **arg) if (paramname == str_name_str) break; } - if (param_index >= numberOfParameters) { - auto msg = fmt::format("Wrong argument for pair coefficients.\n" - "This Model does not have the requested " - "'{}' parameter", paramname); - error->all(FLERR,msg); - } + if (param_index >= numberOfParameters) + error->all(FLERR,fmt::format("Wrong argument for pair coefficients.\n" + "This Model does not have the requested " + "'{}' parameter", paramname)); // Get the index_range for the requested parameter int nlbound(0); @@ -492,12 +490,10 @@ void PairKIM::coeff(int narg, char **arg) std::string argtostr(arg[i++]); // Check to see if the indices range contains only integer numbers & : - if (argtostr.find_first_not_of("0123456789:") != std::string::npos) { - auto msg = fmt::format("Illegal index_range.\nExpected integer " - "parameter(s) instead of '{}' in " - "index_range", argtostr); - error->all(FLERR,msg); - } + if (argtostr.find_first_not_of("0123456789:") != std::string::npos) + error->all(FLERR,fmt::format("Illegal index_range.\nExpected integer" + " parameter(s) instead of '{}' in " + "index_range", argtostr)); std::string::size_type npos = argtostr.find(':'); if (npos != std::string::npos) { @@ -507,21 +503,17 @@ void PairKIM::coeff(int narg, char **arg) nubound = atoi(words[1].c_str()); if (nubound < 1 || nubound > extent || - nlbound < 1 || nlbound > nubound) { - auto msg = fmt::format("Illegal index_range '{}-{}' for '{}' " - "parameter with the extent of '{}'", - nlbound, nubound, paramname, extent); - error->all(FLERR,msg); - } + nlbound < 1 || nlbound > nubound) + error->all(FLERR,fmt::format("Illegal index_range '{}-{}' for '{}' " + "parameter with the extent of '{}'", + nlbound, nubound, paramname, extent)); } else { nlbound = atoi(argtostr.c_str()); - if (nlbound < 1 || nlbound > extent) { - auto msg = fmt::format("Illegal index '{}' for '{}' parameter " - "with the extent of '{}'", nlbound, - paramname, extent); - error->all(FLERR,msg); - } + if (nlbound < 1 || nlbound > extent) + error->all(FLERR,fmt::format("Illegal index '{}' for '{}' parameter " + "with the extent of '{}'", nlbound, + paramname, extent)); nubound = nlbound; } @@ -551,11 +543,10 @@ void PairKIM::coeff(int narg, char **arg) } else error->all(FLERR,"Wrong parameter type to update"); } else { - auto msg = fmt::format("Wrong number of variable values for pair " - "coefficients.\n'{}' values are requested " - "for '{}' parameter", nubound - nlbound + 1, - paramname); - error->all(FLERR,msg); + error->all(FLERR,fmt::format("Wrong number of variable values for pair " + "coefficients.\n'{}' values are requested " + "for '{}' parameter", nubound - nlbound + 1, + paramname)); } } diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index d389b9787e..26d209e7a9 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -58,22 +58,16 @@ FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) : ptr_m = create_manifold(m_name,lmp,narg,arg); // Construct manifold from factory: - if (!ptr_m) { - char msg[2048]; - snprintf(msg,2048,"Manifold pointer for manifold '%s' was NULL for some reason", arg[3]); - error->all(FLERR,msg); - } - + if (!ptr_m) + error->all(FLERR,fmt::format("Manifold pointer for manifold '{}' " + "was NULL for some reason", arg[3])); // After constructing the manifold, you can safely make // room for the parameters nvars = ptr_m->nparams(); - if (narg < nvars+4) { - char msg[2048]; - sprintf(msg,"Manifold %s needs at least %d argument(s)!", - m_name, nvars); - error->all(FLERR,msg); - } + if (narg < nvars+4) + error->all(FLERR,fmt::format("Manifold {} needs at least {} " + "argument(s)!", m_name, nvars)); ptr_m->params = new double[nvars]; if (ptr_m->params == nullptr) { diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index 5d5bdea156..a45d62a588 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -95,9 +95,7 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, max_iter = utils::numeric( FLERR, arg[4] ,false,lmp); ptr_m = create_manifold(arg[5], lmp, narg, arg); - if (!ptr_m) { - error->all(FLERR,"Error creating manifold pointer"); - } + if (!ptr_m) error->all(FLERR,"Error creating manifold pointer"); nvars = ptr_m->nparams(); tstrs = new char*[nvars]; @@ -105,17 +103,13 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, tstyle = new int[nvars]; is_var = new int[nvars]; - if (!tstrs || !tvars || !tstyle || !is_var) { + if (!tstrs || !tvars || !tstyle || !is_var) error->all(FLERR, "Error creating manifold arg arrays"); - } // Check if you have enough args: - if (6 + nvars > narg) { - char msg[2048]; - sprintf(msg, "Not enough args for manifold %s, %d expected but got %d\n", - ptr_m->id(), nvars, narg - 6); - error->all(FLERR, msg); - } + if (6 + nvars > narg) + error->all(FLERR,fmt::format("Not enough args for manifold {}, {} expected " + "but got {}\n",ptr_m->id(),nvars, narg - 6)); // Loop over manifold args: for (int i = 0; i < nvars; ++i) { int len = 0, offset = 0; @@ -154,9 +148,7 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, } argi += 2; } else if (error_on_unknown_keyword) { - char msg[2048]; - sprintf(msg,"Error parsing arg \"%s\".\n", arg[argi]); - error->all(FLERR, msg); + error->all(FLERR,fmt::format("Error parsing arg \"{}\".\n",arg[argi])); } else { argi += 1; } diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index 30e6192275..a81037cad6 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -1183,10 +1183,8 @@ void DihedralTable::spline_table(Table *tb) } } // for (int i=0; ininput; i++) - if ((num_disagreements > tb->ninput/2) && (num_disagreements > 2)) { - std::string msg("Dihedral table has inconsistent forces and energies. (Try \"NOF\".)\n"); - error->all(FLERR, msg); - } + if ((num_disagreements > tb->ninput/2) && (num_disagreements > 2)) + error->all(FLERR,"Dihedral table has inconsistent forces and energies. (Try \"NOF\".)\n"); } // check for consistency if (! tb->f_unspecified) From 4b076e01bec603acb1b7eac8343a669eecaf38ea Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 22 Mar 2021 21:36:33 -0400 Subject: [PATCH 0225/1217] silence compiler warning --- src/fix_property_atom.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 56add7a0d1..6ce5b6360b 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -227,7 +227,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, try { ValueTokenizer values(buf); - if (values.count() != nvalue+1) + if ((int)values.count() != nvalue+1) error->all(FLERR,fmt::format("Incorrect format in {} section " "of data file: {}",keyword,buf)); From 875327117bd4e9d76d39e3548013d2c47b9e5956 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 23 Mar 2021 07:36:12 -0400 Subject: [PATCH 0226/1217] add unit test for dihedral styles table and table/cut --- .../tests/dihedral-table_cut_linear.yaml | 86 + .../tests/dihedral-table_cut_spline.yaml | 86 + .../tests/dihedral-table_linear.yaml | 86 + .../tests/dihedral-table_spline.yaml | 86 + .../force-styles/tests/harmonic_dihedral.txt | 3621 +++++++++++++++++ 5 files changed, 3965 insertions(+) create mode 100644 unittest/force-styles/tests/dihedral-table_cut_linear.yaml create mode 100644 unittest/force-styles/tests/dihedral-table_cut_spline.yaml create mode 100644 unittest/force-styles/tests/dihedral-table_linear.yaml create mode 100644 unittest/force-styles/tests/dihedral-table_spline.yaml create mode 100644 unittest/force-styles/tests/harmonic_dihedral.txt diff --git a/unittest/force-styles/tests/dihedral-table_cut_linear.yaml b/unittest/force-styles/tests/dihedral-table_cut_linear.yaml new file mode 100644 index 0000000000..c34c6269de --- /dev/null +++ b/unittest/force-styles/tests/dihedral-table_cut_linear.yaml @@ -0,0 +1,86 @@ +--- +lammps_version: 10 Mar 2021 +date_generated: Tue Mar 23 08:05:02 202 +epsilon: 1e-14 +prerequisites: ! | + atom full + dihedral table/cut +pre_commands: ! "" +post_commands: ! "" +input_file: in.fourmol +dihedral_style: table/cut linear 3600 +dihedral_coeff: ! | + 1 aat 1.00 170 180 ${input_dir}/harmonic_dihedral.txt HARMONIC_1 + 2 aat 1.00 170 180 ${input_dir}/harmonic_dihedral.txt HARMONIC_2 + 3 aat 0.50 175 180 ${input_dir}/harmonic_dihedral.txt HARMONIC_3 + 4 aat 1.00 170 180 ${input_dir}/harmonic_dihedral.txt HARMONIC_4 + 5 aat 0.25 170 175 ${input_dir}/harmonic_dihedral.txt HARMONIC_5 +extract: ! "" +natoms: 29 +init_energy: 552.225725624496 +init_stress: ! |- + -7.4008882268909986e+01 1.3648518393804071e+02 -6.2476301669130748e+01 3.4620215707793108e+01 1.3017899329318067e+02 1.9706621502063012e+02 +init_forces: ! |2 + 1 -8.1198888996808620e+01 7.1073378215839497e+01 -1.1918247546822441e+02 + 2 3.8575810899979956e+01 -1.9920126773772417e+01 1.8847596663648414e+01 + 3 1.0913741754895571e+02 -7.1292512160682776e+01 7.5572753355603993e+01 + 4 -4.7848742793736733e+01 -7.5245295675494663e+00 6.4464643610526949e+01 + 5 -1.5539692023725792e+01 5.7172364237479494e+00 -1.3226941634858840e+00 + 6 -1.1355716924924745e+02 -8.6143836335725510e+01 -5.7299648623432482e+00 + 7 4.1372375526613887e+01 4.5139121695653614e+01 -7.4310043691848229e+00 + 8 2.1399043677828325e+02 1.8625470581545247e+02 -3.3675100353189755e+00 + 9 5.2653582674682809e+01 5.6583201775589529e+01 -2.5669664860295835e+01 + 10 -4.7984520275438535e+02 -5.1382692638722949e+02 -1.3749287390453020e+02 + 11 1.6539670687119863e+02 1.4091972117987351e+02 -1.2657881071783035e+02 + 12 3.4200742496423310e+01 1.2794076077133660e+02 2.3610219433759886e+02 + 13 1.8270592580559917e+00 4.1997746033241778e+00 8.8146411631557697e+00 + 14 1.8694466162959706e+01 -2.6013807510038696e+01 -9.2498849040619788e+00 + 15 -6.2869548680867373e+00 2.1284514172388507e+00 -6.4318098210331209e+00 + 16 -1.0694908795819050e+02 -5.9251517113768401e+01 1.0405679351593225e+01 + 17 1.7537714042702788e+02 1.4401690395071051e+02 2.8249184624181581e+01 + 18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +run_energy: 549.782031215547 +run_stress: ! |- + -7.5056949042919044e+01 1.3698944188847955e+02 -6.1932492845560127e+01 3.3581673544215263e+01 1.2888596290133776e+02 1.9565093507759894e+02 +run_forces: ! |2 + 1 -8.1850261118769851e+01 7.1565857666082792e+01 -1.1998194154132169e+02 + 2 3.8942730288029111e+01 -2.0139091742218607e+01 1.9096837462073495e+01 + 3 1.0933304895917627e+02 -7.1974713700542679e+01 7.7222647280784500e+01 + 4 -4.7578796179763913e+01 -7.4260553823873163e+00 6.4056709071407184e+01 + 5 -1.5573770424692153e+01 5.7360778752676689e+00 -1.3292716784107659e+00 + 6 -1.1205401245818740e+02 -8.3930835846975214e+01 -6.4629873083122060e+00 + 7 4.1368235883807785e+01 4.5098977123947911e+01 -7.4207495093494247e+00 + 8 2.1112963982593271e+02 1.8319846795829790e+02 -4.5077247269703236e+00 + 9 5.2596180125216748e+01 5.6303309547815658e+01 -2.5556604563933746e+01 + 10 -4.8079664429997507e+02 -5.1197713825609452e+02 -1.3418905325289452e+02 + 11 1.6804796981040414e+02 1.4157399298542791e+02 -1.2667138198231208e+02 + 12 3.3945852325507303e+01 1.2661718822016165e+02 2.3437614824953252e+02 + 13 1.8225699822433148e+00 4.1983174055270061e+00 8.8273571873798709e+00 + 14 1.8256498023781354e+01 -2.5354302062650923e+01 -8.9739201991677255e+00 + 15 -6.2761226111239754e+00 2.1261045368019413e+00 -6.4368032911012207e+00 + 16 -1.0841619930894663e+02 -6.1089982213467948e+01 9.6877249595793860e+00 + 17 1.7710308117736014e+02 1.4547382588500676e+02 2.8263013843016775e+01 + 18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +... diff --git a/unittest/force-styles/tests/dihedral-table_cut_spline.yaml b/unittest/force-styles/tests/dihedral-table_cut_spline.yaml new file mode 100644 index 0000000000..9148e0a80d --- /dev/null +++ b/unittest/force-styles/tests/dihedral-table_cut_spline.yaml @@ -0,0 +1,86 @@ +--- +lammps_version: 10 Mar 2021 +date_generated: Tue Mar 23 08:06:45 202 +epsilon: 1e-14 +prerequisites: ! | + atom full + dihedral table/cut +pre_commands: ! "" +post_commands: ! "" +input_file: in.fourmol +dihedral_style: table/cut spline 3600 +dihedral_coeff: ! | + 1 aat 1.00 170 180 ${input_dir}/harmonic_dihedral.txt HARMONIC_1 + 2 aat 1.00 170 180 ${input_dir}/harmonic_dihedral.txt HARMONIC_2 + 3 aat 0.50 175 180 ${input_dir}/harmonic_dihedral.txt HARMONIC_3 + 4 aat 1.00 170 180 ${input_dir}/harmonic_dihedral.txt HARMONIC_4 + 5 aat 0.25 170 175 ${input_dir}/harmonic_dihedral.txt HARMONIC_5 +extract: ! "" +natoms: 29 +init_energy: 552.218725263499 +init_stress: ! |- + -7.4019824552159534e+01 1.3649499111894895e+02 -6.2475166566789284e+01 3.4617375151088808e+01 1.3019745657214429e+02 1.9709007795400348e+02 +init_forces: ! |2 + 1 -8.1213286444115909e+01 7.1080525227994045e+01 -1.1918872501604099e+02 + 2 3.8585732128399350e+01 -1.9925249987601369e+01 1.8852444035804549e+01 + 3 1.0914957240045973e+02 -7.1293677289031876e+01 7.5564572526931997e+01 + 4 -4.7856039321211888e+01 -7.5256880640368262e+00 6.4474469548287303e+01 + 5 -1.5540068306011690e+01 5.7173997377718440e+00 -1.3227187051350375e+00 + 6 -1.1356202282295826e+02 -8.6148464023143134e+01 -5.7287967059654719e+00 + 7 4.1373182001548223e+01 4.5140001882310173e+01 -7.4311492797065428e+00 + 8 2.1400860040790070e+02 1.8627156816363441e+02 -3.3695416437372394e+00 + 9 5.2656207239745335e+01 5.6586006420025306e+01 -2.5670940543260770e+01 + 10 -4.7989294342864497e+02 -5.1388484267202580e+02 -1.3749831844924219e+02 + 11 1.6541995228367492e+02 1.4093778373411678e+02 -1.2659553837843652e+02 + 12 3.4200230035629019e+01 1.2795430859179336e+02 2.3612094879489862e+02 + 13 1.8271828366360419e+00 4.2000586675545639e+00 8.8152373675940172e+00 + 14 1.8695088969660507e+01 -2.6014674160815950e+01 -9.2501930642549315e+00 + 15 -6.2873518284233292e+00 2.1285858083405422e+00 -6.4322159275576647e+00 + 16 -1.0696654386912348e+02 -5.9261377200437906e+01 1.0407194734343612e+01 + 17 1.7540250771683571e+02 1.4403773516355190e+02 2.8253270705477313e+01 + 18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +run_energy: 549.770211120194 +run_stress: ! 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| + atom full + dihedral table +pre_commands: ! "" +post_commands: ! "" +input_file: in.fourmol +dihedral_style: table linear 3600 +dihedral_coeff: ! | + 1 ${input_dir}/harmonic_dihedral.txt HARMONIC_1 + 2 ${input_dir}/harmonic_dihedral.txt HARMONIC_2 + 3 ${input_dir}/harmonic_dihedral.txt HARMONIC_3 + 4 ${input_dir}/harmonic_dihedral.txt HARMONIC_4 + 5 ${input_dir}/harmonic_dihedral.txt HARMONIC_5 +extract: ! "" +natoms: 29 +init_energy: 789.184256783584 +init_stress: ! |- + -1.6165501104216639e+02 -7.4114380315441565e+01 2.3576939135760787e+02 -2.3488521541598647e+02 3.4341737187983938e+02 -1.5959461001900144e+02 +init_forces: ! |2 + 1 -2.1498835469576278e+01 4.0242705861631180e+01 -9.0007821437717382e+01 + 2 -8.2018888113291979e+00 4.2353656629457461e+00 -4.0073270940910781e+00 + 3 9.1203773212580060e+01 -1.3765900530865244e+02 8.1977349479812418e+01 + 4 -4.8195100042546727e+01 -8.0451084249021534e+00 6.4747111681716376e+01 + 5 -6.2251242080533295e+01 2.2803637398534534e+01 -5.3285420895267421e+00 + 6 9.1265646559106216e+01 1.3743040689865262e+02 -3.9343488033831335e+01 + 7 -4.7432736093120091e+01 -5.1202947877496094e+01 8.4096202947719512e+00 + 8 2.2566883016909227e+02 1.6219571012359663e+02 5.7664673263129927e+01 + 9 -2.0799357954651114e+00 5.0308583175017674e+00 -7.5442843674616533e-01 + 10 -4.0472227269030174e+02 -4.7265020465440665e+02 -9.9994880868353093e+01 + 11 3.9893735247972799e+01 2.0808487532188158e+02 -1.3663466833430391e+02 + 12 6.2491147091194719e+01 7.0245646325825419e+01 1.9568453298435855e+02 + 13 2.9232948128895806e+01 6.7196393653186874e+01 1.4103425861049234e+02 + 14 7.2097046578806413e+01 -1.0032480603588586e+02 -3.5673090473056490e+01 + 15 -1.0059127788938771e+02 3.4055222675821568e+01 -1.0290895713652986e+02 + 16 -9.2256978542416007e+01 -1.2565565388894508e+02 -6.3113527034307076e+01 + 17 1.7537714042702783e+02 1.4401690395071046e+02 2.8249184624181567e+01 + 18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +run_energy: 786.199103735512 +run_stress: ! |- + -1.5979555001643004e+02 -7.4781079673606996e+01 2.3457662969003690e+02 -2.3349637150864024e+02 3.4159374485946643e+02 -1.5956254217954015e+02 +run_forces: ! |2 + 1 -2.2291107377203105e+01 4.0666970718627333e+01 -9.0497211256380396e+01 + 2 -7.6875363073287559e+00 3.9737486142840055e+00 -3.7620801734312614e+00 + 3 9.2103819928191996e+01 -1.3743335232167533e+02 8.2431881459386020e+01 + 4 -4.8290666517219691e+01 -8.1170776132331781e+00 6.4779991104261541e+01 + 5 -6.2246983418905813e+01 2.2813785810311227e+01 -5.3751809499241965e+00 + 6 9.1087481738151070e+01 1.3760819705271160e+02 -3.9500650484032505e+01 + 7 -4.6891554381909977e+01 -5.0621074446115216e+01 8.3775716071879351e+00 + 8 2.2268693398316259e+02 1.5891760123847899e+02 5.7199245600838793e+01 + 9 -1.3435027007714808e+00 5.5949363550589339e+00 -1.0517595721340651e+00 + 10 -4.0565110153193677e+02 -4.7084401363160805e+02 -9.7618847422734831e+01 + 11 4.2251495153612957e+01 2.0872309038043886e+02 -1.3675117078222070e+02 + 12 6.2352820175292266e+01 6.8729440749361473e+01 1.9366789701210121e+02 + 13 2.9032540154457664e+01 6.7387205615336427e+01 1.4127076790322786e+02 + 14 7.1580926568596425e+01 -9.9385928393915108e+01 -3.5110636800452511e+01 + 15 -1.0011174024358218e+02 3.3796455380232061e+01 -1.0280446675457922e+02 + 16 -9.3357186802666320e+01 -1.2692958041908989e+02 -6.3465822450651899e+01 + 17 1.7677536158005910e+02 1.4511959491079591e+02 2.8210471959538260e+01 + 18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +... diff --git a/unittest/force-styles/tests/dihedral-table_spline.yaml b/unittest/force-styles/tests/dihedral-table_spline.yaml new file mode 100644 index 0000000000..90aab98fba --- /dev/null +++ b/unittest/force-styles/tests/dihedral-table_spline.yaml @@ -0,0 +1,86 @@ +--- +lammps_version: 10 Mar 2021 +date_generated: Mon Mar 22 21:19:05 202 +epsilon: 1e-14 +prerequisites: ! | + atom full + dihedral table +pre_commands: ! "" +post_commands: ! "" +input_file: in.fourmol +dihedral_style: table spline 3600 +dihedral_coeff: ! | + 1 ${input_dir}/harmonic_dihedral.txt HARMONIC_1 + 2 ${input_dir}/harmonic_dihedral.txt HARMONIC_2 + 3 ${input_dir}/harmonic_dihedral.txt HARMONIC_3 + 4 ${input_dir}/harmonic_dihedral.txt HARMONIC_4 + 5 ${input_dir}/harmonic_dihedral.txt HARMONIC_5 +extract: ! "" +natoms: 29 +init_energy: 789.17395865366 +init_stress: ! |- + -1.6167160198618581e+02 -7.4120077515581954e+01 2.3579167950176785e+02 -2.3490764576822448e+02 3.4342184840668585e+02 -1.5962456212434762e+02 +init_forces: ! |2 + 1 -2.1511698354927645e+01 4.0249060385771472e+01 -9.0013321064696271e+01 + 2 -8.1931699818042816e+00 4.2308633547530370e+00 -4.0030671970615401e+00 + 3 9.1213724085941266e+01 -1.3766351443388791e+02 8.1969246814730084e+01 + 4 -4.8202572709944334e+01 -8.0465316616826055e+00 6.4757081268568328e+01 + 5 -6.2252471687916213e+01 2.2804485237535822e+01 -5.3285277358374286e+00 + 6 9.1271091175285207e+01 1.3743691094855717e+02 -3.9344000146381845e+01 + 7 -4.7435622491834799e+01 -5.1206081227011012e+01 8.4101355534202042e+00 + 8 2.2568717307036252e+02 1.6221073791401761e+02 5.7667169771245945e+01 + 9 -2.0794865262354030e+00 5.0314964866185363e+00 -7.5468527912272698e-01 + 10 -4.0476567716026062e+02 -4.7270660864081441e+02 -9.9999223852109083e+01 + 11 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+ 6 9.1082266941280153e+01 1.3760435384789912e+02 -3.9497610389853719e+01 + 7 -4.6896901941201634e+01 -5.0626903993409201e+01 8.3785409954385486e+00 + 8 2.2272760597411565e+02 1.5895499661752211e+02 5.7194518486415930e+01 + 9 -1.3424389468966993e+00 5.5961120653727576e+00 -1.0522843110369067e+00 + 10 -4.0569661746613480e+02 -4.7090645573337184e+02 -9.7628440089732422e+01 + 11 4.2260633619776542e+01 2.0874271121537350e+02 -1.3676519708069108e+02 + 12 6.2351939732772273e+01 6.8740733319529681e+01 1.9368291661547465e+02 + 13 2.9034913906341565e+01 6.7392732862315881e+01 1.4128237934676201e+02 + 14 7.1584708176938221e+01 -9.9391162142709391e+01 -3.5112483055478720e+01 + 15 -1.0011391207749671e+02 3.3797184006896543e+01 -1.0280672266200776e+02 + 16 -9.3370883891440556e+01 -1.2693997492906119e+02 -6.3467168010540369e+01 + 17 1.7679515936747723e+02 1.4513584646617855e+02 2.8213604815112788e+01 + 18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 + 29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +... diff --git a/unittest/force-styles/tests/harmonic_dihedral.txt b/unittest/force-styles/tests/harmonic_dihedral.txt new file mode 100644 index 0000000000..3f99f1663c --- /dev/null +++ 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6.09119908946021 3.0652592090369324 31.04442499585652 +699 6.0999257357201815 2.799836877272261 29.78241818880914 +700 6.1086523819801535 2.5455173280956624 28.500000000000014 +701 6.117379028240125 2.3024748594226727 27.198049334797776 +702 6.126105674500097 2.0708760404210143 25.877458485154218 +703 6.134832320760068 1.8508795973526586 24.53913251807294 +704 6.14355896702004 1.6426363047905856 23.183988655320686 +705 6.152285613280012 1.4462888822855477 21.81295564481014 +706 6.161012259539983 1.2619718965531712 20.42697312408222 +707 6.169738905799955 1.0898116692486077 19.02699097632499 +708 6.178465552059926 0.9299261903921019 17.61396867937214 +709 6.187192198319899 0.7824250375043278 16.188874648123534 +710 6.19591884457987 0.6474093005076978 14.75268557084372 +711 6.204645490839842 0.524971512444137 13.306385739786574 +712 6.213372137099813 0.41519558605769824 11.850966376612341 +713 6.222098783359785 0.3181567562848644 10.387424953052408 +714 6.230825429619757 0.2339215286923887 8.916764507293102 +715 6.239552075879728 0.16254763389760063 7.439992956542977 +716 6.2482787221397 0.10408398800281804 5.9581224062562175 +717 6.257005368399671 0.058570659070577125 4.4721684564872275 +718 6.265732014659643 0.02603883966309506 2.9831495058477993 +719 6.274458660919614 0.006510825464412062 1.4920860535488742 From b7296b6d0b456bb1f7520934b2c45a36cfbd3fb0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 23 Mar 2021 13:49:37 -0400 Subject: [PATCH 0227/1217] consolidate documentation for dihedral styles table and table/cut into one file --- doc/src/Commands_bond.rst | 2 +- doc/src/dihedral_style.rst | 2 +- doc/src/dihedral_table.rst | 89 ++++++++++--- doc/src/dihedral_table_cut.rst | 229 --------------------------------- 4 files changed, 72 insertions(+), 250 deletions(-) delete mode 100644 doc/src/dihedral_table_cut.rst diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst index a826228219..70a021849d 100644 --- a/doc/src/Commands_bond.rst +++ b/doc/src/Commands_bond.rst @@ -126,7 +126,7 @@ OPT. * :doc:`quadratic (o) ` * :doc:`spherical ` * :doc:`table (o) ` - * :doc:`table/cut ` + * :doc:`table/cut ` .. _improper: diff --git a/doc/src/dihedral_style.rst b/doc/src/dihedral_style.rst index bf3cf4902a..4301824b40 100644 --- a/doc/src/dihedral_style.rst +++ b/doc/src/dihedral_style.rst @@ -113,7 +113,7 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`quadratic ` - dihedral with quadratic term in angle * :doc:`spherical ` - dihedral which includes angle terms to avoid singularities * :doc:`table ` - tabulated dihedral -* :doc:`table/cut ` - tabulated dihedral with analytic cutoff +* :doc:`table/cut ` - tabulated dihedral with analytic cutoff ---------- diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index ff3e61baee..f1b14065fd 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -1,19 +1,24 @@ .. index:: dihedral_style table .. index:: dihedral_style table/omp +.. index:: dihedral_style table/cut dihedral_style table command ============================ Accelerator Variants: *table/omp* +dihedral_style table/cut command +================================ + Syntax """""" .. code-block:: LAMMPS - dihedral_style table style Ntable + dihedral_style style interp Ntable -* style = *linear* or *spline* = method of interpolation +* style = *table* or *table/cut* +* interp = *linear* or *spline* = method of interpolation * Ntable = size of the internal lookup table Examples @@ -26,13 +31,21 @@ Examples dihedral_coeff 1 file.table DIH_TABLE1 dihedral_coeff 2 file.table DIH_TABLE2 + dihedral_style table/cut spline 400 + dihedral_style table/cut linear 1000 + dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1 + dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2 + Description """"""""""" -The *table* dihedral style creates interpolation tables of length -*Ntable* from dihedral potential and derivative values listed in a -file(s) as a function of the dihedral angle "phi". The files are read -by the :doc:`dihedral_coeff ` command. +The *table* and *table/cut* dihedral styles create interpolation tables +of length *Ntable* from dihedral potential and derivative values listed +in a file(s) as a function of the dihedral angle "phi". The files are +read by the :doc:`dihedral_coeff ` command. For +dihedral style *table/cut* additionally an analytic cutoff that is +quadratic in the bond-angle (theta) is applied in order to regularize +the dihedral interaction. The interpolation tables are created by fitting cubic splines to the file values and interpolating energy and derivative values at each of @@ -51,16 +64,53 @@ interpolated table. For a given dihedral angle (phi), the appropriate coefficients are chosen from this list, and a cubic polynomial is used to compute the energy and the derivative at this angle. -The following coefficients must be defined for each dihedral type via -the :doc:`dihedral_coeff ` command as in the example -above. +For dihedral style *table* the following coefficients must be defined +for each dihedral type via the :doc:`dihedral_coeff ` +command as in the example above. * filename * keyword -The filename specifies a file containing tabulated energy and -derivative values. The keyword specifies a section of the file. The -format of this file is described below. +The filename specifies a file containing tabulated energy and derivative +values. The keyword specifies which section of the file to read. The +format of this file is the same for both dihedral styles and described +below. + +For dihedral style *table/cut* the following coefficients must be +defined for each dihedral type via the :doc:`dihedral_coeff +` command as in the example above. + +* style (aat) +* cutoff prefactor +* cutoff angle1 +* cutoff angle2 +* filename +* keyword + +The cutoff dihedral style uses a tabulated dihedral interaction with a +cutoff function: + +.. math:: + + f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\ + f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2 + +The cutoff specifies an prefactor to the cutoff function. While this +value would ordinarily equal 1 there may be situations where the value +should change. + +The cutoff :math:`\theta_1` specifies the angle (in degrees) below which +the dihedral interaction is unmodified, i.e. the cutoff function is 1. + +The cutoff function is applied between :math:`\theta_1` and +:math:`\theta_2`, which is the angle at which the cutoff function drops +to zero. The value of zero effectively "turns off" the dihedral +interaction. + +The filename specifies a file containing tabulated energy and derivative +values. The keyword specifies which section of the file to read. The +format of this file is the same for both dihedral styles and described +below. ---------- @@ -182,18 +232,19 @@ that matches the specified keyword. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -This dihedral style writes the settings for the "dihedral_style table" -command to :doc:`binary restart files `, so a dihedral_style -command does not need to specified in an input script that reads a -restart file. However, the coefficient information is not stored in -the restart file, since it is tabulated in the potential files. Thus, +These dihedral styles write the settings for the "dihedral_style table" +or "dihedral_style table/cut" command to :doc:`binary restart files +`, so a dihedral_style command does not need to specified in an +input script that reads a restart file. However, the coefficient +information loaded from the table file(s) is not stored in the restart +file, since it is tabulated in the potential files. Thus, suitable dihedral_coeff commands do need to be specified in the restart input -script. +script after reading the restart file. Restrictions """""""""""" -This dihedral style can only be used if LAMMPS was built with the +These dihedral styles can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/dihedral_table_cut.rst b/doc/src/dihedral_table_cut.rst deleted file mode 100644 index a29844da19..0000000000 --- a/doc/src/dihedral_table_cut.rst +++ /dev/null @@ -1,229 +0,0 @@ -.. index:: dihedral_style table/cut - -dihedral_style table/cut command -================================ - -Syntax -"""""" - -.. code-block:: LAMMPS - - dihedral_style table/cut style Ntable - -* style = *linear* or *spline* = method of interpolation -* Ntable = size of the internal lookup table - -Examples -"""""""" - -.. code-block:: LAMMPS - - dihedral_style table/cut spline 400 - dihedral_style table/cut linear 1000 - dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1 - dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2 - -Description -""""""""""" - -The *table/cut* dihedral style creates interpolation tables of length -*Ntable* from dihedral potential and derivative values listed in a -file(s) as a function of the dihedral angle "phi". In addition, an -analytic cutoff that is quadratic in the bond-angle (theta) is applied -in order to regularize the dihedral interaction. The dihedral table -files are read by the :doc:`dihedral_coeff ` command. - -The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy and derivative values at each of -*Ntable* dihedral angles. During a simulation, these tables are used -to interpolate energy and force values on individual atoms as -needed. The interpolation is done in one of 2 styles: *linear* or -*spline*\ . - -For the *linear* style, the dihedral angle (phi) is used to find 2 -surrounding table values from which an energy or its derivative is -computed by linear interpolation. - -For the *spline* style, cubic spline coefficients are computed and -stored at each of the *Ntable* evenly-spaced values in the -interpolated table. For a given dihedral angle (phi), the appropriate -coefficients are chosen from this list, and a cubic polynomial is used -to compute the energy and the derivative at this angle. - -The following coefficients must be defined for each dihedral type via -the :doc:`dihedral_coeff ` command as in the example -above. - -* style (aat) -* cutoff prefactor -* cutoff angle1 -* cutoff angle2 -* filename -* keyword - -The cutoff dihedral style uses a tabulated dihedral interaction with a -cutoff function: - -.. math:: - - f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\ - f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2 - -The cutoff specifies an prefactor to the cutoff function. While this value -would ordinarily equal 1 there may be situations where the value should change. - -The cutoff :math:`\theta_1` specifies the angle (in degrees) below which the dihedral -interaction is unmodified, i.e. the cutoff function is 1. - -The cutoff function is applied between :math:`\theta_1` and :math:`\theta_2`, which is -the angle at which the cutoff function drops to zero. The value of zero effectively -"turns off" the dihedral interaction. - -The filename specifies a file containing tabulated energy and -derivative values. The keyword specifies a section of the file. The -format of this file is described below. - ----------- - -The format of a tabulated file is as follows (without the -parenthesized comments). It can begin with one or more comment -or blank lines. - -.. parsed-literal:: - - # Table of the potential and its negative derivative - - DIH_TABLE1 (keyword is the first text on line) - N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F) - (blank line) - 1 -168.0 -1.40351172223 0.0423346818422 - 2 -156.0 -1.70447981034 0.00811786522531 - 3 -144.0 -1.62956100432 -0.0184129719987 - ... - 30 180.0 -0.707106781187 0.0719306095245 - - # Example 2: table of the potential. Forces omitted - - DIH_TABLE2 - N 30 NOF CHECKU testU.dat CHECKF testF.dat - - 1 -168.0 -1.40351172223 - 2 -156.0 -1.70447981034 - 3 -144.0 -1.62956100432 - ... - 30 180.0 -0.707106781187 - -A section begins with a non-blank line whose first character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the -:doc:`dihedral_coeff ` command. The next line lists (in -any order) one or more parameters for the table. Each parameter is a -keyword followed by one or more numeric values. - -Following a blank line, the next N lines list the tabulated values. On -each line, the first value is the index from 1 to N, the second value is -the angle value, the third value is the energy (in energy units), and -the fourth is -dE/d(phi) also in energy units). The third term is the -energy of the 4-atom configuration for the specified angle. The fourth -term (when present) is the negative derivative of the energy with -respect to the angle (in degrees, or radians depending on whether the -user selected DEGREES or RADIANS). Thus the units of the last term -are still energy, not force. The dihedral angle values must increase -from one line to the next. - -Dihedral table splines are cyclic. There is no discontinuity at 180 -degrees (or at any other angle). Although in the examples above, the -angles range from -180 to 180 degrees, in general, the first angle in -the list can have any value (positive, zero, or negative). However -the *range* of angles represented in the table must be *strictly* less -than 360 degrees (2pi radians) to avoid angle overlap. (You may not -supply entries in the table for both 180 and -180, for example.) If -the user's table covers only a narrow range of dihedral angles, -strange numerical behavior can occur in the large remaining gap. - -**Parameters:** - -The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the N -specified in the :doc:`dihedral_style table ` command. -Let *Ntable* is the number of table entries requested dihedral_style -command, and let *Nfile* be the parameter following "N" in the -tabulated file ("30" in the sparse example above). What LAMMPS does -is a preliminary interpolation by creating splines using the *Nfile* -tabulated values as nodal points. It uses these to interpolate as -needed to generate energy and derivative values at *Ntable* different -points (which are evenly spaced over a 360 degree range, even if the -angles in the file are not). The resulting tables of length *Ntable* -are then used as described above, when computing energy and force for -individual dihedral angles and their atoms. This means that if you -want the interpolation tables of length *Ntable* to match exactly what -is in the tabulated file (with effectively nopreliminary -interpolation), you should set *Ntable* = *Nfile*\ . To insure the -nodal points in the user's file are aligned with the interpolated -table entries, the angles in the table should be integer multiples of -360/\ *Ntable* degrees, or 2\*PI/\ *Ntable* radians (depending on your -choice of angle units). - -The optional "NOF" keyword allows the user to omit the forces -(negative energy derivatives) from the table file (normally located in -the fourth column). In their place, forces will be calculated -automatically by differentiating the potential energy function -indicated by the third column of the table (using either linear or -spline interpolation). - -The optional "DEGREES" keyword allows the user to specify angles in -degrees instead of radians (default). - -The optional "RADIANS" keyword allows the user to specify angles in -radians instead of degrees. (Note: This changes the way the forces -are scaled in the fourth column of the data file.) - -The optional "CHECKU" keyword is followed by a filename. This allows -the user to save all of the *Ntable* different entries in the -interpolated energy table to a file to make sure that the interpolated -function agrees with the user's expectations. (Note: You can -temporarily increase the *Ntable* parameter to a high value for this -purpose. "\ *Ntable*\ " is explained above.) - -The optional "CHECKF" keyword is analogous to the "CHECKU" keyword. -It is followed by a filename, and it allows the user to check the -interpolated force table. This option is available even if the user -selected the "NOF" option. - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds one -that matches the specified keyword. - -Restart, fix_modify, output, run start/stop, minimize info -""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -This dihedral style writes the settings for the "dihedral_style table/cut" -command to :doc:`binary restart files `, so a dihedral_style -command does not need to specified in an input script that reads a -restart file. However, the coefficient information is not stored in -the restart file, since it is tabulated in the potential files. Thus, -dihedral_coeff commands do need to be specified in the restart input -script. - -Restrictions -"""""""""""" - -This dihedral style can only be used if LAMMPS was built with the -USER-MISC package. See the :doc:`Build package ` doc -page for more info. - -Related commands -"""""""""""""""" - -:doc:`dihedral_coeff `, :doc:`dihedral_style table ` - -Default -""""""" - -none - -.. _dihedralcut-Salerno: - -**(Salerno)** Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018). From 08d4fec1429e197494a895446f18b20198b7c32f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 23 Mar 2021 14:38:54 -0400 Subject: [PATCH 0228/1217] add framework for testing the variable command --- unittest/commands/CMakeLists.txt | 4 + unittest/commands/test_variables.cpp | 185 +++++++++++++++++++++++++++ 2 files changed, 189 insertions(+) create mode 100644 unittest/commands/test_variables.cpp diff --git a/unittest/commands/CMakeLists.txt b/unittest/commands/CMakeLists.txt index ee0e89d7e9..b2b8a3b130 100644 --- a/unittest/commands/CMakeLists.txt +++ b/unittest/commands/CMakeLists.txt @@ -11,6 +11,10 @@ add_executable(test_groups test_groups.cpp) target_link_libraries(test_groups PRIVATE lammps GTest::GMock GTest::GTest) add_test(NAME Groups COMMAND test_groups WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) +add_executable(test_variables test_variables.cpp) +target_link_libraries(test_variables PRIVATE lammps GTest::GMock GTest::GTest) +add_test(NAME Variables COMMAND test_variables WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + add_executable(test_kim_commands test_kim_commands.cpp) if(KIM_EXTRA_UNITTESTS) if(CURL_FOUND) diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp new file mode 100644 index 0000000000..32d4a7fa13 --- /dev/null +++ b/unittest/commands/test_variables.cpp @@ -0,0 +1,185 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "lammps.h" + +#include "atom.h" +#include "domain.h" +#include "group.h" +#include "info.h" +#include "input.h" +#include "region.h" +#include "variable.h" + +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include +#include + +// whether to print verbose output (i.e. not capturing LAMMPS screen output). +bool verbose = false; + +#if defined(OMPI_MAJOR_VERSION) +const bool have_openmpi = true; +#else +const bool have_openmpi = false; +#endif + +using LAMMPS_NS::utils::split_words; + +namespace LAMMPS_NS { +using ::testing::ExitedWithCode; +using ::testing::MatchesRegex; +using ::testing::StrEq; + +#define TEST_FAILURE(errmsg, ...) \ + if (Info::has_exceptions()) { \ + ::testing::internal::CaptureStdout(); \ + ASSERT_ANY_THROW({__VA_ARGS__}); \ + auto mesg = ::testing::internal::GetCapturedStdout(); \ + if (verbose) std::cout << mesg; \ + ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ + } else { \ + if (!have_openmpi) { \ + ::testing::internal::CaptureStdout(); \ + ASSERT_DEATH({__VA_ARGS__}, ""); \ + auto mesg = ::testing::internal::GetCapturedStdout(); \ + if (verbose) std::cout << mesg; \ + ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ + } \ + } + +class VariableTest : public ::testing::Test { +protected: + LAMMPS *lmp; + Group *group; + Domain *domain; + Variable *variable; + + void SetUp() override + { + const char *args[] = {"VariableTest", "-log", "none", "-echo", "screen", "-nocite"}; + char **argv = (char **)args; + int argc = sizeof(args) / sizeof(char *); + if (!verbose) ::testing::internal::CaptureStdout(); + lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); + if (!verbose) ::testing::internal::GetCapturedStdout(); + group = lmp->group; + domain = lmp->domain; + variable = lmp->input->variable; + } + + void TearDown() override + { + if (!verbose) ::testing::internal::CaptureStdout(); + delete lmp; + if (!verbose) ::testing::internal::GetCapturedStdout(); + std::cout.flush(); + } + + void command(const std::string &cmd) { lmp->input->one(cmd); } + + void atomic_system() + { + if (!verbose) ::testing::internal::CaptureStdout(); + command("units real"); + command("lattice sc 1.0 origin 0.125 0.125 0.125"); + command("region box block -2 2 -2 2 -2 2"); + command("create_box 8 box"); + command("create_atoms 1 box"); + command("mass * 1.0"); + command("region left block -2.0 -1.0 INF INF INF INF"); + command("region right block 0.5 2.0 INF INF INF INF"); + command("region top block INF INF -2.0 -1.0 INF INF"); + command("set region left type 2"); + command("set region right type 3"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + } + + void molecular_system() + { + if (!verbose) ::testing::internal::CaptureStdout(); + command("fix props all property/atom mol rmass q"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + atomic_system(); + if (!verbose) ::testing::internal::CaptureStdout(); + command("variable molid atom floor(id/4)+1"); + command("variable charge atom 2.0*sin(PI/32*id)"); + command("set atom * mol v_molid"); + command("set atom * charge v_charge"); + command("set type 1 mass 0.5"); + command("set type 2*4 mass 2.0"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + } +}; + +TEST_F(VariableTest, NoBox) +{ + ASSERT_EQ(variable->nvar, 0); + if (!verbose) ::testing::internal::CaptureStdout(); + command("variable one index 1"); + command("variable two equal 2"); + command("variable three string three"); + command("variable four loop 4"); + command("variable five loop 100 pad"); + command("variable six world one"); + command("variable seven format two \"%5.2f\""); + command("variable eight getenv HOME"); + command("variable dummy index 0"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + ASSERT_EQ(variable->nvar, 9); + if (!verbose) ::testing::internal::CaptureStdout(); + command("variable dummy delete"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + ASSERT_EQ(variable->nvar, 8); + + TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable");); +} + +TEST_F(VariableTest, AtomicSystem) +{ + atomic_system(); + + if (!verbose) ::testing::internal::CaptureStdout(); + command("variable id atom id"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + ASSERT_EQ(variable->nvar, 1); +} +} // namespace LAMMPS_NS + +int main(int argc, char **argv) +{ + MPI_Init(&argc, &argv); + ::testing::InitGoogleMock(&argc, argv); + + if (have_openmpi && !LAMMPS_NS::Info::has_exceptions()) + std::cout << "Warning: using OpenMPI without exceptions. " + "Death tests will be skipped\n"; + + // handle arguments passed via environment variable + if (const char *var = getenv("TEST_ARGS")) { + std::vector env = split_words(var); + for (auto arg : env) { + if (arg == "-v") { + verbose = true; + } + } + } + + if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; + + int rv = RUN_ALL_TESTS(); + MPI_Finalize(); + return rv; +} From 16c08516a7947c377ca550a734e8bbc36bc9117c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 23 Mar 2021 16:14:40 -0400 Subject: [PATCH 0229/1217] test definition of more different variable styles --- unittest/commands/test_variables.cpp | 86 ++++++++++++++++++++++------ 1 file changed, 68 insertions(+), 18 deletions(-) diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 32d4a7fa13..85108da4da 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -75,8 +75,8 @@ protected: if (!verbose) ::testing::internal::CaptureStdout(); lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); if (!verbose) ::testing::internal::GetCapturedStdout(); - group = lmp->group; - domain = lmp->domain; + group = lmp->group; + domain = lmp->domain; variable = lmp->input->variable; } @@ -86,6 +86,8 @@ protected: delete lmp; if (!verbose) ::testing::internal::GetCapturedStdout(); std::cout.flush(); + unlink("test_variable.file"); + unlink("test_variable.atomfile"); } void command(const std::string &cmd) { lmp->input->one(cmd); } @@ -122,39 +124,87 @@ protected: command("set type 2*4 mass 2.0"); if (!verbose) ::testing::internal::GetCapturedStdout(); } + + void file_vars() + { + FILE *fp = fopen("test_variable.file", "w"); + fputs("# test file for file style variable\n\n\none\n two \n\n" + "three # with comment\nfour ! with non-comment\n" + "# comments only\n five\n#END\n", + fp); + fclose(fp); + fp = fopen("test_variable.atomfile", "w"); + + fputs("# test file for atomfile style variable\n\n" + "4 # four lines\n4 0.5 #with comment\n" + "2 -0.5 \n3 1.5\n1 -1.5\n\n" + "2\n10 1.0 # test\n13 1.0\n\n######\n" + "4\n1 4.0 # test\n2 3.0\n3 2.0\n4 1.0\n#END\n", + fp); + fclose(fp); + } }; -TEST_F(VariableTest, NoBox) +TEST_F(VariableTest, CreateDelete) { + file_vars(); ASSERT_EQ(variable->nvar, 0); if (!verbose) ::testing::internal::CaptureStdout(); - command("variable one index 1"); - command("variable two equal 2"); - command("variable three string three"); - command("variable four loop 4"); - command("variable five loop 100 pad"); - command("variable six world one"); - command("variable seven format two \"%5.2f\""); - command("variable eight getenv HOME"); - command("variable dummy index 0"); + command("variable one index 1 2 3 4"); + command("variable two equal 1"); + command("variable two equal 2"); + command("variable three string four"); + command("variable three string three"); + command("variable four1 loop 4"); + command("variable four2 loop 2 4"); + command("variable five1 loop 100 pad"); + command("variable five2 loop 100 200 pad"); + command("variable six world one"); + command("variable seven format two \"%5.2f\""); + command("variable eight getenv PWD"); + command("variable eight getenv HOME"); + command("variable nine file test_variable.file"); + command("variable dummy index 0"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 9); + ASSERT_EQ(variable->nvar, 12); if (!verbose) ::testing::internal::CaptureStdout(); - command("variable dummy delete"); + command("variable dummy delete"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 8); - + ASSERT_EQ(variable->nvar, 11); + TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable");); + TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable dummy index");); + TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable dummy delete xxx");); + TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", + command("variable two string xxx");); + TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", + command("variable two getenv xxx");); + TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", + command("variable one equal 2");); + TEST_FAILURE(".*ERROR: Cannot use atomfile-style variable unless an atom map exists.*", + command("variable ten atomfile test_variable.atomfile");); + TEST_FAILURE(".*ERROR on proc 0: Cannot open file variable file test_variable.xxx.*", + command("variable nine1 file test_variable.xxx");); } TEST_F(VariableTest, AtomicSystem) { + command("atom_modify map array"); atomic_system(); + file_vars(); if (!verbose) ::testing::internal::CaptureStdout(); - command("variable id atom id"); + command("variable one index 1 2 3 4"); + command("variable id atom type"); + command("variable id atom id"); + command("variable ten atomfile test_variable.atomfile"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 1); + ASSERT_EQ(variable->nvar, 3); + + TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", + command("variable one atom x");); + TEST_FAILURE(".*ERROR on proc 0: Cannot open file variable file test_variable.xxx.*", + command("variable ten1 atomfile test_variable.xxx");); } } // namespace LAMMPS_NS From 014f9ad527fa5231e0b7bc1b9b10118bbdbadcfa Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 23 Mar 2021 16:47:04 -0400 Subject: [PATCH 0230/1217] simplify Variable::parse_args() by using Tokenizer class --- src/variable.cpp | 33 +++++---------------------------- src/variable.h | 1 - 2 files changed, 5 insertions(+), 29 deletions(-) diff --git a/src/variable.cpp b/src/variable.cpp index 1af4a4728a..6766a67a9a 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -4708,42 +4708,19 @@ double Variable::constant(char *word) int Variable::parse_args(char *str, char **args) { - char *ptrnext; int narg = 0; - char *ptr = str; + Tokenizer values(str,","); - while (ptr && narg < MAXFUNCARG) { - ptrnext = find_next_comma(ptr); - if (ptrnext) *ptrnext = '\0'; - args[narg] = utils::strdup(ptr); + while (values.has_next() && narg < MAXFUNCARG) { + args[narg] = utils::strdup(values.next()); narg++; - ptr = ptrnext; - if (ptr) ptr++; } - if (ptr) error->all(FLERR,"Too many args in variable function"); + if (values.has_next()) + error->all(FLERR,"Too many args in variable function"); return narg; } - -/* ---------------------------------------------------------------------- - find next comma in str - skip commas inside one or more nested parenthesis - only return ptr to comma at level 0, else nullptr if not found -------------------------------------------------------------------------- */ - -char *Variable::find_next_comma(char *str) -{ - int level = 0; - for (char *p = str; *p; ++p) { - if ('(' == *p) level++; - else if (')' == *p) level--; - else if (',' == *p && !level) return p; - } - return nullptr; -} - - /* ---------------------------------------------------------------------- helper routine for printing variable name with error message ------------------------------------------------------------------------- */ diff --git a/src/variable.h b/src/variable.h index 2519bc7ac9..cb74e71b51 100644 --- a/src/variable.h +++ b/src/variable.h @@ -125,7 +125,6 @@ class Variable : protected Pointers { int is_constant(char *); double constant(char *); int parse_args(char *, char **); - char *find_next_comma(char *); void print_var_error(const std::string &, int, const std::string &, int, int global=1); void print_tree(Tree *, int); From 1ebb600829360140e3b0d72ffa08e1b938d56196 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 23 Mar 2021 16:47:40 -0400 Subject: [PATCH 0231/1217] add tests for expressions and functions --- unittest/commands/test_variables.cpp | 36 ++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 85108da4da..5a77c75a6c 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -18,6 +18,7 @@ #include "group.h" #include "info.h" #include "input.h" +#include "math_const.h" #include "region.h" #include "variable.h" @@ -37,6 +38,7 @@ const bool have_openmpi = false; #endif using LAMMPS_NS::utils::split_words; +using LAMMPS_NS::MathConst::MY_PI; namespace LAMMPS_NS { using ::testing::ExitedWithCode; @@ -206,6 +208,40 @@ TEST_F(VariableTest, AtomicSystem) TEST_FAILURE(".*ERROR on proc 0: Cannot open file variable file test_variable.xxx.*", command("variable ten1 atomfile test_variable.xxx");); } + +TEST_F(VariableTest, Expressions) +{ + ASSERT_EQ(variable->nvar, 0); + if (!verbose) ::testing::internal::CaptureStdout(); + command("variable one index 1"); + command("variable two equal 2"); + command("variable three equal v_one+v_two"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + ASSERT_EQ(variable->nvar, 3); + + int ivar = variable->find("one"); + ASSERT_FALSE(variable->equalstyle(ivar)); + ivar = variable->find("two"); + ASSERT_TRUE(variable->equalstyle(ivar)); + ASSERT_DOUBLE_EQ(variable->compute_equal(ivar),2.0); + ivar = variable->find("three"); + ASSERT_DOUBLE_EQ(variable->compute_equal(ivar),3.0); +} + +TEST_F(VariableTest, Functions) +{ + file_vars(); + ASSERT_EQ(variable->nvar, 0); + if (!verbose) ::testing::internal::CaptureStdout(); + command("variable one index 1"); + command("variable two equal PI"); + command("variable three equal atan2(v_one,1)"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + ASSERT_EQ(variable->nvar, 3); + + int ivar = variable->find("three"); + ASSERT_DOUBLE_EQ(variable->compute_equal(ivar),0.25*MY_PI); +} } // namespace LAMMPS_NS int main(int argc, char **argv) From 1efd72eb58cd0b61a7d265847b0c908d06432300 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 23 Mar 2021 16:55:05 -0400 Subject: [PATCH 0232/1217] a couple more expressions and functions --- unittest/commands/test_variables.cpp | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 5a77c75a6c..8c0a24bc0d 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -215,9 +215,10 @@ TEST_F(VariableTest, Expressions) if (!verbose) ::testing::internal::CaptureStdout(); command("variable one index 1"); command("variable two equal 2"); - command("variable three equal v_one+v_two"); + command("variable three equal v_one+v_two"); + command("variable four equal PI"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 3); + ASSERT_EQ(variable->nvar, 4); int ivar = variable->find("one"); ASSERT_FALSE(variable->equalstyle(ivar)); @@ -226,6 +227,8 @@ TEST_F(VariableTest, Expressions) ASSERT_DOUBLE_EQ(variable->compute_equal(ivar),2.0); ivar = variable->find("three"); ASSERT_DOUBLE_EQ(variable->compute_equal(ivar),3.0); + ivar = variable->find("four"); + ASSERT_DOUBLE_EQ(variable->compute_equal(ivar),MY_PI); } TEST_F(VariableTest, Functions) @@ -234,12 +237,15 @@ TEST_F(VariableTest, Functions) ASSERT_EQ(variable->nvar, 0); if (!verbose) ::testing::internal::CaptureStdout(); command("variable one index 1"); - command("variable two equal PI"); + command("variable two equal random(1,2,643532)"); command("variable three equal atan2(v_one,1)"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(variable->nvar, 3); - int ivar = variable->find("three"); + int ivar = variable->find("two"); + ASSERT_GT(variable->compute_equal(ivar),0.99); + ASSERT_LT(variable->compute_equal(ivar),2.01); + ivar = variable->find("three"); ASSERT_DOUBLE_EQ(variable->compute_equal(ivar),0.25*MY_PI); } } // namespace LAMMPS_NS From 346c36e227d152f8bd22d88a83341fdeaaef8eef Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 23 Mar 2021 17:48:47 -0400 Subject: [PATCH 0233/1217] replace redundant functions to handle constants with (unordered) map --- src/variable.cpp | 60 ++++++++++------------------ src/variable.h | 2 - unittest/commands/test_variables.cpp | 12 +++++- 3 files changed, 32 insertions(+), 42 deletions(-) diff --git a/src/variable.cpp b/src/variable.cpp index 6766a67a9a..eb1deaae15 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -39,6 +39,7 @@ #include #include #include +#include #include using namespace LAMMPS_NS; @@ -76,6 +77,20 @@ enum{SUM,XMIN,XMAX,AVE,TRAP,SLOPE}; #define BIG 1.0e20 +// constants for variable expressions. customize by adding new items. +// if needed (cf. 'version') initialize in Variable class constructor. + +static std::unordered_map constants = { + {"PI", MY_PI }, + {"version", -1 }, + {"yes", 1 }, + {"no", 0 }, + {"on", 1 }, + {"off", 0 }, + {"true", 1 }, + {"false", 0 } +}; + /* ---------------------------------------------------------------------- */ Variable::Variable(LAMMPS *lmp) : Pointers(lmp) @@ -98,6 +113,10 @@ Variable::Variable(LAMMPS *lmp) : Pointers(lmp) randomequal = nullptr; randomatom = nullptr; + // override initializer since LAMMPS class needs to be instantiated + + constants["version"] = lmp->num_ver; + // customize by assigning a precedence level precedence[DONE] = 0; @@ -2093,8 +2112,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) // constant // ---------------- - } else if (is_constant(word)) { - value1 = constant(word); + } else if (constants.find(word) != constants.end()) { + value1 = constants[word]; if (tree) { Tree *newtree = new Tree(); newtree->type = VALUE; @@ -4663,43 +4682,6 @@ void Variable::atom_vector(char *word, Tree **tree, } } -/* ---------------------------------------------------------------------- - check if word matches a constant - return 1 if yes, else 0 - customize by adding a constant: PI, version -------------------------------------------------------------------------- */ - -int Variable::is_constant(char *word) -{ - if (strcmp(word,"PI") == 0) return 1; - if (strcmp(word,"version") == 0) return 1; - if (strcmp(word,"yes") == 0) return 1; - if (strcmp(word,"no") == 0) return 1; - if (strcmp(word,"on") == 0) return 1; - if (strcmp(word,"off") == 0) return 1; - if (strcmp(word,"true") == 0) return 1; - if (strcmp(word,"false") == 0) return 1; - return 0; -} - -/* ---------------------------------------------------------------------- - process a constant in formula - customize by adding a constant: PI, version -------------------------------------------------------------------------- */ - -double Variable::constant(char *word) -{ - if (strcmp(word,"PI") == 0) return MY_PI; - if (strcmp(word,"version") == 0) return lmp->num_ver; - if (strcmp(word,"yes") == 0) return 1.0; - if (strcmp(word,"no") == 0) return 0.0; - if (strcmp(word,"on") == 0) return 1.0; - if (strcmp(word,"off") == 0) return 0.0; - if (strcmp(word,"true") == 0) return 1.0; - if (strcmp(word,"false") == 0) return 0.0; - return 0.0; -} - /* ---------------------------------------------------------------------- parse string for comma-separated args store copy of each arg in args array diff --git a/src/variable.h b/src/variable.h index cb74e71b51..5dc8748936 100644 --- a/src/variable.h +++ b/src/variable.h @@ -122,8 +122,6 @@ class Variable : protected Pointers { Tree **, Tree **, int &, double *, int &); int is_atom_vector(char *); void atom_vector(char *, Tree **, Tree **, int &); - int is_constant(char *); - double constant(char *); int parse_args(char *, char **); void print_var_error(const std::string &, int, const std::string &, int, int global=1); diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 8c0a24bc0d..cc20ea2b96 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -211,14 +211,17 @@ TEST_F(VariableTest, AtomicSystem) TEST_F(VariableTest, Expressions) { + atomic_system(); ASSERT_EQ(variable->nvar, 0); if (!verbose) ::testing::internal::CaptureStdout(); command("variable one index 1"); command("variable two equal 2"); command("variable three equal v_one+v_two"); command("variable four equal PI"); + command("variable five equal version"); + command("variable six equal XXX"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 4); + ASSERT_EQ(variable->nvar, 6); int ivar = variable->find("one"); ASSERT_FALSE(variable->equalstyle(ivar)); @@ -229,11 +232,18 @@ TEST_F(VariableTest, Expressions) ASSERT_DOUBLE_EQ(variable->compute_equal(ivar),3.0); ivar = variable->find("four"); ASSERT_DOUBLE_EQ(variable->compute_equal(ivar),MY_PI); + ivar = variable->find("five"); + ASSERT_GE(variable->compute_equal(ivar),20210310); + + TEST_FAILURE(".*ERROR: Variable six: Invalid thermo keyword 'XXX' in variable formula.*", + command("print \"${six}\"");); } TEST_F(VariableTest, Functions) { + atomic_system(); file_vars(); + ASSERT_EQ(variable->nvar, 0); if (!verbose) ::testing::internal::CaptureStdout(); command("variable one index 1"); From 4f46ee30a2dd19fa018fe3c61c6c41018ce6aee4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 23 Mar 2021 18:13:01 -0400 Subject: [PATCH 0234/1217] avoid crash when functions expecting an argument are used without --- src/variable.cpp | 7 ++++++- src/variable.h | 2 +- unittest/commands/test_variables.cpp | 21 ++++++++++++--------- 3 files changed, 19 insertions(+), 11 deletions(-) diff --git a/src/variable.cpp b/src/variable.cpp index eb1deaae15..9a8236fdb4 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -1234,6 +1234,9 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) int i = 0; int expect = ARG; + if (str == nullptr) + print_var_error(FLERR,"Invalid syntax in variable formula",ivar); + while (1) { onechar = str[i]; @@ -4688,9 +4691,11 @@ void Variable::atom_vector(char *word, Tree **tree, max allowed # of args = MAXFUNCARG ------------------------------------------------------------------------- */ -int Variable::parse_args(char *str, char **args) +int Variable::parse_args(const std::string &str, char **args) { int narg = 0; + args[0] = nullptr; + Tokenizer values(str,","); while (values.has_next() && narg < MAXFUNCARG) { diff --git a/src/variable.h b/src/variable.h index 5dc8748936..50d276bb14 100644 --- a/src/variable.h +++ b/src/variable.h @@ -122,7 +122,7 @@ class Variable : protected Pointers { Tree **, Tree **, int &, double *, int &); int is_atom_vector(char *); void atom_vector(char *, Tree **, Tree **, int &); - int parse_args(char *, char **); + int parse_args(const std::string &, char **); void print_var_error(const std::string &, int, const std::string &, int, int global=1); void print_tree(Tree *, int); diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index cc20ea2b96..90a0fe00e7 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -37,8 +37,8 @@ const bool have_openmpi = true; const bool have_openmpi = false; #endif -using LAMMPS_NS::utils::split_words; using LAMMPS_NS::MathConst::MY_PI; +using LAMMPS_NS::utils::split_words; namespace LAMMPS_NS { using ::testing::ExitedWithCode; @@ -227,13 +227,13 @@ TEST_F(VariableTest, Expressions) ASSERT_FALSE(variable->equalstyle(ivar)); ivar = variable->find("two"); ASSERT_TRUE(variable->equalstyle(ivar)); - ASSERT_DOUBLE_EQ(variable->compute_equal(ivar),2.0); + ASSERT_DOUBLE_EQ(variable->compute_equal(ivar), 2.0); ivar = variable->find("three"); - ASSERT_DOUBLE_EQ(variable->compute_equal(ivar),3.0); + ASSERT_DOUBLE_EQ(variable->compute_equal(ivar), 3.0); ivar = variable->find("four"); - ASSERT_DOUBLE_EQ(variable->compute_equal(ivar),MY_PI); + ASSERT_DOUBLE_EQ(variable->compute_equal(ivar), MY_PI); ivar = variable->find("five"); - ASSERT_GE(variable->compute_equal(ivar),20210310); + ASSERT_GE(variable->compute_equal(ivar), 20210310); TEST_FAILURE(".*ERROR: Variable six: Invalid thermo keyword 'XXX' in variable formula.*", command("print \"${six}\"");); @@ -249,14 +249,17 @@ TEST_F(VariableTest, Functions) command("variable one index 1"); command("variable two equal random(1,2,643532)"); command("variable three equal atan2(v_one,1)"); + command("variable four equal atan2()"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 3); + ASSERT_EQ(variable->nvar, 4); int ivar = variable->find("two"); - ASSERT_GT(variable->compute_equal(ivar),0.99); - ASSERT_LT(variable->compute_equal(ivar),2.01); + ASSERT_GT(variable->compute_equal(ivar), 0.99); + ASSERT_LT(variable->compute_equal(ivar), 2.01); ivar = variable->find("three"); - ASSERT_DOUBLE_EQ(variable->compute_equal(ivar),0.25*MY_PI); + ASSERT_DOUBLE_EQ(variable->compute_equal(ivar), 0.25 * MY_PI); + TEST_FAILURE(".*ERROR: Variable four: Invalid syntax in variable formula.*", + command("print \"${four}\"");); } } // namespace LAMMPS_NS From 180e8168862f0d50cd5a6cbed8e5f1a6c8553708 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 23 Mar 2021 19:55:08 -0400 Subject: [PATCH 0235/1217] Simplify PythonPackage tests --- unittest/python/test_python_package.cpp | 44 +++++++++++++------------ 1 file changed, 23 insertions(+), 21 deletions(-) diff --git a/unittest/python/test_python_package.cpp b/unittest/python/test_python_package.cpp index cba77ee2b0..5974592997 100644 --- a/unittest/python/test_python_package.cpp +++ b/unittest/python/test_python_package.cpp @@ -40,6 +40,8 @@ protected: LAMMPS *lmp; Info *info; + void command(const std::string &line) { lmp->input->one(line.c_str()); } + void SetUp() override { const char *args[] = {"PythonPackageTest", "-log", "none", "-echo", "screen", "-nocite"}; @@ -51,16 +53,16 @@ protected: ASSERT_NE(lmp, nullptr); info = new Info(lmp); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units real"); - lmp->input->one("dimension 3"); - lmp->input->one("region box block -4 4 -4 4 -4 4"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 single 0.0 0.0 0.0 units box"); - lmp->input->one("create_atoms 1 single 1.9 -1.9 1.9999 units box"); - lmp->input->one("pair_style zero 2.0"); - lmp->input->one("pair_coeff * *"); - lmp->input->one("mass * 1.0"); - lmp->input->one("variable input_dir index " + INPUT_FOLDER); + command("units real"); + command("dimension 3"); + command("region box block -4 4 -4 4 -4 4"); + command("create_box 1 box"); + command("create_atoms 1 single 0.0 0.0 0.0 units box"); + command("create_atoms 1 single 1.9 -1.9 1.9999 units box"); + command("pair_style zero 2.0"); + command("pair_coeff * *"); + command("mass * 1.0"); + command("variable input_dir index " + INPUT_FOLDER); if (!verbose) ::testing::internal::GetCapturedStdout(); } @@ -78,31 +80,31 @@ TEST_F(PythonPackageTest, python_invoke) if (!info->has_style("command", "python")) GTEST_SKIP(); // execute python function from file if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("python printnum file ${input_dir}/func.py"); + command("python printnum file ${input_dir}/func.py"); if (!verbose) ::testing::internal::GetCapturedStdout(); ::testing::internal::CaptureStdout(); - lmp->input->one("python printnum invoke"); + command("python printnum invoke"); std::string output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; ASSERT_THAT(output, MatchesRegex("python.*2.25.*")); // execute another python function from same file if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("python printtxt exists"); + command("python printtxt exists"); if (!verbose) ::testing::internal::GetCapturedStdout(); ::testing::internal::CaptureStdout(); - lmp->input->one("python printtxt invoke"); + command("python printtxt invoke"); output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; ASSERT_THAT(output, MatchesRegex("python.*sometext.*")); // execute python function that uses the LAMMPS python module if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("variable idx equal 2.25"); - lmp->input->one("python getidxvar input 1 SELF format p exists"); + command("variable idx equal 2.25"); + command("python getidxvar input 1 SELF format p exists"); if (!verbose) ::testing::internal::GetCapturedStdout(); ::testing::internal::CaptureStdout(); - lmp->input->one("python getidxvar invoke"); + command("python getidxvar invoke"); output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; ASSERT_THAT(output, MatchesRegex("python.*2.25.*")); @@ -112,12 +114,12 @@ TEST_F(PythonPackageTest, python_variable) { if (!info->has_style("command", "python")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("variable sq python square"); - lmp->input->one("variable val index 1.5"); - lmp->input->one("python square input 1 v_val return v_sq format ff file ${input_dir}/func.py"); + command("variable sq python square"); + command("variable val index 1.5"); + command("python square input 1 v_val return v_sq format ff file ${input_dir}/func.py"); if (!verbose) ::testing::internal::GetCapturedStdout(); ::testing::internal::CaptureStdout(); - lmp->input->one("print \"${sq}\""); + command("print \"${sq}\""); std::string output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; ASSERT_THAT(output, MatchesRegex("print.*2.25.*")); From 6b24006d43f71f5368d3feedd66e7f48e29de9f1 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 23 Mar 2021 19:56:18 -0400 Subject: [PATCH 0236/1217] Use Info::has_package to check for PYTHON support --- unittest/python/test_python_package.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/unittest/python/test_python_package.cpp b/unittest/python/test_python_package.cpp index 5974592997..110ea24dbc 100644 --- a/unittest/python/test_python_package.cpp +++ b/unittest/python/test_python_package.cpp @@ -77,7 +77,7 @@ protected: TEST_F(PythonPackageTest, python_invoke) { - if (!info->has_style("command", "python")) GTEST_SKIP(); + if (!info->has_package("PYTHON")) GTEST_SKIP(); // execute python function from file if (!verbose) ::testing::internal::CaptureStdout(); command("python printnum file ${input_dir}/func.py"); @@ -112,7 +112,7 @@ TEST_F(PythonPackageTest, python_invoke) TEST_F(PythonPackageTest, python_variable) { - if (!info->has_style("command", "python")) GTEST_SKIP(); + if (!info->has_package("PYTHON")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); command("variable sq python square"); command("variable val index 1.5"); From 359a369573121f9101c0651384a9efd835ffba39 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 23 Mar 2021 19:57:45 -0400 Subject: [PATCH 0237/1217] Ensure that global Py_UnbufferedStdioFlag is set when PYTHONUNBUFFERED=1 --- src/PYTHON/python_impl.cpp | 10 ++++++++++ unittest/python/CMakeLists.txt | 2 +- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index d1f602a1ea..1f45ca6635 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -55,6 +55,16 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp) nfunc = 0; pfuncs = nullptr; + + // check for PYTHONUNBUFFERED environment variable + const char * PYTHONUNBUFFERED = getenv("PYTHONUNBUFFERED"); + + if (PYTHONUNBUFFERED != nullptr && strcmp(PYTHONUNBUFFERED, "1") == 0) { + // Python Global configuration variable + // Force the stdout and stderr streams to be unbuffered. + Py_UnbufferedStdioFlag = 1; + } + // one-time initialization of Python interpreter // pyMain stores pointer to main module external_interpreter = Py_IsInitialized(); diff --git a/unittest/python/CMakeLists.txt b/unittest/python/CMakeLists.txt index d508602c93..d1db17c941 100644 --- a/unittest/python/CMakeLists.txt +++ b/unittest/python/CMakeLists.txt @@ -8,7 +8,7 @@ add_executable(test_python_package test_python_package.cpp) target_link_libraries(test_python_package PRIVATE lammps GTest::GMock GTest::GTest) target_compile_definitions(test_python_package PRIVATE -DTEST_INPUT_FOLDER=${TEST_INPUT_FOLDER}) add_test(NAME PythonPackage COMMAND test_python_package WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) -set_tests_properties(PythonPackage PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}:${LAMMPS_PYTHON_DIR}:$ENV{PYTHONPATH}") +set_tests_properties(PythonPackage PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}:${LAMMPS_PYTHON_DIR}:$ENV{PYTHONPATH};PYTHONUNBUFFERED=1") # we must have shared libraries enabled for testing the python module if(NOT BUILD_SHARED_LIBS) From 23c8d8ccfb9ec206e7acf6035c3adcd0919929b6 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 23 Mar 2021 20:13:39 -0400 Subject: [PATCH 0238/1217] Use HasSubstr since output order is dependent on buffering --- unittest/python/test_python_package.cpp | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/unittest/python/test_python_package.cpp b/unittest/python/test_python_package.cpp index 110ea24dbc..723271c589 100644 --- a/unittest/python/test_python_package.cpp +++ b/unittest/python/test_python_package.cpp @@ -34,6 +34,7 @@ using LAMMPS_NS::utils::split_words; namespace LAMMPS_NS { using ::testing::MatchesRegex; using ::testing::StrEq; +using ::testing::HasSubstr; class PythonPackageTest : public ::testing::Test { protected: @@ -86,7 +87,7 @@ TEST_F(PythonPackageTest, python_invoke) command("python printnum invoke"); std::string output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; - ASSERT_THAT(output, MatchesRegex("python.*2.25.*")); + ASSERT_THAT(output, HasSubstr("2.25\n")); // execute another python function from same file if (!verbose) ::testing::internal::CaptureStdout(); @@ -96,7 +97,7 @@ TEST_F(PythonPackageTest, python_invoke) command("python printtxt invoke"); output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; - ASSERT_THAT(output, MatchesRegex("python.*sometext.*")); + ASSERT_THAT(output, HasSubstr("sometext\n")); // execute python function that uses the LAMMPS python module if (!verbose) ::testing::internal::CaptureStdout(); @@ -107,7 +108,7 @@ TEST_F(PythonPackageTest, python_invoke) command("python getidxvar invoke"); output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; - ASSERT_THAT(output, MatchesRegex("python.*2.25.*")); + ASSERT_THAT(output, HasSubstr("2.25\n")); } TEST_F(PythonPackageTest, python_variable) From 85d1257222797041e7186580d91c931889bc7f3c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 23 Mar 2021 21:41:50 -0400 Subject: [PATCH 0239/1217] move redundant enumerator to Variable class definition in variable.h --- src/info.cpp | 11 +++++------ src/variable.cpp | 4 +--- src/variable.h | 4 ++++ 3 files changed, 10 insertions(+), 9 deletions(-) diff --git a/src/info.cpp b/src/info.cpp index 98ad5a3097..948073bb10 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -64,9 +64,6 @@ #endif namespace LAMMPS_NS { -// same as in variable.cpp -enum {INDEX,LOOP,WORLD,UNIVERSE,ULOOP,STRING,GETENV, - SCALARFILE,ATOMFILE,FORMAT,EQUAL,ATOM,VECTOR,PYTHON,INTERNAL}; enum {COMPUTES=1<<0, DUMPS=1<<1, @@ -106,9 +103,11 @@ static const int STYLES = ATOM_STYLES | INTEGRATE_STYLES | MINIMIZE_STYLES using namespace LAMMPS_NS; +// must match enumerator in variable.h static const char *varstyles[] = { "index", "loop", "world", "universe", "uloop", "string", "getenv", - "file", "atomfile", "format", "equal", "atom", "vector", "python", "internal", "(unknown)"}; + "file", "atomfile", "format", "equal", "atom", "vector", "python", + "internal", "(unknown)"}; static const char *mapstyles[] = { "none", "array", "hash", "yes" }; @@ -649,11 +648,11 @@ void Info::command(int narg, char **arg) fmt::print(out,"Variable[{:3d}]: {:16} style = {:16} def =", i,std::string(names[i])+',', std::string(varstyles[style[i]])+','); - if (style[i] == INTERNAL) { + if (style[i] == Variable::INTERNAL) { fmt::print(out,"{:.8}\n",input->variable->dvalue[i]); continue; } - if ((style[i] != LOOP) && (style[i] != ULOOP)) + if ((style[i] != Variable::LOOP) && (style[i] != Variable::ULOOP)) ndata = input->variable->num[i]; for (int j=0; j < ndata; ++j) if (data[i][j]) fmt::print(out," {}",data[i][j]); diff --git a/src/variable.cpp b/src/variable.cpp index 9a8236fdb4..4646bf98b2 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -54,8 +54,6 @@ using namespace MathConst; #define MYROUND(a) (( a-floor(a) ) >= .5) ? ceil(a) : floor(a) -enum{INDEX,LOOP,WORLD,UNIVERSE,ULOOP,STRING,GETENV, - SCALARFILE,ATOMFILE,FORMAT,EQUAL,ATOM,VECTOR,PYTHON,INTERNAL}; enum{ARG,OP}; // customize by adding a function @@ -5023,7 +5021,7 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) : id_fix = nullptr; buffer = nullptr; - if (style == ATOMFILE) { + if (style == Variable::ATOMFILE) { if (atom->map_style == Atom::MAP_NONE) error->all(FLERR,"Cannot use atomfile-style " "variable unless an atom map exists"); diff --git a/src/variable.h b/src/variable.h index 50d276bb14..e311380971 100644 --- a/src/variable.h +++ b/src/variable.h @@ -53,6 +53,10 @@ class Variable : protected Pointers { int nvar; // # of defined variables char **names; // name of each variable + // must match "varstyles" array in info.cpp + enum{INDEX,LOOP,WORLD,UNIVERSE,ULOOP,STRING,GETENV, + SCALARFILE,ATOMFILE,FORMAT,EQUAL,ATOM,VECTOR,PYTHON,INTERNAL}; + private: int me; int maxvar; // max # of variables following lists can hold From 67f1f12c20134b6db3ea1bf10d6aa45aa61a42d7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 23 Mar 2021 21:42:45 -0400 Subject: [PATCH 0240/1217] more tests for expressions --- src/variable.cpp | 15 ++++----- src/variable.h | 2 +- unittest/commands/test_variables.cpp | 46 ++++++++++++++++++++++------ 3 files changed, 45 insertions(+), 18 deletions(-) diff --git a/src/variable.cpp b/src/variable.cpp index 4646bf98b2..76a4b84f89 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -534,12 +534,10 @@ void Variable::set(int narg, char **arg) if (replaceflag) return; + if (!utils::is_id(arg[0])) + error->all(FLERR,fmt::format("Variable name '{}' must have only alphanu" + "meric characters or underscores",arg[0])); names[nvar] = utils::strdup(arg[0]); - for (auto c : std::string(arg[0])) - if (!isalnum(c) && (c != '_')) - error->all(FLERR,fmt::format("Variable name '{}' must have only " - "alphanumeric characters or underscores", - names[nvar])); nvar++; } @@ -983,9 +981,12 @@ double Variable::compute_equal(int ivar) don't need to flag eval_in_progress since is an immediate variable ------------------------------------------------------------------------- */ -double Variable::compute_equal(char *str) +double Variable::compute_equal(const std::string &str) { - return evaluate(str,nullptr,-1); + char *ptr = utils::strdup(str); + double val = evaluate(ptr,nullptr,-1); + delete[] ptr; + return val; } /* ---------------------------------------------------------------------- diff --git a/src/variable.h b/src/variable.h index e311380971..a43e7f3ad7 100644 --- a/src/variable.h +++ b/src/variable.h @@ -41,7 +41,7 @@ class Variable : protected Pointers { char *retrieve(const char *); double compute_equal(int); - double compute_equal(char *); + double compute_equal(const std::string &); void compute_atom(int, int, double *, int, int); int compute_vector(int, double **); void internal_set(int, double); diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 90a0fe00e7..9f8d08fa31 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -166,13 +166,15 @@ TEST_F(VariableTest, CreateDelete) command("variable eight getenv PWD"); command("variable eight getenv HOME"); command("variable nine file test_variable.file"); + command("variable ten internal 1.0"); + command("variable ten internal 10.0"); command("variable dummy index 0"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 12); + ASSERT_EQ(variable->nvar, 13); if (!verbose) ::testing::internal::CaptureStdout(); command("variable dummy delete"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 11); + ASSERT_EQ(variable->nvar, 12); TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable");); TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable dummy index");); @@ -183,8 +185,10 @@ TEST_F(VariableTest, CreateDelete) command("variable two getenv xxx");); TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", command("variable one equal 2");); + TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", + command("variable one internal 2");); TEST_FAILURE(".*ERROR: Cannot use atomfile-style variable unless an atom map exists.*", - command("variable ten atomfile test_variable.atomfile");); + command("variable eleven atomfile test_variable.atomfile");); TEST_FAILURE(".*ERROR on proc 0: Cannot open file variable file test_variable.xxx.*", command("variable nine1 file test_variable.xxx");); } @@ -220,20 +224,42 @@ TEST_F(VariableTest, Expressions) command("variable four equal PI"); command("variable five equal version"); command("variable six equal XXX"); + command("variable seven equal -v_one"); + command("variable eight equal v_three-0.5"); + command("variable nine equal v_two*(v_one+v_three)"); + command("variable ten equal (1.0/v_two)^2"); + command("variable eleven equal v_three%2"); + command("variable twelve equal 1==2"); + command("variable ten3 equal 1!=v_two"); + command("variable ten4 equal 1<2"); + command("variable ten5 equal 2>1"); + command("variable ten6 equal (1<=v_one)&&(v_ten>=0.2)"); + command("variable ten7 equal !(1nvar, 6); + ASSERT_EQ(variable->nvar, 18); int ivar = variable->find("one"); ASSERT_FALSE(variable->equalstyle(ivar)); ivar = variable->find("two"); ASSERT_TRUE(variable->equalstyle(ivar)); ASSERT_DOUBLE_EQ(variable->compute_equal(ivar), 2.0); - ivar = variable->find("three"); - ASSERT_DOUBLE_EQ(variable->compute_equal(ivar), 3.0); - ivar = variable->find("four"); - ASSERT_DOUBLE_EQ(variable->compute_equal(ivar), MY_PI); - ivar = variable->find("five"); - ASSERT_GE(variable->compute_equal(ivar), 20210310); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_three"), 3.0); + ASSERT_FLOAT_EQ(variable->compute_equal("v_four"), MY_PI); + ASSERT_GE(variable->compute_equal("v_five"), 20210310); + EXPECT_DOUBLE_EQ(variable->compute_equal("v_seven"), -1); + EXPECT_DOUBLE_EQ(variable->compute_equal("v_eight"), 2.5); + EXPECT_DOUBLE_EQ(variable->compute_equal("v_nine"), 8); + EXPECT_DOUBLE_EQ(variable->compute_equal("v_ten"), 0.25); + EXPECT_DOUBLE_EQ(variable->compute_equal("v_eleven"), 1); + EXPECT_DOUBLE_EQ(variable->compute_equal("v_twelve"), 0); + EXPECT_DOUBLE_EQ(variable->compute_equal("v_ten3"), 1); + EXPECT_DOUBLE_EQ(variable->compute_equal("v_ten4"), 1); + EXPECT_DOUBLE_EQ(variable->compute_equal("v_ten5"), 1); + EXPECT_DOUBLE_EQ(variable->compute_equal("v_ten6"), 1); + EXPECT_DOUBLE_EQ(variable->compute_equal("v_ten7"), 0); + EXPECT_DOUBLE_EQ(variable->compute_equal("v_ten8"), 1); TEST_FAILURE(".*ERROR: Variable six: Invalid thermo keyword 'XXX' in variable formula.*", command("print \"${six}\"");); From b6a030532d4f1259279562c3df71456fed11edc4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Mar 2021 10:33:00 -0400 Subject: [PATCH 0241/1217] add tests for boolean evaluation in "if" command --- unittest/commands/test_variables.cpp | 71 +++++++++++++++++++++++----- 1 file changed, 59 insertions(+), 12 deletions(-) diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 9f8d08fa31..5a1d249bd5 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -248,18 +248,18 @@ TEST_F(VariableTest, Expressions) ASSERT_DOUBLE_EQ(variable->compute_equal("v_three"), 3.0); ASSERT_FLOAT_EQ(variable->compute_equal("v_four"), MY_PI); ASSERT_GE(variable->compute_equal("v_five"), 20210310); - EXPECT_DOUBLE_EQ(variable->compute_equal("v_seven"), -1); - EXPECT_DOUBLE_EQ(variable->compute_equal("v_eight"), 2.5); - EXPECT_DOUBLE_EQ(variable->compute_equal("v_nine"), 8); - EXPECT_DOUBLE_EQ(variable->compute_equal("v_ten"), 0.25); - EXPECT_DOUBLE_EQ(variable->compute_equal("v_eleven"), 1); - EXPECT_DOUBLE_EQ(variable->compute_equal("v_twelve"), 0); - EXPECT_DOUBLE_EQ(variable->compute_equal("v_ten3"), 1); - EXPECT_DOUBLE_EQ(variable->compute_equal("v_ten4"), 1); - EXPECT_DOUBLE_EQ(variable->compute_equal("v_ten5"), 1); - EXPECT_DOUBLE_EQ(variable->compute_equal("v_ten6"), 1); - EXPECT_DOUBLE_EQ(variable->compute_equal("v_ten7"), 0); - EXPECT_DOUBLE_EQ(variable->compute_equal("v_ten8"), 1); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_seven"), -1); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_eight"), 2.5); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_nine"), 8); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten"), 0.25); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_eleven"), 1); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_twelve"), 0); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten3"), 1); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten4"), 1); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten5"), 1); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten6"), 1); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten7"), 0); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten8"), 1); TEST_FAILURE(".*ERROR: Variable six: Invalid thermo keyword 'XXX' in variable formula.*", command("print \"${six}\"");); @@ -287,6 +287,53 @@ TEST_F(VariableTest, Functions) TEST_FAILURE(".*ERROR: Variable four: Invalid syntax in variable formula.*", command("print \"${four}\"");); } + +TEST_F(VariableTest, IfCommand) +{ + if (!verbose) ::testing::internal::CaptureStdout(); + command("variable one index 1"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + + ::testing::internal::CaptureStdout(); + command("if 1>0 then 'print \".*bingo!\"'"); + auto text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text,MatchesRegex(".*bingo!.*")); + + ::testing::internal::CaptureStdout(); + command("if (1>=0) then 'print \"bingo!\"'"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text,MatchesRegex(".*bingo!.*")); + + ::testing::internal::CaptureStdout(); + command("if (-1.0e-1<0.0E+0) then 'print \"bingo!\"'"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text,MatchesRegex(".*bingo!.*")); + + ::testing::internal::CaptureStdout(); + command("if (${one}==1.0)&&(2>=1) then 'print \"bingo!\"'"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text,MatchesRegex(".*bingo!.*")); + + ::testing::internal::CaptureStdout(); + command("if !((${one}!=1.0)||(2|^1)) then 'print \"missed\"' else 'print \"bingo!\"'"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text,MatchesRegex(".*bingo!.*")); + + TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", + command("if () then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", + command("if (1)( then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", + command("if (1)1 then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", + command("if (v_one==1.0)&&(2>=1) then 'print \"bingo!\"'");); +} + } // namespace LAMMPS_NS int main(int argc, char **argv) From 8790ecc141cfe52f01d3ec77bcf687bb3808c9da Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 24 Mar 2021 11:18:21 -0400 Subject: [PATCH 0242/1217] Refactor existing tests --- unittest/python/test_python_package.cpp | 130 ++++++++++++++---------- 1 file changed, 76 insertions(+), 54 deletions(-) diff --git a/unittest/python/test_python_package.cpp b/unittest/python/test_python_package.cpp index 723271c589..137278a9d2 100644 --- a/unittest/python/test_python_package.cpp +++ b/unittest/python/test_python_package.cpp @@ -20,6 +20,7 @@ #include #include #include +#include // location of '*.py' files required by tests #define STRINGIFY(val) XSTR(val) @@ -43,86 +44,107 @@ protected: void command(const std::string &line) { lmp->input->one(line.c_str()); } + void HIDE_OUTPUT(std::function f) { + if (!verbose) ::testing::internal::CaptureStdout(); + f(); + if (!verbose) ::testing::internal::GetCapturedStdout(); + } + + std::string CAPTURE_OUTPUT(std::function f) { + ::testing::internal::CaptureStdout(); + f(); + auto output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + return output; + } + void SetUp() override { const char *args[] = {"PythonPackageTest", "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - if (!verbose) ::testing::internal::GetCapturedStdout(); + HIDE_OUTPUT([&] { + lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); + }); ASSERT_NE(lmp, nullptr); info = new Info(lmp); - if (!verbose) ::testing::internal::CaptureStdout(); - command("units real"); - command("dimension 3"); - command("region box block -4 4 -4 4 -4 4"); - command("create_box 1 box"); - command("create_atoms 1 single 0.0 0.0 0.0 units box"); - command("create_atoms 1 single 1.9 -1.9 1.9999 units box"); - command("pair_style zero 2.0"); - command("pair_coeff * *"); - command("mass * 1.0"); - command("variable input_dir index " + INPUT_FOLDER); - if (!verbose) ::testing::internal::GetCapturedStdout(); + if (!info->has_package("PYTHON")) GTEST_SKIP(); + HIDE_OUTPUT([&] { + command("units real"); + command("dimension 3"); + command("region box block -4 4 -4 4 -4 4"); + command("create_box 1 box"); + command("create_atoms 1 single 0.0 0.0 0.0 units box"); + command("create_atoms 1 single 1.9 -1.9 1.9999 units box"); + command("pair_style zero 2.0"); + command("pair_coeff * *"); + command("mass * 1.0"); + command("variable input_dir index " + INPUT_FOLDER); + }); } void TearDown() override { - if (!verbose) ::testing::internal::CaptureStdout(); - delete info; - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); + HIDE_OUTPUT([&] { + delete info; + delete lmp; + info = nullptr; + lmp = nullptr; + }); } }; -TEST_F(PythonPackageTest, python_invoke) +TEST_F(PythonPackageTest, InvokeFunctionFromFile) { - if (!info->has_package("PYTHON")) GTEST_SKIP(); // execute python function from file - if (!verbose) ::testing::internal::CaptureStdout(); - command("python printnum file ${input_dir}/func.py"); - if (!verbose) ::testing::internal::GetCapturedStdout(); - ::testing::internal::CaptureStdout(); - command("python printnum invoke"); - std::string output = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << output; + HIDE_OUTPUT([&] { + command("python printnum file ${input_dir}/func.py"); + }); + + auto output = CAPTURE_OUTPUT([&]() { + command("python printnum invoke"); + }); ASSERT_THAT(output, HasSubstr("2.25\n")); +} +TEST_F(PythonPackageTest, InvokeOtherFunctionFromFile) +{ // execute another python function from same file - if (!verbose) ::testing::internal::CaptureStdout(); - command("python printtxt exists"); - if (!verbose) ::testing::internal::GetCapturedStdout(); - ::testing::internal::CaptureStdout(); - command("python printtxt invoke"); - output = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << output; - ASSERT_THAT(output, HasSubstr("sometext\n")); + HIDE_OUTPUT([&] { + command("python printnum file ${input_dir}/func.py"); + command("python printtxt exists"); + }); + auto output = CAPTURE_OUTPUT([&] { + command("python printtxt invoke"); + }); + ASSERT_THAT(output, HasSubstr("sometext\n")); +} + +TEST_F(PythonPackageTest, InvokeFunctionThatUsesLAMMPSModule) +{ // execute python function that uses the LAMMPS python module - if (!verbose) ::testing::internal::CaptureStdout(); - command("variable idx equal 2.25"); - command("python getidxvar input 1 SELF format p exists"); - if (!verbose) ::testing::internal::GetCapturedStdout(); - ::testing::internal::CaptureStdout(); - command("python getidxvar invoke"); - output = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << output; + HIDE_OUTPUT([&] { + command("python printnum file ${input_dir}/func.py"); + command("variable idx equal 2.25"); + command("python getidxvar input 1 SELF format p exists"); + }); + auto output = CAPTURE_OUTPUT([&] { + command("python getidxvar invoke"); + }); ASSERT_THAT(output, HasSubstr("2.25\n")); } TEST_F(PythonPackageTest, python_variable) { - if (!info->has_package("PYTHON")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); - command("variable sq python square"); - command("variable val index 1.5"); - command("python square input 1 v_val return v_sq format ff file ${input_dir}/func.py"); - if (!verbose) ::testing::internal::GetCapturedStdout(); - ::testing::internal::CaptureStdout(); - command("print \"${sq}\""); - std::string output = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << output; + HIDE_OUTPUT([&] { + command("variable sq python square"); + command("variable val index 1.5"); + command("python square input 1 v_val return v_sq format ff file ${input_dir}/func.py"); + }); + std::string output = CAPTURE_OUTPUT([&] { + command("print \"${sq}\""); + }); ASSERT_THAT(output, MatchesRegex("print.*2.25.*")); } From 487c55edf0d4a5e2811a430d8ac7429d1e63ef92 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Mar 2021 11:24:55 -0400 Subject: [PATCH 0243/1217] simplify and apply clang-format --- unittest/c-library/test_library_mpi.cpp | 2 +- unittest/commands/test_groups.cpp | 2 +- unittest/commands/test_kim_commands.cpp | 612 ++++++++---------- unittest/commands/test_lattice_region.cpp | 259 ++++---- unittest/commands/test_reset_ids.cpp | 132 ++-- unittest/commands/test_simple_commands.cpp | 126 ++-- unittest/commands/test_variables.cpp | 10 +- unittest/force-styles/test_angle_style.cpp | 4 +- unittest/force-styles/test_bond_style.cpp | 4 +- unittest/force-styles/test_config_reader.cpp | 14 +- unittest/force-styles/test_dihedral_style.cpp | 4 +- unittest/force-styles/test_improper_style.cpp | 4 +- unittest/force-styles/test_pair_style.cpp | 9 +- unittest/formats/test_atom_styles.cpp | 5 +- unittest/formats/test_file_operations.cpp | 8 +- unittest/formats/test_image_flags.cpp | 235 +++---- unittest/formats/test_molecule_file.cpp | 21 +- unittest/formats/test_pair_unit_convert.cpp | 500 +++++++------- .../formats/test_potential_file_reader.cpp | 34 +- unittest/utils/test_tokenizer.cpp | 6 +- unittest/utils/test_utils.cpp | 8 +- 21 files changed, 983 insertions(+), 1016 deletions(-) diff --git a/unittest/c-library/test_library_mpi.cpp b/unittest/c-library/test_library_mpi.cpp index 7502da767a..6fdec7b7e4 100644 --- a/unittest/c-library/test_library_mpi.cpp +++ b/unittest/c-library/test_library_mpi.cpp @@ -191,7 +191,7 @@ TEST(MPI, multi_partition) EXPECT_EQ(lammps_extract_setting(lmp, "world_rank"), 0); char *part_id = (char *)lammps_extract_variable(lmp, "partition", nullptr); - ASSERT_THAT(part_id, StrEq(std::to_string(me+1))); + ASSERT_THAT(part_id, StrEq(std::to_string(me + 1))); lammps_close(lmp); }; diff --git a/unittest/commands/test_groups.cpp b/unittest/commands/test_groups.cpp index 7fa7ee721f..3ae1722f4d 100644 --- a/unittest/commands/test_groups.cpp +++ b/unittest/commands/test_groups.cpp @@ -73,7 +73,7 @@ protected: if (!verbose) ::testing::internal::CaptureStdout(); lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); if (!verbose) ::testing::internal::GetCapturedStdout(); - group = lmp->group; + group = lmp->group; domain = lmp->domain; } diff --git a/unittest/commands/test_kim_commands.cpp b/unittest/commands/test_kim_commands.cpp index 311ce6acf1..2d044b86eb 100644 --- a/unittest/commands/test_kim_commands.cpp +++ b/unittest/commands/test_kim_commands.cpp @@ -59,6 +59,7 @@ using ::testing::StrEq; class KimCommandsTest : public ::testing::Test { protected: LAMMPS *lmp; + Variable *variable; void SetUp() override { @@ -68,6 +69,7 @@ protected: if (!verbose) ::testing::internal::CaptureStdout(); lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); if (!verbose) ::testing::internal::GetCapturedStdout(); + variable = lmp->input->variable; } void TearDown() override @@ -76,53 +78,45 @@ protected: delete lmp; if (!verbose) ::testing::internal::GetCapturedStdout(); } + + void command(const std::string &cmd) { lmp->input->one(cmd); } }; TEST_F(KimCommandsTest, kim) { if (!LAMMPS::is_installed_pkg("KIM")) GTEST_SKIP(); - TEST_FAILURE(".*ERROR: Illegal kim command.*", - lmp->input->one("kim");); - TEST_FAILURE(".*ERROR: Unknown kim subcommand.*", - lmp->input->one("kim unknown");); - TEST_FAILURE(".*kim_init.*has been renamed to.*", - lmp->input->one("kim_init");); - TEST_FAILURE(".*kim_interactions.*has been renamed to.*", - lmp->input->one("kim_interactions");); - TEST_FAILURE(".*kim_param.*has been renamed to.*", - lmp->input->one("kim_param");); - TEST_FAILURE(".*kim_property.*has been renamed to.*", - lmp->input->one("kim_property");); - TEST_FAILURE(".*kim_query.*has been renamed to.*", - lmp->input->one("kim_query");); + TEST_FAILURE(".*ERROR: Illegal kim command.*", command("kim");); + TEST_FAILURE(".*ERROR: Unknown kim subcommand.*", command("kim unknown");); + TEST_FAILURE(".*kim_init.*has been renamed to.*", command("kim_init");); + TEST_FAILURE(".*kim_interactions.*has been renamed to.*", command("kim_interactions");); + TEST_FAILURE(".*kim_param.*has been renamed to.*", command("kim_param");); + TEST_FAILURE(".*kim_property.*has been renamed to.*", command("kim_property");); + TEST_FAILURE(".*kim_query.*has been renamed to.*", command("kim_query");); } TEST_F(KimCommandsTest, kim_init) { if (!LAMMPS::is_installed_pkg("KIM")) GTEST_SKIP(); + TEST_FAILURE(".*ERROR: Illegal 'kim init' command.*", command("kim init");); TEST_FAILURE(".*ERROR: Illegal 'kim init' command.*", - lmp->input->one("kim init");); - TEST_FAILURE(".*ERROR: Illegal 'kim init' command.*", - lmp->input->one("kim init LennardJones_Ar real si");); + command("kim init LennardJones_Ar real si");); TEST_FAILURE(".*ERROR: LAMMPS unit_style lj not supported by KIM models.*", - lmp->input->one("kim init LennardJones_Ar lj");); + command("kim init LennardJones_Ar lj");); TEST_FAILURE(".*ERROR: LAMMPS unit_style micro not supported by KIM models.*", - lmp->input->one("kim init LennardJones_Ar micro");); + command("kim init LennardJones_Ar micro");); TEST_FAILURE(".*ERROR: LAMMPS unit_style nano not supported by KIM models.*", - lmp->input->one("kim init LennardJones_Ar nano");); - TEST_FAILURE(".*ERROR: Unknown unit_style.*", - lmp->input->one("kim init LennardJones_Ar new_style");); - TEST_FAILURE(".*ERROR: KIM Model name not found.*", - lmp->input->one("kim init Unknown_Model real");); + command("kim init LennardJones_Ar nano");); + TEST_FAILURE(".*ERROR: Unknown unit_style.*", command("kim init LennardJones_Ar new_style");); + TEST_FAILURE(".*ERROR: KIM Model name not found.*", command("kim init Unknown_Model real");); TEST_FAILURE(".*ERROR: Incompatible units for KIM Simulator Model, required units = metal.*", - lmp->input->one("kim init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu real");); + command("kim init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu real");); // TEST_FAILURE(".*ERROR: KIM Model does not support the requested unit system.*", - // lmp->input->one("kim init ex_model_Ar_P_Morse real");); + // command("kim init ex_model_Ar_P_Morse real");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("kim init LennardJones_Ar real"); + command("kim init LennardJones_Ar real"); if (!verbose) ::testing::internal::GetCapturedStdout(); int ifix = lmp->modify->find_fix("KIM_MODEL_STORE"); @@ -133,124 +127,122 @@ TEST_F(KimCommandsTest, kim_interactions) { if (!LAMMPS::is_installed_pkg("KIM")) GTEST_SKIP(); - TEST_FAILURE(".*ERROR: Illegal 'kim interactions' command.*", - lmp->input->one("kim interactions");); + TEST_FAILURE(".*ERROR: Illegal 'kim interactions' command.*", command("kim interactions");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("kim init LennardJones_Ar real"); + command("kim init LennardJones_Ar real"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Must use 'kim interactions' command " "after simulation box is defined.*", - lmp->input->one("kim interactions Ar");); + command("kim interactions Ar");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("kim init LennardJones_Ar real"); - lmp->input->one("lattice fcc 4.4300"); - lmp->input->one("region box block 0 10 0 10 0 10"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 box"); + command("kim init LennardJones_Ar real"); + command("lattice fcc 4.4300"); + command("region box block 0 10 0 10 0 10"); + command("create_box 1 box"); + command("create_atoms 1 box"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Illegal 'kim interactions' command.*", - lmp->input->one("kim interactions Ar Ar");); + command("kim interactions Ar Ar");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("lattice fcc 4.4300"); - lmp->input->one("region box block 0 20 0 20 0 20"); - lmp->input->one("create_box 4 box"); - lmp->input->one("create_atoms 4 box"); + command("clear"); + command("lattice fcc 4.4300"); + command("region box block 0 20 0 20 0 20"); + command("create_box 4 box"); + command("create_atoms 4 box"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Illegal 'kim interactions' command.*", - lmp->input->one("kim interactions Ar Ar");); + command("kim interactions Ar Ar");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("lattice fcc 4.4300"); - lmp->input->one("region box block 0 10 0 10 0 10"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 box"); + command("clear"); + command("lattice fcc 4.4300"); + command("region box block 0 10 0 10 0 10"); + command("create_box 1 box"); + command("create_atoms 1 box"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Must use 'kim init' before 'kim interactions'.*", - lmp->input->one("kim interactions Ar");); + command("kim interactions Ar");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("kim init LennardJones_Ar real"); - lmp->input->one("lattice fcc 4.4300"); - lmp->input->one("region box block 0 10 0 10 0 10"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 box"); + command("clear"); + command("kim init LennardJones_Ar real"); + command("lattice fcc 4.4300"); + command("region box block 0 10 0 10 0 10"); + command("create_box 1 box"); + command("create_atoms 1 box"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: fixed_types cannot be used with a KIM Portable Model.*", - lmp->input->one("kim interactions fixed_types");); + command("kim interactions fixed_types");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("pair_style kim LennardJones_Ar"); - lmp->input->one("region box block 0 1 0 1 0 1"); - lmp->input->one("create_box 4 box"); - lmp->input->one("pair_coeff * * Ar Ar Ar Ar"); + command("clear"); + command("units real"); + command("pair_style kim LennardJones_Ar"); + command("region box block 0 1 0 1 0 1"); + command("create_box 4 box"); + command("pair_coeff * * Ar Ar Ar Ar"); if (!verbose) ::testing::internal::GetCapturedStdout(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("kim init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu metal"); - lmp->input->one("lattice fcc 4.920"); - lmp->input->one("region box block 0 10 0 10 0 10"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 box"); + command("clear"); + command("kim init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu metal"); + command("lattice fcc 4.920"); + command("region box block 0 10 0 10 0 10"); + command("create_box 1 box"); + command("create_atoms 1 box"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Species 'Ar' is not supported by this KIM Simulator Model.*", - lmp->input->one("kim interactions Ar");); + command("kim interactions Ar");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("kim init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu metal"); - lmp->input->one("lattice fcc 4.08"); - lmp->input->one("region box block 0 10 0 10 0 10"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 box"); - lmp->input->one("kim interactions Au"); + command("clear"); + command("kim init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu metal"); + command("lattice fcc 4.08"); + command("region box block 0 10 0 10 0 10"); + command("create_box 1 box"); + command("create_atoms 1 box"); + command("kim interactions Au"); if (!verbose) ::testing::internal::GetCapturedStdout(); // ASSERT_EQ(lmp->output->var_kim_periodic, 1); // TEST_FAILURE(".*ERROR: Incompatible units for KIM Simulator Model.*", - // lmp->input->one("kim interactions Au");); - + // command("kim interactions Au");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("kim init LennardJones_Ar real"); - lmp->input->one("lattice fcc 4.4300"); - lmp->input->one("region box block 0 10 0 10 0 10"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 box"); - lmp->input->one("kim interactions Ar"); - lmp->input->one("mass 1 39.95"); + command("clear"); + command("kim init LennardJones_Ar real"); + command("lattice fcc 4.4300"); + command("region box block 0 10 0 10 0 10"); + command("create_box 1 box"); + command("create_atoms 1 box"); + command("kim interactions Ar"); + command("mass 1 39.95"); if (!verbose) ::testing::internal::GetCapturedStdout(); int ifix = lmp->modify->find_fix("KIM_MODEL_STORE"); ASSERT_GE(ifix, 0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("kim init LennardJones_Ar real"); - lmp->input->one("lattice fcc 4.4300"); - lmp->input->one("region box block 0 10 0 10 0 10"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 box"); - lmp->input->one("kim interactions Ar"); - lmp->input->one("mass 1 39.95"); - lmp->input->one("run 1"); - lmp->input->one("kim interactions Ar"); - lmp->input->one("run 1"); + command("clear"); + command("kim init LennardJones_Ar real"); + command("lattice fcc 4.4300"); + command("region box block 0 10 0 10 0 10"); + command("create_box 1 box"); + command("create_atoms 1 box"); + command("kim interactions Ar"); + command("mass 1 39.95"); + command("run 1"); + command("kim interactions Ar"); + command("run 1"); if (!verbose) ::testing::internal::GetCapturedStdout(); } @@ -258,189 +250,188 @@ TEST_F(KimCommandsTest, kim_param) { if (!LAMMPS::is_installed_pkg("KIM")) GTEST_SKIP(); - TEST_FAILURE(".*ERROR: Illegal 'kim param' command.*", - lmp->input->one("kim param");); + TEST_FAILURE(".*ERROR: Illegal 'kim param' command.*", command("kim param");); TEST_FAILURE(".*ERROR: Incorrect arguments in 'kim param' command.\n" "'kim param get/set' is mandatory.*", - lmp->input->one("kim param unknown shift 1 shift");); + command("kim param unknown shift 1 shift");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("kim init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu metal"); + command("clear"); + command("kim init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu metal"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: 'kim param' can only be used with a KIM Portable Model.*", - lmp->input->one("kim param get shift 1 shift");); + command("kim param get shift 1 shift");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("kim init LennardJones612_UniversalShifted__MO_959249795837_003 real"); + command("clear"); + command("kim init LennardJones612_UniversalShifted__MO_959249795837_003 real"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Illegal 'kim param get' command.\nTo get the new " "parameter values, pair style must be assigned.\nMust use 'kim" " interactions' or 'pair_style kim' before 'kim param get'.*", - lmp->input->one("kim param get shift 1 shift");); + command("kim param get shift 1 shift");); TEST_FAILURE(".*ERROR: Illegal 'kim param set' command.\nTo set the new " "parameter values, pair style must be assigned.\nMust use 'kim" " interactions' or 'pair_style kim' before 'kim param set'.*", - lmp->input->one("kim param set shift 1 2");); + command("kim param set shift 1 2");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("kim init LennardJones612_UniversalShifted__MO_959249795837_003 real"); - lmp->input->one("lattice fcc 4.4300"); - lmp->input->one("region box block 0 10 0 10 0 10"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 box"); - lmp->input->one("kim interactions Ar"); - lmp->input->one("mass 1 39.95"); + command("clear"); + command("kim init LennardJones612_UniversalShifted__MO_959249795837_003 real"); + command("lattice fcc 4.4300"); + command("region box block 0 10 0 10 0 10"); + command("create_box 1 box"); + command("create_atoms 1 box"); + command("kim interactions Ar"); + command("mass 1 39.95"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Illegal index '0' for " "'shift' parameter with the extent of '1'.*", - lmp->input->one("kim param get shift 0 shift");); + command("kim param get shift 0 shift");); TEST_FAILURE(".*ERROR: Illegal index '2' for " "'shift' parameter with the extent of '1'.*", - lmp->input->one("kim param get shift 2 shift");); + command("kim param get shift 2 shift");); TEST_FAILURE(".*ERROR: Illegal index_range.\nExpected integer " "parameter\\(s\\) instead of '1.' in index_range.*", - lmp->input->one("kim param get shift 1. shift");); + command("kim param get shift 1. shift");); TEST_FAILURE(".*ERROR: Illegal index_range '1-2' for 'shift' " "parameter with the extent of '1'.*", - lmp->input->one("kim param get shift 1:2 shift");); + command("kim param get shift 1:2 shift");); TEST_FAILURE(".*ERROR: Illegal index_range.\nExpected integer " "parameter\\(s\\) instead of '1-2' in index_range.*", - lmp->input->one("kim param get shift 1-2 shift");); + command("kim param get shift 1-2 shift");); TEST_FAILURE(".*ERROR: Wrong number of arguments in 'kim param " "get' command.\nThe LAMMPS '3' variable names or " "'s1 split' is mandatory.*", - lmp->input->one("kim param get sigmas 1:3 s1 s2");); + command("kim param get sigmas 1:3 s1 s2");); TEST_FAILURE(".*ERROR: Wrong argument in 'kim param get' command.\nThis " "Model does not have the requested 'unknown' parameter.*", - lmp->input->one("kim param get unknown 1 unknown");); + command("kim param get unknown 1 unknown");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("kim param get shift 1 shift"); + command("kim param get shift 1 shift"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_FALSE(lmp->input->variable->find("shift") == -1); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("shift")) == "1"); + ASSERT_FALSE(variable->find("shift") == -1); + ASSERT_THAT(variable->retrieve("shift"), StrEq("1")); TEST_FAILURE(".*ERROR: Illegal index '2' for " "'shift' parameter with the extent of '1'.*", - lmp->input->one("kim param set shift 2 2");); + command("kim param set shift 2 2");); TEST_FAILURE(".*ERROR: Illegal index_range.\nExpected integer " "parameter\\(s\\) instead of '1.' in index_range.*", - lmp->input->one("kim param set shift 1. shift");); + command("kim param set shift 1. shift");); TEST_FAILURE(".*ERROR: Illegal index_range '1-2' for " "'shift' parameter with the extent of '1'.*", - lmp->input->one("kim param set shift 1:2 2");); + command("kim param set shift 1:2 2");); TEST_FAILURE(".*ERROR: Wrong number of variable values for pair coefficients.*", - lmp->input->one("kim param set sigmas 1:3 0.5523570 0.4989030");); + command("kim param set sigmas 1:3 0.5523570 0.4989030");); TEST_FAILURE(".*ERROR: Wrong argument for pair coefficients.\nThis " "Model does not have the requested '0.4989030' parameter.*", - lmp->input->one("kim param set sigmas 1:1 0.5523570 0.4989030");); + command("kim param set sigmas 1:1 0.5523570 0.4989030");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("variable new_shift equal 2"); - lmp->input->one("kim param set shift 1 ${new_shift}"); - lmp->input->one("kim param get shift 1 shift"); + command("variable new_shift equal 2"); + command("kim param set shift 1 ${new_shift}"); + command("kim param get shift 1 shift"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("shift")) == "2"); + ASSERT_THAT(variable->retrieve("shift"), StrEq("2")); TEST_FAILURE(".*ERROR: Illegal variable name in 'kim param get'.*", - lmp->input->one("kim param get cutoffs 1:3 list");); + command("kim param get cutoffs 1:3 list");); TEST_FAILURE(".*ERROR: Illegal variable name in 'kim param get'.*", - lmp->input->one("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 list");); + command("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 list");); TEST_FAILURE(".*ERROR: Illegal variable name in 'kim param get'.*", - lmp->input->one("kim param get cutoffs 1:3 split");); + command("kim param get cutoffs 1:3 split");); TEST_FAILURE(".*ERROR: Illegal variable name in 'kim param get'.*", - lmp->input->one("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 split");); + command("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 split");); TEST_FAILURE(".*ERROR: Illegal variable name in 'kim param get'.*", - lmp->input->one("kim param get cutoffs 1:3 explicit");); + command("kim param get cutoffs 1:3 explicit");); TEST_FAILURE(".*ERROR: Illegal variable name in 'kim param get'.*", - lmp->input->one("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 explicit");); + command("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 explicit");); TEST_FAILURE(".*ERROR: Wrong number of arguments in 'kim param get' " "command.\nThe LAMMPS '3' variable names or 'cutoffs " "split/list' is mandatory.*", - lmp->input->one("kim param get cutoffs 1:3 cutoffs");); + command("kim param get cutoffs 1:3 cutoffs");); TEST_FAILURE(".*ERROR: Wrong number of arguments in 'kim param get' " "command.\nThe LAMMPS '3' variable names or 'cutoffs_1 " "split' is mandatory.*", - lmp->input->one("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2");); + command("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 cutoffs_3"); + command("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 cutoffs_3"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("cutoffs_1")) == "2.20943"); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("cutoffs_2")) == "2.10252"); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("cutoffs_3")) == "5.666115"); + ASSERT_THAT(variable->retrieve("cutoffs_1"), StrEq("2.20943")); + ASSERT_THAT(variable->retrieve("cutoffs_2"), StrEq("2.10252")); + ASSERT_THAT(variable->retrieve("cutoffs_3"), StrEq("5.666115")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 cutoffs_3 explicit"); + command("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 cutoffs_3 explicit"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("cutoffs_1")) == "2.20943"); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("cutoffs_2")) == "2.10252"); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("cutoffs_3")) == "5.666115"); + ASSERT_THAT(variable->retrieve("cutoffs_1"), StrEq("2.20943")); + ASSERT_THAT(variable->retrieve("cutoffs_2"), StrEq("2.10252")); + ASSERT_THAT(variable->retrieve("cutoffs_3"), StrEq("5.666115")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("kim param get cutoffs 1:3 cutoffs split"); + command("kim param get cutoffs 1:3 cutoffs split"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("cutoffs_1")) == "2.20943"); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("cutoffs_2")) == "2.10252"); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("cutoffs_3")) == "5.666115"); + ASSERT_THAT(variable->retrieve("cutoffs_1"), StrEq("2.20943")); + ASSERT_THAT(variable->retrieve("cutoffs_2"), StrEq("2.10252")); + ASSERT_THAT(variable->retrieve("cutoffs_3"), StrEq("5.666115")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("kim param get cutoffs 1:3 cutoffs list"); + command("kim param get cutoffs 1:3 cutoffs list"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("cutoffs")) == "2.20943 2.10252 5.666115"); + ASSERT_THAT(variable->retrieve("cutoffs"), StrEq("2.20943 2.10252 5.666115")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("kim param set cutoffs 1 2.21 cutoffs 2 2.11"); - lmp->input->one("kim param get cutoffs 1:2 cutoffs list"); + command("kim param set cutoffs 1 2.21 cutoffs 2 2.11"); + command("kim param get cutoffs 1:2 cutoffs list"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("cutoffs")) == "2.21 2.11"); + ASSERT_THAT(variable->retrieve("cutoffs"), StrEq("2.21 2.11")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("kim param set cutoffs 1:3 2.3 2.2 5.7"); - lmp->input->one("kim param get cutoffs 1:3 cutoffs list"); + command("kim param set cutoffs 1:3 2.3 2.2 5.7"); + command("kim param get cutoffs 1:3 cutoffs list"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("cutoffs")) == "2.3 2.2 5.7"); + ASSERT_THAT(variable->retrieve("cutoffs"), StrEq("2.3 2.2 5.7")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("lattice fcc 4.4300"); - lmp->input->one("region box block 0 10 0 10 0 10"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 box"); - lmp->input->one("mass 1 39.95"); - lmp->input->one("pair_style kim LennardJones612_UniversalShifted__MO_959249795837_003"); - lmp->input->one("pair_coeff * * Ar"); + command("clear"); + command("units real"); + command("lattice fcc 4.4300"); + command("region box block 0 10 0 10 0 10"); + command("create_box 1 box"); + command("create_atoms 1 box"); + command("mass 1 39.95"); + command("pair_style kim LennardJones612_UniversalShifted__MO_959249795837_003"); + command("pair_coeff * * Ar"); if (!verbose) ::testing::internal::GetCapturedStdout(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("kim param get shift 1 shift"); + command("kim param get shift 1 shift"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("shift")) == "1"); + ASSERT_THAT(variable->retrieve("shift"), StrEq("1")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("variable new_shift equal 2"); - lmp->input->one("kim param set shift 1 ${new_shift}"); - lmp->input->one("kim param get shift 1 shift"); + command("variable new_shift equal 2"); + command("kim param set shift 1 ${new_shift}"); + command("kim param get shift 1 shift"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_TRUE(std::string(lmp->input->variable->retrieve("shift")) == "2"); + ASSERT_THAT(variable->retrieve("shift"), StrEq("2")); } TEST_F(KimCommandsTest, kim_property) @@ -452,38 +443,36 @@ TEST_F(KimCommandsTest, kim_property) TEST_FAILURE(".*ERROR: Invalid Python version.\n" "The kim-property Python package requires Python " "3 >= 3.6 support.*", - lmp->input->one("kim property");); + command("kim property");); } else { - TEST_FAILURE(".*ERROR: Invalid 'kim property' command.*", - lmp->input->one("kim property");); - TEST_FAILURE(".*ERROR: Invalid 'kim property' command.*", - lmp->input->one("kim property create");); + TEST_FAILURE(".*ERROR: Invalid 'kim property' command.*", command("kim property");); + TEST_FAILURE(".*ERROR: Invalid 'kim property' command.*", command("kim property create");); TEST_FAILURE(".*ERROR: Incorrect arguments in 'kim property' command." "\n'kim property create/destroy/modify/remove/dump' " "is mandatory.*", - lmp->input->one("kim property unknown 1 atomic-mass");); + command("kim property unknown 1 atomic-mass");); } #if defined(KIM_EXTRA_UNITTESTS) TEST_FAILURE(".*ERROR: Invalid 'kim property create' command.*", - lmp->input->one("kim property create 1");); + command("kim property create 1");); TEST_FAILURE(".*ERROR: Invalid 'kim property destroy' command.*", - lmp->input->one("kim property destroy 1 cohesive-potential-energy-cubic-crystal");); + command("kim property destroy 1 cohesive-potential-energy-cubic-crystal");); TEST_FAILURE(".*ERROR: Invalid 'kim property modify' command.*", - lmp->input->one("kim property modify 1 key short-name");); + command("kim property modify 1 key short-name");); TEST_FAILURE(".*ERROR: There is no property instance to modify the content.*", - lmp->input->one("kim property modify 1 key short-name source-value 1 fcc");); + command("kim property modify 1 key short-name source-value 1 fcc");); TEST_FAILURE(".*ERROR: Invalid 'kim property remove' command.*", - lmp->input->one("kim property remove 1 key");); + command("kim property remove 1 key");); TEST_FAILURE(".*ERROR: There is no property instance to remove the content.*", - lmp->input->one("kim property remove 1 key short-name");); + command("kim property remove 1 key short-name");); TEST_FAILURE(".*ERROR: There is no property instance to dump the content.*", - lmp->input->one("kim property dump results.edn");); + command("kim property dump results.edn");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("kim init LennardJones612_UniversalShifted__MO_959249795837_003 real"); - lmp->input->one("kim property create 1 cohesive-potential-energy-cubic-crystal"); - lmp->input->one("kim property modify 1 key short-name source-value 1 fcc"); - lmp->input->one("kim property destroy 1"); + command("clear"); + command("kim init LennardJones612_UniversalShifted__MO_959249795837_003 real"); + command("kim property create 1 cohesive-potential-energy-cubic-crystal"); + command("kim property modify 1 key short-name source-value 1 fcc"); + command("kim property destroy 1"); if (!verbose) ::testing::internal::GetCapturedStdout(); #endif } @@ -492,264 +481,233 @@ TEST_F(KimCommandsTest, kim_query) { if (!LAMMPS::is_installed_pkg("KIM")) GTEST_SKIP(); - TEST_FAILURE(".*ERROR: Illegal 'kim query' command.*", - lmp->input->one("kim query");); + TEST_FAILURE(".*ERROR: Illegal 'kim query' command.*", command("kim query");); TEST_FAILURE(".*ERROR: Illegal 'kim query' command.\nThe keyword 'split' " "must be followed by the name of the query function.*", - lmp->input->one("kim query a0 split");); + command("kim query a0 split");); TEST_FAILURE(".*ERROR: Illegal 'kim query' command.\nThe keyword 'list' " "must be followed by the name of the query function.*", - lmp->input->one("kim query a0 list");); + command("kim query a0 list");); TEST_FAILURE(".*ERROR: Illegal 'kim query' command.\nThe keyword 'index' " "must be followed by the name of the query function.*", - lmp->input->one("kim query a0 index");); + command("kim query a0 index");); TEST_FAILURE(".*ERROR: Illegal 'kim query' command.\nThe 'list' keyword " "can not be used after 'split'.*", - lmp->input->one("kim query a0 split list");); + command("kim query a0 split list");); TEST_FAILURE(".*ERROR: Illegal 'kim query' command.\nThe 'index' keyword " "can not be used after 'split'.*", - lmp->input->one("kim query a0 split index");); + command("kim query a0 split index");); TEST_FAILURE(".*ERROR: Illegal 'kim query' command.\nThe 'split' keyword " "can not be used after 'list'.*", - lmp->input->one("kim query a0 list split");); + command("kim query a0 list split");); TEST_FAILURE(".*ERROR: Illegal 'kim query' command.\nThe 'index' keyword " "can not be used after 'list'.*", - lmp->input->one("kim query a0 list index");); + command("kim query a0 list index");); TEST_FAILURE(".*ERROR: Illegal 'kim query' command.\nThe 'list' keyword " "can not be used after 'index'.*", - lmp->input->one("kim query a0 index list");); + command("kim query a0 index list");); TEST_FAILURE(".*ERROR: Illegal 'kim query' command.\nThe 'split' keyword " "can not be used after 'index'.*", - lmp->input->one("kim query a0 index split");); + command("kim query a0 index split");); TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `crystal` " "to 'kim query' is wrong. The query format is the " "keyword=\\[value\\], where value is always an array of one " "or more comma-separated items.*", - lmp->input->one("kim query a0 get_lattice_constant_cubic " - "crystal");); + command("kim query a0 get_lattice_constant_cubic " + "crystal");); TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `" "crystal=fcc` to 'kim query' is wrong. The query format is the " "keyword=\\[value\\], where value is always an array of one " "or more comma-separated items.*", - lmp->input->one("kim query a0 get_lattice_constant_cubic " - "crystal=fcc");); + command("kim query a0 get_lattice_constant_cubic " + "crystal=fcc");); TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `" "crystal=\\[fcc` to 'kim query' is wrong. The query format is " "the keyword=\\[value\\], where value is always an array of " "one or more comma-separated items.*", - lmp->input->one("kim query a0 get_lattice_constant_cubic " - "crystal=[fcc");); - TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `" + command("kim query a0 get_lattice_constant_cubic " + "crystal=[fcc");); + TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `" "crystal=fcc\\]` to 'kim query' is wrong. The query format is " "the keyword=\\[value\\], where value is always an array of " "one or more comma-separated items.*", - lmp->input->one("kim query a0 get_lattice_constant_cubic " - "crystal=fcc]");); + command("kim query a0 get_lattice_constant_cubic " + "crystal=fcc]");); - std::string squery("kim query a0 get_lattice_constant_cubic "); - squery += "crystal=[\"fcc\"] species=\"Al\",\"Ni\" units=[\"angstrom\"]"; + std::string squery = "kim query a0 get_lattice_constant_cubic " + "crystal=[\"fcc\"] species=\"Al\",\"Ni\" units=[\"angstrom\"]"; TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `species=" "\"Al\",\"Ni\"` to 'kim query' is wrong. The query format is " "the keyword=\\[value\\], where value is always an array of " "one or more comma-separated items.*", - lmp->input->one(squery);); + command(squery);); - squery = "kim query a0 get_lattice_constant_cubic "; - squery += "crystal=[fcc] species=Al,Ni units=[angstrom]"; + squery = "kim query a0 get_lattice_constant_cubic crystal=[fcc] species=Al,Ni units=[angstrom]"; TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `species=" "Al,Ni` to 'kim query' is wrong. The query format is " "the keyword=\\[value\\], where value is always an array of " "one or more comma-separated items.*", - lmp->input->one(squery);); + command(squery);); - squery = "kim query a0 get_lattice_constant_cubic "; - squery += "crystal=[fcc] species=Al,Ni, units=[angstrom]"; + squery = + "kim query a0 get_lattice_constant_cubic crystal=[fcc] species=Al,Ni, units=[angstrom]"; TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `species=" "Al,Ni,` to 'kim query' is wrong. The query format is " "the keyword=\\[value\\], where value is always an array of " "one or more comma-separated items.*", - lmp->input->one(squery);); + command(squery);); - squery = "kim query a0 get_lattice_constant_cubic "; - squery += "crystal=[fcc] species=[Al,Ni, units=[angstrom]"; + squery = + "kim query a0 get_lattice_constant_cubic crystal=[fcc] species=[Al,Ni, units=[angstrom]"; TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `species=" "\\[Al,Ni,` to 'kim query' is wrong. The query format is " "the keyword=\\[value\\], where value is always an array of " "one or more comma-separated items.*", - lmp->input->one(squery);); + command(squery);); - squery = "kim query a0 get_lattice_constant_cubic "; - squery += "crystal=[fcc] species=Al,Ni], units=[angstrom]"; + squery = + "kim query a0 get_lattice_constant_cubic crystal=[fcc] species=Al,Ni], units=[angstrom]"; TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `species=" "Al,Ni\\],` to 'kim query' is wrong. The query format is " "the keyword=\\[value\\], where value is always an array of " "one or more comma-separated items.*", - lmp->input->one(squery);); + command(squery);); - squery = "kim query a0 get_lattice_constant_cubic "; - squery += "crystal=[fcc] species=Al,\"Ni\"], units=[angstrom]"; + squery = "kim query a0 get_lattice_constant_cubic crystal=[fcc] species=Al,\"Ni\"], " + "units=[angstrom]"; TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `species=" "Al,\"Ni\"\\],` to 'kim query' is wrong. The query format is " "the keyword=\\[value\\], where value is always an array of " "one or more comma-separated items.*", - lmp->input->one(squery);); + command(squery);); - squery = "kim query a0 get_lattice_constant_cubic "; - squery += "crystal=[fcc] species=\"Al\",Ni], units=[angstrom]"; + squery = "kim query a0 get_lattice_constant_cubic crystal=[fcc] species=\"Al\",Ni], " + "units=[angstrom]"; TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `species=" "\"Al\",Ni\\],` to 'kim query' is wrong. The query format is " "the keyword=\\[value\\], where value is always an array of " "one or more comma-separated items.*", - lmp->input->one(squery);); + command(squery);); - squery = "kim query a0 get_lattice_constant_cubic crystal=[\"fcc\"] " - "species=[\"Al\"]"; + squery = "kim query a0 get_lattice_constant_cubic crystal=[\"fcc\"] species=[\"Al\"]"; TEST_FAILURE(".*ERROR: Illegal query format.\nMust use 'kim init' before " "'kim query' or must provide the model name after query " "function with the format of 'model=\\[model_name\\]'.*", - lmp->input->one(squery);); + command(squery);); - squery = "kim query a0 get_lattice_constant_cubic crystal=[fcc] " - "species=[Al]"; + squery = "kim query a0 get_lattice_constant_cubic crystal=[fcc] species=[Al]"; TEST_FAILURE(".*ERROR: Illegal query format.\nMust use 'kim init' before " "'kim query' or must provide the model name after query " "function with the format of 'model=\\[model_name\\]'.*", - lmp->input->one(squery);); + command(squery);); - squery = "kim query a0 get_lattice_constant_cubic crystal=[\"fcc\"] " - "species=[Al]"; + squery = "kim query a0 get_lattice_constant_cubic crystal=[\"fcc\"] species=[Al]"; TEST_FAILURE(".*ERROR: Illegal query format.\nMust use 'kim init' before " "'kim query' or must provide the model name after query " "function with the format of 'model=\\[model_name\\]'.*", - lmp->input->one(squery);); + command(squery);); #if defined(KIM_EXTRA_UNITTESTS) if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - - squery = "kim query latconst_1 get_lattice_constant_cubic "; - squery += "crystal=[fcc] species=[Al] units=[angstrom] "; - squery += "model=[EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005]"; - lmp->input->one(squery); + command("clear"); + command("kim query latconst_1 get_lattice_constant_cubic " + "crystal=[fcc] species=[Al] units=[angstrom] " + "model=[EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005]"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_TRUE((std::string(lmp->input->variable->retrieve("latconst_1")) == - "4.032082033157349")); + ASSERT_THAT(variable->retrieve("latconst_1"), StrEq("4.032082033157349")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal"); + command("clear"); + command("kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal"); + command("kim query latconst_1 get_lattice_constant_cubic crystal=[fcc] species=[Al] " + "units=[angstrom]"); - squery = "kim query latconst_1 get_lattice_constant_cubic "; - squery += "crystal=[fcc] species=[Al] units=[angstrom]"; - lmp->input->one(squery); - - squery = "kim query latconst_2 get_lattice_constant_cubic "; - squery += "crystal=[fcc] species=[Al] units=[angstrom] "; - squery += "model=[LennardJones612_UniversalShifted__MO_959249795837_003]"; - lmp->input->one(squery); + command("kim query latconst_2 get_lattice_constant_cubic crystal=[fcc] species=[Al] " + "units=[angstrom] " + "model=[LennardJones612_UniversalShifted__MO_959249795837_003]"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_TRUE((std::string(lmp->input->variable->retrieve("latconst_1")) == - "4.032082033157349")); - ASSERT_TRUE((std::string(lmp->input->variable->retrieve("latconst_2")) == - "3.328125931322575")); + ASSERT_THAT(variable->retrieve("latconst_1"), StrEq("4.032082033157349")); + ASSERT_THAT(variable->retrieve("latconst_2"), StrEq("3.328125931322575")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("kim init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 metal"); + command("clear"); + command("kim init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 metal"); - squery = "kim query latconst split get_lattice_constant_hexagonal "; - squery += "crystal=[hcp] species=[Zr] units=[angstrom]"; - lmp->input->one(squery); + command("kim query latconst split get_lattice_constant_hexagonal crystal=[hcp] species=[Zr] " + "units=[angstrom]"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_TRUE((std::string(lmp->input->variable->retrieve("latconst_1")) == - "3.234055244384789")); - ASSERT_TRUE((std::string(lmp->input->variable->retrieve("latconst_2")) == - "5.167650199630013")); + ASSERT_THAT(variable->retrieve("latconst_1"), StrEq("3.234055244384789")); + ASSERT_THAT(variable->retrieve("latconst_2"), StrEq("5.167650199630013")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); + command("clear"); - squery = "kim query latconst index get_lattice_constant_hexagonal "; - squery += "crystal=[hcp] species=[Zr] units=[angstrom] "; - squery += "model=[EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000]"; - lmp->input->one(squery); + command("kim query latconst index get_lattice_constant_hexagonal " + "crystal=[hcp] species=[Zr] units=[angstrom] " + "model=[EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000]"); if (!verbose) ::testing::internal::GetCapturedStdout(); - - ASSERT_TRUE((std::string(lmp->input->variable->retrieve("latconst")) == - "3.234055244384789")); + ASSERT_THAT(variable->retrieve("latconst"), StrEq("3.234055244384789")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("variable latconst delete"); - lmp->input->one("clear"); - lmp->input->one("kim init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 metal"); + command("variable latconst delete"); + command("clear"); + command("kim init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 metal"); - squery = "kim query latconst list get_lattice_constant_hexagonal "; - squery += "crystal=[hcp] species=[Zr] units=[angstrom]"; - lmp->input->one(squery); + command("kim query latconst list get_lattice_constant_hexagonal crystal=[hcp] species=[Zr] " + "units=[angstrom]"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_TRUE((std::string(lmp->input->variable->retrieve("latconst")) == - "3.234055244384789 5.167650199630013")); + ASSERT_THAT(variable->retrieve("latconst"), StrEq("3.234055244384789 5.167650199630013")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal"); + command("clear"); + command("kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal"); - squery = "kim query alpha get_linear_thermal_expansion_coefficient_cubic "; - squery += "crystal=[fcc] species=[Al] units=[1/K] temperature=[293.15] "; - squery += "temperature_units=[K]"; - lmp->input->one(squery); + command("kim query alpha get_linear_thermal_expansion_coefficient_cubic " + "crystal=[fcc] species=[Al] units=[1/K] temperature=[293.15] " + "temperature_units=[K]"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_TRUE((std::string(lmp->input->variable->retrieve("alpha")) == - "1.654960564704273e-05")); + ASSERT_THAT(variable->retrieve("alpha"), StrEq("1.654960564704273e-05")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); + command("clear"); - squery = "kim query model_list list get_available_models "; - squery += "species=[Al]"; - lmp->input->one(squery); + command("kim query model_list list get_available_models species=[Al]"); if (!verbose) ::testing::internal::GetCapturedStdout(); - std::string model_list = lmp->input->variable->retrieve("model_list"); + std::string model_list = variable->retrieve("model_list"); auto n = model_list.find("EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005"); ASSERT_TRUE(n != std::string::npos); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); + command("clear"); - squery = "kim query model_name index get_available_models "; - squery += "species=[Al]"; - lmp->input->one(squery); - lmp->input->one("variable model_name delete"); + command("kim query model_name index get_available_models species=[Al]"); + command("variable model_name delete"); if (!verbose) ::testing::internal::GetCapturedStdout(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); + command("clear"); - squery = "kim query model_name index get_available_models "; - squery += "species=[Al] potential_type=[eam,meam]"; - lmp->input->one(squery); - lmp->input->one("variable model_name delete"); + command("kim query model_name index get_available_models " + "species=[Al] potential_type=[eam,meam]"); + command("variable model_name delete"); - squery = "kim query model_name index get_available_models "; - squery += "species=[Al] potential_type=[\"eam\",\"meam\"]"; - lmp->input->one(squery); - lmp->input->one("variable model_name delete"); + command("kim query model_name index get_available_models " + "species=[Al] potential_type=[\"eam\",\"meam\"]"); + command("variable model_name delete"); - squery = "kim query model_name index get_available_models "; - squery += "species=[Al] potential_type=[eam,\"meam\"]"; - lmp->input->one(squery); - lmp->input->one("variable model_name delete"); + command("kim query model_name index get_available_models " + "species=[Al] potential_type=[eam,\"meam\"]"); + command("variable model_name delete"); - squery = "kim query model_name index get_available_models "; - squery += "species=[Al] potential_type=[\"eam\",meam]"; - lmp->input->one(squery); - lmp->input->one("variable model_name delete"); + command("kim query model_name index get_available_models " + "species=[Al] potential_type=[\"eam\",meam]"); + command("variable model_name delete"); if (!verbose) ::testing::internal::GetCapturedStdout(); #endif } diff --git a/unittest/commands/test_lattice_region.cpp b/unittest/commands/test_lattice_region.cpp index b359c90c75..2924c75d9f 100644 --- a/unittest/commands/test_lattice_region.cpp +++ b/unittest/commands/test_lattice_region.cpp @@ -81,12 +81,14 @@ protected: delete lmp; if (!verbose) ::testing::internal::GetCapturedStdout(); } + + void command(const std::string &cmd) { lmp->input->one(cmd); } }; TEST_F(LatticeRegionTest, lattice_none) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice none 2.0"); + command("lattice none 2.0"); if (!verbose) ::testing::internal::GetCapturedStdout(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::NONE); @@ -96,14 +98,14 @@ TEST_F(LatticeRegionTest, lattice_none) ASSERT_EQ(lattice->nbasis, 0); ASSERT_EQ(lattice->basis, nullptr); - TEST_FAILURE(".*ERROR: Illegal lattice command.*", lmp->input->one("lattice");); - TEST_FAILURE(".*ERROR: Illegal lattice command.*", lmp->input->one("lattice xxx");); - TEST_FAILURE(".*ERROR: Illegal lattice command.*", lmp->input->one("lattice none 1.0 origin");); - TEST_FAILURE(".*ERROR: Expected floating point.*", lmp->input->one("lattice none xxx");); + TEST_FAILURE(".*ERROR: Illegal lattice command.*", command("lattice");); + TEST_FAILURE(".*ERROR: Illegal lattice command.*", command("lattice xxx");); + TEST_FAILURE(".*ERROR: Illegal lattice command.*", command("lattice none 1.0 origin");); + TEST_FAILURE(".*ERROR: Expected floating point.*", command("lattice none xxx");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units lj"); - lmp->input->one("lattice none 1.0"); + command("units lj"); + command("lattice none 1.0"); if (!verbose) ::testing::internal::GetCapturedStdout(); lattice = lmp->domain->lattice; ASSERT_EQ(lattice->xlattice, 1.0); @@ -114,7 +116,7 @@ TEST_F(LatticeRegionTest, lattice_none) TEST_F(LatticeRegionTest, lattice_sc) { ::testing::internal::CaptureStdout(); - lmp->input->one("lattice sc 1.0 spacing 1.5 2.0 3.0"); + command("lattice sc 1.0 spacing 1.5 2.0 3.0"); auto output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; ASSERT_THAT(output, MatchesRegex(".*Lattice spacing in x,y,z = 1.50* 2.0* 3.0*.*")); @@ -125,7 +127,7 @@ TEST_F(LatticeRegionTest, lattice_sc) ASSERT_EQ(lattice->zlattice, 3.0); ::testing::internal::CaptureStdout(); - lmp->input->one("lattice sc 2.0"); + command("lattice sc 2.0"); output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; ASSERT_THAT(output, MatchesRegex(".*Lattice spacing in x,y,z = 2.0* 2.0* 2.0*.*")); @@ -151,25 +153,24 @@ TEST_F(LatticeRegionTest, lattice_sc) ASSERT_EQ(lattice->basis[0][2], 0.0); TEST_FAILURE(".*ERROR: Illegal lattice command.*", - lmp->input->one("lattice sc 1.0 origin 1.0 1.0 1.0");); + command("lattice sc 1.0 origin 1.0 1.0 1.0");); + TEST_FAILURE(".*ERROR: Illegal lattice command.*", command("lattice sc 1.0 origin 1.0");); TEST_FAILURE(".*ERROR: Illegal lattice command.*", - lmp->input->one("lattice sc 1.0 origin 1.0");); - TEST_FAILURE(".*ERROR: Illegal lattice command.*", - lmp->input->one("lattice sc 1.0 origin 0.0 0.0 0.0 xxx");); + command("lattice sc 1.0 origin 0.0 0.0 0.0 xxx");); TEST_FAILURE(".*ERROR: Expected floating point.*", - lmp->input->one("lattice sc 1.0 origin xxx 1.0 1.0");); + command("lattice sc 1.0 origin xxx 1.0 1.0");); TEST_FAILURE(".*ERROR: Lattice orient vectors are not orthogonal.*", - lmp->input->one("lattice sc 1.0 orient x 2 2 0");); + command("lattice sc 1.0 orient x 2 2 0");); TEST_FAILURE(".*ERROR: Lattice orient vectors are not right-handed.*", - lmp->input->one("lattice sc 1.0 orient y 0 -1 0");); + command("lattice sc 1.0 orient y 0 -1 0");); TEST_FAILURE(".*ERROR: Lattice spacings are invalid.*", - lmp->input->one("lattice sc 1.0 spacing 0.0 1.0 1.0");); + command("lattice sc 1.0 spacing 0.0 1.0 1.0");); TEST_FAILURE(".*ERROR: Lattice spacings are invalid.*", - lmp->input->one("lattice sc 1.0 spacing 1.0 -0.1 1.0");); + command("lattice sc 1.0 spacing 1.0 -0.1 1.0");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units lj"); - lmp->input->one("lattice sc 2.0"); + command("units lj"); + command("lattice sc 2.0"); if (!verbose) ::testing::internal::GetCapturedStdout(); lattice = lmp->domain->lattice; ASSERT_DOUBLE_EQ(lattice->xlattice, pow(0.5, 1.0 / 3.0)); @@ -177,16 +178,16 @@ TEST_F(LatticeRegionTest, lattice_sc) ASSERT_DOUBLE_EQ(lattice->zlattice, pow(0.5, 1.0 / 3.0)); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("dimension 2"); + command("dimension 2"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", - lmp->input->one("lattice sc 1.0");); + command("lattice sc 1.0");); } TEST_F(LatticeRegionTest, lattice_bcc) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice bcc 4.2 orient x 1 1 0 orient y -1 1 0"); + command("lattice bcc 4.2 orient x 1 1 0 orient y -1 1 0"); if (!verbose) ::testing::internal::GetCapturedStdout(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::BCC); @@ -202,16 +203,16 @@ TEST_F(LatticeRegionTest, lattice_bcc) ASSERT_EQ(lattice->basis[1][2], 0.5); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("dimension 2"); + command("dimension 2"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", - lmp->input->one("lattice bcc 1.0");); + command("lattice bcc 1.0");); } TEST_F(LatticeRegionTest, lattice_fcc) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice fcc 3.5 origin 0.5 0.5 0.5"); + command("lattice fcc 3.5 origin 0.5 0.5 0.5"); if (!verbose) ::testing::internal::GetCapturedStdout(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::FCC); @@ -233,23 +234,22 @@ TEST_F(LatticeRegionTest, lattice_fcc) ASSERT_EQ(lattice->basis[3][2], 0.5); TEST_FAILURE(".*ERROR: Invalid option in lattice command for non-custom style.*", - lmp->input->one("lattice fcc 1.0 basis 0.0 0.0 0.0");); + command("lattice fcc 1.0 basis 0.0 0.0 0.0");); TEST_FAILURE(".*ERROR: Invalid option in lattice command for non-custom style.*", - lmp->input->one("lattice fcc 1.0 a1 0.0 1.0 0.0");); - TEST_FAILURE(".*ERROR: Illegal lattice command.*", - lmp->input->one("lattice fcc 1.0 orient w 1 0 0");); + command("lattice fcc 1.0 a1 0.0 1.0 0.0");); + TEST_FAILURE(".*ERROR: Illegal lattice command.*", command("lattice fcc 1.0 orient w 1 0 0");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("dimension 2"); + command("dimension 2"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", - lmp->input->one("lattice fcc 1.0");); + command("lattice fcc 1.0");); } TEST_F(LatticeRegionTest, lattice_hcp) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice hcp 3.0 orient z 0 0 1"); + command("lattice hcp 3.0 orient z 0 0 1"); if (!verbose) ::testing::internal::GetCapturedStdout(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::HCP); @@ -280,20 +280,20 @@ TEST_F(LatticeRegionTest, lattice_hcp) ASSERT_DOUBLE_EQ(lattice->a3[2], sqrt(8.0 / 3.0)); TEST_FAILURE(".*ERROR: Invalid option in lattice command for non-custom style.*", - lmp->input->one("lattice hcp 1.0 a2 0.0 1.0 0.0");); + command("lattice hcp 1.0 a2 0.0 1.0 0.0");); TEST_FAILURE(".*ERROR: Invalid option in lattice command for non-custom style.*", - lmp->input->one("lattice hcp 1.0 a3 0.0 1.0 0.0");); + command("lattice hcp 1.0 a3 0.0 1.0 0.0");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("dimension 2"); + command("dimension 2"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", - lmp->input->one("lattice hcp 1.0");); + command("lattice hcp 1.0");); } TEST_F(LatticeRegionTest, lattice_diamond) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice diamond 4.1 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1"); + command("lattice diamond 4.1 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1"); if (!verbose) ::testing::internal::GetCapturedStdout(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::DIAMOND); @@ -336,17 +336,17 @@ TEST_F(LatticeRegionTest, lattice_diamond) ASSERT_EQ(lattice->a3[2], 1.0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("dimension 2"); + command("dimension 2"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", - lmp->input->one("lattice diamond 1.0");); + command("lattice diamond 1.0");); } TEST_F(LatticeRegionTest, lattice_sq) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("dimension 2"); - lmp->input->one("lattice sq 3.0"); + command("dimension 2"); + command("lattice sq 3.0"); if (!verbose) ::testing::internal::GetCapturedStdout(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::SQ); @@ -358,22 +358,21 @@ TEST_F(LatticeRegionTest, lattice_sq) ASSERT_EQ(lattice->basis[0][1], 0.0); ASSERT_EQ(lattice->basis[0][2], 0.0); - TEST_FAILURE( - ".*ERROR: Lattice settings are not compatible with 2d simulation.*", - lmp->input->one("lattice sq 1.0 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1");); + TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", + command("lattice sq 1.0 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("dimension 3"); + command("dimension 3"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", - lmp->input->one("lattice sq 1.0");); + command("lattice sq 1.0");); } TEST_F(LatticeRegionTest, lattice_sq2) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("dimension 2"); - lmp->input->one("lattice sq2 2.0"); + command("dimension 2"); + command("lattice sq2 2.0"); if (!verbose) ::testing::internal::GetCapturedStdout(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::SQ2); @@ -389,17 +388,17 @@ TEST_F(LatticeRegionTest, lattice_sq2) ASSERT_EQ(lattice->basis[1][2], 0.0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("dimension 3"); + command("dimension 3"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", - lmp->input->one("lattice sq2 1.0");); + command("lattice sq2 1.0");); } TEST_F(LatticeRegionTest, lattice_hex) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("dimension 2"); - lmp->input->one("lattice hex 2.0"); + command("dimension 2"); + command("lattice hex 2.0"); if (!verbose) ::testing::internal::GetCapturedStdout(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::HEX); @@ -424,32 +423,32 @@ TEST_F(LatticeRegionTest, lattice_hex) ASSERT_EQ(lattice->a3[2], 1.0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("dimension 3"); + command("dimension 3"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", - lmp->input->one("lattice hex 1.0");); + command("lattice hex 1.0");); } TEST_F(LatticeRegionTest, lattice_custom) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("variable a equal 4.34"); - lmp->input->one("variable b equal $a*sqrt(3.0)"); - lmp->input->one("variable c equal $a*sqrt(8.0/3.0)"); - lmp->input->one("variable t equal 1.0/3.0"); - lmp->input->one("variable f equal 5.0/6.0"); - lmp->input->one("lattice custom 1.0 " - "a1 $a 0.0 0.0 " - "a2 0.0 $b 0.0 " - "a3 0.0 0.0 $c " - "basis 0.0 0.0 0.0 " - "basis 0.5 0.5 0.0 " - "basis $t 0.0 0.5 " - "basis $f 0.5 0.5 " - "basis 0.0 0.0 0.625 " - "basis 0.5 0.5 0.625 " - "basis $t 0.0 0.125 " - "basis $f 0.5 0.125 "); + command("variable a equal 4.34"); + command("variable b equal $a*sqrt(3.0)"); + command("variable c equal $a*sqrt(8.0/3.0)"); + command("variable t equal 1.0/3.0"); + command("variable f equal 5.0/6.0"); + command("lattice custom 1.0 " + "a1 $a 0.0 0.0 " + "a2 0.0 $b 0.0 " + "a3 0.0 0.0 $c " + "basis 0.0 0.0 0.0 " + "basis 0.5 0.5 0.0 " + "basis $t 0.0 0.5 " + "basis $f 0.5 0.5 " + "basis 0.0 0.0 0.625 " + "basis 0.5 0.5 0.625 " + "basis $t 0.0 0.125 " + "basis $f 0.5 0.125 "); if (!verbose) ::testing::internal::GetCapturedStdout(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::CUSTOM); @@ -492,47 +491,47 @@ TEST_F(LatticeRegionTest, lattice_custom) ASSERT_DOUBLE_EQ(lattice->a3[2], 4.34 * sqrt(8.0 / 3.0)); TEST_FAILURE(".*ERROR: Illegal lattice command.*", - lmp->input->one("lattice custom 1.0 basis -0.1 0 0");); + command("lattice custom 1.0 basis -0.1 0 0");); TEST_FAILURE(".*ERROR: Illegal lattice command.*", - lmp->input->one("lattice custom 1.0 basis 0.0 1.0 0");); + command("lattice custom 1.0 basis 0.0 1.0 0");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("dimension 2"); + command("dimension 2"); if (!verbose) ::testing::internal::GetCapturedStdout(); - TEST_FAILURE(".*ERROR: No basis atoms in lattice.*", lmp->input->one("lattice custom 1.0");); + TEST_FAILURE(".*ERROR: No basis atoms in lattice.*", command("lattice custom 1.0");); TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", - lmp->input->one("lattice custom 1.0 origin 0.5 0.5 0.5 basis 0.0 0.0 0.0");); + command("lattice custom 1.0 origin 0.5 0.5 0.5 basis 0.0 0.0 0.0");); TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", - lmp->input->one("lattice custom 1.0 a1 1.0 1.0 1.0 basis 0.0 0.0 0.0");); + command("lattice custom 1.0 a1 1.0 1.0 1.0 basis 0.0 0.0 0.0");); TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", - lmp->input->one("lattice custom 1.0 a2 1.0 1.0 1.0 basis 0.0 0.0 0.0");); + command("lattice custom 1.0 a2 1.0 1.0 1.0 basis 0.0 0.0 0.0");); TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", - lmp->input->one("lattice custom 1.0 a3 1.0 1.0 1.0 basis 0.0 0.0 0.0");); + command("lattice custom 1.0 a3 1.0 1.0 1.0 basis 0.0 0.0 0.0");); } TEST_F(LatticeRegionTest, region_fail) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice none 2.0"); - lmp->input->one("region box block 0 1 0 1 0 1"); + command("lattice none 2.0"); + command("region box block 0 1 0 1 0 1"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Create_atoms command before simulation box is defined.*", - lmp->input->one("create_atoms 1 box");); + command("create_atoms 1 box");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("create_box 1 box"); + command("create_box 1 box"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR: Cannot create atoms with undefined lattice.*", - lmp->input->one("create_atoms 1 box");); + command("create_atoms 1 box");); } TEST_F(LatticeRegionTest, region_block_lattice) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice sc 1.5"); - lmp->input->one("region box block 0 2 0 2 0 2 units lattice"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 box"); + command("lattice sc 1.5"); + command("region box block 0 2 0 2 0 2 units lattice"); + command("create_box 1 box"); + command("create_atoms 1 box"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->domain->triclinic, 0); @@ -555,10 +554,10 @@ TEST_F(LatticeRegionTest, region_block_lattice) TEST_F(LatticeRegionTest, region_block_box) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice sc 1.5 origin 0.75 0.75 0.75"); - lmp->input->one("region box block 0 2 0 2 0 2 units box"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 box"); + command("lattice sc 1.5 origin 0.75 0.75 0.75"); + command("region box block 0 2 0 2 0 2 units box"); + command("create_box 1 box"); + command("create_atoms 1 box"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->domain->triclinic, 0); @@ -572,11 +571,11 @@ TEST_F(LatticeRegionTest, region_block_box) TEST_F(LatticeRegionTest, region_cone) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice fcc 2.5 origin 0.5 0.5 0.5"); - lmp->input->one("region box cone x 1.0 1.0 0.5 2.1 0.0 2.0"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 region box"); - lmp->input->one("write_dump all atom init.lammpstrj"); + command("lattice fcc 2.5 origin 0.5 0.5 0.5"); + command("region box cone x 1.0 1.0 0.5 2.1 0.0 2.0"); + command("create_box 1 box"); + command("create_atoms 1 region box"); + command("write_dump all atom init.lammpstrj"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->domain->triclinic, 0); ASSERT_EQ(lmp->atom->natoms, 42); @@ -585,10 +584,10 @@ TEST_F(LatticeRegionTest, region_cone) TEST_F(LatticeRegionTest, region_cylinder) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice fcc 2.5 origin 0.5 0.5 0.5"); - lmp->input->one("region box cylinder z 1.0 1.0 2.1 0.0 2.0 "); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 region box"); + command("lattice fcc 2.5 origin 0.5 0.5 0.5"); + command("region box cylinder z 1.0 1.0 2.1 0.0 2.0 "); + command("create_box 1 box"); + command("create_atoms 1 region box"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->domain->triclinic, 0); ASSERT_EQ(lmp->atom->natoms, 114); @@ -597,10 +596,10 @@ TEST_F(LatticeRegionTest, region_cylinder) TEST_F(LatticeRegionTest, region_prism) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice bcc 2.5 origin 0.75 0.75 0.75"); - lmp->input->one("region box prism 0 2 0 2 0 2 0.5 0.0 0.0"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 box"); + command("lattice bcc 2.5 origin 0.75 0.75 0.75"); + command("region box prism 0 2 0 2 0 2 0.5 0.0 0.0"); + command("create_box 1 box"); + command("create_atoms 1 box"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->domain->triclinic, 1); ASSERT_EQ(lmp->atom->natoms, 16); @@ -609,10 +608,10 @@ TEST_F(LatticeRegionTest, region_prism) TEST_F(LatticeRegionTest, region_sphere) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice fcc 2.5 origin 0.5 0.5 0.5"); - lmp->input->one("region box sphere 1.0 1.0 1.0 1.1"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 region box"); + command("lattice fcc 2.5 origin 0.5 0.5 0.5"); + command("region box sphere 1.0 1.0 1.0 1.1"); + command("create_box 1 box"); + command("create_atoms 1 region box"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->domain->triclinic, 0); ASSERT_EQ(lmp->atom->natoms, 14); @@ -621,12 +620,12 @@ TEST_F(LatticeRegionTest, region_sphere) TEST_F(LatticeRegionTest, region_union) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice fcc 2.5 origin 0.5 0.5 0.5"); - lmp->input->one("region part1 sphere 2.0 1.0 1.0 1.1"); - lmp->input->one("region part2 block 0.0 2.0 0.0 2.0 0.0 2.0"); - lmp->input->one("region box union 2 part1 part2"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 region box"); + command("lattice fcc 2.5 origin 0.5 0.5 0.5"); + command("region part1 sphere 2.0 1.0 1.0 1.1"); + command("region part2 block 0.0 2.0 0.0 2.0 0.0 2.0"); + command("region box union 2 part1 part2"); + command("create_box 1 box"); + command("create_atoms 1 region box"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->domain->triclinic, 0); ASSERT_EQ(lmp->atom->natoms, 67); @@ -635,12 +634,12 @@ TEST_F(LatticeRegionTest, region_union) TEST_F(LatticeRegionTest, region_intersect) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice fcc 2.5 origin 0.5 0.5 0.5"); - lmp->input->one("region part1 sphere 2.0 1.0 1.0 1.8"); - lmp->input->one("region part2 block 0.0 2.0 0.0 2.0 0.0 2.0"); - lmp->input->one("region box intersect 2 part1 part2"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 region box"); + command("lattice fcc 2.5 origin 0.5 0.5 0.5"); + command("region part1 sphere 2.0 1.0 1.0 1.8"); + command("region part2 block 0.0 2.0 0.0 2.0 0.0 2.0"); + command("region box intersect 2 part1 part2"); + command("create_box 1 box"); + command("create_atoms 1 region box"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->domain->triclinic, 0); ASSERT_EQ(lmp->atom->natoms, 21); @@ -649,14 +648,14 @@ TEST_F(LatticeRegionTest, region_intersect) TEST_F(LatticeRegionTest, region_plane) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("lattice fcc 2.5 origin 0.5 0.5 0.5"); - lmp->input->one("region box block 0.0 2.0 0.0 2.0 0.0 2.0"); - lmp->input->one("region part1 plane 0.5 1.0 0.0 0.75 0.0 0.0"); - lmp->input->one("region part2 plane 1.5 1.0 0.0 0.75 0.0 0.0 side out"); - lmp->input->one("region atoms intersect 2 part1 part2"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 region atoms"); - lmp->input->one("write_dump all atom init.lammpstrj"); + command("lattice fcc 2.5 origin 0.5 0.5 0.5"); + command("region box block 0.0 2.0 0.0 2.0 0.0 2.0"); + command("region part1 plane 0.5 1.0 0.0 0.75 0.0 0.0"); + command("region part2 plane 1.5 1.0 0.0 0.75 0.0 0.0 side out"); + command("region atoms intersect 2 part1 part2"); + command("create_box 1 box"); + command("create_atoms 1 region atoms"); + command("write_dump all atom init.lammpstrj"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->domain->triclinic, 0); ASSERT_EQ(lmp->atom->natoms, 16); diff --git a/unittest/commands/test_reset_ids.cpp b/unittest/commands/test_reset_ids.cpp index 3ea2f26cef..89e09b53a6 100644 --- a/unittest/commands/test_reset_ids.cpp +++ b/unittest/commands/test_reset_ids.cpp @@ -85,6 +85,8 @@ protected: delete lmp; if (!verbose) ::testing::internal::GetCapturedStdout(); } + + void command(const std::string &cmd) { lmp->input->one(cmd); } }; TEST_F(ResetIDsTest, MolIDAll) @@ -125,7 +127,7 @@ TEST_F(ResetIDsTest, MolIDAll) // the original data file has two different molecule IDs // for two residues of the same molecule/fragment. if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("reset_mol_ids all"); + command("reset_mol_ids all"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(molid[GETIDX(1)], 1); @@ -167,10 +169,10 @@ TEST_F(ResetIDsTest, DeletePlusAtomID) // delete two water molecules if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("group allwater molecule 3:6"); - lmp->input->one("group twowater molecule 4:6:2"); - lmp->input->one("delete_atoms group twowater compress no bond yes"); - lmp->input->one("reset_mol_ids all"); + command("group allwater molecule 3:6"); + command("group twowater molecule 4:6:2"); + command("delete_atoms group twowater compress no bond yes"); + command("reset_mol_ids all"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->atom->natoms, 23); ASSERT_EQ(lmp->atom->map_tag_max, 26); @@ -229,7 +231,7 @@ TEST_F(ResetIDsTest, DeletePlusAtomID) ASSERT_GE(GETIDX(26), 0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("reset_atom_ids"); + command("reset_atom_ids"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->atom->map_tag_max, 23); @@ -245,9 +247,9 @@ TEST_F(ResetIDsTest, PartialOffset) // delete two water molecules if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("group allwater molecule 3:6"); - lmp->input->one("group nowater subtract all allwater"); - lmp->input->one("reset_mol_ids allwater offset 4"); + command("group allwater molecule 3:6"); + command("group nowater subtract all allwater"); + command("reset_mol_ids allwater offset 4"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->atom->natoms, 29); ASSERT_EQ(lmp->atom->map_tag_max, 29); @@ -283,7 +285,7 @@ TEST_F(ResetIDsTest, PartialOffset) ASSERT_EQ(molid[GETIDX(29)], 8); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("reset_mol_ids nowater offset 0"); + command("reset_mol_ids nowater offset 0"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(molid[GETIDX(1)], 1); @@ -325,11 +327,11 @@ TEST_F(ResetIDsTest, DeleteAdd) // delete two water molecules if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("group allwater molecule 3:6"); - lmp->input->one("group twowater molecule 4:6:2"); - lmp->input->one("group nowater subtract all allwater"); - lmp->input->one("delete_atoms group twowater compress no bond yes mol yes"); - lmp->input->one("reset_mol_ids allwater"); + command("group allwater molecule 3:6"); + command("group twowater molecule 4:6:2"); + command("group nowater subtract all allwater"); + command("delete_atoms group twowater compress no bond yes mol yes"); + command("reset_mol_ids allwater"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->atom->natoms, 23); ASSERT_EQ(lmp->atom->map_tag_max, 26); @@ -388,7 +390,7 @@ TEST_F(ResetIDsTest, DeleteAdd) ASSERT_GE(GETIDX(26), 0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("reset_atom_ids sort yes"); + command("reset_atom_ids sort yes"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->atom->map_tag_max, 23); @@ -396,7 +398,7 @@ TEST_F(ResetIDsTest, DeleteAdd) ASSERT_GE(GETIDX(i), 0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("reset_mol_ids nowater offset 1"); + command("reset_mol_ids nowater offset 1"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(molid[GETIDX(1)], 2); @@ -424,11 +426,11 @@ TEST_F(ResetIDsTest, DeleteAdd) ASSERT_EQ(molid[GETIDX(23)], 4); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("create_atoms 1 single 0.0 0.0 0.0"); - lmp->input->one("create_atoms 2 single 1.0 0.0 0.0"); - lmp->input->one("create_atoms 3 single 2.0 0.0 0.0"); - lmp->input->one("create_atoms 4 single 3.0 0.0 0.0"); - lmp->input->one("reset_mol_ids all single yes"); + command("create_atoms 1 single 0.0 0.0 0.0"); + command("create_atoms 2 single 1.0 0.0 0.0"); + command("create_atoms 3 single 2.0 0.0 0.0"); + command("create_atoms 4 single 3.0 0.0 0.0"); + command("reset_mol_ids all single yes"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->atom->natoms, 27); ASSERT_EQ(lmp->atom->map_tag_max, 27); @@ -442,7 +444,7 @@ TEST_F(ResetIDsTest, DeleteAdd) ASSERT_EQ(molid[GETIDX(27)], 7); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("reset_mol_ids all single no"); + command("reset_mol_ids all single no"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(molid[GETIDX(21)], 3); @@ -454,7 +456,7 @@ TEST_F(ResetIDsTest, DeleteAdd) ASSERT_EQ(molid[GETIDX(27)], 0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("reset_mol_ids all compress no single yes"); + command("reset_mol_ids all compress no single yes"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(molid[GETIDX(21)], 21); @@ -472,20 +474,20 @@ TEST_F(ResetIDsTest, TopologyData) // delete two water molecules if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("group allwater molecule 3:6"); - lmp->input->one("group twowater molecule 4:6:2"); - lmp->input->one("group nowater subtract all allwater"); - lmp->input->one("delete_atoms group twowater compress no bond yes mol yes"); + command("group allwater molecule 3:6"); + command("group twowater molecule 4:6:2"); + command("group nowater subtract all allwater"); + command("delete_atoms group twowater compress no bond yes mol yes"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->atom->natoms, 23); ASSERT_EQ(lmp->atom->map_tag_max, 26); - auto num_bond = lmp->atom->num_bond; - auto num_angle = lmp->atom->num_angle; - auto bond_atom = lmp->atom->bond_atom; - auto angle_atom1 = lmp->atom->angle_atom1; - auto angle_atom2 = lmp->atom->angle_atom2; - auto angle_atom3 = lmp->atom->angle_atom3; + auto num_bond = lmp->atom->num_bond; + auto num_angle = lmp->atom->num_angle; + auto bond_atom = lmp->atom->bond_atom; + auto angle_atom1 = lmp->atom->angle_atom1; + auto angle_atom2 = lmp->atom->angle_atom2; + auto angle_atom3 = lmp->atom->angle_atom3; ASSERT_EQ(num_bond[GETIDX(1)], 2); ASSERT_EQ(bond_atom[GETIDX(1)][0], 2); ASSERT_EQ(bond_atom[GETIDX(1)][1], 3); @@ -561,15 +563,15 @@ TEST_F(ResetIDsTest, TopologyData) ASSERT_EQ(angle_atom3[GETIDX(24)][0], 26); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("reset_atom_ids sort yes"); + command("reset_atom_ids sort yes"); if (!verbose) ::testing::internal::GetCapturedStdout(); - num_bond = lmp->atom->num_bond; - num_angle = lmp->atom->num_angle; - bond_atom = lmp->atom->bond_atom; - angle_atom1 = lmp->atom->angle_atom1; - angle_atom2 = lmp->atom->angle_atom2; - angle_atom3 = lmp->atom->angle_atom3; + num_bond = lmp->atom->num_bond; + num_angle = lmp->atom->num_angle; + bond_atom = lmp->atom->bond_atom; + angle_atom1 = lmp->atom->angle_atom1; + angle_atom2 = lmp->atom->angle_atom2; + angle_atom3 = lmp->atom->angle_atom3; ASSERT_EQ(num_bond[GETIDX(1)], 2); ASSERT_EQ(bond_atom[GETIDX(1)][0], 3); ASSERT_EQ(bond_atom[GETIDX(1)][1], 2); @@ -658,26 +660,23 @@ TEST_F(ResetIDsTest, DeathTests) { if (lmp->atom->natoms == 0) GTEST_SKIP(); - TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", lmp->input->one("reset_mol_ids");); + TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids");); TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", - lmp->input->one("reset_mol_ids all offset 1 1");); + command("reset_mol_ids all offset 1 1");); TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", - lmp->input->one("reset_mol_ids all offset -2");); + command("reset_mol_ids all offset -2");); + TEST_FAILURE(".*ERROR on proc 0: Expected integer.*", command("reset_mol_ids all offset xxx");); TEST_FAILURE(".*ERROR on proc 0: Expected integer.*", - lmp->input->one("reset_mol_ids all offset xxx");); - TEST_FAILURE(".*ERROR on proc 0: Expected integer.*", - lmp->input->one("reset_mol_ids all compress yes single no offset xxx");); + command("reset_mol_ids all compress yes single no offset xxx");); + TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids all offset");); TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", - lmp->input->one("reset_mol_ids all offset");); - TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", - lmp->input->one("reset_mol_ids all compress");); + command("reset_mol_ids all compress");); TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", - lmp->input->one("reset_mol_ids all compress xxx");); + command("reset_mol_ids all compress xxx");); + TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids all single");); TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", - lmp->input->one("reset_mol_ids all single");); - TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", - lmp->input->one("reset_mol_ids all single xxx");); + command("reset_mol_ids all single xxx");); } TEST(ResetMolIds, CMDFail) @@ -693,20 +692,23 @@ TEST(ResetMolIds, CMDFail) TEST_FAILURE(".*ERROR: Reset_mol_ids command before simulation box is.*", lmp->input->one("reset_mol_ids all");); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("atom_modify id no"); - lmp->input->one("region box block 0 1 0 1 0 1"); - lmp->input->one("create_box 1 box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); - TEST_FAILURE(".*ERROR: Cannot use reset_mol_ids unless.*", - lmp->input->one("reset_mol_ids all");); + auto command = [&](const std::string &line) { + lmp->input->one(line.c_str()); + }; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("region box block 0 1 0 1 0 1"); - lmp->input->one("create_box 1 box"); + command("atom_modify id no"); + command("region box block 0 1 0 1 0 1"); + command("create_box 1 box"); if (!verbose) ::testing::internal::GetCapturedStdout(); - TEST_FAILURE(".*ERROR: Can only use reset_mol_ids.*", lmp->input->one("reset_mol_ids all");); + TEST_FAILURE(".*ERROR: Cannot use reset_mol_ids unless.*", command("reset_mol_ids all");); + + if (!verbose) ::testing::internal::CaptureStdout(); + command("clear"); + command("region box block 0 1 0 1 0 1"); + command("create_box 1 box"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + TEST_FAILURE(".*ERROR: Can only use reset_mol_ids.*", command("reset_mol_ids all");); if (!verbose) ::testing::internal::CaptureStdout(); delete lmp; diff --git a/unittest/commands/test_simple_commands.cpp b/unittest/commands/test_simple_commands.cpp index 5fdc1e912b..4261dbd61d 100644 --- a/unittest/commands/test_simple_commands.cpp +++ b/unittest/commands/test_simple_commands.cpp @@ -82,11 +82,13 @@ protected: delete lmp; if (!verbose) ::testing::internal::GetCapturedStdout(); } + + void command(const std::string &cmd) { lmp->input->one(cmd); } }; TEST_F(SimpleCommandsTest, UnknownCommand) { - TEST_FAILURE(".*ERROR: Unknown command.*", lmp->input->one("XXX one two");); + TEST_FAILURE(".*ERROR: Unknown command.*", command("XXX one two");); } TEST_F(SimpleCommandsTest, Echo) @@ -95,31 +97,31 @@ TEST_F(SimpleCommandsTest, Echo) ASSERT_EQ(lmp->input->echo_log, 0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("echo none"); + command("echo none"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->input->echo_screen, 0); ASSERT_EQ(lmp->input->echo_log, 0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("echo both"); + command("echo both"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->input->echo_screen, 1); ASSERT_EQ(lmp->input->echo_log, 1); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("echo screen"); + command("echo screen"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->input->echo_screen, 1); ASSERT_EQ(lmp->input->echo_log, 0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("echo log"); + command("echo log"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->input->echo_screen, 0); ASSERT_EQ(lmp->input->echo_log, 1); - TEST_FAILURE(".*ERROR: Illegal echo command.*", lmp->input->one("echo");); - TEST_FAILURE(".*ERROR: Illegal echo command.*", lmp->input->one("echo xxx");); + TEST_FAILURE(".*ERROR: Illegal echo command.*", command("echo");); + TEST_FAILURE(".*ERROR: Illegal echo command.*", command("echo xxx");); } TEST_F(SimpleCommandsTest, Log) @@ -127,13 +129,13 @@ TEST_F(SimpleCommandsTest, Log) ASSERT_EQ(lmp->logfile, nullptr); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("log simple_command_test.log"); - lmp->input->one("print 'test1'"); + command("log simple_command_test.log"); + command("print 'test1'"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_NE(lmp->logfile, nullptr); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("log none"); + command("log none"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->logfile, nullptr); @@ -145,12 +147,12 @@ TEST_F(SimpleCommandsTest, Log) ASSERT_THAT(text, StrEq("test1")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("log simple_command_test.log append"); - lmp->input->one("print 'test2'"); + command("log simple_command_test.log append"); + command("print 'test2'"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_NE(lmp->logfile, nullptr); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("log none"); + command("log none"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->logfile, nullptr); @@ -162,7 +164,7 @@ TEST_F(SimpleCommandsTest, Log) in.close(); remove("simple_command_test.log"); - TEST_FAILURE(".*ERROR: Illegal log command.*", lmp->input->one("log");); + TEST_FAILURE(".*ERROR: Illegal log command.*", command("log");); } TEST_F(SimpleCommandsTest, Newton) @@ -171,22 +173,22 @@ TEST_F(SimpleCommandsTest, Newton) ASSERT_EQ(lmp->force->newton_pair, 1); ASSERT_EQ(lmp->force->newton_bond, 1); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("newton off"); + command("newton off"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->force->newton_pair, 0); ASSERT_EQ(lmp->force->newton_bond, 0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("newton on off"); + command("newton on off"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->force->newton_pair, 1); ASSERT_EQ(lmp->force->newton_bond, 0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("newton off on"); + command("newton off on"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->force->newton_pair, 0); ASSERT_EQ(lmp->force->newton_bond, 1); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("newton on"); + command("newton on"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->force->newton_pair, 1); ASSERT_EQ(lmp->force->newton_bond, 1); @@ -195,21 +197,20 @@ TEST_F(SimpleCommandsTest, Newton) TEST_F(SimpleCommandsTest, Partition) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("echo none"); + command("echo none"); if (!verbose) ::testing::internal::GetCapturedStdout(); - TEST_FAILURE(".*ERROR: Illegal partition command .*", - lmp->input->one("partition xxx 1 echo none");); + TEST_FAILURE(".*ERROR: Illegal partition command .*", command("partition xxx 1 echo none");); TEST_FAILURE(".*ERROR: Numeric index 2 is out of bounds.*", - lmp->input->one("partition yes 2 echo none");); + command("partition yes 2 echo none");); ::testing::internal::CaptureStdout(); - lmp->input->one("partition yes 1 print 'test'"); + command("partition yes 1 print 'test'"); auto text = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << text; ASSERT_THAT(text, StrEq("test\n")); ::testing::internal::CaptureStdout(); - lmp->input->one("partition no 1 print 'test'"); + command("partition no 1 print 'test'"); text = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << text; ASSERT_THAT(text, StrEq("")); @@ -218,14 +219,14 @@ TEST_F(SimpleCommandsTest, Partition) TEST_F(SimpleCommandsTest, Quit) { ::testing::internal::CaptureStdout(); - lmp->input->one("echo none"); + command("echo none"); ::testing::internal::GetCapturedStdout(); - TEST_FAILURE(".*ERROR: Expected integer .*", lmp->input->one("quit xxx");); + TEST_FAILURE(".*ERROR: Expected integer .*", command("quit xxx");); // the following tests must be skipped with OpenMPI due to using threads if (have_openmpi) GTEST_SKIP(); - ASSERT_EXIT(lmp->input->one("quit"), ExitedWithCode(0), ""); - ASSERT_EXIT(lmp->input->one("quit 9"), ExitedWithCode(9), ""); + ASSERT_EXIT(command("quit"), ExitedWithCode(0), ""); + ASSERT_EXIT(command("quit 9"), ExitedWithCode(9), ""); } TEST_F(SimpleCommandsTest, ResetTimestep) @@ -233,19 +234,19 @@ TEST_F(SimpleCommandsTest, ResetTimestep) ASSERT_EQ(lmp->update->ntimestep, 0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("reset_timestep 10"); + command("reset_timestep 10"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->update->ntimestep, 10); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("reset_timestep 0"); + command("reset_timestep 0"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->update->ntimestep, 0); - TEST_FAILURE(".*ERROR: Timestep must be >= 0.*", lmp->input->one("reset_timestep -10");); - TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", lmp->input->one("reset_timestep");); - TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", lmp->input->one("reset_timestep 10 10");); - TEST_FAILURE(".*ERROR: Expected integer .*", lmp->input->one("reset_timestep xxx");); + TEST_FAILURE(".*ERROR: Timestep must be >= 0.*", command("reset_timestep -10");); + TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep");); + TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep 10 10");); + TEST_FAILURE(".*ERROR: Expected integer .*", command("reset_timestep xxx");); } TEST_F(SimpleCommandsTest, Suffix) @@ -254,39 +255,38 @@ TEST_F(SimpleCommandsTest, Suffix) ASSERT_EQ(lmp->suffix, nullptr); ASSERT_EQ(lmp->suffix2, nullptr); - TEST_FAILURE(".*ERROR: May only enable suffixes after defining one.*", - lmp->input->one("suffix on");); + TEST_FAILURE(".*ERROR: May only enable suffixes after defining one.*", command("suffix on");); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("suffix one"); + command("suffix one"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_THAT(lmp->suffix, StrEq("one")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("suffix hybrid two three"); + command("suffix hybrid two three"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_THAT(lmp->suffix, StrEq("two")); ASSERT_THAT(lmp->suffix2, StrEq("three")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("suffix four"); + command("suffix four"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_THAT(lmp->suffix, StrEq("four")); ASSERT_EQ(lmp->suffix2, nullptr); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("suffix off"); + command("suffix off"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->suffix_enable, 0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("suffix on"); + command("suffix on"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->suffix_enable, 1); - TEST_FAILURE(".*ERROR: Illegal suffix command.*", lmp->input->one("suffix");); - TEST_FAILURE(".*ERROR: Illegal suffix command.*", lmp->input->one("suffix hybrid");); - TEST_FAILURE(".*ERROR: Illegal suffix command.*", lmp->input->one("suffix hybrid one");); + TEST_FAILURE(".*ERROR: Illegal suffix command.*", command("suffix");); + TEST_FAILURE(".*ERROR: Illegal suffix command.*", command("suffix hybrid");); + TEST_FAILURE(".*ERROR: Illegal suffix command.*", command("suffix hybrid one");); } TEST_F(SimpleCommandsTest, Thermo) @@ -294,53 +294,53 @@ TEST_F(SimpleCommandsTest, Thermo) ASSERT_EQ(lmp->output->thermo_every, 0); ASSERT_EQ(lmp->output->var_thermo, nullptr); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("thermo 2"); + command("thermo 2"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->output->thermo_every, 2); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("variable step equal logfreq(10,3,10)"); - lmp->input->one("thermo v_step"); + command("variable step equal logfreq(10,3,10)"); + command("thermo v_step"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_THAT(lmp->output->var_thermo, StrEq("step")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("thermo 10"); + command("thermo 10"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->output->thermo_every, 10); ASSERT_EQ(lmp->output->var_thermo, nullptr); - TEST_FAILURE(".*ERROR: Illegal thermo command.*", lmp->input->one("thermo");); - TEST_FAILURE(".*ERROR: Illegal thermo command.*", lmp->input->one("thermo -1");); - TEST_FAILURE(".*ERROR: Expected integer.*", lmp->input->one("thermo xxx");); + TEST_FAILURE(".*ERROR: Illegal thermo command.*", command("thermo");); + TEST_FAILURE(".*ERROR: Illegal thermo command.*", command("thermo -1");); + TEST_FAILURE(".*ERROR: Expected integer.*", command("thermo xxx");); } TEST_F(SimpleCommandsTest, TimeStep) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("timestep 1"); + command("timestep 1"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->update->dt, 1.0); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("timestep 0.1"); + command("timestep 0.1"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->update->dt, 0.1); // zero timestep is legal and works (atoms don't move) if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("timestep 0.0"); + command("timestep 0.0"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->update->dt, 0.0); // negative timestep also creates a viable MD. if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("timestep -0.1"); + command("timestep -0.1"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->update->dt, -0.1); - TEST_FAILURE(".*ERROR: Illegal timestep command.*", lmp->input->one("timestep");); - TEST_FAILURE(".*ERROR: Expected floating point.*", lmp->input->one("timestep xxx");); + TEST_FAILURE(".*ERROR: Illegal timestep command.*", command("timestep");); + TEST_FAILURE(".*ERROR: Expected floating point.*", command("timestep xxx");); } TEST_F(SimpleCommandsTest, Units) @@ -353,24 +353,24 @@ TEST_F(SimpleCommandsTest, Units) ASSERT_THAT(lmp->update->unit_style, StrEq("lj")); for (std::size_t i = 0; i < num; ++i) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one(fmt::format("units {}", names[i])); + command(fmt::format("units {}", names[i])); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_THAT(lmp->update->unit_style, StrEq(names[i])); ASSERT_EQ(lmp->update->dt, dt[i]); } if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); + command("clear"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_THAT(lmp->update->unit_style, StrEq("lj")); - TEST_FAILURE(".*ERROR: Illegal units command.*", lmp->input->one("units unknown");); + TEST_FAILURE(".*ERROR: Illegal units command.*", command("units unknown");); } TEST_F(SimpleCommandsTest, Shell) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("shell putenv TEST_VARIABLE=simpletest"); + command("shell putenv TEST_VARIABLE=simpletest"); if (!verbose) ::testing::internal::GetCapturedStdout(); char *test_var = getenv("TEST_VARIABLE"); @@ -378,8 +378,8 @@ TEST_F(SimpleCommandsTest, Shell) ASSERT_THAT(test_var, StrEq("simpletest")); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("shell putenv TEST_VARIABLE=simpletest"); - lmp->input->one("shell putenv TEST_VARIABLE2=simpletest2 OTHER_VARIABLE=2"); + command("shell putenv TEST_VARIABLE=simpletest"); + command("shell putenv TEST_VARIABLE2=simpletest2 OTHER_VARIABLE=2"); if (!verbose) ::testing::internal::GetCapturedStdout(); char *test_var2 = getenv("TEST_VARIABLE2"); diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 5a1d249bd5..7106867894 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -298,31 +298,31 @@ TEST_F(VariableTest, IfCommand) command("if 1>0 then 'print \".*bingo!\"'"); auto text = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << text; - ASSERT_THAT(text,MatchesRegex(".*bingo!.*")); + ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); ::testing::internal::CaptureStdout(); command("if (1>=0) then 'print \"bingo!\"'"); text = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << text; - ASSERT_THAT(text,MatchesRegex(".*bingo!.*")); + ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); ::testing::internal::CaptureStdout(); command("if (-1.0e-1<0.0E+0) then 'print \"bingo!\"'"); text = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << text; - ASSERT_THAT(text,MatchesRegex(".*bingo!.*")); + ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); ::testing::internal::CaptureStdout(); command("if (${one}==1.0)&&(2>=1) then 'print \"bingo!\"'"); text = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << text; - ASSERT_THAT(text,MatchesRegex(".*bingo!.*")); + ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); ::testing::internal::CaptureStdout(); command("if !((${one}!=1.0)||(2|^1)) then 'print \"missed\"' else 'print \"bingo!\"'"); text = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << text; - ASSERT_THAT(text,MatchesRegex(".*bingo!.*")); + ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", command("if () then 'print \"bingo!\"'");); diff --git a/unittest/force-styles/test_angle_style.cpp b/unittest/force-styles/test_angle_style.cpp index 7f07052b3d..8cef78c6f8 100644 --- a/unittest/force-styles/test_angle_style.cpp +++ b/unittest/force-styles/test_angle_style.cpp @@ -307,7 +307,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // init_forces block.clear(); - auto f = lmp->atom->f; + auto f = lmp->atom->f; for (int i = 1; i <= natoms; ++i) { const int j = lmp->atom->map(i); block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]); @@ -327,7 +327,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) writer.emit_block("run_stress", block); block.clear(); - f = lmp->atom->f; + f = lmp->atom->f; for (int i = 1; i <= natoms; ++i) { const int j = lmp->atom->map(i); block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]); diff --git a/unittest/force-styles/test_bond_style.cpp b/unittest/force-styles/test_bond_style.cpp index a4956006f5..fa9f8fbc02 100644 --- a/unittest/force-styles/test_bond_style.cpp +++ b/unittest/force-styles/test_bond_style.cpp @@ -307,7 +307,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // init_forces block.clear(); - auto f = lmp->atom->f; + auto f = lmp->atom->f; for (int i = 1; i <= natoms; ++i) { const int j = lmp->atom->map(i); block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]); @@ -327,7 +327,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) writer.emit_block("run_stress", block); block.clear(); - f = lmp->atom->f; + f = lmp->atom->f; for (int i = 1; i <= natoms; ++i) { const int j = lmp->atom->map(i); block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]); diff --git a/unittest/force-styles/test_config_reader.cpp b/unittest/force-styles/test_config_reader.cpp index 4ef3692f56..d4d9d3c854 100644 --- a/unittest/force-styles/test_config_reader.cpp +++ b/unittest/force-styles/test_config_reader.cpp @@ -53,17 +53,17 @@ TestConfigReader::TestConfigReader(TestConfig &config) : YamlReader(), config(co consumers["global_scalar"] = &TestConfigReader::global_scalar; consumers["global_vector"] = &TestConfigReader::global_vector; - consumers["bond_style"] = &TestConfigReader::bond_style; - consumers["bond_coeff"] = &TestConfigReader::bond_coeff; - consumers["angle_style"] = &TestConfigReader::angle_style; - consumers["angle_coeff"] = &TestConfigReader::angle_coeff; + consumers["bond_style"] = &TestConfigReader::bond_style; + consumers["bond_coeff"] = &TestConfigReader::bond_coeff; + consumers["angle_style"] = &TestConfigReader::angle_style; + consumers["angle_coeff"] = &TestConfigReader::angle_coeff; consumers["dihedral_style"] = &TestConfigReader::dihedral_style; consumers["dihedral_coeff"] = &TestConfigReader::dihedral_coeff; consumers["improper_style"] = &TestConfigReader::improper_style; consumers["improper_coeff"] = &TestConfigReader::improper_coeff; - consumers["init_energy"] = &TestConfigReader::init_energy; - consumers["run_energy"] = &TestConfigReader::run_energy; - consumers["equilibrium"] = &TestConfigReader::equilibrium; + consumers["init_energy"] = &TestConfigReader::init_energy; + consumers["run_energy"] = &TestConfigReader::run_energy; + consumers["equilibrium"] = &TestConfigReader::equilibrium; } void TestConfigReader::prerequisites(const yaml_event_t &event) diff --git a/unittest/force-styles/test_dihedral_style.cpp b/unittest/force-styles/test_dihedral_style.cpp index 6dd6a3f205..81df454fcc 100644 --- a/unittest/force-styles/test_dihedral_style.cpp +++ b/unittest/force-styles/test_dihedral_style.cpp @@ -310,7 +310,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // init_forces block.clear(); - auto f = lmp->atom->f; + auto f = lmp->atom->f; for (int i = 1; i <= natoms; ++i) { const int j = lmp->atom->map(i); block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]); @@ -330,7 +330,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) writer.emit_block("run_stress", block); block.clear(); - f = lmp->atom->f; + f = lmp->atom->f; for (int i = 1; i <= natoms; ++i) { const int j = lmp->atom->map(i); block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]); diff --git a/unittest/force-styles/test_improper_style.cpp b/unittest/force-styles/test_improper_style.cpp index 1b97f38faf..33d95820bd 100644 --- a/unittest/force-styles/test_improper_style.cpp +++ b/unittest/force-styles/test_improper_style.cpp @@ -301,7 +301,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // init_forces block.clear(); - auto f = lmp->atom->f; + auto f = lmp->atom->f; for (int i = 1; i <= natoms; ++i) { const int j = lmp->atom->map(i); block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]); @@ -321,7 +321,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) writer.emit_block("run_stress", block); block.clear(); - f = lmp->atom->f; + f = lmp->atom->f; for (int i = 1; i <= natoms; ++i) { const int j = lmp->atom->map(i); block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]); diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index fd8d306538..edfad1f923 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -307,7 +307,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // init_forces block.clear(); - auto f = lmp->atom->f; + auto f = lmp->atom->f; for (int i = 1; i <= natoms; ++i) { const int j = lmp->atom->map(i); block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]); @@ -330,7 +330,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) writer.emit_block("run_stress", block); block.clear(); - f = lmp->atom->f; + f = lmp->atom->f; for (int i = 1; i <= natoms; ++i) { const int j = lmp->atom->map(i); block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]); @@ -829,9 +829,8 @@ TEST(PairStyle, intel) GTEST_SKIP(); } - if ((test_config.pair_style == "rebo") - || utils::strmatch(test_config.pair_style, "^dpd") - || utils::strmatch(test_config.pair_style, "^tersoff.* shift ")) { + if ((test_config.pair_style == "rebo") || utils::strmatch(test_config.pair_style, "^dpd") || + utils::strmatch(test_config.pair_style, "^tersoff.* shift ")) { std::cerr << "Skipping pair style " << lmp->force->pair_style << "\n"; if (!verbose) ::testing::internal::CaptureStdout(); cleanup_lammps(lmp, test_config); diff --git a/unittest/formats/test_atom_styles.cpp b/unittest/formats/test_atom_styles.cpp index 37d436a7a2..b787076495 100644 --- a/unittest/formats/test_atom_styles.cpp +++ b/unittest/formats/test_atom_styles.cpp @@ -102,9 +102,6 @@ class AtomStyleTest : public ::testing::Test { protected: LAMMPS *lmp; - // convenience... - void command(const std::string cmd) { lmp->input->one(cmd); } - void SetUp() override { const char *args[] = {"SimpleCommandsTest", "-log", "none", "-echo", "screen", "-nocite"}; @@ -131,6 +128,8 @@ protected: remove("input_atom_styles.data"); remove("test_atom_styles.restart"); } + + void command(const std::string cmd) { lmp->input->one(cmd); } }; // default class Atom state diff --git a/unittest/formats/test_file_operations.cpp b/unittest/formats/test_file_operations.cpp index 8c4c8bce89..cf85d810df 100644 --- a/unittest/formats/test_file_operations.cpp +++ b/unittest/formats/test_file_operations.cpp @@ -84,6 +84,8 @@ protected: if (!verbose) ::testing::internal::GetCapturedStdout(); remove("safe_file_read_test.txt"); } + + void command(const std::string &cmd) { lmp->input->one(cmd); } }; #define MAX_BUF_SIZE 128 @@ -155,13 +157,13 @@ TEST_F(FileOperationsTest, logmesg) { char buf[8]; ::testing::internal::CaptureStdout(); - lmp->input->one("echo none"); + command("echo none"); ::testing::internal::GetCapturedStdout(); ::testing::internal::CaptureStdout(); utils::logmesg(lmp, "one\n"); - lmp->input->one("log test_logmesg.log"); + command("log test_logmesg.log"); utils::logmesg(lmp, "two\n"); - lmp->input->one("log none"); + command("log none"); std::string out = ::testing::internal::GetCapturedStdout(); memset(buf, 0, 8); FILE *fp = fopen("test_logmesg.log", "r"); diff --git a/unittest/formats/test_image_flags.cpp b/unittest/formats/test_image_flags.cpp index 6d4ae08111..6b3a333328 100644 --- a/unittest/formats/test_image_flags.cpp +++ b/unittest/formats/test_image_flags.cpp @@ -28,7 +28,6 @@ using LAMMPS_NS::utils::split_words; namespace LAMMPS_NS { using ::testing::Eq; - class ImageFlagsTest : public ::testing::Test { protected: LAMMPS *lmp; @@ -43,18 +42,18 @@ protected: if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_NE(lmp, nullptr); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units real"); - lmp->input->one("dimension 3"); - lmp->input->one("region box block -2 2 -2 2 -2 2"); - lmp->input->one("create_box 1 box"); - lmp->input->one("create_atoms 1 single 0.0 0.0 0.0 units box"); - lmp->input->one("create_atoms 1 single 1.9 -1.9 1.9999 units box"); - lmp->input->one("pair_style zero 2.0"); - lmp->input->one("pair_coeff * *"); - lmp->input->one("mass * 1.0"); - lmp->input->one("set atom 1 image -1 2 3"); - lmp->input->one("set atom 2 image -2 1 -1"); - lmp->input->one("write_data test_image_flags.data"); + command("units real"); + command("dimension 3"); + command("region box block -2 2 -2 2 -2 2"); + command("create_box 1 box"); + command("create_atoms 1 single 0.0 0.0 0.0 units box"); + command("create_atoms 1 single 1.9 -1.9 1.9999 units box"); + command("pair_style zero 2.0"); + command("pair_coeff * *"); + command("mass * 1.0"); + command("set atom 1 image -1 2 3"); + command("set atom 2 image -2 1 -1"); + command("write_data test_image_flags.data"); if (!verbose) ::testing::internal::GetCapturedStdout(); } @@ -65,196 +64,198 @@ protected: if (!verbose) ::testing::internal::GetCapturedStdout(); remove("test_image_flags.data"); } + + void command(const std::string &cmd) { lmp->input->one(cmd); } }; TEST_F(ImageFlagsTest, change_box) { auto image = lmp->atom->image; - int imx = (image[0] & IMGMASK) - IMGMAX; - int imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; - int imz = (image[0] >> IMG2BITS) - IMGMAX; + int imx = (image[0] & IMGMASK) - IMGMAX; + int imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; + int imz = (image[0] >> IMG2BITS) - IMGMAX; + + ASSERT_EQ(imx, -1); + ASSERT_EQ(imy, 2); + ASSERT_EQ(imz, 3); - ASSERT_EQ(imx,-1); - ASSERT_EQ(imy,2); - ASSERT_EQ(imz,3); - imx = (image[1] & IMGMASK) - IMGMAX; imy = (image[1] >> IMGBITS & IMGMASK) - IMGMAX; imz = (image[1] >> IMG2BITS) - IMGMAX; - ASSERT_EQ(imx,-2); - ASSERT_EQ(imy,1); - ASSERT_EQ(imz,-1); - + ASSERT_EQ(imx, -2); + ASSERT_EQ(imy, 1); + ASSERT_EQ(imz, -1); + if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("change_box all boundary f p p"); + command("change_box all boundary f p p"); if (!verbose) ::testing::internal::GetCapturedStdout(); image = lmp->atom->image; - imx = (image[0] & IMGMASK) - IMGMAX; - imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; - imz = (image[0] >> IMG2BITS) - IMGMAX; + imx = (image[0] & IMGMASK) - IMGMAX; + imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; + imz = (image[0] >> IMG2BITS) - IMGMAX; - ASSERT_EQ(imx,0); - ASSERT_EQ(imy,2); - ASSERT_EQ(imz,3); + ASSERT_EQ(imx, 0); + ASSERT_EQ(imy, 2); + ASSERT_EQ(imz, 3); imx = (image[1] & IMGMASK) - IMGMAX; imy = (image[1] >> IMGBITS & IMGMASK) - IMGMAX; imz = (image[1] >> IMG2BITS) - IMGMAX; - ASSERT_EQ(imx,0); - ASSERT_EQ(imy,1); - ASSERT_EQ(imz,-1); + ASSERT_EQ(imx, 0); + ASSERT_EQ(imy, 1); + ASSERT_EQ(imz, -1); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("change_box all boundary f s p"); + command("change_box all boundary f s p"); if (!verbose) ::testing::internal::GetCapturedStdout(); image = lmp->atom->image; - imx = (image[0] & IMGMASK) - IMGMAX; - imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; - imz = (image[0] >> IMG2BITS) - IMGMAX; + imx = (image[0] & IMGMASK) - IMGMAX; + imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; + imz = (image[0] >> IMG2BITS) - IMGMAX; - ASSERT_EQ(imx,0); - ASSERT_EQ(imy,0); - ASSERT_EQ(imz,3); + ASSERT_EQ(imx, 0); + ASSERT_EQ(imy, 0); + ASSERT_EQ(imz, 3); imx = (image[1] & IMGMASK) - IMGMAX; imy = (image[1] >> IMGBITS & IMGMASK) - IMGMAX; imz = (image[1] >> IMG2BITS) - IMGMAX; - ASSERT_EQ(imx,0); - ASSERT_EQ(imy,0); - ASSERT_EQ(imz,-1); + ASSERT_EQ(imx, 0); + ASSERT_EQ(imy, 0); + ASSERT_EQ(imz, -1); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("change_box all boundary p p m"); + command("change_box all boundary p p m"); if (!verbose) ::testing::internal::GetCapturedStdout(); image = lmp->atom->image; - imx = (image[0] & IMGMASK) - IMGMAX; - imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; - imz = (image[0] >> IMG2BITS) - IMGMAX; + imx = (image[0] & IMGMASK) - IMGMAX; + imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; + imz = (image[0] >> IMG2BITS) - IMGMAX; - ASSERT_EQ(imx,0); - ASSERT_EQ(imy,0); - ASSERT_EQ(imz,0); + ASSERT_EQ(imx, 0); + ASSERT_EQ(imy, 0); + ASSERT_EQ(imz, 0); imx = (image[1] & IMGMASK) - IMGMAX; imy = (image[1] >> IMGBITS & IMGMASK) - IMGMAX; imz = (image[1] >> IMG2BITS) - IMGMAX; - ASSERT_EQ(imx,0); - ASSERT_EQ(imy,0); - ASSERT_EQ(imz,0); + ASSERT_EQ(imx, 0); + ASSERT_EQ(imy, 0); + ASSERT_EQ(imz, 0); } TEST_F(ImageFlagsTest, read_data) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("dimension 3"); - lmp->input->one("boundary p p p"); - lmp->input->one("pair_style zero 2.0"); - lmp->input->one("read_data test_image_flags.data"); + command("clear"); + command("units real"); + command("dimension 3"); + command("boundary p p p"); + command("pair_style zero 2.0"); + command("read_data test_image_flags.data"); if (!verbose) ::testing::internal::GetCapturedStdout(); - + auto image = lmp->atom->image; - int imx = (image[0] & IMGMASK) - IMGMAX; - int imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; - int imz = (image[0] >> IMG2BITS) - IMGMAX; + int imx = (image[0] & IMGMASK) - IMGMAX; + int imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; + int imz = (image[0] >> IMG2BITS) - IMGMAX; + + ASSERT_EQ(imx, -1); + ASSERT_EQ(imy, 2); + ASSERT_EQ(imz, 3); - ASSERT_EQ(imx,-1); - ASSERT_EQ(imy,2); - ASSERT_EQ(imz,3); - imx = (image[1] & IMGMASK) - IMGMAX; imy = (image[1] >> IMGBITS & IMGMASK) - IMGMAX; imz = (image[1] >> IMG2BITS) - IMGMAX; - ASSERT_EQ(imx,-2); - ASSERT_EQ(imy,1); - ASSERT_EQ(imz,-1); - + ASSERT_EQ(imx, -2); + ASSERT_EQ(imy, 1); + ASSERT_EQ(imz, -1); + if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("dimension 3"); - lmp->input->one("boundary f p p"); - lmp->input->one("pair_style zero 2.0"); - lmp->input->one("read_data test_image_flags.data"); + command("clear"); + command("units real"); + command("dimension 3"); + command("boundary f p p"); + command("pair_style zero 2.0"); + command("read_data test_image_flags.data"); if (!verbose) ::testing::internal::GetCapturedStdout(); image = lmp->atom->image; - imx = (image[0] & IMGMASK) - IMGMAX; - imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; - imz = (image[0] >> IMG2BITS) - IMGMAX; + imx = (image[0] & IMGMASK) - IMGMAX; + imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; + imz = (image[0] >> IMG2BITS) - IMGMAX; - ASSERT_EQ(imx,0); - ASSERT_EQ(imy,2); - ASSERT_EQ(imz,3); + ASSERT_EQ(imx, 0); + ASSERT_EQ(imy, 2); + ASSERT_EQ(imz, 3); imx = (image[1] & IMGMASK) - IMGMAX; imy = (image[1] >> IMGBITS & IMGMASK) - IMGMAX; imz = (image[1] >> IMG2BITS) - IMGMAX; - ASSERT_EQ(imx,0); - ASSERT_EQ(imy,1); - ASSERT_EQ(imz,-1); + ASSERT_EQ(imx, 0); + ASSERT_EQ(imy, 1); + ASSERT_EQ(imz, -1); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("dimension 3"); - lmp->input->one("boundary p s p"); - lmp->input->one("pair_style zero 2.0"); - lmp->input->one("read_data test_image_flags.data"); + command("clear"); + command("units real"); + command("dimension 3"); + command("boundary p s p"); + command("pair_style zero 2.0"); + command("read_data test_image_flags.data"); if (!verbose) ::testing::internal::GetCapturedStdout(); image = lmp->atom->image; - imx = (image[0] & IMGMASK) - IMGMAX; - imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; - imz = (image[0] >> IMG2BITS) - IMGMAX; + imx = (image[0] & IMGMASK) - IMGMAX; + imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; + imz = (image[0] >> IMG2BITS) - IMGMAX; - ASSERT_EQ(imx,-1); - ASSERT_EQ(imy,0); - ASSERT_EQ(imz,3); + ASSERT_EQ(imx, -1); + ASSERT_EQ(imy, 0); + ASSERT_EQ(imz, 3); imx = (image[1] & IMGMASK) - IMGMAX; imy = (image[1] >> IMGBITS & IMGMASK) - IMGMAX; imz = (image[1] >> IMG2BITS) - IMGMAX; - ASSERT_EQ(imx,-2); - ASSERT_EQ(imy,0); - ASSERT_EQ(imz,-1); + ASSERT_EQ(imx, -2); + ASSERT_EQ(imy, 0); + ASSERT_EQ(imz, -1); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("dimension 3"); - lmp->input->one("boundary p p m"); - lmp->input->one("pair_style zero 2.0"); - lmp->input->one("read_data test_image_flags.data"); + command("clear"); + command("units real"); + command("dimension 3"); + command("boundary p p m"); + command("pair_style zero 2.0"); + command("read_data test_image_flags.data"); if (!verbose) ::testing::internal::GetCapturedStdout(); image = lmp->atom->image; - imx = (image[0] & IMGMASK) - IMGMAX; - imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; - imz = (image[0] >> IMG2BITS) - IMGMAX; + imx = (image[0] & IMGMASK) - IMGMAX; + imy = (image[0] >> IMGBITS & IMGMASK) - IMGMAX; + imz = (image[0] >> IMG2BITS) - IMGMAX; - ASSERT_EQ(imx,-1); - ASSERT_EQ(imy,2); - ASSERT_EQ(imz,0); + ASSERT_EQ(imx, -1); + ASSERT_EQ(imy, 2); + ASSERT_EQ(imz, 0); imx = (image[1] & IMGMASK) - IMGMAX; imy = (image[1] >> IMGBITS & IMGMASK) - IMGMAX; imz = (image[1] >> IMG2BITS) - IMGMAX; - ASSERT_EQ(imx,-2); - ASSERT_EQ(imy,1); - ASSERT_EQ(imz,0); + ASSERT_EQ(imx, -2); + ASSERT_EQ(imy, 1); + ASSERT_EQ(imz, 0); } } // namespace LAMMPS_NS diff --git a/unittest/formats/test_molecule_file.cpp b/unittest/formats/test_molecule_file.cpp index 3bfc0dc4fa..204a1bd061 100644 --- a/unittest/formats/test_molecule_file.cpp +++ b/unittest/formats/test_molecule_file.cpp @@ -131,19 +131,20 @@ protected: lmp->input->one(fmt::format("molecule {} {} {}", name, file, args)); remove(file.c_str()); } + + void command(const std::string &cmd) { lmp->input->one(cmd); } }; TEST_F(MoleculeFileTest, nofile) { - TEST_FAILURE(".*Cannot open molecule file nofile.mol.*", - lmp->input->one("molecule 1 nofile.mol");); + TEST_FAILURE(".*Cannot open molecule file nofile.mol.*", command("molecule 1 nofile.mol");); } TEST_F(MoleculeFileTest, badid) { TEST_FAILURE(".*Molecule template ID must have only " "alphanumeric or underscore characters.*", - lmp->input->one("molecule @mol nofile.mol");); + command("molecule @mol nofile.mol");); } TEST_F(MoleculeFileTest, badargs) @@ -223,7 +224,7 @@ TEST_F(MoleculeFileTest, twomols) TEST_F(MoleculeFileTest, twofiles) { ::testing::internal::CaptureStdout(); - lmp->input->one("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); + command("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); auto output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; ASSERT_THAT(output, MatchesRegex(".*Read molecule template twomols:.*1 molecules.*3 atoms " @@ -237,10 +238,10 @@ TEST_F(MoleculeFileTest, twofiles) TEST_F(MoleculeFileTest, bonds) { ::testing::internal::CaptureStdout(); - lmp->input->one("atom_style bond"); - lmp->input->one("region box block 0 1 0 1 0 1"); - lmp->input->one("create_box 2 box bond/types 2 extra/bond/per/atom 2 " - "extra/special/per/atom 4"); + command("atom_style bond"); + command("region box block 0 1 0 1 0 1"); + command("create_box 2 box bond/types 2 extra/bond/per/atom 2 " + "extra/special/per/atom 4"); run_mol_cmd(test_name, "", "Comment\n" "4 atoms\n" @@ -264,8 +265,8 @@ TEST_F(MoleculeFileTest, bonds) "2 bonds.*type.*2.*0 angles.*")); ::testing::internal::CaptureStdout(); - lmp->input->one("mass * 2.0"); - lmp->input->one("create_atoms 0 single 0.5 0.5 0.5 mol bonds 67235"); + command("mass * 2.0"); + command("create_atoms 0 single 0.5 0.5 0.5 mol bonds 67235"); output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; ASSERT_THAT(output, MatchesRegex(".*Created 4 atoms.*")); diff --git a/unittest/formats/test_pair_unit_convert.cpp b/unittest/formats/test_pair_unit_convert.cpp index 712e6ff50c..f0c2f0d031 100644 --- a/unittest/formats/test_pair_unit_convert.cpp +++ b/unittest/formats/test_pair_unit_convert.cpp @@ -59,19 +59,19 @@ protected: ASSERT_NE(lmp, nullptr); if (!verbose) ::testing::internal::CaptureStdout(); info = new Info(lmp); - lmp->input->one("units metal"); - lmp->input->one("dimension 3"); - lmp->input->one("region box block -4 4 -4 4 -4 4"); - lmp->input->one("create_box 2 box"); - lmp->input->one("create_atoms 1 single -1.1 1.2 0.0 units box"); - lmp->input->one("create_atoms 1 single -1.2 -1.1 0.0 units box"); - lmp->input->one("create_atoms 2 single 0.9 1.0 0.0 units box"); - lmp->input->one("create_atoms 2 single 1.0 -0.9 0.0 units box"); - lmp->input->one("pair_style zero 4.0"); - lmp->input->one("pair_coeff * *"); - lmp->input->one("mass * 1.0"); - lmp->input->one("write_data test_pair_unit_convert.data nocoeff"); - lmp->input->one("clear"); + command("units metal"); + command("dimension 3"); + command("region box block -4 4 -4 4 -4 4"); + command("create_box 2 box"); + command("create_atoms 1 single -1.1 1.2 0.0 units box"); + command("create_atoms 1 single -1.2 -1.1 0.0 units box"); + command("create_atoms 2 single 0.9 1.0 0.0 units box"); + command("create_atoms 2 single 1.0 -0.9 0.0 units box"); + command("pair_style zero 4.0"); + command("pair_coeff * *"); + command("mass * 1.0"); + command("write_data test_pair_unit_convert.data nocoeff"); + command("clear"); if (!verbose) ::testing::internal::GetCapturedStdout(); } @@ -83,6 +83,8 @@ protected: if (!verbose) ::testing::internal::GetCapturedStdout(); remove("test_pair_unit_convert.data"); } + + void command(const std::string &cmd) { lmp->input->one(cmd); } }; TEST_F(PairUnitConvertTest, zero) @@ -91,11 +93,11 @@ TEST_F(PairUnitConvertTest, zero) if (!info->has_style("pair", "zero")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style zero 6.0"); - lmp->input->one("pair_coeff * *"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style zero 6.0"); + command("pair_coeff * *"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -108,12 +110,12 @@ TEST_F(PairUnitConvertTest, zero) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style zero 6.0"); - lmp->input->one("pair_coeff * *"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style zero 6.0"); + command("pair_coeff * *"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -134,15 +136,15 @@ TEST_F(PairUnitConvertTest, lj_cut) if (!info->has_style("pair", "lj/cut")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style lj/cut 6.0"); - lmp->input->one("pair_coeff * * 0.01014286346782117 2.0"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style lj/cut 6.0"); + command("pair_coeff * * 0.01014286346782117 2.0"); remove("test.table.metal"); - lmp->input->one("pair_write 1 1 1000 r 0.1 6.0 test.table.metal lj_1_1"); - lmp->input->one("pair_write 1 2 1000 r 0.1 6.0 test.table.metal lj_1_2"); - lmp->input->one("pair_write 2 2 1000 r 0.1 6.0 test.table.metal lj_2_2"); - lmp->input->one("run 0 post no"); + command("pair_write 1 1 1000 r 0.1 6.0 test.table.metal lj_1_1"); + command("pair_write 1 2 1000 r 0.1 6.0 test.table.metal lj_1_2"); + command("pair_write 2 2 1000 r 0.1 6.0 test.table.metal lj_2_2"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -155,16 +157,16 @@ TEST_F(PairUnitConvertTest, lj_cut) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style lj/cut 6.0"); - lmp->input->one("pair_coeff * * 0.2339 2.0"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style lj/cut 6.0"); + command("pair_coeff * * 0.2339 2.0"); remove("test.table.real"); - lmp->input->one("pair_write 1 1 1000 r 0.1 6.0 test.table.real lj_1_1"); - lmp->input->one("pair_write 1 2 1000 r 0.1 6.0 test.table.real lj_1_2"); - lmp->input->one("pair_write 2 2 1000 r 0.1 6.0 test.table.real lj_2_2"); - lmp->input->one("run 0 post no"); + command("pair_write 1 1 1000 r 0.1 6.0 test.table.real lj_1_1"); + command("pair_write 1 2 1000 r 0.1 6.0 test.table.real lj_1_2"); + command("pair_write 2 2 1000 r 0.1 6.0 test.table.real lj_2_2"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -185,11 +187,11 @@ TEST_F(PairUnitConvertTest, eam) if (!info->has_style("pair", "eam")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style eam"); - lmp->input->one("pair_coeff * * Cu_u3.eam"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style eam"); + command("pair_coeff * * Cu_u3.eam"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -202,12 +204,12 @@ TEST_F(PairUnitConvertTest, eam) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style eam"); - lmp->input->one("pair_coeff * * Cu_u3.eam"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style eam"); + command("pair_coeff * * Cu_u3.eam"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -228,11 +230,11 @@ TEST_F(PairUnitConvertTest, eam_alloy) if (!info->has_style("pair", "eam/alloy")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style eam/alloy"); - lmp->input->one("pair_coeff * * AlCu.eam.alloy Al Cu"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style eam/alloy"); + command("pair_coeff * * AlCu.eam.alloy Al Cu"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -245,12 +247,12 @@ TEST_F(PairUnitConvertTest, eam_alloy) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style eam/alloy"); - lmp->input->one("pair_coeff * * AlCu.eam.alloy Al Cu"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style eam/alloy"); + command("pair_coeff * * AlCu.eam.alloy Al Cu"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -271,11 +273,11 @@ TEST_F(PairUnitConvertTest, eam_fs) if (!info->has_style("pair", "eam/fs")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style eam/fs"); - lmp->input->one("pair_coeff * * FeP_mm.eam.fs Fe P"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style eam/fs"); + command("pair_coeff * * FeP_mm.eam.fs Fe P"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -288,12 +290,12 @@ TEST_F(PairUnitConvertTest, eam_fs) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style eam/fs"); - lmp->input->one("pair_coeff * * FeP_mm.eam.fs Fe P"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style eam/fs"); + command("pair_coeff * * FeP_mm.eam.fs Fe P"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -314,11 +316,11 @@ TEST_F(PairUnitConvertTest, eam_cd) if (!info->has_style("pair", "eam/cd")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style eam/cd"); - lmp->input->one("pair_coeff * * FeCr.cdeam Cr Fe"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style eam/cd"); + command("pair_coeff * * FeCr.cdeam Cr Fe"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -331,12 +333,12 @@ TEST_F(PairUnitConvertTest, eam_cd) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style eam/cd"); - lmp->input->one("pair_coeff * * FeCr.cdeam Cr Fe"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style eam/cd"); + command("pair_coeff * * FeCr.cdeam Cr Fe"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -357,11 +359,11 @@ TEST_F(PairUnitConvertTest, eim) if (!info->has_style("pair", "eim")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style eim"); - lmp->input->one("pair_coeff * * Na Cl ffield.eim Na Cl"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style eim"); + command("pair_coeff * * Na Cl ffield.eim Na Cl"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -374,12 +376,12 @@ TEST_F(PairUnitConvertTest, eim) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style eim"); - lmp->input->one("pair_coeff * * Na Cl ffield.eim Na Cl"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style eim"); + command("pair_coeff * * Na Cl ffield.eim Na Cl"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -400,11 +402,11 @@ TEST_F(PairUnitConvertTest, gw) if (!info->has_style("pair", "gw")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style gw"); - lmp->input->one("pair_coeff * * SiC.gw Si C"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style gw"); + command("pair_coeff * * SiC.gw Si C"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -417,12 +419,12 @@ TEST_F(PairUnitConvertTest, gw) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style gw"); - lmp->input->one("pair_coeff * * SiC.gw Si C"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style gw"); + command("pair_coeff * * SiC.gw Si C"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -443,11 +445,11 @@ TEST_F(PairUnitConvertTest, gw_zbl) if (!info->has_style("pair", "gw/zbl")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style gw/zbl"); - lmp->input->one("pair_coeff * * SiC.gw.zbl Si C"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style gw/zbl"); + command("pair_coeff * * SiC.gw.zbl Si C"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -460,12 +462,12 @@ TEST_F(PairUnitConvertTest, gw_zbl) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style gw/zbl"); - lmp->input->one("pair_coeff * * SiC.gw.zbl Si C"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style gw/zbl"); + command("pair_coeff * * SiC.gw.zbl Si C"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -486,11 +488,11 @@ TEST_F(PairUnitConvertTest, nb3b_harmonic) if (!info->has_style("pair", "nb3b/harmonic")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style nb3b/harmonic"); - lmp->input->one("pair_coeff * * MOH.nb3b.harmonic M O"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style nb3b/harmonic"); + command("pair_coeff * * MOH.nb3b.harmonic M O"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -503,12 +505,12 @@ TEST_F(PairUnitConvertTest, nb3b_harmonic) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style nb3b/harmonic"); - lmp->input->one("pair_coeff * * MOH.nb3b.harmonic M O"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style nb3b/harmonic"); + command("pair_coeff * * MOH.nb3b.harmonic M O"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -529,11 +531,11 @@ TEST_F(PairUnitConvertTest, sw) if (!info->has_style("pair", "sw")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style sw"); - lmp->input->one("pair_coeff * * GaN.sw Ga N"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style sw"); + command("pair_coeff * * GaN.sw Ga N"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -546,12 +548,12 @@ TEST_F(PairUnitConvertTest, sw) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style sw"); - lmp->input->one("pair_coeff * * GaN.sw Ga N"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style sw"); + command("pair_coeff * * GaN.sw Ga N"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -572,13 +574,13 @@ TEST_F(PairUnitConvertTest, table_metal2real) if (!info->has_style("pair", "table")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style table linear 1000"); - lmp->input->one("pair_coeff 1 1 test.table.metal lj_1_1"); - lmp->input->one("pair_coeff 1 2 test.table.metal lj_1_2"); - lmp->input->one("pair_coeff 2 2 test.table.metal lj_2_2"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style table linear 1000"); + command("pair_coeff 1 1 test.table.metal lj_1_1"); + command("pair_coeff 1 2 test.table.metal lj_1_2"); + command("pair_coeff 2 2 test.table.metal lj_2_2"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -591,14 +593,14 @@ TEST_F(PairUnitConvertTest, table_metal2real) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style table linear 1000"); - lmp->input->one("pair_coeff 1 1 test.table.metal lj_1_1"); - lmp->input->one("pair_coeff 1 2 test.table.metal lj_1_2"); - lmp->input->one("pair_coeff 2 2 test.table.metal lj_2_2"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style table linear 1000"); + command("pair_coeff 1 1 test.table.metal lj_1_1"); + command("pair_coeff 1 2 test.table.metal lj_1_2"); + command("pair_coeff 2 2 test.table.metal lj_2_2"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -619,13 +621,13 @@ TEST_F(PairUnitConvertTest, table_real2metal) if (!info->has_style("pair", "table")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style table linear 1000"); - lmp->input->one("pair_coeff 1 1 test.table.real lj_1_1"); - lmp->input->one("pair_coeff 1 2 test.table.real lj_1_2"); - lmp->input->one("pair_coeff 2 2 test.table.real lj_2_2"); - lmp->input->one("run 0 post no"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style table linear 1000"); + command("pair_coeff 1 1 test.table.real lj_1_1"); + command("pair_coeff 1 2 test.table.real lj_1_2"); + command("pair_coeff 2 2 test.table.real lj_2_2"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -638,14 +640,14 @@ TEST_F(PairUnitConvertTest, table_real2metal) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style table linear 1000"); - lmp->input->one("pair_coeff 1 1 test.table.real lj_1_1"); - lmp->input->one("pair_coeff 1 2 test.table.real lj_1_2"); - lmp->input->one("pair_coeff 2 2 test.table.real lj_2_2"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style table linear 1000"); + command("pair_coeff 1 1 test.table.real lj_1_1"); + command("pair_coeff 1 2 test.table.real lj_1_2"); + command("pair_coeff 2 2 test.table.real lj_2_2"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -666,11 +668,11 @@ TEST_F(PairUnitConvertTest, tersoff) if (!info->has_style("pair", "tersoff")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style tersoff"); - lmp->input->one("pair_coeff * * SiC.tersoff Si C"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style tersoff"); + command("pair_coeff * * SiC.tersoff Si C"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -683,12 +685,12 @@ TEST_F(PairUnitConvertTest, tersoff) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style tersoff"); - lmp->input->one("pair_coeff * * SiC.tersoff Si C"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style tersoff"); + command("pair_coeff * * SiC.tersoff Si C"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -709,11 +711,11 @@ TEST_F(PairUnitConvertTest, tersoff_mod) if (!info->has_style("pair", "tersoff/mod")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style tersoff/mod"); - lmp->input->one("pair_coeff * * Si.tersoff.mod Si Si"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style tersoff/mod"); + command("pair_coeff * * Si.tersoff.mod Si Si"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -726,12 +728,12 @@ TEST_F(PairUnitConvertTest, tersoff_mod) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style tersoff/mod"); - lmp->input->one("pair_coeff * * Si.tersoff.mod Si Si"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style tersoff/mod"); + command("pair_coeff * * Si.tersoff.mod Si Si"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -752,11 +754,11 @@ TEST_F(PairUnitConvertTest, tersoff_mod_c) if (!info->has_style("pair", "tersoff/mod/c")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style tersoff/mod/c"); - lmp->input->one("pair_coeff * * Si.tersoff.modc Si Si"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style tersoff/mod/c"); + command("pair_coeff * * Si.tersoff.modc Si Si"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -769,12 +771,12 @@ TEST_F(PairUnitConvertTest, tersoff_mod_c) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style tersoff/mod/c"); - lmp->input->one("pair_coeff * * Si.tersoff.modc Si Si"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style tersoff/mod/c"); + command("pair_coeff * * Si.tersoff.modc Si Si"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -795,11 +797,11 @@ TEST_F(PairUnitConvertTest, tersoff_table) if (!info->has_style("pair", "tersoff/table")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style tersoff/table"); - lmp->input->one("pair_coeff * * SiC.tersoff Si C"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style tersoff/table"); + command("pair_coeff * * SiC.tersoff Si C"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -812,12 +814,12 @@ TEST_F(PairUnitConvertTest, tersoff_table) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style tersoff/table"); - lmp->input->one("pair_coeff * * SiC.tersoff Si C"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style tersoff/table"); + command("pair_coeff * * SiC.tersoff Si C"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -838,11 +840,11 @@ TEST_F(PairUnitConvertTest, tersoff_zbl) if (!info->has_style("pair", "tersoff/zbl")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style tersoff/zbl"); - lmp->input->one("pair_coeff * * SiC.tersoff.zbl Si C"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style tersoff/zbl"); + command("pair_coeff * * SiC.tersoff.zbl Si C"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -855,12 +857,12 @@ TEST_F(PairUnitConvertTest, tersoff_zbl) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style tersoff/zbl"); - lmp->input->one("pair_coeff * * SiC.tersoff.zbl Si C"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style tersoff/zbl"); + command("pair_coeff * * SiC.tersoff.zbl Si C"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -881,12 +883,12 @@ TEST_F(PairUnitConvertTest, tersoff_zbl_omp) if (!info->has_style("pair", "tersoff/zbl/omp")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("package omp 4"); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style tersoff/zbl/omp"); - lmp->input->one("pair_coeff * * SiC.tersoff.zbl Si C"); - lmp->input->one("run 0 post no"); + command("package omp 4"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style tersoff/zbl/omp"); + command("pair_coeff * * SiC.tersoff.zbl Si C"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -899,13 +901,13 @@ TEST_F(PairUnitConvertTest, tersoff_zbl_omp) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("package omp 4"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style tersoff/zbl/omp"); - lmp->input->one("pair_coeff * * SiC.tersoff.zbl Si C"); - lmp->input->one("run 0 post no"); + command("clear"); + command("package omp 4"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style tersoff/zbl/omp"); + command("pair_coeff * * SiC.tersoff.zbl Si C"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; @@ -926,11 +928,11 @@ TEST_F(PairUnitConvertTest, vashishta) if (!info->has_style("pair", "vashishta")) GTEST_SKIP(); if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style vashishta"); - lmp->input->one("pair_coeff * * SiC.vashishta Si C"); - lmp->input->one("run 0 post no"); + command("units metal"); + command("read_data test_pair_unit_convert.data"); + command("pair_style vashishta"); + command("pair_coeff * * SiC.vashishta Si C"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); // copy pressure, energy, and force from first step @@ -943,12 +945,12 @@ TEST_F(PairUnitConvertTest, vashishta) fold[i][j] = f[i][j]; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("clear"); - lmp->input->one("units real"); - lmp->input->one("read_data test_pair_unit_convert.data"); - lmp->input->one("pair_style vashishta"); - lmp->input->one("pair_coeff * * SiC.vashishta Si C"); - lmp->input->one("run 0 post no"); + command("clear"); + command("units real"); + command("read_data test_pair_unit_convert.data"); + command("pair_style vashishta"); + command("pair_coeff * * SiC.vashishta Si C"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); double pnew; diff --git a/unittest/formats/test_potential_file_reader.cpp b/unittest/formats/test_potential_file_reader.cpp index 4279c8d1a7..6cf2fd010c 100644 --- a/unittest/formats/test_potential_file_reader.cpp +++ b/unittest/formats/test_potential_file_reader.cpp @@ -96,13 +96,15 @@ protected: delete lmp; if (!verbose) ::testing::internal::GetCapturedStdout(); } + + void command(const std::string &cmd) { lmp->input->one(cmd); } }; // open for native units TEST_F(PotentialFileReaderTest, Sw_native) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); + command("units metal"); PotentialFileReader reader(lmp, "Si.sw", "Stillinger-Weber"); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -114,7 +116,7 @@ TEST_F(PotentialFileReaderTest, Sw_native) TEST_F(PotentialFileReaderTest, Sw_conv) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units real"); + command("units real"); PotentialFileReader reader(lmp, "Si.sw", "Stillinger-Weber", utils::METAL2REAL); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -126,7 +128,7 @@ TEST_F(PotentialFileReaderTest, Sw_conv) TEST_F(PotentialFileReaderTest, Sw_noconv) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units real"); + command("units real"); if (!verbose) ::testing::internal::GetCapturedStdout(); TEST_FAILURE(".*ERROR on proc.*potential.*requires metal units but real.*", @@ -136,7 +138,7 @@ TEST_F(PotentialFileReaderTest, Sw_noconv) TEST_F(PotentialFileReaderTest, Comb) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); + command("units metal"); PotentialFileReader reader(lmp, "ffield.comb", "COMB"); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -147,7 +149,7 @@ TEST_F(PotentialFileReaderTest, Comb) TEST_F(PotentialFileReaderTest, Comb3) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); + command("units metal"); PotentialFileReader reader(lmp, "ffield.comb3", "COMB3"); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -158,7 +160,7 @@ TEST_F(PotentialFileReaderTest, Comb3) TEST_F(PotentialFileReaderTest, Tersoff) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); + command("units metal"); PotentialFileReader reader(lmp, "Si.tersoff", "Tersoff"); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -169,7 +171,7 @@ TEST_F(PotentialFileReaderTest, Tersoff) TEST_F(PotentialFileReaderTest, TersoffMod) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); + command("units metal"); PotentialFileReader reader(lmp, "Si.tersoff.mod", "Tersoff/Mod"); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -180,7 +182,7 @@ TEST_F(PotentialFileReaderTest, TersoffMod) TEST_F(PotentialFileReaderTest, TersoffModC) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); + command("units metal"); PotentialFileReader reader(lmp, "Si.tersoff.modc", "Tersoff/ModC"); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -191,7 +193,7 @@ TEST_F(PotentialFileReaderTest, TersoffModC) TEST_F(PotentialFileReaderTest, TersoffTable) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); + command("units metal"); PotentialFileReader reader(lmp, "Si.tersoff", "TersoffTable"); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -202,7 +204,7 @@ TEST_F(PotentialFileReaderTest, TersoffTable) TEST_F(PotentialFileReaderTest, TersoffZBL) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); + command("units metal"); PotentialFileReader reader(lmp, "SiC.tersoff.zbl", "Tersoff/ZBL"); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -213,7 +215,7 @@ TEST_F(PotentialFileReaderTest, TersoffZBL) TEST_F(PotentialFileReaderTest, GW) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); + command("units metal"); PotentialFileReader reader(lmp, "SiC.gw", "GW"); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -224,7 +226,7 @@ TEST_F(PotentialFileReaderTest, GW) TEST_F(PotentialFileReaderTest, GWZBL) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); + command("units metal"); PotentialFileReader reader(lmp, "SiC.gw.zbl", "GW/ZBL"); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -235,7 +237,7 @@ TEST_F(PotentialFileReaderTest, GWZBL) TEST_F(PotentialFileReaderTest, Nb3bHarmonic) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units real"); + command("units real"); PotentialFileReader reader(lmp, "MOH.nb3b.harmonic", "NB3B Harmonic"); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -246,7 +248,7 @@ TEST_F(PotentialFileReaderTest, Nb3bHarmonic) TEST_F(PotentialFileReaderTest, Vashishta) { if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); + command("units metal"); PotentialFileReader reader(lmp, "SiC.vashishta", "Vashishta"); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -260,7 +262,7 @@ TEST_F(PotentialFileReaderTest, UnitConvert) int unit_convert, flag; if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("units metal"); + command("units metal"); reader = new PotentialFileReader(lmp, "Si.sw", "Stillinger-Weber"); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -288,7 +290,7 @@ TEST_F(PotentialFileReaderTest, UnitConvert) if (!verbose) ::testing::internal::CaptureStdout(); flag = utils::get_supported_conversions(utils::ENERGY); - lmp->input->one("units real"); + command("units real"); reader = new PotentialFileReader(lmp, "Si.sw", "Stillinger-Weber", flag); if (!verbose) ::testing::internal::GetCapturedStdout(); diff --git a/unittest/utils/test_tokenizer.cpp b/unittest/utils/test_tokenizer.cpp index de7472599c..69ec7a55d2 100644 --- a/unittest/utils/test_tokenizer.cpp +++ b/unittest/utils/test_tokenizer.cpp @@ -112,7 +112,7 @@ TEST(Tokenizer, as_vector1) TEST(Tokenizer, as_vector2) { - auto list = Tokenizer("a\\b\\c","\\").as_vector(); + auto list = Tokenizer("a\\b\\c", "\\").as_vector(); ASSERT_THAT(list[0], Eq("a")); ASSERT_THAT(list[1], Eq("b")); ASSERT_THAT(list[2], Eq("c")); @@ -121,14 +121,14 @@ TEST(Tokenizer, as_vector2) TEST(Tokenizer, as_vector3) { - auto list = Tokenizer ("a\\","\\").as_vector(); + auto list = Tokenizer("a\\", "\\").as_vector(); ASSERT_THAT(list[0], Eq("a")); ASSERT_EQ(list.size(), 1); } TEST(Tokenizer, as_vector4) { - auto list = Tokenizer ("\\a","\\").as_vector(); + auto list = Tokenizer("\\a", "\\").as_vector(); ASSERT_THAT(list[0], Eq("a")); ASSERT_EQ(list.size(), 1); } diff --git a/unittest/utils/test_utils.cpp b/unittest/utils/test_utils.cpp index 2fa17a5e5a..56a88e330a 100644 --- a/unittest/utils/test_utils.cpp +++ b/unittest/utils/test_utils.cpp @@ -533,10 +533,12 @@ TEST(Utils, strfind_dot) TEST(Utils, strfind_kim) { - ASSERT_THAT(utils::strfind("n3409jfse MO_004835508849_000 aslfjiaf", - "[MS][MO]_\\d\\d\\d+_\\d\\d\\d"), StrEq("MO_004835508849_000")); + ASSERT_THAT( + utils::strfind("n3409jfse MO_004835508849_000 aslfjiaf", "[MS][MO]_\\d\\d\\d+_\\d\\d\\d"), + StrEq("MO_004835508849_000")); ASSERT_THAT(utils::strfind("VanDuinChakraborty_2003_CHNO__SM_107643900657_000", - "[MS][MO]_\\d\\d\\d+_\\d\\d\\d"), StrEq("SM_107643900657_000")); + "[MS][MO]_\\d\\d\\d+_\\d\\d\\d"), + StrEq("SM_107643900657_000")); } TEST(Utils, bounds_case1) From 51946205ce2b4f90c9b4d1c65a7fca6b9090e5a2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Mar 2021 12:18:12 -0400 Subject: [PATCH 0244/1217] add YAML files for MLIAP nn and quadratic snap model input --- .../tests/manybody-pair-mliap_nn.yaml | 158 ++++++++++++++++++ ...l => manybody-pair-mliap_snap_linear.yaml} | 0 .../manybody-pair-mliap_snap_quadratic.yaml | 158 ++++++++++++++++++ 3 files changed, 316 insertions(+) create mode 100644 unittest/force-styles/tests/manybody-pair-mliap_nn.yaml rename unittest/force-styles/tests/{manybody-pair-mliap_snap.yaml => manybody-pair-mliap_snap_linear.yaml} (100%) create mode 100644 unittest/force-styles/tests/manybody-pair-mliap_snap_quadratic.yaml diff --git a/unittest/force-styles/tests/manybody-pair-mliap_nn.yaml b/unittest/force-styles/tests/manybody-pair-mliap_nn.yaml new file mode 100644 index 0000000000..5270c9571f --- /dev/null +++ b/unittest/force-styles/tests/manybody-pair-mliap_nn.yaml @@ -0,0 +1,158 @@ +--- +lammps_version: 10 Mar 2021 +date_generated: Wed Mar 24 12:18:23 202 +epsilon: 5e-13 +prerequisites: ! | + pair mliap + pair zbl +pre_commands: ! | + variable newton_pair delete + variable newton_pair index on +post_commands: ! "" +input_file: in.manybody +pair_style: hybrid/overlay zbl 4.0 4.8 mliap model nn Ta06A.nn.mliap.model descriptor + sna Ta06A.mliap.descriptor +pair_coeff: ! | + 1*8 1*8 zbl 73 73 + * * mliap Ta Ta Ta Ta Ta Ta Ta Ta +extract: ! 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+ pair mliap + pair zbl +pre_commands: ! | + variable newton_pair delete + variable newton_pair index on +post_commands: ! "" +input_file: in.manybody +pair_style: hybrid/overlay zbl 4.0 4.8 mliap model quadratic W.quadratic.mliap.model + descriptor sna W.quadratic.mliap.descriptor +pair_coeff: ! | + 1*8 1*8 zbl 74 74 + * * mliap W W W W W W W W +extract: ! 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From 9d3e37b1028b16ba14c3fed101e10036440333fd Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 24 Mar 2021 12:43:47 -0400 Subject: [PATCH 0245/1217] Add more python variable tests --- unittest/python/func.py | 10 ++-- unittest/python/test_python_package.cpp | 65 ++++++++++++++++++++++++- 2 files changed, 71 insertions(+), 4 deletions(-) diff --git a/unittest/python/func.py b/unittest/python/func.py index 27704660a6..cc2269c435 100644 --- a/unittest/python/func.py +++ b/unittest/python/func.py @@ -4,6 +4,11 @@ from __future__ import print_function def square(val): return val*val +def bool_to_val(txt): + if txt.upper() in ["TRUE", "YES"]: + return 1.0 + return 0.0 + def printnum(): print("2.25") @@ -11,8 +16,7 @@ def printtxt(): print("sometext") def getidxvar(lmpptr): - from lammps import lammps, LMP_VAR_EQUAL + from lammps import lammps lmp = lammps(ptr=lmpptr) - - val = lmp.extract_variable("idx",None,LMP_VAR_EQUAL) + val = lmp.extract_variable("idx") print(val) diff --git a/unittest/python/test_python_package.cpp b/unittest/python/test_python_package.cpp index 137278a9d2..a7cf52c74e 100644 --- a/unittest/python/test_python_package.cpp +++ b/unittest/python/test_python_package.cpp @@ -14,6 +14,7 @@ #include "atom.h" #include "info.h" #include "input.h" +#include "variable.h" #include "gmock/gmock.h" #include "gtest/gtest.h" @@ -58,6 +59,13 @@ protected: return output; } + double get_variable_value(const std::string & name) { + char * str = utils::strdup(fmt::format("v_{}", name)); + double value = lmp->input->variable->compute_equal(str); + delete [] str; + return value; + } + void SetUp() override { const char *args[] = {"PythonPackageTest", "-log", "none", "-echo", "screen", "-nocite"}; @@ -100,13 +108,67 @@ TEST_F(PythonPackageTest, InvokeFunctionFromFile) HIDE_OUTPUT([&] { command("python printnum file ${input_dir}/func.py"); }); - + auto output = CAPTURE_OUTPUT([&]() { command("python printnum invoke"); }); ASSERT_THAT(output, HasSubstr("2.25\n")); } +TEST_F(PythonPackageTest, InvokeFunctionPassInt) +{ + // execute python function, passing integer as argument + HIDE_OUTPUT([&] { + command("variable sq python square"); + command("python square input 1 2 format ii return v_sq file ${input_dir}/func.py"); + }); + + ASSERT_EQ(get_variable_value("sq"), 4.0); +} + +TEST_F(PythonPackageTest, InvokeFunctionPassFloat) +{ + // execute python function, passing float as argument + HIDE_OUTPUT([&] { + command("variable sq python square"); + command("python square input 1 2.5 format ff return v_sq file ${input_dir}/func.py"); + }); + + ASSERT_EQ(get_variable_value("sq"), 6.25); +} + +TEST_F(PythonPackageTest, InvokeFunctionPassString) +{ + // execute python function, passing string as argument + HIDE_OUTPUT([&] { + command("variable val python bool_to_val"); + command("python bool_to_val input 1 \"true\" format sf return v_val file ${input_dir}/func.py"); + }); + + ASSERT_EQ(get_variable_value("val"), 1.0); +} + +TEST_F(PythonPackageTest, InvokeFunctionPassStringVariable) +{ + // execute python function, passing string variable as argument + HIDE_OUTPUT([&] { + command("variable val python bool_to_val"); + command("python bool_to_val input 1 v_str format sf return v_val file ${input_dir}/func.py"); + }); + + HIDE_OUTPUT([&] { + command("variable str string \"true\""); + }); + + ASSERT_EQ(get_variable_value("val"), 1.0); + + HIDE_OUTPUT([&] { + command("variable str string \"false\""); + }); + + ASSERT_EQ(get_variable_value("val"), 0.0); +} + TEST_F(PythonPackageTest, InvokeOtherFunctionFromFile) { // execute another python function from same file @@ -137,6 +199,7 @@ TEST_F(PythonPackageTest, InvokeFunctionThatUsesLAMMPSModule) TEST_F(PythonPackageTest, python_variable) { + // define variable that evaluates a python function HIDE_OUTPUT([&] { command("variable sq python square"); command("variable val index 1.5"); From cc54f553e0d09ecaa0a15881f1598c33765d2d9c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Mar 2021 14:35:48 -0400 Subject: [PATCH 0246/1217] complete tests for if command booleans --- unittest/commands/test_variables.cpp | 56 ++++++++++++++++++++++++++-- 1 file changed, 52 insertions(+), 4 deletions(-) diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 7106867894..37856184eb 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -295,19 +295,25 @@ TEST_F(VariableTest, IfCommand) if (!verbose) ::testing::internal::GetCapturedStdout(); ::testing::internal::CaptureStdout(); - command("if 1>0 then 'print \".*bingo!\"'"); + command("if 1>0 then 'print \"bingo!\"'"); auto text = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << text; ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); ::testing::internal::CaptureStdout(); - command("if (1>=0) then 'print \"bingo!\"'"); + command("if 1>2 then 'print \"bingo!\"' else 'print \"nope?\"'"); text = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << text; - ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); + ASSERT_THAT(text, MatchesRegex(".*nope\?.*")); ::testing::internal::CaptureStdout(); - command("if (-1.0e-1<0.0E+0) then 'print \"bingo!\"'"); + command("if (1<=0) then 'print \"bingo!\"' else 'print \"nope?\"'"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*nope\?.*")); + + ::testing::internal::CaptureStdout(); + command("if (-1.0e-1<0.0E+0)|^(1<0) then 'print \"bingo!\"'"); text = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << text; ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); @@ -324,8 +330,50 @@ TEST_F(VariableTest, IfCommand) if (verbose) std::cout << text; ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); + ::testing::internal::CaptureStdout(); + command("if (1>=2)&&(0&&1) then 'print \"missed\"' else 'print \"bingo!\"'"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); + + ::testing::internal::CaptureStdout(); + command("if !1 then 'print \"missed\"' else 'print \"bingo!\"'"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); + + ::testing::internal::CaptureStdout(); + command("if !(a==b) then 'print \"bingo!\"'"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); + + ::testing::internal::CaptureStdout(); + command("if x==x|^1==0 then 'print \"bingo!\"'"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); + + ::testing::internal::CaptureStdout(); + command("if x!=x|^a!=b then 'print \"bingo!\"'"); + text = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << text; + ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); + TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", command("if () then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", + command("if \"1 1\" then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", + command("if 1a then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", + command("if 1=<2 then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", + command("if 1!=a then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", + command("if 1&<2 then 'print \"bingo!\"'");); + TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", + command("if 1|<2 then 'print \"bingo!\"'");); TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", command("if (1)( then 'print \"bingo!\"'");); TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", From 407212153ff8a6d24d28dc12d86f209690a406c7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Mar 2021 15:14:58 -0400 Subject: [PATCH 0247/1217] create more variables of different styles --- unittest/commands/test_variables.cpp | 25 ++++++++++++++++++++++--- 1 file changed, 22 insertions(+), 3 deletions(-) diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 37856184eb..c558e02376 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -168,17 +168,22 @@ TEST_F(VariableTest, CreateDelete) command("variable nine file test_variable.file"); command("variable ten internal 1.0"); command("variable ten internal 10.0"); + command("variable ten1 universe 1 2 3 4"); + command("variable ten2 uloop 4"); + command("variable ten3 uloop 4 pad"); command("variable dummy index 0"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 13); + ASSERT_EQ(variable->nvar, 16); if (!verbose) ::testing::internal::CaptureStdout(); command("variable dummy delete"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 12); + ASSERT_EQ(variable->nvar, 15); TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable");); TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable dummy index");); TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable dummy delete xxx");); + TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable dummy loop -1");); + TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable dummy loop 10 1");); TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", command("variable two string xxx");); TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", @@ -191,6 +196,12 @@ TEST_F(VariableTest, CreateDelete) command("variable eleven atomfile test_variable.atomfile");); TEST_FAILURE(".*ERROR on proc 0: Cannot open file variable file test_variable.xxx.*", command("variable nine1 file test_variable.xxx");); + TEST_FAILURE(".*ERROR: World variable count doesn't match # of partitions.*", + command("variable ten10 world xxx xxx");); + TEST_FAILURE(".*ERROR: All universe/uloop variables must have same # of values.*", + command("variable ten4 uloop 2");); + TEST_FAILURE(".*ERROR: Incorrect conversion in format string.*", + command("variable ten11 format two \"%08f\"");); } TEST_F(VariableTest, AtomicSystem) @@ -204,8 +215,16 @@ TEST_F(VariableTest, AtomicSystem) command("variable id atom type"); command("variable id atom id"); command("variable ten atomfile test_variable.atomfile"); + command("compute press all pressure NULL pair"); + command("fix press all ave/time 1 1 1 c_press mode vector"); + command("variable press vector f_press"); + command("variable stress vector v_press+vol"); + command("variable pmax equal max(f_press)"); + command("run 0 post no"); + if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 3); + ASSERT_EQ(variable->nvar, 6); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_pmax"), 0.0); TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", command("variable one atom x");); From 1c9c46d2c1811531a18b05b10ec0f33f8104ecee Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 24 Mar 2021 15:42:38 -0400 Subject: [PATCH 0248/1217] Add tests to cover python command --- src/PYTHON/python_impl.cpp | 1 + unittest/python/func.py | 8 ++ unittest/python/run.py | 2 + unittest/python/test_python_package.cpp | 100 +++++++++++++++++++++++- 4 files changed, 110 insertions(+), 1 deletion(-) create mode 100644 unittest/python/run.py diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index 1f45ca6635..4c43ca3744 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -506,6 +506,7 @@ int PythonImpl::create_entry(char *name) "cannot be used unless output is a string"); pfuncs[ifunc].length_longstr = length_longstr; pfuncs[ifunc].longstr = new char[length_longstr+1]; + pfuncs[ifunc].longstr[length_longstr] = '\0'; } if (strstr(ostr,"v_") != ostr) error->all(FLERR,"Invalid python command"); diff --git a/unittest/python/func.py b/unittest/python/func.py index cc2269c435..cf8db41670 100644 --- a/unittest/python/func.py +++ b/unittest/python/func.py @@ -9,6 +9,11 @@ def bool_to_val(txt): return 1.0 return 0.0 +def val_to_bool(val): + if val != 0: + return "True" + return "False" + def printnum(): print("2.25") @@ -20,3 +25,6 @@ def getidxvar(lmpptr): lmp = lammps(ptr=lmpptr) val = lmp.extract_variable("idx") print(val) + +def longstr(): + return "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent metus." diff --git a/unittest/python/run.py b/unittest/python/run.py new file mode 100644 index 0000000000..7cdb205f50 --- /dev/null +++ b/unittest/python/run.py @@ -0,0 +1,2 @@ +from __future__ import print_function +print("Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent metus.") diff --git a/unittest/python/test_python_package.cpp b/unittest/python/test_python_package.cpp index a7cf52c74e..f7a184b6b3 100644 --- a/unittest/python/test_python_package.cpp +++ b/unittest/python/test_python_package.cpp @@ -15,6 +15,7 @@ #include "info.h" #include "input.h" #include "variable.h" +#include "library.h" #include "gmock/gmock.h" #include "gtest/gtest.h" @@ -31,11 +32,14 @@ std::string INPUT_FOLDER = STRINGIFY(TEST_INPUT_FOLDER); // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; +const char * LOREM_IPSUM = "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent metus."; + using LAMMPS_NS::utils::split_words; namespace LAMMPS_NS { using ::testing::MatchesRegex; using ::testing::StrEq; +using ::testing::Eq; using ::testing::HasSubstr; class PythonPackageTest : public ::testing::Test { @@ -45,6 +49,8 @@ protected: void command(const std::string &line) { lmp->input->one(line.c_str()); } + void command_string(const std::string &lines) { lammps_commands_string(lmp, lines.c_str()); } + void HIDE_OUTPUT(std::function f) { if (!verbose) ::testing::internal::CaptureStdout(); f(); @@ -66,6 +72,10 @@ protected: return value; } + std::string get_variable_string(const std::string & name) { + return lmp->input->variable->retrieve(name.c_str()); + } + void SetUp() override { const char *args[] = {"PythonPackageTest", "-log", "none", "-echo", "screen", "-nocite"}; @@ -121,6 +131,7 @@ TEST_F(PythonPackageTest, InvokeFunctionPassInt) HIDE_OUTPUT([&] { command("variable sq python square"); command("python square input 1 2 format ii return v_sq file ${input_dir}/func.py"); + command("python square invoke"); }); ASSERT_EQ(get_variable_value("sq"), 4.0); @@ -169,6 +180,38 @@ TEST_F(PythonPackageTest, InvokeFunctionPassStringVariable) ASSERT_EQ(get_variable_value("val"), 0.0); } +TEST_F(PythonPackageTest, InvokeStringFunction) +{ + // execute python function, passing string variable as argument + HIDE_OUTPUT([&] { + command("variable str python val_to_bool"); + command("python val_to_bool input 1 v_val format is return v_str file ${input_dir}/func.py"); + }); + + HIDE_OUTPUT([&] { + command("variable val equal 0"); + }); + + ASSERT_THAT(get_variable_string("str"), StrEq("False")); + + HIDE_OUTPUT([&] { + command("variable val equal 1"); + }); + + ASSERT_THAT(get_variable_string("str"), StrEq("True")); +} + +TEST_F(PythonPackageTest, InvokeLongStringFunction) +{ + // execute python function, passing string variable as argument + HIDE_OUTPUT([&] { + command("variable str python longstr"); + command("python longstr format s length 72 return v_str file ${input_dir}/func.py"); + }); + + ASSERT_THAT(get_variable_string("str"), StrEq(LOREM_IPSUM)); +} + TEST_F(PythonPackageTest, InvokeOtherFunctionFromFile) { // execute another python function from same file @@ -211,6 +254,61 @@ TEST_F(PythonPackageTest, python_variable) ASSERT_THAT(output, MatchesRegex("print.*2.25.*")); } +TEST_F(PythonPackageTest, InlineFunction) +{ + // define variable that evaluates a python function + HIDE_OUTPUT([&] { + command("variable fact python factorial"); + command("python factorial input 1 v_n return v_fact format ii here \"\"\"\n" + "def factorial(n):\n" + " if n == 0 or n == 1: return 1\n" + " return n*factorial(n-1)\n" + "\"\"\""); + }); + + HIDE_OUTPUT([&] { + command("variable n equal 1"); + }); + + ASSERT_EQ(get_variable_value("fact"), 1.0); + + HIDE_OUTPUT([&] { + command("variable n equal 2"); + }); + + ASSERT_EQ(get_variable_value("fact"), 2.0); + + HIDE_OUTPUT([&] { + command("variable n equal 3"); + }); + + ASSERT_EQ(get_variable_value("fact"), 6.0); +} + +TEST_F(PythonPackageTest, RunSource) +{ + // execute python script from file + auto output = CAPTURE_OUTPUT([&] { + command("python xyz source ${input_dir}/run.py"); + }); + + ASSERT_THAT(output, HasSubstr(LOREM_IPSUM)); +} + +TEST_F(PythonPackageTest, RunSourceInline) +{ + // execute inline python script + auto output = CAPTURE_OUTPUT([&] { + command("python xyz source \"\"\"\n" + "from __future__ import print_function\n" + "print(2+2)\n" + "\"\"\"" + ); + }); + + ASSERT_THAT(output, HasSubstr("4")); +} + } // namespace LAMMPS_NS int main(int argc, char **argv) @@ -220,7 +318,7 @@ int main(int argc, char **argv) // handle arguments passed via environment variable if (const char *var = getenv("TEST_ARGS")) { - std::vector env = split_words(var); + auto env = split_words(var); for (auto arg : env) { if (arg == "-v") { verbose = true; From b15502ddc861526a72f4041896fbabc5e0b64337 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 24 Mar 2021 15:53:00 -0400 Subject: [PATCH 0249/1217] Add utils::split_lines --- src/utils.cpp | 8 ++++++++ src/utils.h | 6 ++++++ unittest/utils/test_utils.cpp | 17 +++++++++++++---- 3 files changed, 27 insertions(+), 4 deletions(-) diff --git a/src/utils.cpp b/src/utils.cpp index b5576b9f27..e733d7eaae 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -851,6 +851,14 @@ std::vector utils::split_words(const std::string &text) return list; } +/* ---------------------------------------------------------------------- + Convert multi-line string into lines +------------------------------------------------------------------------- */ +std::vector utils::split_lines(const std::string &text) +{ + return Tokenizer(text, "\n").as_vector(); +} + /* ---------------------------------------------------------------------- Return whether string is a valid integer number ------------------------------------------------------------------------- */ diff --git a/src/utils.h b/src/utils.h index eab81f1343..ec4dd6ae85 100644 --- a/src/utils.h +++ b/src/utils.h @@ -321,6 +321,12 @@ namespace LAMMPS_NS { std::vector split_words(const std::string &text); + /** Take multi-line text and split into lines + * + * \param text string that should be split + * \return STL vector with the lines */ + std::vector split_lines(const std::string &text); + /** Check if string can be converted to valid integer * * \param str string that should be checked diff --git a/unittest/utils/test_utils.cpp b/unittest/utils/test_utils.cpp index 2fa17a5e5a..2a87f1c347 100644 --- a/unittest/utils/test_utils.cpp +++ b/unittest/utils/test_utils.cpp @@ -113,7 +113,7 @@ TEST(Utils, count_words_with_extra_spaces) TEST(Utils, split_words_simple) { - std::vector list = utils::split_words("one two three"); + auto list = utils::split_words("one two three"); ASSERT_EQ(list.size(), 3); ASSERT_THAT(list[0], StrEq("one")); ASSERT_THAT(list[1], StrEq("two")); @@ -122,7 +122,7 @@ TEST(Utils, split_words_simple) TEST(Utils, split_words_quoted) { - std::vector list = utils::split_words("one 'two' \"three\""); + auto list = utils::split_words("one 'two' \"three\""); ASSERT_EQ(list.size(), 3); ASSERT_THAT(list[0], StrEq("one")); ASSERT_THAT(list[1], StrEq("two")); @@ -131,7 +131,7 @@ TEST(Utils, split_words_quoted) TEST(Utils, split_words_escaped) { - std::vector list = utils::split_words("1\\' '\"two\"' 3\\\""); + auto list = utils::split_words("1\\' '\"two\"' 3\\\""); ASSERT_EQ(list.size(), 3); ASSERT_THAT(list[0], StrEq("1\\'")); ASSERT_THAT(list[1], StrEq("\"two\"")); @@ -140,13 +140,22 @@ TEST(Utils, split_words_escaped) TEST(Utils, split_words_quote_in_quoted) { - std::vector list = utils::split_words("one 't\\'wo' \"th\\\"ree\""); + auto list = utils::split_words("one 't\\'wo' \"th\\\"ree\""); ASSERT_EQ(list.size(), 3); ASSERT_THAT(list[0], StrEq("one")); ASSERT_THAT(list[1], StrEq("t\\'wo")); ASSERT_THAT(list[2], StrEq("th\\\"ree")); } +TEST(Utils, split_lines) +{ + auto list = utils::split_lines(" line 1\nline 2 \n line 3 \n"); + ASSERT_EQ(list.size(), 3); + ASSERT_THAT(list[0], StrEq(" line 1")); + ASSERT_THAT(list[1], StrEq("line 2 ")); + ASSERT_THAT(list[2], StrEq(" line 3 ")); +} + TEST(Utils, valid_integer1) { ASSERT_TRUE(utils::is_integer("10")); From 45191e9f7c3c21a8f445c3c9699037838bb382cf Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 24 Mar 2021 16:33:39 -0400 Subject: [PATCH 0250/1217] Refactor and add fix python/invoke tests --- unittest/python/test_python_package.cpp | 115 +++++++++++++----------- unittest/testing/core.h | 46 ++++++++-- unittest/testing/systems/melt.h | 28 +++--- 3 files changed, 117 insertions(+), 72 deletions(-) diff --git a/unittest/python/test_python_package.cpp b/unittest/python/test_python_package.cpp index f7a184b6b3..5a36112781 100644 --- a/unittest/python/test_python_package.cpp +++ b/unittest/python/test_python_package.cpp @@ -24,14 +24,14 @@ #include #include +#include "../testing/core.h" +#include "../testing/systems/melt.h" + // location of '*.py' files required by tests #define STRINGIFY(val) XSTR(val) #define XSTR(val) #val std::string INPUT_FOLDER = STRINGIFY(TEST_INPUT_FOLDER); -// whether to print verbose output (i.e. not capturing LAMMPS screen output). -bool verbose = false; - const char * LOREM_IPSUM = "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent metus."; using LAMMPS_NS::utils::split_words; @@ -42,51 +42,12 @@ using ::testing::StrEq; using ::testing::Eq; using ::testing::HasSubstr; -class PythonPackageTest : public ::testing::Test { +class PythonPackageTest : public LAMMPSTest { protected: - LAMMPS *lmp; - Info *info; - - void command(const std::string &line) { lmp->input->one(line.c_str()); } - - void command_string(const std::string &lines) { lammps_commands_string(lmp, lines.c_str()); } - - void HIDE_OUTPUT(std::function f) { - if (!verbose) ::testing::internal::CaptureStdout(); - f(); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - std::string CAPTURE_OUTPUT(std::function f) { - ::testing::internal::CaptureStdout(); - f(); - auto output = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << output; - return output; - } - - double get_variable_value(const std::string & name) { - char * str = utils::strdup(fmt::format("v_{}", name)); - double value = lmp->input->variable->compute_equal(str); - delete [] str; - return value; - } - - std::string get_variable_string(const std::string & name) { - return lmp->input->variable->retrieve(name.c_str()); - } - - void SetUp() override + void InitSystem() override { - const char *args[] = {"PythonPackageTest", "-log", "none", "-echo", "screen", "-nocite"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - HIDE_OUTPUT([&] { - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - }); - ASSERT_NE(lmp, nullptr); - info = new Info(lmp); if (!info->has_package("PYTHON")) GTEST_SKIP(); + HIDE_OUTPUT([&] { command("units real"); command("dimension 3"); @@ -100,15 +61,15 @@ protected: command("variable input_dir index " + INPUT_FOLDER); }); } +}; - void TearDown() override +class FixPythonInvokeTest : public MeltTest { +protected: + void InitSystem() override { - HIDE_OUTPUT([&] { - delete info; - delete lmp; - info = nullptr; - lmp = nullptr; - }); + if (!info->has_package("PYTHON")) GTEST_SKIP(); + + MeltTest::InitSystem(); } }; @@ -309,6 +270,56 @@ TEST_F(PythonPackageTest, RunSourceInline) ASSERT_THAT(output, HasSubstr("4")); } +TEST_F(FixPythonInvokeTest, end_of_step) +{ + HIDE_OUTPUT([&] { + command("python end_of_step_callback here \"\"\"\n" + "from __future__ import print_function\n" + "def end_of_step_callback(ptr):\n" + " print(\"PYTHON_END_OF_STEP\")\n" + "\"\"\""); + command("fix eos all python/invoke 10 end_of_step end_of_step_callback"); + }); + + auto output = CAPTURE_OUTPUT([&] { + command("run 50"); + }); + + auto lines = utils::split_lines(output); + int count = 0; + + for(auto & line : lines) { + if (line == "PYTHON_END_OF_STEP") ++count; + } + + ASSERT_EQ(count, 5); +} + +TEST_F(FixPythonInvokeTest, post_force) +{ + HIDE_OUTPUT([&] { + command("python post_force_callback here \"\"\"\n" + "from __future__ import print_function\n" + "def post_force_callback(ptr, vflag):\n" + " print(\"PYTHON_POST_FORCE\")\n" + "\"\"\""); + command("fix pf all python/invoke 10 post_force post_force_callback"); + }); + + auto output = CAPTURE_OUTPUT([&] { + command("run 50"); + }); + + auto lines = utils::split_lines(output); + int count = 0; + + for(auto & line : lines) { + if (line == "PYTHON_POST_FORCE") ++count; + } + + ASSERT_EQ(count, 5); +} + } // namespace LAMMPS_NS int main(int argc, char **argv) diff --git a/unittest/testing/core.h b/unittest/testing/core.h index 5852f7fd06..4dc15a5327 100644 --- a/unittest/testing/core.h +++ b/unittest/testing/core.h @@ -16,9 +16,12 @@ #include "info.h" #include "input.h" #include "lammps.h" +#include "variable.h" #include "gmock/gmock.h" #include "gtest/gtest.h" +#include + using namespace LAMMPS_NS; using ::testing::MatchesRegex; @@ -45,29 +48,58 @@ class LAMMPSTest : public ::testing::Test { public: void command(const std::string &line) { lmp->input->one(line.c_str()); } + void HIDE_OUTPUT(std::function f) { + if (!verbose) ::testing::internal::CaptureStdout(); + f(); + if (!verbose) ::testing::internal::GetCapturedStdout(); + } + + std::string CAPTURE_OUTPUT(std::function f) { + ::testing::internal::CaptureStdout(); + f(); + auto output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + return output; + } + + double get_variable_value(const std::string & name) { + char * str = utils::strdup(fmt::format("v_{}", name)); + double value = lmp->input->variable->compute_equal(str); + delete [] str; + return value; + } + + std::string get_variable_string(const std::string & name) { + return lmp->input->variable->retrieve(name.c_str()); + } + protected: const char *testbinary = "LAMMPSTest"; LAMMPS *lmp; + Info *info; void SetUp() override { const char *args[] = {testbinary, "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); + HIDE_OUTPUT([&] { + lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); + info = new Info(lmp); + }); InitSystem(); - if (!verbose) ::testing::internal::GetCapturedStdout(); } virtual void InitSystem() {} void TearDown() override { - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - lmp = nullptr; - if (!verbose) ::testing::internal::GetCapturedStdout(); + HIDE_OUTPUT([&] { + delete info; + delete lmp; + info = nullptr; + lmp = nullptr; + }); } }; diff --git a/unittest/testing/systems/melt.h b/unittest/testing/systems/melt.h index 4189a6b771..5ac92f562b 100644 --- a/unittest/testing/systems/melt.h +++ b/unittest/testing/systems/melt.h @@ -19,23 +19,25 @@ class MeltTest : public LAMMPSTest { protected: virtual void InitSystem() override { - command("units lj"); - command("atom_style atomic"); - command("atom_modify map yes"); + HIDE_OUTPUT([&] { + command("units lj"); + command("atom_style atomic"); + command("atom_modify map yes"); - command("lattice fcc 0.8442"); - command("region box block 0 2 0 2 0 2"); - command("create_box 1 box"); - command("create_atoms 1 box"); - command("mass 1 1.0"); + command("lattice fcc 0.8442"); + command("region box block 0 2 0 2 0 2"); + command("create_box 1 box"); + command("create_atoms 1 box"); + command("mass 1 1.0"); - command("velocity all create 3.0 87287"); + command("velocity all create 3.0 87287"); - command("pair_style lj/cut 2.5"); - command("pair_coeff 1 1 1.0 1.0 2.5"); + command("pair_style lj/cut 2.5"); + command("pair_coeff 1 1 1.0 1.0 2.5"); - command("neighbor 0.3 bin"); - command("neigh_modify every 20 delay 0 check no"); + command("neighbor 0.3 bin"); + command("neigh_modify every 20 delay 0 check no"); + }); } }; From 157698543fa85ed6d849f5f1418d658b5e3f42d3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Mar 2021 16:47:08 -0400 Subject: [PATCH 0251/1217] add tests for "next" command --- unittest/commands/test_variables.cpp | 41 ++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index c558e02376..476874ec74 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -401,6 +401,47 @@ TEST_F(VariableTest, IfCommand) command("if (v_one==1.0)&&(2>=1) then 'print \"bingo!\"'");); } +TEST_F(VariableTest, NextCommand) +{ + file_vars(); + + if (!verbose) ::testing::internal::CaptureStdout(); + command("variable one index 1 2"); + command("variable two equal 2"); + command("variable three file test_variable.file"); + command("variable four loop 2 4"); + command("variable five index 1 2"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_one"), 1); + ASSERT_THAT(variable->retrieve("three"), StrEq("one")); + if (!verbose) ::testing::internal::CaptureStdout(); + command("next one"); + command("next three"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_one"), 2); + ASSERT_THAT(variable->retrieve("three"), StrEq("two")); + ASSERT_GE(variable->find("one"), 0); + if (!verbose) ::testing::internal::CaptureStdout(); + command("next one"); + command("next three"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + // index style variable is deleted if no more next element + ASSERT_EQ(variable->find("one"), -1); + ASSERT_GE(variable->find("three"), 0); + if (!verbose) ::testing::internal::CaptureStdout(); + command("next three"); + command("next three"); + command("next three"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + // file style variable is deleted if no more next element + ASSERT_EQ(variable->find("three"), -1); + + TEST_FAILURE(".*ERROR: Illegal next command.*", command("next");); + TEST_FAILURE(".*ERROR: Invalid variable 'xxx' in next command.*", command("next xxx");); + TEST_FAILURE(".*ERROR: Invalid variable style with next command.*", command("next two");); + TEST_FAILURE(".*ERROR: All variables in next command must have same style.*", + command("next five four");); +} } // namespace LAMMPS_NS int main(int argc, char **argv) From aab51fe70e5db178bdac8e5599751e9b2f9e1dba Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Mar 2021 16:47:56 -0400 Subject: [PATCH 0252/1217] more coverage of utility functions in Variable class --- unittest/commands/test_variables.cpp | 61 +++++++++++++++++++++------- 1 file changed, 47 insertions(+), 14 deletions(-) diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 476874ec74..30bbccf4d9 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -71,7 +71,8 @@ protected: void SetUp() override { - const char *args[] = {"VariableTest", "-log", "none", "-echo", "screen", "-nocite"}; + const char *args[] = {"VariableTest", "-log", "none", "-echo", "screen", + "-nocite", "-v", "num", "1"}; char **argv = (char **)args; int argc = sizeof(args) / sizeof(char *); if (!verbose) ::testing::internal::CaptureStdout(); @@ -150,7 +151,7 @@ protected: TEST_F(VariableTest, CreateDelete) { file_vars(); - ASSERT_EQ(variable->nvar, 0); + ASSERT_EQ(variable->nvar, 1); if (!verbose) ::testing::internal::CaptureStdout(); command("variable one index 1 2 3 4"); command("variable two equal 1"); @@ -160,7 +161,7 @@ TEST_F(VariableTest, CreateDelete) command("variable four1 loop 4"); command("variable four2 loop 2 4"); command("variable five1 loop 100 pad"); - command("variable five2 loop 100 200 pad"); + command("variable five2 loop 10 200 pad"); command("variable six world one"); command("variable seven format two \"%5.2f\""); command("variable eight getenv PWD"); @@ -173,17 +174,32 @@ TEST_F(VariableTest, CreateDelete) command("variable ten3 uloop 4 pad"); command("variable dummy index 0"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 16); + ASSERT_EQ(variable->nvar, 17); if (!verbose) ::testing::internal::CaptureStdout(); command("variable dummy delete"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 15); + ASSERT_EQ(variable->nvar, 16); + ASSERT_THAT(variable->retrieve("three"), StrEq("three")); + variable->set_string("three", "four"); + ASSERT_THAT(variable->retrieve("three"), StrEq("four")); + ASSERT_THAT(variable->retrieve("four2"), StrEq("2")); + ASSERT_THAT(variable->retrieve("five1"), StrEq("001")); + ASSERT_THAT(variable->retrieve("seven"), StrEq(" 2.00")); + ASSERT_THAT(variable->retrieve("ten"), StrEq("1")); + + ASSERT_EQ(variable->equalstyle(variable->find("one")), 0); + ASSERT_EQ(variable->equalstyle(variable->find("two")), 1); + ASSERT_EQ(variable->equalstyle(variable->find("ten")), 1); + + ASSERT_EQ(variable->internalstyle(variable->find("two")), 0); + ASSERT_EQ(variable->internalstyle(variable->find("ten")), 1); TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable");); TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable dummy index");); TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable dummy delete xxx");); TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable dummy loop -1");); TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable dummy loop 10 1");); + TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable dummy xxxx");); TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", command("variable two string xxx");); TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", @@ -202,6 +218,8 @@ TEST_F(VariableTest, CreateDelete) command("variable ten4 uloop 2");); TEST_FAILURE(".*ERROR: Incorrect conversion in format string.*", command("variable ten11 format two \"%08f\"");); + TEST_FAILURE(".*ERROR: Variable name 'ten@12' must have only alphanumeric characters or.*", + command("variable ten@12 index one two three");); } TEST_F(VariableTest, AtomicSystem) @@ -218,16 +236,28 @@ TEST_F(VariableTest, AtomicSystem) command("compute press all pressure NULL pair"); command("fix press all ave/time 1 1 1 c_press mode vector"); command("variable press vector f_press"); - command("variable stress vector v_press+vol"); - command("variable pmax equal max(f_press)"); + command("variable press vector f_press+vol"); + command("variable pmax equal max(v_press)"); + command("variable psum equal sum(v_press)"); command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 6); - ASSERT_DOUBLE_EQ(variable->compute_equal("v_pmax"), 0.0); + ASSERT_EQ(variable->nvar, 7); + + ASSERT_EQ(variable->atomstyle(variable->find("one")), 0); + ASSERT_EQ(variable->atomstyle(variable->find("id")), 1); + ASSERT_EQ(variable->atomstyle(variable->find("ten")), 1); + + ASSERT_EQ(variable->vectorstyle(variable->find("one")), 0); + ASSERT_EQ(variable->vectorstyle(variable->find("press")), 1); + + ASSERT_DOUBLE_EQ(variable->compute_equal("v_pmax"), 64.0); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_psum"), 6 * 64.0); TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", command("variable one atom x");); + TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", + command("variable one vector f_press");); TEST_FAILURE(".*ERROR on proc 0: Cannot open file variable file test_variable.xxx.*", command("variable ten1 atomfile test_variable.xxx");); } @@ -235,7 +265,7 @@ TEST_F(VariableTest, AtomicSystem) TEST_F(VariableTest, Expressions) { atomic_system(); - ASSERT_EQ(variable->nvar, 0); + ASSERT_EQ(variable->nvar, 1); if (!verbose) ::testing::internal::CaptureStdout(); command("variable one index 1"); command("variable two equal 2"); @@ -255,9 +285,10 @@ TEST_F(VariableTest, Expressions) command("variable ten6 equal (1<=v_one)&&(v_ten>=0.2)"); command("variable ten7 equal !(1set("dummy index 1 2"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 18); + ASSERT_EQ(variable->nvar, 21); int ivar = variable->find("one"); ASSERT_FALSE(variable->equalstyle(ivar)); @@ -282,6 +313,8 @@ TEST_F(VariableTest, Expressions) TEST_FAILURE(".*ERROR: Variable six: Invalid thermo keyword 'XXX' in variable formula.*", command("print \"${six}\"");); + TEST_FAILURE(".*ERROR: Variable ten9: has a circular dependency.*", + command("print \"${ten9}\"");); } TEST_F(VariableTest, Functions) @@ -289,14 +322,14 @@ TEST_F(VariableTest, Functions) atomic_system(); file_vars(); - ASSERT_EQ(variable->nvar, 0); + ASSERT_EQ(variable->nvar, 1); if (!verbose) ::testing::internal::CaptureStdout(); command("variable one index 1"); command("variable two equal random(1,2,643532)"); command("variable three equal atan2(v_one,1)"); command("variable four equal atan2()"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 4); + ASSERT_EQ(variable->nvar, 5); int ivar = variable->find("two"); ASSERT_GT(variable->compute_equal(ivar), 0.99); From 81e8676c7e8fe1566817decacc2f65cf4e5989fd Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 24 Mar 2021 17:10:15 -0400 Subject: [PATCH 0253/1217] Prepare python/move unittest --- unittest/force-styles/tests/py_nve.py | 75 +++++++++++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 unittest/force-styles/tests/py_nve.py diff --git a/unittest/force-styles/tests/py_nve.py b/unittest/force-styles/tests/py_nve.py new file mode 100644 index 0000000000..4740c85597 --- /dev/null +++ b/unittest/force-styles/tests/py_nve.py @@ -0,0 +1,75 @@ +from __future__ import print_function +from lammps import lammps, LAMMPS_INT, LAMMPS_DOUBLE + +class LAMMPSFix(object): + def __init__(self, ptr, group_name="all"): + self.lmp = lammps(ptr=ptr) + self.group_name = group_name + +class LAMMPSFixMove(LAMMPSFix): + def __init__(self, ptr, group_name="all"): + super(LAMMPSFixMove, self).__init__(ptr, group_name) + + def init(self): + pass + + def initial_integrate(self, vflag): + pass + + def final_integrate(self): + pass + + def initial_integrate_respa(self, vflag, ilevel, iloop): + pass + + def final_integrate_respa(self, ilevel, iloop): + pass + + def reset_dt(self): + pass + + +class NVE(LAMMPSFixMove): + """ Python implementation of fix/nve """ + def __init__(self, ptr, group_name="all"): + super(NVE, self).__init__(ptr) + assert(self.group_name == "all") + + def init(self): + dt = self.lmp.extract_global("dt") + ftm2v = self.lmp.extract_global("ftm2v") + self.ntypes = self.lmp.extract_global("ntypes") + self.dtv = dt + self.dtf = 0.5 * dt * ftm2v + + def initial_integrate(self, vflag): + nlocal = self.lmp.extract_global("nlocal") + mass = self.lmp.extract_atom("mass") + atype = self.lmp.extract_atom("type") + x = self.lmp.extract_atom("x") + v = self.lmp.extract_atom("v") + f = self.lmp.extract_atom("f") + + for i in range(nlocal): + dtfm = self.dtf / mass[int(atype[i])] + v[i][0] += dtfm * f[i][0] + v[i][1] += dtfm * f[i][1] + v[i][2] += dtfm * f[i][2] + x[i][0] += self.dtv * v[i][0] + x[i][1] += self.dtv * v[i][1] + x[i][2] += self.dtv * v[i][2] + + def final_integrate(self): + nlocal = self.lmp.extract_global("nlocal") + mass = self.lmp.extract_atom("mass") + atype = self.lmp.extract_atom("type") + v = self.lmp.extract_atom("v") + f = self.lmp.extract_atom("f") + + for i in range(nlocal): + dtfm = self.dtf / mass[int(atype[i])] + v[i][0] += dtfm * f[i][0] + v[i][1] += dtfm * f[i][1] + v[i][2] += dtfm * f[i][2] + + From b0bc0b9a2f0e39bf936a7b89b10eae3f218bf674 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 24 Mar 2021 17:54:10 -0400 Subject: [PATCH 0254/1217] Use time.strptime instead of datetime.strptime Embedding the Python interpreter multiple times in the same process can cause this issue due to import caching. https://bugs.python.org/issue27400 This seems to be avoidable by using the time module instead. --- python/lammps/__init__.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/python/lammps/__init__.py b/python/lammps/__init__.py index 48839273c5..e6ffd779a9 100644 --- a/python/lammps/__init__.py +++ b/python/lammps/__init__.py @@ -15,7 +15,7 @@ from .pylammps import * # convert module string version to numeric version def get_version_number(): - from datetime import datetime + import time from sys import version_info vstring = None if version_info.major == 3 and version_info.minor >= 8: @@ -32,7 +32,7 @@ def get_version_number(): if not vstring: return 0 - d = datetime.strptime(vstring, "%d%b%Y") - return d.year*10000 + d.month*100 + d.day + t = time.strptime(vstring, "%d%b%Y") + return t.tm_year*10000 + t.tm_mon*100 + t.tm_mday __version__ = get_version_number() From 55b0e33200dceda41397966f2c8999160c95e52d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Mar 2021 18:01:48 -0400 Subject: [PATCH 0255/1217] fix typo --- doc/src/variable.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/variable.rst b/doc/src/variable.rst index ea6b7ef8ec..6a6cdf9a6d 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -429,7 +429,7 @@ argument. For *equal*\ -style variables the formula computes a scalar quantity, which becomes the value of the variable whenever it is evaluated. For *vector*\ -style variables the formula must compute a vector of quantities, which becomes the value of the variable whenever -it is evaluated. The calculated vector can be on length one, but it +it is evaluated. The calculated vector can be of length one, but it cannot be a simple scalar value like that produced by an equal-style compute. I.e. the formula for a vector-style variable must have at least one quantity in it that refers to a global vector produced by a From d04d326413760462d6e670d417610a6bb214514e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Mar 2021 18:02:30 -0400 Subject: [PATCH 0256/1217] more tests for expressions and vector style variables --- unittest/commands/test_variables.cpp | 68 ++++++++++++++++++++++------ 1 file changed, 53 insertions(+), 15 deletions(-) diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 30bbccf4d9..f214dadd36 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -165,7 +165,7 @@ TEST_F(VariableTest, CreateDelete) command("variable six world one"); command("variable seven format two \"%5.2f\""); command("variable eight getenv PWD"); - command("variable eight getenv HOME"); + command("variable eight getenv XXXXX"); command("variable nine file test_variable.file"); command("variable ten internal 1.0"); command("variable ten internal 10.0"); @@ -186,6 +186,9 @@ TEST_F(VariableTest, CreateDelete) ASSERT_THAT(variable->retrieve("five1"), StrEq("001")); ASSERT_THAT(variable->retrieve("seven"), StrEq(" 2.00")); ASSERT_THAT(variable->retrieve("ten"), StrEq("1")); + ASSERT_THAT(variable->retrieve("eight"), StrEq("")); + variable->internal_set(variable->find("ten"), 2.5); + ASSERT_THAT(variable->retrieve("ten"), StrEq("2.5")); ASSERT_EQ(variable->equalstyle(variable->find("one")), 0); ASSERT_EQ(variable->equalstyle(variable->find("two")), 1); @@ -220,6 +223,10 @@ TEST_F(VariableTest, CreateDelete) command("variable ten11 format two \"%08f\"");); TEST_FAILURE(".*ERROR: Variable name 'ten@12' must have only alphanumeric characters or.*", command("variable ten@12 index one two three");); + TEST_FAILURE(".*ERROR: Variable evaluation before simulation box is defined.*", + variable->compute_equal("c_thermo_press");); + TEST_FAILURE(".*ERROR: Invalid variable reference v_unknown in variable formula.*", + variable->compute_equal("v_unknown");); } TEST_F(VariableTest, AtomicSystem) @@ -233,16 +240,29 @@ TEST_F(VariableTest, AtomicSystem) command("variable id atom type"); command("variable id atom id"); command("variable ten atomfile test_variable.atomfile"); - command("compute press all pressure NULL pair"); - command("fix press all ave/time 1 1 1 c_press mode vector"); - command("variable press vector f_press"); - command("variable press vector f_press+vol"); - command("variable pmax equal max(v_press)"); - command("variable psum equal sum(v_press)"); - command("run 0 post no"); + command("compute press all pressure NULL pair"); + command("compute rg all gyration"); + command("compute vacf all vacf"); + command("fix press all ave/time 1 1 1 c_press mode vector"); + command("fix rg all ave/time 1 1 1 c_rg mode vector"); + command("fix vacf all ave/time 1 1 1 c_vacf mode vector"); + + command("variable press vector f_press"); + command("variable rg vector f_rg"); + command("variable vacf vector f_vacf"); + command("variable press vector f_press+0.0"); + command("variable self vector v_self+f_press"); + command("variable circle vector f_press+v_circle"); + command("variable sum vector v_press+v_rg"); + command("variable sum2 vector v_vacf+v_rg"); + command("variable pmax equal max(v_press)"); + command("variable psum equal sum(v_press)"); + command("variable rgmax equal max(v_rg)"); + command("variable rgsum equal sum(v_rg)"); + command("variable loop equal v_loop+1"); + command("run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 7); ASSERT_EQ(variable->atomstyle(variable->find("one")), 0); ASSERT_EQ(variable->atomstyle(variable->find("id")), 1); @@ -251,8 +271,11 @@ TEST_F(VariableTest, AtomicSystem) ASSERT_EQ(variable->vectorstyle(variable->find("one")), 0); ASSERT_EQ(variable->vectorstyle(variable->find("press")), 1); - ASSERT_DOUBLE_EQ(variable->compute_equal("v_pmax"), 64.0); - ASSERT_DOUBLE_EQ(variable->compute_equal("v_psum"), 6 * 64.0); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_pmax"), 0.0); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_psum"), 0.0); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_rgmax"), 1.25); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_rgsum"), 3.75); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_sum[1]"), 1.25); TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", command("variable one atom x");); @@ -260,12 +283,17 @@ TEST_F(VariableTest, AtomicSystem) command("variable one vector f_press");); TEST_FAILURE(".*ERROR on proc 0: Cannot open file variable file test_variable.xxx.*", command("variable ten1 atomfile test_variable.xxx");); + TEST_FAILURE(".*ERROR: Variable loop: has a circular dependency.*", + variable->compute_equal("v_loop");); + TEST_FAILURE(".*Variable self: Vector-style variable in equal-style variable formula.*", + variable->compute_equal("v_self");); + TEST_FAILURE(".*ERROR: Variable sum2: Inconsistent lengths in vector-style variable.*", + variable->compute_equal("max(v_sum2)");); } TEST_F(VariableTest, Expressions) { atomic_system(); - ASSERT_EQ(variable->nvar, 1); if (!verbose) ::testing::internal::CaptureStdout(); command("variable one index 1"); command("variable two equal 2"); @@ -286,9 +314,13 @@ TEST_F(VariableTest, Expressions) command("variable ten7 equal !(12)+(1>=2)+(1&&0)+(0||0)+(1|^1)+10^0"); + command("variable err1 equal v_one/v_ten7"); + command("variable err2 equal v_one%v_ten7"); + command("variable err3 equal v_ten7^-v_one"); variable->set("dummy index 1 2"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 21); int ivar = variable->find("one"); ASSERT_FALSE(variable->equalstyle(ivar)); @@ -310,11 +342,19 @@ TEST_F(VariableTest, Expressions) ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten6"), 1); ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten7"), 0); ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten8"), 1); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten10"), 100); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten11"), 1); TEST_FAILURE(".*ERROR: Variable six: Invalid thermo keyword 'XXX' in variable formula.*", command("print \"${six}\"");); TEST_FAILURE(".*ERROR: Variable ten9: has a circular dependency.*", command("print \"${ten9}\"");); + TEST_FAILURE(".*ERROR on proc 0: Variable err1: Divide by 0 in variable formula.*", + command("print \"${err1}\"");); + TEST_FAILURE(".*ERROR on proc 0: Variable err2: Modulo 0 in variable formula.*", + command("print \"${err2}\"");); + TEST_FAILURE(".*ERROR on proc 0: Variable err3: Invalid power expression in variable formula.*", + command("print \"${err3}\"");); } TEST_F(VariableTest, Functions) @@ -322,14 +362,12 @@ TEST_F(VariableTest, Functions) atomic_system(); file_vars(); - ASSERT_EQ(variable->nvar, 1); if (!verbose) ::testing::internal::CaptureStdout(); command("variable one index 1"); command("variable two equal random(1,2,643532)"); command("variable three equal atan2(v_one,1)"); command("variable four equal atan2()"); if (!verbose) ::testing::internal::GetCapturedStdout(); - ASSERT_EQ(variable->nvar, 5); int ivar = variable->find("two"); ASSERT_GT(variable->compute_equal(ivar), 0.99); From 4fa5ce2dbccd5d6bdcffcce5cce9c2a3bc636585 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 24 Mar 2021 18:11:31 -0400 Subject: [PATCH 0257/1217] Remove unnecessary import --- unittest/force-styles/tests/py_nve.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/force-styles/tests/py_nve.py b/unittest/force-styles/tests/py_nve.py index 4740c85597..1f05be04a8 100644 --- a/unittest/force-styles/tests/py_nve.py +++ b/unittest/force-styles/tests/py_nve.py @@ -1,5 +1,5 @@ from __future__ import print_function -from lammps import lammps, LAMMPS_INT, LAMMPS_DOUBLE +from lammps import lammps class LAMMPSFix(object): def __init__(self, ptr, group_name="all"): From 3c41c12dbc0818b2e93165d436aed45430285188 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 24 Mar 2021 18:58:46 -0400 Subject: [PATCH 0258/1217] Add testcase for python/move --- unittest/force-styles/CMakeLists.txt | 2 +- unittest/force-styles/test_fix_timestep.cpp | 5 +- .../tests/fix-timestep-python_move_nve.yaml | 73 +++++++++++++++++++ 3 files changed, 78 insertions(+), 2 deletions(-) create mode 100644 unittest/force-styles/tests/fix-timestep-python_move_nve.yaml diff --git a/unittest/force-styles/CMakeLists.txt b/unittest/force-styles/CMakeLists.txt index 02300b5ea2..60e83e7e16 100644 --- a/unittest/force-styles/CMakeLists.txt +++ b/unittest/force-styles/CMakeLists.txt @@ -124,7 +124,7 @@ file(GLOB FIX_TIMESTEP_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/fix-tim foreach(TEST ${FIX_TIMESTEP_TESTS}) string(REGEX REPLACE "^.*fix-timestep-(.*)\.yaml" "FixTimestep:\\1" TNAME ${TEST}) add_test(NAME ${TNAME} COMMAND test_fix_timestep ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) - set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};PYTHONPATH=${TEST_INPUT_FOLDER}:$ENV{PYTHONPATH}") + set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};PYTHONPATH=${TEST_INPUT_FOLDER}:${LAMMPS_PYTHON_DIR}:$ENV{PYTHONPATH}") endforeach() # dihedral style tester diff --git a/unittest/force-styles/test_fix_timestep.cpp b/unittest/force-styles/test_fix_timestep.cpp index e4b0fa6e02..aa07f36fb9 100644 --- a/unittest/force-styles/test_fix_timestep.cpp +++ b/unittest/force-styles/test_fix_timestep.cpp @@ -518,9 +518,12 @@ TEST(FixTimestep, plain) // rigid fixes need work to test properly with r-RESPA. // fix nve/limit cannot work with r-RESPA + // fix python/move implementation is missing library interface access to Repsa::step ifix = lmp->modify->find_fix("test"); if (!utils::strmatch(lmp->modify->fix[ifix]->style, "^rigid") && - !utils::strmatch(lmp->modify->fix[ifix]->style, "^nve/limit")) { + !utils::strmatch(lmp->modify->fix[ifix]->style, "^nve/limit") && + !utils::strmatch(lmp->modify->fix[ifix]->style, "^python/move") + ) { if (!verbose) ::testing::internal::CaptureStdout(); cleanup_lammps(lmp, test_config); diff --git a/unittest/force-styles/tests/fix-timestep-python_move_nve.yaml b/unittest/force-styles/tests/fix-timestep-python_move_nve.yaml new file mode 100644 index 0000000000..9c78dbe416 --- /dev/null +++ b/unittest/force-styles/tests/fix-timestep-python_move_nve.yaml @@ -0,0 +1,73 @@ +--- +lammps_version: 10 Mar 2021 +date_generated: Wed Mar 24 18:57:26 202 +epsilon: 9e-12 +prerequisites: ! | + atom full + fix python/move +pre_commands: ! "" +post_commands: ! | + fix test all python/move py_nve.NVE +input_file: in.fourmol +natoms: 29 +run_pos: ! |2 + 1 -2.7045559775384037e-01 2.4912159905679729e+00 -1.6695851791541885e-01 + 2 3.1004029573899528e-01 2.9612354631094391e+00 -8.5466363037021464e-01 + 3 -7.0398551400789477e-01 1.2305509955830618e+00 -6.2777526944456274e-01 + 4 -1.5818159336499285e+00 1.4837407818929933e+00 -1.2538710836062004e+00 + 5 -9.0719763672789266e-01 9.2652103885675297e-01 3.9954210488374786e-01 + 6 2.4831720524855985e-01 2.8313021497871271e-01 -1.2314233331711453e+00 + 7 3.4143527641386412e-01 -2.2646551041391422e-02 -2.5292291414903052e+00 + 8 1.1743552229100009e+00 -4.8863228565853950e-01 -6.3783432910825522e-01 + 9 1.3800524229500313e+00 -2.5274721030406683e-01 2.8353985887095157e-01 + 10 2.0510765220543883e+00 -1.4604063740302866e+00 -9.8323745081712954e-01 + 11 1.7878031944442556e+00 -1.9921863272948861e+00 -1.8890602447625777e+00 + 12 3.0063007039340053e+00 -4.9013350496963298e-01 -1.6231898107386229e+00 + 13 4.0515402959192999e+00 -8.9202011606653986e-01 -1.6400005529924957e+00 + 14 2.6066963345543819e+00 -4.1789253965514150e-01 -2.6634003608794394e+00 + 15 2.9695287185712913e+00 5.5422613165234036e-01 -1.2342022021790127e+00 + 16 2.6747029695228521e+00 -2.4124119054564295e+00 -2.3435746150616148e-02 + 17 2.2153577785283796e+00 -2.0897985186907717e+00 1.1963150794479436e+00 + 18 2.1369701704115704e+00 3.0158507413630606e+00 -3.5179348337215015e+00 + 19 1.5355837136087378e+00 2.6255292355375675e+00 -4.2353987779879052e+00 + 20 2.7727573005678776e+00 3.6923910449610169e+00 -3.9330842459133493e+00 + 21 4.9040128073204299e+00 -4.0752348172957946e+00 -3.6210314709891711e+00 + 22 4.3582355554440841e+00 -4.2126119427287048e+00 -4.4612844196314052e+00 + 23 5.7439382849307599e+00 -3.5821957939275029e+00 -3.8766361295935821e+00 + 24 2.0689243582422630e+00 3.1513346907271012e+00 3.1550389754828800e+00 + 25 1.3045351331492134e+00 3.2665125705842848e+00 2.5111855257433504e+00 + 26 2.5809237402711274e+00 4.0117602605482832e+00 3.2212060529089896e+00 + 27 -1.9611343130357228e+00 -4.3563411931359752e+00 2.1098293115523705e+00 + 28 -2.7473562684513411e+00 -4.0200819932379330e+00 1.5830052163433954e+00 + 29 -1.3126000191359855e+00 -3.5962518039482929e+00 2.2746342468737835e+00 +run_vel: ! |2 + 1 8.1705744183262364e-03 1.6516406176274288e-02 4.7902264318912978e-03 + 2 5.4501493445687759e-03 5.1791699408496334e-03 -1.4372931530376651e-03 + 3 -8.2298292722385643e-03 -1.2926551614621381e-02 -4.0984181178163881e-03 + 4 -3.7699042590093588e-03 -6.5722892098813799e-03 -1.1184640360133230e-03 + 5 -1.1021961004346586e-02 -9.8906780939335987e-03 -2.8410737829284395e-03 + 6 -3.9676663166400034e-02 4.6817061464710256e-02 3.7148491979476124e-02 + 7 9.1033953013898580e-04 -1.0128524411938794e-02 -5.1568251805019748e-02 + 8 7.9064712058855707e-03 -3.3507254552631767e-03 3.4557098492564629e-02 + 9 1.5644176117320923e-03 3.7365546102722164e-03 1.5047408822037646e-02 + 10 2.9201446820573174e-02 -2.9249578745486147e-02 -1.5018077424322538e-02 + 11 -4.7835961513517560e-03 -3.7481385134185206e-03 -2.3464104142290089e-03 + 12 2.2696451841920521e-03 -3.4774154398129479e-04 -3.0640770327796806e-03 + 13 2.7531740451953168e-03 5.8171061612840667e-03 -7.9467454022160518e-04 + 14 3.5246182371994252e-03 -5.7939995585585468e-03 -3.9478431172751344e-03 + 15 -1.8547943640122894e-03 -5.8554729942777743e-03 6.2938485140538649e-03 + 16 1.8681499973445245e-02 -1.3262466204585335e-02 -4.5638651457003243e-02 + 17 -1.2896269981100382e-02 9.7527665265956451e-03 3.7296535360836762e-02 + 18 -8.0065794848261610e-04 -8.6270473212554395e-04 -1.4483040697508738e-03 + 19 1.2452390836182623e-03 -2.5061097118772701e-03 7.2998631009712975e-03 + 20 3.5930060229597042e-03 3.6938860309252966e-03 3.2322732687893028e-03 + 21 -1.4689220370766550e-03 -2.7352129761527741e-04 7.0581624215243391e-04 + 22 -7.0694199254630339e-03 -4.2577148924878554e-03 2.8079117614251796e-04 + 23 6.0446963117374913e-03 -1.4000131614795382e-03 2.5819754847014255e-03 + 24 3.1926367902287940e-04 -9.9445664749276438e-04 1.4999996959365452e-04 + 25 1.3789754514814662e-04 -4.4335894884532569e-03 -8.1808136725080281e-04 + 26 2.0485904035217549e-03 2.7813358633835984e-03 4.3245727149206692e-03 + 27 4.5604120293369857e-04 -1.0305523026921137e-03 2.1188058381358511e-04 + 28 -6.2544520861855116e-03 1.4127711176146942e-03 -1.8429821884794269e-03 + 29 6.4110631534401762e-04 3.1273432719593867e-03 3.7253671105656715e-03 +... From a772c3b7d2ae9c981ce4712f6df1ab739d342640 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Mar 2021 21:27:32 -0400 Subject: [PATCH 0259/1217] test a few more functions and constants --- unittest/commands/test_variables.cpp | 26 +++++++++++++++++++++----- 1 file changed, 21 insertions(+), 5 deletions(-) diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index f214dadd36..45183a2e54 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -316,6 +316,7 @@ TEST_F(VariableTest, Expressions) command("variable ten9 equal v_one-v_ten9"); command("variable ten10 internal 100.0"); command("variable ten11 equal (1!=1)+(2<1)+(2<=1)+(1>2)+(1>=2)+(1&&0)+(0||0)+(1|^1)+10^0"); + command("variable ten12 equal yes+no+on+off+true+false"); command("variable err1 equal v_one/v_ten7"); command("variable err2 equal v_one%v_ten7"); command("variable err3 equal v_ten7^-v_one"); @@ -344,6 +345,7 @@ TEST_F(VariableTest, Expressions) ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten8"), 1); ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten10"), 100); ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten11"), 1); + ASSERT_DOUBLE_EQ(variable->compute_equal("v_ten12"), 3); TEST_FAILURE(".*ERROR: Variable six: Invalid thermo keyword 'XXX' in variable formula.*", command("print \"${six}\"");); @@ -367,13 +369,27 @@ TEST_F(VariableTest, Functions) command("variable two equal random(1,2,643532)"); command("variable three equal atan2(v_one,1)"); command("variable four equal atan2()"); + command("variable five equal sqrt(v_one+v_one)"); + command("variable six equal exp(ln(0.1))"); + command("variable seven equal abs(log(1.0/100.0))"); + command("variable eight equal 0.5*PI"); + command("variable nine equal round(sin(v_eight)+cos(v_eight))"); + command("variable ten equal floor(1.85)+ceil(1.85)"); + command("variable ten1 equal tan(v_eight/2.0)"); + command("variable ten2 equal asin(-1.0)+acos(0.0)"); if (!verbose) ::testing::internal::GetCapturedStdout(); - int ivar = variable->find("two"); - ASSERT_GT(variable->compute_equal(ivar), 0.99); - ASSERT_LT(variable->compute_equal(ivar), 2.01); - ivar = variable->find("three"); - ASSERT_DOUBLE_EQ(variable->compute_equal(ivar), 0.25 * MY_PI); + ASSERT_GT(variable->compute_equal(variable->find("two")), 0.99); + ASSERT_LT(variable->compute_equal(variable->find("two")), 2.01); + ASSERT_DOUBLE_EQ(variable->compute_equal(variable->find("three")), 0.25 * MY_PI); + ASSERT_DOUBLE_EQ(variable->compute_equal(variable->find("five")), sqrt(2.0)); + ASSERT_DOUBLE_EQ(variable->compute_equal(variable->find("six")), 0.1); + ASSERT_DOUBLE_EQ(variable->compute_equal(variable->find("seven")), 2); + ASSERT_DOUBLE_EQ(variable->compute_equal(variable->find("nine")), 1); + ASSERT_DOUBLE_EQ(variable->compute_equal(variable->find("ten")), 3); + ASSERT_FLOAT_EQ(variable->compute_equal(variable->find("ten1")), 1); + ASSERT_DOUBLE_EQ(variable->compute_equal(variable->find("ten2")), 0); + TEST_FAILURE(".*ERROR: Variable four: Invalid syntax in variable formula.*", command("print \"${four}\"");); } From 6d6e2a7920bd9d98f50711f684b51ba527a0e842 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Mar 2021 21:51:55 -0400 Subject: [PATCH 0260/1217] add simple check whether the compiled executable can actually run --- unittest/CMakeLists.txt | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/unittest/CMakeLists.txt b/unittest/CMakeLists.txt index c7f46a7f7b..f5d990d3ed 100644 --- a/unittest/CMakeLists.txt +++ b/unittest/CMakeLists.txt @@ -1,5 +1,14 @@ include(GTest) +# check if we can run the compiled executable and whether it prints +# the LAMMPS version header in the output for an empty input +file(TOUCH ${CMAKE_CURRENT_BINARY_DIR}/in.empty) +add_test(NAME RunLammps + COMMAND $ -log none -echo none -in in.empty + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) +set_tests_properties(RunLammps PROPERTIES + PASS_REGULAR_EXPRESSION "^LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]\\)") + if(BUILD_MPI) function(add_mpi_test) set(MPI_TEST_NUM_PROCS 1) From 28ac1fddc78376698c738e286cb2a0def55255ec Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Mar 2021 14:20:44 -0400 Subject: [PATCH 0261/1217] add tests for fix adapt with pairwise and coulomb interactions --- .../tests/fix-timestep-adapt_coul.yaml | 78 +++++++++++++++++++ .../tests/fix-timestep-adapt_pair.yaml | 77 ++++++++++++++++++ 2 files changed, 155 insertions(+) create mode 100644 unittest/force-styles/tests/fix-timestep-adapt_coul.yaml create mode 100644 unittest/force-styles/tests/fix-timestep-adapt_pair.yaml diff --git a/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml b/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml new file mode 100644 index 0000000000..4bf25f3b33 --- /dev/null +++ b/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml @@ -0,0 +1,78 @@ +--- +lammps_version: 10 Mar 2021 +date_generated: Thu Mar 25 14:07:45 202 +epsilon: 1e-14 +prerequisites: ! | + atom full + fix adapt +pre_commands: ! | + variable scale equal ramp(0.5,1.0) +post_commands: ! | + fix move all nve + pair_style coul/long 8.0 + pair_coeff * * + kspace_style pppm 1.0e-5 + fix test solute adapt 1 pair coul/long scale * * v_scale kspace v_scale scale no +input_file: in.fourmol +natoms: 29 +run_pos: ! |2 + 1 -2.7585387890471996e-01 2.4721267521182790e+00 -1.7590741140808724e-01 + 2 3.0525219871189541e-01 2.9567528136379986e+00 -8.4936576402532038e-01 + 3 -6.9505003051265457e-01 1.2527081545845018e+00 -6.1997181046584049e-01 + 4 -1.5812017862079175e+00 1.4837803436802379e+00 -1.2534501022240629e+00 + 5 -9.0698616844921520e-01 9.2696438488362154e-01 3.9881670647678125e-01 + 6 2.9475212358066677e-01 2.3090672513870800e-01 -1.2850129871041163e+00 + 7 3.3910265413162427e-01 -9.8304106880631008e-03 -2.4646152989509647e+00 + 8 1.1651505006204030e+00 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-4.0744208992376789e+00 -3.6231785861154941e+00 + 22 4.3619404928241057e+00 -4.2118418466324723e+00 -4.4549778550789503e+00 + 23 5.7375471428283742e+00 -3.5861419285984151e+00 -3.8743083628403299e+00 + 24 2.0685472614153846e+00 3.1534292413678289e+00 3.1539268144873454e+00 + 25 1.3099248377134609e+00 3.2652552015323466e+00 2.5158443987470833e+00 + 26 2.5769610944059931e+00 4.0046351067750248e+00 3.2209102828198946e+00 + 27 -1.9616446495134594e+00 -4.3541288139763008e+00 2.1089564303871438e+00 + 28 -2.7409194780982360e+00 -4.0232390590132754e+00 1.5874446954442702e+00 + 29 -1.3169303967683006e+00 -3.6019395338314788e+00 2.2736834157327834e+00 +run_vel: ! |2 + 1 3.2647934948866072e-03 -1.0659515509476220e-03 -3.5596416446573862e-03 + 2 6.5461183155830240e-04 5.3408204488965814e-04 3.7281153774905299e-03 + 3 5.5824606761867453e-04 6.8767077705354802e-03 2.6081254050903369e-03 + 4 -3.0104306057251481e-03 -6.3737880755571717e-03 -5.7689309472175711e-04 + 5 -1.0695603162793169e-02 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b/unittest/force-styles/tests/fix-timestep-adapt_pair.yaml new file mode 100644 index 0000000000..167f531b8e --- /dev/null +++ b/unittest/force-styles/tests/fix-timestep-adapt_pair.yaml @@ -0,0 +1,77 @@ +--- +lammps_version: 10 Mar 2021 +date_generated: Thu Mar 25 14:01:17 202 +epsilon: 1e-14 +prerequisites: ! | + atom full + fix adapt +pre_commands: ! | + variable epsilon equal ramp(0.01,0.03) +post_commands: ! | + fix move all nve + pair_style lj/cut 8.0 + pair_coeff * * 0.02 2.5 + fix test solute adapt 1 pair lj/cut epsilon * * v_epsilon scale no +input_file: in.fourmol +natoms: 29 +run_pos: ! |2 + 1 -3.2551307172152166e-01 2.4346451341937119e+00 -1.1396829659429568e-01 + 2 4.8617926885321056e-01 3.1070882859405997e+00 -1.0606347736697450e+00 + 3 -6.4277692336189840e-01 1.2540574692558419e+00 -6.5067148095539729e-01 + 4 -1.7124546848614086e+00 1.5199062846474698e+00 -1.3466731463120185e+00 + 5 -9.4318702684092770e-01 8.7036167560098177e-01 5.8107949039715845e-01 + 6 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From 27e31c4b151ae6c950d66fe630e45111fa4f4f90 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Mar 2021 14:49:49 -0400 Subject: [PATCH 0262/1217] simplify --- src/ASPHERE/compute_temp_asphere.cpp | 4 +--- src/BODY/compute_temp_body.cpp | 4 +--- src/GPU/fix_npt_gpu.cpp | 32 ++++++---------------------- src/GPU/fix_nvt_gpu.cpp | 19 ++++------------- src/USER-OMP/fix_npt_omp.cpp | 27 ++++------------------- src/USER-OMP/fix_nvt_omp.cpp | 14 ++---------- 6 files changed, 18 insertions(+), 82 deletions(-) diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp index 2fe2e9699c..9afae4d2d9 100644 --- a/src/ASPHERE/compute_temp_asphere.cpp +++ b/src/ASPHERE/compute_temp_asphere.cpp @@ -58,9 +58,7 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) : if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/asphere command"); tempbias = 1; - int n = strlen(arg[iarg+1]) + 1; - id_bias = new char[n]; - strcpy(id_bias,arg[iarg+1]); + id_bias = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"dof") == 0) { if (iarg+2 > narg) diff --git a/src/BODY/compute_temp_body.cpp b/src/BODY/compute_temp_body.cpp index 730a857aec..fb16723b23 100644 --- a/src/BODY/compute_temp_body.cpp +++ b/src/BODY/compute_temp_body.cpp @@ -56,9 +56,7 @@ ComputeTempBody::ComputeTempBody(LAMMPS *lmp, int narg, char **arg) : if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/body command"); tempbias = 1; - int n = strlen(arg[iarg+1]) + 1; - id_bias = new char[n]; - strcpy(id_bias,arg[iarg+1]); + id_bias = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"dof") == 0) { if (iarg+2 > narg) diff --git a/src/GPU/fix_npt_gpu.cpp b/src/GPU/fix_npt_gpu.cpp index 2ba0be29e0..073d5dc6c1 100644 --- a/src/GPU/fix_npt_gpu.cpp +++ b/src/GPU/fix_npt_gpu.cpp @@ -25,44 +25,24 @@ FixNPTGPU::FixNPTGPU(LAMMPS *lmp, int narg, char **arg) : FixNHGPU(lmp, narg, arg) { if (!tstat_flag) - error->all(FLERR,"Temperature control must be used with fix npt/omp"); + error->all(FLERR,"Temperature control must be used with fix npt/gpu"); if (!pstat_flag) - error->all(FLERR,"Pressure control must be used with fix npt/omp"); + error->all(FLERR,"Pressure control must be used with fix npt/gpu"); // create a new compute temp style // id = fix-ID + temp // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id)+"_temp"); + modify->add_compute(id_temp+" all temp"); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id)+"_press"); + modify->add_compute(std::string(id_press)+" all pressure "+id_temp); pcomputeflag = 1; } diff --git a/src/GPU/fix_nvt_gpu.cpp b/src/GPU/fix_nvt_gpu.cpp index 7d7826b6bf..6858c26497 100644 --- a/src/GPU/fix_nvt_gpu.cpp +++ b/src/GPU/fix_nvt_gpu.cpp @@ -26,25 +26,14 @@ FixNVTGPU::FixNVTGPU(LAMMPS *lmp, int narg, char **arg) : FixNHGPU(lmp, narg, arg) { if (!tstat_flag) - error->all(FLERR,"Temperature control must be used with fix nvt"); + error->all(FLERR,"Temperature control must be used with fix nvt/gpu"); if (pstat_flag) - error->all(FLERR,"Pressure control can not be used with fix nvt"); + error->all(FLERR,"Pressure control can not be used with fix nvt/gpu"); // create a new compute temp style // id = fix-ID + temp - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = group->names[igroup]; - newarg[2] = (char *) "temp"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id)+"_temp"); + modify->add_compute(fmt::format("{} {} temp",id_temp,group->names[igroup])); tcomputeflag = 1; } - diff --git a/src/USER-OMP/fix_npt_omp.cpp b/src/USER-OMP/fix_npt_omp.cpp index f3f08c15c2..54328803f4 100644 --- a/src/USER-OMP/fix_npt_omp.cpp +++ b/src/USER-OMP/fix_npt_omp.cpp @@ -34,35 +34,16 @@ FixNPTOMP::FixNPTOMP(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id)+"_temp"); + modify->add_compute(std::string(id_temp)+" all temp"); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id)+"_press"); + modify->add_compute(std::string(id_press)+" all pressure "+id_temp); pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nvt_omp.cpp b/src/USER-OMP/fix_nvt_omp.cpp index bfa2dcbe49..127876b4e8 100644 --- a/src/USER-OMP/fix_nvt_omp.cpp +++ b/src/USER-OMP/fix_nvt_omp.cpp @@ -33,17 +33,7 @@ FixNVTOMP::FixNVTOMP(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = group->names[igroup]; - newarg[2] = (char *) "temp"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id)+"_temp"); + modify->add_compute(fmt::format("{} {} temp",id_temp,group->names[igroup])); tcomputeflag = 1; } From 4efe60ec43e6fba31b9eebfb383ff5dac762097b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Mar 2021 17:14:57 -0400 Subject: [PATCH 0263/1217] compatibility with older CMake versions --- unittest/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/CMakeLists.txt b/unittest/CMakeLists.txt index f5d990d3ed..4e27f4be45 100644 --- a/unittest/CMakeLists.txt +++ b/unittest/CMakeLists.txt @@ -2,7 +2,7 @@ include(GTest) # check if we can run the compiled executable and whether it prints # the LAMMPS version header in the output for an empty input -file(TOUCH ${CMAKE_CURRENT_BINARY_DIR}/in.empty) +file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/in.empty "") add_test(NAME RunLammps COMMAND $ -log none -echo none -in in.empty WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) From 2b34d88b71ce3b3757b1cfbf991e422b8d92e0bb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Mar 2021 17:19:03 -0400 Subject: [PATCH 0264/1217] fix bug --- src/GPU/fix_npt_gpu.cpp | 2 +- src/USER-OMP/fix_npt_omp.cpp | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/src/GPU/fix_npt_gpu.cpp b/src/GPU/fix_npt_gpu.cpp index 073d5dc6c1..3847f31a65 100644 --- a/src/GPU/fix_npt_gpu.cpp +++ b/src/GPU/fix_npt_gpu.cpp @@ -35,7 +35,7 @@ FixNPTGPU::FixNPTGPU(LAMMPS *lmp, int narg, char **arg) : // and thus its KE/temperature contribution should use group all id_temp = utils::strdup(std::string(id)+"_temp"); - modify->add_compute(id_temp+" all temp"); + modify->add_compute(std::string(id_temp)+" all temp"); tcomputeflag = 1; // create a new compute pressure style diff --git a/src/USER-OMP/fix_npt_omp.cpp b/src/USER-OMP/fix_npt_omp.cpp index 54328803f4..4037dd928e 100644 --- a/src/USER-OMP/fix_npt_omp.cpp +++ b/src/USER-OMP/fix_npt_omp.cpp @@ -34,7 +34,6 @@ FixNPTOMP::FixNPTOMP(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - id_temp = utils::strdup(std::string(id)+"_temp"); modify->add_compute(std::string(id_temp)+" all temp"); tcomputeflag = 1; From 2baafda5171a8bf3291162ba4ef225b395695728 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Mar 2021 17:19:11 -0400 Subject: [PATCH 0265/1217] simplify --- src/USER-OMP/fix_nph_omp.cpp | 28 ++++------------------------ 1 file changed, 4 insertions(+), 24 deletions(-) diff --git a/src/USER-OMP/fix_nph_omp.cpp b/src/USER-OMP/fix_nph_omp.cpp index ba7f6e6c26..8c2f9ed3a3 100644 --- a/src/USER-OMP/fix_nph_omp.cpp +++ b/src/USER-OMP/fix_nph_omp.cpp @@ -34,35 +34,15 @@ FixNPHOMP::FixNPHOMP(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id)+"_temp"); + modify->add_compute(std::string(id_temp)+" all temp"); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id)+"_press"); + modify->add_compute(std::string(id_press)+" all pressure "+id_temp); pcomputeflag = 1; } From 53f32cea7e2b42c3ea3bf915ef3dfc3db4be6796 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Mar 2021 19:42:41 -0400 Subject: [PATCH 0266/1217] simplify using utils::strdup() --- src/GRANULAR/fix_pour.cpp | 8 ++----- src/GRANULAR/fix_wall_gran.cpp | 4 +--- src/KOKKOS/atom_kokkos.cpp | 8 ++----- src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 9 +++----- src/KOKKOS/fix_nph_kokkos.cpp | 33 ++++++--------------------- src/KOKKOS/fix_npt_kokkos.cpp | 33 ++++++--------------------- src/KOKKOS/fix_nvt_kokkos.cpp | 18 ++++----------- 7 files changed, 26 insertions(+), 87 deletions(-) diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 3b93722426..08dae55d17 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -948,18 +948,14 @@ void FixPour::options(int narg, char **arg) } else if (strcmp(arg[iarg],"rigid") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix pour command"); - int n = strlen(arg[iarg+1]) + 1; delete [] idrigid; - idrigid = new char[n]; - strcpy(idrigid,arg[iarg+1]); + idrigid = utils::strdup(arg[iarg+1]); rigidflag = 1; iarg += 2; } else if (strcmp(arg[iarg],"shake") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix pour command"); - int n = strlen(arg[iarg+1]) + 1; delete [] idshake; - idshake = new char[n]; - strcpy(idshake,arg[iarg+1]); + idshake = utils::strdup(arg[iarg+1]); shakeflag = 1; iarg += 2; diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 73d2a2f8ba..d18b72aa65 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -338,9 +338,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : } else if (strcmp(arg[iarg],"region") == 0) { if (narg < iarg+2) error->all(FLERR,"Illegal fix wall/gran command"); wallstyle = REGION; - int n = strlen(arg[iarg+1]) + 1; - idregion = new char[n]; - strcpy(idregion,arg[iarg+1]); + idregion = utils::strdup(arg[iarg+1]); iarg += 2; } diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp index c41a42c99a..19cfe02c96 100644 --- a/src/KOKKOS/atom_kokkos.cpp +++ b/src/KOKKOS/atom_kokkos.cpp @@ -257,9 +257,7 @@ int AtomKokkos::add_custom(const char *name, int flag) nivector++; iname = (char **) memory->srealloc(iname,nivector*sizeof(char *), "atom:iname"); - int n = strlen(name) + 1; - iname[index] = new char[n]; - strcpy(iname[index],name); + iname[index] = utils::strdup(name); ivector = (int **) memory->srealloc(ivector,nivector*sizeof(int *), "atom:ivector"); memory->create(ivector[index],nmax,"atom:ivector"); @@ -268,9 +266,7 @@ int AtomKokkos::add_custom(const char *name, int flag) ndvector++; dname = (char **) memory->srealloc(dname,ndvector*sizeof(char *), "atom:dname"); - int n = strlen(name) + 1; - dname[index] = new char[n]; - strcpy(dname[index],name); + dname[index] = utils::strdup(name); this->sync(Device,DVECTOR_MASK); memoryKK->grow_kokkos(k_dvector,dvector,ndvector,nmax, "atom:dvector"); diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index f1390f754b..907d1d555f 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -72,8 +72,7 @@ void AtomVecHybridKokkos::process_args(int narg, char **arg) if (strcmp(arg[iarg],keywords[i]) == 0) error->all(FLERR,"Atom style hybrid cannot use same atom style twice"); styles[nstyles] = atom->new_avec(arg[iarg],1,dummy); - keywords[nstyles] = new char[strlen(arg[iarg])+1]; - strcpy(keywords[nstyles],arg[iarg]); + keywords[nstyles] = utils::strdup(arg[iarg]); jarg = iarg + 1; while (jarg < narg && !known_style(arg[jarg])) jarg++; styles[nstyles]->process_args(jarg-iarg-1,&arg[iarg+1]); @@ -1175,10 +1174,8 @@ void AtomVecHybridKokkos::build_styles() int n; nallstyles = 0; #define ATOM_CLASS -#define AtomStyle(key,Class) \ - n = strlen(#key) + 1; \ - allstyles[nallstyles] = new char[n]; \ - strcpy(allstyles[nallstyles],#key); \ +#define AtomStyle(key,Class) \ + allstyles[nallstyles] = utils::strdup(#key); \ nallstyles++; #include "style_atom.h" // IWYU pragma: keep #undef AtomStyle diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp index 71639083d9..f679940eaf 100644 --- a/src/KOKKOS/fix_nph_kokkos.cpp +++ b/src/KOKKOS/fix_nph_kokkos.cpp @@ -29,45 +29,26 @@ FixNPHKokkos::FixNPHKokkos(LAMMPS *lmp, int narg, char **arg) : { this->kokkosable = 1; if (this->tstat_flag) - this->error->all(FLERR,"Temperature control can not be used with fix nph"); + this->error->all(FLERR,"Temperature control can not be used with fix nph/kk"); if (!this->pstat_flag) - this->error->all(FLERR,"Pressure control must be used with fix nph"); + this->error->all(FLERR,"Pressure control must be used with fix nph/kk"); // create a new compute temp style // id = fix-ID + temp // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(this->id) + 6; - this->id_temp = new char[n]; - strcpy(this->id_temp,this->id); - strcat(this->id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = this->id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp/kk"; - - this->modify->add_compute(3,newarg); - delete [] newarg; + this->id_temp = utils::strdup(std::string(this->id)+"_temp"); + this->modify->add_compute(std::string(this->id_temp)+" all temp/kk"); this->tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(this->id) + 7; - this->id_press = new char[n]; - strcpy(this->id_press,this->id); - strcat(this->id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = this->id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = this->id_temp; - this->modify->add_compute(4,newarg); - delete [] newarg; + this->id_press = utils::strdup(std::string(this->id)+"_press"); + this->modify->add_compute(std::string(this->id_press) + +" all pressure "+this->id_temp); this->pcomputeflag = 1; } diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp index 55c1d9d33f..baa47e026f 100644 --- a/src/KOKKOS/fix_npt_kokkos.cpp +++ b/src/KOKKOS/fix_npt_kokkos.cpp @@ -29,45 +29,26 @@ FixNPTKokkos::FixNPTKokkos(LAMMPS *lmp, int narg, char **arg) : { this->kokkosable = 1; if (!this->tstat_flag) - this->error->all(FLERR,"Temperature control must be used with fix npt"); + this->error->all(FLERR,"Temperature control must be used with fix npt/kk"); if (!this->pstat_flag) - this->error->all(FLERR,"Pressure control must be used with fix npt"); + this->error->all(FLERR,"Pressure control must be used with fix npt/kk"); // create a new compute temp style // id = fix-ID + temp // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(this->id) + 6; - this->id_temp = new char[n]; - strcpy(this->id_temp,this->id); - strcat(this->id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = this->id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp/kk"; - - this->modify->add_compute(3,newarg); - delete [] newarg; + this->id_temp = utils::strdup(std::string(this->id)+"_temp"); + this->modify->add_compute(std::string(this->id_temp)+" all temp/kk"); this->tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(this->id) + 7; - this->id_press = new char[n]; - strcpy(this->id_press,this->id); - strcat(this->id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = this->id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = this->id_temp; - this->modify->add_compute(4,newarg); - delete [] newarg; + this->id_press = utils::strdup(std::string(this->id)+"_press"); + this->modify->add_compute(std::string(this->id_press) + +" all pressure "+this->id_temp); this->pcomputeflag = 1; } diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp index 25984726b7..f589600dde 100644 --- a/src/KOKKOS/fix_nvt_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_kokkos.cpp @@ -30,25 +30,15 @@ FixNVTKokkos::FixNVTKokkos(LAMMPS *lmp, int narg, char **arg) : { this->kokkosable = 1; if (!this->tstat_flag) - this->error->all(FLERR,"Temperature control must be used with fix nvt"); + this->error->all(FLERR,"Temperature control must be used with fix nvt/kk"); if (this->pstat_flag) - this->error->all(FLERR,"Pressure control can not be used with fix nvt"); + this->error->all(FLERR,"Pressure control can not be used with fix nvt/kk"); // create a new compute temp style // id = fix-ID + temp - int n = strlen(this->id) + 6; - this->id_temp = new char[n]; - strcpy(this->id_temp,this->id); - strcat(this->id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = this->id_temp; - newarg[1] = this->group->names[this->igroup]; - newarg[2] = (char *) "temp/kk"; - - this->modify->add_compute(3,newarg); - delete [] newarg; + this->id_temp = utils::strdup(std::string(this->id)+"_temp"); + this->modify->add_compute(std::string(this->id_temp)+" all temp/kk"); this->tcomputeflag = 1; } From e0fdd2ad892531632ce18b6cd929f73367c33b91 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Mar 2021 10:09:08 -0400 Subject: [PATCH 0267/1217] correct lammps.extract_global() method for returned arrays which are returned as list --- python/lammps/core.py | 21 +++++++++++++++++---- unittest/python/python-commands.py | 9 +++++++++ 2 files changed, 26 insertions(+), 4 deletions(-) diff --git a/python/lammps/core.py b/python/lammps/core.py index be026d5e10..279b0a64dc 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -746,12 +746,21 @@ class lammps(object): :type name: string :param dtype: data type of the returned data (see :ref:`py_datatype_constants`) :type dtype: int, optional - :return: value of the property or None - :rtype: int, float, or NoneType + :return: value of the property or list of values or None + :rtype: int, float, list, or NoneType """ + if dtype == LAMMPS_AUTODETECT: dtype = self.extract_global_datatype(name) + # set length of vector for items that are not a scalar + vec_dict = { 'boxlo':3, 'boxhi':3, 'sublo':3, 'subhi':3, + 'sublo_lambda':3, 'subhi_lambda':3, 'periodicity':3 } + if name in vec_dict: + veclen = vec_dict[name] + else: + veclen = 1 + if name: name = name.encode() else: return None @@ -770,10 +779,14 @@ class lammps(object): ptr = self.lib.lammps_extract_global(self.lmp, name) if ptr: - return target_type(ptr[0]) + if veclen > 1: + result = [] + for i in range(0,veclen): + result.append(target_type(ptr[i])) + return result + else: return target_type(ptr[0]) return None - # ------------------------------------------------------------------------- # extract per-atom info datatype diff --git a/unittest/python/python-commands.py b/unittest/python/python-commands.py index c82e2fdb26..c1e4cecef5 100644 --- a/unittest/python/python-commands.py +++ b/unittest/python/python-commands.py @@ -268,6 +268,15 @@ create_atoms 1 single & self.assertEqual(self.lmp.extract_global("boxyhi"), 2.0) self.assertEqual(self.lmp.extract_global("boxzlo"), -3.0) self.assertEqual(self.lmp.extract_global("boxzhi"), 3.0) + self.assertEqual(self.lmp.extract_global("boxlo"), [-1.0, -2.0, -3.0]) + self.assertEqual(self.lmp.extract_global("boxhi"), [1.0, 2.0, 3.0]) + self.assertEqual(self.lmp.extract_global("sublo"), [-1.0, -2.0, -3.0]) + self.assertEqual(self.lmp.extract_global("subhi"), [1.0, 2.0, 3.0]) + self.assertEqual(self.lmp.extract_global("periodicity"), [1,1,1]) + # only valid for triclinic box + self.lmp.command("change_box all triclinic") + self.assertEqual(self.lmp.extract_global("sublo_lambda"), [0.0, 0.0, 0.0]) + self.assertEqual(self.lmp.extract_global("subhi_lambda"), [1.0, 1.0, 1.0]) ############################## if __name__ == "__main__": From b8f02d759abdbbd88407818bef22bcc48abe7e43 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Mar 2021 11:22:22 -0400 Subject: [PATCH 0268/1217] add support for extracting respa levels and timestep values --- python/lammps/core.py | 2 ++ src/library.cpp | 19 ++++++++++++++++++- unittest/python/python-commands.py | 10 ++++++++++ 3 files changed, 30 insertions(+), 1 deletion(-) diff --git a/python/lammps/core.py b/python/lammps/core.py index 279b0a64dc..b3cdceb1a6 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -758,6 +758,8 @@ class lammps(object): 'sublo_lambda':3, 'subhi_lambda':3, 'periodicity':3 } if name in vec_dict: veclen = vec_dict[name] + elif name == 'respa_dt': + veclen = self.extract_global('respa_levels',LAMMPS_INT) else: veclen = 1 diff --git a/src/library.cpp b/src/library.cpp index 8de36a299f..6f08cffcc2 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -31,12 +31,14 @@ #include "group.h" #include "info.h" #include "input.h" +#include "integrate.h" #include "memory.h" #include "modify.h" #include "molecule.h" #include "neigh_list.h" #include "neighbor.h" #include "region.h" +#include "respa.h" #include "output.h" #include "thermo.h" #include "timer.h" @@ -984,12 +986,14 @@ to then decide how to cast the (void*) pointer and access the data. * \return integer constant encoding the data type of the property * or -1 if not found. */ -int lammps_extract_global_datatype(void *handle, const char *name) +int lammps_extract_global_datatype(void * /*handle*/, const char *name) { if (strcmp(name,"dt") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"ntimestep") == 0) return LAMMPS_BIGINT; if (strcmp(name,"atime") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"atimestep") == 0) return LAMMPS_BIGINT; + if (strcmp(name,"respa_levels") == 0) return LAMMPS_INT; + if (strcmp(name,"respa_dt") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"boxlo") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"boxhi") == 0) return LAMMPS_DOUBLE; @@ -1116,6 +1120,14 @@ report the "native" data type. The following tables are provided: - bigint - 1 - the number of the timestep when "atime" was last updated. + * - respa_levels + - int + - 1 + - number of r-RESPA levels. See :doc:`run_style`. + * - respa_dt + - double + - number of r-RESPA levels + - length of the time steps with r-RESPA. See :doc:`run_style`. .. _extract_box_settings: @@ -1366,6 +1378,11 @@ void *lammps_extract_global(void *handle, const char *name) if (strcmp(name,"atime") == 0) return (void *) &lmp->update->atime; if (strcmp(name,"atimestep") == 0) return (void *) &lmp->update->atimestep; + if (utils::strmatch(lmp->update->integrate_style,"^respa")) { + Respa *respa = (Respa *)lmp->update->integrate; + if (strcmp(name,"respa_levels") == 0) return (void *) &respa->nlevels; + if (strcmp(name,"respa_dt") == 0) return (void *) respa->step; + } if (strcmp(name,"boxlo") == 0) return (void *) lmp->domain->boxlo; if (strcmp(name,"boxhi") == 0) return (void *) lmp->domain->boxhi; if (strcmp(name,"sublo") == 0) return (void *) lmp->domain->sublo; diff --git a/unittest/python/python-commands.py b/unittest/python/python-commands.py index c1e4cecef5..3bcb785b74 100644 --- a/unittest/python/python-commands.py +++ b/unittest/python/python-commands.py @@ -274,6 +274,16 @@ create_atoms 1 single & self.assertEqual(self.lmp.extract_global("subhi"), [1.0, 2.0, 3.0]) self.assertEqual(self.lmp.extract_global("periodicity"), [1,1,1]) # only valid for triclinic box + self.assertEqual(self.lmp.extract_global("respa_levels"), None) + self.assertEqual(self.lmp.extract_global("respa_dt"), None) + + # set and initialize r-RESPA + self.lmp.command("run_style respa 3 5 2 pair 2 kspace 3") + self.lmp.command("mass * 1.0") + self.lmp.command("run 1 post no") + self.assertEqual(self.lmp.extract_global("ntimestep"), 1) + self.assertEqual(self.lmp.extract_global("respa_levels"), 3) + self.assertEqual(self.lmp.extract_global("respa_dt"), [0.0005, 0.0025, 0.005]) self.lmp.command("change_box all triclinic") self.assertEqual(self.lmp.extract_global("sublo_lambda"), [0.0, 0.0, 0.0]) self.assertEqual(self.lmp.extract_global("subhi_lambda"), [1.0, 1.0, 1.0]) From a193d9d429ccf8129db46731bf3716b5b58b2c8c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Mar 2021 11:23:28 -0400 Subject: [PATCH 0269/1217] fix several issues when using extract_global() from python exposed by tests --- python/lammps/core.py | 3 ++- src/library.cpp | 9 +++++++-- unittest/python/python-commands.py | 13 +++++++++++-- 3 files changed, 20 insertions(+), 5 deletions(-) diff --git a/python/lammps/core.py b/python/lammps/core.py index b3cdceb1a6..e112c4f3f8 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -777,10 +777,11 @@ class lammps(object): target_type = float elif dtype == LAMMPS_STRING: self.lib.lammps_extract_global.restype = c_char_p - target_type = lambda x: str(x, 'ascii') ptr = self.lib.lammps_extract_global(self.lmp, name) if ptr: + if dtype == LAMMPS_STRING: + return ptr.decode('utf-8') if veclen > 1: result = [] for i in range(0,veclen): diff --git a/src/library.cpp b/src/library.cpp index 6f08cffcc2..a950d31e4e 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -1387,8 +1387,13 @@ void *lammps_extract_global(void *handle, const char *name) if (strcmp(name,"boxhi") == 0) return (void *) lmp->domain->boxhi; if (strcmp(name,"sublo") == 0) return (void *) lmp->domain->sublo; if (strcmp(name,"subhi") == 0) return (void *) lmp->domain->subhi; - if (strcmp(name,"sublo_lambda") == 0) return (void *) lmp->domain->sublo_lamda; - if (strcmp(name,"subhi_lambda") == 0) return (void *) lmp->domain->subhi_lamda; + // these are only valid for a triclinic cell + if (lmp->domain->triclinic) { + if (strcmp(name,"sublo_lambda") == 0) + return (void *) lmp->domain->sublo_lamda; + if (strcmp(name,"subhi_lambda") == 0) + return (void *) lmp->domain->subhi_lamda; + } if (strcmp(name,"boxxlo") == 0) return (void *) &lmp->domain->boxlo[0]; if (strcmp(name,"boxxhi") == 0) return (void *) &lmp->domain->boxhi[0]; if (strcmp(name,"boxylo") == 0) return (void *) &lmp->domain->boxlo[1]; diff --git a/unittest/python/python-commands.py b/unittest/python/python-commands.py index 3bcb785b74..3661feb8a0 100644 --- a/unittest/python/python-commands.py +++ b/unittest/python/python-commands.py @@ -259,9 +259,13 @@ create_atoms 1 single & result = self.lmp.get_thermo(key) self.assertEqual(value, result, key) - def test_extract_global_double(self): + def test_extract_global(self): self.lmp.command("region box block -1 1 -2 2 -3 3") self.lmp.command("create_box 1 box") + self.assertEqual(self.lmp.extract_global("units"), "lj") + self.assertEqual(self.lmp.extract_global("ntimestep"), 0) + self.assertEqual(self.lmp.extract_global("dt"), 0.005) + self.assertEqual(self.lmp.extract_global("boxxlo"), -1.0) self.assertEqual(self.lmp.extract_global("boxxhi"), 1.0) self.assertEqual(self.lmp.extract_global("boxylo"), -2.0) @@ -273,7 +277,9 @@ create_atoms 1 single & self.assertEqual(self.lmp.extract_global("sublo"), [-1.0, -2.0, -3.0]) self.assertEqual(self.lmp.extract_global("subhi"), [1.0, 2.0, 3.0]) self.assertEqual(self.lmp.extract_global("periodicity"), [1,1,1]) - # only valid for triclinic box + self.assertEqual(self.lmp.extract_global("triclinic"), 0) + self.assertEqual(self.lmp.extract_global("sublo_lambda"), None) + self.assertEqual(self.lmp.extract_global("subhi_lambda"), None) self.assertEqual(self.lmp.extract_global("respa_levels"), None) self.assertEqual(self.lmp.extract_global("respa_dt"), None) @@ -284,7 +290,10 @@ create_atoms 1 single & self.assertEqual(self.lmp.extract_global("ntimestep"), 1) self.assertEqual(self.lmp.extract_global("respa_levels"), 3) self.assertEqual(self.lmp.extract_global("respa_dt"), [0.0005, 0.0025, 0.005]) + + # checks only for triclinic boxes self.lmp.command("change_box all triclinic") + self.assertEqual(self.lmp.extract_global("triclinic"), 1) self.assertEqual(self.lmp.extract_global("sublo_lambda"), [0.0, 0.0, 0.0]) self.assertEqual(self.lmp.extract_global("subhi_lambda"), [1.0, 1.0, 1.0]) From cb25e4aa3957b44af87823c2ec9e2f67a28c2845 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 25 Mar 2021 20:08:32 -0400 Subject: [PATCH 0270/1217] Add nve respa testcase for python/move --- unittest/force-styles/test_fix_timestep.cpp | 3 +-- unittest/force-styles/tests/py_nve.py | 29 +++++++++++++++++++++ 2 files changed, 30 insertions(+), 2 deletions(-) diff --git a/unittest/force-styles/test_fix_timestep.cpp b/unittest/force-styles/test_fix_timestep.cpp index aa07f36fb9..f72295716e 100644 --- a/unittest/force-styles/test_fix_timestep.cpp +++ b/unittest/force-styles/test_fix_timestep.cpp @@ -521,8 +521,7 @@ TEST(FixTimestep, plain) // fix python/move implementation is missing library interface access to Repsa::step ifix = lmp->modify->find_fix("test"); if (!utils::strmatch(lmp->modify->fix[ifix]->style, "^rigid") && - !utils::strmatch(lmp->modify->fix[ifix]->style, "^nve/limit") && - !utils::strmatch(lmp->modify->fix[ifix]->style, "^python/move") + !utils::strmatch(lmp->modify->fix[ifix]->style, "^nve/limit") ) { if (!verbose) ::testing::internal::CaptureStdout(); diff --git a/unittest/force-styles/tests/py_nve.py b/unittest/force-styles/tests/py_nve.py index 1f05be04a8..57592ea074 100644 --- a/unittest/force-styles/tests/py_nve.py +++ b/unittest/force-styles/tests/py_nve.py @@ -34,6 +34,7 @@ class NVE(LAMMPSFixMove): def __init__(self, ptr, group_name="all"): super(NVE, self).__init__(ptr) assert(self.group_name == "all") + self._step_respa = None def init(self): dt = self.lmp.extract_global("dt") @@ -42,6 +43,12 @@ class NVE(LAMMPSFixMove): self.dtv = dt self.dtf = 0.5 * dt * ftm2v + @property + def step_respa(self): + if not self._step_respa: + self._step_respa = self.lmp.extract_global("respa_dt") + return self._step_respa + def initial_integrate(self, vflag): nlocal = self.lmp.extract_global("nlocal") mass = self.lmp.extract_atom("mass") @@ -72,4 +79,26 @@ class NVE(LAMMPSFixMove): v[i][1] += dtfm * f[i][1] v[i][2] += dtfm * f[i][2] + def initial_integrate_respa(self, vflag, ilevel, iloop): + ftm2v = self.lmp.extract_global("ftm2v") + self.dtv = self.step_respa[ilevel] + self.dtf = 0.5 * self.step_respa[ilevel] * ftm2v + # innermost level - NVE update of v and x + # all other levels - NVE update of v + + if ilevel == 0: + self.initial_integrate(vflag) + else: + self.final_integrate() + + def final_integrate_respa(self, ilevel, iloop): + ftm2v = self.lmp.extract_global("ftm2v") + self.dtf = 0.5 * self.step_respa[ilevel] * ftm2v + self.final_integrate() + + def reset_dt(self): + dt = self.lmp.extract_global("dt") + ftm2v = self.lmp.extract_global("ftm2v") + self.dtv = dt; + self.dtf = 0.5 * dt * ftm2v; From 029db1413e5248e344df1b1a161b4f90e62932eb Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 25 Mar 2021 21:01:32 -0400 Subject: [PATCH 0271/1217] Add missing verbose after merge --- unittest/python/test_python_package.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/unittest/python/test_python_package.cpp b/unittest/python/test_python_package.cpp index 5a36112781..c240d23875 100644 --- a/unittest/python/test_python_package.cpp +++ b/unittest/python/test_python_package.cpp @@ -33,6 +33,7 @@ std::string INPUT_FOLDER = STRINGIFY(TEST_INPUT_FOLDER); const char * LOREM_IPSUM = "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent metus."; +bool verbose = false; using LAMMPS_NS::utils::split_words; From 756d935d0651768d042dc7c2dcdd91e0d1e68e5b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Mar 2021 21:13:24 -0400 Subject: [PATCH 0272/1217] use std:: namespace for STL containers --- src/USER-AWPMD/pair_awpmd_cut.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index 3d4e1f12a7..54f851171b 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -150,7 +150,7 @@ void PairAWPMDCut::compute(int eflag, int vflag) # if 1 // mapping of the LAMMPS numbers to the AWPMC numbers - vector gmap(ntot,-1); + std::vector gmap(ntot,-1); for (int ii = 0; ii < inum; ii++) { int i = ilist[ii]; @@ -226,7 +226,7 @@ void PairAWPMDCut::compute(int eflag, int vflag) // prepare the solver object wpmd->reset(); - map > etmap; + std::map > etmap; // add particles to the AWPMD solver object for (int i = 0; i < ntot; i++) { //int i = ilist[ii]; @@ -246,8 +246,8 @@ void PairAWPMDCut::compute(int eflag, int vflag) fi= new Vector_3[wpmd->ni]; // adding electrons - for (map >::iterator it=etmap.begin(); it!= etmap.end(); ++it) { - vector &el=it->second; + for (std::map >::iterator it=etmap.begin(); it!= etmap.end(); ++it) { + std::vector &el=it->second; if (!el.size()) // should not happen continue; int s=spin[el[0]] >0 ? 0 : 1; From 664335420aebe34d95fa72382f5b5285d64f621e Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 26 Mar 2021 11:50:58 -0400 Subject: [PATCH 0273/1217] Start refactoring tests --- .../formats/test_potential_file_reader.cpp | 120 ++++++------------ unittest/testing/core.h | 75 ++++++++++- 2 files changed, 107 insertions(+), 88 deletions(-) diff --git a/unittest/formats/test_potential_file_reader.cpp b/unittest/formats/test_potential_file_reader.cpp index 6cf2fd010c..1e3d96d6d7 100644 --- a/unittest/formats/test_potential_file_reader.cpp +++ b/unittest/formats/test_potential_file_reader.cpp @@ -28,37 +28,17 @@ #include "potential_file_reader.h" #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "../testing/core.h" #include #include #include #include -#if defined(OMPI_MAJOR_VERSION) -const bool have_openmpi = true; -#else -const bool have_openmpi = false; -#endif - using namespace LAMMPS_NS; using ::testing::MatchesRegex; using utils::split_words; -#define TEST_FAILURE(errmsg, ...) \ - if (Info::has_exceptions()) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_ANY_THROW({__VA_ARGS__}); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } else { \ - if (!have_openmpi) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_DEATH({__VA_ARGS__}, ""); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } \ - } - // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; @@ -75,38 +55,16 @@ const int LAMMPS_NS::PairNb3bHarmonic::NPARAMS_PER_LINE; const int LAMMPS_NS::PairVashishta::NPARAMS_PER_LINE; const int LAMMPS_NS::PairTersoffTable::NPARAMS_PER_LINE; -class PotentialFileReaderTest : public ::testing::Test { -protected: - LAMMPS *lmp; - - void SetUp() override - { - const char *args[] = { - "PotentialFileReaderTest", "-log", "none", "-echo", "screen", "-nocite"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void TearDown() override - { - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void command(const std::string &cmd) { lmp->input->one(cmd); } +class PotentialFileReaderTest : public LAMMPSTest { }; // open for native units TEST_F(PotentialFileReaderTest, Sw_native) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); PotentialFileReader reader(lmp, "Si.sw", "Stillinger-Weber"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto line = reader.next_line(PairSW::NPARAMS_PER_LINE); ASSERT_EQ(utils::count_words(line), PairSW::NPARAMS_PER_LINE); @@ -115,10 +73,10 @@ TEST_F(PotentialFileReaderTest, Sw_native) // open with supported conversion enabled TEST_F(PotentialFileReaderTest, Sw_conv) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units real"); PotentialFileReader reader(lmp, "Si.sw", "Stillinger-Weber", utils::METAL2REAL); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto line = reader.next_line(PairSW::NPARAMS_PER_LINE); ASSERT_EQ(utils::count_words(line), PairSW::NPARAMS_PER_LINE); @@ -127,9 +85,9 @@ TEST_F(PotentialFileReaderTest, Sw_conv) // open without conversion enabled TEST_F(PotentialFileReaderTest, Sw_noconv) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units real"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR on proc.*potential.*requires metal units but real.*", PotentialFileReader reader(lmp, "Si.sw", "Stillinger-Weber", utils::REAL2METAL);); @@ -137,10 +95,10 @@ TEST_F(PotentialFileReaderTest, Sw_noconv) TEST_F(PotentialFileReaderTest, Comb) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); PotentialFileReader reader(lmp, "ffield.comb", "COMB"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto line = reader.next_line(PairComb::NPARAMS_PER_LINE); ASSERT_EQ(utils::count_words(line), PairComb::NPARAMS_PER_LINE); @@ -148,10 +106,10 @@ TEST_F(PotentialFileReaderTest, Comb) TEST_F(PotentialFileReaderTest, Comb3) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); PotentialFileReader reader(lmp, "ffield.comb3", "COMB3"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto line = reader.next_line(PairComb3::NPARAMS_PER_LINE); ASSERT_EQ(utils::count_words(line), PairComb3::NPARAMS_PER_LINE); @@ -159,10 +117,10 @@ TEST_F(PotentialFileReaderTest, Comb3) TEST_F(PotentialFileReaderTest, Tersoff) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); PotentialFileReader reader(lmp, "Si.tersoff", "Tersoff"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto line = reader.next_line(PairTersoff::NPARAMS_PER_LINE); ASSERT_EQ(utils::count_words(line), PairTersoff::NPARAMS_PER_LINE); @@ -170,10 +128,10 @@ TEST_F(PotentialFileReaderTest, Tersoff) TEST_F(PotentialFileReaderTest, TersoffMod) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); PotentialFileReader reader(lmp, "Si.tersoff.mod", "Tersoff/Mod"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto line = reader.next_line(PairTersoffMOD::NPARAMS_PER_LINE); ASSERT_EQ(utils::count_words(line), PairTersoffMOD::NPARAMS_PER_LINE); @@ -181,10 +139,10 @@ TEST_F(PotentialFileReaderTest, TersoffMod) TEST_F(PotentialFileReaderTest, TersoffModC) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); PotentialFileReader reader(lmp, "Si.tersoff.modc", "Tersoff/ModC"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto line = reader.next_line(PairTersoffMODC::NPARAMS_PER_LINE); ASSERT_EQ(utils::count_words(line), PairTersoffMODC::NPARAMS_PER_LINE); @@ -192,10 +150,10 @@ TEST_F(PotentialFileReaderTest, TersoffModC) TEST_F(PotentialFileReaderTest, TersoffTable) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); PotentialFileReader reader(lmp, "Si.tersoff", "TersoffTable"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto line = reader.next_line(PairTersoffTable::NPARAMS_PER_LINE); ASSERT_EQ(utils::count_words(line), PairTersoffTable::NPARAMS_PER_LINE); @@ -203,10 +161,10 @@ TEST_F(PotentialFileReaderTest, TersoffTable) TEST_F(PotentialFileReaderTest, TersoffZBL) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); PotentialFileReader reader(lmp, "SiC.tersoff.zbl", "Tersoff/ZBL"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto line = reader.next_line(PairTersoffZBL::NPARAMS_PER_LINE); ASSERT_EQ(utils::count_words(line), PairTersoffZBL::NPARAMS_PER_LINE); @@ -214,10 +172,10 @@ TEST_F(PotentialFileReaderTest, TersoffZBL) TEST_F(PotentialFileReaderTest, GW) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); PotentialFileReader reader(lmp, "SiC.gw", "GW"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto line = reader.next_line(PairGW::NPARAMS_PER_LINE); ASSERT_EQ(utils::count_words(line), PairGW::NPARAMS_PER_LINE); @@ -225,10 +183,10 @@ TEST_F(PotentialFileReaderTest, GW) TEST_F(PotentialFileReaderTest, GWZBL) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); PotentialFileReader reader(lmp, "SiC.gw.zbl", "GW/ZBL"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto line = reader.next_line(PairGWZBL::NPARAMS_PER_LINE); ASSERT_EQ(utils::count_words(line), PairGWZBL::NPARAMS_PER_LINE); @@ -236,10 +194,10 @@ TEST_F(PotentialFileReaderTest, GWZBL) TEST_F(PotentialFileReaderTest, Nb3bHarmonic) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units real"); PotentialFileReader reader(lmp, "MOH.nb3b.harmonic", "NB3B Harmonic"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto line = reader.next_line(PairNb3bHarmonic::NPARAMS_PER_LINE); ASSERT_EQ(utils::count_words(line), PairNb3bHarmonic::NPARAMS_PER_LINE); @@ -247,10 +205,10 @@ TEST_F(PotentialFileReaderTest, Nb3bHarmonic) TEST_F(PotentialFileReaderTest, Vashishta) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); PotentialFileReader reader(lmp, "SiC.vashishta", "Vashishta"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto line = reader.next_line(PairVashishta::NPARAMS_PER_LINE); ASSERT_EQ(utils::count_words(line), PairVashishta::NPARAMS_PER_LINE); @@ -261,38 +219,38 @@ TEST_F(PotentialFileReaderTest, UnitConvert) PotentialFileReader *reader; int unit_convert, flag; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); reader = new PotentialFileReader(lmp, "Si.sw", "Stillinger-Weber"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); unit_convert = reader->get_unit_convert(); ASSERT_EQ(unit_convert, 0); delete reader; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); flag = utils::get_supported_conversions(utils::UNKNOWN); reader = new PotentialFileReader(lmp, "Si.sw", "Stillinger-Weber", flag); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); unit_convert = reader->get_unit_convert(); ASSERT_EQ(unit_convert, 0); delete reader; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); flag = utils::get_supported_conversions(utils::ENERGY); reader = new PotentialFileReader(lmp, "Si.sw", "Stillinger-Weber", flag); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); unit_convert = reader->get_unit_convert(); ASSERT_EQ(unit_convert, 0); delete reader; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); flag = utils::get_supported_conversions(utils::ENERGY); command("units real"); reader = new PotentialFileReader(lmp, "Si.sw", "Stillinger-Weber", flag); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); unit_convert = reader->get_unit_convert(); ASSERT_EQ(unit_convert, utils::METAL2REAL); @@ -304,7 +262,7 @@ int main(int argc, char **argv) MPI_Init(&argc, &argv); ::testing::InitGoogleMock(&argc, argv); - if (have_openmpi && !LAMMPS_NS::Info::has_exceptions()) + if (Info::get_mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) std::cout << "Warning: using OpenMPI without exceptions. " "Death tests will be skipped\n"; diff --git a/unittest/testing/core.h b/unittest/testing/core.h index 6243eb219e..19013bf90a 100644 --- a/unittest/testing/core.h +++ b/unittest/testing/core.h @@ -16,8 +16,12 @@ #include "info.h" #include "input.h" #include "lammps.h" +#include "variable.h" #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "exceptions.h" + +#include using namespace LAMMPS_NS; @@ -45,29 +49,86 @@ class LAMMPSTest : public ::testing::Test { public: void command(const std::string &line) { lmp->input->one(line.c_str()); } + void BEGIN_HIDE_OUTPUT() { + if (!verbose) ::testing::internal::CaptureStdout(); + } + + void END_HIDE_OUTPUT() { + if (!verbose) ::testing::internal::GetCapturedStdout(); + } + + void BEGIN_CAPTURE_OUTPUT() { + if (!verbose) ::testing::internal::CaptureStdout(); + } + + std::string END_CAPTURE_OUTPUT() { + auto output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + return output; + } + + void HIDE_OUTPUT(std::function f) { + if (!verbose) ::testing::internal::CaptureStdout(); + try { + f(); + } catch(LAMMPSException & e) { + if (!verbose) std::cout << ::testing::internal::GetCapturedStdout(); + throw e; + } + if (!verbose) ::testing::internal::GetCapturedStdout(); + } + + std::string CAPTURE_OUTPUT(std::function f) { + ::testing::internal::CaptureStdout(); + try { + f(); + } catch(LAMMPSException & e) { + if (verbose) std::cout << ::testing::internal::GetCapturedStdout(); + throw e; + } + auto output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + return output; + } + + double get_variable_value(const std::string & name) { + char * str = utils::strdup(fmt::format("v_{}", name)); + double value = lmp->input->variable->compute_equal(str); + delete [] str; + return value; + } + + std::string get_variable_string(const std::string & name) { + return lmp->input->variable->retrieve(name.c_str()); + } + protected: const char *testbinary = "LAMMPSTest"; LAMMPS *lmp; + Info *info; void SetUp() override { const char *args[] = {testbinary, "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); + HIDE_OUTPUT([&] { + lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); + info = new Info(lmp); + }); InitSystem(); - if (!verbose) ::testing::internal::GetCapturedStdout(); } virtual void InitSystem() {} void TearDown() override { - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - lmp = nullptr; - if (!verbose) ::testing::internal::GetCapturedStdout(); + HIDE_OUTPUT([&] { + delete info; + delete lmp; + info = nullptr; + lmp = nullptr; + }); } }; From 1752bd02765a25caec346d1a034f7226f131679e Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 26 Mar 2021 12:23:58 -0400 Subject: [PATCH 0274/1217] Refactoring of some test files --- unittest/commands/test_groups.cpp | 121 +++++-------- unittest/commands/test_simple_commands.cpp | 201 ++++++++------------- unittest/testing/core.h | 1 + 3 files changed, 122 insertions(+), 201 deletions(-) diff --git a/unittest/commands/test_groups.cpp b/unittest/commands/test_groups.cpp index 3ae1722f4d..181f000a7c 100644 --- a/unittest/commands/test_groups.cpp +++ b/unittest/commands/test_groups.cpp @@ -22,6 +22,7 @@ #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "../testing/core.h" #include #include @@ -29,12 +30,6 @@ // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; -#if defined(OMPI_MAJOR_VERSION) -const bool have_openmpi = true; -#else -const bool have_openmpi = false; -#endif - using LAMMPS_NS::utils::split_words; namespace LAMMPS_NS { @@ -42,54 +37,22 @@ using ::testing::ExitedWithCode; using ::testing::MatchesRegex; using ::testing::StrEq; -#define TEST_FAILURE(errmsg, ...) \ - if (Info::has_exceptions()) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_ANY_THROW({__VA_ARGS__}); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - if (verbose) std::cout << mesg; \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } else { \ - if (!have_openmpi) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_DEATH({__VA_ARGS__}, ""); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - if (verbose) std::cout << mesg; \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } \ - } - -class GroupTest : public ::testing::Test { +class GroupTest : public LAMMPSTest { protected: - LAMMPS *lmp; Group *group; Domain *domain; void SetUp() override { - const char *args[] = {"GroupTest", "-log", "none", "-echo", "screen", "-nocite"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - if (!verbose) ::testing::internal::GetCapturedStdout(); + testbinary = "GroupTest"; + LAMMPSTest::SetUp(); group = lmp->group; domain = lmp->domain; } - void TearDown() override - { - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); - std::cout.flush(); - } - - void command(const std::string &cmd) { lmp->input->one(cmd); } - void atomic_system() { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units real"); command("lattice sc 1.0 origin 0.125 0.125 0.125"); command("region box block -2 2 -2 2 -2 2"); @@ -101,23 +64,25 @@ protected: command("region top block INF INF -2.0 -1.0 INF INF"); command("set region left type 2"); command("set region right type 3"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } void molecular_system() { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("fix props all property/atom mol rmass q"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); + atomic_system(); - if (!verbose) ::testing::internal::CaptureStdout(); + + BEGIN_HIDE_OUTPUT(); command("variable molid atom floor(id/4)+1"); command("variable charge atom 2.0*sin(PI/32*id)"); command("set atom * mol v_molid"); command("set atom * charge v_charge"); command("set type 1 mass 0.5"); command("set type 2*4 mass 2.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } }; @@ -131,7 +96,7 @@ TEST_F(GroupTest, EmptyDelete) { atomic_system(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group new1 empty"); command("group new2 empty"); command("group new2 empty"); @@ -143,16 +108,16 @@ TEST_F(GroupTest, EmptyDelete) command("compute 1 new3 ke"); command("dump 1 new4 atom 50 dump.melt"); command("atom_modify first new5"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(group->ngroup, 7); TEST_FAILURE(".*ERROR: Illegal group command.*", command("group new3 xxx");); TEST_FAILURE(".*ERROR: Illegal group command.*", command("group new3 empty xxx");); TEST_FAILURE(".*ERROR: Group command requires atom attribute molecule.*", command("group new2 include molecule");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); group->assign("new1 delete"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(group->ngroup, 6); TEST_FAILURE(".*ERROR: Illegal group command.*", command("group new2 delete xxx");); @@ -172,13 +137,13 @@ TEST_F(GroupTest, RegionClear) { atomic_system(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group one region left"); command("group two region right"); command("group three empty"); command("group four region left"); command("group four region right"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(group->count(group->find("one")), 16); ASSERT_EQ(group->count(group->find("two")), 16); ASSERT_EQ(group->count(group->find("three")), 0); @@ -189,20 +154,20 @@ TEST_F(GroupTest, RegionClear) TEST_FAILURE(".*ERROR: Illegal group command.*", command("group three region left xxx");); TEST_FAILURE(".*ERROR: Group region ID does not exist.*", command("group four region dummy");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group one clear"); command("group two clear"); command("group three clear"); command("group four clear"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(group->count(group->find("one")), 0); ASSERT_EQ(group->count(group->find("two")), 0); ASSERT_EQ(group->count(group->find("three")), 0); ASSERT_EQ(group->count(group->find("four")), 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("delete_atoms region box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(group->count(group->find("all")), 0); } @@ -214,7 +179,7 @@ TEST_F(GroupTest, SelectRestart) for (int i = 0; i < lmp->atom->natoms; ++i) flags[i] = i & 1; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group one region left"); command("group two region right"); group->create("half", flags); @@ -224,7 +189,7 @@ TEST_F(GroupTest, SelectRestart) command("group five subtract all half four"); command("group top region top"); command("group six intersect half top"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(group->count(group->find("one")), 16); ASSERT_EQ(group->count(group->find("two")), 16); ASSERT_EQ(group->count(group->find("three")), 0); @@ -235,12 +200,12 @@ TEST_F(GroupTest, SelectRestart) ASSERT_EQ(group->count(group->find("half"), domain->find_region("top")), 8); ASSERT_DOUBLE_EQ(group->mass(group->find("half"), domain->find_region("top")), 8.0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("write_restart group.restart"); command("clear"); command("read_restart group.restart"); unlink("group.restart"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); group = lmp->group; ASSERT_EQ(group->count(group->find("one")), 16); ASSERT_EQ(group->count(group->find("two")), 16); @@ -250,11 +215,11 @@ TEST_F(GroupTest, SelectRestart) ASSERT_EQ(group->count(group->find("five")), 16); ASSERT_DOUBLE_EQ(group->mass(group->find("six")), 8.0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group four clear"); command("group five clear"); command("group six clear"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Group ID does not exist.*", command("group four union one two xxx");); TEST_FAILURE(".*ERROR: Group ID does not exist.*", @@ -267,14 +232,14 @@ TEST_F(GroupTest, Molecular) { molecular_system(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group one region left"); command("group two region right"); command("group half id 1:1000:2"); command("group top region top"); command("group three intersect half top"); command("group three include molecule"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(group->count(group->find("one")), 16); ASSERT_EQ(group->count(group->find("two")), 16); ASSERT_EQ(group->count(group->find("three")), 15); @@ -290,36 +255,36 @@ TEST_F(GroupTest, Dynamic) { atomic_system(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("variable step atom id<=step"); command("group half id 1:1000:2"); command("group grow dynamic half var step every 1"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(group->count(group->find("grow")), 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("run 10 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(group->count(group->find("grow")), 5); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group grow dynamic half var step every 1"); command("run 10 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(group->count(group->find("grow")), 10); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group grow static"); command("run 10 post no"); command("group part variable step"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(group->count(group->find("grow")), 10); ASSERT_EQ(group->count(group->find("part")), 30); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group grow dynamic half var step every 1"); command("run 10 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(group->count(group->find("grow")), 20); TEST_FAILURE(".*ERROR: Cannot subtract groups using a dynamic group.*", command("group chunk subtract half grow");); @@ -328,10 +293,10 @@ TEST_F(GroupTest, Dynamic) TEST_FAILURE(".*ERROR: Cannot intersect groups using a dynamic group.*", command("group chunk intersect half grow");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group grow delete"); command("variable ramp equal step"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(group->ngroup, 4); TEST_FAILURE(".*ERROR: Group dynamic cannot reference itself.*", @@ -351,7 +316,7 @@ int main(int argc, char **argv) MPI_Init(&argc, &argv); ::testing::InitGoogleMock(&argc, argv); - if (have_openmpi && !LAMMPS_NS::Info::has_exceptions()) + if (Info::get_mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) std::cout << "Warning: using OpenMPI without exceptions. " "Death tests will be skipped\n"; diff --git a/unittest/commands/test_simple_commands.cpp b/unittest/commands/test_simple_commands.cpp index 4261dbd61d..2ed5e7a989 100644 --- a/unittest/commands/test_simple_commands.cpp +++ b/unittest/commands/test_simple_commands.cpp @@ -24,6 +24,7 @@ #include "fmt/format.h" #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "../testing/core.h" #include #include @@ -34,11 +35,6 @@ // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; -#if defined(OMPI_MAJOR_VERSION) -const bool have_openmpi = true; -#else -const bool have_openmpi = false; -#endif using LAMMPS_NS::utils::split_words; @@ -47,43 +43,7 @@ using ::testing::ExitedWithCode; using ::testing::MatchesRegex; using ::testing::StrEq; -#define TEST_FAILURE(errmsg, ...) \ - if (Info::has_exceptions()) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_ANY_THROW({__VA_ARGS__}); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } else { \ - if (!have_openmpi) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_DEATH({__VA_ARGS__}, ""); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } \ - } - -class SimpleCommandsTest : public ::testing::Test { -protected: - LAMMPS *lmp; - - void SetUp() override - { - const char *args[] = {"SimpleCommandsTest", "-log", "none", "-echo", "screen", "-nocite"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void TearDown() override - { - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void command(const std::string &cmd) { lmp->input->one(cmd); } +class SimpleCommandsTest : public LAMMPSTest { }; TEST_F(SimpleCommandsTest, UnknownCommand) @@ -96,27 +56,27 @@ TEST_F(SimpleCommandsTest, Echo) ASSERT_EQ(lmp->input->echo_screen, 1); ASSERT_EQ(lmp->input->echo_log, 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("echo none"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->input->echo_screen, 0); ASSERT_EQ(lmp->input->echo_log, 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("echo both"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->input->echo_screen, 1); ASSERT_EQ(lmp->input->echo_log, 1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("echo screen"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->input->echo_screen, 1); ASSERT_EQ(lmp->input->echo_log, 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("echo log"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->input->echo_screen, 0); ASSERT_EQ(lmp->input->echo_log, 1); @@ -128,15 +88,15 @@ TEST_F(SimpleCommandsTest, Log) { ASSERT_EQ(lmp->logfile, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("log simple_command_test.log"); command("print 'test1'"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_NE(lmp->logfile, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("log none"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->logfile, nullptr); std::string text; @@ -146,14 +106,14 @@ TEST_F(SimpleCommandsTest, Log) in.close(); ASSERT_THAT(text, StrEq("test1")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("log simple_command_test.log append"); command("print 'test2'"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_NE(lmp->logfile, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("log none"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->logfile, nullptr); in.open("simple_command_test.log"); @@ -172,59 +132,57 @@ TEST_F(SimpleCommandsTest, Newton) // default setting is "on" for both ASSERT_EQ(lmp->force->newton_pair, 1); ASSERT_EQ(lmp->force->newton_bond, 1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("newton off"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->force->newton_pair, 0); ASSERT_EQ(lmp->force->newton_bond, 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("newton on off"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->force->newton_pair, 1); ASSERT_EQ(lmp->force->newton_bond, 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("newton off on"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->force->newton_pair, 0); ASSERT_EQ(lmp->force->newton_bond, 1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("newton on"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->force->newton_pair, 1); ASSERT_EQ(lmp->force->newton_bond, 1); } TEST_F(SimpleCommandsTest, Partition) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("echo none"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Illegal partition command .*", command("partition xxx 1 echo none");); TEST_FAILURE(".*ERROR: Numeric index 2 is out of bounds.*", command("partition yes 2 echo none");); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("partition yes 1 print 'test'"); - auto text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + auto text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, StrEq("test\n")); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("partition no 1 print 'test'"); - text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, StrEq("")); } TEST_F(SimpleCommandsTest, Quit) { - ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("echo none"); - ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Expected integer .*", command("quit xxx");); // the following tests must be skipped with OpenMPI due to using threads - if (have_openmpi) GTEST_SKIP(); + if (Info::get_mpi_vendor() == "Open MPI") GTEST_SKIP(); ASSERT_EXIT(command("quit"), ExitedWithCode(0), ""); ASSERT_EXIT(command("quit 9"), ExitedWithCode(9), ""); } @@ -233,14 +191,14 @@ TEST_F(SimpleCommandsTest, ResetTimestep) { ASSERT_EQ(lmp->update->ntimestep, 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_timestep 10"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->update->ntimestep, 10); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_timestep 0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->update->ntimestep, 0); TEST_FAILURE(".*ERROR: Timestep must be >= 0.*", command("reset_timestep -10");); @@ -257,31 +215,31 @@ TEST_F(SimpleCommandsTest, Suffix) TEST_FAILURE(".*ERROR: May only enable suffixes after defining one.*", command("suffix on");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("suffix one"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(lmp->suffix, StrEq("one")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("suffix hybrid two three"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(lmp->suffix, StrEq("two")); ASSERT_THAT(lmp->suffix2, StrEq("three")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("suffix four"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(lmp->suffix, StrEq("four")); ASSERT_EQ(lmp->suffix2, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("suffix off"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->suffix_enable, 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("suffix on"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->suffix_enable, 1); TEST_FAILURE(".*ERROR: Illegal suffix command.*", command("suffix");); @@ -293,20 +251,20 @@ TEST_F(SimpleCommandsTest, Thermo) { ASSERT_EQ(lmp->output->thermo_every, 0); ASSERT_EQ(lmp->output->var_thermo, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("thermo 2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->output->thermo_every, 2); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("variable step equal logfreq(10,3,10)"); command("thermo v_step"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(lmp->output->var_thermo, StrEq("step")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("thermo 10"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->output->thermo_every, 10); ASSERT_EQ(lmp->output->var_thermo, nullptr); @@ -317,26 +275,26 @@ TEST_F(SimpleCommandsTest, Thermo) TEST_F(SimpleCommandsTest, TimeStep) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("timestep 1"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->update->dt, 1.0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("timestep 0.1"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->update->dt, 0.1); // zero timestep is legal and works (atoms don't move) - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("timestep 0.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->update->dt, 0.0); // negative timestep also creates a viable MD. - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("timestep -0.1"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->update->dt, -0.1); TEST_FAILURE(".*ERROR: Illegal timestep command.*", command("timestep");); @@ -352,16 +310,16 @@ TEST_F(SimpleCommandsTest, Units) ASSERT_THAT(lmp->update->unit_style, StrEq("lj")); for (std::size_t i = 0; i < num; ++i) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("units {}", names[i])); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(lmp->update->unit_style, StrEq(names[i])); ASSERT_EQ(lmp->update->dt, dt[i]); } - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(lmp->update->unit_style, StrEq("lj")); TEST_FAILURE(".*ERROR: Illegal units command.*", command("units unknown");); @@ -369,18 +327,18 @@ TEST_F(SimpleCommandsTest, Units) TEST_F(SimpleCommandsTest, Shell) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("shell putenv TEST_VARIABLE=simpletest"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); char *test_var = getenv("TEST_VARIABLE"); ASSERT_NE(test_var, nullptr); ASSERT_THAT(test_var, StrEq("simpletest")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("shell putenv TEST_VARIABLE=simpletest"); command("shell putenv TEST_VARIABLE2=simpletest2 OTHER_VARIABLE=2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); char *test_var2 = getenv("TEST_VARIABLE2"); char *other_var = getenv("OTHER_VARIABLE"); @@ -398,32 +356,30 @@ TEST_F(SimpleCommandsTest, CiteMe) lmp->citeme = new LAMMPS_NS::CiteMe(lmp, CiteMe::TERSE, CiteMe::TERSE, nullptr); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); lmp->citeme->add("test citation one:\n 1\n"); lmp->citeme->add("test citation two:\n 2\n"); lmp->citeme->add("test citation one:\n 1\n"); lmp->citeme->flush(); - std::string text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + std::string text = END_CAPTURE_OUTPUT(); // find the two unique citations, but not the third ASSERT_THAT(text, MatchesRegex(".*one.*two.*")); ASSERT_THAT(text, Not(MatchesRegex(".*one.*two.*one.*"))); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); lmp->citeme->add("test citation one:\n 0\n"); lmp->citeme->add("test citation two:\n 2\n"); lmp->citeme->add("test citation three:\n 3\n"); lmp->citeme->flush(); - text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + text = END_CAPTURE_OUTPUT(); // find the forth (only differs in long citation) and sixth added citation ASSERT_THAT(text, MatchesRegex(".*one.*three.*")); ASSERT_THAT(text, Not(MatchesRegex(".*two.*"))); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); lmp->citeme->add("test citation one:\n 1\n"); lmp->citeme->add("test citation two:\n 2\n"); lmp->citeme->add("test citation one:\n 0\n"); @@ -431,8 +387,7 @@ TEST_F(SimpleCommandsTest, CiteMe) lmp->citeme->add("test citation three:\n 3\n"); lmp->citeme->flush(); - text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + text = END_CAPTURE_OUTPUT(); // no new citation. no CITE-CITE-CITE- lines ASSERT_THAT(text, Not(MatchesRegex(".*CITE-CITE-CITE-CITE.*"))); @@ -444,7 +399,7 @@ int main(int argc, char **argv) MPI_Init(&argc, &argv); ::testing::InitGoogleMock(&argc, argv); - if (have_openmpi && !LAMMPS_NS::Info::has_exceptions()) + if (Info::get_mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) std::cout << "Warning: using OpenMPI without exceptions. " "Death tests will be skipped\n"; diff --git a/unittest/testing/core.h b/unittest/testing/core.h index 19013bf90a..01c5872579 100644 --- a/unittest/testing/core.h +++ b/unittest/testing/core.h @@ -129,6 +129,7 @@ protected: info = nullptr; lmp = nullptr; }); + std::cout.flush(); } }; From e85f945d8e22ab813c472c6b3857fc5a4576440f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 26 Mar 2021 23:12:29 -0400 Subject: [PATCH 0275/1217] fix typos --- cmake/CMakeLists.txt | 2 +- doc/src/pair_polymorphic.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 06600d02c4..6d98385d02 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -31,7 +31,7 @@ endif() # If enabled, no need to use LD_LIBRARY_PATH / DYLD_LIBRARY_PATH when installed option(LAMMPS_INSTALL_RPATH "Set runtime path for shared libraries linked to LAMMPS binaries" OFF) -if (LAMMPS_INSTALL_RPATH) +if(LAMMPS_INSTALL_RPATH) set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR}) set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON) endif() diff --git a/doc/src/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst index 6abe037581..3df70a017c 100644 --- a/doc/src/pair_polymorphic.rst +++ b/doc/src/pair_polymorphic.rst @@ -319,7 +319,7 @@ This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This pair potential requires the :doc:`newtion ` setting to be +This pair potential requires the :doc:`newton ` setting to be "on" for pair interactions. The potential files provided with LAMMPS (see the potentials directory) From 35abca1b40de24c634bce37c2173f56028d07ae9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 27 Mar 2021 11:18:59 -0400 Subject: [PATCH 0276/1217] we should include when using strcasecmp() --- src/USER-DIFFRACTION/compute_saed.cpp | 1 + src/USER-DIFFRACTION/compute_xrd.cpp | 1 + src/USER-MOLFILE/molfile_interface.cpp | 1 + 3 files changed, 3 insertions(+) diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp index e825006dba..b1fa296315 100644 --- a/src/USER-DIFFRACTION/compute_saed.cpp +++ b/src/USER-DIFFRACTION/compute_saed.cpp @@ -30,6 +30,7 @@ #include #include +#include // for strcasecmp() #include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp index a077df0183..720e5809b1 100644 --- a/src/USER-DIFFRACTION/compute_xrd.cpp +++ b/src/USER-DIFFRACTION/compute_xrd.cpp @@ -31,6 +31,7 @@ #include #include +#include // for strcasecmp() #include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-MOLFILE/molfile_interface.cpp b/src/USER-MOLFILE/molfile_interface.cpp index 1ced86da86..dc40859127 100644 --- a/src/USER-MOLFILE/molfile_interface.cpp +++ b/src/USER-MOLFILE/molfile_interface.cpp @@ -23,6 +23,7 @@ #include #include #include +#include // for strcasecmp() #if defined(_WIN32) #include From 0b73ab96d2fa979f5fe3c8bb9e1c7514c52f97d1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 27 Mar 2021 11:10:36 -0400 Subject: [PATCH 0277/1217] avoid replicated code, consolidate variables and element mapping --- src/GPU/pair_sw_gpu.cpp | 6 +- src/GPU/pair_tersoff_gpu.cpp | 4 +- src/GPU/pair_tersoff_mod_gpu.cpp | 4 +- src/GPU/pair_tersoff_zbl_gpu.cpp | 4 +- src/GPU/pair_vashishta_gpu.cpp | 4 +- src/KOKKOS/pair_sw_kokkos.cpp | 36 ++-- src/KOKKOS/pair_sw_kokkos.h | 2 +- src/KOKKOS/pair_tersoff_kokkos.cpp | 2 +- src/KOKKOS/pair_tersoff_mod_kokkos.cpp | 2 +- src/KOKKOS/pair_tersoff_zbl_kokkos.cpp | 2 +- src/KOKKOS/pair_vashishta_kokkos.cpp | 38 ++-- src/KOKKOS/pair_vashishta_kokkos.h | 2 +- src/MANYBODY/pair_adp.cpp | 2 - src/MANYBODY/pair_adp.h | 2 - src/MANYBODY/pair_bop.cpp | 13 +- src/MANYBODY/pair_bop.h | 5 - src/MANYBODY/pair_comb.cpp | 105 ++-------- src/MANYBODY/pair_comb.h | 6 - src/MANYBODY/pair_comb3.cpp | 183 ++++++------------ src/MANYBODY/pair_comb3.h | 6 - src/MANYBODY/pair_eam.cpp | 4 +- src/MANYBODY/pair_eam.h | 2 - src/MANYBODY/pair_eim.cpp | 63 +----- src/MANYBODY/pair_eim.h | 4 - src/MANYBODY/pair_gw.cpp | 85 +------- src/MANYBODY/pair_gw.h | 6 - src/MANYBODY/pair_lcbop.cpp | 45 +---- src/MANYBODY/pair_lcbop.h | 3 - src/MANYBODY/pair_nb3b_harmonic.cpp | 83 +------- src/MANYBODY/pair_nb3b_harmonic.h | 6 - src/MANYBODY/pair_polymorphic.cpp | 70 +------ src/MANYBODY/pair_polymorphic.h | 5 - src/MANYBODY/pair_sw.cpp | 85 +------- src/MANYBODY/pair_sw.h | 6 - src/MANYBODY/pair_tersoff.cpp | 85 +------- src/MANYBODY/pair_tersoff.h | 6 - src/MANYBODY/pair_tersoff_mod.cpp | 8 +- src/MANYBODY/pair_vashishta.cpp | 85 +------- src/MANYBODY/pair_vashishta.h | 6 - src/MANYBODY/pair_vashishta_table.cpp | 10 +- src/SNAP/pair_snap.cpp | 94 +-------- src/SNAP/pair_snap.h | 3 - src/USER-INTEL/pair_sw_intel.cpp | 4 +- src/USER-INTEL/pair_tersoff_intel.cpp | 4 +- src/USER-MEAMC/pair_meamc.cpp | 119 ++++++------ src/USER-MEAMC/pair_meamc.h | 9 +- src/USER-MISC/pair_agni.cpp | 78 +------- src/USER-MISC/pair_agni.h | 5 - src/USER-MISC/pair_drip.cpp | 78 +------- src/USER-MISC/pair_drip.h | 4 - src/USER-MISC/pair_edip.cpp | 101 ++-------- src/USER-MISC/pair_edip.h | 6 - src/USER-MISC/pair_edip_multi.cpp | 84 +------- src/USER-MISC/pair_edip_multi.h | 6 - src/USER-MISC/pair_extep.cpp | 89 ++------- src/USER-MISC/pair_extep.h | 26 +-- src/USER-MISC/pair_ilp_graphene_hbn.cpp | 85 +------- src/USER-MISC/pair_ilp_graphene_hbn.h | 6 - src/USER-MISC/pair_kolmogorov_crespi_full.cpp | 85 +------- src/USER-MISC/pair_kolmogorov_crespi_full.h | 6 - src/USER-MISC/pair_kolmogorov_crespi_z.cpp | 49 +---- src/USER-MISC/pair_kolmogorov_crespi_z.h | 6 - src/USER-MISC/pair_lebedeva_z.cpp | 54 +----- src/USER-MISC/pair_lebedeva_z.h | 6 - src/USER-MISC/pair_meam_spline.cpp | 27 +-- src/USER-MISC/pair_meam_spline.h | 4 - src/USER-MISC/pair_meam_sw_spline.cpp | 78 +------- src/USER-MISC/pair_meam_sw_spline.h | 3 - src/USER-MISC/pair_tersoff_table.cpp | 130 +++---------- src/USER-MISC/pair_tersoff_table.h | 6 - src/USER-OMP/pair_agni_omp.cpp | 2 +- src/USER-OMP/pair_comb_omp.cpp | 18 +- src/USER-OMP/pair_edip_omp.cpp | 6 +- src/USER-OMP/pair_sw_omp.cpp | 8 +- src/USER-OMP/pair_tersoff_mod_c_omp.cpp | 8 +- src/USER-OMP/pair_tersoff_mod_omp.cpp | 8 +- src/USER-OMP/pair_tersoff_omp.cpp | 8 +- src/USER-OMP/pair_tersoff_table_omp.cpp | 24 +-- src/USER-OMP/pair_vashishta_omp.cpp | 8 +- src/USER-OMP/pair_vashishta_table_omp.cpp | 8 +- src/USER-REAXC/pair_reaxc.cpp | 25 ++- src/USER-REAXC/pair_reaxc.h | 3 - src/USER-SMTBQ/pair_smtbq.cpp | 78 +------- src/USER-SMTBQ/pair_smtbq.h | 9 +- src/input.cpp | 3 + src/pair.cpp | 74 +++++++ src/pair.h | 28 ++- src/pair_coul_streitz.cpp | 84 ++------ src/pair_coul_streitz.h | 8 +- 89 files changed, 601 insertions(+), 2159 deletions(-) diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp index 7bfbe2810f..b819580488 100644 --- a/src/GPU/pair_sw_gpu.cpp +++ b/src/GPU/pair_sw_gpu.cpp @@ -186,7 +186,7 @@ void PairSWGPU::init_style() if (i < 0 || j < 0) continue; else { - int ijparam = elem2param[i][j][j]; + int ijparam = elem3param[i][j][j]; ncutsq[ii][jj] = params[ijparam].cutsq; ncut[ii][jj] = params[ijparam].cut; sigma[ii][jj] = params[ijparam].sigma; @@ -206,7 +206,7 @@ void PairSWGPU::init_style() if (k < 0) continue; else { - int ijkparam = elem2param[i][j][k]; + int ijkparam = elem3param[i][j][k]; costheta[ii][jj][kk] = params[ijkparam].costheta; lambda_epsilon[ii][jj][kk] = params[ijkparam].lambda_epsilon; } @@ -218,7 +218,7 @@ void PairSWGPU::init_style() int success = sw_gpu_init(tp1, atom->nlocal, atom->nlocal+atom->nghost, mnf, cell_size, gpu_mode, screen, ncutsq, ncut, sigma, powerp, powerq, sigma_gamma, c1, c2, c3, c4, c5, - c6, lambda_epsilon, costheta, map, elem2param); + c6, lambda_epsilon, costheta, map, elem3param); memory->destroy(ncutsq); memory->destroy(ncut); diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp index e675ba6903..c2f3413d3d 100644 --- a/src/GPU/pair_tersoff_gpu.cpp +++ b/src/GPU/pair_tersoff_gpu.cpp @@ -41,7 +41,7 @@ using namespace LAMMPS_NS; int tersoff_gpu_init(const int ntypes, const int inum, const int nall, const int max_nbors, const double cell_size, int &gpu_mode, FILE *screen, int* host_map, const int nelements, - int*** host_elem2param, const int nparams, + int*** host_elem3param, const int nparams, const double* ts_lam1, const double* ts_lam2, const double* ts_lam3, const double* ts_powermint, const double* ts_biga, const double* ts_bigb, @@ -218,7 +218,7 @@ void PairTersoffGPU::init_style() int success = tersoff_gpu_init(atom->ntypes+1, atom->nlocal, atom->nlocal+atom->nghost, mnf, cell_size, gpu_mode, screen, map, nelements, - elem2param, nparams, lam1, lam2, lam3, + elem3param, nparams, lam1, lam2, lam3, powermint, biga, bigb, bigr, bigd, c1, c2, c3, c4, c, d, h, gamma, beta, powern, _cutsq); diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp index 98a7248c1f..6a5e9892ec 100644 --- a/src/GPU/pair_tersoff_mod_gpu.cpp +++ b/src/GPU/pair_tersoff_mod_gpu.cpp @@ -40,7 +40,7 @@ using namespace LAMMPS_NS; int tersoff_mod_gpu_init(const int ntypes, const int inum, const int nall, const int max_nbors, const double cell_size, int &gpu_mode, FILE *screen, - int* host_map, const int nelements, int*** host_elem2param, const int nparams, + int* host_map, const int nelements, int*** host_elem3param, const int nparams, const double* ts_lam1, const double* ts_lam2, const double* ts_lam3, const double* ts_powermint, const double* ts_biga, const double* ts_bigb, const double* ts_bigr, const double* ts_bigd, const double* ts_c1, @@ -211,7 +211,7 @@ void PairTersoffMODGPU::init_style() int success = tersoff_mod_gpu_init(atom->ntypes+1, atom->nlocal, atom->nlocal+atom->nghost, mnf, cell_size, gpu_mode, screen, map, nelements, - elem2param, nparams, lam1, lam2, lam3, + elem3param, nparams, lam1, lam2, lam3, powermint, biga, bigb, bigr, bigd, c1, c2, c3, c4, c5, h, beta, powern, powern_del, ca1, _cutsq); diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp index e17b48fec5..0c56212fef 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.cpp +++ b/src/GPU/pair_tersoff_zbl_gpu.cpp @@ -41,7 +41,7 @@ using namespace LAMMPS_NS; int tersoff_zbl_gpu_init(const int ntypes, const int inum, const int nall, const int max_nbors, const double cell_size, int &gpu_mode, FILE *screen, int* host_map, const int nelements, - int*** host_elem2param, const int nparams, + int*** host_elem3param, const int nparams, const double* ts_lam1, const double* ts_lam2, const double* ts_lam3, const double* ts_powermint, const double* ts_biga, const double* ts_bigb, @@ -227,7 +227,7 @@ void PairTersoffZBLGPU::init_style() int success = tersoff_zbl_gpu_init(atom->ntypes+1, atom->nlocal, atom->nlocal+atom->nghost, mnf, cell_size, gpu_mode, screen, map, nelements, - elem2param, nparams, lam1, lam2, lam3, + elem3param, nparams, lam1, lam2, lam3, powermint, biga, bigb, bigr, bigd, c1, c2, c3, c4, c, d, h, gamma, beta, powern, Z_i, Z_j, ZBLcut, ZBLexpscale, diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp index c5dd722974..b3c703952f 100644 --- a/src/GPU/pair_vashishta_gpu.cpp +++ b/src/GPU/pair_vashishta_gpu.cpp @@ -41,7 +41,7 @@ using namespace LAMMPS_NS; int vashishta_gpu_init(const int ntypes, const int inum, const int nall, const int max_nbors, const double cell_size, int &gpu_mode, FILE *screen, int* host_map, - const int nelements, int*** host_elem2param, + const int nelements, int*** host_elem3param, const int nparams, const double* cutsq, const double* r0, const double* gamma, const double* eta, const double* lam1inv, const double* lam4inv, @@ -217,7 +217,7 @@ void PairVashishtaGPU::init_style() int mnf = 5e-2 * neighbor->oneatom; int success = vashishta_gpu_init(atom->ntypes+1, atom->nlocal, atom->nlocal+atom->nghost, mnf, cell_size, gpu_mode, screen, map, nelements, - elem2param, nparams, cutsq, r0, gamma, eta, lam1inv, + elem3param, nparams, cutsq, r0, gamma, eta, lam1inv, lam4inv, zizj, mbigd, dvrc, big6w, heta, bigh, bigw, c0, costheta, bigb, big2b, bigc); memory->destroy(cutsq); diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp index 5d629dc42a..2fb90b7aec 100644 --- a/src/KOKKOS/pair_sw_kokkos.cpp +++ b/src/KOKKOS/pair_sw_kokkos.cpp @@ -289,7 +289,7 @@ void PairSWKokkos::operator()(TagPairSWComputeHalf const X_FLOAT delz = ztmp - x(j,2); const F_FLOAT rsq = delx*delx + dely*dely + delz*delz; - const int ijparam = d_elem2param(itype,jtype,jtype); + const int ijparam = d_elem3param(itype,jtype,jtype); if (rsq >= d_params[ijparam].cutsq) continue; twobody(d_params[ijparam],rsq,fpair,eflag,evdwl); @@ -313,7 +313,7 @@ void PairSWKokkos::operator()(TagPairSWComputeHalf int j = d_neighbors_short(i,jj); j &= NEIGHMASK; const int jtype = d_map[type[j]]; - const int ijparam = d_elem2param(itype,jtype,jtype); + const int ijparam = d_elem3param(itype,jtype,jtype); delr1[0] = x(j,0) - xtmp; delr1[1] = x(j,1) - ytmp; delr1[2] = x(j,2) - ztmp; @@ -328,8 +328,8 @@ void PairSWKokkos::operator()(TagPairSWComputeHalf int k = d_neighbors_short(i,kk); k &= NEIGHMASK; const int ktype = d_map[type[k]]; - const int ikparam = d_elem2param(itype,ktype,ktype); - const int ijkparam = d_elem2param(itype,jtype,ktype); + const int ikparam = d_elem3param(itype,ktype,ktype); + const int ijkparam = d_elem3param(itype,jtype,ktype); delr2[0] = x(k,0) - xtmp; delr2[1] = x(k,1) - ytmp; @@ -412,7 +412,7 @@ void PairSWKokkos::operator()(TagPairSWComputeFullA= d_params[ijparam].cutsq) continue; @@ -434,7 +434,7 @@ void PairSWKokkos::operator()(TagPairSWComputeFullA::operator()(TagPairSWComputeFullA::operator()(TagPairSWComputeFullB= nlocal) continue; const int jtype = d_map[type[j]]; - const int jiparam = d_elem2param(jtype,itype,itype); + const int jiparam = d_elem3param(jtype,itype,itype); const X_FLOAT xtmpj = x(j,0); const X_FLOAT ytmpj = x(j,1); const X_FLOAT ztmpj = x(j,2); @@ -530,8 +530,8 @@ void PairSWKokkos::operator()(TagPairSWComputeFullB::setup_params() { PairSW::setup_params(); - // sync elem2param and params + // sync elem3param and params - tdual_int_3d k_elem2param = tdual_int_3d("pair:elem2param",nelements,nelements,nelements); - t_host_int_3d h_elem2param = k_elem2param.h_view; + tdual_int_3d k_elem3param = tdual_int_3d("pair:elem3param",nelements,nelements,nelements); + t_host_int_3d h_elem3param = k_elem3param.h_view; tdual_param_1d k_params = tdual_param_1d("pair:params",nparams); t_host_param_1d h_params = k_params.h_view; @@ -646,17 +646,17 @@ void PairSWKokkos::setup_params() for (int i = 0; i < nelements; i++) for (int j = 0; j < nelements; j++) for (int k = 0; k < nelements; k++) - h_elem2param(i,j,k) = elem2param[i][j][k]; + h_elem3param(i,j,k) = elem3param[i][j][k]; for (int m = 0; m < nparams; m++) h_params[m] = params[m]; - k_elem2param.template modify(); - k_elem2param.template sync(); + k_elem3param.template modify(); + k_elem3param.template sync(); k_params.template modify(); k_params.template sync(); - d_elem2param = k_elem2param.template view(); + d_elem3param = k_elem3param.template view(); d_params = k_params.template view(); } diff --git a/src/KOKKOS/pair_sw_kokkos.h b/src/KOKKOS/pair_sw_kokkos.h index 31b7f3301d..b9f4559bc2 100644 --- a/src/KOKKOS/pair_sw_kokkos.h +++ b/src/KOKKOS/pair_sw_kokkos.h @@ -102,7 +102,7 @@ class PairSWKokkos : public PairSW { typedef typename tdual_int_3d::t_dev_const_randomread t_int_3d_randomread; typedef typename tdual_int_3d::t_host t_host_int_3d; - t_int_3d_randomread d_elem2param; + t_int_3d_randomread d_elem3param; typename AT::t_int_1d_randomread d_map; typedef Kokkos::DualView tdual_param_1d; diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp index 41a32a61e3..72a79c0b49 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_kokkos.cpp @@ -125,7 +125,7 @@ void PairTersoffKokkos::setup_params() for (i = 1; i <= n; i++) for (j = 1; j <= n; j++) for (k = 1; k <= n; k++) { - m = elem2param[map[i]][map[j]][map[k]]; + m = elem3param[map[i]][map[j]][map[k]]; k_params.h_view(i,j,k).powerm = params[m].powerm; k_params.h_view(i,j,k).gamma = params[m].gamma; k_params.h_view(i,j,k).lam3 = params[m].lam3; diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp index bd8e4d7528..c8431abc4b 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp @@ -124,7 +124,7 @@ void PairTersoffMODKokkos::setup_params() for (i = 1; i <= n; i++) for (j = 1; j <= n; j++) for (k = 1; k <= n; k++) { - m = elem2param[map[i]][map[j]][map[k]]; + m = elem3param[map[i]][map[j]][map[k]]; k_params.h_view(i,j,k).powerm = params[m].powerm; k_params.h_view(i,j,k).lam3 = params[m].lam3; k_params.h_view(i,j,k).h = params[m].h; diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp index 5e201dbc1c..3c362ad340 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp @@ -135,7 +135,7 @@ void PairTersoffZBLKokkos::setup_params() for (i = 1; i <= n; i++) for (j = 1; j <= n; j++) for (k = 1; k <= n; k++) { - m = elem2param[map[i]][map[j]][map[k]]; + m = elem3param[map[i]][map[j]][map[k]]; k_params.h_view(i,j,k).powerm = params[m].powerm; k_params.h_view(i,j,k).gamma = params[m].gamma; k_params.h_view(i,j,k).lam3 = params[m].lam3; diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp index 4b7b50afe9..71f3215931 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.cpp +++ b/src/KOKKOS/pair_vashishta_kokkos.cpp @@ -208,7 +208,7 @@ void PairVashishtaKokkos::operator()(TagPairVashishtaComputeShortNei int j = d_neighbors(i,jj); j &= NEIGHMASK; const int jtype = d_map[type[j]]; - const int ijparam = d_elem2param(itype,jtype,jtype); + const int ijparam = d_elem3param(itype,jtype,jtype); const X_FLOAT delx = xtmp - x(j,0); const X_FLOAT dely = ytmp - x(j,1); @@ -279,7 +279,7 @@ void PairVashishtaKokkos::operator()(TagPairVashishtaComputeHalf::operator()(TagPairVashishtaComputeHalf::operator()(TagPairVashishtaComputeHalf::operator()(TagPairVashishtaComputeFullA::operator()(TagPairVashishtaComputeFullA::operator()(TagPairVashishtaComputeFullA::operator()(TagPairVashishtaComputeFullB= nlocal) continue; const int jtype = d_map[type[j]]; - const int jiparam = d_elem2param(jtype,itype,itype); + const int jiparam = d_elem3param(jtype,itype,itype); const X_FLOAT xtmpj = x(j,0); const X_FLOAT ytmpj = x(j,1); const X_FLOAT ztmpj = x(j,2); @@ -508,8 +508,8 @@ void PairVashishtaKokkos::operator()(TagPairVashishtaComputeFullB::setup_params() { PairVashishta::setup_params(); - // sync elem2param and params + // sync elem3param and params - tdual_int_3d k_elem2param = tdual_int_3d("pair:elem2param",nelements,nelements,nelements); - t_host_int_3d h_elem2param = k_elem2param.h_view; + tdual_int_3d k_elem3param = tdual_int_3d("pair:elem3param",nelements,nelements,nelements); + t_host_int_3d h_elem3param = k_elem3param.h_view; tdual_param_1d k_params = tdual_param_1d("pair:params",nparams); t_host_param_1d h_params = k_params.h_view; @@ -622,17 +622,17 @@ void PairVashishtaKokkos::setup_params() for (int i = 0; i < nelements; i++) for (int j = 0; j < nelements; j++) for (int k = 0; k < nelements; k++) - h_elem2param(i,j,k) = elem2param[i][j][k]; + h_elem3param(i,j,k) = elem3param[i][j][k]; for (int m = 0; m < nparams; m++) h_params[m] = params[m]; - k_elem2param.template modify(); - k_elem2param.template sync(); + k_elem3param.template modify(); + k_elem3param.template sync(); k_params.template modify(); k_params.template sync(); - d_elem2param = k_elem2param.template view(); + d_elem3param = k_elem3param.template view(); d_params = k_params.template view(); } diff --git a/src/KOKKOS/pair_vashishta_kokkos.h b/src/KOKKOS/pair_vashishta_kokkos.h index 14dcf755df..aa8543e751 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.h +++ b/src/KOKKOS/pair_vashishta_kokkos.h @@ -102,7 +102,7 @@ class PairVashishtaKokkos : public PairVashishta { typedef typename tdual_int_3d::t_dev_const_randomread t_int_3d_randomread; typedef typename tdual_int_3d::t_host t_host_int_3d; - t_int_3d_randomread d_elem2param; + t_int_3d_randomread d_elem3param; typename AT::t_int_1d_randomread d_map; typedef Kokkos::DualView tdual_param_1d; diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index aa11e0682a..59afbc280b 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -45,7 +45,6 @@ PairADP::PairADP(LAMMPS *lmp) : Pair(lmp) fp = nullptr; mu = nullptr; lambda = nullptr; - map = nullptr; setfl = nullptr; @@ -86,7 +85,6 @@ PairADP::~PairADP() if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; delete [] type2frho; memory->destroy(type2rhor); memory->destroy(type2z2r); diff --git a/src/MANYBODY/pair_adp.h b/src/MANYBODY/pair_adp.h index 65596113ba..6a292dda14 100644 --- a/src/MANYBODY/pair_adp.h +++ b/src/MANYBODY/pair_adp.h @@ -67,8 +67,6 @@ class PairADP : public Pair { // potentials as file data - int *map; // which element each atom type maps to - struct Setfl { char **elements; int nelements,nrho,nr; diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index be4f17b291..a8f64853bc 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -69,7 +69,6 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp) BOP_index3 = nullptr; BOP_total = nullptr; BOP_total3 = nullptr; - map = nullptr; pi_a = nullptr; pro_delta = nullptr; pi_delta = nullptr; @@ -184,7 +183,6 @@ PairBOP::~PairBOP() if (allocated) { memory_theta_destroy(); if (otfly==0) memory->destroy(cos_index); - delete [] map; memory->destroy(BOP_index); memory->destroy(BOP_total); @@ -620,11 +618,6 @@ void PairBOP::coeff(int narg, char **arg) if (narg != 3 + atom->ntypes) error->all(FLERR,"Incorrect args for pair coefficients"); - // ensure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - // read the potential file nr=2000; nBOt=2000; @@ -657,6 +650,7 @@ void PairBOP::coeff(int narg, char **arg) if (elements) { for (i = 0; i < bop_types; i++) delete [] elements[i]; delete [] elements; + elements = nullptr; } } // clear setflag since coeff() called once with I,J = * * @@ -4922,10 +4916,7 @@ void _noopt PairBOP::read_table(char *filename) ValueTokenizer values = reader.next_values(3); values.next_int(); values.next_double(); - std::string name = values.next_string(); - - elements[i] = new char[name.length()+1]; - strcpy(elements[i], name.c_str()); + elements[i] = utils::strdup(values.next_string()); } ValueTokenizer values = reader.next_values(2); diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h index d61c969094..ba75d5c591 100644 --- a/src/MANYBODY/pair_bop.h +++ b/src/MANYBODY/pair_bop.h @@ -46,17 +46,12 @@ class PairBOP : public Pair { int update_list; // check for changing maximum size of neighbor list int maxbopn; // maximum size of bop neighbor list for allocation int maxnall; // maximum size of bop neighbor list for allocation - int *map; // mapping from atom types to elements - int nelements; // # of unique elements int nr; // increments for the BOP pair potential int ntheta; // increments for the angle function int npower; // power of the angular function int nBOt; // second BO increments int bop_types; // number of elements in potential int npairs; // number of element pairs - char **elements; // names of unique elements - int ***elem2param; - int nparams; int bop_step; int allocate_neigh; int nb_pi,nb_sg; diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index 2d93c6783e..a1fc65deb7 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -62,12 +62,7 @@ PairComb::PairComb(LAMMPS *lmp) : Pair(lmp) map = nullptr; esm = nullptr; - nelements = 0; - elements = nullptr; - nparams = 0; - maxparam = 0; params = nullptr; - elem2param = nullptr; intype = nullptr; fafb = nullptr; @@ -97,12 +92,8 @@ PairComb::~PairComb() { memory->destroy(NCo); - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - - delete [] elements; memory->sfree(params); - memory->destroy(elem2param); + memory->destroy(elem3param); memory->destroy(intype); memory->destroy(fafb); @@ -120,7 +111,6 @@ PairComb::~PairComb() if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; delete [] esm; } } @@ -184,7 +174,7 @@ void PairComb::compute(int eflag, int vflag) iq = q[i]; NCo[i] = 0; nj = 0; - iparam_i = elem2param[itype][itype][itype]; + iparam_i = elem3param[itype][itype][itype]; // self energy, only on i atom @@ -223,7 +213,7 @@ void PairComb::compute(int eflag, int vflag) dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; // long range q-dependent @@ -282,7 +272,7 @@ void PairComb::compute(int eflag, int vflag) for (jj = 0; jj < sht_jnum; jj++) { j = sht_jlist[jj]; jtype = map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; if (params[iparam_ij].hfocor > 0.0) { delr1[0] = x[j][0] - xtmp; @@ -303,7 +293,7 @@ void PairComb::compute(int eflag, int vflag) j = sht_jlist[jj]; jtype = map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; // this Qj for q-dependent BSi @@ -326,7 +316,7 @@ void PairComb::compute(int eflag, int vflag) k = sht_jlist[kk]; if (j == k) continue; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; @@ -370,7 +360,7 @@ void PairComb::compute(int eflag, int vflag) k = sht_jlist[kk]; if (j == k) continue; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; @@ -445,54 +435,15 @@ void PairComb::settings(int narg, char **/*arg*/) void PairComb::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } + map_element2type(narg-3,arg+3); // read potential file and initialize potential parameters read_file(arg[2]); setup_params(); - n = atom->ntypes; - // generate streitz-mintmire direct 1/r energy look-up table if (comm->me == 0 && screen) @@ -506,24 +457,6 @@ void PairComb::coeff(int narg, char **arg) else fputs(" will not apply over-coordination correction ...\n",screen); } - - // clear setflag since coeff() called once with I,J = * * - - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- @@ -741,12 +674,12 @@ void PairComb::setup_params() { int i,j,k,m,n; - // set elem2param for all element triplet combinations + // set elem3param for all element triplet combinations // must be a single exact match to lines read from file // do not allow for ACB in place of ABC - memory->destroy(elem2param); - memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param"); + memory->destroy(elem3param); + memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) @@ -760,7 +693,7 @@ void PairComb::setup_params() } } if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j][k] = n; + elem3param[i][j][k] = n; } // compute parameter values derived from inputs @@ -1403,7 +1336,7 @@ void PairComb::sm_table() if (map[i+1] < 0) continue; r = drin; itype = params[map[i+1]].ielement; - iparam_i = elem2param[itype][itype][itype]; + iparam_i = elem3param[itype][itype][itype]; z = params[iparam_i].esm1; if (comm->me == 0 && screen) @@ -1425,7 +1358,7 @@ void PairComb::sm_table() if (j == i) { itype = params[map[i+1]].ielement; inty = intype[itype][itype]; - iparam_i = elem2param[itype][itype][itype]; + iparam_i = elem3param[itype][itype][itype]; z = params[iparam_i].esm1; zrc = z * rc; exp2ersh = exp(-2.0 * zrc); @@ -1451,10 +1384,10 @@ void PairComb::sm_table() itype = params[map[i+1]].ielement; jtype = params[map[j+1]].ielement; inty = intype[itype][jtype]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; ea = params[iparam_ij].esm1; ea3 = ea*ea*ea; - iparam_ji = elem2param[jtype][itype][itype]; + iparam_ji = elem3param[jtype][itype][itype]; eb = params[iparam_ji].esm1; eb3 = eb*eb*eb; E1 = ea*eb3*eb/((ea+eb)*(ea+eb)*(ea-eb)*(ea-eb)); @@ -1672,7 +1605,7 @@ double PairComb::yasu_char(double *qf_fix, int &igroup) ytmp = x[i][1]; ztmp = x[i][2]; iq = q[i]; - iparam_i = elem2param[itype][itype][itype]; + iparam_i = elem3param[itype][itype][itype]; // charge force from self energy @@ -1706,7 +1639,7 @@ double PairComb::yasu_char(double *qf_fix, int &igroup) delr1[2] = x[j][2] - ztmp; rsq1 = dot3(delr1,delr1); - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; // long range q-dependent @@ -1743,7 +1676,7 @@ double PairComb::yasu_char(double *qf_fix, int &igroup) delr1[2] = x[j][2] - ztmp; rsq1 = dot3(delr1,delr1); - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; if (rsq1 > params[iparam_ij].cutsq) continue; nj ++; diff --git a/src/MANYBODY/pair_comb.h b/src/MANYBODY/pair_comb.h index c127bc0543..51b522badf 100644 --- a/src/MANYBODY/pair_comb.h +++ b/src/MANYBODY/pair_comb.h @@ -62,12 +62,6 @@ class PairComb : public Pair { }; double cutmax; // max cutoff for all elements - int nelements; // # of unique elements - char **elements; // names of unique elements - int ***elem2param; // mapping from element triplets to parameters - int *map; // mapping from atom types to elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets double precision; Param *params; // parameter set for an I-J-K interaction diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index d7814737ea..a0fa3b96b6 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -63,12 +63,7 @@ PairComb3::PairComb3(LAMMPS *lmp) : Pair(lmp) map = nullptr; esm = nullptr; - nelements = 0; - elements = nullptr; - nparams = 0; - maxparam = 0; params = nullptr; - elem2param = nullptr; intype = nullptr; afb = nullptr; @@ -107,12 +102,8 @@ PairComb3::~PairComb3() { memory->destroy(NCo); - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - - delete [] elements; memory->sfree(params); - memory->destroy(elem2param); + memory->destroy(elem3param); memory->destroy(afb); memory->destroy(dpl); @@ -139,7 +130,6 @@ PairComb3::~PairComb3() memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(cutghost); - delete [] map; delete [] esm; } @@ -184,78 +174,31 @@ void PairComb3::settings(int narg, char **arg) void PairComb3::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); + cflag = 0; + for (int i = 3; i < narg; i++) + if (strcmp(arg[i],"C") == 0) { + cflag = 1; + break; + } - // insure I,J args are * * - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if ((strcmp(arg[i],"C") == 0) && (cflag == 0)) { - if (comm->me == 0 && screen) - fputs(" PairComb3: Found C: reading additional library file\n",screen); + if (cflag) { + if (comm->me == 0 && screen) + fputs(" PairComb3: Found C: reading additional library file\n",screen); read_lib(); - cflag = 1; - } - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } } + map_element2type(narg-3,arg+3); + // read potential file and initialize potential parameters read_file(arg[2]); setup_params(); - n = atom->ntypes; - // generate Wolf 1/r energy and van der Waals look-up tables + tables(); - - // clear setflag since coeff() called once with I,J = * * - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); - } /* ---------------------------------------------------------------------- @@ -687,12 +630,12 @@ void PairComb3::setup_params() { int i,j,k,m,n; - // set elem2param for all element triplet combinations + // set elem3param for all element triplet combinations // must be a single exact match to lines read from file // do not allow for ACB in place of ABC - memory->destroy(elem2param); - memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param"); + memory->destroy(elem3param); + memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) @@ -706,7 +649,7 @@ void PairComb3::setup_params() } } if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j][k] = n; + elem3param[i][j][k] = n; } // compute parameter values derived from inputs @@ -804,7 +747,7 @@ void PairComb3::Short_neigh() delrj[2] = x[i][2] - x[j][2]; rsq1 = dot3(delrj,delrj); jtype = map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; if (rsq1 > cutmin) continue; @@ -928,8 +871,8 @@ void PairComb3::compute(int eflag, int vflag) delrj[2] = x[j][2] - ztmp; rsq = dot3(delrj,delrj); - iparam_ij = elem2param[itype][jtype][jtype]; - iparam_ji = elem2param[jtype][itype][itype]; + iparam_ij = elem3param[itype][jtype][jtype]; + iparam_ji = elem3param[jtype][itype][itype]; if (rsq > params[iparam_ij].lcutsq) continue; @@ -950,7 +893,7 @@ void PairComb3::compute(int eflag, int vflag) ztmp = x[i][2]; iq = q[i]; nj = 0; - iparam_i = elem2param[itype][itype][itype]; + iparam_i = elem3param[itype][itype][itype]; // self energy, only on i atom yaself = self(¶ms[iparam_i],iq); @@ -991,8 +934,8 @@ void PairComb3::compute(int eflag, int vflag) dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - iparam_ij = elem2param[itype][jtype][jtype]; - iparam_ji = elem2param[jtype][itype][itype]; + iparam_ij = elem3param[itype][jtype][jtype]; + iparam_ji = elem3param[jtype][itype][itype]; if (rsq > params[iparam_ij].lcutsq) continue; @@ -1091,8 +1034,8 @@ void PairComb3::compute(int eflag, int vflag) ycn = NCo[j]; jtype = map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; - iparam_ji = elem2param[jtype][itype][itype]; + iparam_ij = elem3param[itype][jtype][jtype]; + iparam_ji = elem3param[jtype][itype][itype]; delrj[0] = x[j][0] - xtmp; delrj[1] = x[j][1] - ytmp; @@ -1114,10 +1057,10 @@ void PairComb3::compute(int eflag, int vflag) if (j == k) continue; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; - iparam_ikj = elem2param[itype][ktype][jtype]; - iparam_jik = elem2param[jtype][itype][ktype]; - iparam_ik = elem2param[itype][ktype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; + iparam_ikj = elem3param[itype][ktype][jtype]; + iparam_jik = elem3param[jtype][itype][ktype]; + iparam_ik = elem3param[itype][ktype][ktype]; delrk[0] = x[k][0] - xtmp; delrk[1] = x[k][1] - ytmp; delrk[2] = x[k][2] - ztmp; @@ -1133,7 +1076,7 @@ void PairComb3::compute(int eflag, int vflag) if (params[iparam_ij].rad_flag > 0 && params[iparam_ik].ielementgp == 1 && params[iparam_ik].jelementgp == 1) { - iparam_ki = elem2param[ktype][itype][itype]; + iparam_ki = elem3param[ktype][itype][itype]; kcn=NCo[k]; kconjug += rad_init(rsq2,¶ms[iparam_ki],i,kradtot,kcn); @@ -1157,11 +1100,11 @@ void PairComb3::compute(int eflag, int vflag) delrl[1] = x[l][1] - x[j][1]; delrl[2] = x[l][2] - x[j][2]; rsq3 = dot3(delrl,delrl); - iparam_jl = elem2param[jtype][ltype][ltype]; + iparam_jl = elem3param[jtype][ltype][ltype]; if (rsq3 > params[iparam_jl].cutsq) continue; - iparam_ikl = elem2param[itype][ktype][ltype]; + iparam_ikl = elem3param[itype][ktype][ltype]; torindx = params[iparam_ij].tor_flag; bbtor += bbtor1(torindx, ¶ms[iparam_ikl],¶ms[iparam_jl], rsq1,rsq2,rsq3,delrj,delrk,delrl,srmu); @@ -1178,10 +1121,10 @@ void PairComb3::compute(int eflag, int vflag) if (l == i) continue; ltype = map[type[l]]; - iparam_jil = elem2param[jtype][itype][ltype]; - iparam_ijl = elem2param[itype][jtype][ltype]; - iparam_jl = elem2param[jtype][ltype][ltype]; - iparam_lj = elem2param[ltype][jtype][jtype]; + iparam_jil = elem3param[jtype][itype][ltype]; + iparam_ijl = elem3param[itype][jtype][ltype]; + iparam_jl = elem3param[jtype][ltype][ltype]; + iparam_lj = elem3param[ltype][jtype][jtype]; delrk[0] = x[l][0] - x[j][0]; delrk[1] = x[l][1] - x[j][1]; @@ -1204,7 +1147,7 @@ void PairComb3::compute(int eflag, int vflag) if (params[iparam_ji].rad_flag > 0 && params[iparam_jl].ielementgp == 1 && params[iparam_jl].jelementgp == 1) { - iparam_lj = elem2param[ltype][jtype][jtype]; + iparam_lj = elem3param[ltype][jtype][jtype]; lcn=NCo[l]; lconjug += rad_init(rsq2,¶ms[iparam_lj],j,lradtot,lcn); } @@ -1240,10 +1183,10 @@ void PairComb3::compute(int eflag, int vflag) sht_mnum = sht_num[k]; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; - iparam_ikj = elem2param[itype][ktype][jtype]; - iparam_jik = elem2param[jtype][itype][ktype]; - iparam_ik = elem2param[itype][ktype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; + iparam_ikj = elem3param[itype][ktype][jtype]; + iparam_jik = elem3param[jtype][itype][ktype]; + iparam_ik = elem3param[itype][ktype][ktype]; delrk[0] = x[k][0] - xtmp; delrk[1] = x[k][1] - ytmp; delrk[2] = x[k][2] - ztmp; @@ -1289,9 +1232,9 @@ void PairComb3::compute(int eflag, int vflag) delrl[2] = x[l][2] - x[j][2]; rsq3 = dot3(delrl,delrl); - iparam_jl = elem2param[jtype][ltype][ltype]; + iparam_jl = elem3param[jtype][ltype][ltype]; if (rsq3 > params[iparam_jl].cutsq) continue; - iparam_ikl = elem2param[itype][ktype][ltype]; + iparam_ikl = elem3param[itype][ktype][ltype]; torindx = params[iparam_ij].tor_flag; tor_force(torindx, ¶ms[iparam_ikl], ¶ms[iparam_jl],srmu, rsq1,rsq2,rsq3,delrj,delrk,delrl); @@ -1309,7 +1252,7 @@ void PairComb3::compute(int eflag, int vflag) if ( params[iparam_ijk].rad_flag>=1 && params[iparam_ijk].ielementgp==1 && params[iparam_ijk].kelementgp==1) { - iparam_ki = elem2param[ktype][itype][itype]; + iparam_ki = elem3param[ktype][itype][itype]; kcn=NCo[k]; double rik=sqrt(rsq2); kradtot = -comb_fc(rik,¶ms[iparam_ki])*params[iparam_ki].pcross+kcn; @@ -1333,8 +1276,8 @@ void PairComb3::compute(int eflag, int vflag) delrm[2] = x[m][2] - x[k][2]; rsq3 = dot3(delrm,delrm); - iparam_km = elem2param[ktype][mtype][mtype]; - iparam_ki = elem2param[ktype][itype][itype]; + iparam_km = elem3param[ktype][mtype][mtype]; + iparam_ki = elem3param[ktype][itype][itype]; if (rsq3 > params[iparam_km].cutsq) continue; @@ -1364,10 +1307,10 @@ void PairComb3::compute(int eflag, int vflag) sht_pnum = sht_num[l]; ltype = map[type[l]]; - iparam_jil = elem2param[jtype][itype][ltype]; - iparam_jli = elem2param[jtype][ltype][itype]; - iparam_ijl = elem2param[itype][jtype][ltype]; - iparam_jl = elem2param[jtype][ltype][ltype]; + iparam_jil = elem3param[jtype][itype][ltype]; + iparam_jli = elem3param[jtype][ltype][itype]; + iparam_ijl = elem3param[itype][jtype][ltype]; + iparam_jl = elem3param[jtype][ltype][ltype]; delrk[0] = x[l][0] - x[j][0]; delrk[1] = x[l][1] - x[j][1]; delrk[2] = x[l][2] - x[j][2]; @@ -1405,7 +1348,7 @@ void PairComb3::compute(int eflag, int vflag) if ( params[iparam_jil].rad_flag >= 1 && params[iparam_jil].ielementgp == 1 && params[iparam_jil].kelementgp == 1) { - iparam_lj = elem2param[ltype][jtype][jtype]; + iparam_lj = elem3param[ltype][jtype][jtype]; lcn=NCo[l]; double rjl=sqrt(rsq2); lradtot=-comb_fc(rjl,¶ms[iparam_lj])*params[iparam_lj].pcross +lcn; @@ -1428,7 +1371,7 @@ void PairComb3::compute(int eflag, int vflag) delrp[2] = x[p][2] - x[l][2]; rsq3 = dot3(delrp,delrp); - iparam_lp = elem2param[ltype][ptype][ptype]; + iparam_lp = elem3param[ltype][ptype][ptype]; if (rsq3 > params[iparam_lp].cutsq) continue; @@ -2354,7 +2297,7 @@ void PairComb3::tables() if (map[i+1] < 0) continue; r = drin - dra; itype = map[i+1]; - iparam_i = elem2param[itype][itype][itype]; + iparam_i = elem3param[itype][itype][itype]; z = params[iparam_i].esm; exp2ershift = exp(-2.0*z*rc); afbshift = -exp2ershift*(z+1.0/rc); @@ -2381,7 +2324,7 @@ void PairComb3::tables() if (j == i) { itype = map[i+1]; inty = intype[itype][itype]; - iparam_i = elem2param[itype][itype][itype]; + iparam_i = elem3param[itype][itype][itype]; z = params[iparam_i].esm; zrc = z * rc; exp2ersh = exp(-2.0 * zrc); @@ -2407,10 +2350,10 @@ void PairComb3::tables() itype = map[i+1]; jtype = map[j+1]; inty = intype[itype][jtype]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; ea = params[iparam_ij].esm; ea3 = ea*ea*ea; - iparam_ji = elem2param[jtype][itype][itype]; + iparam_ji = elem3param[jtype][itype][itype]; eb = params[iparam_ji].esm; eb3 = eb*eb*eb; E1 = ea*eb3*eb/((ea+eb)*(ea+eb)*(ea-eb)*(ea-eb)); @@ -2474,7 +2417,7 @@ void PairComb3::tables() itype = ii; jtype = jj; inty = intype[itype][jtype]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; // parameter check: eps > 0 if (params[iparam_ij].vdwflag > 0) { @@ -2521,7 +2464,7 @@ void PairComb3::tables() itype = ii; jtype = jj; inty = intype[itype][jtype]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; r = drin; for (k = 0; k < ncoul; k ++) { r6 = r*r*r*r*r*r; @@ -3229,7 +3172,7 @@ double PairComb3::combqeq(double *qf_fix, int &igroup) ytmp = x[i][1]; ztmp = x[i][2]; iq = q[i]; - iparam_i = elem2param[itype][itype][itype]; + iparam_i = elem3param[itype][itype][itype]; // charge force from self energy fqi = qfo_self(¶ms[iparam_i],iq); @@ -3257,8 +3200,8 @@ double PairComb3::combqeq(double *qf_fix, int &igroup) delrj[2] = ztmp - x[j][2]; rsq1 = dot3(delrj,delrj); - iparam_ij = elem2param[itype][jtype][jtype]; - iparam_ji = elem2param[jtype][itype][itype]; + iparam_ij = elem3param[itype][jtype][jtype]; + iparam_ji = elem3param[jtype][itype][itype]; // long range q-dependent @@ -3304,8 +3247,8 @@ double PairComb3::combqeq(double *qf_fix, int &igroup) delrj[2] = ztmp - x[j][2]; rsq1 = dot3(delrj,delrj); - iparam_ij = elem2param[itype][jtype][jtype]; - iparam_ji = elem2param[jtype][itype][itype]; + iparam_ij = elem3param[itype][jtype][jtype]; + iparam_ji = elem3param[jtype][itype][itype]; if (rsq1 >= params[iparam_ij].cutsq) continue; nj ++; diff --git a/src/MANYBODY/pair_comb3.h b/src/MANYBODY/pair_comb3.h index b999d2cece..d03ee0e474 100644 --- a/src/MANYBODY/pair_comb3.h +++ b/src/MANYBODY/pair_comb3.h @@ -61,16 +61,10 @@ class PairComb3 : public Pair { }; // general setups - int nelements; // # of unique elements - int ***elem2param; // mapping from element triplets to parameters - int *map; // mapping from atom types to elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets double PI,PI2,PI4,PIsq; // PIs double cutmin; // min cutoff for all elements double cutmax; // max cutoff for all elements double precision; // tolerance for QEq convergence - char **elements; // names of unique elements Param *params; // parameter set for an I-J-K interaction int debug_eng1, debug_eng2, debug_fq; // logic controlling debugging outputs int pack_flag; diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 03098904c8..b5fd507687 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -49,7 +49,6 @@ PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp) rho = nullptr; fp = nullptr; numforce = nullptr; - map = nullptr; type2frho = nullptr; nfuncfl = 0; @@ -90,9 +89,7 @@ PairEAM::~PairEAM() if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; delete [] type2frho; - map = nullptr; type2frho = nullptr; memory->destroy(type2rhor); memory->destroy(type2z2r); @@ -348,6 +345,7 @@ void PairEAM::allocate() memory->create(cutsq,n+1,n+1,"pair:cutsq"); + delete[] map; map = new int[n+1]; for (int i = 1; i <= n; i++) map[i] = -1; diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index 7e47c0f4e9..e9cbd15f34 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -75,8 +75,6 @@ class PairEAM : public Pair { // potentials as file data - int *map; // which element each atom type maps to - struct Funcfl { char *file; int nrho,nr; diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index b82a410791..eda1838a5a 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -46,10 +46,6 @@ PairEIM::PairEIM(LAMMPS *lmp) : Pair(lmp) nmax = 0; rho = nullptr; fp = nullptr; - map = nullptr; - - nelements = 0; - elements = nullptr; negativity = nullptr; q0 = nullptr; @@ -80,15 +76,11 @@ PairEIM::~PairEIM() if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; memory->destroy(type2Fij); memory->destroy(type2Gij); memory->destroy(type2phiij); } - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - deallocate_setfl(); delete [] negativity; @@ -353,8 +345,6 @@ void PairEIM::settings(int narg, char **/*arg*/) void PairEIM::coeff(int narg, char **arg) { - int i,j,m,n; - if (!allocated) allocate(); if (narg < 5) error->all(FLERR,"Incorrect args for pair coefficients"); @@ -364,23 +354,8 @@ void PairEIM::coeff(int narg, char **arg) if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) error->all(FLERR,"Incorrect args for pair coefficients"); - // read EIM element names before filename - // nelements = # of EIM elements to read from file - // elements = list of unique element names - - if (nelements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - nelements = narg - 3 - atom->ntypes; - if (nelements < 1) error->all(FLERR,"Incorrect args for pair coefficients"); - elements = new char*[nelements]; - - for (i = 0; i < nelements; i++) { - n = strlen(arg[i+2]) + 1; - elements[i] = new char[n]; - strcpy(elements[i],arg[i+2]); - } + const int ntypes = atom->ntypes; + map_element2type(ntypes,arg+(narg-ntypes)); // read EIM file @@ -388,38 +363,12 @@ void PairEIM::coeff(int narg, char **arg) setfl = new Setfl(); read_file(arg[2+nelements]); - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" + // set per-type atomic masses - for (i = 3 + nelements; i < narg; i++) { - m = i - (3+nelements) + 1; - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - if (j < nelements) map[m] = j; - else if (strcmp(arg[i],"NULL") == 0) map[m] = -1; - else error->all(FLERR,"Incorrect args for pair coefficients"); - } - - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (i = 1; i <= n; i++) - for (j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - // set mass of atom type if i = j - - int count = 0; - for (i = 1; i <= n; i++) - for (j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; + for (int i = 1; i <= ntypes; i++) + for (int j = i; j <= ntypes; j++) + if ((map[i] >= 0) && (map[j] >= 0)) if (i == j) atom->set_mass(FLERR,i,setfl->mass[map[i]]); - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h index 75f8ea6bea..7611898c45 100644 --- a/src/MANYBODY/pair_eim.h +++ b/src/MANYBODY/pair_eim.h @@ -60,10 +60,6 @@ class PairEIM : public Pair { int nmax; double *rho,*fp; int rhofp; - int *map; // which element each atom type maps to - - int nelements; // # of elements to read from potential file - char **elements; // element names Setfl *setfl; diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index 6039e00c0a..7e0cb3a3a2 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -51,12 +51,7 @@ PairGW::PairGW(LAMMPS *lmp) : Pair(lmp) centroidstressflag = CENTROID_NOTAVAIL; unit_convert_flag = utils::get_supported_conversions(utils::ENERGY); - nelements = 0; - elements = nullptr; - nparams = maxparam = 0; params = nullptr; - elem2param = nullptr; - map = nullptr; } /* ---------------------------------------------------------------------- @@ -65,16 +60,12 @@ PairGW::PairGW(LAMMPS *lmp) : Pair(lmp) PairGW::~PairGW() { - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; memory->destroy(params); - memory->destroy(elem2param); + memory->destroy(elem3param); if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; } } @@ -142,7 +133,7 @@ void PairGW::compute(int eflag, int vflag) delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; if (rsq > params[iparam_ij].cutsq) continue; repulsive(¶ms[iparam_ij],rsq,fpair,eflag,evdwl); @@ -165,7 +156,7 @@ void PairGW::compute(int eflag, int vflag) j = jlist[jj]; j &= NEIGHMASK; jtype = map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; delr1[0] = x[j][0] - xtmp; delr1[1] = x[j][1] - ytmp; @@ -182,7 +173,7 @@ void PairGW::compute(int eflag, int vflag) k = jlist[kk]; k &= NEIGHMASK; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; @@ -214,7 +205,7 @@ void PairGW::compute(int eflag, int vflag) k = jlist[kk]; k &= NEIGHMASK; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; @@ -271,70 +262,14 @@ void PairGW::settings(int narg, char **/*arg*/) void PairGW::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } + map_element2type(narg-3,arg+3); // read potential file and initialize potential parameters read_file(arg[2]); setup_params(); - - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (i = 1; i <= n; i++) - for (j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (i = 1; i <= n; i++) - for (j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- @@ -480,12 +415,12 @@ void PairGW::setup_params() { int i,j,k,m,n; - // set elem2param for all element triplet combinations + // set elem3param for all element triplet combinations // must be a single exact match to lines read from file // do not allow for ACB in place of ABC - memory->destroy(elem2param); - memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param"); + memory->destroy(elem3param); + memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) @@ -500,7 +435,7 @@ void PairGW::setup_params() } } if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j][k] = n; + elem3param[i][j][k] = n; } diff --git a/src/MANYBODY/pair_gw.h b/src/MANYBODY/pair_gw.h index 620f0b1af0..a1cbdb5c86 100644 --- a/src/MANYBODY/pair_gw.h +++ b/src/MANYBODY/pair_gw.h @@ -52,13 +52,7 @@ class PairGW : public Pair { }; Param *params; // parameter set for an I-J-K interaction - char **elements; // names of unique elements - int ***elem2param; // mapping from element triplets to paramegw - int *map; // mapping from atom types to elements double cutmax; // max cutoff for all elements - int nelements; // # of unique elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets int **pages; // neighbor list pages int maxlocal; // size of numneigh, firstneigh arrays diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index a2a8c3d1fa..727556dd50 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -74,8 +74,6 @@ PairLCBOP::~PairLCBOP() memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(cutghost); - - delete [] map; } } @@ -128,48 +126,17 @@ void PairLCBOP::coeff(int narg, char **arg) { if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); + map_element2type(narg-3,arg+3); - // insure I,J args are * * + // only element "C" is allowed - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to C and "NULL" - // map[i] = which element (0 for C) the Ith atom type is, -1 if "NULL" - - for (int i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - } else if (strcmp(arg[i],"C") == 0) { - map[i-2] = 0; - } else error->all(FLERR,"Incorrect args for pair coefficients"); - } + if ((nelements != 1) || (strcmp(elements[0],"C") != 0)) + error->all(FLERR,"Incorrect args for pair coefficients"); // read potential file and initialize fitting splines read_file(arg[2]); spline_init(); - - // clear setflag since coeff() called once with I,J = * * - - int n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- @@ -965,11 +932,9 @@ void PairLCBOP::read_file(char *filename) int i,k,l; char s[MAXLINE]; - MPI_Comm_rank(world,&me); - // read file on proc 0 - if (me == 0) { + if (comm->me == 0) { FILE *fp = utils::open_potential(filename,lmp,nullptr); if (fp == nullptr) { char str[128]; diff --git a/src/MANYBODY/pair_lcbop.h b/src/MANYBODY/pair_lcbop.h index dacbe74158..4ee89b4148 100644 --- a/src/MANYBODY/pair_lcbop.h +++ b/src/MANYBODY/pair_lcbop.h @@ -39,9 +39,6 @@ class PairLCBOP : public Pair { protected: int **pages; // neighbor list pages - int *map; // 0 (C) or -1 ("NULL") for each type - - int me; double cutLR; // LR cutoff diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index a1dc903a43..dfc4046eda 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -50,12 +50,7 @@ PairNb3bHarmonic::PairNb3bHarmonic(LAMMPS *lmp) : Pair(lmp) centroidstressflag = CENTROID_NOTAVAIL; unit_convert_flag = utils::get_supported_conversions(utils::ENERGY); - nelements = 0; - elements = nullptr; - nparams = maxparam = 0; params = nullptr; - elem2param = nullptr; - map = nullptr; } /* ---------------------------------------------------------------------- @@ -64,16 +59,12 @@ PairNb3bHarmonic::PairNb3bHarmonic(LAMMPS *lmp) : Pair(lmp) PairNb3bHarmonic::~PairNb3bHarmonic() { - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; memory->destroy(params); - memory->destroy(elem2param); + memory->destroy(elem3param); if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; } } @@ -117,7 +108,7 @@ void PairNb3bHarmonic::compute(int eflag, int vflag) j = jlist[jj]; j &= NEIGHMASK; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; delr1[0] = x[j][0] - xtmp; delr1[1] = x[j][1] - ytmp; delr1[2] = x[j][2] - ztmp; @@ -128,8 +119,8 @@ void PairNb3bHarmonic::compute(int eflag, int vflag) k = jlist[kk]; k &= NEIGHMASK; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; @@ -186,70 +177,14 @@ void PairNb3bHarmonic::settings(int narg, char **/*arg*/) void PairNb3bHarmonic::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } + map_element2type(narg-3,arg+3); // read potential file and initialize potential parameters read_file(arg[2]); setup_params(); - - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } @@ -374,12 +309,12 @@ void PairNb3bHarmonic::setup_params() int i,j,k,m,n; double rtmp; - // set elem2param for all triplet combinations + // set elem3param for all triplet combinations // must be a single exact match to lines read from file // do not allow for ACB in place of ABC - memory->destroy(elem2param); - memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param"); + memory->destroy(elem3param); + memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) @@ -393,7 +328,7 @@ void PairNb3bHarmonic::setup_params() } } if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j][k] = n; + elem3param[i][j][k] = n; } // compute parameter values derived from inputs diff --git a/src/MANYBODY/pair_nb3b_harmonic.h b/src/MANYBODY/pair_nb3b_harmonic.h index b68974e15f..38ec07c78b 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.h +++ b/src/MANYBODY/pair_nb3b_harmonic.h @@ -44,12 +44,6 @@ class PairNb3bHarmonic : public Pair { }; double cutmax; // max cutoff for all elements - int nelements; // # of unique elements - char **elements; // names of unique elements - int ***elem2param; // mapping from element triplets to parameters - int *map; // mapping from atom types to elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets Param *params; // parameter set for an I-J-K interaction void allocate(); diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index a353ad1c47..e267031901 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -49,14 +49,11 @@ PairPolymorphic::PairPolymorphic(LAMMPS *lmp) : Pair(lmp) manybody_flag = 1; centroidstressflag = CENTROID_NOTAVAIL; - nelements = 0; - elements = nullptr; match = nullptr; pairParameters = nullptr; tripletParameters = nullptr; elem2param = nullptr; elem3param = nullptr; - map = nullptr; epsilon = 0.0; neighsize = 0; firstneighV = nullptr; @@ -78,9 +75,6 @@ PairPolymorphic::PairPolymorphic(LAMMPS *lmp) : Pair(lmp) PairPolymorphic::~PairPolymorphic() { - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; delete [] match; delete [] pairParameters; @@ -91,7 +85,6 @@ PairPolymorphic::~PairPolymorphic() if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; delete [] firstneighV; delete [] firstneighW; delete [] firstneighW1; @@ -466,74 +459,19 @@ void PairPolymorphic::settings(int narg, char **/*arg*/) void PairPolymorphic::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg == 4 + atom->ntypes) { - narg--; - epsilon = atof(arg[narg]); - } else if (narg != 3 + atom->ntypes) { - error->all(FLERR,"Incorrect args for pair coefficients"); - } + // parse and remove optional last parameter - // insure I,J args are * * + if (narg == 4 + atom->ntypes) + epsilon = utils::numeric(FLERR,arg[--narg],false,lmp); - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } + map_element2type(narg-3,arg+3); // read potential file and initialize potential parameters read_file(arg[2]); setup_params(); - - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h index c94acd6230..a8a74267cd 100644 --- a/src/MANYBODY/pair_polymorphic.h +++ b/src/MANYBODY/pair_polymorphic.h @@ -302,13 +302,8 @@ class PairPolymorphic : public Pair { double *delxV,*delyV,*delzV,*drV; double *delxW,*delyW,*delzW,*drW; - char **elements; // names of unique elements - int **elem2param; // map: element pairs to parameters - int ***elem3param; // map: element triplets to parameters - int *map; // mapping from atom types to elements double cutmax; // max cutoff for all elements double cutmaxsq; - int nelements; // # of unique elements int npair,ntriple; int *match; diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index e7a334d9a9..fe7e56456e 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -46,12 +46,7 @@ PairSW::PairSW(LAMMPS *lmp) : Pair(lmp) centroidstressflag = CENTROID_NOTAVAIL; unit_convert_flag = utils::get_supported_conversions(utils::ENERGY); - nelements = 0; - elements = nullptr; - nparams = maxparam = 0; params = nullptr; - elem2param = nullptr; - map = nullptr; maxshort = 10; neighshort = nullptr; @@ -65,17 +60,13 @@ PairSW::~PairSW() { if (copymode) return; - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; memory->destroy(params); - memory->destroy(elem2param); + memory->destroy(elem3param); if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(neighshort); - delete [] map; } } @@ -135,7 +126,7 @@ void PairSW::compute(int eflag, int vflag) rsq = delx*delx + dely*dely + delz*delz; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (rsq >= params[ijparam].cutsq) { continue; } else { @@ -175,7 +166,7 @@ void PairSW::compute(int eflag, int vflag) for (jj = 0; jj < jnumm1; jj++) { j = neighshort[jj]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; delr1[0] = x[j][0] - xtmp; delr1[1] = x[j][1] - ytmp; delr1[2] = x[j][2] - ztmp; @@ -187,8 +178,8 @@ void PairSW::compute(int eflag, int vflag) for (kk = jj+1; kk < numshort; kk++) { k = neighshort[kk]; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; @@ -250,70 +241,14 @@ void PairSW::settings(int narg, char **/*arg*/) void PairSW::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } + map_element2type(narg-3,arg+3); // read potential file and initialize potential parameters read_file(arg[2]); setup_params(); - - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- @@ -451,12 +386,12 @@ void PairSW::setup_params() int i,j,k,m,n; double rtmp; - // set elem2param for all triplet combinations + // set elem3param for all triplet combinations // must be a single exact match to lines read from file // do not allow for ACB in place of ABC - memory->destroy(elem2param); - memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param"); + memory->destroy(elem3param); + memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) @@ -470,7 +405,7 @@ void PairSW::setup_params() } } if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j][k] = n; + elem3param[i][j][k] = n; } diff --git a/src/MANYBODY/pair_sw.h b/src/MANYBODY/pair_sw.h index 4fdc538430..4e13caee85 100644 --- a/src/MANYBODY/pair_sw.h +++ b/src/MANYBODY/pair_sw.h @@ -50,12 +50,6 @@ class PairSW : public Pair { protected: double cutmax; // max cutoff for all elements - int nelements; // # of unique elements - char **elements; // names of unique elements - int ***elem2param; // mapping from element triplets to parameters - int *map; // mapping from atom types to elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets Param *params; // parameter set for an I-J-K interaction int maxshort; // size of short neighbor list array int *neighshort; // short neighbor list array diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index dea01589a6..2a642e6244 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -54,12 +54,7 @@ PairTersoff::PairTersoff(LAMMPS *lmp) : Pair(lmp) centroidstressflag = CENTROID_NOTAVAIL; unit_convert_flag = utils::get_supported_conversions(utils::ENERGY); - nelements = 0; - elements = nullptr; - nparams = maxparam = 0; params = nullptr; - elem2param = nullptr; - map = nullptr; maxshort = 10; neighshort = nullptr; @@ -73,17 +68,13 @@ PairTersoff::~PairTersoff() { if (copymode) return; - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; memory->destroy(params); - memory->destroy(elem2param); + memory->destroy(elem3param); if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(neighshort); - delete [] map; } } @@ -204,7 +195,7 @@ void PairTersoff::eval() } jtype = map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; if (rsq >= params[iparam_ij].cutsq) continue; repulsive(¶ms[iparam_ij],rsq,fpair,EFLAG,evdwl); @@ -231,7 +222,7 @@ void PairTersoff::eval() for (jj = 0; jj < numshort; jj++) { j = neighshort[jj]; jtype = map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; delr1[0] = x[j][0] - xtmp; delr1[1] = x[j][1] - ytmp; @@ -255,7 +246,7 @@ void PairTersoff::eval() if (jj == kk) continue; k = neighshort[kk]; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; @@ -295,7 +286,7 @@ void PairTersoff::eval() if (jj == kk) continue; k = neighshort[kk]; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; @@ -383,70 +374,14 @@ void PairTersoff::settings(int narg, char **arg) void PairTersoff::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } + map_element2type(narg-3,arg+3); // read potential file and initialize potential parameters read_file(arg[2]); setup_params(); - - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (i = 1; i <= n; i++) - for (j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (i = 1; i <= n; i++) - for (j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- @@ -598,12 +533,12 @@ void PairTersoff::setup_params() { int i,j,k,m,n; - // set elem2param for all element triplet combinations + // set elem3param for all element triplet combinations // must be a single exact match to lines read from file // do not allow for ACB in place of ABC - memory->destroy(elem2param); - memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param"); + memory->destroy(elem3param); + memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) @@ -617,7 +552,7 @@ void PairTersoff::setup_params() } } if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j][k] = n; + elem3param[i][j][k] = n; } diff --git a/src/MANYBODY/pair_tersoff.h b/src/MANYBODY/pair_tersoff.h index 18c6ebc5f9..a4612d03be 100644 --- a/src/MANYBODY/pair_tersoff.h +++ b/src/MANYBODY/pair_tersoff.h @@ -59,13 +59,7 @@ class PairTersoff : public Pair { }; Param *params; // parameter set for an I-J-K interaction - char **elements; // names of unique elements - int ***elem2param; // mapping from element triplets to parameters - int *map; // mapping from atom types to elements double cutmax; // max cutoff for all elements - int nelements; // # of unique elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets int maxshort; // size of short neighbor list array int *neighshort; // short neighbor list array diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index 86994ccc0e..465bc0ebd0 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -163,12 +163,12 @@ void PairTersoffMOD::setup_params() { int i,j,k,m,n; - // set elem2param for all element triplet combinations + // set elem3param for all element triplet combinations // must be a single exact match to lines read from file // do not allow for ACB in place of ABC - memory->destroy(elem2param); - memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param"); + memory->destroy(elem3param); + memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) @@ -182,7 +182,7 @@ void PairTersoffMOD::setup_params() } } if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j][k] = n; + elem3param[i][j][k] = n; } diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 94f211dd95..cacfa7078e 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -48,12 +48,7 @@ PairVashishta::PairVashishta(LAMMPS *lmp) : Pair(lmp) centroidstressflag = CENTROID_NOTAVAIL; unit_convert_flag = utils::get_supported_conversions(utils::ENERGY); - nelements = 0; - elements = nullptr; - nparams = maxparam = 0; params = nullptr; - elem2param = nullptr; - map = nullptr; r0max = 0.0; maxshort = 10; @@ -68,17 +63,13 @@ PairVashishta::~PairVashishta() { if (copymode) return; - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; memory->destroy(params); - memory->destroy(elem2param); + memory->destroy(elem3param); if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(neighshort); - delete [] map; } } @@ -158,7 +149,7 @@ void PairVashishta::compute(int eflag, int vflag) } jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (rsq >= params[ijparam].cutsq) continue; twobody(¶ms[ijparam],rsq,fpair,eflag,evdwl); @@ -179,7 +170,7 @@ void PairVashishta::compute(int eflag, int vflag) for (jj = 0; jj < jnumm1; jj++) { j = neighshort[jj]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; delr1[0] = x[j][0] - xtmp; delr1[1] = x[j][1] - ytmp; delr1[2] = x[j][2] - ztmp; @@ -192,8 +183,8 @@ void PairVashishta::compute(int eflag, int vflag) for (kk = jj+1; kk < numshort; kk++) { k = neighshort[kk]; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; @@ -257,70 +248,14 @@ void PairVashishta::settings(int narg, char **/*arg*/) void PairVashishta::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } + map_element2type(narg-3,arg+3); // read potential file and initialize potential parameters read_file(arg[2]); setup_params(); - - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- @@ -465,12 +400,12 @@ void PairVashishta::setup_params() { int i,j,k,m,n; - // set elem2param for all triplet combinations + // set elem3param for all triplet combinations // must be a single exact match to lines read from file // do not allow for ACB in place of ABC - memory->destroy(elem2param); - memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param"); + memory->destroy(elem3param); + memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) @@ -484,7 +419,7 @@ void PairVashishta::setup_params() } } if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j][k] = n; + elem3param[i][j][k] = n; } // compute parameter values derived from inputs diff --git a/src/MANYBODY/pair_vashishta.h b/src/MANYBODY/pair_vashishta.h index 19a8e01cd9..06c23b2384 100644 --- a/src/MANYBODY/pair_vashishta.h +++ b/src/MANYBODY/pair_vashishta.h @@ -48,12 +48,6 @@ class PairVashishta : public Pair { }; protected: double cutmax; // max cutoff for all elements - int nelements; // # of unique elements - char **elements; // names of unique elements - int ***elem2param; // mapping from element triplets to parameters - int *map; // mapping from atom types to elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets Param *params; // parameter set for an I-J-K interaction double r0max; // largest value of r0 int maxshort; // size of short neighbor list array diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp index 76b44d8664..14dacdae3f 100644 --- a/src/MANYBODY/pair_vashishta_table.cpp +++ b/src/MANYBODY/pair_vashishta_table.cpp @@ -120,7 +120,7 @@ void PairVashishtaTable::compute(int eflag, int vflag) } jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (rsq >= params[ijparam].cutsq) continue; twobody_table(params[ijparam],rsq,fpair,eflag,evdwl); @@ -141,7 +141,7 @@ void PairVashishtaTable::compute(int eflag, int vflag) for (jj = 0; jj < jnumm1; jj++) { j = neighshort[jj]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; delr1[0] = x[j][0] - xtmp; delr1[1] = x[j][1] - ytmp; delr1[2] = x[j][2] - ztmp; @@ -154,8 +154,8 @@ void PairVashishtaTable::compute(int eflag, int vflag) for (kk = jj+1; kk < numshort; kk++) { k = neighshort[kk]; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; @@ -272,7 +272,7 @@ void PairVashishtaTable::create_tables() for (i = 0; i < nelements; i++) { for (j = 0; j < nelements; j++) { - int ijparam = elem2param[i][j][j]; + int ijparam = elem3param[i][j][j]; for (idx = 0; idx <= ntable; idx++) { rsq = tabinnersq + idx*deltaR2; PairVashishta::twobody(¶ms[ijparam],rsq,fpair,1,eng); diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index 7d57ca3673..ae0023ddec 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -42,8 +42,6 @@ PairSNAP::PairSNAP(LAMMPS *lmp) : Pair(lmp) manybody_flag = 1; centroidstressflag = CENTROID_NOTAVAIL; - nelements = 0; - elements = nullptr; radelem = nullptr; wjelem = nullptr; coeffelem = nullptr; @@ -60,14 +58,9 @@ PairSNAP::~PairSNAP() { if (copymode) return; - if (nelements) { - for (int i = 0; i < nelements; i++) - delete[] elements[i]; - delete[] elements; - memory->destroy(radelem); - memory->destroy(wjelem); - memory->destroy(coeffelem); - } + memory->destroy(radelem); + memory->destroy(wjelem); + memory->destroy(coeffelem); memory->destroy(beta); memory->destroy(bispectrum); @@ -77,7 +70,6 @@ PairSNAP::~PairSNAP() if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - memory->destroy(map); } } @@ -362,7 +354,7 @@ void PairSNAP::allocate() memory->create(setflag,n+1,n+1,"pair:setflag"); memory->create(cutsq,n+1,n+1,"pair:cutsq"); - memory->create(map,n+1,"pair:map"); + map = new int[n+1]; } /* ---------------------------------------------------------------------- @@ -384,61 +376,11 @@ void PairSNAP::coeff(int narg, char **arg) if (!allocated) allocate(); if (narg != 4 + atom->ntypes) error->all(FLERR,"Incorrect args for pair coefficients"); - char* type1 = arg[0]; - char* type2 = arg[1]; - char* coefffilename = arg[2]; - char* paramfilename = arg[3]; - char** elemtypes = &arg[4]; - - // insure I,J args are * * - - if (strcmp(type1,"*") != 0 || strcmp(type2,"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // clean out old arrays - - if (elements) { - for (int i = 0; i < nelements; i++) - delete[] elements[i]; - delete[] elements; - memory->destroy(radelem); - memory->destroy(wjelem); - memory->destroy(coeffelem); - } - - // nelements = # of unique elements declared - // elements = list of unique element names - // allocate as ntypes >= nelements - - elements = new char*[atom->ntypes]; - for (int i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - // read args that map atom types to SNAP elements - // map[i] = which element the Ith atom type is, -1 if not mapped - // map[0] is not used - - nelements = 0; - for (int i = 1; i <= atom->ntypes; i++) { - char* elemstring = elemtypes[i-1]; - if (strcmp(elemstring,"NULL") == 0) { - map[i] = -1; - continue; - } - int j; - for (j = 0; j < nelements; j++) - if (strcmp(elemstring,elements[j]) == 0) break; - map[i] = j; - if (j == nelements) { - int n = strlen(elemstring) + 1; - elements[j] = new char[n]; - strcpy(elements[j],elemstring); - nelements++; - } - } + map_element2type(narg-4,arg+4); // read snapcoeff and snapparam files - read_files(coefffilename,paramfilename); + read_files(arg[2],arg[3]); if (!quadraticflag) ncoeff = ncoeffall - 1; @@ -455,25 +397,6 @@ void PairSNAP::coeff(int narg, char **arg) } } - // clear setflag since coeff() called once with I,J = * * - - int n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); - snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, wselfallflag, nelements); @@ -571,8 +494,11 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) "file: {}", e.what())); } - // set up element lists + // clean out old arrays and set up element lists + memory->destroy(radelem); + memory->destroy(wjelem); + memory->destroy(coeffelem); memory->create(radelem,nelements,"pair:radelem"); memory->create(wjelem,nelements,"pair:wjelem"); memory->create(coeffelem,nelements,ncoeffall,"pair:coeffelem"); diff --git a/src/SNAP/pair_snap.h b/src/SNAP/pair_snap.h index d60000da3a..ee596d2ba7 100644 --- a/src/SNAP/pair_snap.h +++ b/src/SNAP/pair_snap.h @@ -50,14 +50,11 @@ protected: void compute_bispectrum(); double rcutmax; // max cutoff for all elements - int nelements; // # of unique elements - char **elements; // names of unique elements double *radelem; // element radii double *wjelem; // elements weights double **coeffelem; // element bispectrum coefficients double** beta; // betas for all atoms in list double** bispectrum; // bispectrum components for all atoms in list - int *map; // mapping from atom types to elements int twojmax, switchflag, bzeroflag, bnormflag; int chemflag, wselfallflag; int chunksize; diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp index 984b2100a3..bc5c40a258 100644 --- a/src/USER-INTEL/pair_sw_intel.cpp +++ b/src/USER-INTEL/pair_sw_intel.cpp @@ -1204,7 +1204,7 @@ void PairSWIntel::pack_force_const(ForceConst &fc, fc.p2e[ii][jj].c5 = 0; fc.p2e[ii][jj].c6 = 0; } else { - int ijparam = elem2param[i][j][j]; + int ijparam = elem3param[i][j][j]; fc.p2[ii][jj].cutsq = params[ijparam].cutsq; fc.p2[ii][jj].cut = params[ijparam].cut; fc.p2[ii][jj].sigma_gamma = params[ijparam].sigma_gamma; @@ -1237,7 +1237,7 @@ void PairSWIntel::pack_force_const(ForceConst &fc, mytypes++; _onetype = ii * tp1 + jj; _onetype3 = ii * tp1 * tp1 + jj * tp1 + kk; - int ijkparam = elem2param[i][j][k]; + int ijkparam = elem3param[i][j][k]; fc.p3[ii][jj][kk].costheta = params[ijkparam].costheta; fc.p3[ii][jj][kk].lambda_epsilon = params[ijkparam].lambda_epsilon; fc.p3[ii][jj][kk].lambda_epsilon2 = params[ijkparam].lambda_epsilon2; diff --git a/src/USER-INTEL/pair_tersoff_intel.cpp b/src/USER-INTEL/pair_tersoff_intel.cpp index 4284309b74..eb3ce562fa 100644 --- a/src/USER-INTEL/pair_tersoff_intel.cpp +++ b/src/USER-INTEL/pair_tersoff_intel.cpp @@ -482,7 +482,7 @@ void PairTersoffIntel::pack_force_const(ForceConst &fc, fc.c_inner_loop[i][0][j].d2 = 1.0; fc.c_inner_loop[0][i][j].d2 = 1.0; for (int k = 1; k < tp1; k++) { - Param * param = ¶ms[elem2param[map[i]][map[j]][map[k]]]; + Param * param = ¶ms[elem3param[map[i]][map[j]][map[k]]]; fc.c_cutoff_inner[i][k][j].cutsq = static_cast(param->cutsq); fc.c_inner_loop[i][j][k].lam3 = static_cast(param->lam3); fc.c_inner_loop[i][j][k].bigr = static_cast(param->bigr); @@ -504,7 +504,7 @@ void PairTersoffIntel::pack_force_const(ForceConst &fc, fc.c_inner[i][j][k].powermint = static_cast(param->powermint); } - Param * param = ¶ms[elem2param[map[i]][map[j]][map[j]]]; + Param * param = ¶ms[elem3param[map[i]][map[j]][map[j]]]; fc.c_cutoff_outer[i][j].cutsq = static_cast(param->cutsq); fc.c_first_loop[i][j].bigr = static_cast(param->bigr); fc.c_first_loop[i][j].bigd = static_cast(param->bigd); diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index 29d81e9516..67ab3522ad 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -55,7 +55,7 @@ PairMEAMC::PairMEAMC(LAMMPS *lmp) : Pair(lmp) allocated = 0; - nelements = 0; + nlibelements = 0; meam_inst = new MEAM(memory); scale = nullptr; @@ -78,7 +78,6 @@ PairMEAMC::~PairMEAMC() memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(scale); - delete [] map; } } @@ -239,23 +238,23 @@ void PairMEAMC::coeff(int narg, char **arg) error->all(FLERR,"Incorrect args for pair coefficients"); // MEAM element names between 2 filenames - // nelements = # of MEAM elements + // nlibelements = # of MEAM elements // elements = list of unique element names - if (nelements) { - elements.clear(); + if (nlibelements) { + libelements.clear(); mass.clear(); } - nelements = paridx - 3; - if (nelements < 1) error->all(FLERR,"Incorrect args for pair coefficients"); - if (nelements > maxelt) + nlibelements = paridx - 3; + if (nlibelements < 1) error->all(FLERR,"Incorrect args for pair coefficients"); + if (nlibelements > maxelt) error->all(FLERR,fmt::format("Too many elements extracted from MEAM " "library (current limit: {}). Increase " "'maxelt' in meam.h and recompile.", maxelt)); - for (int i = 0; i < nelements; i++) { - elements.push_back(arg[i+3]); + for (int i = 0; i < nlibelements; i++) { + libelements.push_back(arg[i+3]); mass.push_back(0.0); } @@ -269,12 +268,12 @@ void PairMEAMC::coeff(int narg, char **arg) // read args that map atom types to MEAM elements // map[i] = which element the Ith atom type is, -1 if not mapped - for (int i = 4 + nelements; i < narg; i++) { - m = i - (4+nelements) + 1; + for (int i = 4 + nlibelements; i < narg; i++) { + m = i - (4+nlibelements) + 1; int j; - for (j = 0; j < nelements; j++) - if (elements[j] == arg[i]) break; - if (j < nelements) map[m] = j; + for (j = 0; j < nlibelements; j++) + if (libelements[j] == arg[i]) break; + if (j < nlibelements) map[m] = j; else if (strcmp(arg[i],"NULL") == 0) map[m] = -1; else error->all(FLERR,"Incorrect args for pair coefficients"); } @@ -359,25 +358,25 @@ void PairMEAMC::read_files(const std::string &globalfile, void PairMEAMC::read_global_meamc_file(const std::string &globalfile) { // allocate parameter arrays - std::vector lat(nelements); - std::vector ielement(nelements); - std::vector ibar(nelements); - std::vector z(nelements); - std::vector atwt(nelements); - std::vector alpha(nelements); - std::vector b0(nelements); - std::vector b1(nelements); - std::vector b2(nelements); - std::vector b3(nelements); - std::vector alat(nelements); - std::vector esub(nelements); - std::vector asub(nelements); - std::vector t0(nelements); - std::vector t1(nelements); - std::vector t2(nelements); - std::vector t3(nelements); - std::vector rozero(nelements); - std::vector found(nelements, false); + std::vector lat(nlibelements); + std::vector ielement(nlibelements); + std::vector ibar(nlibelements); + std::vector z(nlibelements); + std::vector atwt(nlibelements); + std::vector alpha(nlibelements); + std::vector b0(nlibelements); + std::vector b1(nlibelements); + std::vector b2(nlibelements); + std::vector b3(nlibelements); + std::vector alat(nlibelements); + std::vector esub(nlibelements); + std::vector asub(nlibelements); + std::vector t0(nlibelements); + std::vector t1(nlibelements); + std::vector t2(nlibelements); + std::vector t3(nlibelements); + std::vector rozero(nlibelements); + std::vector found(nlibelements, false); // open global meamf file on proc 0 @@ -401,9 +400,9 @@ void PairMEAMC::read_global_meamc_file(const std::string &globalfile) // skip if element name isn't in element list int index; - for (index = 0; index < nelements; index++) - if (elements[index] == element) break; - if (index == nelements) continue; + for (index = 0; index < nlibelements; index++) + if (libelements[index] == element) break; + if (index == nlibelements) continue; // skip if element already appeared (technically error in library file, but always ignored) @@ -452,47 +451,47 @@ void PairMEAMC::read_global_meamc_file(const std::string &globalfile) // error if didn't find all elements in file - if (nset != nelements) { + if (nset != nlibelements) { std::string msg = "Did not find all elements in MEAM library file, missing:"; - for (int i = 0; i < nelements; i++) + for (int i = 0; i < nlibelements; i++) if (!found[i]) { msg += " "; - msg += elements[i]; + msg += libelements[i]; } error->one(FLERR,msg); } } // distribute complete parameter sets - MPI_Bcast(lat.data(), nelements, MPI_INT, 0, world); - MPI_Bcast(ielement.data(), nelements, MPI_INT, 0, world); - MPI_Bcast(ibar.data(), nelements, MPI_INT, 0, world); - MPI_Bcast(z.data(), nelements, MPI_DOUBLE, 0, world); - MPI_Bcast(atwt.data(), nelements, MPI_DOUBLE, 0, world); - MPI_Bcast(alpha.data(), nelements, MPI_DOUBLE, 0, world); - MPI_Bcast(b0.data(), nelements, MPI_DOUBLE, 0, world); - MPI_Bcast(b1.data(), nelements, MPI_DOUBLE, 0, world); - MPI_Bcast(b2.data(), nelements, MPI_DOUBLE, 0, world); - MPI_Bcast(b3.data(), nelements, MPI_DOUBLE, 0, world); - MPI_Bcast(alat.data(), nelements, MPI_DOUBLE, 0, world); - MPI_Bcast(esub.data(), nelements, MPI_DOUBLE, 0, world); - MPI_Bcast(asub.data(), nelements, MPI_DOUBLE, 0, world); - MPI_Bcast(t0.data(), nelements, MPI_DOUBLE, 0, world); - MPI_Bcast(t1.data(), nelements, MPI_DOUBLE, 0, world); - MPI_Bcast(t2.data(), nelements, MPI_DOUBLE, 0, world); - MPI_Bcast(t3.data(), nelements, MPI_DOUBLE, 0, world); - MPI_Bcast(rozero.data(), nelements, MPI_DOUBLE, 0, world); + MPI_Bcast(lat.data(), nlibelements, MPI_INT, 0, world); + MPI_Bcast(ielement.data(), nlibelements, MPI_INT, 0, world); + MPI_Bcast(ibar.data(), nlibelements, MPI_INT, 0, world); + MPI_Bcast(z.data(), nlibelements, MPI_DOUBLE, 0, world); + MPI_Bcast(atwt.data(), nlibelements, MPI_DOUBLE, 0, world); + MPI_Bcast(alpha.data(), nlibelements, MPI_DOUBLE, 0, world); + MPI_Bcast(b0.data(), nlibelements, MPI_DOUBLE, 0, world); + MPI_Bcast(b1.data(), nlibelements, MPI_DOUBLE, 0, world); + MPI_Bcast(b2.data(), nlibelements, MPI_DOUBLE, 0, world); + MPI_Bcast(b3.data(), nlibelements, MPI_DOUBLE, 0, world); + MPI_Bcast(alat.data(), nlibelements, MPI_DOUBLE, 0, world); + MPI_Bcast(esub.data(), nlibelements, MPI_DOUBLE, 0, world); + MPI_Bcast(asub.data(), nlibelements, MPI_DOUBLE, 0, world); + MPI_Bcast(t0.data(), nlibelements, MPI_DOUBLE, 0, world); + MPI_Bcast(t1.data(), nlibelements, MPI_DOUBLE, 0, world); + MPI_Bcast(t2.data(), nlibelements, MPI_DOUBLE, 0, world); + MPI_Bcast(t3.data(), nlibelements, MPI_DOUBLE, 0, world); + MPI_Bcast(rozero.data(), nlibelements, MPI_DOUBLE, 0, world); // pass element parameters to MEAM package - meam_inst->meam_setup_global(nelements, lat.data(), ielement.data(), atwt.data(), + meam_inst->meam_setup_global(nlibelements, lat.data(), ielement.data(), atwt.data(), alpha.data(), b0.data(), b1.data(), b2.data(), b3.data(), alat.data(), esub.data(), asub.data(), t0.data(), t1.data(), t2.data(), t3.data(), rozero.data(), ibar.data()); // set element masses - for (int i = 0; i < nelements; i++) mass[i] = atwt[i]; + for (int i = 0; i < nlibelements; i++) mass[i] = atwt[i]; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h index 6bf6923869..24625c4076 100644 --- a/src/USER-MEAMC/pair_meamc.h +++ b/src/USER-MEAMC/pair_meamc.h @@ -47,12 +47,11 @@ class PairMEAMC : public Pair { private: class MEAM *meam_inst; - double cutmax; // max cutoff for all elements - int nelements; // # of unique elements - std::vector elements; // names of unique elements - std::vector mass; // mass of each element + double cutmax; // max cutoff for all elements + int nlibelements; // # of library elements + std::vector libelements; // names of library elements + std::vector mass; // mass of library element - int *map; // mapping from atom types (1-indexed) to elements (1-indexed) double **scale; // scaling factor for adapt void allocate(); diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 7481ca35d4..7acaf90e4f 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -67,12 +67,7 @@ PairAGNI::PairAGNI(LAMMPS *lmp) : Pair(lmp) no_virial_fdotr_compute = 1; - nelements = 0; - elements = nullptr; - elem2param = nullptr; - nparams = 0; params = nullptr; - map = nullptr; cutmax = 0.0; } @@ -82,9 +77,6 @@ PairAGNI::PairAGNI(LAMMPS *lmp) : Pair(lmp) PairAGNI::~PairAGNI() { - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; if (params) { for (int i = 0; i < nparams; ++i) { memory->destroy(params[i].eta); @@ -94,12 +86,11 @@ PairAGNI::~PairAGNI() memory->destroy(params); params = nullptr; } - memory->destroy(elem2param); + memory->destroy(elem1param); if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; } } @@ -135,7 +126,7 @@ void PairAGNI::compute(int eflag, int vflag) ztmp = x[i][2]; fxtmp = fytmp = fztmp = 0.0; - const Param &iparam = params[elem2param[itype]]; + const Param &iparam = params[elem1param[itype]]; Vx = new double[iparam.numeta]; Vy = new double[iparam.numeta]; Vz = new double[iparam.numeta]; @@ -238,46 +229,10 @@ void PairAGNI::settings(int narg, char ** /* arg */) void PairAGNI::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); + map_element2type(narg-3,arg+3); - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } if (nelements != 1) error->all(FLERR,"Cannot handle multi-element systems with this potential"); @@ -285,25 +240,6 @@ void PairAGNI::coeff(int narg, char **arg) read_file(arg[2]); setup_params(); - - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- @@ -466,10 +402,10 @@ void PairAGNI::setup_params() int i,m,n; double rtmp; - // set elem2param for all elements + // set elem1param for all elements - memory->destroy(elem2param); - memory->create(elem2param,nelements,"pair:elem2param"); + memory->destroy(elem1param); + memory->create(elem1param,nelements,"pair:elem1param"); for (i = 0; i < nelements; i++) { n = -1; @@ -480,7 +416,7 @@ void PairAGNI::setup_params() } } if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i] = n; + elem1param[i] = n; } // compute parameter values derived from inputs diff --git a/src/USER-MISC/pair_agni.h b/src/USER-MISC/pair_agni.h index 6fba506d04..0a33c11b95 100644 --- a/src/USER-MISC/pair_agni.h +++ b/src/USER-MISC/pair_agni.h @@ -45,11 +45,6 @@ class PairAGNI : public Pair { protected: double cutmax; // max cutoff for all elements - int nelements; // # of unique atom type labels - char **elements; // names of unique elements - int *elem2param; // mapping from element pairs to parameters - int *map; // mapping from atom types to elements - int nparams; // # of stored parameter sets int atomic_feature_version; // version of fingerprint Param *params; // parameter set for an I-J interaction virtual void allocate(); diff --git a/src/USER-MISC/pair_drip.cpp b/src/USER-MISC/pair_drip.cpp index 45b49ee293..0f571dd41e 100644 --- a/src/USER-MISC/pair_drip.cpp +++ b/src/USER-MISC/pair_drip.cpp @@ -22,17 +22,17 @@ #include "pair_drip.h" -#include - -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" + +#include +#include using namespace LAMMPS_NS; @@ -51,10 +51,6 @@ PairDRIP::PairDRIP(LAMMPS *lmp) : Pair(lmp) params = nullptr; nearest3neigh = nullptr; - elements = nullptr; - elem2param = nullptr; - map = nullptr; - nelements = 0; cutmax = 0.0; } @@ -65,14 +61,8 @@ PairDRIP::~PairDRIP() if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; } - if (elements != nullptr) { - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - elements = nullptr; - } memory->destroy(params); memory->destroy(elem2param); memory->destroy(nearest3neigh); @@ -127,64 +117,10 @@ void PairDRIP::settings(int narg, char ** /* arg */) void PairDRIP::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } - + map_element2type(narg-3,arg+3); read_file(arg[2]); - - - // clear setflag since coeff() called once with I,J = * * - n = atom->ntypes; - for (i = 1; i <= n; i++) - for (j = i; j <= n; j++) - setflag[i][j] = 0; - - int count = 0; - for (i = 1; i <= n; i++) - for (j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } diff --git a/src/USER-MISC/pair_drip.h b/src/USER-MISC/pair_drip.h index 3ea6c735a6..59dac076c8 100644 --- a/src/USER-MISC/pair_drip.h +++ b/src/USER-MISC/pair_drip.h @@ -58,10 +58,6 @@ protected: }; Param *params; // parameter set for I-J interactions int **nearest3neigh; // nearest 3 neighbors of atoms - char **elements; // names of unique elements - int **elem2param; // mapping from element pairs to parameters - int *map; // mapping from atom types to elements - int nelements; // # of unique elements double cutmax; // max cutoff for all species void read_file(char *); diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp index 12390ba69d..88b8728c38 100644 --- a/src/USER-MISC/pair_edip.cpp +++ b/src/USER-MISC/pair_edip.cpp @@ -23,18 +23,18 @@ #include "pair_edip.h" -#include -#include - -#include #include "atom.h" -#include "neighbor.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" + +#include +#include +#include using namespace LAMMPS_NS; @@ -64,11 +64,7 @@ PairEDIP::PairEDIP(LAMMPS *lmp) : manybody_flag = 1; centroidstressflag = CENTROID_NOTAVAIL; - nelements = 0; - elements = nullptr; - nparams = maxparam = 0; params = nullptr; - elem2param = nullptr; } /* ---------------------------------------------------------------------- @@ -77,16 +73,12 @@ PairEDIP::PairEDIP(LAMMPS *lmp) : PairEDIP::~PairEDIP() { - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; memory->destroy(params); - memory->destroy(elem2param); + memory->destroy(elem3param); if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; deallocateGrids(); deallocatePreLoops(); @@ -198,7 +190,7 @@ void PairEDIP::compute(int eflag, int vflag) r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (r_ij > params[ijparam].cutsq) continue; r_ij = sqrt(r_ij); @@ -313,7 +305,7 @@ void PairEDIP::compute(int eflag, int vflag) r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (r_ij > params[ijparam].cutsq) continue; r_ij = sqrt(r_ij); @@ -367,7 +359,7 @@ void PairEDIP::compute(int eflag, int vflag) k = jlist[neighbor_k]; k &= NEIGHMASK; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; dr_ik[0] = x[k][0] - xtmp; dr_ik[1] = x[k][1] - ytmp; @@ -766,47 +758,9 @@ void PairEDIP::initGrids(void) void PairEDIP::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } - + map_element2type(narg-3,arg+3); if (nelements != 1) error->all(FLERR,"Pair style edip only supports single element potentials"); @@ -815,25 +769,6 @@ void PairEDIP::coeff(int narg, char **arg) read_file(arg[2]); setup_params(); - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); - // allocate tables and internal structures allocatePreLoops(); @@ -1015,12 +950,12 @@ void PairEDIP::setup_params() int i,j,k,m,n; double rtmp; - // set elem2param for all triplet combinations + // set elem3param for all triplet combinations // must be a single exact match to lines read from file // do not allow for ACB in place of ABC - memory->destroy(elem2param); - memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param"); + memory->destroy(elem3param); + memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) @@ -1034,7 +969,7 @@ void PairEDIP::setup_params() } } if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j][k] = n; + elem3param[i][j][k] = n; } // set cutoff square diff --git a/src/USER-MISC/pair_edip.h b/src/USER-MISC/pair_edip.h index 6c4a37d795..006c124229 100644 --- a/src/USER-MISC/pair_edip.h +++ b/src/USER-MISC/pair_edip.h @@ -87,12 +87,6 @@ class PairEDIP : public Pair { double u4; double cutmax; // max cutoff for all elements - int nelements; // # of unique elements - char **elements; // names of unique elements - int ***elem2param; // mapping from element triplets to parameters - int *map; // mapping from atom types to elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets Param *params; // parameter set for an I-J-K interaction void allocate(); diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp index c0969831b9..4db52da11a 100644 --- a/src/USER-MISC/pair_edip_multi.cpp +++ b/src/USER-MISC/pair_edip_multi.cpp @@ -82,11 +82,7 @@ PairEDIPMulti::PairEDIPMulti(LAMMPS *lmp) : Pair(lmp), preForceCoord(nullptr) manybody_flag = 1; centroidstressflag = CENTROID_NOTAVAIL; - nelements = 0; - elements = nullptr; - nparams = maxparam = 0; params = nullptr; - elem2param = nullptr; } /* ---------------------------------------------------------------------- @@ -95,16 +91,12 @@ PairEDIPMulti::PairEDIPMulti(LAMMPS *lmp) : Pair(lmp), preForceCoord(nullptr) PairEDIPMulti::~PairEDIPMulti() { - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; memory->destroy(params); - memory->destroy(elem2param); + memory->destroy(elem3param); if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; } deallocatePreLoops(); } @@ -173,7 +165,7 @@ void PairEDIPMulti::compute(int eflag, int vflag) r_ij = delx * delx + dely * dely + delz * delz; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (r_ij > params[ijparam].cutsq) continue; r_ij = sqrt(r_ij); @@ -214,7 +206,7 @@ void PairEDIPMulti::compute(int eflag, int vflag) r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (r_ij > params[ijparam].cutsq) continue; r_ij = sqrt(r_ij); @@ -246,8 +238,8 @@ void PairEDIPMulti::compute(int eflag, int vflag) k = jlist[kk]; k &= NEIGHMASK; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; dr_ik[0] = x[k][0] - xtmp; dr_ik[1] = x[k][1] - ytmp; @@ -537,71 +529,15 @@ void PairEDIPMulti::settings(int narg, char **/*arg*/) void PairEDIPMulti::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } + map_element2type(narg-3,arg+3); // read potential file and initialize potential parameters read_file(arg[2]); setup(); - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); - // (re-)allocate tables and internal structures deallocatePreLoops(); @@ -784,12 +720,12 @@ void PairEDIPMulti::setup() int i,j,k,m,n; double rtmp; - // set elem2param for all triplet combinations + // set elem3param for all triplet combinations // must be a single exact match to lines read from file // do not allow for ACB in place of ABC - memory->destroy(elem2param); - memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param"); + memory->destroy(elem3param); + memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) @@ -803,7 +739,7 @@ void PairEDIPMulti::setup() } } if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j][k] = n; + elem3param[i][j][k] = n; } // set cutoff square diff --git a/src/USER-MISC/pair_edip_multi.h b/src/USER-MISC/pair_edip_multi.h index cf1d56945f..2aba064aa9 100644 --- a/src/USER-MISC/pair_edip_multi.h +++ b/src/USER-MISC/pair_edip_multi.h @@ -54,12 +54,6 @@ class PairEDIPMulti : public Pair { double *preForceCoord; double cutmax; // max cutoff for all elements - int nelements; // # of unique elements - char **elements; // names of unique elements - int ***elem2param; // mapping from element triplets to parameters - int *map; // mapping from atom types to elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets Param *params; // parameter set for an I-J-K interaction void allocate(); diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp index ea4a8031a1..c64c7474cd 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/USER-MISC/pair_extep.cpp @@ -52,18 +52,13 @@ PairExTeP::PairExTeP(LAMMPS *lmp) : Pair(lmp) centroidstressflag = CENTROID_NOTAVAIL; ghostneigh = 1; - nelements = 0; - elements = nullptr; - nparams = maxparam = 0; params = nullptr; - elem2param = nullptr; maxlocal = 0; SR_numneigh = nullptr; SR_firstneigh = nullptr; ipage = nullptr; pgsize = oneatom = 0; - map = nullptr; Nt = nullptr; Nd = nullptr; @@ -75,11 +70,8 @@ PairExTeP::PairExTeP(LAMMPS *lmp) : Pair(lmp) PairExTeP::~PairExTeP() { - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; memory->destroy(params); - memory->destroy(elem2param); + memory->destroy(elem3param); memory->destroy(SR_numneigh); memory->sfree(SR_firstneigh); @@ -91,7 +83,6 @@ PairExTeP::~PairExTeP() memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(cutghost); - delete [] map; } } @@ -159,7 +150,7 @@ void PairExTeP::SR_neigh() rsq = delx*delx + dely*dely + delz*delz; jtype=map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; if (rsq < params[iparam_ij].cutsq) { neighptr[n++] = j; @@ -246,7 +237,7 @@ void PairExTeP::compute(int eflag, int vflag) delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; if (rsq > params[iparam_ij].cutsq) continue; repulsive(¶ms[iparam_ij],rsq,fpair,eflag,evdwl); @@ -270,7 +261,7 @@ void PairExTeP::compute(int eflag, int vflag) j &= NEIGHMASK; jtag = tag[j]; jtype = map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; delr1[0] = x[j][0] - xtmp; delr1[1] = x[j][1] - ytmp; @@ -337,7 +328,7 @@ void PairExTeP::compute(int eflag, int vflag) k = jlist[kk]; k &= NEIGHMASK; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; @@ -352,7 +343,7 @@ void PairExTeP::compute(int eflag, int vflag) /* F_IJ (2) */ // compute force components due to spline derivatives // uses only the part with FXY_x (FXY_y is done when i and j are inversed) - int iparam_ik = elem2param[itype][ktype][0]; + int iparam_ik = elem3param[itype][ktype][0]; double fc_ik_d = ters_fc_d(r2,¶ms[iparam_ik]); double fc_prefac_ik_0 = 1.0 * fc_ik_d * fa / r2; double fc_prefac_ik = dFc_dNtij * fc_prefac_ik_0; @@ -396,7 +387,7 @@ void PairExTeP::compute(int eflag, int vflag) k = jlist[kk]; k &= NEIGHMASK; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; @@ -455,71 +446,15 @@ void PairExTeP::settings(int narg, char **/*arg*/) void PairExTeP::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } + map_element2type(narg-3,arg+3); // read potential file and initialize potential parameters read_file(arg[2]); spline_init(); setup(); - - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- @@ -818,12 +753,12 @@ void PairExTeP::setup() { int i,j,k,m,n; - // set elem2param for all element triplet combinations + // set elem3param for all element triplet combinations // must be a single exact match to lines read from file // do not allow for ACB in place of ABC - memory->destroy(elem2param); - memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param"); + memory->destroy(elem3param); + memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) @@ -837,7 +772,7 @@ void PairExTeP::setup() } } if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j][k] = n; + elem3param[i][j][k] = n; } // compute parameter values derived from inputs diff --git a/src/USER-MISC/pair_extep.h b/src/USER-MISC/pair_extep.h index 599147c46e..08ee6d9a82 100644 --- a/src/USER-MISC/pair_extep.h +++ b/src/USER-MISC/pair_extep.h @@ -48,30 +48,24 @@ class PairExTeP : public Pair { double c1,c2,c3,c4; int ielement,jelement,kelement; int powermint; - double Z_i,Z_j; // added for ExTePZBL + double Z_i,Z_j; // added for ExTePZBL double ZBLcut,ZBLexpscale; - double c5,ca1,ca4; // added for ExTePMOD + double c5,ca1,ca4; // added for ExTePMOD double powern_del; }; Param *params; // parameter set for an I-J-K interaction - char **elements; // names of unique elements - int ***elem2param; // mapping from element triplets to parameters - int *map; // mapping from atom types to elements double cutmax; // max cutoff for all elements - int nelements; // # of unique elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets - int maxlocal; // size of numneigh, firstneigh arrays - int maxpage; // # of pages currently allocated - int pgsize; // size of neighbor page - int oneatom; // max # of neighbors for one atom - MyPage *ipage; // neighbor list pages - int *SR_numneigh; // # of pair neighbors for each atom - int **SR_firstneigh; // ptr to 1st neighbor of each atom + int maxlocal; // size of numneigh, firstneigh arrays + int maxpage; // # of pages currently allocated + int pgsize; // size of neighbor page + int oneatom; // max # of neighbors for one atom + MyPage *ipage; // neighbor list pages + int *SR_numneigh; // # of pair neighbors for each atom + int **SR_firstneigh; // ptr to 1st neighbor of each atom - double *Nt, *Nd; // sum of cutoff fns ( f_C ) with SR neighs + double *Nt, *Nd; // sum of cutoff fns ( f_C ) with SR neighs void allocate(); void spline_init(); diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index 982e67d4c1..2870d175c4 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -22,20 +22,19 @@ #include "pair_ilp_graphene_hbn.h" -#include - -#include #include "atom.h" +#include "citeme.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" +#include "memory.h" +#include "my_page.h" #include "neigh_list.h" #include "neigh_request.h" -#include "my_page.h" -#include "memory.h" -#include "error.h" -#include "citeme.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; @@ -66,13 +65,8 @@ PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp) : Pair(lmp) pvector = new double[nextra]; // initialize element to parameter maps - nelements = 0; - elements = nullptr; - nparams = maxparam = 0; params = nullptr; - elem2param = nullptr; cutILPsq = nullptr; - map = nullptr; nmax = 0; maxlocal = 0; @@ -110,13 +104,8 @@ PairILPGrapheneHBN::~PairILPGrapheneHBN() memory->destroy(offset); } - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - memory->destroy(params); memory->destroy(elem2param); memory->destroy(cutILPsq); - if (allocated) delete [] map; } /* ---------------------------------------------------------------------- @@ -168,68 +157,10 @@ void PairILPGrapheneHBN::settings(int narg, char **arg) void PairILPGrapheneHBN::coeff(int narg, char **arg) { - int i,j,n; - - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); if (!allocated) allocate(); - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } - - + map_element2type(narg-3,arg+3); read_file(arg[2]); - - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - cut[i][j] = cut_global; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/USER-MISC/pair_ilp_graphene_hbn.h index aadb792cad..4f5e187782 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.h +++ b/src/USER-MISC/pair_ilp_graphene_hbn.h @@ -56,12 +56,6 @@ class PairILPGrapheneHBN : public Pair { int ielement,jelement; }; Param *params; // parameter set for I-J interactions - char **elements; // names of unique elements - int **elem2param; // mapping from element pairs to parameters - int *map; // mapping from atom types to elements - int nelements; // # of unique elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets int nmax; // max # of atoms double cut_global; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index c5fa33bbac..45ad36dd7c 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -21,21 +21,20 @@ ------------------------------------------------------------------------- */ #include "pair_kolmogorov_crespi_full.h" -#include - -#include #include "atom.h" +#include "citeme.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" +#include "memory.h" +#include "my_page.h" #include "neigh_list.h" #include "neigh_request.h" -#include "my_page.h" -#include "memory.h" -#include "error.h" -#include "citeme.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; @@ -66,13 +65,8 @@ PairKolmogorovCrespiFull::PairKolmogorovCrespiFull(LAMMPS *lmp) : Pair(lmp) pvector = new double[nextra]; // initialize element to parameter maps - nelements = 0; - elements = nullptr; - nparams = maxparam = 0; params = nullptr; - elem2param = nullptr; cutKCsq = nullptr; - map = nullptr; nmax = 0; maxlocal = 0; @@ -111,13 +105,9 @@ PairKolmogorovCrespiFull::~PairKolmogorovCrespiFull() memory->destroy(offset); } - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; memory->destroy(params); memory->destroy(elem2param); memory->destroy(cutKCsq); - if (allocated) delete [] map; } /* ---------------------------------------------------------------------- @@ -169,68 +159,9 @@ void PairKolmogorovCrespiFull::settings(int narg, char **arg) void PairKolmogorovCrespiFull::coeff(int narg, char **arg) { - int i,j,n; - - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); if (!allocated) allocate(); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } - - + map_element2type(narg-3,arg+3); read_file(arg[2]); - - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - cut[i][j] = cut_global; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/USER-MISC/pair_kolmogorov_crespi_full.h index f7d9237be4..dd2721d37e 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.h +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.h @@ -57,12 +57,6 @@ class PairKolmogorovCrespiFull : public Pair { int ielement,jelement; }; Param *params; // parameter set for I-J interactions - char **elements; // names of unique elements - int **elem2param; // mapping from element pairs to parameters - int *map; // mapping from atom types to elements - int nelements; // # of unique elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets int nmax; // max # of atoms double cut_global; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp index 1bea688be5..4b5de2314e 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp @@ -23,16 +23,15 @@ #include "pair_kolmogorov_crespi_z.h" -#include - -#include #include "atom.h" #include "comm.h" -#include "force.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; @@ -69,12 +68,8 @@ PairKolmogorovCrespiZ::~PairKolmogorovCrespiZ() memory->destroy(offset); } - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; memory->destroy(params); memory->destroy(elem2param); - if (allocated) delete [] map; } /* ---------------------------------------------------------------------- */ @@ -221,45 +216,13 @@ void PairKolmogorovCrespiZ::settings(int narg, char **arg) void PairKolmogorovCrespiZ::coeff(int narg, char **arg) { - int i,j,n; - - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } - + map_element2type(narg-3,arg+3,false); read_file(arg[2]); // set setflag only for i,j pairs where both are mapped to elements diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.h b/src/USER-MISC/pair_kolmogorov_crespi_z.h index 1a90fdfa0b..7d242d67fd 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.h +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.h @@ -43,12 +43,6 @@ class PairKolmogorovCrespiZ : public Pair { int ielement,jelement; }; Param *params; // parameter set for I-J interactions - char **elements; // names of unique elements - int **elem2param; // mapping from element pairs to parameters - int *map; // mapping from atom types to elements - int nelements; // # of unique elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets double cut_global; double **cut; diff --git a/src/USER-MISC/pair_lebedeva_z.cpp b/src/USER-MISC/pair_lebedeva_z.cpp index a600f5b761..afd7209c6b 100644 --- a/src/USER-MISC/pair_lebedeva_z.cpp +++ b/src/USER-MISC/pair_lebedeva_z.cpp @@ -24,16 +24,15 @@ #include "pair_lebedeva_z.h" -#include - -#include #include "atom.h" #include "comm.h" -#include "force.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; @@ -48,12 +47,7 @@ PairLebedevaZ::PairLebedevaZ(LAMMPS *lmp) : Pair(lmp) restartinfo = 0; // initialize element to parameter maps - nelements = 0; - elements = nullptr; - nparams = maxparam = 0; params = nullptr; - elem2param = nullptr; - map = nullptr; // always compute energy offset offset_flag = 1; @@ -70,12 +64,8 @@ PairLebedevaZ::~PairLebedevaZ() memory->destroy(offset); } - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; memory->destroy(params); memory->destroy(elem2param); - if (allocated) delete [] map; } /* ---------------------------------------------------------------------- */ @@ -217,45 +207,13 @@ void PairLebedevaZ::settings(int narg, char **arg) void PairLebedevaZ::coeff(int narg, char **arg) { - int i,j,n; - - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } - + map_element2type(narg-3,arg+3,false); read_file(arg[2]); // set setflag only for i,j pairs where both are mapped to elements diff --git a/src/USER-MISC/pair_lebedeva_z.h b/src/USER-MISC/pair_lebedeva_z.h index e221087a0a..57cf445889 100644 --- a/src/USER-MISC/pair_lebedeva_z.h +++ b/src/USER-MISC/pair_lebedeva_z.h @@ -43,12 +43,6 @@ class PairLebedevaZ : public Pair { int ielement,jelement; }; Param *params; // parameter set for I-J interactions - char **elements; // names of unique elements - int **elem2param; // mapping from element pairs to parameters - int *map; // mapping from atom types to elements - int nelements; // # of unique elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets double cut_global; double **cut; diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp index a6bf602c70..e956d96cf2 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/USER-MISC/pair_meam_spline.cpp @@ -32,18 +32,18 @@ ------------------------------------------------------------------------- */ #include "pair_meam_spline.h" -#include -#include #include "atom.h" -#include "force.h" #include "comm.h" -#include "neighbor.h" +#include "error.h" +#include "force.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; @@ -55,10 +55,6 @@ PairMEAMSpline::PairMEAMSpline(LAMMPS *lmp) : Pair(lmp) restartinfo = 0; one_coeff = 1; - nelements = 0; - elements = nullptr; - map = nullptr; - Uprime_values = nullptr; nmax = 0; maxNeighbors = 0; @@ -80,10 +76,6 @@ PairMEAMSpline::PairMEAMSpline(LAMMPS *lmp) : Pair(lmp) PairMEAMSpline::~PairMEAMSpline() { - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - delete[] twoBodyInfo; memory->destroy(Uprime_values); @@ -98,8 +90,6 @@ PairMEAMSpline::~PairMEAMSpline() delete[] gs; delete[] zero_atom_energies; - - delete [] map; } } @@ -389,11 +379,6 @@ void PairMEAMSpline::coeff(int narg, char **arg) if (narg != 3 + atom->ntypes) error->all(FLERR,"Incorrect args for pair coefficients"); - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - // read potential file: also sets the number of elements. read_file(arg[2]); diff --git a/src/USER-MISC/pair_meam_spline.h b/src/USER-MISC/pair_meam_spline.h index d1dc5064f5..b20454f18d 100644 --- a/src/USER-MISC/pair_meam_spline.h +++ b/src/USER-MISC/pair_meam_spline.h @@ -67,10 +67,6 @@ public: double memory_usage(); protected: - char **elements; // names of unique elements - int *map; // mapping from atom types to elements - int nelements; // # of unique elements - class SplineFunction { public: /// Default constructor. diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index 58c0f75546..ff7b89fbe7 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -24,18 +24,18 @@ ------------------------------------------------------------------------- */ #include "pair_meam_sw_spline.h" -#include -#include #include "atom.h" -#include "force.h" #include "comm.h" -#include "neighbor.h" +#include "error.h" +#include "force.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; @@ -49,9 +49,6 @@ PairMEAMSWSpline::PairMEAMSWSpline(LAMMPS *lmp) : Pair(lmp) manybody_flag = 1; centroidstressflag = CENTROID_NOTAVAIL; - nelements = 0; - elements = nullptr; - Uprime_values = nullptr; //ESWprime_values = nullptr; nmax = 0; @@ -66,10 +63,6 @@ PairMEAMSWSpline::PairMEAMSWSpline(LAMMPS *lmp) : Pair(lmp) PairMEAMSWSpline::~PairMEAMSWSpline() { - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - delete[] twoBodyInfo; memory->destroy(Uprime_values); //memory->destroy(ESWprime_values); @@ -77,7 +70,6 @@ PairMEAMSWSpline::~PairMEAMSWSpline() if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; } } @@ -381,46 +373,9 @@ void PairMEAMSWSpline::settings(int narg, char **/*arg*/) void PairMEAMSWSpline::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } + map_element2type(narg-3,arg+3); // for now, only allow single element @@ -431,25 +386,6 @@ void PairMEAMSWSpline::coeff(int narg, char **arg) // read potential file read_file(arg[2]); - - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- diff --git a/src/USER-MISC/pair_meam_sw_spline.h b/src/USER-MISC/pair_meam_sw_spline.h index 7b40d123ed..ecf56c7931 100644 --- a/src/USER-MISC/pair_meam_sw_spline.h +++ b/src/USER-MISC/pair_meam_sw_spline.h @@ -54,9 +54,6 @@ public: double memory_usage(); protected: - char **elements; // names of unique elements - int *map; // mapping from atom types to elements - int nelements; // # of unique elements class SplineFunction { public: diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp index 0d5bbc1147..ed05961fa7 100644 --- a/src/USER-MISC/pair_tersoff_table.cpp +++ b/src/USER-MISC/pair_tersoff_table.cpp @@ -22,21 +22,19 @@ #include "pair_tersoff_table.h" -#include - -#include #include "atom.h" -#include "neighbor.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" -#include "comm.h" -#include "memory.h" - -#include "tokenizer.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "tokenizer.h" -#include "error.h" +#include +#include using namespace LAMMPS_NS; @@ -64,11 +62,7 @@ PairTersoffTable::PairTersoffTable(LAMMPS *lmp) : Pair(lmp) centroidstressflag = CENTROID_NOTAVAIL; unit_convert_flag = utils::get_supported_conversions(utils::ENERGY); - nelements = 0; - elements = nullptr; - nparams = maxparam = 0; params = nullptr; - elem2param = nullptr; allocated = 0; preGtetaFunction = preGtetaFunctionDerived = nullptr; @@ -88,17 +82,12 @@ PairTersoffTable::PairTersoffTable(LAMMPS *lmp) : Pair(lmp) PairTersoffTable::~PairTersoffTable() { - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; memory->destroy(params); - memory->destroy(elem2param); + memory->destroy(elem3param); if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; - } deallocateGrids(); deallocatePreLoops(); @@ -177,7 +166,7 @@ void PairTersoffTable::compute(int eflag, int vflag) r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (r_ij > params[ijparam].cutsq) continue; @@ -208,8 +197,8 @@ void PairTersoffTable::compute(int eflag, int vflag) k = jlist[neighbor_k]; k &= NEIGHMASK; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; dr_ik[0] = xtmp -x[k][0]; dr_ik[1] = ytmp -x[k][1]; @@ -264,7 +253,7 @@ void PairTersoffTable::compute(int eflag, int vflag) r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (r_ij > params[ijparam].cutsq) continue; @@ -308,8 +297,8 @@ void PairTersoffTable::compute(int eflag, int vflag) k = jlist[neighbor_k]; k &= NEIGHMASK; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; dr_ik[0] = xtmp -x[k][0]; dr_ik[1] = ytmp -x[k][1]; @@ -333,8 +322,8 @@ void PairTersoffTable::compute(int eflag, int vflag) k = jlist[neighbor_k]; k &= NEIGHMASK; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; dr_ik[0] = xtmp -x[k][0]; dr_ik[1] = ytmp -x[k][1]; @@ -392,8 +381,8 @@ void PairTersoffTable::compute(int eflag, int vflag) k = jlist[neighbor_k]; k &= NEIGHMASK; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; dr_ik[0] = xtmp -x[k][0]; dr_ik[1] = ytmp -x[k][1]; @@ -457,8 +446,8 @@ void PairTersoffTable::compute(int eflag, int vflag) k = jlist[neighbor_k]; k &= NEIGHMASK; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; dr_ik[0] = xtmp -x[k][0]; dr_ik[1] = ytmp -x[k][1]; @@ -608,7 +597,7 @@ void PairTersoffTable::allocateGrids(void) r = -1.0; deltaArgumentGtetaFunction = 1.0 / GRIDDENSITY_GTETA; - int iparam = elem2param[i][i][i]; + int iparam = elem3param[i][i][i]; double c = params[iparam].c; double d = params[iparam].d; double h = params[iparam].h; @@ -628,7 +617,7 @@ void PairTersoffTable::allocateGrids(void) for (i=0; intypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } + map_element2type(narg-3,arg+3); // read potential file and initialize potential parameters read_file(arg[2]); setup_params(); - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); - // allocate tables and internal structures + allocatePreLoops(); allocateGrids(); } @@ -966,12 +900,12 @@ void PairTersoffTable::setup_params() { int i,j,k,m,n; - // set elem2param for all triplet combinations + // set elem3param for all triplet combinations // must be a single exact match to lines read from file // do not allow for ACB in place of ABC - memory->destroy(elem2param); - memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param"); + memory->destroy(elem3param); + memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) @@ -985,7 +919,7 @@ void PairTersoffTable::setup_params() } } if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j][k] = n; + elem3param[i][j][k] = n; } // set cutoff square diff --git a/src/USER-MISC/pair_tersoff_table.h b/src/USER-MISC/pair_tersoff_table.h index d63a5be5a6..84e6f6fe50 100644 --- a/src/USER-MISC/pair_tersoff_table.h +++ b/src/USER-MISC/pair_tersoff_table.h @@ -59,12 +59,6 @@ class PairTersoffTable : public Pair { double cutmax; // max cutoff for all elements - int nelements; // # of unique elements - char **elements; // names of unique elements - int ***elem2param; // mapping from element triplets to parameters - int *map; // mapping from atom types to elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets Param *params; // parameter set for an I-J-K interaction void allocate(); diff --git a/src/USER-OMP/pair_agni_omp.cpp b/src/USER-OMP/pair_agni_omp.cpp index 02a6126e03..258c833cdf 100644 --- a/src/USER-OMP/pair_agni_omp.cpp +++ b/src/USER-OMP/pair_agni_omp.cpp @@ -101,7 +101,7 @@ void PairAGNIOMP::eval(int iifrom, int iito, ThrData * const thr) ztmp = x[i].z; fxtmp = fytmp = fztmp = 0.0; - const Param &iparam = params[elem2param[itype]]; + const Param &iparam = params[elem1param[itype]]; Vx = new double[iparam.numeta]; Vy = new double[iparam.numeta]; Vz = new double[iparam.numeta]; diff --git a/src/USER-OMP/pair_comb_omp.cpp b/src/USER-OMP/pair_comb_omp.cpp index cfde8ff905..52c8855738 100644 --- a/src/USER-OMP/pair_comb_omp.cpp +++ b/src/USER-OMP/pair_comb_omp.cpp @@ -139,7 +139,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr) iq = q[i]; NCo[i] = 0; nj = 0; - iparam_i = elem2param[itype][itype][itype]; + iparam_i = elem3param[itype][itype][itype]; // self energy, only on i atom @@ -180,7 +180,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr) delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; // long range q-dependent @@ -242,7 +242,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr) for (jj = 0; jj < sht_jnum; jj++) { j = sht_jlist[jj]; jtype = map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; if (params[iparam_ij].hfocor > 0.0) { delr1[0] = x[j][0] - xtmp; @@ -264,7 +264,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr) j = sht_jlist[jj]; jtype = map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; // this Qj for q-dependent BSi @@ -288,7 +288,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr) k = sht_jlist[kk]; if (j == k) continue; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; @@ -332,7 +332,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr) k = sht_jlist[kk]; if (j == k) continue; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; @@ -434,7 +434,7 @@ double PairCombOMP::yasu_char(double *qf_fix, int &igroup) const double ytmp = x[i][1]; const double ztmp = x[i][2]; const double iq = q[i]; - const int iparam_i = elem2param[itype][itype][itype]; + const int iparam_i = elem3param[itype][itype][itype]; // charge force from self energy @@ -467,7 +467,7 @@ double PairCombOMP::yasu_char(double *qf_fix, int &igroup) delr1[2] = x[j][2] - ztmp; double rsq1 = dot3(delr1,delr1); - const int iparam_ij = elem2param[itype][jtype][jtype]; + const int iparam_ij = elem3param[itype][jtype][jtype]; // long range q-dependent @@ -505,7 +505,7 @@ double PairCombOMP::yasu_char(double *qf_fix, int &igroup) delr1[2] = x[j][2] - ztmp; double rsq1 = dot3(delr1,delr1); - const int iparam_ij = elem2param[itype][jtype][jtype]; + const int iparam_ij = elem3param[itype][jtype][jtype]; if (rsq1 > params[iparam_ij].cutsq) continue; nj ++; diff --git a/src/USER-OMP/pair_edip_omp.cpp b/src/USER-OMP/pair_edip_omp.cpp index 106d038743..b2e8708305 100644 --- a/src/USER-OMP/pair_edip_omp.cpp +++ b/src/USER-OMP/pair_edip_omp.cpp @@ -184,7 +184,7 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr) r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (r_ij > params[ijparam].cutsq) continue; r_ij = sqrt(r_ij); @@ -299,7 +299,7 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr) r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (r_ij > params[ijparam].cutsq) continue; r_ij = sqrt(r_ij); @@ -353,7 +353,7 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr) k = jlist[neighbor_k]; k &= NEIGHMASK; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; dr_ik[0] = x[k].x - xtmp; dr_ik[1] = x[k].y - ytmp; diff --git a/src/USER-OMP/pair_sw_omp.cpp b/src/USER-OMP/pair_sw_omp.cpp index 92d0d0c15a..28e450f517 100644 --- a/src/USER-OMP/pair_sw_omp.cpp +++ b/src/USER-OMP/pair_sw_omp.cpp @@ -121,7 +121,7 @@ void PairSWOMP::eval(int iifrom, int iito, ThrData * const thr) rsq = delx*delx + dely*dely + delz*delz; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (rsq >= params[ijparam].cutsq) { continue; } else { @@ -161,7 +161,7 @@ void PairSWOMP::eval(int iifrom, int iito, ThrData * const thr) for (jj = 0; jj < jnumm1; jj++) { j = neighshort_thr[jj]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; delr1[0] = x[j].x - xtmp; delr1[1] = x[j].y - ytmp; delr1[2] = x[j].z - ztmp; @@ -173,8 +173,8 @@ void PairSWOMP::eval(int iifrom, int iito, ThrData * const thr) for (kk = jj+1; kk < numshort; kk++) { k = neighshort_thr[kk]; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; delr2[0] = x[k].x - xtmp; delr2[1] = x[k].y - ytmp; diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp index c6947bbde7..8f255ee1ba 100644 --- a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp @@ -157,7 +157,7 @@ void PairTersoffMODCOMP::eval(int iifrom, int iito, ThrData * const thr) rsq = rsqtmp; } - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; if (rsq > params[iparam_ij].cutsq) continue; repulsive(¶ms[iparam_ij],rsq,fpair,EFLAG,evdwl); @@ -185,7 +185,7 @@ void PairTersoffMODCOMP::eval(int iifrom, int iito, ThrData * const thr) j = jlist[jj]; j &= NEIGHMASK; jtype = map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; delr1[0] = x[j].x - xtmp; delr1[1] = x[j].y - ytmp; @@ -210,7 +210,7 @@ void PairTersoffMODCOMP::eval(int iifrom, int iito, ThrData * const thr) k = jlist[kk]; k &= NEIGHMASK; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k].x - xtmp; delr2[1] = x[k].y - ytmp; @@ -251,7 +251,7 @@ void PairTersoffMODCOMP::eval(int iifrom, int iito, ThrData * const thr) k = jlist[kk]; k &= NEIGHMASK; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k].x - xtmp; delr2[1] = x[k].y - ytmp; diff --git a/src/USER-OMP/pair_tersoff_mod_omp.cpp b/src/USER-OMP/pair_tersoff_mod_omp.cpp index e689803c38..454a387982 100644 --- a/src/USER-OMP/pair_tersoff_mod_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_omp.cpp @@ -159,7 +159,7 @@ void PairTersoffMODOMP::eval(int iifrom, int iito, ThrData * const thr) rsq = rsqtmp; } - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; if (rsq > params[iparam_ij].cutsq) continue; repulsive(¶ms[iparam_ij],rsq,fpair,EFLAG,evdwl); @@ -187,7 +187,7 @@ void PairTersoffMODOMP::eval(int iifrom, int iito, ThrData * const thr) j = jlist[jj]; j &= NEIGHMASK; jtype = map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; delr1[0] = x[j].x - xtmp; delr1[1] = x[j].y - ytmp; @@ -212,7 +212,7 @@ void PairTersoffMODOMP::eval(int iifrom, int iito, ThrData * const thr) k = jlist[kk]; k &= NEIGHMASK; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k].x - xtmp; delr2[1] = x[k].y - ytmp; @@ -253,7 +253,7 @@ void PairTersoffMODOMP::eval(int iifrom, int iito, ThrData * const thr) k = jlist[kk]; k &= NEIGHMASK; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k].x - xtmp; delr2[1] = x[k].y - ytmp; diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/USER-OMP/pair_tersoff_omp.cpp index 7fb3c70d78..c12e3b9859 100644 --- a/src/USER-OMP/pair_tersoff_omp.cpp +++ b/src/USER-OMP/pair_tersoff_omp.cpp @@ -173,7 +173,7 @@ void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr) } jtype = map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; if (rsq >= params[iparam_ij].cutsq) continue; repulsive(¶ms[iparam_ij],rsq,fpair,EFLAG,evdwl); @@ -200,7 +200,7 @@ void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr) for (jj = 0; jj < numshort; jj++) { j = neighshort_thr[jj]; jtype = map[type[j]]; - iparam_ij = elem2param[itype][jtype][jtype]; + iparam_ij = elem3param[itype][jtype][jtype]; delr1[0] = x[j].x - xtmp; delr1[1] = x[j].y - ytmp; @@ -224,7 +224,7 @@ void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr) if (jj == kk) continue; k = neighshort_thr[kk]; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k].x - xtmp; delr2[1] = x[k].y - ytmp; @@ -264,7 +264,7 @@ void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr) if (jj == kk) continue; k = neighshort_thr[kk]; ktype = map[type[k]]; - iparam_ijk = elem2param[itype][jtype][ktype]; + iparam_ijk = elem3param[itype][jtype][ktype]; delr2[0] = x[k].x - xtmp; delr2[1] = x[k].y - ytmp; diff --git a/src/USER-OMP/pair_tersoff_table_omp.cpp b/src/USER-OMP/pair_tersoff_table_omp.cpp index 2e52492491..02752c8577 100644 --- a/src/USER-OMP/pair_tersoff_table_omp.cpp +++ b/src/USER-OMP/pair_tersoff_table_omp.cpp @@ -154,7 +154,7 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr) r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (r_ij > params[ijparam].cutsq) continue; @@ -185,8 +185,8 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr) k = jlist[neighbor_k]; k &= NEIGHMASK; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; dr_ik[0] = xtmp -x[k].x; dr_ik[1] = ytmp -x[k].y; @@ -241,7 +241,7 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr) r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (r_ij > params[ijparam].cutsq) continue; @@ -285,8 +285,8 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr) k = jlist[neighbor_k]; k &= NEIGHMASK; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; dr_ik[0] = xtmp -x[k].x; dr_ik[1] = ytmp -x[k].y; @@ -310,8 +310,8 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr) k = jlist[neighbor_k]; k &= NEIGHMASK; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; dr_ik[0] = xtmp -x[k].x; dr_ik[1] = ytmp -x[k].y; @@ -370,8 +370,8 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr) k = jlist[neighbor_k]; k &= NEIGHMASK; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; dr_ik[0] = xtmp -x[k].x; dr_ik[1] = ytmp -x[k].y; @@ -436,8 +436,8 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr) k = jlist[neighbor_k]; k &= NEIGHMASK; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; dr_ik[0] = xtmp -x[k].x; dr_ik[1] = ytmp -x[k].y; diff --git a/src/USER-OMP/pair_vashishta_omp.cpp b/src/USER-OMP/pair_vashishta_omp.cpp index 303de78e37..23d7235578 100644 --- a/src/USER-OMP/pair_vashishta_omp.cpp +++ b/src/USER-OMP/pair_vashishta_omp.cpp @@ -143,7 +143,7 @@ void PairVashishtaOMP::eval(int iifrom, int iito, ThrData * const thr) } jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (rsq >= params[ijparam].cutsq) continue; twobody(¶ms[ijparam],rsq,fpair,EFLAG,evdwl); @@ -164,7 +164,7 @@ void PairVashishtaOMP::eval(int iifrom, int iito, ThrData * const thr) for (jj = 0; jj < jnumm1; jj++) { j = neighshort_thr[jj]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; delr1[0] = x[j].x - xtmp; delr1[1] = x[j].y - ytmp; delr1[2] = x[j].z - ztmp; @@ -177,8 +177,8 @@ void PairVashishtaOMP::eval(int iifrom, int iito, ThrData * const thr) for (kk = jj+1; kk < numshort; kk++) { k = neighshort_thr[kk]; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; delr2[0] = x[k].x - xtmp; delr2[1] = x[k].y - ytmp; diff --git a/src/USER-OMP/pair_vashishta_table_omp.cpp b/src/USER-OMP/pair_vashishta_table_omp.cpp index 50c985ad68..c03d827d9b 100644 --- a/src/USER-OMP/pair_vashishta_table_omp.cpp +++ b/src/USER-OMP/pair_vashishta_table_omp.cpp @@ -141,7 +141,7 @@ void PairVashishtaTableOMP::eval(int iifrom, int iito, ThrData * const thr) } jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; if (rsq >= params[ijparam].cutsq) continue; twobody_table(params[ijparam],rsq,fpair,EFLAG,evdwl); @@ -162,7 +162,7 @@ void PairVashishtaTableOMP::eval(int iifrom, int iito, ThrData * const thr) for (jj = 0; jj < jnumm1; jj++) { j = neighshort_thr[jj]; jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; + ijparam = elem3param[itype][jtype][jtype]; delr1[0] = x[j].x - xtmp; delr1[1] = x[j].y - ytmp; delr1[2] = x[j].z - ztmp; @@ -175,8 +175,8 @@ void PairVashishtaTableOMP::eval(int iifrom, int iito, ThrData * const thr) for (kk = jj+1; kk < numshort; kk++) { k = neighshort_thr[kk]; ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; delr2[0] = x[k].x - xtmp; delr2[1] = x[k].y - ytmp; diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp index fe78fbbb37..4d6f240ec6 100644 --- a/src/USER-REAXC/pair_reaxc.cpp +++ b/src/USER-REAXC/pair_reaxc.cpp @@ -22,23 +22,23 @@ #include "pair_reaxc.h" -#include - -#include -#include #include "atom.h" -#include "update.h" -#include "force.h" +#include "citeme.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_reaxc.h" -#include "citeme.h" +#include "force.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "update.h" + +#include +#include +#include // for strcasecmp() #include "reaxc_defs.h" #include "reaxc_types.h" @@ -175,7 +175,6 @@ PairReaxC::~PairReaxC() memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(cutghost); - delete [] map; delete [] chi; delete [] eta; diff --git a/src/USER-REAXC/pair_reaxc.h b/src/USER-REAXC/pair_reaxc.h index a833ddbcf0..53b41ba9c8 100644 --- a/src/USER-REAXC/pair_reaxc.h +++ b/src/USER-REAXC/pair_reaxc.h @@ -62,9 +62,6 @@ class PairReaxC : public Pair { protected: char *fix_id; double cutmax; - int nelements; // # of unique elements - char **elements; // names of unique elements - int *map; class FixReaxC *fix_reax; double *chi,*eta,*gamma; diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp index 7ed37fefc4..5a27855a47 100644 --- a/src/USER-SMTBQ/pair_smtbq.cpp +++ b/src/USER-SMTBQ/pair_smtbq.cpp @@ -91,10 +91,6 @@ PairSMTBQ::PairSMTBQ(LAMMPS *lmp) : Pair(lmp) ds = 0.0; kmax = 0; - nelements = 0; - elements = nullptr; - nparams = 0; - maxparam = 0; params = nullptr; intparams = nullptr; @@ -153,8 +149,6 @@ PairSMTBQ::~PairSMTBQ() { int i; if (elements) { - for ( i = 0; i < nelements; i++) delete [] elements[i]; - for (i = 0; i < atom->ntypes ; i++ ) free( params[i].nom); for (i = 1; i <= maxintparam ; i++ ) free( intparams[i].typepot); for (i = 1; i <= maxintparam ; i++ ) free( intparams[i].mode); @@ -166,7 +160,6 @@ PairSMTBQ::~PairSMTBQ() free(writeenerg); free(Bavard); - delete [] elements; memory->sfree(params); memory->sfree(intparams); @@ -216,7 +209,6 @@ PairSMTBQ::~PairSMTBQ() if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] map; delete [] esm; } @@ -252,92 +244,30 @@ void PairSMTBQ::settings(int narg, char ** /* arg */) void PairSMTBQ::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (strstr(force->pair_style,"hybrid")) + if (utils::strmatch(force->pair_style,"^hybrid")) error->all(FLERR,"Pair style SMTBQ is not compatible with hybrid styles"); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } + map_element2type(narg-3,arg+3); // read potential file and initialize potential parameters read_file(arg[2]); - n = atom->ntypes; - // generate Coulomb 1/r energy look-up table - if (comm->me == 0 && screen) fprintf(screen,"Pair SMTBQ:\n"); if (comm->me == 0 && screen) - fprintf(screen," generating Coulomb integral lookup table ...\n"); + fputs("Pair SMTBQ: generating Coulomb integral lookup table ...\n",screen); tabqeq(); // ------------ - if (comm->me == 0 && screen) - fprintf(screen," generating Second Moment integral lookup table ...\n"); + fputs(" generating Second Moment integral lookup table ...\n",screen); tabsm(); - - // ------------ - - // clear setflag since coeff() called once with I,J = * * - - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- diff --git a/src/USER-SMTBQ/pair_smtbq.h b/src/USER-SMTBQ/pair_smtbq.h index 4681c94895..8bf1cba57c 100644 --- a/src/USER-SMTBQ/pair_smtbq.h +++ b/src/USER-SMTBQ/pair_smtbq.h @@ -60,8 +60,6 @@ protected: int loopmax; // max of iteration double cutmax; // max cutoff for all elements - int nelements; // # of unique elements - char **elements; // names of unique elements char *QEqMode; // name of QEqMode char *Bavard; // Verbose parameter char *writepot; // write or not the electronegativity component @@ -70,11 +68,8 @@ protected: double zlim1QEq; // z limit for QEq equilibration double zlim2QEq; // z limit for QEq equilibration double QOxInit; // Initial charge for oxygen atoms (if the charge is not specified) - int *map; // mapping from atom types to elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets - int maxintparam; // max # of interaction sets - int maxintsm; // max # of interaction SM + int maxintparam; // max # of interaction sets + int maxintsm; // max # of interaction SM double r1Coord,r2Coord; Param *params; // parameter set for an I atom Intparam *intparams; // parameter set for an I interaction diff --git a/src/input.cpp b/src/input.cpp index 53fcc606db..f96cf8c75c 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -1697,6 +1697,9 @@ void Input::pair_coeff() error->all(FLERR,"Pair_coeff command before simulation box is defined"); if (force->pair == nullptr) error->all(FLERR,"Pair_coeff command before pair_style is defined"); + if ((narg < 2) || (force->pair->one_coeff && ((strcmp(arg[0],"*") != 0) + || (strcmp(arg[1],"*") != 0)))) + error->all(FLERR,"Incorrect args for pair coefficients"); force->pair->coeff(narg,arg); } diff --git a/src/pair.cpp b/src/pair.cpp index 27a8831eb1..767fa638cf 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -106,6 +106,13 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp) num_tally_compute = 0; list_tally_compute = nullptr; + nelements = nparams = maxparam = 0; + elements = nullptr; + elem1param = nullptr; + elem2param = nullptr; + elem3param = nullptr; + map = nullptr; + nondefault_history_transfer = 0; beyond_contact = 0; @@ -129,6 +136,11 @@ Pair::~Pair() if (copymode) return; + if (elements) + for (int i = 0; i < nelements; i++) delete[] elements[i]; + delete[] elements; + + delete[] map; memory->destroy(eatom); memory->destroy(vatom); memory->destroy(cvatom); @@ -776,6 +788,68 @@ void Pair::del_tally_callback(Compute *ptr) } } +/* ------------------------------------------------------------------- + build element to atom type mapping for manybody potentials + also clear and reset setflag[][] array and check missing entries +---------------------------------------------------------------------- */ + +void Pair::map_element2type(int narg, char **arg, bool update_setflag) +{ + int i,j; + const int ntypes = atom->ntypes; + + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if "NULL" + // nelements = # of unique elements + // elements = list of element names + + if (narg != ntypes) + error->all(FLERR,"Incorrect args for pair coefficients"); + + if (elements) { + for (i = 0; i < nelements; i++) delete[] elements[i]; + delete[] elements; + } + elements = new char*[ntypes]; + for (i = 0; i < ntypes; i++) elements[i] = nullptr; + + nelements = 0; + map[0] = -1; + for (i = 1; i <= narg; i++) { + std::string entry = arg[i-1]; + if (entry == "NULL") { + map[i] = -1; + continue; + } + for (j = 0; j < nelements; j++) + if (entry == elements[j]) break; + map[i] = j; + if (j == nelements) { + elements[j] = utils::strdup(entry); + nelements++; + } + } + + // if requested, clear setflag[i][j] and set it for type pairs + // where both are mapped to elements in map. + + if (update_setflag) { + + int count = 0; + for (i = 1; i <= ntypes; i++) { + for (j = i; j <= ntypes; j++) { + setflag[i][j] = 0; + if ((map[i] >= 0) && (map[j] >= 0)) { + setflag[i][j] = 1; + count++; + } + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + } +} + /* ---------------------------------------------------------------------- setup for energy, virial computation see integrate::ev_set() for bitwise settings of eflag/vflag diff --git a/src/pair.h b/src/pair.h index 9bca64fbf3..b25ad448eb 100644 --- a/src/pair.h +++ b/src/pair.h @@ -216,17 +216,27 @@ class Pair : protected Pointers { virtual void del_tally_callback(class Compute *); protected: - int instance_me; // which Pair class instantiation I am + int instance_me; // which Pair class instantiation I am + int special_lj[4]; // copied from force->special_lj for Kokkos + int suffix_flag; // suffix compatibility flag - int special_lj[4]; // copied from force->special_lj for Kokkos - - int suffix_flag; // suffix compatibility flag - - // pair_modify settings - int offset_flag,mix_flag; // flags for offset and mixing - double tabinner; // inner cutoff for Coulomb table - double tabinner_disp; // inner cutoff for dispersion table + // pair_modify settings + int offset_flag,mix_flag; // flags for offset and mixing + double tabinner; // inner cutoff for Coulomb table + double tabinner_disp; // inner cutoff for dispersion table + protected: + // for mapping of elements to atom types and parameters + // mostly used for manybody potentials + int nelements; // # of unique elements + char **elements; // names of unique elements + int *elem1param; // mapping from elements to parameters + int **elem2param; // mapping from element pairs to parameters + int ***elem3param; // mapping from element triplets to parameters + int *map; // mapping from atom types to elements + int nparams; // # of stored parameter sets + int maxparam; // max # of parameter sets + void map_element2type(int, char**, bool update_setflag=true); public: // custom data type for accessing Coulomb tables diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index 68790c0f03..55529f9eae 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -49,13 +49,8 @@ PairCoulStreitz::PairCoulStreitz(LAMMPS *lmp) : Pair(lmp) restartinfo = 0; one_coeff = 1; nmax = 0; - nelements = 0; - elements = nullptr; - nparams = 0; - maxparam = 0; params = nullptr; - elem2param = nullptr; } /* ---------------------------------------------------------------------- @@ -64,12 +59,8 @@ PairCoulStreitz::PairCoulStreitz(LAMMPS *lmp) : Pair(lmp) PairCoulStreitz::~PairCoulStreitz() { - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - - delete [] elements; memory->sfree(params); - memory->destroy(elem2param); + memory->destroy(elem1param); if (allocated) { memory->destroy(setflag); @@ -80,7 +71,6 @@ PairCoulStreitz::~PairCoulStreitz() memory->destroy(qeq_g); memory->destroy(qeq_z); memory->destroy(qeq_c); - delete [] map; } } @@ -130,69 +120,19 @@ void PairCoulStreitz::settings(int narg, char **arg) void PairCoulStreitz::coeff(int narg, char **arg) { - int i,j,n; - if (!allocated) allocate(); - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if "NULL" - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - elements[j] = utils::strdup(arg[i]); - nelements++; - } - } + map_element2type(narg-3, arg+3); // read potential file and initialize potential parameters read_file(arg[2]); setup_params(); - n = atom->ntypes; - - // clear setflag since coeff() called once with I,J = * * + const int n = atom->ntypes; for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { + for (int j = 1; j <= n; j++) scale[i][j] = 1.0; - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- @@ -308,10 +248,10 @@ void PairCoulStreitz::setup_params() { int i,m,n; - // set elem2param + // set elem1param - memory->destroy(elem2param); - memory->create(elem2param,nelements,"pair:elem2param"); + memory->destroy(elem1param); + memory->create(elem1param,nelements,"pair:elem1param"); for (i = 0; i < nelements; i++) { n = -1; @@ -322,7 +262,7 @@ void PairCoulStreitz::setup_params() } } if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i] = n; + elem1param[i] = n; } // Wolf sum self energy @@ -381,7 +321,7 @@ void PairCoulStreitz::compute(int eflag, int vflag) ytmp = x[i][1]; ztmp = x[i][2]; itype = map[type[i]]; - iparam_i = elem2param[itype]; + iparam_i = elem1param[itype]; qi = q[i]; zei = params[iparam_i].zeta; @@ -401,7 +341,7 @@ void PairCoulStreitz::compute(int eflag, int vflag) j &= NEIGHMASK; jtype = map[type[j]]; - iparam_j = elem2param[jtype]; + iparam_j = elem1param[jtype]; qj = q[j]; zej = params[iparam_j].zeta; zj = params[iparam_j].zcore; @@ -454,7 +394,7 @@ void PairCoulStreitz::compute(int eflag, int vflag) ytmp = x[i][1]; ztmp = x[i][2]; itype = map[type[i]]; - iparam_i = elem2param[itype]; + iparam_i = elem1param[itype]; qi = q[i]; zei = params[iparam_i].zeta; @@ -473,7 +413,7 @@ void PairCoulStreitz::compute(int eflag, int vflag) j = jlist[jj]; j &= NEIGHMASK; jtype = map[type[j]]; - iparam_j = elem2param[jtype]; + iparam_j = elem1param[jtype]; qj = q[j]; zej = params[iparam_j].zeta; zj = params[iparam_j].zcore; diff --git a/src/pair_coul_streitz.h b/src/pair_coul_streitz.h index 2f62846212..12da6afcfe 100644 --- a/src/pair_coul_streitz.h +++ b/src/pair_coul_streitz.h @@ -45,14 +45,8 @@ class PairCoulStreitz : public Pair { }; int nmax; - int nelements; // # of unique elements - char **elements; // names of unique elements - int *elem2param; // mapping from element triplets to parameters - int *map; // mapping from atom types to elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets double precision; - Param *params; // parameter set for an I-J-K interaction + Param *params; // parameter sets for elements // Kspace parameters int kspacetype; From 436be824e14d23115506cf11639bd101818fa084 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Mar 2021 21:13:24 -0400 Subject: [PATCH 0278/1217] use std:: namespace for STL containers --- src/USER-AWPMD/pair_awpmd_cut.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index 3d4e1f12a7..54f851171b 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -150,7 +150,7 @@ void PairAWPMDCut::compute(int eflag, int vflag) # if 1 // mapping of the LAMMPS numbers to the AWPMC numbers - vector gmap(ntot,-1); + std::vector gmap(ntot,-1); for (int ii = 0; ii < inum; ii++) { int i = ilist[ii]; @@ -226,7 +226,7 @@ void PairAWPMDCut::compute(int eflag, int vflag) // prepare the solver object wpmd->reset(); - map > etmap; + std::map > etmap; // add particles to the AWPMD solver object for (int i = 0; i < ntot; i++) { //int i = ilist[ii]; @@ -246,8 +246,8 @@ void PairAWPMDCut::compute(int eflag, int vflag) fi= new Vector_3[wpmd->ni]; // adding electrons - for (map >::iterator it=etmap.begin(); it!= etmap.end(); ++it) { - vector &el=it->second; + for (std::map >::iterator it=etmap.begin(); it!= etmap.end(); ++it) { + std::vector &el=it->second; if (!el.size()) // should not happen continue; int s=spin[el[0]] >0 ? 0 : 1; From dfb18caf5a38b9e32ae6262ce6645f9a37135566 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 27 Mar 2021 15:52:14 -0400 Subject: [PATCH 0279/1217] simplify using utils::strdup(), update order of include files --- src/KOKKOS/pair_exp6_rx_kokkos.cpp | 10 +---- src/KOKKOS/pair_table_rx_kokkos.cpp | 18 +++------ src/LATTE/fix_latte.cpp | 5 +-- src/MC/fix_atom_swap.cpp | 45 +++++++++++---------- src/MC/fix_bond_swap.cpp | 34 ++++++++-------- src/MC/fix_gcmc.cpp | 53 +++++++++++-------------- src/MC/fix_widom.cpp | 4 +- src/MISC/compute_ti.cpp | 26 +++++------- src/MISC/fix_deposit.cpp | 12 ++---- src/MISC/fix_evaporate.cpp | 4 +- src/MISC/fix_oneway.cpp | 4 +- src/MISC/fix_orient_bcc.cpp | 16 ++------ src/MISC/fix_orient_fcc.cpp | 16 ++------ src/MLIAP/mliap_descriptor_snap.cpp | 9 ++--- src/MLIAP/mliap_model_nn.cpp | 2 +- src/REPLICA/compute_event_displace.cpp | 4 +- src/REPLICA/prd.cpp | 22 +++-------- src/REPLICA/tad.cpp | 19 +++------ src/RIGID/compute_erotate_rigid.cpp | 16 ++++---- src/RIGID/compute_ke_rigid.cpp | 16 ++++---- src/RIGID/compute_rigid_local.cpp | 4 +- src/RIGID/fix_ehex.cpp | 22 +++++------ src/RIGID/fix_rigid_nh.cpp | 8 +--- src/RIGID/fix_rigid_nh_small.cpp | 8 +--- src/RIGID/fix_rigid_nph.cpp | 27 ++----------- src/RIGID/fix_rigid_nph_small.cpp | 27 ++----------- src/RIGID/fix_rigid_npt.cpp | 27 ++----------- src/RIGID/fix_rigid_npt_small.cpp | 27 ++----------- src/SHOCK/fix_msst.cpp | 25 ++++++------ src/SHOCK/fix_nphug.cpp | 55 +++++++------------------- src/SPIN/fix_neb_spin.cpp | 28 +++++-------- 31 files changed, 191 insertions(+), 402 deletions(-) diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index 5c1a3b3589..c0cfd11466 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -1800,14 +1800,8 @@ void PairExp6rxKokkos::read_file(char *file) } params[nparams].ispecies = ispecies; - - n = strlen(&atom->dname[ispecies][0]) + 1; - params[nparams].name = new char[n]; - strcpy(params[nparams].name,&atom->dname[ispecies][0]); - - n = strlen(words[1]) + 1; - params[nparams].potential = new char[n]; - strcpy(params[nparams].potential,words[1]); + params[nparams].name = utils::strdup(&atom->dname[ispecies][0]); + params[nparams].potential = utils::strdup(words[1]); if (strcmp(params[nparams].potential,"exp6") == 0) { params[nparams].alpha = atof(words[2]); params[nparams].epsilon = atof(words[3]); diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp index c3e23b6e5e..41b0343443 100644 --- a/src/KOKKOS/pair_table_rx_kokkos.cpp +++ b/src/KOKKOS/pair_table_rx_kokkos.cpp @@ -1040,25 +1040,19 @@ void PairTableRXKokkos::coeff(int narg, char **arg) nspecies = atom->nspecies_dpd; if (nspecies==0) error->all(FLERR,"There are no rx species specified."); - int n; - n = strlen(arg[4]) + 1; - site1 = new char[n]; - strcpy(site1,arg[4]); + site1 = utils::strdup(arg[4]); int ispecies; - for (ispecies = 0; ispecies < nspecies; ispecies++) { + for (ispecies = 0; ispecies < nspecies; ispecies++) if (strcmp(site1,&atom->dname[ispecies][0]) == 0) break; - } + if (ispecies == nspecies && strcmp(site1,"1fluid") != 0) error->all(FLERR,"Site1 name not recognized in pair coefficients"); - n = strlen(arg[5]) + 1; - site2 = new char[n]; - strcpy(site2,arg[5]); - - for (ispecies = 0; ispecies < nspecies; ispecies++) { + site2 = utils::strdup(arg[5]); + for (ispecies = 0; ispecies < nspecies; ispecies++) if (strcmp(site2,&atom->dname[ispecies][0]) == 0) break; - } + if (ispecies == nspecies && strcmp(site2,"1fluid") != 0) error->all(FLERR,"Site2 name not recognized in pair coefficients"); diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index ababe2f185..81d7cb3201 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -84,10 +84,7 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Fix latte does not yet support a LAMMPS calculation " "of a Coulomb potential"); - int n = strlen(arg[3]) + 1; - id_pe = new char[n]; - strcpy(id_pe,arg[3]); - + id_pe = utils::strdup(arg[3]); int ipe = modify->find_compute(id_pe); if (ipe < 0) error->all(FLERR,"Could not find fix latte compute ID"); if (modify->compute[ipe]->peatomflag == 0) diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index 92671fb637..954ce46aa6 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -18,30 +18,31 @@ #include "fix_atom_swap.h" +#include "angle.h" +#include "atom.h" +#include "bond.h" +#include "comm.h" +#include "compute.h" +#include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "group.h" +#include "improper.h" +#include "kspace.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" +#include "pair.h" +#include "random_park.h" +#include "region.h" +#include "update.h" + #include #include #include #include -#include "atom.h" -#include "update.h" -#include "modify.h" -#include "fix.h" -#include "comm.h" -#include "compute.h" -#include "group.h" -#include "domain.h" -#include "region.h" -#include "random_park.h" -#include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" -#include "improper.h" -#include "kspace.h" -#include "memory.h" -#include "error.h" -#include "neighbor.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -138,9 +139,7 @@ void FixAtomSwap::options(int narg, char **arg) iregion = domain->find_region(arg[iarg+1]); if (iregion == -1) error->all(FLERR,"Region ID for fix atom/swap does not exist"); - int n = strlen(arg[iarg+1]) + 1; - idregion = new char[n]; - strcpy(idregion,arg[iarg+1]); + idregion = utils::strdup(arg[iarg+1]); regionflag = 1; iarg += 2; } else if (strcmp(arg[iarg],"ke") == 0) { diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index 119c95d842..84d89a9626 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -13,27 +13,27 @@ #include "fix_bond_swap.h" -#include -#include -#include "atom.h" -#include "force.h" -#include "pair.h" -#include "bond.h" #include "angle.h" -#include "neighbor.h" +#include "atom.h" +#include "bond.h" +#include "citeme.h" +#include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" #include "neigh_list.h" #include "neigh_request.h" -#include "comm.h" -#include "domain.h" -#include "modify.h" -#include "compute.h" +#include "neighbor.h" +#include "pair.h" #include "random_mars.h" -#include "citeme.h" -#include "memory.h" -#include "error.h" - #include "update.h" +#include +#include + using namespace LAMMPS_NS; using namespace FixConst; @@ -642,9 +642,7 @@ int FixBondSwap::modify_param(int narg, char **arg) tflag = 0; } delete [] id_temp; - int n = strlen(arg[1]) + 1; - id_temp = new char[n]; - strcpy(id_temp,arg[1]); + id_temp = utils::strdup(arg[1]); int icompute = modify->find_compute(id_temp); if (icompute < 0) diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index b8eecf95ca..b946615b04 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -17,32 +17,33 @@ #include "fix_gcmc.h" -#include -#include +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "update.h" -#include "modify.h" -#include "fix.h" +#include "bond.h" #include "comm.h" #include "compute.h" -#include "group.h" -#include "domain.h" -#include "region.h" -#include "random_park.h" -#include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "group.h" #include "improper.h" #include "kspace.h" -#include "math_extra.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "molecule.h" #include "neighbor.h" +#include "pair.h" +#include "random_park.h" +#include "region.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -301,9 +302,7 @@ void FixGCMC::options(int narg, char **arg) iregion = domain->find_region(arg[iarg+1]); if (iregion == -1) error->all(FLERR,"Region ID for fix gcmc does not exist"); - int n = strlen(arg[iarg+1]) + 1; - idregion = new char[n]; - strcpy(idregion,arg[iarg+1]); + idregion = utils::strdup(arg[iarg+1]); regionflag = 1; iarg += 2; } else if (strcmp(arg[iarg],"maxangle") == 0) { @@ -327,18 +326,14 @@ void FixGCMC::options(int narg, char **arg) iarg += 2; } else if (strcmp(arg[iarg],"rigid") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command"); - int n = strlen(arg[iarg+1]) + 1; delete [] idrigid; - idrigid = new char[n]; - strcpy(idrigid,arg[iarg+1]); + idrigid = utils::strdup(arg[iarg+1]); rigidflag = 1; iarg += 2; } else if (strcmp(arg[iarg],"shake") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command"); - int n = strlen(arg[iarg+1]) + 1; delete [] idshake; - idshake = new char[n]; - strcpy(idshake,arg[iarg+1]); + idshake = utils::strdup(arg[iarg+1]); shakeflag = 1; iarg += 2; } else if (strcmp(arg[iarg],"full_energy") == 0) { @@ -353,9 +348,7 @@ void FixGCMC::options(int narg, char **arg) ngroupsmax*sizeof(char *), "fix_gcmc:groupstrings"); } - int n = strlen(arg[iarg+1]) + 1; - groupstrings[ngroups] = new char[n]; - strcpy(groupstrings[ngroups],arg[iarg+1]); + groupstrings[ngroups] = utils::strdup(arg[iarg+1]); ngroups++; iarg += 2; } else if (strcmp(arg[iarg],"grouptype") == 0) { @@ -370,9 +363,7 @@ void FixGCMC::options(int narg, char **arg) "fix_gcmc:grouptypestrings"); } grouptypes[ngrouptypes] = utils::inumeric(FLERR,arg[iarg+1],false,lmp); - int n = strlen(arg[iarg+2]) + 1; - grouptypestrings[ngrouptypes] = new char[n]; - strcpy(grouptypestrings[ngrouptypes],arg[iarg+2]); + grouptypestrings[ngrouptypes] = utils::strdup(arg[iarg+2]); ngrouptypes++; iarg += 3; } else if (strcmp(arg[iarg],"intra_energy") == 0) { diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index a1bdc32515..e898196e14 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -224,9 +224,7 @@ void FixWidom::options(int narg, char **arg) iregion = domain->find_region(arg[iarg+1]); if (iregion == -1) error->all(FLERR,"Region ID for fix widom does not exist"); - int n = strlen(arg[iarg+1]) + 1; - idregion = new char[n]; - strcpy(idregion,arg[iarg+1]); + idregion = utils::strdup(arg[iarg+1]); regionflag = 1; iarg += 2; } else if (strcmp(arg[iarg],"charge") == 0) { diff --git a/src/MISC/compute_ti.cpp b/src/MISC/compute_ti.cpp index e81dd81c86..5ba85679a3 100644 --- a/src/MISC/compute_ti.cpp +++ b/src/MISC/compute_ti.cpp @@ -17,17 +17,17 @@ #include "compute_ti.h" -#include #include "atom.h" -#include "update.h" #include "domain.h" -#include "force.h" -#include "pair.h" -#include "kspace.h" -#include "input.h" -#include "variable.h" #include "error.h" +#include "force.h" +#include "input.h" +#include "kspace.h" +#include "pair.h" +#include "update.h" +#include "variable.h" +#include using namespace LAMMPS_NS; @@ -77,21 +77,15 @@ ComputeTI::ComputeTI(LAMMPS *lmp, int narg, char **arg) : else if (strcmp(arg[iarg],"tail") == 0) which[nterms] = TAIL; else which[nterms] = PAIR; - int n = strlen(arg[iarg]) + 1; - pstyle[nterms] = new char[n]; - strcpy(pstyle[nterms],arg[iarg]); + pstyle[nterms] = utils::strdup(arg[iarg]); utils::bounds(FLERR,arg[iarg+1],1,atom->ntypes,ilo[nterms],ihi[nterms],error); iarg += 1; if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) { - int n = strlen(&arg[iarg+1][2]) + 1; - var1[nterms] = new char[n]; - strcpy(var1[nterms],&arg[iarg+1][2]); + var1[nterms] = utils::strdup(&arg[iarg+1][2]); } else error->all(FLERR,"Illegal compute ti command"); if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) { - int n = strlen(&arg[iarg+2][2]) + 1; - var2[nterms] = new char[n]; - strcpy(var2[nterms],&arg[iarg+2][2]); + var2[nterms] = utils::strdup(&arg[iarg+2][2]); } else error->all(FLERR,"Illegal compute ti command"); nterms++; diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp index e832b37e67..6af537f6f4 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/MISC/fix_deposit.cpp @@ -697,9 +697,7 @@ void FixDeposit::options(int narg, char **arg) iregion = domain->find_region(arg[iarg+1]); if (iregion == -1) error->all(FLERR,"Region ID for fix deposit does not exist"); - int n = strlen(arg[iarg+1]) + 1; - idregion = new char[n]; - strcpy(idregion,arg[iarg+1]); + idregion = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"mol") == 0) { @@ -728,18 +726,14 @@ void FixDeposit::options(int narg, char **arg) iarg += nmol+1; } else if (strcmp(arg[iarg],"rigid") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command"); - int n = strlen(arg[iarg+1]) + 1; delete [] idrigid; - idrigid = new char[n]; - strcpy(idrigid,arg[iarg+1]); + idrigid = utils::strdup(arg[iarg+1]); rigidflag = 1; iarg += 2; } else if (strcmp(arg[iarg],"shake") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command"); - int n = strlen(arg[iarg+1]) + 1; delete [] idshake; - idshake = new char[n]; - strcpy(idshake,arg[iarg+1]); + idshake = utils::strdup(arg[iarg+1]); shakeflag = 1; iarg += 2; diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp index d0e016b554..2a11d1675a 100644 --- a/src/MISC/fix_evaporate.cpp +++ b/src/MISC/fix_evaporate.cpp @@ -44,9 +44,7 @@ FixEvaporate::FixEvaporate(LAMMPS *lmp, int narg, char **arg) : nevery = utils::inumeric(FLERR,arg[3],false,lmp); nflux = utils::inumeric(FLERR,arg[4],false,lmp); iregion = domain->find_region(arg[5]); - int n = strlen(arg[5]) + 1; - idregion = new char[n]; - strcpy(idregion,arg[5]); + idregion = utils::strdup(arg[5]); int seed = utils::inumeric(FLERR,arg[6],false,lmp); if (nevery <= 0 || nflux <= 0) diff --git a/src/MISC/fix_oneway.cpp b/src/MISC/fix_oneway.cpp index a2e612730c..7e655e60c6 100644 --- a/src/MISC/fix_oneway.cpp +++ b/src/MISC/fix_oneway.cpp @@ -42,9 +42,7 @@ FixOneWay::FixOneWay(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) nevery = utils::inumeric(FLERR,arg[3],false,lmp); if (nevery < 1) error->all(FLERR,"Illegal fix oneway command"); - int len = strlen(arg[4]); - regionstr = new char[len+1]; - strcpy(regionstr,arg[4]); + regionstr = utils::strdup(arg[4]); if (strcmp(arg[5], "x") == 0) direction = X|PLUS; if (strcmp(arg[5], "X") == 0) direction = X|PLUS; diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index 186e651504..4c6693f729 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -82,19 +82,11 @@ FixOrientBCC::FixOrientBCC(LAMMPS *lmp, int narg, char **arg) : uxif_high = utils::numeric(FLERR,arg[8],false,lmp); if (direction_of_motion == 0) { - int n = strlen(arg[9]) + 1; - chifilename = new char[n]; - strcpy(chifilename,arg[9]); - n = strlen(arg[10]) + 1; - xifilename = new char[n]; - strcpy(xifilename,arg[10]); + chifilename = utils::strdup(arg[9]); + xifilename = utils::strdup(arg[10]); } else if (direction_of_motion == 1) { - int n = strlen(arg[9]) + 1; - xifilename = new char[n]; - strcpy(xifilename,arg[9]); - n = strlen(arg[10]) + 1; - chifilename = new char[n]; - strcpy(chifilename,arg[10]); + xifilename = utils::strdup(arg[9]); + chifilename = utils::strdup(arg[10]); } else error->all(FLERR,"Illegal fix orient/bcc command"); // initializations diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index 04eae4ac3e..a59e412fde 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -80,19 +80,11 @@ FixOrientFCC::FixOrientFCC(LAMMPS *lmp, int narg, char **arg) : uxif_high = utils::numeric(FLERR,arg[8],false,lmp); if (direction_of_motion == 0) { - int n = strlen(arg[9]) + 1; - chifilename = new char[n]; - strcpy(chifilename,arg[9]); - n = strlen(arg[10]) + 1; - xifilename = new char[n]; - strcpy(xifilename,arg[10]); + chifilename = utils::strdup(arg[9]); + xifilename = utils::strdup(arg[10]); } else if (direction_of_motion == 1) { - int n = strlen(arg[9]) + 1; - xifilename = new char[n]; - strcpy(xifilename,arg[9]); - n = strlen(arg[10]) + 1; - chifilename = new char[n]; - strcpy(chifilename,arg[10]); + xifilename = utils::strdup(arg[9]); + chifilename = utils::strdup(arg[10]); } else error->all(FLERR,"Illegal fix orient/fcc command"); // initializations diff --git a/src/MLIAP/mliap_descriptor_snap.cpp b/src/MLIAP/mliap_descriptor_snap.cpp index 388561e248..0fdc548fc1 100644 --- a/src/MLIAP/mliap_descriptor_snap.cpp +++ b/src/MLIAP/mliap_descriptor_snap.cpp @@ -427,22 +427,19 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename) if (strcmp(keywd,"elems") == 0) { for (int ielem = 0; ielem < nelements; ielem++) { - char* elemtmp = keyval; - int n = strlen(elemtmp) + 1; - elements[ielem] = new char[n]; - strcpy(elements[ielem],elemtmp); + elements[ielem] = utils::strdup(keyval); keyval = strtok(nullptr,"' \t\n\r\f"); } elementsflag = 1; } else if (strcmp(keywd,"radelems") == 0) { for (int ielem = 0; ielem < nelements; ielem++) { - radelem[ielem] = atof(keyval); + radelem[ielem] = utils::numeric(FLERR,keyval,false,lmp); keyval = strtok(nullptr,"' \t\n\r\f"); } radelemflag = 1; } else if (strcmp(keywd,"welems") == 0) { for (int ielem = 0; ielem < nelements; ielem++) { - wjelem[ielem] = atof(keyval); + wjelem[ielem] = utils::numeric(FLERR,keyval,false,lmp); keyval = strtok(nullptr,"' \t\n\r\f"); } wjelemflag = 1; diff --git a/src/MLIAP/mliap_model_nn.cpp b/src/MLIAP/mliap_model_nn.cpp index 2bf75385b4..3805a5761b 100644 --- a/src/MLIAP/mliap_model_nn.cpp +++ b/src/MLIAP/mliap_model_nn.cpp @@ -18,9 +18,9 @@ #include "mliap_model_nn.h" #include "pair_mliap.h" #include "mliap_data.h" -#include "error.h" #include "comm.h" +#include "error.h" #include "memory.h" #include "tokenizer.h" diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp index 958c2d3c22..0ef14b8603 100644 --- a/src/REPLICA/compute_event_displace.cpp +++ b/src/REPLICA/compute_event_displace.cpp @@ -206,7 +206,5 @@ void ComputeEventDisplace::reset_extra_compute_fix(const char *id_new) id_event = nullptr; if (id_new == nullptr) return; - int n = strlen(id_new) + 1; - id_event = new char[n]; - strcpy(id_event,id_new); + id_event = utils::strdup(id_new); } diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index de45116194..40e5fc8833 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -77,8 +77,7 @@ void PRD::command(int narg, char **arg) t_dephase = utils::inumeric(FLERR,arg[3],false,lmp); t_corr = utils::inumeric(FLERR,arg[4],false,lmp); - char *id_compute = new char[strlen(arg[5])+1]; - strcpy(id_compute,arg[5]); + char *id_compute = utils::strdup(arg[5]); int seed = utils::inumeric(FLERR,arg[6],false,lmp); options(narg-7,&arg[7]); @@ -875,15 +874,8 @@ void PRD::options(int narg, char **arg) temp_flag = 0; stepmode = 0; - char *str = (char *) "geom"; - int n = strlen(str) + 1; - loop_setting = new char[n]; - strcpy(loop_setting,str); - - str = (char *) "gaussian"; - n = strlen(str) + 1; - dist_setting = new char[n]; - strcpy(dist_setting,str); + loop_setting = utils::strdup("geom"); + dist_setting = utils::strdup("gaussian"); int iarg = 0; while (iarg < narg) { @@ -912,16 +904,12 @@ void PRD::options(int narg, char **arg) else if (strcmp(arg[iarg+1],"local") == 0) loop_setting = nullptr; else if (strcmp(arg[iarg+1],"geom") == 0) loop_setting = nullptr; else error->all(FLERR,"Illegal prd command"); - int n = strlen(arg[iarg+1]) + 1; - loop_setting = new char[n]; - strcpy(loop_setting,arg[iarg+1]); + loop_setting = utils::strdup(arg[iarg+1]); if (strcmp(arg[iarg+2],"uniform") == 0) dist_setting = nullptr; else if (strcmp(arg[iarg+2],"gaussian") == 0) dist_setting = nullptr; else error->all(FLERR,"Illegal prd command"); - n = strlen(arg[iarg+2]) + 1; - dist_setting = new char[n]; - strcpy(dist_setting,arg[iarg+2]); + dist_setting = utils::strdup(arg[iarg+2]); iarg += 3; diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index 0fc611b307..0bab7a31c8 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -89,15 +89,12 @@ void TAD::command(int narg, char **arg) delta_conf = utils::numeric(FLERR,arg[4],false,lmp); tmax = utils::numeric(FLERR,arg[5],false,lmp); - char *id_compute = new char[strlen(arg[6])+1]; - strcpy(id_compute,arg[6]); + char *id_compute = utils::strdup(arg[6]); // quench minimizer is set by min_style command // NEB minimizer is set by options, default = quickmin - int n = strlen(update->minimize_style) + 1; - min_style = new char[n]; - strcpy(min_style,update->minimize_style); + min_style = utils::strdup(update->minimize_style); options(narg-7,&arg[7]); @@ -585,9 +582,7 @@ void TAD::options(int narg, char **arg) n2steps_neb = 100; nevery_neb = 10; - int n = strlen("quickmin") + 1; - min_style_neb = new char[n]; - strcpy(min_style_neb,"quickmin"); + min_style_neb = utils::strdup("quickmin"); dt_neb = update->dt; neb_logfilename = nullptr; @@ -619,9 +614,7 @@ void TAD::options(int narg, char **arg) } else if (strcmp(arg[iarg],"neb_style") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal tad command"); delete [] min_style_neb; - int n = strlen(arg[iarg+1]) + 1; - min_style_neb = new char[n]; - strcpy(min_style_neb,arg[iarg+1]); + min_style_neb = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"neb_step") == 0) { @@ -635,9 +628,7 @@ void TAD::options(int narg, char **arg) if (iarg+2 > narg) error->all(FLERR,"Illegal tad command"); if (strcmp(arg[iarg+1],"none") == 0) neb_logfilename = nullptr; else { - int n = strlen(arg[iarg+1]) + 1; - neb_logfilename = new char[n]; - strcpy(neb_logfilename,arg[iarg+1]); + neb_logfilename = utils::strdup(arg[iarg+1]); } iarg += 2; } else error->all(FLERR,"Illegal tad command"); diff --git a/src/RIGID/compute_erotate_rigid.cpp b/src/RIGID/compute_erotate_rigid.cpp index b20e11e359..d1567cfe2e 100644 --- a/src/RIGID/compute_erotate_rigid.cpp +++ b/src/RIGID/compute_erotate_rigid.cpp @@ -12,14 +12,16 @@ ------------------------------------------------------------------------- */ #include "compute_erotate_rigid.h" -#include -#include "update.h" -#include "force.h" -#include "modify.h" + +#include "error.h" #include "fix.h" #include "fix_rigid.h" #include "fix_rigid_small.h" -#include "error.h" +#include "force.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; @@ -33,9 +35,7 @@ ComputeERotateRigid::ComputeERotateRigid(LAMMPS *lmp, int narg, char **arg) : scalar_flag = 1; extscalar = 1; - int n = strlen(arg[3]) + 1; - rfix = new char[n]; - strcpy(rfix,arg[3]); + rfix = utils::strdup(arg[3]); } /* ---------------------------------------------------------------------- */ diff --git a/src/RIGID/compute_ke_rigid.cpp b/src/RIGID/compute_ke_rigid.cpp index c005f6ac25..9da5aabb9a 100644 --- a/src/RIGID/compute_ke_rigid.cpp +++ b/src/RIGID/compute_ke_rigid.cpp @@ -12,14 +12,16 @@ ------------------------------------------------------------------------- */ #include "compute_ke_rigid.h" -#include -#include "update.h" -#include "force.h" -#include "modify.h" + +#include "error.h" #include "fix.h" #include "fix_rigid.h" #include "fix_rigid_small.h" -#include "error.h" +#include "force.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; @@ -33,9 +35,7 @@ ComputeKERigid::ComputeKERigid(LAMMPS *lmp, int narg, char **arg) : scalar_flag = 1; extscalar = 1; - int n = strlen(arg[3]) + 1; - rfix = new char[n]; - strcpy(rfix,arg[3]); + rfix = utils::strdup(arg[3]); } /* ---------------------------------------------------------------------- */ diff --git a/src/RIGID/compute_rigid_local.cpp b/src/RIGID/compute_rigid_local.cpp index 0a40062055..9de227531d 100644 --- a/src/RIGID/compute_rigid_local.cpp +++ b/src/RIGID/compute_rigid_local.cpp @@ -40,9 +40,7 @@ ComputeRigidLocal::ComputeRigidLocal(LAMMPS *lmp, int narg, char **arg) : local_flag = 1; nvalues = narg - 4; - int n = strlen(arg[3]) + 1; - idrigid = new char[n]; - strcpy(idrigid,arg[3]); + idrigid = utils::strdup(arg[3]); rstyle = new int[nvalues]; diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp index 7229dc8b02..4bfabea3dd 100644 --- a/src/RIGID/fix_ehex.cpp +++ b/src/RIGID/fix_ehex.cpp @@ -24,17 +24,19 @@ #include "fix_ehex.h" -#include -#include #include "atom.h" #include "domain.h" -#include "region.h" -#include "group.h" -#include "force.h" -#include "update.h" -#include "modify.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "region.h" +#include "update.h" + +#include +#include + #include "fix_shake.h" using namespace LAMMPS_NS; @@ -91,9 +93,7 @@ FixEHEX::FixEHEX(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), iregion = domain->find_region(arg[iarg+1]); if (iregion == -1) error->all(FLERR,"Region ID for fix ehex does not exist"); - int n = strlen(arg[iarg+1]) + 1; - idregion = new char[n]; - strcpy(idregion,arg[iarg+1]); + idregion = utils::strdup(arg[iarg+1]); iarg += 2; } diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index a29c8d9863..6fb2bd7a94 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -1202,9 +1202,7 @@ int FixRigidNH::modify_param(int narg, char **arg) tcomputeflag = 0; } delete [] id_temp; - int n = strlen(arg[1]) + 1; - id_temp = new char[n]; - strcpy(id_temp,arg[1]); + id_temp = utils::strdup(arg[1]); int icompute = modify->find_compute(arg[1]); if (icompute < 0) @@ -1236,9 +1234,7 @@ int FixRigidNH::modify_param(int narg, char **arg) pcomputeflag = 0; } delete [] id_press; - int n = strlen(arg[1]) + 1; - id_press = new char[n]; - strcpy(id_press,arg[1]); + id_press = utils::strdup(arg[1]); int icompute = modify->find_compute(arg[1]); if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID"); diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index cfefe285f3..af2adb540d 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -1319,9 +1319,7 @@ int FixRigidNHSmall::modify_param(int narg, char **arg) tcomputeflag = 0; } delete [] id_temp; - int n = strlen(arg[1]) + 1; - id_temp = new char[n]; - strcpy(id_temp,arg[1]); + id_temp = utils::strdup(arg[1]); int icompute = modify->find_compute(arg[1]); if (icompute < 0) @@ -1353,9 +1351,7 @@ int FixRigidNHSmall::modify_param(int narg, char **arg) pcomputeflag = 0; } delete [] id_press; - int n = strlen(arg[1]) + 1; - id_press = new char[n]; - strcpy(id_press,arg[1]); + id_press = utils::strdup(arg[1]); int icompute = modify->find_compute(arg[1]); if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID"); diff --git a/src/RIGID/fix_rigid_nph.cpp b/src/RIGID/fix_rigid_nph.cpp index a2eb079f5c..77c42f0873 100644 --- a/src/RIGID/fix_rigid_nph.cpp +++ b/src/RIGID/fix_rigid_nph.cpp @@ -55,34 +55,15 @@ FixRigidNPH::FixRigidNPH(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id)+"_temp"); + modify->add_compute(std::string(id_temp)+" all temp"); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id)+"_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press,id_temp)); pcomputeflag = 1; } diff --git a/src/RIGID/fix_rigid_nph_small.cpp b/src/RIGID/fix_rigid_nph_small.cpp index 414e408a9a..55c0f55379 100644 --- a/src/RIGID/fix_rigid_nph_small.cpp +++ b/src/RIGID/fix_rigid_nph_small.cpp @@ -58,34 +58,15 @@ FixRigidNPHSmall::FixRigidNPHSmall(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id)+"_temp"); + modify->add_compute(std::string(id_temp)+" all temp"); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id)+"_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press,id_temp)); pcomputeflag = 1; } diff --git a/src/RIGID/fix_rigid_npt.cpp b/src/RIGID/fix_rigid_npt.cpp index e50b1a5045..59d7fa2764 100644 --- a/src/RIGID/fix_rigid_npt.cpp +++ b/src/RIGID/fix_rigid_npt.cpp @@ -65,34 +65,15 @@ FixRigidNPT::FixRigidNPT(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id)+"_temp"); + modify->add_compute(std::string(id_temp)+" all temp"); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id)+"_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press,id_temp)); pcomputeflag = 1; } diff --git a/src/RIGID/fix_rigid_npt_small.cpp b/src/RIGID/fix_rigid_npt_small.cpp index efb9c414f6..5b1ef61865 100644 --- a/src/RIGID/fix_rigid_npt_small.cpp +++ b/src/RIGID/fix_rigid_npt_small.cpp @@ -69,34 +69,15 @@ FixRigidNPTSmall::FixRigidNPTSmall(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id)+"_temp"); + modify->add_compute(std::string(id_temp)+" all temp"); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id)+"_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press,id_temp)); pcomputeflag = 1; } diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp index 10ec0f0351..7a1efa064f 100644 --- a/src/SHOCK/fix_msst.cpp +++ b/src/SHOCK/fix_msst.cpp @@ -19,19 +19,20 @@ #include "fix_msst.h" -#include -#include #include "atom.h" -#include "force.h" #include "comm.h" -#include "modify.h" -#include "fix_external.h" #include "compute.h" -#include "kspace.h" -#include "update.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "fix_external.h" +#include "force.h" +#include "kspace.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -840,9 +841,7 @@ int FixMSST::modify_param(int narg, char **arg) tflag = 0; } delete [] id_temp; - int n = strlen(arg[1]) + 1; - id_temp = new char[n]; - strcpy(id_temp,arg[1]); + id_temp = utils::strdup(arg[1]); int icompute = modify->find_compute(id_temp); if (icompute < 0) @@ -864,9 +863,7 @@ int FixMSST::modify_param(int narg, char **arg) pflag = 0; } delete [] id_press; - int n = strlen(arg[1]) + 1; - id_press = new char[n]; - strcpy(id_press,arg[1]); + id_press = utils::strdup(arg[1]); int icompute = modify->find_compute(id_press); if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID"); diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp index 1fa7b77f6a..7467b7a293 100644 --- a/src/SHOCK/fix_nphug.cpp +++ b/src/SHOCK/fix_nphug.cpp @@ -12,15 +12,17 @@ ------------------------------------------------------------------------- */ #include "fix_nphug.h" -#include -#include -#include "modify.h" -#include "error.h" -#include "update.h" + #include "compute.h" -#include "force.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "group.h" +#include "modify.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -118,51 +120,22 @@ FixNPHug::FixNPHug(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id)+"_temp"); + modify->add_compute(std::string(id_temp)+" all temp"); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id)+"_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press,id_temp)); pcomputeflag = 1; // create a new compute potential energy compute - n = strlen(id) + 4; - id_pe = new char[n]; - strcpy(id_pe,id); - strcat(id_pe,"_pe"); - - newarg = new char*[3]; - newarg[0] = id_pe; - newarg[1] = (char*)"all"; - newarg[2] = (char*)"pe"; - modify->add_compute(3,newarg); - delete [] newarg; + id_pe = utils::strdup(std::string(id)+"_pe"); + modify->add_compute(std::string(id_pe)+" all pe"); peflag = 1; } diff --git a/src/SPIN/fix_neb_spin.cpp b/src/SPIN/fix_neb_spin.cpp index 935365ce1b..620d0a47bd 100644 --- a/src/SPIN/fix_neb_spin.cpp +++ b/src/SPIN/fix_neb_spin.cpp @@ -23,18 +23,19 @@ #include "fix_neb_spin.h" -#include -#include -#include "universe.h" -#include "update.h" #include "atom.h" #include "comm.h" -#include "modify.h" #include "compute.h" -#include "group.h" -#include "memory.h" #include "error.h" #include "force.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -120,17 +121,8 @@ FixNEBSpin::FixNEBSpin(LAMMPS *lmp, int narg, char **arg) : // create a new compute pe style // id = fix-ID + pe, compute group = all - int n = strlen(id) + 4; - id_pe = new char[n]; - strcpy(id_pe,id); - strcat(id_pe,"_pe"); - - char **newarg = new char*[3]; - newarg[0] = id_pe; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pe"; - modify->add_compute(3,newarg); - delete [] newarg; + id_pe = utils::strdup(std::string(id)+"_pe"); + modify->add_compute(std::string(id_pe)+" all pe"); // initialize local storage From 31726f56e6b2605799144f9877b5f52ab803033f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 28 Mar 2021 13:12:39 -0400 Subject: [PATCH 0280/1217] refactor group2ndx and ndx2group commands to use fmtlib, tokenizer and utils --- src/USER-COLVARS/group_ndx.cpp | 189 ++++++++++++-------------- src/USER-COLVARS/group_ndx.h | 2 + src/USER-COLVARS/ndx_group.cpp | 233 ++++++++++++++------------------- src/USER-COLVARS/ndx_group.h | 3 +- src/group.cpp | 2 +- src/group.h | 2 +- 6 files changed, 187 insertions(+), 244 deletions(-) diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp index 96c3663ca0..995f60ac85 100644 --- a/src/USER-COLVARS/group_ndx.cpp +++ b/src/USER-COLVARS/group_ndx.cpp @@ -23,6 +23,8 @@ #include "error.h" #include "group.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- @@ -40,96 +42,6 @@ static int cmptagint(const void *p1, const void *p2) } } -/* ---------------------------------------------------------------------- - helper function. writes out one group to a gromacs style index file - ---------------------------------------------------------------------- */ - -static void write_group(FILE *fp, int gid, Atom *atom, Group *group, int me, - int np, MPI_Comm world, FILE *screen, FILE *logfile) -{ - char fmt[16]; - tagint *sendlist, *recvlist; - bigint num = group->count(gid); - int lnum, cols; - - if (me == 0) { - if (screen) fprintf(screen, " writing group %s... ", group->names[gid]); - if (logfile) fprintf(logfile, " writing group %s... ", group->names[gid]); - - // the "all" group in LAMMPS is called "System" in gromacs - if (gid == 0) { - fputs("[ System ]\n", fp); - } else { - fprintf(fp,"[ %s ]\n", group->names[gid]); - } - - // derive format string for index lists - bigint j = atom->natoms; - int i=0; - while (j > 0) { - ++i; - j /= 10; - } - snprintf(fmt,16,"%%%dd ", i); - cols = 80 / (i+1); - } - - if (num > 0) { - const int * const mask = atom->mask; - const tagint * const tag = atom->tag; - const int groupbit = group->bitmask[gid]; - const int nlocal = atom->nlocal; - int i; - - sendlist = new tagint[nlocal]; - recvlist = new tagint[num]; - lnum = 0; - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) sendlist[lnum++] = tag[i]; - - int nrecv,allrecv; - if (me == 0) { - MPI_Status status; - MPI_Request request; - - for (i=0; i < lnum; i++) - recvlist[i] = sendlist[i]; - - allrecv = lnum; - for (i=1; i < np; ++i) { - MPI_Irecv(recvlist+allrecv,num-allrecv,MPI_LMP_TAGINT,i,0, world,&request); - MPI_Send(&nrecv,0,MPI_INT,i,0,world); - MPI_Wait(&request,&status); - MPI_Get_count(&status,MPI_LMP_TAGINT,&nrecv); - allrecv += nrecv; - } - - // sort received list - qsort((void *)recvlist, num, sizeof(tagint), cmptagint); - } else { - MPI_Recv(&nrecv,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE); - MPI_Rsend(sendlist,lnum,MPI_LMP_TAGINT,0,0,world); - } - delete [] sendlist; - } - - if (me == 0) { - int i, j; - for (i=0, j=0; i < num; ++i) { - fprintf(fp,fmt,recvlist[i]); - ++j; - if (j == cols) { - fputs("\n",fp); - j = 0; - } - } - if (j > 0) fputs("\n",fp); - if (screen) fputs("done\n",screen); - if (logfile) fputs("done\n",logfile); - } - if (num > 0) delete[] recvlist; -} - /* ---------------------------------------------------------------------- */ void Group2Ndx::command(int narg, char **arg) @@ -144,31 +56,100 @@ void Group2Ndx::command(int narg, char **arg) if (comm->me == 0) { fp = fopen(arg[0], "w"); if (fp == nullptr) - error->one(FLERR,"Cannot open index file for writing"); - - if (screen) - fprintf(screen, "Writing groups to index file %s:\n",arg[0]); - if (logfile) - fprintf(logfile,"Writing groups to index file %s:\n",arg[0]); + error->one(FLERR,fmt::format("Cannot open index file for writing: {}", + utils::getsyserror())); + utils::logmesg(lmp,fmt::format("Writing groups to index file {}:\n",arg[0])); } if (narg == 1) { // write out all groups for (int i=0; i < group->ngroup; ++i) { - write_group(fp,i,atom,group,comm->me,comm->nprocs,world,screen,logfile); + write_group(fp,i); } - } else { // write only selected groups for (int i=1; i < narg; ++i) { int gid = group->find(arg[i]); if (gid < 0) error->all(FLERR, "Non-existing group requested"); - write_group(fp,gid,atom,group,comm->me,comm->nprocs,world,screen,logfile); + write_group(fp,gid); } } - if (comm->me == 0) { - if (screen) fputs("\n",screen); - if (logfile) fputs("\n",logfile); - fclose(fp); - } + if (comm->me == 0) fclose(fp); } +/* ---------------------------------------------------------------------- + write out one group to a Gromacs style index file + ---------------------------------------------------------------------- */ +void Group2Ndx::write_group(FILE *fp, int gid) +{ + tagint *sendlist, *recvlist; + bigint gcount = group->count(gid); + int lnum, width, cols; + + if (comm->me == 0) { + utils::logmesg(lmp,fmt::format(" writing group {}...",group->names[gid])); + + // the "all" group in LAMMPS is called "System" in Gromacs + if (gid == 0) { + fputs("[ System ]\n", fp); + } else { + fmt::print(fp,"[ {} ]\n", group->names[gid]); + } + width = log10((double) atom->natoms)+2; + cols = 80 / width; + } + + if (gcount > 0) { + const int * const mask = atom->mask; + const tagint * const tag = atom->tag; + const int groupbit = group->bitmask[gid]; + const int nlocal = atom->nlocal; + int i; + + sendlist = new tagint[nlocal]; + recvlist = new tagint[gcount]; + lnum = 0; + for (i = 0; i < nlocal; i++) + if (mask[i] & groupbit) sendlist[lnum++] = tag[i]; + + int nrecv=0; + bigint allrecv; + if (comm->me == 0) { + MPI_Status status; + MPI_Request request; + + for (i=0; i < lnum; i++) + recvlist[i] = sendlist[i]; + + allrecv = lnum; + for (i=1; i < comm->nprocs; ++i) { + MPI_Irecv(recvlist+allrecv,gcount-allrecv,MPI_LMP_TAGINT,i,0, world,&request); + MPI_Send(&nrecv,0,MPI_INT,i,0,world); // block rank "i" until we are ready to receive + MPI_Wait(&request,&status); + MPI_Get_count(&status,MPI_LMP_TAGINT,&nrecv); + allrecv += nrecv; + } + + // sort received list + qsort((void *)recvlist, allrecv, sizeof(tagint), cmptagint); + } else { + MPI_Recv(&nrecv,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE); + MPI_Rsend(sendlist,lnum,MPI_LMP_TAGINT,0,0,world); + } + delete [] sendlist; + } + + if (comm->me == 0) { + int i, j; + for (i=0, j=0; i < gcount; ++i) { + fmt::print(fp,"{:>{}}",recvlist[i],width); + ++j; + if (j == cols) { + fputs("\n",fp); + j = 0; + } + } + if (j > 0) fputs("\n",fp); + utils::logmesg(lmp,"done\n"); + } + if (gcount > 0) delete[] recvlist; +} diff --git a/src/USER-COLVARS/group_ndx.h b/src/USER-COLVARS/group_ndx.h index 25c38dcf9f..fa15f0e82e 100644 --- a/src/USER-COLVARS/group_ndx.h +++ b/src/USER-COLVARS/group_ndx.h @@ -30,6 +30,8 @@ class Group2Ndx : protected Pointers { public: Group2Ndx(class LAMMPS *lmp) : Pointers(lmp) {}; void command(int, char **); + private: + void write_group(FILE *, int); }; } diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index bf1c5d060a..184faa62cc 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -22,64 +22,52 @@ #include "comm.h" #include "error.h" #include "group.h" +#include "memory.h" +#include "tokenizer.h" -#include +#include using namespace LAMMPS_NS; #define BUFLEN 4096 #define DELTA 16384 -static char *find_section(FILE *fp, const char *name) +// read file until next section "name" or any next section if name == "" + +static std::string find_section(FILE *fp, const std::string &name) { char linebuf[BUFLEN]; - char *n,*p,*t,*r; - while ((p = fgets(linebuf,BUFLEN,fp))) { - t = strtok(p," \t\n\r\f"); - if ((t != nullptr) && *t == '[') { - t = strtok(nullptr," \t\n\r\f"); - if (t != nullptr) { - n = t; - t = strtok(nullptr," \t\n\r\f"); - if ((t != nullptr) && *t == ']') { - if ((name == nullptr) || strcmp(name,n) == 0) { - int l = strlen(n); - r = new char[l+1]; - strncpy(r,n,l+1); - return r; - } - } - } - } + std::string pattern = "^\\s*\\[\\s+\\S+\\s+\\]\\s*$"; + if (!name.empty()) + pattern = fmt::format("^\\s*\\[\\s+{}\\s+\\]\\s*$",name); + + fgets(linebuf,BUFLEN,fp); + while (!feof(fp)) { + if (utils::strmatch(linebuf,pattern)) + return Tokenizer(linebuf).as_vector()[1]; + fgets(linebuf,BUFLEN,fp); } - return nullptr; + return ""; } -static tagint *read_section(FILE *fp, bigint &num) +static std::vector read_section(FILE *fp, std::string &name) { char linebuf[BUFLEN]; - char *p,*t; - tagint *tagbuf; - bigint nmax; + std::vector tagbuf; + std::string pattern = "^\\s*\\[\\s+\\S+\\s+\\]\\s*$"; - num = 0; - nmax = DELTA; - tagbuf = (tagint *)malloc(sizeof(tagint)*nmax); - - while ((p = fgets(linebuf,BUFLEN,fp))) { - t = strtok(p," \t\n\r\f"); - while (t != nullptr) { - // start of a new section. we are done here. - if (*t == '[') return tagbuf; - - tagbuf[num++] = ATOTAGINT(t); - if (num == nmax) { - nmax += DELTA; - tagbuf = (tagint *)realloc(tagbuf,sizeof(tagint)*nmax); - } - t = strtok(nullptr," \t\n\r\f"); + while (fgets(linebuf,BUFLEN,fp)) { + // start of new section. we are done, update "name" + if (utils::strmatch(linebuf,pattern)) { + name = Tokenizer(linebuf).as_vector()[1]; + return tagbuf; } + ValueTokenizer values(linebuf); + while (values.has_next()) + tagbuf.push_back(values.next_tagint()); } + // set empty name to indicate end of file + name = ""; return tagbuf; } @@ -90,151 +78,122 @@ void Ndx2Group::command(int narg, char **arg) int len; bigint num; FILE *fp; - char *name = nullptr; - tagint *tags; + tagint *tagbuf; + std::string name = "", next; if (narg < 1) error->all(FLERR,"Illegal ndx2group command"); - if (atom->tag_enable == 0) - error->all(FLERR,"Must have atom IDs for ndx2group command"); - + error->all(FLERR,"Must have atom IDs for ndx2group command"); if (comm->me == 0) { fp = fopen(arg[0], "r"); if (fp == nullptr) - error->one(FLERR,"Cannot open index file for reading"); - - if (screen) - fprintf(screen, "Reading groups from index file %s:\n",arg[0]); - if (logfile) - fprintf(logfile,"Reading groups from index file %s:\n",arg[0]); + error->one(FLERR,fmt::format("Cannot open index file for reading: {}", + utils::getsyserror())); + utils::logmesg(lmp,fmt::format("Reading groups from index file {}:\n",arg[0])); } - if (narg == 1) { // restore all groups + if (narg == 1) { // restore all groups - do { - if (comm->me == 0) { - len = 0; + if (comm->me == 0) { + name = find_section(fp,""); + while (!name.empty()) { - // find the next section. - // if we had processed a section, before we need to step back - if (name != nullptr) { - rewind(fp); - char *tmp = find_section(fp,name); - delete[] tmp; - delete[] name; - name = nullptr; + // skip over group "all", which is called "System" in gromacs + if (name == "System") { + name = find_section(fp,""); + continue; } - name = find_section(fp,nullptr); - if (name != nullptr) { - len=strlen(name)+1; - // skip over group "all", which is called "System" in gromacs - if (strcmp(name,"System") == 0) continue; - - if (screen) - fprintf(screen," Processing group '%s'\n",name); - if (logfile) - fprintf(logfile," Processing group '%s'\n",name); - } + utils::logmesg(lmp,fmt::format(" Processing group '{}'\n",name)); + len = name.size()+1; MPI_Bcast(&len,1,MPI_INT,0,world); - if (len > 0) { - MPI_Bcast(name,len,MPI_CHAR,0,world); + if (len > 1) { + MPI_Bcast((void *)name.c_str(),len,MPI_CHAR,0,world); // read tags for atoms in group and broadcast - num = 0; - tags = read_section(fp,num); + std::vector tags = read_section(fp,next); + num = tags.size(); MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world); - MPI_Bcast(tags,num,MPI_LMP_TAGINT,0,world); - create(name,num,tags); - free(tags); - } - } else { - MPI_Bcast(&len,1,MPI_INT,0,world); - if (len > 0) { - delete[] name; - name = new char[len]; - MPI_Bcast(name,len,MPI_CHAR,0,world); - - MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world); - tags = (tagint *)malloc(sizeof(tagint)*(num ? num : 1)); - MPI_Bcast(tags,num,MPI_LMP_TAGINT,0,world); - create(name,num,tags); - free(tags); + MPI_Bcast((void *)tags.data(),num,MPI_LMP_TAGINT,0,world); + create(name,tags); + name = next; } } - } while (len); + len = -1; + MPI_Bcast(&len,1,MPI_INT,0,world); + + } else { + + while (1) { + MPI_Bcast(&len,1,MPI_INT,0,world); + if (len < 0) break; + if (len > 1) { + char *buf = new char[len]; + MPI_Bcast(buf,len,MPI_CHAR,0,world); + MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world); + tagint *tbuf = new tagint[num]; + MPI_Bcast(tbuf,num,MPI_LMP_TAGINT,0,world); + create(buf,std::vector(tbuf,tbuf+num)); + delete[] buf; + delete[] tbuf; + } + } + } } else { // restore selected groups - for (int idx=1; idx < narg; ++idx) { + for (int idx=1; idx < narg; ++idx) { if (comm->me == 0) { - len = 0; // find named section, search from beginning of file - if (name != nullptr) delete[] name; rewind(fp); name = find_section(fp,arg[idx]); - if (name != nullptr) len=strlen(name)+1; - - if (screen) - fprintf(screen," %s group '%s'\n", - len ? "Processing" : "Skipping",arg[idx]); - if (logfile) - fprintf(logfile,"%s group '%s'\n", - len ? "Processing" : "Skipping",arg[idx]); - + utils::logmesg(lmp,fmt::format(" {} group '{}'\n", name.size() + ? "Processing" : "Skipping",arg[idx])); + len = name.size()+1; MPI_Bcast(&len,1,MPI_INT,0,world); - if (len > 0) { - MPI_Bcast(name,len,MPI_CHAR,0,world); + if (len > 1) { + MPI_Bcast((void *)name.c_str(),len,MPI_CHAR,0,world); + // read tags for atoms in group and broadcast - num = 0; - tags = read_section(fp,num); + std::vector tags = read_section(fp,name); + num = tags.size(); MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world); - MPI_Bcast(tags,num,MPI_LMP_TAGINT,0,world); - create(name,num,tags); - free(tags); + MPI_Bcast((void *)tags.data(),num,MPI_LMP_TAGINT,0,world); + create(name,tags); } } else { - MPI_Bcast(&len,1,MPI_INT,0,world); - if (len > 0) { - delete[] name; - name = new char[len]; - MPI_Bcast(name,len,MPI_CHAR,0,world); - + if (len > 1) { + char *buf = new char[len]; + MPI_Bcast(buf,len,MPI_CHAR,0,world); MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world); - tags = (tagint *)malloc(sizeof(tagint)*(num ? num : 1)); - MPI_Bcast(tags,num,MPI_LMP_TAGINT,0,world); - create(name,num,tags); - free(tags); + tagint *tbuf = new tagint[num]; + MPI_Bcast(tbuf,num,MPI_LMP_TAGINT,0,world); + create(buf,std::vector(tbuf,tbuf+num)); + delete[] buf; + delete[] tbuf; } } } } - - delete[] name; - if (comm->me == 0) { - if (screen) fputs("\n",screen); - if (logfile) fputs("\n",logfile); - fclose(fp); - } + if (comm->me == 0) fclose(fp); } /* ---------------------------------------------------------------------- */ -void Ndx2Group::create(char *name, bigint num, tagint *tags) +void Ndx2Group::create(const std::string &name, const std::vector &tags) { // wipe out all members if the group exists. gid==0 is group "all" int gid = group->find(name); - if (gid > 0) group->assign(std::string(name) + " clear"); + if (gid > 0) group->assign(name + " clear"); // map from global to local const int nlocal = atom->nlocal; int *flags = (int *)calloc(nlocal,sizeof(int)); - for (bigint i=0; i < num; ++i) { + for (bigint i=0; i < tags.size(); ++i) { const int id = atom->map(tags[i]); - if (id < nlocal && id >= 0) - flags[id] = 1; + if (id < nlocal && id >= 0) flags[id] = 1; } group->create(name,flags); free(flags); diff --git a/src/USER-COLVARS/ndx_group.h b/src/USER-COLVARS/ndx_group.h index cd3250a1d5..ceca1f9570 100644 --- a/src/USER-COLVARS/ndx_group.h +++ b/src/USER-COLVARS/ndx_group.h @@ -23,6 +23,7 @@ CommandStyle(ndx2group,Ndx2Group) #define LMP_NDX_GROUP_H #include "pointers.h" +#include namespace LAMMPS_NS { @@ -30,7 +31,7 @@ class Ndx2Group : protected Pointers { public: Ndx2Group(class LAMMPS *lmp) : Pointers(lmp) {}; void command(int, char **); - void create(char *, bigint, tagint *); + void create(const std::string &, const std::vector &); }; } diff --git a/src/group.cpp b/src/group.cpp index aa05ca6951..ebab78dd0f 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -553,7 +553,7 @@ void Group::assign(const std::string &groupcmd) add flagged atoms to a new or existing group ------------------------------------------------------------------------- */ -void Group::create(const char *name, int *flag) +void Group::create(const std::string &name, int *flag) { int i; diff --git a/src/group.h b/src/group.h index 0c5a18384c..37199712c5 100644 --- a/src/group.h +++ b/src/group.h @@ -32,7 +32,7 @@ class Group : protected Pointers { ~Group(); void assign(int, char **); // assign atoms to a group void assign(const std::string &); // convenience function - void create(const char *, int *); // add flagged atoms to a group + void create(const std::string &, int *); // add flagged atoms to a group int find(const std::string &); // lookup name in list of groups int find_or_create(const char *); // lookup name or create new group void write_restart(FILE *); From b32570c15ebbc0d03da0e03263888c96b15f2ce8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 28 Mar 2021 17:02:49 -0400 Subject: [PATCH 0281/1217] simplify by using utils::strdup() and reorder includes --- src/ASPHERE/fix_nph_asphere.cpp | 17 ++--- src/ASPHERE/fix_npt_asphere.cpp | 17 ++--- src/ASPHERE/fix_nve_asphere.cpp | 3 +- src/ASPHERE/fix_nvt_asphere.cpp | 13 ++-- src/BODY/fix_nph_body.cpp | 19 ++---- src/BODY/fix_npt_body.cpp | 19 ++---- src/BODY/fix_nvt_body.cpp | 13 ++-- src/GPU/fix_npt_gpu.cpp | 6 +- src/GPU/fix_nvt_gpu.cpp | 8 ++- src/KOKKOS/fix_nph_kokkos.cpp | 12 ++-- src/KOKKOS/fix_npt_kokkos.cpp | 12 ++-- src/KOKKOS/fix_nvt_kokkos.cpp | 2 +- src/MC/fix_bond_swap.cpp | 7 +- src/RIGID/fix_rigid_nph.cpp | 6 +- src/RIGID/fix_rigid_nph_small.cpp | 6 +- src/RIGID/fix_rigid_npt.cpp | 6 +- src/RIGID/fix_rigid_npt_small.cpp | 6 +- src/SHOCK/fix_nphug.cpp | 4 +- src/USER-BOCS/compute_pressure_bocs.cpp | 8 +-- src/USER-BOCS/fix_bocs.cpp | 43 +++--------- src/USER-DPD/fix_rx.cpp | 57 ++++------------ src/USER-DPD/pair_exp6_rx.cpp | 31 +++------ src/USER-DPD/pair_multi_lucy_rx.cpp | 9 +-- src/USER-DPD/pair_table_rx.cpp | 10 +-- src/USER-DRUDE/compute_temp_drude.cpp | 17 +++-- src/USER-DRUDE/fix_tgnh_drude.cpp | 32 +++++---- src/USER-DRUDE/fix_tgnpt_drude.cpp | 19 ++---- src/USER-DRUDE/fix_tgnvt_drude.cpp | 13 ++-- src/USER-EFF/compute_temp_region_eff.cpp | 17 +++-- src/USER-EFF/fix_nph_eff.cpp | 32 ++------- src/USER-EFF/fix_npt_eff.cpp | 32 ++------- src/USER-EFF/fix_nvt_eff.cpp | 21 ++---- src/USER-EFF/fix_nvt_sllod_eff.cpp | 32 ++++----- src/USER-EFF/fix_temp_rescale_eff.cpp | 29 +++----- src/USER-INTEL/fix_npt_intel.cpp | 36 +++------- src/USER-INTEL/fix_nvt_intel.cpp | 24 +++---- src/USER-INTEL/fix_nvt_sllod_intel.cpp | 15 +---- src/USER-LB/fix_lb_fluid.cpp | 24 +++---- src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp | 35 +--------- src/USER-MISC/fix_grem.cpp | 67 +++++-------------- src/USER-MISC/fix_npt_cauchy.cpp | 60 ++++++----------- src/USER-OMP/fix_nph_asphere_omp.cpp | 32 ++------- src/USER-OMP/fix_nph_omp.cpp | 12 ++-- src/USER-OMP/fix_nph_sphere_omp.cpp | 32 ++------- src/USER-OMP/fix_npt_asphere_omp.cpp | 32 ++------- src/USER-OMP/fix_npt_omp.cpp | 12 ++-- src/USER-OMP/fix_npt_sphere_omp.cpp | 32 ++------- src/USER-OMP/fix_nvt_asphere_omp.cpp | 15 +---- src/USER-OMP/fix_nvt_omp.cpp | 6 +- src/USER-OMP/fix_nvt_sllod_omp.cpp | 36 +++++----- src/USER-OMP/fix_nvt_sphere_omp.cpp | 19 ++---- src/USER-OMP/fix_rigid_nph_omp.cpp | 31 ++------- src/USER-OMP/fix_rigid_npt_omp.cpp | 33 ++------- src/USER-QTB/fix_qbmsst.cpp | 46 ++++--------- src/USER-UEF/fix_nh_uef.cpp | 54 ++++++--------- src/VORONOI/compute_voronoi_atom.cpp | 4 +- src/fix_box_relax.cpp | 31 ++++----- src/fix_nph.cpp | 19 ++---- src/fix_nph_sphere.cpp | 19 ++---- src/fix_npt.cpp | 19 ++---- src/fix_npt_sphere.cpp | 19 ++---- src/fix_nve.cpp | 12 ++-- src/fix_nvt.cpp | 12 +--- src/fix_nvt_sllod.cpp | 22 +++--- src/fix_nvt_sphere.cpp | 13 ++-- src/fix_press_berendsen.cpp | 31 ++++----- src/fix_temp_berendsen.cpp | 6 +- src/fix_temp_csld.cpp | 6 +- src/fix_temp_csvr.cpp | 6 +- src/fix_temp_rescale.cpp | 6 +- 70 files changed, 447 insertions(+), 1009 deletions(-) diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp index 5231434a45..538e467133 100644 --- a/src/ASPHERE/fix_nph_asphere.cpp +++ b/src/ASPHERE/fix_nph_asphere.cpp @@ -12,10 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_nph_asphere.h" -#include -#include "modify.h" #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -36,21 +35,15 @@ FixNPHAsphere::FixNPHAsphere(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - std::string tcmd = id + std::string("_temp"); - id_temp = new char[tcmd.size()+1]; - strcpy(id_temp,tcmd.c_str()); - - modify->add_compute(tcmd + " all temp/asphere"); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp/asphere",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - std::string pcmd = id + std::string("_press"); - id_press = new char[pcmd.size()+1]; - strcpy(id_press,pcmd.c_str()); - - modify->add_compute(pcmd + " all pressure " + std::string(id_temp)); + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp index 6492dfcde4..99909e5a2a 100644 --- a/src/ASPHERE/fix_npt_asphere.cpp +++ b/src/ASPHERE/fix_npt_asphere.cpp @@ -12,10 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_npt_asphere.h" -#include -#include "modify.h" #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -35,21 +34,15 @@ FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - std::string tcmd = id + std::string("_temp"); - id_temp = new char[tcmd.size()+1]; - strcpy(id_temp,tcmd.c_str()); - - modify->add_compute(tcmd + " all temp/asphere"); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp/asphere",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - std::string pcmd = id + std::string("_press"); - id_press = new char[pcmd.size()+1]; - strcpy(id_press,pcmd.c_str()); - - modify->add_compute(pcmd + " all pressure " + std::string(id_temp)); + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp index 95fb89d5c9..62bb1db172 100644 --- a/src/ASPHERE/fix_nve_asphere.cpp +++ b/src/ASPHERE/fix_nve_asphere.cpp @@ -16,10 +16,11 @@ ------------------------------------------------------------------------- */ #include "fix_nve_asphere.h" -#include "math_extra.h" + #include "atom.h" #include "atom_vec_ellipsoid.h" #include "error.h" +#include "math_extra.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp index 903d88f97a..ef6d97ec99 100644 --- a/src/ASPHERE/fix_nvt_asphere.cpp +++ b/src/ASPHERE/fix_nvt_asphere.cpp @@ -12,12 +12,10 @@ ------------------------------------------------------------------------- */ #include "fix_nvt_asphere.h" -#include +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" - using namespace LAMMPS_NS; using namespace FixConst; @@ -35,11 +33,8 @@ FixNVTAsphere::FixNVTAsphere(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp - std::string cmd = id + std::string("_temp"); - id_temp = new char[cmd.size()+1]; - strcpy(id_temp,cmd.c_str()); - - cmd += fmt::format(" {} temp/asphere",group->names[igroup]); - modify->add_compute(cmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp/asphere", + id_temp,group->names[igroup])); tcomputeflag = 1; } diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp index 1ebde47de6..a876ac9dc7 100644 --- a/src/BODY/fix_nph_body.cpp +++ b/src/BODY/fix_nph_body.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "fix_nph_body.h" -#include +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -41,22 +41,15 @@ FixNPHBody::FixNPHBody(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - std::string tcmd = id + std::string("_temp"); - id_temp = new char[tcmd.size()+1]; - strcpy(id_temp,tcmd.c_str()); - - tcmd += fmt::format(" {} temp/body",group->names[igroup]); - modify->add_compute(tcmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp/body",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - std::string pcmd = id + std::string("_press"); - id_press = new char[pcmd.size()+1]; - strcpy(id_press,pcmd.c_str()); - - modify->add_compute(pcmd + " all pressure " + std::string(id_temp)); + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp index adc5cd4587..bc669fc971 100644 --- a/src/BODY/fix_npt_body.cpp +++ b/src/BODY/fix_npt_body.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "fix_npt_body.h" -#include +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -41,22 +41,15 @@ FixNPTBody::FixNPTBody(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - std::string tcmd = id + std::string("_temp"); - id_temp = new char[tcmd.size()+1]; - strcpy(id_temp,tcmd.c_str()); - - tcmd += fmt::format(" {} temp/body",group->names[igroup]); - modify->add_compute(tcmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp/body",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - std::string pcmd = id + std::string("_press"); - id_press = new char[pcmd.size()+1]; - strcpy(id_press,pcmd.c_str()); - - modify->add_compute(pcmd + " all pressure " + std::string(id_temp)); + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp index a3884f330a..442aed2c94 100644 --- a/src/BODY/fix_nvt_body.cpp +++ b/src/BODY/fix_nvt_body.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "fix_nvt_body.h" -#include +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -39,11 +39,8 @@ FixNVTBody::FixNVTBody(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp - std::string tcmd = id + std::string("_temp"); - id_temp = new char[tcmd.size()+1]; - strcpy(id_temp,tcmd.c_str()); - - tcmd += fmt::format(" {} temp/body",group->names[igroup]); - modify->add_compute(tcmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp/body", + id_temp,group->names[igroup])); tcomputeflag = 1; } diff --git a/src/GPU/fix_npt_gpu.cpp b/src/GPU/fix_npt_gpu.cpp index 3847f31a65..ce601548d4 100644 --- a/src/GPU/fix_npt_gpu.cpp +++ b/src/GPU/fix_npt_gpu.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_gpu.h" -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -35,7 +35,7 @@ FixNPTGPU::FixNPTGPU(LAMMPS *lmp, int narg, char **arg) : // and thus its KE/temperature contribution should use group all id_temp = utils::strdup(std::string(id)+"_temp"); - modify->add_compute(std::string(id_temp)+" all temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style diff --git a/src/GPU/fix_nvt_gpu.cpp b/src/GPU/fix_nvt_gpu.cpp index 6858c26497..191039e343 100644 --- a/src/GPU/fix_nvt_gpu.cpp +++ b/src/GPU/fix_nvt_gpu.cpp @@ -11,11 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_gpu.h" + +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -33,7 +35,7 @@ FixNVTGPU::FixNVTGPU(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp - id_temp = utils::strdup(std::string(id)+"_temp"); + id_temp = utils::strdup(std::string(id) + "_temp"); modify->add_compute(fmt::format("{} {} temp",id_temp,group->names[igroup])); tcomputeflag = 1; } diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp index f679940eaf..e2c3bd8d14 100644 --- a/src/KOKKOS/fix_nph_kokkos.cpp +++ b/src/KOKKOS/fix_nph_kokkos.cpp @@ -16,8 +16,6 @@ #include "modify.h" #include "error.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; @@ -38,17 +36,17 @@ FixNPHKokkos::FixNPHKokkos(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - this->id_temp = utils::strdup(std::string(this->id)+"_temp"); - this->modify->add_compute(std::string(this->id_temp)+" all temp/kk"); + this->id_temp = utils::strdup(std::string(this->id) + "_temp"); + this->modify->add_compute(fmt::format("{} all temp/kk",this->id_temp)); this->tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - this->id_press = utils::strdup(std::string(this->id)+"_press"); - this->modify->add_compute(std::string(this->id_press) - +" all pressure "+this->id_temp); + this->id_press = utils::strdup(std::string(this->id) + "_press"); + this->modify->add_compute(fmt::format("{} all pressure {}", + this->id_press, this->id_temp)); this->pcomputeflag = 1; } diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp index baa47e026f..565703aa35 100644 --- a/src/KOKKOS/fix_npt_kokkos.cpp +++ b/src/KOKKOS/fix_npt_kokkos.cpp @@ -16,8 +16,6 @@ #include "modify.h" #include "error.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; @@ -38,17 +36,17 @@ FixNPTKokkos::FixNPTKokkos(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - this->id_temp = utils::strdup(std::string(this->id)+"_temp"); - this->modify->add_compute(std::string(this->id_temp)+" all temp/kk"); + this->id_temp = utils::strdup(std::string(this->id) + "_temp"); + this->modify->add_compute(fmt::format("{} all temp/kk",this->id_temp)); this->tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - this->id_press = utils::strdup(std::string(this->id)+"_press"); - this->modify->add_compute(std::string(this->id_press) - +" all pressure "+this->id_temp); + this->id_press = utils::strdup(std::string(this->id) + "_press"); + this->modify->add_compute(fmt::format("{} all pressure {}", + this->id_press, this->id_temp)); this->pcomputeflag = 1; } diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp index f589600dde..8eeffcb9f8 100644 --- a/src/KOKKOS/fix_nvt_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_kokkos.cpp @@ -38,7 +38,7 @@ FixNVTKokkos::FixNVTKokkos(LAMMPS *lmp, int narg, char **arg) : // id = fix-ID + temp this->id_temp = utils::strdup(std::string(this->id)+"_temp"); - this->modify->add_compute(std::string(this->id_temp)+" all temp/kk"); + this->modify->add_compute(fmt::format("{} all temp/kk",this->id_temp)); this->tcomputeflag = 1; } diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index 84d89a9626..1f3026888a 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -86,11 +86,8 @@ FixBondSwap::FixBondSwap(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp, compute group = fix group - std::string cmd = id + std::string("_temp"); - id_temp = new char[cmd.size()+1]; - strcpy(id_temp,cmd.c_str()); - - modify->add_compute(cmd + " all temp"); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tflag = 1; // initialize atom list diff --git a/src/RIGID/fix_rigid_nph.cpp b/src/RIGID/fix_rigid_nph.cpp index 77c42f0873..1c93df4599 100644 --- a/src/RIGID/fix_rigid_nph.cpp +++ b/src/RIGID/fix_rigid_nph.cpp @@ -18,9 +18,9 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_nph.h" -#include -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; @@ -56,7 +56,7 @@ FixRigidNPH::FixRigidNPH(LAMMPS *lmp, int narg, char **arg) : // and thus its KE/temperature contribution should use group all id_temp = utils::strdup(std::string(id)+"_temp"); - modify->add_compute(std::string(id_temp)+" all temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style diff --git a/src/RIGID/fix_rigid_nph_small.cpp b/src/RIGID/fix_rigid_nph_small.cpp index 55c0f55379..ad5a48f1c2 100644 --- a/src/RIGID/fix_rigid_nph_small.cpp +++ b/src/RIGID/fix_rigid_nph_small.cpp @@ -18,9 +18,9 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_nph_small.h" -#include -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; @@ -59,7 +59,7 @@ FixRigidNPHSmall::FixRigidNPHSmall(LAMMPS *lmp, int narg, char **arg) : // and thus its KE/temperature contribution should use group all id_temp = utils::strdup(std::string(id)+"_temp"); - modify->add_compute(std::string(id_temp)+" all temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style diff --git a/src/RIGID/fix_rigid_npt.cpp b/src/RIGID/fix_rigid_npt.cpp index 59d7fa2764..4f65929476 100644 --- a/src/RIGID/fix_rigid_npt.cpp +++ b/src/RIGID/fix_rigid_npt.cpp @@ -18,9 +18,9 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_npt.h" -#include -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; @@ -66,7 +66,7 @@ FixRigidNPT::FixRigidNPT(LAMMPS *lmp, int narg, char **arg) : // and thus its KE/temperature contribution should use group all id_temp = utils::strdup(std::string(id)+"_temp"); - modify->add_compute(std::string(id_temp)+" all temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style diff --git a/src/RIGID/fix_rigid_npt_small.cpp b/src/RIGID/fix_rigid_npt_small.cpp index 5b1ef61865..6f7c025bc8 100644 --- a/src/RIGID/fix_rigid_npt_small.cpp +++ b/src/RIGID/fix_rigid_npt_small.cpp @@ -18,9 +18,9 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_npt_small.h" -#include -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; @@ -70,7 +70,7 @@ FixRigidNPTSmall::FixRigidNPTSmall(LAMMPS *lmp, int narg, char **arg) : // and thus its KE/temperature contribution should use group all id_temp = utils::strdup(std::string(id)+"_temp"); - modify->add_compute(std::string(id_temp)+" all temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp index 7467b7a293..20038c7df6 100644 --- a/src/SHOCK/fix_nphug.cpp +++ b/src/SHOCK/fix_nphug.cpp @@ -121,7 +121,7 @@ FixNPHug::FixNPHug(LAMMPS *lmp, int narg, char **arg) : // and thus its KE/temperature contribution should use group all id_temp = utils::strdup(std::string(id)+"_temp"); - modify->add_compute(std::string(id_temp)+" all temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style @@ -135,7 +135,7 @@ FixNPHug::FixNPHug(LAMMPS *lmp, int narg, char **arg) : // create a new compute potential energy compute id_pe = utils::strdup(std::string(id)+"_pe"); - modify->add_compute(std::string(id_pe)+" all pe"); + modify->add_compute(fmt::format("{} all pe",id_pe)); peflag = 1; } diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp index a84442e658..43cf7efb8f 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/USER-BOCS/compute_pressure_bocs.cpp @@ -59,9 +59,7 @@ ComputePressureBocs::ComputePressureBocs(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[3],"NULL") == 0) id_temp = nullptr; else { - int n = strlen(arg[3]) + 1; - id_temp = new char[n]; - strcpy(id_temp,arg[3]); + id_temp = utils::strdup(arg[3]); int icompute = modify->find_compute(id_temp); if (icompute < 0) @@ -446,7 +444,5 @@ void ComputePressureBocs::virial_compute(int n, int ndiag) void ComputePressureBocs::reset_extra_compute_fix(const char *id_new) { delete [] id_temp; - int n = strlen(id_new) + 1; - id_temp = new char[n]; - strcpy(id_temp,id_new); + id_temp = utils::strdup(id_new); } diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index 28a0d6c01a..87d4653da5 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -16,11 +16,6 @@ #include "fix_bocs.h" -#include - -#include -#include - #include "atom.h" #include "citeme.h" #include "comm.h" @@ -29,7 +24,6 @@ #include "domain.h" #include "error.h" #include "fix_deform.h" - #include "force.h" #include "group.h" #include "irregular.h" @@ -40,6 +34,10 @@ #include "respa.h" #include "update.h" +#include +#include +#include + using namespace LAMMPS_NS; using namespace FixConst; @@ -70,7 +68,8 @@ const int NUM_INPUT_DATA_COLUMNS = 2; // columns in the pressure correction FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), - rfix(nullptr), id_dilate(nullptr), irregular(nullptr), id_temp(nullptr), id_press(nullptr), + rfix(nullptr), id_dilate(nullptr), irregular(nullptr), + id_temp(nullptr), id_press(nullptr), eta(nullptr), eta_dot(nullptr), eta_dotdot(nullptr), eta_mass(nullptr), etap(nullptr), etap_dot(nullptr), etap_dotdot(nullptr), etap_mass(nullptr) @@ -403,38 +402,16 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id)+"_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "PRESSURE/BOCS"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id)+"_press"); + modify->add_compute(fmt::format("{} all PRESSURE/BOCS {}",id_press,id_temp)); pcomputeflag = 1; /*~ MRD End of stuff copied from fix_npt.cpp~*/ diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp index c9d12506ab..675c3d6dea 100644 --- a/src/USER-DPD/fix_rx.cpp +++ b/src/USER-DPD/fix_rx.cpp @@ -257,7 +257,6 @@ void FixRX::post_constructor() bool match; char **tmpspecies = new char*[maxspecies]; - int tmpmaxstrlen = 0; for (int jj=0; jj < maxspecies; jj++) tmpspecies[jj] = nullptr; @@ -316,9 +315,7 @@ void FixRX::post_constructor() if (!match) { if (nUniqueSpecies+1>=maxspecies) error->all(FLERR,"Exceeded the maximum number of species permitted in fix rx."); - tmpspecies[nUniqueSpecies] = new char[strlen(word)+1]; - strcpy(tmpspecies[nUniqueSpecies],word); - tmpmaxstrlen = MAX(tmpmaxstrlen,(int)strlen(word)); + tmpspecies[nUniqueSpecies] = utils::strdup(word); nUniqueSpecies++; } word = strtok(nullptr, " \t\n\r\f"); @@ -335,61 +332,31 @@ void FixRX::post_constructor() id_fix_species = nullptr; id_fix_species_old = nullptr; - n = strlen(id) + strlen("_SPECIES") + 1; - id_fix_species = new char[n]; - n = strlen(id) + strlen("_SPECIES_OLD") + 1; - id_fix_species_old = new char[n]; + id_fix_species = utils::strdup(std::string(id)+"_SPECIES"); + id_fix_species_old = utils::strdup(std::string(id)+"_SPECIES_OLD"); - strcpy(id_fix_species,id); - strcat(id_fix_species,"_SPECIES"); - strcpy(id_fix_species_old,id); - strcat(id_fix_species_old,"_SPECIES_OLD"); - - char **newarg = new char*[nspecies+5]; - char **newarg2 = new char*[nspecies+5]; - newarg[0] = id_fix_species; - newarg[1] = group->names[igroup]; - newarg[2] = (char *) "property/atom"; - newarg2[0] = id_fix_species_old; - newarg2[1] = group->names[igroup]; - newarg2[2] = (char *) "property/atom"; - char *str1 = new char[tmpmaxstrlen+3]; - char *str2 = new char[tmpmaxstrlen+6]; + const std::string fmtstr = "{} {} property/atom "; + auto newcmd1 = fmt::format(fmtstr,id_fix_species,group->names[igroup]); + auto newcmd2 = fmt::format(fmtstr,id_fix_species_old,group->names[igroup]); for (int ii=0; iiadd_fix(nspecies+5,newarg,1); + modify->add_fix(newcmd1); fix_species = (FixPropertyAtom *) modify->fix[modify->nfix-1]; restartFlag = modify->fix[modify->nfix-1]->restart_reset; - modify->add_fix(nspecies+5,newarg2,1); + modify->add_fix(newcmd2); fix_species_old = (FixPropertyAtom *) modify->fix[modify->nfix-1]; if (nspecies==0) error->all(FLERR,"There are no rx species specified."); for (int jj=0;jjall(FLERR,"There are no rx species specified."); read_file(arg[2]); - n = strlen(arg[3]) + 1; - site1 = new char[n]; - strcpy(site1,arg[3]); + site1 = utils::strdup(arg[3]); int ispecies; for (ispecies = 0; ispecies < nspecies; ispecies++) { @@ -607,9 +605,7 @@ void PairExp6rx::coeff(int narg, char **arg) if (ispecies == nspecies && strcmp(site1,"1fluid") != 0) error->all(FLERR,"Site1 name not recognized in pair coefficients"); - n = strlen(arg[4]) + 1; - site2 = new char[n]; - strcpy(site2,arg[4]); + site2 = utils::strdup(arg[4]); for (ispecies = 0; ispecies < nspecies; ispecies++) { if (strcmp(site2,&atom->dname[ispecies][0]) == 0) break; @@ -806,17 +802,12 @@ void PairExp6rx::read_file(char *file) params[nparams].ispecies = ispecies; - n = strlen(&atom->dname[ispecies][0]) + 1; - params[nparams].name = new char[n]; - strcpy(params[nparams].name,&atom->dname[ispecies][0]); - - n = strlen(words[1]) + 1; - params[nparams].potential = new char[n]; - strcpy(params[nparams].potential,words[1]); + params[nparams].name = utils::strdup(&atom->dname[ispecies][0]); + params[nparams].potential = utils::strdup(words[1]); if (strcmp(params[nparams].potential,"exp6") == 0) { - params[nparams].alpha = atof(words[2]); - params[nparams].epsilon = atof(words[3]); - params[nparams].rm = atof(words[4]); + params[nparams].alpha = utils::numeric(FLERR,words[2],false,lmp); + params[nparams].epsilon = utils::numeric(FLERR,words[3],false,lmp); + params[nparams].rm = utils::numeric(FLERR,words[4],false,lmp); if (params[nparams].epsilon <= 0.0 || params[nparams].rm <= 0.0 || params[nparams].alpha < 0.0) error->all(FLERR,"Illegal exp6/rx parameters. Rm and Epsilon must be greater than zero. Alpha cannot be negative."); @@ -842,11 +833,9 @@ void PairExp6rx::read_file2(char *file) fp = nullptr; if (comm->me == 0) { fp = fopen(file,"r"); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open polynomial file %s",file); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,fmt::format("Cannot open polynomial file {}: {}", + file,utils::getsyserror())); } // one set of params can span multiple lines diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp index bd720ae138..c0f6af8a7e 100644 --- a/src/USER-DPD/pair_multi_lucy_rx.cpp +++ b/src/USER-DPD/pair_multi_lucy_rx.cpp @@ -387,14 +387,9 @@ void PairMultiLucyRX::coeff(int narg, char **arg) bcast_table(tb); nspecies = atom->nspecies_dpd; - int n; - n = strlen(arg[4]) + 1; - site1 = new char[n]; - strcpy(site1,arg[4]); - n = strlen(arg[5]) + 1; - site2 = new char[n]; - strcpy(site2,arg[5]); + site1 = utils::strdup(arg[4]); + site2 = utils::strdup(arg[5]); // set table cutoff diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp index cefbe5a73d..85879d11fa 100644 --- a/src/USER-DPD/pair_table_rx.cpp +++ b/src/USER-DPD/pair_table_rx.cpp @@ -322,10 +322,8 @@ void PairTableRX::coeff(int narg, char **arg) nspecies = atom->nspecies_dpd; if (nspecies==0) error->all(FLERR,"There are no rx species specified."); - int n; - n = strlen(arg[4]) + 1; - site1 = new char[n]; - strcpy(site1,arg[4]); + + site1 = utils::strdup(arg[4]); int ispecies; for (ispecies = 0; ispecies < nspecies; ispecies++) { @@ -334,9 +332,7 @@ void PairTableRX::coeff(int narg, char **arg) if (ispecies == nspecies && strcmp(site1,"1fluid") != 0) error->all(FLERR,"Site1 name not recognized in pair coefficients"); - n = strlen(arg[5]) + 1; - site2 = new char[n]; - strcpy(site2,arg[5]); + site2 = utils::strdup(arg[5]); for (ispecies = 0; ispecies < nspecies; ispecies++) { if (strcmp(site2,&atom->dname[ispecies][0]) == 0) break; diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/USER-DRUDE/compute_temp_drude.cpp index fe75c10fe3..4325c9d6ae 100644 --- a/src/USER-DRUDE/compute_temp_drude.cpp +++ b/src/USER-DRUDE/compute_temp_drude.cpp @@ -13,15 +13,16 @@ #include "compute_temp_drude.h" -#include #include "atom.h" -#include "update.h" -#include "force.h" -#include "modify.h" -#include "fix_drude.h" +#include "comm.h" #include "domain.h" #include "error.h" -#include "comm.h" +#include "fix_drude.h" +#include "force.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; @@ -116,9 +117,7 @@ int ComputeTempDrude::modify_param(int narg, char **arg) if (strcmp(arg[0],"temp") == 0) { if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); delete [] id_temp; - int n = strlen(arg[1]) + 1; - id_temp = new char[n]; - strcpy(id_temp,arg[1]); + id_temp = utils::strdup(arg[1]); int icompute = modify->find_compute(id_temp); if (icompute < 0) diff --git a/src/USER-DRUDE/fix_tgnh_drude.cpp b/src/USER-DRUDE/fix_tgnh_drude.cpp index 8185b9bcbb..49a4061878 100644 --- a/src/USER-DRUDE/fix_tgnh_drude.cpp +++ b/src/USER-DRUDE/fix_tgnh_drude.cpp @@ -16,23 +16,25 @@ ---------------------------------------------------------------------------------------- */ #include "fix_tgnh_drude.h" -#include -#include + #include "atom.h" +#include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "fix_deform.h" #include "force.h" #include "group.h" -#include "comm.h" -#include "neighbor.h" #include "irregular.h" -#include "modify.h" -#include "fix_deform.h" -#include "compute.h" #include "kspace.h" -#include "update.h" -#include "respa.h" -#include "domain.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -1428,9 +1430,7 @@ int FixTGNHDrude::modify_param(int narg, char **arg) tcomputeflag = 0; } delete [] id_temp; - int n = strlen(arg[1]) + 1; - id_temp = new char[n]; - strcpy(id_temp,arg[1]); + id_temp = utils::strdup(arg[1]); int icompute = modify->find_compute(arg[1]); if (icompute < 0) @@ -1462,9 +1462,7 @@ int FixTGNHDrude::modify_param(int narg, char **arg) pcomputeflag = 0; } delete [] id_press; - int n = strlen(arg[1]) + 1; - id_press = new char[n]; - strcpy(id_press,arg[1]); + id_press = utils::strdup(arg[1]); int icompute = modify->find_compute(arg[1]); if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID"); diff --git a/src/USER-DRUDE/fix_tgnpt_drude.cpp b/src/USER-DRUDE/fix_tgnpt_drude.cpp index 987af367c3..301e0aa029 100644 --- a/src/USER-DRUDE/fix_tgnpt_drude.cpp +++ b/src/USER-DRUDE/fix_tgnpt_drude.cpp @@ -12,10 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_tgnpt_drude.h" -#include -#include "modify.h" #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -35,23 +34,15 @@ FixTGNPTDrude::FixTGNPTDrude(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - std::string tcmd = id + std::string("_temp"); - id_temp = new char[tcmd.size()+1]; - strcpy(id_temp, tcmd.c_str()); - - tcmd += " all temp"; - modify->add_compute(tcmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - std::string pcmd = id + std::string("_press"); - id_press = new char[pcmd.size()+1]; - strcpy(id_press, pcmd.c_str()); - - pcmd += " all pressure " + std::string(id_temp); - modify->add_compute(pcmd); + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/USER-DRUDE/fix_tgnvt_drude.cpp b/src/USER-DRUDE/fix_tgnvt_drude.cpp index bd6809aaed..2339a6f9a7 100644 --- a/src/USER-DRUDE/fix_tgnvt_drude.cpp +++ b/src/USER-DRUDE/fix_tgnvt_drude.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_tgnvt_drude.h" -#include +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -34,11 +35,7 @@ FixTGNVTDrude::FixTGNVTDrude(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp - std::string tcmd = id + std::string("_temp"); - id_temp = new char[tcmd.size()+1]; - strcpy(id_temp, tcmd.c_str()); - - tcmd += fmt::format(" {} temp", group->names[igroup]); - modify->add_compute(tcmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp",id_temp,group->names[igroup])); tcomputeflag = 1; } diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp index 1ca62f39d3..ca13aac06b 100644 --- a/src/USER-EFF/compute_temp_region_eff.cpp +++ b/src/USER-EFF/compute_temp_region_eff.cpp @@ -16,17 +16,18 @@ ------------------------------------------------------------------------- */ -#include - #include "compute_temp_region_eff.h" + #include "atom.h" -#include "update.h" -#include "force.h" #include "domain.h" -#include "region.h" +#include "error.h" +#include "force.h" #include "group.h" #include "memory.h" -#include "error.h" +#include "region.h" +#include "update.h" + +#include using namespace LAMMPS_NS; @@ -43,9 +44,7 @@ ComputeTempRegionEff::ComputeTempRegionEff(LAMMPS *lmp, int narg, char **arg) : iregion = domain->find_region(arg[3]); if (iregion == -1) error->all(FLERR,"Region ID for compute temp/region/eff does not exist"); - int n = strlen(arg[3]) + 1; - idregion = new char[n]; - strcpy(idregion,arg[3]); + idregion = utils::strdup(arg[3]); scalar_flag = vector_flag = 1; size_vector = 6; diff --git a/src/USER-EFF/fix_nph_eff.cpp b/src/USER-EFF/fix_nph_eff.cpp index 2478211c77..1e9871da02 100644 --- a/src/USER-EFF/fix_nph_eff.cpp +++ b/src/USER-EFF/fix_nph_eff.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph_eff.h" -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -34,35 +34,15 @@ FixNPHEff::FixNPHEff(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp/eff"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp/eff",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/USER-EFF/fix_npt_eff.cpp b/src/USER-EFF/fix_npt_eff.cpp index 98b76b1b43..4612810c02 100644 --- a/src/USER-EFF/fix_npt_eff.cpp +++ b/src/USER-EFF/fix_npt_eff.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_eff.h" -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -34,35 +34,15 @@ FixNPTEff::FixNPTEff(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp/eff"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp/eff",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/USER-EFF/fix_nvt_eff.cpp index 8f37cbf2b1..f5358b5db1 100644 --- a/src/USER-EFF/fix_nvt_eff.cpp +++ b/src/USER-EFF/fix_nvt_eff.cpp @@ -11,11 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_eff.h" + +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -33,17 +35,8 @@ FixNVTEff::FixNVTEff(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = group->names[igroup]; - newarg[2] = (char *) "temp/eff"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp/eff", + id_temp,group->names[igroup])); tcomputeflag = 1; } diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp index b5d40251bf..36a5cbb8ab 100644 --- a/src/USER-EFF/fix_nvt_sllod_eff.cpp +++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp @@ -11,19 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include - #include "fix_nvt_sllod_eff.h" -#include "math_extra.h" + #include "atom.h" +#include "compute.h" #include "domain.h" -#include "group.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_deform.h" -#include "compute.h" -#include "error.h" +#include "group.h" +#include "math_extra.h" +#include "modify.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -45,18 +46,9 @@ FixNVTSllodEff::FixNVTSllodEff(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = group->names[igroup]; - newarg[2] = (char *) "temp/deform/eff"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} tmp/deform/eff", + id_temp,group->names[igroup])); tcomputeflag = 1; } diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/USER-EFF/fix_temp_rescale_eff.cpp index f796c7cb02..1ebed8b9ff 100644 --- a/src/USER-EFF/fix_temp_rescale_eff.cpp +++ b/src/USER-EFF/fix_temp_rescale_eff.cpp @@ -15,18 +15,19 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include - -#include #include "fix_temp_rescale_eff.h" + #include "atom.h" -#include "force.h" -#include "group.h" -#include "update.h" #include "comm.h" -#include "modify.h" #include "compute.h" #include "error.h" +#include "force.h" +#include "group.h" +#include "modify.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -56,17 +57,9 @@ FixTempRescaleEff::FixTempRescaleEff(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp/eff // id = fix-ID + temp, compute group = fix group - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[6]; - newarg[0] = id_temp; - newarg[1] = group->names[igroup]; - newarg[2] = (char *) "temp/eff"; - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp/eff", + id_temp,group->names[igroup])); tflag = 1; energy = 0.0; diff --git a/src/USER-INTEL/fix_npt_intel.cpp b/src/USER-INTEL/fix_npt_intel.cpp index 4d69e80515..3f48130f99 100644 --- a/src/USER-INTEL/fix_npt_intel.cpp +++ b/src/USER-INTEL/fix_npt_intel.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_intel.h" -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -25,44 +25,24 @@ FixNPTIntel::FixNPTIntel(LAMMPS *lmp, int narg, char **arg) : FixNHIntel(lmp, narg, arg) { if (!tstat_flag) - error->all(FLERR,"Temperature control must be used with fix npt/omp"); + error->all(FLERR,"Temperature control must be used with fix npt/intel"); if (!pstat_flag) - error->all(FLERR,"Pressure control must be used with fix npt/omp"); + error->all(FLERR,"Pressure control must be used with fix npt/intl"); // create a new compute temp style // id = fix-ID + temp // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/USER-INTEL/fix_nvt_intel.cpp b/src/USER-INTEL/fix_nvt_intel.cpp index b9ceea4c71..61259fba2f 100644 --- a/src/USER-INTEL/fix_nvt_intel.cpp +++ b/src/USER-INTEL/fix_nvt_intel.cpp @@ -11,11 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_intel.h" + +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -26,25 +28,15 @@ FixNVTIntel::FixNVTIntel(LAMMPS *lmp, int narg, char **arg) : FixNHIntel(lmp, narg, arg) { if (!tstat_flag) - error->all(FLERR,"Temperature control must be used with fix nvt"); + error->all(FLERR,"Temperature control must be used with fix nvt/intel"); if (pstat_flag) - error->all(FLERR,"Pressure control can not be used with fix nvt"); + error->all(FLERR,"Pressure control can not be used with fix nvt/intel"); // create a new compute temp style // id = fix-ID + temp - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = group->names[igroup]; - newarg[2] = (char *) "temp"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp",id_temp,group->names[igroup])); tcomputeflag = 1; } diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.cpp b/src/USER-INTEL/fix_nvt_sllod_intel.cpp index 3880adc055..efe124cb2d 100644 --- a/src/USER-INTEL/fix_nvt_sllod_intel.cpp +++ b/src/USER-INTEL/fix_nvt_sllod_intel.cpp @@ -46,18 +46,9 @@ FixNVTSllodIntel::FixNVTSllodIntel(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = group->names[igroup]; - newarg[2] = (char *) "temp/deform"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp/deform", + id_temp,group->names[igroup])); tcomputeflag = 1; } diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp index 351e078dad..dafd5d2a3a 100644 --- a/src/USER-LB/fix_lb_fluid.cpp +++ b/src/USER-LB/fix_lb_fluid.cpp @@ -17,22 +17,22 @@ ------------------------------------------------------------------------- */ #include "fix_lb_fluid.h" + +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "random_mars.h" +#include "update.h" + #include - - #include #include #include -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "domain.h" -#include "atom.h" -#include "group.h" -#include "random_mars.h" -#include "update.h" -#include "force.h" -#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp index 310dae8725..844f99b725 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp @@ -131,24 +131,10 @@ FixNVTManifoldRattle::FixNVTManifoldRattle(LAMMPS *lmp, int narg, char **arg, } // Create temperature compute: - const char *fix_id = arg[1]; - int n = strlen(fix_id)+6; - id_temp = new char[n]; - strcpy(id_temp,fix_id); - strcat(id_temp,"_temp"); - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = group->names[igroup]; - newarg[2] = (char*) "temp"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp",id_temp,group->names[igroup])); int icompute = modify->find_compute(id_temp); - if (icompute < 0) { - error->all(FLERR,"Temperature ID for fix nvt/manifold/rattle " - "does not exist"); - } temperature = modify->compute[icompute]; if (temperature->tempbias) which = BIAS; else which = NOBIAS; @@ -167,8 +153,6 @@ FixNVTManifoldRattle::FixNVTManifoldRattle(LAMMPS *lmp, int narg, char **arg, for (int ich = 0; ich < mtchain; ++ich) { eta[ich] = eta_dot[ich] = eta_dotdot[ich] = 0.0; } - - } /* ---------------------------------------------------------------------- */ @@ -185,9 +169,6 @@ FixNVTManifoldRattle::~FixNVTManifoldRattle() if (id_temp) delete[] id_temp; } - - - int FixNVTManifoldRattle::setmask() { int mask = 0; @@ -198,7 +179,6 @@ int FixNVTManifoldRattle::setmask() return mask; } - /* -------------------------------------------------------------------------- Check that force modification happens before position and velocity update. Make sure respa is not used. @@ -219,8 +199,6 @@ void FixNVTManifoldRattle::init() } - - void FixNVTManifoldRattle::setup(int /*vflag*/) { compute_temp_target(); @@ -359,9 +337,6 @@ void FixNVTManifoldRattle::nh_v_temp() } } - - - // Most of this logic is based on fix_nh: void FixNVTManifoldRattle::initial_integrate(int /*vflag*/) { @@ -381,8 +356,6 @@ void FixNVTManifoldRattle::final_integrate() nhc_temp_integrate(); } - - /* ---------------------------------------------------------------------- */ void FixNVTManifoldRattle::reset_dt() { @@ -395,10 +368,6 @@ void FixNVTManifoldRattle::reset_dt() } - - - - double FixNVTManifoldRattle::memory_usage() { double bytes = FixNVEManifoldRattle::memory_usage(); diff --git a/src/USER-MISC/fix_grem.cpp b/src/USER-MISC/fix_grem.cpp index b1f1bded85..64c7e4a6b7 100644 --- a/src/USER-MISC/fix_grem.cpp +++ b/src/USER-MISC/fix_grem.cpp @@ -23,14 +23,16 @@ ------------------------------------------------------------------------- */ #include "fix_grem.h" -#include + #include "atom.h" -#include "force.h" -#include "update.h" -#include "modify.h" -#include "domain.h" #include "compute.h" +#include "domain.h" #include "error.h" +#include "force.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -65,65 +67,28 @@ FixGrem::FixGrem(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[5]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "PRESSURE/GREM"; - newarg[3] = id_temp; - newarg[4] = id; - modify->add_compute(5,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all PRESSURE/GREM {}", + id_press, id_temp)); // create a new compute ke style // id = fix-ID + ke - n = strlen(id) + 8; - id_ke = new char[n]; - strcpy(id_ke,id); - strcat(id_ke,"_ke"); - - newarg = new char*[3]; - newarg[0] = id_ke; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "ke"; - modify->add_compute(3,newarg); - delete [] newarg; + id_ke = utils::strdup(std::string(id) + "_ke"); + modify->add_compute(fmt::format("{} all ke",id_temp)); // create a new compute pe style // id = fix-ID + pe - n = strlen(id) + 9; - id_pe = new char[n]; - strcpy(id_pe,id); - strcat(id_pe,"_pe"); - - newarg = new char*[3]; - newarg[0] = id_pe; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pe"; - modify->add_compute(3,newarg); - delete [] newarg; + id_pe = utils::strdup(std::string(id) + "_pe"); + modify->add_compute(fmt::format("{} all pe",id_temp)); int ifix = modify->find_fix(id_nh); if (ifix < 0) diff --git a/src/USER-MISC/fix_npt_cauchy.cpp b/src/USER-MISC/fix_npt_cauchy.cpp index 5d51114262..37d6e5286b 100644 --- a/src/USER-MISC/fix_npt_cauchy.cpp +++ b/src/USER-MISC/fix_npt_cauchy.cpp @@ -15,27 +15,28 @@ Contributing authors: ------------------------------------------------------------------------- */ -#include - -#include #include "fix_npt_cauchy.h" -#include "math_extra.h" + #include "atom.h" -#include "force.h" -#include "group.h" #include "comm.h" -#include "neighbor.h" -#include "irregular.h" -#include "modify.h" +#include "compute.h" +#include "domain.h" +#include "error.h" #include "fix_deform.h" #include "fix_store.h" -#include "compute.h" +#include "force.h" +#include "group.h" +#include "irregular.h" #include "kspace.h" -#include "update.h" -#include "respa.h" -#include "domain.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -53,7 +54,8 @@ enum{ISO,ANISO,TRICLINIC}; FixNPTCauchy::FixNPTCauchy(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), - rfix(nullptr), id_dilate(nullptr), irregular(nullptr), id_temp(nullptr), id_press(nullptr), + rfix(nullptr), id_dilate(nullptr), irregular(nullptr), + id_temp(nullptr), id_press(nullptr), eta(nullptr), eta_dot(nullptr), eta_dotdot(nullptr), eta_mass(nullptr), etap(nullptr), etap_dot(nullptr), etap_dotdot(nullptr), etap_mass(nullptr), id_store(nullptr),init_store(nullptr) @@ -604,36 +606,16 @@ FixNPTCauchy::FixNPTCauchy(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nph_asphere_omp.cpp b/src/USER-OMP/fix_nph_asphere_omp.cpp index 4f20d9657c..eeeb4ef2ea 100644 --- a/src/USER-OMP/fix_nph_asphere_omp.cpp +++ b/src/USER-OMP/fix_nph_asphere_omp.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph_asphere_omp.h" -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -34,35 +34,15 @@ FixNPHAsphereOMP::FixNPHAsphereOMP(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp/asphere"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp/asphere",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nph_omp.cpp b/src/USER-OMP/fix_nph_omp.cpp index 8c2f9ed3a3..733600b4bf 100644 --- a/src/USER-OMP/fix_nph_omp.cpp +++ b/src/USER-OMP/fix_nph_omp.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph_omp.h" -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -34,15 +34,15 @@ FixNPHOMP::FixNPHOMP(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - id_temp = utils::strdup(std::string(id)+"_temp"); - modify->add_compute(std::string(id_temp)+" all temp"); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - id_press = utils::strdup(std::string(id)+"_press"); - modify->add_compute(std::string(id_press)+" all pressure "+id_temp); + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nph_sphere_omp.cpp b/src/USER-OMP/fix_nph_sphere_omp.cpp index 0e2a805dcf..35387b51f2 100644 --- a/src/USER-OMP/fix_nph_sphere_omp.cpp +++ b/src/USER-OMP/fix_nph_sphere_omp.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph_sphere_omp.h" -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -34,35 +34,15 @@ FixNPHSphereOMP::FixNPHSphereOMP(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp/sphere"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp/sphere",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_npt_asphere_omp.cpp b/src/USER-OMP/fix_npt_asphere_omp.cpp index c05fca9043..e896db8712 100644 --- a/src/USER-OMP/fix_npt_asphere_omp.cpp +++ b/src/USER-OMP/fix_npt_asphere_omp.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_asphere_omp.h" -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -34,35 +34,15 @@ FixNPTAsphereOMP::FixNPTAsphereOMP(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp/asphere"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp/asphere",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_npt_omp.cpp b/src/USER-OMP/fix_npt_omp.cpp index 4037dd928e..386be81acc 100644 --- a/src/USER-OMP/fix_npt_omp.cpp +++ b/src/USER-OMP/fix_npt_omp.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_omp.h" -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -34,15 +34,15 @@ FixNPTOMP::FixNPTOMP(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - id_temp = utils::strdup(std::string(id)+"_temp"); - modify->add_compute(std::string(id_temp)+" all temp"); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - id_press = utils::strdup(std::string(id)+"_press"); - modify->add_compute(std::string(id_press)+" all pressure "+id_temp); + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_npt_sphere_omp.cpp b/src/USER-OMP/fix_npt_sphere_omp.cpp index 93b6cdda69..4e40fb63d5 100644 --- a/src/USER-OMP/fix_npt_sphere_omp.cpp +++ b/src/USER-OMP/fix_npt_sphere_omp.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_sphere_omp.h" -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -34,35 +34,15 @@ FixNPTSphereOMP::FixNPTSphereOMP(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp/sphere"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp/sphere",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nvt_asphere_omp.cpp b/src/USER-OMP/fix_nvt_asphere_omp.cpp index 353d839b4f..c8db9cc98d 100644 --- a/src/USER-OMP/fix_nvt_asphere_omp.cpp +++ b/src/USER-OMP/fix_nvt_asphere_omp.cpp @@ -33,17 +33,8 @@ FixNVTAsphereOMP::FixNVTAsphereOMP(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = group->names[igroup]; - newarg[2] = (char *) "temp/asphere"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp/asphere", + id_temp,group->names[igroup])); tcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nvt_omp.cpp b/src/USER-OMP/fix_nvt_omp.cpp index 127876b4e8..240825b2c6 100644 --- a/src/USER-OMP/fix_nvt_omp.cpp +++ b/src/USER-OMP/fix_nvt_omp.cpp @@ -11,11 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_omp.h" + +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp index a665241efb..3193d58386 100644 --- a/src/USER-OMP/fix_nvt_sllod_omp.cpp +++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp @@ -15,18 +15,21 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "fix_nvt_sllod_omp.h" -#include -#include "math_extra.h" + #include "atom.h" -#include "group.h" -#include "modify.h" +#include "compute.h" +#include "domain.h" +#include "error.h" #include "fix.h" #include "fix_deform.h" -#include "compute.h" -#include "error.h" -#include "domain.h" +#include "group.h" +#include "math_extra.h" +#include "modify.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -51,18 +54,9 @@ FixNVTSllodOMP::FixNVTSllodOMP(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = group->names[igroup]; - newarg[2] = (char *) "temp/deform"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp/deform", + id_temp,group->names[igroup])); tcomputeflag = 1; } @@ -82,7 +76,7 @@ void FixNVTSllodOMP::init() int i; for (i = 0; i < modify->nfix; i++) - if (strncmp(modify->fix[i]->style,"deform",6) == 0) { + if (utils::strmatch(modify->fix[i]->style,"^deform")) { if (((FixDeform *) modify->fix[i])->remapflag != Domain::V_REMAP) error->all(FLERR,"Using fix nvt/sllod/omp with inconsistent fix " "deform remap option"); diff --git a/src/USER-OMP/fix_nvt_sphere_omp.cpp b/src/USER-OMP/fix_nvt_sphere_omp.cpp index 680ddd7f17..d53d9ec32d 100644 --- a/src/USER-OMP/fix_nvt_sphere_omp.cpp +++ b/src/USER-OMP/fix_nvt_sphere_omp.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_sphere_omp.h" + +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -33,17 +33,8 @@ FixNVTSphereOMP::FixNVTSphereOMP(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = group->names[igroup]; - newarg[2] = (char *) "temp/sphere"; - - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp/sphere", + id_temp,group->names[igroup])); tcomputeflag = 1; } diff --git a/src/USER-OMP/fix_rigid_nph_omp.cpp b/src/USER-OMP/fix_rigid_nph_omp.cpp index cb59ad0828..80bfbe8141 100644 --- a/src/USER-OMP/fix_rigid_nph_omp.cpp +++ b/src/USER-OMP/fix_rigid_nph_omp.cpp @@ -18,9 +18,9 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_nph_omp.h" -#include -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; @@ -57,34 +57,15 @@ FixRigidNPHOMP::FixRigidNPHOMP(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_rigid_npt_omp.cpp b/src/USER-OMP/fix_rigid_npt_omp.cpp index f496dd0a11..f832dda618 100644 --- a/src/USER-OMP/fix_rigid_npt_omp.cpp +++ b/src/USER-OMP/fix_rigid_npt_omp.cpp @@ -18,9 +18,9 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_npt_omp.h" -#include -#include "modify.h" + #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; @@ -67,36 +67,17 @@ FixRigidNPTOMP::FixRigidNPTOMP(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp // compute group = all since pressure is always global (group all) - // and thus its KE/temperature contribution should use group all + // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp index b221ecbca8..0b54811db0 100644 --- a/src/USER-QTB/fix_qbmsst.cpp +++ b/src/USER-QTB/fix_qbmsst.cpp @@ -18,9 +18,6 @@ #include "fix_qbmsst.h" -#include -#include - #include "atom.h" #include "force.h" #include "update.h" @@ -34,6 +31,9 @@ #include "kspace.h" #include "math_const.h" +#include +#include + using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; @@ -204,45 +204,23 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) // id = fix-ID + temp // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = const_cast("all"); - newarg[2] = const_cast("temp"); - modify->add_compute(3,newarg); - delete [] newarg; + + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = const_cast("all"); - newarg[2] = const_cast("pressure"); - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pflag = 1; // create a new compute potential energy compute - n = strlen(id) + 3; - id_pe = new char[n]; - strcpy(id_pe,id); - strcat(id_pe,"_pe"); - newarg = new char*[3]; - newarg[0] = id_pe; - newarg[1] = (char*)"all"; - newarg[2] = (char*)"pe"; - modify->add_compute(3,newarg); - delete [] newarg; + + id_pe = utils::strdup(std::string(id) + "_pe"); + modify->add_compute(fmt::format("{} all pe",id_temp)); peflag = 1; // allocate qbmsst diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp index b757900703..91125fd4ed 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -14,24 +14,26 @@ ------------------------------------------------------------------------- */ #include "fix_nh_uef.h" -#include -#include + #include "atom.h" -#include "force.h" -#include "comm.h" #include "citeme.h" -#include "irregular.h" -#include "modify.h" +#include "comm.h" #include "compute.h" -#include "update.h" -#include "domain.h" -#include "error.h" -#include "output.h" -#include "timer.h" -#include "neighbor.h" #include "compute_pressure_uef.h" #include "compute_temp_uef.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "irregular.h" +#include "modify.h" +#include "neighbor.h" +#include "output.h" +#include "timer.h" #include "uef_utils.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -179,29 +181,12 @@ FixNHUef::FixNHUef(LAMMPS *lmp, int narg, char **arg) : // Create temp and pressure computes for nh/uef - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp/uef"; - modify->add_compute(3,newarg); - delete [] newarg; + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp/uef",id_temp)); tcomputeflag = 1; - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure/uef"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure/uef {}",id_press, id_temp)); pcomputeflag = 1; nevery = 1; @@ -214,8 +199,7 @@ FixNHUef::FixNHUef(LAMMPS *lmp, int narg, char **arg) : FixNHUef::~FixNHUef() { delete uefbox; - if (pcomputeflag && !pstat_flag) - { + if (pcomputeflag && !pstat_flag) { modify->delete_compute(id_press); delete [] id_press; } diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp index bcd9031b6e..d9cd746ca6 100644 --- a/src/VORONOI/compute_voronoi_atom.cpp +++ b/src/VORONOI/compute_voronoi_atom.cpp @@ -80,9 +80,7 @@ ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) : else if (strcmp(arg[iarg], "radius") == 0) { if (iarg + 2 > narg || strstr(arg[iarg+1],"v_") != arg[iarg+1] ) error->all(FLERR,"Illegal compute voronoi/atom command"); - int n = strlen(&arg[iarg+1][2]) + 1; - radstr = new char[n]; - strcpy(radstr,&arg[iarg+1][2]); + radstr = utils::strdup(&arg[iarg+1][2]); iarg += 2; } else if (strcmp(arg[iarg], "surface") == 0) { diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp index ef576e96f6..76bd8f05c2 100644 --- a/src/fix_box_relax.cpp +++ b/src/fix_box_relax.cpp @@ -16,20 +16,20 @@ ------------------------------------------------------------------------- */ #include "fix_box_relax.h" -#include -#include #include "atom.h" -#include "domain.h" -#include "update.h" #include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "modify.h" -#include "compute.h" -#include "error.h" #include "math_extra.h" +#include "modify.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -319,24 +319,17 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - std::string tcmd = id + std::string("_temp"); - id_temp = new char[tcmd.size()+1]; - strcpy(id_temp,tcmd.c_str()); - - tcmd += " all temp"; - modify->add_compute(tcmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tflag = 1; // create a new compute pressure style (virial only) // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - std::string pcmd = id + std::string("_press"); - id_press = new char[pcmd.size()+1]; - strcpy(id_press,pcmd.c_str()); - - pcmd += " all pressure " + std::string(id_temp) + " virial"; - modify->add_compute(pcmd); + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {} virial", + id_press, id_temp)); pflag = 1; dimension = domain->dimension; diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp index 6002d2e40d..5b160689dd 100644 --- a/src/fix_nph.cpp +++ b/src/fix_nph.cpp @@ -12,10 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_nph.h" -#include -#include "modify.h" #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -35,23 +34,15 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - std::string tcmd = id + std::string("_temp"); - id_temp = new char[tcmd.size()+1]; - strcpy(id_temp,tcmd.c_str()); - - tcmd += " all temp"; - modify->add_compute(tcmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - std::string pcmd = id + std::string("_press"); - id_press = new char[pcmd.size()+1]; - strcpy(id_press,pcmd.c_str()); - - pcmd += " all pressure " + std::string(id_temp); - modify->add_compute(pcmd); + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp index 27197c48a7..20e072d5b5 100644 --- a/src/fix_nph_sphere.cpp +++ b/src/fix_nph_sphere.cpp @@ -12,10 +12,11 @@ ------------------------------------------------------------------------- */ #include "fix_nph_sphere.h" -#include -#include "modify.h" #include "error.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -35,21 +36,15 @@ FixNPHSphere::FixNPHSphere(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - std::string tcmd = id + std::string("_temp"); - id_temp = new char[tcmd.size()+1]; - strcpy(id_temp,tcmd.c_str()); - - modify->add_compute(tcmd + " all temp/sphere"); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp/sphere",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - std::string pcmd = id + std::string("_press"); - id_press = new char[pcmd.size()+1]; - strcpy(id_press,pcmd.c_str()); - - modify->add_compute(pcmd + " all pressure " + std::string(id_temp)); + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp index 7ee346985d..78acf0cf7e 100644 --- a/src/fix_npt.cpp +++ b/src/fix_npt.cpp @@ -12,10 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_npt.h" -#include -#include "modify.h" #include "error.h" +#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -35,23 +34,15 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - std::string tcmd = id + std::string("_temp"); - id_temp = new char[tcmd.size()+1]; - strcpy(id_temp,tcmd.c_str()); - - tcmd += " all temp"; - modify->add_compute(tcmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - std::string pcmd = id + std::string("_press"); - id_press = new char[pcmd.size()+1]; - strcpy(id_press,pcmd.c_str()); - - pcmd += " all pressure " + std::string(id_temp); - modify->add_compute(pcmd); + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp index b806cf5362..a6dfeba425 100644 --- a/src/fix_npt_sphere.cpp +++ b/src/fix_npt_sphere.cpp @@ -12,10 +12,11 @@ ------------------------------------------------------------------------- */ #include "fix_npt_sphere.h" -#include -#include "modify.h" #include "error.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -35,21 +36,15 @@ FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - std::string tcmd = id + std::string("_temp"); - id_temp = new char[tcmd.size()+1]; - strcpy(id_temp,tcmd.c_str()); - - modify->add_compute(tcmd + " all temp/sphere"); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp/sphere",id_temp)); tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - std::string pcmd = id + std::string("_press"); - id_press = new char[pcmd.size()+1]; - strcpy(id_press,pcmd.c_str()); - - modify->add_compute(pcmd + " all pressure " + std::string(id_temp)); + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pcomputeflag = 1; } diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp index 23f69abc86..e14ff47e46 100644 --- a/src/fix_nve.cpp +++ b/src/fix_nve.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_nve.h" -#include + #include "atom.h" -#include "force.h" -#include "update.h" -#include "respa.h" #include "error.h" +#include "force.h" +#include "respa.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -27,7 +27,7 @@ using namespace FixConst; FixNVE::FixNVE(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { - if (strcmp(style,"nve/sphere") != 0 && narg < 3) + if (!utils::strmatch(style,"^nve/sphere") && narg < 3) error->all(FLERR,"Illegal fix nve command"); dynamic_group_allow = 1; @@ -53,7 +53,7 @@ void FixNVE::init() dtv = update->dt; dtf = 0.5 * update->dt * force->ftm2v; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) step_respa = ((Respa *) update->integrate)->step; } diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp index ad69e6ee81..14251a269a 100644 --- a/src/fix_nvt.cpp +++ b/src/fix_nvt.cpp @@ -12,12 +12,10 @@ ------------------------------------------------------------------------- */ #include "fix_nvt.h" -#include +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" - using namespace LAMMPS_NS; using namespace FixConst; @@ -35,11 +33,7 @@ FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp - std::string tcmd = id + std::string("_temp"); - id_temp = new char[tcmd.size()+1]; - strcpy(id_temp,tcmd.c_str()); - - tcmd += fmt::format(" {} temp",group->names[igroup]); - modify->add_compute(tcmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp",id_temp,group->names[igroup])); tcomputeflag = 1; } diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp index 2257fa6c56..ba81adee0c 100644 --- a/src/fix_nvt_sllod.cpp +++ b/src/fix_nvt_sllod.cpp @@ -16,17 +16,18 @@ ------------------------------------------------------------------------- */ #include "fix_nvt_sllod.h" -#include -#include "math_extra.h" + #include "atom.h" +#include "compute.h" #include "domain.h" -#include "group.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_deform.h" -#include "compute.h" -#include "error.h" +#include "group.h" +#include "math_extra.h" +#include "modify.h" +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -49,12 +50,9 @@ FixNVTSllod::FixNVTSllod(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp - std::string cmd = id + std::string("_temp"); - id_temp = new char[cmd.size()+1]; - strcpy(id_temp,cmd.c_str()); - - cmd += fmt::format(" {} temp/deform",group->names[igroup]); - modify->add_compute(cmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp/deform", + id_temp,group->names[igroup])); tcomputeflag = 1; } diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp index 1119d345bc..0733a27678 100644 --- a/src/fix_nvt_sphere.cpp +++ b/src/fix_nvt_sphere.cpp @@ -12,12 +12,10 @@ ------------------------------------------------------------------------- */ #include "fix_nvt_sphere.h" -#include +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" - using namespace LAMMPS_NS; using namespace FixConst; @@ -35,11 +33,8 @@ FixNVTSphere::FixNVTSphere(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp - std::string cmd = id + std::string("_temp"); - id_temp = new char[cmd.size()+1]; - strcpy(id_temp,cmd.c_str()); - - cmd += fmt::format(" {} temp/sphere",group->names[igroup]); - modify->add_compute(cmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp/sphere", + id_temp,group->names[igroup])); tcomputeflag = 1; } diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp index d929ca6f28..9cd9de9485 100644 --- a/src/fix_press_berendsen.cpp +++ b/src/fix_press_berendsen.cpp @@ -12,19 +12,20 @@ ------------------------------------------------------------------------- */ #include "fix_press_berendsen.h" -#include -#include #include "atom.h" -#include "force.h" #include "comm.h" -#include "modify.h" -#include "fix_deform.h" #include "compute.h" -#include "kspace.h" -#include "update.h" #include "domain.h" #include "error.h" +#include "fix_deform.h" +#include "force.h" +#include "kspace.h" +#include "modify.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -218,24 +219,16 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) : // compute group = all since pressure is always global (group all) // and thus its KE/temperature contribution should use group all - std::string tcmd = id + std::string("_temp"); - id_temp = new char[tcmd.size()+1]; - strcpy(id_temp,tcmd.c_str()); - - tcmd += " all temp"; - modify->add_compute(tcmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); tflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all // pass id_temp as 4th arg to pressure constructor - std::string pcmd = id + std::string("_press"); - id_press = new char[pcmd.size()+1]; - strcpy(id_press,pcmd.c_str()); - - pcmd += " all pressure " + std::string(id_temp); - modify->add_compute(pcmd); + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pflag = 1; nrigid = 0; diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp index 39b8a5fefd..38ce9de333 100644 --- a/src/fix_temp_berendsen.cpp +++ b/src/fix_temp_berendsen.cpp @@ -72,10 +72,8 @@ FixTempBerendsen::FixTempBerendsen(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp, compute group = fix group - std::string cmd = id + std::string("_temp"); - id_temp = utils::strdup(cmd); - cmd += fmt::format(" {} temp",group->names[igroup]); - modify->add_compute(cmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp",id_temp,group->names[igroup])); tflag = 1; energy = 0; diff --git a/src/fix_temp_csld.cpp b/src/fix_temp_csld.cpp index 787b4dd34e..bf3d0eb7f6 100644 --- a/src/fix_temp_csld.cpp +++ b/src/fix_temp_csld.cpp @@ -81,10 +81,8 @@ FixTempCSLD::FixTempCSLD(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp, compute group = fix group - std::string cmd = id + std::string("_temp"); - id_temp = utils::strdup(cmd); - cmd += fmt::format(" {} temp",group->names[igroup]); - modify->add_compute(cmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp",id_temp,group->names[igroup])); tflag = 1; vhold = nullptr; diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp index 525cf5b74a..2d04243a11 100644 --- a/src/fix_temp_csvr.cpp +++ b/src/fix_temp_csvr.cpp @@ -81,10 +81,8 @@ FixTempCSVR::FixTempCSVR(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp style // id = fix-ID + temp, compute group = fix group - std::string cmd = id + std::string("_temp"); - id_temp = utils::strdup(cmd); - cmd += fmt::format(" {} temp",group->names[igroup]); - modify->add_compute(cmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp",id_temp,group->names[igroup])); tflag = 1; nmax = -1; diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp index b57f6c238c..73c55f2793 100644 --- a/src/fix_temp_rescale.cpp +++ b/src/fix_temp_rescale.cpp @@ -68,10 +68,8 @@ FixTempRescale::FixTempRescale(LAMMPS *lmp, int narg, char **arg) : // create a new compute temp // id = fix-ID + temp, compute group = fix group - std::string cmd = id + std::string("_temp"); - id_temp = utils::strdup(cmd); - cmd += fmt::format(" {} temp",group->names[igroup]); - modify->add_compute(cmd); + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} {} temp",id_temp,group->names[igroup])); tflag = 1; energy = 0.0; From e481eb115456f7332ec7e9dd19151f02e23af515 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Mar 2021 07:29:14 -0400 Subject: [PATCH 0282/1217] simplify by using utils::strdup() fmt::format() and reorder includes --- src/USER-BOCS/fix_bocs.cpp | 8 ++---- src/USER-DPD/fix_eos_table_rx.cpp | 7 +++-- src/USER-DPD/fix_rx.cpp | 26 +++++++++---------- src/USER-DPD/pair_exp6_rx.cpp | 15 +++++------ src/USER-DPD/pair_multi_lucy.cpp | 22 +++++++--------- src/USER-DPD/pair_multi_lucy_rx.cpp | 26 +++++++++---------- src/USER-EFF/fix_temp_rescale_eff.cpp | 4 +-- src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp | 7 ++--- src/USER-MGPT/pair_mgpt.cpp | 16 +++++------- src/USER-MISC/compute_gyration_shape.cpp | 13 +++++----- .../compute_gyration_shape_chunk.cpp | 21 +++++++-------- src/USER-MISC/compute_hma.cpp | 24 +++-------------- src/USER-MISC/compute_pressure_grem.cpp | 8 +++--- 13 files changed, 80 insertions(+), 117 deletions(-) diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index 87d4653da5..60fb03cdf8 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -1525,9 +1525,7 @@ int FixBocs::modify_param(int narg, char **arg) tcomputeflag = 0; } delete [] id_temp; - int n = strlen(arg[1]) + 1; - id_temp = new char[n]; - strcpy(id_temp,arg[1]); + id_temp = utils::strdup(arg[1]); int icompute = modify->find_compute(arg[1]); if (icompute < 0) @@ -1559,9 +1557,7 @@ int FixBocs::modify_param(int narg, char **arg) pcomputeflag = 0; } delete [] id_press; - int n = strlen(arg[1]) + 1; - id_press = new char[n]; - strcpy(id_press,arg[1]); + id_press = utils::strdup(arg[1]); int icompute = modify->find_compute(arg[1]); if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID"); diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp index 28cd4eb4c3..7b0bec93f2 100644 --- a/src/USER-DPD/fix_eos_table_rx.cpp +++ b/src/USER-DPD/fix_eos_table_rx.cpp @@ -17,16 +17,15 @@ #include "fix_eos_table_rx.h" - -#include -#include #include "atom.h" +#include "comm.h" #include "error.h" #include "force.h" #include "memory.h" -#include "comm.h" #include "modify.h" +#include +#include #define MAXLINE 1024 diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp index 675c3d6dea..4f0f381e6d 100644 --- a/src/USER-DPD/fix_rx.cpp +++ b/src/USER-DPD/fix_rx.cpp @@ -13,28 +13,26 @@ #include "fix_rx.h" - -#include -#include -#include // DBL_EPSILON #include "atom.h" -#include "error.h" -#include "group.h" -#include "modify.h" -#include "force.h" -#include "memory.h" #include "comm.h" -#include "update.h" #include "domain.h" -#include "neighbor.h" +#include "error.h" +#include "force.h" +#include "group.h" +#include "math_special.h" +#include "memory.h" +#include "modify.h" #include "neigh_list.h" #include "neigh_request.h" -#include "math_special.h" +#include "neighbor.h" #include "pair_dpd_fdt_energy.h" +#include "update.h" - -#include // std::vector<> #include // std::max +#include // DBL_EPSILON +#include +#include +#include // std::vector<> using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index 036d31060b..ba8d52776f 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -13,20 +13,19 @@ #include "pair_exp6_rx.h" -#include - -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" +#include "fix.h" #include "force.h" -#include "neigh_list.h" #include "math_special.h" #include "memory.h" -#include "error.h" - #include "modify.h" -#include "fix.h" +#include "neigh_list.h" + +#include +#include +#include using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp index 70ea8b40ad..85cab8a37f 100644 --- a/src/USER-DPD/pair_multi_lucy.cpp +++ b/src/USER-DPD/pair_multi_lucy.cpp @@ -21,21 +21,19 @@ The Journal of Chemical Physics, 2016, 144, 104501. ------------------------------------------------------------------------------------------- */ +#include "pair_multi_lucy.h" + +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "neigh_list.h" #include -#include "math_const.h" - #include -#include "pair_multi_lucy.h" -#include "atom.h" -#include "force.h" -#include "comm.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -#include "citeme.h" - using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp index c0f6af8a7e..5bea395725 100644 --- a/src/USER-DPD/pair_multi_lucy_rx.cpp +++ b/src/USER-DPD/pair_multi_lucy_rx.cpp @@ -21,23 +21,21 @@ The Journal of Chemical Physics, 2016, 144, 104501. ------------------------------------------------------------------------------------------- */ +#include "pair_multi_lucy_rx.h" + +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" #include -#include "math_const.h" - #include -#include "pair_multi_lucy_rx.h" -#include "atom.h" -#include "force.h" -#include "comm.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -#include "citeme.h" -#include "modify.h" -#include "fix.h" - using namespace LAMMPS_NS; diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/USER-EFF/fix_temp_rescale_eff.cpp index 1ebed8b9ff..0d3bf6ed43 100644 --- a/src/USER-EFF/fix_temp_rescale_eff.cpp +++ b/src/USER-EFF/fix_temp_rescale_eff.cpp @@ -165,9 +165,7 @@ int FixTempRescaleEff::modify_param(int narg, char **arg) tflag = 0; } delete [] id_temp; - int n = strlen(arg[1]) + 1; - id_temp = new char[n]; - strcpy(id_temp,arg[1]); + id_temp = utils::strdup(arg[1]); int icompute = modify->find_compute(id_temp); if (icompute < 0) error->all(FLERR,"Could not find fix_modify temperature ID"); diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index a45d62a588..4b141a3bd1 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -31,10 +31,8 @@ ------------------------------------------------------------------------- */ - #include "fix_nve_manifold_rattle.h" -#include #include "atom.h" #include "force.h" #include "update.h" @@ -44,18 +42,17 @@ #include "citeme.h" #include "comm.h" +#include + #include "manifold_factory.h" #include "manifold.h" - using namespace LAMMPS_NS; using namespace FixConst; using namespace user_manifold; - enum { CONST, EQUAL }; // For treating the variables. - static const char* cite_fix_nve_manifold_rattle = "fix nve/manifold/rattle command:\n\n" "@article{paquay-2016,\n" diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/USER-MGPT/pair_mgpt.cpp index 75f870e1b2..7061d1f86b 100644 --- a/src/USER-MGPT/pair_mgpt.cpp +++ b/src/USER-MGPT/pair_mgpt.cpp @@ -23,20 +23,18 @@ #include "pair_mgpt.h" -#include - -#include -#include - #include "atom.h" -#include "force.h" #include "comm.h" -#include "neighbor.h" +#include "error.h" +#include "force.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/compute_gyration_shape.cpp b/src/USER-MISC/compute_gyration_shape.cpp index daec7a6b4b..ac073d4cbc 100644 --- a/src/USER-MISC/compute_gyration_shape.cpp +++ b/src/USER-MISC/compute_gyration_shape.cpp @@ -15,17 +15,18 @@ * Contributing author: Evangelos Voyiatzis (Royal DSM) * ------------------------------------------------------------------------- */ - #include "compute_gyration_shape.h" -#include -#include + #include "error.h" -#include "math_extra.h" #include "math_eigen.h" +#include "math_extra.h" #include "math_special.h" #include "modify.h" #include "update.h" +#include +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ @@ -41,9 +42,7 @@ ComputeGyrationShape::ComputeGyrationShape(LAMMPS *lmp, int narg, char **arg) : extvector = 0; // ID of compute gyration - int n = strlen(arg[3]) + 1; - id_gyration = new char[n]; - strcpy(id_gyration,arg[3]); + id_gyration = utils::strdup(arg[3]); init(); diff --git a/src/USER-MISC/compute_gyration_shape_chunk.cpp b/src/USER-MISC/compute_gyration_shape_chunk.cpp index e0ab646ce2..e66173d704 100644 --- a/src/USER-MISC/compute_gyration_shape_chunk.cpp +++ b/src/USER-MISC/compute_gyration_shape_chunk.cpp @@ -15,17 +15,18 @@ * Contributing author: Evangelos Voyiatzis (Royal DSM) * ------------------------------------------------------------------------- */ - #include "compute_gyration_shape_chunk.h" + +#include "error.h" +#include "math_eigen.h" +#include "math_extra.h" +#include "math_special.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + #include #include -#include "error.h" -#include "math_extra.h" -#include "math_eigen.h" -#include "math_special.h" -#include "modify.h" -#include "memory.h" -#include "update.h" using namespace LAMMPS_NS; @@ -37,9 +38,7 @@ ComputeGyrationShapeChunk::ComputeGyrationShapeChunk(LAMMPS *lmp, int narg, char if (narg != 4) error->all(FLERR,"Illegal compute gyration/shape/chunk command"); // ID of compute gyration - int n = strlen(arg[3]) + 1; - id_gyration_chunk = new char[n]; - strcpy(id_gyration_chunk,arg[3]); + id_gyration_chunk = utils::strdup(arg[3]); init(); diff --git a/src/USER-MISC/compute_hma.cpp b/src/USER-MISC/compute_hma.cpp index 8220abebc4..fbe8c67d39 100644 --- a/src/USER-MISC/compute_hma.cpp +++ b/src/USER-MISC/compute_hma.cpp @@ -78,11 +78,7 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : if (narg < 4) error->all(FLERR,"Illegal compute hma command"); if (igroup) error->all(FLERR,"Compute hma must use group all"); if (strcmp(arg[3],"NULL") == 0) {error->all(FLERR,"fix ID specifying the set temperature of canonical simulation is required");} - else { - int n = strlen(arg[3]) + 1; - id_temp = new char[n]; - strcpy(id_temp,arg[3]); - } + else id_temp = utils::strdup(arg[3]); create_attribute = 1; extscalar = 1; @@ -92,23 +88,11 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : // our new fix's id (id_fix)= compute-ID + COMPUTE_STORE // our new fix's group = same as compute group - int n = strlen(id) + strlen("_COMPUTE_STORE") + 1; - id_fix = new char[n]; - strcpy(id_fix,id); - strcat(id_fix,"_COMPUTE_STORE"); - - char **newarg = new char*[6]; - newarg[0] = id_fix; - newarg[1] = group->names[igroup]; - newarg[2] = (char *) "STORE"; - newarg[3] = (char *) "peratom"; - newarg[4] = (char *) "1"; - newarg[5] = (char *) "3"; - modify->add_fix(6,newarg); + id_fix = utils::strdup(std::string(id)+"_COMPUTE_STORE"); + modify->add_fix(fmt::format("{} {} STORE peratom 1 3", + id_fix, group->names[igroup])); fix = (FixStore *) modify->fix[modify->nfix-1]; - delete [] newarg; - // calculate xu,yu,zu for fix store array // skip if reset from restart file diff --git a/src/USER-MISC/compute_pressure_grem.cpp b/src/USER-MISC/compute_pressure_grem.cpp index 6ba4462c29..98f699491f 100644 --- a/src/USER-MISC/compute_pressure_grem.cpp +++ b/src/USER-MISC/compute_pressure_grem.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pressure_grem.h" -#include + #include "update.h" #include "domain.h" #include "modify.h" @@ -21,6 +21,8 @@ #include "kspace.h" #include "error.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- @@ -30,9 +32,7 @@ using namespace LAMMPS_NS; ComputePressureGrem::ComputePressureGrem(LAMMPS *lmp, int narg, char **arg) : ComputePressure(lmp, narg-1, arg) { - int len = strlen(arg[narg-1])+1; - fix_grem = new char[len]; - strcpy(fix_grem,arg[narg-1]); + fix_grem = utils::strdup(arg[narg-1]); } /* ---------------------------------------------------------------------- */ From 806f4e73edf18719a18d9255ac8dbc97b647cd6b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Mar 2021 07:32:43 -0400 Subject: [PATCH 0283/1217] make dihedral style table/cut a derived class from table and remove redundant code --- src/USER-MISC/dihedral_table.cpp | 67 +-- src/USER-MISC/dihedral_table.h | 8 +- src/USER-MISC/dihedral_table_cut.cpp | 842 ++------------------------- src/USER-MISC/dihedral_table_cut.h | 118 +--- 4 files changed, 62 insertions(+), 973 deletions(-) diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index a81037cad6..ffbc9aad31 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -464,7 +464,6 @@ DihedralTable::~DihedralTable() if (allocated) { memory->destroy(setflag); - //memory->destroy(phi0); <- equilibrium angles not supported memory->destroy(tabindex); } } @@ -718,49 +717,18 @@ void DihedralTable::compute(int eflag, int vflag) } } // void DihedralTable::compute() - - - - - - -// single() calculates the dihedral-angle energy of atoms i1, i2, i3, i4. -double DihedralTable::single(int type, int i1, int i2, int i3, int i4) -{ - double vb12[g_dim]; - double vb23[g_dim]; - double vb34[g_dim]; - double n123[g_dim]; - double n234[g_dim]; - - double **x = atom->x; - - double phi = Phi(x[i1], x[i2], x[i3], x[i4], domain, - vb12, vb23, vb34, n123, n234); - - double u=0.0; - u_lookup(type, phi, u); //Calculate the energy, and store it in "u" - - return u; -} - - /* ---------------------------------------------------------------------- */ - - void DihedralTable::allocate() { allocated = 1; int n = atom->ndihedraltypes; memory->create(tabindex,n+1,"dihedral:tabindex"); - //memory->create(phi0,n+1,"dihedral:phi0"); <-equilibrium angles not supported memory->create(setflag,n+1,"dihedral:setflag"); for (int i = 1; i <= n; i++) setflag[i] = 0; } - /* ---------------------------------------------------------------------- global settings ------------------------------------------------------------------------- */ @@ -791,16 +759,13 @@ void DihedralTable::settings(int narg, char **arg) tables = nullptr; } - - /* ---------------------------------------------------------------------- set coeffs for one type ------------------------------------------------------------------------- */ - void DihedralTable::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR,"Illegal dihedral_coeff command"); + if (narg != 3) error->all(FLERR,"Incorrect args for dihedral coefficients"); if (!allocated) allocate(); int ilo,ihi; @@ -815,25 +780,22 @@ void DihedralTable::coeff(int narg, char **arg) if (me == 0) read_table(tb,arg[1],arg[2]); bcast_table(tb); - // --- check the angle data for range errors --- // --- and resolve issues with periodicity --- - if (tb->ninput < 2) { - error->one(FLERR,fmt::format("Invalid dihedral table length ({}).", - arg[2])); - } else if ((tb->ninput == 2) && (tabstyle == SPLINE)) { - error->one(FLERR,fmt::format("Invalid dihedral spline table length. " - "(Try linear)\n ({}).",arg[2])); - } + if (tb->ninput < 2) + error->all(FLERR,fmt::format("Invalid dihedral table length: {}",arg[2])); + else if ((tb->ninput == 2) && (tabstyle == SPLINE)) + error->all(FLERR,fmt::format("Invalid dihedral spline table length: {} " + "(Try linear)",arg[2])); // check for monotonicity for (int i=0; i < tb->ninput-1; i++) { if (tb->phifile[i] >= tb->phifile[i+1]) { auto err_msg = fmt::format("Dihedral table values are not increasing " - "({}, {}th entry)",arg[2],i+1); + "({}, entry {})",arg[2],i+1); if (i==0) - err_msg += std::string("\n(This is probably a mistake with your table format.)\n"); + err_msg += "\n(This is probably a mistake with your table format.)\n"; error->all(FLERR,err_msg); } } @@ -971,15 +933,12 @@ void DihedralTable::coeff(int narg, char **arg) } ntables++; - if (count == 0) - error->all(FLERR,"Illegal dihedral_coeff command"); - -} //DihedralTable::coeff() - + if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients"); +} /* ---------------------------------------------------------------------- - proc 0 writes to restart file - ------------------------------------------------------------------------- */ + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ void DihedralTable::write_restart(FILE *fp) { @@ -1065,7 +1024,6 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword) error->one(FLERR,"Did not find keyword in table file"); } - // read args on 2nd line of section // allocate table arrays for file values @@ -1279,7 +1237,6 @@ void DihedralTable::compute_table(Table *tb) void DihedralTable::param_extract(Table *tb, char *line) { - //tb->theta0 = 180.0; <- equilibrium angles not supported tb->ninput = 0; tb->f_unspecified = false; //default tb->use_degrees = true; //default diff --git a/src/USER-MISC/dihedral_table.h b/src/USER-MISC/dihedral_table.h index a8d1f8f8bb..9d5b03f5cc 100644 --- a/src/USER-MISC/dihedral_table.h +++ b/src/USER-MISC/dihedral_table.h @@ -25,7 +25,6 @@ DihedralStyle(table,DihedralTable) #define LMP_DIHEDRAL_TABLE_H #include "dihedral.h" - namespace LAMMPS_NS { class DihedralTable : public Dihedral { @@ -34,7 +33,7 @@ class DihedralTable : public Dihedral { virtual ~DihedralTable(); virtual void compute(int, int); void settings(int, char **); - void coeff(int, char **); + virtual void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); void write_restart_settings(FILE *); @@ -43,13 +42,11 @@ class DihedralTable : public Dihedral { protected: int tabstyle,tablength; - // double *phi0; <- equilibrium angles not supported std::string checkU_fname; std::string checkF_fname; struct Table { int ninput; - //double phi0; <-equilibrium angles not supported int f_unspecified; // boolean (but MPI does not like type "bool") int use_degrees; // boolean (but MPI does not like type "bool") double *phifile,*efile,*ffile; @@ -62,7 +59,7 @@ class DihedralTable : public Dihedral { Table *tables; int *tabindex; - void allocate(); + virtual void allocate(); void null_table(Table *); void free_table(Table *); void read_table(Table *, char *, char *); @@ -152,6 +149,5 @@ class DihedralTable : public Dihedral { } // namespace LAMMPS_NS - #endif //#ifndef LMP_DIHEDRAL_TABLE_H #endif //#ifdef DIHEDRAL_CLASS ... #else diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index ed7b3ac0d6..dc7a6f9685 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -18,28 +18,23 @@ #include "dihedral_table_cut.h" -#include +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "neighbor.h" +#include "update.h" + #include - #include - #include // IWYU pragma: keep #include // IWYU pragma: keep -#include "atom.h" -#include "neighbor.h" -#include "update.h" -#include "comm.h" -#include "force.h" -#include "citeme.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" - - using namespace LAMMPS_NS; using namespace MathConst; -using namespace std; static const char cite_dihedral_tablecut[] = "dihedral_style table/cut command:\n\n" @@ -89,272 +84,6 @@ enum { //GSL status return codes. }; -static int solve_cyc_tridiag( const double diag[], size_t d_stride, - const double offdiag[], size_t o_stride, - const double b[], size_t b_stride, - double x[], size_t x_stride, - size_t N, bool warn) -{ - int status = GSL_SUCCESS; - double * delta = (double *) malloc (N * sizeof (double)); - double * gamma = (double *) malloc (N * sizeof (double)); - double * alpha = (double *) malloc (N * sizeof (double)); - double * c = (double *) malloc (N * sizeof (double)); - double * z = (double *) malloc (N * sizeof (double)); - - if (delta == 0 || gamma == 0 || alpha == 0 || c == 0 || z == 0) { - if (warn) - fprintf(stderr,"Internal Cyclic Spline Error: failed to allocate working space\n"); - - if (delta) free(delta); - if (gamma) free(gamma); - if (alpha) free(alpha); - if (c) free(c); - if (z) free(z); - return GSL_ENOMEM; - } - else - { - size_t i, j; - double sum = 0.0; - - /* factor */ - - if (N == 1) - { - x[0] = b[0] / diag[0]; - free(delta); - free(gamma); - free(alpha); - free(c); - free(z); - return GSL_SUCCESS; - } - - alpha[0] = diag[0]; - gamma[0] = offdiag[0] / alpha[0]; - delta[0] = offdiag[o_stride * (N-1)] / alpha[0]; - - if (alpha[0] == 0) { - status = GSL_EZERODIV; - } - - for (i = 1; i < N - 2; i++) - { - alpha[i] = diag[d_stride * i] - offdiag[o_stride * (i-1)] * gamma[i - 1]; - gamma[i] = offdiag[o_stride * i] / alpha[i]; - delta[i] = -delta[i - 1] * offdiag[o_stride * (i-1)] / alpha[i]; - if (alpha[i] == 0) { - status = GSL_EZERODIV; - } - } - - for (i = 0; i < N - 2; i++) - { - sum += alpha[i] * delta[i] * delta[i]; - } - - alpha[N - 2] = diag[d_stride * (N - 2)] - offdiag[o_stride * (N - 3)] * gamma[N - 3]; - - gamma[N - 2] = (offdiag[o_stride * (N - 2)] - offdiag[o_stride * (N - 3)] * delta[N - 3]) / alpha[N - 2]; - - alpha[N - 1] = diag[d_stride * (N - 1)] - sum - alpha[(N - 2)] * gamma[N - 2] * gamma[N - 2]; - - /* update */ - z[0] = b[0]; - for (i = 1; i < N - 1; i++) - { - z[i] = b[b_stride * i] - z[i - 1] * gamma[i - 1]; - } - sum = 0.0; - for (i = 0; i < N - 2; i++) - { - sum += delta[i] * z[i]; - } - z[N - 1] = b[b_stride * (N - 1)] - sum - gamma[N - 2] * z[N - 2]; - for (i = 0; i < N; i++) - { - c[i] = z[i] / alpha[i]; - } - - /* backsubstitution */ - x[x_stride * (N - 1)] = c[N - 1]; - x[x_stride * (N - 2)] = c[N - 2] - gamma[N - 2] * x[x_stride * (N - 1)]; - if (N >= 3) - { - for (i = N - 3, j = 0; j <= N - 3; j++, i--) - { - x[x_stride * i] = c[i] - gamma[i] * x[x_stride * (i + 1)] - delta[i] * x[x_stride * (N - 1)]; - } - } - } - - free (z); - free (c); - free (alpha); - free (gamma); - free (delta); - - if ((status == GSL_EZERODIV) && warn) - fprintf(stderr, "Internal Cyclic Spline Error: Matrix must be positive definite.\n"); - - return status; -} //solve_cyc_tridiag() - -/* ---------------------------------------------------------------------- - spline and splint routines modified from Numerical Recipes -------------------------------------------------------------------------- */ - -static int cyc_spline(double const *xa, - double const *ya, - int n, - double period, - double *y2a, bool warn) -{ - - double *diag = new double[n]; - double *offdiag = new double[n]; - double *rhs = new double[n]; - double xa_im1, xa_ip1; - - // In the cyclic case, there are n equations with n unknows. - // The for loop sets up the equations we need to solve. - // Later we invoke the GSL tridiagonal matrix solver to solve them. - - for (int i=0; i < n; i++) { - - // I have to lookup xa[i+1] and xa[i-1]. This gets tricky because of - // periodic boundary conditions. We handle that now. - int im1 = i-1; - if (im1<0) { - im1 += n; - xa_im1 = xa[im1] - period; - } - else - xa_im1 = xa[im1]; - - int ip1 = i+1; - if (ip1>=n) { - ip1 -= n; - xa_ip1 = xa[ip1] + period; - } - else - xa_ip1 = xa[ip1]; - - // Recall that we want to find the y2a[] parameters (there are n of them). - // To solve for them, we have a linear equation with n unknowns - // (in the cyclic case that is). For details, the non-cyclic case is - // explained in equation 3.3.7 in Numerical Recipes in C, p. 115. - diag[i] = (xa_ip1 - xa_im1) / 3.0; - offdiag[i] = (xa_ip1 - xa[i]) / 6.0; - rhs[i] = ((ya[ip1] - ya[i]) / (xa_ip1 - xa[i])) - - ((ya[i] - ya[im1]) / (xa[i] - xa_im1)); - } - - // Because this matrix is tridiagonal (and cyclic), we can use the following - // cheap method to invert it. - if (solve_cyc_tridiag(diag, 1, - offdiag, 1, - rhs, 1, - y2a, 1, - n, warn) != GSL_SUCCESS) { - if (warn) - fprintf(stderr,"Error in inverting matrix for splines.\n"); - - delete [] diag; - delete [] offdiag; - delete [] rhs; - return 1; - } - delete [] diag; - delete [] offdiag; - delete [] rhs; - return 0; -} // cyc_spline() - -/* ---------------------------------------------------------------------- */ - -// cyc_splint(): Evaluates a spline at position x, with n control -// points located at xa[], ya[], and with parameters y2a[] -// The xa[] must be monotonically increasing and their -// range should not exceed period (ie xa[n-1] < xa[0] + period). -// x must lie in the range: [(xa[n-1]-period), (xa[0]+period)] -// "period" is typically 2*PI. -static double cyc_splint(double const *xa, - double const *ya, - double const *y2a, - int n, - double period, - double x) -{ - int klo = -1; - int khi = n; - int k; - double xlo = xa[n-1] - period; - double xhi = xa[0] + period; - while (khi-klo > 1) { - k = (khi+klo) >> 1; //(k=(khi+klo)/2) - if (xa[k] > x) { - khi = k; - xhi = xa[k]; - } - else { - klo = k; - xlo = xa[k]; - } - } - - if (khi == n) khi = 0; - if (klo ==-1) klo = n-1; - - double h = xhi-xlo; - double a = (xhi-x) / h; - double b = (x-xlo) / h; - double y = a*ya[klo] + b*ya[khi] + - ((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0; - - return y; - -} // cyc_splint() - - -static double cyc_lin(double const *xa, - double const *ya, - int n, - double period, - double x) -{ - int klo = -1; - int khi = n; - int k; - double xlo = xa[n-1] - period; - double xhi = xa[0] + period; - while (khi-klo > 1) { - k = (khi+klo) >> 1; //(k=(khi+klo)/2) - if (xa[k] > x) { - khi = k; - xhi = xa[k]; - } - else { - klo = k; - xlo = xa[k]; - } - } - - if (khi == n) khi = 0; - if (klo ==-1) klo = n-1; - - double h = xhi-xlo; - double a = (xhi-x) / h; - double b = (x-xlo) / h; - double y = a*ya[klo] + b*ya[khi]; - - return y; - -} // cyc_lin() - - - // cyc_splintD(): Evaluate the deriviative of a cyclic spline at position x, // with n control points at xa[], ya[], with parameters y2a[]. @@ -405,35 +134,26 @@ static double cyc_splintD(double const *xa, } // cyc_splintD() +// -------------------------------------------- +// ------- Calculate the dihedral angle ------- +// -------------------------------------------- +static const int g_dim=3; /* ---------------------------------------------------------------------- */ -DihedralTableCut::DihedralTableCut(LAMMPS *lmp) : Dihedral(lmp) +DihedralTableCut::DihedralTableCut(LAMMPS *lmp) : DihedralTable(lmp) { if (lmp->citeme) lmp->citeme->add(cite_dihedral_tablecut); - ntables = 0; - tables = nullptr; - checkU_fname = checkF_fname = nullptr; + aat_k = aat_theta0_1 = aat_theta0_2 = nullptr; } /* ---------------------------------------------------------------------- */ DihedralTableCut::~DihedralTableCut() { - if (allocated) { - memory->destroy(aat_k); - memory->destroy(aat_theta0_1); - memory->destroy(aat_theta0_2); - - for (int m = 0; m < ntables; m++) free_table(&tables[m]); - memory->sfree(tables); - memory->sfree(checkU_fname); - memory->sfree(checkF_fname); - - memory->destroy(setflag); - memory->destroy(tabindex); - - } + memory->destroy(aat_k); + memory->destroy(aat_theta0_1); + memory->destroy(aat_theta0_2); } /* ---------------------------------------------------------------------- */ @@ -702,7 +422,7 @@ void DihedralTableCut::compute(int eflag, int vflag) for (i = 0; i < 4; i++) for (j = 0; j < 3; j++) - fabcd[i][j] -= - gt*gtt*fpphi*dphidr[i][j] + fabcd[i][j] -= gt*gtt*fpphi*dphidr[i][j] - gt*gptt*fphi*dthetadr[1][i][j] + gpt*gtt*fphi*dthetadr[0][i][j]; // apply force to each of 4 atoms @@ -751,35 +471,7 @@ void DihedralTableCut::allocate() memory->create(tabindex,n+1,"dihedral:tabindex"); memory->create(setflag,n+1,"dihedral:setflag"); - - for (int i = 1; i <= n; i++) - setflag[i] = 0; -} - -void DihedralTableCut::settings(int narg, char **arg) -{ - if (narg != 2) error->all(FLERR,"Illegal dihedral_style command"); - - if (strcmp(arg[0],"linear") == 0) tabstyle = LINEAR; - else if (strcmp(arg[0],"spline") == 0) tabstyle = SPLINE; - else error->all(FLERR,"Unknown table style in dihedral style table_cut"); - - tablength = utils::inumeric(FLERR,arg[1],false,lmp); - if (tablength < 3) - error->all(FLERR,"Illegal number of dihedral table entries"); - // delete old tables, since cannot just change settings - - for (int m = 0; m < ntables; m++) free_table(&tables[m]); - memory->sfree(tables); - - if (allocated) { - memory->destroy(setflag); - memory->destroy(tabindex); - } - allocated = 0; - - ntables = 0; - tables = nullptr; + for (int i = 1; i <= n; i++) setflag[i] = 0; } /* ---------------------------------------------------------------------- @@ -790,9 +482,9 @@ void DihedralTableCut::settings(int narg, char **arg) void DihedralTableCut::coeff(int narg, char **arg) { - if (narg != 7) error->all(FLERR,"Incorrect args for dihedral coefficients"); if (!allocated) allocate(); + int ilo,ihi; utils::bounds(FLERR,arg[0],1,atom->ndihedraltypes,ilo,ihi,error); @@ -820,29 +512,19 @@ void DihedralTableCut::coeff(int narg, char **arg) // --- check the angle data for range errors --- // --- and resolve issues with periodicity --- - if (tb->ninput < 2) { - string err_msg; - err_msg = string("Invalid dihedral table length (") - + string(arg[5]) + string(")."); - error->one(FLERR,err_msg); - } - else if ((tb->ninput == 2) && (tabstyle == SPLINE)) { - string err_msg; - err_msg = string("Invalid dihedral spline table length. (Try linear)\n (") - + string(arg[5]) + string(")."); - error->one(FLERR,err_msg); - } + if (tb->ninput < 2) + error->all(FLERR,fmt::format("Invalid dihedral table length: {}",arg[5])); + else if ((tb->ninput == 2) && (tabstyle == SPLINE)) + error->all(FLERR,fmt::format("Invalid dihedral spline table length: {} " + "(Try linear)",arg[5])); // check for monotonicity for (int i=0; i < tb->ninput-1; i++) { if (tb->phifile[i] >= tb->phifile[i+1]) { - stringstream i_str; - i_str << i+1; - string err_msg = - string("Dihedral table values are not increasing (") + - string(arg[5]) + string(", ")+i_str.str()+string("th entry)"); + auto err_msg =fmt::format("Dihedral table values are not increasing " + "({}, entry {})",arg[5],i+1); if (i==0) - err_msg += string("\n(This is probably a mistake with your table format.)\n"); + err_msg += "\n(This is probably a mistake with your table format.)\n"; error->all(FLERR,err_msg); } } @@ -851,20 +533,13 @@ void DihedralTableCut::coeff(int narg, char **arg) double philo = tb->phifile[0]; double phihi = tb->phifile[tb->ninput-1]; if (tb->use_degrees) { - if ((phihi - philo) >= 360) { - string err_msg; - err_msg = string("Dihedral table angle range must be < 360 degrees (") - +string(arg[5]) + string(")."); - error->all(FLERR,err_msg); - } - } - else { - if ((phihi - philo) >= MY_2PI) { - string err_msg; - err_msg = string("Dihedral table angle range must be < 2*PI radians (") - + string(arg[5]) + string(")."); - error->all(FLERR,err_msg); - } + if ((phihi - philo) >= 360) + error->all(FLERR,fmt::format("Dihedral table angle range must be < 360 " + "degrees ({})",arg[5])); + } else { + if ((phihi - philo) >= MY_2PI) + error->all(FLERR,fmt::format("Dihedral table angle range must be < 2*PI " + "radians ({})",arg[5])); } // convert phi from degrees to radians @@ -932,10 +607,9 @@ void DihedralTableCut::coeff(int narg, char **arg) // Optional: allow the user to print out the interpolated spline tables if (me == 0) { - if (checkU_fname && (strlen(checkU_fname) != 0)) - { - ofstream checkU_file; - checkU_file.open(checkU_fname, ios::out); + if (!checkU_fname.empty()) { + std::ofstream checkU_file; + checkU_file.open(checkU_fname, std::ios::out); for (int i=0; i < tablength; i++) { double phi = i*MY_2PI/tablength; double u = tb->e[i]; @@ -945,12 +619,10 @@ void DihedralTableCut::coeff(int narg, char **arg) } checkU_file.close(); } - if (checkF_fname && (strlen(checkF_fname) != 0)) - { - ofstream checkF_file; - checkF_file.open(checkF_fname, ios::out); - for (int i=0; i < tablength; i++) - { + if (!checkF_fname.empty()) { + std::ofstream checkF_file; + checkF_file.open(checkF_fname, std::ios::out); + for (int i=0; i < tablength; i++) { double phi = i*MY_2PI/tablength; double f; if ((tabstyle == SPLINE) && (tb->f_unspecified)) { @@ -992,429 +664,3 @@ void DihedralTableCut::coeff(int narg, char **arg) if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients"); } - -/* ---------------------------------------------------------------------- - proc 0 writes out coeffs to restart file -------------------------------------------------------------------------- */ - -void DihedralTableCut::write_restart(FILE *fp) -{ - write_restart_settings(fp); -} - -/* ---------------------------------------------------------------------- - proc 0 reads coeffs from restart file, bcasts them -------------------------------------------------------------------------- */ - -void DihedralTableCut::read_restart(FILE *fp) -{ - read_restart_settings(fp); - allocate(); -} - -/* ---------------------------------------------------------------------- - proc 0 writes out coeffs to restart file -------------------------------------------------------------------------- */ - -void DihedralTableCut::write_restart_settings(FILE *fp) -{ - fwrite(&tabstyle,sizeof(int),1,fp); - fwrite(&tablength,sizeof(int),1,fp); -} - -/* ---------------------------------------------------------------------- - proc 0 reads coeffs from restart file, bcasts them -------------------------------------------------------------------------- */ - -void DihedralTableCut::read_restart_settings(FILE *fp) -{ - if (comm->me == 0) { - utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,nullptr,error); - utils::sfread(FLERR,&tablength,sizeof(int),1,fp,nullptr,error); - } - - MPI_Bcast(&tabstyle,1,MPI_INT,0,world); - MPI_Bcast(&tablength,1,MPI_INT,0,world); -} - -/* ---------------------------------------------------------------------- */ - -void DihedralTableCut::null_table(Table *tb) -{ - tb->phifile = tb->efile = tb->ffile = nullptr; - tb->e2file = tb->f2file = nullptr; - tb->phi = tb->e = tb->de = nullptr; - tb->f = tb->df = tb->e2 = tb->f2 = nullptr; -} - -/* ---------------------------------------------------------------------- */ - -void DihedralTableCut::free_table(Table *tb) -{ - memory->destroy(tb->phifile); - memory->destroy(tb->efile); - memory->destroy(tb->ffile); - memory->destroy(tb->e2file); - memory->destroy(tb->f2file); - - memory->destroy(tb->phi); - memory->destroy(tb->e); - memory->destroy(tb->de); - memory->destroy(tb->f); - memory->destroy(tb->df); - memory->destroy(tb->e2); - memory->destroy(tb->f2); -} - -/* ---------------------------------------------------------------------- - read table file, only called by proc 0 -------------------------------------------------------------------------- */ - -static const int MAXLINE=2048; - -void DihedralTableCut::read_table(Table *tb, char *file, char *keyword) -{ - char line[MAXLINE]; - - // open file - - FILE *fp = utils::open_potential(file,lmp,nullptr); - if (fp == nullptr) { - string err_msg = string("Cannot open file ") + string(file); - error->one(FLERR,err_msg); - } - - // loop until section found with matching keyword - - while (1) { - if (fgets(line,MAXLINE,fp) == nullptr) { - string err_msg=string("Did not find keyword \"") - +string(keyword)+string("\" in dihedral table file."); - error->one(FLERR, err_msg); - } - if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line - if (line[0] == '#') continue; // comment - char *word = strtok(line," \t\n\r"); - if (strcmp(word,keyword) == 0) break; // matching keyword - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section - param_extract(tb,line); - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); - for (int i = 0; i < tb->ninput; i++) - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); - } - - // read args on 2nd line of section - // allocate table arrays for file values - - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); - param_extract(tb,line); - memory->create(tb->phifile,tb->ninput,"dihedral:phifile"); - memory->create(tb->efile,tb->ninput,"dihedral:efile"); - memory->create(tb->ffile,tb->ninput,"dihedral:ffile"); - - // read a,e,f table values from file - - int itmp; - for (int i = 0; i < tb->ninput; i++) { - // Read the next line. Make sure the file is long enough. - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); - - // Skip blank lines and delete text following a '#' character - char *pe = strchr(line, '#'); - if (pe != nullptr) *pe = '\0'; //terminate string at '#' character - char *pc = line; - while ((*pc != '\0') && isspace(*pc)) - pc++; - if (*pc != '\0') { //If line is not a blank line - stringstream line_ss(line); - if (tb->f_unspecified) { - line_ss >> itmp; - line_ss >> tb->phifile[i]; - line_ss >> tb->efile[i]; - } else { - line_ss >> itmp; - line_ss >> tb->phifile[i]; - line_ss >> tb->efile[i]; - line_ss >> tb->ffile[i]; - } - if (! line_ss) { - stringstream err_msg; - err_msg << "Read error in table "<< keyword<<", near line "<f_unspecified) && (i==0)) - err_msg << "\n (This sometimes occurs if users forget to specify the \"NOF\" option.)\n"; - error->one(FLERR, err_msg.str().c_str()); - } - } else //if it is a blank line, then skip it. - i--; - } //for (int i = 0; (i < tb->ninput) && fp; i++) { - - fclose(fp); -} - -/* ---------------------------------------------------------------------- - build spline representation of e,f over entire range of read-in table - this function sets these values in e2file,f2file. - I also perform a crude check for force & energy consistency. -------------------------------------------------------------------------- */ - -void DihedralTableCut::spline_table(Table *tb) -{ - memory->create(tb->e2file,tb->ninput,"dihedral:e2file"); - memory->create(tb->f2file,tb->ninput,"dihedral:f2file"); - - if (cyc_spline(tb->phifile, tb->efile, tb->ninput, - MY_2PI,tb->e2file,comm->me == 0)) - error->one(FLERR,"Error computing dihedral spline tables"); - - if (! tb->f_unspecified) { - if (cyc_spline(tb->phifile, tb->ffile, tb->ninput, - MY_2PI, tb->f2file, comm->me == 0)) - error->one(FLERR,"Error computing dihedral spline tables"); - } - - // CHECK to help make sure the user calculated forces in a way - // which is grossly numerically consistent with the energy table. - if (! tb->f_unspecified) { - int num_disagreements = 0; - for (int i=0; ininput; i++) { - - // Calculate what the force should be at the control points - // by using linear interpolation of the derivatives of the energy: - - double phi_i = tb->phifile[i]; - - // First deal with periodicity - double phi_im1, phi_ip1; - int im1 = i-1; - if (im1 < 0) { - im1 += tb->ninput; - phi_im1 = tb->phifile[im1] - MY_2PI; - } - else - phi_im1 = tb->phifile[im1]; - int ip1 = i+1; - if (ip1 >= tb->ninput) { - ip1 -= tb->ninput; - phi_ip1 = tb->phifile[ip1] + MY_2PI; - } - else - phi_ip1 = tb->phifile[ip1]; - - // Now calculate the midpoints above and below phi_i = tb->phifile[i] - double phi_lo= 0.5*(phi_im1 + phi_i); //midpoint between phi_im1 and phi_i - double phi_hi= 0.5*(phi_i + phi_ip1); //midpoint between phi_i and phi_ip1 - - // Use a linear approximation to the derivative at these two midpoints - double dU_dphi_lo = - (tb->efile[i] - tb->efile[im1]) - / - (phi_i - phi_im1); - double dU_dphi_hi = - (tb->efile[ip1] - tb->efile[i]) - / - (phi_ip1 - phi_i); - - // Now calculate the derivative at position - // phi_i (=tb->phifile[i]) using linear interpolation - - double a = (phi_i - phi_lo) / (phi_hi - phi_lo); - double b = (phi_hi - phi_i) / (phi_hi - phi_lo); - double dU_dphi = a*dU_dphi_lo + b*dU_dphi_hi; - double f = -dU_dphi; - // Alternately, we could use spline interpolation instead: - // double f = - splintD(tb->phifile, tb->efile, tb->e2file, - // tb->ninput, MY_2PI, tb->phifile[i]); - // This is the way I originally did it, but I trust - // the ugly simple linear way above better. - // Recall this entire block of code doess not calculate - // anything important. It does not have to be perfect. - // We are only checking for stupid user errors here. - - if ((f != 0.0) && - (tb->ffile[i] != 0.0) && - ((f/tb->ffile[i] < 0.5) || (f/tb->ffile[i] > 2.0))) { - num_disagreements++; - } - } // for (int i=0; ininput; i++) - - if ((num_disagreements > tb->ninput/2) && (num_disagreements > 2)) { - string msg("Dihedral table has inconsistent forces and energies. (Try \"NOF\".)\n"); - error->all(FLERR,msg.c_str()); - } - - } // check for consistency if (! tb->f_unspecified) - -} // DihedralTable::spline_table() - - -/* ---------------------------------------------------------------------- - compute a,e,f vectors from splined values -------------------------------------------------------------------------- */ - -void DihedralTableCut::compute_table(Table *tb) -{ - //delta = table spacing in dihedral angle for tablength (cyclic) bins - tb->delta = MY_2PI / tablength; - tb->invdelta = 1.0/tb->delta; - tb->deltasq6 = tb->delta*tb->delta / 6.0; - - // N evenly spaced bins in dihedral angle from 0 to 2*PI - // phi,e,f = value at lower edge of bin - // de,df values = delta values of e,f (cyclic, in this case) - // phi,e,f,de,df are arrays containing "tablength" number of entries - - memory->create(tb->phi,tablength,"dihedral:phi"); - memory->create(tb->e,tablength,"dihedral:e"); - memory->create(tb->de,tablength,"dihedral:de"); - memory->create(tb->f,tablength,"dihedral:f"); - memory->create(tb->df,tablength,"dihedral:df"); - memory->create(tb->e2,tablength,"dihedral:e2"); - memory->create(tb->f2,tablength,"dihedral:f2"); - - if (tabstyle == SPLINE) { - // Use cubic spline interpolation to calculate the entries in the - // internal table. (This is true regardless...even if tabstyle!=SPLINE.) - for (int i = 0; i < tablength; i++) { - double phi = i*tb->delta; - tb->phi[i] = phi; - tb->e[i]= cyc_splint(tb->phifile,tb->efile,tb->e2file,tb->ninput,MY_2PI,phi); - if (! tb->f_unspecified) - tb->f[i] = cyc_splint(tb->phifile,tb->ffile,tb->f2file,tb->ninput,MY_2PI,phi); - } - } // if (tabstyle == SPLINE) - else if (tabstyle == LINEAR) { - if (! tb->f_unspecified) { - for (int i = 0; i < tablength; i++) { - double phi = i*tb->delta; - tb->phi[i] = phi; - tb->e[i]= cyc_lin(tb->phifile,tb->efile,tb->ninput,MY_2PI,phi); - tb->f[i]= cyc_lin(tb->phifile,tb->ffile,tb->ninput,MY_2PI,phi); - } - } - else { - for (int i = 0; i < tablength; i++) { - double phi = i*tb->delta; - tb->phi[i] = phi; - tb->e[i]= cyc_lin(tb->phifile,tb->efile,tb->ninput,MY_2PI,phi); - } - // In the linear case, if the user did not specify the forces, then we - // must generate the "f" array. Do this using linear interpolation - // of the e array (which itself was generated above) - for (int i = 0; i < tablength; i++) { - int im1 = i-1; if (im1 < 0) im1 += tablength; - int ip1 = i+1; if (ip1 >= tablength) ip1 -= tablength; - double dedx = (tb->e[ip1] - tb->e[im1]) / (2.0 * tb->delta); - // (This is the average of the linear slopes on either side of the node. - // Note that the nodes in the internal table are evenly spaced.) - tb->f[i] = -dedx; - } - } - - - // Fill the linear interpolation tables (de, df) - for (int i = 0; i < tablength; i++) { - int ip1 = i+1; if (ip1 >= tablength) ip1 -= tablength; - tb->de[i] = tb->e[ip1] - tb->e[i]; - tb->df[i] = tb->f[ip1] - tb->f[i]; - } - } // else if (tabstyle == LINEAR) - - - - cyc_spline(tb->phi, tb->e, tablength, MY_2PI, tb->e2, comm->me == 0); - if (! tb->f_unspecified) - cyc_spline(tb->phi, tb->f, tablength, MY_2PI, tb->f2, comm->me == 0); -} - - -/* ---------------------------------------------------------------------- - extract attributes from parameter line in table section - format of line: N value NOF DEGREES RADIANS - N is required, other params are optional -------------------------------------------------------------------------- */ - -void DihedralTableCut::param_extract(Table *tb, char *line) -{ - //tb->theta0 = 180.0; <- equilibrium angles not supported - tb->ninput = 0; - tb->f_unspecified = false; //default - tb->use_degrees = true; //default - - char *word = strtok(line," \t\n\r\f"); - while (word) { - if (strcmp(word,"N") == 0) { - word = strtok(nullptr," \t\n\r\f"); - tb->ninput = atoi(word); - } - else if (strcmp(word,"NOF") == 0) { - tb->f_unspecified = true; - } - else if ((strcmp(word,"DEGREES") == 0) || (strcmp(word,"degrees") == 0)) { - tb->use_degrees = true; - } - else if ((strcmp(word,"RADIANS") == 0) || (strcmp(word,"radians") == 0)) { - tb->use_degrees = false; - } - else if (strcmp(word,"CHECKU") == 0) { - word = strtok(nullptr," \t\n\r\f"); - memory->sfree(checkU_fname); - memory->create(checkU_fname,strlen(word)+1,"dihedral_table:checkU"); - strcpy(checkU_fname, word); - } - else if (strcmp(word,"CHECKF") == 0) { - word = strtok(nullptr," \t\n\r\f"); - memory->sfree(checkF_fname); - memory->create(checkF_fname,strlen(word)+1,"dihedral_table:checkF"); - strcpy(checkF_fname, word); - } - // COMMENTING OUT: equilibrium angles are not supported - //else if (strcmp(word,"EQ") == 0) { - // word = strtok(nullptr," \t\n\r\f"); - // tb->theta0 = atof(word); - //} - else { - string err_msg("Invalid keyword in dihedral angle table parameters"); - err_msg += string(" (") + string(word) + string(")"); - error->one(FLERR, err_msg); - } - word = strtok(nullptr," \t\n\r\f"); - } - - if (tb->ninput == 0) - error->one(FLERR,"Dihedral table parameters did not set N"); - -} // DihedralTable::param_extract() - - -/* ---------------------------------------------------------------------- - broadcast read-in table info from proc 0 to other procs - this function communicates these values in Table: - ninput,phifile,efile,ffile, - f_unspecified,use_degrees -------------------------------------------------------------------------- */ - -void DihedralTableCut::bcast_table(Table *tb) -{ - MPI_Bcast(&tb->ninput,1,MPI_INT,0,world); - - int me; - MPI_Comm_rank(world,&me); - if (me > 0) { - memory->create(tb->phifile,tb->ninput,"dihedral:phifile"); - memory->create(tb->efile,tb->ninput,"dihedral:efile"); - memory->create(tb->ffile,tb->ninput,"dihedral:ffile"); - } - - MPI_Bcast(tb->phifile,tb->ninput,MPI_DOUBLE,0,world); - MPI_Bcast(tb->efile,tb->ninput,MPI_DOUBLE,0,world); - MPI_Bcast(tb->ffile,tb->ninput,MPI_DOUBLE,0,world); - - MPI_Bcast(&tb->f_unspecified,1,MPI_INT,0,world); - MPI_Bcast(&tb->use_degrees,1,MPI_INT,0,world); - - // COMMENTING OUT: equilibrium angles are not supported - //MPI_Bcast(&tb->theta0,1,MPI_DOUBLE,0,world); -} - - diff --git a/src/USER-MISC/dihedral_table_cut.h b/src/USER-MISC/dihedral_table_cut.h index b07e925f08..b956069e14 100644 --- a/src/USER-MISC/dihedral_table_cut.h +++ b/src/USER-MISC/dihedral_table_cut.h @@ -20,131 +20,21 @@ DihedralStyle(table/cut,DihedralTableCut) #ifndef LMP_DIHEDRAL_TABLE_CUT_H #define LMP_DIHEDRAL_TABLE_CUT_H -#include "dihedral.h" +#include "dihedral_table.h" namespace LAMMPS_NS { -class DihedralTableCut : public Dihedral { +class DihedralTableCut : public DihedralTable { public: DihedralTableCut(class LAMMPS *); virtual ~DihedralTableCut(); virtual void compute(int, int); - void settings(int, char **); - void coeff(int, char **); - void write_restart(FILE *); - void read_restart(FILE *); - void write_restart_settings(FILE *); - void read_restart_settings(FILE *); + virtual void coeff(int, char **); protected: double *aat_k,*aat_theta0_1,*aat_theta0_2; - void allocate(); - - int tabstyle,tablength; - char *checkU_fname; - char *checkF_fname; - - struct Table { - int ninput; - int f_unspecified; // boolean (but MPI does not like type "bool") - int use_degrees; // boolean (but MPI does not like type "bool") - double *phifile,*efile,*ffile; - double *e2file,*f2file; - double delta,invdelta,deltasq6; - double *phi,*e,*de,*f,*df,*e2,*f2; - }; - - int ntables; - Table *tables; - int *tabindex; - - void null_table(Table *); - void free_table(Table *); - void read_table(Table *, char *, char *); - void bcast_table(Table *); - void spline_table(Table *); - void compute_table(Table *); - - void param_extract(Table *, char *); - - // -------------------------------------------- - // ------------ inline functions -------------- - // -------------------------------------------- - - // ----------------------------------------------------------- - // uf_lookup() - // quickly calculate the potential u and force f at angle x, - // using the internal tables tb->e and tb->f (evenly spaced) - // ----------------------------------------------------------- - enum{LINEAR,SPLINE}; - - inline void uf_lookup(int type, double x, double &u, double &f) - { - Table *tb = &tables[tabindex[type]]; - double x_over_delta = x*tb->invdelta; - int i = static_cast (x_over_delta); - double a; - double b = x_over_delta - i; - // Apply periodic boundary conditions to indices i and i+1 - if (i >= tablength) i -= tablength; - int ip1 = i+1; if (ip1 >= tablength) ip1 -= tablength; - - switch(tabstyle) { - case LINEAR: - u = tb->e[i] + b * tb->de[i]; - f = -(tb->f[i] + b * tb->df[i]); //<--works even if tb->f_unspecified==true - break; - case SPLINE: - a = 1.0 - b; - u = a * tb->e[i] + b * tb->e[ip1] + - ((a*a*a-a)*tb->e2[i] + (b*b*b-b)*tb->e2[ip1]) * - tb->deltasq6; - if (tb->f_unspecified) - //Formula below taken from equation3.3.5 of "numerical recipes in c" - //"f"=-derivative of e with respect to x (or "phi" in this case) - f = -((tb->e[i]-tb->e[ip1])*tb->invdelta + - ((3.0*a*a-1.0)*tb->e2[i]+(1.0-3.0*b*b)*tb->e2[ip1])*tb->delta/6.0); - else - f = -(a * tb->f[i] + b * tb->f[ip1] + - ((a*a*a-a)*tb->f2[i] + (b*b*b-b)*tb->f2[ip1]) * - tb->deltasq6); - break; - } // switch(tabstyle) - } // uf_lookup() - - - // ---------------------------------------------------------- - // u_lookup() - // quickly calculate the potential u at angle x using tb->e - //----------------------------------------------------------- - - inline void u_lookup(int type, double x, double &u) - { - Table *tb = &tables[tabindex[type]]; - int N = tablength; - - // i = static_cast ((x - tb->lo) * tb->invdelta); <-general version - double x_over_delta = x*tb->invdelta; - int i = static_cast (x_over_delta); - double b = x_over_delta - i; - - // Apply periodic boundary conditions to indices i and i+1 - if (i >= N) i -= N; - int ip1 = i+1; if (ip1 >= N) ip1 -= N; - - if (tabstyle == LINEAR) { - u = tb->e[i] + b * tb->de[i]; - } - else if (tabstyle == SPLINE) { - double a = 1.0 - b; - u = a * tb->e[i] + b * tb->e[ip1] + - ((a*a*a-a)*tb->e2[i] + (b*b*b-b)*tb->e2[ip1]) * - tb->deltasq6; - } - } // u_lookup() - - + virtual void allocate(); }; } From 1e3f1c584c569601efef6111babd3b3302dde656 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Mar 2021 08:12:37 -0400 Subject: [PATCH 0284/1217] simplify by using utils::strdup() fmt::format() and reorder includes --- src/USER-MISC/fix_orient_eco.cpp | 4 +- src/USER-MISC/fix_pafi.cpp | 4 +- src/USER-MISC/fix_wall_region_ees.cpp | 5 +-- src/USER-MISC/temper_grem.cpp | 26 ++++++------ src/USER-MOLFILE/dump_molfile.cpp | 11 ++--- src/USER-PHONON/fix_phonon.cpp | 61 +++++++++++---------------- src/USER-PLUMED/fix_plumed.cpp | 27 +++++------- src/USER-PTM/compute_ptm_atom.cpp | 11 ++--- src/USER-QTB/fix_qbmsst.cpp | 20 ++++----- src/USER-QTB/fix_qtb.cpp | 24 +++++------ src/USER-QUIP/pair_quip.cpp | 37 +++++++--------- src/USER-REACTION/fix_bond_react.cpp | 48 +++++---------------- src/USER-REAXC/fix_qeq_reax.cpp | 28 ++++++------ src/USER-REAXC/fix_reaxc_species.cpp | 19 +++++---- src/USER-SCAFACOS/scafacos.cpp | 17 ++++---- src/USER-SMD/fix_smd_setvel.cpp | 16 ++----- src/USER-SMD/fix_smd_wall_surface.cpp | 38 +++-------------- src/USER-SMD/fix_smd_wall_surface.h | 1 - 18 files changed, 151 insertions(+), 246 deletions(-) diff --git a/src/USER-MISC/fix_orient_eco.cpp b/src/USER-MISC/fix_orient_eco.cpp index ce412e6fc9..3d6db4cd4f 100644 --- a/src/USER-MISC/fix_orient_eco.cpp +++ b/src/USER-MISC/fix_orient_eco.cpp @@ -87,9 +87,7 @@ FixOrientECO::FixOrientECO(LAMMPS *lmp, int narg, char **arg) : // read reference orientations from file // work on rank 0 only - int n = strlen(arg[6]) + 1; - dir_filename = new char[n]; - strcpy(dir_filename, arg[6]); + dir_filename = utils::strdup(arg[6]); if (me == 0) { char line[IMGMAX]; char *result; diff --git a/src/USER-MISC/fix_pafi.cpp b/src/USER-MISC/fix_pafi.cpp index ec0733657a..c2ad62d7d0 100644 --- a/src/USER-MISC/fix_pafi.cpp +++ b/src/USER-MISC/fix_pafi.cpp @@ -74,9 +74,7 @@ FixPAFI::FixPAFI(LAMMPS *lmp, int narg, char **arg) : com_flag = 1; time_integrate = 1; - int n = strlen(arg[3])+1; - computename = new char[n]; - strcpy(computename,&arg[3][0]); + computename = utils::strdup(&arg[3][0]); icompute = modify->find_compute(computename); if (icompute == -1) diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index 44067b0742..51e0af9dc4 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -52,10 +52,7 @@ FixWallRegionEES::FixWallRegionEES(LAMMPS *lmp, int narg, char **arg) : iregion = domain->find_region(arg[3]); if (iregion == -1) error->all(FLERR,"Region ID for fix wall/region/ees does not exist"); - int n = strlen(arg[3]) + 1; - idregion = new char[n]; - strcpy(idregion,arg[3]); - + idregion = utils::strdup(arg[3]); epsilon = utils::numeric(FLERR,arg[4],false,lmp); sigma = utils::numeric(FLERR,arg[5],false,lmp); cutoff = utils::numeric(FLERR,arg[6],false,lmp); diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp index ee3c5ae5e4..3b987aaad2 100644 --- a/src/USER-MISC/temper_grem.cpp +++ b/src/USER-MISC/temper_grem.cpp @@ -16,21 +16,23 @@ ------------------------------------------------------------------------- */ #include "temper_grem.h" -#include -#include -#include "fix_grem.h" -#include "universe.h" + +#include "compute.h" #include "domain.h" -#include "update.h" +#include "error.h" +#include "finish.h" +#include "fix.h" +#include "fix_grem.h" +#include "force.h" #include "integrate.h" #include "modify.h" -#include "compute.h" -#include "force.h" -#include "fix.h" #include "random_park.h" -#include "finish.h" #include "timer.h" -#include "error.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; @@ -90,9 +92,7 @@ void TemperGrem::command(int narg, char **arg) double pressref = 0; // Get and check for nh fix - int n = strlen(arg[4])+1; - id_nh = new char[n]; - strcpy(id_nh,arg[4]); + id_nh = utils::strdup(arg[4]); int ifix = modify->find_fix(id_nh); if (ifix < 0) error->all(FLERR,"Fix id for nvt or npt fix does not exist"); diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/USER-MOLFILE/dump_molfile.cpp index 9de9a79e26..20790d4b32 100644 --- a/src/USER-MOLFILE/dump_molfile.cpp +++ b/src/USER-MOLFILE/dump_molfile.cpp @@ -17,15 +17,16 @@ #include "dump_molfile.h" -#include -#include -#include "domain.h" #include "atom.h" #include "comm.h" -#include "update.h" +#include "domain.h" +#include "error.h" #include "group.h" #include "memory.h" -#include "error.h" +#include "update.h" + +#include +#include #include "molfile_interface.h" diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp index 30fb7baad5..222f3fa1d2 100644 --- a/src/USER-PHONON/fix_phonon.cpp +++ b/src/USER-PHONON/fix_phonon.cpp @@ -23,21 +23,22 @@ konglt@sjtu.edu.cn; konglt@gmail.com ------------------------------------------------------------------------- */ +#include "fix_phonon.h" + +#include "atom.h" +#include "citeme.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "fft3d_wrap.h" +#include "force.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "update.h" #include #include -#include "fix_phonon.h" -#include "fft3d_wrap.h" -#include "atom.h" -#include "compute.h" -#include "domain.h" -#include "force.h" -#include "group.h" -#include "modify.h" -#include "update.h" -#include "citeme.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -77,15 +78,9 @@ FixPhonon::FixPhonon(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) waitsteps = utils::bnumeric(FLERR,arg[5],false,lmp); // Wait this many timesteps before actually measuring if (waitsteps < 0) error->all(FLERR,"Illegal fix phonon command: waitsteps < 0 !"); - int n = strlen(arg[6]) + 1; // map file - mapfile = new char[n]; - strcpy(mapfile, arg[6]); - - n = strlen(arg[7]) + 1; // prefix of output - prefix = new char[n]; - strcpy(prefix, arg[7]); - logfile = new char[n+4]; - sprintf(logfile,"%s.log",prefix); + mapfile = utils::strdup(arg[6]); + prefix = utils::strdup(arg[7]); + logfile = utils::strdup(std::string(prefix)+".log"); int sdim = sysdim = domain->dimension; int iarg = 8; @@ -184,11 +179,9 @@ FixPhonon::FixPhonon(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) // output some information on the system to log file if (me == 0) { flog = fopen(logfile, "w"); - if (flog == nullptr) { - char str[MAXLINE]; - sprintf(str,"Can not open output file %s",logfile); - error->one(FLERR,str); - } + if (flog == nullptr) + error->one(FLERR,fmt::format("Can not open output file {}: {}", + logfile,utils::getsyserror())); fprintf(flog,"############################################################\n"); fprintf(flog,"# group name of the atoms under study : %s\n", group->names[igroup]); fprintf(flog,"# total number of atoms in the group : %d\n", ngroup); @@ -440,9 +433,7 @@ int FixPhonon::modify_param(int narg, char **arg) if (strcmp(arg[0],"temp") == 0) { if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); delete [] id_temp; - int n = strlen(arg[1]) + 1; - id_temp = new char[n]; - strcpy(id_temp,arg[1]); + id_temp = utils::strdup(arg[1]); int icompute = modify->find_compute(id_temp); if (icompute < 0) error->all(FLERR,"Could not find fix_modify temp ID"); @@ -563,10 +554,9 @@ void FixPhonon::readmap() // read from map file for others char line[MAXLINE]; FILE *fp = fopen(mapfile, "r"); - if (fp == nullptr) { - sprintf(line,"Cannot open input map file %s", mapfile); - error->all(FLERR,line); - } + if (fp == nullptr) + error->all(FLERR,fmt::format("Cannot open input map file {}: {}", + mapfile, utils::getsyserror())); if (fgets(line,MAXLINE,fp) == nullptr) error->all(FLERR,"Error while reading header of mapping file!"); @@ -712,9 +702,8 @@ void FixPhonon::postprocess( ) // write binary file, in fact, it is the force constants matrix that is written // Enforcement of ASR and the conversion of dynamical matrix is done in the postprocessing code - char fname[MAXLINE]; - sprintf(fname,"%s.bin." BIGINT_FORMAT,prefix,update->ntimestep); - FILE *fp_bin = fopen(fname,"wb"); + auto fname = fmt::format("{}.bin.{}",prefix,update->ntimestep); + FILE *fp_bin = fopen(fname.c_str(),"wb"); fwrite(&sysdim, sizeof(int), 1, fp_bin); fwrite(&nx, sizeof(int), 1, fp_bin); diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/USER-PLUMED/fix_plumed.cpp index 1217237e19..8d3cdd5c34 100644 --- a/src/USER-PLUMED/fix_plumed.cpp +++ b/src/USER-PLUMED/fix_plumed.cpp @@ -16,25 +16,24 @@ Pablo Piaggi (EPFL) ------------------------------------------------------------------------- */ -#include - -#include +#include "fix_plumed.h" #include "atom.h" #include "comm.h" -#include "update.h" -#include "force.h" -#include "respa.h" +#include "compute.h" #include "domain.h" #include "error.h" +#include "force.h" #include "group.h" -#include "fix_plumed.h" -#include "universe.h" -#include "compute.h" #include "modify.h" #include "pair.h" - +#include "respa.h" #include "timer.h" +#include "universe.h" +#include "update.h" + +#include +#include #include "plumed/wrapper/Plumed.h" @@ -542,9 +541,7 @@ int FixPlumed::modify_param(int narg, char **arg) if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); modify->delete_compute(id_pe); delete[] id_pe; - int n = strlen(arg[1]) + 1; - id_pe = new char[n]; - strcpy(id_pe,arg[1]); + id_pe = utils::strdup(arg[1]); int icompute = modify->find_compute(arg[1]); if (icompute < 0) error->all(FLERR,"Could not find fix_modify potential energy ID"); @@ -561,9 +558,7 @@ int FixPlumed::modify_param(int narg, char **arg) if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); modify->delete_compute(id_press); delete[] id_press; - int n = strlen(arg[1]) + 1; - id_press = new char[n]; - strcpy(id_press,arg[1]); + id_press = utils::strdup(arg[1]); int icompute = modify->find_compute(arg[1]); if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID"); diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp index 376253dd84..0622b9dcc0 100644 --- a/src/USER-PTM/compute_ptm_atom.cpp +++ b/src/USER-PTM/compute_ptm_atom.cpp @@ -17,23 +17,24 @@ under ------------------------------------------------------------------------- */ #include "compute_ptm_atom.h" -#include -#include -#include -#include #include "atom.h" #include "citeme.h" #include "comm.h" #include "error.h" #include "force.h" +#include "group.h" #include "memory.h" #include "modify.h" #include "neigh_list.h" #include "neigh_request.h" #include "neighbor.h" #include "update.h" -#include "group.h" + +#include +#include +#include +#include #include "ptm_functions.h" diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp index 0b54811db0..a9dfb83f06 100644 --- a/src/USER-QTB/fix_qbmsst.cpp +++ b/src/USER-QTB/fix_qbmsst.cpp @@ -19,17 +19,17 @@ #include "fix_qbmsst.h" #include "atom.h" -#include "force.h" -#include "update.h" -#include "modify.h" +#include "comm.h" #include "compute.h" #include "domain.h" -#include "comm.h" -#include "random_mars.h" -#include "memory.h" #include "error.h" +#include "force.h" #include "kspace.h" #include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "random_mars.h" +#include "update.h" #include #include @@ -869,9 +869,7 @@ int FixQBMSST::modify_param(int narg, char **arg) tflag = 0; } delete [] id_temp; - int n = strlen(arg[1]) + 1; - id_temp = new char[n]; - strcpy(id_temp,arg[1]); + id_temp = utils::strdup(arg[1]); int icompute = modify->find_compute(id_temp); if (icompute < 0) error->all(FLERR,"Could not find fix_modify temperature ID"); @@ -891,9 +889,7 @@ int FixQBMSST::modify_param(int narg, char **arg) pflag = 0; } delete [] id_press; - int n = strlen(arg[1]) + 1; - id_press = new char[n]; - strcpy(id_press,arg[1]); + id_press = utils::strdup(arg[1]); int icompute = modify->find_compute(id_press); if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID"); diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp index 4c79fbeaae..e4e645a1bb 100644 --- a/src/USER-QTB/fix_qtb.cpp +++ b/src/USER-QTB/fix_qtb.cpp @@ -18,20 +18,20 @@ #include "fix_qtb.h" -#include -#include - #include "atom.h" -#include "force.h" -#include "update.h" -#include "modify.h" -#include "compute.h" -#include "respa.h" #include "comm.h" -#include "random_mars.h" +#include "compute.h" +#include "error.h" +#include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "random_mars.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -345,9 +345,7 @@ int FixQTB::modify_param(int narg, char **arg) if (strcmp(arg[0],"temp") == 0) { if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); delete [] id_temp; - int n = strlen(arg[1]) + 1; - id_temp = new char[n]; - strcpy(id_temp,arg[1]); + id_temp = utils::strdup(arg[1]); int icompute = modify->find_compute(id_temp); if (icompute < 0) error->all(FLERR,"Could not find fix_modify temperature ID"); diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp index f850925764..2d338da158 100644 --- a/src/USER-QUIP/pair_quip.cpp +++ b/src/USER-QUIP/pair_quip.cpp @@ -16,21 +16,21 @@ Aidan Thompson (Sandia, athomps@sandia.gov) ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_quip.h" + #include "atom.h" -#include "update.h" -#include "force.h" #include "comm.h" -#include "neighbor.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" -#include "domain.h" +#include "neighbor.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; @@ -252,24 +252,17 @@ void PairQUIP::coeff(int narg, char **arg) if (!allocated) allocate(); int n = atom->ntypes; - if (narg != (4+n)) { - char str[1024]; - sprintf(str,"Number of arguments %d is not correct, it should be %d", narg, 4+n); - error->all(FLERR,str); - } + if (narg != (4+n)) + error->all(FLERR,fmt::format("Number of arguments {} is not correct, " + "it should be {}", narg, 4+n)); // ensure I,J args are * * if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) error->all(FLERR,"Incorrect args for pair coefficients"); - n_quip_file = strlen(arg[2]); - quip_file = new char[n_quip_file+1]; - strcpy(quip_file,arg[2]); - - n_quip_string = strlen(arg[3]); - quip_string = new char[n_quip_string+1]; - strcpy(quip_string,arg[3]); + quip_file = utils::strdup(arg[2]); + quip_string = utils::strdup(arg[3]); for (int i = 4; i < narg; i++) { if (strcmp(arg[i],"NULL") == 0) diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 91354506d1..201949a874 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -169,9 +169,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[iarg+1],"yes") == 0) { if (iarg+4 > narg) error->all(FLERR,"Illegal fix bond/react command:" "'stabilization' keyword has too few arguments"); - int n = strlen(arg[iarg+2]) + 1; - exclude_group = new char[n]; - strcpy(exclude_group,arg[iarg+2]); + exclude_group = utils::strdup(arg[iarg+2]); stabilization_flag = 1; nve_limit_xmax = arg[iarg+3]; iarg += 4; @@ -273,9 +271,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : groupbits[rxn] = group->bitmask[groupid]; if (strncmp(arg[iarg],"v_",2) == 0) { - n = strlen(&arg[iarg][2]) + 1; - char *str = new char[n]; - strcpy(str,&arg[iarg][2]); + char *str = utils::strdup(&arg[iarg][2]); var_id[NEVERY][rxn] = input->variable->find(str); if (var_id[NEVERY][rxn] < 0) error->all(FLERR,"Bond/react: Variable name does not exist"); @@ -291,9 +287,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : iarg++; if (strncmp(arg[iarg],"v_",2) == 0) { - n = strlen(&arg[iarg][2]) + 1; - char *str = new char[n]; - strcpy(str,&arg[iarg][2]); + char *str = utils::strdup(&arg[iarg][2]); var_id[RMIN][rxn] = input->variable->find(str); if (var_id[RMIN][rxn] < 0) error->all(FLERR,"Bond/react: Variable name does not exist"); @@ -312,9 +306,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : iarg++; if (strncmp(arg[iarg],"v_",2) == 0) { - n = strlen(&arg[iarg][2]) + 1; - char *str = new char[n]; - strcpy(str,&arg[iarg][2]); + char *str = utils::strdup(&arg[iarg][2]); var_id[RMAX][rxn] = input->variable->find(str); if (var_id[RMAX][rxn] < 0) error->all(FLERR,"Bond/react: Variable name does not exist"); @@ -340,8 +332,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : "fix bond/react does not exist"); //read superimpose file - files[rxn] = new char[strlen(arg[iarg])+1]; - strcpy(files[rxn],arg[iarg]); + files[rxn] = utils::strdup(arg[iarg]); iarg++; while (iarg < narg && strcmp(arg[iarg],"react") != 0) { @@ -350,9 +341,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : "'prob' keyword has too few arguments"); // check if probability is a variable if (strncmp(arg[iarg+1],"v_",2) == 0) { - int n = strlen(&arg[iarg+1][2]) + 1; - char *str = new char[n]; - strcpy(str,&arg[iarg+1][2]); + char *str = utils::strdup(&arg[iarg+1][2]); var_id[PROB][rxn] = input->variable->find(str); if (var_id[PROB][rxn] < 0) error->all(FLERR,"Bond/react: Variable name does not exist"); @@ -727,21 +716,14 @@ void FixBondReact::post_constructor() fix3 = modify->fix[modify->nfix-1]; } - len = strlen("statted_tags") + 1; - statted_id = new char[len]; - strcpy(statted_id,"statted_tags"); + statted_id = utils::strdup("statted_tags"); // if static group exists, use as parent group // also, rename dynamic exclude_group by appending '_REACT' char *exclude_PARENT_group; - int n = strlen(exclude_group) + 1; - exclude_PARENT_group = new char[n]; - strcpy(exclude_PARENT_group,exclude_group); - n += strlen("_REACT"); + exclude_PARENT_group = utils::strdup(exclude_group); delete [] exclude_group; - exclude_group = new char[n]; - strcpy(exclude_group,exclude_PARENT_group); - strcat(exclude_group,"_REACT"); + exclude_group = utils::strdup(std::string(exclude_PARENT_group)+"_REACT"); group->find_or_create(exclude_group); if (groupid == -1) @@ -766,13 +748,8 @@ void FixBondReact::post_constructor() // sleeping code, for future capabilities custom_exclude_flag = 1; // first we have to find correct fix group reference - int n = strlen("GROUP_") + strlen(exclude_group) + 1; - char *fix_group = new char[n]; - strcpy(fix_group,"GROUP_"); - strcat(fix_group,exclude_group); - int ifix = modify->find_fix(fix_group); + int ifix = modify->find_fix(std::string("GROUP_")+exclude_group); Fix *fix = modify->fix[ifix]; - delete [] fix_group; // this returns names of corresponding property int unused; @@ -780,10 +757,7 @@ void FixBondReact::post_constructor() idprop = (char *) fix->extract("property",unused); if (idprop == nullptr) error->all(FLERR,"Exclude group must be a per-atom property group"); - - len = strlen(idprop) + 1; - statted_id = new char[len]; - strcpy(statted_id,idprop); + statted_id = utils::strdup(idprop); // initialize per-atom statted_tags to 1 // need to correct for smooth restarts diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index 355cbbb770..44088043f0 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -20,22 +20,24 @@ #include "fix_qeq_reax.h" -#include -#include -#include "pair_reaxc.h" #include "atom.h" +#include "citeme.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" +#include "error.h" #include "force.h" #include "group.h" -#include "pair.h" -#include "respa.h" #include "memory.h" -#include "citeme.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "pair_reaxc.h" +#include "respa.h" +#include "update.h" + +#include +#include + #include "reaxc_defs.h" #include "reaxc_types.h" @@ -70,9 +72,7 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) : swa = utils::numeric(FLERR,arg[4],false,lmp); swb = utils::numeric(FLERR,arg[5],false,lmp); tolerance = utils::numeric(FLERR,arg[6],false,lmp); - int len = strlen(arg[7]) + 1; - pertype_option = new char[len]; - strcpy(pertype_option,arg[7]); + pertype_option = utils::strdup(arg[7]); // dual CG support only available for USER-OMP variant // check for compatibility is in Fix::post_constructor() diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp index e90cde2529..81b1dafa61 100644 --- a/src/USER-REAXC/fix_reaxc_species.cpp +++ b/src/USER-REAXC/fix_reaxc_species.cpp @@ -18,20 +18,21 @@ #include "fix_reaxc_species.h" - -#include -#include "fix_ave_atom.h" #include "atom.h" -#include "domain.h" -#include "update.h" -#include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix_ave_atom.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" #include "pair_reaxc.h" +#include "update.h" + +#include + #include "reaxc_defs.h" using namespace LAMMPS_NS; diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index 0ce027ec1e..fa12cffe4c 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -15,21 +15,22 @@ Contributing author: Rene Halver (JSC) ------------------------------------------------------------------------- */ -#include -#include -#include #include "scafacos.h" + #include "atom.h" #include "comm.h" #include "domain.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" + +#include +#include +#include +#include // ScaFaCoS library -#include -#include #include "fcs.h" using namespace LAMMPS_NS; @@ -54,9 +55,7 @@ void Scafacos::settings(int narg, char **arg) { if (narg != 2) error->all(FLERR,"Illegal scafacos command"); - int n = strlen(arg[0]) + 1; - method = new char[n]; - strcpy(method,arg[0]); + method = utils::strdup(arg[0]); tolerance = utils::numeric(FLERR,arg[1],false,lmp); // optional ScaFaCoS library setting defaults diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp index f4c23e9f7a..471159ea53 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/USER-SMD/fix_smd_setvel.cpp @@ -60,9 +60,7 @@ FixSMDSetVel::FixSMDSetVel(LAMMPS *lmp, int narg, char **arg) : xstr = ystr = zstr = nullptr; if (strstr(arg[3], "v_") == arg[3]) { - int n = strlen(&arg[3][2]) + 1; - xstr = new char[n]; - strcpy(xstr, &arg[3][2]); + xstr = utils::strdup( &arg[3][2]); } else if (strcmp(arg[3], "NULL") == 0) { xstyle = NONE; } else { @@ -70,9 +68,7 @@ FixSMDSetVel::FixSMDSetVel(LAMMPS *lmp, int narg, char **arg) : xstyle = CONSTANT; } if (strstr(arg[4], "v_") == arg[4]) { - int n = strlen(&arg[4][2]) + 1; - ystr = new char[n]; - strcpy(ystr, &arg[4][2]); + ystr = utils::strdup( &arg[4][2]); } else if (strcmp(arg[4], "NULL") == 0) { ystyle = NONE; } else { @@ -80,9 +76,7 @@ FixSMDSetVel::FixSMDSetVel(LAMMPS *lmp, int narg, char **arg) : ystyle = CONSTANT; } if (strstr(arg[5], "v_") == arg[5]) { - int n = strlen(&arg[5][2]) + 1; - zstr = new char[n]; - strcpy(zstr, &arg[5][2]); + zstr = utils::strdup( &arg[5][2]); } else if (strcmp(arg[5], "NULL") == 0) { zstyle = NONE; } else { @@ -103,9 +97,7 @@ FixSMDSetVel::FixSMDSetVel(LAMMPS *lmp, int narg, char **arg) : iregion = domain->find_region(arg[iarg + 1]); if (iregion == -1) error->all(FLERR, "Region ID for fix setvelocity does not exist"); - int n = strlen(arg[iarg + 1]) + 1; - idregion = new char[n]; - strcpy(idregion, arg[iarg + 1]); + idregion = utils::strdup( arg[iarg + 1]); iarg += 2; } else error->all(FLERR, "Illegal fix setvelocity command"); diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp index f37c9ec873..e9d32b5684 100644 --- a/src/USER-SMD/fix_smd_wall_surface.cpp +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -184,32 +184,6 @@ void FixSMDWallSurface::setup(int /*vflag*/) { read_triangles(0); } -/* ---------------------------------------------------------------------- - function to determine number of values in a text line - ------------------------------------------------------------------------- */ - -int FixSMDWallSurface::count_words(const char *line) { - int n = strlen(line) + 1; - char *copy; - memory->create(copy, n, "atom:copy"); - strcpy(copy, line); - - char *ptr; - if ((ptr = strchr(copy, '#'))) - *ptr = '\0'; - - if (strtok(copy, " \t\n\r\f") == nullptr) { - memory->destroy(copy); - return 0; - } - n = 1; - while (strtok(nullptr, " \t\n\r\f")) - n++; - - memory->destroy(copy); - return n; -} - /* ---------------------------------------------------------------------- size of atom nlocal's restart data ------------------------------------------------------------------------- */ @@ -265,7 +239,7 @@ void FixSMDWallSurface::read_triangles(int pass) { error->one(FLERR,"error reading number of triangle pairs"); } - nwords = count_words(line); + nwords = utils::count_words(line); if (nwords < 1) { error->one(FLERR,"first line of file is incorrect"); } @@ -290,7 +264,7 @@ void FixSMDWallSurface::read_triangles(int pass) { while (fgets(line, sizeof(line), fp)) { // read a line, should be the facet line // evaluate facet line - nwords = count_words(line); + nwords = utils::count_words(line); if (nwords != 5) { //sprintf(str, "found end solid line"); //error->message(FLERR, str); @@ -322,7 +296,7 @@ void FixSMDWallSurface::read_triangles(int pass) { error->one(FLERR, "error reading outer loop"); } - nwords = count_words(line); + nwords = utils::count_words(line); if (nwords != 2) { error->one(FLERR,"error reading outer loop"); } @@ -335,7 +309,7 @@ void FixSMDWallSurface::read_triangles(int pass) { error->one(FLERR,"error reading vertex line"); } - nwords = count_words(line); + nwords = utils::count_words(line); if (nwords != 4) { error->one(FLERR,"error reading vertex line"); } @@ -366,7 +340,7 @@ void FixSMDWallSurface::read_triangles(int pass) { error->one(FLERR, "error reading endloop"); } - nwords = count_words(line); + nwords = utils::count_words(line); if (nwords != 1) { error->one(FLERR,"error reading endloop"); } @@ -377,7 +351,7 @@ void FixSMDWallSurface::read_triangles(int pass) { error->one(FLERR,"error reading endfacet"); } - nwords = count_words(line); + nwords = utils::count_words(line); if (nwords != 1) { error->one(FLERR,"error reading endfacet"); } diff --git a/src/USER-SMD/fix_smd_wall_surface.h b/src/USER-SMD/fix_smd_wall_surface.h index 10f80c4ca8..3ff2b49737 100644 --- a/src/USER-SMD/fix_smd_wall_surface.h +++ b/src/USER-SMD/fix_smd_wall_surface.h @@ -34,7 +34,6 @@ public: void setup(int); void min_setup(int); - int count_words(const char *line); void read_triangles(int pass); private: From 9058216a5421b2a292711ce06e48360ef23832ed Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Mar 2021 14:11:56 -0400 Subject: [PATCH 0285/1217] silence compiler warnings --- src/USER-COLVARS/ndx_group.cpp | 4 +--- src/USER-DPD/pair_exp6_rx.cpp | 1 - src/USER-MISC/dihedral_table_cut.cpp | 5 ----- 3 files changed, 1 insertion(+), 9 deletions(-) diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index 184faa62cc..d8d5632b06 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -78,7 +78,6 @@ void Ndx2Group::command(int narg, char **arg) int len; bigint num; FILE *fp; - tagint *tagbuf; std::string name = "", next; if (narg < 1) error->all(FLERR,"Illegal ndx2group command"); @@ -191,11 +190,10 @@ void Ndx2Group::create(const std::string &name, const std::vector &tags) // map from global to local const int nlocal = atom->nlocal; int *flags = (int *)calloc(nlocal,sizeof(int)); - for (bigint i=0; i < tags.size(); ++i) { + for (bigint i=0; i < (int)tags.size(); ++i) { const int id = atom->map(tags[i]); if (id < nlocal && id >= 0) flags[id] = 1; } group->create(name,flags); free(flags); } - diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index ba8d52776f..396047fca9 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -587,7 +587,6 @@ void PairExp6rx::coeff(int narg, char **arg) if (!allocated) allocate(); int ilo,ihi,jlo,jhi; - int n; utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index dc7a6f9685..02e6d3e5da 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -134,11 +134,6 @@ static double cyc_splintD(double const *xa, } // cyc_splintD() -// -------------------------------------------- -// ------- Calculate the dihedral angle ------- -// -------------------------------------------- -static const int g_dim=3; - /* ---------------------------------------------------------------------- */ DihedralTableCut::DihedralTableCut(LAMMPS *lmp) : DihedralTable(lmp) From aaf9aa6d69b1ba06ff9df5a40c2384f79b8c32a5 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 29 Mar 2021 14:27:42 -0400 Subject: [PATCH 0286/1217] Refactoring of more tests --- unittest/commands/test_kim_commands.cpp | 183 +++++------ unittest/commands/test_lattice_region.cpp | 170 ++++------ unittest/commands/test_reset_ids.cpp | 149 ++++----- unittest/commands/test_variables.cpp | 153 ++++----- unittest/formats/compressed_dump_test.h | 16 +- unittest/formats/test_atom_styles.cpp | 299 +++++++++--------- unittest/formats/test_dump_atom.cpp | 36 +-- .../formats/test_dump_atom_compressed.cpp | 8 +- unittest/formats/test_dump_cfg.cpp | 8 +- unittest/formats/test_dump_cfg_compressed.cpp | 8 +- unittest/formats/test_dump_custom.cpp | 32 +- .../formats/test_dump_local_compressed.cpp | 12 +- unittest/formats/test_dump_xyz_compressed.cpp | 8 +- .../test_eim_potential_file_reader.cpp | 44 ++- unittest/formats/test_file_operations.cpp | 43 +-- unittest/formats/test_image_flags.cpp | 51 ++- unittest/formats/test_molecule_file.cpp | 47 +-- unittest/formats/test_pair_unit_convert.cpp | 186 ++++++----- unittest/testing/core.h | 21 +- 19 files changed, 627 insertions(+), 847 deletions(-) diff --git a/unittest/commands/test_kim_commands.cpp b/unittest/commands/test_kim_commands.cpp index 2d044b86eb..83e1e5b2d2 100644 --- a/unittest/commands/test_kim_commands.cpp +++ b/unittest/commands/test_kim_commands.cpp @@ -22,6 +22,7 @@ #include "variable.h" #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "../testing/core.h" #include #include @@ -29,57 +30,23 @@ // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; -#if defined(OMPI_MAJOR_VERSION) -const bool have_openmpi = true; -#else -const bool have_openmpi = false; -#endif - using LAMMPS_NS::utils::split_words; namespace LAMMPS_NS { using ::testing::MatchesRegex; using ::testing::StrEq; -#define TEST_FAILURE(errmsg, ...) \ - if (Info::has_exceptions()) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_ANY_THROW({__VA_ARGS__}); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } else { \ - if (!have_openmpi) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_DEATH({__VA_ARGS__}, ""); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } \ - } -class KimCommandsTest : public ::testing::Test { +class KimCommandsTest : public LAMMPSTest { protected: - LAMMPS *lmp; Variable *variable; void SetUp() override { - const char *args[] = {"KimCommandsTest", "-log", "none", "-echo", "screen", "-nocite"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - if (!verbose) ::testing::internal::GetCapturedStdout(); + testbinary = "KimCommandsTest"; + LAMMPSTest::SetUp(); variable = lmp->input->variable; } - - void TearDown() override - { - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void command(const std::string &cmd) { lmp->input->one(cmd); } }; TEST_F(KimCommandsTest, kim) @@ -115,9 +82,9 @@ TEST_F(KimCommandsTest, kim_init) // TEST_FAILURE(".*ERROR: KIM Model does not support the requested unit system.*", // command("kim init ex_model_Ar_P_Morse real");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("kim init LennardJones_Ar real"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); int ifix = lmp->modify->find_fix("KIM_MODEL_STORE"); ASSERT_GE(ifix, 0); @@ -129,81 +96,81 @@ TEST_F(KimCommandsTest, kim_interactions) TEST_FAILURE(".*ERROR: Illegal 'kim interactions' command.*", command("kim interactions");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("kim init LennardJones_Ar real"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Must use 'kim interactions' command " "after simulation box is defined.*", command("kim interactions Ar");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("kim init LennardJones_Ar real"); command("lattice fcc 4.4300"); command("region box block 0 10 0 10 0 10"); command("create_box 1 box"); command("create_atoms 1 box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Illegal 'kim interactions' command.*", command("kim interactions Ar Ar");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("lattice fcc 4.4300"); command("region box block 0 20 0 20 0 20"); command("create_box 4 box"); command("create_atoms 4 box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Illegal 'kim interactions' command.*", command("kim interactions Ar Ar");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("lattice fcc 4.4300"); command("region box block 0 10 0 10 0 10"); command("create_box 1 box"); command("create_atoms 1 box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Must use 'kim init' before 'kim interactions'.*", command("kim interactions Ar");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim init LennardJones_Ar real"); command("lattice fcc 4.4300"); command("region box block 0 10 0 10 0 10"); command("create_box 1 box"); command("create_atoms 1 box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: fixed_types cannot be used with a KIM Portable Model.*", command("kim interactions fixed_types");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("pair_style kim LennardJones_Ar"); command("region box block 0 1 0 1 0 1"); command("create_box 4 box"); command("pair_coeff * * Ar Ar Ar Ar"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu metal"); command("lattice fcc 4.920"); command("region box block 0 10 0 10 0 10"); command("create_box 1 box"); command("create_atoms 1 box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Species 'Ar' is not supported by this KIM Simulator Model.*", command("kim interactions Ar");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu metal"); command("lattice fcc 4.08"); @@ -211,13 +178,13 @@ TEST_F(KimCommandsTest, kim_interactions) command("create_box 1 box"); command("create_atoms 1 box"); command("kim interactions Au"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // ASSERT_EQ(lmp->output->var_kim_periodic, 1); // TEST_FAILURE(".*ERROR: Incompatible units for KIM Simulator Model.*", // command("kim interactions Au");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim init LennardJones_Ar real"); command("lattice fcc 4.4300"); @@ -226,12 +193,12 @@ TEST_F(KimCommandsTest, kim_interactions) command("create_atoms 1 box"); command("kim interactions Ar"); command("mass 1 39.95"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); int ifix = lmp->modify->find_fix("KIM_MODEL_STORE"); ASSERT_GE(ifix, 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim init LennardJones_Ar real"); command("lattice fcc 4.4300"); @@ -243,7 +210,7 @@ TEST_F(KimCommandsTest, kim_interactions) command("run 1"); command("kim interactions Ar"); command("run 1"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } TEST_F(KimCommandsTest, kim_param) @@ -255,18 +222,18 @@ TEST_F(KimCommandsTest, kim_param) "'kim param get/set' is mandatory.*", command("kim param unknown shift 1 shift");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu metal"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: 'kim param' can only be used with a KIM Portable Model.*", command("kim param get shift 1 shift");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim init LennardJones612_UniversalShifted__MO_959249795837_003 real"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Illegal 'kim param get' command.\nTo get the new " "parameter values, pair style must be assigned.\nMust use 'kim" @@ -278,7 +245,7 @@ TEST_F(KimCommandsTest, kim_param) " interactions' or 'pair_style kim' before 'kim param set'.*", command("kim param set shift 1 2");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim init LennardJones612_UniversalShifted__MO_959249795837_003 real"); command("lattice fcc 4.4300"); @@ -287,7 +254,7 @@ TEST_F(KimCommandsTest, kim_param) command("create_atoms 1 box"); command("kim interactions Ar"); command("mass 1 39.95"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Illegal index '0' for " "'shift' parameter with the extent of '1'.*", @@ -312,9 +279,9 @@ TEST_F(KimCommandsTest, kim_param) "Model does not have the requested 'unknown' parameter.*", command("kim param get unknown 1 unknown");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("kim param get shift 1 shift"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_FALSE(variable->find("shift") == -1); ASSERT_THAT(variable->retrieve("shift"), StrEq("1")); @@ -334,11 +301,11 @@ TEST_F(KimCommandsTest, kim_param) "Model does not have the requested '0.4989030' parameter.*", command("kim param set sigmas 1:1 0.5523570 0.4989030");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("variable new_shift equal 2"); command("kim param set shift 1 ${new_shift}"); command("kim param get shift 1 shift"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("shift"), StrEq("2")); @@ -363,51 +330,51 @@ TEST_F(KimCommandsTest, kim_param) "split' is mandatory.*", command("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 cutoffs_3"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("cutoffs_1"), StrEq("2.20943")); ASSERT_THAT(variable->retrieve("cutoffs_2"), StrEq("2.10252")); ASSERT_THAT(variable->retrieve("cutoffs_3"), StrEq("5.666115")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 cutoffs_3 explicit"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("cutoffs_1"), StrEq("2.20943")); ASSERT_THAT(variable->retrieve("cutoffs_2"), StrEq("2.10252")); ASSERT_THAT(variable->retrieve("cutoffs_3"), StrEq("5.666115")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("kim param get cutoffs 1:3 cutoffs split"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("cutoffs_1"), StrEq("2.20943")); ASSERT_THAT(variable->retrieve("cutoffs_2"), StrEq("2.10252")); ASSERT_THAT(variable->retrieve("cutoffs_3"), StrEq("5.666115")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("kim param get cutoffs 1:3 cutoffs list"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("cutoffs"), StrEq("2.20943 2.10252 5.666115")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("kim param set cutoffs 1 2.21 cutoffs 2 2.11"); command("kim param get cutoffs 1:2 cutoffs list"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("cutoffs"), StrEq("2.21 2.11")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("kim param set cutoffs 1:3 2.3 2.2 5.7"); command("kim param get cutoffs 1:3 cutoffs list"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("cutoffs"), StrEq("2.3 2.2 5.7")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("lattice fcc 4.4300"); @@ -417,19 +384,19 @@ TEST_F(KimCommandsTest, kim_param) command("mass 1 39.95"); command("pair_style kim LennardJones612_UniversalShifted__MO_959249795837_003"); command("pair_coeff * * Ar"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("kim param get shift 1 shift"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("shift"), StrEq("1")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("variable new_shift equal 2"); command("kim param set shift 1 ${new_shift}"); command("kim param get shift 1 shift"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("shift"), StrEq("2")); } @@ -467,13 +434,13 @@ TEST_F(KimCommandsTest, kim_property) command("kim property remove 1 key short-name");); TEST_FAILURE(".*ERROR: There is no property instance to dump the content.*", command("kim property dump results.edn");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim init LennardJones612_UniversalShifted__MO_959249795837_003 real"); command("kim property create 1 cohesive-potential-energy-cubic-crystal"); command("kim property modify 1 key short-name source-value 1 fcc"); command("kim property destroy 1"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); #endif } @@ -608,16 +575,16 @@ TEST_F(KimCommandsTest, kim_query) command(squery);); #if defined(KIM_EXTRA_UNITTESTS) - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim query latconst_1 get_lattice_constant_cubic " "crystal=[fcc] species=[Al] units=[angstrom] " "model=[EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005]"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("latconst_1"), StrEq("4.032082033157349")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal"); command("kim query latconst_1 get_lattice_constant_cubic crystal=[fcc] species=[Al] " @@ -626,71 +593,71 @@ TEST_F(KimCommandsTest, kim_query) command("kim query latconst_2 get_lattice_constant_cubic crystal=[fcc] species=[Al] " "units=[angstrom] " "model=[LennardJones612_UniversalShifted__MO_959249795837_003]"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("latconst_1"), StrEq("4.032082033157349")); ASSERT_THAT(variable->retrieve("latconst_2"), StrEq("3.328125931322575")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 metal"); command("kim query latconst split get_lattice_constant_hexagonal crystal=[hcp] species=[Zr] " "units=[angstrom]"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("latconst_1"), StrEq("3.234055244384789")); ASSERT_THAT(variable->retrieve("latconst_2"), StrEq("5.167650199630013")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim query latconst index get_lattice_constant_hexagonal " "crystal=[hcp] species=[Zr] units=[angstrom] " "model=[EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000]"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("latconst"), StrEq("3.234055244384789")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("variable latconst delete"); command("clear"); command("kim init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 metal"); command("kim query latconst list get_lattice_constant_hexagonal crystal=[hcp] species=[Zr] " "units=[angstrom]"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("latconst"), StrEq("3.234055244384789 5.167650199630013")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal"); command("kim query alpha get_linear_thermal_expansion_coefficient_cubic " "crystal=[fcc] species=[Al] units=[1/K] temperature=[293.15] " "temperature_units=[K]"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(variable->retrieve("alpha"), StrEq("1.654960564704273e-05")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim query model_list list get_available_models species=[Al]"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); std::string model_list = variable->retrieve("model_list"); auto n = model_list.find("EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005"); ASSERT_TRUE(n != std::string::npos); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim query model_name index get_available_models species=[Al]"); command("variable model_name delete"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("kim query model_name index get_available_models " @@ -708,7 +675,7 @@ TEST_F(KimCommandsTest, kim_query) command("kim query model_name index get_available_models " "species=[Al] potential_type=[\"eam\",meam]"); command("variable model_name delete"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); #endif } } // namespace LAMMPS_NS @@ -718,7 +685,7 @@ int main(int argc, char **argv) MPI_Init(&argc, &argv); ::testing::InitGoogleMock(&argc, argv); - if (have_openmpi && !LAMMPS_NS::Info::has_exceptions()) + if (Info::get_mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) std::cout << "Warning: using OpenMPI without exceptions. " "Death tests will be skipped\n"; diff --git a/unittest/commands/test_lattice_region.cpp b/unittest/commands/test_lattice_region.cpp index 2924c75d9f..eb6d577652 100644 --- a/unittest/commands/test_lattice_region.cpp +++ b/unittest/commands/test_lattice_region.cpp @@ -22,6 +22,7 @@ #include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "../testing/core.h" #include #include @@ -32,12 +33,6 @@ // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; -#if defined(OMPI_MAJOR_VERSION) -const bool have_openmpi = true; -#else -const bool have_openmpi = false; -#endif - using LAMMPS_NS::utils::split_words; namespace LAMMPS_NS { @@ -45,51 +40,22 @@ using ::testing::ExitedWithCode; using ::testing::MatchesRegex; using ::testing::StrEq; -#define TEST_FAILURE(errmsg, ...) \ - if (Info::has_exceptions()) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_ANY_THROW({__VA_ARGS__}); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } else { \ - if (!have_openmpi) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_DEATH({__VA_ARGS__}, ""); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } \ - } -class LatticeRegionTest : public ::testing::Test { +class LatticeRegionTest : public LAMMPSTest { protected: - LAMMPS *lmp; - void SetUp() override { - const char *args[] = {"LatticeRegionTest", "-log", "none", "-echo", "screen", "-nocite"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - lmp->input->one("units metal"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + testbinary = "LatticeRegionTest"; + LAMMPSTest::SetUp(); + command("units metal"); } - - void TearDown() override - { - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void command(const std::string &cmd) { lmp->input->one(cmd); } }; TEST_F(LatticeRegionTest, lattice_none) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice none 2.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::NONE); ASSERT_EQ(lattice->xlattice, 2.0); @@ -103,10 +69,10 @@ TEST_F(LatticeRegionTest, lattice_none) TEST_FAILURE(".*ERROR: Illegal lattice command.*", command("lattice none 1.0 origin");); TEST_FAILURE(".*ERROR: Expected floating point.*", command("lattice none xxx");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units lj"); command("lattice none 1.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); lattice = lmp->domain->lattice; ASSERT_EQ(lattice->xlattice, 1.0); ASSERT_EQ(lattice->ylattice, 1.0); @@ -168,27 +134,27 @@ TEST_F(LatticeRegionTest, lattice_sc) TEST_FAILURE(".*ERROR: Lattice spacings are invalid.*", command("lattice sc 1.0 spacing 1.0 -0.1 1.0");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units lj"); command("lattice sc 2.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); lattice = lmp->domain->lattice; ASSERT_DOUBLE_EQ(lattice->xlattice, pow(0.5, 1.0 / 3.0)); ASSERT_DOUBLE_EQ(lattice->ylattice, pow(0.5, 1.0 / 3.0)); ASSERT_DOUBLE_EQ(lattice->zlattice, pow(0.5, 1.0 / 3.0)); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dimension 2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", command("lattice sc 1.0");); } TEST_F(LatticeRegionTest, lattice_bcc) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice bcc 4.2 orient x 1 1 0 orient y -1 1 0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::BCC); ASSERT_DOUBLE_EQ(lattice->xlattice, sqrt(2.0) * 4.2); @@ -202,18 +168,18 @@ TEST_F(LatticeRegionTest, lattice_bcc) ASSERT_EQ(lattice->basis[1][1], 0.5); ASSERT_EQ(lattice->basis[1][2], 0.5); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dimension 2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", command("lattice bcc 1.0");); } TEST_F(LatticeRegionTest, lattice_fcc) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice fcc 3.5 origin 0.5 0.5 0.5"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::FCC); ASSERT_DOUBLE_EQ(lattice->xlattice, 3.5); @@ -239,18 +205,18 @@ TEST_F(LatticeRegionTest, lattice_fcc) command("lattice fcc 1.0 a1 0.0 1.0 0.0");); TEST_FAILURE(".*ERROR: Illegal lattice command.*", command("lattice fcc 1.0 orient w 1 0 0");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dimension 2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", command("lattice fcc 1.0");); } TEST_F(LatticeRegionTest, lattice_hcp) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice hcp 3.0 orient z 0 0 1"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::HCP); ASSERT_DOUBLE_EQ(lattice->xlattice, 3.0); @@ -283,18 +249,18 @@ TEST_F(LatticeRegionTest, lattice_hcp) command("lattice hcp 1.0 a2 0.0 1.0 0.0");); TEST_FAILURE(".*ERROR: Invalid option in lattice command for non-custom style.*", command("lattice hcp 1.0 a3 0.0 1.0 0.0");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dimension 2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", command("lattice hcp 1.0");); } TEST_F(LatticeRegionTest, lattice_diamond) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice diamond 4.1 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::DIAMOND); ASSERT_DOUBLE_EQ(lattice->xlattice, 6.6952719636073539); @@ -335,19 +301,19 @@ TEST_F(LatticeRegionTest, lattice_diamond) ASSERT_EQ(lattice->a3[1], 0.0); ASSERT_EQ(lattice->a3[2], 1.0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dimension 2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", command("lattice diamond 1.0");); } TEST_F(LatticeRegionTest, lattice_sq) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dimension 2"); command("lattice sq 3.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::SQ); ASSERT_DOUBLE_EQ(lattice->xlattice, 3.0); @@ -361,19 +327,19 @@ TEST_F(LatticeRegionTest, lattice_sq) TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", command("lattice sq 1.0 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dimension 3"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", command("lattice sq 1.0");); } TEST_F(LatticeRegionTest, lattice_sq2) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dimension 2"); command("lattice sq2 2.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::SQ2); ASSERT_DOUBLE_EQ(lattice->xlattice, 2.0); @@ -387,19 +353,19 @@ TEST_F(LatticeRegionTest, lattice_sq2) ASSERT_EQ(lattice->basis[1][1], 0.5); ASSERT_EQ(lattice->basis[1][2], 0.0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dimension 3"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", command("lattice sq2 1.0");); } TEST_F(LatticeRegionTest, lattice_hex) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dimension 2"); command("lattice hex 2.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::HEX); ASSERT_DOUBLE_EQ(lattice->xlattice, 2.0); @@ -422,16 +388,16 @@ TEST_F(LatticeRegionTest, lattice_hex) ASSERT_EQ(lattice->a3[1], 0.0); ASSERT_EQ(lattice->a3[2], 1.0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dimension 3"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*", command("lattice hex 1.0");); } TEST_F(LatticeRegionTest, lattice_custom) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("variable a equal 4.34"); command("variable b equal $a*sqrt(3.0)"); command("variable c equal $a*sqrt(8.0/3.0)"); @@ -449,7 +415,7 @@ TEST_F(LatticeRegionTest, lattice_custom) "basis 0.5 0.5 0.625 " "basis $t 0.0 0.125 " "basis $f 0.5 0.125 "); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto lattice = lmp->domain->lattice; ASSERT_EQ(lattice->style, Lattice::CUSTOM); ASSERT_DOUBLE_EQ(lattice->xlattice, 4.34); @@ -495,9 +461,9 @@ TEST_F(LatticeRegionTest, lattice_custom) TEST_FAILURE(".*ERROR: Illegal lattice command.*", command("lattice custom 1.0 basis 0.0 1.0 0");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dimension 2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: No basis atoms in lattice.*", command("lattice custom 1.0");); TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", command("lattice custom 1.0 origin 0.5 0.5 0.5 basis 0.0 0.0 0.0");); @@ -511,28 +477,28 @@ TEST_F(LatticeRegionTest, lattice_custom) TEST_F(LatticeRegionTest, region_fail) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice none 2.0"); command("region box block 0 1 0 1 0 1"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Create_atoms command before simulation box is defined.*", command("create_atoms 1 box");); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("create_box 1 box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Cannot create atoms with undefined lattice.*", command("create_atoms 1 box");); } TEST_F(LatticeRegionTest, region_block_lattice) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice sc 1.5"); command("region box block 0 2 0 2 0 2 units lattice"); command("create_box 1 box"); command("create_atoms 1 box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->domain->triclinic, 0); auto x = lmp->atom->x; @@ -553,12 +519,12 @@ TEST_F(LatticeRegionTest, region_block_lattice) TEST_F(LatticeRegionTest, region_block_box) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice sc 1.5 origin 0.75 0.75 0.75"); command("region box block 0 2 0 2 0 2 units box"); command("create_box 1 box"); command("create_atoms 1 box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->domain->triclinic, 0); auto x = lmp->atom->x; @@ -570,84 +536,84 @@ TEST_F(LatticeRegionTest, region_block_box) TEST_F(LatticeRegionTest, region_cone) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice fcc 2.5 origin 0.5 0.5 0.5"); command("region box cone x 1.0 1.0 0.5 2.1 0.0 2.0"); command("create_box 1 box"); command("create_atoms 1 region box"); command("write_dump all atom init.lammpstrj"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->domain->triclinic, 0); ASSERT_EQ(lmp->atom->natoms, 42); } TEST_F(LatticeRegionTest, region_cylinder) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice fcc 2.5 origin 0.5 0.5 0.5"); command("region box cylinder z 1.0 1.0 2.1 0.0 2.0 "); command("create_box 1 box"); command("create_atoms 1 region box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->domain->triclinic, 0); ASSERT_EQ(lmp->atom->natoms, 114); } TEST_F(LatticeRegionTest, region_prism) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice bcc 2.5 origin 0.75 0.75 0.75"); command("region box prism 0 2 0 2 0 2 0.5 0.0 0.0"); command("create_box 1 box"); command("create_atoms 1 box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->domain->triclinic, 1); ASSERT_EQ(lmp->atom->natoms, 16); } TEST_F(LatticeRegionTest, region_sphere) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice fcc 2.5 origin 0.5 0.5 0.5"); command("region box sphere 1.0 1.0 1.0 1.1"); command("create_box 1 box"); command("create_atoms 1 region box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->domain->triclinic, 0); ASSERT_EQ(lmp->atom->natoms, 14); } TEST_F(LatticeRegionTest, region_union) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice fcc 2.5 origin 0.5 0.5 0.5"); command("region part1 sphere 2.0 1.0 1.0 1.1"); command("region part2 block 0.0 2.0 0.0 2.0 0.0 2.0"); command("region box union 2 part1 part2"); command("create_box 1 box"); command("create_atoms 1 region box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->domain->triclinic, 0); ASSERT_EQ(lmp->atom->natoms, 67); } TEST_F(LatticeRegionTest, region_intersect) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice fcc 2.5 origin 0.5 0.5 0.5"); command("region part1 sphere 2.0 1.0 1.0 1.8"); command("region part2 block 0.0 2.0 0.0 2.0 0.0 2.0"); command("region box intersect 2 part1 part2"); command("create_box 1 box"); command("create_atoms 1 region box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->domain->triclinic, 0); ASSERT_EQ(lmp->atom->natoms, 21); } TEST_F(LatticeRegionTest, region_plane) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("lattice fcc 2.5 origin 0.5 0.5 0.5"); command("region box block 0.0 2.0 0.0 2.0 0.0 2.0"); command("region part1 plane 0.5 1.0 0.0 0.75 0.0 0.0"); @@ -656,7 +622,7 @@ TEST_F(LatticeRegionTest, region_plane) command("create_box 1 box"); command("create_atoms 1 region atoms"); command("write_dump all atom init.lammpstrj"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->domain->triclinic, 0); ASSERT_EQ(lmp->atom->natoms, 16); } @@ -668,7 +634,7 @@ int main(int argc, char **argv) MPI_Init(&argc, &argv); ::testing::InitGoogleMock(&argc, argv); - if (have_openmpi && !LAMMPS_NS::Info::has_exceptions()) + if (Info::get_mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) std::cout << "Warning: using OpenMPI without exceptions. " "Death tests will be skipped\n"; diff --git a/unittest/commands/test_reset_ids.cpp b/unittest/commands/test_reset_ids.cpp index 89e09b53a6..694fc9ac77 100644 --- a/unittest/commands/test_reset_ids.cpp +++ b/unittest/commands/test_reset_ids.cpp @@ -21,6 +21,7 @@ #include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "../testing/core.h" #include #include @@ -28,12 +29,6 @@ // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; -#if defined(OMPI_MAJOR_VERSION) -const bool have_openmpi = true; -#else -const bool have_openmpi = false; -#endif - using LAMMPS_NS::utils::split_words; namespace LAMMPS_NS { @@ -41,52 +36,23 @@ using ::testing::MatchesRegex; #define GETIDX(i) lmp->atom->map(i) -#define TEST_FAILURE(errmsg, ...) \ - if (Info::has_exceptions()) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_ANY_THROW({__VA_ARGS__}); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } else { \ - if (!have_openmpi) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_DEATH({__VA_ARGS__}, ""); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } \ - } #define STRINGIFY(val) XSTR(val) #define XSTR(val) #val -class ResetIDsTest : public ::testing::Test { +class ResetIDsTest : public LAMMPSTest { protected: - LAMMPS *lmp; - void SetUp() override { - const char *args[] = {"ResetIDsTest", "-log", "none", "-nocite", "-echo", "screen"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - Info *info = new Info(lmp); + testbinary = "ResetIDsTest"; + LAMMPSTest::SetUp(); if (info->has_style("atom", "full")) { - lmp->input->one("variable input_dir index " STRINGIFY(TEST_INPUT_FOLDER)); - lmp->input->one("include ${input_dir}/in.fourmol"); + BEGIN_HIDE_OUTPUT(); + command("variable input_dir index " STRINGIFY(TEST_INPUT_FOLDER)); + command("include ${input_dir}/in.fourmol"); + END_HIDE_OUTPUT(); } - delete info; - if (!verbose) ::testing::internal::GetCapturedStdout(); } - - void TearDown() override - { - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); - } - - void command(const std::string &cmd) { lmp->input->one(cmd); } }; TEST_F(ResetIDsTest, MolIDAll) @@ -126,9 +92,9 @@ TEST_F(ResetIDsTest, MolIDAll) // the original data file has two different molecule IDs // for two residues of the same molecule/fragment. - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_mol_ids all"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(molid[GETIDX(1)], 1); ASSERT_EQ(molid[GETIDX(2)], 1); @@ -168,12 +134,12 @@ TEST_F(ResetIDsTest, DeletePlusAtomID) auto molid = lmp->atom->molecule; // delete two water molecules - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group allwater molecule 3:6"); command("group twowater molecule 4:6:2"); command("delete_atoms group twowater compress no bond yes"); command("reset_mol_ids all"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->natoms, 23); ASSERT_EQ(lmp->atom->map_tag_max, 26); @@ -230,9 +196,9 @@ TEST_F(ResetIDsTest, DeletePlusAtomID) ASSERT_GE(GETIDX(25), 0); ASSERT_GE(GETIDX(26), 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_atom_ids"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->map_tag_max, 23); for (int i = 1; i <= 23; ++i) @@ -246,11 +212,11 @@ TEST_F(ResetIDsTest, PartialOffset) auto molid = lmp->atom->molecule; // delete two water molecules - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group allwater molecule 3:6"); command("group nowater subtract all allwater"); command("reset_mol_ids allwater offset 4"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->natoms, 29); ASSERT_EQ(lmp->atom->map_tag_max, 29); @@ -284,9 +250,9 @@ TEST_F(ResetIDsTest, PartialOffset) ASSERT_EQ(molid[GETIDX(28)], 8); ASSERT_EQ(molid[GETIDX(29)], 8); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_mol_ids nowater offset 0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(molid[GETIDX(1)], 1); ASSERT_EQ(molid[GETIDX(2)], 1); @@ -326,13 +292,13 @@ TEST_F(ResetIDsTest, DeleteAdd) auto molid = lmp->atom->molecule; // delete two water molecules - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group allwater molecule 3:6"); command("group twowater molecule 4:6:2"); command("group nowater subtract all allwater"); command("delete_atoms group twowater compress no bond yes mol yes"); command("reset_mol_ids allwater"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->natoms, 23); ASSERT_EQ(lmp->atom->map_tag_max, 26); @@ -389,17 +355,17 @@ TEST_F(ResetIDsTest, DeleteAdd) ASSERT_GE(GETIDX(25), 0); ASSERT_GE(GETIDX(26), 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_atom_ids sort yes"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->map_tag_max, 23); for (int i = 1; i <= 23; ++i) ASSERT_GE(GETIDX(i), 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_mol_ids nowater offset 1"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(molid[GETIDX(1)], 2); ASSERT_EQ(molid[GETIDX(2)], 2); @@ -425,13 +391,13 @@ TEST_F(ResetIDsTest, DeleteAdd) ASSERT_EQ(molid[GETIDX(22)], 4); ASSERT_EQ(molid[GETIDX(23)], 4); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("create_atoms 1 single 0.0 0.0 0.0"); command("create_atoms 2 single 1.0 0.0 0.0"); command("create_atoms 3 single 2.0 0.0 0.0"); command("create_atoms 4 single 3.0 0.0 0.0"); command("reset_mol_ids all single yes"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->natoms, 27); ASSERT_EQ(lmp->atom->map_tag_max, 27); @@ -443,9 +409,9 @@ TEST_F(ResetIDsTest, DeleteAdd) ASSERT_EQ(molid[GETIDX(26)], 6); ASSERT_EQ(molid[GETIDX(27)], 7); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_mol_ids all single no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(molid[GETIDX(21)], 3); ASSERT_EQ(molid[GETIDX(22)], 3); @@ -455,9 +421,9 @@ TEST_F(ResetIDsTest, DeleteAdd) ASSERT_EQ(molid[GETIDX(26)], 0); ASSERT_EQ(molid[GETIDX(27)], 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_mol_ids all compress no single yes"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(molid[GETIDX(21)], 21); ASSERT_EQ(molid[GETIDX(22)], 21); @@ -473,12 +439,12 @@ TEST_F(ResetIDsTest, TopologyData) if (lmp->atom->natoms == 0) GTEST_SKIP(); // delete two water molecules - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group allwater molecule 3:6"); command("group twowater molecule 4:6:2"); command("group nowater subtract all allwater"); command("delete_atoms group twowater compress no bond yes mol yes"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->natoms, 23); ASSERT_EQ(lmp->atom->map_tag_max, 26); @@ -562,9 +528,9 @@ TEST_F(ResetIDsTest, TopologyData) ASSERT_EQ(angle_atom2[GETIDX(24)][0], 24); ASSERT_EQ(angle_atom3[GETIDX(24)][0], 26); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_atom_ids sort yes"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); num_bond = lmp->atom->num_bond; num_angle = lmp->atom->num_angle; @@ -679,41 +645,40 @@ TEST_F(ResetIDsTest, DeathTests) command("reset_mol_ids all single xxx");); } -TEST(ResetMolIds, CMDFail) +class ResetMolIDsTest : public LAMMPSTest { +protected: + void SetUp() override + { + testbinary = "ResetIDsTest"; + LAMMPSTest::SetUp(); + } +}; + +TEST_F(ResetMolIDsTest, FailBeforeBox) { - LAMMPS *lmp; - const char *args[] = {"ResetIDsTest", "-log", "none", "-nocite", "-echo", "screen"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - if (!verbose) ::testing::internal::GetCapturedStdout(); - TEST_FAILURE(".*ERROR: Reset_mol_ids command before simulation box is.*", - lmp->input->one("reset_mol_ids all");); + command("reset_mol_ids all");); +} - auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); - }; - - if (!verbose) ::testing::internal::CaptureStdout(); +TEST_F(ResetMolIDsTest, FailMissingId) +{ + BEGIN_HIDE_OUTPUT(); command("atom_modify id no"); command("region box block 0 1 0 1 0 1"); command("create_box 1 box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Cannot use reset_mol_ids unless.*", command("reset_mol_ids all");); +} - if (!verbose) ::testing::internal::CaptureStdout(); +TEST_F(ResetMolIDsTest, FailOnlyMolecular) +{ + BEGIN_HIDE_OUTPUT(); command("clear"); command("region box block 0 1 0 1 0 1"); command("create_box 1 box"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Can only use reset_mol_ids.*", command("reset_mol_ids all");); - - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); -}; +} } // namespace LAMMPS_NS @@ -722,7 +687,7 @@ int main(int argc, char **argv) MPI_Init(&argc, &argv); ::testing::InitGoogleMock(&argc, argv); - if (have_openmpi && !LAMMPS_NS::Info::has_exceptions()) + if (Info::get_mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) std::cout << "Warning: using OpenMPI without exceptions. " "Death tests will be skipped\n"; diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 45183a2e54..d41ad52e57 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -24,6 +24,7 @@ #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "../testing/core.h" #include #include @@ -31,12 +32,6 @@ // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; -#if defined(OMPI_MAJOR_VERSION) -const bool have_openmpi = true; -#else -const bool have_openmpi = false; -#endif - using LAMMPS_NS::MathConst::MY_PI; using LAMMPS_NS::utils::split_words; @@ -45,39 +40,18 @@ using ::testing::ExitedWithCode; using ::testing::MatchesRegex; using ::testing::StrEq; -#define TEST_FAILURE(errmsg, ...) \ - if (Info::has_exceptions()) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_ANY_THROW({__VA_ARGS__}); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - if (verbose) std::cout << mesg; \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } else { \ - if (!have_openmpi) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_DEATH({__VA_ARGS__}, ""); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - if (verbose) std::cout << mesg; \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } \ - } -class VariableTest : public ::testing::Test { +class VariableTest : public LAMMPSTest { protected: - LAMMPS *lmp; Group *group; Domain *domain; Variable *variable; void SetUp() override { - const char *args[] = {"VariableTest", "-log", "none", "-echo", "screen", - "-nocite", "-v", "num", "1"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - if (!verbose) ::testing::internal::GetCapturedStdout(); + testbinary = "VariableTest"; + args = {"-log", "none", "-echo", "screen", "-nocite", "-v", "num", "1"}; + LAMMPSTest::SetUp(); group = lmp->group; domain = lmp->domain; variable = lmp->input->variable; @@ -85,19 +59,14 @@ protected: void TearDown() override { - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); - std::cout.flush(); + LAMMPSTest::TearDown(); unlink("test_variable.file"); unlink("test_variable.atomfile"); } - void command(const std::string &cmd) { lmp->input->one(cmd); } - void atomic_system() { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units real"); command("lattice sc 1.0 origin 0.125 0.125 0.125"); command("region box block -2 2 -2 2 -2 2"); @@ -109,23 +78,23 @@ protected: command("region top block INF INF -2.0 -1.0 INF INF"); command("set region left type 2"); command("set region right type 3"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } void molecular_system() { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("fix props all property/atom mol rmass q"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); atomic_system(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("variable molid atom floor(id/4)+1"); command("variable charge atom 2.0*sin(PI/32*id)"); command("set atom * mol v_molid"); command("set atom * charge v_charge"); command("set type 1 mass 0.5"); command("set type 2*4 mass 2.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } void file_vars() @@ -152,7 +121,7 @@ TEST_F(VariableTest, CreateDelete) { file_vars(); ASSERT_EQ(variable->nvar, 1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("variable one index 1 2 3 4"); command("variable two equal 1"); command("variable two equal 2"); @@ -173,11 +142,11 @@ TEST_F(VariableTest, CreateDelete) command("variable ten2 uloop 4"); command("variable ten3 uloop 4 pad"); command("variable dummy index 0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(variable->nvar, 17); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("variable dummy delete"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(variable->nvar, 16); ASSERT_THAT(variable->retrieve("three"), StrEq("three")); variable->set_string("three", "four"); @@ -235,7 +204,7 @@ TEST_F(VariableTest, AtomicSystem) atomic_system(); file_vars(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("variable one index 1 2 3 4"); command("variable id atom type"); command("variable id atom id"); @@ -262,7 +231,7 @@ TEST_F(VariableTest, AtomicSystem) command("variable rgsum equal sum(v_rg)"); command("variable loop equal v_loop+1"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(variable->atomstyle(variable->find("one")), 0); ASSERT_EQ(variable->atomstyle(variable->find("id")), 1); @@ -294,7 +263,7 @@ TEST_F(VariableTest, AtomicSystem) TEST_F(VariableTest, Expressions) { atomic_system(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("variable one index 1"); command("variable two equal 2"); command("variable three equal v_one+v_two"); @@ -321,7 +290,7 @@ TEST_F(VariableTest, Expressions) command("variable err2 equal v_one%v_ten7"); command("variable err3 equal v_ten7^-v_one"); variable->set("dummy index 1 2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); int ivar = variable->find("one"); ASSERT_FALSE(variable->equalstyle(ivar)); @@ -364,7 +333,7 @@ TEST_F(VariableTest, Functions) atomic_system(); file_vars(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("variable one index 1"); command("variable two equal random(1,2,643532)"); command("variable three equal atan2(v_one,1)"); @@ -377,7 +346,7 @@ TEST_F(VariableTest, Functions) command("variable ten equal floor(1.85)+ceil(1.85)"); command("variable ten1 equal tan(v_eight/2.0)"); command("variable ten2 equal asin(-1.0)+acos(0.0)"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_GT(variable->compute_equal(variable->find("two")), 0.99); ASSERT_LT(variable->compute_equal(variable->find("two")), 2.01); @@ -396,74 +365,64 @@ TEST_F(VariableTest, Functions) TEST_F(VariableTest, IfCommand) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("variable one index 1"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("if 1>0 then 'print \"bingo!\"'"); - auto text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + auto text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("if 1>2 then 'print \"bingo!\"' else 'print \"nope?\"'"); - text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, MatchesRegex(".*nope\?.*")); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("if (1<=0) then 'print \"bingo!\"' else 'print \"nope?\"'"); - text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, MatchesRegex(".*nope\?.*")); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("if (-1.0e-1<0.0E+0)|^(1<0) then 'print \"bingo!\"'"); - text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("if (${one}==1.0)&&(2>=1) then 'print \"bingo!\"'"); - text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("if !((${one}!=1.0)||(2|^1)) then 'print \"missed\"' else 'print \"bingo!\"'"); - text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("if (1>=2)&&(0&&1) then 'print \"missed\"' else 'print \"bingo!\"'"); - text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("if !1 then 'print \"missed\"' else 'print \"bingo!\"'"); - text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("if !(a==b) then 'print \"bingo!\"'"); - text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("if x==x|^1==0 then 'print \"bingo!\"'"); - text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + text = END_CAPTURE_OUTPUT(); ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("if x!=x|^a!=b then 'print \"bingo!\"'"); - text = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << text; + text = END_CAPTURE_OUTPUT(); + ASSERT_THAT(text, MatchesRegex(".*bingo!.*")); TEST_FAILURE(".*ERROR: Invalid Boolean syntax in if command.*", @@ -492,34 +451,34 @@ TEST_F(VariableTest, NextCommand) { file_vars(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("variable one index 1 2"); command("variable two equal 2"); command("variable three file test_variable.file"); command("variable four loop 2 4"); command("variable five index 1 2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_DOUBLE_EQ(variable->compute_equal("v_one"), 1); ASSERT_THAT(variable->retrieve("three"), StrEq("one")); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("next one"); command("next three"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_DOUBLE_EQ(variable->compute_equal("v_one"), 2); ASSERT_THAT(variable->retrieve("three"), StrEq("two")); ASSERT_GE(variable->find("one"), 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("next one"); command("next three"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // index style variable is deleted if no more next element ASSERT_EQ(variable->find("one"), -1); ASSERT_GE(variable->find("three"), 0); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("next three"); command("next three"); command("next three"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // file style variable is deleted if no more next element ASSERT_EQ(variable->find("three"), -1); @@ -536,7 +495,7 @@ int main(int argc, char **argv) MPI_Init(&argc, &argv); ::testing::InitGoogleMock(&argc, argv); - if (have_openmpi && !LAMMPS_NS::Info::has_exceptions()) + if (Info::get_mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) std::cout << "Warning: using OpenMPI without exceptions. " "Death tests will be skipped\n"; diff --git a/unittest/formats/compressed_dump_test.h b/unittest/formats/compressed_dump_test.h index c8afb2aac3..6bc26e123d 100644 --- a/unittest/formats/compressed_dump_test.h +++ b/unittest/formats/compressed_dump_test.h @@ -45,14 +45,14 @@ public: void enable_triclinic() { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("change_box all triclinic"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } void generate_dump(std::string dump_file, std::string dump_modify_options, int ntimesteps) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id all {} 1 {}", dump_style, dump_file)); if (!dump_modify_options.empty()) { @@ -60,7 +60,7 @@ public: } command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, @@ -76,7 +76,7 @@ public: std::string text_modify_options, std::string compressed_modify_options, int ntimesteps) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id0 all {} 1 {} {}", dump_style, text_file, text_options)); command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_file, compressed_options)); @@ -89,17 +89,17 @@ public: } command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } std::string convert_compressed_to_text(std::string compressed_file) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.')); std::string cmdline = fmt::format("{} -d -c {} > {}", COMPRESS_BINARY, compressed_file, converted_file); system(cmdline.c_str()); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); return converted_file; } }; diff --git a/unittest/formats/test_atom_styles.cpp b/unittest/formats/test_atom_styles.cpp index b787076495..67ee9742e5 100644 --- a/unittest/formats/test_atom_styles.cpp +++ b/unittest/formats/test_atom_styles.cpp @@ -24,6 +24,7 @@ #include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "../testing/core.h" #include #include @@ -98,38 +99,28 @@ const double EPSILON = 5.0e-14; namespace LAMMPS_NS { using ::testing::Eq; -class AtomStyleTest : public ::testing::Test { +class AtomStyleTest : public LAMMPSTest { protected: - LAMMPS *lmp; - void SetUp() override { - const char *args[] = {"SimpleCommandsTest", "-log", "none", "-echo", "screen", "-nocite"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - if (!verbose) ::testing::internal::GetCapturedStdout(); + testbinary = "AtomStyleTest"; + LAMMPSTest::SetUp(); ASSERT_NE(lmp, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units real"); command("dimension 3"); command("pair_style zero 4.0"); command("region box block -4 4 -4 4 -4 4"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } void TearDown() override { - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); + LAMMPSTest::TearDown(); remove("test_atom_styles.data"); remove("input_atom_styles.data"); remove("test_atom_styles.restart"); } - - void command(const std::string cmd) { lmp->input->one(cmd); } }; // default class Atom state @@ -503,17 +494,17 @@ TEST_F(AtomStyleTest, atomic_after_charge) expected.has_v = true; expected.has_f = true; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("atom_style charge"); command("atom_style atomic"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_ATOM_STATE_EQ(lmp->atom, expected); } TEST_F(AtomStyleTest, atomic) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("atom_modify map hash"); command("create_box 2 box"); command("create_atoms 1 single -2.0 2.0 0.1"); @@ -523,7 +514,7 @@ TEST_F(AtomStyleTest, atomic) command("mass 1 4.0"); command("mass 2 2.4"); command("pair_coeff * *"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic")); ASSERT_NE(lmp->atom->avec, nullptr); @@ -541,7 +532,7 @@ TEST_F(AtomStyleTest, atomic) ASSERT_EQ(lmp->atom->map_style, Atom::MAP_HASH); ASSERT_EQ(lmp->atom->map_user, 2); ASSERT_EQ(lmp->atom->map_tag_max, 4); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("pair_coeff * *"); command("write_data test_atom_styles.data nocoeff"); command("clear"); @@ -550,7 +541,7 @@ TEST_F(AtomStyleTest, atomic) command("atom_modify map array"); command("units real"); command("read_data test_atom_styles.data"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 4); @@ -598,14 +589,14 @@ TEST_F(AtomStyleTest, atomic) ASSERT_EQ(lmp->atom->map_tag_max, 4); ASSERT_EQ(lmp->atom->tag_consecutive(), 1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("pair_coeff * *"); command("group two id 2:4:2"); command("delete_atoms group two compress no"); command("write_restart test_atom_styles.restart"); command("clear"); command("read_restart test_atom_styles.restart"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 2); @@ -639,16 +630,16 @@ TEST_F(AtomStyleTest, atomic) ASSERT_EQ(lmp->atom->map_style, Atom::MAP_ARRAY); ASSERT_EQ(lmp->atom->map_user, 1); ASSERT_EQ(lmp->atom->map_tag_max, 3); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_atom_ids"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->map_tag_max, 2); ASSERT_EQ(lmp->atom->tag_consecutive(), 1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("comm_style tiled"); command("change_box all triclinic"); command("replicate 2 2 2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->map_tag_max, 16); x = lmp->atom->x; tag = lmp->atom->tag; @@ -704,9 +695,9 @@ TEST_F(AtomStyleTest, atomic) TEST_F(AtomStyleTest, charge) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("atom_style charge"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); AtomState expected; expected.atom_style = "charge"; @@ -721,7 +712,7 @@ TEST_F(AtomStyleTest, charge) expected.q_flag = 1; ASSERT_ATOM_STATE_EQ(lmp->atom, expected); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("create_box 2 box"); command("create_atoms 1 single -2.0 2.0 0.1"); command("create_atoms 1 single -2.0 -2.0 -0.1"); @@ -734,7 +725,7 @@ TEST_F(AtomStyleTest, charge) command("set atom 3 charge -1.0"); command("set atom 4 charge 1.0"); command("pair_coeff * *"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("charge")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 4); @@ -747,7 +738,7 @@ TEST_F(AtomStyleTest, charge) ASSERT_NE(lmp->atom->mass, nullptr); ASSERT_NE(lmp->atom->mass_setflag, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("pair_coeff * *"); command("write_data test_atom_styles.data nocoeff"); command("clear"); @@ -756,7 +747,7 @@ TEST_F(AtomStyleTest, charge) command("units real"); command("atom_modify map array"); command("read_data test_atom_styles.data"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("charge")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 4); @@ -810,7 +801,7 @@ TEST_F(AtomStyleTest, charge) ASSERT_EQ(lmp->atom->mass_setflag[1], 1); ASSERT_EQ(lmp->atom->mass_setflag[2], 1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("pair_coeff * *"); command("group two id 2:4:2"); command("delete_atoms group two compress no"); @@ -818,7 +809,7 @@ TEST_F(AtomStyleTest, charge) command("clear"); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic")); command("read_restart test_atom_styles.restart"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("charge")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 2); @@ -854,11 +845,11 @@ TEST_F(AtomStyleTest, charge) ASSERT_EQ(lmp->atom->mass_setflag[1], 1); ASSERT_EQ(lmp->atom->mass_setflag[2], 1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_atom_ids"); command("change_box all triclinic"); command("replicate 2 2 2 bbox"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->map_tag_max, 16); q = lmp->atom->q; EXPECT_NEAR(q[GETIDX(1)], -0.5, EPSILON); @@ -881,9 +872,9 @@ TEST_F(AtomStyleTest, charge) TEST_F(AtomStyleTest, sphere) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("atom_style sphere"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); AtomState expected; expected.atom_style = "sphere"; @@ -903,7 +894,7 @@ TEST_F(AtomStyleTest, sphere) ASSERT_ATOM_STATE_EQ(lmp->atom, expected); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("create_box 2 box"); command("create_atoms 1 single -2.0 2.0 0.1"); command("create_atoms 1 single -2.0 -2.0 -0.1"); @@ -918,7 +909,7 @@ TEST_F(AtomStyleTest, sphere) command("set atom 3 omega -1.0 0.0 0.0"); command("set atom 4 omega 0.0 1.0 0.0"); command("pair_coeff * *"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("sphere")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 4); @@ -932,7 +923,7 @@ TEST_F(AtomStyleTest, sphere) ASSERT_EQ(lmp->atom->mass, nullptr); ASSERT_EQ(lmp->atom->mass_setflag, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("pair_coeff * *"); command("write_data test_atom_styles.data nocoeff"); command("clear"); @@ -941,7 +932,7 @@ TEST_F(AtomStyleTest, sphere) command("units real"); command("atom_modify map array"); command("read_data test_atom_styles.data"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("sphere")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 4); @@ -1005,7 +996,7 @@ TEST_F(AtomStyleTest, sphere) EXPECT_NEAR(omega[GETIDX(4)][1], 1.0, EPSILON); EXPECT_NEAR(omega[GETIDX(4)][2], 0.0, EPSILON); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("pair_coeff * *"); command("group two id 2:4:2"); command("delete_atoms group two compress no"); @@ -1015,7 +1006,7 @@ TEST_F(AtomStyleTest, sphere) command("read_restart test_atom_styles.restart"); command("replicate 1 1 2"); command("reset_atom_ids"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("sphere")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 4); @@ -1052,9 +1043,9 @@ TEST_F(AtomStyleTest, ellipsoid) { if (!LAMMPS::is_installed_pkg("ASPHERE")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("atom_style ellipsoid"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); AtomState expected; expected.atom_style = "ellipsoid"; @@ -1073,7 +1064,7 @@ TEST_F(AtomStyleTest, ellipsoid) ASSERT_ATOM_STATE_EQ(lmp->atom, expected); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("create_box 3 box"); command("create_atoms 1 single -2.0 2.0 0.1"); command("create_atoms 1 single -2.0 -2.0 -0.1"); @@ -1091,7 +1082,7 @@ TEST_F(AtomStyleTest, ellipsoid) command("set atom 3 quat 1.0 0.0 1.0 30.0"); command("set atom 4 quat 1.0 1.0 1.0 60.0"); command("pair_coeff * *"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("ellipsoid")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 6); @@ -1119,7 +1110,7 @@ TEST_F(AtomStyleTest, ellipsoid) ASSERT_NE(lmp->atom->ellipsoid, nullptr); ASSERT_EQ(lmp->atom->mass_setflag, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("write_data test_atom_styles.data nocoeff"); command("clear"); command("atom_style ellipsoid"); @@ -1128,7 +1119,7 @@ TEST_F(AtomStyleTest, ellipsoid) command("atom_modify map array"); command("read_data test_atom_styles.data"); command("pair_coeff * *"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("ellipsoid")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 6); @@ -1238,7 +1229,7 @@ TEST_F(AtomStyleTest, ellipsoid) EXPECT_NEAR(bonus[3].quat[2], sqrt(5.0 / 30.0), EPSILON); EXPECT_NEAR(bonus[3].quat[3], sqrt(5.0 / 30.0), EPSILON); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group two id 2:4:2"); command("delete_atoms group two compress no"); command("write_restart test_atom_styles.restart"); @@ -1246,7 +1237,7 @@ TEST_F(AtomStyleTest, ellipsoid) command("read_restart test_atom_styles.restart"); command("comm_style tiled"); command("replicate 1 1 2 bbox"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("ellipsoid")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 8); @@ -1319,9 +1310,9 @@ TEST_F(AtomStyleTest, ellipsoid) EXPECT_NEAR(bonus[3].quat[2], 0.0, EPSILON); EXPECT_NEAR(bonus[3].quat[3], 0.25056280708573159, EPSILON); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_atom_ids"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->nellipsoids, 4); ASSERT_EQ(lmp->atom->tag_consecutive(), 1); ASSERT_EQ(lmp->atom->map_tag_max, 8); @@ -1389,10 +1380,10 @@ TEST_F(AtomStyleTest, line) { if (!LAMMPS::is_installed_pkg("ASPHERE")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dimension 2"); command("atom_style line"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); AtomState expected; expected.atom_style = "line"; @@ -1414,7 +1405,7 @@ TEST_F(AtomStyleTest, line) ASSERT_ATOM_STATE_EQ(lmp->atom, expected); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("create_box 3 box"); command("create_atoms 1 single -2.0 2.0 0.0"); command("create_atoms 1 single -2.0 -2.0 0.0"); @@ -1432,7 +1423,7 @@ TEST_F(AtomStyleTest, line) command("set atom 3 theta 30.0"); command("set atom 4 theta 60.0"); command("pair_coeff * *"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("line")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 6); @@ -1448,7 +1439,7 @@ TEST_F(AtomStyleTest, line) ASSERT_NE(lmp->atom->rmass, nullptr); ASSERT_EQ(lmp->atom->mass_setflag, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("write_data test_atom_styles.data nocoeff"); command("clear"); command("dimension 2"); @@ -1457,7 +1448,7 @@ TEST_F(AtomStyleTest, line) command("units real"); command("atom_modify map array"); command("read_data test_atom_styles.data"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("line")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 6); @@ -1547,7 +1538,7 @@ TEST_F(AtomStyleTest, line) EXPECT_NEAR(bonus[3].length, 3.0, EPSILON); EXPECT_NEAR(bonus[3].theta, MathConst::MY_PI / 3.0, EPSILON); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("pair_coeff * *"); command("group two id 2:4:2"); command("delete_atoms group two compress no"); @@ -1557,7 +1548,7 @@ TEST_F(AtomStyleTest, line) command("comm_style tiled"); command("change_box all triclinic"); command("replicate 1 2 1 bbox"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("line")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 8); @@ -1610,9 +1601,9 @@ TEST_F(AtomStyleTest, line) EXPECT_NEAR(bonus[3].length, 3.0, EPSILON); EXPECT_NEAR(bonus[3].theta, MathConst::MY_PI / 6.0, EPSILON); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_atom_ids"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->nlines, 4); ASSERT_EQ(lmp->atom->tag_consecutive(), 1); ASSERT_EQ(lmp->atom->map_tag_max, 8); @@ -1660,9 +1651,9 @@ TEST_F(AtomStyleTest, tri) { if (!LAMMPS::is_installed_pkg("ASPHERE")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("atom_style tri"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); AtomState expected; expected.atom_style = "tri"; @@ -1685,7 +1676,7 @@ TEST_F(AtomStyleTest, tri) ASSERT_ATOM_STATE_EQ(lmp->atom, expected); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("create_box 3 box"); command("create_atoms 1 single -2.0 2.0 0.1"); command("create_atoms 1 single -2.0 -2.0 -0.1"); @@ -1703,7 +1694,7 @@ TEST_F(AtomStyleTest, tri) command("set atom 3 quat 1.0 0.0 1.0 30.0"); command("set atom 4 quat 1.0 1.0 1.0 60.0"); command("pair_coeff * *"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("tri")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 6); @@ -1731,7 +1722,7 @@ TEST_F(AtomStyleTest, tri) ASSERT_NE(lmp->atom->tri, nullptr); ASSERT_EQ(lmp->atom->mass_setflag, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("write_data test_atom_styles.data nocoeff"); command("clear"); command("atom_style tri"); @@ -1740,7 +1731,7 @@ TEST_F(AtomStyleTest, tri) command("atom_modify map array"); command("read_data test_atom_styles.data"); command("pair_coeff * *"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("tri")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 6); @@ -1893,7 +1884,7 @@ TEST_F(AtomStyleTest, tri) EXPECT_NEAR(bonus[3].c3[1], 0.64304946932374796, EPSILON); EXPECT_NEAR(bonus[3].c3[2], -0.32808266428854477, EPSILON); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group two id 2:4:2"); command("delete_atoms group two compress no"); command("write_restart test_atom_styles.restart"); @@ -1901,7 +1892,7 @@ TEST_F(AtomStyleTest, tri) command("read_restart test_atom_styles.restart"); command("change_box all triclinic"); command("replicate 1 1 2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("tri")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 8); @@ -2019,9 +2010,9 @@ TEST_F(AtomStyleTest, tri) EXPECT_NEAR(bonus[3].c3[1], 0.85047049833171351, EPSILON); EXPECT_NEAR(bonus[3].c3[2], -0.15731490073748589, EPSILON); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_atom_ids"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->ntris, 4); ASSERT_EQ(lmp->atom->tag_consecutive(), 1); ASSERT_EQ(lmp->atom->map_tag_max, 8); @@ -2064,9 +2055,9 @@ TEST_F(AtomStyleTest, body_nparticle) { if (!LAMMPS::is_installed_pkg("BODY")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("atom_style body nparticle 2 4"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); AtomState expected; expected.atom_style = "body"; @@ -2129,7 +2120,7 @@ TEST_F(AtomStyleTest, body_nparticle) FILE *fp = fopen("input_atom_styles.data", "w"); fputs(data_file, fp); fclose(fp); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("atom_modify map array"); command("read_data input_atom_styles.data"); command("create_atoms 3 single 2.0 2.0 -2.1"); @@ -2140,7 +2131,7 @@ TEST_F(AtomStyleTest, body_nparticle) command("set atom 3 quat 1.0 0.0 1.0 30.0"); command("set atom 4 quat 1.0 1.0 1.0 60.0"); command("pair_coeff * *"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("body")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 6); @@ -2306,7 +2297,7 @@ TEST_F(AtomStyleTest, body_nparticle) ASSERT_NE(bonus[2].dvalue, nullptr); ASSERT_NE(bonus[3].dvalue, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("write_data test_atom_styles.data nocoeff"); command("clear"); command("atom_style body nparticle 2 4"); @@ -2315,7 +2306,7 @@ TEST_F(AtomStyleTest, body_nparticle) command("atom_modify map array"); command("read_data test_atom_styles.data"); command("pair_coeff * *"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("body")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 6); @@ -2479,7 +2470,7 @@ TEST_F(AtomStyleTest, body_nparticle) ASSERT_NE(bonus[2].dvalue, nullptr); ASSERT_NE(bonus[3].dvalue, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group two id 2:4:2"); command("delete_atoms group two compress no"); command("write_restart test_atom_styles.restart"); @@ -2487,7 +2478,7 @@ TEST_F(AtomStyleTest, body_nparticle) command("read_restart test_atom_styles.restart"); command("comm_style tiled"); command("replicate 1 1 2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("body")); avec = (AtomVecBody *)lmp->atom->avec; ASSERT_THAT(std::string(avec->bptr->style), Eq("nparticle")); @@ -2594,9 +2585,9 @@ TEST_F(AtomStyleTest, body_nparticle) ASSERT_NE(bonus[2].dvalue, nullptr); ASSERT_NE(bonus[3].dvalue, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_atom_ids"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->nbodies, 4); ASSERT_EQ(lmp->atom->tag_consecutive(), 1); ASSERT_EQ(lmp->atom->map_tag_max, 8); @@ -2632,11 +2623,11 @@ TEST_F(AtomStyleTest, template) { if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); create_molecule_files(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); command("atom_style template twomols"); command("newton on"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); AtomState expected; expected.atom_style = "template"; @@ -2658,7 +2649,7 @@ TEST_F(AtomStyleTest, template) ASSERT_ATOM_STATE_EQ(lmp->atom, expected); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("create_box 4 box bond/types 2 angle/types 2 "); command("create_atoms 0 single -2.0 2.0 0.1 mol twomols 65234"); command("create_atoms 0 single -2.0 -2.0 -0.1 mol twomols 62346"); @@ -2676,7 +2667,7 @@ TEST_F(AtomStyleTest, template) command("angle_style zero"); command("angle_coeff * 109.0"); command("pair_coeff * *"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("template")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 12); @@ -2706,7 +2697,7 @@ TEST_F(AtomStyleTest, template) ASSERT_NE(lmp->atom->mass, nullptr); ASSERT_NE(lmp->atom->mass_setflag, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("write_data test_atom_styles.data"); command("clear"); command("units real"); @@ -2718,7 +2709,7 @@ TEST_F(AtomStyleTest, template) command("angle_style zero"); command("atom_modify map array"); command("read_data test_atom_styles.data"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("template")); ASSERT_NE(lmp->atom->avec, nullptr); @@ -2780,7 +2771,7 @@ TEST_F(AtomStyleTest, template) ASSERT_EQ(molatom[GETIDX(11)], -1); ASSERT_EQ(molatom[GETIDX(12)], -1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); @@ -2790,7 +2781,7 @@ TEST_F(AtomStyleTest, template) command("angle_style zero"); command("atom_modify map array"); command("read_data test_atom_styles.data"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("template")); ASSERT_NE(lmp->atom->avec, nullptr); @@ -2902,7 +2893,7 @@ TEST_F(AtomStyleTest, template) ASSERT_EQ(type[GETIDX(11)], 3); ASSERT_EQ(type[GETIDX(12)], 4); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group two id 7:10"); command("delete_atoms group two compress no"); command("write_restart test_atom_styles.restart"); @@ -2910,7 +2901,7 @@ TEST_F(AtomStyleTest, template) command("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); command("read_restart test_atom_styles.restart"); command("replicate 1 1 2 bbox"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("template")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 16); @@ -2980,9 +2971,9 @@ TEST_F(AtomStyleTest, template) ASSERT_EQ(molatom[GETIDX(23)], -1); ASSERT_EQ(molatom[GETIDX(24)], -1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_atom_ids"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->tag_consecutive(), 1); ASSERT_EQ(lmp->atom->map_tag_max, 16); @@ -3028,11 +3019,11 @@ TEST_F(AtomStyleTest, template_charge) { if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); create_molecule_files(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); command("atom_style hybrid template twomols charge"); command("newton on"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); AtomState expected; expected.atom_style = "hybrid"; @@ -3063,7 +3054,7 @@ TEST_F(AtomStyleTest, template_charge) ASSERT_NE(hybrid->styles[0], nullptr); ASSERT_NE(hybrid->styles[1], nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("create_box 4 box bond/types 2 angle/types 2 "); command("create_atoms 0 single -2.0 2.0 0.1 mol twomols 65234"); command("create_atoms 0 single -2.0 -2.0 -0.1 mol twomols 62346"); @@ -3084,7 +3075,7 @@ TEST_F(AtomStyleTest, template_charge) command("angle_style zero"); command("angle_coeff * 109.0"); command("pair_coeff * *"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_NE(lmp->atom->avec, nullptr); hybrid = (AtomVecHybrid *)lmp->atom->avec; ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); @@ -3122,7 +3113,7 @@ TEST_F(AtomStyleTest, template_charge) ASSERT_NE(lmp->atom->mass, nullptr); ASSERT_NE(lmp->atom->mass_setflag, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("write_data test_atom_styles.data"); command("clear"); command("units real"); @@ -3134,7 +3125,7 @@ TEST_F(AtomStyleTest, template_charge) command("angle_style zero"); command("atom_modify map array"); command("read_data test_atom_styles.data"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); ASSERT_NE(lmp->atom->avec, nullptr); @@ -3196,7 +3187,7 @@ TEST_F(AtomStyleTest, template_charge) ASSERT_EQ(molatom[GETIDX(11)], -1); ASSERT_EQ(molatom[GETIDX(12)], -1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); @@ -3206,7 +3197,7 @@ TEST_F(AtomStyleTest, template_charge) command("angle_style zero"); command("atom_modify map array"); command("read_data test_atom_styles.data"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); ASSERT_NE(lmp->atom->avec, nullptr); @@ -3331,7 +3322,7 @@ TEST_F(AtomStyleTest, template_charge) ASSERT_EQ(type[GETIDX(11)], 3); ASSERT_EQ(type[GETIDX(12)], 4); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("group two id 7:10"); command("delete_atoms group two compress no"); command("write_restart test_atom_styles.restart"); @@ -3339,7 +3330,7 @@ TEST_F(AtomStyleTest, template_charge) command("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); command("read_restart test_atom_styles.restart"); command("replicate 1 1 2 bbox"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 16); @@ -3409,9 +3400,9 @@ TEST_F(AtomStyleTest, template_charge) ASSERT_EQ(molatom[GETIDX(23)], -1); ASSERT_EQ(molatom[GETIDX(24)], -1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_atom_ids"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->tag_consecutive(), 1); ASSERT_EQ(lmp->atom->map_tag_max, 16); @@ -3457,10 +3448,10 @@ TEST_F(AtomStyleTest, bond) { if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("atom_style bond"); command("newton on"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); AtomState expected; expected.atom_style = "bond"; @@ -3480,7 +3471,7 @@ TEST_F(AtomStyleTest, bond) ASSERT_ATOM_STATE_EQ(lmp->atom, expected); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("create_box 3 box bond/types 2 " "extra/bond/per/atom 2 extra/special/per/atom 4"); command("create_atoms 1 single -2.0 2.0 0.1"); @@ -3500,7 +3491,7 @@ TEST_F(AtomStyleTest, bond) command("create_bonds single/bond 2 3 5"); command("create_bonds single/bond 2 3 6"); command("create_bonds single/bond 2 5 6"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("bond")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 6); @@ -3533,7 +3524,7 @@ TEST_F(AtomStyleTest, bond) lmp->atom->bond_type[GETIDX(1)][0] *= -1; lmp->atom->bond_type[GETIDX(5)][0] *= -1; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("write_data test_atom_styles.data nocoeff"); command("clear"); command("units real"); @@ -3545,7 +3536,7 @@ TEST_F(AtomStyleTest, bond) command("read_data test_atom_styles.data"); command("pair_coeff * *"); command("bond_coeff * 4.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("bond")); ASSERT_NE(lmp->atom->avec, nullptr); @@ -3594,7 +3585,7 @@ TEST_F(AtomStyleTest, bond) ASSERT_EQ(bond_atom[GETIDX(6)][0], 3); ASSERT_EQ(bond_atom[GETIDX(6)][1], 5); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("atom_style bond"); @@ -3604,7 +3595,7 @@ TEST_F(AtomStyleTest, bond) command("read_data test_atom_styles.data"); command("pair_coeff * *"); command("bond_coeff * 4.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("bond")); ASSERT_NE(lmp->atom->avec, nullptr); @@ -3692,7 +3683,7 @@ TEST_F(AtomStyleTest, bond) lmp->atom->bond_type[GETIDX(1)][0] *= -1; lmp->atom->bond_type[GETIDX(5)][0] *= -1; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("pair_coeff * *"); command("group two id 2:4:2"); command("delete_atoms group two compress no"); @@ -3700,7 +3691,7 @@ TEST_F(AtomStyleTest, bond) command("clear"); command("read_restart test_atom_styles.restart"); command("replicate 1 1 2 bbox"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("bond")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 8); @@ -3754,10 +3745,10 @@ TEST_F(AtomStyleTest, bond) ASSERT_EQ(bond_type[GETIDX(9)][1], 2); ASSERT_EQ(bond_type[GETIDX(11)][0], 2); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("delete_bonds all bond 2"); command("reset_atom_ids"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->tag_consecutive(), 1); ASSERT_EQ(lmp->atom->map_tag_max, 8); @@ -3805,10 +3796,10 @@ TEST_F(AtomStyleTest, angle) { if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("atom_style angle"); command("newton on"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); AtomState expected; expected.atom_style = "angle"; @@ -3829,7 +3820,7 @@ TEST_F(AtomStyleTest, angle) ASSERT_ATOM_STATE_EQ(lmp->atom, expected); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("create_box 3 box bond/types 2 angle/types 2 " "extra/bond/per/atom 2 extra/angle/per/atom 1 " "extra/special/per/atom 4"); @@ -3854,7 +3845,7 @@ TEST_F(AtomStyleTest, angle) command("create_bonds single/bond 2 5 6"); command("create_bonds single/angle 1 1 3 5"); command("create_bonds single/angle 2 3 5 6"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("angle")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 6); @@ -3889,7 +3880,7 @@ TEST_F(AtomStyleTest, angle) lmp->atom->angle_type[GETIDX(3)][0] *= -1; lmp->atom->angle_type[GETIDX(5)][0] *= -1; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("write_data test_atom_styles.data nocoeff"); command("clear"); command("units real"); @@ -3903,7 +3894,7 @@ TEST_F(AtomStyleTest, angle) command("pair_coeff * *"); command("bond_coeff * 4.0"); command("angle_coeff * 90.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("angle")); ASSERT_NE(lmp->atom->avec, nullptr); @@ -3987,7 +3978,7 @@ TEST_F(AtomStyleTest, angle) ASSERT_EQ(angle_atom2[GETIDX(6)][0], 5); ASSERT_EQ(angle_atom3[GETIDX(6)][0], 6); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("atom_style angle"); @@ -3997,7 +3988,7 @@ TEST_F(AtomStyleTest, angle) command("read_data test_atom_styles.data"); command("pair_coeff * *"); command("bond_coeff * 4.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("angle")); ASSERT_NE(lmp->atom->avec, nullptr); @@ -4086,7 +4077,7 @@ TEST_F(AtomStyleTest, angle) ASSERT_EQ(angle_type[GETIDX(3)][0], 1); ASSERT_EQ(angle_type[GETIDX(5)][0], 2); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("pair_coeff * *"); command("group two id 2:4:2"); command("delete_atoms group two compress no"); @@ -4094,7 +4085,7 @@ TEST_F(AtomStyleTest, angle) command("clear"); command("read_restart test_atom_styles.restart"); command("replicate 1 1 2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("angle")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 8); @@ -4131,10 +4122,10 @@ TEST_F(AtomStyleTest, angle) ASSERT_EQ(angle_type[GETIDX(9)][0], 1); ASSERT_EQ(angle_type[GETIDX(11)][0], 2); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("delete_bonds all angle 2"); command("reset_atom_ids"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->tag_consecutive(), 1); ASSERT_EQ(lmp->atom->map_tag_max, 8); @@ -4166,9 +4157,9 @@ TEST_F(AtomStyleTest, full_ellipsoid) if (!LAMMPS::is_installed_pkg("ASPHERE")) GTEST_SKIP(); if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("atom_style hybrid full ellipsoid"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); AtomState expected; expected.atom_style = "hybrid"; @@ -4204,7 +4195,7 @@ TEST_F(AtomStyleTest, full_ellipsoid) ASSERT_NE(hybrid->styles[0], nullptr); ASSERT_NE(hybrid->styles[1], nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("create_box 3 box bond/types 2 " "extra/bond/per/atom 2 extra/special/per/atom 4"); command("create_atoms 1 single -2.0 2.0 0.1"); @@ -4239,7 +4230,7 @@ TEST_F(AtomStyleTest, full_ellipsoid) command("create_bonds single/bond 2 3 5"); command("create_bonds single/bond 2 3 6"); command("create_bonds single/bond 2 5 6"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 6); @@ -4269,7 +4260,7 @@ TEST_F(AtomStyleTest, full_ellipsoid) ASSERT_NE(lmp->atom->ellipsoid, nullptr); ASSERT_NE(lmp->atom->mass_setflag, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("write_data test_atom_styles.data nocoeff"); command("clear"); command("units real"); @@ -4280,7 +4271,7 @@ TEST_F(AtomStyleTest, full_ellipsoid) command("read_data test_atom_styles.data"); command("pair_coeff * *"); command("bond_coeff * 4.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); ASSERT_NE(lmp->atom->avec, nullptr); hybrid = (AtomVecHybrid *)lmp->atom->avec; @@ -4405,7 +4396,7 @@ TEST_F(AtomStyleTest, full_ellipsoid) EXPECT_NEAR(bonus[3].quat[2], sqrt(5.0 / 30.0), EPSILON); EXPECT_NEAR(bonus[3].quat[3], sqrt(5.0 / 30.0), EPSILON); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("pair_coeff * *"); command("group two id 2:4:2"); command("delete_atoms group two compress no"); @@ -4413,7 +4404,7 @@ TEST_F(AtomStyleTest, full_ellipsoid) command("clear"); command("read_restart test_atom_styles.restart"); command("replicate 1 1 2 bbox"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); hybrid = (AtomVecHybrid *)lmp->atom->avec; ASSERT_EQ(hybrid->nstyles, 2); @@ -4492,9 +4483,9 @@ TEST_F(AtomStyleTest, full_ellipsoid) EXPECT_NEAR(bonus[3].quat[2], 0.0, EPSILON); EXPECT_NEAR(bonus[3].quat[3], 0.25056280708573159, EPSILON); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_atom_ids"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->nellipsoids, 4); ASSERT_EQ(lmp->atom->tag_consecutive(), 1); ASSERT_EQ(lmp->atom->map_tag_max, 8); @@ -4561,10 +4552,10 @@ TEST_F(AtomStyleTest, full_ellipsoid) TEST_F(AtomStyleTest, property_atom) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("atom_modify map array"); command("fix Properties all property/atom i_one d_two mol d_three q rmass ghost yes"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); AtomState expected; expected.atom_style = "atomic"; @@ -4596,7 +4587,7 @@ TEST_F(AtomStyleTest, property_atom) expected.nextra_border_max = 1; ASSERT_ATOM_STATE_EQ(lmp->atom, expected); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("create_box 2 box"); command("create_atoms 1 single -2.0 2.0 0.1"); command("create_atoms 1 single -2.0 -2.0 -0.1"); @@ -4623,7 +4614,7 @@ TEST_F(AtomStyleTest, property_atom) command("set atom 3 d_three 0.5"); command("set atom 4 d_three 2.0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); expected.natoms = 4; expected.nlocal = 4; expected.map_tag_max = 4; @@ -4637,7 +4628,7 @@ TEST_F(AtomStyleTest, property_atom) ASSERT_NE(lmp->atom->nmax, -1); ASSERT_NE(lmp->atom->rmass, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("pair_coeff * *"); command("write_data test_atom_styles.data nocoeff"); command("clear"); @@ -4648,7 +4639,7 @@ TEST_F(AtomStyleTest, property_atom) command("fix props all property/atom i_one d_two mol d_three q rmass ghost yes"); command("read_data test_atom_styles.data fix props NULL Properties"); command("pair_coeff * *"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 4); @@ -4726,7 +4717,7 @@ TEST_F(AtomStyleTest, property_atom) EXPECT_NEAR(three[GETIDX(3)], 0.5, EPSILON); EXPECT_NEAR(three[GETIDX(4)], 2.0, EPSILON); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("pair_coeff * *"); command("group two id 2:4:2"); command("delete_atoms group two compress no"); @@ -4735,7 +4726,7 @@ TEST_F(AtomStyleTest, property_atom) ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic")); command("read_restart test_atom_styles.restart"); command("fix props all property/atom i_one d_two mol d_three q rmass ghost yes"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); expected.natoms = 2; expected.nlocal = 2; expected.nghost = 0; @@ -4773,10 +4764,10 @@ TEST_F(AtomStyleTest, property_atom) EXPECT_NEAR(three[GETIDX(1)], -2.5, EPSILON); EXPECT_NEAR(three[GETIDX(3)], 0.5, EPSILON); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("reset_atom_ids"); command("change_box all triclinic"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->map_tag_max, 2); q = lmp->atom->q; EXPECT_NEAR(q[GETIDX(1)], -0.5, EPSILON); diff --git a/unittest/formats/test_dump_atom.cpp b/unittest/formats/test_dump_atom.cpp index 39cefdccea..46c6b7dfa7 100644 --- a/unittest/formats/test_dump_atom.cpp +++ b/unittest/formats/test_dump_atom.cpp @@ -32,14 +32,14 @@ class DumpAtomTest : public MeltTest { public: void enable_triclinic() { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("change_box all triclinic"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } void generate_dump(std::string dump_file, std::string dump_modify_options, int ntimesteps) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id all {} 1 {}", dump_style, dump_file)); if (!dump_modify_options.empty()) { @@ -47,13 +47,13 @@ public: } command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } void generate_text_and_binary_dump(std::string text_file, std::string binary_file, std::string dump_modify_options, int ntimesteps) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id0 all {} 1 {}", dump_style, text_file)); command(fmt::format("dump id1 all {} 1 {}", dump_style, binary_file)); @@ -63,15 +63,15 @@ public: } command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } std::string convert_binary_to_text(std::string binary_file) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); std::string cmdline = fmt::format("{} {}", BINARY2TXT_BINARY, binary_file); system(cmdline.c_str()); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); return fmt::format("{}.txt", binary_file); } }; @@ -504,27 +504,27 @@ TEST_F(DumpAtomTest, per_processor_multi_file_run1) TEST_F(DumpAtomTest, dump_modify_scale_invalid) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dump id all atom 1 dump.txt"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*Illegal dump_modify command.*", command("dump_modify id scale true");); } TEST_F(DumpAtomTest, dump_modify_image_invalid) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dump id all atom 1 dump.txt"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*Illegal dump_modify command.*", command("dump_modify id image true");); } TEST_F(DumpAtomTest, dump_modify_invalid) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("dump id all atom 1 dump.txt"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*Illegal dump_modify command.*", command("dump_modify id true");); } @@ -534,12 +534,12 @@ TEST_F(DumpAtomTest, write_dump) auto reference = "dump_ref_run0.melt"; auto dump_file = "write_dump_atom_run0.melt"; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id all atom 1 {}", reference)); command("dump_modify id scale no units yes"); command("run 0"); command("write_dump all atom write_dump_atom_run*.melt modify scale no units yes"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_FILE_EXISTS(reference); ASSERT_FILE_EXISTS(dump_file); @@ -556,12 +556,12 @@ TEST_F(DumpAtomTest, binary_write_dump) auto reference = "dump_run0.melt.bin"; auto dump_file = "write_dump_atom_run0_p0.melt.bin"; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id all atom 1 {}", reference)); command("dump_modify id scale no units yes"); command("run 0"); command("write_dump all atom write_dump_atom_run*_p%.melt.bin modify scale no units yes"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); ASSERT_FILE_EXISTS(reference); ASSERT_FILE_EXISTS(dump_file); diff --git a/unittest/formats/test_dump_atom_compressed.cpp b/unittest/formats/test_dump_atom_compressed.cpp index ed591184c3..5a519e06a1 100644 --- a/unittest/formats/test_dump_atom_compressed.cpp +++ b/unittest/formats/test_dump_atom_compressed.cpp @@ -340,9 +340,9 @@ TEST_F(DumpAtomCompressTest, compressed_modify_bad_param) { if (compression_style != "atom/gz") GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt"))); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 compression_level 12"); @@ -353,9 +353,9 @@ TEST_F(DumpAtomCompressTest, compressed_modify_multi_bad_param) { if (compression_style != "atom/gz") GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt"))); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); diff --git a/unittest/formats/test_dump_cfg.cpp b/unittest/formats/test_dump_cfg.cpp index 327a9caca7..b8f879de6f 100644 --- a/unittest/formats/test_dump_cfg.cpp +++ b/unittest/formats/test_dump_cfg.cpp @@ -30,7 +30,7 @@ public: void generate_dump(std::string dump_file, std::string fields, std::string dump_modify_options, int ntimesteps) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id all {} 1 {} {}", dump_style, dump_file, fields)); if (!dump_modify_options.empty()) { @@ -38,7 +38,7 @@ public: } command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } }; @@ -54,9 +54,9 @@ TEST_F(DumpCfgTest, require_multifile) auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz xu yu zu xsu ysu zsu vx vy vz fx fy fz"; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id all cfg 1 {} {}", dump_file, fields)); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*Dump cfg requires one snapshot per file.*", command("run 0");); } diff --git a/unittest/formats/test_dump_cfg_compressed.cpp b/unittest/formats/test_dump_cfg_compressed.cpp index 834a71db70..20f902091b 100644 --- a/unittest/formats/test_dump_cfg_compressed.cpp +++ b/unittest/formats/test_dump_cfg_compressed.cpp @@ -230,9 +230,9 @@ TEST_F(DumpCfgCompressTest, compressed_modify_bad_param) if (compression_style != "cfg/gz") GTEST_SKIP(); auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.cfg"), fields)); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 compression_level 12"); @@ -244,9 +244,9 @@ TEST_F(DumpCfgCompressTest, compressed_modify_multi_bad_param) if (compression_style != "cfg/gz") GTEST_SKIP(); auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.cfg"), fields)); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); diff --git a/unittest/formats/test_dump_custom.cpp b/unittest/formats/test_dump_custom.cpp index f2d7935426..b90d77e966 100644 --- a/unittest/formats/test_dump_custom.cpp +++ b/unittest/formats/test_dump_custom.cpp @@ -30,15 +30,15 @@ class DumpCustomTest : public MeltTest { public: void enable_triclinic() { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("change_box all triclinic"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } void generate_dump(std::string dump_file, std::string fields, std::string dump_modify_options, int ntimesteps) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id all {} 1 {} {}", dump_style, dump_file, fields)); if (!dump_modify_options.empty()) { @@ -46,14 +46,14 @@ public: } command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } void generate_text_and_binary_dump(std::string text_file, std::string binary_file, std::string fields, std::string dump_modify_options, int ntimesteps) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id0 all {} 1 {} {}", dump_style, text_file, fields)); command(fmt::format("dump id1 all {} 1 {} {}", dump_style, binary_file, fields)); @@ -63,15 +63,15 @@ public: } command(fmt::format("run {}", ntimesteps)); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } std::string convert_binary_to_text(std::string binary_file) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); std::string cmdline = fmt::format("{} {}", BINARY2TXT_BINARY, binary_file); system(cmdline.c_str()); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); return fmt::format("{}.txt", binary_file); } }; @@ -113,9 +113,9 @@ TEST_F(DumpCustomTest, thresh_run0) TEST_F(DumpCustomTest, compute_run0) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("compute comp all property/atom x y z"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto dump_file = "dump_custom_compute_run0.melt"; auto fields = "id type x y z c_comp[1] c_comp[2] c_comp[3]"; @@ -134,9 +134,9 @@ TEST_F(DumpCustomTest, compute_run0) TEST_F(DumpCustomTest, fix_run0) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("fix numdiff all numdiff 1 0.0001"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto dump_file = "dump_custom_compute_run0.melt"; auto fields = "id x y z f_numdiff[1] f_numdiff[2] f_numdiff[3]"; @@ -155,10 +155,10 @@ TEST_F(DumpCustomTest, fix_run0) TEST_F(DumpCustomTest, custom_run0) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("fix prop all property/atom i_flag1 d_flag2"); command("compute 1 all property/atom i_flag1 d_flag2"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto dump_file = "dump_custom_custom_run0.melt"; auto fields = "id x y z i_flag1 d_flag2"; @@ -242,10 +242,10 @@ TEST_F(DumpCustomTest, binary_triclinic_run1) TEST_F(DumpCustomTest, with_variable_run1) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("compute 1 all property/atom proc"); command("variable p atom (c_1%10)+1"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto dump_file = "dump_custom_with_variable_run1.melt"; auto fields = "id type x y z v_p"; diff --git a/unittest/formats/test_dump_local_compressed.cpp b/unittest/formats/test_dump_local_compressed.cpp index 20f90984a1..95656071fc 100644 --- a/unittest/formats/test_dump_local_compressed.cpp +++ b/unittest/formats/test_dump_local_compressed.cpp @@ -31,9 +31,9 @@ public: void SetUp() override { CompressedDumpTest::SetUp(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("compute comp all pair/local dist eng"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } }; @@ -205,9 +205,9 @@ TEST_F(DumpLocalCompressTest, compressed_modify_bad_param) auto fields = "index c_comp[1]"; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.local"), fields)); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 compression_level 12"); @@ -220,9 +220,9 @@ TEST_F(DumpLocalCompressTest, compressed_modify_multi_bad_param) auto fields = "index c_comp[1]"; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.local"), fields)); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); diff --git a/unittest/formats/test_dump_xyz_compressed.cpp b/unittest/formats/test_dump_xyz_compressed.cpp index f80201872c..dad7911b4c 100644 --- a/unittest/formats/test_dump_xyz_compressed.cpp +++ b/unittest/formats/test_dump_xyz_compressed.cpp @@ -191,9 +191,9 @@ TEST_F(DumpXYZCompressTest, compressed_modify_bad_param) { if (compression_style != "xyz/gz") GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.xyz"))); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 compression_level 12"); @@ -204,9 +204,9 @@ TEST_F(DumpXYZCompressTest, compressed_modify_multi_bad_param) { if (compression_style != "xyz/gz") GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.xyz"))); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); diff --git a/unittest/formats/test_eim_potential_file_reader.cpp b/unittest/formats/test_eim_potential_file_reader.cpp index 9992fb8662..26f2795a85 100644 --- a/unittest/formats/test_eim_potential_file_reader.cpp +++ b/unittest/formats/test_eim_potential_file_reader.cpp @@ -18,6 +18,7 @@ #include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "../testing/core.h" #include #include @@ -28,28 +29,23 @@ using utils::split_words; // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; -class EIMPotentialFileReaderTest : public ::testing::Test { +class EIMPotentialFileReaderTest : public LAMMPSTest { protected: - LAMMPS *lmp; PairEIM::Setfl setfl; static const int nelements = 9; void SetUp() override { - const char *args[] = { - "PotentialFileReaderTest", "-log", "none", "-echo", "screen", "-nocite"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - lmp->input->one("units metal"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + testbinary = "EIMPotentialFileReaderTest"; + LAMMPSTest::SetUp(); ASSERT_NE(lmp, nullptr); + + BEGIN_HIDE_OUTPUT(); + command("units metal"); + END_HIDE_OUTPUT(); // check if the prerequisite eim pair style is available - Info *info = new Info(lmp); ASSERT_TRUE(info->has_style("pair", "eim")); - delete info; int npair = nelements * (nelements + 1) / 2; setfl.ielement = new int[nelements]; @@ -99,17 +95,15 @@ protected: delete[] setfl.rs; delete[] setfl.tp; - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); + LAMMPSTest::TearDown(); } }; TEST_F(EIMPotentialFileReaderTest, global_line) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); EIMPotentialFileReader reader(lmp, "ffield.eim"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); reader.get_global(&setfl); ASSERT_DOUBLE_EQ(setfl.division, 2.0); @@ -119,9 +113,9 @@ TEST_F(EIMPotentialFileReaderTest, global_line) TEST_F(EIMPotentialFileReaderTest, element_line_sequential) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); EIMPotentialFileReader reader(lmp, "ffield.eim"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); reader.get_element(&setfl, 0, "Li"); ASSERT_EQ(setfl.ielement[0], 3); @@ -144,9 +138,9 @@ TEST_F(EIMPotentialFileReaderTest, element_line_sequential) TEST_F(EIMPotentialFileReaderTest, element_line_random) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); EIMPotentialFileReader reader(lmp, "ffield.eim"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); reader.get_element(&setfl, 0, "Id"); ASSERT_EQ(setfl.ielement[0], 53); @@ -160,9 +154,9 @@ TEST_F(EIMPotentialFileReaderTest, element_line_random) TEST_F(EIMPotentialFileReaderTest, pair_line) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); EIMPotentialFileReader reader(lmp, "ffield.eim"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); reader.get_pair(&setfl, 0, "Li", "Li"); ASSERT_DOUBLE_EQ(setfl.rcutphiA[0], 6.0490e+00); @@ -183,9 +177,9 @@ TEST_F(EIMPotentialFileReaderTest, pair_line) TEST_F(EIMPotentialFileReaderTest, pair_identical) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); EIMPotentialFileReader reader(lmp, "ffield.eim"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); reader.get_pair(&setfl, 0, "Li", "Na"); reader.get_pair(&setfl, 1, "Na", "Li"); diff --git a/unittest/formats/test_file_operations.cpp b/unittest/formats/test_file_operations.cpp index cf85d810df..80082bc53c 100644 --- a/unittest/formats/test_file_operations.cpp +++ b/unittest/formats/test_file_operations.cpp @@ -17,6 +17,7 @@ #include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "../testing/core.h" #include #include @@ -31,43 +32,17 @@ using utils::sfgets; using utils::sfread; using utils::split_words; -#if defined(OMPI_MAJOR_VERSION) -const bool have_openmpi = true; -#else -const bool have_openmpi = false; -#endif - -#define TEST_FAILURE(errmsg, ...) \ - if (Info::has_exceptions()) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_ANY_THROW({__VA_ARGS__}); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } else { \ - if (!have_openmpi) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_DEATH({__VA_ARGS__}, ""); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } \ - } - // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; -class FileOperationsTest : public ::testing::Test { +class FileOperationsTest : public LAMMPSTest { protected: - LAMMPS *lmp; - void SetUp() override { - const char *args[] = {"FileOperationsTest", "-log", "none", "-echo", "screen", "-nocite"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - if (!verbose) ::testing::internal::GetCapturedStdout(); + testbinary = "FileOperationsTest"; + LAMMPSTest::SetUp(); ASSERT_NE(lmp, nullptr); + FILE *fp = fopen("safe_file_read_test.txt", "wb"); ASSERT_NE(fp, nullptr); fputs("one line\n", fp); @@ -79,13 +54,9 @@ protected: void TearDown() override { - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); + LAMMPSTest::TearDown(); remove("safe_file_read_test.txt"); } - - void command(const std::string &cmd) { lmp->input->one(cmd); } }; #define MAX_BUF_SIZE 128 @@ -179,7 +150,7 @@ int main(int argc, char **argv) MPI_Init(&argc, &argv); ::testing::InitGoogleMock(&argc, argv); - if (have_openmpi && !LAMMPS_NS::Info::has_exceptions()) + if (Info::get_mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) std::cout << "Warning: using OpenMPI without exceptions. " "Death tests will be skipped\n"; diff --git a/unittest/formats/test_image_flags.cpp b/unittest/formats/test_image_flags.cpp index 6b3a333328..63d85789e6 100644 --- a/unittest/formats/test_image_flags.cpp +++ b/unittest/formats/test_image_flags.cpp @@ -15,6 +15,7 @@ #include "input.h" #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "../testing/core.h" #include #include @@ -28,20 +29,14 @@ using LAMMPS_NS::utils::split_words; namespace LAMMPS_NS { using ::testing::Eq; -class ImageFlagsTest : public ::testing::Test { +class ImageFlagsTest : public LAMMPSTest { protected: - LAMMPS *lmp; - void SetUp() override { - const char *args[] = {"ImageFlagsTest", "-log", "none", "-echo", "screen", "-nocite"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - if (!verbose) ::testing::internal::GetCapturedStdout(); + testbinary = "ImageFlagsTest"; + LAMMPSTest::SetUp(); ASSERT_NE(lmp, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units real"); command("dimension 3"); command("region box block -2 2 -2 2 -2 2"); @@ -54,18 +49,14 @@ protected: command("set atom 1 image -1 2 3"); command("set atom 2 image -2 1 -1"); command("write_data test_image_flags.data"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } void TearDown() override { - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); + LAMMPSTest::TearDown(); remove("test_image_flags.data"); } - - void command(const std::string &cmd) { lmp->input->one(cmd); } }; TEST_F(ImageFlagsTest, change_box) @@ -87,9 +78,9 @@ TEST_F(ImageFlagsTest, change_box) ASSERT_EQ(imy, 1); ASSERT_EQ(imz, -1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("change_box all boundary f p p"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); image = lmp->atom->image; imx = (image[0] & IMGMASK) - IMGMAX; @@ -108,9 +99,9 @@ TEST_F(ImageFlagsTest, change_box) ASSERT_EQ(imy, 1); ASSERT_EQ(imz, -1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("change_box all boundary f s p"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); image = lmp->atom->image; imx = (image[0] & IMGMASK) - IMGMAX; @@ -129,9 +120,9 @@ TEST_F(ImageFlagsTest, change_box) ASSERT_EQ(imy, 0); ASSERT_EQ(imz, -1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("change_box all boundary p p m"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); image = lmp->atom->image; imx = (image[0] & IMGMASK) - IMGMAX; @@ -153,14 +144,14 @@ TEST_F(ImageFlagsTest, change_box) TEST_F(ImageFlagsTest, read_data) { - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("dimension 3"); command("boundary p p p"); command("pair_style zero 2.0"); command("read_data test_image_flags.data"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); auto image = lmp->atom->image; int imx = (image[0] & IMGMASK) - IMGMAX; @@ -179,14 +170,14 @@ TEST_F(ImageFlagsTest, read_data) ASSERT_EQ(imy, 1); ASSERT_EQ(imz, -1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("dimension 3"); command("boundary f p p"); command("pair_style zero 2.0"); command("read_data test_image_flags.data"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); image = lmp->atom->image; imx = (image[0] & IMGMASK) - IMGMAX; @@ -205,14 +196,14 @@ TEST_F(ImageFlagsTest, read_data) ASSERT_EQ(imy, 1); ASSERT_EQ(imz, -1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("dimension 3"); command("boundary p s p"); command("pair_style zero 2.0"); command("read_data test_image_flags.data"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); image = lmp->atom->image; imx = (image[0] & IMGMASK) - IMGMAX; @@ -231,14 +222,14 @@ TEST_F(ImageFlagsTest, read_data) ASSERT_EQ(imy, 0); ASSERT_EQ(imz, -1); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("dimension 3"); command("boundary p p m"); command("pair_style zero 2.0"); command("read_data test_image_flags.data"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); image = lmp->atom->image; imx = (image[0] & IMGMASK) - IMGMAX; diff --git a/unittest/formats/test_molecule_file.cpp b/unittest/formats/test_molecule_file.cpp index 204a1bd061..4bcf375dff 100644 --- a/unittest/formats/test_molecule_file.cpp +++ b/unittest/formats/test_molecule_file.cpp @@ -19,6 +19,7 @@ #include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "../testing/core.h" #include #include @@ -33,26 +34,6 @@ using utils::split_words; #define test_name test_info_->name() -#if defined(OMPI_MAJOR_VERSION) -const bool have_openmpi = true; -#else -const bool have_openmpi = false; -#endif - -#define TEST_FAILURE(errmsg, ...) \ - if (Info::has_exceptions()) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_ANY_THROW({__VA_ARGS__}); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } else { \ - if (!have_openmpi) { \ - ::testing::internal::CaptureStdout(); \ - ASSERT_DEATH({__VA_ARGS__}, ""); \ - auto mesg = ::testing::internal::GetCapturedStdout(); \ - ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ - } \ - } static void create_molecule_files() { @@ -96,27 +77,21 @@ static void create_molecule_files() // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; -class MoleculeFileTest : public ::testing::Test { +class MoleculeFileTest : public LAMMPSTest { protected: - LAMMPS *lmp; - void SetUp() override { - const char *args[] = {"MoleculeFileTest", "-log", "none", "-echo", "screen", "-nocite"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - create_molecule_files(); - if (!verbose) ::testing::internal::GetCapturedStdout(); + testbinary = "MoleculeFileTest"; + LAMMPSTest::SetUp(); ASSERT_NE(lmp, nullptr); + BEGIN_HIDE_OUTPUT(); + create_molecule_files(); + END_HIDE_OUTPUT(); } void TearDown() override { - if (!verbose) ::testing::internal::CaptureStdout(); - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); + LAMMPSTest::TearDown(); remove("h2o.mol"); remove("co2.mol"); } @@ -128,11 +103,9 @@ protected: fputs(content.c_str(), fp); fclose(fp); - lmp->input->one(fmt::format("molecule {} {} {}", name, file, args)); + command(fmt::format("molecule {} {} {}", name, file, args)); remove(file.c_str()); } - - void command(const std::string &cmd) { lmp->input->one(cmd); } }; TEST_F(MoleculeFileTest, nofile) @@ -292,7 +265,7 @@ int main(int argc, char **argv) MPI_Init(&argc, &argv); ::testing::InitGoogleMock(&argc, argv); - if (have_openmpi && !LAMMPS_NS::Info::has_exceptions()) + if (Info::get_mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) std::cout << "Warning: using OpenMPI without exceptions. " "Death tests will be skipped\n"; diff --git a/unittest/formats/test_pair_unit_convert.cpp b/unittest/formats/test_pair_unit_convert.cpp index f0c2f0d031..bdd66f67a6 100644 --- a/unittest/formats/test_pair_unit_convert.cpp +++ b/unittest/formats/test_pair_unit_convert.cpp @@ -20,6 +20,7 @@ #include "thermo.h" #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "../testing/core.h" #include #include @@ -42,23 +43,17 @@ const double p_convert = 1.01325; // of data in update.cpp. could be 1.0e-12 const double rel_error = 5.0e-7; -class PairUnitConvertTest : public ::testing::Test { +class PairUnitConvertTest : public LAMMPSTest { protected: - LAMMPS *lmp; - Info *info; double fold[4][3]; void SetUp() override { - const char *args[] = {"PairUnitConvertTest", "-log", "none", "-echo", "screen", "-nocite"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); - if (!verbose) ::testing::internal::GetCapturedStdout(); + testbinary = "PairUnitConvertTest"; + LAMMPSTest::SetUp(); ASSERT_NE(lmp, nullptr); - if (!verbose) ::testing::internal::CaptureStdout(); - info = new Info(lmp); + + BEGIN_HIDE_OUTPUT(); command("units metal"); command("dimension 3"); command("region box block -4 4 -4 4 -4 4"); @@ -72,19 +67,14 @@ protected: command("mass * 1.0"); command("write_data test_pair_unit_convert.data nocoeff"); command("clear"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); } void TearDown() override { - if (!verbose) ::testing::internal::CaptureStdout(); - delete info; - delete lmp; - if (!verbose) ::testing::internal::GetCapturedStdout(); + LAMMPSTest::TearDown(); remove("test_pair_unit_convert.data"); } - - void command(const std::string &cmd) { lmp->input->one(cmd); } }; TEST_F(PairUnitConvertTest, zero) @@ -92,13 +82,13 @@ TEST_F(PairUnitConvertTest, zero) // check if the prerequisite pair style is available if (!info->has_style("pair", "zero")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style zero 6.0"); command("pair_coeff * *"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -109,14 +99,14 @@ TEST_F(PairUnitConvertTest, zero) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style zero 6.0"); command("pair_coeff * *"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -135,7 +125,7 @@ TEST_F(PairUnitConvertTest, lj_cut) // check if the prerequisite pair style is available if (!info->has_style("pair", "lj/cut")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style lj/cut 6.0"); @@ -145,7 +135,7 @@ TEST_F(PairUnitConvertTest, lj_cut) command("pair_write 1 2 1000 r 0.1 6.0 test.table.metal lj_1_2"); command("pair_write 2 2 1000 r 0.1 6.0 test.table.metal lj_2_2"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -156,7 +146,7 @@ TEST_F(PairUnitConvertTest, lj_cut) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); @@ -167,7 +157,7 @@ TEST_F(PairUnitConvertTest, lj_cut) command("pair_write 1 2 1000 r 0.1 6.0 test.table.real lj_1_2"); command("pair_write 2 2 1000 r 0.1 6.0 test.table.real lj_2_2"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -186,13 +176,13 @@ TEST_F(PairUnitConvertTest, eam) // check if the prerequisite pair style is available if (!info->has_style("pair", "eam")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style eam"); command("pair_coeff * * Cu_u3.eam"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -203,14 +193,14 @@ TEST_F(PairUnitConvertTest, eam) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style eam"); command("pair_coeff * * Cu_u3.eam"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -229,13 +219,13 @@ TEST_F(PairUnitConvertTest, eam_alloy) // check if the prerequisite pair style is available if (!info->has_style("pair", "eam/alloy")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style eam/alloy"); command("pair_coeff * * AlCu.eam.alloy Al Cu"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -246,14 +236,14 @@ TEST_F(PairUnitConvertTest, eam_alloy) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style eam/alloy"); command("pair_coeff * * AlCu.eam.alloy Al Cu"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -272,13 +262,13 @@ TEST_F(PairUnitConvertTest, eam_fs) // check if the prerequisite pair style is available if (!info->has_style("pair", "eam/fs")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style eam/fs"); command("pair_coeff * * FeP_mm.eam.fs Fe P"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -289,14 +279,14 @@ TEST_F(PairUnitConvertTest, eam_fs) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style eam/fs"); command("pair_coeff * * FeP_mm.eam.fs Fe P"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -315,13 +305,13 @@ TEST_F(PairUnitConvertTest, eam_cd) // check if the prerequisite pair style is available if (!info->has_style("pair", "eam/cd")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style eam/cd"); command("pair_coeff * * FeCr.cdeam Cr Fe"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -332,14 +322,14 @@ TEST_F(PairUnitConvertTest, eam_cd) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style eam/cd"); command("pair_coeff * * FeCr.cdeam Cr Fe"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -358,13 +348,13 @@ TEST_F(PairUnitConvertTest, eim) // check if the prerequisite pair style is available if (!info->has_style("pair", "eim")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style eim"); command("pair_coeff * * Na Cl ffield.eim Na Cl"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -375,14 +365,14 @@ TEST_F(PairUnitConvertTest, eim) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style eim"); command("pair_coeff * * Na Cl ffield.eim Na Cl"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -401,13 +391,13 @@ TEST_F(PairUnitConvertTest, gw) // check if the prerequisite pair style is available if (!info->has_style("pair", "gw")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style gw"); command("pair_coeff * * SiC.gw Si C"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -418,14 +408,14 @@ TEST_F(PairUnitConvertTest, gw) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style gw"); command("pair_coeff * * SiC.gw Si C"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -444,13 +434,13 @@ TEST_F(PairUnitConvertTest, gw_zbl) // check if the prerequisite pair style is available if (!info->has_style("pair", "gw/zbl")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style gw/zbl"); command("pair_coeff * * SiC.gw.zbl Si C"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -461,14 +451,14 @@ TEST_F(PairUnitConvertTest, gw_zbl) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style gw/zbl"); command("pair_coeff * * SiC.gw.zbl Si C"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -487,13 +477,13 @@ TEST_F(PairUnitConvertTest, nb3b_harmonic) // check if the prerequisite pair style is available if (!info->has_style("pair", "nb3b/harmonic")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style nb3b/harmonic"); command("pair_coeff * * MOH.nb3b.harmonic M O"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -504,14 +494,14 @@ TEST_F(PairUnitConvertTest, nb3b_harmonic) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style nb3b/harmonic"); command("pair_coeff * * MOH.nb3b.harmonic M O"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -530,13 +520,13 @@ TEST_F(PairUnitConvertTest, sw) // check if the prerequisite pair style is available if (!info->has_style("pair", "sw")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style sw"); command("pair_coeff * * GaN.sw Ga N"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -547,14 +537,14 @@ TEST_F(PairUnitConvertTest, sw) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style sw"); command("pair_coeff * * GaN.sw Ga N"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -573,7 +563,7 @@ TEST_F(PairUnitConvertTest, table_metal2real) // check if the prerequisite pair style is available if (!info->has_style("pair", "table")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style table linear 1000"); @@ -581,7 +571,7 @@ TEST_F(PairUnitConvertTest, table_metal2real) command("pair_coeff 1 2 test.table.metal lj_1_2"); command("pair_coeff 2 2 test.table.metal lj_2_2"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -592,7 +582,7 @@ TEST_F(PairUnitConvertTest, table_metal2real) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); @@ -601,7 +591,7 @@ TEST_F(PairUnitConvertTest, table_metal2real) command("pair_coeff 1 2 test.table.metal lj_1_2"); command("pair_coeff 2 2 test.table.metal lj_2_2"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -620,7 +610,7 @@ TEST_F(PairUnitConvertTest, table_real2metal) // check if the prerequisite pair style is available if (!info->has_style("pair", "table")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style table linear 1000"); @@ -628,7 +618,7 @@ TEST_F(PairUnitConvertTest, table_real2metal) command("pair_coeff 1 2 test.table.real lj_1_2"); command("pair_coeff 2 2 test.table.real lj_2_2"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -639,7 +629,7 @@ TEST_F(PairUnitConvertTest, table_real2metal) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units metal"); command("read_data test_pair_unit_convert.data"); @@ -648,7 +638,7 @@ TEST_F(PairUnitConvertTest, table_real2metal) command("pair_coeff 1 2 test.table.real lj_1_2"); command("pair_coeff 2 2 test.table.real lj_2_2"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -667,13 +657,13 @@ TEST_F(PairUnitConvertTest, tersoff) // check if the prerequisite pair style is available if (!info->has_style("pair", "tersoff")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style tersoff"); command("pair_coeff * * SiC.tersoff Si C"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -684,14 +674,14 @@ TEST_F(PairUnitConvertTest, tersoff) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style tersoff"); command("pair_coeff * * SiC.tersoff Si C"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -710,13 +700,13 @@ TEST_F(PairUnitConvertTest, tersoff_mod) // check if the prerequisite pair style is available if (!info->has_style("pair", "tersoff/mod")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style tersoff/mod"); command("pair_coeff * * Si.tersoff.mod Si Si"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -727,14 +717,14 @@ TEST_F(PairUnitConvertTest, tersoff_mod) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style tersoff/mod"); command("pair_coeff * * Si.tersoff.mod Si Si"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -753,13 +743,13 @@ TEST_F(PairUnitConvertTest, tersoff_mod_c) // check if the prerequisite pair style is available if (!info->has_style("pair", "tersoff/mod/c")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style tersoff/mod/c"); command("pair_coeff * * Si.tersoff.modc Si Si"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -770,14 +760,14 @@ TEST_F(PairUnitConvertTest, tersoff_mod_c) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style tersoff/mod/c"); command("pair_coeff * * Si.tersoff.modc Si Si"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -796,13 +786,13 @@ TEST_F(PairUnitConvertTest, tersoff_table) // check if the prerequisite pair style is available if (!info->has_style("pair", "tersoff/table")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style tersoff/table"); command("pair_coeff * * SiC.tersoff Si C"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -813,14 +803,14 @@ TEST_F(PairUnitConvertTest, tersoff_table) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style tersoff/table"); command("pair_coeff * * SiC.tersoff Si C"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -839,13 +829,13 @@ TEST_F(PairUnitConvertTest, tersoff_zbl) // check if the prerequisite pair style is available if (!info->has_style("pair", "tersoff/zbl")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style tersoff/zbl"); command("pair_coeff * * SiC.tersoff.zbl Si C"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -856,14 +846,14 @@ TEST_F(PairUnitConvertTest, tersoff_zbl) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style tersoff/zbl"); command("pair_coeff * * SiC.tersoff.zbl Si C"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -882,14 +872,14 @@ TEST_F(PairUnitConvertTest, tersoff_zbl_omp) // check if the prerequisite pair style is available if (!info->has_style("pair", "tersoff/zbl/omp")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("package omp 4"); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style tersoff/zbl/omp"); command("pair_coeff * * SiC.tersoff.zbl Si C"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -900,7 +890,7 @@ TEST_F(PairUnitConvertTest, tersoff_zbl_omp) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("package omp 4"); command("units real"); @@ -908,7 +898,7 @@ TEST_F(PairUnitConvertTest, tersoff_zbl_omp) command("pair_style tersoff/zbl/omp"); command("pair_coeff * * SiC.tersoff.zbl Si C"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); @@ -927,13 +917,13 @@ TEST_F(PairUnitConvertTest, vashishta) // check if the prerequisite pair style is available if (!info->has_style("pair", "vashishta")) GTEST_SKIP(); - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("units metal"); command("read_data test_pair_unit_convert.data"); command("pair_style vashishta"); command("pair_coeff * * SiC.vashishta Si C"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); // copy pressure, energy, and force from first step double pold; @@ -944,14 +934,14 @@ TEST_F(PairUnitConvertTest, vashishta) for (int j = 0; j < 3; ++j) fold[i][j] = f[i][j]; - if (!verbose) ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("clear"); command("units real"); command("read_data test_pair_unit_convert.data"); command("pair_style vashishta"); command("pair_coeff * * SiC.vashishta Si C"); command("run 0 post no"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + END_HIDE_OUTPUT(); double pnew; lmp->output->thermo->evaluate_keyword("press", &pnew); diff --git a/unittest/testing/core.h b/unittest/testing/core.h index 01c5872579..deab845573 100644 --- a/unittest/testing/core.h +++ b/unittest/testing/core.h @@ -22,6 +22,8 @@ #include "exceptions.h" #include +#include +#include using namespace LAMMPS_NS; @@ -103,20 +105,31 @@ public: } protected: - const char *testbinary = "LAMMPSTest"; + std::string testbinary = "LAMMPSTest"; + std::vector args = {"-log", "none", "-echo", "screen", "-nocite"}; LAMMPS *lmp; Info *info; void SetUp() override { - const char *args[] = {testbinary, "-log", "none", "-echo", "screen", "-nocite"}; - char **argv = (char **)args; - int argc = sizeof(args) / sizeof(char *); + int argc = args.size() + 1; + char ** argv = new char*[argc]; + argv[0] = utils::strdup(testbinary); + for(int i = 1; i < argc; i++) { + argv[i] = utils::strdup(args[i-1]); + } + HIDE_OUTPUT([&] { lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); info = new Info(lmp); }); InitSystem(); + + for(int i = 0; i < argc; i++) { + delete [] argv[i]; + argv[i] = nullptr; + } + delete [] argv; } virtual void InitSystem() {} From dca9cd9c1c8118db7c928a532182f58fca6d7680 Mon Sep 17 00:00:00 2001 From: Trung Nguyen Date: Mon, 29 Mar 2021 13:46:16 -0500 Subject: [PATCH 0287/1217] Kept the .cubin files so that they are only rebuilt whenever changes are made to the relevant source files --- lib/gpu/Makefile.cuda | 3 +-- lib/gpu/Makefile.cuda_mps | 3 +-- lib/gpu/Nvidia.makefile | 5 +---- lib/gpu/Nvidia.makefile_multi | 3 +-- 4 files changed, 4 insertions(+), 10 deletions(-) diff --git a/lib/gpu/Makefile.cuda b/lib/gpu/Makefile.cuda index 7020f18cf3..e02501d080 100644 --- a/lib/gpu/Makefile.cuda +++ b/lib/gpu/Makefile.cuda @@ -45,7 +45,7 @@ CUDA_INCLUDE = -I$(CUDA_HOME)/include CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC CUDA_LINK = $(CUDA_LIB) -lcudart -CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) -Icudpp_mini $(CUDA_ARCH) \ +CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) $(CUDA_ARCH) \ $(CUDA_PRECISION) BIN2C = $(CUDA_HOME)/bin/bin2c @@ -103,7 +103,6 @@ $(OBJ_DIR)/pppm_d_cubin.h: $(OBJ_DIR)/pppm_d.cubin $(OBJ_DIR)/%_cubin.h: lal_%.cu $(ALL_H) $(CUDA) --fatbin -DNV_KERNEL -o $(OBJ_DIR)/$*.cubin $(OBJ_DIR)/lal_$*.cu $(BIN2C) -c -n $* $(OBJ_DIR)/$*.cubin > $@ - @rm $(OBJ_DIR)/$*.cubin # host code compilation diff --git a/lib/gpu/Makefile.cuda_mps b/lib/gpu/Makefile.cuda_mps index 21aac89151..f52bd07fcf 100644 --- a/lib/gpu/Makefile.cuda_mps +++ b/lib/gpu/Makefile.cuda_mps @@ -44,7 +44,7 @@ CUDA_INCLUDE = -I$(CUDA_HOME)/include CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC CUDA_LINK = $(CUDA_LIB) -lcudart -CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) -Icudpp_mini $(CUDA_ARCH) \ +CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) $(CUDA_ARCH) \ $(CUDA_PRECISION) BIN2C = $(CUDA_HOME)/bin/bin2c @@ -102,7 +102,6 @@ $(OBJ_DIR)/pppm_d_cubin.h: $(OBJ_DIR)/pppm_d.cubin $(OBJ_DIR)/%_cubin.h: lal_%.cu $(ALL_H) $(CUDA) --fatbin -DNV_KERNEL -o $(OBJ_DIR)/$*.cubin $(OBJ_DIR)/lal_$*.cu $(BIN2C) -c -n $* $(OBJ_DIR)/$*.cubin > $@ - @rm $(OBJ_DIR)/$*.cubin # host code compilation diff --git a/lib/gpu/Nvidia.makefile b/lib/gpu/Nvidia.makefile index d3275b890f..56942d3f3c 100644 --- a/lib/gpu/Nvidia.makefile +++ b/lib/gpu/Nvidia.makefile @@ -30,7 +30,7 @@ $(OBJ_DIR): # Compilers and linkers -CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) -Icudpp_mini $(CUDA_ARCH) \ +CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) $(CUDA_ARCH) \ $(CUDA_PRECISION) CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_PRECISION) $(CUDA_INCLUDE) \ $(CUDPP_OPT) @@ -46,7 +46,6 @@ $(OBJ_DIR)/pppm_f.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h \ $(OBJ_DIR)/pppm_f_cubin.h: $(OBJ_DIR)/pppm_f.cubin $(BIN2C) -c -n pppm_f $(OBJ_DIR)/pppm_f.cubin > $(OBJ_DIR)/pppm_f_cubin.h - rm $(OBJ_DIR)/pppm_f.cubin $(OBJ_DIR)/pppm_d.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h \ lal_pre_cuda_hip.h @@ -54,12 +53,10 @@ $(OBJ_DIR)/pppm_d.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h \ $(OBJ_DIR)/pppm_d_cubin.h: $(OBJ_DIR)/pppm_d.cubin $(BIN2C) -c -n pppm_d $(OBJ_DIR)/pppm_d.cubin > $(OBJ_DIR)/pppm_d_cubin.h - rm $(OBJ_DIR)/pppm_d.cubin $(OBJ_DIR)/%_cubin.h: lal_%.cu $(ALL_H) $(CUDA) --fatbin -DNV_KERNEL -o $(OBJ_DIR)/$*.cubin $(OBJ_DIR)/lal_$*.cu $(BIN2C) -c -n $* $(OBJ_DIR)/$*.cubin > $@ - @rm $(OBJ_DIR)/$*.cubin # host code compilation diff --git a/lib/gpu/Nvidia.makefile_multi b/lib/gpu/Nvidia.makefile_multi index 6716388562..ddbee4f2a1 100644 --- a/lib/gpu/Nvidia.makefile_multi +++ b/lib/gpu/Nvidia.makefile_multi @@ -29,7 +29,7 @@ $(OBJ_DIR): # Compilers and linkers -CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) -Icudpp_mini $(CUDA_ARCH) \ +CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) $(CUDA_ARCH) \ $(CUDA_PRECISION) CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_PRECISION) $(CUDA_INCLUDE) \ $(CUDPP_OPT) @@ -54,7 +54,6 @@ $(OBJ_DIR)/pppm_d_cubin.h: $(OBJ_DIR)/pppm_d.cubin $(OBJ_DIR)/%_cubin.h: lal_%.cu $(ALL_H) $(CUDA) --fatbin -DNV_KERNEL -o $(OBJ_DIR)/$*.cubin $(OBJ_DIR)/lal_$*.cu $(BIN2C) -c -n $* $(OBJ_DIR)/$*.cubin > $@ - @rm $(OBJ_DIR)/$*.cubin # host code compilation From 6f986eee4eb5ef72c46fb1d8a0c0dc00f6918712 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 29 Mar 2021 15:01:29 -0400 Subject: [PATCH 0288/1217] Add missing changes --- unittest/commands/test_lattice_region.cpp | 10 +++----- unittest/formats/test_file_operations.cpp | 8 +++--- unittest/formats/test_molecule_file.cpp | 30 +++++++++-------------- 3 files changed, 20 insertions(+), 28 deletions(-) diff --git a/unittest/commands/test_lattice_region.cpp b/unittest/commands/test_lattice_region.cpp index eb6d577652..ae38f3a7f5 100644 --- a/unittest/commands/test_lattice_region.cpp +++ b/unittest/commands/test_lattice_region.cpp @@ -81,10 +81,9 @@ TEST_F(LatticeRegionTest, lattice_none) TEST_F(LatticeRegionTest, lattice_sc) { - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("lattice sc 1.0 spacing 1.5 2.0 3.0"); - auto output = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << output; + auto output = END_CAPTURE_OUTPUT(); ASSERT_THAT(output, MatchesRegex(".*Lattice spacing in x,y,z = 1.50* 2.0* 3.0*.*")); auto lattice = lmp->domain->lattice; @@ -92,10 +91,9 @@ TEST_F(LatticeRegionTest, lattice_sc) ASSERT_EQ(lattice->ylattice, 2.0); ASSERT_EQ(lattice->zlattice, 3.0); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("lattice sc 2.0"); - output = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << output; + output = END_CAPTURE_OUTPUT(); ASSERT_THAT(output, MatchesRegex(".*Lattice spacing in x,y,z = 2.0* 2.0* 2.0*.*")); lattice = lmp->domain->lattice; diff --git a/unittest/formats/test_file_operations.cpp b/unittest/formats/test_file_operations.cpp index 80082bc53c..700990fb72 100644 --- a/unittest/formats/test_file_operations.cpp +++ b/unittest/formats/test_file_operations.cpp @@ -127,15 +127,15 @@ TEST_F(FileOperationsTest, safe_fread) TEST_F(FileOperationsTest, logmesg) { char buf[8]; - ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); command("echo none"); - ::testing::internal::GetCapturedStdout(); - ::testing::internal::CaptureStdout(); + END_HIDE_OUTPUT(); + BEGIN_CAPTURE_OUTPUT(); utils::logmesg(lmp, "one\n"); command("log test_logmesg.log"); utils::logmesg(lmp, "two\n"); command("log none"); - std::string out = ::testing::internal::GetCapturedStdout(); + std::string out = END_CAPTURE_OUTPUT(); memset(buf, 0, 8); FILE *fp = fopen("test_logmesg.log", "r"); fread(buf, 1, 8, fp); diff --git a/unittest/formats/test_molecule_file.cpp b/unittest/formats/test_molecule_file.cpp index 4bcf375dff..9928ec4b7c 100644 --- a/unittest/formats/test_molecule_file.cpp +++ b/unittest/formats/test_molecule_file.cpp @@ -174,32 +174,29 @@ TEST_F(MoleculeFileTest, nospecial) TEST_F(MoleculeFileTest, minimal) { - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); run_mol_cmd(test_name, "", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"); - auto output = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << output; + auto output = END_CAPTURE_OUTPUT(); ASSERT_THAT(output, MatchesRegex(".*Read molecule template.*1 molecules.*1 atoms.*0 bonds.*")); } TEST_F(MoleculeFileTest, twomols) { - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); run_mol_cmd(test_name, "", "Comment\n2 atoms\n\n" " Coords\n\n 1 0.0 0.0 0.0\n 2 0.0 0.0 1.0\n" " Molecules\n\n 1 1\n 2 2\n\n Types\n\n 1 1\n 2 2\n\n"); - auto output = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << output; + auto output = END_CAPTURE_OUTPUT(); ASSERT_THAT(output, MatchesRegex(".*Read molecule template.*2 molecules.*2 atoms " "with max type 2.*0 bonds.*")); } TEST_F(MoleculeFileTest, twofiles) { - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); - auto output = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << output; + auto output = END_CAPTURE_OUTPUT(); ASSERT_THAT(output, MatchesRegex(".*Read molecule template twomols:.*1 molecules.*3 atoms " "with max type 2.*2 bonds with max type 1.*" "1 angles with max type 1.*0 dihedrals.*" @@ -210,7 +207,7 @@ TEST_F(MoleculeFileTest, twofiles) TEST_F(MoleculeFileTest, bonds) { - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("atom_style bond"); command("region box block 0 1 0 1 0 1"); command("create_box 2 box bond/types 2 extra/bond/per/atom 2 " @@ -232,19 +229,17 @@ TEST_F(MoleculeFileTest, bonds) " Bonds\n\n" " 1 1 1 2\n" " 2 2 1 3\n\n"); - auto output = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << output; + auto output = END_CAPTURE_OUTPUT(); ASSERT_THAT(output, MatchesRegex(".*Read molecule template.*1 molecules.*4 atoms.*type.*2.*" "2 bonds.*type.*2.*0 angles.*")); - ::testing::internal::CaptureStdout(); + BEGIN_CAPTURE_OUTPUT(); command("mass * 2.0"); command("create_atoms 0 single 0.5 0.5 0.5 mol bonds 67235"); - output = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << output; + output = END_CAPTURE_OUTPUT(); ASSERT_THAT(output, MatchesRegex(".*Created 4 atoms.*")); - ::testing::internal::CaptureStdout(); + BEGIN_HIDE_OUTPUT(); Molecule *mol = lmp->atom->molecules[0]; ASSERT_EQ(mol->natoms, 4); ASSERT_EQ(lmp->atom->natoms, 4); @@ -256,8 +251,7 @@ TEST_F(MoleculeFileTest, bonds) EXPECT_DOUBLE_EQ(mol->com[2], 0.5); EXPECT_DOUBLE_EQ(mol->maxextent, sqrt(2)); EXPECT_EQ(mol->comatom, 1); - output = ::testing::internal::GetCapturedStdout(); - if (verbose) std::cout << output; + END_HIDE_OUTPUT(); } int main(int argc, char **argv) From 2b11848fcca79cfc1ef1ffdbbb1e34f4d4833004 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Mar 2021 15:26:57 -0400 Subject: [PATCH 0289/1217] bugfix from dan bolintineanu for issue reported on lammps-users by Deng Pan --- src/GRANULAR/pair_granular.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index cc210138eb..bcf262aa2c 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -446,9 +446,9 @@ void PairGranular::compute(int eflag, int vflag) if (tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_FORCE || tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_RESCALE_FORCE) - frameupdate = fabs(rsht) < EPSILON*Fscrit; + frameupdate = fabs(rsht) > EPSILON*Fscrit; else - frameupdate = fabs(rsht)*k_tangential < EPSILON*Fscrit; + frameupdate = fabs(rsht)*k_tangential > EPSILON*Fscrit; if (frameupdate) { shrmag = sqrt(history[0]*history[0] + history[1]*history[1] + history[2]*history[2]); @@ -568,7 +568,7 @@ void PairGranular::compute(int eflag, int vflag) if (historyupdate) { rolldotn = history[rhist0]*nx + history[rhist1]*ny + history[rhist2]*nz; - frameupdate = fabs(rolldotn)*k_roll < EPSILON*Frcrit; + frameupdate = fabs(rolldotn)*k_roll > EPSILON*Frcrit; if (frameupdate) { // rotate into tangential plane rollmag = sqrt(history[rhist0]*history[rhist0] + history[rhist1]*history[rhist1] + From 4ea9a9bf049e7185b949a5f52d83ddb14563e071 Mon Sep 17 00:00:00 2001 From: kipbarrett Date: Mon, 29 Mar 2021 15:23:22 -0500 Subject: [PATCH 0290/1217] Removed screening symmetry and added rann example --- examples/USER/rann/TiZr_2.nn | 277 +++++++++++++++++++++++++++++++++++ examples/USER/rann/in.lammps | 45 ++++++ src/USER-RANN/pair_rann.cpp | 3 - 3 files changed, 322 insertions(+), 3 deletions(-) create mode 100644 examples/USER/rann/TiZr_2.nn create mode 100644 examples/USER/rann/in.lammps diff --git a/examples/USER/rann/TiZr_2.nn b/examples/USER/rann/TiZr_2.nn new file mode 100644 index 0000000000..7ebdebf320 --- /dev/null +++ b/examples/USER/rann/TiZr_2.nn @@ -0,0 +1,277 @@ +#iter: 3957, evals: 6770, e_err: 1.2959304580e-05, e1: 1.2959304580e-05, ev_err 1.4570936792e-05, r_err: 1.0147937957e-06, lambda: 1.4986245485e+50 +atomtypes: +Ti Zr +mass:Ti: +47.867000 +mass:Zr: +91.224000 +fingerprintsperelement:Ti: +3 +fingerprintsperelement:Zr: +3 +fingerprints:Ti_Ti: +radialscreened_0 +fingerprints:Ti_all_all: +bondscreened_0 +fingerprints:Ti_Zr: +radialscreened_0 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+2.227387923911460e+01 +8.401986227903949e+00 +bias:Zr:1: +-1.947972075332220e+01 +activationfunctions:Ti:0: +sigI +activationfunctions:Ti:1: +linear +activationfunctions:Zr:0: +sigI +activationfunctions:Zr:1: +linear +calibrationparameters:algorithm: +LM_ch +calibrationparameters:dumpdirectory: +. +calibrationparameters:doforces: +0 +calibrationparameters:normalizeinput: +1 +calibrationparameters:tolerance: +1.0000000000e-07 +calibrationparameters:regularizer: +1.0000000000e-04 +calibrationparameters:logfile: +TiZr.log +calibrationparameters:potentialoutputfile: +TiZr_output_2.nn +calibrationparameters:potentialoutputfreq: +10 +calibrationparameters:maxepochs: +10000000 +calibrationparameters:dimsreserved:Ti:0: +45 +calibrationparameters:dimsreserved:Ti:1: +20 +calibrationparameters:dimsreserved:Ti:2: +0 +calibrationparameters:dimsreserved:Zr:0: +37 +calibrationparameters:dimsreserved:Zr:1: +20 +calibrationparameters:dimsreserved:Zr:2: +0 +calibrationparameters:validation: +0.100000 diff --git a/examples/USER/rann/in.lammps b/examples/USER/rann/in.lammps new file mode 100644 index 0000000000..3f831fca21 --- /dev/null +++ b/examples/USER/rann/in.lammps @@ -0,0 +1,45 @@ +units metal +dimension 3 +boundary p p p +atom_style atomic + + +lattice hcp 2.9962594 +region whole block 0 10 0 10 0 10 units lattice +create_box 2 whole +create_atoms 2 box +timestep 0.001 +set group all type 1 +set group all type/fraction 2 0.10 486 + +pair_style rann +pair_coeff * * TiZr_2.nn Ti Zr + + + +compute peratom all pe/atom +shell mkdir ovito_files2 +dump 1 all custom 10 ovito_files2/dump.*.gz id type x y z c_peratom +dump_modify 1 element Ti Zr + +thermo 1 +thermo_style custom step lx ly lz press pxx pyy pzz pxy pxz pyz pe temp + +variable etol equal 1.0e-32 +variable ftol equal 1.0e-32 +variable maxiter equal 1.0e+9 +variable maxeval equal 1.0e+9 +variable dmax equal 1.0e-2 + +fix 1 all box/relax aniso 0.0 +min_style cg +minimize ${etol} ${ftol} ${maxiter} ${maxeval} +unfix 1 +write_restart TiZr.min + +#-------------------------EQUILIBRATION-------------------------------- + +velocity all create 300 12345 mom yes rot no +fix 1 all npt temp 300 300 0.1 aniso 0 0 1 +run 100 +unfix 1 diff --git a/src/USER-RANN/pair_rann.cpp b/src/USER-RANN/pair_rann.cpp index 0dcf3740a6..6a100db244 100644 --- a/src/USER-RANN/pair_rann.cpp +++ b/src/USER-RANN/pair_rann.cpp @@ -619,14 +619,11 @@ void PairRANN::read_screening(std::vector line,std::vectorone(filename,linenum-1,"unrecognized screening keyword"); } From 213fc06321270fa11eff0255e1d5bb16190546d4 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 29 Mar 2021 18:05:04 -0400 Subject: [PATCH 0291/1217] Add GzFileWriter implementation --- src/COMPRESS/dump_atom_gz.cpp | 89 +++++++-------- src/COMPRESS/dump_atom_gz.h | 5 +- src/COMPRESS/dump_atom_zstd.cpp | 6 +- src/COMPRESS/gz_file_writer.cpp | 105 ++++++++++++++++++ src/COMPRESS/gz_file_writer.h | 47 ++++++++ src/COMPRESS/zstd_file_writer.cpp | 8 +- src/COMPRESS/zstd_file_writer.h | 2 +- src/file_writer.h | 2 +- .../formats/test_dump_atom_compressed.cpp | 4 +- 9 files changed, 207 insertions(+), 61 deletions(-) create mode 100644 src/COMPRESS/gz_file_writer.cpp create mode 100644 src/COMPRESS/gz_file_writer.h diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index f252e32064..071af2167d 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -14,6 +14,7 @@ #include "dump_atom_gz.h" #include "domain.h" #include "error.h" +#include "file_writer.h" #include "update.h" @@ -25,10 +26,6 @@ using namespace LAMMPS_NS; DumpAtomGZ::DumpAtomGZ(LAMMPS *lmp, int narg, char **arg) : DumpAtom(lmp, narg, arg) { - gzFp = nullptr; - - compression_level = Z_BEST_COMPRESSION; - if (!compressed) error->all(FLERR,"Dump atom/gz only writes compressed files"); } @@ -37,9 +34,6 @@ DumpAtomGZ::DumpAtomGZ(LAMMPS *lmp, int narg, char **arg) : DumpAtomGZ::~DumpAtomGZ() { - if (gzFp) gzclose(gzFp); - gzFp = nullptr; - fp = nullptr; } /* ---------------------------------------------------------------------- @@ -91,17 +85,12 @@ void DumpAtomGZ::openfile() // each proc with filewriter = 1 opens a file if (filewriter) { - std::string mode; - if (append_flag) { - mode = fmt::format("ab{}", compression_level); - } else { - mode = fmt::format("wb{}", compression_level); + try { + writer.open(filecurrent, append_flag); + } catch (FileWriterException &e) { + error->one(FLERR, e.what()); } - - gzFp = gzopen(filecurrent, mode.c_str()); - - if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file"); - } else gzFp = nullptr; + } // delete string with timestep replaced @@ -112,29 +101,34 @@ void DumpAtomGZ::openfile() void DumpAtomGZ::write_header(bigint ndump) { + std::string header; + if ((multiproc) || (!multiproc && me == 0)) { if (unit_flag && !unit_count) { ++unit_count; - gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style); + header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style); } - if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time()); - gzprintf(gzFp,"ITEM: TIMESTEP\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); - gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); - if (domain->triclinic == 0) { - gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi); - } else { - gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz); + if (time_flag) { + header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); } - gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); + + header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep); + header += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump); + if (domain->triclinic == 0) { + header += fmt::format("ITEM: BOX BOUNDS {}\n", boundstr); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxxlo, boxxhi); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxylo, boxyhi); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxzlo, boxzhi); + } else { + header += fmt::format("ITEM: BOX BOUNDS xy xz yz {}\n", boundstr); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxxlo, boxxhi, boxxy); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxylo, boxyhi, boxxz); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxzlo, boxzhi, boxyz); + } + header += fmt::format("ITEM: ATOMS {}\n", columns); + + writer.write(header.c_str(), header.length()); } } @@ -142,7 +136,7 @@ void DumpAtomGZ::write_header(bigint ndump) void DumpAtomGZ::write_data(int n, double *mybuf) { - gzwrite(gzFp,mybuf,sizeof(char)*n); + writer.write(mybuf, n); } /* ---------------------------------------------------------------------- */ @@ -152,11 +146,11 @@ void DumpAtomGZ::write() DumpAtom::write(); if (filewriter) { if (multifile) { - gzclose(gzFp); - gzFp = nullptr; + writer.close(); } else { - if (flush_flag) - gzflush(gzFp,Z_SYNC_FLUSH); + if (flush_flag && writer.isopen()) { + writer.flush(); + } } } } @@ -167,14 +161,15 @@ int DumpAtomGZ::modify_param(int narg, char **arg) { int consumed = DumpAtom::modify_param(narg, arg); if (consumed == 0) { - if (strcmp(arg[0],"compression_level") == 0) { - if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); - int min_level = Z_DEFAULT_COMPRESSION; - int max_level = Z_BEST_COMPRESSION; - compression_level = utils::inumeric(FLERR, arg[1], false, lmp); - if (compression_level < min_level || compression_level > max_level) - error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level)); - return 2; + try { + if (strcmp(arg[0],"compression_level") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + int compression_level = utils::inumeric(FLERR, arg[1], false, lmp); + writer.setCompressionLevel(compression_level); + return 2; + } + } catch (FileWriterException &e) { + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/src/COMPRESS/dump_atom_gz.h b/src/COMPRESS/dump_atom_gz.h index 0c0b95974f..d540f5300a 100644 --- a/src/COMPRESS/dump_atom_gz.h +++ b/src/COMPRESS/dump_atom_gz.h @@ -21,7 +21,7 @@ DumpStyle(atom/gz,DumpAtomGZ) #define LMP_DUMP_ATOM_GZ_H #include "dump_atom.h" -#include +#include "gz_file_writer.h" namespace LAMMPS_NS { @@ -31,8 +31,7 @@ class DumpAtomGZ : public DumpAtom { virtual ~DumpAtomGZ(); protected: - int compression_level; - gzFile gzFp; // file pointer for the compressed output stream + GzFileWriter writer; virtual void openfile(); virtual void write_header(bigint); diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index 3dde07bbf4..300a4c81cb 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -90,12 +90,8 @@ void DumpAtomZstd::openfile() // each proc with filewriter = 1 opens a file if (filewriter) { - if (append_flag) { - error->one(FLERR, "dump/zstd currently doesn't support append"); - } - try { - writer.open(filecurrent); + writer.open(filecurrent, append_flag); } catch (FileWriterException &e) { error->one(FLERR, e.what()); } diff --git a/src/COMPRESS/gz_file_writer.cpp b/src/COMPRESS/gz_file_writer.cpp new file mode 100644 index 0000000000..d24d77b21a --- /dev/null +++ b/src/COMPRESS/gz_file_writer.cpp @@ -0,0 +1,105 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Richard Berger (Temple U) +------------------------------------------------------------------------- */ + +#include "gz_file_writer.h" +#include +#include "fmt/format.h" + +using namespace LAMMPS_NS; + +GzFileWriter::GzFileWriter() : FileWriter(), + compression_level(Z_BEST_COMPRESSION), + gzFp(nullptr) +{ +} + +/* ---------------------------------------------------------------------- */ + +GzFileWriter::~GzFileWriter() +{ + close(); +} + +/* ---------------------------------------------------------------------- */ + +void GzFileWriter::open(const std::string &path, bool append) +{ + if (isopen()) return; + + std::string mode; + if (append) { + mode = fmt::format("ab{}", mode, compression_level); + } else { + mode = fmt::format("wb{}", mode, compression_level); + } + + gzFp = gzopen(path.c_str(), mode.c_str()); + + if (gzFp == nullptr) + throw FileWriterException(fmt::format("Could not open file '{}'", path)); +} + +/* ---------------------------------------------------------------------- */ + +size_t GzFileWriter::write(const void * buffer, size_t length) +{ + if (!isopen()) return 0; + + return gzwrite(gzFp, buffer, length); +} + +/* ---------------------------------------------------------------------- */ + +void GzFileWriter::flush() +{ + if (!isopen()) return; + + gzflush(gzFp, Z_SYNC_FLUSH); +} + +/* ---------------------------------------------------------------------- */ + +void GzFileWriter::close() +{ + if (!isopen()) return; + + gzclose(gzFp); + gzFp = nullptr; +} + +/* ---------------------------------------------------------------------- */ + +bool GzFileWriter::isopen() const +{ + return gzFp; +} + +/* ---------------------------------------------------------------------- */ + +void GzFileWriter::setCompressionLevel(int level) +{ + if (isopen()) + throw FileWriterException("Compression level can not be changed while file is open"); + + const int min_level = Z_DEFAULT_COMPRESSION; + const int max_level = Z_BEST_COMPRESSION; + + if (level < min_level || level > max_level) + throw FileWriterException(fmt::format("Compression level must in the range of [{}, {}]", min_level, max_level)); + + compression_level = level; +} diff --git a/src/COMPRESS/gz_file_writer.h b/src/COMPRESS/gz_file_writer.h new file mode 100644 index 0000000000..28473b1164 --- /dev/null +++ b/src/COMPRESS/gz_file_writer.h @@ -0,0 +1,47 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Richard Berger (Temple U) +------------------------------------------------------------------------- */ + +#ifndef LMP_GZ_FILE_WRITER_H +#define LMP_GZ_FILE_WRITER_H + +#include "file_writer.h" +#include +#include +#include + +namespace LAMMPS_NS { + +class GzFileWriter : public FileWriter { + int compression_level; + + gzFile gzFp; // file pointer for the compressed output stream +public: + GzFileWriter(); + virtual ~GzFileWriter(); + virtual void open(const std::string &path, bool append = false) override; + virtual void close() override; + virtual void flush() override; + virtual size_t write(const void * buffer, size_t length) override; + virtual bool isopen() const override; + + void setCompressionLevel(int level); +}; + + +} + +#endif diff --git a/src/COMPRESS/zstd_file_writer.cpp b/src/COMPRESS/zstd_file_writer.cpp index f82ade605c..3356fc1ad5 100644 --- a/src/COMPRESS/zstd_file_writer.cpp +++ b/src/COMPRESS/zstd_file_writer.cpp @@ -46,11 +46,15 @@ ZstdFileWriter::~ZstdFileWriter() /* ---------------------------------------------------------------------- */ -void ZstdFileWriter::open(const std::string &path) +void ZstdFileWriter::open(const std::string &path, bool append) { if (isopen()) return; - fp = fopen(path.c_str(), "wb"); + if (append) { + fp = fopen(path.c_str(), "ab"); + } else { + fp = fopen(path.c_str(), "wb"); + } if (!fp) { throw FileWriterException(fmt::format("Could not open file '{}'", path)); diff --git a/src/COMPRESS/zstd_file_writer.h b/src/COMPRESS/zstd_file_writer.h index 30afc86994..a4dbbdff64 100644 --- a/src/COMPRESS/zstd_file_writer.h +++ b/src/COMPRESS/zstd_file_writer.h @@ -38,7 +38,7 @@ class ZstdFileWriter : public FileWriter { public: ZstdFileWriter(); virtual ~ZstdFileWriter(); - virtual void open(const std::string &path) override; + virtual void open(const std::string &path, bool append = false) override; virtual void close() override; virtual void flush() override; virtual size_t write(const void * buffer, size_t length) override; diff --git a/src/file_writer.h b/src/file_writer.h index 8597ab570d..02eef6ad70 100644 --- a/src/file_writer.h +++ b/src/file_writer.h @@ -27,7 +27,7 @@ class FileWriter { public: FileWriter() = default; virtual ~FileWriter() = default; - virtual void open(const std::string &path) = 0; + virtual void open(const std::string &path, bool append = false) = 0; virtual void close() = 0; virtual void flush() = 0; virtual size_t write(const void * buffer, size_t length) = 0; diff --git a/unittest/formats/test_dump_atom_compressed.cpp b/unittest/formats/test_dump_atom_compressed.cpp index ed591184c3..51ce44fbb4 100644 --- a/unittest/formats/test_dump_atom_compressed.cpp +++ b/unittest/formats/test_dump_atom_compressed.cpp @@ -344,7 +344,7 @@ TEST_F(DumpAtomCompressTest, compressed_modify_bad_param) command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt"))); if (!verbose) ::testing::internal::GetCapturedStdout(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 compression_level 12"); ); } @@ -357,7 +357,7 @@ TEST_F(DumpAtomCompressTest, compressed_modify_multi_bad_param) command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt"))); if (!verbose) ::testing::internal::GetCapturedStdout(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); ); } From 20e6174e59fab97366f89f9ea8a7280e5299027a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Mar 2021 21:11:07 -0400 Subject: [PATCH 0292/1217] cannot use tokenizer for parse_args() as the search for commata must be away of parenthesis --- src/variable.cpp | 36 +++++++++++++++++++++------- src/variable.h | 3 ++- unittest/commands/test_variables.cpp | 7 ++++-- 3 files changed, 35 insertions(+), 11 deletions(-) diff --git a/src/variable.cpp b/src/variable.cpp index 76a4b84f89..3bf88db55e 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -4690,23 +4690,43 @@ void Variable::atom_vector(char *word, Tree **tree, max allowed # of args = MAXFUNCARG ------------------------------------------------------------------------- */ -int Variable::parse_args(const std::string &str, char **args) +int Variable::parse_args(char *str, char **args) { + char *ptrnext; int narg = 0; - args[0] = nullptr; + char *ptr = str; - Tokenizer values(str,","); - - while (values.has_next() && narg < MAXFUNCARG) { - args[narg] = utils::strdup(values.next()); + while (ptr && narg < MAXFUNCARG) { + ptrnext = find_next_comma(ptr); + if (ptrnext) *ptrnext = '\0'; + args[narg] = utils::strdup(ptr); narg++; + ptr = ptrnext; + if (ptr) ptr++; } - if (values.has_next()) - error->all(FLERR,"Too many args in variable function"); + if (ptr) error->all(FLERR,"Too many args in variable function"); return narg; } +/* ---------------------------------------------------------------------- + find next comma in str + skip commas inside one or more nested parenthesis + only return ptr to comma at level 0, else nullptr if not found +------------------------------------------------------------------------- */ + +char *Variable::find_next_comma(char *str) +{ + int level = 0; + for (char *p = str; *p; ++p) { + if ('(' == *p) level++; + else if (')' == *p) level--; + else if (',' == *p && !level) return p; + } + return nullptr; +} + + /* ---------------------------------------------------------------------- helper routine for printing variable name with error message ------------------------------------------------------------------------- */ diff --git a/src/variable.h b/src/variable.h index a43e7f3ad7..da759ecf6a 100644 --- a/src/variable.h +++ b/src/variable.h @@ -126,7 +126,8 @@ class Variable : protected Pointers { Tree **, Tree **, int &, double *, int &); int is_atom_vector(char *); void atom_vector(char *, Tree **, Tree **, int &); - int parse_args(const std::string &, char **); + int parse_args(char *, char **); + char *find_next_comma(char *); void print_var_error(const std::string &, int, const std::string &, int, int global=1); void print_tree(Tree *, int); diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index d41ad52e57..eb533aee86 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -334,8 +334,9 @@ TEST_F(VariableTest, Functions) file_vars(); BEGIN_HIDE_OUTPUT(); + command("variable seed index 643532"); command("variable one index 1"); - command("variable two equal random(1,2,643532)"); + command("variable two equal random(1,2,v_seed)"); command("variable three equal atan2(v_one,1)"); command("variable four equal atan2()"); command("variable five equal sqrt(v_one+v_one)"); @@ -346,6 +347,7 @@ TEST_F(VariableTest, Functions) command("variable ten equal floor(1.85)+ceil(1.85)"); command("variable ten1 equal tan(v_eight/2.0)"); command("variable ten2 equal asin(-1.0)+acos(0.0)"); + command("variable ten3 equal floor(100*random(0.2,0.8,v_seed)+1)"); END_HIDE_OUTPUT(); ASSERT_GT(variable->compute_equal(variable->find("two")), 0.99); @@ -357,7 +359,8 @@ TEST_F(VariableTest, Functions) ASSERT_DOUBLE_EQ(variable->compute_equal(variable->find("nine")), 1); ASSERT_DOUBLE_EQ(variable->compute_equal(variable->find("ten")), 3); ASSERT_FLOAT_EQ(variable->compute_equal(variable->find("ten1")), 1); - ASSERT_DOUBLE_EQ(variable->compute_equal(variable->find("ten2")), 0); + ASSERT_GT(variable->compute_equal(variable->find("ten3")), 19); + ASSERT_LT(variable->compute_equal(variable->find("ten3")), 81); TEST_FAILURE(".*ERROR: Variable four: Invalid syntax in variable formula.*", command("print \"${four}\"");); From 41de02ee9dd48569456532bf875344d1846a6b60 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Mar 2021 23:44:38 -0400 Subject: [PATCH 0293/1217] update granular howto --- doc/src/Howto_granular.rst | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/doc/src/Howto_granular.rst b/doc/src/Howto_granular.rst index c696d44249..70c2b2fbb7 100644 --- a/doc/src/Howto_granular.rst +++ b/doc/src/Howto_granular.rst @@ -18,12 +18,13 @@ This compute calculates rotational kinetic energy which can be :doc:`output with thermodynamic info `. -Use one of these 3 pair potentials, which compute forces and torques +Use one of these 4 pair potentials, which compute forces and torques between interacting pairs of particles: -* :doc:`pair_style ` gran/history -* :doc:`pair_style ` gran/no_history -* :doc:`pair_style ` gran/hertzian +* :doc:`pair_style gran/history ` +* :doc:`pair_style gran/no_history ` +* :doc:`pair_style gran/hertzian ` +* :doc:`pair_style granular ` These commands implement fix options specific to granular systems: @@ -31,6 +32,7 @@ These commands implement fix options specific to granular systems: * :doc:`fix pour ` * :doc:`fix viscous ` * :doc:`fix wall/gran ` +* :doc:`fix wall/gran/region ` The fix style *freeze* zeroes both the force and torque of frozen atoms, and should be used for granular system instead of the fix style From ea105a3c9a15d4958a46b079416d6dd10ca18407 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Mar 2021 07:36:22 -0400 Subject: [PATCH 0294/1217] fix typo --- doc/src/pair_dpd.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index d1d84407c4..62cf94786d 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -150,7 +150,7 @@ shifted to be 0.0 at the cutoff distance Rc. The :doc:`pair_modify ` table option is not relevant for these pair styles. -These pair style do not support the :doc:`pair_modify ` +These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. From 304156138347f16f77fcc15908ba9a9112cb822f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Mar 2021 07:36:53 -0400 Subject: [PATCH 0295/1217] add proper r-RESPA support for fix cmap --- doc/src/fix_cmap.rst | 5 +++++ src/MOLECULE/fix_cmap.cpp | 17 ++++++++++++----- src/MOLECULE/fix_cmap.h | 2 +- 3 files changed, 18 insertions(+), 6 deletions(-) diff --git a/doc/src/fix_cmap.rst b/doc/src/fix_cmap.rst index 892fd4ab41..e6e8d0c627 100644 --- a/doc/src/fix_cmap.rst +++ b/doc/src/fix_cmap.rst @@ -127,6 +127,11 @@ the :doc:`run ` command. The forces due to this fix are imposed during an energy minimization, invoked by the :doc:`minimize ` command. +The :doc:`fix_modify ` *respa* option is supported by this +fix. This allows to set at which level of the :doc:`r-RESPA +` integrator the fix is adding its forces. Default is the +outermost level. + .. note:: If you want the potential energy associated with the CMAP terms diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index 6da259f6ca..1b58037eb7 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -81,6 +81,8 @@ FixCMAP::FixCMAP(LAMMPS *lmp, int narg, char **arg) : extvector = 1; wd_header = 1; wd_section = 1; + respa_level_support = 1; + ilevel_respa = 0; MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); @@ -182,6 +184,11 @@ void FixCMAP::init() // define newton_bond here in case restart file was read (not data file) newton_bond = force->newton_bond; + + if (utils::strmatch(update->integrate_style,"^respa")) { + ilevel_respa = ((Respa *) update->integrate)->nlevels-1; + if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); + } } /* --------------------------------------------------------------------- */ @@ -190,12 +197,12 @@ void FixCMAP::setup(int vflag) { pre_neighbor(); - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { - ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); - post_force_respa(vflag,nlevels_respa-1,0); - ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); + ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); + post_force_respa(vflag,ilevel_respa,0); + ((Respa *) update->integrate)->copy_f_flevel(ilevel_respa); } } @@ -596,7 +603,7 @@ void FixCMAP::post_force(int vflag) void FixCMAP::post_force_respa(int vflag, int ilevel, int /*iloop*/) { - if (ilevel == nlevels_respa-1) post_force(vflag); + if (ilevel == ilevel_respa) post_force(vflag); } /* ---------------------------------------------------------------------- */ diff --git a/src/MOLECULE/fix_cmap.h b/src/MOLECULE/fix_cmap.h index 39d10bd77b..cd0c01a921 100644 --- a/src/MOLECULE/fix_cmap.h +++ b/src/MOLECULE/fix_cmap.h @@ -67,7 +67,7 @@ class FixCMAP : public Fix { private: int nprocs,me; int newton_bond,eflag_caller; - int ctype,nlevels_respa; + int ctype,ilevel_respa; int ncrosstermtypes,crossterm_per_atom,maxcrossterm; int ncrosstermlist; bigint ncmap; From 40f1a74a7f39f0a281652ed611d3ecc3fc95ec9e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Mar 2021 07:37:39 -0400 Subject: [PATCH 0296/1217] use more precise detection of verlet and respa run styles --- src/fix_addforce.cpp | 4 ++-- src/fix_recenter.cpp | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp index 07031a40a4..a9f6248995 100644 --- a/src/fix_addforce.cpp +++ b/src/fix_addforce.cpp @@ -193,7 +193,7 @@ void FixAddForce::init() update->whichflag == 2 && estyle == NONE) error->all(FLERR,"Must use variable energy with fix addforce"); - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -203,7 +203,7 @@ void FixAddForce::init() void FixAddForce::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp index 1db74981b6..f5e4513d74 100644 --- a/src/fix_recenter.cpp +++ b/src/fix_recenter.cpp @@ -144,7 +144,7 @@ void FixRecenter::init() zinit = xcm[2]; } - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } From bfca619957830e7a8168753c7ae778e5e3e947f8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Mar 2021 07:49:15 -0400 Subject: [PATCH 0297/1217] fix typos --- doc/src/pair_fep_soft.rst | 2 +- doc/src/pair_gayberne.rst | 2 +- doc/src/pair_vashishta.rst | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index 109ddfdf21..1bb50fad1f 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -363,7 +363,7 @@ Mixing, shift, table, tail correction, restart, rRESPA info The different versions of the *lj/cut/soft* pair styles support mixing. For atom type pairs I,J and I != J, the :math:`\epsilon` and :math:`\sigma` -coefficients and cutoff distance for these pair style can be mixed. The default +coefficients and cutoff distance for these pair styles can be mixed. The default mix value is *geometric* for 12-6 styles. The mixing rule for epsilon and sigma for *lj/class2/soft* 9-6 potentials is to diff --git a/doc/src/pair_gayberne.rst b/doc/src/pair_gayberne.rst index 19597b9018..448f3a26de 100644 --- a/doc/src/pair_gayberne.rst +++ b/doc/src/pair_gayberne.rst @@ -188,7 +188,7 @@ Restrictions The *gayberne* style is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -These pair style require that atoms store torque and a quaternion to +These pair styles require that atoms store torque and a quaternion to represent their orientation, as defined by the :doc:`atom_style `. It also require they store a per-type :doc:`shape `. The particles cannot store a per-particle diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst index aef401ec7c..9edb77ecbe 100644 --- a/doc/src/pair_vashishta.rst +++ b/doc/src/pair_vashishta.rst @@ -217,7 +217,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -These pair style are part of the MANYBODY package. They is only +These pair styles are part of the MANYBODY package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. These pair styles requires the :doc:`newton ` setting to be "on" From 57ad6d50f45ed5974d8cecf1ca0ed08ced0975b3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Mar 2021 10:35:04 -0400 Subject: [PATCH 0298/1217] silence compiler warnings --- src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 1 - src/USER-REACTION/fix_bond_react.cpp | 1 - 2 files changed, 2 deletions(-) diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 907d1d555f..c962ed0c71 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -1171,7 +1171,6 @@ void AtomVecHybridKokkos::build_styles() allstyles = new char*[nallstyles]; - int n; nallstyles = 0; #define ATOM_CLASS #define AtomStyle(key,Class) \ diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 17754c8297..2b88a8a264 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -682,7 +682,6 @@ it will have the name 'i_limit_tags' and will be intitialized to 0 (not in group void FixBondReact::post_constructor() { - int len; // let's add the limit_tags per-atom property fix std::string cmd = std::string("bond_react_props_internal"); id_fix2 = new char[cmd.size()+1]; From 71dbf43e090a6c6e93126efa4a4e293f29fae9df Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Mar 2021 11:10:59 -0400 Subject: [PATCH 0299/1217] error our when Fix:set_molecule() is called with unsupported fixes also add example input for using fix rigid/small with fix deposit --- .../deposit/in.deposit.molecule.rigid-small | 56 +++++ examples/deposit/in.deposit.molecule.shake | 4 +- ...10Mar21.deposit.molecule.rigid-small.g++.1 | 218 ++++++++++++++++++ ...10Mar21.deposit.molecule.rigid-small.g++.4 | 218 ++++++++++++++++++ src/RIGID/fix_rigid_nh_small.cpp | 13 ++ src/RIGID/fix_rigid_nh_small.h | 1 + src/RIGID/fix_rigid_small.h | 2 +- src/fix.cpp | 6 + src/fix.h | 2 +- 9 files changed, 516 insertions(+), 4 deletions(-) create mode 100644 examples/deposit/in.deposit.molecule.rigid-small create mode 100644 examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.1 create mode 100644 examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.4 diff --git a/examples/deposit/in.deposit.molecule.rigid-small b/examples/deposit/in.deposit.molecule.rigid-small new file mode 100644 index 0000000000..2e6a84e54b --- /dev/null +++ b/examples/deposit/in.deposit.molecule.rigid-small @@ -0,0 +1,56 @@ +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +region slab block 0 5 0 5 8 9 + +group addatoms empty +region mobile block 0 5 0 5 2 INF +group mobile region mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/small molecule mol dimer +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 & + mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type & +# axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type & +# axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 diff --git a/examples/deposit/in.deposit.molecule.shake b/examples/deposit/in.deposit.molecule.shake index 7bd701c924..30c6bd7a53 100644 --- a/examples/deposit/in.deposit.molecule.shake +++ b/examples/deposit/in.deposit.molecule.shake @@ -21,11 +21,11 @@ bond_coeff 1 5.0 1.0 neigh_modify delay 0 -group addatoms type 2 +group addatoms empty region mobile block 0 5 0 5 2 INF group mobile region mobile -compute add addatoms temp +compute add addatoms temp compute_modify add dynamic/dof yes extra/dof 0 fix 1 addatoms nve diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.1 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.1 new file mode 100644 index 0000000000..0f5a1afcfa --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.1 @@ -0,0 +1,218 @@ +LAMMPS (10 Mar 2021) + using 1 OpenMP thread(s) per MPI task +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) + 1 by 1 by 1 MPI processor grid + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate +Created 350 atoms + create_atoms CPU = 0.001 seconds + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +Read molecule template dimer: + 1 molecules + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region slab block 0 5 0 5 8 9 + +group addatoms empty +0 atoms in group addatoms +region mobile block 0 5 0 5 2 INF +group mobile region mobile +150 atoms in group mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/small molecule mol dimer + create bodies CPU = 0.000 seconds + 0 rigid bodies with 0 atoms + 1.0000000 = max distance from body owner to body atom +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468) + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 +WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes +Step Atoms Temp E_pair TotEng Press + 0 350 0 -6.9215833 -6.9215833 -1.0052629 + 100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914 + 200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276 + 300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826 + 400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699 + 500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307 + 600 362 1.026148 -6.7105231 -6.6680032 -0.68314418 + 700 364 1.0683344 -6.6725162 -6.621154 -0.65747369 + 800 366 1.0958952 -6.6412275 -6.5813425 -0.68789614 + 900 368 1.1250033 -6.6101882 -6.541404 -0.66674346 + 1000 370 1.2326373 -6.5993719 -6.5160856 -0.6968868 + 1100 372 1.1397426 -6.5912861 -6.5070309 -0.63330356 + 1200 374 1.0514292 -6.5905747 -6.5062354 -0.71020362 + 1300 376 1.003296 -6.5747765 -6.4880555 -0.65459732 + 1400 378 0.82999289 -6.5681797 -6.4913285 -0.60438126 + 1500 380 0.90239175 -6.575298 -6.4862461 -0.66528725 + 1600 382 0.86399799 -6.5692206 -6.4787496 -0.65027781 + 1700 384 0.64747231 -6.5644237 -6.4927634 -0.6304614 + 1800 386 0.74288971 -6.5515735 -6.4649672 -0.67772325 + 1900 388 0.7257202 -6.5565091 -6.4676644 -0.66173549 + 2000 390 0.73381036 -6.5631515 -6.4690733 -0.64685916 + 2100 392 0.76476562 -6.5574124 -6.4549885 -0.68866192 + 2200 394 0.65932468 -6.5511557 -6.459118 -0.71728829 + 2300 396 0.70269509 -6.5728146 -6.4707819 -0.64362081 + 2400 398 0.60528919 -6.5845991 -6.4933494 -0.63956327 + 2500 400 0.51025744 -6.5812452 -6.5015175 -0.68706961 + 2600 402 0.5245131 -6.6003894 -6.5155801 -0.68972215 + 2700 404 0.46330251 -6.5659175 -6.4885092 -0.72870942 + 2800 406 0.48039778 -6.5715192 -6.488692 -0.753758 + 2900 408 0.53698616 -6.5813154 -6.4858951 -0.67117541 + 3000 410 0.50231419 -6.5886963 -6.4968096 -0.71905351 + 3100 412 0.49420225 -6.596733 -6.5037702 -0.65947518 + 3200 414 0.42703699 -6.5879338 -6.5054146 -0.80033546 + 3300 416 0.44306009 -6.580249 -6.4923825 -0.76503083 + 3400 418 0.55620672 -6.5923388 -6.4792346 -0.69367877 + 3500 420 0.39815033 -6.5911154 -6.5081674 -0.65569211 + 3600 422 0.44197847 -6.6026382 -6.5083774 -0.73299102 + 3700 424 0.45049389 -6.6060616 -6.5077817 -0.7552914 + 3800 426 0.43047295 -6.6079275 -6.51193 -0.71501328 + 3900 428 0.43779129 -6.6099306 -6.5102001 -0.71539515 + 4000 430 0.41113503 -6.6123009 -6.5166881 -0.74177096 + 4100 432 0.32800011 -6.5983566 -6.5205325 -0.71688103 + 4200 434 0.39168203 -6.6110342 -6.5162724 -0.78927697 + 4300 436 0.48151013 -6.6183315 -6.4996106 -0.70523035 + 4400 438 0.45391027 -6.6331732 -6.5191775 -0.7270855 + 4500 440 0.349126 -6.6091657 -6.5199006 -0.76974115 + 4600 442 0.43375023 -6.6219188 -6.5090653 -0.74576212 + 4700 444 0.40071749 -6.6184164 -6.5123707 -0.71919052 + 4800 446 0.414292 -6.6298132 -6.5183445 -0.76237313 + 4900 448 0.44210681 -6.6364174 -6.5155288 -0.78753121 + 5000 450 0.36101771 -6.6232703 -6.5229876 -0.73927083 + 5100 452 0.41481171 -6.6442404 -6.5272305 -0.76316209 + 5200 454 0.40283527 -6.6512252 -6.5358759 -0.79645689 + 5300 456 0.3642061 -6.6530346 -6.5472072 -0.77458364 + 5400 458 0.38449826 -6.6514864 -6.5381518 -0.73083784 + 5500 460 0.42559408 -6.6769326 -6.5497169 -0.78932279 + 5600 462 0.38905756 -6.6698705 -6.5519743 -0.77118812 + 5700 464 0.38354955 -6.6706904 -6.5528977 -0.75067129 + 5800 466 0.36760943 -6.6942519 -6.5798669 -0.685487 + 5900 468 0.30783118 -6.6838159 -6.5867965 -0.79233808 + 6000 470 0.33145368 -6.6733504 -6.5675673 -0.84390449 + 6100 472 0.39252324 -6.6912189 -6.5643973 -0.83342022 + 6200 474 0.32342144 -6.6906083 -6.5848481 -0.71262158 + 6300 476 0.34445238 -6.7008453 -6.5868721 -0.76650756 + 6400 478 0.38152782 -6.7017838 -6.5740758 -0.77113022 + 6500 480 0.37540166 -6.7119996 -6.5849105 -0.79907635 + 6600 482 0.3579419 -6.7034721 -6.5809401 -0.8141269 + 6700 484 0.33538235 -6.6916682 -6.575601 -0.83265486 + 6800 486 0.34081871 -6.6931924 -6.573976 -0.80582583 + 6900 488 0.3555283 -6.6939997 -6.5683263 -0.74771423 + 7000 490 0.3543769 -6.7093364 -6.5827732 -0.77643516 + 7100 492 0.31263107 -6.698361 -6.5855723 -0.73108333 + 7200 494 0.32107 -6.6959056 -6.5789166 -0.7575478 + 7300 496 0.32908165 -6.7137605 -6.592677 -0.86538023 + 7400 498 0.32539571 -6.7030353 -6.5821554 -0.79337428 + 7500 500 0.33902577 -6.7078178 -6.5806832 -0.85408988 + 7600 502 0.35530921 -6.707507 -6.5730274 -0.79914613 + 7700 504 0.32391812 -6.6978823 -6.5741635 -0.78603595 + 7800 506 0.36390015 -6.7151325 -6.5748943 -0.83164222 + 7900 508 0.3372561 -6.7086718 -6.5775535 -0.7949992 + 8000 510 0.36612946 -6.7225238 -6.5789437 -0.80322866 + 8100 512 0.34622305 -6.7229825 -6.5860486 -0.70478659 + 8200 514 0.3212233 -6.7202524 -6.5921381 -0.91836713 + 8300 516 0.3402461 -6.721488 -6.5846642 -0.88273592 + 8400 518 0.34070258 -6.7268378 -6.5887152 -0.76057264 + 8500 520 0.36267747 -6.744602 -6.5963924 -0.81051317 + 8600 522 0.3439948 -6.7376267 -6.595943 -0.84600203 + 8700 524 0.30960289 -6.7276471 -6.5991382 -0.90965986 + 8800 526 0.28868972 -6.7159628 -6.595218 -0.876093 + 8900 528 0.31020216 -6.7162903 -6.5855707 -0.83193125 + 9000 530 0.31836275 -6.7171479 -6.5819939 -0.82093897 + 9100 532 0.32543293 -6.724167 -6.5850016 -0.7690143 + 9200 534 0.32644265 -6.7139575 -6.5733549 -0.86903096 + 9300 536 0.33050759 -6.7254715 -6.5821077 -0.94504522 + 9400 538 0.30372582 -6.7139931 -6.5813247 -0.91128612 + 9500 540 0.32943659 -6.7206223 -6.5757312 -0.87818439 + 9600 542 0.30911968 -6.708091 -6.5712114 -0.79092372 + 9700 544 0.33909826 -6.7222948 -6.5711342 -0.80266151 + 9800 546 0.29015141 -6.7086869 -6.5784908 -0.87763769 + 9900 548 0.33838474 -6.7384955 -6.5856667 -0.85630604 + 10000 550 0.30213198 -6.7338924 -6.5965597 -0.75738882 +Loop time of 17.2852 on 1 procs for 10000 steps with 550 atoms + +Performance: 249924.414 tau/day, 578.529 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.637 | 9.637 | 9.637 | 0.0 | 55.75 +Bond | 0.025444 | 0.025444 | 0.025444 | 0.0 | 0.15 +Neigh | 4.6852 | 4.6852 | 4.6852 | 0.0 | 27.11 +Comm | 0.65556 | 0.65556 | 0.65556 | 0.0 | 3.79 +Output | 0.0099883 | 0.0099883 | 0.0099883 | 0.0 | 0.06 +Modify | 2.1895 | 2.1895 | 2.1895 | 0.0 | 12.67 +Other | | 0.08248 | | | 0.48 + +Nlocal: 550.000 ave 550 max 550 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2367.00 ave 2367 max 2367 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 36781.0 ave 36781 max 36781 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 36781 +Ave neighs/atom = 66.874545 +Ave special neighs/atom = 0.36363636 +Neighbor list builds = 840 +Dangerous builds = 0 +Total wall time: 0:00:17 diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.4 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.4 new file mode 100644 index 0000000000..0dcae43ba2 --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.4 @@ -0,0 +1,218 @@ +LAMMPS (10 Mar 2021) + using 1 OpenMP thread(s) per MPI task +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) + 1 by 1 by 4 MPI processor grid + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate +Created 350 atoms + create_atoms CPU = 0.139 seconds + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +Read molecule template dimer: + 1 molecules + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region slab block 0 5 0 5 8 9 + +group addatoms empty +0 atoms in group addatoms +region mobile block 0 5 0 5 2 INF +group mobile region mobile +150 atoms in group mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/small molecule mol dimer + create bodies CPU = 0.006 seconds + 0 rigid bodies with 0 atoms + 1.0000000 = max distance from body owner to body atom +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468) + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 +WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes +Step Atoms Temp E_pair TotEng Press + 0 350 0 -6.9215833 -6.9215833 -1.0052629 + 100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337 + 200 354 1.0081552 -6.8645575 -6.850318 -0.69629729 + 300 356 1.0085803 -6.821677 -6.8004288 -0.69532657 + 400 358 1.0099188 -6.7837923 -6.7555822 -0.68879568 + 500 360 1.0140221 -6.7446709 -6.7094618 -0.72991641 + 600 362 1.026146 -6.7129201 -6.6704003 -0.67063836 + 700 364 1.0683193 -6.6776523 -6.6262908 -0.65572472 + 800 366 1.0958893 -6.6402029 -6.5803182 -0.66307281 + 900 368 1.1231768 -6.6050912 -6.5364187 -0.64076928 + 1000 370 1.1976283 -6.5942507 -6.5133299 -0.69249019 + 1100 372 1.0506263 -6.5772313 -6.499564 -0.63072939 + 1200 374 0.93724351 -6.5732957 -6.4981157 -0.64963897 + 1300 376 0.93899686 -6.5578406 -6.4766773 -0.65096289 + 1400 378 0.8704974 -6.5468498 -6.4662482 -0.67613931 + 1500 380 0.84490693 -6.5401094 -6.4567304 -0.64385968 + 1600 382 0.9243154 -6.5611604 -6.4643734 -0.62096869 + 1700 384 0.67202953 -6.5590557 -6.4846775 -0.67807465 + 1800 386 0.8712464 -6.5654953 -6.4639251 -0.65860236 + 1900 388 0.70011668 -6.5808612 -6.495151 -0.65146463 + 2000 390 0.64019295 -6.5652168 -6.4831408 -0.70291888 + 2100 392 0.67578277 -6.5596196 -6.469113 -0.63315981 + 2200 394 0.60785287 -6.558941 -6.4740885 -0.7133822 + 2300 396 0.8155086 -6.5756022 -6.4571887 -0.69176417 + 2400 398 0.69028748 -6.5875474 -6.483484 -0.63743938 + 2500 400 0.5013913 -6.5871851 -6.5088427 -0.65872179 + 2600 402 0.51268385 -6.5782356 -6.495339 -0.74289067 + 2700 404 0.57745388 -6.5815718 -6.4850912 -0.67922914 + 2800 406 0.47317895 -6.5974978 -6.5159152 -0.64657562 + 2900 408 0.50593124 -6.6019054 -6.5120034 -0.64211427 + 3000 410 0.44423233 -6.5956684 -6.5144064 -0.66526127 + 3100 412 0.40808865 -6.5949863 -6.5182221 -0.62722445 + 3200 414 0.40692632 -6.5866689 -6.5080358 -0.76440608 + 3300 416 0.43908529 -6.5851721 -6.4980939 -0.69345883 + 3400 418 0.53825907 -6.5880076 -6.478553 -0.69726204 + 3500 420 0.46363057 -6.6135193 -6.5169296 -0.58015901 + 3600 422 0.39262699 -6.621857 -6.5381213 -0.74921264 + 3700 424 0.42679205 -6.6146579 -6.5215488 -0.69040431 + 3800 426 0.38997492 -6.6139725 -6.5270063 -0.78237667 + 3900 428 0.5222531 -6.6403886 -6.5214174 -0.78298122 + 4000 430 0.47841128 -6.6502681 -6.5390097 -0.68125967 + 4100 432 0.44609186 -6.6610827 -6.5552392 -0.81157037 + 4200 434 0.4591431 -6.6858064 -6.5747234 -0.79000753 + 4300 436 0.40690573 -6.6800195 -6.579693 -0.6781696 + 4400 438 0.43023944 -6.6849804 -6.5769294 -0.7620548 + 4500 440 0.40889421 -6.6783124 -6.5737656 -0.8577593 + 4600 442 0.41452051 -6.6968565 -6.5890061 -0.70427746 + 4700 444 0.36740394 -6.6920933 -6.5948636 -0.69303162 + 4800 446 0.40112316 -6.6869413 -6.5790158 -0.84792822 + 4900 448 0.42437165 -6.6789835 -6.5629444 -0.82278531 + 5000 450 0.41822898 -6.6770254 -6.5608507 -0.72224472 + 5100 452 0.38445688 -6.6738997 -6.5654522 -0.7022418 + 5200 454 0.39998238 -6.6670536 -6.5525212 -0.73639959 + 5300 456 0.39471029 -6.6728592 -6.5581681 -0.70419927 + 5400 458 0.35817807 -6.6702423 -6.5646658 -0.81657219 + 5500 460 0.37151428 -6.6690855 -6.558035 -0.78076653 + 5600 462 0.32642513 -6.6622352 -6.5633185 -0.69118644 + 5700 464 0.43665879 -6.6811227 -6.5470195 -0.77500043 + 5800 466 0.40704721 -6.6858874 -6.5592311 -0.72683597 + 5900 468 0.3861903 -6.6896953 -6.5679794 -0.78001958 + 6000 470 0.34073346 -6.6833717 -6.574627 -0.78170837 + 6100 472 0.39953874 -6.7083668 -6.5792785 -0.81791744 + 6200 474 0.36685189 -6.7114648 -6.5915027 -0.80545451 + 6300 476 0.35851799 -6.7261023 -6.607475 -0.77350495 + 6400 478 0.41771823 -6.7427425 -6.6029205 -0.85319003 + 6500 480 0.36519478 -6.732662 -6.6090284 -0.78712805 + 6600 482 0.30669571 -6.7269784 -6.6219892 -0.76698134 + 6700 484 0.3384344 -6.7261448 -6.6090213 -0.79935239 + 6800 486 0.36420902 -6.7320259 -6.6046277 -0.84650552 + 6900 488 0.40181215 -6.7490619 -6.6070279 -0.75753238 + 7000 490 0.30536068 -6.7398924 -6.6308351 -0.73210162 + 7100 492 0.28813004 -6.7257287 -6.6217794 -0.92178435 + 7200 494 0.30956277 -6.7342688 -6.6214727 -0.77532949 + 7300 496 0.36625115 -6.7528159 -6.6180561 -0.76247835 + 7400 498 0.30935271 -6.7401433 -6.6252231 -0.82809158 + 7500 500 0.33222282 -6.7410421 -6.6164585 -0.81948236 + 7600 502 0.33318693 -6.7488106 -6.622704 -0.82395904 + 7700 504 0.34570598 -6.7547394 -6.6226989 -0.85644369 + 7800 506 0.34587242 -6.7446006 -6.6113099 -0.82476511 + 7900 508 0.2969166 -6.7305429 -6.6151078 -0.8210214 + 8000 510 0.32355758 -6.7437629 -6.6168776 -0.81719054 + 8100 512 0.33784479 -6.7545537 -6.6209335 -0.78082067 + 8200 514 0.32351289 -6.7525032 -6.6234757 -0.87093587 + 8300 516 0.31900134 -6.7550972 -6.6268166 -0.79928704 + 8400 518 0.3338521 -6.7588757 -6.6235302 -0.81699503 + 8500 520 0.33115184 -6.7614854 -6.6261589 -0.79958489 + 8600 522 0.29478929 -6.7490188 -6.6276018 -0.81954456 + 8700 524 0.267993 -6.7467764 -6.6355389 -0.76642994 + 8800 526 0.28792085 -6.7527118 -6.6322887 -0.86911619 + 8900 528 0.32430992 -6.75901 -6.6223453 -0.87087898 + 9000 530 0.33151321 -6.7534845 -6.6127478 -0.79309499 + 9100 532 0.32760982 -6.7599992 -6.6199028 -0.7506309 + 9200 534 0.32579101 -6.7671489 -6.6268269 -0.94238755 + 9300 536 0.35144354 -6.7782581 -6.625813 -0.77952234 + 9400 538 0.33689976 -6.7804455 -6.6332867 -0.75768501 + 9500 540 0.3052486 -6.7745436 -6.6402908 -0.89621525 + 9600 542 0.30617581 -6.7648172 -6.6292412 -0.90623541 + 9700 544 0.30097715 -6.7714379 -6.6372707 -0.85534149 + 9800 546 0.31297479 -6.7814978 -6.6410604 -0.88651064 + 9900 548 0.31832347 -6.790661 -6.6468926 -1.006 + 10000 550 0.29239559 -6.7823137 -6.6494066 -1.0337518 +Loop time of 34.7661 on 4 procs for 10000 steps with 550 atoms + +Performance: 124259.065 tau/day, 287.637 timesteps/s +73.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0076709 | 3.1286 | 9.1834 | 211.7 | 9.00 +Bond | 0.0040276 | 0.010416 | 0.022169 | 7.0 | 0.03 +Neigh | 0.052413 | 1.5948 | 4.885 | 155.3 | 4.59 +Comm | 4.9736 | 12.242 | 20.073 | 166.2 | 35.21 +Output | 0.053549 | 0.10104 | 0.21642 | 21.0 | 0.29 +Modify | 13.435 | 16.191 | 23.851 | 110.0 | 46.57 +Other | | 1.499 | | | 4.31 + +Nlocal: 137.500 ave 299 max 2 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1898.75 ave 2679 max 524 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Neighs: 9204.00 ave 23014 max 0 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 36816 +Ave neighs/atom = 66.938182 +Ave special neighs/atom = 0.36363636 +Neighbor list builds = 832 +Dangerous builds = 0 +Total wall time: 0:00:34 diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index af2adb540d..3956fcf35d 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -1365,6 +1365,19 @@ int FixRigidNHSmall::modify_param(int narg, char **arg) return FixRigidSmall::modify_param(narg,arg); } +/* ---------------------------------------------------------------------- + disallow using fix rigid/n??/small fixes with fix deposit + we would need custom functionality to update data structures + used by all fixes derived from this class but not fix rigid/small +------------------------------------------------------------------------- */ + +void FixRigidNHSmall::set_molecule(int, tagint, int, + double *, double *, double *) +{ + error->all(FLERR,fmt::format("Molecule update not (yet) implemented for " + "fix {}", style)); +} + /* ---------------------------------------------------------------------- */ void FixRigidNHSmall::allocate_chain() diff --git a/src/RIGID/fix_rigid_nh_small.h b/src/RIGID/fix_rigid_nh_small.h index e04290aee8..32c4c1ab74 100644 --- a/src/RIGID/fix_rigid_nh_small.h +++ b/src/RIGID/fix_rigid_nh_small.h @@ -80,6 +80,7 @@ class FixRigidNHSmall : public FixRigidSmall { void nh_epsilon_dot(); void compute_dof(); + void set_molecule(int, tagint, int, double *, double *, double *); void allocate_chain(); void allocate_order(); void deallocate_chain(); diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h index d6e97c06fd..6534017971 100644 --- a/src/RIGID/fix_rigid_small.h +++ b/src/RIGID/fix_rigid_small.h @@ -43,7 +43,7 @@ class FixRigidSmall : public Fix { void grow_arrays(int); void copy_arrays(int, int, int); void set_arrays(int); - void set_molecule(int, tagint, int, double *, double *, double *); + virtual void set_molecule(int, tagint, int, double *, double *, double *); int pack_exchange(int, double *); int unpack_exchange(int, double *); diff --git a/src/fix.cpp b/src/fix.cpp index b9d9fb3969..32a76cc125 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -174,6 +174,12 @@ void Fix::modify_params(int narg, char **arg) } } +void::Fix::set_molecule(int, tagint, int, double *, double *, double *) +{ + error->all(FLERR,fmt::format("Molecule update not implemented for " + "fix {}", style)); +} + /* ---------------------------------------------------------------------- setup for peratom energy and global/peratom virial computation see integrate::ev_set() for values of eflag (0-3) and vflag (0-6) diff --git a/src/fix.h b/src/fix.h index 7092b56c8f..31add74ee4 100644 --- a/src/fix.h +++ b/src/fix.h @@ -155,7 +155,7 @@ class Fix : protected Pointers { virtual void copy_arrays(int, int, int) {} virtual void set_arrays(int) {} virtual void update_arrays(int, int) {} - virtual void set_molecule(int, tagint, int, double *, double *, double *) {} + virtual void set_molecule(int, tagint, int, double *, double *, double *); virtual void clear_bonus() {} virtual int pack_border(int, int *, double *) {return 0;} From 24d9d6d17d1fbe1485b86debdf7c3bdac854bca0 Mon Sep 17 00:00:00 2001 From: "Ronald E. Miller" Date: Tue, 30 Mar 2021 11:27:39 -0400 Subject: [PATCH 0300/1217] update to kim_interactions to correctly handle incorrect combinations of periodic and f/s boundary conditions when the SM has to choose between kspace or real space coulomb calculations. This version treats "p p p" in kspace, "f f f" or "s s s" in realspace, and "p p f" with kspace-slab. all others are sent to kspace-slab and then caught there as an error. --- src/KIM/kim_interactions.cpp | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp index b6a1ed6f47..c3da21b50d 100644 --- a/src/KIM/kim_interactions.cpp +++ b/src/KIM/kim_interactions.cpp @@ -94,6 +94,7 @@ void KimInteractions::command(int narg, char **arg) void KimInteractions::do_setup(int narg, char **arg) { + static bool kim_update=0; bool fixed_types; if ((narg == 1) && (0 == strcmp("fixed_types",arg[0]))) { fixed_types = true; @@ -185,9 +186,11 @@ void KimInteractions::do_setup(int narg, char **arg) KIM_SimulatorModel_GetSimulatorFieldMetadata( simulatorModel,i,&sim_lines,&sim_field); if (0 == strcmp(sim_field,"model-defn")) { + if (kim_update) input->one("variable kim_update equal 1"); + else input->one("variable kim_update equal 0"); if (domain->periodicity[0]&&domain->periodicity[1]&&domain->periodicity[2]) input->one("variable kim_periodic equal 1"); - else if (domain->periodicity[0]&&domain->periodicity[1]&&!domain->periodicity[2]) input->one("variable kim_periodic equal 2"); - else input->one("variable kim_periodic equal 0"); + else if (!domain->periodicity[0]&&!domain->periodicity[1]&&!domain->periodicity[2]) input->one("variable kim_periodic equal 0"); + else input->one("variable kim_periodic equal 2"); sim_model_idx = i; for (int j=0; j < sim_lines; ++j) { KIM_SimulatorModel_GetSimulatorFieldLine( @@ -217,7 +220,8 @@ void KimInteractions::do_setup(int narg, char **arg) KIM_SimulatorModel_OpenAndInitializeTemplateMap(simulatorModel); - } else { + } else if (!kim_update) { + // not a simulator model. issue pair_style and pair_coeff commands. @@ -242,6 +246,7 @@ void KimInteractions::do_setup(int narg, char **arg) // End output to log file input->write_echo("#=== END kim_interactions ====================================\n\n"); + kim_update=1; } /* ---------------------------------------------------------------------- */ From 2dbf59efa9fb4f30456a7cbb00f5a2b8eaeaecbe Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Mar 2021 11:43:56 -0400 Subject: [PATCH 0301/1217] update install instructions for updates via patch and git for CMake/GNU make --- doc/src/Install_git.rst | 70 +++++++++++++++++++++++++++------------ doc/src/Install_patch.rst | 62 +++++++++++++++++++++++++--------- 2 files changed, 94 insertions(+), 38 deletions(-) diff --git a/doc/src/Install_git.rst b/doc/src/Install_git.rst index a84f31a80d..3c10171ea3 100644 --- a/doc/src/Install_git.rst +++ b/doc/src/Install_git.rst @@ -86,33 +86,59 @@ check out any other desired branch) first. Once you have updated your local files with a ``git pull`` (or ``git checkout``), you still need to re-build LAMMPS if any source files have -changed. To do this, you should cd to the src directory and type: +changed. How to do this depends on the build system you are using. -.. code-block:: bash +.. tabs:: - $ make purge # remove any deprecated src files - $ make package-update # sync package files with src files - $ make foo # re-build for your machine (mpi, serial, etc) + .. tab:: CMake build -just as described on the :doc:`Apply patch ` page, -after a patch has been installed. + Change to your build folder and type: -.. warning:: + .. code-block:: bash - If you wish to edit/change a src file that is from a - package, you should edit the version of the file inside the package - sub-directory with src, then re-install the package. The version in - the source directory is merely a copy and will be wiped out if you type "make - package-update". + cmake . --build -.. warning:: + CMake should auto-detect whether it needs to re-run the CMake + configuration step and otherwise redo the build for all files + that have been changed or files that depend on changed files. + In case some build options have been changed or renamed, you + may have to update those by running: - The GitHub servers support both the "git://" and - "https://" access protocols for anonymous read-only access. If you - have a correspondingly configured GitHub account, you may also use - SSH access with the URL "git@github.com:lammps/lammps.git". + .. code-block:: bash -The LAMMPS GitHub project is managed by Christoph Junghans (LANL, -junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at -gmail.com) and Richard Berger (Temple U, richard.berger at -temple.edu). + cmake . + + and then rebuild. + + .. tab:: Traditional make + + Switch to the src directory and type: + + .. code-block:: bash + + $ make purge # remove any deprecated src files + $ make package-update # sync package files with src files + $ make foo # re-build for your machine (mpi, serial, etc) + + Just as described on the :doc:`Apply patch ` page, + after a patch has been installed. + + .. warning:: + + If you wish to edit/change a src file that is from a package, + you should edit the version of the file inside the package + sub-directory with src, then re-install the package. The + version in the source directory is merely a copy and will be + wiped out if you type "make package-update". + +.. admonition:: Git protocols + :class: note + + The servers at github.com support the "git://" and "https://" access + protocols for anonymous, read-only access. If you have a suitably + configured GitHub account, you may also use SSH protocol with the + URL "git@github.com:lammps/lammps.git". + +The LAMMPS GitHub project is currently managed by Axel Kohlmeyer +(Temple U, akohlmey at gmail.com) and Richard Berger (Temple U, +richard.berger at temple.edu). diff --git a/doc/src/Install_patch.rst b/doc/src/Install_patch.rst index 39e007bb67..b1f36b19e0 100644 --- a/doc/src/Install_patch.rst +++ b/doc/src/Install_patch.rst @@ -43,24 +43,54 @@ up to date. * A list of updated files print out to the screen. The -b switch creates backup files of your originals (e.g. src/force.cpp.orig), so you can manually undo the patch if something goes wrong. -* Type the following from the src directory, to enforce consistency - between the src and package directories. This is OK to do even if you - don't use one or more packages. If you are applying several patches - successively, you only need to type this once at the end. The purge - command removes deprecated src files if any were removed by the patch - from package sub-directories. - .. code-block:: bash +* Once you have updated your local files you need to re-build LAMMPS. + If you are applying several patches successively, you only need to + do the rebuild once at the end. How to do it depends on the build + system you are using. - $ make purge - $ make package-update + .. tabs:: -* Re-build LAMMPS via the "make" command. + .. tab:: CMake build -.. warning:: + Change to your build folder and type: - If you wish to edit/change a source file that is part of a package, - you should edit the version of the file inside the package folder in - src, and then re-install or update the package. The version in the - src directory is merely a copy and will be wiped out when you type - "make package-update". + .. code-block:: bash + + cmake . --build + + CMake should auto-detect whether it needs to re-run the CMake + configuration step and otherwise redo the build for all files + that have been changed or files that depend on changed files. + In case some build options have been changed or renamed, you + may have to update those by running: + + .. code-block:: bash + + cmake . + + and then rebuild. + + .. tab:: Traditional make + + Switch to the src directory and type: + + .. code-block:: bash + + $ make purge # remove any deprecated src files + $ make package-update # sync package files with src files + $ make foo # re-build for your machine (mpi, serial, etc) + + to enforce consistency of the source between the src folder + and package directories. This is OK to do even if you don't + use any packages. The "make purge" command removes any deprecated + src files if they were removed by the patch from a package + sub-directory. + + .. warning:: + + If you wish to edit/change a src file that is from a package, + you should edit the version of the file inside the package + sub-directory with src, then re-install the package. The + version in the source directory is merely a copy and will be + wiped out if you type "make package-update". From 4ee24b85b0e786b6bf98f998fd4d45e8994da20b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Mar 2021 11:45:47 -0400 Subject: [PATCH 0302/1217] fix a few minor issues with the docs --- doc/src/Build_basics.rst | 2 +- doc/src/angle_cosine_periodic.rst | 6 ------ doc/src/dihedral_table.rst | 4 ++-- 3 files changed, 3 insertions(+), 9 deletions(-) diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst index af6120630d..30e668a283 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -1,7 +1,7 @@ Basic build options =================== -The following topics are covered on this page, for building both with +The following topics are covered on this page, for building with both CMake and make: * :ref:`Serial vs parallel build ` diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index 8c60ac1ebb..4983745618 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -71,9 +71,3 @@ Default none ----------- - -.. _cosine-Mayo: - -**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990). diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index f1b14065fd..a456fecebd 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -15,10 +15,10 @@ Syntax .. code-block:: LAMMPS - dihedral_style style interp Ntable + dihedral_style style interpolation Ntable * style = *table* or *table/cut* -* interp = *linear* or *spline* = method of interpolation +* interpolation = *linear* or *spline* = method of interpolation * Ntable = size of the internal lookup table Examples From 39dc3e69ba716d63298cc8aca7e973268a94f8fe Mon Sep 17 00:00:00 2001 From: julient31 Date: Tue, 30 Mar 2021 10:35:25 -0600 Subject: [PATCH 0303/1217] Commit before pull --- doc/src/Howto_spins.rst | 4 ++-- .../validation_damped_exchange/run-test-exchange.sh | 12 +++++++++--- .../test-spin-precession.in | 8 +++++++- src/SPIN/pair_spin_exchange_biquadratic.cpp | 2 +- 4 files changed, 19 insertions(+), 7 deletions(-) diff --git a/doc/src/Howto_spins.rst b/doc/src/Howto_spins.rst index 0afcc12c91..87e30a5f6f 100644 --- a/doc/src/Howto_spins.rst +++ b/doc/src/Howto_spins.rst @@ -21,8 +21,8 @@ orientations and their associated inter-atomic distances. The command :doc:`fix precession/spin ` allows to apply a constant magnetic torque on all the spins in the system. This -torque can be an external magnetic field (Zeeman interaction), or an -uniaxial magnetic anisotropy. +torque can be an external magnetic field (Zeeman interaction), and an +uniaxial or cubic magnetic anisotropy. A Langevin thermostat can be applied to those magnetic spins using :doc:`fix langevin/spin `. Typically, this thermostat diff --git a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh index bd878a52de..a714e22fcf 100755 --- a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh +++ b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh @@ -3,9 +3,15 @@ # clean old res rm res_*.dat -# compute Lammps -./../../../../src/lmp_serial \ - -in test-spin-precession.in +# test standard Lammps +# ./../../../../src/lmp_serial \ +# -in test-spin-precession.in + +# test spin/kk with Kokkos Lammps +mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ + -k on -sf kk -in test-spin-precession.in + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" diff --git a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in index 9dfb4a98d6..bea5f53bf4 100644 --- a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in +++ b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in @@ -1,16 +1,22 @@ #LAMMPS in.run units metal -atom_style spin +# atom_style spin +atom_style spin/kk atom_modify map array boundary f f f +shell echo "test1" atom_modify map array lattice sc 3.0 region box block 0 2 0 1 0 1 +shell echo "test1" create_box 1 box +shell echo "test1" create_atoms 1 box +shell echo "test1" + mass 1 55.845 set atom 1 spin 2.0 1.0 0.0 0.0 set atom 2 spin 2.0 0.0 1.0 0.0 diff --git a/src/SPIN/pair_spin_exchange_biquadratic.cpp b/src/SPIN/pair_spin_exchange_biquadratic.cpp index 352949e5c3..a00d1cc8b0 100644 --- a/src/SPIN/pair_spin_exchange_biquadratic.cpp +++ b/src/SPIN/pair_spin_exchange_biquadratic.cpp @@ -393,7 +393,7 @@ void PairSpinExchangeBiquadratic::compute_exchange(int i, int j, double rsq, jtype = type[j]; r2j = rsq/J3[itype][jtype]/J3[itype][jtype]; - r2k = rsq/J3[itype][jtype]/J3[itype][jtype]; + r2k = rsq/K3[itype][jtype]/K3[itype][jtype]; Jex = 4.0*J1_mag[itype][jtype]*r2j; Jex *= (1.0-J2[itype][jtype]*r2j); From 8f5d11c0c576e4ea4b3a8682a329ee949438124a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Mar 2021 13:34:31 -0400 Subject: [PATCH 0304/1217] add missing return --- src/deprecated.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/deprecated.cpp b/src/deprecated.cpp index 40974e202b..4e596abb43 100644 --- a/src/deprecated.cpp +++ b/src/deprecated.cpp @@ -47,6 +47,7 @@ void Deprecated::command(int narg, char **arg) newcmd.append(arg[i]); } input->one(newcmd); + return; } error->all(FLERR,"This command is no longer available"); } From 2e86cb4176743859deb289e3018be9df92288d43 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Mar 2021 15:33:11 -0400 Subject: [PATCH 0305/1217] for atom style template number of bonds does not depend on newton_bond --- src/read_data.cpp | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/src/read_data.cpp b/src/read_data.cpp index 90aafd4b98..09fb8f3eae 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -793,7 +793,7 @@ void ReadData::command(int narg, char **arg) special.build(); } - // for atom style template systems, count total bonds,angles,etc + // for atom style template just count total bonds, etc. from template(s) if (atom->molecular == Atom::TEMPLATE) { Molecule **onemols = atom->avec->onemols; @@ -821,13 +821,6 @@ void ReadData::command(int narg, char **arg) MPI_Allreduce(&ndihedrals,&atom->ndihedrals,1,MPI_LMP_BIGINT,MPI_SUM,world); MPI_Allreduce(&nimpropers,&atom->nimpropers,1,MPI_LMP_BIGINT,MPI_SUM,world); - if (!force->newton_bond) { - atom->nbonds /= 2; - atom->nangles /= 3; - atom->ndihedrals /= 4; - atom->nimpropers /= 4; - } - if (me == 0) { std::string mesg; From e22f9c4768fb29f3dd0646ea303a623b79d15a74 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Mar 2021 16:48:51 -0400 Subject: [PATCH 0306/1217] newton bond off does not work with atom style template currently --- src/neighbor.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 0055678f41..68fa3ca96e 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1363,6 +1363,10 @@ void Neighbor::init_topology() onoff = improper_off; MPI_Allreduce(&onoff,&improper_off,1,MPI_INT,MPI_MAX,world); + // newton_bond off is not supported with atom style template + if ((atom->molecular == Atom::TEMPLATE) && (force->newton_bond == 0)) + error->all(FLERR,"Must use 'newton bond on' with atom style template"); + // instantiate NTopo classes if (atom->avec->bonds_allow) { From eea2f45a95d7c43df38df672a882933ae3e9e8ea Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Mar 2021 17:19:28 -0400 Subject: [PATCH 0307/1217] force newton bond to be on since we don't support it to be off (yet) --- unittest/formats/test_atom_styles.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/unittest/formats/test_atom_styles.cpp b/unittest/formats/test_atom_styles.cpp index 37d436a7a2..a08bddcba4 100644 --- a/unittest/formats/test_atom_styles.cpp +++ b/unittest/formats/test_atom_styles.cpp @@ -2711,7 +2711,7 @@ TEST_F(AtomStyleTest, template) command("write_data test_atom_styles.data"); command("clear"); command("units real"); - command("newton off"); + command("newton off on"); command("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); command("atom_style template twomols"); command("pair_style zero 4.0"); @@ -3127,7 +3127,7 @@ TEST_F(AtomStyleTest, template_charge) command("write_data test_atom_styles.data"); command("clear"); command("units real"); - command("newton off"); + command("newton off on"); command("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); command("atom_style hybrid template twomols charge"); command("pair_style zero 4.0"); From 183b30abd7d66d66bbe4d577c9ffdc844b533ea3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Mar 2021 18:30:22 -0400 Subject: [PATCH 0308/1217] use strmatch() consistently to detect respa and verlet runstyles with optional suffix --- src/BODY/fix_wall_body_polygon.cpp | 2 +- src/BODY/fix_wall_body_polyhedron.cpp | 2 +- src/CLASS2/pair_lj_class2.cpp | 4 ++-- src/CLASS2/pair_lj_class2_coul_long.cpp | 4 ++-- src/GPU/fix_gpu.cpp | 2 +- src/GPU/fix_nh_gpu.cpp | 2 +- src/GPU/fix_nve_gpu.cpp | 2 +- src/GPU/pppm_gpu.cpp | 2 +- src/GRANULAR/fix_freeze.cpp | 2 +- src/GRANULAR/fix_wall_gran.cpp | 4 ++-- src/KOKKOS/fix_setforce_kokkos.cpp | 2 +- src/KOKKOS/fix_shake_kokkos.cpp | 2 +- src/KOKKOS/pair_buck_coul_cut_kokkos.cpp | 2 +- src/KOKKOS/pair_buck_coul_long_kokkos.cpp | 2 +- src/KOKKOS/pair_buck_kokkos.cpp | 2 +- src/KOKKOS/pair_coul_long_kokkos.cpp | 2 +- src/KOKKOS/pair_hybrid_kokkos.cpp | 2 +- .../pair_lj_charmm_coul_charmm_implicit_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_class2_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_cut_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_expand_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_gromacs_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_sdk_kokkos.cpp | 2 +- src/KOKKOS/pair_morse_kokkos.cpp | 2 +- src/KOKKOS/pair_yukawa_kokkos.cpp | 2 +- src/KOKKOS/pair_zbl_kokkos.cpp | 2 +- src/KSPACE/pair_buck_long_coul_long.cpp | 4 ++-- src/KSPACE/pair_lj_charmmfsw_coul_long.cpp | 4 ++-- src/KSPACE/pair_lj_long_coul_long.cpp | 4 ++-- src/MANYBODY/fix_qeq_comb.cpp | 2 +- src/MC/fix_bond_break.cpp | 2 +- src/MC/fix_bond_create.cpp | 2 +- src/MISC/fix_efield.cpp | 4 ++-- src/MISC/fix_gld.cpp | 2 +- src/MISC/fix_orient_bcc.cpp | 4 ++-- src/MISC/fix_orient_fcc.cpp | 4 ++-- src/MISC/fix_ttm.cpp | 2 +- src/MOLECULE/dihedral_charmm.cpp | 2 +- src/MOLECULE/dihedral_charmmfsw.cpp | 2 +- src/POEMS/fix_poems.cpp | 2 +- src/QEQ/fix_qeq_dynamic.cpp | 2 +- src/QEQ/fix_qeq_fire.cpp | 2 +- src/QEQ/fix_qeq_point.cpp | 2 +- src/QEQ/fix_qeq_shielded.cpp | 2 +- src/QEQ/fix_qeq_slater.cpp | 2 +- src/RIGID/fix_rigid.cpp | 2 +- src/RIGID/fix_rigid_small.cpp | 2 +- src/RIGID/fix_shake.cpp | 4 ++-- src/SPIN/fix_precession_spin.cpp | 4 ++-- src/USER-BOCS/fix_bocs.cpp | 4 ++-- src/USER-COLVARS/fix_colvars.cpp | 4 ++-- src/USER-DRUDE/fix_langevin_drude.cpp | 2 +- src/USER-DRUDE/fix_tgnh_drude.cpp | 4 ++-- src/USER-EFF/fix_nve_eff.cpp | 2 +- src/USER-FEP/fix_adapt_fep.cpp | 2 +- src/USER-INTEL/fix_nh_intel.cpp | 2 +- src/USER-LB/fix_lb_viscous.cpp | 4 ++-- src/USER-MANIFOLD/fix_manifoldforce.cpp | 2 +- src/USER-MISC/fix_addtorque.cpp | 4 ++-- src/USER-MISC/fix_electron_stopping_fit.cpp | 2 +- src/USER-MISC/fix_ffl.cpp | 4 ++-- src/USER-MISC/fix_filter_corotate.cpp | 2 +- src/USER-MISC/fix_flow_gauss.cpp | 4 ++-- src/USER-MISC/fix_gle.cpp | 4 ++-- src/USER-MISC/fix_grem.cpp | 4 ++-- src/USER-MISC/fix_imd.cpp | 2 +- src/USER-MISC/fix_npt_cauchy.cpp | 4 ++-- src/USER-MISC/fix_nvk.cpp | 2 +- src/USER-MISC/fix_orient_eco.cpp | 4 ++-- src/USER-MISC/fix_pafi.cpp | 4 ++-- src/USER-MISC/fix_rhok.cpp | 4 ++-- src/USER-MISC/fix_smd.cpp | 10 +++++----- src/USER-MISC/fix_ti_spring.cpp | 4 ++-- src/USER-MISC/fix_ttm_mod.cpp | 2 +- src/USER-MISC/fix_wall_region_ees.cpp | 4 ++-- src/USER-MISC/pair_lj_expand_coul_long.cpp | 4 ++-- src/USER-OMP/fix_omp.cpp | 5 ++--- src/USER-OMP/fix_qeq_comb_omp.cpp | 2 +- src/USER-QMMM/fix_qmmm.cpp | 2 +- src/USER-QTB/fix_qtb.cpp | 4 ++-- src/USER-REAXC/fix_qeq_reax.cpp | 2 +- src/USER-SMD/fix_smd_setvel.cpp | 2 +- src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp | 4 ++-- src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp | 4 ++-- src/fix_adapt.cpp | 2 +- src/fix_aveforce.cpp | 4 ++-- src/fix_drag.cpp | 4 ++-- src/fix_dt_reset.cpp | 2 +- src/fix_enforce2d.cpp | 2 +- src/fix_gravity.cpp | 4 ++-- src/fix_indent.cpp | 4 ++-- src/fix_langevin.cpp | 4 ++-- src/fix_lineforce.cpp | 2 +- src/fix_move.cpp | 2 +- src/fix_nh.cpp | 4 ++-- src/fix_numdiff.cpp | 4 ++-- src/fix_nve_limit.cpp | 2 +- src/fix_nve_noforce.cpp | 2 +- src/fix_planeforce.cpp | 2 +- src/fix_restrain.cpp | 4 ++-- src/fix_setforce.cpp | 4 ++-- src/fix_spring.cpp | 4 ++-- src/fix_spring_chunk.cpp | 4 ++-- src/fix_spring_rg.cpp | 4 ++-- src/fix_spring_self.cpp | 4 ++-- src/fix_store_force.cpp | 4 ++-- src/fix_viscous.cpp | 4 ++-- src/fix_wall.cpp | 4 ++-- src/fix_wall_region.cpp | 4 ++-- src/neighbor.cpp | 2 +- src/pair_hybrid.cpp | 2 +- src/pair_lj96_cut.cpp | 4 ++-- src/pair_mie_cut.cpp | 4 ++-- src/run.cpp | 2 +- 123 files changed, 177 insertions(+), 178 deletions(-) diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp index 63df8d2a5c..027c0dbd5a 100644 --- a/src/BODY/fix_wall_body_polygon.cpp +++ b/src/BODY/fix_wall_body_polygon.cpp @@ -195,7 +195,7 @@ void FixWallBodyPolygon::init() void FixWallBodyPolygon::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); } diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp index 45edf28c98..acfafaefbe 100644 --- a/src/BODY/fix_wall_body_polyhedron.cpp +++ b/src/BODY/fix_wall_body_polyhedron.cpp @@ -202,7 +202,7 @@ void FixWallBodyPolyhedron::init() void FixWallBodyPolyhedron::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); } diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index 3727b17493..23b0be7396 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -491,7 +491,7 @@ void PairLJClass2::init_style() int irequest; int respa = 0; - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; } @@ -506,7 +506,7 @@ void PairLJClass2::init_style() // set rRESPA cutoffs - if (strstr(update->integrate_style,"respa") && + if (utils::strmatch(update->integrate_style,"^respa") && ((Respa *) update->integrate)->level_inner >= 0) cut_respa = ((Respa *) update->integrate)->cutoff; else cut_respa = nullptr; diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index 8b4a6bd732..9bebae15c8 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -671,7 +671,7 @@ void PairLJClass2CoulLong::init_style() int irequest; int respa = 0; - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; } @@ -688,7 +688,7 @@ void PairLJClass2CoulLong::init_style() // set rRESPA cutoffs - if (strstr(update->integrate_style,"respa") && + if (utils::strmatch(update->integrate_style,"^respa") && ((Respa *) update->integrate)->level_inner >= 0) cut_respa = ((Respa *) update->integrate)->cutoff; else cut_respa = nullptr; diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index 9fc3e67e5c..66a3e85941 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -297,7 +297,7 @@ void FixGPU::setup(int vflag) error->all(FLERR, "Cannot use neigh_modify exclude with GPU neighbor builds"); - if (strstr(update->integrate_style,"verlet")) post_force(vflag); + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { // In setup only, all forces calculated on GPU are put in the outer level ((Respa *) update->integrate)->copy_flevel_f(_nlevels_respa-1); diff --git a/src/GPU/fix_nh_gpu.cpp b/src/GPU/fix_nh_gpu.cpp index 8b57289a50..c41099c6d2 100644 --- a/src/GPU/fix_nh_gpu.cpp +++ b/src/GPU/fix_nh_gpu.cpp @@ -63,7 +63,7 @@ FixNHGPU::~FixNHGPU() void FixNHGPU::setup(int vflag) { FixNH::setup(vflag); - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) _respa_on = 1; else _respa_on = 0; diff --git a/src/GPU/fix_nve_gpu.cpp b/src/GPU/fix_nve_gpu.cpp index c3dd5b6ae2..9c6705deac 100644 --- a/src/GPU/fix_nve_gpu.cpp +++ b/src/GPU/fix_nve_gpu.cpp @@ -52,7 +52,7 @@ FixNVEGPU::~FixNVEGPU() void FixNVEGPU::setup(int vflag) { FixNVE::setup(vflag); - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) _respa_on = 1; else _respa_on = 0; diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp index 61d0144b73..d6a827354c 100644 --- a/src/GPU/pppm_gpu.cpp +++ b/src/GPU/pppm_gpu.cpp @@ -149,7 +149,7 @@ void PPPMGPU::init() // GPU precision specific init bool respa_value=false; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) respa_value=true; if (order>8) diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp index a343683b03..6a16bbb1f6 100644 --- a/src/GRANULAR/fix_freeze.cpp +++ b/src/GRANULAR/fix_freeze.cpp @@ -69,7 +69,7 @@ void FixFreeze::init() void FixFreeze::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { int nlevels_respa = ((Respa *) update->integrate)->nlevels; diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index d18b72aa65..5e8d568b7a 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -464,7 +464,7 @@ void FixWallGran::init() dt = update->dt; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; // check for FixRigid so can extract rigid body masses @@ -511,7 +511,7 @@ void FixWallGran::init() void FixWallGran::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp index 81de089960..30899bf402 100644 --- a/src/KOKKOS/fix_setforce_kokkos.cpp +++ b/src/KOKKOS/fix_setforce_kokkos.cpp @@ -67,7 +67,7 @@ void FixSetForceKokkos::init() { FixSetForce::init(); - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) error->all(FLERR,"Cannot (yet) use respa with Kokkos"); } diff --git a/src/KOKKOS/fix_shake_kokkos.cpp b/src/KOKKOS/fix_shake_kokkos.cpp index 97a2932415..253c7ee7e0 100644 --- a/src/KOKKOS/fix_shake_kokkos.cpp +++ b/src/KOKKOS/fix_shake_kokkos.cpp @@ -156,7 +156,7 @@ void FixShakeKokkos::init() { FixShake::init(); - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) error->all(FLERR,"Cannot yet use respa with Kokkos"); if (rattle) diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp index 1b6139a61a..975c191c3d 100644 --- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp @@ -285,7 +285,7 @@ void PairBuckCoulCutKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp index 771258f18b..2812abb026 100644 --- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp @@ -447,7 +447,7 @@ void PairBuckCoulLongKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp index bc25a26ded..b51bde119c 100644 --- a/src/KOKKOS/pair_buck_kokkos.cpp +++ b/src/KOKKOS/pair_buck_kokkos.cpp @@ -205,7 +205,7 @@ void PairBuckKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp index affdf76ab0..4075108823 100644 --- a/src/KOKKOS/pair_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_coul_long_kokkos.cpp @@ -405,7 +405,7 @@ void PairCoulLongKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_hybrid_kokkos.cpp b/src/KOKKOS/pair_hybrid_kokkos.cpp index 540a6a368a..5ef2edf1b6 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_kokkos.cpp @@ -90,7 +90,7 @@ void PairHybridKokkos::compute(int eflag, int vflag) Respa *respa = nullptr; respaflag = 0; - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { respa = (Respa *) update->integrate; if (respa->nhybrid_styles > 0) respaflag = 1; } diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp index b8fcc04b00..a0abce1510 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp @@ -450,7 +450,7 @@ void PairLJCharmmCoulCharmmImplicitKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp index 8391338037..f683204d9d 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp @@ -451,7 +451,7 @@ void PairLJCharmmCoulCharmmKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp index b54e5c96c9..7f9876a76f 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp @@ -459,7 +459,7 @@ void PairLJCharmmCoulLongKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp index 281f29405f..36a15da628 100644 --- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp @@ -287,7 +287,7 @@ void PairLJClass2CoulCutKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp index de7b04159a..031d025544 100644 --- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp @@ -442,7 +442,7 @@ void PairLJClass2CoulLongKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp index 12b0c02421..cef3c1f8d8 100644 --- a/src/KOKKOS/pair_lj_class2_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp @@ -223,7 +223,7 @@ void PairLJClass2Kokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp index e2bf45c00a..636a72b5e1 100644 --- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp @@ -278,7 +278,7 @@ void PairLJCutCoulCutKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp index 29eacfa774..8b4e189442 100644 --- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp @@ -307,7 +307,7 @@ void PairLJCutCoulDebyeKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp index 31380d88a8..cbeb0ab70a 100644 --- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp @@ -300,7 +300,7 @@ void PairLJCutCoulDSFKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp index 4270238c71..244acc644a 100644 --- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp @@ -440,7 +440,7 @@ void PairLJCutCoulLongKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp index 2a900dac7a..bffb921490 100644 --- a/src/KOKKOS/pair_lj_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp @@ -217,7 +217,7 @@ void PairLJCutKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp index 3e6e955f02..d351f2d5fc 100644 --- a/src/KOKKOS/pair_lj_expand_kokkos.cpp +++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp @@ -227,7 +227,7 @@ void PairLJExpandKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp index ca59ec9d01..fa4a3ca06d 100644 --- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp @@ -436,7 +436,7 @@ void PairLJGromacsCoulGromacsKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp index c7bcacc778..58fe845b71 100644 --- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp @@ -272,7 +272,7 @@ void PairLJGromacsKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_sdk_kokkos.cpp index b752225902..f8f1fa87cc 100644 --- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp +++ b/src/KOKKOS/pair_lj_sdk_kokkos.cpp @@ -255,7 +255,7 @@ void PairLJSDKKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp index bab19c2f44..74c2934510 100644 --- a/src/KOKKOS/pair_morse_kokkos.cpp +++ b/src/KOKKOS/pair_morse_kokkos.cpp @@ -234,7 +234,7 @@ void PairMorseKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_yukawa_kokkos.cpp b/src/KOKKOS/pair_yukawa_kokkos.cpp index 39e604c9aa..123b0a2d84 100644 --- a/src/KOKKOS/pair_yukawa_kokkos.cpp +++ b/src/KOKKOS/pair_yukawa_kokkos.cpp @@ -107,7 +107,7 @@ void PairYukawaKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KOKKOS/pair_zbl_kokkos.cpp b/src/KOKKOS/pair_zbl_kokkos.cpp index a530b66ee0..954c2edf26 100644 --- a/src/KOKKOS/pair_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_zbl_kokkos.cpp @@ -81,7 +81,7 @@ void PairZBLKokkos::init_style() // error if rRESPA with inner levels - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { int respa = 0; if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index c2c46f359b..f392179152 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -248,7 +248,7 @@ void PairBuckLongCoulLong::init_style() // set rRESPA cutoffs - if (strstr(update->integrate_style,"respa") && + if (utils::strmatch(update->integrate_style,"^respa") && ((Respa *) update->integrate)->level_inner >= 0) cut_respa = ((Respa *) update->integrate)->cutoff; else cut_respa = nullptr; @@ -264,7 +264,7 @@ void PairBuckLongCoulLong::init_style() int irequest; int respa = 0; - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; } diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index 459eac1687..ea48f0676f 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -740,7 +740,7 @@ void PairLJCharmmfswCoulLong::init_style() int irequest; int respa = 0; - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; } @@ -779,7 +779,7 @@ void PairLJCharmmfswCoulLong::init_style() // set & error check interior rRESPA cutoffs - if (strstr(update->integrate_style,"respa") && + if (utils::strmatch(update->integrate_style,"^respa") && ((Respa *) update->integrate)->level_inner >= 0) { cut_respa = ((Respa *) update->integrate)->cutoff; if (MIN(cut_lj,cut_coul) < cut_respa[3]) diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp index 2b34cf7f1b..da3b3c19e0 100644 --- a/src/KSPACE/pair_lj_long_coul_long.cpp +++ b/src/KSPACE/pair_lj_long_coul_long.cpp @@ -242,7 +242,7 @@ void PairLJLongCoulLong::init_style() // set rRESPA cutoffs - if (strstr(update->integrate_style,"respa") && + if (utils::strmatch(update->integrate_style,"^respa") && ((Respa *) update->integrate)->level_inner >= 0) cut_respa = ((Respa *) update->integrate)->cutoff; else cut_respa = nullptr; @@ -258,7 +258,7 @@ void PairLJLongCoulLong::init_style() int irequest; int respa = 0; - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; } diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index 7c2d18fc13..910db90822 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -138,7 +138,7 @@ void FixQEQComb::init() void FixQEQComb::setup(int vflag) { firstflag = 1; - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp index 56da69a7bc..8974b9039f 100644 --- a/src/MC/fix_bond_break.cpp +++ b/src/MC/fix_bond_break.cpp @@ -143,7 +143,7 @@ int FixBondBreak::setmask() void FixBondBreak::init() { - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; // enable angle/dihedral/improper breaking if any defined diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp index c8c0af3a3e..634837595b 100644 --- a/src/MC/fix_bond_create.cpp +++ b/src/MC/fix_bond_create.cpp @@ -232,7 +232,7 @@ int FixBondCreate::setmask() void FixBondCreate::init() { - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; // check cutoff for iatomtype,jatomtype diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp index 1181f554cf..5eb3caf5ea 100644 --- a/src/MISC/fix_efield.cpp +++ b/src/MISC/fix_efield.cpp @@ -209,7 +209,7 @@ void FixEfield::init() update->whichflag == 2 && estyle == NONE) error->all(FLERR,"Must use variable energy with fix efield"); - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -219,7 +219,7 @@ void FixEfield::init() void FixEfield::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp index 3f6c3da258..d0ad26c740 100644 --- a/src/MISC/fix_gld.cpp +++ b/src/MISC/fix_gld.cpp @@ -206,7 +206,7 @@ void FixGLD::init() dtv = update->dt; dtf = 0.5 * update->dt * force->ftm2v; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) step_respa = ((Respa *) update->integrate)->step; } diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index 4c6693f729..520940f2f0 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -202,7 +202,7 @@ int FixOrientBCC::setmask() void FixOrientBCC::init() { - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -228,7 +228,7 @@ void FixOrientBCC::init_list(int /*id*/, NeighList *ptr) void FixOrientBCC::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index a59e412fde..c94e91a0b5 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -200,7 +200,7 @@ int FixOrientFCC::setmask() void FixOrientFCC::init() { - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -226,7 +226,7 @@ void FixOrientFCC::init_list(int /*id*/, NeighList *ptr) void FixOrientFCC::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index 4658c0c943..da71d736c2 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -207,7 +207,7 @@ void FixTTM::init() for (int iznode = 0; iznode < nznodes; iznode++) net_energy_transfer_all[ixnode][iynode][iznode] = 0; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index cc60dbec2b..d56c875744 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -368,7 +368,7 @@ void DihedralCharmm::coeff(int narg, char **arg) void DihedralCharmm::init_style() { - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { Respa *r = (Respa *) update->integrate; if (r->level_pair >= 0 && (r->level_pair != r->level_dihedral)) error->all(FLERR,"Dihedral style charmm must be set to same" diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index 1164e93f18..09372f67ac 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -386,7 +386,7 @@ void DihedralCharmmfsw::coeff(int narg, char **arg) void DihedralCharmmfsw::init_style() { - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { Respa *r = (Respa *) update->integrate; if (r->level_pair >= 0 && (r->level_pair != r->level_dihedral)) error->all(FLERR,"Dihedral style charmmfsw must be set to same" diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index bb74e90850..3d5b3697f7 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -389,7 +389,7 @@ void FixPOEMS::init() // rRESPA info - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { step_respa = ((Respa *) update->integrate)->step; nlevels_respa = ((Respa *) update->integrate)->nlevels; } diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index 2bd63b718d..b06bde223b 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -78,7 +78,7 @@ void FixQEqDynamic::init() error->warning(FLERR,"Fix qeq/dynamic tolerance may be too small" " for damped dynamics"); - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index 6e51c906bc..b33a7745e0 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -91,7 +91,7 @@ void FixQEqFire::init() error->warning(FLERR,"Fix qeq/fire tolerance may be too small" " for damped fires"); - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; comb = (PairComb *) force->pair_match("comb",1); diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index f112c4859f..3d71135ae1 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -57,7 +57,7 @@ void FixQEqPoint::init() int ntypes = atom->ntypes; memory->create(shld,ntypes+1,ntypes+1,"qeq:shielding"); - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index decfe69ccc..356a747ed3 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -68,7 +68,7 @@ void FixQEqShielded::init() error->all(FLERR,"Invalid param file for fix qeq/shielded"); } - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 5cab1f1979..9b90f78d7a 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -79,7 +79,7 @@ void FixQEqSlater::init() error->all(FLERR,"Invalid param file for fix qeq/slater"); } - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index c211e0e4ca..a8a0e1409f 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -750,7 +750,7 @@ void FixRigid::init() dtf = 0.5 * update->dt * force->ftm2v; dtq = 0.5 * update->dt; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) step_respa = ((Respa *) update->integrate)->step; // setup rigid bodies, using current atom info. if reinitflag is not set, diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index bdc7330d6d..b7e0a1b2ac 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -600,7 +600,7 @@ void FixRigidSmall::init() dtf = 0.5 * update->dt * force->ftm2v; dtq = 0.5 * update->dt; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) step_respa = ((Respa *) update->integrate)->step; } diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index adef291ed9..390fe88309 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -456,7 +456,7 @@ void FixShake::setup(int vflag) // set respa to 0 if verlet is used and to 1 otherwise - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) respa = 0; else respa = 1; @@ -2956,7 +2956,7 @@ void FixShake::unpack_forward_comm(int n, int first, double *buf) void FixShake::reset_dt() { - if (strstr(update->integrate_style,"verlet")) { + if (utils::strmatch(update->integrate_style,"^verlet")) { dtv = update->dt; if (rattle) dtfsq = 0.5 * update->dt * update->dt * force->ftm2v; else dtfsq = update->dt * update->dt * force->ftm2v; diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 70ea7e1a09..17b9d3eb22 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -186,7 +186,7 @@ void FixPrecessionSpin::init() k1ch = k1c/hbar; k2ch = k2c/hbar; - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -225,7 +225,7 @@ void FixPrecessionSpin::init() void FixPrecessionSpin::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index 60fb03cdf8..bd217e60a8 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -590,7 +590,7 @@ void FixBocs::init() if (force->kspace) kspace_flag = 1; else kspace_flag = 0; - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { nlevels_respa = ((Respa *) update->integrate)->nlevels; step_respa = ((Respa *) update->integrate)->step; dto = 0.5*step_respa[0]; @@ -1850,7 +1850,7 @@ void FixBocs::reset_dt() // If using respa, then remap is performed in innermost level - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) dto = 0.5*step_respa[0]; if (pstat_flag) diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp index 74972a8076..a1b992059e 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/USER-COLVARS/fix_colvars.cpp @@ -412,7 +412,7 @@ void FixColvars::init() if ((me == 0) && (update->whichflag == 2)) error->warning(FLERR,"Using fix colvars with minimization"); - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } @@ -680,7 +680,7 @@ void FixColvars::setup(int vflag) proxy->setup(); // initialize forces - if (strstr(update->integrate_style,"verlet") || (update->whichflag == 2)) + if (utils::strmatch(update->integrate_style,"^verlet") || (update->whichflag == 2)) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp index 2dabec3a30..44d2556b61 100644 --- a/src/USER-DRUDE/fix_langevin_drude.cpp +++ b/src/USER-DRUDE/fix_langevin_drude.cpp @@ -156,7 +156,7 @@ void FixLangevinDrude::init() void FixLangevinDrude::setup(int /*vflag*/) { - if (!strstr(update->integrate_style,"verlet")) + if (!utils::strmatch(update->integrate_style,"^verlet")) error->all(FLERR,"RESPA style not compatible with fix langevin/drude"); if (!comm->ghost_velocity) error->all(FLERR,"fix langevin/drude requires ghost velocities. Use comm_modify vel yes"); diff --git a/src/USER-DRUDE/fix_tgnh_drude.cpp b/src/USER-DRUDE/fix_tgnh_drude.cpp index 49a4061878..d8bf1d76f9 100644 --- a/src/USER-DRUDE/fix_tgnh_drude.cpp +++ b/src/USER-DRUDE/fix_tgnh_drude.cpp @@ -671,7 +671,7 @@ void FixTGNHDrude::init() if (force->kspace) kspace_flag = 1; else kspace_flag = 0; - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { nlevels_respa = ((Respa *) update->integrate)->nlevels; step_respa = ((Respa *) update->integrate)->step; dto = 0.5*step_respa[0]; @@ -1593,7 +1593,7 @@ void FixTGNHDrude::reset_dt() // If using respa, then remap is performed in innermost level - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) dto = 0.5*step_respa[0]; } diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp index 58acdcc258..bfdd85df49 100644 --- a/src/USER-EFF/fix_nve_eff.cpp +++ b/src/USER-EFF/fix_nve_eff.cpp @@ -58,7 +58,7 @@ void FixNVEEff::init() dtv = update->dt; dtf = 0.5 * update->dt * force->ftm2v; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) step_respa = ((Respa *) update->integrate)->step; } diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp index c8a65539b4..7f17179087 100644 --- a/src/USER-FEP/fix_adapt_fep.cpp +++ b/src/USER-FEP/fix_adapt_fep.cpp @@ -356,7 +356,7 @@ void FixAdaptFEP::init() fix_chg = (FixStore *) modify->fix[ifix]; } - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } diff --git a/src/USER-INTEL/fix_nh_intel.cpp b/src/USER-INTEL/fix_nh_intel.cpp index 19245cccbf..6105892041 100644 --- a/src/USER-INTEL/fix_nh_intel.cpp +++ b/src/USER-INTEL/fix_nh_intel.cpp @@ -317,7 +317,7 @@ void FixNHIntel::reset_dt() // If using respa, then remap is performed in innermost level - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) dto = 0.5*step_respa[0]; if (pstat_flag) diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/USER-LB/fix_lb_viscous.cpp index 08a0a10356..a13fea3a1a 100644 --- a/src/USER-LB/fix_lb_viscous.cpp +++ b/src/USER-LB/fix_lb_viscous.cpp @@ -79,7 +79,7 @@ int FixLbViscous::setmask() void FixLbViscous::init() { - if (strcmp(update->integrate_style,"respa") == 0) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } @@ -88,7 +88,7 @@ void FixLbViscous::init() void FixLbViscous::setup(int vflag) { - if (strstr(update->integrate_style,"verlet") != nullptr) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index 26d209e7a9..b48decddba 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -120,7 +120,7 @@ void FixManifoldForce::init() void FixManifoldForce::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { int nlevels_respa = ((Respa *) update->integrate)->nlevels; diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp index b19f51a10b..59f2560e0b 100644 --- a/src/USER-MISC/fix_addtorque.cpp +++ b/src/USER-MISC/fix_addtorque.cpp @@ -130,7 +130,7 @@ void FixAddTorque::init() varflag = EQUAL; else varflag = CONSTANT; - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -140,7 +140,7 @@ void FixAddTorque::init() void FixAddTorque::setup(int vflag) { - if (strcmp(update->integrate_style,"verlet") == 0) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/USER-MISC/fix_electron_stopping_fit.cpp b/src/USER-MISC/fix_electron_stopping_fit.cpp index 2d9034aaef..8768ed5f3d 100644 --- a/src/USER-MISC/fix_electron_stopping_fit.cpp +++ b/src/USER-MISC/fix_electron_stopping_fit.cpp @@ -140,7 +140,7 @@ void FixElectronStoppingFit::init() void FixElectronStoppingFit::setup(int vflag) { - if (strcmp(update->integrate_style,"verlet") == 0) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp index eb9f033afc..6dfa9eb2ca 100644 --- a/src/USER-MISC/fix_ffl.cpp +++ b/src/USER-MISC/fix_ffl.cpp @@ -156,7 +156,7 @@ void FixFFL::init() { } } - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { nlevels_respa = ((Respa *) update->integrate)->nlevels; step_respa = ((Respa *) update->integrate)->step; } @@ -178,7 +178,7 @@ void FixFFL::init_ffl() { /* ---------------------------------------------------------------------- */ void FixFFL::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp index 38b22c1189..6e6dce84a7 100644 --- a/src/USER-MISC/fix_filter_corotate.cpp +++ b/src/USER-MISC/fix_filter_corotate.cpp @@ -277,7 +277,7 @@ void FixFilterCorotate::init() // could have changed locations in fix list since created // set ptrs to rRESPA variables - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { nlevels_respa = ((Respa *) update->integrate)->nlevels; } else error->all(FLERR,"Fix filter/corotate requires rRESPA!"); diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index 3c913f8039..9e6a2c0174 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -123,7 +123,7 @@ void FixFlowGauss::init() { //if respa level specified by fix_modify, then override default (outermost) //if specified level too high, set to max level - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); @@ -146,7 +146,7 @@ void FixFlowGauss::setup(int vflag) if (mTot <= 0.0) error->all(FLERR,"Invalid group mass in fix flow/gauss"); - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); post_force_respa(vflag,ilevel_respa,0); ((Respa *) update->integrate)->copy_f_flevel(ilevel_respa); diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp index a83ab0f9ce..8a7459b79d 100644 --- a/src/USER-MISC/fix_gle.cpp +++ b/src/USER-MISC/fix_gle.cpp @@ -416,7 +416,7 @@ void FixGLE::init() } } - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { nlevels_respa = ((Respa *) update->integrate)->nlevels; step_respa = ((Respa *) update->integrate)->step; } @@ -502,7 +502,7 @@ void FixGLE::init_gles() void FixGLE::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); diff --git a/src/USER-MISC/fix_grem.cpp b/src/USER-MISC/fix_grem.cpp index 64c7e4a6b7..e036eff205 100644 --- a/src/USER-MISC/fix_grem.cpp +++ b/src/USER-MISC/fix_grem.cpp @@ -200,10 +200,10 @@ void FixGrem::init() void FixGrem::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) error->all(FLERR,"Run style 'respa' is not supported"); } diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp index 8796de289e..f9591db4d3 100644 --- a/src/USER-MISC/fix_imd.cpp +++ b/src/USER-MISC/fix_imd.cpp @@ -601,7 +601,7 @@ int FixIMD::setmask() /* ---------------------------------------------------------------------- */ void FixIMD::init() { - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; return; diff --git a/src/USER-MISC/fix_npt_cauchy.cpp b/src/USER-MISC/fix_npt_cauchy.cpp index 37d6e5286b..802cabea67 100644 --- a/src/USER-MISC/fix_npt_cauchy.cpp +++ b/src/USER-MISC/fix_npt_cauchy.cpp @@ -765,7 +765,7 @@ void FixNPTCauchy::init() if (force->kspace) kspace_flag = 1; else kspace_flag = 0; - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { nlevels_respa = ((Respa *) update->integrate)->nlevels; step_respa = ((Respa *) update->integrate)->step; dto = 0.5*step_respa[0]; @@ -1752,7 +1752,7 @@ void FixNPTCauchy::reset_dt() // If using respa, then remap is performed in innermost level - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) dto = 0.5*step_respa[0]; if (pstat_flag) diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp index d21f4efe4e..ef6c390f95 100644 --- a/src/USER-MISC/fix_nvk.cpp +++ b/src/USER-MISC/fix_nvk.cpp @@ -59,7 +59,7 @@ void FixNVK::init() dtv = update->dt; dtf = 0.5 * update->dt; - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { error->all(FLERR,"Fix nvk not yet enabled for RESPA"); step_respa = ((Respa *) update->integrate)->step; } diff --git a/src/USER-MISC/fix_orient_eco.cpp b/src/USER-MISC/fix_orient_eco.cpp index 3d6db4cd4f..56da3cd6a1 100644 --- a/src/USER-MISC/fix_orient_eco.cpp +++ b/src/USER-MISC/fix_orient_eco.cpp @@ -177,7 +177,7 @@ void FixOrientECO::init() { MPI_Bcast(&norm_fac, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&inv_norm_fac, 1, MPI_DOUBLE, 0, world); - if (strstr(update->integrate_style, "respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels - 1; if (respa_level >= 0) ilevel_respa = MIN(respa_level, ilevel_respa); } @@ -201,7 +201,7 @@ void FixOrientECO::init_list(int /* id */, NeighList *ptr) { /* ---------------------------------------------------------------------- */ void FixOrientECO::setup(int vflag) { - if (strstr(update->integrate_style, "verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/USER-MISC/fix_pafi.cpp b/src/USER-MISC/fix_pafi.cpp index c2ad62d7d0..7d5216f540 100644 --- a/src/USER-MISC/fix_pafi.cpp +++ b/src/USER-MISC/fix_pafi.cpp @@ -180,7 +180,7 @@ void FixPAFI::init() error->all(FLERR,"Compute for fix pafi must have 9 fields per atom"); - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { step_respa = ((Respa *) update->integrate)->step; // nve nlevels_respa = ((Respa *) update->integrate)->nlevels; if (respa_level >= 0) ilevel_respa = MIN(respa_level,nlevels_respa-1); @@ -191,7 +191,7 @@ void FixPAFI::init() void FixPAFI::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else for (int ilevel = 0; ilevel < nlevels_respa; ilevel++) { diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp index f546b9a814..18e1ed195f 100644 --- a/src/USER-MISC/fix_rhok.cpp +++ b/src/USER-MISC/fix_rhok.cpp @@ -95,7 +95,7 @@ int FixRhok::setmask() void FixRhok::init() { // RESPA boilerplate - if (strcmp( update->integrate_style, "respa" ) == 0) + if (utils::strmatch(update->integrate_style,"^respa")) mNLevelsRESPA = ((Respa *) update->integrate)->nlevels; // Count the number of affected particles @@ -117,7 +117,7 @@ void FixRhok::init() // Initial application of the fix to a system (when doing MD) void FixRhok::setup( int inVFlag ) { - if (strcmp( update->integrate_style, "verlet" ) == 0) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force( inVFlag ); else { diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp index 8ea1beac71..bc8ede4a17 100644 --- a/src/USER-MISC/fix_smd.cpp +++ b/src/USER-MISC/fix_smd.cpp @@ -159,7 +159,7 @@ void FixSMD::init() zn = dz/r_old; } - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -169,7 +169,7 @@ void FixSMD::init() void FixSMD::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); @@ -190,7 +190,7 @@ void FixSMD::post_force(int vflag) else smd_couple(); if (styleflag & SMD_CVEL) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) r_old += v_smd * update->dt; else r_old += v_smd * ((Respa *) update->integrate)->step[ilevel_respa]; @@ -205,7 +205,7 @@ void FixSMD::smd_tether() group->xcm(igroup,masstotal,xcm); double dt = update->dt; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) dt = ((Respa *) update->integrate)->step[ilevel_respa]; // fx,fy,fz = components of k * (r-r0) @@ -311,7 +311,7 @@ void FixSMD::smd_couple() group->xcm(igroup2,masstotal2,xcm2); double dt = update->dt; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) dt = ((Respa *) update->integrate)->step[ilevel_respa]; // renormalize direction of spring diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp index 766b9df5eb..1d6079d4d6 100644 --- a/src/USER-MISC/fix_ti_spring.cpp +++ b/src/USER-MISC/fix_ti_spring.cpp @@ -141,7 +141,7 @@ int FixTISpring::setmask() void FixTISpring::init() { - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } @@ -149,7 +149,7 @@ void FixTISpring::init() void FixTISpring::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index 7056ad6a00..d4023b6011 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -230,7 +230,7 @@ void FixTTMMod::init() for (int iznode = 0; iznode < nznodes; iznode++) net_energy_transfer_all[ixnode][iynode][iznode] = 0; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index 51e0af9dc4..8a79b73034 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -118,7 +118,7 @@ void FixWallRegionEES::init() offset = 0; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } @@ -126,7 +126,7 @@ void FixWallRegionEES::init() void FixWallRegionEES::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/USER-MISC/pair_lj_expand_coul_long.cpp index f49d181e0f..84eb86aaa8 100644 --- a/src/USER-MISC/pair_lj_expand_coul_long.cpp +++ b/src/USER-MISC/pair_lj_expand_coul_long.cpp @@ -690,7 +690,7 @@ void PairLJExpandCoulLong::init_style() int irequest; int respa = 0; - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; } @@ -707,7 +707,7 @@ void PairLJExpandCoulLong::init_style() // set rRESPA cutoffs - if (strstr(update->integrate_style,"respa") && + if (utils::strmatch(update->integrate_style,"^respa") && ((Respa *) update->integrate)->level_inner >= 0) cut_respa = ((Respa *) update->integrate)->cutoff; else cut_respa = nullptr; diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp index 23671f4c7e..678df7c22a 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/USER-OMP/fix_omp.cpp @@ -203,9 +203,8 @@ void FixOMP::init() thr[i]->_timer_active=-1; } - if ((strstr(update->integrate_style,"respa") != nullptr) - && (strstr(update->integrate_style,"respa/omp") == nullptr)) - error->all(FLERR,"Need to use respa/omp for r-RESPA with /omp styles"); + if (!utils::strmatch(update->integrate_style,"^respa/omp")) + error->all(FLERR,"Must use respa/omp for r-RESPA with /omp styles"); if (force->pair && force->pair->compute_flag) _pair_compute_flag = true; else _pair_compute_flag = false; diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp index aceff62ebc..6844729e92 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.cpp +++ b/src/USER-OMP/fix_qeq_comb_omp.cpp @@ -58,7 +58,7 @@ void FixQEQCombOMP::init() error->all(FLERR,"Must use pair_style comb or " "comb/omp with fix qeq/comb/omp"); - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } diff --git a/src/USER-QMMM/fix_qmmm.cpp b/src/USER-QMMM/fix_qmmm.cpp index 6689ebdb9d..fab658f8f2 100644 --- a/src/USER-QMMM/fix_qmmm.cpp +++ b/src/USER-QMMM/fix_qmmm.cpp @@ -651,7 +651,7 @@ void FixQMMM::exchange_forces() void FixQMMM::init() { - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) error->all(FLERR,"Fix qmmm does not currently support r-RESPA"); if (do_init) { diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp index e4e645a1bb..a4f6e8678f 100644 --- a/src/USER-QTB/fix_qtb.cpp +++ b/src/USER-QTB/fix_qtb.cpp @@ -216,7 +216,7 @@ void FixQTB::init() } // respa - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } @@ -225,7 +225,7 @@ void FixQTB::init() ------------------------------------------------------------------------- */ void FixQTB::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index 44088043f0..3109950ff2 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -370,7 +370,7 @@ void FixQEqReax::init() init_shielding(); init_taper(); - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp index 471159ea53..312deb4d19 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/USER-SMD/fix_smd_setvel.cpp @@ -208,7 +208,7 @@ void FixSMDSetVel::init() { /* ---------------------------------------------------------------------- */ void FixSMDSetVel::setup(int vflag) { - if (strstr(update->integrate_style, "verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else error->all(FLERR,"Fix smd/setvel does not support RESPA"); diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index 556d303d30..c1bf0a308d 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -338,7 +338,7 @@ void PairLJSwitch3CoulGaussLong::init_style() int irequest; int respa = 0; - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; } @@ -355,7 +355,7 @@ void PairLJSwitch3CoulGaussLong::init_style() // set rRESPA cutoffs - if (strstr(update->integrate_style,"respa") && + if (utils::strmatch(update->integrate_style,"^respa") && ((Respa *) update->integrate)->level_inner >= 0) cut_respa = ((Respa *) update->integrate)->cutoff; else cut_respa = nullptr; diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp index 47ddf8c7ad..187778bb66 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -340,7 +340,7 @@ void PairMM3Switch3CoulGaussLong::init_style() int irequest; int respa = 0; - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; } @@ -357,7 +357,7 @@ void PairMM3Switch3CoulGaussLong::init_style() // set rRESPA cutoffs - if (strstr(update->integrate_style,"respa") && + if (utils::strmatch(update->integrate_style,"^respa") && ((Respa *) update->integrate)->level_inner >= 0) cut_respa = ((Respa *) update->integrate)->cutoff; else cut_respa = nullptr; diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index c09b6481f6..51fdb16d5d 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -462,7 +462,7 @@ void FixAdapt::init() fix_chg = (FixStore *) modify->fix[ifix]; } - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp index 5ce50aafea..867643499a 100644 --- a/src/fix_aveforce.cpp +++ b/src/fix_aveforce.cpp @@ -155,7 +155,7 @@ void FixAveForce::init() if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL) varflag = EQUAL; else varflag = CONSTANT; - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { nlevels_respa = ((Respa *) update->integrate)->nlevels; if (respa_level >= 0) ilevel_respa = MIN(respa_level,nlevels_respa-1); else ilevel_respa = nlevels_respa-1; @@ -166,7 +166,7 @@ void FixAveForce::init() void FixAveForce::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else for (int ilevel = 0; ilevel < nlevels_respa; ilevel++) { diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp index 40b8af7f9a..03209ce729 100644 --- a/src/fix_drag.cpp +++ b/src/fix_drag.cpp @@ -69,7 +69,7 @@ int FixDrag::setmask() void FixDrag::init() { - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -79,7 +79,7 @@ void FixDrag::init() void FixDrag::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp index 336911e8c7..34cecc45de 100644 --- a/src/fix_dt_reset.cpp +++ b/src/fix_dt_reset.cpp @@ -112,7 +112,7 @@ void FixDtReset::init() // set rRESPA flag respaflag = 0; - if (strstr(update->integrate_style,"respa")) respaflag = 1; + if (utils::strmatch(update->integrate_style,"^respa")) respaflag = 1; // check for DCD or XTC dumps diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index c1b8285a4b..1284a9b78c 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -90,7 +90,7 @@ void FixEnforce2D::init() void FixEnforce2D::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { int nlevels_respa = ((Respa *) update->integrate)->nlevels; diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp index 194f5731bc..8c6baab1ee 100644 --- a/src/fix_gravity.cpp +++ b/src/fix_gravity.cpp @@ -181,7 +181,7 @@ int FixGravity::setmask() void FixGravity::init() { - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -243,7 +243,7 @@ void FixGravity::init() void FixGravity::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index 48355446d1..d2a7ba0d2a 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -153,7 +153,7 @@ void FixIndent::init() error->all(FLERR,"Variable for fix indent is not equal style"); } - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -163,7 +163,7 @@ void FixIndent::init() void FixIndent::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index 66da7a9633..bf9d5cad23 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -310,7 +310,7 @@ void FixLangevin::init() if (temperature && temperature->tempbias) tbiasflag = BIAS; else tbiasflag = NOBIAS; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; if (utils::strmatch(update->integrate_style,"^respa") && gjfflag) @@ -367,7 +367,7 @@ void FixLangevin::setup(int vflag) } } } - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp index 9582d8db51..6a77442ea4 100644 --- a/src/fix_lineforce.cpp +++ b/src/fix_lineforce.cpp @@ -59,7 +59,7 @@ int FixLineForce::setmask() void FixLineForce::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { int nlevels_respa = ((Respa *) update->integrate)->nlevels; diff --git a/src/fix_move.cpp b/src/fix_move.cpp index e37fe52cc9..6b640cd747 100644 --- a/src/fix_move.cpp +++ b/src/fix_move.cpp @@ -433,7 +433,7 @@ void FixMove::init() if (velocityflag) memory->create(velocity,maxatom,3,"move:velocity"); else velocity = nullptr; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index 120aeeb7de..d95763f06b 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -728,7 +728,7 @@ void FixNH::init() if (force->kspace) kspace_flag = 1; else kspace_flag = 0; - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { nlevels_respa = ((Respa *) update->integrate)->nlevels; step_respa = ((Respa *) update->integrate)->step; dto = 0.5*step_respa[0]; @@ -1722,7 +1722,7 @@ void FixNH::reset_dt() // If using respa, then remap is performed in innermost level - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) dto = 0.5*step_respa[0]; if (pstat_flag) diff --git a/src/fix_numdiff.cpp b/src/fix_numdiff.cpp index 10926ec440..495e196749 100644 --- a/src/fix_numdiff.cpp +++ b/src/fix_numdiff.cpp @@ -120,7 +120,7 @@ void FixNumDiff::init() if (force->kspace && force->kspace->compute_flag) kspace_compute_flag = 1; else kspace_compute_flag = 0; - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -130,7 +130,7 @@ void FixNumDiff::init() void FixNumDiff::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp index 7ee0e6f80e..58db5e25d9 100644 --- a/src/fix_nve_limit.cpp +++ b/src/fix_nve_limit.cpp @@ -66,7 +66,7 @@ void FixNVELimit::init() vlimitsq = (xlimit/dtv) * (xlimit/dtv); ncount = 0; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) step_respa = ((Respa *) update->integrate)->step; // warn if using fix shake, which will lead to invalid constraint forces diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp index 3a9c1c6442..61528a0024 100644 --- a/src/fix_nve_noforce.cpp +++ b/src/fix_nve_noforce.cpp @@ -47,7 +47,7 @@ void FixNVENoforce::init() { dtv = update->dt; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) step_respa = ((Respa *) update->integrate)->step; } diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp index cc0b43054a..783d26ac9e 100644 --- a/src/fix_planeforce.cpp +++ b/src/fix_planeforce.cpp @@ -59,7 +59,7 @@ int FixPlaneForce::setmask() void FixPlaneForce::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { int nlevels_respa = ((Respa *) update->integrate)->nlevels; diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index 82e91c8289..ff61703c1a 100644 --- a/src/fix_restrain.cpp +++ b/src/fix_restrain.cpp @@ -185,7 +185,7 @@ int FixRestrain::setmask() void FixRestrain::init() { - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -195,7 +195,7 @@ void FixRestrain::init() void FixRestrain::setup(int vflag) { - if (strcmp(update->integrate_style,"verlet") == 0) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp index 7d41b428c9..d59d091f42 100644 --- a/src/fix_setforce.cpp +++ b/src/fix_setforce.cpp @@ -166,7 +166,7 @@ void FixSetForce::init() varflag = EQUAL; else varflag = CONSTANT; - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { nlevels_respa = ((Respa *) update->integrate)->nlevels; if (respa_level >= 0) ilevel_respa = MIN(respa_level,nlevels_respa-1); else ilevel_respa = nlevels_respa-1; @@ -192,7 +192,7 @@ void FixSetForce::init() void FixSetForce::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else for (int ilevel = 0; ilevel < nlevels_respa; ilevel++) { diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index 89d569fc8b..200d9f072a 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -128,7 +128,7 @@ void FixSpring::init() masstotal = group->mass(igroup); if (styleflag == COUPLE) masstotal2 = group->mass(igroup2); - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -138,7 +138,7 @@ void FixSpring::init() void FixSpring::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp index 8eb35e74aa..a007aabefc 100644 --- a/src/fix_spring_chunk.cpp +++ b/src/fix_spring_chunk.cpp @@ -112,7 +112,7 @@ void FixSpringChunk::init() if (strcmp(idchunk,ccom->idchunk) != 0) error->all(FLERR,"Fix spring chunk chunkID not same as comID chunkID"); - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -122,7 +122,7 @@ void FixSpringChunk::init() void FixSpringChunk::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index cabdc4b11f..58249bbd2d 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -77,7 +77,7 @@ void FixSpringRG::init() rg0_flag = 0; } - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -87,7 +87,7 @@ void FixSpringRG::init() void FixSpringRG::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp index 7a22cbd3f8..9f649faec0 100644 --- a/src/fix_spring_self.cpp +++ b/src/fix_spring_self.cpp @@ -120,7 +120,7 @@ int FixSpringSelf::setmask() void FixSpringSelf::init() { - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -130,7 +130,7 @@ void FixSpringSelf::init() void FixSpringSelf::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp index 460422aee9..1541294f6c 100644 --- a/src/fix_store_force.cpp +++ b/src/fix_store_force.cpp @@ -68,7 +68,7 @@ int FixStoreForce::setmask() void FixStoreForce::init() { - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; } @@ -76,7 +76,7 @@ void FixStoreForce::init() void FixStoreForce::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp index 7bdac6aeaf..0c7d682ae2 100644 --- a/src/fix_viscous.cpp +++ b/src/fix_viscous.cpp @@ -80,7 +80,7 @@ void FixViscous::init() { int max_respa = 0; - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = max_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,max_respa); } @@ -90,7 +90,7 @@ void FixViscous::init() void FixViscous::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index 677085854c..280ce848c6 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -263,7 +263,7 @@ void FixWall::init() for (int m = 0; m < nwall; m++) precompute(m); - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -273,7 +273,7 @@ void FixWall::init() void FixWall::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) { + if (utils::strmatch(update->integrate_style,"^verlet")) { if (!fldflag) post_force(vflag); } else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index 7e30fe2361..e5c9167ce4 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -187,7 +187,7 @@ void FixWallRegion::init() offset = coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv; } - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -197,7 +197,7 @@ void FixWallRegion::init() void FixWallRegion::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 68fa3ca96e..fb0a244cc0 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -319,7 +319,7 @@ void Neighbor::init() // rRESPA cutoffs int respa = 0; - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; } diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 377364b8e5..c7b6048139 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -114,7 +114,7 @@ void PairHybrid::compute(int eflag, int vflag) Respa *respa = nullptr; respaflag = 0; - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { respa = (Respa *) update->integrate; if (respa->nhybrid_styles > 0) respaflag = 1; } diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index b68d595098..65f2d40e00 100644 --- a/src/pair_lj96_cut.cpp +++ b/src/pair_lj96_cut.cpp @@ -490,7 +490,7 @@ void PairLJ96Cut::init_style() int irequest; int respa = 0; - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; } @@ -505,7 +505,7 @@ void PairLJ96Cut::init_style() // set rRESPA cutoffs - if (strstr(update->integrate_style,"respa") && + if (utils::strmatch(update->integrate_style,"^respa") && ((Respa *) update->integrate)->level_inner >= 0) cut_respa = ((Respa *) update->integrate)->cutoff; else cut_respa = nullptr; diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp index 043ad3aeaa..503ed60d1b 100644 --- a/src/pair_mie_cut.cpp +++ b/src/pair_mie_cut.cpp @@ -499,7 +499,7 @@ void PairMIECut::init_style() int irequest; int respa = 0; - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; } @@ -514,7 +514,7 @@ void PairMIECut::init_style() // set rRESPA cutoffs - if (strstr(update->integrate_style,"respa") && + if (utils::strmatch(update->integrate_style,"^respa") && ((Respa *) update->integrate)->level_inner >= 0) cut_respa = ((Respa *) update->integrate)->cutoff; else cut_respa = nullptr; diff --git a/src/run.cpp b/src/run.cpp index fedf020d9d..c503e174ff 100644 --- a/src/run.cpp +++ b/src/run.cpp @@ -134,7 +134,7 @@ void Run::command(int narg, char **arg) error->all(FLERR,"Run command stop value is before end of run"); } - if (!preflag && strstr(update->integrate_style,"respa")) + if (!preflag && utils::strmatch(update->integrate_style,"^respa")) error->all(FLERR,"Run flag 'pre no' not compatible with r-RESPA"); // if nevery, make copies of arg strings that are commands From 7092a7769c8cce2dd9e81aa6381cf2c2af72882c Mon Sep 17 00:00:00 2001 From: Bhanuday Sharma <55601693+bhanudaysharma@users.noreply.github.com> Date: Wed, 31 Mar 2021 06:44:52 +0530 Subject: [PATCH 0309/1217] Update units.rst In LJ units, the conversion formula between rho and rho* should be corrected to \rho^* = \rho \frac{\sigma^{dim}}{m} --- doc/src/units.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/units.rst b/doc/src/units.rst index 8ca29f4c49..3c0f4a220a 100644 --- a/doc/src/units.rst +++ b/doc/src/units.rst @@ -87,7 +87,7 @@ energy is a derived unit (in SI units you equivalently have the relation * charge = reduced LJ charge, where :math:`q^* = q \frac{1}{\sqrt{4 \pi \varepsilon_0 \sigma \epsilon}}` * dipole = reduced LJ dipole, moment where :math:`\mu^* = \mu \frac{1}{\sqrt{4 \pi \varepsilon_0 \sigma^3 \epsilon}}` * electric field = force/charge, where :math:`E^* = E \frac{\sqrt{4 \pi \varepsilon_0 \sigma \epsilon} \sigma}{\epsilon}` -* density = mass/volume, where :math:`\rho^* = \rho \sigma^{dim}` +* density = mass/volume, where :math:`\rho^* = \rho \frac{\sigma^{dim}}{m}` Note that for LJ units, the default mode of thermodynamic output via the :doc:`thermo_style ` command is to normalize all From 7e0d44e0ca471495e5a8dd4bb90040fd14a6aa84 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 30 Mar 2021 20:51:23 -0600 Subject: [PATCH 0310/1217] Adding no_attraction flag to granular pair and wall styles --- doc/src/fix_wall_gran.rst | 10 ++++++++-- doc/src/fix_wall_gran_region.rst | 10 +++++++++- doc/src/pair_gran.rst | 15 ++++++++++++++- doc/src/pair_granular.rst | 6 ++++++ src/GRANULAR/fix_wall_gran.cpp | 14 +++++++++++++- src/GRANULAR/fix_wall_gran.h | 1 + src/GRANULAR/pair_gran_hertz_history.cpp | 2 ++ src/GRANULAR/pair_gran_hooke.cpp | 2 ++ src/GRANULAR/pair_gran_hooke_history.cpp | 12 +++++++++++- src/GRANULAR/pair_gran_hooke_history.h | 1 + src/GRANULAR/pair_granular.cpp | 14 +++++++++++++- src/GRANULAR/pair_granular.h | 1 + src/KOKKOS/pair_gran_hooke_history_kokkos.cpp | 1 + 13 files changed, 82 insertions(+), 7 deletions(-) diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index 1eefc4aeae..73fa7e367b 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -45,7 +45,7 @@ Syntax radius = cylinder radius (distance units) * zero or more keyword/value pairs may be appended to args -* keyword = *wiggle* or *shear* or *contacts* +* keyword = *wiggle* or *shear* or *contacts* or *no_attraction* .. parsed-literal:: @@ -58,6 +58,8 @@ Syntax vshear = magnitude of shear velocity (velocity units) *contacts* value = none generate contact information for each particle + *no_attraction* value = none + turn off possibility for attractive interactions Examples @@ -175,8 +177,12 @@ the clockwise direction for *vshear* > 0 or counter-clockwise for *vshear* < 0. In this case, *vshear* is the tangential velocity of the wall at whatever *radius* has been defined. +If a particle is moving away from the wall while in contact, there +is a possibility that the particle could experience an effective attractive +force due to damping. If the *no_attraction* keyword is used, this fix +will zero out the normal component of the force if there is an effective +attractive force. This keyword cannot be used with the JKR or DMT models. -Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the shear friction state of atoms interacting with the diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 9ed5bb7bcc..356c8427b0 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -36,12 +36,14 @@ Syntax * wallstyle = region (see :doc:`fix wall/gran ` for options for other kinds of walls) * region-ID = region whose boundary will act as wall -* keyword = *contacts* +* keyword = *contacts* or *no_attraction* .. parsed-literal:: *contacts* value = none generate contact information for each particle + *no_attraction* value = none + turn off possibility for attractive interactions Examples """""""" @@ -199,6 +201,12 @@ values for the 6 wall/particle coefficients than for particle/particle interactions. E.g. if you wish to model the wall as a different material. +If a particle is moving away from the wall while in contact, there +is a possibility that the particle could experience an effective attractive +force due to damping. If the *no_attraction* keyword is used, this fix +will zero out the normal component of the force if there is an effective +attractive force. This keyword cannot be used with the JKR or DMT models. + Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index d3f87839e8..aa2e42d339 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -26,7 +26,7 @@ Syntax .. code-block:: LAMMPS - pair_style style Kn Kt gamma_n gamma_t xmu dampflag + pair_style style Kn Kt gamma_n gamma_t xmu dampflag keyword * style = *gran/hooke* or *gran/hooke/history* or *gran/hertz/history* * Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) @@ -36,6 +36,13 @@ Syntax * xmu = static yield criterion (unitless value between 0.0 and 1.0e4) * dampflag = 0 or 1 if tangential damping force is excluded or included +* keyword = *no_attraction* + + .. parsed-literal:: + + *no_attraction* value = none + turn off possibility for attractive interactions + .. note:: Versions of LAMMPS before 9Jan09 had different style names for @@ -208,6 +215,12 @@ potential is used as a sub-style of :doc:`pair_style hybrid `, then pair_coeff command to determine which atoms interact via a granular potential. +If two particles are moving away from each other while in contact, there +is a possibility that the particles could experience an effective attractive +force due to damping. If the *no_attraction* keyword is used, this fix +will zero out the normal component of the force if there is an effective +attractive force. + ---------- .. include:: accel_styles.rst diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index 80663b7d49..cb65a58777 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -657,6 +657,12 @@ then LAMMPS will use that cutoff for the specified atom type combination, and automatically set pairwise cutoffs for the remaining atom types. +If two particles are moving away from each other while in contact, there +is a possibility that the particles could experience an effective attractive +force due to damping. If the *no_attraction* keyword is used, this fix +will zero out the normal component of the force if there is an effective +attractive force. This keyword cannot be used with the JKR or DMT models. + ---------- .. include:: accel_styles.rst diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index d18b72aa65..9c17a323c5 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -347,6 +347,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : wiggle = 0; wshear = 0; peratom_flag = 0; + noattraction_flag = 0; while (iarg < narg) { if (strcmp(arg[iarg],"wiggle") == 0) { @@ -373,6 +374,13 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : size_peratom_cols = 8; peratom_freq = 1; iarg += 1; + } else if (strcmp(arg[iarg],"no_attraction") == 0) { + noattraction_flag = 1; + if(normal_model == JKR) + error->all(FLERR,"Cannot turn off attraction with JRK model"); + if(normal_model == DMT) + error->all(FLERR,"Cannot turn off attraction with DMT model"); + iarg += 1; } else error->all(FLERR,"Illegal fix wall/gran command"); } @@ -761,6 +769,7 @@ void FixWallGran::hooke(double rsq, double dx, double dy, double dz, damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radius-r)*rinv - damp; + if(noattraction_flag and ccel < 0.0) ccel = 0.0; // relative velocities @@ -853,6 +862,7 @@ void FixWallGran::hooke_history(double rsq, double dx, double dy, double dz, damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radius-r)*rinv - damp; + if(noattraction_flag and ccel < 0.0) ccel = 0.0; // relative velocities @@ -984,7 +994,8 @@ void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz, if (rwall == 0.0) polyhertz = sqrt((radius-r)*radius); else polyhertz = sqrt((radius-r)*radius*rwall/(rwall+radius)); ccel *= polyhertz; - + if(noattraction_flag and ccel < 0.0) ccel = 0.0; + // relative velocities vtr1 = vt1 - (dz*wr2-dy*wr3); @@ -1177,6 +1188,7 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; + if(noattraction_flag and Fntot < 0.0) Fntot = 0.0; //**************************************** // tangential force, including history effects diff --git a/src/GRANULAR/fix_wall_gran.h b/src/GRANULAR/fix_wall_gran.h index a81a4c787c..3963b22a2c 100644 --- a/src/GRANULAR/fix_wall_gran.h +++ b/src/GRANULAR/fix_wall_gran.h @@ -69,6 +69,7 @@ class FixWallGran : public Fix { // for granular model choices int normal_model, damping_model; int tangential_model, roll_model, twist_model; + int noattraction_flag; // history flags int normal_history, tangential_history, roll_history, twist_history; diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index e7193140b9..7da0c6142d 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -181,6 +181,7 @@ void PairGranHertzHistory::compute(int eflag, int vflag) ccel = kn*(radsum-r)*rinv - damp; polyhertz = sqrt((radsum-r)*radi*radj / radsum); ccel *= polyhertz; + if(noattractionflag and ccel < 0.0) ccel = 0.0; // relative velocities @@ -388,6 +389,7 @@ double PairGranHertzHistory::single(int i, int j, int /*itype*/, int /*jtype*/, ccel = kn*(radsum-r)*rinv - damp; polyhertz = sqrt((radsum-r)*radi*radj / radsum); ccel *= polyhertz; + if(noattractionflag and ccel < 0.0) ccel = 0.0; // relative velocities diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp index 3875d12a0f..76946701cb 100644 --- a/src/GRANULAR/pair_gran_hooke.cpp +++ b/src/GRANULAR/pair_gran_hooke.cpp @@ -158,6 +158,7 @@ void PairGranHooke::compute(int eflag, int vflag) damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; + if(noattractionflag and ccel < 0.0) ccel = 0.0; // relative velocities @@ -299,6 +300,7 @@ double PairGranHooke::single(int i, int j, int /*itype*/, int /*jtype*/, double damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; + if(noattractionflag and ccel < 0.0) ccel = 0.0; // relative velocities diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 4deb828d76..4893be4084 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -237,6 +237,7 @@ void PairGranHookeHistory::compute(int eflag, int vflag) damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; + if(noattractionflag and ccel < 0.0) ccel = 0.0; // relative velocities @@ -356,7 +357,7 @@ void PairGranHookeHistory::allocate() void PairGranHookeHistory::settings(int narg, char **arg) { - if (narg != 6) error->all(FLERR,"Illegal pair_style command"); + if (narg != 6 and narg != 7) error->all(FLERR,"Illegal pair_style command"); kn = utils::numeric(FLERR,arg[0],false,lmp); if (strcmp(arg[1],"NULL") == 0) kt = kn * 2.0/7.0; @@ -369,6 +370,14 @@ void PairGranHookeHistory::settings(int narg, char **arg) xmu = utils::numeric(FLERR,arg[4],false,lmp); dampflag = utils::inumeric(FLERR,arg[5],false,lmp); if (dampflag == 0) gammat = 0.0; + + noattractionflag = 0; + if(narg == 7) { + if(strcmp(arg[6], "no_attraction")) + noattractionflag = 1; + else + error->all(FLERR,"Illegal pair_style command"); + } if (kn < 0.0 || kt < 0.0 || gamman < 0.0 || gammat < 0.0 || xmu < 0.0 || xmu > 10000.0 || dampflag < 0 || dampflag > 1) @@ -686,6 +695,7 @@ double PairGranHookeHistory::single(int i, int j, int /*itype*/, int /*jtype*/, damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; + if(noattractionflag and ccel < 0.0) ccel = 0.0; // relative velocities diff --git a/src/GRANULAR/pair_gran_hooke_history.h b/src/GRANULAR/pair_gran_hooke_history.h index c27ce8a9af..bf40097f9d 100644 --- a/src/GRANULAR/pair_gran_hooke_history.h +++ b/src/GRANULAR/pair_gran_hooke_history.h @@ -49,6 +49,7 @@ class PairGranHookeHistory : public Pair { double dt; int freeze_group_bit; int history; + int noattractionflag; int neighprev; double *onerad_dynamic,*onerad_frozen; diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index cc210138eb..7c1a1f2b29 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -793,6 +793,7 @@ void PairGranular::coeff(int narg, char **arg) roll_model_one = ROLL_NONE; twist_model_one = TWIST_NONE; damping_model_one = VISCOELASTIC; + noattractionflag = 0; int iarg = 2; while (iarg < narg) { @@ -1030,7 +1031,18 @@ void PairGranular::coeff(int narg, char **arg) count++; } } - + + if(noattraction flag) { + for(int i = 1; i <= ntypes; i++) { + for(int j = 1; j <= ntypes; j++) { + if(normal_model[i][j] == JKR) + error->all(FLERR,"Cannot turn off attraction with JKR pairstyle"); + if(normal_model[i][j] == DMT) + error->all(FLERR,"Cannot turn off attraction with DMT pairstyle"); + } + } + } + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } diff --git a/src/GRANULAR/pair_granular.h b/src/GRANULAR/pair_granular.h index 7ef4f2af98..1e4e8c8fc4 100644 --- a/src/GRANULAR/pair_granular.h +++ b/src/GRANULAR/pair_granular.h @@ -70,6 +70,7 @@ class PairGranular : public Pair { // model choices int **normal_model, **damping_model; int **tangential_model, **roll_model, **twist_model; + int **noattractionflag; // history flags int normal_history, tangential_history, roll_history, twist_history; diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp index 81c82ab826..caa19ffdef 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp @@ -392,6 +392,7 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC F_FLOAT damp = meff*gamman*vnnr*rsqinv; F_FLOAT ccel = kn*(radsum-r)*rinv - damp; + if(noattractionflag & ccel < 0.0) ccel = 0.0; // relative velocities From 2988aa2d1f6cc3d6a67bc7b03021d898656a30f9 Mon Sep 17 00:00:00 2001 From: Dan Bolintineanu Date: Tue, 30 Mar 2021 21:55:06 -0600 Subject: [PATCH 0311/1217] Fixes bug where accumulated tangential and rolling displacements are not rotated correctly. Pointed out by Deng Pan on LAMMPS mailing list 3/26/21 --- src/GRANULAR/pair_granular.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index cc210138eb..bcf262aa2c 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -446,9 +446,9 @@ void PairGranular::compute(int eflag, int vflag) if (tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_FORCE || tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_RESCALE_FORCE) - frameupdate = fabs(rsht) < EPSILON*Fscrit; + frameupdate = fabs(rsht) > EPSILON*Fscrit; else - frameupdate = fabs(rsht)*k_tangential < EPSILON*Fscrit; + frameupdate = fabs(rsht)*k_tangential > EPSILON*Fscrit; if (frameupdate) { shrmag = sqrt(history[0]*history[0] + history[1]*history[1] + history[2]*history[2]); @@ -568,7 +568,7 @@ void PairGranular::compute(int eflag, int vflag) if (historyupdate) { rolldotn = history[rhist0]*nx + history[rhist1]*ny + history[rhist2]*nz; - frameupdate = fabs(rolldotn)*k_roll < EPSILON*Frcrit; + frameupdate = fabs(rolldotn)*k_roll > EPSILON*Frcrit; if (frameupdate) { // rotate into tangential plane rollmag = sqrt(history[rhist0]*history[rhist0] + history[rhist1]*history[rhist1] + From d36894ccf5691ca9ba6e85d264a3cb435526ce44 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 30 Mar 2021 22:16:47 -0600 Subject: [PATCH 0312/1217] Adding pertype flag to pair granular --- doc/src/fix_wall_gran.rst | 2 +- doc/src/fix_wall_gran_region.rst | 2 +- doc/src/pair_gran.rst | 2 +- doc/src/pair_granular.rst | 8 ++++++++ src/GRANULAR/pair_granular.cpp | 34 ++++++++++++++++++++------------ 5 files changed, 32 insertions(+), 16 deletions(-) diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index 73fa7e367b..bfe06bf7a0 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -59,7 +59,7 @@ Syntax *contacts* value = none generate contact information for each particle *no_attraction* value = none - turn off possibility for attractive interactions + turn off possibility of attractive interactions Examples diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 356c8427b0..00eb19ba1c 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -43,7 +43,7 @@ Syntax *contacts* value = none generate contact information for each particle *no_attraction* value = none - turn off possibility for attractive interactions + turn off possibility of attractive interactions Examples """""""" diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index aa2e42d339..8145f7fb7a 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -41,7 +41,7 @@ Syntax .. parsed-literal:: *no_attraction* value = none - turn off possibility for attractive interactions + turn off possibility of attractive interactions .. note:: diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index cb65a58777..0076994e25 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -623,6 +623,14 @@ Finally, the twisting torque on each particle is given by: ---------- +If two particles are moving away from each other while in contact, there +is a possibility that the particles could experience an effective attractive +force due to damping. If the optional *no_attraction* keyword is used, this fix +will zero out the normal component of the force if there is an effective +attractive force. This keyword cannot be used with the JKR or DMT models. + +---------- + The *granular* pair style can reproduce the behavior of the *pair gran/\** styles with the appropriate settings (some very minor differences can be expected due to corrections in diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 7c1a1f2b29..256acd5a6a 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -130,6 +130,7 @@ PairGranular::~PairGranular() memory->destroy(tangential_model); memory->destroy(roll_model); memory->destroy(twist_model); + memory->destroy(noattraction_flag); delete [] onerad_dynamic; delete [] onerad_frozen; @@ -370,6 +371,7 @@ void PairGranular::compute(int eflag, int vflag) Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; + if(noattraction_flag[itype][jtype] and Fntot < 0.0) Fntot = 0.0; //**************************************** // tangential force, including history effects @@ -740,6 +742,7 @@ void PairGranular::allocate() memory->create(tangential_model,n+1,n+1,"pair:tangential_model"); memory->create(roll_model,n+1,n+1,"pair:roll_model"); memory->create(twist_model,n+1,n+1,"pair:twist_model"); + memory->create(noattraction_flag,n+1,n+1,"pair:noattraction_flag"); onerad_dynamic = new double[n+1]; onerad_frozen = new double[n+1]; @@ -793,8 +796,8 @@ void PairGranular::coeff(int narg, char **arg) roll_model_one = ROLL_NONE; twist_model_one = TWIST_NONE; damping_model_one = VISCOELASTIC; - noattractionflag = 0; - + int na_flag = 0; + int iarg = 2; while (iarg < narg) { if (strcmp(arg[iarg], "hooke") == 0) { @@ -968,6 +971,9 @@ void PairGranular::coeff(int narg, char **arg) error->all(FLERR, "Illegal pair_coeff command, not enough parameters"); cutoff_one = utils::numeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; + } else if (strcmp(arg[iarg], "no_attraction") == 0) { + na_flag = 1; + iarg += 1; } else error->all(FLERR, "Illegal pair coeff command"); } @@ -985,6 +991,12 @@ void PairGranular::coeff(int narg, char **arg) 27.467*powint(cor,4)-18.022*powint(cor,5)+4.8218*powint(cor,6); } else damp = normal_coeffs_one[1]; + if(na_flag and normal_model_one == JKR) + error->all(FLERR,"Cannot turn off attraction with JKR pairstyle"); + + if(na_flag and normal_model_one == DMT) + error->all(FLERR,"Cannot turn off attraction with DMT pairstyle"); + for (int i = ilo; i <= ihi; i++) { for (int j = MAX(jlo,i); j <= jhi; j++) { normal_model[i][j] = normal_model[j][i] = normal_model_one; @@ -1027,21 +1039,13 @@ void PairGranular::coeff(int narg, char **arg) cutoff_type[i][j] = cutoff_type[j][i] = cutoff_one; + noattraction_flag[i][j] = na_flag; + setflag[i][j] = 1; count++; } } - - if(noattraction flag) { - for(int i = 1; i <= ntypes; i++) { - for(int j = 1; j <= ntypes; j++) { - if(normal_model[i][j] == JKR) - error->all(FLERR,"Cannot turn off attraction with JKR pairstyle"); - if(normal_model[i][j] == DMT) - error->all(FLERR,"Cannot turn off attraction with DMT pairstyle"); - } - } - } + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } @@ -1315,6 +1319,7 @@ void PairGranular::write_restart(FILE *fp) fwrite(&tangential_model[i][j],sizeof(int),1,fp); fwrite(&roll_model[i][j],sizeof(int),1,fp); fwrite(&twist_model[i][j],sizeof(int),1,fp); + fwrite(&noattraction_flag[i][j],sizeof(int),1,fp); fwrite(normal_coeffs[i][j],sizeof(double),4,fp); fwrite(tangential_coeffs[i][j],sizeof(double),3,fp); fwrite(roll_coeffs[i][j],sizeof(double),3,fp); @@ -1345,6 +1350,7 @@ void PairGranular::read_restart(FILE *fp) utils::sfread(FLERR,&tangential_model[i][j],sizeof(int),1,fp,nullptr,error); utils::sfread(FLERR,&roll_model[i][j],sizeof(int),1,fp,nullptr,error); utils::sfread(FLERR,&twist_model[i][j],sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&noattraction_flag[i][j],sizeof(int),1,fp,nullptr,error); utils::sfread(FLERR,normal_coeffs[i][j],sizeof(double),4,fp,nullptr,error); utils::sfread(FLERR,tangential_coeffs[i][j],sizeof(double),3,fp,nullptr,error); utils::sfread(FLERR,roll_coeffs[i][j],sizeof(double),3,fp,nullptr,error); @@ -1356,6 +1362,7 @@ void PairGranular::read_restart(FILE *fp) MPI_Bcast(&tangential_model[i][j],1,MPI_INT,0,world); MPI_Bcast(&roll_model[i][j],1,MPI_INT,0,world); MPI_Bcast(&twist_model[i][j],1,MPI_INT,0,world); + MPI_Bcast(&noattraction_flag[i][j],1,MPI_INT,0,world); MPI_Bcast(normal_coeffs[i][j],4,MPI_DOUBLE,0,world); MPI_Bcast(tangential_coeffs[i][j],3,MPI_DOUBLE,0,world); MPI_Bcast(roll_coeffs[i][j],3,MPI_DOUBLE,0,world); @@ -1541,6 +1548,7 @@ double PairGranular::single(int i, int j, int itype, int jtype, Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; + if(noattraction_flag[itype][jtype] and Fntot < 0.0) Fntot = 0.0; jnum = list->numneigh[i]; jlist = list->firstneigh[i]; From e1cf6a312fabb721d7ee7103c619064e2e532ddd Mon Sep 17 00:00:00 2001 From: Oliver Henrich Date: Wed, 31 Mar 2021 18:56:50 +0100 Subject: [PATCH 0313/1217] Corrected error message --- src/USER-CGDNA/pair_oxdna2_coaxstk.cpp | 4 ++-- src/USER-CGDNA/pair_oxdna2_dh.cpp | 4 ++-- src/USER-CGDNA/pair_oxrna2_stk.cpp | 2 +- src/USER-CGDNA/pair_oxrna2_xstk.cpp | 4 ++-- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index f0b3386478..47d16c4806 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -551,7 +551,7 @@ void PairOxdna2Coaxstk::coeff(int narg, char **arg) { int count; - if (narg != 21) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/coaxstk"); + if (narg != 21) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/coaxstk"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -673,7 +673,7 @@ void PairOxdna2Coaxstk::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/coaxstk"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/coaxstk"); } diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index d877e0bf9a..6b0df2cde6 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -273,7 +273,7 @@ void PairOxdna2Dh::coeff(int narg, char **arg) { int count; - if (narg != 5) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/dh"); + if (narg != 5) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/dh"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -356,7 +356,7 @@ void PairOxdna2Dh::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/dh"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/dh"); } /* ---------------------------------------------------------------------- diff --git a/src/USER-CGDNA/pair_oxrna2_stk.cpp b/src/USER-CGDNA/pair_oxrna2_stk.cpp index 33480aa380..3b02a57501 100644 --- a/src/USER-CGDNA/pair_oxrna2_stk.cpp +++ b/src/USER-CGDNA/pair_oxrna2_stk.cpp @@ -1022,7 +1022,7 @@ void PairOxrna2Stk::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/stk"); } diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.cpp b/src/USER-CGDNA/pair_oxrna2_xstk.cpp index c3b97bfa9c..71c6ca0356 100644 --- a/src/USER-CGDNA/pair_oxrna2_xstk.cpp +++ b/src/USER-CGDNA/pair_oxrna2_xstk.cpp @@ -576,7 +576,7 @@ void PairOxrna2Xstk::coeff(int narg, char **arg) { int count; - if (narg != 22) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk"); + if (narg != 22) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/xstk"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -707,7 +707,7 @@ void PairOxrna2Xstk::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/xstk"); } From 0bde6c82a3630ec29381bdcc736a016c6c46782c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 31 Mar 2021 14:40:54 -0400 Subject: [PATCH 0314/1217] remove newton bond off check again --- src/neighbor.cpp | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/neighbor.cpp b/src/neighbor.cpp index fb0a244cc0..704d94c77c 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1363,10 +1363,6 @@ void Neighbor::init_topology() onoff = improper_off; MPI_Allreduce(&onoff,&improper_off,1,MPI_INT,MPI_MAX,world); - // newton_bond off is not supported with atom style template - if ((atom->molecular == Atom::TEMPLATE) && (force->newton_bond == 0)) - error->all(FLERR,"Must use 'newton bond on' with atom style template"); - // instantiate NTopo classes if (atom->avec->bonds_allow) { From 9e412bb7a661088a9bc7b43cf0585fb9c9fb25ae Mon Sep 17 00:00:00 2001 From: Michael Brown Date: Wed, 31 Mar 2021 11:42:39 -0700 Subject: [PATCH 0315/1217] Fixing bug with GPU neighboring when using builds supporting CUDPP. ...introduced in Feb 2021 GPU package update. Manifests when GPU library is built with -DUSE_CUDPP and -DLAL_USE_OLD_NEIGHBOR (latter forced with CUDA 11.2). --- lib/gpu/lal_neighbor.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/gpu/lal_neighbor.cpp b/lib/gpu/lal_neighbor.cpp index aabba49575..a0d2eaa8c3 100644 --- a/lib/gpu/lal_neighbor.cpp +++ b/lib/gpu/lal_neighbor.cpp @@ -740,6 +740,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum, // If binning on GPU, do this now if (_gpu_nbor==1) { + mn = _max_nbors; const numtyp i_cell_size=static_cast(1.0/_cell_size); const int neigh_block=_block_cell_id; const int GX=(int)ceil((float)nall/neigh_block); From c53f2d4629acfa1b88416e886bb1f2e498620bef Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 31 Mar 2021 14:55:07 -0400 Subject: [PATCH 0316/1217] correct USER-OMP respa/omp check --- src/USER-OMP/fix_omp.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp index 678df7c22a..ccc86325db 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/USER-OMP/fix_omp.cpp @@ -203,7 +203,8 @@ void FixOMP::init() thr[i]->_timer_active=-1; } - if (!utils::strmatch(update->integrate_style,"^respa/omp")) + if (utils::strmatch(update->integrate_style,"^respa") + && !utils::strmatch(update->integrate_style,"^respa/omp")) error->all(FLERR,"Must use respa/omp for r-RESPA with /omp styles"); if (force->pair && force->pair->compute_flag) _pair_compute_flag = true; From 7699fb37080d55ac041611983ef3889905afc4e1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 31 Mar 2021 15:55:31 -0400 Subject: [PATCH 0317/1217] generalize some checks in fix rigid and rigid/small --- src/RIGID/fix_rigid.cpp | 15 ++++++--------- src/RIGID/fix_rigid_nh_small.cpp | 24 +++++++++++++----------- src/RIGID/fix_rigid_small.cpp | 14 ++++++-------- 3 files changed, 25 insertions(+), 28 deletions(-) diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index a8a0e1409f..985554f738 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -720,17 +720,14 @@ void FixRigid::init() } } - // error if npt,nph fix comes before rigid fix - - for (i = 0; i < modify->nfix; i++) { - if (strcmp(modify->fix[i]->style,"npt") == 0) break; - if (strcmp(modify->fix[i]->style,"nph") == 0) break; - } + // error if a fix changing the box comes before rigid fix + for (i = 0; i < modify->nfix; i++) + if (modify->fix[i]->box_change) break; if (i < modify->nfix) { for (int j = i; j < modify->nfix; j++) - if (strcmp(modify->fix[j]->style,"rigid") == 0) - error->all(FLERR,"Rigid fix must come before NPT/NPH fix"); + if (utils::strmatch(modify->fix[j]->style,"^rigid")) + error->all(FLERR,"Rigid fixes must come before any box changing fix"); } // add gravity forces based on gravity vector from fix @@ -738,7 +735,7 @@ void FixRigid::init() if (id_gravity) { int ifix = modify->find_fix(id_gravity); if (ifix < 0) error->all(FLERR,"Fix rigid cannot find fix gravity ID"); - if (strcmp(modify->fix[ifix]->style,"gravity") != 0) + if (!utils::strmatch(modify->fix[ifix]->style,"^gravity")) error->all(FLERR,"Fix rigid gravity fix is invalid"); int tmp; gvec = (double *) modify->fix[ifix]->extract("gvec",tmp); diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 3956fcf35d..454f240bb4 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -19,22 +19,24 @@ #include "fix_rigid_nh_small.h" -#include -#include -#include "math_extra.h" #include "atom.h" +#include "comm.h" #include "compute.h" #include "domain.h" -#include "update.h" -#include "modify.h" -#include "fix_deform.h" -#include "group.h" -#include "comm.h" -#include "force.h" -#include "kspace.h" -#include "memory.h" #include "error.h" +#include "fix_deform.h" +#include "force.h" +#include "group.h" +#include "kspace.h" +#include "math_extra.h" +#include "memory.h" +#include "modify.h" +#include "molecule.h" #include "rigid_const.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index b7e0a1b2ac..d9a0b82ae8 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -571,16 +571,14 @@ void FixRigidSmall::init() } } - // error if npt,nph fix comes before rigid fix + // error if a fix changing the box comes before rigid fix - for (i = 0; i < modify->nfix; i++) { - if (strcmp(modify->fix[i]->style,"npt") == 0) break; - if (strcmp(modify->fix[i]->style,"nph") == 0) break; - } + for (i = 0; i < modify->nfix; i++) + if (modify->fix[i]->box_change) break; if (i < modify->nfix) { for (int j = i; j < modify->nfix; j++) - if (strcmp(modify->fix[j]->style,"rigid") == 0) - error->all(FLERR,"Rigid fix must come before NPT/NPH fix"); + if (utils::strmatch(modify->fix[j]->style,"^rigid")) + error->all(FLERR,"Rigid fixes must come before any box changing fix"); } // add gravity forces based on gravity vector from fix @@ -588,7 +586,7 @@ void FixRigidSmall::init() if (id_gravity) { int ifix = modify->find_fix(id_gravity); if (ifix < 0) error->all(FLERR,"Fix rigid/small cannot find fix gravity ID"); - if (strcmp(modify->fix[ifix]->style,"gravity") != 0) + if (!utils::strmatch(modify->fix[ifix]->style,"^gravity")) error->all(FLERR,"Fix rigid/small gravity fix is invalid"); int tmp; gvec = (double *) modify->fix[ifix]->extract("gvec",tmp); From bed57e02f71168fabd0f7e2895e08162c2a0797b Mon Sep 17 00:00:00 2001 From: "Ronald E. Miller" Date: Wed, 31 Mar 2021 16:18:05 -0400 Subject: [PATCH 0318/1217] avoiding static variable --- src/KIM/kim_interactions.cpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp index 3b37c96870..9b63224f0f 100644 --- a/src/KIM/kim_interactions.cpp +++ b/src/KIM/kim_interactions.cpp @@ -65,6 +65,7 @@ #include "error.h" #include "fix_store_kim.h" #include "input.h" +#include "variable.h" #include "modify.h" #include "update.h" @@ -96,7 +97,6 @@ void KimInteractions::command(int narg, char **arg) void KimInteractions::do_setup(int narg, char **arg) { - static bool kim_update=0; bool fixed_types; const std::string arg_str(arg[0]); if ((narg == 1) && (arg_str == "fixed_types")) { @@ -130,6 +130,7 @@ void KimInteractions::do_setup(int narg, char **arg) "=======\n"); if (simulatorModel) { + auto first_visit = input->variable->find("kim_update"); if (!fixed_types) { std::string atom_type_sym_list = fmt::format("{}", fmt::join(arg, arg + narg, " ")); @@ -199,8 +200,8 @@ void KimInteractions::do_setup(int narg, char **arg) const std::string sim_field_str(sim_field); if (sim_field_str == "model-defn") { - if (kim_update) input->one("variable kim_update equal 1"); - else input->one("variable kim_update equal 0"); + if (first_visit<0) input->one("variable kim_update equal 0"); + else input->one("variable kim_update equal 1"); if (domain->periodicity[0] && domain->periodicity[1] && domain->periodicity[2]) @@ -242,7 +243,7 @@ void KimInteractions::do_setup(int narg, char **arg) KIM_SimulatorModel_OpenAndInitializeTemplateMap(simulatorModel); - } else if (!kim_update) { + } else { // not a simulator model. issue pair_style and pair_coeff commands. @@ -264,7 +265,6 @@ void KimInteractions::do_setup(int narg, char **arg) // End output to log file input->write_echo("#=== END kim interactions =============================" "=======\n\n"); - kim_update=1; } /* ---------------------------------------------------------------------- */ From 7b9dfb296daf7e4147d6bb2c5e12fcd798ab1422 Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Thu, 1 Apr 2021 00:35:17 +0200 Subject: [PATCH 0319/1217] Renamed pair style, user package: nnp => hdnnp --- cmake/CMakeLists.txt | 7 +- cmake/Modules/FindN2P2.cmake | 10 +-- cmake/presets/all_off.cmake | 10 +-- cmake/presets/all_on.cmake | 10 +-- cmake/presets/nolib.cmake | 6 +- doc/src/Build_extras.rst | 84 +++++++++---------- doc/src/Build_package.rst | 4 +- doc/src/Commands_pair.rst | 2 +- doc/src/Packages_details.rst | 68 +++++++-------- doc/src/Packages_user.rst | 4 +- doc/src/{pair_nnp.rst => pair_hdnnp.rst} | 32 +++---- doc/src/pair_style.rst | 2 +- doc/utils/sphinx-config/false_positives.txt | 4 +- examples/USER/{nnp => hdnnp}/data.H2O-360mol | 0 .../nnp-data => hdnnp/hdnnp-data}/input.nn | 0 .../hdnnp-data}/scaling.data | 0 .../hdnnp-data}/weights.001.data | 0 .../hdnnp-data}/weights.008.data | 0 examples/USER/{nnp/in.nnp => hdnnp/in.hdnnp} | 16 ++-- lib/README | 4 +- lib/{nnp => hdnnp}/Makefile.lammps | 12 +-- lib/{nnp => hdnnp}/README | 42 +++++----- src/.gitignore | 4 +- src/Makefile | 10 +-- src/{USER-NNP => USER-HDNNP}/Install.sh | 16 ++-- src/{USER-NNP => USER-HDNNP}/README | 10 +-- .../pair_hdnnp.cpp} | 40 ++++----- .../pair_nnp.h => USER-HDNNP/pair_hdnnp.h} | 12 +-- 28 files changed, 204 insertions(+), 205 deletions(-) rename doc/src/{pair_nnp.rst => pair_hdnnp.rst} (90%) rename examples/USER/{nnp => hdnnp}/data.H2O-360mol (100%) rename examples/USER/{nnp/nnp-data => hdnnp/hdnnp-data}/input.nn (100%) rename examples/USER/{nnp/nnp-data => hdnnp/hdnnp-data}/scaling.data (100%) rename examples/USER/{nnp/nnp-data => hdnnp/hdnnp-data}/weights.001.data (100%) rename examples/USER/{nnp/nnp-data => hdnnp/hdnnp-data}/weights.008.data (100%) rename examples/USER/{nnp/in.nnp => hdnnp/in.hdnnp} (81%) rename lib/{nnp => hdnnp}/Makefile.lammps (62%) rename lib/{nnp => hdnnp}/README (68%) rename src/{USER-NNP => USER-HDNNP}/Install.sh (66%) rename src/{USER-NNP => USER-HDNNP}/README (75%) rename src/{USER-NNP/pair_nnp.cpp => USER-HDNNP/pair_hdnnp.cpp} (94%) rename src/{USER-NNP/pair_nnp.h => USER-HDNNP/pair_hdnnp.h} (91%) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 2efd36b1f4..94f419bd37 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -116,8 +116,8 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF - USER-MOLFILE USER-NETCDF USER-NNP USER-PHONON USER-PLUMED USER-PTM USER-QTB + USER-HDNNP USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC + USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF) @@ -381,8 +381,7 @@ else() set(CUDA_REQUEST_PIC) endif() -foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE - USER-NETCDF USER-NNP USER-PLUMED USER-QMMM +foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-HDNNP USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS) if(PKG_${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL}) diff --git a/cmake/Modules/FindN2P2.cmake b/cmake/Modules/FindN2P2.cmake index a06850f07f..cae5de5342 100644 --- a/cmake/Modules/FindN2P2.cmake +++ b/cmake/Modules/FindN2P2.cmake @@ -3,9 +3,9 @@ include(FindPackageHandleStandardArgs) # Check if N2P2_DIR is set manually. if (DEFINED ENV{N2P2_DIR}) set(N2P2_DIR "${N2P2_DIR}") -# If not, try if directory "lib/nnp/n2p2" exists. +# If not, try if directory "lib/hdnnp/n2p2" exists. else() - get_filename_component(_fullpath "${LAMMPS_LIB_SOURCE_DIR}/nnp/n2p2" REALPATH) + get_filename_component(_fullpath "${LAMMPS_LIB_SOURCE_DIR}/hdnnp/n2p2" REALPATH) if (EXISTS ${_fullpath}) set(N2P2_DIR "${_fullpath}") endif() @@ -17,12 +17,12 @@ find_path(N2P2_INCLUDE_DIR InterfaceLammps.h PATHS "${N2P2_DIR}/include") find_library(N2P2_LIBNNP NAMES nnp PATHS "${N2P2_DIR}/lib") find_library(N2P2_LIBNNPIF NAMES nnpif PATHS "${N2P2_DIR}/lib") # Users could compile n2p2 with extra flags which are then also required for -# pair_nnp.cpp compilation. To forward them to the LAMMPS build process n2p2 +# pair_hdnnp.cpp compilation. To forward them to the LAMMPS build process n2p2 # writes a file with cmake commands, e.g. # -# target_compile_definitions(lammps PRIVATE -DNNP_NO_SF_GROUPS) +# target_compile_definitions(lammps PRIVATE -DN2P2_NO_SF_GROUPS) # -# to "lib/lammps-extra.cmake" which is then included by USER-NNP.cmake. +# to "lib/lammps-extra.cmake" which is then included by USER-HDNNP.cmake. find_file(N2P2_CMAKE_EXTRA NAMES lammps-extra.cmake PATHS "${N2P2_DIR}/lib") find_package_handle_standard_args(N2P2 DEFAULT_MSG diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index d567b141bf..7f3caebf8c 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -7,11 +7,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU SNAP SPIN SRD VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP - USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD - USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-NNP - USER-OMP USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP - USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ - USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) + USER-H5MD USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC + USER-MESODPD USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB + USER-QUIP USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD + USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 2b879e9ecf..fbc78ededf 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -9,11 +9,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU SNAP SPIN SRD VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP - USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD - USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-NNP - USER-OMP USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP - USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ - USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) + USER-H5MD USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC + USER-MESODPD USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB + USER-QUIP USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD + USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index c0236347cb..a819e6a347 100644 --- a/cmake/presets/nolib.cmake +++ b/cmake/presets/nolib.cmake @@ -2,9 +2,9 @@ # library or special compiler (fortran or cuda) or equivalent. set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON - VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB - USER-MOLFILE USER-MESONT USER-NETCDF USER-NNP USER-PLUMED USER-QMMM - USER-QUIP USER-SCAFACOS USER-SMD USER-VTK) + VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-HDNNP USER-LB + USER-MOLFILE USER-MESONT USER-NETCDF USER-PLUMED USER-QMMM + USER-QUIP USER-SCAFACOS USER-SMD USER-VTK) foreach(PKG ${PACKAGES_WITH_LIB}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 545a86c04e..30f4bb711d 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -48,11 +48,11 @@ This is the list of packages that may require additional steps. * :ref:`USER-AWPMD ` * :ref:`USER-COLVARS ` * :ref:`USER-H5MD ` + * :ref:`USER-HDNNP ` * :ref:`USER-INTEL ` * :ref:`USER-MESONT ` * :ref:`USER-MOLFILE ` * :ref:`USER-NETCDF ` - * :ref:`USER-NNP ` * :ref:`USER-PLUMED ` * :ref:`USER-OMP ` * :ref:`USER-QMMM ` @@ -1416,6 +1416,47 @@ the HDF5 library. ---------- +.. _user-hdnnp: + +USER-HDNNP package +--------------------------------- + +To build with the USER-HDNNP package it is required to download and build the +external `n2p2 `__ library ``v2.2.0`` +(or higher) before starting the LAMMPS build process. More specifically, only +the *n2p2* core library ``libnnp`` and interface library ``libnnpif`` are +actually needed: when using GCC it should suffice to execute ``make libnnpif`` +in the *n2p2* ``src`` directory. For more details please see +``lib/hdnnp/README`` and the `n2p2 build documentation +`__. If *n2p2* is +downloaded and compiled in the LAMMPS directory ``lib/hdnnp/n2p2`` no special +flags need to be set besides the usual package activation. If you prefer to +install *n2p2* somewhere else on your system you must specify the path via the +``N2P2_DIR`` variable. + +.. tabs:: + + .. tab:: CMake build + + There is one additional setting besides ``-D PKG_USER-HDNNP=yes`` in case + *n2p2* is not installed in the ``lib/hdnnp/n2p2`` directory: + + .. code-block:: bash + + -D N2P2_DIR=path # path ... n2p2 installation path + + .. tab:: Traditional make + + There is one additional variable that needs to be set besides ``make + yes-user-hdnnp`` in case *n2p2* is not installed in the ``lib/hdnnp/n2p2`` + directory: + + .. code-block:: bash + + make N2P2_DIR=path ... + +---------- + .. _user-intel: USER-INTEL package @@ -1597,47 +1638,6 @@ on your system. ---------- -.. _user-nnp: - -USER-NNP package ---------------------------------- - -To build with the USER-NNP package it is required to download and build the -external `n2p2 `__ library ``v2.2.0`` -(or higher) before starting the LAMMPS build process. More specifically, only -the *n2p2* core library ``libnnp`` and interface library ``libnnpif`` are -actually needed: when using GCC it should suffice to execute ``make libnnpif`` -in the *n2p2* ``src`` directory. For more details please see ``lib/nnp/README`` -and the `n2p2 build documentation -`__. If *n2p2* is -downloaded and compiled in the LAMMPS directory ``lib/nnp/n2p2`` no special -flags need to be set besides the usual package activation. If you prefer to -install *n2p2* somewhere else on your system you must specify the path via the -``N2P2_DIR`` variable. - -.. tabs:: - - .. tab:: CMake build - - There is one additional setting besides ``-D PKG_USER-NNP=yes`` in case - *n2p2* is not installed in the ``lib/nnp/n2p2`` directory: - - .. code-block:: bash - - -D N2P2_DIR=path # path ... n2p2 installation path - - .. tab:: Traditional make - - There is one additional variable that needs to be set besides ``make - yes-user-nnp`` in case *n2p2* is not installed in the ``lib/nnp/n2p2`` - directory: - - .. code-block:: bash - - make N2P2_DIR=path ... - ----------- - .. _user-omp: USER-OMP package diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index 36a7bce482..d069dc8a84 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -35,9 +35,9 @@ packages: +--------------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ | :ref:`MSCG ` | :ref:`OPT ` | :ref:`POEMS ` | :ref:`PYTHON ` | :ref:`VORONOI ` | :ref:`USER-ADIOS ` | +--------------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`USER-INTEL ` | :ref:`USER-MOLFILE ` | +| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`USER-HDNNP ` | :ref:`USER-INTEL ` | +--------------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-NETCDF ` | :ref:`USER-NNP ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | :ref:`USER-QUIP ` | +| :ref:`USER-MOLFILE ` | :ref:`USER-NETCDF ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | :ref:`USER-QUIP ` | +--------------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ | :ref:`USER-SCAFACOS ` | :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | | +--------------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index b074c2f8c3..d17f81f411 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -115,6 +115,7 @@ OPT. * :doc:`gw/zbl ` * :doc:`hbond/dreiding/lj (o) ` * :doc:`hbond/dreiding/morse (o) ` + * :doc:`hdnnp ` * :doc:`ilp/graphene/hbn ` * :doc:`kolmogorov/crespi/full ` * :doc:`kolmogorov/crespi/z ` @@ -198,7 +199,6 @@ OPT. * :doc:`nm/cut (o) ` * :doc:`nm/cut/coul/cut (o) ` * :doc:`nm/cut/coul/long (o) ` - * :doc:`nnp ` * :doc:`oxdna/coaxstk ` * :doc:`oxdna/excv ` * :doc:`oxdna/hbond ` diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index ed89341d0c..df57ff63a0 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -77,6 +77,7 @@ page gives those details. * :ref:`USER-EFF ` * :ref:`USER-FEP ` * :ref:`USER-H5MD ` + * :ref:`USER-HDNNP ` * :ref:`USER-INTEL ` * :ref:`USER-LB ` * :ref:`USER-MANIFOLD ` @@ -88,7 +89,6 @@ page gives those details. * :ref:`USER-MOFFF ` * :ref:`USER-MOLFILE ` * :ref:`USER-NETCDF ` - * :ref:`USER-NNP ` * :ref:`USER-OMP ` * :ref:`USER-PHONON ` * :ref:`USER-PLUMED ` @@ -1550,6 +1550,39 @@ This package has :ref:`specific installation instructions ` on the :d ---------- +.. _PKG-USER-HDNNP: + +USER-HDNNP package +------------------ + +**Contents:** + +A :doc:`pair_style hdnnp ` command which allows to use +high-dimensional neural network potentials (HDNNPs), a form of machine learning +potentials. HDNNPs must be carefully trained prior to their application in a +molecular dynamics simulation. + +.. _n2p2: https://github.com/CompPhysVienna/n2p2 + +To use this package you must have the `n2p2 `_ library installed and +compiled on your system. + +**Author:** Andreas Singraber + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/USER-HDNNP: filenames -> commands +* src/USER-HDNNP/README +* lib/hdnnp/README +* :doc:`pair_style hdnnp ` +* examples/USER/hdnnp + +---------- + .. _PKG-USER-INTEL: USER-INTEL package @@ -1924,39 +1957,6 @@ This package has :ref:`specific installation instructions ` on the ---------- -.. _PKG-USER-NNP: - -USER-NNP package ----------------- - -**Contents:** - -A :doc:`pair_style nnp ` command which allows to use high-dimensional -neural network potentials (HDNNPs), a form of machine learning potentials. -HDNNPs must be carefully trained prior to their application in a molecular -dynamics simulation. - -.. _n2p2: https://github.com/CompPhysVienna/n2p2 - -To use this package you must have the `n2p2 `_ library installed and -compiled on your system. - -**Author:** Andreas Singraber - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-NNP: filenames -> commands -* src/USER-NNP/README -* lib/nnp/README -* :doc:`pair_style nnp ` -* examples/USER/nnp - ----------- - .. _PKG-USER-OMP: USER-OMP package diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index 77bf13cde6..0b25389032 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -57,6 +57,8 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-H5MD ` | dump output via HDF5 | :doc:`dump h5md ` | n/a | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-HDNNP ` | High-dimensional neural network potentials | :doc:`pair_style hdnnp ` | USER/hdnnp | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-INTEL ` | optimized Intel CPU and KNL styles | :doc:`Speed intel ` | `Benchmarks `_ | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-LB ` | Lattice Boltzmann fluid | :doc:`fix lb/fluid ` | USER/lb | no | @@ -79,8 +81,6 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-NETCDF ` | dump output via NetCDF | :doc:`dump netcdf ` | n/a | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-NNP ` | High-dimensional neural network potentials | :doc:`pair_style nnp ` | USER/nnp | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-OMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-PHONON ` | phonon dynamical matrix | :doc:`fix phonon ` | USER/phonon | no | diff --git a/doc/src/pair_nnp.rst b/doc/src/pair_hdnnp.rst similarity index 90% rename from doc/src/pair_nnp.rst rename to doc/src/pair_hdnnp.rst index 3141dce317..b34c00f982 100644 --- a/doc/src/pair_nnp.rst +++ b/doc/src/pair_hdnnp.rst @@ -1,14 +1,14 @@ -.. index:: pair_style nnp +.. index:: pair_style hdnnp -pair_style nnp command -====================== +pair_style hdnnp command +======================== Syntax """""" .. code-block:: LAMMPS - pair_style nnp keyword value ... + pair_style hdnnp keyword value ... * zero or more keyword/value pairs may be appended * keyword = *dir* or *showew* or *showewsum* or *maxew* or *resetew* or *cflength* or *cfenergy* @@ -19,7 +19,7 @@ Syntax *emap* value = mapping mapping = Element mapping from LAMMPS atom types to n2p2 elements *dir* value = directory - directory = Path to NNP configuration files + directory = Path to HDNNP configuration files *showew* value = *yes* or *no* *showewsum* value = summary summary = Write EW summary every this many timesteps (*0* turns summary off) @@ -36,10 +36,10 @@ Examples .. code-block:: LAMMPS - pair_style nnp showew yes showewsum 100 maxew 1000 resetew yes cflength 1.8897261328 cfenergy 0.0367493254 emap "1:H,2:O" + pair_style hdnnp showew yes showewsum 100 maxew 1000 resetew yes cflength 1.8897261328 cfenergy 0.0367493254 emap "1:H,2:O" pair_coeff * * 6.35 - pair_style nnp dir "./" showewsum 10000 + pair_style hdnnp dir "./" showewsum 10000 pair_coeff * * 6.01 Description @@ -81,15 +81,15 @@ If provided, the keyword *emap* determines the mapping from LAMMPS atom types to n2p2 elements. The format is a comma-separated list of ``atom type:element`` pairs, e.g. ``"1:Cu,2:Zn"`` will map atom types 1 and 2 to elements Cu and Zn, respectively. Atom types not present in the list will be completely ignored by -the NNP. The keyword *emap* is mandatory in a "hybrid" setup (see +the HDNNP. The keyword *emap* is mandatory in a "hybrid" setup (see :doc:`pair_hybrid `) with "extra" atom types in the simulation -which are not handled by the NNP. +which are not handled by the HDNNP. .. warning:: Without an explicit mapping it is by default assumed that the atom type specifications in LAMMPS configuration files are consistent with the ordering - of elements in the NNP library. Thus, without the *emap* keyword present + of elements in the *n2p2* library. Thus, without the *emap* keyword present atom types must be sorted in order of ascending atomic number, e.g. the only correct mapping for a configuration containing hydrogen, oxygen and zinc atoms would be: @@ -104,7 +104,7 @@ which are not handled by the NNP. | Zn | 30 | 3 | +---------+---------------+-------------+ -Use the *dir* keyword to specify the directory containing the NNP configuration +Use the *dir* keyword to specify the directory containing the HDNNP configuration files. The directory must contain ``input.nn`` with neural network and symmetry function setup, ``scaling.data`` with symmetry function scaling data and ``weights.???.data`` with weight parameters for each element. @@ -128,7 +128,7 @@ used to print out the MPI rank the atom belongs to. The *showew* keyword should only be set to *yes* for debugging purposes. Extrapolation warnings may add lots of overhead as they are communicated each - timestep. Also, if the simulation is run in a region where the NNP was not + timestep. Also, if the simulation is run in a region where the HDNNP was not correctly trained, lots of extrapolation warnings may clog log files and the console. In a production run use *showewsum* instead. @@ -160,7 +160,7 @@ whole trajectory. If the training of a neural network potential has been performed with different physical units for length and energy than those set in LAMMPS, it is still possible to use the potential when the unit conversion factors are provided via -the *cflength* and *cfenergy* keywords. If for example, the NNP was +the *cflength* and *cfenergy* keywords. If for example, the HDNNP was parameterized with Bohr and Hartree training data and symmetry function parameters (i.e. distances and energies in "input.nn" are given in Bohr and Hartree) but LAMMPS is set to use *metal* units (Angstrom and eV) the correct @@ -174,7 +174,7 @@ conversion factors are: Thus, arguments of *cflength* and *cfenergy* are the multiplicative factors required to convert lengths and energies given in LAMMPS units to respective -quantities in native NNP units (1 Angstrom = 1.8897261328 Bohr, 1 eV = +quantities in native HDNNP units (1 Angstrom = 1.8897261328 Bohr, 1 eV = 0.0367493254 Hartree). ---- @@ -199,7 +199,7 @@ keywords. Restrictions """""""""""" -This pair style is part of the USER-NNP package. It is only enabled if LAMMPS +This pair style is part of the USER-HDNNP package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -214,7 +214,7 @@ Related commands Default ^^^^^^^ -The default options are *dir* = "nnp/", *showew* = yes, *showewsum* = 0, *maxew* +The default options are *dir* = "hdnnp/", *showew* = yes, *showewsum* = 0, *maxew* = 0, *resetew* = no, *cflength* = 1.0, *cfenergy* = 1.0. The default atom type mapping is determined automatically according to ascending atomic number of present elements (see above). diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 4872f2328a..f3a59fd8bc 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -178,6 +178,7 @@ accelerated styles exist. * :doc:`gw/zbl ` - Gao-Weber potential with a repulsive ZBL core * :doc:`hbond/dreiding/lj ` - DREIDING hydrogen bonding LJ potential * :doc:`hbond/dreiding/morse ` - DREIDING hydrogen bonding Morse potential +* :doc:`hdnnp ` - High-dimensional neural network potential * :doc:`ilp/graphene/hbn ` - registry-dependent interlayer potential (ILP) * :doc:`kim ` - interface to potentials provided by KIM project * :doc:`kolmogorov/crespi/full ` - Kolmogorov-Crespi (KC) potential with no simplifications @@ -261,7 +262,6 @@ accelerated styles exist. * :doc:`nm/cut ` - N-M potential * :doc:`nm/cut/coul/cut ` - N-M potential with cutoff Coulomb * :doc:`nm/cut/coul/long ` - N-M potential with long-range Coulomb -* :doc:`nnp ` - High-dimensional neural network potential * :doc:`oxdna/coaxstk ` - * :doc:`oxdna/excv ` - * :doc:`oxdna/hbond ` - diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index e2900468fa..7d49568c55 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1211,6 +1211,8 @@ hbn hbnewflag hbond hcp +hdnnp +HDNNP heatconduction Hebenstreit Hecht @@ -2178,8 +2180,6 @@ nmin Nmols nn nnodes -nnp -NNP Nocedal nocite nocoeff diff --git a/examples/USER/nnp/data.H2O-360mol b/examples/USER/hdnnp/data.H2O-360mol similarity index 100% rename from examples/USER/nnp/data.H2O-360mol rename to examples/USER/hdnnp/data.H2O-360mol diff --git a/examples/USER/nnp/nnp-data/input.nn b/examples/USER/hdnnp/hdnnp-data/input.nn similarity index 100% rename from examples/USER/nnp/nnp-data/input.nn rename to examples/USER/hdnnp/hdnnp-data/input.nn diff --git a/examples/USER/nnp/nnp-data/scaling.data b/examples/USER/hdnnp/hdnnp-data/scaling.data similarity index 100% rename from examples/USER/nnp/nnp-data/scaling.data rename to examples/USER/hdnnp/hdnnp-data/scaling.data diff --git a/examples/USER/nnp/nnp-data/weights.001.data b/examples/USER/hdnnp/hdnnp-data/weights.001.data similarity index 100% rename from examples/USER/nnp/nnp-data/weights.001.data rename to examples/USER/hdnnp/hdnnp-data/weights.001.data diff --git a/examples/USER/nnp/nnp-data/weights.008.data b/examples/USER/hdnnp/hdnnp-data/weights.008.data similarity index 100% rename from examples/USER/nnp/nnp-data/weights.008.data rename to examples/USER/hdnnp/hdnnp-data/weights.008.data diff --git a/examples/USER/nnp/in.nnp b/examples/USER/hdnnp/in.hdnnp similarity index 81% rename from examples/USER/nnp/in.nnp rename to examples/USER/hdnnp/in.hdnnp index d4664d1c83..112fb24515 100644 --- a/examples/USER/nnp/in.nnp +++ b/examples/USER/hdnnp/in.hdnnp @@ -1,5 +1,5 @@ ############################################################################### -# MD simulation for NN water +# MD simulation for HDNNP water ############################################################################### ############################################################################### @@ -11,9 +11,9 @@ variable cfgFile string "data.H2O-360mol" # Timesteps variable numSteps equal 10 variable dt equal 0.0005 -# NN -variable nnpCutoff equal 6.36 -variable nnpDir string "nnp-data" +# HDNNP +variable hdnnpCutoff equal 6.36 +variable hdnnpDir string "hdnnp-data" ############################################################################### # GENERAL SETUP @@ -26,10 +26,10 @@ timestep ${dt} thermo 1 ############################################################################### -# NN +# HDNNP ############################################################################### -pair_style nnp dir ${nnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254 emap "1:H,2:O" -pair_coeff * * ${nnpCutoff} +pair_style hdnnp dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254 emap "1:H,2:O" +pair_coeff * * ${hdnnpCutoff} ############################################################################### # INTEGRATOR @@ -39,7 +39,7 @@ fix INT all nve ############################################################################### # OUTPUT ############################################################################### -dump 1 all atom 1 dump.nnp +dump 1 all atom 1 dump.hdnnp ############################################################################### # SIMULATION diff --git a/lib/README b/lib/README index 535f2b228e..8709c7784c 100644 --- a/lib/README +++ b/lib/README @@ -27,6 +27,8 @@ gpu general GPU routines, GPU package from Mike Brown (ORNL) h5md ch5md library for output of MD data in HDF5 format from Pierre de Buyl (KU Leuven) +hdnnp hooks to n2p2, neural network potential package, used by USER-HDNNP + from Andreas Singraber kim hooks to the KIM library, used by KIM package from Ryan Elliott and Ellad Tadmor (U Minn) kokkos Kokkos package for GPU and many-core acceleration @@ -41,8 +43,6 @@ mscg hooks to the MSCG library, used by fix_mscg command from Jacob Wagner and Greg Voth group (U Chicago) netcdf hooks to a NetCDF library installed on your system from Lars Pastewka (Karlsruhe Institute of Technology) -nnp hooks to n2p2, neural network potential package, used by USER-NNP - from Andreas Singraber poems POEMS rigid-body integration package, POEMS package from Rudranarayan Mukherjee (RPI) python hooks to the system Python library, used by the PYTHON package diff --git a/lib/nnp/Makefile.lammps b/lib/hdnnp/Makefile.lammps similarity index 62% rename from lib/nnp/Makefile.lammps rename to lib/hdnnp/Makefile.lammps index fb5b939541..3b5ce3ab42 100644 --- a/lib/nnp/Makefile.lammps +++ b/lib/hdnnp/Makefile.lammps @@ -2,7 +2,7 @@ # Normally, you do NOT need to edit this file! # Check out if n2p2 or a link is right here. -N2P2_LOCALDIR=$(realpath ../../lib/nnp/n2p2) +N2P2_LOCALDIR=$(realpath ../../lib/hdnnp/n2p2) ifeq ($(N2P2_DIR),) N2P2_DIR=$(shell test -d $(N2P2_LOCALDIR) && echo $(N2P2_LOCALDIR)) else @@ -12,13 +12,13 @@ endif # Give up if n2p2 not found yet. ifeq ($(N2P2_DIR),) -$(error Cannot find library for USER-NNP package, please set environment or make variable N2P2_DIR manually.) +$(error Cannot find library for USER-HDNNP package, please set environment or make variable N2P2_DIR manually.) endif -# Read extra NNP_ compilation flags from makefile provided by n2p2: +# Read extra N2P2_ compilation flags from makefile provided by n2p2: include $(N2P2_DIR)/lib/Makefile.lammps-extra # Next, add general info to include/lib/path variables. -nnp_SYSINC += -I$(N2P2_DIR)/include -nnp_SYSLIB += -L$(N2P2_DIR)/lib -lnnpif -lnnp -nnp_SYSPATH += +hdnnp_SYSINC += -I$(N2P2_DIR)/include +hdnnp_SYSLIB += -L$(N2P2_DIR)/lib -lnnpif -lnnp +hdnnp_SYSPATH += diff --git a/lib/nnp/README b/lib/hdnnp/README similarity index 68% rename from lib/nnp/README rename to lib/hdnnp/README index 004d60df0b..d92fac5301 100644 --- a/lib/nnp/README +++ b/lib/hdnnp/README @@ -1,4 +1,4 @@ -The USER-NNP package requires access to pre-compiled libraries of the n2p2 +The USER-HDNNP package requires access to pre-compiled libraries of the n2p2 package (https://github.com/CompPhysVienna/n2p2). More precisely, the n2p2 core library ("libnnp"), the interface library ("libnnpif"), some headers and extra build helper files are needed. These files will be created automatically during @@ -10,17 +10,17 @@ Basic build instructions for n2p2 ================================= The n2p2 software package comes with lots of useful tools for creating and -applying neural network potentials (NNPs). In order to use n2p2 together with -LAMMPS only some parts of the n2p2 code need to be compiled. As an example, -everything related to NNP training is not required and would only add unwanted -library dependencies. Hence, the build infrastructure of n2p2 is designed to allow -a separate build of the LAMMPS interface. +applying high-dimensional neural network potentials (HDNNPs). In order to use +n2p2 together with LAMMPS only some parts of the n2p2 code need to be compiled. +As an example, everything related to HDNNP training is not required and would +only add unwanted library dependencies. Hence, the build infrastructure of n2p2 +is designed to allow a separate build of the LAMMPS interface. After downloading n2p2, change to the "src" directory and simply execute make libnnpif -which should create the following files needed by the USER-NNP package: +which should create the following files needed by the USER-HDNNP package: * "n2p2/lib/libnnp.a" * "n2p2/lib/libnnpif.a" @@ -43,7 +43,7 @@ also available (e.g. "makefile.intel") and can be activated by supplying the Please make sure that your compiler settings for n2p2 and LAMMPS are compatible (avoid mixing different compilers). -If you want to build a serial version of LAMMPS with USER-NNP package n2p2 must +If you want to build a serial version of LAMMPS with USER-HDNNP package n2p2 must also be built with MPI disabled. This can be achieved with a preprocessor flag (-DN2P2_NO_MPI) which is (among others) prepared, but commented out, in the provided compiler-specific settings makefiles. For example, if you use the GNU @@ -65,12 +65,12 @@ Installation directory of n2p2 You can install n2p2 either in this folder (1) or somewhere else on your system (2): (1) If n2p2 is installed here, please make sure that the directory is also named - "n2p2", i.e. within "lib/nnp/n2p2" you can see the n2p2 folder structure, in + "n2p2", i.e. within "lib/hdnnp/n2p2" you can see the n2p2 folder structure, in particular "lib" and "include": lib | - nnp + hdnnp | n2p2 | @@ -79,27 +79,27 @@ You can install n2p2 either in this folder (1) or somewhere else on your system include lib src ... In this case LAMMPS will automatically find n2p2 during the build process - and you only need to enable the USER-NNP package via CMake (-D PKG_USER-NNP=yes) - or the traditional makefile approach (make yes-user-nnp). It is also valid to - create a link here named "n2p2" which points to the n2p2 installation - directory. + and you only need to enable the USER-HDNNP package via CMake (-D + PKG_USER-HDNNP=yes) or the traditional makefile approach (make yes-user-hdnnp). + It is also valid to create a link here named "n2p2" which points to the n2p2 + installation directory. (2) If n2p2 is installed somewhere else the path must be given as an additional setting (variable N2P2_DIR) to the build tool. For example, with CMake use - cmake -D PKG_USER-NNP=yes -D N2P2_DIR= ../cmake/ + cmake -D PKG_USER-HDNNP=yes -D N2P2_DIR= ../cmake/ and for the traditional makefiles use - make yes-user-nnp + make yes-user-hdnnp make N2P2_DIR= mpi -Testing a successful build of LAMMPS with USER-NNP -================================================== +Testing a successful build of LAMMPS with USER-HDNNP +==================================================== -An example is provided in the LAMMPS directory "examples/USER/nnp" which runs +An example is provided in the LAMMPS directory "examples/USER/hdnnp" which runs 10 timesteps with 360 water molecules. The neural network potential is defined -via files in the "nnp-data" subdirectory. Use the "in.nnp" LAMMPS script file +via files in the "hdnnp-data" subdirectory. Use the "in.hdnnp" LAMMPS script file to run the simulation. You should see a large output of the n2p2 library when -the pair style "nnp" is initialized, followed by the LAMMPS per-timestep +the pair style "hdnnp" is initialized, followed by the LAMMPS per-timestep output. diff --git a/src/.gitignore b/src/.gitignore index 9e37dc316c..b02a44705c 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -971,6 +971,8 @@ /pair_hbond_dreiding_lj.h /pair_hbond_dreiding_morse.cpp /pair_hbond_dreiding_morse.h +/pair_hdnnp.cpp +/pair_hdnnp.h /pair_ilp_graphene_hbn.cpp /pair_ilp_graphene_hbn.h /pair_kolmogorov_crespi_full.cpp @@ -1079,8 +1081,6 @@ /pair_nm_cut_coul_cut.h /pair_nm_cut_coul_long.cpp /pair_nm_cut_coul_long.h -/pair_nnp.cpp -/pair_nnp.h /pair_oxdna_*.cpp /pair_oxdna_*.h /pair_oxdna2_*.cpp diff --git a/src/Makefile b/src/Makefile index 3afe821db7..7fce8e5354 100644 --- a/src/Makefile +++ b/src/Makefile @@ -52,17 +52,17 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ python qeq replica rigid shock snap spin srd voronoi PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ - user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ + user-diffraction user-dpd user-drude user-eff user-fep user-h5md user-hdnnp \ user-intel user-lb user-manifold user-meamc user-mesodpd user-mesont \ user-mgpt user-misc user-mofff user-molfile \ - user-netcdf user-nnp user-omp user-phonon user-plumed user-ptm user-qmmm \ + user-netcdf user-omp user-phonon user-plumed user-ptm user-qmmm \ user-qtb user-quip user-reaction user-reaxc user-scafacos user-smd user-smtbq \ user-sdpd user-sph user-tally user-uef user-vtk user-yaff PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \ python voronoi \ - user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ - user-netcdf user-nnp user-plumed user-qmmm user-quip user-scafacos \ + user-adios user-atc user-awpmd user-colvars user-h5md user-hdnnp user-lb user-molfile \ + user-netcdf user-plumed user-qmmm user-quip user-scafacos \ user-smd user-vtk user-mesont PACKSYS = compress mpiio python user-lb @@ -70,7 +70,7 @@ PACKSYS = compress mpiio python user-lb PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont PACKEXT = kim latte mscg voronoi \ - user-adios user-h5md user-molfile user-netcdf user-nnp user-plumed user-qmmm \ + user-adios user-h5md user-hdnnp user-molfile user-netcdf user-plumed user-qmmm \ user-quip user-smd user-vtk PACKALL = $(PACKAGE) $(PACKUSER) diff --git a/src/USER-NNP/Install.sh b/src/USER-HDNNP/Install.sh similarity index 66% rename from src/USER-NNP/Install.sh rename to src/USER-HDNNP/Install.sh index cd60ba1598..8ee16c53ca 100644 --- a/src/USER-NNP/Install.sh +++ b/src/USER-HDNNP/Install.sh @@ -37,17 +37,17 @@ done if (test $1 = 1) then if (test -e ../Makefile.package) then - sed -i -e 's/[^ \t]*nnp[^ \t]* //g' ../Makefile.package - sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(nnp_SYSINC) |' ../Makefile.package - sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(nnp_SYSLIB) |' ../Makefile.package - sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(nnp_SYSPATH) |' ../Makefile.package + sed -i -e 's/[^ \t]*hdnnp[^ \t]* //g' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(hdnnp_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(hdnnp_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(hdnnp_SYSPATH) |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*nnp.*$/d' ../Makefile.package.settings + sed -i -e '/^include.*hdnnp.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ -include ..\/..\/lib\/nnp\/Makefile.lammps\ +include ..\/..\/lib\/hdnnp\/Makefile.lammps\ ' ../Makefile.package.settings fi @@ -55,11 +55,11 @@ include ..\/..\/lib\/nnp\/Makefile.lammps\ elif (test $1 = 0) then if (test -e ../Makefile.package) then - sed -i -e 's/[^ \t]*nnp[^ \t]* //g' ../Makefile.package + sed -i -e 's/[^ \t]*hdnnp[^ \t]* //g' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*nnp.*$/d' ../Makefile.package.settings + sed -i -e '/^include.*hdnnp.*$/d' ../Makefile.package.settings fi fi diff --git a/src/USER-NNP/README b/src/USER-HDNNP/README similarity index 75% rename from src/USER-NNP/README rename to src/USER-HDNNP/README index a8eae3d865..690db8a714 100644 --- a/src/USER-NNP/README +++ b/src/USER-HDNNP/README @@ -1,15 +1,15 @@ -This package implements the "pair_style nnp" command which can be used in a +This package implements the "pair_style hdnnp" command which can be used in a LAMMPS input script. This pair style allows to use pre-trained high-dimensional neural network potentials[1] via an interface to the n2p2 library (https://github.com/CompPhysVienna/n2p2)[2]. -Please see the main documentation for the "pair_style nnp" command for further +Please see the main documentation for the "pair_style hdnnp" command for further details on how the pair style is used. An example is provided in the -"examples/USER/nnp" directory of LAMMPS. +"examples/USER/hdnnp" directory of LAMMPS. -The USER-NNP package requires the external library n2p2 which must be +The USER-HDNNP package requires the external library n2p2 which must be downloaded and compiled before starting the build process of LAMMPS. A -guideline on how to build n2p2 is presented in "lib/nnp/README". This package +guideline on how to build n2p2 is presented in "lib/hdnnp/README". This package supports the LAMMPS build process via CMake and traditional makefiles, please see the LAMMPS manual section on building with external libraries for more details. diff --git a/src/USER-NNP/pair_nnp.cpp b/src/USER-HDNNP/pair_hdnnp.cpp similarity index 94% rename from src/USER-NNP/pair_nnp.cpp rename to src/USER-HDNNP/pair_hdnnp.cpp index b2dae5a969..213574327c 100644 --- a/src/USER-NNP/pair_nnp.cpp +++ b/src/USER-HDNNP/pair_hdnnp.cpp @@ -18,7 +18,7 @@ Contributing author: Andreas Singraber ------------------------------------------------------------------------- */ -#include "pair_nnp.h" +#include "pair_hdnnp.h" #include #include "atom.h" #include "citeme.h" @@ -34,8 +34,8 @@ using namespace LAMMPS_NS; -static const char cite_user_nnp_package[] = - "USER-NNP package:\n\n" +static const char cite_user_hdnnp_package[] = + "USER-HDNNP package:\n\n" "@Article{Singraber19,\n" " author = {Singraber, Andreas and Behler, J{\"o}rg and Dellago, Christoph},\n" " title = {Library-{{Based LAMMPS Implementation}} of {{High}}-{{Dimensional Neural Network Potentials}}},\n" @@ -50,23 +50,23 @@ static const char cite_user_nnp_package[] = /* ---------------------------------------------------------------------- */ -PairNNP::PairNNP(LAMMPS *lmp) : Pair(lmp) +PairHDNNP::PairHDNNP(LAMMPS *lmp) : Pair(lmp) { - if (lmp->citeme) lmp->citeme->add(cite_user_nnp_package); + if (lmp->citeme) lmp->citeme->add(cite_user_hdnnp_package); interface = new nnp::InterfaceLammps(); } /* ---------------------------------------------------------------------- */ -PairNNP::~PairNNP() +PairHDNNP::~PairHDNNP() { delete interface; } /* ---------------------------------------------------------------------- */ -void PairNNP::compute(int eflag, int vflag) +void PairHDNNP::compute(int eflag, int vflag) { if(eflag || vflag) ev_setup(eflag,vflag); else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; @@ -78,7 +78,7 @@ void PairNNP::compute(int eflag, int vflag) // (tagint = int64_t) interface->setLocalTags(atom->tag); - // Transfer local neighbor list to NNP interface. + // Transfer local neighbor list to n2p2 interface. transferNeighborList(); // Compute symmetry functions, atomic neural networks and add up energy. @@ -109,7 +109,7 @@ void PairNNP::compute(int eflag, int vflag) global settings ------------------------------------------------------------------------- */ -void PairNNP::settings(int narg, char **arg) +void PairHDNNP::settings(int narg, char **arg) { single_enable = 0; // 1 if single() routine exists single_hessian_enable = 0; // 1 if single_hessian() routine exists @@ -128,9 +128,9 @@ void PairNNP::settings(int narg, char **arg) if (narg == 0) error->all(FLERR,"Illegal pair_style command"); // default settings - int len = strlen("nnp/") + 1; + int len = strlen("hdnnp/") + 1; directory = new char[len]; - strcpy(directory,"nnp/"); + strcpy(directory,"hdnnp/"); showew = true; showewsum = 0; maxew = 0; @@ -144,7 +144,7 @@ void PairNNP::settings(int narg, char **arg) numExtrapolationWarningsSummary = 0; while(iarg < narg) { - // set NNP directory + // set HDNNP directory if (strcmp(arg[iarg],"dir") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style command"); @@ -216,7 +216,7 @@ void PairNNP::settings(int narg, char **arg) set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void PairNNP::coeff(int narg, char **arg) +void PairHDNNP::coeff(int narg, char **arg) { if (!allocated) allocate(); @@ -244,14 +244,14 @@ void PairNNP::coeff(int narg, char **arg) init specific to this pair style ------------------------------------------------------------------------- */ -void PairNNP::init_style() +void PairHDNNP::init_style() { int irequest = neighbor->request((void *) this); neighbor->requests[irequest]->pair = 1; neighbor->requests[irequest]->half = 0; neighbor->requests[irequest]->full = 1; - // Return immediately if NNP setup is already completed. + // Return immediately if HDNNP setup is already completed. if (interface->isInitialized()) return; // Activate screen and logfile output only for rank 0. @@ -285,7 +285,7 @@ void PairNNP::init_style() init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairNNP::init_one(int i, int j) +double PairHDNNP::init_one(int i, int j) { return maxCutoffRadius; } @@ -294,7 +294,7 @@ double PairNNP::init_one(int i, int j) allocate all arrays ------------------------------------------------------------------------- */ -void PairNNP::allocate() +void PairHDNNP::allocate() { allocated = 1; int n = atom->ntypes; @@ -307,9 +307,9 @@ void PairNNP::allocate() memory->create(cutsq,n+1,n+1,"pair:cutsq"); } -void PairNNP::transferNeighborList() +void PairHDNNP::transferNeighborList() { - // Transfer neighbor list to NNP. + // Transfer neighbor list to n2p2. double rc2 = maxCutoffRadius * maxCutoffRadius; for (int ii = 0; ii < list->inum; ++ii) { int i = list->ilist[ii]; @@ -327,7 +327,7 @@ void PairNNP::transferNeighborList() } } -void PairNNP::handleExtrapolationWarnings() +void PairHDNNP::handleExtrapolationWarnings() { // Get number of extrapolation warnings for local atoms. long numCurrentEW = (long)interface->getNumExtrapolationWarnings(); diff --git a/src/USER-NNP/pair_nnp.h b/src/USER-HDNNP/pair_hdnnp.h similarity index 91% rename from src/USER-NNP/pair_nnp.h rename to src/USER-HDNNP/pair_hdnnp.h index 8a41d1a5d6..a3488bbad4 100644 --- a/src/USER-NNP/pair_nnp.h +++ b/src/USER-HDNNP/pair_hdnnp.h @@ -20,12 +20,12 @@ #ifdef PAIR_CLASS -PairStyle(nnp,PairNNP) +PairStyle(hdnnp,PairHDNNP) #else -#ifndef LMP_PAIR_NNP_H -#define LMP_PAIR_NNP_H +#ifndef LMP_PAIR_HDNNP_H +#define LMP_PAIR_HDNNP_H #include "pair.h" @@ -35,12 +35,12 @@ namespace nnp { namespace LAMMPS_NS { -class PairNNP : public Pair { +class PairHDNNP : public Pair { public: - PairNNP(class LAMMPS *); - virtual ~PairNNP(); + PairHDNNP(class LAMMPS *); + virtual ~PairHDNNP(); virtual void compute(int, int); virtual void settings(int, char **); virtual void coeff(int, char **); From 8e4a2e4c7bbc23b74be0c13339bcc768fc94007f Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Thu, 1 Apr 2021 00:41:27 +0200 Subject: [PATCH 0320/1217] Renamed a missing cmake file, NNP => HDNNP --- cmake/Modules/Packages/{USER-NNP.cmake => USER-HDNNP.cmake} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename cmake/Modules/Packages/{USER-NNP.cmake => USER-HDNNP.cmake} (100%) diff --git a/cmake/Modules/Packages/USER-NNP.cmake b/cmake/Modules/Packages/USER-HDNNP.cmake similarity index 100% rename from cmake/Modules/Packages/USER-NNP.cmake rename to cmake/Modules/Packages/USER-HDNNP.cmake From 8b2676a103c8fc220fe404c547d1e40ea3d78d5f Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Wed, 31 Mar 2021 16:57:13 -0600 Subject: [PATCH 0321/1217] Moving arguments in gran wall, renaming toarg limit_damping --- src/GRANULAR/fix_wall_gran.cpp | 31 ++++++++++++------- src/GRANULAR/fix_wall_gran.h | 2 +- src/GRANULAR/pair_gran_hertz_history.cpp | 4 +-- src/GRANULAR/pair_gran_hooke.cpp | 4 +-- src/GRANULAR/pair_gran_hooke_history.cpp | 10 +++--- src/GRANULAR/pair_gran_hooke_history.h | 2 +- src/GRANULAR/pair_granular.cpp | 30 +++++++++--------- src/GRANULAR/pair_granular.h | 2 +- src/KOKKOS/pair_gran_hooke_history_kokkos.cpp | 2 +- 9 files changed, 47 insertions(+), 40 deletions(-) diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 9c17a323c5..c9d00ccdd3 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -116,6 +116,12 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : kt /= force->nktv2p; } iarg = 10; + + if (strcmp(arg[iarg],"limit_damping") == 0) { + limit_damping = 1; + iarg += 1; + } + } else { iarg = 4; damping_model = VISCOELASTIC; @@ -292,6 +298,9 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : strcmp(arg[iarg], "zcylinder") == 0 || strcmp(arg[iarg], "region") == 0) { break; + } else if (strcmp(arg[iarg],"limit_damping") == 0) { + limit_damping = 1; + iarg += 1; } else { error->all(FLERR, "Illegal fix wall/gran command"); } @@ -301,6 +310,11 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : if (tangential_model == TANGENTIAL_MINDLIN_RESCALE) size_history += 1; } + if(normal_model == JKR) + error->all(FLERR,"Cannot limit damping with JRK model"); + if(normal_model == DMT) + error->all(FLERR,"Cannot limit damping with DMT model"); + // wallstyle args idregion = nullptr; @@ -347,7 +361,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : wiggle = 0; wshear = 0; peratom_flag = 0; - noattraction_flag = 0; + limit_damping = 0; while (iarg < narg) { if (strcmp(arg[iarg],"wiggle") == 0) { @@ -374,13 +388,6 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : size_peratom_cols = 8; peratom_freq = 1; iarg += 1; - } else if (strcmp(arg[iarg],"no_attraction") == 0) { - noattraction_flag = 1; - if(normal_model == JKR) - error->all(FLERR,"Cannot turn off attraction with JRK model"); - if(normal_model == DMT) - error->all(FLERR,"Cannot turn off attraction with DMT model"); - iarg += 1; } else error->all(FLERR,"Illegal fix wall/gran command"); } @@ -769,7 +776,7 @@ void FixWallGran::hooke(double rsq, double dx, double dy, double dz, damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radius-r)*rinv - damp; - if(noattraction_flag and ccel < 0.0) ccel = 0.0; + if(limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities @@ -862,7 +869,7 @@ void FixWallGran::hooke_history(double rsq, double dx, double dy, double dz, damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radius-r)*rinv - damp; - if(noattraction_flag and ccel < 0.0) ccel = 0.0; + if(limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities @@ -994,7 +1001,7 @@ void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz, if (rwall == 0.0) polyhertz = sqrt((radius-r)*radius); else polyhertz = sqrt((radius-r)*radius*rwall/(rwall+radius)); ccel *= polyhertz; - if(noattraction_flag and ccel < 0.0) ccel = 0.0; + if(limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities @@ -1188,7 +1195,7 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; - if(noattraction_flag and Fntot < 0.0) Fntot = 0.0; + if(limit_damping and Fntot < 0.0) Fntot = 0.0; //**************************************** // tangential force, including history effects diff --git a/src/GRANULAR/fix_wall_gran.h b/src/GRANULAR/fix_wall_gran.h index 3963b22a2c..473f26cca4 100644 --- a/src/GRANULAR/fix_wall_gran.h +++ b/src/GRANULAR/fix_wall_gran.h @@ -69,7 +69,7 @@ class FixWallGran : public Fix { // for granular model choices int normal_model, damping_model; int tangential_model, roll_model, twist_model; - int noattraction_flag; + int limit_damping; // history flags int normal_history, tangential_history, roll_history, twist_history; diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index 7da0c6142d..40c6c3a41d 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -181,7 +181,7 @@ void PairGranHertzHistory::compute(int eflag, int vflag) ccel = kn*(radsum-r)*rinv - damp; polyhertz = sqrt((radsum-r)*radi*radj / radsum); ccel *= polyhertz; - if(noattractionflag and ccel < 0.0) ccel = 0.0; + if(limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities @@ -389,7 +389,7 @@ double PairGranHertzHistory::single(int i, int j, int /*itype*/, int /*jtype*/, ccel = kn*(radsum-r)*rinv - damp; polyhertz = sqrt((radsum-r)*radi*radj / radsum); ccel *= polyhertz; - if(noattractionflag and ccel < 0.0) ccel = 0.0; + if(limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp index 76946701cb..0e3ffc7293 100644 --- a/src/GRANULAR/pair_gran_hooke.cpp +++ b/src/GRANULAR/pair_gran_hooke.cpp @@ -158,7 +158,7 @@ void PairGranHooke::compute(int eflag, int vflag) damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if(noattractionflag and ccel < 0.0) ccel = 0.0; + if(limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities @@ -300,7 +300,7 @@ double PairGranHooke::single(int i, int j, int /*itype*/, int /*jtype*/, double damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if(noattractionflag and ccel < 0.0) ccel = 0.0; + if(limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 4893be4084..d3c1cf7672 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -237,7 +237,7 @@ void PairGranHookeHistory::compute(int eflag, int vflag) damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if(noattractionflag and ccel < 0.0) ccel = 0.0; + if(limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities @@ -371,10 +371,10 @@ void PairGranHookeHistory::settings(int narg, char **arg) dampflag = utils::inumeric(FLERR,arg[5],false,lmp); if (dampflag == 0) gammat = 0.0; - noattractionflag = 0; + limit_damping = 0; if(narg == 7) { - if(strcmp(arg[6], "no_attraction")) - noattractionflag = 1; + if(strcmp(arg[6], "limit_damping")) + limit_damping = 1; else error->all(FLERR,"Illegal pair_style command"); } @@ -695,7 +695,7 @@ double PairGranHookeHistory::single(int i, int j, int /*itype*/, int /*jtype*/, damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if(noattractionflag and ccel < 0.0) ccel = 0.0; + if(limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities diff --git a/src/GRANULAR/pair_gran_hooke_history.h b/src/GRANULAR/pair_gran_hooke_history.h index bf40097f9d..f511d30237 100644 --- a/src/GRANULAR/pair_gran_hooke_history.h +++ b/src/GRANULAR/pair_gran_hooke_history.h @@ -49,7 +49,7 @@ class PairGranHookeHistory : public Pair { double dt; int freeze_group_bit; int history; - int noattractionflag; + int limit_damping; int neighprev; double *onerad_dynamic,*onerad_frozen; diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 256acd5a6a..dd22f03fa8 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -130,7 +130,7 @@ PairGranular::~PairGranular() memory->destroy(tangential_model); memory->destroy(roll_model); memory->destroy(twist_model); - memory->destroy(noattraction_flag); + memory->destroy(limit_damping); delete [] onerad_dynamic; delete [] onerad_frozen; @@ -371,7 +371,7 @@ void PairGranular::compute(int eflag, int vflag) Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; - if(noattraction_flag[itype][jtype] and Fntot < 0.0) Fntot = 0.0; + if(limit_damping[itype][jtype] and Fntot < 0.0) Fntot = 0.0; //**************************************** // tangential force, including history effects @@ -742,7 +742,7 @@ void PairGranular::allocate() memory->create(tangential_model,n+1,n+1,"pair:tangential_model"); memory->create(roll_model,n+1,n+1,"pair:roll_model"); memory->create(twist_model,n+1,n+1,"pair:twist_model"); - memory->create(noattraction_flag,n+1,n+1,"pair:noattraction_flag"); + memory->create(limit_damping,n+1,n+1,"pair:limit_damping"); onerad_dynamic = new double[n+1]; onerad_frozen = new double[n+1]; @@ -796,7 +796,7 @@ void PairGranular::coeff(int narg, char **arg) roll_model_one = ROLL_NONE; twist_model_one = TWIST_NONE; damping_model_one = VISCOELASTIC; - int na_flag = 0; + int ld_flag = 0; int iarg = 2; while (iarg < narg) { @@ -971,8 +971,8 @@ void PairGranular::coeff(int narg, char **arg) error->all(FLERR, "Illegal pair_coeff command, not enough parameters"); cutoff_one = utils::numeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; - } else if (strcmp(arg[iarg], "no_attraction") == 0) { - na_flag = 1; + } else if (strcmp(arg[iarg], "limit_damping") == 0) { + ld_flag = 1; iarg += 1; } else error->all(FLERR, "Illegal pair coeff command"); } @@ -991,11 +991,11 @@ void PairGranular::coeff(int narg, char **arg) 27.467*powint(cor,4)-18.022*powint(cor,5)+4.8218*powint(cor,6); } else damp = normal_coeffs_one[1]; - if(na_flag and normal_model_one == JKR) - error->all(FLERR,"Cannot turn off attraction with JKR pairstyle"); + if(ld_flag and normal_model_one == JKR) + error->all(FLERR,"Cannot limit damping with JKR model"); - if(na_flag and normal_model_one == DMT) - error->all(FLERR,"Cannot turn off attraction with DMT pairstyle"); + if(ld_flag and normal_model_one == DMT) + error->all(FLERR,"Cannot limit damping with DMT model"); for (int i = ilo; i <= ihi; i++) { for (int j = MAX(jlo,i); j <= jhi; j++) { @@ -1039,7 +1039,7 @@ void PairGranular::coeff(int narg, char **arg) cutoff_type[i][j] = cutoff_type[j][i] = cutoff_one; - noattraction_flag[i][j] = na_flag; + limit_damping[i][j] = ld_flag; setflag[i][j] = 1; count++; @@ -1319,7 +1319,7 @@ void PairGranular::write_restart(FILE *fp) fwrite(&tangential_model[i][j],sizeof(int),1,fp); fwrite(&roll_model[i][j],sizeof(int),1,fp); fwrite(&twist_model[i][j],sizeof(int),1,fp); - fwrite(&noattraction_flag[i][j],sizeof(int),1,fp); + fwrite(&limit_damping[i][j],sizeof(int),1,fp); fwrite(normal_coeffs[i][j],sizeof(double),4,fp); fwrite(tangential_coeffs[i][j],sizeof(double),3,fp); fwrite(roll_coeffs[i][j],sizeof(double),3,fp); @@ -1350,7 +1350,7 @@ void PairGranular::read_restart(FILE *fp) utils::sfread(FLERR,&tangential_model[i][j],sizeof(int),1,fp,nullptr,error); utils::sfread(FLERR,&roll_model[i][j],sizeof(int),1,fp,nullptr,error); utils::sfread(FLERR,&twist_model[i][j],sizeof(int),1,fp,nullptr,error); - utils::sfread(FLERR,&noattraction_flag[i][j],sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&limit_damping[i][j],sizeof(int),1,fp,nullptr,error); utils::sfread(FLERR,normal_coeffs[i][j],sizeof(double),4,fp,nullptr,error); utils::sfread(FLERR,tangential_coeffs[i][j],sizeof(double),3,fp,nullptr,error); utils::sfread(FLERR,roll_coeffs[i][j],sizeof(double),3,fp,nullptr,error); @@ -1362,7 +1362,7 @@ void PairGranular::read_restart(FILE *fp) MPI_Bcast(&tangential_model[i][j],1,MPI_INT,0,world); MPI_Bcast(&roll_model[i][j],1,MPI_INT,0,world); MPI_Bcast(&twist_model[i][j],1,MPI_INT,0,world); - MPI_Bcast(&noattraction_flag[i][j],1,MPI_INT,0,world); + MPI_Bcast(&limit_damping[i][j],1,MPI_INT,0,world); MPI_Bcast(normal_coeffs[i][j],4,MPI_DOUBLE,0,world); MPI_Bcast(tangential_coeffs[i][j],3,MPI_DOUBLE,0,world); MPI_Bcast(roll_coeffs[i][j],3,MPI_DOUBLE,0,world); @@ -1548,7 +1548,7 @@ double PairGranular::single(int i, int j, int itype, int jtype, Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; - if(noattraction_flag[itype][jtype] and Fntot < 0.0) Fntot = 0.0; + if(limit_damping[itype][jtype] and Fntot < 0.0) Fntot = 0.0; jnum = list->numneigh[i]; jlist = list->firstneigh[i]; diff --git a/src/GRANULAR/pair_granular.h b/src/GRANULAR/pair_granular.h index 1e4e8c8fc4..49eb457f0d 100644 --- a/src/GRANULAR/pair_granular.h +++ b/src/GRANULAR/pair_granular.h @@ -70,7 +70,7 @@ class PairGranular : public Pair { // model choices int **normal_model, **damping_model; int **tangential_model, **roll_model, **twist_model; - int **noattractionflag; + int **limit_damping; // history flags int normal_history, tangential_history, roll_history, twist_history; diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp index caa19ffdef..8d853b7dae 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp @@ -392,7 +392,7 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC F_FLOAT damp = meff*gamman*vnnr*rsqinv; F_FLOAT ccel = kn*(radsum-r)*rinv - damp; - if(noattractionflag & ccel < 0.0) ccel = 0.0; + if(limit_damping & ccel < 0.0) ccel = 0.0; // relative velocities From 8b37f3c04448bc3d3ed7a9f416cde67e8ad8e802 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Wed, 31 Mar 2021 17:25:41 -0600 Subject: [PATCH 0322/1217] Fixing incorrect arg for pair gran --- doc/src/fix_wall_gran.rst | 14 ++++---------- doc/src/fix_wall_gran_region.rst | 9 ++------- doc/src/pair_gran.rst | 6 +++--- doc/src/pair_granular.rst | 2 +- src/GRANULAR/pair_gran_hooke_history.cpp | 6 ++---- 5 files changed, 12 insertions(+), 25 deletions(-) diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index bfe06bf7a0..02d52ef1a6 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -29,6 +29,7 @@ Syntax gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) xmu = static yield criterion (unitless value between 0.0 and 1.0e4) dampflag = 0 or 1 if tangential damping force is excluded or included + optional keyword = *limit_damping*, limit damping to prevent attractive interaction .. parsed-literal:: @@ -45,7 +46,7 @@ Syntax radius = cylinder radius (distance units) * zero or more keyword/value pairs may be appended to args -* keyword = *wiggle* or *shear* or *contacts* or *no_attraction* +* keyword = *wiggle* or *shear* or *contacts* .. parsed-literal:: @@ -58,8 +59,6 @@ Syntax vshear = magnitude of shear velocity (velocity units) *contacts* value = none generate contact information for each particle - *no_attraction* value = none - turn off possibility of attractive interactions Examples @@ -97,7 +96,8 @@ Specifically, delta = radius - r = overlap of particle with wall, m_eff = mass of particle, and the effective radius of contact = RiRj/Ri+Rj is set to the radius of the particle. -The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu* and *dampflag* +The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*, +and the optional keyword *limit_damping* have the same meaning and units as those specified with the :doc:`pair_style gran/\* ` commands. This means a NULL can be used for either *Kt* or *gamma_t* as described on that page. If a @@ -177,12 +177,6 @@ the clockwise direction for *vshear* > 0 or counter-clockwise for *vshear* < 0. In this case, *vshear* is the tangential velocity of the wall at whatever *radius* has been defined. -If a particle is moving away from the wall while in contact, there -is a possibility that the particle could experience an effective attractive -force due to damping. If the *no_attraction* keyword is used, this fix -will zero out the normal component of the force if there is an effective -attractive force. This keyword cannot be used with the JKR or DMT models. - """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the shear friction state of atoms interacting with the diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 00eb19ba1c..b7a9ff6bd7 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -183,7 +183,8 @@ radius - r = overlap of particle with wall, m_eff = mass of particle, and the effective radius of contact is just the radius of the particle. -The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu* and *dampflag* +The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*, +and the optional keyword *limit_damping* have the same meaning and units as those specified with the :doc:`pair_style gran/\* ` commands. This means a NULL can be used for either *Kt* or *gamma_t* as described on that page. If a @@ -201,12 +202,6 @@ values for the 6 wall/particle coefficients than for particle/particle interactions. E.g. if you wish to model the wall as a different material. -If a particle is moving away from the wall while in contact, there -is a possibility that the particle could experience an effective attractive -force due to damping. If the *no_attraction* keyword is used, this fix -will zero out the normal component of the force if there is an effective -attractive force. This keyword cannot be used with the JKR or DMT models. - Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index 8145f7fb7a..b918e38da6 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -40,8 +40,8 @@ Syntax .. parsed-literal:: - *no_attraction* value = none - turn off possibility of attractive interactions + *limit_damping* value = none + limit damping to prevent attractive interaction .. note:: @@ -217,7 +217,7 @@ potential. If two particles are moving away from each other while in contact, there is a possibility that the particles could experience an effective attractive -force due to damping. If the *no_attraction* keyword is used, this fix +force due to damping. If the *limit_damping* keyword is used, this fix will zero out the normal component of the force if there is an effective attractive force. diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index 0076994e25..04c9d45afd 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -625,7 +625,7 @@ Finally, the twisting torque on each particle is given by: If two particles are moving away from each other while in contact, there is a possibility that the particles could experience an effective attractive -force due to damping. If the optional *no_attraction* keyword is used, this fix +force due to damping. If the optional *limit_damping* keyword is used, this fix will zero out the normal component of the force if there is an effective attractive force. This keyword cannot be used with the JKR or DMT models. diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index d3c1cf7672..a86af2116e 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -373,10 +373,8 @@ void PairGranHookeHistory::settings(int narg, char **arg) limit_damping = 0; if(narg == 7) { - if(strcmp(arg[6], "limit_damping")) - limit_damping = 1; - else - error->all(FLERR,"Illegal pair_style command"); + if(strcmp(arg[6], "limit_damping") == 0) limit_damping = 1; + else error->all(FLERR,"Illegal pair_style command"); } if (kn < 0.0 || kt < 0.0 || gamman < 0.0 || gammat < 0.0 || From b34585762b2d87cb8a931b5ef344b9d1f501339d Mon Sep 17 00:00:00 2001 From: snikolo Date: Thu, 1 Apr 2021 01:00:25 -0600 Subject: [PATCH 0323/1217] updated sectoring function to account for triclinic cells. I didn't see a triclinic cell error warnings in SPIN/* or KOKKOS/atom_vec_spin_kokkos.cpp files. --- src/SPIN/fix_nve_spin.cpp | 22 +++++++++++++++++----- 1 file changed, 17 insertions(+), 5 deletions(-) diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 364994741e..0df63951e4 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -507,13 +507,25 @@ void FixNVESpin::sectoring() { int sec[3]; double sublo[3],subhi[3]; - double* sublotmp = domain->sublo; - double* subhitmp = domain->subhi; - for (int dim = 0 ; dim < 3 ; dim++) { - sublo[dim]=sublotmp[dim]; - subhi[dim]=subhitmp[dim]; + + if (domain->triclinic == 1){ + double* sublotmp = domain->sublo_lamda; + double* subhitmp = domain->subhi_lamda; + for (int dim = 0 ; dim < 3 ; dim++) { + sublo[dim]=sublotmp[dim]*domain->boxhi[dim]; + subhi[dim]=subhitmp[dim]*domain->boxhi[dim]; + } } + else { + double* sublotmp = domain->sublo; + double* subhitmp = domain->subhi; + for (int dim = 0 ; dim < 3 ; dim++) { + sublo[dim]=sublotmp[dim]; + subhi[dim]=subhitmp[dim]; + } + } + const double rsx = subhi[0] - sublo[0]; const double rsy = subhi[1] - sublo[1]; const double rsz = subhi[2] - sublo[2]; From f48af95d499536dd5da692ba0b3ea9c6361ffcee Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Apr 2021 08:23:10 -0400 Subject: [PATCH 0324/1217] update gcmc example to use fix rigid/small --- examples/gcmc/in.gcmc.co2 | 48 +++--- examples/gcmc/log.27Nov18.gcmc.co2.g++.1 | 196 ----------------------- examples/gcmc/log.31Mar21.gcmc.co2.g++.1 | 196 +++++++++++++++++++++++ 3 files changed, 220 insertions(+), 220 deletions(-) delete mode 100644 examples/gcmc/log.27Nov18.gcmc.co2.g++.1 create mode 100644 examples/gcmc/log.31Mar21.gcmc.co2.g++.1 diff --git a/examples/gcmc/in.gcmc.co2 b/examples/gcmc/in.gcmc.co2 index b5e11d212d..1da9020a64 100644 --- a/examples/gcmc/in.gcmc.co2 +++ b/examples/gcmc/in.gcmc.co2 @@ -1,4 +1,4 @@ -# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics +# GCMC for CO2 molecular fluid, rigid/small dynamics # Rigid CO2 TraPPE model # [Potoff and J.I. Siepmann, Vapor-liquid equilibria of # mixtures containing alkanes, carbon dioxide and @@ -7,7 +7,7 @@ # variables available on command line variable mu index -8.1 -variable disp index 0.5 +variable disp index 0.5 variable temp index 338.0 variable lbox index 10.0 variable spacing index 5.0 @@ -17,7 +17,7 @@ variable spacing index 5.0 units real atom_style full boundary p p p -pair_style lj/cut/coul/long 14 +pair_style lj/cut/coul/long 14 pair_modify mix arithmetic tail yes kspace_style ewald 0.0001 bond_style harmonic @@ -25,7 +25,7 @@ angle_style harmonic # box, start molecules on simple cubic lattice -lattice sc ${spacing} +lattice sc ${spacing} region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box create_box 2 box & bond/types 1 & @@ -34,56 +34,56 @@ create_box 2 box & extra/angle/per/atom 1 & extra/special/per/atom 2 molecule co2mol CO2.txt -create_atoms 0 box mol co2mol 464563 units box - -# rigid CO2 TraPPE model +create_atoms 0 box mol co2mol 464563 units box + +# rigid CO2 TraPPE model pair_coeff 1 1 0.053649 2.8 -pair_coeff 2 2 0.156973 3.05 -bond_coeff 1 0 1.16 -angle_coeff 1 0 180 +pair_coeff 2 2 0.156973 3.05 +bond_coeff 1 0 1.16 +angle_coeff 1 0 180 # masses -mass 1 12.0107 -mass 2 15.9994 +mass 1 12.0107 +mass 2 15.9994 # MD settings group co2 type 1 2 neighbor 2.0 bin neigh_modify every 1 delay 10 check yes -velocity all create ${temp} 54654 +velocity all create ${temp} 54654 timestep 1.0 -# rigid constraints with thermostat +# rigid constraints with thermostat -fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol +fix myrigid co2 rigid/small molecule mol co2mol # dynamically update fix rigid/nvt/small temperature ndof -fix_modify myrigidnvt dynamic/dof yes +fix_modify myrigid dynamic/dof yes # gcmc variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol & - co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt + co2mol tfac_insert ${tfac} group co2 rigid myrigid # atom counts -variable carbon atom "type==1" +variable carbon atom "type==1" variable oxygen atom "type==2" -group carbon dynamic co2 var carbon -group oxygen dynamic co2 var oxygen +group carbon dynamic co2 var carbon +group oxygen dynamic co2 var oxygen variable nC equal count(carbon) variable nO equal count(oxygen) # output -variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) -variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) -variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) -variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) +variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) +variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) +variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) +variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) # dynamically update default temperature ndof compute_modify thermo_temp dynamic/dof yes diff --git a/examples/gcmc/log.27Nov18.gcmc.co2.g++.1 b/examples/gcmc/log.27Nov18.gcmc.co2.g++.1 deleted file mode 100644 index 4ed9056d04..0000000000 --- a/examples/gcmc/log.27Nov18.gcmc.co2.g++.1 +++ /dev/null @@ -1,196 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics -# Rigid CO2 TraPPE model -# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of -# mixtures containing alkanes, carbon dioxide and -# nitrogen AIChE J., 47,1676-1682 (2001)]. - -# variables available on command line - -variable mu index -8.1 -variable disp index 0.5 -variable temp index 338.0 -variable lbox index 10.0 -variable spacing index 5.0 - -# global model settings - -units real -atom_style full -boundary p p p -pair_style lj/cut/coul/long 14 -pair_modify mix arithmetic tail yes -kspace_style ewald 0.0001 -bond_style harmonic -angle_style harmonic - -# box, start molecules on simple cubic lattice - -lattice sc ${spacing} -lattice sc 5.0 -Lattice spacing in x,y,z = 5 5 5 -region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 10.0 units box -create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 -Created orthogonal box = (0 0 0) to (10 10 10) - 1 by 1 by 1 MPI processor grid -molecule co2mol CO2.txt -Read molecule co2mol: - 3 atoms with max type 2 - 2 bonds with max type 1 - 1 angles with max type 1 - 0 dihedrals with max type 0 - 0 impropers with max type 0 -create_atoms 0 box mol co2mol 464563 units box -Created 24 atoms - Time spent = 0.00134993 secs - -# rigid CO2 TraPPE model - -pair_coeff 1 1 0.053649 2.8 -pair_coeff 2 2 0.156973 3.05 -bond_coeff 1 0 1.16 -angle_coeff 1 0 180 - -# masses - -mass 1 12.0107 -mass 2 15.9994 - -# MD settings - -group co2 type 1 2 -24 atoms in group co2 -neighbor 2.0 bin -neigh_modify every 1 delay 10 check yes -velocity all create ${temp} 54654 -velocity all create 338.0 54654 -timestep 1.0 - -# rigid constraints with thermostat - -fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol -fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol -fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol -8 rigid bodies with 24 atoms - 1.16 = max distance from body owner to body atom - -# dynamically update fix rigid/nvt/small temperature ndof -fix_modify myrigidnvt dynamic/dof yes - -# gcmc - -variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt - -# atom counts - -variable carbon atom "type==1" -variable oxygen atom "type==2" -group carbon dynamic co2 var carbon -dynamic group carbon defined -group oxygen dynamic co2 var oxygen -dynamic group oxygen defined -variable nC equal count(carbon) -variable nO equal count(oxygen) - -# output - -variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) -variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) -variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) -variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) - -# dynamically update default temperature ndof -compute_modify thermo_temp dynamic/dof yes - -thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO -thermo 1000 - -# run - -run 20000 -Ewald initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - G vector (1/distance) = 0.164636 - estimated absolute RMS force accuracy = 0.0332064 - estimated relative force accuracy = 0.0001 - KSpace vectors: actual max1d max3d = 16 2 62 - kxmax kymax kzmax = 2 2 2 -WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:487) -0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc -0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc -WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:471) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 16 - ghost atom cutoff = 16 - binsize = 8, bins = 2 2 2 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes -Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO - 0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16 - 1000 267.9799 -73.919548 -3.6735999 5.8578459 0.36539744 15 0.23663972 0.2494423 0 0 5 10 - 2000 409.06596 -98.033864 -6.7570039 10.974131 0.43847693 18 0.29379544 0.29816284 0 0 6 12 - 3000 279.3225 -836.47758 -26.434976 15.819539 0.87695385 36 0.23798567 0.24203908 0 0 12 24 - 4000 333.6181 606.63478 -30.35312 18.894592 0.87695385 36 0.19121778 0.19481508 0 0 12 24 - 5000 405.98741 -103.97582 -14.180277 16.942399 0.65771539 27 0.15272841 0.15982952 0 0 9 18 - 6000 283.5835 -240.01076 -6.7198093 7.607777 0.43847693 18 0.1606796 0.16536735 0 0 6 12 - 7000 142.00717 154.95914 -0.74192319 0.98769159 0.14615898 6 0.19501993 0.20103405 0 0 2 4 - 8000 376.67702 -118.12474 -10.774631 13.847899 0.5846359 24 0.20133396 0.20468352 0 0 8 16 - 9000 305.43166 -1095.8633 -10.388279 9.7112935 0.51155641 21 0.19445239 0.19869334 0 0 7 14 - 10000 244.08225 -179.31274 -12.974988 8.9732748 0.5846359 24 0.19098971 0.19586397 0 0 8 16 - 11000 305.03389 -568.94714 -21.745425 14.244887 0.73079488 30 0.18517522 0.18978828 0 0 10 20 - 12000 318.29735 767.76579 -37.184231 21.189508 1.0231128 42 0.17256426 0.17580267 0 0 14 28 - 13000 411.21707 433.01125 -4.5149215 8.9889065 0.36539744 15 0.16329385 0.16767604 0 0 5 10 - 14000 304.29535 148.28607 -2.3505844 6.6516754 0.36539744 15 0.17435868 0.17897674 0 0 5 10 - 15000 338.00555 2384.1424 -21.438264 17.463859 0.80387436 33 0.17237066 0.17634112 0 0 11 22 - 16000 613.56062 610.93867 -0.057364228 1.2192718 0.073079488 3 0.17128158 0.1758886 0 0 1 2 - 17000 432.63323 -980.52384 -15.79844 18.054365 0.65771539 27 0.17145651 0.17504846 0 0 9 18 - 18000 181.74572 -352.81765 -1.8617959 2.1669979 0.21923846 9 0.17292463 0.17654774 0 0 3 6 - 19000 208.55292 -248.38735 -4.2287767 4.5588154 0.36539744 15 0.18168324 0.18454331 0 0 5 10 - 20000 304.73317 -649.9896 -16.532405 12.716924 0.65771539 27 0.18085983 0.18345574 0 0 9 18 -Loop time of 21.0434 on 1 procs for 20000 steps with 27 atoms - -Performance: 82.116 ns/day, 0.292 hours/ns, 950.415 timesteps/s -98.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.2373 | 2.2373 | 2.2373 | 0.0 | 10.63 -Bond | 0.022895 | 0.022895 | 0.022895 | 0.0 | 0.11 -Kspace | 0.16756 | 0.16756 | 0.16756 | 0.0 | 0.80 -Neigh | 0.11436 | 0.11436 | 0.11436 | 0.0 | 0.54 -Comm | 0.26988 | 0.26988 | 0.26988 | 0.0 | 1.28 -Output | 0.0014684 | 0.0014684 | 0.0014684 | 0.0 | 0.01 -Modify | 18.193 | 18.193 | 18.193 | 0.0 | 86.45 -Other | | 0.03692 | | | 0.18 - -Nlocal: 27 ave 27 max 27 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2081 ave 2081 max 2081 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 6264 ave 6264 max 6264 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 6264 -Ave neighs/atom = 232 -Ave special neighs/atom = 2 -Neighbor list builds = 20177 -Dangerous builds = 0 - -Total wall time: 0:00:21 diff --git a/examples/gcmc/log.31Mar21.gcmc.co2.g++.1 b/examples/gcmc/log.31Mar21.gcmc.co2.g++.1 new file mode 100644 index 0000000000..80de6554e4 --- /dev/null +++ b/examples/gcmc/log.31Mar21.gcmc.co2.g++.1 @@ -0,0 +1,196 @@ +LAMMPS (10 Mar 2021) + using 1 OpenMP thread(s) per MPI task +# GCMC for CO2 molecular fluid, rigid/small dynamics +# Rigid CO2 TraPPE model +# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of +# mixtures containing alkanes, carbon dioxide and +# nitrogen AIChE J., 47,1676-1682 (2001)]. + +# variables available on command line + +variable mu index -8.1 +variable disp index 0.5 +variable temp index 338.0 +variable lbox index 10.0 +variable spacing index 5.0 + +# global model settings + +units real +atom_style full +boundary p p p +pair_style lj/cut/coul/long 14 +pair_modify mix arithmetic tail yes +kspace_style ewald 0.0001 +bond_style harmonic +angle_style harmonic + +# box, start molecules on simple cubic lattice + +lattice sc ${spacing} +lattice sc 5.0 +Lattice spacing in x,y,z = 5.0000000 5.0000000 5.0000000 +region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box +region box block 0 10.0 0 ${lbox} 0 ${lbox} units box +region box block 0 10.0 0 10.0 0 ${lbox} units box +region box block 0 10.0 0 10.0 0 10.0 units box +create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.000000 10.000000 10.000000) + 1 by 1 by 1 MPI processor grid +molecule co2mol CO2.txt +Read molecule template co2mol: + 1 molecules + 3 atoms with max type 2 + 2 bonds with max type 1 + 1 angles with max type 1 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +create_atoms 0 box mol co2mol 464563 units box +Created 24 atoms + create_atoms CPU = 0.002 seconds + +# rigid CO2 TraPPE model + +pair_coeff 1 1 0.053649 2.8 +pair_coeff 2 2 0.156973 3.05 +bond_coeff 1 0 1.16 +angle_coeff 1 0 180 + +# masses + +mass 1 12.0107 +mass 2 15.9994 + +# MD settings + +group co2 type 1 2 +24 atoms in group co2 +neighbor 2.0 bin +neigh_modify every 1 delay 10 check yes +velocity all create ${temp} 54654 +velocity all create 338.0 54654 +timestep 1.0 + +# rigid constraints with thermostat + +fix myrigid co2 rigid/small molecule mol co2mol + create bodies CPU = 0.000 seconds + 8 rigid bodies with 24 atoms + 1.1600000 = max distance from body owner to body atom + +# dynamically update fix rigid/nvt/small temperature ndof +fix_modify myrigid dynamic/dof yes + +# gcmc + +variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) +fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigid +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigid + +# atom counts + +variable carbon atom "type==1" +variable oxygen atom "type==2" +group carbon dynamic co2 var carbon +dynamic group carbon defined +group oxygen dynamic co2 var oxygen +dynamic group oxygen defined +variable nC equal count(carbon) +variable nO equal count(oxygen) + +# output + +variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) +variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) +variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) +variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) + +# dynamically update default temperature ndof +compute_modify thermo_temp dynamic/dof yes + +thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO +thermo 1000 + +# run + +run 20000 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.16463644 + estimated absolute RMS force accuracy = 0.033206372 + estimated relative force accuracy = 0.0001 + KSpace vectors: actual max1d max3d = 16 2 62 + kxmax kymax kzmax = 2 2 2 +WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:482) +0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc +0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8, bins = 2 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes +Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO + 0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16 + 1000 261.50949 -204.60974 -9.6459249 8.3147747 0.51155641 21 0.096366192 0.097590121 0 0 7 14 + 2000 479.39697 231.28436 -7.0089345 10.47927 0.36539744 15 0.085531005 0.085453295 0 0 5 10 + 3000 318.31766 -433.17133 -7.3680951 8.5396005 0.43847693 18 0.078556687 0.080101462 0 0 6 12 + 4000 357.40776 -186.78 -16.453111 14.915105 0.65771539 27 0.082003877 0.08249082 0 0 9 18 + 5000 399.94731 1524.2909 -16.624678 18.677282 0.73079488 30 0.071285101 0.072731705 0 0 10 20 + 6000 354.71736 60.134827 -18.988979 16.565073 0.73079488 30 0.071615663 0.071713414 0 0 10 20 + 7000 483.32057 966.32174 -5.7393251 10.565037 0.36539744 15 0.087027775 0.089855826 0 0 5 10 + 8000 547.68562 494.96891 -4.125626 11.97201 0.36539744 15 0.11738082 0.11937373 0 0 5 10 + 9000 433.76488 390.91467 -0.85312985 5.1718828 0.21923846 9 0.13265238 0.13513212 0 0 3 6 + 10000 330.01685 -862.07457 -26.494645 18.690633 0.87695385 36 0.13775034 0.13905403 0 0 12 24 + 11000 334.26318 -578.48274 -13.236965 12.288625 0.5846359 24 0.13713936 0.13960485 0 0 8 16 + 12000 243.68657 -1244.7156 -25.757644 12.590645 0.80387436 33 0.1339588 0.13588739 0 0 11 22 + 13000 307.66758 -429.66928 -17.864639 14.367878 0.73079488 30 0.12604721 0.1278094 0 0 10 20 + 14000 330.91434 495.97112 -15.374248 13.809499 0.65771539 27 0.12011756 0.12145865 0 0 9 18 + 15000 564.87966 982.72332 -14.810525 26.379517 0.73079488 30 0.12164324 0.12343521 0 0 10 20 + 16000 342.63867 -54.776299 -2.2580523 5.7875978 0.29231795 12 0.13535812 0.13790758 0 0 4 8 + 17000 461.07005 -2.4317694 -1.145154 3.2068452 0.14615898 6 0.1444739 0.14730804 0 0 2 4 + 18000 197.21207 -40.124433 -7.0857418 5.2906654 0.43847693 18 0.14403997 0.14574329 0 0 6 12 + 19000 393.36395 -420.49802 -11.172739 14.461366 0.5846359 24 0.15005606 0.15142063 0 0 8 16 + 20000 356.48539 56.071962 -1.7861789 4.2504609 0.21923846 9 0.15422732 0.15627984 0 0 3 6 +Loop time of 19.5982 on 1 procs for 20000 steps with 9 atoms + +Performance: 88.171 ns/day, 0.272 hours/ns, 1020.502 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.3404 | 2.3404 | 2.3404 | 0.0 | 11.94 +Bond | 0.033919 | 0.033919 | 0.033919 | 0.0 | 0.17 +Kspace | 0.19974 | 0.19974 | 0.19974 | 0.0 | 1.02 +Neigh | 0.11478 | 0.11478 | 0.11478 | 0.0 | 0.59 +Comm | 0.22538 | 0.22538 | 0.22538 | 0.0 | 1.15 +Output | 0.00096536 | 0.00096536 | 0.00096536 | 0.0 | 0.00 +Modify | 16.627 | 16.627 | 16.627 | 0.0 | 84.84 +Other | | 0.05594 | | | 0.29 + +Nlocal: 9.00000 ave 9 max 9 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 703.000 ave 703 max 703 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 719.000 ave 719 max 719 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 719 +Ave neighs/atom = 79.888889 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 20196 +Dangerous builds = 0 + +Total wall time: 0:00:19 From d72b390c41f63bae8f6cde7c9d4a56e6a9abf042 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Apr 2021 08:48:39 -0400 Subject: [PATCH 0325/1217] correct check for box changing fixes --- src/RIGID/fix_rigid.cpp | 4 ++-- src/RIGID/fix_rigid_small.cpp | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 985554f738..26bbb9477f 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -725,7 +725,7 @@ void FixRigid::init() for (i = 0; i < modify->nfix; i++) if (modify->fix[i]->box_change) break; if (i < modify->nfix) { - for (int j = i; j < modify->nfix; j++) + for (int j = i+1; j < modify->nfix; j++) if (utils::strmatch(modify->fix[j]->style,"^rigid")) error->all(FLERR,"Rigid fixes must come before any box changing fix"); } @@ -736,7 +736,7 @@ void FixRigid::init() int ifix = modify->find_fix(id_gravity); if (ifix < 0) error->all(FLERR,"Fix rigid cannot find fix gravity ID"); if (!utils::strmatch(modify->fix[ifix]->style,"^gravity")) - error->all(FLERR,"Fix rigid gravity fix is invalid"); + error->all(FLERR,"Fix rigid gravity fix ID is not a gravity fix style"); int tmp; gvec = (double *) modify->fix[ifix]->extract("gvec",tmp); } diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index d9a0b82ae8..14bd9f7a55 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -576,7 +576,7 @@ void FixRigidSmall::init() for (i = 0; i < modify->nfix; i++) if (modify->fix[i]->box_change) break; if (i < modify->nfix) { - for (int j = i; j < modify->nfix; j++) + for (int j = i+1; j < modify->nfix; j++) if (utils::strmatch(modify->fix[j]->style,"^rigid")) error->all(FLERR,"Rigid fixes must come before any box changing fix"); } @@ -587,7 +587,7 @@ void FixRigidSmall::init() int ifix = modify->find_fix(id_gravity); if (ifix < 0) error->all(FLERR,"Fix rigid/small cannot find fix gravity ID"); if (!utils::strmatch(modify->fix[ifix]->style,"^gravity")) - error->all(FLERR,"Fix rigid/small gravity fix is invalid"); + error->all(FLERR,"Fix rigid gravity fix ID is not a gravity fix style"); int tmp; gvec = (double *) modify->fix[ifix]->extract("gvec",tmp); } From c9652f3aa695f95d62914cc94000cdcd51f4fd98 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Apr 2021 09:31:54 -0400 Subject: [PATCH 0326/1217] update documentation for the extract_global() method of the lammps.lammps class --- python/lammps/core.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/python/lammps/core.py b/python/lammps/core.py index e112c4f3f8..3118cb3d99 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -729,12 +729,11 @@ class lammps(object): def extract_global(self, name, dtype=LAMMPS_AUTODETECT): """Query LAMMPS about global settings of different types. - This is a wrapper around the :cpp:func:`lammps_extract_global` - function of the C-library interface. Unlike the C function - this method returns the value and not a pointer and thus can - only return the first value for keywords representing a list - of values. The :cpp:func:`lammps_extract_global` documentation - includes a list of the supported keywords and their data types. + This is a wrapper around the :cpp:func:`lammps_extract_global` function + of the C-library interface. Since there are no pointers in Python, this + method will - unlike the C function - return the value or a list of + values. The :cpp:func:`lammps_extract_global` documentation includes a + list of the supported keywords and their data types. Since Python needs to know the data type to be able to interpret the result, by default, this function will try to auto-detect the data type by asking the library. You can also force a specific data type. For that From f867e69290beea676eb86b0cabae44768349df9f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Apr 2021 09:35:52 -0400 Subject: [PATCH 0327/1217] include new split_lines() function in Developer docs --- doc/src/Developer_utils.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/doc/src/Developer_utils.rst b/doc/src/Developer_utils.rst index 992df6ba63..17b4715dc7 100644 --- a/doc/src/Developer_utils.rst +++ b/doc/src/Developer_utils.rst @@ -101,6 +101,9 @@ and parsing files or arguments. .. doxygenfunction:: split_words :project: progguide +.. doxygenfunction:: split_lines + :project: progguide + .. doxygenfunction:: strmatch :project: progguide From e0aec1b5d9ba2c3d26d16beb11d5a100853b195f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Apr 2021 09:39:17 -0400 Subject: [PATCH 0328/1217] remove obsoleted comment --- unittest/force-styles/test_fix_timestep.cpp | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/unittest/force-styles/test_fix_timestep.cpp b/unittest/force-styles/test_fix_timestep.cpp index f72295716e..e4b0fa6e02 100644 --- a/unittest/force-styles/test_fix_timestep.cpp +++ b/unittest/force-styles/test_fix_timestep.cpp @@ -518,11 +518,9 @@ TEST(FixTimestep, plain) // rigid fixes need work to test properly with r-RESPA. // fix nve/limit cannot work with r-RESPA - // fix python/move implementation is missing library interface access to Repsa::step ifix = lmp->modify->find_fix("test"); if (!utils::strmatch(lmp->modify->fix[ifix]->style, "^rigid") && - !utils::strmatch(lmp->modify->fix[ifix]->style, "^nve/limit") - ) { + !utils::strmatch(lmp->modify->fix[ifix]->style, "^nve/limit")) { if (!verbose) ::testing::internal::CaptureStdout(); cleanup_lammps(lmp, test_config); From b5d2f5f2b27828a3544cb42a05ad0906044ab1f2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Apr 2021 09:45:01 -0400 Subject: [PATCH 0329/1217] address whitespace issues --- src/KIM/kim_interactions.cpp | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp index 9b63224f0f..f12c1774d2 100644 --- a/src/KIM/kim_interactions.cpp +++ b/src/KIM/kim_interactions.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing authors: Axel Kohlmeyer (Temple U), - Ryan S. Elliott (UMN) - Ellad B. Tadmor (UMN) - Ronald Miller (Carleton U) - Yaser Afshar (UMN) + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN), + Ellad B. Tadmor (UMN), + Ronald Miller (Carleton U), + Yaser Afshar (UMN) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- @@ -200,8 +200,8 @@ void KimInteractions::do_setup(int narg, char **arg) const std::string sim_field_str(sim_field); if (sim_field_str == "model-defn") { - if (first_visit<0) input->one("variable kim_update equal 0"); - else input->one("variable kim_update equal 1"); + if (first_visit < 0) input->one("variable kim_update equal 0"); + else input->one("variable kim_update equal 1"); if (domain->periodicity[0] && domain->periodicity[1] && domain->periodicity[2]) From 4c2fb7a4312501d59ab530a09a5c5054272d53bf Mon Sep 17 00:00:00 2001 From: Nick Curtis Date: Thu, 1 Apr 2021 09:43:13 -0500 Subject: [PATCH 0330/1217] Porting to new default platform for AMD/HIP in ROCm 4.1 --- cmake/Modules/Packages/GPU.cmake | 12 +++++++++--- doc/src/Build_extras.rst | 13 ++++++++++--- lib/gpu/Makefile.hip | 6 +++++- lib/gpu/README | 5 ++--- lib/gpu/lal_pre_cuda_hip.h | 8 ++++---- 5 files changed, 30 insertions(+), 14 deletions(-) diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index 9aa917144b..68d74ea42e 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -218,7 +218,7 @@ elseif(GPU_API STREQUAL "HIP") if(NOT DEFINED HIP_PLATFORM) if(NOT DEFINED ENV{HIP_PLATFORM}) - set(HIP_PLATFORM "hcc" CACHE PATH "HIP Platform to be used during compilation") + set(HIP_PLATFORM "amd" CACHE PATH "HIP Platform to be used during compilation") else() set(HIP_PLATFORM $ENV{HIP_PLATFORM} CACHE PATH "HIP Platform used during compilation") endif() @@ -226,7 +226,7 @@ elseif(GPU_API STREQUAL "HIP") set(ENV{HIP_PLATFORM} ${HIP_PLATFORM}) - if(HIP_PLATFORM STREQUAL "hcc") + if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd") set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture") elseif(HIP_PLATFORM STREQUAL "nvcc") find_package(CUDA REQUIRED) @@ -284,7 +284,7 @@ elseif(GPU_API STREQUAL "HIP") set(CUBIN_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin") set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h") - if(HIP_PLATFORM STREQUAL "hcc") + if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd") configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY) if(HIP_COMPILER STREQUAL "clang") @@ -381,6 +381,12 @@ elseif(GPU_API STREQUAL "HIP") target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__) target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include) + elseif(HIP_PLATFORM STREQUAL "amd") + target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_AMD__) + target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include) + + target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_AMD__) + target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include) endif() target_link_libraries(lammps PRIVATE gpu) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 2081dc4bcd..3af018c656 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -125,7 +125,7 @@ CMake build # default is sm_50 -D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip # value depends on selected HIP_PLATFORM - # default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc + # default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc -D HIP_USE_DEVICE_SORT=value # enables GPU sorting # value = yes (default) or no -D CUDPP_OPT=value # use GPU binning on with CUDA (should be off for modern GPUs) @@ -169,17 +169,24 @@ desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`. If you are compiling with HIP, note that before running CMake you will have to set appropriate environment variables. Some variables such as -:code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc` +:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc` and the linker to work correctly. .. code:: bash - # AMDGPU target + # AMDGPU target (ROCm <= 4.0) export HIP_PLATFORM=hcc export HCC_AMDGPU_TARGET=gfx906 cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc .. make -j 4 +.. code:: bash + + # AMDGPU target (ROCm >= 4.1) + export HIP_PLATFORM=amd + cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc .. + make -j 4 + .. code:: bash # CUDA target (not recommended, use GPU_ARCH=cuda) diff --git a/lib/gpu/Makefile.hip b/lib/gpu/Makefile.hip index dbdef433ec..a736988596 100644 --- a/lib/gpu/Makefile.hip +++ b/lib/gpu/Makefile.hip @@ -1,6 +1,6 @@ # /* ---------------------------------------------------------------------- # Generic Linux Makefile for HIP -# - export HIP_PLATFORM=hcc (or nvcc) before execution +# - export HIP_PLATFORM=amd (or nvcc) before execution # - change HIP_ARCH for your GPU # ------------------------------------------------------------------------- */ @@ -42,6 +42,10 @@ ifeq (hcc,$(HIP_PLATFORM)) HIP_OPTS += -ffast-math # possible values: gfx803,gfx900,gfx906 HIP_ARCH = gfx906 +else ifeq (amd,$(HIP_PLATFORM)) + HIP_OPTS += -ffast-math + # possible values: gfx803,gfx900,gfx906 + HIP_ARCH = gfx906 else ifeq (nvcc,$(HIP_PLATFORM)) HIP_OPTS += --use_fast_math HIP_ARCH = -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_32,code=[sm_32,compute_32] -gencode arch=compute_35,code=[sm_35,compute_35] \ diff --git a/lib/gpu/README b/lib/gpu/README index dfffe11b81..eb22839a59 100644 --- a/lib/gpu/README +++ b/lib/gpu/README @@ -212,8 +212,8 @@ additionally requires cub (https://nvlabs.github.io/cub). Download and extract the cub directory to lammps/lib/gpu/ or specify an appropriate path in lammps/lib/gpu/Makefile.hip. 2. In Makefile.hip it is possible to specify the target platform via -export HIP_PLATFORM=hcc or HIP_PLATFORM=nvcc as well as the target -architecture (gfx803, gfx900, gfx906 etc.) +export HIP_PLATFORM=amd (ROCm >= 4.1), HIP_PLATFORM=hcc (ROCm <= 4.0) +or HIP_PLATFORM=nvcc as well as the target architecture (gfx803, gfx900, gfx906 etc.) 3. If your MPI implementation does not support `mpicxx --showme` command, it is required to specify the corresponding MPI compiler and linker flags in lammps/lib/gpu/Makefile.hip and in lammps/src/MAKE/OPTIONS/Makefile.hip. @@ -278,4 +278,3 @@ and Brown, W.M., Masako, Y. Implementing Molecular Dynamics on Hybrid High Performance Computers - Three-Body Potentials. Computer Physics Communications. 2013. 184: p. 2785–2793. - diff --git a/lib/gpu/lal_pre_cuda_hip.h b/lib/gpu/lal_pre_cuda_hip.h index d37b4a94c2..dfb6229bed 100644 --- a/lib/gpu/lal_pre_cuda_hip.h +++ b/lib/gpu/lal_pre_cuda_hip.h @@ -30,7 +30,7 @@ // ------------------------------------------------------------------------- -#ifdef __HIP_PLATFORM_HCC__ +#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) #define CONFIG_ID 303 #define SIMD_SIZE 64 #else @@ -161,7 +161,7 @@ // KERNEL MACROS - TEXTURES // ------------------------------------------------------------------------- -#ifdef __HIP_PLATFORM_HCC__ +#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) #define _texture(name, type) __device__ type* name #define _texture_2d(name, type) __device__ type* name #else @@ -201,7 +201,7 @@ #define mu_tex mu_ #endif -#ifdef __HIP_PLATFORM_HCC__ +#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) #undef fetch4 #undef fetch @@ -266,7 +266,7 @@ typedef struct _double4 double4; #endif #endif -#if defined(CUDA_PRE_NINE) || defined(__HIP_PLATFORM_HCC__) +#if defined(CUDA_PRE_NINE) || defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) #ifdef _SINGLE_SINGLE #define shfl_down __shfl_down From e7422a6bf73f836db3bd7689a30cbaf8a96174df Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Apr 2021 11:26:54 -0400 Subject: [PATCH 0331/1217] silence compiler warnings --- src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp | 5 ++--- src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp | 5 ++--- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index 556d303d30..ce0090ce5e 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -611,7 +611,7 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype, { double r2inv,r6inv,r,grij,expm2,t,erfc1,prefactor,prefactor2; double fraction,table,forcecoul,forcecoul2,forcelj,phicoul; - double rrij,expn2,erfc2,expb,ecoul,evdwl,trx,tr,ftr; + double rrij,expn2,erfc2,expb,evdwl,trx,tr,ftr; int itable; @@ -657,7 +657,7 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype, prefactor2 = -force->qqrd2e * atom->q[i]*atom->q[j]/r; forcecoul2 = prefactor2 * (erfc2 + EWALD_F*rrij*expn2); forcelj = expb*lj1[itype][jtype]*r-6.0*lj4[itype][jtype]*r6inv; - } else forcelj = 0.0; + } else forcelj = forcecoul2 = 0.0; double eng = 0.0; if (rsq < cut_coulsq) { @@ -672,7 +672,6 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype, } if (rsq < cut_ljsq[itype][jtype]) { - ecoul += prefactor2*erfc2*factor_coul; evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) - offset[itype][jtype]; } else evdwl = 0.0; diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp index 47ddf8c7ad..4416a7c932 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -611,7 +611,7 @@ double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype, { double r2inv,r6inv,r,grij,expm2,t,erfc1,prefactor,prefactor2; double fraction,table,forcecoul,forcecoul2,forcelj,phicoul; - double expb,rrij,expn2,erfc2,ecoul,evdwl,trx,tr,ftr; + double expb,rrij,expn2,erfc2,evdwl,trx,tr,ftr; int itable; @@ -658,7 +658,7 @@ double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype, prefactor2 = -force->qqrd2e * atom->q[i]*atom->q[j]/r; forcecoul2 = prefactor2 * (erfc2 + EWALD_F*rrij*expn2); forcelj = expb*lj1[itype][jtype]*r-6.0*lj4[itype][jtype]*r6inv; - } else forcelj = 0.0; + } else forcelj = forcecoul2 = 0.0; double eng = 0.0; if (rsq < cut_coulsq) { @@ -673,7 +673,6 @@ double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype, } if (rsq < cut_ljsq[itype][jtype]) { - ecoul += prefactor2*erfc2*factor_coul; evdwl = expb-lj4[itype][jtype]*r6inv-offset[itype][jtype]; } else evdwl = 0.0; From 9ac246011e2d15f594bee7aedd61527897ee394a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Apr 2021 11:48:54 -0400 Subject: [PATCH 0332/1217] remove flags and setup for multi-cutoff r-RESPA support which is missing --- .../pair_lj_switch3_coulgauss_long.cpp | 54 +++++-------------- .../pair_mm3_switch3_coulgauss_long.cpp | 50 ++++------------- 2 files changed, 22 insertions(+), 82 deletions(-) diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index ce0090ce5e..f406965e9b 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -17,21 +17,20 @@ #include "pair_lj_switch3_coulgauss_long.h" -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "respa.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -49,7 +48,6 @@ using namespace MathConst; PairLJSwitch3CoulGaussLong::PairLJSwitch3CoulGaussLong(LAMMPS *lmp) : Pair(lmp) { ewaldflag = pppmflag = 1; - respa_enable = 1; writedata = 1; ftable = nullptr; qdist = 0.0; @@ -170,8 +168,8 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag) expn2 = 0.0; erfc2 = 0.0; forcecoul2 = 0.0; - } - else { + prefactor2 = 0.0; + } else { rrij = lj2[itype][jtype]*r; expn2 = exp(-rrij*rrij); erfc2 = erfc(rrij); @@ -333,42 +331,19 @@ void PairLJSwitch3CoulGaussLong::init_style() if (!atom->q_flag) error->all(FLERR,"Pair style lj/switch3/coulgauss/long requires atom attribute q"); - // request regular or rRESPA neighbor list - - int irequest; - int respa = 0; - - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { - if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; - if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; - } - - irequest = neighbor->request(this,instance_me); - - if (respa >= 1) { - neighbor->requests[irequest]->respaouter = 1; - neighbor->requests[irequest]->respainner = 1; - } - if (respa == 2) neighbor->requests[irequest]->respamiddle = 1; - cut_coulsq = cut_coul * cut_coul; - // set rRESPA cutoffs - - if (strstr(update->integrate_style,"respa") && - ((Respa *) update->integrate)->level_inner >= 0) - cut_respa = ((Respa *) update->integrate)->cutoff; - else cut_respa = nullptr; - // insure use of KSpace long-range solver, set g_ewald if (force->kspace == nullptr) error->all(FLERR,"Pair style requires a KSpace style"); g_ewald = force->kspace->g_ewald; + neighbor->request(this,instance_me); + // setup force tables - if (ncoultablebits) init_tables(cut_coul,cut_respa); + if (ncoultablebits) init_tables(cut_coul,nullptr); } /* ---------------------------------------------------------------------- @@ -413,11 +388,6 @@ double PairLJSwitch3CoulGaussLong::init_one(int i, int j) lj4[j][i] = lj4[i][j]; offset[j][i] = offset[i][j]; - // check interior rRESPA cutoff - - if (cut_respa && MIN(cut_lj[i][j],cut_coul) < cut_respa[3]) - error->all(FLERR,"Pair cutoff < Respa interior cutoff"); - // compute I,J contribution to long-range tail correction // count total # of atoms of type I and J via Allreduce diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp index 4416a7c932..64ea669a30 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -17,21 +17,20 @@ #include "pair_mm3_switch3_coulgauss_long.h" -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "respa.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -49,7 +48,6 @@ using namespace MathConst; PairMM3Switch3CoulGaussLong::PairMM3Switch3CoulGaussLong(LAMMPS *lmp) : Pair(lmp) { ewaldflag = pppmflag = 1; - respa_enable = 1; writedata = 1; ftable = nullptr; qdist = 0.0; @@ -335,42 +333,19 @@ void PairMM3Switch3CoulGaussLong::init_style() if (!atom->q_flag) error->all(FLERR,"Pair style mm3/switch3/coulgauss/long requires atom attribute q"); - // request regular or rRESPA neighbor list - - int irequest; - int respa = 0; - - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { - if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; - if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; - } - - irequest = neighbor->request(this,instance_me); - - if (respa >= 1) { - neighbor->requests[irequest]->respaouter = 1; - neighbor->requests[irequest]->respainner = 1; - } - if (respa == 2) neighbor->requests[irequest]->respamiddle = 1; - cut_coulsq = cut_coul * cut_coul; - // set rRESPA cutoffs - - if (strstr(update->integrate_style,"respa") && - ((Respa *) update->integrate)->level_inner >= 0) - cut_respa = ((Respa *) update->integrate)->cutoff; - else cut_respa = nullptr; - // insure use of KSpace long-range solver, set g_ewald if (force->kspace == nullptr) error->all(FLERR,"Pair style requires a KSpace style"); g_ewald = force->kspace->g_ewald; + irequest = neighbor->request(this,instance_me); + // setup force tables - if (ncoultablebits) init_tables(cut_coul,cut_respa); + if (ncoultablebits) init_tables(cut_coul,nullptr); } /* ---------------------------------------------------------------------- @@ -414,11 +389,6 @@ double PairMM3Switch3CoulGaussLong::init_one(int i, int j) lj4[j][i] = lj4[i][j]; offset[j][i] = offset[i][j]; - // check interior rRESPA cutoff - - if (cut_respa && MIN(cut_lj[i][j],cut_coul) < cut_respa[3]) - error->all(FLERR,"Pair cutoff < Respa interior cutoff"); - // compute I,J contribution to long-range tail correction // count total # of atoms of type I and J via Allreduce From b5ef98cc22ea023579351a3c7fc2f1210f1801e3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Apr 2021 12:42:07 -0400 Subject: [PATCH 0333/1217] consolidate the documentation for lj/switch3/coulgauss/long and mm3/switch3/coulgauss/long into a single file --- doc/src/Commands_pair.rst | 2 +- doc/src/Packages_details.rst | 2 +- doc/src/pair_lj_switch3_coulgauss_long.rst | 55 +++++++++- doc/src/pair_mm3_switch3_coulgauss_long.rst | 109 -------------------- doc/src/pair_style.rst | 2 +- 5 files changed, 53 insertions(+), 117 deletions(-) delete mode 100644 doc/src/pair_mm3_switch3_coulgauss_long.rst diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index da403aa87e..080f3eff20 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -187,7 +187,7 @@ OPT. * :doc:`mgpt ` * :doc:`mie/cut (g) ` * :doc:`mliap ` - * :doc:`mm3/switch3/coulgauss/long ` + * :doc:`mm3/switch3/coulgauss/long ` * :doc:`momb ` * :doc:`morse (gkot) ` * :doc:`morse/smooth/linear (o) ` diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index e858593c4c..173c515fc2 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -2456,6 +2456,6 @@ which discuss the `QuickFF `_ methodology. * :doc:`bond_style mm3 ` * :doc:`improper_style distharm ` * :doc:`improper_style sqdistharm ` -* :doc:`pair_style mm3/switch3/coulgauss/long ` +* :doc:`pair_style mm3/switch3/coulgauss/long ` * :doc:`pair_style lj/switch3/coulgauss/long ` * examples/USER/yaff diff --git a/doc/src/pair_lj_switch3_coulgauss_long.rst b/doc/src/pair_lj_switch3_coulgauss_long.rst index f791b9836b..6b918c1071 100644 --- a/doc/src/pair_lj_switch3_coulgauss_long.rst +++ b/doc/src/pair_lj_switch3_coulgauss_long.rst @@ -1,8 +1,12 @@ .. index:: pair_style lj/switch3/coulgauss/long +.. index:: pair_style mm3/switch3/coulgauss/long pair_style lj/switch3/coulgauss/long command ============================================ +pair_style mm3/switch3/coulgauss/long command +============================================= + Syntax """""" @@ -10,7 +14,7 @@ Syntax pair_style style args -* style = *lj/switch3/coulgauss/long* +* style = *lj/switch3/coulgauss/long* or *mm3/switch3/coulgauss/long* * args = list of arguments for a particular style .. parsed-literal:: @@ -20,6 +24,11 @@ Syntax cutoff2 = global cutoff for Coulombic (optional) (distance units) width = width parameter of the smoothing function (distance units) + *mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width + cutoff = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) + width = width parameter of the smoothing function (distance units) + Examples """""""" @@ -31,6 +40,12 @@ Examples pair_style lj/switch3/coulgauss/long 12.0 10.0 3.0 pair_coeff 1 0.2 2.5 1.2 + pair_style mm3/switch3/coulgauss/long 12.0 3.0 + pair_coeff 1 0.2 2.5 1.2 + + pair_style mm3/switch3/coulgauss/long 12.0 10.0 3.0 + pair_coeff 1 0.2 2.5 1.2 + Description """"""""""" @@ -41,8 +56,17 @@ vdW potential E = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12}-\left(\frac{\sigma}{r}\right)^{6} \right] -, which goes smoothly to zero at the cutoff r_c as defined -by the switching function +The *mm3/switch3/coulgauss/long* style evaluates the MM3 +vdW potential :ref:`(Allinger) ` + +.. math:: + + E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\ + r_{v,ij} & = r_{v,i} + r_{v,j} \\ + \epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j} + +Both potentials go smoothly to zero at the cutoff r_c as defined by the +switching function .. math:: @@ -85,14 +109,35 @@ commands: Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" +For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distance for all of the lj/long pair styles can be mixed. +The default mix value is *geometric*\ . See the "pair_modify" command +for details. + Shifting the potential energy is not necessary because the switching function ensures that the potential is zero at the cut-off. +These pair styles support the :doc:`pair_modify ` table and +options since they can tabulate the short-range portion of the +long-range Coulombic interactions. + +Thes pair styles do not support the :doc:`pair_modify ` +tail option for adding a long-range tail correction to the +Lennard-Jones portion of the energy and pressure. + +These pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. + +These pair styles can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. They do not support the +*inner*\ , *middle*\ , *outer* keywords. + Restrictions """""""""""" -These styles are part of the USER-YAFF package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +These styles are part of the USER-YAFF package. They are only enabled +if LAMMPS was built with that package. See the :doc:`Build package +` doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_mm3_switch3_coulgauss_long.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst deleted file mode 100644 index 798df0bf7a..0000000000 --- a/doc/src/pair_mm3_switch3_coulgauss_long.rst +++ /dev/null @@ -1,109 +0,0 @@ -.. index:: pair_style mm3/switch3/coulgauss/long - -pair_style mm3/switch3/coulgauss/long command -============================================= - -Syntax -"""""" - -.. code-block:: LAMMPS - - pair_style style args - -* style = *mm3/switch3/coulgauss/long* -* args = list of arguments for a particular style - -.. parsed-literal:: - - *mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width - cutoff = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - width = width parameter of the smoothing function (distance units) - -Examples -"""""""" - -.. code-block:: LAMMPS - - pair_style mm3/switch3/coulgauss/long 12.0 3.0 - pair_coeff 1 0.2 2.5 1.2 - - pair_style mm3/switch3/coulgauss/long 12.0 10.0 3.0 - pair_coeff 1 0.2 2.5 1.2 - -Description -""""""""""" - -The *mm3/switch3/coulgauss/long* style evaluates the MM3 -vdW potential :ref:`(Allinger) ` - -.. math:: - - E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\ - r_{v,ij} & = r_{v,i} + r_{v,j} \\ - \epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j} - -, which goes smoothly to zero at the cutoff r_c as defined -by the switching function - -.. math:: - - S_3(r) = \left\lbrace \begin{array}{ll} - 1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\ - 3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\ - 0 & \quad\mathrm{if}\quad r >= r_\mathrm{c} - \end{array} \right. - -where w is the width defined in the arguments. This potential -is combined with Coulomb interaction between Gaussian charge densities: - -.. math:: - - E = \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}} - -where :math:`q_i` and :math:`q_j` are the charges on the 2 atoms, -epsilon is the dielectric constant which can be set by the -:doc:`dielectric ` command, ::math:`\gamma_i` and -:math:`\gamma_j` are the widths of the Gaussian charge distribution and -erf() is the error-function. This style has to be used in conjunction -with the :doc:`kspace_style ` command - -If one cutoff is specified it is used for both the vdW and Coulomb -terms. If two cutoffs are specified, the first is used as the cutoff -for the vdW terms, and the second is the cutoff for the Coulombic term. - -The following coefficients must be defined for each pair of atoms -types via the :doc:`pair_coeff ` command as in the examples -above, or in the data file or restart files read by the -:doc:`read_data ` or :doc:`read_restart ` -commands: - -* :math:`\epsilon` (energy) -* :math:`r_v` (distance) -* :math:`\gamma` (distance) - ----------- - -Mixing, shift, table, tail correction, restart, rRESPA info -""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -Mixing rules are fixed for this style as defined above. - -Shifting the potential energy is not necessary because the switching -function ensures that the potential is zero at the cut-off. - -Restrictions -"""""""""""" - -These styles are part of the USER-YAFF package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. - -Related commands -"""""""""""""""" - -:doc:`pair_coeff ` - -Default -""""""" - -none diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index fc66b778a1..89530895c4 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -250,7 +250,7 @@ accelerated styles exist. * :doc:`mgpt ` - simplified model generalized pseudopotential theory (MGPT) potential * :doc:`mesont/tpm ` - nanotubes mesoscopic force field * :doc:`mie/cut ` - Mie potential -* :doc:`mm3/switch3/coulgauss/long ` - smoothed MM3 vdW potential with Gaussian electrostatics +* :doc:`mm3/switch3/coulgauss/long ` - smoothed MM3 vdW potential with Gaussian electrostatics * :doc:`momb ` - Many-Body Metal-Organic (MOMB) force field * :doc:`morse ` - Morse potential * :doc:`morse/smooth/linear ` - linear smoothed Morse potential From 994ee59fd55200b74b80f1738f53b295bf4ee9ad Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Apr 2021 12:42:48 -0400 Subject: [PATCH 0334/1217] correct single() functions for USER-YAFF pair styles to be consistent with compute() --- .../pair_lj_switch3_coulgauss_long.cpp | 37 ++++++++------- .../pair_mm3_switch3_coulgauss_long.cpp | 46 ++++++++++--------- 2 files changed, 42 insertions(+), 41 deletions(-) diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index f406965e9b..c6bc65c196 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -580,8 +580,8 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype, double &fforce) { double r2inv,r6inv,r,grij,expm2,t,erfc1,prefactor,prefactor2; - double fraction,table,forcecoul,forcecoul2,forcelj,phicoul; - double rrij,expn2,erfc2,expb,evdwl,trx,tr,ftr; + double fraction,table,forcecoul,forcecoul2,forcelj; + double rrij,expn2,erfc2,expb,ecoul,evdwl,trx,tr,ftr; int itable; @@ -613,41 +613,41 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype, } else forcecoul = 0.0; if (rsq < cut_ljsq[itype][jtype]) { - r = sqrt(rsq); r6inv = r2inv*r2inv*r2inv; - rrij = lj2[itype][jtype] * r; - if (rrij==0.0) { + forcelj = r6inv*(12.0*lj3[itype][jtype]*r6inv-6.0*lj4[itype][jtype]); + if (lj2[itype][jtype] == 0.0) { expn2 = 0.0; erfc2 = 0.0; - } - else { + forcecoul2 = 0.0; + } else { + r = sqrt(rsq); + rrij = lj2[itype][jtype]*r; expn2 = exp(-rrij*rrij); erfc2 = erfc(rrij); + prefactor2 = -force->qqrd2e*atom->q[i]*atom->q[j]/r; + forcecoul2 = prefactor2*(erfc2+EWALD_F*rrij*expn2); } - prefactor2 = -force->qqrd2e * atom->q[i]*atom->q[j]/r; - forcecoul2 = prefactor2 * (erfc2 + EWALD_F*rrij*expn2); - forcelj = expb*lj1[itype][jtype]*r-6.0*lj4[itype][jtype]*r6inv; - } else forcelj = forcecoul2 = 0.0; + } else forcelj = 0.0; - double eng = 0.0; + evdwl = ecoul = 0.0; if (rsq < cut_coulsq) { if (!ncoultablebits || rsq <= tabinnersq) - phicoul = prefactor*erfc1; + ecoul = prefactor*erfc1; else { table = etable[itable] + fraction*detable[itable]; - phicoul = atom->q[i]*atom->q[j] * table; + ecoul = atom->q[i]*atom->q[j] * table; } - if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor; - eng += phicoul; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; } if (rsq < cut_ljsq[itype][jtype]) { + ecoul += prefactor2*erfc2*factor_coul; evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) - offset[itype][jtype]; } else evdwl = 0.0; // Truncation, see Yaff Switch3 - if (truncw>0) { + if (truncw > 0) { if (rsq < cut_ljsq[itype][jtype]) { if (r>cut_lj[itype][jtype]-truncw) { trx = (cut_lj[itype][jtype]-r)*truncwi; @@ -658,10 +658,9 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype, } } } - eng += evdwl*factor_lj; fforce = (forcecoul + factor_coul*forcecoul2 + factor_lj*forcelj) * r2inv; - return eng; + return evdwl*factor_lj + ecoul; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp index 64ea669a30..e91ea5c695 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -171,8 +171,7 @@ void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag) expn2 = 0.0; erfc2 = 0.0; forcecoul2 = 0.0; - } - else { + } else { rrij = lj2[itype][jtype]*r; expn2 = exp(-rrij*rrij); erfc2 = erfc(rrij); @@ -341,7 +340,7 @@ void PairMM3Switch3CoulGaussLong::init_style() error->all(FLERR,"Pair style requires a KSpace style"); g_ewald = force->kspace->g_ewald; - irequest = neighbor->request(this,instance_me); + neighbor->request(this,instance_me); // setup force tables @@ -580,8 +579,8 @@ double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype, double &fforce) { double r2inv,r6inv,r,grij,expm2,t,erfc1,prefactor,prefactor2; - double fraction,table,forcecoul,forcecoul2,forcelj,phicoul; - double expb,rrij,expn2,erfc2,evdwl,trx,tr,ftr; + double fraction,table,forcecoul,forcecoul2,forcelj; + double expb,rrij,expn2,erfc2,evdwl,ecoul,trx,tr,ftr; int itable; @@ -614,40 +613,43 @@ double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype, if (rsq < cut_ljsq[itype][jtype]) { r = sqrt(rsq); - r6inv = r2inv*r2inv*r2inv; expb = lj3[itype][jtype]*exp(-lj1[itype][jtype]*r); - rrij = lj2[itype][jtype] * r; - if (rrij==0.0) { + forcelj = expb*lj1[itype][jtype]*r; + r6inv = r2inv*r2inv*r2inv; + forcelj -= 6.0*lj4[itype][jtype]*r6inv; + + if (lj2[itype][jtype] == 0.0) { expn2 = 0.0; erfc2 = 0.0; - } - else { + forcecoul2 = 0.0; + prefactor2 = 0.0; + } else { + rrij = lj2[itype][jtype]*r; expn2 = exp(-rrij*rrij); erfc2 = erfc(rrij); + prefactor2 = -force->qqrd2e * atom->q[i]*atom->q[j]/r; + forcecoul2 = prefactor2 * (erfc2 + EWALD_F*rrij*expn2); } - prefactor2 = -force->qqrd2e * atom->q[i]*atom->q[j]/r; - forcecoul2 = prefactor2 * (erfc2 + EWALD_F*rrij*expn2); - forcelj = expb*lj1[itype][jtype]*r-6.0*lj4[itype][jtype]*r6inv; - } else forcelj = forcecoul2 = 0.0; + } else expb = forcelj = 0.0; - double eng = 0.0; + evdwl = ecoul = 0.0; if (rsq < cut_coulsq) { if (!ncoultablebits || rsq <= tabinnersq) - phicoul = prefactor*erfc1; + ecoul = prefactor*erfc1; else { table = etable[itable] + fraction*detable[itable]; - phicoul = atom->q[i]*atom->q[j] * table; + ecoul = atom->q[i]*atom->q[j] * table; } - if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor; - eng += phicoul; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; } if (rsq < cut_ljsq[itype][jtype]) { + ecoul += prefactor2*erfc2*factor_coul; evdwl = expb-lj4[itype][jtype]*r6inv-offset[itype][jtype]; } else evdwl = 0.0; // Truncation, see Yaff Switch3 - if (truncw>0) { + if (truncw > 0) { if (rsq < cut_ljsq[itype][jtype]) { if (r>cut_lj[itype][jtype]-truncw) { trx = (cut_lj[itype][jtype]-r)*truncwi; @@ -658,10 +660,10 @@ double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype, } } } - eng += evdwl*factor_lj; fforce = (forcecoul + factor_coul*forcecoul2 + factor_lj*forcelj) * r2inv; - return eng; + return ecoul + evdwl*factor_lj; +; } /* ---------------------------------------------------------------------- */ From c3eb52f46ab37f77748c35620e1052130ab96b2e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Apr 2021 12:43:24 -0400 Subject: [PATCH 0335/1217] add force tests for USER-YAFF pair styles --- .../mol-pair-lj_switch3_coulgauss_long.yaml | 99 +++++++++++++++++++ .../mol-pair-lj_switch3_coulgauss_table.yaml | 99 +++++++++++++++++++ .../mol-pair-mm3_switch3_coulgauss_long.yaml | 99 +++++++++++++++++++ .../mol-pair-mm3_switch3_coulgauss_table.yaml | 99 +++++++++++++++++++ 4 files changed, 396 insertions(+) create mode 100644 unittest/force-styles/tests/mol-pair-lj_switch3_coulgauss_long.yaml create mode 100644 unittest/force-styles/tests/mol-pair-lj_switch3_coulgauss_table.yaml create mode 100644 unittest/force-styles/tests/mol-pair-mm3_switch3_coulgauss_long.yaml create mode 100644 unittest/force-styles/tests/mol-pair-mm3_switch3_coulgauss_table.yaml diff --git a/unittest/force-styles/tests/mol-pair-lj_switch3_coulgauss_long.yaml b/unittest/force-styles/tests/mol-pair-lj_switch3_coulgauss_long.yaml new file mode 100644 index 0000000000..e14044f9a0 --- /dev/null +++ b/unittest/force-styles/tests/mol-pair-lj_switch3_coulgauss_long.yaml @@ -0,0 +1,99 @@ +--- +lammps_version: 10 Mar 2021 +date_generated: Thu Apr 1 12:05:31 202 +epsilon: 7.5e-14 +prerequisites: ! | + atom full + pair lj/switch3/coulgauss/long + kspace ewald +pre_commands: ! "" +post_commands: ! | + pair_modify mix arithmetic + pair_modify table 0 + kspace_style ewald 1.0e-6 + kspace_modify gewald 0.3 + kspace_modify compute no +input_file: in.fourmol +pair_style: lj/switch3/coulgauss/long 8.0 2.0 +pair_coeff: ! | + 1 1 0.02 2.5 1.0 + 2 2 0.005 1.0 0.7 + 2 4 0.005 0.5 0.7 + 3 3 0.02 3.2 1.3 + 4 4 0.015 3.1 1.2 + 5 5 0.015 3.1 1.2 +extract: ! | + epsilon 2 + sigma 2 + gamma 2 + cut_coul 0 +natoms: 29 +init_vdwl: 749.239201392283 +init_coul: 262.63137433058 +init_stress: ! |2- + 2.1905445805730942e+03 2.1830788072793757e+03 4.6581902800701146e+03 -7.4288115309776367e+02 2.6990012828168151e+01 6.7591505796334252e+02 +init_forces: ! |2 + 1 -2.2440985285095003e+01 2.6839510386427128e+02 3.3548778459373403e+02 + 2 1.6014525975608947e+02 1.2916401608538342e+02 -1.9007855889522560e+02 + 3 -1.3523588460187835e+02 -3.8701969631758487e+02 -1.4563951593124975e+02 + 4 -8.1626375608064503e+00 2.0129840978934559e+00 -5.9838237090267477e+00 + 5 -3.2509810426586694e+00 -3.8006496952690405e+00 1.2238094761779506e+01 + 6 -8.3272100467340556e+02 9.6240884847023358e+02 1.1512799880160530e+03 + 7 5.9109223946129624e+01 -3.3613343492781996e+02 -1.7166010182633938e+03 + 8 1.4374025374023395e+02 -1.0687979059788748e+02 3.9897084761513247e+02 + 9 8.0822098286061347e+01 8.1693084015402164e+01 3.5446319638063176e+02 + 10 5.3122611725677234e+02 -6.1057993090036803e+02 -1.8379536842135653e+02 + 11 -3.0599394771020791e+00 -5.2185583295434022e+00 -1.0179624348800495e+01 + 12 1.9237456341967800e+01 1.0181865500248987e+01 -6.1597937746835436e+00 + 13 8.3909903723672699e+00 -3.3718280449484173e+00 -3.3038121588715319e-01 + 14 -4.1292661630995928e+00 9.9336707464018092e-01 -9.3350058002796388e+00 + 15 4.2168785095757555e-01 8.7977955328786113e+00 2.0699990715180956e+00 + 16 4.6411046171725997e+02 -3.3264571918035432e+02 -1.1912223271773271e+03 + 17 -4.5697820722395699e+02 3.2194358869766086e+02 1.2030903913181610e+03 + 18 -2.9720972086277636e-01 1.7565528490258597e+00 2.4294604263813859e+00 + 19 -2.6658339749427125e+00 -3.5543359860963246e+00 -7.0028176604540848e-01 + 20 2.3030703223874878e+00 1.6788085961460804e+00 8.8715814688464914e-02 + 21 -7.2491063430524989e+01 -8.0704358691908013e+01 2.2713112476019884e+02 + 22 -1.1047017798074540e+02 -2.7622195109041627e+01 -1.7106972908159221e+02 + 23 1.8254515612066885e+02 1.0874225091685935e+02 -5.5558584096022528e+01 + 24 3.7139490938880684e+01 -2.1182968679989389e+02 1.1239472278345924e+02 + 25 -1.5173442669154963e+02 2.2482896227152501e+01 -1.2683235954885029e+02 + 26 1.1404997762743471e+02 1.8910942097520967e+02 1.3865307057956501e+01 + 27 5.1263700969024825e+01 -2.2708329767472884e+02 9.0733209359745530e+01 + 28 -1.8280634435959598e+02 7.6676771027308675e+01 -1.2320543486529729e+02 + 29 1.3193901693998819e+02 1.5040612832512986e+02 3.2448964935598738e+01 +run_vdwl: 719.395943067584 +run_coul: 262.577357625246 +run_stress: ! |2- + 2.1439469903049130e+03 2.1388099416476502e+03 4.3901771762143671e+03 -7.2215136136852652e+02 4.3981220891989977e+01 6.3726346095247902e+02 +run_forces: ! |2 + 1 -1.9342111296614632e+01 2.6536048036936916e+02 3.2628113020689460e+02 + 2 1.5478381002242270e+02 1.2483653341336152e+02 -1.8332859341112297e+02 + 3 -1.3348486669886435e+02 -3.7921582819403795e+02 -1.4287155661999228e+02 + 4 -8.1288301070929982e+00 2.0080316198654273e+00 -5.9722562656827858e+00 + 5 -3.2351829753164845e+00 -3.7719427860922665e+00 1.2190138978995325e+01 + 6 -8.0768848311420356e+02 9.2016491680294996e+02 1.0274658369925041e+03 + 7 5.6698550383493917e+01 -3.1122940570534678e+02 -1.5733988978986536e+03 + 8 1.3387241605110836e+02 -9.8275697925936129e+01 3.8773060932891792e+02 + 9 7.8389121495727082e+01 7.8858365413426057e+01 3.4347185476758511e+02 + 10 5.2128680605857573e+02 -5.9933944295277558e+02 -1.8148565911030960e+02 + 11 -3.0663895518130402e+00 -5.1690166614639725e+00 -1.0127704831021171e+01 + 12 1.9218490979542565e+01 1.0175625089829989e+01 -6.2912885237383334e+00 + 13 8.3443094714464650e+00 -3.3361880724739623e+00 -3.2980152351128239e-01 + 14 -4.0925411684752673e+00 9.7261482089301243e-01 -9.2160488176079518e+00 + 15 4.0396689631175081e-01 8.8125643989717197e+00 2.0895512608739368e+00 + 16 4.3558458306026108e+02 -3.1347365130054965e+02 -1.1153604445579856e+03 + 17 -4.2831293616595980e+02 3.0256033131579363e+02 1.1274168049543377e+03 + 18 -3.0240289244505925e-01 1.7692205043557692e+00 2.4421829464376694e+00 + 19 -2.6549690010635465e+00 -3.5598277436632562e+00 -6.9536112330149602e-01 + 20 2.2933819335528716e+00 1.6713255394851048e+00 7.9301163390346582e-02 + 21 -7.1399138479900728e+01 -7.8808617837125738e+01 2.2288288096726535e+02 + 22 -1.0872540509179575e+02 -2.7364445523270156e+01 -1.6789056923341974e+02 + 23 1.7970587875020576e+02 1.0659054948727307e+02 -5.4485902397030543e+01 + 24 3.8719492068991073e+01 -2.1018768384060851e+02 1.1276643199107306e+02 + 25 -1.5234502496218383e+02 2.2328379592897981e+01 -1.2741458364942766e+02 + 26 1.1307896673604499e+02 1.8762340967163530e+02 1.4075792400442774e+01 + 27 5.0253213702344411e+01 -2.2292638222448988e+02 8.8474597952361989e+01 + 28 -1.7928804250876811e+02 7.5155358290636585e+01 -1.2061205300179266e+02 + 29 1.2943333640446872e+02 1.4777042443708973e+02 3.2113607053518280e+01 +... diff --git a/unittest/force-styles/tests/mol-pair-lj_switch3_coulgauss_table.yaml b/unittest/force-styles/tests/mol-pair-lj_switch3_coulgauss_table.yaml new file mode 100644 index 0000000000..973ed7051e --- /dev/null +++ b/unittest/force-styles/tests/mol-pair-lj_switch3_coulgauss_table.yaml @@ -0,0 +1,99 @@ +--- +lammps_version: 10 Mar 2021 +date_generated: Thu Apr 1 12:05:32 202 +epsilon: 5e-13 +prerequisites: ! | + atom full + pair lj/switch3/coulgauss/long + kspace ewald +pre_commands: ! "" +post_commands: ! | + pair_modify mix arithmetic + pair_modify table 16 + kspace_style ewald 1.0e-6 + kspace_modify gewald 0.3 + kspace_modify compute no +input_file: in.fourmol +pair_style: lj/switch3/coulgauss/long 8.0 2.0 +pair_coeff: ! | + 1 1 0.02 2.5 1.0 + 2 2 0.005 1.0 0.7 + 2 4 0.005 0.5 0.7 + 3 3 0.02 3.2 1.3 + 4 4 0.015 3.1 1.2 + 5 5 0.015 3.1 1.2 +extract: ! | + epsilon 2 + sigma 2 + gamma 2 + cut_coul 0 +natoms: 29 +init_vdwl: 749.239201392283 +init_coul: 262.631410551483 +init_stress: ! |2- + 2.1905446008358158e+03 2.1830788130354440e+03 4.6581902934947393e+03 -7.4288114980317005e+02 2.6990022323315568e+01 6.7591506205400140e+02 +init_forces: ! |2 + 1 -2.2440986789065228e+01 2.6839510344190973e+02 3.3548778280211798e+02 + 2 1.6014525925595575e+02 1.2916401535280644e+02 -1.9007855755707530e+02 + 3 -1.3523588449321372e+02 -3.8701969643290909e+02 -1.4563951605577458e+02 + 4 -8.1626375642225835e+00 2.0129845605828729e+00 -5.9838235187927911e+00 + 5 -3.2509808748500135e+00 -3.8006487477814463e+00 1.2238094996907998e+01 + 6 -8.3272100512926681e+02 9.6240884941333036e+02 1.1512799862203640e+03 + 7 5.9109223148516158e+01 -3.3613343497406407e+02 -1.7166010203250210e+03 + 8 1.4374025301066052e+02 -1.0687979086260394e+02 3.9897084965667705e+02 + 9 8.0822100084645626e+01 8.1693083424499093e+01 3.5446319827945621e+02 + 10 5.3122611737361080e+02 -6.1057993046376589e+02 -1.8379536902952145e+02 + 11 -3.0599395914956227e+00 -5.2185576282473036e+00 -1.0179624244755713e+01 + 12 1.9237456510724858e+01 1.0181865558167726e+01 -6.1597946782797850e+00 + 13 8.3909904522091470e+00 -3.3718281778746344e+00 -3.3038108557256562e-01 + 14 -4.1292663075103953e+00 9.9336695410995779e-01 -9.3350056582436061e+00 + 15 4.2168780003223016e-01 8.7977952410479840e+00 2.0699996667940117e+00 + 16 4.6411046291217519e+02 -3.3264572037764498e+02 -1.1912223268528312e+03 + 17 -4.5697820745668372e+02 3.2194358895792664e+02 1.2030903912557251e+03 + 18 -2.9720916995537250e-01 1.7565528041526848e+00 2.4294595600637425e+00 + 19 -2.6658359770891962e+00 -3.5543374045750902e+00 -7.0028189781643846e-01 + 20 2.3030721439983917e+00 1.6788097920639553e+00 8.8716903513438167e-02 + 21 -7.2491063802446362e+01 -8.0704358127081790e+01 2.2713112533044830e+02 + 22 -1.1047018068190837e+02 -2.7622196765220032e+01 -1.7106973071745716e+02 + 23 1.8254515931328083e+02 1.0874225209184637e+02 -5.5558583211276250e+01 + 24 3.7139491235265282e+01 -2.1182968640787311e+02 1.1239472233677957e+02 + 25 -1.5173442866720330e+02 2.2482894929853938e+01 -1.2683236039424271e+02 + 26 1.1404997991795076e+02 1.8910942242955088e+02 1.3865308691923977e+01 + 27 5.1263700853661504e+01 -2.2708329750901160e+02 9.0733209165823396e+01 + 28 -1.8280634707113845e+02 7.6676770092406045e+01 -1.2320543608135794e+02 + 29 1.3193901956336219e+02 1.5040612883439849e+02 3.2448966441423750e+01 +run_vdwl: 719.3959430344 +run_coul: 262.577390407319 +run_stress: ! |2- + 2.1439470065972137e+03 2.1388099427650550e+03 4.3901771876285757e+03 -7.2215135528838152e+02 4.3981227731157169e+01 6.3726346514781233e+02 +run_forces: ! |2 + 1 -1.9342112777764044e+01 2.6536047986408227e+02 3.2628112882188066e+02 + 2 1.5478380987853197e+02 1.2483653254176838e+02 -1.8332859191802055e+02 + 3 -1.3348486656752218e+02 -3.7921582829992821e+02 -1.4287155674732023e+02 + 4 -8.1288300595478145e+00 2.0080320707984289e+00 -5.9722560784187575e+00 + 5 -3.2351826602132863e+00 -3.7719418655198664e+00 1.2190139134122882e+01 + 6 -8.0768848338103430e+02 9.2016491733383600e+02 1.0274658351618857e+03 + 7 5.6698550307468736e+01 -3.1122940556308856e+02 -1.5733989002062301e+03 + 8 1.3387241574644310e+02 -9.8275698627583083e+01 3.8773061254696188e+02 + 9 7.8389123166777367e+01 7.8858364582844956e+01 3.4347185682031875e+02 + 10 5.2128680625044581e+02 -5.9933944258147972e+02 -1.8148565985727146e+02 + 11 -3.0663897393660062e+00 -5.1690158790311020e+00 -1.0127704822035417e+01 + 12 1.9218491178640956e+01 1.0175625315025894e+01 -6.2912900026938683e+00 + 13 8.3443096072761875e+00 -3.3361882591914980e+00 -3.2980142478029900e-01 + 14 -4.0925412507338894e+00 9.7261457606495283e-01 -9.2160486509597419e+00 + 15 4.0396659601733209e-01 8.8125640821770475e+00 2.0895518255992327e+00 + 16 4.3558458334132916e+02 -3.1347365174745744e+02 -1.1153604446371062e+03 + 17 -4.2831293628122177e+02 3.0256033223226825e+02 1.1274168046352991e+03 + 18 -3.0240272912362937e-01 1.7692204105371876e+00 2.4421821828695935e+00 + 19 -2.6549708608109603e+00 -3.5598291696654596e+00 -6.9536106786938656e-01 + 20 2.2933837220124476e+00 1.6713266856927325e+00 7.9302040608548133e-02 + 21 -7.1399139014949796e+01 -7.8808617040884513e+01 2.2288288163778361e+02 + 22 -1.0872540740988465e+02 -2.7364447046562592e+01 -1.6789057060588300e+02 + 23 1.7970588157677136e+02 1.0659055047797085e+02 -5.4485901626092641e+01 + 24 3.8719492028250940e+01 -2.1018768371930031e+02 1.1276643093423978e+02 + 25 -1.5234502685835807e+02 2.2328378412375191e+01 -1.2741458439419397e+02 + 26 1.1307896905891306e+02 1.8762341114219453e+02 1.4075794088855011e+01 + 27 5.0253213439313768e+01 -2.2292638208302930e+02 8.8474597770747309e+01 + 28 -1.7928804514846018e+02 7.5155357340410589e+01 -1.2061205423392185e+02 + 29 1.2943333884079848e+02 1.4777042481467481e+02 3.2113608671625300e+01 +... diff --git a/unittest/force-styles/tests/mol-pair-mm3_switch3_coulgauss_long.yaml b/unittest/force-styles/tests/mol-pair-mm3_switch3_coulgauss_long.yaml new file mode 100644 index 0000000000..d74aba7143 --- /dev/null +++ b/unittest/force-styles/tests/mol-pair-mm3_switch3_coulgauss_long.yaml @@ -0,0 +1,99 @@ +--- +lammps_version: 10 Mar 2021 +date_generated: Thu Apr 1 12:40:49 202 +epsilon: 7.5e-14 +prerequisites: ! | + atom full + pair mm3/switch3/coulgauss/long + kspace ewald +pre_commands: ! "" +post_commands: ! | + pair_modify mix arithmetic + pair_modify table 0 + kspace_style ewald 1.0e-6 + kspace_modify gewald 0.3 + kspace_modify compute no +input_file: in.fourmol +pair_style: mm3/switch3/coulgauss/long 8.0 2.0 +pair_coeff: ! | + 1 1 0.02 2.5 1.0 + 2 2 0.005 1.0 0.7 + 2 4 0.005 0.5 0.7 + 3 3 0.02 3.2 1.3 + 4 4 0.015 3.1 1.2 + 5 5 0.015 3.1 1.2 +extract: ! | + epsilon 2 + sigma 2 + gamma 2 + cut_coul 0 +natoms: 29 +init_vdwl: 38.1287498820824 +init_coul: 262.63137433058 +init_stress: ! |- + -9.1891442318066098e+01 -1.3287972066289731e+02 -3.2601698046780012e+02 3.0074181349476991e+01 -4.6650805915669622e+00 -8.2199038214680613e+01 +init_forces: ! |2 + 1 2.0409906927303840e+00 -1.8543276343677643e+01 -3.5869856577020748e+01 + 2 -1.8468129335667530e+01 -1.7027855689261912e+01 2.0713359151753043e+01 + 3 1.0001881298085964e+01 5.9235891506906007e+01 2.4372336208613245e+01 + 4 -4.5761624241138597e+00 -9.8945397153998949e-01 -3.3785801701857485e+00 + 5 -3.6934402656902114e+00 -4.0696606560869748e+00 3.8826787260480975e+00 + 6 7.6754814037515942e+01 -9.5808744511121716e+01 -9.3227045949147495e+01 + 7 -2.1177649780159676e+01 2.8793163914062454e+01 1.2529350681895039e+02 + 8 -2.1450096176689623e+01 1.0356391751725083e+01 -2.8955420955058667e+01 + 9 -8.2497939748793154e+00 -1.3077027567751550e+01 -3.6173491871315754e+01 + 10 -5.3511691146997535e+01 6.0900974965221437e+01 1.8391821307129032e+01 + 11 -1.3170240621133327e+00 -3.2364695484525727e+00 -4.4029422841407655e+00 + 12 2.5797191091185894e+01 -7.5496414014335278e-01 -2.6346161145571760e+00 + 13 3.3781782842360095e+00 -7.7635850626588521e-01 -6.1835215466770443e-01 + 14 -2.5357285341105120e-02 9.3547318559063564e-01 -4.9468893910982210e+00 + 15 4.2707742121454375e+00 4.7941154645598454e+00 -1.2015244265327498e+00 + 16 -3.6573746563916743e+01 1.8565541369425805e+01 1.1446966549457964e+02 + 17 4.3913383545862132e+01 -3.3849656320211224e+01 -9.5337593733730870e+01 + 18 2.6570097579579910e+00 6.2826343323709564e+00 -1.0356872257658154e+00 + 19 -2.6993382209993975e+00 -3.5969189205658059e+00 -6.8072388138355555e-01 + 20 2.3243788182239480e+00 1.6918048474772680e+00 1.0886178998340870e-01 + 21 8.8572294982176594e+00 1.1602893199785523e+01 -3.0057630309158139e+01 + 22 1.2429506519553414e+01 2.1605554971279792e+00 2.1808499086967526e+01 + 23 -2.1432721217228789e+01 -1.3678275101206289e+01 8.4081109687741140e+00 + 24 -3.9016922943010681e+00 2.9074424568745080e+01 -1.3996421656066522e+01 + 25 1.7462841196067998e+01 -4.6818042132561875e+00 1.5548837958928004e+01 + 26 -1.2984517260341663e+01 -2.4211628682033979e+01 -4.8885242451183231e-01 + 27 -7.1989693245110757e+00 3.0862600015720503e+01 -1.2113492397573609e+01 + 28 2.1728885747832702e+01 -1.1241487657358419e+01 1.5185683466068600e+01 + 29 -1.4356735366664552e+01 -1.9712882789785066e+01 -3.0642394558798047e+00 +run_vdwl: 37.7351028273436 +run_coul: 262.634961661768 +run_stress: ! |- + -9.3272108018189712e+01 -1.3382217126586661e+02 -3.2672293936615591e+02 2.9759545957029179e+01 -4.9209094100413031e+00 -8.2642487904188499e+01 +run_forces: ! |2 + 1 2.0020649788635687e+00 -1.8597539511786593e+01 -3.5898845980394640e+01 + 2 -1.8527112215088330e+01 -1.7111766426267462e+01 2.0691354848190322e+01 + 3 1.0099460867786970e+01 5.9365750003142132e+01 2.4423492212473526e+01 + 4 -4.5756546931309785e+00 -9.8171265309239830e-01 -3.3833947541955820e+00 + 5 -3.6935770918861186e+00 -4.0701905608402482e+00 3.8892344342573999e+00 + 6 7.6571694717448139e+01 -9.5745009991872053e+01 -9.3149401161723290e+01 + 7 -2.1146519945476555e+01 2.8805358955193604e+01 1.2508940744689353e+02 + 8 -2.1038405837727929e+01 9.9856756739362105e+00 -2.8916679506818486e+01 + 9 -8.2725059756602182e+00 -1.3032514603603040e+01 -3.6169609418536254e+01 + 10 -5.3760826931047106e+01 6.1170224214358463e+01 1.8495907821099792e+01 + 11 -1.3253792323264064e+00 -3.2541587509559888e+00 -4.4355038136226383e+00 + 12 2.5785718250683153e+01 -7.4878886859791716e-01 -2.6134474044331246e+00 + 13 3.3829109925579108e+00 -7.7854283145617098e-01 -6.1471416338880658e-01 + 14 -4.1269999117458912e-02 9.3253553809356449e-01 -4.9663548861610076e+00 + 15 4.2930245502032669e+00 4.8016878244809185e+00 -1.2067988554549580e+00 + 16 -3.6783956118288792e+01 1.8760442771705005e+01 1.1514035612976591e+02 + 17 4.4141165055486525e+01 -3.4054760176447999e+01 -9.5996384977569576e+01 + 18 2.6593312590300169e+00 6.2866044197349034e+00 -1.0406390620860617e+00 + 19 -2.6868912576483734e+00 -3.5919428389901107e+00 -6.7199629496476021e-01 + 20 2.3122559534773646e+00 1.6848231900639974e+00 1.0223174367536356e-01 + 21 9.0047861017105912e+00 1.1657532054221129e+01 -3.0300252008113389e+01 + 22 1.2602723597354565e+01 2.2333302149108087e+00 2.1993415039821400e+01 + 23 -2.1752703090839589e+01 -1.3807398281546009e+01 8.4647717981317978e+00 + 24 -4.1597044706741348e+00 2.9600068810024190e+01 -1.4377966609809059e+01 + 25 1.8008123772533907e+01 -4.7255601865067156e+00 1.6011744232774660e+01 + 26 -1.3270414090792938e+01 -2.4692000422804888e+01 -5.6774111520305048e-01 + 27 -7.3472295182173077e+00 3.1133794558171346e+01 -1.2191686027733443e+01 + 28 2.2002916813161221e+01 -1.1345147346836630e+01 1.5336216642368582e+01 + 29 -1.4484026442375008e+01 -1.9880794776432037e+01 -3.1367163092441239e+00 +... diff --git a/unittest/force-styles/tests/mol-pair-mm3_switch3_coulgauss_table.yaml b/unittest/force-styles/tests/mol-pair-mm3_switch3_coulgauss_table.yaml new file mode 100644 index 0000000000..e1b11baa5d --- /dev/null +++ b/unittest/force-styles/tests/mol-pair-mm3_switch3_coulgauss_table.yaml @@ -0,0 +1,99 @@ +--- +lammps_version: 10 Mar 2021 +date_generated: Thu Apr 1 12:40:49 202 +epsilon: 5e-13 +prerequisites: ! | + atom full + pair mm3/switch3/coulgauss/long + kspace ewald +pre_commands: ! "" +post_commands: ! | + pair_modify mix arithmetic + pair_modify table 16 + kspace_style ewald 1.0e-6 + kspace_modify gewald 0.3 + kspace_modify compute no +input_file: in.fourmol +pair_style: mm3/switch3/coulgauss/long 8.0 2.0 +pair_coeff: ! | + 1 1 0.02 2.5 1.0 + 2 2 0.005 1.0 0.7 + 2 4 0.005 0.5 0.7 + 3 3 0.02 3.2 1.3 + 4 4 0.015 3.1 1.2 + 5 5 0.015 3.1 1.2 +extract: ! | + epsilon 2 + sigma 2 + gamma 2 + cut_coul 0 +natoms: 29 +init_vdwl: 38.1287498820824 +init_coul: 262.631410551483 +init_stress: ! |- + -9.1891422055344222e+01 -1.3287971490682878e+02 -3.2601696704317601e+02 3.0074184644070325e+01 -4.6650710964193243e+00 -8.2199034124021594e+01 +init_forces: ! |2 + 1 2.0409891887601410e+00 -1.8543276766039128e+01 -3.5869858368636784e+01 + 2 -1.8468129835801221e+01 -1.7027856421838862e+01 2.0713360489903284e+01 + 3 1.0001881406750512e+01 5.9235891391581845e+01 2.4372336084088403e+01 + 4 -4.5761624275299884e+00 -9.8945350885057237e-01 -3.3785799799517919e+00 + 5 -3.6934400978815565e+00 -4.0696597085993824e+00 3.8826789611765924e+00 + 6 7.6754813581654659e+01 -9.5808743568025008e+01 -9.3227047744836440e+01 + 7 -2.1177650577773125e+01 2.8793163867818368e+01 1.2529350475732382e+02 + 8 -2.1450096906263081e+01 1.0356391487008732e+01 -2.8955418913514073e+01 + 9 -8.2497921762950064e+00 -1.3077028158654645e+01 -3.6173489972491325e+01 + 10 -5.3511691030159355e+01 6.0900975401823587e+01 1.8391820698964121e+01 + 11 -1.3170241765068751e+00 -3.2364688471564778e+00 -4.4029421800959856e+00 + 12 2.5797191259942942e+01 -7.5496408222462352e-01 -2.6346170181534139e+00 + 13 3.3781783640778875e+00 -7.7635863919210357e-01 -6.1835202435311720e-01 + 14 -2.5357429751907436e-02 9.3547306506041328e-01 -4.9468892490621892e+00 + 15 4.2707741612200945e+00 4.7941151727292111e+00 -1.2015238312568339e+00 + 16 -3.6573745369001358e+01 1.8565540172135101e+01 1.1446966581907569e+02 + 17 4.3913383313135455e+01 -3.3849656059945403e+01 -9.5337593796166914e+01 + 18 2.6570103088653938e+00 6.2826342874977836e+00 -1.0356880920834588e+00 + 19 -2.6993402231458812e+00 -3.5969203390445723e+00 -6.8072401315458542e-01 + 20 2.3243806398348510e+00 1.6918060433951427e+00 1.0886287880838207e-01 + 21 8.8572291262962786e+00 1.1602893764611768e+01 -3.0057629738908702e+01 + 22 1.2429503818390431e+01 2.1605538409495715e+00 2.1808497451102578e+01 + 23 -2.1432718024616804e+01 -1.3678273926219282e+01 8.4081118535203938e+00 + 24 -3.9016919979164766e+00 2.9074424960765882e+01 -1.3996422102746218e+01 + 25 1.7462839220414320e+01 -4.6818055105547502e+00 1.5548837113535589e+01 + 26 -1.2984514969825625e+01 -2.4211627227692777e+01 -4.8885079054435532e-01 + 27 -7.1989694398744213e+00 3.0862600181437756e+01 -1.2113492591495778e+01 + 28 2.1728883036290242e+01 -1.1241488592261051e+01 1.5185682250007966e+01 + 29 -1.4356732743290538e+01 -1.9712882280516450e+01 -3.0642379500547996e+00 +run_vdwl: 37.735102831577 +run_coul: 262.634996567417 +run_stress: ! |- + -9.3272087816450096e+01 -1.3382216892660497e+02 -3.2672292496064199e+02 2.9759550012391575e+01 -4.9209020012813669e+00 -8.2642482482441096e+01 +run_forces: ! |2 + 1 2.0020633315697571e+00 -1.8597540312576371e+01 -3.5898847150887825e+01 + 2 -1.8527112685977595e+01 -1.7111767435468980e+01 2.0691356245503808e+01 + 3 1.0099461000123771e+01 5.9365749899001820e+01 2.4423492074447349e+01 + 4 -4.5756545930134305e+00 -9.8171217238369679e-01 -3.3833945796207656e+00 + 5 -3.6935769629718820e+00 -4.0701894718259650e+00 3.8892346120926988e+00 + 6 7.6571693742405060e+01 -9.5745009619986718e+01 -9.3149402824851791e+01 + 7 -2.1146520723115522e+01 2.8805359357005347e+01 1.2508940510400312e+02 + 8 -2.1038406658511651e+01 9.9856753020536395e+00 -2.8916677199745425e+01 + 9 -8.2725040661224440e+00 -1.3032515389877304e+01 -3.6169607187530971e+01 + 10 -5.3760826866916233e+01 6.1170224662661617e+01 1.8495907188455345e+01 + 11 -1.3253793686585611e+00 -3.2541579724226799e+00 -4.4355037885599886e+00 + 12 2.5785718921609639e+01 -7.4878876652861359e-01 -2.6134482478760357e+00 + 13 3.3829110641517599e+00 -7.7854300168776425e-01 -6.1471395974905052e-01 + 14 -4.1270221660368221e-02 9.3253524130353482e-01 -4.9663546372704301e+00 + 15 4.2930244204525003e+00 4.8016875903370053e+00 -1.2067983339497499e+00 + 16 -3.6783955303667234e+01 1.8760441796324653e+01 1.1514035663250905e+02 + 17 4.4141164796979076e+01 -3.4054759175778408e+01 -9.5996385613193283e+01 + 18 2.6593320216432965e+00 6.2866046080770897e+00 -1.0406402388907743e+00 + 19 -2.6868932719674365e+00 -3.5919446222505456e+00 -6.7199643833073341e-01 + 20 2.3122579672731871e+00 1.6848245740968735e+00 1.0223265461108680e-01 + 21 9.0047857933168434e+00 1.1657532538116142e+01 -3.0300251561127794e+01 + 22 1.2602721079420199e+01 2.2333285795234898e+00 2.1993413545558095e+01 + 23 -2.1752700027690018e+01 -1.3807397168507773e+01 8.4647725463156984e+00 + 24 -4.1597043845955195e+00 2.9600069115788433e+01 -1.4377967328816560e+01 + 25 1.8008122136440438e+01 -4.7255613901672264e+00 1.6011743726111732e+01 + 26 -1.3270411937489305e+01 -2.4691999045812377e+01 -5.6773953378636655e-01 + 27 -7.3472299042491755e+00 3.1133794605717583e+01 -1.2191686159483819e+01 + 28 2.2002914561082278e+01 -1.1345148097691201e+01 1.5336215539418586e+01 + 29 -1.4484023859861420e+01 -1.9880794227041598e+01 -3.1367150853552728e+00 +... From 4975295e0fa3221a442aa7a459adb91a841f02f1 Mon Sep 17 00:00:00 2001 From: julient31 Date: Thu, 1 Apr 2021 11:45:16 -0600 Subject: [PATCH 0336/1217] - adding a force/clear equivalent for spins in verlet/kk - setting all validation problems for spin/kk --- .../llg_exchange.py | 2 +- .../run-test-exchange.sh | 8 +++--- .../test-spin-precession.in | 4 +-- .../run-test-prec.sh | 8 +++++- .../test-spin-precession.in | 1 + .../run-test-prec.sh | 7 +++++ .../test-prec-spin.template | 1 + .../validation_nve/in.spin.iron-nve | 4 +-- .../validation_nve/run-test-nve.sh | 8 ++++-- .../validation_nvt/in.spin.nvt_lattice | 1 + .../validation_nvt/in.spin.nvt_spin | 1 + .../validation_nvt/run-test-nvt.sh | 20 ++++++++++++-- src/KOKKOS/atom_vec_spin_kokkos.cpp | 8 +++--- src/KOKKOS/verlet_kokkos.cpp | 27 +++++++++++++++++++ 14 files changed, 82 insertions(+), 18 deletions(-) diff --git a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py index 5b93ac5c2d..a4cba3a940 100755 --- a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py +++ b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py @@ -6,7 +6,7 @@ import matplotlib.pyplot as plt import mpmath as mp hbar=0.658212 # Planck's constant (eV.fs/rad) -# J0=0.05 # per-neighbor exchange interaction (eV) +J0=0.05 # per-neighbor exchange interaction (eV) # exchange interaction parameters J1 = 11.254 # in eV diff --git a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh index a714e22fcf..9d00318473 100755 --- a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh +++ b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh @@ -4,12 +4,12 @@ rm res_*.dat # test standard Lammps -# ./../../../../src/lmp_serial \ -# -in test-spin-precession.in +./../../../../src/lmp_serial \ + -in test-spin-precession.in # test spin/kk with Kokkos Lammps -mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ - -k on -sf kk -in test-spin-precession.in +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in test-spin-precession.in # extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" diff --git a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in index 0615d384ec..c195c046ec 100644 --- a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in +++ b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in @@ -1,8 +1,8 @@ #LAMMPS in.run units metal -# atom_style spin -atom_style spin/kk +atom_style spin +# atom_style spin/kk atom_modify map array boundary f f f shell echo "test1" diff --git a/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh b/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh index 8609179376..e7a943beef 100755 --- a/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh +++ b/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh @@ -3,9 +3,15 @@ # clean old res rm res_*.dat -# compute Lammps +# test standard Lammps ./../../../../src/lmp_serial \ -in test-spin-precession.in + +# test spin/kk with Kokkos Lammps +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in test-spin-precession.in + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" diff --git a/examples/SPIN/test_problems/validation_damped_precession/test-spin-precession.in b/examples/SPIN/test_problems/validation_damped_precession/test-spin-precession.in index b8e943e579..56abdded15 100644 --- a/examples/SPIN/test_problems/validation_damped_precession/test-spin-precession.in +++ b/examples/SPIN/test_problems/validation_damped_precession/test-spin-precession.in @@ -2,6 +2,7 @@ units metal atom_style spin +# atom_style spin/kk atom_modify map array boundary f f f diff --git a/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh b/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh index bcdd337903..ecdbb2c156 100755 --- a/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh +++ b/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh @@ -12,7 +12,14 @@ do temp="$(echo "$tempi+$i*($tempf-$tempi)/$N" | bc -l)" sed s/temperature/${temp}/g test-prec-spin.template > \ test-prec-spin.in + + # test standard Lammps ./../../../../src/lmp_serial -in test-prec-spin.in + + # test spin/kk with Kokkos Lammps + # mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ + # -k on -sf kk -in test-prec-spin.in + Hz="$(tail -n 1 average_spin | awk -F " " '{print $3}')" sz="$(tail -n 1 average_spin | awk -F " " '{print $5}')" en="$(tail -n 1 average_spin | awk -F " " '{print $6}')" diff --git a/examples/SPIN/test_problems/validation_langevin_precession/test-prec-spin.template b/examples/SPIN/test_problems/validation_langevin_precession/test-prec-spin.template index 52f6a105ea..bec7126e69 100644 --- a/examples/SPIN/test_problems/validation_langevin_precession/test-prec-spin.template +++ b/examples/SPIN/test_problems/validation_langevin_precession/test-prec-spin.template @@ -2,6 +2,7 @@ units metal atom_style spin +# atom_style spin/kk atom_modify map array boundary p p p diff --git a/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve b/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve index a29d0158cf..38c669e166 100644 --- a/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve +++ b/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve @@ -50,5 +50,5 @@ thermo 200 compute outsp all property/atom spx spy spz sp fmx fmy fmz dump 1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] -# run 100000 -run 10000 +run 100000 +# run 1 diff --git a/examples/SPIN/test_problems/validation_nve/run-test-nve.sh b/examples/SPIN/test_problems/validation_nve/run-test-nve.sh index a349fb91f7..04d3d60847 100755 --- a/examples/SPIN/test_problems/validation_nve/run-test-nve.sh +++ b/examples/SPIN/test_problems/validation_nve/run-test-nve.sh @@ -3,10 +3,14 @@ # clean old res rm res_*.dat -# compute Lammps +# test standard Lammps +../../../../src/lmp_serial -in in.spin.iron-nve + +# test spin/kk with Kokkos Lammps # mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ # -k on -sf kk -in in.spin.iron-nve -../../../../src/lmp_serial -in in.spin.iron-nve + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" diff --git a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice index 2375c0ff8d..cc7bcfa68d 100644 --- a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice +++ b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice @@ -3,6 +3,7 @@ clear units metal atom_style spin +# atom_style spin/kk dimension 3 boundary p p p diff --git a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin index 6b65df7109..7e8152f481 100644 --- a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin +++ b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin @@ -3,6 +3,7 @@ clear units metal atom_style spin +# atom_style spin/kk dimension 3 boundary p p p diff --git a/examples/SPIN/test_problems/validation_nvt/run-test-nvt.sh b/examples/SPIN/test_problems/validation_nvt/run-test-nvt.sh index d3abbbe1a5..1372e1bd2c 100755 --- a/examples/SPIN/test_problems/validation_nvt/run-test-nvt.sh +++ b/examples/SPIN/test_problems/validation_nvt/run-test-nvt.sh @@ -3,16 +3,32 @@ # clean old res rm res_*.dat -# compute NVT Spin -> Lattice +### compute NVT Spin -> Lattice + +# test standard Lammps ./../../../../src/lmp_serial -in in.spin.nvt_spin + +# test spin/kk with Kokkos Lammps +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in in.spin.nvt_spin + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" en="$(echo "$en-$in" | bc -l)" tail -n +$in log.lammps | head -n $en > res_nvt_spin.dat -# compute NVT Lattice -> Spin +### compute NVT Lattice -> Spin + +# test standard Lammps ./../../../../src/lmp_serial -in in.spin.nvt_lattice + +# test spin/kk with Kokkos Lammps +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in in.spin.nvt_lattice + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp index 188748d655..e513ff2ffa 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.cpp +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -1303,9 +1303,9 @@ void AtomVecSpinKokkos::sync_overlapping_device(ExecutionSpace space, unsigned i clear all forces (mech and mag) ------------------------------------------------------------------------- */ -void AtomVecSpinKokkos::force_clear(int /*n*/, size_t nbytes) +void AtomVecSpinKokkos::force_clear(int n, size_t nbytes) { - memset(&atom->f[0][0],0,3*nbytes); - memset(&atom->fm[0][0],0,3*nbytes); - memset(&atom->fm_long[0][0],0,3*nbytes); + memset(&f[n][0],0,3*nbytes); + memset(&fm[n][0],0,3*nbytes); + memset(&fm_long[n][0],0,3*nbytes); } diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 3aa7a3575a..27f4646366 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -594,6 +594,15 @@ void VerletKokkos::force_clear() Kokkos::parallel_for(nall, Zero::t_f_array>(atomKK->k_torque.view())); atomKK->modified(Device,TORQUE_MASK); } + + // reset SPIN forces + + if (extraflag) { + Kokkos::parallel_for(nall, Zero::t_fm_array>(atomKK->k_fm.view())); + atomKK->modified(Device,FM_MASK); + Kokkos::parallel_for(nall, Zero::t_fm_array>(atomKK->k_fm_long.view())); + atomKK->modified(Device,FML_MASK); + } // neighbor includegroup flag is set // clear force only on initial nfirst particles @@ -607,6 +616,15 @@ void VerletKokkos::force_clear() Kokkos::parallel_for(atomKK->nfirst, Zero::t_f_array>(atomKK->k_torque.view())); atomKK->modified(Device,TORQUE_MASK); } + + // reset SPIN forces + + if (extraflag) { + Kokkos::parallel_for(atomKK->nfirst, Zero::t_fm_array>(atomKK->k_fm.view())); + atomKK->modified(Device,FM_MASK); + Kokkos::parallel_for(atomKK->nfirst, Zero::t_fm_array>(atomKK->k_fm_long.view())); + atomKK->modified(Device,FML_MASK); + } if (force->newton) { auto range = Kokkos::RangePolicy(atomKK->nlocal, atomKK->nlocal + atomKK->nghost); @@ -617,6 +635,15 @@ void VerletKokkos::force_clear() Kokkos::parallel_for(range, Zero::t_f_array>(atomKK->k_torque.view())); atomKK->modified(Device,TORQUE_MASK); } + + // reset SPIN forces + + if (extraflag) { + Kokkos::parallel_for(range, Zero::t_fm_array>(atomKK->k_fm.view())); + atomKK->modified(Device,FM_MASK); + Kokkos::parallel_for(range, Zero::t_fm_array>(atomKK->k_fm_long.view())); + atomKK->modified(Device,FML_MASK); + } } } } From 2dfafe4adb8eb7646f1587c59410681538adabb4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 12:07:43 -0400 Subject: [PATCH 0337/1217] add is_file() special variable function and unit tests for it --- doc/src/variable.rst | 8 ++++++-- src/variable.cpp | 24 ++++++++++++++++++++++-- unittest/commands/test_variables.cpp | 14 +++++++++++--- 3 files changed, 39 insertions(+), 7 deletions(-) diff --git a/doc/src/variable.rst b/doc/src/variable.rst index 6a6cdf9a6d..af324c180f 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -65,8 +65,8 @@ Syntax bound(group,dir,region), gyration(group,region), ke(group,reigon), angmom(group,dim,region), torque(group,dim,region), inertia(group,dimdim,region), omega(group,dim,region) - special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x) - feature functions = is_active(category,feature,exact), is_defined(category,id,exact) + special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name) + feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id) atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q compute references = c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i] @@ -821,6 +821,10 @@ Special Functions Special functions take specific kinds of arguments, meaning their arguments cannot be formulas themselves. +The is_file(x) function is a test whether 'x' is a (readable) file +and returns 1 in this case, otherwise it returns 0. For that 'x' +is taken as a literal string and must not have any blanks in it. + The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions each take 1 argument which is of the form "c_ID" or "c_ID[N]" or "f_ID" or "f_ID[N]" or "v_name". The first two are computes and the diff --git a/src/variable.cpp b/src/variable.cpp index 3bf88db55e..1a4feb3573 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -65,7 +65,7 @@ enum{DONE,ADD,SUBTRACT,MULTIPLY,DIVIDE,CARAT,MODULO,UNARY, SQRT,EXP,LN,LOG,ABS,SIN,COS,TAN,ASIN,ACOS,ATAN,ATAN2, RANDOM,NORMAL,CEIL,FLOOR,ROUND,RAMP,STAGGER,LOGFREQ,LOGFREQ2, LOGFREQ3,STRIDE,STRIDE2,VDISPLACE,SWIGGLE,CWIGGLE,GMASK,RMASK, - GRMASK,IS_ACTIVE,IS_DEFINED,IS_AVAILABLE, + GRMASK,IS_ACTIVE,IS_DEFINED,IS_AVAILABLE,IS_FILE, VALUE,ATOMARRAY,TYPEARRAY,INTARRAY,BIGINTARRAY,VECTORARRAY}; // customize by adding a special function @@ -4079,7 +4079,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, strcmp(word,"gmask") && strcmp(word,"rmask") && strcmp(word,"grmask") && strcmp(word,"next") && strcmp(word,"is_active") && strcmp(word,"is_defined") && - strcmp(word,"is_available")) + strcmp(word,"is_available") && strcmp(word,"is_file")) return 0; // parse contents for comma-separated args @@ -4488,6 +4488,26 @@ int Variable::special_function(char *word, char *contents, Tree **tree, // save value in tree or on argstack + if (tree) { + Tree *newtree = new Tree(); + newtree->type = VALUE; + newtree->value = value; + newtree->first = newtree->second = nullptr; + newtree->nextra = 0; + treestack[ntreestack++] = newtree; + } else argstack[nargstack++] = value; + + } else if (strcmp(word,"is_file") == 0) { + if (narg != 1) + print_var_error(FLERR,"Invalid is_file() function in " + "variable formula",ivar); + + FILE *fp = fopen(args[0],"r"); + value = (fp == nullptr) ? 0.0 : 1.0; + if (fp) fclose(fp); + + // save value in tree or on argstack + if (tree) { Tree *newtree = new Tree(); newtree->type = VALUE; diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index eb533aee86..97f874a856 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -142,12 +142,13 @@ TEST_F(VariableTest, CreateDelete) command("variable ten2 uloop 4"); command("variable ten3 uloop 4 pad"); command("variable dummy index 0"); + command("variable file equal is_file(MYFILE)"); END_HIDE_OUTPUT(); - ASSERT_EQ(variable->nvar, 17); + ASSERT_EQ(variable->nvar, 18); BEGIN_HIDE_OUTPUT(); command("variable dummy delete"); END_HIDE_OUTPUT(); - ASSERT_EQ(variable->nvar, 16); + ASSERT_EQ(variable->nvar, 17); ASSERT_THAT(variable->retrieve("three"), StrEq("three")); variable->set_string("three", "four"); ASSERT_THAT(variable->retrieve("three"), StrEq("four")); @@ -158,6 +159,13 @@ TEST_F(VariableTest, CreateDelete) ASSERT_THAT(variable->retrieve("eight"), StrEq("")); variable->internal_set(variable->find("ten"), 2.5); ASSERT_THAT(variable->retrieve("ten"), StrEq("2.5")); + ASSERT_THAT(variable->retrieve("file"), StrEq("0")); + FILE *fp = fopen("MYFILE","w"); + fputs(" ",fp); + fclose(fp); + ASSERT_THAT(variable->retrieve("file"), StrEq("1")); + unlink("MYFILE"); + ASSERT_THAT(variable->retrieve("file"), StrEq("0")); ASSERT_EQ(variable->equalstyle(variable->find("one")), 0); ASSERT_EQ(variable->equalstyle(variable->find("two")), 1); @@ -200,7 +208,7 @@ TEST_F(VariableTest, CreateDelete) TEST_F(VariableTest, AtomicSystem) { - command("atom_modify map array"); + HIDE_OUTPUT([&] { command("atom_modify map array"); }); atomic_system(); file_vars(); From 887eb40ad493eedf61f21ca9c19186c8181fb7a1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 12:07:59 -0400 Subject: [PATCH 0338/1217] fix crash when requesting verbose output. --- unittest/testing/core.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/testing/core.h b/unittest/testing/core.h index deab845573..75b0564d02 100644 --- a/unittest/testing/core.h +++ b/unittest/testing/core.h @@ -60,7 +60,7 @@ public: } void BEGIN_CAPTURE_OUTPUT() { - if (!verbose) ::testing::internal::CaptureStdout(); + ::testing::internal::CaptureStdout(); } std::string END_CAPTURE_OUTPUT() { From 366b49c5811316cabae57bfbfbe7dfe810632834 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 12:14:34 -0400 Subject: [PATCH 0339/1217] copy NeighRequest::id to NeighList::id so we can identify them when a style has multiple requests --- src/neigh_list.cpp | 1 + src/neigh_list.h | 1 + 2 files changed, 2 insertions(+) diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp index 308ecbbf6e..a51ecb7518 100644 --- a/src/neigh_list.cpp +++ b/src/neigh_list.cpp @@ -143,6 +143,7 @@ void NeighList::post_constructor(NeighRequest *nq) respamiddle = nq->respamiddle; respainner = nq->respainner; copy = nq->copy; + id = nq->id; if (nq->copy) { listcopy = neighbor->lists[nq->copylist]; diff --git a/src/neigh_list.h b/src/neigh_list.h index d69b844dc8..ad8e104f2a 100644 --- a/src/neigh_list.h +++ b/src/neigh_list.h @@ -44,6 +44,7 @@ class NeighList : protected Pointers { int copy; // 1 if this list is copied from another list int kk2cpu; // 1 if this list is copied from Kokkos to CPU int copymode; // 1 if this is a Kokkos on-device copy + int id; // copied from neighbor list request // data structs to store neighbor pairs I,J and associated values From d24f74b582408a308bc0fd37fda06e175239b1d8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 12:31:46 -0400 Subject: [PATCH 0340/1217] add stop on file example to fix halt docs --- doc/src/fix_halt.rst | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index 964132518d..06f068bb7d 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -115,6 +115,18 @@ The version with "bondmax" will just run somewhat faster, due to less overhead in computing bond lengths and not storing them in a separate compute. +A variable can be used to implement a large variety of conditions, +including to stop when a specific file exists. Example: + +.. code-block:: LAMMPS + + variable exit equal is_file(EXIT) + fix 10 all halt 100 v_exit != 0 error soft + +Will stop the current run command when a file ``EXIT`` is created +in the current working directory. The condition can be cleared +by removing the file through the :doc:`shell ` command. + The choice of operators listed above are the usual comparison operators. The XOR operation (exclusive or) is also included as "\|\^". In this context, XOR means that if either the attribute or avalue is From 43735fd3f5c52670b87706076de01c2c8b4ab83e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 13:50:50 -0400 Subject: [PATCH 0341/1217] update neighbor list library interface to use ID field in neighbor list to uniquely identify lists --- src/library.cpp | 135 ++++++++++++++++++++++-------------------------- 1 file changed, 62 insertions(+), 73 deletions(-) diff --git a/src/library.cpp b/src/library.cpp index a950d31e4e..2129ebeff8 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -3914,40 +3914,43 @@ int lammps_create_atoms(void *handle, int n, tagint *id, int *type, // Library functions for accessing neighbor lists // ---------------------------------------------------------------------- -/** Find neighbor list index of pair style neighbor list +/** Find index of a neighbor list requested by a pair style * - * Try finding pair instance that matches style. If exact is set, the pair must - * match style exactly. If exact is 0, style must only be contained. If pair is - * of style pair/hybrid, style is instead matched the nsub-th hybrid sub-style. + * This function determines which of the available neighbor lists for + * pair styles matches the given conditions. It first matches the style + * name. If exact is 1 the name must match exactly, if exact is 0, a + * regular expression or substring match is done. If the pair style is + * hybrid or hybrid/overlay the style is matched against the sub styles + * instead. + * If a the same pair style is used multiple times as a sub-style, the + * nsub argument must be > 0 and represents the nth instance of the sub-style + * (same as for the pair_coeff command, for example). In that case + * nsub=0 will not produce a match and this function will return -1. * - * Once the pair instance has been identified, multiple neighbor list requests - * may be found. Every neighbor list is uniquely identified by its request - * index. Thus, providing this request index ensures that the correct neighbor - * list index is returned. + * The final condition to be checked is the request ID (reqid). This + * will normally be 0, but some pair styles request multiple neighbor + * lists and set the request ID to a value > 0. * * \param handle pointer to a previously created LAMMPS instance cast to ``void *``. * \param style String used to search for pair style instance * \param exact Flag to control whether style should match exactly or only - * must be contained in pair style name - * \param nsub match nsub-th hybrid sub-style - * \param request request index that specifies which neighbor list should be - * returned, in case there are multiple neighbor lists requests - * for the found pair style + * a regular expression / substring match is applied. + * \param nsub match nsub-th hybrid sub-style instance of the same style + * \param reqid request id to identify neighbor list in case there are + * multiple requests from the same pair style instance * \return return neighbor list index if found, otherwise -1 */ -int lammps_find_pair_neighlist(void* handle, char * style, int exact, int nsub, int request) { - LAMMPS * lmp = (LAMMPS *) handle; - Pair* pair = lmp->force->pair_match(style, exact, nsub); +int lammps_find_pair_neighlist(void *handle, char *style, int exact, int nsub, int reqid) { + LAMMPS *lmp = (LAMMPS *) handle; + Pair *pair = lmp->force->pair_match(style, exact, nsub); if (pair != nullptr) { // find neigh list for (int i = 0; i < lmp->neighbor->nlist; i++) { - NeighList * list = lmp->neighbor->lists[i]; - if (list->requestor_type != NeighList::PAIR || pair != list->requestor) continue; - - if (list->index == request) { - return i; - } + NeighList *list = lmp->neighbor->lists[i]; + if ( (list->requestor_type == NeighList::PAIR) + && (pair == list->requestor) + && (list->id == reqid) ) return i; } } return -1; @@ -3955,74 +3958,60 @@ int lammps_find_pair_neighlist(void* handle, char * style, int exact, int nsub, /* ---------------------------------------------------------------------- */ -/** Find neighbor list index of fix neighbor list +/** Find index of a neighbor list requested by a fix + * + * The neighbor list request from a fix is identified by the fix ID and + * the request ID. The request ID is typically 0, but will be > 0 in + * case a fix has multiple neighbor list requests. * * \param handle pointer to a previously created LAMMPS instance cast to ``void *``. * \param id Identifier of fix instance - * \param request request index that specifies which request should be returned, - * in case there are multiple neighbor lists for this fix + * \param reqid request id to identify neighbor list in case there are + * multiple requests from the same fix * \return return neighbor list index if found, otherwise -1 */ -int lammps_find_fix_neighlist(void* handle, char *id, int request) { - LAMMPS * lmp = (LAMMPS *) handle; - Fix* fix = nullptr; - const int nfix = lmp->modify->nfix; +int lammps_find_fix_neighlist(void *handle, char *id, int reqid) { + LAMMPS *lmp = (LAMMPS *) handle; + const int ifix = lmp->modify->find_fix(id); + if (ifix < 0) return -1; - // find fix with name - for (int ifix = 0; ifix < nfix; ifix++) { - if (strcmp(lmp->modify->fix[ifix]->id, id) == 0) { - fix = lmp->modify->fix[ifix]; - break; - } - } - - if (fix != nullptr) { - // find neigh list - for (int i = 0; i < lmp->neighbor->nlist; i++) { - NeighList * list = lmp->neighbor->lists[i]; - if (list->requestor_type != NeighList::FIX || fix != list->requestor) continue; - - if (list->index == request) { - return i; - } - } + Fix *fix = lmp->modify->fix[ifix]; + // find neigh list + for (int i = 0; i < lmp->neighbor->nlist; i++) { + NeighList *list = lmp->neighbor->lists[i]; + if ( (list->requestor_type == NeighList::FIX) + && (fix == list->requestor) + && (list->id == reqid) ) return i; } return -1; } /* ---------------------------------------------------------------------- */ -/** Find neighbor list index of compute neighbor list +/** Find index of a neighbor list requested by a compute + * + * The neighbor list request from a compute is identified by the compute + * ID and the request ID. The request ID is typically 0, but will be + * > 0 in case a compute has multiple neighbor list requests. * * \param handle pointer to a previously created LAMMPS instance cast to ``void *``. - * \param id Identifier of fix instance - * \param request request index that specifies which request should be returned, - * in case there are multiple neighbor lists for this fix + * \param id Identifier of compute instance + * \param reqid request id to identify neighbor list in case there are + * multiple requests from the same compute * \return return neighbor list index if found, otherwise -1 */ -int lammps_find_compute_neighlist(void* handle, char *id, int request) { - LAMMPS * lmp = (LAMMPS *) handle; - Compute* compute = nullptr; - const int ncompute = lmp->modify->ncompute; +int lammps_find_compute_neighlist(void* handle, char *id, int reqid) { + LAMMPS *lmp = (LAMMPS *) handle; + const int icompute = lmp->modify->find_compute(id); + if (icompute < 0) return -1; - // find compute with name - for (int icompute = 0; icompute < ncompute; icompute++) { - if (strcmp(lmp->modify->compute[icompute]->id, id) == 0) { - compute = lmp->modify->compute[icompute]; - break; - } - } - - if (compute != nullptr) { - // find neigh list - for (int i = 0; i < lmp->neighbor->nlist; i++) { - NeighList * list = lmp->neighbor->lists[i]; - if (list->requestor_type != NeighList::COMPUTE || compute != list->requestor) continue; - - if (list->index == request) { - return i; - } - } + Compute *compute = lmp->modify->compute[icompute]; + // find neigh list + for (int i = 0; i < lmp->neighbor->nlist; i++) { + NeighList * list = lmp->neighbor->lists[i]; + if ( (list->requestor_type == NeighList::COMPUTE) + && (compute == list->requestor) + && (list->id == reqid) ) return i; } return -1; } From 5583901b2c77d6882f3a8b762e4ba15500954faf Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 13:51:42 -0400 Subject: [PATCH 0342/1217] should not set neighbor list request id to non-zero when just requesting a single neighbor list --- src/USER-QUIP/pair_quip.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp index 2d338da158..20a6c98cb8 100644 --- a/src/USER-QUIP/pair_quip.cpp +++ b/src/USER-QUIP/pair_quip.cpp @@ -318,7 +318,6 @@ void PairQUIP::init_style() // Initialise neighbor list int irequest_full = neighbor->request(this); - neighbor->requests[irequest_full]->id = 1; neighbor->requests[irequest_full]->half = 0; neighbor->requests[irequest_full]->full = 1; } From c4f59764d43e36b5caa87939c2185e579f5e45fb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 15:28:09 -0400 Subject: [PATCH 0343/1217] reformat pair_coeff section that got misformatted as string --- .../force-styles/tests/mol-pair-born.yaml | 36 +++++++++---------- .../tests/mol-pair-born_coul_dsf.yaml | 36 +++++++++---------- .../tests/mol-pair-born_coul_long.yaml | 36 +++++++++---------- .../tests/mol-pair-born_coul_msm.yaml | 36 +++++++++---------- .../tests/mol-pair-born_coul_msm_table.yaml | 36 +++++++++---------- .../tests/mol-pair-born_coul_wolf.yaml | 36 +++++++++---------- .../force-styles/tests/mol-pair-morse.yaml | 31 +++++++++------- .../tests/mol-pair-morse_smooth_linear.yaml | 31 +++++++++------- 8 files changed, 144 insertions(+), 134 deletions(-) diff --git a/unittest/force-styles/tests/mol-pair-born.yaml b/unittest/force-styles/tests/mol-pair-born.yaml index 05e77a49b5..f411505f74 100644 --- a/unittest/force-styles/tests/mol-pair-born.yaml +++ b/unittest/force-styles/tests/mol-pair-born.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:10 202 +lammps_version: 10 Mar 2021 +date_generated: Fri Apr 2 15:14:43 202 epsilon: 5e-14 prerequisites: ! | atom full @@ -9,22 +9,22 @@ pre_commands: ! "" post_commands: ! "" input_file: in.fourmol pair_style: born 8.0 -pair_coeff: ! "1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 - 141.547923828784 \n1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 - 4.09225030876458 \n1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 - 403.51858739517 \n1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 - 303.336540547726 \n1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 - 303.336540547726 \n2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 - 0.177172207445923 \n2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 - 17.5662073921955 \n2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 - 0.000703093129207124 \n2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 - 12.548008396489 \n3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 - 1019.38354056979 \n3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 - 778.254162800904 \n3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 - 778.254162800904 \n4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722\n" +pair_coeff: ! | + 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 + 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 + 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 + 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 + 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 + 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 + 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 + 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 + 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 extract: ! | a 2 c 2 diff --git a/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml b/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml index c139bd0bc2..a3bacb3f7c 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:10 202 +lammps_version: 10 Mar 2021 +date_generated: Fri Apr 2 15:14:43 202 epsilon: 5e-14 prerequisites: ! | atom full @@ -9,22 +9,22 @@ pre_commands: ! "" post_commands: ! "" input_file: in.fourmol pair_style: born/coul/dsf 0.25 8.0 -pair_coeff: ! "1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 - 141.547923828784 \n1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 - 4.09225030876458 \n1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 - 403.51858739517 \n1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 - 303.336540547726 \n1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 - 303.336540547726 \n2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 - 0.177172207445923 \n2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 - 17.5662073921955 \n2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 - 0.000703093129207124 \n2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 - 12.548008396489 \n3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 - 1019.38354056979 \n3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 - 778.254162800904 \n3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 - 778.254162800904 \n4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722\n" +pair_coeff: ! | + 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 + 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 + 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 + 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 + 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 + 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 + 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 + 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 + 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 extract: ! "" natoms: 29 init_vdwl: 225.01325775005 diff --git a/unittest/force-styles/tests/mol-pair-born_coul_long.yaml b/unittest/force-styles/tests/mol-pair-born_coul_long.yaml index e831e0da9c..7f99ac0b15 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:10 202 +lammps_version: 10 Mar 2021 +date_generated: Fri Apr 2 15:14:43 202 epsilon: 7.5e-14 prerequisites: ! | atom full @@ -14,22 +14,22 @@ post_commands: ! | kspace_modify compute no input_file: in.fourmol pair_style: born/coul/long 8.0 -pair_coeff: ! "1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 - 141.547923828784 \n1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 - 4.09225030876458 \n1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 - 403.51858739517 \n1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 - 303.336540547726 \n1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 - 303.336540547726 \n2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 - 0.177172207445923 \n2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 - 17.5662073921955 \n2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 - 0.000703093129207124 \n2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 - 12.548008396489 \n3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 - 1019.38354056979 \n3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 - 778.254162800904 \n3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 - 778.254162800904 \n4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n" +pair_coeff: ! | + 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 + 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 + 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 + 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 + 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 + 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 + 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 + 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 + 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 extract: ! | cut_coul 0 natoms: 29 diff --git a/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml index e0def1f392..e805c24b28 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:10 202 +lammps_version: 10 Mar 2021 +date_generated: Fri Apr 2 15:14:43 202 epsilon: 5e-14 prerequisites: ! | atom full @@ -15,22 +15,22 @@ post_commands: ! | kspace_modify pressure/scalar no # required for USER-OMP with msm input_file: in.fourmol pair_style: born/coul/msm 12.0 -pair_coeff: ! "1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 - 141.547923828784 \n1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 - 4.09225030876458 \n1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 - 403.51858739517 \n1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 - 303.336540547726 \n1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 - 303.336540547726 \n2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 - 0.177172207445923 \n2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 - 17.5662073921955 \n2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 - 0.000703093129207124 \n2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 - 12.548008396489 \n3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 - 1019.38354056979 \n3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 - 778.254162800904 \n3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 - 778.254162800904 \n4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n" +pair_coeff: ! | + 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 + 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 + 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 + 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 + 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 + 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 + 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 + 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 + 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 extract: ! | cut_coul 0 natoms: 29 diff --git a/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml index fe6a0faf84..75f0f76a44 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:10 202 +lammps_version: 10 Mar 2021 +date_generated: Fri Apr 2 15:14:43 202 epsilon: 5e-14 prerequisites: ! | atom full @@ -15,22 +15,22 @@ post_commands: ! | kspace_modify pressure/scalar no # required for USER-OMP with msm input_file: in.fourmol pair_style: born/coul/msm 12.0 -pair_coeff: ! "1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 - 141.547923828784 \n1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 - 4.09225030876458 \n1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 - 403.51858739517 \n1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 - 303.336540547726 \n1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 - 303.336540547726 \n2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 - 0.177172207445923 \n2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 - 17.5662073921955 \n2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 - 0.000703093129207124 \n2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 - 12.548008396489 \n3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 - 1019.38354056979 \n3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 - 778.254162800904 \n3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 - 778.254162800904 \n4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n" +pair_coeff: ! | + 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 + 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 + 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 + 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 + 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 + 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 + 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 + 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 + 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 extract: ! | cut_coul 0 natoms: 29 diff --git a/unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml b/unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml index f3c37e100a..db4ad73e30 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:11 202 +lammps_version: 10 Mar 2021 +date_generated: Fri Apr 2 15:14:44 202 epsilon: 5e-14 prerequisites: ! | atom full @@ -9,22 +9,22 @@ pre_commands: ! "" post_commands: ! "" input_file: in.fourmol pair_style: born/coul/wolf 0.25 8.0 -pair_coeff: ! "1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 - 141.547923828784 \n1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 - 4.09225030876458 \n1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 - 403.51858739517 \n1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 - 303.336540547726 \n1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 - 303.336540547726 \n2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 - 0.177172207445923 \n2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 - 17.5662073921955 \n2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 - 0.000703093129207124 \n2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 - 12.548008396489 \n3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 - 1019.38354056979 \n3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 - 778.254162800904 \n3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 - 778.254162800904 \n4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722 \n5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 - 592.979935420722\n" +pair_coeff: ! | + 1 1 2.51937098847838 0.148356076521964 1.82166848001002 29.0375806150613 141.547923828784 + 1 2 2.87560097202631 0.103769845319212 1.18949647259382 1.7106306969663 4.09225030876458 + 1 3 2.73333746288062 0.169158133709025 2.06291417638668 63.7180294456725 403.51858739517 + 1 4 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 1 5 2.51591531388789 0.166186965980131 2.01659390849669 49.622913109061 303.336540547726 + 2 2 1.0594557710255 0.281261664467988 0.314884389172266 0.271080184997071 0.177172207445923 + 2 3 2.12127488295383 0.124576922646243 1.46526793359105 5.10367785279284 17.5662073921955 + 2 4 0.523836115049206 0.140093804714855 0.262040872137659 0.00432916334694855 0.000703093129207124 + 2 5 2.36887234111228 0.121604450909563 1.39946581861656 3.82529730669145 12.548008396489 + 3 3 2.81831917530019 0.189944649028137 2.31041576143228 127.684271782117 1019.38354056979 + 3 4 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 3 5 2.5316180773506 0.186976803503293 2.26748506873271 100.602835334624 778.254162800904 + 4 4 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 4 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 + 5 5 2.63841820292211 0.184008285863681 2.19742633928911 79.1465822481912 592.979935420722 extract: ! "" natoms: 29 init_vdwl: 225.01325775005 diff --git a/unittest/force-styles/tests/mol-pair-morse.yaml b/unittest/force-styles/tests/mol-pair-morse.yaml index cf75cd6dbd..61a66d8ac5 100644 --- a/unittest/force-styles/tests/mol-pair-morse.yaml +++ b/unittest/force-styles/tests/mol-pair-morse.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:19 202 +lammps_version: 10 Mar 2021 +date_generated: Fri Apr 2 15:27:01 202 epsilon: 5e-14 prerequisites: ! | atom full @@ -9,17 +9,22 @@ pre_commands: ! "" post_commands: ! "" input_file: in.fourmol pair_style: morse 8.0 -pair_coeff: ! "1 1 0.0202798941614106 2.78203488021395 2.725417159299 \n1 2 0.0101167811264648 - 3.9793050302425 1.90749569018897 \n1 3 0.0202934330695928 2.43948720203264 3.10711749999622 - \n1 4 0.0175731334238374 2.48316585521317 3.05258880102438 \n1 5 0.0175731334238374 - 2.48316585521317 3.05258880102438 \n2 2 0.00503064360487288 6.98433077606902 1.08960295117864 - \n2 3 0.0101296013842819 3.31380153807866 2.28919067558352 \n2 4 0.00497405122588691 - 14.0508902925745 0.544416409093563 \n2 5 0.00877114211614446 3.39491256196178 2.23466262511073 - \n3 3 0.0203039874239943 2.17204344301477 3.48881895084762 \n3 4 0.0175825321440736 - 2.20660439192238 3.43428999287994 \n3 5 0.0175825321440736 2.20660439192238 3.43428999287994 - \n4 4 0.0152259201379927 2.24227873774009 3.37976131582396 \n4 5 0.0152259201379927 - 2.24227873774009 3.37976131582396 \n5 5 0.0152259201379927 2.24227873774009 3.37976131582396 - \n" +pair_coeff: ! | + 1 1 0.0202798941614106 2.78203488021395 2.725417159299 + 1 2 0.0101167811264648 3.9793050302425 1.90749569018897 + 1 3 0.0202934330695928 2.43948720203264 3.10711749999622 + 1 4 0.0175731334238374 2.48316585521317 3.05258880102438 + 1 5 0.0175731334238374 2.48316585521317 3.05258880102438 + 2 2 0.00503064360487288 6.98433077606902 1.08960295117864 + 2 3 0.0101296013842819 3.31380153807866 2.28919067558352 + 2 4 0.00497405122588691 14.0508902925745 0.544416409093563 + 2 5 0.00877114211614446 3.39491256196178 2.23466262511073 + 3 3 0.0203039874239943 2.17204344301477 3.48881895084762 + 3 4 0.0175825321440736 2.20660439192238 3.43428999287994 + 3 5 0.0175825321440736 2.20660439192238 3.43428999287994 + 4 4 0.0152259201379927 2.24227873774009 3.37976131582396 + 4 5 0.0152259201379927 2.24227873774009 3.37976131582396 + 5 5 0.0152259201379927 2.24227873774009 3.37976131582396 extract: ! | d0 2 r0 2 diff --git a/unittest/force-styles/tests/mol-pair-morse_smooth_linear.yaml b/unittest/force-styles/tests/mol-pair-morse_smooth_linear.yaml index e933b47a0b..86d749ba25 100644 --- a/unittest/force-styles/tests/mol-pair-morse_smooth_linear.yaml +++ b/unittest/force-styles/tests/mol-pair-morse_smooth_linear.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 24 Aug 2020 -date_generated: Tue Sep 15 09:44:19 202 +lammps_version: 10 Mar 2021 +date_generated: Fri Apr 2 15:27:01 202 epsilon: 5e-14 prerequisites: ! | atom full @@ -9,17 +9,22 @@ pre_commands: ! "" post_commands: ! "" input_file: in.fourmol pair_style: morse/smooth/linear 8.0 -pair_coeff: ! "1 1 0.0202798941614106 2.78203488021395 2.725417159299 \n1 2 0.0101167811264648 - 3.9793050302425 1.90749569018897 \n1 3 0.0202934330695928 2.43948720203264 3.10711749999622 - \n1 4 0.0175731334238374 2.48316585521317 3.05258880102438 \n1 5 0.0175731334238374 - 2.48316585521317 3.05258880102438 \n2 2 0.00503064360487288 6.98433077606902 1.08960295117864 - \n2 3 0.0101296013842819 3.31380153807866 2.28919067558352 \n2 4 0.00497405122588691 - 14.0508902925745 0.544416409093563 \n2 5 0.00877114211614446 3.39491256196178 2.23466262511073 - \n3 3 0.0203039874239943 2.17204344301477 3.48881895084762 \n3 4 0.0175825321440736 - 2.20660439192238 3.43428999287994 \n3 5 0.0175825321440736 2.20660439192238 3.43428999287994 - \n4 4 0.0152259201379927 2.24227873774009 3.37976131582396 \n4 5 0.0152259201379927 - 2.24227873774009 3.37976131582396 \n5 5 0.0152259201379927 2.24227873774009 3.37976131582396 - \n" +pair_coeff: ! | + 1 1 0.0202798941614106 2.78203488021395 2.725417159299 + 1 2 0.0101167811264648 3.9793050302425 1.90749569018897 + 1 3 0.0202934330695928 2.43948720203264 3.10711749999622 + 1 4 0.0175731334238374 2.48316585521317 3.05258880102438 + 1 5 0.0175731334238374 2.48316585521317 3.05258880102438 + 2 2 0.00503064360487288 6.98433077606902 1.08960295117864 + 2 3 0.0101296013842819 3.31380153807866 2.28919067558352 + 2 4 0.00497405122588691 14.0508902925745 0.544416409093563 + 2 5 0.00877114211614446 3.39491256196178 2.23466262511073 + 3 3 0.0203039874239943 2.17204344301477 3.48881895084762 + 3 4 0.0175825321440736 2.20660439192238 3.43428999287994 + 3 5 0.0175825321440736 2.20660439192238 3.43428999287994 + 4 4 0.0152259201379927 2.24227873774009 3.37976131582396 + 4 5 0.0152259201379927 2.24227873774009 3.37976131582396 + 5 5 0.0152259201379927 2.24227873774009 3.37976131582396 extract: ! | d0 2 r0 2 From 160f2cc6307cb5c7e7b3179ca93e0d01de7b8b9f Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 2 Apr 2021 16:11:23 -0400 Subject: [PATCH 0344/1217] Update ROCm container definitions --- tools/singularity/ubuntu18.04_amd_rocm.def | 2 +- tools/singularity/ubuntu20.04_amd_rocm.def | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tools/singularity/ubuntu18.04_amd_rocm.def b/tools/singularity/ubuntu18.04_amd_rocm.def index bb04c738c4..7b06970110 100644 --- a/tools/singularity/ubuntu18.04_amd_rocm.def +++ b/tools/singularity/ubuntu18.04_amd_rocm.def @@ -94,7 +94,7 @@ From: ubuntu:18.04 ########################################################################### export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64 - git clone -b rocm-3.7.x https://github.com/ROCmSoftwarePlatform/hipCUB.git + git clone -b rocm-4.1.x https://github.com/ROCmSoftwarePlatform/hipCUB.git mkdir hipCUB/build cd hipCUB/build CXX=hipcc cmake -D BUILD_TEST=off .. diff --git a/tools/singularity/ubuntu20.04_amd_rocm.def b/tools/singularity/ubuntu20.04_amd_rocm.def index 28d57be341..4eee97ffec 100644 --- a/tools/singularity/ubuntu20.04_amd_rocm.def +++ b/tools/singularity/ubuntu20.04_amd_rocm.def @@ -2,7 +2,7 @@ BootStrap: docker From: ubuntu:20.04 %environment - export PATH=/usr/lib/ccache:/usr/local/cuda-11.0/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64 + export PATH=/usr/lib/ccache:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64 %post export DEBIAN_FRONTEND=noninteractive apt-get update @@ -90,7 +90,7 @@ From: ubuntu:20.04 ########################################################################### export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64 - git clone -b rocm-3.7.x https://github.com/ROCmSoftwarePlatform/hipCUB.git + git clone -b rocm-4.1.x https://github.com/ROCmSoftwarePlatform/hipCUB.git mkdir hipCUB/build cd hipCUB/build CXX=hipcc cmake -D BUILD_TEST=off .. From 79a413aeea135e0968edc9b8dfc1b73b3f6a5886 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 16:15:28 -0400 Subject: [PATCH 0345/1217] replace calls to sqrt() in constant initializers with precomputed numbers. this also moves those arrays into a separate file and out of the header --- src/USER-PTM/ptm_constants.cpp | 156 +++++++++++++++++++++++ src/USER-PTM/ptm_constants.h | 220 ++++++++------------------------- 2 files changed, 205 insertions(+), 171 deletions(-) create mode 100644 src/USER-PTM/ptm_constants.cpp diff --git a/src/USER-PTM/ptm_constants.cpp b/src/USER-PTM/ptm_constants.cpp new file mode 100644 index 0000000000..82bead2101 --- /dev/null +++ b/src/USER-PTM/ptm_constants.cpp @@ -0,0 +1,156 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +#include "ptm_constants.h" +#include + +const int ptm_num_nbrs[9] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS_BCC, PTM_NUM_NBRS_ICO, PTM_NUM_NBRS_SC, PTM_NUM_NBRS_DCUB, PTM_NUM_NBRS_DHEX, PTM_NUM_NBRS_GRAPHENE}; + +//------------------------------------ +// template structures +//------------------------------------ + +#define MYSQRT2 1.41421356237309504880 +#define MYSQRT3 1.73205080756887729352 +#define MYSQRT5 2.23606797749978969640 +#define MYSQRT6 2.44948974278317809819 +// sqrt((5.0-sqrt(5.0))/10.0): +#define MY5MINUSSQRT5BY10 0.52573111211913360602 +// sqrt((5.0+sqrt(5.0))/10.0): +#define MY5PLUSSQRT5BY10 0.85065080835203993218 +//these point sets have barycentre {0, 0, 0} and are scaled such that the mean neighbour distance is 1 + +const double ptm_template_fcc[PTM_NUM_POINTS_FCC][3] = { + { 0, 0, 0 }, + { MYSQRT2/2, MYSQRT2/2, 0 }, + { 0, MYSQRT2/2, MYSQRT2/2 }, + { MYSQRT2/2, 0, MYSQRT2/2 }, + { -MYSQRT2/2, -MYSQRT2/2, 0 }, + { 0, -MYSQRT2/2, -MYSQRT2/2 }, + { -MYSQRT2/2, 0, -MYSQRT2/2 }, + { -MYSQRT2/2, MYSQRT2/2, 0 }, + { 0, -MYSQRT2/2, MYSQRT2/2 }, + { -MYSQRT2/2, 0, MYSQRT2/2 }, + { MYSQRT2/2, -MYSQRT2/2, 0 }, + { 0, MYSQRT2/2, -MYSQRT2/2 }, + { MYSQRT2/2, 0, -MYSQRT2/2 }, +}; + +const double ptm_template_hcp[PTM_NUM_POINTS_HCP][3] = { + { 0, 0, 0 }, + { 0.5, -MYSQRT3/2, 0 }, + { -1, 0, 0 }, + { -0.5, MYSQRT3/6, -MYSQRT6/3 }, + { 0.5, MYSQRT3/6, -MYSQRT6/3 }, + { 0, -MYSQRT3/3, -MYSQRT6/3 }, + { -0.5, MYSQRT3/2, 0 }, + { 0.5, MYSQRT3/2, 0 }, + { 1, 0, 0 }, + { -0.5, -MYSQRT3/2, 0 }, + { 0, -MYSQRT3/3, MYSQRT6/3 }, + { 0.5, MYSQRT3/6, MYSQRT6/3 }, + { -0.5, MYSQRT3/6, MYSQRT6/3 }, +}; + +const double ptm_template_bcc[PTM_NUM_POINTS_BCC][3] = { + { 0, 0, 0 }, + { 7*MYSQRT3/3-7./2, 7*MYSQRT3/3-7./2, 7*MYSQRT3/3-7./2 }, + { 7./2-7*MYSQRT3/3, 7*MYSQRT3/3-7./2, 7*MYSQRT3/3-7./2 }, + { 7*MYSQRT3/3-7./2, 7*MYSQRT3/3-7./2, 7./2-7*MYSQRT3/3 }, + { 7./2-7*MYSQRT3/3, 7./2-7*MYSQRT3/3, 7*MYSQRT3/3-7./2 }, + { 7*MYSQRT3/3-7./2, 7./2-7*MYSQRT3/3, 7*MYSQRT3/3-7./2 }, + { 7./2-7*MYSQRT3/3, 7*MYSQRT3/3-7./2, 7./2-7*MYSQRT3/3 }, + { 7./2-7*MYSQRT3/3, 7./2-7*MYSQRT3/3, 7./2-7*MYSQRT3/3 }, + { 7*MYSQRT3/3-7./2, 7./2-7*MYSQRT3/3, 7./2-7*MYSQRT3/3 }, + { 14*MYSQRT3/3-7, 0, 0 }, + { 7-14*MYSQRT3/3, 0, 0 }, + { 0, 14*MYSQRT3/3-7, 0 }, + { 0, 7-14*MYSQRT3/3, 0 }, + { 0, 0, 14*MYSQRT3/3-7 }, + { 0, 0, 7-14*MYSQRT3/3 }, +}; + +const double ptm_template_ico[PTM_NUM_POINTS_ICO][3] = { + { 0, 0, 0 }, + { 0, 0, 1 }, + { 0, 0, -1 }, + { -MY5MINUSSQRT5BY10, (5+MYSQRT5)/10, -MYSQRT5/5 }, + { MY5MINUSSQRT5BY10, -(5+MYSQRT5)/10, MYSQRT5/5 }, + { 0, -2*MYSQRT5/5, -MYSQRT5/5 }, + { 0, 2*MYSQRT5/5, MYSQRT5/5 }, + { MY5PLUSSQRT5BY10, -(5-MYSQRT5)/10, -MYSQRT5/5 }, + { -MY5PLUSSQRT5BY10, (5-MYSQRT5)/10, MYSQRT5/5 }, + { -MY5PLUSSQRT5BY10, -(5-MYSQRT5)/10, -MYSQRT5/5 }, + { MY5PLUSSQRT5BY10, (5-MYSQRT5)/10, MYSQRT5/5 }, + { MY5MINUSSQRT5BY10, (5+MYSQRT5)/10, -MYSQRT5/5 }, + { -MY5MINUSSQRT5BY10, -(5+MYSQRT5)/10, MYSQRT5/5 }, +}; + +const double ptm_template_sc[PTM_NUM_POINTS_SC][3] = { + { 0, 0, 0 }, + { 0, 0, -1 }, + { 0, 0, 1 }, + { 0, -1, 0 }, + { 0, 1, 0 }, + { -1, 0, 0 }, + { 1, 0, 0 }, +}; + +const double ptm_template_dcub[PTM_NUM_POINTS_DCUB][3] = { + { 0, 0, 0 }, + { 4/(MYSQRT3+6*MYSQRT2), 4/(MYSQRT3+6*MYSQRT2), 4/(MYSQRT3+6*MYSQRT2) }, + { 4/(MYSQRT3+6*MYSQRT2), -4/(MYSQRT3+6*MYSQRT2), -4/(MYSQRT3+6*MYSQRT2) }, + { -4/(MYSQRT3+6*MYSQRT2), -4/(MYSQRT3+6*MYSQRT2), 4/(MYSQRT3+6*MYSQRT2) }, + { -4/(MYSQRT3+6*MYSQRT2), 4/(MYSQRT3+6*MYSQRT2), -4/(MYSQRT3+6*MYSQRT2) }, + { 8/(MYSQRT3+6*MYSQRT2), 8/(MYSQRT3+6*MYSQRT2), 0 }, + { 0, 8/(MYSQRT3+6*MYSQRT2), 8/(MYSQRT3+6*MYSQRT2) }, + { 8/(MYSQRT3+6*MYSQRT2), 0, 8/(MYSQRT3+6*MYSQRT2) }, + { 0, -8/(MYSQRT3+6*MYSQRT2), -8/(MYSQRT3+6*MYSQRT2) }, + { 8/(MYSQRT3+6*MYSQRT2), -8/(MYSQRT3+6*MYSQRT2), 0 }, + { 8/(MYSQRT3+6*MYSQRT2), 0, -8/(MYSQRT3+6*MYSQRT2) }, + { -8/(MYSQRT3+6*MYSQRT2), -8/(MYSQRT3+6*MYSQRT2), 0 }, + { 0, -8/(MYSQRT3+6*MYSQRT2), 8/(MYSQRT3+6*MYSQRT2) }, + { -8/(MYSQRT3+6*MYSQRT2), 0, 8/(MYSQRT3+6*MYSQRT2) }, + { -8/(MYSQRT3+6*MYSQRT2), 0, -8/(MYSQRT3+6*MYSQRT2) }, + { -8/(MYSQRT3+6*MYSQRT2), 8/(MYSQRT3+6*MYSQRT2), 0 }, + { 0, 8/(MYSQRT3+6*MYSQRT2), -8/(MYSQRT3+6*MYSQRT2) }, +}; + +const double ptm_template_dhex[PTM_NUM_POINTS_DHEX][3] = { + { 0, 0, 0 }, + { -4*MYSQRT2/(MYSQRT3+6*MYSQRT2), 4*MYSQRT6/(3*(MYSQRT3+6*MYSQRT2)), -4*MYSQRT3/(3*MYSQRT3+18*MYSQRT2) }, + { 0, -8*MYSQRT6/(3*MYSQRT3+18*MYSQRT2), -4*MYSQRT3/(3*MYSQRT3+18*MYSQRT2) }, + { 4*MYSQRT2/(MYSQRT3+6*MYSQRT2), 4*MYSQRT6/(3*(MYSQRT3+6*MYSQRT2)), -4*MYSQRT3/(3*MYSQRT3+18*MYSQRT2) }, + { 0, 0, 4*MYSQRT3/(MYSQRT3+6*MYSQRT2) }, + { -8*MYSQRT2/(MYSQRT3+6*MYSQRT2), 0, 0 }, + { -4*MYSQRT2/(MYSQRT3+6*MYSQRT2), 4*MYSQRT6/(3*(MYSQRT3+6*MYSQRT2)), -16*MYSQRT3/(3*(MYSQRT3+6*MYSQRT2)) }, + { -4*MYSQRT2/(MYSQRT3+6*MYSQRT2), 4*MYSQRT6/(MYSQRT3+6*MYSQRT2), 0 }, + { 4*MYSQRT2/(MYSQRT3+6*MYSQRT2), -4*MYSQRT6/(MYSQRT3+6*MYSQRT2), 0 }, + { 0, -8*MYSQRT6/(3*MYSQRT3+18*MYSQRT2), -16*MYSQRT3/(3*(MYSQRT3+6*MYSQRT2)) }, + { -4*MYSQRT2/(MYSQRT3+6*MYSQRT2), -4*MYSQRT6/(MYSQRT3+6*MYSQRT2), 0 }, + { 4*MYSQRT2/(MYSQRT3+6*MYSQRT2), 4*MYSQRT6/(3*(MYSQRT3+6*MYSQRT2)), -16*MYSQRT3/(3*(MYSQRT3+6*MYSQRT2)) }, + { 4*MYSQRT2/(MYSQRT3+6*MYSQRT2), 4*MYSQRT6/(MYSQRT3+6*MYSQRT2), 0 }, + { 8*MYSQRT2/(MYSQRT3+6*MYSQRT2), 0, 0 }, + { 0, -8*MYSQRT6/(3*MYSQRT3+18*MYSQRT2), 16*MYSQRT3/(3*(MYSQRT3+6*MYSQRT2)) }, + { 4*MYSQRT2/(MYSQRT3+6*MYSQRT2), 4*MYSQRT6/(3*(MYSQRT3+6*MYSQRT2)), 16*MYSQRT3/(3*(MYSQRT3+6*MYSQRT2)) }, + { -4*MYSQRT2/(MYSQRT3+6*MYSQRT2), 4*MYSQRT6/(3*(MYSQRT3+6*MYSQRT2)), 16*MYSQRT3/(3*(MYSQRT3+6*MYSQRT2)) }, +}; + +const double ptm_template_graphene[PTM_NUM_POINTS_GRAPHENE][3] = { + { 0, 0, 0 }, + { 0, -3./11+6*MYSQRT3/11, 0 }, + { -3*MYSQRT3/22+9./11, -3*MYSQRT3/11+3./22, 0 }, + { -9./11+3*MYSQRT3/22, -3*MYSQRT3/11+3./22, 0 }, + { -9./11+3*MYSQRT3/22, -9./22+9*MYSQRT3/11, 0 }, + { -3*MYSQRT3/22+9./11, -9./22+9*MYSQRT3/11, 0 }, + { -3*MYSQRT3/11+18./11, 0, 0 }, + { -3*MYSQRT3/22+9./11, -9*MYSQRT3/11+9./22, 0 }, + { -9./11+3*MYSQRT3/22, -9*MYSQRT3/11+9./22, 0 }, + { -18./11+3*MYSQRT3/11, 0, 0 }, +}; diff --git a/src/USER-PTM/ptm_constants.h b/src/USER-PTM/ptm_constants.h index c3882f622c..898ded6b49 100644 --- a/src/USER-PTM/ptm_constants.h +++ b/src/USER-PTM/ptm_constants.h @@ -10,63 +10,61 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #ifndef PTM_CONSTANTS_H #define PTM_CONSTANTS_H -#include - //------------------------------------ // definitions //------------------------------------ -#define PTM_NO_ERROR 0 +#define PTM_NO_ERROR 0 -#define PTM_CHECK_FCC (1 << 0) -#define PTM_CHECK_HCP (1 << 1) -#define PTM_CHECK_BCC (1 << 2) -#define PTM_CHECK_ICO (1 << 3) -#define PTM_CHECK_SC (1 << 4) -#define PTM_CHECK_DCUB (1 << 5) -#define PTM_CHECK_DHEX (1 << 6) -#define PTM_CHECK_GRAPHENE (1 << 7) -#define PTM_CHECK_DEFAULT (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC) +#define PTM_CHECK_FCC (1 << 0) +#define PTM_CHECK_HCP (1 << 1) +#define PTM_CHECK_BCC (1 << 2) +#define PTM_CHECK_ICO (1 << 3) +#define PTM_CHECK_SC (1 << 4) +#define PTM_CHECK_DCUB (1 << 5) +#define PTM_CHECK_DHEX (1 << 6) +#define PTM_CHECK_GRAPHENE (1 << 7) +#define PTM_CHECK_DEFAULT (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC) #define PTM_CHECK_ALL (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC | PTM_CHECK_DCUB | PTM_CHECK_DHEX | PTM_CHECK_GRAPHENE) -#define PTM_MATCH_NONE 0 -#define PTM_MATCH_FCC 1 -#define PTM_MATCH_HCP 2 -#define PTM_MATCH_BCC 3 -#define PTM_MATCH_ICO 4 -#define PTM_MATCH_SC 5 -#define PTM_MATCH_DCUB 6 -#define PTM_MATCH_DHEX 7 -#define PTM_MATCH_GRAPHENE 8 +#define PTM_MATCH_NONE 0 +#define PTM_MATCH_FCC 1 +#define PTM_MATCH_HCP 2 +#define PTM_MATCH_BCC 3 +#define PTM_MATCH_ICO 4 +#define PTM_MATCH_SC 5 +#define PTM_MATCH_DCUB 6 +#define PTM_MATCH_DHEX 7 +#define PTM_MATCH_GRAPHENE 8 -#define PTM_ALLOY_NONE 0 -#define PTM_ALLOY_PURE 1 -#define PTM_ALLOY_L10 2 -#define PTM_ALLOY_L12_CU 3 -#define PTM_ALLOY_L12_AU 4 -#define PTM_ALLOY_B2 5 -#define PTM_ALLOY_SIC 6 -#define PTM_ALLOY_BN 7 +#define PTM_ALLOY_NONE 0 +#define PTM_ALLOY_PURE 1 +#define PTM_ALLOY_L10 2 +#define PTM_ALLOY_L12_CU 3 +#define PTM_ALLOY_L12_AU 4 +#define PTM_ALLOY_B2 5 +#define PTM_ALLOY_SIC 6 +#define PTM_ALLOY_BN 7 #define PTM_MAX_INPUT_POINTS 19 -#define PTM_MAX_NBRS 16 -#define PTM_MAX_POINTS (PTM_MAX_NBRS + 1) -#define PTM_MAX_FACETS 28 //2 * PTM_MAX_NBRS - 4 -#define PTM_MAX_EDGES 42 //3 * PTM_MAX_NBRS - 6 +#define PTM_MAX_NBRS 16 +#define PTM_MAX_POINTS (PTM_MAX_NBRS + 1) +#define PTM_MAX_FACETS 28 //2 * PTM_MAX_NBRS - 4 +#define PTM_MAX_EDGES 42 //3 * PTM_MAX_NBRS - 6 //------------------------------------ // number of neighbours //------------------------------------ -#define PTM_NUM_NBRS_FCC 12 -#define PTM_NUM_NBRS_HCP 12 -#define PTM_NUM_NBRS_BCC 14 -#define PTM_NUM_NBRS_ICO 12 -#define PTM_NUM_NBRS_SC 6 -#define PTM_NUM_NBRS_DCUB 16 -#define PTM_NUM_NBRS_DHEX 16 -#define PTM_NUM_NBRS_GRAPHENE 9 +#define PTM_NUM_NBRS_FCC 12 +#define PTM_NUM_NBRS_HCP 12 +#define PTM_NUM_NBRS_BCC 14 +#define PTM_NUM_NBRS_ICO 12 +#define PTM_NUM_NBRS_SC 6 +#define PTM_NUM_NBRS_DCUB 16 +#define PTM_NUM_NBRS_DHEX 16 +#define PTM_NUM_NBRS_GRAPHENE 9 #define PTM_NUM_POINTS_FCC (PTM_NUM_NBRS_FCC + 1) #define PTM_NUM_POINTS_HCP (PTM_NUM_NBRS_HCP + 1) @@ -77,142 +75,22 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #define PTM_NUM_POINTS_DHEX (PTM_NUM_NBRS_DHEX + 1) #define PTM_NUM_POINTS_GRAPHENE (PTM_NUM_NBRS_GRAPHENE + 1) -const int ptm_num_nbrs[9] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS_BCC, PTM_NUM_NBRS_ICO, PTM_NUM_NBRS_SC, PTM_NUM_NBRS_DCUB, PTM_NUM_NBRS_DHEX, PTM_NUM_NBRS_GRAPHENE}; +extern const int ptm_num_nbrs[9]; //------------------------------------ // template structures //------------------------------------ -//these point sets have barycentre {0, 0, 0} and are scaled such that the mean neighbour distance is 1 +// these point sets have barycentre {0, 0, 0} and are scaled such that the mean neighbour distance is 1 -const double ptm_template_fcc[PTM_NUM_POINTS_FCC][3] = { - { 0, 0, 0 }, - { sqrt(2)/2, sqrt(2)/2, 0 }, - { 0, sqrt(2)/2, sqrt(2)/2 }, - { sqrt(2)/2, 0, sqrt(2)/2 }, - { -sqrt(2)/2, -sqrt(2)/2, 0 }, - { 0, -sqrt(2)/2, -sqrt(2)/2 }, - { -sqrt(2)/2, 0, -sqrt(2)/2 }, - { -sqrt(2)/2, sqrt(2)/2, 0 }, - { 0, -sqrt(2)/2, sqrt(2)/2 }, - { -sqrt(2)/2, 0, sqrt(2)/2 }, - { sqrt(2)/2, -sqrt(2)/2, 0 }, - { 0, sqrt(2)/2, -sqrt(2)/2 }, - { sqrt(2)/2, 0, -sqrt(2)/2 }, -}; - -const double ptm_template_hcp[PTM_NUM_POINTS_HCP][3] = { - { 0, 0, 0 }, - { 0.5, -sqrt(3)/2, 0 }, - { -1, 0, 0 }, - { -0.5, sqrt(3)/6, -sqrt(6)/3 }, - { 0.5, sqrt(3)/6, -sqrt(6)/3 }, - { 0, -sqrt(3)/3, -sqrt(6)/3 }, - { -0.5, sqrt(3)/2, 0 }, - { 0.5, sqrt(3)/2, 0 }, - { 1, 0, 0 }, - { -0.5, -sqrt(3)/2, 0 }, - { 0, -sqrt(3)/3, sqrt(6)/3 }, - { 0.5, sqrt(3)/6, sqrt(6)/3 }, - { -0.5, sqrt(3)/6, sqrt(6)/3 }, -}; - -const double ptm_template_bcc[PTM_NUM_POINTS_BCC][3] = { - { 0, 0, 0 }, - { 7*sqrt(3)/3-7./2, 7*sqrt(3)/3-7./2, 7*sqrt(3)/3-7./2 }, - { 7./2-7*sqrt(3)/3, 7*sqrt(3)/3-7./2, 7*sqrt(3)/3-7./2 }, - { 7*sqrt(3)/3-7./2, 7*sqrt(3)/3-7./2, 7./2-7*sqrt(3)/3 }, - { 7./2-7*sqrt(3)/3, 7./2-7*sqrt(3)/3, 7*sqrt(3)/3-7./2 }, - { 7*sqrt(3)/3-7./2, 7./2-7*sqrt(3)/3, 7*sqrt(3)/3-7./2 }, - { 7./2-7*sqrt(3)/3, 7*sqrt(3)/3-7./2, 7./2-7*sqrt(3)/3 }, - { 7./2-7*sqrt(3)/3, 7./2-7*sqrt(3)/3, 7./2-7*sqrt(3)/3 }, - { 7*sqrt(3)/3-7./2, 7./2-7*sqrt(3)/3, 7./2-7*sqrt(3)/3 }, - { 14*sqrt(3)/3-7, 0, 0 }, - { 7-14*sqrt(3)/3, 0, 0 }, - { 0, 14*sqrt(3)/3-7, 0 }, - { 0, 7-14*sqrt(3)/3, 0 }, - { 0, 0, 14*sqrt(3)/3-7 }, - { 0, 0, 7-14*sqrt(3)/3 }, -}; - -const double ptm_template_ico[PTM_NUM_POINTS_ICO][3] = { - { 0, 0, 0 }, - { 0, 0, 1 }, - { 0, 0, -1 }, - { -sqrt((5-sqrt(5))/10), (5+sqrt(5))/10, -sqrt(5)/5 }, - { sqrt((5-sqrt(5))/10), -(5+sqrt(5))/10, sqrt(5)/5 }, - { 0, -2*sqrt(5)/5, -sqrt(5)/5 }, - { 0, 2*sqrt(5)/5, sqrt(5)/5 }, - { sqrt((5+sqrt(5))/10), -(5-sqrt(5))/10, -sqrt(5)/5 }, - { -sqrt((5+sqrt(5))/10), (5-sqrt(5))/10, sqrt(5)/5 }, - { -sqrt((5+sqrt(5))/10), -(5-sqrt(5))/10, -sqrt(5)/5 }, - { sqrt((5+sqrt(5))/10), (5-sqrt(5))/10, sqrt(5)/5 }, - { sqrt((5-sqrt(5))/10), (5+sqrt(5))/10, -sqrt(5)/5 }, - { -sqrt((5-sqrt(5))/10), -(5+sqrt(5))/10, sqrt(5)/5 }, -}; - -const double ptm_template_sc[PTM_NUM_POINTS_SC][3] = { - { 0, 0, 0 }, - { 0, 0, -1 }, - { 0, 0, 1 }, - { 0, -1, 0 }, - { 0, 1, 0 }, - { -1, 0, 0 }, - { 1, 0, 0 }, -}; - -const double ptm_template_dcub[PTM_NUM_POINTS_DCUB][3] = { - { 0, 0, 0 }, - { 4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)) }, - { 4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)) }, - { -4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)) }, - { -4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)) }, - { 8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)), 0 }, - { 0, 8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)) }, - { 8/(sqrt(3)+6*sqrt(2)), 0, 8/(sqrt(3)+6*sqrt(2)) }, - { 0, -8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)) }, - { 8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)), 0 }, - { 8/(sqrt(3)+6*sqrt(2)), 0, -8/(sqrt(3)+6*sqrt(2)) }, - { -8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)), 0 }, - { 0, -8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)) }, - { -8/(sqrt(3)+6*sqrt(2)), 0, 8/(sqrt(3)+6*sqrt(2)) }, - { -8/(sqrt(3)+6*sqrt(2)), 0, -8/(sqrt(3)+6*sqrt(2)) }, - { -8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)), 0 }, - { 0, 8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)) }, -}; - -const double ptm_template_dhex[PTM_NUM_POINTS_DHEX][3] = { - { 0, 0, 0 }, - { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, - { 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, - { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, - { 0, 0, 4*sqrt(3)/(sqrt(3)+6*sqrt(2)) }, - { -8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 }, - { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, - { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, - { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, - { 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, - { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, - { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, - { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, - { 8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 }, - { 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, - { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, - { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, -}; - -const double ptm_template_graphene[PTM_NUM_POINTS_GRAPHENE][3] = { - { 0, 0, 0 }, - { 0, -3./11+6*sqrt(3)/11, 0 }, - { -3*sqrt(3)/22+9./11, -3*sqrt(3)/11+3./22, 0 }, - { -9./11+3*sqrt(3)/22, -3*sqrt(3)/11+3./22, 0 }, - { -9./11+3*sqrt(3)/22, -9./22+9*sqrt(3)/11, 0 }, - { -3*sqrt(3)/22+9./11, -9./22+9*sqrt(3)/11, 0 }, - { -3*sqrt(3)/11+18./11, 0, 0 }, - { -3*sqrt(3)/22+9./11, -9*sqrt(3)/11+9./22, 0 }, - { -9./11+3*sqrt(3)/22, -9*sqrt(3)/11+9./22, 0 }, - { -18./11+3*sqrt(3)/11, 0, 0 }, -}; +extern const double ptm_template_fcc[PTM_NUM_POINTS_FCC][3]; +extern const double ptm_template_hcp[PTM_NUM_POINTS_HCP][3]; +extern const double ptm_template_bcc[PTM_NUM_POINTS_BCC][3]; +extern const double ptm_template_ico[PTM_NUM_POINTS_ICO][3]; +extern const double ptm_template_sc[PTM_NUM_POINTS_SC][3]; +extern const double ptm_template_dcub[PTM_NUM_POINTS_DCUB][3]; +extern const double ptm_template_dhex[PTM_NUM_POINTS_DHEX][3]; +extern const double ptm_template_graphene[PTM_NUM_POINTS_GRAPHENE][3]; #endif From 7d85461e9798793bc2ecbc8aaba5175de05fe92b Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 2 Apr 2021 16:32:25 -0400 Subject: [PATCH 0346/1217] Prevent compilation from breaking with Python 2 --- src/PYTHON/python_impl.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index 4c43ca3744..c83385410a 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -56,6 +56,8 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp) nfunc = 0; pfuncs = nullptr; +#if PY_MAJOR_VERSION >= 3 +#ifndef Py_LIMITED_API // check for PYTHONUNBUFFERED environment variable const char * PYTHONUNBUFFERED = getenv("PYTHONUNBUFFERED"); @@ -64,6 +66,8 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp) // Force the stdout and stderr streams to be unbuffered. Py_UnbufferedStdioFlag = 1; } +#endif +#endif // one-time initialization of Python interpreter // pyMain stores pointer to main module From af6452065fbaa5bedcb3a942115384cf8f88e2e0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 16:48:13 -0400 Subject: [PATCH 0347/1217] correct URL to XTC file format docs on the gromacs homepage --- doc/src/dump.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/dump.rst b/doc/src/dump.rst index c94d9a8007..a5f11a792a 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -349,7 +349,7 @@ the box size stored with the snapshot. The *xtc* style writes XTC files, a compressed trajectory format used by the GROMACS molecular dynamics package, and described -`here `_. +`here `_. The precision used in XTC files can be adjusted via the :doc:`dump_modify ` command. The default value of 1000 means that coordinates are stored to 1/1000 nanometer accuracy. XTC From 2a10b5ba69010cb7df3901876273984a9ff1bbd7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 17:21:34 -0400 Subject: [PATCH 0348/1217] fix bug causing segfaults --- src/domain.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/domain.cpp b/src/domain.cpp index abf0d70079..8e666f2a45 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -1826,7 +1826,7 @@ void Domain::delete_region(int iregion) // delete and move other Regions down in list one slot delete regions[iregion]; - for (int i = iregion+1; iregion < nregion; ++i) + for (int i = iregion+1; i < nregion; ++i) regions[i-1] = regions[i]; nregion--; } From abfe8bab5915d833fa88c274ce221dbc8612f7dc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 17:32:29 -0400 Subject: [PATCH 0349/1217] fix uninitialized memory access issues. consolidate enumerators. --- src/GRANULAR/fix_wall_gran.cpp | 45 ++++++++++++++------------- src/GRANULAR/fix_wall_gran.h | 4 +++ src/GRANULAR/fix_wall_gran_region.cpp | 33 +++++++++----------- 3 files changed, 41 insertions(+), 41 deletions(-) diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 5e8d568b7a..2efc189e6d 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -17,29 +17,25 @@ ------------------------------------------------------------------------- */ #include "fix_wall_gran.h" -#include -#include + #include "atom.h" #include "domain.h" -#include "update.h" +#include "error.h" #include "force.h" -#include "modify.h" -#include "respa.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "modify.h" #include "neighbor.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; -// XYZ PLANE need to be 0,1,2 - -enum{XPLANE=0,YPLANE=1,ZPLANE=2,ZCYLINDER,REGION}; -enum{HOOKE,HOOKE_HISTORY,HERTZ_HISTORY,GRANULAR}; -enum{NONE,CONSTANT,EQUAL}; - #define PI27SQ 266.47931882941264802866 // 27*PI**2 #define THREEROOT3 5.19615242270663202362 // 3*sqrt(3) #define SIXROOT6 14.69693845669906728801 // 6*sqrt(6) @@ -48,18 +44,20 @@ enum{NONE,CONSTANT,EQUAL}; #define THREEQUARTERS 0.75 // 3/4 #define TWOPI 6.28318530717959 // 2*PI -#define EPSILON 1e-10 - -enum {NORMAL_HOOKE, NORMAL_HERTZ, HERTZ_MATERIAL, DMT, JKR}; -enum {VELOCITY, MASS_VELOCITY, VISCOELASTIC, TSUJI}; -enum {TANGENTIAL_NOHISTORY, TANGENTIAL_HISTORY, - TANGENTIAL_MINDLIN, TANGENTIAL_MINDLIN_RESCALE}; -enum {TWIST_NONE, TWIST_SDS, TWIST_MARSHALL}; -enum {ROLL_NONE, ROLL_SDS}; - #define BIG 1.0e20 #define EPSILON 1e-10 +// XYZ PLANE need to be 0,1,2 + +enum {XPLANE=0,YPLANE=1,ZPLANE=2,ZCYLINDER,REGION}; + +enum {NONE,CONSTANT,EQUAL}; +enum {DAMPING_NONE, VELOCITY, MASS_VELOCITY, VISCOELASTIC, TSUJI}; +enum {TANGENTIAL_NONE, TANGENTIAL_NOHISTORY, TANGENTIAL_HISTORY, + TANGENTIAL_MINDLIN, TANGENTIAL_MINDLIN_RESCALE}; +enum {TWIST_NONE, TWIST_SDS, TWIST_MARSHALL}; +enum {ROLL_NONE, ROLL_SDS}; + /* ---------------------------------------------------------------------- */ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : @@ -84,6 +82,10 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : use_history = restart_peratom = 1; if (pairstyle == HOOKE) use_history = restart_peratom = 0; + tangential_history = roll_history = twist_history = 0; + normal_model = NORMAL_NONE; + tangential_model = TANGENTIAL_NONE; + damping_model = DAMPING_NONE; // wall/particle coefficients @@ -120,7 +122,6 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : iarg = 4; damping_model = VISCOELASTIC; roll_model = twist_model = NONE; - tangential_history = roll_history = twist_history = 0; while (iarg < narg) { if (strcmp(arg[iarg], "hooke") == 0) { if (iarg + 2 >= narg) diff --git a/src/GRANULAR/fix_wall_gran.h b/src/GRANULAR/fix_wall_gran.h index a81a4c787c..bf4797e960 100644 --- a/src/GRANULAR/fix_wall_gran.h +++ b/src/GRANULAR/fix_wall_gran.h @@ -26,6 +26,10 @@ namespace LAMMPS_NS { class FixWallGran : public Fix { public: + + enum {HOOKE,HOOKE_HISTORY,HERTZ_HISTORY,GRANULAR}; + enum {NORMAL_NONE, NORMAL_HOOKE, NORMAL_HERTZ, HERTZ_MATERIAL, DMT, JKR}; + FixWallGran(class LAMMPS *, int, char **); virtual ~FixWallGran(); int setmask(); diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index 5e670a0a07..b051fbea57 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -16,26 +16,21 @@ ------------------------------------------------------------------------- */ #include "fix_wall_gran_region.h" -#include -#include "region.h" + #include "atom.h" -#include "domain.h" -#include "update.h" -#include "memory.h" -#include "error.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "memory.h" #include "neighbor.h" +#include "region.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; -// same as FixWallGran - -enum{HOOKE,HOOKE_HISTORY,HERTZ_HISTORY,GRANULAR}; -enum {NORMAL_HOOKE, NORMAL_HERTZ, HERTZ_MATERIAL, DMT, JKR}; - -#define BIG 1.0e20 - /* ---------------------------------------------------------------------- */ FixWallGranRegion::FixWallGranRegion(LAMMPS *lmp, int narg, char **arg) : @@ -186,7 +181,7 @@ void FixWallGranRegion::post_force(int /*vflag*/) if (mask[i] & groupbit) { if (!region->match(x[i][0],x[i][1],x[i][2])) continue; - if (pairstyle == GRANULAR && normal_model == JKR) { + if (pairstyle == FixWallGran::GRANULAR && normal_model == FixWallGran::JKR) { nc = region->surface(x[i][0],x[i][1],x[i][2], radius[i]+pulloff_distance(radius[i])); } @@ -228,7 +223,7 @@ void FixWallGranRegion::post_force(int /*vflag*/) rsq = region->contact[ic].r*region->contact[ic].r; - if (pairstyle == GRANULAR && normal_model == JKR) { + if (pairstyle == FixWallGran::GRANULAR && normal_model == FixWallGran::JKR) { if (history_many[i][c2r[ic]][0] == 0.0 && rsq > radius[i]*radius[i]) { for (m = 0; m < size_history; m++) history_many[i][0][m] = 0.0; @@ -264,18 +259,18 @@ void FixWallGranRegion::post_force(int /*vflag*/) else contact = nullptr; - if (pairstyle == HOOKE) + if (pairstyle == FixWallGran::HOOKE) hooke(rsq,dx,dy,dz,vwall,v[i],f[i], omega[i],torque[i],radius[i],meff, contact); - else if (pairstyle == HOOKE_HISTORY) + else if (pairstyle == FixWallGran::HOOKE_HISTORY) hooke_history(rsq,dx,dy,dz,vwall,v[i],f[i], omega[i],torque[i],radius[i],meff, history_many[i][c2r[ic]], contact); - else if (pairstyle == HERTZ_HISTORY) + else if (pairstyle == FixWallGran::HERTZ_HISTORY) hertz_history(rsq,dx,dy,dz,vwall,region->contact[ic].radius, v[i],f[i],omega[i],torque[i], radius[i],meff,history_many[i][c2r[ic]], contact); - else if (pairstyle == GRANULAR) + else if (pairstyle == FixWallGran::GRANULAR) granular(rsq,dx,dy,dz,vwall,region->contact[ic].radius, v[i],f[i],omega[i],torque[i], radius[i],meff,history_many[i][c2r[ic]],contact); From 2c00136f2219760e961baaa2604cc1f3bab849b2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 17:49:15 -0400 Subject: [PATCH 0350/1217] used correct suffix when installing plugin binaries for testing --- unittest/commands/CMakeLists.txt | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/unittest/commands/CMakeLists.txt b/unittest/commands/CMakeLists.txt index a658c8a25d..7cd2687fb7 100644 --- a/unittest/commands/CMakeLists.txt +++ b/unittest/commands/CMakeLists.txt @@ -11,13 +11,13 @@ if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows" AND PKG_PLUGIN) -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE} - BUILD_BYPRODUCTS /morse2plugin${CMAKE_SHARED_LIBRARY_SUFFIX} - /nve2plugin${CMAKE_SHARED_LIBRARY_SUFFIX} - /helloplugin${CMAKE_SHARED_LIBRARY_SUFFIX} + BUILD_BYPRODUCTS /morse2plugin${CMAKE_SHARED_MODULE_SUFFIX} + /nve2plugin${CMAKE_SHARED_MODULE_SUFFIX} + /helloplugin${CMAKE_SHARED_MODULE_SUFFIX} INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_if_different - /morse2plugin${CMAKE_SHARED_LIBRARY_SUFFIX} - /nve2plugin${CMAKE_SHARED_LIBRARY_SUFFIX} - /helloplugin${CMAKE_SHARED_LIBRARY_SUFFIX} + /morse2plugin${CMAKE_SHARED_MODULE_SUFFIX} + /nve2plugin${CMAKE_SHARED_MODULE_SUFFIX} + /helloplugin${CMAKE_SHARED_MODULE_SUFFIX} ${CMAKE_CURRENT_BINARY_DIR} TEST_COMMAND "") endif() From 51212e62d968f441a94bafcc5ee3f59385d99498 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 19:55:53 -0400 Subject: [PATCH 0351/1217] correct/update docs and parameter names for finding neighbor lists --- python/lammps/core.py | 64 ++++++++++++++++++++++++++++--------------- python/lammps/data.py | 2 +- 2 files changed, 43 insertions(+), 23 deletions(-) diff --git a/python/lammps/core.py b/python/lammps/core.py index 3118cb3d99..823175e65a 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -1721,17 +1721,23 @@ class lammps(object): # ------------------------------------------------------------------------- - def find_pair_neighlist(self, style, exact=True, nsub=0, request=0): + def find_pair_neighlist(self, style, exact=True, nsub=0, reqid=0): """Find neighbor list index of pair style neighbor list - Try finding pair instance that matches style. If exact is set, the pair must - match style exactly. If exact is 0, style must only be contained. If pair is - of style pair/hybrid, style is instead matched the nsub-th hybrid sub-style. + Search for a neighbor list requested by a pair style instance that + matches "style". If exact is True, the pair style name must match + exactly. If exact is False, the pair style name is matched against + "style" as regular expression or substring. If the pair style is a + hybrid pair style, the style is instead matched against the hybrid + sub-styles. If the same pair style is used as substyle multiple + types, you must set nsub to a value n > 0 which indicates the nth + instance of that sub-style to be used (same as for the pair_coeff + command). The default value of 0 will fail to match in that case. - Once the pair instance has been identified, multiple neighbor list requests - may be found. Every neighbor list is uniquely identified by its request - index. Thus, providing this request index ensures that the correct neighbor - list index is returned. + Once the pair style instance has been identified, it may have + requested multiple neighbor lists. Those are uniquely identified by + a request ID > 0 as set by the pair style. Otherwise the request + ID is 0. :param style: name of pair style that should be searched for :type style: string @@ -1739,44 +1745,58 @@ class lammps(object): :type exact: bool, optional :param nsub: match nsub-th hybrid sub-style, defaults to 0 :type nsub: int, optional - :param request: index of neighbor list request, in case there are more than one, defaults to 0 - :type request: int, optional + :param reqid: list request id, > 0 in case there are more than one, defaults to 0 + :type reqid: int, optional :return: neighbor list index if found, otherwise -1 :rtype: int - """ + + """ style = style.encode() exact = int(exact) - idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, exact, nsub, request) + idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, exact, nsub, reqid) return idx # ------------------------------------------------------------------------- - def find_fix_neighlist(self, fixid, request=0): + def find_fix_neighlist(self, fixid, reqid=0): """Find neighbor list index of fix neighbor list + The fix instance requesting the neighbor list is uniquely identified + by the fix ID. In case the fix has requested multiple neighbor + lists, those are uniquely identified by a request ID > 0 as set by + the fix. Otherwise the request ID is 0 (the default). + :param fixid: name of fix :type fixid: string - :param request: index of neighbor list request, in case there are more than one, defaults to 0 - :type request: int, optional + :param reqid: id of neighbor list request, in case there are more than one request, defaults to 0 + :type reqid: int, optional :return: neighbor list index if found, otherwise -1 :rtype: int - """ + + """ fixid = fixid.encode() - idx = self.lib.lammps_find_fix_neighlist(self.lmp, fixid, request) + idx = self.lib.lammps_find_fix_neighlist(self.lmp, fixid, reqid) return idx # ------------------------------------------------------------------------- - def find_compute_neighlist(self, computeid, request=0): + def find_compute_neighlist(self, computeid, reqid=0): """Find neighbor list index of compute neighbor list + The compute instance requesting the neighbor list is uniquely + identified by the compute ID. In case the compute has requested + multiple neighbor lists, those are uniquely identified by a request + ID > 0 as set by the compute. Otherwise the request ID is 0 (the + default). + :param computeid: name of compute :type computeid: string - :param request: index of neighbor list request, in case there are more than one, defaults to 0 - :type request: int, optional + :param reqid: index of neighbor list request, in case there are more than one request, defaults to 0 + :type reqid: int, optional :return: neighbor list index if found, otherwise -1 :rtype: int - """ + + """ computeid = computeid.encode() - idx = self.lib.lammps_find_compute_neighlist(self.lmp, computeid, request) + idx = self.lib.lammps_find_compute_neighlist(self.lmp, computeid, reqid) return idx diff --git a/python/lammps/data.py b/python/lammps/data.py index 2cf100ed82..1613936ddf 100644 --- a/python/lammps/data.py +++ b/python/lammps/data.py @@ -52,7 +52,7 @@ class NeighList: def get(self, element): """ - :return: tuple with atom local index, numpy array of neighbor local atom indices + :return: tuple with atom local index, number of neighbors and ctypes pointer to neighbor's local atom indices :rtype: (int, int, ctypes.POINTER(c_int)) """ iatom, numneigh, neighbors = self.lmp.get_neighlist_element_neighbors(self.idx, element) From c74bb9b56bfcce915287937af8c4dcf27cca3eee Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 21:00:26 -0400 Subject: [PATCH 0352/1217] add more unit tests for neighbor list access --- unittest/python/CMakeLists.txt | 1 + unittest/python/python-commands.py | 230 ++++++++++++++++++++++++++--- 2 files changed, 209 insertions(+), 22 deletions(-) diff --git a/unittest/python/CMakeLists.txt b/unittest/python/CMakeLists.txt index d1db17c941..b51d6e340a 100644 --- a/unittest/python/CMakeLists.txt +++ b/unittest/python/CMakeLists.txt @@ -28,6 +28,7 @@ endif() if(Python_EXECUTABLE) # prepare to augment the environment so that the LAMMPS python module and the shared library is found. set(PYTHON_TEST_ENVIRONMENT PYTHONPATH=${LAMMPS_PYTHON_DIR}:$ENV{PYTHONPATH}) + list(APPEND PYTHON_TEST_ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") if(APPLE) list(APPEND PYTHON_TEST_ENVIRONMENT "DYLD_LIBRARY_PATH=${CMAKE_BINARY_DIR}:$ENV{DYLD_LIBRARY_PATH};LAMMPS_CMAKE_CACHE=${CMAKE_BINARY_DIR}/CMakeCache.txt") else() diff --git a/unittest/python/python-commands.py b/unittest/python/python-commands.py index 3661feb8a0..1c388460d1 100644 --- a/unittest/python/python-commands.py +++ b/unittest/python/python-commands.py @@ -1,6 +1,17 @@ import sys,os,unittest -from lammps import lammps, LMP_VAR_ATOM +from lammps import lammps, LMP_VAR_ATOM, LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR + +has_manybody=False +try: + machine=None + if 'LAMMPS_MACHINE_NAME' in os.environ: + machine=os.environ['LAMMPS_MACHINE_NAME'] + lmp=lammps(name=machine) + has_manybody = lmp.has_style("pair","sw") + lmp.close() +except: + pass class PythonCommand(unittest.TestCase): @@ -85,35 +96,34 @@ create_atoms 1 single & natoms = self.lmp.get_natoms() self.assertEqual(natoms,2) - def testNeighborList(self): - self.lmp.command("units lj") - self.lmp.command("atom_style atomic") - self.lmp.command("atom_modify map array") - self.lmp.command("boundary f f f") - self.lmp.command("region box block 0 2 0 2 0 2") - self.lmp.command("create_box 1 box") - - x = [ - 1.0, 1.0, 1.0, - 1.0, 1.0, 1.5 - ] + def testNeighborListSimple(self): + self.lmp.commands_string(""" + units lj + atom_style atomic + atom_modify map array + boundary f f f + region box block 0 2 0 2 0 2 + create_box 1 box""") + x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5 ] types = [1, 1] self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 2) - self.lmp.command("mass 1 1.0") - self.lmp.command("velocity all create 3.0 87287") - self.lmp.command("pair_style lj/cut 2.5") - self.lmp.command("pair_coeff 1 1 1.0 1.0 2.5") - self.lmp.command("neighbor 0.1 bin") - self.lmp.command("neigh_modify every 20 delay 0 check no") + self.lmp.commands_string(""" + mass 1 1.0 + velocity all create 3.0 87287 + pair_style lj/cut 2.5 + pair_coeff 1 1 1.0 1.0 2.5 + neighbor 0.1 bin + neigh_modify every 20 delay 0 check no + run 0 post no""") - self.lmp.command("run 0") - - self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"), 0) + idx = self.lmp.find_pair_neighlist("lj/cut") + self.assertEqual(0, 0) + self.assertEqual(self.lmp.find_pair_neighlist("morse"), -1) nlist = self.lmp.get_neighlist(0) self.assertEqual(len(nlist), 2) atom_i, numneigh_i, neighbors_i = nlist[0] @@ -127,6 +137,182 @@ create_atoms 1 single & self.assertEqual(1, neighbors_i[0]) + def testNeighborListHalf(self): + self.lmp.commands_string(""" + boundary f f f + units real + region box block -5 5 -5 5 -5 5 + create_box 1 box + mass 1 1.0 + pair_style lj/cut 4.0 + pair_coeff 1 1 0.2 2.0 + """) + x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, + 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, + 0.0, 0.0, 1.0 ] + tags = [1, 2, 3, 4, 5, 6, 7] + types = [1, 1, 1, 1, 1, 1, 1] + + self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) + nlocal = self.lmp.extract_global("nlocal") + self.assertEqual(nlocal, 7) + + self.lmp.command("run 0 post no") + + self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"),0) + nlist = self.lmp.get_neighlist(0) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, num, neighs = nlist.get(i) + self.assertEqual(idx,i) + self.assertEqual(num,nlocal-1-i) + + @unittest.skipIf(not has_manybody,"Full neighbor list test for manybody potential") + def testNeighborListFull(self): + self.lmp.commands_string(""" + boundary f f f + units metal + region box block -5 5 -5 5 -5 5 + create_box 1 box + mass 1 1.0 + pair_style sw + pair_coeff * * Si.sw Si + """) + x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, + 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, + 0.0, 0.0, 1.0 ] + tags = [1, 2, 3, 4, 5, 6, 7] + types = [1, 1, 1, 1, 1, 1, 1] + + self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) + nlocal = self.lmp.extract_global("nlocal") + self.assertEqual(nlocal, 7) + + self.lmp.command("run 0 post no") + + self.assertEqual(self.lmp.find_pair_neighlist("sw"),0) + nlist = self.lmp.get_neighlist(0) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, num, neighs = nlist.get(i) + self.assertEqual(idx,i) + self.assertEqual(num,nlocal-1) + + @unittest.skipIf(not has_manybody,"Hybrid neighbor list test for manybody potential") + def testNeighborListHybrid(self): + self.lmp.commands_string(""" + boundary f f f + units metal + region box block -5 5 -5 5 -5 5 + create_box 2 box + mass * 1.0 + pair_style hybrid/overlay morse 4.0 lj/cut 4.0 lj/cut 4.0 sw + pair_coeff * * sw Si.sw Si NULL + pair_coeff 1 2 morse 0.2 2.0 2.0 + pair_coeff 2 2 lj/cut 1 0.1 2.0 + pair_coeff * * lj/cut 2 0.01 2.0 + """) + x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, + 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, + 0.0, 0.0, 1.0 ] + tags = [1, 2, 3, 4, 5, 6, 7] + types = [1, 1, 1, 1, 2, 2, 2] + + self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) + nlocal = self.lmp.extract_global("nlocal") + self.assertEqual(nlocal, 7) + + self.lmp.command("run 0 post no") + + # valid and invalid lookups + self.assertNotEqual(self.lmp.find_pair_neighlist("sw"),-1) + self.assertNotEqual(self.lmp.find_pair_neighlist("morse"),-1) + self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut",nsub=1),-1) + self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut",nsub=2),-1) + self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"),-1) + self.assertEqual(self.lmp.find_pair_neighlist("hybrid/overlay"),-1) + self.assertNotEqual(self.lmp.get_neighlist(4).size,0) + self.assertEqual(self.lmp.get_neighlist(5).size,-1) + + # full neighbor list for 4 type 1 atoms + # all have 3 type 1 atom neighbors + nlist = self.lmp.get_neighlist(self.lmp.find_pair_neighlist("sw")) + self.assertEqual(nlist.size, 4) + for i in range(0,nlist.size): + idx, num, neighs = nlist.get(i) + self.assertEqual(idx,i) + self.assertEqual(num,3) + + # half neighbor list for all pairs between type 1 and type 2 + # 4 type 1 atoms with 3 type 2 neighbors and 3 type 2 atoms without neighbors + nlist = self.lmp.get_neighlist(self.lmp.find_pair_neighlist("morse")) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, num, neighs = nlist.get(i) + if (i < 4): self.assertEqual(num,3) + else: self.assertEqual(num,0) + + # half neighbor list between type 2 atoms only + # 3 pairs with 2, 1, 0 neighbors + nlist = self.lmp.get_neighlist(self.lmp.find_pair_neighlist("lj/cut",nsub=1)) + self.assertEqual(nlist.size, 3) + for i in range(0,nlist.size): + idx, num, neighs = nlist.get(i) + self.assertEqual(num,2-i) + + # half neighbor list between all pairs. same as simple lj/cut case + nlist = self.lmp.get_neighlist(self.lmp.find_pair_neighlist("lj/cut",nsub=2)) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, num, neighs = nlist.get(i) + self.assertEqual(num,nlocal-1-i) + + def testNeighborListCompute(self): + self.lmp.commands_string(""" + boundary f f f + units real + region box block -5 5 -5 5 -5 5 + create_box 1 box + mass 1 1.0 + pair_style lj/cut 4.0 + pair_coeff 1 1 0.2 2.0 + compute dist all pair/local dist + fix dist all ave/histo 1 1 1 0.0 3.0 4 c_dist mode vector + thermo_style custom f_dist[*] + """) + x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, + 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, + 0.0, 0.0, 1.0 ] + tags = [1, 2, 3, 4, 5, 6, 7] + types = [1, 1, 1, 1, 1, 1, 1] + + self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) + nlocal = self.lmp.extract_global("nlocal") + self.assertEqual(nlocal, 7) + + self.lmp.command("run 0 post no") + # check compute data from histogram summary + nhisto = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=0) + nskip = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=1) + minval = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=2) + maxval = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=3) + # 21 pair distances counted, none skipped, smallest 1.0, largest 2.1 + self.assertEqual(nhisto,21) + self.assertEqual(nskip,0) + self.assertEqual(minval,1.0) + self.assertEqual(maxval,2.1) + + self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut"),-1) + self.assertNotEqual(self.lmp.find_compute_neighlist("dist"),-1) + + # the compute has a half neighbor list + nlist = self.lmp.get_neighlist(self.lmp.find_compute_neighlist("dist")) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, num, neighs = nlist.get(i) + self.assertEqual(idx,i) + self.assertEqual(num,nlocal-1-i) + def test_extract_box_non_periodic(self): self.lmp.command("boundary f f f") self.lmp.command("region box block 0 2 0 2 0 2") From 7e70def4cc64d704866735e6ffbc59448f62e18b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 21:00:42 -0400 Subject: [PATCH 0353/1217] fix errors/typos in manual --- doc/src/Python_module.rst | 2 +- doc/src/fix_ave_histo.rst | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/src/Python_module.rst b/doc/src/Python_module.rst index d2564986de..c19d4b0345 100644 --- a/doc/src/Python_module.rst +++ b/doc/src/Python_module.rst @@ -142,7 +142,7 @@ Style Constants Type Constants -------------- -.. py:data:: LMP_TYPE_SCALAR, LMP_TYLE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS +.. py:data:: LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS :type: int Constants in the :py:mod:`lammps` module to select what type of data diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index d50112ac48..3a2857f383 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -138,8 +138,8 @@ vector or columns of the array had been listed one by one. E.g. these .. code-block:: LAMMPS compute myCOM all com/chunk - fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector - fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector + fix 1 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[*] file tmp1.com mode vector + fix 2 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector If the fix ave/histo/weight command is used, exactly two values must be specified. If the values are vectors, they must be the same From 85a5698c1b93d22c5e29de49dcc4fe66518945cf Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 21:40:45 -0400 Subject: [PATCH 0354/1217] add find method to neighbor list wrapper classes --- python/lammps/data.py | 19 +++++++++++++++++++ python/lammps/numpy_wrapper.py | 17 +++++++++++++++++ unittest/python/python-commands.py | 13 +++++++++++-- 3 files changed, 47 insertions(+), 2 deletions(-) diff --git a/python/lammps/data.py b/python/lammps/data.py index 1613936ddf..892d628356 100644 --- a/python/lammps/data.py +++ b/python/lammps/data.py @@ -52,6 +52,8 @@ class NeighList: def get(self, element): """ + Access a specific neighbor list entry. "element" must be a number from 0 to the size-1 of the list + :return: tuple with atom local index, number of neighbors and ctypes pointer to neighbor's local atom indices :rtype: (int, int, ctypes.POINTER(c_int)) """ @@ -71,3 +73,20 @@ class NeighList: for ii in range(inum): yield self.get(ii) + + def find(self, iatom): + """ + Find the neighbor list for a specific (local) atom iatom. + If there is no list for iatom, (-1, None) is returned. + + :return: tuple with number of neighbors and ctypes pointer to neighbor's local atom indices + :rtype: (int, ctypes.POINTER(c_int)) + """ + + inum = self.size + for ii in range(inum): + idx, numneigh, neighbors = self.get(ii) + if idx == iatom: + return numneigh, neighbors + + return -1, None diff --git a/python/lammps/numpy_wrapper.py b/python/lammps/numpy_wrapper.py index ce64d68c90..1ecaf3163b 100644 --- a/python/lammps/numpy_wrapper.py +++ b/python/lammps/numpy_wrapper.py @@ -331,8 +331,25 @@ class NumPyNeighList(NeighList): def get(self, element): """ + Access a specific neighbor list entry. "element" must be a number from 0 to the size-1 of the list + :return: tuple with atom local index, numpy array of neighbor local atom indices :rtype: (int, numpy.array) """ iatom, neighbors = self.lmp.numpy.get_neighlist_element_neighbors(self.idx, element) return iatom, neighbors + + def find(self, iatom): + """ + Find the neighbor list for a specific (local) atom iatom. + If there is no list for iatom, None is returned. + + :return: numpy array of neighbor local atom indices + :rtype: numpy.array or None + """ + inum = self.size + for ii in range(inum): + idx, neighbors = self.get(ii) + if idx == iatom: + return neighbors + return None diff --git a/unittest/python/python-commands.py b/unittest/python/python-commands.py index 1c388460d1..530cea8b13 100644 --- a/unittest/python/python-commands.py +++ b/unittest/python/python-commands.py @@ -122,9 +122,9 @@ create_atoms 1 single & run 0 post no""") idx = self.lmp.find_pair_neighlist("lj/cut") - self.assertEqual(0, 0) + self.assertNotEqual(idx, -1) self.assertEqual(self.lmp.find_pair_neighlist("morse"), -1) - nlist = self.lmp.get_neighlist(0) + nlist = self.lmp.get_neighlist(idx) self.assertEqual(len(nlist), 2) atom_i, numneigh_i, neighbors_i = nlist[0] atom_j, numneigh_j, _ = nlist[1] @@ -167,6 +167,15 @@ create_atoms 1 single & self.assertEqual(idx,i) self.assertEqual(num,nlocal-1-i) + # look up neighbor list by atom index + num, neighs = nlist.find(2) + self.assertEqual(num,4) + self.assertIsNotNone(neighs,None) + # this one will fail + num, neighs = nlist.find(10) + self.assertEqual(num,-1) + self.assertIsNone(neighs,None) + @unittest.skipIf(not has_manybody,"Full neighbor list test for manybody potential") def testNeighborListFull(self): self.lmp.commands_string(""" From d3b2ccf9dd5b6f0f6265db73b12b5e6115cfd80f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 21:41:26 -0400 Subject: [PATCH 0355/1217] numpy version of neighbor list tests --- unittest/python/python-numpy.py | 237 +++++++++++++++++++++++++++++--- 1 file changed, 215 insertions(+), 22 deletions(-) diff --git a/unittest/python/python-numpy.py b/unittest/python/python-numpy.py index 9f1d5f12c8..f3a116b91b 100644 --- a/unittest/python/python-numpy.py +++ b/unittest/python/python-numpy.py @@ -4,6 +4,17 @@ from lammps import lammps, LAMMPS_INT, LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL, \ LMP_VAR_ATOM from ctypes import c_void_p +has_manybody=False +try: + machine=None + if 'LAMMPS_MACHINE_NAME' in os.environ: + machine=os.environ['LAMMPS_MACHINE_NAME'] + lmp=lammps(name=machine) + has_manybody = lmp.has_style("pair","sw") + lmp.close() +except: + pass + try: import numpy NUMPY_INSTALLED = True @@ -137,36 +148,34 @@ class PythonNumpy(unittest.TestCase): self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all()) self.assertEqual(len(v), 2) - def testNeighborList(self): - self.lmp.command("units lj") - self.lmp.command("atom_style atomic") - self.lmp.command("atom_modify map array") - self.lmp.command("boundary f f f") - self.lmp.command("region box block 0 2 0 2 0 2") - self.lmp.command("create_box 1 box") - - x = [ - 1.0, 1.0, 1.0, - 1.0, 1.0, 1.5 - ] + def testNeighborListSimple(self): + self.lmp.commands_string(""" + units lj + atom_style atomic + atom_modify map array + boundary f f f + region box block 0 2 0 2 0 2 + create_box 1 box""") + x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5 ] types = [1, 1] self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 2) - self.lmp.command("mass 1 1.0") - self.lmp.command("velocity all create 3.0 87287") - self.lmp.command("pair_style lj/cut 2.5") - self.lmp.command("pair_coeff 1 1 1.0 1.0 2.5") - self.lmp.command("neighbor 0.1 bin") - self.lmp.command("neigh_modify every 20 delay 0 check no") + self.lmp.commands_string(""" + mass 1 1.0 + velocity all create 3.0 87287 + pair_style lj/cut 2.5 + pair_coeff 1 1 1.0 1.0 2.5 + neighbor 0.1 bin + neigh_modify every 20 delay 0 check no + run 0 post no""") - self.lmp.command("run 0") - - self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"), 0) - nlist = self.lmp.numpy.get_neighlist(0) + idx = self.lmp.find_pair_neighlist("lj/cut") + self.assertNotEqual(idx, -1) + nlist = self.lmp.numpy.get_neighlist(idx) self.assertEqual(len(nlist), 2) atom_i, neighbors_i = nlist[0] atom_j, neighbors_j = nlist[1] @@ -180,6 +189,190 @@ class PythonNumpy(unittest.TestCase): self.assertIn(1, neighbors_i) self.assertNotIn(0, neighbors_j) + def testNeighborListHalf(self): + self.lmp.commands_string(""" + boundary f f f + units real + region box block -5 5 -5 5 -5 5 + create_box 1 box + mass 1 1.0 + pair_style lj/cut 4.0 + pair_coeff 1 1 0.2 2.0 + """) + x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, + 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, + 0.0, 0.0, 1.0 ] + tags = [1, 2, 3, 4, 5, 6, 7] + types = [1, 1, 1, 1, 1, 1, 1] + + self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) + nlocal = self.lmp.extract_global("nlocal") + self.assertEqual(nlocal, 7) + + self.lmp.command("run 0 post no") + + self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"),0) + nlist = self.lmp.numpy.get_neighlist(0) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, neighs = nlist.get(i) + self.assertEqual(idx,i) + self.assertEqual(neighs.size,nlocal-1-i) + + # look up neighbor list by atom index + neighs = nlist.find(2) + self.assertEqual(neighs.size,4) + self.assertIsNotNone(neighs,None) + # this one will fail + neighs = nlist.find(10) + self.assertIsNone(neighs,None) + + @unittest.skipIf(not has_manybody,"Full neighbor list test for manybody potential") + def testNeighborListFull(self): + self.lmp.commands_string(""" + boundary f f f + units metal + region box block -5 5 -5 5 -5 5 + create_box 1 box + mass 1 1.0 + pair_style sw + pair_coeff * * Si.sw Si + """) + x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, + 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, + 0.0, 0.0, 1.0 ] + tags = [1, 2, 3, 4, 5, 6, 7] + types = [1, 1, 1, 1, 1, 1, 1] + + self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) + nlocal = self.lmp.extract_global("nlocal") + self.assertEqual(nlocal, 7) + + self.lmp.command("run 0 post no") + + self.assertEqual(self.lmp.find_pair_neighlist("sw"),0) + nlist = self.lmp.numpy.get_neighlist(0) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, neighs = nlist.get(i) + self.assertEqual(idx,i) + self.assertEqual(neighs.size,nlocal-1) + + @unittest.skipIf(not has_manybody,"Hybrid neighbor list test for manybody potential") + def testNeighborListHybrid(self): + self.lmp.commands_string(""" + boundary f f f + units metal + region box block -5 5 -5 5 -5 5 + create_box 2 box + mass * 1.0 + pair_style hybrid/overlay morse 4.0 lj/cut 4.0 lj/cut 4.0 sw + pair_coeff * * sw Si.sw Si NULL + pair_coeff 1 2 morse 0.2 2.0 2.0 + pair_coeff 2 2 lj/cut 1 0.1 2.0 + pair_coeff * * lj/cut 2 0.01 2.0 + """) + x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, + 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, + 0.0, 0.0, 1.0 ] + tags = [1, 2, 3, 4, 5, 6, 7] + types = [1, 1, 1, 1, 2, 2, 2] + + self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) + nlocal = self.lmp.extract_global("nlocal") + self.assertEqual(nlocal, 7) + + self.lmp.command("run 0 post no") + + # valid and invalid lookups + self.assertNotEqual(self.lmp.find_pair_neighlist("sw"),-1) + self.assertNotEqual(self.lmp.find_pair_neighlist("morse"),-1) + self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut",nsub=1),-1) + self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut",nsub=2),-1) + self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"),-1) + self.assertEqual(self.lmp.find_pair_neighlist("hybrid/overlay"),-1) + self.assertNotEqual(self.lmp.numpy.get_neighlist(4).size,0) + self.assertEqual(self.lmp.numpy.get_neighlist(5).size,-1) + + # full neighbor list for 4 type 1 atoms + # all have 3 type 1 atom neighbors + nlist = self.lmp.numpy.get_neighlist(self.lmp.find_pair_neighlist("sw")) + self.assertEqual(nlist.size, 4) + for i in range(0,nlist.size): + idx, neighs = nlist.get(i) + self.assertEqual(idx,i) + self.assertEqual(neighs.size,3) + + # half neighbor list for all pairs between type 1 and type 2 + # 4 type 1 atoms with 3 type 2 neighbors and 3 type 2 atoms without neighbors + nlist = self.lmp.numpy.get_neighlist(self.lmp.find_pair_neighlist("morse")) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, neighs = nlist.get(i) + if (i < 4): self.assertEqual(neighs.size,3) + else: self.assertEqual(neighs.size,0) + + # half neighbor list between type 2 atoms only + # 3 pairs with 2, 1, 0 neighbors + nlist = self.lmp.numpy.get_neighlist(self.lmp.find_pair_neighlist("lj/cut",nsub=1)) + self.assertEqual(nlist.size, 3) + for i in range(0,nlist.size): + idx, neighs = nlist.get(i) + self.assertEqual(neighs.size,2-i) + + # half neighbor list between all pairs. same as simple lj/cut case + nlist = self.lmp.numpy.get_neighlist(self.lmp.find_pair_neighlist("lj/cut",nsub=2)) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, neighs = nlist.get(i) + self.assertEqual(neighs.size,nlocal-1-i) + + def testNeighborListCompute(self): + self.lmp.commands_string(""" + boundary f f f + units real + region box block -5 5 -5 5 -5 5 + create_box 1 box + mass 1 1.0 + pair_style lj/cut 4.0 + pair_coeff 1 1 0.2 2.0 + compute dist all pair/local dist + fix dist all ave/histo 1 1 1 0.0 3.0 4 c_dist mode vector + thermo_style custom f_dist[*] + """) + x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, + 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, + 0.0, 0.0, 1.0 ] + tags = [1, 2, 3, 4, 5, 6, 7] + types = [1, 1, 1, 1, 1, 1, 1] + + self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) + nlocal = self.lmp.extract_global("nlocal") + self.assertEqual(nlocal, 7) + + self.lmp.command("run 0 post no") + # check compute data from histogram summary + nhisto = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=0) + nskip = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=1) + minval = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=2) + maxval = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=3) + # 21 pair distances counted, none skipped, smallest 1.0, largest 2.1 + self.assertEqual(nhisto,21) + self.assertEqual(nskip,0) + self.assertEqual(minval,1.0) + self.assertEqual(maxval,2.1) + + self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut"),-1) + self.assertNotEqual(self.lmp.find_compute_neighlist("dist"),-1) + + # the compute has a half neighbor list + nlist = self.lmp.numpy.get_neighlist(self.lmp.find_compute_neighlist("dist")) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, neighs = nlist.get(i) + self.assertEqual(idx,i) + self.assertEqual(neighs.size,nlocal-1-i) + def test_extract_variable_equalstyle(self): self.lmp.command("variable a equal 100") a = self.lmp.numpy.extract_variable("a") From 678302bfcb33486ea6cf1320538b203796e02306 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Apr 2021 22:08:39 -0400 Subject: [PATCH 0356/1217] avoid a floating point exception in RanMars::rayleigh() from taking log(0) --- src/random_mars.cpp | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/src/random_mars.cpp b/src/random_mars.cpp index 621d7d3008..78c6f93ba4 100644 --- a/src/random_mars.cpp +++ b/src/random_mars.cpp @@ -136,13 +136,16 @@ double RanMars::gaussian(double mu, double sigma) double RanMars::rayleigh(double sigma) { - double first,v1; + double v1; - if (sigma <= 0) error->all(FLERR,"Invalid Rayleigh parameter"); + if (sigma <= 0.0) error->all(FLERR,"Invalid Rayleigh parameter"); v1 = uniform(); - first = sigma*sqrt(-2.0*log(v1)); - return first; + // avoid a floating point exception due to log(0.0) + // and just return a very big number + if (v1 == 0.0) return 1.0e300; + + return sigma*sqrt(-2.0*log(v1)); } /* ---------------------------------------------------------------------- From b1faf17eeb4ee978e25a034f4804afdf176c2f46 Mon Sep 17 00:00:00 2001 From: Dan Bolintineanu Date: Sat, 3 Apr 2021 00:48:00 -0600 Subject: [PATCH 0357/1217] Updates fix wall/gran to mirror recent updates to pair granular. Also some minor changes related to the limit_damping option --- doc/src/pair_gran.rst | 4 +- doc/src/pair_granular.rst | 2 +- src/GRANULAR/fix_wall_gran.cpp | 174 ++- src/GRANULAR/pair_gran_hooke_history.cpp | 6 +- src/GRANULAR/pair_granular.cpp | 31 +- src/GRANULAR/pair_granular_corrected.cpp | 1821 ++++++++++++++++++++++ 6 files changed, 1968 insertions(+), 70 deletions(-) create mode 100644 src/GRANULAR/pair_granular_corrected.cpp diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index b918e38da6..7d6189fda1 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -36,7 +36,7 @@ Syntax * xmu = static yield criterion (unitless value between 0.0 and 1.0e4) * dampflag = 0 or 1 if tangential damping force is excluded or included -* keyword = *no_attraction* +* keyword = *limit_damping* .. parsed-literal:: @@ -61,6 +61,8 @@ Examples pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1 pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0 + pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0 limit_damping + Description """"""""""" diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index 04c9d45afd..e0a33f31d0 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -24,7 +24,7 @@ Examples pair_coeff * * hooke 1000.0 50.0 tangential linear_history 500.0 1.0 0.4 damping mass_velocity pair_style granular - pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 + pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 limit_damping pair_style granular pair_coeff * * hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index c9d00ccdd3..1d27e21162 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -53,7 +53,8 @@ enum{NONE,CONSTANT,EQUAL}; enum {NORMAL_HOOKE, NORMAL_HERTZ, HERTZ_MATERIAL, DMT, JKR}; enum {VELOCITY, MASS_VELOCITY, VISCOELASTIC, TSUJI}; enum {TANGENTIAL_NOHISTORY, TANGENTIAL_HISTORY, - TANGENTIAL_MINDLIN, TANGENTIAL_MINDLIN_RESCALE}; + TANGENTIAL_MINDLIN, TANGENTIAL_MINDLIN_RESCALE, + TANGENTIAL_MINDLIN_FORCE, TANGENTIAL_MINDLIN_RESCALE_FORCE}; enum {TWIST_NONE, TWIST_SDS, TWIST_MARSHALL}; enum {ROLL_NONE, ROLL_SDS}; @@ -216,7 +217,9 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : iarg += 4; } else if ((strcmp(arg[iarg+1], "linear_history") == 0) || (strcmp(arg[iarg+1], "mindlin") == 0) || - (strcmp(arg[iarg+1], "mindlin_rescale") == 0)) { + (strcmp(arg[iarg+1], "mindlin_rescale") == 0) || + (strcmp(arg[iarg+1], "mindlin/force") == 0) || + (strcmp(arg[iarg+1], "mindlin_rescale/force") == 0)) { if (iarg + 4 >= narg) error->all(FLERR,"Illegal pair_coeff command, " "not enough parameters provided for tangential model"); @@ -226,8 +229,14 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : tangential_model = TANGENTIAL_MINDLIN; else if (strcmp(arg[iarg+1], "mindlin_rescale") == 0) tangential_model = TANGENTIAL_MINDLIN_RESCALE; + else if (strcmp(arg[iarg+1], "mindlin/force") == 0) + tangential_model = TANGENTIAL_MINDLIN_FORCE; + else if (strcmp(arg[iarg+1], "mindlin_rescale/force") == 0) + tangential_model = TANGENTIAL_MINDLIN_RESCALE_FORCE; if ((tangential_model == TANGENTIAL_MINDLIN || - tangential_model == TANGENTIAL_MINDLIN_RESCALE) && + tangential_model == TANGENTIAL_MINDLIN_RESCALE || + tangential_model == TANGENTIAL_MINDLIN_FORCE || + tangential_model == TANGENTIAL_MINDLIN_RESCALE_FORCE) && (strcmp(arg[iarg+2], "NULL") == 0)) { if (normal_model == NORMAL_HERTZ || normal_model == NORMAL_HOOKE) { error->all(FLERR, "NULL setting for Mindlin tangential " @@ -306,14 +315,20 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : } } size_history = 3*tangential_history + 3*roll_history + twist_history; + //Unlike the pair style, the wall style does not have a 'touch' + //array. Hence, an additional entry in the history is used to + //determine if particles previously contacted for JKR cohesion purposes. if (normal_model == JKR) size_history += 1; - if (tangential_model == TANGENTIAL_MINDLIN_RESCALE) size_history += 1; + if (tangential_model == TANGENTIAL_MINDLIN_RESCALE || + tangential_model == TANGENTIAL_MINDLIN_RESCALE_FORCE) size_history += 1; } - if(normal_model == JKR) - error->all(FLERR,"Cannot limit damping with JRK model"); - if(normal_model == DMT) - error->all(FLERR,"Cannot limit damping with DMT model"); + if (limit_damping and normal_model == JKR) + error->all(FLERR,"Illegal pair_coeff command, " + "cannot limit damping with JRK model"); + if (limit_damping and normal_model == DMT) + error->all(FLERR,"Illegal pair_coeff command, " + "Cannot limit damping with DMT model"); // wallstyle args @@ -509,7 +524,8 @@ void FixWallGran::init() roll_history_index += 1; twist_history_index += 1; } - if (tangential_model == TANGENTIAL_MINDLIN_RESCALE) { + if (tangential_model == TANGENTIAL_MINDLIN_RESCALE || + tangential_model == TANGENTIAL_MINDLIN_RESCALE_FORCE) { roll_history_index += 1; twist_history_index += 1; } @@ -1120,7 +1136,8 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, double signtwist, magtwist, magtortwist, Mtcrit; double tortwist1, tortwist2, tortwist3; - double shrmag,rsht; + double shrmag,rsht,prjmag; + bool frameupdate; r = sqrt(rsq); E = normal_coeffs[0]; @@ -1195,12 +1212,18 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; - if(limit_damping and Fntot < 0.0) Fntot = 0.0; + if (limit_damping and Fntot < 0.0) Fntot = 0.0; //**************************************** // tangential force, including history effects //**************************************** + // For linear, mindlin, mindlin_rescale: + // history = cumulative tangential displacement + // + // For mindlin/force, mindlin_rescale/force: + // history = cumulative tangential elastic force + // tangential component vt1 = vr1 - vn1; vt2 = vr2 - vn2; @@ -1242,69 +1265,115 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, int thist2 = thist1 + 1; if (tangential_history) { - if (tangential_model == TANGENTIAL_MINDLIN) { + if (tangential_model == TANGENTIAL_MINDLIN || + tangential_model == TANGENTIAL_MINDLIN_FORCE) { k_tangential *= a; } - else if (tangential_model == TANGENTIAL_MINDLIN_RESCALE) { + else if (tangential_model == + TANGENTIAL_MINDLIN_RESCALE || + tangential_model == + TANGENTIAL_MINDLIN_RESCALE_FORCE){ k_tangential *= a; - if (a < history[3]) { //On unloading, rescale the shear displacements + // on unloading, rescale the shear displacements/force + if (a < history[thist2+1]) { double factor = a/history[thist2+1]; history[thist0] *= factor; history[thist1] *= factor; history[thist2] *= factor; } } - shrmag = sqrt(history[thist0]*history[thist0] + - history[thist1]*history[thist1] + - history[thist2]*history[thist2]); + // rotate and update displacements. // see e.g. eq. 17 of Luding, Gran. Matter 2008, v10,p235 if (history_update) { rsht = history[thist0]*nx + history[thist1]*ny + history[thist2]*nz; - if (fabs(rsht) < EPSILON) rsht = 0; - if (rsht > 0) { - // if rhst == shrmag, contacting pair has rotated 90 deg in one step, - // in which case you deserve a crash! - scalefac = shrmag/(shrmag - rsht); + if (tangential_model == TANGENTIAL_MINDLIN_FORCE || + tangential_model == TANGENTIAL_MINDLIN_RESCALE_FORCE) + frameupdate = fabs(rsht) > EPSILON*Fscrit; + else + frameupdate = fabs(rsht)*k_tangential > EPSILON*Fscrit; + if (frameupdate) { + shrmag = sqrt(history[thist0]*history[thist0] + + history[thist1]*history[thist1] + + history[thist2]*history[thist2]); + // projection history[thist0] -= rsht*nx; history[thist1] -= rsht*ny; history[thist2] -= rsht*nz; + // also rescale to preserve magnitude + prjmag = sqrt(history[0]*history[0] + history[1]*history[1] + + history[2]*history[2]); + if (prjmag > 0) scalefac = shrmag/prjmag; + else scalefac = 0; history[thist0] *= scalefac; history[thist1] *= scalefac; history[thist2] *= scalefac; } // update history + if (tangential_model == TANGENTIAL_HISTORY || + tangential_model == TANGENTIAL_MINDLIN || + tangential_model == TANGENTIAL_MINDLIN_RESCALE) { history[thist0] += vtr1*dt; history[thist1] += vtr2*dt; history[thist2] += vtr3*dt; + } else{ + // tangential force + // see e.g. eq. 18 of Thornton et al, Pow. Tech. 2013, v223,p30-46 + history[thist0] -= k_tangential*vtr1*dt; + history[thist1] -= k_tangential*vtr2*dt; + history[thist2] -= k_tangential*vtr3*dt; + } + if (tangential_model == TANGENTIAL_MINDLIN_RESCALE || + tangential_model == TANGENTIAL_MINDLIN_RESCALE_FORCE) + history[thist2+1] = a; } // tangential forces = history + tangential velocity damping - fs1 = -k_tangential*history[thist0] - damp_tangential*vtr1; - fs2 = -k_tangential*history[thist1] - damp_tangential*vtr2; - fs3 = -k_tangential*history[thist2] - damp_tangential*vtr3; + if (tangential_model == TANGENTIAL_HISTORY || + tangential_model == TANGENTIAL_MINDLIN || + tangential_model == TANGENTIAL_MINDLIN_RESCALE) { + fs1 = -k_tangential*history[thist0] - damp_tangential*vtr1; + fs2 = -k_tangential*history[thist1] - damp_tangential*vtr2; + fs3 = -k_tangential*history[thist2] - damp_tangential*vtr3; + } else { + fs1 = history[thist0] - damp_tangential*vtr1; + fs2 = history[thist1] - damp_tangential*vtr2; + fs3 = history[thist2] - damp_tangential*vtr3; + } // rescale frictional displacements and forces if needed Fscrit = tangential_coeffs[2] * Fncrit; fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3); if (fs > Fscrit) { + shrmag = sqrt(history[thist0]*history[thist0] + + history[thist1]*history[thist1] + + history[thist2]*history[thist2]); if (shrmag != 0.0) { - history[thist0] = -1.0/k_tangential*(Fscrit*fs1/fs + - damp_tangential*vtr1); - history[thist1] = -1.0/k_tangential*(Fscrit*fs2/fs + - damp_tangential*vtr2); - history[thist2] = -1.0/k_tangential*(Fscrit*fs3/fs + - damp_tangential*vtr3); + if (tangential_model == TANGENTIAL_HISTORY || + tangential_model == TANGENTIAL_MINDLIN || + tangential_model == + TANGENTIAL_MINDLIN_RESCALE) { + history[thist0] = -1.0/k_tangential*(Fscrit*fs1/fs + + damp_tangential*vtr1); + history[thist1] = -1.0/k_tangential*(Fscrit*fs2/fs + + damp_tangential*vtr2); + history[thist2] = -1.0/k_tangential*(Fscrit*fs3/fs + + damp_tangential*vtr3); + } else { + history[thist0] = Fscrit*fs1/fs + damp_tangential*vtr1; + history[thist1] = Fscrit*fs2/fs + damp_tangential*vtr2; + history[thist2] = Fscrit*fs3/fs + damp_tangential*vtr3; + } fs1 *= Fscrit/fs; fs2 *= Fscrit/fs; fs3 *= Fscrit/fs; } else fs1 = fs2 = fs3 = 0.0; } } else { // classic pair gran/hooke (no history) - fs = meff*damp_tangential*vrel; - if (vrel != 0.0) Ft = MIN(Fne,fs) / vrel; + fs = damp_tangential*vrel; + if (vrel != 0.0) Ft = MIN(Fscrit,fs) / vrel; else Ft = 0.0; fs1 = -Ft*vtr1; fs2 = -Ft*vtr2; @@ -1315,14 +1384,14 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, // rolling resistance //**************************************** - if (roll_model != ROLL_NONE || twist_model != NONE) { + if (roll_model != ROLL_NONE || twist_model != TWIST_NONE) { relrot1 = omega[0]; relrot2 = omega[1]; relrot3 = omega[2]; } if (roll_model != ROLL_NONE) { - - // rolling velocity, see eq. 31 of Wang et al, Particuology v 23, p 49 (2015) + // rolling velocity, + // see eq. 31 of Wang et al, Particuology v 23, p 49 (2015) // This is different from the Marshall papers, // which use the Bagi/Kuhn formulation // for rolling velocity (see Wang et al for why the latter is wrong) @@ -1334,21 +1403,29 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, int rhist1 = rhist0 + 1; int rhist2 = rhist1 + 1; - // rolling displacement - rollmag = sqrt(history[rhist0]*history[rhist0] + - history[rhist1]*history[rhist1] + - history[rhist2]*history[rhist2]); - - rolldotn = history[rhist0]*nx + history[rhist1]*ny + history[rhist2]*nz; + k_roll = roll_coeffs[0]; + damp_roll = roll_coeffs[1]; + Frcrit = roll_coeffs[2] * Fncrit; if (history_update) { - if (fabs(rolldotn) < EPSILON) rolldotn = 0; - if (rolldotn > 0) { // rotate into tangential plane - scalefac = rollmag/(rollmag - rolldotn); + rolldotn = history[rhist0]*nx + history[rhist1]*ny + history[rhist2]*nz; + frameupdate = fabs(rolldotn)*k_roll > EPSILON*Frcrit; + if (frameupdate) { // rotate into tangential plane + rollmag = sqrt(history[rhist0]*history[rhist0] + + history[rhist1]*history[rhist1] + + history[rhist2]*history[rhist2]); + // projection history[rhist0] -= rolldotn*nx; history[rhist1] -= rolldotn*ny; history[rhist2] -= rolldotn*nz; + // also rescale to preserve magnitude + prjmag = sqrt(history[rhist0]*history[rhist0] + + history[rhist1]*history[rhist1] + + history[rhist2]*history[rhist2]); + + if (prjmag > 0) scalefac = rollmag/prjmag; + else scalefac = 0; history[rhist0] *= scalefac; history[rhist1] *= scalefac; history[rhist2] *= scalefac; @@ -1358,17 +1435,16 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, history[rhist2] += vrl3*dt; } - k_roll = roll_coeffs[0]; - damp_roll = roll_coeffs[1]; fr1 = -k_roll*history[rhist0] - damp_roll*vrl1; fr2 = -k_roll*history[rhist1] - damp_roll*vrl2; fr3 = -k_roll*history[rhist2] - damp_roll*vrl3; // rescale frictional displacements and forces if needed - Frcrit = roll_coeffs[2] * Fncrit; - fr = sqrt(fr1*fr1 + fr2*fr2 + fr3*fr3); if (fr > Frcrit) { + rollmag = sqrt(history[rhist0]*history[rhist0] + + history[rhist1]*history[rhist1] + + history[rhist2]*history[rhist2]); if (rollmag != 0.0) { history[rhist0] = -1.0/k_roll*(Frcrit*fr1/fr + damp_roll*vrl1); history[rhist1] = -1.0/k_roll*(Frcrit*fr2/fr + damp_roll*vrl2); diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index a86af2116e..4f7a6e20ec 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -237,7 +237,7 @@ void PairGranHookeHistory::compute(int eflag, int vflag) damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if(limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities @@ -372,8 +372,8 @@ void PairGranHookeHistory::settings(int narg, char **arg) if (dampflag == 0) gammat = 0.0; limit_damping = 0; - if(narg == 7) { - if(strcmp(arg[6], "limit_damping") == 0) limit_damping = 1; + if (narg == 7) { + if (strcmp(arg[6], "limit_damping") == 0) limit_damping = 1; else error->all(FLERR,"Illegal pair_style command"); } diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index dc829879e8..8bf9b0c4ed 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -365,13 +365,13 @@ void PairGranular::compute(int eflag, int vflag) damp_normal = a*meff; } else if (damping_model[itype][jtype] == TSUJI) { damp_normal = sqrt(meff*knfac); - } + } else damp_normal = 0.0; damp_normal_prefactor = normal_coeffs[itype][jtype][1]*damp_normal; Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; - if(limit_damping[itype][jtype] and Fntot < 0.0) Fntot = 0.0; + if (limit_damping[itype][jtype] and Fntot < 0.0) Fntot = 0.0; //**************************************** // tangential force, including history effects @@ -542,20 +542,17 @@ void PairGranular::compute(int eflag, int vflag) relrot1 = omega[i][0] - omega[j][0]; relrot2 = omega[i][1] - omega[j][1]; relrot3 = omega[i][2] - omega[j][2]; - // rolling velocity, - // see eq. 31 of Wang et al, Particuology v 23, p 49 (2015) - // this is different from the Marshall papers, - // which use the Bagi/Kuhn formulation - // for rolling velocity (see Wang et al for why the latter is wrong) - // - 0.5*((radj-radi)/radsum)*vtr1; - // - 0.5*((radj-radi)/radsum)*vtr2; - // - 0.5*((radj-radi)/radsum)*vtr3; } //**************************************** // rolling resistance //**************************************** if (roll_model[itype][jtype] != ROLL_NONE) { + // rolling velocity, + // see eq. 31 of Wang et al, Particuology v 23, p 49 (2015) + // this is different from the Marshall papers, + // which use the Bagi/Kuhn formulation + // for rolling velocity (see Wang et al for why the latter is wrong) vrl1 = Reff*(relrot2*nz - relrot3*ny); vrl2 = Reff*(relrot3*nx - relrot1*nz); vrl3 = Reff*(relrot1*ny - relrot2*nx); @@ -974,12 +971,12 @@ void PairGranular::coeff(int narg, char **arg) } else if (strcmp(arg[iarg], "limit_damping") == 0) { ld_flag = 1; iarg += 1; - } else error->all(FLERR, "Illegal pair coeff command"); + } else error->all(FLERR, "Illegal pair_coeff command"); } // error not to specify normal or tangential model if ((normal_model_one < 0) || (tangential_model_one < 0)) - error->all(FLERR, "Illegal pair coeff command, " + error->all(FLERR, "Illegal pair_coeff command, " "must specify normal or tangential contact model"); int count = 0; @@ -991,11 +988,13 @@ void PairGranular::coeff(int narg, char **arg) 27.467*powint(cor,4)-18.022*powint(cor,5)+4.8218*powint(cor,6); } else damp = normal_coeffs_one[1]; - if(ld_flag and normal_model_one == JKR) - error->all(FLERR,"Cannot limit damping with JKR model"); + if (ld_flag and normal_model_one == JKR) + error->all(FLERR,"Illegal pair_coeff command, " + "Cannot limit damping with JKR model"); - if(ld_flag and normal_model_one == DMT) - error->all(FLERR,"Cannot limit damping with DMT model"); + if (ld_flag and normal_model_one == DMT) + error->all(FLERR,"Illegal pair_coeff command, " + "Cannot limit damping with DMT model"); for (int i = ilo; i <= ihi; i++) { for (int j = MAX(jlo,i); j <= jhi; j++) { diff --git a/src/GRANULAR/pair_granular_corrected.cpp b/src/GRANULAR/pair_granular_corrected.cpp new file mode 100644 index 0000000000..bcf262aa2c --- /dev/null +++ b/src/GRANULAR/pair_granular_corrected.cpp @@ -0,0 +1,1821 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: + Dan Bolintineanu (SNL), Ishan Srivastava (SNL), Jeremy Lechman(SNL) + Leo Silbert (SNL), Gary Grest (SNL) +----------------------------------------------------------------------- */ + +#include "pair_granular.h" + +#include +#include + +#include "atom.h" +#include "force.h" +#include "update.h" +#include "modify.h" +#include "fix.h" +#include "fix_dummy.h" +#include "fix_neigh_history.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "memory.h" +#include "error.h" +#include "math_const.h" +#include "math_special.h" + + +using namespace LAMMPS_NS; +using namespace MathConst; +using namespace MathSpecial; + +#define PI27SQ 266.47931882941264802866 // 27*PI**2 +#define THREEROOT3 5.19615242270663202362 // 3*sqrt(3) +#define SIXROOT6 14.69693845669906728801 // 6*sqrt(6) +#define INVROOT6 0.40824829046386307274 // 1/sqrt(6) +#define FOURTHIRDS 4.0/3.0 // 4/3 +#define THREEQUARTERS 0.75 // 3/4 + +#define EPSILON 1e-10 + +enum {HOOKE, HERTZ, HERTZ_MATERIAL, DMT, JKR}; +enum {VELOCITY, MASS_VELOCITY, VISCOELASTIC, TSUJI}; +enum {TANGENTIAL_NOHISTORY, TANGENTIAL_HISTORY, + TANGENTIAL_MINDLIN, TANGENTIAL_MINDLIN_RESCALE, + TANGENTIAL_MINDLIN_FORCE, TANGENTIAL_MINDLIN_RESCALE_FORCE}; +enum {TWIST_NONE, TWIST_SDS, TWIST_MARSHALL}; +enum {ROLL_NONE, ROLL_SDS}; + +/* ---------------------------------------------------------------------- */ + +PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 1; + no_virial_fdotr_compute = 1; + centroidstressflag = CENTROID_NOTAVAIL; + + single_extra = 12; + svector = new double[single_extra]; + + neighprev = 0; + + nmax = 0; + mass_rigid = nullptr; + + onerad_dynamic = nullptr; + onerad_frozen = nullptr; + maxrad_dynamic = nullptr; + maxrad_frozen = nullptr; + + history_transfer_factors = nullptr; + + dt = update->dt; + + // set comm size needed by this Pair if used with fix rigid + + comm_forward = 1; + + use_history = 0; + beyond_contact = 0; + nondefault_history_transfer = 0; + tangential_history_index = 0; + roll_history_index = twist_history_index = 0; + + // create dummy fix as placeholder for FixNeighHistory + // this is so final order of Modify:fix will conform to input script + + fix_history = nullptr; + modify->add_fix("NEIGH_HISTORY_GRANULAR_DUMMY all DUMMY"); + fix_dummy = (FixDummy *) modify->fix[modify->nfix-1]; +} + +/* ---------------------------------------------------------------------- */ + +PairGranular::~PairGranular() +{ + delete [] svector; + + if (!fix_history) modify->delete_fix("NEIGH_HISTORY_GRANULAR_DUMMY"); + else modify->delete_fix("NEIGH_HISTORY_GRANULAR"); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(cutoff_type); + + memory->destroy(normal_coeffs); + memory->destroy(tangential_coeffs); + memory->destroy(roll_coeffs); + memory->destroy(twist_coeffs); + + memory->destroy(Emod); + memory->destroy(poiss); + + memory->destroy(normal_model); + memory->destroy(damping_model); + memory->destroy(tangential_model); + memory->destroy(roll_model); + memory->destroy(twist_model); + + delete [] onerad_dynamic; + delete [] onerad_frozen; + delete [] maxrad_dynamic; + delete [] maxrad_frozen; + } + + memory->destroy(mass_rigid); +} + +/* ---------------------------------------------------------------------- */ + +void PairGranular::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz,nx,ny,nz; + double radi,radj,radsum,rsq,r,rinv; + double Reff, delta, dR, dR2, dist_to_contact; + + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double wr1,wr2,wr3; + double vtr1,vtr2,vtr3,vrel; + + double knfac, damp_normal=0.0, damp_normal_prefactor; + double k_tangential, damp_tangential; + double Fne, Ft, Fdamp, Fntot, Fncrit, Fscrit, Frcrit; + double fs, fs1, fs2, fs3, tor1, tor2, tor3; + + double mi,mj,meff; + double relrot1,relrot2,relrot3,vrl1,vrl2,vrl3; + + // for JKR + double R2, coh, F_pulloff, delta_pulloff, dist_pulloff, a, a2, E; + double t0, t1, t2, t3, t4, t5, t6; + double sqrt1, sqrt2, sqrt3; + + // rolling + double k_roll, damp_roll; + double torroll1, torroll2, torroll3; + double rollmag, rolldotn, scalefac; + double fr, fr1, fr2, fr3; + + // twisting + double k_twist, damp_twist, mu_twist; + double signtwist, magtwist, magtortwist, Mtcrit; + double tortwist1, tortwist2, tortwist3; + + double shrmag,rsht,prjmag; + bool frameupdate; + int *ilist,*jlist,*numneigh,**firstneigh; + int *touch,**firsttouch; + double *history,*allhistory,**firsthistory; + + bool touchflag = false; + const bool historyupdate = (update->setupflag) ? false : true; + + ev_init(eflag,vflag); + + // update rigid body info for owned & ghost atoms if using FixRigid masses + // body[i] = which body atom I is in, -1 if none + // mass_body = mass of each rigid body + + if (fix_rigid && neighbor->ago == 0) { + int tmp; + int *body = (int *) fix_rigid->extract("body",tmp); + double *mass_body = (double *) fix_rigid->extract("masstotal",tmp); + if (atom->nmax > nmax) { + memory->destroy(mass_rigid); + nmax = atom->nmax; + memory->create(mass_rigid,nmax,"pair:mass_rigid"); + } + int nlocal = atom->nlocal; + for (i = 0; i < nlocal; i++) + if (body[i] >= 0) mass_rigid[i] = mass_body[body[i]]; + else mass_rigid[i] = 0.0; + comm->forward_comm_pair(this); + } + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + int *type = atom->type; + double **omega = atom->omega; + double **torque = atom->torque; + double *radius = atom->radius; + double *rmass = atom->rmass; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + if (use_history) { + firsttouch = fix_history->firstflag; + firsthistory = fix_history->firstvalue; + } + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + radi = radius[i]; + if (use_history) { + touch = firsttouch[i]; + allhistory = firsthistory[i]; + } + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + jtype = type[j]; + rsq = delx*delx + dely*dely + delz*delz; + radj = radius[j]; + radsum = radi + radj; + + E = normal_coeffs[itype][jtype][0]; + Reff = radi*radj/radsum; + touchflag = false; + + if (normal_model[itype][jtype] == JKR) { + E *= THREEQUARTERS; + if (touch[jj]) { + R2 = Reff*Reff; + coh = normal_coeffs[itype][jtype][3]; + a = cbrt(9.0*MY_PI*coh*R2/(4*E)); + delta_pulloff = a*a/Reff - 2*sqrt(MY_PI*coh*a/E); + dist_pulloff = radsum-delta_pulloff; + touchflag = (rsq < dist_pulloff*dist_pulloff); + } else { + touchflag = (rsq < radsum*radsum); + } + } else { + touchflag = (rsq < radsum*radsum); + } + + if (!touchflag) { + // unset non-touching neighbors + if (use_history) { + touch[jj] = 0; + history = &allhistory[size_history*jj]; + for (int k = 0; k < size_history; k++) history[k] = 0.0; + } + } else { + r = sqrt(rsq); + rinv = 1.0/r; + + nx = delx*rinv; + ny = dely*rinv; + nz = delz*rinv; + + // relative translational velocity + + vr1 = v[i][0] - v[j][0]; + vr2 = v[i][1] - v[j][1]; + vr3 = v[i][2] - v[j][2]; + + // normal component + + vnnr = vr1*nx + vr2*ny + vr3*nz; //v_R . n + vn1 = nx*vnnr; + vn2 = ny*vnnr; + vn3 = nz*vnnr; + + // meff = effective mass of pair of particles + // if I or J part of rigid body, use body mass + // if I or J is frozen, meff is other particle + + mi = rmass[i]; + mj = rmass[j]; + if (fix_rigid) { + if (mass_rigid[i] > 0.0) mi = mass_rigid[i]; + if (mass_rigid[j] > 0.0) mj = mass_rigid[j]; + } + + meff = mi*mj / (mi+mj); + if (mask[i] & freeze_group_bit) meff = mj; + if (mask[j] & freeze_group_bit) meff = mi; + + delta = radsum - r; + dR = delta*Reff; + + if (normal_model[itype][jtype] == JKR) { + touch[jj] = 1; + R2=Reff*Reff; + coh = normal_coeffs[itype][jtype][3]; + dR2 = dR*dR; + t0 = coh*coh*R2*R2*E; + t1 = PI27SQ*t0; + t2 = 8*dR*dR2*E*E*E; + t3 = 4*dR2*E; + // in case sqrt(0) < 0 due to precision issues + sqrt1 = MAX(0, t0*(t1+2*t2)); + t4 = cbrt(t1+t2+THREEROOT3*MY_PI*sqrt(sqrt1)); + t5 = t3/t4 + t4/E; + sqrt2 = MAX(0, 2*dR + t5); + t6 = sqrt(sqrt2); + sqrt3 = MAX(0, 4*dR - t5 + SIXROOT6*coh*MY_PI*R2/(E*t6)); + a = INVROOT6*(t6 + sqrt(sqrt3)); + a2 = a*a; + knfac = normal_coeffs[itype][jtype][0]*a; + Fne = knfac*a2/Reff - MY_2PI*a2*sqrt(4*coh*E/(MY_PI*a)); + } else { + knfac = E; // Hooke + Fne = knfac*delta; + a = sqrt(dR); + if (normal_model[itype][jtype] != HOOKE) { + Fne *= a; + knfac *= a; + } + if (normal_model[itype][jtype] == DMT) + Fne -= 4*MY_PI*normal_coeffs[itype][jtype][3]*Reff; + } + + // NOTE: consider restricting Hooke to only have + // 'velocity' as an option for damping? + + if (damping_model[itype][jtype] == VELOCITY) { + damp_normal = 1; + } else if (damping_model[itype][jtype] == MASS_VELOCITY) { + damp_normal = meff; + } else if (damping_model[itype][jtype] == VISCOELASTIC) { + damp_normal = a*meff; + } else if (damping_model[itype][jtype] == TSUJI) { + damp_normal = sqrt(meff*knfac); + } + + damp_normal_prefactor = normal_coeffs[itype][jtype][1]*damp_normal; + Fdamp = -damp_normal_prefactor*vnnr; + + Fntot = Fne + Fdamp; + + //**************************************** + // tangential force, including history effects + //**************************************** + + // For linear, mindlin, mindlin_rescale: + // history = cumulative tangential displacement + // + // For mindlin/force, mindlin_rescale/force: + // history = cumulative tangential elastic force + + // tangential component + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // relative rotational velocity + wr1 = (radi*omega[i][0] + radj*omega[j][0]); + wr2 = (radi*omega[i][1] + radj*omega[j][1]); + wr3 = (radi*omega[i][2] + radj*omega[j][2]); + + // relative tangential velocities + vtr1 = vt1 - (nz*wr2-ny*wr3); + vtr2 = vt2 - (nx*wr3-nz*wr1); + vtr3 = vt3 - (ny*wr1-nx*wr2); + vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3; + vrel = sqrt(vrel); + + // if any history is needed + if (use_history) { + touch[jj] = 1; + history = &allhistory[size_history*jj]; + } + + if (normal_model[itype][jtype] == JKR) { + F_pulloff = 3*MY_PI*coh*Reff; + Fncrit = fabs(Fne + 2*F_pulloff); + } else if (normal_model[itype][jtype] == DMT) { + F_pulloff = 4*MY_PI*coh*Reff; + Fncrit = fabs(Fne + 2*F_pulloff); + } else { + Fncrit = fabs(Fntot); + } + Fscrit = tangential_coeffs[itype][jtype][2] * Fncrit; + + //------------------------------ + // tangential forces + //------------------------------ + k_tangential = tangential_coeffs[itype][jtype][0]; + damp_tangential = tangential_coeffs[itype][jtype][1] * + damp_normal_prefactor; + + if (tangential_history) { + if (tangential_model[itype][jtype] == TANGENTIAL_MINDLIN || + tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_FORCE) { + k_tangential *= a; + } else if (tangential_model[itype][jtype] == + TANGENTIAL_MINDLIN_RESCALE || + tangential_model[itype][jtype] == + TANGENTIAL_MINDLIN_RESCALE_FORCE) { + k_tangential *= a; + // on unloading, rescale the shear displacements/force + if (a < history[3]) { + double factor = a/history[3]; + history[0] *= factor; + history[1] *= factor; + history[2] *= factor; + } + } + // rotate and update displacements / force. + // see e.g. eq. 17 of Luding, Gran. Matter 2008, v10,p235 + if (historyupdate) { + rsht = history[0]*nx + history[1]*ny + history[2]*nz; + if (tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_FORCE || + tangential_model[itype][jtype] == + TANGENTIAL_MINDLIN_RESCALE_FORCE) + frameupdate = fabs(rsht) > EPSILON*Fscrit; + else + frameupdate = fabs(rsht)*k_tangential > EPSILON*Fscrit; + if (frameupdate) { + shrmag = sqrt(history[0]*history[0] + history[1]*history[1] + + history[2]*history[2]); + // projection + history[0] -= rsht*nx; + history[1] -= rsht*ny; + history[2] -= rsht*nz; + + // also rescale to preserve magnitude + prjmag = sqrt(history[0]*history[0] + history[1]*history[1] + + history[2]*history[2]); + if (prjmag > 0) scalefac = shrmag/prjmag; + else scalefac = 0; + history[0] *= scalefac; + history[1] *= scalefac; + history[2] *= scalefac; + } + // update history + if (tangential_model[itype][jtype] == TANGENTIAL_HISTORY || + tangential_model[itype][jtype] == TANGENTIAL_MINDLIN || + tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_RESCALE) { + // tangential displacement + history[0] += vtr1*dt; + history[1] += vtr2*dt; + history[2] += vtr3*dt; + } else { + // tangential force + // see e.g. eq. 18 of Thornton et al, Pow. Tech. 2013, v223,p30-46 + history[0] -= k_tangential*vtr1*dt; + history[1] -= k_tangential*vtr2*dt; + history[2] -= k_tangential*vtr3*dt; + } + if (tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_RESCALE || + tangential_model[itype][jtype] == + TANGENTIAL_MINDLIN_RESCALE_FORCE) + history[3] = a; + } + + // tangential forces = history + tangential velocity damping + if (tangential_model[itype][jtype] == TANGENTIAL_HISTORY || + tangential_model[itype][jtype] == TANGENTIAL_MINDLIN || + tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_RESCALE) { + fs1 = -k_tangential*history[0] - damp_tangential*vtr1; + fs2 = -k_tangential*history[1] - damp_tangential*vtr2; + fs3 = -k_tangential*history[2] - damp_tangential*vtr3; + } else { + fs1 = history[0] - damp_tangential*vtr1; + fs2 = history[1] - damp_tangential*vtr2; + fs3 = history[2] - damp_tangential*vtr3; + } + + // rescale frictional displacements and forces if needed + fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3); + if (fs > Fscrit) { + shrmag = sqrt(history[0]*history[0] + history[1]*history[1] + + history[2]*history[2]); + if (shrmag != 0.0) { + if (tangential_model[itype][jtype] == TANGENTIAL_HISTORY || + tangential_model[itype][jtype] == TANGENTIAL_MINDLIN || + tangential_model[itype][jtype] == + TANGENTIAL_MINDLIN_RESCALE) { + history[0] = -1.0/k_tangential*(Fscrit*fs1/fs + + damp_tangential*vtr1); + history[1] = -1.0/k_tangential*(Fscrit*fs2/fs + + damp_tangential*vtr2); + history[2] = -1.0/k_tangential*(Fscrit*fs3/fs + + damp_tangential*vtr3); + } else { + history[0] = Fscrit*fs1/fs + damp_tangential*vtr1; + history[1] = Fscrit*fs2/fs + damp_tangential*vtr2; + history[2] = Fscrit*fs3/fs + damp_tangential*vtr3; + } + fs1 *= Fscrit/fs; + fs2 *= Fscrit/fs; + fs3 *= Fscrit/fs; + } else fs1 = fs2 = fs3 = 0.0; + } + } else { // classic pair gran/hooke (no history) + fs = damp_tangential*vrel; + if (vrel != 0.0) Ft = MIN(Fscrit,fs) / vrel; + else Ft = 0.0; + fs1 = -Ft*vtr1; + fs2 = -Ft*vtr2; + fs3 = -Ft*vtr3; + } + + if (roll_model[itype][jtype] != ROLL_NONE || + twist_model[itype][jtype] != TWIST_NONE) { + relrot1 = omega[i][0] - omega[j][0]; + relrot2 = omega[i][1] - omega[j][1]; + relrot3 = omega[i][2] - omega[j][2]; + // rolling velocity, + // see eq. 31 of Wang et al, Particuology v 23, p 49 (2015) + // this is different from the Marshall papers, + // which use the Bagi/Kuhn formulation + // for rolling velocity (see Wang et al for why the latter is wrong) + // - 0.5*((radj-radi)/radsum)*vtr1; + // - 0.5*((radj-radi)/radsum)*vtr2; + // - 0.5*((radj-radi)/radsum)*vtr3; + } + //**************************************** + // rolling resistance + //**************************************** + + if (roll_model[itype][jtype] != ROLL_NONE) { + vrl1 = Reff*(relrot2*nz - relrot3*ny); + vrl2 = Reff*(relrot3*nx - relrot1*nz); + vrl3 = Reff*(relrot1*ny - relrot2*nx); + + int rhist0 = roll_history_index; + int rhist1 = rhist0 + 1; + int rhist2 = rhist1 + 1; + + k_roll = roll_coeffs[itype][jtype][0]; + damp_roll = roll_coeffs[itype][jtype][1]; + Frcrit = roll_coeffs[itype][jtype][2] * Fncrit; + + if (historyupdate) { + rolldotn = history[rhist0]*nx + history[rhist1]*ny + history[rhist2]*nz; + frameupdate = fabs(rolldotn)*k_roll > EPSILON*Frcrit; + if (frameupdate) { // rotate into tangential plane + rollmag = sqrt(history[rhist0]*history[rhist0] + + history[rhist1]*history[rhist1] + + history[rhist2]*history[rhist2]); + // projection + history[rhist0] -= rolldotn*nx; + history[rhist1] -= rolldotn*ny; + history[rhist2] -= rolldotn*nz; + // also rescale to preserve magnitude + prjmag = sqrt(history[rhist0]*history[rhist0] + + history[rhist1]*history[rhist1] + + history[rhist2]*history[rhist2]); + if (prjmag > 0) scalefac = rollmag/prjmag; + else scalefac = 0; + history[rhist0] *= scalefac; + history[rhist1] *= scalefac; + history[rhist2] *= scalefac; + } + history[rhist0] += vrl1*dt; + history[rhist1] += vrl2*dt; + history[rhist2] += vrl3*dt; + } + + fr1 = -k_roll*history[rhist0] - damp_roll*vrl1; + fr2 = -k_roll*history[rhist1] - damp_roll*vrl2; + fr3 = -k_roll*history[rhist2] - damp_roll*vrl3; + + // rescale frictional displacements and forces if needed + + fr = sqrt(fr1*fr1 + fr2*fr2 + fr3*fr3); + if (fr > Frcrit) { + rollmag = sqrt(history[rhist0]*history[rhist0] + + history[rhist1]*history[rhist1] + + history[rhist2]*history[rhist2]); + if (rollmag != 0.0) { + history[rhist0] = -1.0/k_roll*(Frcrit*fr1/fr + damp_roll*vrl1); + history[rhist1] = -1.0/k_roll*(Frcrit*fr2/fr + damp_roll*vrl2); + history[rhist2] = -1.0/k_roll*(Frcrit*fr3/fr + damp_roll*vrl3); + fr1 *= Frcrit/fr; + fr2 *= Frcrit/fr; + fr3 *= Frcrit/fr; + } else fr1 = fr2 = fr3 = 0.0; + } + } + + //**************************************** + // twisting torque, including history effects + //**************************************** + + if (twist_model[itype][jtype] != TWIST_NONE) { + // omega_T (eq 29 of Marshall) + magtwist = relrot1*nx + relrot2*ny + relrot3*nz; + if (twist_model[itype][jtype] == TWIST_MARSHALL) { + k_twist = 0.5*k_tangential*a*a;; // eq 32 of Marshall paper + damp_twist = 0.5*damp_tangential*a*a; + mu_twist = TWOTHIRDS*a*tangential_coeffs[itype][jtype][2]; + } else { + k_twist = twist_coeffs[itype][jtype][0]; + damp_twist = twist_coeffs[itype][jtype][1]; + mu_twist = twist_coeffs[itype][jtype][2]; + } + if (historyupdate) { + history[twist_history_index] += magtwist*dt; + } + magtortwist = -k_twist*history[twist_history_index] - + damp_twist*magtwist; // M_t torque (eq 30) + signtwist = (magtwist > 0) - (magtwist < 0); + Mtcrit = mu_twist*Fncrit; // critical torque (eq 44) + if (fabs(magtortwist) > Mtcrit) { + history[twist_history_index] = 1.0/k_twist*(Mtcrit*signtwist - + damp_twist*magtwist); + magtortwist = -Mtcrit * signtwist; // eq 34 + } + } + + // apply forces & torques + + fx = nx*Fntot + fs1; + fy = ny*Fntot + fs2; + fz = nz*Fntot + fs3; + + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + + tor1 = ny*fs3 - nz*fs2; + tor2 = nz*fs1 - nx*fs3; + tor3 = nx*fs2 - ny*fs1; + + dist_to_contact = radi-0.5*delta; + torque[i][0] -= dist_to_contact*tor1; + torque[i][1] -= dist_to_contact*tor2; + torque[i][2] -= dist_to_contact*tor3; + + if (twist_model[itype][jtype] != TWIST_NONE) { + tortwist1 = magtortwist * nx; + tortwist2 = magtortwist * ny; + tortwist3 = magtortwist * nz; + + torque[i][0] += tortwist1; + torque[i][1] += tortwist2; + torque[i][2] += tortwist3; + } + + if (roll_model[itype][jtype] != ROLL_NONE) { + torroll1 = Reff*(ny*fr3 - nz*fr2); // n cross fr + torroll2 = Reff*(nz*fr1 - nx*fr3); + torroll3 = Reff*(nx*fr2 - ny*fr1); + + torque[i][0] += torroll1; + torque[i][1] += torroll2; + torque[i][2] += torroll3; + } + + if (force->newton_pair || j < nlocal) { + f[j][0] -= fx; + f[j][1] -= fy; + f[j][2] -= fz; + + dist_to_contact = radj-0.5*delta; + torque[j][0] -= dist_to_contact*tor1; + torque[j][1] -= dist_to_contact*tor2; + torque[j][2] -= dist_to_contact*tor3; + + if (twist_model[itype][jtype] != TWIST_NONE) { + torque[j][0] -= tortwist1; + torque[j][1] -= tortwist2; + torque[j][2] -= tortwist3; + } + if (roll_model[itype][jtype] != ROLL_NONE) { + torque[j][0] -= torroll1; + torque[j][1] -= torroll2; + torque[j][2] -= torroll3; + } + } + if (evflag) ev_tally_xyz(i,j,nlocal,force->newton_pair, + 0.0,0.0,fx,fy,fz,delx,dely,delz); + } + } + } +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairGranular::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cutoff_type,n+1,n+1,"pair:cutoff_type"); + memory->create(normal_coeffs,n+1,n+1,4,"pair:normal_coeffs"); + memory->create(tangential_coeffs,n+1,n+1,3,"pair:tangential_coeffs"); + memory->create(roll_coeffs,n+1,n+1,3,"pair:roll_coeffs"); + memory->create(twist_coeffs,n+1,n+1,3,"pair:twist_coeffs"); + + memory->create(Emod,n+1,n+1,"pair:Emod"); + memory->create(poiss,n+1,n+1,"pair:poiss"); + + memory->create(normal_model,n+1,n+1,"pair:normal_model"); + memory->create(damping_model,n+1,n+1,"pair:damping_model"); + memory->create(tangential_model,n+1,n+1,"pair:tangential_model"); + memory->create(roll_model,n+1,n+1,"pair:roll_model"); + memory->create(twist_model,n+1,n+1,"pair:twist_model"); + + onerad_dynamic = new double[n+1]; + onerad_frozen = new double[n+1]; + maxrad_dynamic = new double[n+1]; + maxrad_frozen = new double[n+1]; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairGranular::settings(int narg, char **arg) +{ + if (narg == 1) { + cutoff_global = utils::numeric(FLERR,arg[0],false,lmp); + } else { + cutoff_global = -1; // will be set based on particle sizes, model choice + } + + normal_history = tangential_history = 0; + roll_history = twist_history = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairGranular::coeff(int narg, char **arg) +{ + int normal_model_one, damping_model_one; + int tangential_model_one, roll_model_one, twist_model_one; + + double normal_coeffs_one[4]; + double tangential_coeffs_one[4]; + double roll_coeffs_one[4]; + double twist_coeffs_one[4]; + + double cutoff_one = -1; + + if (narg < 2) + error->all(FLERR,"Incorrect args for pair coefficients"); + + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + + //Defaults + normal_model_one = tangential_model_one = -1; + roll_model_one = ROLL_NONE; + twist_model_one = TWIST_NONE; + damping_model_one = VISCOELASTIC; + + int iarg = 2; + while (iarg < narg) { + if (strcmp(arg[iarg], "hooke") == 0) { + if (iarg + 2 >= narg) + error->all(FLERR,"Illegal pair_coeff command, " + "not enough parameters provided for Hooke option"); + normal_model_one = HOOKE; + normal_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+1],false,lmp); // kn + normal_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); // damping + iarg += 3; + } else if (strcmp(arg[iarg], "hertz") == 0) { + if (iarg + 2 >= narg) + error->all(FLERR,"Illegal pair_coeff command, " + "not enough parameters provided for Hertz option"); + normal_model_one = HERTZ; + normal_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+1],false,lmp); // kn + normal_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); // damping + iarg += 3; + } else if (strcmp(arg[iarg], "hertz/material") == 0) { + if (iarg + 3 >= narg) + error->all(FLERR,"Illegal pair_coeff command, " + "not enough parameters provided for Hertz/material option"); + normal_model_one = HERTZ_MATERIAL; + normal_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+1],false,lmp); // E + normal_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); // damping + normal_coeffs_one[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp); // Poisson's ratio + iarg += 4; + } else if (strcmp(arg[iarg], "dmt") == 0) { + if (iarg + 4 >= narg) + error->all(FLERR,"Illegal pair_coeff command, " + "not enough parameters provided for Hertz option"); + normal_model_one = DMT; + normal_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+1],false,lmp); // E + normal_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); // damping + normal_coeffs_one[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp); // Poisson's ratio + normal_coeffs_one[3] = utils::numeric(FLERR,arg[iarg+4],false,lmp); // cohesion + iarg += 5; + } else if (strcmp(arg[iarg], "jkr") == 0) { + if (iarg + 4 >= narg) + error->all(FLERR,"Illegal pair_coeff command, " + "not enough parameters provided for JKR option"); + beyond_contact = 1; + normal_model_one = JKR; + normal_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+1],false,lmp); // E + normal_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); // damping + normal_coeffs_one[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp); // Poisson's ratio + normal_coeffs_one[3] = utils::numeric(FLERR,arg[iarg+4],false,lmp); // cohesion + iarg += 5; + } else if (strcmp(arg[iarg], "damping") == 0) { + if (iarg+1 >= narg) + error->all(FLERR, "Illegal pair_coeff command, " + "not enough parameters provided for damping model"); + if (strcmp(arg[iarg+1], "velocity") == 0) { + damping_model_one = VELOCITY; + iarg += 1; + } else if (strcmp(arg[iarg+1], "mass_velocity") == 0) { + damping_model_one = MASS_VELOCITY; + iarg += 1; + } else if (strcmp(arg[iarg+1], "viscoelastic") == 0) { + damping_model_one = VISCOELASTIC; + iarg += 1; + } else if (strcmp(arg[iarg+1], "tsuji") == 0) { + damping_model_one = TSUJI; + iarg += 1; + } else error->all(FLERR, "Illegal pair_coeff command, " + "unrecognized damping model"); + iarg += 1; + } else if (strcmp(arg[iarg], "tangential") == 0) { + if (iarg + 1 >= narg) + error->all(FLERR,"Illegal pair_coeff command, must specify " + "tangential model after tangential keyword"); + if (strcmp(arg[iarg+1], "linear_nohistory") == 0) { + if (iarg + 3 >= narg) + error->all(FLERR,"Illegal pair_coeff command, " + "not enough parameters provided for tangential model"); + tangential_model_one = TANGENTIAL_NOHISTORY; + tangential_coeffs_one[0] = 0; + // gammat and friction coeff + tangential_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); + tangential_coeffs_one[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp); + iarg += 4; + } else if ((strcmp(arg[iarg+1], "linear_history") == 0) || + (strcmp(arg[iarg+1], "mindlin") == 0) || + (strcmp(arg[iarg+1], "mindlin_rescale") == 0) || + (strcmp(arg[iarg+1], "mindlin/force") == 0) || + (strcmp(arg[iarg+1], "mindlin_rescale/force") == 0)) { + if (iarg + 4 >= narg) + error->all(FLERR,"Illegal pair_coeff command, " + "not enough parameters provided for tangential model"); + if (strcmp(arg[iarg+1], "linear_history") == 0) + tangential_model_one = TANGENTIAL_HISTORY; + else if (strcmp(arg[iarg+1], "mindlin") == 0) + tangential_model_one = TANGENTIAL_MINDLIN; + else if (strcmp(arg[iarg+1], "mindlin_rescale") == 0) + tangential_model_one = TANGENTIAL_MINDLIN_RESCALE; + else if (strcmp(arg[iarg+1], "mindlin/force") == 0) + tangential_model_one = TANGENTIAL_MINDLIN_FORCE; + else if (strcmp(arg[iarg+1], "mindlin_rescale/force") == 0) + tangential_model_one = TANGENTIAL_MINDLIN_RESCALE_FORCE; + tangential_history = 1; + if ((tangential_model_one == TANGENTIAL_MINDLIN || + tangential_model_one == TANGENTIAL_MINDLIN_RESCALE || + tangential_model_one == TANGENTIAL_MINDLIN_FORCE || + tangential_model_one == TANGENTIAL_MINDLIN_RESCALE_FORCE) && + (strcmp(arg[iarg+2], "NULL") == 0)) { + if (normal_model_one == HERTZ || normal_model_one == HOOKE) { + error->all(FLERR, "NULL setting for Mindlin tangential " + "stiffness requires a normal contact model that " + "specifies material properties"); + } + tangential_coeffs_one[0] = -1; + } else { + tangential_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+2],false,lmp); // kt + } + // gammat and friction coeff + tangential_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+3],false,lmp); + tangential_coeffs_one[2] = utils::numeric(FLERR,arg[iarg+4],false,lmp); + iarg += 5; + } else { + error->all(FLERR, "Illegal pair_coeff command, " + "tangential model not recognized"); + } + } else if (strcmp(arg[iarg], "rolling") == 0) { + if (iarg + 1 >= narg) + error->all(FLERR, "Illegal pair_coeff command, not enough parameters"); + if (strcmp(arg[iarg+1], "none") == 0) { + roll_model_one = ROLL_NONE; + iarg += 2; + } else if (strcmp(arg[iarg+1], "sds") == 0) { + if (iarg + 4 >= narg) + error->all(FLERR,"Illegal pair_coeff command, " + "not enough parameters provided for rolling model"); + roll_model_one = ROLL_SDS; + roll_history = 1; + // kR and gammaR and rolling friction coeff + roll_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+2],false,lmp); + roll_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+3],false,lmp); + roll_coeffs_one[2] = utils::numeric(FLERR,arg[iarg+4],false,lmp); + iarg += 5; + } else { + error->all(FLERR, "Illegal pair_coeff command, " + "rolling friction model not recognized"); + } + } else if (strcmp(arg[iarg], "twisting") == 0) { + if (iarg + 1 >= narg) + error->all(FLERR, "Illegal pair_coeff command, not enough parameters"); + if (strcmp(arg[iarg+1], "none") == 0) { + twist_model_one = TWIST_NONE; + iarg += 2; + } else if (strcmp(arg[iarg+1], "marshall") == 0) { + twist_model_one = TWIST_MARSHALL; + twist_history = 1; + iarg += 2; + } else if (strcmp(arg[iarg+1], "sds") == 0) { + if (iarg + 4 >= narg) + error->all(FLERR,"Illegal pair_coeff command, " + "not enough parameters provided for twist model"); + twist_model_one = TWIST_SDS; + twist_history = 1; + // kt and gammat and friction coeff + twist_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+2],false,lmp); + twist_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+3],false,lmp); + twist_coeffs_one[2] = utils::numeric(FLERR,arg[iarg+4],false,lmp); + iarg += 5; + } else { + error->all(FLERR, "Illegal pair_coeff command, " + "twisting friction model not recognized"); + } + } else if (strcmp(arg[iarg], "cutoff") == 0) { + if (iarg + 1 >= narg) + error->all(FLERR, "Illegal pair_coeff command, not enough parameters"); + cutoff_one = utils::numeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + } else error->all(FLERR, "Illegal pair coeff command"); + } + + // error not to specify normal or tangential model + if ((normal_model_one < 0) || (tangential_model_one < 0)) + error->all(FLERR, "Illegal pair coeff command, " + "must specify normal or tangential contact model"); + + int count = 0; + double damp; + if (damping_model_one == TSUJI) { + double cor; + cor = normal_coeffs_one[1]; + damp = 1.2728-4.2783*cor+11.087*square(cor)-22.348*cube(cor)+ + 27.467*powint(cor,4)-18.022*powint(cor,5)+4.8218*powint(cor,6); + } else damp = normal_coeffs_one[1]; + + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + normal_model[i][j] = normal_model[j][i] = normal_model_one; + normal_coeffs[i][j][1] = normal_coeffs[j][i][1] = damp; + if (normal_model_one != HERTZ && normal_model_one != HOOKE) { + Emod[i][j] = Emod[j][i] = normal_coeffs_one[0]; + poiss[i][j] = poiss[j][i] = normal_coeffs_one[2]; + normal_coeffs[i][j][0] = normal_coeffs[j][i][0] = + FOURTHIRDS*mix_stiffnessE(Emod[i][j],Emod[i][j], + poiss[i][j],poiss[i][j]); + } else { + normal_coeffs[i][j][0] = normal_coeffs[j][i][0] = normal_coeffs_one[0]; + } + if ((normal_model_one == JKR) || (normal_model_one == DMT)) + normal_coeffs[i][j][3] = normal_coeffs[j][i][3] = normal_coeffs_one[3]; + + damping_model[i][j] = damping_model[j][i] = damping_model_one; + + tangential_model[i][j] = tangential_model[j][i] = tangential_model_one; + if (tangential_coeffs_one[0] == -1) { + tangential_coeffs[i][j][0] = tangential_coeffs[j][i][0] = + 8*mix_stiffnessG(Emod[i][j],Emod[i][j],poiss[i][j],poiss[i][j]); + } else { + tangential_coeffs[i][j][0] = tangential_coeffs[j][i][0] = + tangential_coeffs_one[0]; + } + for (int k = 1; k < 3; k++) + tangential_coeffs[i][j][k] = tangential_coeffs[j][i][k] = + tangential_coeffs_one[k]; + + roll_model[i][j] = roll_model[j][i] = roll_model_one; + if (roll_model_one != ROLL_NONE) + for (int k = 0; k < 3; k++) + roll_coeffs[i][j][k] = roll_coeffs[j][i][k] = roll_coeffs_one[k]; + + twist_model[i][j] = twist_model[j][i] = twist_model_one; + if (twist_model_one != TWIST_NONE && twist_model_one != TWIST_MARSHALL) + for (int k = 0; k < 3; k++) + twist_coeffs[i][j][k] = twist_coeffs[j][i][k] = twist_coeffs_one[k]; + + cutoff_type[i][j] = cutoff_type[j][i] = cutoff_one; + + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairGranular::init_style() +{ + int i; + + // error and warning checks + + if (!atom->radius_flag || !atom->rmass_flag) + error->all(FLERR,"Pair granular requires atom attributes radius, rmass"); + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair granular requires ghost atoms store velocity"); + + // determine whether we need a granular neigh list, how large it needs to be + + use_history = normal_history || tangential_history || + roll_history || twist_history; + + // for JKR, will need fix/neigh/history to keep track of touch arrays + + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + if (normal_model[i][j] == JKR) use_history = 1; + + size_history = 3*tangential_history + 3*roll_history + twist_history; + + // determine location of tangential/roll/twist histories in array + + if (roll_history) { + if (tangential_history) roll_history_index = 3; + else roll_history_index = 0; + } + if (twist_history) { + if (tangential_history) { + if (roll_history) twist_history_index = 6; + else twist_history_index = 3; + } else { + if (roll_history) twist_history_index = 3; + else twist_history_index = 0; + } + } + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + if (tangential_model[i][j] == TANGENTIAL_MINDLIN_RESCALE || + tangential_model[i][j] == TANGENTIAL_MINDLIN_RESCALE_FORCE) { + size_history += 1; + roll_history_index += 1; + twist_history_index += 1; + nondefault_history_transfer = 1; + history_transfer_factors = new int[size_history]; + for (int ii = 0; ii < size_history; ++ii) + history_transfer_factors[ii] = -1; + history_transfer_factors[3] = 1; + break; + } + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->size = 1; + if (use_history) neighbor->requests[irequest]->history = 1; + + dt = update->dt; + + // if history is stored and first init, create Fix to store history + // it replaces FixDummy, created in the constructor + // this is so its order in the fix list is preserved + + if (use_history && fix_history == nullptr) { + modify->replace_fix("NEIGH_HISTORY_GRANULAR_DUMMY","NEIGH_HISTORY_GRANULAR" + " all NEIGH_HISTORY " + std::to_string(size_history),1); + int ifix = modify->find_fix("NEIGH_HISTORY_GRANULAR"); + fix_history = (FixNeighHistory *) modify->fix[ifix]; + fix_history->pair = this; + } + + // check for FixFreeze and set freeze_group_bit + + for (i = 0; i < modify->nfix; i++) + if (strcmp(modify->fix[i]->style,"freeze") == 0) break; + if (i < modify->nfix) freeze_group_bit = modify->fix[i]->groupbit; + else freeze_group_bit = 0; + + // check for FixRigid so can extract rigid body masses + + fix_rigid = nullptr; + for (i = 0; i < modify->nfix; i++) + if (modify->fix[i]->rigid_flag) break; + if (i < modify->nfix) fix_rigid = modify->fix[i]; + + // check for FixPour and FixDeposit so can extract particle radii + + int ipour; + for (ipour = 0; ipour < modify->nfix; ipour++) + if (strcmp(modify->fix[ipour]->style,"pour") == 0) break; + if (ipour == modify->nfix) ipour = -1; + + int idep; + for (idep = 0; idep < modify->nfix; idep++) + if (strcmp(modify->fix[idep]->style,"deposit") == 0) break; + if (idep == modify->nfix) idep = -1; + + // set maxrad_dynamic and maxrad_frozen for each type + // include future FixPour and FixDeposit particles as dynamic + + int itype; + for (i = 1; i <= atom->ntypes; i++) { + onerad_dynamic[i] = onerad_frozen[i] = 0.0; + if (ipour >= 0) { + itype = i; + double radmax = *((double *) modify->fix[ipour]->extract("radius",itype)); + onerad_dynamic[i] = radmax; + } + if (idep >= 0) { + itype = i; + double radmax = *((double *) modify->fix[idep]->extract("radius",itype)); + onerad_dynamic[i] = radmax; + } + } + + double *radius = atom->radius; + int *mask = atom->mask; + int *type = atom->type; + int nlocal = atom->nlocal; + + for (i = 0; i < nlocal; i++) { + double radius_cut = radius[i]; + if (mask[i] & freeze_group_bit) { + onerad_frozen[type[i]] = MAX(onerad_frozen[type[i]],radius_cut); + } else { + onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]],radius_cut); + } + } + + MPI_Allreduce(&onerad_dynamic[1],&maxrad_dynamic[1],atom->ntypes, + MPI_DOUBLE,MPI_MAX,world); + MPI_Allreduce(&onerad_frozen[1],&maxrad_frozen[1],atom->ntypes, + MPI_DOUBLE,MPI_MAX,world); + + // set fix which stores history info + + if (size_history > 0) { + int ifix = modify->find_fix("NEIGH_HISTORY_GRANULAR"); + if (ifix < 0) error->all(FLERR,"Could not find pair fix neigh history ID"); + fix_history = (FixNeighHistory *) modify->fix[ifix]; + } +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairGranular::init_one(int i, int j) +{ + double cutoff=0.0; + + if (setflag[i][j] == 0) { + if ((normal_model[i][i] != normal_model[j][j]) || + (damping_model[i][i] != damping_model[j][j]) || + (tangential_model[i][i] != tangential_model[j][j]) || + (roll_model[i][i] != roll_model[j][j]) || + (twist_model[i][i] != twist_model[j][j])) { + + char str[512]; + sprintf(str,"Granular pair style functional forms are different, " + "cannot mix coefficients for types %d and %d. \n" + "This combination must be set explicitly " + "via pair_coeff command",i,j); + error->one(FLERR,str); + } + + if (normal_model[i][j] == HERTZ || normal_model[i][j] == HOOKE) + normal_coeffs[i][j][0] = normal_coeffs[j][i][0] = + mix_geom(normal_coeffs[i][i][0], normal_coeffs[j][j][0]); + else + normal_coeffs[i][j][0] = normal_coeffs[j][i][0] = + mix_stiffnessE(Emod[i][i], Emod[j][j], poiss[i][i], poiss[j][j]); + + normal_coeffs[i][j][1] = normal_coeffs[j][i][1] = + mix_geom(normal_coeffs[i][i][1], normal_coeffs[j][j][1]); + if ((normal_model[i][j] == JKR) || (normal_model[i][j] == DMT)) + normal_coeffs[i][j][3] = normal_coeffs[j][i][3] = + mix_geom(normal_coeffs[i][i][3], normal_coeffs[j][j][3]); + + for (int k = 0; k < 3; k++) + tangential_coeffs[i][j][k] = tangential_coeffs[j][i][k] = + mix_geom(tangential_coeffs[i][i][k], tangential_coeffs[j][j][k]); + + if (roll_model[i][j] != ROLL_NONE) { + for (int k = 0; k < 3; k++) + roll_coeffs[i][j][k] = roll_coeffs[j][i][k] = + mix_geom(roll_coeffs[i][i][k], roll_coeffs[j][j][k]); + } + + if (twist_model[i][j] != TWIST_NONE && twist_model[i][j] != TWIST_MARSHALL) { + for (int k = 0; k < 3; k++) + twist_coeffs[i][j][k] = twist_coeffs[j][i][k] = + mix_geom(twist_coeffs[i][i][k], twist_coeffs[j][j][k]); + } + } + + // It is possible that cut[i][j] at this point is still 0.0. + // This can happen when + // there is a future fix_pour after the current run. A cut[i][j] = 0.0 creates + // problems because neighbor.cpp uses min(cut[i][j]) to decide on the bin size + // To avoid this issue, for cases involving cut[i][j] = 0.0 (possible only + // if there is no current information about radius/cutoff of type i and j). + // we assign cutoff = max(cut[i][j]) for i,j such that cut[i][j] > 0.0. + + double pulloff; + + if (cutoff_type[i][j] < 0 && cutoff_global < 0) { + if (((maxrad_dynamic[i] > 0.0) && (maxrad_dynamic[j] > 0.0)) || + ((maxrad_dynamic[i] > 0.0) && (maxrad_frozen[j] > 0.0)) || + // radius info about both i and j exist + ((maxrad_frozen[i] > 0.0) && (maxrad_dynamic[j] > 0.0))) { + cutoff = maxrad_dynamic[i]+maxrad_dynamic[j]; + pulloff = 0.0; + if (normal_model[i][j] == JKR) { + pulloff = pulloff_distance(maxrad_dynamic[i], maxrad_dynamic[j], i, j); + cutoff += pulloff; + } + + if (normal_model[i][j] == JKR) + pulloff = pulloff_distance(maxrad_frozen[i], maxrad_dynamic[j], i, j); + cutoff = MAX(cutoff, maxrad_frozen[i]+maxrad_dynamic[j]+pulloff); + + if (normal_model[i][j] == JKR) + pulloff = pulloff_distance(maxrad_dynamic[i], maxrad_frozen[j], i, j); + cutoff = MAX(cutoff,maxrad_dynamic[i]+maxrad_frozen[j]+pulloff); + + } else { + + // radius info about either i or j does not exist + // (i.e. not present and not about to get poured; + // set to largest value to not interfere with neighbor list) + + double cutmax = 0.0; + for (int k = 1; k <= atom->ntypes; k++) { + cutmax = MAX(cutmax,2.0*maxrad_dynamic[k]); + cutmax = MAX(cutmax,2.0*maxrad_frozen[k]); + } + cutoff = cutmax; + } + } else if (cutoff_type[i][j] > 0) { + cutoff = cutoff_type[i][j]; + } else if (cutoff_global > 0) { + cutoff = cutoff_global; + } + + return cutoff; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairGranular::write_restart(FILE *fp) +{ + int i,j; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&normal_model[i][j],sizeof(int),1,fp); + fwrite(&damping_model[i][j],sizeof(int),1,fp); + fwrite(&tangential_model[i][j],sizeof(int),1,fp); + fwrite(&roll_model[i][j],sizeof(int),1,fp); + fwrite(&twist_model[i][j],sizeof(int),1,fp); + fwrite(normal_coeffs[i][j],sizeof(double),4,fp); + fwrite(tangential_coeffs[i][j],sizeof(double),3,fp); + fwrite(roll_coeffs[i][j],sizeof(double),3,fp); + fwrite(twist_coeffs[i][j],sizeof(double),3,fp); + fwrite(&cutoff_type[i][j],sizeof(double),1,fp); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairGranular::read_restart(FILE *fp) +{ + allocate(); + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + utils::sfread(FLERR,&normal_model[i][j],sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&damping_model[i][j],sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&tangential_model[i][j],sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&roll_model[i][j],sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&twist_model[i][j],sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,normal_coeffs[i][j],sizeof(double),4,fp,nullptr,error); + utils::sfread(FLERR,tangential_coeffs[i][j],sizeof(double),3,fp,nullptr,error); + utils::sfread(FLERR,roll_coeffs[i][j],sizeof(double),3,fp,nullptr,error); + utils::sfread(FLERR,twist_coeffs[i][j],sizeof(double),3,fp,nullptr,error); + utils::sfread(FLERR,&cutoff_type[i][j],sizeof(double),1,fp,nullptr,error); + } + MPI_Bcast(&normal_model[i][j],1,MPI_INT,0,world); + MPI_Bcast(&damping_model[i][j],1,MPI_INT,0,world); + MPI_Bcast(&tangential_model[i][j],1,MPI_INT,0,world); + MPI_Bcast(&roll_model[i][j],1,MPI_INT,0,world); + MPI_Bcast(&twist_model[i][j],1,MPI_INT,0,world); + MPI_Bcast(normal_coeffs[i][j],4,MPI_DOUBLE,0,world); + MPI_Bcast(tangential_coeffs[i][j],3,MPI_DOUBLE,0,world); + MPI_Bcast(roll_coeffs[i][j],3,MPI_DOUBLE,0,world); + MPI_Bcast(twist_coeffs[i][j],3,MPI_DOUBLE,0,world); + MPI_Bcast(&cutoff_type[i][j],1,MPI_DOUBLE,0,world); + } + } + } +} + +/* ---------------------------------------------------------------------- */ + +void PairGranular::reset_dt() +{ + dt = update->dt; +} + +/* ---------------------------------------------------------------------- */ + +double PairGranular::single(int i, int j, int itype, int jtype, + double rsq, double /* factor_coul */, + double /* factor_lj */, double &fforce) +{ + double radi,radj,radsum; + double r,rinv,delx,dely,delz, nx, ny, nz, Reff; + double dR, dR2; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3,wr1,wr2,wr3; + double vtr1,vtr2,vtr3,vrel; + double mi,mj,meff; + double relrot1,relrot2,relrot3,vrl1,vrl2,vrl3; + + double knfac, damp_normal, damp_normal_prefactor; + double k_tangential, damp_tangential; + double Fne, Ft, Fdamp, Fntot, Fncrit, Fscrit, Frcrit; + double fs, fs1, fs2, fs3; + + // for JKR + double R2, coh, F_pulloff, delta_pulloff, dist_pulloff, a, a2, E; + double delta, t0, t1, t2, t3, t4, t5, t6; + double sqrt1, sqrt2, sqrt3; + + // rolling + double k_roll, damp_roll; + double rollmag; + double fr, fr1, fr2, fr3; + + // twisting + double k_twist, damp_twist, mu_twist; + double signtwist, magtwist, magtortwist, Mtcrit; + + double shrmag; + int jnum; + int *jlist; + double *history,*allhistory; + + int nall = atom->nlocal + atom->nghost; + if ((i >= nall) || (j >= nall)) + error->all(FLERR,"Not enough atoms for pair granular single function"); + + double *radius = atom->radius; + radi = radius[i]; + radj = radius[j]; + radsum = radi + radj; + Reff = (radsum > 0.0) ? radi*radj/radsum : 0.0; + + bool touchflag; + E = normal_coeffs[itype][jtype][0]; + if (normal_model[itype][jtype] == JKR) { + E *= THREEQUARTERS; + R2 = Reff*Reff; + coh = normal_coeffs[itype][jtype][3]; + a = cbrt(9.0*MY_PI*coh*R2/(4*E)); + delta_pulloff = a*a/Reff - 2*sqrt(MY_PI*coh*a/E); + dist_pulloff = radsum+delta_pulloff; + touchflag = (rsq <= dist_pulloff*dist_pulloff); + } else touchflag = (rsq <= radsum*radsum); + + if (!touchflag) { + fforce = 0.0; + for (int m = 0; m < single_extra; m++) svector[m] = 0.0; + return 0.0; + } + + double **x = atom->x; + delx = x[i][0] - x[j][0]; + dely = x[i][1] - x[j][1]; + delz = x[i][2] - x[j][2]; + r = sqrt(rsq); + rinv = 1.0/r; + + nx = delx*rinv; + ny = dely*rinv; + nz = delz*rinv; + + // relative translational velocity + + double **v = atom->v; + vr1 = v[i][0] - v[j][0]; + vr2 = v[i][1] - v[j][1]; + vr3 = v[i][2] - v[j][2]; + + // normal component + + vnnr = vr1*nx + vr2*ny + vr3*nz; + vn1 = nx*vnnr; + vn2 = ny*vnnr; + vn3 = nz*vnnr; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // relative rotational velocity + + double **omega = atom->omega; + wr1 = (radi*omega[i][0] + radj*omega[j][0]); + wr2 = (radi*omega[i][1] + radj*omega[j][1]); + wr3 = (radi*omega[i][2] + radj*omega[j][2]); + + // meff = effective mass of pair of particles + // if I or J part of rigid body, use body mass + // if I or J is frozen, meff is other particle + + double *rmass = atom->rmass; + int *mask = atom->mask; + + mi = rmass[i]; + mj = rmass[j]; + if (fix_rigid) { + // NOTE: ensure mass_rigid is current for owned+ghost atoms? + if (mass_rigid[i] > 0.0) mi = mass_rigid[i]; + if (mass_rigid[j] > 0.0) mj = mass_rigid[j]; + } + + meff = mi*mj / (mi+mj); + if (mask[i] & freeze_group_bit) meff = mj; + if (mask[j] & freeze_group_bit) meff = mi; + + delta = radsum - r; + dR = delta*Reff; + if (normal_model[itype][jtype] == JKR) { + dR2 = dR*dR; + t0 = coh*coh*R2*R2*E; + t1 = PI27SQ*t0; + t2 = 8*dR*dR2*E*E*E; + t3 = 4*dR2*E; + // in case sqrt(0) < 0 due to precision issues + sqrt1 = MAX(0, t0*(t1+2*t2)); + t4 = cbrt(t1+t2+THREEROOT3*MY_PI*sqrt(sqrt1)); + t5 = t3/t4 + t4/E; + sqrt2 = MAX(0, 2*dR + t5); + t6 = sqrt(sqrt2); + sqrt3 = MAX(0, 4*dR - t5 + SIXROOT6*coh*MY_PI*R2/(E*t6)); + a = INVROOT6*(t6 + sqrt(sqrt3)); + a2 = a*a; + knfac = normal_coeffs[itype][jtype][0]*a; + Fne = knfac*a2/Reff - MY_2PI*a2*sqrt(4*coh*E/(MY_PI*a)); + } else { + knfac = E; + Fne = knfac*delta; + a = sqrt(dR); + if (normal_model[itype][jtype] != HOOKE) { + Fne *= a; + knfac *= a; + } + if (normal_model[itype][jtype] == DMT) + Fne -= 4*MY_PI*normal_coeffs[itype][jtype][3]*Reff; + } + + if (damping_model[itype][jtype] == VELOCITY) { + damp_normal = 1; + } else if (damping_model[itype][jtype] == MASS_VELOCITY) { + damp_normal = meff; + } else if (damping_model[itype][jtype] == VISCOELASTIC) { + damp_normal = a*meff; + } else if (damping_model[itype][jtype] == TSUJI) { + damp_normal = sqrt(meff*knfac); + } else damp_normal = 0.0; + + damp_normal_prefactor = normal_coeffs[itype][jtype][1]*damp_normal; + Fdamp = -damp_normal_prefactor*vnnr; + + Fntot = Fne + Fdamp; + + jnum = list->numneigh[i]; + jlist = list->firstneigh[i]; + + if (use_history) { + if ((fix_history == nullptr) || (fix_history->firstvalue == nullptr)) + error->one(FLERR,"Pair granular single computation needs history"); + allhistory = fix_history->firstvalue[i]; + for (int jj = 0; jj < jnum; jj++) { + neighprev++; + if (neighprev >= jnum) neighprev = 0; + if (jlist[neighprev] == j) break; + } + history = &allhistory[size_history*neighprev]; + } + + //**************************************** + // tangential force, including history effects + //**************************************** + + // For linear, mindlin, mindlin_rescale: + // history = cumulative tangential displacement + // + // For mindlin/force, mindlin_rescale/force: + // history = cumulative tangential elastic force + + // tangential component + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // relative rotational velocity + wr1 = (radi*omega[i][0] + radj*omega[j][0]); + wr2 = (radi*omega[i][1] + radj*omega[j][1]); + wr3 = (radi*omega[i][2] + radj*omega[j][2]); + + // relative tangential velocities + vtr1 = vt1 - (nz*wr2-ny*wr3); + vtr2 = vt2 - (nx*wr3-nz*wr1); + vtr3 = vt3 - (ny*wr1-nx*wr2); + vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3; + vrel = sqrt(vrel); + + if (normal_model[itype][jtype] == JKR) { + F_pulloff = 3*MY_PI*coh*Reff; + Fncrit = fabs(Fne + 2*F_pulloff); + } else if (normal_model[itype][jtype] == DMT) { + F_pulloff = 4*MY_PI*coh*Reff; + Fncrit = fabs(Fne + 2*F_pulloff); + } else { + Fncrit = fabs(Fntot); + } + Fscrit = tangential_coeffs[itype][jtype][2] * Fncrit; + + //------------------------------ + // tangential forces + //------------------------------ + k_tangential = tangential_coeffs[itype][jtype][0]; + damp_tangential = tangential_coeffs[itype][jtype][1]*damp_normal_prefactor; + + if (tangential_history) { + if (tangential_model[itype][jtype] != TANGENTIAL_HISTORY) { + k_tangential *= a; + } + + shrmag = sqrt(history[0]*history[0] + history[1]*history[1] + + history[2]*history[2]); + + // tangential forces = history + tangential velocity damping + if (tangential_model[itype][jtype] == TANGENTIAL_HISTORY || + tangential_model[itype][jtype] == TANGENTIAL_MINDLIN || + tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_RESCALE) { + fs1 = -k_tangential*history[0] - damp_tangential*vtr1; + fs2 = -k_tangential*history[1] - damp_tangential*vtr2; + fs3 = -k_tangential*history[2] - damp_tangential*vtr3; + } else { + fs1 = history[0] - damp_tangential*vtr1; + fs2 = history[1] - damp_tangential*vtr2; + fs3 = history[2] - damp_tangential*vtr3; + } + + // rescale frictional forces if needed + fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3); + if (fs > Fscrit) { + if (shrmag != 0.0) { + fs1 *= Fscrit/fs; + fs2 *= Fscrit/fs; + fs3 *= Fscrit/fs; + fs *= Fscrit/fs; + } else fs1 = fs2 = fs3 = fs = 0.0; + } + + // classic pair gran/hooke (no history) + } else { + fs = damp_tangential*vrel; + if (vrel != 0.0) Ft = MIN(Fscrit,fs) / vrel; + else Ft = 0.0; + fs1 = -Ft*vtr1; + fs2 = -Ft*vtr2; + fs3 = -Ft*vtr3; + fs = Ft*vrel; + } + + //**************************************** + // rolling resistance + //**************************************** + + if ((roll_model[itype][jtype] != ROLL_NONE) + || (twist_model[itype][jtype] != TWIST_NONE)) { + relrot1 = omega[i][0] - omega[j][0]; + relrot2 = omega[i][1] - omega[j][1]; + relrot3 = omega[i][2] - omega[j][2]; + + // rolling velocity, see eq. 31 of Wang et al, Particuology v 23, p 49 (2015) + // this is different from the Marshall papers, + // which use the Bagi/Kuhn formulation + // for rolling velocity (see Wang et al for why the latter is wrong) + + vrl1 = Reff*(relrot2*nz - relrot3*ny); //- 0.5*((radj-radi)/radsum)*vtr1; + vrl2 = Reff*(relrot3*nx - relrot1*nz); //- 0.5*((radj-radi)/radsum)*vtr2; + vrl3 = Reff*(relrot1*ny - relrot2*nx); //- 0.5*((radj-radi)/radsum)*vtr3; + + int rhist0 = roll_history_index; + int rhist1 = rhist0 + 1; + int rhist2 = rhist1 + 1; + + // rolling displacement + rollmag = sqrt(history[rhist0]*history[rhist0] + + history[rhist1]*history[rhist1] + + history[rhist2]*history[rhist2]); + + k_roll = roll_coeffs[itype][jtype][0]; + damp_roll = roll_coeffs[itype][jtype][1]; + fr1 = -k_roll*history[rhist0] - damp_roll*vrl1; + fr2 = -k_roll*history[rhist1] - damp_roll*vrl2; + fr3 = -k_roll*history[rhist2] - damp_roll*vrl3; + + // rescale frictional displacements and forces if needed + Frcrit = roll_coeffs[itype][jtype][2] * Fncrit; + + fr = sqrt(fr1*fr1 + fr2*fr2 + fr3*fr3); + if (fr > Frcrit) { + if (rollmag != 0.0) { + fr1 *= Frcrit/fr; + fr2 *= Frcrit/fr; + fr3 *= Frcrit/fr; + fr *= Frcrit/fr; + } else fr1 = fr2 = fr3 = fr = 0.0; + } + } else fr1 = fr2 = fr3 = fr = 0.0; + + //**************************************** + // twisting torque, including history effects + //**************************************** + + if (twist_model[itype][jtype] != TWIST_NONE) { + // omega_T (eq 29 of Marshall) + magtwist = relrot1*nx + relrot2*ny + relrot3*nz; + if (twist_model[itype][jtype] == TWIST_MARSHALL) { + k_twist = 0.5*k_tangential*a*a;; //eq 32 + damp_twist = 0.5*damp_tangential*a*a; + mu_twist = TWOTHIRDS*a*tangential_coeffs[itype][jtype][2];; + } else { + k_twist = twist_coeffs[itype][jtype][0]; + damp_twist = twist_coeffs[itype][jtype][1]; + mu_twist = twist_coeffs[itype][jtype][2]; + } + // M_t torque (eq 30) + magtortwist = -k_twist*history[twist_history_index] - damp_twist*magtwist; + signtwist = (magtwist > 0) - (magtwist < 0); + Mtcrit = mu_twist*Fncrit; // critical torque (eq 44) + if (fabs(magtortwist) > Mtcrit) { + magtortwist = -Mtcrit * signtwist; // eq 34 + } else magtortwist = 0.0; + } else magtortwist = 0.0; + + // set force and return no energy + + fforce = Fntot*rinv; + + // set single_extra quantities + + svector[0] = fs1; + svector[1] = fs2; + svector[2] = fs3; + svector[3] = fs; + svector[4] = fr1; + svector[5] = fr2; + svector[6] = fr3; + svector[7] = fr; + svector[8] = magtortwist; + svector[9] = delx; + svector[10] = dely; + svector[11] = delz; + return 0.0; +} + +/* ---------------------------------------------------------------------- */ + +int PairGranular::pack_forward_comm(int n, int *list, double *buf, + int /* pbc_flag */, int * /* pbc */) +{ + int i,j,m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = mass_rigid[j]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void PairGranular::unpack_forward_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) + mass_rigid[i] = buf[m++]; +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based arrays +------------------------------------------------------------------------- */ + +double PairGranular::memory_usage() +{ + double bytes = (double)nmax * sizeof(double); + return bytes; +} + +/* ---------------------------------------------------------------------- + mixing of Young's modulus (E) +------------------------------------------------------------------------- */ + +double PairGranular::mix_stiffnessE(double Eii, double Ejj, + double poisii, double poisjj) +{ + return 1/((1-poisii*poisii)/Eii+(1-poisjj*poisjj)/Ejj); +} + +/* ---------------------------------------------------------------------- + mixing of shear modulus (G) +------------------------------------------------------------------------ */ + +double PairGranular::mix_stiffnessG(double Eii, double Ejj, + double poisii, double poisjj) +{ + return 1/((2*(2-poisii)*(1+poisii)/Eii) + (2*(2-poisjj)*(1+poisjj)/Ejj)); +} + +/* ---------------------------------------------------------------------- + mixing of everything else +------------------------------------------------------------------------- */ + +double PairGranular::mix_geom(double valii, double valjj) +{ + return sqrt(valii*valjj); +} + + +/* ---------------------------------------------------------------------- + compute pull-off distance (beyond contact) for a given radius and atom type +------------------------------------------------------------------------- */ + +double PairGranular::pulloff_distance(double radi, double radj, + int itype, int jtype) +{ + double E, coh, a, Reff; + Reff = radi*radj/(radi+radj); + if (Reff <= 0) return 0; + coh = normal_coeffs[itype][jtype][3]; + E = normal_coeffs[itype][jtype][0]*THREEQUARTERS; + a = cbrt(9*MY_PI*coh*Reff*Reff/(4*E)); + return a*a/Reff - 2*sqrt(MY_PI*coh*a/E); +} + +/* ---------------------------------------------------------------------- + transfer history during fix/neigh/history exchange + only needed if any history entries i-j are not just negative of j-i entries +------------------------------------------------------------------------- */ + +void PairGranular::transfer_history(double* source, double* target) +{ + for (int i = 0; i < size_history; i++) + target[i] = history_transfer_factors[i]*source[i]; +} From 46f98ec4dc85d04d0f5e65cb2155e6b3e3a24fcb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Apr 2021 10:23:16 -0400 Subject: [PATCH 0358/1217] make compatible with const data pointers as arguments --- src/library.cpp | 18 +++++++++++------- src/library.h | 14 +++++++------- 2 files changed, 18 insertions(+), 14 deletions(-) diff --git a/src/library.cpp b/src/library.cpp index 7dbe5f9467..ac059f53ae 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -3822,8 +3822,8 @@ X(1),Y(1),Z(1),X(2),Y(2),Z(2),...,X(N),Y(N),Z(N). * \return number of atoms created on success; -1 on failure (no box, no atom IDs, etc.) */ -int lammps_create_atoms(void *handle, int n, tagint *id, int *type, - double *x, double *v, imageint *image, +int lammps_create_atoms(void *handle, int n, const tagint *id, const int *type, + const double *x, const double *v, const imageint *image, int bexpand) { LAMMPS *lmp = (LAMMPS *) handle; @@ -3859,13 +3859,17 @@ int lammps_create_atoms(void *handle, int n, tagint *id, int *type, int nlocal_prev = nlocal; double xdata[3]; + imageint idata, *img; for (int i = 0; i < n; i++) { xdata[0] = x[3*i]; xdata[1] = x[3*i+1]; xdata[2] = x[3*i+2]; - imageint * img = image ? image + i : nullptr; - tagint tag = id ? id[i] : 0; + if (image) { + idata = image[i]; + img = &idata; + } else img = nullptr; + const tagint tag = id ? id[i] : 0; // create atom only on MPI rank that would own it @@ -3943,7 +3947,7 @@ int lammps_create_atoms(void *handle, int n, tagint *id, int *type, * multiple requests from the same pair style instance * \return return neighbor list index if found, otherwise -1 */ -int lammps_find_pair_neighlist(void *handle, char *style, int exact, int nsub, int reqid) { +int lammps_find_pair_neighlist(void *handle, const char *style, int exact, int nsub, int reqid) { LAMMPS *lmp = (LAMMPS *) handle; Pair *pair = lmp->force->pair_match(style, exact, nsub); @@ -3973,7 +3977,7 @@ int lammps_find_pair_neighlist(void *handle, char *style, int exact, int nsub, i * multiple requests from the same fix * \return return neighbor list index if found, otherwise -1 */ -int lammps_find_fix_neighlist(void *handle, char *id, int reqid) { +int lammps_find_fix_neighlist(void *handle, const char *id, int reqid) { LAMMPS *lmp = (LAMMPS *) handle; const int ifix = lmp->modify->find_fix(id); if (ifix < 0) return -1; @@ -4003,7 +4007,7 @@ int lammps_find_fix_neighlist(void *handle, char *id, int reqid) { * multiple requests from the same compute * \return return neighbor list index if found, otherwise -1 */ -int lammps_find_compute_neighlist(void* handle, char *id, int reqid) { +int lammps_find_compute_neighlist(void* handle, const char *id, int reqid) { LAMMPS *lmp = (LAMMPS *) handle; const int icompute = lmp->modify->find_compute(id); if (icompute < 0) return -1; diff --git a/src/library.h b/src/library.h index 11cd72388a..3500e1b65e 100644 --- a/src/library.h +++ b/src/library.h @@ -160,20 +160,20 @@ void lammps_scatter(void *handle, char *name, int type, int count, void *data); void lammps_scatter_subset(void *handle, char *name, int type, int count, int ndata, int *ids, void *data); #if !defined(LAMMPS_BIGBIG) -int lammps_create_atoms(void *handle, int n, int *id, int *type, - double *x, double *v, int *image, int bexpand); +int lammps_create_atoms(void *handle, int n, const int *id, const int *type, + const double *x, const double *v, const int *image, int bexpand); #else -int lammps_create_atoms(void *handle, int n, int64_t *id, int *type, - double *x, double *v, int64_t* image, int bexpand); +int lammps_create_atoms(void *handle, int n, const int64_t *id, const int *type, + const double *x, const double *v, const int64_t* image, int bexpand); #endif /* ---------------------------------------------------------------------- * Library functions for accessing neighbor lists * ---------------------------------------------------------------------- */ -int lammps_find_pair_neighlist(void *handle, char *style, int exact, int nsub, int request); -int lammps_find_fix_neighlist(void *handle, char *id, int request); -int lammps_find_compute_neighlist(void *handle, char *id, int request); +int lammps_find_pair_neighlist(void *handle, const char *style, int exact, int nsub, int request); +int lammps_find_fix_neighlist(void *handle, const char *id, int request); +int lammps_find_compute_neighlist(void *handle, const char *id, int request); int lammps_neighlist_num_elements(void *handle, int idx); void lammps_neighlist_element_neighbors(void *handle, int idx, int element, int *iatom, int *numneigh, int **neighbors); From 432ccffb3e7a719d5b0db9cc8a992ef105f2266a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Apr 2021 09:58:20 -0400 Subject: [PATCH 0359/1217] find manybody potentials --- unittest/c-library/CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/unittest/c-library/CMakeLists.txt b/unittest/c-library/CMakeLists.txt index 121c42f7fd..3c24cdcff4 100644 --- a/unittest/c-library/CMakeLists.txt +++ b/unittest/c-library/CMakeLists.txt @@ -11,6 +11,7 @@ add_executable(test_library_properties test_library_properties.cpp test_main.cpp target_link_libraries(test_library_properties PRIVATE lammps GTest::GTest GTest::GMock) target_compile_definitions(test_library_properties PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR}) add_test(LibraryProperties test_library_properties) +set_tests_properties(LibraryProperties PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") set(TEST_CONFIG_DEFS "-DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR};-DLAMMPS_${LAMMPS_SIZES}") set(PKG_COUNT 0) From 5520d6edd737af74792386e0c7f4759757a9ff90 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Apr 2021 10:24:46 -0400 Subject: [PATCH 0360/1217] confirm that no incompatible neighbor lists are found --- unittest/python/python-commands.py | 2 ++ unittest/python/python-numpy.py | 2 ++ 2 files changed, 4 insertions(+) diff --git a/unittest/python/python-commands.py b/unittest/python/python-commands.py index 530cea8b13..f3526d6d4b 100644 --- a/unittest/python/python-commands.py +++ b/unittest/python/python-commands.py @@ -313,6 +313,8 @@ create_atoms 1 single & self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut"),-1) self.assertNotEqual(self.lmp.find_compute_neighlist("dist"),-1) + self.assertEqual(self.lmp.find_compute_neighlist("xxx"),-1) + self.assertEqual(self.lmp.find_fix_neighlist("dist"),-1) # the compute has a half neighbor list nlist = self.lmp.get_neighlist(self.lmp.find_compute_neighlist("dist")) diff --git a/unittest/python/python-numpy.py b/unittest/python/python-numpy.py index f3a116b91b..dc121691ab 100644 --- a/unittest/python/python-numpy.py +++ b/unittest/python/python-numpy.py @@ -364,6 +364,8 @@ class PythonNumpy(unittest.TestCase): self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut"),-1) self.assertNotEqual(self.lmp.find_compute_neighlist("dist"),-1) + self.assertEqual(self.lmp.find_compute_neighlist("xxx"),-1) + self.assertEqual(self.lmp.find_fix_neighlist("dist"),-1) # the compute has a half neighbor list nlist = self.lmp.numpy.get_neighlist(self.lmp.find_compute_neighlist("dist")) From cea4298946f8be5a7c605e6d1f9d55abb32ca8cd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Apr 2021 09:59:09 -0400 Subject: [PATCH 0361/1217] silence LAMMPS output, if requested --- unittest/c-library/test_library_properties.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/unittest/c-library/test_library_properties.cpp b/unittest/c-library/test_library_properties.cpp index 182beee7d0..2b2b1cd58e 100644 --- a/unittest/c-library/test_library_properties.cpp +++ b/unittest/c-library/test_library_properties.cpp @@ -160,7 +160,9 @@ TEST_F(LibraryProperties, box) boxlo[0] = -6.1; boxhi[1] = 7.3; xy = 0.1; + if (!verbose) ::testing::internal::CaptureStdout(); lammps_reset_box(lmp, boxlo, boxhi, xy, yz, xz); + if (!verbose) ::testing::internal::GetCapturedStdout(); lammps_extract_box(lmp, boxlo, boxhi, &xy, &yz, &xz, pflags, &boxflag); EXPECT_DOUBLE_EQ(boxlo[0], -6.1); EXPECT_DOUBLE_EQ(boxlo[1], -7.692866); From 1a48667026821125717e3410d268e96cf428747b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Apr 2021 10:00:14 -0400 Subject: [PATCH 0362/1217] add minimal test for neighbor list functions --- .../c-library/test_library_properties.cpp | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/unittest/c-library/test_library_properties.cpp b/unittest/c-library/test_library_properties.cpp index 2b2b1cd58e..19e881e32b 100644 --- a/unittest/c-library/test_library_properties.cpp +++ b/unittest/c-library/test_library_properties.cpp @@ -315,6 +315,60 @@ TEST_F(LibraryProperties, global) EXPECT_DOUBLE_EQ((*d_ptr), 0.1); }; +TEST_F(LibraryProperties, neighlist) +{ + if (!lammps_has_style(lmp, "pair", "sw")) GTEST_SKIP(); + const char sysinit[] = "boundary f f f\n" + "units real\n" + "region box block -5 5 -5 5 -5 5\n" + "create_box 2 box\n" + "mass 1 1.0\n" + "mass 2 1.0\n" + "pair_style hybrid/overlay lj/cut 4.0 lj/cut 4.0 morse 4.0 sw\n" + "pair_coeff * * sw Si.sw Si NULL\n" + "pair_coeff 1 2 morse 0.2 2.0 2.0\n" + "pair_coeff 2 2 lj/cut 1 0.1 2.0\n" + "pair_coeff * * lj/cut 2 0.01 2.0\n" + "compute dist all pair/local dist\n" + "fix dist all ave/histo 1 1 1 0.0 3.0 4 c_dist mode vector\n" + "thermo_style custom f_dist[*]"; + + const double pos[] = {0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, + 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0}; + const tagint ids[] = {1, 2, 3, 4, 5, 6, 7}; + const int types[] = {1, 1, 1, 1, 2, 2, 2}; + + const int numatoms = sizeof(ids) / sizeof(tagint); + + if (!verbose) ::testing::internal::CaptureStdout(); + lammps_commands_string(lmp, sysinit); + lammps_create_atoms(lmp, numatoms, ids, types, pos, nullptr, nullptr, 0); + lammps_command(lmp, "run 0 post no"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + + int nhisto = *(double *)lammps_extract_fix(lmp,"dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,0,0); + int nskip = *(double *)lammps_extract_fix(lmp,"dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,1,0); + double minval = *(double *)lammps_extract_fix(lmp,"dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,2,0); + double maxval = *(double *)lammps_extract_fix(lmp,"dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,3,0); + // 21 pair distances counted, none skipped, smallest 1.0, largest 2.1 + EXPECT_EQ(nhisto,21); + EXPECT_EQ(nskip,0); + EXPECT_DOUBLE_EQ(minval,1.0); + EXPECT_DOUBLE_EQ(maxval,2.1); + + const int nlocal = lammps_extract_setting(lmp, "nlocal"); + EXPECT_EQ(nlocal, numatoms); + EXPECT_NE(lammps_find_pair_neighlist(lmp, "sw", 1, 0, 0), -1); + EXPECT_NE(lammps_find_pair_neighlist(lmp, "morse", 1, 0, 0), -1); + EXPECT_NE(lammps_find_pair_neighlist(lmp, "lj/cut", 1, 1, 0), -1); + EXPECT_NE(lammps_find_pair_neighlist(lmp, "lj/cut", 1, 2, 0), -1); + EXPECT_EQ(lammps_find_pair_neighlist(lmp, "lj/cut", 1, 0, 0), -1); + EXPECT_EQ(lammps_find_pair_neighlist(lmp, "hybrid/overlay", 1, 0, 0), -1); + EXPECT_NE(lammps_find_compute_neighlist(lmp, "dist", 0),-1); + EXPECT_EQ(lammps_find_fix_neighlist(lmp, "dist", 0),-1); + EXPECT_EQ(lammps_find_compute_neighlist(lmp, "xxx", 0),-1); +}; + class AtomProperties : public ::testing::Test { protected: void *lmp; From 6205375c0317ec93fe1bb4715cef61bff1f969eb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Apr 2021 10:04:16 -0400 Subject: [PATCH 0363/1217] allow const char for compute/fix id arguments --- src/library.cpp | 4 ++-- src/library.h | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/library.cpp b/src/library.cpp index ac059f53ae..8f23ffcb6c 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -1615,7 +1615,7 @@ lists the available options. * \return pointer (cast to ``void *``) to the location of the * requested data or ``NULL`` if not found. */ -void *lammps_extract_compute(void *handle, char *id, int style, int type) +void *lammps_extract_compute(void *handle, const char *id, int style, int type) { LAMMPS *lmp = (LAMMPS *) handle; @@ -1801,7 +1801,7 @@ The following table lists the available options. * \return pointer (cast to ``void *``) to the location of the * requested data or ``NULL`` if not found. */ -void *lammps_extract_fix(void *handle, char *id, int style, int type, +void *lammps_extract_fix(void *handle, const char *id, int style, int type, int nrow, int ncol) { LAMMPS *lmp = (LAMMPS *) handle; diff --git a/src/library.h b/src/library.h index 3500e1b65e..8db19f7eb2 100644 --- a/src/library.h +++ b/src/library.h @@ -138,8 +138,8 @@ void *lammps_extract_atom(void *handle, const char *name); * Library functions to access data from computes, fixes, variables in LAMMPS * ---------------------------------------------------------------------- */ -void *lammps_extract_compute(void *handle, char *id, int, int); -void *lammps_extract_fix(void *handle, char *, int, int, int, int); +void *lammps_extract_compute(void *handle, const char *, int, int); +void *lammps_extract_fix(void *handle, const char *, int, int, int, int); void *lammps_extract_variable(void *handle, const char *, const char *); int lammps_set_variable(void *, char *, char *); From cfc39b5a7338e8e621542cfaea10c29adbbd08c7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Apr 2021 10:44:07 -0400 Subject: [PATCH 0364/1217] complete porting python neighborlist test to c-library version --- .../c-library/test_library_properties.cpp | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/unittest/c-library/test_library_properties.cpp b/unittest/c-library/test_library_properties.cpp index 19e881e32b..de40c85617 100644 --- a/unittest/c-library/test_library_properties.cpp +++ b/unittest/c-library/test_library_properties.cpp @@ -367,6 +367,62 @@ TEST_F(LibraryProperties, neighlist) EXPECT_NE(lammps_find_compute_neighlist(lmp, "dist", 0),-1); EXPECT_EQ(lammps_find_fix_neighlist(lmp, "dist", 0),-1); EXPECT_EQ(lammps_find_compute_neighlist(lmp, "xxx", 0),-1); + + // full neighbor list for 4 type 1 atoms + // all have 3 type 1 atom neighbors + int idx = lammps_find_pair_neighlist(lmp, "sw", 1, 0, 0); + int num = lammps_neighlist_num_elements(lmp, idx); + EXPECT_EQ(num, 4); + int iatom, inum, *neighbors; + for (int i=0; i < num; ++i) { + lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors); + EXPECT_EQ(iatom,i); + EXPECT_EQ(inum,3); + EXPECT_NE(neighbors,nullptr); + } + + // half neighbor list for all pairs between type 1 and type 2 + // 4 type 1 atoms with 3 type 2 neighbors and 3 type 2 atoms without neighbors + idx = lammps_find_pair_neighlist(lmp, "morse", 0, 0, 0); + num = lammps_neighlist_num_elements(lmp, idx); + EXPECT_EQ(num, nlocal); + for (int i=0; i < num; ++i) { + lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors); + if (i < 4) EXPECT_EQ(inum, 3); + else EXPECT_EQ(inum,0); + EXPECT_NE(neighbors,nullptr); + } + + // half neighbor list between type 2 atoms only + // 3 pairs with 2, 1, 0 neighbors + idx = lammps_find_pair_neighlist(lmp, "lj/cut", 1, 1, 0); + num = lammps_neighlist_num_elements(lmp, idx); + EXPECT_EQ(num, 3); + for (int i=0; i < num; ++i) { + lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors); + EXPECT_EQ(inum,2-i); + EXPECT_NE(neighbors,nullptr); + } + + // half neighbor list between all pairs. same as simple lj/cut case + idx = lammps_find_pair_neighlist(lmp, "lj/cut", 1, 2, 0); + num = lammps_neighlist_num_elements(lmp, idx); + EXPECT_EQ(num, nlocal); + for (int i=0; i < num; ++i) { + lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors); + EXPECT_EQ(inum,nlocal-1-i); + EXPECT_NE(neighbors,nullptr); + } + + // the compute has a half neighbor list + idx = lammps_find_compute_neighlist(lmp, "dist", 0); + num = lammps_neighlist_num_elements(lmp, idx); + EXPECT_EQ(num, nlocal); + for (int i=0; i < num; ++i) { + lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors); + EXPECT_EQ(inum,nlocal-1-i); + EXPECT_NE(neighbors,nullptr); + } }; class AtomProperties : public ::testing::Test { From 7244ccf8b14c784aef356735df242f92368db681 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Apr 2021 11:04:02 -0400 Subject: [PATCH 0365/1217] update format --- .../c-library/test_library_properties.cpp | 61 ++++++++++--------- 1 file changed, 33 insertions(+), 28 deletions(-) diff --git a/unittest/c-library/test_library_properties.cpp b/unittest/c-library/test_library_properties.cpp index de40c85617..07e920bda7 100644 --- a/unittest/c-library/test_library_properties.cpp +++ b/unittest/c-library/test_library_properties.cpp @@ -346,15 +346,18 @@ TEST_F(LibraryProperties, neighlist) lammps_command(lmp, "run 0 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); - int nhisto = *(double *)lammps_extract_fix(lmp,"dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,0,0); - int nskip = *(double *)lammps_extract_fix(lmp,"dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,1,0); - double minval = *(double *)lammps_extract_fix(lmp,"dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,2,0); - double maxval = *(double *)lammps_extract_fix(lmp,"dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,3,0); + int nhisto = + *(double *)lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 0, 0); + int nskip = *(double *)lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 1, 0); + double minval = + *(double *)lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 2, 0); + double maxval = + *(double *)lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 3, 0); // 21 pair distances counted, none skipped, smallest 1.0, largest 2.1 - EXPECT_EQ(nhisto,21); - EXPECT_EQ(nskip,0); - EXPECT_DOUBLE_EQ(minval,1.0); - EXPECT_DOUBLE_EQ(maxval,2.1); + EXPECT_EQ(nhisto, 21); + EXPECT_EQ(nskip, 0); + EXPECT_DOUBLE_EQ(minval, 1.0); + EXPECT_DOUBLE_EQ(maxval, 2.1); const int nlocal = lammps_extract_setting(lmp, "nlocal"); EXPECT_EQ(nlocal, numatoms); @@ -364,9 +367,9 @@ TEST_F(LibraryProperties, neighlist) EXPECT_NE(lammps_find_pair_neighlist(lmp, "lj/cut", 1, 2, 0), -1); EXPECT_EQ(lammps_find_pair_neighlist(lmp, "lj/cut", 1, 0, 0), -1); EXPECT_EQ(lammps_find_pair_neighlist(lmp, "hybrid/overlay", 1, 0, 0), -1); - EXPECT_NE(lammps_find_compute_neighlist(lmp, "dist", 0),-1); - EXPECT_EQ(lammps_find_fix_neighlist(lmp, "dist", 0),-1); - EXPECT_EQ(lammps_find_compute_neighlist(lmp, "xxx", 0),-1); + EXPECT_NE(lammps_find_compute_neighlist(lmp, "dist", 0), -1); + EXPECT_EQ(lammps_find_fix_neighlist(lmp, "dist", 0), -1); + EXPECT_EQ(lammps_find_compute_neighlist(lmp, "xxx", 0), -1); // full neighbor list for 4 type 1 atoms // all have 3 type 1 atom neighbors @@ -374,11 +377,11 @@ TEST_F(LibraryProperties, neighlist) int num = lammps_neighlist_num_elements(lmp, idx); EXPECT_EQ(num, 4); int iatom, inum, *neighbors; - for (int i=0; i < num; ++i) { + for (int i = 0; i < num; ++i) { lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors); - EXPECT_EQ(iatom,i); - EXPECT_EQ(inum,3); - EXPECT_NE(neighbors,nullptr); + EXPECT_EQ(iatom, i); + EXPECT_EQ(inum, 3); + EXPECT_NE(neighbors, nullptr); } // half neighbor list for all pairs between type 1 and type 2 @@ -386,11 +389,13 @@ TEST_F(LibraryProperties, neighlist) idx = lammps_find_pair_neighlist(lmp, "morse", 0, 0, 0); num = lammps_neighlist_num_elements(lmp, idx); EXPECT_EQ(num, nlocal); - for (int i=0; i < num; ++i) { + for (int i = 0; i < num; ++i) { lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors); - if (i < 4) EXPECT_EQ(inum, 3); - else EXPECT_EQ(inum,0); - EXPECT_NE(neighbors,nullptr); + if (i < 4) + EXPECT_EQ(inum, 3); + else + EXPECT_EQ(inum, 0); + EXPECT_NE(neighbors, nullptr); } // half neighbor list between type 2 atoms only @@ -398,30 +403,30 @@ TEST_F(LibraryProperties, neighlist) idx = lammps_find_pair_neighlist(lmp, "lj/cut", 1, 1, 0); num = lammps_neighlist_num_elements(lmp, idx); EXPECT_EQ(num, 3); - for (int i=0; i < num; ++i) { + for (int i = 0; i < num; ++i) { lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors); - EXPECT_EQ(inum,2-i); - EXPECT_NE(neighbors,nullptr); + EXPECT_EQ(inum, 2 - i); + EXPECT_NE(neighbors, nullptr); } // half neighbor list between all pairs. same as simple lj/cut case idx = lammps_find_pair_neighlist(lmp, "lj/cut", 1, 2, 0); num = lammps_neighlist_num_elements(lmp, idx); EXPECT_EQ(num, nlocal); - for (int i=0; i < num; ++i) { + for (int i = 0; i < num; ++i) { lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors); - EXPECT_EQ(inum,nlocal-1-i); - EXPECT_NE(neighbors,nullptr); + EXPECT_EQ(inum, nlocal - 1 - i); + EXPECT_NE(neighbors, nullptr); } // the compute has a half neighbor list idx = lammps_find_compute_neighlist(lmp, "dist", 0); num = lammps_neighlist_num_elements(lmp, idx); EXPECT_EQ(num, nlocal); - for (int i=0; i < num; ++i) { + for (int i = 0; i < num; ++i) { lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors); - EXPECT_EQ(inum,nlocal-1-i); - EXPECT_NE(neighbors,nullptr); + EXPECT_EQ(inum, nlocal - 1 - i); + EXPECT_NE(neighbors, nullptr); } }; From a4a23f3ef18cf0a82de27208e13e09ad2fea3011 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Apr 2021 11:04:24 -0400 Subject: [PATCH 0366/1217] add an example for looking up and looping over a neighbor list --- doc/src/Python_neighbor.rst | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/doc/src/Python_neighbor.rst b/doc/src/Python_neighbor.rst index cba117ad20..416fcb30a8 100644 --- a/doc/src/Python_neighbor.rst +++ b/doc/src/Python_neighbor.rst @@ -1,6 +1,43 @@ Neighbor list access ==================== +Access to neighbor lists is handled through a couple of wrapper classes +that allows to treat it like either a python list or a NumPy array. The +access procedure is similar to that of the C-library interface: use one +of the "find" functions to look up the index of the neighbor list in the +global table of neighbor lists and then get access to the neigbor list +data. The code sample below demonstrates reading the neighbor list data +using the NumPy access method. + +.. code-block:: python + + from lammps import lammps + import numpy as np + + lmp = lammps() + lmp.commands_string(""" + region box block -2 2 -2 2 -2 2 + lattice fcc 1.0 + create_box 1 box + create_atoms 1 box + mass 1 1.0 + pair_style lj/cut 2.5 + pair_coeff 1 1 1.0 1.0 + run 0 post no""") + + # look up the neighbor list + nlidx = lmp.find_pair_neighlist('lj/cut') + nl = lmp.numpy.get_neighlist(nlidx) + tags = lmp.extract_atom('id') + print("half neighbor list with {} entries".format(nl.size)) + # print neighbor list contents + for i in range(0,nl.size): + idx, nlist = nl.get(i) + print("\natom {} with ID {} has {} neighbors:".format(idx,tags[idx],nlist.size)) + if nlist.size > 0: + for n in np.nditer(nlist): + print(" atom {} with ID {}".format(n,tags[n])) + **Methods:** * :py:meth:`lammps.get_neighlist() `: Get neighbor list for given index From 17355f967a383968d7f618afde28b38ecbe4bce4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Apr 2021 11:11:18 -0400 Subject: [PATCH 0367/1217] address spelling and manual processing issues --- doc/src/Library_scatter.rst | 2 +- doc/src/Python_neighbor.rst | 2 +- doc/utils/sphinx-config/false_positives.txt | 1 + python/lammps/core.py | 4 ++-- src/library.cpp | 4 ++-- 5 files changed, 7 insertions(+), 6 deletions(-) diff --git a/doc/src/Library_scatter.rst b/doc/src/Library_scatter.rst index 40a79c2d9b..b45f45f6fb 100644 --- a/doc/src/Library_scatter.rst +++ b/doc/src/Library_scatter.rst @@ -76,7 +76,7 @@ It documents the following functions: ----------------------- -.. doxygenfunction:: lammps_create_atoms(void *handle, int n, int *id, int *type, double *x, double *v, int *image, int bexpand) +.. doxygenfunction:: lammps_create_atoms(void *handle, int n, const int *id, const int *type, const double *x, const double *v, const int *image, int bexpand) :project: progguide diff --git a/doc/src/Python_neighbor.rst b/doc/src/Python_neighbor.rst index 416fcb30a8..00c4cc8996 100644 --- a/doc/src/Python_neighbor.rst +++ b/doc/src/Python_neighbor.rst @@ -5,7 +5,7 @@ Access to neighbor lists is handled through a couple of wrapper classes that allows to treat it like either a python list or a NumPy array. The access procedure is similar to that of the C-library interface: use one of the "find" functions to look up the index of the neighbor list in the -global table of neighbor lists and then get access to the neigbor list +global table of neighbor lists and then get access to the neighbor list data. The code sample below demonstrates reading the neighbor list data using the NumPy access method. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 38a6971f4c..c10e978428 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2681,6 +2681,7 @@ representable Reproducibility reproducibility repuls +reqid rescale rescaled rescales diff --git a/python/lammps/core.py b/python/lammps/core.py index 11adecdca1..1f606f67f4 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -1753,9 +1753,9 @@ class lammps(object): Search for a neighbor list requested by a pair style instance that matches "style". If exact is True, the pair style name must match exactly. If exact is False, the pair style name is matched against - "style" as regular expression or substring. If the pair style is a + "style" as regular expression or sub-string. If the pair style is a hybrid pair style, the style is instead matched against the hybrid - sub-styles. If the same pair style is used as substyle multiple + sub-styles. If the same pair style is used as sub-style multiple types, you must set nsub to a value n > 0 which indicates the nth instance of that sub-style to be used (same as for the pair_coeff command). The default value of 0 will fail to match in that case. diff --git a/src/library.cpp b/src/library.cpp index 8f23ffcb6c..b72c8d7220 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -3926,7 +3926,7 @@ int lammps_create_atoms(void *handle, int n, const tagint *id, const int *type, * This function determines which of the available neighbor lists for * pair styles matches the given conditions. It first matches the style * name. If exact is 1 the name must match exactly, if exact is 0, a - * regular expression or substring match is done. If the pair style is + * regular expression or sub-string match is done. If the pair style is * hybrid or hybrid/overlay the style is matched against the sub styles * instead. * If a the same pair style is used multiple times as a sub-style, the @@ -3941,7 +3941,7 @@ int lammps_create_atoms(void *handle, int n, const tagint *id, const int *type, * \param handle pointer to a previously created LAMMPS instance cast to ``void *``. * \param style String used to search for pair style instance * \param exact Flag to control whether style should match exactly or only - * a regular expression / substring match is applied. + * a regular expression / sub-string match is applied. * \param nsub match nsub-th hybrid sub-style instance of the same style * \param reqid request id to identify neighbor list in case there are * multiple requests from the same pair style instance From b2e9ffa67371f340ebae59e1285b26e1945b8f07 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Apr 2021 11:15:00 -0400 Subject: [PATCH 0368/1217] add missing entry to standard packages list --- doc/src/Packages_standard.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/src/Packages_standard.rst b/doc/src/Packages_standard.rst index ab9be69ab3..81623c8d4a 100644 --- a/doc/src/Packages_standard.rst +++ b/doc/src/Packages_standard.rst @@ -71,6 +71,8 @@ package: +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`PERI ` | Peridynamics models | :doc:`pair_style peri ` | peri | no | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`PLUGIN ` | Plugin loader command | :doc:`plugin ` | plugins | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`POEMS ` | coupled rigid body motion | :doc:`fix poems ` | rigid | int | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`PYTHON ` | embed Python code in an input script | :doc:`python ` | python | sys | From f0e3786ded9641ca0a911e374cae587a5de8a06e Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Sun, 4 Apr 2021 22:48:25 +0200 Subject: [PATCH 0369/1217] Minor changes to conform with coding standards --- src/USER-HDNNP/pair_hdnnp.cpp | 34 ++++++++++++---------------------- 1 file changed, 12 insertions(+), 22 deletions(-) diff --git a/src/USER-HDNNP/pair_hdnnp.cpp b/src/USER-HDNNP/pair_hdnnp.cpp index 213574327c..c7318ec0b5 100644 --- a/src/USER-HDNNP/pair_hdnnp.cpp +++ b/src/USER-HDNNP/pair_hdnnp.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "pair_hdnnp.h" -#include + #include "atom.h" #include "citeme.h" #include "comm.h" @@ -29,7 +29,7 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "utils.h" + #include "InterfaceLammps.h" // n2p2 interface header using namespace LAMMPS_NS; @@ -54,6 +54,13 @@ PairHDNNP::PairHDNNP(LAMMPS *lmp) : Pair(lmp) { if (lmp->citeme) lmp->citeme->add(cite_user_hdnnp_package); + single_enable = 0; // 1 if single() routine exists + restartinfo = 0; // 1 if pair style writes restart info + one_coeff = 1; // 1 if allows only one coeff * * call + manybody_flag = 1; // 1 if a manybody potential + unit_convert_flag = 0; // TODO: Check possible values. value != 0 indicates support for unit conversion. + reinitflag = 0; // 1 if compatible with fix adapt and alike + interface = new nnp::InterfaceLammps(); } @@ -68,8 +75,7 @@ PairHDNNP::~PairHDNNP() void PairHDNNP::compute(int eflag, int vflag) { - if(eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); // Set number of local atoms and add element. interface->setLocalAtoms(atom->nlocal,atom->type); @@ -111,35 +117,19 @@ void PairHDNNP::compute(int eflag, int vflag) void PairHDNNP::settings(int narg, char **arg) { - single_enable = 0; // 1 if single() routine exists - single_hessian_enable = 0; // 1 if single_hessian() routine exists - restartinfo = 0; // 1 if pair style writes restart info - respa_enable = 0; // 1 if inner/middle/outer rRESPA routines - one_coeff = 1; // 1 if allows only one coeff * * call - manybody_flag = 1; // 1 if a manybody potential - unit_convert_flag = 0; // value != 0 indicates support for unit conversion. - no_virial_fdotr_compute = 0; // 1 if does not invoke virial_fdotr_compute() - writedata = 0; // 1 if writes coeffs to data file - ghostneigh = 0; // 1 if pair style needs neighbors of ghosts - reinitflag = 0; // 1 if compatible with fix adapt and alike - int iarg = 0; if (narg == 0) error->all(FLERR,"Illegal pair_style command"); // default settings - int len = strlen("hdnnp/") + 1; - directory = new char[len]; - strcpy(directory,"hdnnp/"); + directory = utils::strdup("hdnnp/"); showew = true; showewsum = 0; maxew = 0; resetew = false; cflength = 1.0; cfenergy = 1.0; - len = strlen("") + 1; - emap = new char[len]; - strcpy(emap,""); + emap = utils::strdup(""); numExtrapolationWarningsTotal = 0; numExtrapolationWarningsSummary = 0; From 5e0b017d30281b7fb94e23a4c53d84defb7467d2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 4 Apr 2021 20:51:58 -0400 Subject: [PATCH 0370/1217] update information about adding unit tests to reflect recent changes --- doc/src/Developer_unittest.rst | 45 ++++++++++++++++++++++------------ 1 file changed, 29 insertions(+), 16 deletions(-) diff --git a/doc/src/Developer_unittest.rst b/doc/src/Developer_unittest.rst index 4487dff11c..52753ee1b4 100644 --- a/doc/src/Developer_unittest.rst +++ b/doc/src/Developer_unittest.rst @@ -4,10 +4,10 @@ Adding tests for unit testing This section discusses adding or expanding tests for the unit test infrastructure included into the LAMMPS source code distribution. Unlike example inputs, unit tests focus on testing the "local" behavior -of individual features, tend to run very fast, and should be set up to -cover as much of the added code as possible. When contributing code to -the distribution, the LAMMPS developers will appreciate if additions -to the integrated unit test facility are included. +of individual features, tend to run fast, and should be set up to cover +as much of the added code as possible. When contributing code to the +distribution, the LAMMPS developers will appreciate if additions to the +integrated unit test facility are included. Given the complex nature of MD simulations where many operations can only be performed when suitable "real" simulation environment has been @@ -50,6 +50,9 @@ available: * - File name: - Test name: - Description: + * - ``test_argutils.cpp`` + - ArgInfo + - Tests for ``ArgInfo`` class used by LAMMPS * - ``test_fmtlib.cpp`` - FmtLib - Tests for ``fmtlib::`` functions used by LAMMPS @@ -155,23 +158,27 @@ have the desired effect: { ASSERT_EQ(lmp->update->ntimestep, 0); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("reset_timestep 10"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + BEGIN_HIDE_OUTPUT(); + command("reset_timestep 10"); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->update->ntimestep, 10); - if (!verbose) ::testing::internal::CaptureStdout(); - lmp->input->one("reset_timestep 0"); - if (!verbose) ::testing::internal::GetCapturedStdout(); + BEGIN_HIDE_OUTPUT(); + command("reset_timestep 0"); + END_HIDE_OUTPUT(); ASSERT_EQ(lmp->update->ntimestep, 0); + + TEST_FAILURE(".*ERROR: Timestep must be >= 0.*", command("reset_timestep -10");); + TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep");); + TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep 10 10");); + TEST_FAILURE(".*ERROR: Expected integer .*", command("reset_timestep xxx");); } -Please note the use of the (global) verbose variable to control whether -the LAMMPS command will be silent by capturing the output or not. In -the default case, verbose == false, the test output will be compact and -not mixed with LAMMPS output. However setting the verbose flag (via -setting the ``TEST_ARGS`` environment variable, ``TEST_ARGS=-v``) can be -helpful to understand why tests fail unexpectedly. +Please note the use of the ``BEGIN_HIDE_OUTPUT`` and ``END_HIDE_OUTPUT`` +functions that will capture output from running LAMMPS. This is normally +discarded but by setting the verbose flag (via setting the ``TEST_ARGS`` +environment variable, ``TEST_ARGS=-v``) it can be printed and used to +understand why tests fail unexpectedly. Another complexity of these tests stems from the need to capture situations where LAMMPS will stop with an error, i.e. handle so-called @@ -210,6 +217,12 @@ The following test programs are currently available: * - ``test_lattice_region.cpp`` - LatticeRegion - Tests to validate the :doc:`lattice ` and :doc:`region ` commands + * - ``test_groups.cpp`` + - GroupTest + - Tests to validate the :doc:`group ` command + * - ``test_variables.cpp`` + - VariableTest + - Tests to validate the :doc:`variable ` command * - ``test_kim_commands.cpp`` - KimCommands - Tests for several commands from the :ref:`KIM package ` From d1b6aaa3f3a6e1524864c6d582b9a0220ea5980c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 4 Apr 2021 20:57:29 -0400 Subject: [PATCH 0371/1217] plugins also have a .so suffix on MacOS (unlike shared libs) --- unittest/commands/test_simple_commands.cpp | 4 ---- 1 file changed, 4 deletions(-) diff --git a/unittest/commands/test_simple_commands.cpp b/unittest/commands/test_simple_commands.cpp index 9173909806..9bd6e74c9b 100644 --- a/unittest/commands/test_simple_commands.cpp +++ b/unittest/commands/test_simple_commands.cpp @@ -328,11 +328,7 @@ TEST_F(SimpleCommandsTest, Units) #if defined(LMP_PLUGIN) TEST_F(SimpleCommandsTest, Plugin) { -#if defined(__APPLE__) - std::string loadfmt("plugin load {}plugin.dylib"); -#else std::string loadfmt("plugin load {}plugin.so"); -#endif ::testing::internal::CaptureStdout(); lmp->input->one(fmt::format(loadfmt, "hello")); auto text = ::testing::internal::GetCapturedStdout(); From 36c6410fd8fff5a583b8429f4a1c78cecdb87772 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 4 Apr 2021 21:14:12 -0400 Subject: [PATCH 0372/1217] make skip() function argument optional and default to 1 --- src/tokenizer.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/tokenizer.h b/src/tokenizer.h index 2db9870866..b3bbf05296 100644 --- a/src/tokenizer.h +++ b/src/tokenizer.h @@ -41,7 +41,7 @@ public: Tokenizer& operator=(Tokenizer&&) = default; void reset(); - void skip(int n); + void skip(int n=1); bool has_next() const; bool contains(const std::string &str) const; std::string next(); @@ -104,7 +104,7 @@ public: bool has_next() const; bool contains(const std::string &value) const; - void skip(int ntokens); + void skip(int ntokens=1); size_t count(); }; From 1e7e930d55ca27103cdc601860c6c53fbfaeef8f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 4 Apr 2021 21:14:40 -0400 Subject: [PATCH 0373/1217] generalize match to fit all rigid/small derived fixes --- src/velocity.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/velocity.cpp b/src/velocity.cpp index b8d2e5229a..f4483074aa 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -108,7 +108,7 @@ void Velocity::command(int narg, char **arg) int initcomm = 0; if (style == ZERO && rfix >= 0 && - utils::strmatch(modify->fix[rfix]->style,"^rigid/small")) initcomm = 1; + utils::strmatch(modify->fix[rfix]->style,"^rigid.*/small.*")) initcomm = 1; if ((style == CREATE || style == SET) && temperature && strcmp(temperature->style,"temp/cs") == 0) initcomm = 1; From 67d4302fc7befe67ff157b4e1584067efabea171 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 4 Apr 2021 21:51:06 -0400 Subject: [PATCH 0374/1217] add tests for tokenizer skip() function and throwing an exception --- unittest/utils/test_tokenizer.cpp | 44 +++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/unittest/utils/test_tokenizer.cpp b/unittest/utils/test_tokenizer.cpp index 69ec7a55d2..ec097abf62 100644 --- a/unittest/utils/test_tokenizer.cpp +++ b/unittest/utils/test_tokenizer.cpp @@ -43,6 +43,18 @@ TEST(Tokenizer, two_words) ASSERT_EQ(t.count(), 2); } +TEST(Tokenizer, skip) +{ + Tokenizer t("test word", " "); + ASSERT_TRUE(t.has_next()); + t.skip(); + ASSERT_TRUE(t.has_next()); + t.skip(1); + ASSERT_FALSE(t.has_next()); + ASSERT_EQ(t.count(), 2); + ASSERT_THROW(t.skip(), TokenizerException); +} + TEST(Tokenizer, prefix_separators) { Tokenizer t(" test word", " "); @@ -63,6 +75,18 @@ TEST(Tokenizer, iterate_words) ASSERT_EQ(t.count(), 2); } +TEST(Tokenizer, copy_constructor) +{ + Tokenizer t(" test word ", " "); + ASSERT_THAT(t.next(), Eq("test")); + ASSERT_THAT(t.next(), Eq("word")); + ASSERT_EQ(t.count(), 2); + Tokenizer u(t); + ASSERT_THAT(u.next(), Eq("test")); + ASSERT_THAT(u.next(), Eq("word")); + ASSERT_EQ(u.count(), 2); +} + TEST(Tokenizer, no_separator_path) { Tokenizer t("one", ":"); @@ -139,6 +163,26 @@ TEST(ValueTokenizer, empty_string) ASSERT_FALSE(values.has_next()); } +TEST(ValueTokenizer, two_words) +{ + ValueTokenizer t("test word", " "); + ASSERT_THAT(t.next_string(), Eq("test")); + ASSERT_THAT(t.next_string(), Eq("word")); + ASSERT_THROW(t.next_string(), TokenizerException); +} + +TEST(ValueTokenizer, skip) +{ + ValueTokenizer t("test word", " "); + ASSERT_TRUE(t.has_next()); + t.skip(); + ASSERT_TRUE(t.has_next()); + t.skip(1); + ASSERT_FALSE(t.has_next()); + ASSERT_EQ(t.count(), 2); + ASSERT_THROW(t.skip(), TokenizerException); +} + TEST(ValueTokenizer, bad_integer) { ValueTokenizer values("f10"); From a858c07e8a7ff8c11a939fbb6a9c3e9430634ca9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 4 Apr 2021 21:51:48 -0400 Subject: [PATCH 0375/1217] add unit tests for empty id, invalid timespecs, and merge sort --- unittest/utils/test_utils.cpp | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/unittest/utils/test_utils.cpp b/unittest/utils/test_utils.cpp index 81dda11615..0c6e38e342 100644 --- a/unittest/utils/test_utils.cpp +++ b/unittest/utils/test_utils.cpp @@ -331,6 +331,11 @@ TEST(Utils, valid_id7) ASSERT_TRUE(utils::is_id("___")); } +TEST(Utils, empty_id) +{ + ASSERT_FALSE(utils::is_id("")); +} + TEST(Utils, invalid_id1) { ASSERT_FALSE(utils::is_id("+abc")); @@ -780,6 +785,11 @@ TEST(Utils, unit_conversion) ASSERT_DOUBLE_EQ(factor, 1.0 / 23.060549); } +TEST(Utils, timespec2seconds_off) +{ + ASSERT_DOUBLE_EQ(utils::timespec2seconds("off"), -1.0); +} + TEST(Utils, timespec2seconds_ss) { ASSERT_DOUBLE_EQ(utils::timespec2seconds("45"), 45.0); @@ -795,6 +805,11 @@ TEST(Utils, timespec2seconds_hhmmss) ASSERT_DOUBLE_EQ(utils::timespec2seconds("2:10:45"), 7845.0); } +TEST(Utils, timespec2seconds_invalid) +{ + ASSERT_DOUBLE_EQ(utils::timespec2seconds("2:aa:45"), -1.0); +} + TEST(Utils, date2num) { ASSERT_EQ(utils::date2num("1Jan05"), 20050101); @@ -810,3 +825,32 @@ TEST(Utils, date2num) ASSERT_EQ(utils::date2num("30November 02"), 20021130); ASSERT_EQ(utils::date2num("31December100"), 1001231); } + +static int compare(int a, int b, void *) +{ + if (a < b) + return -1; + else if (a > b) + return 1; + else + return 0; +} + +TEST(Utils, merge_sort) +{ + int data[] = {773, 405, 490, 830, 632, 96, 428, 728, 912, 840, 878, 745, 213, 219, 249, 380, + 894, 758, 575, 690, 61, 849, 19, 577, 338, 569, 898, 873, 448, 940, 431, 780, + 472, 289, 65, 491, 641, 37, 367, 33, 407, 854, 594, 611, 845, 136, 107, 592, + 275, 865, 158, 626, 399, 703, 686, 734, 188, 559, 781, 558, 737, 281, 638, 664, + 533, 529, 62, 969, 595, 661, 837, 463, 624, 568, 615, 936, 206, 637, 91, 694, + 214, 872, 468, 66, 775, 949, 486, 576, 255, 961, 480, 138, 177, 509, 333, 705, + 10, 375, 321, 952, 210, 111, 475, 268, 708, 864, 244, 121, 988, 540, 942, 682, + 750, 473, 478, 714, 955, 911, 482, 384, 144, 757, 697, 791, 420, 605, 447, 320}; + + const int num = sizeof(data) / sizeof(int); + utils::merge_sort(data, num, nullptr, &compare); + bool sorted = true; + for (int i = 1; i < num; ++i) + if (data[i - 1] > data[i]) sorted = false; + ASSERT_TRUE(sorted); +} From e00e2676fca98a56f87775fa7820aab19a6019b3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 4 Apr 2021 22:23:13 -0400 Subject: [PATCH 0376/1217] add tests for utils::open_potential() --- .../formats/test_potential_file_reader.cpp | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) diff --git a/unittest/formats/test_potential_file_reader.cpp b/unittest/formats/test_potential_file_reader.cpp index 1e3d96d6d7..f270f6e1f1 100644 --- a/unittest/formats/test_potential_file_reader.cpp +++ b/unittest/formats/test_potential_file_reader.cpp @@ -28,6 +28,7 @@ #include "potential_file_reader.h" #include "gmock/gmock.h" #include "gtest/gtest.h" + #include "../testing/core.h" #include @@ -257,6 +258,67 @@ TEST_F(PotentialFileReaderTest, UnitConvert) delete reader; } +class OpenPotentialTest : public LAMMPSTest { +}; + +// open for native units +TEST_F(OpenPotentialTest, Sw_native) +{ + int convert_flag = utils::get_supported_conversions(utils::ENERGY); + BEGIN_CAPTURE_OUTPUT(); + command("units metal"); + FILE *fp = utils::open_potential("Si.sw", lmp, &convert_flag); + auto text = END_CAPTURE_OUTPUT(); + double conv = utils::get_conversion_factor(utils::ENERGY, convert_flag); + + ASSERT_NE(fp, nullptr); + ASSERT_DOUBLE_EQ(conv, 1.0); + fclose(fp); +} + +// open with supported conversion enabled +TEST_F(OpenPotentialTest, Sw_conv) +{ + int convert_flag = utils::get_supported_conversions(utils::ENERGY); + ASSERT_EQ(convert_flag, utils::METAL2REAL | utils::REAL2METAL); + BEGIN_HIDE_OUTPUT(); + command("units real"); + FILE *fp = utils::open_potential("Si.sw", lmp, &convert_flag); + auto text = END_CAPTURE_OUTPUT(); + double conv = utils::get_conversion_factor(utils::ENERGY, convert_flag); + + ASSERT_NE(fp, nullptr); + ASSERT_EQ(convert_flag, utils::METAL2REAL); + ASSERT_DOUBLE_EQ(conv, 23.060549); + fclose(fp); +} + +// open with conversion disabled +TEST_F(OpenPotentialTest, Sw_noconv) +{ + BEGIN_HIDE_OUTPUT(); + command("units real"); + END_HIDE_OUTPUT(); + TEST_FAILURE(".*potential.*requires metal units but real.*", + utils::open_potential("Si.sw", lmp, nullptr);); + BEGIN_HIDE_OUTPUT(); + command("units lj"); + END_HIDE_OUTPUT(); + int convert_flag = utils::get_supported_conversions(utils::UNKNOWN); + ASSERT_EQ(convert_flag, utils::NOCONVERT); +} + +// open non-existing potential +TEST_F(OpenPotentialTest, No_file) +{ + int convert_flag = utils::get_supported_conversions(utils::ENERGY); + BEGIN_HIDE_OUTPUT(); + command("units metal"); + FILE *fp = utils::open_potential("Unknown.sw", lmp, &convert_flag); + END_HIDE_OUTPUT(); + ASSERT_EQ(fp,nullptr); +} + int main(int argc, char **argv) { MPI_Init(&argc, &argv); From 773ec40d3a83008e0e9bcfc0d51443ba9b6e2dd0 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 5 Apr 2021 11:37:35 -0600 Subject: [PATCH 0377/1217] Misc small fixes --- src/GRANULAR/fix_wall_gran.cpp | 11 +- src/GRANULAR/pair_gran_hertz_history.cpp | 4 +- src/GRANULAR/pair_gran_hooke.cpp | 4 +- src/GRANULAR/pair_granular.cpp | 2 +- src/GRANULAR/pair_granular_corrected.cpp | 1821 ---------------------- 5 files changed, 10 insertions(+), 1832 deletions(-) delete mode 100644 src/GRANULAR/pair_granular_corrected.cpp diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 1d27e21162..7ce8e49008 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -376,7 +376,6 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : wiggle = 0; wshear = 0; peratom_flag = 0; - limit_damping = 0; while (iarg < narg) { if (strcmp(arg[iarg],"wiggle") == 0) { @@ -792,7 +791,7 @@ void FixWallGran::hooke(double rsq, double dx, double dy, double dz, damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radius-r)*rinv - damp; - if(limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities @@ -885,7 +884,7 @@ void FixWallGran::hooke_history(double rsq, double dx, double dy, double dz, damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radius-r)*rinv - damp; - if(limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities @@ -1017,7 +1016,7 @@ void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz, if (rwall == 0.0) polyhertz = sqrt((radius-r)*radius); else polyhertz = sqrt((radius-r)*radius*rwall/(rwall+radius)); ccel *= polyhertz; - if(limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities @@ -1303,8 +1302,8 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, history[thist2] -= rsht*nz; // also rescale to preserve magnitude - prjmag = sqrt(history[0]*history[0] + history[1]*history[1] + - history[2]*history[2]); + prjmag = sqrt(history[thist0]*history[thist0] + + history[thist1]*history[thist1] + history[thist2]*history[thist2]); if (prjmag > 0) scalefac = shrmag/prjmag; else scalefac = 0; history[thist0] *= scalefac; diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index 40c6c3a41d..e21ec727d6 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -181,7 +181,7 @@ void PairGranHertzHistory::compute(int eflag, int vflag) ccel = kn*(radsum-r)*rinv - damp; polyhertz = sqrt((radsum-r)*radi*radj / radsum); ccel *= polyhertz; - if(limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities @@ -389,7 +389,7 @@ double PairGranHertzHistory::single(int i, int j, int /*itype*/, int /*jtype*/, ccel = kn*(radsum-r)*rinv - damp; polyhertz = sqrt((radsum-r)*radi*radj / radsum); ccel *= polyhertz; - if(limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp index 0e3ffc7293..c28bbd007f 100644 --- a/src/GRANULAR/pair_gran_hooke.cpp +++ b/src/GRANULAR/pair_gran_hooke.cpp @@ -158,7 +158,7 @@ void PairGranHooke::compute(int eflag, int vflag) damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if(limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities @@ -300,7 +300,7 @@ double PairGranHooke::single(int i, int j, int /*itype*/, int /*jtype*/, double damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if(limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping and ccel < 0.0) ccel = 0.0; // relative velocities diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 8bf9b0c4ed..ac98a6e27c 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -1547,7 +1547,7 @@ double PairGranular::single(int i, int j, int itype, int jtype, Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; - if(limit_damping[itype][jtype] and Fntot < 0.0) Fntot = 0.0; + if (limit_damping[itype][jtype] and Fntot < 0.0) Fntot = 0.0; jnum = list->numneigh[i]; jlist = list->firstneigh[i]; diff --git a/src/GRANULAR/pair_granular_corrected.cpp b/src/GRANULAR/pair_granular_corrected.cpp deleted file mode 100644 index bcf262aa2c..0000000000 --- a/src/GRANULAR/pair_granular_corrected.cpp +++ /dev/null @@ -1,1821 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing authors: - Dan Bolintineanu (SNL), Ishan Srivastava (SNL), Jeremy Lechman(SNL) - Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------ */ - -#include "pair_granular.h" - -#include -#include - -#include "atom.h" -#include "force.h" -#include "update.h" -#include "modify.h" -#include "fix.h" -#include "fix_dummy.h" -#include "fix_neigh_history.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" -#include "error.h" -#include "math_const.h" -#include "math_special.h" - - -using namespace LAMMPS_NS; -using namespace MathConst; -using namespace MathSpecial; - -#define PI27SQ 266.47931882941264802866 // 27*PI**2 -#define THREEROOT3 5.19615242270663202362 // 3*sqrt(3) -#define SIXROOT6 14.69693845669906728801 // 6*sqrt(6) -#define INVROOT6 0.40824829046386307274 // 1/sqrt(6) -#define FOURTHIRDS 4.0/3.0 // 4/3 -#define THREEQUARTERS 0.75 // 3/4 - -#define EPSILON 1e-10 - -enum {HOOKE, HERTZ, HERTZ_MATERIAL, DMT, JKR}; -enum {VELOCITY, MASS_VELOCITY, VISCOELASTIC, TSUJI}; -enum {TANGENTIAL_NOHISTORY, TANGENTIAL_HISTORY, - TANGENTIAL_MINDLIN, TANGENTIAL_MINDLIN_RESCALE, - TANGENTIAL_MINDLIN_FORCE, TANGENTIAL_MINDLIN_RESCALE_FORCE}; -enum {TWIST_NONE, TWIST_SDS, TWIST_MARSHALL}; -enum {ROLL_NONE, ROLL_SDS}; - -/* ---------------------------------------------------------------------- */ - -PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp) -{ - single_enable = 1; - no_virial_fdotr_compute = 1; - centroidstressflag = CENTROID_NOTAVAIL; - - single_extra = 12; - svector = new double[single_extra]; - - neighprev = 0; - - nmax = 0; - mass_rigid = nullptr; - - onerad_dynamic = nullptr; - onerad_frozen = nullptr; - maxrad_dynamic = nullptr; - maxrad_frozen = nullptr; - - history_transfer_factors = nullptr; - - dt = update->dt; - - // set comm size needed by this Pair if used with fix rigid - - comm_forward = 1; - - use_history = 0; - beyond_contact = 0; - nondefault_history_transfer = 0; - tangential_history_index = 0; - roll_history_index = twist_history_index = 0; - - // create dummy fix as placeholder for FixNeighHistory - // this is so final order of Modify:fix will conform to input script - - fix_history = nullptr; - modify->add_fix("NEIGH_HISTORY_GRANULAR_DUMMY all DUMMY"); - fix_dummy = (FixDummy *) modify->fix[modify->nfix-1]; -} - -/* ---------------------------------------------------------------------- */ - -PairGranular::~PairGranular() -{ - delete [] svector; - - if (!fix_history) modify->delete_fix("NEIGH_HISTORY_GRANULAR_DUMMY"); - else modify->delete_fix("NEIGH_HISTORY_GRANULAR"); - - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - memory->destroy(cutoff_type); - - memory->destroy(normal_coeffs); - memory->destroy(tangential_coeffs); - memory->destroy(roll_coeffs); - memory->destroy(twist_coeffs); - - memory->destroy(Emod); - memory->destroy(poiss); - - memory->destroy(normal_model); - memory->destroy(damping_model); - memory->destroy(tangential_model); - memory->destroy(roll_model); - memory->destroy(twist_model); - - delete [] onerad_dynamic; - delete [] onerad_frozen; - delete [] maxrad_dynamic; - delete [] maxrad_frozen; - } - - memory->destroy(mass_rigid); -} - -/* ---------------------------------------------------------------------- */ - -void PairGranular::compute(int eflag, int vflag) -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz,nx,ny,nz; - double radi,radj,radsum,rsq,r,rinv; - double Reff, delta, dR, dR2, dist_to_contact; - - double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; - double wr1,wr2,wr3; - double vtr1,vtr2,vtr3,vrel; - - double knfac, damp_normal=0.0, damp_normal_prefactor; - double k_tangential, damp_tangential; - double Fne, Ft, Fdamp, Fntot, Fncrit, Fscrit, Frcrit; - double fs, fs1, fs2, fs3, tor1, tor2, tor3; - - double mi,mj,meff; - double relrot1,relrot2,relrot3,vrl1,vrl2,vrl3; - - // for JKR - double R2, coh, F_pulloff, delta_pulloff, dist_pulloff, a, a2, E; - double t0, t1, t2, t3, t4, t5, t6; - double sqrt1, sqrt2, sqrt3; - - // rolling - double k_roll, damp_roll; - double torroll1, torroll2, torroll3; - double rollmag, rolldotn, scalefac; - double fr, fr1, fr2, fr3; - - // twisting - double k_twist, damp_twist, mu_twist; - double signtwist, magtwist, magtortwist, Mtcrit; - double tortwist1, tortwist2, tortwist3; - - double shrmag,rsht,prjmag; - bool frameupdate; - int *ilist,*jlist,*numneigh,**firstneigh; - int *touch,**firsttouch; - double *history,*allhistory,**firsthistory; - - bool touchflag = false; - const bool historyupdate = (update->setupflag) ? false : true; - - ev_init(eflag,vflag); - - // update rigid body info for owned & ghost atoms if using FixRigid masses - // body[i] = which body atom I is in, -1 if none - // mass_body = mass of each rigid body - - if (fix_rigid && neighbor->ago == 0) { - int tmp; - int *body = (int *) fix_rigid->extract("body",tmp); - double *mass_body = (double *) fix_rigid->extract("masstotal",tmp); - if (atom->nmax > nmax) { - memory->destroy(mass_rigid); - nmax = atom->nmax; - memory->create(mass_rigid,nmax,"pair:mass_rigid"); - } - int nlocal = atom->nlocal; - for (i = 0; i < nlocal; i++) - if (body[i] >= 0) mass_rigid[i] = mass_body[body[i]]; - else mass_rigid[i] = 0.0; - comm->forward_comm_pair(this); - } - - double **x = atom->x; - double **v = atom->v; - double **f = atom->f; - int *type = atom->type; - double **omega = atom->omega; - double **torque = atom->torque; - double *radius = atom->radius; - double *rmass = atom->rmass; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - if (use_history) { - firsttouch = fix_history->firstflag; - firsthistory = fix_history->firstvalue; - } - - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - itype = type[i]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - radi = radius[i]; - if (use_history) { - touch = firsttouch[i]; - allhistory = firsthistory[i]; - } - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - jtype = type[j]; - rsq = delx*delx + dely*dely + delz*delz; - radj = radius[j]; - radsum = radi + radj; - - E = normal_coeffs[itype][jtype][0]; - Reff = radi*radj/radsum; - touchflag = false; - - if (normal_model[itype][jtype] == JKR) { - E *= THREEQUARTERS; - if (touch[jj]) { - R2 = Reff*Reff; - coh = normal_coeffs[itype][jtype][3]; - a = cbrt(9.0*MY_PI*coh*R2/(4*E)); - delta_pulloff = a*a/Reff - 2*sqrt(MY_PI*coh*a/E); - dist_pulloff = radsum-delta_pulloff; - touchflag = (rsq < dist_pulloff*dist_pulloff); - } else { - touchflag = (rsq < radsum*radsum); - } - } else { - touchflag = (rsq < radsum*radsum); - } - - if (!touchflag) { - // unset non-touching neighbors - if (use_history) { - touch[jj] = 0; - history = &allhistory[size_history*jj]; - for (int k = 0; k < size_history; k++) history[k] = 0.0; - } - } else { - r = sqrt(rsq); - rinv = 1.0/r; - - nx = delx*rinv; - ny = dely*rinv; - nz = delz*rinv; - - // relative translational velocity - - vr1 = v[i][0] - v[j][0]; - vr2 = v[i][1] - v[j][1]; - vr3 = v[i][2] - v[j][2]; - - // normal component - - vnnr = vr1*nx + vr2*ny + vr3*nz; //v_R . n - vn1 = nx*vnnr; - vn2 = ny*vnnr; - vn3 = nz*vnnr; - - // meff = effective mass of pair of particles - // if I or J part of rigid body, use body mass - // if I or J is frozen, meff is other particle - - mi = rmass[i]; - mj = rmass[j]; - if (fix_rigid) { - if (mass_rigid[i] > 0.0) mi = mass_rigid[i]; - if (mass_rigid[j] > 0.0) mj = mass_rigid[j]; - } - - meff = mi*mj / (mi+mj); - if (mask[i] & freeze_group_bit) meff = mj; - if (mask[j] & freeze_group_bit) meff = mi; - - delta = radsum - r; - dR = delta*Reff; - - if (normal_model[itype][jtype] == JKR) { - touch[jj] = 1; - R2=Reff*Reff; - coh = normal_coeffs[itype][jtype][3]; - dR2 = dR*dR; - t0 = coh*coh*R2*R2*E; - t1 = PI27SQ*t0; - t2 = 8*dR*dR2*E*E*E; - t3 = 4*dR2*E; - // in case sqrt(0) < 0 due to precision issues - sqrt1 = MAX(0, t0*(t1+2*t2)); - t4 = cbrt(t1+t2+THREEROOT3*MY_PI*sqrt(sqrt1)); - t5 = t3/t4 + t4/E; - sqrt2 = MAX(0, 2*dR + t5); - t6 = sqrt(sqrt2); - sqrt3 = MAX(0, 4*dR - t5 + SIXROOT6*coh*MY_PI*R2/(E*t6)); - a = INVROOT6*(t6 + sqrt(sqrt3)); - a2 = a*a; - knfac = normal_coeffs[itype][jtype][0]*a; - Fne = knfac*a2/Reff - MY_2PI*a2*sqrt(4*coh*E/(MY_PI*a)); - } else { - knfac = E; // Hooke - Fne = knfac*delta; - a = sqrt(dR); - if (normal_model[itype][jtype] != HOOKE) { - Fne *= a; - knfac *= a; - } - if (normal_model[itype][jtype] == DMT) - Fne -= 4*MY_PI*normal_coeffs[itype][jtype][3]*Reff; - } - - // NOTE: consider restricting Hooke to only have - // 'velocity' as an option for damping? - - if (damping_model[itype][jtype] == VELOCITY) { - damp_normal = 1; - } else if (damping_model[itype][jtype] == MASS_VELOCITY) { - damp_normal = meff; - } else if (damping_model[itype][jtype] == VISCOELASTIC) { - damp_normal = a*meff; - } else if (damping_model[itype][jtype] == TSUJI) { - damp_normal = sqrt(meff*knfac); - } - - damp_normal_prefactor = normal_coeffs[itype][jtype][1]*damp_normal; - Fdamp = -damp_normal_prefactor*vnnr; - - Fntot = Fne + Fdamp; - - //**************************************** - // tangential force, including history effects - //**************************************** - - // For linear, mindlin, mindlin_rescale: - // history = cumulative tangential displacement - // - // For mindlin/force, mindlin_rescale/force: - // history = cumulative tangential elastic force - - // tangential component - vt1 = vr1 - vn1; - vt2 = vr2 - vn2; - vt3 = vr3 - vn3; - - // relative rotational velocity - wr1 = (radi*omega[i][0] + radj*omega[j][0]); - wr2 = (radi*omega[i][1] + radj*omega[j][1]); - wr3 = (radi*omega[i][2] + radj*omega[j][2]); - - // relative tangential velocities - vtr1 = vt1 - (nz*wr2-ny*wr3); - vtr2 = vt2 - (nx*wr3-nz*wr1); - vtr3 = vt3 - (ny*wr1-nx*wr2); - vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3; - vrel = sqrt(vrel); - - // if any history is needed - if (use_history) { - touch[jj] = 1; - history = &allhistory[size_history*jj]; - } - - if (normal_model[itype][jtype] == JKR) { - F_pulloff = 3*MY_PI*coh*Reff; - Fncrit = fabs(Fne + 2*F_pulloff); - } else if (normal_model[itype][jtype] == DMT) { - F_pulloff = 4*MY_PI*coh*Reff; - Fncrit = fabs(Fne + 2*F_pulloff); - } else { - Fncrit = fabs(Fntot); - } - Fscrit = tangential_coeffs[itype][jtype][2] * Fncrit; - - //------------------------------ - // tangential forces - //------------------------------ - k_tangential = tangential_coeffs[itype][jtype][0]; - damp_tangential = tangential_coeffs[itype][jtype][1] * - damp_normal_prefactor; - - if (tangential_history) { - if (tangential_model[itype][jtype] == TANGENTIAL_MINDLIN || - tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_FORCE) { - k_tangential *= a; - } else if (tangential_model[itype][jtype] == - TANGENTIAL_MINDLIN_RESCALE || - tangential_model[itype][jtype] == - TANGENTIAL_MINDLIN_RESCALE_FORCE) { - k_tangential *= a; - // on unloading, rescale the shear displacements/force - if (a < history[3]) { - double factor = a/history[3]; - history[0] *= factor; - history[1] *= factor; - history[2] *= factor; - } - } - // rotate and update displacements / force. - // see e.g. eq. 17 of Luding, Gran. Matter 2008, v10,p235 - if (historyupdate) { - rsht = history[0]*nx + history[1]*ny + history[2]*nz; - if (tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_FORCE || - tangential_model[itype][jtype] == - TANGENTIAL_MINDLIN_RESCALE_FORCE) - frameupdate = fabs(rsht) > EPSILON*Fscrit; - else - frameupdate = fabs(rsht)*k_tangential > EPSILON*Fscrit; - if (frameupdate) { - shrmag = sqrt(history[0]*history[0] + history[1]*history[1] + - history[2]*history[2]); - // projection - history[0] -= rsht*nx; - history[1] -= rsht*ny; - history[2] -= rsht*nz; - - // also rescale to preserve magnitude - prjmag = sqrt(history[0]*history[0] + history[1]*history[1] + - history[2]*history[2]); - if (prjmag > 0) scalefac = shrmag/prjmag; - else scalefac = 0; - history[0] *= scalefac; - history[1] *= scalefac; - history[2] *= scalefac; - } - // update history - if (tangential_model[itype][jtype] == TANGENTIAL_HISTORY || - tangential_model[itype][jtype] == TANGENTIAL_MINDLIN || - tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_RESCALE) { - // tangential displacement - history[0] += vtr1*dt; - history[1] += vtr2*dt; - history[2] += vtr3*dt; - } else { - // tangential force - // see e.g. eq. 18 of Thornton et al, Pow. Tech. 2013, v223,p30-46 - history[0] -= k_tangential*vtr1*dt; - history[1] -= k_tangential*vtr2*dt; - history[2] -= k_tangential*vtr3*dt; - } - if (tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_RESCALE || - tangential_model[itype][jtype] == - TANGENTIAL_MINDLIN_RESCALE_FORCE) - history[3] = a; - } - - // tangential forces = history + tangential velocity damping - if (tangential_model[itype][jtype] == TANGENTIAL_HISTORY || - tangential_model[itype][jtype] == TANGENTIAL_MINDLIN || - tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_RESCALE) { - fs1 = -k_tangential*history[0] - damp_tangential*vtr1; - fs2 = -k_tangential*history[1] - damp_tangential*vtr2; - fs3 = -k_tangential*history[2] - damp_tangential*vtr3; - } else { - fs1 = history[0] - damp_tangential*vtr1; - fs2 = history[1] - damp_tangential*vtr2; - fs3 = history[2] - damp_tangential*vtr3; - } - - // rescale frictional displacements and forces if needed - fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3); - if (fs > Fscrit) { - shrmag = sqrt(history[0]*history[0] + history[1]*history[1] + - history[2]*history[2]); - if (shrmag != 0.0) { - if (tangential_model[itype][jtype] == TANGENTIAL_HISTORY || - tangential_model[itype][jtype] == TANGENTIAL_MINDLIN || - tangential_model[itype][jtype] == - TANGENTIAL_MINDLIN_RESCALE) { - history[0] = -1.0/k_tangential*(Fscrit*fs1/fs + - damp_tangential*vtr1); - history[1] = -1.0/k_tangential*(Fscrit*fs2/fs + - damp_tangential*vtr2); - history[2] = -1.0/k_tangential*(Fscrit*fs3/fs + - damp_tangential*vtr3); - } else { - history[0] = Fscrit*fs1/fs + damp_tangential*vtr1; - history[1] = Fscrit*fs2/fs + damp_tangential*vtr2; - history[2] = Fscrit*fs3/fs + damp_tangential*vtr3; - } - fs1 *= Fscrit/fs; - fs2 *= Fscrit/fs; - fs3 *= Fscrit/fs; - } else fs1 = fs2 = fs3 = 0.0; - } - } else { // classic pair gran/hooke (no history) - fs = damp_tangential*vrel; - if (vrel != 0.0) Ft = MIN(Fscrit,fs) / vrel; - else Ft = 0.0; - fs1 = -Ft*vtr1; - fs2 = -Ft*vtr2; - fs3 = -Ft*vtr3; - } - - if (roll_model[itype][jtype] != ROLL_NONE || - twist_model[itype][jtype] != TWIST_NONE) { - relrot1 = omega[i][0] - omega[j][0]; - relrot2 = omega[i][1] - omega[j][1]; - relrot3 = omega[i][2] - omega[j][2]; - // rolling velocity, - // see eq. 31 of Wang et al, Particuology v 23, p 49 (2015) - // this is different from the Marshall papers, - // which use the Bagi/Kuhn formulation - // for rolling velocity (see Wang et al for why the latter is wrong) - // - 0.5*((radj-radi)/radsum)*vtr1; - // - 0.5*((radj-radi)/radsum)*vtr2; - // - 0.5*((radj-radi)/radsum)*vtr3; - } - //**************************************** - // rolling resistance - //**************************************** - - if (roll_model[itype][jtype] != ROLL_NONE) { - vrl1 = Reff*(relrot2*nz - relrot3*ny); - vrl2 = Reff*(relrot3*nx - relrot1*nz); - vrl3 = Reff*(relrot1*ny - relrot2*nx); - - int rhist0 = roll_history_index; - int rhist1 = rhist0 + 1; - int rhist2 = rhist1 + 1; - - k_roll = roll_coeffs[itype][jtype][0]; - damp_roll = roll_coeffs[itype][jtype][1]; - Frcrit = roll_coeffs[itype][jtype][2] * Fncrit; - - if (historyupdate) { - rolldotn = history[rhist0]*nx + history[rhist1]*ny + history[rhist2]*nz; - frameupdate = fabs(rolldotn)*k_roll > EPSILON*Frcrit; - if (frameupdate) { // rotate into tangential plane - rollmag = sqrt(history[rhist0]*history[rhist0] + - history[rhist1]*history[rhist1] + - history[rhist2]*history[rhist2]); - // projection - history[rhist0] -= rolldotn*nx; - history[rhist1] -= rolldotn*ny; - history[rhist2] -= rolldotn*nz; - // also rescale to preserve magnitude - prjmag = sqrt(history[rhist0]*history[rhist0] + - history[rhist1]*history[rhist1] + - history[rhist2]*history[rhist2]); - if (prjmag > 0) scalefac = rollmag/prjmag; - else scalefac = 0; - history[rhist0] *= scalefac; - history[rhist1] *= scalefac; - history[rhist2] *= scalefac; - } - history[rhist0] += vrl1*dt; - history[rhist1] += vrl2*dt; - history[rhist2] += vrl3*dt; - } - - fr1 = -k_roll*history[rhist0] - damp_roll*vrl1; - fr2 = -k_roll*history[rhist1] - damp_roll*vrl2; - fr3 = -k_roll*history[rhist2] - damp_roll*vrl3; - - // rescale frictional displacements and forces if needed - - fr = sqrt(fr1*fr1 + fr2*fr2 + fr3*fr3); - if (fr > Frcrit) { - rollmag = sqrt(history[rhist0]*history[rhist0] + - history[rhist1]*history[rhist1] + - history[rhist2]*history[rhist2]); - if (rollmag != 0.0) { - history[rhist0] = -1.0/k_roll*(Frcrit*fr1/fr + damp_roll*vrl1); - history[rhist1] = -1.0/k_roll*(Frcrit*fr2/fr + damp_roll*vrl2); - history[rhist2] = -1.0/k_roll*(Frcrit*fr3/fr + damp_roll*vrl3); - fr1 *= Frcrit/fr; - fr2 *= Frcrit/fr; - fr3 *= Frcrit/fr; - } else fr1 = fr2 = fr3 = 0.0; - } - } - - //**************************************** - // twisting torque, including history effects - //**************************************** - - if (twist_model[itype][jtype] != TWIST_NONE) { - // omega_T (eq 29 of Marshall) - magtwist = relrot1*nx + relrot2*ny + relrot3*nz; - if (twist_model[itype][jtype] == TWIST_MARSHALL) { - k_twist = 0.5*k_tangential*a*a;; // eq 32 of Marshall paper - damp_twist = 0.5*damp_tangential*a*a; - mu_twist = TWOTHIRDS*a*tangential_coeffs[itype][jtype][2]; - } else { - k_twist = twist_coeffs[itype][jtype][0]; - damp_twist = twist_coeffs[itype][jtype][1]; - mu_twist = twist_coeffs[itype][jtype][2]; - } - if (historyupdate) { - history[twist_history_index] += magtwist*dt; - } - magtortwist = -k_twist*history[twist_history_index] - - damp_twist*magtwist; // M_t torque (eq 30) - signtwist = (magtwist > 0) - (magtwist < 0); - Mtcrit = mu_twist*Fncrit; // critical torque (eq 44) - if (fabs(magtortwist) > Mtcrit) { - history[twist_history_index] = 1.0/k_twist*(Mtcrit*signtwist - - damp_twist*magtwist); - magtortwist = -Mtcrit * signtwist; // eq 34 - } - } - - // apply forces & torques - - fx = nx*Fntot + fs1; - fy = ny*Fntot + fs2; - fz = nz*Fntot + fs3; - - f[i][0] += fx; - f[i][1] += fy; - f[i][2] += fz; - - tor1 = ny*fs3 - nz*fs2; - tor2 = nz*fs1 - nx*fs3; - tor3 = nx*fs2 - ny*fs1; - - dist_to_contact = radi-0.5*delta; - torque[i][0] -= dist_to_contact*tor1; - torque[i][1] -= dist_to_contact*tor2; - torque[i][2] -= dist_to_contact*tor3; - - if (twist_model[itype][jtype] != TWIST_NONE) { - tortwist1 = magtortwist * nx; - tortwist2 = magtortwist * ny; - tortwist3 = magtortwist * nz; - - torque[i][0] += tortwist1; - torque[i][1] += tortwist2; - torque[i][2] += tortwist3; - } - - if (roll_model[itype][jtype] != ROLL_NONE) { - torroll1 = Reff*(ny*fr3 - nz*fr2); // n cross fr - torroll2 = Reff*(nz*fr1 - nx*fr3); - torroll3 = Reff*(nx*fr2 - ny*fr1); - - torque[i][0] += torroll1; - torque[i][1] += torroll2; - torque[i][2] += torroll3; - } - - if (force->newton_pair || j < nlocal) { - f[j][0] -= fx; - f[j][1] -= fy; - f[j][2] -= fz; - - dist_to_contact = radj-0.5*delta; - torque[j][0] -= dist_to_contact*tor1; - torque[j][1] -= dist_to_contact*tor2; - torque[j][2] -= dist_to_contact*tor3; - - if (twist_model[itype][jtype] != TWIST_NONE) { - torque[j][0] -= tortwist1; - torque[j][1] -= tortwist2; - torque[j][2] -= tortwist3; - } - if (roll_model[itype][jtype] != ROLL_NONE) { - torque[j][0] -= torroll1; - torque[j][1] -= torroll2; - torque[j][2] -= torroll3; - } - } - if (evflag) ev_tally_xyz(i,j,nlocal,force->newton_pair, - 0.0,0.0,fx,fy,fz,delx,dely,delz); - } - } - } -} - -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ - -void PairGranular::allocate() -{ - allocated = 1; - int n = atom->ntypes; - - memory->create(setflag,n+1,n+1,"pair:setflag"); - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - memory->create(cutoff_type,n+1,n+1,"pair:cutoff_type"); - memory->create(normal_coeffs,n+1,n+1,4,"pair:normal_coeffs"); - memory->create(tangential_coeffs,n+1,n+1,3,"pair:tangential_coeffs"); - memory->create(roll_coeffs,n+1,n+1,3,"pair:roll_coeffs"); - memory->create(twist_coeffs,n+1,n+1,3,"pair:twist_coeffs"); - - memory->create(Emod,n+1,n+1,"pair:Emod"); - memory->create(poiss,n+1,n+1,"pair:poiss"); - - memory->create(normal_model,n+1,n+1,"pair:normal_model"); - memory->create(damping_model,n+1,n+1,"pair:damping_model"); - memory->create(tangential_model,n+1,n+1,"pair:tangential_model"); - memory->create(roll_model,n+1,n+1,"pair:roll_model"); - memory->create(twist_model,n+1,n+1,"pair:twist_model"); - - onerad_dynamic = new double[n+1]; - onerad_frozen = new double[n+1]; - maxrad_dynamic = new double[n+1]; - maxrad_frozen = new double[n+1]; -} - -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ - -void PairGranular::settings(int narg, char **arg) -{ - if (narg == 1) { - cutoff_global = utils::numeric(FLERR,arg[0],false,lmp); - } else { - cutoff_global = -1; // will be set based on particle sizes, model choice - } - - normal_history = tangential_history = 0; - roll_history = twist_history = 0; -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairGranular::coeff(int narg, char **arg) -{ - int normal_model_one, damping_model_one; - int tangential_model_one, roll_model_one, twist_model_one; - - double normal_coeffs_one[4]; - double tangential_coeffs_one[4]; - double roll_coeffs_one[4]; - double twist_coeffs_one[4]; - - double cutoff_one = -1; - - if (narg < 2) - error->all(FLERR,"Incorrect args for pair coefficients"); - - if (!allocated) allocate(); - - int ilo,ihi,jlo,jhi; - utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); - utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); - - //Defaults - normal_model_one = tangential_model_one = -1; - roll_model_one = ROLL_NONE; - twist_model_one = TWIST_NONE; - damping_model_one = VISCOELASTIC; - - int iarg = 2; - while (iarg < narg) { - if (strcmp(arg[iarg], "hooke") == 0) { - if (iarg + 2 >= narg) - error->all(FLERR,"Illegal pair_coeff command, " - "not enough parameters provided for Hooke option"); - normal_model_one = HOOKE; - normal_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+1],false,lmp); // kn - normal_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); // damping - iarg += 3; - } else if (strcmp(arg[iarg], "hertz") == 0) { - if (iarg + 2 >= narg) - error->all(FLERR,"Illegal pair_coeff command, " - "not enough parameters provided for Hertz option"); - normal_model_one = HERTZ; - normal_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+1],false,lmp); // kn - normal_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); // damping - iarg += 3; - } else if (strcmp(arg[iarg], "hertz/material") == 0) { - if (iarg + 3 >= narg) - error->all(FLERR,"Illegal pair_coeff command, " - "not enough parameters provided for Hertz/material option"); - normal_model_one = HERTZ_MATERIAL; - normal_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+1],false,lmp); // E - normal_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); // damping - normal_coeffs_one[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp); // Poisson's ratio - iarg += 4; - } else if (strcmp(arg[iarg], "dmt") == 0) { - if (iarg + 4 >= narg) - error->all(FLERR,"Illegal pair_coeff command, " - "not enough parameters provided for Hertz option"); - normal_model_one = DMT; - normal_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+1],false,lmp); // E - normal_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); // damping - normal_coeffs_one[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp); // Poisson's ratio - normal_coeffs_one[3] = utils::numeric(FLERR,arg[iarg+4],false,lmp); // cohesion - iarg += 5; - } else if (strcmp(arg[iarg], "jkr") == 0) { - if (iarg + 4 >= narg) - error->all(FLERR,"Illegal pair_coeff command, " - "not enough parameters provided for JKR option"); - beyond_contact = 1; - normal_model_one = JKR; - normal_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+1],false,lmp); // E - normal_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); // damping - normal_coeffs_one[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp); // Poisson's ratio - normal_coeffs_one[3] = utils::numeric(FLERR,arg[iarg+4],false,lmp); // cohesion - iarg += 5; - } else if (strcmp(arg[iarg], "damping") == 0) { - if (iarg+1 >= narg) - error->all(FLERR, "Illegal pair_coeff command, " - "not enough parameters provided for damping model"); - if (strcmp(arg[iarg+1], "velocity") == 0) { - damping_model_one = VELOCITY; - iarg += 1; - } else if (strcmp(arg[iarg+1], "mass_velocity") == 0) { - damping_model_one = MASS_VELOCITY; - iarg += 1; - } else if (strcmp(arg[iarg+1], "viscoelastic") == 0) { - damping_model_one = VISCOELASTIC; - iarg += 1; - } else if (strcmp(arg[iarg+1], "tsuji") == 0) { - damping_model_one = TSUJI; - iarg += 1; - } else error->all(FLERR, "Illegal pair_coeff command, " - "unrecognized damping model"); - iarg += 1; - } else if (strcmp(arg[iarg], "tangential") == 0) { - if (iarg + 1 >= narg) - error->all(FLERR,"Illegal pair_coeff command, must specify " - "tangential model after tangential keyword"); - if (strcmp(arg[iarg+1], "linear_nohistory") == 0) { - if (iarg + 3 >= narg) - error->all(FLERR,"Illegal pair_coeff command, " - "not enough parameters provided for tangential model"); - tangential_model_one = TANGENTIAL_NOHISTORY; - tangential_coeffs_one[0] = 0; - // gammat and friction coeff - tangential_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); - tangential_coeffs_one[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp); - iarg += 4; - } else if ((strcmp(arg[iarg+1], "linear_history") == 0) || - (strcmp(arg[iarg+1], "mindlin") == 0) || - (strcmp(arg[iarg+1], "mindlin_rescale") == 0) || - (strcmp(arg[iarg+1], "mindlin/force") == 0) || - (strcmp(arg[iarg+1], "mindlin_rescale/force") == 0)) { - if (iarg + 4 >= narg) - error->all(FLERR,"Illegal pair_coeff command, " - "not enough parameters provided for tangential model"); - if (strcmp(arg[iarg+1], "linear_history") == 0) - tangential_model_one = TANGENTIAL_HISTORY; - else if (strcmp(arg[iarg+1], "mindlin") == 0) - tangential_model_one = TANGENTIAL_MINDLIN; - else if (strcmp(arg[iarg+1], "mindlin_rescale") == 0) - tangential_model_one = TANGENTIAL_MINDLIN_RESCALE; - else if (strcmp(arg[iarg+1], "mindlin/force") == 0) - tangential_model_one = TANGENTIAL_MINDLIN_FORCE; - else if (strcmp(arg[iarg+1], "mindlin_rescale/force") == 0) - tangential_model_one = TANGENTIAL_MINDLIN_RESCALE_FORCE; - tangential_history = 1; - if ((tangential_model_one == TANGENTIAL_MINDLIN || - tangential_model_one == TANGENTIAL_MINDLIN_RESCALE || - tangential_model_one == TANGENTIAL_MINDLIN_FORCE || - tangential_model_one == TANGENTIAL_MINDLIN_RESCALE_FORCE) && - (strcmp(arg[iarg+2], "NULL") == 0)) { - if (normal_model_one == HERTZ || normal_model_one == HOOKE) { - error->all(FLERR, "NULL setting for Mindlin tangential " - "stiffness requires a normal contact model that " - "specifies material properties"); - } - tangential_coeffs_one[0] = -1; - } else { - tangential_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+2],false,lmp); // kt - } - // gammat and friction coeff - tangential_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+3],false,lmp); - tangential_coeffs_one[2] = utils::numeric(FLERR,arg[iarg+4],false,lmp); - iarg += 5; - } else { - error->all(FLERR, "Illegal pair_coeff command, " - "tangential model not recognized"); - } - } else if (strcmp(arg[iarg], "rolling") == 0) { - if (iarg + 1 >= narg) - error->all(FLERR, "Illegal pair_coeff command, not enough parameters"); - if (strcmp(arg[iarg+1], "none") == 0) { - roll_model_one = ROLL_NONE; - iarg += 2; - } else if (strcmp(arg[iarg+1], "sds") == 0) { - if (iarg + 4 >= narg) - error->all(FLERR,"Illegal pair_coeff command, " - "not enough parameters provided for rolling model"); - roll_model_one = ROLL_SDS; - roll_history = 1; - // kR and gammaR and rolling friction coeff - roll_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+2],false,lmp); - roll_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+3],false,lmp); - roll_coeffs_one[2] = utils::numeric(FLERR,arg[iarg+4],false,lmp); - iarg += 5; - } else { - error->all(FLERR, "Illegal pair_coeff command, " - "rolling friction model not recognized"); - } - } else if (strcmp(arg[iarg], "twisting") == 0) { - if (iarg + 1 >= narg) - error->all(FLERR, "Illegal pair_coeff command, not enough parameters"); - if (strcmp(arg[iarg+1], "none") == 0) { - twist_model_one = TWIST_NONE; - iarg += 2; - } else if (strcmp(arg[iarg+1], "marshall") == 0) { - twist_model_one = TWIST_MARSHALL; - twist_history = 1; - iarg += 2; - } else if (strcmp(arg[iarg+1], "sds") == 0) { - if (iarg + 4 >= narg) - error->all(FLERR,"Illegal pair_coeff command, " - "not enough parameters provided for twist model"); - twist_model_one = TWIST_SDS; - twist_history = 1; - // kt and gammat and friction coeff - twist_coeffs_one[0] = utils::numeric(FLERR,arg[iarg+2],false,lmp); - twist_coeffs_one[1] = utils::numeric(FLERR,arg[iarg+3],false,lmp); - twist_coeffs_one[2] = utils::numeric(FLERR,arg[iarg+4],false,lmp); - iarg += 5; - } else { - error->all(FLERR, "Illegal pair_coeff command, " - "twisting friction model not recognized"); - } - } else if (strcmp(arg[iarg], "cutoff") == 0) { - if (iarg + 1 >= narg) - error->all(FLERR, "Illegal pair_coeff command, not enough parameters"); - cutoff_one = utils::numeric(FLERR,arg[iarg+1],false,lmp); - iarg += 2; - } else error->all(FLERR, "Illegal pair coeff command"); - } - - // error not to specify normal or tangential model - if ((normal_model_one < 0) || (tangential_model_one < 0)) - error->all(FLERR, "Illegal pair coeff command, " - "must specify normal or tangential contact model"); - - int count = 0; - double damp; - if (damping_model_one == TSUJI) { - double cor; - cor = normal_coeffs_one[1]; - damp = 1.2728-4.2783*cor+11.087*square(cor)-22.348*cube(cor)+ - 27.467*powint(cor,4)-18.022*powint(cor,5)+4.8218*powint(cor,6); - } else damp = normal_coeffs_one[1]; - - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - normal_model[i][j] = normal_model[j][i] = normal_model_one; - normal_coeffs[i][j][1] = normal_coeffs[j][i][1] = damp; - if (normal_model_one != HERTZ && normal_model_one != HOOKE) { - Emod[i][j] = Emod[j][i] = normal_coeffs_one[0]; - poiss[i][j] = poiss[j][i] = normal_coeffs_one[2]; - normal_coeffs[i][j][0] = normal_coeffs[j][i][0] = - FOURTHIRDS*mix_stiffnessE(Emod[i][j],Emod[i][j], - poiss[i][j],poiss[i][j]); - } else { - normal_coeffs[i][j][0] = normal_coeffs[j][i][0] = normal_coeffs_one[0]; - } - if ((normal_model_one == JKR) || (normal_model_one == DMT)) - normal_coeffs[i][j][3] = normal_coeffs[j][i][3] = normal_coeffs_one[3]; - - damping_model[i][j] = damping_model[j][i] = damping_model_one; - - tangential_model[i][j] = tangential_model[j][i] = tangential_model_one; - if (tangential_coeffs_one[0] == -1) { - tangential_coeffs[i][j][0] = tangential_coeffs[j][i][0] = - 8*mix_stiffnessG(Emod[i][j],Emod[i][j],poiss[i][j],poiss[i][j]); - } else { - tangential_coeffs[i][j][0] = tangential_coeffs[j][i][0] = - tangential_coeffs_one[0]; - } - for (int k = 1; k < 3; k++) - tangential_coeffs[i][j][k] = tangential_coeffs[j][i][k] = - tangential_coeffs_one[k]; - - roll_model[i][j] = roll_model[j][i] = roll_model_one; - if (roll_model_one != ROLL_NONE) - for (int k = 0; k < 3; k++) - roll_coeffs[i][j][k] = roll_coeffs[j][i][k] = roll_coeffs_one[k]; - - twist_model[i][j] = twist_model[j][i] = twist_model_one; - if (twist_model_one != TWIST_NONE && twist_model_one != TWIST_MARSHALL) - for (int k = 0; k < 3; k++) - twist_coeffs[i][j][k] = twist_coeffs[j][i][k] = twist_coeffs_one[k]; - - cutoff_type[i][j] = cutoff_type[j][i] = cutoff_one; - - setflag[i][j] = 1; - count++; - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairGranular::init_style() -{ - int i; - - // error and warning checks - - if (!atom->radius_flag || !atom->rmass_flag) - error->all(FLERR,"Pair granular requires atom attributes radius, rmass"); - if (comm->ghost_velocity == 0) - error->all(FLERR,"Pair granular requires ghost atoms store velocity"); - - // determine whether we need a granular neigh list, how large it needs to be - - use_history = normal_history || tangential_history || - roll_history || twist_history; - - // for JKR, will need fix/neigh/history to keep track of touch arrays - - for (int i = 1; i <= atom->ntypes; i++) - for (int j = i; j <= atom->ntypes; j++) - if (normal_model[i][j] == JKR) use_history = 1; - - size_history = 3*tangential_history + 3*roll_history + twist_history; - - // determine location of tangential/roll/twist histories in array - - if (roll_history) { - if (tangential_history) roll_history_index = 3; - else roll_history_index = 0; - } - if (twist_history) { - if (tangential_history) { - if (roll_history) twist_history_index = 6; - else twist_history_index = 3; - } else { - if (roll_history) twist_history_index = 3; - else twist_history_index = 0; - } - } - for (int i = 1; i <= atom->ntypes; i++) - for (int j = i; j <= atom->ntypes; j++) - if (tangential_model[i][j] == TANGENTIAL_MINDLIN_RESCALE || - tangential_model[i][j] == TANGENTIAL_MINDLIN_RESCALE_FORCE) { - size_history += 1; - roll_history_index += 1; - twist_history_index += 1; - nondefault_history_transfer = 1; - history_transfer_factors = new int[size_history]; - for (int ii = 0; ii < size_history; ++ii) - history_transfer_factors[ii] = -1; - history_transfer_factors[3] = 1; - break; - } - - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->size = 1; - if (use_history) neighbor->requests[irequest]->history = 1; - - dt = update->dt; - - // if history is stored and first init, create Fix to store history - // it replaces FixDummy, created in the constructor - // this is so its order in the fix list is preserved - - if (use_history && fix_history == nullptr) { - modify->replace_fix("NEIGH_HISTORY_GRANULAR_DUMMY","NEIGH_HISTORY_GRANULAR" - " all NEIGH_HISTORY " + std::to_string(size_history),1); - int ifix = modify->find_fix("NEIGH_HISTORY_GRANULAR"); - fix_history = (FixNeighHistory *) modify->fix[ifix]; - fix_history->pair = this; - } - - // check for FixFreeze and set freeze_group_bit - - for (i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"freeze") == 0) break; - if (i < modify->nfix) freeze_group_bit = modify->fix[i]->groupbit; - else freeze_group_bit = 0; - - // check for FixRigid so can extract rigid body masses - - fix_rigid = nullptr; - for (i = 0; i < modify->nfix; i++) - if (modify->fix[i]->rigid_flag) break; - if (i < modify->nfix) fix_rigid = modify->fix[i]; - - // check for FixPour and FixDeposit so can extract particle radii - - int ipour; - for (ipour = 0; ipour < modify->nfix; ipour++) - if (strcmp(modify->fix[ipour]->style,"pour") == 0) break; - if (ipour == modify->nfix) ipour = -1; - - int idep; - for (idep = 0; idep < modify->nfix; idep++) - if (strcmp(modify->fix[idep]->style,"deposit") == 0) break; - if (idep == modify->nfix) idep = -1; - - // set maxrad_dynamic and maxrad_frozen for each type - // include future FixPour and FixDeposit particles as dynamic - - int itype; - for (i = 1; i <= atom->ntypes; i++) { - onerad_dynamic[i] = onerad_frozen[i] = 0.0; - if (ipour >= 0) { - itype = i; - double radmax = *((double *) modify->fix[ipour]->extract("radius",itype)); - onerad_dynamic[i] = radmax; - } - if (idep >= 0) { - itype = i; - double radmax = *((double *) modify->fix[idep]->extract("radius",itype)); - onerad_dynamic[i] = radmax; - } - } - - double *radius = atom->radius; - int *mask = atom->mask; - int *type = atom->type; - int nlocal = atom->nlocal; - - for (i = 0; i < nlocal; i++) { - double radius_cut = radius[i]; - if (mask[i] & freeze_group_bit) { - onerad_frozen[type[i]] = MAX(onerad_frozen[type[i]],radius_cut); - } else { - onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]],radius_cut); - } - } - - MPI_Allreduce(&onerad_dynamic[1],&maxrad_dynamic[1],atom->ntypes, - MPI_DOUBLE,MPI_MAX,world); - MPI_Allreduce(&onerad_frozen[1],&maxrad_frozen[1],atom->ntypes, - MPI_DOUBLE,MPI_MAX,world); - - // set fix which stores history info - - if (size_history > 0) { - int ifix = modify->find_fix("NEIGH_HISTORY_GRANULAR"); - if (ifix < 0) error->all(FLERR,"Could not find pair fix neigh history ID"); - fix_history = (FixNeighHistory *) modify->fix[ifix]; - } -} - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairGranular::init_one(int i, int j) -{ - double cutoff=0.0; - - if (setflag[i][j] == 0) { - if ((normal_model[i][i] != normal_model[j][j]) || - (damping_model[i][i] != damping_model[j][j]) || - (tangential_model[i][i] != tangential_model[j][j]) || - (roll_model[i][i] != roll_model[j][j]) || - (twist_model[i][i] != twist_model[j][j])) { - - char str[512]; - sprintf(str,"Granular pair style functional forms are different, " - "cannot mix coefficients for types %d and %d. \n" - "This combination must be set explicitly " - "via pair_coeff command",i,j); - error->one(FLERR,str); - } - - if (normal_model[i][j] == HERTZ || normal_model[i][j] == HOOKE) - normal_coeffs[i][j][0] = normal_coeffs[j][i][0] = - mix_geom(normal_coeffs[i][i][0], normal_coeffs[j][j][0]); - else - normal_coeffs[i][j][0] = normal_coeffs[j][i][0] = - mix_stiffnessE(Emod[i][i], Emod[j][j], poiss[i][i], poiss[j][j]); - - normal_coeffs[i][j][1] = normal_coeffs[j][i][1] = - mix_geom(normal_coeffs[i][i][1], normal_coeffs[j][j][1]); - if ((normal_model[i][j] == JKR) || (normal_model[i][j] == DMT)) - normal_coeffs[i][j][3] = normal_coeffs[j][i][3] = - mix_geom(normal_coeffs[i][i][3], normal_coeffs[j][j][3]); - - for (int k = 0; k < 3; k++) - tangential_coeffs[i][j][k] = tangential_coeffs[j][i][k] = - mix_geom(tangential_coeffs[i][i][k], tangential_coeffs[j][j][k]); - - if (roll_model[i][j] != ROLL_NONE) { - for (int k = 0; k < 3; k++) - roll_coeffs[i][j][k] = roll_coeffs[j][i][k] = - mix_geom(roll_coeffs[i][i][k], roll_coeffs[j][j][k]); - } - - if (twist_model[i][j] != TWIST_NONE && twist_model[i][j] != TWIST_MARSHALL) { - for (int k = 0; k < 3; k++) - twist_coeffs[i][j][k] = twist_coeffs[j][i][k] = - mix_geom(twist_coeffs[i][i][k], twist_coeffs[j][j][k]); - } - } - - // It is possible that cut[i][j] at this point is still 0.0. - // This can happen when - // there is a future fix_pour after the current run. A cut[i][j] = 0.0 creates - // problems because neighbor.cpp uses min(cut[i][j]) to decide on the bin size - // To avoid this issue, for cases involving cut[i][j] = 0.0 (possible only - // if there is no current information about radius/cutoff of type i and j). - // we assign cutoff = max(cut[i][j]) for i,j such that cut[i][j] > 0.0. - - double pulloff; - - if (cutoff_type[i][j] < 0 && cutoff_global < 0) { - if (((maxrad_dynamic[i] > 0.0) && (maxrad_dynamic[j] > 0.0)) || - ((maxrad_dynamic[i] > 0.0) && (maxrad_frozen[j] > 0.0)) || - // radius info about both i and j exist - ((maxrad_frozen[i] > 0.0) && (maxrad_dynamic[j] > 0.0))) { - cutoff = maxrad_dynamic[i]+maxrad_dynamic[j]; - pulloff = 0.0; - if (normal_model[i][j] == JKR) { - pulloff = pulloff_distance(maxrad_dynamic[i], maxrad_dynamic[j], i, j); - cutoff += pulloff; - } - - if (normal_model[i][j] == JKR) - pulloff = pulloff_distance(maxrad_frozen[i], maxrad_dynamic[j], i, j); - cutoff = MAX(cutoff, maxrad_frozen[i]+maxrad_dynamic[j]+pulloff); - - if (normal_model[i][j] == JKR) - pulloff = pulloff_distance(maxrad_dynamic[i], maxrad_frozen[j], i, j); - cutoff = MAX(cutoff,maxrad_dynamic[i]+maxrad_frozen[j]+pulloff); - - } else { - - // radius info about either i or j does not exist - // (i.e. not present and not about to get poured; - // set to largest value to not interfere with neighbor list) - - double cutmax = 0.0; - for (int k = 1; k <= atom->ntypes; k++) { - cutmax = MAX(cutmax,2.0*maxrad_dynamic[k]); - cutmax = MAX(cutmax,2.0*maxrad_frozen[k]); - } - cutoff = cutmax; - } - } else if (cutoff_type[i][j] > 0) { - cutoff = cutoff_type[i][j]; - } else if (cutoff_global > 0) { - cutoff = cutoff_global; - } - - return cutoff; -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairGranular::write_restart(FILE *fp) -{ - int i,j; - for (i = 1; i <= atom->ntypes; i++) { - for (j = i; j <= atom->ntypes; j++) { - fwrite(&setflag[i][j],sizeof(int),1,fp); - if (setflag[i][j]) { - fwrite(&normal_model[i][j],sizeof(int),1,fp); - fwrite(&damping_model[i][j],sizeof(int),1,fp); - fwrite(&tangential_model[i][j],sizeof(int),1,fp); - fwrite(&roll_model[i][j],sizeof(int),1,fp); - fwrite(&twist_model[i][j],sizeof(int),1,fp); - fwrite(normal_coeffs[i][j],sizeof(double),4,fp); - fwrite(tangential_coeffs[i][j],sizeof(double),3,fp); - fwrite(roll_coeffs[i][j],sizeof(double),3,fp); - fwrite(twist_coeffs[i][j],sizeof(double),3,fp); - fwrite(&cutoff_type[i][j],sizeof(double),1,fp); - } - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairGranular::read_restart(FILE *fp) -{ - allocate(); - int i,j; - int me = comm->me; - for (i = 1; i <= atom->ntypes; i++) { - for (j = i; j <= atom->ntypes; j++) { - if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); - if (setflag[i][j]) { - if (me == 0) { - utils::sfread(FLERR,&normal_model[i][j],sizeof(int),1,fp,nullptr,error); - utils::sfread(FLERR,&damping_model[i][j],sizeof(int),1,fp,nullptr,error); - utils::sfread(FLERR,&tangential_model[i][j],sizeof(int),1,fp,nullptr,error); - utils::sfread(FLERR,&roll_model[i][j],sizeof(int),1,fp,nullptr,error); - utils::sfread(FLERR,&twist_model[i][j],sizeof(int),1,fp,nullptr,error); - utils::sfread(FLERR,normal_coeffs[i][j],sizeof(double),4,fp,nullptr,error); - utils::sfread(FLERR,tangential_coeffs[i][j],sizeof(double),3,fp,nullptr,error); - utils::sfread(FLERR,roll_coeffs[i][j],sizeof(double),3,fp,nullptr,error); - utils::sfread(FLERR,twist_coeffs[i][j],sizeof(double),3,fp,nullptr,error); - utils::sfread(FLERR,&cutoff_type[i][j],sizeof(double),1,fp,nullptr,error); - } - MPI_Bcast(&normal_model[i][j],1,MPI_INT,0,world); - MPI_Bcast(&damping_model[i][j],1,MPI_INT,0,world); - MPI_Bcast(&tangential_model[i][j],1,MPI_INT,0,world); - MPI_Bcast(&roll_model[i][j],1,MPI_INT,0,world); - MPI_Bcast(&twist_model[i][j],1,MPI_INT,0,world); - MPI_Bcast(normal_coeffs[i][j],4,MPI_DOUBLE,0,world); - MPI_Bcast(tangential_coeffs[i][j],3,MPI_DOUBLE,0,world); - MPI_Bcast(roll_coeffs[i][j],3,MPI_DOUBLE,0,world); - MPI_Bcast(twist_coeffs[i][j],3,MPI_DOUBLE,0,world); - MPI_Bcast(&cutoff_type[i][j],1,MPI_DOUBLE,0,world); - } - } - } -} - -/* ---------------------------------------------------------------------- */ - -void PairGranular::reset_dt() -{ - dt = update->dt; -} - -/* ---------------------------------------------------------------------- */ - -double PairGranular::single(int i, int j, int itype, int jtype, - double rsq, double /* factor_coul */, - double /* factor_lj */, double &fforce) -{ - double radi,radj,radsum; - double r,rinv,delx,dely,delz, nx, ny, nz, Reff; - double dR, dR2; - double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3,wr1,wr2,wr3; - double vtr1,vtr2,vtr3,vrel; - double mi,mj,meff; - double relrot1,relrot2,relrot3,vrl1,vrl2,vrl3; - - double knfac, damp_normal, damp_normal_prefactor; - double k_tangential, damp_tangential; - double Fne, Ft, Fdamp, Fntot, Fncrit, Fscrit, Frcrit; - double fs, fs1, fs2, fs3; - - // for JKR - double R2, coh, F_pulloff, delta_pulloff, dist_pulloff, a, a2, E; - double delta, t0, t1, t2, t3, t4, t5, t6; - double sqrt1, sqrt2, sqrt3; - - // rolling - double k_roll, damp_roll; - double rollmag; - double fr, fr1, fr2, fr3; - - // twisting - double k_twist, damp_twist, mu_twist; - double signtwist, magtwist, magtortwist, Mtcrit; - - double shrmag; - int jnum; - int *jlist; - double *history,*allhistory; - - int nall = atom->nlocal + atom->nghost; - if ((i >= nall) || (j >= nall)) - error->all(FLERR,"Not enough atoms for pair granular single function"); - - double *radius = atom->radius; - radi = radius[i]; - radj = radius[j]; - radsum = radi + radj; - Reff = (radsum > 0.0) ? radi*radj/radsum : 0.0; - - bool touchflag; - E = normal_coeffs[itype][jtype][0]; - if (normal_model[itype][jtype] == JKR) { - E *= THREEQUARTERS; - R2 = Reff*Reff; - coh = normal_coeffs[itype][jtype][3]; - a = cbrt(9.0*MY_PI*coh*R2/(4*E)); - delta_pulloff = a*a/Reff - 2*sqrt(MY_PI*coh*a/E); - dist_pulloff = radsum+delta_pulloff; - touchflag = (rsq <= dist_pulloff*dist_pulloff); - } else touchflag = (rsq <= radsum*radsum); - - if (!touchflag) { - fforce = 0.0; - for (int m = 0; m < single_extra; m++) svector[m] = 0.0; - return 0.0; - } - - double **x = atom->x; - delx = x[i][0] - x[j][0]; - dely = x[i][1] - x[j][1]; - delz = x[i][2] - x[j][2]; - r = sqrt(rsq); - rinv = 1.0/r; - - nx = delx*rinv; - ny = dely*rinv; - nz = delz*rinv; - - // relative translational velocity - - double **v = atom->v; - vr1 = v[i][0] - v[j][0]; - vr2 = v[i][1] - v[j][1]; - vr3 = v[i][2] - v[j][2]; - - // normal component - - vnnr = vr1*nx + vr2*ny + vr3*nz; - vn1 = nx*vnnr; - vn2 = ny*vnnr; - vn3 = nz*vnnr; - - // tangential component - - vt1 = vr1 - vn1; - vt2 = vr2 - vn2; - vt3 = vr3 - vn3; - - // relative rotational velocity - - double **omega = atom->omega; - wr1 = (radi*omega[i][0] + radj*omega[j][0]); - wr2 = (radi*omega[i][1] + radj*omega[j][1]); - wr3 = (radi*omega[i][2] + radj*omega[j][2]); - - // meff = effective mass of pair of particles - // if I or J part of rigid body, use body mass - // if I or J is frozen, meff is other particle - - double *rmass = atom->rmass; - int *mask = atom->mask; - - mi = rmass[i]; - mj = rmass[j]; - if (fix_rigid) { - // NOTE: ensure mass_rigid is current for owned+ghost atoms? - if (mass_rigid[i] > 0.0) mi = mass_rigid[i]; - if (mass_rigid[j] > 0.0) mj = mass_rigid[j]; - } - - meff = mi*mj / (mi+mj); - if (mask[i] & freeze_group_bit) meff = mj; - if (mask[j] & freeze_group_bit) meff = mi; - - delta = radsum - r; - dR = delta*Reff; - if (normal_model[itype][jtype] == JKR) { - dR2 = dR*dR; - t0 = coh*coh*R2*R2*E; - t1 = PI27SQ*t0; - t2 = 8*dR*dR2*E*E*E; - t3 = 4*dR2*E; - // in case sqrt(0) < 0 due to precision issues - sqrt1 = MAX(0, t0*(t1+2*t2)); - t4 = cbrt(t1+t2+THREEROOT3*MY_PI*sqrt(sqrt1)); - t5 = t3/t4 + t4/E; - sqrt2 = MAX(0, 2*dR + t5); - t6 = sqrt(sqrt2); - sqrt3 = MAX(0, 4*dR - t5 + SIXROOT6*coh*MY_PI*R2/(E*t6)); - a = INVROOT6*(t6 + sqrt(sqrt3)); - a2 = a*a; - knfac = normal_coeffs[itype][jtype][0]*a; - Fne = knfac*a2/Reff - MY_2PI*a2*sqrt(4*coh*E/(MY_PI*a)); - } else { - knfac = E; - Fne = knfac*delta; - a = sqrt(dR); - if (normal_model[itype][jtype] != HOOKE) { - Fne *= a; - knfac *= a; - } - if (normal_model[itype][jtype] == DMT) - Fne -= 4*MY_PI*normal_coeffs[itype][jtype][3]*Reff; - } - - if (damping_model[itype][jtype] == VELOCITY) { - damp_normal = 1; - } else if (damping_model[itype][jtype] == MASS_VELOCITY) { - damp_normal = meff; - } else if (damping_model[itype][jtype] == VISCOELASTIC) { - damp_normal = a*meff; - } else if (damping_model[itype][jtype] == TSUJI) { - damp_normal = sqrt(meff*knfac); - } else damp_normal = 0.0; - - damp_normal_prefactor = normal_coeffs[itype][jtype][1]*damp_normal; - Fdamp = -damp_normal_prefactor*vnnr; - - Fntot = Fne + Fdamp; - - jnum = list->numneigh[i]; - jlist = list->firstneigh[i]; - - if (use_history) { - if ((fix_history == nullptr) || (fix_history->firstvalue == nullptr)) - error->one(FLERR,"Pair granular single computation needs history"); - allhistory = fix_history->firstvalue[i]; - for (int jj = 0; jj < jnum; jj++) { - neighprev++; - if (neighprev >= jnum) neighprev = 0; - if (jlist[neighprev] == j) break; - } - history = &allhistory[size_history*neighprev]; - } - - //**************************************** - // tangential force, including history effects - //**************************************** - - // For linear, mindlin, mindlin_rescale: - // history = cumulative tangential displacement - // - // For mindlin/force, mindlin_rescale/force: - // history = cumulative tangential elastic force - - // tangential component - vt1 = vr1 - vn1; - vt2 = vr2 - vn2; - vt3 = vr3 - vn3; - - // relative rotational velocity - wr1 = (radi*omega[i][0] + radj*omega[j][0]); - wr2 = (radi*omega[i][1] + radj*omega[j][1]); - wr3 = (radi*omega[i][2] + radj*omega[j][2]); - - // relative tangential velocities - vtr1 = vt1 - (nz*wr2-ny*wr3); - vtr2 = vt2 - (nx*wr3-nz*wr1); - vtr3 = vt3 - (ny*wr1-nx*wr2); - vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3; - vrel = sqrt(vrel); - - if (normal_model[itype][jtype] == JKR) { - F_pulloff = 3*MY_PI*coh*Reff; - Fncrit = fabs(Fne + 2*F_pulloff); - } else if (normal_model[itype][jtype] == DMT) { - F_pulloff = 4*MY_PI*coh*Reff; - Fncrit = fabs(Fne + 2*F_pulloff); - } else { - Fncrit = fabs(Fntot); - } - Fscrit = tangential_coeffs[itype][jtype][2] * Fncrit; - - //------------------------------ - // tangential forces - //------------------------------ - k_tangential = tangential_coeffs[itype][jtype][0]; - damp_tangential = tangential_coeffs[itype][jtype][1]*damp_normal_prefactor; - - if (tangential_history) { - if (tangential_model[itype][jtype] != TANGENTIAL_HISTORY) { - k_tangential *= a; - } - - shrmag = sqrt(history[0]*history[0] + history[1]*history[1] + - history[2]*history[2]); - - // tangential forces = history + tangential velocity damping - if (tangential_model[itype][jtype] == TANGENTIAL_HISTORY || - tangential_model[itype][jtype] == TANGENTIAL_MINDLIN || - tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_RESCALE) { - fs1 = -k_tangential*history[0] - damp_tangential*vtr1; - fs2 = -k_tangential*history[1] - damp_tangential*vtr2; - fs3 = -k_tangential*history[2] - damp_tangential*vtr3; - } else { - fs1 = history[0] - damp_tangential*vtr1; - fs2 = history[1] - damp_tangential*vtr2; - fs3 = history[2] - damp_tangential*vtr3; - } - - // rescale frictional forces if needed - fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3); - if (fs > Fscrit) { - if (shrmag != 0.0) { - fs1 *= Fscrit/fs; - fs2 *= Fscrit/fs; - fs3 *= Fscrit/fs; - fs *= Fscrit/fs; - } else fs1 = fs2 = fs3 = fs = 0.0; - } - - // classic pair gran/hooke (no history) - } else { - fs = damp_tangential*vrel; - if (vrel != 0.0) Ft = MIN(Fscrit,fs) / vrel; - else Ft = 0.0; - fs1 = -Ft*vtr1; - fs2 = -Ft*vtr2; - fs3 = -Ft*vtr3; - fs = Ft*vrel; - } - - //**************************************** - // rolling resistance - //**************************************** - - if ((roll_model[itype][jtype] != ROLL_NONE) - || (twist_model[itype][jtype] != TWIST_NONE)) { - relrot1 = omega[i][0] - omega[j][0]; - relrot2 = omega[i][1] - omega[j][1]; - relrot3 = omega[i][2] - omega[j][2]; - - // rolling velocity, see eq. 31 of Wang et al, Particuology v 23, p 49 (2015) - // this is different from the Marshall papers, - // which use the Bagi/Kuhn formulation - // for rolling velocity (see Wang et al for why the latter is wrong) - - vrl1 = Reff*(relrot2*nz - relrot3*ny); //- 0.5*((radj-radi)/radsum)*vtr1; - vrl2 = Reff*(relrot3*nx - relrot1*nz); //- 0.5*((radj-radi)/radsum)*vtr2; - vrl3 = Reff*(relrot1*ny - relrot2*nx); //- 0.5*((radj-radi)/radsum)*vtr3; - - int rhist0 = roll_history_index; - int rhist1 = rhist0 + 1; - int rhist2 = rhist1 + 1; - - // rolling displacement - rollmag = sqrt(history[rhist0]*history[rhist0] + - history[rhist1]*history[rhist1] + - history[rhist2]*history[rhist2]); - - k_roll = roll_coeffs[itype][jtype][0]; - damp_roll = roll_coeffs[itype][jtype][1]; - fr1 = -k_roll*history[rhist0] - damp_roll*vrl1; - fr2 = -k_roll*history[rhist1] - damp_roll*vrl2; - fr3 = -k_roll*history[rhist2] - damp_roll*vrl3; - - // rescale frictional displacements and forces if needed - Frcrit = roll_coeffs[itype][jtype][2] * Fncrit; - - fr = sqrt(fr1*fr1 + fr2*fr2 + fr3*fr3); - if (fr > Frcrit) { - if (rollmag != 0.0) { - fr1 *= Frcrit/fr; - fr2 *= Frcrit/fr; - fr3 *= Frcrit/fr; - fr *= Frcrit/fr; - } else fr1 = fr2 = fr3 = fr = 0.0; - } - } else fr1 = fr2 = fr3 = fr = 0.0; - - //**************************************** - // twisting torque, including history effects - //**************************************** - - if (twist_model[itype][jtype] != TWIST_NONE) { - // omega_T (eq 29 of Marshall) - magtwist = relrot1*nx + relrot2*ny + relrot3*nz; - if (twist_model[itype][jtype] == TWIST_MARSHALL) { - k_twist = 0.5*k_tangential*a*a;; //eq 32 - damp_twist = 0.5*damp_tangential*a*a; - mu_twist = TWOTHIRDS*a*tangential_coeffs[itype][jtype][2];; - } else { - k_twist = twist_coeffs[itype][jtype][0]; - damp_twist = twist_coeffs[itype][jtype][1]; - mu_twist = twist_coeffs[itype][jtype][2]; - } - // M_t torque (eq 30) - magtortwist = -k_twist*history[twist_history_index] - damp_twist*magtwist; - signtwist = (magtwist > 0) - (magtwist < 0); - Mtcrit = mu_twist*Fncrit; // critical torque (eq 44) - if (fabs(magtortwist) > Mtcrit) { - magtortwist = -Mtcrit * signtwist; // eq 34 - } else magtortwist = 0.0; - } else magtortwist = 0.0; - - // set force and return no energy - - fforce = Fntot*rinv; - - // set single_extra quantities - - svector[0] = fs1; - svector[1] = fs2; - svector[2] = fs3; - svector[3] = fs; - svector[4] = fr1; - svector[5] = fr2; - svector[6] = fr3; - svector[7] = fr; - svector[8] = magtortwist; - svector[9] = delx; - svector[10] = dely; - svector[11] = delz; - return 0.0; -} - -/* ---------------------------------------------------------------------- */ - -int PairGranular::pack_forward_comm(int n, int *list, double *buf, - int /* pbc_flag */, int * /* pbc */) -{ - int i,j,m; - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = mass_rigid[j]; - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -void PairGranular::unpack_forward_comm(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) - mass_rigid[i] = buf[m++]; -} - -/* ---------------------------------------------------------------------- - memory usage of local atom-based arrays -------------------------------------------------------------------------- */ - -double PairGranular::memory_usage() -{ - double bytes = (double)nmax * sizeof(double); - return bytes; -} - -/* ---------------------------------------------------------------------- - mixing of Young's modulus (E) -------------------------------------------------------------------------- */ - -double PairGranular::mix_stiffnessE(double Eii, double Ejj, - double poisii, double poisjj) -{ - return 1/((1-poisii*poisii)/Eii+(1-poisjj*poisjj)/Ejj); -} - -/* ---------------------------------------------------------------------- - mixing of shear modulus (G) ------------------------------------------------------------------------- */ - -double PairGranular::mix_stiffnessG(double Eii, double Ejj, - double poisii, double poisjj) -{ - return 1/((2*(2-poisii)*(1+poisii)/Eii) + (2*(2-poisjj)*(1+poisjj)/Ejj)); -} - -/* ---------------------------------------------------------------------- - mixing of everything else -------------------------------------------------------------------------- */ - -double PairGranular::mix_geom(double valii, double valjj) -{ - return sqrt(valii*valjj); -} - - -/* ---------------------------------------------------------------------- - compute pull-off distance (beyond contact) for a given radius and atom type -------------------------------------------------------------------------- */ - -double PairGranular::pulloff_distance(double radi, double radj, - int itype, int jtype) -{ - double E, coh, a, Reff; - Reff = radi*radj/(radi+radj); - if (Reff <= 0) return 0; - coh = normal_coeffs[itype][jtype][3]; - E = normal_coeffs[itype][jtype][0]*THREEQUARTERS; - a = cbrt(9*MY_PI*coh*Reff*Reff/(4*E)); - return a*a/Reff - 2*sqrt(MY_PI*coh*a/E); -} - -/* ---------------------------------------------------------------------- - transfer history during fix/neigh/history exchange - only needed if any history entries i-j are not just negative of j-i entries -------------------------------------------------------------------------- */ - -void PairGranular::transfer_history(double* source, double* target) -{ - for (int i = 0; i < size_history; i++) - target[i] = history_transfer_factors[i]*source[i]; -} From 6bdf0138acbeb53101bc7ac3b2e42cfd995470da Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 5 Apr 2021 11:50:53 -0600 Subject: [PATCH 0378/1217] Typos in documentation --- doc/src/pair_gran.rst | 2 +- doc/src/pair_granular.rst | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index 7d6189fda1..5bccdfd8b4 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -219,7 +219,7 @@ potential. If two particles are moving away from each other while in contact, there is a possibility that the particles could experience an effective attractive -force due to damping. If the *limit_damping* keyword is used, this fix +force due to damping. If the *limit_damping* keyword is used, this option will zero out the normal component of the force if there is an effective attractive force. diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index e0a33f31d0..a9ca437370 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -625,7 +625,7 @@ Finally, the twisting torque on each particle is given by: If two particles are moving away from each other while in contact, there is a possibility that the particles could experience an effective attractive -force due to damping. If the optional *limit_damping* keyword is used, this fix +force due to damping. If the optional *limit_damping* keyword is used, this option will zero out the normal component of the force if there is an effective attractive force. This keyword cannot be used with the JKR or DMT models. @@ -667,7 +667,7 @@ atom types. If two particles are moving away from each other while in contact, there is a possibility that the particles could experience an effective attractive -force due to damping. If the *no_attraction* keyword is used, this fix +force due to damping. If the *limit_damping* keyword is used, this option will zero out the normal component of the force if there is an effective attractive force. This keyword cannot be used with the JKR or DMT models. From f323fb29b3cc6e96a643b9de94c73472c3f9bccd Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Mon, 5 Apr 2021 11:53:49 -0600 Subject: [PATCH 0379/1217] Reverting no_attraction option in wall gran region docu --- doc/src/fix_wall_gran_region.rst | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index b7a9ff6bd7..35fe1fab72 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -36,14 +36,12 @@ Syntax * wallstyle = region (see :doc:`fix wall/gran ` for options for other kinds of walls) * region-ID = region whose boundary will act as wall -* keyword = *contacts* or *no_attraction* +* keyword = *contacts* .. parsed-literal:: *contacts* value = none generate contact information for each particle - *no_attraction* value = none - turn off possibility of attractive interactions Examples """""""" From 4e4a571dbda05a29dff342d163f4059b0aac5117 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 14:31:13 -0400 Subject: [PATCH 0380/1217] Add advanced LAMMPS_DOWNLOADS_URL cmake option --- cmake/CMakeLists.txt | 5 +++++ cmake/Modules/LAMMPSUtils.cmake | 1 - 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 21d965ebba..4c94a5037a 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -22,6 +22,11 @@ set(LAMMPS_TOOLS_DIR ${LAMMPS_DIR}/tools) set(LAMMPS_PYTHON_DIR ${LAMMPS_DIR}/python) set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials) +set(LAMMPS_DOWNLOADS_URL "https://download.lammps.org" CACHE STRING "Base URL for LAMMPS downloads") +set(LAMMPS_POTENTIALS_URL "${LAMMPS_DOWNLOADS_URL}/potentials") +set(LAMMPS_THIRDPARTY_URL "${LAMMPS_DOWNLOADS_URL}/thirdparty") +mark_as_advanced(LAMMPS_DOWNLOADS_URL) + find_package(Git) # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed diff --git a/cmake/Modules/LAMMPSUtils.cmake b/cmake/Modules/LAMMPSUtils.cmake index 37275843fa..acaef19498 100644 --- a/cmake/Modules/LAMMPSUtils.cmake +++ b/cmake/Modules/LAMMPSUtils.cmake @@ -86,7 +86,6 @@ endfunction(GenerateBinaryHeader) # fetch missing potential files function(FetchPotentials pkgfolder potfolder) if (EXISTS "${pkgfolder}/potentials.txt") - set(LAMMPS_POTENTIALS_URL "https://download.lammps.org/potentials") file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].") foreach(line ${linelist}) string(FIND ${line} " " blank) From 8533bb17e7cf3913600f139de54edaab2cf01108 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 14:36:38 -0400 Subject: [PATCH 0381/1217] Update cmake/Modules/OpenCLLoader.cmake --- cmake/Modules/OpenCLLoader.cmake | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/cmake/Modules/OpenCLLoader.cmake b/cmake/Modules/OpenCLLoader.cmake index 5ab121f841..54eaab4795 100644 --- a/cmake/Modules/OpenCLLoader.cmake +++ b/cmake/Modules/OpenCLLoader.cmake @@ -1,11 +1,13 @@ message(STATUS "Downloading and building OpenCL loader library") +set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball") +set(OPENCL_LOADER_MD5 "011cdcbd41030be94f3fced6d763a52a" CACHE STRING "MD5 checksum of OpenCL loader tarball") +mark_as_advanced(OPENCL_LOADER_URL) +mark_as_advanced(OPENCL_LOADER_MD5) include(ExternalProject) -set(OPENCL_LOADER_URL "https://download.lammps.org/thirdparty/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball") -mark_as_advanced(OPENCL_LOADER_URL) ExternalProject_Add(opencl_loader - URL ${OPENCL_LOADER_URL} - URL_MD5 011cdcbd41030be94f3fced6d763a52a + URL ${OPENCL_LOADER_URL} + URL_MD5 ${OPENCL_LOADER_MD5} SOURCE_DIR "${CMAKE_BINARY_DIR}/opencl_loader-src" BINARY_DIR "${CMAKE_BINARY_DIR}/opencl_loader-build" CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS} From 3b14606f063f8fa72470697a495a3441df2e00ca Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 14:43:05 -0400 Subject: [PATCH 0382/1217] Update cmake/Modules/MPI4WIN.cmake --- cmake/Modules/MPI4WIN.cmake | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/cmake/Modules/MPI4WIN.cmake b/cmake/Modules/MPI4WIN.cmake index 529cefeab0..aa0c9e1833 100644 --- a/cmake/Modules/MPI4WIN.cmake +++ b/cmake/Modules/MPI4WIN.cmake @@ -1,16 +1,25 @@ # Download and configure custom MPICH files for Windows message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows") +set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball") +set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball") +set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball") +set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball") +mark_as_advanced(MPICH2_WIN64_DEVEL_URL) +mark_as_advanced(MPICH2_WIN32_DEVEL_URL) +mark_as_advanced(MPICH2_WIN64_DEVEL_MD5) +mark_as_advanced(MPICH2_WIN32_DEVEL_MD5) + include(ExternalProject) if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64") ExternalProject_Add(mpi4win_build - URL https://download.lammps.org/thirdparty/mpich2-win64-devel.tar.gz - URL_MD5 4939fdb59d13182fd5dd65211e469f14 + URL ${MPICH2_WIN64_DEVEL_URL} + URL_MD5 ${MPICH2_WIN64_DEVEL_MD5} CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" BUILD_BYPRODUCTS /lib/libmpi.a) else() ExternalProject_Add(mpi4win_build - URL https://download.lammps.org/thirdparty/mpich2-win32-devel.tar.gz - URL_MD5 a61d153500dce44e21b755ee7257e031 + URL ${MPICH2_WIN32_DEVEL_URL} + URL_MD5 ${MPICH2_WIN32_DEVEL_MD5} CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" BUILD_BYPRODUCTS /lib/libmpi.a) endif() From 614411130b2aa3312b5ab12a02db3132f31a56ec Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 14:44:27 -0400 Subject: [PATCH 0383/1217] Update cmake/Modules/Documentation.cmake --- cmake/Modules/Documentation.cmake | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Documentation.cmake b/cmake/Modules/Documentation.cmake index 5a42244b9e..c0028676b7 100644 --- a/cmake/Modules/Documentation.cmake +++ b/cmake/Modules/Documentation.cmake @@ -55,11 +55,15 @@ if(BUILD_DOC) COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade ) + set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" CACHE STRING "URL for MathJax tarball") + set(MATHJAX_MD5 "a4a6a093a89bc2ccab1452d766b98e53" CACHE STRING "MD5 checksum of MathJax tarball") + mark_as_advanced(MATHJAX_URL) + # download mathjax distribution and unpack to folder "mathjax" if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5) - file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" + file(DOWNLOAD ${MATHJAX_URL} "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz" - EXPECTED_MD5 a4a6a093a89bc2ccab1452d766b98e53) + EXPECTED_MD5 ${MATHJAX_MD5}) execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*) execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax) From 192ee276b16c3d67838ce58d50f9a85c41abe141 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 14:46:50 -0400 Subject: [PATCH 0384/1217] Update cmake/Modules/Packages/KOKKOS.cmake --- cmake/Modules/Packages/KOKKOS.cmake | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index 1dfb0bf389..1f00516e08 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -37,9 +37,13 @@ if(DOWNLOAD_KOKKOS) list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}") list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}") include(ExternalProject) + set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball") + set(KOKKOS_MD5 "08201d1c7cf5bc458ce0f5b44a629d5a" CACHE STRING "MD5 checksum of KOKKOS tarball") + mark_as_advanced(KOKKOS_URL) + mark_as_advanced(KOKKOS_MD5) ExternalProject_Add(kokkos_build - URL https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz - URL_MD5 08201d1c7cf5bc458ce0f5b44a629d5a + URL ${KOKKOS_URL} + URL_MD5 ${KOKKOS_MD5} CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS} BUILD_BYPRODUCTS /lib/libkokkoscore.a ) From 42ca8c5ba09762c43602614feee0363a25f9273d Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 14:55:56 -0400 Subject: [PATCH 0385/1217] Update cmake/Modules/Packages/VORONOI.cmake --- cmake/Modules/Packages/VORONOI.cmake | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Packages/VORONOI.cmake b/cmake/Modules/Packages/VORONOI.cmake index 1d6893a978..7feea4c52e 100644 --- a/cmake/Modules/Packages/VORONOI.cmake +++ b/cmake/Modules/Packages/VORONOI.cmake @@ -7,6 +7,11 @@ endif() option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT}) if(DOWNLOAD_VORO) message(STATUS "Voro++ download requested - we will build our own") + set(VORO_URL "${LAMMPS_THIRDPARTY_URL}/voro++-0.4.6.tar.gz" CACHE STRING "URL for Voro++ tarball") + set(VORO_MD5 "2338b824c3b7b25590e18e8df5d68af9" CACHE STRING "MD5 checksum for Voro++ tarball") + mark_as_advanced(VORO_URL) + mark_as_advanced(VORO_MD5) + include(ExternalProject) if(BUILD_SHARED_LIBS) @@ -22,8 +27,8 @@ if(DOWNLOAD_VORO) endif() ExternalProject_Add(voro_build - URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz - URL_MD5 2338b824c3b7b25590e18e8df5d68af9 + URL ${VORO_URL} + URL_MD5 ${VORO_MD5} PATCH_COMMAND patch -b -p0 < ${LAMMPS_LIB_SOURCE_DIR}/voronoi/voro-make.patch CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} From 725332614a95131a855cfc8bc74edd98dcb5dccd Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 14:56:47 -0400 Subject: [PATCH 0386/1217] Update cmake/Modules/Packages/MSCG.cmake --- cmake/Modules/Packages/MSCG.cmake | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Packages/MSCG.cmake b/cmake/Modules/Packages/MSCG.cmake index 6cb389fb13..6ac62cb012 100644 --- a/cmake/Modules/Packages/MSCG.cmake +++ b/cmake/Modules/Packages/MSCG.cmake @@ -7,10 +7,15 @@ else() endif() option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT}) if(DOWNLOAD_MSCG) + set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz" CACHE STRING "URL for MSCG tarball") + set(MSCG_MD5 "8c45e269ee13f60b303edd7823866a91" CACHE STRING "MD5 checksum of MSCG tarball") + mark_as_advanced(MSCG_URL) + mark_as_advanced(MSCG_MD5) + include(ExternalProject) ExternalProject_Add(mscg_build - URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz - URL_MD5 8c45e269ee13f60b303edd7823866a91 + URL ${MSCG_URL} + URL_MD5 ${MSCG_MD5} SOURCE_SUBDIR src/CMake CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} From 0277883fb2271a31ed0d07f4b64098ee4655b436 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 15:00:06 -0400 Subject: [PATCH 0387/1217] Update cmake/Modules/Packages/USER-SCAFACOS.cmake --- cmake/Modules/Packages/USER-SCAFACOS.cmake | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/cmake/Modules/Packages/USER-SCAFACOS.cmake b/cmake/Modules/Packages/USER-SCAFACOS.cmake index dc5c400c36..fd355420c3 100644 --- a/cmake/Modules/Packages/USER-SCAFACOS.cmake +++ b/cmake/Modules/Packages/USER-SCAFACOS.cmake @@ -14,15 +14,19 @@ endif() option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT}) if(DOWNLOAD_SCAFACOS) message(STATUS "ScaFaCoS download requested - we will build our own") + set(SCAFACOS_URL "https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz" CACHE STRING "URL for SCAFACOS tarball") + set(SCAFACOS_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of SCAFACOS tarball") + mark_as_advanced(SCAFACOS_URL) + mark_as_advanced(SCAFACOS_MD5) # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later. - file(DOWNLOAD https://download.lammps.org/thirdparty/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff + file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032) include(ExternalProject) ExternalProject_Add(scafacos_build - URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz - URL_MD5 bd46d74e3296bd8a444d731bb10c1738 + URL ${SCAFACOS_URL} + URL_MD5 ${SCAFACOS_MD5} PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff CONFIGURE_COMMAND /configure --prefix= --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m From 8ccc19bb2a272ec593da61515a1a313e1ff6d35f Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 15:03:05 -0400 Subject: [PATCH 0388/1217] Update cmake/Modules/Packages/LATTE.cmake --- cmake/Modules/Packages/LATTE.cmake | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Packages/LATTE.cmake b/cmake/Modules/Packages/LATTE.cmake index e66f83fa43..ddf31a68ed 100644 --- a/cmake/Modules/Packages/LATTE.cmake +++ b/cmake/Modules/Packages/LATTE.cmake @@ -15,10 +15,14 @@ endif() option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT}) if(DOWNLOAD_LATTE) message(STATUS "LATTE download requested - we will build our own") + set(LATTE_URL "https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz" CACHE STRING "URL for LATTE tarball") + set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball") + mark_as_advanced(LATTE_URL) + mark_as_advanced(LATTE_MD5) include(ExternalProject) ExternalProject_Add(latte_build - URL https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz - URL_MD5 820e73a457ced178c08c71389a385de7 + URL ${LATTE_URL} + URL_MD5 ${LATTE_MD5} SOURCE_SUBDIR cmake CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES} From b718903efc36ce9d15218f425cc74a4f180170d6 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 15:10:01 -0400 Subject: [PATCH 0389/1217] Update cmake/Modules/Packages/USER-PLUMED.cmake --- cmake/Modules/Packages/USER-PLUMED.cmake | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/USER-PLUMED.cmake index 53abf5771a..8719e8179d 100644 --- a/cmake/Modules/Packages/USER-PLUMED.cmake +++ b/cmake/Modules/Packages/USER-PLUMED.cmake @@ -53,10 +53,16 @@ if(DOWNLOAD_PLUMED) elseif(PLUMED_MODE STREQUAL "RUNTIME") set(PLUMED_BUILD_BYPRODUCTS "/lib/libplumedWrapper.a") endif() + + set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz" CACHE STRING "URL for PLUMED tarball") + set(PLUMED_MD5 "95f29dd0c067577f11972ff90dfc7d12" CACHE STRING "MD5 checksum of PLUMED tarball") + mark_as_advanced(PLUMED_URL) + mark_as_advanced(PLUMED_MD5) + include(ExternalProject) ExternalProject_Add(plumed_build - URL https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz - URL_MD5 95f29dd0c067577f11972ff90dfc7d12 + URL ${PLUMED_URL} + URL_MD5 ${PLUMED_MD5} BUILD_IN_SOURCE 1 CONFIGURE_COMMAND /configure --prefix= ${CONFIGURE_REQUEST_PIC} From 88b9e99707c95bd6ede9f47672536ded23fe66d0 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 15:26:58 -0400 Subject: [PATCH 0390/1217] Update cmake/Modules/Packages/GPU.cmake --- cmake/Modules/Packages/GPU.cmake | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index 9aa917144b..115d81af2a 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -338,11 +338,16 @@ elseif(GPU_API STREQUAL "HIP") if(DOWNLOAD_CUB) message(STATUS "CUB download requested") + set(CUB_URL "https://github.com/NVlabs/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball") + set(CUB_MD5 "1cf595beacafff104700921bac8519f3" CACHE STRING "MD5 checksum of CUB tarball") + mark_as_advanced(CUB_URL) + mark_as_advanced(CUB_MD5) + include(ExternalProject) ExternalProject_Add(CUB - GIT_REPOSITORY https://github.com/NVlabs/cub - TIMEOUT 5 + URL ${CUB_URL} + URL_MD5 ${CUB_MD5} PREFIX "${CMAKE_CURRENT_BINARY_DIR}" CONFIGURE_COMMAND "" BUILD_COMMAND "" @@ -354,7 +359,7 @@ elseif(GPU_API STREQUAL "HIP") else() find_package(CUB) if(NOT CUB_FOUND) - message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it") + message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_CUB=ON to download it") endif() endif() From 2509190daec63d7942334ed5556ff72abc175574 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 15:29:33 -0400 Subject: [PATCH 0391/1217] Update cmake/Modules/YAML.cmake --- cmake/Modules/YAML.cmake | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/cmake/Modules/YAML.cmake b/cmake/Modules/YAML.cmake index f2ba34e1b6..c50773568c 100644 --- a/cmake/Modules/YAML.cmake +++ b/cmake/Modules/YAML.cmake @@ -2,10 +2,13 @@ message(STATUS "Downloading and building YAML library") include(ExternalProject) set(YAML_URL "https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz" CACHE STRING "URL for libyaml tarball") +set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of libyaml tarball") mark_as_advanced(YAML_URL) +mark_as_advanced(YAML_MD5) + ExternalProject_Add(libyaml URL ${YAML_URL} - URL_MD5 bb15429d8fb787e7d3f1c83ae129a999 + URL_MD5 ${YAML_MD5} SOURCE_DIR "${CMAKE_BINARY_DIR}/yaml-src" BINARY_DIR "${CMAKE_BINARY_DIR}/yaml-build" CONFIGURE_COMMAND /configure ${CONFIGURE_REQUEST_PIC} From d4550dbb4b218541af2754bba41db856ad227f6e Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 15:32:18 -0400 Subject: [PATCH 0392/1217] Update cmake/Modules/Packages/USER-SMD.cmake --- cmake/Modules/Packages/USER-SMD.cmake | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Packages/USER-SMD.cmake b/cmake/Modules/Packages/USER-SMD.cmake index 67f4aae99d..6d941f9798 100644 --- a/cmake/Modules/Packages/USER-SMD.cmake +++ b/cmake/Modules/Packages/USER-SMD.cmake @@ -7,10 +7,14 @@ endif() option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT}) if(DOWNLOAD_EIGEN3) message(STATUS "Eigen3 download requested - we will build our own") + set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz" CACHE STRING "URL for Eigen3 tarball") + set(EIGEN3_MD5 "9e30f67e8531477de4117506fe44669b" CACHE STRING "MD5 checksum of Eigen3 tarball") + mark_as_advanced(EIGEN3_URL) + mark_as_advanced(EIGEN3_MD5) include(ExternalProject) ExternalProject_Add(Eigen3_build - URL https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz - URL_MD5 9e30f67e8531477de4117506fe44669b + URL ${EIGEN3_URL} + URL_MD5 ${EIGEN3_MD5} CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" ) ExternalProject_get_property(Eigen3_build SOURCE_DIR) From cbd439692ebfb2c070ed307998471b4e15523849 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 15:36:14 -0400 Subject: [PATCH 0393/1217] Update cmake/Modules/Packages/KIM.cmake --- cmake/Modules/Packages/KIM.cmake | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake index 5482d3071c..2a2a1cde78 100644 --- a/cmake/Modules/Packages/KIM.cmake +++ b/cmake/Modules/Packages/KIM.cmake @@ -35,9 +35,13 @@ if(DOWNLOAD_KIM) include(ExternalProject) enable_language(C) enable_language(Fortran) + set(KIM_URL "https://s3.openkim.org/kim-api/kim-api-2.2.1.txz" CACHE STRING "URL for KIM tarball") + set(KIM_MD5 "ae1ddda2ef7017ea07934e519d023dca" CACHE STRING "MD5 checksum of KIM tarball") + mark_as_advanced(KIM_URL) + mark_as_advanced(KIM_MD5) ExternalProject_Add(kim_build - URL https://s3.openkim.org/kim-api/kim-api-2.2.1.txz - URL_MD5 ae1ddda2ef7017ea07934e519d023dca + URL ${KIM_URL} + URL_MD5 ${KIM_MD5} BINARY_DIR build CMAKE_ARGS ${CMAKE_REQUEST_PIC} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} From fc6e10921d26c5c9e0a446cec7246dad005324f6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 5 Apr 2021 15:38:59 -0400 Subject: [PATCH 0394/1217] add post yes/no keyword to rerun commmand (with default to no) --- doc/src/rerun.rst | 9 +++++++-- src/rerun.cpp | 12 +++++++++++- 2 files changed, 18 insertions(+), 3 deletions(-) diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst index 7d51fba868..e9e23afba8 100644 --- a/doc/src/rerun.rst +++ b/doc/src/rerun.rst @@ -15,7 +15,7 @@ Syntax .. parsed-literal:: - keyword = *first* or *last* or *every* or *skip* or *start* or *stop* or *dump* + keyword = *first* or *last* or *every* or *skip* or *start* or *stop* or *post* or *dump* *first* args = Nfirst Nfirst = dump timestep to start on *last* args = Nlast @@ -28,6 +28,7 @@ Syntax Nstart = timestep on which pseudo run will start *stop* args = Nstop Nstop = timestep to which pseudo run will end + *post* value = *yes* or *no* *dump* args = same as :doc:`read_dump ` command starting with its field arguments Examples @@ -154,6 +155,10 @@ Also note that an error will occur if you read a snapshot from the dump file with a timestep value larger than the *stop* setting you have specified. +The *post* keyword can be used to minimize the output to the screen that +happens after a *rerun* command, similar to the post keyword of the +:doc:`run command `. It is set to *no* by default. + The *dump* keyword is required and must be the last keyword specified. Its arguments are passed internally to the :doc:`read_dump ` command. The first argument following the *dump* keyword should be @@ -226,4 +231,4 @@ Default The option defaults are first = 0, last = a huge value (effectively infinity), start = same as first, stop = same as last, every = 0, skip -= 1; += 1, post = no; diff --git a/src/rerun.cpp b/src/rerun.cpp index 648874420a..8615b02d95 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -51,6 +51,7 @@ void Rerun::command(int narg, char **arg) if (strcmp(arg[iarg],"start") == 0) break; if (strcmp(arg[iarg],"stop") == 0) break; if (strcmp(arg[iarg],"dump") == 0) break; + if (strcmp(arg[iarg],"post") == 0) break; iarg++; } int nfile = iarg; @@ -65,6 +66,7 @@ void Rerun::command(int narg, char **arg) int nskip = 1; int startflag = 0; int stopflag = 0; + int postflag = 0; bigint start = -1; bigint stop = -1; @@ -101,6 +103,14 @@ void Rerun::command(int narg, char **arg) stop = utils::bnumeric(FLERR,arg[iarg+1],false,lmp); if (stop < 0) error->all(FLERR,"Illegal rerun command"); iarg += 2; + } else if (strcmp(arg[iarg],"post") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command"); + if (strcmp(arg[iarg+1],"yes") == 0) { + postflag = 1; + } else if (strcmp(arg[iarg+1],"no") == 0) { + postflag = 0; + } else error->all(FLERR,"Illegal rerun command"); + iarg += 2; } else if (strcmp(arg[iarg],"dump") == 0) { break; } else error->all(FLERR,"Illegal rerun command"); @@ -182,7 +192,7 @@ void Rerun::command(int narg, char **arg) update->nsteps = ndump; Finish finish(lmp); - finish.end(1); + finish.end(postflag); update->whichflag = 0; update->firststep = update->laststep = 0; From 7e57d6a334b0493698827f4a78b204ec5e064de9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 5 Apr 2021 15:39:31 -0400 Subject: [PATCH 0395/1217] add tests for "rerun" --- unittest/formats/test_dump_atom.cpp | 50 ++++++++++++++++-- unittest/formats/test_dump_custom.cpp | 73 +++++++++++++++++++++++++-- 2 files changed, 115 insertions(+), 8 deletions(-) diff --git a/unittest/formats/test_dump_atom.cpp b/unittest/formats/test_dump_atom.cpp index 46c6b7dfa7..5161eece3e 100644 --- a/unittest/formats/test_dump_atom.cpp +++ b/unittest/formats/test_dump_atom.cpp @@ -15,6 +15,8 @@ #include "../testing/systems/melt.h" #include "../testing/utils.h" #include "fmt/format.h" +#include "output.h" +#include "thermo.h" #include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" @@ -24,7 +26,7 @@ using ::testing::Eq; char *BINARY2TXT_BINARY = nullptr; -bool verbose = false; +bool verbose = false; class DumpAtomTest : public MeltTest { std::string dump_style = "atom"; @@ -46,7 +48,14 @@ public: command(fmt::format("dump_modify id {}", dump_modify_options)); } - command(fmt::format("run {}", ntimesteps)); + command(fmt::format("run {} post no", ntimesteps)); + END_HIDE_OUTPUT(); + } + + void continue_dump(int ntimesteps) + { + BEGIN_HIDE_OUTPUT(); + command(fmt::format("run {} pre no post no", ntimesteps)); END_HIDE_OUTPUT(); } @@ -62,7 +71,7 @@ public: command(fmt::format("dump_modify id1 {}", dump_modify_options)); } - command(fmt::format("run {}", ntimesteps)); + command(fmt::format("run {} post no", ntimesteps)); END_HIDE_OUTPUT(); } @@ -446,13 +455,16 @@ TEST_F(DumpAtomTest, binary_triclinic_with_image_run0) delete_file(converted_file); } -TEST_F(DumpAtomTest, run1) +TEST_F(DumpAtomTest, run1plus1) { - auto dump_file = "dump_run1.melt"; + auto dump_file = "dump_run1plus1.melt"; generate_dump(dump_file, "", 1); ASSERT_FILE_EXISTS(dump_file); ASSERT_EQ(count_lines(dump_file), 82); + continue_dump(1); + ASSERT_FILE_EXISTS(dump_file); + ASSERT_EQ(count_lines(dump_file), 123); delete_file(dump_file); } @@ -466,6 +478,34 @@ TEST_F(DumpAtomTest, run2) delete_file(dump_file); } +TEST_F(DumpAtomTest, rerun) +{ + auto dump_file = "dump_rerun.melt"; + HIDE_OUTPUT([&] { + command("fix 1 all nve"); + }); + generate_dump(dump_file, "format line \"%d %d %20.15g %20.15g %20.15g\"", 1); + double pe_1, pe_2, pe_rerun; + lmp->output->thermo->evaluate_keyword("pe", &pe_1); + ASSERT_FILE_EXISTS(dump_file); + ASSERT_EQ(count_lines(dump_file), 82); + continue_dump(1); + lmp->output->thermo->evaluate_keyword("pe", &pe_2); + ASSERT_FILE_EXISTS(dump_file); + ASSERT_EQ(count_lines(dump_file), 123); + HIDE_OUTPUT([&] { + command(fmt::format("rerun {} first 1 last 1 every 1 post no dump x y z", dump_file)); + }); + lmp->output->thermo->evaluate_keyword("pe", &pe_rerun); + ASSERT_DOUBLE_EQ(pe_1, pe_rerun); + HIDE_OUTPUT([&] { + command(fmt::format("rerun {} first 2 last 2 every 1 post yes dump x y z", dump_file)); + }); + lmp->output->thermo->evaluate_keyword("pe", &pe_rerun); + ASSERT_DOUBLE_EQ(pe_2, pe_rerun); + delete_file(dump_file); +} + TEST_F(DumpAtomTest, multi_file_run1) { auto dump_file = "dump_run1_*.melt"; diff --git a/unittest/formats/test_dump_custom.cpp b/unittest/formats/test_dump_custom.cpp index b90d77e966..f8a55bb2fb 100644 --- a/unittest/formats/test_dump_custom.cpp +++ b/unittest/formats/test_dump_custom.cpp @@ -15,6 +15,8 @@ #include "../testing/systems/melt.h" #include "../testing/utils.h" #include "fmt/format.h" +#include "output.h" +#include "thermo.h" #include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" @@ -22,7 +24,7 @@ using ::testing::Eq; char *BINARY2TXT_BINARY = nullptr; -bool verbose = false; +bool verbose = false; class DumpCustomTest : public MeltTest { std::string dump_style = "custom"; @@ -45,7 +47,14 @@ public: command(fmt::format("dump_modify id {}", dump_modify_options)); } - command(fmt::format("run {}", ntimesteps)); + command(fmt::format("run {} post no", ntimesteps)); + END_HIDE_OUTPUT(); + } + + void continue_dump(int ntimesteps) + { + BEGIN_HIDE_OUTPUT(); + command(fmt::format("run {} pre no post no", ntimesteps)); END_HIDE_OUTPUT(); } @@ -62,7 +71,7 @@ public: command(fmt::format("dump_modify id1 {}", dump_modify_options)); } - command(fmt::format("run {}", ntimesteps)); + command(fmt::format("run {} post no", ntimesteps)); END_HIDE_OUTPUT(); } @@ -262,6 +271,64 @@ TEST_F(DumpCustomTest, with_variable_run1) delete_file(dump_file); } +TEST_F(DumpCustomTest, run1plus1) +{ + auto dump_file = "dump_custom_run1plus1.melt"; + auto fields = "id type x y z"; + + generate_dump(dump_file, fields, "units yes", 1); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + ASSERT_EQ(lines.size(), 84); + continue_dump(1); + ASSERT_FILE_EXISTS(dump_file); + lines = read_lines(dump_file); + ASSERT_EQ(lines.size(), 125); + delete_file(dump_file); +} + +TEST_F(DumpCustomTest, run2) +{ + auto dump_file = "dump_custom_run2.melt"; + auto fields = "id type x y z"; + generate_dump(dump_file, fields, "", 2); + + ASSERT_FILE_EXISTS(dump_file); + ASSERT_EQ(count_lines(dump_file), 123); + delete_file(dump_file); +} + +TEST_F(DumpCustomTest, rerun) +{ + auto dump_file = "dump_rerun.melt"; + auto fields = "id type xs ys zs"; + + HIDE_OUTPUT([&] { + command("fix 1 all nve"); + }); + generate_dump(dump_file, fields, "format float %20.15g", 1); + double pe_1, pe_2, pe_rerun; + lmp->output->thermo->evaluate_keyword("pe", &pe_1); + ASSERT_FILE_EXISTS(dump_file); + ASSERT_EQ(count_lines(dump_file), 82); + continue_dump(1); + lmp->output->thermo->evaluate_keyword("pe", &pe_2); + ASSERT_FILE_EXISTS(dump_file); + ASSERT_EQ(count_lines(dump_file), 123); + HIDE_OUTPUT([&] { + command(fmt::format("rerun {} first 1 last 1 every 1 post no dump x y z", dump_file)); + }); + lmp->output->thermo->evaluate_keyword("pe", &pe_rerun); + ASSERT_DOUBLE_EQ(pe_1, pe_rerun); + HIDE_OUTPUT([&] { + command(fmt::format("rerun {} first 2 last 2 every 1 post yes dump x y z", dump_file)); + }); + lmp->output->thermo->evaluate_keyword("pe", &pe_rerun); + ASSERT_DOUBLE_EQ(pe_2, pe_rerun); + delete_file(dump_file); +} + int main(int argc, char **argv) { MPI_Init(&argc, &argv); From 94068cc4c7b8465dc3beb91dde1eecfc0cbeb33e Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Apr 2021 16:17:41 -0400 Subject: [PATCH 0396/1217] Add missing GTEST_MD5 --- cmake/Modules/GTest.cmake | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/GTest.cmake b/cmake/Modules/GTest.cmake index 0c62291d5e..677ed5f4af 100644 --- a/cmake/Modules/GTest.cmake +++ b/cmake/Modules/GTest.cmake @@ -8,10 +8,12 @@ endif() include(ExternalProject) set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball") +set(GTEST_MD5 "ecd1fa65e7de707cd5c00bdac56022cd" CACHE STRING "MD5 checksum of GTest tarball") mark_as_advanced(GTEST_URL) +mark_as_advanced(GTEST_MD5) ExternalProject_Add(googletest - URL ${GTEST_URL} - URL_MD5 ecd1fa65e7de707cd5c00bdac56022cd + URL ${GTEST_URL} + URL_MD5 ${GTEST_MD5} SOURCE_DIR "${CMAKE_BINARY_DIR}/gtest-src" BINARY_DIR "${CMAKE_BINARY_DIR}/gtest-build" CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS} From 2fc9734fab1ea44a50505f383a69104b965b6953 Mon Sep 17 00:00:00 2001 From: Trung Nguyen Date: Mon, 5 Apr 2021 23:51:11 -0500 Subject: [PATCH 0397/1217] Fixed a bug with rigid/*/small when starting with an empty group of rigid bodies such as when using fix deposit --- src/RIGID/fix_rigid_nh_small.cpp | 19 ++++--------------- src/RIGID/fix_rigid_nh_small.h | 2 -- 2 files changed, 4 insertions(+), 17 deletions(-) diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 454f240bb4..242c33eb3a 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -754,6 +754,8 @@ void FixRigidNHSmall::final_integrate() void FixRigidNHSmall::nhc_temp_integrate() { + if (g_f == 0) return; + int i,j,k; double kt,gfkt_t,gfkt_r,tmp,ms,s,s2; @@ -1148,6 +1150,8 @@ void FixRigidNHSmall::compute_press_target() void FixRigidNHSmall::nh_epsilon_dot() { + if (g_f == 0) return; + int i; double volume,scale,f_epsilon; @@ -1204,8 +1208,6 @@ void FixRigidNHSmall::compute_dof() nf_r = nfall[1]; g_f = nf_t + nf_r; - onednft = 1.0 + (double)(dimension) / (double)g_f; - onednfr = (double) (dimension) / (double)g_f; } /* ---------------------------------------------------------------------- @@ -1367,19 +1369,6 @@ int FixRigidNHSmall::modify_param(int narg, char **arg) return FixRigidSmall::modify_param(narg,arg); } -/* ---------------------------------------------------------------------- - disallow using fix rigid/n??/small fixes with fix deposit - we would need custom functionality to update data structures - used by all fixes derived from this class but not fix rigid/small -------------------------------------------------------------------------- */ - -void FixRigidNHSmall::set_molecule(int, tagint, int, - double *, double *, double *) -{ - error->all(FLERR,fmt::format("Molecule update not (yet) implemented for " - "fix {}", style)); -} - /* ---------------------------------------------------------------------- */ void FixRigidNHSmall::allocate_chain() diff --git a/src/RIGID/fix_rigid_nh_small.h b/src/RIGID/fix_rigid_nh_small.h index 32c4c1ab74..899cec1122 100644 --- a/src/RIGID/fix_rigid_nh_small.h +++ b/src/RIGID/fix_rigid_nh_small.h @@ -38,7 +38,6 @@ class FixRigidNHSmall : public FixRigidSmall { int dimension; // # of dimensions int nf_t,nf_r; // trans/rot degrees of freedom - double onednft,onednfr; // factors 1 + dimension/trans(rot) degrees of freedom double *w,*wdti1,*wdti2,*wdti4; // Yoshida-Suzuki coefficients double *q_t,*q_r; // trans/rot thermostat masses double *eta_t,*eta_r; // trans/rot thermostat positions @@ -80,7 +79,6 @@ class FixRigidNHSmall : public FixRigidSmall { void nh_epsilon_dot(); void compute_dof(); - void set_molecule(int, tagint, int, double *, double *, double *); void allocate_chain(); void allocate_order(); void deallocate_chain(); From 8e28252ac936efea29e20a92a99ccedddfa8f1ed Mon Sep 17 00:00:00 2001 From: Trung Nguyen Date: Tue, 6 Apr 2021 00:19:20 -0500 Subject: [PATCH 0398/1217] Updated fix rigid/nh for the (g_f == 0) case --- src/RIGID/fix_rigid_nh.cpp | 6 ++++-- src/RIGID/fix_rigid_nh.h | 2 -- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 6fb2bd7a94..4dec04370e 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -234,8 +234,6 @@ void FixRigidNH::init() } g_f = nf_t + nf_r; - onednft = 1.0 + (double)(dimension) / (double)g_f; - onednfr = (double) (dimension) / (double)g_f; // see Table 1 in Kamberaj et al @@ -719,6 +717,8 @@ void FixRigidNH::final_integrate() void FixRigidNH::nhc_temp_integrate() { + if (g_f == 0) return; + int i,j,k; double kt,gfkt_t,gfkt_r,tmp,ms,s,s2; @@ -1063,6 +1063,8 @@ void FixRigidNH::compute_press_target() void FixRigidNH::nh_epsilon_dot() { + if (g_f == 0) return; + int i; double volume,scale,f_epsilon; diff --git a/src/RIGID/fix_rigid_nh.h b/src/RIGID/fix_rigid_nh.h index a8850413eb..10ad9b24fb 100644 --- a/src/RIGID/fix_rigid_nh.h +++ b/src/RIGID/fix_rigid_nh.h @@ -38,8 +38,6 @@ class FixRigidNH : public FixRigid { double boltz,nktv2p,mvv2e; // boltzman constant, conversion factors int nf_t,nf_r; // trans/rot degrees of freedom - double onednft,onednfr; // factors 1 + dimension/trans(rot) - // degrees of freedom double *w,*wdti1,*wdti2,*wdti4; // Yoshida-Suzuki coefficients double *q_t,*q_r; // trans/rot thermostat masses double *eta_t,*eta_r; // trans/rot thermostat positions From 1fe284dbba8aeb980ce9ef6658bb4b1c4c343ab5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 6 Apr 2021 07:55:43 -0400 Subject: [PATCH 0399/1217] add examples for using fix rigid/nv?/small with fix deposit --- .../in.deposit.molecule.rigid-nve-small | 56 +++++ .../in.deposit.molecule.rigid-nvt-small | 56 +++++ ...r21.deposit.molecule.rigid-nve-small.g++.1 | 218 ++++++++++++++++++ ...r21.deposit.molecule.rigid-nve-small.g++.4 | 218 ++++++++++++++++++ ...r21.deposit.molecule.rigid-nvt-small.g++.1 | 218 ++++++++++++++++++ ...r21.deposit.molecule.rigid-nvt-small.g++.4 | 218 ++++++++++++++++++ 6 files changed, 984 insertions(+) create mode 100644 examples/deposit/in.deposit.molecule.rigid-nve-small create mode 100644 examples/deposit/in.deposit.molecule.rigid-nvt-small create mode 100644 examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.1 create mode 100644 examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.4 create mode 100644 examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.1 create mode 100644 examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.4 diff --git a/examples/deposit/in.deposit.molecule.rigid-nve-small b/examples/deposit/in.deposit.molecule.rigid-nve-small new file mode 100644 index 0000000000..b2af77ac00 --- /dev/null +++ b/examples/deposit/in.deposit.molecule.rigid-nve-small @@ -0,0 +1,56 @@ +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +region slab block 0 5 0 5 8 9 + +group addatoms empty +region mobile block 0 5 0 5 2 INF +group mobile region mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/nve/small molecule mol dimer +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 & + mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type & +# axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type & +# axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 diff --git a/examples/deposit/in.deposit.molecule.rigid-nvt-small b/examples/deposit/in.deposit.molecule.rigid-nvt-small new file mode 100644 index 0000000000..9ceb1b3984 --- /dev/null +++ b/examples/deposit/in.deposit.molecule.rigid-nvt-small @@ -0,0 +1,56 @@ +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +region slab block 0 5 0 5 8 9 + +group addatoms empty +region mobile block 0 5 0 5 2 INF +group mobile region mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/nvt/small molecule temp 0.1 0.1 0.1 mol dimer +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 & + mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type & +# axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type & +# axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.1 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.1 new file mode 100644 index 0000000000..792d3954c1 --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.1 @@ -0,0 +1,218 @@ +LAMMPS (10 Mar 2021) + using 1 OpenMP thread(s) per MPI task +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) + 1 by 1 by 1 MPI processor grid + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate +Created 350 atoms + create_atoms CPU = 0.001 seconds + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +Read molecule template dimer: + 1 molecules + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region slab block 0 5 0 5 8 9 + +group addatoms empty +0 atoms in group addatoms +region mobile block 0 5 0 5 2 INF +group mobile region mobile +150 atoms in group mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/nve/small molecule mol dimer + create bodies CPU = 0.000 seconds + 0 rigid bodies with 0 atoms + 1.0000000 = max distance from body owner to body atom +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468) + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 +WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes +Step Atoms Temp E_pair TotEng Press + 0 350 0 -6.9215833 -6.9215833 -1.0052629 + 100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914 + 200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276 + 300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826 + 400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699 + 500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307 + 600 362 1.026148 -6.7105231 -6.6680032 -0.68314418 + 700 364 1.0683344 -6.6725162 -6.621154 -0.65747369 + 800 366 1.0958953 -6.6412275 -6.5813425 -0.68789615 + 900 368 1.1250034 -6.6101882 -6.541404 -0.66674346 + 1000 370 1.2326365 -6.5993719 -6.5160856 -0.69688655 + 1100 372 1.1397444 -6.5912865 -6.5070312 -0.6333041 + 1200 374 1.0514447 -6.5905753 -6.5062348 -0.71020272 + 1300 376 1.0033284 -6.5747792 -6.4880554 -0.65459641 + 1400 378 0.82996548 -6.5681806 -6.4913319 -0.60438595 + 1500 380 0.90239071 -6.5752982 -6.4862465 -0.66528503 + 1600 382 0.86403681 -6.5692212 -6.4787461 -0.65027922 + 1700 384 0.64748046 -6.5644242 -6.4927629 -0.63046709 + 1800 386 0.74288742 -6.5515741 -6.4649681 -0.67770665 + 1900 388 0.72584537 -6.5565195 -6.4676596 -0.66175025 + 2000 390 0.73351281 -6.5631154 -6.4690753 -0.64686647 + 2100 392 0.76490681 -6.5573734 -6.4549305 -0.68861526 + 2200 394 0.65926638 -6.5511574 -6.4591279 -0.71726284 + 2300 396 0.70267414 -6.5728555 -6.4708258 -0.64360436 + 2400 398 0.60523691 -6.5845973 -6.4933555 -0.63956839 + 2500 400 0.5103586 -6.5812006 -6.5014571 -0.68698448 + 2600 402 0.52401744 -6.6003358 -6.5156066 -0.68987222 + 2700 404 0.46421291 -6.5662747 -6.4887143 -0.72872856 + 2800 406 0.48254258 -6.5724266 -6.4892296 -0.75447872 + 2900 408 0.53073083 -6.5809842 -6.4866754 -0.67592283 + 3000 410 0.55314547 -6.5922077 -6.4910226 -0.74646953 + 3100 412 0.47150308 -6.5907273 -6.5020344 -0.64994935 + 3200 414 0.43047803 -6.5836315 -6.5004473 -0.79764713 + 3300 416 0.46289353 -6.5739439 -6.4821441 -0.76441674 + 3400 418 0.59724106 -6.5980575 -6.4766089 -0.73735626 + 3500 420 0.43571285 -6.5955972 -6.5048237 -0.64145941 + 3600 422 0.42461639 -6.6060271 -6.5154691 -0.70124484 + 3700 424 0.44323254 -6.6059723 -6.5092766 -0.74498147 + 3800 426 0.4037907 -6.592043 -6.5019958 -0.72171799 + 3900 428 0.41668443 -6.5975302 -6.5026079 -0.68327878 + 4000 430 0.44895183 -6.5958671 -6.4914597 -0.73939433 + 4100 432 0.39798052 -6.5952115 -6.5007833 -0.74871822 + 4200 434 0.45156734 -6.6237274 -6.5144772 -0.75111778 + 4300 436 0.48297356 -6.6395283 -6.5204465 -0.76105913 + 4400 438 0.43595234 -6.6347133 -6.5252276 -0.72858275 + 4500 440 0.44683726 -6.6385398 -6.5242916 -0.74280051 + 4600 442 0.47875512 -6.6419903 -6.5174274 -0.75579572 + 4700 444 0.43972605 -6.6406078 -6.5242388 -0.72196509 + 4800 446 0.43572615 -6.6495404 -6.5323047 -0.7135049 + 4900 448 0.38063437 -6.6432385 -6.5391588 -0.77087429 + 5000 450 0.4239223 -6.6617795 -6.5440233 -0.784531 + 5100 452 0.37201988 -6.6581813 -6.5532421 -0.74611403 + 5200 454 0.41765777 -6.6661321 -6.5465385 -0.75422239 + 5300 456 0.38015287 -6.6606624 -6.5502013 -0.78866702 + 5400 458 0.40549607 -6.6807118 -6.5611878 -0.78932883 + 5500 460 0.34444407 -6.6720564 -6.5690976 -0.77859171 + 5600 462 0.36572308 -6.6730078 -6.5621827 -0.85672419 + 5700 464 0.40055073 -6.6976989 -6.574685 -0.74251563 + 5800 466 0.36037213 -6.7022014 -6.5900685 -0.66239625 + 5900 468 0.32810921 -6.6952135 -6.591803 -0.83981757 + 6000 470 0.35110886 -6.6986862 -6.5866302 -0.82474047 + 6100 472 0.29965884 -6.6839503 -6.5871326 -0.7864913 + 6200 474 0.32402637 -6.6902745 -6.5843165 -0.74531083 + 6300 476 0.35042653 -6.6990084 -6.5830585 -0.74839967 + 6400 478 0.32695511 -6.6909459 -6.5815048 -0.76549489 + 6500 480 0.35209088 -6.6902987 -6.5711013 -0.71281516 + 6600 482 0.354106 -6.6890268 -6.567808 -0.81897158 + 6700 484 0.3504816 -6.681739 -6.5604463 -0.811609 + 6800 486 0.37396733 -6.7018369 -6.5710253 -0.80383296 + 6900 488 0.36435774 -6.7010114 -6.5722169 -0.72063651 + 7000 490 0.35631012 -6.7089806 -6.581727 -0.74152078 + 7100 492 0.37646659 -6.719154 -6.5833352 -0.77739001 + 7200 494 0.36546269 -6.7223269 -6.5891623 -0.8288767 + 7300 496 0.37688206 -6.7457243 -6.607053 -0.80062121 + 7400 498 0.30331409 -6.7284953 -6.6158184 -0.79894584 + 7500 500 0.30382936 -6.7333804 -6.6194444 -0.86924602 + 7600 502 0.30163143 -6.7294737 -6.6153104 -0.7689497 + 7700 504 0.30281215 -6.7233976 -6.6077402 -0.8557548 + 7800 506 0.33378009 -6.7244958 -6.5958651 -0.82584084 + 7900 508 0.31843128 -6.7250998 -6.6013002 -0.82424684 + 8000 510 0.35912946 -6.7399052 -6.5990701 -0.81879575 + 8100 512 0.31405017 -6.733487 -6.6092777 -0.72940457 + 8200 514 0.30475 -6.7271485 -6.6056043 -0.87958287 + 8300 516 0.30717434 -6.7277574 -6.6042329 -0.81700937 + 8400 518 0.33032462 -6.7382165 -6.6043011 -0.75436496 + 8500 520 0.32218568 -6.7351971 -6.6035347 -0.77661738 + 8600 522 0.30922651 -6.7275431 -6.6001797 -0.85334327 + 8700 524 0.30728021 -6.7237477 -6.5962029 -0.94977016 + 8800 526 0.31061903 -6.7181672 -6.5882505 -0.86132456 + 8900 528 0.33543344 -6.728929 -6.5875768 -0.87545919 + 9000 530 0.31887735 -6.7265066 -6.5911341 -0.76892061 + 9100 532 0.31888326 -6.7216274 -6.5852629 -0.83190298 + 9200 534 0.33310892 -6.7111349 -6.567661 -0.94282671 + 9300 536 0.34737171 -6.722515 -6.5718361 -0.95235602 + 9400 538 0.32752858 -6.7246204 -6.5815549 -0.86227131 + 9500 540 0.30665764 -6.7225391 -6.5876665 -0.87144326 + 9600 542 0.32747382 -6.7149245 -6.5699176 -0.86863105 + 9700 544 0.32463079 -6.7205757 -6.5758643 -0.85393932 + 9800 546 0.31517825 -6.7178961 -6.5764699 -0.81017759 + 9900 548 0.33649933 -6.7380644 -6.5860871 -0.80769312 + 10000 550 0.37394555 -6.7612874 -6.5913121 -0.82102213 +Loop time of 16.7275 on 1 procs for 10000 steps with 550 atoms + +Performance: 258256.688 tau/day, 597.816 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.2508 | 9.2508 | 9.2508 | 0.0 | 55.30 +Bond | 0.021603 | 0.021603 | 0.021603 | 0.0 | 0.13 +Neigh | 4.5325 | 4.5325 | 4.5325 | 0.0 | 27.10 +Comm | 0.62777 | 0.62777 | 0.62777 | 0.0 | 3.75 +Output | 0.006916 | 0.006916 | 0.006916 | 0.0 | 0.04 +Modify | 2.218 | 2.218 | 2.218 | 0.0 | 13.26 +Other | | 0.07002 | | | 0.42 + +Nlocal: 550.000 ave 550 max 550 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2344.00 ave 2344 max 2344 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 36607.0 ave 36607 max 36607 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 36607 +Ave neighs/atom = 66.558182 +Ave special neighs/atom = 0.36363636 +Neighbor list builds = 847 +Dangerous builds = 0 +Total wall time: 0:00:16 diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.4 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.4 new file mode 100644 index 0000000000..e9158cd7ec --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.4 @@ -0,0 +1,218 @@ +LAMMPS (10 Mar 2021) + using 1 OpenMP thread(s) per MPI task +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) + 1 by 1 by 4 MPI processor grid + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate +Created 350 atoms + create_atoms CPU = 0.002 seconds + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +Read molecule template dimer: + 1 molecules + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region slab block 0 5 0 5 8 9 + +group addatoms empty +0 atoms in group addatoms +region mobile block 0 5 0 5 2 INF +group mobile region mobile +150 atoms in group mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/nve/small molecule mol dimer + create bodies CPU = 0.000 seconds + 0 rigid bodies with 0 atoms + 1.0000000 = max distance from body owner to body atom +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468) + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 +WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes +Step Atoms Temp E_pair TotEng Press + 0 350 0 -6.9215833 -6.9215833 -1.0052629 + 100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337 + 200 354 1.0081552 -6.8645575 -6.850318 -0.69629729 + 300 356 1.0085803 -6.821677 -6.8004288 -0.69532657 + 400 358 1.0099188 -6.7837923 -6.7555822 -0.68879568 + 500 360 1.0140221 -6.7446709 -6.7094618 -0.72991641 + 600 362 1.026146 -6.7129201 -6.6704003 -0.67063836 + 700 364 1.0683193 -6.6776523 -6.6262908 -0.65572472 + 800 366 1.0958894 -6.6402029 -6.5803182 -0.66307282 + 900 368 1.1231769 -6.6050912 -6.5364187 -0.64076928 + 1000 370 1.1976289 -6.5942508 -6.51333 -0.69249047 + 1100 372 1.05061 -6.5772306 -6.4995645 -0.6307289 + 1200 374 0.93723829 -6.5732962 -6.4981166 -0.64963821 + 1300 376 0.93899122 -6.5578418 -6.476679 -0.65096688 + 1400 378 0.87050694 -6.546852 -6.4662495 -0.67613401 + 1500 380 0.84462904 -6.5400883 -6.4567368 -0.64376986 + 1600 382 0.92417795 -6.5611292 -6.4643567 -0.62092779 + 1700 384 0.67296541 -6.5589985 -6.4845167 -0.6779111 + 1800 386 0.87159158 -6.5655058 -6.4638954 -0.6582786 + 1900 388 0.67504975 -6.5772537 -6.4946123 -0.665098 + 2000 390 0.65034978 -6.5717854 -6.4884072 -0.73162072 + 2100 392 0.63389859 -6.5652907 -6.4803935 -0.64937411 + 2200 394 0.6265637 -6.5582412 -6.4707767 -0.70819854 + 2300 396 0.85352983 -6.5750751 -6.4511408 -0.69995918 + 2400 398 0.69792348 -6.5938659 -6.4886513 -0.63755214 + 2500 400 0.45320495 -6.595022 -6.5242087 -0.70462183 + 2600 402 0.46824374 -6.5697613 -6.4940502 -0.75497893 + 2700 404 0.46605975 -6.5599272 -6.4820583 -0.66778506 + 2800 406 0.50637604 -6.5700492 -6.482743 -0.63812082 + 2900 408 0.55335921 -6.5873352 -6.4890054 -0.62891652 + 3000 410 0.51731142 -6.5890566 -6.4944264 -0.64305355 + 3100 412 0.59439734 -6.6003127 -6.4885025 -0.67140541 + 3200 414 0.53413632 -6.595564 -6.4923492 -0.76242248 + 3300 416 0.49221593 -6.5990831 -6.5014681 -0.71330819 + 3400 418 0.55006126 -6.6015725 -6.4897179 -0.72044309 + 3500 420 0.49065348 -6.6329864 -6.5307669 -0.65775397 + 3600 422 0.41907335 -6.6219753 -6.5325995 -0.75936391 + 3700 424 0.38720116 -6.6153349 -6.5308629 -0.74166397 + 3800 426 0.40625994 -6.6150209 -6.5244231 -0.7595111 + 3900 428 0.40460547 -6.6122642 -6.5200936 -0.70484465 + 4000 430 0.45014991 -6.6254404 -6.5207544 -0.70069933 + 4100 432 0.44820466 -6.640222 -6.5338771 -0.805972 + 4200 434 0.39767521 -6.6450316 -6.5488199 -0.72841414 + 4300 436 0.4155331 -6.6547917 -6.5523381 -0.6894484 + 4400 438 0.43034353 -6.6615074 -6.5534303 -0.74026062 + 4500 440 0.38062977 -6.6541618 -6.5568417 -0.85911194 + 4600 442 0.39357419 -6.6522517 -6.5498512 -0.66232114 + 4700 444 0.40296801 -6.6647029 -6.5580616 -0.67307577 + 4800 446 0.38194993 -6.6510248 -6.548258 -0.77887746 + 4900 448 0.40739835 -6.6601751 -6.5487771 -0.84146416 + 5000 450 0.38392807 -6.6560665 -6.5494198 -0.77343399 + 5100 452 0.35209286 -6.6481476 -6.5488294 -0.68065755 + 5200 454 0.41355143 -6.6615988 -6.543181 -0.81611092 + 5300 456 0.42200484 -6.6627494 -6.5401273 -0.7774134 + 5400 458 0.37764326 -6.661431 -6.550117 -0.72187808 + 5500 460 0.41857405 -6.6674232 -6.542306 -0.74929745 + 5600 462 0.41682611 -6.6710961 -6.5447852 -0.7557454 + 5700 464 0.44396148 -6.6924346 -6.5560887 -0.78018312 + 5800 466 0.37058077 -6.6865013 -6.5711919 -0.74146125 + 5900 468 0.346812 -6.681215 -6.57191 -0.81184233 + 6000 470 0.34919462 -6.6827931 -6.571348 -0.87330821 + 6100 472 0.39360936 -6.6933359 -6.5661634 -0.79237598 + 6200 474 0.33270778 -6.6847095 -6.5759127 -0.77978526 + 6300 476 0.35973804 -6.6951254 -6.5760944 -0.80340174 + 6400 478 0.38124318 -6.7045984 -6.5769857 -0.81628407 + 6500 480 0.41188302 -6.7133356 -6.573896 -0.7940289 + 6600 482 0.36998039 -6.7079555 -6.5813025 -0.75055442 + 6700 484 0.37615026 -6.722917 -6.592741 -0.76534055 + 6800 486 0.3466597 -6.7188712 -6.5976116 -0.77986211 + 6900 488 0.32902492 -6.7247054 -6.6084005 -0.75702458 + 7000 490 0.31856427 -6.7167709 -6.6029979 -0.76014555 + 7100 492 0.30233891 -6.7144406 -6.6053651 -0.96246708 + 7200 494 0.32557309 -6.7315347 -6.6129049 -0.8122153 + 7300 496 0.29919611 -6.7186327 -6.6085455 -0.71917931 + 7400 498 0.29778169 -6.7259455 -6.6153238 -0.88199391 + 7500 500 0.35535305 -6.7419073 -6.6086499 -0.90344083 + 7600 502 0.31979187 -6.7326802 -6.6116434 -0.78324572 + 7700 504 0.30821359 -6.72895 -6.6112295 -0.81363335 + 7800 506 0.31374993 -6.7255461 -6.6046346 -0.89904197 + 7900 508 0.29072338 -6.7177355 -6.6047082 -0.81423073 + 8000 510 0.30557494 -6.7208283 -6.600995 -0.85853575 + 8100 512 0.30521237 -6.726874 -6.6061601 -0.75361257 + 8200 514 0.29622226 -6.7152225 -6.5970794 -0.85766132 + 8300 516 0.28337698 -6.7023552 -6.5884003 -0.8985415 + 8400 518 0.32860902 -6.7211074 -6.5878875 -0.89758921 + 8500 520 0.35483743 -6.7406183 -6.5956126 -0.77602077 + 8600 522 0.32928486 -6.7326607 -6.5970358 -0.75070137 + 8700 524 0.36008106 -6.7474714 -6.5980103 -0.87093836 + 8800 526 0.36082301 -6.743579 -6.5926644 -0.90132107 + 8900 528 0.35010285 -6.7501553 -6.6026214 -0.85238959 + 9000 530 0.31513985 -6.7411795 -6.6073937 -0.75884529 + 9100 532 0.30895083 -6.7421063 -6.6099891 -0.74482692 + 9200 534 0.33631849 -6.751265 -6.6064087 -0.95632911 + 9300 536 0.33306096 -6.759187 -6.6147156 -0.76275935 + 9400 538 0.34582537 -6.7706766 -6.619619 -0.72251598 + 9500 540 0.32003146 -6.772057 -6.6313024 -0.88195851 + 9600 542 0.32439637 -6.7743569 -6.6307127 -0.90233104 + 9700 544 0.33988235 -6.7763721 -6.624862 -0.85185581 + 9800 546 0.32877587 -6.7744977 -6.62697 -0.8550905 + 9900 548 0.29570051 -6.7623752 -6.6288243 -1.0371157 + 10000 550 0.33675914 -6.7757315 -6.6226591 -1.0082157 +Loop time of 16.2553 on 4 procs for 10000 steps with 550 atoms + +Performance: 265759.101 tau/day, 615.183 timesteps/s +97.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0034051 | 2.6646 | 8.0317 | 200.7 | 16.39 +Bond | 0.0022626 | 0.0072971 | 0.019437 | 8.3 | 0.04 +Neigh | 0.018657 | 1.218 | 3.7621 | 137.5 | 7.49 +Comm | 1.1497 | 6.7957 | 12.192 | 164.2 | 41.81 +Output | 0.010692 | 0.01431 | 0.019901 | 3.2 | 0.09 +Modify | 3.1502 | 5.3779 | 11.342 | 149.0 | 33.08 +Other | | 0.1775 | | | 1.09 + +Nlocal: 137.500 ave 299 max 2 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1903.75 ave 2686 max 529 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Neighs: 9209.75 ave 23206 max 0 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 36839 +Ave neighs/atom = 66.980000 +Ave special neighs/atom = 0.36363636 +Neighbor list builds = 829 +Dangerous builds = 0 +Total wall time: 0:00:16 diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.1 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.1 new file mode 100644 index 0000000000..5abc557d8b --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.1 @@ -0,0 +1,218 @@ +LAMMPS (10 Mar 2021) + using 1 OpenMP thread(s) per MPI task +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) + 1 by 1 by 1 MPI processor grid + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate +Created 350 atoms + create_atoms CPU = 0.001 seconds + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +Read molecule template dimer: + 1 molecules + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region slab block 0 5 0 5 8 9 + +group addatoms empty +0 atoms in group addatoms +region mobile block 0 5 0 5 2 INF +group mobile region mobile +150 atoms in group mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/nvt/small molecule temp 0.1 0.1 0.1 mol dimer + create bodies CPU = 0.000 seconds + 0 rigid bodies with 0 atoms + 1.0000000 = max distance from body owner to body atom +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468) + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 +WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes +Step Atoms Temp E_pair TotEng Press + 0 350 0 -6.9215833 -6.9215833 -1.0052629 + 100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914 + 200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276 + 300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826 + 400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699 + 500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307 + 600 362 1.026148 -6.7105231 -6.6680032 -0.68314418 + 700 364 1.0683344 -6.6725162 -6.621154 -0.65747369 + 800 366 1.0958953 -6.6412275 -6.5813425 -0.68789615 + 900 368 1.1250034 -6.6101882 -6.541404 -0.66674346 + 1000 370 1.2326365 -6.5993719 -6.5160856 -0.69688655 + 1100 372 1.1397444 -6.5912865 -6.5070312 -0.6333041 + 1200 374 1.0514447 -6.5905753 -6.5062348 -0.71020272 + 1300 376 1.0033284 -6.5747792 -6.4880554 -0.65459641 + 1400 378 0.82996548 -6.5681806 -6.4913319 -0.60438595 + 1500 380 0.90239071 -6.5752982 -6.4862465 -0.66528503 + 1600 382 0.86403681 -6.5692212 -6.4787461 -0.65027922 + 1700 384 0.64748046 -6.5644242 -6.4927629 -0.63046709 + 1800 386 0.74288742 -6.5515741 -6.4649681 -0.67770665 + 1900 388 0.72584537 -6.5565195 -6.4676596 -0.66175025 + 2000 390 0.73351281 -6.5631154 -6.4690753 -0.64686647 + 2100 392 0.76490681 -6.5573734 -6.4549305 -0.68861526 + 2200 394 0.65926638 -6.5511574 -6.4591279 -0.71726284 + 2300 396 0.70267414 -6.5728555 -6.4708258 -0.64360436 + 2400 398 0.60523691 -6.5845973 -6.4933555 -0.63956839 + 2500 400 0.5103586 -6.5812006 -6.5014571 -0.68698448 + 2600 402 0.52401744 -6.6003358 -6.5156066 -0.68987222 + 2700 404 0.46421291 -6.5662747 -6.4887143 -0.72872856 + 2800 406 0.48254258 -6.5724266 -6.4892296 -0.75447872 + 2900 408 0.53073083 -6.5809842 -6.4866754 -0.67592283 + 3000 410 0.55314547 -6.5922077 -6.4910226 -0.74646953 + 3100 412 0.47150308 -6.5907273 -6.5020344 -0.64994935 + 3200 414 0.43047803 -6.5836315 -6.5004473 -0.79764713 + 3300 416 0.46289353 -6.5739439 -6.4821441 -0.76441674 + 3400 418 0.59724106 -6.5980575 -6.4766089 -0.73735626 + 3500 420 0.43571285 -6.5955972 -6.5048237 -0.64145941 + 3600 422 0.42461639 -6.6060271 -6.5154691 -0.70124484 + 3700 424 0.44323254 -6.6059723 -6.5092766 -0.74498147 + 3800 426 0.4037907 -6.592043 -6.5019958 -0.72171799 + 3900 428 0.41668443 -6.5975302 -6.5026079 -0.68327878 + 4000 430 0.44895183 -6.5958671 -6.4914597 -0.73939433 + 4100 432 0.39798052 -6.5952115 -6.5007833 -0.74871822 + 4200 434 0.45156734 -6.6237274 -6.5144772 -0.75111778 + 4300 436 0.48297356 -6.6395283 -6.5204465 -0.76105913 + 4400 438 0.43595234 -6.6347133 -6.5252276 -0.72858275 + 4500 440 0.44683726 -6.6385398 -6.5242916 -0.74280051 + 4600 442 0.47875512 -6.6419903 -6.5174274 -0.75579572 + 4700 444 0.43972605 -6.6406078 -6.5242388 -0.72196509 + 4800 446 0.43572615 -6.6495404 -6.5323047 -0.7135049 + 4900 448 0.38063437 -6.6432385 -6.5391588 -0.77087429 + 5000 450 0.4239223 -6.6617795 -6.5440233 -0.784531 + 5100 452 0.37201988 -6.6581813 -6.5532421 -0.74611403 + 5200 454 0.41765777 -6.6661321 -6.5465385 -0.75422239 + 5300 456 0.38015287 -6.6606624 -6.5502013 -0.78866702 + 5400 458 0.40549607 -6.6807118 -6.5611878 -0.78932883 + 5500 460 0.34444407 -6.6720564 -6.5690976 -0.77859171 + 5600 462 0.36572308 -6.6730078 -6.5621827 -0.85672419 + 5700 464 0.40055073 -6.6976989 -6.574685 -0.74251563 + 5800 466 0.36037213 -6.7022014 -6.5900685 -0.66239625 + 5900 468 0.32810921 -6.6952135 -6.591803 -0.83981757 + 6000 470 0.35110886 -6.6986862 -6.5866302 -0.82474047 + 6100 472 0.29965884 -6.6839503 -6.5871326 -0.7864913 + 6200 474 0.32402637 -6.6902745 -6.5843165 -0.74531083 + 6300 476 0.35042653 -6.6990084 -6.5830585 -0.74839967 + 6400 478 0.32695511 -6.6909459 -6.5815048 -0.76549489 + 6500 480 0.35209088 -6.6902987 -6.5711013 -0.71281516 + 6600 482 0.354106 -6.6890268 -6.567808 -0.81897158 + 6700 484 0.3504816 -6.681739 -6.5604463 -0.811609 + 6800 486 0.37396733 -6.7018369 -6.5710253 -0.80383296 + 6900 488 0.36435774 -6.7010114 -6.5722169 -0.72063651 + 7000 490 0.35631012 -6.7089806 -6.581727 -0.74152078 + 7100 492 0.37646659 -6.719154 -6.5833352 -0.77739001 + 7200 494 0.36546269 -6.7223269 -6.5891623 -0.8288767 + 7300 496 0.37688206 -6.7457243 -6.607053 -0.80062121 + 7400 498 0.30331409 -6.7284953 -6.6158184 -0.79894584 + 7500 500 0.30382936 -6.7333804 -6.6194444 -0.86924602 + 7600 502 0.30163143 -6.7294737 -6.6153104 -0.7689497 + 7700 504 0.30281215 -6.7233976 -6.6077402 -0.8557548 + 7800 506 0.33378009 -6.7244958 -6.5958651 -0.82584084 + 7900 508 0.31843128 -6.7250998 -6.6013002 -0.82424684 + 8000 510 0.35912946 -6.7399052 -6.5990701 -0.81879575 + 8100 512 0.31405017 -6.733487 -6.6092777 -0.72940457 + 8200 514 0.30475 -6.7271485 -6.6056043 -0.87958287 + 8300 516 0.30717434 -6.7277574 -6.6042329 -0.81700937 + 8400 518 0.33032462 -6.7382165 -6.6043011 -0.75436496 + 8500 520 0.32218568 -6.7351971 -6.6035347 -0.77661738 + 8600 522 0.30922651 -6.7275431 -6.6001797 -0.85334327 + 8700 524 0.30728021 -6.7237477 -6.5962029 -0.94977016 + 8800 526 0.31061903 -6.7181672 -6.5882505 -0.86132456 + 8900 528 0.33543344 -6.728929 -6.5875768 -0.87545919 + 9000 530 0.31887735 -6.7265066 -6.5911341 -0.76892061 + 9100 532 0.31888326 -6.7216274 -6.5852629 -0.83190298 + 9200 534 0.33310892 -6.7111349 -6.567661 -0.94282671 + 9300 536 0.34737171 -6.722515 -6.5718361 -0.95235602 + 9400 538 0.32752858 -6.7246204 -6.5815549 -0.86227131 + 9500 540 0.30665764 -6.7225391 -6.5876665 -0.87144326 + 9600 542 0.32747382 -6.7149245 -6.5699176 -0.86863105 + 9700 544 0.32463079 -6.7205757 -6.5758643 -0.85393932 + 9800 546 0.31517825 -6.7178961 -6.5764699 -0.81017759 + 9900 548 0.33649933 -6.7380644 -6.5860871 -0.80769312 + 10000 550 0.37394555 -6.7612874 -6.5913121 -0.82102213 +Loop time of 16.6615 on 1 procs for 10000 steps with 550 atoms + +Performance: 259279.806 tau/day, 600.185 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.2639 | 9.2639 | 9.2639 | 0.0 | 55.60 +Bond | 0.021559 | 0.021559 | 0.021559 | 0.0 | 0.13 +Neigh | 4.544 | 4.544 | 4.544 | 0.0 | 27.27 +Comm | 0.62792 | 0.62792 | 0.62792 | 0.0 | 3.77 +Output | 0.0069666 | 0.0069666 | 0.0069666 | 0.0 | 0.04 +Modify | 2.1282 | 2.1282 | 2.1282 | 0.0 | 12.77 +Other | | 0.06897 | | | 0.41 + +Nlocal: 550.000 ave 550 max 550 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2344.00 ave 2344 max 2344 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 36607.0 ave 36607 max 36607 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 36607 +Ave neighs/atom = 66.558182 +Ave special neighs/atom = 0.36363636 +Neighbor list builds = 847 +Dangerous builds = 0 +Total wall time: 0:00:16 diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.4 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.4 new file mode 100644 index 0000000000..7239fc9bb9 --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.4 @@ -0,0 +1,218 @@ +LAMMPS (10 Mar 2021) + using 1 OpenMP thread(s) per MPI task +# sample surface deposition script for molecules + +units lj +atom_style bond +boundary p p f + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 +region box block 0 5 0 5 0 10 +create_box 3 box bond/types 1 extra/bond/per/atom 1 +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) + 1 by 1 by 4 MPI processor grid + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate +Created 350 atoms + create_atoms CPU = 0.002 seconds + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 1.0 1.0 5.0 +mass * 1.0 + +bond_style harmonic +bond_coeff 1 5.0 1.0 + +neigh_modify delay 0 + +molecule dimer molecule.dimer +Read molecule template dimer: + 1 molecules + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region slab block 0 5 0 5 8 9 + +group addatoms empty +0 atoms in group addatoms +region mobile block 0 5 0 5 2 INF +group mobile region mobile +150 atoms in group mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/nvt/small molecule temp 0.1 0.1 0.1 mol dimer + create bodies CPU = 0.000 seconds + 0 rigid bodies with 0 atoms + 1.0000000 = max distance from body owner to body atom +fix 2 mobile langevin 0.1 0.1 0.1 587283 +fix 3 mobile nve + +fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1 +fix 5 addatoms wall/reflect zhi EDGE + +thermo_style custom step atoms temp epair etotal press +thermo 100 +thermo_modify temp add lost/bond ignore lost warn +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468) + +#dump 1 all atom 50 dump.deposit.atom + +#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30 +#dump_modify 3 pad 5 + +run 10000 +WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes +Step Atoms Temp E_pair TotEng Press + 0 350 0 -6.9215833 -6.9215833 -1.0052629 + 100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337 + 200 354 1.0081552 -6.8645575 -6.850318 -0.69629729 + 300 356 1.0085803 -6.821677 -6.8004288 -0.69532657 + 400 358 1.0099188 -6.7837923 -6.7555822 -0.68879568 + 500 360 1.0140221 -6.7446709 -6.7094618 -0.72991641 + 600 362 1.026146 -6.7129201 -6.6704003 -0.67063836 + 700 364 1.0683193 -6.6776523 -6.6262908 -0.65572472 + 800 366 1.0958894 -6.6402029 -6.5803182 -0.66307282 + 900 368 1.1231769 -6.6050912 -6.5364187 -0.64076928 + 1000 370 1.1976289 -6.5942508 -6.51333 -0.69249047 + 1100 372 1.05061 -6.5772306 -6.4995645 -0.6307289 + 1200 374 0.93723829 -6.5732962 -6.4981166 -0.64963821 + 1300 376 0.93899122 -6.5578418 -6.476679 -0.65096688 + 1400 378 0.87050694 -6.546852 -6.4662495 -0.67613401 + 1500 380 0.84462904 -6.5400883 -6.4567368 -0.64376986 + 1600 382 0.92417795 -6.5611292 -6.4643567 -0.62092779 + 1700 384 0.67296541 -6.5589985 -6.4845167 -0.6779111 + 1800 386 0.87159158 -6.5655058 -6.4638954 -0.6582786 + 1900 388 0.67504975 -6.5772537 -6.4946123 -0.665098 + 2000 390 0.65034978 -6.5717854 -6.4884072 -0.73162072 + 2100 392 0.63389859 -6.5652907 -6.4803935 -0.64937411 + 2200 394 0.6265637 -6.5582412 -6.4707767 -0.70819854 + 2300 396 0.85352983 -6.5750751 -6.4511408 -0.69995918 + 2400 398 0.69792348 -6.5938659 -6.4886513 -0.63755214 + 2500 400 0.45320495 -6.595022 -6.5242087 -0.70462183 + 2600 402 0.46824374 -6.5697613 -6.4940502 -0.75497893 + 2700 404 0.46605975 -6.5599272 -6.4820583 -0.66778506 + 2800 406 0.50637604 -6.5700492 -6.482743 -0.63812082 + 2900 408 0.55335921 -6.5873352 -6.4890054 -0.62891652 + 3000 410 0.51731142 -6.5890566 -6.4944264 -0.64305355 + 3100 412 0.59439734 -6.6003127 -6.4885025 -0.67140541 + 3200 414 0.53413632 -6.595564 -6.4923492 -0.76242248 + 3300 416 0.49221593 -6.5990831 -6.5014681 -0.71330819 + 3400 418 0.55006126 -6.6015725 -6.4897179 -0.72044309 + 3500 420 0.49065348 -6.6329864 -6.5307669 -0.65775397 + 3600 422 0.41907335 -6.6219753 -6.5325995 -0.75936391 + 3700 424 0.38720116 -6.6153349 -6.5308629 -0.74166397 + 3800 426 0.40625994 -6.6150209 -6.5244231 -0.7595111 + 3900 428 0.40460547 -6.6122642 -6.5200936 -0.70484465 + 4000 430 0.45014991 -6.6254404 -6.5207544 -0.70069933 + 4100 432 0.44820466 -6.640222 -6.5338771 -0.805972 + 4200 434 0.39767521 -6.6450316 -6.5488199 -0.72841414 + 4300 436 0.4155331 -6.6547917 -6.5523381 -0.6894484 + 4400 438 0.43034353 -6.6615074 -6.5534303 -0.74026062 + 4500 440 0.38062977 -6.6541618 -6.5568417 -0.85911194 + 4600 442 0.39357419 -6.6522517 -6.5498512 -0.66232114 + 4700 444 0.40296801 -6.6647029 -6.5580616 -0.67307577 + 4800 446 0.38194993 -6.6510248 -6.548258 -0.77887746 + 4900 448 0.40739835 -6.6601751 -6.5487771 -0.84146416 + 5000 450 0.38392807 -6.6560665 -6.5494198 -0.77343399 + 5100 452 0.35209286 -6.6481476 -6.5488294 -0.68065755 + 5200 454 0.41355143 -6.6615988 -6.543181 -0.81611092 + 5300 456 0.42200484 -6.6627494 -6.5401273 -0.7774134 + 5400 458 0.37764326 -6.661431 -6.550117 -0.72187808 + 5500 460 0.41857405 -6.6674232 -6.542306 -0.74929745 + 5600 462 0.41682611 -6.6710961 -6.5447852 -0.7557454 + 5700 464 0.44396148 -6.6924346 -6.5560887 -0.78018312 + 5800 466 0.37058077 -6.6865013 -6.5711919 -0.74146125 + 5900 468 0.346812 -6.681215 -6.57191 -0.81184233 + 6000 470 0.34919462 -6.6827931 -6.571348 -0.87330821 + 6100 472 0.39360936 -6.6933359 -6.5661634 -0.79237598 + 6200 474 0.33270778 -6.6847095 -6.5759127 -0.77978526 + 6300 476 0.35973804 -6.6951254 -6.5760944 -0.80340174 + 6400 478 0.38124318 -6.7045984 -6.5769857 -0.81628407 + 6500 480 0.41188302 -6.7133356 -6.573896 -0.7940289 + 6600 482 0.36998039 -6.7079555 -6.5813025 -0.75055442 + 6700 484 0.37615026 -6.722917 -6.592741 -0.76534055 + 6800 486 0.3466597 -6.7188712 -6.5976116 -0.77986211 + 6900 488 0.32902492 -6.7247054 -6.6084005 -0.75702458 + 7000 490 0.31856427 -6.7167709 -6.6029979 -0.76014555 + 7100 492 0.30233891 -6.7144406 -6.6053651 -0.96246708 + 7200 494 0.32557309 -6.7315347 -6.6129049 -0.8122153 + 7300 496 0.29919611 -6.7186327 -6.6085455 -0.71917931 + 7400 498 0.29778169 -6.7259455 -6.6153238 -0.88199391 + 7500 500 0.35535305 -6.7419073 -6.6086499 -0.90344083 + 7600 502 0.31979187 -6.7326802 -6.6116434 -0.78324572 + 7700 504 0.30821359 -6.72895 -6.6112295 -0.81363335 + 7800 506 0.31374993 -6.7255461 -6.6046346 -0.89904197 + 7900 508 0.29072338 -6.7177355 -6.6047082 -0.81423073 + 8000 510 0.30557494 -6.7208283 -6.600995 -0.85853575 + 8100 512 0.30521237 -6.726874 -6.6061601 -0.75361257 + 8200 514 0.29622226 -6.7152225 -6.5970794 -0.85766132 + 8300 516 0.28337698 -6.7023552 -6.5884003 -0.8985415 + 8400 518 0.32860902 -6.7211074 -6.5878875 -0.89758921 + 8500 520 0.35483743 -6.7406183 -6.5956126 -0.77602077 + 8600 522 0.32928486 -6.7326607 -6.5970358 -0.75070137 + 8700 524 0.36008106 -6.7474714 -6.5980103 -0.87093836 + 8800 526 0.36082301 -6.743579 -6.5926644 -0.90132107 + 8900 528 0.35010285 -6.7501553 -6.6026214 -0.85238959 + 9000 530 0.31513985 -6.7411795 -6.6073937 -0.75884529 + 9100 532 0.30895083 -6.7421063 -6.6099891 -0.74482692 + 9200 534 0.33631849 -6.751265 -6.6064087 -0.95632911 + 9300 536 0.33306096 -6.759187 -6.6147156 -0.76275935 + 9400 538 0.34582537 -6.7706766 -6.619619 -0.72251598 + 9500 540 0.32003146 -6.772057 -6.6313024 -0.88195851 + 9600 542 0.32439637 -6.7743569 -6.6307127 -0.90233104 + 9700 544 0.33988235 -6.7763721 -6.624862 -0.85185581 + 9800 546 0.32877587 -6.7744977 -6.62697 -0.8550905 + 9900 548 0.29570051 -6.7623752 -6.6288243 -1.0371157 + 10000 550 0.33675914 -6.7757315 -6.6226591 -1.0082157 +Loop time of 16.1559 on 4 procs for 10000 steps with 550 atoms + +Performance: 267395.139 tau/day, 618.970 timesteps/s +96.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0035574 | 2.5467 | 7.5373 | 192.6 | 15.76 +Bond | 0.0022929 | 0.0073138 | 0.019471 | 8.3 | 0.05 +Neigh | 0.018645 | 1.2357 | 3.8167 | 138.4 | 7.65 +Comm | 1.1946 | 6.6335 | 11.87 | 158.8 | 41.06 +Output | 0.010714 | 0.014391 | 0.020006 | 3.2 | 0.09 +Modify | 3.4474 | 5.6081 | 11.47 | 143.2 | 34.71 +Other | | 0.1102 | | | 0.68 + +Nlocal: 137.500 ave 299 max 2 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1903.75 ave 2686 max 529 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Neighs: 9209.75 ave 23206 max 0 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 36839 +Ave neighs/atom = 66.980000 +Ave special neighs/atom = 0.36363636 +Neighbor list builds = 829 +Dangerous builds = 0 +Total wall time: 0:00:16 From 11d62b71c382ef202cee84602e35984b3e0b98a7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 6 Apr 2021 11:11:01 -0400 Subject: [PATCH 0400/1217] use clang preset when compiling on MacOS --- .github/workflows/unittest-macos.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/unittest-macos.yml b/.github/workflows/unittest-macos.yml index a65db7636b..f62b3046c9 100644 --- a/.github/workflows/unittest-macos.yml +++ b/.github/workflows/unittest-macos.yml @@ -24,7 +24,9 @@ jobs: shell: bash working-directory: ${{github.workspace}}/build run: | - cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake \ + cmake -C $GITHUB_WORKSPACE/cmake/presets/clang.cmake \ + -C $GITHUB_WORKSPACE/cmake/presets/most.cmake \ + $GITHUB_WORKSPACE/cmake \ -DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON cmake --build . --parallel 2 From 6a99f5b5c54e0385aa314afd1e7f1c3d187196ce Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Tue, 6 Apr 2021 17:24:54 +0200 Subject: [PATCH 0401/1217] WIP: - no auto-download of user-pace src yet - lib/pace/*.cpp,*.h are provided explicitly yet. - implement CMake integration in USER-PACE.cmake and in CMakeLists.txt --- cmake/CMakeLists.txt | 6 +- cmake/Modules/Packages/USER-PACE.cmake | 14 + lib/pace/Install.py | 1 + lib/pace/LICENSE | 674 ++++++++ lib/pace/README | 0 lib/pace/TODO | 30 + lib/pace/ace_abstract_basis.cpp | 184 +++ lib/pace/ace_abstract_basis.h | 169 ++ lib/pace/ace_array2dlm.h | 579 +++++++ lib/pace/ace_arraynd.h | 1949 ++++++++++++++++++++++++ lib/pace/ace_c_basis.cpp | 980 ++++++++++++ lib/pace/ace_c_basis.h | 155 ++ lib/pace/ace_c_basisfunction.h | 251 +++ lib/pace/ace_complex.h | 266 ++++ lib/pace/ace_contigous_array.h | 249 +++ lib/pace/ace_evaluator.cpp | 660 ++++++++ lib/pace/ace_evaluator.h | 230 +++ lib/pace/ace_flatten_basis.cpp | 130 ++ lib/pace/ace_flatten_basis.h | 135 ++ lib/pace/ace_radial.cpp | 566 +++++++ lib/pace/ace_radial.h | 324 ++++ lib/pace/ace_recursive.cpp | 1340 ++++++++++++++++ lib/pace/ace_recursive.h | 247 +++ lib/pace/ace_spherical_cart.cpp | 221 +++ lib/pace/ace_spherical_cart.h | 134 ++ lib/pace/ace_timing.h | 126 ++ lib/pace/ace_types.h | 45 + lib/pace/ace_version.h | 39 + lib/pace/ships_radial.cpp | 388 +++++ lib/pace/ships_radial.h | 158 ++ src/Makefile | 4 +- src/USER-PACE/Install.sh | 68 + src/USER-PACE/LICENSE | 674 ++++++++ src/USER-PACE/pair_pace.cpp | 458 ++++++ src/USER-PACE/pair_pace.h | 97 ++ 35 files changed, 11546 insertions(+), 5 deletions(-) create mode 100644 cmake/Modules/Packages/USER-PACE.cmake create mode 100644 lib/pace/Install.py create mode 100644 lib/pace/LICENSE create mode 100644 lib/pace/README create mode 100644 lib/pace/TODO create mode 100644 lib/pace/ace_abstract_basis.cpp create mode 100644 lib/pace/ace_abstract_basis.h create mode 100644 lib/pace/ace_array2dlm.h create mode 100644 lib/pace/ace_arraynd.h create mode 100644 lib/pace/ace_c_basis.cpp create mode 100644 lib/pace/ace_c_basis.h create mode 100644 lib/pace/ace_c_basisfunction.h create mode 100644 lib/pace/ace_complex.h create mode 100644 lib/pace/ace_contigous_array.h create mode 100644 lib/pace/ace_evaluator.cpp create mode 100644 lib/pace/ace_evaluator.h create mode 100644 lib/pace/ace_flatten_basis.cpp create mode 100644 lib/pace/ace_flatten_basis.h create mode 100644 lib/pace/ace_radial.cpp create mode 100644 lib/pace/ace_radial.h create mode 100644 lib/pace/ace_recursive.cpp create mode 100644 lib/pace/ace_recursive.h create mode 100644 lib/pace/ace_spherical_cart.cpp create mode 100644 lib/pace/ace_spherical_cart.h create mode 100644 lib/pace/ace_timing.h create mode 100644 lib/pace/ace_types.h create mode 100644 lib/pace/ace_version.h create mode 100644 lib/pace/ships_radial.cpp create mode 100644 lib/pace/ships_radial.h create mode 100644 src/USER-PACE/Install.sh create mode 100644 src/USER-PACE/LICENSE create mode 100644 src/USER-PACE/pair_pace.cpp create mode 100644 src/USER-PACE/pair_pace.h diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 21d965ebba..4bd5ea8fec 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -119,7 +119,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF) + USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE) set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP) @@ -382,9 +382,9 @@ else() endif() foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM - USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS) + USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE) if(PKG_${PKG_WITH_INCL}) - include(Packages/${PKG_WITH_INCL}) + include(Packages/${PKG_WITH_INCL}) endif() endforeach() diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/USER-PACE.cmake new file mode 100644 index 0000000000..c9e8e1bcfe --- /dev/null +++ b/cmake/Modules/Packages/USER-PACE.cmake @@ -0,0 +1,14 @@ +set(PACE_EVALUATOR_PATH ${LAMMPS_LIB_SOURCE_DIR}/pace) +message("CMakeLists.txt DEBUG: PACE_EVALUATOR_PATH=${PACE_EVALUATOR_PATH}") +set(PACE_EVALUATOR_SRC_PATH ${PACE_EVALUATOR_PATH}) + +FILE(GLOB PACE_EVALUATOR_SOURCE_FILES ${PACE_EVALUATOR_SRC_PATH}/*.cpp) +set(PACE_EVALUATOR_INCLUDE_DIR ${PACE_EVALUATOR_SRC_PATH}) + + +##### aceevaluator ##### +add_library(aceevaluator ${PACE_EVALUATOR_SOURCE_FILES}) +target_include_directories(aceevaluator PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) +target_compile_options(aceevaluator PRIVATE -O2) +set_target_properties(aceevaluator PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE}) +target_link_libraries(lammps PRIVATE aceevaluator) \ No newline at end of file diff --git a/lib/pace/Install.py b/lib/pace/Install.py new file mode 100644 index 0000000000..f87f5c14cb --- /dev/null +++ b/lib/pace/Install.py @@ -0,0 +1 @@ +# TODO \ No newline at end of file diff --git a/lib/pace/LICENSE b/lib/pace/LICENSE new file mode 100644 index 0000000000..f288702d2f --- /dev/null +++ b/lib/pace/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/lib/pace/README b/lib/pace/README new file mode 100644 index 0000000000..e69de29bb2 diff --git a/lib/pace/TODO b/lib/pace/TODO new file mode 100644 index 0000000000..8021916923 --- /dev/null +++ b/lib/pace/TODO @@ -0,0 +1,30 @@ +[TODO/DONE] pair_pace.cpp and pair_pace.h will have to go into src/USER-PACE and thus also need to conform to our requirements. + +[TODO] also src/USER-PACE would need to have an Install.sh file that integrates the settings from the lib folder into the conventional build process. +[TODO] there would have to be a lib/pace folder for building/interfacing to the library. + +[TODO] how you organize your repo is up to you. a better way to describe what you would have to do is to point you to examples. +which of the examples is relevant depends on what build system you are using for your "PACE" external package. + +If you are using CMake to build it, you can look at the KIM package +If you are using autoconf/automake, you can look at the USER-PLUMED package +If you are using neither (just a plain Makefile), you can look at the VORONOI or QUIP package +The following additional modifications are needed: + +[TODO] lib/pace: needs one or more Makefile.lammps, a README and an Install.py file +[TODO] src/Makefile: needs support for the USER-PACE package and compiling via lib-pace. Also the package needs to be added to the PACKEXT and PACKLIB variables + +[DONE] cmake/Modules/Packages/USER-PACE.cmake needs to be added +[DONE] cmake/CMakeLists.txt needs to include it in case the package is enabled. + +[TODO] doc/src/Build_extra.rst needs to include the build instructions for CMake and traditional make +[TODO] doc/src/Package_user.rst and doc/src/Package_details.rst needs to contain relevant information and links + + +Because of the different build systems, there are different steps required, but each of the examples I've pointed out are tested and used regularly and thus should be working sufficiently well. +Mind you the QUIP package is set up in such a way, that no automatic download is possible and a manual download and compilation is required. So that is the least preferred and least convenient option. + +We are happy to provide more details, but that requires that you first have something that already is following either of the suggested variants, so that we don't have to discuss in all generality. + +I would also suggest to close this pull request here, leave all files in place, but then start a new branch from the current master and then move the few things over you need to retain, +add the build environment files and then start working on getting it to do what it should. \ No newline at end of file diff --git a/lib/pace/ace_abstract_basis.cpp b/lib/pace/ace_abstract_basis.cpp new file mode 100644 index 0000000000..3d8afafdaf --- /dev/null +++ b/lib/pace/ace_abstract_basis.cpp @@ -0,0 +1,184 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Lysogorskiy Yury on 28.04.2020. + +#include "ace_abstract_basis.h" + +////embedding function +////case nemb = 1 only implementation +////F = sign(x)*( ( 1 - exp(-(w*x)^3) )*abs(x)^m + ((1/w)^(m-1))*exp(-(w*x)^3)*abs(x) ) +//// !! no prefactor wpre +void Fexp(DOUBLE_TYPE x, DOUBLE_TYPE m, DOUBLE_TYPE &F, DOUBLE_TYPE &DF) { + DOUBLE_TYPE w = 1.e6; + DOUBLE_TYPE eps = 1e-10; + + DOUBLE_TYPE lambda = pow(1.0 / w, m - 1.0); + if (abs(x) > eps) { + DOUBLE_TYPE g; + DOUBLE_TYPE a = abs(x); + DOUBLE_TYPE am = pow(a, m); + DOUBLE_TYPE w3x3 = pow(w * a, 3); + DOUBLE_TYPE sign_factor = (signbit(x) ? -1 : 1); + if (w3x3 > 30.0) + g = 0.0; + else + g = exp(-w3x3); + + DOUBLE_TYPE omg = 1.0 - g; + F = sign_factor * (omg * am + lambda * g * a); + DOUBLE_TYPE dg = -3.0 * w * w * w * a * a * g; + DF = m * pow(a, m - 1.0) * omg - am * dg + lambda * dg * a + lambda * g; + } else { + F = lambda * x; + DF = lambda; + } +} + + +//Scaled-shifted embedding function +//F = sign(x)*( ( 1 - exp(-(w*x)^3) )*abs(x)^m + ((1/w)^(m-1))*exp(-(w*x)^3)*abs(x) ) +// !! no prefactor wpre +void FexpShiftedScaled(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF) { + DOUBLE_TYPE eps = 1e-10; + DOUBLE_TYPE a, xoff, yoff, nx, exprho; + + if (abs(mexp - 1.0) < eps) { + F = rho; + DF = 1; + } else { + a = abs(rho); + exprho = exp(-a); + nx = 1. / mexp; + xoff = pow(nx, (nx / (1.0 - nx))) * exprho; + yoff = pow(nx, (1 / (1.0 - nx))) * exprho; + DOUBLE_TYPE sign_factor = (signbit(rho) ? -1 : 1); + F = sign_factor * (pow(xoff + a, mexp) - yoff); + DF = yoff + mexp * (-xoff + 1.0) * pow(xoff + a, mexp - 1.); + } +} + +void ACEAbstractBasisSet::inner_cutoff(DOUBLE_TYPE rho_core, DOUBLE_TYPE rho_cut, DOUBLE_TYPE drho_cut, + DOUBLE_TYPE &fcut, DOUBLE_TYPE &dfcut) { + + DOUBLE_TYPE rho_low = rho_cut - drho_cut; + if (rho_core >= rho_cut) { + fcut = 0; + dfcut = 0; + } else if (rho_core <= rho_low) { + fcut = 1; + dfcut = 0; + } else { + fcut = 0.5 * (1 + cos(M_PI * (rho_core - rho_low) / drho_cut)); + dfcut = -0.5 * sin(M_PI * (rho_core - rho_low) / drho_cut) * M_PI / drho_cut; + } +} + +void ACEAbstractBasisSet::FS_values_and_derivatives(Array1D &rhos, DOUBLE_TYPE &value, + Array1D &derivatives, DENSITY_TYPE ndensity) { + DOUBLE_TYPE F, DF = 0, wpre, mexp; + for (int p = 0; p < ndensity; p++) { + wpre = FS_parameters.at(p * ndensity + 0); + mexp = FS_parameters.at(p * ndensity + 1); + if (this->npoti == "FinnisSinclair") + Fexp(rhos(p), mexp, F, DF); + else if (this->npoti == "FinnisSinclairShiftedScaled") + FexpShiftedScaled(rhos(p), mexp, F, DF); + value += F * wpre; // * weight (wpre) + derivatives(p) = DF * wpre;// * weight (wpre) + } +} + +void ACEAbstractBasisSet::_clean() { + + delete[] elements_name; + elements_name = nullptr; + delete radial_functions; + radial_functions = nullptr; +} + +ACEAbstractBasisSet::ACEAbstractBasisSet(const ACEAbstractBasisSet &other) { + ACEAbstractBasisSet::_copy_scalar_memory(other); + ACEAbstractBasisSet::_copy_dynamic_memory(other); +} + +ACEAbstractBasisSet &ACEAbstractBasisSet::operator=(const ACEAbstractBasisSet &other) { + if (this != &other) { + // deallocate old memory + ACEAbstractBasisSet::_clean(); + //copy scalar values + ACEAbstractBasisSet::_copy_scalar_memory(other); + //copy dynamic memory + ACEAbstractBasisSet::_copy_dynamic_memory(other); + } + return *this; +} + +ACEAbstractBasisSet::~ACEAbstractBasisSet() { + ACEAbstractBasisSet::_clean(); +} + +void ACEAbstractBasisSet::_copy_scalar_memory(const ACEAbstractBasisSet &src) { + deltaSplineBins = src.deltaSplineBins; + FS_parameters = src.FS_parameters; + npoti = src.npoti; + + nelements = src.nelements; + rankmax = src.rankmax; + ndensitymax = src.ndensitymax; + nradbase = src.nradbase; + lmax = src.lmax; + nradmax = src.nradmax; + cutoffmax = src.cutoffmax; + + spherical_harmonics = src.spherical_harmonics; + + rho_core_cutoffs = src.rho_core_cutoffs; + drho_core_cutoffs = src.drho_core_cutoffs; + + + E0vals = src.E0vals; +} + +void ACEAbstractBasisSet::_copy_dynamic_memory(const ACEAbstractBasisSet &src) {//allocate new memory + if (src.elements_name == nullptr) + throw runtime_error("Could not copy ACEAbstractBasisSet::elements_name - array not initialized"); + elements_name = new string[nelements]; + //copy + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + elements_name[mu] = src.elements_name[mu]; + } + radial_functions = src.radial_functions->clone(); +} + +SPECIES_TYPE ACEAbstractBasisSet::get_species_index_by_name(const string &elemname) { + for (SPECIES_TYPE t = 0; t < nelements; t++) { + if (this->elements_name[t] == elemname) + return t; + } + return -1; +} \ No newline at end of file diff --git a/lib/pace/ace_abstract_basis.h b/lib/pace/ace_abstract_basis.h new file mode 100644 index 0000000000..165ea9496f --- /dev/null +++ b/lib/pace/ace_abstract_basis.h @@ -0,0 +1,169 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Lysogorskiy Yury on 28.04.2020. + +#ifndef ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H +#define ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H + +#include +#include + +#include "ace_c_basisfunction.h" +#include "ace_contigous_array.h" +#include "ace_radial.h" +#include "ace_spherical_cart.h" +#include "ace_types.h" + +using namespace std; + +/** + * Abstract basis set class + */ +class ACEAbstractBasisSet { +public: + SPECIES_TYPE nelements = 0; ///< number of elements in basis set + RANK_TYPE rankmax = 0; ///< maximum value of rank + DENSITY_TYPE ndensitymax = 0; ///< maximum number of densities \f$ \rho^{(p)} \f$ + NS_TYPE nradbase = 0; ///< maximum number of radial \f$\textbf{basis}\f$ function \f$ g_{k}(r) \f$ + LS_TYPE lmax = 0; ///< \f$ l_\textrm{max} \f$ - maximum value of orbital moment \f$ l \f$ + NS_TYPE nradmax = 0; ///< maximum number \f$ n \f$ of radial function \f$ R_{nl}(r) \f$ + DOUBLE_TYPE cutoffmax = 0; ///< maximum value of cutoff distance among all species in basis set + DOUBLE_TYPE deltaSplineBins = 0; ///< Spline interpolation density + + string npoti = "FinnisSinclair"; ///< FS and embedding function combination + + string *elements_name = nullptr; ///< Array of elements name for mapping from index (0..nelements-1) to element symbol (string) + + AbstractRadialBasis *radial_functions = nullptr; ///< object to work with radial functions + ACECartesianSphericalHarmonics spherical_harmonics; ///< object to work with spherical harmonics in Cartesian representation + + + Array1D rho_core_cutoffs; ///< energy-based inner cut-off + Array1D drho_core_cutoffs; ///< decay of energy-based inner cut-off + + vector FS_parameters; ///< parameters for cluster functional, see Eq.(3) in implementation notes or Eq.(53) in PRB 99, 014104 (2019) + + // E0 values + Array1D E0vals; + + /** + * Default empty constructor + */ + ACEAbstractBasisSet() = default; + + // copy constructor, operator= and destructor (see. Rule of Three) + + /** + * Copy constructor (see. Rule of Three) + * @param other + */ + ACEAbstractBasisSet(const ACEAbstractBasisSet &other); + + /** + * operator= (see. Rule of Three) + * @param other + * @return + */ + ACEAbstractBasisSet &operator=(const ACEAbstractBasisSet &other); + + /** + * virtual destructor (see. Rule of Three) + */ + virtual ~ACEAbstractBasisSet(); + + /** + * Computing cluster functional \f$ F(\rho_i^{(1)}, \dots, \rho_i^{(P)}) \f$ + * and its derivatives \f$ (\partial F/\partial\rho_i^{(1)}, \dots, \partial F/\partial \rho_i^{(P)} ) \f$ + * @param rhos array with densities \f$ \rho^{(p)} \f$ + * @param value (out) return value of cluster functional + * @param derivatives (out) array of derivatives \f$ (\partial F/\partial\rho_i^{(1)}, \dots, \partial F/\partial \rho_i^{(P)} ) \f$ + * @param ndensity number \f$ P \f$ of densities to use + */ + void FS_values_and_derivatives(Array1D &rhos, DOUBLE_TYPE &value, Array1D &derivatives, + DENSITY_TYPE ndensity); + + /** + * Computing hard core pairwise repulsive potential \f$ f_{cut}(\rho_i^{(\textrm{core})})\f$ and its derivative, + * see Eq.(29) of implementation notes + * @param rho_core value of \f$ \rho_i^{(\textrm{core})} \f$ + * @param rho_cut \f$ \rho_{cut}^{\mu_i} \f$ value + * @param drho_cut \f$ \Delta_{cut}^{\mu_i} \f$ value + * @param fcut (out) return inner cutoff function + * @param dfcut (out) return derivative of inner cutoff function + */ + static void inner_cutoff(DOUBLE_TYPE rho_core, DOUBLE_TYPE rho_cut, DOUBLE_TYPE drho_cut, DOUBLE_TYPE &fcut, + DOUBLE_TYPE &dfcut); + + + /** + * Virtual method to save potential to file + * @param filename file name + */ + virtual void save(const string &filename) = 0; + + /** + * Virtual method to load potential from file + * @param filename file name + */ + virtual void load(const string filename) = 0; + + /** + * Get the species index by its element name + * @param elemname element name + * @return species index + */ + SPECIES_TYPE get_species_index_by_name(const string &elemname); + + + // routines for copying and cleaning dynamic memory of the class (see. Rule of Three) + + /** + * Routine for clean the dynamically allocated memory\n + * IMPORTANT! It must be idempotent for safety. + */ + virtual void _clean(); + + /** + * Copy dynamic memory from src. Must be override and extended in derived classes! + * @param src source object to copy from + */ + virtual void _copy_dynamic_memory(const ACEAbstractBasisSet &src); + + /** + * Copy scalar values from src. Must be override and extended in derived classes! + * @param src source object to copy from + */ + virtual void _copy_scalar_memory(const ACEAbstractBasisSet &src); +}; + +void Fexp(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF); + +void FexpShiftedScaled(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF); + +#endif //ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H diff --git a/lib/pace/ace_array2dlm.h b/lib/pace/ace_array2dlm.h new file mode 100644 index 0000000000..2b38602bc7 --- /dev/null +++ b/lib/pace/ace_array2dlm.h @@ -0,0 +1,579 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Yury Lysogorskiy on 11.01.20. + + +#ifndef ACE_ARRAY2DLM_H +#define ACE_ARRAY2DLM_H + +#include +#include + +#include "ace_arraynd.h" +#include "ace_contigous_array.h" +#include "ace_types.h" + +using namespace std; + +/** + * Contiguous array to organize values by \f$ (l,m) \f$ indiced (orbital moment and its projection). + * Only \f$ l_\textrm{max}\f$ should be provided, \f$ m = -l, \dots,l \f$ + * for \f$ l = 0, \dots, l_\textrm{max}\f$ + * @tparam T type of values to store + */ +template +class Array2DLM : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + + LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$ + + bool is_proxy = false; ///< flag to show, if object is owning the memory or just represent it (proxying)dimensions + +public: + /** + * Default empty constructor + */ + Array2DLM() = default; + + /** + * Parametrized constructor + * @param lmax maximum value of \f$ l \f$ + * @param array_name name of the array + */ + explicit Array2DLM(LS_TYPE lmax, string array_name = "Array2DLM") { + init(lmax, array_name); + } + + + /** + * Constructor to create slices-proxy array, i.e. to provide access to the memory, but not to own it. + * @param lmax maximum value of \f$ l \f$ + * @param data_ptr pointer to original data + * @param array_name name of the array + */ + Array2DLM(LS_TYPE lmax, T *data_ptr, string array_name = "Array2DLM") { + this->lmax = lmax; + this->size = (lmax + 1) * (lmax + 1); + this->data = data_ptr; + this->array_name = array_name; + is_proxy = true; + }; + + /** + * Destructor + */ + ~Array2DLM() { + if (!is_proxy) { + if (data != nullptr) delete[] data; + } + data = nullptr; + } + + /** + * Initialize array, allocate memory + * @param lmax maximum value of l + * @param array_name name of the array + */ + void init(LS_TYPE lmax, string array_name = "Array2DLM") { + if (is_proxy) { + char s[1024]; + sprintf(s, "Could not re-initialize proxy-array %s\n", this->array_name.c_str()); + throw logic_error(s); + } + this->lmax = lmax; + this->array_name = array_name; + //for m = -l .. l + if (size != (lmax + 1) * (lmax + 1)) { + size = (lmax + 1) * (lmax + 1); + if (data) delete[] data; + data = new T[size]{}; + memset(data, 0.0, size * sizeof(T)); + } else { + memset(data, 0, size * sizeof(T)); + } + } + +#ifdef MULTIARRAY_INDICES_CHECK +/** + * Check if indices (l,m) are within array + */ + void check_indices(LS_TYPE l, MS_TYPE m) const { + + if ((l < 0) | (l > lmax)) { + fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax); + exit(EXIT_FAILURE); + } + + if ((m < -l) | (m > l)) { + fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l); + exit(EXIT_FAILURE); + } + size_t ii = l * (l + 1) + m; + if (ii >= size) { + fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size); + exit(EXIT_FAILURE); + } + } +#endif + + /** + * Accessing the array value by index (l,m) for reading + * @param l + * @param m + * @return array value + */ + inline const T &operator()(LS_TYPE l, MS_TYPE m) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(l, m); +#endif + //l^2 + l + m + return data[l * (l + 1) + m]; + } + + /** + * Accessing the array value by index (l,m) for writing + * @param l + * @param m + * @return array value + */ + inline T &operator()(LS_TYPE l, MS_TYPE m) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(l, m); +#endif + //l^2 + l + m + return data[l * (l + 1) + m]; + } + + /** + * Convert array to STL vector> container + * @return vector> container + */ + vector> to_vector() const { + vector> res; + res.resize(lmax + 1); + + for (int i = 0; i < lmax + 1; i++) { + res[i].resize(i + 1); + for (int j = 0; j < i + 1; j++) { + res[i][j] = operator()(i, j); + } + } + return res; + } +}; + +/** + * Contiguous array to organize values by \f$ (i_0, l , m) \f$ indices. + * Only \f$ d_{0}, l_\textrm{max}\f$ should be provided: \f$ m = -l, \dots,l \f$ + * for \f$ l = 0, \dots, l_\textrm{max}\f$ + * @tparam T type of values to store + */ +template +class Array3DLM : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + + LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$ + + + size_t dim[1] = {0}; ///< linear dimension \f$ d_{0} \f$ + + size_t s[1] = {0}; ///< strides for linear dimensions + + Array1D *> _proxy_slices; ///< slices representation +public: + /** + * Default empty constructor + */ + Array3DLM() = default; + + /** + * Parametrized constructor + * @param array_name name of the array + */ + Array3DLM(string array_name) { + this->array_name = array_name; + }; + + /** + * Parametrized constructor + * @param d0 maximum value of \f$ i_0 \f$ + * @param lmax maximum value of \f$ l \f$ + * @param array_name name of the array + */ + explicit Array3DLM(size_t d0, LS_TYPE lmax, string array_name = "Array3DLM") { + init(d0, lmax, array_name); + } + + /** + * Initialize array and its slices + * @param d0 maximum value of \f$ i_0 \f$ + * @param lmax maximum value of \f$ l \f$ + * @param array_name name of the array + */ + void init(size_t d0, LS_TYPE lmax, string array_name = "Array3DLM") { + this->array_name = array_name; + this->lmax = lmax; + dim[0] = d0; + s[0] = lmax * lmax; + if (size != s[0] * dim[0]) { + size = s[0] * dim[0]; + if (data) delete[] data; + data = new T[size]{}; + memset(data, 0, size * sizeof(T)); + } else { + memset(data, 0, size * sizeof(T)); + } + + _proxy_slices.set_array_name(array_name + "_proxy"); + //arrange proxy-slices + _clear_proxies(); + _proxy_slices.resize(dim[0]); + for (size_t i0 = 0; i0 < dim[0]; ++i0) { + _proxy_slices(i0) = new Array2DLM(this->lmax, &this->data[i0 * s[0]], + array_name + "_slice"); + } + } + + /** + * Release pointers to slices + */ + void _clear_proxies() { + for (size_t i0 = 0; i0 < _proxy_slices.get_dim(0); ++i0) { + delete _proxy_slices(i0); + _proxy_slices(i0) = nullptr; + } + } + + /** + * Destructor, clear proxies + */ + ~Array3DLM() { + _clear_proxies(); + } + + /** + * Resize array to new dimensions + * @param d0 + * @param lmax + */ + void resize(size_t d0, LS_TYPE lmax) { + _clear_proxies(); + init(d0, lmax, this->array_name); + } + + /** + * Get array dimensions + * @param d dimension index + * @return dimension along axis 'd' + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + /** + * Check if indices (i0, l,m) are within array + */ + void check_indices(size_t i0, LS_TYPE l, MS_TYPE m) const { + if ((l < 0) | (l > lmax)) { + fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax); + exit(EXIT_FAILURE); + } + + if ((m < -l) | (m > l)) { + fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l); + exit(EXIT_FAILURE); + } + + if ((i0 < 0) | (i0 >= dim[0])) { + fprintf(stderr, "%s: index i0 = %ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + exit(EXIT_FAILURE); + } + + size_t ii = i0 * s[0] + l * (l + 1) + m; + if (ii >= size) { + fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size); + exit(EXIT_FAILURE); + } + } +#endif + + /** + * Accessing the array value by index (i0,l,m) for reading + * @param i0 + * @param l + * @param m + * @return array value + */ + inline const T &operator()(size_t i0, LS_TYPE l, MS_TYPE m) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, l, m); +#endif + return data[i0 * s[0] + l * (l + 1) + m]; + } + + /** + * Accessing the array value by index (i0,l,m) for writing + * @param i0 + * @param l + * @param m + * @return array value + */ + inline T &operator()(size_t i0, LS_TYPE l, MS_TYPE m) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, l, m); +#endif + return data[i0 * s[0] + l * (l + 1) + m]; + } + + /** + * Return proxy Array2DLM pointing to i0, l=0, m=0 to read + * @param i0 + * @return proxy Array2DLM pointing to i0, l=0, m=0 + */ + inline const Array2DLM &operator()(size_t i0) const { + return *_proxy_slices(i0); + } + + /** + * Return proxy Array2DLM pointing to i0, l=0, m=0 to write + * @param i0 + * @return proxy Array2DLM pointing to i0, l=0, m=0 + */ + inline Array2DLM &operator()(size_t i0) { + return *_proxy_slices(i0); + } +}; + + +/** + * Contiguous array to organize values by \f$ (i_0, i_1, l , m) \f$ indices. + * Only \f$ d_{0}, d_{1}, l_\textrm{max}\f$ should be provided: \f$ m = -l, \dots,l \f$ + * for \f$ l = 0, \dots, l_\textrm{max}\f$ + * @tparam T type of values to store + */ +template +class Array4DLM : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + + LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$ + size_t dim[2] = {0, 0}; ///< linear dimension \f$ d_{0}, d_{1} \f$ + size_t s[2] = {0, 0}; ///< strides for linear dimensions + + Array2D *> _proxy_slices; ///< slices representation +public: + /** + * Default empty constructor + */ + Array4DLM() = default; + + /** + * Parametrized constructor + * @param array_name name of the array + */ + Array4DLM(string array_name) { + this->array_name = array_name; + }; + + /** + * Parametrized constructor + * @param d0 maximum value of \f$ i_0 \f$ + * @param d1 maximum value of \f$ i_1 \f$ + * @param lmax maximum value of \f$ l \f$ + * @param array_name name of the array + */ + explicit Array4DLM(size_t d0, size_t d1, LS_TYPE lmax, string array_name = "Array4DLM") { + init(d0, d1, lmax, array_name); + } + + /** + * Initialize array, reallocate memory and its slices + * @param d0 maximum value of \f$ i_0 \f$ + * @param d1 maximum value of \f$ i_1 \f$ + * @param lmax maximum value of \f$ l \f$ + * @param array_name name of the array + */ + void init(size_t d0, size_t d1, LS_TYPE lmax, string array_name = "Array4DLM") { + this->array_name = array_name; + this->lmax = lmax; + dim[1] = d1; + dim[0] = d0; + s[1] = lmax * lmax; + s[0] = s[1] * dim[1]; + if (size != s[0] * dim[0]) { + size = s[0] * dim[0]; + if (data) delete[] data; + data = new T[size]{}; + memset(data, 0, size * sizeof(T)); + } else { + memset(data, 0, size * sizeof(T)); + } + + _proxy_slices.set_array_name(array_name + "_proxy"); + //release old memory if there is any + _clear_proxies(); + //arrange proxy-slices + _proxy_slices.resize(dim[0], dim[1]); + for (size_t i0 = 0; i0 < dim[0]; ++i0) + for (size_t i1 = 0; i1 < dim[1]; ++i1) { + _proxy_slices(i0, i1) = new Array2DLM(this->lmax, &this->data[i0 * s[0] + i1 * s[1]], + array_name + "_slice"); + } + } + + /** + * Release pointers to slices + */ + void _clear_proxies() { + + for (size_t i0 = 0; i0 < _proxy_slices.get_dim(0); ++i0) + for (size_t i1 = 0; i1 < _proxy_slices.get_dim(1); ++i1) { + delete _proxy_slices(i0, i1); + _proxy_slices(i0, i1) = nullptr; + } + } + + /** + * Destructor, clear proxies + */ + ~Array4DLM() { + _clear_proxies(); + } + + /** + * Deallocate memory, reallocate with the new dimensions + * @param d0 + * @param lmax + */ + void resize(size_t d0, size_t d1, LS_TYPE lmax) { + _clear_proxies(); + init(d0, d1, lmax, this->array_name); + } + + /** + * Get array dimensions + * @param d dimension index + * @return dimension along axis 'd' + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + /** + * Check if indices (i0, l,m) are within array + */ + void check_indices(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) const { + if ((l < 0) | (l > lmax)) { + fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax); + exit(EXIT_FAILURE); + } + + if ((m < -l) | (m > l)) { + fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l); + exit(EXIT_FAILURE); + } + + if ((i0 < 0) | (i0 >= dim[0])) { + fprintf(stderr, "%s: index i0 = %ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + exit(EXIT_FAILURE); + } + + + if ((i1 < 0) | (i1 >= dim[1])) { + fprintf(stderr, "%s: index i1 = %ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); + exit(EXIT_FAILURE); + } + + size_t ii = i0 * s[0] + i1 * s[1] + l * (l + 1) + m; + if (ii >= size) { + fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size); + exit(EXIT_FAILURE); + } + } +#endif + + /** + * Accessing the array value by index (i0,l,m) for reading + * @param i0 + * @param i1 + * @param l + * @param m + * @return array value + */ + inline const T &operator()(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, l, m); +#endif + return data[i0 * s[0] + i1 * s[1] + l * (l + 1) + m]; + } + + /** + * Accessing the array value by index (i0,l,m) for writing + * @param i0 + * @param i1 + * @param l + * @param m + * @return array value + */ + inline T &operator()(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, l, m); +#endif + return data[i0 * s[0] + i1 * s[1] + l * (l + 1) + m]; + } + + /** + * Return proxy Array2DLM pointing to i0, i1, l=0, m=0 to read + * @param i0 + * @param i1 + * @return proxy Array2DLM pointing to i0, l=0, m=0 + */ + inline const Array2DLM &operator()(size_t i0, size_t i1) const { + return *_proxy_slices(i0, i1); + } + + /** + * Return proxy Array2DLM pointing to i0, i1, l=0, m=0 to write + * @param i0 + * @param i1 + * @return proxy Array2DLM pointing to i0, l=0, m=0 + */ + inline Array2DLM &operator()(size_t i0, size_t i1) { + return *_proxy_slices(i0, i1); + } +}; + +#endif //ACE_ARRAY2DLM_H \ No newline at end of file diff --git a/lib/pace/ace_arraynd.h b/lib/pace/ace_arraynd.h new file mode 100644 index 0000000000..1044b5654e --- /dev/null +++ b/lib/pace/ace_arraynd.h @@ -0,0 +1,1949 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +//automatically generate source code + +#ifndef ACE_MULTIARRAY_H +#define ACE_MULTIARRAY_H + +#include +#include +#include + +#include "ace_contigous_array.h" + +using namespace std; + + +/** + * Multidimensional (1 - dimensional) array of type T with contiguous memory layout. + * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @tparam T data type + */ +template +class Array1D : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + using ContiguousArrayND::is_proxy_; + + size_t dim[1] = {0}; ///< dimensions + size_t s[1] = {0}; ///< strides + int ndim = 1; ///< number of dimensions +public: + + /** + * Default empty constructor + */ + Array1D() = default; + + /** + * Parametrized constructor with array name + * @param array_name name of array (for error logging) + */ + Array1D(const string &array_name) { this->array_name = array_name; } + + /** + * Parametrized constructor + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + Array1D(size_t d0, const string &array_name = "Array1D", T *new_data = nullptr) { + init(d0, array_name, new_data); + } + + /** + * Setup the dimensions and strides of array + * @param d0,... array sizes for different dimensions + */ + void set_dimensions(size_t d0) { + + dim[0] = d0; + + s[0] = 1; + + size = s[0] * dim[0]; + }; + + /** + * Initialize array storage, dimensions and strides + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + void init(size_t d0, const string &array_name = "Array1D", T *new_data = nullptr) { + this->array_name = array_name; + + size_t old_size = size; + set_dimensions(d0); + + bool new_is_proxy = (new_data != nullptr); + + if (new_is_proxy) { + if (!is_proxy_) delete[] data; + data = new_data; + } else { + if (size != old_size) { + T *old_data = data; //preserve the pointer to the old data + data = new T[size]; // allocate new data + if (old_data != nullptr) { // + size_t min_size = old_size < size ? old_size : size; + memcpy(data, old_data, min_size * sizeof(T)); + if (!is_proxy_) delete[] old_data; + } + //memset(data, 0, size * sizeof(T)); + } else { + //memset(data, 0, size * sizeof(T)); + } + } + + is_proxy_ = new_is_proxy; + } + + /** + * Resize array + * @param d0,... array sizes for different dimensions + */ + void resize(size_t d0) { + init(d0, this->array_name); + } + + /** + * Reshape array without reset the data + * @param d0,... array sizes for different dimensions + */ + void reshape(size_t d0) { + //check data size consistency + size_t new_size = d0; + if (new_size != size) + throw invalid_argument("Couldn't reshape array when the size is not conserved"); + set_dimensions(d0); + } + + /** + * Get array size in dimension "d" + * @param d dimension index + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + + /** + * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + void check_indices(size_t i0) const { + + if ((i0 < 0) | (i0 >= dim[0])) { + char buf[1024]; + sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + throw std::out_of_range(buf); + } + + } + +#endif + + /** + * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline const T &operator()(size_t i0) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0); +#endif + + return data[i0]; + + } + + /** + * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline T &operator()(size_t i0) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0); +#endif + + return data[i0]; + + } + + /** + * Array comparison operator + * @param other + */ + bool operator==(const Array1D &other) const { + //compare dimensions + for (int d = 0; d < ndim; d++) { + if (this->dim[d] != other.dim[d]) + return false; + } + return ContiguousArrayND::operator==(other); + } + + /** + * Convert to nested vector> container + * @return vector container + */ + vector to_vector() const { + vector res; + + res.resize(dim[0]); + + for (int i0 = 0; i0 < dim[0]; i0++) { + res[i0] = operator()(i0); + + } + + + return res; + } // end to_vector() + + + /** + * Set values to vector> container + * @param vec container + */ + void set_vector(const vector &vec) { + size_t d0 = 0; + d0 = vec.size(); + + + init(d0, array_name); + for (int i0 = 0; i0 < dim[0]; i0++) { + operator()(i0) = vec.at(i0); + + } + + } + + /** + * Parametrized constructor from vector> container + * @param vec container + * @param array_name array name + */ + Array1D(const vector &vec, const string &array_name = "Array1D") { + this->set_vector(vec); + this->array_name = array_name; + } + + /** + * operator= to vector> container + * @param vec container + */ + Array1D &operator=(const vector &vec) { + this->set_vector(vec); + return *this; + } + + + vector get_shape() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = dim[d]; + return sh; + } + + vector get_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d]; + return sh; + } + + vector get_memory_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d] * sizeof(T); + return sh; + } +}; + + +/** + * Multidimensional (2 - dimensional) array of type T with contiguous memory layout. + * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @tparam T data type + */ +template +class Array2D : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + using ContiguousArrayND::is_proxy_; + + size_t dim[2] = {0}; ///< dimensions + size_t s[2] = {0}; ///< strides + int ndim = 2; ///< number of dimensions +public: + + /** + * Default empty constructor + */ + Array2D() = default; + + /** + * Parametrized constructor with array name + * @param array_name name of array (for error logging) + */ + Array2D(const string &array_name) { this->array_name = array_name; } + + /** + * Parametrized constructor + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + Array2D(size_t d0, size_t d1, const string &array_name = "Array2D", T *new_data = nullptr) { + init(d0, d1, array_name, new_data); + } + + /** + * Setup the dimensions and strides of array + * @param d0,... array sizes for different dimensions + */ + void set_dimensions(size_t d0, size_t d1) { + + dim[0] = d0; + dim[1] = d1; + + s[1] = 1; + s[0] = s[1] * dim[1]; + + size = s[0] * dim[0]; + }; + + /** + * Initialize array storage, dimensions and strides + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + void init(size_t d0, size_t d1, const string &array_name = "Array2D", T *new_data = nullptr) { + this->array_name = array_name; + + size_t old_size = size; + set_dimensions(d0, d1); + + bool new_is_proxy = (new_data != nullptr); + + if (new_is_proxy) { + if (!is_proxy_) delete[] data; + data = new_data; + } else { + if (size != old_size) { + T *old_data = data; //preserve the pointer to the old data + data = new T[size]; // allocate new data + if (old_data != nullptr) { // + size_t min_size = old_size < size ? old_size : size; + memcpy(data, old_data, min_size * sizeof(T)); + if (!is_proxy_) delete[] old_data; + } + //memset(data, 0, size * sizeof(T)); + } else { + //memset(data, 0, size * sizeof(T)); + } + } + + is_proxy_ = new_is_proxy; + } + + /** + * Resize array + * @param d0,... array sizes for different dimensions + */ + void resize(size_t d0, size_t d1) { + init(d0, d1, this->array_name); + } + + /** + * Reshape array without reset the data + * @param d0,... array sizes for different dimensions + */ + void reshape(size_t d0, size_t d1) { + //check data size consistency + size_t new_size = d0 * d1; + if (new_size != size) + throw invalid_argument("Couldn't reshape array when the size is not conserved"); + set_dimensions(d0, d1); + } + + /** + * Get array size in dimension "d" + * @param d dimension index + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + + /** + * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + void check_indices(size_t i0, size_t i1) const { + + if ((i0 < 0) | (i0 >= dim[0])) { + char buf[1024]; + sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + throw std::out_of_range(buf); + } + + if ((i1 < 0) | (i1 >= dim[1])) { + char buf[1024]; + sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); + throw std::out_of_range(buf); + } + + } + +#endif + + /** + * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline const T &operator()(size_t i0, size_t i1) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1); +#endif + + return data[i0 * s[0] + i1]; + + } + + /** + * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline T &operator()(size_t i0, size_t i1) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1); +#endif + + return data[i0 * s[0] + i1]; + + } + + /** + * Array comparison operator + * @param other + */ + bool operator==(const Array2D &other) const { + //compare dimensions + for (int d = 0; d < ndim; d++) { + if (this->dim[d] != other.dim[d]) + return false; + } + return ContiguousArrayND::operator==(other); + } + + /** + * Convert to nested vector> container + * @return vector container + */ + vector> to_vector() const { + vector> res; + + res.resize(dim[0]); + + for (int i0 = 0; i0 < dim[0]; i0++) { + res[i0].resize(dim[1]); + + + for (int i1 = 0; i1 < dim[1]; i1++) { + res[i0][i1] = operator()(i0, i1); + + } + } + + + return res; + } // end to_vector() + + + /** + * Set values to vector> container + * @param vec container + */ + void set_vector(const vector> &vec) { + size_t d0 = 0; + size_t d1 = 0; + d0 = vec.size(); + + if (d0 > 0) { + d1 = vec.at(0).size(); + + + } + + init(d0, d1, array_name); + for (int i0 = 0; i0 < dim[0]; i0++) { + if (vec.at(i0).size() != d1) + throw std::invalid_argument("Vector size is not constant at dimension 1"); + + for (int i1 = 0; i1 < dim[1]; i1++) { + operator()(i0, i1) = vec.at(i0).at(i1); + + } + } + + } + + /** + * Parametrized constructor from vector> container + * @param vec container + * @param array_name array name + */ + Array2D(const vector> &vec, const string &array_name = "Array2D") { + this->set_vector(vec); + this->array_name = array_name; + } + + /** + * operator= to vector> container + * @param vec container + */ + Array2D &operator=(const vector> &vec) { + this->set_vector(vec); + return *this; + } + + + /** + * operator= to flatten vector container + * @param vec container + */ + Array2D &operator=(const vector &vec) { + this->set_flatten_vector(vec); + return *this; + } + + + vector get_shape() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = dim[d]; + return sh; + } + + vector get_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d]; + return sh; + } + + vector get_memory_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d] * sizeof(T); + return sh; + } +}; + + +/** + * Multidimensional (3 - dimensional) array of type T with contiguous memory layout. + * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @tparam T data type + */ +template +class Array3D : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + using ContiguousArrayND::is_proxy_; + + size_t dim[3] = {0}; ///< dimensions + size_t s[3] = {0}; ///< strides + int ndim = 3; ///< number of dimensions +public: + + /** + * Default empty constructor + */ + Array3D() = default; + + /** + * Parametrized constructor with array name + * @param array_name name of array (for error logging) + */ + Array3D(const string &array_name) { this->array_name = array_name; } + + /** + * Parametrized constructor + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + Array3D(size_t d0, size_t d1, size_t d2, const string &array_name = "Array3D", T *new_data = nullptr) { + init(d0, d1, d2, array_name, new_data); + } + + /** + * Setup the dimensions and strides of array + * @param d0,... array sizes for different dimensions + */ + void set_dimensions(size_t d0, size_t d1, size_t d2) { + + dim[0] = d0; + dim[1] = d1; + dim[2] = d2; + + s[2] = 1; + s[1] = s[2] * dim[2]; + s[0] = s[1] * dim[1]; + + size = s[0] * dim[0]; + }; + + /** + * Initialize array storage, dimensions and strides + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + void init(size_t d0, size_t d1, size_t d2, const string &array_name = "Array3D", T *new_data = nullptr) { + this->array_name = array_name; + + size_t old_size = size; + set_dimensions(d0, d1, d2); + + bool new_is_proxy = (new_data != nullptr); + + if (new_is_proxy) { + if (!is_proxy_) delete[] data; + data = new_data; + } else { + if (size != old_size) { + T *old_data = data; //preserve the pointer to the old data + data = new T[size]; // allocate new data + if (old_data != nullptr) { // + size_t min_size = old_size < size ? old_size : size; + memcpy(data, old_data, min_size * sizeof(T)); + if (!is_proxy_) delete[] old_data; + } + //memset(data, 0, size * sizeof(T)); + } else { + //memset(data, 0, size * sizeof(T)); + } + } + + is_proxy_ = new_is_proxy; + } + + /** + * Resize array + * @param d0,... array sizes for different dimensions + */ + void resize(size_t d0, size_t d1, size_t d2) { + init(d0, d1, d2, this->array_name); + } + + /** + * Reshape array without reset the data + * @param d0,... array sizes for different dimensions + */ + void reshape(size_t d0, size_t d1, size_t d2) { + //check data size consistency + size_t new_size = d0 * d1 * d2; + if (new_size != size) + throw invalid_argument("Couldn't reshape array when the size is not conserved"); + set_dimensions(d0, d1, d2); + } + + /** + * Get array size in dimension "d" + * @param d dimension index + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + + /** + * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + void check_indices(size_t i0, size_t i1, size_t i2) const { + + if ((i0 < 0) | (i0 >= dim[0])) { + char buf[1024]; + sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + throw std::out_of_range(buf); + } + + if ((i1 < 0) | (i1 >= dim[1])) { + char buf[1024]; + sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); + throw std::out_of_range(buf); + } + + if ((i2 < 0) | (i2 >= dim[2])) { + char buf[1024]; + sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); + throw std::out_of_range(buf); + } + + } + +#endif + + /** + * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline const T &operator()(size_t i0, size_t i1, size_t i2) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2]; + + } + + /** + * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline T &operator()(size_t i0, size_t i1, size_t i2) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2]; + + } + + /** + * Array comparison operator + * @param other + */ + bool operator==(const Array3D &other) const { + //compare dimensions + for (int d = 0; d < ndim; d++) { + if (this->dim[d] != other.dim[d]) + return false; + } + return ContiguousArrayND::operator==(other); + } + + /** + * Convert to nested vector> container + * @return vector container + */ + vector>> to_vector() const { + vector>> res; + + res.resize(dim[0]); + + for (int i0 = 0; i0 < dim[0]; i0++) { + res[i0].resize(dim[1]); + + + for (int i1 = 0; i1 < dim[1]; i1++) { + res[i0][i1].resize(dim[2]); + + + for (int i2 = 0; i2 < dim[2]; i2++) { + res[i0][i1][i2] = operator()(i0, i1, i2); + + } + } + } + + + return res; + } // end to_vector() + + + /** + * Set values to vector> container + * @param vec container + */ + void set_vector(const vector>> &vec) { + size_t d0 = 0; + size_t d1 = 0; + size_t d2 = 0; + d0 = vec.size(); + + if (d0 > 0) { + d1 = vec.at(0).size(); + if (d1 > 0) { + d2 = vec.at(0).at(0).size(); + + + } + } + + init(d0, d1, d2, array_name); + for (int i0 = 0; i0 < dim[0]; i0++) { + if (vec.at(i0).size() != d1) + throw std::invalid_argument("Vector size is not constant at dimension 1"); + + for (int i1 = 0; i1 < dim[1]; i1++) { + if (vec.at(i0).at(i1).size() != d2) + throw std::invalid_argument("Vector size is not constant at dimension 2"); + + for (int i2 = 0; i2 < dim[2]; i2++) { + operator()(i0, i1, i2) = vec.at(i0).at(i1).at(i2); + + } + } + } + + } + + /** + * Parametrized constructor from vector> container + * @param vec container + * @param array_name array name + */ + Array3D(const vector>> &vec, const string &array_name = "Array3D") { + this->set_vector(vec); + this->array_name = array_name; + } + + /** + * operator= to vector> container + * @param vec container + */ + Array3D &operator=(const vector>> &vec) { + this->set_vector(vec); + return *this; + } + + + /** + * operator= to flatten vector container + * @param vec container + */ + Array3D &operator=(const vector &vec) { + this->set_flatten_vector(vec); + return *this; + } + + + vector get_shape() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = dim[d]; + return sh; + } + + vector get_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d]; + return sh; + } + + vector get_memory_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d] * sizeof(T); + return sh; + } +}; + + +/** + * Multidimensional (4 - dimensional) array of type T with contiguous memory layout. + * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @tparam T data type + */ +template +class Array4D : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + using ContiguousArrayND::is_proxy_; + + size_t dim[4] = {0}; ///< dimensions + size_t s[4] = {0}; ///< strides + int ndim = 4; ///< number of dimensions +public: + + /** + * Default empty constructor + */ + Array4D() = default; + + /** + * Parametrized constructor with array name + * @param array_name name of array (for error logging) + */ + Array4D(const string &array_name) { this->array_name = array_name; } + + /** + * Parametrized constructor + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + Array4D(size_t d0, size_t d1, size_t d2, size_t d3, const string &array_name = "Array4D", T *new_data = nullptr) { + init(d0, d1, d2, d3, array_name, new_data); + } + + /** + * Setup the dimensions and strides of array + * @param d0,... array sizes for different dimensions + */ + void set_dimensions(size_t d0, size_t d1, size_t d2, size_t d3) { + + dim[0] = d0; + dim[1] = d1; + dim[2] = d2; + dim[3] = d3; + + s[3] = 1; + s[2] = s[3] * dim[3]; + s[1] = s[2] * dim[2]; + s[0] = s[1] * dim[1]; + + size = s[0] * dim[0]; + }; + + /** + * Initialize array storage, dimensions and strides + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + void init(size_t d0, size_t d1, size_t d2, size_t d3, const string &array_name = "Array4D", T *new_data = nullptr) { + this->array_name = array_name; + + size_t old_size = size; + set_dimensions(d0, d1, d2, d3); + + bool new_is_proxy = (new_data != nullptr); + + if (new_is_proxy) { + if (!is_proxy_) delete[] data; + data = new_data; + } else { + if (size != old_size) { + T *old_data = data; //preserve the pointer to the old data + data = new T[size]; // allocate new data + if (old_data != nullptr) { // + size_t min_size = old_size < size ? old_size : size; + memcpy(data, old_data, min_size * sizeof(T)); + if (!is_proxy_) delete[] old_data; + } + //memset(data, 0, size * sizeof(T)); + } else { + //memset(data, 0, size * sizeof(T)); + } + } + + is_proxy_ = new_is_proxy; + } + + /** + * Resize array + * @param d0,... array sizes for different dimensions + */ + void resize(size_t d0, size_t d1, size_t d2, size_t d3) { + init(d0, d1, d2, d3, this->array_name); + } + + /** + * Reshape array without reset the data + * @param d0,... array sizes for different dimensions + */ + void reshape(size_t d0, size_t d1, size_t d2, size_t d3) { + //check data size consistency + size_t new_size = d0 * d1 * d2 * d3; + if (new_size != size) + throw invalid_argument("Couldn't reshape array when the size is not conserved"); + set_dimensions(d0, d1, d2, d3); + } + + /** + * Get array size in dimension "d" + * @param d dimension index + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + + /** + * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + void check_indices(size_t i0, size_t i1, size_t i2, size_t i3) const { + + if ((i0 < 0) | (i0 >= dim[0])) { + char buf[1024]; + sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + throw std::out_of_range(buf); + } + + if ((i1 < 0) | (i1 >= dim[1])) { + char buf[1024]; + sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); + throw std::out_of_range(buf); + } + + if ((i2 < 0) | (i2 >= dim[2])) { + char buf[1024]; + sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); + throw std::out_of_range(buf); + } + + if ((i3 < 0) | (i3 >= dim[3])) { + char buf[1024]; + sprintf(buf, "%s: index i3=%ld out of range (0, %ld)\n", array_name.c_str(), i3, dim[3] - 1); + throw std::out_of_range(buf); + } + + } + +#endif + + /** + * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline const T &operator()(size_t i0, size_t i1, size_t i2, size_t i3) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2, i3); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3]; + + } + + /** + * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline T &operator()(size_t i0, size_t i1, size_t i2, size_t i3) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2, i3); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3]; + + } + + /** + * Array comparison operator + * @param other + */ + bool operator==(const Array4D &other) const { + //compare dimensions + for (int d = 0; d < ndim; d++) { + if (this->dim[d] != other.dim[d]) + return false; + } + return ContiguousArrayND::operator==(other); + } + + /** + * Convert to nested vector> container + * @return vector container + */ + vector>>> to_vector() const { + vector>>> res; + + res.resize(dim[0]); + + for (int i0 = 0; i0 < dim[0]; i0++) { + res[i0].resize(dim[1]); + + + for (int i1 = 0; i1 < dim[1]; i1++) { + res[i0][i1].resize(dim[2]); + + + for (int i2 = 0; i2 < dim[2]; i2++) { + res[i0][i1][i2].resize(dim[3]); + + + for (int i3 = 0; i3 < dim[3]; i3++) { + res[i0][i1][i2][i3] = operator()(i0, i1, i2, i3); + + } + } + } + } + + + return res; + } // end to_vector() + + + /** + * Set values to vector> container + * @param vec container + */ + void set_vector(const vector>>> &vec) { + size_t d0 = 0; + size_t d1 = 0; + size_t d2 = 0; + size_t d3 = 0; + d0 = vec.size(); + + if (d0 > 0) { + d1 = vec.at(0).size(); + if (d1 > 0) { + d2 = vec.at(0).at(0).size(); + if (d2 > 0) { + d3 = vec.at(0).at(0).at(0).size(); + + + } + } + } + + init(d0, d1, d2, d3, array_name); + for (int i0 = 0; i0 < dim[0]; i0++) { + if (vec.at(i0).size() != d1) + throw std::invalid_argument("Vector size is not constant at dimension 1"); + + for (int i1 = 0; i1 < dim[1]; i1++) { + if (vec.at(i0).at(i1).size() != d2) + throw std::invalid_argument("Vector size is not constant at dimension 2"); + + for (int i2 = 0; i2 < dim[2]; i2++) { + if (vec.at(i0).at(i1).at(i2).size() != d3) + throw std::invalid_argument("Vector size is not constant at dimension 3"); + + for (int i3 = 0; i3 < dim[3]; i3++) { + operator()(i0, i1, i2, i3) = vec.at(i0).at(i1).at(i2).at(i3); + + } + } + } + } + + } + + /** + * Parametrized constructor from vector> container + * @param vec container + * @param array_name array name + */ + Array4D(const vector>>> &vec, const string &array_name = "Array4D") { + this->set_vector(vec); + this->array_name = array_name; + } + + /** + * operator= to vector> container + * @param vec container + */ + Array4D &operator=(const vector>>> &vec) { + this->set_vector(vec); + return *this; + } + + + /** + * operator= to flatten vector container + * @param vec container + */ + Array4D &operator=(const vector &vec) { + this->set_flatten_vector(vec); + return *this; + } + + + vector get_shape() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = dim[d]; + return sh; + } + + vector get_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d]; + return sh; + } + + vector get_memory_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d] * sizeof(T); + return sh; + } +}; + + +/** + * Multidimensional (5 - dimensional) array of type T with contiguous memory layout. + * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @tparam T data type + */ +template +class Array5D : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + using ContiguousArrayND::is_proxy_; + + size_t dim[5] = {0}; ///< dimensions + size_t s[5] = {0}; ///< strides + int ndim = 5; ///< number of dimensions +public: + + /** + * Default empty constructor + */ + Array5D() = default; + + /** + * Parametrized constructor with array name + * @param array_name name of array (for error logging) + */ + Array5D(const string &array_name) { this->array_name = array_name; } + + /** + * Parametrized constructor + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + Array5D(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, const string &array_name = "Array5D", + T *new_data = nullptr) { + init(d0, d1, d2, d3, d4, array_name, new_data); + } + + /** + * Setup the dimensions and strides of array + * @param d0,... array sizes for different dimensions + */ + void set_dimensions(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4) { + + dim[0] = d0; + dim[1] = d1; + dim[2] = d2; + dim[3] = d3; + dim[4] = d4; + + s[4] = 1; + s[3] = s[4] * dim[4]; + s[2] = s[3] * dim[3]; + s[1] = s[2] * dim[2]; + s[0] = s[1] * dim[1]; + + size = s[0] * dim[0]; + }; + + /** + * Initialize array storage, dimensions and strides + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + void init(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, const string &array_name = "Array5D", + T *new_data = nullptr) { + this->array_name = array_name; + + size_t old_size = size; + set_dimensions(d0, d1, d2, d3, d4); + + bool new_is_proxy = (new_data != nullptr); + + if (new_is_proxy) { + if (!is_proxy_) delete[] data; + data = new_data; + } else { + if (size != old_size) { + T *old_data = data; //preserve the pointer to the old data + data = new T[size]; // allocate new data + if (old_data != nullptr) { // + size_t min_size = old_size < size ? old_size : size; + memcpy(data, old_data, min_size * sizeof(T)); + if (!is_proxy_) delete[] old_data; + } + //memset(data, 0, size * sizeof(T)); + } else { + //memset(data, 0, size * sizeof(T)); + } + } + + is_proxy_ = new_is_proxy; + } + + /** + * Resize array + * @param d0,... array sizes for different dimensions + */ + void resize(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4) { + init(d0, d1, d2, d3, d4, this->array_name); + } + + /** + * Reshape array without reset the data + * @param d0,... array sizes for different dimensions + */ + void reshape(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4) { + //check data size consistency + size_t new_size = d0 * d1 * d2 * d3 * d4; + if (new_size != size) + throw invalid_argument("Couldn't reshape array when the size is not conserved"); + set_dimensions(d0, d1, d2, d3, d4); + } + + /** + * Get array size in dimension "d" + * @param d dimension index + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + + /** + * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + void check_indices(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4) const { + + if ((i0 < 0) | (i0 >= dim[0])) { + char buf[1024]; + sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + throw std::out_of_range(buf); + } + + if ((i1 < 0) | (i1 >= dim[1])) { + char buf[1024]; + sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); + throw std::out_of_range(buf); + } + + if ((i2 < 0) | (i2 >= dim[2])) { + char buf[1024]; + sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); + throw std::out_of_range(buf); + } + + if ((i3 < 0) | (i3 >= dim[3])) { + char buf[1024]; + sprintf(buf, "%s: index i3=%ld out of range (0, %ld)\n", array_name.c_str(), i3, dim[3] - 1); + throw std::out_of_range(buf); + } + + if ((i4 < 0) | (i4 >= dim[4])) { + char buf[1024]; + sprintf(buf, "%s: index i4=%ld out of range (0, %ld)\n", array_name.c_str(), i4, dim[4] - 1); + throw std::out_of_range(buf); + } + + } + +#endif + + /** + * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline const T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2, i3, i4); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4]; + + } + + /** + * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2, i3, i4); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4]; + + } + + /** + * Array comparison operator + * @param other + */ + bool operator==(const Array5D &other) const { + //compare dimensions + for (int d = 0; d < ndim; d++) { + if (this->dim[d] != other.dim[d]) + return false; + } + return ContiguousArrayND::operator==(other); + } + + /** + * Convert to nested vector> container + * @return vector container + */ + vector>>>> to_vector() const { + vector>>>> res; + + res.resize(dim[0]); + + for (int i0 = 0; i0 < dim[0]; i0++) { + res[i0].resize(dim[1]); + + + for (int i1 = 0; i1 < dim[1]; i1++) { + res[i0][i1].resize(dim[2]); + + + for (int i2 = 0; i2 < dim[2]; i2++) { + res[i0][i1][i2].resize(dim[3]); + + + for (int i3 = 0; i3 < dim[3]; i3++) { + res[i0][i1][i2][i3].resize(dim[4]); + + + for (int i4 = 0; i4 < dim[4]; i4++) { + res[i0][i1][i2][i3][i4] = operator()(i0, i1, i2, i3, i4); + + } + } + } + } + } + + + return res; + } // end to_vector() + + + /** + * Set values to vector> container + * @param vec container + */ + void set_vector(const vector>>>> &vec) { + size_t d0 = 0; + size_t d1 = 0; + size_t d2 = 0; + size_t d3 = 0; + size_t d4 = 0; + d0 = vec.size(); + + if (d0 > 0) { + d1 = vec.at(0).size(); + if (d1 > 0) { + d2 = vec.at(0).at(0).size(); + if (d2 > 0) { + d3 = vec.at(0).at(0).at(0).size(); + if (d3 > 0) { + d4 = vec.at(0).at(0).at(0).at(0).size(); + + + } + } + } + } + + init(d0, d1, d2, d3, d4, array_name); + for (int i0 = 0; i0 < dim[0]; i0++) { + if (vec.at(i0).size() != d1) + throw std::invalid_argument("Vector size is not constant at dimension 1"); + + for (int i1 = 0; i1 < dim[1]; i1++) { + if (vec.at(i0).at(i1).size() != d2) + throw std::invalid_argument("Vector size is not constant at dimension 2"); + + for (int i2 = 0; i2 < dim[2]; i2++) { + if (vec.at(i0).at(i1).at(i2).size() != d3) + throw std::invalid_argument("Vector size is not constant at dimension 3"); + + for (int i3 = 0; i3 < dim[3]; i3++) { + if (vec.at(i0).at(i1).at(i2).at(i3).size() != d4) + throw std::invalid_argument("Vector size is not constant at dimension 4"); + + for (int i4 = 0; i4 < dim[4]; i4++) { + operator()(i0, i1, i2, i3, i4) = vec.at(i0).at(i1).at(i2).at(i3).at(i4); + + } + } + } + } + } + + } + + /** + * Parametrized constructor from vector> container + * @param vec container + * @param array_name array name + */ + Array5D(const vector>>>> &vec, const string &array_name = "Array5D") { + this->set_vector(vec); + this->array_name = array_name; + } + + /** + * operator= to vector> container + * @param vec container + */ + Array5D &operator=(const vector>>>> &vec) { + this->set_vector(vec); + return *this; + } + + + /** + * operator= to flatten vector container + * @param vec container + */ + Array5D &operator=(const vector &vec) { + this->set_flatten_vector(vec); + return *this; + } + + + vector get_shape() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = dim[d]; + return sh; + } + + vector get_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d]; + return sh; + } + + vector get_memory_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d] * sizeof(T); + return sh; + } +}; + + +/** + * Multidimensional (6 - dimensional) array of type T with contiguous memory layout. + * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @tparam T data type + */ +template +class Array6D : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + using ContiguousArrayND::is_proxy_; + + size_t dim[6] = {0}; ///< dimensions + size_t s[6] = {0}; ///< strides + int ndim = 6; ///< number of dimensions +public: + + /** + * Default empty constructor + */ + Array6D() = default; + + /** + * Parametrized constructor with array name + * @param array_name name of array (for error logging) + */ + Array6D(const string &array_name) { this->array_name = array_name; } + + /** + * Parametrized constructor + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + Array6D(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5, const string &array_name = "Array6D", + T *new_data = nullptr) { + init(d0, d1, d2, d3, d4, d5, array_name, new_data); + } + + /** + * Setup the dimensions and strides of array + * @param d0,... array sizes for different dimensions + */ + void set_dimensions(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5) { + + dim[0] = d0; + dim[1] = d1; + dim[2] = d2; + dim[3] = d3; + dim[4] = d4; + dim[5] = d5; + + s[5] = 1; + s[4] = s[5] * dim[5]; + s[3] = s[4] * dim[4]; + s[2] = s[3] * dim[3]; + s[1] = s[2] * dim[2]; + s[0] = s[1] * dim[1]; + + size = s[0] * dim[0]; + }; + + /** + * Initialize array storage, dimensions and strides + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + void init(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5, const string &array_name = "Array6D", + T *new_data = nullptr) { + this->array_name = array_name; + + size_t old_size = size; + set_dimensions(d0, d1, d2, d3, d4, d5); + + bool new_is_proxy = (new_data != nullptr); + + if (new_is_proxy) { + if (!is_proxy_) delete[] data; + data = new_data; + } else { + if (size != old_size) { + T *old_data = data; //preserve the pointer to the old data + data = new T[size]; // allocate new data + if (old_data != nullptr) { // + size_t min_size = old_size < size ? old_size : size; + memcpy(data, old_data, min_size * sizeof(T)); + if (!is_proxy_) delete[] old_data; + } + //memset(data, 0, size * sizeof(T)); + } else { + //memset(data, 0, size * sizeof(T)); + } + } + + is_proxy_ = new_is_proxy; + } + + /** + * Resize array + * @param d0,... array sizes for different dimensions + */ + void resize(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5) { + init(d0, d1, d2, d3, d4, d5, this->array_name); + } + + /** + * Reshape array without reset the data + * @param d0,... array sizes for different dimensions + */ + void reshape(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5) { + //check data size consistency + size_t new_size = d0 * d1 * d2 * d3 * d4 * d5; + if (new_size != size) + throw invalid_argument("Couldn't reshape array when the size is not conserved"); + set_dimensions(d0, d1, d2, d3, d4, d5); + } + + /** + * Get array size in dimension "d" + * @param d dimension index + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + + /** + * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + void check_indices(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4, size_t i5) const { + + if ((i0 < 0) | (i0 >= dim[0])) { + char buf[1024]; + sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + throw std::out_of_range(buf); + } + + if ((i1 < 0) | (i1 >= dim[1])) { + char buf[1024]; + sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); + throw std::out_of_range(buf); + } + + if ((i2 < 0) | (i2 >= dim[2])) { + char buf[1024]; + sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); + throw std::out_of_range(buf); + } + + if ((i3 < 0) | (i3 >= dim[3])) { + char buf[1024]; + sprintf(buf, "%s: index i3=%ld out of range (0, %ld)\n", array_name.c_str(), i3, dim[3] - 1); + throw std::out_of_range(buf); + } + + if ((i4 < 0) | (i4 >= dim[4])) { + char buf[1024]; + sprintf(buf, "%s: index i4=%ld out of range (0, %ld)\n", array_name.c_str(), i4, dim[4] - 1); + throw std::out_of_range(buf); + } + + if ((i5 < 0) | (i5 >= dim[5])) { + char buf[1024]; + sprintf(buf, "%s: index i5=%ld out of range (0, %ld)\n", array_name.c_str(), i5, dim[5] - 1); + throw std::out_of_range(buf); + } + + } + +#endif + + /** + * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline const T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4, size_t i5) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2, i3, i4, i5); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4 * s[4] + i5]; + + } + + /** + * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4, size_t i5) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2, i3, i4, i5); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4 * s[4] + i5]; + + } + + /** + * Array comparison operator + * @param other + */ + bool operator==(const Array6D &other) const { + //compare dimensions + for (int d = 0; d < ndim; d++) { + if (this->dim[d] != other.dim[d]) + return false; + } + return ContiguousArrayND::operator==(other); + } + + /** + * Convert to nested vector> container + * @return vector container + */ + vector>>>>> to_vector() const { + vector>>>>> res; + + res.resize(dim[0]); + + for (int i0 = 0; i0 < dim[0]; i0++) { + res[i0].resize(dim[1]); + + + for (int i1 = 0; i1 < dim[1]; i1++) { + res[i0][i1].resize(dim[2]); + + + for (int i2 = 0; i2 < dim[2]; i2++) { + res[i0][i1][i2].resize(dim[3]); + + + for (int i3 = 0; i3 < dim[3]; i3++) { + res[i0][i1][i2][i3].resize(dim[4]); + + + for (int i4 = 0; i4 < dim[4]; i4++) { + res[i0][i1][i2][i3][i4].resize(dim[5]); + + + for (int i5 = 0; i5 < dim[5]; i5++) { + res[i0][i1][i2][i3][i4][i5] = operator()(i0, i1, i2, i3, i4, i5); + + } + } + } + } + } + } + + + return res; + } // end to_vector() + + + /** + * Set values to vector> container + * @param vec container + */ + void set_vector(const vector>>>>> &vec) { + size_t d0 = 0; + size_t d1 = 0; + size_t d2 = 0; + size_t d3 = 0; + size_t d4 = 0; + size_t d5 = 0; + d0 = vec.size(); + + if (d0 > 0) { + d1 = vec.at(0).size(); + if (d1 > 0) { + d2 = vec.at(0).at(0).size(); + if (d2 > 0) { + d3 = vec.at(0).at(0).at(0).size(); + if (d3 > 0) { + d4 = vec.at(0).at(0).at(0).at(0).size(); + if (d4 > 0) { + d5 = vec.at(0).at(0).at(0).at(0).at(0).size(); + + + } + } + } + } + } + + init(d0, d1, d2, d3, d4, d5, array_name); + for (int i0 = 0; i0 < dim[0]; i0++) { + if (vec.at(i0).size() != d1) + throw std::invalid_argument("Vector size is not constant at dimension 1"); + + for (int i1 = 0; i1 < dim[1]; i1++) { + if (vec.at(i0).at(i1).size() != d2) + throw std::invalid_argument("Vector size is not constant at dimension 2"); + + for (int i2 = 0; i2 < dim[2]; i2++) { + if (vec.at(i0).at(i1).at(i2).size() != d3) + throw std::invalid_argument("Vector size is not constant at dimension 3"); + + for (int i3 = 0; i3 < dim[3]; i3++) { + if (vec.at(i0).at(i1).at(i2).at(i3).size() != d4) + throw std::invalid_argument("Vector size is not constant at dimension 4"); + + for (int i4 = 0; i4 < dim[4]; i4++) { + if (vec.at(i0).at(i1).at(i2).at(i3).at(i4).size() != d5) + throw std::invalid_argument("Vector size is not constant at dimension 5"); + + for (int i5 = 0; i5 < dim[5]; i5++) { + operator()(i0, i1, i2, i3, i4, i5) = vec.at(i0).at(i1).at(i2).at(i3).at(i4).at(i5); + + } + } + } + } + } + } + + } + + /** + * Parametrized constructor from vector> container + * @param vec container + * @param array_name array name + */ + Array6D(const vector>>>>> &vec, const string &array_name = "Array6D") { + this->set_vector(vec); + this->array_name = array_name; + } + + /** + * operator= to vector> container + * @param vec container + */ + Array6D &operator=(const vector>>>>> &vec) { + this->set_vector(vec); + return *this; + } + + + /** + * operator= to flatten vector container + * @param vec container + */ + Array6D &operator=(const vector &vec) { + this->set_flatten_vector(vec); + return *this; + } + + + vector get_shape() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = dim[d]; + return sh; + } + + vector get_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d]; + return sh; + } + + vector get_memory_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d] * sizeof(T); + return sh; + } +}; + + +#endif //ACE_MULTIARRAY_H diff --git a/lib/pace/ace_c_basis.cpp b/lib/pace/ace_c_basis.cpp new file mode 100644 index 0000000000..d1c55700b7 --- /dev/null +++ b/lib/pace/ace_c_basis.cpp @@ -0,0 +1,980 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Yury Lysogorskiy on 1.04.20. + +#include "ace_c_basis.h" +#include "ships_radial.h" + +using namespace std; + +ACECTildeBasisSet::ACECTildeBasisSet(string filename) { + load(filename); +} + +ACECTildeBasisSet::ACECTildeBasisSet(const ACECTildeBasisSet &other) { + ACECTildeBasisSet::_copy_scalar_memory(other); + ACECTildeBasisSet::_copy_dynamic_memory(other); + pack_flatten_basis(); +} + + +ACECTildeBasisSet &ACECTildeBasisSet::operator=(const ACECTildeBasisSet &other) { + if (this != &other) { + _clean(); + _copy_scalar_memory(other); + _copy_dynamic_memory(other); + pack_flatten_basis(); + } + return *this; +} + + +ACECTildeBasisSet::~ACECTildeBasisSet() { + ACECTildeBasisSet::_clean(); +} + +void ACECTildeBasisSet::_clean() { + // call parent method + ACEFlattenBasisSet::_clean(); + _clean_contiguous_arrays(); + _clean_basis_arrays(); +} + +void ACECTildeBasisSet::_copy_scalar_memory(const ACECTildeBasisSet &src) { + ACEFlattenBasisSet::_copy_scalar_memory(src); + num_ctilde_max = src.num_ctilde_max; +} + +void ACECTildeBasisSet::_copy_dynamic_memory(const ACECTildeBasisSet &src) {//allocate new memory + ACEFlattenBasisSet::_copy_dynamic_memory(src); + + if (src.basis_rank1 == nullptr) + throw runtime_error("Could not copy ACECTildeBasisSet::basis_rank1 - array not initialized"); + if (src.basis == nullptr) throw runtime_error("Could not copy ACECTildeBasisSet::basis - array not initialized"); + + + basis_rank1 = new ACECTildeBasisFunction *[src.nelements]; + basis = new ACECTildeBasisFunction *[src.nelements]; + + //copy basis arrays + for (SPECIES_TYPE mu = 0; mu < src.nelements; ++mu) { + basis_rank1[mu] = new ACECTildeBasisFunction[src.total_basis_size_rank1[mu]]; + + for (size_t i = 0; i < src.total_basis_size_rank1[mu]; i++) { + basis_rank1[mu][i] = src.basis_rank1[mu][i]; + } + + + basis[mu] = new ACECTildeBasisFunction[src.total_basis_size[mu]]; + for (size_t i = 0; i < src.total_basis_size[mu]; i++) { + basis[mu][i] = src.basis[mu][i]; + } + } + //DON"T COPY CONTIGUOUS ARRAY, REBUILD THEM +} + +void ACECTildeBasisSet::_clean_contiguous_arrays() { + ACEFlattenBasisSet::_clean_contiguous_arrays(); + + delete[] full_c_tildes_rank1; + full_c_tildes_rank1 = nullptr; + + delete[] full_c_tildes; + full_c_tildes = nullptr; +} + +//re-pack the constituent dynamic arrays of all basis functions in contiguous arrays +void ACECTildeBasisSet::pack_flatten_basis() { + compute_array_sizes(basis_rank1, basis); + + //1. clean contiguous arrays + _clean_contiguous_arrays(); + //2. allocate contiguous arrays + delete[] full_ns_rank1; + full_ns_rank1 = new NS_TYPE[rank_array_total_size_rank1]; + delete[] full_ls_rank1; + full_ls_rank1 = new NS_TYPE[rank_array_total_size_rank1]; + delete[] full_mus_rank1; + full_mus_rank1 = new SPECIES_TYPE[rank_array_total_size_rank1]; + delete[] full_ms_rank1; + full_ms_rank1 = new MS_TYPE[rank_array_total_size_rank1]; + + delete[] full_c_tildes_rank1; + full_c_tildes_rank1 = new DOUBLE_TYPE[coeff_array_total_size_rank1]; + + + delete[] full_ns; + full_ns = new NS_TYPE[rank_array_total_size]; + delete[] full_ls; + full_ls = new LS_TYPE[rank_array_total_size]; + delete[] full_mus; + full_mus = new SPECIES_TYPE[rank_array_total_size]; + delete[] full_ms; + full_ms = new MS_TYPE[ms_array_total_size]; + + delete[] full_c_tildes; + full_c_tildes = new DOUBLE_TYPE[coeff_array_total_size]; + + + //3. copy the values from private C_tilde_B_basis_function arrays to new contigous space + //4. clean private memory + //5. reassign private array pointers + + //r = 0, rank = 1 + size_t rank_array_ind_rank1 = 0; + size_t coeff_array_ind_rank1 = 0; + size_t ms_array_ind_rank1 = 0; + + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + for (int func_ind_r1 = 0; func_ind_r1 < total_basis_size_rank1[mu]; ++func_ind_r1) { + ACECTildeBasisFunction &func = basis_rank1[mu][func_ind_r1]; + + //copy values ns from c_tilde_basis_function private memory to contigous memory part + full_ns_rank1[rank_array_ind_rank1] = func.ns[0]; + + //copy values ls from c_tilde_basis_function private memory to contigous memory part + full_ls_rank1[rank_array_ind_rank1] = func.ls[0]; + + //copy values mus from c_tilde_basis_function private memory to contigous memory part + full_mus_rank1[rank_array_ind_rank1] = func.mus[0]; + + //copy values ctildes from c_tilde_basis_function private memory to contigous memory part + memcpy(&full_c_tildes_rank1[coeff_array_ind_rank1], func.ctildes, + func.ndensity * sizeof(DOUBLE_TYPE)); + + + //copy values mus from c_tilde_basis_function private memory to contigous memory part + memcpy(&full_ms_rank1[ms_array_ind_rank1], func.ms_combs, + func.num_ms_combs * + func.rank * sizeof(MS_TYPE)); + + //release memory of each ACECTildeBasisFunction if it is not proxy + func._clean(); + + func.mus = &full_mus_rank1[rank_array_ind_rank1]; + func.ns = &full_ns_rank1[rank_array_ind_rank1]; + func.ls = &full_ls_rank1[rank_array_ind_rank1]; + func.ms_combs = &full_ms_rank1[ms_array_ind_rank1]; + func.ctildes = &full_c_tildes_rank1[coeff_array_ind_rank1]; + func.is_proxy = true; + + rank_array_ind_rank1 += func.rank; + ms_array_ind_rank1 += func.rank * + func.num_ms_combs; + coeff_array_ind_rank1 += func.num_ms_combs * func.ndensity; + + } + } + + + //rank>1, r>0 + size_t rank_array_ind = 0; + size_t coeff_array_ind = 0; + size_t ms_array_ind = 0; + + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + for (int func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) { + ACECTildeBasisFunction &func = basis[mu][func_ind]; + + //copy values mus from c_tilde_basis_function private memory to contigous memory part + memcpy(&full_mus[rank_array_ind], func.mus, + func.rank * sizeof(SPECIES_TYPE)); + + //copy values ns from c_tilde_basis_function private memory to contigous memory part + memcpy(&full_ns[rank_array_ind], func.ns, + func.rank * sizeof(NS_TYPE)); + //copy values ls from c_tilde_basis_function private memory to contigous memory part + memcpy(&full_ls[rank_array_ind], func.ls, + func.rank * sizeof(LS_TYPE)); + //copy values mus from c_tilde_basis_function private memory to contigous memory part + memcpy(&full_ms[ms_array_ind], func.ms_combs, + func.num_ms_combs * + func.rank * sizeof(MS_TYPE)); + + //copy values ctildes from c_tilde_basis_function private memory to contigous memory part + memcpy(&full_c_tildes[coeff_array_ind], func.ctildes, + func.num_ms_combs * func.ndensity * sizeof(DOUBLE_TYPE)); + + + //release memory of each ACECTildeBasisFunction if it is not proxy + func._clean(); + + func.ns = &full_ns[rank_array_ind]; + func.ls = &full_ls[rank_array_ind]; + func.mus = &full_mus[rank_array_ind]; + func.ctildes = &full_c_tildes[coeff_array_ind]; + func.ms_combs = &full_ms[ms_array_ind]; + func.is_proxy = true; + + rank_array_ind += func.rank; + ms_array_ind += func.rank * + func.num_ms_combs; + coeff_array_ind += func.num_ms_combs * func.ndensity; + } + } +} + +void fwrite_c_tilde_b_basis_func(FILE *fptr, ACECTildeBasisFunction &func) { + RANK_TYPE r; + fprintf(fptr, "ctilde_basis_func: "); + fprintf(fptr, "rank=%d ndens=%d mu0=%d ", func.rank, func.ndensity, func.mu0); + + fprintf(fptr, "mu=("); + for (r = 0; r < func.rank; ++r) + fprintf(fptr, " %d ", func.mus[r]); + fprintf(fptr, ")\n"); + + fprintf(fptr, "n=("); + for (r = 0; r < func.rank; ++r) + fprintf(fptr, " %d ", func.ns[r]); + fprintf(fptr, ")\n"); + + fprintf(fptr, "l=("); + for (r = 0; r < func.rank; ++r) + fprintf(fptr, " %d ", func.ls[r]); + fprintf(fptr, ")\n"); + + fprintf(fptr, "num_ms=%d\n", func.num_ms_combs); + + for (int m_ind = 0; m_ind < func.num_ms_combs; m_ind++) { + fprintf(fptr, "<"); + for (r = 0; r < func.rank; ++r) + fprintf(fptr, " %d ", func.ms_combs[m_ind * func.rank + r]); + fprintf(fptr, ">: "); + for (DENSITY_TYPE p = 0; p < func.ndensity; p++) + fprintf(fptr, " %.18f ", func.ctildes[m_ind * func.ndensity + p]); + fprintf(fptr, "\n"); + } + +} + +void ACECTildeBasisSet::save(const string &filename) { + FILE *fptr; + fptr = fopen(filename.c_str(), "w"); + + fprintf(fptr, "nelements=%d\n", nelements); + + //elements mapping + fprintf(fptr, "elements:"); + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) + fprintf(fptr, " %s", elements_name[mu].c_str()); + fprintf(fptr, "\n\n"); + + fprintf(fptr, "lmax=%d\n\n", lmax); + + fprintf(fptr, "embedding-function: %s\n", npoti.c_str()); + + fprintf(fptr, "%ld FS parameters: ", FS_parameters.size()); + for (int i = 0; i < FS_parameters.size(); ++i) { + fprintf(fptr, " %f", FS_parameters.at(i)); + } + fprintf(fptr, "\n"); + + //hard-core energy cutoff repulsion + fprintf(fptr, "core energy-cutoff parameters: "); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + fprintf(fptr, "%.18f %.18f\n", rho_core_cutoffs(mu_i), drho_core_cutoffs(mu_i)); + + // save E0 values + fprintf(fptr, "E0:"); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + fprintf(fptr, " %.18f", E0vals(mu_i)); + fprintf(fptr, "\n"); + + + fprintf(fptr, "\n"); + + + fprintf(fptr, "radbasename=%s\n", radial_functions->radbasename.c_str()); + fprintf(fptr, "nradbase=%d\n", nradbase); + fprintf(fptr, "nradmax=%d\n", nradmax); + + + fprintf(fptr, "cutoffmax=%f\n", cutoffmax); + + fprintf(fptr, "deltaSplineBins=%f\n", deltaSplineBins); + + //hard-core repulsion + fprintf(fptr, "core repulsion parameters: "); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) + fprintf(fptr, "%.18f %.18f\n", radial_functions->prehc(mu_i, mu_j), radial_functions->lambdahc(mu_j, mu_j)); + + + + + + //TODO: radial functions + //radparameter + fprintf(fptr, "radparameter="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) + fprintf(fptr, " %.18f", radial_functions->lambda(mu_i, mu_j)); + fprintf(fptr, "\n"); + + fprintf(fptr, "cutoff="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) + fprintf(fptr, " %.18f", radial_functions->cut(mu_i, mu_j)); + fprintf(fptr, "\n"); + + fprintf(fptr, "dcut="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) + fprintf(fptr, " %.18f", radial_functions->dcut(mu_i, mu_j)); + fprintf(fptr, "\n"); + + fprintf(fptr, "crad="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { + for (NS_TYPE k = 0; k < nradbase; k++) { + for (NS_TYPE n = 0; n < nradmax; n++) { + for (LS_TYPE l = 0; l <= lmax; l++) { + fprintf(fptr, " %.18f", radial_functions->crad(mu_i, mu_j, n, l, k)); + } + fprintf(fptr, "\n"); + } + } + } + + fprintf(fptr, "\n"); + + fprintf(fptr, "rankmax=%d\n", rankmax); + fprintf(fptr, "ndensitymax=%d\n", ndensitymax); + fprintf(fptr, "\n"); + + //num_c_tilde_max + fprintf(fptr, "num_c_tilde_max=%d\n", num_ctilde_max); + fprintf(fptr, "num_ms_combinations_max=%d\n", num_ms_combinations_max); + + + //write total_basis_size and total_basis_size_rank1 + fprintf(fptr, "total_basis_size_rank1: "); + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + fprintf(fptr, "%d ", total_basis_size_rank1[mu]); + } + fprintf(fptr, "\n"); + + for (SPECIES_TYPE mu = 0; mu < nelements; mu++) + for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size_rank1[mu]; ++func_ind) + fwrite_c_tilde_b_basis_func(fptr, basis_rank1[mu][func_ind]); + + fprintf(fptr, "total_basis_size: "); + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + fprintf(fptr, "%d ", total_basis_size[mu]); + } + fprintf(fptr, "\n"); + + for (SPECIES_TYPE mu = 0; mu < nelements; mu++) + for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) + fwrite_c_tilde_b_basis_func(fptr, basis[mu][func_ind]); + + + fclose(fptr); +} + +void fread_c_tilde_b_basis_func(FILE *fptr, ACECTildeBasisFunction &func) { + RANK_TYPE r; + int res; + char buf[3][128]; + + res = fscanf(fptr, " ctilde_basis_func: "); + + res = fscanf(fptr, "rank=%s ndens=%s mu0=%s ", buf[0], buf[1], buf[2]); + if (res != 3) + throw invalid_argument("Could not read C-tilde basis function"); + + func.rank = (RANK_TYPE) stol(buf[0]); + func.ndensity = (DENSITY_TYPE) stol(buf[1]); + func.mu0 = (SPECIES_TYPE) stol(buf[2]); + + func.mus = new SPECIES_TYPE[func.rank]; + func.ns = new NS_TYPE[func.rank]; + func.ls = new LS_TYPE[func.rank]; + + res = fscanf(fptr, " mu=("); + for (r = 0; r < func.rank; ++r) { + res = fscanf(fptr, "%s", buf[0]); + if (res != 1) + throw invalid_argument("Could not read C-tilde basis function"); + func.mus[r] = (SPECIES_TYPE) stol(buf[0]); + } + res = fscanf(fptr, " )"); // ")" + + res = fscanf(fptr, " n=("); // "n=" + for (r = 0; r < func.rank; ++r) { + res = fscanf(fptr, "%s", buf[0]); + if (res != 1) + throw invalid_argument("Could not read C-tilde basis function"); + + func.ns[r] = (NS_TYPE) stol(buf[0]); + } + res = fscanf(fptr, " )"); + + res = fscanf(fptr, " l=("); + for (r = 0; r < func.rank; ++r) { + res = fscanf(fptr, "%s", buf[0]); + if (res != 1) + throw invalid_argument("Could not read C-tilde basis function"); + func.ls[r] = (NS_TYPE) stol(buf[0]); + } + res = fscanf(fptr, " )"); + + res = fscanf(fptr, " num_ms=%s\n", buf[0]); + if (res != 1) + throw invalid_argument("Could not read C-tilde basis function"); + + func.num_ms_combs = (SHORT_INT_TYPE) stoi(buf[0]); + + func.ms_combs = new MS_TYPE[func.rank * func.num_ms_combs]; + func.ctildes = new DOUBLE_TYPE[func.ndensity * func.num_ms_combs]; + + for (int m_ind = 0; m_ind < func.num_ms_combs; m_ind++) { + res = fscanf(fptr, " <"); + for (r = 0; r < func.rank; ++r) { + res = fscanf(fptr, "%s", buf[0]); + if (res != 1) + throw invalid_argument("Could not read C-tilde basis function"); + func.ms_combs[m_ind * func.rank + r] = stoi(buf[0]); + } + res = fscanf(fptr, " >:"); + for (DENSITY_TYPE p = 0; p < func.ndensity; p++) { + res = fscanf(fptr, "%s", buf[0]); + if (res != 1) + throw invalid_argument("Could not read C-tilde basis function"); + func.ctildes[m_ind * func.ndensity + p] = stod(buf[0]); + } + } +} + +string +format_error_message(const char *buffer, const string &filename, const string &var_name, const string &expected) { + string err_message = "File '" + filename + "': couldn't read '" + var_name + "'"; + if (buffer) + err_message = err_message + ", read:'" + buffer + "'"; + if (!expected.empty()) + err_message = err_message + ". Expected format: '" + expected + "'"; + return err_message; +} + +void throw_error(const string &filename, const string &var_name, const string expected = "") { + throw invalid_argument(format_error_message(nullptr, filename, var_name, expected)); +} + +DOUBLE_TYPE stod_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") { + try { + return stod(buffer); + } catch (invalid_argument &exc) { + throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str()); + } +} + +int stoi_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") { + try { + return stoi(buffer); + } catch (invalid_argument &exc) { + throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str()); + } +} + +long int stol_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") { + try { + return stol(buffer); + } catch (invalid_argument &exc) { + throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str()); + } +} + +void ACECTildeBasisSet::load(const string filename) { + int res; + char buffer[1024], buffer2[1024]; + string radbasename = "ChebExpCos"; + + FILE *fptr; + fptr = fopen(filename.c_str(), "r"); + if (fptr == NULL) + throw invalid_argument("Could not open file " + filename); + + //read number of elements + res = fscanf(fptr, " nelements="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "nelements", "nelements=[number]"); + nelements = stoi_err(buffer, filename, "nelements", "nelements=[number]"); + + //elements mapping + elements_name = new string[nelements]; + res = fscanf(fptr, " elements:"); + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "elements", "elements: Ele1 Ele2 ..."); + elements_name[mu] = buffer; + } + + // load angular basis - only need spherical harmonics parameter + res = fscanf(fptr, " lmax=%s\n", buffer); + if (res != 1) + throw_error(filename, "lmax", "lmax=[number]"); + lmax = stoi_err(buffer, filename, "lmax", "lmax=[number]"); + spherical_harmonics.init(lmax); + + + // reading "embedding-function:" + bool is_embedding_function_specified = false; + res = fscanf(fptr, " embedding-function: %s", buffer); + if (res == 0) { + //throw_error(filename, "E0", " E0: E0-species1 E0-species2 ..."); + this->npoti = "FinnisSinclair"; // default values + //printf("Warning! No embedding-function is specified, embedding-function: FinnisSinclair would be assumed\n"); + is_embedding_function_specified = false; + } else { + this->npoti = buffer; + is_embedding_function_specified = true; + } + int parameters_size; + res = fscanf(fptr, "%s FS parameters:", buffer); + if (res != 1) + throw_error(filename, "FS parameters size", "[number] FS parameters: par1 par2 ..."); + parameters_size = stoi_err(buffer, filename, "FS parameters size", "[number] FS parameters"); + FS_parameters.resize(parameters_size); + for (int i = 0; i < FS_parameters.size(); ++i) { + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "FS parameter", "[number] FS parameters: [par1] [par2] ..."); + FS_parameters[i] = stod_err(buffer, filename, "FS parameter", "[number] FS parameters: [par1] [par2] ..."); + } + + if (!is_embedding_function_specified) { + // assuming non-linear potential, and embedding function type is important + for (int j = 1; j < parameters_size; j += 2) + if (FS_parameters[j] != 1.0) { //if not ensure linearity of embedding function parameters + printf("ERROR! Your potential is non-linear\n"); + printf("Please specify 'embedding-function: FinnisSinclair' or 'embedding-function: FinnisSinclairShiftedScaled' before 'FS parameters size' line\n"); + throw_error(filename, "embedding-function", "FinnisSinclair or FinnisSinclairShiftedScaled"); + } + printf("Notice! No embedding-function is specified, but potential has linear embedding, default embedding-function: FinnisSinclair would be assumed\n"); + } + + //hard-core energy cutoff repulsion + res = fscanf(fptr, " core energy-cutoff parameters:"); + if (res != 0) + throw_error(filename, "core energy-cutoff parameters", "core energy-cutoff parameters: [par1] [par2]"); + + rho_core_cutoffs.init(nelements, "rho_core_cutoffs"); + drho_core_cutoffs.init(nelements, "drho_core_cutoffs"); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) { + res = fscanf(fptr, "%s %s", buffer, buffer2); + if (res != 2) + throw_error(filename, "core energy-cutoff parameters", + "core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ..."); + rho_core_cutoffs(mu_i) = stod_err(buffer, filename, "rho core cutoff", + "core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ..."); + drho_core_cutoffs(mu_i) = stod_err(buffer2, filename, "drho_core_cutoff", + "core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ..."); + } + + // atom energy shift E0 (energy of isolated atom) + E0vals.init(nelements); + + // reading "E0:" + res = fscanf(fptr, " E0: %s", buffer); + if (res == 0) { + //throw_error(filename, "E0", " E0: E0-species1 E0-species2 ..."); + E0vals.fill(0.0); + } else { + double E0 = atof(buffer); + E0vals(0) = E0; + + for (SPECIES_TYPE mu_i = 1; mu_i < nelements; ++mu_i) { + res = fscanf(fptr, " %lf", &E0); + if (res != 1) + throw_error(filename, "E0", " couldn't read one of the E0 values"); + E0vals(mu_i) = E0; + } + res = fscanf(fptr, "\n"); + if (res != 0) + printf("file %s : format seems broken near E0; trying to continue...\n", filename.c_str()); + } + + // check which radial basis we need to load + res = fscanf(fptr, " radbasename=%s\n", buffer); + if (res != 1) { + throw_error(filename, "radbasename", "rabbasename=ChebExpCos|ChebPow|ACE.jl.Basic"); + } else { + radbasename = buffer; + } + +// printf("radbasename = `%s`\n", radbasename.c_str()); + if (radbasename == "ChebExpCos" | radbasename == "ChebPow") { + _load_radial_ACERadial(fptr, filename, radbasename); + } else if (radbasename == "ACE.jl.Basic") { + _load_radial_SHIPsBasic(fptr, filename, radbasename); + } else { + throw invalid_argument( + ("File '" + filename + "': I don't know how to read radbasename = " + radbasename).c_str()); + } + + res = fscanf(fptr, " rankmax="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "rankmax", "rankmax=[number]"); + rankmax = stoi_err(buffer, filename, "rankmax", "rankmax=[number]"); + + res = fscanf(fptr, " ndensitymax="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "ndensitymax", "ndensitymax=[number]"); + ndensitymax = stoi_err(buffer, filename, "ndensitymax", "ndensitymax=[number]"); + + // read the list of correlations to be put into the basis + //num_c_tilde_max + res = fscanf(fptr, " num_c_tilde_max="); + res = fscanf(fptr, "%s\n", buffer); + if (res != 1) + throw_error(filename, "num_c_tilde_max", "num_c_tilde_max=[number]"); + num_ctilde_max = stol_err(buffer, filename, "num_c_tilde_max", "num_c_tilde_max=[number]"); + + res = fscanf(fptr, " num_ms_combinations_max="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "num_ms_combinations_max", "num_ms_combinations_max=[number]"); +// throw invalid_argument(("File '" + filename + "': couldn't read num_ms_combinations_max").c_str()); + num_ms_combinations_max = stol_err(buffer, filename, "num_ms_combinations_max", "num_ms_combinations_max=[number]"); + + //read total_basis_size_rank1 + total_basis_size_rank1 = new SHORT_INT_TYPE[nelements]; + basis_rank1 = new ACECTildeBasisFunction *[nelements]; + res = fscanf(fptr, " total_basis_size_rank1: "); + + + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "total_basis_size_rank1", "total_basis_size_rank1: [size_ele1] [size_ele2] ..."); +// throw invalid_argument(("File '" + filename + "': couldn't read total_basis_size_rank1").c_str()); + total_basis_size_rank1[mu] = stoi_err(buffer, filename, "total_basis_size_rank1", + "total_basis_size_rank1: [size_ele1] [size_ele2] ..."); + basis_rank1[mu] = new ACECTildeBasisFunction[total_basis_size_rank1[mu]]; + } + for (SPECIES_TYPE mu = 0; mu < nelements; mu++) + for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size_rank1[mu]; ++func_ind) { + fread_c_tilde_b_basis_func(fptr, basis_rank1[mu][func_ind]); + } + + //read total_basis_size + res = fscanf(fptr, " total_basis_size: "); + total_basis_size = new SHORT_INT_TYPE[nelements]; + basis = new ACECTildeBasisFunction *[nelements]; + + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "total_basis_size", "total_basis_size: [size_ele1] [size_ele2] ..."); + total_basis_size[mu] = stoi_err(buffer, filename, "total_basis_size", + "total_basis_size: [size_ele1] [size_ele2] ..."); + basis[mu] = new ACECTildeBasisFunction[total_basis_size[mu]]; + } + for (SPECIES_TYPE mu = 0; mu < nelements; mu++) + for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) { + fread_c_tilde_b_basis_func(fptr, basis[mu][func_ind]); + } + + fclose(fptr); + +// radial_functions->radbasename = radbasename; + radial_functions->setuplookupRadspline(); + pack_flatten_basis(); +} + +void ACECTildeBasisSet::compute_array_sizes(ACECTildeBasisFunction **basis_rank1, ACECTildeBasisFunction **basis) { + //compute arrays sizes + rank_array_total_size_rank1 = 0; + //ms_array_total_size_rank1 = rank_array_total_size_rank1; + coeff_array_total_size_rank1 = 0; + + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + if (total_basis_size_rank1[mu] > 0) { + rank_array_total_size_rank1 += total_basis_size_rank1[mu]; + + ACEAbstractBasisFunction &func = basis_rank1[mu][0];//TODO: get total density instead of density from first function + coeff_array_total_size_rank1 += total_basis_size_rank1[mu] * func.ndensity; + } + } + + rank_array_total_size = 0; + coeff_array_total_size = 0; + + ms_array_total_size = 0; + max_dB_array_size = 0; + + + max_B_array_size = 0; + + size_t cur_ms_size = 0; + size_t cur_ms_rank_size = 0; + + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + + cur_ms_size = 0; + cur_ms_rank_size = 0; + for (int func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) { + auto &func = basis[mu][func_ind]; + rank_array_total_size += func.rank; + ms_array_total_size += func.rank * func.num_ms_combs; + coeff_array_total_size += func.ndensity * func.num_ms_combs; + + cur_ms_size += func.num_ms_combs; + cur_ms_rank_size += func.rank * func.num_ms_combs; + } + + if (cur_ms_size > max_B_array_size) + max_B_array_size = cur_ms_size; + + if (cur_ms_rank_size > max_dB_array_size) + max_dB_array_size = cur_ms_rank_size; + } +} + +void ACECTildeBasisSet::_clean_basis_arrays() { + if (basis_rank1 != nullptr) + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + delete[] basis_rank1[mu]; + basis_rank1[mu] = nullptr; + } + + if (basis != nullptr) + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + delete[] basis[mu]; + basis[mu] = nullptr; + } + delete[] basis; + basis = nullptr; + + delete[] basis_rank1; + basis_rank1 = nullptr; +} + +//pack into 1D array with all basis functions +void ACECTildeBasisSet::flatten_basis(C_tilde_full_basis_vector2d &mu0_ctilde_basis_vector) { + + _clean_basis_arrays(); + basis_rank1 = new ACECTildeBasisFunction *[nelements]; + basis = new ACECTildeBasisFunction *[nelements]; + + delete[] total_basis_size_rank1; + delete[] total_basis_size; + total_basis_size_rank1 = new SHORT_INT_TYPE[nelements]; + total_basis_size = new SHORT_INT_TYPE[nelements]; + + + size_t tot_size_rank1 = 0; + size_t tot_size = 0; + + for (SPECIES_TYPE mu = 0; mu < this->nelements; ++mu) { + tot_size = 0; + tot_size_rank1 = 0; + + for (auto &func: mu0_ctilde_basis_vector[mu]) { + if (func.rank == 1) tot_size_rank1 += 1; + else tot_size += 1; + } + + total_basis_size_rank1[mu] = tot_size_rank1; + basis_rank1[mu] = new ACECTildeBasisFunction[tot_size_rank1]; + + total_basis_size[mu] = tot_size; + basis[mu] = new ACECTildeBasisFunction[tot_size]; + } + + + for (SPECIES_TYPE mu = 0; mu < this->nelements; ++mu) { + size_t ind_rank1 = 0; + size_t ind = 0; + + for (auto &func: mu0_ctilde_basis_vector[mu]) { + if (func.rank == 1) { //r=0, rank=1 + basis_rank1[mu][ind_rank1] = func; + ind_rank1 += 1; + } else { //r>0, rank>1 + basis[mu][ind] = func; + ind += 1; + } + } + + } +} + + +void ACECTildeBasisSet::_load_radial_ACERadial(FILE *fptr, + const string filename, + const string radbasename) { + int res; + char buffer[1024], buffer2[1024]; + + res = fscanf(fptr, " nradbase="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "nradbase", "nradbase=[number]"); +// throw invalid_argument(("File '" + filename + "': couldn't read nradbase").c_str()); + nradbase = stoi_err(buffer, filename, "nradbase", "nradbase=[number]"); + + res = fscanf(fptr, " nradmax="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "nradmax", "nradmax=[number]"); + nradmax = stoi_err(buffer, filename, "nradmax", "nradmax=[number]"); + + res = fscanf(fptr, " cutoffmax="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "cutoffmax", "cutoffmax=[number]"); + cutoffmax = stod_err(buffer, filename, "cutoffmax", "cutoffmax=[number]"); + + + res = fscanf(fptr, " deltaSplineBins="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "deltaSplineBins", "deltaSplineBins=[spline density, Angstroms]"); +// throw invalid_argument(("File '" + filename + "': couldn't read ntot").c_str()); + deltaSplineBins = stod_err(buffer, filename, "deltaSplineBins", "deltaSplineBins=[spline density, Angstroms]"); + + + if (radial_functions == nullptr) + radial_functions = new ACERadialFunctions(nradbase, lmax, nradmax, + deltaSplineBins, + nelements, + cutoffmax, radbasename); + else + radial_functions->init(nradbase, lmax, nradmax, + deltaSplineBins, + nelements, + cutoffmax, radbasename); + + + //hard-core repulsion + res = fscanf(fptr, " core repulsion parameters:"); + if (res != 0) + throw_error(filename, "core repulsion parameters", "core repulsion parameters: [prehc lambdahc] ..."); +// throw invalid_argument(("File '" + filename + "': couldn't read core repulsion parameters").c_str()); + + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { + res = fscanf(fptr, "%s %s", buffer, buffer2); + if (res != 2) + throw_error(filename, "core repulsion parameters", "core repulsion parameters: [prehc lambdahc] ..."); + radial_functions->prehc(mu_i, mu_j) = stod_err(buffer, filename, "core repulsion parameters", + "core repulsion parameters: [prehc lambdahc] ..."); + radial_functions->lambdahc(mu_i, mu_j) = stod_err(buffer2, filename, "core repulsion parameters", + "core repulsion parameters: [prehc lambdahc] ..."); + } + + + + //read radial functions parameter + res = fscanf(fptr, " radparameter="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "radparameter", "radparameter=[param_ele1] [param_ele2]"); + radial_functions->lambda(mu_i, mu_j) = stod_err(buffer, filename, "radparameter", + "radparameter=[param_ele1] [param_ele2]"); + } + + + res = fscanf(fptr, " cutoff="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "cutoff", "cutoff=[param_ele1] [param_ele2]"); + radial_functions->cut(mu_i, mu_j) = stod_err(buffer, filename, "cutoff", + "cutoff=[param_ele1] [param_ele2]"); + } + + + res = fscanf(fptr, " dcut="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { + res = fscanf(fptr, " %s", buffer); + if (res != 1) + throw_error(filename, "dcut", "dcut=[param_ele1] [param_ele2]"); + radial_functions->dcut(mu_i, mu_j) = stod_err(buffer, filename, "dcut", "dcut=[param_ele1] [param_ele2]"); + } + + + res = fscanf(fptr, " crad="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) + for (NS_TYPE k = 0; k < nradbase; k++) + for (NS_TYPE n = 0; n < nradmax; n++) + for (LS_TYPE l = 0; l <= lmax; l++) { + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "crad", "crad=[crad_]...[crad_knl]: nradbase*nrad*(l+1) times"); + radial_functions->crad(mu_i, mu_j, n, l, k) = stod_err(buffer, filename, "crad", + "crad=[crad_]...[crad_knl]: nradbase*nrad*(l+1) times"); + } +} + +void ACECTildeBasisSet::_load_radial_SHIPsBasic(FILE *fptr, + const string filename, + const string radbasename) { + // create a radial basis object, and read it from the file pointer + SHIPsRadialFunctions *ships_radial_functions = new SHIPsRadialFunctions(); + ships_radial_functions->fread(fptr); + + //mimic ships_radial_functions to ACERadialFunctions + ships_radial_functions->nradial = ships_radial_functions->get_maxn(); + ships_radial_functions->nradbase = ships_radial_functions->get_maxn(); + + nradbase = ships_radial_functions->get_maxn(); + nradmax = ships_radial_functions->get_maxn(); + cutoffmax = ships_radial_functions->get_rcut(); + deltaSplineBins = 0.001; + + ships_radial_functions->init(nradbase, lmax, nradmax, + deltaSplineBins, + nelements, + cutoffmax, radbasename); + + + if (radial_functions) delete radial_functions; + radial_functions = ships_radial_functions; + radial_functions->prehc.fill(0); + radial_functions->lambdahc.fill(1); + radial_functions->lambda.fill(0); + + + radial_functions->cut.fill(ships_radial_functions->get_rcut()); + radial_functions->dcut.fill(0); + + radial_functions->crad.fill(0); + +} \ No newline at end of file diff --git a/lib/pace/ace_c_basis.h b/lib/pace/ace_c_basis.h new file mode 100644 index 0000000000..ec6b9e8afc --- /dev/null +++ b/lib/pace/ace_c_basis.h @@ -0,0 +1,155 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Yury Lysogorskiy on 1.04.20. + +#ifndef ACE_C_BASIS_H +#define ACE_C_BASIS_H + +#include "ace_flatten_basis.h" + +typedef vector> C_tilde_full_basis_vector2d; + +/** + * ACE basis set of C-tilde basis functions + */ +class ACECTildeBasisSet : public ACEFlattenBasisSet { +public: + + ACECTildeBasisFunction **basis_rank1 = nullptr; ///< two-dimensional array of first-rank basis function with indices: [species index][func index] + ACECTildeBasisFunction **basis = nullptr; ///< two-dimensional array of higher rank basis function with indices: [species index][func index] + + DOUBLE_TYPE *full_c_tildes_rank1 = nullptr; ///< C_tilde coefficients contiguous package, size: coeff_array_total_size_rank1 + DOUBLE_TYPE *full_c_tildes = nullptr; ///< C_tilde coefficients contiguous package, size: coeff_array_total_size + + //TODO: remove? + SHORT_INT_TYPE num_ctilde_max = 0; + + + /** + * Default constructor + */ + ACECTildeBasisSet() = default; + + /** + * Constructor from .ace file + */ + ACECTildeBasisSet(const string filename); + + /** + * Copy constructor (see. Rule of Three) + * @param other + */ + ACECTildeBasisSet(const ACECTildeBasisSet &other); + + /** + * operator= (see. Rule of Three) + * @param other + * @return + */ + ACECTildeBasisSet &operator=(const ACECTildeBasisSet &other); + + /** + * Destructor (see. Rule of Three) + */ + ~ACECTildeBasisSet() override; + + /** + * Cleaning dynamic memory of the class (see. Rule of Three) + */ + void _clean() override; + + /** + * Copying and cleaning dynamic memory of the class (see. Rule of Three) + * @param src + */ + void _copy_dynamic_memory(const ACECTildeBasisSet &src); + + /** + * Copying scalar variables + * @param src + */ + void _copy_scalar_memory(const ACECTildeBasisSet &src); + + /** + * Clean contiguous arrays (full_c_tildes_rank1, full_c_tildes) and those of base class + */ + void _clean_contiguous_arrays() override ; + + /** + * Save potential to .ace file + * @param filename .ace file name + */ + void save(const string &filename) override; + + /** + * Load potential from .ace + * @param filename .ace file name + */ + void load(const string filename) override; + + /** + * Load the ACE type radial basis + */ + void _load_radial_ACERadial(FILE *fptr, + const string filename, + const string radbasename); + + void _load_radial_SHIPsBasic(FILE * fptr, + const string filename, + const string radbasename ); + + /** + * Re-pack the constituent dynamic arrays of all basis functions in contiguous arrays + */ + void pack_flatten_basis() override; + + /** + * Computes flatten array sizes + * @param basis_rank1 two-dimensional array of first-rank ACECTildeBasisFunctions + * @param basis two-dimensional array of higher-rank ACECTildeBasisFunctions + */ + void compute_array_sizes(ACECTildeBasisFunction** basis_rank1, ACECTildeBasisFunction** basis); + + /** + * Clean basis arrays 'basis_rank1' and 'basis' + */ + void _clean_basis_arrays(); + + /** + * Pack two-dimensional vector of ACECTildeBasisFunction into 1D dynami array with all basis functions + * @param mu0_ctilde_basis_vector vector> + */ + void flatten_basis(C_tilde_full_basis_vector2d& mu0_ctilde_basis_vector); + + /** + * Empty stub implementation + */ + void flatten_basis() override{}; +}; + +#endif //ACE_C_BASIS_H diff --git a/lib/pace/ace_c_basisfunction.h b/lib/pace/ace_c_basisfunction.h new file mode 100644 index 0000000000..4e2795590e --- /dev/null +++ b/lib/pace/ace_c_basisfunction.h @@ -0,0 +1,251 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Yury Lysogorskiy on 26.02.20. + +#ifndef ACE_C_BASISFUNCTION_H +#define ACE_C_BASISFUNCTION_H + +#include +#include +#include +#include + +#include "ace_types.h" + +//macros for copying the member-array from "other" object for C-tilde and B-basis +#define basis_mem_copy(other, array, size, type) if(other.array) { \ + if(!is_proxy) delete[] array;\ + array = new type[(size)];\ + is_proxy = false;\ + memcpy(array, other.array, (size) * sizeof(type));\ +} + +/** + * Abstract basis function, that stores general quantities + */ +struct ACEAbstractBasisFunction { + /** + * flattened array of computed combinations of (m1, m2, ..., m_rank) + * which have non-zero general Clebsch-Gordan coefficient: + * \f$ \mathbf{m}_1, \dots, \mathbf{m}_\mathrm{num ms combs}\f$ = + * \f$ (m_1, m_2, \dots, m_{rank})_1, \dots, (m_1, m_2, \dots, m_{rank})_{\mathrm{num ms combs}} \f$, + * size = num_ms_combs * rank, + * effective shape: [num_ms_combs][rank] + */ + MS_TYPE *ms_combs = nullptr; + + /** + * species types of neighbours atoms \f$ \mathbf{\mu} = (\mu_1, \mu_2, \dots, \mu_{rank}) \f$, + * should be lexicographically sorted, + * size = rank, + * effective shape: [rank] + */ + SPECIES_TYPE *mus = nullptr; + + /** + * indices for radial part \f$ \mathbf{n} = (n_1, n_2, \dots, n_{rank}) \f$, + * should be lexicographically sorted, + * size = rank, + * effective shape: [rank] + */ + NS_TYPE *ns = nullptr; + + + /** + * indices for radial part \f$ \mathbf{l} = (l_1, l_2, \dots, l_{rank}) \f$, + * should be lexicographically sorted, + * size = rank, + * effective shape: [rank] + */ + LS_TYPE *ls = nullptr; + + SHORT_INT_TYPE num_ms_combs = 0; ///< number of different ms-combinations + + RANK_TYPE rank = 0; ///< number of atomic base functions "A"s in basis function product B + + DENSITY_TYPE ndensity = 0; ///< number of densities + + SPECIES_TYPE mu0 = 0; ///< species type of central atom + + /** + * whether ms array contains only "non-negative" ms-combinations. + * positive ms-combination is when the first non-zero m is positive (0 1 -1) + * negative ms-combination is when the first non-zero m is negative (0 -1 1) + */ + bool is_half_ms_basis = false; + + /* + * flag, whether object is "owner" (i.e. responsible for memory cleaning) of + * the ms, ns, ls, mus and other dynamically allocated arrases or just a proxy for them + */ + bool is_proxy = false; + + /** + * Copying static and dynamic memory variables from another ACEAbstractBasisFunction. + * Always copy the dynamic memory, even if the source is a proxy object + * @param other + */ + virtual void _copy_from(const ACEAbstractBasisFunction &other) { + rank = other.rank; + ndensity = other.ndensity; + mu0 = other.mu0; + num_ms_combs = other.num_ms_combs; + is_half_ms_basis = other.is_half_ms_basis; + is_proxy = false; + + basis_mem_copy(other, mus, rank, SPECIES_TYPE) + basis_mem_copy(other, ns, rank, NS_TYPE) + basis_mem_copy(other, ls, rank, LS_TYPE) + basis_mem_copy(other, ms_combs, num_ms_combs * rank, MS_TYPE) + } + + /** + * Clean the dynamically allocated memory if object is responsible for it + */ + virtual void _clean() { + //release memory if the structure is not proxy + if (!is_proxy) { + delete[] mus; + delete[] ns; + delete[] ls; + delete[] ms_combs; + } + + mus = nullptr; + ns = nullptr; + ls = nullptr; + ms_combs = nullptr; + } + +}; + +/** + * Representation of C-tilde basis function, i.e. the function that is summed up over a group of B-functions + * that differs only by intermediate coupling orbital moment \f$ L \f$ and coefficients. + */ +struct ACECTildeBasisFunction : public ACEAbstractBasisFunction { + + /** + * c_tilde coefficients for all densities, + * size = num_ms_combs*ndensity, + * effective shape [num_ms_combs][ndensity] + */ + DOUBLE_TYPE *ctildes = nullptr; + + /* + * Default constructor + */ + ACECTildeBasisFunction() = default; + + // Because the ACECTildeBasisFunction contains dynamically allocated arrays, the Rule of Three should be + // fulfilled, i.e. copy constructor (copy the dynamic arrays), operator= (release previous arrays and + // copy the new dynamic arrays) and destructor (release all dynamically allocated memory) + + /** + * Copy constructor, to fulfill the Rule of Three. + * Always copy the dynamic memory, even if the source is a proxy object. + */ + ACECTildeBasisFunction(const ACECTildeBasisFunction &other) { + _copy_from(other); + } + + /* + * operator=, to fulfill the Rule of Three. + * Always copy the dynamic memory, even if the source is a proxy object + */ + ACECTildeBasisFunction &operator=(const ACECTildeBasisFunction &other) { + _clean(); + _copy_from(other); + return *this; + } + + /* + * Destructor + */ + ~ACECTildeBasisFunction() { + _clean(); + } + + /** + * Copy from another object, always copy the memory, even if the source is a proxy object + * @param other + */ + void _copy_from(const ACECTildeBasisFunction &other) { + ACEAbstractBasisFunction::_copy_from(other); + is_proxy = false; + basis_mem_copy(other, ctildes, num_ms_combs * ndensity, DOUBLE_TYPE) + } + + /** + * Clean the dynamically allocated memory if object is responsible for it + */ + void _clean() override { + ACEAbstractBasisFunction::_clean(); + //release memory if the structure is not proxy + if (!is_proxy) { + delete[] ctildes; + } + ctildes = nullptr; + } + + /** + * Print the information about basis function to cout, in order to ease the output redirection. + */ + void print() const { + using namespace std; + cout << "ACECTildeBasisFunction: ndensity= " << (int) this->ndensity << ", mu0 = " << (int) this->mu0 << " "; + cout << " mus=("; + for (RANK_TYPE r = 0; r < this->rank; r++) + cout << (int) this->mus[r] << " "; + cout << "), ns=("; + for (RANK_TYPE r = 0; r < this->rank; r++) + cout << this->ns[r] << " "; + cout << "), ls=("; + for (RANK_TYPE r = 0; r < this->rank; r++) + cout << this->ls[r] << " "; + + cout << "), " << this->num_ms_combs << " m_s combinations: {" << endl; + + for (int i = 0; i < this->num_ms_combs; i++) { + cout << "\t< "; + for (RANK_TYPE r = 0; r < this->rank; r++) + cout << this->ms_combs[i * this->rank + r] << " "; + cout << " >: c_tilde="; + for (DENSITY_TYPE p = 0; p < this->ndensity; ++p) + cout << " " << this->ctildes[i * this->ndensity + p] << " "; + cout << endl; + } + if (this->is_proxy) + cout << "proxy "; + if (this->is_half_ms_basis) + cout << "half_ms_basis"; + cout << "}" << endl; + } +}; + +#endif //ACE_C_BASISFUNCTION_H diff --git a/lib/pace/ace_complex.h b/lib/pace/ace_complex.h new file mode 100644 index 0000000000..5fdb4b5b93 --- /dev/null +++ b/lib/pace/ace_complex.h @@ -0,0 +1,266 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Yury Lysogorskiy on 26.02.20. + +#ifndef ACE_COMPLEX_H +#define ACE_COMPLEX_H + + +/** +A custom data structure for complex numbers and overloaded operations with them. +*/ +struct ACEComplex { +public: + /** + Double, real part of the complex number + */ + DOUBLE_TYPE real; + /** + Double, imaginary part of the complex number + */ + DOUBLE_TYPE img; + + ACEComplex &operator=(const ACEComplex &rhs) = default; + + ACEComplex &operator=(const DOUBLE_TYPE &rhs) { + this->real = rhs; + this->img = 0.; + return *this; + } + + /** + Overloading of arithmetical operator += ACEComplex + */ + ACEComplex &operator+=(const ACEComplex &rhs) { + this->real += rhs.real; + this->img += rhs.img; + return *this; // return the result by reference + } + + /** + Overloading of arithmetical operator += DOUBLE_TYPE + */ + ACEComplex &operator+=(const DOUBLE_TYPE &rhs) { + this->real += rhs; + return *this; // return the result by reference + } + + /** + Overloading of arithmetical operator *= DOUBLE_TYPE + */ + ACEComplex &operator*=(const DOUBLE_TYPE &rhs) { + this->real *= rhs; + this->img *= rhs; + return *this; // return the result by reference + } + + /** + Overloading of arithmetical operator *= ACEComplex + */ + ACEComplex &operator*=(const ACEComplex &rhs) { + DOUBLE_TYPE old_real = this->real; + this->real = old_real * rhs.real - this->img * rhs.img; + this->img = old_real * rhs.img + this->img * rhs.real; + return *this; // return the result by reference + } + + /** + Overloading of arithmetical operator * ACEComplex + */ + ACEComplex operator*(const ACEComplex &cm2) const { + ACEComplex res{real * cm2.real - img * cm2.img, + real * cm2.img + img * cm2.real}; + return res; + } + + /* + * Return complex conjugated copy of itself + */ + ACEComplex conjugated() const { + ACEComplex res{real, -img}; + return res; + } + + /* + * Complex conjugate itself inplace + */ + void conjugate() { + img = -img; + } + + /* + * Multiplication by ACEComplex and return real-part only + */ + DOUBLE_TYPE real_part_product(const ACEComplex &cm2) const { + return real * cm2.real - img * cm2.img; + } + + /* + * Multiplication by DOUBLE_TYPE and return real-part only + */ + DOUBLE_TYPE real_part_product(const DOUBLE_TYPE &cm2) const { + return real * cm2; + } + + /* + * Overloading of arithmetical operator * by DOUBLE_TYPE + */ + ACEComplex operator*(const DOUBLE_TYPE &cm2) const { + ACEComplex res{real * cm2, + img * cm2}; + return res; + } + + /* + * Overloading of arithmetical operator + ACEComplex + */ + ACEComplex operator+(const ACEComplex &cm2) const { + ACEComplex res{real + cm2.real, + img + cm2.img}; + return res; + } + + /* + * Overloading of arithmetical operator + with DOUBLE_TYPE + */ + ACEComplex operator+(const DOUBLE_TYPE &cm2) const { + ACEComplex res{real + cm2, img}; + return res; + } + + /* + * Overloading of arithmetical operator == ACEComplex + */ + bool operator==(const ACEComplex &c2) const { + return (real == c2.real) && (img == c2.img); + } + + /* + * Overloading of arithmetical operator == DOUBLE_TYPE + */ + bool operator==(const DOUBLE_TYPE &d2) const { + return (real == d2) && (img == 0.); + } + + /* + * Overloading of arithmetical operator != ACEComplex + */ + bool operator!=(const ACEComplex &c2) const { + return (real != c2.real) || (img != c2.img); + } + + /* + * Overloading of arithmetical operator != DOUBLE_TYPE + */ + bool operator!=(const DOUBLE_TYPE &d2) const { + return (real != d2) || (img != 0.); + } + +}; + +/* + * double * complex for commutativity with complex * double + */ +inline ACEComplex operator*(const DOUBLE_TYPE &real, const ACEComplex &cm) { + return cm * real; +} + +/* + * double + complex for commutativity with complex + double + */ +inline ACEComplex operator+(const DOUBLE_TYPE &real, const ACEComplex &cm) { + return cm + real; +} + +/** +A structure to store the derivative of \f$ Y_{lm} \f$ +*/ +struct ACEDYcomponent { +public: + /** + complex, contains the three components of derivative of Ylm, + \f$ \frac{dY_{lm}}{dx}, \frac{dY_{lm}}{dy} and \frac{dY_{lm}}{dz}\f$ + */ + ACEComplex a[3]; + + /* + * Overloading of arithmetical operator*= DOUBLE_TYPE + */ + ACEDYcomponent &operator*=(const DOUBLE_TYPE &rhs) { + this->a[0] *= rhs; + this->a[1] *= rhs; + this->a[2] *= rhs; + return *this; + } + + /* + * Overloading of arithmetical operator * ACEComplex + */ + ACEDYcomponent operator*(const ACEComplex &rhs) const { + ACEDYcomponent res; + res.a[0] = this->a[0] * rhs; + res.a[1] = this->a[1] * rhs; + res.a[2] = this->a[2] * rhs; + return res; + } + + /* + * Overloading of arithmetical operator * DOUBLE_TYPE + */ + ACEDYcomponent operator*(const DOUBLE_TYPE &rhs) const { + ACEDYcomponent res; + res.a[0] = this->a[0] * rhs; + res.a[1] = this->a[1] * rhs; + res.a[2] = this->a[2] * rhs; + return res; + } + + /* + * Return conjugated copy of itself + */ + ACEDYcomponent conjugated() const { + ACEDYcomponent res; + res.a[0] = this->a[0].conjugated(); + res.a[1] = this->a[1].conjugated(); + res.a[2] = this->a[2].conjugated(); + return res; + } + + /* + * Conjugated itself in-place + */ + void conjugate() { + this->a[0].conjugate(); + this->a[1].conjugate(); + this->a[2].conjugate(); + } + +}; + + +#endif //ACE_COMPLEX_H diff --git a/lib/pace/ace_contigous_array.h b/lib/pace/ace_contigous_array.h new file mode 100644 index 0000000000..f008fa203f --- /dev/null +++ b/lib/pace/ace_contigous_array.h @@ -0,0 +1,249 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Yury Lysogorskiy on 11.01.20. +#ifndef ACE_CONTIGUOUSARRAYND_H +#define ACE_CONTIGUOUSARRAYND_H + +#include + +#include "ace_types.h" + +using namespace std; + +/** + * Common predecessor class to represent multidimensional array of type T + * and store it in memory contiguous form + * + * @tparam T data type + */ +template +class ContiguousArrayND { +protected: + T *data = nullptr; ///< pointer to contiguous data + size_t size = 0; ///< total array size + string array_name = "Array"; /// 0) { + data = new T[size]; + for (size_t ind = 0; ind < size; ind++) + data[ind] = other.data[ind]; + } + } else { //is proxy, then copy the pointer + data = other.data; + } + } + + /** + * Overload operator= + * @param other another ContiguousArrayND + * @return itself + */ + + ContiguousArrayND &operator=(const ContiguousArrayND &other) { +#ifdef MULTIARRAY_LIFE_CYCLE + cout< 0) { + + if(data!=nullptr) delete[] data; + data = new T[size]; + + for (size_t ind = 0; ind < size; ind++) + data[ind] = other.data[ind]; + } + } else { //is proxy, then copy the pointer + data = other.data; + } + } + return *this; + } + + + //TODO: make destructor virtual, check the destructors in inherited classes + + /** + * Destructor + */ + ~ContiguousArrayND() { +#ifdef MULTIARRAY_LIFE_CYCLE + cout<array_name = name; + } + + /** + * Get total number of elements in array (its size) + * @return array size + */ + size_t get_size() const { + return size; + } + + /** + * Fill array with value + * @param value value to fill + */ + void fill(T value) { + for (size_t ind = 0; ind < size; ind++) + data[ind] = value; + } + + /** + * Get array data at absolute index ind for reading + * @param ind absolute index + * @return array value + */ + inline const T &get_data(size_t ind) const { +#ifdef MULTIARRAY_INDICES_CHECK + if ((ind < 0) | (ind >= size)) { + printf("%s: get_data ind=%d out of range (0, %d)\n", array_name, ind, size); + exit(EXIT_FAILURE); + } +#endif + return data[ind]; + } + + /** + * Get array data at absolute index ind for writing + * @param ind absolute index + * @return array value + */ + inline T &get_data(size_t ind) { +#ifdef MULTIARRAY_INDICES_CHECK + if ((ind < 0) | (ind >= size)) { + printf("%s: get_data ind=%ld out of range (0, %ld)\n", array_name.c_str(), ind, size); + exit(EXIT_FAILURE); + } +#endif + return data[ind]; + } + + /** + * Get array data pointer + * @return data array pointer + */ + inline T* get_data() const { + return data; + } + + /** + * Overload comparison operator== + * Compare the total size and array values elementwise. + * + * @param other another array + * @return + */ + bool operator==(const ContiguousArrayND &other) const { + if (this->size != other.size) + return false; + + for (size_t i = 0; i < this->size; ++i) + if (this->data[i] != other.data[i]) + return false; + + return true; + } + + + /** + * Convert to flatten vector container + * @return vector container + */ + vector to_flatten_vector() const { + vector res; + + res.resize(size); + size_t vec_ind = 0; + + for (int vec_ind = 0; vec_ind < size; vec_ind++) + res.at(vec_ind) = data[vec_ind]; + + return res; + } // end to_flatten_vector() + + + /** + * Set values from flatten vector container + * @param vec container + */ + void set_flatten_vector(const vector &vec) { + if (vec.size() != size) + throw std::invalid_argument("Flatten vector size is not consistent with expected size"); + for (size_t i = 0; i < size; i++) { + data[i] = vec[i]; + } + } + + bool is_proxy(){ + return is_proxy_; + } + +}; + + +#endif //ACE_CONTIGUOUSARRAYND_H \ No newline at end of file diff --git a/lib/pace/ace_evaluator.cpp b/lib/pace/ace_evaluator.cpp new file mode 100644 index 0000000000..987f4502bf --- /dev/null +++ b/lib/pace/ace_evaluator.cpp @@ -0,0 +1,660 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Yury Lysogorskiy on 31.01.20. + +#include "ace_evaluator.h" + +#include "ace_abstract_basis.h" +#include "ace_types.h" + +void ACEEvaluator::init(ACEAbstractBasisSet *basis_set) { + A.init(basis_set->nelements, basis_set->nradmax + 1, basis_set->lmax + 1, "A"); + A_rank1.init(basis_set->nelements, basis_set->nradbase, "A_rank1"); + + rhos.init(basis_set->ndensitymax + 1, "rhos"); // +1 density for core repulsion + dF_drho.init(basis_set->ndensitymax + 1, "dF_drho"); // +1 density for core repulsion +} + +void ACEEvaluator::init_timers() { + loop_over_neighbour_timer.init(); + forces_calc_loop_timer.init(); + forces_calc_neighbour_timer.init(); + energy_calc_timer.init(); + per_atom_calc_timer.init(); + total_time_calc_timer.init(); +} + +//================================================================================================================ + +void ACECTildeEvaluator::set_basis(ACECTildeBasisSet &bas) { + basis_set = &bas; + init(basis_set); +} + +void ACECTildeEvaluator::init(ACECTildeBasisSet *basis_set) { + + ACEEvaluator::init(basis_set); + + + weights.init(basis_set->nelements, basis_set->nradmax + 1, basis_set->lmax + 1, + "weights"); + + weights_rank1.init(basis_set->nelements, basis_set->nradbase, "weights_rank1"); + + + DG_cache.init(1, basis_set->nradbase, "DG_cache"); + DG_cache.fill(0); + + R_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "R_cache"); + R_cache.fill(0); + + DR_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "DR_cache"); + DR_cache.fill(0); + + Y_cache.init(1, basis_set->lmax + 1, "Y_cache"); + Y_cache.fill({0, 0}); + + DY_cache.init(1, basis_set->lmax + 1, "dY_dense_cache"); + DY_cache.fill({0.}); + + //hard-core repulsion + DCR_cache.init(1, "DCR_cache"); + DCR_cache.fill(0); + dB_flatten.init(basis_set->max_dB_array_size, "dB_flatten"); + + +} + +void ACECTildeEvaluator::resize_neighbours_cache(int max_jnum) { + if(basis_set== nullptr) { + throw std::invalid_argument("ACECTildeEvaluator: basis set is not assigned"); + } + if (R_cache.get_dim(0) < max_jnum) { + + //TODO: implement grow + R_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); + R_cache.fill(0); + + DR_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); + DR_cache.fill(0); + + DG_cache.resize(max_jnum, basis_set->nradbase); + DG_cache.fill(0); + + Y_cache.resize(max_jnum, basis_set->lmax + 1); + Y_cache.fill({0, 0}); + + DY_cache.resize(max_jnum, basis_set->lmax + 1); + DY_cache.fill({0}); + + //hard-core repulsion + DCR_cache.init(max_jnum, "DCR_cache"); + DCR_cache.fill(0); + } +} + + + +// double** r - atomic coordinates of atom I +// int* types - atomic types if atom I +// int **firstneigh - ptr to 1st J int value of each I atom. Usage: jlist = firstneigh[i]; +// Usage: j = jlist_of_i[jj]; +// jnum - number of J neighbors for each I atom. jnum = numneigh[i]; + +void +ACECTildeEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) { + if(basis_set== nullptr) { + throw std::invalid_argument("ACECTildeEvaluator: basis set is not assigned"); + } + per_atom_calc_timer.start(); +#ifdef PRINT_MAIN_STEPS + printf("\n ATOM: ind = %d r_norm=(%f, %f, %f)\n",i, x[i][0], x[i][1], x[i][2]); +#endif + DOUBLE_TYPE evdwl = 0, evdwl_cut = 0, rho_core = 0; + DOUBLE_TYPE r_norm; + DOUBLE_TYPE xn, yn, zn, r_xyz; + DOUBLE_TYPE R, GR, DGR, R_over_r, DR, DCR; + DOUBLE_TYPE *r_hat; + + SPECIES_TYPE mu_j; + RANK_TYPE r, rank, t; + NS_TYPE n; + LS_TYPE l; + MS_TYPE m, m_t; + + SPECIES_TYPE *mus; + NS_TYPE *ns; + LS_TYPE *ls; + MS_TYPE *ms; + + int j, jj, func_ind, ms_ind; + SHORT_INT_TYPE factor; + + ACEComplex Y{0}, Y_DR{0.}; + ACEComplex B{0.}; + ACEComplex dB{0}; + ACEComplex A_cache[basis_set->rankmax]; + + dB_flatten.fill({0.}); + + ACEDYcomponent grad_phi_nlm{0}, DY{0.}; + + //size is +1 of max to avoid out-of-boundary array access in double-triangular scheme + ACEComplex A_forward_prod[basis_set->rankmax + 1]; + ACEComplex A_backward_prod[basis_set->rankmax + 1]; + + DOUBLE_TYPE inv_r_norm; + DOUBLE_TYPE r_norms[jnum]; + DOUBLE_TYPE inv_r_norms[jnum]; + DOUBLE_TYPE rhats[jnum][3];//normalized vector + SPECIES_TYPE elements[jnum]; + const DOUBLE_TYPE xtmp = x[i][0]; + const DOUBLE_TYPE ytmp = x[i][1]; + const DOUBLE_TYPE ztmp = x[i][2]; + DOUBLE_TYPE f_ji[3]; + + bool is_element_mapping = element_type_mapping.get_size() > 0; + SPECIES_TYPE mu_i; + if (is_element_mapping) + mu_i = element_type_mapping(type[i]); + else + mu_i = type[i]; + + const SHORT_INT_TYPE total_basis_size_rank1 = basis_set->total_basis_size_rank1[mu_i]; + const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; + + ACECTildeBasisFunction *basis_rank1 = basis_set->basis_rank1[mu_i]; + ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; + + DOUBLE_TYPE rho_cut, drho_cut, fcut, dfcut; + DOUBLE_TYPE dF_drho_core; + + //TODO: lmax -> lmaxi (get per-species type) + const LS_TYPE lmaxi = basis_set->lmax; + + //TODO: nradmax -> nradiali (get per-species type) + const NS_TYPE nradiali = basis_set->nradmax; + + //TODO: nradbase -> nradbasei (get per-species type) + const NS_TYPE nradbasei = basis_set->nradbase; + + //TODO: get per-species type number of densities + const DENSITY_TYPE ndensity= basis_set->ndensitymax; + + neighbours_forces.resize(jnum, 3); + neighbours_forces.fill(0); + + //TODO: shift nullifications to place where arrays are used + weights.fill({0}); + weights_rank1.fill(0); + A.fill({0}); + A_rank1.fill(0); + rhos.fill(0); + dF_drho.fill(0); + +#ifdef EXTRA_C_PROJECTIONS + basis_projections_rank1.init(total_basis_size_rank1, ndensity, "c_projections_rank1"); + basis_projections.init(total_basis_size, ndensity, "c_projections"); +#endif + + //proxy references to spherical harmonics and radial functions arrays + const Array2DLM &ylm = basis_set->spherical_harmonics.ylm; + const Array2DLM &dylm = basis_set->spherical_harmonics.dylm; + + const Array2D &fr = basis_set->radial_functions->fr; + const Array2D &dfr = basis_set->radial_functions->dfr; + + const Array1D &gr = basis_set->radial_functions->gr; + const Array1D &dgr = basis_set->radial_functions->dgr; + + loop_over_neighbour_timer.start(); + + int jj_actual = 0; + SPECIES_TYPE type_j = 0; + int neighbour_index_mapping[jnum]; // jj_actual -> jj + //loop over neighbours, compute distance, consider only atoms within with rradial_functions->cut(mu_i, mu_j); + r_xyz = sqrt(xn * xn + yn * yn + zn * zn); + + if (r_xyz >= current_cutoff) + continue; + + inv_r_norm = 1 / r_xyz; + + r_norms[jj_actual] = r_xyz; + inv_r_norms[jj_actual] = inv_r_norm; + rhats[jj_actual][0] = xn * inv_r_norm; + rhats[jj_actual][1] = yn * inv_r_norm; + rhats[jj_actual][2] = zn * inv_r_norm; + elements[jj_actual] = mu_j; + neighbour_index_mapping[jj_actual] = jj; + jj_actual++; + } + + int jnum_actual = jj_actual; + + //ALGORITHM 1: Atomic base A + for (jj = 0; jj < jnum_actual; ++jj) { + r_norm = r_norms[jj]; + mu_j = elements[jj]; + r_hat = rhats[jj]; + + //proxies + Array2DLM &Y_jj = Y_cache(jj); + Array2DLM &DY_jj = DY_cache(jj); + + + basis_set->radial_functions->evaluate(r_norm, basis_set->nradbase, nradiali, mu_i, mu_j); + basis_set->spherical_harmonics.compute_ylm(r_hat[0], r_hat[1], r_hat[2], lmaxi); + //loop for computing A's + //rank = 1 + for (n = 0; n < basis_set->nradbase; n++) { + GR = gr(n); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("-neigh atom %d\n", jj); + printf("gr(n=%d)(r=%f) = %f\n", n, r_norm, gr(n)); + printf("dgr(n=%d)(r=%f) = %f\n", n, r_norm, dgr(n)); +#endif + DG_cache(jj, n) = dgr(n); + A_rank1(mu_j, n) += GR * Y00; + } + //loop for computing A's + // for rank > 1 + for (n = 0; n < nradiali; n++) { + auto &A_lm = A(mu_j, n); + for (l = 0; l <= lmaxi; l++) { + R = fr(n, l); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("R(nl=%d,%d)(r=%f)=%f\n", n + 1, l, r_norm, R); +#endif + + DR_cache(jj, n, l) = dfr(n, l); + R_cache(jj, n, l) = R; + + for (m = 0; m <= l; m++) { + Y = ylm(l, m); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("Y(lm=%d,%d)=(%f, %f)\n", l, m, Y.real, Y.img); +#endif + A_lm(l, m) += R * Y; //accumulation sum over neighbours + Y_jj(l, m) = Y; + DY_jj(l, m) = dylm(l, m); + } + } + } + + //hard-core repulsion + rho_core += basis_set->radial_functions->cr; + DCR_cache(jj) = basis_set->radial_functions->dcr; + + } //end loop over neighbours + + //complex conjugate A's (for NEGATIVE (-m) terms) + // for rank > 1 + for (mu_j = 0; mu_j < basis_set->nelements; mu_j++) { + for (n = 0; n < nradiali; n++) { + auto &A_lm = A(mu_j, n); + for (l = 0; l <= lmaxi; l++) { + //fill in -m part in the outer loop using the same m <-> -m symmetry as for Ylm + for (m = 1; m <= l; m++) { + factor = m % 2 == 0 ? 1 : -1; + A_lm(l, -m) = A_lm(l, m).conjugated() * factor; + } + } + } + } //now A's are constructed + loop_over_neighbour_timer.stop(); + + // ==================== ENERGY ==================== + + energy_calc_timer.start(); +#ifdef EXTRA_C_PROJECTIONS + basis_projections_rank1.fill(0); + basis_projections.fill(0); +#endif + + //ALGORITHM 2: Basis functions B with iterative product and density rho(p) calculation + //rank=1 + for (int func_rank1_ind = 0; func_rank1_ind < total_basis_size_rank1; ++func_rank1_ind) { + ACECTildeBasisFunction *func = &basis_rank1[func_rank1_ind]; +// ndensity = func->ndensity; +#ifdef PRINT_LOOPS_INDICES + printf("Num density = %d r = 0\n",(int) ndensity ); + print_C_tilde_B_basis_function(*func); +#endif + double A_cur = A_rank1(func->mus[0], func->ns[0] - 1); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("A_r=1(x=%d, n=%d)=(%f)\n", func->mus[0], func->ns[0], A_cur); + printf(" coeff[0] = %f\n", func->ctildes[0]); +#endif + for (DENSITY_TYPE p = 0; p < ndensity; ++p) { + //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 + rhos(p) += func->ctildes[p] * A_cur; +#ifdef EXTRA_C_PROJECTIONS + //aggregate C-projections separately + basis_projections_rank1(func_rank1_ind, p)+= func->ctildes[p] * A_cur; +#endif + } + } // end loop for rank=1 + + //rank>1 + int func_ms_ind = 0; + int func_ms_t_ind = 0;// index for dB + + for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { + ACECTildeBasisFunction *func = &basis[func_ind]; + //TODO: check if func->ctildes are zero, then skip +// ndensity = func->ndensity; + rank = func->rank; + r = rank - 1; +#ifdef PRINT_LOOPS_INDICES + printf("Num density = %d r = %d\n",(int) ndensity, (int)r ); + print_C_tilde_B_basis_function(*func); +#endif + mus = func->mus; + ns = func->ns; + ls = func->ls; + + //loop over {ms} combinations in sum + for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { + ms = &func->ms_combs[ms_ind * rank]; // current ms-combination (of length = rank) + + //loop over m, collect B = product of A with given ms + A_forward_prod[0] = 1; + A_backward_prod[r] = 1; + + //fill forward A-product triangle + for (t = 0; t < rank; t++) { + //TODO: optimize ns[t]-1 -> ns[t] during functions construction + A_cache[t] = A(mus[t], ns[t] - 1, ls[t], ms[t]); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("A(x=%d, n=%d, l=%d, m=%d)=(%f,%f)\n", mus[t], ns[t], ls[t], ms[t], A_cache[t].real, + A_cache[t].img); +#endif + A_forward_prod[t + 1] = A_forward_prod[t] * A_cache[t]; + } + + B = A_forward_prod[t]; + +#ifdef DEBUG_FORCES_CALCULATIONS + printf("B = (%f, %f)\n", (B).real, (B).img); +#endif + //fill backward A-product triangle + for (t = r; t >= 1; t--) { + A_backward_prod[t - 1] = + A_backward_prod[t] * A_cache[t]; + } + + for (t = 0; t < rank; ++t, ++func_ms_t_ind) { + dB = A_forward_prod[t] * A_backward_prod[t]; //dB - product of all A's except t-th + dB_flatten(func_ms_t_ind) = dB; +#ifdef DEBUG_FORCES_CALCULATIONS + m_t = ms[t]; + printf("dB(n,l,m)(%d,%d,%d) = (%f, %f)\n", ns[t], ls[t], m_t, (dB).real, (dB).img); +#endif + } + + for (DENSITY_TYPE p = 0; p < ndensity; ++p) { + //real-part only multiplication + rhos(p) += B.real_part_product(func->ctildes[ms_ind * ndensity + p]); + +#ifdef EXTRA_C_PROJECTIONS + //aggregate C-projections separately + basis_projections(func_ind, p)+=B.real_part_product(func->ctildes[ms_ind * ndensity + p]); +#endif + +#ifdef PRINT_INTERMEDIATE_VALUES + printf("rhos(%d) += %f\n", p, B.real_part_product(func->ctildes[ms_ind * ndensity + p])); + printf("Rho[i = %d][p = %d] = %f\n", i , p , rhos(p)); +#endif + } + }//end of loop over {ms} combinations in sum + }// end loop for rank>1 + +#ifdef DEBUG_FORCES_CALCULATIONS + printf("rhos = "); + for(DENSITY_TYPE p =0; prho_core_cutoffs(mu_i); + drho_cut = basis_set->drho_core_cutoffs(mu_i); + + basis_set->inner_cutoff(rho_core, rho_cut, drho_cut, fcut, dfcut); + basis_set->FS_values_and_derivatives(rhos, evdwl, dF_drho, ndensity); + + dF_drho_core = evdwl * dfcut + 1; + for (DENSITY_TYPE p = 0; p < ndensity; ++p) + dF_drho(p) *= fcut; + evdwl_cut = evdwl * fcut + rho_core; + + // E0 shift + evdwl_cut += basis_set->E0vals(mu_i); + +#ifdef DEBUG_FORCES_CALCULATIONS + printf("dFrhos = "); + for(DENSITY_TYPE p =0; pndensity; + for (DENSITY_TYPE p = 0; p < ndensity; ++p) { + //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 + weights_rank1(func->mus[0], func->ns[0] - 1) += dF_drho(p) * func->ctildes[p]; + } + } + + // rank>1 + func_ms_ind = 0; + func_ms_t_ind = 0;// index for dB + DOUBLE_TYPE theta = 0; + for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { + ACECTildeBasisFunction *func = &basis[func_ind]; +// ndensity = func->ndensity; + rank = func->rank; + mus = func->mus; + ns = func->ns; + ls = func->ls; + for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { + ms = &func->ms_combs[ms_ind * rank]; + theta = 0; + for (DENSITY_TYPE p = 0; p < ndensity; ++p) { + theta += dF_drho(p) * func->ctildes[ms_ind * ndensity + p]; +#ifdef DEBUG_FORCES_CALCULATIONS + printf("(p=%d) theta += dF_drho[p] * func.ctildes[ms_ind * ndensity + p] = %f * %f = %f\n",p, dF_drho(p), func->ctildes[ms_ind * ndensity + p],dF_drho(p)*func->ctildes[ms_ind * ndensity + p]); + printf("theta=%f\n",theta); +#endif + } + + theta *= 0.5; // 0.5 factor due to possible double counting ??? + for (t = 0; t < rank; ++t, ++func_ms_t_ind) { + m_t = ms[t]; + factor = (m_t % 2 == 0 ? 1 : -1); + dB = dB_flatten(func_ms_t_ind); + weights(mus[t], ns[t] - 1, ls[t], m_t) += theta * dB; //Theta_array(func_ms_ind); + // update -m_t (that could also be positive), because the basis is half_basis + weights(mus[t], ns[t] - 1, ls[t], -m_t) += + theta * (dB).conjugated() * factor;// Theta_array(func_ms_ind); +#ifdef DEBUG_FORCES_CALCULATIONS + printf("dB(n,l,m)(%d,%d,%d) = (%f, %f)\n", ns[t], ls[t], m_t, (dB).real, (dB).img); + printf("theta = %f\n",theta); + printf("weights(n,l,m)(%d,%d,%d) += (%f, %f)\n", ns[t], ls[t], m_t, (theta * dB * 0.5).real, + (theta * dB * 0.5).img); + printf("weights(n,l,-m)(%d,%d,%d) += (%f, %f)\n", ns[t], ls[t], -m_t, + ( theta * (dB).conjugated() * factor * 0.5).real, + ( theta * (dB).conjugated() * factor * 0.5).img); +#endif + } + } + } + energy_calc_timer.stop(); + +// ==================== FORCES ==================== +#ifdef PRINT_MAIN_STEPS + printf("\nFORCE CALCULATION\n"); + printf("loop over neighbours\n"); +#endif + + forces_calc_loop_timer.start(); +// loop over neighbour atoms for force calculations + for (jj = 0; jj < jnum_actual; ++jj) { + mu_j = elements[jj]; + r_hat = rhats[jj]; + inv_r_norm = inv_r_norms[jj]; + + Array2DLM &Y_cache_jj = Y_cache(jj); + Array2DLM &DY_cache_jj = DY_cache(jj); + +#ifdef PRINT_LOOPS_INDICES + printf("\nneighbour atom #%d\n", jj); + printf("rhat = (%f, %f, %f)\n", r_hat[0], r_hat[1], r_hat[2]); +#endif + + forces_calc_neighbour_timer.start(); + + f_ji[0] = f_ji[1] = f_ji[2] = 0; + +//for rank = 1 + for (n = 0; n < nradbasei; ++n) { + if (weights_rank1(mu_j, n) == 0) + continue; + auto &DG = DG_cache(jj, n); + DGR = DG * Y00; + DGR *= weights_rank1(mu_j, n); +#ifdef DEBUG_FORCES_CALCULATIONS + printf("r=1: (n,l,m)=(%d, 0, 0)\n",n+1); + printf("\tGR(n=%d, r=%f)=%f\n",n+1,r_norm, gr(n)); + printf("\tDGR(n=%d, r=%f)=%f\n",n+1,r_norm, dgr(n)); + printf("\tdF+=(%f, %f, %f)\n",DGR * r_hat[0], DGR * r_hat[1], DGR * r_hat[2]); +#endif + f_ji[0] += DGR * r_hat[0]; + f_ji[1] += DGR * r_hat[1]; + f_ji[2] += DGR * r_hat[2]; + } + +//for rank > 1 + for (n = 0; n < nradiali; n++) { + for (l = 0; l <= lmaxi; l++) { + R_over_r = R_cache(jj, n, l) * inv_r_norm; + DR = DR_cache(jj, n, l); + + // for m>=0 + for (m = 0; m <= l; m++) { + ACEComplex w = weights(mu_j, n, l, m); + if (w == 0) + continue; + //counting for -m cases if m>0 + if (m > 0) w *= 2; + + DY = DY_cache_jj(l, m); + Y_DR = Y_cache_jj(l, m) * DR; + + grad_phi_nlm.a[0] = Y_DR * r_hat[0] + DY.a[0] * R_over_r; + grad_phi_nlm.a[1] = Y_DR * r_hat[1] + DY.a[1] * R_over_r; + grad_phi_nlm.a[2] = Y_DR * r_hat[2] + DY.a[2] * R_over_r; +#ifdef DEBUG_FORCES_CALCULATIONS + printf("d_phi(n=%d, l=%d, m=%d) = ((%f,%f), (%f,%f), (%f,%f))\n",n+1,l,m, + grad_phi_nlm.a[0].real, grad_phi_nlm.a[0].img, + grad_phi_nlm.a[1].real, grad_phi_nlm.a[1].img, + grad_phi_nlm.a[2].real, grad_phi_nlm.a[2].img); + + printf("weights(n,l,m)(%d,%d,%d) = (%f,%f)\n", n+1, l, m,w.real, w.img); + //if (m>0) w*=2; + printf("dF(n,l,m)(%d, %d, %d) += (%f, %f, %f)\n", n + 1, l, m, + w.real_part_product(grad_phi_nlm.a[0]), + w.real_part_product(grad_phi_nlm.a[1]), + w.real_part_product(grad_phi_nlm.a[2]) + ); +#endif +// real-part multiplication only + f_ji[0] += w.real_part_product(grad_phi_nlm.a[0]); + f_ji[1] += w.real_part_product(grad_phi_nlm.a[1]); + f_ji[2] += w.real_part_product(grad_phi_nlm.a[2]); + } + } + } + + +#ifdef PRINT_INTERMEDIATE_VALUES + printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, + f_ji[0], f_ji[1], f_ji[2] + ); +#endif + + //hard-core repulsion + DCR = DCR_cache(jj); +#ifdef DEBUG_FORCES_CALCULATIONS + printf("DCR = %f\n",DCR); +#endif + f_ji[0] += dF_drho_core * DCR * r_hat[0]; + f_ji[1] += dF_drho_core * DCR * r_hat[1]; + f_ji[2] += dF_drho_core * DCR * r_hat[2]; +#ifdef PRINT_INTERMEDIATE_VALUES + printf("with core-repulsion\n"); + printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, + f_ji[0], f_ji[1], f_ji[2] + ); + printf("neighbour_index_mapping[jj=%d]=%d\n",jj,neighbour_index_mapping[jj]); +#endif + + neighbours_forces(neighbour_index_mapping[jj], 0) = f_ji[0]; + neighbours_forces(neighbour_index_mapping[jj], 1) = f_ji[1]; + neighbours_forces(neighbour_index_mapping[jj], 2) = f_ji[2]; + + forces_calc_neighbour_timer.stop(); + }// end loop over neighbour atoms for forces + + forces_calc_loop_timer.stop(); + + //now, energies and forces are ready + //energies(i) = evdwl + rho_core; + e_atom = evdwl_cut; + +#ifdef PRINT_INTERMEDIATE_VALUES + printf("energies(i) = FS(...rho_p_accum...) = %f\n", evdwl); +#endif + per_atom_calc_timer.stop(); +} \ No newline at end of file diff --git a/lib/pace/ace_evaluator.h b/lib/pace/ace_evaluator.h new file mode 100644 index 0000000000..356ea52563 --- /dev/null +++ b/lib/pace/ace_evaluator.h @@ -0,0 +1,230 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Yury Lysogorskiy on 31.01.20. + +#ifndef ACE_EVALUATOR_H +#define ACE_EVALUATOR_H + +#include "ace_abstract_basis.h" +#include "ace_arraynd.h" +#include "ace_array2dlm.h" +#include "ace_c_basis.h" +#include "ace_complex.h" +#include "ace_timing.h" +#include "ace_types.h" + +/** + * Basic evaluator class, that should accept the basis set and implement the "compute_atom" method using given basis set. + */ +class ACEEvaluator { +protected: + + Array2D A_rank1 = Array2D("A_rank1"); ///< 2D-array for storing A's for rank=1, shape: A(mu_j,n) + Array4DLM A = Array4DLM("A"); ///< 4D array with (l,m) last indices for storing A's for rank>1: A(mu_j, n, l, m) + + Array1D rhos = Array1D("rhos"); ///< densities \f$ \rho^{(p)} \f$(ndensity), p = 0 .. ndensity-1 + Array1D dF_drho = Array1D("dF_drho"); ///< derivatives of cluster functional wrt. densities, index = 0 .. ndensity-1 + + /** + * Initialize internal arrays according to basis set sizes + * @param basis_set + */ + void init(ACEAbstractBasisSet *basis_set); + +public: + // set of timers for code profiling + + ACETimer loop_over_neighbour_timer; ///< timer for loop over neighbours when constructing A's for single central atom + ACETimer per_atom_calc_timer; ///< timer for single compute_atom call + + + ACETimer forces_calc_loop_timer; ///< timer for forces calculations for single central atom + ACETimer forces_calc_neighbour_timer; ///< timer for loop over neighbour atoms for force calculations + + ACETimer energy_calc_timer; ///< timer for energy calculation + ACETimer total_time_calc_timer; ///< timer for total calculations of all atoms within given atomic environment system + + /** + * Initialize all timers + */ + void init_timers(); + + /** + * Mapping from external atoms types, i.e. LAMMPS, to internal SPECIES_TYPE, used in basis functions + */ + Array1D element_type_mapping = Array1D("element_type_mapping"); + + + DOUBLE_TYPE e_atom = 0; ///< energy of current atom, including core-repulsion + + /** + * temporary array for the pair forces between current atom_i and its neighbours atom_k + * neighbours_forces(k,3), k = 0..num_of_neighbours(atom_i)-1 + */ + Array2D neighbours_forces = Array2D("neighbours_forces"); + + ACEEvaluator() = default; + + virtual ~ACEEvaluator() = default; + + /** + * The key method to compute energy and forces for atom 'i'. + * Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array + * + * @param i atom index + * @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3] + * @param type atomic types array of the real and ghost atoms, shape: [atom_ind] + * @param jnum number of neighbours of atom_i + * @param jlist array of neighbour indices, shape: [jnum] + */ + virtual void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) = 0; + + /** + * Resize all caches over neighbours atoms + * @param max_jnum maximum number of neighbours + */ + virtual void resize_neighbours_cache(int max_jnum) = 0; + +#ifdef EXTRA_C_PROJECTIONS + /** + * 2D array to store projections of basis function for rank = 1, shape: [func_ind][ndensity] + */ + Array2D basis_projections_rank1 = Array2D("basis_projections_rank1"); + + /** + * 2D array to store projections of basis function for rank > 1, shape: [func_ind][ndensity] + */ + Array2D basis_projections = Array2D("basis_projections"); +#endif +}; + +//TODO: split into separate file +/** + * Evaluator for C-tilde basis set, that should accept the basis set and implement the "compute_atom" method using given basis set. + */ +class ACECTildeEvaluator : public ACEEvaluator { + + /** + * Weights \f$ \omega_{i \mu n 0 0} \f$ for rank = 1, see Eq.(10) from implementation notes, + * 'i' is fixed for the current atom, shape: [nelements][nradbase] + */ + Array2D weights_rank1 = Array2D("weights_rank1"); + + /** + * Weights \f$ \omega_{i \mu n l m} \f$ for rank > 1, see Eq.(10) from implementation notes, + * 'i' is fixed for the current atom, shape: [nelements][nradbase][l=0..lmax, m] + */ + Array4DLM weights = Array4DLM("weights"); + + /** + * cache for gradients of \f$ g(r)\f$: grad_phi(jj,n)=A2DLM(l,m) + * shape:[max_jnum][nradbase] + */ + Array2D DG_cache = Array2D("DG_cache"); + + + /** + * cache for \f$ R_{nl}(r)\f$ + * shape:[max_jnum][nradbase][0..lmax] + */ + Array3D R_cache = Array3D("R_cache"); + /** + * cache for derivatives of \f$ R_{nl}(r)\f$ + * shape:[max_jnum][nradbase][0..lmax] + */ + Array3D DR_cache = Array3D("DR_cache"); + /** + * cache for \f$ Y_{lm}(\hat{r})\f$ + * shape:[max_jnum][0..lmax][m] + */ + Array3DLM Y_cache = Array3DLM("Y_cache"); + /** + * cache for \f$ \nabla Y_{lm}(\hat{r})\f$ + * shape:[max_jnum][0..lmax][m] + */ + Array3DLM DY_cache = Array3DLM("dY_dense_cache"); + + /** + * cache for derivatives of hard-core repulsion + * shape:[max_jnum] + */ + Array1D DCR_cache = Array1D("DCR_cache"); + + /** + * Partial derivatives \f$ dB_{i \mu n l m t}^{(r)} \f$ with sequential numbering over [func_ind][ms_ind][r], + * shape:[func_ms_r_ind] + */ + Array1D dB_flatten = Array1D("dB_flatten"); + + /** + * pointer to the ACEBasisSet object + */ + ACECTildeBasisSet *basis_set = nullptr; + + /** + * Initialize internal arrays according to basis set sizes + * @param basis_set + */ + void init(ACECTildeBasisSet *basis_set); + +public: + + ACECTildeEvaluator() = default; + + explicit ACECTildeEvaluator(ACECTildeBasisSet &bas) { + set_basis(bas); + } + + /** + * set the basis function to the ACE evaluator + * @param bas + */ + void set_basis(ACECTildeBasisSet &bas); + + /** + * The key method to compute energy and forces for atom 'i'. + * Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array + * + * @param i atom index + * @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3] + * @param type atomic types array of the real and ghost atoms, shape: [atom_ind] + * @param jnum number of neighbours of atom_i + * @param jlist array of neighbour indices, shape: [jnum] + */ + void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) override; + + /** + * Resize all caches over neighbours atoms + * @param max_jnum maximum number of neighbours + */ + void resize_neighbours_cache(int max_jnum) override; +}; + + +#endif //ACE_EVALUATOR_H \ No newline at end of file diff --git a/lib/pace/ace_flatten_basis.cpp b/lib/pace/ace_flatten_basis.cpp new file mode 100644 index 0000000000..541785a202 --- /dev/null +++ b/lib/pace/ace_flatten_basis.cpp @@ -0,0 +1,130 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by yury on 28.04.2020. + +#include "ace_flatten_basis.h" + +ACEFlattenBasisSet::ACEFlattenBasisSet(const ACEFlattenBasisSet &other) { + _copy_scalar_memory(other); + _copy_dynamic_memory(other); +} + +ACEFlattenBasisSet &ACEFlattenBasisSet::operator=(const ACEFlattenBasisSet &other) { + if (this != &other) { + _clean(); + _copy_scalar_memory(other); + _copy_dynamic_memory(other); + } + return *this; +} + + +ACEFlattenBasisSet::~ACEFlattenBasisSet() { + ACEFlattenBasisSet::_clean(); +} + +void ACEFlattenBasisSet::_clean() { + //chained call of base class method + ACEAbstractBasisSet::_clean(); + _clean_contiguous_arrays(); + _clean_basissize_arrays(); + +} + +void ACEFlattenBasisSet::_clean_basissize_arrays() { + delete[] total_basis_size; + total_basis_size = nullptr; + + delete[] total_basis_size_rank1; + total_basis_size_rank1 = nullptr; +} + +void ACEFlattenBasisSet::_clean_contiguous_arrays() { + delete[] full_ns_rank1; + full_ns_rank1 = nullptr; + + delete[] full_ls_rank1; + full_ls_rank1 = nullptr; + + delete[] full_mus_rank1; + full_mus_rank1 = nullptr; + + delete[] full_ms_rank1; + full_ms_rank1 = nullptr; + + ////// + + delete[] full_ns; + full_ns = nullptr; + + delete[] full_ls; + full_ls = nullptr; + + delete[] full_mus; + full_mus = nullptr; + + delete[] full_ms; + full_ms = nullptr; +} + +void ACEFlattenBasisSet::_copy_scalar_memory(const ACEFlattenBasisSet &src) { + ACEAbstractBasisSet::_copy_scalar_memory(src); + + rank_array_total_size_rank1 = src.rank_array_total_size_rank1; + coeff_array_total_size_rank1 = src.coeff_array_total_size_rank1; + rank_array_total_size = src.rank_array_total_size; + ms_array_total_size = src.ms_array_total_size; + coeff_array_total_size = src.coeff_array_total_size; + + max_B_array_size = src.max_B_array_size; + max_dB_array_size = src.max_dB_array_size; + num_ms_combinations_max = src.num_ms_combinations_max; +} + +void ACEFlattenBasisSet::_copy_dynamic_memory(const ACEFlattenBasisSet &src) { //allocate new memory + + ACEAbstractBasisSet::_copy_dynamic_memory(src); + + if (src.total_basis_size_rank1 == nullptr) + throw runtime_error("Could not copy ACEFlattenBasisSet::total_basis_size_rank1 - array not initialized"); + if (src.total_basis_size == nullptr) + throw runtime_error("Could not copy ACEFlattenBasisSet::total_basis_size - array not initialized"); + + delete[] total_basis_size_rank1; + total_basis_size_rank1 = new SHORT_INT_TYPE[nelements]; + delete[] total_basis_size; + total_basis_size = new SHORT_INT_TYPE[nelements]; + + //copy + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + total_basis_size_rank1[mu] = src.total_basis_size_rank1[mu]; + total_basis_size[mu] = src.total_basis_size[mu]; + } +} + diff --git a/lib/pace/ace_flatten_basis.h b/lib/pace/ace_flatten_basis.h new file mode 100644 index 0000000000..e21cbb749a --- /dev/null +++ b/lib/pace/ace_flatten_basis.h @@ -0,0 +1,135 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Lysogroskiy Yury on 28.04.2020. + +#ifndef ACE_EVALUATOR_ACE_FLATTEN_BASIS_H +#define ACE_EVALUATOR_ACE_FLATTEN_BASIS_H + + +#include "ace_abstract_basis.h" +#include "ace_c_basisfunction.h" +#include "ace_radial.h" +#include "ace_spherical_cart.h" +#include "ace_types.h" + +/** + * Basis set with basis function attributes, i.e. \f$ \mathbf{n}, \mathbf{l}, \mathbf{m}\f$, etc. + * packed into contiguous arrays for the cache-friendly memory layout. + */ +class ACEFlattenBasisSet : public ACEAbstractBasisSet { +public: + //arrays and its sizes for rank = 1 basis functions for packed basis + + size_t rank_array_total_size_rank1 = 0; ///< size for full_ns_rank1, full_ls_rank1, full_Xs_rank1 + size_t coeff_array_total_size_rank1 = 0; ///< size for full coefficients array (depends on B or C-Tilde basis) + + NS_TYPE *full_ns_rank1 = nullptr; ///< ns contiguous package [rank_array_total_size_rank1] + LS_TYPE *full_ls_rank1 = nullptr; ///< ls contiguous package [rank_array_total_size_rank1] + SPECIES_TYPE *full_mus_rank1 = nullptr; ///< mus contiguous package [rank_array_total_size_rank1] + MS_TYPE *full_ms_rank1 = nullptr; ///< m_s contiguous package[rank_array_total_size_rank1] + + //arrays and its sizes for rank > 1 basis functions for packed basis + size_t rank_array_total_size = 0; ///< size for full_ns, full_ls, full_Xs + size_t ms_array_total_size = 0; ///< size for full_ms array + size_t coeff_array_total_size = 0;///< size for full coefficients arrays (depends on B- or C- basis) + + NS_TYPE *full_ns = nullptr; ///< ns contiguous package [rank_array_total_size] + LS_TYPE *full_ls = nullptr; ///< ls contiguous package [rank_array_total_size] + SPECIES_TYPE *full_mus = nullptr; ///< mus contiguous package [rank_array_total_size] + MS_TYPE *full_ms = nullptr; ///< //m_s contiguous package [ms_array_total_size] + + /** + * Rearrange basis functions in contiguous memory to optimize cache access + */ + virtual void pack_flatten_basis() = 0; + + virtual void flatten_basis() = 0; + + //1D flat array basis representation: [mu] + SHORT_INT_TYPE *total_basis_size_rank1 = nullptr; ///< per-species type array of total_basis_rank1[mu] sizes + SHORT_INT_TYPE *total_basis_size = nullptr; ///< per-species type array of total_basis[mu] sizes + + size_t max_B_array_size = 0; ///< maximum over elements array size for B[func_ind][ms_ind] + size_t max_dB_array_size = 0; ///< maximum over elements array size for dB[func_ind][ms_ind][r] + + SHORT_INT_TYPE num_ms_combinations_max = 0; ///< maximum number of ms combinations among all basis functions + + /** + * Default constructor + */ + ACEFlattenBasisSet() = default; + + /** + * Copy constructor (see Rule of Three) + * @param other + */ + ACEFlattenBasisSet(const ACEFlattenBasisSet &other); + + /** + * operator= (see Rule of Three) + * @param other + * @return + */ + ACEFlattenBasisSet &operator=(const ACEFlattenBasisSet &other); + + /** + * Destructor (see Rule of Three) + */ + ~ACEFlattenBasisSet() override; + + // routines for copying and cleaning dynamic memory of the class (see Rule of Three) + /** + * Cleaning dynamic memory of the class (see. Rule of Three), + * must be idempotent for safety + */ + void _clean() override; + + /** + * Copying scalar variables + * @param src + */ + void _copy_scalar_memory(const ACEFlattenBasisSet &src); + + /** + * Copying and cleaning dynamic memory of the class (see. Rule of Three) + * @param src + */ + void _copy_dynamic_memory(const ACEFlattenBasisSet &src); + + /** + * Clean contiguous arrays + */ + virtual void _clean_contiguous_arrays(); + + /** + * Release dynamic arrays with basis set sizes + */ + void _clean_basissize_arrays(); +}; + +#endif //ACE_EVALUATOR_ACE_FLATTEN_BASIS_H diff --git a/lib/pace/ace_radial.cpp b/lib/pace/ace_radial.cpp new file mode 100644 index 0000000000..01348a719c --- /dev/null +++ b/lib/pace/ace_radial.cpp @@ -0,0 +1,566 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +#include +#include +#include + +#include "ace_radial.h" + +const DOUBLE_TYPE pi = 3.14159265358979323846264338327950288419; // pi + +ACERadialFunctions::ACERadialFunctions(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, + SPECIES_TYPE nelements, + DOUBLE_TYPE cutoff, string radbasename) { + init(nradb, lmax, nradial, deltaSplineBins, nelements, cutoff, radbasename); +} + +void ACERadialFunctions::init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, + SPECIES_TYPE nelements, + DOUBLE_TYPE cutoff, string radbasename) { + this->nradbase = nradb; + this->lmax = lmax; + this->nradial = nradial; + this->deltaSplineBins = deltaSplineBins; + this->nelements = nelements; + this->cutoff = cutoff; + this->radbasename = radbasename; + + gr.init(nradbase, "gr"); + dgr.init(nradbase, "dgr"); + d2gr.init(nradbase, "d2gr"); + + + fr.init(nradial, lmax + 1, "fr"); + dfr.init(nradial, lmax + 1, "dfr"); + d2fr.init(nradial, lmax + 1, "d2fr"); + + + cheb.init(nradbase + 1, "cheb"); + dcheb.init(nradbase + 1, "dcheb"); + cheb2.init(nradbase + 1, "cheb2"); + + + splines_gk.init(nelements, nelements, "splines_gk"); + splines_rnl.init(nelements, nelements, "splines_rnl"); + splines_hc.init(nelements, nelements, "splines_hc"); + + lambda.init(nelements, nelements, "lambda"); + lambda.fill(1.); + + cut.init(nelements, nelements, "cut"); + cut.fill(1.); + + dcut.init(nelements, nelements, "dcut"); + dcut.fill(1.); + + crad.init(nelements, nelements, nradial, (lmax + 1), nradbase, "crad"); + crad.fill(0.); + + //hard-core repulsion + prehc.init(nelements, nelements, "prehc"); + prehc.fill(0.); + + lambdahc.init(nelements, nelements, "lambdahc"); + lambdahc.fill(1.); + +} + + +/** +Function that computes Chebyshev polynomials of first and second kind + to setup the radial functions and the derivatives + +@param n, x + +@returns cheb1, dcheb1 +*/ +void ACERadialFunctions::calcCheb(NS_TYPE n, DOUBLE_TYPE x) { + if (n < 0) { + char s[1024]; + sprintf(s, "The order n of the polynomials should be positive %d\n", n); + throw std::invalid_argument(s); + } + DOUBLE_TYPE twox = 2.0 * x; + cheb(0) = 1.; + dcheb(0) = 0.; + cheb2(0) = 1.; + + if (nradbase > 1) { + cheb(1) = x; + cheb2(1) = twox; + } + for (NS_TYPE m = 1; m <= n - 1; m++) { + cheb(m + 1) = twox * cheb(m) - cheb(m - 1); + cheb2(m + 1) = twox * cheb2(m) - cheb2(m - 1); + } + for (NS_TYPE m = 1; m <= n; m++) { + dcheb(m) = m * cheb2(m - 1); + } +#ifdef DEBUG_RADIAL + for ( NS_TYPE m=0; m<=n; m++ ) { + printf(" m %d cheb %f dcheb %f \n", m, cheb(m), dcheb(m)); + } +#endif +} + +/** +Function that computes radial basis. + +@param lam, nradbase, cut, dcut, r + +@returns gr, dgr +*/ +void ACERadialFunctions::radbase(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { + /*lam is given by the formula (24), that contains cut */ + + if (r < cut) { + if (radbasename == "ChebExpCos") { + chebExpCos(lam, cut, dcut, r); + } else if (radbasename == "ChebPow") { + chebPow(lam, cut, dcut, r); + } else if (radbasename == "ChebLinear") { + chebLinear(lam, cut, dcut, r); + } else { + throw invalid_argument("Unknown radial basis function name: " + radbasename); + } + } else { + gr.fill(0); + dgr.fill(0); + } +} + +/*** + * Radial function: ChebExpCos, cheb exp scaling including cos envelope + * @param lam function parameter + * @param cut cutoff distance + * @param r function input argument + * @return fills in gr and dgr arrays + */ +void +ACERadialFunctions::chebExpCos(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { + DOUBLE_TYPE y2, y1, x, dx; + DOUBLE_TYPE env, denv, fcut, dfcut; + /* scaled distance x and derivative*/ + y1 = exp(-lam * r / cut); + y2 = exp(-lam); + x = 1.0 - 2.0 * ((y1 - y2) / (1 - y2)); + dx = 2 * (lam / cut) * (y1 / (1 - y2)); + /* calculation of Chebyshev polynomials from the recursion */ + calcCheb(nradbase - 1, x); + gr(0) = cheb(0); + dgr(0) = dcheb(0) * dx; + for (NS_TYPE n = 2; n <= nradbase; n++) { + gr(n - 1) = 0.5 - 0.5 * cheb(n - 1); + dgr(n - 1) = -0.5 * dcheb(n - 1) * dx; + } + env = 0.5 * (1.0 + cos(M_PI * r / cut)); + denv = -0.5 * sin(M_PI * r / cut) * M_PI / cut; + for (NS_TYPE n = 0; n < nradbase; n++) { + dgr(n) = gr(n) * denv + dgr(n) * env; + gr(n) = gr(n) * env; + } + // for radtype = 3 a smooth cut is already included in the basis function + dx = cut - dcut; + if (r > dx) { + fcut = 0.5 * (1.0 + cos(M_PI * (r - dx) / dcut)); + dfcut = -0.5 * sin(M_PI * (r - dx) / dcut) * M_PI / dcut; + for (NS_TYPE n = 0; n < nradbase; n++) { + dgr(n) = gr(n) * dfcut + dgr(n) * fcut; + gr(n) = gr(n) * fcut; + } + } +} + +/*** +* Radial function: ChebPow, Radial function: ChebPow +* - argument of Chebyshev polynomials +* x = 2.0*( 1.0 - (1.0 - r/rcut)^lam ) - 1.0 +* - radial function +* gr(n) = ( 1.0 - Cheb(n) )/2.0, n = 1,...,nradbase +* - the function fulfills: +* gr(n) = 0 at rcut +* dgr(n) = 0 at rcut for lam >= 1 +* second derivative zero at rcut for lam >= 2 +* -> the radial function does not require a separate cutoff function +* - corresponds to radial basis radtype=5 in Fortran code +* +* @param lam function parameter +* @param cut cutoff distance +* @param r function input argument +* @return fills in gr and dgr arrays +*/ +void +ACERadialFunctions::chebPow(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { + DOUBLE_TYPE y, dy, x, dx; + /* scaled distance x and derivative*/ + y = (1.0 - r / cut); + dy = pow(y, (lam - 1.0)); + y = dy * y; + dy = -lam / cut * dy; + + x = 2.0 * (1.0 - y) - 1.0; + dx = -2.0 * dy; + calcCheb(nradbase, x); + for (NS_TYPE n = 1; n <= nradbase; n++) { + gr(n - 1) = 0.5 - 0.5 * cheb(n); + dgr(n - 1) = -0.5 * dcheb(n) * dx; + } +} + + +void +ACERadialFunctions::chebLinear(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { + DOUBLE_TYPE x, dx; + /* scaled distance x and derivative*/ + x = (1.0 - r / cut); + dx = -1 / cut; + calcCheb(nradbase, x); + for (NS_TYPE n = 1; n <= nradbase; n++) { + gr(n - 1) = 0.5 - 0.5 * cheb(n); + dgr(n - 1) = -0.5 * dcheb(n) * dx; + } +} + +/** +Function that computes radial functions. + +@param nradbase, nelements, elei, elej + +@returns fr, dfr +*/ +void ACERadialFunctions::radfunc(SPECIES_TYPE elei, SPECIES_TYPE elej) { + DOUBLE_TYPE frval, dfrval; + for (NS_TYPE n = 0; n < nradial; n++) { + for (LS_TYPE l = 0; l <= lmax; l++) { + frval = 0.0; + dfrval = 0.0; + for (NS_TYPE k = 0; k < nradbase; k++) { + frval += crad(elei, elej, n, l, k) * gr(k); + dfrval += crad(elei, elej, n, l, k) * dgr(k); + } + fr(n, l) = frval; + dfr(n, l) = dfrval; + } + } +} + + +void ACERadialFunctions::all_radfunc(SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, DOUBLE_TYPE r) { + DOUBLE_TYPE lam = lambda(mu_i, mu_j); + DOUBLE_TYPE r_cut = cut(mu_i, mu_j); + DOUBLE_TYPE dr_cut = dcut(mu_i, mu_j); + // set up radial functions + radbase(lam, r_cut, dr_cut, r); //update gr, dgr + radfunc(mu_i, mu_j); // update fr(nr, l), dfr(nr, l) +} + + +void ACERadialFunctions::setuplookupRadspline() { + using namespace std::placeholders; + DOUBLE_TYPE lam, r_cut, dr_cut; + DOUBLE_TYPE cr_c, dcr_c, pre, lamhc; + + // at r = rcut + eps the function and its derivatives is zero + for (SPECIES_TYPE elei = 0; elei < nelements; elei++) { + for (SPECIES_TYPE elej = 0; elej < nelements; elej++) { + + lam = lambda(elei, elej); + r_cut = cut(elei, elej); + dr_cut = dcut(elei, elej); + + splines_gk(elei, elej).setupSplines(gr.get_size(), + std::bind(&ACERadialFunctions::radbase, this, lam, r_cut, dr_cut, + _1),//update gr, dgr + gr.get_data(), + dgr.get_data(), deltaSplineBins, cutoff); + + splines_rnl(elei, elej).setupSplines(fr.get_size(), + std::bind(&ACERadialFunctions::all_radfunc, this, elei, elej, + _1), // update fr(nr, l), dfr(nr, l) + fr.get_data(), + dfr.get_data(), deltaSplineBins, cutoff); + + + pre = prehc(elei, elej); + lamhc = lambdahc(elei, elej); +// radcore(r, pre, lamhc, cutoff, cr_c, dcr_c); + splines_hc(elei, elej).setupSplines(1, + std::bind(&ACERadialFunctions::radcore, _1, pre, lamhc, cutoff, + std::ref(cr_c), std::ref(dcr_c)), + &cr_c, + &dcr_c, deltaSplineBins, cutoff); + } + } + +} + +/** +Function that gets radial function from look-up table using splines. + +@param r, nradbase_c, nradial_c, lmax, mu_i, mu_j + +@returns fr, dfr, gr, dgr, cr, dcr +*/ +void +ACERadialFunctions::evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, + SPECIES_TYPE mu_j, bool calc_second_derivatives) { + auto &spline_gk = splines_gk(mu_i, mu_j); + auto &spline_rnl = splines_rnl(mu_i, mu_j); + auto &spline_hc = splines_hc(mu_i, mu_j); + + spline_gk.calcSplines(r, calc_second_derivatives); // populate splines_gk.values, splines_gk.derivatives; + for (NS_TYPE nr = 0; nr < nradbase_c; nr++) { + gr(nr) = spline_gk.values(nr); + dgr(nr) = spline_gk.derivatives(nr); + if (calc_second_derivatives) + d2gr(nr) = spline_gk.second_derivatives(nr); + } + + spline_rnl.calcSplines(r, calc_second_derivatives); + for (size_t ind = 0; ind < fr.get_size(); ind++) { + fr.get_data(ind) = spline_rnl.values.get_data(ind); + dfr.get_data(ind) = spline_rnl.derivatives.get_data(ind); + if (calc_second_derivatives) + d2fr.get_data(ind) = spline_rnl.second_derivatives.get_data(ind); + } + + spline_hc.calcSplines(r, calc_second_derivatives); + cr = spline_hc.values(0); + dcr = spline_hc.derivatives(0); + if (calc_second_derivatives) + d2cr = spline_hc.second_derivatives(0); +} + + +void +ACERadialFunctions::radcore(DOUBLE_TYPE r, DOUBLE_TYPE pre, DOUBLE_TYPE lambda, DOUBLE_TYPE cutoff, DOUBLE_TYPE &cr, + DOUBLE_TYPE &dcr) { +/* pseudocode for hard core repulsion +in: + r: distance + pre: prefactor: read from input, depends on pair of atoms mu_i mu_j + lambda: exponent: read from input, depends on pair of atoms mu_i mu_j + cutoff: cutoff distance: read from input, depends on pair of atoms mu_i mu_j +out: +cr: hard core repulsion +dcr: derivative of hard core repulsion + + function + \$f f_{core} = pre \exp( - \lambda r^2 ) / r \$f + +*/ + + DOUBLE_TYPE r2, lr2, y, x0, env, denv; + +// repulsion strictly positive and decaying + pre = abs(pre); + lambda = abs(lambda); + + r2 = r * r; + lr2 = lambda * r2; + if (lr2 < 50.0) { + y = exp(-lr2); + cr = pre * y / r; + dcr = -pre * y * (2.0 * lr2 + 1.0) / r2; + + x0 = r / cutoff; + env = 0.5 * (1.0 + cos(pi * x0)); + denv = -0.5 * sin(pi * x0) * pi / cutoff; + dcr = cr * denv + dcr * env; + cr = cr * env; + } else { + cr = 0.0; + dcr = 0.0; + } + +} + +void +ACERadialFunctions::evaluate_range(vector r_vec, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, + SPECIES_TYPE mu_j) { + if (nradbase_c > nradbase) + throw invalid_argument("nradbase_c couldn't be larger than nradbase"); + if (nradial_c > nradial) + throw invalid_argument("nradial_c couldn't be larger than nradial"); + if (mu_i > nelements) + throw invalid_argument("mu_i couldn't be larger than nelements"); + if (mu_j > nelements) + throw invalid_argument("mu_j couldn't be larger than nelements"); + + gr_vec.resize(r_vec.size(), nradbase_c); + dgr_vec.resize(r_vec.size(), nradbase_c); + d2gr_vec.resize(r_vec.size(), nradbase_c); + + fr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1)); + dfr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1)); + d2fr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1)); + + for (size_t i = 0; i < r_vec.size(); i++) { + DOUBLE_TYPE r = r_vec[i]; + this->evaluate(r, nradbase_c, nradial_c, mu_i, mu_j, true); + for (NS_TYPE nr = 0; nr < nradbase_c; nr++) { + gr_vec(i, nr) = gr(nr); + dgr_vec(i, nr) = dgr(nr); + d2gr_vec(i, nr) = d2gr(nr); + } + + for (NS_TYPE nr = 0; nr < nradial_c; nr++) { + for (LS_TYPE l = 0; l <= lmax; l++) { + fr_vec(i, nr, l) = fr(nr, l); + dfr_vec(i, nr, l) = dfr(nr, l); + d2fr_vec(i, nr, l) = d2fr(nr, l); + + } + } + } + +} + +void SplineInterpolator::setupSplines(int num_of_functions, RadialFunctions func, + DOUBLE_TYPE *values, + DOUBLE_TYPE *dvalues, DOUBLE_TYPE deltaSplineBins, DOUBLE_TYPE cutoff) { + + this->deltaSplineBins = deltaSplineBins; + this->cutoff = cutoff; + this->ntot = static_cast(cutoff / deltaSplineBins); + + DOUBLE_TYPE r, c[4]; + this->num_of_functions = num_of_functions; + this->values.resize(num_of_functions); + this->derivatives.resize(num_of_functions); + this->second_derivatives.resize(num_of_functions); + + Array1D f1g(num_of_functions); + Array1D f1gd1(num_of_functions); + f1g.fill(0); + f1gd1.fill(0); + + nlut = ntot; + DOUBLE_TYPE f0, f1, f0d1, f1d1; + int idx; + + // cutoff is global cutoff + rscalelookup = (DOUBLE_TYPE) nlut / cutoff; + invrscalelookup = 1.0 / rscalelookup; + + lookupTable.init(ntot + 1, num_of_functions, 4); + if (values == nullptr & num_of_functions > 0) + throw invalid_argument("SplineInterpolator::setupSplines: values could not be null"); + if (dvalues == nullptr & num_of_functions > 0) + throw invalid_argument("SplineInterpolator::setupSplines: dvalues could not be null"); + + for (int n = nlut; n >= 1; n--) { + r = invrscalelookup * DOUBLE_TYPE(n); + func(r); //populate values and dvalues arrays + for (int func_id = 0; func_id < num_of_functions; func_id++) { + f0 = values[func_id]; + f1 = f1g(func_id); + f0d1 = dvalues[func_id] * invrscalelookup; + f1d1 = f1gd1(func_id); + // evaluate coefficients + c[0] = f0; + c[1] = f0d1; + c[2] = 3.0 * (f1 - f0) - f1d1 - 2.0 * f0d1; + c[3] = -2.0 * (f1 - f0) + f1d1 + f0d1; + // store coefficients + for (idx = 0; idx <= 3; idx++) + lookupTable(n, func_id, idx) = c[idx]; + + // evaluate function values and derivatives at current position + f1g(func_id) = c[0]; + f1gd1(func_id) = c[1]; + } + } + + +} + + +void SplineInterpolator::calcSplines(DOUBLE_TYPE r, bool calc_second_derivatives) { + DOUBLE_TYPE wl, wl2, wl3, w2l1, w3l2, w4l2; + DOUBLE_TYPE c[4]; + int func_id, idx; + DOUBLE_TYPE x = r * rscalelookup; + int nl = static_cast(floor(x)); + + if (nl <= 0) + throw std::invalid_argument("Encountered very small distance. Stopping."); + + if (nl < nlut) { + wl = x - DOUBLE_TYPE(nl); + wl2 = wl * wl; + wl3 = wl2 * wl; + w2l1 = 2.0 * wl; + w3l2 = 3.0 * wl2; + w4l2 = 6.0 * wl; + for (func_id = 0; func_id < num_of_functions; func_id++) { + for (idx = 0; idx <= 3; idx++) { + c[idx] = lookupTable(nl, func_id, idx); + } + values(func_id) = c[0] + c[1] * wl + c[2] * wl2 + c[3] * wl3; + derivatives(func_id) = (c[1] + c[2] * w2l1 + c[3] * w3l2) * rscalelookup; + if (calc_second_derivatives) + second_derivatives(func_id) = (c[2] + c[3] * w4l2) * rscalelookup * rscalelookup * 2; + } + } else { // fill with zeroes + values.fill(0); + derivatives.fill(0); + if (calc_second_derivatives) + second_derivatives.fill(0); + } +} + +void SplineInterpolator::calcSplines(DOUBLE_TYPE r, SHORT_INT_TYPE func_ind) { + DOUBLE_TYPE wl, wl2, wl3, w2l1, w3l2; + DOUBLE_TYPE c[4]; + int idx; + DOUBLE_TYPE x = r * rscalelookup; + int nl = static_cast(floor(x)); + + if (nl <= 0) + throw std::invalid_argument("Encountered very small distance. Stopping."); + + if (nl < nlut) { + wl = x - DOUBLE_TYPE(nl); + wl2 = wl * wl; + wl3 = wl2 * wl; + w2l1 = 2.0 * wl; + w3l2 = 3.0 * wl2; + + for (idx = 0; idx <= 3; idx++) { + c[idx] = lookupTable(nl, func_ind, idx); + } + values(func_ind) = c[0] + c[1] * wl + c[2] * wl2 + c[3] * wl3; + derivatives(func_ind) = (c[1] + c[2] * w2l1 + c[3] * w3l2) * rscalelookup; + + } else { // fill with zeroes + values(func_ind) = 0; + derivatives(func_ind) = 0; + } +} diff --git a/lib/pace/ace_radial.h b/lib/pace/ace_radial.h new file mode 100644 index 0000000000..e45cfaec79 --- /dev/null +++ b/lib/pace/ace_radial.h @@ -0,0 +1,324 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#ifndef ACE_RADIAL_FUNCTIONS_H +#define ACE_RADIAL_FUNCTIONS_H + +#include "ace_arraynd.h" +#include "ace_types.h" +#include + +using namespace std; + +//typedef void (*RadialFunctions)(DOUBLE_TYPE x); +typedef std::function RadialFunctions; + +/** + * Class that implement spline interpolation and caching for radial functions + */ +class SplineInterpolator { +public: + DOUBLE_TYPE cutoff = 0; ///< cutoff + DOUBLE_TYPE deltaSplineBins = 0.001; + int ntot = 10000; ///< Number of bins for look-up tables. + int nlut = 10000; ///< number of nodes in look-up table + DOUBLE_TYPE invrscalelookup = 1; ///< inverse of conversion coefficient from distance to lookup table within cutoff range + DOUBLE_TYPE rscalelookup = 1; ///< conversion coefficient from distance to lookup table within cutoff range + int num_of_functions = 0;///< number of functions to spline-interpolation + + Array1D values;// = Array1D("values"); ///< shape: [func_ind] + Array1D derivatives;// = Array1D("derivatives");///< shape: [func_ind] + Array1D second_derivatives;// = Array1D("second_derivatives");///< shape: [func_ind] + + Array3D lookupTable = Array3D("lookupTable");///< shape: [ntot+1][func_ind][4] + + /** + * Setup splines + * + * @param num_of_functions number of functions + * @param func subroutine, that update `values` and `dvalues` arrays + * @param values values + * @param dvalues derivatives + */ + void setupSplines(int num_of_functions, RadialFunctions func, + DOUBLE_TYPE *values, + DOUBLE_TYPE *dvalues, DOUBLE_TYPE deltaSplineBins, DOUBLE_TYPE cutoff); + + /** + * Populate `values` and `derivatives` arrays with a spline-interpolation for + * all functions + * + * @param r + * + * @return: populate 'values' and 'derivatives' + */ + void calcSplines(DOUBLE_TYPE r, bool calc_second_derivatives = false); + + /** + * Populate `values` and `derivatives` arrays with a spline-interpolation for + * all functions + * + * @param r + * + * @return: populate 'values' and 'derivatives' + */ + void calcSplines(DOUBLE_TYPE r, SHORT_INT_TYPE func_ind); +}; + +/** + * Interface class for radial basis functions with rank=1 (g_k), R_nl (rank>1) and hard-core repulsion radial functions + */ +class AbstractRadialBasis { +public: + SPECIES_TYPE nelements = 0; ///< number of elements + Array2D cut = Array2D("cut"); ///< cutoffs, shape: [nelements][nelements] + Array2D dcut = Array2D("dcut"); ///< decay of cutoff, shape: [nelements][nelements] + DOUBLE_TYPE cutoff = 0; ///< cutoff + +// int ntot = 10000; ///< Number of bins for look-up tables. + DOUBLE_TYPE deltaSplineBins; + LS_TYPE lmax = 0; ///< maximum value of `l` + NS_TYPE nradial = 0; ///< maximum number `n` of radial functions \f$ R_{nl}(r) \f$ + NS_TYPE nradbase = 0; ///< number of radial basis functions \f$ g_k(r) \f$ + + // Arrays for look-up tables. + Array2D splines_gk; ///< array of spline interpolator to store g_k, shape: [nelements][nelements] + Array2D splines_rnl; ///< array of spline interpolator to store R_nl, shape: [nelements][nelements] + Array2D splines_hc; ///< array of spline interpolator to store R_nl shape: [nelements][nelements] + //-------------------------------------------------------------------------- + + string radbasename = "ChebExpCos"; ///< type of radial basis functions \f$ g_{k}(r) \f$ (default="ChebExpCos") + + /** + Arrays to store radial functions. + */ + Array1D gr = Array1D("gr"); ///< g_k(r) functions, shape: [nradbase] + Array1D dgr = Array1D("dgr"); ///< derivatives of g_k(r) functions, shape: [nradbase] + Array1D d2gr = Array1D("d2gr"); ///< derivatives of g_k(r) functions, shape: [nradbase] + + Array2D fr = Array2D("fr"); ///< R_nl(r) functions, shape: [nradial][lmax+1] + Array2D dfr = Array2D( + "dfr"); ///< derivatives of R_nl(r) functions, shape: [nradial][lmax+1] + Array2D d2fr = Array2D( + "d2fr"); ///< derivatives of R_nl(r) functions, shape: [nradial][lmax+1] + + + + DOUBLE_TYPE cr; ///< hard-core repulsion + DOUBLE_TYPE dcr; ///< derivative of hard-core repulsion + DOUBLE_TYPE d2cr; ///< derivative of hard-core repulsion + + Array5D crad = Array5D( + "crad"); ///< expansion coefficients of radial functions into radial basis function, see Eq. (27) of PRB, shape: [nelements][nelements][lmax + 1][nradial][nradbase] + Array2D lambda = Array2D( + "lambda"); ///< distance scaling parameter Eq.(24) of PRB, shape: [nelements][nelements] + + Array2D prehc = Array2D( + "prehc"); ///< hard-core repulsion coefficients (prefactor), shape: [nelements][nelements] + Array2D lambdahc = Array2D( + "lambdahc");; ///< hard-core repulsion coefficients (lambdahc), shape: [nelements][nelements] + + virtual void + evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, + bool calc_second_derivatives = false) = 0; + + virtual void + init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements, + DOUBLE_TYPE cutoff, + string radbasename = "ChebExpCos") = 0; + + /** + * Function that sets up the look-up tables for spline-representation of radial functions. + */ + virtual void setuplookupRadspline() = 0; + + virtual AbstractRadialBasis *clone() const = 0; + + virtual ~AbstractRadialBasis() = default; +}; + + +/** +Class to store radial functions and their associated functions. \n +*/ +class ACERadialFunctions final : public AbstractRadialBasis { +public: + + //-------------------------------------------------------------------------- + + /** + Arrays to store Chebyshev polynomials. + */ + Array1D cheb = Array1D( + "cheb"); ///< Chebyshev polynomials of the first kind, shape: [nradbase+1] + Array1D dcheb = Array1D( + "dcheb"); ///< derivatives Chebyshev polynomials of the first kind, shape: [nradbase+1] + Array1D cheb2 = Array1D( + "cheb2"); ///< Chebyshev polynomials of the second kind, shape: [nradbase+1] + + //-------------------------------------------------------------------------- + + Array2D gr_vec; + Array2D dgr_vec; + Array2D d2gr_vec; + + Array3D fr_vec; + Array3D dfr_vec; + Array3D d2fr_vec; + //------------------------------------------------------------------------ + /** + * Default constructor + */ + ACERadialFunctions() = default; + + /** + * Parametrized constructor + * + * @param nradb number of radial basis function \f$ g_k(r) \f$ - nradbase + * @param lmax maximum orbital moment - lmax + * @param nradial maximum n-index of radial functions \f$ R_{nl}(r) \f$ - nradial + * @param ntot Number of bins for spline look-up tables. + * @param nelements numer of elements + * @param cutoff cutoff + * @param radbasename type of radial basis function \f$ g_k(r) \f$ (default: "ChebExpCos") + */ + ACERadialFunctions(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, + SPECIES_TYPE nelements, + DOUBLE_TYPE cutoff, string radbasename = "ChebExpCos"); + + /** + * Initialize arrays for given parameters + * + * @param nradb number of radial basis function \f$ g_k(r) \f$ - nradbase + * @param lmax maximum orbital moment - lmax + * @param nradial maximum n-index of radial functions \f$ R_{nl}(r) \f$ - nradial + * @param ntot Number of bins for spline look-up tables. + * @param nelements numer of elements + * @param cutoff cutoff + * @param radbasename type of radial basis function \f$ g_k(r) \f$ (default: "ChebExpCos") + */ + void init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements, + DOUBLE_TYPE cutoff, + string radbasename = "ChebExpCos") final; + + /** + * Destructor + */ + ~ACERadialFunctions() final = default; + + /** + * Function that computes Chebyshev polynomials of first and second kind + * to setup the radial functions and the derivatives + * + * @param n maximum polynom order + * @param x + * + * @returns fills cheb, dcheb and cheb2 arrays + */ + void calcCheb(NS_TYPE n, DOUBLE_TYPE x); + + /** + * Function that computes radial basis functions \$f g_k(r) \$f, see Eq.(21) of PRB paper + * @param lam \$f \lambda \$f parameter, see eq. (24) of PRB paper + * @param cut cutoff + * @param dcut cutoff decay + * @param r distance + * + * @return function fills gr and dgr arrays + */ + void radbase(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); + + /** + * Function that computes radial core repulsion \$f f_{core} = pre \exp( - \lambda r^2 ) / r \$f, + * and its derivative, see Eq.(27) of implementation notes. + * + * @param r distance + * @param pre prefactor: read from input, depends on pair of atoms mu_i mu_j + * @param lambda exponent: read from input, depends on pair of atoms mu_i mu_j + * @param cutoff cutoff distance: read from input, depends on pair of atoms mu_i mu_j + * @param cr (out) hard core repulsion + * @param dcr (out) derivative of hard core repulsion + */ + static void radcore(DOUBLE_TYPE r, DOUBLE_TYPE pre, DOUBLE_TYPE lambda, DOUBLE_TYPE cutoff, DOUBLE_TYPE &cr, + DOUBLE_TYPE &dcr); + + /** + * Function that sets up the look-up tables for spline-representation of radial functions. + */ + void setuplookupRadspline() final; + + /** + * Function that computes radial functions \f$ R_{nl}(r)\f$ (see Eq. 27 from PRB paper) + * and its derivatives for all range of n,l, + * ONLY if radial basis functions (gr and dgr) are computed. + * @param elei first species type + * @param elej second species type + * + * @return fills in fr, dfr arrays + */ + void radfunc(SPECIES_TYPE elei, SPECIES_TYPE elej); + + /** + * Compute all radial functions R_nl(r), radial basis functions g_k(r) and hard-core repulsion function hc(r) + * + * @param r distance + * @param nradbase_c + * @param nradial_c + * @param mu_i + * @param mu_j + * + * @return update gr(k), dgr(k), fr(n,l), dfr(n,l), cr, dcr + */ + void evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, + bool calc_second_derivatives = false) final; + + + void + evaluate_range(vector r_vec, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, + SPECIES_TYPE mu_j); + + void chebExpCos(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); + + void chebPow(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); + + void chebLinear(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); + + /** + * Setup all radial functions for element pair mu_i-mu_j and distance r + * @param mu_i first specie type + * @param mu_j second specie type + * @param r distance + * @return update fr(nr, l), dfr(nr, l) + */ + void all_radfunc(SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, DOUBLE_TYPE r); + + ACERadialFunctions *clone() const override { + return new ACERadialFunctions(*this); + }; +}; + +#endif \ No newline at end of file diff --git a/lib/pace/ace_recursive.cpp b/lib/pace/ace_recursive.cpp new file mode 100644 index 0000000000..c895418943 --- /dev/null +++ b/lib/pace/ace_recursive.cpp @@ -0,0 +1,1340 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Christoph Ortner on 20.12.2020 + +#include "ace_recursive.h" + +#include "ace_abstract_basis.h" +#include "ace_types.h" + +/* ------------------------------------------------------------ + * ACEDAG Implementation + * (just the DAG construction, not the traversal) + * ------------------------------------------------------------ */ + +/* Notes on different Tags: + * rec1 - first basic implementation + * rec2 - avoid index arithmetic, contiguous layout, + * canonical evaluator in ACE.jl format + * rec3 - split nodes into interior and leaf nodes + */ + +void ACEDAG::init(Array2D xAspec, + Array2D AAspec, + Array1D orders, + Array2D jl_coeffs, + int _heuristic ) { + + // remember which heuristic we want to use! + heuristic = _heuristic; + + /* stage one of the graph is just extracting the A basis from + * the tensor product format into the linear list; all information + * for that is already stored in Aspec, and the only thing to do here is + * to construct zero-coefficients. Still we have to copy Aspec, since + * the one we have here will (may?) be deleted. */ + int num1 = xAspec.get_dim(0); + Aspec = xAspec; //YL: just copying the multiarray: Aspec = xAspec; + + /* fill the one-particle basis into the DAGmap + * DAGmap[ (i1,...,in) ] = iAA index where the (i1,...,in) basis functions + * lives. + */ + TDAGMAP DAGmap; + for (int iA = 0; iA < num1; iA++) { + vector a(1); + a[0] = iA; + DAGmap[a] = iA; + } + + /* For stage 2 we now want to construct the actual recursion; the + recursion info will be stored in DAGspec, while the + coefficients go into DAGcoeffs. These arrays are initialized to + length `num2`, but they will have to grow as we add additional + artificial nodes into the graph. + + initially we treat all nodes as having children, but then in a + second stage below we reorganize. */ + int num2 = AAspec.get_dim(0); + int ndensity = jl_coeffs.get_dim(1); + nodes_pre.resize(2*num2, 2); + coeffs_pre.resize(2*num2, ndensity); + + /* the first basis function we construct will get index num1, + * since there are already num1 one-particle basis functions + * to collect during stage 1 */ + dag_idx = num1; + /* main loop over AA basis set to transform into DAG */ + for (int iAA = 0; iAA < num2; iAA++) { + // create a vector representing the current basis function + int ord = orders(iAA); + vector aa(ord); + for (int t = 0; t < ord; t++) aa[t] = AAspec(iAA, t); + vector c(ndensity); + for (int p = 0; p < ndensity; p++) c[p] = jl_coeffs(iAA, p); + insert_node(DAGmap, aa, c); + } + + /* convert to 3-stage format through reordering + * interior nodes first, then leaf nodes */ + + // allocate storage + num_nodes = dag_idx; // store total size of dag + // num_nodes - num1 = number of many-body nodes. + nodes.resize(num_nodes - num1, 2); + coeffs.resize(num_nodes - num1, ndensity); + + // find out which nodes have children + haschild.resize(num_nodes - num1); + haschild.fill(false); + for (int iAA = 0; iAA < num_nodes - num1; iAA++) { + if (nodes_pre(iAA, 0) >= num1) + haschild(nodes_pre(iAA, 0)-num1) = true; + if (nodes_pre(iAA, 1) >= num1) + haschild(nodes_pre(iAA, 1)-num1) = true; + } + + // to reorder the graph we need a fresh map from preordered indices to + // postordered indices; for the 1-particle basis the order remains the same. + // TODO: doesn't need to be a map, could be a vector. + map neworder; + for (int iA = 0; iA < num1; iA++) + neworder[iA] = iA; + + // insert all interior nodes + num2_int = 0; + num2_leaf = 0; + dag_idx = num1; + int i1, i2, i1pre, i2pre; + for (int iAA = 0; iAA < num_nodes - num1; iAA++) { + if (haschild(iAA)) { + num2_int += 1; + // indices into AAbuf before reordering + i1pre = nodes_pre(iAA, 0); + i2pre = nodes_pre(iAA, 1); + // indices into AAbuf after reordering + i1 = neworder[i1pre]; + i2 = neworder[i2pre]; + // insert the current node : iAA is old order, dag_idx is new order + neworder[num1+iAA] = dag_idx; + nodes(dag_idx-num1, 0) = i1; + nodes(dag_idx-num1, 1) = i2; + for (int t = 0; t < ndensity; t++) + coeffs(dag_idx-num1, t) = coeffs_pre(iAA, t); + dag_idx++; + } + } + + // insert all leaf nodes + for (int iAA = 0; iAA < num_nodes - num1; iAA++) { + if (!haschild(iAA)) { + num2_leaf += 1; + // indices into AAbuf before reordering + i1pre = nodes_pre(iAA, 0); + i2pre = nodes_pre(iAA, 1); + // insert the current node : no need to remember the new order now + nodes(dag_idx-num1, 0) = neworder[i1pre]; + nodes(dag_idx-num1, 1) = neworder[i2pre]; + for (int t = 0; t < ndensity; t++) + coeffs(dag_idx-num1, t) = coeffs_pre(iAA, t); + dag_idx++; + } + } +#ifdef DEBUG + cout << "num2_int = " << num2_int << "; num2_leaf = " << num2_leaf << "\n"; +#endif + // free up memory that is no longer needed + nodes_pre.resize(0, 0); + coeffs_pre.resize(0, 0); + haschild.resize(0); + + /* finalize dag: allocate buffer storage */ + AAbuf.resize(num1 + num2_int); + w.resize(num_nodes); + // TODO: technically only need num1 + num2_int for w, this can save one + // memory access later, probably not worth the crazy code duplication. +} + +void ACEDAG::insert_node(TDAGMAP &DAGmap, vector a, vector c) { + /* start with a list of all possible partitions into 2 groups + * and check whether any of these nodes are already in the dag */ + auto partitions = find_2partitions(a); + int ndensity = c.size(); + int num1 = get_num1(); + + // TODO: first try to find partitions into nodes that are already parents + // that way we will get more leaf nodes! + for (TPARTITION const& p : partitions) { + /* this is the good case; the parent nodes are both already in the + * graph; add the new node and return. This is also the only place in the + * code where an actual insert happens. */ + if (DAGmap.count(p.first) && DAGmap.count(p.second)) { + if (nodes_pre.get_dim(0) < dag_idx + 1) { //check if array is sufficiently large + int newsize = (dag_idx * 3) / 2; + nodes_pre.resize(newsize, 2); // grow arrays if necessary + coeffs_pre.resize(newsize, ndensity); + } + int i1 = DAGmap[p.first]; + int i2 = DAGmap[p.second]; + nodes_pre(dag_idx - num1, 0) = i1; + nodes_pre(dag_idx - num1, 1) = i2; + DAGmap[a] = dag_idx; + for (int p = 0; p < ndensity; p++) + coeffs_pre(dag_idx - num1, p) = c[p]; + dag_idx += 1; + return; + } + } + + /* if we are here, then this means, the new node cannot yet be inserted. + * We first need to insert some intermediate auxiliary nodes. For this + * we use a simple heuristic: + * try to find a partition where one of the two nodes are already + * in the graph, if there are several, then we remember the longest + * (this is a very greedy heuristic!!) + * .... (continue below) .... + */ + TPARTITION longest; + int longest_length = 0; + for (auto const& p : partitions) { + int len = 0; + if (DAGmap.count(p.first)) { + len = p.first.size(); + } else if (DAGmap.count(p.second)) { + len = p.second.size(); + } + if ((len > 0) && (len > longest_length)) { + longest_length = len; + longest = p; + } + } + + /* sanity check */ + if (longest_length == 0) { + std::stringstream error_message; + error_message << "WARNING : something has gone horribly wrong! `longest_length == 0`! \n"; + error_message << "a = ["; + for (int t = 0; t < a.size(); t++) + error_message << a[t] << ", "; + error_message << "]\n"; + throw std::logic_error(error_message.str()); +// return; + } + + /* If there is a partition with one component already in the graph, + * then we only need to add in the other component. Note that there will + * always be at least one such partition, namely all those containing + * a one-element node e.g. (1,2,3,4) -> (1,) (2,3,4) then (1,) is + * a one-particle basis function and hence always in the graph. + * If heuristic == 0, then we just take one of those partitionas and move on. + * + * We also accept the found partition if longest_length > 1. + * And we also accept it if we have a 2- or 3-correlation. + */ + + if ( (heuristic == 0) + || (longest_length > 1) + || (a.size() <= 3)) { + /* insert the other node that isn't in the DAG yet + * this is an artificial node so it gets zero-coefficients + * This step is recursive, so more than one node might be inserted here */ + vector cz(ndensity); + for (int i = 0; i < ndensity; i++) cz[i] = 0.0; + TPARTITION p = longest; + if (DAGmap.count(p.first)) + insert_node(DAGmap, p.second, cz); + else + insert_node(DAGmap, p.first, cz); + } + + /* Second heuristic : heuristic == 1 + * Focus on inserting artificial 2-correlations + */ + else if (heuristic == 1) { + // and we also know that longest_length == 1 and nu = a.size >= 4. + int nu = a.size(); + // generate an artificial partition + vector a1(2); + for (int i = 0; i < 2; i++) a1[i] = a[i]; + vector a2(nu - 2); + for (int i = 0; i < nu - 2; i++) a2[i] = a[2 + i]; + vector cz(ndensity); + for (int i = 0; i < cz.size(); i++) cz[i] = 0.0; + // and insert both (we know neither are in the DAG yet) + insert_node(DAGmap, a1, cz); + insert_node(DAGmap, a2, cz); + } else { + cout << "WARNING : something has gone horribly wrong! \n"; + // TODO: Throw and error here?!? + return; + } + + + + /* now we should be ready to insert the entire tuple `a` since there is now + * an eligible parent pair. Here we recompute the partition of `a`, but + * that's a small price to pay for a clearer code. Maybe this can be + * optimized a bit by wrapping it all into a while loop or having a second + * version of `insert_node` ... */ + insert_node(DAGmap, a, c); +} + +TPARTITIONS ACEDAG::find_2partitions(vector v) { + int N = v.size(); + int zo; + TPARTITIONS partitions; + TPARTITION part; + /* This is a fun little hack to extract all subsets of the indices 1:N + * the number i will have binary representation with each digit indicating + * whether or not that index belongs to the selected subset */ + for (int i = 1; i < (1< v1(N1); + vector v2(N2); + int i1 =0, i2 = 0; + p = 1; + for (int n = 0; n < N; n++) { + zo = ((i / p) % 2); + p *= 2; + if (zo == 1) { + v1[i1] = v[n]; + i1 += 1; + } else { + v2[i2] = v[n]; + i2 += 1; + } + } + part = make_pair(v1, v2); + partitions.push_back(part); + } + return partitions; +} + +void ACEDAG::print() { + cout << "DAG Specification: \n" ; + cout << " n1 : " << get_num1() << "\n"; + cout << " n2 : " << get_num2() << "\n"; + cout << " num_nodes : " << num_nodes << "\n"; + cout << "--------------------\n"; + cout << "A-spec: \n"; + for (int iA = 0; iA < get_num1(); iA++) { + cout << iA << " : " << Aspec(iA, 0) << + Aspec(iA, 1) << Aspec(iA, 2) << Aspec(iA, 3) << "\n"; + } + + cout << "-----------\n"; + cout << "AA-tree\n"; + + for (int iAA = 0; iAA < get_num2(); iAA++) { + cout << iAA + get_num1() << " : " << + nodes(iAA, 0) << ", " << nodes(iAA, 1) << "\n"; + } +} + + +/* ------------------------------------------------------------ + * ACERecursiveEvaluator + * ------------------------------------------------------------ */ + + +void ACERecursiveEvaluator::set_basis(ACECTildeBasisSet &bas, int heuristic) { + basis_set = &bas; + init(basis_set, heuristic); +} + +void ACERecursiveEvaluator::init(ACECTildeBasisSet *basis_set, int heuristic) { + + ACEEvaluator::init(basis_set); + + + weights.init(basis_set->nelements, basis_set->nradmax + 1, basis_set->lmax + 1, + "weights"); + + weights_rank1.init(basis_set->nelements, basis_set->nradbase, "weights_rank1"); + + + DG_cache.init(1, basis_set->nradbase, "DG_cache"); + DG_cache.fill(0); + + R_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "R_cache"); + R_cache.fill(0); + + DR_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "DR_cache"); + DR_cache.fill(0); + + Y_cache.init(1, basis_set->lmax + 1, "Y_cache"); + Y_cache.fill({0, 0}); + + DY_cache.init(1, basis_set->lmax + 1, "dY_dense_cache"); + DY_cache.fill({0.}); + + //hard-core repulsion + DCR_cache.init(1, "DCR_cache"); + DCR_cache.fill(0); + dB_flatten.init(basis_set->max_dB_array_size, "dB_flatten"); + + /* convert to ACE.jl format to prepare for construction of DAG + * This will fill the arrays jl_Aspec, jl_AAspec, jl_orders + */ + acejlformat(); + + // test_acejlformat(); + + // now pass this info into the DAG + dag.init(jl_Aspec, jl_AAspec, jl_orders, jl_coeffs, heuristic); + + // finally empty the temporary arrays to clear up the memory... + // TODO +} + + +void ACERecursiveEvaluator::acejlformat() { + + int func_ms_ind = 0; + int func_ms_t_ind = 0;// index for dB + int j, jj, func_ind, ms_ind; + + SPECIES_TYPE mu_i = 0;//TODO: multispecies + const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; + ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; + + int AAidx = 0; + RANK_TYPE order, t; + SPECIES_TYPE *mus; + NS_TYPE *ns; + LS_TYPE *ls; + MS_TYPE *ms; + + /* transform basis into new format: + [A1 ... A_num1] + [(i1,i2)(i1,i2)(...)(i1,i2,i3)(...)] + where each ia represents an A_{ia} + */ + + /* compute max values for mu, n, l, m */ + SPECIES_TYPE maxmu = 0; //TODO: multispecies + NS_TYPE maxn = basis_set->nradmax; + LS_TYPE maxl = basis_set->lmax; + RANK_TYPE maxorder = basis_set->rankmax; + const DENSITY_TYPE ndensity = basis_set->ndensitymax; + + int num1 = 0; + + + /* create a 4D lookup table for the 1-p basis + * TODO: replace with a map?? + */ + Array4D A_lookup(int(maxmu+1), int(maxn), int(maxl+1), int(2*maxl+1)); + for (int mu = 0; mu < maxmu+1; mu++) + for (int n = 0; n < maxn; n++) + for (int l = 0; l < maxl+1; l++) + for (int m = 0; m < 2*maxl+1; m++) + A_lookup(mu, n, l, m) = -1; + int A_idx = 0; // linear index of A basis function (1-particle) + for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { + ACECTildeBasisFunction *func = &basis[func_ind]; +// func->print(); + order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; + for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { + ms = &func->ms_combs[ms_ind * order]; + for (t = 0; t < order; t++) { + int iA = A_lookup(mus[t], ns[t]-1, ls[t], ms[t]+ls[t]); + if (iA == -1) { + A_lookup(mus[t], ns[t] - 1, ls[t], ms[t] + ls[t]) = A_idx; + A_idx += 1; + } + } + } + } + + /* create the reverse list: linear indixes to mu,l,m,n + this keeps only the basis functions we really need */ + num1 = A_idx; + Array2D & Aspec = jl_Aspec; + Aspec.resize(num1, 4); + // Array2D Aspec(num1, 4); + for (int mu = 0; mu <= maxmu; mu++) + for (int n = 1; n <= maxn; n++) + for (int l = 0; l <= maxl; l++) + for (int m = -l; m <= l; m++) { + int iA = A_lookup(mu, n-1, l, l+m); + if (iA != -1) { + Aspec(iA, 0) = mu; + Aspec(iA, 1) = n; + Aspec(iA, 2) = l; + Aspec(iA, 3) = m; + } + } + + /* ============ HALF-BASIS TRICK START ============ */ + for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { + ACECTildeBasisFunction *func = &basis[func_ind]; + order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; + if (!( (mus[0] <= maxmu) && (ns[0] <= maxn) && (ls[0] <= maxl) )) + continue; + + for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { + ms = &func->ms_combs[ms_ind * order]; + + // find first positive and negative index + int pos_idx = order + 1; + int neg_idx = order + 1; + for (t = order-1; t >= 0; t--) + if (ms[t] > 0) pos_idx = t; + else if (ms[t] < 0) neg_idx = t; + + // if neg_idx < pos_idx then this means that ms is non-zero + // and that the first non-zero index is negative, hence this is + // a negative-sign tuple which we want to combine into + // its opposite. + if (neg_idx < pos_idx) { + // find the opposite tuple + int ms_ind2 = 0; + MS_TYPE *ms2; + bool found_opposite = false; + for (ms_ind2 = 0; ms_ind2 < func->num_ms_combs; ++ms_ind2) { + ms2 = &func->ms_combs[ms_ind2 * order]; + bool isopposite = true; + for (t = 0; t < order; t++) + if (ms[t] != -ms2[t]) { + isopposite = false; + break; + } + if (isopposite) { + found_opposite = true; + break; + } + } + + if (ms_ind == ms_ind2) { + cout << "WARNING - ms_ind == ms_ind2 \n"; + } + + // now we need to overwrite the coefficients + if (found_opposite) { + int sig = 1; + for (t = 0; t < order; t++) + if (ms[t] < 0) + sig *= -1; + for (int p = 0; p < ndensity; ++p) { + func->ctildes[ms_ind2 * ndensity + p] += + func->ctildes[ms_ind * ndensity + p]; + func->ctildes[ms_ind * ndensity + p] = 0.0; + } + } + } + } + } + + // /* ============ HALF-BASIS TRICK END ============ */ + + + /* count number of basis functions, keep only non-zero!! */ + int num2 = 0; + for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { + ACECTildeBasisFunction *func = &basis[func_ind]; + for (ms_ind = 0; ms_ind < (&basis[func_ind])->num_ms_combs; ++ms_ind, ++func_ms_ind) { + // check that the coefficients are actually non-zero + bool isnonzero = false; + for (DENSITY_TYPE p = 0; p < ndensity; ++p) + if (func->ctildes[ms_ind * ndensity + p] != 0.0) + isnonzero = true; + if (isnonzero) + num2++; + } + } + + + /* Now create the AA basis links into the A basis */ + num1 = A_idx; // total number of A-basis functions that we keep + // Array1D AAorders(num2); + Array1D & AAorders = jl_orders; + AAorders.resize(num2); + // Array2D AAspec(num2, maxorder); // specs of AA basis functions + Array2D & AAspec = jl_AAspec; + AAspec.resize(num2, maxorder); + jl_coeffs.resize(num2, ndensity); + AAidx = 0; // linear index into AA basis function + int len_flat = 0; + for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { + ACECTildeBasisFunction *func = &basis[func_ind]; + order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; + if (!((mus[0] <= maxmu) && (ns[0] <= maxn) && (ls[0] <= maxl))) //fool-proofing of functions + continue; + + for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { + ms = &func->ms_combs[ms_ind * order]; + + // check that the coefficients are actually non-zero + bool iszero = true; + for (DENSITY_TYPE p = 0; p < ndensity; ++p) + if (func->ctildes[ms_ind * ndensity + p] != 0.0) + iszero = false; + if (iszero) continue; + + AAorders(AAidx) = order; + for (t = 0; t < order; t++) { + int Ait = A_lookup(int(mus[t]), int(ns[t]-1), int(ls[t]), int(ms[t])+int(ls[t])); + AAspec(AAidx, t) = Ait; + len_flat += 1; + } + for (t = order; t < maxorder; t++) AAspec(AAidx, t) = -1; + /* copy over the coefficients */ + for (DENSITY_TYPE p = 0; p < ndensity; ++p) + jl_coeffs(AAidx, p) = func->ctildes[ms_ind * ndensity + p]; + AAidx += 1; + } + } + + // flatten the AAspec array + jl_AAspec_flat.resize(len_flat); + int idx_spec = 0; + for (int AAidx = 0; AAidx < jl_AAspec.get_dim(0); AAidx++) + for (int p = 0; p < jl_orders(AAidx); p++, idx_spec++) + jl_AAspec_flat(idx_spec) = jl_AAspec(AAidx, p); + +} + +void ACERecursiveEvaluator::test_acejlformat() { + + Array2D AAspec = jl_AAspec; + Array2D Aspec = jl_Aspec; + Array1D AAorders = jl_orders; + cout << "num2 = " << AAorders.get_dim(0) << "\n"; + int func_ms_ind = 0; + int func_ms_t_ind = 0;// index for dB + int j, jj, func_ind, ms_ind; + + SPECIES_TYPE mu_i = 0; + const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; + ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; + + RANK_TYPE order, t; + SPECIES_TYPE *mus; + NS_TYPE *ns; + LS_TYPE *ls; + MS_TYPE *ms; + + /* ==== test by printing the basis spec ====*/ + // TODO: convert this into an automatic consistency test + int iAA = 0; + for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { + ACECTildeBasisFunction *func = &basis[func_ind]; + order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; + // func->print(); + //loop over {ms} combinations in sum + for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { + ms = &func->ms_combs[ms_ind * order]; + + + cout << iAA << " : |"; + for (t = 0; t < order; t++) + cout << mus[t] << ";" << ns[t] << "," << ls[t] << "," << ms[t] << "|"; + cout << "\n"; + + cout << " ["; + for (t = 0; t < AAorders(iAA); t++) + cout << AAspec(iAA, int(t)) << ","; + cout << "]\n"; + cout << " |"; + for (t = 0; t < AAorders(iAA); t++) { + int iA = AAspec(iAA, t); + // cout << iA << ","; + cout << Aspec(iA, 0) << ";" + << Aspec(iA, 1) << "," + << Aspec(iA, 2) << "," + << Aspec(iA, 3) << "|"; + } + cout << "\n"; + iAA += 1; + } + } + /* ==== END TEST ==== */ + + +} + + + + +void ACERecursiveEvaluator::resize_neighbours_cache(int max_jnum) { + if(basis_set== nullptr) { + throw std::invalid_argument("ACERecursiveEvaluator: basis set is not assigned"); + } + if (R_cache.get_dim(0) < max_jnum) { + + //TODO: implement grow + R_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); + R_cache.fill(0); + + DR_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); + DR_cache.fill(0); + + DG_cache.resize(max_jnum, basis_set->nradbase); + DG_cache.fill(0); + + Y_cache.resize(max_jnum, basis_set->lmax + 1); + Y_cache.fill({0, 0}); + + DY_cache.resize(max_jnum, basis_set->lmax + 1); + DY_cache.fill({0}); + + //hard-core repulsion + DCR_cache.init(max_jnum, "DCR_cache"); + DCR_cache.fill(0); + } +} + + + +// double** r - atomic coordinates of atom I +// int* types - atomic types if atom I +// int **firstneigh - ptr to 1st J int value of each I atom. Usage: jlist = firstneigh[i]; +// Usage: j = jlist_of_i[jj]; +// jnum - number of J neighbors for each I atom. jnum = numneigh[i]; + +void +ACERecursiveEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) { + if(basis_set== nullptr) { + throw std::invalid_argument("ACERecursiveEvaluator: basis set is not assigned"); + } + per_atom_calc_timer.start(); +#ifdef PRINT_MAIN_STEPS + printf("\n ATOM: ind = %d r_norm=(%f, %f, %f)\n",i, x[i][0], x[i][1], x[i][2]); +#endif + DOUBLE_TYPE evdwl = 0, evdwl_cut = 0, rho_core = 0; + DOUBLE_TYPE r_norm; + DOUBLE_TYPE xn, yn, zn, r_xyz; + DOUBLE_TYPE R, GR, DGR, R_over_r, DR, DCR; + DOUBLE_TYPE *r_hat; + + SPECIES_TYPE mu_j; + RANK_TYPE r, rank, t; + NS_TYPE n; + LS_TYPE l; + MS_TYPE m, m_t; + + SPECIES_TYPE *mus; + NS_TYPE *ns; + LS_TYPE *ls; + MS_TYPE *ms; + + int j, jj, func_ind, ms_ind; + SHORT_INT_TYPE factor; + + ACEComplex Y{0}, Y_DR{0.}; + ACEComplex B{0.}; + ACEComplex dB{0}; + ACEComplex A_cache[basis_set->rankmax]; + + ACEComplex dA[basis_set->rankmax]; + int spec[basis_set->rankmax]; + + dB_flatten.fill({0.}); + + ACEDYcomponent grad_phi_nlm{0}, DY{0.}; + + //size is +1 of max to avoid out-of-boundary array access in double-triangular scheme + ACEComplex A_forward_prod[basis_set->rankmax + 1]; + ACEComplex A_backward_prod[basis_set->rankmax + 1]; + + DOUBLE_TYPE inv_r_norm; + DOUBLE_TYPE r_norms[jnum]; + DOUBLE_TYPE inv_r_norms[jnum]; + DOUBLE_TYPE rhats[jnum][3];//normalized vector + SPECIES_TYPE elements[jnum]; + const DOUBLE_TYPE xtmp = x[i][0]; + const DOUBLE_TYPE ytmp = x[i][1]; + const DOUBLE_TYPE ztmp = x[i][2]; + DOUBLE_TYPE f_ji[3]; + + bool is_element_mapping = element_type_mapping.get_size() > 0; + SPECIES_TYPE mu_i; + if (is_element_mapping) + mu_i = element_type_mapping(type[i]); + else + mu_i = type[i]; + + const SHORT_INT_TYPE total_basis_size_rank1 = basis_set->total_basis_size_rank1[mu_i]; + const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; + + ACECTildeBasisFunction *basis_rank1 = basis_set->basis_rank1[mu_i]; + ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; + + DOUBLE_TYPE rho_cut, drho_cut, fcut, dfcut; + DOUBLE_TYPE dF_drho_core; + + //TODO: lmax -> lmaxi (get per-species type) + const LS_TYPE lmaxi = basis_set->lmax; + + //TODO: nradmax -> nradiali (get per-species type) + const NS_TYPE nradiali = basis_set->nradmax; + + //TODO: nradbase -> nradbasei (get per-species type) + const NS_TYPE nradbasei = basis_set->nradbase; + + //TODO: get per-species type number of densities + const DENSITY_TYPE ndensity= basis_set->ndensitymax; + + neighbours_forces.resize(jnum, 3); + neighbours_forces.fill(0); + + //TODO: shift nullifications to place where arrays are used + weights.fill({0}); + weights_rank1.fill(0); + A.fill({0}); + A_rank1.fill(0); + rhos.fill(0); + dF_drho.fill(0); + +#ifdef EXTRA_C_PROJECTIONS + basis_projections_rank1.init(total_basis_size_rank1, ndensity, "c_projections_rank1"); + basis_projections.init(total_basis_size, ndensity, "c_projections"); +#endif + + //proxy references to spherical harmonics and radial functions arrays + const Array2DLM &ylm = basis_set->spherical_harmonics.ylm; + const Array2DLM &dylm = basis_set->spherical_harmonics.dylm; + + const Array2D &fr = basis_set->radial_functions->fr; + const Array2D &dfr = basis_set->radial_functions->dfr; + + const Array1D &gr = basis_set->radial_functions->gr; + const Array1D &dgr = basis_set->radial_functions->dgr; + + loop_over_neighbour_timer.start(); + + int jj_actual = 0; + SPECIES_TYPE type_j = 0; + int neighbour_index_mapping[jnum]; // jj_actual -> jj + //loop over neighbours, compute distance, consider only atoms within with rradial_functions->cut(mu_i, mu_j); + r_xyz = sqrt(xn * xn + yn * yn + zn * zn); + + if (r_xyz >= current_cutoff) + continue; + + inv_r_norm = 1 / r_xyz; + + r_norms[jj_actual] = r_xyz; + inv_r_norms[jj_actual] = inv_r_norm; + rhats[jj_actual][0] = xn * inv_r_norm; + rhats[jj_actual][1] = yn * inv_r_norm; + rhats[jj_actual][2] = zn * inv_r_norm; + elements[jj_actual] = mu_j; + neighbour_index_mapping[jj_actual] = jj; + jj_actual++; + } + + int jnum_actual = jj_actual; + + //ALGORITHM 1: Atomic base A + for (jj = 0; jj < jnum_actual; ++jj) { + r_norm = r_norms[jj]; + mu_j = elements[jj]; + r_hat = rhats[jj]; + + //proxies + Array2DLM &Y_jj = Y_cache(jj); + Array2DLM &DY_jj = DY_cache(jj); + + + basis_set->radial_functions->evaluate(r_norm, basis_set->nradbase, nradiali, mu_i, mu_j); + basis_set->spherical_harmonics.compute_ylm(r_hat[0], r_hat[1], r_hat[2], lmaxi); + //loop for computing A's + //rank = 1 + for (n = 0; n < basis_set->nradbase; n++) { + GR = gr(n); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("-neigh atom %d\n", jj); + printf("gr(n=%d)(r=%f) = %f\n", n, r_norm, gr(n)); + printf("dgr(n=%d)(r=%f) = %f\n", n, r_norm, dgr(n)); +#endif + DG_cache(jj, n) = dgr(n); + A_rank1(mu_j, n) += GR * Y00; + } + //loop for computing A's + // for rank > 1 + for (n = 0; n < nradiali; n++) { + auto &A_lm = A(mu_j, n); + for (l = 0; l <= lmaxi; l++) { + R = fr(n, l); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("R(nl=%d,%d)(r=%f)=%f\n", n + 1, l, r_norm, R); +#endif + + DR_cache(jj, n, l) = dfr(n, l); + R_cache(jj, n, l) = R; + + for (m = 0; m <= l; m++) { + Y = ylm(l, m); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("Y(lm=%d,%d)=(%f, %f)\n", l, m, Y.real, Y.img); +#endif + A_lm(l, m) += R * Y; //accumulation sum over neighbours + Y_jj(l, m) = Y; + DY_jj(l, m) = dylm(l, m); + } + } + } + + //hard-core repulsion + rho_core += basis_set->radial_functions->cr; + DCR_cache(jj) = basis_set->radial_functions->dcr; + + } //end loop over neighbours + + //complex conjugate A's (for NEGATIVE (-m) terms) + // for rank > 1 + for (mu_j = 0; mu_j < basis_set->nelements; mu_j++) { + for (n = 0; n < nradiali; n++) { + auto &A_lm = A(mu_j, n); + for (l = 0; l <= lmaxi; l++) { + //fill in -m part in the outer loop using the same m <-> -m symmetry as for Ylm + for (m = 1; m <= l; m++) { + factor = m % 2 == 0 ? 1 : -1; + A_lm(l, -m) = A_lm(l, m).conjugated() * factor; + } + } + } + } //now A's are constructed + loop_over_neighbour_timer.stop(); + + // ==================== ENERGY ==================== + + energy_calc_timer.start(); +#ifdef EXTRA_C_PROJECTIONS + basis_projections_rank1.fill(0); + basis_projections.fill(0); +#endif + + //ALGORITHM 2: Basis functions B with iterative product and density rho(p) calculation + //rank=1 + for (int func_rank1_ind = 0; func_rank1_ind < total_basis_size_rank1; ++func_rank1_ind) { + ACECTildeBasisFunction *func = &basis_rank1[func_rank1_ind]; +// ndensity = func->ndensity; +#ifdef PRINT_LOOPS_INDICES + printf("Num density = %d r = 0\n",(int) ndensity ); + print_C_tilde_B_basis_function(*func); +#endif + double A_cur = A_rank1(func->mus[0], func->ns[0] - 1); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("A_r=1(x=%d, n=%d)=(%f)\n", func->mus[0], func->ns[0], A_cur); + printf(" coeff[0] = %f\n", func->ctildes[0]); +#endif + for (DENSITY_TYPE p = 0; p < ndensity; ++p) { + //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 + rhos(p) += func->ctildes[p] * A_cur; +#ifdef EXTRA_C_PROJECTIONS + //aggregate C-projections separately + basis_projections_rank1(func_rank1_ind, p)+= func->ctildes[p] * A_cur; +#endif + } + } // end loop for rank=1 + + // ================ START RECURSIVE EVALUATOR ==================== + // (rank > 1 only) + + /* STAGE 1: + * 1-particle basis is already evaluated, so we only need to + * copy it into the AA value buffer + */ + int num1 = dag.get_num1(); + for (int idx = 0; idx < num1; idx++) + dag.AAbuf(idx) = A( dag.Aspec(idx, 0), + dag.Aspec(idx, 1)-1, + dag.Aspec(idx, 2), + dag.Aspec(idx, 3) ); + + + if (recursive) { + /* STAGE 2: FORWARD PASS + * Forward pass: go through the dag and store all intermediate results + */ + + // rhos.fill(0); note the rhos are already reset and started filling above! + ACEComplex AAcur{0.0}; + int i1, i2; + + int * dag_nodes = dag.nodes.get_data(); + int idx_nodes = 0; + + DOUBLE_TYPE * dag_coefs = dag.coeffs.get_data(); + int idx_coefs = 0; + + int num2_int = dag.get_num2_int(); + int num2_leaf = dag.get_num2_leaf(); + + // interior nodes (save AA) + for (int idx = num1; idx < num1+num2_int; idx++) { + i1 = dag_nodes[idx_nodes]; idx_nodes++; + i2 = dag_nodes[idx_nodes]; idx_nodes++; + AAcur = dag.AAbuf(i1) * dag.AAbuf(i2); + dag.AAbuf(idx) = AAcur; + for (int p = 0; p < ndensity; p++, idx_coefs++) + rhos(p) += AAcur.real_part_product(dag_coefs[idx_coefs]); + } + + // leaf nodes -> no need to store in AAbuf + DOUBLE_TYPE AAcur_re = 0.0; + for (int _idx = 0; _idx < num2_leaf; _idx++) { + i1 = dag_nodes[idx_nodes]; idx_nodes++; + i2 = dag_nodes[idx_nodes]; idx_nodes++; + AAcur_re = dag.AAbuf(i1).real_part_product(dag.AAbuf(i2)); + for (int p = 0; p < ndensity; p++, idx_coefs++) + rhos(p) += AAcur_re * dag_coefs[idx_coefs]; + } + + } else { + + /* non-recursive Julia-style evaluator implementation */ + // TODO: fix array access to enable bounds checking again??? + ACEComplex AAcur{1.0}; + int *AAspec = jl_AAspec_flat.get_data(); + DOUBLE_TYPE *coeffs = jl_coeffs.get_data(); + int idx_spec = 0; + int idx_coefs = 0; + int order = 0; + int max_order = jl_AAspec.get_dim(1); + for (int iAA = 0; iAA < jl_AAspec.get_dim(0); iAA ++) { + AAcur = 1.0; + order = jl_orders(iAA); + for (int r = 0; r < order; r++, idx_spec++) + AAcur *= dag.AAbuf( AAspec[idx_spec] ); + for (int p = 0; p < ndensity; p++, idx_coefs++) + rhos(p) += AAcur.real_part_product(coeffs[idx_coefs]); + } + } + + /* we now have rho and can evaluate lots of things. + -------- this is back to the original PACE code --------- */ + +#ifdef DEBUG_FORCES_CALCULATIONS + printf("rhos = "); + for(DENSITY_TYPE p =0; prho_core_cutoffs(mu_i); + drho_cut = basis_set->drho_core_cutoffs(mu_i); + + basis_set->inner_cutoff(rho_core, rho_cut, drho_cut, fcut, dfcut); + basis_set->FS_values_and_derivatives(rhos, evdwl, dF_drho, ndensity); + + dF_drho_core = evdwl * dfcut + 1; + for (DENSITY_TYPE p = 0; p < ndensity; ++p) + dF_drho(p) *= fcut; + evdwl_cut = evdwl * fcut + rho_core; + + // E0 shift + evdwl_cut += basis_set->E0vals(mu_i); + + /* I've moved this from below the weight calculation + since I believe it only times the energy? the weights + are only needed for the forces? + But I believe we could add a third timer for computing just + the weights; this will allow us to check better where the + bottleneck is. + */ + energy_calc_timer.stop(); + + forces_calc_loop_timer.start(); + + +#ifdef DEBUG_FORCES_CALCULATIONS + printf("dFrhos = "); + for(DENSITY_TYPE p =0; pndensity; + for (DENSITY_TYPE p = 0; p < ndensity; ++p) { + //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 + weights_rank1(func->mus[0], func->ns[0] - 1) += dF_drho(p) * func->ctildes[p]; + } + } + + /* --------- we now continue with the recursive code --------- */ + + if (recursive) { + /* STAGE 2: BACKWARD PASS */ + int i1, i2; + ACEComplex AA1{0.0}; + ACEComplex AA2{0.0}; + ACEComplex wcur{0.0}; + int num2_int = dag.get_num2_int(); + int num2_leaf = dag.get_num2_leaf(); + /* to prepare for the backward we first need to zero the weights */ + dag.w.fill({0.0}); + + int * dag_nodes = dag.nodes.get_data(); + int idx_nodes = 2 * (num2_int + num2_leaf) - 1; + + DOUBLE_TYPE * dag_coefs = dag.coeffs.get_data(); + int idx_coefs = ndensity * (num2_int + num2_leaf) - 1; + + for (int idx = num1+num2_int+num2_leaf - 1; idx >= num1; idx--) { + i2 = dag_nodes[idx_nodes]; idx_nodes--; + i1 = dag_nodes[idx_nodes]; idx_nodes--; + AA1 = dag.AAbuf(i1); + AA2 = dag.AAbuf(i2); + wcur = dag.w(idx); // [***] + for (int p = ndensity-1; p >= 0; p--, idx_coefs--) + wcur += dF_drho(p) * dag_coefs[idx_coefs]; + dag.w(i1) += wcur * AA2; // TODO: replace with explicit muladd? + dag.w(i2) += wcur * AA1; + } + + /* [***] + * Note that these weights don't really need to be stored for the + * leaf nodes. We tested splitting this for loop into two where + * for the leaf nodes the weight would just be initialized to 0.0 + * instead of reading from an array. The improvement was barely + * measurable, ca 3%, so we reverted to this simpler algorithm + */ + + + } else { + + // non-recursive ACE.jl style implemenation of gradients, but with + // a backward differentiation approach to the prod-A + // (cf. Algorithm 3 in the manuscript) + + dag.w.fill({0.0}); + ACEComplex AAf{1.0}, AAb{1.0}, theta{0.0}; + + int *AAspec = jl_AAspec_flat.get_data(); + DOUBLE_TYPE *coeffs = jl_coeffs.get_data(); + int idx_spec = 0; + int idx_coefs = 0; + int order = 0; + int max_order = jl_AAspec.get_dim(1); + for (int iAA = 0; iAA < jl_AAspec.get_dim(0); iAA ++ ) { + order = jl_orders(iAA); + theta = 0.0; + for (int p = 0; p < ndensity; p++, idx_coefs++) + theta += dF_drho(p) * coeffs[idx_coefs]; + dA[0] = 1.0; + AAf = 1.0; + for (int t = 0; t < order-1; t++, idx_spec++) { + spec[t] = AAspec[idx_spec]; + A_cache[t] = dag.AAbuf(spec[t]); + AAf *= A_cache[t]; + dA[t+1] = AAf; + } + spec[order-1] = AAspec[idx_spec]; idx_spec++; + A_cache[order-1] = dag.AAbuf(spec[order-1]); + AAb = 1.0; + for (int t = order-1; t >= 1; t--) { + AAb *= A_cache[t]; + dA[t-1] *= AAb; + dag.w(spec[t]) += theta * dA[t]; + } + dag.w(spec[0]) += theta * dA[0]; + } + + } + + /* STAGE 3: + * get the gradients from the 1-particle basis gradients and write them + * into the dF/drho derivatives. + */ + /* In order to reuse the original PACE code, we copy the weights back + * into the the PACE datastructure. */ + + for (int idx = 0; idx < num1; idx++) { + int m = dag.Aspec(idx, 3); + if (m >= 0) { + weights(dag.Aspec(idx, 0), // mu + dag.Aspec(idx, 1) - 1, // n + dag.Aspec(idx, 2), // l + m ) += dag.w(idx); + } else { + int factor = (m % 2 == 0 ? 1 : -1); + weights(dag.Aspec(idx, 0), // mu + dag.Aspec(idx, 1) - 1, // n + dag.Aspec(idx, 2), // l + -m ) += factor * dag.w(idx).conjugated(); + } + } + + + /* ------ From here we are now back to the original PACE code ---- */ + +// ==================== FORCES ==================== +#ifdef PRINT_MAIN_STEPS + printf("\nFORCE CALCULATION\n"); + printf("loop over neighbours\n"); +#endif + +// loop over neighbour atoms for force calculations + for (jj = 0; jj < jnum_actual; ++jj) { + mu_j = elements[jj]; + r_hat = rhats[jj]; + inv_r_norm = inv_r_norms[jj]; + + Array2DLM &Y_cache_jj = Y_cache(jj); + Array2DLM &DY_cache_jj = DY_cache(jj); + +#ifdef PRINT_LOOPS_INDICES + printf("\nneighbour atom #%d\n", jj); + printf("rhat = (%f, %f, %f)\n", r_hat[0], r_hat[1], r_hat[2]); +#endif + + forces_calc_neighbour_timer.start(); + + f_ji[0] = f_ji[1] = f_ji[2] = 0; + +//for rank = 1 + for (n = 0; n < nradbasei; ++n) { + if (weights_rank1(mu_j, n) == 0) + continue; + auto &DG = DG_cache(jj, n); + DGR = DG * Y00; + DGR *= weights_rank1(mu_j, n); +#ifdef DEBUG_FORCES_CALCULATIONS + printf("r=1: (n,l,m)=(%d, 0, 0)\n",n+1); + printf("\tGR(n=%d, r=%f)=%f\n",n+1,r_norm, gr(n)); + printf("\tDGR(n=%d, r=%f)=%f\n",n+1,r_norm, dgr(n)); + printf("\tdF+=(%f, %f, %f)\n",DGR * r_hat[0], DGR * r_hat[1], DGR * r_hat[2]); +#endif + f_ji[0] += DGR * r_hat[0]; + f_ji[1] += DGR * r_hat[1]; + f_ji[2] += DGR * r_hat[2]; + } + +//for rank > 1 + for (n = 0; n < nradiali; n++) { + for (l = 0; l <= lmaxi; l++) { + R_over_r = R_cache(jj, n, l) * inv_r_norm; + DR = DR_cache(jj, n, l); + + // for m>=0 + for (m = 0; m <= l; m++) { + ACEComplex w = weights(mu_j, n, l, m); + if (w == 0) + continue; + //counting for -m cases if m>0 + // if (m > 0) w *= 2; // not needed for recursive eval + + DY = DY_cache_jj(l, m); + Y_DR = Y_cache_jj(l, m) * DR; + + grad_phi_nlm.a[0] = Y_DR * r_hat[0] + DY.a[0] * R_over_r; + grad_phi_nlm.a[1] = Y_DR * r_hat[1] + DY.a[1] * R_over_r; + grad_phi_nlm.a[2] = Y_DR * r_hat[2] + DY.a[2] * R_over_r; +#ifdef DEBUG_FORCES_CALCULATIONS + printf("d_phi(n=%d, l=%d, m=%d) = ((%f,%f), (%f,%f), (%f,%f))\n",n+1,l,m, + grad_phi_nlm.a[0].real, grad_phi_nlm.a[0].img, + grad_phi_nlm.a[1].real, grad_phi_nlm.a[1].img, + grad_phi_nlm.a[2].real, grad_phi_nlm.a[2].img); + + printf("weights(n,l,m)(%d,%d,%d) = (%f,%f)\n", n+1, l, m, w.real, w.img); + //if (m>0) w*=2; + printf("dF(n,l,m)(%d, %d, %d) += (%f, %f, %f)\n", n + 1, l, m, + w.real_part_product(grad_phi_nlm.a[0]), + w.real_part_product(grad_phi_nlm.a[1]), + w.real_part_product(grad_phi_nlm.a[2]) + ); +#endif +// real-part multiplication only + f_ji[0] += w.real_part_product(grad_phi_nlm.a[0]); + f_ji[1] += w.real_part_product(grad_phi_nlm.a[1]); + f_ji[2] += w.real_part_product(grad_phi_nlm.a[2]); + } + } + } + + +#ifdef PRINT_INTERMEDIATE_VALUES + printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, + f_ji[0], f_ji[1], f_ji[2] + ); +#endif + + //hard-core repulsion + DCR = DCR_cache(jj); +#ifdef DEBUG_FORCES_CALCULATIONS + printf("DCR = %f\n",DCR); +#endif + f_ji[0] += dF_drho_core * DCR * r_hat[0]; + f_ji[1] += dF_drho_core * DCR * r_hat[1]; + f_ji[2] += dF_drho_core * DCR * r_hat[2]; +#ifdef PRINT_INTERMEDIATE_VALUES + printf("with core-repulsion\n"); + printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, + f_ji[0], f_ji[1], f_ji[2] + ); + printf("neighbour_index_mapping[jj=%d]=%d\n",jj,neighbour_index_mapping[jj]); +#endif + + neighbours_forces(neighbour_index_mapping[jj], 0) = f_ji[0]; + neighbours_forces(neighbour_index_mapping[jj], 1) = f_ji[1]; + neighbours_forces(neighbour_index_mapping[jj], 2) = f_ji[2]; + + forces_calc_neighbour_timer.stop(); + }// end loop over neighbour atoms for forces + + forces_calc_loop_timer.stop(); + + //now, energies and forces are ready + //energies(i) = evdwl + rho_core; + e_atom = evdwl_cut; + +#ifdef PRINT_INTERMEDIATE_VALUES + printf("energies(i) = FS(...rho_p_accum...) = %f\n", evdwl); +#endif + per_atom_calc_timer.stop(); +} \ No newline at end of file diff --git a/lib/pace/ace_recursive.h b/lib/pace/ace_recursive.h new file mode 100644 index 0000000000..78e74feb86 --- /dev/null +++ b/lib/pace/ace_recursive.h @@ -0,0 +1,247 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Christoph Ortner on 20.12.2020 + +#ifndef ACE_RECURSIVE_H +#define ACE_RECURSIVE_H + +#include "ace_abstract_basis.h" +#include "ace_arraynd.h" +#include "ace_array2dlm.h" +#include "ace_c_basis.h" +#include "ace_complex.h" +#include "ace_timing.h" +#include "ace_types.h" +#include "ace_evaluator.h" + +#include +#include +#include +#include +#include + +using namespace std; + + +typedef pair, vector > TPARTITION; +typedef list TPARTITIONS; + +typedef map, int> TDAGMAP; + +class ACEDAG { + + TPARTITIONS find_2partitions(vector v); + + void insert_node(TDAGMAP &dagmap, + vector node, + vector c); + + // the following fields are used only for *construction*, not evaluation + int dag_idx; // current index of dag node + Array2D nodes_pre; //TODO: YL: better to use vector<> + Array2D coeffs_pre; //TODO: YL: better to use vector<> + Array1D haschild; //TODO: YL: better to use vector<> + + /* which heuristic to choose for DAG construction? + * 0 : the simple original heuristic + * 1 : prioritize 2-correlation nodes and build the rest from those + */ + int heuristic = 0; + +public: + + ACEDAG() = default; + + void init(Array2D Aspec, Array2D AAspec, + Array1D orders, Array2D coeffs, + int heuristic ); + + Array1D AAbuf; + Array1D w; + + Array2D Aspec; + + // nodes in the graph + Array2D nodes; + Array2D coeffs; + + // total number of nodes in the dag + int num_nodes; + // number of interior nodes (with children) + int num2_int; + // number of leaf nodes (nc = no child) + int num2_leaf; + + + // number of 1-particle basis functions + // (these will be stored in the first num1 entries of AAbuf) + int get_num1() { return Aspec.get_dim(0); }; + // total number of n-correlation basis functions n > 1. + int get_num2() { return num_nodes - get_num1(); }; + int get_num2_int() { return num2_int; }; // with children + int get_num2_leaf() { return num2_leaf; }; // without children + + // debugging tool + void print(); +}; + + +/** + * Recursive Variant of the ACETildeEvaluator; should be 100% compatible + */ +class ACERecursiveEvaluator : public ACEEvaluator { + + /** + * Weights \f$ \omega_{i \mu n 0 0} \f$ for rank = 1, see Eq.(10) from implementation notes, + * 'i' is fixed for the current atom, shape: [nelements][nradbase] + */ + Array2D weights_rank1 = Array2D("weights_rank1"); + + /** + * Weights \f$ \omega_{i \mu n l m} \f$ for rank > 1, see Eq.(10) from implementation notes, + * 'i' is fixed for the current atom, shape: [nelements][nradbase][l=0..lmax, m] + */ + Array4DLM weights = Array4DLM("weights"); + + /** + * cache for gradients of \f$ g(r)\f$: grad_phi(jj,n)=A2DLM(l,m) + * shape:[max_jnum][nradbase] + */ + Array2D DG_cache = Array2D("DG_cache"); + + + /** + * cache for \f$ R_{nl}(r)\f$ + * shape:[max_jnum][nradbase][0..lmax] + */ + Array3D R_cache = Array3D("R_cache"); + /** + * cache for derivatives of \f$ R_{nl}(r)\f$ + * shape:[max_jnum][nradbase][0..lmax] + */ + Array3D DR_cache = Array3D("DR_cache"); + /** + * cache for \f$ Y_{lm}(\hat{r})\f$ + * shape:[max_jnum][0..lmax][m] + */ + Array3DLM Y_cache = Array3DLM("Y_cache"); + /** + * cache for \f$ \nabla Y_{lm}(\hat{r})\f$ + * shape:[max_jnum][0..lmax][m] + */ + Array3DLM DY_cache = Array3DLM("dY_dense_cache"); + + /** + * cache for derivatives of hard-core repulsion + * shape:[max_jnum] + */ + Array1D DCR_cache = Array1D("DCR_cache"); + + /** + * Partial derivatives \f$ dB_{i \mu n l m t}^{(r)} \f$ with sequential numbering over [func_ind][ms_ind][r], + * shape:[func_ms_r_ind] + */ + Array1D dB_flatten = Array1D("dB_flatten"); + + /** + * pointer to the ACEBasisSet object + */ + ACECTildeBasisSet *basis_set = nullptr; + + /** + * Initialize internal arrays according to basis set sizes + * @param basis_set + */ + void init(ACECTildeBasisSet *basis_set, int heuristic); + + /* convert the PACE to the ACE.jl format to prepare for DAG construction*/ + Array2D jl_Aspec; + Array2D jl_AAspec; + Array1D jl_AAspec_flat; + Array1D jl_orders; + Array2D jl_coeffs; + void acejlformat(); + + /* the main event : the computational graph */ + ACEDAG dag; + + bool recursive = true; + +public: + + + ACERecursiveEvaluator() = default; + + explicit ACERecursiveEvaluator(ACECTildeBasisSet &bas, + bool recursive = true) { + set_recursive(recursive); + set_basis(bas); + } + + /** + * set the basis function to the ACE evaluator + * @param bas + */ + void set_basis(ACECTildeBasisSet &bas, int heuristic = 0); + + /** + * The key method to compute energy and forces for atom 'i'. + * Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array + * + * @param i atom index + * @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3] + * @param type atomic types array of the real and ghost atoms, shape: [atom_ind] + * @param jnum number of neighbours of atom_i + * @param jlist array of neighbour indices, shape: [jnum] + */ + void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) override; + + /** + * Resize all caches over neighbours atoms + * @param max_jnum maximum number of neighbours + */ + void resize_neighbours_cache(int max_jnum) override; + + /******* public functions related to recursive evaluator ********/ + + // print out the DAG for visual inspection + void print_dag() {dag.print();} + + // print out the jl format for visual inspection + // should be converted into a proper test + void test_acejlformat(); + + void set_recursive(bool tf) { recursive = tf; } + + /********************************/ + +}; + + +#endif //ACE_RECURSIVE_H \ No newline at end of file diff --git a/lib/pace/ace_spherical_cart.cpp b/lib/pace/ace_spherical_cart.cpp new file mode 100644 index 0000000000..f1f0fccced --- /dev/null +++ b/lib/pace/ace_spherical_cart.cpp @@ -0,0 +1,221 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Ralf Drautz, Yury Lysogorskiy + +#include + +#include "ace_spherical_cart.h" + +ACECartesianSphericalHarmonics::ACECartesianSphericalHarmonics(LS_TYPE lm) { + init(lm); +} + +void ACECartesianSphericalHarmonics::init(LS_TYPE lm) { + lmax = lm; + + alm.init(lmax, "alm"); + blm.init(lmax, "blm"); + cl.init(lmax + 1); + dl.init(lmax + 1); + + plm.init(lmax, "plm"); + dplm.init(lmax, "dplm"); + + ylm.init(lmax, "ylm"); + dylm.init(lmax, "dylm"); + + pre_compute(); +} + +/** +Destructor for ACECartesianSphericalHarmonics. + +@param None + +@returns None +*/ +ACECartesianSphericalHarmonics::~ACECartesianSphericalHarmonics() {} + + +void ACECartesianSphericalHarmonics::pre_compute() { + + DOUBLE_TYPE a, b; + DOUBLE_TYPE lsq, ld, l1, l2; + DOUBLE_TYPE msq; + + for (LS_TYPE l = 1; l <= lmax; l++) { + lsq = l * l; + ld = 2 * l; + l1 = (4 * lsq - 1); + l2 = lsq - ld + 1; + for (MS_TYPE m = 0; m < l - 1; m++) { + msq = m * m; + a = sqrt((DOUBLE_TYPE(l1)) / (DOUBLE_TYPE(lsq - msq))); + b = -sqrt((DOUBLE_TYPE(l2 - msq)) / (DOUBLE_TYPE(4 * l2 - 1))); + alm(l, m) = a; + blm(l, m) = b; + } + } + + for (LS_TYPE l = 1; l <= lmax; l++) { + cl(l) = -sqrt(1.0 + 0.5 / (DOUBLE_TYPE(l))); + dl(l) = sqrt(DOUBLE_TYPE(2 * (l - 1) + 3)); + } +} + + +void ACECartesianSphericalHarmonics::compute_barplm(DOUBLE_TYPE rz, LS_TYPE lmaxi) { + + // requires -1 <= rz <= 1 , NO CHECKING IS PERFORMED !!!!!!!!! + // prefactors include 1/sqrt(2) factor compared to reference + DOUBLE_TYPE t; + + // l=0, m=0 + //plm(0, 0) = Y00/sq1o4pi; //= sq1o4pi; + plm(0, 0) = Y00; //= 1; + dplm(0, 0) = 0.0; + + if (lmaxi > 0) { + + // l=1, m=0 + plm(1, 0) = Y00 * sq3 * rz; + dplm(1, 0) = Y00 * sq3; + + // l=1, m=1 + plm(1, 1) = -sq3o2 * Y00; + dplm(1, 1) = 0.0; + + // loop l = 2, lmax + for (LS_TYPE l = 2; l <= lmaxi; l++) { + for (MS_TYPE m = 0; m < l - 1; m++) { + plm(l, m) = alm(l, m) * (rz * plm(l - 1, m) + blm(l, m) * plm(l - 2, m)); + dplm(l, m) = alm(l, m) * (plm(l - 1, m) + rz * dplm(l - 1, m) + blm(l, m) * dplm(l - 2, m)); + } + t = dl(l) * plm(l - 1, l - 1); + plm(l, l - 1) = t * rz; + dplm(l, l - 1) = t; + plm(l, l) = cl(l) * plm(l - 1, l - 1); + dplm(l, l) = 0.0; + } + } +} //end compute_barplm + + +void ACECartesianSphericalHarmonics::compute_ylm(DOUBLE_TYPE rx, DOUBLE_TYPE ry, DOUBLE_TYPE rz, LS_TYPE lmaxi) { + + // requires rx^2 + ry^2 + rz^2 = 1 , NO CHECKING IS PERFORMED !!!!!!!!! + + DOUBLE_TYPE real; + DOUBLE_TYPE img; + MS_TYPE m; + ACEComplex phase; + ACEComplex phasem, mphasem1; + ACEComplex dyx, dyy, dyz; + ACEComplex rdy; + + phase.real = rx; + phase.img = ry; + //compute barplm + compute_barplm(rz, lmaxi); + + //m = 0 + m = 0; + for (LS_TYPE l = 0; l <= lmaxi; l++) { + + ylm(l, m).real = plm(l, m); + ylm(l, m).img = 0.0; + + dyz.real = dplm(l, m); + rdy.real = dyz.real * rz; + + dylm(l, m).a[0].real = -rdy.real * rx; + dylm(l, m).a[0].img = 0.0; + dylm(l, m).a[1].real = -rdy.real * ry; + dylm(l, m).a[1].img = 0.0; + dylm(l, m).a[2].real = dyz.real - rdy.real * rz; + dylm(l, m).a[2].img = 0; + } + //m = 0 + m = 1; + for (LS_TYPE l = 1; l <= lmaxi; l++) { + + ylm(l, m) = phase * plm(l, m); + +// std::cout << "Re ylm(" << l << "," << m <<")= " << ylm(l, m).real << std::endl; +// std::cout << "Im ylm(" << l << "," << m <<")= " << ylm(l, m).img << std::endl; + + dyx.real = plm(l, m); + dyx.img = 0.0; + dyy.real = 0.0; + dyy.img = plm(l, m); + dyz.real = phase.real * dplm(l, m); + dyz.img = phase.img * dplm(l, m); + + rdy.real = rx * dyx.real + +rz * dyz.real; + rdy.img = ry * dyy.img + rz * dyz.img; + + dylm(l, m).a[0].real = dyx.real - rdy.real * rx; + dylm(l, m).a[0].img = -rdy.img * rx; + dylm(l, m).a[1].real = -rdy.real * ry; + dylm(l, m).a[1].img = dyy.img - rdy.img * ry; + dylm(l, m).a[2].real = dyz.real - rdy.real * rz; + dylm(l, m).a[2].img = dyz.img - rdy.img * rz; + } + + // m > 1 + phasem = phase; + for (MS_TYPE m = 2; m <= lmaxi; m++) { + + mphasem1.real = phasem.real * DOUBLE_TYPE(m); + mphasem1.img = phasem.img * DOUBLE_TYPE(m); + phasem = phasem * phase; + + for (LS_TYPE l = m; l <= lmaxi; l++) { + + ylm(l, m).real = phasem.real * plm(l, m); + ylm(l, m).img = phasem.img * plm(l, m); + + dyx = mphasem1 * plm(l, m); + dyy.real = -dyx.img; + dyy.img = dyx.real; + dyz = phasem * dplm(l, m); + + rdy.real = rx * dyx.real + ry * dyy.real + rz * dyz.real; + rdy.img = rx * dyx.img + ry * dyy.img + rz * dyz.img; + + dylm(l, m).a[0].real = dyx.real - rdy.real * rx; + dylm(l, m).a[0].img = dyx.img - rdy.img * rx; + dylm(l, m).a[1].real = dyy.real - rdy.real * ry; + dylm(l, m).a[1].img = dyy.img - rdy.img * ry; + dylm(l, m).a[2].real = dyz.real - rdy.real * rz; + dylm(l, m).a[2].img = dyz.img - rdy.img * rz; + } + } + +} + diff --git a/lib/pace/ace_spherical_cart.h b/lib/pace/ace_spherical_cart.h new file mode 100644 index 0000000000..b2a0cb5913 --- /dev/null +++ b/lib/pace/ace_spherical_cart.h @@ -0,0 +1,134 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Ralf Drautz, Yury Lysogorskiy + +#ifndef ACE_SPHERICAL_CART_H +#define ACE_SPHERICAL_CART_H + +#include + +#include "ace_arraynd.h" +#include "ace_array2dlm.h" +#include "ace_complex.h" +#include "ace_types.h" + + +using namespace std; + +const DOUBLE_TYPE sq1o4pi = 0.28209479177387814347; // sqrt(1/(4*pi)) +const DOUBLE_TYPE sq4pi = 3.54490770181103176384; // sqrt(4*pi) +const DOUBLE_TYPE sq3 = 1.73205080756887719318;//sqrt(3), numpy +const DOUBLE_TYPE sq3o2 = 1.22474487139158894067;//sqrt(3/2), numpy + +//definition of common factor for spherical harmonics = Y00 +//const DOUBLE_TYPE Y00 = sq1o4pi; +const DOUBLE_TYPE Y00 = 1; + +/** +Class to store spherical harmonics and their associated functions. \n +All the associated members such as \f$ P_{lm}, Y_{lm}\f$ etc are one dimensional arrays of length (L+1)*(L+2)/2. \n +The value that corresponds to a particular l, m configuration can be accessed through a \code ylm(l,m) \endcode \n +*/ +class ACECartesianSphericalHarmonics { +public: + + /** + int, the number of spherical harmonics to be found + */ + LS_TYPE lmax; + + /** + * Default constructor + */ + ACECartesianSphericalHarmonics() = default; + + /** + * Parametrized constructor. Dynamically initialises all the arrays. + * @param lmax maximum orbital moment + */ + explicit ACECartesianSphericalHarmonics(LS_TYPE lmax); + + /** + * Initialize internal arrays and precompute necessary coefficients + * @param lm maximum orbital moment + */ + void init(LS_TYPE lm); + + /** + * Destructor + */ + ~ACECartesianSphericalHarmonics(); + + /** + * Precompute necessaary helper arrays Precomputes the value of \f$ a_{lm}, b_{lm}, c_l, d_l \f$ + */ + void pre_compute(); + + /** + Function that computes \f$ \bar{P}_{lm} \f$ for the corresponding lmax value + Input is \f$ \hat{r}_z \f$ which is the $z$-component of the bond direction. + + For each \f$ \hat{r}_z \f$, this computes the whole range of \f$ \bar{P}_{lm} \f$ values + and its derivatives upto the lmax specified, which is a member of the class. + + @param rz, DOUBLE_TYPE + + @returns None + */ + void compute_barplm(DOUBLE_TYPE rz, LS_TYPE lmaxi); + + /** + Function that computes \f$ Y_{lm} \f$ for the corresponding lmax value + Input is the bond-directon vector \f$ \hat{r}_x, \hat{r}_y, \hat{r}_z \f$ + + Each \f$ Y_{lm} \f$ value is a ACEComplex object with real and imaginary parts. This function also + finds the derivatives, which are stored in the Dycomponent class, with each component being a + ACEComplex object. + + @param rx, DOUBLE_TYPE + @param ry, DOUBLE_TYPE + @param rz, DOUBLE_TYPE + @param lmaxi, int + */ + void compute_ylm(DOUBLE_TYPE rx, DOUBLE_TYPE ry, DOUBLE_TYPE rz, LS_TYPE lmaxi); + + Array2DLM alm; + Array2DLM blm; + Array1D cl; + Array1D dl; + + Array2DLM plm; + Array2DLM dplm; + + Array2DLM ylm; ///< Values of all spherical harmonics after \code compute_ylm(rx,ry,rz, lmaxi) \endcode call + Array2DLM dylm;///< Values of gradients of all spherical harmonics after \code compute_ylm(rx,ry,rz, lmaxi) \endcode call + +}; + + +#endif diff --git a/lib/pace/ace_timing.h b/lib/pace/ace_timing.h new file mode 100644 index 0000000000..7f5243eb99 --- /dev/null +++ b/lib/pace/ace_timing.h @@ -0,0 +1,126 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Yury Lysogorskiy on 19.02.20. + +#ifndef ACE_TIMING_H +#define ACE_TIMING_H + +#include + +using namespace std::chrono; +using Clock = std::chrono::high_resolution_clock; +using TimePoint = std::chrono::time_point; +using Duration = Clock::duration; + +////////////////////////////////////////// +#ifdef FINE_TIMING +/** + * Helper class for timing the code. + * The timer should be initialized to reset measured time and + * then call "start" and "stop" before and after measured code. + * The measured time is stored in "duration" variable + */ +struct ACETimer { + Duration duration; ///< measured duration + TimePoint start_moment; ///< start moment of current measurement + + ACETimer() { init(); }; + + /** + * Reset timer + */ + void init() { duration = std::chrono::nanoseconds(0); } + + /** + * Start timer + */ + void start() { start_moment = Clock::now(); } + + /** + * Stop timer, update measured "duration" + */ + void stop() { duration += Clock::now() - start_moment; } + + /** + * Get duration in microseconds + */ + long as_microseconds() { return std::chrono::duration_cast(duration).count(); } + + /** + * Get duration in nanoseconds + */ + long as_nanoseconds() { return std::chrono::duration_cast(duration).count(); } + +}; + +#else // EMPTY Definitions +/** + * Helper class for timing the code. + * The timer should be initialized to reset measured time and + * then call "start" and "stop" before and after measured code. + * The measured time is stored in "duration" variable + */ +struct ACETimer { + Duration duration; ///< measured duration + TimePoint start_moment; ///< start moment of current measurement + + ACETimer() {}; + + /** + * Reset timer + */ + void init() {} + + /** + * Start timer + */ + void start() {} + + /** + * Stop timer, update measured "duration" + */ + void stop() {} + + /** + * Get duration in microseconds + */ + long as_microseconds() {return 0; } + + /** + * Get duration in nanoseconds + */ + long as_nanoseconds() {return 0; } + +}; + +#endif +////////////////////////////////////////// + + +#endif //ACE_TIMING_H diff --git a/lib/pace/ace_types.h b/lib/pace/ace_types.h new file mode 100644 index 0000000000..f9b3cf7267 --- /dev/null +++ b/lib/pace/ace_types.h @@ -0,0 +1,45 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Yury Lysogorskiy on 20.01.20. + +#ifndef ACE_TYPES_H +#define ACE_TYPES_H + +typedef char RANK_TYPE; +typedef int SPECIES_TYPE; +typedef short int NS_TYPE; +typedef short int LS_TYPE; + +typedef short int DENSITY_TYPE; + +typedef short int MS_TYPE; + +typedef short int SHORT_INT_TYPE; +typedef double DOUBLE_TYPE; + +#endif \ No newline at end of file diff --git a/lib/pace/ace_version.h b/lib/pace/ace_version.h new file mode 100644 index 0000000000..9d61e5c505 --- /dev/null +++ b/lib/pace/ace_version.h @@ -0,0 +1,39 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Lysogorskiy Yury on 07.04.2020. + +#ifndef ACE_VERSION_H +#define ACE_VERSION_H + +#define VERSION_YEAR 2021 +#define VERSION_MONTH 2 +#define VERSION_DAY 3 + +#endif //ACE_VERSION_Hls + diff --git a/lib/pace/ships_radial.cpp b/lib/pace/ships_radial.cpp new file mode 100644 index 0000000000..e948f03f21 --- /dev/null +++ b/lib/pace/ships_radial.cpp @@ -0,0 +1,388 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Christoph Ortner on 03.06.2020 + +#include "ships_radial.h" + +#include +#include +#include + + +using namespace std; + +void SHIPsRadPolyBasis::_init(DOUBLE_TYPE r0, int p, DOUBLE_TYPE rcut, + DOUBLE_TYPE xl, DOUBLE_TYPE xr, + int pl, int pr, size_t maxn) { + this->p = p; + this->r0 = r0; + this->rcut = rcut; + this->xl = xl; + this->xr = xr; + this->pl = pl; + this->pr = pr; + this->maxn = maxn; + this->A.resize(maxn); + this->B.resize(maxn); + this->C.resize(maxn); + this->P.resize(maxn); + this->dP_dr.resize(maxn); +} + + +void SHIPsRadPolyBasis::fread(FILE *fptr) +{ + int res; //for fscanf result + int maxn, p, pl, pr, ntests; + double r0, xl, xr, a, b, c, rcut; + + // transform parameters + res = fscanf(fptr, "transform parameters: p=%d r0=%lf\n", &p, &r0); + if (res != 2) + throw invalid_argument("Couldn't read line: transform parameters: p=%d r0=%lf"); + // cutoff parameters + res = fscanf(fptr, "cutoff parameters: rcut=%lf xl=%lf xr=%lf pl=%d pr=%d\n", + &rcut, &xl, &xr, &pl, &pr); + if (res != 5) + throw invalid_argument("Couldn't read cutoff parameters: rcut=%lf xl=%lf xr=%lf pl=%d pr=%d"); + // basis size + res = fscanf(fptr, "recursion coefficients: maxn = %d\n", &maxn); + if (res != 1) + throw invalid_argument("Couldn't read recursion coefficients: maxn = %d"); + // initialize and allocate + this->_init(r0, p, rcut, xl, xr, pl, pr, maxn); + + // read basis coefficients + for (int i = 0; i < maxn; i++) { + res = fscanf(fptr, " %lf %lf %lf\n", &a, &b, &c); + if (res != 3) + throw invalid_argument("Couldn't read line: A_n B_n C_n"); + this->A(i) = DOUBLE_TYPE(a); + this->B(i) = DOUBLE_TYPE(b); + this->C(i) = DOUBLE_TYPE(c); + } + + // // check there are no consistency tests (I don't have time to fix this now) + // res = fscanf(fptr, "tests: ntests = %d\n", &ntests); + // if (res != 1) + // throw invalid_argument("Couldn't read line: tests: ntests = %d"); + // if (ntests != 0) + // throw invalid_argument("must have ntests = 0!"); + + // --------------------------------------------------------------------- + // run the consistency test this could be moved into a separate function + double r, Pn, dPn; + double err = 0.0; + + res = fscanf(fptr, "tests: ntests = %d\n", &ntests); + if (res != 1) + throw invalid_argument("Couldn't read line: tests: ntests = %d"); + for (size_t itest = 0; itest < ntests; itest++) { + // read an r argument + res = fscanf(fptr, " r=%lf\n", &r); + // printf("r = %lf \n", r); + if (res != 1) + throw invalid_argument("Couldn't read line: r=%lf"); + // printf("test %d, r=%f, maxn=%d \n", itest, r, maxn); + // evaluate the basis + this->calcP(r, maxn, SPECIES_TYPE(0), SPECIES_TYPE(0)); + // compare against the stored values + for (size_t n = 0; n < maxn; n++) { + res = fscanf(fptr, " %lf %lf\n", &Pn, &dPn); + if (res != 2) + throw invalid_argument("Couldn't read test value line: %lf %lf"); + err = max(err, abs(Pn - this->P(n)) + abs(dPn - this->dP_dr(n))); + // printf(" %d %e %e \n", int(n), + // abs(Pn - this->P(n)), + // abs(dPn - this->dP_dr(n))); + } + } + if (ntests > 0) + printf("Maximum Test error = %e\n", err); + // --------------------------------------------------------------------- + +} + + + + +size_t SHIPsRadPolyBasis::get_maxn() +{ + return this->maxn; +} + + +// Julia code: ((1+r0)/(1+r))^p +void SHIPsRadPolyBasis::transform(const DOUBLE_TYPE r, DOUBLE_TYPE &x_out, DOUBLE_TYPE &dx_out) const { + x_out = pow((1 + r0) / (1 + r), p); // ==pow( (1 + r) / (1 + r0), -p ); + dx_out = -p * pow((1 + r) / (1 + r0), -p - 1) / (1 + r0); +} + +void SHIPsRadPolyBasis::fcut(const DOUBLE_TYPE x, DOUBLE_TYPE &f_out, DOUBLE_TYPE &df_out) const { + if ( ((x < xl) && (pl > 0)) || ((x > xr) && (pr > 0)) ) { + f_out = 0.0; + df_out = 0.0; + } else { + f_out = pow(x - xl, pl) * pow(x - xr, pr); + df_out = pl * pow(x - xl, pl - 1) * pow(x - xr, pr) + pow(x - xl, pl) * pr * pow(x - xr, pr - 1); + } +} + + /* ------------------------------------------------------------------------ +Julia Code +P[1] = J.A[1] * _fcut_(J.pl, J.tl, J.pr, J.tr, t) +if length(J) == 1; return P; end +P[2] = (J.A[2] * t + J.B[2]) * P[1] +@inbounds for n = 3:length(J) + P[n] = (J.A[n] * t + J.B[n]) * P[n-1] + J.C[n] * P[n-2] +end +return P +------------------------------------------------------------------------ */ + +void SHIPsRadPolyBasis::calcP(DOUBLE_TYPE r, size_t maxn, + SPECIES_TYPE z1, SPECIES_TYPE z2) { + if (maxn > this->maxn) + throw invalid_argument("Given maxn couldn't be larger than global maxn"); + + if (maxn > P.get_size()) + throw invalid_argument("Given maxn couldn't be larger than global length of P"); + + DOUBLE_TYPE x, dx_dr; // dx -> dx/dr + transform(r, x, dx_dr); + // printf("r = %f, x = %f, fcut = %f \n", r, x, fcut(x)); + DOUBLE_TYPE f, df_dx; + fcut(x, f, df_dx); // df -> df/dx + + //fill with zeros + P.fill(0); + dP_dr.fill(0); + + P(0) = A(0) * f; + dP_dr(0) = A(0) * df_dx * dx_dr; // dP/dr; chain rule: df_cut/dr = df_cut/dx * dx/dr + if (maxn > 0) { + P(1) = (A(1) * x + B(1)) * P(0); + dP_dr(1) = A(1) * dx_dr * P(0) + (A(1) * x + B(1)) * dP_dr(0); + } + for (size_t n = 2; n < maxn; n++) { + P(n) = (A(n) * x + B(n)) * P(n - 1) + C(n) * P(n - 2); + dP_dr(n) = A(n) * dx_dr * P(n - 1) + (A(n) * x + B(n)) * dP_dr(n - 1) + C(n) * dP_dr(n - 2); + } +} + + +// ==================================================================== + + +bool SHIPsRadialFunctions::has_pair() { + return this->haspair; +} + +void SHIPsRadialFunctions::load(string fname) { + FILE * fptr = fopen(fname.data(), "r"); + size_t res = fscanf(fptr, "radbasename=ACE.jl.Basic\n"); + if (res != 0) + throw("SHIPsRadialFunctions::load : couldnt read radbasename=ACE.jl.Basic"); + this->fread(fptr); + fclose(fptr); +} + +void SHIPsRadialFunctions::fread(FILE *fptr){ + int res; + size_t maxn; + char hasE0, haspair; + DOUBLE_TYPE c; + + // check whether we have a pair potential + res = fscanf(fptr, "haspair: %c\n", &haspair); + if (res != 1) + throw("SHIPsRadialFunctions::load : couldn't read haspair"); + + // read the radial basis + this->radbasis.fread(fptr); + + // read the pair potential + if (haspair == 't') { + this->haspair=true; + fscanf(fptr, "begin repulsive potential\n"); + fscanf(fptr, "begin polypairpot\n"); + // read the basis parameters + pairbasis.fread(fptr); + maxn = pairbasis.get_maxn(); + // read the coefficients + fscanf(fptr, "coefficients\n"); + paircoeffs.resize(maxn); + for (size_t n = 0; n < maxn; n++) { + fscanf(fptr, "%lf\n", &c); + paircoeffs(n) = c; + } + fscanf(fptr, "end polypairpot\n"); + // read the spline parameters + fscanf(fptr, "spline parameters\n"); + fscanf(fptr, " e_0 + B exp(-A*(r/ri-1)) * (ri/r)\n"); + fscanf(fptr, "ri=%lf\n", &(this->ri)); + fscanf(fptr, "e0=%lf\n", &(this->e0)); + fscanf(fptr, "A=%lf\n", &(this->A)); + fscanf(fptr, "B=%lf\n", &(this->B)); + fscanf(fptr, "end repulsive potential\n"); + } +} + + +size_t SHIPsRadialFunctions::get_maxn() +{ + return this->radbasis.get_maxn(); +} + +DOUBLE_TYPE SHIPsRadialFunctions::get_rcut() +{ + return max(radbasis.rcut, pairbasis.rcut); +} + + +void SHIPsRadialFunctions::fill_gk(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2) { + radbasis.calcP(r, maxn, z1, z2); + for (NS_TYPE n = 0; n < maxn; n++) { + gr(n) = radbasis.P(n); + dgr(n) = radbasis.dP_dr(n); + } +} + + +void SHIPsRadialFunctions::fill_Rnl(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2) { + radbasis.calcP(r, maxn, z1, z2); + for (NS_TYPE n = 0; n < maxn; n++) { + for (LS_TYPE l = 0; l <= lmax; l++) { + fr(n, l) = radbasis.P(n); + dfr(n, l) = radbasis.dP_dr(n); + } + } +} + + +void SHIPsRadialFunctions::setuplookupRadspline() { +} + + +void SHIPsRadialFunctions::init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, + SPECIES_TYPE nelements, + DOUBLE_TYPE cutoff, string radbasename) { + //mimic ACERadialFunctions::init + this->nradbase = nradb; + this->lmax = lmax; + this->nradial = nradial; + this->deltaSplineBins = deltaSplineBins; + this->nelements = nelements; + this->cutoff = cutoff; + this->radbasename = radbasename; + + gr.init(nradbase, "gr"); + dgr.init(nradbase, "dgr"); + + + fr.init(nradial, lmax + 1, "fr"); + dfr.init(nradial, lmax + 1, "dfr"); + + splines_gk.init(nelements, nelements, "splines_gk"); + splines_rnl.init(nelements, nelements, "splines_rnl"); + splines_hc.init(nelements, nelements, "splines_hc"); + + lambda.init(nelements, nelements, "lambda"); + lambda.fill(1.); + + cut.init(nelements, nelements, "cut"); + cut.fill(1.); + + dcut.init(nelements, nelements, "dcut"); + dcut.fill(1.); + + crad.init(nelements, nelements, (lmax + 1), nradial, nradbase, "crad"); + crad.fill(0.); + + //hard-core repulsion + prehc.init(nelements, nelements, "prehc"); + prehc.fill(0.); + + lambdahc.init(nelements, nelements, "lambdahc"); + lambdahc.fill(1.); +} + + +void SHIPsRadialFunctions::evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, + SPECIES_TYPE mu_j, bool calc_second_derivatives) { + if (calc_second_derivatives) + throw invalid_argument("SHIPsRadialFunctions has not `calc_second_derivatives` option"); + + radbasis.calcP(r, nradbase_c, mu_i, mu_j); + for (NS_TYPE nr = 0; nr < nradbase_c; nr++) { + gr(nr) = radbasis.P(nr); + dgr(nr) = radbasis.dP_dr(nr); + } + for (NS_TYPE nr = 0; nr < nradial_c; nr++) { + for (LS_TYPE l = 0; l <= this->lmax; l++) { + fr(nr, l) = radbasis.P(nr); + dfr(nr, l) = radbasis.dP_dr(nr); + } + } + + if (this->has_pair()) + this->evaluate_pair(r, mu_i, mu_j); + else { + cr = 0; + dcr = 0; + } +} + +void SHIPsRadialFunctions::evaluate_pair(DOUBLE_TYPE r, + SPECIES_TYPE mu_i, + SPECIES_TYPE mu_j, + bool calc_second_derivatives) { + // spline_hc.calcSplines(r); + // cr = spline_hc.values(0); + // dcr = spline_hc.derivatives(0); + + // the outer polynomial potential + if (r > ri) { + pairbasis.calcP(r, pairbasis.get_maxn(), mu_i, mu_j); + cr = 0; + dcr = 0; + for (size_t n = 0; n < pairbasis.get_maxn(); n++) { + cr += paircoeffs(n) * pairbasis.P(n); + dcr += paircoeffs(n) * pairbasis.dP_dr(n); + } + } + else { // the repulsive core part + cr = e0 + B * exp(-A * (r/ri - 1)) * (ri/r); + dcr = B * exp( - A * (r/ri-1) ) * ri * ( - A / ri / r - 1/(r*r) ); + } + // fix double-counting + cr *= 0.5; + dcr *= 0.5; +} + + + diff --git a/lib/pace/ships_radial.h b/lib/pace/ships_radial.h new file mode 100644 index 0000000000..60a82448cd --- /dev/null +++ b/lib/pace/ships_radial.h @@ -0,0 +1,158 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Christoph Ortner on 03.06.2020 + +#ifndef SHIPs_RADIAL_FUNCTIONS_H +#define SHIPs_RADIAL_FUNCTIONS_H + +#include "ace_arraynd.h" +#include "ace_types.h" +#include "ace_radial.h" + +class SHIPsRadPolyBasis { + +public: + + // transform parameters + int p = 0; + DOUBLE_TYPE r0 = 0.0; + + // cutoff parameters + DOUBLE_TYPE rcut = 0.0; + DOUBLE_TYPE xl = 0.0; + DOUBLE_TYPE xr = 0.0; + int pl = 0; + int pr = 0; + + // basis size + size_t maxn = 0; + + // recursion parameters + Array1D A = Array1D("SHIPs radial basis: A"); + Array1D B = Array1D("SHIPs radial basis: B"); + Array1D C = Array1D("SHIPs radial basis: C"); + + // temporary storage for evaluating the basis + Array1D P = Array1D("SHIPs radial basis: P"); + Array1D dP_dr = Array1D("SHIPs radial basis: dP"); + +////////////////////////////////// + + SHIPsRadPolyBasis() = default; + + ~SHIPsRadPolyBasis() = default; + + // distance transform + void transform(const DOUBLE_TYPE r, DOUBLE_TYPE &x_out, DOUBLE_TYPE &dx_out) const; + + // cutoff function + void fcut(const DOUBLE_TYPE x, DOUBLE_TYPE &f_out, DOUBLE_TYPE &df_out) const; + + void fread(FILE *fptr); + + void _init(DOUBLE_TYPE r0, int p, DOUBLE_TYPE rcut, + DOUBLE_TYPE xl, DOUBLE_TYPE xr, + int pl, int pr, size_t maxn); + + void calcP(DOUBLE_TYPE r, size_t maxn, SPECIES_TYPE z1, SPECIES_TYPE z2); + + size_t get_maxn(); + +}; + + + + +class SHIPsRadialFunctions : public AbstractRadialBasis { +public: + + // radial basis + SHIPsRadPolyBasis radbasis; + + // pair potential basis + bool haspair = false; + SHIPsRadPolyBasis pairbasis; + + // pair potential coefficients + Array1D paircoeffs = Array1D("SHIPs pairpot coeffs: paircoeffs"); + + // spline parameters for repulsive core + DOUBLE_TYPE ri = 0.0; + DOUBLE_TYPE e0 = 0.0; + DOUBLE_TYPE A = 0.0; + DOUBLE_TYPE B = 0.0; + +////////////////////////////////// + + SHIPsRadialFunctions() = default; + + ~SHIPsRadialFunctions() override = default; + + + void fread(FILE *fptr); + + void load(string fname); + + size_t get_maxn(); + DOUBLE_TYPE get_rcut(); + + bool has_pair(); + + void init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements, + DOUBLE_TYPE cutoff, + string radbasename) override; + + void + evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, + bool calc_second_derivatives = false) override; + + void + evaluate_pair(DOUBLE_TYPE r, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, + bool calc_second_derivatives = false); + + void setuplookupRadspline() override; + + SHIPsRadialFunctions *clone() const override { + return new SHIPsRadialFunctions(*this); + }; + + /** + * Helper method, that populate `fr` and `dfr` 2D-arrays (n,l) with P(n), dP_dr for given coordinate r + * @param r + * @param maxn + * @param z1 + * @param z2 + */ + void fill_Rnl(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2); + + void fill_gk(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2); +}; + + +#endif diff --git a/src/Makefile b/src/Makefile index a63c49e344..bec0a2b16b 100644 --- a/src/Makefile +++ b/src/Makefile @@ -63,7 +63,7 @@ PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \ python voronoi \ user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ user-netcdf user-plumed user-qmmm user-quip user-scafacos \ - user-smd user-vtk user-mesont + user-smd user-vtk user-mesont user-pace PACKSYS = compress mpiio python user-lb @@ -71,7 +71,7 @@ PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont PACKEXT = kim latte mscg voronoi \ user-adios user-h5md user-molfile user-netcdf user-plumed user-qmmm user-quip \ - user-smd user-vtk + user-smd user-vtk user-pace PACKALL = $(PACKAGE) $(PACKUSER) diff --git a/src/USER-PACE/Install.sh b/src/USER-PACE/Install.sh new file mode 100644 index 0000000000..4d87b0e3ed --- /dev/null +++ b/src/USER-PACE/Install.sh @@ -0,0 +1,68 @@ +# Install.sh file that integrates the settings from the lib folder into the conventional build process (make build?) + +# COPIED FROM src/KIM/Install.sh: + +# # Install/unInstall package files in LAMMPS +# # mode = 0/1/2 for uninstall/install/update + +# mode=$1 + +# # enforce using portable C locale +# LC_ALL=C +# export LC_ALL + +# # arg1 = file, arg2 = file it depends on + +# action () { +# if (test $mode = 0) then +# rm -f ../$1 +# elif (! cmp -s $1 ../$1) then +# if (test -z "$2" || test -e ../$2) then +# cp $1 .. +# if (test $mode = 2) then +# echo " updating src/$1" +# fi +# fi +# elif (test -n "$2") then +# if (test ! -e ../$2) then +# rm -f ../$1 +# fi +# fi +# } + +# # all package files with no dependencies + +# for file in *.cpp *.h; do +# test -f ${file} && action $file +# done + +# # edit 2 Makefile.package files to include/exclude package info + +# if (test $1 = 1) then + +# if (test -e ../Makefile.package) then +# sed -i -e 's/[^ \t]*kim[^ \t]* //' ../Makefile.package +# sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(kim_SYSINC) |' ../Makefile.package +# sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(kim_SYSLIB) |' ../Makefile.package +# sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(kim_SYSPATH) |' ../Makefile.package +# fi + +# if (test -e ../Makefile.package.settings) then +# sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings +# # multiline form needed for BSD sed on Macs +# sed -i -e '4 i \ +# include ..\/..\/lib\/kim\/Makefile.lammps +# ' ../Makefile.package.settings +# fi + +# elif (test $1 = 0) then + +# if (test -e ../Makefile.package) then +# sed -i -e 's/[^ \t]*kim[^ \t]* //' ../Makefile.package +# fi + +# if (test -e ../Makefile.package.settings) then +# sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings +# fi + +# fi diff --git a/src/USER-PACE/LICENSE b/src/USER-PACE/LICENSE new file mode 100644 index 0000000000..f288702d2f --- /dev/null +++ b/src/USER-PACE/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp new file mode 100644 index 0000000000..a515b7b4b0 --- /dev/null +++ b/src/USER-PACE/pair_pace.cpp @@ -0,0 +1,458 @@ +/* +Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + +^1: Ruhr-University Bochum, Bochum, Germany +^2: University of Cambridge, Cambridge, United Kingdom +^3: Sandia National Laboratories, Albuquerque, New Mexico, USA +^4: University of British Columbia, Vancouver, BC, Canada + + + This FILENAME is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + */ + + +// +// Created by Lysogorskiy Yury on 27.02.20. +// + +#include +#include +#include +#include +#include "pair_pace.h" +#include "atom.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "force.h" +#include "comm.h" +#include "memory.h" +#include "error.h" + + +#include "math_const.h" + +#include "ace_version.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define MAXLINE 1024 +#define DELTA 4 + +//added YL + +//keywords for ACE evaluator style +#define RECURSIVE_KEYWORD "recursive" +#define PRODUCT_KEYWORD "product" + + +int elements_num_pace = 104; +char const *const elements_pace[104] = {"X", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", + "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", + "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", + "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", + "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", + "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", + "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", + "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr" +}; + +int AtomicNumberByName_pace(char *elname) { + for (int i = 1; i < elements_num_pace; i++) + if (strcmp(elname, elements_pace[i]) == 0) + return i; + return -1; +} + + +/* ---------------------------------------------------------------------- */ +PairPACE::PairPACE(LAMMPS *lmp) : Pair(lmp) { + //single_enable = 0; + restartinfo = 0; + one_coeff = 1; + manybody_flag = 1; + + nelements = 0; + + ace = NULL; + potential_file_name = NULL; + elements = NULL; + map = NULL; +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete +------------------------------------------------------------------------- */ + +PairPACE::~PairPACE() { + if (copymode) return; + + if (elements) + for (int i = 0; i < nelements; i++) delete[] elements[i]; + delete[] elements; + + + delete[] potential_file_name; + + delete basis_set; + delete ace; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(map); + memory->destroy(scale); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairPACE::compute(int eflag, int vflag) { + int i, j, ii, jj, inum, jnum; + double delx, dely, delz, evdwl; + double fij[3]; + int *ilist, *jlist, *numneigh, **firstneigh; + + ev_init(eflag, vflag); + + // downwards modified by YL + + double **x = atom->x; + double **f = atom->f; + tagint *tag = atom->tag; + int *type = atom->type; + + // number of atoms in cell + int nlocal = atom->nlocal; + + int newton_pair = force->newton_pair; + + // number of atoms including ghost atoms + int nall = nlocal + atom->nghost; + + // inum: length of the neighborlists list + inum = list->inum; + + // ilist: list of "i" atoms for which neighbor lists exist + ilist = list->ilist; + + //numneigh: the length of each these neigbor list + numneigh = list->numneigh; + + // the pointer to the list of neighbors of "i" + firstneigh = list->firstneigh; + + if (inum != nlocal) { + char str[128]; + snprintf(str,128,"inum: %d nlocal: %d are different",inum, nlocal); + error->all(FLERR,str); + } + + + // Aidan Thompson told RD (26 July 2019) that practically always holds: + // inum = nlocal + // i = ilist(ii) < inum + // j = jlist(jj) < nall + // neighborlist contains neighbor atoms plus skin atoms, + // skin atoms can be removed by setting skin to zero but here + // they are disregarded anyway + + + //determine the maximum number of neighbours + int max_jnum = -1; + int nei = 0; + for (ii = 0; ii < list->inum; ii++) { + i = ilist[ii]; + jnum = numneigh[i]; + nei = nei + jnum; + if (jnum > max_jnum) + max_jnum = jnum; + } + + ace->resize_neighbours_cache(max_jnum); + + //loop over atoms + for (ii = 0; ii < list->inum; ii++) { + i = list->ilist[ii]; + const int itype = type[i]; + + const double xtmp = x[i][0]; + const double ytmp = x[i][1]; + const double ztmp = x[i][2]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // checking if neighbours are actually within cutoff range is done inside compute_atom + // mapping from LAMMPS atom types ('type' array) to ACE species is done inside compute_atom + // by using 'ace->element_type_mapping' array + // x: [r0 ,r1, r2, ..., r100] + // i = 0 ,1 + // jnum(0) = 50 + // jlist(neigh ind of 0-atom) = [1,2,10,7,99,25, .. 50 element in total] + try { + ace->compute_atom(i, x, type, jnum, jlist); + } catch (exception &e) { + error->all(FLERR, e.what()); + exit(EXIT_FAILURE); + } + // 'compute_atom' will update the `ace->e_atom` and `ace->neighbours_forces(jj, alpha)` arrays + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + const int jtype = type[j]; + j &= NEIGHMASK; + delx = x[j][0] - xtmp; + dely = x[j][1] - ytmp; + delz = x[j][2] - ztmp; + + fij[0] = scale[itype][jtype]*ace->neighbours_forces(jj, 0); + fij[1] = scale[itype][jtype]*ace->neighbours_forces(jj, 1); + fij[2] = scale[itype][jtype]*ace->neighbours_forces(jj, 2); + + + f[i][0] += fij[0]; + f[i][1] += fij[1]; + f[i][2] += fij[2]; + f[j][0] -= fij[0]; + f[j][1] -= fij[1]; + f[j][2] -= fij[2]; + + // tally per-atom virial contribution + if (vflag) + ev_tally_xyz(i, j, nlocal, newton_pair, 0.0, 0.0, + fij[0], fij[1], fij[2], + -delx, -dely, -delz); + } + + // tally energy contribution + if (eflag) { + // evdwl = energy of atom I + evdwl = scale[1][1]*ace->e_atom; + ev_tally_full(i, 2.0 * evdwl, 0.0, 0.0, 0.0, 0.0, 0.0); + } + } + + if (vflag_fdotr) virial_fdotr_compute(); + + + // end modifications YL +} + +/* ---------------------------------------------------------------------- */ + +void PairPACE::allocate() { + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); + memory->create(map, n + 1, "pair:map"); + memory->create(scale, n + 1, n + 1,"pair:scale"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairPACE::settings(int narg, char **arg) { + if (narg > 1) { + error->all(FLERR, + "Illegal pair_style command. Correct form:\n\tpair_style pace\nor\n\tpair_style pace "); + error->all(FLERR, RECURSIVE_KEYWORD); + error->all(FLERR, "or\n\tpair_style pace "); + error->all(FLERR, PRODUCT_KEYWORD); + } + recursive = true; // default evaluator style: RECURSIVE + if (narg > 0) { + if (strcmp(arg[0], RECURSIVE_KEYWORD) == 0) + recursive = true; + else if (strcmp(arg[0], PRODUCT_KEYWORD) == 0) { + recursive = false; + } else { + error->all(FLERR, + "Illegal pair_style command: pair_style pace "); + error->all(FLERR, arg[0]); + error->all(FLERR, "\nCorrect form:\n\tpair_style pace\nor\n\tpair_style pace recursive"); + } + } + + if (comm->me == 0) { + if (screen) fprintf(screen, "ACE version: %d.%d.%d\n", VERSION_YEAR, VERSION_MONTH, VERSION_DAY); + if (logfile) fprintf(logfile, "ACE version: %d.%d.%d\n", VERSION_YEAR, VERSION_MONTH, VERSION_DAY); + + if (recursive) { + if (screen) fprintf(screen, "Recursive evaluator is used\n"); + if (logfile) fprintf(logfile, "Recursive evaluator is used\n"); + } else { + if (screen) fprintf(screen, "Product evaluator is used\n"); + if (logfile) fprintf(logfile, "Product evaluator is used\n"); + } + } + + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairPACE::coeff(int narg, char **arg) { + + if (narg < 4) + error->all(FLERR, + "Incorrect args for pair coefficients. Correct form:\npair_coeff * * elem1 elem2 ..."); + + if (!allocated) allocate(); + + //number of provided elements in pair_coeff line + int ntypes_coeff = narg - 3; + + if (ntypes_coeff != atom->ntypes) { + char error_message[1024]; + snprintf(error_message, 1024, + "Incorrect args for pair coefficients. You provided %d elements in pair_coeff, but structure has %d atom types", + ntypes_coeff, atom->ntypes); + error->all(FLERR, error_message); + } + + char *type1 = arg[0]; + char *type2 = arg[1]; + char *potential_file_name = arg[2]; + char **elemtypes = &arg[3]; + + // insure I,J args are * * + + if (strcmp(type1, "*") != 0 || strcmp(type2, "*") != 0) + error->all(FLERR, "Incorrect args for pair coefficients"); + + + //load potential file + basis_set = new ACECTildeBasisSet(); + if (comm->me == 0) { + if (screen) fprintf(screen, "Loading %s\n", potential_file_name); + if (logfile) fprintf(logfile, "Loading %s\n", potential_file_name); + } + basis_set->load(potential_file_name); + + if (comm->me == 0) { + if (screen) fprintf(screen, "Total number of basis functions\n"); + if (logfile) fprintf(logfile, "Total number of basis functions\n"); + + for (SPECIES_TYPE mu = 0; mu < basis_set->nelements; mu++) { + int n_r1 = basis_set->total_basis_size_rank1[mu]; + int n = basis_set->total_basis_size[mu]; + if (screen) fprintf(screen, "\t%s: %d (r=1) %d (r>1)\n", basis_set->elements_name[mu].c_str(), n_r1, n); + if (logfile) fprintf(logfile, "\t%s: %d (r=1) %d (r>1)\n", basis_set->elements_name[mu].c_str(), n_r1, n); + } + } + + // read args that map atom types to pACE elements + // map[i] = which element the Ith atom type is, -1 if not mapped + // map[0] is not used + + ace = new ACERecursiveEvaluator(); + ace->set_recursive(recursive); + ace->element_type_mapping.init(atom->ntypes + 1); + + for (int i = 1; i <= atom->ntypes; i++) { + char *elemname = elemtypes[i - 1]; + int atomic_number = AtomicNumberByName_pace(elemname); + if (atomic_number == -1) { + char error_msg[1024]; + snprintf(error_msg, 1024, "String '%s' is not a valid element\n", elemname); + error->all(FLERR, error_msg); + } + SPECIES_TYPE mu = basis_set->get_species_index_by_name(elemname); + if (mu != -1) { + if (comm->me == 0) { + if (screen) + fprintf(screen, "Mapping LAMMPS atom type #%d(%s) -> ACE species type #%d\n", i, elemname, mu); + if (logfile) + fprintf(logfile, "Mapping LAMMPS atom type #%d(%s) -> ACE species type #%d\n", i, elemname, mu); + } + map[i] = mu; + ace->element_type_mapping(i) = mu; // set up LAMMPS atom type to ACE species mapping for ace evaluator + } else { + char error_msg[1024]; + snprintf(error_msg, 1024, "Element %s is not supported by ACE-potential from file %s", elemname, + potential_file_name); + error->all(FLERR, error_msg); + } + } + + // clear setflag since coeff() called once with I,J = * * + int n = atom->ntypes; + for (int i = 1; i <= n; i++) { + for (int j = i; j <= n; j++) { + setflag[i][j] = 1; + scale[i][j] = 1.0; + } + } + + // set setflag i,j for type pairs where both are mapped to elements + + int count = 1; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + if (map[i] >= 0 && map[j] >= 0) { + setflag[i][j] = 1; + count++; + } + + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + + ace->set_basis(*basis_set, 1); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairPACE::init_style() { + if (atom->tag_enable == 0) + error->all(FLERR, "Pair style pACE requires atom IDs"); + if (force->newton_pair == 0) + error->all(FLERR, "Pair style pACE requires newton pair on"); + + // request a full neighbor list + int irequest = neighbor->request(this, instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairPACE::init_one(int i, int j) { + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); + //cutoff from the basis set's radial functions settings + scale[j][i] = scale[i][j]; + return basis_set->radial_functions->cut(map[i], map[j]); +} + +/* ---------------------------------------------------------------------- + extract method for extracting value of scale variable + ---------------------------------------------------------------------- */ +void *PairPACE::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str,"scale") == 0) return (void *) scale; + return NULL; +} + diff --git a/src/USER-PACE/pair_pace.h b/src/USER-PACE/pair_pace.h new file mode 100644 index 0000000000..3fccbd98f0 --- /dev/null +++ b/src/USER-PACE/pair_pace.h @@ -0,0 +1,97 @@ +/* +Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + +^1: Ruhr-University Bochum, Bochum, Germany +^2: University of Cambridge, Cambridge, United Kingdom +^3: Sandia National Laboratories, Albuquerque, New Mexico, USA +^4: University of British Columbia, Vancouver, BC, Canada + + + This FILENAME is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + */ + + +// +// Created by Lysogorskiy Yury on 27.02.20. +// + + +#ifdef PAIR_CLASS + +PairStyle(pace,PairPACE) + +#else + +#ifndef LMP_PAIR_PACE_H +#define LMP_PAIR_PACE_H + +#include "pair.h" +#include "ace_evaluator.h" +#include "ace_recursive.h" +#include "ace_c_basis.h" + +namespace LAMMPS_NS { + + class PairPACE : public Pair { + public: + PairPACE(class LAMMPS *); + + virtual ~PairPACE(); + + virtual void compute(int, int); + + void settings(int, char **); + + void coeff(int, char **); + + virtual void init_style(); + + double init_one(int, int); + + void *extract(const char *, int &); + + // virtual double memory_usage(); + + protected: + ACECTildeBasisSet *basis_set = nullptr; + + ACERecursiveEvaluator *ace = nullptr; + + char *potential_file_name; + + virtual void allocate(); + + void read_files(char *, char *); + + inline int equal(double *x, double *y); + + + double rcutmax; // max cutoff for all elements + int nelements; // # of unique elements + char **elements; // names of unique elements + + int *map; // mapping from atom types to elements + int *jlist_local; + int *type_local; + double **scale; + + bool recursive = false; // "recursive" option for ACERecursiveEvaluator + }; + +} + +#endif +#endif \ No newline at end of file From d346c539147ae666741494657646a8d885741312 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 6 Apr 2021 11:28:19 -0400 Subject: [PATCH 0402/1217] silence compiler warnings about formats --- src/USER-REAXC/reaxc_tool_box.cpp | 45 +++++++++++++++---------------- src/USER-REAXC/reaxc_traj.h | 16 ++++++----- 2 files changed, 31 insertions(+), 30 deletions(-) diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/USER-REAXC/reaxc_tool_box.cpp index f0171d2108..abab3f2b43 100644 --- a/src/USER-REAXC/reaxc_tool_box.cpp +++ b/src/USER-REAXC/reaxc_tool_box.cpp @@ -25,10 +25,11 @@ ----------------------------------------------------------------------*/ #include "reaxc_tool_box.h" +#include "reaxc_defs.h" + #include #include #include -#include "reaxc_defs.h" #include "error.h" @@ -49,62 +50,58 @@ int Tokenize( char* s, char*** tok ) return count; } - - /* safe malloc */ void *smalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, const char *name ) { void *ptr; - char errmsg[256]; if (n <= 0) { - snprintf(errmsg, 256, "Trying to allocate %ld bytes for array %s. " - "returning NULL.", n, name); + auto errmsg = fmt::format("Trying to allocate {} bytes for array {}. " + "returning NULL.", n, name); if (error_ptr) error_ptr->one(FLERR,errmsg); - else fputs(errmsg,stderr); + else fputs(errmsg.c_str(),stderr); return nullptr; } ptr = malloc( n ); if (ptr == nullptr) { - snprintf(errmsg, 256, "Failed to allocate %ld bytes for array %s", n, name); + auto errmsg = fmt::format("Failed to allocate {} bytes for array {}", + n, name); if (error_ptr) error_ptr->one(FLERR,errmsg); - else fputs(errmsg,stderr); + else fputs(errmsg.c_str(),stderr); } return ptr; } - /* safe calloc */ void *scalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const char *name ) { void *ptr; - char errmsg[256]; if (n <= 0) { - snprintf(errmsg, 256, "Trying to allocate %ld elements for array %s. " - "returning NULL.\n", n, name ); + auto errmsg = fmt::format("Trying to allocate {} elements for array {}. " + "returning NULL.\n", n, name); if (error_ptr) error_ptr->one(FLERR,errmsg); - else fputs(errmsg,stderr); + else fputs(errmsg.c_str(),stderr); return nullptr; } if (size <= 0) { - snprintf(errmsg, 256, "Elements size for array %s is %ld. " - "returning NULL", name, size ); + auto errmsg = fmt::format("Elements size for array {} is {}. " + "returning NULL", name, size); if (error_ptr) error_ptr->one(FLERR,errmsg); - else fputs(errmsg,stderr); + else fputs(errmsg.c_str(),stderr); return nullptr; } ptr = calloc( n, size ); if (ptr == nullptr) { - char errmsg[256]; - snprintf(errmsg, 256, "Failed to allocate %ld bytes for array %s", n*size, name); + auto errmsg = fmt::format("Failed to allocate {} bytes for array {}", + n*size, name); if (error_ptr) error_ptr->one(FLERR,errmsg); - else fputs(errmsg,stderr); + else fputs(errmsg.c_str(),stderr); } return ptr; @@ -115,14 +112,14 @@ void *scalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const c void sfree( LAMMPS_NS::Error* error_ptr, void *ptr, const char *name ) { if (ptr == nullptr) { - char errmsg[256]; - snprintf(errmsg, 256, "Trying to free the already NULL pointer %s", name ); + auto errmsg = fmt::format("Trying to free the already free()'d pointer {}", + name); if (error_ptr) error_ptr->one(FLERR,errmsg); - else fputs(errmsg,stderr); + else fputs(errmsg.c_str(),stderr); return; } - free( ptr ); + free(ptr); ptr = nullptr; } diff --git a/src/USER-REAXC/reaxc_traj.h b/src/USER-REAXC/reaxc_traj.h index 4966bf11d8..2ff5995204 100644 --- a/src/USER-REAXC/reaxc_traj.h +++ b/src/USER-REAXC/reaxc_traj.h @@ -36,14 +36,18 @@ #define HEADER_LINE_LEN 62 #define STR_LINE "%-37s%-24s\n" #define INT_LINE "%-37s%-24d\n" -#define BIGINT_LINE "%-37s%-24ld\n" +#if defined(LAMMPS_SMALLSMALL) +#define BIGINT_LINE "%-37s%-24d\n" +#else +#define BIGINT_LINE "%-37s%-24lld\n" +#endif #define INT2_LINE "%-36s%-12d,%-12d\n" #define REAL_LINE "%-37s%-24.3f\n" #define SCI_LINE "%-37s%-24g\n" #define REAL3_LINE "%-32s%9.3f,%9.3f,%9.3f\n" #if defined(LAMMPS_BIGBIG) -#define INIT_DESC "%9ld%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass +#define INIT_DESC "%9lld%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass #else #define INIT_DESC "%9d%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass #endif @@ -56,7 +60,7 @@ #define SIZE_INFO_LEN3 31 #if defined(LAMMPS_BIGBIG) -#define ATOM_BASIC "%9ld%10.3f%10.3f%10.3f%10.3f\n" //AtomID AtomType (X Y Z) Charge +#define ATOM_BASIC "%9lld%10.3f%10.3f%10.3f%10.3f\n" //AtomID AtomType (X Y Z) Charge #define ATOM_wV "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) Charge #define ATOM_wF "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Fx Fy Fz) Charge #define ATOM_FULL "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) (Fx Fy Fz) Charge @@ -72,9 +76,9 @@ #define ATOM_FULL_LEN 110 #if defined(LAMMPS_BIGBIG) -#define BOND_BASIC "%9ld%9ld%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO -#define BOND_FULL "%9ld%9ld%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2 -#define ANGLE_BASIC "%9ld%9ld%9ld%10.3f\n" // Atom1 Atom2 Atom3 Theta +#define BOND_BASIC "%9lld%9lld%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO +#define BOND_FULL "%9lld%9lld%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2 +#define ANGLE_BASIC "%9lld%9lld%9lld%10.3f\n" // Atom1 Atom2 Atom3 Theta #else #define BOND_BASIC "%9d%9d%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO #define BOND_FULL "%9d%9d%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2 From db400c91aec560f8b04a83c8de4141724d1df89e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 6 Apr 2021 11:37:59 -0400 Subject: [PATCH 0403/1217] relax error a little bit to avoid failure on macos --- unittest/force-styles/tests/fix-timestep-adapt_coul.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml b/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml index 4bf25f3b33..cd7f9aa87d 100644 --- a/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml +++ b/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Mar 2021 date_generated: Thu Mar 25 14:07:45 202 -epsilon: 1e-14 +epsilon: 7.5e-14 prerequisites: ! | atom full fix adapt From e01e0298cb9587cac513face286643ff1e7d6b07 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 6 Apr 2021 13:25:24 -0400 Subject: [PATCH 0404/1217] fix uninitialized data access after restart bug in USER-YAFF pair styles also fix some source formatting issues --- src/KSPACE/pair_lj_cut_coul_long.cpp | 16 +++++++------- .../pair_lj_switch3_coulgauss_long.cpp | 22 ++++++++++--------- .../pair_mm3_switch3_coulgauss_long.cpp | 20 +++++++++-------- 3 files changed, 31 insertions(+), 27 deletions(-) diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index fcb39b8c6e..5d04fd1cfb 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -17,21 +17,21 @@ #include "pair_lj_cut_coul_long.h" -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "respa.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index 6e4c0587f7..2247a9467c 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -106,6 +106,7 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag) firstneigh = list->firstneigh; // loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { i = ilist[ii]; qtmp = q[i]; @@ -193,7 +194,7 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag) offset[itype][jtype]; } else evdwl = 0.0; - // Truncation, see Yaff Switch33 + // Truncation, see Yaff Switch3 if (truncw>0) { if (rsq < cut_ljsq[itype][jtype]) { if (r>cut_lj[itype][jtype]-truncw) { @@ -262,19 +263,18 @@ void PairLJSwitch3CoulGaussLong::allocate() void PairLJSwitch3CoulGaussLong::settings(int narg, char **arg) { - if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command"); + if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command"); cut_lj_global = utils::numeric(FLERR,arg[0],false,lmp); + if (narg == 2) { cut_coul = cut_lj_global; truncw = utils::numeric(FLERR,arg[1],false,lmp); - } - else { + } else { cut_coul = utils::numeric(FLERR,arg[1],false,lmp); truncw = utils::numeric(FLERR,arg[2],false,lmp); } - if (truncw>0.0) truncwi = 1.0/truncw; - else truncwi = 0.0; + // reset cutoffs that have been explicitly set if (allocated) { @@ -332,6 +332,9 @@ void PairLJSwitch3CoulGaussLong::init_style() cut_coulsq = cut_coul * cut_coul; + if (truncw>0.0) truncwi = 1.0/truncw; + else truncwi = 0.0; + // insure use of KSpace long-range solver, set g_ewald if (force->kspace == nullptr) @@ -375,8 +378,7 @@ double PairLJSwitch3CoulGaussLong::init_one(int i, int j) double r6inv = r2inv*r2inv*r2inv; double r12inv = r6inv*r6inv; offset[i][j] = lj3[i][j]*r12inv-lj4[i][j]*r6inv; - } - else {offset[i][j] = 0.0;} + } else {offset[i][j] = 0.0;} } else offset[i][j] = 0.0; cut_ljsq[j][i] = cut_ljsq[i][j]; @@ -431,8 +433,7 @@ double PairLJSwitch3CoulGaussLong::init_one(int i, int j) double t71 = -0.4e1 * cg * (0.2e1 * t10 * t11 - 0.2e1 * t10 * t14 + (cg5 - 0.2e1 * cg1) * t58 * cg5) * t26 / t4 / t41 / t9; etail_ij = 2.0*MY_PI*all[0]*all[1]*t71; ptail_ij = 2.0*MY_PI*all[0]*all[1]*t71; - } - else { + } else { double t1 = pow(cg3, 0.2e1); double t2 = t1 * t1; double t3 = t2 * t1; @@ -618,6 +619,7 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype, expn2 = 0.0; erfc2 = 0.0; forcecoul2 = 0.0; + prefactor2 = 0.0; } else { r = sqrt(rsq); rrij = lj2[itype][jtype]*r; diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp index 67a322ca24..c7fcac855a 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -106,6 +106,7 @@ void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag) firstneigh = list->firstneigh; // loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { i = ilist[ii]; qtmp = q[i]; @@ -170,6 +171,7 @@ void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag) expn2 = 0.0; erfc2 = 0.0; forcecoul2 = 0.0; + prefactor2 = 0.0; } else { rrij = lj2[itype][jtype]*r; expn2 = exp(-rrij*rrij); @@ -263,19 +265,18 @@ void PairMM3Switch3CoulGaussLong::allocate() void PairMM3Switch3CoulGaussLong::settings(int narg, char **arg) { - if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command"); + if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command"); cut_lj_global = utils::numeric(FLERR,arg[0],false,lmp); + if (narg == 2) { cut_coul = cut_lj_global; truncw = utils::numeric(FLERR,arg[1],false,lmp); - } - else { + } else { cut_coul = utils::numeric(FLERR,arg[1],false,lmp); truncw = utils::numeric(FLERR,arg[2],false,lmp); } - if (truncw>0.0) truncwi = 1.0/truncw; - else truncwi = 0.0; + // reset cutoffs that have been explicitly set if (allocated) { @@ -333,6 +334,9 @@ void PairMM3Switch3CoulGaussLong::init_style() cut_coulsq = cut_coul * cut_coul; + if (truncw>0.0) truncwi = 1.0/truncw; + else truncwi = 0.0; + // insure use of KSpace long-range solver, set g_ewald if (force->kspace == nullptr) @@ -375,8 +379,7 @@ double PairMM3Switch3CoulGaussLong::init_one(int i, int j) double r6inv = r2inv*r2inv*r2inv; double expb = lj3[i][j]*exp(-lj1[i][j]*r); offset[i][j] = expb-lj4[i][j]*r6inv; - } - else {offset[i][j] = 0.0;} + } else {offset[i][j] = 0.0;} } else offset[i][j] = 0.0; cut_ljsq[j][i] = cut_ljsq[i][j]; @@ -426,8 +429,7 @@ double PairMM3Switch3CoulGaussLong::init_one(int i, int j) double t64 = cg * (0.6388888889e3 * ((-t3 + (0.7e1 / 0.36e2 * cg5 - t5) * t1 - 0.2e1 / 0.3e1 * t8 * (cg5 - cg1 / 0.4e1) * cg3 + cg5 * t14) * t20 + t3 + (cg5 / 0.12e2 + t5) * t1 + (cg5 + cg1 / 0.3e1) * cg1 * cg3 / 0.2e1 + t30 * cg5) * t2 * t36 * t39 - 0.225e1 * (0.2e1 * t43 * t44 - 0.2e1 * t43 * t47 + cg5 * (cg5 - 0.2e1 * cg1)) * t54 * t1 / cg1 / t8 * t39); etail_ij = 2.0*MY_PI*all[0]*all[1]*t64; ptail_ij = 2.0*MY_PI*all[0]*all[1]*t64; - } - else { + } else { double t2 = pow(cg3, 0.2e1); double t3 = t2 * t2; double t7 = 0.12e2 / cg3 * cg1; From 698b9b9519000b8976084714a977a6ce25a880d3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 6 Apr 2021 13:36:27 -0400 Subject: [PATCH 0405/1217] relax epsilon some more --- unittest/force-styles/tests/fix-timestep-adapt_coul.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml b/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml index cd7f9aa87d..f0ec2f1292 100644 --- a/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml +++ b/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Mar 2021 date_generated: Thu Mar 25 14:07:45 202 -epsilon: 7.5e-14 +epsilon: 5e-13 prerequisites: ! | atom full fix adapt From e5a665c1d97f48041e8be7760dcfe53aae509233 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 6 Apr 2021 14:45:07 -0400 Subject: [PATCH 0406/1217] Add utilities for Python code --- src/PYTHON/python_utils.h | 42 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 src/PYTHON/python_utils.h diff --git a/src/PYTHON/python_utils.h b/src/PYTHON/python_utils.h new file mode 100644 index 0000000000..82422916ff --- /dev/null +++ b/src/PYTHON/python_utils.h @@ -0,0 +1,42 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_PYTHON_UTILS_H +#define LMP_PYTHON_UTILS_H + +#include + +namespace LAMMPS_NS { + +namespace PyUtils { + +class GIL { + PyGILState_STATE gstate; +public: + GIL() : gstate(PyGILState_Ensure()) { + } + ~GIL() { + PyGILState_Release(gstate); + } +}; + +static void Print_Errors() { + PyErr_Print(); + PyErr_Clear(); +} + +} + +} + +#endif From da5bd578ad826a6f83542251e3f9bd61d552afd9 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 6 Apr 2021 14:46:35 -0400 Subject: [PATCH 0407/1217] Simplify python_impl.cpp --- src/PYTHON/python_impl.cpp | 62 ++++++++++++++------------------------ 1 file changed, 22 insertions(+), 40 deletions(-) diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index c83385410a..7e46da4c49 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -21,6 +21,7 @@ #include "input.h" #include "memory.h" #include "python_compat.h" +#include "python_utils.h" #include "variable.h" #include @@ -91,13 +92,12 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp) } #endif - PyGILState_STATE gstate = PyGILState_Ensure(); + PyUtils::GIL lock; PyObject *pModule = PyImport_AddModule("__main__"); if (!pModule) error->all(FLERR,"Could not initialize embedded Python"); pyMain = (void *) pModule; - PyGILState_Release(gstate); } /* ---------------------------------------------------------------------- */ @@ -106,23 +106,19 @@ PythonImpl::~PythonImpl() { if (pyMain) { // clean up - PyGILState_STATE gstate = PyGILState_Ensure(); + PyUtils::GIL lock; for (int i = 0; i < nfunc; i++) { delete [] pfuncs[i].name; deallocate(i); - PyObject *pFunc = (PyObject *) pfuncs[i].pFunc; - Py_XDECREF(pFunc); + Py_CLEAR(pfuncs[i].pFunc); } + } - // shutdown Python interpreter - - if (!external_interpreter) { - Py_Finalize(); - } - else { - PyGILState_Release(gstate); - } + // shutdown Python interpreter + if (!external_interpreter) { + PyGILState_STATE gstate = PyGILState_Ensure(); + Py_Finalize(); } memory->sfree(pfuncs); @@ -228,7 +224,7 @@ void PythonImpl::command(int narg, char **arg) int ifunc = create_entry(arg[0]); - PyGILState_STATE gstate = PyGILState_Ensure(); + PyUtils::GIL lock; // send Python code to Python interpreter // file: read the file via PyRun_SimpleFile() @@ -239,14 +235,14 @@ void PythonImpl::command(int narg, char **arg) FILE *fp = fopen(pyfile,"r"); if (fp == nullptr) { - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Could not open Python file"); } int err = PyRun_SimpleFile(fp,pyfile); if (err) { - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Could not process Python file"); } @@ -255,7 +251,7 @@ void PythonImpl::command(int narg, char **arg) int err = PyRun_SimpleString(herestr); if (err) { - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Could not process Python string"); } } @@ -266,13 +262,13 @@ void PythonImpl::command(int narg, char **arg) PyObject *pFunc = PyObject_GetAttrString(pModule,pfuncs[ifunc].name); if (!pFunc) { - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,fmt::format("Could not find Python function {}", pfuncs[ifunc].name)); } if (!PyCallable_Check(pFunc)) { - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,fmt::format("Python function {} is not callable", pfuncs[ifunc].name)); } @@ -284,14 +280,13 @@ void PythonImpl::command(int narg, char **arg) delete [] istr; delete [] format; delete [] pyfile; - PyGILState_Release(gstate); } /* ------------------------------------------------------------------ */ void PythonImpl::invoke_function(int ifunc, char *result) { - PyGILState_STATE gstate = PyGILState_Ensure(); + PyUtils::GIL lock; PyObject *pValue; char *str; @@ -303,7 +298,6 @@ void PythonImpl::invoke_function(int ifunc, char *result) PyObject *pArgs = PyTuple_New(ninput); if (!pArgs) { - PyGILState_Release(gstate); error->all(FLERR,"Could not create Python function arguments"); } @@ -314,7 +308,6 @@ void PythonImpl::invoke_function(int ifunc, char *result) str = input->variable->retrieve(pfuncs[ifunc].svalue[i]); if (!str) { - PyGILState_Release(gstate); error->all(FLERR,"Could not evaluate Python function input variable"); } @@ -327,7 +320,6 @@ void PythonImpl::invoke_function(int ifunc, char *result) str = input->variable->retrieve(pfuncs[ifunc].svalue[i]); if (!str) { - PyGILState_Release(gstate); error->all(FLERR,"Could not evaluate Python function input variable"); } @@ -339,7 +331,6 @@ void PythonImpl::invoke_function(int ifunc, char *result) if (pfuncs[ifunc].ivarflag[i]) { str = input->variable->retrieve(pfuncs[ifunc].svalue[i]); if (!str) { - PyGILState_Release(gstate); error->all(FLERR,"Could not evaluate Python function input variable"); } @@ -350,7 +341,6 @@ void PythonImpl::invoke_function(int ifunc, char *result) } else if (itype == PTR) { pValue = PY_VOID_POINTER(lmp); } else { - PyGILState_Release(gstate); error->all(FLERR,"Unsupported variable type"); } PyTuple_SetItem(pArgs,i,pValue); @@ -360,15 +350,13 @@ void PythonImpl::invoke_function(int ifunc, char *result) // error check with one() since only some procs may fail pValue = PyObject_CallObject(pFunc,pArgs); + Py_CLEAR(pArgs); if (!pValue) { - PyErr_Print(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->one(FLERR,"Python function evaluation failed"); } - Py_DECREF(pArgs); - // function returned a value // assign it to result string stored by python-style variable // or if user specified a length, assign it to longstr @@ -385,10 +373,8 @@ void PythonImpl::invoke_function(int ifunc, char *result) strncpy(pfuncs[ifunc].longstr,pystr,pfuncs[ifunc].length_longstr); else strncpy(result,pystr,VALUELENGTH-1); } - Py_DECREF(pValue); } - - PyGILState_Release(gstate); + Py_CLEAR(pValue); } /* ------------------------------------------------------------------ */ @@ -523,11 +509,8 @@ int PythonImpl::create_entry(char *name) int PythonImpl::execute_string(char *cmd) { - PyGILState_STATE gstate = PyGILState_Ensure(); - int err = PyRun_SimpleString(cmd); - PyGILState_Release(gstate); - - return err; + PyUtils::GIL lock; + return PyRun_SimpleString(cmd); } /* ---------------------------------------------------------------------- */ @@ -537,9 +520,8 @@ int PythonImpl::execute_file(char *fname) FILE *fp = fopen(fname,"r"); if (fp == nullptr) return -1; - PyGILState_STATE gstate = PyGILState_Ensure(); + PyUtils::GIL lock; int err = PyRun_SimpleFile(fp,fname); - PyGILState_Release(gstate); if (fp) fclose(fp); return err; From 5ee24c5b8994bd12555e40f3a9717c1d6d0cd96c Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 6 Apr 2021 14:47:20 -0400 Subject: [PATCH 0408/1217] Update fix_python_invoke --- src/PYTHON/fix_python_invoke.cpp | 49 ++++++++++++++++++-------------- src/PYTHON/fix_python_invoke.h | 4 ++- 2 files changed, 30 insertions(+), 23 deletions(-) diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 23c4197dca..6483e21f91 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -21,6 +21,7 @@ #include "error.h" #include "lmppython.h" #include "python_compat.h" +#include "python_utils.h" #include "update.h" #include @@ -51,12 +52,12 @@ FixPythonInvoke::FixPythonInvoke(LAMMPS *lmp, int narg, char **arg) : } // get Python function - PyGILState_STATE gstate = PyGILState_Ensure(); + PyUtils::GIL lock; PyObject *pyMain = PyImport_AddModule("__main__"); if (!pyMain) { - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Could not initialize embedded Python"); } @@ -64,11 +65,19 @@ FixPythonInvoke::FixPythonInvoke(LAMMPS *lmp, int narg, char **arg) : pFunc = PyObject_GetAttrString(pyMain, fname); if (!pFunc) { - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Could not find Python function"); } - PyGILState_Release(gstate); + lmpPtr = PY_VOID_POINTER(lmp); +} + +/* ---------------------------------------------------------------------- */ + +FixPythonInvoke::~FixPythonInvoke() +{ + PyUtils::GIL lock; + Py_CLEAR(lmpPtr); } /* ---------------------------------------------------------------------- */ @@ -82,18 +91,16 @@ int FixPythonInvoke::setmask() void FixPythonInvoke::end_of_step() { - PyGILState_STATE gstate = PyGILState_Ensure(); + PyUtils::GIL lock; - PyObject *ptr = PY_VOID_POINTER(lmp); - PyObject *arglist = Py_BuildValue("(O)", ptr); + PyObject * result = PyObject_CallFunction((PyObject*)pFunc, "O", (PyObject*)lmpPtr); - PyObject *result = PyEval_CallObject((PyObject*)pFunc, arglist); - Py_DECREF(arglist); - if (!result && (comm->me == 0)) PyErr_Print(); - - PyGILState_Release(gstate); - if (!result) + if (!result) { + PyUtils::Print_Errors(); error->all(FLERR,"Fix python/invoke end_of_step() method failed"); + } + + Py_CLEAR(result); } /* ---------------------------------------------------------------------- */ @@ -102,16 +109,14 @@ void FixPythonInvoke::post_force(int vflag) { if (update->ntimestep % nevery != 0) return; - PyGILState_STATE gstate = PyGILState_Ensure(); + PyUtils::GIL lock; - PyObject *ptr = PY_VOID_POINTER(lmp); - PyObject *arglist = Py_BuildValue("(Oi)", ptr, vflag); + PyObject * result = PyObject_CallFunction((PyObject*)pFunc, "Oi", (PyObject*)lmpPtr, vflag); - PyObject *result = PyEval_CallObject((PyObject*)pFunc, arglist); - Py_DECREF(arglist); - if (!result && (comm->me == 0)) PyErr_Print(); - - PyGILState_Release(gstate); - if (!result) + if (!result) { + PyUtils::Print_Errors(); error->all(FLERR,"Fix python/invoke post_force() method failed"); + } + + Py_CLEAR(result); } diff --git a/src/PYTHON/fix_python_invoke.h b/src/PYTHON/fix_python_invoke.h index 89310eeded..48fb0b404f 100644 --- a/src/PYTHON/fix_python_invoke.h +++ b/src/PYTHON/fix_python_invoke.h @@ -21,6 +21,7 @@ FixStyle(python,FixPythonInvoke) #ifndef LMP_FIX_PYTHON_INVOKE_H #define LMP_FIX_PYTHON_INVOKE_H + #include "fix.h" namespace LAMMPS_NS { @@ -28,12 +29,13 @@ namespace LAMMPS_NS { class FixPythonInvoke : public Fix { public: FixPythonInvoke(class LAMMPS *, int, char **); - virtual ~FixPythonInvoke() {} + virtual ~FixPythonInvoke(); int setmask(); virtual void end_of_step(); virtual void post_force(int); private: + void * lmpPtr; void * pFunc; int selected_callback; }; From 7e9fa25121a4f1e5ed1c2a25f0e8486c9c1d8076 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 6 Apr 2021 14:48:44 -0400 Subject: [PATCH 0409/1217] Update fix_python_move.cpp --- src/PYTHON/fix_python_move.cpp | 177 +++++++++++---------------------- 1 file changed, 59 insertions(+), 118 deletions(-) diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index 5425b78193..e04a32afe4 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -21,8 +21,9 @@ #include "error.h" #include "lmppython.h" #include "python_compat.h" +#include "python_utils.h" -#include +#include #include // IWYU pragma: export using namespace LAMMPS_NS; @@ -40,7 +41,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) : py_move = nullptr; - PyGILState_STATE gstate = PyGILState_Ensure(); + PyUtils::GIL lock; // add current directory to PYTHONPATH PyObject *py_path = PySys_GetObject((char *)"path"); @@ -48,70 +49,50 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) : // create integrator instance - char *full_cls_name = arg[3]; - char *lastpos = strrchr(full_cls_name, '.'); + std::string full_cls_name = arg[3]; + size_t lastpos = full_cls_name.rfind("."); - if (lastpos == nullptr) { + if (lastpos == std::string::npos) { error->all(FLERR,"Fix python/integrate requires fully qualified class name"); } - size_t module_name_length = strlen(full_cls_name) - strlen(lastpos); - size_t cls_name_length = strlen(lastpos)-1; + std::string module_name = full_cls_name.substr(0, lastpos); + std::string cls_name = full_cls_name.substr(lastpos+1); - char *module_name = new char[module_name_length+1]; - char *cls_name = new char[cls_name_length+1]; - strncpy(module_name, full_cls_name, module_name_length); - module_name[module_name_length] = 0; - - strcpy(cls_name, lastpos+1); - - PyObject *pModule = PyImport_ImportModule(module_name); + PyObject *pModule = PyImport_ImportModule(module_name.c_str()); if (!pModule) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Loading python integrator module failure"); } // create LAMMPS atom type to potential file type mapping in python class // by calling 'lammps_pair_style.map_coeff(name,type)' - PyObject *py_move_type = PyObject_GetAttrString(pModule, cls_name); + PyObject *py_move_type = PyObject_GetAttrString(pModule, cls_name.c_str()); if (!py_move_type) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Could not find integrator class in module'"); } - delete [] module_name; - delete [] cls_name; - PyObject *ptr = PY_VOID_POINTER(lmp); - PyObject *arglist = Py_BuildValue("(O)", ptr); - PyObject *py_move_obj = PyObject_CallObject(py_move_type, arglist); - Py_DECREF(arglist); + PyObject *py_move_obj = PyObject_CallFunction(py_move_type, "O", ptr); + Py_CLEAR(ptr); if (!py_move_obj) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Could not instantiate instance of integrator class'"); } // check object interface py_move = (void *) py_move_obj; - - PyGILState_Release(gstate); } /* ---------------------------------------------------------------------- */ FixPythonMove::~FixPythonMove() { - PyGILState_STATE gstate = PyGILState_Ensure(); - if (py_move) Py_DECREF((PyObject*) py_move); - PyGILState_Release(gstate); + PyUtils::GIL lock; + Py_CLEAR(py_move); } /* ---------------------------------------------------------------------- */ @@ -130,122 +111,82 @@ int FixPythonMove::setmask() void FixPythonMove::init() { - PyGILState_STATE gstate = PyGILState_Ensure(); - PyObject *py_move_obj = (PyObject *) py_move; - PyObject *py_init = PyObject_GetAttrString(py_move_obj,(char *)"init"); - if (!py_init) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Could not find 'init()' method'"); + PyUtils::GIL lock; + PyObject * result = PyObject_CallMethod((PyObject *)py_move, "init", nullptr); + + if (!result) { + PyUtils::Print_Errors(); + error->all(FLERR,"Fix python/move init() method failed"); } - PyObject *result = PyEval_CallObject(py_init, nullptr); - if (!result && (comm->me == 0)) PyErr_Print(); - PyGILState_Release(gstate); - if (!result) error->all(FLERR,"Fix python/move init() method failed"); + Py_CLEAR(result); } /* ---------------------------------------------------------------------- */ void FixPythonMove::initial_integrate(int vflag) { - PyGILState_STATE gstate = PyGILState_Ensure(); - PyObject *py_move_obj = (PyObject *) py_move; - PyObject *py_initial_integrate = PyObject_GetAttrString(py_move_obj,"initial_integrate"); - if (!py_initial_integrate) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Could not find 'initial_integrate' method'"); + PyUtils::GIL lock; + PyObject * result = PyObject_CallMethod((PyObject*)py_move, "initial_integrate", "i", vflag); + + if (!result) { + PyUtils::Print_Errors(); + error->all(FLERR,"Fix python/move initial_integrate() method failed"); } - PyObject *arglist = Py_BuildValue("(i)", vflag); - PyObject *result = PyEval_CallObject(py_initial_integrate, arglist); - Py_DECREF(arglist); - if (!result && (comm->me == 0)) PyErr_Print(); - PyGILState_Release(gstate); - if (!result) error->all(FLERR,"Fix python/move initial_integrate() " - "method failed"); + Py_CLEAR(result); } /* ---------------------------------------------------------------------- */ void FixPythonMove::final_integrate() { - PyGILState_STATE gstate = PyGILState_Ensure(); - PyObject *py_move_obj = (PyObject *) py_move; - PyObject *py_final_integrate = PyObject_GetAttrString(py_move_obj,"final_integrate"); - if (!py_final_integrate) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Could not find 'final_integrate' method'"); + PyUtils::GIL lock; + PyObject * result = PyObject_CallMethod((PyObject*)py_move, "final_integrate", nullptr); + + if (!result) { + PyUtils::Print_Errors(); + error->all(FLERR,"Fix python/move final_integrate() method failed"); } - PyObject *result = PyEval_CallObject(py_final_integrate, nullptr); - if (!result && (comm->me == 0)) PyErr_Print(); - PyGILState_Release(gstate); - if (!result) error->all(FLERR,"Fix python/move final_integrate() method " - "failed"); + Py_CLEAR(result); } /* ---------------------------------------------------------------------- */ void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop) { - PyGILState_STATE gstate = PyGILState_Ensure(); - PyObject *py_move_obj = (PyObject *) py_move; - PyObject *py_initial_integrate_respa = PyObject_GetAttrString(py_move_obj,"initial_integrate_respa"); - if (!py_initial_integrate_respa) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Could not find 'initial_integrate_respa' method'"); + PyUtils::GIL lock; + PyObject * result = PyObject_CallMethod((PyObject*)py_move, "initial_integrate_respa", "iii", vflag, ilevel, iloop); + + if (!result) { + PyUtils::Print_Errors(); + error->all(FLERR,"Fix python/move initial_integrate_respa() method failed"); } - PyObject *arglist = Py_BuildValue("(iii)", vflag, ilevel, iloop); - PyObject *result = PyEval_CallObject(py_initial_integrate_respa, arglist); - Py_DECREF(arglist); - if (!result && (comm->me == 0)) PyErr_Print(); - PyGILState_Release(gstate); - if (!result) error->all(FLERR,"Fix python/move initial_integrate_respa() " - "method failed"); + Py_CLEAR(result); } /* ---------------------------------------------------------------------- */ void FixPythonMove::final_integrate_respa(int ilevel, int iloop) { - PyGILState_STATE gstate = PyGILState_Ensure(); - PyObject *py_move_obj = (PyObject *) py_move; - PyObject *py_final_integrate_respa = PyObject_GetAttrString(py_move_obj,"final_integrate_respa"); - if (!py_final_integrate_respa) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Could not find 'final_integrate_respa' method'"); + PyUtils::GIL lock; + PyObject * result = PyObject_CallMethod((PyObject*)py_move, "final_integrate_respa", "ii", ilevel, iloop); + + if (!result) { + PyUtils::Print_Errors(); + error->all(FLERR,"Fix python/move final_integrate_respa() method failed"); } - PyObject *arglist = Py_BuildValue("(ii)", ilevel, iloop); - PyObject *result = PyEval_CallObject(py_final_integrate_respa, arglist); - Py_DECREF(arglist); - if (!result && (comm->me == 0)) PyErr_Print(); - PyGILState_Release(gstate); - if (!result) error->all(FLERR,"Fix python/move final_integrate_respa() " - "method failed"); + Py_CLEAR(result); } /* ---------------------------------------------------------------------- */ void FixPythonMove::reset_dt() { - PyGILState_STATE gstate = PyGILState_Ensure(); - PyObject *py_move_obj = (PyObject *) py_move; - PyObject *py_reset_dt = PyObject_GetAttrString(py_move_obj,"reset_dt"); - if (!py_reset_dt) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Could not find 'reset_dt' method'"); + PyUtils::GIL lock; + PyObject * result = PyObject_CallMethod((PyObject*)py_move, "reset_dt", nullptr); + + if (!result) { + PyUtils::Print_Errors(); + error->all(FLERR,"Fix python/move reset_dt() method failed"); } - PyObject *result = PyEval_CallObject(py_reset_dt, nullptr); - if (!result && (comm->me == 0)) PyErr_Print(); - PyGILState_Release(gstate); - if (!result) error->all(FLERR,"Fix python/move reset_dt() method failed"); + Py_CLEAR(result); } From 0aa9aa96f69e8e9fbdb5384827f52acd99df91f4 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 6 Apr 2021 14:50:08 -0400 Subject: [PATCH 0410/1217] Update pair_python --- src/PYTHON/pair_python.cpp | 237 +++++++++++-------------------------- src/PYTHON/pair_python.h | 1 + 2 files changed, 70 insertions(+), 168 deletions(-) diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index b5d6021e1e..f3a16612b6 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -24,9 +24,10 @@ #include "memory.h" #include "neigh_list.h" #include "python_compat.h" +#include "python_utils.h" #include "update.h" -#include +#include #include // IWYU pragma: export using namespace LAMMPS_NS; @@ -50,7 +51,7 @@ PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) { // add current directory to PYTHONPATH - PyGILState_STATE gstate = PyGILState_Ensure(); + PyUtils::GIL lock; PyObject *py_path = PySys_GetObject((char *)"path"); PyList_Append(py_path, PY_STRING_FROM_STRING(".")); @@ -61,14 +62,14 @@ PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) { if (potentials_path != nullptr) { PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path)); } - PyGILState_Release(gstate); } /* ---------------------------------------------------------------------- */ PairPython::~PairPython() { - if (py_potential) Py_DECREF((PyObject*) py_potential); + PyUtils::GIL lock; + Py_CLEAR(py_potential); delete[] skip_types; if (allocated) { @@ -103,41 +104,31 @@ void PairPython::compute(int eflag, int vflag) // prepare access to compute_force and compute_energy functions - PyGILState_STATE gstate = PyGILState_Ensure(); + PyUtils::GIL lock; PyObject *py_pair_instance = (PyObject *) py_potential; PyObject *py_compute_force = PyObject_GetAttrString(py_pair_instance,"compute_force"); if (!py_compute_force) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Could not find 'compute_force' method'"); } if (!PyCallable_Check(py_compute_force)) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Python 'compute_force' is not callable"); } PyObject *py_compute_energy = PyObject_GetAttrString(py_pair_instance,"compute_energy"); if (!py_compute_energy) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Could not find 'compute_energy' method'"); } if (!PyCallable_Check(py_compute_energy)) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Python 'compute_energy' is not callable"); } PyObject *py_compute_args = PyTuple_New(3); if (!py_compute_args) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Could not create tuple for 'compute' function arguments"); } @@ -179,13 +170,11 @@ void PairPython::compute(int eflag, int vflag) PyTuple_SetItem(py_compute_args,0,py_rsq); py_value = PyObject_CallObject(py_compute_force,py_compute_args); if (!py_value) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Calling 'compute_force' function failed"); } fpair = factor_lj*PyFloat_AsDouble(py_value); - Py_DECREF(py_value); + Py_CLEAR(py_value); f[i][0] += delx*fpair; f[i][1] += dely*fpair; @@ -198,8 +187,12 @@ void PairPython::compute(int eflag, int vflag) if (eflag) { py_value = PyObject_CallObject(py_compute_energy,py_compute_args); + if (!py_value) { + PyUtils::Print_Errors(); + error->all(FLERR,"Calling 'compute_energy' function failed"); + } evdwl = factor_lj*PyFloat_AsDouble(py_value); - Py_DECREF(py_value); + Py_CLEAR(py_value); } else evdwl = 0.0; if (evflag) ev_tally(i,j,nlocal,newton_pair, @@ -207,8 +200,7 @@ void PairPython::compute(int eflag, int vflag) } } } - Py_DECREF(py_compute_args); - PyGILState_Release(gstate); + Py_CLEAR(py_compute_args); if (vflag_fdotr) virial_fdotr_compute(); } @@ -261,112 +253,49 @@ void PairPython::coeff(int narg, char **arg) error->all(FLERR,"Incorrect args for pair coefficients"); // check if python potential file exists and source it - char * full_cls_name = arg[2]; - char * lastpos = strrchr(full_cls_name, '.'); + std::string full_cls_name = arg[2]; + size_t lastpos = full_cls_name.rfind("."); - if (lastpos == nullptr) { + if (lastpos == std::string::npos) { error->all(FLERR,"Python pair style requires fully qualified class name"); } - size_t module_name_length = strlen(full_cls_name) - strlen(lastpos); - size_t cls_name_length = strlen(lastpos)-1; + std::string module_name = full_cls_name.substr(0, lastpos); + std::string cls_name = full_cls_name.substr(lastpos+1); - char * module_name = new char[module_name_length+1]; - char * cls_name = new char[cls_name_length+1]; - strncpy(module_name, full_cls_name, module_name_length); - module_name[module_name_length] = 0; + PyUtils::GIL lock; - strcpy(cls_name, lastpos+1); - - PyGILState_STATE gstate = PyGILState_Ensure(); - - PyObject * pModule = PyImport_ImportModule(module_name); + PyObject * pModule = PyImport_ImportModule(module_name.c_str()); if (!pModule) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Loading python pair style module failure"); } // create LAMMPS atom type to potential file type mapping in python class // by calling 'lammps_pair_style.map_coeff(name,type)' - PyObject *py_pair_type = PyObject_GetAttrString(pModule, cls_name); + PyObject *py_pair_type = PyObject_GetAttrString(pModule, cls_name.c_str()); if (!py_pair_type) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Could not find pair style class in module'"); } - delete [] module_name; - delete [] cls_name; - PyObject * py_pair_instance = PyObject_CallObject(py_pair_type, nullptr); if (!py_pair_instance) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Could not instantiate instance of pair style class'"); } py_potential = (void *) py_pair_instance; - PyObject *py_check_units = PyObject_GetAttrString(py_pair_instance,"check_units"); - if (!py_check_units) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Could not find 'check_units' method'"); - } - if (!PyCallable_Check(py_check_units)) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Python 'check_units' is not callable"); - } - PyObject *py_units_args = PyTuple_New(1); - if (!py_units_args) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Could not create tuple for 'check_units' function arguments"); - } - - PyObject *py_name = PY_STRING_FROM_STRING(update->unit_style); - PyTuple_SetItem(py_units_args,0,py_name); - PyObject *py_value = PyObject_CallObject(py_check_units,py_units_args); + PyObject *py_value = PyObject_CallMethod(py_pair_instance, "check_units", "s", update->unit_style); if (!py_value) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Calling 'check_units' function failed"); } - Py_DECREF(py_units_args); + Py_CLEAR(py_value); - PyObject *py_map_coeff = PyObject_GetAttrString(py_pair_instance,"map_coeff"); - if (!py_map_coeff) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Could not find 'map_coeff' method'"); - } - if (!PyCallable_Check(py_map_coeff)) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Python 'map_coeff' is not callable"); - } - - PyObject *py_map_args = PyTuple_New(2); - if (!py_map_args) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Could not create tuple for 'map_coeff' function arguments"); - } - delete[] skip_types; skip_types = new int[ntypes+1]; skip_types[0] = 1; @@ -375,25 +304,20 @@ void PairPython::coeff(int narg, char **arg) skip_types[i] = 1; continue; } else skip_types[i] = 0; - PyObject *py_type = PY_INT_FROM_LONG(i); - py_name = PY_STRING_FROM_STRING(arg[2+i]); - PyTuple_SetItem(py_map_args,0,py_name); - PyTuple_SetItem(py_map_args,1,py_type); - py_value = PyObject_CallObject(py_map_coeff,py_map_args); + const int type = i; + const char * name = arg[2+i]; + py_value = PyObject_CallMethod(py_pair_instance, "map_coeff", "si", name, type); if (!py_value) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Calling 'map_coeff' function failed"); } + Py_CLEAR(py_value); for (int j = i; j <= ntypes ; j++) { setflag[i][j] = 1; cutsq[i][j] = cut_global*cut_global; } } - Py_DECREF(py_map_args); - PyGILState_Release(gstate); } /* ---------------------------------------------------------------------- */ @@ -417,76 +341,53 @@ double PairPython::single(int /* i */, int /* j */, int itype, int jtype, // prepare access to compute_force and compute_energy functions - PyGILState_STATE gstate = PyGILState_Ensure(); + PyUtils::GIL lock; PyObject *py_pair_instance = (PyObject *) py_potential; - PyObject *py_compute_force - = PyObject_GetAttrString(py_pair_instance,"compute_force"); - if (!py_compute_force) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Could not find 'compute_force' method'"); - } - if (!PyCallable_Check(py_compute_force)) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Python 'compute_force' is not callable"); - } + PyObject *py_compute_force = (PyObject *) get_member_function("compute_force"); + PyObject *py_compute_energy = (PyObject *) get_member_function("compute_energy"); + PyObject *py_compute_args = Py_BuildValue("(dii)", rsq, itype, jtype); - PyObject *py_compute_energy - = PyObject_GetAttrString(py_pair_instance,"compute_energy"); - if (!py_compute_energy) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Could not find 'compute_energy' method'"); - } - if (!PyCallable_Check(py_compute_energy)) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); - error->all(FLERR,"Python 'compute_energy' is not callable"); - } - - PyObject *py_rsq, *py_itype, *py_jtype, *py_value; - PyObject *py_compute_args = PyTuple_New(3); if (!py_compute_args) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Could not create tuple for 'compute' function arguments"); } - py_itype = PY_INT_FROM_LONG(itype); - PyTuple_SetItem(py_compute_args,1,py_itype); - py_jtype = PY_INT_FROM_LONG(jtype); - PyTuple_SetItem(py_compute_args,2,py_jtype); - py_rsq = PyFloat_FromDouble(rsq); - PyTuple_SetItem(py_compute_args,0,py_rsq); - - py_value = PyObject_CallObject(py_compute_force,py_compute_args); + PyObject * py_value = PyObject_CallObject(py_compute_force, py_compute_args); if (!py_value) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Calling 'compute_force' function failed"); } fforce = factor_lj*PyFloat_AsDouble(py_value); - Py_DECREF(py_value); + Py_CLEAR(py_value); - py_value = PyObject_CallObject(py_compute_energy,py_compute_args); + py_value = PyObject_CallObject(py_compute_energy, py_compute_args); if (!py_value) { - PyErr_Print(); - PyErr_Clear(); - PyGILState_Release(gstate); + PyUtils::Print_Errors(); error->all(FLERR,"Calling 'compute_energy' function failed"); } double evdwl = factor_lj*PyFloat_AsDouble(py_value); - Py_DECREF(py_value); - Py_DECREF(py_compute_args); - PyGILState_Release(gstate); + Py_CLEAR(py_value); + Py_CLEAR(py_compute_args); return evdwl; } + + +/* ---------------------------------------------------------------------- */ + +void * PairPython::get_member_function(const char * name) +{ + PyUtils::GIL lock; + PyObject *py_pair_instance = (PyObject *) py_potential; + PyObject * py_mfunc = PyObject_GetAttrString(py_pair_instance, name); + if (!py_mfunc) { + PyUtils::Print_Errors(); + error->all(FLERR, fmt::format("Could not find '{}' method'", name)); + } + if (!PyCallable_Check(py_mfunc)) { + PyUtils::Print_Errors(); + error->all(FLERR, fmt::format("Python '{}' is not callable", name)); + } + return py_mfunc; +} diff --git a/src/PYTHON/pair_python.h b/src/PYTHON/pair_python.h index 4c3c00a70d..881bfe2835 100644 --- a/src/PYTHON/pair_python.h +++ b/src/PYTHON/pair_python.h @@ -50,6 +50,7 @@ class PairPython : public Pair { int * skip_types; virtual void allocate(); + void * get_member_function(const char *); }; } From 80a65150c22c186e230cb7d2902f2951065dc83a Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 6 Apr 2021 13:08:48 -0600 Subject: [PATCH 0411/1217] Patching uninitialized values, replacing lines in documentation --- doc/src/fix_wall_gran.rst | 2 + src/GRANULAR/fix_wall_gran.cpp | 76 ++++++++++++------------ src/GRANULAR/pair_gran_hertz_history.cpp | 8 ++- src/GRANULAR/pair_granular.cpp | 2 +- 4 files changed, 49 insertions(+), 39 deletions(-) diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index 02d52ef1a6..95a4b5d818 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -177,6 +177,8 @@ the clockwise direction for *vshear* > 0 or counter-clockwise for *vshear* < 0. In this case, *vshear* is the tangential velocity of the wall at whatever *radius* has been defined. + +Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the shear friction state of atoms interacting with the diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index d746923ab0..f9840c9d5e 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -71,6 +71,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Fix wall/gran requires atom style sphere"); create_attribute = 1; + limit_damping = 0; // set interaction style // disable bonded/history option for now @@ -91,7 +92,6 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : // wall/particle coefficients int iarg; - if (pairstyle != GRANULAR) { size_history = 3; if (narg < 11) error->all(FLERR,"Illegal fix wall/gran command"); @@ -322,14 +322,14 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : if (normal_model == JKR) size_history += 1; if (tangential_model == TANGENTIAL_MINDLIN_RESCALE || tangential_model == TANGENTIAL_MINDLIN_RESCALE_FORCE) size_history += 1; - } - if (limit_damping and normal_model == JKR) - error->all(FLERR,"Illegal pair_coeff command, " - "cannot limit damping with JRK model"); - if (limit_damping and normal_model == DMT) - error->all(FLERR,"Illegal pair_coeff command, " - "Cannot limit damping with DMT model"); + if (limit_damping and normal_model == JKR) + error->all(FLERR,"Illegal pair_coeff command, " + "cannot limit damping with JRK model"); + if (limit_damping and normal_model == DMT) + error->all(FLERR,"Illegal pair_coeff command, " + "Cannot limit damping with DMT model"); + } // wallstyle args @@ -504,37 +504,39 @@ void FixWallGran::init() if (modify->fix[i]->rigid_flag) break; if (i < modify->nfix) fix_rigid = modify->fix[i]; - tangential_history_index = 0; - if (roll_history) { - if (tangential_history) roll_history_index = 3; - else roll_history_index = 0; - } - if (twist_history) { - if (tangential_history) { - if (roll_history) twist_history_index = 6; - else twist_history_index = 3; + if(pairstyle == GRANULAR) { + tangential_history_index = 0; + if (roll_history) { + if (tangential_history) roll_history_index = 3; + else roll_history_index = 0; } - else{ - if (roll_history) twist_history_index = 3; - else twist_history_index = 0; + if (twist_history) { + if (tangential_history) { + if (roll_history) twist_history_index = 6; + else twist_history_index = 3; + } + else{ + if (roll_history) twist_history_index = 3; + else twist_history_index = 0; + } + } + if (normal_model == JKR) { + tangential_history_index += 1; + roll_history_index += 1; + twist_history_index += 1; + } + if (tangential_model == TANGENTIAL_MINDLIN_RESCALE || + tangential_model == TANGENTIAL_MINDLIN_RESCALE_FORCE) { + roll_history_index += 1; + twist_history_index += 1; + } + + if (damping_model == TSUJI) { + double cor = normal_coeffs[1]; + normal_coeffs[1] = 1.2728-4.2783*cor+11.087*pow(cor,2)-22.348*pow(cor,3)+ + 27.467*pow(cor,4)-18.022*pow(cor,5)+ + 4.8218*pow(cor,6); } - } - if (normal_model == JKR) { - tangential_history_index += 1; - roll_history_index += 1; - twist_history_index += 1; - } - if (tangential_model == TANGENTIAL_MINDLIN_RESCALE || - tangential_model == TANGENTIAL_MINDLIN_RESCALE_FORCE) { - roll_history_index += 1; - twist_history_index += 1; - } - - if (damping_model == TSUJI) { - double cor = normal_coeffs[1]; - normal_coeffs[1] = 1.2728-4.2783*cor+11.087*pow(cor,2)-22.348*pow(cor,3)+ - 27.467*pow(cor,4)-18.022*pow(cor,5)+ - 4.8218*pow(cor,6); } } diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index e21ec727d6..be2a3c2558 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -278,7 +278,7 @@ void PairGranHertzHistory::compute(int eflag, int vflag) void PairGranHertzHistory::settings(int narg, char **arg) { - if (narg != 6) error->all(FLERR,"Illegal pair_style command"); + if (narg != 6 and narg != 7) error->all(FLERR,"Illegal pair_style command"); kn = utils::numeric(FLERR,arg[0],false,lmp); if (strcmp(arg[1],"NULL") == 0) kt = kn * 2.0/7.0; @@ -296,6 +296,12 @@ void PairGranHertzHistory::settings(int narg, char **arg) xmu < 0.0 || xmu > 10000.0 || dampflag < 0 || dampflag > 1) error->all(FLERR,"Illegal pair_style command"); + limit_damping = 0; + if (narg == 7) { + if (strcmp(arg[6], "limit_damping") == 0) limit_damping = 1; + else error->all(FLERR,"Illegal pair_style command"); + } + // convert Kn and Kt from pressure units to force/distance^2 kn /= force->nktv2p; diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index ac98a6e27c..653d5c70a1 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -1038,7 +1038,7 @@ void PairGranular::coeff(int narg, char **arg) cutoff_type[i][j] = cutoff_type[j][i] = cutoff_one; - limit_damping[i][j] = ld_flag; + limit_damping[i][j] = limit_damping[j][i] = ld_flag; setflag[i][j] = 1; count++; From 8e43d58faba0bcb520bdaa0e21c9a5f1eb601017 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 6 Apr 2021 13:48:56 -0600 Subject: [PATCH 0412/1217] Switching logical operators to match preferred style --- src/GRANULAR/fix_wall_gran.cpp | 12 ++++++------ src/GRANULAR/pair_gran_hertz_history.cpp | 6 +++--- src/GRANULAR/pair_gran_hooke.cpp | 4 ++-- src/GRANULAR/pair_gran_hooke_history.cpp | 6 +++--- src/GRANULAR/pair_granular.cpp | 8 ++++---- src/KOKKOS/pair_gran_hooke_history_kokkos.cpp | 2 +- 6 files changed, 19 insertions(+), 19 deletions(-) diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index f9840c9d5e..11cf0a9bc9 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -323,10 +323,10 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : if (tangential_model == TANGENTIAL_MINDLIN_RESCALE || tangential_model == TANGENTIAL_MINDLIN_RESCALE_FORCE) size_history += 1; - if (limit_damping and normal_model == JKR) + if (limit_damping && normal_model == JKR) error->all(FLERR,"Illegal pair_coeff command, " "cannot limit damping with JRK model"); - if (limit_damping and normal_model == DMT) + if (limit_damping && normal_model == DMT) error->all(FLERR,"Illegal pair_coeff command, " "Cannot limit damping with DMT model"); } @@ -794,7 +794,7 @@ void FixWallGran::hooke(double rsq, double dx, double dy, double dz, damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radius-r)*rinv - damp; - if (limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping && ccel < 0.0) ccel = 0.0; // relative velocities @@ -887,7 +887,7 @@ void FixWallGran::hooke_history(double rsq, double dx, double dy, double dz, damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radius-r)*rinv - damp; - if (limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping && ccel < 0.0) ccel = 0.0; // relative velocities @@ -1019,7 +1019,7 @@ void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz, if (rwall == 0.0) polyhertz = sqrt((radius-r)*radius); else polyhertz = sqrt((radius-r)*radius*rwall/(rwall+radius)); ccel *= polyhertz; - if (limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping && ccel < 0.0) ccel = 0.0; // relative velocities @@ -1214,7 +1214,7 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; - if (limit_damping and Fntot < 0.0) Fntot = 0.0; + if (limit_damping && Fntot < 0.0) Fntot = 0.0; //**************************************** // tangential force, including history effects diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index be2a3c2558..e40a9be2bd 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -181,7 +181,7 @@ void PairGranHertzHistory::compute(int eflag, int vflag) ccel = kn*(radsum-r)*rinv - damp; polyhertz = sqrt((radsum-r)*radi*radj / radsum); ccel *= polyhertz; - if (limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping && ccel < 0.0) ccel = 0.0; // relative velocities @@ -278,7 +278,7 @@ void PairGranHertzHistory::compute(int eflag, int vflag) void PairGranHertzHistory::settings(int narg, char **arg) { - if (narg != 6 and narg != 7) error->all(FLERR,"Illegal pair_style command"); + if (narg != 6 && narg != 7) error->all(FLERR,"Illegal pair_style command"); kn = utils::numeric(FLERR,arg[0],false,lmp); if (strcmp(arg[1],"NULL") == 0) kt = kn * 2.0/7.0; @@ -395,7 +395,7 @@ double PairGranHertzHistory::single(int i, int j, int /*itype*/, int /*jtype*/, ccel = kn*(radsum-r)*rinv - damp; polyhertz = sqrt((radsum-r)*radi*radj / radsum); ccel *= polyhertz; - if (limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping && ccel < 0.0) ccel = 0.0; // relative velocities diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp index c28bbd007f..0f45fadca9 100644 --- a/src/GRANULAR/pair_gran_hooke.cpp +++ b/src/GRANULAR/pair_gran_hooke.cpp @@ -158,7 +158,7 @@ void PairGranHooke::compute(int eflag, int vflag) damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if (limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping && ccel < 0.0) ccel = 0.0; // relative velocities @@ -300,7 +300,7 @@ double PairGranHooke::single(int i, int j, int /*itype*/, int /*jtype*/, double damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if (limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping && ccel < 0.0) ccel = 0.0; // relative velocities diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 4f7a6e20ec..48c30c761e 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -237,7 +237,7 @@ void PairGranHookeHistory::compute(int eflag, int vflag) damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if (limit_damping and ccel < 0.0) ccel = 0.0; + if (limit_damping && ccel < 0.0) ccel = 0.0; // relative velocities @@ -357,7 +357,7 @@ void PairGranHookeHistory::allocate() void PairGranHookeHistory::settings(int narg, char **arg) { - if (narg != 6 and narg != 7) error->all(FLERR,"Illegal pair_style command"); + if (narg != 6 && narg != 7) error->all(FLERR,"Illegal pair_style command"); kn = utils::numeric(FLERR,arg[0],false,lmp); if (strcmp(arg[1],"NULL") == 0) kt = kn * 2.0/7.0; @@ -693,7 +693,7 @@ double PairGranHookeHistory::single(int i, int j, int /*itype*/, int /*jtype*/, damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if(limit_damping and ccel < 0.0) ccel = 0.0; + if(limit_damping && ccel < 0.0) ccel = 0.0; // relative velocities diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 653d5c70a1..e787e305ff 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -371,7 +371,7 @@ void PairGranular::compute(int eflag, int vflag) Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; - if (limit_damping[itype][jtype] and Fntot < 0.0) Fntot = 0.0; + if (limit_damping[itype][jtype] && Fntot < 0.0) Fntot = 0.0; //**************************************** // tangential force, including history effects @@ -988,11 +988,11 @@ void PairGranular::coeff(int narg, char **arg) 27.467*powint(cor,4)-18.022*powint(cor,5)+4.8218*powint(cor,6); } else damp = normal_coeffs_one[1]; - if (ld_flag and normal_model_one == JKR) + if (ld_flag && normal_model_one == JKR) error->all(FLERR,"Illegal pair_coeff command, " "Cannot limit damping with JKR model"); - if (ld_flag and normal_model_one == DMT) + if (ld_flag && normal_model_one == DMT) error->all(FLERR,"Illegal pair_coeff command, " "Cannot limit damping with DMT model"); @@ -1547,7 +1547,7 @@ double PairGranular::single(int i, int j, int itype, int jtype, Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; - if (limit_damping[itype][jtype] and Fntot < 0.0) Fntot = 0.0; + if (limit_damping[itype][jtype] && Fntot < 0.0) Fntot = 0.0; jnum = list->numneigh[i]; jlist = list->firstneigh[i]; diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp index 8d853b7dae..95be9843b9 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp @@ -392,7 +392,7 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC F_FLOAT damp = meff*gamman*vnnr*rsqinv; F_FLOAT ccel = kn*(radsum-r)*rinv - damp; - if(limit_damping & ccel < 0.0) ccel = 0.0; + if(limit_damping && ccel < 0.0) ccel = 0.0; // relative velocities From c44b8f18ee49326cf63bf14410bb1c4493cfb700 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Tue, 6 Apr 2021 13:54:11 -0600 Subject: [PATCH 0413/1217] Adding explicit parentheses to logical operations --- src/GRANULAR/fix_wall_gran.cpp | 8 ++++---- src/GRANULAR/pair_gran_hertz_history.cpp | 4 ++-- src/GRANULAR/pair_gran_hooke.cpp | 4 ++-- src/GRANULAR/pair_gran_hooke_history.cpp | 4 ++-- src/GRANULAR/pair_granular.cpp | 4 ++-- src/KOKKOS/pair_gran_hooke_history_kokkos.cpp | 2 +- 6 files changed, 13 insertions(+), 13 deletions(-) diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 11cf0a9bc9..0611a54efd 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -794,7 +794,7 @@ void FixWallGran::hooke(double rsq, double dx, double dy, double dz, damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radius-r)*rinv - damp; - if (limit_damping && ccel < 0.0) ccel = 0.0; + if (limit_damping && (ccel < 0.0)) ccel = 0.0; // relative velocities @@ -887,7 +887,7 @@ void FixWallGran::hooke_history(double rsq, double dx, double dy, double dz, damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radius-r)*rinv - damp; - if (limit_damping && ccel < 0.0) ccel = 0.0; + if (limit_damping && (ccel < 0.0)) ccel = 0.0; // relative velocities @@ -1019,7 +1019,7 @@ void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz, if (rwall == 0.0) polyhertz = sqrt((radius-r)*radius); else polyhertz = sqrt((radius-r)*radius*rwall/(rwall+radius)); ccel *= polyhertz; - if (limit_damping && ccel < 0.0) ccel = 0.0; + if (limit_damping && (ccel < 0.0)) ccel = 0.0; // relative velocities @@ -1214,7 +1214,7 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; - if (limit_damping && Fntot < 0.0) Fntot = 0.0; + if (limit_damping && (Fntot < 0.0)) Fntot = 0.0; //**************************************** // tangential force, including history effects diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index e40a9be2bd..56e9691fad 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -181,7 +181,7 @@ void PairGranHertzHistory::compute(int eflag, int vflag) ccel = kn*(radsum-r)*rinv - damp; polyhertz = sqrt((radsum-r)*radi*radj / radsum); ccel *= polyhertz; - if (limit_damping && ccel < 0.0) ccel = 0.0; + if (limit_damping && (ccel < 0.0)) ccel = 0.0; // relative velocities @@ -395,7 +395,7 @@ double PairGranHertzHistory::single(int i, int j, int /*itype*/, int /*jtype*/, ccel = kn*(radsum-r)*rinv - damp; polyhertz = sqrt((radsum-r)*radi*radj / radsum); ccel *= polyhertz; - if (limit_damping && ccel < 0.0) ccel = 0.0; + if (limit_damping && (ccel < 0.0)) ccel = 0.0; // relative velocities diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp index 0f45fadca9..eb5ccec680 100644 --- a/src/GRANULAR/pair_gran_hooke.cpp +++ b/src/GRANULAR/pair_gran_hooke.cpp @@ -158,7 +158,7 @@ void PairGranHooke::compute(int eflag, int vflag) damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if (limit_damping && ccel < 0.0) ccel = 0.0; + if (limit_damping && (ccel < 0.0)) ccel = 0.0; // relative velocities @@ -300,7 +300,7 @@ double PairGranHooke::single(int i, int j, int /*itype*/, int /*jtype*/, double damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if (limit_damping && ccel < 0.0) ccel = 0.0; + if (limit_damping && (ccel < 0.0)) ccel = 0.0; // relative velocities diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 48c30c761e..0f9682a133 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -237,7 +237,7 @@ void PairGranHookeHistory::compute(int eflag, int vflag) damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if (limit_damping && ccel < 0.0) ccel = 0.0; + if (limit_damping && (ccel < 0.0)) ccel = 0.0; // relative velocities @@ -693,7 +693,7 @@ double PairGranHookeHistory::single(int i, int j, int /*itype*/, int /*jtype*/, damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; - if(limit_damping && ccel < 0.0) ccel = 0.0; + if(limit_damping && (ccel < 0.0)) ccel = 0.0; // relative velocities diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index e787e305ff..dc367dcc0a 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -371,7 +371,7 @@ void PairGranular::compute(int eflag, int vflag) Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; - if (limit_damping[itype][jtype] && Fntot < 0.0) Fntot = 0.0; + if (limit_damping[itype][jtype] && (Fntot < 0.0)) Fntot = 0.0; //**************************************** // tangential force, including history effects @@ -1547,7 +1547,7 @@ double PairGranular::single(int i, int j, int itype, int jtype, Fdamp = -damp_normal_prefactor*vnnr; Fntot = Fne + Fdamp; - if (limit_damping[itype][jtype] && Fntot < 0.0) Fntot = 0.0; + if (limit_damping[itype][jtype] && (Fntot < 0.0)) Fntot = 0.0; jnum = list->numneigh[i]; jlist = list->firstneigh[i]; diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp index 95be9843b9..01ac1ea54f 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp @@ -392,7 +392,7 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC F_FLOAT damp = meff*gamman*vnnr*rsqinv; F_FLOAT ccel = kn*(radsum-r)*rinv - damp; - if(limit_damping && ccel < 0.0) ccel = 0.0; + if(limit_damping && (ccel < 0.0)) ccel = 0.0; // relative velocities From 5af294d49edb013699863b48cc24f374de641389 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 6 Apr 2021 16:47:06 -0400 Subject: [PATCH 0414/1217] Update test_potential_file_reader.cpp --- .../formats/test_potential_file_reader.cpp | 26 ++++++++++--------- 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/unittest/formats/test_potential_file_reader.cpp b/unittest/formats/test_potential_file_reader.cpp index 1e3d96d6d7..6331db28a7 100644 --- a/unittest/formats/test_potential_file_reader.cpp +++ b/unittest/formats/test_potential_file_reader.cpp @@ -42,18 +42,20 @@ using utils::split_words; // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; -const int LAMMPS_NS::PairSW::NPARAMS_PER_LINE; -const int LAMMPS_NS::PairComb::NPARAMS_PER_LINE; -const int LAMMPS_NS::PairComb3::NPARAMS_PER_LINE; -const int LAMMPS_NS::PairTersoff::NPARAMS_PER_LINE; -const int LAMMPS_NS::PairTersoffMOD::NPARAMS_PER_LINE; -const int LAMMPS_NS::PairTersoffMODC::NPARAMS_PER_LINE; -const int LAMMPS_NS::PairTersoffZBL::NPARAMS_PER_LINE; -const int LAMMPS_NS::PairGW::NPARAMS_PER_LINE; -const int LAMMPS_NS::PairGWZBL::NPARAMS_PER_LINE; -const int LAMMPS_NS::PairNb3bHarmonic::NPARAMS_PER_LINE; -const int LAMMPS_NS::PairVashishta::NPARAMS_PER_LINE; -const int LAMMPS_NS::PairTersoffTable::NPARAMS_PER_LINE; +#if __cplusplus < 201703L +constexpr int LAMMPS_NS::PairSW::NPARAMS_PER_LINE; +constexpr int LAMMPS_NS::PairComb::NPARAMS_PER_LINE; +constexpr int LAMMPS_NS::PairComb3::NPARAMS_PER_LINE; +constexpr int LAMMPS_NS::PairTersoff::NPARAMS_PER_LINE; +constexpr int LAMMPS_NS::PairTersoffMOD::NPARAMS_PER_LINE; +constexpr int LAMMPS_NS::PairTersoffMODC::NPARAMS_PER_LINE; +constexpr int LAMMPS_NS::PairTersoffZBL::NPARAMS_PER_LINE; +constexpr int LAMMPS_NS::PairGW::NPARAMS_PER_LINE; +constexpr int LAMMPS_NS::PairGWZBL::NPARAMS_PER_LINE; +constexpr int LAMMPS_NS::PairNb3bHarmonic::NPARAMS_PER_LINE; +constexpr int LAMMPS_NS::PairVashishta::NPARAMS_PER_LINE; +constexpr int LAMMPS_NS::PairTersoffTable::NPARAMS_PER_LINE; +#endif class PotentialFileReaderTest : public LAMMPSTest { }; From b6776ca3debf462dcaf2320015d80337a83ae483 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 6 Apr 2021 16:48:18 -0400 Subject: [PATCH 0415/1217] Remove GCC optimization pragma for GCC < 4.9 due to compiler segfault --- unittest/formats/test_atom_styles.cpp | 4 ---- 1 file changed, 4 deletions(-) diff --git a/unittest/formats/test_atom_styles.cpp b/unittest/formats/test_atom_styles.cpp index 8166a5d1f0..8a031fe308 100644 --- a/unittest/formats/test_atom_styles.cpp +++ b/unittest/formats/test_atom_styles.cpp @@ -40,11 +40,7 @@ #elif defined(__GNUC__) #if (__GNUC__ > 4) || ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 9)) #pragma GCC optimize("no-var-tracking-assignments", "O0") -#else -#pragma GCC optimize("no-var-tracking-assignments") #endif -#else -#define _do_nothing #endif #endif From 0ae75aabcd4c1b72945092618e4039e01a1a02d5 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 6 Apr 2021 17:10:16 -0400 Subject: [PATCH 0416/1217] Remove unused variables --- src/PYTHON/pair_python.cpp | 1 - src/PYTHON/python_impl.cpp | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index f3a16612b6..b147c9cb79 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -342,7 +342,6 @@ double PairPython::single(int /* i */, int /* j */, int itype, int jtype, // prepare access to compute_force and compute_energy functions PyUtils::GIL lock; - PyObject *py_pair_instance = (PyObject *) py_potential; PyObject *py_compute_force = (PyObject *) get_member_function("compute_force"); PyObject *py_compute_energy = (PyObject *) get_member_function("compute_energy"); PyObject *py_compute_args = Py_BuildValue("(dii)", rsq, itype, jtype); diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index 7e46da4c49..c84d04b4b7 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -117,7 +117,7 @@ PythonImpl::~PythonImpl() // shutdown Python interpreter if (!external_interpreter) { - PyGILState_STATE gstate = PyGILState_Ensure(); + PyGILState_Ensure(); Py_Finalize(); } From 932ea80b253e89c826b97c53bc5ffe22f00989a9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 6 Apr 2021 18:39:37 -0400 Subject: [PATCH 0417/1217] update reference data for angle style cosine/periodic --- unittest/force-styles/tests/angle-cosine_periodic.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/unittest/force-styles/tests/angle-cosine_periodic.yaml b/unittest/force-styles/tests/angle-cosine_periodic.yaml index 55beb13fdd..1c6cb7158d 100644 --- a/unittest/force-styles/tests/angle-cosine_periodic.yaml +++ b/unittest/force-styles/tests/angle-cosine_periodic.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 10 Feb 2021 -date_generated: Fri Feb 26 23:09:23 2021 +lammps_version: 10 Mar 2021 +date_generated: Tue Apr 6 18:38:56 2021 epsilon: 2.5e-13 prerequisites: ! | atom full @@ -14,7 +14,7 @@ angle_coeff: ! | 2 45.0 1 2 3 50.0 -1 3 4 100.0 -1 4 -equilibrium: 4 3.141592653589793 3.141592653589793 3.141592653589793 3.141592653589793 +equilibrium: 4 1.5707963267948966 1.5707963267948966 0 0 extract: ! "" natoms: 29 init_energy: 946.676664091363 From 717faa65155e5071c2ef6c09b8bc525af573cf78 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 6 Apr 2021 19:12:28 -0400 Subject: [PATCH 0418/1217] correctly detect GPU package with CUDA api --- cmake/Modules/Packages/GPU.cmake | 2 +- lib/gpu/lal_device.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index 74a023685d..b706537825 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -131,7 +131,7 @@ if(GPU_API STREQUAL "CUDA") add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS}) target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY}) target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS}) - target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS}) + target_compile_definitions(gpu PRIVATE -DUSE_CUDA -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS}) if(CUDPP_OPT) target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini) target_compile_definitions(gpu PRIVATE -DUSE_CUDPP) diff --git a/lib/gpu/lal_device.cpp b/lib/gpu/lal_device.cpp index a65c3d8810..b42aa8e21d 100644 --- a/lib/gpu/lal_device.cpp +++ b/lib/gpu/lal_device.cpp @@ -1061,7 +1061,7 @@ bool lmp_gpu_config(const std::string &category, const std::string &setting) return setting == "opencl"; #elif defined(USE_HIP) return setting == "hip"; -#elif defined(USE_CUDA) +#elif defined(USE_CUDA) || defined(USE_CUDART) return setting == "cuda"; #endif return false; From 3de33027677ec318fe2d0f2f80a63ac35671ca07 Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Wed, 7 Apr 2021 12:20:24 +0200 Subject: [PATCH 0419/1217] remove source files from lib/pace; add lib/pace/Install.py to automatically download the source files from github/ICAMS/lammps-user-pace; add lib/pace/CMakeLists.txt to build libpace.a add lib/pace/README update src/USER-PACE/Install.sh --- lib/pace/CMakeLists.txt | 19 + lib/pace/Install.py | 112 +- lib/pace/LICENSE | 674 ----------- lib/pace/README | 9 + lib/pace/ace_abstract_basis.cpp | 184 --- lib/pace/ace_abstract_basis.h | 169 --- lib/pace/ace_array2dlm.h | 579 --------- lib/pace/ace_arraynd.h | 1949 ------------------------------- lib/pace/ace_c_basis.cpp | 980 ---------------- lib/pace/ace_c_basis.h | 155 --- lib/pace/ace_c_basisfunction.h | 251 ---- lib/pace/ace_complex.h | 266 ----- lib/pace/ace_contigous_array.h | 249 ---- lib/pace/ace_evaluator.cpp | 660 ----------- lib/pace/ace_evaluator.h | 230 ---- lib/pace/ace_flatten_basis.cpp | 130 --- lib/pace/ace_flatten_basis.h | 135 --- lib/pace/ace_radial.cpp | 566 --------- lib/pace/ace_radial.h | 324 ----- lib/pace/ace_recursive.cpp | 1340 --------------------- lib/pace/ace_recursive.h | 247 ---- lib/pace/ace_spherical_cart.cpp | 221 ---- lib/pace/ace_spherical_cart.h | 134 --- lib/pace/ace_timing.h | 126 -- lib/pace/ace_types.h | 45 - lib/pace/ace_version.h | 39 - lib/pace/ships_radial.cpp | 388 ------ lib/pace/ships_radial.h | 158 --- src/USER-PACE/Install.sh | 104 +- 29 files changed, 189 insertions(+), 10254 deletions(-) create mode 100644 lib/pace/CMakeLists.txt delete mode 100644 lib/pace/LICENSE delete mode 100644 lib/pace/ace_abstract_basis.cpp delete mode 100644 lib/pace/ace_abstract_basis.h delete mode 100644 lib/pace/ace_array2dlm.h delete mode 100644 lib/pace/ace_arraynd.h delete mode 100644 lib/pace/ace_c_basis.cpp delete mode 100644 lib/pace/ace_c_basis.h delete mode 100644 lib/pace/ace_c_basisfunction.h delete mode 100644 lib/pace/ace_complex.h delete mode 100644 lib/pace/ace_contigous_array.h delete mode 100644 lib/pace/ace_evaluator.cpp delete mode 100644 lib/pace/ace_evaluator.h delete mode 100644 lib/pace/ace_flatten_basis.cpp delete mode 100644 lib/pace/ace_flatten_basis.h delete mode 100644 lib/pace/ace_radial.cpp delete mode 100644 lib/pace/ace_radial.h delete mode 100644 lib/pace/ace_recursive.cpp delete mode 100644 lib/pace/ace_recursive.h delete mode 100644 lib/pace/ace_spherical_cart.cpp delete mode 100644 lib/pace/ace_spherical_cart.h delete mode 100644 lib/pace/ace_timing.h delete mode 100644 lib/pace/ace_types.h delete mode 100644 lib/pace/ace_version.h delete mode 100644 lib/pace/ships_radial.cpp delete mode 100644 lib/pace/ships_radial.h diff --git a/lib/pace/CMakeLists.txt b/lib/pace/CMakeLists.txt new file mode 100644 index 0000000000..2884c83cb9 --- /dev/null +++ b/lib/pace/CMakeLists.txt @@ -0,0 +1,19 @@ +cmake_minimum_required(VERSION 3.7) # CMake version check +project(aceevaluator) +set(CMAKE_CXX_STANDARD 11) # Enable c++11 standard + + +set(PACE_EVALUATOR_PATH ${CMAKE_CURRENT_LIST_DIR}/src/USER-PACE) +# message("CMakeLists.txt DEBUG: PACE_EVALUATOR_PATH=${PACE_EVALUATOR_PATH}") +set(PACE_EVALUATOR_SRC_PATH ${PACE_EVALUATOR_PATH}) + +FILE(GLOB PACE_EVALUATOR_SOURCE_FILES ${PACE_EVALUATOR_SRC_PATH}/*.cpp) +list(FILTER PACE_EVALUATOR_SOURCE_FILES EXCLUDE REGEX ".*pair_pace.*") +set(PACE_EVALUATOR_INCLUDE_DIR ${PACE_EVALUATOR_SRC_PATH}) + + +##### aceevaluator ##### +add_library(aceevaluator ${PACE_EVALUATOR_SOURCE_FILES}) +target_include_directories(aceevaluator PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) +target_compile_options(aceevaluator PRIVATE -O3) +set_target_properties(aceevaluator PROPERTIES OUTPUT_NAME pace${LAMMPS_MACHINE}) diff --git a/lib/pace/Install.py b/lib/pace/Install.py index f87f5c14cb..640971e011 100644 --- a/lib/pace/Install.py +++ b/lib/pace/Install.py @@ -1 +1,111 @@ -# TODO \ No newline at end of file +# TODO#!/usr/bin/env python + +""" +Install.py tool to download, compile, and setup the pace library +used to automate the steps described in the README file in this dir +""" + +from __future__ import print_function +import sys, os, subprocess, shutil +from argparse import ArgumentParser + +sys.path.append('..') +from install_helpers import fullpath, geturl, checkmd5sum + +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + +# settings + +thisdir = fullpath('.') +version = "v.2021.2.3" + +# known checksums for different PACE versions. used to validate the download. +checksums = { \ + 'v.2021.2.3' : '9ebb087cba7e4ca041fde52f7e9e640c', \ + } + + +# help message + +HELP = """ +Syntax from src dir: make lib-pace args="-b" + or: make lib-pace args="-b -v version" +Syntax from lib dir: python Install.py -b + or: python Install.py -b -v version + +Examples: + +make lib-pace args="-b" # install default version of PACE lib +make lib-pace args="-b -v version" # install specified version of PACE lib + + +""" + +pgroup = parser.add_mutually_exclusive_group() +pgroup.add_argument("-b", "--build", action="store_true", + help="download and build base PACE library") +parser.add_argument("-v", "--version", default=version, choices=checksums.keys(), + help="set version of PACE library to download and build (default: %s)" % version) +parser.add_argument("-vv", "--verbose", action="store_true", + help="be more verbose about is happening while this script runs") + +args = parser.parse_args() + +# print help message and exit, if neither build nor path options are given +if not args.build: + parser.print_help() + sys.exit(HELP) + +buildflag = args.build + +verboseflag = args.verbose +version = args.version + + +archive_extension = "tar.gz" +url = "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/%s.%s" % (version, archive_extension) +unarchived_folder_name = "lammps-user-pace-%s"%(version) + +# download PACE tarball, unpack, build PACE +if buildflag: + + # download entire tarball + + print("Downloading pace tarball ...") + archive_filename = "%s.%s" % (version, archive_extension) + download_filename = "%s/%s" % (thisdir, archive_filename) + print("Downloading from ",url," to ",download_filename, end=" ") + geturl(url, download_filename) + print(" done") + + # verify downloaded archive integrity via md5 checksum, if known. + if version in checksums: + if not checkmd5sum(checksums[version], archive_filename): + sys.exit("Checksum for pace library does not match") + + print("Unpacking pace tarball ...") + src_folder = thisdir+"/src" + cmd = 'cd "%s"; rm -rf "%s"; tar -xvf %s; mv %s %s' % (thisdir, src_folder, archive_filename, unarchived_folder_name, src_folder) + subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + + # configure + + build_folder = "%s/build"%(thisdir) + print("Configuring libpace ...") + cmd = 'cd %s && mkdir build && cd build && cmake .. -DCMAKE_BUILD_TYPE=Release' % (thisdir) + txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + if verboseflag: print(txt.decode("UTF-8")) + + # build + print("Building libpace ...") + cmd = 'cd "%s" && make -j2 && cp libpace.a %s/' % (build_folder, thisdir) + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + if verboseflag: + print(txt.decode("UTF-8")) + +# remove source files + + print("Removing pace build files and archive ...") + cmd = 'rm %s; rm -rf %s' % (download_filename, build_folder) + subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) \ No newline at end of file diff --git a/lib/pace/LICENSE b/lib/pace/LICENSE deleted file mode 100644 index f288702d2f..0000000000 --- a/lib/pace/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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If not, see . - -Also add information on how to contact you by electronic and paper mail. - - If the program does terminal interaction, make it output a short -notice like this when it starts in an interactive mode: - - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. - - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. diff --git a/lib/pace/README b/lib/pace/README index e69de29bb2..e9a1ab820a 100644 --- a/lib/pace/README +++ b/lib/pace/README @@ -0,0 +1,9 @@ +This directory contains files required to use the USER-PACE package. + +You can type "make lib-pace" from the src directory to see help on +how to download and build this library via make commands, or you can +do the same thing by typing "python Install.py" from within this +directory. + + + diff --git a/lib/pace/ace_abstract_basis.cpp b/lib/pace/ace_abstract_basis.cpp deleted file mode 100644 index 3d8afafdaf..0000000000 --- a/lib/pace/ace_abstract_basis.cpp +++ /dev/null @@ -1,184 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Lysogorskiy Yury on 28.04.2020. - -#include "ace_abstract_basis.h" - -////embedding function -////case nemb = 1 only implementation -////F = sign(x)*( ( 1 - exp(-(w*x)^3) )*abs(x)^m + ((1/w)^(m-1))*exp(-(w*x)^3)*abs(x) ) -//// !! no prefactor wpre -void Fexp(DOUBLE_TYPE x, DOUBLE_TYPE m, DOUBLE_TYPE &F, DOUBLE_TYPE &DF) { - DOUBLE_TYPE w = 1.e6; - DOUBLE_TYPE eps = 1e-10; - - DOUBLE_TYPE lambda = pow(1.0 / w, m - 1.0); - if (abs(x) > eps) { - DOUBLE_TYPE g; - DOUBLE_TYPE a = abs(x); - DOUBLE_TYPE am = pow(a, m); - DOUBLE_TYPE w3x3 = pow(w * a, 3); - DOUBLE_TYPE sign_factor = (signbit(x) ? -1 : 1); - if (w3x3 > 30.0) - g = 0.0; - else - g = exp(-w3x3); - - DOUBLE_TYPE omg = 1.0 - g; - F = sign_factor * (omg * am + lambda * g * a); - DOUBLE_TYPE dg = -3.0 * w * w * w * a * a * g; - DF = m * pow(a, m - 1.0) * omg - am * dg + lambda * dg * a + lambda * g; - } else { - F = lambda * x; - DF = lambda; - } -} - - -//Scaled-shifted embedding function -//F = sign(x)*( ( 1 - exp(-(w*x)^3) )*abs(x)^m + ((1/w)^(m-1))*exp(-(w*x)^3)*abs(x) ) -// !! no prefactor wpre -void FexpShiftedScaled(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF) { - DOUBLE_TYPE eps = 1e-10; - DOUBLE_TYPE a, xoff, yoff, nx, exprho; - - if (abs(mexp - 1.0) < eps) { - F = rho; - DF = 1; - } else { - a = abs(rho); - exprho = exp(-a); - nx = 1. / mexp; - xoff = pow(nx, (nx / (1.0 - nx))) * exprho; - yoff = pow(nx, (1 / (1.0 - nx))) * exprho; - DOUBLE_TYPE sign_factor = (signbit(rho) ? -1 : 1); - F = sign_factor * (pow(xoff + a, mexp) - yoff); - DF = yoff + mexp * (-xoff + 1.0) * pow(xoff + a, mexp - 1.); - } -} - -void ACEAbstractBasisSet::inner_cutoff(DOUBLE_TYPE rho_core, DOUBLE_TYPE rho_cut, DOUBLE_TYPE drho_cut, - DOUBLE_TYPE &fcut, DOUBLE_TYPE &dfcut) { - - DOUBLE_TYPE rho_low = rho_cut - drho_cut; - if (rho_core >= rho_cut) { - fcut = 0; - dfcut = 0; - } else if (rho_core <= rho_low) { - fcut = 1; - dfcut = 0; - } else { - fcut = 0.5 * (1 + cos(M_PI * (rho_core - rho_low) / drho_cut)); - dfcut = -0.5 * sin(M_PI * (rho_core - rho_low) / drho_cut) * M_PI / drho_cut; - } -} - -void ACEAbstractBasisSet::FS_values_and_derivatives(Array1D &rhos, DOUBLE_TYPE &value, - Array1D &derivatives, DENSITY_TYPE ndensity) { - DOUBLE_TYPE F, DF = 0, wpre, mexp; - for (int p = 0; p < ndensity; p++) { - wpre = FS_parameters.at(p * ndensity + 0); - mexp = FS_parameters.at(p * ndensity + 1); - if (this->npoti == "FinnisSinclair") - Fexp(rhos(p), mexp, F, DF); - else if (this->npoti == "FinnisSinclairShiftedScaled") - FexpShiftedScaled(rhos(p), mexp, F, DF); - value += F * wpre; // * weight (wpre) - derivatives(p) = DF * wpre;// * weight (wpre) - } -} - -void ACEAbstractBasisSet::_clean() { - - delete[] elements_name; - elements_name = nullptr; - delete radial_functions; - radial_functions = nullptr; -} - -ACEAbstractBasisSet::ACEAbstractBasisSet(const ACEAbstractBasisSet &other) { - ACEAbstractBasisSet::_copy_scalar_memory(other); - ACEAbstractBasisSet::_copy_dynamic_memory(other); -} - -ACEAbstractBasisSet &ACEAbstractBasisSet::operator=(const ACEAbstractBasisSet &other) { - if (this != &other) { - // deallocate old memory - ACEAbstractBasisSet::_clean(); - //copy scalar values - ACEAbstractBasisSet::_copy_scalar_memory(other); - //copy dynamic memory - ACEAbstractBasisSet::_copy_dynamic_memory(other); - } - return *this; -} - -ACEAbstractBasisSet::~ACEAbstractBasisSet() { - ACEAbstractBasisSet::_clean(); -} - -void ACEAbstractBasisSet::_copy_scalar_memory(const ACEAbstractBasisSet &src) { - deltaSplineBins = src.deltaSplineBins; - FS_parameters = src.FS_parameters; - npoti = src.npoti; - - nelements = src.nelements; - rankmax = src.rankmax; - ndensitymax = src.ndensitymax; - nradbase = src.nradbase; - lmax = src.lmax; - nradmax = src.nradmax; - cutoffmax = src.cutoffmax; - - spherical_harmonics = src.spherical_harmonics; - - rho_core_cutoffs = src.rho_core_cutoffs; - drho_core_cutoffs = src.drho_core_cutoffs; - - - E0vals = src.E0vals; -} - -void ACEAbstractBasisSet::_copy_dynamic_memory(const ACEAbstractBasisSet &src) {//allocate new memory - if (src.elements_name == nullptr) - throw runtime_error("Could not copy ACEAbstractBasisSet::elements_name - array not initialized"); - elements_name = new string[nelements]; - //copy - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - elements_name[mu] = src.elements_name[mu]; - } - radial_functions = src.radial_functions->clone(); -} - -SPECIES_TYPE ACEAbstractBasisSet::get_species_index_by_name(const string &elemname) { - for (SPECIES_TYPE t = 0; t < nelements; t++) { - if (this->elements_name[t] == elemname) - return t; - } - return -1; -} \ No newline at end of file diff --git a/lib/pace/ace_abstract_basis.h b/lib/pace/ace_abstract_basis.h deleted file mode 100644 index 165ea9496f..0000000000 --- a/lib/pace/ace_abstract_basis.h +++ /dev/null @@ -1,169 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Lysogorskiy Yury on 28.04.2020. - -#ifndef ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H -#define ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H - -#include -#include - -#include "ace_c_basisfunction.h" -#include "ace_contigous_array.h" -#include "ace_radial.h" -#include "ace_spherical_cart.h" -#include "ace_types.h" - -using namespace std; - -/** - * Abstract basis set class - */ -class ACEAbstractBasisSet { -public: - SPECIES_TYPE nelements = 0; ///< number of elements in basis set - RANK_TYPE rankmax = 0; ///< maximum value of rank - DENSITY_TYPE ndensitymax = 0; ///< maximum number of densities \f$ \rho^{(p)} \f$ - NS_TYPE nradbase = 0; ///< maximum number of radial \f$\textbf{basis}\f$ function \f$ g_{k}(r) \f$ - LS_TYPE lmax = 0; ///< \f$ l_\textrm{max} \f$ - maximum value of orbital moment \f$ l \f$ - NS_TYPE nradmax = 0; ///< maximum number \f$ n \f$ of radial function \f$ R_{nl}(r) \f$ - DOUBLE_TYPE cutoffmax = 0; ///< maximum value of cutoff distance among all species in basis set - DOUBLE_TYPE deltaSplineBins = 0; ///< Spline interpolation density - - string npoti = "FinnisSinclair"; ///< FS and embedding function combination - - string *elements_name = nullptr; ///< Array of elements name for mapping from index (0..nelements-1) to element symbol (string) - - AbstractRadialBasis *radial_functions = nullptr; ///< object to work with radial functions - ACECartesianSphericalHarmonics spherical_harmonics; ///< object to work with spherical harmonics in Cartesian representation - - - Array1D rho_core_cutoffs; ///< energy-based inner cut-off - Array1D drho_core_cutoffs; ///< decay of energy-based inner cut-off - - vector FS_parameters; ///< parameters for cluster functional, see Eq.(3) in implementation notes or Eq.(53) in PRB 99, 014104 (2019) - - // E0 values - Array1D E0vals; - - /** - * Default empty constructor - */ - ACEAbstractBasisSet() = default; - - // copy constructor, operator= and destructor (see. Rule of Three) - - /** - * Copy constructor (see. Rule of Three) - * @param other - */ - ACEAbstractBasisSet(const ACEAbstractBasisSet &other); - - /** - * operator= (see. Rule of Three) - * @param other - * @return - */ - ACEAbstractBasisSet &operator=(const ACEAbstractBasisSet &other); - - /** - * virtual destructor (see. Rule of Three) - */ - virtual ~ACEAbstractBasisSet(); - - /** - * Computing cluster functional \f$ F(\rho_i^{(1)}, \dots, \rho_i^{(P)}) \f$ - * and its derivatives \f$ (\partial F/\partial\rho_i^{(1)}, \dots, \partial F/\partial \rho_i^{(P)} ) \f$ - * @param rhos array with densities \f$ \rho^{(p)} \f$ - * @param value (out) return value of cluster functional - * @param derivatives (out) array of derivatives \f$ (\partial F/\partial\rho_i^{(1)}, \dots, \partial F/\partial \rho_i^{(P)} ) \f$ - * @param ndensity number \f$ P \f$ of densities to use - */ - void FS_values_and_derivatives(Array1D &rhos, DOUBLE_TYPE &value, Array1D &derivatives, - DENSITY_TYPE ndensity); - - /** - * Computing hard core pairwise repulsive potential \f$ f_{cut}(\rho_i^{(\textrm{core})})\f$ and its derivative, - * see Eq.(29) of implementation notes - * @param rho_core value of \f$ \rho_i^{(\textrm{core})} \f$ - * @param rho_cut \f$ \rho_{cut}^{\mu_i} \f$ value - * @param drho_cut \f$ \Delta_{cut}^{\mu_i} \f$ value - * @param fcut (out) return inner cutoff function - * @param dfcut (out) return derivative of inner cutoff function - */ - static void inner_cutoff(DOUBLE_TYPE rho_core, DOUBLE_TYPE rho_cut, DOUBLE_TYPE drho_cut, DOUBLE_TYPE &fcut, - DOUBLE_TYPE &dfcut); - - - /** - * Virtual method to save potential to file - * @param filename file name - */ - virtual void save(const string &filename) = 0; - - /** - * Virtual method to load potential from file - * @param filename file name - */ - virtual void load(const string filename) = 0; - - /** - * Get the species index by its element name - * @param elemname element name - * @return species index - */ - SPECIES_TYPE get_species_index_by_name(const string &elemname); - - - // routines for copying and cleaning dynamic memory of the class (see. Rule of Three) - - /** - * Routine for clean the dynamically allocated memory\n - * IMPORTANT! It must be idempotent for safety. - */ - virtual void _clean(); - - /** - * Copy dynamic memory from src. Must be override and extended in derived classes! - * @param src source object to copy from - */ - virtual void _copy_dynamic_memory(const ACEAbstractBasisSet &src); - - /** - * Copy scalar values from src. Must be override and extended in derived classes! - * @param src source object to copy from - */ - virtual void _copy_scalar_memory(const ACEAbstractBasisSet &src); -}; - -void Fexp(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF); - -void FexpShiftedScaled(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF); - -#endif //ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H diff --git a/lib/pace/ace_array2dlm.h b/lib/pace/ace_array2dlm.h deleted file mode 100644 index 2b38602bc7..0000000000 --- a/lib/pace/ace_array2dlm.h +++ /dev/null @@ -1,579 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Yury Lysogorskiy on 11.01.20. - - -#ifndef ACE_ARRAY2DLM_H -#define ACE_ARRAY2DLM_H - -#include -#include - -#include "ace_arraynd.h" -#include "ace_contigous_array.h" -#include "ace_types.h" - -using namespace std; - -/** - * Contiguous array to organize values by \f$ (l,m) \f$ indiced (orbital moment and its projection). - * Only \f$ l_\textrm{max}\f$ should be provided, \f$ m = -l, \dots,l \f$ - * for \f$ l = 0, \dots, l_\textrm{max}\f$ - * @tparam T type of values to store - */ -template -class Array2DLM : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - - LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$ - - bool is_proxy = false; ///< flag to show, if object is owning the memory or just represent it (proxying)dimensions - -public: - /** - * Default empty constructor - */ - Array2DLM() = default; - - /** - * Parametrized constructor - * @param lmax maximum value of \f$ l \f$ - * @param array_name name of the array - */ - explicit Array2DLM(LS_TYPE lmax, string array_name = "Array2DLM") { - init(lmax, array_name); - } - - - /** - * Constructor to create slices-proxy array, i.e. to provide access to the memory, but not to own it. - * @param lmax maximum value of \f$ l \f$ - * @param data_ptr pointer to original data - * @param array_name name of the array - */ - Array2DLM(LS_TYPE lmax, T *data_ptr, string array_name = "Array2DLM") { - this->lmax = lmax; - this->size = (lmax + 1) * (lmax + 1); - this->data = data_ptr; - this->array_name = array_name; - is_proxy = true; - }; - - /** - * Destructor - */ - ~Array2DLM() { - if (!is_proxy) { - if (data != nullptr) delete[] data; - } - data = nullptr; - } - - /** - * Initialize array, allocate memory - * @param lmax maximum value of l - * @param array_name name of the array - */ - void init(LS_TYPE lmax, string array_name = "Array2DLM") { - if (is_proxy) { - char s[1024]; - sprintf(s, "Could not re-initialize proxy-array %s\n", this->array_name.c_str()); - throw logic_error(s); - } - this->lmax = lmax; - this->array_name = array_name; - //for m = -l .. l - if (size != (lmax + 1) * (lmax + 1)) { - size = (lmax + 1) * (lmax + 1); - if (data) delete[] data; - data = new T[size]{}; - memset(data, 0.0, size * sizeof(T)); - } else { - memset(data, 0, size * sizeof(T)); - } - } - -#ifdef MULTIARRAY_INDICES_CHECK -/** - * Check if indices (l,m) are within array - */ - void check_indices(LS_TYPE l, MS_TYPE m) const { - - if ((l < 0) | (l > lmax)) { - fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax); - exit(EXIT_FAILURE); - } - - if ((m < -l) | (m > l)) { - fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l); - exit(EXIT_FAILURE); - } - size_t ii = l * (l + 1) + m; - if (ii >= size) { - fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size); - exit(EXIT_FAILURE); - } - } -#endif - - /** - * Accessing the array value by index (l,m) for reading - * @param l - * @param m - * @return array value - */ - inline const T &operator()(LS_TYPE l, MS_TYPE m) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(l, m); -#endif - //l^2 + l + m - return data[l * (l + 1) + m]; - } - - /** - * Accessing the array value by index (l,m) for writing - * @param l - * @param m - * @return array value - */ - inline T &operator()(LS_TYPE l, MS_TYPE m) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(l, m); -#endif - //l^2 + l + m - return data[l * (l + 1) + m]; - } - - /** - * Convert array to STL vector> container - * @return vector> container - */ - vector> to_vector() const { - vector> res; - res.resize(lmax + 1); - - for (int i = 0; i < lmax + 1; i++) { - res[i].resize(i + 1); - for (int j = 0; j < i + 1; j++) { - res[i][j] = operator()(i, j); - } - } - return res; - } -}; - -/** - * Contiguous array to organize values by \f$ (i_0, l , m) \f$ indices. - * Only \f$ d_{0}, l_\textrm{max}\f$ should be provided: \f$ m = -l, \dots,l \f$ - * for \f$ l = 0, \dots, l_\textrm{max}\f$ - * @tparam T type of values to store - */ -template -class Array3DLM : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - - LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$ - - - size_t dim[1] = {0}; ///< linear dimension \f$ d_{0} \f$ - - size_t s[1] = {0}; ///< strides for linear dimensions - - Array1D *> _proxy_slices; ///< slices representation -public: - /** - * Default empty constructor - */ - Array3DLM() = default; - - /** - * Parametrized constructor - * @param array_name name of the array - */ - Array3DLM(string array_name) { - this->array_name = array_name; - }; - - /** - * Parametrized constructor - * @param d0 maximum value of \f$ i_0 \f$ - * @param lmax maximum value of \f$ l \f$ - * @param array_name name of the array - */ - explicit Array3DLM(size_t d0, LS_TYPE lmax, string array_name = "Array3DLM") { - init(d0, lmax, array_name); - } - - /** - * Initialize array and its slices - * @param d0 maximum value of \f$ i_0 \f$ - * @param lmax maximum value of \f$ l \f$ - * @param array_name name of the array - */ - void init(size_t d0, LS_TYPE lmax, string array_name = "Array3DLM") { - this->array_name = array_name; - this->lmax = lmax; - dim[0] = d0; - s[0] = lmax * lmax; - if (size != s[0] * dim[0]) { - size = s[0] * dim[0]; - if (data) delete[] data; - data = new T[size]{}; - memset(data, 0, size * sizeof(T)); - } else { - memset(data, 0, size * sizeof(T)); - } - - _proxy_slices.set_array_name(array_name + "_proxy"); - //arrange proxy-slices - _clear_proxies(); - _proxy_slices.resize(dim[0]); - for (size_t i0 = 0; i0 < dim[0]; ++i0) { - _proxy_slices(i0) = new Array2DLM(this->lmax, &this->data[i0 * s[0]], - array_name + "_slice"); - } - } - - /** - * Release pointers to slices - */ - void _clear_proxies() { - for (size_t i0 = 0; i0 < _proxy_slices.get_dim(0); ++i0) { - delete _proxy_slices(i0); - _proxy_slices(i0) = nullptr; - } - } - - /** - * Destructor, clear proxies - */ - ~Array3DLM() { - _clear_proxies(); - } - - /** - * Resize array to new dimensions - * @param d0 - * @param lmax - */ - void resize(size_t d0, LS_TYPE lmax) { - _clear_proxies(); - init(d0, lmax, this->array_name); - } - - /** - * Get array dimensions - * @param d dimension index - * @return dimension along axis 'd' - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - /** - * Check if indices (i0, l,m) are within array - */ - void check_indices(size_t i0, LS_TYPE l, MS_TYPE m) const { - if ((l < 0) | (l > lmax)) { - fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax); - exit(EXIT_FAILURE); - } - - if ((m < -l) | (m > l)) { - fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l); - exit(EXIT_FAILURE); - } - - if ((i0 < 0) | (i0 >= dim[0])) { - fprintf(stderr, "%s: index i0 = %ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - exit(EXIT_FAILURE); - } - - size_t ii = i0 * s[0] + l * (l + 1) + m; - if (ii >= size) { - fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size); - exit(EXIT_FAILURE); - } - } -#endif - - /** - * Accessing the array value by index (i0,l,m) for reading - * @param i0 - * @param l - * @param m - * @return array value - */ - inline const T &operator()(size_t i0, LS_TYPE l, MS_TYPE m) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, l, m); -#endif - return data[i0 * s[0] + l * (l + 1) + m]; - } - - /** - * Accessing the array value by index (i0,l,m) for writing - * @param i0 - * @param l - * @param m - * @return array value - */ - inline T &operator()(size_t i0, LS_TYPE l, MS_TYPE m) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, l, m); -#endif - return data[i0 * s[0] + l * (l + 1) + m]; - } - - /** - * Return proxy Array2DLM pointing to i0, l=0, m=0 to read - * @param i0 - * @return proxy Array2DLM pointing to i0, l=0, m=0 - */ - inline const Array2DLM &operator()(size_t i0) const { - return *_proxy_slices(i0); - } - - /** - * Return proxy Array2DLM pointing to i0, l=0, m=0 to write - * @param i0 - * @return proxy Array2DLM pointing to i0, l=0, m=0 - */ - inline Array2DLM &operator()(size_t i0) { - return *_proxy_slices(i0); - } -}; - - -/** - * Contiguous array to organize values by \f$ (i_0, i_1, l , m) \f$ indices. - * Only \f$ d_{0}, d_{1}, l_\textrm{max}\f$ should be provided: \f$ m = -l, \dots,l \f$ - * for \f$ l = 0, \dots, l_\textrm{max}\f$ - * @tparam T type of values to store - */ -template -class Array4DLM : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - - LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$ - size_t dim[2] = {0, 0}; ///< linear dimension \f$ d_{0}, d_{1} \f$ - size_t s[2] = {0, 0}; ///< strides for linear dimensions - - Array2D *> _proxy_slices; ///< slices representation -public: - /** - * Default empty constructor - */ - Array4DLM() = default; - - /** - * Parametrized constructor - * @param array_name name of the array - */ - Array4DLM(string array_name) { - this->array_name = array_name; - }; - - /** - * Parametrized constructor - * @param d0 maximum value of \f$ i_0 \f$ - * @param d1 maximum value of \f$ i_1 \f$ - * @param lmax maximum value of \f$ l \f$ - * @param array_name name of the array - */ - explicit Array4DLM(size_t d0, size_t d1, LS_TYPE lmax, string array_name = "Array4DLM") { - init(d0, d1, lmax, array_name); - } - - /** - * Initialize array, reallocate memory and its slices - * @param d0 maximum value of \f$ i_0 \f$ - * @param d1 maximum value of \f$ i_1 \f$ - * @param lmax maximum value of \f$ l \f$ - * @param array_name name of the array - */ - void init(size_t d0, size_t d1, LS_TYPE lmax, string array_name = "Array4DLM") { - this->array_name = array_name; - this->lmax = lmax; - dim[1] = d1; - dim[0] = d0; - s[1] = lmax * lmax; - s[0] = s[1] * dim[1]; - if (size != s[0] * dim[0]) { - size = s[0] * dim[0]; - if (data) delete[] data; - data = new T[size]{}; - memset(data, 0, size * sizeof(T)); - } else { - memset(data, 0, size * sizeof(T)); - } - - _proxy_slices.set_array_name(array_name + "_proxy"); - //release old memory if there is any - _clear_proxies(); - //arrange proxy-slices - _proxy_slices.resize(dim[0], dim[1]); - for (size_t i0 = 0; i0 < dim[0]; ++i0) - for (size_t i1 = 0; i1 < dim[1]; ++i1) { - _proxy_slices(i0, i1) = new Array2DLM(this->lmax, &this->data[i0 * s[0] + i1 * s[1]], - array_name + "_slice"); - } - } - - /** - * Release pointers to slices - */ - void _clear_proxies() { - - for (size_t i0 = 0; i0 < _proxy_slices.get_dim(0); ++i0) - for (size_t i1 = 0; i1 < _proxy_slices.get_dim(1); ++i1) { - delete _proxy_slices(i0, i1); - _proxy_slices(i0, i1) = nullptr; - } - } - - /** - * Destructor, clear proxies - */ - ~Array4DLM() { - _clear_proxies(); - } - - /** - * Deallocate memory, reallocate with the new dimensions - * @param d0 - * @param lmax - */ - void resize(size_t d0, size_t d1, LS_TYPE lmax) { - _clear_proxies(); - init(d0, d1, lmax, this->array_name); - } - - /** - * Get array dimensions - * @param d dimension index - * @return dimension along axis 'd' - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - /** - * Check if indices (i0, l,m) are within array - */ - void check_indices(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) const { - if ((l < 0) | (l > lmax)) { - fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax); - exit(EXIT_FAILURE); - } - - if ((m < -l) | (m > l)) { - fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l); - exit(EXIT_FAILURE); - } - - if ((i0 < 0) | (i0 >= dim[0])) { - fprintf(stderr, "%s: index i0 = %ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - exit(EXIT_FAILURE); - } - - - if ((i1 < 0) | (i1 >= dim[1])) { - fprintf(stderr, "%s: index i1 = %ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); - exit(EXIT_FAILURE); - } - - size_t ii = i0 * s[0] + i1 * s[1] + l * (l + 1) + m; - if (ii >= size) { - fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size); - exit(EXIT_FAILURE); - } - } -#endif - - /** - * Accessing the array value by index (i0,l,m) for reading - * @param i0 - * @param i1 - * @param l - * @param m - * @return array value - */ - inline const T &operator()(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, l, m); -#endif - return data[i0 * s[0] + i1 * s[1] + l * (l + 1) + m]; - } - - /** - * Accessing the array value by index (i0,l,m) for writing - * @param i0 - * @param i1 - * @param l - * @param m - * @return array value - */ - inline T &operator()(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, l, m); -#endif - return data[i0 * s[0] + i1 * s[1] + l * (l + 1) + m]; - } - - /** - * Return proxy Array2DLM pointing to i0, i1, l=0, m=0 to read - * @param i0 - * @param i1 - * @return proxy Array2DLM pointing to i0, l=0, m=0 - */ - inline const Array2DLM &operator()(size_t i0, size_t i1) const { - return *_proxy_slices(i0, i1); - } - - /** - * Return proxy Array2DLM pointing to i0, i1, l=0, m=0 to write - * @param i0 - * @param i1 - * @return proxy Array2DLM pointing to i0, l=0, m=0 - */ - inline Array2DLM &operator()(size_t i0, size_t i1) { - return *_proxy_slices(i0, i1); - } -}; - -#endif //ACE_ARRAY2DLM_H \ No newline at end of file diff --git a/lib/pace/ace_arraynd.h b/lib/pace/ace_arraynd.h deleted file mode 100644 index 1044b5654e..0000000000 --- a/lib/pace/ace_arraynd.h +++ /dev/null @@ -1,1949 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -//automatically generate source code - -#ifndef ACE_MULTIARRAY_H -#define ACE_MULTIARRAY_H - -#include -#include -#include - -#include "ace_contigous_array.h" - -using namespace std; - - -/** - * Multidimensional (1 - dimensional) array of type T with contiguous memory layout. - * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @tparam T data type - */ -template -class Array1D : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - using ContiguousArrayND::is_proxy_; - - size_t dim[1] = {0}; ///< dimensions - size_t s[1] = {0}; ///< strides - int ndim = 1; ///< number of dimensions -public: - - /** - * Default empty constructor - */ - Array1D() = default; - - /** - * Parametrized constructor with array name - * @param array_name name of array (for error logging) - */ - Array1D(const string &array_name) { this->array_name = array_name; } - - /** - * Parametrized constructor - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - Array1D(size_t d0, const string &array_name = "Array1D", T *new_data = nullptr) { - init(d0, array_name, new_data); - } - - /** - * Setup the dimensions and strides of array - * @param d0,... array sizes for different dimensions - */ - void set_dimensions(size_t d0) { - - dim[0] = d0; - - s[0] = 1; - - size = s[0] * dim[0]; - }; - - /** - * Initialize array storage, dimensions and strides - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - void init(size_t d0, const string &array_name = "Array1D", T *new_data = nullptr) { - this->array_name = array_name; - - size_t old_size = size; - set_dimensions(d0); - - bool new_is_proxy = (new_data != nullptr); - - if (new_is_proxy) { - if (!is_proxy_) delete[] data; - data = new_data; - } else { - if (size != old_size) { - T *old_data = data; //preserve the pointer to the old data - data = new T[size]; // allocate new data - if (old_data != nullptr) { // - size_t min_size = old_size < size ? old_size : size; - memcpy(data, old_data, min_size * sizeof(T)); - if (!is_proxy_) delete[] old_data; - } - //memset(data, 0, size * sizeof(T)); - } else { - //memset(data, 0, size * sizeof(T)); - } - } - - is_proxy_ = new_is_proxy; - } - - /** - * Resize array - * @param d0,... array sizes for different dimensions - */ - void resize(size_t d0) { - init(d0, this->array_name); - } - - /** - * Reshape array without reset the data - * @param d0,... array sizes for different dimensions - */ - void reshape(size_t d0) { - //check data size consistency - size_t new_size = d0; - if (new_size != size) - throw invalid_argument("Couldn't reshape array when the size is not conserved"); - set_dimensions(d0); - } - - /** - * Get array size in dimension "d" - * @param d dimension index - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - - /** - * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - void check_indices(size_t i0) const { - - if ((i0 < 0) | (i0 >= dim[0])) { - char buf[1024]; - sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - throw std::out_of_range(buf); - } - - } - -#endif - - /** - * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline const T &operator()(size_t i0) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0); -#endif - - return data[i0]; - - } - - /** - * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline T &operator()(size_t i0) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0); -#endif - - return data[i0]; - - } - - /** - * Array comparison operator - * @param other - */ - bool operator==(const Array1D &other) const { - //compare dimensions - for (int d = 0; d < ndim; d++) { - if (this->dim[d] != other.dim[d]) - return false; - } - return ContiguousArrayND::operator==(other); - } - - /** - * Convert to nested vector> container - * @return vector container - */ - vector to_vector() const { - vector res; - - res.resize(dim[0]); - - for (int i0 = 0; i0 < dim[0]; i0++) { - res[i0] = operator()(i0); - - } - - - return res; - } // end to_vector() - - - /** - * Set values to vector> container - * @param vec container - */ - void set_vector(const vector &vec) { - size_t d0 = 0; - d0 = vec.size(); - - - init(d0, array_name); - for (int i0 = 0; i0 < dim[0]; i0++) { - operator()(i0) = vec.at(i0); - - } - - } - - /** - * Parametrized constructor from vector> container - * @param vec container - * @param array_name array name - */ - Array1D(const vector &vec, const string &array_name = "Array1D") { - this->set_vector(vec); - this->array_name = array_name; - } - - /** - * operator= to vector> container - * @param vec container - */ - Array1D &operator=(const vector &vec) { - this->set_vector(vec); - return *this; - } - - - vector get_shape() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = dim[d]; - return sh; - } - - vector get_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d]; - return sh; - } - - vector get_memory_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d] * sizeof(T); - return sh; - } -}; - - -/** - * Multidimensional (2 - dimensional) array of type T with contiguous memory layout. - * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @tparam T data type - */ -template -class Array2D : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - using ContiguousArrayND::is_proxy_; - - size_t dim[2] = {0}; ///< dimensions - size_t s[2] = {0}; ///< strides - int ndim = 2; ///< number of dimensions -public: - - /** - * Default empty constructor - */ - Array2D() = default; - - /** - * Parametrized constructor with array name - * @param array_name name of array (for error logging) - */ - Array2D(const string &array_name) { this->array_name = array_name; } - - /** - * Parametrized constructor - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - Array2D(size_t d0, size_t d1, const string &array_name = "Array2D", T *new_data = nullptr) { - init(d0, d1, array_name, new_data); - } - - /** - * Setup the dimensions and strides of array - * @param d0,... array sizes for different dimensions - */ - void set_dimensions(size_t d0, size_t d1) { - - dim[0] = d0; - dim[1] = d1; - - s[1] = 1; - s[0] = s[1] * dim[1]; - - size = s[0] * dim[0]; - }; - - /** - * Initialize array storage, dimensions and strides - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - void init(size_t d0, size_t d1, const string &array_name = "Array2D", T *new_data = nullptr) { - this->array_name = array_name; - - size_t old_size = size; - set_dimensions(d0, d1); - - bool new_is_proxy = (new_data != nullptr); - - if (new_is_proxy) { - if (!is_proxy_) delete[] data; - data = new_data; - } else { - if (size != old_size) { - T *old_data = data; //preserve the pointer to the old data - data = new T[size]; // allocate new data - if (old_data != nullptr) { // - size_t min_size = old_size < size ? old_size : size; - memcpy(data, old_data, min_size * sizeof(T)); - if (!is_proxy_) delete[] old_data; - } - //memset(data, 0, size * sizeof(T)); - } else { - //memset(data, 0, size * sizeof(T)); - } - } - - is_proxy_ = new_is_proxy; - } - - /** - * Resize array - * @param d0,... array sizes for different dimensions - */ - void resize(size_t d0, size_t d1) { - init(d0, d1, this->array_name); - } - - /** - * Reshape array without reset the data - * @param d0,... array sizes for different dimensions - */ - void reshape(size_t d0, size_t d1) { - //check data size consistency - size_t new_size = d0 * d1; - if (new_size != size) - throw invalid_argument("Couldn't reshape array when the size is not conserved"); - set_dimensions(d0, d1); - } - - /** - * Get array size in dimension "d" - * @param d dimension index - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - - /** - * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - void check_indices(size_t i0, size_t i1) const { - - if ((i0 < 0) | (i0 >= dim[0])) { - char buf[1024]; - sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - throw std::out_of_range(buf); - } - - if ((i1 < 0) | (i1 >= dim[1])) { - char buf[1024]; - sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); - throw std::out_of_range(buf); - } - - } - -#endif - - /** - * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline const T &operator()(size_t i0, size_t i1) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1); -#endif - - return data[i0 * s[0] + i1]; - - } - - /** - * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline T &operator()(size_t i0, size_t i1) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1); -#endif - - return data[i0 * s[0] + i1]; - - } - - /** - * Array comparison operator - * @param other - */ - bool operator==(const Array2D &other) const { - //compare dimensions - for (int d = 0; d < ndim; d++) { - if (this->dim[d] != other.dim[d]) - return false; - } - return ContiguousArrayND::operator==(other); - } - - /** - * Convert to nested vector> container - * @return vector container - */ - vector> to_vector() const { - vector> res; - - res.resize(dim[0]); - - for (int i0 = 0; i0 < dim[0]; i0++) { - res[i0].resize(dim[1]); - - - for (int i1 = 0; i1 < dim[1]; i1++) { - res[i0][i1] = operator()(i0, i1); - - } - } - - - return res; - } // end to_vector() - - - /** - * Set values to vector> container - * @param vec container - */ - void set_vector(const vector> &vec) { - size_t d0 = 0; - size_t d1 = 0; - d0 = vec.size(); - - if (d0 > 0) { - d1 = vec.at(0).size(); - - - } - - init(d0, d1, array_name); - for (int i0 = 0; i0 < dim[0]; i0++) { - if (vec.at(i0).size() != d1) - throw std::invalid_argument("Vector size is not constant at dimension 1"); - - for (int i1 = 0; i1 < dim[1]; i1++) { - operator()(i0, i1) = vec.at(i0).at(i1); - - } - } - - } - - /** - * Parametrized constructor from vector> container - * @param vec container - * @param array_name array name - */ - Array2D(const vector> &vec, const string &array_name = "Array2D") { - this->set_vector(vec); - this->array_name = array_name; - } - - /** - * operator= to vector> container - * @param vec container - */ - Array2D &operator=(const vector> &vec) { - this->set_vector(vec); - return *this; - } - - - /** - * operator= to flatten vector container - * @param vec container - */ - Array2D &operator=(const vector &vec) { - this->set_flatten_vector(vec); - return *this; - } - - - vector get_shape() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = dim[d]; - return sh; - } - - vector get_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d]; - return sh; - } - - vector get_memory_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d] * sizeof(T); - return sh; - } -}; - - -/** - * Multidimensional (3 - dimensional) array of type T with contiguous memory layout. - * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @tparam T data type - */ -template -class Array3D : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - using ContiguousArrayND::is_proxy_; - - size_t dim[3] = {0}; ///< dimensions - size_t s[3] = {0}; ///< strides - int ndim = 3; ///< number of dimensions -public: - - /** - * Default empty constructor - */ - Array3D() = default; - - /** - * Parametrized constructor with array name - * @param array_name name of array (for error logging) - */ - Array3D(const string &array_name) { this->array_name = array_name; } - - /** - * Parametrized constructor - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - Array3D(size_t d0, size_t d1, size_t d2, const string &array_name = "Array3D", T *new_data = nullptr) { - init(d0, d1, d2, array_name, new_data); - } - - /** - * Setup the dimensions and strides of array - * @param d0,... array sizes for different dimensions - */ - void set_dimensions(size_t d0, size_t d1, size_t d2) { - - dim[0] = d0; - dim[1] = d1; - dim[2] = d2; - - s[2] = 1; - s[1] = s[2] * dim[2]; - s[0] = s[1] * dim[1]; - - size = s[0] * dim[0]; - }; - - /** - * Initialize array storage, dimensions and strides - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - void init(size_t d0, size_t d1, size_t d2, const string &array_name = "Array3D", T *new_data = nullptr) { - this->array_name = array_name; - - size_t old_size = size; - set_dimensions(d0, d1, d2); - - bool new_is_proxy = (new_data != nullptr); - - if (new_is_proxy) { - if (!is_proxy_) delete[] data; - data = new_data; - } else { - if (size != old_size) { - T *old_data = data; //preserve the pointer to the old data - data = new T[size]; // allocate new data - if (old_data != nullptr) { // - size_t min_size = old_size < size ? old_size : size; - memcpy(data, old_data, min_size * sizeof(T)); - if (!is_proxy_) delete[] old_data; - } - //memset(data, 0, size * sizeof(T)); - } else { - //memset(data, 0, size * sizeof(T)); - } - } - - is_proxy_ = new_is_proxy; - } - - /** - * Resize array - * @param d0,... array sizes for different dimensions - */ - void resize(size_t d0, size_t d1, size_t d2) { - init(d0, d1, d2, this->array_name); - } - - /** - * Reshape array without reset the data - * @param d0,... array sizes for different dimensions - */ - void reshape(size_t d0, size_t d1, size_t d2) { - //check data size consistency - size_t new_size = d0 * d1 * d2; - if (new_size != size) - throw invalid_argument("Couldn't reshape array when the size is not conserved"); - set_dimensions(d0, d1, d2); - } - - /** - * Get array size in dimension "d" - * @param d dimension index - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - - /** - * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - void check_indices(size_t i0, size_t i1, size_t i2) const { - - if ((i0 < 0) | (i0 >= dim[0])) { - char buf[1024]; - sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - throw std::out_of_range(buf); - } - - if ((i1 < 0) | (i1 >= dim[1])) { - char buf[1024]; - sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); - throw std::out_of_range(buf); - } - - if ((i2 < 0) | (i2 >= dim[2])) { - char buf[1024]; - sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); - throw std::out_of_range(buf); - } - - } - -#endif - - /** - * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline const T &operator()(size_t i0, size_t i1, size_t i2) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2]; - - } - - /** - * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline T &operator()(size_t i0, size_t i1, size_t i2) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2]; - - } - - /** - * Array comparison operator - * @param other - */ - bool operator==(const Array3D &other) const { - //compare dimensions - for (int d = 0; d < ndim; d++) { - if (this->dim[d] != other.dim[d]) - return false; - } - return ContiguousArrayND::operator==(other); - } - - /** - * Convert to nested vector> container - * @return vector container - */ - vector>> to_vector() const { - vector>> res; - - res.resize(dim[0]); - - for (int i0 = 0; i0 < dim[0]; i0++) { - res[i0].resize(dim[1]); - - - for (int i1 = 0; i1 < dim[1]; i1++) { - res[i0][i1].resize(dim[2]); - - - for (int i2 = 0; i2 < dim[2]; i2++) { - res[i0][i1][i2] = operator()(i0, i1, i2); - - } - } - } - - - return res; - } // end to_vector() - - - /** - * Set values to vector> container - * @param vec container - */ - void set_vector(const vector>> &vec) { - size_t d0 = 0; - size_t d1 = 0; - size_t d2 = 0; - d0 = vec.size(); - - if (d0 > 0) { - d1 = vec.at(0).size(); - if (d1 > 0) { - d2 = vec.at(0).at(0).size(); - - - } - } - - init(d0, d1, d2, array_name); - for (int i0 = 0; i0 < dim[0]; i0++) { - if (vec.at(i0).size() != d1) - throw std::invalid_argument("Vector size is not constant at dimension 1"); - - for (int i1 = 0; i1 < dim[1]; i1++) { - if (vec.at(i0).at(i1).size() != d2) - throw std::invalid_argument("Vector size is not constant at dimension 2"); - - for (int i2 = 0; i2 < dim[2]; i2++) { - operator()(i0, i1, i2) = vec.at(i0).at(i1).at(i2); - - } - } - } - - } - - /** - * Parametrized constructor from vector> container - * @param vec container - * @param array_name array name - */ - Array3D(const vector>> &vec, const string &array_name = "Array3D") { - this->set_vector(vec); - this->array_name = array_name; - } - - /** - * operator= to vector> container - * @param vec container - */ - Array3D &operator=(const vector>> &vec) { - this->set_vector(vec); - return *this; - } - - - /** - * operator= to flatten vector container - * @param vec container - */ - Array3D &operator=(const vector &vec) { - this->set_flatten_vector(vec); - return *this; - } - - - vector get_shape() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = dim[d]; - return sh; - } - - vector get_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d]; - return sh; - } - - vector get_memory_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d] * sizeof(T); - return sh; - } -}; - - -/** - * Multidimensional (4 - dimensional) array of type T with contiguous memory layout. - * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @tparam T data type - */ -template -class Array4D : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - using ContiguousArrayND::is_proxy_; - - size_t dim[4] = {0}; ///< dimensions - size_t s[4] = {0}; ///< strides - int ndim = 4; ///< number of dimensions -public: - - /** - * Default empty constructor - */ - Array4D() = default; - - /** - * Parametrized constructor with array name - * @param array_name name of array (for error logging) - */ - Array4D(const string &array_name) { this->array_name = array_name; } - - /** - * Parametrized constructor - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - Array4D(size_t d0, size_t d1, size_t d2, size_t d3, const string &array_name = "Array4D", T *new_data = nullptr) { - init(d0, d1, d2, d3, array_name, new_data); - } - - /** - * Setup the dimensions and strides of array - * @param d0,... array sizes for different dimensions - */ - void set_dimensions(size_t d0, size_t d1, size_t d2, size_t d3) { - - dim[0] = d0; - dim[1] = d1; - dim[2] = d2; - dim[3] = d3; - - s[3] = 1; - s[2] = s[3] * dim[3]; - s[1] = s[2] * dim[2]; - s[0] = s[1] * dim[1]; - - size = s[0] * dim[0]; - }; - - /** - * Initialize array storage, dimensions and strides - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - void init(size_t d0, size_t d1, size_t d2, size_t d3, const string &array_name = "Array4D", T *new_data = nullptr) { - this->array_name = array_name; - - size_t old_size = size; - set_dimensions(d0, d1, d2, d3); - - bool new_is_proxy = (new_data != nullptr); - - if (new_is_proxy) { - if (!is_proxy_) delete[] data; - data = new_data; - } else { - if (size != old_size) { - T *old_data = data; //preserve the pointer to the old data - data = new T[size]; // allocate new data - if (old_data != nullptr) { // - size_t min_size = old_size < size ? old_size : size; - memcpy(data, old_data, min_size * sizeof(T)); - if (!is_proxy_) delete[] old_data; - } - //memset(data, 0, size * sizeof(T)); - } else { - //memset(data, 0, size * sizeof(T)); - } - } - - is_proxy_ = new_is_proxy; - } - - /** - * Resize array - * @param d0,... array sizes for different dimensions - */ - void resize(size_t d0, size_t d1, size_t d2, size_t d3) { - init(d0, d1, d2, d3, this->array_name); - } - - /** - * Reshape array without reset the data - * @param d0,... array sizes for different dimensions - */ - void reshape(size_t d0, size_t d1, size_t d2, size_t d3) { - //check data size consistency - size_t new_size = d0 * d1 * d2 * d3; - if (new_size != size) - throw invalid_argument("Couldn't reshape array when the size is not conserved"); - set_dimensions(d0, d1, d2, d3); - } - - /** - * Get array size in dimension "d" - * @param d dimension index - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - - /** - * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - void check_indices(size_t i0, size_t i1, size_t i2, size_t i3) const { - - if ((i0 < 0) | (i0 >= dim[0])) { - char buf[1024]; - sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - throw std::out_of_range(buf); - } - - if ((i1 < 0) | (i1 >= dim[1])) { - char buf[1024]; - sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); - throw std::out_of_range(buf); - } - - if ((i2 < 0) | (i2 >= dim[2])) { - char buf[1024]; - sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); - throw std::out_of_range(buf); - } - - if ((i3 < 0) | (i3 >= dim[3])) { - char buf[1024]; - sprintf(buf, "%s: index i3=%ld out of range (0, %ld)\n", array_name.c_str(), i3, dim[3] - 1); - throw std::out_of_range(buf); - } - - } - -#endif - - /** - * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline const T &operator()(size_t i0, size_t i1, size_t i2, size_t i3) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2, i3); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3]; - - } - - /** - * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline T &operator()(size_t i0, size_t i1, size_t i2, size_t i3) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2, i3); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3]; - - } - - /** - * Array comparison operator - * @param other - */ - bool operator==(const Array4D &other) const { - //compare dimensions - for (int d = 0; d < ndim; d++) { - if (this->dim[d] != other.dim[d]) - return false; - } - return ContiguousArrayND::operator==(other); - } - - /** - * Convert to nested vector> container - * @return vector container - */ - vector>>> to_vector() const { - vector>>> res; - - res.resize(dim[0]); - - for (int i0 = 0; i0 < dim[0]; i0++) { - res[i0].resize(dim[1]); - - - for (int i1 = 0; i1 < dim[1]; i1++) { - res[i0][i1].resize(dim[2]); - - - for (int i2 = 0; i2 < dim[2]; i2++) { - res[i0][i1][i2].resize(dim[3]); - - - for (int i3 = 0; i3 < dim[3]; i3++) { - res[i0][i1][i2][i3] = operator()(i0, i1, i2, i3); - - } - } - } - } - - - return res; - } // end to_vector() - - - /** - * Set values to vector> container - * @param vec container - */ - void set_vector(const vector>>> &vec) { - size_t d0 = 0; - size_t d1 = 0; - size_t d2 = 0; - size_t d3 = 0; - d0 = vec.size(); - - if (d0 > 0) { - d1 = vec.at(0).size(); - if (d1 > 0) { - d2 = vec.at(0).at(0).size(); - if (d2 > 0) { - d3 = vec.at(0).at(0).at(0).size(); - - - } - } - } - - init(d0, d1, d2, d3, array_name); - for (int i0 = 0; i0 < dim[0]; i0++) { - if (vec.at(i0).size() != d1) - throw std::invalid_argument("Vector size is not constant at dimension 1"); - - for (int i1 = 0; i1 < dim[1]; i1++) { - if (vec.at(i0).at(i1).size() != d2) - throw std::invalid_argument("Vector size is not constant at dimension 2"); - - for (int i2 = 0; i2 < dim[2]; i2++) { - if (vec.at(i0).at(i1).at(i2).size() != d3) - throw std::invalid_argument("Vector size is not constant at dimension 3"); - - for (int i3 = 0; i3 < dim[3]; i3++) { - operator()(i0, i1, i2, i3) = vec.at(i0).at(i1).at(i2).at(i3); - - } - } - } - } - - } - - /** - * Parametrized constructor from vector> container - * @param vec container - * @param array_name array name - */ - Array4D(const vector>>> &vec, const string &array_name = "Array4D") { - this->set_vector(vec); - this->array_name = array_name; - } - - /** - * operator= to vector> container - * @param vec container - */ - Array4D &operator=(const vector>>> &vec) { - this->set_vector(vec); - return *this; - } - - - /** - * operator= to flatten vector container - * @param vec container - */ - Array4D &operator=(const vector &vec) { - this->set_flatten_vector(vec); - return *this; - } - - - vector get_shape() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = dim[d]; - return sh; - } - - vector get_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d]; - return sh; - } - - vector get_memory_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d] * sizeof(T); - return sh; - } -}; - - -/** - * Multidimensional (5 - dimensional) array of type T with contiguous memory layout. - * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @tparam T data type - */ -template -class Array5D : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - using ContiguousArrayND::is_proxy_; - - size_t dim[5] = {0}; ///< dimensions - size_t s[5] = {0}; ///< strides - int ndim = 5; ///< number of dimensions -public: - - /** - * Default empty constructor - */ - Array5D() = default; - - /** - * Parametrized constructor with array name - * @param array_name name of array (for error logging) - */ - Array5D(const string &array_name) { this->array_name = array_name; } - - /** - * Parametrized constructor - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - Array5D(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, const string &array_name = "Array5D", - T *new_data = nullptr) { - init(d0, d1, d2, d3, d4, array_name, new_data); - } - - /** - * Setup the dimensions and strides of array - * @param d0,... array sizes for different dimensions - */ - void set_dimensions(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4) { - - dim[0] = d0; - dim[1] = d1; - dim[2] = d2; - dim[3] = d3; - dim[4] = d4; - - s[4] = 1; - s[3] = s[4] * dim[4]; - s[2] = s[3] * dim[3]; - s[1] = s[2] * dim[2]; - s[0] = s[1] * dim[1]; - - size = s[0] * dim[0]; - }; - - /** - * Initialize array storage, dimensions and strides - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - void init(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, const string &array_name = "Array5D", - T *new_data = nullptr) { - this->array_name = array_name; - - size_t old_size = size; - set_dimensions(d0, d1, d2, d3, d4); - - bool new_is_proxy = (new_data != nullptr); - - if (new_is_proxy) { - if (!is_proxy_) delete[] data; - data = new_data; - } else { - if (size != old_size) { - T *old_data = data; //preserve the pointer to the old data - data = new T[size]; // allocate new data - if (old_data != nullptr) { // - size_t min_size = old_size < size ? old_size : size; - memcpy(data, old_data, min_size * sizeof(T)); - if (!is_proxy_) delete[] old_data; - } - //memset(data, 0, size * sizeof(T)); - } else { - //memset(data, 0, size * sizeof(T)); - } - } - - is_proxy_ = new_is_proxy; - } - - /** - * Resize array - * @param d0,... array sizes for different dimensions - */ - void resize(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4) { - init(d0, d1, d2, d3, d4, this->array_name); - } - - /** - * Reshape array without reset the data - * @param d0,... array sizes for different dimensions - */ - void reshape(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4) { - //check data size consistency - size_t new_size = d0 * d1 * d2 * d3 * d4; - if (new_size != size) - throw invalid_argument("Couldn't reshape array when the size is not conserved"); - set_dimensions(d0, d1, d2, d3, d4); - } - - /** - * Get array size in dimension "d" - * @param d dimension index - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - - /** - * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - void check_indices(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4) const { - - if ((i0 < 0) | (i0 >= dim[0])) { - char buf[1024]; - sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - throw std::out_of_range(buf); - } - - if ((i1 < 0) | (i1 >= dim[1])) { - char buf[1024]; - sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); - throw std::out_of_range(buf); - } - - if ((i2 < 0) | (i2 >= dim[2])) { - char buf[1024]; - sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); - throw std::out_of_range(buf); - } - - if ((i3 < 0) | (i3 >= dim[3])) { - char buf[1024]; - sprintf(buf, "%s: index i3=%ld out of range (0, %ld)\n", array_name.c_str(), i3, dim[3] - 1); - throw std::out_of_range(buf); - } - - if ((i4 < 0) | (i4 >= dim[4])) { - char buf[1024]; - sprintf(buf, "%s: index i4=%ld out of range (0, %ld)\n", array_name.c_str(), i4, dim[4] - 1); - throw std::out_of_range(buf); - } - - } - -#endif - - /** - * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline const T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2, i3, i4); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4]; - - } - - /** - * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2, i3, i4); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4]; - - } - - /** - * Array comparison operator - * @param other - */ - bool operator==(const Array5D &other) const { - //compare dimensions - for (int d = 0; d < ndim; d++) { - if (this->dim[d] != other.dim[d]) - return false; - } - return ContiguousArrayND::operator==(other); - } - - /** - * Convert to nested vector> container - * @return vector container - */ - vector>>>> to_vector() const { - vector>>>> res; - - res.resize(dim[0]); - - for (int i0 = 0; i0 < dim[0]; i0++) { - res[i0].resize(dim[1]); - - - for (int i1 = 0; i1 < dim[1]; i1++) { - res[i0][i1].resize(dim[2]); - - - for (int i2 = 0; i2 < dim[2]; i2++) { - res[i0][i1][i2].resize(dim[3]); - - - for (int i3 = 0; i3 < dim[3]; i3++) { - res[i0][i1][i2][i3].resize(dim[4]); - - - for (int i4 = 0; i4 < dim[4]; i4++) { - res[i0][i1][i2][i3][i4] = operator()(i0, i1, i2, i3, i4); - - } - } - } - } - } - - - return res; - } // end to_vector() - - - /** - * Set values to vector> container - * @param vec container - */ - void set_vector(const vector>>>> &vec) { - size_t d0 = 0; - size_t d1 = 0; - size_t d2 = 0; - size_t d3 = 0; - size_t d4 = 0; - d0 = vec.size(); - - if (d0 > 0) { - d1 = vec.at(0).size(); - if (d1 > 0) { - d2 = vec.at(0).at(0).size(); - if (d2 > 0) { - d3 = vec.at(0).at(0).at(0).size(); - if (d3 > 0) { - d4 = vec.at(0).at(0).at(0).at(0).size(); - - - } - } - } - } - - init(d0, d1, d2, d3, d4, array_name); - for (int i0 = 0; i0 < dim[0]; i0++) { - if (vec.at(i0).size() != d1) - throw std::invalid_argument("Vector size is not constant at dimension 1"); - - for (int i1 = 0; i1 < dim[1]; i1++) { - if (vec.at(i0).at(i1).size() != d2) - throw std::invalid_argument("Vector size is not constant at dimension 2"); - - for (int i2 = 0; i2 < dim[2]; i2++) { - if (vec.at(i0).at(i1).at(i2).size() != d3) - throw std::invalid_argument("Vector size is not constant at dimension 3"); - - for (int i3 = 0; i3 < dim[3]; i3++) { - if (vec.at(i0).at(i1).at(i2).at(i3).size() != d4) - throw std::invalid_argument("Vector size is not constant at dimension 4"); - - for (int i4 = 0; i4 < dim[4]; i4++) { - operator()(i0, i1, i2, i3, i4) = vec.at(i0).at(i1).at(i2).at(i3).at(i4); - - } - } - } - } - } - - } - - /** - * Parametrized constructor from vector> container - * @param vec container - * @param array_name array name - */ - Array5D(const vector>>>> &vec, const string &array_name = "Array5D") { - this->set_vector(vec); - this->array_name = array_name; - } - - /** - * operator= to vector> container - * @param vec container - */ - Array5D &operator=(const vector>>>> &vec) { - this->set_vector(vec); - return *this; - } - - - /** - * operator= to flatten vector container - * @param vec container - */ - Array5D &operator=(const vector &vec) { - this->set_flatten_vector(vec); - return *this; - } - - - vector get_shape() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = dim[d]; - return sh; - } - - vector get_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d]; - return sh; - } - - vector get_memory_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d] * sizeof(T); - return sh; - } -}; - - -/** - * Multidimensional (6 - dimensional) array of type T with contiguous memory layout. - * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @tparam T data type - */ -template -class Array6D : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - using ContiguousArrayND::is_proxy_; - - size_t dim[6] = {0}; ///< dimensions - size_t s[6] = {0}; ///< strides - int ndim = 6; ///< number of dimensions -public: - - /** - * Default empty constructor - */ - Array6D() = default; - - /** - * Parametrized constructor with array name - * @param array_name name of array (for error logging) - */ - Array6D(const string &array_name) { this->array_name = array_name; } - - /** - * Parametrized constructor - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - Array6D(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5, const string &array_name = "Array6D", - T *new_data = nullptr) { - init(d0, d1, d2, d3, d4, d5, array_name, new_data); - } - - /** - * Setup the dimensions and strides of array - * @param d0,... array sizes for different dimensions - */ - void set_dimensions(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5) { - - dim[0] = d0; - dim[1] = d1; - dim[2] = d2; - dim[3] = d3; - dim[4] = d4; - dim[5] = d5; - - s[5] = 1; - s[4] = s[5] * dim[5]; - s[3] = s[4] * dim[4]; - s[2] = s[3] * dim[3]; - s[1] = s[2] * dim[2]; - s[0] = s[1] * dim[1]; - - size = s[0] * dim[0]; - }; - - /** - * Initialize array storage, dimensions and strides - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - void init(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5, const string &array_name = "Array6D", - T *new_data = nullptr) { - this->array_name = array_name; - - size_t old_size = size; - set_dimensions(d0, d1, d2, d3, d4, d5); - - bool new_is_proxy = (new_data != nullptr); - - if (new_is_proxy) { - if (!is_proxy_) delete[] data; - data = new_data; - } else { - if (size != old_size) { - T *old_data = data; //preserve the pointer to the old data - data = new T[size]; // allocate new data - if (old_data != nullptr) { // - size_t min_size = old_size < size ? old_size : size; - memcpy(data, old_data, min_size * sizeof(T)); - if (!is_proxy_) delete[] old_data; - } - //memset(data, 0, size * sizeof(T)); - } else { - //memset(data, 0, size * sizeof(T)); - } - } - - is_proxy_ = new_is_proxy; - } - - /** - * Resize array - * @param d0,... array sizes for different dimensions - */ - void resize(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5) { - init(d0, d1, d2, d3, d4, d5, this->array_name); - } - - /** - * Reshape array without reset the data - * @param d0,... array sizes for different dimensions - */ - void reshape(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5) { - //check data size consistency - size_t new_size = d0 * d1 * d2 * d3 * d4 * d5; - if (new_size != size) - throw invalid_argument("Couldn't reshape array when the size is not conserved"); - set_dimensions(d0, d1, d2, d3, d4, d5); - } - - /** - * Get array size in dimension "d" - * @param d dimension index - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - - /** - * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - void check_indices(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4, size_t i5) const { - - if ((i0 < 0) | (i0 >= dim[0])) { - char buf[1024]; - sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - throw std::out_of_range(buf); - } - - if ((i1 < 0) | (i1 >= dim[1])) { - char buf[1024]; - sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); - throw std::out_of_range(buf); - } - - if ((i2 < 0) | (i2 >= dim[2])) { - char buf[1024]; - sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); - throw std::out_of_range(buf); - } - - if ((i3 < 0) | (i3 >= dim[3])) { - char buf[1024]; - sprintf(buf, "%s: index i3=%ld out of range (0, %ld)\n", array_name.c_str(), i3, dim[3] - 1); - throw std::out_of_range(buf); - } - - if ((i4 < 0) | (i4 >= dim[4])) { - char buf[1024]; - sprintf(buf, "%s: index i4=%ld out of range (0, %ld)\n", array_name.c_str(), i4, dim[4] - 1); - throw std::out_of_range(buf); - } - - if ((i5 < 0) | (i5 >= dim[5])) { - char buf[1024]; - sprintf(buf, "%s: index i5=%ld out of range (0, %ld)\n", array_name.c_str(), i5, dim[5] - 1); - throw std::out_of_range(buf); - } - - } - -#endif - - /** - * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline const T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4, size_t i5) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2, i3, i4, i5); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4 * s[4] + i5]; - - } - - /** - * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4, size_t i5) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2, i3, i4, i5); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4 * s[4] + i5]; - - } - - /** - * Array comparison operator - * @param other - */ - bool operator==(const Array6D &other) const { - //compare dimensions - for (int d = 0; d < ndim; d++) { - if (this->dim[d] != other.dim[d]) - return false; - } - return ContiguousArrayND::operator==(other); - } - - /** - * Convert to nested vector> container - * @return vector container - */ - vector>>>>> to_vector() const { - vector>>>>> res; - - res.resize(dim[0]); - - for (int i0 = 0; i0 < dim[0]; i0++) { - res[i0].resize(dim[1]); - - - for (int i1 = 0; i1 < dim[1]; i1++) { - res[i0][i1].resize(dim[2]); - - - for (int i2 = 0; i2 < dim[2]; i2++) { - res[i0][i1][i2].resize(dim[3]); - - - for (int i3 = 0; i3 < dim[3]; i3++) { - res[i0][i1][i2][i3].resize(dim[4]); - - - for (int i4 = 0; i4 < dim[4]; i4++) { - res[i0][i1][i2][i3][i4].resize(dim[5]); - - - for (int i5 = 0; i5 < dim[5]; i5++) { - res[i0][i1][i2][i3][i4][i5] = operator()(i0, i1, i2, i3, i4, i5); - - } - } - } - } - } - } - - - return res; - } // end to_vector() - - - /** - * Set values to vector> container - * @param vec container - */ - void set_vector(const vector>>>>> &vec) { - size_t d0 = 0; - size_t d1 = 0; - size_t d2 = 0; - size_t d3 = 0; - size_t d4 = 0; - size_t d5 = 0; - d0 = vec.size(); - - if (d0 > 0) { - d1 = vec.at(0).size(); - if (d1 > 0) { - d2 = vec.at(0).at(0).size(); - if (d2 > 0) { - d3 = vec.at(0).at(0).at(0).size(); - if (d3 > 0) { - d4 = vec.at(0).at(0).at(0).at(0).size(); - if (d4 > 0) { - d5 = vec.at(0).at(0).at(0).at(0).at(0).size(); - - - } - } - } - } - } - - init(d0, d1, d2, d3, d4, d5, array_name); - for (int i0 = 0; i0 < dim[0]; i0++) { - if (vec.at(i0).size() != d1) - throw std::invalid_argument("Vector size is not constant at dimension 1"); - - for (int i1 = 0; i1 < dim[1]; i1++) { - if (vec.at(i0).at(i1).size() != d2) - throw std::invalid_argument("Vector size is not constant at dimension 2"); - - for (int i2 = 0; i2 < dim[2]; i2++) { - if (vec.at(i0).at(i1).at(i2).size() != d3) - throw std::invalid_argument("Vector size is not constant at dimension 3"); - - for (int i3 = 0; i3 < dim[3]; i3++) { - if (vec.at(i0).at(i1).at(i2).at(i3).size() != d4) - throw std::invalid_argument("Vector size is not constant at dimension 4"); - - for (int i4 = 0; i4 < dim[4]; i4++) { - if (vec.at(i0).at(i1).at(i2).at(i3).at(i4).size() != d5) - throw std::invalid_argument("Vector size is not constant at dimension 5"); - - for (int i5 = 0; i5 < dim[5]; i5++) { - operator()(i0, i1, i2, i3, i4, i5) = vec.at(i0).at(i1).at(i2).at(i3).at(i4).at(i5); - - } - } - } - } - } - } - - } - - /** - * Parametrized constructor from vector> container - * @param vec container - * @param array_name array name - */ - Array6D(const vector>>>>> &vec, const string &array_name = "Array6D") { - this->set_vector(vec); - this->array_name = array_name; - } - - /** - * operator= to vector> container - * @param vec container - */ - Array6D &operator=(const vector>>>>> &vec) { - this->set_vector(vec); - return *this; - } - - - /** - * operator= to flatten vector container - * @param vec container - */ - Array6D &operator=(const vector &vec) { - this->set_flatten_vector(vec); - return *this; - } - - - vector get_shape() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = dim[d]; - return sh; - } - - vector get_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d]; - return sh; - } - - vector get_memory_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d] * sizeof(T); - return sh; - } -}; - - -#endif //ACE_MULTIARRAY_H diff --git a/lib/pace/ace_c_basis.cpp b/lib/pace/ace_c_basis.cpp deleted file mode 100644 index d1c55700b7..0000000000 --- a/lib/pace/ace_c_basis.cpp +++ /dev/null @@ -1,980 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Yury Lysogorskiy on 1.04.20. - -#include "ace_c_basis.h" -#include "ships_radial.h" - -using namespace std; - -ACECTildeBasisSet::ACECTildeBasisSet(string filename) { - load(filename); -} - -ACECTildeBasisSet::ACECTildeBasisSet(const ACECTildeBasisSet &other) { - ACECTildeBasisSet::_copy_scalar_memory(other); - ACECTildeBasisSet::_copy_dynamic_memory(other); - pack_flatten_basis(); -} - - -ACECTildeBasisSet &ACECTildeBasisSet::operator=(const ACECTildeBasisSet &other) { - if (this != &other) { - _clean(); - _copy_scalar_memory(other); - _copy_dynamic_memory(other); - pack_flatten_basis(); - } - return *this; -} - - -ACECTildeBasisSet::~ACECTildeBasisSet() { - ACECTildeBasisSet::_clean(); -} - -void ACECTildeBasisSet::_clean() { - // call parent method - ACEFlattenBasisSet::_clean(); - _clean_contiguous_arrays(); - _clean_basis_arrays(); -} - -void ACECTildeBasisSet::_copy_scalar_memory(const ACECTildeBasisSet &src) { - ACEFlattenBasisSet::_copy_scalar_memory(src); - num_ctilde_max = src.num_ctilde_max; -} - -void ACECTildeBasisSet::_copy_dynamic_memory(const ACECTildeBasisSet &src) {//allocate new memory - ACEFlattenBasisSet::_copy_dynamic_memory(src); - - if (src.basis_rank1 == nullptr) - throw runtime_error("Could not copy ACECTildeBasisSet::basis_rank1 - array not initialized"); - if (src.basis == nullptr) throw runtime_error("Could not copy ACECTildeBasisSet::basis - array not initialized"); - - - basis_rank1 = new ACECTildeBasisFunction *[src.nelements]; - basis = new ACECTildeBasisFunction *[src.nelements]; - - //copy basis arrays - for (SPECIES_TYPE mu = 0; mu < src.nelements; ++mu) { - basis_rank1[mu] = new ACECTildeBasisFunction[src.total_basis_size_rank1[mu]]; - - for (size_t i = 0; i < src.total_basis_size_rank1[mu]; i++) { - basis_rank1[mu][i] = src.basis_rank1[mu][i]; - } - - - basis[mu] = new ACECTildeBasisFunction[src.total_basis_size[mu]]; - for (size_t i = 0; i < src.total_basis_size[mu]; i++) { - basis[mu][i] = src.basis[mu][i]; - } - } - //DON"T COPY CONTIGUOUS ARRAY, REBUILD THEM -} - -void ACECTildeBasisSet::_clean_contiguous_arrays() { - ACEFlattenBasisSet::_clean_contiguous_arrays(); - - delete[] full_c_tildes_rank1; - full_c_tildes_rank1 = nullptr; - - delete[] full_c_tildes; - full_c_tildes = nullptr; -} - -//re-pack the constituent dynamic arrays of all basis functions in contiguous arrays -void ACECTildeBasisSet::pack_flatten_basis() { - compute_array_sizes(basis_rank1, basis); - - //1. clean contiguous arrays - _clean_contiguous_arrays(); - //2. allocate contiguous arrays - delete[] full_ns_rank1; - full_ns_rank1 = new NS_TYPE[rank_array_total_size_rank1]; - delete[] full_ls_rank1; - full_ls_rank1 = new NS_TYPE[rank_array_total_size_rank1]; - delete[] full_mus_rank1; - full_mus_rank1 = new SPECIES_TYPE[rank_array_total_size_rank1]; - delete[] full_ms_rank1; - full_ms_rank1 = new MS_TYPE[rank_array_total_size_rank1]; - - delete[] full_c_tildes_rank1; - full_c_tildes_rank1 = new DOUBLE_TYPE[coeff_array_total_size_rank1]; - - - delete[] full_ns; - full_ns = new NS_TYPE[rank_array_total_size]; - delete[] full_ls; - full_ls = new LS_TYPE[rank_array_total_size]; - delete[] full_mus; - full_mus = new SPECIES_TYPE[rank_array_total_size]; - delete[] full_ms; - full_ms = new MS_TYPE[ms_array_total_size]; - - delete[] full_c_tildes; - full_c_tildes = new DOUBLE_TYPE[coeff_array_total_size]; - - - //3. copy the values from private C_tilde_B_basis_function arrays to new contigous space - //4. clean private memory - //5. reassign private array pointers - - //r = 0, rank = 1 - size_t rank_array_ind_rank1 = 0; - size_t coeff_array_ind_rank1 = 0; - size_t ms_array_ind_rank1 = 0; - - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - for (int func_ind_r1 = 0; func_ind_r1 < total_basis_size_rank1[mu]; ++func_ind_r1) { - ACECTildeBasisFunction &func = basis_rank1[mu][func_ind_r1]; - - //copy values ns from c_tilde_basis_function private memory to contigous memory part - full_ns_rank1[rank_array_ind_rank1] = func.ns[0]; - - //copy values ls from c_tilde_basis_function private memory to contigous memory part - full_ls_rank1[rank_array_ind_rank1] = func.ls[0]; - - //copy values mus from c_tilde_basis_function private memory to contigous memory part - full_mus_rank1[rank_array_ind_rank1] = func.mus[0]; - - //copy values ctildes from c_tilde_basis_function private memory to contigous memory part - memcpy(&full_c_tildes_rank1[coeff_array_ind_rank1], func.ctildes, - func.ndensity * sizeof(DOUBLE_TYPE)); - - - //copy values mus from c_tilde_basis_function private memory to contigous memory part - memcpy(&full_ms_rank1[ms_array_ind_rank1], func.ms_combs, - func.num_ms_combs * - func.rank * sizeof(MS_TYPE)); - - //release memory of each ACECTildeBasisFunction if it is not proxy - func._clean(); - - func.mus = &full_mus_rank1[rank_array_ind_rank1]; - func.ns = &full_ns_rank1[rank_array_ind_rank1]; - func.ls = &full_ls_rank1[rank_array_ind_rank1]; - func.ms_combs = &full_ms_rank1[ms_array_ind_rank1]; - func.ctildes = &full_c_tildes_rank1[coeff_array_ind_rank1]; - func.is_proxy = true; - - rank_array_ind_rank1 += func.rank; - ms_array_ind_rank1 += func.rank * - func.num_ms_combs; - coeff_array_ind_rank1 += func.num_ms_combs * func.ndensity; - - } - } - - - //rank>1, r>0 - size_t rank_array_ind = 0; - size_t coeff_array_ind = 0; - size_t ms_array_ind = 0; - - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - for (int func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) { - ACECTildeBasisFunction &func = basis[mu][func_ind]; - - //copy values mus from c_tilde_basis_function private memory to contigous memory part - memcpy(&full_mus[rank_array_ind], func.mus, - func.rank * sizeof(SPECIES_TYPE)); - - //copy values ns from c_tilde_basis_function private memory to contigous memory part - memcpy(&full_ns[rank_array_ind], func.ns, - func.rank * sizeof(NS_TYPE)); - //copy values ls from c_tilde_basis_function private memory to contigous memory part - memcpy(&full_ls[rank_array_ind], func.ls, - func.rank * sizeof(LS_TYPE)); - //copy values mus from c_tilde_basis_function private memory to contigous memory part - memcpy(&full_ms[ms_array_ind], func.ms_combs, - func.num_ms_combs * - func.rank * sizeof(MS_TYPE)); - - //copy values ctildes from c_tilde_basis_function private memory to contigous memory part - memcpy(&full_c_tildes[coeff_array_ind], func.ctildes, - func.num_ms_combs * func.ndensity * sizeof(DOUBLE_TYPE)); - - - //release memory of each ACECTildeBasisFunction if it is not proxy - func._clean(); - - func.ns = &full_ns[rank_array_ind]; - func.ls = &full_ls[rank_array_ind]; - func.mus = &full_mus[rank_array_ind]; - func.ctildes = &full_c_tildes[coeff_array_ind]; - func.ms_combs = &full_ms[ms_array_ind]; - func.is_proxy = true; - - rank_array_ind += func.rank; - ms_array_ind += func.rank * - func.num_ms_combs; - coeff_array_ind += func.num_ms_combs * func.ndensity; - } - } -} - -void fwrite_c_tilde_b_basis_func(FILE *fptr, ACECTildeBasisFunction &func) { - RANK_TYPE r; - fprintf(fptr, "ctilde_basis_func: "); - fprintf(fptr, "rank=%d ndens=%d mu0=%d ", func.rank, func.ndensity, func.mu0); - - fprintf(fptr, "mu=("); - for (r = 0; r < func.rank; ++r) - fprintf(fptr, " %d ", func.mus[r]); - fprintf(fptr, ")\n"); - - fprintf(fptr, "n=("); - for (r = 0; r < func.rank; ++r) - fprintf(fptr, " %d ", func.ns[r]); - fprintf(fptr, ")\n"); - - fprintf(fptr, "l=("); - for (r = 0; r < func.rank; ++r) - fprintf(fptr, " %d ", func.ls[r]); - fprintf(fptr, ")\n"); - - fprintf(fptr, "num_ms=%d\n", func.num_ms_combs); - - for (int m_ind = 0; m_ind < func.num_ms_combs; m_ind++) { - fprintf(fptr, "<"); - for (r = 0; r < func.rank; ++r) - fprintf(fptr, " %d ", func.ms_combs[m_ind * func.rank + r]); - fprintf(fptr, ">: "); - for (DENSITY_TYPE p = 0; p < func.ndensity; p++) - fprintf(fptr, " %.18f ", func.ctildes[m_ind * func.ndensity + p]); - fprintf(fptr, "\n"); - } - -} - -void ACECTildeBasisSet::save(const string &filename) { - FILE *fptr; - fptr = fopen(filename.c_str(), "w"); - - fprintf(fptr, "nelements=%d\n", nelements); - - //elements mapping - fprintf(fptr, "elements:"); - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) - fprintf(fptr, " %s", elements_name[mu].c_str()); - fprintf(fptr, "\n\n"); - - fprintf(fptr, "lmax=%d\n\n", lmax); - - fprintf(fptr, "embedding-function: %s\n", npoti.c_str()); - - fprintf(fptr, "%ld FS parameters: ", FS_parameters.size()); - for (int i = 0; i < FS_parameters.size(); ++i) { - fprintf(fptr, " %f", FS_parameters.at(i)); - } - fprintf(fptr, "\n"); - - //hard-core energy cutoff repulsion - fprintf(fptr, "core energy-cutoff parameters: "); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - fprintf(fptr, "%.18f %.18f\n", rho_core_cutoffs(mu_i), drho_core_cutoffs(mu_i)); - - // save E0 values - fprintf(fptr, "E0:"); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - fprintf(fptr, " %.18f", E0vals(mu_i)); - fprintf(fptr, "\n"); - - - fprintf(fptr, "\n"); - - - fprintf(fptr, "radbasename=%s\n", radial_functions->radbasename.c_str()); - fprintf(fptr, "nradbase=%d\n", nradbase); - fprintf(fptr, "nradmax=%d\n", nradmax); - - - fprintf(fptr, "cutoffmax=%f\n", cutoffmax); - - fprintf(fptr, "deltaSplineBins=%f\n", deltaSplineBins); - - //hard-core repulsion - fprintf(fptr, "core repulsion parameters: "); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) - fprintf(fptr, "%.18f %.18f\n", radial_functions->prehc(mu_i, mu_j), radial_functions->lambdahc(mu_j, mu_j)); - - - - - - //TODO: radial functions - //radparameter - fprintf(fptr, "radparameter="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) - fprintf(fptr, " %.18f", radial_functions->lambda(mu_i, mu_j)); - fprintf(fptr, "\n"); - - fprintf(fptr, "cutoff="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) - fprintf(fptr, " %.18f", radial_functions->cut(mu_i, mu_j)); - fprintf(fptr, "\n"); - - fprintf(fptr, "dcut="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) - fprintf(fptr, " %.18f", radial_functions->dcut(mu_i, mu_j)); - fprintf(fptr, "\n"); - - fprintf(fptr, "crad="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { - for (NS_TYPE k = 0; k < nradbase; k++) { - for (NS_TYPE n = 0; n < nradmax; n++) { - for (LS_TYPE l = 0; l <= lmax; l++) { - fprintf(fptr, " %.18f", radial_functions->crad(mu_i, mu_j, n, l, k)); - } - fprintf(fptr, "\n"); - } - } - } - - fprintf(fptr, "\n"); - - fprintf(fptr, "rankmax=%d\n", rankmax); - fprintf(fptr, "ndensitymax=%d\n", ndensitymax); - fprintf(fptr, "\n"); - - //num_c_tilde_max - fprintf(fptr, "num_c_tilde_max=%d\n", num_ctilde_max); - fprintf(fptr, "num_ms_combinations_max=%d\n", num_ms_combinations_max); - - - //write total_basis_size and total_basis_size_rank1 - fprintf(fptr, "total_basis_size_rank1: "); - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - fprintf(fptr, "%d ", total_basis_size_rank1[mu]); - } - fprintf(fptr, "\n"); - - for (SPECIES_TYPE mu = 0; mu < nelements; mu++) - for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size_rank1[mu]; ++func_ind) - fwrite_c_tilde_b_basis_func(fptr, basis_rank1[mu][func_ind]); - - fprintf(fptr, "total_basis_size: "); - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - fprintf(fptr, "%d ", total_basis_size[mu]); - } - fprintf(fptr, "\n"); - - for (SPECIES_TYPE mu = 0; mu < nelements; mu++) - for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) - fwrite_c_tilde_b_basis_func(fptr, basis[mu][func_ind]); - - - fclose(fptr); -} - -void fread_c_tilde_b_basis_func(FILE *fptr, ACECTildeBasisFunction &func) { - RANK_TYPE r; - int res; - char buf[3][128]; - - res = fscanf(fptr, " ctilde_basis_func: "); - - res = fscanf(fptr, "rank=%s ndens=%s mu0=%s ", buf[0], buf[1], buf[2]); - if (res != 3) - throw invalid_argument("Could not read C-tilde basis function"); - - func.rank = (RANK_TYPE) stol(buf[0]); - func.ndensity = (DENSITY_TYPE) stol(buf[1]); - func.mu0 = (SPECIES_TYPE) stol(buf[2]); - - func.mus = new SPECIES_TYPE[func.rank]; - func.ns = new NS_TYPE[func.rank]; - func.ls = new LS_TYPE[func.rank]; - - res = fscanf(fptr, " mu=("); - for (r = 0; r < func.rank; ++r) { - res = fscanf(fptr, "%s", buf[0]); - if (res != 1) - throw invalid_argument("Could not read C-tilde basis function"); - func.mus[r] = (SPECIES_TYPE) stol(buf[0]); - } - res = fscanf(fptr, " )"); // ")" - - res = fscanf(fptr, " n=("); // "n=" - for (r = 0; r < func.rank; ++r) { - res = fscanf(fptr, "%s", buf[0]); - if (res != 1) - throw invalid_argument("Could not read C-tilde basis function"); - - func.ns[r] = (NS_TYPE) stol(buf[0]); - } - res = fscanf(fptr, " )"); - - res = fscanf(fptr, " l=("); - for (r = 0; r < func.rank; ++r) { - res = fscanf(fptr, "%s", buf[0]); - if (res != 1) - throw invalid_argument("Could not read C-tilde basis function"); - func.ls[r] = (NS_TYPE) stol(buf[0]); - } - res = fscanf(fptr, " )"); - - res = fscanf(fptr, " num_ms=%s\n", buf[0]); - if (res != 1) - throw invalid_argument("Could not read C-tilde basis function"); - - func.num_ms_combs = (SHORT_INT_TYPE) stoi(buf[0]); - - func.ms_combs = new MS_TYPE[func.rank * func.num_ms_combs]; - func.ctildes = new DOUBLE_TYPE[func.ndensity * func.num_ms_combs]; - - for (int m_ind = 0; m_ind < func.num_ms_combs; m_ind++) { - res = fscanf(fptr, " <"); - for (r = 0; r < func.rank; ++r) { - res = fscanf(fptr, "%s", buf[0]); - if (res != 1) - throw invalid_argument("Could not read C-tilde basis function"); - func.ms_combs[m_ind * func.rank + r] = stoi(buf[0]); - } - res = fscanf(fptr, " >:"); - for (DENSITY_TYPE p = 0; p < func.ndensity; p++) { - res = fscanf(fptr, "%s", buf[0]); - if (res != 1) - throw invalid_argument("Could not read C-tilde basis function"); - func.ctildes[m_ind * func.ndensity + p] = stod(buf[0]); - } - } -} - -string -format_error_message(const char *buffer, const string &filename, const string &var_name, const string &expected) { - string err_message = "File '" + filename + "': couldn't read '" + var_name + "'"; - if (buffer) - err_message = err_message + ", read:'" + buffer + "'"; - if (!expected.empty()) - err_message = err_message + ". Expected format: '" + expected + "'"; - return err_message; -} - -void throw_error(const string &filename, const string &var_name, const string expected = "") { - throw invalid_argument(format_error_message(nullptr, filename, var_name, expected)); -} - -DOUBLE_TYPE stod_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") { - try { - return stod(buffer); - } catch (invalid_argument &exc) { - throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str()); - } -} - -int stoi_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") { - try { - return stoi(buffer); - } catch (invalid_argument &exc) { - throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str()); - } -} - -long int stol_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") { - try { - return stol(buffer); - } catch (invalid_argument &exc) { - throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str()); - } -} - -void ACECTildeBasisSet::load(const string filename) { - int res; - char buffer[1024], buffer2[1024]; - string radbasename = "ChebExpCos"; - - FILE *fptr; - fptr = fopen(filename.c_str(), "r"); - if (fptr == NULL) - throw invalid_argument("Could not open file " + filename); - - //read number of elements - res = fscanf(fptr, " nelements="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "nelements", "nelements=[number]"); - nelements = stoi_err(buffer, filename, "nelements", "nelements=[number]"); - - //elements mapping - elements_name = new string[nelements]; - res = fscanf(fptr, " elements:"); - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "elements", "elements: Ele1 Ele2 ..."); - elements_name[mu] = buffer; - } - - // load angular basis - only need spherical harmonics parameter - res = fscanf(fptr, " lmax=%s\n", buffer); - if (res != 1) - throw_error(filename, "lmax", "lmax=[number]"); - lmax = stoi_err(buffer, filename, "lmax", "lmax=[number]"); - spherical_harmonics.init(lmax); - - - // reading "embedding-function:" - bool is_embedding_function_specified = false; - res = fscanf(fptr, " embedding-function: %s", buffer); - if (res == 0) { - //throw_error(filename, "E0", " E0: E0-species1 E0-species2 ..."); - this->npoti = "FinnisSinclair"; // default values - //printf("Warning! No embedding-function is specified, embedding-function: FinnisSinclair would be assumed\n"); - is_embedding_function_specified = false; - } else { - this->npoti = buffer; - is_embedding_function_specified = true; - } - int parameters_size; - res = fscanf(fptr, "%s FS parameters:", buffer); - if (res != 1) - throw_error(filename, "FS parameters size", "[number] FS parameters: par1 par2 ..."); - parameters_size = stoi_err(buffer, filename, "FS parameters size", "[number] FS parameters"); - FS_parameters.resize(parameters_size); - for (int i = 0; i < FS_parameters.size(); ++i) { - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "FS parameter", "[number] FS parameters: [par1] [par2] ..."); - FS_parameters[i] = stod_err(buffer, filename, "FS parameter", "[number] FS parameters: [par1] [par2] ..."); - } - - if (!is_embedding_function_specified) { - // assuming non-linear potential, and embedding function type is important - for (int j = 1; j < parameters_size; j += 2) - if (FS_parameters[j] != 1.0) { //if not ensure linearity of embedding function parameters - printf("ERROR! Your potential is non-linear\n"); - printf("Please specify 'embedding-function: FinnisSinclair' or 'embedding-function: FinnisSinclairShiftedScaled' before 'FS parameters size' line\n"); - throw_error(filename, "embedding-function", "FinnisSinclair or FinnisSinclairShiftedScaled"); - } - printf("Notice! No embedding-function is specified, but potential has linear embedding, default embedding-function: FinnisSinclair would be assumed\n"); - } - - //hard-core energy cutoff repulsion - res = fscanf(fptr, " core energy-cutoff parameters:"); - if (res != 0) - throw_error(filename, "core energy-cutoff parameters", "core energy-cutoff parameters: [par1] [par2]"); - - rho_core_cutoffs.init(nelements, "rho_core_cutoffs"); - drho_core_cutoffs.init(nelements, "drho_core_cutoffs"); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) { - res = fscanf(fptr, "%s %s", buffer, buffer2); - if (res != 2) - throw_error(filename, "core energy-cutoff parameters", - "core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ..."); - rho_core_cutoffs(mu_i) = stod_err(buffer, filename, "rho core cutoff", - "core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ..."); - drho_core_cutoffs(mu_i) = stod_err(buffer2, filename, "drho_core_cutoff", - "core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ..."); - } - - // atom energy shift E0 (energy of isolated atom) - E0vals.init(nelements); - - // reading "E0:" - res = fscanf(fptr, " E0: %s", buffer); - if (res == 0) { - //throw_error(filename, "E0", " E0: E0-species1 E0-species2 ..."); - E0vals.fill(0.0); - } else { - double E0 = atof(buffer); - E0vals(0) = E0; - - for (SPECIES_TYPE mu_i = 1; mu_i < nelements; ++mu_i) { - res = fscanf(fptr, " %lf", &E0); - if (res != 1) - throw_error(filename, "E0", " couldn't read one of the E0 values"); - E0vals(mu_i) = E0; - } - res = fscanf(fptr, "\n"); - if (res != 0) - printf("file %s : format seems broken near E0; trying to continue...\n", filename.c_str()); - } - - // check which radial basis we need to load - res = fscanf(fptr, " radbasename=%s\n", buffer); - if (res != 1) { - throw_error(filename, "radbasename", "rabbasename=ChebExpCos|ChebPow|ACE.jl.Basic"); - } else { - radbasename = buffer; - } - -// printf("radbasename = `%s`\n", radbasename.c_str()); - if (radbasename == "ChebExpCos" | radbasename == "ChebPow") { - _load_radial_ACERadial(fptr, filename, radbasename); - } else if (radbasename == "ACE.jl.Basic") { - _load_radial_SHIPsBasic(fptr, filename, radbasename); - } else { - throw invalid_argument( - ("File '" + filename + "': I don't know how to read radbasename = " + radbasename).c_str()); - } - - res = fscanf(fptr, " rankmax="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "rankmax", "rankmax=[number]"); - rankmax = stoi_err(buffer, filename, "rankmax", "rankmax=[number]"); - - res = fscanf(fptr, " ndensitymax="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "ndensitymax", "ndensitymax=[number]"); - ndensitymax = stoi_err(buffer, filename, "ndensitymax", "ndensitymax=[number]"); - - // read the list of correlations to be put into the basis - //num_c_tilde_max - res = fscanf(fptr, " num_c_tilde_max="); - res = fscanf(fptr, "%s\n", buffer); - if (res != 1) - throw_error(filename, "num_c_tilde_max", "num_c_tilde_max=[number]"); - num_ctilde_max = stol_err(buffer, filename, "num_c_tilde_max", "num_c_tilde_max=[number]"); - - res = fscanf(fptr, " num_ms_combinations_max="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "num_ms_combinations_max", "num_ms_combinations_max=[number]"); -// throw invalid_argument(("File '" + filename + "': couldn't read num_ms_combinations_max").c_str()); - num_ms_combinations_max = stol_err(buffer, filename, "num_ms_combinations_max", "num_ms_combinations_max=[number]"); - - //read total_basis_size_rank1 - total_basis_size_rank1 = new SHORT_INT_TYPE[nelements]; - basis_rank1 = new ACECTildeBasisFunction *[nelements]; - res = fscanf(fptr, " total_basis_size_rank1: "); - - - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "total_basis_size_rank1", "total_basis_size_rank1: [size_ele1] [size_ele2] ..."); -// throw invalid_argument(("File '" + filename + "': couldn't read total_basis_size_rank1").c_str()); - total_basis_size_rank1[mu] = stoi_err(buffer, filename, "total_basis_size_rank1", - "total_basis_size_rank1: [size_ele1] [size_ele2] ..."); - basis_rank1[mu] = new ACECTildeBasisFunction[total_basis_size_rank1[mu]]; - } - for (SPECIES_TYPE mu = 0; mu < nelements; mu++) - for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size_rank1[mu]; ++func_ind) { - fread_c_tilde_b_basis_func(fptr, basis_rank1[mu][func_ind]); - } - - //read total_basis_size - res = fscanf(fptr, " total_basis_size: "); - total_basis_size = new SHORT_INT_TYPE[nelements]; - basis = new ACECTildeBasisFunction *[nelements]; - - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "total_basis_size", "total_basis_size: [size_ele1] [size_ele2] ..."); - total_basis_size[mu] = stoi_err(buffer, filename, "total_basis_size", - "total_basis_size: [size_ele1] [size_ele2] ..."); - basis[mu] = new ACECTildeBasisFunction[total_basis_size[mu]]; - } - for (SPECIES_TYPE mu = 0; mu < nelements; mu++) - for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) { - fread_c_tilde_b_basis_func(fptr, basis[mu][func_ind]); - } - - fclose(fptr); - -// radial_functions->radbasename = radbasename; - radial_functions->setuplookupRadspline(); - pack_flatten_basis(); -} - -void ACECTildeBasisSet::compute_array_sizes(ACECTildeBasisFunction **basis_rank1, ACECTildeBasisFunction **basis) { - //compute arrays sizes - rank_array_total_size_rank1 = 0; - //ms_array_total_size_rank1 = rank_array_total_size_rank1; - coeff_array_total_size_rank1 = 0; - - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - if (total_basis_size_rank1[mu] > 0) { - rank_array_total_size_rank1 += total_basis_size_rank1[mu]; - - ACEAbstractBasisFunction &func = basis_rank1[mu][0];//TODO: get total density instead of density from first function - coeff_array_total_size_rank1 += total_basis_size_rank1[mu] * func.ndensity; - } - } - - rank_array_total_size = 0; - coeff_array_total_size = 0; - - ms_array_total_size = 0; - max_dB_array_size = 0; - - - max_B_array_size = 0; - - size_t cur_ms_size = 0; - size_t cur_ms_rank_size = 0; - - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - - cur_ms_size = 0; - cur_ms_rank_size = 0; - for (int func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) { - auto &func = basis[mu][func_ind]; - rank_array_total_size += func.rank; - ms_array_total_size += func.rank * func.num_ms_combs; - coeff_array_total_size += func.ndensity * func.num_ms_combs; - - cur_ms_size += func.num_ms_combs; - cur_ms_rank_size += func.rank * func.num_ms_combs; - } - - if (cur_ms_size > max_B_array_size) - max_B_array_size = cur_ms_size; - - if (cur_ms_rank_size > max_dB_array_size) - max_dB_array_size = cur_ms_rank_size; - } -} - -void ACECTildeBasisSet::_clean_basis_arrays() { - if (basis_rank1 != nullptr) - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - delete[] basis_rank1[mu]; - basis_rank1[mu] = nullptr; - } - - if (basis != nullptr) - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - delete[] basis[mu]; - basis[mu] = nullptr; - } - delete[] basis; - basis = nullptr; - - delete[] basis_rank1; - basis_rank1 = nullptr; -} - -//pack into 1D array with all basis functions -void ACECTildeBasisSet::flatten_basis(C_tilde_full_basis_vector2d &mu0_ctilde_basis_vector) { - - _clean_basis_arrays(); - basis_rank1 = new ACECTildeBasisFunction *[nelements]; - basis = new ACECTildeBasisFunction *[nelements]; - - delete[] total_basis_size_rank1; - delete[] total_basis_size; - total_basis_size_rank1 = new SHORT_INT_TYPE[nelements]; - total_basis_size = new SHORT_INT_TYPE[nelements]; - - - size_t tot_size_rank1 = 0; - size_t tot_size = 0; - - for (SPECIES_TYPE mu = 0; mu < this->nelements; ++mu) { - tot_size = 0; - tot_size_rank1 = 0; - - for (auto &func: mu0_ctilde_basis_vector[mu]) { - if (func.rank == 1) tot_size_rank1 += 1; - else tot_size += 1; - } - - total_basis_size_rank1[mu] = tot_size_rank1; - basis_rank1[mu] = new ACECTildeBasisFunction[tot_size_rank1]; - - total_basis_size[mu] = tot_size; - basis[mu] = new ACECTildeBasisFunction[tot_size]; - } - - - for (SPECIES_TYPE mu = 0; mu < this->nelements; ++mu) { - size_t ind_rank1 = 0; - size_t ind = 0; - - for (auto &func: mu0_ctilde_basis_vector[mu]) { - if (func.rank == 1) { //r=0, rank=1 - basis_rank1[mu][ind_rank1] = func; - ind_rank1 += 1; - } else { //r>0, rank>1 - basis[mu][ind] = func; - ind += 1; - } - } - - } -} - - -void ACECTildeBasisSet::_load_radial_ACERadial(FILE *fptr, - const string filename, - const string radbasename) { - int res; - char buffer[1024], buffer2[1024]; - - res = fscanf(fptr, " nradbase="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "nradbase", "nradbase=[number]"); -// throw invalid_argument(("File '" + filename + "': couldn't read nradbase").c_str()); - nradbase = stoi_err(buffer, filename, "nradbase", "nradbase=[number]"); - - res = fscanf(fptr, " nradmax="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "nradmax", "nradmax=[number]"); - nradmax = stoi_err(buffer, filename, "nradmax", "nradmax=[number]"); - - res = fscanf(fptr, " cutoffmax="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "cutoffmax", "cutoffmax=[number]"); - cutoffmax = stod_err(buffer, filename, "cutoffmax", "cutoffmax=[number]"); - - - res = fscanf(fptr, " deltaSplineBins="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "deltaSplineBins", "deltaSplineBins=[spline density, Angstroms]"); -// throw invalid_argument(("File '" + filename + "': couldn't read ntot").c_str()); - deltaSplineBins = stod_err(buffer, filename, "deltaSplineBins", "deltaSplineBins=[spline density, Angstroms]"); - - - if (radial_functions == nullptr) - radial_functions = new ACERadialFunctions(nradbase, lmax, nradmax, - deltaSplineBins, - nelements, - cutoffmax, radbasename); - else - radial_functions->init(nradbase, lmax, nradmax, - deltaSplineBins, - nelements, - cutoffmax, radbasename); - - - //hard-core repulsion - res = fscanf(fptr, " core repulsion parameters:"); - if (res != 0) - throw_error(filename, "core repulsion parameters", "core repulsion parameters: [prehc lambdahc] ..."); -// throw invalid_argument(("File '" + filename + "': couldn't read core repulsion parameters").c_str()); - - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { - res = fscanf(fptr, "%s %s", buffer, buffer2); - if (res != 2) - throw_error(filename, "core repulsion parameters", "core repulsion parameters: [prehc lambdahc] ..."); - radial_functions->prehc(mu_i, mu_j) = stod_err(buffer, filename, "core repulsion parameters", - "core repulsion parameters: [prehc lambdahc] ..."); - radial_functions->lambdahc(mu_i, mu_j) = stod_err(buffer2, filename, "core repulsion parameters", - "core repulsion parameters: [prehc lambdahc] ..."); - } - - - - //read radial functions parameter - res = fscanf(fptr, " radparameter="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "radparameter", "radparameter=[param_ele1] [param_ele2]"); - radial_functions->lambda(mu_i, mu_j) = stod_err(buffer, filename, "radparameter", - "radparameter=[param_ele1] [param_ele2]"); - } - - - res = fscanf(fptr, " cutoff="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "cutoff", "cutoff=[param_ele1] [param_ele2]"); - radial_functions->cut(mu_i, mu_j) = stod_err(buffer, filename, "cutoff", - "cutoff=[param_ele1] [param_ele2]"); - } - - - res = fscanf(fptr, " dcut="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { - res = fscanf(fptr, " %s", buffer); - if (res != 1) - throw_error(filename, "dcut", "dcut=[param_ele1] [param_ele2]"); - radial_functions->dcut(mu_i, mu_j) = stod_err(buffer, filename, "dcut", "dcut=[param_ele1] [param_ele2]"); - } - - - res = fscanf(fptr, " crad="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) - for (NS_TYPE k = 0; k < nradbase; k++) - for (NS_TYPE n = 0; n < nradmax; n++) - for (LS_TYPE l = 0; l <= lmax; l++) { - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "crad", "crad=[crad_]...[crad_knl]: nradbase*nrad*(l+1) times"); - radial_functions->crad(mu_i, mu_j, n, l, k) = stod_err(buffer, filename, "crad", - "crad=[crad_]...[crad_knl]: nradbase*nrad*(l+1) times"); - } -} - -void ACECTildeBasisSet::_load_radial_SHIPsBasic(FILE *fptr, - const string filename, - const string radbasename) { - // create a radial basis object, and read it from the file pointer - SHIPsRadialFunctions *ships_radial_functions = new SHIPsRadialFunctions(); - ships_radial_functions->fread(fptr); - - //mimic ships_radial_functions to ACERadialFunctions - ships_radial_functions->nradial = ships_radial_functions->get_maxn(); - ships_radial_functions->nradbase = ships_radial_functions->get_maxn(); - - nradbase = ships_radial_functions->get_maxn(); - nradmax = ships_radial_functions->get_maxn(); - cutoffmax = ships_radial_functions->get_rcut(); - deltaSplineBins = 0.001; - - ships_radial_functions->init(nradbase, lmax, nradmax, - deltaSplineBins, - nelements, - cutoffmax, radbasename); - - - if (radial_functions) delete radial_functions; - radial_functions = ships_radial_functions; - radial_functions->prehc.fill(0); - radial_functions->lambdahc.fill(1); - radial_functions->lambda.fill(0); - - - radial_functions->cut.fill(ships_radial_functions->get_rcut()); - radial_functions->dcut.fill(0); - - radial_functions->crad.fill(0); - -} \ No newline at end of file diff --git a/lib/pace/ace_c_basis.h b/lib/pace/ace_c_basis.h deleted file mode 100644 index ec6b9e8afc..0000000000 --- a/lib/pace/ace_c_basis.h +++ /dev/null @@ -1,155 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Yury Lysogorskiy on 1.04.20. - -#ifndef ACE_C_BASIS_H -#define ACE_C_BASIS_H - -#include "ace_flatten_basis.h" - -typedef vector> C_tilde_full_basis_vector2d; - -/** - * ACE basis set of C-tilde basis functions - */ -class ACECTildeBasisSet : public ACEFlattenBasisSet { -public: - - ACECTildeBasisFunction **basis_rank1 = nullptr; ///< two-dimensional array of first-rank basis function with indices: [species index][func index] - ACECTildeBasisFunction **basis = nullptr; ///< two-dimensional array of higher rank basis function with indices: [species index][func index] - - DOUBLE_TYPE *full_c_tildes_rank1 = nullptr; ///< C_tilde coefficients contiguous package, size: coeff_array_total_size_rank1 - DOUBLE_TYPE *full_c_tildes = nullptr; ///< C_tilde coefficients contiguous package, size: coeff_array_total_size - - //TODO: remove? - SHORT_INT_TYPE num_ctilde_max = 0; - - - /** - * Default constructor - */ - ACECTildeBasisSet() = default; - - /** - * Constructor from .ace file - */ - ACECTildeBasisSet(const string filename); - - /** - * Copy constructor (see. Rule of Three) - * @param other - */ - ACECTildeBasisSet(const ACECTildeBasisSet &other); - - /** - * operator= (see. Rule of Three) - * @param other - * @return - */ - ACECTildeBasisSet &operator=(const ACECTildeBasisSet &other); - - /** - * Destructor (see. Rule of Three) - */ - ~ACECTildeBasisSet() override; - - /** - * Cleaning dynamic memory of the class (see. Rule of Three) - */ - void _clean() override; - - /** - * Copying and cleaning dynamic memory of the class (see. Rule of Three) - * @param src - */ - void _copy_dynamic_memory(const ACECTildeBasisSet &src); - - /** - * Copying scalar variables - * @param src - */ - void _copy_scalar_memory(const ACECTildeBasisSet &src); - - /** - * Clean contiguous arrays (full_c_tildes_rank1, full_c_tildes) and those of base class - */ - void _clean_contiguous_arrays() override ; - - /** - * Save potential to .ace file - * @param filename .ace file name - */ - void save(const string &filename) override; - - /** - * Load potential from .ace - * @param filename .ace file name - */ - void load(const string filename) override; - - /** - * Load the ACE type radial basis - */ - void _load_radial_ACERadial(FILE *fptr, - const string filename, - const string radbasename); - - void _load_radial_SHIPsBasic(FILE * fptr, - const string filename, - const string radbasename ); - - /** - * Re-pack the constituent dynamic arrays of all basis functions in contiguous arrays - */ - void pack_flatten_basis() override; - - /** - * Computes flatten array sizes - * @param basis_rank1 two-dimensional array of first-rank ACECTildeBasisFunctions - * @param basis two-dimensional array of higher-rank ACECTildeBasisFunctions - */ - void compute_array_sizes(ACECTildeBasisFunction** basis_rank1, ACECTildeBasisFunction** basis); - - /** - * Clean basis arrays 'basis_rank1' and 'basis' - */ - void _clean_basis_arrays(); - - /** - * Pack two-dimensional vector of ACECTildeBasisFunction into 1D dynami array with all basis functions - * @param mu0_ctilde_basis_vector vector> - */ - void flatten_basis(C_tilde_full_basis_vector2d& mu0_ctilde_basis_vector); - - /** - * Empty stub implementation - */ - void flatten_basis() override{}; -}; - -#endif //ACE_C_BASIS_H diff --git a/lib/pace/ace_c_basisfunction.h b/lib/pace/ace_c_basisfunction.h deleted file mode 100644 index 4e2795590e..0000000000 --- a/lib/pace/ace_c_basisfunction.h +++ /dev/null @@ -1,251 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Yury Lysogorskiy on 26.02.20. - -#ifndef ACE_C_BASISFUNCTION_H -#define ACE_C_BASISFUNCTION_H - -#include -#include -#include -#include - -#include "ace_types.h" - -//macros for copying the member-array from "other" object for C-tilde and B-basis -#define basis_mem_copy(other, array, size, type) if(other.array) { \ - if(!is_proxy) delete[] array;\ - array = new type[(size)];\ - is_proxy = false;\ - memcpy(array, other.array, (size) * sizeof(type));\ -} - -/** - * Abstract basis function, that stores general quantities - */ -struct ACEAbstractBasisFunction { - /** - * flattened array of computed combinations of (m1, m2, ..., m_rank) - * which have non-zero general Clebsch-Gordan coefficient: - * \f$ \mathbf{m}_1, \dots, \mathbf{m}_\mathrm{num ms combs}\f$ = - * \f$ (m_1, m_2, \dots, m_{rank})_1, \dots, (m_1, m_2, \dots, m_{rank})_{\mathrm{num ms combs}} \f$, - * size = num_ms_combs * rank, - * effective shape: [num_ms_combs][rank] - */ - MS_TYPE *ms_combs = nullptr; - - /** - * species types of neighbours atoms \f$ \mathbf{\mu} = (\mu_1, \mu_2, \dots, \mu_{rank}) \f$, - * should be lexicographically sorted, - * size = rank, - * effective shape: [rank] - */ - SPECIES_TYPE *mus = nullptr; - - /** - * indices for radial part \f$ \mathbf{n} = (n_1, n_2, \dots, n_{rank}) \f$, - * should be lexicographically sorted, - * size = rank, - * effective shape: [rank] - */ - NS_TYPE *ns = nullptr; - - - /** - * indices for radial part \f$ \mathbf{l} = (l_1, l_2, \dots, l_{rank}) \f$, - * should be lexicographically sorted, - * size = rank, - * effective shape: [rank] - */ - LS_TYPE *ls = nullptr; - - SHORT_INT_TYPE num_ms_combs = 0; ///< number of different ms-combinations - - RANK_TYPE rank = 0; ///< number of atomic base functions "A"s in basis function product B - - DENSITY_TYPE ndensity = 0; ///< number of densities - - SPECIES_TYPE mu0 = 0; ///< species type of central atom - - /** - * whether ms array contains only "non-negative" ms-combinations. - * positive ms-combination is when the first non-zero m is positive (0 1 -1) - * negative ms-combination is when the first non-zero m is negative (0 -1 1) - */ - bool is_half_ms_basis = false; - - /* - * flag, whether object is "owner" (i.e. responsible for memory cleaning) of - * the ms, ns, ls, mus and other dynamically allocated arrases or just a proxy for them - */ - bool is_proxy = false; - - /** - * Copying static and dynamic memory variables from another ACEAbstractBasisFunction. - * Always copy the dynamic memory, even if the source is a proxy object - * @param other - */ - virtual void _copy_from(const ACEAbstractBasisFunction &other) { - rank = other.rank; - ndensity = other.ndensity; - mu0 = other.mu0; - num_ms_combs = other.num_ms_combs; - is_half_ms_basis = other.is_half_ms_basis; - is_proxy = false; - - basis_mem_copy(other, mus, rank, SPECIES_TYPE) - basis_mem_copy(other, ns, rank, NS_TYPE) - basis_mem_copy(other, ls, rank, LS_TYPE) - basis_mem_copy(other, ms_combs, num_ms_combs * rank, MS_TYPE) - } - - /** - * Clean the dynamically allocated memory if object is responsible for it - */ - virtual void _clean() { - //release memory if the structure is not proxy - if (!is_proxy) { - delete[] mus; - delete[] ns; - delete[] ls; - delete[] ms_combs; - } - - mus = nullptr; - ns = nullptr; - ls = nullptr; - ms_combs = nullptr; - } - -}; - -/** - * Representation of C-tilde basis function, i.e. the function that is summed up over a group of B-functions - * that differs only by intermediate coupling orbital moment \f$ L \f$ and coefficients. - */ -struct ACECTildeBasisFunction : public ACEAbstractBasisFunction { - - /** - * c_tilde coefficients for all densities, - * size = num_ms_combs*ndensity, - * effective shape [num_ms_combs][ndensity] - */ - DOUBLE_TYPE *ctildes = nullptr; - - /* - * Default constructor - */ - ACECTildeBasisFunction() = default; - - // Because the ACECTildeBasisFunction contains dynamically allocated arrays, the Rule of Three should be - // fulfilled, i.e. copy constructor (copy the dynamic arrays), operator= (release previous arrays and - // copy the new dynamic arrays) and destructor (release all dynamically allocated memory) - - /** - * Copy constructor, to fulfill the Rule of Three. - * Always copy the dynamic memory, even if the source is a proxy object. - */ - ACECTildeBasisFunction(const ACECTildeBasisFunction &other) { - _copy_from(other); - } - - /* - * operator=, to fulfill the Rule of Three. - * Always copy the dynamic memory, even if the source is a proxy object - */ - ACECTildeBasisFunction &operator=(const ACECTildeBasisFunction &other) { - _clean(); - _copy_from(other); - return *this; - } - - /* - * Destructor - */ - ~ACECTildeBasisFunction() { - _clean(); - } - - /** - * Copy from another object, always copy the memory, even if the source is a proxy object - * @param other - */ - void _copy_from(const ACECTildeBasisFunction &other) { - ACEAbstractBasisFunction::_copy_from(other); - is_proxy = false; - basis_mem_copy(other, ctildes, num_ms_combs * ndensity, DOUBLE_TYPE) - } - - /** - * Clean the dynamically allocated memory if object is responsible for it - */ - void _clean() override { - ACEAbstractBasisFunction::_clean(); - //release memory if the structure is not proxy - if (!is_proxy) { - delete[] ctildes; - } - ctildes = nullptr; - } - - /** - * Print the information about basis function to cout, in order to ease the output redirection. - */ - void print() const { - using namespace std; - cout << "ACECTildeBasisFunction: ndensity= " << (int) this->ndensity << ", mu0 = " << (int) this->mu0 << " "; - cout << " mus=("; - for (RANK_TYPE r = 0; r < this->rank; r++) - cout << (int) this->mus[r] << " "; - cout << "), ns=("; - for (RANK_TYPE r = 0; r < this->rank; r++) - cout << this->ns[r] << " "; - cout << "), ls=("; - for (RANK_TYPE r = 0; r < this->rank; r++) - cout << this->ls[r] << " "; - - cout << "), " << this->num_ms_combs << " m_s combinations: {" << endl; - - for (int i = 0; i < this->num_ms_combs; i++) { - cout << "\t< "; - for (RANK_TYPE r = 0; r < this->rank; r++) - cout << this->ms_combs[i * this->rank + r] << " "; - cout << " >: c_tilde="; - for (DENSITY_TYPE p = 0; p < this->ndensity; ++p) - cout << " " << this->ctildes[i * this->ndensity + p] << " "; - cout << endl; - } - if (this->is_proxy) - cout << "proxy "; - if (this->is_half_ms_basis) - cout << "half_ms_basis"; - cout << "}" << endl; - } -}; - -#endif //ACE_C_BASISFUNCTION_H diff --git a/lib/pace/ace_complex.h b/lib/pace/ace_complex.h deleted file mode 100644 index 5fdb4b5b93..0000000000 --- a/lib/pace/ace_complex.h +++ /dev/null @@ -1,266 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Yury Lysogorskiy on 26.02.20. - -#ifndef ACE_COMPLEX_H -#define ACE_COMPLEX_H - - -/** -A custom data structure for complex numbers and overloaded operations with them. -*/ -struct ACEComplex { -public: - /** - Double, real part of the complex number - */ - DOUBLE_TYPE real; - /** - Double, imaginary part of the complex number - */ - DOUBLE_TYPE img; - - ACEComplex &operator=(const ACEComplex &rhs) = default; - - ACEComplex &operator=(const DOUBLE_TYPE &rhs) { - this->real = rhs; - this->img = 0.; - return *this; - } - - /** - Overloading of arithmetical operator += ACEComplex - */ - ACEComplex &operator+=(const ACEComplex &rhs) { - this->real += rhs.real; - this->img += rhs.img; - return *this; // return the result by reference - } - - /** - Overloading of arithmetical operator += DOUBLE_TYPE - */ - ACEComplex &operator+=(const DOUBLE_TYPE &rhs) { - this->real += rhs; - return *this; // return the result by reference - } - - /** - Overloading of arithmetical operator *= DOUBLE_TYPE - */ - ACEComplex &operator*=(const DOUBLE_TYPE &rhs) { - this->real *= rhs; - this->img *= rhs; - return *this; // return the result by reference - } - - /** - Overloading of arithmetical operator *= ACEComplex - */ - ACEComplex &operator*=(const ACEComplex &rhs) { - DOUBLE_TYPE old_real = this->real; - this->real = old_real * rhs.real - this->img * rhs.img; - this->img = old_real * rhs.img + this->img * rhs.real; - return *this; // return the result by reference - } - - /** - Overloading of arithmetical operator * ACEComplex - */ - ACEComplex operator*(const ACEComplex &cm2) const { - ACEComplex res{real * cm2.real - img * cm2.img, - real * cm2.img + img * cm2.real}; - return res; - } - - /* - * Return complex conjugated copy of itself - */ - ACEComplex conjugated() const { - ACEComplex res{real, -img}; - return res; - } - - /* - * Complex conjugate itself inplace - */ - void conjugate() { - img = -img; - } - - /* - * Multiplication by ACEComplex and return real-part only - */ - DOUBLE_TYPE real_part_product(const ACEComplex &cm2) const { - return real * cm2.real - img * cm2.img; - } - - /* - * Multiplication by DOUBLE_TYPE and return real-part only - */ - DOUBLE_TYPE real_part_product(const DOUBLE_TYPE &cm2) const { - return real * cm2; - } - - /* - * Overloading of arithmetical operator * by DOUBLE_TYPE - */ - ACEComplex operator*(const DOUBLE_TYPE &cm2) const { - ACEComplex res{real * cm2, - img * cm2}; - return res; - } - - /* - * Overloading of arithmetical operator + ACEComplex - */ - ACEComplex operator+(const ACEComplex &cm2) const { - ACEComplex res{real + cm2.real, - img + cm2.img}; - return res; - } - - /* - * Overloading of arithmetical operator + with DOUBLE_TYPE - */ - ACEComplex operator+(const DOUBLE_TYPE &cm2) const { - ACEComplex res{real + cm2, img}; - return res; - } - - /* - * Overloading of arithmetical operator == ACEComplex - */ - bool operator==(const ACEComplex &c2) const { - return (real == c2.real) && (img == c2.img); - } - - /* - * Overloading of arithmetical operator == DOUBLE_TYPE - */ - bool operator==(const DOUBLE_TYPE &d2) const { - return (real == d2) && (img == 0.); - } - - /* - * Overloading of arithmetical operator != ACEComplex - */ - bool operator!=(const ACEComplex &c2) const { - return (real != c2.real) || (img != c2.img); - } - - /* - * Overloading of arithmetical operator != DOUBLE_TYPE - */ - bool operator!=(const DOUBLE_TYPE &d2) const { - return (real != d2) || (img != 0.); - } - -}; - -/* - * double * complex for commutativity with complex * double - */ -inline ACEComplex operator*(const DOUBLE_TYPE &real, const ACEComplex &cm) { - return cm * real; -} - -/* - * double + complex for commutativity with complex + double - */ -inline ACEComplex operator+(const DOUBLE_TYPE &real, const ACEComplex &cm) { - return cm + real; -} - -/** -A structure to store the derivative of \f$ Y_{lm} \f$ -*/ -struct ACEDYcomponent { -public: - /** - complex, contains the three components of derivative of Ylm, - \f$ \frac{dY_{lm}}{dx}, \frac{dY_{lm}}{dy} and \frac{dY_{lm}}{dz}\f$ - */ - ACEComplex a[3]; - - /* - * Overloading of arithmetical operator*= DOUBLE_TYPE - */ - ACEDYcomponent &operator*=(const DOUBLE_TYPE &rhs) { - this->a[0] *= rhs; - this->a[1] *= rhs; - this->a[2] *= rhs; - return *this; - } - - /* - * Overloading of arithmetical operator * ACEComplex - */ - ACEDYcomponent operator*(const ACEComplex &rhs) const { - ACEDYcomponent res; - res.a[0] = this->a[0] * rhs; - res.a[1] = this->a[1] * rhs; - res.a[2] = this->a[2] * rhs; - return res; - } - - /* - * Overloading of arithmetical operator * DOUBLE_TYPE - */ - ACEDYcomponent operator*(const DOUBLE_TYPE &rhs) const { - ACEDYcomponent res; - res.a[0] = this->a[0] * rhs; - res.a[1] = this->a[1] * rhs; - res.a[2] = this->a[2] * rhs; - return res; - } - - /* - * Return conjugated copy of itself - */ - ACEDYcomponent conjugated() const { - ACEDYcomponent res; - res.a[0] = this->a[0].conjugated(); - res.a[1] = this->a[1].conjugated(); - res.a[2] = this->a[2].conjugated(); - return res; - } - - /* - * Conjugated itself in-place - */ - void conjugate() { - this->a[0].conjugate(); - this->a[1].conjugate(); - this->a[2].conjugate(); - } - -}; - - -#endif //ACE_COMPLEX_H diff --git a/lib/pace/ace_contigous_array.h b/lib/pace/ace_contigous_array.h deleted file mode 100644 index f008fa203f..0000000000 --- a/lib/pace/ace_contigous_array.h +++ /dev/null @@ -1,249 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Yury Lysogorskiy on 11.01.20. -#ifndef ACE_CONTIGUOUSARRAYND_H -#define ACE_CONTIGUOUSARRAYND_H - -#include - -#include "ace_types.h" - -using namespace std; - -/** - * Common predecessor class to represent multidimensional array of type T - * and store it in memory contiguous form - * - * @tparam T data type - */ -template -class ContiguousArrayND { -protected: - T *data = nullptr; ///< pointer to contiguous data - size_t size = 0; ///< total array size - string array_name = "Array"; /// 0) { - data = new T[size]; - for (size_t ind = 0; ind < size; ind++) - data[ind] = other.data[ind]; - } - } else { //is proxy, then copy the pointer - data = other.data; - } - } - - /** - * Overload operator= - * @param other another ContiguousArrayND - * @return itself - */ - - ContiguousArrayND &operator=(const ContiguousArrayND &other) { -#ifdef MULTIARRAY_LIFE_CYCLE - cout< 0) { - - if(data!=nullptr) delete[] data; - data = new T[size]; - - for (size_t ind = 0; ind < size; ind++) - data[ind] = other.data[ind]; - } - } else { //is proxy, then copy the pointer - data = other.data; - } - } - return *this; - } - - - //TODO: make destructor virtual, check the destructors in inherited classes - - /** - * Destructor - */ - ~ContiguousArrayND() { -#ifdef MULTIARRAY_LIFE_CYCLE - cout<array_name = name; - } - - /** - * Get total number of elements in array (its size) - * @return array size - */ - size_t get_size() const { - return size; - } - - /** - * Fill array with value - * @param value value to fill - */ - void fill(T value) { - for (size_t ind = 0; ind < size; ind++) - data[ind] = value; - } - - /** - * Get array data at absolute index ind for reading - * @param ind absolute index - * @return array value - */ - inline const T &get_data(size_t ind) const { -#ifdef MULTIARRAY_INDICES_CHECK - if ((ind < 0) | (ind >= size)) { - printf("%s: get_data ind=%d out of range (0, %d)\n", array_name, ind, size); - exit(EXIT_FAILURE); - } -#endif - return data[ind]; - } - - /** - * Get array data at absolute index ind for writing - * @param ind absolute index - * @return array value - */ - inline T &get_data(size_t ind) { -#ifdef MULTIARRAY_INDICES_CHECK - if ((ind < 0) | (ind >= size)) { - printf("%s: get_data ind=%ld out of range (0, %ld)\n", array_name.c_str(), ind, size); - exit(EXIT_FAILURE); - } -#endif - return data[ind]; - } - - /** - * Get array data pointer - * @return data array pointer - */ - inline T* get_data() const { - return data; - } - - /** - * Overload comparison operator== - * Compare the total size and array values elementwise. - * - * @param other another array - * @return - */ - bool operator==(const ContiguousArrayND &other) const { - if (this->size != other.size) - return false; - - for (size_t i = 0; i < this->size; ++i) - if (this->data[i] != other.data[i]) - return false; - - return true; - } - - - /** - * Convert to flatten vector container - * @return vector container - */ - vector to_flatten_vector() const { - vector res; - - res.resize(size); - size_t vec_ind = 0; - - for (int vec_ind = 0; vec_ind < size; vec_ind++) - res.at(vec_ind) = data[vec_ind]; - - return res; - } // end to_flatten_vector() - - - /** - * Set values from flatten vector container - * @param vec container - */ - void set_flatten_vector(const vector &vec) { - if (vec.size() != size) - throw std::invalid_argument("Flatten vector size is not consistent with expected size"); - for (size_t i = 0; i < size; i++) { - data[i] = vec[i]; - } - } - - bool is_proxy(){ - return is_proxy_; - } - -}; - - -#endif //ACE_CONTIGUOUSARRAYND_H \ No newline at end of file diff --git a/lib/pace/ace_evaluator.cpp b/lib/pace/ace_evaluator.cpp deleted file mode 100644 index 987f4502bf..0000000000 --- a/lib/pace/ace_evaluator.cpp +++ /dev/null @@ -1,660 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Yury Lysogorskiy on 31.01.20. - -#include "ace_evaluator.h" - -#include "ace_abstract_basis.h" -#include "ace_types.h" - -void ACEEvaluator::init(ACEAbstractBasisSet *basis_set) { - A.init(basis_set->nelements, basis_set->nradmax + 1, basis_set->lmax + 1, "A"); - A_rank1.init(basis_set->nelements, basis_set->nradbase, "A_rank1"); - - rhos.init(basis_set->ndensitymax + 1, "rhos"); // +1 density for core repulsion - dF_drho.init(basis_set->ndensitymax + 1, "dF_drho"); // +1 density for core repulsion -} - -void ACEEvaluator::init_timers() { - loop_over_neighbour_timer.init(); - forces_calc_loop_timer.init(); - forces_calc_neighbour_timer.init(); - energy_calc_timer.init(); - per_atom_calc_timer.init(); - total_time_calc_timer.init(); -} - -//================================================================================================================ - -void ACECTildeEvaluator::set_basis(ACECTildeBasisSet &bas) { - basis_set = &bas; - init(basis_set); -} - -void ACECTildeEvaluator::init(ACECTildeBasisSet *basis_set) { - - ACEEvaluator::init(basis_set); - - - weights.init(basis_set->nelements, basis_set->nradmax + 1, basis_set->lmax + 1, - "weights"); - - weights_rank1.init(basis_set->nelements, basis_set->nradbase, "weights_rank1"); - - - DG_cache.init(1, basis_set->nradbase, "DG_cache"); - DG_cache.fill(0); - - R_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "R_cache"); - R_cache.fill(0); - - DR_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "DR_cache"); - DR_cache.fill(0); - - Y_cache.init(1, basis_set->lmax + 1, "Y_cache"); - Y_cache.fill({0, 0}); - - DY_cache.init(1, basis_set->lmax + 1, "dY_dense_cache"); - DY_cache.fill({0.}); - - //hard-core repulsion - DCR_cache.init(1, "DCR_cache"); - DCR_cache.fill(0); - dB_flatten.init(basis_set->max_dB_array_size, "dB_flatten"); - - -} - -void ACECTildeEvaluator::resize_neighbours_cache(int max_jnum) { - if(basis_set== nullptr) { - throw std::invalid_argument("ACECTildeEvaluator: basis set is not assigned"); - } - if (R_cache.get_dim(0) < max_jnum) { - - //TODO: implement grow - R_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); - R_cache.fill(0); - - DR_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); - DR_cache.fill(0); - - DG_cache.resize(max_jnum, basis_set->nradbase); - DG_cache.fill(0); - - Y_cache.resize(max_jnum, basis_set->lmax + 1); - Y_cache.fill({0, 0}); - - DY_cache.resize(max_jnum, basis_set->lmax + 1); - DY_cache.fill({0}); - - //hard-core repulsion - DCR_cache.init(max_jnum, "DCR_cache"); - DCR_cache.fill(0); - } -} - - - -// double** r - atomic coordinates of atom I -// int* types - atomic types if atom I -// int **firstneigh - ptr to 1st J int value of each I atom. Usage: jlist = firstneigh[i]; -// Usage: j = jlist_of_i[jj]; -// jnum - number of J neighbors for each I atom. jnum = numneigh[i]; - -void -ACECTildeEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) { - if(basis_set== nullptr) { - throw std::invalid_argument("ACECTildeEvaluator: basis set is not assigned"); - } - per_atom_calc_timer.start(); -#ifdef PRINT_MAIN_STEPS - printf("\n ATOM: ind = %d r_norm=(%f, %f, %f)\n",i, x[i][0], x[i][1], x[i][2]); -#endif - DOUBLE_TYPE evdwl = 0, evdwl_cut = 0, rho_core = 0; - DOUBLE_TYPE r_norm; - DOUBLE_TYPE xn, yn, zn, r_xyz; - DOUBLE_TYPE R, GR, DGR, R_over_r, DR, DCR; - DOUBLE_TYPE *r_hat; - - SPECIES_TYPE mu_j; - RANK_TYPE r, rank, t; - NS_TYPE n; - LS_TYPE l; - MS_TYPE m, m_t; - - SPECIES_TYPE *mus; - NS_TYPE *ns; - LS_TYPE *ls; - MS_TYPE *ms; - - int j, jj, func_ind, ms_ind; - SHORT_INT_TYPE factor; - - ACEComplex Y{0}, Y_DR{0.}; - ACEComplex B{0.}; - ACEComplex dB{0}; - ACEComplex A_cache[basis_set->rankmax]; - - dB_flatten.fill({0.}); - - ACEDYcomponent grad_phi_nlm{0}, DY{0.}; - - //size is +1 of max to avoid out-of-boundary array access in double-triangular scheme - ACEComplex A_forward_prod[basis_set->rankmax + 1]; - ACEComplex A_backward_prod[basis_set->rankmax + 1]; - - DOUBLE_TYPE inv_r_norm; - DOUBLE_TYPE r_norms[jnum]; - DOUBLE_TYPE inv_r_norms[jnum]; - DOUBLE_TYPE rhats[jnum][3];//normalized vector - SPECIES_TYPE elements[jnum]; - const DOUBLE_TYPE xtmp = x[i][0]; - const DOUBLE_TYPE ytmp = x[i][1]; - const DOUBLE_TYPE ztmp = x[i][2]; - DOUBLE_TYPE f_ji[3]; - - bool is_element_mapping = element_type_mapping.get_size() > 0; - SPECIES_TYPE mu_i; - if (is_element_mapping) - mu_i = element_type_mapping(type[i]); - else - mu_i = type[i]; - - const SHORT_INT_TYPE total_basis_size_rank1 = basis_set->total_basis_size_rank1[mu_i]; - const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; - - ACECTildeBasisFunction *basis_rank1 = basis_set->basis_rank1[mu_i]; - ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; - - DOUBLE_TYPE rho_cut, drho_cut, fcut, dfcut; - DOUBLE_TYPE dF_drho_core; - - //TODO: lmax -> lmaxi (get per-species type) - const LS_TYPE lmaxi = basis_set->lmax; - - //TODO: nradmax -> nradiali (get per-species type) - const NS_TYPE nradiali = basis_set->nradmax; - - //TODO: nradbase -> nradbasei (get per-species type) - const NS_TYPE nradbasei = basis_set->nradbase; - - //TODO: get per-species type number of densities - const DENSITY_TYPE ndensity= basis_set->ndensitymax; - - neighbours_forces.resize(jnum, 3); - neighbours_forces.fill(0); - - //TODO: shift nullifications to place where arrays are used - weights.fill({0}); - weights_rank1.fill(0); - A.fill({0}); - A_rank1.fill(0); - rhos.fill(0); - dF_drho.fill(0); - -#ifdef EXTRA_C_PROJECTIONS - basis_projections_rank1.init(total_basis_size_rank1, ndensity, "c_projections_rank1"); - basis_projections.init(total_basis_size, ndensity, "c_projections"); -#endif - - //proxy references to spherical harmonics and radial functions arrays - const Array2DLM &ylm = basis_set->spherical_harmonics.ylm; - const Array2DLM &dylm = basis_set->spherical_harmonics.dylm; - - const Array2D &fr = basis_set->radial_functions->fr; - const Array2D &dfr = basis_set->radial_functions->dfr; - - const Array1D &gr = basis_set->radial_functions->gr; - const Array1D &dgr = basis_set->radial_functions->dgr; - - loop_over_neighbour_timer.start(); - - int jj_actual = 0; - SPECIES_TYPE type_j = 0; - int neighbour_index_mapping[jnum]; // jj_actual -> jj - //loop over neighbours, compute distance, consider only atoms within with rradial_functions->cut(mu_i, mu_j); - r_xyz = sqrt(xn * xn + yn * yn + zn * zn); - - if (r_xyz >= current_cutoff) - continue; - - inv_r_norm = 1 / r_xyz; - - r_norms[jj_actual] = r_xyz; - inv_r_norms[jj_actual] = inv_r_norm; - rhats[jj_actual][0] = xn * inv_r_norm; - rhats[jj_actual][1] = yn * inv_r_norm; - rhats[jj_actual][2] = zn * inv_r_norm; - elements[jj_actual] = mu_j; - neighbour_index_mapping[jj_actual] = jj; - jj_actual++; - } - - int jnum_actual = jj_actual; - - //ALGORITHM 1: Atomic base A - for (jj = 0; jj < jnum_actual; ++jj) { - r_norm = r_norms[jj]; - mu_j = elements[jj]; - r_hat = rhats[jj]; - - //proxies - Array2DLM &Y_jj = Y_cache(jj); - Array2DLM &DY_jj = DY_cache(jj); - - - basis_set->radial_functions->evaluate(r_norm, basis_set->nradbase, nradiali, mu_i, mu_j); - basis_set->spherical_harmonics.compute_ylm(r_hat[0], r_hat[1], r_hat[2], lmaxi); - //loop for computing A's - //rank = 1 - for (n = 0; n < basis_set->nradbase; n++) { - GR = gr(n); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("-neigh atom %d\n", jj); - printf("gr(n=%d)(r=%f) = %f\n", n, r_norm, gr(n)); - printf("dgr(n=%d)(r=%f) = %f\n", n, r_norm, dgr(n)); -#endif - DG_cache(jj, n) = dgr(n); - A_rank1(mu_j, n) += GR * Y00; - } - //loop for computing A's - // for rank > 1 - for (n = 0; n < nradiali; n++) { - auto &A_lm = A(mu_j, n); - for (l = 0; l <= lmaxi; l++) { - R = fr(n, l); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("R(nl=%d,%d)(r=%f)=%f\n", n + 1, l, r_norm, R); -#endif - - DR_cache(jj, n, l) = dfr(n, l); - R_cache(jj, n, l) = R; - - for (m = 0; m <= l; m++) { - Y = ylm(l, m); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("Y(lm=%d,%d)=(%f, %f)\n", l, m, Y.real, Y.img); -#endif - A_lm(l, m) += R * Y; //accumulation sum over neighbours - Y_jj(l, m) = Y; - DY_jj(l, m) = dylm(l, m); - } - } - } - - //hard-core repulsion - rho_core += basis_set->radial_functions->cr; - DCR_cache(jj) = basis_set->radial_functions->dcr; - - } //end loop over neighbours - - //complex conjugate A's (for NEGATIVE (-m) terms) - // for rank > 1 - for (mu_j = 0; mu_j < basis_set->nelements; mu_j++) { - for (n = 0; n < nradiali; n++) { - auto &A_lm = A(mu_j, n); - for (l = 0; l <= lmaxi; l++) { - //fill in -m part in the outer loop using the same m <-> -m symmetry as for Ylm - for (m = 1; m <= l; m++) { - factor = m % 2 == 0 ? 1 : -1; - A_lm(l, -m) = A_lm(l, m).conjugated() * factor; - } - } - } - } //now A's are constructed - loop_over_neighbour_timer.stop(); - - // ==================== ENERGY ==================== - - energy_calc_timer.start(); -#ifdef EXTRA_C_PROJECTIONS - basis_projections_rank1.fill(0); - basis_projections.fill(0); -#endif - - //ALGORITHM 2: Basis functions B with iterative product and density rho(p) calculation - //rank=1 - for (int func_rank1_ind = 0; func_rank1_ind < total_basis_size_rank1; ++func_rank1_ind) { - ACECTildeBasisFunction *func = &basis_rank1[func_rank1_ind]; -// ndensity = func->ndensity; -#ifdef PRINT_LOOPS_INDICES - printf("Num density = %d r = 0\n",(int) ndensity ); - print_C_tilde_B_basis_function(*func); -#endif - double A_cur = A_rank1(func->mus[0], func->ns[0] - 1); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("A_r=1(x=%d, n=%d)=(%f)\n", func->mus[0], func->ns[0], A_cur); - printf(" coeff[0] = %f\n", func->ctildes[0]); -#endif - for (DENSITY_TYPE p = 0; p < ndensity; ++p) { - //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 - rhos(p) += func->ctildes[p] * A_cur; -#ifdef EXTRA_C_PROJECTIONS - //aggregate C-projections separately - basis_projections_rank1(func_rank1_ind, p)+= func->ctildes[p] * A_cur; -#endif - } - } // end loop for rank=1 - - //rank>1 - int func_ms_ind = 0; - int func_ms_t_ind = 0;// index for dB - - for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { - ACECTildeBasisFunction *func = &basis[func_ind]; - //TODO: check if func->ctildes are zero, then skip -// ndensity = func->ndensity; - rank = func->rank; - r = rank - 1; -#ifdef PRINT_LOOPS_INDICES - printf("Num density = %d r = %d\n",(int) ndensity, (int)r ); - print_C_tilde_B_basis_function(*func); -#endif - mus = func->mus; - ns = func->ns; - ls = func->ls; - - //loop over {ms} combinations in sum - for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { - ms = &func->ms_combs[ms_ind * rank]; // current ms-combination (of length = rank) - - //loop over m, collect B = product of A with given ms - A_forward_prod[0] = 1; - A_backward_prod[r] = 1; - - //fill forward A-product triangle - for (t = 0; t < rank; t++) { - //TODO: optimize ns[t]-1 -> ns[t] during functions construction - A_cache[t] = A(mus[t], ns[t] - 1, ls[t], ms[t]); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("A(x=%d, n=%d, l=%d, m=%d)=(%f,%f)\n", mus[t], ns[t], ls[t], ms[t], A_cache[t].real, - A_cache[t].img); -#endif - A_forward_prod[t + 1] = A_forward_prod[t] * A_cache[t]; - } - - B = A_forward_prod[t]; - -#ifdef DEBUG_FORCES_CALCULATIONS - printf("B = (%f, %f)\n", (B).real, (B).img); -#endif - //fill backward A-product triangle - for (t = r; t >= 1; t--) { - A_backward_prod[t - 1] = - A_backward_prod[t] * A_cache[t]; - } - - for (t = 0; t < rank; ++t, ++func_ms_t_ind) { - dB = A_forward_prod[t] * A_backward_prod[t]; //dB - product of all A's except t-th - dB_flatten(func_ms_t_ind) = dB; -#ifdef DEBUG_FORCES_CALCULATIONS - m_t = ms[t]; - printf("dB(n,l,m)(%d,%d,%d) = (%f, %f)\n", ns[t], ls[t], m_t, (dB).real, (dB).img); -#endif - } - - for (DENSITY_TYPE p = 0; p < ndensity; ++p) { - //real-part only multiplication - rhos(p) += B.real_part_product(func->ctildes[ms_ind * ndensity + p]); - -#ifdef EXTRA_C_PROJECTIONS - //aggregate C-projections separately - basis_projections(func_ind, p)+=B.real_part_product(func->ctildes[ms_ind * ndensity + p]); -#endif - -#ifdef PRINT_INTERMEDIATE_VALUES - printf("rhos(%d) += %f\n", p, B.real_part_product(func->ctildes[ms_ind * ndensity + p])); - printf("Rho[i = %d][p = %d] = %f\n", i , p , rhos(p)); -#endif - } - }//end of loop over {ms} combinations in sum - }// end loop for rank>1 - -#ifdef DEBUG_FORCES_CALCULATIONS - printf("rhos = "); - for(DENSITY_TYPE p =0; prho_core_cutoffs(mu_i); - drho_cut = basis_set->drho_core_cutoffs(mu_i); - - basis_set->inner_cutoff(rho_core, rho_cut, drho_cut, fcut, dfcut); - basis_set->FS_values_and_derivatives(rhos, evdwl, dF_drho, ndensity); - - dF_drho_core = evdwl * dfcut + 1; - for (DENSITY_TYPE p = 0; p < ndensity; ++p) - dF_drho(p) *= fcut; - evdwl_cut = evdwl * fcut + rho_core; - - // E0 shift - evdwl_cut += basis_set->E0vals(mu_i); - -#ifdef DEBUG_FORCES_CALCULATIONS - printf("dFrhos = "); - for(DENSITY_TYPE p =0; pndensity; - for (DENSITY_TYPE p = 0; p < ndensity; ++p) { - //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 - weights_rank1(func->mus[0], func->ns[0] - 1) += dF_drho(p) * func->ctildes[p]; - } - } - - // rank>1 - func_ms_ind = 0; - func_ms_t_ind = 0;// index for dB - DOUBLE_TYPE theta = 0; - for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { - ACECTildeBasisFunction *func = &basis[func_ind]; -// ndensity = func->ndensity; - rank = func->rank; - mus = func->mus; - ns = func->ns; - ls = func->ls; - for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { - ms = &func->ms_combs[ms_ind * rank]; - theta = 0; - for (DENSITY_TYPE p = 0; p < ndensity; ++p) { - theta += dF_drho(p) * func->ctildes[ms_ind * ndensity + p]; -#ifdef DEBUG_FORCES_CALCULATIONS - printf("(p=%d) theta += dF_drho[p] * func.ctildes[ms_ind * ndensity + p] = %f * %f = %f\n",p, dF_drho(p), func->ctildes[ms_ind * ndensity + p],dF_drho(p)*func->ctildes[ms_ind * ndensity + p]); - printf("theta=%f\n",theta); -#endif - } - - theta *= 0.5; // 0.5 factor due to possible double counting ??? - for (t = 0; t < rank; ++t, ++func_ms_t_ind) { - m_t = ms[t]; - factor = (m_t % 2 == 0 ? 1 : -1); - dB = dB_flatten(func_ms_t_ind); - weights(mus[t], ns[t] - 1, ls[t], m_t) += theta * dB; //Theta_array(func_ms_ind); - // update -m_t (that could also be positive), because the basis is half_basis - weights(mus[t], ns[t] - 1, ls[t], -m_t) += - theta * (dB).conjugated() * factor;// Theta_array(func_ms_ind); -#ifdef DEBUG_FORCES_CALCULATIONS - printf("dB(n,l,m)(%d,%d,%d) = (%f, %f)\n", ns[t], ls[t], m_t, (dB).real, (dB).img); - printf("theta = %f\n",theta); - printf("weights(n,l,m)(%d,%d,%d) += (%f, %f)\n", ns[t], ls[t], m_t, (theta * dB * 0.5).real, - (theta * dB * 0.5).img); - printf("weights(n,l,-m)(%d,%d,%d) += (%f, %f)\n", ns[t], ls[t], -m_t, - ( theta * (dB).conjugated() * factor * 0.5).real, - ( theta * (dB).conjugated() * factor * 0.5).img); -#endif - } - } - } - energy_calc_timer.stop(); - -// ==================== FORCES ==================== -#ifdef PRINT_MAIN_STEPS - printf("\nFORCE CALCULATION\n"); - printf("loop over neighbours\n"); -#endif - - forces_calc_loop_timer.start(); -// loop over neighbour atoms for force calculations - for (jj = 0; jj < jnum_actual; ++jj) { - mu_j = elements[jj]; - r_hat = rhats[jj]; - inv_r_norm = inv_r_norms[jj]; - - Array2DLM &Y_cache_jj = Y_cache(jj); - Array2DLM &DY_cache_jj = DY_cache(jj); - -#ifdef PRINT_LOOPS_INDICES - printf("\nneighbour atom #%d\n", jj); - printf("rhat = (%f, %f, %f)\n", r_hat[0], r_hat[1], r_hat[2]); -#endif - - forces_calc_neighbour_timer.start(); - - f_ji[0] = f_ji[1] = f_ji[2] = 0; - -//for rank = 1 - for (n = 0; n < nradbasei; ++n) { - if (weights_rank1(mu_j, n) == 0) - continue; - auto &DG = DG_cache(jj, n); - DGR = DG * Y00; - DGR *= weights_rank1(mu_j, n); -#ifdef DEBUG_FORCES_CALCULATIONS - printf("r=1: (n,l,m)=(%d, 0, 0)\n",n+1); - printf("\tGR(n=%d, r=%f)=%f\n",n+1,r_norm, gr(n)); - printf("\tDGR(n=%d, r=%f)=%f\n",n+1,r_norm, dgr(n)); - printf("\tdF+=(%f, %f, %f)\n",DGR * r_hat[0], DGR * r_hat[1], DGR * r_hat[2]); -#endif - f_ji[0] += DGR * r_hat[0]; - f_ji[1] += DGR * r_hat[1]; - f_ji[2] += DGR * r_hat[2]; - } - -//for rank > 1 - for (n = 0; n < nradiali; n++) { - for (l = 0; l <= lmaxi; l++) { - R_over_r = R_cache(jj, n, l) * inv_r_norm; - DR = DR_cache(jj, n, l); - - // for m>=0 - for (m = 0; m <= l; m++) { - ACEComplex w = weights(mu_j, n, l, m); - if (w == 0) - continue; - //counting for -m cases if m>0 - if (m > 0) w *= 2; - - DY = DY_cache_jj(l, m); - Y_DR = Y_cache_jj(l, m) * DR; - - grad_phi_nlm.a[0] = Y_DR * r_hat[0] + DY.a[0] * R_over_r; - grad_phi_nlm.a[1] = Y_DR * r_hat[1] + DY.a[1] * R_over_r; - grad_phi_nlm.a[2] = Y_DR * r_hat[2] + DY.a[2] * R_over_r; -#ifdef DEBUG_FORCES_CALCULATIONS - printf("d_phi(n=%d, l=%d, m=%d) = ((%f,%f), (%f,%f), (%f,%f))\n",n+1,l,m, - grad_phi_nlm.a[0].real, grad_phi_nlm.a[0].img, - grad_phi_nlm.a[1].real, grad_phi_nlm.a[1].img, - grad_phi_nlm.a[2].real, grad_phi_nlm.a[2].img); - - printf("weights(n,l,m)(%d,%d,%d) = (%f,%f)\n", n+1, l, m,w.real, w.img); - //if (m>0) w*=2; - printf("dF(n,l,m)(%d, %d, %d) += (%f, %f, %f)\n", n + 1, l, m, - w.real_part_product(grad_phi_nlm.a[0]), - w.real_part_product(grad_phi_nlm.a[1]), - w.real_part_product(grad_phi_nlm.a[2]) - ); -#endif -// real-part multiplication only - f_ji[0] += w.real_part_product(grad_phi_nlm.a[0]); - f_ji[1] += w.real_part_product(grad_phi_nlm.a[1]); - f_ji[2] += w.real_part_product(grad_phi_nlm.a[2]); - } - } - } - - -#ifdef PRINT_INTERMEDIATE_VALUES - printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, - f_ji[0], f_ji[1], f_ji[2] - ); -#endif - - //hard-core repulsion - DCR = DCR_cache(jj); -#ifdef DEBUG_FORCES_CALCULATIONS - printf("DCR = %f\n",DCR); -#endif - f_ji[0] += dF_drho_core * DCR * r_hat[0]; - f_ji[1] += dF_drho_core * DCR * r_hat[1]; - f_ji[2] += dF_drho_core * DCR * r_hat[2]; -#ifdef PRINT_INTERMEDIATE_VALUES - printf("with core-repulsion\n"); - printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, - f_ji[0], f_ji[1], f_ji[2] - ); - printf("neighbour_index_mapping[jj=%d]=%d\n",jj,neighbour_index_mapping[jj]); -#endif - - neighbours_forces(neighbour_index_mapping[jj], 0) = f_ji[0]; - neighbours_forces(neighbour_index_mapping[jj], 1) = f_ji[1]; - neighbours_forces(neighbour_index_mapping[jj], 2) = f_ji[2]; - - forces_calc_neighbour_timer.stop(); - }// end loop over neighbour atoms for forces - - forces_calc_loop_timer.stop(); - - //now, energies and forces are ready - //energies(i) = evdwl + rho_core; - e_atom = evdwl_cut; - -#ifdef PRINT_INTERMEDIATE_VALUES - printf("energies(i) = FS(...rho_p_accum...) = %f\n", evdwl); -#endif - per_atom_calc_timer.stop(); -} \ No newline at end of file diff --git a/lib/pace/ace_evaluator.h b/lib/pace/ace_evaluator.h deleted file mode 100644 index 356ea52563..0000000000 --- a/lib/pace/ace_evaluator.h +++ /dev/null @@ -1,230 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Yury Lysogorskiy on 31.01.20. - -#ifndef ACE_EVALUATOR_H -#define ACE_EVALUATOR_H - -#include "ace_abstract_basis.h" -#include "ace_arraynd.h" -#include "ace_array2dlm.h" -#include "ace_c_basis.h" -#include "ace_complex.h" -#include "ace_timing.h" -#include "ace_types.h" - -/** - * Basic evaluator class, that should accept the basis set and implement the "compute_atom" method using given basis set. - */ -class ACEEvaluator { -protected: - - Array2D A_rank1 = Array2D("A_rank1"); ///< 2D-array for storing A's for rank=1, shape: A(mu_j,n) - Array4DLM A = Array4DLM("A"); ///< 4D array with (l,m) last indices for storing A's for rank>1: A(mu_j, n, l, m) - - Array1D rhos = Array1D("rhos"); ///< densities \f$ \rho^{(p)} \f$(ndensity), p = 0 .. ndensity-1 - Array1D dF_drho = Array1D("dF_drho"); ///< derivatives of cluster functional wrt. densities, index = 0 .. ndensity-1 - - /** - * Initialize internal arrays according to basis set sizes - * @param basis_set - */ - void init(ACEAbstractBasisSet *basis_set); - -public: - // set of timers for code profiling - - ACETimer loop_over_neighbour_timer; ///< timer for loop over neighbours when constructing A's for single central atom - ACETimer per_atom_calc_timer; ///< timer for single compute_atom call - - - ACETimer forces_calc_loop_timer; ///< timer for forces calculations for single central atom - ACETimer forces_calc_neighbour_timer; ///< timer for loop over neighbour atoms for force calculations - - ACETimer energy_calc_timer; ///< timer for energy calculation - ACETimer total_time_calc_timer; ///< timer for total calculations of all atoms within given atomic environment system - - /** - * Initialize all timers - */ - void init_timers(); - - /** - * Mapping from external atoms types, i.e. LAMMPS, to internal SPECIES_TYPE, used in basis functions - */ - Array1D element_type_mapping = Array1D("element_type_mapping"); - - - DOUBLE_TYPE e_atom = 0; ///< energy of current atom, including core-repulsion - - /** - * temporary array for the pair forces between current atom_i and its neighbours atom_k - * neighbours_forces(k,3), k = 0..num_of_neighbours(atom_i)-1 - */ - Array2D neighbours_forces = Array2D("neighbours_forces"); - - ACEEvaluator() = default; - - virtual ~ACEEvaluator() = default; - - /** - * The key method to compute energy and forces for atom 'i'. - * Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array - * - * @param i atom index - * @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3] - * @param type atomic types array of the real and ghost atoms, shape: [atom_ind] - * @param jnum number of neighbours of atom_i - * @param jlist array of neighbour indices, shape: [jnum] - */ - virtual void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) = 0; - - /** - * Resize all caches over neighbours atoms - * @param max_jnum maximum number of neighbours - */ - virtual void resize_neighbours_cache(int max_jnum) = 0; - -#ifdef EXTRA_C_PROJECTIONS - /** - * 2D array to store projections of basis function for rank = 1, shape: [func_ind][ndensity] - */ - Array2D basis_projections_rank1 = Array2D("basis_projections_rank1"); - - /** - * 2D array to store projections of basis function for rank > 1, shape: [func_ind][ndensity] - */ - Array2D basis_projections = Array2D("basis_projections"); -#endif -}; - -//TODO: split into separate file -/** - * Evaluator for C-tilde basis set, that should accept the basis set and implement the "compute_atom" method using given basis set. - */ -class ACECTildeEvaluator : public ACEEvaluator { - - /** - * Weights \f$ \omega_{i \mu n 0 0} \f$ for rank = 1, see Eq.(10) from implementation notes, - * 'i' is fixed for the current atom, shape: [nelements][nradbase] - */ - Array2D weights_rank1 = Array2D("weights_rank1"); - - /** - * Weights \f$ \omega_{i \mu n l m} \f$ for rank > 1, see Eq.(10) from implementation notes, - * 'i' is fixed for the current atom, shape: [nelements][nradbase][l=0..lmax, m] - */ - Array4DLM weights = Array4DLM("weights"); - - /** - * cache for gradients of \f$ g(r)\f$: grad_phi(jj,n)=A2DLM(l,m) - * shape:[max_jnum][nradbase] - */ - Array2D DG_cache = Array2D("DG_cache"); - - - /** - * cache for \f$ R_{nl}(r)\f$ - * shape:[max_jnum][nradbase][0..lmax] - */ - Array3D R_cache = Array3D("R_cache"); - /** - * cache for derivatives of \f$ R_{nl}(r)\f$ - * shape:[max_jnum][nradbase][0..lmax] - */ - Array3D DR_cache = Array3D("DR_cache"); - /** - * cache for \f$ Y_{lm}(\hat{r})\f$ - * shape:[max_jnum][0..lmax][m] - */ - Array3DLM Y_cache = Array3DLM("Y_cache"); - /** - * cache for \f$ \nabla Y_{lm}(\hat{r})\f$ - * shape:[max_jnum][0..lmax][m] - */ - Array3DLM DY_cache = Array3DLM("dY_dense_cache"); - - /** - * cache for derivatives of hard-core repulsion - * shape:[max_jnum] - */ - Array1D DCR_cache = Array1D("DCR_cache"); - - /** - * Partial derivatives \f$ dB_{i \mu n l m t}^{(r)} \f$ with sequential numbering over [func_ind][ms_ind][r], - * shape:[func_ms_r_ind] - */ - Array1D dB_flatten = Array1D("dB_flatten"); - - /** - * pointer to the ACEBasisSet object - */ - ACECTildeBasisSet *basis_set = nullptr; - - /** - * Initialize internal arrays according to basis set sizes - * @param basis_set - */ - void init(ACECTildeBasisSet *basis_set); - -public: - - ACECTildeEvaluator() = default; - - explicit ACECTildeEvaluator(ACECTildeBasisSet &bas) { - set_basis(bas); - } - - /** - * set the basis function to the ACE evaluator - * @param bas - */ - void set_basis(ACECTildeBasisSet &bas); - - /** - * The key method to compute energy and forces for atom 'i'. - * Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array - * - * @param i atom index - * @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3] - * @param type atomic types array of the real and ghost atoms, shape: [atom_ind] - * @param jnum number of neighbours of atom_i - * @param jlist array of neighbour indices, shape: [jnum] - */ - void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) override; - - /** - * Resize all caches over neighbours atoms - * @param max_jnum maximum number of neighbours - */ - void resize_neighbours_cache(int max_jnum) override; -}; - - -#endif //ACE_EVALUATOR_H \ No newline at end of file diff --git a/lib/pace/ace_flatten_basis.cpp b/lib/pace/ace_flatten_basis.cpp deleted file mode 100644 index 541785a202..0000000000 --- a/lib/pace/ace_flatten_basis.cpp +++ /dev/null @@ -1,130 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by yury on 28.04.2020. - -#include "ace_flatten_basis.h" - -ACEFlattenBasisSet::ACEFlattenBasisSet(const ACEFlattenBasisSet &other) { - _copy_scalar_memory(other); - _copy_dynamic_memory(other); -} - -ACEFlattenBasisSet &ACEFlattenBasisSet::operator=(const ACEFlattenBasisSet &other) { - if (this != &other) { - _clean(); - _copy_scalar_memory(other); - _copy_dynamic_memory(other); - } - return *this; -} - - -ACEFlattenBasisSet::~ACEFlattenBasisSet() { - ACEFlattenBasisSet::_clean(); -} - -void ACEFlattenBasisSet::_clean() { - //chained call of base class method - ACEAbstractBasisSet::_clean(); - _clean_contiguous_arrays(); - _clean_basissize_arrays(); - -} - -void ACEFlattenBasisSet::_clean_basissize_arrays() { - delete[] total_basis_size; - total_basis_size = nullptr; - - delete[] total_basis_size_rank1; - total_basis_size_rank1 = nullptr; -} - -void ACEFlattenBasisSet::_clean_contiguous_arrays() { - delete[] full_ns_rank1; - full_ns_rank1 = nullptr; - - delete[] full_ls_rank1; - full_ls_rank1 = nullptr; - - delete[] full_mus_rank1; - full_mus_rank1 = nullptr; - - delete[] full_ms_rank1; - full_ms_rank1 = nullptr; - - ////// - - delete[] full_ns; - full_ns = nullptr; - - delete[] full_ls; - full_ls = nullptr; - - delete[] full_mus; - full_mus = nullptr; - - delete[] full_ms; - full_ms = nullptr; -} - -void ACEFlattenBasisSet::_copy_scalar_memory(const ACEFlattenBasisSet &src) { - ACEAbstractBasisSet::_copy_scalar_memory(src); - - rank_array_total_size_rank1 = src.rank_array_total_size_rank1; - coeff_array_total_size_rank1 = src.coeff_array_total_size_rank1; - rank_array_total_size = src.rank_array_total_size; - ms_array_total_size = src.ms_array_total_size; - coeff_array_total_size = src.coeff_array_total_size; - - max_B_array_size = src.max_B_array_size; - max_dB_array_size = src.max_dB_array_size; - num_ms_combinations_max = src.num_ms_combinations_max; -} - -void ACEFlattenBasisSet::_copy_dynamic_memory(const ACEFlattenBasisSet &src) { //allocate new memory - - ACEAbstractBasisSet::_copy_dynamic_memory(src); - - if (src.total_basis_size_rank1 == nullptr) - throw runtime_error("Could not copy ACEFlattenBasisSet::total_basis_size_rank1 - array not initialized"); - if (src.total_basis_size == nullptr) - throw runtime_error("Could not copy ACEFlattenBasisSet::total_basis_size - array not initialized"); - - delete[] total_basis_size_rank1; - total_basis_size_rank1 = new SHORT_INT_TYPE[nelements]; - delete[] total_basis_size; - total_basis_size = new SHORT_INT_TYPE[nelements]; - - //copy - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - total_basis_size_rank1[mu] = src.total_basis_size_rank1[mu]; - total_basis_size[mu] = src.total_basis_size[mu]; - } -} - diff --git a/lib/pace/ace_flatten_basis.h b/lib/pace/ace_flatten_basis.h deleted file mode 100644 index e21cbb749a..0000000000 --- a/lib/pace/ace_flatten_basis.h +++ /dev/null @@ -1,135 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Lysogroskiy Yury on 28.04.2020. - -#ifndef ACE_EVALUATOR_ACE_FLATTEN_BASIS_H -#define ACE_EVALUATOR_ACE_FLATTEN_BASIS_H - - -#include "ace_abstract_basis.h" -#include "ace_c_basisfunction.h" -#include "ace_radial.h" -#include "ace_spherical_cart.h" -#include "ace_types.h" - -/** - * Basis set with basis function attributes, i.e. \f$ \mathbf{n}, \mathbf{l}, \mathbf{m}\f$, etc. - * packed into contiguous arrays for the cache-friendly memory layout. - */ -class ACEFlattenBasisSet : public ACEAbstractBasisSet { -public: - //arrays and its sizes for rank = 1 basis functions for packed basis - - size_t rank_array_total_size_rank1 = 0; ///< size for full_ns_rank1, full_ls_rank1, full_Xs_rank1 - size_t coeff_array_total_size_rank1 = 0; ///< size for full coefficients array (depends on B or C-Tilde basis) - - NS_TYPE *full_ns_rank1 = nullptr; ///< ns contiguous package [rank_array_total_size_rank1] - LS_TYPE *full_ls_rank1 = nullptr; ///< ls contiguous package [rank_array_total_size_rank1] - SPECIES_TYPE *full_mus_rank1 = nullptr; ///< mus contiguous package [rank_array_total_size_rank1] - MS_TYPE *full_ms_rank1 = nullptr; ///< m_s contiguous package[rank_array_total_size_rank1] - - //arrays and its sizes for rank > 1 basis functions for packed basis - size_t rank_array_total_size = 0; ///< size for full_ns, full_ls, full_Xs - size_t ms_array_total_size = 0; ///< size for full_ms array - size_t coeff_array_total_size = 0;///< size for full coefficients arrays (depends on B- or C- basis) - - NS_TYPE *full_ns = nullptr; ///< ns contiguous package [rank_array_total_size] - LS_TYPE *full_ls = nullptr; ///< ls contiguous package [rank_array_total_size] - SPECIES_TYPE *full_mus = nullptr; ///< mus contiguous package [rank_array_total_size] - MS_TYPE *full_ms = nullptr; ///< //m_s contiguous package [ms_array_total_size] - - /** - * Rearrange basis functions in contiguous memory to optimize cache access - */ - virtual void pack_flatten_basis() = 0; - - virtual void flatten_basis() = 0; - - //1D flat array basis representation: [mu] - SHORT_INT_TYPE *total_basis_size_rank1 = nullptr; ///< per-species type array of total_basis_rank1[mu] sizes - SHORT_INT_TYPE *total_basis_size = nullptr; ///< per-species type array of total_basis[mu] sizes - - size_t max_B_array_size = 0; ///< maximum over elements array size for B[func_ind][ms_ind] - size_t max_dB_array_size = 0; ///< maximum over elements array size for dB[func_ind][ms_ind][r] - - SHORT_INT_TYPE num_ms_combinations_max = 0; ///< maximum number of ms combinations among all basis functions - - /** - * Default constructor - */ - ACEFlattenBasisSet() = default; - - /** - * Copy constructor (see Rule of Three) - * @param other - */ - ACEFlattenBasisSet(const ACEFlattenBasisSet &other); - - /** - * operator= (see Rule of Three) - * @param other - * @return - */ - ACEFlattenBasisSet &operator=(const ACEFlattenBasisSet &other); - - /** - * Destructor (see Rule of Three) - */ - ~ACEFlattenBasisSet() override; - - // routines for copying and cleaning dynamic memory of the class (see Rule of Three) - /** - * Cleaning dynamic memory of the class (see. Rule of Three), - * must be idempotent for safety - */ - void _clean() override; - - /** - * Copying scalar variables - * @param src - */ - void _copy_scalar_memory(const ACEFlattenBasisSet &src); - - /** - * Copying and cleaning dynamic memory of the class (see. Rule of Three) - * @param src - */ - void _copy_dynamic_memory(const ACEFlattenBasisSet &src); - - /** - * Clean contiguous arrays - */ - virtual void _clean_contiguous_arrays(); - - /** - * Release dynamic arrays with basis set sizes - */ - void _clean_basissize_arrays(); -}; - -#endif //ACE_EVALUATOR_ACE_FLATTEN_BASIS_H diff --git a/lib/pace/ace_radial.cpp b/lib/pace/ace_radial.cpp deleted file mode 100644 index 01348a719c..0000000000 --- a/lib/pace/ace_radial.cpp +++ /dev/null @@ -1,566 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -#include -#include -#include - -#include "ace_radial.h" - -const DOUBLE_TYPE pi = 3.14159265358979323846264338327950288419; // pi - -ACERadialFunctions::ACERadialFunctions(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, - SPECIES_TYPE nelements, - DOUBLE_TYPE cutoff, string radbasename) { - init(nradb, lmax, nradial, deltaSplineBins, nelements, cutoff, radbasename); -} - -void ACERadialFunctions::init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, - SPECIES_TYPE nelements, - DOUBLE_TYPE cutoff, string radbasename) { - this->nradbase = nradb; - this->lmax = lmax; - this->nradial = nradial; - this->deltaSplineBins = deltaSplineBins; - this->nelements = nelements; - this->cutoff = cutoff; - this->radbasename = radbasename; - - gr.init(nradbase, "gr"); - dgr.init(nradbase, "dgr"); - d2gr.init(nradbase, "d2gr"); - - - fr.init(nradial, lmax + 1, "fr"); - dfr.init(nradial, lmax + 1, "dfr"); - d2fr.init(nradial, lmax + 1, "d2fr"); - - - cheb.init(nradbase + 1, "cheb"); - dcheb.init(nradbase + 1, "dcheb"); - cheb2.init(nradbase + 1, "cheb2"); - - - splines_gk.init(nelements, nelements, "splines_gk"); - splines_rnl.init(nelements, nelements, "splines_rnl"); - splines_hc.init(nelements, nelements, "splines_hc"); - - lambda.init(nelements, nelements, "lambda"); - lambda.fill(1.); - - cut.init(nelements, nelements, "cut"); - cut.fill(1.); - - dcut.init(nelements, nelements, "dcut"); - dcut.fill(1.); - - crad.init(nelements, nelements, nradial, (lmax + 1), nradbase, "crad"); - crad.fill(0.); - - //hard-core repulsion - prehc.init(nelements, nelements, "prehc"); - prehc.fill(0.); - - lambdahc.init(nelements, nelements, "lambdahc"); - lambdahc.fill(1.); - -} - - -/** -Function that computes Chebyshev polynomials of first and second kind - to setup the radial functions and the derivatives - -@param n, x - -@returns cheb1, dcheb1 -*/ -void ACERadialFunctions::calcCheb(NS_TYPE n, DOUBLE_TYPE x) { - if (n < 0) { - char s[1024]; - sprintf(s, "The order n of the polynomials should be positive %d\n", n); - throw std::invalid_argument(s); - } - DOUBLE_TYPE twox = 2.0 * x; - cheb(0) = 1.; - dcheb(0) = 0.; - cheb2(0) = 1.; - - if (nradbase > 1) { - cheb(1) = x; - cheb2(1) = twox; - } - for (NS_TYPE m = 1; m <= n - 1; m++) { - cheb(m + 1) = twox * cheb(m) - cheb(m - 1); - cheb2(m + 1) = twox * cheb2(m) - cheb2(m - 1); - } - for (NS_TYPE m = 1; m <= n; m++) { - dcheb(m) = m * cheb2(m - 1); - } -#ifdef DEBUG_RADIAL - for ( NS_TYPE m=0; m<=n; m++ ) { - printf(" m %d cheb %f dcheb %f \n", m, cheb(m), dcheb(m)); - } -#endif -} - -/** -Function that computes radial basis. - -@param lam, nradbase, cut, dcut, r - -@returns gr, dgr -*/ -void ACERadialFunctions::radbase(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { - /*lam is given by the formula (24), that contains cut */ - - if (r < cut) { - if (radbasename == "ChebExpCos") { - chebExpCos(lam, cut, dcut, r); - } else if (radbasename == "ChebPow") { - chebPow(lam, cut, dcut, r); - } else if (radbasename == "ChebLinear") { - chebLinear(lam, cut, dcut, r); - } else { - throw invalid_argument("Unknown radial basis function name: " + radbasename); - } - } else { - gr.fill(0); - dgr.fill(0); - } -} - -/*** - * Radial function: ChebExpCos, cheb exp scaling including cos envelope - * @param lam function parameter - * @param cut cutoff distance - * @param r function input argument - * @return fills in gr and dgr arrays - */ -void -ACERadialFunctions::chebExpCos(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { - DOUBLE_TYPE y2, y1, x, dx; - DOUBLE_TYPE env, denv, fcut, dfcut; - /* scaled distance x and derivative*/ - y1 = exp(-lam * r / cut); - y2 = exp(-lam); - x = 1.0 - 2.0 * ((y1 - y2) / (1 - y2)); - dx = 2 * (lam / cut) * (y1 / (1 - y2)); - /* calculation of Chebyshev polynomials from the recursion */ - calcCheb(nradbase - 1, x); - gr(0) = cheb(0); - dgr(0) = dcheb(0) * dx; - for (NS_TYPE n = 2; n <= nradbase; n++) { - gr(n - 1) = 0.5 - 0.5 * cheb(n - 1); - dgr(n - 1) = -0.5 * dcheb(n - 1) * dx; - } - env = 0.5 * (1.0 + cos(M_PI * r / cut)); - denv = -0.5 * sin(M_PI * r / cut) * M_PI / cut; - for (NS_TYPE n = 0; n < nradbase; n++) { - dgr(n) = gr(n) * denv + dgr(n) * env; - gr(n) = gr(n) * env; - } - // for radtype = 3 a smooth cut is already included in the basis function - dx = cut - dcut; - if (r > dx) { - fcut = 0.5 * (1.0 + cos(M_PI * (r - dx) / dcut)); - dfcut = -0.5 * sin(M_PI * (r - dx) / dcut) * M_PI / dcut; - for (NS_TYPE n = 0; n < nradbase; n++) { - dgr(n) = gr(n) * dfcut + dgr(n) * fcut; - gr(n) = gr(n) * fcut; - } - } -} - -/*** -* Radial function: ChebPow, Radial function: ChebPow -* - argument of Chebyshev polynomials -* x = 2.0*( 1.0 - (1.0 - r/rcut)^lam ) - 1.0 -* - radial function -* gr(n) = ( 1.0 - Cheb(n) )/2.0, n = 1,...,nradbase -* - the function fulfills: -* gr(n) = 0 at rcut -* dgr(n) = 0 at rcut for lam >= 1 -* second derivative zero at rcut for lam >= 2 -* -> the radial function does not require a separate cutoff function -* - corresponds to radial basis radtype=5 in Fortran code -* -* @param lam function parameter -* @param cut cutoff distance -* @param r function input argument -* @return fills in gr and dgr arrays -*/ -void -ACERadialFunctions::chebPow(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { - DOUBLE_TYPE y, dy, x, dx; - /* scaled distance x and derivative*/ - y = (1.0 - r / cut); - dy = pow(y, (lam - 1.0)); - y = dy * y; - dy = -lam / cut * dy; - - x = 2.0 * (1.0 - y) - 1.0; - dx = -2.0 * dy; - calcCheb(nradbase, x); - for (NS_TYPE n = 1; n <= nradbase; n++) { - gr(n - 1) = 0.5 - 0.5 * cheb(n); - dgr(n - 1) = -0.5 * dcheb(n) * dx; - } -} - - -void -ACERadialFunctions::chebLinear(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { - DOUBLE_TYPE x, dx; - /* scaled distance x and derivative*/ - x = (1.0 - r / cut); - dx = -1 / cut; - calcCheb(nradbase, x); - for (NS_TYPE n = 1; n <= nradbase; n++) { - gr(n - 1) = 0.5 - 0.5 * cheb(n); - dgr(n - 1) = -0.5 * dcheb(n) * dx; - } -} - -/** -Function that computes radial functions. - -@param nradbase, nelements, elei, elej - -@returns fr, dfr -*/ -void ACERadialFunctions::radfunc(SPECIES_TYPE elei, SPECIES_TYPE elej) { - DOUBLE_TYPE frval, dfrval; - for (NS_TYPE n = 0; n < nradial; n++) { - for (LS_TYPE l = 0; l <= lmax; l++) { - frval = 0.0; - dfrval = 0.0; - for (NS_TYPE k = 0; k < nradbase; k++) { - frval += crad(elei, elej, n, l, k) * gr(k); - dfrval += crad(elei, elej, n, l, k) * dgr(k); - } - fr(n, l) = frval; - dfr(n, l) = dfrval; - } - } -} - - -void ACERadialFunctions::all_radfunc(SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, DOUBLE_TYPE r) { - DOUBLE_TYPE lam = lambda(mu_i, mu_j); - DOUBLE_TYPE r_cut = cut(mu_i, mu_j); - DOUBLE_TYPE dr_cut = dcut(mu_i, mu_j); - // set up radial functions - radbase(lam, r_cut, dr_cut, r); //update gr, dgr - radfunc(mu_i, mu_j); // update fr(nr, l), dfr(nr, l) -} - - -void ACERadialFunctions::setuplookupRadspline() { - using namespace std::placeholders; - DOUBLE_TYPE lam, r_cut, dr_cut; - DOUBLE_TYPE cr_c, dcr_c, pre, lamhc; - - // at r = rcut + eps the function and its derivatives is zero - for (SPECIES_TYPE elei = 0; elei < nelements; elei++) { - for (SPECIES_TYPE elej = 0; elej < nelements; elej++) { - - lam = lambda(elei, elej); - r_cut = cut(elei, elej); - dr_cut = dcut(elei, elej); - - splines_gk(elei, elej).setupSplines(gr.get_size(), - std::bind(&ACERadialFunctions::radbase, this, lam, r_cut, dr_cut, - _1),//update gr, dgr - gr.get_data(), - dgr.get_data(), deltaSplineBins, cutoff); - - splines_rnl(elei, elej).setupSplines(fr.get_size(), - std::bind(&ACERadialFunctions::all_radfunc, this, elei, elej, - _1), // update fr(nr, l), dfr(nr, l) - fr.get_data(), - dfr.get_data(), deltaSplineBins, cutoff); - - - pre = prehc(elei, elej); - lamhc = lambdahc(elei, elej); -// radcore(r, pre, lamhc, cutoff, cr_c, dcr_c); - splines_hc(elei, elej).setupSplines(1, - std::bind(&ACERadialFunctions::radcore, _1, pre, lamhc, cutoff, - std::ref(cr_c), std::ref(dcr_c)), - &cr_c, - &dcr_c, deltaSplineBins, cutoff); - } - } - -} - -/** -Function that gets radial function from look-up table using splines. - -@param r, nradbase_c, nradial_c, lmax, mu_i, mu_j - -@returns fr, dfr, gr, dgr, cr, dcr -*/ -void -ACERadialFunctions::evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, - SPECIES_TYPE mu_j, bool calc_second_derivatives) { - auto &spline_gk = splines_gk(mu_i, mu_j); - auto &spline_rnl = splines_rnl(mu_i, mu_j); - auto &spline_hc = splines_hc(mu_i, mu_j); - - spline_gk.calcSplines(r, calc_second_derivatives); // populate splines_gk.values, splines_gk.derivatives; - for (NS_TYPE nr = 0; nr < nradbase_c; nr++) { - gr(nr) = spline_gk.values(nr); - dgr(nr) = spline_gk.derivatives(nr); - if (calc_second_derivatives) - d2gr(nr) = spline_gk.second_derivatives(nr); - } - - spline_rnl.calcSplines(r, calc_second_derivatives); - for (size_t ind = 0; ind < fr.get_size(); ind++) { - fr.get_data(ind) = spline_rnl.values.get_data(ind); - dfr.get_data(ind) = spline_rnl.derivatives.get_data(ind); - if (calc_second_derivatives) - d2fr.get_data(ind) = spline_rnl.second_derivatives.get_data(ind); - } - - spline_hc.calcSplines(r, calc_second_derivatives); - cr = spline_hc.values(0); - dcr = spline_hc.derivatives(0); - if (calc_second_derivatives) - d2cr = spline_hc.second_derivatives(0); -} - - -void -ACERadialFunctions::radcore(DOUBLE_TYPE r, DOUBLE_TYPE pre, DOUBLE_TYPE lambda, DOUBLE_TYPE cutoff, DOUBLE_TYPE &cr, - DOUBLE_TYPE &dcr) { -/* pseudocode for hard core repulsion -in: - r: distance - pre: prefactor: read from input, depends on pair of atoms mu_i mu_j - lambda: exponent: read from input, depends on pair of atoms mu_i mu_j - cutoff: cutoff distance: read from input, depends on pair of atoms mu_i mu_j -out: -cr: hard core repulsion -dcr: derivative of hard core repulsion - - function - \$f f_{core} = pre \exp( - \lambda r^2 ) / r \$f - -*/ - - DOUBLE_TYPE r2, lr2, y, x0, env, denv; - -// repulsion strictly positive and decaying - pre = abs(pre); - lambda = abs(lambda); - - r2 = r * r; - lr2 = lambda * r2; - if (lr2 < 50.0) { - y = exp(-lr2); - cr = pre * y / r; - dcr = -pre * y * (2.0 * lr2 + 1.0) / r2; - - x0 = r / cutoff; - env = 0.5 * (1.0 + cos(pi * x0)); - denv = -0.5 * sin(pi * x0) * pi / cutoff; - dcr = cr * denv + dcr * env; - cr = cr * env; - } else { - cr = 0.0; - dcr = 0.0; - } - -} - -void -ACERadialFunctions::evaluate_range(vector r_vec, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, - SPECIES_TYPE mu_j) { - if (nradbase_c > nradbase) - throw invalid_argument("nradbase_c couldn't be larger than nradbase"); - if (nradial_c > nradial) - throw invalid_argument("nradial_c couldn't be larger than nradial"); - if (mu_i > nelements) - throw invalid_argument("mu_i couldn't be larger than nelements"); - if (mu_j > nelements) - throw invalid_argument("mu_j couldn't be larger than nelements"); - - gr_vec.resize(r_vec.size(), nradbase_c); - dgr_vec.resize(r_vec.size(), nradbase_c); - d2gr_vec.resize(r_vec.size(), nradbase_c); - - fr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1)); - dfr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1)); - d2fr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1)); - - for (size_t i = 0; i < r_vec.size(); i++) { - DOUBLE_TYPE r = r_vec[i]; - this->evaluate(r, nradbase_c, nradial_c, mu_i, mu_j, true); - for (NS_TYPE nr = 0; nr < nradbase_c; nr++) { - gr_vec(i, nr) = gr(nr); - dgr_vec(i, nr) = dgr(nr); - d2gr_vec(i, nr) = d2gr(nr); - } - - for (NS_TYPE nr = 0; nr < nradial_c; nr++) { - for (LS_TYPE l = 0; l <= lmax; l++) { - fr_vec(i, nr, l) = fr(nr, l); - dfr_vec(i, nr, l) = dfr(nr, l); - d2fr_vec(i, nr, l) = d2fr(nr, l); - - } - } - } - -} - -void SplineInterpolator::setupSplines(int num_of_functions, RadialFunctions func, - DOUBLE_TYPE *values, - DOUBLE_TYPE *dvalues, DOUBLE_TYPE deltaSplineBins, DOUBLE_TYPE cutoff) { - - this->deltaSplineBins = deltaSplineBins; - this->cutoff = cutoff; - this->ntot = static_cast(cutoff / deltaSplineBins); - - DOUBLE_TYPE r, c[4]; - this->num_of_functions = num_of_functions; - this->values.resize(num_of_functions); - this->derivatives.resize(num_of_functions); - this->second_derivatives.resize(num_of_functions); - - Array1D f1g(num_of_functions); - Array1D f1gd1(num_of_functions); - f1g.fill(0); - f1gd1.fill(0); - - nlut = ntot; - DOUBLE_TYPE f0, f1, f0d1, f1d1; - int idx; - - // cutoff is global cutoff - rscalelookup = (DOUBLE_TYPE) nlut / cutoff; - invrscalelookup = 1.0 / rscalelookup; - - lookupTable.init(ntot + 1, num_of_functions, 4); - if (values == nullptr & num_of_functions > 0) - throw invalid_argument("SplineInterpolator::setupSplines: values could not be null"); - if (dvalues == nullptr & num_of_functions > 0) - throw invalid_argument("SplineInterpolator::setupSplines: dvalues could not be null"); - - for (int n = nlut; n >= 1; n--) { - r = invrscalelookup * DOUBLE_TYPE(n); - func(r); //populate values and dvalues arrays - for (int func_id = 0; func_id < num_of_functions; func_id++) { - f0 = values[func_id]; - f1 = f1g(func_id); - f0d1 = dvalues[func_id] * invrscalelookup; - f1d1 = f1gd1(func_id); - // evaluate coefficients - c[0] = f0; - c[1] = f0d1; - c[2] = 3.0 * (f1 - f0) - f1d1 - 2.0 * f0d1; - c[3] = -2.0 * (f1 - f0) + f1d1 + f0d1; - // store coefficients - for (idx = 0; idx <= 3; idx++) - lookupTable(n, func_id, idx) = c[idx]; - - // evaluate function values and derivatives at current position - f1g(func_id) = c[0]; - f1gd1(func_id) = c[1]; - } - } - - -} - - -void SplineInterpolator::calcSplines(DOUBLE_TYPE r, bool calc_second_derivatives) { - DOUBLE_TYPE wl, wl2, wl3, w2l1, w3l2, w4l2; - DOUBLE_TYPE c[4]; - int func_id, idx; - DOUBLE_TYPE x = r * rscalelookup; - int nl = static_cast(floor(x)); - - if (nl <= 0) - throw std::invalid_argument("Encountered very small distance. Stopping."); - - if (nl < nlut) { - wl = x - DOUBLE_TYPE(nl); - wl2 = wl * wl; - wl3 = wl2 * wl; - w2l1 = 2.0 * wl; - w3l2 = 3.0 * wl2; - w4l2 = 6.0 * wl; - for (func_id = 0; func_id < num_of_functions; func_id++) { - for (idx = 0; idx <= 3; idx++) { - c[idx] = lookupTable(nl, func_id, idx); - } - values(func_id) = c[0] + c[1] * wl + c[2] * wl2 + c[3] * wl3; - derivatives(func_id) = (c[1] + c[2] * w2l1 + c[3] * w3l2) * rscalelookup; - if (calc_second_derivatives) - second_derivatives(func_id) = (c[2] + c[3] * w4l2) * rscalelookup * rscalelookup * 2; - } - } else { // fill with zeroes - values.fill(0); - derivatives.fill(0); - if (calc_second_derivatives) - second_derivatives.fill(0); - } -} - -void SplineInterpolator::calcSplines(DOUBLE_TYPE r, SHORT_INT_TYPE func_ind) { - DOUBLE_TYPE wl, wl2, wl3, w2l1, w3l2; - DOUBLE_TYPE c[4]; - int idx; - DOUBLE_TYPE x = r * rscalelookup; - int nl = static_cast(floor(x)); - - if (nl <= 0) - throw std::invalid_argument("Encountered very small distance. Stopping."); - - if (nl < nlut) { - wl = x - DOUBLE_TYPE(nl); - wl2 = wl * wl; - wl3 = wl2 * wl; - w2l1 = 2.0 * wl; - w3l2 = 3.0 * wl2; - - for (idx = 0; idx <= 3; idx++) { - c[idx] = lookupTable(nl, func_ind, idx); - } - values(func_ind) = c[0] + c[1] * wl + c[2] * wl2 + c[3] * wl3; - derivatives(func_ind) = (c[1] + c[2] * w2l1 + c[3] * w3l2) * rscalelookup; - - } else { // fill with zeroes - values(func_ind) = 0; - derivatives(func_ind) = 0; - } -} diff --git a/lib/pace/ace_radial.h b/lib/pace/ace_radial.h deleted file mode 100644 index e45cfaec79..0000000000 --- a/lib/pace/ace_radial.h +++ /dev/null @@ -1,324 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -#ifndef ACE_RADIAL_FUNCTIONS_H -#define ACE_RADIAL_FUNCTIONS_H - -#include "ace_arraynd.h" -#include "ace_types.h" -#include - -using namespace std; - -//typedef void (*RadialFunctions)(DOUBLE_TYPE x); -typedef std::function RadialFunctions; - -/** - * Class that implement spline interpolation and caching for radial functions - */ -class SplineInterpolator { -public: - DOUBLE_TYPE cutoff = 0; ///< cutoff - DOUBLE_TYPE deltaSplineBins = 0.001; - int ntot = 10000; ///< Number of bins for look-up tables. - int nlut = 10000; ///< number of nodes in look-up table - DOUBLE_TYPE invrscalelookup = 1; ///< inverse of conversion coefficient from distance to lookup table within cutoff range - DOUBLE_TYPE rscalelookup = 1; ///< conversion coefficient from distance to lookup table within cutoff range - int num_of_functions = 0;///< number of functions to spline-interpolation - - Array1D values;// = Array1D("values"); ///< shape: [func_ind] - Array1D derivatives;// = Array1D("derivatives");///< shape: [func_ind] - Array1D second_derivatives;// = Array1D("second_derivatives");///< shape: [func_ind] - - Array3D lookupTable = Array3D("lookupTable");///< shape: [ntot+1][func_ind][4] - - /** - * Setup splines - * - * @param num_of_functions number of functions - * @param func subroutine, that update `values` and `dvalues` arrays - * @param values values - * @param dvalues derivatives - */ - void setupSplines(int num_of_functions, RadialFunctions func, - DOUBLE_TYPE *values, - DOUBLE_TYPE *dvalues, DOUBLE_TYPE deltaSplineBins, DOUBLE_TYPE cutoff); - - /** - * Populate `values` and `derivatives` arrays with a spline-interpolation for - * all functions - * - * @param r - * - * @return: populate 'values' and 'derivatives' - */ - void calcSplines(DOUBLE_TYPE r, bool calc_second_derivatives = false); - - /** - * Populate `values` and `derivatives` arrays with a spline-interpolation for - * all functions - * - * @param r - * - * @return: populate 'values' and 'derivatives' - */ - void calcSplines(DOUBLE_TYPE r, SHORT_INT_TYPE func_ind); -}; - -/** - * Interface class for radial basis functions with rank=1 (g_k), R_nl (rank>1) and hard-core repulsion radial functions - */ -class AbstractRadialBasis { -public: - SPECIES_TYPE nelements = 0; ///< number of elements - Array2D cut = Array2D("cut"); ///< cutoffs, shape: [nelements][nelements] - Array2D dcut = Array2D("dcut"); ///< decay of cutoff, shape: [nelements][nelements] - DOUBLE_TYPE cutoff = 0; ///< cutoff - -// int ntot = 10000; ///< Number of bins for look-up tables. - DOUBLE_TYPE deltaSplineBins; - LS_TYPE lmax = 0; ///< maximum value of `l` - NS_TYPE nradial = 0; ///< maximum number `n` of radial functions \f$ R_{nl}(r) \f$ - NS_TYPE nradbase = 0; ///< number of radial basis functions \f$ g_k(r) \f$ - - // Arrays for look-up tables. - Array2D splines_gk; ///< array of spline interpolator to store g_k, shape: [nelements][nelements] - Array2D splines_rnl; ///< array of spline interpolator to store R_nl, shape: [nelements][nelements] - Array2D splines_hc; ///< array of spline interpolator to store R_nl shape: [nelements][nelements] - //-------------------------------------------------------------------------- - - string radbasename = "ChebExpCos"; ///< type of radial basis functions \f$ g_{k}(r) \f$ (default="ChebExpCos") - - /** - Arrays to store radial functions. - */ - Array1D gr = Array1D("gr"); ///< g_k(r) functions, shape: [nradbase] - Array1D dgr = Array1D("dgr"); ///< derivatives of g_k(r) functions, shape: [nradbase] - Array1D d2gr = Array1D("d2gr"); ///< derivatives of g_k(r) functions, shape: [nradbase] - - Array2D fr = Array2D("fr"); ///< R_nl(r) functions, shape: [nradial][lmax+1] - Array2D dfr = Array2D( - "dfr"); ///< derivatives of R_nl(r) functions, shape: [nradial][lmax+1] - Array2D d2fr = Array2D( - "d2fr"); ///< derivatives of R_nl(r) functions, shape: [nradial][lmax+1] - - - - DOUBLE_TYPE cr; ///< hard-core repulsion - DOUBLE_TYPE dcr; ///< derivative of hard-core repulsion - DOUBLE_TYPE d2cr; ///< derivative of hard-core repulsion - - Array5D crad = Array5D( - "crad"); ///< expansion coefficients of radial functions into radial basis function, see Eq. (27) of PRB, shape: [nelements][nelements][lmax + 1][nradial][nradbase] - Array2D lambda = Array2D( - "lambda"); ///< distance scaling parameter Eq.(24) of PRB, shape: [nelements][nelements] - - Array2D prehc = Array2D( - "prehc"); ///< hard-core repulsion coefficients (prefactor), shape: [nelements][nelements] - Array2D lambdahc = Array2D( - "lambdahc");; ///< hard-core repulsion coefficients (lambdahc), shape: [nelements][nelements] - - virtual void - evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, - bool calc_second_derivatives = false) = 0; - - virtual void - init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements, - DOUBLE_TYPE cutoff, - string radbasename = "ChebExpCos") = 0; - - /** - * Function that sets up the look-up tables for spline-representation of radial functions. - */ - virtual void setuplookupRadspline() = 0; - - virtual AbstractRadialBasis *clone() const = 0; - - virtual ~AbstractRadialBasis() = default; -}; - - -/** -Class to store radial functions and their associated functions. \n -*/ -class ACERadialFunctions final : public AbstractRadialBasis { -public: - - //-------------------------------------------------------------------------- - - /** - Arrays to store Chebyshev polynomials. - */ - Array1D cheb = Array1D( - "cheb"); ///< Chebyshev polynomials of the first kind, shape: [nradbase+1] - Array1D dcheb = Array1D( - "dcheb"); ///< derivatives Chebyshev polynomials of the first kind, shape: [nradbase+1] - Array1D cheb2 = Array1D( - "cheb2"); ///< Chebyshev polynomials of the second kind, shape: [nradbase+1] - - //-------------------------------------------------------------------------- - - Array2D gr_vec; - Array2D dgr_vec; - Array2D d2gr_vec; - - Array3D fr_vec; - Array3D dfr_vec; - Array3D d2fr_vec; - //------------------------------------------------------------------------ - /** - * Default constructor - */ - ACERadialFunctions() = default; - - /** - * Parametrized constructor - * - * @param nradb number of radial basis function \f$ g_k(r) \f$ - nradbase - * @param lmax maximum orbital moment - lmax - * @param nradial maximum n-index of radial functions \f$ R_{nl}(r) \f$ - nradial - * @param ntot Number of bins for spline look-up tables. - * @param nelements numer of elements - * @param cutoff cutoff - * @param radbasename type of radial basis function \f$ g_k(r) \f$ (default: "ChebExpCos") - */ - ACERadialFunctions(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, - SPECIES_TYPE nelements, - DOUBLE_TYPE cutoff, string radbasename = "ChebExpCos"); - - /** - * Initialize arrays for given parameters - * - * @param nradb number of radial basis function \f$ g_k(r) \f$ - nradbase - * @param lmax maximum orbital moment - lmax - * @param nradial maximum n-index of radial functions \f$ R_{nl}(r) \f$ - nradial - * @param ntot Number of bins for spline look-up tables. - * @param nelements numer of elements - * @param cutoff cutoff - * @param radbasename type of radial basis function \f$ g_k(r) \f$ (default: "ChebExpCos") - */ - void init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements, - DOUBLE_TYPE cutoff, - string radbasename = "ChebExpCos") final; - - /** - * Destructor - */ - ~ACERadialFunctions() final = default; - - /** - * Function that computes Chebyshev polynomials of first and second kind - * to setup the radial functions and the derivatives - * - * @param n maximum polynom order - * @param x - * - * @returns fills cheb, dcheb and cheb2 arrays - */ - void calcCheb(NS_TYPE n, DOUBLE_TYPE x); - - /** - * Function that computes radial basis functions \$f g_k(r) \$f, see Eq.(21) of PRB paper - * @param lam \$f \lambda \$f parameter, see eq. (24) of PRB paper - * @param cut cutoff - * @param dcut cutoff decay - * @param r distance - * - * @return function fills gr and dgr arrays - */ - void radbase(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); - - /** - * Function that computes radial core repulsion \$f f_{core} = pre \exp( - \lambda r^2 ) / r \$f, - * and its derivative, see Eq.(27) of implementation notes. - * - * @param r distance - * @param pre prefactor: read from input, depends on pair of atoms mu_i mu_j - * @param lambda exponent: read from input, depends on pair of atoms mu_i mu_j - * @param cutoff cutoff distance: read from input, depends on pair of atoms mu_i mu_j - * @param cr (out) hard core repulsion - * @param dcr (out) derivative of hard core repulsion - */ - static void radcore(DOUBLE_TYPE r, DOUBLE_TYPE pre, DOUBLE_TYPE lambda, DOUBLE_TYPE cutoff, DOUBLE_TYPE &cr, - DOUBLE_TYPE &dcr); - - /** - * Function that sets up the look-up tables for spline-representation of radial functions. - */ - void setuplookupRadspline() final; - - /** - * Function that computes radial functions \f$ R_{nl}(r)\f$ (see Eq. 27 from PRB paper) - * and its derivatives for all range of n,l, - * ONLY if radial basis functions (gr and dgr) are computed. - * @param elei first species type - * @param elej second species type - * - * @return fills in fr, dfr arrays - */ - void radfunc(SPECIES_TYPE elei, SPECIES_TYPE elej); - - /** - * Compute all radial functions R_nl(r), radial basis functions g_k(r) and hard-core repulsion function hc(r) - * - * @param r distance - * @param nradbase_c - * @param nradial_c - * @param mu_i - * @param mu_j - * - * @return update gr(k), dgr(k), fr(n,l), dfr(n,l), cr, dcr - */ - void evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, - bool calc_second_derivatives = false) final; - - - void - evaluate_range(vector r_vec, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, - SPECIES_TYPE mu_j); - - void chebExpCos(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); - - void chebPow(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); - - void chebLinear(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); - - /** - * Setup all radial functions for element pair mu_i-mu_j and distance r - * @param mu_i first specie type - * @param mu_j second specie type - * @param r distance - * @return update fr(nr, l), dfr(nr, l) - */ - void all_radfunc(SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, DOUBLE_TYPE r); - - ACERadialFunctions *clone() const override { - return new ACERadialFunctions(*this); - }; -}; - -#endif \ No newline at end of file diff --git a/lib/pace/ace_recursive.cpp b/lib/pace/ace_recursive.cpp deleted file mode 100644 index c895418943..0000000000 --- a/lib/pace/ace_recursive.cpp +++ /dev/null @@ -1,1340 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Christoph Ortner on 20.12.2020 - -#include "ace_recursive.h" - -#include "ace_abstract_basis.h" -#include "ace_types.h" - -/* ------------------------------------------------------------ - * ACEDAG Implementation - * (just the DAG construction, not the traversal) - * ------------------------------------------------------------ */ - -/* Notes on different Tags: - * rec1 - first basic implementation - * rec2 - avoid index arithmetic, contiguous layout, - * canonical evaluator in ACE.jl format - * rec3 - split nodes into interior and leaf nodes - */ - -void ACEDAG::init(Array2D xAspec, - Array2D AAspec, - Array1D orders, - Array2D jl_coeffs, - int _heuristic ) { - - // remember which heuristic we want to use! - heuristic = _heuristic; - - /* stage one of the graph is just extracting the A basis from - * the tensor product format into the linear list; all information - * for that is already stored in Aspec, and the only thing to do here is - * to construct zero-coefficients. Still we have to copy Aspec, since - * the one we have here will (may?) be deleted. */ - int num1 = xAspec.get_dim(0); - Aspec = xAspec; //YL: just copying the multiarray: Aspec = xAspec; - - /* fill the one-particle basis into the DAGmap - * DAGmap[ (i1,...,in) ] = iAA index where the (i1,...,in) basis functions - * lives. - */ - TDAGMAP DAGmap; - for (int iA = 0; iA < num1; iA++) { - vector a(1); - a[0] = iA; - DAGmap[a] = iA; - } - - /* For stage 2 we now want to construct the actual recursion; the - recursion info will be stored in DAGspec, while the - coefficients go into DAGcoeffs. These arrays are initialized to - length `num2`, but they will have to grow as we add additional - artificial nodes into the graph. - - initially we treat all nodes as having children, but then in a - second stage below we reorganize. */ - int num2 = AAspec.get_dim(0); - int ndensity = jl_coeffs.get_dim(1); - nodes_pre.resize(2*num2, 2); - coeffs_pre.resize(2*num2, ndensity); - - /* the first basis function we construct will get index num1, - * since there are already num1 one-particle basis functions - * to collect during stage 1 */ - dag_idx = num1; - /* main loop over AA basis set to transform into DAG */ - for (int iAA = 0; iAA < num2; iAA++) { - // create a vector representing the current basis function - int ord = orders(iAA); - vector aa(ord); - for (int t = 0; t < ord; t++) aa[t] = AAspec(iAA, t); - vector c(ndensity); - for (int p = 0; p < ndensity; p++) c[p] = jl_coeffs(iAA, p); - insert_node(DAGmap, aa, c); - } - - /* convert to 3-stage format through reordering - * interior nodes first, then leaf nodes */ - - // allocate storage - num_nodes = dag_idx; // store total size of dag - // num_nodes - num1 = number of many-body nodes. - nodes.resize(num_nodes - num1, 2); - coeffs.resize(num_nodes - num1, ndensity); - - // find out which nodes have children - haschild.resize(num_nodes - num1); - haschild.fill(false); - for (int iAA = 0; iAA < num_nodes - num1; iAA++) { - if (nodes_pre(iAA, 0) >= num1) - haschild(nodes_pre(iAA, 0)-num1) = true; - if (nodes_pre(iAA, 1) >= num1) - haschild(nodes_pre(iAA, 1)-num1) = true; - } - - // to reorder the graph we need a fresh map from preordered indices to - // postordered indices; for the 1-particle basis the order remains the same. - // TODO: doesn't need to be a map, could be a vector. - map neworder; - for (int iA = 0; iA < num1; iA++) - neworder[iA] = iA; - - // insert all interior nodes - num2_int = 0; - num2_leaf = 0; - dag_idx = num1; - int i1, i2, i1pre, i2pre; - for (int iAA = 0; iAA < num_nodes - num1; iAA++) { - if (haschild(iAA)) { - num2_int += 1; - // indices into AAbuf before reordering - i1pre = nodes_pre(iAA, 0); - i2pre = nodes_pre(iAA, 1); - // indices into AAbuf after reordering - i1 = neworder[i1pre]; - i2 = neworder[i2pre]; - // insert the current node : iAA is old order, dag_idx is new order - neworder[num1+iAA] = dag_idx; - nodes(dag_idx-num1, 0) = i1; - nodes(dag_idx-num1, 1) = i2; - for (int t = 0; t < ndensity; t++) - coeffs(dag_idx-num1, t) = coeffs_pre(iAA, t); - dag_idx++; - } - } - - // insert all leaf nodes - for (int iAA = 0; iAA < num_nodes - num1; iAA++) { - if (!haschild(iAA)) { - num2_leaf += 1; - // indices into AAbuf before reordering - i1pre = nodes_pre(iAA, 0); - i2pre = nodes_pre(iAA, 1); - // insert the current node : no need to remember the new order now - nodes(dag_idx-num1, 0) = neworder[i1pre]; - nodes(dag_idx-num1, 1) = neworder[i2pre]; - for (int t = 0; t < ndensity; t++) - coeffs(dag_idx-num1, t) = coeffs_pre(iAA, t); - dag_idx++; - } - } -#ifdef DEBUG - cout << "num2_int = " << num2_int << "; num2_leaf = " << num2_leaf << "\n"; -#endif - // free up memory that is no longer needed - nodes_pre.resize(0, 0); - coeffs_pre.resize(0, 0); - haschild.resize(0); - - /* finalize dag: allocate buffer storage */ - AAbuf.resize(num1 + num2_int); - w.resize(num_nodes); - // TODO: technically only need num1 + num2_int for w, this can save one - // memory access later, probably not worth the crazy code duplication. -} - -void ACEDAG::insert_node(TDAGMAP &DAGmap, vector a, vector c) { - /* start with a list of all possible partitions into 2 groups - * and check whether any of these nodes are already in the dag */ - auto partitions = find_2partitions(a); - int ndensity = c.size(); - int num1 = get_num1(); - - // TODO: first try to find partitions into nodes that are already parents - // that way we will get more leaf nodes! - for (TPARTITION const& p : partitions) { - /* this is the good case; the parent nodes are both already in the - * graph; add the new node and return. This is also the only place in the - * code where an actual insert happens. */ - if (DAGmap.count(p.first) && DAGmap.count(p.second)) { - if (nodes_pre.get_dim(0) < dag_idx + 1) { //check if array is sufficiently large - int newsize = (dag_idx * 3) / 2; - nodes_pre.resize(newsize, 2); // grow arrays if necessary - coeffs_pre.resize(newsize, ndensity); - } - int i1 = DAGmap[p.first]; - int i2 = DAGmap[p.second]; - nodes_pre(dag_idx - num1, 0) = i1; - nodes_pre(dag_idx - num1, 1) = i2; - DAGmap[a] = dag_idx; - for (int p = 0; p < ndensity; p++) - coeffs_pre(dag_idx - num1, p) = c[p]; - dag_idx += 1; - return; - } - } - - /* if we are here, then this means, the new node cannot yet be inserted. - * We first need to insert some intermediate auxiliary nodes. For this - * we use a simple heuristic: - * try to find a partition where one of the two nodes are already - * in the graph, if there are several, then we remember the longest - * (this is a very greedy heuristic!!) - * .... (continue below) .... - */ - TPARTITION longest; - int longest_length = 0; - for (auto const& p : partitions) { - int len = 0; - if (DAGmap.count(p.first)) { - len = p.first.size(); - } else if (DAGmap.count(p.second)) { - len = p.second.size(); - } - if ((len > 0) && (len > longest_length)) { - longest_length = len; - longest = p; - } - } - - /* sanity check */ - if (longest_length == 0) { - std::stringstream error_message; - error_message << "WARNING : something has gone horribly wrong! `longest_length == 0`! \n"; - error_message << "a = ["; - for (int t = 0; t < a.size(); t++) - error_message << a[t] << ", "; - error_message << "]\n"; - throw std::logic_error(error_message.str()); -// return; - } - - /* If there is a partition with one component already in the graph, - * then we only need to add in the other component. Note that there will - * always be at least one such partition, namely all those containing - * a one-element node e.g. (1,2,3,4) -> (1,) (2,3,4) then (1,) is - * a one-particle basis function and hence always in the graph. - * If heuristic == 0, then we just take one of those partitionas and move on. - * - * We also accept the found partition if longest_length > 1. - * And we also accept it if we have a 2- or 3-correlation. - */ - - if ( (heuristic == 0) - || (longest_length > 1) - || (a.size() <= 3)) { - /* insert the other node that isn't in the DAG yet - * this is an artificial node so it gets zero-coefficients - * This step is recursive, so more than one node might be inserted here */ - vector cz(ndensity); - for (int i = 0; i < ndensity; i++) cz[i] = 0.0; - TPARTITION p = longest; - if (DAGmap.count(p.first)) - insert_node(DAGmap, p.second, cz); - else - insert_node(DAGmap, p.first, cz); - } - - /* Second heuristic : heuristic == 1 - * Focus on inserting artificial 2-correlations - */ - else if (heuristic == 1) { - // and we also know that longest_length == 1 and nu = a.size >= 4. - int nu = a.size(); - // generate an artificial partition - vector a1(2); - for (int i = 0; i < 2; i++) a1[i] = a[i]; - vector a2(nu - 2); - for (int i = 0; i < nu - 2; i++) a2[i] = a[2 + i]; - vector cz(ndensity); - for (int i = 0; i < cz.size(); i++) cz[i] = 0.0; - // and insert both (we know neither are in the DAG yet) - insert_node(DAGmap, a1, cz); - insert_node(DAGmap, a2, cz); - } else { - cout << "WARNING : something has gone horribly wrong! \n"; - // TODO: Throw and error here?!? - return; - } - - - - /* now we should be ready to insert the entire tuple `a` since there is now - * an eligible parent pair. Here we recompute the partition of `a`, but - * that's a small price to pay for a clearer code. Maybe this can be - * optimized a bit by wrapping it all into a while loop or having a second - * version of `insert_node` ... */ - insert_node(DAGmap, a, c); -} - -TPARTITIONS ACEDAG::find_2partitions(vector v) { - int N = v.size(); - int zo; - TPARTITIONS partitions; - TPARTITION part; - /* This is a fun little hack to extract all subsets of the indices 1:N - * the number i will have binary representation with each digit indicating - * whether or not that index belongs to the selected subset */ - for (int i = 1; i < (1< v1(N1); - vector v2(N2); - int i1 =0, i2 = 0; - p = 1; - for (int n = 0; n < N; n++) { - zo = ((i / p) % 2); - p *= 2; - if (zo == 1) { - v1[i1] = v[n]; - i1 += 1; - } else { - v2[i2] = v[n]; - i2 += 1; - } - } - part = make_pair(v1, v2); - partitions.push_back(part); - } - return partitions; -} - -void ACEDAG::print() { - cout << "DAG Specification: \n" ; - cout << " n1 : " << get_num1() << "\n"; - cout << " n2 : " << get_num2() << "\n"; - cout << " num_nodes : " << num_nodes << "\n"; - cout << "--------------------\n"; - cout << "A-spec: \n"; - for (int iA = 0; iA < get_num1(); iA++) { - cout << iA << " : " << Aspec(iA, 0) << - Aspec(iA, 1) << Aspec(iA, 2) << Aspec(iA, 3) << "\n"; - } - - cout << "-----------\n"; - cout << "AA-tree\n"; - - for (int iAA = 0; iAA < get_num2(); iAA++) { - cout << iAA + get_num1() << " : " << - nodes(iAA, 0) << ", " << nodes(iAA, 1) << "\n"; - } -} - - -/* ------------------------------------------------------------ - * ACERecursiveEvaluator - * ------------------------------------------------------------ */ - - -void ACERecursiveEvaluator::set_basis(ACECTildeBasisSet &bas, int heuristic) { - basis_set = &bas; - init(basis_set, heuristic); -} - -void ACERecursiveEvaluator::init(ACECTildeBasisSet *basis_set, int heuristic) { - - ACEEvaluator::init(basis_set); - - - weights.init(basis_set->nelements, basis_set->nradmax + 1, basis_set->lmax + 1, - "weights"); - - weights_rank1.init(basis_set->nelements, basis_set->nradbase, "weights_rank1"); - - - DG_cache.init(1, basis_set->nradbase, "DG_cache"); - DG_cache.fill(0); - - R_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "R_cache"); - R_cache.fill(0); - - DR_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "DR_cache"); - DR_cache.fill(0); - - Y_cache.init(1, basis_set->lmax + 1, "Y_cache"); - Y_cache.fill({0, 0}); - - DY_cache.init(1, basis_set->lmax + 1, "dY_dense_cache"); - DY_cache.fill({0.}); - - //hard-core repulsion - DCR_cache.init(1, "DCR_cache"); - DCR_cache.fill(0); - dB_flatten.init(basis_set->max_dB_array_size, "dB_flatten"); - - /* convert to ACE.jl format to prepare for construction of DAG - * This will fill the arrays jl_Aspec, jl_AAspec, jl_orders - */ - acejlformat(); - - // test_acejlformat(); - - // now pass this info into the DAG - dag.init(jl_Aspec, jl_AAspec, jl_orders, jl_coeffs, heuristic); - - // finally empty the temporary arrays to clear up the memory... - // TODO -} - - -void ACERecursiveEvaluator::acejlformat() { - - int func_ms_ind = 0; - int func_ms_t_ind = 0;// index for dB - int j, jj, func_ind, ms_ind; - - SPECIES_TYPE mu_i = 0;//TODO: multispecies - const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; - ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; - - int AAidx = 0; - RANK_TYPE order, t; - SPECIES_TYPE *mus; - NS_TYPE *ns; - LS_TYPE *ls; - MS_TYPE *ms; - - /* transform basis into new format: - [A1 ... A_num1] - [(i1,i2)(i1,i2)(...)(i1,i2,i3)(...)] - where each ia represents an A_{ia} - */ - - /* compute max values for mu, n, l, m */ - SPECIES_TYPE maxmu = 0; //TODO: multispecies - NS_TYPE maxn = basis_set->nradmax; - LS_TYPE maxl = basis_set->lmax; - RANK_TYPE maxorder = basis_set->rankmax; - const DENSITY_TYPE ndensity = basis_set->ndensitymax; - - int num1 = 0; - - - /* create a 4D lookup table for the 1-p basis - * TODO: replace with a map?? - */ - Array4D A_lookup(int(maxmu+1), int(maxn), int(maxl+1), int(2*maxl+1)); - for (int mu = 0; mu < maxmu+1; mu++) - for (int n = 0; n < maxn; n++) - for (int l = 0; l < maxl+1; l++) - for (int m = 0; m < 2*maxl+1; m++) - A_lookup(mu, n, l, m) = -1; - int A_idx = 0; // linear index of A basis function (1-particle) - for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { - ACECTildeBasisFunction *func = &basis[func_ind]; -// func->print(); - order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; - for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { - ms = &func->ms_combs[ms_ind * order]; - for (t = 0; t < order; t++) { - int iA = A_lookup(mus[t], ns[t]-1, ls[t], ms[t]+ls[t]); - if (iA == -1) { - A_lookup(mus[t], ns[t] - 1, ls[t], ms[t] + ls[t]) = A_idx; - A_idx += 1; - } - } - } - } - - /* create the reverse list: linear indixes to mu,l,m,n - this keeps only the basis functions we really need */ - num1 = A_idx; - Array2D & Aspec = jl_Aspec; - Aspec.resize(num1, 4); - // Array2D Aspec(num1, 4); - for (int mu = 0; mu <= maxmu; mu++) - for (int n = 1; n <= maxn; n++) - for (int l = 0; l <= maxl; l++) - for (int m = -l; m <= l; m++) { - int iA = A_lookup(mu, n-1, l, l+m); - if (iA != -1) { - Aspec(iA, 0) = mu; - Aspec(iA, 1) = n; - Aspec(iA, 2) = l; - Aspec(iA, 3) = m; - } - } - - /* ============ HALF-BASIS TRICK START ============ */ - for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { - ACECTildeBasisFunction *func = &basis[func_ind]; - order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; - if (!( (mus[0] <= maxmu) && (ns[0] <= maxn) && (ls[0] <= maxl) )) - continue; - - for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { - ms = &func->ms_combs[ms_ind * order]; - - // find first positive and negative index - int pos_idx = order + 1; - int neg_idx = order + 1; - for (t = order-1; t >= 0; t--) - if (ms[t] > 0) pos_idx = t; - else if (ms[t] < 0) neg_idx = t; - - // if neg_idx < pos_idx then this means that ms is non-zero - // and that the first non-zero index is negative, hence this is - // a negative-sign tuple which we want to combine into - // its opposite. - if (neg_idx < pos_idx) { - // find the opposite tuple - int ms_ind2 = 0; - MS_TYPE *ms2; - bool found_opposite = false; - for (ms_ind2 = 0; ms_ind2 < func->num_ms_combs; ++ms_ind2) { - ms2 = &func->ms_combs[ms_ind2 * order]; - bool isopposite = true; - for (t = 0; t < order; t++) - if (ms[t] != -ms2[t]) { - isopposite = false; - break; - } - if (isopposite) { - found_opposite = true; - break; - } - } - - if (ms_ind == ms_ind2) { - cout << "WARNING - ms_ind == ms_ind2 \n"; - } - - // now we need to overwrite the coefficients - if (found_opposite) { - int sig = 1; - for (t = 0; t < order; t++) - if (ms[t] < 0) - sig *= -1; - for (int p = 0; p < ndensity; ++p) { - func->ctildes[ms_ind2 * ndensity + p] += - func->ctildes[ms_ind * ndensity + p]; - func->ctildes[ms_ind * ndensity + p] = 0.0; - } - } - } - } - } - - // /* ============ HALF-BASIS TRICK END ============ */ - - - /* count number of basis functions, keep only non-zero!! */ - int num2 = 0; - for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { - ACECTildeBasisFunction *func = &basis[func_ind]; - for (ms_ind = 0; ms_ind < (&basis[func_ind])->num_ms_combs; ++ms_ind, ++func_ms_ind) { - // check that the coefficients are actually non-zero - bool isnonzero = false; - for (DENSITY_TYPE p = 0; p < ndensity; ++p) - if (func->ctildes[ms_ind * ndensity + p] != 0.0) - isnonzero = true; - if (isnonzero) - num2++; - } - } - - - /* Now create the AA basis links into the A basis */ - num1 = A_idx; // total number of A-basis functions that we keep - // Array1D AAorders(num2); - Array1D & AAorders = jl_orders; - AAorders.resize(num2); - // Array2D AAspec(num2, maxorder); // specs of AA basis functions - Array2D & AAspec = jl_AAspec; - AAspec.resize(num2, maxorder); - jl_coeffs.resize(num2, ndensity); - AAidx = 0; // linear index into AA basis function - int len_flat = 0; - for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { - ACECTildeBasisFunction *func = &basis[func_ind]; - order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; - if (!((mus[0] <= maxmu) && (ns[0] <= maxn) && (ls[0] <= maxl))) //fool-proofing of functions - continue; - - for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { - ms = &func->ms_combs[ms_ind * order]; - - // check that the coefficients are actually non-zero - bool iszero = true; - for (DENSITY_TYPE p = 0; p < ndensity; ++p) - if (func->ctildes[ms_ind * ndensity + p] != 0.0) - iszero = false; - if (iszero) continue; - - AAorders(AAidx) = order; - for (t = 0; t < order; t++) { - int Ait = A_lookup(int(mus[t]), int(ns[t]-1), int(ls[t]), int(ms[t])+int(ls[t])); - AAspec(AAidx, t) = Ait; - len_flat += 1; - } - for (t = order; t < maxorder; t++) AAspec(AAidx, t) = -1; - /* copy over the coefficients */ - for (DENSITY_TYPE p = 0; p < ndensity; ++p) - jl_coeffs(AAidx, p) = func->ctildes[ms_ind * ndensity + p]; - AAidx += 1; - } - } - - // flatten the AAspec array - jl_AAspec_flat.resize(len_flat); - int idx_spec = 0; - for (int AAidx = 0; AAidx < jl_AAspec.get_dim(0); AAidx++) - for (int p = 0; p < jl_orders(AAidx); p++, idx_spec++) - jl_AAspec_flat(idx_spec) = jl_AAspec(AAidx, p); - -} - -void ACERecursiveEvaluator::test_acejlformat() { - - Array2D AAspec = jl_AAspec; - Array2D Aspec = jl_Aspec; - Array1D AAorders = jl_orders; - cout << "num2 = " << AAorders.get_dim(0) << "\n"; - int func_ms_ind = 0; - int func_ms_t_ind = 0;// index for dB - int j, jj, func_ind, ms_ind; - - SPECIES_TYPE mu_i = 0; - const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; - ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; - - RANK_TYPE order, t; - SPECIES_TYPE *mus; - NS_TYPE *ns; - LS_TYPE *ls; - MS_TYPE *ms; - - /* ==== test by printing the basis spec ====*/ - // TODO: convert this into an automatic consistency test - int iAA = 0; - for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { - ACECTildeBasisFunction *func = &basis[func_ind]; - order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; - // func->print(); - //loop over {ms} combinations in sum - for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { - ms = &func->ms_combs[ms_ind * order]; - - - cout << iAA << " : |"; - for (t = 0; t < order; t++) - cout << mus[t] << ";" << ns[t] << "," << ls[t] << "," << ms[t] << "|"; - cout << "\n"; - - cout << " ["; - for (t = 0; t < AAorders(iAA); t++) - cout << AAspec(iAA, int(t)) << ","; - cout << "]\n"; - cout << " |"; - for (t = 0; t < AAorders(iAA); t++) { - int iA = AAspec(iAA, t); - // cout << iA << ","; - cout << Aspec(iA, 0) << ";" - << Aspec(iA, 1) << "," - << Aspec(iA, 2) << "," - << Aspec(iA, 3) << "|"; - } - cout << "\n"; - iAA += 1; - } - } - /* ==== END TEST ==== */ - - -} - - - - -void ACERecursiveEvaluator::resize_neighbours_cache(int max_jnum) { - if(basis_set== nullptr) { - throw std::invalid_argument("ACERecursiveEvaluator: basis set is not assigned"); - } - if (R_cache.get_dim(0) < max_jnum) { - - //TODO: implement grow - R_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); - R_cache.fill(0); - - DR_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); - DR_cache.fill(0); - - DG_cache.resize(max_jnum, basis_set->nradbase); - DG_cache.fill(0); - - Y_cache.resize(max_jnum, basis_set->lmax + 1); - Y_cache.fill({0, 0}); - - DY_cache.resize(max_jnum, basis_set->lmax + 1); - DY_cache.fill({0}); - - //hard-core repulsion - DCR_cache.init(max_jnum, "DCR_cache"); - DCR_cache.fill(0); - } -} - - - -// double** r - atomic coordinates of atom I -// int* types - atomic types if atom I -// int **firstneigh - ptr to 1st J int value of each I atom. Usage: jlist = firstneigh[i]; -// Usage: j = jlist_of_i[jj]; -// jnum - number of J neighbors for each I atom. jnum = numneigh[i]; - -void -ACERecursiveEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) { - if(basis_set== nullptr) { - throw std::invalid_argument("ACERecursiveEvaluator: basis set is not assigned"); - } - per_atom_calc_timer.start(); -#ifdef PRINT_MAIN_STEPS - printf("\n ATOM: ind = %d r_norm=(%f, %f, %f)\n",i, x[i][0], x[i][1], x[i][2]); -#endif - DOUBLE_TYPE evdwl = 0, evdwl_cut = 0, rho_core = 0; - DOUBLE_TYPE r_norm; - DOUBLE_TYPE xn, yn, zn, r_xyz; - DOUBLE_TYPE R, GR, DGR, R_over_r, DR, DCR; - DOUBLE_TYPE *r_hat; - - SPECIES_TYPE mu_j; - RANK_TYPE r, rank, t; - NS_TYPE n; - LS_TYPE l; - MS_TYPE m, m_t; - - SPECIES_TYPE *mus; - NS_TYPE *ns; - LS_TYPE *ls; - MS_TYPE *ms; - - int j, jj, func_ind, ms_ind; - SHORT_INT_TYPE factor; - - ACEComplex Y{0}, Y_DR{0.}; - ACEComplex B{0.}; - ACEComplex dB{0}; - ACEComplex A_cache[basis_set->rankmax]; - - ACEComplex dA[basis_set->rankmax]; - int spec[basis_set->rankmax]; - - dB_flatten.fill({0.}); - - ACEDYcomponent grad_phi_nlm{0}, DY{0.}; - - //size is +1 of max to avoid out-of-boundary array access in double-triangular scheme - ACEComplex A_forward_prod[basis_set->rankmax + 1]; - ACEComplex A_backward_prod[basis_set->rankmax + 1]; - - DOUBLE_TYPE inv_r_norm; - DOUBLE_TYPE r_norms[jnum]; - DOUBLE_TYPE inv_r_norms[jnum]; - DOUBLE_TYPE rhats[jnum][3];//normalized vector - SPECIES_TYPE elements[jnum]; - const DOUBLE_TYPE xtmp = x[i][0]; - const DOUBLE_TYPE ytmp = x[i][1]; - const DOUBLE_TYPE ztmp = x[i][2]; - DOUBLE_TYPE f_ji[3]; - - bool is_element_mapping = element_type_mapping.get_size() > 0; - SPECIES_TYPE mu_i; - if (is_element_mapping) - mu_i = element_type_mapping(type[i]); - else - mu_i = type[i]; - - const SHORT_INT_TYPE total_basis_size_rank1 = basis_set->total_basis_size_rank1[mu_i]; - const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; - - ACECTildeBasisFunction *basis_rank1 = basis_set->basis_rank1[mu_i]; - ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; - - DOUBLE_TYPE rho_cut, drho_cut, fcut, dfcut; - DOUBLE_TYPE dF_drho_core; - - //TODO: lmax -> lmaxi (get per-species type) - const LS_TYPE lmaxi = basis_set->lmax; - - //TODO: nradmax -> nradiali (get per-species type) - const NS_TYPE nradiali = basis_set->nradmax; - - //TODO: nradbase -> nradbasei (get per-species type) - const NS_TYPE nradbasei = basis_set->nradbase; - - //TODO: get per-species type number of densities - const DENSITY_TYPE ndensity= basis_set->ndensitymax; - - neighbours_forces.resize(jnum, 3); - neighbours_forces.fill(0); - - //TODO: shift nullifications to place where arrays are used - weights.fill({0}); - weights_rank1.fill(0); - A.fill({0}); - A_rank1.fill(0); - rhos.fill(0); - dF_drho.fill(0); - -#ifdef EXTRA_C_PROJECTIONS - basis_projections_rank1.init(total_basis_size_rank1, ndensity, "c_projections_rank1"); - basis_projections.init(total_basis_size, ndensity, "c_projections"); -#endif - - //proxy references to spherical harmonics and radial functions arrays - const Array2DLM &ylm = basis_set->spherical_harmonics.ylm; - const Array2DLM &dylm = basis_set->spherical_harmonics.dylm; - - const Array2D &fr = basis_set->radial_functions->fr; - const Array2D &dfr = basis_set->radial_functions->dfr; - - const Array1D &gr = basis_set->radial_functions->gr; - const Array1D &dgr = basis_set->radial_functions->dgr; - - loop_over_neighbour_timer.start(); - - int jj_actual = 0; - SPECIES_TYPE type_j = 0; - int neighbour_index_mapping[jnum]; // jj_actual -> jj - //loop over neighbours, compute distance, consider only atoms within with rradial_functions->cut(mu_i, mu_j); - r_xyz = sqrt(xn * xn + yn * yn + zn * zn); - - if (r_xyz >= current_cutoff) - continue; - - inv_r_norm = 1 / r_xyz; - - r_norms[jj_actual] = r_xyz; - inv_r_norms[jj_actual] = inv_r_norm; - rhats[jj_actual][0] = xn * inv_r_norm; - rhats[jj_actual][1] = yn * inv_r_norm; - rhats[jj_actual][2] = zn * inv_r_norm; - elements[jj_actual] = mu_j; - neighbour_index_mapping[jj_actual] = jj; - jj_actual++; - } - - int jnum_actual = jj_actual; - - //ALGORITHM 1: Atomic base A - for (jj = 0; jj < jnum_actual; ++jj) { - r_norm = r_norms[jj]; - mu_j = elements[jj]; - r_hat = rhats[jj]; - - //proxies - Array2DLM &Y_jj = Y_cache(jj); - Array2DLM &DY_jj = DY_cache(jj); - - - basis_set->radial_functions->evaluate(r_norm, basis_set->nradbase, nradiali, mu_i, mu_j); - basis_set->spherical_harmonics.compute_ylm(r_hat[0], r_hat[1], r_hat[2], lmaxi); - //loop for computing A's - //rank = 1 - for (n = 0; n < basis_set->nradbase; n++) { - GR = gr(n); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("-neigh atom %d\n", jj); - printf("gr(n=%d)(r=%f) = %f\n", n, r_norm, gr(n)); - printf("dgr(n=%d)(r=%f) = %f\n", n, r_norm, dgr(n)); -#endif - DG_cache(jj, n) = dgr(n); - A_rank1(mu_j, n) += GR * Y00; - } - //loop for computing A's - // for rank > 1 - for (n = 0; n < nradiali; n++) { - auto &A_lm = A(mu_j, n); - for (l = 0; l <= lmaxi; l++) { - R = fr(n, l); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("R(nl=%d,%d)(r=%f)=%f\n", n + 1, l, r_norm, R); -#endif - - DR_cache(jj, n, l) = dfr(n, l); - R_cache(jj, n, l) = R; - - for (m = 0; m <= l; m++) { - Y = ylm(l, m); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("Y(lm=%d,%d)=(%f, %f)\n", l, m, Y.real, Y.img); -#endif - A_lm(l, m) += R * Y; //accumulation sum over neighbours - Y_jj(l, m) = Y; - DY_jj(l, m) = dylm(l, m); - } - } - } - - //hard-core repulsion - rho_core += basis_set->radial_functions->cr; - DCR_cache(jj) = basis_set->radial_functions->dcr; - - } //end loop over neighbours - - //complex conjugate A's (for NEGATIVE (-m) terms) - // for rank > 1 - for (mu_j = 0; mu_j < basis_set->nelements; mu_j++) { - for (n = 0; n < nradiali; n++) { - auto &A_lm = A(mu_j, n); - for (l = 0; l <= lmaxi; l++) { - //fill in -m part in the outer loop using the same m <-> -m symmetry as for Ylm - for (m = 1; m <= l; m++) { - factor = m % 2 == 0 ? 1 : -1; - A_lm(l, -m) = A_lm(l, m).conjugated() * factor; - } - } - } - } //now A's are constructed - loop_over_neighbour_timer.stop(); - - // ==================== ENERGY ==================== - - energy_calc_timer.start(); -#ifdef EXTRA_C_PROJECTIONS - basis_projections_rank1.fill(0); - basis_projections.fill(0); -#endif - - //ALGORITHM 2: Basis functions B with iterative product and density rho(p) calculation - //rank=1 - for (int func_rank1_ind = 0; func_rank1_ind < total_basis_size_rank1; ++func_rank1_ind) { - ACECTildeBasisFunction *func = &basis_rank1[func_rank1_ind]; -// ndensity = func->ndensity; -#ifdef PRINT_LOOPS_INDICES - printf("Num density = %d r = 0\n",(int) ndensity ); - print_C_tilde_B_basis_function(*func); -#endif - double A_cur = A_rank1(func->mus[0], func->ns[0] - 1); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("A_r=1(x=%d, n=%d)=(%f)\n", func->mus[0], func->ns[0], A_cur); - printf(" coeff[0] = %f\n", func->ctildes[0]); -#endif - for (DENSITY_TYPE p = 0; p < ndensity; ++p) { - //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 - rhos(p) += func->ctildes[p] * A_cur; -#ifdef EXTRA_C_PROJECTIONS - //aggregate C-projections separately - basis_projections_rank1(func_rank1_ind, p)+= func->ctildes[p] * A_cur; -#endif - } - } // end loop for rank=1 - - // ================ START RECURSIVE EVALUATOR ==================== - // (rank > 1 only) - - /* STAGE 1: - * 1-particle basis is already evaluated, so we only need to - * copy it into the AA value buffer - */ - int num1 = dag.get_num1(); - for (int idx = 0; idx < num1; idx++) - dag.AAbuf(idx) = A( dag.Aspec(idx, 0), - dag.Aspec(idx, 1)-1, - dag.Aspec(idx, 2), - dag.Aspec(idx, 3) ); - - - if (recursive) { - /* STAGE 2: FORWARD PASS - * Forward pass: go through the dag and store all intermediate results - */ - - // rhos.fill(0); note the rhos are already reset and started filling above! - ACEComplex AAcur{0.0}; - int i1, i2; - - int * dag_nodes = dag.nodes.get_data(); - int idx_nodes = 0; - - DOUBLE_TYPE * dag_coefs = dag.coeffs.get_data(); - int idx_coefs = 0; - - int num2_int = dag.get_num2_int(); - int num2_leaf = dag.get_num2_leaf(); - - // interior nodes (save AA) - for (int idx = num1; idx < num1+num2_int; idx++) { - i1 = dag_nodes[idx_nodes]; idx_nodes++; - i2 = dag_nodes[idx_nodes]; idx_nodes++; - AAcur = dag.AAbuf(i1) * dag.AAbuf(i2); - dag.AAbuf(idx) = AAcur; - for (int p = 0; p < ndensity; p++, idx_coefs++) - rhos(p) += AAcur.real_part_product(dag_coefs[idx_coefs]); - } - - // leaf nodes -> no need to store in AAbuf - DOUBLE_TYPE AAcur_re = 0.0; - for (int _idx = 0; _idx < num2_leaf; _idx++) { - i1 = dag_nodes[idx_nodes]; idx_nodes++; - i2 = dag_nodes[idx_nodes]; idx_nodes++; - AAcur_re = dag.AAbuf(i1).real_part_product(dag.AAbuf(i2)); - for (int p = 0; p < ndensity; p++, idx_coefs++) - rhos(p) += AAcur_re * dag_coefs[idx_coefs]; - } - - } else { - - /* non-recursive Julia-style evaluator implementation */ - // TODO: fix array access to enable bounds checking again??? - ACEComplex AAcur{1.0}; - int *AAspec = jl_AAspec_flat.get_data(); - DOUBLE_TYPE *coeffs = jl_coeffs.get_data(); - int idx_spec = 0; - int idx_coefs = 0; - int order = 0; - int max_order = jl_AAspec.get_dim(1); - for (int iAA = 0; iAA < jl_AAspec.get_dim(0); iAA ++) { - AAcur = 1.0; - order = jl_orders(iAA); - for (int r = 0; r < order; r++, idx_spec++) - AAcur *= dag.AAbuf( AAspec[idx_spec] ); - for (int p = 0; p < ndensity; p++, idx_coefs++) - rhos(p) += AAcur.real_part_product(coeffs[idx_coefs]); - } - } - - /* we now have rho and can evaluate lots of things. - -------- this is back to the original PACE code --------- */ - -#ifdef DEBUG_FORCES_CALCULATIONS - printf("rhos = "); - for(DENSITY_TYPE p =0; prho_core_cutoffs(mu_i); - drho_cut = basis_set->drho_core_cutoffs(mu_i); - - basis_set->inner_cutoff(rho_core, rho_cut, drho_cut, fcut, dfcut); - basis_set->FS_values_and_derivatives(rhos, evdwl, dF_drho, ndensity); - - dF_drho_core = evdwl * dfcut + 1; - for (DENSITY_TYPE p = 0; p < ndensity; ++p) - dF_drho(p) *= fcut; - evdwl_cut = evdwl * fcut + rho_core; - - // E0 shift - evdwl_cut += basis_set->E0vals(mu_i); - - /* I've moved this from below the weight calculation - since I believe it only times the energy? the weights - are only needed for the forces? - But I believe we could add a third timer for computing just - the weights; this will allow us to check better where the - bottleneck is. - */ - energy_calc_timer.stop(); - - forces_calc_loop_timer.start(); - - -#ifdef DEBUG_FORCES_CALCULATIONS - printf("dFrhos = "); - for(DENSITY_TYPE p =0; pndensity; - for (DENSITY_TYPE p = 0; p < ndensity; ++p) { - //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 - weights_rank1(func->mus[0], func->ns[0] - 1) += dF_drho(p) * func->ctildes[p]; - } - } - - /* --------- we now continue with the recursive code --------- */ - - if (recursive) { - /* STAGE 2: BACKWARD PASS */ - int i1, i2; - ACEComplex AA1{0.0}; - ACEComplex AA2{0.0}; - ACEComplex wcur{0.0}; - int num2_int = dag.get_num2_int(); - int num2_leaf = dag.get_num2_leaf(); - /* to prepare for the backward we first need to zero the weights */ - dag.w.fill({0.0}); - - int * dag_nodes = dag.nodes.get_data(); - int idx_nodes = 2 * (num2_int + num2_leaf) - 1; - - DOUBLE_TYPE * dag_coefs = dag.coeffs.get_data(); - int idx_coefs = ndensity * (num2_int + num2_leaf) - 1; - - for (int idx = num1+num2_int+num2_leaf - 1; idx >= num1; idx--) { - i2 = dag_nodes[idx_nodes]; idx_nodes--; - i1 = dag_nodes[idx_nodes]; idx_nodes--; - AA1 = dag.AAbuf(i1); - AA2 = dag.AAbuf(i2); - wcur = dag.w(idx); // [***] - for (int p = ndensity-1; p >= 0; p--, idx_coefs--) - wcur += dF_drho(p) * dag_coefs[idx_coefs]; - dag.w(i1) += wcur * AA2; // TODO: replace with explicit muladd? - dag.w(i2) += wcur * AA1; - } - - /* [***] - * Note that these weights don't really need to be stored for the - * leaf nodes. We tested splitting this for loop into two where - * for the leaf nodes the weight would just be initialized to 0.0 - * instead of reading from an array. The improvement was barely - * measurable, ca 3%, so we reverted to this simpler algorithm - */ - - - } else { - - // non-recursive ACE.jl style implemenation of gradients, but with - // a backward differentiation approach to the prod-A - // (cf. Algorithm 3 in the manuscript) - - dag.w.fill({0.0}); - ACEComplex AAf{1.0}, AAb{1.0}, theta{0.0}; - - int *AAspec = jl_AAspec_flat.get_data(); - DOUBLE_TYPE *coeffs = jl_coeffs.get_data(); - int idx_spec = 0; - int idx_coefs = 0; - int order = 0; - int max_order = jl_AAspec.get_dim(1); - for (int iAA = 0; iAA < jl_AAspec.get_dim(0); iAA ++ ) { - order = jl_orders(iAA); - theta = 0.0; - for (int p = 0; p < ndensity; p++, idx_coefs++) - theta += dF_drho(p) * coeffs[idx_coefs]; - dA[0] = 1.0; - AAf = 1.0; - for (int t = 0; t < order-1; t++, idx_spec++) { - spec[t] = AAspec[idx_spec]; - A_cache[t] = dag.AAbuf(spec[t]); - AAf *= A_cache[t]; - dA[t+1] = AAf; - } - spec[order-1] = AAspec[idx_spec]; idx_spec++; - A_cache[order-1] = dag.AAbuf(spec[order-1]); - AAb = 1.0; - for (int t = order-1; t >= 1; t--) { - AAb *= A_cache[t]; - dA[t-1] *= AAb; - dag.w(spec[t]) += theta * dA[t]; - } - dag.w(spec[0]) += theta * dA[0]; - } - - } - - /* STAGE 3: - * get the gradients from the 1-particle basis gradients and write them - * into the dF/drho derivatives. - */ - /* In order to reuse the original PACE code, we copy the weights back - * into the the PACE datastructure. */ - - for (int idx = 0; idx < num1; idx++) { - int m = dag.Aspec(idx, 3); - if (m >= 0) { - weights(dag.Aspec(idx, 0), // mu - dag.Aspec(idx, 1) - 1, // n - dag.Aspec(idx, 2), // l - m ) += dag.w(idx); - } else { - int factor = (m % 2 == 0 ? 1 : -1); - weights(dag.Aspec(idx, 0), // mu - dag.Aspec(idx, 1) - 1, // n - dag.Aspec(idx, 2), // l - -m ) += factor * dag.w(idx).conjugated(); - } - } - - - /* ------ From here we are now back to the original PACE code ---- */ - -// ==================== FORCES ==================== -#ifdef PRINT_MAIN_STEPS - printf("\nFORCE CALCULATION\n"); - printf("loop over neighbours\n"); -#endif - -// loop over neighbour atoms for force calculations - for (jj = 0; jj < jnum_actual; ++jj) { - mu_j = elements[jj]; - r_hat = rhats[jj]; - inv_r_norm = inv_r_norms[jj]; - - Array2DLM &Y_cache_jj = Y_cache(jj); - Array2DLM &DY_cache_jj = DY_cache(jj); - -#ifdef PRINT_LOOPS_INDICES - printf("\nneighbour atom #%d\n", jj); - printf("rhat = (%f, %f, %f)\n", r_hat[0], r_hat[1], r_hat[2]); -#endif - - forces_calc_neighbour_timer.start(); - - f_ji[0] = f_ji[1] = f_ji[2] = 0; - -//for rank = 1 - for (n = 0; n < nradbasei; ++n) { - if (weights_rank1(mu_j, n) == 0) - continue; - auto &DG = DG_cache(jj, n); - DGR = DG * Y00; - DGR *= weights_rank1(mu_j, n); -#ifdef DEBUG_FORCES_CALCULATIONS - printf("r=1: (n,l,m)=(%d, 0, 0)\n",n+1); - printf("\tGR(n=%d, r=%f)=%f\n",n+1,r_norm, gr(n)); - printf("\tDGR(n=%d, r=%f)=%f\n",n+1,r_norm, dgr(n)); - printf("\tdF+=(%f, %f, %f)\n",DGR * r_hat[0], DGR * r_hat[1], DGR * r_hat[2]); -#endif - f_ji[0] += DGR * r_hat[0]; - f_ji[1] += DGR * r_hat[1]; - f_ji[2] += DGR * r_hat[2]; - } - -//for rank > 1 - for (n = 0; n < nradiali; n++) { - for (l = 0; l <= lmaxi; l++) { - R_over_r = R_cache(jj, n, l) * inv_r_norm; - DR = DR_cache(jj, n, l); - - // for m>=0 - for (m = 0; m <= l; m++) { - ACEComplex w = weights(mu_j, n, l, m); - if (w == 0) - continue; - //counting for -m cases if m>0 - // if (m > 0) w *= 2; // not needed for recursive eval - - DY = DY_cache_jj(l, m); - Y_DR = Y_cache_jj(l, m) * DR; - - grad_phi_nlm.a[0] = Y_DR * r_hat[0] + DY.a[0] * R_over_r; - grad_phi_nlm.a[1] = Y_DR * r_hat[1] + DY.a[1] * R_over_r; - grad_phi_nlm.a[2] = Y_DR * r_hat[2] + DY.a[2] * R_over_r; -#ifdef DEBUG_FORCES_CALCULATIONS - printf("d_phi(n=%d, l=%d, m=%d) = ((%f,%f), (%f,%f), (%f,%f))\n",n+1,l,m, - grad_phi_nlm.a[0].real, grad_phi_nlm.a[0].img, - grad_phi_nlm.a[1].real, grad_phi_nlm.a[1].img, - grad_phi_nlm.a[2].real, grad_phi_nlm.a[2].img); - - printf("weights(n,l,m)(%d,%d,%d) = (%f,%f)\n", n+1, l, m, w.real, w.img); - //if (m>0) w*=2; - printf("dF(n,l,m)(%d, %d, %d) += (%f, %f, %f)\n", n + 1, l, m, - w.real_part_product(grad_phi_nlm.a[0]), - w.real_part_product(grad_phi_nlm.a[1]), - w.real_part_product(grad_phi_nlm.a[2]) - ); -#endif -// real-part multiplication only - f_ji[0] += w.real_part_product(grad_phi_nlm.a[0]); - f_ji[1] += w.real_part_product(grad_phi_nlm.a[1]); - f_ji[2] += w.real_part_product(grad_phi_nlm.a[2]); - } - } - } - - -#ifdef PRINT_INTERMEDIATE_VALUES - printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, - f_ji[0], f_ji[1], f_ji[2] - ); -#endif - - //hard-core repulsion - DCR = DCR_cache(jj); -#ifdef DEBUG_FORCES_CALCULATIONS - printf("DCR = %f\n",DCR); -#endif - f_ji[0] += dF_drho_core * DCR * r_hat[0]; - f_ji[1] += dF_drho_core * DCR * r_hat[1]; - f_ji[2] += dF_drho_core * DCR * r_hat[2]; -#ifdef PRINT_INTERMEDIATE_VALUES - printf("with core-repulsion\n"); - printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, - f_ji[0], f_ji[1], f_ji[2] - ); - printf("neighbour_index_mapping[jj=%d]=%d\n",jj,neighbour_index_mapping[jj]); -#endif - - neighbours_forces(neighbour_index_mapping[jj], 0) = f_ji[0]; - neighbours_forces(neighbour_index_mapping[jj], 1) = f_ji[1]; - neighbours_forces(neighbour_index_mapping[jj], 2) = f_ji[2]; - - forces_calc_neighbour_timer.stop(); - }// end loop over neighbour atoms for forces - - forces_calc_loop_timer.stop(); - - //now, energies and forces are ready - //energies(i) = evdwl + rho_core; - e_atom = evdwl_cut; - -#ifdef PRINT_INTERMEDIATE_VALUES - printf("energies(i) = FS(...rho_p_accum...) = %f\n", evdwl); -#endif - per_atom_calc_timer.stop(); -} \ No newline at end of file diff --git a/lib/pace/ace_recursive.h b/lib/pace/ace_recursive.h deleted file mode 100644 index 78e74feb86..0000000000 --- a/lib/pace/ace_recursive.h +++ /dev/null @@ -1,247 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Christoph Ortner on 20.12.2020 - -#ifndef ACE_RECURSIVE_H -#define ACE_RECURSIVE_H - -#include "ace_abstract_basis.h" -#include "ace_arraynd.h" -#include "ace_array2dlm.h" -#include "ace_c_basis.h" -#include "ace_complex.h" -#include "ace_timing.h" -#include "ace_types.h" -#include "ace_evaluator.h" - -#include -#include -#include -#include -#include - -using namespace std; - - -typedef pair, vector > TPARTITION; -typedef list TPARTITIONS; - -typedef map, int> TDAGMAP; - -class ACEDAG { - - TPARTITIONS find_2partitions(vector v); - - void insert_node(TDAGMAP &dagmap, - vector node, - vector c); - - // the following fields are used only for *construction*, not evaluation - int dag_idx; // current index of dag node - Array2D nodes_pre; //TODO: YL: better to use vector<> - Array2D coeffs_pre; //TODO: YL: better to use vector<> - Array1D haschild; //TODO: YL: better to use vector<> - - /* which heuristic to choose for DAG construction? - * 0 : the simple original heuristic - * 1 : prioritize 2-correlation nodes and build the rest from those - */ - int heuristic = 0; - -public: - - ACEDAG() = default; - - void init(Array2D Aspec, Array2D AAspec, - Array1D orders, Array2D coeffs, - int heuristic ); - - Array1D AAbuf; - Array1D w; - - Array2D Aspec; - - // nodes in the graph - Array2D nodes; - Array2D coeffs; - - // total number of nodes in the dag - int num_nodes; - // number of interior nodes (with children) - int num2_int; - // number of leaf nodes (nc = no child) - int num2_leaf; - - - // number of 1-particle basis functions - // (these will be stored in the first num1 entries of AAbuf) - int get_num1() { return Aspec.get_dim(0); }; - // total number of n-correlation basis functions n > 1. - int get_num2() { return num_nodes - get_num1(); }; - int get_num2_int() { return num2_int; }; // with children - int get_num2_leaf() { return num2_leaf; }; // without children - - // debugging tool - void print(); -}; - - -/** - * Recursive Variant of the ACETildeEvaluator; should be 100% compatible - */ -class ACERecursiveEvaluator : public ACEEvaluator { - - /** - * Weights \f$ \omega_{i \mu n 0 0} \f$ for rank = 1, see Eq.(10) from implementation notes, - * 'i' is fixed for the current atom, shape: [nelements][nradbase] - */ - Array2D weights_rank1 = Array2D("weights_rank1"); - - /** - * Weights \f$ \omega_{i \mu n l m} \f$ for rank > 1, see Eq.(10) from implementation notes, - * 'i' is fixed for the current atom, shape: [nelements][nradbase][l=0..lmax, m] - */ - Array4DLM weights = Array4DLM("weights"); - - /** - * cache for gradients of \f$ g(r)\f$: grad_phi(jj,n)=A2DLM(l,m) - * shape:[max_jnum][nradbase] - */ - Array2D DG_cache = Array2D("DG_cache"); - - - /** - * cache for \f$ R_{nl}(r)\f$ - * shape:[max_jnum][nradbase][0..lmax] - */ - Array3D R_cache = Array3D("R_cache"); - /** - * cache for derivatives of \f$ R_{nl}(r)\f$ - * shape:[max_jnum][nradbase][0..lmax] - */ - Array3D DR_cache = Array3D("DR_cache"); - /** - * cache for \f$ Y_{lm}(\hat{r})\f$ - * shape:[max_jnum][0..lmax][m] - */ - Array3DLM Y_cache = Array3DLM("Y_cache"); - /** - * cache for \f$ \nabla Y_{lm}(\hat{r})\f$ - * shape:[max_jnum][0..lmax][m] - */ - Array3DLM DY_cache = Array3DLM("dY_dense_cache"); - - /** - * cache for derivatives of hard-core repulsion - * shape:[max_jnum] - */ - Array1D DCR_cache = Array1D("DCR_cache"); - - /** - * Partial derivatives \f$ dB_{i \mu n l m t}^{(r)} \f$ with sequential numbering over [func_ind][ms_ind][r], - * shape:[func_ms_r_ind] - */ - Array1D dB_flatten = Array1D("dB_flatten"); - - /** - * pointer to the ACEBasisSet object - */ - ACECTildeBasisSet *basis_set = nullptr; - - /** - * Initialize internal arrays according to basis set sizes - * @param basis_set - */ - void init(ACECTildeBasisSet *basis_set, int heuristic); - - /* convert the PACE to the ACE.jl format to prepare for DAG construction*/ - Array2D jl_Aspec; - Array2D jl_AAspec; - Array1D jl_AAspec_flat; - Array1D jl_orders; - Array2D jl_coeffs; - void acejlformat(); - - /* the main event : the computational graph */ - ACEDAG dag; - - bool recursive = true; - -public: - - - ACERecursiveEvaluator() = default; - - explicit ACERecursiveEvaluator(ACECTildeBasisSet &bas, - bool recursive = true) { - set_recursive(recursive); - set_basis(bas); - } - - /** - * set the basis function to the ACE evaluator - * @param bas - */ - void set_basis(ACECTildeBasisSet &bas, int heuristic = 0); - - /** - * The key method to compute energy and forces for atom 'i'. - * Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array - * - * @param i atom index - * @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3] - * @param type atomic types array of the real and ghost atoms, shape: [atom_ind] - * @param jnum number of neighbours of atom_i - * @param jlist array of neighbour indices, shape: [jnum] - */ - void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) override; - - /** - * Resize all caches over neighbours atoms - * @param max_jnum maximum number of neighbours - */ - void resize_neighbours_cache(int max_jnum) override; - - /******* public functions related to recursive evaluator ********/ - - // print out the DAG for visual inspection - void print_dag() {dag.print();} - - // print out the jl format for visual inspection - // should be converted into a proper test - void test_acejlformat(); - - void set_recursive(bool tf) { recursive = tf; } - - /********************************/ - -}; - - -#endif //ACE_RECURSIVE_H \ No newline at end of file diff --git a/lib/pace/ace_spherical_cart.cpp b/lib/pace/ace_spherical_cart.cpp deleted file mode 100644 index f1f0fccced..0000000000 --- a/lib/pace/ace_spherical_cart.cpp +++ /dev/null @@ -1,221 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Ralf Drautz, Yury Lysogorskiy - -#include - -#include "ace_spherical_cart.h" - -ACECartesianSphericalHarmonics::ACECartesianSphericalHarmonics(LS_TYPE lm) { - init(lm); -} - -void ACECartesianSphericalHarmonics::init(LS_TYPE lm) { - lmax = lm; - - alm.init(lmax, "alm"); - blm.init(lmax, "blm"); - cl.init(lmax + 1); - dl.init(lmax + 1); - - plm.init(lmax, "plm"); - dplm.init(lmax, "dplm"); - - ylm.init(lmax, "ylm"); - dylm.init(lmax, "dylm"); - - pre_compute(); -} - -/** -Destructor for ACECartesianSphericalHarmonics. - -@param None - -@returns None -*/ -ACECartesianSphericalHarmonics::~ACECartesianSphericalHarmonics() {} - - -void ACECartesianSphericalHarmonics::pre_compute() { - - DOUBLE_TYPE a, b; - DOUBLE_TYPE lsq, ld, l1, l2; - DOUBLE_TYPE msq; - - for (LS_TYPE l = 1; l <= lmax; l++) { - lsq = l * l; - ld = 2 * l; - l1 = (4 * lsq - 1); - l2 = lsq - ld + 1; - for (MS_TYPE m = 0; m < l - 1; m++) { - msq = m * m; - a = sqrt((DOUBLE_TYPE(l1)) / (DOUBLE_TYPE(lsq - msq))); - b = -sqrt((DOUBLE_TYPE(l2 - msq)) / (DOUBLE_TYPE(4 * l2 - 1))); - alm(l, m) = a; - blm(l, m) = b; - } - } - - for (LS_TYPE l = 1; l <= lmax; l++) { - cl(l) = -sqrt(1.0 + 0.5 / (DOUBLE_TYPE(l))); - dl(l) = sqrt(DOUBLE_TYPE(2 * (l - 1) + 3)); - } -} - - -void ACECartesianSphericalHarmonics::compute_barplm(DOUBLE_TYPE rz, LS_TYPE lmaxi) { - - // requires -1 <= rz <= 1 , NO CHECKING IS PERFORMED !!!!!!!!! - // prefactors include 1/sqrt(2) factor compared to reference - DOUBLE_TYPE t; - - // l=0, m=0 - //plm(0, 0) = Y00/sq1o4pi; //= sq1o4pi; - plm(0, 0) = Y00; //= 1; - dplm(0, 0) = 0.0; - - if (lmaxi > 0) { - - // l=1, m=0 - plm(1, 0) = Y00 * sq3 * rz; - dplm(1, 0) = Y00 * sq3; - - // l=1, m=1 - plm(1, 1) = -sq3o2 * Y00; - dplm(1, 1) = 0.0; - - // loop l = 2, lmax - for (LS_TYPE l = 2; l <= lmaxi; l++) { - for (MS_TYPE m = 0; m < l - 1; m++) { - plm(l, m) = alm(l, m) * (rz * plm(l - 1, m) + blm(l, m) * plm(l - 2, m)); - dplm(l, m) = alm(l, m) * (plm(l - 1, m) + rz * dplm(l - 1, m) + blm(l, m) * dplm(l - 2, m)); - } - t = dl(l) * plm(l - 1, l - 1); - plm(l, l - 1) = t * rz; - dplm(l, l - 1) = t; - plm(l, l) = cl(l) * plm(l - 1, l - 1); - dplm(l, l) = 0.0; - } - } -} //end compute_barplm - - -void ACECartesianSphericalHarmonics::compute_ylm(DOUBLE_TYPE rx, DOUBLE_TYPE ry, DOUBLE_TYPE rz, LS_TYPE lmaxi) { - - // requires rx^2 + ry^2 + rz^2 = 1 , NO CHECKING IS PERFORMED !!!!!!!!! - - DOUBLE_TYPE real; - DOUBLE_TYPE img; - MS_TYPE m; - ACEComplex phase; - ACEComplex phasem, mphasem1; - ACEComplex dyx, dyy, dyz; - ACEComplex rdy; - - phase.real = rx; - phase.img = ry; - //compute barplm - compute_barplm(rz, lmaxi); - - //m = 0 - m = 0; - for (LS_TYPE l = 0; l <= lmaxi; l++) { - - ylm(l, m).real = plm(l, m); - ylm(l, m).img = 0.0; - - dyz.real = dplm(l, m); - rdy.real = dyz.real * rz; - - dylm(l, m).a[0].real = -rdy.real * rx; - dylm(l, m).a[0].img = 0.0; - dylm(l, m).a[1].real = -rdy.real * ry; - dylm(l, m).a[1].img = 0.0; - dylm(l, m).a[2].real = dyz.real - rdy.real * rz; - dylm(l, m).a[2].img = 0; - } - //m = 0 - m = 1; - for (LS_TYPE l = 1; l <= lmaxi; l++) { - - ylm(l, m) = phase * plm(l, m); - -// std::cout << "Re ylm(" << l << "," << m <<")= " << ylm(l, m).real << std::endl; -// std::cout << "Im ylm(" << l << "," << m <<")= " << ylm(l, m).img << std::endl; - - dyx.real = plm(l, m); - dyx.img = 0.0; - dyy.real = 0.0; - dyy.img = plm(l, m); - dyz.real = phase.real * dplm(l, m); - dyz.img = phase.img * dplm(l, m); - - rdy.real = rx * dyx.real + +rz * dyz.real; - rdy.img = ry * dyy.img + rz * dyz.img; - - dylm(l, m).a[0].real = dyx.real - rdy.real * rx; - dylm(l, m).a[0].img = -rdy.img * rx; - dylm(l, m).a[1].real = -rdy.real * ry; - dylm(l, m).a[1].img = dyy.img - rdy.img * ry; - dylm(l, m).a[2].real = dyz.real - rdy.real * rz; - dylm(l, m).a[2].img = dyz.img - rdy.img * rz; - } - - // m > 1 - phasem = phase; - for (MS_TYPE m = 2; m <= lmaxi; m++) { - - mphasem1.real = phasem.real * DOUBLE_TYPE(m); - mphasem1.img = phasem.img * DOUBLE_TYPE(m); - phasem = phasem * phase; - - for (LS_TYPE l = m; l <= lmaxi; l++) { - - ylm(l, m).real = phasem.real * plm(l, m); - ylm(l, m).img = phasem.img * plm(l, m); - - dyx = mphasem1 * plm(l, m); - dyy.real = -dyx.img; - dyy.img = dyx.real; - dyz = phasem * dplm(l, m); - - rdy.real = rx * dyx.real + ry * dyy.real + rz * dyz.real; - rdy.img = rx * dyx.img + ry * dyy.img + rz * dyz.img; - - dylm(l, m).a[0].real = dyx.real - rdy.real * rx; - dylm(l, m).a[0].img = dyx.img - rdy.img * rx; - dylm(l, m).a[1].real = dyy.real - rdy.real * ry; - dylm(l, m).a[1].img = dyy.img - rdy.img * ry; - dylm(l, m).a[2].real = dyz.real - rdy.real * rz; - dylm(l, m).a[2].img = dyz.img - rdy.img * rz; - } - } - -} - diff --git a/lib/pace/ace_spherical_cart.h b/lib/pace/ace_spherical_cart.h deleted file mode 100644 index b2a0cb5913..0000000000 --- a/lib/pace/ace_spherical_cart.h +++ /dev/null @@ -1,134 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Ralf Drautz, Yury Lysogorskiy - -#ifndef ACE_SPHERICAL_CART_H -#define ACE_SPHERICAL_CART_H - -#include - -#include "ace_arraynd.h" -#include "ace_array2dlm.h" -#include "ace_complex.h" -#include "ace_types.h" - - -using namespace std; - -const DOUBLE_TYPE sq1o4pi = 0.28209479177387814347; // sqrt(1/(4*pi)) -const DOUBLE_TYPE sq4pi = 3.54490770181103176384; // sqrt(4*pi) -const DOUBLE_TYPE sq3 = 1.73205080756887719318;//sqrt(3), numpy -const DOUBLE_TYPE sq3o2 = 1.22474487139158894067;//sqrt(3/2), numpy - -//definition of common factor for spherical harmonics = Y00 -//const DOUBLE_TYPE Y00 = sq1o4pi; -const DOUBLE_TYPE Y00 = 1; - -/** -Class to store spherical harmonics and their associated functions. \n -All the associated members such as \f$ P_{lm}, Y_{lm}\f$ etc are one dimensional arrays of length (L+1)*(L+2)/2. \n -The value that corresponds to a particular l, m configuration can be accessed through a \code ylm(l,m) \endcode \n -*/ -class ACECartesianSphericalHarmonics { -public: - - /** - int, the number of spherical harmonics to be found - */ - LS_TYPE lmax; - - /** - * Default constructor - */ - ACECartesianSphericalHarmonics() = default; - - /** - * Parametrized constructor. Dynamically initialises all the arrays. - * @param lmax maximum orbital moment - */ - explicit ACECartesianSphericalHarmonics(LS_TYPE lmax); - - /** - * Initialize internal arrays and precompute necessary coefficients - * @param lm maximum orbital moment - */ - void init(LS_TYPE lm); - - /** - * Destructor - */ - ~ACECartesianSphericalHarmonics(); - - /** - * Precompute necessaary helper arrays Precomputes the value of \f$ a_{lm}, b_{lm}, c_l, d_l \f$ - */ - void pre_compute(); - - /** - Function that computes \f$ \bar{P}_{lm} \f$ for the corresponding lmax value - Input is \f$ \hat{r}_z \f$ which is the $z$-component of the bond direction. - - For each \f$ \hat{r}_z \f$, this computes the whole range of \f$ \bar{P}_{lm} \f$ values - and its derivatives upto the lmax specified, which is a member of the class. - - @param rz, DOUBLE_TYPE - - @returns None - */ - void compute_barplm(DOUBLE_TYPE rz, LS_TYPE lmaxi); - - /** - Function that computes \f$ Y_{lm} \f$ for the corresponding lmax value - Input is the bond-directon vector \f$ \hat{r}_x, \hat{r}_y, \hat{r}_z \f$ - - Each \f$ Y_{lm} \f$ value is a ACEComplex object with real and imaginary parts. This function also - finds the derivatives, which are stored in the Dycomponent class, with each component being a - ACEComplex object. - - @param rx, DOUBLE_TYPE - @param ry, DOUBLE_TYPE - @param rz, DOUBLE_TYPE - @param lmaxi, int - */ - void compute_ylm(DOUBLE_TYPE rx, DOUBLE_TYPE ry, DOUBLE_TYPE rz, LS_TYPE lmaxi); - - Array2DLM alm; - Array2DLM blm; - Array1D cl; - Array1D dl; - - Array2DLM plm; - Array2DLM dplm; - - Array2DLM ylm; ///< Values of all spherical harmonics after \code compute_ylm(rx,ry,rz, lmaxi) \endcode call - Array2DLM dylm;///< Values of gradients of all spherical harmonics after \code compute_ylm(rx,ry,rz, lmaxi) \endcode call - -}; - - -#endif diff --git a/lib/pace/ace_timing.h b/lib/pace/ace_timing.h deleted file mode 100644 index 7f5243eb99..0000000000 --- a/lib/pace/ace_timing.h +++ /dev/null @@ -1,126 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Yury Lysogorskiy on 19.02.20. - -#ifndef ACE_TIMING_H -#define ACE_TIMING_H - -#include - -using namespace std::chrono; -using Clock = std::chrono::high_resolution_clock; -using TimePoint = std::chrono::time_point; -using Duration = Clock::duration; - -////////////////////////////////////////// -#ifdef FINE_TIMING -/** - * Helper class for timing the code. - * The timer should be initialized to reset measured time and - * then call "start" and "stop" before and after measured code. - * The measured time is stored in "duration" variable - */ -struct ACETimer { - Duration duration; ///< measured duration - TimePoint start_moment; ///< start moment of current measurement - - ACETimer() { init(); }; - - /** - * Reset timer - */ - void init() { duration = std::chrono::nanoseconds(0); } - - /** - * Start timer - */ - void start() { start_moment = Clock::now(); } - - /** - * Stop timer, update measured "duration" - */ - void stop() { duration += Clock::now() - start_moment; } - - /** - * Get duration in microseconds - */ - long as_microseconds() { return std::chrono::duration_cast(duration).count(); } - - /** - * Get duration in nanoseconds - */ - long as_nanoseconds() { return std::chrono::duration_cast(duration).count(); } - -}; - -#else // EMPTY Definitions -/** - * Helper class for timing the code. - * The timer should be initialized to reset measured time and - * then call "start" and "stop" before and after measured code. - * The measured time is stored in "duration" variable - */ -struct ACETimer { - Duration duration; ///< measured duration - TimePoint start_moment; ///< start moment of current measurement - - ACETimer() {}; - - /** - * Reset timer - */ - void init() {} - - /** - * Start timer - */ - void start() {} - - /** - * Stop timer, update measured "duration" - */ - void stop() {} - - /** - * Get duration in microseconds - */ - long as_microseconds() {return 0; } - - /** - * Get duration in nanoseconds - */ - long as_nanoseconds() {return 0; } - -}; - -#endif -////////////////////////////////////////// - - -#endif //ACE_TIMING_H diff --git a/lib/pace/ace_types.h b/lib/pace/ace_types.h deleted file mode 100644 index f9b3cf7267..0000000000 --- a/lib/pace/ace_types.h +++ /dev/null @@ -1,45 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Yury Lysogorskiy on 20.01.20. - -#ifndef ACE_TYPES_H -#define ACE_TYPES_H - -typedef char RANK_TYPE; -typedef int SPECIES_TYPE; -typedef short int NS_TYPE; -typedef short int LS_TYPE; - -typedef short int DENSITY_TYPE; - -typedef short int MS_TYPE; - -typedef short int SHORT_INT_TYPE; -typedef double DOUBLE_TYPE; - -#endif \ No newline at end of file diff --git a/lib/pace/ace_version.h b/lib/pace/ace_version.h deleted file mode 100644 index 9d61e5c505..0000000000 --- a/lib/pace/ace_version.h +++ /dev/null @@ -1,39 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Lysogorskiy Yury on 07.04.2020. - -#ifndef ACE_VERSION_H -#define ACE_VERSION_H - -#define VERSION_YEAR 2021 -#define VERSION_MONTH 2 -#define VERSION_DAY 3 - -#endif //ACE_VERSION_Hls - diff --git a/lib/pace/ships_radial.cpp b/lib/pace/ships_radial.cpp deleted file mode 100644 index e948f03f21..0000000000 --- a/lib/pace/ships_radial.cpp +++ /dev/null @@ -1,388 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Christoph Ortner on 03.06.2020 - -#include "ships_radial.h" - -#include -#include -#include - - -using namespace std; - -void SHIPsRadPolyBasis::_init(DOUBLE_TYPE r0, int p, DOUBLE_TYPE rcut, - DOUBLE_TYPE xl, DOUBLE_TYPE xr, - int pl, int pr, size_t maxn) { - this->p = p; - this->r0 = r0; - this->rcut = rcut; - this->xl = xl; - this->xr = xr; - this->pl = pl; - this->pr = pr; - this->maxn = maxn; - this->A.resize(maxn); - this->B.resize(maxn); - this->C.resize(maxn); - this->P.resize(maxn); - this->dP_dr.resize(maxn); -} - - -void SHIPsRadPolyBasis::fread(FILE *fptr) -{ - int res; //for fscanf result - int maxn, p, pl, pr, ntests; - double r0, xl, xr, a, b, c, rcut; - - // transform parameters - res = fscanf(fptr, "transform parameters: p=%d r0=%lf\n", &p, &r0); - if (res != 2) - throw invalid_argument("Couldn't read line: transform parameters: p=%d r0=%lf"); - // cutoff parameters - res = fscanf(fptr, "cutoff parameters: rcut=%lf xl=%lf xr=%lf pl=%d pr=%d\n", - &rcut, &xl, &xr, &pl, &pr); - if (res != 5) - throw invalid_argument("Couldn't read cutoff parameters: rcut=%lf xl=%lf xr=%lf pl=%d pr=%d"); - // basis size - res = fscanf(fptr, "recursion coefficients: maxn = %d\n", &maxn); - if (res != 1) - throw invalid_argument("Couldn't read recursion coefficients: maxn = %d"); - // initialize and allocate - this->_init(r0, p, rcut, xl, xr, pl, pr, maxn); - - // read basis coefficients - for (int i = 0; i < maxn; i++) { - res = fscanf(fptr, " %lf %lf %lf\n", &a, &b, &c); - if (res != 3) - throw invalid_argument("Couldn't read line: A_n B_n C_n"); - this->A(i) = DOUBLE_TYPE(a); - this->B(i) = DOUBLE_TYPE(b); - this->C(i) = DOUBLE_TYPE(c); - } - - // // check there are no consistency tests (I don't have time to fix this now) - // res = fscanf(fptr, "tests: ntests = %d\n", &ntests); - // if (res != 1) - // throw invalid_argument("Couldn't read line: tests: ntests = %d"); - // if (ntests != 0) - // throw invalid_argument("must have ntests = 0!"); - - // --------------------------------------------------------------------- - // run the consistency test this could be moved into a separate function - double r, Pn, dPn; - double err = 0.0; - - res = fscanf(fptr, "tests: ntests = %d\n", &ntests); - if (res != 1) - throw invalid_argument("Couldn't read line: tests: ntests = %d"); - for (size_t itest = 0; itest < ntests; itest++) { - // read an r argument - res = fscanf(fptr, " r=%lf\n", &r); - // printf("r = %lf \n", r); - if (res != 1) - throw invalid_argument("Couldn't read line: r=%lf"); - // printf("test %d, r=%f, maxn=%d \n", itest, r, maxn); - // evaluate the basis - this->calcP(r, maxn, SPECIES_TYPE(0), SPECIES_TYPE(0)); - // compare against the stored values - for (size_t n = 0; n < maxn; n++) { - res = fscanf(fptr, " %lf %lf\n", &Pn, &dPn); - if (res != 2) - throw invalid_argument("Couldn't read test value line: %lf %lf"); - err = max(err, abs(Pn - this->P(n)) + abs(dPn - this->dP_dr(n))); - // printf(" %d %e %e \n", int(n), - // abs(Pn - this->P(n)), - // abs(dPn - this->dP_dr(n))); - } - } - if (ntests > 0) - printf("Maximum Test error = %e\n", err); - // --------------------------------------------------------------------- - -} - - - - -size_t SHIPsRadPolyBasis::get_maxn() -{ - return this->maxn; -} - - -// Julia code: ((1+r0)/(1+r))^p -void SHIPsRadPolyBasis::transform(const DOUBLE_TYPE r, DOUBLE_TYPE &x_out, DOUBLE_TYPE &dx_out) const { - x_out = pow((1 + r0) / (1 + r), p); // ==pow( (1 + r) / (1 + r0), -p ); - dx_out = -p * pow((1 + r) / (1 + r0), -p - 1) / (1 + r0); -} - -void SHIPsRadPolyBasis::fcut(const DOUBLE_TYPE x, DOUBLE_TYPE &f_out, DOUBLE_TYPE &df_out) const { - if ( ((x < xl) && (pl > 0)) || ((x > xr) && (pr > 0)) ) { - f_out = 0.0; - df_out = 0.0; - } else { - f_out = pow(x - xl, pl) * pow(x - xr, pr); - df_out = pl * pow(x - xl, pl - 1) * pow(x - xr, pr) + pow(x - xl, pl) * pr * pow(x - xr, pr - 1); - } -} - - /* ------------------------------------------------------------------------ -Julia Code -P[1] = J.A[1] * _fcut_(J.pl, J.tl, J.pr, J.tr, t) -if length(J) == 1; return P; end -P[2] = (J.A[2] * t + J.B[2]) * P[1] -@inbounds for n = 3:length(J) - P[n] = (J.A[n] * t + J.B[n]) * P[n-1] + J.C[n] * P[n-2] -end -return P ------------------------------------------------------------------------- */ - -void SHIPsRadPolyBasis::calcP(DOUBLE_TYPE r, size_t maxn, - SPECIES_TYPE z1, SPECIES_TYPE z2) { - if (maxn > this->maxn) - throw invalid_argument("Given maxn couldn't be larger than global maxn"); - - if (maxn > P.get_size()) - throw invalid_argument("Given maxn couldn't be larger than global length of P"); - - DOUBLE_TYPE x, dx_dr; // dx -> dx/dr - transform(r, x, dx_dr); - // printf("r = %f, x = %f, fcut = %f \n", r, x, fcut(x)); - DOUBLE_TYPE f, df_dx; - fcut(x, f, df_dx); // df -> df/dx - - //fill with zeros - P.fill(0); - dP_dr.fill(0); - - P(0) = A(0) * f; - dP_dr(0) = A(0) * df_dx * dx_dr; // dP/dr; chain rule: df_cut/dr = df_cut/dx * dx/dr - if (maxn > 0) { - P(1) = (A(1) * x + B(1)) * P(0); - dP_dr(1) = A(1) * dx_dr * P(0) + (A(1) * x + B(1)) * dP_dr(0); - } - for (size_t n = 2; n < maxn; n++) { - P(n) = (A(n) * x + B(n)) * P(n - 1) + C(n) * P(n - 2); - dP_dr(n) = A(n) * dx_dr * P(n - 1) + (A(n) * x + B(n)) * dP_dr(n - 1) + C(n) * dP_dr(n - 2); - } -} - - -// ==================================================================== - - -bool SHIPsRadialFunctions::has_pair() { - return this->haspair; -} - -void SHIPsRadialFunctions::load(string fname) { - FILE * fptr = fopen(fname.data(), "r"); - size_t res = fscanf(fptr, "radbasename=ACE.jl.Basic\n"); - if (res != 0) - throw("SHIPsRadialFunctions::load : couldnt read radbasename=ACE.jl.Basic"); - this->fread(fptr); - fclose(fptr); -} - -void SHIPsRadialFunctions::fread(FILE *fptr){ - int res; - size_t maxn; - char hasE0, haspair; - DOUBLE_TYPE c; - - // check whether we have a pair potential - res = fscanf(fptr, "haspair: %c\n", &haspair); - if (res != 1) - throw("SHIPsRadialFunctions::load : couldn't read haspair"); - - // read the radial basis - this->radbasis.fread(fptr); - - // read the pair potential - if (haspair == 't') { - this->haspair=true; - fscanf(fptr, "begin repulsive potential\n"); - fscanf(fptr, "begin polypairpot\n"); - // read the basis parameters - pairbasis.fread(fptr); - maxn = pairbasis.get_maxn(); - // read the coefficients - fscanf(fptr, "coefficients\n"); - paircoeffs.resize(maxn); - for (size_t n = 0; n < maxn; n++) { - fscanf(fptr, "%lf\n", &c); - paircoeffs(n) = c; - } - fscanf(fptr, "end polypairpot\n"); - // read the spline parameters - fscanf(fptr, "spline parameters\n"); - fscanf(fptr, " e_0 + B exp(-A*(r/ri-1)) * (ri/r)\n"); - fscanf(fptr, "ri=%lf\n", &(this->ri)); - fscanf(fptr, "e0=%lf\n", &(this->e0)); - fscanf(fptr, "A=%lf\n", &(this->A)); - fscanf(fptr, "B=%lf\n", &(this->B)); - fscanf(fptr, "end repulsive potential\n"); - } -} - - -size_t SHIPsRadialFunctions::get_maxn() -{ - return this->radbasis.get_maxn(); -} - -DOUBLE_TYPE SHIPsRadialFunctions::get_rcut() -{ - return max(radbasis.rcut, pairbasis.rcut); -} - - -void SHIPsRadialFunctions::fill_gk(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2) { - radbasis.calcP(r, maxn, z1, z2); - for (NS_TYPE n = 0; n < maxn; n++) { - gr(n) = radbasis.P(n); - dgr(n) = radbasis.dP_dr(n); - } -} - - -void SHIPsRadialFunctions::fill_Rnl(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2) { - radbasis.calcP(r, maxn, z1, z2); - for (NS_TYPE n = 0; n < maxn; n++) { - for (LS_TYPE l = 0; l <= lmax; l++) { - fr(n, l) = radbasis.P(n); - dfr(n, l) = radbasis.dP_dr(n); - } - } -} - - -void SHIPsRadialFunctions::setuplookupRadspline() { -} - - -void SHIPsRadialFunctions::init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, - SPECIES_TYPE nelements, - DOUBLE_TYPE cutoff, string radbasename) { - //mimic ACERadialFunctions::init - this->nradbase = nradb; - this->lmax = lmax; - this->nradial = nradial; - this->deltaSplineBins = deltaSplineBins; - this->nelements = nelements; - this->cutoff = cutoff; - this->radbasename = radbasename; - - gr.init(nradbase, "gr"); - dgr.init(nradbase, "dgr"); - - - fr.init(nradial, lmax + 1, "fr"); - dfr.init(nradial, lmax + 1, "dfr"); - - splines_gk.init(nelements, nelements, "splines_gk"); - splines_rnl.init(nelements, nelements, "splines_rnl"); - splines_hc.init(nelements, nelements, "splines_hc"); - - lambda.init(nelements, nelements, "lambda"); - lambda.fill(1.); - - cut.init(nelements, nelements, "cut"); - cut.fill(1.); - - dcut.init(nelements, nelements, "dcut"); - dcut.fill(1.); - - crad.init(nelements, nelements, (lmax + 1), nradial, nradbase, "crad"); - crad.fill(0.); - - //hard-core repulsion - prehc.init(nelements, nelements, "prehc"); - prehc.fill(0.); - - lambdahc.init(nelements, nelements, "lambdahc"); - lambdahc.fill(1.); -} - - -void SHIPsRadialFunctions::evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, - SPECIES_TYPE mu_j, bool calc_second_derivatives) { - if (calc_second_derivatives) - throw invalid_argument("SHIPsRadialFunctions has not `calc_second_derivatives` option"); - - radbasis.calcP(r, nradbase_c, mu_i, mu_j); - for (NS_TYPE nr = 0; nr < nradbase_c; nr++) { - gr(nr) = radbasis.P(nr); - dgr(nr) = radbasis.dP_dr(nr); - } - for (NS_TYPE nr = 0; nr < nradial_c; nr++) { - for (LS_TYPE l = 0; l <= this->lmax; l++) { - fr(nr, l) = radbasis.P(nr); - dfr(nr, l) = radbasis.dP_dr(nr); - } - } - - if (this->has_pair()) - this->evaluate_pair(r, mu_i, mu_j); - else { - cr = 0; - dcr = 0; - } -} - -void SHIPsRadialFunctions::evaluate_pair(DOUBLE_TYPE r, - SPECIES_TYPE mu_i, - SPECIES_TYPE mu_j, - bool calc_second_derivatives) { - // spline_hc.calcSplines(r); - // cr = spline_hc.values(0); - // dcr = spline_hc.derivatives(0); - - // the outer polynomial potential - if (r > ri) { - pairbasis.calcP(r, pairbasis.get_maxn(), mu_i, mu_j); - cr = 0; - dcr = 0; - for (size_t n = 0; n < pairbasis.get_maxn(); n++) { - cr += paircoeffs(n) * pairbasis.P(n); - dcr += paircoeffs(n) * pairbasis.dP_dr(n); - } - } - else { // the repulsive core part - cr = e0 + B * exp(-A * (r/ri - 1)) * (ri/r); - dcr = B * exp( - A * (r/ri-1) ) * ri * ( - A / ri / r - 1/(r*r) ); - } - // fix double-counting - cr *= 0.5; - dcr *= 0.5; -} - - - diff --git a/lib/pace/ships_radial.h b/lib/pace/ships_radial.h deleted file mode 100644 index 60a82448cd..0000000000 --- a/lib/pace/ships_radial.h +++ /dev/null @@ -1,158 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Christoph Ortner on 03.06.2020 - -#ifndef SHIPs_RADIAL_FUNCTIONS_H -#define SHIPs_RADIAL_FUNCTIONS_H - -#include "ace_arraynd.h" -#include "ace_types.h" -#include "ace_radial.h" - -class SHIPsRadPolyBasis { - -public: - - // transform parameters - int p = 0; - DOUBLE_TYPE r0 = 0.0; - - // cutoff parameters - DOUBLE_TYPE rcut = 0.0; - DOUBLE_TYPE xl = 0.0; - DOUBLE_TYPE xr = 0.0; - int pl = 0; - int pr = 0; - - // basis size - size_t maxn = 0; - - // recursion parameters - Array1D A = Array1D("SHIPs radial basis: A"); - Array1D B = Array1D("SHIPs radial basis: B"); - Array1D C = Array1D("SHIPs radial basis: C"); - - // temporary storage for evaluating the basis - Array1D P = Array1D("SHIPs radial basis: P"); - Array1D dP_dr = Array1D("SHIPs radial basis: dP"); - -////////////////////////////////// - - SHIPsRadPolyBasis() = default; - - ~SHIPsRadPolyBasis() = default; - - // distance transform - void transform(const DOUBLE_TYPE r, DOUBLE_TYPE &x_out, DOUBLE_TYPE &dx_out) const; - - // cutoff function - void fcut(const DOUBLE_TYPE x, DOUBLE_TYPE &f_out, DOUBLE_TYPE &df_out) const; - - void fread(FILE *fptr); - - void _init(DOUBLE_TYPE r0, int p, DOUBLE_TYPE rcut, - DOUBLE_TYPE xl, DOUBLE_TYPE xr, - int pl, int pr, size_t maxn); - - void calcP(DOUBLE_TYPE r, size_t maxn, SPECIES_TYPE z1, SPECIES_TYPE z2); - - size_t get_maxn(); - -}; - - - - -class SHIPsRadialFunctions : public AbstractRadialBasis { -public: - - // radial basis - SHIPsRadPolyBasis radbasis; - - // pair potential basis - bool haspair = false; - SHIPsRadPolyBasis pairbasis; - - // pair potential coefficients - Array1D paircoeffs = Array1D("SHIPs pairpot coeffs: paircoeffs"); - - // spline parameters for repulsive core - DOUBLE_TYPE ri = 0.0; - DOUBLE_TYPE e0 = 0.0; - DOUBLE_TYPE A = 0.0; - DOUBLE_TYPE B = 0.0; - -////////////////////////////////// - - SHIPsRadialFunctions() = default; - - ~SHIPsRadialFunctions() override = default; - - - void fread(FILE *fptr); - - void load(string fname); - - size_t get_maxn(); - DOUBLE_TYPE get_rcut(); - - bool has_pair(); - - void init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements, - DOUBLE_TYPE cutoff, - string radbasename) override; - - void - evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, - bool calc_second_derivatives = false) override; - - void - evaluate_pair(DOUBLE_TYPE r, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, - bool calc_second_derivatives = false); - - void setuplookupRadspline() override; - - SHIPsRadialFunctions *clone() const override { - return new SHIPsRadialFunctions(*this); - }; - - /** - * Helper method, that populate `fr` and `dfr` 2D-arrays (n,l) with P(n), dP_dr for given coordinate r - * @param r - * @param maxn - * @param z1 - * @param z2 - */ - void fill_Rnl(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2); - - void fill_gk(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2); -}; - - -#endif diff --git a/src/USER-PACE/Install.sh b/src/USER-PACE/Install.sh index 4d87b0e3ed..c099ddd2c4 100644 --- a/src/USER-PACE/Install.sh +++ b/src/USER-PACE/Install.sh @@ -1,68 +1,64 @@ -# Install.sh file that integrates the settings from the lib folder into the conventional build process (make build?) +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update -# COPIED FROM src/KIM/Install.sh: +mode=$1 -# # Install/unInstall package files in LAMMPS -# # mode = 0/1/2 for uninstall/install/update +# enforce using portable C locale +LC_ALL=C +export LC_ALL -# mode=$1 +# arg1 = file, arg2 = file it depends on -# # enforce using portable C locale -# LC_ALL=C -# export LC_ALL +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} -# # arg1 = file, arg2 = file it depends on +# all package files with no dependencies -# action () { -# if (test $mode = 0) then -# rm -f ../$1 -# elif (! cmp -s $1 ../$1) then -# if (test -z "$2" || test -e ../$2) then -# cp $1 .. -# if (test $mode = 2) then -# echo " updating src/$1" -# fi -# fi -# elif (test -n "$2") then -# if (test ! -e ../$2) then -# rm -f ../$1 -# fi -# fi -# } +for file in *.cpp *.h; do + test -f ${file} && action $file +done -# # all package files with no dependencies +# edit 2 Makefile.package files to include/exclude package info -# for file in *.cpp *.h; do -# test -f ${file} && action $file -# done +if (test $1 = 1) then -# # edit 2 Makefile.package files to include/exclude package info + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*pace[^ \t]* //' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(pace_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(pace_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(pace_SYSPATH) |' ../Makefile.package + fi -# if (test $1 = 1) then + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*pace.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ +include ..\/..\/lib\/pace\/Makefile.lammps +' ../Makefile.package.settings + fi -# if (test -e ../Makefile.package) then -# sed -i -e 's/[^ \t]*kim[^ \t]* //' ../Makefile.package -# sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(kim_SYSINC) |' ../Makefile.package -# sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(kim_SYSLIB) |' ../Makefile.package -# sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(kim_SYSPATH) |' ../Makefile.package -# fi +elif (test $1 = 0) then -# if (test -e ../Makefile.package.settings) then -# sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings -# # multiline form needed for BSD sed on Macs -# sed -i -e '4 i \ -# include ..\/..\/lib\/kim\/Makefile.lammps -# ' ../Makefile.package.settings -# fi + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*pace[^ \t]* //' ../Makefile.package + fi -# elif (test $1 = 0) then + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*pace.*$/d' ../Makefile.package.settings + fi -# if (test -e ../Makefile.package) then -# sed -i -e 's/[^ \t]*kim[^ \t]* //' ../Makefile.package -# fi - -# if (test -e ../Makefile.package.settings) then -# sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings -# fi - -# fi +fi From 0d1ccbe1b542fdcfb8259c23c501be756307798c Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Wed, 7 Apr 2021 12:43:28 +0200 Subject: [PATCH 0420/1217] Move A.Thomson's modifications on doc and examples in: - doc/src/.rst - examples/USER/pace - potentials --- doc/src/Commands_pair.rst | 1 + doc/src/Packages_details.rst | 37 + doc/src/pair_pace.rst | 114 + examples/USER/pace/Cu-PBE-core-rep.ace | 1 + examples/USER/pace/in.pace.product | 38 + examples/USER/pace/in.pace.recursive | 38 + .../pace/log.03Feb2021.pace.product.g++.1 | 108 + .../pace/log.03Feb2021.pace.product.g++.4 | 108 + .../pace/log.03Feb2021.pace.recursive.g++.1 | 108 + .../pace/log.03Feb2021.pace.recursive.g++.4 | 108 + potentials/Cu-PBE-core-rep.ace | 8980 +++++++++++++++++ 11 files changed, 9641 insertions(+) create mode 100644 doc/src/pair_pace.rst create mode 120000 examples/USER/pace/Cu-PBE-core-rep.ace create mode 100644 examples/USER/pace/in.pace.product create mode 100644 examples/USER/pace/in.pace.recursive create mode 100644 examples/USER/pace/log.03Feb2021.pace.product.g++.1 create mode 100644 examples/USER/pace/log.03Feb2021.pace.product.g++.4 create mode 100644 examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 create mode 100644 examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 create mode 100644 potentials/Cu-PBE-core-rep.ace diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 080f3eff20..1d15b93edf 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -215,6 +215,7 @@ OPT. * :doc:`oxrna2/stk ` * :doc:`oxrna2/xstk ` * :doc:`oxrna2/coaxstk ` + * :doc:`pace ` * :doc:`peri/eps ` * :doc:`peri/lps (o) ` * :doc:`peri/pmb (o) ` diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index b662ae73c7..549ab3d8f0 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -90,6 +90,7 @@ page gives those details. * :ref:`USER-MOLFILE ` * :ref:`USER-NETCDF ` * :ref:`USER-OMP ` + * :ref:`USER-PACE ` * :ref:`USER-PHONON ` * :ref:`USER-PLUMED ` * :ref:`USER-PTM ` @@ -1349,6 +1350,42 @@ This package has :ref:`specific installation instructions ` on the ---------- +.. _PKG-USER-PACE: + +USER-PACE package +------------------- + +**Contents:** + +A pair style for the Atomic Cluster Expansion potential (ACE). +ACE is a methodology for deriving a highly accurate classical potential +fit to a large archive of quantum mechanical (DFT) data. The USER-PACE +package provides an efficient implementation for running simulations +with ACE potentials. + +**Authors:** + +This package was written by Yury Lysogorskiy^1, +Cas van der Oord^2, Anton Bochkarev^1, +Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, +Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1. + + ^1: Ruhr-University Bochum, Bochum, Germany + + ^2: University of Cambridge, Cambridge, United Kingdom + + ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + + ^4: University of British Columbia, Vancouver, BC, Canada + +**Supporting info:** + +* src/USER-PACE: filenames -> commands +* :doc:`pair_style pace ` +* examples/USER/pace + +---------- + .. _PKG-USER-PLUMED: USER-PLUMED package diff --git a/doc/src/pair_pace.rst b/doc/src/pair_pace.rst new file mode 100644 index 0000000000..1ebf6210cd --- /dev/null +++ b/doc/src/pair_pace.rst @@ -0,0 +1,114 @@ +.. index:: pair_style pace + +pair_style pace command +======================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style pace ... keyword values ... + +* an optional keyword may be appended +* keyword = *product* or *recursive* + + .. parsed-literal:: + + *product* = use product algorithm for basis functions + *recursive* = use recursive algorithm for basis functions + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style pace + pair_style pace product + pair_coeff * * Cu-PBE-core-rep.ace Cu + +Description +""""""""""" + +Pair style *pace* computes interactions using the Atomic Cluster +Expansion (ACE), which is a general expansion of the atomic energy in +multi-body basis functions. :ref:`(Drautz) `. +The *pace* pair style +provides an efficient implementation that +is described in this paper :ref:`(Lysogorskiy) `. + +In ACE, the total energy is decomposed into a sum over +atomic energies. The energy of atom *i* is expressed as a +linear or non-linear function of one or more density functions. +By projecting the +density onto a local atomic base, the lowest order contributions +to the energy can be expressed as a set of scalar polynomials in +basis function contributions summed over neighbor atoms. + +Only a single pair_coeff command is used with the *pace* style which +specifies an ACE coefficient file followed by N additional arguments +specifying the mapping of ACE elements to LAMMPS atom types, +where N is the number of LAMMPS atom types: + +* ACE coefficient file +* N element names = mapping of ACE elements to atom types + +Only a single pair_coeff command is used with the *pace* style which +specifies an ACE file that fully defines the potential. +Note that unlike for other potentials, cutoffs are +not set in the pair_style or pair_coeff command; they are specified in +the ACE file. + +The pair_style *mliap* may be followed by an optional keyword +*product* or *recursive*, which determines which of two algorithms + is used for the calculation of basis functions and derivatives. +The default is *recursive*. + +See the :doc:`pair_coeff ` doc page for alternate ways +to specify the path for the ACE coefficient file. + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +For atom type pairs I,J and I != J, where types I and J correspond to +two different element types, mixing is performed by LAMMPS with +user-specifiable parameters as described above. You never need to +specify a pair_coeff command with I != J arguments for this style. + +This pair style does not support the :doc:`pair_modify ` +shift, table, and tail options. + +This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +This pair style can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. It does not support the +*inner*\ , *middle*\ , *outer* keywords. + +---------- + +Restrictions +"""""""""""" + +This pair style is part of the USER-PACE package. It is only enabled if LAMMPS +was built with that package. +See the :doc:`Build package ` doc page for more info. + +Related commands +"""""""""""""""" + +:doc:`pair_style snap ` + +Default +""""""" + +recursive + +.. _Drautz20191: + +**(Drautz)** Drautz, Phys Rev B, 99, 014104 (2019). + +.. _Lysogorskiy20211: + +**(Lysogorskiy)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, TBD (2021). diff --git a/examples/USER/pace/Cu-PBE-core-rep.ace b/examples/USER/pace/Cu-PBE-core-rep.ace new file mode 120000 index 0000000000..4414592f78 --- /dev/null +++ b/examples/USER/pace/Cu-PBE-core-rep.ace @@ -0,0 +1 @@ +../../../potentials/Cu-PBE-core-rep.ace \ No newline at end of file diff --git a/examples/USER/pace/in.pace.product b/examples/USER/pace/in.pace.product new file mode 100644 index 0000000000..d70bb0f67c --- /dev/null +++ b/examples/USER/pace/in.pace.product @@ -0,0 +1,38 @@ +# simple test of fcc Cu with ACE product + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +region box block 0 4 0 4 0 4 +create_box 1 box +create_atoms 1 box + +mass 1 26.98 + +group Al type 1 + +pair_style pace product +pair_coeff * * Cu-PBE-core-rep.ace Cu + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 + diff --git a/examples/USER/pace/in.pace.recursive b/examples/USER/pace/in.pace.recursive new file mode 100644 index 0000000000..dd655eb18d --- /dev/null +++ b/examples/USER/pace/in.pace.recursive @@ -0,0 +1,38 @@ +# simple test of fcc Cu with ACE recursive + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +region box block 0 4 0 4 0 4 +create_box 1 box +create_atoms 1 box + +mass 1 26.98 + +group Al type 1 + +pair_style pace recursive +pair_coeff * * Cu-PBE-core-rep.ace Cu + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 + diff --git a/examples/USER/pace/log.03Feb2021.pace.product.g++.1 b/examples/USER/pace/log.03Feb2021.pace.product.g++.1 new file mode 100644 index 0000000000..01ba9c25a4 --- /dev/null +++ b/examples/USER/pace/log.03Feb2021.pace.product.g++.1 @@ -0,0 +1,108 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +# simple test of fcc Cu with ACE product + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +lattice fcc 3.597 +Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000 +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 256 atoms + create_atoms CPU = 0.000 seconds + +mass 1 26.98 + +group Al type 1 +256 atoms in group Al + +pair_style pace product +ACE version: 2021.2.3 +Product evaluator is used +pair_coeff * * Cu-PBE-core-rep.ace Cu +Loading Cu-PBE-core-rep.ace +Total number of basis functions + Cu: 16 (r=1) 726 (r>1) +Mapping LAMMPS atom type #1(Cu) -> ACE species type #0 + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 +Neighbor list info ... + update every 2 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.7 + ghost atom cutoff = 7.7 + binsize = 3.85, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pace, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes +Step Temp E_pair TotEng Press v_delenergy v_delpress + 0 300 -945.9873 -936.0989 45359.818 0 2.1827873e-11 + 10 280.68558 -945.35055 -936.09878 46326.919 0 2.910383e-11 + 20 228.73618 -943.63789 -936.09844 48903.598 0 -2.910383e-11 + 30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11 + 40 97.732944 -939.31899 -936.09758 55176.875 0 2.1827873e-11 + 50 59.165961 -938.04759 -936.0974 56850.103 0 2.910383e-11 + 60 53.124678 -937.84857 -936.09751 56878.948 0 0 + 70 74.623347 -938.5575 -936.09782 55565.237 0 4.3655746e-11 + 80 109.4762 -939.70663 -936.09815 53665.652 0 2.910383e-11 + 90 142.02657 -940.77975 -936.09837 52001.1 0 0 + 100 161.73598 -941.42945 -936.09842 51114.997 0 1.4551915e-11 +Loop time of 11.4718 on 1 procs for 100 steps with 256 atoms + +Performance: 0.377 ns/day, 63.732 hours/ns, 8.717 timesteps/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.468 | 11.468 | 11.468 | 0.0 | 99.96 +Neigh | 0.001181 | 0.001181 | 0.001181 | 0.0 | 0.01 +Comm | 0.001207 | 0.001207 | 0.001207 | 0.0 | 0.01 +Output | 0.000876 | 0.000876 | 0.000876 | 0.0 | 0.01 +Modify | 0.000455 | 0.000455 | 0.000455 | 0.0 | 0.00 +Other | | 0.000397 | | | 0.00 + +Nlocal: 256.000 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2201.00 ave 2201 max 2201 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 43118.0 ave 43118 max 43118 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 43118 +Ave neighs/atom = 168.42969 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:11 diff --git a/examples/USER/pace/log.03Feb2021.pace.product.g++.4 b/examples/USER/pace/log.03Feb2021.pace.product.g++.4 new file mode 100644 index 0000000000..052becb7d6 --- /dev/null +++ b/examples/USER/pace/log.03Feb2021.pace.product.g++.4 @@ -0,0 +1,108 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +# simple test of fcc Cu with ACE product + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +lattice fcc 3.597 +Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000 +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 256 atoms + create_atoms CPU = 0.000 seconds + +mass 1 26.98 + +group Al type 1 +256 atoms in group Al + +pair_style pace product +ACE version: 2021.2.3 +Product evaluator is used +pair_coeff * * Cu-PBE-core-rep.ace Cu +Loading Cu-PBE-core-rep.ace +Total number of basis functions + Cu: 16 (r=1) 726 (r>1) +Mapping LAMMPS atom type #1(Cu) -> ACE species type #0 + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 +Neighbor list info ... + update every 2 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.7 + ghost atom cutoff = 7.7 + binsize = 3.85, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pace, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes +Step Temp E_pair TotEng Press v_delenergy v_delpress + 0 300 -945.9873 -936.0989 45359.818 0 -1.4551915e-11 + 10 280.68558 -945.35055 -936.09878 46326.919 0 2.910383e-11 + 20 228.73618 -943.63789 -936.09844 48903.598 0 0 + 30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11 + 40 97.732944 -939.31899 -936.09758 55176.875 0 2.1827873e-11 + 50 59.165961 -938.04759 -936.0974 56850.103 0 -1.4551915e-11 + 60 53.124678 -937.84857 -936.09751 56878.948 0 7.2759576e-12 + 70 74.623347 -938.5575 -936.09782 55565.237 0 0 + 80 109.4762 -939.70663 -936.09815 53665.652 0 2.1827873e-11 + 90 142.02657 -940.77975 -936.09837 52001.1 0 -1.4551915e-11 + 100 161.73598 -941.42945 -936.09842 51114.997 0 1.4551915e-11 +Loop time of 3.54317 on 4 procs for 100 steps with 256 atoms + +Performance: 1.219 ns/day, 19.684 hours/ns, 28.223 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.1375 | 3.3058 | 3.469 | 6.5 | 93.30 +Neigh | 0.000284 | 0.00031975 | 0.000352 | 0.0 | 0.01 +Comm | 0.071607 | 0.23492 | 0.40336 | 24.6 | 6.63 +Output | 0.001189 | 0.0012315 | 0.001347 | 0.2 | 0.03 +Modify | 0.000311 | 0.00032725 | 0.000351 | 0.0 | 0.01 +Other | | 0.0005298 | | | 0.01 + +Nlocal: 64.0000 ave 71 max 57 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 1373.00 ave 1380 max 1366 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 10779.5 ave 11978 max 9604 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 43118 +Ave neighs/atom = 168.42969 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 b/examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 new file mode 100644 index 0000000000..e6de3bd5c6 --- /dev/null +++ b/examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 @@ -0,0 +1,108 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +# simple test of fcc Cu with ACE recursive + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +lattice fcc 3.597 +Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000 +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 256 atoms + create_atoms CPU = 0.000 seconds + +mass 1 26.98 + +group Al type 1 +256 atoms in group Al + +pair_style pace recursive +ACE version: 2021.2.3 +Recursive evaluator is used +pair_coeff * * Cu-PBE-core-rep.ace Cu +Loading Cu-PBE-core-rep.ace +Total number of basis functions + Cu: 16 (r=1) 726 (r>1) +Mapping LAMMPS atom type #1(Cu) -> ACE species type #0 + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 +Neighbor list info ... + update every 2 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.7 + ghost atom cutoff = 7.7 + binsize = 3.85, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pace, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes +Step Temp E_pair TotEng Press v_delenergy v_delpress + 0 300 -945.9873 -936.0989 45359.818 0 0 + 10 280.68558 -945.35055 -936.09878 46326.919 0 5.8207661e-11 + 20 228.73618 -943.63789 -936.09844 48903.598 0 1.4551915e-11 + 30 160.53661 -941.38948 -936.09798 52222.083 0 7.2759576e-11 + 40 97.732944 -939.31899 -936.09758 55176.875 0 -5.8207661e-11 + 50 59.165961 -938.04759 -936.0974 56850.103 0 0 + 60 53.124678 -937.84857 -936.09751 56878.948 0 8.7311491e-11 + 70 74.623347 -938.5575 -936.09782 55565.237 0 -1.4551915e-11 + 80 109.4762 -939.70663 -936.09815 53665.652 0 2.1827873e-11 + 90 142.02657 -940.77975 -936.09837 52001.1 0 2.910383e-11 + 100 161.73598 -941.42945 -936.09842 51114.997 0 0 +Loop time of 9.31437 on 1 procs for 100 steps with 256 atoms + +Performance: 0.464 ns/day, 51.746 hours/ns, 10.736 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.3103 | 9.3103 | 9.3103 | 0.0 | 99.96 +Neigh | 0.001214 | 0.001214 | 0.001214 | 0.0 | 0.01 +Comm | 0.001176 | 0.001176 | 0.001176 | 0.0 | 0.01 +Output | 0.000827 | 0.000827 | 0.000827 | 0.0 | 0.01 +Modify | 0.000479 | 0.000479 | 0.000479 | 0.0 | 0.01 +Other | | 0.000363 | | | 0.00 + +Nlocal: 256.000 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2201.00 ave 2201 max 2201 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 43118.0 ave 43118 max 43118 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 43118 +Ave neighs/atom = 168.42969 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:09 diff --git a/examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 b/examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 new file mode 100644 index 0000000000..b816f8e570 --- /dev/null +++ b/examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 @@ -0,0 +1,108 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +# simple test of fcc Cu with ACE recursive + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +lattice fcc 3.597 +Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000 +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 256 atoms + create_atoms CPU = 0.000 seconds + +mass 1 26.98 + +group Al type 1 +256 atoms in group Al + +pair_style pace recursive +ACE version: 2021.2.3 +Recursive evaluator is used +pair_coeff * * Cu-PBE-core-rep.ace Cu +Loading Cu-PBE-core-rep.ace +Total number of basis functions + Cu: 16 (r=1) 726 (r>1) +Mapping LAMMPS atom type #1(Cu) -> ACE species type #0 + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 +Neighbor list info ... + update every 2 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.7 + ghost atom cutoff = 7.7 + binsize = 3.85, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pace, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes +Step Temp E_pair TotEng Press v_delenergy v_delpress + 0 300 -945.9873 -936.0989 45359.818 0 -5.0931703e-11 + 10 280.68558 -945.35055 -936.09878 46326.919 0 1.4551915e-11 + 20 228.73618 -943.63789 -936.09844 48903.598 0 0 + 30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11 + 40 97.732944 -939.31899 -936.09758 55176.875 0 0 + 50 59.165961 -938.04759 -936.0974 56850.103 0 -2.910383e-11 + 60 53.124678 -937.84857 -936.09751 56878.948 0 1.4551915e-11 + 70 74.623347 -938.5575 -936.09782 55565.237 0 3.6379788e-11 + 80 109.4762 -939.70663 -936.09815 53665.652 0 -7.2759576e-12 + 90 142.02657 -940.77975 -936.09837 52001.1 0 -2.910383e-11 + 100 161.73598 -941.42945 -936.09842 51114.997 0 7.2759576e-12 +Loop time of 2.91339 on 4 procs for 100 steps with 256 atoms + +Performance: 1.483 ns/day, 16.185 hours/ns, 34.324 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5753 | 2.723 | 2.8656 | 6.3 | 93.46 +Neigh | 0.000308 | 0.000365 | 0.00046 | 0.0 | 0.01 +Comm | 0.045106 | 0.18792 | 0.33552 | 24.1 | 6.45 +Output | 0.001213 | 0.001259 | 0.001388 | 0.2 | 0.04 +Modify | 0.000304 | 0.00033 | 0.00037 | 0.0 | 0.01 +Other | | 0.0005595 | | | 0.02 + +Nlocal: 64.0000 ave 71 max 57 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 1373.00 ave 1380 max 1366 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 10779.5 ave 11978 max 9604 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 43118 +Ave neighs/atom = 168.42969 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/potentials/Cu-PBE-core-rep.ace b/potentials/Cu-PBE-core-rep.ace new file mode 100644 index 0000000000..338675f718 --- /dev/null +++ b/potentials/Cu-PBE-core-rep.ace @@ -0,0 +1,8980 @@ +nelements=1 +elements: Cu + +lmax=6 + +embedding-function: FinnisSinclairShiftedScaled +4 FS parameters: 1.000000 1.000000 1.000000 0.500000 +core energy-cutoff parameters: 100000.000000000000000000 250.000000000000000000 +E0: 0.000000000000000000 + +radbasename=ChebPow +nradbase=16 +nradmax=5 +cutoffmax=7.400000 +deltaSplineBins=0.001000 +core repulsion parameters: 400.000000000000000000 7.000000000000000000 +radparameter= 2.000000000000000000 +cutoff= 7.400000000000000355 +dcut= 0.010000000000000000 +crad= 1.620882954168367363 1.226870698977090335 0.999546737553742348 1.448717152469839231 0.789126334259324436 0.990815368777163696 1.019809595831713933 + -0.010015984641177847 0.177152406295798537 -0.099297777289971231 0.173787043169736394 -0.226947223064932313 -0.058969556614429458 0.008323578427593646 + 0.037392073193535026 0.101922365253167557 0.446201407295113706 -0.369069422111282963 -0.101863282196291566 -0.029626931322193999 0.097875222496131745 + 0.002819311425100959 0.000151479194773449 -0.214871024239485592 -0.069350620490777212 0.231426164941363366 -0.026191321598537990 -0.242936254601765322 + 0.186424171366563085 -0.103524085445276359 0.830521273247123437 0.062832162628560284 -0.106558674195482483 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-0.002303680195516651 0.026862055083389711 +ctilde_basis_func: rank=2 ndens=2 mu0=0 mu=( 0 0 ) +n=( 5 4 ) +l=( 5 5 ) +num_ms=6 +< 0 0 >: -0.000652423778863231 0.026695406667047394 +< 1 -1 >: 0.001304847557726462 -0.053390813334094789 +< 2 -2 >: -0.001304847557726462 0.053390813334094796 +< 3 -3 >: 0.001304847557726462 -0.053390813334094803 +< 4 -4 >: -0.001304847557726462 0.053390813334094796 +< 5 -5 >: 0.001304847557726461 -0.053390813334094740 +ctilde_basis_func: rank=2 ndens=2 mu0=0 mu=( 0 0 ) +n=( 5 4 ) +l=( 6 6 ) +num_ms=7 +< 0 0 >: -0.022661669008512072 -0.089577314277810058 +< 1 -1 >: 0.045323338017024151 0.179154628555620143 +< 2 -2 >: -0.045323338017024137 -0.179154628555620060 +< 3 -3 >: 0.045323338017024151 0.179154628555620143 +< 4 -4 >: -0.045323338017024123 -0.179154628555620032 +< 5 -5 >: 0.045323338017024137 0.179154628555620060 +< 6 -6 >: -0.045323338017024109 -0.179154628555619949 +ctilde_basis_func: rank=2 ndens=2 mu0=0 mu=( 0 0 ) +n=( 5 5 ) +l=( 0 0 ) +num_ms=1 +< 0 0 >: 0.000927204096660696 0.214065283656125371 +ctilde_basis_func: rank=2 ndens=2 mu0=0 mu=( 0 0 ) +n=( 5 5 ) +l=( 1 1 ) +num_ms=2 +< 0 0 >: 0.000094655033139699 0.004208753371838363 +< 1 -1 >: -0.000189310066279397 -0.008417506743676724 +ctilde_basis_func: rank=2 ndens=2 mu0=0 mu=( 0 0 ) +n=( 5 5 ) +l=( 2 2 ) +num_ms=3 +< 0 0 >: 0.000351584678183165 0.036688837956052121 +< 1 -1 >: -0.000703169356366331 -0.073377675912104257 +< 2 -2 >: 0.000703169356366331 0.073377675912104270 +ctilde_basis_func: rank=2 ndens=2 mu0=0 mu=( 0 0 ) +n=( 5 5 ) +l=( 3 3 ) +num_ms=4 +< 0 0 >: 0.002788351180694639 -0.034407768721874142 +< 1 -1 >: -0.005576702361389278 0.068815537443748284 +< 2 -2 >: 0.005576702361389277 -0.068815537443748284 +< 3 -3 >: -0.005576702361389277 0.068815537443748284 +ctilde_basis_func: rank=2 ndens=2 mu0=0 mu=( 0 0 ) +n=( 5 5 ) +l=( 4 4 ) +num_ms=5 +< 0 0 >: 0.000317570803659664 -0.001123830834830057 +< 1 -1 >: -0.000635141607319327 0.002247661669660114 +< 2 -2 >: 0.000635141607319327 -0.002247661669660114 +< 3 -3 >: -0.000635141607319327 0.002247661669660114 +< 4 -4 >: 0.000635141607319327 -0.002247661669660114 +ctilde_basis_func: rank=2 ndens=2 mu0=0 mu=( 0 0 ) +n=( 5 5 ) +l=( 5 5 ) +num_ms=6 +< 0 0 >: 0.000488890061324461 -0.017808170881300944 +< 1 -1 >: -0.000977780122648922 0.035616341762601887 +< 2 -2 >: 0.000977780122648922 -0.035616341762601894 +< 3 -3 >: -0.000977780122648922 0.035616341762601901 +< 4 -4 >: 0.000977780122648922 -0.035616341762601894 +< 5 -5 >: -0.000977780122648921 0.035616341762601852 +ctilde_basis_func: rank=2 ndens=2 mu0=0 mu=( 0 0 ) +n=( 5 5 ) +l=( 6 6 ) +num_ms=7 +< 0 0 >: 0.005721847329407898 0.062910453316038589 +< 1 -1 >: -0.011443694658815798 -0.125820906632077206 +< 2 -2 >: 0.011443694658815794 0.125820906632077151 +< 3 -3 >: -0.011443694658815798 -0.125820906632077206 +< 4 -4 >: 0.011443694658815791 0.125820906632077123 +< 5 -5 >: -0.011443694658815794 -0.125820906632077151 +< 6 -6 >: 0.011443694658815787 0.125820906632077067 From da56b9de569ac6546df64872283ae6f2eadde983 Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Wed, 7 Apr 2021 07:48:43 -0600 Subject: [PATCH 0421/1217] Adding user-omp support --- src/USER-OMP/pair_gran_hertz_history_omp.cpp | 1 + src/USER-OMP/pair_gran_hooke_history_omp.cpp | 1 + src/USER-OMP/pair_gran_hooke_omp.cpp | 1 + 3 files changed, 3 insertions(+) diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.cpp b/src/USER-OMP/pair_gran_hertz_history_omp.cpp index 2187dcbe90..200075a316 100644 --- a/src/USER-OMP/pair_gran_hertz_history_omp.cpp +++ b/src/USER-OMP/pair_gran_hertz_history_omp.cpp @@ -224,6 +224,7 @@ void PairGranHertzHistoryOMP::eval(int iifrom, int iito, ThrData * const thr) ccel = kn*(radsum-r)*rinv - damp; polyhertz = sqrt((radsum-r)*radi*radj / radsum); ccel *= polyhertz; + if (limit_damping && (ccel < 0.0)) ccel = 0.0; // relative velocities diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.cpp b/src/USER-OMP/pair_gran_hooke_history_omp.cpp index 7894d1e963..0ba9607bd9 100644 --- a/src/USER-OMP/pair_gran_hooke_history_omp.cpp +++ b/src/USER-OMP/pair_gran_hooke_history_omp.cpp @@ -223,6 +223,7 @@ void PairGranHookeHistoryOMP::eval(int iifrom, int iito, ThrData * const thr) damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; + if (limit_damping && (ccel < 0.0)) ccel = 0.0; // relative velocities diff --git a/src/USER-OMP/pair_gran_hooke_omp.cpp b/src/USER-OMP/pair_gran_hooke_omp.cpp index 08ae07c6f5..451b074fa9 100644 --- a/src/USER-OMP/pair_gran_hooke_omp.cpp +++ b/src/USER-OMP/pair_gran_hooke_omp.cpp @@ -197,6 +197,7 @@ void PairGranHookeOMP::eval(int iifrom, int iito, ThrData * const thr) damp = meff*gamman*vnnr*rsqinv; ccel = kn*(radsum-r)*rinv - damp; + if (limit_damping && (ccel < 0.0)) ccel = 0.0; // relative velocities From 29c78d022a1351f2f89d0bdd3dd274e0ad19ed08 Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Wed, 7 Apr 2021 19:54:35 +0200 Subject: [PATCH 0422/1217] add lib/pace/Makefile.lammps --- lib/pace/Makefile.lammps | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 lib/pace/Makefile.lammps diff --git a/lib/pace/Makefile.lammps b/lib/pace/Makefile.lammps new file mode 100644 index 0000000000..17820716df --- /dev/null +++ b/lib/pace/Makefile.lammps @@ -0,0 +1,3 @@ +pace_SYSINC =-I../../lib/pace/src/USER-PACE +pace_SYSLIB = -L../../lib/pace/ -lpace +pace_SYSPATH = From 5d00fa7ec5106229561e12cab93fb7b0a680e58b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 14:00:14 -0400 Subject: [PATCH 0423/1217] update constants for lj/cubic/gpu from CPU version --- lib/gpu/lal_lj_cubic.cu | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/lib/gpu/lal_lj_cubic.cu b/lib/gpu/lal_lj_cubic.cu index a91326d521..df3398afd7 100644 --- a/lib/gpu/lal_lj_cubic.cu +++ b/lib/gpu/lal_lj_cubic.cu @@ -26,10 +26,10 @@ _texture_2d( pos_tex,int4); // LJ quantities scaled by epsilon and rmin = sigma*2^1/6 (see src/pair_lj_cubic.h) -#define _RT6TWO (numtyp)1.1224621 -#define _PHIS (numtyp)-0.7869823 /* energy at s */ -#define _DPHIDS (numtyp)2.6899009 /* gradient at s */ -#define _A3 (numtyp)27.93357 /* cubic coefficient */ +#define _RT6TWO (numtyp)1.1224620483093730 /* 2^1/6 */ +#define _PHIS (numtyp)-0.7869822485207097 /* energy at s */ +#define _DPHIDS (numtyp)2.6899008972047196 /* gradient at s */ +#define _A3 (numtyp)27.9335700460986445 /* cubic coefficient */ __kernel void k_lj_cubic(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict lj1, From 835820ba00227fc1e294163f2d19f44effa951c7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 14:00:27 -0400 Subject: [PATCH 0424/1217] reorder includes --- src/GPU/pair_lj_cubic_gpu.cpp | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp index 2c6231ca89..73839bdbed 100644 --- a/src/GPU/pair_lj_cubic_gpu.cpp +++ b/src/GPU/pair_lj_cubic_gpu.cpp @@ -17,25 +17,24 @@ #include "pair_lj_cubic_gpu.h" -#include -#include -#include - #include "atom.h" #include "atom_vec.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" +#include "gpu_extra.h" #include "integrate.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" +#include "suffix.h" #include "universe.h" #include "update.h" -#include "domain.h" -#include "gpu_extra.h" -#include "suffix.h" + +#include +#include #include "pair_lj_cubic_const.h" From 9af086916b7764b746a174eb40cb74a461480432 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 14:11:25 -0400 Subject: [PATCH 0425/1217] skip GPU tests for a couple more tabulated coulomb tests --- unittest/force-styles/tests/mol-pair-born_coul_table_cs.yaml | 1 + unittest/force-styles/tests/mol-pair-coul_table_cs.yaml | 1 + 2 files changed, 2 insertions(+) diff --git a/unittest/force-styles/tests/mol-pair-born_coul_table_cs.yaml b/unittest/force-styles/tests/mol-pair-born_coul_table_cs.yaml index 32a2b44328..d2ff07b2b8 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_table_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_table_cs.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:39 2021 epsilon: 7.5e-14 +skip_tests: gpu prerequisites: ! | atom full pair born/coul/long/cs diff --git a/unittest/force-styles/tests/mol-pair-coul_table_cs.yaml b/unittest/force-styles/tests/mol-pair-coul_table_cs.yaml index d5ed5fab83..983053a88b 100644 --- a/unittest/force-styles/tests/mol-pair-coul_table_cs.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_table_cs.yaml @@ -2,6 +2,7 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:44 2021 epsilon: 7.5e-14 +skip_tests: gpu prerequisites: ! | atom full pair coul/long/cs From 7b18bc1fecfe282b656841bd156dbac43e4f6052 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 14:26:27 -0400 Subject: [PATCH 0426/1217] correctly handle r-RESPA for lj/class2 and lj/class2/gpu --- src/CLASS2/pair_lj_class2.cpp | 17 +++++----- src/GPU/pair_lj_class2_gpu.cpp | 32 +++++++++---------- .../tests/mol-pair-lj_class2.yaml | 1 - 3 files changed, 25 insertions(+), 25 deletions(-) diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index 23b0be7396..a0cb122494 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -11,20 +11,20 @@ #include "pair_lj_class2.h" -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "respa.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -36,6 +36,7 @@ PairLJClass2::PairLJClass2(LAMMPS *lmp) : Pair(lmp) respa_enable = 1; writedata = 1; centroidstressflag = CENTROID_SAME; + cut_respa = nullptr; } /* ---------------------------------------------------------------------- */ diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp index 06ab116a7e..e32561ab59 100644 --- a/src/GPU/pair_lj_class2_gpu.cpp +++ b/src/GPU/pair_lj_class2_gpu.cpp @@ -16,25 +16,24 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_gpu.h" -#include -#include -#include #include "atom.h" #include "atom_vec.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" +#include "gpu_extra.h" #include "integrate.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" +#include "suffix.h" #include "universe.h" #include "update.h" -#include "domain.h" -#include "gpu_extra.h" -#include "suffix.h" + +#include using namespace LAMMPS_NS; @@ -46,13 +45,13 @@ int lj96_gpu_init(const int ntypes, double **cutsq, double **host_lj1, const int nall, const int max_nbors, const int maxspecial, const double cell_size, int &gpu_mode, FILE *screen); void lj96_gpu_clear(); -int ** lj96_gpu_compute_n(const int ago, const int inum, const int nall, - double **host_x, int *host_type, double *sublo, - double *subhi, tagint *tag, int **nspecial, - tagint **special, const bool eflag, const bool vflag, - const bool eatom, const bool vatom, int &host_start, - int **ilist, int **jnum, - const double cpu_time, bool &success); +int **lj96_gpu_compute_n(const int ago, const int inum, const int nall, + double **host_x, int *host_type, double *sublo, + double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, + const double cpu_time, bool &success); void lj96_gpu_compute(const int ago, const int inum, const int nall, double **host_x, int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag, const bool vflag, @@ -64,6 +63,7 @@ double lj96_gpu_bytes(); PairLJClass2GPU::PairLJClass2GPU(LAMMPS *lmp) : PairLJClass2(lmp), gpu_mode(GPU_FORCE) { + respa_enable = 0; reinitflag = 0; cpu_time = 0.0; suffix_flag |= Suffix::GPU; diff --git a/unittest/force-styles/tests/mol-pair-lj_class2.yaml b/unittest/force-styles/tests/mol-pair-lj_class2.yaml index 779bb4def2..ba4989e6e2 100644 --- a/unittest/force-styles/tests/mol-pair-lj_class2.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_class2.yaml @@ -2,7 +2,6 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:46 2021 epsilon: 5e-14 -skip_tests: gpu prerequisites: ! | atom full pair lj/class2 From f072289ac1ad17fca3aaf23046ca8ca0aa1bb74c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 14:52:36 -0400 Subject: [PATCH 0427/1217] need to initialize limit_damping array to NULL --- src/GRANULAR/pair_granular.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index dc367dcc0a..faeaaacd88 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -80,6 +80,8 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp) onerad_frozen = nullptr; maxrad_dynamic = nullptr; maxrad_frozen = nullptr; + + limit_damping = nullptr; history_transfer_factors = nullptr; From ea8277ce87d8e5b7fe5be83117f9e4025687662f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 14:59:33 -0400 Subject: [PATCH 0428/1217] whitespace fixes --- doc/src/fix_wall_gran.rst | 4 ++-- doc/src/fix_wall_gran_region.rst | 4 ++-- doc/src/pair_gran.rst | 8 ++++---- doc/src/pair_granular.rst | 12 ++++++------ src/GRANULAR/fix_wall_gran.cpp | 14 +++++++------- src/GRANULAR/pair_gran_hooke_history.cpp | 2 +- src/GRANULAR/pair_granular.cpp | 10 +++++----- 7 files changed, 27 insertions(+), 27 deletions(-) diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index 95a4b5d818..57bec679e4 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -96,8 +96,8 @@ Specifically, delta = radius - r = overlap of particle with wall, m_eff = mass of particle, and the effective radius of contact = RiRj/Ri+Rj is set to the radius of the particle. -The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*, -and the optional keyword *limit_damping* +The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*, +and the optional keyword *limit_damping* have the same meaning and units as those specified with the :doc:`pair_style gran/\* ` commands. This means a NULL can be used for either *Kt* or *gamma_t* as described on that page. If a diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 35fe1fab72..0a252b162a 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -181,8 +181,8 @@ radius - r = overlap of particle with wall, m_eff = mass of particle, and the effective radius of contact is just the radius of the particle. -The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*, -and the optional keyword *limit_damping* +The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*, +and the optional keyword *limit_damping* have the same meaning and units as those specified with the :doc:`pair_style gran/\* ` commands. This means a NULL can be used for either *Kt* or *gamma_t* as described on that page. If a diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index 5bccdfd8b4..fbcacb5c76 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -217,11 +217,11 @@ potential is used as a sub-style of :doc:`pair_style hybrid `, then pair_coeff command to determine which atoms interact via a granular potential. -If two particles are moving away from each other while in contact, there -is a possibility that the particles could experience an effective attractive -force due to damping. If the *limit_damping* keyword is used, this option +If two particles are moving away from each other while in contact, there +is a possibility that the particles could experience an effective attractive +force due to damping. If the *limit_damping* keyword is used, this option will zero out the normal component of the force if there is an effective -attractive force. +attractive force. ---------- diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index a9ca437370..432fd29584 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -623,9 +623,9 @@ Finally, the twisting torque on each particle is given by: ---------- -If two particles are moving away from each other while in contact, there -is a possibility that the particles could experience an effective attractive -force due to damping. If the optional *limit_damping* keyword is used, this option +If two particles are moving away from each other while in contact, there +is a possibility that the particles could experience an effective attractive +force due to damping. If the optional *limit_damping* keyword is used, this option will zero out the normal component of the force if there is an effective attractive force. This keyword cannot be used with the JKR or DMT models. @@ -665,9 +665,9 @@ then LAMMPS will use that cutoff for the specified atom type combination, and automatically set pairwise cutoffs for the remaining atom types. -If two particles are moving away from each other while in contact, there -is a possibility that the particles could experience an effective attractive -force due to damping. If the *limit_damping* keyword is used, this option +If two particles are moving away from each other while in contact, there +is a possibility that the particles could experience an effective attractive +force due to damping. If the *limit_damping* keyword is used, this option will zero out the normal component of the force if there is an effective attractive force. This keyword cannot be used with the JKR or DMT models. diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 0611a54efd..51dca15e7b 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -119,12 +119,12 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : kt /= force->nktv2p; } iarg = 10; - + if (strcmp(arg[iarg],"limit_damping") == 0) { limit_damping = 1; - iarg += 1; + iarg += 1; } - + } else { iarg = 4; damping_model = VISCOELASTIC; @@ -310,7 +310,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : break; } else if (strcmp(arg[iarg],"limit_damping") == 0) { limit_damping = 1; - iarg += 1; + iarg += 1; } else { error->all(FLERR, "Illegal fix wall/gran command"); } @@ -530,7 +530,7 @@ void FixWallGran::init() roll_history_index += 1; twist_history_index += 1; } - + if (damping_model == TSUJI) { double cor = normal_coeffs[1]; normal_coeffs[1] = 1.2728-4.2783*cor+11.087*pow(cor,2)-22.348*pow(cor,3)+ @@ -1020,7 +1020,7 @@ void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz, else polyhertz = sqrt((radius-r)*radius*rwall/(rwall+radius)); ccel *= polyhertz; if (limit_damping && (ccel < 0.0)) ccel = 0.0; - + // relative velocities vtr1 = vt1 - (dz*wr2-dy*wr3); @@ -1305,7 +1305,7 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, history[thist2] -= rsht*nz; // also rescale to preserve magnitude - prjmag = sqrt(history[thist0]*history[thist0] + + prjmag = sqrt(history[thist0]*history[thist0] + history[thist1]*history[thist1] + history[thist2]*history[thist2]); if (prjmag > 0) scalefac = shrmag/prjmag; else scalefac = 0; diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 0f9682a133..ac26ffbf1b 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -370,7 +370,7 @@ void PairGranHookeHistory::settings(int narg, char **arg) xmu = utils::numeric(FLERR,arg[4],false,lmp); dampflag = utils::inumeric(FLERR,arg[5],false,lmp); if (dampflag == 0) gammat = 0.0; - + limit_damping = 0; if (narg == 7) { if (strcmp(arg[6], "limit_damping") == 0) limit_damping = 1; diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index faeaaacd88..52971f920f 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -80,7 +80,7 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp) onerad_frozen = nullptr; maxrad_dynamic = nullptr; maxrad_frozen = nullptr; - + limit_damping = nullptr; history_transfer_factors = nullptr; @@ -796,7 +796,7 @@ void PairGranular::coeff(int narg, char **arg) twist_model_one = TWIST_NONE; damping_model_one = VISCOELASTIC; int ld_flag = 0; - + int iarg = 2; while (iarg < narg) { if (strcmp(arg[iarg], "hooke") == 0) { @@ -971,7 +971,7 @@ void PairGranular::coeff(int narg, char **arg) cutoff_one = utils::numeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg], "limit_damping") == 0) { - ld_flag = 1; + ld_flag = 1; iarg += 1; } else error->all(FLERR, "Illegal pair_coeff command"); } @@ -1047,7 +1047,7 @@ void PairGranular::coeff(int narg, char **arg) } } - + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } @@ -1320,7 +1320,7 @@ void PairGranular::write_restart(FILE *fp) fwrite(&tangential_model[i][j],sizeof(int),1,fp); fwrite(&roll_model[i][j],sizeof(int),1,fp); fwrite(&twist_model[i][j],sizeof(int),1,fp); - fwrite(&limit_damping[i][j],sizeof(int),1,fp); + fwrite(&limit_damping[i][j],sizeof(int),1,fp); fwrite(normal_coeffs[i][j],sizeof(double),4,fp); fwrite(tangential_coeffs[i][j],sizeof(double),3,fp); fwrite(roll_coeffs[i][j],sizeof(double),3,fp); From 5bc630f00858e773028397ee38c8a36e8ab25ec4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 15:07:06 -0400 Subject: [PATCH 0429/1217] step version strings for next patch release --- doc/lammps.1 | 2 +- src/version.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/lammps.1 b/doc/lammps.1 index 6ce463bfba..c10950643d 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,4 +1,4 @@ -.TH LAMMPS "10 March 2021" "2021-03-10" +.TH LAMMPS "8 April 2021" "2021-04-08" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. diff --git a/src/version.h b/src/version.h index d16067e41c..d7839fcbfe 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "10 Mar 2021" +#define LAMMPS_VERSION "8 Apr 2021" From feda2dc08dc11502dd24dd7c2bc835a21924be95 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Wed, 7 Apr 2021 14:07:58 -0600 Subject: [PATCH 0430/1217] Updated doc page and spelling --- doc/src/pair_pace.rst | 4 ++-- doc/utils/sphinx-config/false_positives.txt | 14 ++++++++++++++ 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/doc/src/pair_pace.rst b/doc/src/pair_pace.rst index 1ebf6210cd..36baaa7ef9 100644 --- a/doc/src/pair_pace.rst +++ b/doc/src/pair_pace.rst @@ -59,9 +59,9 @@ Note that unlike for other potentials, cutoffs are not set in the pair_style or pair_coeff command; they are specified in the ACE file. -The pair_style *mliap* may be followed by an optional keyword +The pair_style *pace* command may be followed by an optional keyword *product* or *recursive*, which determines which of two algorithms - is used for the calculation of basis functions and derivatives. +is used for the calculation of basis functions and derivatives. The default is *recursive*. See the :doc:`pair_coeff ` doc page for alternate ways diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 38a6971f4c..9689125753 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -268,6 +268,7 @@ blueviolet bn bni bo +Bochkarev Bochum bocs bodyflag @@ -343,6 +344,7 @@ Cao Capolungo Caro cartesian +Cas CasP Caswell Cates @@ -1069,6 +1071,7 @@ fuer fx fy fz +Gabor Gahler gainsboro Galindo @@ -1193,6 +1196,7 @@ Halperin Halver Hamaker Hamel +Hammerschmidt haptic Hara Harpertown @@ -1743,6 +1747,7 @@ lx ly Lybrand lyon +Lysogorskiy Lyulin lz Maaravi @@ -1801,8 +1806,10 @@ Materias mathbf mathjax matlab +Matous matplotlib Matsubara +Matteo Mattice Mattox Mattson @@ -1863,6 +1870,7 @@ MEMALIGN membered memcheck Mendelev +Menon mer Meremianin Mersenne @@ -1986,6 +1994,7 @@ mpiio mpirun mplayer mps +Mrovec Mryglod mscg MSCG @@ -2311,6 +2320,7 @@ oneway onn ons OO +Oord opencl openKIM openmp @@ -2331,6 +2341,7 @@ Orsi ortho orthonormal orthorhombic +Ortner oso Otype Ouldridge @@ -2620,6 +2631,7 @@ radians Rafferty rahman Rahman +Ralf Raman ramped ramping @@ -2726,6 +2738,7 @@ Rij RIj Rik Rin +Rinaldi Rino RiRj Risi @@ -2814,6 +2827,7 @@ Sandia sandybrown sanitizer Sanyal +Sarath sc scafacos SCAFACOS From 0151fd00c281aac40fdebd88b76b5ef80e3c2c81 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 17:37:30 -0400 Subject: [PATCH 0431/1217] correct CMake support for USER-PACE package and align with recent conventions for downloading external code --- cmake/Modules/Packages/USER-PACE.cmake | 34 +++++++++++++++++--------- 1 file changed, 23 insertions(+), 11 deletions(-) diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/USER-PACE.cmake index c9e8e1bcfe..008d32444c 100644 --- a/cmake/Modules/Packages/USER-PACE.cmake +++ b/cmake/Modules/Packages/USER-PACE.cmake @@ -1,14 +1,26 @@ -set(PACE_EVALUATOR_PATH ${LAMMPS_LIB_SOURCE_DIR}/pace) -message("CMakeLists.txt DEBUG: PACE_EVALUATOR_PATH=${PACE_EVALUATOR_PATH}") -set(PACE_EVALUATOR_SRC_PATH ${PACE_EVALUATOR_PATH}) -FILE(GLOB PACE_EVALUATOR_SOURCE_FILES ${PACE_EVALUATOR_SRC_PATH}/*.cpp) -set(PACE_EVALUATOR_INCLUDE_DIR ${PACE_EVALUATOR_SRC_PATH}) +set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.2.3.tar.gz" CACHE STRING "URL for PACE evaluator library sources") +set(PACELIB_MD5 "9ebb087cba7e4ca041fde52f7e9e640c" CACHE STRING "MD5 checksum of PACE evaluator library tarball") +mark_as_advanced(PACELIB_URL) +mark_as_advanced(PACELIB_MD5) + +# download library sources to build folder +file(DOWNLOAD ${PACELIB_URL} libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5}) + +# uncompress downloaded sources +execute_process( + COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace* + COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz + WORKING_DIRECTORY ${CMAKE_BINARY_DIR} +) -##### aceevaluator ##### -add_library(aceevaluator ${PACE_EVALUATOR_SOURCE_FILES}) -target_include_directories(aceevaluator PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) -target_compile_options(aceevaluator PRIVATE -O2) -set_target_properties(aceevaluator PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE}) -target_link_libraries(lammps PRIVATE aceevaluator) \ No newline at end of file +file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE) +file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp) +list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp) + +add_library(pace STATIC ${PACE_EVALUATOR_SOURCES}) +set_target_properties(pace PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE}) +target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) +target_link_libraries(lammps PRIVATE pace) + From 7b34f025ee088212ee5d26ad62c993e8e7d80678 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 17:46:18 -0400 Subject: [PATCH 0432/1217] correct src/Makefile for USER-PACE --- src/Makefile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/Makefile b/src/Makefile index bec0a2b16b..d5f0e600d6 100644 --- a/src/Makefile +++ b/src/Makefile @@ -55,7 +55,7 @@ PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-c user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ user-intel user-lb user-manifold user-meamc user-mesodpd user-mesont \ user-mgpt user-misc user-mofff user-molfile \ - user-netcdf user-omp user-phonon user-plumed user-ptm user-qmmm \ + user-netcdf user-omp user-phonon user-pace user-plumed user-ptm user-qmmm \ user-qtb user-quip user-reaction user-reaxc user-scafacos user-smd user-smtbq \ user-sdpd user-sph user-tally user-uef user-vtk user-yaff @@ -70,8 +70,8 @@ PACKSYS = compress mpiio python user-lb PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont PACKEXT = kim latte mscg voronoi \ - user-adios user-h5md user-molfile user-netcdf user-plumed user-qmmm user-quip \ - user-smd user-vtk user-pace + user-adios user-h5md user-molfile user-netcdf user-pace user-plumed \ + user-qmmm user-quip user-smd user-vtk PACKALL = $(PACKAGE) $(PACKUSER) From 084c0713d6e69fad23459782978fa4c73889f82b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 18:05:00 -0400 Subject: [PATCH 0433/1217] resolve whitespace issues --- doc/src/Packages_details.rst | 4 ++-- doc/src/pair_pace.rst | 26 +++++++++++++------------- src/USER-PACE/pair_pace.cpp | 2 +- src/USER-PACE/pair_pace.h | 2 +- 4 files changed, 17 insertions(+), 17 deletions(-) diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 549ab3d8f0..1964a83717 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -1363,9 +1363,9 @@ fit to a large archive of quantum mechanical (DFT) data. The USER-PACE package provides an efficient implementation for running simulations with ACE potentials. -**Authors:** +**Authors:** -This package was written by Yury Lysogorskiy^1, +This package was written by Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1. diff --git a/doc/src/pair_pace.rst b/doc/src/pair_pace.rst index 36baaa7ef9..56ae0f32dc 100644 --- a/doc/src/pair_pace.rst +++ b/doc/src/pair_pace.rst @@ -15,8 +15,8 @@ Syntax .. parsed-literal:: - *product* = use product algorithm for basis functions - *recursive* = use recursive algorithm for basis functions + *product* = use product algorithm for basis functions + *recursive* = use recursive algorithm for basis functions Examples """""""" @@ -30,24 +30,24 @@ Examples Description """"""""""" -Pair style *pace* computes interactions using the Atomic Cluster -Expansion (ACE), which is a general expansion of the atomic energy in -multi-body basis functions. :ref:`(Drautz) `. -The *pace* pair style -provides an efficient implementation that +Pair style *pace* computes interactions using the Atomic Cluster +Expansion (ACE), which is a general expansion of the atomic energy in +multi-body basis functions. :ref:`(Drautz) `. +The *pace* pair style +provides an efficient implementation that is described in this paper :ref:`(Lysogorskiy) `. In ACE, the total energy is decomposed into a sum over -atomic energies. The energy of atom *i* is expressed as a -linear or non-linear function of one or more density functions. +atomic energies. The energy of atom *i* is expressed as a +linear or non-linear function of one or more density functions. By projecting the density onto a local atomic base, the lowest order contributions to the energy can be expressed as a set of scalar polynomials in basis function contributions summed over neighbor atoms. Only a single pair_coeff command is used with the *pace* style which -specifies an ACE coefficient file followed by N additional arguments -specifying the mapping of ACE elements to LAMMPS atom types, +specifies an ACE coefficient file followed by N additional arguments +specifying the mapping of ACE elements to LAMMPS atom types, where N is the number of LAMMPS atom types: * ACE coefficient file @@ -61,7 +61,7 @@ the ACE file. The pair_style *pace* command may be followed by an optional keyword *product* or *recursive*, which determines which of two algorithms -is used for the calculation of basis functions and derivatives. +is used for the calculation of basis functions and derivatives. The default is *recursive*. See the :doc:`pair_coeff ` doc page for alternate ways @@ -92,7 +92,7 @@ Restrictions """""""""""" This pair style is part of the USER-PACE package. It is only enabled if LAMMPS -was built with that package. +was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index a515b7b4b0..ee1922d886 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -446,7 +446,7 @@ double PairPACE::init_one(int i, int j) { return basis_set->radial_functions->cut(map[i], map[j]); } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- extract method for extracting value of scale variable ---------------------------------------------------------------------- */ void *PairPACE::extract(const char *str, int &dim) diff --git a/src/USER-PACE/pair_pace.h b/src/USER-PACE/pair_pace.h index 3fccbd98f0..76b08a65c0 100644 --- a/src/USER-PACE/pair_pace.h +++ b/src/USER-PACE/pair_pace.h @@ -94,4 +94,4 @@ namespace LAMMPS_NS { } #endif -#endif \ No newline at end of file +#endif From 2d1fc67b5df7d47c425565c96e208794e7c2a5bb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 19:09:43 -0400 Subject: [PATCH 0434/1217] update .gitignore --- src/.gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/.gitignore b/src/.gitignore index 6fa3aef513..96a89ae667 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -32,6 +32,9 @@ /pair_kim.cpp /pair_kim.h +/pair_pace.cpp +/pair_pace.h + /superpose3d.h /kokkos.cpp From 2d4b05ffa6db866f30ae100754677ae6bdcd9d6d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 19:13:10 -0400 Subject: [PATCH 0435/1217] refactor code to more closely match LAMMPS coding conventions - update indentation to 2 characters - remove dead code and unused class members - use convenience functions in many places - reuse code and members from Pair base class - declare local functions/variables static - PIMPL-ify access to the ACE evaluator library functions/classes - correct settings member variables to match implementation --- src/USER-PACE/pair_pace.cpp | 538 ++++++++++++++++-------------------- src/USER-PACE/pair_pace.h | 60 ++-- 2 files changed, 250 insertions(+), 348 deletions(-) diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index ee1922d886..527f2a6f06 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -28,25 +28,33 @@ Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, // Created by Lysogorskiy Yury on 27.02.20. // -#include -#include -#include -#include #include "pair_pace.h" + #include "atom.h" -#include "neighbor.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" +#include +#include -#include "math_const.h" - +#include "ace_evaluator.h" +#include "ace_recursive.h" +#include "ace_c_basis.h" #include "ace_version.h" +namespace LAMMPS_NS { + struct ACEImpl { + ACECTildeBasisSet *basis_set; + ACERecursiveEvaluator *ace; + }; +} + using namespace LAMMPS_NS; using namespace MathConst; @@ -59,9 +67,8 @@ using namespace MathConst; #define RECURSIVE_KEYWORD "recursive" #define PRODUCT_KEYWORD "product" - -int elements_num_pace = 104; -char const *const elements_pace[104] = {"X", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", +static int elements_num_pace = 104; +static char const *const elements_pace[104] = {"X", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", @@ -71,27 +78,26 @@ char const *const elements_pace[104] = {"X", "H", "He", "Li", "Be", "B", "C", "N "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr" }; -int AtomicNumberByName_pace(char *elname) { - for (int i = 1; i < elements_num_pace; i++) - if (strcmp(elname, elements_pace[i]) == 0) - return i; - return -1; +static int AtomicNumberByName_pace(char *elname) { + for (int i = 1; i < elements_num_pace; i++) + if (strcmp(elname, elements_pace[i]) == 0) + return i; + return -1; } - /* ---------------------------------------------------------------------- */ PairPACE::PairPACE(LAMMPS *lmp) : Pair(lmp) { - //single_enable = 0; - restartinfo = 0; - one_coeff = 1; - manybody_flag = 1; + single_enable = 0; + restartinfo = 0; + one_coeff = 1; + manybody_flag = 1; - nelements = 0; + aceimpl = new ACEImpl; + aceimpl->ace = nullptr; + aceimpl->basis_set = nullptr; + recursive = false; - ace = NULL; - potential_file_name = NULL; - elements = NULL; - map = NULL; + scale = nullptr; } /* ---------------------------------------------------------------------- @@ -99,170 +105,157 @@ PairPACE::PairPACE(LAMMPS *lmp) : Pair(lmp) { ------------------------------------------------------------------------- */ PairPACE::~PairPACE() { - if (copymode) return; + if (copymode) return; - if (elements) - for (int i = 0; i < nelements; i++) delete[] elements[i]; - delete[] elements; + delete aceimpl->basis_set; + delete aceimpl->ace; + delete aceimpl; - - delete[] potential_file_name; - - delete basis_set; - delete ace; - - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - memory->destroy(map); - memory->destroy(scale); - } + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(scale); + } } /* ---------------------------------------------------------------------- */ void PairPACE::compute(int eflag, int vflag) { - int i, j, ii, jj, inum, jnum; - double delx, dely, delz, evdwl; - double fij[3]; - int *ilist, *jlist, *numneigh, **firstneigh; + int i, j, ii, jj, inum, jnum; + double delx, dely, delz, evdwl; + double fij[3]; + int *ilist, *jlist, *numneigh, **firstneigh; - ev_init(eflag, vflag); + ev_init(eflag, vflag); - // downwards modified by YL + // downwards modified by YL - double **x = atom->x; - double **f = atom->f; - tagint *tag = atom->tag; - int *type = atom->type; + double **x = atom->x; + double **f = atom->f; + tagint *tag = atom->tag; + int *type = atom->type; - // number of atoms in cell - int nlocal = atom->nlocal; + // number of atoms in cell + int nlocal = atom->nlocal; - int newton_pair = force->newton_pair; + int newton_pair = force->newton_pair; - // number of atoms including ghost atoms - int nall = nlocal + atom->nghost; + // number of atoms including ghost atoms + int nall = nlocal + atom->nghost; - // inum: length of the neighborlists list - inum = list->inum; + // inum: length of the neighborlists list + inum = list->inum; - // ilist: list of "i" atoms for which neighbor lists exist - ilist = list->ilist; + // ilist: list of "i" atoms for which neighbor lists exist + ilist = list->ilist; - //numneigh: the length of each these neigbor list - numneigh = list->numneigh; + //numneigh: the length of each these neigbor list + numneigh = list->numneigh; - // the pointer to the list of neighbors of "i" - firstneigh = list->firstneigh; + // the pointer to the list of neighbors of "i" + firstneigh = list->firstneigh; - if (inum != nlocal) { - char str[128]; - snprintf(str,128,"inum: %d nlocal: %d are different",inum, nlocal); - error->all(FLERR,str); + if (inum != nlocal) + error->all(FLERR,fmt::format("inum: {} nlocal: {} are different",inum, nlocal)); + + // Aidan Thompson told RD (26 July 2019) that practically always holds: + // inum = nlocal + // i = ilist(ii) < inum + // j = jlist(jj) < nall + // neighborlist contains neighbor atoms plus skin atoms, + // skin atoms can be removed by setting skin to zero but here + // they are disregarded anyway + + + //determine the maximum number of neighbours + int max_jnum = -1; + int nei = 0; + for (ii = 0; ii < list->inum; ii++) { + i = ilist[ii]; + jnum = numneigh[i]; + nei = nei + jnum; + if (jnum > max_jnum) + max_jnum = jnum; + } + + aceimpl->ace->resize_neighbours_cache(max_jnum); + + //loop over atoms + for (ii = 0; ii < list->inum; ii++) { + i = list->ilist[ii]; + const int itype = type[i]; + + const double xtmp = x[i][0]; + const double ytmp = x[i][1]; + const double ztmp = x[i][2]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // checking if neighbours are actually within cutoff range is done inside compute_atom + // mapping from LAMMPS atom types ('type' array) to ACE species is done inside compute_atom + // by using 'aceimpl->ace->element_type_mapping' array + // x: [r0 ,r1, r2, ..., r100] + // i = 0 ,1 + // jnum(0) = 50 + // jlist(neigh ind of 0-atom) = [1,2,10,7,99,25, .. 50 element in total] + + try { + aceimpl->ace->compute_atom(i, x, type, jnum, jlist); + } catch (exception &e) { + error->one(FLERR, e.what()); + } + // 'compute_atom' will update the `aceimpl->ace->e_atom` and `aceimpl->ace->neighbours_forces(jj, alpha)` arrays + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + const int jtype = type[j]; + j &= NEIGHMASK; + delx = x[j][0] - xtmp; + dely = x[j][1] - ytmp; + delz = x[j][2] - ztmp; + + fij[0] = scale[itype][jtype]*aceimpl->ace->neighbours_forces(jj, 0); + fij[1] = scale[itype][jtype]*aceimpl->ace->neighbours_forces(jj, 1); + fij[2] = scale[itype][jtype]*aceimpl->ace->neighbours_forces(jj, 2); + + f[i][0] += fij[0]; + f[i][1] += fij[1]; + f[i][2] += fij[2]; + f[j][0] -= fij[0]; + f[j][1] -= fij[1]; + f[j][2] -= fij[2]; + + // tally per-atom virial contribution + if (vflag) + ev_tally_xyz(i, j, nlocal, newton_pair, 0.0, 0.0, + fij[0], fij[1], fij[2], + -delx, -dely, -delz); } - - // Aidan Thompson told RD (26 July 2019) that practically always holds: - // inum = nlocal - // i = ilist(ii) < inum - // j = jlist(jj) < nall - // neighborlist contains neighbor atoms plus skin atoms, - // skin atoms can be removed by setting skin to zero but here - // they are disregarded anyway - - - //determine the maximum number of neighbours - int max_jnum = -1; - int nei = 0; - for (ii = 0; ii < list->inum; ii++) { - i = ilist[ii]; - jnum = numneigh[i]; - nei = nei + jnum; - if (jnum > max_jnum) - max_jnum = jnum; + // tally energy contribution + if (eflag) { + // evdwl = energy of atom I + evdwl = scale[1][1]*aceimpl->ace->e_atom; + ev_tally_full(i, 2.0 * evdwl, 0.0, 0.0, 0.0, 0.0, 0.0); } + } - ace->resize_neighbours_cache(max_jnum); + if (vflag_fdotr) virial_fdotr_compute(); - //loop over atoms - for (ii = 0; ii < list->inum; ii++) { - i = list->ilist[ii]; - const int itype = type[i]; - - const double xtmp = x[i][0]; - const double ytmp = x[i][1]; - const double ztmp = x[i][2]; - - jlist = firstneigh[i]; - jnum = numneigh[i]; - - // checking if neighbours are actually within cutoff range is done inside compute_atom - // mapping from LAMMPS atom types ('type' array) to ACE species is done inside compute_atom - // by using 'ace->element_type_mapping' array - // x: [r0 ,r1, r2, ..., r100] - // i = 0 ,1 - // jnum(0) = 50 - // jlist(neigh ind of 0-atom) = [1,2,10,7,99,25, .. 50 element in total] - try { - ace->compute_atom(i, x, type, jnum, jlist); - } catch (exception &e) { - error->all(FLERR, e.what()); - exit(EXIT_FAILURE); - } - // 'compute_atom' will update the `ace->e_atom` and `ace->neighbours_forces(jj, alpha)` arrays - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - const int jtype = type[j]; - j &= NEIGHMASK; - delx = x[j][0] - xtmp; - dely = x[j][1] - ytmp; - delz = x[j][2] - ztmp; - - fij[0] = scale[itype][jtype]*ace->neighbours_forces(jj, 0); - fij[1] = scale[itype][jtype]*ace->neighbours_forces(jj, 1); - fij[2] = scale[itype][jtype]*ace->neighbours_forces(jj, 2); - - - f[i][0] += fij[0]; - f[i][1] += fij[1]; - f[i][2] += fij[2]; - f[j][0] -= fij[0]; - f[j][1] -= fij[1]; - f[j][2] -= fij[2]; - - // tally per-atom virial contribution - if (vflag) - ev_tally_xyz(i, j, nlocal, newton_pair, 0.0, 0.0, - fij[0], fij[1], fij[2], - -delx, -dely, -delz); - } - - // tally energy contribution - if (eflag) { - // evdwl = energy of atom I - evdwl = scale[1][1]*ace->e_atom; - ev_tally_full(i, 2.0 * evdwl, 0.0, 0.0, 0.0, 0.0, 0.0); - } - } - - if (vflag_fdotr) virial_fdotr_compute(); - - - // end modifications YL + // end modifications YL } /* ---------------------------------------------------------------------- */ void PairPACE::allocate() { - allocated = 1; - int n = atom->ntypes; + allocated = 1; + int n = atom->ntypes; - memory->create(setflag, n + 1, n + 1, "pair:setflag"); - memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); - memory->create(map, n + 1, "pair:map"); - memory->create(scale, n + 1, n + 1,"pair:scale"); + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); + memory->create(scale, n + 1, n + 1,"pair:scale"); + map = new int[n+1]; } /* ---------------------------------------------------------------------- @@ -270,41 +263,24 @@ void PairPACE::allocate() { ------------------------------------------------------------------------- */ void PairPACE::settings(int narg, char **arg) { - if (narg > 1) { - error->all(FLERR, - "Illegal pair_style command. Correct form:\n\tpair_style pace\nor\n\tpair_style pace "); - error->all(FLERR, RECURSIVE_KEYWORD); - error->all(FLERR, "or\n\tpair_style pace "); - error->all(FLERR, PRODUCT_KEYWORD); - } - recursive = true; // default evaluator style: RECURSIVE - if (narg > 0) { - if (strcmp(arg[0], RECURSIVE_KEYWORD) == 0) - recursive = true; - else if (strcmp(arg[0], PRODUCT_KEYWORD) == 0) { - recursive = false; - } else { - error->all(FLERR, - "Illegal pair_style command: pair_style pace "); - error->all(FLERR, arg[0]); - error->all(FLERR, "\nCorrect form:\n\tpair_style pace\nor\n\tpair_style pace recursive"); - } - } - - if (comm->me == 0) { - if (screen) fprintf(screen, "ACE version: %d.%d.%d\n", VERSION_YEAR, VERSION_MONTH, VERSION_DAY); - if (logfile) fprintf(logfile, "ACE version: %d.%d.%d\n", VERSION_YEAR, VERSION_MONTH, VERSION_DAY); - - if (recursive) { - if (screen) fprintf(screen, "Recursive evaluator is used\n"); - if (logfile) fprintf(logfile, "Recursive evaluator is used\n"); - } else { - if (screen) fprintf(screen, "Product evaluator is used\n"); - if (logfile) fprintf(logfile, "Product evaluator is used\n"); - } - } + if (narg > 1) + error->all(FLERR,"Illegal pair_style command."); + recursive = true; // default evaluator style: RECURSIVE + if (narg > 0) { + if (strcmp(arg[0], RECURSIVE_KEYWORD) == 0) + recursive = true; + else if (strcmp(arg[0], PRODUCT_KEYWORD) == 0) { + recursive = false; + } else error->all(FLERR,"Illegal pair_style command"); + } + if (comm->me == 0) { + utils::logmesg(lmp,fmt::format("ACE version: {}.{}.{}\n", + VERSION_YEAR, VERSION_MONTH, VERSION_DAY)); + if (recursive) utils::logmesg(lmp,"Recursive evaluator is used\n"); + else utils::logmesg(lmp,"Product evaluator is used\n"); + } } /* ---------------------------------------------------------------------- @@ -313,110 +289,64 @@ void PairPACE::settings(int narg, char **arg) { void PairPACE::coeff(int narg, char **arg) { - if (narg < 4) - error->all(FLERR, - "Incorrect args for pair coefficients. Correct form:\npair_coeff * * elem1 elem2 ..."); + if (!allocated) allocate(); - if (!allocated) allocate(); + map_element2type(narg-3,arg+3); - //number of provided elements in pair_coeff line - int ntypes_coeff = narg - 3; + char *potential_file_name = arg[2]; + char **elemtypes = &arg[3]; - if (ntypes_coeff != atom->ntypes) { - char error_message[1024]; - snprintf(error_message, 1024, - "Incorrect args for pair coefficients. You provided %d elements in pair_coeff, but structure has %d atom types", - ntypes_coeff, atom->ntypes); - error->all(FLERR, error_message); + //load potential file + aceimpl->basis_set = new ACECTildeBasisSet(); + if (comm->me == 0) + utils::logmesg(lmp,fmt::format("Loading {}\n", potential_file_name)); + aceimpl->basis_set->load(potential_file_name); + + if (comm->me == 0) { + utils::logmesg(lmp,"Total number of basis functions\n"); + + for (SPECIES_TYPE mu = 0; mu < aceimpl->basis_set->nelements; mu++) { + int n_r1 = aceimpl->basis_set->total_basis_size_rank1[mu]; + int n = aceimpl->basis_set->total_basis_size[mu]; + utils::logmesg(lmp,fmt::format("\t{}: {} (r=1) {} (r>1)\n", aceimpl->basis_set->elements_name[mu], n_r1, n)); } + } - char *type1 = arg[0]; - char *type2 = arg[1]; - char *potential_file_name = arg[2]; - char **elemtypes = &arg[3]; + // read args that map atom types to pACE elements + // map[i] = which element the Ith atom type is, -1 if not mapped + // map[0] is not used - // insure I,J args are * * + aceimpl->ace = new ACERecursiveEvaluator(); + aceimpl->ace->set_recursive(recursive); + aceimpl->ace->element_type_mapping.init(atom->ntypes + 1); - if (strcmp(type1, "*") != 0 || strcmp(type2, "*") != 0) - error->all(FLERR, "Incorrect args for pair coefficients"); + const int n = atom->ntypes; + for (int i = 1; i <= n; i++) { + char *elemname = elemtypes[i - 1]; + int atomic_number = AtomicNumberByName_pace(elemname); + if (atomic_number == -1) + error->all(FLERR,fmt::format("'{}' is not a valid element\n", elemname)); - - //load potential file - basis_set = new ACECTildeBasisSet(); - if (comm->me == 0) { - if (screen) fprintf(screen, "Loading %s\n", potential_file_name); - if (logfile) fprintf(logfile, "Loading %s\n", potential_file_name); + SPECIES_TYPE mu = aceimpl->basis_set->get_species_index_by_name(elemname); + if (mu != -1) { + if (comm->me == 0) + utils::logmesg(lmp,fmt::format("Mapping LAMMPS atom type #{}({}) -> " + "ACE species type #{}\n", i, elemname, mu)); + map[i] = mu; + aceimpl->ace->element_type_mapping(i) = mu; // set up LAMMPS atom type to ACE species mapping for ace evaluator + } else { + error->all(FLERR, fmt::format("Element {} is not supported by ACE-potential from file {}", elemname,potential_file_name)); } - basis_set->load(potential_file_name); + } - if (comm->me == 0) { - if (screen) fprintf(screen, "Total number of basis functions\n"); - if (logfile) fprintf(logfile, "Total number of basis functions\n"); - - for (SPECIES_TYPE mu = 0; mu < basis_set->nelements; mu++) { - int n_r1 = basis_set->total_basis_size_rank1[mu]; - int n = basis_set->total_basis_size[mu]; - if (screen) fprintf(screen, "\t%s: %d (r=1) %d (r>1)\n", basis_set->elements_name[mu].c_str(), n_r1, n); - if (logfile) fprintf(logfile, "\t%s: %d (r=1) %d (r>1)\n", basis_set->elements_name[mu].c_str(), n_r1, n); - } + // initialize scale factor + for (int i = 1; i <= n; i++) { + for (int j = i; j <= n; j++) { + scale[i][j] = 1.0; } + } - // read args that map atom types to pACE elements - // map[i] = which element the Ith atom type is, -1 if not mapped - // map[0] is not used - - ace = new ACERecursiveEvaluator(); - ace->set_recursive(recursive); - ace->element_type_mapping.init(atom->ntypes + 1); - - for (int i = 1; i <= atom->ntypes; i++) { - char *elemname = elemtypes[i - 1]; - int atomic_number = AtomicNumberByName_pace(elemname); - if (atomic_number == -1) { - char error_msg[1024]; - snprintf(error_msg, 1024, "String '%s' is not a valid element\n", elemname); - error->all(FLERR, error_msg); - } - SPECIES_TYPE mu = basis_set->get_species_index_by_name(elemname); - if (mu != -1) { - if (comm->me == 0) { - if (screen) - fprintf(screen, "Mapping LAMMPS atom type #%d(%s) -> ACE species type #%d\n", i, elemname, mu); - if (logfile) - fprintf(logfile, "Mapping LAMMPS atom type #%d(%s) -> ACE species type #%d\n", i, elemname, mu); - } - map[i] = mu; - ace->element_type_mapping(i) = mu; // set up LAMMPS atom type to ACE species mapping for ace evaluator - } else { - char error_msg[1024]; - snprintf(error_msg, 1024, "Element %s is not supported by ACE-potential from file %s", elemname, - potential_file_name); - error->all(FLERR, error_msg); - } - } - - // clear setflag since coeff() called once with I,J = * * - int n = atom->ntypes; - for (int i = 1; i <= n; i++) { - for (int j = i; j <= n; j++) { - setflag[i][j] = 1; - scale[i][j] = 1.0; - } - } - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 1; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); - - ace->set_basis(*basis_set, 1); + aceimpl->ace->set_basis(*aceimpl->basis_set, 1); } /* ---------------------------------------------------------------------- @@ -424,15 +354,15 @@ void PairPACE::coeff(int narg, char **arg) { ------------------------------------------------------------------------- */ void PairPACE::init_style() { - if (atom->tag_enable == 0) - error->all(FLERR, "Pair style pACE requires atom IDs"); - if (force->newton_pair == 0) - error->all(FLERR, "Pair style pACE requires newton pair on"); + if (atom->tag_enable == 0) + error->all(FLERR, "Pair style pACE requires atom IDs"); + if (force->newton_pair == 0) + error->all(FLERR, "Pair style pACE requires newton pair on"); - // request a full neighbor list - int irequest = neighbor->request(this, instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + // request a full neighbor list + int irequest = neighbor->request(this, instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; } /* ---------------------------------------------------------------------- @@ -440,10 +370,10 @@ void PairPACE::init_style() { ------------------------------------------------------------------------- */ double PairPACE::init_one(int i, int j) { - if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); - //cutoff from the basis set's radial functions settings - scale[j][i] = scale[i][j]; - return basis_set->radial_functions->cut(map[i], map[j]); + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); + //cutoff from the basis set's radial functions settings + scale[j][i] = scale[i][j]; + return aceimpl->basis_set->radial_functions->cut(map[i], map[j]); } /* ---------------------------------------------------------------------- @@ -451,8 +381,8 @@ double PairPACE::init_one(int i, int j) { ---------------------------------------------------------------------- */ void *PairPACE::extract(const char *str, int &dim) { - dim = 2; - if (strcmp(str,"scale") == 0) return (void *) scale; - return NULL; + dim = 2; + if (strcmp(str,"scale") == 0) return (void *) scale; + return nullptr; } diff --git a/src/USER-PACE/pair_pace.h b/src/USER-PACE/pair_pace.h index 76b08a65c0..b29ee3a7a9 100644 --- a/src/USER-PACE/pair_pace.h +++ b/src/USER-PACE/pair_pace.h @@ -39,58 +39,30 @@ PairStyle(pace,PairPACE) #define LMP_PAIR_PACE_H #include "pair.h" -#include "ace_evaluator.h" -#include "ace_recursive.h" -#include "ace_c_basis.h" namespace LAMMPS_NS { - class PairPACE : public Pair { - public: - PairPACE(class LAMMPS *); +class PairPACE : public Pair { + public: + PairPACE(class LAMMPS *); + virtual ~PairPACE(); - virtual ~PairPACE(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + virtual void init_style(); + double init_one(int, int); - virtual void compute(int, int); + void *extract(const char *, int &); - void settings(int, char **); + protected: + struct ACEImpl *aceimpl; - void coeff(int, char **); - - virtual void init_style(); - - double init_one(int, int); - - void *extract(const char *, int &); - - // virtual double memory_usage(); - - protected: - ACECTildeBasisSet *basis_set = nullptr; - - ACERecursiveEvaluator *ace = nullptr; - - char *potential_file_name; - - virtual void allocate(); - - void read_files(char *, char *); - - inline int equal(double *x, double *y); - - - double rcutmax; // max cutoff for all elements - int nelements; // # of unique elements - char **elements; // names of unique elements - - int *map; // mapping from atom types to elements - int *jlist_local; - int *type_local; - double **scale; - - bool recursive = false; // "recursive" option for ACERecursiveEvaluator - }; + virtual void allocate(); + double **scale; + bool recursive; // "recursive" option for ACERecursiveEvaluator +}; } #endif From bd6dd658d6b037c03203d413fdff71f358cbc15b Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Wed, 7 Apr 2021 17:21:16 -0600 Subject: [PATCH 0436/1217] Updating to master, misc style changes --- src/USER-OMP/npair_full_multi_omp.cpp | 2 +- src/USER-OMP/npair_half_multi_newtoff_omp.cpp | 4 +- src/USER-OMP/npair_half_multi_newton_omp.cpp | 8 +- .../npair_half_multi_newton_tri_omp.cpp | 4 +- src/comm.cpp | 18 ++-- src/comm_brick.cpp | 26 ++--- src/comm_tiled.cpp | 22 ++--- src/nbin_multi.cpp | 2 +- src/neighbor.cpp | 98 +++++++++---------- src/npair_half_multi_newtoff.cpp | 4 +- src/npair_half_multi_newton.cpp | 4 +- src/npair_half_multi_newton_tri.cpp | 2 +- src/npair_half_size_multi_newtoff.cpp | 4 +- src/npair_half_size_multi_newton.cpp | 8 +- src/npair_half_size_multi_newton_tri.cpp | 4 +- src/nstencil.cpp | 6 +- src/pair_hybrid.cpp | 8 +- 17 files changed, 112 insertions(+), 112 deletions(-) diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp index 4fc6fb4a68..a6df0c6dbe 100755 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -98,7 +98,7 @@ void NPairFullMultiOmp::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // loop over all atoms in surrounding bins in stencil including self diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp index ed0e770b2f..bf5d5efa69 100755 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -100,7 +100,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // loop over all atoms in other bins in stencil including self @@ -114,7 +114,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; - for (j = js; j >=0; j = bins[j]) { + for (j = js; j >= 0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index 13d286ab5b..00e4b6c624 100755 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -99,13 +99,13 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // if same size: uses half stencil so check central bin - if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - if(icollection == jcollection) js = bins[i]; + if (icollection == jcollection) js = bins[i]; else js = binhead_multi[jcollection][jbin]; // if same collection, @@ -117,7 +117,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) // if j is ghost, only store if j coords are "above and to the right" of i for (j = js; j >= 0; j = bins[j]) { - if(icollection != jcollection and j < i) continue; + if ((icollection != jcollection) && (j < i)) continue; if (j >= nlocal) { if (x[j][2] < ztmp) continue; diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index cb758673d4..31e7635414 100755 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -100,7 +100,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // loop over all atoms in bins in stencil @@ -120,7 +120,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) for (j = js; j >= 0; j = bins[j]) { // if same size (same collection), use half stencil - if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/comm.cpp b/src/comm.cpp index 7e3d6d839b..dc6d75dd79 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -246,15 +246,15 @@ void Comm::init() for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; - if(mode == Comm::MULTI and neighbor->style != Neighbor::MULTI) + if ((mode == Comm::MULTI) && (neighbor->style != Neighbor::MULTI)) error->all(FLERR,"Cannot use comm mode multi without multi-style neighbor lists"); - if(multi_reduce){ + if (multi_reduce) { if (force->newton == 0) error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); if (neighbor->any_full()) error->all(FLERR,"Cannot use multi/reduce communication with a full neighbor list"); - if(mode != Comm::MULTI) + if (mode != Comm::MULTI) error->all(FLERR,"Cannot use multi/reduce communication without mode multi"); } } @@ -293,11 +293,11 @@ void Comm::modify_params(int narg, char **arg) // need to reset cutghostuser when switching comm mode if (mode == Comm::MULTI) cutghostuser = 0.0; if (mode == Comm::MULTIOLD) cutghostuser = 0.0; - if(cutusermulti){ + if (cutusermulti) { memory->destroy(cutusermulti); cutusermulti = nullptr; } - if(cutusermultiold){ + if (cutusermultiold) { memory->destroy(cutusermultiold); cutusermultiold = nullptr; } @@ -306,7 +306,7 @@ void Comm::modify_params(int narg, char **arg) // need to reset cutghostuser when switching comm mode if (mode == Comm::SINGLE) cutghostuser = 0.0; if (mode == Comm::MULTIOLD) cutghostuser = 0.0; - if(cutusermultiold){ + if (cutusermultiold) { memory->destroy(cutusermultiold); cutusermultiold = nullptr; } @@ -315,7 +315,7 @@ void Comm::modify_params(int narg, char **arg) // need to reset cutghostuser when switching comm mode if (mode == Comm::SINGLE) cutghostuser = 0.0; if (mode == Comm::MULTI) cutghostuser = 0.0; - if(cutusermulti){ + if (cutusermulti) { memory->destroy(cutusermulti); cutusermulti = nullptr; } @@ -743,8 +743,8 @@ double Comm::get_comm_cutoff() } // Check maximum interval size for neighbor multi - if(neighbor->interval_collection_flag){ - for(int i = 0; i < neighbor->ncollections; i++){ + if (neighbor->interval_collection_flag) { + for (int i = 0; i < neighbor->ncollections; i++){ maxcommcutoff = MAX(maxcommcutoff, neighbor->collection2cut[i]); } } diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 50c18e5fe7..b6306eb042 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -145,9 +145,9 @@ void CommBrick::init() ncollections = neighbor->ncollections; allocate_multi(maxswap); memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); - if(cutusermultiflag) { + if (cutusermultiflag) { memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); - for(int i = ncollections_prior; i < ncollections; i++) + for (int i = ncollections_prior; i < ncollections; i++) cutusermulti[i] = -1.0; } @@ -206,15 +206,15 @@ void CommBrick::setup() ncollections = neighbor->ncollections; // reallocate memory for multi-style communication at setup if ncollections change - if(ncollections_prior != ncollections){ - if(multilo) free_multi(); - if(cutghostmulti) memory->destroy(cutghostmulti); + if (ncollections_prior != ncollections) { + if (multilo) free_multi(); + if (cutghostmulti) memory->destroy(cutghostmulti); allocate_multi(maxswap); memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); - if(cutusermultiflag) { + if (cutusermultiflag) { memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); - for(i = ncollections_prior; i < ncollections; i++) + for (i = ncollections_prior; i < ncollections; i++) cutusermulti[i] = -1.0; } @@ -223,11 +223,11 @@ void CommBrick::setup() // parse any cutoff/multi commands int nhi, nlo; - for(auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { + for (auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { utils::bounds(FLERR,it->first,0,ncollections,nlo,nhi,error); - if(nhi >= ncollections) + if (nhi >= ncollections) error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command"); - for (j=nlo; j<=nhi; ++j) + for (j = nlo; j<=nhi; ++j) cutusermulti[j] = it->second; } usermultiargs.clear(); @@ -249,7 +249,7 @@ void CommBrick::setup() } for (j = 0; j < ncollections; j++){ - if(multi_reduce and cutcollectionsq[j][j] > cutcollectionsq[i][i]) continue; + if (multi_reduce && (cutcollectionsq[j][j] > cutcollectionsq[i][i])) continue; cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j])); cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j])); cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j])); @@ -815,7 +815,7 @@ void CommBrick::borders() AtomVec *avec = atom->avec; // After exchanging/sorting, need to reconstruct collection array for border communication - if(mode == Comm::MULTI) neighbor->build_collection(0); + if (mode == Comm::MULTI) neighbor->build_collection(0); // do swaps over all 3 dimensions @@ -989,7 +989,7 @@ void CommBrick::borders() firstrecv[iswap] = atom->nlocal + atom->nghost; nprior = atom->nlocal + atom->nghost; atom->nghost += nrecv; - if(neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); + if (neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); iswap++; } diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 27f630f720..da3bb3a65f 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -191,16 +191,16 @@ void CommTiled::setup() ncollections = neighbor->ncollections; // allocate memory for multi-style communication at setup as ncollections can change - if(ncollections_prior != ncollections){ + if (ncollections_prior != ncollections) { memory->destroy(cutghostmulti); if (mode == Comm::MULTI) memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); - for(i = 0; i < maxswap; i ++) + for (i = 0; i < maxswap; i ++) grow_swap_send_multi(i,DELTA_PROCS); - if(cutusermultiflag){ + if (cutusermultiflag) { memory->grow(cutusermulti,ncollections,"comm:cutusermulti"); - for(i = ncollections_prior; i < ncollections; i++) + for (i = ncollections_prior; i < ncollections; i++) cutusermulti[i] = -1.0; } @@ -209,12 +209,12 @@ void CommTiled::setup() // parse any cutoff/multi commands int nhi, nlo; - for(auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { + for (auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) { utils::bounds(FLERR,it->first,0,ncollections,nlo,nhi,error); - if(nhi >= ncollections) + if (nhi >= ncollections) error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command"); - for (j=nlo; j<=nhi; ++j) + for (j = nlo; j <= nhi; ++j) cutusermulti[j] = it->second; } usermultiargs.clear(); @@ -236,7 +236,7 @@ void CommTiled::setup() } for (j = 0; j < ncollections; j++){ - if(multi_reduce and cutcollectionsq[j][j] > cutcollectionsq[i][i]) continue; + if (multi_reduce && (cutcollectionsq[j][j] > cutcollectionsq[i][i])) continue; cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j])); cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j])); cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j])); @@ -1066,7 +1066,7 @@ void CommTiled::borders() AtomVec *avec = atom->avec; // After exchanging, need to reconstruct collection array for border communication - if(mode == Comm::MULTI) neighbor->build_collection(0); + if (mode == Comm::MULTI) neighbor->build_collection(0); // send/recv max one = max # of atoms in single send/recv for any swap // send/recv max all = max # of atoms in all sends/recvs within any swap @@ -1357,7 +1357,7 @@ void CommTiled::borders() if (n) { nprior = atom->nghost + atom->nlocal; atom->nghost += forward_recv_offset[iswap][n-1] + recvnum[iswap][n-1]; - if(neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); + if (neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); } } @@ -2405,7 +2405,7 @@ void CommTiled::grow_swap_send_multi(int i, int n) { memory->destroy(sendbox_multi[i]); - if(ncollections > 0) + if (ncollections > 0) memory->create(sendbox_multi[i],n,ncollections,6,"comm:sendbox_multi"); } diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index a39f10d074..3bfe26239b 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -234,7 +234,7 @@ void NBinMulti::setup_bins(int /*style*/) if (binsize_optimal*bininvx_multi[n] > CUT2BIN_RATIO || binsize_optimal*bininvy_multi[n] > CUT2BIN_RATIO) error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); - if(dimension == 3 and binsize_optimal*bininvz_multi[n] > CUT2BIN_RATIO) + if ((dimension == 3) && (binsize_optimal*bininvz_multi[n] > CUT2BIN_RATIO)) error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); // mbinlo/hi = lowest and highest global bins my ghost atoms could be in diff --git a/src/neighbor.cpp b/src/neighbor.cpp index def4cbd228..5a4c574ce9 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -359,16 +359,16 @@ void Neighbor::init() cutneighmaxsq = cutneighmax * cutneighmax; // Define cutoffs for multi - if(style == Neighbor::MULTI){ + if (style == Neighbor::MULTI) { int icollection, jcollection; // If collections not yet defined, create default map using types - if(not custom_collection_flag) { + if (not custom_collection_flag) { ncollections = n; interval_collection_flag = 0; - if(not type2collection) + if (not type2collection) memory->create(type2collection,n+1,"neigh:type2collection"); - for(i = 1; i <= n; i++) + for (i = 1; i <= n; i++) type2collection[i] = i-1; } @@ -384,30 +384,30 @@ void Neighbor::init() // // Define collection cutoffs - for(i = 0; i < ncollections; i++) - for(j = 0; j < ncollections; j++) + for (i = 0; i < ncollections; i++) + for (j = 0; j < ncollections; j++) cutcollectionsq[i][j] = 0.0; - if(not interval_collection_flag){ + if (not interval_collection_flag) { finite_cut_flag = 0; - for(i = 1; i <= n; i++){ + for (i = 1; i <= n; i++){ icollection = type2collection[i]; - for(j = 1; j <= n; j++){ + for (j = 1; j <= n; j++){ jcollection = type2collection[j]; - if(cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) { + if (cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) { cutcollectionsq[icollection][jcollection] = cutneighsq[i][j]; cutcollectionsq[jcollection][icollection] = cutneighsq[i][j]; } } } } else { - if(force->pair->finitecutflag){ + if (force->pair->finitecutflag) { finite_cut_flag = 1; // If cutoffs depend on finite atom sizes, use radii of intervals to find cutoffs double ri, rj, tmp; - for(i = 0; i < ncollections; i++){ + for (i = 0; i < ncollections; i++){ ri = collection2cut[i]*0.5; - for(j = 0; j < ncollections; j++){ + for (j = 0; j < ncollections; j++){ rj = collection2cut[j]*0.5; tmp = force->pair->radii2cut(ri, rj) + skin; cutcollectionsq[i][j] = tmp*tmp; @@ -417,33 +417,33 @@ void Neighbor::init() finite_cut_flag = 0; // Map types to collections - if(not type2collection) + if (not type2collection) memory->create(type2collection,n+1,"neigh:type2collection"); - for(i = 1; i <= n; i++) + for (i = 1; i <= n; i++) type2collection[i] = -1; double cuttmp; - for(i = 1; i <= n; i++){ + for (i = 1; i <= n; i++){ // Remove skin added to cutneighsq cuttmp = sqrt(cutneighsq[i][i]) - skin; - for(icollection = 0; icollection < ncollections; icollection ++){ - if(collection2cut[icollection] >= cuttmp) { + for (icollection = 0; icollection < ncollections; icollection ++){ + if (collection2cut[icollection] >= cuttmp) { type2collection[i] = icollection; break; } } - if(type2collection[i] == -1) + if (type2collection[i] == -1) error->all(FLERR, "Pair cutoff exceeds interval cutoffs for multi"); } // Define cutoffs - for(i = 1; i <= n; i++){ + for (i = 1; i <= n; i++){ icollection = type2collection[i]; - for(j = 1; j <= n; j++){ + for (j = 1; j <= n; j++){ jcollection = type2collection[j]; - if(cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) { + if (cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) { cutcollectionsq[icollection][jcollection] = cutneighsq[i][j]; cutcollectionsq[jcollection][icollection] = cutneighsq[i][j]; } @@ -2175,7 +2175,7 @@ void Neighbor::build(int topoflag) int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; // rebuild collection array from scratch - if(style == Neighbor::MULTI) build_collection(0); + if (style == Neighbor::MULTI) build_collection(0); // check that using special bond flags will not overflow neigh lists @@ -2500,15 +2500,15 @@ void Neighbor::modify_params(int narg, char **arg) } else error->all(FLERR,"Illegal neigh_modify command"); } else if (strcmp(arg[iarg],"collection/interval") == 0) { - if(style != Neighbor::MULTI) + if (style != Neighbor::MULTI) error->all(FLERR,"Cannot use collection/interval command without multi setting"); - if(iarg+2 > narg) + if (iarg+2 > narg) error->all(FLERR,"Invalid collection/interval command"); ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); - if(ncollections < 1) + if (ncollections < 1) error->all(FLERR,"Invalid collection/interval command"); - if(iarg+1+ncollections > narg) + if (iarg+1+ncollections > narg) error->all(FLERR,"Invalid collection/interval command"); int ntypes = atom->ntypes; @@ -2521,26 +2521,26 @@ void Neighbor::modify_params(int narg, char **arg) // Set upper cutoff for each collection char *id; double cut_interval; - for(i = 0; i < ncollections; i++){ + for (i = 0; i < ncollections; i++){ cut_interval = utils::numeric(FLERR,arg[iarg+2+i],false,lmp); collection2cut[i] = cut_interval; - if(i != 0) - if(collection2cut[i-1] >= collection2cut[i]) + if (i != 0) + if (collection2cut[i-1] >= collection2cut[i]) error->all(FLERR,"Nonsequential interval cutoffs in collection/interval setting"); } iarg += 2 + ncollections; } else if (strcmp(arg[iarg],"collection/type") == 0) { - if(style != Neighbor::MULTI) + if (style != Neighbor::MULTI) error->all(FLERR,"Cannot use collection/type command without multi setting"); - if(iarg+2 > narg) + if (iarg+2 > narg) error->all(FLERR,"Invalid collection/type command"); ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); - if(ncollections < 1) + if (ncollections < 1) error->all(FLERR,"Invalid collection/interval command"); - if(iarg+1+ncollections > narg) + if (iarg+1+ncollections > narg) error->all(FLERR,"Invalid collection/type command"); int ntypes = atom->ntypes; @@ -2548,17 +2548,17 @@ void Neighbor::modify_params(int narg, char **arg) interval_collection_flag = 0; custom_collection_flag = 1; - if(not type2collection) + if (not type2collection) memory->create(type2collection,ntypes+1,"neigh:type2collection"); // Erase previous mapping - for(i = 1; i <= ntypes; i++) + for (i = 1; i <= ntypes; i++) type2collection[i] = -1; // For each custom range, define mapping for types in interval int nfield; char *str; - for(i = 0; i < ncollections; i++){ + for (i = 0; i < ncollections; i++){ n = strlen(arg[iarg+2+i]) + 1; str = new char[n]; strcpy(str,arg[iarg+2+i]); @@ -2570,7 +2570,7 @@ void Neighbor::modify_params(int narg, char **arg) utils::bounds(FLERR,field,1,ntypes,nlo,nhi,error); for (k = nlo; k <= nhi; k++) { - if(type2collection[k] != -1) + if (type2collection[k] != -1) error->all(FLERR,"Type specified more than once in collection/type commnd"); type2collection[k] = i; } @@ -2580,8 +2580,8 @@ void Neighbor::modify_params(int narg, char **arg) } // Check for undefined atom type - for(i = 1; i <= ntypes; i++){ - if(type2collection[i] == -1){ + for (i = 1; i <= ntypes; i++){ + if (type2collection[i] == -1) { error->all(FLERR,"Type missing in collection/type commnd"); } } @@ -2632,8 +2632,8 @@ int Neighbor::exclude_setting() int Neighbor::any_full() { int any_full = 0; - for(int i = 0; i < old_nrequest; i++) { - if(old_requests[i]->full) any_full = 1; + for (int i = 0; i < old_nrequest; i++) { + if (old_requests[i]->full) any_full = 1; } return any_full; } @@ -2648,31 +2648,31 @@ void Neighbor::build_collection(int istart) error->all(FLERR, "Cannot define atom collections without neighbor style multi"); int nmax = atom->nlocal+atom->nghost; - if(nmax > nmax_collection){ + if (nmax > nmax_collection) { nmax_collection = nmax+DELTA_PERATOM; memory->grow(collection, nmax_collection, "neigh:collection"); } - if(finite_cut_flag){ + if (finite_cut_flag) { double cut; int icollection; - for(int i = istart; i < nmax; i++){ + for (int i = istart; i < nmax; i++){ cut = force->pair->atom2cut(i); collection[i] = -1; - for(icollection = 0; icollection < ncollections; icollection++){ - if(collection2cut[icollection] >= cut) { + for (icollection = 0; icollection < ncollections; icollection++){ + if (collection2cut[icollection] >= cut) { collection[i] = icollection; break; } } - if(collection[i] == -1) + if (collection[i] == -1) error->one(FLERR, "Atom cutoff exceeds interval cutoffs for multi"); } } else { int *type = atom->type; - for(int i = istart; i < nmax; i++){ + for (int i = istart; i < nmax; i++){ collection[i] = type2collection[type[i]]; } } diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp index 5f050429ac..e1f66800dc 100755 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -88,7 +88,7 @@ void NPairHalfMultiNewtoff::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // loop over all atoms in other bins in stencil including self @@ -102,7 +102,7 @@ void NPairHalfMultiNewtoff::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; - for (j = js; j >=0; j = bins[j]) { + for (j = js; j >= 0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index 18e66d4adb..4cf30f0ce5 100755 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -93,7 +93,7 @@ void NPairHalfMultiNewton::build(NeighList *list) // if same size: uses half stencil so check central bin if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - if(icollection == jcollection) js = bins[i]; + if (icollection == jcollection) js = bins[i]; else js = binhead_multi[jcollection][jbin]; // if same collection, @@ -105,7 +105,7 @@ void NPairHalfMultiNewton::build(NeighList *list) // if j is ghost, only store if j coords are "above and to the right" of i for (j = js; j >= 0; j = bins[j]) { - if(icollection != jcollection and j < i) continue; + if((icollection != jcollection) && (j < i)) continue; if (j >= nlocal) { if (x[j][2] < ztmp) continue; diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp index 90c6cf714d..556529eba6 100755 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -87,7 +87,7 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // loop over all atoms in bins in stencil diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp index 77aa4f746b..23ea27b209 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -79,7 +79,7 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // loop over all atoms in other bins in stencil including self @@ -93,7 +93,7 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) for (k = 0; k < ns; k++) { js = binhead_multi[jcollection][jbin + s[k]]; - for (j = js; j >=0; j = bins[j]) { + for (j = js; j >= 0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index 67715ebe68..50db6c19ec 100755 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -76,13 +76,13 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // if same size: uses half stencil so check central bin - if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ - if(icollection == jcollection) js = bins[i]; + if (icollection == jcollection) js = bins[i]; else js = binhead_multi[jcollection][jbin]; // if same collection, @@ -94,7 +94,7 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) // if j is ghost, only store if j coords are "above and to the right" of i for (j = js; j >= 0; j = bins[j]) { - if(icollection != jcollection and j < i) continue; + if ((icollection != jcollection) && (j < i)) continue; if (j >= nlocal) { if (x[j][2] < ztmp) continue; diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 2bf033781e..290c8c76f4 100755 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -76,7 +76,7 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) for (jcollection = 0; jcollection < ncollections; jcollection++) { // if same collection use own bin - if(icollection == jcollection) jbin = ibin; + if (icollection == jcollection) jbin = ibin; else jbin = coord2bin(x[i], jcollection); // loop over all atoms in bins in stencil @@ -96,7 +96,7 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) for (j = js; j >= 0; j = bins[j]) { // if same size (same collection), use half stencil - if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; diff --git a/src/nstencil.cpp b/src/nstencil.cpp index ba7259a9fc..729b690ba1 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -272,10 +272,10 @@ void NStencil::create_setup() double stencil_range; int n = ncollections; - if(nb) copy_bin_info_multi(); + if (nb) copy_bin_info_multi(); // Deallocate arrays if previously allocated - if(n > maxcollections and stencil_multi){ + if((n > maxcollections) && stencil_multi){ memory->destroy(nstencil_multi); for (i = 0; i < maxcollections; i++) { for (j = 0; j < maxcollections; j++) @@ -299,7 +299,7 @@ void NStencil::create_setup() } // Allocate arrays - if(!maxstencil_multi) { + if (!maxstencil_multi) { memory->create(flag_half_multi, n, n, "neighstencil:flag_half_multi"); memory->create(flag_skip_multi, n, n, diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 6e8b55fd67..075290ef38 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -1083,9 +1083,9 @@ double PairHybrid::atom2cut(int i) cut = 0.0; for (int m = 0; m < nstyles; m++) { - if (styles[m]->finitecutflag){ + if (styles[m]->finitecutflag) { temp = styles[m]->atom2cut(i); - if(temp > cut) cut = temp; + if (temp > cut) cut = temp; } } return cut; @@ -1101,9 +1101,9 @@ double PairHybrid::radii2cut(double r1, double r2) cut = 0.0; for (int m = 0; m < nstyles; m++) { - if (styles[m]->finitecutflag){ + if (styles[m]->finitecutflag) { temp = styles[m]->radii2cut(r1,r2); - if(temp > cut) cut = temp; + if (temp > cut) cut = temp; } } return cut; From b57025523f58da4ceab22319986e06db4e29ac6a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 19:28:02 -0400 Subject: [PATCH 0437/1217] honor LAMMPS_POTENTIALS environment variable when loading potential file --- src/USER-PACE/pair_pace.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index 527f2a6f06..41551e454c 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -293,7 +293,7 @@ void PairPACE::coeff(int narg, char **arg) { map_element2type(narg-3,arg+3); - char *potential_file_name = arg[2]; + auto potential_file_name = utils::get_potential_file_path(arg[2]); char **elemtypes = &arg[3]; //load potential file From f6f383bf99b33e745be64d6734dd204d87a009f5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 19:29:22 -0400 Subject: [PATCH 0438/1217] add .gitignore file to lib/pace folder --- lib/pace/.gitignore | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 lib/pace/.gitignore diff --git a/lib/pace/.gitignore b/lib/pace/.gitignore new file mode 100644 index 0000000000..0598083baa --- /dev/null +++ b/lib/pace/.gitignore @@ -0,0 +1,2 @@ +/src +/libpace.a From 8a233a5ec77292123670e5e0856bd032530e0fad Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 19:30:38 -0400 Subject: [PATCH 0439/1217] add unit test reference data for USER-PACE --- .../tests/manybody-pair-pace_product.yaml | 156 ++++++++++++++++++ .../tests/manybody-pair-pace_recursive.yaml | 156 ++++++++++++++++++ 2 files changed, 312 insertions(+) create mode 100644 unittest/force-styles/tests/manybody-pair-pace_product.yaml create mode 100644 unittest/force-styles/tests/manybody-pair-pace_recursive.yaml diff --git a/unittest/force-styles/tests/manybody-pair-pace_product.yaml b/unittest/force-styles/tests/manybody-pair-pace_product.yaml new file mode 100644 index 0000000000..21c37c49be --- /dev/null +++ b/unittest/force-styles/tests/manybody-pair-pace_product.yaml @@ -0,0 +1,156 @@ +--- +lammps_version: 10 Mar 2021 +date_generated: Wed Apr 7 19:29:52 2021 +epsilon: 5e-13 +skip_tests: +prerequisites: ! | + pair pace +pre_commands: ! | + variable newton_pair delete + variable newton_pair index on +post_commands: ! "" +input_file: in.manybody +pair_style: pace product +pair_coeff: ! | + * * Cu-PBE-core-rep.ace Cu Cu Cu Cu Cu Cu Cu Cu +extract: ! 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6.9831995565982619e-01 -2.3722369658580467e-01 + 62 -1.1615014571620641e+00 1.1805918165226632e+00 -9.2596032516965732e-01 + 63 9.6753599487408937e-01 -1.4353996747437299e+00 -6.7618187950266095e-01 + 64 1.3730994742564451e+00 1.5481237027388630e+00 2.7374902138995694e+00 +... diff --git a/unittest/force-styles/tests/manybody-pair-pace_recursive.yaml b/unittest/force-styles/tests/manybody-pair-pace_recursive.yaml new file mode 100644 index 0000000000..43b52a5391 --- /dev/null +++ b/unittest/force-styles/tests/manybody-pair-pace_recursive.yaml @@ -0,0 +1,156 @@ +--- +lammps_version: 10 Mar 2021 +date_generated: Wed Apr 7 19:30:07 2021 +epsilon: 5e-13 +skip_tests: +prerequisites: ! | + pair pace +pre_commands: ! | + variable newton_pair delete + variable newton_pair index on +post_commands: ! "" +input_file: in.manybody +pair_style: pace recursive +pair_coeff: ! | + * * Cu-PBE-core-rep.ace Cu Cu Cu Cu Cu Cu Cu Cu +extract: ! 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From a84ac392a34c7e3f6d33e8fc5aea33ac8963ac40 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 23:25:22 -0400 Subject: [PATCH 0440/1217] silence compiler warnings --- src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index 2247a9467c..d1f9d33e8a 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -581,7 +581,7 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype, { double r2inv,r6inv,r,grij,expm2,t,erfc1,prefactor,prefactor2; double fraction,table,forcecoul,forcecoul2,forcelj; - double rrij,expn2,erfc2,expb,ecoul,evdwl,trx,tr,ftr; + double rrij,expn2,erfc2,ecoul,evdwl,trx,tr,ftr; int itable; From 1ca38db9dfde1b3c34bf9e1eb804f484f8dcc753 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 23:26:21 -0400 Subject: [PATCH 0441/1217] simplify and avoid temporary buffers when piping to/from gzip --- src/dump.cpp | 32 ++++++++++++++----------------- src/fix_tmd.cpp | 49 ++++++++++++++++++++++------------------------- src/library.cpp | 15 +++++---------- src/read_data.cpp | 16 +++++++++------- src/reader.cpp | 16 +++++++++------- 5 files changed, 60 insertions(+), 68 deletions(-) diff --git a/src/dump.cpp b/src/dump.cpp index 031364dada..c483d90fc3 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -14,16 +14,16 @@ #include "dump.h" #include "atom.h" -#include "irregular.h" -#include "update.h" -#include "domain.h" -#include "group.h" -#include "output.h" -#include "modify.h" -#include "fix.h" #include "compute.h" -#include "memory.h" +#include "domain.h" #include "error.h" +#include "fix.h" +#include "group.h" +#include "irregular.h" +#include "memory.h" +#include "modify.h" +#include "output.h" +#include "update.h" #include @@ -141,12 +141,9 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp) if (strchr(filename,'*')) multifile = 1; - char *suffix = filename + strlen(filename) - strlen(".bin"); - if (suffix > filename && strcmp(suffix,".bin") == 0) binary = 1; - suffix = filename + strlen(filename) - strlen(".gz"); - if (suffix > filename && strcmp(suffix,".gz") == 0) compressed = 1; - suffix = filename + strlen(filename) - strlen(".zst"); - if (suffix > filename && strcmp(suffix,".zst") == 0) compressed = 1; + if (utils::strmatch(filename, "\\.bin$")) binary = 1; + if (utils::strmatch(filename, "\\.gz$") + || utils::strmatch(filename, "\\.zst$")) compressed = 1; } /* ---------------------------------------------------------------------- */ @@ -582,12 +579,11 @@ void Dump::openfile() if (filewriter) { if (compressed) { #ifdef LAMMPS_GZIP - char gzip[128]; - sprintf(gzip,"gzip -6 > %s",filecurrent); + auto gzip = fmt::format("gzip -6 > {}",filecurrent); #ifdef _WIN32 - fp = _popen(gzip,"wb"); + fp = _popen(gzip.c_str(),"wb"); #else - fp = popen(gzip,"w"); + fp = popen(gzip.c_str(),"w"); #endif #else error->one(FLERR,"Cannot open gzipped file"); diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index 8cff132c63..f462b0633b 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -18,19 +18,18 @@ #include "fix_tmd.h" +#include "atom.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "respa.h" +#include "update.h" + #include #include -#include "atom.h" -#include "update.h" -#include "modify.h" -#include "domain.h" -#include "group.h" -#include "respa.h" -#include "force.h" -#include "memory.h" -#include "error.h" - - using namespace LAMMPS_NS; using namespace FixConst; @@ -520,31 +519,29 @@ void FixTMD::readfile(char *file) void FixTMD::open(char *file) { - compressed = 0; - char *suffix = file + strlen(file) - 3; - if (suffix > file && strcmp(suffix,".gz") == 0) compressed = 1; - if (!compressed) fp = fopen(file,"r"); - else { + if (utils::strmatch(file,"\\.gz$")) { + compressed = 1; + #ifdef LAMMPS_GZIP - char gunzip[128]; - snprintf(gunzip,128,"gzip -c -d %s",file); + auto gunzip = fmt::format("gzip -c -d {}",file); #ifdef _WIN32 - fp = _popen(gunzip,"rb"); + fp = _popen(gunzip.c_str(),"rb"); #else - fp = popen(gunzip,"r"); + fp = popen(gunzip.c_str(),"r"); #endif #else - error->one(FLERR,"Cannot open gzipped file"); + error->one(FLERR,"Cannot open gzipped file without gzip support"); #endif + } else { + compressed = 0; + fp = fopen(file,"r"); } - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open file %s",file); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,fmt::format("Cannot open file {}: {}", + file, utils::getsyserror())); } /* ---------------------------------------------------------------------- */ diff --git a/src/library.cpp b/src/library.cpp index b72c8d7220..300aafc293 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -4734,19 +4734,14 @@ void lammps_set_fix_external_callback(void *handle, char *id, FixExternalFnPtr c BEGIN_CAPTURE { int ifix = lmp->modify->find_fix(id); - if (ifix < 0) { - char str[128]; - snprintf(str, 128, "Can not find fix with ID '%s'!", id); - lmp->error->all(FLERR,str); - } + if (ifix < 0) + lmp->error->all(FLERR,fmt::format("Cannot find fix with ID '{}'!", id)); Fix *fix = lmp->modify->fix[ifix]; - if (strcmp("external",fix->style) != 0) { - char str[128]; - snprintf(str, 128, "Fix '%s' is not of style external!", id); - lmp->error->all(FLERR,str); - } + if (strcmp("external",fix->style) != 0) + lmp->error->all(FLERR,fmt::format("Fix '{}' is not of style " + "external!", id)); FixExternal * fext = (FixExternal*) fix; fext->set_callback(callback, caller); diff --git a/src/read_data.cpp b/src/read_data.cpp index 09fb8f3eae..cc3b2e5965 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -1954,13 +1954,12 @@ int ReadData::reallocate(int **pcount, int cmax, int amax) void ReadData::open(char *file) { - compressed = 0; - char *suffix = file + strlen(file) - 3; - if (suffix > file && strcmp(suffix,".gz") == 0) compressed = 1; - if (!compressed) fp = fopen(file,"r"); - else { + if (utils::strmatch(file,"\\.gz$")) { + compressed = 1; + #ifdef LAMMPS_GZIP - std::string gunzip = fmt::format("gzip -c -d {}",file); + auto gunzip = fmt::format("gzip -c -d {}",file); + #ifdef _WIN32 fp = _popen(gunzip.c_str(),"rb"); #else @@ -1968,8 +1967,11 @@ void ReadData::open(char *file) #endif #else - error->one(FLERR,"Cannot open gzipped file: " + utils::getsyserror()); + error->one(FLERR,"Cannot open gzipped file without gzip support"); #endif + } else { + compressed = 0; + fp = fopen(file,"r"); } if (fp == nullptr) diff --git a/src/reader.cpp b/src/reader.cpp index a4bc8d816f..c22a9f7e5d 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -37,13 +37,12 @@ void Reader::open_file(const char *file) { if (fp != nullptr) close_file(); - compressed = 0; - const char *suffix = file + strlen(file) - 3; - if (suffix > file && strcmp(suffix,".gz") == 0) compressed = 1; - if (!compressed) fp = fopen(file,"r"); - else { + if (utils::strmatch(file,"\\.gz$")) { + compressed = 1; + #ifdef LAMMPS_GZIP - std::string gunzip = fmt::format("gzip -c -d {}",file); + auto gunzip = fmt::format("gzip -c -d {}",file); + #ifdef _WIN32 fp = _popen(gunzip.c_str(),"rb"); #else @@ -51,8 +50,11 @@ void Reader::open_file(const char *file) #endif #else - error->one(FLERR,"Cannot open gzipped file: " + utils::getsyserror()); + error->one(FLERR,"Cannot open gzipped file without gzip support"); #endif + } else { + compressed = 0; + fp = fopen(file,"r"); } if (fp == nullptr) From d22d6ad45d97028977f916b92276d1cad819874a Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Thu, 8 Apr 2021 11:52:49 +0200 Subject: [PATCH 0442/1217] cmake/USER-PACE.cmake: update PACELIB_URL and PACELIB_MD5 (new source files with whitespaces) lib/pace: add Makefile, Install.py use make remove the LICENSE from src/USER-PACE --- cmake/Modules/Packages/USER-PACE.cmake | 8 +- lib/pace/Install.py | 16 +- lib/pace/Makefile | 38 ++ src/USER-PACE/LICENSE | 674 ------------------------- 4 files changed, 46 insertions(+), 690 deletions(-) create mode 100644 lib/pace/Makefile delete mode 100644 src/USER-PACE/LICENSE diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/USER-PACE.cmake index 008d32444c..b953278e75 100644 --- a/cmake/Modules/Packages/USER-PACE.cmake +++ b/cmake/Modules/Packages/USER-PACE.cmake @@ -1,11 +1,11 @@ -set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.2.3.tar.gz" CACHE STRING "URL for PACE evaluator library sources") -set(PACELIB_MD5 "9ebb087cba7e4ca041fde52f7e9e640c" CACHE STRING "MD5 checksum of PACE evaluator library tarball") +set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.2.3.upd.tar.gz" CACHE STRING "URL for PACE evaluator library sources") +set(PACELIB_MD5 "8041e3de7254815eb3ff0a11e2cc84ea" CACHE STRING "MD5 checksum of PACE evaluator library tarball") mark_as_advanced(PACELIB_URL) mark_as_advanced(PACELIB_MD5) # download library sources to build folder -file(DOWNLOAD ${PACELIB_URL} libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5}) +file(DOWNLOAD ${PACELIB_URL} ./libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5}) # uncompress downloaded sources execute_process( @@ -20,7 +20,7 @@ file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PAC list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp) add_library(pace STATIC ${PACE_EVALUATOR_SOURCES}) -set_target_properties(pace PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE}) +set_target_properties(pace PROPERTIES OUTPUT_NAME pace${LAMMPS_MACHINE}) target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) target_link_libraries(lammps PRIVATE pace) diff --git a/lib/pace/Install.py b/lib/pace/Install.py index 640971e011..5f72157611 100644 --- a/lib/pace/Install.py +++ b/lib/pace/Install.py @@ -18,11 +18,11 @@ parser = ArgumentParser(prog='Install.py', # settings thisdir = fullpath('.') -version = "v.2021.2.3" +version = "v.2021.2.3.upd" # known checksums for different PACE versions. used to validate the download. checksums = { \ - 'v.2021.2.3' : '9ebb087cba7e4ca041fde52f7e9e640c', \ + 'v.2021.2.3.upd' : '8041e3de7254815eb3ff0a11e2cc84ea', \ } @@ -89,17 +89,9 @@ if buildflag: cmd = 'cd "%s"; rm -rf "%s"; tar -xvf %s; mv %s %s' % (thisdir, src_folder, archive_filename, unarchived_folder_name, src_folder) subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) - # configure - - build_folder = "%s/build"%(thisdir) - print("Configuring libpace ...") - cmd = 'cd %s && mkdir build && cd build && cmake .. -DCMAKE_BUILD_TYPE=Release' % (thisdir) - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - if verboseflag: print(txt.decode("UTF-8")) - # build print("Building libpace ...") - cmd = 'cd "%s" && make -j2 && cp libpace.a %s/' % (build_folder, thisdir) + cmd = 'make lib -j2' txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) if verboseflag: print(txt.decode("UTF-8")) @@ -107,5 +99,5 @@ if buildflag: # remove source files print("Removing pace build files and archive ...") - cmd = 'rm %s; rm -rf %s' % (download_filename, build_folder) + cmd = 'rm %s; make clean-build' % (download_filename) subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) \ No newline at end of file diff --git a/lib/pace/Makefile b/lib/pace/Makefile new file mode 100644 index 0000000000..baaef0b837 --- /dev/null +++ b/lib/pace/Makefile @@ -0,0 +1,38 @@ +SHELL = /bin/sh + +# ------ FILES ------ + +SRC_FILES = $(wildcard src/USER-PACE/*.cpp) +SRC = $(filter-out src/USER-PACE/pair_pace.cpp, $(SRC_FILES)) + +# ------ DEFINITIONS ------ + +LIB = libpace.a +OBJ = $(SRC:.cpp=.o) + + +# ------ SETTINGS ------ +CXXFLAGS = -O2 -fPIC -Isrc/USER-PACE + +ARCHIVE = ar +ARCHFLAG = -rc +DEPFLAGS = -M +USRLIB = +SYSLIB = + +# ------ MAKE PROCEDURE ------ + +lib: $(OBJ) + $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) + +# ------ COMPILE RULES ------ + +%.o: %.cpp + $(CXX) $(CXXFLAGS) -c $< -o $@ + +# ------ CLEAN ------ +clean-all: + -rm -f *~ $(OBJ) $(LIB) + +clean-build: + -rm -f *~ $(OBJ) \ No newline at end of file diff --git a/src/USER-PACE/LICENSE b/src/USER-PACE/LICENSE deleted file mode 100644 index f288702d2f..0000000000 --- a/src/USER-PACE/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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From 73ee7805dc9dae77d2adf005925cf63ca4a69a7e Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Thu, 8 Apr 2021 12:13:33 +0200 Subject: [PATCH 0443/1217] remove GPL3 license terms from src/USER-PACE/pair_pace.* delete lib/pace/CMakeLists.txt --- lib/pace/CMakeLists.txt | 19 ------------------- lib/pace/TODO | 30 ------------------------------ src/USER-PACE/pair_pace.cpp | 16 +--------------- src/USER-PACE/pair_pace.h | 16 +--------------- 4 files changed, 2 insertions(+), 79 deletions(-) delete mode 100644 lib/pace/CMakeLists.txt delete mode 100644 lib/pace/TODO diff --git a/lib/pace/CMakeLists.txt b/lib/pace/CMakeLists.txt deleted file mode 100644 index 2884c83cb9..0000000000 --- a/lib/pace/CMakeLists.txt +++ /dev/null @@ -1,19 +0,0 @@ -cmake_minimum_required(VERSION 3.7) # CMake version check -project(aceevaluator) -set(CMAKE_CXX_STANDARD 11) # Enable c++11 standard - - -set(PACE_EVALUATOR_PATH ${CMAKE_CURRENT_LIST_DIR}/src/USER-PACE) -# message("CMakeLists.txt DEBUG: PACE_EVALUATOR_PATH=${PACE_EVALUATOR_PATH}") -set(PACE_EVALUATOR_SRC_PATH ${PACE_EVALUATOR_PATH}) - -FILE(GLOB PACE_EVALUATOR_SOURCE_FILES ${PACE_EVALUATOR_SRC_PATH}/*.cpp) -list(FILTER PACE_EVALUATOR_SOURCE_FILES EXCLUDE REGEX ".*pair_pace.*") -set(PACE_EVALUATOR_INCLUDE_DIR ${PACE_EVALUATOR_SRC_PATH}) - - -##### aceevaluator ##### -add_library(aceevaluator ${PACE_EVALUATOR_SOURCE_FILES}) -target_include_directories(aceevaluator PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) -target_compile_options(aceevaluator PRIVATE -O3) -set_target_properties(aceevaluator PROPERTIES OUTPUT_NAME pace${LAMMPS_MACHINE}) diff --git a/lib/pace/TODO b/lib/pace/TODO deleted file mode 100644 index 8021916923..0000000000 --- a/lib/pace/TODO +++ /dev/null @@ -1,30 +0,0 @@ -[TODO/DONE] pair_pace.cpp and pair_pace.h will have to go into src/USER-PACE and thus also need to conform to our requirements. - -[TODO] also src/USER-PACE would need to have an Install.sh file that integrates the settings from the lib folder into the conventional build process. -[TODO] there would have to be a lib/pace folder for building/interfacing to the library. - -[TODO] how you organize your repo is up to you. a better way to describe what you would have to do is to point you to examples. -which of the examples is relevant depends on what build system you are using for your "PACE" external package. - -If you are using CMake to build it, you can look at the KIM package -If you are using autoconf/automake, you can look at the USER-PLUMED package -If you are using neither (just a plain Makefile), you can look at the VORONOI or QUIP package -The following additional modifications are needed: - -[TODO] lib/pace: needs one or more Makefile.lammps, a README and an Install.py file -[TODO] src/Makefile: needs support for the USER-PACE package and compiling via lib-pace. Also the package needs to be added to the PACKEXT and PACKLIB variables - -[DONE] cmake/Modules/Packages/USER-PACE.cmake needs to be added -[DONE] cmake/CMakeLists.txt needs to include it in case the package is enabled. - -[TODO] doc/src/Build_extra.rst needs to include the build instructions for CMake and traditional make -[TODO] doc/src/Package_user.rst and doc/src/Package_details.rst needs to contain relevant information and links - - -Because of the different build systems, there are different steps required, but each of the examples I've pointed out are tested and used regularly and thus should be working sufficiently well. -Mind you the QUIP package is set up in such a way, that no automatic download is possible and a manual download and compilation is required. So that is the least preferred and least convenient option. - -We are happy to provide more details, but that requires that you first have something that already is following either of the suggested variants, so that we don't have to discuss in all generality. - -I would also suggest to close this pull request here, leave all files in place, but then start a new branch from the current master and then move the few things over you need to retain, -add the build environment files and then start working on getting it to do what it should. \ No newline at end of file diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index 41551e454c..c12753603a 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -7,21 +7,7 @@ Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, ^2: University of Cambridge, Cambridge, United Kingdom ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA ^4: University of British Columbia, Vancouver, BC, Canada - - - This FILENAME is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . - */ +*/ // diff --git a/src/USER-PACE/pair_pace.h b/src/USER-PACE/pair_pace.h index b29ee3a7a9..37509cff5e 100644 --- a/src/USER-PACE/pair_pace.h +++ b/src/USER-PACE/pair_pace.h @@ -7,21 +7,7 @@ Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, ^2: University of Cambridge, Cambridge, United Kingdom ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA ^4: University of British Columbia, Vancouver, BC, Canada - - - This FILENAME is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . - */ +*/ // From ac5bd8a4f7e7f759a0505afa3f3cbdf97fcbb846 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 8 Apr 2021 08:44:18 -0400 Subject: [PATCH 0444/1217] correct the description of how the F dot r contributions are computed --- doc/src/compute_pressure.rst | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index f69f70daba..3c98208261 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -46,13 +46,14 @@ system volume (or area in 2d). The second term is the virial, equal to -dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body, many-body, and long-range interactions, where :math:`r_i` and :math:`f_i` are the position and force vector of atom *i*, and the black -dot indicates a dot product. When periodic boundary conditions are -used, N' necessarily includes periodic image (ghost) atoms outside the -central box, and the position and force vectors of ghost atoms are thus -included in the summation. When periodic boundary conditions are not -used, N' = N = the number of atoms in the system. :doc:`Fixes ` -that impose constraints (e.g. the :doc:`fix shake ` command) -also contribute to the virial term. +dot indicates a dot product. This is computed in parallel for each +sub-domain and then summed over all parallel processes. Thus N' +necessarily includes atoms from neighboring sub-domains (so-called ghost +atoms) and the position and force vectors of ghost atoms are thus +included in the summation. Only when running in serial and without +periodic boundary conditions is N' = N = the number of atoms in the +system. :doc:`Fixes ` that impose constraints (e.g. the :doc:`fix +shake ` command) may also contribute to the virial term. A symmetric pressure tensor, stored as a 6-element vector, is also calculated by this compute. The 6 components of the vector are From 74a37964188469aad2fa5d57bb1858cf7b048bf4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 8 Apr 2021 08:51:33 -0400 Subject: [PATCH 0445/1217] avoid ambiguous precedence through using parentheses. update unit test reference --- src/MOLECULE/angle_cosine_periodic.cpp | 10 +-- .../tests/angle-cosine_periodic.yaml | 80 +++++++++---------- 2 files changed, 45 insertions(+), 45 deletions(-) diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp index 0df103c333..6d4252e8b3 100644 --- a/src/MOLECULE/angle_cosine_periodic.cpp +++ b/src/MOLECULE/angle_cosine_periodic.cpp @@ -17,17 +17,17 @@ #include "angle_cosine_periodic.h" -#include #include "atom.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" #include "math_const.h" #include "math_special.h" #include "memory.h" -#include "error.h" +#include "neighbor.h" +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -224,7 +224,7 @@ void AngleCosinePeriodic::coeff(int narg, char **arg) double AngleCosinePeriodic::equilibrium_angle(int i) { - return MY_PI*(1.0 - (b[i]>0)?0.0:1.0/static_cast(multiplicity[i])); + return MY_PI*(1.0 - ((b[i]>0) ? 0.0 : (1.0/static_cast(multiplicity[i])))); } /* ---------------------------------------------------------------------- diff --git a/unittest/force-styles/tests/angle-cosine_periodic.yaml b/unittest/force-styles/tests/angle-cosine_periodic.yaml index 1c6cb7158d..84d8ff1194 100644 --- a/unittest/force-styles/tests/angle-cosine_periodic.yaml +++ b/unittest/force-styles/tests/angle-cosine_periodic.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 10 Mar 2021 -date_generated: Tue Apr 6 18:38:56 2021 +lammps_version: 8 Apr 2021 +date_generated: Thu Apr 8 09:28:11 2021 epsilon: 2.5e-13 prerequisites: ! | atom full @@ -11,32 +11,32 @@ input_file: in.fourmol angle_style: cosine/periodic angle_coeff: ! | 1 75.0 1 2 - 2 45.0 1 2 + 2 45.0 -1 2 3 50.0 -1 3 4 100.0 -1 4 -equilibrium: 4 1.5707963267948966 1.5707963267948966 0 0 +equilibrium: 4 3.141592653589793 1.5707963267948966 2.0943951023931957 2.356194490192345 extract: ! "" natoms: 29 -init_energy: 946.676664091363 -init_stress: ! |2- - 3.8581448829084906e+00 -6.3926599144452858e+01 6.0068454261544439e+01 1.4347370855129017e+02 1.0109551149053127e+02 4.9470344115369670e+01 +init_energy: 605.3643061001458 +init_stress: ! |- + -1.7082420754402889e+01 -7.3281097507808681e+00 2.4410530505183818e+01 8.5827033671406951e+01 1.4260977966148616e+02 4.1579557432232576e+01 init_forces: ! |2 1 7.9609486050127529e+00 -3.9274211736421961e+01 -3.8917410871887981e+01 2 4.6997439470662350e+00 3.8052682089524090e+01 3.0599010994189470e+01 - 3 -4.4330179925982058e+01 -1.6514501437366098e+00 1.9894582317318523e+01 - 4 1.1465928779203908e+01 -7.1462736556935234e+00 -1.8983545733370338e+01 - 5 2.7634466780141157e+01 1.5504150132065057e+01 1.0078115065618357e+01 - 6 2.2512674572611367e+01 -5.4260358088923418e+01 -6.0646506351853276e+01 + 3 -7.1532072701475698e+01 9.6873528247272844e+01 7.3410935137796983e+01 + 4 3.1784763224659116e+01 -4.4133218046130608e+01 -6.2234613362865147e+01 + 5 5.8817481848549889e+01 -2.5112568523390145e+01 3.9611729278121981e+00 + 6 -8.7258065964885336e+00 -4.2663580774228997e+01 -1.6819642012415606e+01 7 -1.5578858996464229e+01 1.3895348629116569e+01 -3.3939856789628062e+00 - 8 -2.6028225001107934e+00 4.7418887884887312e+01 1.2659217319984802e+02 - 9 9.4419020144376677e+00 -1.3812152922900303e+01 1.2280697239365450e+00 - 10 3.7181742871134183e+01 -2.6592777970320334e+01 -1.0034832175946605e+02 - 11 1.1888648487599809e+01 -1.7288532453781471e+00 -1.8714004234488471e+00 - 12 1.3452345752647041e+01 3.9195153629390539e+01 -3.9429673136141247e+01 - 13 -4.6656310032990458e+00 -1.2502935413462930e+01 1.4918864440944628e+01 - 14 -2.1383527724886850e+01 -9.3422692044635554e+00 7.5125645645164223e+00 - 15 -8.0644375221897171e+00 -2.6783296801963008e+00 6.9267625241565547e+00 - 16 -7.0395776185793807e+01 4.3227686209287491e+01 3.0567216126495769e+01 + 8 -1.6678237064738614e+01 -2.6557373913973738e+01 8.7708427797183326e+00 + 9 -9.4419020144376677e+00 1.3812152922900303e+01 -1.2280697239365450e+00 + 10 1.0844630504236606e+02 1.9274264686364820e+01 1.2594098114786526e+01 + 11 -1.1888648487599809e+01 1.7288532453781471e+00 1.8714004234488471e+00 + 12 9.7432958614920665e+01 1.1284647087939499e+02 -1.3445218835244805e+02 + 13 -2.2887258478933525e+01 -5.9815335453575649e+01 4.1237962971772127e+01 + 14 -4.6498844054867675e+01 -3.0251289808967520e+01 1.5556535565006259e+01 + 15 -5.3477741242848616e+01 -1.7885978453267143e+01 4.6284681424489207e+01 + 16 -7.3215663693592745e+01 1.7514552522777997e+01 7.4857846653898914e+00 17 2.0782832048872386e+01 -2.8304296512773977e+01 1.5273484998106287e+01 18 1.6481336531704756e+00 1.7222946144801426e+01 -6.9896289164966490e+01 19 -2.0180190840279820e+01 -2.5140421523544326e+01 2.9933594625645306e+01 @@ -50,27 +50,27 @@ init_forces: ! |2 27 -8.7971258084923178e+00 7.2217511410368814e+01 -2.4599681382405976e+01 28 -1.9235439225569891e+01 -4.3179911322776611e+01 1.0030656861974458e+00 29 2.8032565034062209e+01 -2.9037600087592210e+01 2.3596615696208531e+01 -run_energy: 945.667120914027 -run_stress: ! |2- - 4.9007195370705645e+00 -6.4584848054201885e+01 5.9684128517131313e+01 1.4440631784196160e+02 1.0147779649040916e+02 5.0605123164347972e+01 +run_energy: 603.8182365368202 +run_stress: ! |- + -1.6098625319219664e+01 -7.7961962067566510e+00 2.3894821525976329e+01 8.7036156470651477e+01 1.4262918929621054e+02 4.2523803236880880e+01 run_forces: ! |2 - 1 8.0595707378962782e+00 -3.9275884216073550e+01 -3.8921834622274609e+01 - 2 4.6450877231394490e+00 3.7989319504376653e+01 3.0709930231636147e+01 - 3 -4.4174062041610540e+01 -1.3116774304574319e+00 1.9852389406583850e+01 - 4 1.1432955350908090e+01 -7.3978491536336328e+00 -1.8963452260213845e+01 - 5 2.7565769765719310e+01 1.5533965769082254e+01 1.0064393083030197e+01 - 6 2.2437947870916961e+01 -5.4321180615060769e+01 -6.0748488446866872e+01 - 7 -1.5585343433722571e+01 1.3904433399215314e+01 -3.4020204287915634e+00 - 8 -2.7173598979194153e+00 4.7428178462168347e+01 1.2654691883960646e+02 - 9 9.4915406599908749e+00 -1.3885257714808199e+01 1.2160209239091246e+00 - 10 3.7036130179485966e+01 -2.6384482125884212e+01 -1.0013051660330657e+02 - 11 1.1913327728618880e+01 -1.7105485662994653e+00 -1.8898750666441195e+00 - 12 1.3449580650332301e+01 3.9344535800585398e+01 -3.9552691785632291e+01 - 13 -4.6002052262583266e+00 -1.2370495939576998e+01 1.4765847794019894e+01 - 14 -2.1313398317698834e+01 -9.6666833306404527e+00 7.4826992840481967e+00 - 15 -8.0459573339780484e+00 -2.8098768831377434e+00 7.2021609989661499e+00 - 16 -7.0394187900784956e+01 4.3284348202675552e+01 3.0478355256814506e+01 - 17 2.0798603484964556e+01 -2.8350845162531051e+01 1.5290163395115368e+01 + 1 8.1036664069391833e+00 -3.9279459516104339e+01 -3.8959949625007155e+01 + 2 4.6488532958171156e+00 3.7987813821226069e+01 3.0712083303318757e+01 + 3 -7.1419656269516480e+01 9.7015207052323333e+01 7.3123837986656483e+01 + 4 3.1774739774255771e+01 -4.4324760214341296e+01 -6.1918121921961003e+01 + 5 5.8630133295649813e+01 -2.5003101567718115e+01 3.8957656941403842e+00 + 6 -8.6686835699933500e+00 -4.2717543793109854e+01 -1.6944132920021204e+01 + 7 -1.5605967450730276e+01 1.3924972058096937e+01 -3.4081311693274161e+00 + 8 -1.6735469954990947e+01 -2.6654949908594496e+01 8.9412902423392993e+00 + 9 -9.4705763934675620e+00 1.3861186924074314e+01 -1.2218212802251793e+00 + 10 1.0864309846473817e+02 1.9311615651482960e+01 1.2534898619395602e+01 + 11 -1.1889594908454491e+01 1.6849924892427488e+00 1.9039966312260486e+00 + 12 9.6643785665770423e+01 1.1329932305772147e+02 -1.3435213826206018e+02 + 13 -2.2815824864999897e+01 -5.9701629573330088e+01 4.1148977584672039e+01 + 14 -4.6226658006998740e+01 -3.0469540424436548e+01 1.5534272011399247e+01 + 15 -5.3141801628038777e+01 -1.8156497866651446e+01 4.6272398149175629e+01 + 16 -7.3254211788300807e+01 1.7569251761827239e+01 7.4522974142679850e+00 + 17 2.0784167932320894e+01 -2.8346879951708846e+01 1.5284477542010659e+01 18 1.7456021018344252e+00 1.7528557172698406e+01 -7.0852460721917453e+01 19 -2.0389936120749365e+01 -2.5462340563923114e+01 3.0421727677614534e+01 20 1.8644334018914940e+01 7.9337833912247095e+00 4.0430733044302912e+01 From 492ddbbcfa1361c979b80650587da9f63de6b049 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 8 Apr 2021 09:32:24 -0400 Subject: [PATCH 0446/1217] simplify --- unittest/force-styles/yaml_writer.cpp | 31 ++++----------------------- 1 file changed, 4 insertions(+), 27 deletions(-) diff --git a/unittest/force-styles/yaml_writer.cpp b/unittest/force-styles/yaml_writer.cpp index b5082c361f..d299b7a879 100644 --- a/unittest/force-styles/yaml_writer.cpp +++ b/unittest/force-styles/yaml_writer.cpp @@ -13,6 +13,7 @@ #include "yaml_writer.h" #include "yaml.h" +#include "fmt/format.h" #include #include @@ -51,41 +52,17 @@ YamlWriter::~YamlWriter() void YamlWriter::emit(const std::string &key, const double value) { - yaml_scalar_event_initialize(&event, NULL, (yaml_char_t *)YAML_STR_TAG, - (yaml_char_t *)key.c_str(), key.size(), 1, 0, - YAML_PLAIN_SCALAR_STYLE); - yaml_emitter_emit(&emitter, &event); - char buf[256]; - snprintf(buf, 256, "%.15g", value); - yaml_scalar_event_initialize(&event, NULL, (yaml_char_t *)YAML_STR_TAG, (yaml_char_t *)buf, - strlen(buf), 1, 0, YAML_PLAIN_SCALAR_STYLE); - yaml_emitter_emit(&emitter, &event); + emit(key,fmt::format("{}",value)); } void YamlWriter::emit(const std::string &key, const long value) { - yaml_scalar_event_initialize(&event, NULL, (yaml_char_t *)YAML_STR_TAG, - (yaml_char_t *)key.c_str(), key.size(), 1, 0, - YAML_PLAIN_SCALAR_STYLE); - yaml_emitter_emit(&emitter, &event); - char buf[256]; - snprintf(buf, 256, "%ld", value); - yaml_scalar_event_initialize(&event, NULL, (yaml_char_t *)YAML_STR_TAG, (yaml_char_t *)buf, - strlen(buf), 1, 0, YAML_PLAIN_SCALAR_STYLE); - yaml_emitter_emit(&emitter, &event); + emit(key,fmt::format("{}",value)); } void YamlWriter::emit(const std::string &key, const int value) { - yaml_scalar_event_initialize(&event, NULL, (yaml_char_t *)YAML_STR_TAG, - (yaml_char_t *)key.c_str(), key.size(), 1, 0, - YAML_PLAIN_SCALAR_STYLE); - yaml_emitter_emit(&emitter, &event); - char buf[256]; - snprintf(buf, 256, "%d", value); - yaml_scalar_event_initialize(&event, NULL, (yaml_char_t *)YAML_STR_TAG, (yaml_char_t *)buf, - strlen(buf), 1, 0, YAML_PLAIN_SCALAR_STYLE); - yaml_emitter_emit(&emitter, &event); + emit(key,fmt::format("{}",value)); } void YamlWriter::emit(const std::string &key, const std::string &value) From d1fd2f74d1046e4177b8714f4cf72ed47f7c87c8 Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Thu, 8 Apr 2021 16:06:05 +0200 Subject: [PATCH 0447/1217] update PACELIB_URL (tackling some PGI warnings): v.2021.2.3.upd2 update lib/pace/Makefile: -O3 optimization --- cmake/Modules/Packages/USER-PACE.cmake | 4 ++-- lib/pace/Install.py | 4 ++-- lib/pace/Makefile | 5 ++--- 3 files changed, 6 insertions(+), 7 deletions(-) diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/USER-PACE.cmake index b953278e75..e8262f7d40 100644 --- a/cmake/Modules/Packages/USER-PACE.cmake +++ b/cmake/Modules/Packages/USER-PACE.cmake @@ -1,6 +1,6 @@ -set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.2.3.upd.tar.gz" CACHE STRING "URL for PACE evaluator library sources") -set(PACELIB_MD5 "8041e3de7254815eb3ff0a11e2cc84ea" CACHE STRING "MD5 checksum of PACE evaluator library tarball") +set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.2.3.upd2.tar.gz" CACHE STRING "URL for PACE evaluator library sources") +set(PACELIB_MD5 "8fd1162724d349b930e474927197f20d" CACHE STRING "MD5 checksum of PACE evaluator library tarball") mark_as_advanced(PACELIB_URL) mark_as_advanced(PACELIB_MD5) diff --git a/lib/pace/Install.py b/lib/pace/Install.py index 5f72157611..91aa8b3a46 100644 --- a/lib/pace/Install.py +++ b/lib/pace/Install.py @@ -18,11 +18,11 @@ parser = ArgumentParser(prog='Install.py', # settings thisdir = fullpath('.') -version = "v.2021.2.3.upd" +version = "v.2021.2.3.upd2" # known checksums for different PACE versions. used to validate the download. checksums = { \ - 'v.2021.2.3.upd' : '8041e3de7254815eb3ff0a11e2cc84ea', \ + 'v.2021.2.3.upd2' : '8fd1162724d349b930e474927197f20d', \ } diff --git a/lib/pace/Makefile b/lib/pace/Makefile index baaef0b837..c2e1892ddd 100644 --- a/lib/pace/Makefile +++ b/lib/pace/Makefile @@ -12,11 +12,10 @@ OBJ = $(SRC:.cpp=.o) # ------ SETTINGS ------ -CXXFLAGS = -O2 -fPIC -Isrc/USER-PACE +CXXFLAGS = -O3 -fPIC -Isrc/USER-PACE ARCHIVE = ar ARCHFLAG = -rc -DEPFLAGS = -M USRLIB = SYSLIB = @@ -35,4 +34,4 @@ clean-all: -rm -f *~ $(OBJ) $(LIB) clean-build: - -rm -f *~ $(OBJ) \ No newline at end of file + -rm -f *~ $(OBJ) From 2d19282961eb2af5195f1038111ed3c5164e51b3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 8 Apr 2021 13:45:37 -0400 Subject: [PATCH 0448/1217] reorder include statements in RIGID package --- src/RIGID/fix_rattle.cpp | 15 +++++++------- src/RIGID/fix_rigid.cpp | 32 +++++++++++++++--------------- src/RIGID/fix_rigid_nh.cpp | 24 +++++++++++----------- src/RIGID/fix_rigid_nvt_small.cpp | 1 + src/RIGID/fix_shake.cpp | 33 ++++++++++++++++--------------- 5 files changed, 55 insertions(+), 50 deletions(-) diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp index aef3cb3964..90aa6d487a 100644 --- a/src/RIGID/fix_rattle.cpp +++ b/src/RIGID/fix_rattle.cpp @@ -17,17 +17,18 @@ #include "fix_rattle.h" -#include -#include #include "atom.h" -#include "update.h" -#include "modify.h" -#include "domain.h" -#include "force.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" #include "math_extra.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 26bbb9477f..3cd4f5dbc8 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -13,29 +13,29 @@ #include "fix_rigid.h" -#include - -#include -#include "math_extra.h" -#include "math_eigen.h" #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "domain.h" -#include "update.h" -#include "respa.h" -#include "modify.h" -#include "group.h" #include "comm.h" -#include "random_mars.h" -#include "force.h" -#include "input.h" -#include "variable.h" -#include "math_const.h" -#include "memory.h" +#include "domain.h" #include "error.h" +#include "force.h" +#include "group.h" +#include "input.h" +#include "math_const.h" +#include "math_eigen.h" +#include "math_extra.h" +#include "memory.h" +#include "modify.h" +#include "random_mars.h" +#include "respa.h" #include "rigid_const.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 4dec04370e..3c4e332fd2 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -18,22 +18,24 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_nh.h" -#include -#include -#include "math_extra.h" + #include "atom.h" +#include "comm.h" #include "compute.h" #include "domain.h" -#include "update.h" -#include "modify.h" -#include "fix_deform.h" -#include "group.h" -#include "comm.h" -#include "force.h" -#include "kspace.h" -#include "memory.h" #include "error.h" +#include "fix_deform.h" +#include "force.h" +#include "group.h" +#include "kspace.h" +#include "math_extra.h" +#include "memory.h" +#include "modify.h" #include "rigid_const.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/RIGID/fix_rigid_nvt_small.cpp b/src/RIGID/fix_rigid_nvt_small.cpp index 0bcebd866d..0392f9c881 100644 --- a/src/RIGID/fix_rigid_nvt_small.cpp +++ b/src/RIGID/fix_rigid_nvt_small.cpp @@ -18,6 +18,7 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_nvt_small.h" + #include "error.h" using namespace LAMMPS_NS; diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 390fe88309..5662e63c88 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -13,25 +13,26 @@ #include "fix_shake.h" +#include "angle.h" +#include "atom.h" +#include "atom_vec.h" +#include "bond.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix_respa.h" +#include "force.h" +#include "group.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "molecule.h" +#include "respa.h" +#include "update.h" + #include #include #include -#include "atom.h" -#include "atom_vec.h" -#include "molecule.h" -#include "update.h" -#include "respa.h" -#include "modify.h" -#include "domain.h" -#include "force.h" -#include "bond.h" -#include "angle.h" -#include "comm.h" -#include "group.h" -#include "fix_respa.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; From 22a337b3935de957c94184d0859dfc3c0778903b Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Thu, 8 Apr 2021 13:00:20 -0600 Subject: [PATCH 0449/1217] Updated READMEs in lib/pace and src/USER-PACE --- lib/pace/README | 13 +++++++++++-- src/USER-PACE/README | 23 +++++++++++++++++++++++ 2 files changed, 34 insertions(+), 2 deletions(-) create mode 100644 src/USER-PACE/README diff --git a/lib/pace/README b/lib/pace/README index e9a1ab820a..ddc6f7f7a7 100644 --- a/lib/pace/README +++ b/lib/pace/README @@ -1,9 +1,18 @@ -This directory contains files required to use the USER-PACE package. +This directory contains files required to use the USER-PACE package, +which provides the pace pair style, an efficient implementation of +the Atomic Cluster Expansion potential (ACE). +ACE is a methodology for deriving a highly accurate classical potential +fit to a large archive of quantum mechanical (DFT) data. +This package was written by Yury Lysogorskiy and others +at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, +Ruhr University Bochum, Germany, http://www.icams.de You can type "make lib-pace" from the src directory to see help on how to download and build this library via make commands, or you can do the same thing by typing "python Install.py" from within this directory. +More information about the USER-PACE implementation of ACE +is available here: - +https://github.com/ICAMS/lammps-user-pace diff --git a/src/USER-PACE/README b/src/USER-PACE/README new file mode 100644 index 0000000000..476edaef76 --- /dev/null +++ b/src/USER-PACE/README @@ -0,0 +1,23 @@ +The USER-PACE package, +provides the pace pair style, an efficient implementation of +the Atomic Cluster Expansion potential (ACE). +ACE is a methodology for deriving a highly accurate classical potential +fit to a large archive of quantum mechanical (DFT) data. +This package was written by Yury Lysogorskiy and others +at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, +Ruhr University Bochum, Germany, http://www.icams.de + +This package requires a library that can be downloaded and built +in lib/pace or somewhere else, +which must be done before building LAMMPS with this +package. Details of the download, build, and install process for +this package usng traditional make (not CMake) are given in the +lib/pace/README file, and scripts are +provided to help automate the process. Also see the LAMMPS manual for +general information on building LAMMPS with external libraries +using either traditional make or CMake. + +More information about the USER-PACE implementation of ACE +is available here: + +https://github.com/ICAMS/lammps-user-pace From a39dc9f9b224118e54330e67d6a240dfab91d352 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Thu, 8 Apr 2021 13:36:04 -0600 Subject: [PATCH 0450/1217] Added minimal info on downloading and building PACE library --- doc/src/Build_extras.rst | 32 ++++++++++++++++++++++++++++++++ doc/src/Packages_details.rst | 4 ++++ src/USER-PACE/README | 22 +++++++++++----------- 3 files changed, 47 insertions(+), 11 deletions(-) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 3af018c656..726374a012 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -52,6 +52,7 @@ This is the list of packages that may require additional steps. * :ref:`USER-MESONT ` * :ref:`USER-MOLFILE ` * :ref:`USER-NETCDF ` + * :ref:`USER-PACE ` * :ref:`USER-PLUMED ` * :ref:`USER-OMP ` * :ref:`USER-QMMM ` @@ -1247,6 +1248,37 @@ be built for the most part with all major versions of the C++ language. ---------- +.. _user-pace: + +USER-PACE package +----------------------------- + +This package requires a library that can be downloaded and built +in lib/pace or somewhere else, which must be done before building +LAMMPS with this package. + +.. tabs:: + + .. tab:: CMake build + + The library download and build will happen automatically when USER-PACE + is requested. + + .. tab:: Traditional make + + You can download and build the USER-PACE library + in one step from the ``lammps/src`` dir, using these commands, + which invoke the ``lib/pace/Install.py`` script. + + .. code-block:: bash + + $ make lib-pace # print help message + $ make lib-pace args="-b" # download and build the default version in lib/pace + + You should not need to edit the ``lib/pace/Makefile.lammps`` file. + +---------- + .. _user-plumed: USER-PLUMED package diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 1964a83717..b10983a35b 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -1378,6 +1378,10 @@ Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1. ^4: University of British Columbia, Vancouver, BC, Canada +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + **Supporting info:** * src/USER-PACE: filenames -> commands diff --git a/src/USER-PACE/README b/src/USER-PACE/README index 476edaef76..3d85c806e9 100644 --- a/src/USER-PACE/README +++ b/src/USER-PACE/README @@ -1,18 +1,18 @@ -The USER-PACE package, -provides the pace pair style, an efficient implementation of -the Atomic Cluster Expansion potential (ACE). -ACE is a methodology for deriving a highly accurate classical potential -fit to a large archive of quantum mechanical (DFT) data. +The USER-PACE package provides the pace pair style, +an efficient implementation of the Atomic Cluster Expansion +potential (ACE). + +ACE is a methodology for deriving a highly accurate classical +potential fit to a large archive of quantum mechanical (DFT) data. This package was written by Yury Lysogorskiy and others at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, -Ruhr University Bochum, Germany, http://www.icams.de +Ruhr University Bochum, Germany (http://www.icams.de). This package requires a library that can be downloaded and built -in lib/pace or somewhere else, -which must be done before building LAMMPS with this -package. Details of the download, build, and install process for -this package usng traditional make (not CMake) are given in the -lib/pace/README file, and scripts are +in lib/pace or somewhere else, which must be done before building +LAMMPS with this package. Details of the download, build, and +install process for this package using traditional make (not CMake) +are given in the lib/pace/README file, and scripts are provided to help automate the process. Also see the LAMMPS manual for general information on building LAMMPS with external libraries using either traditional make or CMake. From 0aee75857a6e7fa320862255b81eff32f30c336f Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Thu, 8 Apr 2021 14:09:19 -0600 Subject: [PATCH 0451/1217] Eliminated doc build warnings --- doc/src/Build_package.rst | 22 +++++++++++----------- doc/src/Packages_user.rst | 2 ++ doc/src/pair_style.rst | 5 +++-- 3 files changed, 16 insertions(+), 13 deletions(-) diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index f9fc52f8db..91531f51ec 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -30,17 +30,17 @@ steps, as explained on the :doc:`Build extras ` page. These links take you to the extra instructions for those select packages: -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`COMPRESS ` | :ref:`GPU ` | :ref:`KIM ` | :ref:`KOKKOS ` | :ref:`LATTE ` | :ref:`MESSAGE ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`MSCG ` | :ref:`OPT ` | :ref:`POEMS ` | :ref:`PYTHON ` | :ref:`VORONOI ` | :ref:`USER-ADIOS ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`USER-INTEL ` | :ref:`USER-MOLFILE ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-NETCDF ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | :ref:`USER-QUIP ` | :ref:`USER-SCAFACOS ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | | | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ ++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`COMPRESS ` | :ref:`GPU ` | :ref:`KIM ` | :ref:`KOKKOS ` | :ref:`LATTE ` | :ref:`MESSAGE ` | ++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`MSCG ` | :ref:`OPT ` | :ref:`POEMS ` | :ref:`PYTHON ` | :ref:`VORONOI ` | :ref:`USER-ADIOS ` | ++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`USER-INTEL ` | :ref:`USER-MOLFILE ` | ++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`USER-NETCDF ` | :ref:`USER-PACE ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | :ref:`USER-QUIP ` | ++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`USER-SCAFACOS ` | :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | | ++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ The mechanism for including packages is simple but different for CMake versus make. diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index a3efaf15c8..00d1dfb67b 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -81,6 +81,8 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-OMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-PACE ` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace ` | USER/pace | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-PHONON ` | phonon dynamical matrix | :doc:`fix phonon ` | USER/phonon | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-PLUMED ` | :ref:`PLUMED ` free energy library | :doc:`fix plumed ` | USER/plumed | ext | diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 89530895c4..a64fc67194 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -98,7 +98,7 @@ accelerated styles exist. * :doc:`zero ` - neighbor list but no interactions * :doc:`adp ` - angular dependent potential (ADP) of Mishin -* :doc:`agni ` - machine learned potential mapping atomic environment to forces +* :doc:`agni ` - AGNI machine-learning potential * :doc:`airebo ` - AIREBO potential of Stuart * :doc:`airebo/morse ` - AIREBO with Morse instead of LJ * :doc:`atm ` - Axilrod-Teller-Muto potential @@ -278,6 +278,7 @@ accelerated styles exist. * :doc:`oxrna2/hbond ` - * :doc:`oxrna2/stk ` - * :doc:`oxrna2/xstk ` - +* :doc:`pace ` - Atomic Cluster Expansion (ACE) machine-learning potential * :doc:`peri/eps ` - peridynamic EPS potential * :doc:`peri/lps ` - peridynamic LPS potential * :doc:`peri/pmb ` - peridynamic PMB potential @@ -295,7 +296,7 @@ accelerated styles exist. * :doc:`smd/ulsph ` - * :doc:`smtbq ` - * :doc:`mliap ` - Multiple styles of machine-learning potential -* :doc:`snap ` - SNAP quantum-accurate potential +* :doc:`snap ` - SNAP machine-learning potential * :doc:`soft ` - Soft (cosine) potential * :doc:`sph/heatconduction ` - * :doc:`sph/idealgas ` - From c660dcefd2c6bcf7d6811c158a65b68a85b000d6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 8 Apr 2021 17:42:32 -0400 Subject: [PATCH 0452/1217] add minimal framework for pair style hybrid/scaled --- src/pair_hybrid_scaled.cpp | 201 +++++++++++++++++++++++++++++++++++++ src/pair_hybrid_scaled.h | 63 ++++++++++++ 2 files changed, 264 insertions(+) create mode 100644 src/pair_hybrid_scaled.cpp create mode 100644 src/pair_hybrid_scaled.h diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp new file mode 100644 index 0000000000..9f3a5d44be --- /dev/null +++ b/src/pair_hybrid_scaled.cpp @@ -0,0 +1,201 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "pair_hybrid_scaled.h" + +#include "atom.h" +#include "error.h" +#include "memory.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairHybridScaled::PairHybridScaled(LAMMPS *lmp) : + PairHybrid(lmp), fsum(nullptr), + scaleval(nullptr), scaleidx(nullptr), scalevar(nullptr) +{ + nscalevar = 0; + nmaxfsum = -1; +} + +/* ---------------------------------------------------------------------- */ + +PairHybridScaled::~PairHybridScaled() +{ + for (int i=0; i < nscalevar; ++i) + delete[] scalevar[i]; + delete[] scalevar; + + if (nmaxfsum > 0) + memory->destroy(fsum); + + if (allocated) { + memory->destroy(scaleval); + memory->destroy(scaleidx); + } +} +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairHybridScaled::allocate() +{ + PairHybrid::allocate(); + + const int n = atom->ntypes; + + memory->create(scaleval,n+1,n+1,"pair:scaleval"); + memory->create(scaleidx,n+1,n+1,"pair:scaleidx"); + for (int i = 1; i <= n; i++) { + for (int j = i; j <= n; j++) { + scaleval[i][j] = 0.0; + scaleidx[i][j] = -1; + } + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairHybridScaled::coeff(int narg, char **arg) +{ + if (narg < 3) error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + + // 3rd arg = scale factor for sub-style, must be either + // a constant or equal stye or compatible variable + + double scale = utils::numeric(FLERR,arg[2],false,lmp); + + // 4th arg = pair sub-style name + // 5th arg = pair sub-style index if name used multiple times + // + // allow for "none" as valid sub-style name + + int multflag; + int m; + + for (m = 0; m < nstyles; m++) { + multflag = 0; + if (strcmp(arg[3],keywords[m]) == 0) { + if (multiple[m]) { + multflag = 1; + if (narg < 5) error->all(FLERR,"Incorrect args for pair coefficients"); + if (multiple[m] == utils::inumeric(FLERR,arg[4],false,lmp)) break; + else continue; + } else break; + } + } + + int none = 0; + if (m == nstyles) { + if (strcmp(arg[3],"none") == 0) none = 1; + else error->all(FLERR,"Pair coeff for hybrid has invalid style"); + } + + // move 1st/2nd args to 3rd/4th args + // if multflag: move 1st/2nd args to 4th/5th args + // just copy ptrs, since arg[] points into original input line + + arg[3+multflag] = arg[1]; + arg[2+multflag] = arg[0]; + + // invoke sub-style coeff() starting with 1st remaining arg + + if (!none) styles[m]->coeff(narg-2-multflag,arg+2+multflag); + + // set setflag and which type pairs map to which sub-style + // if sub-style is none: set hybrid subflag, wipe out map + // else: set hybrid setflag & map only if substyle setflag is set + // if sub-style is new for type pair, add as multiple mapping + // if sub-style exists for type pair, don't add, just update coeffs + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + if (none) { + setflag[i][j] = 1; + nmap[i][j] = 0; + count++; + } else if (styles[m]->setflag[i][j]) { + int k; + for (k = 0; k < nmap[i][j]; k++) + if (map[i][j][k] == m) break; + if (k == nmap[i][j]) map[i][j][nmap[i][j]++] = m; + setflag[i][j] = 1; + scaleval[i][j] = scale; + scaleidx[i][j] = -1; + count++; + } + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + + +/* ---------------------------------------------------------------------- + we need to handle Pair::svector special for hybrid/scaled +------------------------------------------------------------------------- */ + +void PairHybridScaled::init_svector() +{ + // single_extra = list all sub-style single_extra + // allocate svector + + single_extra = 0; + for (int m = 0; m < nstyles; m++) + single_extra += styles[m]->single_extra; + + if (single_extra) { + delete [] svector; + svector = new double[single_extra]; + } +} + +/* ---------------------------------------------------------------------- + we need to handle Pair::svector special for hybrid/scaled +------------------------------------------------------------------------- */ + +void PairHybridScaled::copy_svector(int itype, int jtype) +{ + int n=0; + Pair *this_style; + + // fill svector array. + // copy data from active styles and use 0.0 for inactive ones + for (int m = 0; m < nstyles; m++) { + for (int k = 0; k < nmap[itype][jtype]; ++k) { + if (m == map[itype][jtype][k]) { + this_style = styles[m]; + } else { + this_style = nullptr; + } + } + for (int l = 0; l < styles[m]->single_extra; ++l) { + if (this_style) { + svector[n++] = this_style->svector[l]; + } else { + svector[n++] = 0.0; + } + } + } +} diff --git a/src/pair_hybrid_scaled.h b/src/pair_hybrid_scaled.h new file mode 100644 index 0000000000..d0d2d8838a --- /dev/null +++ b/src/pair_hybrid_scaled.h @@ -0,0 +1,63 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(hybrid/scaled,PairHybridScaled) + +#else + +#ifndef LMP_PAIR_HYBRID_SCALED_H +#define LMP_PAIR_HYBRID_SCALED_H + +#include "pair_hybrid.h" + +namespace LAMMPS_NS { + +class PairHybridScaled : public PairHybrid { + public: + PairHybridScaled(class LAMMPS *); + virtual ~PairHybridScaled(); + void coeff(int, char **); + //void compute(int, int); + + void init_svector(); + void copy_svector(int,int); + + protected: + double **fsum; + double **scaleval; + int **scaleidx; + char **scalevar; + int nscalevar; + int nmaxfsum; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair coeff for hybrid has invalid style + +Style in pair coeff must have been listed in pair_style command. + +*/ From a441c7b379b38ecda9a19415d167d246b2da5409 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 8 Apr 2021 17:44:13 -0400 Subject: [PATCH 0453/1217] simplify hybrid coeff parsing. check for number is already done with conversion --- src/pair_hybrid.cpp | 7 ++----- src/pair_hybrid_overlay.cpp | 8 ++------ 2 files changed, 4 insertions(+), 11 deletions(-) diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index c7b6048139..c12ec67351 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -468,10 +468,7 @@ void PairHybrid::coeff(int narg, char **arg) if (multiple[m]) { multflag = 1; if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients"); - if (!isdigit(arg[3][0])) - error->all(FLERR,"Incorrect args for pair coefficients"); - int index = utils::inumeric(FLERR,arg[3],false,lmp); - if (index == multiple[m]) break; + if (multiple[m] == utils::inumeric(FLERR,arg[3],false,lmp)) break; else continue; } else break; } @@ -492,7 +489,7 @@ void PairHybrid::coeff(int narg, char **arg) // invoke sub-style coeff() starting with 1st remaining arg - if (!none) styles[m]->coeff(narg-1-multflag,&arg[1+multflag]); + if (!none) styles[m]->coeff(narg-1-multflag,arg+1+multflag); // if sub-style only allows one pair coeff call (with * * and type mapping) // then unset setflag/map assigned to that style before setting it below diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index fc78a8aef7..814b3b2f20 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -17,7 +17,6 @@ #include "error.h" #include -#include using namespace LAMMPS_NS; @@ -51,10 +50,7 @@ void PairHybridOverlay::coeff(int narg, char **arg) if (multiple[m]) { multflag = 1; if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients"); - if (!isdigit(arg[3][0])) - error->all(FLERR,"Incorrect args for pair coefficients"); - int index = utils::inumeric(FLERR,arg[3],false,lmp); - if (index == multiple[m]) break; + if (multiple[m] == utils::inumeric(FLERR,arg[3],false,lmp)) break; else continue; } else break; } @@ -75,7 +71,7 @@ void PairHybridOverlay::coeff(int narg, char **arg) // invoke sub-style coeff() starting with 1st remaining arg - if (!none) styles[m]->coeff(narg-1-multflag,&arg[1+multflag]); + if (!none) styles[m]->coeff(narg-1-multflag,arg+1+multflag); // set setflag and which type pairs map to which sub-style // if sub-style is none: set hybrid subflag, wipe out map From ee240f93d935a087ef9313ea87143b6fdc2a482b Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Thu, 8 Apr 2021 23:54:26 +0200 Subject: [PATCH 0454/1217] Rearranged cutoff and element map user input Cutoff radius is now mandatory argument of pair_style. "emap" keyword is removed and replaced by additional pair_coeff arguments (similar to pair_airebo.cpp). Changes in docs are still missing. --- examples/USER/hdnnp/in.hdnnp | 4 +-- src/USER-HDNNP/pair_hdnnp.cpp | 59 ++++++++++++++++++----------------- src/USER-HDNNP/pair_hdnnp.h | 2 +- 3 files changed, 34 insertions(+), 31 deletions(-) diff --git a/examples/USER/hdnnp/in.hdnnp b/examples/USER/hdnnp/in.hdnnp index 112fb24515..79edc605be 100644 --- a/examples/USER/hdnnp/in.hdnnp +++ b/examples/USER/hdnnp/in.hdnnp @@ -28,8 +28,8 @@ thermo 1 ############################################################################### # HDNNP ############################################################################### -pair_style hdnnp dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254 emap "1:H,2:O" -pair_coeff * * ${hdnnpCutoff} +pair_style hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254 +pair_coeff * * H O ############################################################################### # INTEGRATOR diff --git a/src/USER-HDNNP/pair_hdnnp.cpp b/src/USER-HDNNP/pair_hdnnp.cpp index c7318ec0b5..598189b1f1 100644 --- a/src/USER-HDNNP/pair_hdnnp.cpp +++ b/src/USER-HDNNP/pair_hdnnp.cpp @@ -119,7 +119,10 @@ void PairHDNNP::settings(int narg, char **arg) { int iarg = 0; - if (narg == 0) error->all(FLERR,"Illegal pair_style command"); + if (narg < 1) error->all(FLERR,"Illegal pair_style command"); + + maxCutoffRadius = utils::numeric(FLERR,arg[0],false,lmp); + iarg++; // default settings directory = utils::strdup("hdnnp/"); @@ -129,7 +132,6 @@ void PairHDNNP::settings(int narg, char **arg) resetew = false; cflength = 1.0; cfenergy = 1.0; - emap = utils::strdup(""); numExtrapolationWarningsTotal = 0; numExtrapolationWarningsSummary = 0; @@ -139,18 +141,7 @@ void PairHDNNP::settings(int narg, char **arg) if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style command"); delete[] directory; - len = strlen(arg[iarg+1]) + 2; - directory = new char[len]; - sprintf(directory, "%s/", arg[iarg+1]); - iarg += 2; - // element mapping - } else if (strcmp(arg[iarg],"emap") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal pair_style command"); - delete[] emap; - len = strlen(arg[iarg+1]) + 1; - emap = new char[len]; - sprintf(emap, "%s", arg[iarg+1]); + directory = utils::strdup(arg[iarg+1]); iarg += 2; // show extrapolation warnings } else if (strcmp(arg[iarg],"showew") == 0) { @@ -208,26 +199,39 @@ void PairHDNNP::settings(int narg, char **arg) void PairHDNNP::coeff(int narg, char **arg) { + int n = atom->ntypes; + if (!allocated) allocate(); - if (narg != 3) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg != 2 + n) + error->all(FLERR,"Incorrect args for pair coefficients"); - int ilo,ihi,jlo,jhi; - utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); - utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); - maxCutoffRadius = utils::numeric(FLERR,arg[2],false,lmp); + int *map = new int[n+1]; + for (int i = 0; i < n; i++) map[i] = 0; - // TODO: Check how this flag is set. - int count = 0; - for(int i=ilo; i<=ihi; i++) { - for(int j=MAX(jlo,i); j<=jhi; j++) { - setflag[i][j] = 1; - count++; + emap = ""; + for (int i = 2; i < narg; i++) { + if (strcmp(arg[i],"NULL") != 0) { + if (i != 2) emap += ","; + emap += std::to_string(i-1) + ":" + arg[i]; + map[i-1] = 1; } } + int count = 0; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + if (map[i] > 0 && map[j] > 0) { + setflag[i][j] = 1; + count++; + } + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + + delete[] map; } /* ---------------------------------------------------------------------- @@ -237,7 +241,6 @@ void PairHDNNP::coeff(int narg, char **arg) void PairHDNNP::init_style() { int irequest = neighbor->request((void *) this); - neighbor->requests[irequest]->pair = 1; neighbor->requests[irequest]->half = 0; neighbor->requests[irequest]->full = 1; @@ -254,7 +257,7 @@ void PairHDNNP::init_style() // Initialize interface on all processors. interface->initialize(directory, - emap, + emap.c_str(), showew, resetew, showewsum, @@ -294,7 +297,7 @@ void PairHDNNP::allocate() for (int j = i; j <= n; j++) setflag[i][j] = 0; - memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cutsq,n+1,n+1,"pair:cutsq"); // TODO: Is this required? } void PairHDNNP::transferNeighborList() diff --git a/src/USER-HDNNP/pair_hdnnp.h b/src/USER-HDNNP/pair_hdnnp.h index a3488bbad4..913da97933 100644 --- a/src/USER-HDNNP/pair_hdnnp.h +++ b/src/USER-HDNNP/pair_hdnnp.h @@ -63,7 +63,7 @@ class PairHDNNP : public Pair { double cfenergy; double maxCutoffRadius; char *directory; - char *emap; + std::string emap; nnp::InterfaceLammps *interface; }; From 8ed6d80b851a4dbe02aa61bcd50ca12e5d3c15b1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 8 Apr 2021 21:02:28 -0400 Subject: [PATCH 0455/1217] first working version, forces only, no restart --- doc/src/pair_hybrid.rst | 98 ++++++---- src/pair_hybrid.h | 2 +- src/pair_hybrid_scaled.cpp | 358 ++++++++++++++++++++++++++++++++----- src/pair_hybrid_scaled.h | 17 +- 4 files changed, 386 insertions(+), 89 deletions(-) diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index 558c326175..c851423029 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -2,6 +2,7 @@ .. index:: pair_style hybrid/kk .. index:: pair_style hybrid/overlay .. index:: pair_style hybrid/overlay/kk +.. index:: pair_style hybrid/scaled pair_style hybrid command ========================= @@ -13,6 +14,8 @@ pair_style hybrid/overlay command Accelerator Variants: *hybrid/overlay/kk* +pair_style hybrid/scale command + Syntax """""" @@ -20,8 +23,10 @@ Syntax pair_style hybrid style1 args style2 args ... pair_style hybrid/overlay style1 args style2 args ... + pair_style hybrid/scaled factor1 style1 args factor2 style 2 args ... * style1,style2 = list of one or more pair styles and their arguments +* factor1,factor2 = scale factors for pair styles, may be a variable Examples """""""" @@ -37,15 +42,24 @@ Examples pair_coeff * * lj/cut 1.0 1.0 pair_coeff * * coul/long + variable one equal ramp(1.0,0.0) + variable two equal 1.0-v_one + pair_style hybrid/scaled v_one lj/cut 2.5 v_two morse 2.5 + pair_coeff 1 1 lj/cut 1.0 1.0 2.5 + pair_coeff 1 1 morse 1.0 1.0 1.0 2.5 + Description """"""""""" -The *hybrid* and *hybrid/overlay* styles enable the use of multiple -pair styles in one simulation. With the *hybrid* style, exactly one -pair style is assigned to each pair of atom types. With the -*hybrid/overlay* style, one or more pair styles can be assigned to -each pair of atom types. The assignment of pair styles to type pairs -is made via the :doc:`pair_coeff ` command. +The *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles enable the +use of multiple pair styles in one simulation. With the *hybrid* style, +exactly one pair style is assigned to each pair of atom types. With the +*hybrid/overlay* and *hybrid/scaled* styles, one or more pair styles can +be assigned to each pair of atom types. The assignment of pair styles +to type pairs is made via the :doc:`pair_coeff ` command. +The *hybrid/scaled* style differs from the *hybrid/overlay* style by +requiring a factor for each pair style that is used to scale all +forces and energies computed by the pair style. Here are two examples of hybrid simulations. The *hybrid* style could be used for a simulation of a metal droplet on a LJ surface. The @@ -61,12 +75,19 @@ it would be more efficient to use the single combined potential, but in general any combination of pair potentials can be used together in to produce an interaction that is not encoded in any single pair_style file, e.g. adding Coulombic forces between granular particles. +The *hybrid/scaled* style enables more complex combinations of pair +styles than a simple sum as *hybrid/overlay* does. Furthermore, since +the scale factors can be variables, they can change during a simulation +which would allow to smoothly switch between two different pair styles +or two different parameter sets. All pair styles that will be used are listed as "sub-styles" following -the *hybrid* or *hybrid/overlay* keyword, in any order. Each -sub-style's name is followed by its usual arguments, as illustrated in -the example above. See the doc pages of individual pair styles for a -listing and explanation of the appropriate arguments. +the *hybrid* or *hybrid/overlay* keyword, in any order. In case of the +*hybrid/scaled* pair style each sub-style is prefixed with its scale +factor. The scale factor may be an equal style (or equivalent) +variable. Each sub-style's name is followed by its usual arguments, as +illustrated in the example above. See the doc pages of individual pair +styles for a listing and explanation of the appropriate arguments. Note that an individual pair style can be used multiple times as a sub-style. For efficiency this should only be done if your model @@ -143,16 +164,16 @@ one sub-style. Just as with a simulation using a single pair style, if you specify the same atom type pair in a second pair_coeff command, the previous assignment will be overwritten. -For the *hybrid/overlay* style, each atom type pair I,J can be -assigned to one or more sub-styles. If you specify the same atom type -pair in a second pair_coeff command with a new sub-style, then the -second sub-style is added to the list of potentials that will be -calculated for two interacting atoms of those types. If you specify -the same atom type pair in a second pair_coeff command with a -sub-style that has already been defined for that pair of atoms, then -the new pair coefficients simply override the previous ones, as in the -normal usage of the pair_coeff command. E.g. these two sets of -commands are the same: +For the *hybrid/overlay* and *hybrid/scaled* style, each atom type pair +I,J can be assigned to one or more sub-styles. If you specify the same +atom type pair in a second pair_coeff command with a new sub-style, then +the second sub-style is added to the list of potentials that will be +calculated for two interacting atoms of those types. If you specify the +same atom type pair in a second pair_coeff command with a sub-style that +has already been defined for that pair of atoms, then the new pair +coefficients simply override the previous ones, as in the normal usage +of the pair_coeff command. E.g. these two sets of commands are the +same: .. code-block:: LAMMPS @@ -170,19 +191,20 @@ data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below. -For both the *hybrid* and *hybrid/overlay* styles, every atom type -pair I,J (where I <= J) must be assigned to at least one sub-style via -the :doc:`pair_coeff ` command as in the examples above, or -in the data file read by the :doc:`read_data `, or by mixing -as described below. +For all of the *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles, +every atom type pair I,J (where I <= J) must be assigned to at least one +sub-style via the :doc:`pair_coeff ` command as in the +examples above, or in the data file read by the :doc:`read_data +`, or by mixing as described below. If you want there to be no interactions between a particular pair of atom types, you have 3 choices. You can assign the type pair to some sub-style and use the :doc:`neigh_modify exclude type ` command. You can assign it to some sub-style and set the coefficients -so that there is effectively no interaction (e.g. epsilon = 0.0 in a -LJ potential). Or, for *hybrid* and *hybrid/overlay* simulations, you -can use this form of the pair_coeff command in your input script: +so that there is effectively no interaction (e.g. epsilon = 0.0 in a LJ +potential). Or, for *hybrid*, *hybrid/overlay*, or *hybrid/scaled* +simulations, you can use this form of the pair_coeff command in your +input script: .. code-block:: LAMMPS @@ -260,7 +282,10 @@ the specific syntax, requirements and restrictions. ---------- The potential energy contribution to the overall system due to an -individual sub-style can be accessed and output via the :doc:`compute pair ` command. +individual sub-style can be accessed and output via the :doc:`compute +pair ` command. Note that in the case of pair style +*hybrid/scaled* this is the **unscaled** potential energy of the +selected sub-style. ---------- @@ -388,12 +413,12 @@ The hybrid pair styles supports the :doc:`pair_modify ` shift, table, and tail options for an I,J pair interaction, if the associated sub-style supports it. -For the hybrid pair styles, the list of sub-styles and their -respective settings are written to :doc:`binary restart files `, so a :doc:`pair_style ` command does -not need to specified in an input script that reads a restart file. -However, the coefficient information is not stored in the restart -file. Thus, pair_coeff commands need to be re-specified in the -restart input script. +For the hybrid pair styles, the list of sub-styles and their respective +settings are written to :doc:`binary restart files `, so a +:doc:`pair_style ` command does not need to specified in an +input script that reads a restart file. However, the coefficient +information is not stored in the restart file. Thus, pair_coeff +commands need to be re-specified in the restart input script. These pair styles support the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, if @@ -409,6 +434,9 @@ e.g. *lj/cut/coul/long* or *buck/coul/long*\ . You must insure that the short-range Coulombic cutoff used by each of these long pair styles is the same or else LAMMPS will generate an error. +Pair style *hybrid/scaled* currently only works for non-accelerated +pair styles. + Related commands """""""""""""""" diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index 7717d1fd51..3bde620514 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -37,7 +37,7 @@ class PairHybrid : public Pair { PairHybrid(class LAMMPS *); virtual ~PairHybrid(); virtual void compute(int, int); - void settings(int, char **); + virtual void settings(int, char **); virtual void coeff(int, char **); void init_style(); double init_one(int, int); diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index 9f3a5d44be..7e1d634627 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -15,7 +15,12 @@ #include "atom.h" #include "error.h" +#include "force.h" +#include "input.h" #include "memory.h" +#include "respa.h" +#include "update.h" +#include "variable.h" #include @@ -23,11 +28,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairHybridScaled::PairHybridScaled(LAMMPS *lmp) : - PairHybrid(lmp), fsum(nullptr), - scaleval(nullptr), scaleidx(nullptr), scalevar(nullptr) +PairHybridScaled::PairHybridScaled(LAMMPS *lmp) + : PairHybrid(lmp), fsum(nullptr), scaleval(nullptr), scaleidx(nullptr) { - nscalevar = 0; nmaxfsum = -1; } @@ -35,36 +38,307 @@ PairHybridScaled::PairHybridScaled(LAMMPS *lmp) : PairHybridScaled::~PairHybridScaled() { - for (int i=0; i < nscalevar; ++i) - delete[] scalevar[i]; - delete[] scalevar; - - if (nmaxfsum > 0) - memory->destroy(fsum); - - if (allocated) { - memory->destroy(scaleval); - memory->destroy(scaleidx); - } + memory->destroy(fsum); + memory->destroy(scaleval); } + /* ---------------------------------------------------------------------- - allocate all arrays + call each sub-style's compute() or compute_outer() function + accumulate sub-style global/peratom energy/virial in hybrid + for global vflag = VIRIAL_PAIR: + each sub-style computes own virial[6] + sum sub-style virial[6] to hybrid's virial[6] + for global vflag = VIRIAL_FDOTR: + call sub-style with adjusted vflag to prevent it calling + virial_fdotr_compute() + hybrid calls virial_fdotr_compute() on final accumulated f ------------------------------------------------------------------------- */ -void PairHybridScaled::allocate() +void PairHybridScaled::compute(int eflag, int vflag) { - PairHybrid::allocate(); + int i,j,m,n; - const int n = atom->ntypes; + // update scale values from variables where needed - memory->create(scaleval,n+1,n+1,"pair:scaleval"); - memory->create(scaleidx,n+1,n+1,"pair:scaleidx"); - for (int i = 1; i <= n; i++) { - for (int j = i; j <= n; j++) { - scaleval[i][j] = 0.0; - scaleidx[i][j] = -1; + const int nvars = scalevars.size(); + if (nvars > 0) { + double *vals = new double[nvars]; + for (i = 0; i < nvars; ++i) { + j = input->variable->find(scalevars[i].c_str()); + vals[i] = input->variable->compute_equal(j); + } + for (i = 0; i < nstyles; ++i) { + if (scaleidx[i] >= 0) + scaleval[i] = vals[scaleidx[i]]; + } + delete[] vals; + } + + // check if no_virial_fdotr_compute is set and global component of + // incoming vflag = VIRIAL_FDOTR + // if so, reset vflag as if global component were VIRIAL_PAIR + // necessary since one or more sub-styles cannot compute virial as F dot r + + if (no_virial_fdotr_compute && (vflag & VIRIAL_FDOTR)) + vflag = VIRIAL_PAIR | (vflag & ~VIRIAL_FDOTR); + + ev_init(eflag,vflag); + + // grow fsum array if needed, and copy existing forces (usually 0.0) to it. + + if (atom->nmax > nmaxfsum) { + memory->destroy(fsum); + nmaxfsum = atom->nmax; + memory->create(fsum,nmaxfsum,3,"pair:fsum"); + } + const int nall = atom->nlocal + atom->nghost; + auto f = atom->f; + for (i = 0; i < nall; ++i) { + fsum[i][0] = f[i][0]; + fsum[i][1] = f[i][1]; + fsum[i][2] = f[i][2]; + } + + // check if global component of incoming vflag = VIRIAL_FDOTR + // if so, reset vflag passed to substyle so VIRIAL_FDOTR is turned off + // necessary so substyle will not invoke virial_fdotr_compute() + + int vflag_substyle; + if (vflag & VIRIAL_FDOTR) vflag_substyle = vflag & ~VIRIAL_FDOTR; + else vflag_substyle = vflag; + + double *saved_special = save_special(); + + // check if we are running with r-RESPA using the hybrid keyword + + Respa *respa = nullptr; + respaflag = 0; + if (utils::strmatch(update->integrate_style,"^respa")) { + respa = (Respa *) update->integrate; + if (respa->nhybrid_styles > 0) respaflag = 1; + } + + for (m = 0; m < nstyles; m++) { + + // clear forces + + memset(&f[0][0],0,nall*3*sizeof(double)); + + set_special(m); + + if (!respaflag || (respaflag && respa->hybrid_compute[m])) { + + // invoke compute() unless compute flag is turned off or + // outerflag is set and sub-style has a compute_outer() method + + if (styles[m]->compute_flag == 0) continue; + if (outerflag && styles[m]->respa_enable) + styles[m]->compute_outer(eflag,vflag_substyle); + else styles[m]->compute(eflag,vflag_substyle); + } + + // add scaled forces to global sum + const double scale = scaleval[m]; + for (i = 0; i < nall; ++i) { + fsum[i][0] += scale*f[i][0]; + fsum[i][1] += scale*f[i][1]; + fsum[i][2] += scale*f[i][2]; + } + + restore_special(saved_special); + + // jump to next sub-style if r-RESPA does not want global accumulated data + + if (respaflag && !respa->tally_global) continue; + + if (eflag_global) { + eng_vdwl += scale * styles[m]->eng_vdwl; + eng_coul += scale * styles[m]->eng_coul; + } + if (vflag_global) { + for (n = 0; n < 6; n++) virial[n] += scale * styles[m]->virial[n]; + } + if (eflag_atom) { + n = atom->nlocal; + if (force->newton_pair) n += atom->nghost; + double *eatom_substyle = styles[m]->eatom; + for (i = 0; i < n; i++) eatom[i] += scale * eatom_substyle[i]; + } + if (vflag_atom) { + n = atom->nlocal; + if (force->newton_pair) n += atom->nghost; + double **vatom_substyle = styles[m]->vatom; + for (i = 0; i < n; i++) + for (j = 0; j < 6; j++) + vatom[i][j] += scale * vatom_substyle[i][j]; + } + + // substyles may be CENTROID_SAME or CENTROID_AVAIL + + if (cvflag_atom) { + n = atom->nlocal; + if (force->newton_pair) n += atom->nghost; + if (styles[m]->centroidstressflag == CENTROID_AVAIL) { + double **cvatom_substyle = styles[m]->cvatom; + for (i = 0; i < n; i++) + for (j = 0; j < 9; j++) + cvatom[i][j] += scale * cvatom_substyle[i][j]; + } else { + double **vatom_substyle = styles[m]->vatom; + for (i = 0; i < n; i++) { + for (j = 0; j < 6; j++) { + cvatom[i][j] += scale * vatom_substyle[i][j]; + } + for (j = 6; j < 9; j++) { + cvatom[i][j] += scale * vatom_substyle[i][j-3]; + } + } + } } } + + // copy accumulated forces to original force array + + for (i = 0; i < nall; ++i) { + f[i][0] = fsum[i][0]; + f[i][1] = fsum[i][1]; + f[i][2] = fsum[i][2]; + } + delete [] saved_special; + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + create one pair style for each arg in list +------------------------------------------------------------------------- */ + +void PairHybridScaled::settings(int narg, char **arg) +{ + if (narg < 1) error->all(FLERR,"Illegal pair_style command"); + if (lmp->kokkos && !utils::strmatch(force->pair_style,"^hybrid.*/kk$")) + error->all(FLERR,fmt::format("Must use pair_style {}/kk with Kokkos", + force->pair_style)); + + // delete old lists, since cannot just change settings + + if (nstyles > 0) { + for (int m = 0; m < nstyles; m++) { + delete styles[m]; + delete [] keywords[m]; + if (special_lj[m]) delete [] special_lj[m]; + if (special_coul[m]) delete [] special_coul[m]; + } + delete[] styles; + delete[] keywords; + delete[] multiple; + delete[] special_lj; + delete[] special_coul; + delete[] compute_tally; + delete[] scaleval; + delete[] scaleidx; + scalevars.clear(); + } + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(cutghost); + memory->destroy(nmap); + memory->destroy(map); + } + allocated = 0; + + // allocate list of sub-styles as big as possibly needed if no extra args + + styles = new Pair*[narg]; + keywords = new char*[narg]; + multiple = new int[narg]; + + special_lj = new double*[narg]; + special_coul = new double*[narg]; + compute_tally = new int[narg]; + + scaleval = new double[narg]; + scaleidx = new int[narg]; + scalevars.reserve(narg); + + // allocate each sub-style + // allocate uses suffix, but don't store suffix version in keywords, + // else syntax in coeff() will not match + // call settings() with set of args that are not pair style names + // use force->pair_map to determine which args these are + + int iarg,jarg,dummy; + + iarg = 0; + nstyles = 0; + while (iarg < narg-1) { + + // first process scale factor or variable + // idx < 0 indicates constant value otherwise index in variable name list + + double val = 0.0; + int idx = -1; + if (utils::strmatch(arg[iarg],"^v_")) { + for (std::size_t i=0; i < scalevars.size(); ++i) { + if (scalevars[i] == arg[iarg]+2) { + idx = i; + break; + } + } + if (idx < 0) { + idx = scalevars.size(); + scalevars.push_back(arg[iarg]+2); + } + } else { + val = utils::numeric(FLERR,arg[iarg],false,lmp); + } + scaleval[nstyles] = val; + scaleidx[nstyles] = idx; + ++iarg; + + if (utils::strmatch(arg[iarg],"^hybrid")) + error->all(FLERR,"Pair style hybrid cannot have hybrid as an argument"); + if (strcmp(arg[iarg],"none") == 0) + error->all(FLERR,"Pair style hybrid cannot have none as an argument"); + + styles[nstyles] = force->new_pair(arg[iarg],1,dummy); + force->store_style(keywords[nstyles],arg[iarg],0); + special_lj[nstyles] = special_coul[nstyles] = nullptr; + compute_tally[nstyles] = 1; + + // determine list of arguments for pair style settings + // by looking for the next known pair style name. + + jarg = iarg + 1; + while ((jarg < narg) + && !force->pair_map->count(arg[jarg]) + && !lmp->match_style("pair",arg[jarg])) jarg++; + + // decrement to account for scale factor except when last argument + + if (jarg < narg) --jarg; + + styles[nstyles]->settings(jarg-iarg-1,arg+iarg+1); + iarg = jarg; + nstyles++; + } + + // multiple[i] = 1 to M if sub-style used multiple times, else 0 + + for (int i = 0; i < nstyles; i++) { + int count = 0; + for (int j = 0; j < nstyles; j++) { + if (strcmp(keywords[j],keywords[i]) == 0) count++; + if (j == i) multiple[i] = count; + } + if (count == 1) multiple[i] = 0; + } + + // set pair flags from sub-style flags + + flags(); } /* ---------------------------------------------------------------------- @@ -80,14 +354,8 @@ void PairHybridScaled::coeff(int narg, char **arg) utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); - // 3rd arg = scale factor for sub-style, must be either - // a constant or equal stye or compatible variable - - double scale = utils::numeric(FLERR,arg[2],false,lmp); - - // 4th arg = pair sub-style name - // 5th arg = pair sub-style index if name used multiple times - // + // 3rd arg = pair sub-style name + // 4th arg = pair sub-style index if name used multiple times // allow for "none" as valid sub-style name int multflag; @@ -95,11 +363,14 @@ void PairHybridScaled::coeff(int narg, char **arg) for (m = 0; m < nstyles; m++) { multflag = 0; - if (strcmp(arg[3],keywords[m]) == 0) { + if (strcmp(arg[2],keywords[m]) == 0) { if (multiple[m]) { multflag = 1; - if (narg < 5) error->all(FLERR,"Incorrect args for pair coefficients"); - if (multiple[m] == utils::inumeric(FLERR,arg[4],false,lmp)) break; + if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients"); + if (!isdigit(arg[3][0])) + error->all(FLERR,"Incorrect args for pair coefficients"); + int index = utils::inumeric(FLERR,arg[3],false,lmp); + if (index == multiple[m]) break; else continue; } else break; } @@ -107,20 +378,20 @@ void PairHybridScaled::coeff(int narg, char **arg) int none = 0; if (m == nstyles) { - if (strcmp(arg[3],"none") == 0) none = 1; + if (strcmp(arg[2],"none") == 0) none = 1; else error->all(FLERR,"Pair coeff for hybrid has invalid style"); } - // move 1st/2nd args to 3rd/4th args - // if multflag: move 1st/2nd args to 4th/5th args + // move 1st/2nd args to 2nd/3rd args + // if multflag: move 1st/2nd args to 3rd/4th args // just copy ptrs, since arg[] points into original input line - arg[3+multflag] = arg[1]; - arg[2+multflag] = arg[0]; + arg[2+multflag] = arg[1]; + arg[1+multflag] = arg[0]; // invoke sub-style coeff() starting with 1st remaining arg - if (!none) styles[m]->coeff(narg-2-multflag,arg+2+multflag); + if (!none) styles[m]->coeff(narg-1-multflag,&arg[1+multflag]); // set setflag and which type pairs map to which sub-style // if sub-style is none: set hybrid subflag, wipe out map @@ -141,8 +412,6 @@ void PairHybridScaled::coeff(int narg, char **arg) if (map[i][j][k] == m) break; if (k == nmap[i][j]) map[i][j][nmap[i][j]++] = m; setflag[i][j] = 1; - scaleval[i][j] = scale; - scaleidx[i][j] = -1; count++; } } @@ -151,7 +420,6 @@ void PairHybridScaled::coeff(int narg, char **arg) if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } - /* ---------------------------------------------------------------------- we need to handle Pair::svector special for hybrid/scaled ------------------------------------------------------------------------- */ diff --git a/src/pair_hybrid_scaled.h b/src/pair_hybrid_scaled.h index d0d2d8838a..a8bd5517ec 100644 --- a/src/pair_hybrid_scaled.h +++ b/src/pair_hybrid_scaled.h @@ -22,27 +22,28 @@ PairStyle(hybrid/scaled,PairHybridScaled) #include "pair_hybrid.h" +#include +#include + namespace LAMMPS_NS { class PairHybridScaled : public PairHybrid { public: PairHybridScaled(class LAMMPS *); virtual ~PairHybridScaled(); - void coeff(int, char **); - //void compute(int, int); + virtual void compute(int, int); + virtual void settings(int, char**); + virtual void coeff(int, char **); void init_svector(); void copy_svector(int,int); protected: double **fsum; - double **scaleval; - int **scaleidx; - char **scalevar; - int nscalevar; + double *scaleval; + int *scaleidx; + std::vector scalevars; int nmaxfsum; - - void allocate(); }; } From ae27d3bf4cdea5a86b8f3bfe1681c2cb3d990fc6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 00:31:43 -0400 Subject: [PATCH 0456/1217] add support for single() and read/write_restart() --- src/pair_hybrid.h | 6 +- src/pair_hybrid_scaled.cpp | 126 ++++++++++++++++++++++++++++++++++++- src/pair_hybrid_scaled.h | 4 ++ 3 files changed, 130 insertions(+), 6 deletions(-) diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index 3bde620514..ca79163fc2 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -42,9 +42,9 @@ class PairHybrid : public Pair { void init_style(); double init_one(int, int); void setup(); - void write_restart(FILE *); - void read_restart(FILE *); - double single(int, int, int, int, double, double, double, double &); + virtual void write_restart(FILE *); + virtual void read_restart(FILE *); + virtual double single(int, int, int, int, double, double, double, double &); void modify_params(int narg, char **arg); double memory_usage(); diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index 7e1d634627..da8631dcf8 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -14,11 +14,13 @@ #include "pair_hybrid_scaled.h" #include "atom.h" +#include "comm.h" #include "error.h" #include "force.h" #include "input.h" #include "memory.h" #include "respa.h" +#include "suffix.h" #include "update.h" #include "variable.h" @@ -39,7 +41,9 @@ PairHybridScaled::PairHybridScaled(LAMMPS *lmp) PairHybridScaled::~PairHybridScaled() { memory->destroy(fsum); - memory->destroy(scaleval); + memory->destroy(tsum); + delete[] scaleval; + delete[] scaleidx; } /* ---------------------------------------------------------------------- @@ -299,15 +303,20 @@ void PairHybridScaled::settings(int narg, char **arg) ++iarg; if (utils::strmatch(arg[iarg],"^hybrid")) - error->all(FLERR,"Pair style hybrid cannot have hybrid as an argument"); + error->all(FLERR,"Pair style hybrid/scaled cannot have hybrid as an argument"); if (strcmp(arg[iarg],"none") == 0) - error->all(FLERR,"Pair style hybrid cannot have none as an argument"); + error->all(FLERR,"Pair style hybrid/scaled cannot have none as an argument"); styles[nstyles] = force->new_pair(arg[iarg],1,dummy); force->store_style(keywords[nstyles],arg[iarg],0); special_lj[nstyles] = special_coul[nstyles] = nullptr; compute_tally[nstyles] = 1; + if ((((PairHybridScaled *)styles[nstyles])->suffix_flag + & (Suffix::INTEL|Suffix::GPU|Suffix::OMP)) != 0) + error->all(FLERR,"Pair style hybrid/scaled does not support " + "accelerator styles"); + // determine list of arguments for pair style settings // by looking for the next known pair style name. @@ -341,6 +350,60 @@ void PairHybridScaled::settings(int narg, char **arg) flags(); } +/* ---------------------------------------------------------------------- + call sub-style to compute single interaction + error if sub-style does not support single() call + since overlay could have multiple sub-styles, sum results explicitly +------------------------------------------------------------------------- */ + +double PairHybridScaled::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_lj, double &fforce) +{ + if (nmap[itype][jtype] == 0) + error->one(FLERR,"Invoked pair single on pair style none"); + + // update scale values from variables where needed + + const int nvars = scalevars.size(); + if (nvars > 0) { + double *vals = new double[nvars]; + for (i = 0; i < nvars; ++i) { + j = input->variable->find(scalevars[i].c_str()); + vals[i] = input->variable->compute_equal(j); + } + for (i = 0; i < nstyles; ++i) { + if (scaleidx[i] >= 0) + scaleval[i] = vals[scaleidx[i]]; + } + delete[] vals; + } + + double fone; + fforce = 0.0; + double esum = 0.0; + double scale; + + for (int m = 0; m < nmap[itype][jtype]; m++) { + if (rsq < styles[map[itype][jtype][m]]->cutsq[itype][jtype]) { + if (styles[map[itype][jtype][m]]->single_enable == 0) + error->one(FLERR,"Pair hybrid sub-style does not support single call"); + + if ((special_lj[map[itype][jtype][m]] != nullptr) || + (special_coul[map[itype][jtype][m]] != nullptr)) + error->one(FLERR,"Pair hybrid single calls do not support" + " per sub-style special bond values"); + + scale = scaleval[map[itype][jtype][m]]; + esum += scale * styles[map[itype][jtype][m]]->single(i,j,itype,jtype,rsq, + factor_coul,factor_lj,fone); + fforce += scale * fone; + } + } + + if (single_extra) copy_svector(itype,jtype); + return esum; +} + /* ---------------------------------------------------------------------- set coeffs for one or more type pairs ------------------------------------------------------------------------- */ @@ -420,6 +483,63 @@ void PairHybridScaled::coeff(int narg, char **arg) if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairHybridScaled::write_restart(FILE *fp) +{ + PairHybrid::write_restart(fp); + + fwrite(scaleval,sizeof(double),nstyles,fp); + fwrite(scaleidx,sizeof(int),nstyles,fp); + + int n = scalevars.size(); + fwrite(&n,sizeof(int),1,fp); + for (auto var : scalevars) { + n = var.size() + 1; + fwrite(&n,sizeof(int),1,fp); + fwrite(var.c_str(),sizeof(char),n,fp); + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairHybridScaled::read_restart(FILE *fp) +{ + PairHybrid::read_restart(fp); + + delete[] scaleval; + delete[] scaleidx; + scalevars.clear(); + scaleval = new double[nstyles]; + scaleidx = new int[nstyles]; + + int n, me = comm->me; + if (me == 0) { + utils::sfread(FLERR,scaleval,sizeof(double),nstyles,fp,nullptr,error); + utils::sfread(FLERR,scaleidx,sizeof(int),nstyles,fp,nullptr,error); + } + MPI_Bcast(scaleval,nstyles,MPI_DOUBLE,0,world); + MPI_Bcast(scaleidx,nstyles,MPI_INT,0,world); + + char *tmp; + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,nullptr,error); + MPI_Bcast(&n,1,MPI_INT,0,world); + scalevars.resize(n); + for (size_t j=0; j < scalevars.size(); ++j) { + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,nullptr,error); + MPI_Bcast(&n,1,MPI_INT,0,world); + tmp = new char[n]; + if (me == 0) utils::sfread(FLERR,tmp,sizeof(char),n,fp,nullptr,error); + MPI_Bcast(tmp,n,MPI_CHAR,0,world); + scalevars[j] = tmp; + delete[] tmp; + } +} + /* ---------------------------------------------------------------------- we need to handle Pair::svector special for hybrid/scaled ------------------------------------------------------------------------- */ diff --git a/src/pair_hybrid_scaled.h b/src/pair_hybrid_scaled.h index a8bd5517ec..fbfcdab23a 100644 --- a/src/pair_hybrid_scaled.h +++ b/src/pair_hybrid_scaled.h @@ -35,6 +35,10 @@ class PairHybridScaled : public PairHybrid { virtual void settings(int, char**); virtual void coeff(int, char **); + virtual void write_restart(FILE *); + virtual void read_restart(FILE *); + virtual double single(int, int, int, int, double, double, double, double &); + void init_svector(); void copy_svector(int,int); From 73a33abb44fe8bd2907c044a1652867db3d82e83 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 00:32:06 -0400 Subject: [PATCH 0457/1217] add unit test for hybrid/scaled --- .../tests/mol-pair-hybrid-scaled.yaml | 104 ++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 unittest/force-styles/tests/mol-pair-hybrid-scaled.yaml diff --git a/unittest/force-styles/tests/mol-pair-hybrid-scaled.yaml b/unittest/force-styles/tests/mol-pair-hybrid-scaled.yaml new file mode 100644 index 0000000000..cc3acb50f0 --- /dev/null +++ b/unittest/force-styles/tests/mol-pair-hybrid-scaled.yaml @@ -0,0 +1,104 @@ +--- +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:45 2021 +epsilon: 5e-14 +skip_tests: gpu intel omp +prerequisites: ! | + atom full + pair lj/cut + pair coul/cut +pre_commands: ! | + variable scale equal 1.0 +post_commands: ! | + pair_modify mix arithmetic +input_file: in.fourmol +pair_style: hybrid/scaled v_scale lj/cut 8.0 0.6 coul/cut 8.0 0.4 coul/cut 8.0 +pair_coeff: ! | + 1 1 lj/cut 0.02 2.5 8 + 1 2 lj/cut 0.01 1.75 8 + 1 3 lj/cut 0.02 2.85 8 + 1 4 lj/cut 0.0173205 2.8 8 + 1 5 lj/cut 0.0173205 2.8 8 + 2 2 lj/cut 0.005 1 8 + 2 3 lj/cut 0.01 2.1 8 + 2 4 lj/cut 0.005 0.5 8 + 2 5 lj/cut 0.00866025 2.05 8 + 3 3 lj/cut 0.02 3.2 8 + 3 4 lj/cut 0.0173205 3.15 8 + 3 5 lj/cut 0.0173205 3.15 8 + 4 4 lj/cut 0.015 3.1 8 + 4 5 lj/cut 0.015 3.1 8 + 5 5 lj/cut 0.015 3.1 8 + * * coul/cut 1 + * * coul/cut 2 +extract: ! "" +natoms: 29 +init_vdwl: 749.237031537357 +init_coul: -127.494586297384 +init_stress: ! |2- + 2.1525607963688685e+03 2.1557327421151899e+03 4.6078904881742919e+03 -7.6038602729615206e+02 1.6844266627640316e+01 6.6957549356541904e+02 +init_forces: ! |2 + 1 -2.1092656751925425e+01 2.6988675971196511e+02 3.3315496490210148e+02 + 2 1.5859534558925552e+02 1.2807631885753918e+02 -1.8817306436807144e+02 + 3 -1.3530454720678361e+02 -3.8712939850050407e+02 -1.4565941679363837e+02 + 4 -7.8195539840070643e+00 2.1451967639963558e+00 -5.9041143405612999e+00 + 5 -2.9163954623584245e+00 -3.3469203159528891e+00 1.2074681739853981e+01 + 6 -8.2989063447195736e+02 9.6019318342576571e+02 1.1479359629470548e+03 + 7 5.7874538635311936e+01 -3.3533985555183068e+02 -1.7140659049826711e+03 + 8 1.4280513303191131e+02 -1.0509295075299345e+02 4.0233495763755388e+02 + 9 8.0984846358566287e+01 7.9600519879262990e+01 3.5197302607961126e+02 + 10 5.3089511229361369e+02 -6.0998478582862322e+02 -1.8376190026890427e+02 + 11 -3.3416993160125812e+00 -4.7792759715873308e+00 -1.0199030124309976e+01 + 12 2.0837574127335213e+01 9.8678992274266921e+00 -6.6547856883058829e+00 + 13 7.7163253261199216e+00 -3.2213746930547997e+00 -1.5767800864580894e-01 + 14 -4.6138299494911639e+00 1.1336312962250332e+00 -8.7660603717255832e+00 + 15 1.6301594996052212e-02 8.3212544078493291e+00 2.0473863128880430e+00 + 16 4.6221152690976908e+02 -3.3124444344467344e+02 -1.1865036959698600e+03 + 17 -4.5568726200724092e+02 3.2159231068141992e+02 1.1980747895060381e+03 + 18 1.2559081069243214e+00 6.6417071126352401e+00 -9.8829024661057083e+00 + 19 1.6184514948299680e+00 -1.6594104323923884e+00 5.6561121961572223e+00 + 20 -3.4526823962510336e+00 -3.1794201827804485e+00 4.2593058942069533e+00 + 21 -6.9075184494915916e+01 -8.0130885501011278e+01 2.1539206802020570e+02 + 22 -1.0659100672969126e+02 -2.5122518903211912e+01 -1.6283765584018167e+02 + 23 1.7515797811309091e+02 1.0400246780074602e+02 -5.2024018223038112e+01 + 24 3.4171625917777114e+01 -2.0194713552213176e+02 1.0982444762500101e+02 + 25 -1.4493448920889654e+02 2.0799041369281703e+01 -1.2091050237305346e+02 + 26 1.0983611557367320e+02 1.8026252731144598e+02 1.2199612526237862e+01 + 27 4.8962849172262665e+01 -2.1594262411895852e+02 8.6423873663236122e+01 + 28 -1.7556665080686602e+02 7.2243004627719102e+01 -1.1798867746650107e+02 + 29 1.2734696054095977e+02 1.4335517724642804e+02 3.2138218235426962e+01 +run_vdwl: 719.583657033589 +run_coul: -127.40544584254 +run_stress: ! |2- + 2.1066855251881925e+03 2.1118463017620702e+03 4.3411898896739367e+03 -7.3939094916433964e+02 3.4004309224046892e+01 6.3091802194682043e+02 +run_forces: ! |2 + 1 -1.8063372896871861e+01 2.6678105157873705e+02 3.2402996659149238e+02 + 2 1.5330358878115447e+02 1.2380492572678898e+02 -1.8151333240574237e+02 + 3 -1.3354888440944052e+02 -3.7931758440809585e+02 -1.4288689214683646e+02 + 4 -7.7881294728555828e+00 2.1395223669670709e+00 -5.8946911982403414e+00 + 5 -2.9015406841040750e+00 -3.3190775902304690e+00 1.2028378254388521e+01 + 6 -8.0488833369818803e+02 9.1802981835006187e+02 1.0244099127408372e+03 + 7 5.5465440662485150e+01 -3.1049131627300432e+02 -1.5711945284966396e+03 + 8 1.3295629283853211e+02 -9.6566834572636509e+01 3.9097872808487460e+02 + 9 7.8594917874857543e+01 7.6787239820699739e+01 3.4114513928465578e+02 + 10 5.2093084326233679e+02 -5.9871672888830824e+02 -1.8144904320802175e+02 + 11 -3.3489474910616370e+00 -4.7299066233626039e+00 -1.0148722292306179e+01 + 12 2.0817110693939330e+01 9.8621648346024777e+00 -6.7801624810903709e+00 + 13 7.6705047254095406e+00 -3.1868508087899996e+00 -1.5820764985177732e-01 + 14 -4.5784791310044675e+00 1.1138053855319887e+00 -8.6502065778611730e+00 + 15 -2.0858645012343142e-03 8.3343285345071436e+00 2.0653788728248101e+00 + 16 4.3381526742384807e+02 -3.1216388880293573e+02 -1.1109931745334770e+03 + 17 -4.2715774864577224e+02 3.0231264864237801e+02 1.1227484174344033e+03 + 18 1.2031503133104606e+00 6.6109154581424221e+00 -9.8172457746610178e+00 + 19 1.6542029696015907e+00 -1.6435312394752812e+00 5.6634735276627497e+00 + 20 -3.4397850729417945e+00 -3.1640002526012512e+00 4.1983600861482540e+00 + 21 -6.8065111490654829e+01 -7.8373161130023504e+01 2.1145341222255522e+02 + 22 -1.0497862711706458e+02 -2.4878742273401844e+01 -1.5988817620288421e+02 + 23 1.7253257365878264e+02 1.0200250230245655e+02 -5.1030905034776815e+01 + 24 3.5759299481226734e+01 -2.0057859782619599e+02 1.1032111627497152e+02 + 25 -1.4570195714964908e+02 2.0679748005808605e+01 -1.2162175868970056e+02 + 26 1.0901403460528100e+02 1.7901644500696690e+02 1.2412674623332103e+01 + 27 4.8035883250870448e+01 -2.1205445789284894e+02 8.4315888267103702e+01 + 28 -1.7229323056476886e+02 7.0823266235363889e+01 -1.1557273097021344e+02 + 29 1.2500312314724302e+02 1.4088629633289813e+02 3.1828931397054006e+01 +... From f2039b56675cce11f90c09b0cd4ad23d0f4b4e00 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 00:36:29 -0400 Subject: [PATCH 0458/1217] add hybrid/scaled pair style to summary tables --- doc/src/Commands_pair.rst | 2 +- doc/src/pair_style.rst | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 080f3eff20..e82713f8a4 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -26,6 +26,7 @@ OPT. * :doc:`zero ` * :doc:`hybrid (k) ` * :doc:`hybrid/overlay (k) ` + * :doc:`hybrid/scaled ` * :doc:`kim ` * :doc:`list ` * @@ -33,7 +34,6 @@ OPT. * * * - * * :doc:`adp (o) ` * :doc:`agni (o) ` * :doc:`airebo (io) ` diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 89530895c4..bc2340d729 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -95,6 +95,7 @@ accelerated styles exist. * :doc:`none ` - turn off pairwise interactions * :doc:`hybrid ` - multiple styles of pairwise interactions * :doc:`hybrid/overlay ` - multiple styles of superposed pairwise interactions +* :doc:`hybrid/scaled ` - multiple styles of scaled superposed pairwise interactions * :doc:`zero ` - neighbor list but no interactions * :doc:`adp ` - angular dependent potential (ADP) of Mishin From de158c40ad83a815546a1e07884c1ca37eb2a310 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 00:38:58 -0400 Subject: [PATCH 0459/1217] add support for torque --- src/pair_hybrid_scaled.cpp | 21 ++++++++++++++++++++- src/pair_hybrid_scaled.h | 2 +- 2 files changed, 21 insertions(+), 2 deletions(-) diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index da8631dcf8..92cdc767fe 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -31,7 +31,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ PairHybridScaled::PairHybridScaled(LAMMPS *lmp) - : PairHybrid(lmp), fsum(nullptr), scaleval(nullptr), scaleidx(nullptr) + : PairHybrid(lmp), fsum(nullptr), tsum(nullptr), + scaleval(nullptr), scaleidx(nullptr) { nmaxfsum = -1; } @@ -92,15 +93,23 @@ void PairHybridScaled::compute(int eflag, int vflag) if (atom->nmax > nmaxfsum) { memory->destroy(fsum); + if (atom->torque_flag) memory->destroy(tsum); nmaxfsum = atom->nmax; memory->create(fsum,nmaxfsum,3,"pair:fsum"); + if (atom->torque_flag) memory->create(tsum,nmaxfsum,3,"pair:tsum"); } const int nall = atom->nlocal + atom->nghost; auto f = atom->f; + auto t = atom->torque; for (i = 0; i < nall; ++i) { fsum[i][0] = f[i][0]; fsum[i][1] = f[i][1]; fsum[i][2] = f[i][2]; + if (atom->torque_flag) { + tsum[i][0] = t[i][0]; + tsum[i][1] = t[i][1]; + tsum[i][2] = t[i][2]; + } } // check if global component of incoming vflag = VIRIAL_FDOTR @@ -147,6 +156,11 @@ void PairHybridScaled::compute(int eflag, int vflag) fsum[i][0] += scale*f[i][0]; fsum[i][1] += scale*f[i][1]; fsum[i][2] += scale*f[i][2]; + if (atom->torque_flag) { + tsum[i][0] += scale*t[i][0]; + tsum[i][1] += scale*t[i][1]; + tsum[i][2] += scale*t[i][2]; + } } restore_special(saved_special); @@ -207,6 +221,11 @@ void PairHybridScaled::compute(int eflag, int vflag) f[i][0] = fsum[i][0]; f[i][1] = fsum[i][1]; f[i][2] = fsum[i][2]; + if (atom->torque_flag) { + t[i][0] = tsum[i][0]; + t[i][1] = tsum[i][1]; + t[i][2] = tsum[i][2]; + } } delete [] saved_special; diff --git a/src/pair_hybrid_scaled.h b/src/pair_hybrid_scaled.h index fbfcdab23a..38a031ad84 100644 --- a/src/pair_hybrid_scaled.h +++ b/src/pair_hybrid_scaled.h @@ -43,7 +43,7 @@ class PairHybridScaled : public PairHybrid { void copy_svector(int,int); protected: - double **fsum; + double **fsum, **tsum; double *scaleval; int *scaleidx; std::vector scalevars; From 4c23ecfd4ff4c856e3b65d48fa4aad3f36409b46 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 00:47:22 -0400 Subject: [PATCH 0460/1217] error out on special atom styles --- src/pair_hybrid_scaled.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index 92cdc767fe..27a02a8d90 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -14,6 +14,7 @@ #include "pair_hybrid_scaled.h" #include "atom.h" +#include "atom_vec.h" #include "comm.h" #include "error.h" #include "force.h" @@ -243,6 +244,9 @@ void PairHybridScaled::settings(int narg, char **arg) error->all(FLERR,fmt::format("Must use pair_style {}/kk with Kokkos", force->pair_style)); + if (atom->avec->forceclearflag) + error->all(FLERR,"Atom style is not compatible with pair_style hybrid/scaled"); + // delete old lists, since cannot just change settings if (nstyles > 0) { From 7b45b691f4a926328f53fdcc95c9d78261656269 Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Fri, 9 Apr 2021 13:31:40 +0200 Subject: [PATCH 0461/1217] pair_pace.cpp: check that units are "metal" update ace-evaluator (download link + md5sum in cmake and make build systems): accept multilines comment at the beginning of potential.ace file add first comment line for potentials/Cu-PBE-core-rep.ace --- cmake/Modules/Packages/USER-PACE.cmake | 4 ++-- lib/pace/Install.py | 12 +++++++----- potentials/Cu-PBE-core-rep.ace | 2 ++ src/USER-PACE/pair_pace.cpp | 5 +++++ 4 files changed, 16 insertions(+), 7 deletions(-) diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/USER-PACE.cmake index e8262f7d40..df1fb023a5 100644 --- a/cmake/Modules/Packages/USER-PACE.cmake +++ b/cmake/Modules/Packages/USER-PACE.cmake @@ -1,6 +1,6 @@ -set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.2.3.upd2.tar.gz" CACHE STRING "URL for PACE evaluator library sources") -set(PACELIB_MD5 "8fd1162724d349b930e474927197f20d" CACHE STRING "MD5 checksum of PACE evaluator library tarball") +set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz" CACHE STRING "URL for PACE evaluator library sources") +set(PACELIB_MD5 "4db54962fbd6adcf8c18d46e1798ceb5" CACHE STRING "MD5 checksum of PACE evaluator library tarball") mark_as_advanced(PACELIB_URL) mark_as_advanced(PACELIB_MD5) diff --git a/lib/pace/Install.py b/lib/pace/Install.py index 91aa8b3a46..08bbb331bb 100644 --- a/lib/pace/Install.py +++ b/lib/pace/Install.py @@ -12,20 +12,22 @@ from argparse import ArgumentParser sys.path.append('..') from install_helpers import fullpath, geturl, checkmd5sum -parser = ArgumentParser(prog='Install.py', - description="LAMMPS library build wrapper script") - # settings thisdir = fullpath('.') -version = "v.2021.2.3.upd2" +version = 'v.2021.4.9' # known checksums for different PACE versions. used to validate the download. checksums = { \ - 'v.2021.2.3.upd2' : '8fd1162724d349b930e474927197f20d', \ + 'v.2021.2.3.upd2' : '8fd1162724d349b930e474927197f20d', + 'v.2021.4.9' : '4db54962fbd6adcf8c18d46e1798ceb5', } +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + + # help message HELP = """ diff --git a/potentials/Cu-PBE-core-rep.ace b/potentials/Cu-PBE-core-rep.ace index 338675f718..511bb9af7f 100644 --- a/potentials/Cu-PBE-core-rep.ace +++ b/potentials/Cu-PBE-core-rep.ace @@ -1,3 +1,5 @@ +# DATE: 2021-04-08 UNITS: metal CONTRIBUTOR: Yury Lysogorskiy CITATION: npj Comp. Mat., submitted (2021) + nelements=1 elements: Cu diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index c12753603a..f59291b33e 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -25,6 +25,7 @@ Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, #include "neigh_list.h" #include "neigh_request.h" #include "neighbor.h" +#include "update.h" #include #include @@ -252,6 +253,10 @@ void PairPACE::settings(int narg, char **arg) { if (narg > 1) error->all(FLERR,"Illegal pair_style command."); + // ACE potentials are parameterized in metal units + if (strcmp("metal",update->unit_style) != 0) + error->all(FLERR,"ACE potentials require 'metal' units"); + recursive = true; // default evaluator style: RECURSIVE if (narg > 0) { if (strcmp(arg[0], RECURSIVE_KEYWORD) == 0) From 924a331342b5a1a57df988c4656b25992ecab067 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 09:08:39 -0400 Subject: [PATCH 0462/1217] avoid uninitialized data usage reported by coverity scan --- src/GRANULAR/fix_wall_gran.cpp | 2 +- src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp | 3 +-- src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp | 3 +-- 3 files changed, 3 insertions(+), 5 deletions(-) diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 51dca15e7b..136472f1cd 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -1261,6 +1261,7 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, k_tangential = tangential_coeffs[0]; damp_tangential = tangential_coeffs[1]*damp_normal_prefactor; + Fscrit = tangential_coeffs[2] * Fncrit; int thist0 = tangential_history_index; int thist1 = thist0 + 1; @@ -1346,7 +1347,6 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, } // rescale frictional displacements and forces if needed - Fscrit = tangential_coeffs[2] * Fncrit; fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3); if (fs > Fscrit) { shrmag = sqrt(history[thist0]*history[thist0] + diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index d1f9d33e8a..72fa4ff064 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -586,9 +586,9 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype, int itable; r2inv = 1.0/rsq; + r = sqrt(rsq); if (rsq < cut_coulsq) { if (!ncoultablebits || rsq <= tabinnersq) { - r = sqrt(rsq); grij = g_ewald * r; expm2 = exp(-grij*grij); t = 1.0 / (1.0 + EWALD_P*grij); @@ -621,7 +621,6 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype, forcecoul2 = 0.0; prefactor2 = 0.0; } else { - r = sqrt(rsq); rrij = lj2[itype][jtype]*r; expn2 = exp(-rrij*rrij); erfc2 = erfc(rrij); diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp index c7fcac855a..4e52226eaf 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -586,9 +586,9 @@ double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype, int itable; r2inv = 1.0/rsq; + r = sqrt(rsq); if (rsq < cut_coulsq) { if (!ncoultablebits || rsq <= tabinnersq) { - r = sqrt(rsq); grij = g_ewald * r; expm2 = exp(-grij*grij); t = 1.0 / (1.0 + EWALD_P*grij); @@ -613,7 +613,6 @@ double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype, } else forcecoul = 0.0; if (rsq < cut_ljsq[itype][jtype]) { - r = sqrt(rsq); expb = lj3[itype][jtype]*exp(-lj1[itype][jtype]*r); forcelj = expb*lj1[itype][jtype]*r; r6inv = r2inv*r2inv*r2inv; From 97977e3e68d1e60e84c3883cfa8ec7f986eef730 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 09:44:23 -0400 Subject: [PATCH 0463/1217] incorrect check for additional argument in pair_modify nofdotr --- src/pair.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/pair.cpp b/src/pair.cpp index 767fa638cf..0d90b0ce39 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -204,7 +204,6 @@ void Pair::modify_params(int narg, char **arg) else error->all(FLERR,"Illegal pair_modify command"); iarg += 2; } else if (strcmp(arg[iarg],"nofdotr") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command"); no_virial_fdotr_compute = 1; ++iarg; } else error->all(FLERR,"Illegal pair_modify command"); From d507c57c8a0b7c22b978e49a03a750433d4073d7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 09:45:09 -0400 Subject: [PATCH 0464/1217] add missing zeroing of the torque array, reformat code --- src/pair_hybrid_scaled.cpp | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index 27a02a8d90..62b94d9ba9 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -134,9 +134,10 @@ void PairHybridScaled::compute(int eflag, int vflag) for (m = 0; m < nstyles; m++) { - // clear forces + // clear forces and torques memset(&f[0][0],0,nall*3*sizeof(double)); + if (atom->torque_flag) memset(&t[0][0],0,nall*3*sizeof(double)); set_special(m); @@ -171,17 +172,17 @@ void PairHybridScaled::compute(int eflag, int vflag) if (respaflag && !respa->tally_global) continue; if (eflag_global) { - eng_vdwl += scale * styles[m]->eng_vdwl; - eng_coul += scale * styles[m]->eng_coul; + eng_vdwl += scale*styles[m]->eng_vdwl; + eng_coul += scale*styles[m]->eng_coul; } if (vflag_global) { - for (n = 0; n < 6; n++) virial[n] += scale * styles[m]->virial[n]; + for (n = 0; n < 6; n++) virial[n] += scale*styles[m]->virial[n]; } if (eflag_atom) { n = atom->nlocal; if (force->newton_pair) n += atom->nghost; double *eatom_substyle = styles[m]->eatom; - for (i = 0; i < n; i++) eatom[i] += scale * eatom_substyle[i]; + for (i = 0; i < n; i++) eatom[i] += scale*eatom_substyle[i]; } if (vflag_atom) { n = atom->nlocal; @@ -189,7 +190,7 @@ void PairHybridScaled::compute(int eflag, int vflag) double **vatom_substyle = styles[m]->vatom; for (i = 0; i < n; i++) for (j = 0; j < 6; j++) - vatom[i][j] += scale * vatom_substyle[i][j]; + vatom[i][j] += scale*vatom_substyle[i][j]; } // substyles may be CENTROID_SAME or CENTROID_AVAIL @@ -201,22 +202,22 @@ void PairHybridScaled::compute(int eflag, int vflag) double **cvatom_substyle = styles[m]->cvatom; for (i = 0; i < n; i++) for (j = 0; j < 9; j++) - cvatom[i][j] += scale * cvatom_substyle[i][j]; + cvatom[i][j] += scale*cvatom_substyle[i][j]; } else { double **vatom_substyle = styles[m]->vatom; for (i = 0; i < n; i++) { for (j = 0; j < 6; j++) { - cvatom[i][j] += scale * vatom_substyle[i][j]; + cvatom[i][j] += scale*vatom_substyle[i][j]; } for (j = 6; j < 9; j++) { - cvatom[i][j] += scale * vatom_substyle[i][j-3]; + cvatom[i][j] += scale*vatom_substyle[i][j-3]; } } } } } - // copy accumulated forces to original force array + // copy accumulated scaled forces to original force array for (i = 0; i < nall; ++i) { f[i][0] = fsum[i][0]; From b6b101f29af3c18df6bc223c5e12aa2e8e0fb376 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 09:54:47 -0400 Subject: [PATCH 0465/1217] update melt example to use velocity with loop geom for consistent velocities --- examples/melt/in.melt | 2 +- examples/melt/log.27Nov18.melt.g++.4 | 85 ------------------- ...Nov18.melt.g++.1 => log.8Apr21.melt.g++.1} | 50 +++++------ examples/melt/log.8Apr21.melt.g++.4 | 85 +++++++++++++++++++ 4 files changed, 111 insertions(+), 111 deletions(-) delete mode 100644 examples/melt/log.27Nov18.melt.g++.4 rename examples/melt/{log.27Nov18.melt.g++.1 => log.8Apr21.melt.g++.1} (51%) create mode 100644 examples/melt/log.8Apr21.melt.g++.4 diff --git a/examples/melt/in.melt b/examples/melt/in.melt index 8431a4344e..f169dc2ffc 100644 --- a/examples/melt/in.melt +++ b/examples/melt/in.melt @@ -9,7 +9,7 @@ create_box 1 box create_atoms 1 box mass 1 1.0 -velocity all create 3.0 87287 +velocity all create 3.0 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 diff --git a/examples/melt/log.27Nov18.melt.g++.4 b/examples/melt/log.27Nov18.melt.g++.4 deleted file mode 100644 index 927895b1cd..0000000000 --- a/examples/melt/log.27Nov18.melt.g++.4 +++ /dev/null @@ -1,85 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# 3d Lennard-Jones melt - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 -region box block 0 10 0 10 0 10 -create_box 1 box -Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 4000 atoms - Time spent = 0.00041604 secs -mass 1 1.0 - -velocity all create 3.0 87287 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify every 20 delay 0 check no - -fix 1 all nve - -#dump id all atom 50 dump.melt - -#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -thermo 50 -run 250 -Neighbor list info ... - update every 20 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 12 12 12 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 3 -6.7733681 0 -2.2744931 -3.7033504 - 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 - 100 1.6503357 -4.756014 0 -2.2811293 5.8050524 - 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 - 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 - 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 -Loop time of 0.223329 on 4 procs for 250 steps with 4000 atoms - -Performance: 483592.231 tau/day, 1119.426 timesteps/s -97.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.15881 | 0.16314 | 0.16859 | 0.9 | 73.05 -Neigh | 0.02472 | 0.025218 | 0.025828 | 0.3 | 11.29 -Comm | 0.025185 | 0.030091 | 0.034351 | 1.9 | 13.47 -Output | 0.00015163 | 0.00019169 | 0.00030899 | 0.0 | 0.09 -Modify | 0.0037532 | 0.0038366 | 0.0040054 | 0.2 | 1.72 -Other | | 0.00085 | | | 0.38 - -Nlocal: 1000 ave 1010 max 982 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 2703.75 ave 2713 max 2689 min -Histogram: 1 0 0 0 0 0 0 2 0 1 -Neighs: 37915.5 ave 39239 max 36193 min -Histogram: 1 0 0 0 0 1 1 0 0 1 - -Total # of neighbors = 151662 -Ave neighs/atom = 37.9155 -Neighbor list builds = 12 -Dangerous builds not checked -Total wall time: 0:00:00 diff --git a/examples/melt/log.27Nov18.melt.g++.1 b/examples/melt/log.8Apr21.melt.g++.1 similarity index 51% rename from examples/melt/log.27Nov18.melt.g++.1 rename to examples/melt/log.8Apr21.melt.g++.1 index 69b39e6011..a3b6d003db 100644 --- a/examples/melt/log.27Nov18.melt.g++.1 +++ b/examples/melt/log.8Apr21.melt.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (27 Nov 2018) +LAMMPS (8 Apr 2021) using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt @@ -6,17 +6,17 @@ units lj atom_style atomic lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 region box block 0 10 0 10 0 10 create_box 1 box -Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.795962 16.795962 16.795962) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms - Time spent = 0.000645638 secs + create_atoms CPU = 0.002 seconds mass 1 1.0 -velocity all create 3.0 87287 +velocity all create 3.0 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 @@ -48,38 +48,38 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.222 | 3.222 | 3.222 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733681 0 -2.2744931 -3.7033504 - 50 1.6758903 -4.7955425 0 -2.2823355 5.670064 - 100 1.6458363 -4.7492704 0 -2.2811332 5.8691042 - 150 1.6324555 -4.7286791 0 -2.280608 5.9589514 - 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 - 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 -Loop time of 0.729809 on 1 procs for 250 steps with 4000 atoms + 50 1.6842865 -4.8082494 0 -2.2824513 5.5666131 + 100 1.6712577 -4.7875609 0 -2.281301 5.6613913 + 150 1.6444751 -4.7471034 0 -2.2810074 5.8614211 + 200 1.6471542 -4.7509053 0 -2.2807916 5.8805431 + 250 1.6645597 -4.7774327 0 -2.2812174 5.7526089 +Loop time of 1.61045 on 1 procs for 250 steps with 4000 atoms -Performance: 147983.915 tau/day, 342.555 timesteps/s +Performance: 67062.020 tau/day, 155.236 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.60661 | 0.60661 | 0.60661 | 0.0 | 83.12 -Neigh | 0.092198 | 0.092198 | 0.092198 | 0.0 | 12.63 -Comm | 0.013581 | 0.013581 | 0.013581 | 0.0 | 1.86 -Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.02 -Modify | 0.014395 | 0.014395 | 0.014395 | 0.0 | 1.97 -Other | | 0.002878 | | | 0.39 +Pair | 1.3961 | 1.3961 | 1.3961 | 0.0 | 86.69 +Neigh | 0.13555 | 0.13555 | 0.13555 | 0.0 | 8.42 +Comm | 0.037732 | 0.037732 | 0.037732 | 0.0 | 2.34 +Output | 0.0003345 | 0.0003345 | 0.0003345 | 0.0 | 0.02 +Modify | 0.038016 | 0.038016 | 0.038016 | 0.0 | 2.36 +Other | | 0.002731 | | | 0.17 -Nlocal: 4000 ave 4000 max 4000 min +Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5499 ave 5499 max 5499 min +Nghost: 5506.00 ave 5506 max 5506 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 151513 ave 151513 max 151513 min +Neighs: 151788.0 ave 151788 max 151788 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 151513 -Ave neighs/atom = 37.8783 +Total # of neighbors = 151788 +Ave neighs/atom = 37.947000 Neighbor list builds = 12 Dangerous builds not checked -Total wall time: 0:00:00 +Total wall time: 0:00:01 diff --git a/examples/melt/log.8Apr21.melt.g++.4 b/examples/melt/log.8Apr21.melt.g++.4 new file mode 100644 index 0000000000..1edbeac7aa --- /dev/null +++ b/examples/melt/log.8Apr21.melt.g++.4 @@ -0,0 +1,85 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.795962 16.795962 16.795962) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4000 atoms + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 3.0 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +#dump id all atom 50 dump.melt + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.706 | 2.706 | 2.706 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733681 0 -2.2744931 -3.7033504 + 50 1.6842865 -4.8082494 0 -2.2824513 5.5666131 + 100 1.6712577 -4.7875609 0 -2.281301 5.6613913 + 150 1.6444751 -4.7471034 0 -2.2810074 5.8614211 + 200 1.6471542 -4.7509053 0 -2.2807916 5.8805431 + 250 1.6645597 -4.7774327 0 -2.2812174 5.7526089 +Loop time of 0.490832 on 4 procs for 250 steps with 4000 atoms + +Performance: 220034.754 tau/day, 509.340 timesteps/s +96.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.35932 | 0.37256 | 0.38746 | 1.9 | 75.90 +Neigh | 0.035928 | 0.038449 | 0.042344 | 1.3 | 7.83 +Comm | 0.053452 | 0.068917 | 0.08485 | 5.3 | 14.04 +Output | 0.00015545 | 0.00023746 | 0.00047684 | 0.0 | 0.05 +Modify | 0.0096958 | 0.0097951 | 0.0098989 | 0.1 | 2.00 +Other | | 0.0008721 | | | 0.18 + +Nlocal: 1000.00 ave 1008 max 987 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 2711.25 ave 2728 max 2693 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 37947.0 ave 38966 max 37338 min +Histogram: 1 1 0 1 0 0 0 0 0 1 + +Total # of neighbors = 151788 +Ave neighs/atom = 37.947000 +Neighbor list builds = 12 +Dangerous builds not checked +Total wall time: 0:00:00 From 08471cb88ed0a88d6dc0e83d2dc758ab73080124 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 10:29:36 -0400 Subject: [PATCH 0466/1217] update path to updated log file --- unittest/python/python-formats.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/python/python-formats.py b/unittest/python/python-formats.py index c093e9bebb..ca877b8305 100644 --- a/unittest/python/python-formats.py +++ b/unittest/python/python-formats.py @@ -4,7 +4,7 @@ from lammps.formats import LogFile, AvgChunkFile EXAMPLES_DIR=os.path.abspath(os.path.join(__file__, '..', '..', '..', 'examples')) -DEFAULT_STYLE_EXAMPLE_LOG="melt/log.27Nov18.melt.g++.1" +DEFAULT_STYLE_EXAMPLE_LOG="melt/log.8Apr21.melt.g++.1" MULTI_STYLE_EXAMPLE_LOG="peptide/log.27Nov18.peptide.g++.1" AVG_CHUNK_FILE="VISCOSITY/profile.13Oct16.nemd.2d.g++.1" From ded22bf8bc68cc20cc6333866fe447af0d7d3c02 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 11:36:10 -0400 Subject: [PATCH 0467/1217] Minor changes to dump_atom_gz/dump_atom_zstd --- src/COMPRESS/dump_atom_gz.cpp | 5 +---- src/COMPRESS/dump_atom_zstd.cpp | 4 ++-- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index 071af2167d..254e146800 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -11,16 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "dump_atom_gz.h" #include "domain.h" +#include "dump_atom_gz.h" #include "error.h" -#include "file_writer.h" #include "update.h" - #include - using namespace LAMMPS_NS; DumpAtomGZ::DumpAtomGZ(LAMMPS *lmp, int narg, char **arg) : diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index 300a4c81cb..dd744b5d49 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -43,7 +43,7 @@ DumpAtomZstd::~DumpAtomZstd() /* ---------------------------------------------------------------------- generic opening of a dump file - ASCII or binary or zstdipped + ASCII or binary or compressed some derived classes override this function ------------------------------------------------------------------------- */ @@ -180,7 +180,7 @@ int DumpAtomZstd::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, e.what()); + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; From 2682663df6ac7ee5092b2df090a95c5349074471 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 11:41:45 -0400 Subject: [PATCH 0468/1217] Use GzFileWriter in dump cfg/gz --- src/COMPRESS/dump_cfg_gz.cpp | 88 ++++++++----------- src/COMPRESS/dump_cfg_gz.h | 5 +- src/COMPRESS/dump_cfg_zstd.cpp | 3 +- unittest/formats/test_dump_cfg_compressed.cpp | 4 +- 4 files changed, 41 insertions(+), 59 deletions(-) diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp index 378baf502f..6bbf118789 100644 --- a/src/COMPRESS/dump_cfg_gz.cpp +++ b/src/COMPRESS/dump_cfg_gz.cpp @@ -11,41 +11,30 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "dump_cfg_gz.h" #include "atom.h" #include "domain.h" +#include "dump_cfg_gz.h" #include "error.h" #include "update.h" - #include - using namespace LAMMPS_NS; #define UNWRAPEXPAND 10.0 DumpCFGGZ::DumpCFGGZ(LAMMPS *lmp, int narg, char **arg) : DumpCFG(lmp, narg, arg) { - gzFp = nullptr; - - compression_level = Z_BEST_COMPRESSION; - if (!compressed) error->all(FLERR,"Dump cfg/gz only writes compressed files"); } - /* ---------------------------------------------------------------------- */ DumpCFGGZ::~DumpCFGGZ() { - if (gzFp) gzclose(gzFp); - gzFp = nullptr; - fp = nullptr; } - /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or gzipped @@ -95,17 +84,12 @@ void DumpCFGGZ::openfile() // each proc with filewriter = 1 opens a file if (filewriter) { - std::string mode; - if (append_flag) { - mode = fmt::format("ab{}", compression_level); - } else { - mode = fmt::format("wb{}", compression_level); + try { + writer.open(filecurrent, append_flag); + } catch (FileWriterException &e) { + error->one(FLERR, e.what()); } - - gzFp = gzopen(filecurrent, mode.c_str()); - - if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file"); - } else gzFp = nullptr; + } // delete string with timestep replaced @@ -127,30 +111,30 @@ void DumpCFGGZ::write_header(bigint n) if (atom->peri_flag) scale = atom->pdscale; else if (unwrapflag == 1) scale = UNWRAPEXPAND; - char str[64]; - sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT); - gzprintf(gzFp,str,n); - gzprintf(gzFp,"A = %g Angstrom (basic length-scale)\n",scale); - gzprintf(gzFp,"H0(1,1) = %g A\n",domain->xprd); - gzprintf(gzFp,"H0(1,2) = 0 A \n"); - gzprintf(gzFp,"H0(1,3) = 0 A \n"); - gzprintf(gzFp,"H0(2,1) = %g A \n",domain->xy); - gzprintf(gzFp,"H0(2,2) = %g A\n",domain->yprd); - gzprintf(gzFp,"H0(2,3) = 0 A \n"); - gzprintf(gzFp,"H0(3,1) = %g A \n",domain->xz); - gzprintf(gzFp,"H0(3,2) = %g A \n",domain->yz); - gzprintf(gzFp,"H0(3,3) = %g A\n",domain->zprd); - gzprintf(gzFp,".NO_VELOCITY.\n"); - gzprintf(gzFp,"entry_count = %d\n",nfield-2); + std::string header = fmt::format("Number of particles = {}\n", n); + header += fmt::format("A = {0:g} Angstrom (basic length-scale)\n", scale); + header += fmt::format("H0(1,1) = {0:g} A\n",domain->xprd); + header += fmt::format("H0(1,2) = 0 A \n"); + header += fmt::format("H0(1,3) = 0 A \n"); + header += fmt::format("H0(2,1) = {0:g} A \n",domain->xy); + header += fmt::format("H0(2,2) = {0:g} A\n",domain->yprd); + header += fmt::format("H0(2,3) = 0 A \n"); + header += fmt::format("H0(3,1) = {0:g} A \n",domain->xz); + header += fmt::format("H0(3,2) = {0:g} A \n",domain->yz); + header += fmt::format("H0(3,3) = {0:g} A\n",domain->zprd); + header += fmt::format(".NO_VELOCITY.\n"); + header += fmt::format("entry_count = {}\n",nfield-2); for (int i = 0; i < nfield-5; i++) - gzprintf(gzFp,"auxiliary[%d] = %s\n",i,auxname[i]); + header += fmt::format("auxiliary[{}] = {}\n",i,auxname[i]); + + writer.write(header.c_str(), header.length()); } /* ---------------------------------------------------------------------- */ void DumpCFGGZ::write_data(int n, double *mybuf) { - gzwrite(gzFp,mybuf,sizeof(char)*n); + writer.write(mybuf, n); } /* ---------------------------------------------------------------------- */ @@ -160,11 +144,11 @@ void DumpCFGGZ::write() DumpCFG::write(); if (filewriter) { if (multifile) { - gzclose(gzFp); - gzFp = nullptr; + writer.close(); } else { - if (flush_flag) - gzflush(gzFp,Z_SYNC_FLUSH); + if (flush_flag && writer.isopen()) { + writer.flush(); + } } } } @@ -175,16 +159,16 @@ int DumpCFGGZ::modify_param(int narg, char **arg) { int consumed = DumpCFG::modify_param(narg, arg); if (consumed == 0) { - if (strcmp(arg[0],"compression_level") == 0) { - if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); - int min_level = Z_DEFAULT_COMPRESSION; - int max_level = Z_BEST_COMPRESSION; - compression_level = utils::inumeric(FLERR, arg[1], false, lmp); - if (compression_level < min_level || compression_level > max_level) - error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level)); - return 2; + try { + if (strcmp(arg[0],"compression_level") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + int compression_level = utils::inumeric(FLERR, arg[1], false, lmp); + writer.setCompressionLevel(compression_level); + return 2; + } + } catch (FileWriterException &e) { + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; } - diff --git a/src/COMPRESS/dump_cfg_gz.h b/src/COMPRESS/dump_cfg_gz.h index 0c6ed24f06..2844902a38 100644 --- a/src/COMPRESS/dump_cfg_gz.h +++ b/src/COMPRESS/dump_cfg_gz.h @@ -21,7 +21,7 @@ DumpStyle(cfg/gz,DumpCFGGZ) #define LMP_DUMP_CFG_GZ_H #include "dump_cfg.h" -#include +#include "gz_file_writer.h" namespace LAMMPS_NS { @@ -31,8 +31,7 @@ class DumpCFGGZ : public DumpCFG { virtual ~DumpCFGGZ(); protected: - int compression_level; - gzFile gzFp; // file pointer for the compressed output stream + GzFileWriter writer; virtual void openfile(); virtual void write_header(bigint); diff --git a/src/COMPRESS/dump_cfg_zstd.cpp b/src/COMPRESS/dump_cfg_zstd.cpp index 459649c70a..978e695d1a 100644 --- a/src/COMPRESS/dump_cfg_zstd.cpp +++ b/src/COMPRESS/dump_cfg_zstd.cpp @@ -21,7 +21,6 @@ #include "domain.h" #include "dump_cfg_zstd.h" #include "error.h" -#include "file_writer.h" #include "update.h" #include @@ -46,7 +45,7 @@ DumpCFGZstd::~DumpCFGZstd() /* ---------------------------------------------------------------------- generic opening of a dump file - ASCII or binary or zstdipped + ASCII or binary or compressed some derived classes override this function ------------------------------------------------------------------------- */ diff --git a/unittest/formats/test_dump_cfg_compressed.cpp b/unittest/formats/test_dump_cfg_compressed.cpp index 20f902091b..6d5e8bcf04 100644 --- a/unittest/formats/test_dump_cfg_compressed.cpp +++ b/unittest/formats/test_dump_cfg_compressed.cpp @@ -234,7 +234,7 @@ TEST_F(DumpCfgCompressTest, compressed_modify_bad_param) command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.cfg"), fields)); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 compression_level 12"); ); } @@ -248,7 +248,7 @@ TEST_F(DumpCfgCompressTest, compressed_modify_multi_bad_param) command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.cfg"), fields)); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); ); } From 77de0273be242bd6bae9bd0e59fd99a69ff1449d Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 12:37:14 -0400 Subject: [PATCH 0469/1217] Fix typo --- src/dump_local.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 53a82b496f..8b9b309aff 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -112,7 +112,7 @@ DumpLocal::DumpLocal(LAMMPS *lmp, int narg, char **arg) : label = utils::strdup("ENTRIES"); - // if wildcard expansion occurred, free earg memory from exapnd_args() + // if wildcard expansion occurred, free earg memory from expand_args() if (expand) { for (int i = 0; i < nfield; i++) delete [] earg[i]; From e0e031aa4324082c53654df333b82ea2d4b9b0c0 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 13:38:18 -0400 Subject: [PATCH 0470/1217] Correct dump_modify example in docs --- doc/src/dump_modify.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 753cce703c..d072df5d4d 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -362,7 +362,7 @@ settings, reverting all values to their default format. compute 1 all property/local batom1 batom2 dump 1 all local 100 tmp.bonds index c_1[1] c_1[2] - dump_modify 1 format "%d %0.0f %0.0f" + dump_modify 1 format line "%d %0.0f %0.0f" will output the two atom IDs for atoms in each bond as integers. If the dump_modify command were omitted, they would appear as From 5c9a5ba8ac03f51ac1e3bf0457cc1742f003e4e7 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 14:48:38 -0400 Subject: [PATCH 0471/1217] Add missing code to allow customized formatting in dump local --- src/dump_local.cpp | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 8b9b309aff..dac8066236 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -225,6 +225,46 @@ int DumpLocal::modify_param(int narg, char **arg) delete [] label; label = utils::strdup(arg[1]); return 2; + } else if (strcmp(arg[0],"format") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + + if (strcmp(arg[1],"none") == 0) { + // just clear format_column_user allocated by this dump child class + for (int i = 0; i < nfield; i++) { + delete [] format_column_user[i]; + format_column_user[i] = nullptr; + } + return 2; + } else if (strcmp(arg[1],"int") == 0) { + delete [] format_int_user; + format_int_user = utils::strdup(arg[2]); + delete [] format_bigint_user; + int n = strlen(format_int_user) + 8; + format_bigint_user = new char[n]; + // replace "d" in format_int_user with bigint format specifier + // use of &str[1] removes leading '%' from BIGINT_FORMAT string + char *ptr = strchr(format_int_user,'d'); + if (ptr == nullptr) + error->all(FLERR, + "Dump_modify int format does not contain d character"); + char str[8]; + sprintf(str,"%s",BIGINT_FORMAT); + *ptr = '\0'; + sprintf(format_bigint_user,"%s%s%s",format_int_user,&str[1],ptr+1); + *ptr = 'd'; + + } else if (strcmp(arg[1],"float") == 0) { + delete [] format_float_user; + format_float_user = utils::strdup(arg[2]); + + } else { + int i = utils::inumeric(FLERR,arg[1],false,lmp) - 1; + if (i < 0 || i >= nfield) + error->all(FLERR,"Illegal dump_modify command"); + if (format_column_user[i]) delete [] format_column_user[i]; + format_column_user[i] = utils::strdup(arg[2]); + } + return 3; } return 0; } From dc71d8030694fb6c55588b94913182aa8f482f70 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 14:49:07 -0400 Subject: [PATCH 0472/1217] Add dump local tests --- unittest/formats/CMakeLists.txt | 5 + unittest/formats/test_dump_local.cpp | 195 +++++++++++++++++++++++++++ 2 files changed, 200 insertions(+) create mode 100644 unittest/formats/test_dump_local.cpp diff --git a/unittest/formats/CMakeLists.txt b/unittest/formats/CMakeLists.txt index be0d14c47d..4c6de98729 100644 --- a/unittest/formats/CMakeLists.txt +++ b/unittest/formats/CMakeLists.txt @@ -102,6 +102,11 @@ target_link_libraries(test_dump_cfg PRIVATE lammps GTest::GMock GTest::GTest) add_test(NAME DumpCfg COMMAND test_dump_cfg WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(DumpCfg PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") +add_executable(test_dump_local test_dump_local.cpp) +target_link_libraries(test_dump_local PRIVATE lammps GTest::GMock GTest::GTest) +add_test(NAME DumpLocal COMMAND test_dump_local WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) +set_tests_properties(DumpLocal PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") + if(BUILD_TOOLS) set_tests_properties(DumpAtom PROPERTIES ENVIRONMENT "BINARY2TXT_BINARY=$") set_tests_properties(DumpCustom PROPERTIES ENVIRONMENT "BINARY2TXT_BINARY=$") diff --git a/unittest/formats/test_dump_local.cpp b/unittest/formats/test_dump_local.cpp new file mode 100644 index 0000000000..fb38ca08ad --- /dev/null +++ b/unittest/formats/test_dump_local.cpp @@ -0,0 +1,195 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "../testing/core.h" +#include "../testing/systems/melt.h" +#include "../testing/utils.h" +#include "fmt/format.h" +#include "output.h" +#include "thermo.h" +#include "utils.h" +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include + +using ::testing::Eq; + +char *BINARY2TXT_BINARY = nullptr; +bool verbose = false; + +class DumpLocalTest : public MeltTest { + std::string dump_style = "local"; + +public: + void enable_triclinic() + { + BEGIN_HIDE_OUTPUT(); + command("change_box all triclinic"); + END_HIDE_OUTPUT(); + } + + void generate_dump(std::string dump_file, std::string dump_options, std::string dump_modify_options, int ntimesteps) + { + BEGIN_HIDE_OUTPUT(); + command(fmt::format("dump id all {} 1 {} {}", dump_style, dump_file, dump_options)); + + if (!dump_modify_options.empty()) { + command(fmt::format("dump_modify id {}", dump_modify_options)); + } + + command(fmt::format("run {} post no", ntimesteps)); + END_HIDE_OUTPUT(); + } + + void continue_dump(int ntimesteps) + { + BEGIN_HIDE_OUTPUT(); + command(fmt::format("run {} pre no post no", ntimesteps)); + END_HIDE_OUTPUT(); + } + + void SetUp() override { + MeltTest::SetUp(); + + BEGIN_HIDE_OUTPUT(); + command("compute comp all pair/local dist eng"); + END_HIDE_OUTPUT(); + } +}; + +TEST_F(DumpLocalTest, run0) +{ + auto dump_file = "dump_local_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + ASSERT_EQ(lines.size(), 873); + + ASSERT_THAT(lines[0], Eq("ITEM: TIMESTEP")); + ASSERT_EQ(std::stoi(lines[1]), 0); + + ASSERT_THAT(lines[2], Eq("ITEM: NUMBER OF ENTRIES")); + ASSERT_EQ(std::stoi(lines[3]), 864); + + ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS pp pp pp")); + ASSERT_EQ(utils::split_words(lines[5]).size(), 2); + ASSERT_EQ(utils::split_words(lines[6]).size(), 2); + ASSERT_EQ(utils::split_words(lines[7]).size(), 2); + ASSERT_THAT(lines[8], Eq("ITEM: ENTRIES index c_comp[1] ")); + ASSERT_EQ(utils::split_words(lines[9]).size(), 2); + ASSERT_THAT(lines[9], Eq("1 1.18765 ")); + delete_file(dump_file); +} + +TEST_F(DumpLocalTest, format_line_run0) +{ + auto dump_file = "dump_local_format_line_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "format line \"%d %20.8g\"", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + + ASSERT_EQ(utils::split_words(lines[9]).size(), 2); + ASSERT_THAT(lines[9], Eq("1 1.1876539 ")); + delete_file(dump_file); +} + +TEST_F(DumpLocalTest, format_int_run0) +{ + auto dump_file = "dump_local_format_int_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "format int \"%20d\"", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + + ASSERT_EQ(utils::split_words(lines[9]).size(), 2); + ASSERT_THAT(lines[9], Eq(" 1 1.18765 ")); + delete_file(dump_file); +} + +TEST_F(DumpLocalTest, format_float_run0) +{ + auto dump_file = "dump_local_format_float_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "format float \"%20.5g\"", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + + ASSERT_EQ(utils::split_words(lines[9]).size(), 2); + ASSERT_THAT(lines[9], Eq("1 1.1877 ")); + delete_file(dump_file); +} + +TEST_F(DumpLocalTest, format_column_run0) +{ + auto dump_file = "dump_local_format_column_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "format 1 \"%20d\"", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + + ASSERT_EQ(utils::split_words(lines[9]).size(), 2); + ASSERT_THAT(lines[9], Eq(" 1 1.18765 ")); + delete_file(dump_file); +} + +TEST_F(DumpLocalTest, no_buffer_run0) +{ + auto dump_file = "dump_local_format_line_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "buffer no", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + ASSERT_EQ(lines.size(), 873); + + ASSERT_THAT(lines[0], Eq("ITEM: TIMESTEP")); + ASSERT_EQ(std::stoi(lines[1]), 0); + + ASSERT_THAT(lines[2], Eq("ITEM: NUMBER OF ENTRIES")); + ASSERT_EQ(std::stoi(lines[3]), 864); + + ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS pp pp pp")); + ASSERT_EQ(utils::split_words(lines[5]).size(), 2); + ASSERT_EQ(utils::split_words(lines[6]).size(), 2); + ASSERT_EQ(utils::split_words(lines[7]).size(), 2); + ASSERT_THAT(lines[8], Eq("ITEM: ENTRIES index c_comp[1] ")); + ASSERT_EQ(utils::split_words(lines[9]).size(), 2); + ASSERT_THAT(lines[9], Eq("1 1.18765 ")); + delete_file(dump_file); +} + +int main(int argc, char **argv) +{ + MPI_Init(&argc, &argv); + ::testing::InitGoogleMock(&argc, argv); + + // handle arguments passed via environment variable + if (const char *var = getenv("TEST_ARGS")) { + std::vector env = utils::split_words(var); + for (auto arg : env) { + if (arg == "-v") { + verbose = true; + } + } + } + + BINARY2TXT_BINARY = getenv("BINARY2TXT_BINARY"); + + if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; + + int rv = RUN_ALL_TESTS(); + MPI_Finalize(); + return rv; +} From d19cd8fb115bcab444b10742a692d913253a3231 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 14:49:45 -0400 Subject: [PATCH 0473/1217] Fix test --- unittest/formats/test_dump_atom.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/formats/test_dump_atom.cpp b/unittest/formats/test_dump_atom.cpp index 5161eece3e..669f4d38bd 100644 --- a/unittest/formats/test_dump_atom.cpp +++ b/unittest/formats/test_dump_atom.cpp @@ -135,7 +135,7 @@ TEST_F(DumpAtomTest, no_scale_run0) TEST_F(DumpAtomTest, no_buffer_no_scale_run0) { auto dump_file = "dump_no_buffer_no_scale_run0.melt"; - generate_dump(dump_file, "scale no", 0); + generate_dump(dump_file, "buffer no scale no", 0); ASSERT_FILE_EXISTS(dump_file); auto lines = read_lines(dump_file); From cf41ea6fafae8f9d69cd32429c433856f2c7b10f Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 15:42:28 -0400 Subject: [PATCH 0474/1217] Update dump local and local/gz --- src/COMPRESS/dump_local_gz.cpp | 118 ++++++++-------- src/COMPRESS/dump_local_gz.h | 5 +- src/COMPRESS/dump_local_zstd.cpp | 33 ++++- unittest/formats/test_dump_local.cpp | 66 +++++++++ .../formats/test_dump_local_compressed.cpp | 133 +++++++++++++++++- 5 files changed, 285 insertions(+), 70 deletions(-) diff --git a/src/COMPRESS/dump_local_gz.cpp b/src/COMPRESS/dump_local_gz.cpp index e8065a848a..a0a39b51e0 100644 --- a/src/COMPRESS/dump_local_gz.cpp +++ b/src/COMPRESS/dump_local_gz.cpp @@ -11,24 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "dump_local_gz.h" #include "domain.h" +#include "dump_local_gz.h" #include "error.h" #include "update.h" - #include - using namespace LAMMPS_NS; DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) : DumpLocal(lmp, narg, arg) { - gzFp = nullptr; - - compression_level = Z_BEST_COMPRESSION; - if (!compressed) error->all(FLERR,"Dump local/gz only writes compressed files"); } @@ -38,12 +32,8 @@ DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) : DumpLocalGZ::~DumpLocalGZ() { - if (gzFp) gzclose(gzFp); - gzFp = nullptr; - fp = nullptr; } - /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or gzipped @@ -93,17 +83,12 @@ void DumpLocalGZ::openfile() // each proc with filewriter = 1 opens a file if (filewriter) { - std::string mode; - if (append_flag) { - mode = fmt::format("ab{}", compression_level); - } else { - mode = fmt::format("wb{}", compression_level); + try { + writer.open(filecurrent, append_flag); + } catch (FileWriterException &e) { + error->one(FLERR, e.what()); } - - gzFp = gzopen(filecurrent, mode.c_str()); - - if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file"); - } else gzFp = nullptr; + } // delete string with timestep replaced @@ -112,29 +97,34 @@ void DumpLocalGZ::openfile() void DumpLocalGZ::write_header(bigint ndump) { + std::string header; + if ((multiproc) || (!multiproc && me == 0)) { if (unit_flag && !unit_count) { ++unit_count; - gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style); + header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style); } - if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time()); - gzprintf(gzFp,"ITEM: TIMESTEP\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); - gzprintf(gzFp,"ITEM: NUMBER OF %s\n",label); - gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); - if (domain->triclinic) { - gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz); - } else { - gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi); + if (time_flag) { + header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); } - gzprintf(gzFp,"ITEM: %s %s\n",label,columns); + + header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep); + header += fmt::format("ITEM: NUMBER OF {}\n{}\n", label, ndump); + if (domain->triclinic == 0) { + header += fmt::format("ITEM: BOX BOUNDS {}\n", boundstr); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxxlo, boxxhi); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxylo, boxyhi); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxzlo, boxzhi); + } else { + header += fmt::format("ITEM: BOX BOUNDS xy xz yz {}\n", boundstr); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxxlo, boxxhi, boxxy); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxylo, boxyhi, boxxz); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxzlo, boxzhi, boxyz); + } + header += fmt::format("ITEM: {} {}\n", label, columns); + + writer.write(header.c_str(), header.length()); } } @@ -143,19 +133,28 @@ void DumpLocalGZ::write_header(bigint ndump) void DumpLocalGZ::write_data(int n, double *mybuf) { if (buffer_flag == 1) { - gzwrite(gzFp,mybuf,sizeof(char)*n); - + writer.write(mybuf, sizeof(char)*n); } else { - int i,j; + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; int m = 0; - for (i = 0; i < n; i++) { - for (j = 0; j < size_one; j++) { - if (vtype[j] == INT) - gzprintf(gzFp,vformat[j],static_cast (mybuf[m])); - else gzprintf(gzFp,vformat[j],mybuf[m]); + for (int i = 0; i < n; i++) { + for (int j = 0; j < size_one; j++) { + int written = 0; + if (vtype[j] == Dump::INT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } else { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + } + + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump local/gz output"); + } m++; } - gzprintf(gzFp,"\n"); + writer.write("\n", 1); } } } @@ -167,11 +166,11 @@ void DumpLocalGZ::write() DumpLocal::write(); if (filewriter) { if (multifile) { - gzclose(gzFp); - gzFp = nullptr; + writer.close(); } else { - if (flush_flag) - gzflush(gzFp,Z_SYNC_FLUSH); + if (flush_flag && writer.isopen()) { + writer.flush(); + } } } } @@ -182,14 +181,15 @@ int DumpLocalGZ::modify_param(int narg, char **arg) { int consumed = DumpLocal::modify_param(narg, arg); if (consumed == 0) { - if (strcmp(arg[0],"compression_level") == 0) { - if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); - int min_level = Z_DEFAULT_COMPRESSION; - int max_level = Z_BEST_COMPRESSION; - compression_level = utils::inumeric(FLERR, arg[1], false, lmp); - if (compression_level < min_level || compression_level > max_level) - error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level)); - return 2; + try { + if (strcmp(arg[0],"compression_level") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + int compression_level = utils::inumeric(FLERR, arg[1], false, lmp); + writer.setCompressionLevel(compression_level); + return 2; + } + } catch (FileWriterException &e) { + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/src/COMPRESS/dump_local_gz.h b/src/COMPRESS/dump_local_gz.h index b3f7c7dcf8..7feb6a8945 100644 --- a/src/COMPRESS/dump_local_gz.h +++ b/src/COMPRESS/dump_local_gz.h @@ -21,7 +21,7 @@ DumpStyle(local/gz,DumpLocalGZ) #define LMP_DUMP_LOCAL_GZ_H #include "dump_local.h" -#include +#include "gz_file_writer.h" namespace LAMMPS_NS { @@ -31,8 +31,7 @@ class DumpLocalGZ : public DumpLocal { virtual ~DumpLocalGZ(); protected: - int compression_level; - gzFile gzFp; // file pointer for the compressed output stream + GzFileWriter writer; virtual void openfile(); virtual void write_header(bigint); diff --git a/src/COMPRESS/dump_local_zstd.cpp b/src/COMPRESS/dump_local_zstd.cpp index d26555d282..a4303f3b25 100644 --- a/src/COMPRESS/dump_local_zstd.cpp +++ b/src/COMPRESS/dump_local_zstd.cpp @@ -17,15 +17,13 @@ #ifdef LAMMPS_ZSTD -#include "dump_local_zstd.h" #include "domain.h" +#include "dump_local_zstd.h" #include "error.h" #include "update.h" - #include - using namespace LAMMPS_NS; DumpLocalZstd::DumpLocalZstd(LAMMPS *lmp, int narg, char **arg) : @@ -42,7 +40,6 @@ DumpLocalZstd::~DumpLocalZstd() { } - /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or gzipped @@ -145,7 +142,31 @@ void DumpLocalZstd::write_header(bigint ndump) void DumpLocalZstd::write_data(int n, double *mybuf) { - writer.write(mybuf, sizeof(char)*n); + if (buffer_flag == 1) { + writer.write(mybuf, sizeof(char)*n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < size_one; j++) { + int written = 0; + if (vtype[j] == Dump::INT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } else { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + } + + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump local/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } } /* ---------------------------------------------------------------------- */ @@ -184,7 +205,7 @@ int DumpLocalZstd::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, e.what()); + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/unittest/formats/test_dump_local.cpp b/unittest/formats/test_dump_local.cpp index fb38ca08ad..b122d71849 100644 --- a/unittest/formats/test_dump_local.cpp +++ b/unittest/formats/test_dump_local.cpp @@ -93,6 +93,18 @@ TEST_F(DumpLocalTest, run0) delete_file(dump_file); } +TEST_F(DumpLocalTest, label_run0) +{ + auto dump_file = "dump_local_label_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "label ELEMENTS", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + ASSERT_THAT(lines[2], Eq("ITEM: NUMBER OF ELEMENTS")); + ASSERT_THAT(lines[8], Eq("ITEM: ELEMENTS index c_comp[1] ")); + delete_file(dump_file); +} + TEST_F(DumpLocalTest, format_line_run0) { auto dump_file = "dump_local_format_line_run0.melt"; @@ -170,6 +182,60 @@ TEST_F(DumpLocalTest, no_buffer_run0) delete_file(dump_file); } +TEST_F(DumpLocalTest, with_units_run0) +{ + auto dump_file = "dump_with_units_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "units yes", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + ASSERT_EQ(lines.size(), 875); + + ASSERT_THAT(lines[0], Eq("ITEM: UNITS")); + ASSERT_THAT(lines[1], Eq("lj")); + + ASSERT_THAT(lines[2], Eq("ITEM: TIMESTEP")); + ASSERT_EQ(std::stoi(lines[3]), 0); + + ASSERT_THAT(lines[4], Eq("ITEM: NUMBER OF ENTRIES")); + ASSERT_EQ(std::stoi(lines[5]), 864); +} + +TEST_F(DumpLocalTest, with_time_run0) +{ + auto dump_file = "dump_with_time_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "time yes", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + ASSERT_EQ(lines.size(), 875); + + ASSERT_THAT(lines[0], Eq("ITEM: TIME")); + ASSERT_THAT(std::stof(lines[1]), 0.0); + + ASSERT_THAT(lines[2], Eq("ITEM: TIMESTEP")); + ASSERT_EQ(std::stoi(lines[3]), 0); + + ASSERT_THAT(lines[4], Eq("ITEM: NUMBER OF ENTRIES")); + ASSERT_EQ(std::stoi(lines[5]), 864); +} + +TEST_F(DumpLocalTest, triclinic_run0) +{ + auto dump_file = "dump_local_triclinic_run0.melt"; + enable_triclinic(); + generate_dump(dump_file, "index c_comp[1]", "", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + + ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS xy xz yz pp pp pp")); + ASSERT_EQ(utils::split_words(lines[5]).size(), 3); + ASSERT_EQ(utils::split_words(lines[6]).size(), 3); + ASSERT_EQ(utils::split_words(lines[7]).size(), 3); + delete_file(dump_file); +} + int main(int argc, char **argv) { MPI_Init(&argc, &argv); diff --git a/unittest/formats/test_dump_local_compressed.cpp b/unittest/formats/test_dump_local_compressed.cpp index 95656071fc..cd217354af 100644 --- a/unittest/formats/test_dump_local_compressed.cpp +++ b/unittest/formats/test_dump_local_compressed.cpp @@ -69,6 +69,135 @@ TEST_F(DumpLocalCompressTest, compressed_run0) delete_file(converted_file_0); } +TEST_F(DumpLocalCompressTest, compressed_no_buffer_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "no_buffer_run*.melt.local"; + auto base_name_0 = "no_buffer_run0.melt.local"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "index c_comp[1]"; + + if(compression_style == "local/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "buffer no", "buffer no checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "buffer no", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + +TEST_F(DumpLocalCompressTest, compressed_with_time_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "with_time_run*.melt.local"; + auto base_name_0 = "with_time_run0.melt.local"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "index c_comp[1]"; + + if(compression_style == "local/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "time yes", "time yes checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "time yes", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + +TEST_F(DumpLocalCompressTest, compressed_with_units_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "with_units_run*.melt.local"; + auto base_name_0 = "with_units_run0.melt.local"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "index c_comp[1]"; + + if(compression_style == "local/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "units yes", "units yes checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "units yes", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + +TEST_F(DumpLocalCompressTest, compressed_triclinic_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + enable_triclinic(); + + auto base_name = "triclinic_run*.melt.local"; + auto base_name_0 = "triclinic_run0.melt.local"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "index c_comp[1]"; + + if(compression_style == "local/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "", "checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + TEST_F(DumpLocalCompressTest, compressed_multi_file_run1) { if (!COMPRESS_BINARY) GTEST_SKIP(); @@ -209,7 +338,7 @@ TEST_F(DumpLocalCompressTest, compressed_modify_bad_param) command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.local"), fields)); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 compression_level 12"); ); } @@ -224,7 +353,7 @@ TEST_F(DumpLocalCompressTest, compressed_modify_multi_bad_param) command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.local"), fields)); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); ); } From eb3cddb028f475b3a3478dbba5abe358bfc4539a Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 15:46:18 -0400 Subject: [PATCH 0475/1217] Update docs to include format support in dump local variants --- doc/src/dump_modify.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index d072df5d4d..07f00c4030 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -308,9 +308,9 @@ performed with dump style *xtc*\ . ---------- -The *format* keyword can be used to change the default numeric format -output by the text-based dump styles: *atom*\ , *custom*\ , *cfg*\ , and -*xyz* styles, and their MPIIO variants. Only the *line* or *none* +The *format* keyword can be used to change the default numeric format output +by the text-based dump styles: *atom*\ , *local*\ , *custom*\ , *cfg*\ , and +*xyz* styles, and their MPIIO variants. Only the *line* or *none* options can be used with the *atom* and *xyz* styles. All the specified format strings are C-style formats, e.g. as used by From c17ee12989b95e2fc160032494d19380230879f3 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 15:57:17 -0400 Subject: [PATCH 0476/1217] Update dump xyz/gz --- src/COMPRESS/dump_xyz_gz.cpp | 57 +++++++------------ src/COMPRESS/dump_xyz_gz.h | 5 +- src/COMPRESS/dump_xyz_zstd.cpp | 3 +- unittest/formats/test_dump_xyz_compressed.cpp | 4 +- 4 files changed, 27 insertions(+), 42 deletions(-) diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index c63d354e80..5c90c48d0f 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -15,19 +15,13 @@ #include "error.h" #include "update.h" - #include - using namespace LAMMPS_NS; DumpXYZGZ::DumpXYZGZ(LAMMPS *lmp, int narg, char **arg) : DumpXYZ(lmp, narg, arg) { - gzFp = nullptr; - - compression_level = Z_BEST_COMPRESSION; - if (!compressed) error->all(FLERR,"Dump xyz/gz only writes compressed files"); } @@ -37,12 +31,8 @@ DumpXYZGZ::DumpXYZGZ(LAMMPS *lmp, int narg, char **arg) : DumpXYZGZ::~DumpXYZGZ() { - if (gzFp) gzclose(gzFp); - gzFp = nullptr; - fp = nullptr; } - /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or gzipped @@ -92,17 +82,12 @@ void DumpXYZGZ::openfile() // each proc with filewriter = 1 opens a file if (filewriter) { - std::string mode; - if (append_flag) { - mode = fmt::format("ab{}", compression_level); - } else { - mode = fmt::format("wb{}", compression_level); + try { + writer.open(filecurrent, append_flag); + } catch (FileWriterException &e) { + error->one(FLERR, e.what()); } - - gzFp = gzopen(filecurrent, mode.c_str()); - - if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file"); - } else gzFp = nullptr; + } // delete string with timestep replaced @@ -112,8 +97,9 @@ void DumpXYZGZ::openfile() void DumpXYZGZ::write_header(bigint ndump) { if (me == 0) { - gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); - gzprintf(gzFp,"Atoms. Timestep: " BIGINT_FORMAT "\n",update->ntimestep); + std::string header = fmt::format("{}\n", ndump); + header += fmt::format("Atoms. Timestep: {}\n", update->ntimestep); + writer.write(header.c_str(), header.length()); } } @@ -121,7 +107,7 @@ void DumpXYZGZ::write_header(bigint ndump) void DumpXYZGZ::write_data(int n, double *mybuf) { - gzwrite(gzFp,mybuf,sizeof(char)*n); + writer.write(mybuf, n); } /* ---------------------------------------------------------------------- */ @@ -131,11 +117,11 @@ void DumpXYZGZ::write() DumpXYZ::write(); if (filewriter) { if (multifile) { - gzclose(gzFp); - gzFp = nullptr; + writer.close(); } else { - if (flush_flag) - gzflush(gzFp,Z_SYNC_FLUSH); + if (flush_flag && writer.isopen()) { + writer.flush(); + } } } } @@ -146,14 +132,15 @@ int DumpXYZGZ::modify_param(int narg, char **arg) { int consumed = DumpXYZ::modify_param(narg, arg); if (consumed == 0) { - if (strcmp(arg[0],"compression_level") == 0) { - if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); - int min_level = Z_DEFAULT_COMPRESSION; - int max_level = Z_BEST_COMPRESSION; - compression_level = utils::inumeric(FLERR, arg[1], false, lmp); - if (compression_level < min_level || compression_level > max_level) - error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level)); - return 2; + try { + if (strcmp(arg[0],"compression_level") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + int compression_level = utils::inumeric(FLERR, arg[1], false, lmp); + writer.setCompressionLevel(compression_level); + return 2; + } + } catch (FileWriterException &e) { + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/src/COMPRESS/dump_xyz_gz.h b/src/COMPRESS/dump_xyz_gz.h index 834db488a5..2fce0a3f5a 100644 --- a/src/COMPRESS/dump_xyz_gz.h +++ b/src/COMPRESS/dump_xyz_gz.h @@ -21,7 +21,7 @@ DumpStyle(xyz/gz,DumpXYZGZ) #define LMP_DUMP_XYZ_GZ_H #include "dump_xyz.h" -#include +#include "gz_file_writer.h" namespace LAMMPS_NS { @@ -31,8 +31,7 @@ class DumpXYZGZ : public DumpXYZ { virtual ~DumpXYZGZ(); protected: - int compression_level; - gzFile gzFp; // file pointer for the compressed output stream + GzFileWriter writer; virtual void openfile(); virtual void write_header(bigint); diff --git a/src/COMPRESS/dump_xyz_zstd.cpp b/src/COMPRESS/dump_xyz_zstd.cpp index 7c5b73d0ba..03edf561b1 100644 --- a/src/COMPRESS/dump_xyz_zstd.cpp +++ b/src/COMPRESS/dump_xyz_zstd.cpp @@ -19,7 +19,6 @@ #include "dump_xyz_zstd.h" #include "error.h" -#include "file_writer.h" #include "update.h" #include @@ -158,7 +157,7 @@ int DumpXYZZstd::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, e.what()); + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/unittest/formats/test_dump_xyz_compressed.cpp b/unittest/formats/test_dump_xyz_compressed.cpp index dad7911b4c..b627cb5a99 100644 --- a/unittest/formats/test_dump_xyz_compressed.cpp +++ b/unittest/formats/test_dump_xyz_compressed.cpp @@ -195,7 +195,7 @@ TEST_F(DumpXYZCompressTest, compressed_modify_bad_param) command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.xyz"))); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 compression_level 12"); ); } @@ -208,7 +208,7 @@ TEST_F(DumpXYZCompressTest, compressed_modify_multi_bad_param) command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.xyz"))); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); ); } From 511f64fde4ab569d2ac9bde67c9e9c6d6aa7e3da Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 16:36:30 -0400 Subject: [PATCH 0477/1217] Update dump custom/gz --- src/COMPRESS/dump_atom_gz.cpp | 4 +- src/COMPRESS/dump_atom_zstd.cpp | 4 +- src/COMPRESS/dump_cfg_gz.cpp | 4 +- src/COMPRESS/dump_cfg_zstd.cpp | 4 +- src/COMPRESS/dump_custom_gz.cpp | 98 +++++++++---------- src/COMPRESS/dump_custom_gz.h | 5 +- src/COMPRESS/dump_custom_zstd.cpp | 7 +- src/COMPRESS/dump_local_gz.cpp | 5 +- src/COMPRESS/dump_local_zstd.cpp | 4 +- src/COMPRESS/dump_xyz_gz.cpp | 4 +- src/COMPRESS/dump_xyz_zstd.cpp | 4 +- .../formats/test_dump_custom_compressed.cpp | 33 ++++++- 12 files changed, 106 insertions(+), 70 deletions(-) diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index 254e146800..b3b202e373 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -71,7 +71,9 @@ void DumpAtomGZ::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index dd744b5d49..f739a53322 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -79,7 +79,9 @@ void DumpAtomZstd::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp index 6bbf118789..23c0d82429 100644 --- a/src/COMPRESS/dump_cfg_gz.cpp +++ b/src/COMPRESS/dump_cfg_gz.cpp @@ -73,7 +73,9 @@ void DumpCFGGZ::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/src/COMPRESS/dump_cfg_zstd.cpp b/src/COMPRESS/dump_cfg_zstd.cpp index 978e695d1a..5bc6ac86dc 100644 --- a/src/COMPRESS/dump_cfg_zstd.cpp +++ b/src/COMPRESS/dump_cfg_zstd.cpp @@ -81,7 +81,9 @@ void DumpCFGZstd::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp index 4f03a4a232..5cecf22b5d 100644 --- a/src/COMPRESS/dump_custom_gz.cpp +++ b/src/COMPRESS/dump_custom_gz.cpp @@ -11,39 +11,28 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "dump_custom_gz.h" #include "domain.h" +#include "dump_custom_gz.h" #include "error.h" #include "update.h" - #include - using namespace LAMMPS_NS; DumpCustomGZ::DumpCustomGZ(LAMMPS *lmp, int narg, char **arg) : DumpCustom(lmp, narg, arg) { - gzFp = nullptr; - - compression_level = Z_BEST_COMPRESSION; - if (!compressed) error->all(FLERR,"Dump custom/gz only writes compressed files"); } - /* ---------------------------------------------------------------------- */ DumpCustomGZ::~DumpCustomGZ() { - if (gzFp) gzclose(gzFp); - gzFp = nullptr; - fp = nullptr; } - /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or gzipped @@ -82,7 +71,9 @@ void DumpCustomGZ::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; @@ -93,17 +84,12 @@ void DumpCustomGZ::openfile() // each proc with filewriter = 1 opens a file if (filewriter) { - std::string mode; - if (append_flag) { - mode = fmt::format("ab{}", compression_level); - } else { - mode = fmt::format("wb{}", compression_level); + try { + writer.open(filecurrent, append_flag); + } catch (FileWriterException &e) { + error->one(FLERR, e.what()); } - - gzFp = gzopen(filecurrent, mode.c_str()); - - if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file"); - } else gzFp = nullptr; + } // delete string with timestep replaced @@ -112,29 +98,34 @@ void DumpCustomGZ::openfile() void DumpCustomGZ::write_header(bigint ndump) { + std::string header; + if ((multiproc) || (!multiproc && me == 0)) { if (unit_flag && !unit_count) { ++unit_count; - gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style); + header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style); } - if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time()); - gzprintf(gzFp,"ITEM: TIMESTEP\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); - gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); - if (domain->triclinic == 0) { - gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi); - } else { - gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz); + if (time_flag) { + header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); } - gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); + + header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep); + header += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump); + if (domain->triclinic == 0) { + header += fmt::format("ITEM: BOX BOUNDS {}\n", boundstr); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxxlo, boxxhi); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxylo, boxyhi); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxzlo, boxzhi); + } else { + header += fmt::format("ITEM: BOX BOUNDS xy xz yz {}\n", boundstr); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxxlo, boxxhi, boxxy); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxylo, boxyhi, boxxz); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxzlo, boxzhi, boxyz); + } + header += fmt::format("ITEM: ATOMS {}\n", columns); + + writer.write(header.c_str(), header.length()); } } @@ -142,7 +133,7 @@ void DumpCustomGZ::write_header(bigint ndump) void DumpCustomGZ::write_data(int n, double *mybuf) { - gzwrite(gzFp,mybuf,sizeof(char)*n); + writer.write(mybuf, n); } /* ---------------------------------------------------------------------- */ @@ -152,11 +143,11 @@ void DumpCustomGZ::write() DumpCustom::write(); if (filewriter) { if (multifile) { - gzclose(gzFp); - gzFp = nullptr; + writer.close(); } else { - if (flush_flag) - gzflush(gzFp,Z_SYNC_FLUSH); + if (flush_flag && writer.isopen()) { + writer.flush(); + } } } } @@ -167,14 +158,15 @@ int DumpCustomGZ::modify_param(int narg, char **arg) { int consumed = DumpCustom::modify_param(narg, arg); if (consumed == 0) { - if (strcmp(arg[0],"compression_level") == 0) { - if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); - int min_level = Z_DEFAULT_COMPRESSION; - int max_level = Z_BEST_COMPRESSION; - compression_level = utils::inumeric(FLERR, arg[1], false, lmp); - if (compression_level < min_level || compression_level > max_level) - error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level)); - return 2; + try { + if (strcmp(arg[0],"compression_level") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + int compression_level = utils::inumeric(FLERR, arg[1], false, lmp); + writer.setCompressionLevel(compression_level); + return 2; + } + } catch (FileWriterException &e) { + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/src/COMPRESS/dump_custom_gz.h b/src/COMPRESS/dump_custom_gz.h index 184f3563f1..db30b944ec 100644 --- a/src/COMPRESS/dump_custom_gz.h +++ b/src/COMPRESS/dump_custom_gz.h @@ -21,7 +21,7 @@ DumpStyle(custom/gz,DumpCustomGZ) #define LMP_DUMP_CUSTOM_GZ_H #include "dump_custom.h" -#include +#include "gz_file_writer.h" namespace LAMMPS_NS { @@ -31,8 +31,7 @@ class DumpCustomGZ : public DumpCustom { virtual ~DumpCustomGZ(); protected: - int compression_level; - gzFile gzFp; // file pointer for the compressed output stream + GzFileWriter writer; virtual void openfile(); virtual void write_header(bigint); diff --git a/src/COMPRESS/dump_custom_zstd.cpp b/src/COMPRESS/dump_custom_zstd.cpp index 3aa3f874ea..bd248bd0fc 100644 --- a/src/COMPRESS/dump_custom_zstd.cpp +++ b/src/COMPRESS/dump_custom_zstd.cpp @@ -20,7 +20,6 @@ #include "domain.h" #include "dump_custom_zstd.h" #include "error.h" -#include "file_writer.h" #include "update.h" #include @@ -79,7 +78,9 @@ void DumpCustomZstd::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; @@ -184,7 +185,7 @@ int DumpCustomZstd::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, e.what()); + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/src/COMPRESS/dump_local_gz.cpp b/src/COMPRESS/dump_local_gz.cpp index a0a39b51e0..9b0ac0c344 100644 --- a/src/COMPRESS/dump_local_gz.cpp +++ b/src/COMPRESS/dump_local_gz.cpp @@ -27,7 +27,6 @@ DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Dump local/gz only writes compressed files"); } - /* ---------------------------------------------------------------------- */ DumpLocalGZ::~DumpLocalGZ() @@ -72,7 +71,9 @@ void DumpLocalGZ::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/src/COMPRESS/dump_local_zstd.cpp b/src/COMPRESS/dump_local_zstd.cpp index a4303f3b25..05cd0bb1ae 100644 --- a/src/COMPRESS/dump_local_zstd.cpp +++ b/src/COMPRESS/dump_local_zstd.cpp @@ -78,7 +78,9 @@ void DumpLocalZstd::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index 5c90c48d0f..0697f19ce3 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -71,7 +71,9 @@ void DumpXYZGZ::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/src/COMPRESS/dump_xyz_zstd.cpp b/src/COMPRESS/dump_xyz_zstd.cpp index 03edf561b1..cb75542337 100644 --- a/src/COMPRESS/dump_xyz_zstd.cpp +++ b/src/COMPRESS/dump_xyz_zstd.cpp @@ -78,7 +78,9 @@ void DumpXYZZstd::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/unittest/formats/test_dump_custom_compressed.cpp b/unittest/formats/test_dump_custom_compressed.cpp index fb70206590..5ad231d440 100644 --- a/unittest/formats/test_dump_custom_compressed.cpp +++ b/unittest/formats/test_dump_custom_compressed.cpp @@ -58,6 +58,35 @@ TEST_F(DumpCustomCompressTest, compressed_run1) delete_file(converted_file); } +TEST_F(DumpCustomCompressTest, compressed_with_time_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "with_time_custom_run1.melt"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); + auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; + + if(compression_style == "custom/zstd") { + generate_text_and_compressed_dump(text_file, compressed_file, fields, fields, "time yes", "time yes checksum yes", 1); + } else { + generate_text_and_compressed_dump(text_file, compressed_file, fields, "time yes", 1); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file); + ASSERT_FILE_EXISTS(compressed_file); + + auto converted_file = convert_compressed_to_text(compressed_file); + + ASSERT_FILE_EXISTS(converted_file); + ASSERT_FILE_EQUAL(text_file, converted_file); + delete_file(text_file); + delete_file(compressed_file); + delete_file(converted_file); +} + TEST_F(DumpCustomCompressTest, compressed_triclinic_run1) { if (!COMPRESS_BINARY) GTEST_SKIP(); @@ -222,7 +251,7 @@ TEST_F(DumpCustomCompressTest, compressed_modify_bad_param) auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.custom"), fields)); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 compression_level 12"); ); } @@ -234,7 +263,7 @@ TEST_F(DumpCustomCompressTest, compressed_modify_multi_bad_param) auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.custom"), fields)); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); ); } From 234c75550722fa48ceff16456696e71628567124 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 17:08:57 -0400 Subject: [PATCH 0478/1217] Add missing types in dump local --- src/COMPRESS/dump_local_gz.cpp | 4 ++++ src/COMPRESS/dump_local_zstd.cpp | 4 ++++ src/dump_local.cpp | 8 ++++++++ 3 files changed, 16 insertions(+) diff --git a/src/COMPRESS/dump_local_gz.cpp b/src/COMPRESS/dump_local_gz.cpp index 9b0ac0c344..7ffb8d80ff 100644 --- a/src/COMPRESS/dump_local_gz.cpp +++ b/src/COMPRESS/dump_local_gz.cpp @@ -144,6 +144,10 @@ void DumpLocalGZ::write_data(int n, double *mybuf) int written = 0; if (vtype[j] == Dump::INT) { written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } else if (vtype[j] == Dump::DOUBLE) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + } else if (vtype[j] == Dump::BIGINT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); } else { written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); } diff --git a/src/COMPRESS/dump_local_zstd.cpp b/src/COMPRESS/dump_local_zstd.cpp index 05cd0bb1ae..4d7fe9361b 100644 --- a/src/COMPRESS/dump_local_zstd.cpp +++ b/src/COMPRESS/dump_local_zstd.cpp @@ -155,6 +155,10 @@ void DumpLocalZstd::write_data(int n, double *mybuf) int written = 0; if (vtype[j] == Dump::INT) { written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } else if (vtype[j] == Dump::DOUBLE) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + } else if (vtype[j] == Dump::BIGINT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); } else { written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); } diff --git a/src/dump_local.cpp b/src/dump_local.cpp index dac8066236..0f8d139f66 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -179,6 +179,8 @@ void DumpLocal::init_style() vformat[i] = utils::strdup(std::string(format_int_user) + " "); else if (vtype[i] == Dump::DOUBLE && format_float_user) vformat[i] = utils::strdup(std::string(format_float_user) + " "); + else if (vtype[i] == Dump::BIGINT && format_bigint_user) + vformat[i] = utils::strdup(std::string(format_bigint_user) + " "); else vformat[i] = utils::strdup(word + " "); ++i; } @@ -375,6 +377,10 @@ int DumpLocal::convert_string(int n, double *mybuf) for (j = 0; j < size_one; j++) { if (vtype[j] == Dump::INT) offset += sprintf(&sbuf[offset],vformat[j],static_cast (mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) + offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]); + else if (vtype[j] == Dump::BIGINT) + offset += sprintf(&sbuf[offset],vformat[j],static_cast (mybuf[m])); else offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]); m++; @@ -409,6 +415,8 @@ void DumpLocal::write_lines(int n, double *mybuf) for (i = 0; i < n; i++) { for (j = 0; j < size_one; j++) { if (vtype[j] == Dump::INT) fprintf(fp,vformat[j],static_cast (mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) fprintf(fp,vformat[j],mybuf[m]); + else if (vtype[j] == Dump::BIGINT) fprintf(fp,vformat[j],static_cast(mybuf[m])); else fprintf(fp,vformat[j],mybuf[m]); m++; } From 242881af55578f6ca137865241415d3ba45a787b Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 17:45:45 -0400 Subject: [PATCH 0479/1217] Make dump custom/gz, custom/zstd compatible to 'buffer no' option --- src/COMPRESS/dump_custom_gz.cpp | 30 ++++++++++++++++++- src/COMPRESS/dump_custom_zstd.cpp | 30 ++++++++++++++++++- .../formats/test_dump_custom_compressed.cpp | 29 ++++++++++++++++++ 3 files changed, 87 insertions(+), 2 deletions(-) diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp index 5cecf22b5d..9a3fc39d0a 100644 --- a/src/COMPRESS/dump_custom_gz.cpp +++ b/src/COMPRESS/dump_custom_gz.cpp @@ -133,7 +133,35 @@ void DumpCustomGZ::write_header(bigint ndump) void DumpCustomGZ::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag == 1) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < nfield; j++) { + int written = 0; + if (vtype[j] == Dump::INT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } else if (vtype[j] == Dump::DOUBLE) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + } else if (vtype[j] == Dump::STRING) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]); + } else if (vtype[j] == Dump::BIGINT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } + + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump custom/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } } /* ---------------------------------------------------------------------- */ diff --git a/src/COMPRESS/dump_custom_zstd.cpp b/src/COMPRESS/dump_custom_zstd.cpp index bd248bd0fc..b3f0971bf5 100644 --- a/src/COMPRESS/dump_custom_zstd.cpp +++ b/src/COMPRESS/dump_custom_zstd.cpp @@ -146,7 +146,35 @@ void DumpCustomZstd::write_header(bigint ndump) void DumpCustomZstd::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag == 1) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < nfield; j++) { + int written = 0; + if (vtype[j] == Dump::INT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } else if (vtype[j] == Dump::DOUBLE) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + } else if (vtype[j] == Dump::STRING) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]); + } else if (vtype[j] == Dump::BIGINT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } + + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump custom/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } } /* ---------------------------------------------------------------------- */ diff --git a/unittest/formats/test_dump_custom_compressed.cpp b/unittest/formats/test_dump_custom_compressed.cpp index 5ad231d440..cb45c1b837 100644 --- a/unittest/formats/test_dump_custom_compressed.cpp +++ b/unittest/formats/test_dump_custom_compressed.cpp @@ -87,6 +87,35 @@ TEST_F(DumpCustomCompressTest, compressed_with_time_run1) delete_file(converted_file); } +TEST_F(DumpCustomCompressTest, compressed_no_buffer_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "no_buffer_custom_run1.melt"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); + auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; + + if(compression_style == "custom/zstd") { + generate_text_and_compressed_dump(text_file, compressed_file, fields, fields, "buffer no", "buffer no checksum yes", 1); + } else { + generate_text_and_compressed_dump(text_file, compressed_file, fields, "buffer no", 1); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file); + ASSERT_FILE_EXISTS(compressed_file); + + auto converted_file = convert_compressed_to_text(compressed_file); + + ASSERT_FILE_EXISTS(converted_file); + ASSERT_FILE_EQUAL(text_file, converted_file); + delete_file(text_file); + delete_file(compressed_file); + delete_file(converted_file); +} + TEST_F(DumpCustomCompressTest, compressed_triclinic_run1) { if (!COMPRESS_BINARY) GTEST_SKIP(); From e5ee210f58a380b605a94f2539a67f34ecfe4807 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 18:02:55 -0400 Subject: [PATCH 0480/1217] Make dump atom/gz, atom/zstd compatible to 'buffer no' option --- src/COMPRESS/dump_atom_gz.cpp | 28 ++++++++++++++++++- src/COMPRESS/dump_atom_zstd.cpp | 28 ++++++++++++++++++- .../formats/test_dump_atom_compressed.cpp | 28 +++++++++++++++++++ 3 files changed, 82 insertions(+), 2 deletions(-) diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index b3b202e373..7b54fd8e62 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -135,7 +135,33 @@ void DumpAtomGZ::write_header(bigint ndump) void DumpAtomGZ::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag == 1) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + int written = 0; + if (image_flag == 1) { + written = snprintf(vbuffer, VBUFFER_SIZE, format, + static_cast (mybuf[m]), static_cast (mybuf[m+1]), + mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast (mybuf[m+5]), + static_cast (mybuf[m+6]), static_cast (mybuf[m+7])); + } else { + written = snprintf(vbuffer, VBUFFER_SIZE, format, + static_cast (mybuf[m]), static_cast (mybuf[m+1]), + mybuf[m+2],mybuf[m+3],mybuf[m+4]); + } + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump atom/gz output"); + } + + m += size_one; + } + } } /* ---------------------------------------------------------------------- */ diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index f739a53322..b53ebb2269 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -143,7 +143,33 @@ void DumpAtomZstd::write_header(bigint ndump) void DumpAtomZstd::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag == 1) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + int written = 0; + if (image_flag == 1) { + written = snprintf(vbuffer, VBUFFER_SIZE, format, + static_cast (mybuf[m]), static_cast (mybuf[m+1]), + mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast (mybuf[m+5]), + static_cast (mybuf[m+6]), static_cast (mybuf[m+7])); + } else { + written = snprintf(vbuffer, VBUFFER_SIZE, format, + static_cast (mybuf[m]), static_cast (mybuf[m+1]), + mybuf[m+2],mybuf[m+3],mybuf[m+4]); + } + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump atom/gz output"); + } + + m += size_one; + } + } } /* ---------------------------------------------------------------------- */ diff --git a/unittest/formats/test_dump_atom_compressed.cpp b/unittest/formats/test_dump_atom_compressed.cpp index da68acee2a..aeb747004e 100644 --- a/unittest/formats/test_dump_atom_compressed.cpp +++ b/unittest/formats/test_dump_atom_compressed.cpp @@ -61,6 +61,34 @@ TEST_F(DumpAtomCompressTest, compressed_run0) delete_file(converted_file); } +TEST_F(DumpAtomCompressTest, compressed_no_buffer_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto text_file = text_dump_filename("no_buffer_run0.melt"); + auto compressed_file = compressed_dump_filename("no_buffer_run0.melt"); + + if(compression_style == "atom/zstd") { + generate_text_and_compressed_dump(text_file, compressed_file, "", "", "buffer no", "buffer no checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_file, compressed_file, "", "buffer no", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file); + ASSERT_FILE_EXISTS(compressed_file); + + auto converted_file = convert_compressed_to_text(compressed_file); + + ASSERT_THAT(converted_file, Eq(converted_dump_filename("no_buffer_run0.melt"))); + ASSERT_FILE_EXISTS(converted_file); + ASSERT_FILE_EQUAL(text_file, converted_file); + delete_file(text_file); + delete_file(compressed_file); + delete_file(converted_file); +} + TEST_F(DumpAtomCompressTest, compressed_multi_file_run1) { if (!COMPRESS_BINARY) GTEST_SKIP(); From a69c5a5cae0f745adcb09d638de1cf1ceacb575c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 20:19:04 -0400 Subject: [PATCH 0481/1217] fix bugs in shell putenv and getenv style variables. add more unit tests. --- src/input.cpp | 4 ++-- src/variable.cpp | 3 +-- unittest/commands/test_simple_commands.cpp | 13 +++++++++---- unittest/commands/test_variables.cpp | 14 ++++++++++++-- 4 files changed, 24 insertions(+), 10 deletions(-) diff --git a/src/input.cpp b/src/input.cpp index f96cf8c75c..3f3c7cb2e6 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -1250,9 +1250,9 @@ void Input::shell() for (int i = 1; i < narg; i++) { rv = 0; #ifdef _WIN32 - if (arg[i]) rv = _putenv(arg[i]); + if (arg[i]) rv = _putenv(utils::strdup(arg[i])); #else - if (arg[i]) rv = putenv(arg[i]); + if (arg[i]) rv = putenv(utils::strdup(arg[i])); #endif rv = (rv < 0) ? errno : 0; MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world); diff --git a/src/variable.cpp b/src/variable.cpp index 1a4feb3573..437efaf540 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -341,8 +341,7 @@ void Variable::set(int narg, char **arg) which[nvar] = 0; pad[nvar] = 0; data[nvar] = new char*[num[nvar]]; - copy(1,&arg[2],data[nvar]); - data[nvar][1] = utils::strdup("(undefined)"); + data[nvar][0] = utils::strdup(arg[2]); // SCALARFILE for strings or numbers // which = 1st value diff --git a/unittest/commands/test_simple_commands.cpp b/unittest/commands/test_simple_commands.cpp index 9bd6e74c9b..6ee783a8e1 100644 --- a/unittest/commands/test_simple_commands.cpp +++ b/unittest/commands/test_simple_commands.cpp @@ -20,8 +20,8 @@ #include "output.h" #include "update.h" #include "utils.h" +#include "variable.h" -#include "fmt/format.h" #include "gmock/gmock.h" #include "gtest/gtest.h" #include "../testing/core.h" @@ -398,6 +398,7 @@ TEST_F(SimpleCommandsTest, Shell) { BEGIN_HIDE_OUTPUT(); command("shell putenv TEST_VARIABLE=simpletest"); + command("variable simple1 getenv TEST_VARIABLE"); END_HIDE_OUTPUT(); char *test_var = getenv("TEST_VARIABLE"); @@ -405,18 +406,22 @@ TEST_F(SimpleCommandsTest, Shell) ASSERT_THAT(test_var, StrEq("simpletest")); BEGIN_HIDE_OUTPUT(); - command("shell putenv TEST_VARIABLE=simpletest"); - command("shell putenv TEST_VARIABLE2=simpletest2 OTHER_VARIABLE=2"); + command("shell putenv TEST_VARIABLE=simpletest2"); + command("shell putenv TEST_VARIABLE2=simpletest OTHER_VARIABLE=2"); END_HIDE_OUTPUT(); char *test_var2 = getenv("TEST_VARIABLE2"); char *other_var = getenv("OTHER_VARIABLE"); ASSERT_NE(test_var2, nullptr); - ASSERT_THAT(test_var2, StrEq("simpletest2")); + ASSERT_THAT(test_var2, StrEq("simpletest")); ASSERT_NE(other_var, nullptr); ASSERT_THAT(other_var, StrEq("2")); + + test_var = getenv("TEST_VARIABLE"); + ASSERT_NE(test_var, nullptr); + ASSERT_THAT(test_var, StrEq("simpletest2")); } TEST_F(SimpleCommandsTest, CiteMe) diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 97f874a856..f31959c3ff 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -122,6 +122,8 @@ TEST_F(VariableTest, CreateDelete) file_vars(); ASSERT_EQ(variable->nvar, 1); BEGIN_HIDE_OUTPUT(); + command("shell putenv TEST_VARIABLE=simpletest2"); + command("shell putenv TEST_VARIABLE2=simpletest OTHER_VARIABLE=2"); command("variable one index 1 2 3 4"); command("variable two equal 1"); command("variable two equal 2"); @@ -133,8 +135,8 @@ TEST_F(VariableTest, CreateDelete) command("variable five2 loop 10 200 pad"); command("variable six world one"); command("variable seven format two \"%5.2f\""); - command("variable eight getenv PWD"); - command("variable eight getenv XXXXX"); + command("variable eight getenv TEST_VARIABLE2"); + command("variable eight getenv XXX"); command("variable nine file test_variable.file"); command("variable ten internal 1.0"); command("variable ten internal 10.0"); @@ -167,6 +169,14 @@ TEST_F(VariableTest, CreateDelete) unlink("MYFILE"); ASSERT_THAT(variable->retrieve("file"), StrEq("0")); + BEGIN_HIDE_OUTPUT(); + command("variable seven delete"); + command("variable seven getenv TEST_VARIABLE"); + command("variable eight getenv OTHER_VARIABLE"); + END_HIDE_OUTPUT(); + ASSERT_THAT(variable->retrieve("seven"), StrEq("simpletest2")); + ASSERT_THAT(variable->retrieve("eight"), StrEq("2")); + ASSERT_EQ(variable->equalstyle(variable->find("one")), 0); ASSERT_EQ(variable->equalstyle(variable->find("two")), 1); ASSERT_EQ(variable->equalstyle(variable->find("ten")), 1); From c16e4f241fbc00ed6dbf30ca7d74cce360db068f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 20:37:01 -0400 Subject: [PATCH 0482/1217] replace "leaky" call to putenv() with setenv() on non-windows platforms --- src/input.cpp | 11 ++++++++++- unittest/commands/test_simple_commands.cpp | 20 +++++++++----------- 2 files changed, 19 insertions(+), 12 deletions(-) diff --git a/src/input.cpp b/src/input.cpp index 3f3c7cb2e6..9079cdd76c 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -1252,7 +1252,16 @@ void Input::shell() #ifdef _WIN32 if (arg[i]) rv = _putenv(utils::strdup(arg[i])); #else - if (arg[i]) rv = putenv(utils::strdup(arg[i])); + if (arg[i]) { + std::string vardef(arg[i]); + auto found = vardef.find_first_of("="); + if (found == std::string::npos) { + rv = setenv(vardef.c_str(),"",1); + } else { + rv = setenv(vardef.substr(0,found).c_str(), + vardef.substr(found+1).c_str(),1); + } + } #endif rv = (rv < 0) ? errno : 0; MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world); diff --git a/unittest/commands/test_simple_commands.cpp b/unittest/commands/test_simple_commands.cpp index 6ee783a8e1..e8cebe98e2 100644 --- a/unittest/commands/test_simple_commands.cpp +++ b/unittest/commands/test_simple_commands.cpp @@ -398,30 +398,28 @@ TEST_F(SimpleCommandsTest, Shell) { BEGIN_HIDE_OUTPUT(); command("shell putenv TEST_VARIABLE=simpletest"); - command("variable simple1 getenv TEST_VARIABLE"); END_HIDE_OUTPUT(); - char *test_var = getenv("TEST_VARIABLE"); + const char *test_var = getenv("TEST_VARIABLE"); ASSERT_NE(test_var, nullptr); ASSERT_THAT(test_var, StrEq("simpletest")); BEGIN_HIDE_OUTPUT(); - command("shell putenv TEST_VARIABLE=simpletest2"); + command("shell putenv TEST_VARIABLE"); command("shell putenv TEST_VARIABLE2=simpletest OTHER_VARIABLE=2"); END_HIDE_OUTPUT(); - char *test_var2 = getenv("TEST_VARIABLE2"); - char *other_var = getenv("OTHER_VARIABLE"); + test_var = getenv("TEST_VARIABLE2"); + ASSERT_NE(test_var, nullptr); + ASSERT_THAT(test_var, StrEq("simpletest")); - ASSERT_NE(test_var2, nullptr); - ASSERT_THAT(test_var2, StrEq("simpletest")); - - ASSERT_NE(other_var, nullptr); - ASSERT_THAT(other_var, StrEq("2")); + test_var = getenv("OTHER_VARIABLE"); + ASSERT_NE(test_var, nullptr); + ASSERT_THAT(test_var, StrEq("2")); test_var = getenv("TEST_VARIABLE"); ASSERT_NE(test_var, nullptr); - ASSERT_THAT(test_var, StrEq("simpletest2")); + ASSERT_THAT(test_var, StrEq("")); } TEST_F(SimpleCommandsTest, CiteMe) From 552d13b9e4141ec90899325234b41ef7bf896218 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 21:43:02 -0400 Subject: [PATCH 0483/1217] print message only on MPI rank 0 --- src/finish.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/finish.cpp b/src/finish.cpp index 810155f1b0..28596e3a72 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -401,7 +401,7 @@ void Finish::end(int flag) } #endif - if (lmp->kokkos && lmp->kokkos->ngpus > 0) + if ((comm->me == 0) && lmp->kokkos && (lmp->kokkos->ngpus > 0)) if (const char* env_clb = getenv("CUDA_LAUNCH_BLOCKING")) if (!(strcmp(env_clb,"1") == 0)) { error->warning(FLERR,"Timing breakdown may not be accurate " From 7a2910f05feef1bb460d48f7beb3c11573eb698e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 21:44:34 -0400 Subject: [PATCH 0484/1217] must have num == 2 for getenv style variables --- src/variable.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/variable.cpp b/src/variable.cpp index 437efaf540..5c22981255 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -337,11 +337,12 @@ void Variable::set(int narg, char **arg) } if (nvar == maxvar) grow(); style[nvar] = GETENV; - num[nvar] = 1; + num[nvar] = 2; which[nvar] = 0; pad[nvar] = 0; data[nvar] = new char*[num[nvar]]; data[nvar][0] = utils::strdup(arg[2]); + data[nvar][1] = utils::strdup("(undefined)"); // SCALARFILE for strings or numbers // which = 1st value From 96f59a58d3738104bae82dcc91868aeb042d09eb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 21:53:18 -0400 Subject: [PATCH 0485/1217] be a little more paranoid about avoiding memory leakage --- src/variable.cpp | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/variable.cpp b/src/variable.cpp index 5c22981255..d903490219 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -1252,7 +1252,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) print_var_error(FLERR,"Invalid syntax in variable formula",ivar); expect = OP; - char *contents; + char *contents = nullptr; i = find_matching_paren(str,i,contents,ivar); i++; @@ -2068,7 +2068,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) // ---------------- if (str[i] == '(') { - char *contents; + char *contents = nullptr; i = find_matching_paren(str,i,contents,ivar); i++; @@ -3286,6 +3286,7 @@ int Variable::find_matching_paren(char *str, int i, char *&contents, int ivar) int istop = i; int n = istop - istart - 1; + delete[] contents; contents = new char[n+1]; strncpy(contents,&str[istart+1],n); contents[n] = '\0'; @@ -4827,7 +4828,7 @@ double Variable::evaluate_boolean(char *str) error->all(FLERR,"Invalid Boolean syntax in if command"); expect = OP; - char *contents; + char *contents = nullptr; i = find_matching_paren(str,i,contents,-1); i++; From 0496fd27dbb8cace53090f3e4fb81abdad489816 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 22:49:25 -0400 Subject: [PATCH 0486/1217] reorder include files --- src/pair_hybrid.cpp | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index c12ec67351..48ba1ccff7 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -14,20 +14,19 @@ #include "pair_hybrid.h" -#include -#include #include "atom.h" -#include "force.h" -#include "pair.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "update.h" #include "comm.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" #include "respa.h" - #include "suffix.h" +#include "update.h" + +#include using namespace LAMMPS_NS; From 0d325f22219239a52d3b2b7ca8344749814b51bc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 22:50:16 -0400 Subject: [PATCH 0487/1217] error out when scale factor variables do not exist --- src/pair_hybrid_scaled.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index 62b94d9ba9..7a30c9a3ee 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -71,6 +71,9 @@ void PairHybridScaled::compute(int eflag, int vflag) double *vals = new double[nvars]; for (i = 0; i < nvars; ++i) { j = input->variable->find(scalevars[i].c_str()); + if (j < 0) + error->all(FLERR,fmt::format("Variable '{}' not found when updating " + "scale factors",scalevars[i])); vals[i] = input->variable->compute_equal(j); } for (i = 0; i < nstyles; ++i) { From ec6e2d35cbd46fe5cdbcb3bacfebc0bd6c06dbf6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 22:50:51 -0400 Subject: [PATCH 0488/1217] complete update of the hybrid documentation for hybrid/scaled --- doc/src/pair_hybrid.rst | 157 +++++++++++++++++++++------------------- 1 file changed, 83 insertions(+), 74 deletions(-) diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index c851423029..9fdba318d9 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -59,35 +59,40 @@ be assigned to each pair of atom types. The assignment of pair styles to type pairs is made via the :doc:`pair_coeff ` command. The *hybrid/scaled* style differs from the *hybrid/overlay* style by requiring a factor for each pair style that is used to scale all -forces and energies computed by the pair style. +forces, energies and stresses computed by each sub-style. Because of +the additional complexity, the *hybrid/scaled* style will have more +overhead and thus will be a bit slower than *hybrid/overlay*. Here are two examples of hybrid simulations. The *hybrid* style could -be used for a simulation of a metal droplet on a LJ surface. The -metal atoms interact with each other via an *eam* potential, the -surface atoms interact with each other via a *lj/cut* potential, and -the metal/surface interaction is also computed via a *lj/cut* -potential. The *hybrid/overlay* style could be used as in the second -example above, where multiple potentials are superposed in an additive -fashion to compute the interaction between atoms. In this example, -using *lj/cut* and *coul/long* together gives the same result as if -the *lj/cut/coul/long* potential were used by itself. In this case, -it would be more efficient to use the single combined potential, but -in general any combination of pair potentials can be used together in -to produce an interaction that is not encoded in any single pair_style -file, e.g. adding Coulombic forces between granular particles. -The *hybrid/scaled* style enables more complex combinations of pair -styles than a simple sum as *hybrid/overlay* does. Furthermore, since -the scale factors can be variables, they can change during a simulation -which would allow to smoothly switch between two different pair styles -or two different parameter sets. +be used for a simulation of a metal droplet on a LJ surface. The metal +atoms interact with each other via an *eam* potential, the surface atoms +interact with each other via a *lj/cut* potential, and the metal/surface +interaction is also computed via a *lj/cut* potential. The +*hybrid/overlay* style could be used as in the second example above, +where multiple potentials are superposed in an additive fashion to +compute the interaction between atoms. In this example, using *lj/cut* +and *coul/long* together gives the same result as if the +*lj/cut/coul/long* potential were used by itself. In this case, it +would be more efficient to use the single combined potential, but in +general any combination of pair potentials can be used together in to +produce an interaction that is not encoded in any single pair_style +file, e.g. adding Coulombic forces between granular particles. The +*hybrid/scaled* style enables more complex combinations of pair styles +than a simple sum as *hybrid/overlay* does; there may be fractional +contributions from sub-styles or contributions may be subtracted with a +negative scale factor. Furthermore, since the scale factors can be +variables that may change during a simulation, which would allow, for +instance, to smoothly switch between two different pair styles or two +different parameter sets. All pair styles that will be used are listed as "sub-styles" following the *hybrid* or *hybrid/overlay* keyword, in any order. In case of the -*hybrid/scaled* pair style each sub-style is prefixed with its scale -factor. The scale factor may be an equal style (or equivalent) -variable. Each sub-style's name is followed by its usual arguments, as -illustrated in the example above. See the doc pages of individual pair -styles for a listing and explanation of the appropriate arguments. +*hybrid/scaled* pair style, each sub-style is prefixed with a scale +factor. The scale factor is either a floating point number or an equal +style (or equivalent) variable. Each sub-style's name is followed by its +usual arguments, as illustrated in the examples above. See the doc +pages of individual pair styles for a listing and explanation of the +appropriate arguments. Note that an individual pair style can be used multiple times as a sub-style. For efficiency this should only be done if your model @@ -164,7 +169,7 @@ one sub-style. Just as with a simulation using a single pair style, if you specify the same atom type pair in a second pair_coeff command, the previous assignment will be overwritten. -For the *hybrid/overlay* and *hybrid/scaled* style, each atom type pair +For the *hybrid/overlay* and *hybrid/scaled* styles, each atom type pair I,J can be assigned to one or more sub-styles. If you specify the same atom type pair in a second pair_coeff command with a new sub-style, then the second sub-style is added to the list of potentials that will be @@ -187,15 +192,15 @@ same: Coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as described above, or in the -data file or restart files read by the :doc:`read_data ` or -:doc:`read_restart ` commands, or by mixing as described -below. +data file read by the :doc:`read_data ` commands, or by +mixing as described below. For all of the *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles, every atom type pair I,J (where I <= J) must be assigned to at least one sub-style via the :doc:`pair_coeff ` command as in the examples above, or in the data file read by the :doc:`read_data -`, or by mixing as described below. +`, or by mixing as described below. Also all sub-styles +must be used at least once in a :doc:`pair_coeff ` command. If you want there to be no interactions between a particular pair of atom types, you have 3 choices. You can assign the type pair to some @@ -208,22 +213,22 @@ input script: .. code-block:: LAMMPS - pair_coeff 2 3 none + pair_coeff 2 3 none or this form in the "Pair Coeffs" section of the data file: .. parsed-literal:: - 3 none + 3 none If an assignment to *none* is made in a simulation with the -*hybrid/overlay* pair style, it wipes out all previous assignments of -that atom type pair to sub-styles. +*hybrid/overlay* or *hybrid/scaled* pair style, it wipes out all +previous assignments of that pair of atom types to sub-styles. Note that you may need to use an :doc:`atom_style ` hybrid command in your input script, if atoms in the simulation will need attributes from several atom styles, due to using multiple pair -potentials. +styles with different requirements. ---------- @@ -232,8 +237,9 @@ for applying weightings that change the strength of pairwise interactions between pairs of atoms that are also 1-2, 1-3, and 1-4 neighbors in the molecular bond topology, as normally set by the :doc:`special_bonds ` command. Different weights can be -assigned to different pair hybrid sub-styles via the :doc:`pair_modify special ` command. This allows multiple force fields -to be used in a model of a hybrid system, however, there is no consistent +assigned to different pair hybrid sub-styles via the :doc:`pair_modify +special ` command. This allows multiple force fields to be +used in a model of a hybrid system, however, there is no consistent approach to determine parameters automatically for the interactions between the two force fields, this is only recommended when particles described by the different force fields do not mix. @@ -307,28 +313,27 @@ Pair_style hybrid allows interactions between type pairs 2-2, 1-2, could even add a second interaction for 1-1 to be computed by another pair style, assuming pair_style hybrid/overlay is used. -But you should not, as a general rule, attempt to exclude the -many-body interactions for some subset of the type pairs within the -set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions. That -is not conceptually well-defined for many-body interactions, since the +But you should not, as a general rule, attempt to exclude the many-body +interactions for some subset of the type pairs within the set of 1,3,4 +interactions, e.g. exclude 1-1 or 1-3 interactions. That is not +conceptually well-defined for many-body interactions, since the potential will typically calculate energies and foces for small groups of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to -find the additional atoms in the group. It is typically non-physical -to think of excluding an interaction between a particular pair of -atoms when the potential computes 3-body or 4-body interactions. +find the additional atoms in the group. However, you can still use the pair_coeff none setting or the :doc:`neigh_modify exclude ` command to exclude certain type pairs from the neighbor list that will be passed to a many-body sub-style. This will alter the calculations made by a many-body -potential, since it builds its list of 3-body, 4-body, etc -interactions from the pair list. You will need to think carefully as -to whether it produces a physically meaningful result for your model. +potential beyond the specific pairs, since it builds its list of 3-body, +4-body, etc interactions from the pair lists. You will need to think +**carefully** as to whether excluding such pairs produces a physically +meaningful result for your model. For example, imagine you have two atom types in your model, type 1 for atoms in one surface, and type 2 for atoms in the other, and you wish to use a Tersoff potential to compute interactions within each -surface, but not between surfaces. Then either of these two command +surface, but not between the surfaces. Then either of these two command sequences would implement that model: .. code-block:: LAMMPS @@ -345,9 +350,9 @@ Either way, only neighbor lists with 1-1 or 2-2 interactions would be passed to the Tersoff potential, which means it would compute no 3-body interactions containing both type 1 and 2 atoms. -Here is another example, using hybrid/overlay, to use 2 many-body -potentials together, in an overlapping manner. Imagine you have CNT -(C atoms) on a Si surface. You want to use Tersoff for Si/Si and Si/C +Here is another example to use 2 many-body potentials together in an +overlapping manner using hybrid/overlay. Imagine you have CNT (C atoms) +on a Si surface. You want to use Tersoff for Si/Si and Si/C interactions, and AIREBO for C/C interactions. Si atoms are type 1; C atoms are type 2. Something like this will work: @@ -358,9 +363,9 @@ atoms are type 2. Something like this will work: pair_coeff * * airebo CH.airebo NULL C Note that to prevent the Tersoff potential from computing C/C -interactions, you would need to modify the SiC.tersoff file to turn -off C/C interaction, i.e. by setting the appropriate coefficients to -0.0. +interactions, you would need to **modify** the SiC.tersoff potential +file to turn off C/C interaction, i.e. by setting the appropriate +coefficients to 0.0. ---------- @@ -368,18 +373,19 @@ Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc -page. +page. Pair style *hybrid/scaled* does (currently) not support the +*gpu*, *omp*, *kk*, or *intel* suffix. -Since the *hybrid* and *hybrid/overlay* styles delegate computation to -the individual sub-styles, the suffix versions of the *hybrid* and -*hybrid/overlay* styles are used to propagate the corresponding suffix -to all sub-styles, if those versions exist. Otherwise the -non-accelerated version will be used. +Since the *hybrid*, *hybrid/overlay*, *hybrid/scaled* styles delegate +computation to the individual sub-styles, the suffix versions of the +*hybrid* and *hybrid/overlay* styles are used to propagate the +corresponding suffix to all sub-styles, if those versions +exist. Otherwise the non-accelerated version will be used. -The individual accelerated sub-styles are part of the GPU, USER-OMP -and OPT packages, respectively. They are only enabled if LAMMPS was -built with those packages. See the :doc:`Build package ` -doc page for more info. +The individual accelerated sub-styles are part of the GPU, KOKKOS, +USER-INTEL, USER-OMP, and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :doc:`Build +package ` doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the @@ -397,17 +403,17 @@ Any pair potential settings made via the :doc:`pair_modify ` command are passed along to all sub-styles of the hybrid potential. -For atom type pairs I,J and I != J, if the sub-style assigned to I,I -and J,J is the same, and if the sub-style allows for mixing, then the +For atom type pairs I,J and I != J, if the sub-style assigned to I,I and +J,J is the same, and if the sub-style allows for mixing, then the coefficients for I,J can be mixed. This means you do not have to specify a pair_coeff command for I,J since the I,J type pair will be -assigned automatically to the sub-style defined for both I,I and J,J -and its coefficients generated by the mixing rule used by that -sub-style. For the *hybrid/overlay* style, there is an additional -requirement that both the I,I and J,J pairs are assigned to a single -sub-style. See the "pair_modify" command for details of mixing rules. -See the See the doc page for the sub-style to see if allows for -mixing. +assigned automatically to the sub-style defined for both I,I and J,J and +its coefficients generated by the mixing rule used by that sub-style. +For the *hybrid/overlay* and *hybrid/scaled* style, there is an +additional requirement that both the I,I and J,J pairs are assigned to a +single sub-style. See the :doc:`pair_modify ` command for +details of mixing rules. See the See the doc page for the sub-style to +see if allows for mixing. The hybrid pair styles supports the :doc:`pair_modify ` shift, table, and tail options for an I,J pair interaction, if the @@ -418,7 +424,10 @@ settings are written to :doc:`binary restart files `, so a :doc:`pair_style ` command does not need to specified in an input script that reads a restart file. However, the coefficient information is not stored in the restart file. Thus, pair_coeff -commands need to be re-specified in the restart input script. +commands need to be re-specified in the restart input script. For pair +style *hybrid/scaled* also the names of any variables used as scale +factors are restored, but not the variables themselves, so those may +need to be redefined when continuing from a restart. These pair styles support the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, if @@ -435,7 +444,7 @@ short-range Coulombic cutoff used by each of these long pair styles is the same or else LAMMPS will generate an error. Pair style *hybrid/scaled* currently only works for non-accelerated -pair styles. +pair styles and pair styles from the OPT package. Related commands """""""""""""""" From d88cf587b2743e1b94436acc293a14ad5def69ee Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 10 Apr 2021 00:25:00 -0400 Subject: [PATCH 0489/1217] add pair style coul/cut/global and fix restart/data bugs in coul/cut --- doc/src/Commands_pair.rst | 1 + doc/src/pair_coul.rst | 14 ++- doc/src/pair_style.rst | 1 + src/pair_coul_cut.cpp | 61 ++++++++-- src/pair_coul_cut.h | 6 +- src/pair_coul_cut_global.cpp | 44 +++++++ src/pair_coul_cut_global.h | 55 +++++++++ unittest/force-styles/test_pair_style.cpp | 1 - .../force-styles/tests/mol-pair-coul_cut.yaml | 114 +++++++++--------- .../tests/mol-pair-coul_cut_global.yaml | 85 +++++++++++++ 10 files changed, 311 insertions(+), 71 deletions(-) create mode 100644 src/pair_coul_cut_global.cpp create mode 100644 src/pair_coul_cut_global.h create mode 100644 unittest/force-styles/tests/mol-pair-coul_cut_global.yaml diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index e82713f8a4..60996b9c65 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -69,6 +69,7 @@ OPT. * :doc:`comb3 ` * :doc:`cosine/squared ` * :doc:`coul/cut (gko) ` + * :doc:`coul/cut/global (o) ` * :doc:`coul/cut/soft (o) ` * :doc:`coul/debye (gko) ` * :doc:`coul/diel (o) ` diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index 4def43647f..b8303622aa 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -10,6 +10,8 @@ .. index:: pair_style coul/dsf/gpu .. index:: pair_style coul/dsf/kk .. index:: pair_style coul/dsf/omp +.. index:: pair_style coul/cut/global +.. index:: pair_style coul/cut/global/omp .. index:: pair_style coul/long .. index:: pair_style coul/long/omp .. index:: pair_style coul/long/kk @@ -40,6 +42,11 @@ pair_style coul/dsf command Accelerator Variants: *coul/dsf/gpu*, *coul/dsf/kk*, *coul/dsf/omp* +pair_style coul/cut/global command +================================== + +Accelerator Variants: *coul/cut/omp* + pair_style coul/long command ============================ @@ -76,8 +83,8 @@ Syntax pair_style coul/cut cutoff pair_style coul/debye kappa cutoff pair_style coul/dsf alpha cutoff + pair_style coul/cut/global cutoff pair_style coul/long cutoff - pair_style coul/long/gpu cutoff pair_style coul/wolf alpha cutoff pair_style coul/streitz cutoff keyword alpha pair_style tip4p/cut otype htype btype atype qdist cutoff @@ -245,6 +252,11 @@ Streitz-Mintmire parameterization for the material being modeled. ---------- +Pair style *coul/cut/global* computes the same Coulombic interactions +as style *coul/cut* except that it allows only a single global cutoff +and thus makes it compatible for use in combination with long-range +coulomb styles in :doc:`hybrid pair styles `. + Styles *coul/long* and *coul/msm* compute the same Coulombic interactions as style *coul/cut* except that an additional damping factor is applied so it can be used in conjunction with the diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index bc2340d729..49eac18aa8 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -133,6 +133,7 @@ accelerated styles exist. * :doc:`comb3 ` - charge-optimized many-body (COMB3) potential * :doc:`cosine/squared ` - Cooke-Kremer-Deserno membrane model potential * :doc:`coul/cut ` - cutoff Coulomb potential +* :doc:`coul/cut/global ` - cutoff Coulomb potential * :doc:`coul/cut/soft ` - Coulomb potential with a soft core * :doc:`coul/debye ` - cutoff Coulomb potential with Debye screening * :doc:`coul/diel ` - Coulomb potential with dielectric permittivity diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index 44ddd424d9..428c12c2e0 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -13,22 +13,24 @@ #include "pair_coul_cut.h" -#include -#include #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairCoulCut::PairCoulCut(LAMMPS *lmp) : Pair(lmp) {} +PairCoulCut::PairCoulCut(LAMMPS *lmp) : Pair(lmp) { + writedata = 1; +} /* ---------------------------------------------------------------------- */ @@ -208,8 +210,10 @@ void PairCoulCut::init_style() double PairCoulCut::init_one(int i, int j) { - if (setflag[i][j] == 0) + if (setflag[i][j] == 0) { cut[i][j] = mix_distance(cut[i][i],cut[j][j]); + scale[i][j] = 1.0; + } scale[j][i] = scale[i][j]; @@ -225,11 +229,15 @@ void PairCoulCut::write_restart(FILE *fp) write_restart_settings(fp); int i,j; - for (i = 1; i <= atom->ntypes; i++) + for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { + fwrite(&scale[i][j],sizeof(double),1,fp); fwrite(&setflag[i][j],sizeof(int),1,fp); - if (setflag[i][j]) fwrite(&cut[i][j],sizeof(double),1,fp); + if (setflag[i][j]) { + fwrite(&cut[i][j],sizeof(double),1,fp); + } } + } } /* ---------------------------------------------------------------------- @@ -243,15 +251,21 @@ void PairCoulCut::read_restart(FILE *fp) int i,j; int me = comm->me; - for (i = 1; i <= atom->ntypes; i++) + for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { - if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); + if (me == 0) { + utils::sfread(FLERR,&scale[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); + } + MPI_Bcast(&scale[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { - if (me == 0) utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + if (me == 0) + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); } } + } } /* ---------------------------------------------------------------------- @@ -281,6 +295,27 @@ void PairCoulCut::read_restart_settings(FILE *fp) MPI_Bcast(&mix_flag,1,MPI_INT,0,world); } +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairCoulCut::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d\n",i); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairCoulCut::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g\n",i,j,cut[i][j]); +} + /* ---------------------------------------------------------------------- */ double PairCoulCut::single(int i, int j, int /*itype*/, int /*jtype*/, diff --git a/src/pair_coul_cut.h b/src/pair_coul_cut.h index 5fed8344e2..fe44c0d8a4 100644 --- a/src/pair_coul_cut.h +++ b/src/pair_coul_cut.h @@ -30,15 +30,17 @@ class PairCoulCut : public Pair { virtual ~PairCoulCut(); virtual void compute(int, int); virtual void settings(int, char **); - void coeff(int, char **); + virtual void coeff(int, char **); void init_style(); double init_one(int, int); void write_restart(FILE *); void read_restart(FILE *); virtual void write_restart_settings(FILE *); virtual void read_restart_settings(FILE *); + virtual void write_data(FILE *); + virtual void write_data_all(FILE *); virtual double single(int, int, int, int, double, double, double, double &); - void *extract(const char *, int &); + virtual void *extract(const char *, int &); protected: double cut_global; diff --git a/src/pair_coul_cut_global.cpp b/src/pair_coul_cut_global.cpp new file mode 100644 index 0000000000..fa3d394092 --- /dev/null +++ b/src/pair_coul_cut_global.cpp @@ -0,0 +1,44 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "pair_coul_cut_global.h" + +#include "error.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairCoulCutGlobal::coeff(int narg, char **arg) +{ + if (narg != 2) + error->all(FLERR,"Incorrect args for pair coefficients"); + + PairCoulCut::coeff(narg,arg); +} + + +/* ---------------------------------------------------------------------- */ + +void *PairCoulCutGlobal::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_global; + dim = 2; + if (strcmp(str,"scale") == 0) return (void *) scale; + return nullptr; +} diff --git a/src/pair_coul_cut_global.h b/src/pair_coul_cut_global.h new file mode 100644 index 0000000000..4b3a8ddbaa --- /dev/null +++ b/src/pair_coul_cut_global.h @@ -0,0 +1,55 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(coul/cut/global,PairCoulCutGlobal) + +#else + +#ifndef LMP_PAIR_COUL_CUT_GLOBAL_H +#define LMP_PAIR_COUL_CUT_GLOBAL_H + +#include "pair_coul_cut.h" + +namespace LAMMPS_NS { + +class PairCoulCutGlobal : public PairCoulCut { + public: + PairCoulCutGlobal(class LAMMPS *lmp) : PairCoulCut(lmp) {} + void coeff(int, char **); + void *extract(const char *, int &); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair style coul/cut requires atom attribute q + +The atom style defined does not have these attributes. + +*/ diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index 5ea7fc371c..057f2b5352 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -25,7 +25,6 @@ #include "atom.h" #include "compute.h" -#include "fmt/format.h" #include "force.h" #include "info.h" #include "input.h" diff --git a/unittest/force-styles/tests/mol-pair-coul_cut.yaml b/unittest/force-styles/tests/mol-pair-coul_cut.yaml index 921e682a9a..09e97a3a8d 100644 --- a/unittest/force-styles/tests/mol-pair-coul_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_cut.yaml @@ -1,7 +1,8 @@ --- -lammps_version: 10 Feb 2021 -date_generated: Fri Feb 26 23:08:42 2021 +lammps_version: 8 Apr 2021 +date_generated: Sat Apr 10 00:22:24 2021 epsilon: 1e-13 +skip_tests: prerequisites: ! | atom full pair coul/cut @@ -11,17 +12,22 @@ post_commands: ! | input_file: in.fourmol pair_style: coul/cut 8.0 pair_coeff: ! | - * * + 1 1 + 2 2 7.0 + 2 3 7.5 + 3 3 + 4 4 8.0 + 5 5 extract: ! | cut_coul 2 natoms: 29 init_vdwl: 0 -init_coul: -127.494586297384 +init_coul: -93.55664334073657 init_stress: ! |- - -2.6824547034957277e+01 -4.3162775104089022e+01 -5.7507264158338124e+01 -8.2055093564543602e-01 -7.9072701063929465e+00 3.0552092014126533e+00 + -2.0535385669481379e+01 -1.6145387915767863e+01 -5.6875869755487301e+01 -4.1550674863524968e+00 -7.0519267473420957e+00 2.6305371873347489e+00 init_forces: ! |2 1 2.2407335289699457e+00 -5.8916421262140251e-02 4.2668639853362533e-01 - 2 3.0979928510686561e-01 -2.1737695778193569e+00 -1.8762407787145119e+00 + 2 -1.2152150177208687e-01 -3.4650575893033708e+00 -1.3360477574570087e+00 3 -1.5509825092714681e-02 -8.6264917303471161e-02 3.0367577692877928e-02 4 5.1555686582278520e-02 1.0144901459000669e-02 -3.0866112200648410e-01 5 -3.9871973553557233e-01 7.0523075214913145e-01 -7.8022318023030612e-02 @@ -30,57 +36,57 @@ init_forces: ! |2 8 -1.7087898110045159e+00 4.1818078578969917e+00 2.4290227133489601e+00 9 1.8279010754687195e+00 -5.6724899047236770e+00 1.6512690951588267e+00 10 -2.9363989744075952e-01 4.2512276557131090e-01 -2.0317384271111175e-01 - 11 -9.8868358921602750e-01 1.1284880357946445e+00 -5.3995772876854398e-01 + 11 -9.6854530039287257e-01 1.2818484089934798e+00 -4.0964874266313867e-01 12 3.3104189805348057e+00 -7.6522029601079322e-01 1.2706541181424338e+00 - 13 -3.8231563183336364e-01 -1.1565866576649098e-02 -8.7140102078706039e-03 - 14 -1.2285578202646528e+00 4.4726948380599840e-01 -1.5341285475604788e-02 - 15 2.2085158688210516e-01 -1.6336214445566244e-01 -9.6577522905262758e-01 + 13 -3.0889352958622951e-01 2.5103266106999866e-01 1.0669227367631845e-01 + 14 -1.2634615134073266e+00 5.9356329877397740e-01 2.0097321421686021e-01 + 15 3.4164194917662777e-01 -1.3968217225075463e-02 -1.0754490238146823e+00 16 -1.0515762083518698e+00 -3.6728607969167482e-01 2.7987602083946292e+00 - 17 -2.3442527695736954e+00 6.0494781225943264e+00 -7.7669898420813883e+00 - 18 1.2747707302049942e+00 6.6751091235431907e+00 -9.9139029454048035e+00 - 19 1.6181330640335625e+00 -1.6591712461142003e+00 5.6543694708933723e+00 - 20 -3.4516847879389365e+00 -3.1783992642977736e+00 4.2589367844805865e+00 - 21 2.4909407783496178e+00 1.4847928289095484e+00 -1.0503546063193097e+01 - 22 1.4973505700836185e+00 1.0712683327319574e+00 6.7413935914321712e+00 - 23 -4.4865766347042468e+00 -3.8185091520236116e+00 4.2817682561025867e+00 - 24 -2.4197806588078703e+00 9.8687406957238029e+00 -2.3585711007230041e+00 - 25 3.5804022684917332e+00 -3.1080767536674005e+00 3.9458463586096970e+00 - 26 -2.0751789623087848e+00 -7.6352193307876766e+00 -4.5052467808202223e-01 - 27 -2.8475395052833852e+00 1.1111959093179417e+01 -4.4252374188335644e+00 - 28 4.8464204075747359e+00 -5.2910383050538492e+00 4.0808901405648896e+00 - 29 -1.2636120082903082e+00 -6.1719354975176035e+00 9.2219267915908476e-01 + 17 -2.4272925242862877e+00 5.1482976415440387e+00 -6.9745861917436480e+00 + 18 -3.3422585449197340e-01 1.0468316830549977e+01 -9.5556804718861983e+00 + 19 1.8166530000757015e+00 -1.4461616747597046e+00 7.5536140661465714e+00 + 20 -3.2356613999008608e+00 -3.8668819868868143e+00 5.3737386596536343e+00 + 21 4.0222635030104259e+00 1.6132349119387515e+00 -1.0241718963154419e+01 + 22 1.4374544034911272e+00 -9.5656370964487103e-01 6.5980789669241569e+00 + 23 -4.4376821117692176e+00 -3.8947548010087796e+00 4.1208787227921038e+00 + 24 -1.5247815933638265e+00 1.1713843272625617e+01 -6.0248223323521604e+00 + 25 3.1898863386468577e+00 -4.1364515802851436e+00 3.9097585091440594e+00 + 26 -2.2629415636619381e+00 -8.5609820249335087e+00 -1.1581224704665538e+00 + 27 -3.6829593583586151e+00 1.0444039166475267e+01 -3.7821850434646627e+00 + 28 5.4031537104784855e+00 -4.4754845440910707e+00 3.6816742644554843e+00 + 29 -1.2926003313820287e+00 -6.0718114858636643e+00 7.3448520698640607e-02 run_vdwl: 0 -run_coul: -127.551092913469 +run_coul: -93.61491356191763 run_stress: ! |- - -2.6928416018548067e+01 -4.3177725729834854e+01 -5.7444951165085541e+01 -8.5814323779813129e-01 -7.9912081348585087e+00 2.9897259857467389e+00 + -2.0637957613066451e+01 -1.6150296923318230e+01 -5.6826659025532969e+01 -4.1943798944102859e+00 -7.1336719665040942e+00 2.5570315775315215e+00 run_forces: ! |2 - 1 2.2424368291189611e+00 -5.7157845887417236e-02 4.3210281185121069e-01 - 2 3.0183044940246062e-01 -2.1770211242302246e+00 -1.8796316672405435e+00 - 3 -1.5579134024760494e-02 -8.6577075665555045e-02 3.0374580927846943e-02 - 4 5.2605597845996610e-02 1.0081774332824270e-02 -3.0969764881211892e-01 - 5 -3.9802063955902828e-01 7.0541551998225649e-01 -7.9105180426906119e-02 - 6 2.0115016302231399e+00 -3.7433268305651115e+00 -2.9688564502920158e+00 - 7 -3.2650169036425236e-01 7.4540116984953042e-01 3.8864116015671808e+00 - 8 -1.6992053224967520e+00 4.1770597030834642e+00 2.4329396564406349e+00 - 9 1.8250267620013743e+00 -5.6775189439742455e+00 1.6562371734234631e+00 - 10 -2.9411864176775349e-01 4.2484150168808632e-01 -2.0454722162066086e-01 - 11 -9.8864600485826815e-01 1.1292383541031983e+00 -5.3894807546123469e-01 - 12 3.3107287761242974e+00 -7.6414239662660099e-01 1.2747075215620911e+00 - 13 -3.8336813011366144e-01 -1.2486400314578122e-02 -9.4718485253563467e-03 - 14 -1.2290837060322926e+00 4.4862678961891689e-01 -1.5069551071827086e-02 - 15 2.2244012017801007e-01 -1.6546887582342559e-01 -9.6944707732754809e-01 - 16 -1.0531155341397860e+00 -3.6654926990083037e-01 2.7960996028622298e+00 - 17 -2.3452245945824948e+00 6.0586966641613316e+00 -7.7701709031633026e+00 - 18 1.2287925114358347e+00 6.6283596097346500e+00 -9.8694991818018014e+00 - 19 1.6548495610099294e+00 -1.6299328734082061e+00 5.6681416753764280e+00 - 20 -3.4405939298489487e+00 -3.1595057592530829e+00 4.2031829943411507e+00 - 21 2.4999236613139768e+00 1.4581441593082431e+00 -1.0498791509490704e+01 - 22 1.5230738475837411e+00 1.0948611353935194e+00 6.7461577757855986e+00 - 23 -4.5208030817248321e+00 -3.8176488387685179e+00 4.2715025892256220e+00 - 24 -2.4424910840260479e+00 9.8889784537097576e+00 -2.3784455147561552e+00 - 25 3.6199382208005479e+00 -3.1023007862101899e+00 3.9803408068580102e+00 - 26 -2.0901080780170158e+00 -7.6586474495008154e+00 -4.6300658746615819e-01 - 27 -2.8661140489132810e+00 1.1127847846706011e+01 -4.4084385064798797e+00 - 28 4.8657388732889295e+00 -5.2969930881855793e+00 4.0790567237989928e+00 - 29 -1.2659132198580254e+00 -6.1822751233574085e+00 9.0587140991575621e-01 + 1 2.2425199864949272e+00 -5.7185268117056043e-02 4.3203484436437956e-01 + 2 -1.2953282231918894e-01 -3.4675950045872330e+00 -1.3398768542921780e+00 + 3 -1.5576933865004368e-02 -8.6576616933096762e-02 3.0374805119446222e-02 + 4 5.2594937495592908e-02 1.0083837924927244e-02 -3.0970246073870022e-01 + 5 -3.9802884083965534e-01 7.0541446618110337e-01 -7.9104505633399519e-02 + 6 2.0114733380305516e+00 -3.7433607398217483e+00 -2.9688665724203247e+00 + 7 -3.2646062589844127e-01 7.4545113602886504e-01 3.8864515374233779e+00 + 8 -1.6992144552176487e+00 4.1770867949498349e+00 2.4329479646797592e+00 + 9 1.8250302102601557e+00 -5.6775183441065051e+00 1.6562334058459376e+00 + 10 -2.9411499784567297e-01 4.2483825717579743e-01 -2.0454944575981404e-01 + 11 -9.6852892734814910e-01 1.2825160904684365e+00 -4.0863298208468957e-01 + 12 3.3107072705734946e+00 -7.6411402305007570e-01 1.2747076834264663e+00 + 13 -3.0999843695510060e-01 2.5003385487095964e-01 1.0600468871727173e-01 + 14 -1.2638813019667337e+00 5.9487350384637094e-01 2.0105698487957110e-01 + 15 3.4335793714273627e-01 -1.5950553742170387e-02 -1.0791712067698431e+00 + 16 -1.0530808398954454e+00 -3.6657367999349177e-01 2.7960862384014673e+00 + 17 -2.4285042656947571e+00 5.1576639561985473e+00 -6.9782029543394053e+00 + 18 -3.7929628350149169e-01 1.0420786070107907e+01 -9.5123267863543006e+00 + 19 1.8527235581340016e+00 -1.4163845910512083e+00 7.5667871079591533e+00 + 20 -3.2257007148929735e+00 -3.8484754900366887e+00 5.3176481256299590e+00 + 21 4.0318672433929734e+00 1.5871903248026678e+00 -1.0237421892763503e+01 + 22 1.4629760972442929e+00 -9.3386175185967235e-01 6.6032592166314519e+00 + 23 -4.4717803858275476e+00 -3.8939153227171523e+00 4.1111064353488365e+00 + 24 -1.5477331915053858e+00 1.1733740828713346e+01 -6.0432763590713154e+00 + 25 3.2290132418876336e+00 -4.1305242042670889e+00 3.9442459043882159e+00 + 26 -2.2770020178904948e+00 -8.5834251121651697e+00 -1.1704818988226089e+00 + 27 -3.7015228676694329e+00 1.0459984537547431e+01 -3.7654963783953805e+00 + 28 5.4222452431134922e+00 -4.4818388539753489e+00 3.6800169942739531e+00 + 29 -1.2945511546367356e+00 -6.0823641023924875e+00 5.8148360356210294e-02 ... diff --git a/unittest/force-styles/tests/mol-pair-coul_cut_global.yaml b/unittest/force-styles/tests/mol-pair-coul_cut_global.yaml new file mode 100644 index 0000000000..817c7c76ca --- /dev/null +++ b/unittest/force-styles/tests/mol-pair-coul_cut_global.yaml @@ -0,0 +1,85 @@ +--- +lammps_version: 10 Feb 2021 +date_generated: Fri Feb 26 23:08:42 2021 +epsilon: 1e-13 +prerequisites: ! | + atom full + pair coul/cut/global +pre_commands: ! "" +post_commands: ! "" +input_file: in.fourmol +pair_style: coul/cut/global 8.0 +pair_coeff: ! | + * * +extract: ! | + cut_coul 0 +natoms: 29 +init_vdwl: 0 +init_coul: -127.494586297384 +init_stress: ! |- + -2.6824547034957277e+01 -4.3162775104089022e+01 -5.7507264158338124e+01 -8.2055093564543602e-01 -7.9072701063929465e+00 3.0552092014126533e+00 +init_forces: ! |2 + 1 2.2407335289699457e+00 -5.8916421262140251e-02 4.2668639853362533e-01 + 2 3.0979928510686561e-01 -2.1737695778193569e+00 -1.8762407787145119e+00 + 3 -1.5509825092714681e-02 -8.6264917303471161e-02 3.0367577692877928e-02 + 4 5.1555686582278520e-02 1.0144901459000669e-02 -3.0866112200648410e-01 + 5 -3.9871973553557233e-01 7.0523075214913145e-01 -7.8022318023030612e-02 + 6 2.0159901805654243e+00 -3.7483112004912753e+00 -2.9733937038705189e+00 + 7 -3.2885029720170206e-01 7.5012396443748963e-01 3.8958946746344409e+00 + 8 -1.7087898110045159e+00 4.1818078578969917e+00 2.4290227133489601e+00 + 9 1.8279010754687195e+00 -5.6724899047236770e+00 1.6512690951588267e+00 + 10 -2.9363989744075952e-01 4.2512276557131090e-01 -2.0317384271111175e-01 + 11 -9.8868358921602750e-01 1.1284880357946445e+00 -5.3995772876854398e-01 + 12 3.3104189805348057e+00 -7.6522029601079322e-01 1.2706541181424338e+00 + 13 -3.8231563183336364e-01 -1.1565866576649098e-02 -8.7140102078706039e-03 + 14 -1.2285578202646528e+00 4.4726948380599840e-01 -1.5341285475604788e-02 + 15 2.2085158688210516e-01 -1.6336214445566244e-01 -9.6577522905262758e-01 + 16 -1.0515762083518698e+00 -3.6728607969167482e-01 2.7987602083946292e+00 + 17 -2.3442527695736954e+00 6.0494781225943264e+00 -7.7669898420813883e+00 + 18 1.2747707302049942e+00 6.6751091235431907e+00 -9.9139029454048035e+00 + 19 1.6181330640335625e+00 -1.6591712461142003e+00 5.6543694708933723e+00 + 20 -3.4516847879389365e+00 -3.1783992642977736e+00 4.2589367844805865e+00 + 21 2.4909407783496178e+00 1.4847928289095484e+00 -1.0503546063193097e+01 + 22 1.4973505700836185e+00 1.0712683327319574e+00 6.7413935914321712e+00 + 23 -4.4865766347042468e+00 -3.8185091520236116e+00 4.2817682561025867e+00 + 24 -2.4197806588078703e+00 9.8687406957238029e+00 -2.3585711007230041e+00 + 25 3.5804022684917332e+00 -3.1080767536674005e+00 3.9458463586096970e+00 + 26 -2.0751789623087848e+00 -7.6352193307876766e+00 -4.5052467808202223e-01 + 27 -2.8475395052833852e+00 1.1111959093179417e+01 -4.4252374188335644e+00 + 28 4.8464204075747359e+00 -5.2910383050538492e+00 4.0808901405648896e+00 + 29 -1.2636120082903082e+00 -6.1719354975176035e+00 9.2219267915908476e-01 +run_vdwl: 0 +run_coul: -127.551092913469 +run_stress: ! |- + -2.6928416018548067e+01 -4.3177725729834854e+01 -5.7444951165085541e+01 -8.5814323779813129e-01 -7.9912081348585087e+00 2.9897259857467389e+00 +run_forces: ! |2 + 1 2.2424368291189611e+00 -5.7157845887417236e-02 4.3210281185121069e-01 + 2 3.0183044940246062e-01 -2.1770211242302246e+00 -1.8796316672405435e+00 + 3 -1.5579134024760494e-02 -8.6577075665555045e-02 3.0374580927846943e-02 + 4 5.2605597845996610e-02 1.0081774332824270e-02 -3.0969764881211892e-01 + 5 -3.9802063955902828e-01 7.0541551998225649e-01 -7.9105180426906119e-02 + 6 2.0115016302231399e+00 -3.7433268305651115e+00 -2.9688564502920158e+00 + 7 -3.2650169036425236e-01 7.4540116984953042e-01 3.8864116015671808e+00 + 8 -1.6992053224967520e+00 4.1770597030834642e+00 2.4329396564406349e+00 + 9 1.8250267620013743e+00 -5.6775189439742455e+00 1.6562371734234631e+00 + 10 -2.9411864176775349e-01 4.2484150168808632e-01 -2.0454722162066086e-01 + 11 -9.8864600485826815e-01 1.1292383541031983e+00 -5.3894807546123469e-01 + 12 3.3107287761242974e+00 -7.6414239662660099e-01 1.2747075215620911e+00 + 13 -3.8336813011366144e-01 -1.2486400314578122e-02 -9.4718485253563467e-03 + 14 -1.2290837060322926e+00 4.4862678961891689e-01 -1.5069551071827086e-02 + 15 2.2244012017801007e-01 -1.6546887582342559e-01 -9.6944707732754809e-01 + 16 -1.0531155341397860e+00 -3.6654926990083037e-01 2.7960996028622298e+00 + 17 -2.3452245945824948e+00 6.0586966641613316e+00 -7.7701709031633026e+00 + 18 1.2287925114358347e+00 6.6283596097346500e+00 -9.8694991818018014e+00 + 19 1.6548495610099294e+00 -1.6299328734082061e+00 5.6681416753764280e+00 + 20 -3.4405939298489487e+00 -3.1595057592530829e+00 4.2031829943411507e+00 + 21 2.4999236613139768e+00 1.4581441593082431e+00 -1.0498791509490704e+01 + 22 1.5230738475837411e+00 1.0948611353935194e+00 6.7461577757855986e+00 + 23 -4.5208030817248321e+00 -3.8176488387685179e+00 4.2715025892256220e+00 + 24 -2.4424910840260479e+00 9.8889784537097576e+00 -2.3784455147561552e+00 + 25 3.6199382208005479e+00 -3.1023007862101899e+00 3.9803408068580102e+00 + 26 -2.0901080780170158e+00 -7.6586474495008154e+00 -4.6300658746615819e-01 + 27 -2.8661140489132810e+00 1.1127847846706011e+01 -4.4084385064798797e+00 + 28 4.8657388732889295e+00 -5.2969930881855793e+00 4.0790567237989928e+00 + 29 -1.2659132198580254e+00 -6.1822751233574085e+00 9.0587140991575621e-01 +... From 39a00e2901019e37d8bb3d50ffdbeedc9ed224f6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 11 Apr 2021 06:03:46 -0400 Subject: [PATCH 0490/1217] reformat --- doc/src/fix_qeq.rst | 125 ++++++++++++++++++++++++-------------------- 1 file changed, 67 insertions(+), 58 deletions(-) diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index 56fde059e8..c655076ce8 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -56,27 +56,28 @@ Examples Description """"""""""" -Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) ` and formulated in :ref:`(Nakano) ` (also known -as the matrix inversion method) and in :ref:`(Rick and Stuart) ` (also -known as the extended Lagrangian method) based on the -electronegativity equilization principle. +Perform the charge equilibration (QEq) method as described in +:ref:`(Rappe and Goddard) ` and formulated in :ref:`(Nakano) +` (also known as the matrix inversion method) and in +:ref:`(Rick and Stuart) ` (also known as the extended Lagrangian +method) based on the electronegativity equilization principle. These fixes can be used with any :doc:`pair style ` in LAMMPS, so long as per-atom charges are defined. The most typical use-case is in conjunction with a :doc:`pair style ` that performs charge equilibration periodically (e.g. every timestep), such -as the ReaxFF or Streitz-Mintmire potential. -But these fixes can also be used with -potentials that normally assume per-atom charges are fixed, e.g. a -:doc:`Buckingham ` or :doc:`LJ/Coulombic ` potential. +as the ReaxFF or Streitz-Mintmire potential. But these fixes can also +be used with potentials that normally assume per-atom charges are fixed, +e.g. a :doc:`Buckingham ` or :doc:`LJ/Coulombic ` +potential. -Because the charge equilibration calculation is effectively -independent of the pair style, these fixes can also be used to perform -a one-time assignment of charges to atoms. For example, you could -define the QEq fix, perform a zero-timestep run via the :doc:`run ` -command without any pair style defined which would set per-atom -charges (based on the current atom configuration), then remove the fix -via the :doc:`unfix ` command before performing further dynamics. +Because the charge equilibration calculation is effectively independent +of the pair style, these fixes can also be used to perform a one-time +assignment of charges to atoms. For example, you could define the QEq +fix, perform a zero-timestep run via the :doc:`run ` command +without any pair style defined which would set per-atom charges (based +on the current atom configuration), then remove the fix via the +:doc:`unfix ` command before performing further dynamics. .. note:: @@ -87,11 +88,14 @@ via the :doc:`unfix ` command before performing further dynamics. .. note:: - The :doc:`fix qeq/comb ` command must still be used - to perform charge equilibration with the :doc:`COMB potential `. The :doc:`fix qeq/reax ` - command can be used to perform charge equilibration with the :doc:`ReaxFF force field `, although fix qeq/shielded yields the - same results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance* - are the same. Eventually the fix qeq/reax command will be deprecated. + The :doc:`fix qeq/comb ` command must still be used to + perform charge equilibration with the :doc:`COMB potential + `. The :doc:`fix qeq/reax ` command can be + used to perform charge equilibration with the :doc:`ReaxFF force + field `, although fix qeq/shielded yields the same + results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance* + are the same. Eventually the fix qeq/reax command will be + deprecated. The QEq method minimizes the electrostatic energy of the system (or equalizes the derivative of energy with respect to charge of all the @@ -134,55 +138,57 @@ usually a good number. The *qeq/shielded* style describes partial charges on atoms also as point charges, but uses a shielded Coulomb potential to describe the interaction between a pair of charged particles. Interaction through -the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force field ` paper. The shielding accounts for charge overlap +the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force +field ` paper. The shielding accounts for charge overlap between charged particles at small separation. This style is the same -as :doc:`fix qeq/reax `, and can be used with :doc:`pair_style reax/c `. Only the *chi*\ , *eta*\ , and *gamma* -parameters from the *qfile* file are used. When using the string -*reax/c* as filename, these parameters are extracted directly from -an active *reax/c* pair style. This style solves partial -charges on atoms via the matrix inversion method. A tolerance of -1.0e-6 is usually a good number. +as :doc:`fix qeq/reax `, and can be used with +:doc:`pair_style reax/c `. Only the *chi*\ , *eta*\ , and +*gamma* parameters from the *qfile* file are used. When using the string +*reax/c* as filename, these parameters are extracted directly from an +active *reax/c* pair style. This style solves partial charges on atoms +via the matrix inversion method. A tolerance of 1.0e-6 is usually a +good number. The *qeq/slater* style describes partial charges on atoms as spherical charge densities centered around atoms via the Slater 1\ *s* orbital, so -that the interaction between a pair of charged particles is the -product of two Slater 1\ *s* orbitals. The expression for the Slater -1\ *s* orbital is given under equation (6) of the -:ref:`Streitz-Mintmire ` paper. Only the *chi*\ , *eta*\ , *zeta*\ , and -*qcore* parameters from the *qfile* file are used. When using the string +that the interaction between a pair of charged particles is the product +of two Slater 1\ *s* orbitals. The expression for the Slater 1\ *s* +orbital is given under equation (6) of the :ref:`Streitz-Mintmire +` paper. Only the *chi*\ , *eta*\ , *zeta*\ , and *qcore* +parameters from the *qfile* file are used. When using the string *coul/streitz* as filename, these parameters are extracted directly from -an active *coul/streitz* pair style. This style solves -partial charges on atoms via the matrix inversion method. A tolerance -of 1.0e-6 is usually a good number. Keyword *alpha* can be used to -change the Slater type orbital exponent. +an active *coul/streitz* pair style. This style solves partial charges +on atoms via the matrix inversion method. A tolerance of 1.0e-6 is +usually a good number. Keyword *alpha* can be used to change the Slater +type orbital exponent. The *qeq/dynamic* style describes partial charges on atoms as point -charges that interact through 1/r, but the extended Lagrangian method -is used to solve partial charges on atoms. Only the *chi* and *eta* +charges that interact through 1/r, but the extended Lagrangian method is +used to solve partial charges on atoms. Only the *chi* and *eta* parameters from the *qfile* file are used. Note that Coulomb -catastrophe can occur if repulsion between the pair of charged -particles is too weak. A tolerance of 1.0e-3 is usually a good -number. Keyword *qdamp* can be used to change the damping factor, while -keyword *qstep* can be used to change the time step size. +catastrophe can occur if repulsion between the pair of charged particles +is too weak. A tolerance of 1.0e-3 is usually a good number. Keyword +*qdamp* can be used to change the damping factor, while keyword *qstep* +can be used to change the time step size. -The :ref:`\ *qeq/fire*\ ` style describes the same charge model and charge -solver as the *qeq/dynamic* style, but employs a FIRE minimization -algorithm to solve for equilibrium charges. -Keyword *qdamp* can be used to change the damping factor, while -keyword *qstep* can be used to change the time step size. +The :ref:`\ *qeq/fire*\ ` style describes the same charge model +and charge solver as the *qeq/dynamic* style, but employs a FIRE +minimization algorithm to solve for equilibrium charges. Keyword +*qdamp* can be used to change the damping factor, while keyword *qstep* +can be used to change the time step size. Note that *qeq/point*\ , *qeq/shielded*\ , and *qeq/slater* describe different charge models, whereas the matrix inversion method and the extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are different solvers. -Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all describe -charges as point charges that interact through 1/r relationship, but -solve partial charges on atoms using different solvers. These three -styles should yield comparable results if -the QEq parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the -same. Style *qeq/point* is typically faster, *qeq/dynamic* scales -better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ . +Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all +describe charges as point charges that interact through 1/r +relationship, but solve partial charges on atoms using different +solvers. These three styles should yield comparable results if the QEq +parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the same. +Style *qeq/point* is typically faster, *qeq/dynamic* scales better on +larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ . .. note:: @@ -200,9 +206,11 @@ better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ . Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No information about these fixes is written to :doc:`binary restart files `. No global scalar or vector or per-atom -quantities are stored by these fixes for access by various :doc:`output commands `. No parameter of these fixes can be used -with the *start/stop* keywords of the :doc:`run ` command. +No information about these fixes is written to :doc:`binary restart +files `. No global scalar or vector or per-atom quantities are +stored by these fixes for access by various :doc:`output commands +`. No parameter of these fixes can be used with the +*start/stop* keywords of the :doc:`run ` command. Thexe fixes are invoked during :doc:`energy minimization `. @@ -210,7 +218,8 @@ Restrictions """""""""""" These fixes are part of the QEQ package. They are only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package +` doc page for more info. Related commands """""""""""""""" From e1418a341a6cc0f196ae958807160e250229b5c9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 11 Apr 2021 06:05:41 -0400 Subject: [PATCH 0491/1217] ensure that only one of comb/comb3 is matched and called --- src/MANYBODY/fix_qeq_comb.cpp | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index 910db90822..7c23e6c218 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -17,21 +17,21 @@ #include "fix_qeq_comb.h" -#include -#include -#include "pair_comb.h" -#include "pair_comb3.h" -#include "neigh_list.h" #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "group.h" +#include "memory.h" +#include "neigh_list.h" #include "respa.h" #include "update.h" -#include "memory.h" -#include "error.h" +#include +#include +#include "pair_comb.h" +#include "pair_comb3.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -85,9 +85,6 @@ FixQEQComb::FixQEQComb(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) qf[i] = 0.0; - comb = nullptr; - comb3 = nullptr; - comm_forward = 1; } @@ -119,8 +116,9 @@ void FixQEQComb::init() if (!atom->q_flag) error->all(FLERR,"Fix qeq/comb requires atom attribute q"); - comb = (PairComb *) force->pair_match("^comb",0); comb3 = (PairComb3 *) force->pair_match("^comb3",0); + if (!comb3) comb = (PairComb *) force->pair_match("^comb",0); + if (comb == nullptr && comb3 == nullptr) error->all(FLERR,"Must use pair_style comb or comb3 with fix qeq/comb"); @@ -204,14 +202,17 @@ void FixQEQComb::post_force(int /*vflag*/) double *q = atom->q; int *mask = atom->mask; - if (comb) { + if (comb) { inum = comb->list->inum; ilist = comb->list->ilist; - } - if (comb3) { + } else if (comb3) { inum = comb3->list->inum; ilist = comb3->list->ilist; + } else { + inum = 0; + ilist = nullptr; } + for (ii = 0; ii < inum; ii++) { i = ilist[ii]; q1[i] = q2[i] = qf[i] = 0.0; @@ -227,8 +228,9 @@ void FixQEQComb::post_force(int /*vflag*/) } comm->forward_comm_fix(this); + enegtot = 0.0; if (comb) enegtot = comb->yasu_char(qf,igroup); - if (comb3) enegtot = comb3->combqeq(qf,igroup); + else if (comb3) enegtot = comb3->combqeq(qf,igroup); enegtot /= ngroup; enegchk = enegmax = 0.0; From bb0be962a91702abcd57b24651c898f60724555e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 11 Apr 2021 16:44:46 -0400 Subject: [PATCH 0492/1217] eliminate use of s(n)printf() in QEQ package --- src/QEQ/fix_qeq.cpp | 30 ++++++++++++--------------- src/QEQ/fix_qeq_dynamic.cpp | 27 ++++++++++--------------- src/QEQ/fix_qeq_fire.cpp | 39 ++++++++++++++---------------------- src/QEQ/fix_qeq_point.cpp | 28 ++++++++++++-------------- src/QEQ/fix_qeq_shielded.cpp | 32 ++++++++++++++--------------- src/QEQ/fix_qeq_slater.cpp | 30 ++++++++++++--------------- 6 files changed, 80 insertions(+), 106 deletions(-) diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index a63e008b36..e592ed2af4 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -18,16 +18,16 @@ #include "fix_qeq.h" -#include -#include #include "atom.h" #include "comm.h" -#include "neigh_list.h" -#include "update.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -386,13 +386,11 @@ int FixQEq::CG( double *b, double *x ) vector_sum( d, 1., p, beta, d, inum ); } - if (loop >= maxiter && comm->me == 0) { - char str[128]; - sprintf(str,"Fix qeq CG convergence failed (%g) after %d iterations " - "at " BIGINT_FORMAT " step",sqrt(sig_new)/b_norm,loop,update->ntimestep); - error->warning(FLERR,str); - } - + if ((comm->me == 0) && (loop >= maxiter)) + error->warning(FLERR,fmt::format("Fix qeq CG convergence failed ({}) " + "after {} iterations at step {}", + sqrt(sig_new)/b_norm,loop, + update->ntimestep)); return loop; } @@ -708,11 +706,9 @@ void FixQEq::read_file(char *file) FILE *fp; if (comm->me == 0) { fp = utils::open_potential(file,lmp,nullptr); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open fix qeq parameter file %s",file); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,fmt::format("Cannot open fix qeq parameter file {}: {}", + file,utils::getsyserror())); } // read each line out of file, skipping blank lines or leading '#' diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index b06bde223b..397393b786 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -17,20 +17,20 @@ #include "fix_qeq_dynamic.h" -#include - -#include #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" +#include "error.h" #include "force.h" #include "group.h" #include "kspace.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "respa.h" -#include "error.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; @@ -154,14 +154,9 @@ void FixQEqDynamic::pre_force(int /*vflag*/) } } - if (comm->me == 0) { - if (iloop == maxiter) { - char str[128]; - sprintf(str,"Charges did not converge at step " BIGINT_FORMAT - ": %lg",update->ntimestep,enegchk); - error->warning(FLERR,str); - } - } + if ((comm->me == 0) && (iloop >= maxiter)) + error->warning(FLERR,fmt::format("Charges did not converge at step " + "{}: {}",update->ntimestep,enegchk)); if (force->kspace) force->kspace->qsum_qsq(); } diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index b33a7745e0..0bdf65dc18 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -17,22 +17,22 @@ #include "fix_qeq_fire.h" -#include - -#include #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" +#include "error.h" #include "force.h" #include "group.h" +#include "kspace.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "pair_comb.h" #include "pair_comb3.h" -#include "kspace.h" #include "respa.h" -#include "error.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -47,7 +47,7 @@ using namespace FixConst; /* ---------------------------------------------------------------------- */ FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) : - FixQEq(lmp, narg, arg) + FixQEq(lmp, narg, arg), comb(nullptr), comb3(nullptr) { qdamp = 0.20; qstep = 0.20; @@ -65,9 +65,6 @@ FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) : iarg += 2; } else error->all(FLERR,"Illegal fix qeq/fire command"); } - - comb = nullptr; - comb3 = nullptr; } /* ---------------------------------------------------------------------- */ @@ -94,9 +91,8 @@ void FixQEqFire::init() if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; - comb = (PairComb *) force->pair_match("comb",1); - comb3 = (PairComb3 *) force->pair_match("comb3",1); - + comb3 = (PairComb3 *) force->pair_match("^comb3",0); + if (!comb3) comb = (PairComb *) force->pair_match("^comb",0); } /* ---------------------------------------------------------------------- */ @@ -218,14 +214,9 @@ void FixQEqFire::pre_force(int /*vflag*/) if (enegchk < tolerance) break; } - if (comm->me == 0) { - if (iloop == maxiter) { - char str[128]; - sprintf(str,"Charges did not converge at step " BIGINT_FORMAT - ": %lg",update->ntimestep,enegchk); - error->warning(FLERR,str); - } - } + if ((comm->me == 0) && (iloop >= maxiter)) + error->warning(FLERR,fmt::format("Charges did not converge at step " + "{}: {}",update->ntimestep,enegchk)); if (force->kspace) force->kspace->qsum_qsq(); } diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index 3d71135ae1..ac31f906e0 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -16,20 +16,22 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_point.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" +#include "error.h" #include "force.h" #include "group.h" #include "kspace.h" -#include "respa.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; @@ -158,13 +160,9 @@ void FixQEqPoint::compute_H() } } - if (m_fill >= H.m) { - char str[128]; - sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n", - m_fill, H.m ); - error->warning(FLERR,str); - error->all(FLERR,"Fix qeq/point has insufficient QEq matrix size"); - } + if (m_fill >= H.m) + error->all(FLERR,fmt::format("Fix qeq/point has insufficient H matrix " + "size: m_fill={} H.m={}\n",m_fill, H.m)); } /* ---------------------------------------------------------------------- */ diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index 356a747ed3..ad6202abd8 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -16,21 +16,23 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_shielded.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" +#include "error.h" #include "force.h" #include "group.h" -#include "pair.h" #include "kspace.h" -#include "respa.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; @@ -223,13 +225,9 @@ void FixQEqShielded::compute_H() } } - if (m_fill >= H.m) { - char str[128]; - sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n", - m_fill, H.m ); - error->warning(FLERR,str); - error->all(FLERR,"Fix qeq/shielded has insufficient QEq matrix size"); - } + if (m_fill >= H.m) + error->all(FLERR,fmt::format("Fix qeq/shielded has insufficient H matrix " + "size: m_fill={} H.m={}\n",m_fill,H.m)); } /* ---------------------------------------------------------------------- */ @@ -247,7 +245,7 @@ double FixQEqShielded::calculate_H( double r, double gamma ) Taper = Taper * r + Tap[0]; denom = r * r * r + gamma; - denom = pow(denom,0.3333333333333); + denom = pow(denom,1.0/3.0); return Taper * EV_TO_KCAL_PER_MOL / denom; } diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 9b90f78d7a..326d71c93b 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -16,22 +16,23 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_slater.h" -#include -#include #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" +#include "error.h" #include "force.h" #include "group.h" -#include "pair.h" #include "kspace.h" -#include "respa.h" #include "math_const.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -207,14 +208,9 @@ void FixQEqSlater::compute_H() chizj[i] = zjtmp; } - if (m_fill >= H.m) { - char str[128]; - sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n", - m_fill, H.m ); - error->warning(FLERR,str); - error->all(FLERR,"Fix qeq/slater has insufficient QEq matrix size"); - } - + if (m_fill >= H.m) + error->all(FLERR,fmt::format(FLERR,"Fix qeq/slater has insufficient H " + "matrix size:m_fill={} H.m={}\n",m_fill,H.m)); } /* ---------------------------------------------------------------------- */ From 38d5798223a6946e688749b2d3dabe13810f659b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 11 Apr 2021 21:36:18 -0400 Subject: [PATCH 0493/1217] must not look for package metadata when using python module from source tree --- python/lammps/__init__.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/python/lammps/__init__.py b/python/lammps/__init__.py index e6ffd779a9..93c46819c0 100644 --- a/python/lammps/__init__.py +++ b/python/lammps/__init__.py @@ -13,10 +13,16 @@ from .core import * from .data import * from .pylammps import * -# convert module string version to numeric version +# convert installed module string version to numeric version def get_version_number(): import time + from os.path import join from sys import version_info + + # must report 0 when inside LAMMPS source tree + if __file__.find(join('python', 'lammps', '__init__.py')) > 0: + return 0 + vstring = None if version_info.major == 3 and version_info.minor >= 8: from importlib.metadata import version From d81f03706cb8783020c990f6701933036c05e16f Mon Sep 17 00:00:00 2001 From: tc387 Date: Mon, 12 Apr 2021 01:30:36 -0500 Subject: [PATCH 0494/1217] Added an example using real units. --- .../charge_regulation/data.chreg-acid-real | 235 ++++++++++++++++++ .../misc/charge_regulation/in.chreg-acid-real | 44 ++++ .../log.11Apr21.chreg-acid-real.g++.1 | 145 +++++++++++ .../log.11Apr21.chreg-acid-real.g++.4 | 145 +++++++++++ 4 files changed, 569 insertions(+) create mode 100644 examples/USER/misc/charge_regulation/data.chreg-acid-real create mode 100644 examples/USER/misc/charge_regulation/in.chreg-acid-real create mode 100644 examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 create mode 100644 examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 diff --git a/examples/USER/misc/charge_regulation/data.chreg-acid-real b/examples/USER/misc/charge_regulation/data.chreg-acid-real new file mode 100644 index 0000000000..1f005a155b --- /dev/null +++ b/examples/USER/misc/charge_regulation/data.chreg-acid-real @@ -0,0 +1,235 @@ +LAMMPS data file generated by get_input.py + +219 atoms +3 atom types +-180 180 xlo xhi +-180 180 ylo yhi +-180 180 zlo zhi + +Masses + +1 20 +2 20 +3 20 + +Atoms + +1 1 0 18.70795854 -60.24998141 144.0092784 +2 1 -1 -130.9166548 -58.17450505 59.42690807 +3 1 -1 -125.5489258 58.46696329 77.38308245 +4 1 -1 46.8178314 -169.1807517 143.6272062 +5 1 -1 -162.2028908 -135.2407217 -129.3455357 +6 1 -1 -69.93717134 136.6009615 -140.3684699 +7 1 -1 -92.39022725 0.88313303 -156.091658 +8 1 -1 150.5452585 -15.59052452 3.326246397 +9 1 -1 171.8072626 172.9794849 75.84528386 +10 1 -1 -3.808294794 171.5056017 -19.13183671 +11 1 -1 68.90552852 86.21187482 24.628687 +12 1 -1 -73.4512319 54.41387468 86.90435812 +13 1 -1 35.26889793 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-29.14739431 94.50860741 -51.527097 +122 2 1 -145.9322739 154.5384232 112.3421798 +123 2 1 -32.24342538 -22.90490626 -133.4101075 +124 2 1 155.0953371 97.30799449 -13.02231424 +125 2 1 -109.6079033 -42.89844953 -51.80376701 +126 2 1 -150.2770445 -55.20818421 147.7312972 +127 2 1 -26.96028917 151.3053234 51.82429115 +128 2 1 -42.51040448 55.12547194 -10.01649745 +129 2 1 -154.7332138 -166.4922488 75.56066422 +130 2 1 179.3252381 50.98353603 -103.842222 +131 2 1 -87.64561442 -167.4026399 -37.04977996 +132 2 1 -141.7543098 32.23109989 44.99445113 +133 2 1 121.3596596 -6.092779973 129.6856923 +134 2 1 124.4836766 -86.35531223 85.50625099 +135 2 1 140.6305506 -165.9843021 -35.3966949 +136 2 1 -89.51258901 36.2123163 54.25434215 +137 2 1 107.5306105 58.22419926 141.7457531 +138 2 1 -51.03564423 -166.277591 119.3103596 +139 2 1 106.3738063 153.673561 100.7747233 +140 2 1 -105.1662471 -49.88388187 -163.5658795 +141 2 1 -123.4063552 104.6405545 -157.1806703 +142 2 1 30.68517662 111.7365757 -128.0988407 +143 2 1 -70.66650991 -36.87088431 101.1920697 +144 2 1 59.85584345 28.56015074 -148.8751279 +145 2 1 76.34296857 -18.88899045 11.99663247 +146 2 1 -127.898772 9.029786744 -155.2067979 +147 2 1 -61.47407783 106.6906337 -32.24644961 +148 2 1 -41.82882356 105.2048819 95.67134776 +149 2 1 64.70518204 -125.5606981 -130.2221179 +150 2 1 -95.86998176 64.01110464 -62.69889224 +151 2 1 -3.893149866 -170.4938796 -173.9425756 +152 2 1 -142.5571999 -115.9852755 -42.33527796 +153 2 1 -170.1094774 67.22933296 -69.41406448 +154 2 1 -135.7002446 -117.3853245 -77.66219554 +155 2 1 97.68794466 -176.3481416 64.0577303 +156 2 1 98.30084322 -179.1048324 157.6098802 +157 2 1 -61.74657154 71.45180441 36.21267022 +158 2 1 148.9924395 8.130617629 2.580809806 +159 2 1 -7.179797893 131.8852645 48.92705878 +160 2 1 166.7210737 111.3028256 122.5151765 +161 2 1 160.4061661 105.4292149 147.9164951 +162 2 1 70.35573238 -156.217711 -37.86968306 +163 2 1 37.82167168 128.9612675 113.5371453 +164 2 1 -149.4650805 40.2544478 -89.16446826 +165 2 1 23.15794976 -35.62998186 -128.5225995 +166 2 1 148.5909499 65.59167763 44.47571026 +167 2 1 38.20567747 91.06090259 167.2556933 +168 2 1 -173.8935359 124.3001041 -123.4154022 +169 2 1 -113.0780192 -112.7185827 -75.51909042 +170 2 1 -47.52814398 -162.0232543 -40.84518679 +171 2 1 164.6580923 96.26106544 -67.52475023 +172 2 1 -166.687599 -28.28821753 -80.04284273 +173 2 1 9.786487166 -133.5748603 -110.4924395 +174 2 1 73.69685916 -130.6229707 -12.1566579 +175 2 1 90.69039384 -12.53964183 -156.8650452 +176 2 1 -1.065055548 123.2458955 9.207883208 +177 2 1 175.3144942 -62.38332615 89.50309521 +178 2 1 -135.5554643 -135.3786299 -12.22599884 +179 2 1 -65.15130962 -12.87802388 -85.25728639 +180 2 1 -161.9760397 -159.2069523 72.10033228 +181 2 1 -116.5200037 9.430944126 5.8294178 +182 2 1 -28.85454266 -176.0245493 -141.7245957 +183 2 1 63.2968571 -114.4145268 -168.891953 +184 2 1 -61.61686575 -158.2947391 162.9099557 +185 2 1 51.43661765 119.3411567 4.253266919 +186 2 1 50.78017633 47.93871152 129.5527454 +187 2 1 151.0842128 -27.15258927 -161.0800505 +188 2 1 -63.76595621 -118.2333675 -55.31381078 +189 2 1 -103.5498203 -55.20725862 -73.28180307 +190 2 1 -165.1300235 72.52455317 27.04945294 +191 2 1 68.10471264 124.0704131 -0.252243467 +192 2 1 79.29794618 142.8637277 -42.01908928 +193 2 1 167.6806551 20.41616629 -147.6924841 +194 2 1 -135.8036012 64.48710622 102.1923975 +195 2 1 98.55703781 -115.0070794 78.85760695 +196 2 1 15.16187488 19.73322691 -170.7866955 +197 2 1 151.0729333 50.92372407 -173.3272023 +198 2 1 42.92899709 -139.8564977 161.7836767 +199 2 1 -123.3797296 144.2768906 93.18435951 +200 2 1 83.46684339 160.4439871 16.84583748 +201 2 1 -9.982765467 138.2373541 -55.3263136 +202 2 1 -161.6023131 -141.5797686 -64.66795638 +203 2 1 2.63144963 -54.92560391 117.5540027 +204 2 1 -70.31638318 175.5673808 -103.3383852 +205 2 1 -4.543770763 -40.50287551 98.39515078 +206 2 1 19.2926167 -2.671035153 112.1413205 +207 2 1 76.93260202 177.3949067 -126.2787212 +208 2 1 131.8183006 132.4167597 131.6586696 +209 2 1 -82.9844547 -85.47123292 92.81285561 +210 3 -1 115.4743016 -5.981969165 65.81311346 +211 3 -1 -86.91538943 171.1823129 -45.00079 +212 3 -1 174.0893311 141.4009485 159.8631805 +213 3 -1 164.8739505 64.21237704 -8.113691614 +214 3 -1 -75.49748308 40.97887837 158.0779944 +215 3 -1 45.16399203 72.25791157 159.9861897 +216 3 -1 105.7676225 -56.05853127 3.624467826 +217 3 -1 166.8523536 -151.4993186 -151.6124408 +218 3 -1 -43.30886503 46.05330597 155.3934201 +219 3 -1 -5.592027058 2.85325065 11.39381158 \ No newline at end of file diff --git a/examples/USER/misc/charge_regulation/in.chreg-acid-real b/examples/USER/misc/charge_regulation/in.chreg-acid-real new file mode 100644 index 0000000000..195b163d96 --- /dev/null +++ b/examples/USER/misc/charge_regulation/in.chreg-acid-real @@ -0,0 +1,44 @@ +# Charge regulation lammps for simple weak electrolyte + +units real +atom_style charge +neighbor 3.0 bin +read_data data.chreg-acid-real + +#real units +variable sigma equal 7.2 # particle diameter 0.72 nm +variable temperature equal 298 # temperature 298 K +variable kb index 0.0019872067 # kB in Kcal/mol/K +variable epsilon equal ${kb}*${temperature} +variable tunit equal 2000 # time unit is 2000 fs +variable timestep equal 0.005*${tunit} + +variable cut_long equal 12.5*${sigma} +variable nevery equal 100 +variable nmc equal 100 +variable pH equal 7.0 +variable pKa equal 6.0 +variable pIm equal 3.0 +variable pIp equal 3.0 + +variable cut_lj equal 2^(1.0/6.0)*${sigma} +velocity all create ${temperature} 8008 loop geom + +pair_style lj/cut/coul/long ${cut_lj} ${cut_long} +pair_coeff * * ${epsilon} ${sigma} +kspace_style pppm 1.0e-3 +dielectric 78 +pair_modify shift yes + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123 +fix_modify fT temp dtemp + +fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +thermo 100 +thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] +timestep ${timestep} +run 2000 diff --git a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 new file mode 100644 index 0000000000..3b766d662d --- /dev/null +++ b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 @@ -0,0 +1,145 @@ +LAMMPS (10 Feb 2021) +# Charge regulation lammps for simple weak electrolyte + +units real +atom_style charge +neighbor 3.0 bin +read_data data.chreg-acid-real +Reading data file ... + orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 219 atoms + read_data CPU = 0.002 seconds + +#real units +variable sigma equal 7.2 # particle diameter 0.72 nm +variable temperature equal 298 # temperature 298 K +variable kb index 0.0019872067 # kB in Kcal/mol/K +variable epsilon equal ${kb}*${temperature} +variable epsilon equal 0.0019872067*${temperature} +variable epsilon equal 0.0019872067*298 +variable tunit equal 2000 # time unit is 2000 fs +variable timestep equal 0.005*${tunit} +variable timestep equal 0.005*2000 + +variable cut_long equal 12.5*${sigma} +variable cut_long equal 12.5*7.2 +variable nevery equal 100 +variable nmc equal 100 +variable pH equal 7.0 +variable pKa equal 6.0 +variable pIm equal 3.0 +variable pIp equal 3.0 + +variable cut_lj equal 2^(1.0/6.0)*${sigma} +variable cut_lj equal 2^(1.0/6.0)*7.2 +velocity all create ${temperature} 8008 loop geom +velocity all create 298 8008 loop geom + +pair_style lj/cut/coul/long ${cut_lj} ${cut_long} +pair_style lj/cut/coul/long 8.08172674782749 ${cut_long} +pair_style lj/cut/coul/long 8.08172674782749 90 +pair_coeff * * ${epsilon} ${sigma} +pair_coeff * * 0.5921875966 ${sigma} +pair_coeff * * 0.5921875966 7.2 +kspace_style pppm 1.0e-3 +dielectric 78 +pair_modify shift yes + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123 +fix fT all langevin 298 $(v_temperature) $(v_tunit) 123 +fix fT all langevin 298 298 $(v_tunit) 123 +fix fT all langevin 298 298 2000 123 +fix_modify fT temp dtemp + +fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc 100 seed 2345 tempfixid fT +thermo 100 +thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] +timestep ${timestep} +timestep 10 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:339) + G vector (1/distance) = 0.019408615 + grid = 8 8 8 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00012527706 + estimated relative force accuracy = 3.7726815e-07 + using double precision KISS FFT + 3d grid and FFT values/proc = 2197 512 +0 atoms in group FixChargeRegulation:exclusion_group:chareg +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 93 + ghost atom cutoff = 93 + binsize = 46.5, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.707 | 3.707 | 3.707 Mbytes +Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] + 0 -6.4798431 298 0 0 1 99 0 0 109 10 + 100 -6.9219668 306.44177 100 77 15 85 0 0 94 9 + 200 -6.8175255 306.64254 200 164 23 77 0 0 87 10 + 300 -5.2482381 331.67831 300 248 21 79 0 0 85 6 + 400 -7.4531538 285.3495 400 326 17 83 0 0 89 6 + 500 -6.9662528 286.2123 500 408 14 86 0 0 95 9 + 600 -6.528214 291.41762 600 492 14 86 0 0 95 9 + 700 -6.290871 271.50948 700 567 14 86 0 0 96 10 + 800 -6.4944741 300.66261 800 650 23 77 0 0 83 6 + 900 -8.0414672 305.6179 900 731 25 75 0 0 84 9 + 1000 -8.5694583 297.69733 1000 810 25 75 0 0 83 8 + 1100 -8.9364878 292.52429 1100 891 22 78 0 0 88 10 + 1200 -8.733737 316.79814 1200 963 21 79 0 0 88 9 + 1300 -8.0946506 350.85016 1300 1043 21 79 0 0 88 9 + 1400 -7.1835794 283.90836 1400 1128 17 83 0 0 93 10 + 1500 -6.5673667 306.70066 1500 1208 23 77 0 0 87 10 + 1600 -7.0819412 272.07245 1600 1288 21 79 0 0 89 10 + 1700 -5.8907481 301.00694 1700 1365 28 72 0 0 84 12 + 1800 -4.9932405 282.95729 1800 1447 24 76 0 0 82 6 + 1900 -4.3273176 296.96436 1900 1527 22 78 0 0 86 8 + 2000 -4.4859306 299.76741 2000 1600 26 74 0 0 81 7 +Loop time of 1.15911 on 1 procs for 2000 steps with 188 atoms + +Performance: 1490.798 ns/day, 0.016 hours/ns, 1725.460 timesteps/s +99.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.036171 | 0.036171 | 0.036171 | 0.0 | 3.12 +Kspace | 0.37716 | 0.37716 | 0.37716 | 0.0 | 32.54 +Neigh | 0.022399 | 0.022399 | 0.022399 | 0.0 | 1.93 +Comm | 0.005311 | 0.005311 | 0.005311 | 0.0 | 0.46 +Output | 0.000745 | 0.000745 | 0.000745 | 0.0 | 0.06 +Modify | 0.71566 | 0.71566 | 0.71566 | 0.0 | 61.74 +Other | | 0.001663 | | | 0.14 + +Nlocal: 188.000 ave 188 max 188 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 411.000 ave 411 max 411 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1268.00 ave 1268 max 1268 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1268 +Ave neighs/atom = 6.7446809 +Neighbor list builds = 2195 +Dangerous builds = 15 +Total wall time: 0:00:01 diff --git a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 new file mode 100644 index 0000000000..7ab22c1f36 --- /dev/null +++ b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 @@ -0,0 +1,145 @@ +LAMMPS (10 Feb 2021) +# Charge regulation lammps for simple weak electrolyte + +units real +atom_style charge +neighbor 3.0 bin +read_data data.chreg-acid-real +Reading data file ... + orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 219 atoms + read_data CPU = 0.002 seconds + +#real units +variable sigma equal 7.2 # particle diameter 0.72 nm +variable temperature equal 298 # temperature 298 K +variable kb index 0.0019872067 # kB in Kcal/mol/K +variable epsilon equal ${kb}*${temperature} +variable epsilon equal 0.0019872067*${temperature} +variable epsilon equal 0.0019872067*298 +variable tunit equal 2000 # time unit is 2000 fs +variable timestep equal 0.005*${tunit} +variable timestep equal 0.005*2000 + +variable cut_long equal 12.5*${sigma} +variable cut_long equal 12.5*7.2 +variable nevery equal 100 +variable nmc equal 100 +variable pH equal 7.0 +variable pKa equal 6.0 +variable pIm equal 3.0 +variable pIp equal 3.0 + +variable cut_lj equal 2^(1.0/6.0)*${sigma} +variable cut_lj equal 2^(1.0/6.0)*7.2 +velocity all create ${temperature} 8008 loop geom +velocity all create 298 8008 loop geom + +pair_style lj/cut/coul/long ${cut_lj} ${cut_long} +pair_style lj/cut/coul/long 8.08172674782749 ${cut_long} +pair_style lj/cut/coul/long 8.08172674782749 90 +pair_coeff * * ${epsilon} ${sigma} +pair_coeff * * 0.5921875966 ${sigma} +pair_coeff * * 0.5921875966 7.2 +kspace_style pppm 1.0e-3 +dielectric 78 +pair_modify shift yes + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123 +fix fT all langevin 298 $(v_temperature) $(v_tunit) 123 +fix fT all langevin 298 298 $(v_tunit) 123 +fix fT all langevin 298 298 2000 123 +fix_modify fT temp dtemp + +fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc 100 seed 2345 tempfixid fT +thermo 100 +thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] +timestep ${timestep} +timestep 10 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:339) + G vector (1/distance) = 0.019408615 + grid = 8 8 8 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00012527706 + estimated relative force accuracy = 3.7726815e-07 + using double precision KISS FFT + 3d grid and FFT values/proc = 1053 128 +0 atoms in group FixChargeRegulation:exclusion_group:chareg +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 93 + ghost atom cutoff = 93 + binsize = 46.5, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.624 | 3.624 | 3.624 Mbytes +Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] + 0 -6.4798431 298 0 0 1 99 0 0 109 10 + 100 -7.9144028 317.49717 100 73 15 85 0 0 94 9 + 200 -5.9183735 315.31348 200 157 24 76 0 0 86 10 + 300 -6.7851544 295.82718 300 243 21 79 0 0 86 7 + 400 -6.3777493 297.53619 400 316 16 84 0 0 91 7 + 500 -6.0281518 287.62012 500 398 15 85 0 0 93 8 + 600 -8.4403907 301.30302 600 483 14 86 0 0 94 8 + 700 -9.6450828 305.33793 700 563 15 85 0 0 96 11 + 800 -6.1034312 307.18396 800 646 20 80 0 0 85 5 + 900 -7.3098915 295.21039 900 729 24 76 0 0 86 10 + 1000 -6.721795 316.34459 1000 803 25 75 0 0 84 9 + 1100 -7.389073 326.53025 1100 882 23 77 0 0 87 10 + 1200 -9.6721231 327.15878 1200 958 20 80 0 0 89 9 + 1300 -7.4738885 295.09338 1300 1045 20 80 0 0 88 8 + 1400 -7.8136191 297.62074 1400 1127 18 82 0 0 92 10 + 1500 -7.6522652 284.20977 1500 1204 24 76 0 0 85 9 + 1600 -8.473883 293.37704 1600 1283 22 78 0 0 92 14 + 1700 -5.7030629 327.53233 1700 1366 26 74 0 0 83 9 + 1800 -6.1817998 278.22073 1800 1447 21 79 0 0 84 5 + 1900 -5.3113964 293.69193 1900 1526 24 76 0 0 85 9 + 2000 -5.5827334 307.91424 2000 1599 26 74 0 0 80 6 +Loop time of 0.547632 on 4 procs for 2000 steps with 186 atoms + +Performance: 3155.407 ns/day, 0.008 hours/ns, 3652.091 timesteps/s +99.5% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.008417 | 0.01004 | 0.010817 | 1.0 | 1.83 +Kspace | 0.17103 | 0.17157 | 0.17208 | 0.1 | 31.33 +Neigh | 0.004536 | 0.0052815 | 0.005857 | 0.7 | 0.96 +Comm | 0.023141 | 0.02398 | 0.02617 | 0.8 | 4.38 +Output | 0.000556 | 0.00063325 | 0.000864 | 0.0 | 0.12 +Modify | 0.33403 | 0.33441 | 0.33471 | 0.1 | 61.07 +Other | | 0.001711 | | | 0.31 + +Nlocal: 46.5000 ave 48 max 44 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 241.500 ave 244 max 238 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Neighs: 303.750 ave 333 max 286 min +Histogram: 2 0 0 0 1 0 0 0 0 1 + +Total # of neighbors = 1215 +Ave neighs/atom = 6.5322581 +Neighbor list builds = 2196 +Dangerous builds = 12 +Total wall time: 0:00:00 From 7d95943b7e2ddb500addba2f69e78d7821eed3b5 Mon Sep 17 00:00:00 2001 From: tc387 Date: Mon, 12 Apr 2021 01:46:39 -0500 Subject: [PATCH 0495/1217] increased bin size in example input file to avoid dangerous builds --- .../misc/charge_regulation/in.chreg-acid-real | 2 +- .../log.11Apr21.chreg-acid-real.g++.1 | 66 +++++++------- .../log.11Apr21.chreg-acid-real.g++.4 | 88 +++++++++---------- 3 files changed, 78 insertions(+), 78 deletions(-) diff --git a/examples/USER/misc/charge_regulation/in.chreg-acid-real b/examples/USER/misc/charge_regulation/in.chreg-acid-real index 195b163d96..d7225f33ea 100644 --- a/examples/USER/misc/charge_regulation/in.chreg-acid-real +++ b/examples/USER/misc/charge_regulation/in.chreg-acid-real @@ -2,7 +2,7 @@ units real atom_style charge -neighbor 3.0 bin +neighbor 10.0 bin read_data data.chreg-acid-real #real units diff --git a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 index 3b766d662d..6e50ea5ef3 100644 --- a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 +++ b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 @@ -3,7 +3,7 @@ LAMMPS (10 Feb 2021) units real atom_style charge -neighbor 3.0 bin +neighbor 10.0 bin read_data data.chreg-acid-real Reading data file ... orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000) @@ -83,16 +83,16 @@ WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulo Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 93 - ghost atom cutoff = 93 - binsize = 46.5, bins = 8 8 8 + master list distance cutoff = 100 + ghost atom cutoff = 100 + binsize = 50, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.707 | 3.707 | 3.707 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.708 | 3.708 | 3.708 Mbytes Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] 0 -6.4798431 298 0 0 1 99 0 0 109 10 100 -6.9219668 306.44177 100 77 15 85 0 0 94 9 @@ -104,42 +104,42 @@ Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] 700 -6.290871 271.50948 700 567 14 86 0 0 96 10 800 -6.4944741 300.66261 800 650 23 77 0 0 83 6 900 -8.0414672 305.6179 900 731 25 75 0 0 84 9 - 1000 -8.5694583 297.69733 1000 810 25 75 0 0 83 8 - 1100 -8.9364878 292.52429 1100 891 22 78 0 0 88 10 - 1200 -8.733737 316.79814 1200 963 21 79 0 0 88 9 - 1300 -8.0946506 350.85016 1300 1043 21 79 0 0 88 9 - 1400 -7.1835794 283.90836 1400 1128 17 83 0 0 93 10 - 1500 -6.5673667 306.70066 1500 1208 23 77 0 0 87 10 - 1600 -7.0819412 272.07245 1600 1288 21 79 0 0 89 10 - 1700 -5.8907481 301.00694 1700 1365 28 72 0 0 84 12 - 1800 -4.9932405 282.95729 1800 1447 24 76 0 0 82 6 - 1900 -4.3273176 296.96436 1900 1527 22 78 0 0 86 8 - 2000 -4.4859306 299.76741 2000 1600 26 74 0 0 81 7 -Loop time of 1.15911 on 1 procs for 2000 steps with 188 atoms + 1000 -8.5694583 298.73349 1000 810 25 75 0 0 83 8 + 1100 -8.6677368 269.67435 1100 894 22 78 0 0 87 9 + 1200 -8.2246183 284.14886 1200 969 22 78 0 0 88 10 + 1300 -7.7674621 320.04838 1300 1040 23 77 0 0 85 8 + 1400 -9.5186335 303.48091 1400 1124 18 82 0 0 93 11 + 1500 -5.8437493 271.40712 1500 1204 25 75 0 0 83 8 + 1600 -5.9149181 268.24708 1600 1285 23 77 0 0 90 13 + 1700 -6.5047738 303.79732 1700 1369 27 73 0 0 84 11 + 1800 -7.3010139 308.98213 1800 1450 22 78 0 0 83 5 + 1900 -6.3505397 306.94357 1900 1527 22 78 0 0 86 8 + 2000 -5.7144173 287.06184 2000 1605 27 73 0 0 80 7 +Loop time of 1.17189 on 1 procs for 2000 steps with 187 atoms -Performance: 1490.798 ns/day, 0.016 hours/ns, 1725.460 timesteps/s -99.5% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1474.535 ns/day, 0.016 hours/ns, 1706.638 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.036171 | 0.036171 | 0.036171 | 0.0 | 3.12 -Kspace | 0.37716 | 0.37716 | 0.37716 | 0.0 | 32.54 -Neigh | 0.022399 | 0.022399 | 0.022399 | 0.0 | 1.93 -Comm | 0.005311 | 0.005311 | 0.005311 | 0.0 | 0.46 -Output | 0.000745 | 0.000745 | 0.000745 | 0.0 | 0.06 -Modify | 0.71566 | 0.71566 | 0.71566 | 0.0 | 61.74 -Other | | 0.001663 | | | 0.14 +Pair | 0.035807 | 0.035807 | 0.035807 | 0.0 | 3.06 +Kspace | 0.37689 | 0.37689 | 0.37689 | 0.0 | 32.16 +Neigh | 0.008694 | 0.008694 | 0.008694 | 0.0 | 0.74 +Comm | 0.004793 | 0.004793 | 0.004793 | 0.0 | 0.41 +Output | 0.000746 | 0.000746 | 0.000746 | 0.0 | 0.06 +Modify | 0.74292 | 0.74292 | 0.74292 | 0.0 | 63.39 +Other | | 0.00205 | | | 0.17 -Nlocal: 188.000 ave 188 max 188 min +Nlocal: 187.000 ave 187 max 187 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 411.000 ave 411 max 411 min +Nghost: 437.000 ave 437 max 437 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1268.00 ave 1268 max 1268 min +Neighs: 1500.00 ave 1500 max 1500 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 1268 -Ave neighs/atom = 6.7446809 -Neighbor list builds = 2195 -Dangerous builds = 15 +Total # of neighbors = 1500 +Ave neighs/atom = 8.0213904 +Neighbor list builds = 2080 +Dangerous builds = 0 Total wall time: 0:00:01 diff --git a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 index 7ab22c1f36..927e29c1f3 100644 --- a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 +++ b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 @@ -3,7 +3,7 @@ LAMMPS (10 Feb 2021) units real atom_style charge -neighbor 3.0 bin +neighbor 10.0 bin read_data data.chreg-acid-real Reading data file ... orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000) @@ -83,9 +83,9 @@ WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulo Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 93 - ghost atom cutoff = 93 - binsize = 46.5, bins = 8 8 8 + master list distance cutoff = 100 + ghost atom cutoff = 100 + binsize = 50, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long, perpetual attributes: half, newton on @@ -95,51 +95,51 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.624 | 3.624 | 3.624 Mbytes Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] 0 -6.4798431 298 0 0 1 99 0 0 109 10 - 100 -7.9144028 317.49717 100 73 15 85 0 0 94 9 - 200 -5.9183735 315.31348 200 157 24 76 0 0 86 10 - 300 -6.7851544 295.82718 300 243 21 79 0 0 86 7 - 400 -6.3777493 297.53619 400 316 16 84 0 0 91 7 - 500 -6.0281518 287.62012 500 398 15 85 0 0 93 8 - 600 -8.4403907 301.30302 600 483 14 86 0 0 94 8 - 700 -9.6450828 305.33793 700 563 15 85 0 0 96 11 - 800 -6.1034312 307.18396 800 646 20 80 0 0 85 5 - 900 -7.3098915 295.21039 900 729 24 76 0 0 86 10 - 1000 -6.721795 316.34459 1000 803 25 75 0 0 84 9 - 1100 -7.389073 326.53025 1100 882 23 77 0 0 87 10 - 1200 -9.6721231 327.15878 1200 958 20 80 0 0 89 9 - 1300 -7.4738885 295.09338 1300 1045 20 80 0 0 88 8 - 1400 -7.8136191 297.62074 1400 1127 18 82 0 0 92 10 - 1500 -7.6522652 284.20977 1500 1204 24 76 0 0 85 9 - 1600 -8.473883 293.37704 1600 1283 22 78 0 0 92 14 - 1700 -5.7030629 327.53233 1700 1366 26 74 0 0 83 9 - 1800 -6.1817998 278.22073 1800 1447 21 79 0 0 84 5 - 1900 -5.3113964 293.69193 1900 1526 24 76 0 0 85 9 - 2000 -5.5827334 307.91424 2000 1599 26 74 0 0 80 6 -Loop time of 0.547632 on 4 procs for 2000 steps with 186 atoms + 100 -7.6327126 304.68909 100 73 15 85 0 0 94 9 + 200 -6.1699041 272.19597 200 156 24 76 0 0 87 11 + 300 -7.7876571 288.90801 300 240 20 80 0 0 87 7 + 400 -6.3239918 274.65708 400 315 16 84 0 0 90 6 + 500 -5.3978659 257.49208 500 398 15 85 0 0 93 8 + 600 -5.6433949 322.52048 600 477 18 82 0 0 90 8 + 700 -6.5351367 269.20244 700 558 18 82 0 0 91 9 + 800 -6.2093085 315.21326 800 638 24 76 0 0 83 7 + 900 -7.0795998 311.93228 900 719 28 72 0 0 82 10 + 1000 -6.4668438 281.72674 1000 796 27 73 0 0 81 8 + 1100 -6.2377994 318.48594 1100 875 25 75 0 0 84 9 + 1200 -6.6305072 304.9091 1200 950 23 77 0 0 87 10 + 1300 -5.9624552 286.05027 1300 1029 22 78 0 0 86 8 + 1400 -4.4695814 261.81053 1400 1111 20 80 0 0 90 10 + 1500 -5.6928652 293.72403 1500 1191 24 76 0 0 86 10 + 1600 -6.8715413 290.47065 1600 1275 22 78 0 0 90 12 + 1700 -6.5067505 292.74735 1700 1356 25 75 0 0 85 10 + 1800 -5.3902702 307.79012 1800 1434 22 78 0 0 83 5 + 1900 -5.1407153 318.48918 1900 1510 21 79 0 0 87 8 + 2000 -4.9514719 281.87771 2000 1589 25 75 0 0 82 7 +Loop time of 0.562889 on 4 procs for 2000 steps with 189 atoms -Performance: 3155.407 ns/day, 0.008 hours/ns, 3652.091 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3069.876 ns/day, 0.008 hours/ns, 3553.097 timesteps/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.008417 | 0.01004 | 0.010817 | 1.0 | 1.83 -Kspace | 0.17103 | 0.17157 | 0.17208 | 0.1 | 31.33 -Neigh | 0.004536 | 0.0052815 | 0.005857 | 0.7 | 0.96 -Comm | 0.023141 | 0.02398 | 0.02617 | 0.8 | 4.38 -Output | 0.000556 | 0.00063325 | 0.000864 | 0.0 | 0.12 -Modify | 0.33403 | 0.33441 | 0.33471 | 0.1 | 61.07 -Other | | 0.001711 | | | 0.31 +Pair | 0.008399 | 0.010383 | 0.011765 | 1.2 | 1.84 +Kspace | 0.17501 | 0.17543 | 0.1757 | 0.1 | 31.17 +Neigh | 0.001833 | 0.0021325 | 0.002293 | 0.4 | 0.38 +Comm | 0.023099 | 0.024255 | 0.026645 | 0.9 | 4.31 +Output | 0.000465 | 0.000546 | 0.000783 | 0.0 | 0.10 +Modify | 0.3464 | 0.34669 | 0.34698 | 0.0 | 61.59 +Other | | 0.003452 | | | 0.61 -Nlocal: 46.5000 ave 48 max 44 min -Histogram: 1 0 0 0 0 1 0 0 0 2 -Nghost: 241.500 ave 244 max 238 min -Histogram: 1 0 0 0 0 1 0 0 1 1 -Neighs: 303.750 ave 333 max 286 min -Histogram: 2 0 0 0 1 0 0 0 0 1 +Nlocal: 47.2500 ave 57 max 41 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 285.750 ave 303 max 263 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Neighs: 403.500 ave 548 max 324 min +Histogram: 2 0 0 1 0 0 0 0 0 1 -Total # of neighbors = 1215 -Ave neighs/atom = 6.5322581 -Neighbor list builds = 2196 -Dangerous builds = 12 +Total # of neighbors = 1614 +Ave neighs/atom = 8.5396825 +Neighbor list builds = 2081 +Dangerous builds = 0 Total wall time: 0:00:00 From bc25fa82688cb7506143454774115f0471dada1f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 09:59:02 -0400 Subject: [PATCH 0496/1217] full integration into documentation build system --- doc/src/Commands_fix.rst | 1 + doc/src/fix.rst | 1 + doc/src/fix_charge_regulation.rst | 14 ++++++++++---- 3 files changed, 12 insertions(+), 4 deletions(-) diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index 4793568288..671716e89d 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -46,6 +46,7 @@ OPT. * :doc:`bond/react ` * :doc:`bond/swap ` * :doc:`box/relax ` + * :doc:`charge/regulation ` * :doc:`client/md ` * :doc:`cmap ` * :doc:`colvars ` diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 2e516faa4e..109bfb00be 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -189,6 +189,7 @@ accelerated styles exist. * :doc:`bond/react ` - apply topology changes to model reactions * :doc:`bond/swap ` - Monte Carlo bond swapping * :doc:`box/relax ` - relax box size during energy minimization +* :doc:`charge/regulation ` - Monte Carlo sampling of charge regulation * :doc:`client/md ` - MD client for client/server simulations * :doc:`cmap ` - enables CMAP cross-terms of the CHARMM force field * :doc:`colvars ` - interface to the collective variables "Colvars" library diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index fb63c8d7a5..ef91db1e59 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/doc/src/fix_charge_regulation.rst @@ -225,7 +225,7 @@ quantities: Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if LAMMPS +This fix is part of the MC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -243,7 +243,9 @@ the LJ potential must be shifted so that it vanishes at the cutoff. This can be easily achieved using the :doc:`pair_modify ` command, i.e., by using: *pair_modify shift yes*. -Note: Region restrictions are not yet implemented. +.. note:: + + Region restrictions are not yet implemented. Related commands """""""""""""""" @@ -253,7 +255,11 @@ Related commands Default """"""" -pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0; acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery = 100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves = [1/3, 1/3, 1/3], group-ID = all + +pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0; +acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery = +100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves = +[1/3, 1/3, 1/3], group-ID = all ---------- @@ -267,4 +273,4 @@ pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0; acid_type .. _Landsgesell: -**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, "Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning", Macromolecules 53, 3007–3020 (2020). +**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, "Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning", Macromolecules 53, 3007-3020 (2020). From 0c2fc07cc5462e28cd228028aea4be3070c981d0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 10:00:52 -0400 Subject: [PATCH 0497/1217] add USER-OMP version of pair style coul/cut/global --- src/USER-OMP/pair_coul_cut_global_omp.cpp | 44 ++++++++++++++++++ src/USER-OMP/pair_coul_cut_global_omp.h | 55 +++++++++++++++++++++++ 2 files changed, 99 insertions(+) create mode 100644 src/USER-OMP/pair_coul_cut_global_omp.cpp create mode 100644 src/USER-OMP/pair_coul_cut_global_omp.h diff --git a/src/USER-OMP/pair_coul_cut_global_omp.cpp b/src/USER-OMP/pair_coul_cut_global_omp.cpp new file mode 100644 index 0000000000..36fee39fc8 --- /dev/null +++ b/src/USER-OMP/pair_coul_cut_global_omp.cpp @@ -0,0 +1,44 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "pair_coul_cut_global_omp.h" + +#include "error.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairCoulCutGlobalOMP::coeff(int narg, char **arg) +{ + if (narg != 2) + error->all(FLERR,"Incorrect args for pair coefficients"); + + PairCoulCut::coeff(narg,arg); +} + + +/* ---------------------------------------------------------------------- */ + +void *PairCoulCutGlobalOMP::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_global; + dim = 2; + if (strcmp(str,"scale") == 0) return (void *) scale; + return nullptr; +} diff --git a/src/USER-OMP/pair_coul_cut_global_omp.h b/src/USER-OMP/pair_coul_cut_global_omp.h new file mode 100644 index 0000000000..a2cb4a1dbe --- /dev/null +++ b/src/USER-OMP/pair_coul_cut_global_omp.h @@ -0,0 +1,55 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(coul/cut/global/omp,PairCoulCutGlobalOMP) + +#else + +#ifndef LMP_PAIR_COUL_CUT_GLOBAL_OMP_H +#define LMP_PAIR_COUL_CUT_GLOBAL_OMP_H + +#include "pair_coul_cut_omp.h" + +namespace LAMMPS_NS { + +class PairCoulCutGlobalOMP : public PairCoulCutOMP { + public: + PairCoulCutGlobalOMP(class LAMMPS *lmp) : PairCoulCutOMP(lmp) {} + void coeff(int, char **); + void *extract(const char *, int &); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair style coul/cut requires atom attribute q + +The atom style defined does not have these attributes. + +*/ From 9658b8e645f1fb611e52e1771e3a4b4cd6be7224 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 10:05:52 -0400 Subject: [PATCH 0498/1217] move fix charge/regulation to MC package (examples stay in place for now) --- doc/src/Packages_details.rst | 6 +++++- src/{USER-MISC => MC}/fix_charge_regulation.cpp | 0 src/{USER-MISC => MC}/fix_charge_regulation.h | 0 src/USER-MISC/README | 1 - 4 files changed, 5 insertions(+), 2 deletions(-) rename src/{USER-MISC => MC}/fix_charge_regulation.cpp (100%) rename src/{USER-MISC => MC}/fix_charge_regulation.h (100%) diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index b662ae73c7..d5c011012d 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -585,7 +585,7 @@ MC package Several fixes and a pair style that have Monte Carlo (MC) or MC-like attributes. These include fixes for creating, breaking, and swapping bonds, for performing atomic swaps, and performing grand-canonical MC -(GCMC) in conjunction with dynamics. +(GCMC) or similar processes in conjunction with dynamics. **Supporting info:** @@ -593,8 +593,12 @@ bonds, for performing atomic swaps, and performing grand-canonical MC * :doc:`fix atom/swap ` * :doc:`fix bond/break ` * :doc:`fix bond/create ` +* :doc:`fix bond/create/angle ` * :doc:`fix bond/swap ` +* :doc:`fix charge/regulation ` * :doc:`fix gcmc ` +* :doc:`fix tfmc ` +* :doc:`fix widom ` * :doc:`pair_style dsmc ` * https://lammps.sandia.gov/movies.html#gcmc diff --git a/src/USER-MISC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp similarity index 100% rename from src/USER-MISC/fix_charge_regulation.cpp rename to src/MC/fix_charge_regulation.cpp diff --git a/src/USER-MISC/fix_charge_regulation.h b/src/MC/fix_charge_regulation.h similarity index 100% rename from src/USER-MISC/fix_charge_regulation.h rename to src/MC/fix_charge_regulation.h diff --git a/src/USER-MISC/README b/src/USER-MISC/README index ef25a0c116..314fe6146e 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -53,7 +53,6 @@ dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18 fix accelerate/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 -fix charge_regulation, Tine Curk and Jiaxing Yuan, tcurk5@gmail.com, 02 Feb 2021 fix electron/stopping/fit, James Stewart (SNL), jstewa .at. sandia.gov, 23 Sep 2020 fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019 fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018 From 0c79673d931091f8628c2f705c5133c39a471fed Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 10:14:31 -0400 Subject: [PATCH 0499/1217] make fix charge/regulation compatible with USER-INTEL package --- src/MC/fix_charge_regulation.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 5479082158..0aa3def153 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -45,7 +45,6 @@ #include #include - using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; @@ -1082,6 +1081,7 @@ double FixChargeRegulation::energy_full() { if (force->kspace) force->kspace->compute(eflag, vflag); + if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag); if (modify->n_post_force) modify->post_force(vflag); if (modify->n_end_of_step) modify->end_of_step(); update->eflag_global = update->ntimestep; From a572142e6f4088eddf0f48e8a5d76232a0ee23ec Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 10:25:10 -0400 Subject: [PATCH 0500/1217] fix inconsistent new/delete --- src/MC/fix_charge_regulation.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 0aa3def153..797d7fb5b0 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -130,7 +130,7 @@ FixChargeRegulation::~FixChargeRegulation() { delete random_equal; delete random_unequal; - delete idftemp; + delete[] idftemp; if (group) { int igroupall = group->find("all"); From 65ba022c2a0ce3ab6e4822bfdc279679e511822c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 10:25:24 -0400 Subject: [PATCH 0501/1217] simplify --- src/MC/fix_charge_regulation.cpp | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 797d7fb5b0..47adad3f6d 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -1295,10 +1295,7 @@ void FixChargeRegulation::options(int narg, char **arg) { } else if (strcmp(arg[iarg], "tempfixid") == 0) { if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge/regulation command"); - int n = strlen(arg[iarg + 1]) + 1; - delete[] idftemp; - idftemp = new char[n]; - strcpy(idftemp, arg[iarg + 1]); + idftemp = utils::strdup(arg[iarg+1]); setThermoTemperaturePointer(); iarg += 2; } else if (strcmp(arg[iarg], "rxd") == 0) { @@ -1371,9 +1368,7 @@ void FixChargeRegulation::options(int narg, char **arg) { ngroupsmax * sizeof(char *), "fix_charge_regulation:groupstrings"); } - int n = strlen(arg[iarg + 1]) + 1; - groupstrings[ngroups] = new char[n]; - strcpy(groupstrings[ngroups], arg[iarg + 1]); + groupstrings[ngroups] = utils::strdup(arg[iarg+1]); ngroups++; iarg += 2; } else error->all(FLERR, "Illegal fix charge/regulation command"); From 82e1c4fb121c7e5c33f40406b0ed0c6f1b831121 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 10:25:39 -0400 Subject: [PATCH 0502/1217] silence compiler warnings --- src/MC/fix_charge_regulation.cpp | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 47adad3f6d..34391b86fb 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -14,6 +14,7 @@ /* ---------------------------------------------------------------------- Contributing author: Tine Curk (tcurk5@gmail.com) and Jiaxing Yuan (yuanjiaxing123@hotmail.com) ------------------------------------------------------------------------- */ + #include "fix_charge_regulation.h" #include "angle.h" @@ -652,7 +653,7 @@ void FixChargeRegulation::backward_ions() { double energy_before = energy_stored; double factor; - int mask1_tmp, mask2_tmp; + int mask1_tmp = 0, mask2_tmp = 0; double *dummyp = nullptr; int m1 = -1, m2 = -1; @@ -724,12 +725,6 @@ void FixChargeRegulation::backward_ions() { atom->mask[m2] = mask2_tmp; } } - } else { - // reassign original charge and mask - if (m1 >= 0) { - atom->q[m1] = 1; - atom->mask[m1] = mask1_tmp; - } } } } @@ -738,7 +733,7 @@ void FixChargeRegulation::forward_ions_multival() { double energy_before = energy_stored; double factor = 1; - double *dummyp; + double *dummyp = nullptr; int mm[salt_charge_ratio + 1];// particle ID array for all ions to be inserted if (salt_charge[0] <= -salt_charge[1]) { @@ -792,7 +787,7 @@ void FixChargeRegulation::backward_ions_multival() { double energy_before = energy_stored; double factor = 1; - double *dummyp; // dummy pointer + double *dummyp = nullptr; // dummy pointer int mm[salt_charge_ratio + 1]; // particle ID array for all deleted ions double qq[salt_charge_ratio + 1]; // charge array for all deleted ions int mask_tmp[salt_charge_ratio + 1]; // temporary mask array From c324d754a0644f2a50c5b376ca3318b8fc1a3396 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 10:51:44 -0400 Subject: [PATCH 0503/1217] when installing the LAMMPS python package create a valid version id --- python/install.py | 8 +++++--- python/lammps/__init__.py | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/python/install.py b/python/install.py index 6e4c509f07..fbff02a1b5 100644 --- a/python/install.py +++ b/python/install.py @@ -10,7 +10,7 @@ build target in the conventional and CMake based build systems # copy LAMMPS shared library and lammps package to system dirs from __future__ import print_function -import sys,os,shutil +import sys,os,shutil,time from argparse import ArgumentParser parser = ArgumentParser(prog='install.py', @@ -80,13 +80,15 @@ if args.dir: sys.exit() -# extract version string from header +# extract LAMMPS version string from header +# and convert to python packaging compatible version def get_lammps_version(header): with open(header, 'r') as f: line = f.readline() start_pos = line.find('"')+1 end_pos = line.find('"', start_pos) - return "".join(line[start_pos:end_pos].split()) + t = time.strptime("".join(line[start_pos:end_pos].split()), "%d%b%Y") + return "{}.{}.{}".format(t.tm_year,t.tm_mon,t.tm_mday) verstr = get_lammps_version(args.version) diff --git a/python/lammps/__init__.py b/python/lammps/__init__.py index 93c46819c0..2c0e7a6fe3 100644 --- a/python/lammps/__init__.py +++ b/python/lammps/__init__.py @@ -38,7 +38,7 @@ def get_version_number(): if not vstring: return 0 - t = time.strptime(vstring, "%d%b%Y") + t = time.strptime(vstring, "%Y.%m.%d") return t.tm_year*10000 + t.tm_mon*100 + t.tm_mday __version__ = get_version_number() From 5605a237cf74184581cb1cffca17cba9b6b617c8 Mon Sep 17 00:00:00 2001 From: julient31 Date: Mon, 12 Apr 2021 10:27:20 -0600 Subject: [PATCH 0504/1217] working on the typedef correction --- src/KOKKOS/atom_kokkos.h | 9 ++- src/KOKKOS/atom_vec_spin_kokkos.cpp | 27 +++++-- src/KOKKOS/kokkos_type.h | 108 ++++++++++++++++++---------- 3 files changed, 95 insertions(+), 49 deletions(-) diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index 908958ab14..f5649f927e 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -56,9 +56,12 @@ class AtomKokkos : public Atom { // SPIN package - DAT::tdual_sp_array k_sp; - DAT::tdual_fm_array k_fm; - DAT::tdual_fm_long_array k_fm_long; + // DAT::tdual_sp_array k_sp; + // DAT::tdual_fm_array k_fm; + // DAT::tdual_fm_long_array k_fm_long; + DAT::tdual_float_1d_4 k_sp; + DAT::tdual_f_array k_fm; + DAT::tdual_f_array k_fm_long; // USER-DPD package DAT::tdual_efloat_1d k_uCond, k_uMech, k_uChem, k_uCG, k_uCGnew, diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp index e513ff2ffa..5e3ff19831 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.cpp +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -189,7 +189,8 @@ struct AtomVecSpinKokkos_PackComm { AtomVecSpinKokkos_PackComm( const typename DAT::tdual_x_array &x, - const typename DAT::tdual_sp_array &sp, + // const typename DAT::tdual_sp_array &sp, + const typename DAT::tdual_float_1d_4 &sp, const typename DAT::tdual_xfloat_2d &buf, const typename DAT::tdual_int_2d &list, const int & iswap, @@ -1269,12 +1270,18 @@ void AtomVecSpinKokkos::sync_overlapping_device(ExecutionSpace space, unsigned i perform_async_copy(atomKK->k_mask,space); if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync()) perform_async_copy(atomKK->k_image,space); + // if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) + // perform_async_copy(atomKK->k_sp,space); if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) - perform_async_copy(atomKK->k_sp,space); + perform_async_copy(atomKK->k_sp,space); + // if ((mask & FM_MASK) && atomKK->k_sp.need_sync()) + // perform_async_copy(atomKK->k_fm,space); if ((mask & FM_MASK) && atomKK->k_sp.need_sync()) - perform_async_copy(atomKK->k_fm,space); + perform_async_copy(atomKK->k_fm,space); + // if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) + // perform_async_copy(atomKK->k_fm_long,space); if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) - perform_async_copy(atomKK->k_fm_long,space); + perform_async_copy(atomKK->k_fm_long,space); } else { if ((mask & X_MASK) && atomKK->k_x.need_sync()) perform_async_copy(atomKK->k_x,space); @@ -1290,12 +1297,18 @@ void AtomVecSpinKokkos::sync_overlapping_device(ExecutionSpace space, unsigned i perform_async_copy(atomKK->k_mask,space); if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync()) perform_async_copy(atomKK->k_image,space); + // if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) + // perform_async_copy(atomKK->k_sp,space); if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) - perform_async_copy(atomKK->k_sp,space); + perform_async_copy(atomKK->k_sp,space); + // if ((mask & FM_MASK) && atomKK->k_fm.need_sync()) + // perform_async_copy(atomKK->k_fm,space); if ((mask & FM_MASK) && atomKK->k_fm.need_sync()) - perform_async_copy(atomKK->k_fm,space); + perform_async_copy(atomKK->k_fm,space); + // if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) + // perform_async_copy(atomKK->k_fm_long,space); if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) - perform_async_copy(atomKK->k_fm_long,space); + perform_async_copy(atomKK->k_fm_long,space); } } diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index e0e1dc8269..b0fbdf1f9f 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -773,33 +773,50 @@ typedef tdual_virial_array::t_dev_const_randomread t_virial_array_randomread; //3d SP_FLOAT array n*4 #ifdef LMP_KOKKOS_NO_LEGACY -typedef Kokkos::DualView tdual_sp_array; +// typedef Kokkos::DualView tdual_sp_array; +typedef Kokkos::DualView tdual_float_1d_4; #else -typedef Kokkos::DualView tdual_sp_array; +// typedef Kokkos::DualView tdual_sp_array; +typedef Kokkos::DualView tdual_float_1d_4; #endif -typedef tdual_sp_array::t_dev t_sp_array; -typedef tdual_sp_array::t_dev_const t_sp_array_const; -typedef tdual_sp_array::t_dev_um t_sp_array_um; -typedef tdual_sp_array::t_dev_const_um t_sp_array_const_um; -typedef tdual_sp_array::t_dev_const_randomread t_sp_array_randomread; +// typedef tdual_sp_array::t_dev t_sp_array; +// typedef tdual_sp_array::t_dev_const t_sp_array_const; +// typedef tdual_sp_array::t_dev_um t_sp_array_um; +// typedef tdual_sp_array::t_dev_const_um t_sp_array_const_um; +// typedef tdual_sp_array::t_dev_const_randomread t_sp_array_randomread; +typedef tdual_float_1d_4::t_dev t_sp_array; +typedef tdual_float_1d_4::t_dev_const t_sp_array_const; +typedef tdual_float_1d_4::t_dev_um t_sp_array_um; +typedef tdual_float_1d_4::t_dev_const_um t_sp_array_const_um; +typedef tdual_float_1d_4::t_dev_const_randomread t_sp_array_randomread; //3d FM_FLOAT array n*3 -typedef Kokkos::DualView tdual_fm_array; -typedef tdual_fm_array::t_dev t_fm_array; -typedef tdual_fm_array::t_dev_const t_fm_array_const; -typedef tdual_fm_array::t_dev_um t_fm_array_um; -typedef tdual_fm_array::t_dev_const_um t_fm_array_const_um; -typedef tdual_fm_array::t_dev_const_randomread t_fm_array_randomread; +// typedef Kokkos::DualView tdual_fm_array; +// typedef tdual_fm_array::t_dev t_fm_array; +// typedef tdual_fm_array::t_dev_const t_fm_array_const; +// typedef tdual_fm_array::t_dev_um t_fm_array_um; +// typedef tdual_fm_array::t_dev_const_um t_fm_array_const_um; +// typedef tdual_fm_array::t_dev_const_randomread t_fm_array_randomread; +typedef tdual_f_array::t_dev t_fm_array; +typedef tdual_f_array::t_dev_const t_fm_array_const; +typedef tdual_f_array::t_dev_um t_fm_array_um; +typedef tdual_f_array::t_dev_const_um t_fm_array_const_um; +typedef tdual_f_array::t_dev_const_randomread t_fm_array_randomread; //3d FML_FLOAT array n*3 -typedef Kokkos::DualView tdual_fm_long_array; -typedef tdual_fm_long_array::t_dev t_fm_long_array; -typedef tdual_fm_long_array::t_dev_const t_fm_long_array_const; -typedef tdual_fm_long_array::t_dev_um t_fm_long_array_um; -typedef tdual_fm_long_array::t_dev_const_um t_fm_long_array_const_um; -typedef tdual_fm_long_array::t_dev_const_randomread t_fm_long_array_randomread; +// typedef Kokkos::DualView tdual_fm_long_array; +// typedef tdual_fm_long_array::t_dev t_fm_long_array; +// typedef tdual_fm_long_array::t_dev_const t_fm_long_array_const; +// typedef tdual_fm_long_array::t_dev_um t_fm_long_array_um; +// typedef tdual_fm_long_array::t_dev_const_um t_fm_long_array_const_um; +// typedef tdual_fm_long_array::t_dev_const_randomread t_fm_long_array_randomread; +typedef tdual_f_array::t_dev t_fm_long_array; +typedef tdual_f_array::t_dev_const t_fm_long_array_const; +typedef tdual_f_array::t_dev_um t_fm_long_array_um; +typedef tdual_f_array::t_dev_const_um t_fm_long_array_const_um; +typedef tdual_f_array::t_dev_const_randomread t_fm_long_array_randomread; //Energy Types //1d E_FLOAT array n @@ -1040,30 +1057,43 @@ typedef tdual_virial_array::t_host_const_randomread t_virial_array_randomread; // Spin types //2d X_FLOAT array n*4 -typedef Kokkos::DualView tdual_sp_array; -typedef tdual_sp_array::t_host t_sp_array; -typedef tdual_sp_array::t_host_const t_sp_array_const; -typedef tdual_sp_array::t_host_um t_sp_array_um; -typedef tdual_sp_array::t_host_const_um t_sp_array_const_um; -typedef tdual_sp_array::t_host_const_randomread t_sp_array_randomread; +// typedef Kokkos::DualView tdual_sp_array; +// typedef tdual_sp_array::t_host t_sp_array; +// typedef tdual_sp_array::t_host_const t_sp_array_const; +// typedef tdual_sp_array::t_host_um t_sp_array_um; +// typedef tdual_sp_array::t_host_const_um t_sp_array_const_um; +// typedef tdual_sp_array::t_host_const_randomread t_sp_array_randomread; +typedef tdual_float_1d_4::t_host t_sp_array; +typedef tdual_float_1d_4::t_host_const t_sp_array_const; +typedef tdual_float_1d_4::t_host_um t_sp_array_um; +typedef tdual_float_1d_4::t_host_const_um t_sp_array_const_um; +typedef tdual_float_1d_4::t_host_const_randomread t_sp_array_randomread; //2d F_FLOAT array n*3 -typedef Kokkos::DualView tdual_fm_array; -//typedef Kokkos::DualView tdual_f_array; -typedef tdual_fm_array::t_host t_fm_array; -typedef tdual_fm_array::t_host_const t_fm_array_const; -typedef tdual_fm_array::t_host_um t_fm_array_um; -typedef tdual_fm_array::t_host_const_um t_fm_array_const_um; -typedef tdual_fm_array::t_host_const_randomread t_fm_array_randomread; +// typedef Kokkos::DualView tdual_fm_array; +// typedef tdual_fm_array::t_host t_fm_array; +// typedef tdual_fm_array::t_host_const t_fm_array_const; +// typedef tdual_fm_array::t_host_um t_fm_array_um; +// typedef tdual_fm_array::t_host_const_um t_fm_array_const_um; +// typedef tdual_fm_array::t_host_const_randomread t_fm_array_randomread; +typedef tdual_f_array::t_host t_fm_array; +typedef tdual_f_array::t_host_const t_fm_array_const; +typedef tdual_f_array::t_host_um t_fm_array_um; +typedef tdual_f_array::t_host_const_um t_fm_array_const_um; +typedef tdual_f_array::t_host_const_randomread t_fm_array_randomread; //2d F_FLOAT array n*3 -typedef Kokkos::DualView tdual_fm_long_array; -//typedef Kokkos::DualView tdual_f_array; -typedef tdual_fm_long_array::t_host t_fm_long_array; -typedef tdual_fm_long_array::t_host_const t_fm_long_array_const; -typedef tdual_fm_long_array::t_host_um t_fm_long_array_um; -typedef tdual_fm_long_array::t_host_const_um t_fm_long_array_const_um; -typedef tdual_fm_long_array::t_host_const_randomread t_fm_long_array_randomread; +// typedef Kokkos::DualView tdual_fm_long_array; +// typedef tdual_fm_long_array::t_host t_fm_long_array; +// typedef tdual_fm_long_array::t_host_const t_fm_long_array_const; +// typedef tdual_fm_long_array::t_host_um t_fm_long_array_um; +// typedef tdual_fm_long_array::t_host_const_um t_fm_long_array_const_um; +// typedef tdual_fm_long_array::t_host_const_randomread t_fm_long_array_randomread; +typedef tdual_f_array::t_host t_fm_long_array; +typedef tdual_f_array::t_host_const t_fm_long_array_const; +typedef tdual_f_array::t_host_um t_fm_long_array_um; +typedef tdual_f_array::t_host_const_um t_fm_long_array_const_um; +typedef tdual_f_array::t_host_const_randomread t_fm_long_array_randomread; //Energy Types From 3925bcc1dee5be618f25b293ad234ced6e5e5366 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 13:35:42 -0400 Subject: [PATCH 0505/1217] apply requested changes do pair style hybrid doc --- doc/src/pair_hybrid.rst | 60 ++++++++++++++++++++++------------------- 1 file changed, 33 insertions(+), 27 deletions(-) diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index 9fdba318d9..e4e253caf9 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -14,7 +14,8 @@ pair_style hybrid/overlay command Accelerator Variants: *hybrid/overlay/kk* -pair_style hybrid/scale command +pair_style hybrid/scaled command +================================== Syntax """""" @@ -42,6 +43,10 @@ Examples pair_coeff * * lj/cut 1.0 1.0 pair_coeff * * coul/long + pair_style hybrid/scaled 0.5 tersoff 0.5 sw + pair_coeff * * tersoff Si.tersoff Si + pair_coeff * * sw Si.sw Si + variable one equal ramp(1.0,0.0) variable two equal 1.0-v_one pair_style hybrid/scaled v_one lj/cut 2.5 v_two morse 2.5 @@ -57,11 +62,11 @@ exactly one pair style is assigned to each pair of atom types. With the *hybrid/overlay* and *hybrid/scaled* styles, one or more pair styles can be assigned to each pair of atom types. The assignment of pair styles to type pairs is made via the :doc:`pair_coeff ` command. -The *hybrid/scaled* style differs from the *hybrid/overlay* style by -requiring a factor for each pair style that is used to scale all -forces, energies and stresses computed by each sub-style. Because of -the additional complexity, the *hybrid/scaled* style will have more -overhead and thus will be a bit slower than *hybrid/overlay*. +The major difference between the *hybrid/overlay* and *hybrid/scaled* +styles is that the *hybrid/scaled* adds a scale factor for each +sub-style contribution to forces, energies and stresses. Because of the +added complexity, the *hybrid/scaled* style has more overhead and thus +may be slower than *hybrid/overlay*. Here are two examples of hybrid simulations. The *hybrid* style could be used for a simulation of a metal droplet on a LJ surface. The metal @@ -76,34 +81,35 @@ and *coul/long* together gives the same result as if the would be more efficient to use the single combined potential, but in general any combination of pair potentials can be used together in to produce an interaction that is not encoded in any single pair_style -file, e.g. adding Coulombic forces between granular particles. The -*hybrid/scaled* style enables more complex combinations of pair styles -than a simple sum as *hybrid/overlay* does; there may be fractional -contributions from sub-styles or contributions may be subtracted with a -negative scale factor. Furthermore, since the scale factors can be -variables that may change during a simulation, which would allow, for -instance, to smoothly switch between two different pair styles or two -different parameter sets. +file, e.g. adding Coulombic forces between granular particles. + +If the *hybrid/scaled* style is used instead of *hybrid/overlay*\ , +contributions from sub-styles are weighted by their scale factors, which +may be fractional or even negative. Furthermore the scale factors may +be variables that may change during a simulation. This enables +switching smoothly between two different pair styles or two different +parameter sets during a run. All pair styles that will be used are listed as "sub-styles" following the *hybrid* or *hybrid/overlay* keyword, in any order. In case of the *hybrid/scaled* pair style, each sub-style is prefixed with a scale factor. The scale factor is either a floating point number or an equal -style (or equivalent) variable. Each sub-style's name is followed by its -usual arguments, as illustrated in the examples above. See the doc -pages of individual pair styles for a listing and explanation of the -appropriate arguments. +style (or equivalent) variable. Each sub-style's name is followed by +its usual arguments, as illustrated in the examples above. See the doc +pages of the individual pair styles for a listing and explanation of the +appropriate arguments for them. Note that an individual pair style can be used multiple times as a -sub-style. For efficiency this should only be done if your model -requires it. E.g. if you have different regions of Si and C atoms and -wish to use a Tersoff potential for pure Si for one set of atoms, and -a Tersoff potential for pure C for the other set (presumably with some -third potential for Si-C interactions), then the sub-style *tersoff* -could be listed twice. But if you just want to use a Lennard-Jones or -other pairwise potential for several different atom type pairs in your -model, then you should just list the sub-style once and use the -pair_coeff command to assign parameters for the different type pairs. +sub-style. For efficiency reasons this should only be done if your +model requires it. E.g. if you have different regions of Si and C atoms +and wish to use a Tersoff potential for pure Si for one set of atoms, +and a Tersoff potential for pure C for the other set (presumably with +some third potential for Si-C interactions), then the sub-style +*tersoff* could be listed twice. But if you just want to use a +Lennard-Jones or other pairwise potential for several different atom +type pairs in your model, then you should just list the sub-style once +and use the pair_coeff command to assign parameters for the different +type pairs. .. note:: From ee38452f14d3cd1d8549cae15223443606c7dd46 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 14:52:17 -0400 Subject: [PATCH 0506/1217] fix bug causing a failed download when using cmake -B --- cmake/Modules/Packages/USER-PACE.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/USER-PACE.cmake index df1fb023a5..66f228017c 100644 --- a/cmake/Modules/Packages/USER-PACE.cmake +++ b/cmake/Modules/Packages/USER-PACE.cmake @@ -5,7 +5,7 @@ mark_as_advanced(PACELIB_URL) mark_as_advanced(PACELIB_MD5) # download library sources to build folder -file(DOWNLOAD ${PACELIB_URL} ./libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5}) +file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5}) # uncompress downloaded sources execute_process( From 04248c2ccdf41f8e2977e72ce99f1a45715e3463 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 14:52:35 -0400 Subject: [PATCH 0507/1217] finalize CMake build docs --- doc/src/Build_extras.rst | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 726374a012..12bb33f264 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -1255,14 +1255,23 @@ USER-PACE package This package requires a library that can be downloaded and built in lib/pace or somewhere else, which must be done before building -LAMMPS with this package. +LAMMPS with this package. The code for the library can be found +at: `https://github.com/ICAMS/lammps-user-pace/ `_ .. tabs:: .. tab:: CMake build - The library download and build will happen automatically when USER-PACE - is requested. + By default the library will be downloaded from the git repository + and built automatically when the USER-PACE package is enabled with + ``-D PKG_USER-PACE=yes``. The location for the sources may be + customized by setting the variable ``PACELIB_URL`` when + configuring with CMake (e.g. to use a local archive on machines + without internet access). Since CMake checks the validity of the + archive with ``md5sum`` you may also need to set ``PACELIB_MD5`` + if you provide a different library version than what is downloaded + automatically. + .. tab:: Traditional make From f1e5d1115169ecbdb8977ed3bfd57d24667b2d51 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 14:52:53 -0400 Subject: [PATCH 0508/1217] add LAMMPS distribution header --- src/USER-PACE/pair_pace.cpp | 13 +++++++++++++ src/USER-PACE/pair_pace.h | 10 ++++++++++ 2 files changed, 23 insertions(+) diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index f59291b33e..d6eda0f511 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + /* Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, diff --git a/src/USER-PACE/pair_pace.h b/src/USER-PACE/pair_pace.h index 37509cff5e..4d5ddcb9e8 100644 --- a/src/USER-PACE/pair_pace.h +++ b/src/USER-PACE/pair_pace.h @@ -1,3 +1,13 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + This software is distributed under the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + /* Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, From d08d59acb3cd4e271cc8d106ead2865636d3128c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 15:00:21 -0400 Subject: [PATCH 0509/1217] whitespace fix --- src/pair_coul_cut.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index 428c12c2e0..629d39a9c5 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -260,7 +260,7 @@ void PairCoulCut::read_restart(FILE *fp) MPI_Bcast(&scale[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { - if (me == 0) + if (me == 0) utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); } From 573aebf06fe0379c530f2b9598e7f8efff7b7790 Mon Sep 17 00:00:00 2001 From: julient31 Date: Mon, 12 Apr 2021 14:52:47 -0600 Subject: [PATCH 0510/1217] adding possibility of one or more fix prec/spin in fix nve/spin --- src/SPIN/fix_nve_spin.cpp | 57 ++++++++++++++++++++++++++++++++------- src/SPIN/fix_nve_spin.h | 7 ++++- 2 files changed, 53 insertions(+), 11 deletions(-) diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 30a18fb301..97e3237fda 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -74,6 +74,9 @@ FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) : nlocal_max = 0; npairs = 0; npairspin = 0; + + // test nprec + nprecspin = 0; // checking if map array or hash is defined @@ -189,20 +192,20 @@ void FixNVESpin::init() // loop 2: fill vector with ptrs to Pair/Spin styles - int count = 0; + int count1 = 0; if (npairspin == 1) { - count = 1; + count1 = 1; spin_pairs[0] = (PairSpin *) force->pair_match("spin",0,0); } else if (npairspin > 1) { for (int i = 0; ipair_match("spin",0,i)) { - spin_pairs[count] = (PairSpin *) force->pair_match("spin",0,i); - count++; + spin_pairs[count1] = (PairSpin *) force->pair_match("spin",0,i); + count1++; } } } - if (count != npairspin) + if (count1 != npairspin) error->all(FLERR,"Incorrect number of spin pairs"); // set pair/spin and long/spin flags @@ -215,15 +218,48 @@ void FixNVESpin::init() } } - // ptrs FixPrecessionSpin classes + // // ptrs FixPrecessionSpin classes + // int iforce; + // for (iforce = 0; iforce < modify->nfix; iforce++) { + // if (strstr(modify->fix[iforce]->style,"precession/spin")) { + // precession_spin_flag = 1; + // lockprecessionspin = (FixPrecessionSpin *) modify->fix[iforce]; + // } + // } + + // set ptrs for fix precession/spin styles + + // loop 1: obtain # of fix precession/spin styles + int iforce; for (iforce = 0; iforce < modify->nfix; iforce++) { if (strstr(modify->fix[iforce]->style,"precession/spin")) { - precession_spin_flag = 1; - lockprecessionspin = (FixPrecessionSpin *) modify->fix[iforce]; + nprecspin++; } } + + // init length of vector of ptrs to precession/spin styles + + if (nprecspin > 0) { + lockprecessionspin = new FixPrecessionSpin*[nprecspin]; + } + + // loop 2: fill vector with ptrs to precession/spin styles + + int count2 = 0; + if (nprecspin > 0) { + for (iforce = 0; iforce < modify->nfix; iforce++) { + if (strstr(modify->fix[iforce]->style,"precession/spin")) { + precession_spin_flag = 1; + lockprecessionspin[count2] = (FixPrecessionSpin *) modify->fix[iforce]; + count2++; + } + } + } + + if (count2 != nprecspin) + error->all(FLERR,"Incorrect number of fix precession/spin"); // ptrs on the FixLangevinSpin class @@ -471,7 +507,9 @@ void FixNVESpin::ComputeInteractionsSpin(int i) // update magnetic precession interactions if (precession_spin_flag) { - lockprecessionspin->compute_single_precession(i,spi,fmi); + for (int k = 0; k < nprecspin; k++) { + lockprecessionspin[k]->compute_single_precession(i,spi,fmi); + } } // update langevin damping and random force @@ -496,7 +534,6 @@ void FixNVESpin::ComputeInteractionsSpin(int i) fm[i][0] = fmi[0]; fm[i][1] = fmi[1]; fm[i][2] = fmi[2]; - } /* ---------------------------------------------------------------------- diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h index 5aa6b8e4e4..a4b89c1727 100644 --- a/src/SPIN/fix_nve_spin.h +++ b/src/SPIN/fix_nve_spin.h @@ -63,9 +63,14 @@ friend class PairSpin; // pointers to magnetic fixes - class FixPrecessionSpin *lockprecessionspin; + // class FixPrecessionSpin *lockprecessionspin; class FixLangevinSpin *locklangevinspin; class FixSetForceSpin *locksetforcespin; + + // pointers to fix precession/spin styles + + int nprecspin; + class FixPrecessionSpin **lockprecessionspin; // pointers to magnetic pair styles From bb52cf93778f8d2f9a92d91171f622a516b11546 Mon Sep 17 00:00:00 2001 From: julient31 Date: Mon, 12 Apr 2021 15:01:29 -0600 Subject: [PATCH 0511/1217] adding mask check for fix prec/spin --- src/SPIN/fix_precession_spin.cpp | 181 ++++++++++++++++++++++++++++--- src/SPIN/fix_precession_spin.h | 25 ++++- 2 files changed, 191 insertions(+), 15 deletions(-) diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 17b9d3eb22..873a21ea66 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -67,6 +67,9 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : H_field = 0.0; nhx = nhy = nhz = 0.0; hx = hy = hz = 0.0; + stt_field = 0.0; + nsttx = nstty = nsttz = 0.0; + sttx = stty = sttz = 0.0; Ka = 0.0; nax = nay = naz = 0.0; Kax = Kay = Kaz = 0.0; @@ -74,8 +77,11 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : nc1x = nc1y = nc1z = 0.0; nc2x = nc2y = nc2z = 0.0; nc3x = nc3y = nc3z = 0.0; + K6 = 0.0; + n6x = n6y = n6z = 0.0; + m6x = m6y = m6z = 0.0; - zeeman_flag = aniso_flag = cubic_flag = 0; + zeeman_flag = stt_flag = aniso_flag = cubic_flag = hexaniso_flag = 0; int iarg = 3; while (iarg < narg) { @@ -87,6 +93,14 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : nhy = utils::numeric(FLERR,arg[iarg+3],false,lmp); nhz = utils::numeric(FLERR,arg[iarg+4],false,lmp); iarg += 5; + } else if (strcmp(arg[iarg],"stt") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix precession/spin command"); + stt_flag = 1; + stt_field = utils::numeric(FLERR,arg[iarg+1],false,lmp); + nsttx = utils::numeric(FLERR,arg[iarg+2],false,lmp); + nstty = utils::numeric(FLERR,arg[iarg+3],false,lmp); + nsttz = utils::numeric(FLERR,arg[iarg+4],false,lmp); + iarg += 5; } else if (strcmp(arg[iarg],"anisotropy") == 0) { if (iarg+4 > narg) error->all(FLERR,"Illegal fix precession/spin command"); aniso_flag = 1; @@ -110,6 +124,17 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : nc3y = utils::numeric(FLERR,arg[iarg+10],false,lmp); nc3z = utils::numeric(FLERR,arg[iarg+11],false,lmp); iarg += 12; + } else if (strcmp(arg[iarg],"hexaniso") == 0) { + if (iarg+7 > narg) error->all(FLERR,"Illegal fix precession/spin command"); + hexaniso_flag = 1; + K6 = utils::numeric(FLERR,arg[iarg+1],false,lmp); + n6x = utils::numeric(FLERR,arg[iarg+2],false,lmp); + n6y = utils::numeric(FLERR,arg[iarg+3],false,lmp); + n6z = utils::numeric(FLERR,arg[iarg+4],false,lmp); + m6x = utils::numeric(FLERR,arg[iarg+5],false,lmp); + m6y = utils::numeric(FLERR,arg[iarg+6],false,lmp); + m6z = utils::numeric(FLERR,arg[iarg+7],false,lmp); + iarg += 8; } else error->all(FLERR,"Illegal precession/spin command"); } @@ -123,6 +148,13 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : nhz *= inorm; } + if (stt_flag) { + inorm = 1.0/sqrt(nsttx*nsttx + nstty*nstty + nsttz*nsttz); + nsttx *= inorm; + nstty *= inorm; + nsttz *= inorm; + } + if (aniso_flag) { inorm = 1.0/sqrt(nax*nax + nay*nay + naz*naz); nax *= inorm; @@ -144,6 +176,27 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : nc3y *= inorm; nc3z *= inorm; } + + if (hexaniso_flag) { + inorm = 1.0/sqrt(n6x*n6x + n6y*n6y + n6z*n6z); + n6x *= inorm; + n6y *= inorm; + n6z *= inorm; + inorm = 1.0/sqrt(m6x*m6x + m6y*m6y + m6z*m6z); + m6x *= inorm; + m6y *= inorm; + m6z *= inorm; + l6x = (n6z*m6y-n6y*m6z); + l6y = (n6x*m6z-n6z*m6x); + l6z = (n6y*m6x-n6x*m6y); + inorm = 1.0/sqrt(l6x*l6x + l6y*l6y + l6z*l6z); + l6x *= inorm; + l6y *= inorm; + l6z *= inorm; + m6x = (l6z*n6y-l6y*n6z); + m6y = (l6x*n6z-l6z*n6x); + m6z = (l6y*n6x-l6x*n6y); + } degree2rad = MY_PI/180.0; time_origin = update->ntimestep; @@ -185,8 +238,9 @@ void FixPrecessionSpin::init() Kah = Ka/hbar; k1ch = k1c/hbar; k2ch = k2c/hbar; + K6h = K6/hbar; - if (utils::strmatch(update->integrate_style,"^respa")) { + if (strstr(update->integrate_style,"respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -201,12 +255,11 @@ void FixPrecessionSpin::init() // check that fix precession/spin is only declared once - int iprec = 0; - for (int iforce = 0; iforce < modify->nfix; iforce++) - if (strstr(modify->fix[iforce]->style,"precession/spin")) iprec++; - if (iprec > 1) - error->all(FLERR,"precession/spin command can only be declared once"); - + // int iprec = 0; + // for (int iforce = 0; iforce < modify->nfix; iforce++) + // if (strstr(modify->fix[iforce]->style,"precession/spin")) iprec++; + // if (iprec > 1) + // error->all(FLERR,"precession/spin command can only be declared once"); varflag = CONSTANT; if (magfieldstyle != CONSTANT) varflag = EQUAL; @@ -225,7 +278,7 @@ void FixPrecessionSpin::init() void FixPrecessionSpin::setup(int vflag) { - if (utils::strmatch(update->integrate_style,"^verlet")) + if (strstr(update->integrate_style,"verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); @@ -283,16 +336,26 @@ void FixPrecessionSpin::post_force(int /* vflag */) epreci -= compute_zeeman_energy(spi); } + if (stt_flag) { // compute Spin Transfer Torque + compute_stt(spi,fmi); + epreci -= compute_stt_energy(spi); + } + if (aniso_flag) { // compute magnetic anisotropy compute_anisotropy(spi,fmi); epreci -= compute_anisotropy_energy(spi); } - if (cubic_flag) { // compute cubic anisotropy + if (cubic_flag) { // compute cubic anisotropy compute_cubic(spi,fmi); epreci -= compute_cubic_energy(spi); } + if (hexaniso_flag) { // compute hexagonal anisotropy + compute_hexaniso(spi,fmi); + epreci -= compute_hexaniso_energy(spi); + } + emag[i] += epreci; eprec += epreci; fm[i][0] += fmi[0]; @@ -309,12 +372,16 @@ void FixPrecessionSpin::compute_single_precession(int i, double spi[3], double f int *mask = atom->mask; if (mask[i] & groupbit) { if (zeeman_flag) compute_zeeman(i,fmi); + if (stt_flag) compute_stt(spi,fmi); if (aniso_flag) compute_anisotropy(spi,fmi); if (cubic_flag) compute_cubic(spi,fmi); + if (hexaniso_flag) compute_hexaniso(spi,fmi); } } -/* ---------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Zeeman +------------------------------------------------------------------------- */ void FixPrecessionSpin::compute_zeeman(int i, double fmi[3]) { @@ -334,14 +401,39 @@ double FixPrecessionSpin::compute_zeeman_energy(double spi[4]) return energy; } +/* ---------------------------------------------------------------------- + STT +------------------------------------------------------------------------- */ + +void FixPrecessionSpin::compute_stt(double spi[3], double fmi[3]) +{ + double sx = spi[0]; + double sy = spi[1]; + double sz = spi[2]; + fmi[0] += 1.0*stt_field*( sy*nsttz-sz*nstty); + fmi[1] += 1.0*stt_field*(-sx*nsttz+sz*nsttx); + fmi[2] += 1.0*stt_field*( sx*nstty-sy*nsttx); +} + /* ---------------------------------------------------------------------- */ +double FixPrecessionSpin::compute_stt_energy(double spi[3]) +{ + double energy = 0.0; // Non-conservative force + return energy; +} + +/* ---------------------------------------------------------------------- + compute uniaxial anisotropy interaction for spin i +------------------------------------------------------------------------- */ + void FixPrecessionSpin::compute_anisotropy(double spi[3], double fmi[3]) { double scalar = nax*spi[0] + nay*spi[1] + naz*spi[2]; fmi[0] += scalar*Kax; fmi[1] += scalar*Kay; fmi[2] += scalar*Kaz; + // printf("fm pres1: %g %g %g \n",fmi[0],fmi[1],fmi[2]); } /* ---------------------------------------------------------------------- */ @@ -393,9 +485,7 @@ void FixPrecessionSpin::compute_cubic(double spi[3], double fmi[3]) fmi[2] += (fourz + sixz); } -/* ---------------------------------------------------------------------- - compute cubic aniso energy of spin i -------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- */ double FixPrecessionSpin::compute_cubic_energy(double spi[3]) { @@ -412,6 +502,62 @@ double FixPrecessionSpin::compute_cubic_energy(double spi[3]) return energy; } +/* ---------------------------------------------------------------------- + compute hexagonal anisotropy interaction for spin i +------------------------------------------------------------------------- */ + +void FixPrecessionSpin::compute_hexaniso(double spi[3], double fmi[3]) +{ + double s_x,s_y,s_z; + double pf, phi, ssint2; + + // changing to the axes' frame + + s_x = l6x*spi[0]+l6y*spi[1]+l6z*spi[2]; + s_y = m6x*spi[0]+m6y*spi[1]+m6z*spi[2]; + s_z = n6x*spi[0]+n6y*spi[1]+n6z*spi[2]; + + // hexagonal anisotropy in the axes' frame + + phi = atan2(s_y,s_x); + ssint2 = s_x*s_x + s_y*s_y; // s^2sin^2(theta) + pf = 6.0 * K6h * ssint2*ssint2*sqrt(ssint2); // 6*K_6*s^5*sin^5(theta) + double fm_x = pf*cos(5*phi); + double fm_y = -pf*sin(5*phi); + double fm_z = 0; + + // back to the lab's frame + + fmi[0] += fm_x*l6x+fm_y*m6x+fm_z*n6x; + fmi[1] += fm_x*l6y+fm_y*m6y+fm_z*n6y; + fmi[2] += fm_x*l6z+fm_y*m6z+fm_z*n6z; +} + +/* ---------------------------------------------------------------------- + compute hexagonal aniso energy of spin i +------------------------------------------------------------------------- */ + +double FixPrecessionSpin::compute_hexaniso_energy(double spi[3]) +{ + double energy = 0.0; + double s_x,s_y,s_z, phi,ssint2; + + // changing to the axes' frame + + s_x = l6x*spi[0]+l6y*spi[1]+l6z*spi[2]; + s_y = m6x*spi[0]+m6y*spi[1]+m6z*spi[2]; + s_z = n6x*spi[0]+n6y*spi[1]+n6z*spi[2]; + + // hexagonal anisotropy in the axes' frame + + phi = atan2(s_y,s_z); + ssint2 = s_x*s_x + s_y*s_y; + + energy = K6 * ssint2*ssint2*ssint2*cos(6*phi); + + return 2.0*energy; +} + /* ---------------------------------------------------------------------- */ void FixPrecessionSpin::set_magneticprecession() @@ -421,6 +567,13 @@ void FixPrecessionSpin::set_magneticprecession() hy = H_field*nhy; hz = H_field*nhz; } + + if (stt_flag) { + sttx = stt_field*nsttx; + stty = stt_field*nstty; + sttz = stt_field*nsttz; + } + if (aniso_flag) { Kax = 2.0*Kah*nax; Kay = 2.0*Kah*nay; diff --git a/src/SPIN/fix_precession_spin.h b/src/SPIN/fix_precession_spin.h index 9c3c616077..d06a04f8f1 100644 --- a/src/SPIN/fix_precession_spin.h +++ b/src/SPIN/fix_precession_spin.h @@ -39,7 +39,7 @@ class FixPrecessionSpin : public Fix { void min_post_force(int); double compute_scalar(); - int zeeman_flag, aniso_flag, cubic_flag; + int zeeman_flag, stt_flag, aniso_flag, cubic_flag, hexaniso_flag; void compute_single_precession(int, double *, double *); // zeeman calculations @@ -47,6 +47,11 @@ class FixPrecessionSpin : public Fix { void compute_zeeman(int, double *); double compute_zeeman_energy(double *); + // stt calculations + + void compute_stt(double *, double *); + double compute_stt_energy(double *); + // uniaxial aniso calculations void compute_anisotropy(double *, double *); @@ -57,6 +62,11 @@ class FixPrecessionSpin : public Fix { void compute_cubic(double *, double *); double compute_cubic_energy(double *); + // hexagonal aniso calculations + + void compute_hexaniso(double *, double *); + double compute_hexaniso_energy(double *); + // storing magnetic energies int nlocal_max; // max nlocal (for list size) @@ -83,6 +93,12 @@ class FixPrecessionSpin : public Fix { double nhx, nhy, nhz; double hx, hy, hz; // temp. force variables + // STT intensity and direction + + double stt_field; + double nsttx, nstty, nsttz; + double sttx, stty, sttz; + // magnetic anisotropy intensity and direction double Ka; // aniso const. in eV @@ -98,6 +114,13 @@ class FixPrecessionSpin : public Fix { double nc2x,nc2y,nc2z; double nc3x,nc3y,nc3z; + // hexagonal anisotropy + double K6; // hexagonal aniso const. in eV + double K6h; // hexagonal aniso const. in rad.THz + double n6x,n6y,n6z; // main axis + double m6x,m6y,m6z; // secondary (perpendicular) axis + double l6x,l6y,l6z; // =(m x n) + void set_magneticprecession(); }; From 455bb933c8b59177b73d911b686db814f6ba6a64 Mon Sep 17 00:00:00 2001 From: julient31 Date: Mon, 12 Apr 2021 16:18:22 -0600 Subject: [PATCH 0512/1217] adding modifications for more than one fix langevin/spin in fix nve/spin --- .../llg_exchange.py | 2 +- .../validation_nvt/in.spin.nvt_lattice | 4 +- .../validation_nvt/in.spin.nvt_spin | 9 ++- src/SPIN/fix_langevin_spin.cpp | 12 ++++ src/SPIN/fix_langevin_spin.h | 3 +- src/SPIN/fix_nve_spin.cpp | 67 ++++++++++++++----- src/SPIN/fix_nve_spin.h | 12 ++-- src/SPIN/fix_precession_spin.cpp | 1 - 8 files changed, 83 insertions(+), 27 deletions(-) diff --git a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py index 5b93ac5c2d..a4cba3a940 100755 --- a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py +++ b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py @@ -6,7 +6,7 @@ import matplotlib.pyplot as plt import mpmath as mp hbar=0.658212 # Planck's constant (eV.fs/rad) -# J0=0.05 # per-neighbor exchange interaction (eV) +J0=0.05 # per-neighbor exchange interaction (eV) # exchange interaction parameters J1 = 11.254 # in eV diff --git a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice index 2375c0ff8d..6f995fa071 100644 --- a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice +++ b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice @@ -30,8 +30,8 @@ neighbor 0.1 bin neigh_modify every 10 check yes delay 20 fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin 200.0 200.0 1.0 48279 -fix 3 all langevin/spin 0.0 0.00001 321 +fix 2 all langevin 200.0 200.0 0.1 48279 +fix 3 all langevin/spin 0.0 0.0 321 fix 4 all nve/spin lattice moving timestep 0.001 diff --git a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin index 6b65df7109..b33789cec6 100644 --- a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin +++ b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin @@ -21,16 +21,19 @@ mass 1 55.845 set group all spin 2.2 0.0 0.0 1.0 velocity all create 0 4928459 rot yes dist gaussian -pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +# pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0 pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe pair_coeff * * spin/exchange exchange 3.4 0.1 0.2171 1.841 +pair_coeff * * spin/neel neel 4.0 0.02 0.0 1.841 0.0 0.0 1.0 neighbor 0.1 bin neigh_modify every 10 check yes delay 20 fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 200.0 0.01 321 -fix 3 all nve/spin lattice moving +fix 2 all langevin 0.0 0.0 0.0 48279 +fix 3 all langevin/spin 200.0 0.01 321 +fix 4 all nve/spin lattice moving timestep 0.001 # compute and output options diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index c9cb0fa2ec..209eaa5632 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -24,6 +24,7 @@ #include "fix_langevin_spin.h" #include #include +#include "atom.h" #include "comm.h" #include "error.h" #include "force.h" @@ -163,3 +164,14 @@ void FixLangevinSpin::add_temperature(double fmi[3]) fmi[1] *= gil_factor; fmi[2] *= gil_factor; } + +/* ---------------------------------------------------------------------- */ + +void FixLangevinSpin::compute_single_langevin(int i, double spi[3], double fmi[3]) +{ + int *mask = atom->mask; + if (mask[i] & groupbit) { + if (tdamp_flag) add_tdamping(spi,fmi); + if (temp_flag) add_temperature(fmi); + } +} diff --git a/src/SPIN/fix_langevin_spin.h b/src/SPIN/fix_langevin_spin.h index c73b33353b..89267f7d4d 100644 --- a/src/SPIN/fix_langevin_spin.h +++ b/src/SPIN/fix_langevin_spin.h @@ -26,7 +26,7 @@ namespace LAMMPS_NS { class FixLangevinSpin : public Fix { public: - int tdamp_flag,ldamp_flag,temp_flag; // damping and temperature flags + int tdamp_flag,temp_flag; // damping and temperature flags FixLangevinSpin(class LAMMPS *, int, char **); virtual ~FixLangevinSpin(); @@ -35,6 +35,7 @@ class FixLangevinSpin : public Fix { void setup(int); void add_tdamping(double *, double *); // add transverse damping void add_temperature(double *); // add temperature + void compute_single_langevin(int, double *, double *); protected: double alpha_t; // transverse mag. damping diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 97e3237fda..266f0bd690 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -60,7 +60,8 @@ enum{NONE}; FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), - pair(nullptr), spin_pairs(nullptr), + pair(nullptr), spin_pairs(nullptr), locklangevinspin(nullptr), + locksetforcespin(nullptr), lockprecessionspin(nullptr), rsec(nullptr), stack_head(nullptr), stack_foot(nullptr), backward_stacks(nullptr), forward_stacks(nullptr) { @@ -76,7 +77,7 @@ FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) : npairspin = 0; // test nprec - nprecspin = 0; + nprecspin = nlangspin = nsetspin = 0; // checking if map array or hash is defined @@ -128,7 +129,6 @@ FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) : maglangevin_flag = 0; tdamp_flag = temp_flag = 0; setforce_spin_flag = 0; - } /* ---------------------------------------------------------------------- */ @@ -141,6 +141,8 @@ FixNVESpin::~FixNVESpin() memory->destroy(forward_stacks); memory->destroy(backward_stacks); delete [] spin_pairs; + delete [] locklangevinspin; + delete [] lockprecessionspin; } /* ---------------------------------------------------------------------- */ @@ -261,19 +263,51 @@ void FixNVESpin::init() if (count2 != nprecspin) error->all(FLERR,"Incorrect number of fix precession/spin"); - // ptrs on the FixLangevinSpin class - + // set ptrs for fix langevin/spin styles + + // loop 1: obtain # of fix langevin/spin styles + for (iforce = 0; iforce < modify->nfix; iforce++) { if (strstr(modify->fix[iforce]->style,"langevin/spin")) { - maglangevin_flag = 1; - locklangevinspin = (FixLangevinSpin *) modify->fix[iforce]; + nlangspin++; } } + + // init length of vector of ptrs to precession/spin styles - if (maglangevin_flag) { - if (locklangevinspin->tdamp_flag == 1) tdamp_flag = 1; - if (locklangevinspin->temp_flag == 1) temp_flag = 1; + if (nlangspin > 0) { + locklangevinspin = new FixLangevinSpin*[nprecspin]; } + + // loop 2: fill vector with ptrs to precession/spin styles + + count2 = 0; + if (nlangspin > 0) { + for (iforce = 0; iforce < modify->nfix; iforce++) { + if (strstr(modify->fix[iforce]->style,"langevin/spin")) { + maglangevin_flag = 1; + locklangevinspin[count2] = (FixLangevinSpin *) modify->fix[iforce]; + count2++; + } + } + } + + if (count2 != nlangspin) + error->all(FLERR,"Incorrect number of fix precession/spin"); + + // // ptrs on the FixLangevinSpin class + + // for (iforce = 0; iforce < modify->nfix; iforce++) { + // if (strstr(modify->fix[iforce]->style,"langevin/spin")) { + // maglangevin_flag = 1; + // locklangevinspin = (FixLangevinSpin *) modify->fix[iforce]; + // } + // } + + // if (maglangevin_flag) { + // if (locklangevinspin->tdamp_flag == 1) tdamp_flag = 1; + // if (locklangevinspin->temp_flag == 1) temp_flag = 1; + // } // ptrs FixSetForceSpin classes @@ -515,12 +549,15 @@ void FixNVESpin::ComputeInteractionsSpin(int i) // update langevin damping and random force if (maglangevin_flag) { // mag. langevin - if (tdamp_flag) { // transverse damping - locklangevinspin->add_tdamping(spi,fmi); - } - if (temp_flag) { // spin temperature - locklangevinspin->add_temperature(fmi); + for (int k = 0; k < nlangspin; k++) { + locklangevinspin[k]->compute_single_langevin(i,spi,fmi); } + // if (tdamp_flag) { // transverse damping + // locklangevinspin->add_tdamping(spi,fmi); + // } + // if (temp_flag) { // spin temperature + // locklangevinspin->add_temperature(fmi); + // } } // update setforce of magnetic interactions diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h index a4b89c1727..ac5bc57b25 100644 --- a/src/SPIN/fix_nve_spin.h +++ b/src/SPIN/fix_nve_spin.h @@ -61,11 +61,15 @@ friend class PairSpin; int tdamp_flag, temp_flag; int setforce_spin_flag; - // pointers to magnetic fixes + // pointers to fix langevin/spin styles - // class FixPrecessionSpin *lockprecessionspin; - class FixLangevinSpin *locklangevinspin; - class FixSetForceSpin *locksetforcespin; + int nlangspin; + class FixLangevinSpin **locklangevinspin; + + // pointers to fix setforce/spin styles + + int nsetspin; + class FixSetForceSpin *locksetforcespin; // to be done // pointers to fix precession/spin styles diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 873a21ea66..a6bb19907a 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -433,7 +433,6 @@ void FixPrecessionSpin::compute_anisotropy(double spi[3], double fmi[3]) fmi[0] += scalar*Kax; fmi[1] += scalar*Kay; fmi[2] += scalar*Kaz; - // printf("fm pres1: %g %g %g \n",fmi[0],fmi[1],fmi[2]); } /* ---------------------------------------------------------------------- */ From 47814292a119f42bd77881e1854c5fae23449695 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 12 Apr 2021 19:57:27 -0400 Subject: [PATCH 0513/1217] Make dump cfg/gz, cfg/zstd compatible to 'buffer no' option --- src/COMPRESS/dump_cfg_gz.cpp | 67 ++++++++++++++++++- src/COMPRESS/dump_cfg_zstd.cpp | 67 ++++++++++++++++++- unittest/formats/test_dump_cfg_compressed.cpp | 33 +++++++++ 3 files changed, 165 insertions(+), 2 deletions(-) diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp index 23c0d82429..c5942c1fc5 100644 --- a/src/COMPRESS/dump_cfg_gz.cpp +++ b/src/COMPRESS/dump_cfg_gz.cpp @@ -136,7 +136,72 @@ void DumpCFGGZ::write_header(bigint n) void DumpCFGGZ::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + if (unwrapflag == 0) { + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < size_one; j++) { + int written = 0; + if (j == 0) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%f \n", mybuf[m]); + } else if (j == 1) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]); + } else if (j >= 2) { + if (vtype[j] == Dump::INT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + else if (vtype[j] == Dump::STRING) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]); + else if (vtype[j] == Dump::BIGINT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump cfg/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } else if (unwrapflag == 1) { + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < size_one; j++) { + int written = 0; + if (j == 0) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%f \n", mybuf[m]); + } else if (j == 1) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]); + } else if (j >= 2 && j <= 4) { + double unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5; + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], unwrap_coord); + } else if (j >= 5) { + if (vtype[j] == Dump::INT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + else if (vtype[j] == Dump::STRING) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]); + else if (vtype[j] == Dump::BIGINT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump cfg/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } + } } /* ---------------------------------------------------------------------- */ diff --git a/src/COMPRESS/dump_cfg_zstd.cpp b/src/COMPRESS/dump_cfg_zstd.cpp index 5bc6ac86dc..0ea92f3807 100644 --- a/src/COMPRESS/dump_cfg_zstd.cpp +++ b/src/COMPRESS/dump_cfg_zstd.cpp @@ -148,7 +148,72 @@ void DumpCFGZstd::write_header(bigint n) void DumpCFGZstd::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + if (unwrapflag == 0) { + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < size_one; j++) { + int written = 0; + if (j == 0) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%f \n", mybuf[m]); + } else if (j == 1) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]); + } else if (j >= 2) { + if (vtype[j] == Dump::INT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + else if (vtype[j] == Dump::STRING) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]); + else if (vtype[j] == Dump::BIGINT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump cfg/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } else if (unwrapflag == 1) { + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < size_one; j++) { + int written = 0; + if (j == 0) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%f \n", mybuf[m]); + } else if (j == 1) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]); + } else if (j >= 2 && j <= 4) { + double unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5; + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], unwrap_coord); + } else if (j >= 5) { + if (vtype[j] == Dump::INT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + else if (vtype[j] == Dump::STRING) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]); + else if (vtype[j] == Dump::BIGINT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump cfg/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } + } } /* ---------------------------------------------------------------------- */ diff --git a/unittest/formats/test_dump_cfg_compressed.cpp b/unittest/formats/test_dump_cfg_compressed.cpp index 6d5e8bcf04..1a00f9520e 100644 --- a/unittest/formats/test_dump_cfg_compressed.cpp +++ b/unittest/formats/test_dump_cfg_compressed.cpp @@ -66,6 +66,39 @@ TEST_F(DumpCfgCompressTest, compressed_run0) delete_file(converted_file_0); } +TEST_F(DumpCfgCompressTest, compressed_no_buffer_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "no_buffer_run*.melt.cfg"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + + auto base_name_0 = "no_buffer_run0.melt.cfg"; + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; + + if(compression_style == "cfg/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "buffer no", "buffer no", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "buffer no", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + TEST_F(DumpCfgCompressTest, compressed_unwrap_run0) { if (!COMPRESS_BINARY) GTEST_SKIP(); From dba3cce883b8c89fa5a012818990f4d851532bc1 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 12 Apr 2021 20:03:58 -0400 Subject: [PATCH 0514/1217] Make dump xyz/gz, xyz/zstd compatible to 'buffer no' option --- src/COMPRESS/dump_xyz_gz.cpp | 19 +++++++++++- src/COMPRESS/dump_xyz_zstd.cpp | 19 +++++++++++- unittest/formats/test_dump_xyz_compressed.cpp | 31 +++++++++++++++++++ 3 files changed, 67 insertions(+), 2 deletions(-) diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index 0697f19ce3..abd6e7fa78 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -109,7 +109,24 @@ void DumpXYZGZ::write_header(bigint ndump) void DumpXYZGZ::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + int written = snprintf(vbuffer, VBUFFER_SIZE, format, + typenames[static_cast (mybuf[m+1])], + mybuf[m+2],mybuf[m+3],mybuf[m+4]); + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump xyz/gz output"); + } + m += size_one; + } + } } /* ---------------------------------------------------------------------- */ diff --git a/src/COMPRESS/dump_xyz_zstd.cpp b/src/COMPRESS/dump_xyz_zstd.cpp index cb75542337..74e482717b 100644 --- a/src/COMPRESS/dump_xyz_zstd.cpp +++ b/src/COMPRESS/dump_xyz_zstd.cpp @@ -120,7 +120,24 @@ void DumpXYZZstd::write_header(bigint ndump) void DumpXYZZstd::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + int written = snprintf(vbuffer, VBUFFER_SIZE, format, + typenames[static_cast (mybuf[m+1])], + mybuf[m+2],mybuf[m+3],mybuf[m+4]); + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump xyz/gz output"); + } + m += size_one; + } + } } /* ---------------------------------------------------------------------- */ diff --git a/unittest/formats/test_dump_xyz_compressed.cpp b/unittest/formats/test_dump_xyz_compressed.cpp index b627cb5a99..d9aa8e370d 100644 --- a/unittest/formats/test_dump_xyz_compressed.cpp +++ b/unittest/formats/test_dump_xyz_compressed.cpp @@ -60,6 +60,37 @@ TEST_F(DumpXYZCompressTest, compressed_run0) delete_file(converted_file_0); } +TEST_F(DumpXYZCompressTest, compressed_no_buffer_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "no_buffer_run*.melt.xyz"; + auto base_name_0 = "no_buffer_run0.melt.xyz"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + + if(compression_style == "xyz/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, "", "", "buffer no", "buffer no", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, "", "buffer no", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + TEST_F(DumpXYZCompressTest, compressed_multi_file_run1) { if (!COMPRESS_BINARY) GTEST_SKIP(); From e49e505b9f096bb1e954e99e51544353eff4ceb8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 23:16:02 -0400 Subject: [PATCH 0515/1217] make utility function private --- src/USER-COLVARS/ndx_group.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/USER-COLVARS/ndx_group.h b/src/USER-COLVARS/ndx_group.h index ceca1f9570..944638017d 100644 --- a/src/USER-COLVARS/ndx_group.h +++ b/src/USER-COLVARS/ndx_group.h @@ -31,6 +31,7 @@ class Ndx2Group : protected Pointers { public: Ndx2Group(class LAMMPS *lmp) : Pointers(lmp) {}; void command(int, char **); + private: void create(const std::string &, const std::vector &); }; From d8c68dec6f9f38e162cf428a231c70c44bc866ae Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 23:32:26 -0400 Subject: [PATCH 0516/1217] whitespace fixes --- doc/src/Build_extras.rst | 8 ++++---- src/COMPRESS/gz_file_writer.cpp | 2 +- src/MC/fix_charge_regulation.cpp | 2 +- src/USER-PACE/README | 20 ++++++++++---------- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 12bb33f264..d375d33e56 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -1253,8 +1253,8 @@ be built for the most part with all major versions of the C++ language. USER-PACE package ----------------------------- -This package requires a library that can be downloaded and built -in lib/pace or somewhere else, which must be done before building +This package requires a library that can be downloaded and built +in lib/pace or somewhere else, which must be done before building LAMMPS with this package. The code for the library can be found at: `https://github.com/ICAMS/lammps-user-pace/ `_ @@ -1276,8 +1276,8 @@ at: `https://github.com/ICAMS/lammps-user-pace/ triclinic; + triclinic = domain->triclinic; int ipe = modify->find_compute("thermo_pe"); c_pe = modify->compute[ipe]; diff --git a/src/USER-PACE/README b/src/USER-PACE/README index 3d85c806e9..c701a615f7 100644 --- a/src/USER-PACE/README +++ b/src/USER-PACE/README @@ -1,23 +1,23 @@ -The USER-PACE package provides the pace pair style, -an efficient implementation of the Atomic Cluster Expansion +The USER-PACE package provides the pace pair style, +an efficient implementation of the Atomic Cluster Expansion potential (ACE). -ACE is a methodology for deriving a highly accurate classical -potential fit to a large archive of quantum mechanical (DFT) data. +ACE is a methodology for deriving a highly accurate classical +potential fit to a large archive of quantum mechanical (DFT) data. This package was written by Yury Lysogorskiy and others -at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, +at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, Ruhr University Bochum, Germany (http://www.icams.de). -This package requires a library that can be downloaded and built -in lib/pace or somewhere else, which must be done before building -LAMMPS with this package. Details of the download, build, and -install process for this package using traditional make (not CMake) +This package requires a library that can be downloaded and built +in lib/pace or somewhere else, which must be done before building +LAMMPS with this package. Details of the download, build, and +install process for this package using traditional make (not CMake) are given in the lib/pace/README file, and scripts are provided to help automate the process. Also see the LAMMPS manual for general information on building LAMMPS with external libraries using either traditional make or CMake. -More information about the USER-PACE implementation of ACE +More information about the USER-PACE implementation of ACE is available here: https://github.com/ICAMS/lammps-user-pace From 02612047c34aac6dd90082b7c90c85df001cdf9e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 23:57:30 -0400 Subject: [PATCH 0517/1217] must set CMAKE_EXPORT_COMPILE_COMMANDS ON for using iwyu --- cmake/CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index f567a15d25..a11c7575d2 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -269,6 +269,7 @@ endif() set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool") mark_as_advanced(ENABLE_IWYU) if(ENABLE_IWYU) + set(CMAKE_EXPORT_COMPILE_COMMANDS ON) find_program(IWYU_EXE NAMES include-what-you-use iwyu) find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py) if (IWYU_EXE AND IWYU_TOOL) From fab571cf6bc1a1ba3aaa5b261f0244fda49a46b7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 00:32:11 -0400 Subject: [PATCH 0518/1217] IWYU reported header updates --- src/body.cpp | 1 - src/compute.cpp | 1 - src/compute_chunk_spread_atom.cpp | 2 ++ src/compute_reduce.cpp | 2 ++ src/compute_temp_region.cpp | 9 ++++----- src/fix.cpp | 1 - src/fix_controller.cpp | 2 -- src/fix_enforce2d.cpp | 7 +++---- src/fix_lineforce.cpp | 1 - src/fix_nph_sphere.cpp | 2 -- src/fix_npt_sphere.cpp | 2 -- src/fix_nve_limit.cpp | 11 +++++------ src/fix_nve_noforce.cpp | 6 +++--- src/fix_planeforce.cpp | 1 - src/fix_store_force.cpp | 8 ++++---- src/fix_vector.cpp | 2 -- src/group.cpp | 1 - src/imbalance_store.cpp | 2 -- src/imbalance_var.cpp | 2 -- src/info.cpp | 1 - src/library.cpp | 1 - src/math_eigen.cpp | 4 +++- src/math_special.cpp | 2 -- src/my_pool_chunk.cpp | 1 - src/npair_full_bin_atomonly.cpp | 6 +++--- src/npair_half_bin_atomonly_newton.cpp | 6 +++--- src/npair_half_size_bin_newtoff.cpp | 6 +++--- src/npair_half_size_bin_newton.cpp | 6 +++--- src/npair_half_size_bin_newton_tri.cpp | 6 +++--- src/npair_half_size_multi_newtoff.cpp | 6 +++--- src/npair_half_size_multi_newton.cpp | 6 +++--- src/npair_half_size_multi_newton_tri.cpp | 6 +++--- src/npair_half_size_nsq_newtoff.cpp | 6 +++--- src/npair_half_size_nsq_newton.cpp | 6 +++--- src/npair_halffull_newtoff.cpp | 6 +++--- src/npair_halffull_newton.cpp | 6 +++--- src/npair_skip.cpp | 6 +++--- src/npair_skip_respa.cpp | 6 +++--- src/npair_skip_size.cpp | 6 +++--- src/npair_skip_size_off2on.cpp | 6 +++--- src/npair_skip_size_off2on_oneside.cpp | 6 +++--- src/output.cpp | 3 --- src/pair_lj96_cut.cpp | 15 +++++++-------- src/pair_lj_relres.cpp | 1 - src/reader.cpp | 2 -- src/region_sphere.cpp | 1 - src/tokenizer.cpp | 1 - src/universe.cpp | 2 -- src/variable.cpp | 1 - src/write_coeff.cpp | 1 - src/write_data.cpp | 1 - src/write_restart.cpp | 1 - 52 files changed, 84 insertions(+), 119 deletions(-) diff --git a/src/body.cpp b/src/body.cpp index 89bb2fc1d9..2c4121b0cc 100644 --- a/src/body.cpp +++ b/src/body.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "body.h" -#include using namespace LAMMPS_NS; diff --git a/src/compute.cpp b/src/compute.cpp index 81e317076c..46bd0d0fc8 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -22,7 +22,6 @@ #include "modify.h" #include -#include using namespace LAMMPS_NS; diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp index d817141064..f552454e72 100644 --- a/src/compute_chunk_spread_atom.cpp +++ b/src/compute_chunk_spread_atom.cpp @@ -23,6 +23,8 @@ #include "modify.h" #include "update.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index 30b4fcb98a..6e961df47a 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -25,6 +25,8 @@ #include "update.h" #include "variable.h" +#include + using namespace LAMMPS_NS; #define BIG 1.0e20 diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index 036f118a30..535a0166c5 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -13,15 +13,14 @@ #include "compute_temp_region.h" -#include #include "atom.h" -#include "update.h" -#include "force.h" #include "domain.h" -#include "region.h" +#include "error.h" +#include "force.h" #include "group.h" #include "memory.h" -#include "error.h" +#include "region.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/fix.cpp b/src/fix.cpp index 32a76cc125..14c04bf4b5 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -21,7 +21,6 @@ #include "memory.h" #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp index 21d1ccf751..c611dee271 100644 --- a/src/fix_controller.cpp +++ b/src/fix_controller.cpp @@ -21,8 +21,6 @@ #include "update.h" #include "variable.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index 1284a9b78c..11e041fcf4 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -12,14 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_enforce2d.h" -#include + #include "atom.h" -#include "update.h" #include "domain.h" +#include "error.h" #include "modify.h" #include "respa.h" -#include "error.h" - +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp index 6a77442ea4..d95aacfd93 100644 --- a/src/fix_lineforce.cpp +++ b/src/fix_lineforce.cpp @@ -19,7 +19,6 @@ #include "update.h" #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp index 20e072d5b5..1266cb2b9d 100644 --- a/src/fix_nph_sphere.cpp +++ b/src/fix_nph_sphere.cpp @@ -16,8 +16,6 @@ #include "error.h" #include "modify.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp index a6dfeba425..8bbd43d4cf 100644 --- a/src/fix_npt_sphere.cpp +++ b/src/fix_npt_sphere.cpp @@ -16,8 +16,6 @@ #include "error.h" #include "modify.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp index 58db5e25d9..58dc023991 100644 --- a/src/fix_nve_limit.cpp +++ b/src/fix_nve_limit.cpp @@ -13,16 +13,15 @@ #include "fix_nve_limit.h" -#include -#include #include "atom.h" -#include "force.h" -#include "update.h" -#include "respa.h" -#include "modify.h" #include "comm.h" #include "error.h" +#include "force.h" +#include "modify.h" +#include "respa.h" +#include "update.h" +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp index 61528a0024..e6bca3b608 100644 --- a/src/fix_nve_noforce.cpp +++ b/src/fix_nve_noforce.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "fix_nve_noforce.h" -#include + #include "atom.h" -#include "update.h" -#include "respa.h" #include "error.h" +#include "respa.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp index 783d26ac9e..fe6f3d6500 100644 --- a/src/fix_planeforce.cpp +++ b/src/fix_planeforce.cpp @@ -19,7 +19,6 @@ #include "update.h" #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp index 1541294f6c..7ebd4db75a 100644 --- a/src/fix_store_force.cpp +++ b/src/fix_store_force.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_store_force.h" -#include + #include "atom.h" -#include "update.h" -#include "respa.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "respa.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index afd3778841..71a8bb3d3c 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -22,8 +22,6 @@ #include "update.h" #include "variable.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/group.cpp b/src/group.cpp index ebab78dd0f..0143008a72 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -35,7 +35,6 @@ #include #include #include -#include using namespace LAMMPS_NS; diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp index 879b434bfd..e72ef4d50b 100644 --- a/src/imbalance_store.cpp +++ b/src/imbalance_store.cpp @@ -16,8 +16,6 @@ #include "atom.h" #include "error.h" -#include - using namespace LAMMPS_NS; /* -------------------------------------------------------------------- */ diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp index d2a4f0d691..64f98a6a26 100644 --- a/src/imbalance_var.cpp +++ b/src/imbalance_var.cpp @@ -20,8 +20,6 @@ #include "memory.h" #include "variable.h" -#include - using namespace LAMMPS_NS; /* -------------------------------------------------------------------- */ diff --git a/src/info.cpp b/src/info.cpp index 948073bb10..f1ee327191 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -39,7 +39,6 @@ #include "pair.h" #include "pair_hybrid.h" #include "region.h" -#include "universe.h" #include "update.h" #include "variable.h" diff --git a/src/library.cpp b/src/library.cpp index 300aafc293..c51006f8d8 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -31,7 +31,6 @@ #include "group.h" #include "info.h" #include "input.h" -#include "integrate.h" #include "memory.h" #include "modify.h" #include "molecule.h" diff --git a/src/math_eigen.cpp b/src/math_eigen.cpp index ab00e42ae0..10caccd0e5 100644 --- a/src/math_eigen.cpp +++ b/src/math_eigen.cpp @@ -18,7 +18,9 @@ #include "math_eigen.h" #include "math_eigen_impl.h" -#include +#include +#include +#include using std::vector; using std::array; diff --git a/src/math_special.cpp b/src/math_special.cpp index 243d5a05f3..8d48158e72 100644 --- a/src/math_special.cpp +++ b/src/math_special.cpp @@ -4,8 +4,6 @@ #include // IWYU pragma: keep #include -#include "error.h" - using namespace LAMMPS_NS; static constexpr int nmaxfactorial = 167; diff --git a/src/my_pool_chunk.cpp b/src/my_pool_chunk.cpp index d866804adc..d824b0557b 100644 --- a/src/my_pool_chunk.cpp +++ b/src/my_pool_chunk.cpp @@ -14,7 +14,6 @@ #include "my_pool_chunk.h" #include -#include #if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32) #define LAMMPS_MEMALIGN 64 diff --git a/src/npair_full_bin_atomonly.cpp b/src/npair_full_bin_atomonly.cpp index 4e05c2c17a..8ace197e30 100644 --- a/src/npair_full_bin_atomonly.cpp +++ b/src/npair_full_bin_atomonly.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin_atomonly.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_bin_atomonly_newton.cpp b/src/npair_half_bin_atomonly_newton.cpp index 2dd0bd0b96..2007bda728 100644 --- a/src/npair_half_bin_atomonly_newton.cpp +++ b/src/npair_half_bin_atomonly_newton.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_atomonly_newton.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_bin_newtoff.cpp b/src/npair_half_size_bin_newtoff.cpp index 2d406d533c..5b9eee3672 100644 --- a/src/npair_half_size_bin_newtoff.cpp +++ b/src/npair_half_size_bin_newtoff.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_bin_newtoff.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_bin_newton.cpp b/src/npair_half_size_bin_newton.cpp index 820b293414..9cf4e744ab 100644 --- a/src/npair_half_size_bin_newton.cpp +++ b/src/npair_half_size_bin_newton.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_bin_newton.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_bin_newton_tri.cpp b/src/npair_half_size_bin_newton_tri.cpp index ea878ef440..83f903c864 100644 --- a/src/npair_half_size_bin_newton_tri.cpp +++ b/src/npair_half_size_bin_newton_tri.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_bin_newton_tri.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp index d57542f562..f1bc93de38 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_multi_newtoff.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index 01065876af..22a02899ca 100644 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_multi_newton.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 361c0ba260..268ca81f3d 100644 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_multi_newton_tri.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_nsq_newtoff.cpp b/src/npair_half_size_nsq_newtoff.cpp index 38594ebcb1..79302042a6 100644 --- a/src/npair_half_size_nsq_newtoff.cpp +++ b/src/npair_half_size_nsq_newtoff.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_nsq_newtoff.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" +#include "error.h" #include "group.h" #include "my_page.h" -#include "error.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_nsq_newton.cpp b/src/npair_half_size_nsq_newton.cpp index 9010ca9a86..1ac6223afa 100644 --- a/src/npair_half_size_nsq_newton.cpp +++ b/src/npair_half_size_nsq_newton.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_nsq_newton.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" +#include "error.h" #include "group.h" #include "my_page.h" -#include "error.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_halffull_newtoff.cpp b/src/npair_halffull_newtoff.cpp index e2965b4a46..52f981e843 100644 --- a/src/npair_halffull_newtoff.cpp +++ b/src/npair_halffull_newtoff.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_newtoff.h" -#include "neigh_list.h" -#include "atom_vec.h" -#include "my_page.h" + #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_halffull_newton.cpp b/src/npair_halffull_newton.cpp index 99b5493f3e..cf15af8f18 100644 --- a/src/npair_halffull_newton.cpp +++ b/src/npair_halffull_newton.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_newton.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_skip.cpp b/src/npair_skip.cpp index 45540ab2fa..6046464ecf 100644 --- a/src/npair_skip.cpp +++ b/src/npair_skip.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_skip.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_skip_respa.cpp b/src/npair_skip_respa.cpp index 3479a5d8ce..d24a30794e 100644 --- a/src/npair_skip_respa.cpp +++ b/src/npair_skip_respa.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_skip_respa.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_skip_size.cpp b/src/npair_skip_size.cpp index d3810e6acc..40b70aed21 100644 --- a/src/npair_skip_size.cpp +++ b/src/npair_skip_size.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_skip_size.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_skip_size_off2on.cpp b/src/npair_skip_size_off2on.cpp index 0d7630aaa9..994910852b 100644 --- a/src/npair_skip_size_off2on.cpp +++ b/src/npair_skip_size_off2on.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_skip_size_off2on.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_skip_size_off2on_oneside.cpp b/src/npair_skip_size_off2on_oneside.cpp index eab98de035..30ee2ff6ba 100644 --- a/src/npair_skip_size_off2on_oneside.cpp +++ b/src/npair_skip_size_off2on_oneside.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "npair_skip_size_off2on_oneside.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" #include "domain.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/output.cpp b/src/output.cpp index 988ef04409..d7be9b8cd6 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -14,18 +14,15 @@ #include "output.h" #include "style_dump.h" // IWYU pragma: keep -#include "atom.h" #include "comm.h" #include "domain.h" #include "dump.h" #include "error.h" -#include "force.h" #include "group.h" #include "info.h" #include "input.h" #include "memory.h" #include "modify.h" -#include "neighbor.h" #include "thermo.h" #include "update.h" #include "variable.h" diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index 65f2d40e00..92cbb47440 100644 --- a/src/pair_lj96_cut.cpp +++ b/src/pair_lj96_cut.cpp @@ -17,20 +17,19 @@ #include "pair_lj96_cut.h" -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "respa.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_relres.cpp b/src/pair_lj_relres.cpp index 1f40d03aa9..306b68684e 100644 --- a/src/pair_lj_relres.cpp +++ b/src/pair_lj_relres.cpp @@ -26,7 +26,6 @@ #include "memory.h" #include -#include using namespace LAMMPS_NS; diff --git a/src/reader.cpp b/src/reader.cpp index c22a9f7e5d..ba172f58ee 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -15,8 +15,6 @@ #include "error.h" -#include - using namespace LAMMPS_NS; // only proc 0 calls methods of this class, except for constructor/destructor diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp index 8921cbd456..3a5a51834b 100644 --- a/src/region_sphere.cpp +++ b/src/region_sphere.cpp @@ -19,7 +19,6 @@ #include "variable.h" #include -#include using namespace LAMMPS_NS; diff --git a/src/tokenizer.cpp b/src/tokenizer.cpp index d26a5199f9..ea8ff2ce43 100644 --- a/src/tokenizer.cpp +++ b/src/tokenizer.cpp @@ -19,7 +19,6 @@ #include "utils.h" #include "fmt/format.h" -#include #include using namespace LAMMPS_NS; diff --git a/src/universe.cpp b/src/universe.cpp index a7fa8fc2e2..79de6948df 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -15,9 +15,7 @@ #include "error.h" #include "memory.h" -#include "version.h" -#include #include using namespace LAMMPS_NS; diff --git a/src/variable.cpp b/src/variable.cpp index d903490219..f66b99d6e5 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -40,7 +40,6 @@ #include #include #include -#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 485bc3b29b..79a99502a6 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -22,7 +22,6 @@ #include "force.h" #include "improper.h" #include "pair.h" -#include "universe.h" #include #include diff --git a/src/write_data.cpp b/src/write_data.cpp index 6d10359e8b..8ec24bb4cf 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -29,7 +29,6 @@ #include "output.h" #include "pair.h" #include "thermo.h" -#include "universe.h" #include "update.h" #include diff --git a/src/write_restart.cpp b/src/write_restart.cpp index afe1d2d528..795e93b05e 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -32,7 +32,6 @@ #include "output.h" #include "pair.h" #include "thermo.h" -#include "universe.h" #include "update.h" #include From b9cb63ae56832ae2c10e102280032bee7f71cbea Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 00:47:58 -0400 Subject: [PATCH 0519/1217] remove redundant check --- src/pair_hybrid_scaled.cpp | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index 7a30c9a3ee..cdbccbf7c7 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -457,8 +457,6 @@ void PairHybridScaled::coeff(int narg, char **arg) if (multiple[m]) { multflag = 1; if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients"); - if (!isdigit(arg[3][0])) - error->all(FLERR,"Incorrect args for pair coefficients"); int index = utils::inumeric(FLERR,arg[3],false,lmp); if (index == multiple[m]) break; else continue; From bddc6d58201b3ef4618de87732118341a8a34a05 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 09:58:19 -0400 Subject: [PATCH 0520/1217] make installation procedure consistent with install.py --- python/setup.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/python/setup.py b/python/setup.py index aff0b14671..2f2b67b6f1 100644 --- a/python/setup.py +++ b/python/setup.py @@ -1,7 +1,8 @@ # this only installs the LAMMPS python package # it assumes the LAMMPS shared library is already installed from distutils.core import setup -import os +from sys import version_info +import os,time LAMMPS_PYTHON_DIR = os.path.dirname(os.path.realpath(__file__)) LAMMPS_DIR = os.path.dirname(LAMMPS_PYTHON_DIR) @@ -12,7 +13,13 @@ def get_lammps_version(): line = f.readline() start_pos = line.find('"')+1 end_pos = line.find('"', start_pos) - return "".join(line[start_pos:end_pos].split()) + t = time.strptime("".join(line[start_pos:end_pos].split()), "%d%b%Y") + return "{}.{}.{}".format(t.tm_year,t.tm_mon,t.tm_mday) + +if version_info.major >= 3: + pkgs = ['lammps', 'lammps.mliap'] +else: + pkgs = ['lammps'] setup( name = "lammps", @@ -22,5 +29,5 @@ setup( url = "https://lammps.sandia.gov", description = "LAMMPS Molecular Dynamics Python package", license = "GPL", - packages=["lammps","lammps.mliap"], + packages=pkgs, ) From 82337c8cc574bc454a5ceb4618151fdaf04e24b9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 09:58:41 -0400 Subject: [PATCH 0521/1217] silence compiler warnings when compiling with python 2 --- src/PYTHON/fix_python_invoke.cpp | 6 ++++-- src/PYTHON/fix_python_move.cpp | 14 +++++++------- src/PYTHON/pair_python.cpp | 4 ++-- 3 files changed, 13 insertions(+), 11 deletions(-) diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 6483e21f91..7d981a749e 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -92,8 +92,9 @@ int FixPythonInvoke::setmask() void FixPythonInvoke::end_of_step() { PyUtils::GIL lock; + char fmt[] = "O"; - PyObject * result = PyObject_CallFunction((PyObject*)pFunc, "O", (PyObject*)lmpPtr); + PyObject * result = PyObject_CallFunction((PyObject*)pFunc, fmt, (PyObject*)lmpPtr); if (!result) { PyUtils::Print_Errors(); @@ -110,8 +111,9 @@ void FixPythonInvoke::post_force(int vflag) if (update->ntimestep % nevery != 0) return; PyUtils::GIL lock; + char fmt[] = "Oi"; - PyObject * result = PyObject_CallFunction((PyObject*)pFunc, "Oi", (PyObject*)lmpPtr, vflag); + PyObject * result = PyObject_CallFunction((PyObject*)pFunc, fmt, (PyObject*)lmpPtr, vflag); if (!result) { PyUtils::Print_Errors(); diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index e04a32afe4..8ec2e1b74d 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -75,7 +75,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) : } PyObject *ptr = PY_VOID_POINTER(lmp); - PyObject *py_move_obj = PyObject_CallFunction(py_move_type, "O", ptr); + PyObject *py_move_obj = PyObject_CallFunction(py_move_type, (char *)"O", ptr); Py_CLEAR(ptr); if (!py_move_obj) { @@ -112,7 +112,7 @@ int FixPythonMove::setmask() void FixPythonMove::init() { PyUtils::GIL lock; - PyObject * result = PyObject_CallMethod((PyObject *)py_move, "init", nullptr); + PyObject * result = PyObject_CallMethod((PyObject *)py_move, (char *)"init", nullptr); if (!result) { PyUtils::Print_Errors(); @@ -126,7 +126,7 @@ void FixPythonMove::init() void FixPythonMove::initial_integrate(int vflag) { PyUtils::GIL lock; - PyObject * result = PyObject_CallMethod((PyObject*)py_move, "initial_integrate", "i", vflag); + PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"initial_integrate", (char *)"i", vflag); if (!result) { PyUtils::Print_Errors(); @@ -140,7 +140,7 @@ void FixPythonMove::initial_integrate(int vflag) void FixPythonMove::final_integrate() { PyUtils::GIL lock; - PyObject * result = PyObject_CallMethod((PyObject*)py_move, "final_integrate", nullptr); + PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"final_integrate", nullptr); if (!result) { PyUtils::Print_Errors(); @@ -154,7 +154,7 @@ void FixPythonMove::final_integrate() void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop) { PyUtils::GIL lock; - PyObject * result = PyObject_CallMethod((PyObject*)py_move, "initial_integrate_respa", "iii", vflag, ilevel, iloop); + PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"initial_integrate_respa", (char *)"iii", vflag, ilevel, iloop); if (!result) { PyUtils::Print_Errors(); @@ -168,7 +168,7 @@ void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop) void FixPythonMove::final_integrate_respa(int ilevel, int iloop) { PyUtils::GIL lock; - PyObject * result = PyObject_CallMethod((PyObject*)py_move, "final_integrate_respa", "ii", ilevel, iloop); + PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"final_integrate_respa", (char *)"ii", ilevel, iloop); if (!result) { PyUtils::Print_Errors(); @@ -182,7 +182,7 @@ void FixPythonMove::final_integrate_respa(int ilevel, int iloop) void FixPythonMove::reset_dt() { PyUtils::GIL lock; - PyObject * result = PyObject_CallMethod((PyObject*)py_move, "reset_dt", nullptr); + PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"reset_dt", nullptr); if (!result) { PyUtils::Print_Errors(); diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index b147c9cb79..5020119e0d 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -288,7 +288,7 @@ void PairPython::coeff(int narg, char **arg) py_potential = (void *) py_pair_instance; - PyObject *py_value = PyObject_CallMethod(py_pair_instance, "check_units", "s", update->unit_style); + PyObject *py_value = PyObject_CallMethod(py_pair_instance, (char *)"check_units", (char *)"s", update->unit_style); if (!py_value) { PyUtils::Print_Errors(); error->all(FLERR,"Calling 'check_units' function failed"); @@ -306,7 +306,7 @@ void PairPython::coeff(int narg, char **arg) } else skip_types[i] = 0; const int type = i; const char * name = arg[2+i]; - py_value = PyObject_CallMethod(py_pair_instance, "map_coeff", "si", name, type); + py_value = PyObject_CallMethod(py_pair_instance, (char *)"map_coeff", (char *)"si", name, type); if (!py_value) { PyUtils::Print_Errors(); error->all(FLERR,"Calling 'map_coeff' function failed"); From 208d9f1fce3b8cb7c2f3bca4dc93d746c38982ef Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 09:59:15 -0400 Subject: [PATCH 0522/1217] use safe fread function to silence compiler warnings --- src/pair_lj_relres.cpp | 30 +++++++++++++++--------------- src/pair_morse.cpp | 11 ++++++----- 2 files changed, 21 insertions(+), 20 deletions(-) diff --git a/src/pair_lj_relres.cpp b/src/pair_lj_relres.cpp index 306b68684e..2131907f3a 100644 --- a/src/pair_lj_relres.cpp +++ b/src/pair_lj_relres.cpp @@ -607,18 +607,18 @@ void PairLJRelRes::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilonf[i][j],sizeof(double),1,fp); - fread(&sigmaf[i][j],sizeof(double),1,fp); - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cutf_inner[i][j],sizeof(double),1,fp); - fread(&cutf[i][j],sizeof(double),1,fp); - fread(&cut_inner[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilonf[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&sigmaf[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cutf_inner[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cutf[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); } MPI_Bcast(&epsilonf[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigmaf[i][j],1,MPI_DOUBLE,0,world); @@ -654,12 +654,12 @@ void PairLJRelRes::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cutf_inner_global,sizeof(double),1,fp); - fread(&cutf_global,sizeof(double),1,fp); - fread(&cut_inner_global,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cutf_inner_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cutf_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); } MPI_Bcast(&cutf_inner_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cutf_global,1,MPI_DOUBLE,0,world); diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index 6c67a8ef55..e6d924dab6 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -13,14 +13,15 @@ #include "pair_morse.h" -#include -#include #include "atom.h" #include "comm.h" -#include "force.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; From 107d112265dab7c59fc672996b65a520180dbaac Mon Sep 17 00:00:00 2001 From: snikolo Date: Tue, 13 Apr 2021 09:43:28 -0600 Subject: [PATCH 0523/1217] updates for thermo energy output --- src/SPIN/fix_langevin_spin.cpp | 29 +++++++++++++++++++++++++++-- src/SPIN/fix_langevin_spin.h | 7 +++++-- 2 files changed, 32 insertions(+), 4 deletions(-) diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index 209eaa5632..b4de180406 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -35,6 +35,8 @@ #include "random_mars.h" #include "respa.h" #include "update.h" +#include "compute.h" +#include "group.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -51,6 +53,14 @@ FixLangevinSpin::FixLangevinSpin(LAMMPS *lmp, int narg, char **arg) : alpha_t = utils::numeric(FLERR,arg[4],false,lmp); seed = utils::inumeric(FLERR,arg[5],false,lmp); + dynamic_group_allow = 1; + scalar_flag = 1; + global_freq = 1; + extscalar = 1; + ecouple_flag = 1; + nevery = 1; + tallyflag = 1; + if (alpha_t < 0.0) { error->all(FLERR,"Illegal langevin/spin command"); } else if (alpha_t == 0.0) { @@ -143,7 +153,7 @@ void FixLangevinSpin::add_tdamping(double spi[3], double fmi[3]) /* ---------------------------------------------------------------------- */ -void FixLangevinSpin::add_temperature(double fmi[3]) +void FixLangevinSpin::add_temperature(int i, double spi[3], double fmi[3]) { // double rx = sigma*(2.0*random->uniform() - 1.0); // double ry = sigma*(2.0*random->uniform() - 1.0); @@ -151,7 +161,9 @@ void FixLangevinSpin::add_temperature(double fmi[3]) double rx = sigma*random->gaussian(); double ry = sigma*random->gaussian(); double rz = sigma*random->gaussian(); + double hbar = force->hplanck/MY_2PI; + energyS += 0.25*hbar*(rx*spi[0]+ry*spi[1]+rz*spi[2])*update->dt; // adding the random field fmi[0] += rx; @@ -172,6 +184,19 @@ void FixLangevinSpin::compute_single_langevin(int i, double spi[3], double fmi[3 int *mask = atom->mask; if (mask[i] & groupbit) { if (tdamp_flag) add_tdamping(spi,fmi); - if (temp_flag) add_temperature(fmi); + if (temp_flag) add_temperature(i,spi,fmi); } } + +/* ---------------------------------------------------------------------- */ + +double FixLangevinSpin::compute_scalar() +{ + if (!tallyflag) return 0.0; + + double energy_all; + MPI_Allreduce(&energyS,&energy_all,1,MPI_DOUBLE,MPI_SUM,world); + return -energy_all; +} + +/* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/fix_langevin_spin.h b/src/SPIN/fix_langevin_spin.h index 89267f7d4d..2a8a654597 100644 --- a/src/SPIN/fix_langevin_spin.h +++ b/src/SPIN/fix_langevin_spin.h @@ -34,8 +34,9 @@ class FixLangevinSpin : public Fix { void init(); void setup(int); void add_tdamping(double *, double *); // add transverse damping - void add_temperature(double *); // add temperature + void add_temperature(int, double *, double *); void compute_single_langevin(int, double *, double *); + virtual double compute_scalar(); protected: double alpha_t; // transverse mag. damping @@ -43,7 +44,9 @@ class FixLangevinSpin : public Fix { double temp; // spin bath temperature double D,sigma; // bath intensity var. double gil_factor; // gilbert's prefactor - + double energyS; + int nlocal_max; + int tallyflag; char *id_temp; class Compute *temperature; From 3b2c0871ccc766a4e66174880f4524c86079d435 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 14:53:03 -0400 Subject: [PATCH 0524/1217] add and use Neighbor::modify_params() convenience function --- src/MC/fix_charge_regulation.cpp | 9 +-------- src/MC/fix_gcmc.cpp | 9 +-------- src/MC/fix_widom.cpp | 9 +-------- src/USER-MISC/fix_srp.cpp | 12 +----------- src/neighbor.cpp | 16 ++++++++++++++++ src/neighbor.h | 1 + 6 files changed, 21 insertions(+), 35 deletions(-) diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 6775b4e4ca..17d3af3e34 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -187,14 +187,7 @@ void FixChargeRegulation::init() { // neighbor list exclusion setup // turn off interactions between group all and the exclusion group - int narg = 4; - char **arg = new char*[narg];; - arg[0] = (char *) "exclude"; - arg[1] = (char *) "group"; - arg[2] = (char *) group_id.c_str(); - arg[3] = (char *) "all"; - neighbor->modify_params(narg,arg); - delete [] arg; + neighbor->modify_params(fmt::format("exclude group {} all",group_id)); } // check that no deletable atoms are in atom->firstgroup diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index b946615b04..ff894d976b 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -580,14 +580,7 @@ void FixGCMC::init() // neighbor list exclusion setup // turn off interactions between group all and the exclusion group - int narg = 4; - char **arg = new char*[narg];; - arg[0] = (char *) "exclude"; - arg[1] = (char *) "group"; - arg[2] = (char *) group_id.c_str(); - arg[3] = (char *) "all"; - neighbor->modify_params(narg,arg); - delete [] arg; + neighbor->modify_params(fmt::format("exclude group {} all",group_id); } // create a new group for temporary use with selected molecules diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index e898196e14..65f00811c1 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -342,14 +342,7 @@ void FixWidom::init() // neighbor list exclusion setup // turn off interactions between group all and the exclusion group - int narg = 4; - char **arg = new char*[narg];; - arg[0] = (char *) "exclude"; - arg[1] = (char *) "group"; - arg[2] = (char *) group_id.c_str(); - arg[3] = (char *) "all"; - neighbor->modify_params(narg,arg); - delete [] arg; + neighbor->modify_params(fmt::format("exclude group {} all",group_id)); } // create a new group for temporary use with selected molecules diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index eb57da30e9..51047dfaa6 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -128,20 +128,10 @@ void FixSRP::init() // bond particles do not interact with other types // type bptype only interacts with itself - char* arg1[4]; - arg1[0] = (char *) "exclude"; - arg1[1] = (char *) "type"; - char c0[20]; - char c1[20]; - for (int z = 1; z < atom->ntypes; z++) { if (z == bptype) continue; - sprintf(c0, "%d", z); - arg1[2] = c0; - sprintf(c1, "%d", bptype); - arg1[3] = c1; - neighbor->modify_params(4, arg1); + neighbor->modify_params(fmt::format("exclude type {} {}",z,bptype)); } } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 704d94c77c..ee4226f43e 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -2356,6 +2356,22 @@ void Neighbor::modify_params(int narg, char **arg) } } +/* ---------------------------------------------------------------------- + convenience function to allow modifying parameters from a single string +------------------------------------------------------------------------- */ + +void Neighbor::modify_params(const std::string &modcmd) +{ + auto args = utils::split_words(modcmd); + char **newarg = new char*[args.size()]; + int i=0; + for (const auto &arg : args) { + newarg[i++] = (char *)arg.c_str(); + } + modify_params(args.size(),newarg); + delete[] newarg; +} + /* ---------------------------------------------------------------------- remove the first group-group exclusion matching group1, group2 ------------------------------------------------------------------------- */ diff --git a/src/neighbor.h b/src/neighbor.h index b9b40bcf1a..0babfae9ef 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -118,6 +118,7 @@ class Neighbor : protected Pointers { void set(int, char **); // set neighbor style and skin distance void reset_timestep(bigint); // reset of timestep counter void modify_params(int, char**); // modify params that control builds + void modify_params(const std::string &); // convenience overload void exclusion_group_group_delete(int, int); // rm a group-group exclusion int exclude_setting(); // return exclude value to accelerator pkg From 533739b1287e04e431ddca4966a6d547763b80e8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 14:53:51 -0400 Subject: [PATCH 0525/1217] avoid NULL pointer dereference / slience warnings issued by static code analysis --- src/MC/fix_charge_regulation.cpp | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 17d3af3e34..4e7e5ab5a0 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -349,7 +349,7 @@ void FixChargeRegulation::forward_acid() { double energy_before = energy_stored; double factor; - double *dummyp = nullptr; + double dummyp[3]; double pos[3]; pos[0] = 0; pos[1] = 0; @@ -408,7 +408,7 @@ void FixChargeRegulation::backward_acid() { double energy_before = energy_stored; double factor; int mask_tmp; - double *dummyp = nullptr; + double dummyp[3]; double pos[3]; pos[0] = 0; pos[1] = 0; @@ -481,7 +481,7 @@ void FixChargeRegulation::forward_base() { double energy_before = energy_stored; double factor; - double *dummyp = nullptr; + double dummyp[3]; double pos[3]; pos[0] = 0; pos[1] = 0; @@ -539,7 +539,7 @@ void FixChargeRegulation::backward_base() { double energy_before = energy_stored; double factor; - double *dummyp = nullptr; + double dummyp[3]; int mask_tmp; double pos[3]; pos[0] = 0; @@ -612,7 +612,7 @@ void FixChargeRegulation::forward_ions() { double energy_before = energy_stored; double factor; - double *dummyp = nullptr; + double dummyp[3]; int m1 = -1, m2 = -1; factor = volume_rx * volume_rx * c10pI_plus * c10pI_minus / ((1 + ncation) * (1 + nanion)); @@ -647,7 +647,7 @@ void FixChargeRegulation::backward_ions() { double energy_before = energy_stored; double factor; int mask1_tmp = 0, mask2_tmp = 0; - double *dummyp = nullptr; + double dummyp[3]; int m1 = -1, m2 = -1; m1 = get_random_particle(cation_type, +1, 0, dummyp); @@ -726,7 +726,7 @@ void FixChargeRegulation::forward_ions_multival() { double energy_before = energy_stored; double factor = 1; - double *dummyp = nullptr; + double dummyp[3]; int mm[salt_charge_ratio + 1];// particle ID array for all ions to be inserted if (salt_charge[0] <= -salt_charge[1]) { @@ -780,7 +780,7 @@ void FixChargeRegulation::backward_ions_multival() { double energy_before = energy_stored; double factor = 1; - double *dummyp = nullptr; // dummy pointer + double dummyp[3]; // dummy particle int mm[salt_charge_ratio + 1]; // particle ID array for all deleted ions double qq[salt_charge_ratio + 1]; // charge array for all deleted ions int mask_tmp[salt_charge_ratio + 1]; // temporary mask array From 680e6a389dac748000bf9a8e53a20b4e14cae26a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 14:54:04 -0400 Subject: [PATCH 0526/1217] use type cast consistently --- src/PYTHON/fix_python_invoke.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 7d981a749e..82baef909b 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -92,9 +92,8 @@ int FixPythonInvoke::setmask() void FixPythonInvoke::end_of_step() { PyUtils::GIL lock; - char fmt[] = "O"; - PyObject * result = PyObject_CallFunction((PyObject*)pFunc, fmt, (PyObject*)lmpPtr); + PyObject * result = PyObject_CallFunction((PyObject*)pFunc, (char *)"O", (PyObject*)lmpPtr); if (!result) { PyUtils::Print_Errors(); From 9dbdb4386b6e74f020c594218fa4a175e056dd54 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 14:54:47 -0400 Subject: [PATCH 0527/1217] fix typo --- src/MC/fix_gcmc.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index ff894d976b..3ab6327404 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -580,7 +580,7 @@ void FixGCMC::init() // neighbor list exclusion setup // turn off interactions between group all and the exclusion group - neighbor->modify_params(fmt::format("exclude group {} all",group_id); + neighbor->modify_params(fmt::format("exclude group {} all",group_id)); } // create a new group for temporary use with selected molecules From 8aed7e55b37752e574116e40d7210d63a99b4d32 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 14:59:37 -0400 Subject: [PATCH 0528/1217] add error check when updating variables in ::single() function --- src/pair_hybrid_scaled.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index cdbccbf7c7..de8801fe24 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -396,6 +396,9 @@ double PairHybridScaled::single(int i, int j, int itype, int jtype, double rsq, double *vals = new double[nvars]; for (i = 0; i < nvars; ++i) { j = input->variable->find(scalevars[i].c_str()); + if (j < 0) + error->all(FLERR,fmt::format("Variable '{}' not found when updating " + "scale factors",scalevars[i])); vals[i] = input->variable->compute_equal(j); } for (i = 0; i < nstyles; ++i) { From b53822da467caed956bb205562abe74bd407374b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 17:47:00 -0400 Subject: [PATCH 0529/1217] provide Command base class in command.h for deriving command styles from --- examples/plugins/helloplugin.cpp | 6 +- src/KIM/kim_command.h | 6 +- src/MESSAGE/message.h | 6 +- src/MESSAGE/server.h | 6 +- src/PLUGIN/plugin.cpp | 2 +- src/PLUGIN/plugin.h | 4 +- src/REPLICA/hyper.cpp | 2 +- src/REPLICA/hyper.h | 4 +- src/REPLICA/neb.cpp | 4 +- src/REPLICA/neb.h | 4 +- src/REPLICA/prd.cpp | 2 +- src/REPLICA/prd.h | 4 +- src/REPLICA/tad.cpp | 2 +- src/REPLICA/tad.h | 4 +- src/REPLICA/temper.cpp | 2 +- src/REPLICA/temper.h | 4 +- src/SPIN/neb_spin.cpp | 2 +- src/SPIN/neb_spin.h | 4 +- src/USER-COLVARS/group_ndx.h | 6 +- src/USER-COLVARS/ndx_group.h | 6 +- src/USER-MISC/temper_grem.cpp | 2 +- src/USER-MISC/temper_grem.h | 4 +- src/USER-MISC/temper_npt.cpp | 2 +- src/USER-MISC/temper_npt.h | 4 +- src/USER-PHONON/dynamical_matrix.cpp | 2 +- src/USER-PHONON/dynamical_matrix.h | 86 ++++++++++++++-------------- src/USER-PHONON/third_order.cpp | 2 +- src/USER-PHONON/third_order.h | 4 +- src/balance.cpp | 2 +- src/balance.h | 4 +- src/change_box.cpp | 2 +- src/change_box.h | 4 +- src/command.h | 29 ++++++++++ src/create_atoms.cpp | 2 +- src/create_atoms.h | 4 +- src/create_bonds.cpp | 2 +- src/create_bonds.h | 4 +- src/create_box.cpp | 12 ++-- src/create_box.h | 4 +- src/delete_atoms.cpp | 2 +- src/delete_atoms.h | 4 +- src/delete_bonds.cpp | 2 +- src/delete_bonds.h | 4 +- src/deprecated.h | 6 +- src/displace_atoms.cpp | 2 +- src/displace_atoms.h | 4 +- src/info.h | 6 +- src/minimize.cpp | 2 +- src/minimize.h | 4 +- src/read_data.cpp | 6 +- src/read_data.h | 4 +- src/read_dump.cpp | 6 +- src/read_dump.h | 4 +- src/read_restart.cpp | 2 +- src/read_restart.h | 4 +- src/replicate.cpp | 2 +- src/replicate.h | 4 +- src/rerun.cpp | 2 +- src/rerun.h | 4 +- src/reset_atom_ids.cpp | 2 +- src/reset_atom_ids.h | 4 +- src/reset_mol_ids.cpp | 2 +- src/reset_mol_ids.h | 4 +- src/run.cpp | 2 +- src/run.h | 4 +- src/set.h | 6 +- src/velocity.cpp | 2 +- src/velocity.h | 4 +- src/write_coeff.h | 6 +- src/write_data.cpp | 2 +- src/write_data.h | 4 +- src/write_dump.h | 6 +- src/write_restart.cpp | 2 +- src/write_restart.h | 4 +- 74 files changed, 203 insertions(+), 180 deletions(-) create mode 100644 src/command.h diff --git a/examples/plugins/helloplugin.cpp b/examples/plugins/helloplugin.cpp index 11f2cfb891..f453add374 100644 --- a/examples/plugins/helloplugin.cpp +++ b/examples/plugins/helloplugin.cpp @@ -2,16 +2,16 @@ #include "lammpsplugin.h" #include "comm.h" +#include "command.h" #include "error.h" -#include "pointers.h" #include "version.h" #include namespace LAMMPS_NS { - class Hello : protected Pointers { + class Hello : protected Command { public: - Hello(class LAMMPS *lmp) : Pointers(lmp) {}; + Hello(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); }; } diff --git a/src/KIM/kim_command.h b/src/KIM/kim_command.h index f327e4f2f3..64abeed9e0 100644 --- a/src/KIM/kim_command.h +++ b/src/KIM/kim_command.h @@ -62,13 +62,13 @@ CommandStyle(kim,KimCommand) #ifndef LMP_KIM_COMMAND_H #define LMP_KIM_COMMAND_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class KimCommand : protected Pointers { +class KimCommand : protected Command { public: - KimCommand(class LAMMPS *lmp) : Pointers(lmp) {}; + KimCommand(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); }; diff --git a/src/MESSAGE/message.h b/src/MESSAGE/message.h index f8b2d47a21..c499ff6537 100644 --- a/src/MESSAGE/message.h +++ b/src/MESSAGE/message.h @@ -20,13 +20,13 @@ CommandStyle(message,Message) #ifndef LMP_MESSAGE_H #define LMP_MESSAGE_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Message : protected Pointers { +class Message : protected Command { public: - Message(class LAMMPS *lmp) : Pointers(lmp) {}; + Message(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); private: diff --git a/src/MESSAGE/server.h b/src/MESSAGE/server.h index 579f6ab6f1..63191ccf33 100644 --- a/src/MESSAGE/server.h +++ b/src/MESSAGE/server.h @@ -20,13 +20,13 @@ CommandStyle(server,Server) #ifndef LMP_SERVER_H #define LMP_SERVER_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Server : protected Pointers { +class Server : protected Command { public: - Server(class LAMMPS *lmp) : Pointers(lmp) {}; + Server(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); }; diff --git a/src/PLUGIN/plugin.cpp b/src/PLUGIN/plugin.cpp index b52e1a1959..a2f74060f1 100644 --- a/src/PLUGIN/plugin.cpp +++ b/src/PLUGIN/plugin.cpp @@ -41,7 +41,7 @@ namespace LAMMPS_NS /* ---------------------------------------------------------------------- */ - Plugin::Plugin(LAMMPS *lmp) : Pointers(lmp) {} + Plugin::Plugin(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/PLUGIN/plugin.h b/src/PLUGIN/plugin.h index 946b08db1a..61355f4113 100644 --- a/src/PLUGIN/plugin.h +++ b/src/PLUGIN/plugin.h @@ -21,12 +21,12 @@ CommandStyle(plugin,Plugin) #define LMP_PLUGIN_H #include "lammpsplugin.h" -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { - class Plugin : protected Pointers { + class Plugin : protected Command { public: Plugin(class LAMMPS *); void command(int, char **); diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp index 5a9cf8520e..8eb1c143e9 100644 --- a/src/REPLICA/hyper.cpp +++ b/src/REPLICA/hyper.cpp @@ -38,7 +38,7 @@ enum{NOHYPER,GLOBAL,LOCAL}; /* ---------------------------------------------------------------------- */ -Hyper::Hyper(LAMMPS *lmp) : Pointers(lmp), dumplist(nullptr) {} +Hyper::Hyper(LAMMPS *lmp) : Command(lmp), dumplist(nullptr) {} /* ---------------------------------------------------------------------- perform hyperdynamics simulation diff --git a/src/REPLICA/hyper.h b/src/REPLICA/hyper.h index 1b05172bcf..faad58994b 100644 --- a/src/REPLICA/hyper.h +++ b/src/REPLICA/hyper.h @@ -20,11 +20,11 @@ CommandStyle(hyper,Hyper) #ifndef LMP_HYPER_H #define LMP_HYPER_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Hyper : protected Pointers { +class Hyper : protected Command { public: Hyper(class LAMMPS *); ~Hyper() {} diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index a6a70fde38..7183bdd168 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -42,7 +42,7 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -NEB::NEB(LAMMPS *lmp) : Pointers(lmp), all(nullptr), rdist(nullptr) {} +NEB::NEB(LAMMPS *lmp) : Command(lmp), all(nullptr), rdist(nullptr) {} /* ---------------------------------------------------------------------- internal NEB constructor, called from TAD @@ -50,7 +50,7 @@ NEB::NEB(LAMMPS *lmp) : Pointers(lmp), all(nullptr), rdist(nullptr) {} NEB::NEB(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in, int n2steps_in, int nevery_in, double *buf_init, double *buf_final) - : Pointers(lmp), all(nullptr), rdist(nullptr) + : Command(lmp), all(nullptr), rdist(nullptr) { double delx,dely,delz; diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h index b53992711c..d8a9d5d3e4 100644 --- a/src/REPLICA/neb.h +++ b/src/REPLICA/neb.h @@ -20,11 +20,11 @@ CommandStyle(neb,NEB) #ifndef LMP_NEB_H #define LMP_NEB_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class NEB : protected Pointers { +class NEB : protected Command { public: NEB(class LAMMPS *); NEB(class LAMMPS *, double, double, int, int, int, double *, double *); diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index 40e5fc8833..2ba0340109 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -46,7 +46,7 @@ enum{SINGLE_PROC_DIRECT,SINGLE_PROC_MAP,MULTI_PROC}; /* ---------------------------------------------------------------------- */ -PRD::PRD(LAMMPS *lmp) : Pointers(lmp) {} +PRD::PRD(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- perform PRD simulation on one or more replicas diff --git a/src/REPLICA/prd.h b/src/REPLICA/prd.h index 3539987093..b331f7dc02 100644 --- a/src/REPLICA/prd.h +++ b/src/REPLICA/prd.h @@ -20,11 +20,11 @@ CommandStyle(prd,PRD) #ifndef LMP_PRD_H #define LMP_PRD_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class PRD : protected Pointers { +class PRD : protected Command { public: PRD(class LAMMPS *); ~PRD() {} diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index 0bab7a31c8..a849e7a242 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -43,7 +43,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -TAD::TAD(LAMMPS *lmp) : Pointers(lmp) {} +TAD::TAD(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/REPLICA/tad.h b/src/REPLICA/tad.h index d44b226643..3a525146a6 100644 --- a/src/REPLICA/tad.h +++ b/src/REPLICA/tad.h @@ -20,11 +20,11 @@ CommandStyle(tad,TAD) #ifndef LMP_TAD_H #define LMP_TAD_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class TAD : protected Pointers { +class TAD : protected Command { public: TAD(class LAMMPS *); ~TAD(); diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index 63b34b9b1d..d3894060a3 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -40,7 +40,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Temper::Temper(LAMMPS *lmp) : Pointers(lmp) {} +Temper::Temper(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/REPLICA/temper.h b/src/REPLICA/temper.h index 883ec30b94..ce7944da95 100644 --- a/src/REPLICA/temper.h +++ b/src/REPLICA/temper.h @@ -20,11 +20,11 @@ CommandStyle(temper,Temper) #ifndef LMP_TEMPER_H #define LMP_TEMPER_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Temper : protected Pointers { +class Temper : protected Command { public: Temper(class LAMMPS *); ~Temper(); diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index cbb495db8e..88a0ffc402 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -67,7 +67,7 @@ static const char cite_neb_spin[] = /* ---------------------------------------------------------------------- */ -NEBSpin::NEBSpin(LAMMPS *lmp) : Pointers(lmp) { +NEBSpin::NEBSpin(LAMMPS *lmp) : Command(lmp) { if (lmp->citeme) lmp->citeme->add(cite_neb_spin); } diff --git a/src/SPIN/neb_spin.h b/src/SPIN/neb_spin.h index 568eca0957..3dbae09297 100644 --- a/src/SPIN/neb_spin.h +++ b/src/SPIN/neb_spin.h @@ -20,11 +20,11 @@ CommandStyle(neb/spin,NEBSpin) #ifndef LMP_NEB_SPIN_H #define LMP_NEB_SPIN_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class NEBSpin : protected Pointers { +class NEBSpin : protected Command { public: NEBSpin(class LAMMPS *); ~NEBSpin(); diff --git a/src/USER-COLVARS/group_ndx.h b/src/USER-COLVARS/group_ndx.h index fa15f0e82e..46ba86c860 100644 --- a/src/USER-COLVARS/group_ndx.h +++ b/src/USER-COLVARS/group_ndx.h @@ -22,13 +22,13 @@ CommandStyle(group2ndx,Group2Ndx) #ifndef LMP_GROUP_NDX_H #define LMP_GROUP_NDX_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Group2Ndx : protected Pointers { +class Group2Ndx : protected Command { public: - Group2Ndx(class LAMMPS *lmp) : Pointers(lmp) {}; + Group2Ndx(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); private: void write_group(FILE *, int); diff --git a/src/USER-COLVARS/ndx_group.h b/src/USER-COLVARS/ndx_group.h index ceca1f9570..1c881a65bf 100644 --- a/src/USER-COLVARS/ndx_group.h +++ b/src/USER-COLVARS/ndx_group.h @@ -22,14 +22,14 @@ CommandStyle(ndx2group,Ndx2Group) #ifndef LMP_NDX_GROUP_H #define LMP_NDX_GROUP_H -#include "pointers.h" +#include "command.h" #include namespace LAMMPS_NS { -class Ndx2Group : protected Pointers { +class Ndx2Group : protected Command { public: - Ndx2Group(class LAMMPS *lmp) : Pointers(lmp) {}; + Ndx2Group(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); void create(const std::string &, const std::vector &); }; diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp index 3b987aaad2..ee60ab375d 100644 --- a/src/USER-MISC/temper_grem.cpp +++ b/src/USER-MISC/temper_grem.cpp @@ -40,7 +40,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -TemperGrem::TemperGrem(LAMMPS *lmp) : Pointers(lmp) {} +TemperGrem::TemperGrem(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/temper_grem.h b/src/USER-MISC/temper_grem.h index f379814c61..b720aeb45c 100644 --- a/src/USER-MISC/temper_grem.h +++ b/src/USER-MISC/temper_grem.h @@ -20,11 +20,11 @@ CommandStyle(temper/grem,TemperGrem) #ifndef LMP_TEMPER_GREM_H #define LMP_TEMPER_GREM_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class TemperGrem : protected Pointers { +class TemperGrem : protected Command { public: TemperGrem(class LAMMPS *); ~TemperGrem(); diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp index 08fa2246c3..1ed55a9cf3 100644 --- a/src/USER-MISC/temper_npt.cpp +++ b/src/USER-MISC/temper_npt.cpp @@ -42,7 +42,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -TemperNPT::TemperNPT(LAMMPS *lmp) : Pointers(lmp) {} +TemperNPT::TemperNPT(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/temper_npt.h b/src/USER-MISC/temper_npt.h index 6beae68c6a..5c285f083c 100644 --- a/src/USER-MISC/temper_npt.h +++ b/src/USER-MISC/temper_npt.h @@ -21,11 +21,11 @@ CommandStyle(temper/npt,TemperNPT) #ifndef LMP_TEMPERNPT_H #define LMP_TEMPERNPT_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class TemperNPT : protected Pointers { +class TemperNPT : protected Command { public: TemperNPT(class LAMMPS *); ~TemperNPT(); diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp index 798b50fdf7..0476c734a5 100644 --- a/src/USER-PHONON/dynamical_matrix.cpp +++ b/src/USER-PHONON/dynamical_matrix.cpp @@ -32,7 +32,7 @@ enum{REGULAR,ESKM}; /* ---------------------------------------------------------------------- */ -DynamicalMatrix::DynamicalMatrix(LAMMPS *lmp) : Pointers(lmp), fp(nullptr) +DynamicalMatrix::DynamicalMatrix(LAMMPS *lmp) : Command(lmp), fp(nullptr) { external_force_clear = 1; } diff --git a/src/USER-PHONON/dynamical_matrix.h b/src/USER-PHONON/dynamical_matrix.h index 8ff11044ea..30baeda27f 100644 --- a/src/USER-PHONON/dynamical_matrix.h +++ b/src/USER-PHONON/dynamical_matrix.h @@ -11,62 +11,62 @@ CommandStyle(dynamical_matrix,DynamicalMatrix) #ifndef LMP_DYNAMICAL_MATRIX_H #define LMP_DYNAMICAL_MATRIX_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { - class DynamicalMatrix : protected Pointers { - public: - DynamicalMatrix(class LAMMPS *); - virtual ~DynamicalMatrix(); - void command(int, char **); - void setup(); +class DynamicalMatrix : protected Command { + public: + DynamicalMatrix(class LAMMPS *); + virtual ~DynamicalMatrix(); + void command(int, char **); + void setup(); - protected: - int eflag,vflag; // flags for energy/virial computation - int external_force_clear; // clear forces locally or externally + protected: + int eflag,vflag; // flags for energy/virial computation + int external_force_clear; // clear forces locally or externally - int triclinic; // 0 if domain is orthog, 1 if triclinic - int pairflag; + int triclinic; // 0 if domain is orthog, 1 if triclinic + int pairflag; - int pair_compute_flag; // 0 if pair->compute is skipped - int kspace_compute_flag; // 0 if kspace->compute is skipped + int pair_compute_flag; // 0 if pair->compute is skipped + int kspace_compute_flag; // 0 if kspace->compute is skipped - int nvec; // local atomic dof = length of xvec + int nvec; // local atomic dof = length of xvec - void update_force(); - void force_clear(); - virtual void openfile(const char* filename); + void update_force(); + void force_clear(); + virtual void openfile(const char* filename); - private: - void options(int, char **); - void calculateMatrix(); - void dynmat_clear(double **dynmat); - void create_groupmap(); - void writeMatrix(double **dynmat); - void convert_units(const char *style); - void displace_atom(int local_idx, int direction, int magnitude); + private: + void options(int, char **); + void calculateMatrix(); + void dynmat_clear(double **dynmat); + void create_groupmap(); + void writeMatrix(double **dynmat); + void convert_units(const char *style); + void displace_atom(int local_idx, int direction, int magnitude); - double conversion; - double conv_energy; - double conv_distance; - double conv_mass; - double del; - int igroup,groupbit; - bigint gcount; // number of atoms in group - bigint dynlen; // rank of dynamical matrix - int scaleflag; - int me; - bigint *groupmap; + double conversion; + double conv_energy; + double conv_distance; + double conv_mass; + double del; + int igroup,groupbit; + bigint gcount; // number of atoms in group + bigint dynlen; // rank of dynamical matrix + int scaleflag; + int me; + bigint *groupmap; - int compressed; // 1 if dump file is written compressed, 0 no - int binaryflag; // 1 if dump file is written binary, 0 no - int file_opened; // 1 if openfile method has been called, 0 no - int file_flag; // 1 custom file name, 0 dynmat.dat + int compressed; // 1 if dump file is written compressed, 0 no + int binaryflag; // 1 if dump file is written binary, 0 no + int file_opened; // 1 if openfile method has been called, 0 no + int file_flag; // 1 custom file name, 0 dynmat.dat - FILE *fp; - }; + FILE *fp; +}; } diff --git a/src/USER-PHONON/third_order.cpp b/src/USER-PHONON/third_order.cpp index 875490d643..ebcc682d7a 100644 --- a/src/USER-PHONON/third_order.cpp +++ b/src/USER-PHONON/third_order.cpp @@ -32,7 +32,7 @@ enum{REGULAR,BALLISTICO}; /* ---------------------------------------------------------------------- */ -ThirdOrder::ThirdOrder(LAMMPS *lmp) : Pointers(lmp), fp(nullptr) +ThirdOrder::ThirdOrder(LAMMPS *lmp) : Command(lmp), fp(nullptr) { external_force_clear = 1; } diff --git a/src/USER-PHONON/third_order.h b/src/USER-PHONON/third_order.h index 83062b6b1f..87b0c695f6 100644 --- a/src/USER-PHONON/third_order.h +++ b/src/USER-PHONON/third_order.h @@ -12,11 +12,11 @@ CommandStyle(third_order,ThirdOrder) #ifndef LMP_THIRD_ORDER_H #define LMP_THIRD_ORDER_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { - class ThirdOrder : protected Pointers { + class ThirdOrder : protected Command { public: ThirdOrder(class LAMMPS *); virtual ~ThirdOrder(); diff --git a/src/balance.cpp b/src/balance.cpp index 6294e023b3..bf037e8f8f 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -51,7 +51,7 @@ enum{X,Y,Z}; /* ---------------------------------------------------------------------- */ -Balance::Balance(LAMMPS *lmp) : Pointers(lmp) +Balance::Balance(LAMMPS *lmp) : Command(lmp) { MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); diff --git a/src/balance.h b/src/balance.h index 424da33757..25ccac85ae 100644 --- a/src/balance.h +++ b/src/balance.h @@ -20,11 +20,11 @@ CommandStyle(balance,Balance) #ifndef LMP_BALANCE_H #define LMP_BALANCE_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Balance : protected Pointers { +class Balance : protected Command { public: class RCB *rcb; class FixStore *fixstore; // per-atom weights stored in FixStore diff --git a/src/change_box.cpp b/src/change_box.cpp index ba99e1b6e1..4471d85132 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -35,7 +35,7 @@ enum{X=0,Y,Z,YZ,XZ,XY}; /* ---------------------------------------------------------------------- */ -ChangeBox::ChangeBox(LAMMPS *lmp) : Pointers(lmp) {} +ChangeBox::ChangeBox(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/change_box.h b/src/change_box.h index d8a057f9a6..2f6802194b 100644 --- a/src/change_box.h +++ b/src/change_box.h @@ -20,11 +20,11 @@ CommandStyle(change_box,ChangeBox) #ifndef LMP_CHANGE_BOX_H #define LMP_CHANGE_BOX_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class ChangeBox : protected Pointers { +class ChangeBox : protected Command { public: ChangeBox(class LAMMPS *); void command(int, char **); diff --git a/src/command.h b/src/command.h new file mode 100644 index 0000000000..6abbc167ac --- /dev/null +++ b/src/command.h @@ -0,0 +1,29 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_COMMAND_H +#define LMP_COMMAND_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class Command : protected Pointers { + public: + Command(class LAMMPS *lmp) : Pointers(lmp) {}; + virtual void command(int, char **) = 0; +}; + +} + +#endif diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 46aff081d9..7591ae7587 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -52,7 +52,7 @@ enum{NONE,RATIO,SUBSET}; /* ---------------------------------------------------------------------- */ -CreateAtoms::CreateAtoms(LAMMPS *lmp) : Pointers(lmp), basistype(nullptr) {} +CreateAtoms::CreateAtoms(LAMMPS *lmp) : Command(lmp), basistype(nullptr) {} /* ---------------------------------------------------------------------- */ diff --git a/src/create_atoms.h b/src/create_atoms.h index 5508752f00..8f0e016192 100644 --- a/src/create_atoms.h +++ b/src/create_atoms.h @@ -20,11 +20,11 @@ CommandStyle(create_atoms,CreateAtoms) #ifndef LMP_CREATE_ATOMS_H #define LMP_CREATE_ATOMS_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class CreateAtoms : protected Pointers { +class CreateAtoms : protected Command { public: CreateAtoms(class LAMMPS *); void command(int, char **); diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index 494e743c05..bedbe4b436 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -38,7 +38,7 @@ enum{MANY,SBOND,SANGLE,SDIHEDRAL,SIMPROPER}; /* ---------------------------------------------------------------------- */ -CreateBonds::CreateBonds(LAMMPS *lmp) : Pointers(lmp) {} +CreateBonds::CreateBonds(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/create_bonds.h b/src/create_bonds.h index eea99b0113..f25cb6d1bc 100644 --- a/src/create_bonds.h +++ b/src/create_bonds.h @@ -20,11 +20,11 @@ CommandStyle(create_bonds,CreateBonds) #ifndef LMP_CREATE_BONDS_H #define LMP_CREATE_BONDS_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class CreateBonds : protected Pointers { +class CreateBonds : protected Command { public: CreateBonds(class LAMMPS *); void command(int, char **); diff --git a/src/create_box.cpp b/src/create_box.cpp index 000fb42495..1350b6f392 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -12,22 +12,24 @@ ------------------------------------------------------------------------- */ #include "create_box.h" -#include + #include "atom.h" #include "atom_vec.h" +#include "comm.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "region.h" #include "region_prism.h" -#include "force.h" -#include "comm.h" #include "update.h" -#include "error.h" + +#include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -CreateBox::CreateBox(LAMMPS *lmp) : Pointers(lmp) {} +CreateBox::CreateBox(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/create_box.h b/src/create_box.h index 740769b4de..846af6bcee 100644 --- a/src/create_box.h +++ b/src/create_box.h @@ -20,11 +20,11 @@ CommandStyle(create_box,CreateBox) #ifndef LMP_CREATE_BOX_H #define LMP_CREATE_BOX_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class CreateBox : protected Pointers { +class CreateBox : protected Command { public: CreateBox(class LAMMPS *); void command(int, char **); diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index 3dbf21ae59..326201c9a2 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -41,7 +41,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Pointers(lmp) {} +DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/delete_atoms.h b/src/delete_atoms.h index 5eab7f6ba7..e43bebfa54 100644 --- a/src/delete_atoms.h +++ b/src/delete_atoms.h @@ -20,12 +20,12 @@ CommandStyle(delete_atoms,DeleteAtoms) #ifndef LMP_DELETE_ATOMS_H #define LMP_DELETE_ATOMS_H -#include "pointers.h" +#include "command.h" #include namespace LAMMPS_NS { -class DeleteAtoms : protected Pointers { +class DeleteAtoms : protected Command { public: DeleteAtoms(class LAMMPS *); void command(int, char **); diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp index 5a487743e1..2bb46e7564 100644 --- a/src/delete_bonds.cpp +++ b/src/delete_bonds.cpp @@ -30,7 +30,7 @@ enum{MULTI,ATOM,BOND,ANGLE,DIHEDRAL,IMPROPER,STATS}; /* ---------------------------------------------------------------------- */ -DeleteBonds::DeleteBonds(LAMMPS *lmp) : Pointers(lmp) {} +DeleteBonds::DeleteBonds(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/delete_bonds.h b/src/delete_bonds.h index 60d76b9086..2f255e12d6 100644 --- a/src/delete_bonds.h +++ b/src/delete_bonds.h @@ -20,11 +20,11 @@ CommandStyle(delete_bonds,DeleteBonds) #ifndef LMP_DELETE_BONDS_H #define LMP_DELETE_BONDS_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class DeleteBonds : protected Pointers { +class DeleteBonds : protected Command { public: DeleteBonds(class LAMMPS *); void command(int, char **); diff --git a/src/deprecated.h b/src/deprecated.h index aceb1181c1..4b6cba7f30 100644 --- a/src/deprecated.h +++ b/src/deprecated.h @@ -26,13 +26,13 @@ CommandStyle(kim_query,Deprecated) #ifndef LMP_DEPRECATED_H #define LMP_DEPRECATED_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Deprecated : protected Pointers { +class Deprecated : protected Command { public: - Deprecated(class LAMMPS *lmp) : Pointers(lmp) {}; + Deprecated(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); }; diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index dd71e944ef..6bc3b0ab35 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -42,7 +42,7 @@ enum{MOVE,RAMP,RANDOM,ROTATE}; /* ---------------------------------------------------------------------- */ -DisplaceAtoms::DisplaceAtoms(LAMMPS *lmp) : Pointers(lmp) +DisplaceAtoms::DisplaceAtoms(LAMMPS *lmp) : Command(lmp) { mvec = nullptr; } diff --git a/src/displace_atoms.h b/src/displace_atoms.h index 737d55dbdd..98247b7244 100644 --- a/src/displace_atoms.h +++ b/src/displace_atoms.h @@ -20,11 +20,11 @@ CommandStyle(displace_atoms,DisplaceAtoms) #ifndef LMP_DISPLACE_ATOMS_H #define LMP_DISPLACE_ATOMS_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class DisplaceAtoms : protected Pointers { +class DisplaceAtoms : protected Command { public: DisplaceAtoms(class LAMMPS *); ~DisplaceAtoms(); diff --git a/src/info.h b/src/info.h index d8fa23489e..536a93c559 100644 --- a/src/info.h +++ b/src/info.h @@ -20,15 +20,15 @@ CommandStyle(info,Info) #ifndef LMP_INFO_H #define LMP_INFO_H -#include "pointers.h" +#include "command.h" #include namespace LAMMPS_NS { -class Info : protected Pointers { +class Info : protected Command { public: - Info(class LAMMPS *lmp) : Pointers(lmp) {}; + Info(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); bool is_active(const char *, const char *); diff --git a/src/minimize.cpp b/src/minimize.cpp index 8e55d6e0ea..1fb0d219cd 100644 --- a/src/minimize.cpp +++ b/src/minimize.cpp @@ -25,7 +25,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Minimize::Minimize(LAMMPS *lmp) : Pointers(lmp) {} +Minimize::Minimize(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/minimize.h b/src/minimize.h index 42a2fcaf02..10b244130a 100644 --- a/src/minimize.h +++ b/src/minimize.h @@ -20,11 +20,11 @@ CommandStyle(minimize,Minimize) #ifndef LMP_MINIMIZE_H #define LMP_MINIMIZE_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Minimize : protected Pointers { +class Minimize : protected Command { public: Minimize(class LAMMPS *); void command(int, char **); diff --git a/src/read_data.cpp b/src/read_data.cpp index cc3b2e5965..c0085f19d1 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -11,10 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - #include "read_data.h" #include "angle.h" @@ -66,7 +62,7 @@ const char *suffixes[] = {"/cuda","/gpu","/opt","/omp","/kk", /* ---------------------------------------------------------------------- */ -ReadData::ReadData(LAMMPS *lmp) : Pointers(lmp) +ReadData::ReadData(LAMMPS *lmp) : Command(lmp) { MPI_Comm_rank(world,&me); line = new char[MAXLINE]; diff --git a/src/read_data.h b/src/read_data.h index 68b40fc529..d251259a08 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -20,11 +20,11 @@ CommandStyle(read_data,ReadData) #ifndef LMP_READ_DATA_H #define LMP_READ_DATA_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class ReadData : protected Pointers { +class ReadData : protected Command { public: ReadData(class LAMMPS *); ~ReadData(); diff --git a/src/read_dump.cpp b/src/read_dump.cpp index 0282e2d039..ddb793c629 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -15,10 +15,6 @@ Contributing author: Timothy Sirk (ARL) ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - #include "read_dump.h" #include "atom.h" @@ -46,7 +42,7 @@ enum{NOADD,YESADD,KEEPADD}; /* ---------------------------------------------------------------------- */ -ReadDump::ReadDump(LAMMPS *lmp) : Pointers(lmp) +ReadDump::ReadDump(LAMMPS *lmp) : Command(lmp) { MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); diff --git a/src/read_dump.h b/src/read_dump.h index 93fb4bc713..ba59cc9224 100644 --- a/src/read_dump.h +++ b/src/read_dump.h @@ -22,11 +22,11 @@ CommandStyle(read_dump,ReadDump) #ifndef LMP_READ_DUMP_H #define LMP_READ_DUMP_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class ReadDump : protected Pointers { +class ReadDump : protected Command { public: ReadDump(class LAMMPS *); ~ReadDump(); diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 9e8fbce91c..7983a25ae9 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -43,7 +43,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -ReadRestart::ReadRestart(LAMMPS *lmp) : Pointers(lmp) {} +ReadRestart::ReadRestart(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/read_restart.h b/src/read_restart.h index 99b37cfa45..3a2c7965b3 100644 --- a/src/read_restart.h +++ b/src/read_restart.h @@ -20,11 +20,11 @@ CommandStyle(read_restart,ReadRestart) #ifndef LMP_READ_RESTART_H #define LMP_READ_RESTART_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class ReadRestart : protected Pointers { +class ReadRestart : protected Command { public: ReadRestart(class LAMMPS *); void command(int, char **); diff --git a/src/replicate.cpp b/src/replicate.cpp index 6877ec091c..95bf615d04 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -31,7 +31,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Replicate::Replicate(LAMMPS *lmp) : Pointers(lmp) {} +Replicate::Replicate(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/replicate.h b/src/replicate.h index 58c0010aa3..fd865a9c71 100644 --- a/src/replicate.h +++ b/src/replicate.h @@ -20,11 +20,11 @@ CommandStyle(replicate,Replicate) #ifndef LMP_REPLICATE_H #define LMP_REPLICATE_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Replicate : protected Pointers { +class Replicate : protected Command { public: Replicate(class LAMMPS *); void command(int, char **); diff --git a/src/rerun.cpp b/src/rerun.cpp index 8615b02d95..9571724e2d 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -29,7 +29,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Rerun::Rerun(LAMMPS *lmp) : Pointers(lmp) {} +Rerun::Rerun(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/rerun.h b/src/rerun.h index ea1d0221c3..57aa32227f 100644 --- a/src/rerun.h +++ b/src/rerun.h @@ -20,11 +20,11 @@ CommandStyle(rerun,Rerun) #ifndef LMP_RERUN_H #define LMP_RERUN_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Rerun : protected Pointers { +class Rerun : protected Command { public: Rerun(class LAMMPS *); void command(int, char **); diff --git a/src/reset_atom_ids.cpp b/src/reset_atom_ids.cpp index 7298103b80..47dae3cb56 100644 --- a/src/reset_atom_ids.cpp +++ b/src/reset_atom_ids.cpp @@ -43,7 +43,7 @@ static int compare_coords(const int, const int, void *); /* ---------------------------------------------------------------------- */ -ResetIDs::ResetIDs(LAMMPS *lmp) : Pointers(lmp) {} +ResetIDs::ResetIDs(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/reset_atom_ids.h b/src/reset_atom_ids.h index 02a7f77e8d..a017abbbc8 100644 --- a/src/reset_atom_ids.h +++ b/src/reset_atom_ids.h @@ -20,11 +20,11 @@ CommandStyle(reset_atom_ids,ResetIDs) #ifndef LMP_RESET_IDS_H #define LMP_RESET_IDS_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class ResetIDs : protected Pointers { +class ResetIDs : protected Command { public: struct AtomRvous { bigint ibin; diff --git a/src/reset_mol_ids.cpp b/src/reset_mol_ids.cpp index aed26b4568..39f7307ca1 100644 --- a/src/reset_mol_ids.cpp +++ b/src/reset_mol_ids.cpp @@ -32,7 +32,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -ResetMolIDs::ResetMolIDs(LAMMPS *lmp) : Pointers(lmp) { +ResetMolIDs::ResetMolIDs(LAMMPS *lmp) : Command(lmp) { cfa = nullptr; cca = nullptr; diff --git a/src/reset_mol_ids.h b/src/reset_mol_ids.h index fbb6fceb03..c25f64fe43 100644 --- a/src/reset_mol_ids.h +++ b/src/reset_mol_ids.h @@ -20,11 +20,11 @@ CommandStyle(reset_mol_ids,ResetMolIDs) #ifndef LMP_RESET_MOL_IDS_H #define LMP_RESET_MOL_IDS_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class ResetMolIDs : protected Pointers { +class ResetMolIDs : protected Command { public: ResetMolIDs(class LAMMPS *); ~ResetMolIDs(); diff --git a/src/run.cpp b/src/run.cpp index c503e174ff..379cf8015a 100644 --- a/src/run.cpp +++ b/src/run.cpp @@ -31,7 +31,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Run::Run(LAMMPS *lmp) : Pointers(lmp) {} +Run::Run(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/run.h b/src/run.h index 5578ea9598..a9a4a556f0 100644 --- a/src/run.h +++ b/src/run.h @@ -20,11 +20,11 @@ CommandStyle(run,Run) #ifndef LMP_RUN_H #define LMP_RUN_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Run : protected Pointers { +class Run : protected Command { public: Run(class LAMMPS *); void command(int, char **); diff --git a/src/set.h b/src/set.h index 29f1ea526e..02e81b057a 100644 --- a/src/set.h +++ b/src/set.h @@ -20,13 +20,13 @@ CommandStyle(set,Set) #ifndef LMP_SET_H #define LMP_SET_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Set : protected Pointers { +class Set : protected Command { public: - Set(class LAMMPS *lmp) : Pointers(lmp) {}; + Set(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); private: diff --git a/src/velocity.cpp b/src/velocity.cpp index f4483074aa..e0c80baa91 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -42,7 +42,7 @@ enum{NONE,CONSTANT,EQUAL,ATOM}; /* ---------------------------------------------------------------------- */ -Velocity::Velocity(LAMMPS *lmp) : Pointers(lmp) {} +Velocity::Velocity(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/velocity.h b/src/velocity.h index e14c0d0d1c..5c54302a1e 100644 --- a/src/velocity.h +++ b/src/velocity.h @@ -20,11 +20,11 @@ CommandStyle(velocity,Velocity) #ifndef LMP_VELOCITY_H #define LMP_VELOCITY_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Velocity : protected Pointers { +class Velocity : protected Command { public: Velocity(class LAMMPS *); void command(int, char **); diff --git a/src/write_coeff.h b/src/write_coeff.h index b995e60d63..2555454db0 100644 --- a/src/write_coeff.h +++ b/src/write_coeff.h @@ -20,13 +20,13 @@ CommandStyle(write_coeff,WriteCoeff) #ifndef LMP_WRITE_COEFF_H #define LMP_WRITE_COEFF_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class WriteCoeff : protected Pointers { +class WriteCoeff : protected Command { public: - WriteCoeff(class LAMMPS *lmp) : Pointers(lmp) {}; + WriteCoeff(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); }; diff --git a/src/write_data.cpp b/src/write_data.cpp index 6d10359e8b..d8b37ca265 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -41,7 +41,7 @@ enum{ELLIPSOID,LINE,TRIANGLE,BODY}; // also in AtomVecHybrid /* ---------------------------------------------------------------------- */ -WriteData::WriteData(LAMMPS *lmp) : Pointers(lmp) +WriteData::WriteData(LAMMPS *lmp) : Command(lmp) { MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); diff --git a/src/write_data.h b/src/write_data.h index a4e71c9cda..c9ba5a4a52 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -20,11 +20,11 @@ CommandStyle(write_data,WriteData) #ifndef LMP_WRITE_DATA_H #define LMP_WRITE_DATA_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class WriteData : protected Pointers { +class WriteData : protected Command { public: WriteData(class LAMMPS *); void command(int, char **); diff --git a/src/write_dump.h b/src/write_dump.h index db39a75d4b..5d1499934a 100644 --- a/src/write_dump.h +++ b/src/write_dump.h @@ -20,13 +20,13 @@ CommandStyle(write_dump,WriteDump) #ifndef LMP_WRITE_DUMP_H #define LMP_WRITE_DUMP_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class WriteDump : protected Pointers { +class WriteDump : protected Command { public: - WriteDump(class LAMMPS *lmp) : Pointers(lmp) {}; + WriteDump(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); }; diff --git a/src/write_restart.cpp b/src/write_restart.cpp index afe1d2d528..ce0eddcd73 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -43,7 +43,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -WriteRestart::WriteRestart(LAMMPS *lmp) : Pointers(lmp) +WriteRestart::WriteRestart(LAMMPS *lmp) : Command(lmp) { MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); diff --git a/src/write_restart.h b/src/write_restart.h index a4a606482e..0b8826f10b 100644 --- a/src/write_restart.h +++ b/src/write_restart.h @@ -20,11 +20,11 @@ CommandStyle(write_restart,WriteRestart) #ifndef LMP_WRITE_RESTART_H #define LMP_WRITE_RESTART_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class WriteRestart : protected Pointers { +class WriteRestart : protected Command { public: WriteRestart(class LAMMPS *); void command(int, char **); From 81578d99343f1b53bec4ec5e6c65651de1fbac19 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 17:47:21 -0400 Subject: [PATCH 0530/1217] update docs for change in class topology --- doc/graphviz/lammps-classes.dot | 10 +++++++--- doc/src/Developer_org.rst | 16 ++++++++-------- doc/src/JPG/lammps-classes.png | Bin 260274 -> 293226 bytes doc/src/Modify_command.rst | 17 +++++++++-------- 4 files changed, 24 insertions(+), 19 deletions(-) diff --git a/doc/graphviz/lammps-classes.dot b/doc/graphviz/lammps-classes.dot index 3c2d2f418d..390dd2cc4b 100644 --- a/doc/graphviz/lammps-classes.dot +++ b/doc/graphviz/lammps-classes.dot @@ -18,8 +18,8 @@ digraph lammps { Up [shape=box label="Update" color=blue] Un [shape=box label="Universe" color=blue] Ti [shape=box label="Timer" color=blue] - Lt [label="Lattice"] Rg [label="Region" color=red] + Lt [label="Lattice"] Rb [shape=box label="RegionBlock"] Rs [shape=box label="RegionSphere"] Av [label="AtomVec" color=red] @@ -34,6 +34,7 @@ digraph lammps { Du [label="Dump" color=red] Fi [label="Fix" color=red] Cp [label="Compute" color=red] + Cm [label="Command" color=red] Th [label="Thermo"] Va [label="Variable"] Ew [shape=box label="Ewald"] @@ -71,16 +72,19 @@ digraph lammps { Dg [shape=box label="DumpCFG"] Ve [shape=box label="Verlet"] Rr [shape=box label="Respa"] + Ru [shape=box label="Run"] + Se [shape=box label="Set"] Pt [shape=box label="PPPMTIP4P"] Vs [shape=box label="VerletSplit"] Ro [shape=box label="RespaOMP"] Mc [shape=box label="MinCG"] Mf [shape=box label="MinFire"] La -> {At Ci Co Do Er Fo Gr In Me Mo Ne Ou Ti Up Un} [penwidth=2] - Do -> {Lt Rg} [penwidth=2] + Do -> {Rg Lt} [penwidth=2] Rg -> {Rb Rs} [style=dashed penwidth=2] Co -> {Cb Ct} [style=dashed penwidth=2] - In -> Va [penwidth=2] + In -> {Va Cm} [penwidth=2] + Cm -> {Ru Se} [style=dashed penwidth=2] Mo -> {Fi Cp} [penwidth=2] Fo -> {Pa Bo An Di Im Ks} [penwidth=2] Ks -> {Ew Pp} [style=dashed penwidth=2] diff --git a/doc/src/Developer_org.rst b/doc/src/Developer_org.rst index 6ecccf084d..133d567cb3 100644 --- a/doc/src/Developer_org.rst +++ b/doc/src/Developer_org.rst @@ -49,8 +49,8 @@ underscore character '_' to separate words. Outside of bundled libraries which may have different conventions, all C and C++ header files have a ``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a ``.c`` extension. A small number of C++ classes and utility functions -are implemented with only a ``.h`` file. Examples are the Pointer class -or the MathVec functions. +are implemented with only a ``.h`` file. Examples are the Pointers and +Commands classes or the MathVec functions. Class topology -------------- @@ -144,7 +144,7 @@ implement specific commands that can be invoked before, after, or in between runs. For these an instance of the class is created, its command() method called and then, after completion, the class instance deleted. Examples for this are the create_box, create_atoms, minimize, -run, or velocity command styles. +run, set, or velocity command styles. For all those ``styles`` certain naming conventions are employed: for the fix nve command the class is called FixNVE and the source files are @@ -175,11 +175,11 @@ follows: - The Input class reads and processes input input strings and files, stores variables, and invokes :doc:`commands `. -- As discussed above, command style classes are directly derived from - the Pointers class. They provide input script commands that perform - one-time operations before/after/between simulations or which invoke a - simulation. They are instantiated from within the Input class, - invoked, then immediately destructed. +- Command style classes are derived from the Command class. They provide + input script commands that perform one-time operations + before/after/between simulations or which invoke a simulation. 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znBfGTuritiZNF+w4%sYB9=sbzkhq`oUxaW;&5K2z^27qz_Um!mP`9x#rcpA{F*iq;}mEeG}#b75ns+D04C(|=t_0{q^9B_Nu^Gn zUS4VTK}Vg@xbkc0k{YObQyb{5T9k{Nd^Nzm;#N*G`*3&8qX|CGQQuv=Ii-T?phOE5 z1IFwBOvst^c5nw091{pLRk5)Nj{^% zvYURQwgb)}N-lN^qULz5=09BS3j``&{{eW=ydT!58O)F+!}9>zrzbSlf(aG1id_@9 zEJJmHyTHMy{6l0JSy>A4R;R;%!K~sU%FMaIWt!JNOG5llmUx!G{@4(dar4Ho%wv9e Q;t#eHCXYWR_xS0*0HRiBzW@LL diff --git a/doc/src/Modify_command.rst b/doc/src/Modify_command.rst index 2d0a1d99d9..e0e3ecbb8d 100644 --- a/doc/src/Modify_command.rst +++ b/doc/src/Modify_command.rst @@ -1,14 +1,15 @@ Input script command style ========================== -New commands can be added to LAMMPS input scripts by adding new -classes that have a "command" method. For example, the create_atoms, -read_data, velocity, and run commands are all implemented in this -fashion. When such a command is encountered in the LAMMPS input -script, LAMMPS simply creates a class with the corresponding name, -invokes the "command" method of the class, and passes it the arguments -from the input script. The command method can perform whatever -operations it wishes on LAMMPS data structures. +New commands can be added to LAMMPS input scripts by adding new classes +that are derived from the Command class and thus must have a "command" +method. For example, the create_atoms, read_data, velocity, and run +commands are all implemented in this fashion. When such a command is +encountered in the LAMMPS input script, LAMMPS simply creates a class +instance with the corresponding name, invokes the "command" method of +the class, and passes it the arguments from the input script. The +command method can perform whatever operations it wishes on LAMMPS data +structures. The single method your new class must define is as follows: From 75579fc1003b815bdecd8e62f2e0d0de0daa13c8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 14 Apr 2021 07:05:00 -0400 Subject: [PATCH 0531/1217] take advantage of having the common Command base class to unify code paths --- doc/src/Developer_plugins.rst | 61 +++++++++++++----------------- examples/plugins/helloplugin.cpp | 11 +++--- src/KIM/kim_command.h | 2 +- src/MESSAGE/message.h | 2 +- src/MESSAGE/server.h | 2 +- src/PLUGIN/plugin.cpp | 2 +- src/PLUGIN/plugin.h | 2 +- src/REPLICA/hyper.h | 2 +- src/REPLICA/neb.h | 2 +- src/REPLICA/prd.h | 2 +- src/REPLICA/tad.h | 2 +- src/REPLICA/temper.h | 2 +- src/SPIN/neb_spin.h | 2 +- src/USER-COLVARS/group_ndx.h | 2 +- src/USER-COLVARS/ndx_group.h | 2 +- src/USER-MISC/temper_grem.h | 2 +- src/USER-MISC/temper_npt.h | 2 +- src/USER-PHONON/dynamical_matrix.h | 2 +- src/USER-PHONON/third_order.h | 2 +- src/balance.h | 2 +- src/change_box.h | 2 +- src/create_atoms.h | 2 +- src/create_bonds.h | 2 +- src/create_box.h | 2 +- src/delete_atoms.h | 2 +- src/delete_bonds.h | 2 +- src/deprecated.h | 2 +- src/displace_atoms.h | 2 +- src/info.h | 2 +- src/input.cpp | 11 +++--- src/input.h | 5 ++- src/lammpsplugin.h | 2 - src/minimize.h | 2 +- src/read_data.h | 2 +- src/read_dump.h | 2 +- src/read_restart.h | 2 +- src/replicate.h | 2 +- src/rerun.h | 2 +- src/reset_atom_ids.h | 2 +- src/reset_mol_ids.h | 2 +- src/run.h | 2 +- src/set.h | 2 +- src/velocity.h | 2 +- src/write_coeff.h | 2 +- src/write_data.h | 2 +- src/write_dump.h | 2 +- src/write_restart.h | 2 +- 47 files changed, 83 insertions(+), 91 deletions(-) diff --git a/doc/src/Developer_plugins.rst b/doc/src/Developer_plugins.rst index 68f1f1387c..1beedcf213 100644 --- a/doc/src/Developer_plugins.rst +++ b/doc/src/Developer_plugins.rst @@ -59,31 +59,25 @@ Members of ``lammpsplugin_t`` * - author - String with the name and email of the author * - creator.v1 - - Pointer to factory function for pair, bond, angle, dihedral, or improper styles + - Pointer to factory function for pair, bond, angle, dihedral, improper or command styles * - creator.v2 - Pointer to factory function for compute, fix, or region styles - * - creator.v3 - - Pointer to factory function for command styles * - handle - Pointer to the open DSO file handle Only one of the three alternate creator entries can be used at a time -and which of those is determined by the style of plugin. The "creator.v1" -element is for factory functions of supported styles computing forces (i.e. -pair, bond, angle, dihedral, or improper styles) and the function takes -as single argument the pointer to the LAMMPS instance. The factory function -is cast to the ``lammpsplugin_factory1`` type before assignment. The -"creator.v2" element is for factory functions creating an instance of -a fix, compute, or region style and takes three arguments: a pointer to -the LAMMPS instance, an integer with the length of the argument list and -a ``char **`` pointer to the list of arguments. The factory function pointer -needs to be cast to the ``lammpsplugin_factory2`` type before assignment. -The "creator.v3" element takes the same arguments as "creator.v3" but is -specific to creating command styles: the factory function has to instantiate -the command style locally passing the LAMMPS pointer as argument and then -call its "command" member function with the number and list of arguments. -The factory function pointer needs to be cast to the -``lammpsplugin_factory3`` type before assignment. +and which of those is determined by the style of plugin. The +"creator.v1" element is for factory functions of supported styles +computing forces (i.e. command, pair, bond, angle, dihedral, or +improper styles) and the function takes as single argument the pointer +to the LAMMPS instance. The factory function is cast to the +``lammpsplugin_factory1`` type before assignment. The "creator.v2" +element is for factory functions creating an instance of a fix, compute, +or region style and takes three arguments: a pointer to the LAMMPS +instance, an integer with the length of the argument list and a ``char +**`` pointer to the list of arguments. The factory function pointer +needs to be cast to the ``lammpsplugin_factory2`` type before +assignment. Pair style example ^^^^^^^^^^^^^^^^^^ @@ -123,12 +117,12 @@ function would look like this: The factory function in this example is called ``morse2creator()``. It receives a pointer to the LAMMPS class as only argument and thus has to -be assigned to the *creator.v1* member of the plugin struct and cast to the -``lammpsplugin_factory1`` pointer type. It returns a +be assigned to the *creator.v1* member of the plugin struct and cast to +the ``lammpsplugin_factory1`` function pointer type. It returns a pointer to the allocated class instance derived from the ``Pair`` class. -This function may be declared static to avoid clashes with other plugins. -The name of the derived class, ``PairMorse2``, must be unique inside -the entire LAMMPS executable. +This function may be declared static to avoid clashes with other +plugins. The name of the derived class, ``PairMorse2``, however must be +unique inside the entire LAMMPS executable. Fix style example ^^^^^^^^^^^^^^^^^ @@ -169,9 +163,9 @@ Below is an example for that: Command style example ^^^^^^^^^^^^^^^^^^^^^ -For command styles there is a third variant of factory function as +Command styles also use the first variant of factory function as demonstrated in the following example, which also shows that the -implementation of the plugin class may also be within the same +implementation of the plugin class may be within the same source file as the plugin interface code: .. code-block:: C++ @@ -180,15 +174,15 @@ file as the plugin interface code: #include "comm.h" #include "error.h" - #include "pointers.h" + #include "command.h" #include "version.h" #include namespace LAMMPS_NS { - class Hello : protected Pointers { + class Hello : public Command { public: - Hello(class LAMMPS *lmp) : Pointers(lmp) {}; + Hello(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); }; } @@ -202,10 +196,9 @@ file as the plugin interface code: utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0])); } - static void hellocreator(LAMMPS *lmp, int argc, char **argv) + static void hellocreator(LAMMPS *lmp) { - Hello hello(lmp); - hello.command(argc,argv); + return new Hello(lmp); } extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) @@ -216,9 +209,9 @@ file as the plugin interface code: plugin.version = LAMMPS_VERSION; plugin.style = "command"; plugin.name = "hello"; - plugin.info = "Hello world command v1.0"; + plugin.info = "Hello world command v1.1"; plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; - plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator; + plugin.creator.v1 = (lammpsplugin_factory1 *) &hellocreator; plugin.handle = handle; (*register_plugin)(&plugin,lmp); } diff --git a/examples/plugins/helloplugin.cpp b/examples/plugins/helloplugin.cpp index f453add374..f4a49c1a5a 100644 --- a/examples/plugins/helloplugin.cpp +++ b/examples/plugins/helloplugin.cpp @@ -9,7 +9,7 @@ #include namespace LAMMPS_NS { - class Hello : protected Command { + class Hello : public Command { public: Hello(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); @@ -25,10 +25,9 @@ void Hello::command(int argc, char **argv) utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0])); } -static void hellocreator(LAMMPS *lmp, int argc, char **argv) +static Command *hellocreator(LAMMPS *lmp) { - Hello hello(lmp); - hello.command(argc,argv); + return new Hello(lmp); } extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) @@ -39,9 +38,9 @@ extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) plugin.version = LAMMPS_VERSION; plugin.style = "command"; plugin.name = "hello"; - plugin.info = "Hello world command v1.0"; + plugin.info = "Hello world command v1.1"; plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; - plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator; + plugin.creator.v1 = (lammpsplugin_factory1 *) &hellocreator; plugin.handle = handle; (*register_plugin)(&plugin,lmp); } diff --git a/src/KIM/kim_command.h b/src/KIM/kim_command.h index 64abeed9e0..b27b0e0873 100644 --- a/src/KIM/kim_command.h +++ b/src/KIM/kim_command.h @@ -66,7 +66,7 @@ CommandStyle(kim,KimCommand) namespace LAMMPS_NS { -class KimCommand : protected Command { +class KimCommand : public Command { public: KimCommand(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/MESSAGE/message.h b/src/MESSAGE/message.h index c499ff6537..88c658e44b 100644 --- a/src/MESSAGE/message.h +++ b/src/MESSAGE/message.h @@ -24,7 +24,7 @@ CommandStyle(message,Message) namespace LAMMPS_NS { -class Message : protected Command { +class Message : public Command { public: Message(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/MESSAGE/server.h b/src/MESSAGE/server.h index 63191ccf33..7c93db8c64 100644 --- a/src/MESSAGE/server.h +++ b/src/MESSAGE/server.h @@ -24,7 +24,7 @@ CommandStyle(server,Server) namespace LAMMPS_NS { -class Server : protected Command { +class Server : public Command { public: Server(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/PLUGIN/plugin.cpp b/src/PLUGIN/plugin.cpp index a2f74060f1..d311b64520 100644 --- a/src/PLUGIN/plugin.cpp +++ b/src/PLUGIN/plugin.cpp @@ -257,7 +257,7 @@ namespace LAMMPS_NS "style {} from plugin", plugin->name)); } - (*command_map)[plugin->name] = (Input::CommandCreator)plugin->creator.v3; + (*command_map)[plugin->name] = (Input::CommandCreator)plugin->creator.v1; } else { utils::logmesg(lmp,fmt::format("Loading plugin for {} styles not " diff --git a/src/PLUGIN/plugin.h b/src/PLUGIN/plugin.h index 61355f4113..4b4bca9878 100644 --- a/src/PLUGIN/plugin.h +++ b/src/PLUGIN/plugin.h @@ -26,7 +26,7 @@ CommandStyle(plugin,Plugin) namespace LAMMPS_NS { - class Plugin : protected Command { + class Plugin : public Command { public: Plugin(class LAMMPS *); void command(int, char **); diff --git a/src/REPLICA/hyper.h b/src/REPLICA/hyper.h index faad58994b..a96ccf3727 100644 --- a/src/REPLICA/hyper.h +++ b/src/REPLICA/hyper.h @@ -24,7 +24,7 @@ CommandStyle(hyper,Hyper) namespace LAMMPS_NS { -class Hyper : protected Command { +class Hyper : public Command { public: Hyper(class LAMMPS *); ~Hyper() {} diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h index d8a9d5d3e4..8298766ccf 100644 --- a/src/REPLICA/neb.h +++ b/src/REPLICA/neb.h @@ -24,7 +24,7 @@ CommandStyle(neb,NEB) namespace LAMMPS_NS { -class NEB : protected Command { +class NEB : public Command { public: NEB(class LAMMPS *); NEB(class LAMMPS *, double, double, int, int, int, double *, double *); diff --git a/src/REPLICA/prd.h b/src/REPLICA/prd.h index b331f7dc02..0d8fde1bfe 100644 --- a/src/REPLICA/prd.h +++ b/src/REPLICA/prd.h @@ -24,7 +24,7 @@ CommandStyle(prd,PRD) namespace LAMMPS_NS { -class PRD : protected Command { +class PRD : public Command { public: PRD(class LAMMPS *); ~PRD() {} diff --git a/src/REPLICA/tad.h b/src/REPLICA/tad.h index 3a525146a6..91e570c707 100644 --- a/src/REPLICA/tad.h +++ b/src/REPLICA/tad.h @@ -24,7 +24,7 @@ CommandStyle(tad,TAD) namespace LAMMPS_NS { -class TAD : protected Command { +class TAD : public Command { public: TAD(class LAMMPS *); ~TAD(); diff --git a/src/REPLICA/temper.h b/src/REPLICA/temper.h index ce7944da95..3f7d813f2a 100644 --- a/src/REPLICA/temper.h +++ b/src/REPLICA/temper.h @@ -24,7 +24,7 @@ CommandStyle(temper,Temper) namespace LAMMPS_NS { -class Temper : protected Command { +class Temper : public Command { public: Temper(class LAMMPS *); ~Temper(); diff --git a/src/SPIN/neb_spin.h b/src/SPIN/neb_spin.h index 3dbae09297..54d85093a5 100644 --- a/src/SPIN/neb_spin.h +++ b/src/SPIN/neb_spin.h @@ -24,7 +24,7 @@ CommandStyle(neb/spin,NEBSpin) namespace LAMMPS_NS { -class NEBSpin : protected Command { +class NEBSpin : public Command { public: NEBSpin(class LAMMPS *); ~NEBSpin(); diff --git a/src/USER-COLVARS/group_ndx.h b/src/USER-COLVARS/group_ndx.h index 46ba86c860..58b210937a 100644 --- a/src/USER-COLVARS/group_ndx.h +++ b/src/USER-COLVARS/group_ndx.h @@ -26,7 +26,7 @@ CommandStyle(group2ndx,Group2Ndx) namespace LAMMPS_NS { -class Group2Ndx : protected Command { +class Group2Ndx : public Command { public: Group2Ndx(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/USER-COLVARS/ndx_group.h b/src/USER-COLVARS/ndx_group.h index 1c881a65bf..e0fc6cf527 100644 --- a/src/USER-COLVARS/ndx_group.h +++ b/src/USER-COLVARS/ndx_group.h @@ -27,7 +27,7 @@ CommandStyle(ndx2group,Ndx2Group) namespace LAMMPS_NS { -class Ndx2Group : protected Command { +class Ndx2Group : public Command { public: Ndx2Group(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/USER-MISC/temper_grem.h b/src/USER-MISC/temper_grem.h index b720aeb45c..3c1891f22d 100644 --- a/src/USER-MISC/temper_grem.h +++ b/src/USER-MISC/temper_grem.h @@ -24,7 +24,7 @@ CommandStyle(temper/grem,TemperGrem) namespace LAMMPS_NS { -class TemperGrem : protected Command { +class TemperGrem : public Command { public: TemperGrem(class LAMMPS *); ~TemperGrem(); diff --git a/src/USER-MISC/temper_npt.h b/src/USER-MISC/temper_npt.h index 5c285f083c..a0eb1c1e9b 100644 --- a/src/USER-MISC/temper_npt.h +++ b/src/USER-MISC/temper_npt.h @@ -25,7 +25,7 @@ CommandStyle(temper/npt,TemperNPT) namespace LAMMPS_NS { -class TemperNPT : protected Command { +class TemperNPT : public Command { public: TemperNPT(class LAMMPS *); ~TemperNPT(); diff --git a/src/USER-PHONON/dynamical_matrix.h b/src/USER-PHONON/dynamical_matrix.h index 30baeda27f..d8c3ad411b 100644 --- a/src/USER-PHONON/dynamical_matrix.h +++ b/src/USER-PHONON/dynamical_matrix.h @@ -15,7 +15,7 @@ CommandStyle(dynamical_matrix,DynamicalMatrix) namespace LAMMPS_NS { -class DynamicalMatrix : protected Command { +class DynamicalMatrix : public Command { public: DynamicalMatrix(class LAMMPS *); virtual ~DynamicalMatrix(); diff --git a/src/USER-PHONON/third_order.h b/src/USER-PHONON/third_order.h index 87b0c695f6..56a0266937 100644 --- a/src/USER-PHONON/third_order.h +++ b/src/USER-PHONON/third_order.h @@ -16,7 +16,7 @@ CommandStyle(third_order,ThirdOrder) namespace LAMMPS_NS { - class ThirdOrder : protected Command { + class ThirdOrder : public Command { public: ThirdOrder(class LAMMPS *); virtual ~ThirdOrder(); diff --git a/src/balance.h b/src/balance.h index 25ccac85ae..0642fe04f6 100644 --- a/src/balance.h +++ b/src/balance.h @@ -24,7 +24,7 @@ CommandStyle(balance,Balance) namespace LAMMPS_NS { -class Balance : protected Command { +class Balance : public Command { public: class RCB *rcb; class FixStore *fixstore; // per-atom weights stored in FixStore diff --git a/src/change_box.h b/src/change_box.h index 2f6802194b..f48edb2d9f 100644 --- a/src/change_box.h +++ b/src/change_box.h @@ -24,7 +24,7 @@ CommandStyle(change_box,ChangeBox) namespace LAMMPS_NS { -class ChangeBox : protected Command { +class ChangeBox : public Command { public: ChangeBox(class LAMMPS *); void command(int, char **); diff --git a/src/create_atoms.h b/src/create_atoms.h index 8f0e016192..deb155b96a 100644 --- a/src/create_atoms.h +++ b/src/create_atoms.h @@ -24,7 +24,7 @@ CommandStyle(create_atoms,CreateAtoms) namespace LAMMPS_NS { -class CreateAtoms : protected Command { +class CreateAtoms : public Command { public: CreateAtoms(class LAMMPS *); void command(int, char **); diff --git a/src/create_bonds.h b/src/create_bonds.h index f25cb6d1bc..d2d50c86c6 100644 --- a/src/create_bonds.h +++ b/src/create_bonds.h @@ -24,7 +24,7 @@ CommandStyle(create_bonds,CreateBonds) namespace LAMMPS_NS { -class CreateBonds : protected Command { +class CreateBonds : public Command { public: CreateBonds(class LAMMPS *); void command(int, char **); diff --git a/src/create_box.h b/src/create_box.h index 846af6bcee..26a2be6fe1 100644 --- a/src/create_box.h +++ b/src/create_box.h @@ -24,7 +24,7 @@ CommandStyle(create_box,CreateBox) namespace LAMMPS_NS { -class CreateBox : protected Command { +class CreateBox : public Command { public: CreateBox(class LAMMPS *); void command(int, char **); diff --git a/src/delete_atoms.h b/src/delete_atoms.h index e43bebfa54..5ff1d12f65 100644 --- a/src/delete_atoms.h +++ b/src/delete_atoms.h @@ -25,7 +25,7 @@ CommandStyle(delete_atoms,DeleteAtoms) namespace LAMMPS_NS { -class DeleteAtoms : protected Command { +class DeleteAtoms : public Command { public: DeleteAtoms(class LAMMPS *); void command(int, char **); diff --git a/src/delete_bonds.h b/src/delete_bonds.h index 2f255e12d6..5c56a67f68 100644 --- a/src/delete_bonds.h +++ b/src/delete_bonds.h @@ -24,7 +24,7 @@ CommandStyle(delete_bonds,DeleteBonds) namespace LAMMPS_NS { -class DeleteBonds : protected Command { +class DeleteBonds : public Command { public: DeleteBonds(class LAMMPS *); void command(int, char **); diff --git a/src/deprecated.h b/src/deprecated.h index 4b6cba7f30..d5997d7199 100644 --- a/src/deprecated.h +++ b/src/deprecated.h @@ -30,7 +30,7 @@ CommandStyle(kim_query,Deprecated) namespace LAMMPS_NS { -class Deprecated : protected Command { +class Deprecated : public Command { public: Deprecated(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/displace_atoms.h b/src/displace_atoms.h index 98247b7244..c2c2e8306f 100644 --- a/src/displace_atoms.h +++ b/src/displace_atoms.h @@ -24,7 +24,7 @@ CommandStyle(displace_atoms,DisplaceAtoms) namespace LAMMPS_NS { -class DisplaceAtoms : protected Command { +class DisplaceAtoms : public Command { public: DisplaceAtoms(class LAMMPS *); ~DisplaceAtoms(); diff --git a/src/info.h b/src/info.h index 536a93c559..386d38c39f 100644 --- a/src/info.h +++ b/src/info.h @@ -26,7 +26,7 @@ CommandStyle(info,Info) namespace LAMMPS_NS { -class Info : protected Command { +class Info : public Command { public: Info(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/input.cpp b/src/input.cpp index 9079cdd76c..16cef08c36 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -21,6 +21,7 @@ #include "comm.h" #include "comm_brick.h" #include "comm_tiled.h" +#include "command.h" #include "compute.h" #include "dihedral.h" #include "domain.h" @@ -82,7 +83,7 @@ command line flags, holds the factory of commands and creates and initializes an instance of the Variable class. To execute a command, a specific class instance, derived from -:cpp:class:`Pointers`, is created, then its ``command()`` member +:cpp:class:`Command`, is created, then its ``command()`` member function executed, and finally the class instance is deleted. \endverbatim @@ -789,7 +790,8 @@ int Input::execute_command() if (command_map->find(command) != command_map->end()) { CommandCreator &command_creator = (*command_map)[command]; - command_creator(lmp,narg,arg); + Command *cmd = command_creator(lmp); + cmd->command(narg,arg); return 0; } @@ -803,10 +805,9 @@ int Input::execute_command() ------------------------------------------------------------------------- */ template -void Input::command_creator(LAMMPS *lmp, int narg, char **arg) +Command *Input::command_creator(LAMMPS *lmp) { - T cmd(lmp); - cmd.command(narg,arg); + return new T(lmp); } /* ---------------------------------------------------------------------- */ diff --git a/src/input.h b/src/input.h index 809a7a5f94..59be026640 100644 --- a/src/input.h +++ b/src/input.h @@ -19,6 +19,7 @@ #include namespace LAMMPS_NS { + class Command; class Input : protected Pointers { friend class Info; @@ -59,12 +60,12 @@ class Input : protected Pointers { FILE **infiles; // list of open input files public: - typedef void (*CommandCreator)(LAMMPS *, int, char **); + typedef Command * (*CommandCreator)(LAMMPS *); typedef std::map CommandCreatorMap; CommandCreatorMap *command_map; protected: - template static void command_creator(LAMMPS *, int, char **); + template static Command *command_creator(LAMMPS *); private: void parse(); // parse an input text line diff --git a/src/lammpsplugin.h b/src/lammpsplugin.h index 1baed9799d..e544e8bffe 100644 --- a/src/lammpsplugin.h +++ b/src/lammpsplugin.h @@ -20,7 +20,6 @@ extern "C" { typedef void *(lammpsplugin_factory1)(void *); typedef void *(lammpsplugin_factory2)(void *, int, char **); - typedef void (lammpsplugin_factory3)(void *, int, char **); typedef struct { const char *version; @@ -31,7 +30,6 @@ extern "C" { union { lammpsplugin_factory1 *v1; lammpsplugin_factory2 *v2; - lammpsplugin_factory3 *v3; } creator; void *handle; } lammpsplugin_t; diff --git a/src/minimize.h b/src/minimize.h index 10b244130a..32d08c5f52 100644 --- a/src/minimize.h +++ b/src/minimize.h @@ -24,7 +24,7 @@ CommandStyle(minimize,Minimize) namespace LAMMPS_NS { -class Minimize : protected Command { +class Minimize : public Command { public: Minimize(class LAMMPS *); void command(int, char **); diff --git a/src/read_data.h b/src/read_data.h index d251259a08..7ccbeebd58 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -24,7 +24,7 @@ CommandStyle(read_data,ReadData) namespace LAMMPS_NS { -class ReadData : protected Command { +class ReadData : public Command { public: ReadData(class LAMMPS *); ~ReadData(); diff --git a/src/read_dump.h b/src/read_dump.h index ba59cc9224..842b629fa4 100644 --- a/src/read_dump.h +++ b/src/read_dump.h @@ -26,7 +26,7 @@ CommandStyle(read_dump,ReadDump) namespace LAMMPS_NS { -class ReadDump : protected Command { +class ReadDump : public Command { public: ReadDump(class LAMMPS *); ~ReadDump(); diff --git a/src/read_restart.h b/src/read_restart.h index 3a2c7965b3..fc2a27fa67 100644 --- a/src/read_restart.h +++ b/src/read_restart.h @@ -24,7 +24,7 @@ CommandStyle(read_restart,ReadRestart) namespace LAMMPS_NS { -class ReadRestart : protected Command { +class ReadRestart : public Command { public: ReadRestart(class LAMMPS *); void command(int, char **); diff --git a/src/replicate.h b/src/replicate.h index fd865a9c71..b4be578b23 100644 --- a/src/replicate.h +++ b/src/replicate.h @@ -24,7 +24,7 @@ CommandStyle(replicate,Replicate) namespace LAMMPS_NS { -class Replicate : protected Command { +class Replicate : public Command { public: Replicate(class LAMMPS *); void command(int, char **); diff --git a/src/rerun.h b/src/rerun.h index 57aa32227f..c10ca8780e 100644 --- a/src/rerun.h +++ b/src/rerun.h @@ -24,7 +24,7 @@ CommandStyle(rerun,Rerun) namespace LAMMPS_NS { -class Rerun : protected Command { +class Rerun : public Command { public: Rerun(class LAMMPS *); void command(int, char **); diff --git a/src/reset_atom_ids.h b/src/reset_atom_ids.h index a017abbbc8..6c262f2bd8 100644 --- a/src/reset_atom_ids.h +++ b/src/reset_atom_ids.h @@ -24,7 +24,7 @@ CommandStyle(reset_atom_ids,ResetIDs) namespace LAMMPS_NS { -class ResetIDs : protected Command { +class ResetIDs : public Command { public: struct AtomRvous { bigint ibin; diff --git a/src/reset_mol_ids.h b/src/reset_mol_ids.h index c25f64fe43..5759cf8b4e 100644 --- a/src/reset_mol_ids.h +++ b/src/reset_mol_ids.h @@ -24,7 +24,7 @@ CommandStyle(reset_mol_ids,ResetMolIDs) namespace LAMMPS_NS { -class ResetMolIDs : protected Command { +class ResetMolIDs : public Command { public: ResetMolIDs(class LAMMPS *); ~ResetMolIDs(); diff --git a/src/run.h b/src/run.h index a9a4a556f0..747af6a61c 100644 --- a/src/run.h +++ b/src/run.h @@ -24,7 +24,7 @@ CommandStyle(run,Run) namespace LAMMPS_NS { -class Run : protected Command { +class Run : public Command { public: Run(class LAMMPS *); void command(int, char **); diff --git a/src/set.h b/src/set.h index 02e81b057a..330bd484a3 100644 --- a/src/set.h +++ b/src/set.h @@ -24,7 +24,7 @@ CommandStyle(set,Set) namespace LAMMPS_NS { -class Set : protected Command { +class Set : public Command { public: Set(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/velocity.h b/src/velocity.h index 5c54302a1e..d7405f87fd 100644 --- a/src/velocity.h +++ b/src/velocity.h @@ -24,7 +24,7 @@ CommandStyle(velocity,Velocity) namespace LAMMPS_NS { -class Velocity : protected Command { +class Velocity : public Command { public: Velocity(class LAMMPS *); void command(int, char **); diff --git a/src/write_coeff.h b/src/write_coeff.h index 2555454db0..8815162c48 100644 --- a/src/write_coeff.h +++ b/src/write_coeff.h @@ -24,7 +24,7 @@ CommandStyle(write_coeff,WriteCoeff) namespace LAMMPS_NS { -class WriteCoeff : protected Command { +class WriteCoeff : public Command { public: WriteCoeff(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/write_data.h b/src/write_data.h index c9ba5a4a52..cecfaa4800 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -24,7 +24,7 @@ CommandStyle(write_data,WriteData) namespace LAMMPS_NS { -class WriteData : protected Command { +class WriteData : public Command { public: WriteData(class LAMMPS *); void command(int, char **); diff --git a/src/write_dump.h b/src/write_dump.h index 5d1499934a..763fd12f60 100644 --- a/src/write_dump.h +++ b/src/write_dump.h @@ -24,7 +24,7 @@ CommandStyle(write_dump,WriteDump) namespace LAMMPS_NS { -class WriteDump : protected Command { +class WriteDump : public Command { public: WriteDump(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/write_restart.h b/src/write_restart.h index 0b8826f10b..05f5c45ec6 100644 --- a/src/write_restart.h +++ b/src/write_restart.h @@ -24,7 +24,7 @@ CommandStyle(write_restart,WriteRestart) namespace LAMMPS_NS { -class WriteRestart : protected Command { +class WriteRestart : public Command { public: WriteRestart(class LAMMPS *); void command(int, char **); From 2e5079371ad9f5e2edb3eaf093167451605a9b38 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 14 Apr 2021 07:26:34 -0400 Subject: [PATCH 0532/1217] must delete command explicitly now --- src/input.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/input.cpp b/src/input.cpp index 16cef08c36..d3352b380a 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -792,6 +792,7 @@ int Input::execute_command() CommandCreator &command_creator = (*command_map)[command]; Command *cmd = command_creator(lmp); cmd->command(narg,arg); + delete cmd; return 0; } From 91dfc6875bc086666ce6e85421d1973fe423a8ce Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 14 Apr 2021 17:02:12 -0400 Subject: [PATCH 0533/1217] Silence compiler warnings about unused variables --- src/KSPACE/fft3d.cpp | 35 +++++++++++++++++------------------ 1 file changed, 17 insertions(+), 18 deletions(-) diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp index 7a271326f7..6a05be4e6f 100644 --- a/src/KSPACE/fft3d.cpp +++ b/src/KSPACE/fft3d.cpp @@ -69,7 +69,6 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) { - int i,total,length,offset,num; FFT_SCALAR norm; #if defined(FFT_FFTW3) FFT_SCALAR *out_ptr; @@ -99,9 +98,6 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) // 1d FFTs along fast axis - total = plan->total1; - length = plan->length1; - #if defined(FFT_MKL) if (flag == 1) DftiComputeForward(plan->handle_fast,data); @@ -114,11 +110,14 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) theplan=plan->plan_fast_backward; FFTW_API(execute_dft)(theplan,data,data); #else + int total = plan->total1; + int length = plan->length1; + if (flag == 1) - for (offset = 0; offset < total; offset += length) + for (int offset = 0; offset < total; offset += length) kiss_fft(plan->cfg_fast_forward,&data[offset],&data[offset]); else - for (offset = 0; offset < total; offset += length) + for (int offset = 0; offset < total; offset += length) kiss_fft(plan->cfg_fast_backward,&data[offset],&data[offset]); #endif @@ -133,9 +132,6 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) // 1d FFTs along mid axis - total = plan->total2; - length = plan->length2; - #if defined(FFT_MKL) if (flag == 1) DftiComputeForward(plan->handle_mid,data); @@ -148,11 +144,14 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) theplan=plan->plan_mid_backward; FFTW_API(execute_dft)(theplan,data,data); #else + total = plan->total2; + length = plan->length2; + if (flag == 1) - for (offset = 0; offset < total; offset += length) + for (int offset = 0; offset < total; offset += length) kiss_fft(plan->cfg_mid_forward,&data[offset],&data[offset]); else - for (offset = 0; offset < total; offset += length) + for (int offset = 0; offset < total; offset += length) kiss_fft(plan->cfg_mid_backward,&data[offset],&data[offset]); #endif @@ -167,9 +166,6 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) // 1d FFTs along slow axis - total = plan->total3; - length = plan->length3; - #if defined(FFT_MKL) if (flag == 1) DftiComputeForward(plan->handle_slow,data); @@ -182,11 +178,14 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) theplan=plan->plan_slow_backward; FFTW_API(execute_dft)(theplan,data,data); #else + total = plan->total3; + length = plan->length3; + if (flag == 1) - for (offset = 0; offset < total; offset += length) + for (int offset = 0; offset < total; offset += length) kiss_fft(plan->cfg_slow_forward,&data[offset],&data[offset]); else - for (offset = 0; offset < total; offset += length) + for (int offset = 0; offset < total; offset += length) kiss_fft(plan->cfg_slow_backward,&data[offset],&data[offset]); #endif @@ -201,11 +200,11 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) if (flag == -1 && plan->scaled) { norm = plan->norm; - num = plan->normnum; + const int num = plan->normnum; #if defined(FFT_FFTW3) out_ptr = (FFT_SCALAR *)out; #endif - for (i = 0; i < num; i++) { + for (int i = 0; i < num; i++) { #if defined(FFT_FFTW3) *(out_ptr++) *= norm; *(out_ptr++) *= norm; From d5661e06ae266dee138e432f732922ab91b1b37e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 14 Apr 2021 20:00:38 -0400 Subject: [PATCH 0534/1217] Detect linux distribution and version --- cmake/Modules/LAMMPSUtils.cmake | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/cmake/Modules/LAMMPSUtils.cmake b/cmake/Modules/LAMMPSUtils.cmake index acaef19498..41dcfc5b2f 100644 --- a/cmake/Modules/LAMMPSUtils.cmake +++ b/cmake/Modules/LAMMPSUtils.cmake @@ -104,3 +104,13 @@ function(FetchPotentials pkgfolder potfolder) endforeach() endif() endfunction(FetchPotentials) + +# set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux +if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (EXISTS /etc/os-release)) + file(STRINGS /etc/os-release distro REGEX "^NAME=") + string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}") + file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=") + string(REGEX REPLACE "VERSION_ID=\"?([^\"]*)\"?" "\\1" disversion "${disversion}") + set(CMAKE_LINUX_DISTRO ${distro}) + set(CMAKE_DISTRO_VERSION ${disversion}) +endif() From 2a81411029c6410d4e979c9f3ac5b27d6f795d70 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 14 Apr 2021 20:01:46 -0400 Subject: [PATCH 0535/1217] use linux distro and version info to decide when to look for faster linkers --- cmake/CMakeLists.txt | 2 +- cmake/Modules/Testing.cmake | 13 ++++++++----- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index a11c7575d2..263b5a566d 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -731,7 +731,7 @@ get_target_property(DEFINES lammps COMPILE_DEFINITIONS) include(FeatureSummary) feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND) message(STATUS "<<< Build configuration >>> - Operating System: ${CMAKE_SYSTEM_NAME} + Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION} Build type: ${CMAKE_BUILD_TYPE} Install path: ${CMAKE_INSTALL_PREFIX} Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}") diff --git a/cmake/Modules/Testing.cmake b/cmake/Modules/Testing.cmake index 6d2f39b0f3..7fbd8212de 100644 --- a/cmake/Modules/Testing.cmake +++ b/cmake/Modules/Testing.cmake @@ -16,11 +16,14 @@ if(ENABLE_TESTING) set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command") set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options") - # check if a faster linker is available. - # only verified with GNU and Clang compilers and new CMake - if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13) - if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") - OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")) + # we need to build and link a LOT of tester executables, so it is worth checking if + # a faster linker is available. requires GNU or Clang compiler, newer CMake. + # also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails) + if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13) + AND ((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") + OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))) + if (((CMAKE_LINUX_DISTRO STREQUAL Ubuntu) AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04)) + OR ((CMAKE_LINUX_DISTRO STREQUAL Fedora) AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30))) include(CheckCXXCompilerFlag) set(CMAKE_CUSTOM_LINKER_DEFAULT default) check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG) From 6e739c04e43951596a6a13a4b8db374e03026e96 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 14 Apr 2021 20:02:05 -0400 Subject: [PATCH 0536/1217] use safe fread() call --- src/read_restart.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 9e8fbce91c..d3fecd9d80 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -1195,7 +1195,7 @@ void ReadRestart::check_eof_magic() if (me == 0) { long curpos = ftell(fp); fseek(fp,(long)-n,SEEK_END); - fread(str,sizeof(char),n,fp); + utils::sfread(FLERR,str,sizeof(char),n,fp,nullptr,error); fseek(fp,curpos,SEEK_SET); } From 0870a560939079644892c9ff2e650e2a45339243 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 15 Apr 2021 11:57:48 -0400 Subject: [PATCH 0537/1217] expand exception message to include cause of file open failure --- src/potential_file_reader.cpp | 3 ++- src/text_file_reader.cpp | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/potential_file_reader.cpp b/src/potential_file_reader.cpp index 2730a3d109..bddfca9bce 100644 --- a/src/potential_file_reader.cpp +++ b/src/potential_file_reader.cpp @@ -62,7 +62,8 @@ PotentialFileReader::PotentialFileReader(LAMMPS *lmp, try { reader = open_potential(filename); if (!reader) { - error->one(FLERR, fmt::format("cannot open {} potential file {}", potential_name, filename)); + error->one(FLERR, fmt::format("cannot open {} potential file {}: {}", + potential_name, filename, utils::getsyserror())); } } catch (FileReaderException &e) { error->one(FLERR, e.what()); diff --git a/src/text_file_reader.cpp b/src/text_file_reader.cpp index af27bfb16d..7a6e914639 100644 --- a/src/text_file_reader.cpp +++ b/src/text_file_reader.cpp @@ -46,7 +46,8 @@ TextFileReader::TextFileReader(const std::string &filename, const std::string &f fp = fopen(filename.c_str(), "r"); if (fp == nullptr) { - throw FileReaderException(fmt::format("cannot open {} file {}", filetype, filename)); + throw FileReaderException(fmt::format("cannot open {} file {}: {}", + filetype, filename, utils::getsyserror())); } } From 9168f949e6b84e356533c0ac5efd0c755af639cb Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 15 Apr 2021 16:06:47 -0400 Subject: [PATCH 0538/1217] bond/react: custom constraint --- src/USER-REACTION/fix_bond_react.cpp | 138 +++++++++++++++++++++++++-- src/USER-REACTION/fix_bond_react.h | 7 ++ 2 files changed, 139 insertions(+), 6 deletions(-) mode change 100644 => 100755 src/USER-REACTION/fix_bond_react.cpp mode change 100644 => 100755 src/USER-REACTION/fix_bond_react.h diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp old mode 100644 new mode 100755 index 2b88a8a264..ebaeaa6a7e --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -80,7 +80,7 @@ static const char cite_fix_bond_react[] = enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE}; // types of available reaction constraints -enum{DISTANCE,ANGLE,DIHEDRAL,ARRHENIUS,RMSD}; +enum{DISTANCE,ANGLE,DIHEDRAL,ARRHENIUS,RMSD,CUSTOM}; // ID type used by constraint enum{ATOM,FRAG}; @@ -125,6 +125,14 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : narrhenius = 0; status = PROCEED; + // reaction functions used by 'custom' constraint + nrxnfunction = 2; + rxnfunclist.resize(nrxnfunction); + rxnfunclist[0] = "rxnsum"; + rxnfunclist[1] = "rxnave"; + nvvec = 0; + vvec = nullptr; + nxspecial = nullptr; onemol_nxspecial = nullptr; twomol_nxspecial = nullptr; @@ -582,6 +590,7 @@ FixBondReact::~FixBondReact() memory->destroy(delete_atoms); memory->destroy(create_atoms); memory->destroy(chiral_atoms); + if (vvec != nullptr) memory->destroy(vvec); memory->destroy(rxn_name); memory->destroy(nevery); @@ -1971,6 +1980,8 @@ int FixBondReact::check_constraints() memory->destroy(xfrozen); memory->destroy(xmobile); if (rmsd > constraints[i][rxnID].par[0]) satisfied[i] = 0; + } else if (constraints[i][rxnID].type == CUSTOM) { + satisfied[i] = custom_constraint(constraints[i][rxnID].str); } } @@ -2085,6 +2096,118 @@ double FixBondReact::get_temperature(tagint **myglove, int row_offset, int col) return t; } +/* ---------------------------------------------------------------------- +evaulate expression for variable constraint +------------------------------------------------------------------------- */ + +double FixBondReact::custom_constraint(std::string varstr) +{ + int pos,pos1,pos2,pos3,irxnfunc; + int prev3 = -1; + double val; + std::string argstr,varid,fragid,evlcat; + std::vector evlstr; + + // search varstr for special 'rxn' functions + while (true) { + // find next reaction special function occurrence + pos1 = INT_MAX; + for (int i = 0; i < nrxnfunction; i++) { + pos = varstr.find(rxnfunclist[i],prev3+1); + if (pos == std::string::npos) continue; + if (pos < pos1) { + pos1 = pos; + irxnfunc = i; + } + } + if (pos1 == INT_MAX) break; + + fragid = "all"; // operate over entire reaction site by default + pos2 = varstr.find("(",pos1); + pos3 = varstr.find(")",pos2); + if (pos2 == std::string::npos || pos3 == std::string::npos) + error->one(FLERR,"Bond/react: Illegal rxn function syntax\n"); + evlstr.push_back(varstr.substr(prev3+1,pos1-(prev3+1))); + prev3 = pos3; + argstr = varstr.substr(pos2+1,pos3-pos2-1); + pos2 = argstr.find(","); + if (pos2 != std::string::npos) { + varid = argstr.substr(0,pos2); + fragid = argstr.substr(pos2+1); + } else varid = argstr; + evlstr.push_back(std::to_string(rxnfunction(rxnfunclist[irxnfunc], varid, fragid))); + } + evlstr.push_back(varstr.substr(prev3+1)); + + for (int i = 0; i < evlstr.size(); i++) + evlcat += evlstr[i]; + + char *cstr = new char[evlcat.length() + 1]; + strcpy(cstr, evlcat.c_str()); + + val = input->variable->compute_equal(cstr); + delete [] cstr; + return val; +} + +/* ---------------------------------------------------------------------- +current two 'rxn' functions: rxnsum and rxnave +------------------------------------------------------------------------- */ + +double FixBondReact::rxnfunction(std::string rxnfunc, std::string varid, + std::string fragid) +{ + if (varid.substr(0,2) != "v_") error->one(FLERR,"Bond/react: Reaction special function variable " + "name should begin with 'v_'"); + varid = varid.substr(2); + int ivar = input->variable->find(varid.c_str()); + if (ivar < 0) + error->one(FLERR,"Bond/react: Reaction special function variable " + "name does not exist"); + if (!input->variable->atomstyle(ivar)) + error->one(FLERR,"Bond/react: Reaction special function must " + "reference an atom-style variable"); + if (vvec == nullptr) { + memory->create(vvec,atom->nlocal,"bond/react:vvec"); + nvvec = atom->nlocal; + } + if (nvvec < atom->nlocal) { + memory->grow(vvec,atom->nlocal,"bond/react:vvec"); + nvvec = atom->nlocal; + } + input->variable->compute_atom(ivar,igroup,vvec,1,0); + int ifrag = -1; + if (fragid != "all") { + ifrag = onemol->findfragment(fragid.c_str()); + if (ifrag < 0) error->one(FLERR,"Bond/react: Molecule fragment " + "in reaction special function does not exist"); + } + + int iatom; + int nsum = 0; + double sumvvec = 0; + if (rxnfunc == "rxnsum" || rxnfunc == "rxnave") { + if (fragid == "all") { + for (int i = 0; i < onemol->natoms; i++) { + iatom = atom->map(glove[i][1]); + sumvvec += vvec[iatom]; + } + nsum = onemol->natoms; + } else { + for (int i = 0; i < onemol->natoms; i++) { + if (onemol->fragmentmask[ifrag][i]) { + iatom = atom->map(glove[i][1]); + sumvvec += vvec[iatom]; + nsum++; + } + } + } + } + + if (rxnfunc == "rxnsum") return sumvvec; + if (rxnfunc == "rxnave") return sumvvec/nsum; +} + /* ---------------------------------------------------------------------- return handedness (1 or -1) of a chiral center, given ordered set of coordinates ------------------------------------------------------------------------- */ @@ -3705,13 +3828,13 @@ void FixBondReact::ReadConstraints(char *line, int myrxn) strcpy(constraintstr[myrxn],"("); // string for boolean constraint logic for (int i = 0; i < nconstraints[myrxn]; i++) { readline(line); - if ((ptr = strrchr(line,'('))) { // reverse char search + if ((ptr = strrchr(line,'{'))) { // reverse char search strncat(constraintstr[myrxn],line,ptr-line+1); line = ptr + 1; } // 'C' indicates where to sub in next constraint strcat(constraintstr[myrxn],"C"); - if ((ptr = strchr(line,')'))) { + if ((ptr = strchr(line,'}'))) { strncat(constraintstr[myrxn],ptr,strrchr(line,')')-ptr+1); } if ((ptr = strstr(line,"&&"))) { @@ -3723,7 +3846,7 @@ void FixBondReact::ReadConstraints(char *line, int myrxn) } else if (i+1 < nconstraints[myrxn]) { strcat(constraintstr[myrxn],"&&"); } - if ((ptr = strchr(line,')'))) + if ((ptr = strchr(line,'}'))) *ptr = '\0'; sscanf(line,"%s",constraint_type); if (strcmp(constraint_type,"distance") == 0) { @@ -3775,8 +3898,11 @@ void FixBondReact::ReadConstraints(char *line, int myrxn) if (ifragment < 0) error->one(FLERR,"Bond/react: Molecule fragment does not exist"); else constraints[i][myrxn].id[0] = ifragment; } - } else - error->one(FLERR,"Bond/react: Illegal constraint type in 'Constraints' section of map file"); + } else if (strcmp(constraint_type,"custom") == 0) { + constraints[i][myrxn].type = CUSTOM; + strtok(line," \t\n\r\f"); + constraints[i][myrxn].str = strtok(nullptr,"\"\t\n\r\f"); + } else error->one(FLERR,"Bond/react: Illegal constraint type in 'Constraints' section of map file"); } strcat(constraintstr[myrxn],")"); // close boolean constraint logic string delete [] constraint_type; diff --git a/src/USER-REACTION/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h old mode 100644 new mode 100755 index 67788df217..b54e5b6b24 --- a/src/USER-REACTION/fix_bond_react.h +++ b/src/USER-REACTION/fix_bond_react.h @@ -74,6 +74,8 @@ class FixBondReact : public Fix { int maxnconstraints; int *nconstraints; char **constraintstr; + int nrxnfunction; + std::vector rxnfunclist; int narrhenius; int **var_flag,**var_id; // for keyword values with variable inputs int status; @@ -138,6 +140,8 @@ class FixBondReact : public Fix { int **delete_atoms; // atoms in pre-reacted templates to delete int **create_atoms; // atoms in post-reacted templates to create int ***chiral_atoms; // pre-react chiral atoms. 1) flag 2) orientation 3-4) ordered atom types + int nvvec; + double *vvec; // per-atom vector to store variable constraint atom-style variable values int **nxspecial,**onemol_nxspecial,**twomol_nxspecial; // full number of 1-4 neighbors tagint **xspecial,**onemol_xspecial,**twomol_xspecial; // full 1-4 neighbor list @@ -175,6 +179,8 @@ class FixBondReact : public Fix { int check_constraints(); void get_IDcoords(int, int, double *); double get_temperature(tagint **, int, int); + double custom_constraint(std::string); + double rxnfunction(std::string, std::string, std::string); int get_chirality(double[12]); // get handedness given an ordered set of coordinates void open(char *); @@ -209,6 +215,7 @@ class FixBondReact : public Fix { int id[MAXCONIDS]; int idtype[MAXCONIDS]; double par[MAXCONPAR]; + std::string str; }; Constraint **constraints; From 21a38c203a893a8aa3b87b2b1b596b0300542968 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 15 Apr 2021 16:11:39 -0400 Subject: [PATCH 0539/1217] bond/react: custom constraint docs --- doc/src/fix_bond_react.rst | 43 ++++++++++++++++++++++++++++++++++++-- 1 file changed, 41 insertions(+), 2 deletions(-) diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index 5291aff81b..f42952ecdc 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -328,8 +328,8 @@ keyword 'ChiralIDs' lists the atom IDs of chiral atoms whose handedness should be enforced. The fifth optional section begins with the keyword 'Constraints' and lists additional criteria that must be satisfied in order for the reaction to occur. Currently, there are -five types of constraints available, as discussed below: 'distance', -'angle', 'dihedral', 'arrhenius', and 'rmsd'. +six types of constraints available, as discussed below: 'distance', +'angle', 'dihedral', 'arrhenius', 'rmsd', and 'custom'. A sample map file is given below: @@ -500,6 +500,45 @@ example, the molecule fragment could consist of only the backbone atoms of a polymer chain. This constraint can be used to enforce a specific relative position and orientation between reacting molecules. +The constraint of type 'custom' has the following syntax: + +.. parsed-literal:: + + custom *varstring* + +where 'custom' is the required keyword, and *varstring* is a +variable expression. The expression must be a valid equal-style +variable formula that can be read by the :doc:`variable ` command, +after any special reaction functions are evaluated. If the resulting +expression is zero, the reaction is prevented from occurring; +otherwise, it is permitted to occur. There are two special reaction +functions available, 'rxnsum' and 'rxnave'. These functions operate +over the atoms in a given reaction site, and have one mandatory +argument and one optional argument. The mandatory argument is the +identifier for an atom-style variable. The second, optional argument +is the name of a molecule fragment in the pre-reaction template, and +can be used to operate over a subset of atoms in the reaction site. +The 'rxnsum' function sums the atom-style variable over the reaction +site, while the 'rxnave' returns the average value. For example, a +constraint on the total potential energy of atoms involved in the +reaction can be imposed as follows: + +.. code-block:: LAMMPS + +compute 1 all pe/atom # in LAMMPS input script +variable my_pe atom c_1 # in LAMMPS input script + +.. code-block:: LAMMPS + +custom "rxnsum(v_my_pe) > 100" # in Constraints section of map file + +The above example prevents the reaction from occurring unless the +total potential energy of the reaction site is above 100. The variable +expression can be interpreted as the probability of the reaction +occurring by using an inequality and the 'random(x,y,z)' function +available as an equal-style variable input, similar to the 'arrhenius' +constraint above. + By default, all constraints must be satisfied for the reaction to occur. In other words, constraints are evaluated as a series of logical values using the logical AND operator "&&". More complex logic From 024725c3e0667ac1ed9db86f8bce21d62d9582d0 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 15 Apr 2021 16:19:09 -0400 Subject: [PATCH 0540/1217] notation update constraints can be grouped logically with curly brackets now, instead of parentheses --- doc/src/fix_bond_react.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index f42952ecdc..ec6123f0f1 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -546,15 +546,15 @@ can be achieved by explicitly adding the logical AND operator "&&" or the logical OR operator "||" after a given constraint command. If a logical operator is specified after a constraint, it must be placed after all constraint parameters, on the same line as the constraint -(one per line). Similarly, parentheses can be used to group +(one per line). Similarly, curly brackets can be used to group constraints. The expression that results from concatenating all constraints should be a valid logical expression that can be read by the :doc:`variable ` command after converting each constraint to a logical value. Because exactly one constraint is allowed per line, having a valid logical expression implies that left -parentheses "(" should only appear before a constraint, and right -parentheses ")" should only appear after a constraint and before any -logical operator. +curly brackets "{" should only appear before a constraint, and right +curly brackets "}" should only appear after a constraint and before +any logical operator. Once a reaction site has been successfully identified, data structures within LAMMPS that store bond topology are updated to reflect the From 7300e5c4bd6632a5d9a1458a5003d93caeccc8d7 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 15 Apr 2021 18:33:21 -0400 Subject: [PATCH 0541/1217] Use C++ for AtomVec::Method --- src/atom_vec.cpp | 142 ++++++++++++++++++----------------------------- src/atom_vec.h | 22 ++++---- 2 files changed, 66 insertions(+), 98 deletions(-) diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index 7d7cfa4878..78903d6a7f 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -71,21 +71,6 @@ AtomVec::AtomVec(LAMMPS *lmp) : Pointers(lmp) default_create = "id type mask image x v"; default_data_atom = ""; default_data_vel = ""; - - // initializations - - init_method(&mgrow); - init_method(&mcopy); - init_method(&mcomm); - init_method(&mcomm_vel); - init_method(&mreverse); - init_method(&mborder); - init_method(&mborder_vel); - init_method(&mexchange); - init_method(&mrestart); - init_method(&mcreate); - init_method(&mdata_atom); - init_method(&mdata_vel); } /* ---------------------------------------------------------------------- */ @@ -129,19 +114,6 @@ AtomVec::~AtomVec() } } - destroy_method(&mgrow); - destroy_method(&mcopy); - destroy_method(&mcomm); - destroy_method(&mcomm_vel); - destroy_method(&mreverse); - destroy_method(&mborder); - destroy_method(&mborder_vel); - destroy_method(&mexchange); - destroy_method(&mrestart); - destroy_method(&mcreate); - destroy_method(&mdata_atom); - destroy_method(&mdata_vel); - delete [] threads; } @@ -2395,18 +2367,18 @@ void AtomVec::setup_fields() // populate field-based data struct for each method to use - create_method(ngrow,&mgrow); - create_method(ncopy,&mcopy); - create_method(ncomm,&mcomm); - create_method(ncomm_vel,&mcomm_vel); - create_method(nreverse,&mreverse); - create_method(nborder,&mborder); - create_method(nborder_vel,&mborder_vel); - create_method(nexchange,&mexchange); - create_method(nrestart,&mrestart); - create_method(ncreate,&mcreate); - create_method(ndata_atom,&mdata_atom); - create_method(ndata_vel,&mdata_vel); + init_method(ngrow,&mgrow); + init_method(ncopy,&mcopy); + init_method(ncomm,&mcomm); + init_method(ncomm_vel,&mcomm_vel); + init_method(nreverse,&mreverse); + init_method(nborder,&mborder); + init_method(nborder_vel,&mborder_vel); + init_method(nexchange,&mexchange); + init_method(nrestart,&mrestart); + init_method(ncreate,&mcreate); + init_method(ndata_atom,&mdata_atom); + init_method(ndata_vel,&mdata_vel); // create threads data struct for grow and memory_usage to use @@ -2480,7 +2452,6 @@ void AtomVec::setup_fields() int AtomVec::process_fields(char *str, const char *default_str, Method *method) { if (str == nullptr) { - method->index = nullptr; return 0; } @@ -2496,17 +2467,19 @@ int AtomVec::process_fields(char *str, const char *default_str, Method *method) Atom::PerAtom *peratom = atom->peratom; int nperatom = atom->nperatom; - int *index; + // allocate memory in method + method->resize(nfield); + + int *index = method->index; int match; - if (nfield) index = new int[nfield]; for (int i = 0; i < nfield; i++) { - const char * field = words[i].c_str(); + const std::string & field = words[i]; // find field in master Atom::peratom list for (match = 0; match < nperatom; match++) - if (strcmp(field, peratom[match].name) == 0) break; + if (field == peratom[match].name) break; if (match == nperatom) error->all(FLERR,fmt::format("Peratom field {} not recognized", field)); index[i] = match; @@ -2520,38 +2493,19 @@ int AtomVec::process_fields(char *str, const char *default_str, Method *method) // error if field is in default str for (match = 0; match < ndef; match++) - if (strcmp(field, def_words[match].c_str()) == 0) + if (field == def_words[match]) error->all(FLERR,fmt::format("Peratom field {} is a default", field)); } - if (nfield) method->index = index; - else method->index = nullptr; return nfield; } /* ---------------------------------------------------------------------- - create a method data structs for processing fields + init method data structs for processing fields ------------------------------------------------------------------------- */ -void AtomVec::create_method(int nfield, Method *method) +void AtomVec::init_method(int nfield, Method *method) { - if (nfield > 0) { - method->pdata = new void*[nfield]; - method->datatype = new int[nfield]; - method->cols = new int[nfield]; - method->maxcols = new int*[nfield]; - method->collength = new int[nfield]; - method->plength = new void*[nfield]; - } else { - method->pdata = nullptr; - method->datatype = nullptr; - method->cols = nullptr; - method->maxcols = nullptr; - method->collength = nullptr; - method->plength = nullptr; - return; - } - for (int i = 0; i < nfield; i++) { Atom::PerAtom *field = &atom->peratom[method->index[i]]; method->pdata[i] = (void *) field->address; @@ -2566,31 +2520,43 @@ void AtomVec::create_method(int nfield, Method *method) } /* ---------------------------------------------------------------------- - free memory in a method data structs + Method class members ------------------------------------------------------------------------- */ -void AtomVec::init_method(Method *method) +AtomVec::Method::~Method() { - method->pdata = nullptr; - method->datatype = nullptr; - method->cols = nullptr; - method->maxcols = nullptr; - method->collength = nullptr; - method->plength = nullptr; - method->index = nullptr; + delete [] pdata; + delete [] datatype; + delete [] cols; + delete [] maxcols; + delete [] collength; + delete [] plength; + delete [] index; } -/* ---------------------------------------------------------------------- - free memory in a method data structs -------------------------------------------------------------------------- */ +void AtomVec::Method::resize(int nfield) { + delete [] pdata; + delete [] datatype; + delete [] cols; + delete [] maxcols; + delete [] collength; + delete [] plength; + delete [] index; + pdata = nullptr; + datatype = nullptr; + cols = nullptr; + maxcols = nullptr; + collength = nullptr; + plength = nullptr; + index = nullptr; -void AtomVec::destroy_method(Method *method) -{ - delete [] method->pdata; - delete [] method->datatype; - delete [] method->cols; - delete [] method->maxcols; - delete [] method->collength; - delete [] method->plength; - delete [] method->index; + if (nfield > 0) { + pdata = new void*[nfield]; + datatype = new int[nfield]; + cols = new int[nfield]; + maxcols = new int*[nfield]; + collength = new int[nfield]; + plength = new void*[nfield]; + index = new int[nfield]; + } } diff --git a/src/atom_vec.h b/src/atom_vec.h index 8e670304ed..d1915ba508 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -191,13 +191,17 @@ class AtomVec : protected Pointers { const char *default_create,*default_data_atom,*default_data_vel; struct Method { - void **pdata; - int *datatype; - int *cols; - int **maxcols; - int *collength; - void **plength; - int *index; + void **pdata = nullptr; + int *datatype = nullptr; + int *cols = nullptr; + int **maxcols = nullptr; + int *collength = nullptr; + void **plength = nullptr; + int *index = nullptr; + + Method() = default; + ~Method(); + void resize(int nfield); }; Method mgrow,mcopy; @@ -219,9 +223,7 @@ class AtomVec : protected Pointers { int grow_nmax_bonus(int); void setup_fields(); int process_fields(char *, const char *, Method *); - void create_method(int, Method *); - void init_method(Method *); - void destroy_method(Method *); + void init_method(int, Method *); }; } From b15a813a591c0f297c9c86b0033e59025877e43a Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 15 Apr 2021 18:46:59 -0400 Subject: [PATCH 0542/1217] Avoid manual new / delete[] in AtomVec::Method --- src/atom_vec.cpp | 44 ++++++++------------------------------------ src/atom_vec.h | 16 +++++++--------- 2 files changed, 15 insertions(+), 45 deletions(-) diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index 78903d6a7f..eec09cf58a 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -2470,7 +2470,7 @@ int AtomVec::process_fields(char *str, const char *default_str, Method *method) // allocate memory in method method->resize(nfield); - int *index = method->index; + std::vector & index = method->index; int match; for (int i = 0; i < nfield; i++) { @@ -2523,40 +2523,12 @@ void AtomVec::init_method(int nfield, Method *method) Method class members ------------------------------------------------------------------------- */ -AtomVec::Method::~Method() -{ - delete [] pdata; - delete [] datatype; - delete [] cols; - delete [] maxcols; - delete [] collength; - delete [] plength; - delete [] index; -} - void AtomVec::Method::resize(int nfield) { - delete [] pdata; - delete [] datatype; - delete [] cols; - delete [] maxcols; - delete [] collength; - delete [] plength; - delete [] index; - pdata = nullptr; - datatype = nullptr; - cols = nullptr; - maxcols = nullptr; - collength = nullptr; - plength = nullptr; - index = nullptr; - - if (nfield > 0) { - pdata = new void*[nfield]; - datatype = new int[nfield]; - cols = new int[nfield]; - maxcols = new int*[nfield]; - collength = new int[nfield]; - plength = new void*[nfield]; - index = new int[nfield]; - } + pdata.resize(nfield); + datatype.resize(nfield); + cols.resize(nfield); + maxcols.resize(nfield); + collength.resize(nfield); + plength.resize(nfield); + index.resize(nfield); } diff --git a/src/atom_vec.h b/src/atom_vec.h index d1915ba508..a8f5f5ec22 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -191,16 +191,14 @@ class AtomVec : protected Pointers { const char *default_create,*default_data_atom,*default_data_vel; struct Method { - void **pdata = nullptr; - int *datatype = nullptr; - int *cols = nullptr; - int **maxcols = nullptr; - int *collength = nullptr; - void **plength = nullptr; - int *index = nullptr; + std::vector pdata; + std::vector datatype; + std::vector cols; + std::vector maxcols; + std::vector collength; + std::vector plength; + std::vector index; - Method() = default; - ~Method(); void resize(int nfield); }; From 9031c230801cc60fca3445134224337880466fca Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 16 Apr 2021 14:14:18 +0200 Subject: [PATCH 0543/1217] add extended dpd (dpdext & dpdext_tstat) --- doc/src/pair_dpdext.rst | 137 + examples/USER/dpdext/README | 10 + examples/USER/dpdext/dpdext/dpdext.data | 2196 +++++++++++++++++ examples/USER/dpdext/dpdext/in.dpdext | 44 + .../dpdext/dpdext/log.10Mar21.dpdext.g++.1 | 201 ++ .../dpdext/dpdext/log.10Mar21.dpdext.g++.4 | 201 ++ .../USER/dpdext/dpdext_tstat/cg_spce.data | 2196 +++++++++++++++++ .../dpdext/dpdext_tstat/cg_spce_table.pot | 354 +++ examples/USER/dpdext/dpdext_tstat/in.cg_spce | 31 + .../dpdext_tstat/log.10Mar21.dpdext.g++.1 | 293 +++ .../dpdext_tstat/log.10Mar21.dpdext.g++.4 | 293 +++ src/Makefile | 2 +- src/USER-DPDEXT/README | 10 + src/USER-DPDEXT/pair_dpd_ext.cpp | 496 ++++ src/USER-DPDEXT/pair_dpd_ext.h | 86 + src/USER-DPDEXT/pair_dpd_tstat_ext.cpp | 376 +++ src/USER-DPDEXT/pair_dpd_tstat_ext.h | 62 + 17 files changed, 6987 insertions(+), 1 deletion(-) create mode 100644 doc/src/pair_dpdext.rst create mode 100644 examples/USER/dpdext/README create mode 100755 examples/USER/dpdext/dpdext/dpdext.data create mode 100755 examples/USER/dpdext/dpdext/in.dpdext create mode 100644 examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 create mode 100644 examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 create mode 100755 examples/USER/dpdext/dpdext_tstat/cg_spce.data create mode 100755 examples/USER/dpdext/dpdext_tstat/cg_spce_table.pot create mode 100755 examples/USER/dpdext/dpdext_tstat/in.cg_spce create mode 100644 examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 create mode 100644 examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 create mode 100644 src/USER-DPDEXT/README create mode 100644 src/USER-DPDEXT/pair_dpd_ext.cpp create mode 100644 src/USER-DPDEXT/pair_dpd_ext.h create mode 100644 src/USER-DPDEXT/pair_dpd_tstat_ext.cpp create mode 100644 src/USER-DPDEXT/pair_dpd_tstat_ext.h diff --git a/doc/src/pair_dpdext.rst b/doc/src/pair_dpdext.rst new file mode 100644 index 0000000000..301f9f3ea0 --- /dev/null +++ b/doc/src/pair_dpdext.rst @@ -0,0 +1,137 @@ +.. index:: pair_style dpdext + +pair_style dpdext command +========================== + +pair_style dpdext/tstat command +================================ + +Syntax +"""""" + + +.. code-block:: LAMMPS + + pair_style dpdext T cutoff seed + pair_style dpdext/tstat Tstart Tstop cutoff seed + +* T = temperature (temperature units) +* Tstart,Tstop = desired temperature at start/end of run (temperature units) +* cutoff = global cutoff for DPD interactions (distance units) +* seed = random # seed (positive integer) + +Examples +"""""""" + + +.. code-block:: LAMMPS + + pair_style dpdext 1.0 2.5 34387 + pair_coeff 1 1 25.0 4.5 4.5 0.5 0.5 1.2 + pair_coeff 1 2 40.0 4.5 4.5 0.5 0.5 1.2 + + pair_style dpdext/tstat 1.0 1.0 2.5 34387 + pair_coeff 1 1 4.5 4.5 0.5 0.5 1.2 + pair_coeff 1 2 4.5 4.5 0.5 0.5 1.2 + +Description +""""""""""" + +The style *dpdext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) `, :ref:`(Junghans) `. + +Style *dpdext/tstat* invokes an extended DPD thermostat on pairwise interactions, which is equivalent to the non-conservative portion of the extended DPD force field. To use *dpdext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay ` command to compute both the desired pair interaction and the thermostat for each pair of particles. + +For the style *dpdext*\ , the force on atom I due to atom J is given as a sum +of 3 terms + +.. math:: + + \mathbf{f} = & f^C + f^D + f^R \qquad \qquad r < r_c \\ + f^C = & A_{ij} w(r) \hat{\mathbf{r}}_{ij} \\ + f^D = & - \gamma_{\parallel} w_{\parallel}^2(r) (\hat{\mathbf{r}}_{ij} \cdot \mathbf{v}_{ij}) \hat{\mathbf{r}}_{ij} - \gamma_{\perp} w_{\perp}^2 (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \mathbf{v}_{ij} \\ + f^R = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij} + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\ + w(r) = & 1 - r/r_c \\ + +where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\a` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command. + +For the style *dpdext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. + +For the style *dpdext*\ , the pairwise energy associated with style *dpdext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. For style *dpdext/tstat* there is no pairwise energy, but the last two terms of the formula make a contribution to the virial. + +For the style *dpdext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. + +For the style *dpdext*\ , the pairwise energy associated with style *dpdext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. For style *dpdext/tstat* there is no pairwise energy, but the last two terms of the formula make a contribution to the virial. + +For the style *dpdext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above: + +* A (force units) +* :math:`\gamma_{\perp}` (force/velocity units) +* :math:`\gamma_{\parallel}` (force/velocity units) +* :math:`s_{\perp}` (unitless) +* :math:`s_{\parallel}` (unitless) +* :math:`r_c` (distance units) + +The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that :math:`\sigma`'s are set equal to :math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by the :doc:`pair_style ` command so it does not need to be specified. + + +For the style *dpdext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff ` command is the same, except that A is not included. + +.. note:: + + If you are modeling DPD polymer chains, you may want to use the :doc:`pair_style srp ` command in conjunction with these pair styles. It is a soft segmental repulsive potential (SRP) that can prevent DPD polymer chains from crossing each other. + +.. note:: + + The virial calculation for pressure when using this pair style includes all the components of force listed above, including the random force. + +---------- + + +**Mixing, shift, table, tail correction, restart, rRESPA info**\ : + +The style *dpdext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. + +The pair styles do not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. Note that as discussed above, the energy due to the conservative :math:`\mathbf{f}^C` term is already shifted to be zero at the cutoff distance :math:`r_c`. + +The :doc:`pair_modify ` table option is not relevant for the style *dpdext*. + +The style *dpdext* does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. + +The pair styles can only be used via the pair keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , and *outer*\ keywords. + +The style *dpdext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. + +---------- + + +Restrictions +"""""""""""" + +The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too infrequent for style *dpdext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. + +The pair styles require to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. + +The pair styles will not restart exactly when using the :doc:`read_restart ` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the :doc:`read_restart ` command for more details. + +Related commands +"""""""""""""""" + +:doc:`pair_style dpd `, :doc:`pair_coeff `, :doc:`fix nvt `, :doc:`fix langevin `, :doc:`pair_style srp ` + +**Default:** none + + +---------- + + +.. _Groot: + + + +**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997). + +.. _Junghans: + + + +**(Junghans)** Junghans, Praprotnik and Kremer, Soft Matter 4, 156, 1119-1128 (2008). diff --git a/examples/USER/dpdext/README b/examples/USER/dpdext/README new file mode 100644 index 0000000000..43d66c4bd3 --- /dev/null +++ b/examples/USER/dpdext/README @@ -0,0 +1,10 @@ +Examples for Extended Dissipative Particle Dynamics (DPD) +--------------------------------------------------------- +This directory contains examples for extended DPD simulations + +1) 'dpdext' - test case (DPD fluid) for 'dpdext' pair style (in.dpdext) and an initial + configuration (dpdext.data) + +2) 'dpdext_tstat' - test case (coarse-grained SPC/E water) for 'dpdext/tstat' pair style + (in.cg_spce), an initial configuration (dpdext.data) and tabulated potential + (cg_spce_table.pot) obtained by bottom-up coarse-graining of the atomistic SPC/E water. diff --git a/examples/USER/dpdext/dpdext/dpdext.data b/examples/USER/dpdext/dpdext/dpdext.data new file mode 100755 index 0000000000..dddbf6ad6c --- /dev/null +++ b/examples/USER/dpdext/dpdext/dpdext.data @@ -0,0 +1,2196 @@ + DPD Fluid + + 2180 atoms + + 1 atom types + + 0.0000000E+00 40.310000000000 xlo xhi + 0.0000000E+00 40.310000000000 ylo yhi + 0.0000000E+00 40.310000000000 zlo zhi + + Masses + +1 18.01540 + + Atoms + +1 1 2.815000E+01 5.430000E+00 2.370000E+00 +2 1 1.890000E+00 2.957000E+01 1.761000E+01 +3 1 8.920000E+00 3.556000E+01 8.240000E+00 +4 1 2.307000E+01 9.600000E+00 4.710000E+00 +5 1 1.688000E+01 8.940000E+00 3.880000E+00 +6 1 2.571000E+01 1.277000E+01 1.056000E+01 +7 1 2.788000E+01 3.328000E+01 1.300000E-01 +8 1 3.287000E+01 2.050000E+00 1.368000E+01 +9 1 4.900000E+00 2.183000E+01 1.751000E+01 +10 1 9.670000E+00 3.108000E+01 1.843000E+01 +11 1 1.233000E+01 3.490000E+00 1.091000E+01 +12 1 6.630000E+00 1.581000E+01 3.455000E+01 +13 1 3.951000E+01 2.047000E+01 2.288000E+01 +14 1 3.977000E+01 3.173000E+01 9.060000E+00 +15 1 5.370000E+00 8.940000E+00 3.646000E+01 +16 1 2.129000E+01 3.853000E+01 3.468000E+01 +17 1 1.987000E+01 2.677000E+01 3.762000E+01 +18 1 2.658000E+01 3.167000E+01 2.280000E+00 +19 1 1.231000E+01 3.336000E+01 1.098000E+01 +20 1 7.310000E+00 1.410000E+01 1.654000E+01 +21 1 3.388000E+01 2.584000E+01 1.677000E+01 +22 1 1.115000E+01 3.070000E+00 3.992000E+01 +23 1 3.171000E+01 3.195000E+01 2.267000E+01 +24 1 5.960000E+00 3.507000E+01 1.230000E+01 +25 1 2.904000E+01 1.740000E+00 9.460000E+00 +26 1 1.539000E+01 2.686000E+01 2.030000E+00 +27 1 3.890000E+00 2.148000E+01 2.877000E+01 +28 1 4.550000E+00 2.800000E+01 2.431000E+01 +29 1 9.680000E+00 3.992000E+01 2.964000E+01 +30 1 2.560000E+00 3.939000E+01 2.987000E+01 +31 1 4.960000E+00 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2.253000E+01 1.992000E+01 1.380000E+01 +2113 1 1.176000E+01 1.405000E+01 3.903000E+01 +2114 1 1.018000E+01 9.280000E+00 8.030000E+00 +2115 1 1.445000E+01 2.184000E+01 3.200000E+01 +2116 1 1.692000E+01 2.470000E+01 1.871000E+01 +2117 1 2.841000E+01 2.090000E+01 1.081000E+01 +2118 1 1.582000E+01 9.670000E+00 1.823000E+01 +2119 1 3.260000E+00 4.080000E+00 3.358000E+01 +2120 1 3.262000E+01 2.107000E+01 3.990000E+00 +2121 1 1.652000E+01 1.218000E+01 3.564000E+01 +2122 1 2.648000E+01 2.505000E+01 2.501000E+01 +2123 1 3.168000E+01 8.160000E+00 2.482000E+01 +2124 1 1.468000E+01 1.968000E+01 2.087000E+01 +2125 1 1.103000E+01 2.608000E+01 6.010000E+00 +2126 1 1.102000E+01 1.184000E+01 2.603000E+01 +2127 1 3.776000E+01 3.770000E+00 1.490000E+00 +2128 1 2.031000E+01 2.734000E+01 6.700000E-01 +2129 1 3.770000E+00 3.563000E+01 4.170000E+00 +2130 1 4.490000E+00 2.167000E+01 1.302000E+01 +2131 1 3.730000E+00 2.565000E+01 1.098000E+01 +2132 1 3.893000E+01 2.628000E+01 3.085000E+01 +2133 1 1.716000E+01 7.780000E+00 1.678000E+01 +2134 1 3.330000E+01 3.916000E+01 1.899000E+01 +2135 1 3.264000E+01 4.210000E+00 2.427000E+01 +2136 1 1.114000E+01 8.100000E+00 2.329000E+01 +2137 1 1.026000E+01 8.900000E-01 2.724000E+01 +2138 1 2.257000E+01 2.754000E+01 3.789000E+01 +2139 1 2.495000E+01 2.840000E+01 3.687000E+01 +2140 1 3.977000E+01 2.981000E+01 5.800000E+00 +2141 1 2.256000E+01 3.840000E+00 6.270000E+00 +2142 1 7.580000E+00 1.410000E+01 3.520000E+00 +2143 1 1.702000E+01 3.918000E+01 9.200000E+00 +2144 1 2.898000E+01 1.973000E+01 3.924000E+01 +2145 1 4.020000E+01 1.529000E+01 2.723000E+01 +2146 1 7.220000E+00 2.652000E+01 2.819000E+01 +2147 1 1.020000E+01 4.510000E+00 2.913000E+01 +2148 1 1.075000E+01 1.786000E+01 8.600000E+00 +2149 1 2.851000E+01 6.170000E+00 2.682000E+01 +2150 1 1.450000E+00 2.132000E+01 4.020000E+00 +2151 1 4.360000E+00 1.142000E+01 4.500000E-01 +2152 1 6.800000E+00 2.136000E+01 2.166000E+01 +2153 1 1.803000E+01 3.907000E+01 4.900000E+00 +2154 1 3.187000E+01 1.368000E+01 1.983000E+01 +2155 1 3.040000E+01 9.820000E+00 3.786000E+01 +2156 1 3.694000E+01 5.550000E+00 1.614000E+01 +2157 1 1.520000E+00 2.840000E+00 7.180000E+00 +2158 1 7.550000E+00 3.788000E+01 1.150000E+00 +2159 1 3.262000E+01 8.680000E+00 1.004000E+01 +2160 1 9.400000E+00 1.616000E+01 1.029000E+01 +2161 1 5.980000E+00 1.628000E+01 2.001000E+01 +2162 1 1.590000E+00 2.898000E+01 2.510000E+00 +2163 1 2.260000E+00 2.503000E+01 2.702000E+01 +2164 1 3.725000E+01 2.886000E+01 1.681000E+01 +2165 1 1.751000E+01 3.490000E+01 2.327000E+01 +2166 1 2.729000E+01 1.952000E+01 2.661000E+01 +2167 1 8.190000E+00 3.201000E+01 2.417000E+01 +2168 1 7.080000E+00 2.577000E+01 1.091000E+01 +2169 1 3.065000E+01 6.030000E+00 2.910000E+00 +2170 1 2.078000E+01 1.994000E+01 1.970000E+01 +2171 1 7.100000E-01 7.250000E+00 1.784000E+01 +2172 1 3.287000E+01 8.740000E+00 1.891000E+01 +2173 1 1.178000E+01 2.800000E+01 1.470000E+01 +2174 1 2.178000E+01 2.015000E+01 3.462000E+01 +2175 1 3.874000E+01 1.992000E+01 1.613000E+01 +2176 1 3.554000E+01 3.239000E+01 3.856000E+01 +2177 1 1.772000E+01 4.020000E+01 1.210000E+00 +2178 1 2.093000E+01 1.558000E+01 2.323000E+01 +2179 1 8.900000E+00 2.592000E+01 3.849000E+01 +2180 1 1.428000E+01 6.460000E+00 3.351000E+01 diff --git a/examples/USER/dpdext/dpdext/in.dpdext b/examples/USER/dpdext/dpdext/in.dpdext new file mode 100755 index 0000000000..3101be9a1c --- /dev/null +++ b/examples/USER/dpdext/dpdext/in.dpdext @@ -0,0 +1,44 @@ +# DPD Fluid + +variable T equal 1.0 +variable rc equal 1.0 +variable rcD equal 1.2 + +units lj +boundary p p p +atom_style atomic +dimension 3 +newton on +comm_modify vel yes + +### create box and configuration +variable L equal 5.0 +lattice fcc 3.0 +region simBox block 0 ${L} 0 ${L} 0 ${L} +create_box 2 simBox +#create_atoms 1 region simBox +create_atoms 1 random 100 132456 simBox +create_atoms 2 random 100 132456 simBox +mass 1 1.0 +mass 2 2.0 +### + +pair_style dpdext ${T} ${rc} 3854262 + +pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD} +pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD} +pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD} + +timestep 0.01 +run_style verlet + +velocity all create ${T} 68768932 + +thermo_style custom step time temp press +thermo 500 + +fix 1 all nve + +run 50000 + +write_data final.data pair ij \ No newline at end of file diff --git a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 b/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 new file mode 100644 index 0000000000..ef61ed11b8 --- /dev/null +++ b/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 @@ -0,0 +1,201 @@ +LAMMPS (10 Mar 2021) +# DPD Fluid + +variable T equal 1.0 +variable rc equal 1.0 +variable rcD equal 1.2 + +units lj +boundary p p p +atom_style atomic +dimension 3 +newton on +comm_modify vel yes + +### create box and configuration +variable L equal 5.0 +lattice fcc 3.0 +Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424 +region simBox block 0 ${L} 0 ${L} 0 ${L} +region simBox block 0 5 0 ${L} 0 ${L} +region simBox block 0 5 0 5 0 ${L} +region simBox block 0 5 0 5 0 5 +create_box 2 simBox +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.5032121 5.5032121 5.5032121) + 1 by 1 by 1 MPI processor grid +#create_atoms 1 region simBox +create_atoms 1 random 100 132456 simBox +Created 100 atoms + create_atoms CPU = 0.001 seconds +create_atoms 2 random 100 132456 simBox +Created 100 atoms + create_atoms CPU = 0.000 seconds +mass 1 1.0 +mass 2 2.0 +### + +pair_style dpdext ${T} ${rc} 3854262 +pair_style dpdext 1 ${rc} 3854262 +pair_style dpdext 1 1 3854262 + +pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD} +pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD} +pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD} + +timestep 0.01 +run_style verlet + +velocity all create ${T} 68768932 +velocity all create 1 68768932 + +thermo_style custom step time temp press +thermo 500 + +fix 1 all nve + +run 50000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.52 + ghost atom cutoff = 1.52 + binsize = 0.76, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair dpdext, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.087 | 3.087 | 3.087 Mbytes +Step Time Temp Press + 0 0 1 8.8992215 + 500 5 0.93699892 8.1219621 + 1000 10 0.99211009 7.4709658 + 1500 15 0.91190984 8.828742 + 2000 20 0.90749036 9.1258378 + 2500 25 0.97960404 7.085574 + 3000 30 1.0314836 6.8400202 + 3500 35 1.0137019 7.2346862 + 4000 40 0.98189616 6.7265624 + 4500 45 1.0127497 6.6718402 + 5000 50 0.90659787 7.4911309 + 5500 55 1.0257891 6.8163777 + 6000 60 1.0596209 7.8511522 + 6500 65 0.95679865 8.4091947 + 7000 70 1.012617 7.4162991 + 7500 75 1.0990412 7.160905 + 8000 80 0.91085269 7.6861008 + 8500 85 1.1000209 6.4818934 + 9000 90 0.99982282 8.1312206 + 9500 95 1.1330979 7.7167159 + 10000 100 0.98147521 8.4394218 + 10500 105 1.0254021 7.23574 + 11000 110 0.94064194 7.9766833 + 11500 115 1.012364 8.4285752 + 12000 120 0.94787277 7.0819132 + 12500 125 1.13729 7.9636837 + 13000 130 1.1200519 7.1570016 + 13500 135 0.96797085 8.9794827 + 14000 140 1.0271217 7.4193307 + 14500 145 1.0154843 7.3495938 + 15000 150 1.0408558 7.3047404 + 15500 155 1.0801685 6.8072764 + 16000 160 0.9921089 7.3200563 + 16500 165 0.92952943 7.281934 + 17000 170 0.87149276 7.6508951 + 17500 175 0.92808338 6.4774803 + 18000 180 1.008898 7.1954708 + 18500 185 0.95962238 8.0257166 + 19000 190 0.99501354 8.5364854 + 19500 195 0.97420657 8.3140832 + 20000 200 0.99926953 7.7840117 + 20500 205 1.0503096 7.9214552 + 21000 210 0.97782558 7.4084605 + 21500 215 0.90363877 7.2867997 + 22000 220 1.0045369 7.7341956 + 22500 225 1.0319487 8.4140146 + 23000 230 1.006863 7.6023442 + 23500 235 0.90302749 8.0230562 + 24000 240 1.0768463 7.7315652 + 24500 245 1.0529241 7.9835388 + 25000 250 0.96057288 6.9591339 + 25500 255 0.98941425 7.4287206 + 26000 260 0.99120107 7.0440907 + 26500 265 0.94017831 7.9499345 + 27000 270 0.93766339 8.118634 + 27500 275 0.98309918 7.9865412 + 28000 280 1.0191736 8.3330592 + 28500 285 0.99546328 8.3419405 + 29000 290 0.95703084 7.313665 + 29500 295 1.0122694 8.1900103 + 30000 300 1.0758207 8.2876755 + 30500 305 1.0981472 6.4742286 + 31000 310 1.0356215 6.4857599 + 31500 315 0.95584989 8.4446078 + 32000 320 1.0591455 8.3936647 + 32500 325 0.92674627 7.0391747 + 33000 330 0.93486399 7.6892746 + 33500 335 1.0772579 7.1395468 + 34000 340 1.1029975 7.4249835 + 34500 345 0.9845352 6.3478805 + 35000 350 1.1004884 8.0179815 + 35500 355 0.97596833 8.1652441 + 36000 360 1.0026086 7.8100907 + 36500 365 1.0242946 7.4683685 + 37000 370 0.98485255 7.9021959 + 37500 375 1.078371 8.726722 + 38000 380 0.99139516 7.3585787 + 38500 385 1.0531594 8.5221732 + 39000 390 1.0290073 7.0905003 + 39500 395 1.0368491 8.0293456 + 40000 400 1.0520724 7.6372283 + 40500 405 0.94925657 8.9578914 + 41000 410 0.99919726 7.7207005 + 41500 415 1.0507736 6.9924906 + 42000 420 1.0442899 7.8115665 + 42500 425 1.0192672 8.5123404 + 43000 430 0.9784861 8.0556966 + 43500 435 0.99592222 8.0665153 + 44000 440 0.95621235 8.4132911 + 44500 445 0.93400296 7.3266133 + 45000 450 1.0389454 7.2458003 + 45500 455 1.1076673 6.5868539 + 46000 460 1.0826918 7.9286381 + 46500 465 0.93589963 8.5310745 + 47000 470 1.0352143 6.6366463 + 47500 475 1.0497186 8.5074329 + 48000 480 0.96107226 7.7505527 + 48500 485 1.1061337 8.2753596 + 49000 490 1.0337198 7.5777833 + 49500 495 0.94052507 7.3661443 + 50000 500 0.98527818 7.1746325 +Loop time of 10.2559 on 1 procs for 50000 steps with 200 atoms + +Performance: 4212216.548 tau/day, 4875.251 timesteps/s +99.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.9888 | 8.9888 | 8.9888 | 0.0 | 87.65 +Neigh | 0.832 | 0.832 | 0.832 | 0.0 | 8.11 +Comm | 0.30913 | 0.30913 | 0.30913 | 0.0 | 3.01 +Output | 0.0021966 | 0.0021966 | 0.0021966 | 0.0 | 0.02 +Modify | 0.084161 | 0.084161 | 0.084161 | 0.0 | 0.82 +Other | | 0.03957 | | | 0.39 + +Nlocal: 200.000 ave 200 max 200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 547.000 ave 547 max 547 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1651.00 ave 1651 max 1651 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1651 +Ave neighs/atom = 8.2550000 +Neighbor list builds = 5000 +Dangerous builds = 5000 + +write_data final.data pair ij +System init for write_data ... +Total wall time: 0:00:10 diff --git a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 b/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 new file mode 100644 index 0000000000..bbbf47a46c --- /dev/null +++ b/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 @@ -0,0 +1,201 @@ +LAMMPS (10 Mar 2021) +# DPD Fluid + +variable T equal 1.0 +variable rc equal 1.0 +variable rcD equal 1.2 + +units lj +boundary p p p +atom_style atomic +dimension 3 +newton on +comm_modify vel yes + +### create box and configuration +variable L equal 5.0 +lattice fcc 3.0 +Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424 +region simBox block 0 ${L} 0 ${L} 0 ${L} +region simBox block 0 5 0 ${L} 0 ${L} +region simBox block 0 5 0 5 0 ${L} +region simBox block 0 5 0 5 0 5 +create_box 2 simBox +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.5032121 5.5032121 5.5032121) + 1 by 2 by 2 MPI processor grid +#create_atoms 1 region simBox +create_atoms 1 random 100 132456 simBox +Created 100 atoms + create_atoms CPU = 0.001 seconds +create_atoms 2 random 100 132456 simBox +Created 100 atoms + create_atoms CPU = 0.000 seconds +mass 1 1.0 +mass 2 2.0 +### + +pair_style dpdext ${T} ${rc} 3854262 +pair_style dpdext 1 ${rc} 3854262 +pair_style dpdext 1 1 3854262 + +pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD} +pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD} +pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD} + +timestep 0.01 +run_style verlet + +velocity all create ${T} 68768932 +velocity all create 1 68768932 + +thermo_style custom step time temp press +thermo 500 + +fix 1 all nve + +run 50000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.52 + ghost atom cutoff = 1.52 + binsize = 0.76, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair dpdext, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.064 | 3.064 | 3.064 Mbytes +Step Time Temp Press + 0 0 1 7.9021356 + 500 5 0.937908 7.0735774 + 1000 10 0.89467862 7.7074585 + 1500 15 1.0197239 8.6662041 + 2000 20 1.0306203 8.0831978 + 2500 25 0.94106312 7.4609953 + 3000 30 1.0217162 7.7000536 + 3500 35 0.9694633 6.9496101 + 4000 40 0.89886564 7.5844291 + 4500 45 0.9914389 6.5459858 + 5000 50 1.0503316 7.1639528 + 5500 55 0.95397384 7.2900451 + 6000 60 0.91097079 7.4484481 + 6500 65 1.0212125 8.6396803 + 7000 70 0.84788375 9.2247619 + 7500 75 1.0477577 7.9631111 + 8000 80 1.0473514 7.2904431 + 8500 85 1.0482936 7.9668363 + 9000 90 1.0239558 7.1715815 + 9500 95 1.0727305 8.2075133 + 10000 100 0.96755536 7.8062307 + 10500 105 1.0357222 8.2249507 + 11000 110 1.053488 6.8283393 + 11500 115 0.89283913 8.9044509 + 12000 120 1.0085932 8.1844316 + 12500 125 0.84259725 6.9608932 + 13000 130 1.0559908 7.5907714 + 13500 135 0.95175487 8.8486631 + 14000 140 0.954129 8.2199072 + 14500 145 1.0034836 8.6956618 + 15000 150 0.99411864 7.3723436 + 15500 155 1.0876662 8.5906664 + 16000 160 0.98613154 7.6599681 + 16500 165 1.0355659 6.7243908 + 17000 170 1.0838802 7.5905171 + 17500 175 0.95966717 7.3268842 + 18000 180 0.91267962 8.1126836 + 18500 185 0.9625394 8.0889468 + 19000 190 1.0209688 7.2104928 + 19500 195 0.93315956 8.3484128 + 20000 200 1.0430989 6.4154856 + 20500 205 1.037892 7.3727084 + 21000 210 1.0551654 8.3732908 + 21500 215 0.97922101 8.0403654 + 22000 220 1.0480356 9.2304431 + 22500 225 1.0009668 8.0807868 + 23000 230 1.0808549 7.9128664 + 23500 235 0.99282487 7.550466 + 24000 240 0.96893196 8.0123396 + 24500 245 0.96945612 6.9129899 + 25000 250 0.9373397 6.2942852 + 25500 255 0.98958822 7.8259805 + 26000 260 0.97971277 7.3263113 + 26500 265 0.91588062 8.284996 + 27000 270 1.0045677 7.490418 + 27500 275 0.92664827 7.2434156 + 28000 280 0.98527367 7.1695053 + 28500 285 0.97862372 8.2272887 + 29000 290 1.067876 8.3157621 + 29500 295 1.0688998 7.5106281 + 30000 300 1.117583 8.8135518 + 30500 305 1.035452 7.3572033 + 31000 310 1.03275 8.1486503 + 31500 315 0.96000074 7.6740792 + 32000 320 0.91763282 7.6603754 + 32500 325 0.99394287 8.8127132 + 33000 330 1.0021499 7.9881263 + 33500 335 0.97639399 8.2361021 + 34000 340 1.0309313 8.2918535 + 34500 345 1.0214124 7.3886765 + 35000 350 1.0029326 8.2745874 + 35500 355 1.0634485 6.4161924 + 36000 360 1.0242523 7.4099968 + 36500 365 1.0302234 8.0604043 + 37000 370 1.0143945 7.34914 + 37500 375 0.99553421 6.8818266 + 38000 380 1.0073546 7.6254332 + 38500 385 1.0068118 7.4673312 + 39000 390 0.95181135 6.1644033 + 39500 395 0.98964849 8.501371 + 40000 400 0.99441011 8.1515808 + 40500 405 1.0339683 7.6747037 + 41000 410 0.99467835 7.8743708 + 41500 415 1.0231331 7.3169584 + 42000 420 0.94617359 8.0079888 + 42500 425 1.0163237 7.7949198 + 43000 430 0.97039825 8.8842702 + 43500 435 1.0326956 7.6700965 + 44000 440 1.1106283 8.2900664 + 44500 445 0.96697428 7.0408563 + 45000 450 1.0137186 6.8316108 + 45500 455 1.0531692 8.0051631 + 46000 460 1.0382619 7.2937333 + 46500 465 0.90277459 7.9676952 + 47000 470 1.00751 8.7594948 + 47500 475 0.95565907 8.320444 + 48000 480 1.0396091 7.9262425 + 48500 485 1.0349892 8.333501 + 49000 490 0.9759139 7.4839858 + 49500 495 0.91538068 7.1780491 + 50000 500 1.0310634 7.1522794 +Loop time of 9.14414 on 4 procs for 50000 steps with 200 atoms + +Performance: 4724338.550 tau/day, 5467.984 timesteps/s +96.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.0824 | 5.212 | 5.3376 | 5.1 | 57.00 +Neigh | 0.49498 | 0.50029 | 0.505 | 0.6 | 5.47 +Comm | 3.1637 | 3.2822 | 3.4143 | 6.3 | 35.89 +Output | 0.0025831 | 0.003088 | 0.004569 | 1.5 | 0.03 +Modify | 0.067261 | 0.068927 | 0.070535 | 0.5 | 0.75 +Other | | 0.07762 | | | 0.85 + +Nlocal: 50.0000 ave 53 max 46 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Nghost: 296.000 ave 301 max 290 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 410.750 ave 431 max 357 min +Histogram: 1 0 0 0 0 0 0 0 0 3 + +Total # of neighbors = 1643 +Ave neighs/atom = 8.2150000 +Neighbor list builds = 5000 +Dangerous builds = 5000 + +write_data final.data pair ij +System init for write_data ... +Total wall time: 0:00:09 diff --git a/examples/USER/dpdext/dpdext_tstat/cg_spce.data b/examples/USER/dpdext/dpdext_tstat/cg_spce.data new file mode 100755 index 0000000000..d487e2c73c --- /dev/null +++ b/examples/USER/dpdext/dpdext_tstat/cg_spce.data @@ -0,0 +1,2196 @@ + Coarse-Grained SPC/E Water + + 2180 atoms + + 1 atom types + + 0.0000000E+00 40.310000000000 xlo xhi + 0.0000000E+00 40.310000000000 ylo yhi + 0.0000000E+00 40.310000000000 zlo zhi + + Masses + +1 18.01540 + + Atoms + +1 1 2.815000E+01 5.430000E+00 2.370000E+00 +2 1 1.890000E+00 2.957000E+01 1.761000E+01 +3 1 8.920000E+00 3.556000E+01 8.240000E+00 +4 1 2.307000E+01 9.600000E+00 4.710000E+00 +5 1 1.688000E+01 8.940000E+00 3.880000E+00 +6 1 2.571000E+01 1.277000E+01 1.056000E+01 +7 1 2.788000E+01 3.328000E+01 1.300000E-01 +8 1 3.287000E+01 2.050000E+00 1.368000E+01 +9 1 4.900000E+00 2.183000E+01 1.751000E+01 +10 1 9.670000E+00 3.108000E+01 1.843000E+01 +11 1 1.233000E+01 3.490000E+00 1.091000E+01 +12 1 6.630000E+00 1.581000E+01 3.455000E+01 +13 1 3.951000E+01 2.047000E+01 2.288000E+01 +14 1 3.977000E+01 3.173000E+01 9.060000E+00 +15 1 5.370000E+00 8.940000E+00 3.646000E+01 +16 1 2.129000E+01 3.853000E+01 3.468000E+01 +17 1 1.987000E+01 2.677000E+01 3.762000E+01 +18 1 2.658000E+01 3.167000E+01 2.280000E+00 +19 1 1.231000E+01 3.336000E+01 1.098000E+01 +20 1 7.310000E+00 1.410000E+01 1.654000E+01 +21 1 3.388000E+01 2.584000E+01 1.677000E+01 +22 1 1.115000E+01 3.070000E+00 3.992000E+01 +23 1 3.171000E+01 3.195000E+01 2.267000E+01 +24 1 5.960000E+00 3.507000E+01 1.230000E+01 +25 1 2.904000E+01 1.740000E+00 9.460000E+00 +26 1 1.539000E+01 2.686000E+01 2.030000E+00 +27 1 3.890000E+00 2.148000E+01 2.877000E+01 +28 1 4.550000E+00 2.800000E+01 2.431000E+01 +29 1 9.680000E+00 3.992000E+01 2.964000E+01 +30 1 2.560000E+00 3.939000E+01 2.987000E+01 +31 1 4.960000E+00 2.280000E+01 6.230000E+00 +32 1 2.795000E+01 3.511000E+01 9.810000E+00 +33 1 3.254000E+01 3.032000E+01 3.025000E+01 +34 1 2.292000E+01 3.033000E+01 1.730000E+01 +35 1 2.190000E+00 2.025000E+01 3.929000E+01 +36 1 9.460000E+00 3.815000E+01 6.950000E+00 +37 1 2.409000E+01 2.885000E+01 7.730000E+00 +38 1 3.711000E+01 3.888000E+01 3.314000E+01 +39 1 3.492000E+01 1.987000E+01 8.240000E+00 +40 1 1.350000E+00 3.799000E+01 3.885000E+01 +41 1 3.289000E+01 3.289000E+01 1.859000E+01 +42 1 3.337000E+01 1.603000E+01 3.141000E+01 +43 1 5.120000E+00 6.540000E+00 3.231000E+01 +44 1 5.080000E+00 3.640000E+00 2.178000E+01 +45 1 7.090000E+00 1.072000E+01 1.911000E+01 +46 1 2.804000E+01 1.444000E+01 2.027000E+01 +47 1 2.972000E+01 3.928000E+01 2.997000E+01 +48 1 2.170000E+01 3.263000E+01 3.100000E+01 +49 1 3.063000E+01 8.940000E+00 3.410000E+00 +50 1 2.400000E+00 1.484000E+01 2.534000E+01 +51 1 2.128000E+01 3.944000E+01 1.892000E+01 +52 1 3.616000E+01 3.993000E+01 1.443000E+01 +53 1 2.416000E+01 2.414000E+01 1.280000E+01 +54 1 3.177000E+01 1.047000E+01 1.568000E+01 +55 1 4.024000E+01 1.188000E+01 3.343000E+01 +56 1 6.040000E+00 1.367000E+01 4.028000E+01 +57 1 1.537000E+01 3.589000E+01 6.930000E+00 +58 1 1.231000E+01 2.220000E+00 1.471000E+01 +59 1 3.450000E+00 4.810000E+00 2.487000E+01 +60 1 1.589000E+01 2.520000E+00 1.705000E+01 +61 1 3.705000E+01 3.620000E+01 6.730000E+00 +62 1 3.777000E+01 2.710000E+01 4.029000E+01 +63 1 8.260000E+00 2.033000E+01 4.030000E+01 +64 1 8.210000E+00 3.558000E+01 1.717000E+01 +65 1 3.338000E+01 1.389000E+01 2.210000E+01 +66 1 1.454000E+01 1.650000E+00 1.300000E+01 +67 1 1.977000E+01 3.489000E+01 1.751000E+01 +68 1 5.630000E+00 4.220000E+00 3.875000E+01 +69 1 7.570000E+00 2.576000E+01 1.371000E+01 +70 1 9.340000E+00 3.392000E+01 3.538000E+01 +71 1 2.116000E+01 8.590000E+00 1.475000E+01 +72 1 2.328000E+01 4.022000E+01 1.138000E+01 +73 1 1.298000E+01 3.479000E+01 2.338000E+01 +74 1 2.232000E+01 3.339000E+01 5.320000E+00 +75 1 3.290000E+00 3.240000E+01 2.024000E+01 +76 1 3.794000E+01 3.982000E+01 1.790000E+00 +77 1 1.111000E+01 1.440000E+01 2.301000E+01 +78 1 2.556000E+01 1.714000E+01 1.684000E+01 +79 1 2.500000E+00 2.474000E+01 2.028000E+01 +80 1 1.692000E+01 3.837000E+01 1.303000E+01 +81 1 6.310000E+00 2.551000E+01 3.960000E+01 +82 1 2.402000E+01 1.966000E+01 2.905000E+01 +83 1 2.216000E+01 9.500000E+00 2.543000E+01 +84 1 2.006000E+01 3.431000E+01 4.260000E+00 +85 1 2.198000E+01 8.670000E+00 2.806000E+01 +86 1 1.465000E+01 2.763000E+01 8.340000E+00 +87 1 3.975000E+01 3.870000E+00 3.701000E+01 +88 1 2.952000E+01 7.340000E+00 5.310000E+00 +89 1 2.759000E+01 1.589000E+01 3.402000E+01 +90 1 3.746000E+01 3.945000E+01 2.486000E+01 +91 1 2.370000E+01 2.429000E+01 2.803000E+01 +92 1 1.270000E+01 1.653000E+01 2.314000E+01 +93 1 1.653000E+01 2.786000E+01 2.885000E+01 +94 1 3.146000E+01 2.340000E+00 8.320000E+00 +95 1 3.406000E+01 2.124000E+01 2.389000E+01 +96 1 5.130000E+00 1.574000E+01 8.360000E+00 +97 1 3.087000E+01 6.020000E+00 2.295000E+01 +98 1 3.607000E+01 3.674000E+01 9.200000E+00 +99 1 2.507000E+01 2.107000E+01 3.778000E+01 +100 1 3.351000E+01 4.870000E+00 1.301000E+01 +101 1 2.978000E+01 1.879000E+01 1.277000E+01 +102 1 2.496000E+01 1.400000E-01 3.900000E+01 +103 1 3.761000E+01 3.179000E+01 2.540000E+00 +104 1 2.600000E+00 6.800000E+00 3.347000E+01 +105 1 2.570000E+01 3.173000E+01 1.831000E+01 +106 1 9.460000E+00 1.524000E+01 2.542000E+01 +107 1 2.255000E+01 2.515000E+01 2.190000E+00 +108 1 1.902000E+01 1.988000E+01 3.138000E+01 +109 1 9.450000E+00 3.164000E+01 2.652000E+01 +110 1 6.810000E+00 9.420000E+00 1.463000E+01 +111 1 1.651000E+01 5.200000E+00 2.836000E+01 +112 1 2.234000E+01 2.475000E+01 3.956000E+01 +113 1 3.805000E+01 2.946000E+01 9.080000E+00 +114 1 3.553000E+01 1.590000E+01 1.032000E+01 +115 1 2.565000E+01 3.402000E+01 1.062000E+01 +116 1 1.554000E+01 5.410000E+00 3.926000E+01 +117 1 2.449000E+01 1.282000E+01 1.305000E+01 +118 1 1.590000E+00 3.743000E+01 3.398000E+01 +119 1 1.954000E+01 9.570000E+00 1.179000E+01 +120 1 9.870000E+00 1.497000E+01 1.872000E+01 +121 1 2.925000E+01 3.397000E+01 7.650000E+00 +122 1 2.738000E+01 3.514000E+01 2.980000E+01 +123 1 3.704000E+01 2.310000E+00 2.189000E+01 +124 1 1.988000E+01 1.471000E+01 1.600000E-01 +125 1 1.118000E+01 1.476000E+01 3.354000E+01 +126 1 3.100000E-01 2.588000E+01 3.313000E+01 +127 1 3.437000E+01 2.586000E+01 2.337000E+01 +128 1 3.931000E+01 3.398000E+01 3.424000E+01 +129 1 7.070000E+00 3.063000E+01 2.188000E+01 +130 1 1.840000E+00 1.104000E+01 1.974000E+01 +131 1 1.924000E+01 3.244000E+01 3.670000E+01 +132 1 1.675000E+01 3.463000E+01 1.524000E+01 +133 1 1.670000E+01 3.557000E+01 2.765000E+01 +134 1 3.999000E+01 3.970000E+01 2.385000E+01 +135 1 3.096000E+01 5.990000E+00 1.962000E+01 +136 1 2.357000E+01 1.297000E+01 2.012000E+01 +137 1 5.010000E+00 1.524000E+01 3.843000E+01 +138 1 6.180000E+00 1.152000E+01 2.331000E+01 +139 1 1.200000E+00 2.550000E+01 2.334000E+01 +140 1 4.210000E+00 2.882000E+01 1.460000E+00 +141 1 5.750000E+00 2.729000E+01 7.300000E+00 +142 1 2.792000E+01 6.980000E+00 2.345000E+01 +143 1 9.150000E+00 1.540000E+00 3.415000E+01 +144 1 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+347 8.920000E+00 6.079481E-04 -2.335309E-04 +348 8.940000E+00 5.700798E-04 3.964121E-03 +349 8.960000E+00 4.516330E-04 7.824320E-03 +350 8.980000E+00 2.593567E-04 1.134707E-02 +351 9.000000E+00 0.000000E+00 1.453236E-02 diff --git a/examples/USER/dpdext/dpdext_tstat/in.cg_spce b/examples/USER/dpdext/dpdext_tstat/in.cg_spce new file mode 100755 index 0000000000..ea1a3dfcba --- /dev/null +++ b/examples/USER/dpdext/dpdext_tstat/in.cg_spce @@ -0,0 +1,31 @@ +# Coarse-Grained SPC/E Water + +variable T equal 300.0 +variable rc equal 9.0 +variable rcD equal 10.0 + +units real +boundary p p p +atom_style atomic +dimension 3 +newton on +comm_modify vel yes + +read_data cg_spce.data + +pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262 + +pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc} +pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD} + +timestep 1.0 +run_style verlet + +velocity all create ${T} 68768932 + +thermo_style custom step time temp press +thermo 10 + +fix 1 all nve + +run 2000 diff --git a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 b/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 new file mode 100644 index 0000000000..6916a5dd6e --- /dev/null +++ b/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 @@ -0,0 +1,293 @@ +LAMMPS (10 Mar 2021) +# Coarse-Grained SPC/E Water + +variable T equal 300.0 +variable rc equal 9.0 +variable rcD equal 10.0 + +units real +boundary p p p +atom_style atomic +dimension 3 +newton on +comm_modify vel yes + +read_data cg_spce.data +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.310000 40.310000 40.310000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2180 atoms + read_data CPU = 0.037 seconds + +pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 9 385262 + +pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc} +pair_coeff 1 1 table cg_spce_table.pot VOTCA 9 +WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:461) +pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD} +pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 10 + +timestep 1.0 +run_style verlet + +velocity all create ${T} 68768932 +velocity all create 300 68768932 + +thermo_style custom step time temp press +thermo 10 + +fix 1 all nve + +run 2000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 7 7 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair dpdext/tstat, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 5.380 | 5.380 | 5.380 Mbytes +Step Time Temp Press + 0 0 300 7368.7186 + 10 10 298.34842 6443.6033 + 20 20 303.36187 9303.0158 + 30 30 301.59356 7533.7912 + 40 40 300.97217 5623.9089 + 50 50 300.31652 9105.8093 + 60 60 296.92173 9213.304 + 70 70 294.36593 12701.327 + 80 80 295.30077 6098.4732 + 90 90 296.35396 8051.719 + 100 100 293.72532 5555.983 + 110 110 290.95711 9001.8346 + 120 120 290.91972 10264.241 + 130 130 294.14911 11450.959 + 140 140 299.11994 7244.1639 + 150 150 301.20082 7675.7516 + 160 160 300.71883 9718.1901 + 170 170 295.47176 8931.1414 + 180 180 290.45284 7381.7674 + 190 190 291.66922 11028.436 + 200 200 294.0543 11897.269 + 210 210 299.17955 8939.2171 + 220 220 298.45193 8047.038 + 230 230 300.48548 10033.64 + 240 240 299.24752 6310.7247 + 250 250 304.51487 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1250 1250 300.56214 7877.4055 + 1260 1260 308.03086 5644.2135 + 1270 1270 311.12289 6875.5126 + 1280 1280 307.83182 7204.9894 + 1290 1290 309.58491 9993.2255 + 1300 1300 305.36536 8626.859 + 1310 1310 304.35084 3471.1205 + 1320 1320 304.40125 2149.2701 + 1330 1330 295.74547 6252.9592 + 1340 1340 293.16034 3407.4408 + 1350 1350 298.6302 10139.977 + 1360 1360 300.46627 7312.9011 + 1370 1370 298.00367 2780.8886 + 1380 1380 300.97807 9403.3451 + 1390 1390 294.32612 12005.453 + 1400 1400 296.13403 5569.4907 + 1410 1410 297.86152 9558.6064 + 1420 1420 303.01992 8678.345 + 1430 1430 298.53849 5544.6316 + 1440 1440 293.60633 12879.765 + 1450 1450 296.28813 9312.4229 + 1460 1460 292.64466 8344.5877 + 1470 1470 295.28975 7689.9396 + 1480 1480 300.10761 7436.7346 + 1490 1490 291.6152 8909.6757 + 1500 1500 286.644 9756.5014 + 1510 1510 294.52064 10383.164 + 1520 1520 297.49618 4972.89 + 1530 1530 295.63379 6192.5729 + 1540 1540 295.04528 4987.7191 + 1550 1550 290.41403 7013.6076 + 1560 1560 295.62326 7222.5009 + 1570 1570 299.90584 4282.5688 + 1580 1580 299.04532 7885.433 + 1590 1590 300.03907 5508.0652 + 1600 1600 298.05683 9262.3744 + 1610 1610 297.50015 9544.6913 + 1620 1620 303.21217 6393.6756 + 1630 1630 304.44383 9674.6583 + 1640 1640 302.68977 9065.4408 + 1650 1650 303.62415 6851.1575 + 1660 1660 306.11103 8592.0481 + 1670 1670 300.84566 8483.551 + 1680 1680 303.92882 10113.096 + 1690 1690 305.02534 7389.9402 + 1700 1700 303.52902 5541.9256 + 1710 1710 299.27905 9547.7344 + 1720 1720 294.14366 7269.2402 + 1730 1730 299.49977 8086.0601 + 1740 1740 298.66942 7026.6067 + 1750 1750 296.94428 9595.2435 + 1760 1760 297.36921 6268.7436 + 1770 1770 299.88423 10598.189 + 1780 1780 293.76868 7405.7641 + 1790 1790 297.19444 10837.102 + 1800 1800 296.46054 8345.699 + 1810 1810 299.06801 5256.5992 + 1820 1820 294.17725 5510.7529 + 1830 1830 286.78527 6310.8881 + 1840 1840 284.89686 8249.1144 + 1850 1850 293.79389 4578.9263 + 1860 1860 298.31279 8752.305 + 1870 1870 295.31087 8401.2736 + 1880 1880 298.13297 4354.8694 + 1890 1890 298.90786 11454.088 + 1900 1900 299.1416 9121.4138 + 1910 1910 296.43134 12157.884 + 1920 1920 292.05445 8613.1522 + 1930 1930 300.3421 7898.3626 + 1940 1940 304.55746 6311.259 + 1950 1950 304.03899 8789.3537 + 1960 1960 305.08259 7243.5622 + 1970 1970 304.0858 8712.4796 + 1980 1980 299.14574 5166.3501 + 1990 1990 300.07254 10019.769 + 2000 2000 301.78176 8789.7968 +Loop time of 79.8698 on 1 procs for 2000 steps with 2180 atoms + +Performance: 2.164 ns/day, 11.093 hours/ns, 25.041 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 79.378 | 79.378 | 79.378 | 0.0 | 99.38 +Neigh | 0.22454 | 0.22454 | 0.22454 | 0.0 | 0.28 +Comm | 0.17969 | 0.17969 | 0.17969 | 0.0 | 0.22 +Output | 0.0063846 | 0.0063846 | 0.0063846 | 0.0 | 0.01 +Modify | 0.044496 | 0.044496 | 0.044496 | 0.0 | 0.06 +Other | | 0.03671 | | | 0.05 + +Nlocal: 2180.00 ave 2180 max 2180 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 6693.00 ave 6693 max 6693 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 261496.0 ave 261496 max 261496 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 261496 +Ave neighs/atom = 119.95229 +Neighbor list builds = 25 +Dangerous builds = 0 +Total wall time: 0:01:20 diff --git a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 b/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 new file mode 100644 index 0000000000..890414d580 --- /dev/null +++ b/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 @@ -0,0 +1,293 @@ +LAMMPS (10 Mar 2021) +# Coarse-Grained SPC/E Water + +variable T equal 300.0 +variable rc equal 9.0 +variable rcD equal 10.0 + +units real +boundary p p p +atom_style atomic +dimension 3 +newton on +comm_modify vel yes + +read_data cg_spce.data +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.310000 40.310000 40.310000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2180 atoms + read_data CPU = 0.012 seconds + +pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 9 385262 + +pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc} +pair_coeff 1 1 table cg_spce_table.pot VOTCA 9 +WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:461) +pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD} +pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 10 + +timestep 1.0 +run_style verlet + +velocity all create ${T} 68768932 +velocity all create 300 68768932 + +thermo_style custom step time temp press +thermo 10 + +fix 1 all nve + +run 2000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 7 7 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair dpdext/tstat, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.695 | 3.696 | 3.697 Mbytes +Step Time Temp Press + 0 0 300 5965.5396 + 10 10 303.16391 8779.1574 + 20 20 306.9014 8268.573 + 30 30 305.84291 9976.0547 + 40 40 301.20527 8832.3902 + 50 50 305.72012 8041.0146 + 60 60 305.1676 7118.8042 + 70 70 305.01132 9423.9307 + 80 80 308.10236 10781.423 + 90 90 309.18703 3637.9961 + 100 100 305.11814 7726.7672 + 110 110 298.37346 8575.1602 + 120 120 304.79786 8910.8048 + 130 130 309.05401 6351.4839 + 140 140 304.28367 4805.137 + 150 150 300.28903 7412.6411 + 160 160 299.39358 10183.593 + 170 170 296.80729 5437.1054 + 180 180 295.2755 8317.0414 + 190 190 303.25949 8338.3453 + 200 200 303.24607 9636.5224 + 210 210 298.56684 10288.264 + 220 220 293.42999 9001.0482 + 230 230 293.12497 9083.5194 + 240 240 291.92847 9659.3388 + 250 250 299.2202 6328.759 + 260 260 297.45209 10405.677 + 270 270 292.12257 7273.9369 + 280 280 289.81113 8957.8747 + 290 290 299.06683 6695.3776 + 300 300 300.75468 6298.5705 + 310 310 296.26524 7432.4815 + 320 320 294.21403 9941.7038 + 330 330 293.01776 4750.2993 + 340 340 295.22553 4968.3595 + 350 350 293.95589 9224.5496 + 360 360 297.94278 8792.0395 + 370 370 298.99075 5453.7814 + 380 380 302.1188 6229.2283 + 390 390 298.48943 8517.5273 + 400 400 295.3701 11328.394 + 410 410 287.74238 4058.0382 + 420 420 288.83732 5706.6773 + 430 430 298.8242 6178.7142 + 440 440 304.42682 10138.321 + 450 450 300.28695 9731.3417 + 460 460 300.34539 9249.4691 + 470 470 303.32231 11638.718 + 480 480 301.46777 4186.402 + 490 490 292.56069 9184.8386 + 500 500 297.26162 11766.733 + 510 510 295.34018 6436.33 + 520 520 300.16314 9325.3669 + 530 530 305.00513 5947.6408 + 540 540 300.88805 5222.7384 + 550 550 301.56707 6669.1808 + 560 560 304.89854 10730.053 + 570 570 299.50424 7956.1042 + 580 580 301.23382 10192.246 + 590 590 298.81222 6017.2125 + 600 600 300.57891 4575.433 + 610 610 301.95936 6309.7515 + 620 620 301.09393 5993.6489 + 630 630 300.47565 4388.7137 + 640 640 299.31886 9535.6093 + 650 650 295.06025 7954.5811 + 660 660 298.72666 8630.7466 + 670 670 302.53833 5636.1305 + 680 680 306.32833 12539.149 + 690 690 296.1951 11345.293 + 700 700 297.00325 6352.1448 + 710 710 298.51181 6922.4379 + 720 720 293.80125 4849.4922 + 730 730 296.52677 11141.583 + 740 740 294.15306 3527.8677 + 750 750 294.74737 8454.0815 + 760 760 292.53913 8187.9032 + 770 770 294.37078 7487.5703 + 780 780 297.50085 9198.7697 + 790 790 298.37773 8969.0024 + 800 800 293.29879 6506.6479 + 810 810 296.58266 8805.7872 + 820 820 290.85616 5248.8123 + 830 830 292.29488 5123.8203 + 840 840 292.77623 8263.5675 + 850 850 297.88225 6777.7444 + 860 860 300.01913 10439.087 + 870 870 295.79578 7318.1322 + 880 880 301.5994 8242.4774 + 890 890 306.63208 8090.6106 + 900 900 303.53759 6831.2666 + 910 910 300.70481 3811.0498 + 920 920 299.96274 8351.1573 + 930 930 299.67435 7046.0534 + 940 940 310.81742 6887.6925 + 950 950 305.09984 4811.088 + 960 960 301.33039 4184.851 + 970 970 301.19205 6417.6542 + 980 980 299.6491 7738.2233 + 990 990 297.33655 9264.0874 + 1000 1000 302.33418 7166.2751 + 1010 1010 300.08402 9121.0882 + 1020 1020 302.82225 6405.7109 + 1030 1030 304.01683 6944.0839 + 1040 1040 305.82618 6160.3838 + 1050 1050 308.12518 4356.0931 + 1060 1060 307.64811 6954.7245 + 1070 1070 313.70509 5558.9804 + 1080 1080 316.09239 7250.6147 + 1090 1090 310.2845 5441.3722 + 1100 1100 300.18899 4417.8774 + 1110 1110 304.02471 5609.1668 + 1120 1120 303.46016 10355.031 + 1130 1130 305.68165 6400.913 + 1140 1140 308.78348 7235.1894 + 1150 1150 299.30025 9246.4856 + 1160 1160 302.70799 9866.9536 + 1170 1170 302.0977 8643.5532 + 1180 1180 307.15407 8866.4664 + 1190 1190 305.78146 7562.4911 + 1200 1200 302.54605 7974.9973 + 1210 1210 306.14264 9554.2381 + 1220 1220 308.89843 6219.5361 + 1230 1230 305.71844 7633.9105 + 1240 1240 306.51911 7705.4795 + 1250 1250 304.78473 8590.5595 + 1260 1260 300.82969 9281.5964 + 1270 1270 305.9271 4951.1323 + 1280 1280 310.32728 9446.3989 + 1290 1290 318.27879 9102.5544 + 1300 1300 310.45777 5931.5457 + 1310 1310 304.81268 1214.4291 + 1320 1320 307.08811 10315.961 + 1330 1330 306.86917 8584.9658 + 1340 1340 307.26912 7254.864 + 1350 1350 310.02754 8508.6256 + 1360 1360 306.12763 4912.6641 + 1370 1370 301.67924 6715.8196 + 1380 1380 298.37239 6149.8821 + 1390 1390 299.62894 8181.4761 + 1400 1400 301.60395 6714.4244 + 1410 1410 297.65752 7035.6575 + 1420 1420 297.02817 7510.2637 + 1430 1430 303.59177 10361.937 + 1440 1440 300.10771 8473.2311 + 1450 1450 291.21837 6097.9954 + 1460 1460 291.58663 7729.0841 + 1470 1470 292.52447 6555.8661 + 1480 1480 294.48264 6960.0201 + 1490 1490 298.34869 8044.2321 + 1500 1500 296.8193 11731.289 + 1510 1510 296.52073 5452.8935 + 1520 1520 294.54819 9591.7969 + 1530 1530 297.36394 5148.5383 + 1540 1540 289.08137 6057.0981 + 1550 1550 288.27007 8965.1965 + 1560 1560 294.84398 8316.9487 + 1570 1570 299.79573 8760.7322 + 1580 1580 295.66745 5045.5322 + 1590 1590 298.14356 7161.1834 + 1600 1600 297.10402 6529.9938 + 1610 1610 299.69137 7741.6027 + 1620 1620 304.93043 11222.109 + 1630 1630 302.01322 10893.107 + 1640 1640 295.47422 8400.3124 + 1650 1650 301.93122 7190.2609 + 1660 1660 305.02639 6140.5552 + 1670 1670 302.86047 8651.5366 + 1680 1680 304.82151 9909.407 + 1690 1690 300.48426 8428.8845 + 1700 1700 293.06643 5333.8144 + 1710 1710 295.43687 9103.4353 + 1720 1720 298.77208 8162.1053 + 1730 1730 300.08189 9603.4371 + 1740 1740 303.16004 10693.291 + 1750 1750 303.54199 9151.023 + 1760 1760 300.99281 4641.2985 + 1770 1770 297.36657 3888.5753 + 1780 1780 298.32969 7286.2299 + 1790 1790 297.34183 8975.8956 + 1800 1800 295.83042 6366.7607 + 1810 1810 295.92044 9308.4953 + 1820 1820 298.10087 7117.2369 + 1830 1830 296.13936 4849.3739 + 1840 1840 296.5869 8321.4011 + 1850 1850 296.74513 9530.6806 + 1860 1860 298.57398 8788.0603 + 1870 1870 299.12825 6015.4777 + 1880 1880 301.91639 11706.441 + 1890 1890 309.85968 10909.493 + 1900 1900 302.64998 8779.8967 + 1910 1910 301.62919 9176.3902 + 1920 1920 300.66238 5369.8681 + 1930 1930 297.64499 8185.09 + 1940 1940 296.47852 10188.803 + 1950 1950 297.802 6679.4466 + 1960 1960 299.78754 7316.8198 + 1970 1970 300.09083 6008.9414 + 1980 1980 297.94119 5615.6403 + 1990 1990 298.37687 9727.308 + 2000 2000 296.08394 6400.2746 +Loop time of 40.5503 on 4 procs for 2000 steps with 2180 atoms + +Performance: 4.261 ns/day, 5.632 hours/ns, 49.321 timesteps/s +99.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 37.953 | 38.022 | 38.132 | 1.1 | 93.77 +Neigh | 0.10585 | 0.10835 | 0.10994 | 0.5 | 0.27 +Comm | 2.2287 | 2.3368 | 2.405 | 4.6 | 5.76 +Output | 0.0072037 | 0.0081832 | 0.011022 | 1.8 | 0.02 +Modify | 0.023132 | 0.024188 | 0.025948 | 0.7 | 0.06 +Other | | 0.05032 | | | 0.12 + +Nlocal: 545.000 ave 559 max 531 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 3619.00 ave 3655 max 3594 min +Histogram: 1 1 0 0 1 0 0 0 0 1 +Neighs: 65415.5 ave 66835 max 64310 min +Histogram: 1 0 0 2 0 0 0 0 0 1 + +Total # of neighbors = 261662 +Ave neighs/atom = 120.02844 +Neighbor list builds = 26 +Dangerous builds = 0 +Total wall time: 0:00:40 diff --git a/src/Makefile b/src/Makefile index 679cbe7b97..41d2a91c31 100644 --- a/src/Makefile +++ b/src/Makefile @@ -52,7 +52,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ python qeq replica rigid shock snap spin srd voronoi PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ - user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ + user-diffraction user-dpd user-dpdext user-drude user-eff user-fep user-h5md \ user-intel user-lb user-manifold user-meamc user-mesodpd user-mesont \ user-mgpt user-misc user-mofff user-molfile \ user-netcdf user-omp user-phonon user-plumed user-ptm user-qmmm \ diff --git a/src/USER-DPDEXT/README b/src/USER-DPDEXT/README new file mode 100644 index 0000000000..73f8d047f8 --- /dev/null +++ b/src/USER-DPDEXT/README @@ -0,0 +1,10 @@ +Martin Svoboda (ICPF, UJEP) - svobod.martin@gmail.com +Karel Sindelka (ICPF) - sindelka@icpf.cas.cz +Martin Lisal (ICPF, UJEP) - lisal@icpf.cas.cz + +This package implements a generalised force field for dissipative +particle dynamics (DPD). The extension divides contributions +of dissipative and random forces to parrallel and perpendicular parts. +See the doc pages for "pair_style dpdext" and "pair_style dpdext/tstat". + +There are example scripts for using this package in examples/USER/dpdext. diff --git a/src/USER-DPDEXT/pair_dpd_ext.cpp b/src/USER-DPDEXT/pair_dpd_ext.cpp new file mode 100644 index 0000000000..e5405cf071 --- /dev/null +++ b/src/USER-DPDEXT/pair_dpd_ext.cpp @@ -0,0 +1,496 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Kurt Smith (U Pittsburgh) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Martin Svoboda (ICPF, UJEP), Martin Lísal (ICPF, UJEP) +------------------------------------------------------------------------- */ +#include "pair_dpd_ext.h" + +#include +#include "atom.h" +#include "comm.h" +#include "update.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "random_mars.h" +#include "memory.h" +#include "error.h" + + +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-10 + +/* ---------------------------------------------------------------------- */ + +PairDPDExt::PairDPDExt(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; + random = nullptr; +} + +/* ---------------------------------------------------------------------- */ + +PairDPDExt::~PairDPDExt() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(a0); + memory->destroy(gamma); + memory->destroy(gammaT); + memory->destroy(sigma); + memory->destroy(sigmaT); + memory->destroy(ws); + memory->destroy(wsT); + } + + if (random) delete random; +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDExt::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpairx,fpairy,fpairz,fpair; + double vxtmp,vytmp,vztmp,delvx,delvy,delvz; + double rsq,r,rinv,dot,wd,wdPar,wdPerp,randnum,randnumx,randnumy,randnumz,factor_dpd; + double P[3][3]; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double dtinvsqrt = 1.0/sqrt(update->dt); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + vxtmp = v[i][0]; + vytmp = v[i][1]; + vztmp = v[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_dpd = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + if (r < EPSILON) continue; // r can be 0.0 in DPD systems + rinv = 1.0/r; + delvx = vxtmp - v[j][0]; + delvy = vytmp - v[j][1]; + delvz = vztmp - v[j][2]; + dot = delx*delvx + dely*delvy + delz*delvz; + + P[0][0] = 1.0 - delx*delx*rinv*rinv; + P[0][1] = - delx*dely*rinv*rinv; + P[0][2] = - delx*delz*rinv*rinv; + + P[1][0] = P[0][1]; + P[1][1] = 1.0 - dely*dely*rinv*rinv; + P[1][2] = - dely*delz*rinv*rinv; + + P[2][0] = P[0][2]; + P[2][1] = P[1][2]; + P[2][2] = 1.0 - delz*delz*rinv*rinv; + + wd = 1.0 - r/cut[itype][jtype]; + wdPar = pow(wd,ws[itype][jtype]); + wdPerp = pow(wd,wsT[itype][jtype]); + + randnum = random->gaussian(); + randnumx = random->gaussian(); + randnumy = random->gaussian(); + randnumz = random->gaussian(); + + // conservative force + fpair = a0[itype][jtype]*wd; + + // drag force - parallel + fpair -= gamma[itype][jtype]*wdPar*wdPar*dot*rinv; + + // random force - parallel + fpair += sigma[itype][jtype]*wdPar*randnum*dtinvsqrt; + + fpairx = fpair*rinv*delx; + fpairy = fpair*rinv*dely; + fpairz = fpair*rinv*delz; + + // drag force - perpendicular + fpairx -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[0][0]*delvx + P[0][1]*delvy + P[0][2]*delvz); + fpairy -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[1][0]*delvx + P[1][1]*delvy + P[1][2]*delvz); + fpairz -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[2][0]*delvx + P[2][1]*delvy + P[2][2]*delvz); + + // random force - perpendicular + fpairx += sigmaT[itype][jtype]*wdPerp* + (P[0][0]*randnumx + P[0][1]*randnumy + P[0][2]*randnumz)*dtinvsqrt; + fpairy += sigmaT[itype][jtype]*wdPerp* + (P[1][0]*randnumx + P[1][1]*randnumy + P[1][2]*randnumz)*dtinvsqrt; + fpairz += sigmaT[itype][jtype]*wdPerp* + (P[2][0]*randnumx + P[2][1]*randnumy + P[2][2]*randnumz)*dtinvsqrt; + + fpairx *= factor_dpd; + fpairy *= factor_dpd; + fpairz *= factor_dpd; + + f[i][0] += fpairx; + f[i][1] += fpairy; + f[i][2] += fpairz; + if (newton_pair || j < nlocal) { + f[j][0] -= fpairx; + f[j][1] -= fpairy; + f[j][2] -= fpairz; + } + + if (eflag) { + // unshifted eng of conservative term: + // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]); + // eng shifted to 0.0 at cutoff + evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd; + evdwl *= factor_dpd; + } + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, + evdwl,0.0, + fpairx, fpairy, fpairz, + delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairDPDExt::allocate() +{ + int i,j; + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (i = 1; i <= n; i++) + for (j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(a0,n+1,n+1,"pair:a0"); + memory->create(gamma,n+1,n+1,"pair:gamma"); + memory->create(gammaT,n+1,n+1,"pair:gammaT"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + memory->create(sigmaT,n+1,n+1,"pair:sigmaT"); + memory->create(ws,n+1,n+1,"pair:ws"); + memory->create(wsT,n+1,n+1,"pair:wsT"); + for (i = 0; i <= atom->ntypes; i++) + { + for (j = 0; j <= atom->ntypes; j++) + { + sigma[i][j] = gamma[i][j] =sigmaT[i][j] = gammaT[i][j] = 0.0; + ws[i][j] = wsT[i][j] = 1.0; + } + } +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairDPDExt::settings(int narg, char **arg) +{ + if (narg != 3) error->all(FLERR,"Illegal pair_style command"); + + temperature = utils::numeric(FLERR,arg[0],false,lmp); + cut_global = utils::numeric(FLERR,arg[1],false,lmp); + seed = utils::inumeric(FLERR,arg[2],false,lmp); + + // initialize Marsaglia RNG with processor-unique seed + + if (seed <= 0) error->all(FLERR,"Illegal pair_style command"); + delete random; + random = new RanMars(lmp,seed + comm->me); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) { + cut[i][j] = cut_global; + cutsq[i][j] = cut_global*cut_global; + } + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairDPDExt::coeff(int narg, char **arg) +{ + if (narg < 7 || narg > 8) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + + double a0_one = utils::numeric(FLERR,arg[2],false,lmp); + double gamma_one = utils::numeric(FLERR,arg[3],false,lmp); + double gammaT_one = utils::numeric(FLERR,arg[4],false,lmp); + double ws_one = utils::numeric(FLERR,arg[5],false,lmp); + double wsT_one = utils::numeric(FLERR,arg[6],false,lmp); + + double cut_one = cut_global; + if (narg == 8) cut_one = utils::numeric(FLERR,arg[7],false,lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + a0[i][j] = a0_one; + gamma[i][j] = gamma_one; + gammaT[i][j] = gammaT_one; + ws[i][j] = ws_one; + wsT[i][j] = wsT_one; + cut[i][j] = cut_one; + cutsq[i][j] = cut_one*cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairDPDExt::init_style() +{ + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair dpd requires ghost atoms store velocity"); + + // if newton off, forces between atoms ij will be double computed + // using different random numbers + + if (force->newton_pair == 0 && comm->me == 0) error->warning(FLERR, + "Pair dpd needs newton pair on for momentum conservation"); + + neighbor->request(this,instance_me); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairDPDExt::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + sigma[i][j] = sqrt(2.0*force->boltz*temperature*gamma[i][j]); + sigmaT[i][j] = sqrt(2.0*force->boltz*temperature*gammaT[i][j]); + + cut[j][i] = cut[i][j]; + cutsq[j][i] = cutsq[i][j]; + a0[j][i] = a0[i][j]; + gamma[j][i] = gamma[i][j]; + gammaT[j][i] = gammaT[i][j]; + sigma[j][i] = sigma[i][j]; + sigmaT[j][i] = sigmaT[i][j]; + ws[j][i] = ws[i][j]; + wsT[j][i] = wsT[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDExt::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&a0[i][j],sizeof(double),1,fp); + fwrite(&gamma[i][j],sizeof(double),1,fp); + fwrite(&gammaT[i][j],sizeof(double),1,fp); + fwrite(&ws[i][j],sizeof(double),1,fp); + fwrite(&wsT[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDExt::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&gammaT[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&ws[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&wsT[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + } + MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&gammaT[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&ws[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&wsT[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDExt::write_restart_settings(FILE *fp) +{ + fwrite(&temperature,sizeof(double),1,fp); + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&seed,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDExt::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + utils::sfread(FLERR,&temperature,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&seed,sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); + } + MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&seed,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + + // initialize Marsaglia RNG with processor-unique seed + // same seed that pair_style command initially specified + + if (random) delete random; + random = new RanMars(lmp,seed + comm->me); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairDPDExt::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g %g %g\n",i, + a0[i][i],gamma[i][i],gammaT[i][i],ws[i][i],wsT[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairDPDExt::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g %g %g %g\n",i,j, + a0[i][j],gamma[i][j],gammaT[i][j],ws[i][j],wsT[i][j],cut[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairDPDExt::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_dpd, double &fforce) +{ + double r,rinv,wd,phi; + + r = sqrt(rsq); + if (r < EPSILON) { + fforce = 0.0; + return 0.0; + } + + rinv = 1.0/r; + wd = 1.0 - r/cut[itype][jtype]; + fforce = a0[itype][jtype]*wd * factor_dpd*rinv; + + phi = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd; + return factor_dpd*phi; +} diff --git a/src/USER-DPDEXT/pair_dpd_ext.h b/src/USER-DPDEXT/pair_dpd_ext.h new file mode 100644 index 0000000000..e85c3451c5 --- /dev/null +++ b/src/USER-DPDEXT/pair_dpd_ext.h @@ -0,0 +1,86 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(dpdext,PairDPDExt) + +#else + +#ifndef LMP_PAIR_DPD_EXT_H +#define LMP_PAIR_DPD_EXT_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairDPDExt : public Pair { + public: + PairDPDExt(class LAMMPS *); + virtual ~PairDPDExt(); + virtual void compute(int, int); + virtual void settings(int, char **); + virtual void coeff(int, char **); + void init_style(); + double init_one(int, int); + virtual void write_restart(FILE *); + virtual void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + virtual void write_data(FILE *); + virtual void write_data_all(FILE *); + double single(int, int, int, int, double, double, double, double &); + + protected: + double cut_global,temperature; + int seed; + double **cut; + double **a0,**gamma,**gammaII,**gammaT; + double **sigma,**sigmaT; + double **ws,**wsT; + class RanMars *random; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair dpd requires ghost atoms store velocity + +Use the comm_modify vel yes command to enable this. + +W: Pair dpd needs newton pair on for momentum conservation + +Self-explanatory. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +*/ diff --git a/src/USER-DPDEXT/pair_dpd_tstat_ext.cpp b/src/USER-DPDEXT/pair_dpd_tstat_ext.cpp new file mode 100644 index 0000000000..bfd10c1374 --- /dev/null +++ b/src/USER-DPDEXT/pair_dpd_tstat_ext.cpp @@ -0,0 +1,376 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Martin Svoboda (ICPF, UJEP), Martin Lísal (ICPF, UJEP) +------------------------------------------------------------------------- */ + +#include "pair_dpd_tstat_ext.h" + +#include +#include "atom.h" +#include "update.h" +#include "force.h" +#include "neigh_list.h" +#include "comm.h" +#include "random_mars.h" +#include "error.h" + + +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-10 + +/* ---------------------------------------------------------------------- */ + +PairDPDTstatExt::PairDPDTstatExt(LAMMPS *lmp) : PairDPDExt(lmp) +{ + single_enable = 0; + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDTstatExt::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,fpairx,fpairy,fpairz,fpair; + double vxtmp,vytmp,vztmp,delvx,delvy,delvz; + double rsq,r,rinv,dot,wd,wdPar,wdPerp,randnum,randnumx,randnumy,randnumz,factor_dpd; + double P[3][3]; + int *ilist,*jlist,*numneigh,**firstneigh; + + ev_init(eflag,vflag); + + // adjust sigma if target T is changing + + if (t_start != t_stop) { + double delta = update->ntimestep - update->beginstep; + if (delta != 0.0) delta /= update->endstep - update->beginstep; + temperature = t_start + delta * (t_stop-t_start); + double boltz = force->boltz; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]); + sigmaT[i][j] = sigmaT[j][i] = sqrt(2.0*boltz*temperature*gammaT[i][j]); + } + } + } + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double dtinvsqrt = 1.0/sqrt(update->dt); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + vxtmp = v[i][0]; + vytmp = v[i][1]; + vztmp = v[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_dpd = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + if (r < EPSILON) continue; // r can be 0.0 in DPD systems + rinv = 1.0/r; + delvx = vxtmp - v[j][0]; + delvy = vytmp - v[j][1]; + delvz = vztmp - v[j][2]; + dot = delx*delvx + dely*delvy + delz*delvz; + + P[0][0] = 1.0 - delx*delx*rinv*rinv; + P[0][1] = - delx*dely*rinv*rinv; + P[0][2] = - delx*delz*rinv*rinv; + + P[1][0] = P[0][1]; + P[1][1] = 1.0 - dely*dely*rinv*rinv; + P[1][2] = - dely*delz*rinv*rinv; + + P[2][0] = P[0][2]; + P[2][1] = P[1][2]; + P[2][2] = 1.0 - delz*delz*rinv*rinv; + + wd = 1.0 - r/cut[itype][jtype]; + wdPar = pow(wd,ws[itype][jtype]); + wdPerp = pow(wd,wsT[itype][jtype]); + + randnum = random->gaussian(); + randnumx = random->gaussian(); + randnumy = random->gaussian(); + randnumz = random->gaussian(); + + // drag force - parallel + fpair = -gamma[itype][jtype]*wdPar*wdPar*dot*rinv; + + // random force - parallel + fpair += sigma[itype][jtype]*wdPar*randnum*dtinvsqrt; + + fpairx = fpair*rinv*delx; + fpairy = fpair*rinv*dely; + fpairz = fpair*rinv*delz; + + // drag force - perpendicular + fpairx -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[0][0]*delvx + P[0][1]*delvy + P[0][2]*delvz); + fpairy -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[1][0]*delvx + P[1][1]*delvy + P[1][2]*delvz); + fpairz -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[2][0]*delvx + P[2][1]*delvy + P[2][2]*delvz); + + // random force - perpendicular + fpairx += sigmaT[itype][jtype]*wdPerp* + (P[0][0]*randnumx + P[0][1]*randnumy + P[0][2]*randnumz)*dtinvsqrt; + fpairy += sigmaT[itype][jtype]*wdPerp* + (P[1][0]*randnumx + P[1][1]*randnumy + P[1][2]*randnumz)*dtinvsqrt; + fpairz += sigmaT[itype][jtype]*wdPerp* + (P[2][0]*randnumx + P[2][1]*randnumy + P[2][2]*randnumz)*dtinvsqrt; + + fpairx *= factor_dpd; + fpairy *= factor_dpd; + fpairz *= factor_dpd; + + f[i][0] += fpairx; + f[i][1] += fpairy; + f[i][2] += fpairz; + if (newton_pair || j < nlocal) { + f[j][0] -= fpairx; + f[j][1] -= fpairy; + f[j][2] -= fpairz; + } + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, + 0.0,0.0, + fpairx, fpairy, fpairz, + delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::settings(int narg, char **arg) +{ + if (narg != 4) error->all(FLERR,"Illegal pair_style command"); + + t_start = utils::numeric(FLERR,arg[0],false,lmp); + t_stop = utils::numeric(FLERR,arg[1],false,lmp); + cut_global = utils::numeric(FLERR,arg[2],false,lmp); + seed = utils::inumeric(FLERR,arg[3],false,lmp); + + temperature = t_start; + + // initialize Marsaglia RNG with processor-unique seed + + if (seed <= 0) error->all(FLERR,"Illegal pair_style command"); + delete random; + random = new RanMars(lmp,seed + comm->me); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::coeff(int narg, char **arg) +{ + if (narg < 6 || narg > 7) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + + double a0_one = 0.0; + double gamma_one = utils::numeric(FLERR,arg[2],false,lmp); + double gammaT_one = utils::numeric(FLERR,arg[3],false,lmp); + double ws_one = utils::numeric(FLERR,arg[4],false,lmp); + double wsT_one = utils::numeric(FLERR,arg[5],false,lmp); + + double cut_one = cut_global; + if (narg == 7) cut_one = utils::numeric(FLERR,arg[6],false,lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + a0[i][j] = a0_one; + gamma[i][j] = gamma_one; + gammaT[i][j] = gammaT_one; + ws[i][j] = ws_one; + wsT[i][j] = wsT_one; + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&gamma[i][j],sizeof(double),1,fp); + fwrite(&gammaT[i][j],sizeof(double),1,fp); + fwrite(&ws[i][j],sizeof(double),1,fp); + fwrite(&wsT[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&gammaT[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&ws[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&wsT[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + } + MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&gammaT[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&ws[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&wsT[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::write_restart_settings(FILE *fp) +{ + fwrite(&t_start,sizeof(double),1,fp); + fwrite(&t_stop,sizeof(double),1,fp); + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&seed,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + utils::sfread(FLERR,&t_start,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&t_stop,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&seed,sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); + } + MPI_Bcast(&t_start,1,MPI_DOUBLE,0,world); + MPI_Bcast(&t_stop,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&seed,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + + temperature = t_start; + + // initialize Marsaglia RNG with processor-unique seed + // same seed that pair_style command initially specified + + if (random) delete random; + random = new RanMars(lmp,seed + comm->me); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g %g\n",i,gamma[i][i],gammaT[i][i],ws[i][i],wsT[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairDPDTstatExt::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g %g %g\n",i,j, + gamma[i][j],gammaT[i][j],ws[i][j],wsT[i][j],cut[i][j]); +} diff --git a/src/USER-DPDEXT/pair_dpd_tstat_ext.h b/src/USER-DPDEXT/pair_dpd_tstat_ext.h new file mode 100644 index 0000000000..c8441f90bd --- /dev/null +++ b/src/USER-DPDEXT/pair_dpd_tstat_ext.h @@ -0,0 +1,62 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(dpdext/tstat,PairDPDTstatExt) + +#else + +#ifndef LMP_PAIR_DPD_TSTAT_EXT_H +#define LMP_PAIR_DPD_TSTAT_EXT_H + +#include "pair_dpd_ext.h" + +namespace LAMMPS_NS { + +class PairDPDTstatExt : public PairDPDExt { + public: + PairDPDTstatExt(class LAMMPS *); + ~PairDPDTstatExt() {} + void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + + protected: + double t_start,t_stop; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +*/ From 4041a07e6670ba1dbd089665e5252e3fcb36dc35 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 16 Apr 2021 15:43:03 +0200 Subject: [PATCH 0544/1217] add USER-DPDEXT to CMakeLists.txt --- cmake/CMakeLists.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index f567a15d25..d840dedf6c 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -120,9 +120,9 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF - USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB + USER-COLVARS USER-DIFFRACTION USER-DPD USER-DPDEXT USER-DRUDE USER-EFF USER-FEP + USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC + USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE) From ce51305b2d0559b3d31c67fc9fa8e8541721a224 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 16 Apr 2021 15:44:20 +0200 Subject: [PATCH 0545/1217] fix typing error in doc file --- doc/src/pair_dpdext.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/pair_dpdext.rst b/doc/src/pair_dpdext.rst index 301f9f3ea0..4b6855774d 100644 --- a/doc/src/pair_dpdext.rst +++ b/doc/src/pair_dpdext.rst @@ -52,7 +52,7 @@ of 3 terms f^R = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij} + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\ w(r) = & 1 - r/r_c \\ -where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\a` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command. +where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command. For the style *dpdext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. From 7a97331e510aa53635a5b469deceb445e785c99a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 16 Apr 2021 12:38:00 -0400 Subject: [PATCH 0546/1217] add support for Plumed2 version 2.5.7, 2.6.3, 2.7.1 --- cmake/Modules/Packages/USER-PLUMED.cmake | 5 +++-- lib/plumed/Install.py | 5 ++++- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/USER-PLUMED.cmake index 8719e8179d..e71542cfc5 100644 --- a/cmake/Modules/Packages/USER-PLUMED.cmake +++ b/cmake/Modules/Packages/USER-PLUMED.cmake @@ -54,8 +54,9 @@ if(DOWNLOAD_PLUMED) set(PLUMED_BUILD_BYPRODUCTS "/lib/libplumedWrapper.a") endif() - set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz" CACHE STRING "URL for PLUMED tarball") - set(PLUMED_MD5 "95f29dd0c067577f11972ff90dfc7d12" CACHE STRING "MD5 checksum of PLUMED tarball") + set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.1/plumed-src-2.7.1.tgz" CACHE STRING "URL for PLUMED tarball") + set(PLUMED_MD5 "4eac6a462ec84dfe0cec96c82421b8e8" CACHE STRING "MD5 checksum of PLUMED tarball") + mark_as_advanced(PLUMED_URL) mark_as_advanced(PLUMED_MD5) diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py index c11d5bfee9..e3858b39d3 100644 --- a/lib/plumed/Install.py +++ b/lib/plumed/Install.py @@ -17,7 +17,7 @@ parser = ArgumentParser(prog='Install.py', # settings -version = "2.7.0" +version = "2.7.1" mode = "static" # help message @@ -47,9 +47,12 @@ checksums = { \ '2.5.2' : 'bd2f18346c788eb54e1e52f4f6acf41a', \ '2.5.3' : 'de30d6e7c2dcc0973298e24a6da24286', \ '2.5.4' : 'f31b7d16a4be2e30aa7d5c19c3d37853', \ + '2.5.7' : '1ca36226fdb8110b1009aa61d615d4e5', \ '2.6.0' : '204d2edae58d9b10ba3ad460cad64191', \ '2.6.1' : '89a9a450fc6025299fe16af235957163', \ + '2.6.3' : 'a9f8028fd74528c2024781ea1fdefeee', \ '2.7.0' : '95f29dd0c067577f11972ff90dfc7d12', \ + '2.7.1' : '4eac6a462ec84dfe0cec96c82421b8e8', \ } # parse and process arguments From e4e20b67a8afe7471c56c01203eadbf45cc0d7af Mon Sep 17 00:00:00 2001 From: gugmelik <72472448+gugmelik@users.noreply.github.com> Date: Fri, 16 Apr 2021 20:02:32 +0300 Subject: [PATCH 0547/1217] Update lal_lj_smooth.cpp Added new line at the end of file. --- lib/gpu/lal_lj_smooth.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/gpu/lal_lj_smooth.cpp b/lib/gpu/lal_lj_smooth.cpp index 5e4785230b..c936b7ca31 100644 --- a/lib/gpu/lal_lj_smooth.cpp +++ b/lib/gpu/lal_lj_smooth.cpp @@ -183,4 +183,4 @@ void LJSMOOTHT::loop(const bool _eflag, const bool _vflag) { } template class LJSMOOTH; -} \ No newline at end of file +} From 5b9c0ff6432ca1c209a157e8fc7db4ccaec17f95 Mon Sep 17 00:00:00 2001 From: gugmelik <72472448+gugmelik@users.noreply.github.com> Date: Fri, 16 Apr 2021 20:03:30 +0300 Subject: [PATCH 0548/1217] Update lal_lj_smooth.cu Added new line at the end of file. --- lib/gpu/lal_lj_smooth.cu | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/gpu/lal_lj_smooth.cu b/lib/gpu/lal_lj_smooth.cu index c02e1b5ae0..fa87e6fcee 100644 --- a/lib/gpu/lal_lj_smooth.cu +++ b/lib/gpu/lal_lj_smooth.cu @@ -232,4 +232,4 @@ __kernel void k_lj_smooth_fast(const __global numtyp4 *restrict x_, store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, ans,engv); } // if ii -} \ No newline at end of file +} From 87a60da150c25ff87ac65d66dd3a52385be68fc8 Mon Sep 17 00:00:00 2001 From: gugmelik <72472448+gugmelik@users.noreply.github.com> Date: Fri, 16 Apr 2021 20:05:58 +0300 Subject: [PATCH 0549/1217] Update lal_lj_smooth.h Added new line at the end of file. --- lib/gpu/lal_lj_smooth.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/gpu/lal_lj_smooth.h b/lib/gpu/lal_lj_smooth.h index f869977c58..ae7d628b3b 100644 --- a/lib/gpu/lal_lj_smooth.h +++ b/lib/gpu/lal_lj_smooth.h @@ -88,4 +88,4 @@ class LJSMOOTH : public BaseAtomic { } -#endif \ No newline at end of file +#endif From 99035dc68096170e570f0213d6a388b6f06925a8 Mon Sep 17 00:00:00 2001 From: julient31 Date: Fri, 16 Apr 2021 11:59:37 -0600 Subject: [PATCH 0550/1217] removing all commented lines --- src/KOKKOS/atom_kokkos.h | 3 --- src/KOKKOS/atom_vec_spin_kokkos.cpp | 14 ----------- src/KOKKOS/kokkos_type.h | 37 ----------------------------- 3 files changed, 54 deletions(-) diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index f5649f927e..f5cf4916cf 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -56,9 +56,6 @@ class AtomKokkos : public Atom { // SPIN package - // DAT::tdual_sp_array k_sp; - // DAT::tdual_fm_array k_fm; - // DAT::tdual_fm_long_array k_fm_long; DAT::tdual_float_1d_4 k_sp; DAT::tdual_f_array k_fm; DAT::tdual_f_array k_fm_long; diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp index 5e3ff19831..e9bbeebe28 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.cpp +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -189,7 +189,6 @@ struct AtomVecSpinKokkos_PackComm { AtomVecSpinKokkos_PackComm( const typename DAT::tdual_x_array &x, - // const typename DAT::tdual_sp_array &sp, const typename DAT::tdual_float_1d_4 &sp, const typename DAT::tdual_xfloat_2d &buf, const typename DAT::tdual_int_2d &list, @@ -201,7 +200,6 @@ struct AtomVecSpinKokkos_PackComm { _xprd(xprd),_yprd(yprd),_zprd(zprd), _xy(xy),_xz(xz),_yz(yz) { const size_t maxsend = (buf.view().extent(0)*buf.view().extent(1))/3; - // const size_t elements = 3; const size_t elements = 7; buffer_view(_buf,buf,maxsend,elements); _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2]; @@ -1270,16 +1268,10 @@ void AtomVecSpinKokkos::sync_overlapping_device(ExecutionSpace space, unsigned i perform_async_copy(atomKK->k_mask,space); if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync()) perform_async_copy(atomKK->k_image,space); - // if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) - // perform_async_copy(atomKK->k_sp,space); if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) perform_async_copy(atomKK->k_sp,space); - // if ((mask & FM_MASK) && atomKK->k_sp.need_sync()) - // perform_async_copy(atomKK->k_fm,space); if ((mask & FM_MASK) && atomKK->k_sp.need_sync()) perform_async_copy(atomKK->k_fm,space); - // if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) - // perform_async_copy(atomKK->k_fm_long,space); if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) perform_async_copy(atomKK->k_fm_long,space); } else { @@ -1297,16 +1289,10 @@ void AtomVecSpinKokkos::sync_overlapping_device(ExecutionSpace space, unsigned i perform_async_copy(atomKK->k_mask,space); if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync()) perform_async_copy(atomKK->k_image,space); - // if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) - // perform_async_copy(atomKK->k_sp,space); if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) perform_async_copy(atomKK->k_sp,space); - // if ((mask & FM_MASK) && atomKK->k_fm.need_sync()) - // perform_async_copy(atomKK->k_fm,space); if ((mask & FM_MASK) && atomKK->k_fm.need_sync()) perform_async_copy(atomKK->k_fm,space); - // if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) - // perform_async_copy(atomKK->k_fm_long,space); if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) perform_async_copy(atomKK->k_fm_long,space); } diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index b0fbdf1f9f..af5adeee73 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -773,17 +773,10 @@ typedef tdual_virial_array::t_dev_const_randomread t_virial_array_randomread; //3d SP_FLOAT array n*4 #ifdef LMP_KOKKOS_NO_LEGACY -// typedef Kokkos::DualView tdual_sp_array; typedef Kokkos::DualView tdual_float_1d_4; #else -// typedef Kokkos::DualView tdual_sp_array; typedef Kokkos::DualView tdual_float_1d_4; #endif -// typedef tdual_sp_array::t_dev t_sp_array; -// typedef tdual_sp_array::t_dev_const t_sp_array_const; -// typedef tdual_sp_array::t_dev_um t_sp_array_um; -// typedef tdual_sp_array::t_dev_const_um t_sp_array_const_um; -// typedef tdual_sp_array::t_dev_const_randomread t_sp_array_randomread; typedef tdual_float_1d_4::t_dev t_sp_array; typedef tdual_float_1d_4::t_dev_const t_sp_array_const; typedef tdual_float_1d_4::t_dev_um t_sp_array_um; @@ -792,12 +785,6 @@ typedef tdual_float_1d_4::t_dev_const_randomread t_sp_array_randomread; //3d FM_FLOAT array n*3 -// typedef Kokkos::DualView tdual_fm_array; -// typedef tdual_fm_array::t_dev t_fm_array; -// typedef tdual_fm_array::t_dev_const t_fm_array_const; -// typedef tdual_fm_array::t_dev_um t_fm_array_um; -// typedef tdual_fm_array::t_dev_const_um t_fm_array_const_um; -// typedef tdual_fm_array::t_dev_const_randomread t_fm_array_randomread; typedef tdual_f_array::t_dev t_fm_array; typedef tdual_f_array::t_dev_const t_fm_array_const; typedef tdual_f_array::t_dev_um t_fm_array_um; @@ -806,12 +793,6 @@ typedef tdual_f_array::t_dev_const_randomread t_fm_array_randomread; //3d FML_FLOAT array n*3 -// typedef Kokkos::DualView tdual_fm_long_array; -// typedef tdual_fm_long_array::t_dev t_fm_long_array; -// typedef tdual_fm_long_array::t_dev_const t_fm_long_array_const; -// typedef tdual_fm_long_array::t_dev_um t_fm_long_array_um; -// typedef tdual_fm_long_array::t_dev_const_um t_fm_long_array_const_um; -// typedef tdual_fm_long_array::t_dev_const_randomread t_fm_long_array_randomread; typedef tdual_f_array::t_dev t_fm_long_array; typedef tdual_f_array::t_dev_const t_fm_long_array_const; typedef tdual_f_array::t_dev_um t_fm_long_array_um; @@ -1057,12 +1038,6 @@ typedef tdual_virial_array::t_host_const_randomread t_virial_array_randomread; // Spin types //2d X_FLOAT array n*4 -// typedef Kokkos::DualView tdual_sp_array; -// typedef tdual_sp_array::t_host t_sp_array; -// typedef tdual_sp_array::t_host_const t_sp_array_const; -// typedef tdual_sp_array::t_host_um t_sp_array_um; -// typedef tdual_sp_array::t_host_const_um t_sp_array_const_um; -// typedef tdual_sp_array::t_host_const_randomread t_sp_array_randomread; typedef tdual_float_1d_4::t_host t_sp_array; typedef tdual_float_1d_4::t_host_const t_sp_array_const; typedef tdual_float_1d_4::t_host_um t_sp_array_um; @@ -1070,12 +1045,6 @@ typedef tdual_float_1d_4::t_host_const_um t_sp_array_const_um; typedef tdual_float_1d_4::t_host_const_randomread t_sp_array_randomread; //2d F_FLOAT array n*3 -// typedef Kokkos::DualView tdual_fm_array; -// typedef tdual_fm_array::t_host t_fm_array; -// typedef tdual_fm_array::t_host_const t_fm_array_const; -// typedef tdual_fm_array::t_host_um t_fm_array_um; -// typedef tdual_fm_array::t_host_const_um t_fm_array_const_um; -// typedef tdual_fm_array::t_host_const_randomread t_fm_array_randomread; typedef tdual_f_array::t_host t_fm_array; typedef tdual_f_array::t_host_const t_fm_array_const; typedef tdual_f_array::t_host_um t_fm_array_um; @@ -1083,12 +1052,6 @@ typedef tdual_f_array::t_host_const_um t_fm_array_const_um; typedef tdual_f_array::t_host_const_randomread t_fm_array_randomread; //2d F_FLOAT array n*3 -// typedef Kokkos::DualView tdual_fm_long_array; -// typedef tdual_fm_long_array::t_host t_fm_long_array; -// typedef tdual_fm_long_array::t_host_const t_fm_long_array_const; -// typedef tdual_fm_long_array::t_host_um t_fm_long_array_um; -// typedef tdual_fm_long_array::t_host_const_um t_fm_long_array_const_um; -// typedef tdual_fm_long_array::t_host_const_randomread t_fm_long_array_randomread; typedef tdual_f_array::t_host t_fm_long_array; typedef tdual_f_array::t_host_const t_fm_long_array_const; typedef tdual_f_array::t_host_um t_fm_long_array_um; From e906fae88ce7c7421858ec05a3dfa40678ea62e0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 16 Apr 2021 17:10:07 -0400 Subject: [PATCH 0551/1217] whitespace fixes --- src/KOKKOS/atom_vec_spin_kokkos.cpp | 24 ++++++++++++------------ src/KOKKOS/atom_vec_spin_kokkos.h | 2 +- src/KOKKOS/verlet_kokkos.cpp | 6 +++--- src/SPIN/fix_nve_spin.cpp | 2 +- 4 files changed, 17 insertions(+), 17 deletions(-) diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp index e9bbeebe28..399ab23a5f 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.cpp +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -56,7 +56,7 @@ AtomVecSpinKokkos::AtomVecSpinKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) xcol_data = 4; atom->sp_flag = 1; - + k_count = DAT::tdual_int_1d("atom::k_count",1); atomKK = (AtomKokkos *) atom; commKK = (CommKokkos *) comm; @@ -84,13 +84,13 @@ void AtomVecSpinKokkos::grow(int n) memoryKK->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type"); memoryKK->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask"); memoryKK->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image"); - + // allocating mech. quantities memoryKK->grow_kokkos(atomKK->k_x,atomKK->x,nmax,"atom:x"); memoryKK->grow_kokkos(atomKK->k_v,atomKK->v,nmax,"atom:v"); memoryKK->grow_kokkos(atomKK->k_f,atomKK->f,nmax,"atom:f"); - + // allocating mag. quantities memoryKK->grow_kokkos(atomKK->k_sp,atomKK->sp,nmax,"atom:sp"); @@ -134,11 +134,11 @@ void AtomVecSpinKokkos::grow_pointers() f = atomKK->f; d_f = atomKK->k_f.d_view; h_f = atomKK->k_f.h_view; - - sp = atomKK->sp; + + sp = atomKK->sp; d_sp = atomKK->k_sp.d_view; h_sp = atomKK->k_sp.h_view; - fm = atomKK->fm; + fm = atomKK->fm; d_fm = atomKK->k_fm.d_view; h_fm = atomKK->k_fm.h_view; fm_long = atomKK->fm_long; @@ -163,7 +163,7 @@ void AtomVecSpinKokkos::copy(int i, int j, int delflag) h_v(j,1) = h_v(i,1); h_v(j,2) = h_v(i,2); - h_sp(j,0) = h_sp(i,0); + h_sp(j,0) = h_sp(i,0); h_sp(j,1) = h_sp(i,1); h_sp(j,2) = h_sp(i,2); h_sp(j,3) = h_sp(i,3); @@ -186,7 +186,7 @@ struct AtomVecSpinKokkos_PackComm { const int _iswap; X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz; X_FLOAT _pbc[6]; - + AtomVecSpinKokkos_PackComm( const typename DAT::tdual_x_array &x, const typename DAT::tdual_float_1d_4 &sp, @@ -268,7 +268,7 @@ struct AtomVecSpinKokkos_PackBorder { _buf(buf),_list(list),_iswap(iswap), _x(x),_tag(tag),_type(type),_mask(mask),_sp(sp), _dx(dx),_dy(dy),_dz(dz) {} - + KOKKOS_INLINE_FUNCTION void operator() (const int& i) const { const int j = _list(_iswap,i); @@ -741,9 +741,9 @@ struct AtomVecSpinKokkos_PackExchangeFunctor { } } }; - + /* ---------------------------------------------------------------------- */ - + int AtomVecSpinKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &k_buf, DAT::tdual_int_1d k_sendlist, DAT::tdual_int_1d k_copylist, @@ -768,7 +768,7 @@ int AtomVecSpinKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2 } /* ---------------------------------------------------------------------- */ - + int AtomVecSpinKokkos::pack_exchange(int i, double *buf) { int m = 1; diff --git a/src/KOKKOS/atom_vec_spin_kokkos.h b/src/KOKKOS/atom_vec_spin_kokkos.h index 5dca7b4e13..bcb5ea3b45 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.h +++ b/src/KOKKOS/atom_vec_spin_kokkos.h @@ -51,7 +51,7 @@ class AtomVecSpinKokkos : public AtomVecKokkos { void write_data(FILE *, int, double **); int write_data_hybrid(FILE *, double *); double memory_usage(); - + // clear magnetic and mechanic forces void force_clear(int, size_t); diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 27f4646366..254e269671 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -594,7 +594,7 @@ void VerletKokkos::force_clear() Kokkos::parallel_for(nall, Zero::t_f_array>(atomKK->k_torque.view())); atomKK->modified(Device,TORQUE_MASK); } - + // reset SPIN forces if (extraflag) { @@ -616,7 +616,7 @@ void VerletKokkos::force_clear() Kokkos::parallel_for(atomKK->nfirst, Zero::t_f_array>(atomKK->k_torque.view())); atomKK->modified(Device,TORQUE_MASK); } - + // reset SPIN forces if (extraflag) { @@ -635,7 +635,7 @@ void VerletKokkos::force_clear() Kokkos::parallel_for(range, Zero::t_f_array>(atomKK->k_torque.view())); atomKK->modified(Device,TORQUE_MASK); } - + // reset SPIN forces if (extraflag) { diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index faf9e5c1db..eb6d918ab0 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -524,7 +524,7 @@ void FixNVESpin::sectoring() sublo[dim]=sublotmp[dim]; subhi[dim]=subhitmp[dim]; } - } + } const double rsx = subhi[0] - sublo[0]; const double rsy = subhi[1] - sublo[1]; From a91e904f349d49b7015345a5e5d00aeeed6649f7 Mon Sep 17 00:00:00 2001 From: Gurgen Date: Sat, 17 Apr 2021 14:56:16 +0300 Subject: [PATCH 0552/1217] minor changes --- lib/gpu/lal_lj_smooth.cpp | 4 ++-- lib/gpu/lal_lj_smooth.cu | 2 +- lib/gpu/lal_lj_smooth.h | 8 ++++---- lib/gpu/lal_lj_smooth_ext.cpp | 2 -- 4 files changed, 7 insertions(+), 9 deletions(-) diff --git a/lib/gpu/lal_lj_smooth.cpp b/lib/gpu/lal_lj_smooth.cpp index 5e4785230b..47ca4ab6fa 100644 --- a/lib/gpu/lal_lj_smooth.cpp +++ b/lib/gpu/lal_lj_smooth.cpp @@ -145,7 +145,7 @@ double LJSMOOTHT::host_memory_usage() const { // Calculate energies, forces, and torques // --------------------------------------------------------------------------- template -void LJSMOOTHT::loop(const bool _eflag, const bool _vflag) { +int LJSMOOTHT::loop(const bool _eflag, const bool _vflag) { // Compute the block size and grid size to keep all cores busy const int BX=this->block_size(); int eflag, vflag; @@ -183,4 +183,4 @@ void LJSMOOTHT::loop(const bool _eflag, const bool _vflag) { } template class LJSMOOTH; -} \ No newline at end of file +} diff --git a/lib/gpu/lal_lj_smooth.cu b/lib/gpu/lal_lj_smooth.cu index c02e1b5ae0..fa87e6fcee 100644 --- a/lib/gpu/lal_lj_smooth.cu +++ b/lib/gpu/lal_lj_smooth.cu @@ -232,4 +232,4 @@ __kernel void k_lj_smooth_fast(const __global numtyp4 *restrict x_, store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, ans,engv); } // if ii -} \ No newline at end of file +} diff --git a/lib/gpu/lal_lj_smooth.h b/lib/gpu/lal_lj_smooth.h index f869977c58..fec39c95c6 100644 --- a/lib/gpu/lal_lj_smooth.h +++ b/lib/gpu/lal_lj_smooth.h @@ -1,13 +1,13 @@ /*************************************************************************** lj_smooth.h ------------------- - W. Michael Brown (ORNL) + G. Melikyan Class for acceleration of the lj/smooth pair style. __________________________________________________________________________ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) __________________________________________________________________________ begin : - email : brownw@ornl.gov + email : gkmelikyan@edu.hse.ru ***************************************************************************/ #ifndef LAL_LJ_SMOOTH_H @@ -83,9 +83,9 @@ class LJSMOOTH : public BaseAtomic { private: bool _allocated; - void loop(const bool _eflag, const bool _vflag); + int loop(const int _eflag, const int _vflag); }; } -#endif \ No newline at end of file +#endif diff --git a/lib/gpu/lal_lj_smooth_ext.cpp b/lib/gpu/lal_lj_smooth_ext.cpp index fd4dfd46be..aaebbe1493 100644 --- a/lib/gpu/lal_lj_smooth_ext.cpp +++ b/lib/gpu/lal_lj_smooth_ext.cpp @@ -142,5 +142,3 @@ void ljsmt_gpu_compute(const int ago, const int inum_full, const int nall, double ljsmt_gpu_bytes() { return LJSMTMF.host_memory_usage(); } - - From e5877d8aa971c23251f49baae17d88e134b2af51 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 17 Apr 2021 11:01:42 -0400 Subject: [PATCH 0553/1217] More explicit code in simple case --- src/variable.cpp | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/variable.cpp b/src/variable.cpp index d903490219..1306061875 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -413,7 +413,7 @@ void Variable::set(int narg, char **arg) if (style[ivar] != EQUAL) error->all(FLERR,"Cannot redefine variable as a different style"); delete [] data[ivar][0]; - copy(1,&arg[2],data[ivar]); + data[ivar][0] = utils::strdup(arg[2]); replaceflag = 1; } else { if (nvar == maxvar) grow(); @@ -422,7 +422,7 @@ void Variable::set(int narg, char **arg) which[nvar] = 0; pad[nvar] = 0; data[nvar] = new char*[num[nvar]]; - copy(1,&arg[2],data[nvar]); + data[nvar][0] = utils::strdup(arg[2]); data[nvar][1] = new char[VALUELENGTH]; strcpy(data[nvar][1],"(undefined)"); } @@ -439,7 +439,7 @@ void Variable::set(int narg, char **arg) if (style[ivar] != ATOM) error->all(FLERR,"Cannot redefine variable as a different style"); delete [] data[ivar][0]; - copy(1,&arg[2],data[ivar]); + data[ivar][0] = utils::strdup(arg[2]); replaceflag = 1; } else { if (nvar == maxvar) grow(); @@ -448,7 +448,7 @@ void Variable::set(int narg, char **arg) which[nvar] = 0; pad[nvar] = 0; data[nvar] = new char*[num[nvar]]; - copy(1,&arg[2],data[nvar]); + data[nvar][0] = utils::strdup(arg[2]); } // VECTOR @@ -463,7 +463,7 @@ void Variable::set(int narg, char **arg) if (style[ivar] != VECTOR) error->all(FLERR,"Cannot redefine variable as a different style"); delete [] data[ivar][0]; - copy(1,&arg[2],data[ivar]); + data[ivar][0] = utils::strdup(arg[2]); replaceflag = 1; } else { if (nvar == maxvar) grow(); @@ -472,7 +472,7 @@ void Variable::set(int narg, char **arg) which[nvar] = 0; pad[nvar] = 0; data[nvar] = new char*[num[nvar]]; - copy(1,&arg[2],data[nvar]); + data[nvar][0] = utils::strdup(arg[2]); } // PYTHON @@ -489,7 +489,7 @@ void Variable::set(int narg, char **arg) if (style[ivar] != PYTHON) error->all(FLERR,"Cannot redefine variable as a different style"); delete [] data[ivar][0]; - copy(1,&arg[2],data[ivar]); + data[ivar][0] = utils::strdup(arg[2]); replaceflag = 1; } else { if (nvar == maxvar) grow(); @@ -498,7 +498,7 @@ void Variable::set(int narg, char **arg) which[nvar] = 1; pad[nvar] = 0; data[nvar] = new char*[num[nvar]]; - copy(1,&arg[2],data[nvar]); + data[nvar][0] = utils::strdup(arg[2]); data[nvar][1] = new char[VALUELENGTH]; strcpy(data[nvar][1],"(undefined)"); } From 18e5e42ce3f91d58cb425310ec16e52f14e7fc4d Mon Sep 17 00:00:00 2001 From: Gurgen Date: Sun, 18 Apr 2021 04:30:59 +0300 Subject: [PATCH 0554/1217] minor change --- lib/gpu/lal_lj_smooth.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/gpu/lal_lj_smooth.cpp b/lib/gpu/lal_lj_smooth.cpp index 47ca4ab6fa..59ebd0f636 100644 --- a/lib/gpu/lal_lj_smooth.cpp +++ b/lib/gpu/lal_lj_smooth.cpp @@ -145,7 +145,7 @@ double LJSMOOTHT::host_memory_usage() const { // Calculate energies, forces, and torques // --------------------------------------------------------------------------- template -int LJSMOOTHT::loop(const bool _eflag, const bool _vflag) { +int LJSMOOTHT::loop(const int _eflag, const int _vflag) { // Compute the block size and grid size to keep all cores busy const int BX=this->block_size(); int eflag, vflag; From 3d5897c9263ec2e4ecf39970409e705b2536a6cc Mon Sep 17 00:00:00 2001 From: Michael Brown Date: Sun, 18 Apr 2021 01:40:33 -0700 Subject: [PATCH 0555/1217] Fixes issue from Feb 2021 GPU package update for tersoff styles using multiple types. --- lib/gpu/lal_tersoff.cpp | 12 +++--------- lib/gpu/lal_tersoff.cu | 16 ++-------------- lib/gpu/lal_tersoff.h | 2 +- lib/gpu/lal_tersoff_extra.h | 5 ++++- lib/gpu/lal_tersoff_mod.cpp | 12 +++--------- lib/gpu/lal_tersoff_mod.cu | 22 +++++----------------- lib/gpu/lal_tersoff_mod.h | 2 +- lib/gpu/lal_tersoff_zbl.cpp | 12 +++--------- lib/gpu/lal_tersoff_zbl.cu | 22 +++++----------------- lib/gpu/lal_tersoff_zbl.h | 2 +- 10 files changed, 28 insertions(+), 79 deletions(-) diff --git a/lib/gpu/lal_tersoff.cpp b/lib/gpu/lal_tersoff.cpp index e0e87d9148..ac5e5bc600 100644 --- a/lib/gpu/lal_tersoff.cpp +++ b/lib/gpu/lal_tersoff.cpp @@ -108,10 +108,7 @@ int TersoffT::init(const int ntypes, const int nlocal, const int nall, const int _nparams = nparams; _nelements = nelements; - UCL_H_Vec host_write(ntypes*ntypes,*(this->ucl_device), - UCL_READ_WRITE); - host_write.zero(); - cutsq_pair.alloc(ntypes*ntypes,*(this->ucl_device),UCL_READ_ONLY); + _cutsq_max=0.0; for (int ii=1; iihost_write[ii*ntypes+jj]) - host_write[ii*ntypes+jj]=host_cutsq[ijkparam]; + if (host_cutsq[ijkparam]>_cutsq_max) _cutsq_max=host_cutsq[ijkparam]; } } } - ucl_copy(cutsq_pair,host_write,ntypes*ntypes); // -------------------------------------------------------------------- UCL_H_Vec dview(nparams,*(this->ucl_device), @@ -235,7 +230,6 @@ void TersoffT::clear() { ts3.clear(); ts4.clear(); ts5.clear(); - cutsq_pair.clear(); map.clear(); elem2param.clear(); _zetaij.clear(); @@ -286,7 +280,7 @@ int TersoffT::loop(const int eflag, const int vflag, const int evatom, int BX=this->block_pair(); int GX=static_cast(ceil(static_cast(ainum)/BX)); this->k_short_nbor.set_size(GX,BX); - this->k_short_nbor.run(&this->atom->x, &cutsq_pair, &_ntypes, + this->k_short_nbor.run(&this->atom->x, &_cutsq_max, &_ntypes, &this->nbor->dev_nbor, &this->nbor->dev_packed, &ainum, &nbor_pitch, &this->_threads_per_atom); diff --git a/lib/gpu/lal_tersoff.cu b/lib/gpu/lal_tersoff.cu index 03ce68be77..8baa5ce12a 100644 --- a/lib/gpu/lal_tersoff.cu +++ b/lib/gpu/lal_tersoff.cu @@ -226,17 +226,13 @@ _texture_2d( pos_tex,int4); #endif __kernel void k_tersoff_short_nbor(const __global numtyp4 *restrict x_, - const __global numtyp *restrict cutsq_pair, - const int ntypes, __global int * dev_nbor, + const numtyp cutsq, const int ntypes, + __global int * dev_nbor, const __global int * dev_packed, const int inum, const int nbor_pitch, const int t_per_atom_in) { const int ii=GLOBAL_ID_X; - #ifdef ONETYPE - const numtyp cutsq=cutsq_pair[ONETYPE]; - #endif - if (ii { /// ts5.x = beta, ts5.y = powern, ts5.z = lam2, ts5.w = bigb UCL_D_Vec ts5; - UCL_D_Vec cutsq_pair; + numtyp _cutsq_max; UCL_D_Vec elem2param; UCL_D_Vec map; diff --git a/lib/gpu/lal_tersoff_extra.h b/lib/gpu/lal_tersoff_extra.h index da2568aa1b..9fe2c63176 100644 --- a/lib/gpu/lal_tersoff_extra.h +++ b/lib/gpu/lal_tersoff_extra.h @@ -142,7 +142,10 @@ ucl_inline numtyp ters_fa_d(const numtyp r, numtyp *ans_d) { #ifndef ONETYPE - if (r > param_bigr + param_bigd) return (numtyp)0.0; + if (r > param_bigr + param_bigd) { + *ans_d = (numtyp)0.0; + return (numtyp)0.0; + } #endif numtyp dfc; const numtyp fc=ters_fc_d(r,param_bigr,param_bigd,&dfc); diff --git a/lib/gpu/lal_tersoff_mod.cpp b/lib/gpu/lal_tersoff_mod.cpp index b7b0fff1b9..347feab06f 100644 --- a/lib/gpu/lal_tersoff_mod.cpp +++ b/lib/gpu/lal_tersoff_mod.cpp @@ -105,10 +105,7 @@ int TersoffMT::init(const int ntypes, const int nlocal, const int nall, const in _nparams = nparams; _nelements = nelements; - UCL_H_Vec host_write(ntypes*ntypes,*(this->ucl_device), - UCL_READ_WRITE); - host_write.zero(); - cutsq_pair.alloc(ntypes*ntypes,*(this->ucl_device),UCL_READ_ONLY); + _cutsq_max=0.0; for (int ii=1; iihost_write[ii*ntypes+jj]) - host_write[ii*ntypes+jj]=host_cutsq[ijkparam]; + if (host_cutsq[ijkparam]>_cutsq_max) _cutsq_max=host_cutsq[ijkparam]; } } } - ucl_copy(cutsq_pair,host_write,ntypes*ntypes); UCL_H_Vec dview(nparams,*(this->ucl_device), UCL_WRITE_ONLY); @@ -229,7 +224,6 @@ void TersoffMT::clear() { ts3.clear(); ts4.clear(); ts5.clear(); - cutsq_pair.clear(); map.clear(); elem2param.clear(); _zetaij.clear(); @@ -275,7 +269,7 @@ int TersoffMT::loop(const int eflag, const int vflag, const int evatom, int BX=this->block_pair(); int GX=static_cast(ceil(static_cast(ainum)/BX)); this->k_short_nbor.set_size(GX,BX); - this->k_short_nbor.run(&this->atom->x, &cutsq_pair, &_ntypes, + this->k_short_nbor.run(&this->atom->x, &_cutsq_max, &_ntypes, &this->nbor->dev_nbor, &this->nbor->dev_packed, &ainum, &nbor_pitch, &this->_threads_per_atom); diff --git a/lib/gpu/lal_tersoff_mod.cu b/lib/gpu/lal_tersoff_mod.cu index 44b04c6933..1eb57683d5 100644 --- a/lib/gpu/lal_tersoff_mod.cu +++ b/lib/gpu/lal_tersoff_mod.cu @@ -220,17 +220,13 @@ _texture_2d( pos_tex,int4); #endif __kernel void k_tersoff_mod_short_nbor(const __global numtyp4 *restrict x_, - const __global numtyp *restrict cutsq_pair, - const int ntypes, __global int * dev_nbor, - const __global int * dev_packed, - const int inum, const int nbor_pitch, - const int t_per_atom) { + const numtyp cutsq, const int ntypes, + __global int * dev_nbor, + const __global int * dev_packed, + const int inum, const int nbor_pitch, + const int t_per_atom) { const int ii=GLOBAL_ID_X; - #ifdef ONETYPE - const numtyp cutsq=cutsq_pair[ONETYPE]; - #endif - if (ii { /// ts5.x = c5, ts5.y = h UCL_D_Vec ts5; - UCL_D_Vec cutsq_pair; + numtyp _cutsq_max; UCL_D_Vec elem2param; UCL_D_Vec map; diff --git a/lib/gpu/lal_tersoff_zbl.cpp b/lib/gpu/lal_tersoff_zbl.cpp index 4456712b0a..4fba97606c 100644 --- a/lib/gpu/lal_tersoff_zbl.cpp +++ b/lib/gpu/lal_tersoff_zbl.cpp @@ -112,10 +112,7 @@ int TersoffZT::init(const int ntypes, const int nlocal, const int nall, _nparams = nparams; _nelements = nelements; - UCL_H_Vec host_write(ntypes*ntypes,*(this->ucl_device), - UCL_READ_WRITE); - host_write.zero(); - cutsq_pair.alloc(ntypes*ntypes,*(this->ucl_device),UCL_READ_ONLY); + _cutsq_max=0.0; for (int ii=1; iihost_write[ii*ntypes+jj]) - host_write[ii*ntypes+jj]=host_cutsq[ijkparam]; + if (host_cutsq[ijkparam]>_cutsq_max) _cutsq_max=host_cutsq[ijkparam]; } } } - ucl_copy(cutsq_pair,host_write,ntypes*ntypes); UCL_H_Vec dview(nparams,*(this->ucl_device), UCL_WRITE_ONLY); @@ -253,7 +248,6 @@ void TersoffZT::clear() { ts4.clear(); ts5.clear(); ts6.clear(); - cutsq_pair.clear(); map.clear(); elem2param.clear(); _zetaij.clear(); @@ -299,7 +293,7 @@ int TersoffZT::loop(const int eflag, const int vflag, const int evatom, int BX=this->block_pair(); int GX=static_cast(ceil(static_cast(ainum)/BX)); this->k_short_nbor.set_size(GX,BX); - this->k_short_nbor.run(&this->atom->x, &cutsq_pair, &_ntypes, + this->k_short_nbor.run(&this->atom->x, &_cutsq_max, &_ntypes, &this->nbor->dev_nbor, &this->nbor->dev_packed, &ainum, &nbor_pitch, &this->_threads_per_atom); diff --git a/lib/gpu/lal_tersoff_zbl.cu b/lib/gpu/lal_tersoff_zbl.cu index fce1ccc406..6250fa55de 100644 --- a/lib/gpu/lal_tersoff_zbl.cu +++ b/lib/gpu/lal_tersoff_zbl.cu @@ -238,17 +238,13 @@ _texture( ts6_tex,int4); #endif __kernel void k_tersoff_zbl_short_nbor(const __global numtyp4 *restrict x_, - const __global numtyp *restrict cutsq_pair, - const int ntypes, __global int * dev_nbor, - const __global int * dev_packed, - const int inum, const int nbor_pitch, - const int t_per_atom) { + const numtyp cutsq, const int ntypes, + __global int * dev_nbor, + const __global int * dev_packed, + const int inum, const int nbor_pitch, + const int t_per_atom) { const int ii=GLOBAL_ID_X; - #ifdef ONETYPE - const numtyp cutsq=cutsq_pair[ONETYPE]; - #endif - if (ii { /// ts6.x = Z_i, ts6.y = Z_j, ts6.z = ZBLcut, ts6.w = ZBLexpscale UCL_D_Vec ts6; - UCL_D_Vec cutsq_pair; + numtyp _cutsq_max; UCL_D_Vec elem2param; UCL_D_Vec map; From 8d10f35acb7dfa336e32d185a3b8dae11f28c56d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 18 Apr 2021 20:43:03 -0400 Subject: [PATCH 0556/1217] display more info about the GPU package setting in the CMake config summary --- cmake/CMakeLists.txt | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 263b5a566d..7f99b04cd6 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -800,9 +800,12 @@ if(BUILD_MPI) endif() if(PKG_GPU) message(STATUS "<<< GPU package settings >>> --- GPU API: ${GPU_API}") +-- GPU API: ${GPU_API}") if(GPU_API STREQUAL "CUDA") + message(STATUS "CUDA Compiler: ${CUDA_NVCC_EXECUTABLE}") message(STATUS "GPU default architecture: ${GPU_ARCH}") + message(STATUS "GPU binning with CUDPP: ${CUDPP_OPT}") + message(STATUS "CUDA MPS support: ${CUDA_MPS_SUPPORT}") elseif(GPU_API STREQUAL "HIP") message(STATUS "HIP platform: ${HIP_PLATFORM}") message(STATUS "HIP architecture: ${HIP_ARCH}") @@ -812,7 +815,7 @@ if(PKG_GPU) message(STATUS "HIP GPU sorting: off") endif() endif() - message(STATUS "GPU precision: ${GPU_PREC}") + message(STATUS "GPU precision: ${GPU_PREC}") endif() if(PKG_KOKKOS) message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}") From f1680b0fdd846863c4ade9d61a70da75fc5e1790 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 18 Apr 2021 20:43:48 -0400 Subject: [PATCH 0557/1217] enable unit test runs on the GPU for tersoff and tersoff/zbl --- unittest/force-styles/tests/manybody-pair-tersoff.yaml | 1 - unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml | 3 +-- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/unittest/force-styles/tests/manybody-pair-tersoff.yaml b/unittest/force-styles/tests/manybody-pair-tersoff.yaml index 7626e4e5de..366810b84e 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff.yaml @@ -2,7 +2,6 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:20 2021 epsilon: 5e-13 -skip_tests: gpu prerequisites: ! | pair tersoff pre_commands: ! | diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml index a8d668ac3b..c1da0c1543 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_zbl.yaml @@ -1,8 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:20 2021 -epsilon: 5e-11 -skip_tests: gpu +epsilon: 5e-9 prerequisites: ! | pair tersoff/zbl pre_commands: ! | From bb7931c9890c8059ae4ad0a4ec2c15393b8becef Mon Sep 17 00:00:00 2001 From: Michael Brown Date: Sun, 18 Apr 2021 09:35:54 -0700 Subject: [PATCH 0558/1217] Fixing bugs in slow (non-shared memory) variant of lj/charmm/coul/charmm/gpu --- lib/gpu/lal_charmm.cpp | 2 +- lib/gpu/lal_charmm.cu | 21 ++++++++------------- 2 files changed, 9 insertions(+), 14 deletions(-) diff --git a/lib/gpu/lal_charmm.cpp b/lib/gpu/lal_charmm.cpp index 811a431cc7..a78043af40 100644 --- a/lib/gpu/lal_charmm.cpp +++ b/lib/gpu/lal_charmm.cpp @@ -150,7 +150,7 @@ int CHARMMT::loop(const int eflag, const int vflag) { &_cut_coul_innersq, &this->_threads_per_atom); } else { this->k_pair.set_size(GX,BX); - this->k_pair.run(&this->atom->x, &ljd, &sp_lj, + this->k_pair.run(&this->atom->x, &lj1, &_lj_types, &sp_lj, &this->nbor->dev_nbor, this->_nbor_data, &this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->atom->q, diff --git a/lib/gpu/lal_charmm.cu b/lib/gpu/lal_charmm.cu index 304dc34e8b..589d9adc91 100644 --- a/lib/gpu/lal_charmm.cu +++ b/lib/gpu/lal_charmm.cu @@ -29,7 +29,8 @@ _texture(q_tex, int2); #endif __kernel void k_charmm(const __global numtyp4 *restrict x_, - const __global numtyp2 *restrict ljd, + const __global numtyp4 *restrict lj1, + const int lj_types, const __global numtyp *restrict sp_lj, const __global int *dev_nbor, const __global int *dev_packed, @@ -88,20 +89,14 @@ __kernel void k_charmm(const __global numtyp4 *restrict x_, numtyp delz = ix.z-jx.z; numtyp rsq = delx*delx+dely*dely+delz*delz; + int mtype=itype*lj_types+jtype; if (rsq cut_lj_innersq) { switch1 = (cut_ljsq-rsq); numtyp switch2 = (numtyp)12.0*rsq*switch1*(rsq-cut_lj_innersq)* @@ -109,7 +104,7 @@ __kernel void k_charmm(const __global numtyp4 *restrict x_, switch1 *= switch1; switch1 *= (cut_ljsq+(numtyp)2.0*rsq-(numtyp)3.0*cut_lj_innersq)* denom_lj; - switch2 *= lj3-lj4; + switch2 *= r6inv*(lj1[mtype].z*r6inv-lj1[mtype].w); force_lj = force_lj*switch1+switch2; } } else @@ -137,7 +132,7 @@ __kernel void k_charmm(const __global numtyp4 *restrict x_, if (EVFLAG && eflag) { e_coul += forcecoul; if (rsq < cut_ljsq) { - numtyp e=lj3-lj4; + numtyp e=r6inv*(lj1[mtype].z*r6inv-lj1[mtype].w); if (rsq > cut_lj_innersq) e *= switch1; energy+=factor_lj*e; From 101deae472b87a29b6591291bd1b533dbc6bc8c8 Mon Sep 17 00:00:00 2001 From: Stephen Sanderson Date: Mon, 19 Apr 2021 10:19:44 +1000 Subject: [PATCH 0559/1217] Removed error thrown when bound xxx upper is used --- src/compute_chunk_atom.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index be1e1e1035..ed36929e4e 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -245,7 +245,6 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) : else maxflag[idim] = COORD; if (maxflag[idim] == COORD) maxvalue[idim] = utils::numeric(FLERR,arg[iarg+3],false,lmp); - else error->all(FLERR,"Illegal compute chunk/atom command"); iarg += 4; } else if (strcmp(arg[iarg],"units") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal compute chunk/atom command"); From 9469cba0818924f17ef15104bcf54e192a23f8d1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 19 Apr 2021 00:34:22 -0400 Subject: [PATCH 0560/1217] enable GPU unit test for pair style lj/charmm/coul/charmm --- unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm.yaml index db8265a6b2..452a1b58d6 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm.yaml @@ -2,7 +2,6 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:45 2021 epsilon: 7e-14 -skip_tests: gpu prerequisites: ! | atom full pair lj/charmm/coul/charmm From f3eb577b3bdb5a3dfce958ae743e7ce4b4acafaa Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 19 Apr 2021 01:14:25 -0400 Subject: [PATCH 0561/1217] update hybrid tests, enable test for hybrid with CPU neigh list and no multiples of the same style --- .../tests/mol-pair-hybrid-overlay.yaml | 1 - .../force-styles/tests/mol-pair-hybrid.yaml | 152 +++++++++--------- .../tests/mol-pair-hybrid_multiple.yaml | 99 ++++++++++++ 3 files changed, 175 insertions(+), 77 deletions(-) create mode 100644 unittest/force-styles/tests/mol-pair-hybrid_multiple.yaml diff --git a/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml b/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml index 0967d5727b..a264411788 100644 --- a/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml +++ b/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml @@ -2,7 +2,6 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:45 2021 epsilon: 5e-14 -skip_tests: gpu prerequisites: ! | atom full pair lj/cut diff --git a/unittest/force-styles/tests/mol-pair-hybrid.yaml b/unittest/force-styles/tests/mol-pair-hybrid.yaml index 95bec97279..713f3d6d26 100644 --- a/unittest/force-styles/tests/mol-pair-hybrid.yaml +++ b/unittest/force-styles/tests/mol-pair-hybrid.yaml @@ -1,99 +1,99 @@ --- -lammps_version: 10 Feb 2021 -date_generated: Fri Feb 26 23:08:45 2021 +lammps_version: 8 Apr 2021 +date_generated: Mon Apr 19 01:11:57 2021 epsilon: 5e-14 -skip_tests: gpu prerequisites: ! | atom full pair lj/cut + pair lj96/cut pre_commands: ! "" post_commands: ! "" input_file: in.fourmol -pair_style: hybrid lj/cut 8.0 lj/cut 8.0 +pair_style: hybrid lj/cut 8.0 lj96/cut 8.0 pair_coeff: ! | - 1 1 lj/cut 1 0.02 2.5 8 - 1 2 lj/cut 1 0.01 1.75 8 - 1 3 lj/cut 1 0.02 2.85 8 - 1 4 lj/cut 1 0.0173205 2.8 8 - 1 5 lj/cut 1 0.0173205 2.8 8 - 2 2 lj/cut 1 0.005 1 8 - 2 3 lj/cut 1 0.01 2.1 8 - 2 4 lj/cut 2 0.005 0.5 8 - 2 5 lj/cut 2 0.00866025 2.05 8 - 3 3 lj/cut 2 0.02 3.2 8 - 3 4 lj/cut 2 0.0173205 3.15 8 - 3 5 lj/cut 2 0.0173205 3.15 8 - 4 4 lj/cut 2 0.015 3.1 8 - 4 5 lj/cut 2 0.015 3.1 8 - 5 5 lj/cut 2 0.015 3.1 8 + 1 1 lj/cut 0.02 2.5 8 + 1 2 lj/cut 0.01 1.75 8 + 1 3 lj/cut 0.02 2.85 8 + 1 4 lj/cut 0.0173205 2.8 8 + 1 5 lj/cut 0.0173205 2.8 8 + 2 2 lj/cut 0.005 1 8 + 2 3 lj/cut 0.01 2.1 8 + 2 4 lj96/cut 0.005 0.5 8 + 2 5 lj96/cut 0.00866025 2.05 8 + 3 3 lj96/cut 0.02 3.2 8 + 3 4 lj96/cut 0.0173205 3.15 8 + 3 5 lj96/cut 0.0173205 3.15 8 + 4 4 lj96/cut 0.015 3.1 8 + 4 5 lj96/cut 0.015 3.1 8 + 5 5 lj96/cut 0.015 3.1 8 extract: ! "" natoms: 29 -init_vdwl: 749.237031537357 +init_vdwl: 652.4184565002801 init_coul: 0 init_stress: ! |2- - 2.1793853434038251e+03 2.1988955172192786e+03 4.6653977523326275e+03 -7.5956547636050641e+02 2.4751536734034119e+01 6.6652028436400667e+02 + 1.6199109282483769e+03 1.8651693243367095e+03 4.3554637539217792e+03 -9.5632074111864961e+02 -2.2843566340523523e+02 6.9979931660192312e+02 init_forces: ! |2 - 1 -2.3333390280895383e+01 2.6994567613322732e+02 3.3272827850356794e+02 - 2 1.5828554630414868e+02 1.3025008843535846e+02 -1.8629682358935690e+02 + 1 -2.3333467289742931e+01 2.6993142283476851e+02 3.3272495963292283e+02 + 2 1.5828552013445056e+02 1.3025008546972211e+02 -1.8629688302475225e+02 3 -1.3528903738169089e+02 -3.8704313358320059e+02 -1.4568978437133126e+02 - 4 -7.8711096705893420e+00 2.1350518625373542e+00 -5.5954532185548151e+00 - 5 -2.5176757268228527e+00 -4.0521510681020221e+00 1.2152704057877008e+01 + 4 -7.8711116846129050e+00 2.1350517679284451e+00 -5.5954561911890046e+00 + 5 -2.5177006460693390e+00 -4.0521653208614632e+00 1.2152678277353530e+01 6 -8.3190662465252262e+02 9.6394149462625705e+02 1.1509093566509250e+03 - 7 5.8203388932513640e+01 -3.3608997951626816e+02 -1.7179617996573054e+03 - 8 1.4451392284291583e+02 -1.0927475861089046e+02 3.9990593492420493e+02 - 9 7.9156945283097571e+01 8.5273009783986680e+01 3.5032175698445252e+02 + 7 6.4962361232321371e+01 -3.3998931142273761e+02 -1.7032944435177421e+03 + 8 1.3800067755917669e+02 -1.0575764259058835e+02 3.8568183849544192e+02 + 9 7.9156940582018805e+01 8.5272978047670051e+01 3.5032172427046436e+02 10 5.3118875219105416e+02 -6.1040990859419469e+02 -1.8355872642619312e+02 - 11 -2.3530157267965532e+00 -5.9077640073819744e+00 -9.6590723955414326e+00 + 11 -2.3531003777844695e+00 -5.9077049537176469e+00 -9.6590265504356907e+00 12 1.7527155146800411e+01 1.0633119523437488e+01 -7.9254398064483143e+00 - 13 8.0986409579532861e+00 -3.2098088264781510e+00 -1.4896399843793828e-01 - 14 -3.3852721292265100e+00 6.8636181241903504e-01 -8.7507190862499726e+00 - 15 -2.0454999188605286e-01 8.4846165523049883e+00 3.0131615419406708e+00 + 13 8.0985903919880737e+00 -3.2096212808671210e+00 -1.4884740337815178e-01 + 14 -3.3853022166233191e+00 6.8640988271648729e-01 -8.7507072432538457e+00 + 15 -2.0454983537269980e-01 8.4846157143527687e+00 3.0131531921339136e+00 16 4.6326310311812085e+02 -3.3087715736498177e+02 -1.1893024561782547e+03 - 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"" +post_commands: ! "" +input_file: in.fourmol +pair_style: hybrid lj/cut 8.0 lj/cut 8.0 +pair_coeff: ! | + 1 1 lj/cut 1 0.02 2.5 8 + 1 2 lj/cut 1 0.01 1.75 8 + 1 3 lj/cut 1 0.02 2.85 8 + 1 4 lj/cut 1 0.0173205 2.8 8 + 1 5 lj/cut 1 0.0173205 2.8 8 + 2 2 lj/cut 1 0.005 1 8 + 2 3 lj/cut 1 0.01 2.1 8 + 2 4 lj/cut 2 0.005 0.5 8 + 2 5 lj/cut 2 0.00866025 2.05 8 + 3 3 lj/cut 2 0.02 3.2 8 + 3 4 lj/cut 2 0.0173205 3.15 8 + 3 5 lj/cut 2 0.0173205 3.15 8 + 4 4 lj/cut 2 0.015 3.1 8 + 4 5 lj/cut 2 0.015 3.1 8 + 5 5 lj/cut 2 0.015 3.1 8 +extract: ! "" +natoms: 29 +init_vdwl: 749.2370315373572 +init_coul: 0 +init_stress: ! |2- + 2.1793853434038251e+03 2.1988955172192786e+03 4.6653977523326275e+03 -7.5956547636050641e+02 2.4751536734034119e+01 6.6652028436400667e+02 +init_forces: ! |2 + 1 -2.3333390280895383e+01 2.6994567613322732e+02 3.3272827850356794e+02 + 2 1.5828554630414868e+02 1.3025008843535846e+02 -1.8629682358935690e+02 + 3 -1.3528903738169089e+02 -3.8704313358320059e+02 -1.4568978437133126e+02 + 4 -7.8711096705893420e+00 2.1350518625373542e+00 -5.5954532185548151e+00 + 5 -2.5176757268228527e+00 -4.0521510681020221e+00 1.2152704057877008e+01 + 6 -8.3190662465252262e+02 9.6394149462625705e+02 1.1509093566509250e+03 + 7 5.8203388932513640e+01 -3.3608997951626816e+02 -1.7179617996573054e+03 + 8 1.4451392284291583e+02 -1.0927475861089046e+02 3.9990593492420493e+02 + 9 7.9156945283097571e+01 8.5273009783986680e+01 3.5032175698445252e+02 + 10 5.3118875219105416e+02 -6.1040990859419469e+02 -1.8355872642619312e+02 + 11 -2.3530157267965532e+00 -5.9077640073819744e+00 -9.6590723955414326e+00 + 12 1.7527155146800411e+01 1.0633119523437488e+01 -7.9254398064483143e+00 + 13 8.0986409579532861e+00 -3.2098088264781510e+00 -1.4896399843793828e-01 + 14 -3.3852721292265100e+00 6.8636181241903504e-01 -8.7507190862499726e+00 + 15 -2.0454999188605286e-01 8.4846165523049883e+00 3.0131615419406708e+00 + 16 4.6326310311812085e+02 -3.3087715736498177e+02 -1.1893024561782547e+03 + 17 -4.5334300923766710e+02 3.1554283255882558e+02 1.2058417793481196e+03 + 18 -1.8862623280672657e-02 -3.3402010907951640e-02 3.1000479299095243e-02 + 19 3.1843079640570080e-04 -2.3918627818763423e-04 1.7427252638513441e-03 + 20 -9.9760831209706009e-04 -1.0209184826753088e-03 3.6910972636601454e-04 + 21 -7.1566125273265527e+01 -8.1615678329920812e+01 2.2589561408339878e+02 + 22 -1.0808835729977487e+02 -2.6193787235943859e+01 -1.6957904943161384e+02 + 23 1.7964455474779510e+02 1.0782097695276961e+02 -5.6305786479140700e+01 + 24 3.6591406576585001e+01 -2.1181587621785556e+02 1.1218301872572404e+02 + 25 -1.4851489147738829e+02 2.3907118122949107e+01 -1.2485634873166315e+02 + 26 1.1191129453598201e+02 1.8789774664223359e+02 1.2650137204319886e+01 + 27 5.1810388677546058e+01 -2.2705458321213791e+02 9.0849111082069683e+01 + 28 -1.8041307121444072e+02 7.7534042932772934e+01 -1.2206956760706599e+02 + 29 1.2861057254925004e+02 1.4952711274394565e+02 3.1216025556267869e+01 +run_vdwl: 719.4432816774656 +run_coul: 0 +run_stress: ! |2- + 2.1330153957371017e+03 2.1547728168285512e+03 4.3976497417710170e+03 -7.3873328448298525e+02 4.1743821105367225e+01 6.2788012209191243e+02 +run_forces: ! |2 + 1 -2.0299419751359796e+01 2.6686193378822901e+02 3.2358785870694004e+02 + 2 1.5298617928491248e+02 1.2596516341409225e+02 -1.7961292655338647e+02 + 3 -1.3353630652439793e+02 -3.7923748696131213e+02 -1.4291839793625775e+02 + 4 -7.8374717836161771e+00 2.1276610789823414e+00 -5.5845014473820624e+00 + 5 -2.5014258630866699e+00 -4.0250131424704385e+00 1.2103512372025625e+01 + 6 -8.0681462887292412e+02 9.2165637136761688e+02 1.0270795806932804e+03 + 7 5.5780279349903594e+01 -3.1117530951561696e+02 -1.5746991292869038e+03 + 8 1.3452983055534955e+02 -1.0064659350255846e+02 3.8851791558207583e+02 + 9 7.6746213883426122e+01 8.2501469877402286e+01 3.3944351200617950e+02 + 10 5.2128033527695618e+02 -5.9920098848285909e+02 -1.8126029815043356e+02 + 11 -2.3573118090915246e+00 -5.8616944550888350e+00 -9.6049808811326240e+00 + 12 1.7503975847822890e+01 1.0626930310560827e+01 -8.0603160272054950e+00 + 13 8.0530313322973104e+00 -3.1756495170399104e+00 -1.4618315664740525e-01 + 14 -3.3416065168069760e+00 6.6492606336082127e-01 -8.6345131440469647e+00 + 15 -2.2253843262374870e-01 8.5025661635348619e+00 3.0369735873081569e+00 + 16 4.3476311264989528e+02 -3.1171086735551455e+02 -1.1135217194927461e+03 + 17 -4.2469846140777202e+02 2.9615411776780638e+02 1.1302573488400678e+03 + 18 -1.8849981672825901e-02 -3.3371636477421286e-02 3.0986293443778724e-02 + 19 3.0940277774413972e-04 -2.4634536455373055e-04 1.7433360008861018e-03 + 20 -9.8648131277150768e-04 -1.0112587134526944e-03 3.6932948773965422e-04 + 21 -7.0490745283106705e+01 -7.9749153581142281e+01 2.2171003384646417e+02 + 22 -1.0638717908920059e+02 -2.5949502163177943e+01 -1.6645589526812256e+02 + 23 1.7686797710735050e+02 1.0571018898885526e+02 -5.5243337084099444e+01 + 24 3.8206017656281247e+01 -2.1022820141992992e+02 1.1260711266189016e+02 + 25 -1.4918881473530885e+02 2.3762151395876515e+01 -1.2549188139143089e+02 + 26 1.1097059498808326e+02 1.8645503634228552e+02 1.2861559677865269e+01 + 27 5.0800844984832011e+01 -2.2296588090685447e+02 8.8607367716323097e+01 + 28 -1.7694190504288861e+02 7.6029945485181912e+01 -1.1950518150242056e+02 + 29 1.2614894925528131e+02 1.4694250820033537e+02 3.0893386672863009e+01 +... From 48e9f451f44131b759c859d458773ef0a637f293 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 19 Apr 2021 01:23:54 -0400 Subject: [PATCH 0562/1217] disallow using the same GPU pair style multiple times as hybrid sub-style --- src/pair_hybrid.cpp | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 48ba1ccff7..b67f98a726 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -547,6 +547,15 @@ void PairHybrid::init_style() if (used == 0) error->all(FLERR,"Pair hybrid sub-style is not used"); } + // The GPU library uses global data for each pair style, so the + // same style must not be used multiple times + + for (istyle = 0; istyle < nstyles; istyle++) { + bool is_gpu = (((PairHybrid *)styles[m])->suffix_flag & Suffix::GPU); + if (multiple[istyle] && is_gpu) + error->all(FLERR,"GPU package styles must not be used multiple times"); + } + // check if special_lj/special_coul overrides are compatible for (istyle = 0; istyle < nstyles; istyle++) { From 5409a2a8070c7fc320c1819a2ebe22d86cb7a490 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 19 Apr 2021 07:55:10 -0400 Subject: [PATCH 0563/1217] rearrange for better readability --- src/compute_chunk_atom.cpp | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index ed36929e4e..5960e1fc6f 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -237,14 +237,12 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) : else if (strcmp(arg[iarg+1],"y") == 0) idim = 1; else if (strcmp(arg[iarg+1],"z") == 0) idim = 2; else error->all(FLERR,"Illegal compute chunk/atom command"); + minflag[idim] = COORD; if (strcmp(arg[iarg+2],"lower") == 0) minflag[idim] = LOWER; - else minflag[idim] = COORD; - if (minflag[idim] == COORD) - minvalue[idim] = utils::numeric(FLERR,arg[iarg+2],false,lmp); + else minvalue[idim] = utils::numeric(FLERR,arg[iarg+2],false,lmp); + maxflag[idim] = COORD; if (strcmp(arg[iarg+3],"upper") == 0) maxflag[idim] = UPPER; - else maxflag[idim] = COORD; - if (maxflag[idim] == COORD) - maxvalue[idim] = utils::numeric(FLERR,arg[iarg+3],false,lmp); + else maxvalue[idim] = utils::numeric(FLERR,arg[iarg+3],false,lmp); iarg += 4; } else if (strcmp(arg[iarg],"units") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal compute chunk/atom command"); From 1ad45d65d6ea6c45c4df71d56fb626c5353281ac Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 19 Apr 2021 08:09:02 -0400 Subject: [PATCH 0564/1217] document limitation of not using GPU pair styles as the same style multiple times with hybrid --- doc/src/pair_hybrid.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index e4e253caf9..868d645b83 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -452,6 +452,9 @@ the same or else LAMMPS will generate an error. Pair style *hybrid/scaled* currently only works for non-accelerated pair styles and pair styles from the OPT package. +When using pair styles from the GPU package they must not be listed +multiple times. LAMMPS will detect this and abort. + Related commands """""""""""""""" From d60a247138fe0cfb4f7ac9ed6a3d428fbcbd8512 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 19 Apr 2021 08:44:46 -0400 Subject: [PATCH 0565/1217] fix typo --- src/pair_hybrid.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index b67f98a726..002429e7b3 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -551,7 +551,7 @@ void PairHybrid::init_style() // same style must not be used multiple times for (istyle = 0; istyle < nstyles; istyle++) { - bool is_gpu = (((PairHybrid *)styles[m])->suffix_flag & Suffix::GPU); + bool is_gpu = (((PairHybrid *)styles[istyle])->suffix_flag & Suffix::GPU); if (multiple[istyle] && is_gpu) error->all(FLERR,"GPU package styles must not be used multiple times"); } From c46f1b52416980b4e17024279dc4200bb9564dfb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 19 Apr 2021 08:51:53 -0400 Subject: [PATCH 0566/1217] modify tests for hybrid pair styles to include some pair_coeff none settings --- .../tests/atomic-pair-hybrid-eam.yaml | 8 +- .../tests/atomic-pair-hybrid-eam_fs.yaml | 8 +- .../tests/mol-pair-hybrid-overlay.yaml | 105 +++++++------- .../tests/mol-pair-hybrid-scaled.yaml | 129 +++++++++--------- .../force-styles/tests/mol-pair-hybrid.yaml | 94 ++++++------- .../tests/mol-pair-hybrid_multiple.yaml | 114 ++++++++-------- .../tests/mol-pair-python_hybrid.yaml | 12 +- 7 files changed, 235 insertions(+), 235 deletions(-) diff --git a/unittest/force-styles/tests/atomic-pair-hybrid-eam.yaml b/unittest/force-styles/tests/atomic-pair-hybrid-eam.yaml index a681657b65..4c8e040200 100644 --- a/unittest/force-styles/tests/atomic-pair-hybrid-eam.yaml +++ b/unittest/force-styles/tests/atomic-pair-hybrid-eam.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 10 Feb 2021 -date_generated: Fri Feb 26 23:09:02 2021 +lammps_version: 8 Apr 2021 +date_generated: Mon Apr 19 08:49:08 2021 epsilon: 1e-11 prerequisites: ! | pair eam/fs @@ -13,7 +13,7 @@ pair_coeff: ! | 2 2 eam Ni_u3.eam extract: ! "" natoms: 32 -init_vdwl: 0.713225916338978 +init_vdwl: 0.7132259163389776 init_coul: 0 init_stress: ! |2- 2.6556151567263032e+02 2.6660724159085703e+02 2.4812081237895359e+02 6.0264893464561915e+00 -6.6027371615114303e+00 -1.4187579099120772e+01 @@ -50,7 +50,7 @@ init_forces: ! |2 30 -8.7442364632334701e-01 -8.5922993943854902e+00 -3.1671240722317777e+00 31 3.1880080741982892e+00 -5.0021160844369490e+00 -2.7083467494366831e-01 32 -1.5986786450380142e+01 -5.5759911113046883e+00 -1.5504124024744577e+00 -run_vdwl: 0.669352105052575 +run_vdwl: 0.6693521050525746 run_coul: 0 run_stress: ! |2- 2.6541041873586806e+02 2.6644256162479292e+02 2.4793398704069506e+02 5.9903981717659827e+00 -6.6045526000630410e+00 -1.4160943794248436e+01 diff --git a/unittest/force-styles/tests/atomic-pair-hybrid-eam_fs.yaml b/unittest/force-styles/tests/atomic-pair-hybrid-eam_fs.yaml index d2f511b3ea..be3889de90 100644 --- a/unittest/force-styles/tests/atomic-pair-hybrid-eam_fs.yaml +++ b/unittest/force-styles/tests/atomic-pair-hybrid-eam_fs.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 10 Feb 2021 -date_generated: Fri Feb 26 23:09:03 2021 +lammps_version: 8 Apr 2021 +date_generated: Mon Apr 19 08:49:08 2021 epsilon: 5e-12 prerequisites: ! | pair eam/fs @@ -13,7 +13,7 @@ pair_coeff: ! | * * eam/fs AlFe_mm.eam.fs NULL Al extract: ! "" natoms: 32 -init_vdwl: 15.6583494469006 +init_vdwl: 15.658349446900637 init_coul: 0 init_stress: ! |2- 3.1757662346015599e+02 3.1488042003987044e+02 2.9518192213010605e+02 8.0970202601485379e+00 -4.6038792816319125e+00 -1.1521259274290610e+01 @@ -50,7 +50,7 @@ init_forces: ! |2 30 -2.0584055270338175e+00 -5.2207163606526530e+00 -4.6304543222177532e+00 31 1.2014109675977875e+00 -6.5554529419137078e+00 2.1453874832093329e+00 32 -1.5986786450380142e+01 -5.5759911113046883e+00 -1.5504124024744577e+00 -run_vdwl: 15.6055369596825 +run_vdwl: 15.605536959682482 run_coul: 0 run_stress: ! |2- 3.1739734448741643e+02 3.1467775824072135e+02 2.9494960877836593e+02 8.0575431550134713e+00 -4.6069278562709943e+00 -1.1484582135772436e+01 diff --git a/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml b/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml index a264411788..4aeae6cd1b 100644 --- a/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml +++ b/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml @@ -1,7 +1,7 @@ --- -lammps_version: 10 Feb 2021 -date_generated: Fri Feb 26 23:08:45 2021 -epsilon: 5e-14 +lammps_version: 8 Apr 2021 +date_generated: Mon Apr 19 08:49:07 2021 +epsilon: 7.5e-14 prerequisites: ! | atom full pair lj/cut @@ -16,86 +16,85 @@ pair_coeff: ! | 1 2 lj/cut 0.01 1.75 8 1 3 lj/cut 0.02 2.85 8 1 4 lj/cut 0.0173205 2.8 8 - 1 5 lj/cut 0.0173205 2.8 8 2 2 lj/cut 0.005 1 8 2 3 lj/cut 0.01 2.1 8 2 4 lj/cut 0.005 0.5 8 2 5 lj/cut 0.00866025 2.05 8 3 3 lj/cut 0.02 3.2 8 - 3 4 lj/cut 0.0173205 3.15 8 3 5 lj/cut 0.0173205 3.15 8 4 4 lj/cut 0.015 3.1 8 4 5 lj/cut 0.015 3.1 8 5 5 lj/cut 0.015 3.1 8 * * coul/cut + 3 3 none extract: ! "" natoms: 29 -init_vdwl: 749.237031537357 -init_coul: -127.494586297384 +init_vdwl: 745.8729165577952 +init_coul: -138.51281549901438 init_stress: ! |2- - 2.1525607963688685e+03 2.1557327421151899e+03 4.6078904881742919e+03 -7.6038602729615206e+02 1.6844266627640316e+01 6.6957549356541904e+02 + 2.1433945387773583e+03 2.1438418525427405e+03 4.5749493230631624e+03 -7.5161300805564053e+02 2.2812993218099149e+00 6.7751226426357493e+02 init_forces: ! |2 - 1 -2.1092656751925425e+01 2.6988675971196511e+02 3.3315496490210148e+02 + 1 -1.9649291084632637e+01 2.6691357149380127e+02 3.3265232188338541e+02 2 1.5859534558925552e+02 1.2807631885753918e+02 -1.8817306436807144e+02 - 3 -1.3530454720678361e+02 -3.8712939850050407e+02 -1.4565941679363837e+02 + 3 -1.3530567831970495e+02 -3.8712983044177196e+02 -1.4566129338928388e+02 4 -7.8195539840070643e+00 2.1451967639963558e+00 -5.9041143405612999e+00 5 -2.9163954623584245e+00 -3.3469203159528891e+00 1.2074681739853981e+01 - 6 -8.2989063447195736e+02 9.6019318342576571e+02 1.1479359629470548e+03 - 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"" natoms: 29 -init_vdwl: 749.237031537357 -init_coul: -127.494586297384 +init_vdwl: 695.3728483503972 +init_coul: 118.95803822933868 init_stress: ! |2- - 2.1525607963688685e+03 2.1557327421151899e+03 4.6078904881742919e+03 -7.6038602729615206e+02 1.6844266627640316e+01 6.6957549356541904e+02 + 2.1020038760662910e+03 2.1696900014167491e+03 4.2400143530641753e+03 -8.4820804228720078e+02 3.1662186032408862e+01 6.7609982605789560e+02 init_forces: ! |2 - 1 -2.1092656751925425e+01 2.6988675971196511e+02 3.3315496490210148e+02 - 2 1.5859534558925552e+02 1.2807631885753918e+02 -1.8817306436807144e+02 + 1 1.2395744433084418e+02 4.0360040310773837e+02 1.4710329775938777e+02 + 2 2.0403866219573294e+00 3.7427015227202860e+00 -5.2095053499948687e+00 3 -1.3530454720678361e+02 -3.8712939850050407e+02 -1.4565941679363837e+02 - 4 -7.8195539840070643e+00 2.1451967639963558e+00 -5.9041143405612999e+00 - 5 -2.9163954623584245e+00 -3.3469203159528891e+00 1.2074681739853981e+01 - 6 -8.2989063447195736e+02 9.6019318342576571e+02 1.1479359629470548e+03 - 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25 -1.4570195714964908e+02 2.0679748005808605e+01 -1.2162175868970056e+02 - 26 1.0901403460528100e+02 1.7901644500696690e+02 1.2412674623332103e+01 - 27 4.8035883250870448e+01 -2.1205445789284894e+02 8.4315888267103702e+01 - 28 -1.7229323056476886e+02 7.0823266235363889e+01 -1.1557273097021344e+02 - 29 1.2500312314724302e+02 1.4088629633289813e+02 3.1828931397054006e+01 + 1 1.2147752778287347e+02 3.9534374510798301e+02 1.4413605468707195e+02 + 2 2.0399930128993224e+00 3.7557805682682748e+00 -5.2058063128492336e+00 + 3 -1.3333096721751764e+02 -3.7844737951764535e+02 -1.4238961467845959e+02 + 4 -8.8134959904656007e+00 2.0713309772867512e+00 -6.4488585600230390e+00 + 5 -3.8477726201647444e+00 -3.3895758075040905e+00 1.2617145909886416e+01 + 6 -8.0167356407303771e+02 9.1511139207343115e+02 1.0260272560535318e+03 + 7 5.5505611657656395e+01 -3.1051895449278589e+02 -1.5710947343097826e+03 + 8 2.0529374503578478e+02 -2.0214215494247814e+01 7.2625230302681450e+02 + 9 5.2759827822743706e+00 -8.5029606929125237e+00 6.9437749095564918e+00 + 10 5.1965622207475565e+02 -5.9755369618722887e+02 -1.8157960265809501e+02 + 11 -2.8945778423069450e+00 -5.7662137070620867e+00 -1.0795655996511190e+01 + 12 2.0805414458419623e+01 9.8601745071951186e+00 -6.7782082590913761e+00 + 13 8.7071353977142216e+00 -3.5468381013374746e+00 -5.0622413568933977e-01 + 14 -3.5154376369702902e+00 7.7780954572734984e-01 -9.9213826027447922e+00 + 15 1.9841048852047882e+00 8.5994997942103542e+00 1.4318674533257378e+00 + 16 4.3381844145946962e+02 -3.1216471119732176e+02 -1.1109885080754987e+03 + 17 -4.2715530816964593e+02 3.0229606646197493e+02 1.1227416717947804e+03 + 18 1.2084471423281700e+00 6.6044276302722391e+00 -9.8277754487894136e+00 + 19 3.2313284340457584e+00 3.9423765207539685e-01 4.3538203547548804e-01 + 20 -1.1969830459758257e+00 -8.8960771143457151e-01 9.2526061301410900e-01 + 21 -6.8060732684000939e+01 -7.8361174093266939e+01 2.1144116321844479e+02 + 22 -1.0408301224632098e+02 -2.5910595170511762e+01 -1.6092979318531198e+02 + 23 1.7368084263289987e+02 1.0120586644080414e+02 -5.1841492516928824e+01 + 24 3.5901478353702402e+01 -2.0053113579605662e+02 1.1040539818330446e+02 + 25 -1.4257916099779564e+02 2.4374225442971877e+01 -1.1459703108843671e+02 + 26 1.1121725716987784e+02 1.8123540984908496e+02 1.5706480723289609e+01 + 27 4.7997433858479745e+01 -2.1209575374436324e+02 8.4297950741699410e+01 + 28 -1.7410976565710496e+02 6.8409754929264125e+01 -1.1446187451410728e+02 + 29 1.2345981204292134e+02 1.3785309073312925e+02 3.4004852992123624e+01 ... diff --git a/unittest/force-styles/tests/mol-pair-hybrid.yaml b/unittest/force-styles/tests/mol-pair-hybrid.yaml index 713f3d6d26..ab25a334c6 100644 --- a/unittest/force-styles/tests/mol-pair-hybrid.yaml +++ b/unittest/force-styles/tests/mol-pair-hybrid.yaml @@ -1,6 +1,6 @@ --- lammps_version: 8 Apr 2021 -date_generated: Mon Apr 19 01:11:57 2021 +date_generated: Mon Apr 19 08:49:07 2021 epsilon: 5e-14 prerequisites: ! | atom full @@ -15,7 +15,7 @@ pair_coeff: ! | 1 2 lj/cut 0.01 1.75 8 1 3 lj/cut 0.02 2.85 8 1 4 lj/cut 0.0173205 2.8 8 - 1 5 lj/cut 0.0173205 2.8 8 + 1 5 none 2 2 lj/cut 0.005 1 8 2 3 lj/cut 0.01 2.1 8 2 4 lj96/cut 0.005 0.5 8 @@ -24,76 +24,76 @@ pair_coeff: ! | 3 4 lj96/cut 0.0173205 3.15 8 3 5 lj96/cut 0.0173205 3.15 8 4 4 lj96/cut 0.015 3.1 8 - 4 5 lj96/cut 0.015 3.1 8 + 4 5 none 5 5 lj96/cut 0.015 3.1 8 extract: ! "" natoms: 29 -init_vdwl: 652.4184565002801 +init_vdwl: 652.4450882982227 init_coul: 0 init_stress: ! |2- - 1.6199109282483769e+03 1.8651693243367095e+03 4.3554637539217792e+03 -9.5632074111864961e+02 -2.2843566340523523e+02 6.9979931660192312e+02 + 1.6199549089538609e+03 1.8652222871458566e+03 4.3555170935393007e+03 -9.5632547516887212e+02 -2.2845869578774162e+02 6.9982627975055175e+02 init_forces: ! |2 1 -2.3333467289742931e+01 2.6993142283476851e+02 3.3272495963292283e+02 2 1.5828552013445056e+02 1.3025008546972211e+02 -1.8629688302475225e+02 - 3 -1.3528903738169089e+02 -3.8704313358320059e+02 -1.4568978437133126e+02 + 3 -1.3529016849461223e+02 -3.8704356552446848e+02 -1.4569166096697677e+02 4 -7.8711116846129050e+00 2.1350517679284451e+00 -5.5954561911890046e+00 5 -2.5177006460693390e+00 -4.0521653208614632e+00 1.2152678277353530e+01 - 6 -8.3190662465252262e+02 9.6394149462625705e+02 1.1509093566509250e+03 - 7 6.4962361232321371e+01 -3.3998931142273761e+02 -1.7032944435177421e+03 + 6 -8.3190697480339566e+02 9.6394156556954056e+02 1.1509082485986419e+03 + 7 6.4961865086373535e+01 -3.3998877273576284e+02 -1.7032949977108992e+03 8 1.3800067755917669e+02 -1.0575764259058835e+02 3.8568183849544192e+02 9 7.9156940582018805e+01 8.5272978047670051e+01 3.5032172427046436e+02 - 10 5.3118875219105416e+02 -6.1040990859419469e+02 -1.8355872642619312e+02 + 10 5.3118723340662132e+02 -6.1040797933322176e+02 -1.8355763882870201e+02 11 -2.3531003777844695e+00 -5.9077049537176469e+00 -9.6590265504356907e+00 - 12 1.7527155146800411e+01 1.0633119523437488e+01 -7.9254398064483143e+00 + 12 1.7525454559786660e+01 1.0636445740481784e+01 -7.9240149067722738e+00 13 8.0985903919880737e+00 -3.2096212808671210e+00 -1.4884740337815178e-01 14 -3.3853022166233191e+00 6.8640988271648729e-01 -8.7507072432538457e+00 15 -2.0454983537269980e-01 8.4846157143527687e+00 3.0131531921339136e+00 - 16 4.6326310311812085e+02 -3.3087715736498177e+02 -1.1893024561782547e+03 - 17 -4.5359750947639009e+02 3.1593101129176102e+02 1.2054041942174727e+03 - 18 -1.2247799307716830e-02 -2.5549356154280022e-02 2.3426146878445887e-02 + 16 4.6326233922126522e+02 -3.3087556531781973e+02 -1.1892999860848122e+03 + 17 -4.5359533332836713e+02 3.1593155242296575e+02 1.2054040116538242e+03 + 18 -1.2313292578060062e-02 -2.5378393942268991e-02 2.2968315649798128e-02 19 3.0439100375925543e-04 -2.4779478988349023e-04 1.7258398467618651e-03 20 -9.8045055969651082e-04 -1.0028949153285463e-03 3.5715001758946177e-04 - 21 -5.7259654105550446e+00 -6.6261603981115007e+00 1.8662334963157239e+01 + 21 -5.7186294103147572e+00 -6.6344147796080684e+00 1.8654007864095536e+01 22 -8.9567671655515344e+00 -2.1701845330290590e+00 -1.4052631842883260e+01 23 1.4673371058172327e+01 8.8071981142288021e+00 -4.5994772330864269e+00 - 24 3.2754323123828888e+00 -1.7320890380029486e+01 9.3837561146006259e+00 + 24 3.2769508891728725e+00 -1.7316771489185900e+01 9.3887574366841235e+00 25 -1.2406052232816045e+01 1.9955673026898786e+00 -1.0432202322872895e+01 26 9.1216838958879958e+00 1.5316110435596807e+01 1.0304939537049307e+00 - 27 3.8505279402678756e+00 -1.8674981408870256e+01 7.2374473540380091e+00 + 27 3.8455233865293490e+00 -1.8678583225803411e+01 7.2399697763695485e+00 28 -1.4536949587460585e+01 6.2480560831561052e+00 -9.8361741655762192e+00 29 1.0692946253413785e+01 1.2432540782763471e+01 2.5948100184389560e+00 -run_vdwl: 624.0931724812624 +run_vdwl: 624.1198434527859 run_coul: 0 run_stress: ! |2- - 1.5810614921207168e+03 1.8259496400572398e+03 4.0927586908511830e+03 -9.3274460917940576e+02 -2.0867274108457650e+02 6.5972860402326364e+02 + 1.5811055300513408e+03 1.8260026652593124e+03 4.0928122296059910e+03 -9.3274940961565028e+02 -2.0869586127604293e+02 6.5975565836651401e+02 run_forces: ! |2 - 1 -2.0299541691313117e+01 2.6684808661567672e+02 3.2358468742419683e+02 - 2 1.5298613011067428e+02 1.2596515037057534e+02 -1.7961295709437377e+02 - 3 -1.3353640466567978e+02 -3.7923755350333602e+02 -1.4291841089088308e+02 - 4 -7.8374737454652808e+00 2.1276609324255480e+00 -5.5845044191605586e+00 - 5 -2.5014508748542599e+00 -4.0250275085278417e+00 1.2103486568405946e+01 - 6 -8.0709581424168800e+02 9.2196946936473341e+02 1.0273855514262461e+03 - 7 6.2369460347918640e+01 -3.1506026103586646e+02 -1.5609068887693647e+03 - 8 1.2853744772540196e+02 -9.7465102833516411e+01 3.7497118964197733e+02 - 9 7.6715909805418633e+01 8.2459997331121102e+01 3.3929722448588177e+02 - 10 5.2124066201315134e+02 -5.9915158589906139e+02 -1.8122187177576421e+02 - 11 -2.3573942943424457e+00 -5.8616371525570177e+00 -9.6049341235370651e+00 - 12 1.7504085531188526e+01 1.0626906235157978e+01 -8.0602559985143234e+00 - 13 8.0529810484635167e+00 -3.1754618743136067e+00 -1.4606675720625387e-01 - 14 -3.3416364933094522e+00 6.6497439746567266e-01 -8.6345017171716023e+00 - 15 -2.2253806720629177e-01 8.5025652150980289e+00 3.0369656856596272e+00 - 16 4.3476579887679043e+02 -3.1171316950942264e+02 -1.1135265898068189e+03 - 17 -4.2495551400860438e+02 2.9654448375995389e+02 1.1298239898107718e+03 - 18 -1.2238729800031808e-02 -2.5522946873703746e-02 2.3420684481679759e-02 - 19 2.9523284696012181e-04 -2.5507040699961720e-04 1.7263527154627954e-03 - 20 -9.6972071699707053e-04 -9.9365617328814326e-04 3.5770286403774917e-04 - 21 -5.7852799713364247e+00 -6.6291063289513819e+00 1.8725369889018072e+01 - 22 -9.0188467780616044e+00 -2.2015412590920249e+00 -1.4100629864742880e+01 - 23 1.4794748132410522e+01 8.8415190746034931e+00 -4.6144919806087472e+00 - 24 3.4156814089933589e+00 -1.7553199977900867e+01 9.5679676502289812e+00 - 25 -1.2674531267261465e+01 2.0106983101785691e+00 -1.0661185224301247e+01 - 26 9.2499105004052797e+00 1.5533291582421921e+01 1.0752649123326561e+00 - 27 3.9148625428118144e+00 -1.8756087716965553e+01 7.2481567158739484e+00 - 28 -1.4631015201690607e+01 6.2801030048063575e+00 -9.8799556023515258e+00 - 29 1.0722676474855227e+01 1.2481600078747476e+01 2.6278850741448676e+00 + 1 -2.0299545735132892e+01 2.6684807204226053e+02 3.2358468359237850e+02 + 2 1.5298613010577799e+02 1.2596515036763115e+02 -1.7961295708782035e+02 + 3 -1.3353752998744326e+02 -3.7923796991710333e+02 -1.4292028045209116e+02 + 4 -7.8374742335759366e+00 2.1276610876297597e+00 -5.5845047399918775e+00 + 5 -2.5014507165598512e+00 -4.0250273077928105e+00 1.2103486006755219e+01 + 6 -8.0709614974024726e+02 9.2196952917801661e+02 1.0273844835710092e+03 + 7 6.2368964790102126e+01 -3.1505972760991460e+02 -1.5609074758304780e+03 + 8 1.2853739032019485e+02 -9.7465044500250556e+01 3.7497119240743029e+02 + 9 7.6715909814250395e+01 8.2459997325499288e+01 3.3929722449258207e+02 + 10 5.2123917690492942e+02 -5.9914969452129674e+02 -1.8122078898785443e+02 + 11 -2.3573941156945706e+00 -5.8616368783617920e+00 -9.6049336125719105e+00 + 12 1.7502383808896312e+01 1.0630235744520755e+01 -8.0588289450962680e+00 + 13 8.0529802801748964e+00 -3.1754616291151323e+00 -1.4606677296755816e-01 + 14 -3.3416363973176253e+00 6.6497430894639287e-01 -8.6345016037082427e+00 + 15 -2.2253805990966902e-01 8.5025662406844038e+00 3.0369660480415672e+00 + 16 4.3476506269170443e+02 -3.1171159958023998e+02 -1.1135242200065077e+03 + 17 -4.2495337371832613e+02 2.9654505216420324e+02 1.1298239214745126e+03 + 18 -1.2304275579819248e-02 -2.5351950229154721e-02 2.2962838569349546e-02 + 19 2.9523284665120854e-04 -2.5507040924857842e-04 1.7263527188201720e-03 + 20 -9.6972071754998339e-04 -9.9365617456234753e-04 3.5770286471788313e-04 + 21 -5.7779283683910396e+00 -6.6373783567402054e+00 1.8717023177597437e+01 + 22 -9.0188479017520962e+00 -2.2015411814231656e+00 -1.4100630927846634e+01 + 23 1.4794749299535622e+01 8.8415202426425061e+00 -4.6144921197234865e+00 + 24 3.4171983592341331e+00 -1.7549081284618467e+01 9.5729670271818517e+00 + 25 -1.2674530181010821e+01 2.0106979870159911e+00 -1.0661184439552951e+01 + 26 9.2499114441813344e+00 1.5533293107821931e+01 1.0752648395769842e+00 + 27 3.9098603108147572e+00 -1.8759688298395208e+01 7.2506773670471274e+00 + 28 -1.4631015477945336e+01 6.2801033491768763e+00 -9.8799560206646078e+00 + 29 1.0722675266961424e+01 1.2481598596015642e+01 2.6278846486097209e+00 ... diff --git a/unittest/force-styles/tests/mol-pair-hybrid_multiple.yaml b/unittest/force-styles/tests/mol-pair-hybrid_multiple.yaml index 658f3a2e1a..59a5098238 100644 --- a/unittest/force-styles/tests/mol-pair-hybrid_multiple.yaml +++ b/unittest/force-styles/tests/mol-pair-hybrid_multiple.yaml @@ -1,6 +1,6 @@ --- lammps_version: 8 Apr 2021 -date_generated: Mon Apr 19 01:10:13 2021 +date_generated: Mon Apr 19 08:49:08 2021 epsilon: 5e-14 skip_tests: gpu prerequisites: ! | @@ -17,83 +17,83 @@ pair_coeff: ! | 1 4 lj/cut 1 0.0173205 2.8 8 1 5 lj/cut 1 0.0173205 2.8 8 2 2 lj/cut 1 0.005 1 8 - 2 3 lj/cut 1 0.01 2.1 8 + 2 3 none 2 4 lj/cut 2 0.005 0.5 8 2 5 lj/cut 2 0.00866025 2.05 8 3 3 lj/cut 2 0.02 3.2 8 3 4 lj/cut 2 0.0173205 3.15 8 3 5 lj/cut 2 0.0173205 3.15 8 - 4 4 lj/cut 2 0.015 3.1 8 + 4 4 none 4 5 lj/cut 2 0.015 3.1 8 5 5 lj/cut 2 0.015 3.1 8 extract: ! "" natoms: 29 -init_vdwl: 749.2370315373572 +init_vdwl: 695.3923515458562 init_coul: 0 init_stress: ! |2- - 2.1793853434038251e+03 2.1988955172192786e+03 4.6653977523326275e+03 -7.5956547636050641e+02 2.4751536734034119e+01 6.6652028436400667e+02 + 2.0701694962880379e+03 2.1161697936676396e+03 4.2064778387649758e+03 -8.5392301766114281e+02 5.8381311611070338e+01 6.7526909503583579e+02 init_forces: ! |2 - 1 -2.3333390280895383e+01 2.6994567613322732e+02 3.3272827850356794e+02 - 2 1.5828554630414868e+02 1.3025008843535846e+02 -1.8629682358935690e+02 + 1 1.3470193899351008e+02 3.9971667505559770e+02 1.4653534158640173e+02 + 2 -2.5920146506056333e-04 -3.7955921659898438e-03 1.6073626919112927e-04 3 -1.3528903738169089e+02 -3.8704313358320059e+02 -1.4568978437133126e+02 - 4 -7.8711096705893420e+00 2.1350518625373542e+00 -5.5954532185548151e+00 - 5 -2.5176757268228527e+00 -4.0521510681020221e+00 1.2152704057877008e+01 + 4 -7.8050743980642938e+00 2.1869547823331810e+00 -5.5398195700937443e+00 + 5 -2.3463115265684147e+00 -3.6110080311379984e+00 1.1991043207479338e+01 6 -8.3190662465252262e+02 9.6394149462625705e+02 1.1509093566509250e+03 - 7 5.8203388932513640e+01 -3.3608997951626816e+02 -1.7179617996573054e+03 - 8 1.4451392284291583e+02 -1.0927475861089046e+02 3.9990593492420493e+02 - 9 7.9156945283097571e+01 8.5273009783986680e+01 3.5032175698445252e+02 + 7 5.8196056725569250e+01 -3.3609532232737348e+02 -1.7179637678770343e+03 + 8 2.2371752997318714e+02 -2.4044581303870338e+01 7.5018536133648945e+02 + 9 -1.9409760262620549e-03 7.2485476558358224e-03 5.8859368216628563e-03 10 5.3118875219105416e+02 -6.1040990859419469e+02 -1.8355872642619312e+02 - 11 -2.3530157267965532e+00 -5.9077640073819744e+00 -9.6590723955414326e+00 + 11 -2.3694888595131456e+00 -5.8683646131501845e+00 -9.6273569602169200e+00 12 1.7527155146800411e+01 1.0633119523437488e+01 -7.9254398064483143e+00 - 13 8.0986409579532861e+00 -3.2098088264781510e+00 -1.4896399843793828e-01 - 14 -3.3852721292265100e+00 6.8636181241903504e-01 -8.7507190862499726e+00 - 15 -2.0454999188605286e-01 8.4846165523049883e+00 3.0131615419406708e+00 + 13 8.1017386753150031e+00 -3.2103099553624541e+00 -1.4999876338278073e-01 + 14 -3.3827233651141047e+00 6.8626763970182614e-01 -8.7541119515926020e+00 + 15 -2.2835033173800551e-01 8.4695347876005833e+00 3.0205948609978988e+00 16 4.6326310311812085e+02 -3.3087715736498177e+02 -1.1893024561782547e+03 - 17 -4.5334300923766710e+02 3.1554283255882558e+02 1.2058417793481196e+03 - 18 -1.8862623280672657e-02 -3.3402010907951640e-02 3.1000479299095243e-02 - 19 3.1843079640570080e-04 -2.3918627818763423e-04 1.7427252638513441e-03 - 20 -9.9760831209706009e-04 -1.0209184826753088e-03 3.6910972636601454e-04 + 17 -4.5334049545249684e+02 3.1553975228548006e+02 1.2058468481979494e+03 + 18 -1.4044201506550015e-02 -2.4978926457057571e-02 2.7899849198216014e-02 + 19 5.7908066872909211e-04 2.3580122518177659e-05 9.4432839946607169e-04 + 20 -7.9929144000317922e-04 -8.5923998915859100e-04 9.3688470857894682e-05 21 -7.1566125273265527e+01 -8.1615678329920812e+01 2.2589561408339878e+02 - 22 -1.0808835729977487e+02 -2.6193787235943859e+01 -1.6957904943161384e+02 - 23 1.7964455474779510e+02 1.0782097695276961e+02 -5.6305786479140700e+01 + 22 -1.0808832728447032e+02 -2.6193822094038484e+01 -1.6957908491609356e+02 + 23 1.7964458878508086e+02 1.0782095393625858e+02 -5.6305810335528790e+01 24 3.6591406576585001e+01 -2.1181587621785556e+02 1.1218301872572404e+02 - 25 -1.4851489147738829e+02 2.3907118122949107e+01 -1.2485634873166315e+02 - 26 1.1191129453598201e+02 1.8789774664223359e+02 1.2650137204319886e+01 + 25 -1.4851247198601720e+02 2.3908563011127814e+01 -1.2485206982576771e+02 + 26 1.1191155617819715e+02 1.8789792679177191e+02 1.2650470167620387e+01 27 5.1810388677546058e+01 -2.2705458321213791e+02 9.0849111082069683e+01 - 28 -1.8041307121444072e+02 7.7534042932772934e+01 -1.2206956760706599e+02 - 29 1.2861057254925004e+02 1.4952711274394565e+02 3.1216025556267869e+01 -run_vdwl: 719.4432816774656 + 28 -1.8041314710135907e+02 7.7533961534478649e+01 -1.2206952271304674e+02 + 29 1.2861042716162333e+02 1.4952690328401346e+02 3.1216205256769118e+01 +run_vdwl: 666.4782147617275 run_coul: 0 run_stress: ! |2- - 2.1330153957371017e+03 2.1547728168285512e+03 4.3976497417710170e+03 -7.3873328448298525e+02 4.1743821105367225e+01 6.2788012209191243e+02 + 2.0230459789503245e+03 2.0702509496053467e+03 3.9518738620330496e+03 -8.2693736200387241e+02 7.2394119974104541e+01 6.3708810010786885e+02 run_forces: ! |2 - 1 -2.0299419751359796e+01 2.6686193378822901e+02 3.2358785870694004e+02 - 2 1.5298617928491248e+02 1.2596516341409225e+02 -1.7961292655338647e+02 - 3 -1.3353630652439793e+02 -3.7923748696131213e+02 -1.4291839793625775e+02 - 4 -7.8374717836161771e+00 2.1276610789823414e+00 -5.5845014473820624e+00 - 5 -2.5014258630866699e+00 -4.0250131424704385e+00 1.2103512372025625e+01 - 6 -8.0681462887292412e+02 9.2165637136761688e+02 1.0270795806932804e+03 - 7 5.5780279349903594e+01 -3.1117530951561696e+02 -1.5746991292869038e+03 - 8 1.3452983055534955e+02 -1.0064659350255846e+02 3.8851791558207583e+02 - 9 7.6746213883426122e+01 8.2501469877402286e+01 3.3944351200617950e+02 - 10 5.2128033527695618e+02 -5.9920098848285909e+02 -1.8126029815043356e+02 - 11 -2.3573118090915246e+00 -5.8616944550888350e+00 -9.6049808811326240e+00 - 12 1.7503975847822890e+01 1.0626930310560827e+01 -8.0603160272054950e+00 - 13 8.0530313322973104e+00 -3.1756495170399104e+00 -1.4618315664740525e-01 - 14 -3.3416065168069760e+00 6.6492606336082127e-01 -8.6345131440469647e+00 - 15 -2.2253843262374870e-01 8.5025661635348619e+00 3.0369735873081569e+00 - 16 4.3476311264989528e+02 -3.1171086735551455e+02 -1.1135217194927461e+03 - 17 -4.2469846140777202e+02 2.9615411776780638e+02 1.1302573488400678e+03 - 18 -1.8849981672825901e-02 -3.3371636477421286e-02 3.0986293443778724e-02 - 19 3.0940277774413972e-04 -2.4634536455373055e-04 1.7433360008861018e-03 - 20 -9.8648131277150768e-04 -1.0112587134526944e-03 3.6932948773965422e-04 - 21 -7.0490745283106705e+01 -7.9749153581142281e+01 2.2171003384646417e+02 - 22 -1.0638717908920059e+02 -2.5949502163177943e+01 -1.6645589526812256e+02 - 23 1.7686797710735050e+02 1.0571018898885526e+02 -5.5243337084099444e+01 - 24 3.8206017656281247e+01 -2.1022820141992992e+02 1.1260711266189016e+02 - 25 -1.4918881473530885e+02 2.3762151395876515e+01 -1.2549188139143089e+02 - 26 1.1097059498808326e+02 1.8645503634228552e+02 1.2861559677865269e+01 - 27 5.0800844984832011e+01 -2.2296588090685447e+02 8.8607367716323097e+01 - 28 -1.7694190504288861e+02 7.6029945485181912e+01 -1.1950518150242056e+02 - 29 1.2614894925528131e+02 1.4694250820033537e+02 3.0893386672863009e+01 + 1 1.3222884765649096e+02 3.9147464530754542e+02 1.4358022294156322e+02 + 2 -3.0864727869908275e-04 -3.8828117503160744e-03 1.7172318042670622e-04 + 3 -1.3332620470087795e+02 -3.7836092101534376e+02 -1.4242041283928734e+02 + 4 -7.7728646036501301e+00 2.1785693730418103e+00 -5.5299592481691731e+00 + 5 -2.3308414297947593e+00 -3.5861079994724223e+00 1.1943272718268586e+01 + 6 -8.0362787449170855e+02 9.1873908852320062e+02 1.0286784127827473e+03 + 7 5.5811219820327509e+01 -3.1120381969697877e+02 -1.5746114945931058e+03 + 8 2.0944769168608951e+02 -1.6467844308363212e+01 7.2633940157846291e+02 + 9 -1.8576332682468917e-03 7.0788521064532543e-03 5.6952330037911550e-03 + 10 5.1993646731938259e+02 -5.9797705136296099e+02 -1.8137145374090557e+02 + 11 -2.3735947029864999e+00 -5.8227345663909000e+00 -9.5735721932593005e+00 + 12 1.7496750082385656e+01 1.0626428651973894e+01 -8.0588816332352362e+00 + 13 8.0561193459222018e+00 -3.1761461937053199e+00 -1.4721657561379659e-01 + 14 -3.3390327331317540e+00 6.6483212295920502e-01 -8.6379436016166640e+00 + 15 -2.4691219203353357e-01 8.4871512091352503e+00 3.0445957174405320e+00 + 16 4.3476322109548175e+02 -3.1171106479661643e+02 -1.1135217352066604e+03 + 17 -4.2469483753690730e+02 2.9614920041309318e+02 1.1302640053436066e+03 + 18 -1.4041685725000265e-02 -2.4956350669900162e-02 2.7904010910612693e-02 + 19 5.7049372682756931e-04 1.6554736417528457e-05 9.4341990684141492e-04 + 20 -7.8849148841722897e-04 -8.4994368910122327e-04 9.4566031895818034e-05 + 21 -7.0490744649332854e+01 -7.9749153638697052e+01 2.2171003329264727e+02 + 22 -1.0638714881331208e+02 -2.5949537046722948e+01 -1.6645593048575904e+02 + 23 1.7686801069212282e+02 1.0571016567965997e+02 -5.5243360803916154e+01 + 24 3.8206094080913594e+01 -2.1022820935692107e+02 1.1260716750436217e+02 + 25 -1.4918646093941553e+02 2.3763610305920544e+01 -1.2548765023777884e+02 + 26 1.1097085296101896e+02 1.8645520999549970e+02 1.2861892631557549e+01 + 27 5.0800842221321886e+01 -2.2296588391583720e+02 8.8607366497542188e+01 + 28 -1.7694198089845398e+02 7.6029863930484495e+01 -1.1950513646089449e+02 + 29 1.2614880669418112e+02 1.4694230208476219e+02 3.0893567658970003e+01 ... diff --git a/unittest/force-styles/tests/mol-pair-python_hybrid.yaml b/unittest/force-styles/tests/mol-pair-python_hybrid.yaml index 663e3efa2d..5383ee113f 100644 --- a/unittest/force-styles/tests/mol-pair-python_hybrid.yaml +++ b/unittest/force-styles/tests/mol-pair-python_hybrid.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 10 Feb 2021 -date_generated: Fri Feb 26 23:08:56 2021 +lammps_version: 8 Apr 2021 +date_generated: Mon Apr 19 08:49:08 2021 epsilon: 5e-14 prerequisites: ! | atom full @@ -15,8 +15,8 @@ pair_coeff: ! | * * python py_pot.LJCutFourMol 1 2 3 4 5 extract: ! "" natoms: 29 -init_vdwl: 769.435514792906 -init_coul: -127.494586297384 +init_vdwl: 769.4355147929056 +init_coul: -127.49458629738443 init_stress: ! |2- 2.2678521911648518e+03 2.2247029630324569e+03 4.6668446509523028e+03 -7.1863043563709800e+02 6.6980305204573611e+01 6.6425623166019000e+02 init_forces: ! |2 @@ -49,8 +49,8 @@ init_forces: ! |2 27 5.8858131514524516e+01 -2.5934658519982310e+02 1.0378659589349859e+02 28 -2.1004851662389484e+02 8.7061736878465183e+01 -1.4131944246679177e+02 29 1.5193395589309270e+02 1.7194075642255194e+02 3.8106025733269696e+01 -run_vdwl: 738.975921529802 -run_coul: -127.388878149465 +run_vdwl: 738.9759215298017 +run_coul: -127.38887814946516 run_stress: ! |2- 2.2173727908784563e+03 2.1780484935540412e+03 4.3978310588967724e+03 -6.9936430337437957e+02 8.2321786589523725e+01 6.2596079360064653e+02 run_forces: ! |2 From cf62dbf96aeabd0be34ccd979d295921de7aa28a Mon Sep 17 00:00:00 2001 From: Agilio Padua Date: Mon, 19 Apr 2021 18:23:33 +0200 Subject: [PATCH 0567/1217] In manual pages point to examples --- doc/src/Howto_drude2.rst | 2 ++ doc/src/compute_fep.rst | 2 ++ doc/src/compute_temp_drude.rst | 2 ++ doc/src/fix_adapt_fep.rst | 3 +++ doc/src/fix_drude.rst | 2 ++ doc/src/fix_drude_transform.rst | 2 ++ doc/src/fix_langevin_drude.rst | 2 ++ doc/src/fix_tgnh_drude.rst | 2 ++ doc/src/pair_coul_tt.rst | 1 + doc/src/pair_fep_soft.rst | 2 ++ doc/src/pair_thole.rst | 2 ++ 11 files changed, 22 insertions(+) diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index d95f5c02aa..24c21f27b1 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -9,6 +9,8 @@ USER-DRUDE package activated. Then, the data file and input scripts have to be modified to include the Drude dipoles and how to handle them. +Example input scripts available: examples/USER/drude + ---------- **Overview of Drude induced dipoles** diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index 279148a55d..ef908acfc0 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -48,6 +48,8 @@ Examples compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes compute 1 all fep 300 atom charge 2 v_delta +Example input scripts available: examples/USER/fep + Description """"""""""" diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst index 418f2e1e5d..7e0f5f6555 100644 --- a/doc/src/compute_temp_drude.rst +++ b/doc/src/compute_temp_drude.rst @@ -20,6 +20,8 @@ Examples compute TDRUDE all temp/drude +Example input scripts available: examples/USER/drude + Description """"""""""" diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index b45ac80429..81a34ab75e 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -56,6 +56,9 @@ Examples fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes fix 1 all adapt/fep 10 atom diameter 1 v_size + +Example input scripts available: examples/USER/fep + Description """"""""""" diff --git a/doc/src/fix_drude.rst b/doc/src/fix_drude.rst index 385a847749..a879f1594b 100644 --- a/doc/src/fix_drude.rst +++ b/doc/src/fix_drude.rst @@ -22,6 +22,8 @@ Examples fix 1 all drude 1 1 0 1 0 2 2 2 fix 1 all drude C C N C N D D D +Example input scripts available: examples/USER/drude + Description """"""""""" diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index 792b041576..28d57306ea 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -25,6 +25,8 @@ Examples fix 3 all drude/transform/direct fix 1 all drude/transform/inverse +Example input scripts available: examples/USER/drude + Description """"""""""" diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst index ad5a876712..c075a56549 100644 --- a/doc/src/fix_langevin_drude.rst +++ b/doc/src/fix_langevin_drude.rst @@ -35,6 +35,8 @@ Examples fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451 fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes +Example input scripts available: examples/USER/drude + Description """"""""""" diff --git a/doc/src/fix_tgnh_drude.rst b/doc/src/fix_tgnh_drude.rst index 1854655a82..a6e9832833 100644 --- a/doc/src/fix_tgnh_drude.rst +++ b/doc/src/fix_tgnh_drude.rst @@ -62,6 +62,8 @@ Examples fix 2 jello tgnpt/drude temp 300.0 300.0 100.0 1.0 20.0 tri 5.0 5.0 1000.0 fix 2 ice tgnpt/drude temp 250.0 250.0 100.0 1.0 20.0 x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 +Example input scripts available: examples/USER/drude + Description """"""""""" diff --git a/doc/src/pair_coul_tt.rst b/doc/src/pair_coul_tt.rst index 11b4e72a60..b01d46d7ae 100644 --- a/doc/src/pair_coul_tt.rst +++ b/doc/src/pair_coul_tt.rst @@ -29,6 +29,7 @@ Examples pair_coeff 1 2 coul/tt 4.0 1.0 4 12.0 pair_coeff 1 3* coul/tt 4.5 1.0 4 +Example input scripts available: examples/USER/drude Description """"""""""" diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index 109ddfdf21..f3000a47a1 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -182,6 +182,8 @@ Examples pair_coeff * * 100.0 2.0 1.5 1.0 pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 +Example input scripts available: examples/USER/fep + Description """"""""""" diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst index a8cf8ee044..183bab48c9 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -42,6 +42,8 @@ Examples pair_style lj/cut/thole/long 2.6 12.0 +Example input scripts available: examples/USER/drude + Description """"""""""" From 92abca3910137e02845d563185edece6661d9cd1 Mon Sep 17 00:00:00 2001 From: kipbarrett Date: Mon, 19 Apr 2021 13:40:19 -0500 Subject: [PATCH 0568/1217] bug fixes --- src/USER-RANN/pair_rann.cpp | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/src/USER-RANN/pair_rann.cpp b/src/USER-RANN/pair_rann.cpp index 6a100db244..d2b9535b56 100644 --- a/src/USER-RANN/pair_rann.cpp +++ b/src/USER-RANN/pair_rann.cpp @@ -164,12 +164,12 @@ PairRANN::~PairRANN() memory->destroy(sx); memory->destroy(sy); memory->destroy(sz); - memory->destroy(dlayerx); - memory->destroy(dlayery); - memory->destroy(dlayerz); - memory->destroy(dlayersumx); - memory->destroy(dlayersumy); - memory->destroy(dlayersumz); + memory->destroy(dsx); + memory->destroy(dsy); + memory->destroy(dsz); + memory->destroy(dssumx); + memory->destroy(dssumy); + memory->destroy(dssumz); } } @@ -538,7 +538,7 @@ void PairRANN::read_weight(std::vector line,std::vectorone(filename,*linenum,"unexpected end of potential file!"); @@ -569,7 +569,7 @@ void PairRANN::read_bias(std::vector line,std::vector net[l].Biases[i][0] = utils::numeric(filename,*linenum,line1[0].c_str(),1,lmp); for (j=1;jcreate(sx,fmax*nmax2,"pair:sx"); memory->create(sy,fmax*nmax2,"pair:sy"); memory->create(sz,fmax*nmax2,"pair:sz"); - memory->create(dlayerx,nmax2,fnmax,"pair:dsx"); - memory->create(dlayery,nmax2,fnmax,"pair:dsy"); - memory->create(dlayerz,nmax2,fnmax,"pair:dsz"); - memory->create(dlayersumx,nmax2,fnmax,"pair:dssumx"); - memory->create(dlayersumy,nmax2,fnmax,"pair:dssumy"); - memory->create(dlayersumz,nmax2,fnmax,"pair:dssumz"); + memory->create(dsx,nmax2,fnmax,"pair:dsx"); + memory->create(dsy,nmax2,fnmax,"pair:dsy"); + memory->create(dsz,nmax2,fnmax,"pair:dsz"); + memory->create(dssumx,nmax2,fnmax,"pair:dssumx"); + memory->create(dssumy,nmax2,fnmax,"pair:dssumy"); + memory->create(dssumz,nmax2,fnmax,"pair:dssumz"); } return false;//everything looks good } From bc4b4147efc391f82bf5de616815fd398fcde6ed Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 19 Apr 2021 14:57:41 -0400 Subject: [PATCH 0569/1217] Avoid filename collisions with AtomStyles test --- unittest/formats/test_molecule_file.cpp | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/unittest/formats/test_molecule_file.cpp b/unittest/formats/test_molecule_file.cpp index 9928ec4b7c..4e3e374889 100644 --- a/unittest/formats/test_molecule_file.cpp +++ b/unittest/formats/test_molecule_file.cpp @@ -60,18 +60,18 @@ static void create_molecule_files() "Special Bond Counts\n\n1 2 0 0\n2 1 1 0\n3 1 1 0\n\n" "Special Bonds\n\n1 2 3\n2 1 3\n3 1 2\n\n"; - FILE *fp = fopen("tmp.h2o.mol", "w"); + FILE *fp = fopen("tmp.moltest.h2o.mol", "w"); if (fp) { fputs(h2o_file, fp); fclose(fp); } - rename("tmp.h2o.mol", "h2o.mol"); - fp = fopen("tmp.co2.mol", "w"); + rename("tmp.moltest.h2o.mol", "moltest.h2o.mol"); + fp = fopen("tmp.moltest.co2.mol", "w"); if (fp) { fputs(co2_file, fp); fclose(fp); } - rename("tmp.co2.mol", "co2.mol"); + rename("tmp.moltest.co2.mol", "moltest.co2.mol"); } // whether to print verbose output (i.e. not capturing LAMMPS screen output). @@ -92,13 +92,13 @@ protected: void TearDown() override { LAMMPSTest::TearDown(); - remove("h2o.mol"); - remove("co2.mol"); + remove("moltest.h2o.mol"); + remove("moltest.co2.mol"); } void run_mol_cmd(const std::string &name, const std::string &args, const std::string &content) { - std::string file = name + ".mol"; + std::string file = fmt::format("moltest_{}.mol", name); FILE *fp = fopen(file.c_str(), "w"); fputs(content.c_str(), fp); fclose(fp); @@ -195,7 +195,7 @@ TEST_F(MoleculeFileTest, twomols) TEST_F(MoleculeFileTest, twofiles) { BEGIN_CAPTURE_OUTPUT(); - command("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); + command("molecule twomols moltest.h2o.mol moltest.co2.mol offset 2 1 1 0 0"); auto output = END_CAPTURE_OUTPUT(); ASSERT_THAT(output, MatchesRegex(".*Read molecule template twomols:.*1 molecules.*3 atoms " "with max type 2.*2 bonds with max type 1.*" From a6efdf9b9f90baa421babeb7c22aca59b913ddec Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 19 Apr 2021 15:14:01 -0400 Subject: [PATCH 0570/1217] Clean up molecule files creation --- unittest/formats/test_atom_styles.cpp | 19 ++++++++++++------- unittest/formats/test_molecule_file.cpp | 22 ++++++++++++---------- 2 files changed, 24 insertions(+), 17 deletions(-) diff --git a/unittest/formats/test_atom_styles.cpp b/unittest/formats/test_atom_styles.cpp index 8a031fe308..980afc3182 100644 --- a/unittest/formats/test_atom_styles.cpp +++ b/unittest/formats/test_atom_styles.cpp @@ -48,7 +48,7 @@ using LAMMPS_NS::utils::split_words; -static void create_molecule_files() +static void create_molecule_files(const std::string & h2o_filename, const std::string & co2_filename) { // create molecule files const char h2o_file[] = "# Water molecule. SPC/E model.\n\n3 atoms\n2 bonds\n1 angles\n\n" @@ -73,18 +73,16 @@ static void create_molecule_files() "Special Bond Counts\n\n1 2 0 0\n2 1 1 0\n3 1 1 0\n\n" "Special Bonds\n\n1 2 3\n2 1 3\n3 1 2\n\n"; - FILE *fp = fopen("tmp.h2o.mol", "w"); + FILE *fp = fopen(h2o_filename.c_str(), "w"); if (fp) { fputs(h2o_file, fp); fclose(fp); } - rename("tmp.h2o.mol", "h2o.mol"); - fp = fopen("tmp.co2.mol", "w"); + fp = fopen(co2_filename.c_str(), "w"); if (fp) { fputs(co2_file, fp); fclose(fp); } - rename("tmp.co2.mol", "co2.mol"); } // whether to print verbose output (i.e. not capturing LAMMPS screen output). @@ -97,6 +95,15 @@ using ::testing::Eq; class AtomStyleTest : public LAMMPSTest { protected: + static void SetUpTestSuite() { + create_molecule_files("h2o.mol", "co2.mol"); + } + + static void TearDownTestSuite() { + remove("h2o.mol"); + remove("co2.mol"); + } + void SetUp() override { testbinary = "AtomStyleTest"; @@ -2618,7 +2625,6 @@ TEST_F(AtomStyleTest, body_nparticle) TEST_F(AtomStyleTest, template) { if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); - create_molecule_files(); BEGIN_HIDE_OUTPUT(); command("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); command("atom_style template twomols"); @@ -3014,7 +3020,6 @@ TEST_F(AtomStyleTest, template) TEST_F(AtomStyleTest, template_charge) { if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); - create_molecule_files(); BEGIN_HIDE_OUTPUT(); command("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); command("atom_style hybrid template twomols charge"); diff --git a/unittest/formats/test_molecule_file.cpp b/unittest/formats/test_molecule_file.cpp index 4e3e374889..5712e31a30 100644 --- a/unittest/formats/test_molecule_file.cpp +++ b/unittest/formats/test_molecule_file.cpp @@ -35,7 +35,7 @@ using utils::split_words; #define test_name test_info_->name() -static void create_molecule_files() +static void create_molecule_files(const std::string & h2o_filename, const std::string & co2_filename) { // create molecule files const char h2o_file[] = "# Water molecule. SPC/E model.\n\n3 atoms\n2 bonds\n1 angles\n\n" @@ -60,18 +60,16 @@ static void create_molecule_files() "Special Bond Counts\n\n1 2 0 0\n2 1 1 0\n3 1 1 0\n\n" "Special Bonds\n\n1 2 3\n2 1 3\n3 1 2\n\n"; - FILE *fp = fopen("tmp.moltest.h2o.mol", "w"); + FILE *fp = fopen(h2o_filename.c_str(), "w"); if (fp) { fputs(h2o_file, fp); fclose(fp); } - rename("tmp.moltest.h2o.mol", "moltest.h2o.mol"); - fp = fopen("tmp.moltest.co2.mol", "w"); + fp = fopen(co2_filename.c_str(), "w"); if (fp) { fputs(co2_file, fp); fclose(fp); } - rename("tmp.moltest.co2.mol", "moltest.co2.mol"); } // whether to print verbose output (i.e. not capturing LAMMPS screen output). @@ -79,21 +77,25 @@ bool verbose = false; class MoleculeFileTest : public LAMMPSTest { protected: + static void SetUpTestSuite() { + create_molecule_files("moltest.h2o.mol", "moltest.co2.mol"); + } + + static void TearDownTestSuite() { + remove("moltest.h2o.mol"); + remove("moltest.co2.mol"); + } + void SetUp() override { testbinary = "MoleculeFileTest"; LAMMPSTest::SetUp(); ASSERT_NE(lmp, nullptr); - BEGIN_HIDE_OUTPUT(); - create_molecule_files(); - END_HIDE_OUTPUT(); } void TearDown() override { LAMMPSTest::TearDown(); - remove("moltest.h2o.mol"); - remove("moltest.co2.mol"); } void run_mol_cmd(const std::string &name, const std::string &args, const std::string &content) From f2096ded96f5321f942ea86a2770f9178056e255 Mon Sep 17 00:00:00 2001 From: julient31 Date: Mon, 19 Apr 2021 17:09:53 -0600 Subject: [PATCH 0571/1217] - improved design of test_problem - cleaned up langevin/spin - started doc for stt and hexaniso --- doc/src/fix_precession_spin.rst | 11 +++++++---- examples/SPIN/test_problems/README | 11 +++++++++++ examples/SPIN/test_problems/run_all.sh | 25 +++++++++++++++++++++++++ src/SPIN/fix_langevin_spin.cpp | 26 +------------------------- src/SPIN/fix_langevin_spin.h | 6 ------ 5 files changed, 44 insertions(+), 35 deletions(-) create mode 100755 examples/SPIN/test_problems/run_all.sh diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst index 5e818374a0..033c244131 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -12,7 +12,7 @@ Syntax * ID, group are documented in :doc:`fix ` command * precession/spin = style name of this fix command -* style = *zeeman* or *anisotropy* or *cubic* +* style = *zeeman* or *anisotropy* or *cubic* or *stt* or *hexaniso* .. parsed-literal:: @@ -22,12 +22,15 @@ Syntax *anisotropy* args = K x y z K = intensity of the magnetic anisotropy (in eV) x y z = vector direction of the anisotropy - - .. parsed-literal:: - *cubic* args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z K1 and K2c = intensity of the magnetic anisotropy (in eV) n1x to n3z = three direction vectors of the cubic anisotropy + *stt* args = J x y z + H = intensity of the spin-transfer torque field (in Tesla) + x y z = vector direction of the field + *hexaniso* args = K6 x y z + H = intensity of the spin-transfer torque field (in Tesla) + x y z = vector direction of the field Examples """""""" diff --git a/examples/SPIN/test_problems/README b/examples/SPIN/test_problems/README index 0a1362ec9c..17e0935a35 100644 --- a/examples/SPIN/test_problems/README +++ b/examples/SPIN/test_problems/README @@ -45,3 +45,14 @@ directory. results (computed by the python script). Note: This example is a reworked version of a test problem provided by Martin Kroger (ETHZ). + +- validation_nve: + simulates a small assembly of magnetic atoms (54). The atoms are + coupled by an exchange interaction and a mechanical potential + (EAM here). + This example represents an NVE run: the total energy of the + system is preserved, whereas the spin and lattice energy + reservoirs are exchanging energy. + Run as: ./run-test-nve.sh + Output: res_lammps.dat contains the data. The results are displayed + by nve_spin_lattice.pdf. diff --git a/examples/SPIN/test_problems/run_all.sh b/examples/SPIN/test_problems/run_all.sh new file mode 100755 index 0000000000..fb682e3ef5 --- /dev/null +++ b/examples/SPIN/test_problems/run_all.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# test 1: damping and exchange +cd validation_damped_exchange/ +./run-test-exchange.sh +rm dump.data res_lammps.dat res_llg.dat +cd .. + +# test 2: damping and Zeeman +cd validation_damped_precession/ +./run-test-prec.sh +rm res_lammps.dat res_llg.dat +cd .. + +# test 3: langevin, damping and Zeeman +cd validation_langevin_precession/ +./run-test-prec.sh +rm average_spin test-prec-spin.in res_lammps.dat res_langevin.dat +cd .. + +# test 4: NVE run, test Etot preservation +cd validation_nve/ +./run-test-nve.sh +rm nve_spin_lattice.pdf res_lammps.dat +cd .. diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index b4de180406..0b566ce60b 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -45,7 +45,7 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ FixLangevinSpin::FixLangevinSpin(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), id_temp(nullptr), random(nullptr) + Fix(lmp, narg, arg), random(nullptr) { if (narg != 6) error->all(FLERR,"Illegal langevin/spin command"); @@ -53,14 +53,6 @@ FixLangevinSpin::FixLangevinSpin(LAMMPS *lmp, int narg, char **arg) : alpha_t = utils::numeric(FLERR,arg[4],false,lmp); seed = utils::inumeric(FLERR,arg[5],false,lmp); - dynamic_group_allow = 1; - scalar_flag = 1; - global_freq = 1; - extscalar = 1; - ecouple_flag = 1; - nevery = 1; - tallyflag = 1; - if (alpha_t < 0.0) { error->all(FLERR,"Illegal langevin/spin command"); } else if (alpha_t == 0.0) { @@ -117,10 +109,8 @@ void FixLangevinSpin::init() double hbar = force->hplanck/MY_2PI; // eV/(rad.THz) double kb = force->boltz; // eV/K - // D = (MY_2PI*alpha_t*gil_factor*kb*temp); D = (alpha_t*gil_factor*kb*temp); - // D = (12.0/MY_2PI)*(MY_2PI*alpha_t*gil_factor*kb*temp); D /= (hbar*dts); sigma = sqrt(2.0*D); } @@ -163,7 +153,6 @@ void FixLangevinSpin::add_temperature(int i, double spi[3], double fmi[3]) double rz = sigma*random->gaussian(); double hbar = force->hplanck/MY_2PI; - energyS += 0.25*hbar*(rx*spi[0]+ry*spi[1]+rz*spi[2])*update->dt; // adding the random field fmi[0] += rx; @@ -187,16 +176,3 @@ void FixLangevinSpin::compute_single_langevin(int i, double spi[3], double fmi[3 if (temp_flag) add_temperature(i,spi,fmi); } } - -/* ---------------------------------------------------------------------- */ - -double FixLangevinSpin::compute_scalar() -{ - if (!tallyflag) return 0.0; - - double energy_all; - MPI_Allreduce(&energyS,&energy_all,1,MPI_DOUBLE,MPI_SUM,world); - return -energy_all; -} - -/* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/fix_langevin_spin.h b/src/SPIN/fix_langevin_spin.h index 2a8a654597..090e5b666a 100644 --- a/src/SPIN/fix_langevin_spin.h +++ b/src/SPIN/fix_langevin_spin.h @@ -36,7 +36,6 @@ class FixLangevinSpin : public Fix { void add_tdamping(double *, double *); // add transverse damping void add_temperature(int, double *, double *); void compute_single_langevin(int, double *, double *); - virtual double compute_scalar(); protected: double alpha_t; // transverse mag. damping @@ -44,11 +43,6 @@ class FixLangevinSpin : public Fix { double temp; // spin bath temperature double D,sigma; // bath intensity var. double gil_factor; // gilbert's prefactor - double energyS; - int nlocal_max; - int tallyflag; - char *id_temp; - class Compute *temperature; int nlevels_respa; class RanMars *random; From 10ea64fb0c4f8e274cbe830a8cc4a05d7495bbf8 Mon Sep 17 00:00:00 2001 From: julient31 Date: Mon, 19 Apr 2021 17:25:14 -0600 Subject: [PATCH 0572/1217] Improving the doc for the STT term --- doc/src/fix_precession_spin.rst | 23 +++++++++++++---------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst index 033c244131..2d6d8e2f7b 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -12,7 +12,7 @@ Syntax * ID, group are documented in :doc:`fix ` command * precession/spin = style name of this fix command -* style = *zeeman* or *anisotropy* or *cubic* or *stt* or *hexaniso* +* style = *zeeman* or *anisotropy* or *cubic* or *stt* .. parsed-literal:: @@ -26,10 +26,7 @@ Syntax K1 and K2c = intensity of the magnetic anisotropy (in eV) n1x to n3z = three direction vectors of the cubic anisotropy *stt* args = J x y z - H = intensity of the spin-transfer torque field (in Tesla) - x y z = vector direction of the field - *hexaniso* args = K6 x y z - H = intensity of the spin-transfer torque field (in Tesla) + J = intensity of the spin-transfer torque field x y z = vector direction of the field Examples @@ -128,6 +125,11 @@ axis along the :math:`(1 1 1)`-type cube diagonals). :math:`K_2^c > diagonals. See chapter 2 of :ref:`(Skomski) ` for more details on cubic anisotropies. +Style *stt* is used to simulate the interaction between the spins and +a spin-transfer torque. +See equation(7) of :ref:`(Chirac) ` for more details about the +implemented spin-transfer torque term. + In all cases, the choice of :math:`(x y z)` only imposes the vector directions for the forces. Only the direction of the vector is important; its length is ignored (the entered vectors are @@ -165,11 +167,6 @@ is only enabled if LAMMPS was built with this package, and if the atom_style "spin" was declared. See the :doc:`Build package ` doc page for more info. -The *precession/spin* style can only be declared once. If more than -one precession type (for example combining an anisotropy and a Zeeman -interactions) has to be declared, they have to be chained in the same -command line (as shown in the examples above). - Related commands """""""""""""""" @@ -187,3 +184,9 @@ none **(Skomski)** Skomski, R. (2008). Simple models of magnetism. Oxford University Press. + +.. _Chirac1: + +**(Chirac)** Chirac, Théophile, et al. Ultrafast antiferromagnetic +switching in NiO induced by spin transfer torques. +Physical Review B 102.13 (2020): 134415. From a64378ba5b92cc5baf4676f66234ef1c86575fb5 Mon Sep 17 00:00:00 2001 From: julient31 Date: Mon, 19 Apr 2021 17:29:47 -0600 Subject: [PATCH 0573/1217] cleaning-up fix nve/spin and precession/spin --- src/SPIN/fix_nve_spin.cpp | 30 ------------------------------ src/SPIN/fix_precession_spin.cpp | 8 -------- 2 files changed, 38 deletions(-) diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 266f0bd690..7b96c88a6a 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -220,16 +220,6 @@ void FixNVESpin::init() } } - // // ptrs FixPrecessionSpin classes - - // int iforce; - // for (iforce = 0; iforce < modify->nfix; iforce++) { - // if (strstr(modify->fix[iforce]->style,"precession/spin")) { - // precession_spin_flag = 1; - // lockprecessionspin = (FixPrecessionSpin *) modify->fix[iforce]; - // } - // } - // set ptrs for fix precession/spin styles // loop 1: obtain # of fix precession/spin styles @@ -295,20 +285,6 @@ void FixNVESpin::init() if (count2 != nlangspin) error->all(FLERR,"Incorrect number of fix precession/spin"); - // // ptrs on the FixLangevinSpin class - - // for (iforce = 0; iforce < modify->nfix; iforce++) { - // if (strstr(modify->fix[iforce]->style,"langevin/spin")) { - // maglangevin_flag = 1; - // locklangevinspin = (FixLangevinSpin *) modify->fix[iforce]; - // } - // } - - // if (maglangevin_flag) { - // if (locklangevinspin->tdamp_flag == 1) tdamp_flag = 1; - // if (locklangevinspin->temp_flag == 1) temp_flag = 1; - // } - // ptrs FixSetForceSpin classes for (iforce = 0; iforce < modify->nfix; iforce++) { @@ -552,12 +528,6 @@ void FixNVESpin::ComputeInteractionsSpin(int i) for (int k = 0; k < nlangspin; k++) { locklangevinspin[k]->compute_single_langevin(i,spi,fmi); } - // if (tdamp_flag) { // transverse damping - // locklangevinspin->add_tdamping(spi,fmi); - // } - // if (temp_flag) { // spin temperature - // locklangevinspin->add_temperature(fmi); - // } } // update setforce of magnetic interactions diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index a6bb19907a..34d3fbe8a3 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -253,14 +253,6 @@ void FixPrecessionSpin::init() error->all(FLERR,"Illegal precession/spin command"); } - // check that fix precession/spin is only declared once - - // int iprec = 0; - // for (int iforce = 0; iforce < modify->nfix; iforce++) - // if (strstr(modify->fix[iforce]->style,"precession/spin")) iprec++; - // if (iprec > 1) - // error->all(FLERR,"precession/spin command can only be declared once"); - varflag = CONSTANT; if (magfieldstyle != CONSTANT) varflag = EQUAL; From 33556e3745d53f6f6acc08ef545c56749ed296db Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 20 Apr 2021 11:44:39 -0400 Subject: [PATCH 0574/1217] Remove unused defines --- src/force.cpp | 2 -- src/pair_coul_streitz.cpp | 1 - src/run.cpp | 2 -- 3 files changed, 5 deletions(-) diff --git a/src/force.cpp b/src/force.cpp index e56e250ffc..80f5ef22a7 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -36,8 +36,6 @@ using namespace LAMMPS_NS; -#define MAXLINE 1024 - /* ---------------------------------------------------------------------- */ Force::Force(LAMMPS *lmp) : Pointers(lmp) diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index 55529f9eae..87bcd45736 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -36,7 +36,6 @@ using namespace LAMMPS_NS; using namespace MathConst; -#define MAXLINE 1024 #define DELTA 4 #define PGDELTA 1 #define MAXNEIGH 24 diff --git a/src/run.cpp b/src/run.cpp index 379cf8015a..1534d506d6 100644 --- a/src/run.cpp +++ b/src/run.cpp @@ -27,8 +27,6 @@ using namespace LAMMPS_NS; -#define MAXLINE 2048 - /* ---------------------------------------------------------------------- */ Run::Run(LAMMPS *lmp) : Command(lmp) {} From 8826e962def3fc1240aa58b26e1e8ce78e63ab85 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 20 Apr 2021 14:06:08 -0400 Subject: [PATCH 0575/1217] Add info message when death test is skipped --- unittest/testing/core.h | 3 +++ 1 file changed, 3 insertions(+) diff --git a/unittest/testing/core.h b/unittest/testing/core.h index 75b0564d02..843d135645 100644 --- a/unittest/testing/core.h +++ b/unittest/testing/core.h @@ -42,6 +42,9 @@ using ::testing::MatchesRegex; auto mesg = ::testing::internal::GetCapturedStdout(); \ ASSERT_THAT(mesg, MatchesRegex(errmsg)); \ } \ + else { \ + std::cerr << "[ ] [ INFO ] Skipping death test (no exception support) \n"; \ + } \ } // whether to print verbose output (i.e. not capturing LAMMPS screen output). From aba4dfc42e8154dc09049ec3c61180b3e4d48b81 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 20 Apr 2021 14:06:53 -0400 Subject: [PATCH 0576/1217] Avoid leaking memory in error cases --- src/group.cpp | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/src/group.cpp b/src/group.cpp index 0143008a72..38ffa79a22 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -35,6 +35,7 @@ #include #include #include +#include using namespace LAMMPS_NS; @@ -380,7 +381,7 @@ void Group::assign(int narg, char **arg) if (narg < 4) error->all(FLERR,"Illegal group command"); int length = narg-2; - int *list = new int[length]; + std::vector list(length); int jgroup; for (int iarg = 2; iarg < narg; iarg++) { @@ -409,8 +410,6 @@ void Group::assign(int narg, char **arg) if (mask[i] & otherbit) mask[i] &= inverse; } - delete [] list; - // style = union } else if (strcmp(arg[1],"union") == 0) { @@ -418,7 +417,7 @@ void Group::assign(int narg, char **arg) if (narg < 3) error->all(FLERR,"Illegal group command"); int length = narg-2; - int *list = new int[length]; + std::vector list(length); int jgroup; for (int iarg = 2; iarg < narg; iarg++) { @@ -439,8 +438,6 @@ void Group::assign(int narg, char **arg) if (mask[i] & otherbit) mask[i] |= bit; } - delete [] list; - // style = intersect } else if (strcmp(arg[1],"intersect") == 0) { @@ -448,7 +445,7 @@ void Group::assign(int narg, char **arg) if (narg < 4) error->all(FLERR,"Illegal group command"); int length = narg-2; - int *list = new int[length]; + std::vector list(length); int jgroup; for (int iarg = 2; iarg < narg; iarg++) { @@ -472,8 +469,6 @@ void Group::assign(int narg, char **arg) if (ok) mask[i] |= bit; } - delete [] list; - // style = dynamic // create a new FixGroup to dynamically determine atoms in group @@ -539,13 +534,12 @@ void Group::assign(int narg, char **arg) void Group::assign(const std::string &groupcmd) { auto args = utils::split_words(groupcmd); - char **newarg = new char*[args.size()]; + std::vector newarg(args.size()); int i=0; for (const auto &arg : args) { newarg[i++] = (char *)arg.c_str(); } - assign(args.size(),newarg); - delete[] newarg; + assign(args.size(),newarg.data()); } /* ---------------------------------------------------------------------- From fcf17a709ef810ed38f6833f8ac6260b7778c4d9 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 20 Apr 2021 14:24:07 -0400 Subject: [PATCH 0577/1217] Don't store group if initial assignment failed --- src/group.cpp | 664 +++++++++++++++--------------- unittest/commands/test_groups.cpp | 2 +- 2 files changed, 340 insertions(+), 326 deletions(-) diff --git a/src/group.cpp b/src/group.cpp index 38ffa79a22..9e140779ef 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -30,6 +30,7 @@ #include "region.h" #include "tokenizer.h" #include "variable.h" +#include "exceptions.h" #include #include @@ -152,12 +153,14 @@ void Group::assign(int narg, char **arg) // add a new group if igroup = -1 int igroup = find(arg[0]); + bool created = false; if (igroup == -1) { if (ngroup == MAX_GROUP) error->all(FLERR,"Too many groups"); igroup = find_unused(); names[igroup] = utils::strdup(arg[0]); ngroup++; + created = true; } double **x = atom->x; @@ -165,349 +168,360 @@ void Group::assign(int narg, char **arg) int nlocal = atom->nlocal; int bit = bitmask[igroup]; - // style = region - // add to group if atom is in region + try { + // style = region + // add to group if atom is in region - if (strcmp(arg[1],"region") == 0) { + if (strcmp(arg[1],"region") == 0) { - if (narg != 3) error->all(FLERR,"Illegal group command"); + if (narg != 3) error->all(FLERR,"Illegal group command"); - int iregion = domain->find_region(arg[2]); - if (iregion == -1) error->all(FLERR,"Group region ID does not exist"); - domain->regions[iregion]->init(); - domain->regions[iregion]->prematch(); + int iregion = domain->find_region(arg[2]); + if (iregion == -1) error->all(FLERR,"Group region ID does not exist"); + domain->regions[iregion]->init(); + domain->regions[iregion]->prematch(); - for (i = 0; i < nlocal; i++) - if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) - mask[i] |= bit; + for (i = 0; i < nlocal; i++) + if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) + mask[i] |= bit; - // create an empty group + // create an empty group - } else if (strcmp(arg[1],"empty") == 0) { + } else if (strcmp(arg[1],"empty") == 0) { - if (narg != 2) error->all(FLERR,"Illegal group command"); - // nothing else to do here + if (narg != 2) error->all(FLERR,"Illegal group command"); + // nothing else to do here - // style = type, molecule, id - // add to group if atom matches type/molecule/id or condition + // style = type, molecule, id + // add to group if atom matches type/molecule/id or condition - } else if (strcmp(arg[1],"type") == 0 || strcmp(arg[1],"molecule") == 0 || - strcmp(arg[1],"id") == 0) { + } else if (strcmp(arg[1],"type") == 0 || strcmp(arg[1],"molecule") == 0 || + strcmp(arg[1],"id") == 0) { - if (narg < 3) error->all(FLERR,"Illegal group command"); + if (narg < 3) error->all(FLERR,"Illegal group command"); - int category=NONE; - if (strcmp(arg[1],"type") == 0) category = TYPE; - else if (strcmp(arg[1],"molecule") == 0) category = MOLECULE; - else if (strcmp(arg[1],"id") == 0) category = ID; + int category=NONE; + if (strcmp(arg[1],"type") == 0) category = TYPE; + else if (strcmp(arg[1],"molecule") == 0) category = MOLECULE; + else if (strcmp(arg[1],"id") == 0) category = ID; - if ((category == MOLECULE) && (!atom->molecule_flag)) - error->all(FLERR,"Group command requires atom attribute molecule"); - - if ((category == ID) && (!atom->tag_enable)) - error->all(FLERR,"Group command requires atom IDs"); - - // args = logical condition - - if (narg > 3 && - (strcmp(arg[2],"<") == 0 || strcmp(arg[2],">") == 0 || - strcmp(arg[2],"<=") == 0 || strcmp(arg[2],">=") == 0 || - strcmp(arg[2],"==") == 0 || strcmp(arg[2],"!=") == 0 || - strcmp(arg[2],"<>") == 0)) { - - int condition = -1; - if (strcmp(arg[2],"<") == 0) condition = LT; - else if (strcmp(arg[2],"<=") == 0) condition = LE; - else if (strcmp(arg[2],">") == 0) condition = GT; - else if (strcmp(arg[2],">=") == 0) condition = GE; - else if (strcmp(arg[2],"==") == 0) condition = EQ; - else if (strcmp(arg[2],"!=") == 0) condition = NEQ; - else if (strcmp(arg[2],"<>") == 0) condition = BETWEEN; - else error->all(FLERR,"Illegal group command"); - - tagint bound1,bound2; - bound1 = utils::tnumeric(FLERR,arg[3],false,lmp); - bound2 = -1; - - if (condition == BETWEEN) { - if (narg != 5) error->all(FLERR,"Illegal group command"); - bound2 = utils::tnumeric(FLERR,arg[4],false,lmp); - } else if (narg != 4) error->all(FLERR,"Illegal group command"); - - int *attribute = nullptr; - tagint *tattribute = nullptr; - if (category == TYPE) attribute = atom->type; - else if (category == MOLECULE) tattribute = atom->molecule; - else if (category == ID) tattribute = atom->tag; - - // add to group if meets condition - - if (attribute) { - if (condition == LT) { - for (i = 0; i < nlocal; i++) - if (attribute[i] < bound1) mask[i] |= bit; - } else if (condition == LE) { - for (i = 0; i < nlocal; i++) - if (attribute[i] <= bound1) mask[i] |= bit; - } else if (condition == GT) { - for (i = 0; i < nlocal; i++) - if (attribute[i] > bound1) mask[i] |= bit; - } else if (condition == GE) { - for (i = 0; i < nlocal; i++) - if (attribute[i] >= bound1) mask[i] |= bit; - } else if (condition == EQ) { - for (i = 0; i < nlocal; i++) - if (attribute[i] == bound1) mask[i] |= bit; - } else if (condition == NEQ) { - for (i = 0; i < nlocal; i++) - if (attribute[i] != bound1) mask[i] |= bit; - } else if (condition == BETWEEN) { - for (i = 0; i < nlocal; i++) - if (attribute[i] >= bound1 && attribute[i] <= bound2) - mask[i] |= bit; - } - } else { - if (condition == LT) { - for (i = 0; i < nlocal; i++) - if (tattribute[i] < bound1) mask[i] |= bit; - } else if (condition == LE) { - for (i = 0; i < nlocal; i++) - if (tattribute[i] <= bound1) mask[i] |= bit; - } else if (condition == GT) { - for (i = 0; i < nlocal; i++) - if (tattribute[i] > bound1) mask[i] |= bit; - } else if (condition == GE) { - for (i = 0; i < nlocal; i++) - if (tattribute[i] >= bound1) mask[i] |= bit; - } else if (condition == EQ) { - for (i = 0; i < nlocal; i++) - if (tattribute[i] == bound1) mask[i] |= bit; - } else if (condition == NEQ) { - for (i = 0; i < nlocal; i++) - if (tattribute[i] != bound1) mask[i] |= bit; - } else if (condition == BETWEEN) { - for (i = 0; i < nlocal; i++) - if (tattribute[i] >= bound1 && tattribute[i] <= bound2) - mask[i] |= bit; - } - } - - // args = list of values - - } else { - int *attribute = nullptr; - tagint *tattribute = nullptr; - if (category == TYPE) attribute = atom->type; - else if (category == MOLECULE) tattribute = atom->molecule; - else if (category == ID) tattribute = atom->tag; - - tagint start,stop,delta; - - for (int iarg = 2; iarg < narg; iarg++) { - delta = 1; - try { - ValueTokenizer values(arg[iarg],":"); - start = values.next_tagint(); - if (utils::strmatch(arg[iarg],"^-?\\d+$")) { - stop = start; - } else if (utils::strmatch(arg[iarg],"^-?\\d+:-?\\d+$")) { - stop = values.next_tagint(); - } else if (utils::strmatch(arg[iarg],"^-?\\d+:-?\\d+:\\d+$")) { - stop = values.next_tagint(); - delta = values.next_tagint(); - } else throw TokenizerException("Syntax error",""); - } catch (TokenizerException &e) { - error->all(FLERR,fmt::format("Incorrect range string " - "'{}': {}",arg[iarg],e.what())); - } - if (delta < 1) - error->all(FLERR,"Illegal range increment value"); - - // add to group if attribute matches value or sequence - - if (attribute) { - for (i = 0; i < nlocal; i++) - if (attribute[i] >= start && attribute[i] <= stop && - (attribute[i]-start) % delta == 0) mask[i] |= bit; - } else { - for (i = 0; i < nlocal; i++) - if (tattribute[i] >= start && tattribute[i] <= stop && - (tattribute[i]-start) % delta == 0) mask[i] |= bit; - } - } - } - - // style = variable - // add to group if atom-atyle variable is non-zero - - } else if (strcmp(arg[1],"variable") == 0) { - - int ivar = input->variable->find(arg[2]); - if (ivar < 0) error->all(FLERR,"Variable name for group does not exist"); - if (!input->variable->atomstyle(ivar)) - error->all(FLERR,"Variable for group is invalid style"); - - double *aflag; - - // aflag = evaluation of per-atom variable - - memory->create(aflag,nlocal,"group:aflag"); - input->variable->compute_atom(ivar,0,aflag,1,0); - - // add to group if per-atom variable evaluated to non-zero - - for (i = 0; i < nlocal; i++) - if (aflag[i] != 0.0) mask[i] |= bit; - - memory->destroy(aflag); - - // style = include - - } else if (strcmp(arg[1],"include") == 0) { - - if (narg != 3) error->all(FLERR,"Illegal group command"); - if (strcmp(arg[2],"molecule") == 0) { - if (!atom->molecule_flag) + if ((category == MOLECULE) && (!atom->molecule_flag)) error->all(FLERR,"Group command requires atom attribute molecule"); - add_molecules(igroup,bit); + if ((category == ID) && (!atom->tag_enable)) + error->all(FLERR,"Group command requires atom IDs"); + + // args = logical condition + + if (narg > 3 && + (strcmp(arg[2],"<") == 0 || strcmp(arg[2],">") == 0 || + strcmp(arg[2],"<=") == 0 || strcmp(arg[2],">=") == 0 || + strcmp(arg[2],"==") == 0 || strcmp(arg[2],"!=") == 0 || + strcmp(arg[2],"<>") == 0)) { + + int condition = -1; + if (strcmp(arg[2],"<") == 0) condition = LT; + else if (strcmp(arg[2],"<=") == 0) condition = LE; + else if (strcmp(arg[2],">") == 0) condition = GT; + else if (strcmp(arg[2],">=") == 0) condition = GE; + else if (strcmp(arg[2],"==") == 0) condition = EQ; + else if (strcmp(arg[2],"!=") == 0) condition = NEQ; + else if (strcmp(arg[2],"<>") == 0) condition = BETWEEN; + else error->all(FLERR,"Illegal group command"); + + tagint bound1,bound2; + bound1 = utils::tnumeric(FLERR,arg[3],false,lmp); + bound2 = -1; + + if (condition == BETWEEN) { + if (narg != 5) error->all(FLERR,"Illegal group command"); + bound2 = utils::tnumeric(FLERR,arg[4],false,lmp); + } else if (narg != 4) error->all(FLERR,"Illegal group command"); + + int *attribute = nullptr; + tagint *tattribute = nullptr; + if (category == TYPE) attribute = atom->type; + else if (category == MOLECULE) tattribute = atom->molecule; + else if (category == ID) tattribute = atom->tag; + + // add to group if meets condition + + if (attribute) { + if (condition == LT) { + for (i = 0; i < nlocal; i++) + if (attribute[i] < bound1) mask[i] |= bit; + } else if (condition == LE) { + for (i = 0; i < nlocal; i++) + if (attribute[i] <= bound1) mask[i] |= bit; + } else if (condition == GT) { + for (i = 0; i < nlocal; i++) + if (attribute[i] > bound1) mask[i] |= bit; + } else if (condition == GE) { + for (i = 0; i < nlocal; i++) + if (attribute[i] >= bound1) mask[i] |= bit; + } else if (condition == EQ) { + for (i = 0; i < nlocal; i++) + if (attribute[i] == bound1) mask[i] |= bit; + } else if (condition == NEQ) { + for (i = 0; i < nlocal; i++) + if (attribute[i] != bound1) mask[i] |= bit; + } else if (condition == BETWEEN) { + for (i = 0; i < nlocal; i++) + if (attribute[i] >= bound1 && attribute[i] <= bound2) + mask[i] |= bit; + } + } else { + if (condition == LT) { + for (i = 0; i < nlocal; i++) + if (tattribute[i] < bound1) mask[i] |= bit; + } else if (condition == LE) { + for (i = 0; i < nlocal; i++) + if (tattribute[i] <= bound1) mask[i] |= bit; + } else if (condition == GT) { + for (i = 0; i < nlocal; i++) + if (tattribute[i] > bound1) mask[i] |= bit; + } else if (condition == GE) { + for (i = 0; i < nlocal; i++) + if (tattribute[i] >= bound1) mask[i] |= bit; + } else if (condition == EQ) { + for (i = 0; i < nlocal; i++) + if (tattribute[i] == bound1) mask[i] |= bit; + } else if (condition == NEQ) { + for (i = 0; i < nlocal; i++) + if (tattribute[i] != bound1) mask[i] |= bit; + } else if (condition == BETWEEN) { + for (i = 0; i < nlocal; i++) + if (tattribute[i] >= bound1 && tattribute[i] <= bound2) + mask[i] |= bit; + } + } + + // args = list of values + + } else { + int *attribute = nullptr; + tagint *tattribute = nullptr; + if (category == TYPE) attribute = atom->type; + else if (category == MOLECULE) tattribute = atom->molecule; + else if (category == ID) tattribute = atom->tag; + + tagint start,stop,delta; + + for (int iarg = 2; iarg < narg; iarg++) { + delta = 1; + try { + ValueTokenizer values(arg[iarg],":"); + start = values.next_tagint(); + if (utils::strmatch(arg[iarg],"^-?\\d+$")) { + stop = start; + } else if (utils::strmatch(arg[iarg],"^-?\\d+:-?\\d+$")) { + stop = values.next_tagint(); + } else if (utils::strmatch(arg[iarg],"^-?\\d+:-?\\d+:\\d+$")) { + stop = values.next_tagint(); + delta = values.next_tagint(); + } else throw TokenizerException("Syntax error",""); + } catch (TokenizerException &e) { + error->all(FLERR,fmt::format("Incorrect range string " + "'{}': {}",arg[iarg],e.what())); + } + if (delta < 1) + error->all(FLERR,"Illegal range increment value"); + + // add to group if attribute matches value or sequence + + if (attribute) { + for (i = 0; i < nlocal; i++) + if (attribute[i] >= start && attribute[i] <= stop && + (attribute[i]-start) % delta == 0) mask[i] |= bit; + } else { + for (i = 0; i < nlocal; i++) + if (tattribute[i] >= start && tattribute[i] <= stop && + (tattribute[i]-start) % delta == 0) mask[i] |= bit; + } + } + } + + // style = variable + // add to group if atom-atyle variable is non-zero + + } else if (strcmp(arg[1],"variable") == 0) { + + int ivar = input->variable->find(arg[2]); + if (ivar < 0) error->all(FLERR,"Variable name for group does not exist"); + if (!input->variable->atomstyle(ivar)) + error->all(FLERR,"Variable for group is invalid style"); + + double *aflag; + + // aflag = evaluation of per-atom variable + + memory->create(aflag,nlocal,"group:aflag"); + input->variable->compute_atom(ivar,0,aflag,1,0); + + // add to group if per-atom variable evaluated to non-zero + + for (i = 0; i < nlocal; i++) + if (aflag[i] != 0.0) mask[i] |= bit; + + memory->destroy(aflag); + + // style = include + + } else if (strcmp(arg[1],"include") == 0) { + + if (narg != 3) error->all(FLERR,"Illegal group command"); + if (strcmp(arg[2],"molecule") == 0) { + if (!atom->molecule_flag) + error->all(FLERR,"Group command requires atom attribute molecule"); + + add_molecules(igroup,bit); + + } else error->all(FLERR,"Illegal group command"); + + // style = subtract + + } else if (strcmp(arg[1],"subtract") == 0) { + + if (narg < 4) error->all(FLERR,"Illegal group command"); + + int length = narg-2; + std::vector list(length); + + int jgroup; + for (int iarg = 2; iarg < narg; iarg++) { + jgroup = find(arg[iarg]); + if (jgroup == -1) error->all(FLERR,"Group ID does not exist"); + if (dynamic[jgroup]) + error->all(FLERR,"Cannot subtract groups using a dynamic group"); + list[iarg-2] = jgroup; + } + + // add to group if in 1st group in list + + int otherbit = bitmask[list[0]]; + + for (i = 0; i < nlocal; i++) + if (mask[i] & otherbit) mask[i] |= bit; + + // remove atoms if they are in any of the other groups + // AND with inverse mask removes the atom from group + + int inverse = inversemask[igroup]; + + for (int ilist = 1; ilist < length; ilist++) { + otherbit = bitmask[list[ilist]]; + for (i = 0; i < nlocal; i++) + if (mask[i] & otherbit) mask[i] &= inverse; + } + + // style = union + + } else if (strcmp(arg[1],"union") == 0) { + + if (narg < 3) error->all(FLERR,"Illegal group command"); + + int length = narg-2; + std::vector list(length); + + int jgroup; + for (int iarg = 2; iarg < narg; iarg++) { + jgroup = find(arg[iarg]); + if (jgroup == -1) error->all(FLERR,"Group ID does not exist"); + if (dynamic[jgroup]) + error->all(FLERR,"Cannot union groups using a dynamic group"); + list[iarg-2] = jgroup; + } + + // add to group if in any other group in list + + int otherbit; + + for (int ilist = 0; ilist < length; ilist++) { + otherbit = bitmask[list[ilist]]; + for (i = 0; i < nlocal; i++) + if (mask[i] & otherbit) mask[i] |= bit; + } + + // style = intersect + + } else if (strcmp(arg[1],"intersect") == 0) { + + if (narg < 4) error->all(FLERR,"Illegal group command"); + + int length = narg-2; + std::vector list(length); + + int jgroup; + for (int iarg = 2; iarg < narg; iarg++) { + jgroup = find(arg[iarg]); + if (jgroup == -1) error->all(FLERR,"Group ID does not exist"); + if (dynamic[jgroup]) + error->all(FLERR,"Cannot intersect groups using a dynamic group"); + list[iarg-2] = jgroup; + } + + // add to group if in all groups in list + + int otherbit,ok,ilist; + + for (i = 0; i < nlocal; i++) { + ok = 1; + for (ilist = 0; ilist < length; ilist++) { + otherbit = bitmask[list[ilist]]; + if ((mask[i] & otherbit) == 0) ok = 0; + } + if (ok) mask[i] |= bit; + } + + // style = dynamic + // create a new FixGroup to dynamically determine atoms in group + + } else if (strcmp(arg[1],"dynamic") == 0) { + + if (narg < 4) error->all(FLERR,"Illegal group command"); + if (strcmp(arg[0],arg[2]) == 0) + error->all(FLERR,"Group dynamic cannot reference itself"); + if (find(arg[2]) < 0) + error->all(FLERR,"Group dynamic parent group does not exist"); + if (igroup == 0) error->all(FLERR,"Group all cannot be made dynamic"); + + // if group is already dynamic, delete existing FixGroup + + if (dynamic[igroup]) + modify->delete_fix(std::string("GROUP_") + names[igroup]); + + dynamic[igroup] = 1; + + std::string fixcmd = "GROUP_"; + fixcmd += fmt::format("{} {} GROUP",names[igroup],arg[2]); + for (int i = 3; i < narg; i++) fixcmd += std::string(" ") + arg[i]; + modify->add_fix(fixcmd); + + // style = static + // remove dynamic FixGroup if necessary + + } else if (strcmp(arg[1],"static") == 0) { + + if (narg != 2) error->all(FLERR,"Illegal group command"); + + if (dynamic[igroup]) + modify->delete_fix(std::string("GROUP_") + names[igroup]); + + dynamic[igroup] = 0; + + // not a valid group style } else error->all(FLERR,"Illegal group command"); - // style = subtract - - } else if (strcmp(arg[1],"subtract") == 0) { - - if (narg < 4) error->all(FLERR,"Illegal group command"); - - int length = narg-2; - std::vector list(length); - - int jgroup; - for (int iarg = 2; iarg < narg; iarg++) { - jgroup = find(arg[iarg]); - if (jgroup == -1) error->all(FLERR,"Group ID does not exist"); - if (dynamic[jgroup]) - error->all(FLERR,"Cannot subtract groups using a dynamic group"); - list[iarg-2] = jgroup; + } catch (LAMMPSException & e) { + // undo created group in case of an error + if (created) { + delete [] names[igroup]; + names[igroup] = nullptr; + ngroup--; } - - // add to group if in 1st group in list - - int otherbit = bitmask[list[0]]; - - for (i = 0; i < nlocal; i++) - if (mask[i] & otherbit) mask[i] |= bit; - - // remove atoms if they are in any of the other groups - // AND with inverse mask removes the atom from group - - int inverse = inversemask[igroup]; - - for (int ilist = 1; ilist < length; ilist++) { - otherbit = bitmask[list[ilist]]; - for (i = 0; i < nlocal; i++) - if (mask[i] & otherbit) mask[i] &= inverse; - } - - // style = union - - } else if (strcmp(arg[1],"union") == 0) { - - if (narg < 3) error->all(FLERR,"Illegal group command"); - - int length = narg-2; - std::vector list(length); - - int jgroup; - for (int iarg = 2; iarg < narg; iarg++) { - jgroup = find(arg[iarg]); - if (jgroup == -1) error->all(FLERR,"Group ID does not exist"); - if (dynamic[jgroup]) - error->all(FLERR,"Cannot union groups using a dynamic group"); - list[iarg-2] = jgroup; - } - - // add to group if in any other group in list - - int otherbit; - - for (int ilist = 0; ilist < length; ilist++) { - otherbit = bitmask[list[ilist]]; - for (i = 0; i < nlocal; i++) - if (mask[i] & otherbit) mask[i] |= bit; - } - - // style = intersect - - } else if (strcmp(arg[1],"intersect") == 0) { - - if (narg < 4) error->all(FLERR,"Illegal group command"); - - int length = narg-2; - std::vector list(length); - - int jgroup; - for (int iarg = 2; iarg < narg; iarg++) { - jgroup = find(arg[iarg]); - if (jgroup == -1) error->all(FLERR,"Group ID does not exist"); - if (dynamic[jgroup]) - error->all(FLERR,"Cannot intersect groups using a dynamic group"); - list[iarg-2] = jgroup; - } - - // add to group if in all groups in list - - int otherbit,ok,ilist; - - for (i = 0; i < nlocal; i++) { - ok = 1; - for (ilist = 0; ilist < length; ilist++) { - otherbit = bitmask[list[ilist]]; - if ((mask[i] & otherbit) == 0) ok = 0; - } - if (ok) mask[i] |= bit; - } - - // style = dynamic - // create a new FixGroup to dynamically determine atoms in group - - } else if (strcmp(arg[1],"dynamic") == 0) { - - if (narg < 4) error->all(FLERR,"Illegal group command"); - if (strcmp(arg[0],arg[2]) == 0) - error->all(FLERR,"Group dynamic cannot reference itself"); - if (find(arg[2]) < 0) - error->all(FLERR,"Group dynamic parent group does not exist"); - if (igroup == 0) error->all(FLERR,"Group all cannot be made dynamic"); - - // if group is already dynamic, delete existing FixGroup - - if (dynamic[igroup]) - modify->delete_fix(std::string("GROUP_") + names[igroup]); - - dynamic[igroup] = 1; - - std::string fixcmd = "GROUP_"; - fixcmd += fmt::format("{} {} GROUP",names[igroup],arg[2]); - for (int i = 3; i < narg; i++) fixcmd += std::string(" ") + arg[i]; - modify->add_fix(fixcmd); - - // style = static - // remove dynamic FixGroup if necessary - - } else if (strcmp(arg[1],"static") == 0) { - - if (narg != 2) error->all(FLERR,"Illegal group command"); - - if (dynamic[igroup]) - modify->delete_fix(std::string("GROUP_") + names[igroup]); - - dynamic[igroup] = 0; - - // not a valid group style - - } else error->all(FLERR,"Illegal group command"); + throw e; + } // print stats for changed group diff --git a/unittest/commands/test_groups.cpp b/unittest/commands/test_groups.cpp index 181f000a7c..7feddcc685 100644 --- a/unittest/commands/test_groups.cpp +++ b/unittest/commands/test_groups.cpp @@ -297,7 +297,7 @@ TEST_F(GroupTest, Dynamic) command("group grow delete"); command("variable ramp equal step"); END_HIDE_OUTPUT(); - ASSERT_EQ(group->ngroup, 4); + ASSERT_EQ(group->ngroup, 3); TEST_FAILURE(".*ERROR: Group dynamic cannot reference itself.*", command("group half dynamic half region top");); From a4e2255c872d45ba1fdb43da0c604ed1509bf0fa Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 20 Apr 2021 14:31:11 -0400 Subject: [PATCH 0578/1217] Avoid memory leak in case of errors/exceptions in add_fix --- src/modify.cpp | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/modify.cpp b/src/modify.cpp index 79a0ecd41f..246b855913 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -964,13 +964,12 @@ void Modify::add_fix(int narg, char **arg, int trysuffix) void Modify::add_fix(const std::string &fixcmd, int trysuffix) { auto args = utils::split_words(fixcmd); - char **newarg = new char*[args.size()]; - int i=0; + std::vector newarg(args.size()); + int i = 0; for (const auto &arg : args) { newarg[i++] = (char *)arg.c_str(); } - add_fix(args.size(),newarg,trysuffix); - delete[] newarg; + add_fix(args.size(),newarg.data(),trysuffix); } From 7696d0f84c2cb9d83451b9bfacd38f4c0dbaf47c Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 20 Apr 2021 15:40:59 -0400 Subject: [PATCH 0579/1217] Add ENVIRONMENT to RunLammps test --- unittest/CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/unittest/CMakeLists.txt b/unittest/CMakeLists.txt index 4e27f4be45..412cf8d3d6 100644 --- a/unittest/CMakeLists.txt +++ b/unittest/CMakeLists.txt @@ -7,6 +7,7 @@ add_test(NAME RunLammps COMMAND $ -log none -echo none -in in.empty WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(RunLammps PROPERTIES + ENVIRONMENT "TSAN_OPTIONS='ignore_noninstrumented_modules=1'" PASS_REGULAR_EXPRESSION "^LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]\\)") if(BUILD_MPI) From 90d3b65691dc10c213dbbb5c136352b5ebe930e4 Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Tue, 20 Apr 2021 22:55:26 +0200 Subject: [PATCH 0580/1217] Minor changes for CMake build tested --- cmake/Modules/FindN2P2.cmake | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/cmake/Modules/FindN2P2.cmake b/cmake/Modules/FindN2P2.cmake index cae5de5342..95413edfb1 100644 --- a/cmake/Modules/FindN2P2.cmake +++ b/cmake/Modules/FindN2P2.cmake @@ -12,10 +12,10 @@ else() endif() # Set path to include directory. -find_path(N2P2_INCLUDE_DIR InterfaceLammps.h PATHS "${N2P2_DIR}/include") +find_path(N2P2_INCLUDE_DIR InterfaceLammps.h HINTS "${N2P2_DIR}/include") # Two libraries need to be linked: libnnp and libnnpif. -find_library(N2P2_LIBNNP NAMES nnp PATHS "${N2P2_DIR}/lib") -find_library(N2P2_LIBNNPIF NAMES nnpif PATHS "${N2P2_DIR}/lib") +find_library(N2P2_LIBNNP NAMES nnp HINTS "${N2P2_DIR}/lib") +find_library(N2P2_LIBNNPIF NAMES nnpif HINTS "${N2P2_DIR}/lib") # Users could compile n2p2 with extra flags which are then also required for # pair_hdnnp.cpp compilation. To forward them to the LAMMPS build process n2p2 # writes a file with cmake commands, e.g. @@ -23,7 +23,7 @@ find_library(N2P2_LIBNNPIF NAMES nnpif PATHS "${N2P2_DIR}/lib") # target_compile_definitions(lammps PRIVATE -DN2P2_NO_SF_GROUPS) # # to "lib/lammps-extra.cmake" which is then included by USER-HDNNP.cmake. -find_file(N2P2_CMAKE_EXTRA NAMES lammps-extra.cmake PATHS "${N2P2_DIR}/lib") +find_file(N2P2_CMAKE_EXTRA NAMES lammps-extra.cmake HINTS "${N2P2_DIR}/lib") find_package_handle_standard_args(N2P2 DEFAULT_MSG N2P2_DIR From 0e38bfb58bef85040dbb9d92c5bdcfc11578759d Mon Sep 17 00:00:00 2001 From: julient31 Date: Wed, 21 Apr 2021 07:25:12 -0600 Subject: [PATCH 0581/1217] adding "division by zero" checks in fix precession/spin --- src/SPIN/fix_langevin_spin.cpp | 3 +-- src/SPIN/fix_precession_spin.cpp | 42 ++++++++++++++++++++++++-------- 2 files changed, 33 insertions(+), 12 deletions(-) diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index 0b566ce60b..949833caa7 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -28,6 +28,7 @@ #include "comm.h" #include "error.h" #include "force.h" +#include "group.h" #include "math_const.h" #include "memory.h" #include "modify.h" @@ -35,8 +36,6 @@ #include "random_mars.h" #include "respa.h" #include "update.h" -#include "compute.h" -#include "group.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 34d3fbe8a3..01df9d3750 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -140,56 +140,78 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : // normalize vectors - double inorm; + double norm2,inorm; if (zeeman_flag) { - inorm = 1.0/sqrt(nhx*nhx + nhy*nhy + nhz*nhz); + norm2 = nhx*nhx + nhy*nhy + nhz*nhz; + if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + inorm = 1.0/sqrt(norm2); nhx *= inorm; nhy *= inorm; nhz *= inorm; } if (stt_flag) { - inorm = 1.0/sqrt(nsttx*nsttx + nstty*nstty + nsttz*nsttz); + norm2 = nsttx*nsttx + nstty*nstty + nsttz*nsttz; + if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + inorm = 1.0/sqrt(norm2); nsttx *= inorm; nstty *= inorm; nsttz *= inorm; } if (aniso_flag) { - inorm = 1.0/sqrt(nax*nax + nay*nay + naz*naz); + norm2 = nax*nax + nay*nay + naz*naz; + if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + inorm = 1.0/sqrt(norm2); nax *= inorm; nay *= inorm; naz *= inorm; } if (cubic_flag) { - inorm = 1.0/sqrt(nc1x*nc1x + nc1y*nc1y + nc1z*nc1z); + norm2 = nc1x*nc1x + nc1y*nc1y + nc1z*nc1z; + if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + inorm = 1.0/sqrt(norm2); nc1x *= inorm; nc1y *= inorm; nc1z *= inorm; - inorm = 1.0/sqrt(nc2x*nc2x + nc2y*nc2y + nc2z*nc2z); + + norm2 = nc2x*nc2x + nc2y*nc2y + nc2z*nc2z; + if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + inorm = 1.0/sqrt(norm2); nc2x *= inorm; nc2y *= inorm; nc2z *= inorm; - inorm = 1.0/sqrt(nc3x*nc3x + nc3y*nc3y + nc3z*nc3z); + + norm2 = nc3x*nc3x + nc3y*nc3y + nc3z*nc3z; + if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + inorm = 1.0/sqrt(norm2); nc3x *= inorm; nc3y *= inorm; nc3z *= inorm; } if (hexaniso_flag) { - inorm = 1.0/sqrt(n6x*n6x + n6y*n6y + n6z*n6z); + norm2 = n6x*n6x + n6y*n6y + n6z*n6z; + if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + inorm = 1.0/sqrt(norm2); n6x *= inorm; n6y *= inorm; n6z *= inorm; - inorm = 1.0/sqrt(m6x*m6x + m6y*m6y + m6z*m6z); + + norm2 = m6x*m6x + m6y*m6y + m6z*m6z; + if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + inorm = 1.0/sqrt(norm2); m6x *= inorm; m6y *= inorm; m6z *= inorm; l6x = (n6z*m6y-n6y*m6z); l6y = (n6x*m6z-n6z*m6x); l6z = (n6y*m6x-n6x*m6y); - inorm = 1.0/sqrt(l6x*l6x + l6y*l6y + l6z*l6z); + + norm2 = l6x*l6x + l6y*l6y + l6z*l6z; + if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + inorm = 1.0/sqrt(norm2); l6x *= inorm; l6y *= inorm; l6z *= inorm; From b1dd616a2f7fcd87b6ba7dc2c7bf03cefe40aca1 Mon Sep 17 00:00:00 2001 From: julient31 Date: Wed, 21 Apr 2021 07:43:00 -0600 Subject: [PATCH 0582/1217] correcting a small typo in the checks, and adding a note in the documentation of fix precession/spin about the error if a (0,0,0) vector is given as an input. --- doc/src/fix_precession_spin.rst | 12 +++++++++++- src/SPIN/fix_precession_spin.cpp | 27 ++++++++++++++++++--------- 2 files changed, 29 insertions(+), 10 deletions(-) diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst index 2d6d8e2f7b..183753db5f 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -127,7 +127,7 @@ details on cubic anisotropies. Style *stt* is used to simulate the interaction between the spins and a spin-transfer torque. -See equation(7) of :ref:`(Chirac) ` for more details about the +See equation (7) of :ref:`(Chirac) ` for more details about the implemented spin-transfer torque term. In all cases, the choice of :math:`(x y z)` only imposes the vector @@ -137,6 +137,16 @@ normalized). Those styles can be combined within one single command line. +.. note:: + + The norm of all vectors defined with the precession/spin command + have to be non-zero. For example, defining + "fix 1 all precession/spin zeeman 0.1 0.0 0.0 0.0" would result + in an error message. + Since those vector components are used to compute the inverse of the + field (or anisotropy) vector norm, setting a zero-vector would result + in a division by zero. + ---------- Restart, fix_modify, output, run start/stop, minimize info diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 01df9d3750..7cfbe6e1a7 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -143,7 +143,8 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : double norm2,inorm; if (zeeman_flag) { norm2 = nhx*nhx + nhy*nhy + nhz*nhz; - if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + if (norm2 == 0.0) + error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); nhx *= inorm; nhy *= inorm; @@ -152,7 +153,8 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : if (stt_flag) { norm2 = nsttx*nsttx + nstty*nstty + nsttz*nsttz; - if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + if (norm2 == 0.0) + error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); nsttx *= inorm; nstty *= inorm; @@ -161,7 +163,8 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : if (aniso_flag) { norm2 = nax*nax + nay*nay + naz*naz; - if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + if (norm2 == 0.0) + error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); nax *= inorm; nay *= inorm; @@ -170,21 +173,24 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : if (cubic_flag) { norm2 = nc1x*nc1x + nc1y*nc1y + nc1z*nc1z; - if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + if (norm2 == 0.0) + error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); nc1x *= inorm; nc1y *= inorm; nc1z *= inorm; norm2 = nc2x*nc2x + nc2y*nc2y + nc2z*nc2z; - if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + if (norm2 == 0.0) + error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); nc2x *= inorm; nc2y *= inorm; nc2z *= inorm; norm2 = nc3x*nc3x + nc3y*nc3y + nc3z*nc3z; - if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + if (norm2 == 0.0) + error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); nc3x *= inorm; nc3y *= inorm; @@ -193,14 +199,16 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : if (hexaniso_flag) { norm2 = n6x*n6x + n6y*n6y + n6z*n6z; - if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + if (norm2 == 0.0) + error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); n6x *= inorm; n6y *= inorm; n6z *= inorm; norm2 = m6x*m6x + m6y*m6y + m6z*m6z; - if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + if (norm2 == 0.0) + error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); m6x *= inorm; m6y *= inorm; @@ -210,7 +218,8 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : l6z = (n6y*m6x-n6x*m6y); norm2 = l6x*l6x + l6y*l6y + l6z*l6z; - if (norm2 == 0.0) else error->all(FLERR,"Illegal precession/spin command"); + if (norm2 == 0.0) + error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); l6x *= inorm; l6y *= inorm; From f270b600f78e1c0574bd9387c43efec363de9708 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 21 Apr 2021 08:17:17 -0600 Subject: [PATCH 0583/1217] Fix compile error in kokkos_type --- src/KOKKOS/kokkos_type.h | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index af5adeee73..8eb9744a94 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -1038,6 +1038,11 @@ typedef tdual_virial_array::t_host_const_randomread t_virial_array_randomread; // Spin types //2d X_FLOAT array n*4 +#ifdef LMP_KOKKOS_NO_LEGACY +typedef Kokkos::DualView tdual_float_1d_4; +#else +typedef Kokkos::DualView tdual_float_1d_4; +#endif typedef tdual_float_1d_4::t_host t_sp_array; typedef tdual_float_1d_4::t_host_const t_sp_array_const; typedef tdual_float_1d_4::t_host_um t_sp_array_um; From 1656661fc21312ab4feca464900cd1be1327162b Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 21 Apr 2021 11:17:32 -0400 Subject: [PATCH 0584/1217] Disable rcb_min_size test --- unittest/commands/test_mpi_load_balancing.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/unittest/commands/test_mpi_load_balancing.cpp b/unittest/commands/test_mpi_load_balancing.cpp index cbdea26981..39e39e5da8 100644 --- a/unittest/commands/test_mpi_load_balancing.cpp +++ b/unittest/commands/test_mpi_load_balancing.cpp @@ -195,6 +195,9 @@ TEST_F(MPILoadBalanceTest, rcb) TEST_F(MPILoadBalanceTest, rcb_min_size) { + GTEST_SKIP(); + // TODO minimum domain size is not enforced right now + // skipping for now to allow other MPI tests to get merged command("comm_style tiled"); command("create_atoms 1 single 0 0 0"); command("create_atoms 1 single 0 0 0.25"); From 6cad2ba829a5b4ea9e0679a730ef3d851bf3e9b4 Mon Sep 17 00:00:00 2001 From: julient31 Date: Wed, 21 Apr 2021 10:55:43 -0600 Subject: [PATCH 0585/1217] reverting changes in fix precession/spin --- src/SPIN/fix_precession_spin.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 7cfbe6e1a7..389ab1838d 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -271,7 +271,7 @@ void FixPrecessionSpin::init() k2ch = k2c/hbar; K6h = K6/hbar; - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } @@ -301,7 +301,7 @@ void FixPrecessionSpin::init() void FixPrecessionSpin::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); From 1c80c9455bd9edc29364146fe203faa73893b111 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 21 Apr 2021 14:58:57 -0400 Subject: [PATCH 0586/1217] whitespace fixes --- doc/src/fix_precession_spin.rst | 16 +++++++------- src/SPIN/fix_langevin_spin.h | 2 +- src/SPIN/fix_nve_spin.cpp | 26 +++++++++++------------ src/SPIN/fix_nve_spin.h | 8 +++---- src/SPIN/fix_precession_spin.cpp | 36 ++++++++++++++++---------------- src/SPIN/fix_precession_spin.h | 2 +- 6 files changed, 45 insertions(+), 45 deletions(-) diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst index 183753db5f..9bf9db24e1 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -125,10 +125,10 @@ axis along the :math:`(1 1 1)`-type cube diagonals). :math:`K_2^c > diagonals. See chapter 2 of :ref:`(Skomski) ` for more details on cubic anisotropies. -Style *stt* is used to simulate the interaction between the spins and +Style *stt* is used to simulate the interaction between the spins and a spin-transfer torque. -See equation (7) of :ref:`(Chirac) ` for more details about the -implemented spin-transfer torque term. +See equation (7) of :ref:`(Chirac) ` for more details about the +implemented spin-transfer torque term. In all cases, the choice of :math:`(x y z)` only imposes the vector directions for the forces. Only the direction of the vector is @@ -139,12 +139,12 @@ Those styles can be combined within one single command line. .. note:: - The norm of all vectors defined with the precession/spin command + The norm of all vectors defined with the precession/spin command have to be non-zero. For example, defining "fix 1 all precession/spin zeeman 0.1 0.0 0.0 0.0" would result - in an error message. + in an error message. Since those vector components are used to compute the inverse of the - field (or anisotropy) vector norm, setting a zero-vector would result + field (or anisotropy) vector norm, setting a zero-vector would result in a division by zero. ---------- @@ -197,6 +197,6 @@ Oxford University Press. .. _Chirac1: -**(Chirac)** Chirac, Théophile, et al. Ultrafast antiferromagnetic -switching in NiO induced by spin transfer torques. +**(Chirac)** Chirac, Théophile, et al. Ultrafast antiferromagnetic +switching in NiO induced by spin transfer torques. Physical Review B 102.13 (2020): 134415. diff --git a/src/SPIN/fix_langevin_spin.h b/src/SPIN/fix_langevin_spin.h index 090e5b666a..baa1cb1c84 100644 --- a/src/SPIN/fix_langevin_spin.h +++ b/src/SPIN/fix_langevin_spin.h @@ -34,7 +34,7 @@ class FixLangevinSpin : public Fix { void init(); void setup(int); void add_tdamping(double *, double *); // add transverse damping - void add_temperature(int, double *, double *); + void add_temperature(int, double *, double *); void compute_single_langevin(int, double *, double *); protected: diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 5da7c32b6c..c394b943b7 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -60,7 +60,7 @@ enum{NONE}; FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), - pair(nullptr), spin_pairs(nullptr), locklangevinspin(nullptr), + pair(nullptr), spin_pairs(nullptr), locklangevinspin(nullptr), locksetforcespin(nullptr), lockprecessionspin(nullptr), rsec(nullptr), stack_head(nullptr), stack_foot(nullptr), backward_stacks(nullptr), forward_stacks(nullptr) @@ -75,7 +75,7 @@ FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) : nlocal_max = 0; npairs = 0; npairspin = 0; - + // test nprec nprecspin = nlangspin = nsetspin = 0; @@ -221,22 +221,22 @@ void FixNVESpin::init() } // set ptrs for fix precession/spin styles - + // loop 1: obtain # of fix precession/spin styles - + int iforce; for (iforce = 0; iforce < modify->nfix; iforce++) { if (strstr(modify->fix[iforce]->style,"precession/spin")) { nprecspin++; } } - + // init length of vector of ptrs to precession/spin styles if (nprecspin > 0) { lockprecessionspin = new FixPrecessionSpin*[nprecspin]; } - + // loop 2: fill vector with ptrs to precession/spin styles int count2 = 0; @@ -249,26 +249,26 @@ void FixNVESpin::init() } } } - + if (count2 != nprecspin) error->all(FLERR,"Incorrect number of fix precession/spin"); // set ptrs for fix langevin/spin styles - + // loop 1: obtain # of fix langevin/spin styles - + for (iforce = 0; iforce < modify->nfix; iforce++) { if (strstr(modify->fix[iforce]->style,"langevin/spin")) { nlangspin++; } } - + // init length of vector of ptrs to precession/spin styles if (nlangspin > 0) { locklangevinspin = new FixLangevinSpin*[nprecspin]; } - + // loop 2: fill vector with ptrs to precession/spin styles count2 = 0; @@ -281,10 +281,10 @@ void FixNVESpin::init() } } } - + if (count2 != nlangspin) error->all(FLERR,"Incorrect number of fix precession/spin"); - + // ptrs FixSetForceSpin classes for (iforce = 0; iforce < modify->nfix; iforce++) { diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h index ac5bc57b25..73716bac26 100644 --- a/src/SPIN/fix_nve_spin.h +++ b/src/SPIN/fix_nve_spin.h @@ -65,15 +65,15 @@ friend class PairSpin; int nlangspin; class FixLangevinSpin **locklangevinspin; - + // pointers to fix setforce/spin styles - + int nsetspin; class FixSetForceSpin *locksetforcespin; // to be done - + // pointers to fix precession/spin styles - int nprecspin; + int nprecspin; class FixPrecessionSpin **lockprecessionspin; // pointers to magnetic pair styles diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 389ab1838d..c3f8a4d7df 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -143,7 +143,7 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : double norm2,inorm; if (zeeman_flag) { norm2 = nhx*nhx + nhy*nhy + nhz*nhz; - if (norm2 == 0.0) + if (norm2 == 0.0) error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); nhx *= inorm; @@ -153,7 +153,7 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : if (stt_flag) { norm2 = nsttx*nsttx + nstty*nstty + nsttz*nsttz; - if (norm2 == 0.0) + if (norm2 == 0.0) error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); nsttx *= inorm; @@ -163,7 +163,7 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : if (aniso_flag) { norm2 = nax*nax + nay*nay + naz*naz; - if (norm2 == 0.0) + if (norm2 == 0.0) error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); nax *= inorm; @@ -173,41 +173,41 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : if (cubic_flag) { norm2 = nc1x*nc1x + nc1y*nc1y + nc1z*nc1z; - if (norm2 == 0.0) + if (norm2 == 0.0) error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); nc1x *= inorm; nc1y *= inorm; nc1z *= inorm; - + norm2 = nc2x*nc2x + nc2y*nc2y + nc2z*nc2z; - if (norm2 == 0.0) + if (norm2 == 0.0) error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); nc2x *= inorm; nc2y *= inorm; nc2z *= inorm; - + norm2 = nc3x*nc3x + nc3y*nc3y + nc3z*nc3z; - if (norm2 == 0.0) + if (norm2 == 0.0) error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); nc3x *= inorm; nc3y *= inorm; nc3z *= inorm; } - + if (hexaniso_flag) { norm2 = n6x*n6x + n6y*n6y + n6z*n6z; - if (norm2 == 0.0) + if (norm2 == 0.0) error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); n6x *= inorm; n6y *= inorm; n6z *= inorm; - + norm2 = m6x*m6x + m6y*m6y + m6z*m6z; - if (norm2 == 0.0) + if (norm2 == 0.0) error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); m6x *= inorm; @@ -216,9 +216,9 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : l6x = (n6z*m6y-n6y*m6z); l6y = (n6x*m6z-n6z*m6x); l6z = (n6y*m6x-n6x*m6y); - + norm2 = l6x*l6x + l6y*l6y + l6z*l6z; - if (norm2 == 0.0) + if (norm2 == 0.0) error->all(FLERR,"Illegal precession/spin command"); inorm = 1.0/sqrt(norm2); l6x *= inorm; @@ -534,7 +534,7 @@ void FixPrecessionSpin::compute_hexaniso(double spi[3], double fmi[3]) double pf, phi, ssint2; // changing to the axes' frame - + s_x = l6x*spi[0]+l6y*spi[1]+l6z*spi[2]; s_y = m6x*spi[0]+m6y*spi[1]+m6z*spi[2]; s_z = n6x*spi[0]+n6y*spi[1]+n6z*spi[2]; @@ -571,7 +571,7 @@ double FixPrecessionSpin::compute_hexaniso_energy(double spi[3]) s_z = n6x*spi[0]+n6y*spi[1]+n6z*spi[2]; // hexagonal anisotropy in the axes' frame - + phi = atan2(s_y,s_z); ssint2 = s_x*s_x + s_y*s_y; @@ -589,13 +589,13 @@ void FixPrecessionSpin::set_magneticprecession() hy = H_field*nhy; hz = H_field*nhz; } - + if (stt_flag) { sttx = stt_field*nsttx; stty = stt_field*nstty; sttz = stt_field*nsttz; } - + if (aniso_flag) { Kax = 2.0*Kah*nax; Kay = 2.0*Kah*nay; diff --git a/src/SPIN/fix_precession_spin.h b/src/SPIN/fix_precession_spin.h index d06a04f8f1..ae3c94a94c 100644 --- a/src/SPIN/fix_precession_spin.h +++ b/src/SPIN/fix_precession_spin.h @@ -63,7 +63,7 @@ class FixPrecessionSpin : public Fix { double compute_cubic_energy(double *); // hexagonal aniso calculations - + void compute_hexaniso(double *, double *); double compute_hexaniso_energy(double *); From b4efeb977d5ffa62bf21e4620102e47ea9c46e0f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 21 Apr 2021 18:12:24 -0400 Subject: [PATCH 0587/1217] update and sort lists of packages for different presets and categories --- cmake/presets/all_off.cmake | 20 ++++++++++---------- cmake/presets/all_on.cmake | 20 ++++++++++---------- cmake/presets/nolib.cmake | 9 +++++---- src/Makefile | 11 +++++------ 4 files changed, 30 insertions(+), 30 deletions(-) diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index bd94b9dbe5..9be6cfe54b 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -2,16 +2,16 @@ # an existing package selection without losing any other settings set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP - MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK - SNAP SPIN SRD VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP - USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD - USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP - USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP - USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ - USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE + MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN + SRD VORONOI + USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL + USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT + USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON + USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC + USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF + USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 438c119c4c..411fb09d6b 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -4,16 +4,16 @@ # with just a working C++ compiler and an MPI library. set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP - MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK - SNAP SPIN SRD VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP - USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD - USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP - USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP - USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ - USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE + MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN + SRD VORONOI + USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL + USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT + USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON + USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC + USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF + USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index 0245b58cc7..c9abb00a15 100644 --- a/cmake/presets/nolib.cmake +++ b/cmake/presets/nolib.cmake @@ -1,10 +1,11 @@ # preset that turns off all packages that require some form of external # library or special compiler (fortran or cuda) or equivalent. -set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON - VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB - USER-MOLFILE USER-MESONT USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP - USER-SCAFACOS USER-SMD USER-VTK) +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG + PYTHON VORONOI + USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB USER-MOLFILE USER-MESONT + USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS + USER-SMD USER-VTK) foreach(PKG ${PACKAGES_WITH_LIB}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/src/Makefile b/src/Makefile index d5f0e600d6..1606f9b239 100644 --- a/src/Makefile +++ b/src/Makefile @@ -59,11 +59,10 @@ PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-c user-qtb user-quip user-reaction user-reaxc user-scafacos user-smd user-smtbq \ user-sdpd user-sph user-tally user-uef user-vtk user-yaff -PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \ - python voronoi \ - user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ - user-netcdf user-plumed user-qmmm user-quip user-scafacos \ - user-smd user-vtk user-mesont user-pace +PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems python voronoi \ + user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-mesont \ + user-molfile user-netcdf user-pace user-plumed user-qmmm user-quip \ + user-scafacos user-smd user-vtk PACKSYS = compress mpiio python user-lb @@ -71,7 +70,7 @@ PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont PACKEXT = kim latte mscg voronoi \ user-adios user-h5md user-molfile user-netcdf user-pace user-plumed \ - user-qmmm user-quip user-smd user-vtk + user-qmmm user-quip user-scafacos user-smd user-vtk PACKALL = $(PACKAGE) $(PACKUSER) From 96baae29d0ff1c7c8011f2cbe73664dd1b420aba Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 21 Apr 2021 22:01:07 -0400 Subject: [PATCH 0588/1217] fix bug flagged by compiler warning --- src/KOKKOS/atom_vec_spin_kokkos.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp index 399ab23a5f..c3464d3267 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.cpp +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -637,11 +637,12 @@ int AtomVecSpinKokkos::unpack_border_hybrid(int n, int first, double *buf) m = 0; last = first + n; - for (i = first; i < last; i++) + for (i = first; i < last; i++) { h_sp(i,0) = buf[m++]; h_sp(i,1) = buf[m++]; h_sp(i,2) = buf[m++]; h_sp(i,3) = buf[m++]; + } return m; } From a1e07d3f7547e219ca48c8392d163e786fa627be Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 21 Apr 2021 22:01:33 -0400 Subject: [PATCH 0589/1217] fix memory leak in fix atom/swap reported on MatSci forum: https://matsci.org/t/question-to-fix-atom-swap-function/36135 --- src/MC/fix_atom_swap.cpp | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index 954ce46aa6..d055d57b88 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -117,6 +117,21 @@ FixAtomSwap::FixAtomSwap(LAMMPS *lmp, int narg, char **arg) : } +/* ---------------------------------------------------------------------- */ + +FixAtomSwap::~FixAtomSwap() +{ + memory->destroy(type_list); + memory->destroy(mu); + memory->destroy(qtype); + memory->destroy(sqrt_mass_ratio); + memory->destroy(local_swap_iatom_list); + memory->destroy(local_swap_jatom_list); + if (regionflag) delete [] idregion; + delete random_equal; + delete random_unequal; +} + /* ---------------------------------------------------------------------- parse optional parameters at end of input line ------------------------------------------------------------------------- */ @@ -180,19 +195,6 @@ void FixAtomSwap::options(int narg, char **arg) /* ---------------------------------------------------------------------- */ -FixAtomSwap::~FixAtomSwap() -{ - memory->destroy(type_list); - memory->destroy(mu); - memory->destroy(qtype); - memory->destroy(sqrt_mass_ratio); - if (regionflag) delete [] idregion; - delete random_equal; - delete random_unequal; -} - -/* ---------------------------------------------------------------------- */ - int FixAtomSwap::setmask() { int mask = 0; From 4127faacec2253d8fdd4eb00a1621b6bfa548ee6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 21 Apr 2021 22:02:18 -0400 Subject: [PATCH 0590/1217] substitute unicode general punctuation left/right single/double quotes --- src/utils.cpp | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/utils.cpp b/src/utils.cpp index e733d7eaae..e8f1c63606 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -673,6 +673,18 @@ std::string utils::utf8_subst(const std::string &line) // ZERO WIDTH SPACE (U+200B) if ((in[i] == 0xe2U) && (in[i+1] == 0x80U) && (in[i+2] == 0x8bU)) out += ' ', i += 2; + // LEFT SINGLE QUOTATION MARK (U+2018) + if ((in[i] == 0xe2U) && (in[i+1] == 0x80U) && (in[i+2] == 0x98U)) + out += '\'', i += 2; + // RIGHT SINGLE QUOTATION MARK (U+2019) + if ((in[i] == 0xe2U) && (in[i+1] == 0x80U) && (in[i+2] == 0x99U)) + out += '\'', i += 2; + // LEFT DOUBLE QUOTATION MARK (U+201C) + if ((in[i] == 0xe2U) && (in[i+1] == 0x80U) && (in[i+2] == 0x9cU)) + out += '"', i += 2; + // RIGHT DOUBLE QUOTATION MARK (U+201D) + if ((in[i] == 0xe2U) && (in[i+1] == 0x80U) && (in[i+2] == 0x9dU)) + out += '"', i += 2; // NARROW NO-BREAK SPACE (U+202F) if ((in[i] == 0xe2U) && (in[i+1] == 0x80U) && (in[i+2] == 0xafU)) out += ' ', i += 2; From 0cf1252f1fbf56bfb74d0b8f143547b54ed0c65f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 21 Apr 2021 22:52:32 -0400 Subject: [PATCH 0591/1217] add overload to utils::logmesg() that handles format strings and variable arguments this reduces utils::logmesg(lmp,fmt::format(...)) to utils::logmesg(lmp,...) while still allowing just a single string argument. --- src/utils.cpp | 14 ++++++++------ src/utils.h | 28 +++++++++++++++++++++++++--- 2 files changed, 33 insertions(+), 9 deletions(-) diff --git a/src/utils.cpp b/src/utils.cpp index e733d7eaae..4071b7b61b 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -123,12 +123,7 @@ std::string utils::strfind(const std::string &text, const std::string &pattern) return ""; } -/** This function simplifies the repetitive task of outputting some - * message to both the screen and/or the log file. In combination - * with using fmt::format(), which returns the formatted text - * in a std::string() instance, this can be used to reduce - * operations previously requiring several lines of code to - * a single statement. */ +/* specialization for the case of just a single string argument */ void utils::logmesg(LAMMPS *lmp, const std::string &mesg) { @@ -136,6 +131,13 @@ void utils::logmesg(LAMMPS *lmp, const std::string &mesg) if (lmp->logfile) fputs(mesg.c_str(), lmp->logfile); } +void utils::_internal_logmesg(LAMMPS *lmp, fmt::string_view format, + fmt::format_args args) +{ + if (lmp->screen) fmt::vprint(lmp->screen, format, args); + if (lmp->logfile) fmt::vprint(lmp->logfile, format, args); +} + /* define this here, so we won't have to include the headers everywhere and utils.h will more likely be included anyway. */ diff --git a/src/utils.h b/src/utils.h index ec4dd6ae85..6eed8fd3bc 100644 --- a/src/utils.h +++ b/src/utils.h @@ -17,6 +17,8 @@ /*! \file utils.h */ #include "lmptype.h" +#include "fmt/format.h" + #include #include #include @@ -45,10 +47,30 @@ namespace LAMMPS_NS { std::string strfind(const std::string &text, const std::string &pattern); - /** Send message to screen and logfile, if available + /* Internal function handling the argument list for logmesg(). */ + + void _internal_logmesg(LAMMPS *lmp, fmt::string_view format, + fmt::format_args args); + + /** Send formatted message to screen and logfile, if available * - * \param lmp pointer to LAMMPS class instance - * \param mesg message to be printed */ + * This function simplifies the repetitive task of outputting some + * message to both the screen and/or the log file. The template + * wrapper with fmtlib format and argument processing allows + * this function to work similar to fmt::print(). + * The specialization overload handles the case of no arguments. + * + * \param lmp pointer to LAMMPS class instance + * \param format format string of message to be printed + * \param args arguments to format string */ + + template + void logmesg(LAMMPS *lmp, const S &format, Args&&... args) { + _internal_logmesg(lmp, format, + fmt::make_args_checked(format, args...)); + } + + /** \overload */ void logmesg(LAMMPS *lmp, const std::string &mesg); From d2cdb318aba4058e0458bf5fe4973654217c9228 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 21 Apr 2021 22:53:41 -0400 Subject: [PATCH 0592/1217] apply new logmesg() overload to a bunch of cases. --- src/KSPACE/ewald_disp.cpp | 7 +- src/KSPACE/fix_tune_kspace.cpp | 16 ++-- src/KSPACE/msm_cg.cpp | 9 +-- src/KSPACE/pppm_cg.cpp | 9 +-- src/KSPACE/pppm_disp.cpp | 6 +- src/MC/pair_dsmc.cpp | 3 +- src/MLIAP/mliap_descriptor_snap.cpp | 5 +- src/PLUGIN/plugin.cpp | 40 +++++----- src/POEMS/fix_poems.cpp | 4 +- src/RIGID/fix_rigid.cpp | 3 +- src/RIGID/fix_rigid_small.cpp | 11 ++- src/RIGID/fix_shake.cpp | 14 ++-- src/SHOCK/fix_msst.cpp | 13 ++-- src/SNAP/pair_snap.cpp | 6 +- src/USER-COLVARS/group_ndx.cpp | 4 +- src/USER-COLVARS/ndx_group.cpp | 8 +- src/USER-MISC/fix_orient_eco.cpp | 4 +- src/USER-MISC/fix_pafi.cpp | 2 +- src/USER-PACE/pair_pace.cpp | 12 +-- src/USER-QTB/fix_qbmsst.cpp | 12 +-- src/bond.cpp | 8 +- src/comm.cpp | 2 +- src/create_atoms.cpp | 7 +- src/create_bonds.cpp | 4 +- src/delete_bonds.cpp | 20 ++--- src/finish.cpp | 112 +++++++++++++--------------- src/group.cpp | 4 +- src/lattice.cpp | 5 +- src/modify.cpp | 20 ++--- src/molecule.cpp | 18 ++--- src/output.cpp | 5 +- src/pair.cpp | 8 +- src/potential_file_reader.cpp | 4 +- src/read_data.cpp | 27 ++++--- src/read_dump.cpp | 15 ++-- src/read_restart.cpp | 35 +++++---- src/replicate.cpp | 18 ++--- src/reset_mol_ids.cpp | 8 +- src/set.cpp | 8 +- src/special.cpp | 29 ++++--- src/timer.cpp | 5 +- src/utils.cpp | 6 +- 42 files changed, 259 insertions(+), 297 deletions(-) diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index 89eeb4b3eb..927485ef84 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -274,8 +274,8 @@ void EwaldDisp::init() } if (comm->me == 0) - utils::logmesg(lmp,fmt::format(" G vector = {:.8g}, accuracy = {:.8g}\n", - g_ewald,accuracy)); + utils::logmesg(lmp," G vector = {:.8g}, accuracy = {:.8g}\n", + g_ewald,accuracy); // apply coulomb g_ewald to dispersion unless it is explicitly set @@ -339,8 +339,7 @@ void EwaldDisp::setup() if (!(first_output||comm->me)) { first_output = 1; - utils::logmesg(lmp,fmt::format(" vectors: nbox = {}, nkvec = {}\n", - nbox, nkvec)); + utils::logmesg(lmp," vectors: nbox = {}, nkvec = {}\n", nbox, nkvec); } } diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index 5f53561e20..55960f1c33 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -151,10 +151,8 @@ void FixTuneKspace::pre_exchange() } else if (niter == 4) { store_old_kspace_settings(); if (comm->me == 0) - utils::logmesg(lmp,fmt::format("ewald_time = {}\n" - "pppm_time = {}\n" - "msm_time = {}\n", - ewald_time, pppm_time, msm_time)); + utils::logmesg(lmp,"ewald_time = {}\npppm_time = {}\nmsm_time = {}\n", + ewald_time, pppm_time, msm_time); // switch to fastest one if (msm_time == 0.0) msm_time = 1.0e300; kspace_style = "ewald"; @@ -243,7 +241,7 @@ void FixTuneKspace::update_pair_style(const std::string &new_pair_style, force->pair->write_restart(p_pair_settings_file); rewind(p_pair_settings_file); if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Creating new pair style: {}\n",new_pair_style)); + utils::logmesg(lmp,"Creating new pair style: {}\n",new_pair_style); // delete old pair style and create new one force->create_pair(new_pair_style.c_str(),1); @@ -254,8 +252,7 @@ void FixTuneKspace::update_pair_style(const std::string &new_pair_style, double *pcutoff = (double *) force->pair->extract("cut_coul",itmp); double current_cutoff = *pcutoff; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Coulomb cutoff for real space: {}\n", - current_cutoff)); + utils::logmesg(lmp,"Coulomb cutoff for real space: {}\n",current_cutoff); // close temporary file fclose(p_pair_settings_file); @@ -310,8 +307,7 @@ void FixTuneKspace::adjust_rcut(double time) double *p_cutoff = (double *) force->pair->extract("cut_coul",itmp); double current_cutoff = *p_cutoff; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Old Coulomb cutoff for real space: {}\n", - current_cutoff)); + utils::logmesg(lmp,"Old Coulomb cutoff for real space: {}\n",current_cutoff); // use Brent's method from Numerical Recipes to find optimal real space cutoff @@ -382,7 +378,7 @@ void FixTuneKspace::adjust_rcut(double time) double *new_cutoff = (double *) force->pair->extract("cut_coul",itmp); current_cutoff = *new_cutoff; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Adjusted Coulomb cutoff for real space: {}\n", current_cutoff)); + utils::logmesg(lmp,"Adjusted Coulomb cutoff for real space: {}\n", current_cutoff); store_old_kspace_settings(); update_pair_style(pair_style,pair_cut_coul); diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp index 4c9384f13e..9781dee2ea 100644 --- a/src/KSPACE/msm_cg.cpp +++ b/src/KSPACE/msm_cg.cpp @@ -132,11 +132,10 @@ void MSMCG::compute(int eflag, int vflag) / static_cast(atom->natoms); if (me == 0) - utils::logmesg(lmp,fmt::format(" MSM/cg optimization cutoff: {:.8}\n" - " Total charged atoms: {:.1f}%\n" - " Min/max charged atoms/proc: {:.1f}%" - " {:.1f}%\n",smallq, - charged_frac,charged_fmin,charged_fmax)); + utils::logmesg(lmp," MSM/cg optimization cutoff: {:.8}\n" + " Total charged atoms: {:.1f}%\n" + " Min/max charged atoms/proc: {:.1f}% {:.1f}%\n", + smallq,charged_frac,charged_fmin,charged_fmax); } // only need to rebuild this list after a neighbor list update diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp index a96e112393..b31919f767 100644 --- a/src/KSPACE/pppm_cg.cpp +++ b/src/KSPACE/pppm_cg.cpp @@ -148,11 +148,10 @@ void PPPMCG::compute(int eflag, int vflag) / static_cast(atom->natoms); if (me == 0) - utils::logmesg(lmp,fmt::format(" PPPM/cg optimization cutoff: {:.8g}\n" - " Total charged atoms: {:.1f}%\n" - " Min/max charged atoms/proc: {:.1f}%" - " {:.1f}%\n",smallq, - charged_frac,charged_fmin,charged_fmax)); + utils::logmesg(lmp," PPPM/cg optimization cutoff: {:.8g}\n" + " Total charged atoms: {:.1f}%\n" + " Min/max charged atoms/proc: {:.1f}% {:.1f}%\n", + smallq,charged_frac,charged_fmin,charged_fmax); } // only need to rebuild this list after a neighbor list update diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index 58db6e51fc..1844301ac5 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -1392,8 +1392,7 @@ void PPPMDisp::init_coeffs() if (function[2] && nsplit <= 6) { if (me == 0) - utils::logmesg(lmp,fmt::format(" Using {} instead of 7 structure " - "factors\n",nsplit)); + utils::logmesg(lmp," Using {} instead of 7 structure factors\n",nsplit); //function[3] = 1; //function[2] = 0; if (B) delete [] B; // remove this when un-comment previous 2 lines @@ -1406,8 +1405,7 @@ void PPPMDisp::init_coeffs() if (function[3]) { if (me == 0) - utils::logmesg(lmp,fmt::format(" Using {} structure factors\n", - nsplit)); + utils::logmesg(lmp," Using {} structure factors\n",nsplit); if (nsplit > 9) error->warning(FLERR,"Simulations might be very slow " "because of large number of structure factors"); diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index 1bcb9f6493..7064a500d2 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -283,8 +283,7 @@ void PairDSMC::init_style() cellz = (domain->boxhi[2] - domain->boxlo[2])/ncellsz; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("DSMC cell size = {} x {} x {}\n", - cellx,celly,cellz)); + utils::logmesg(lmp,"DSMC cell size = {} x {} x {}\n",cellx,celly,cellz); total_ncells = ncellsx*ncellsy*ncellsz; vol = cellx*celly*cellz; diff --git a/src/MLIAP/mliap_descriptor_snap.cpp b/src/MLIAP/mliap_descriptor_snap.cpp index 0fdc548fc1..5c73cb64df 100644 --- a/src/MLIAP/mliap_descriptor_snap.cpp +++ b/src/MLIAP/mliap_descriptor_snap.cpp @@ -412,9 +412,8 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename) char* keywd = strtok(line,"' \t\n\r\f"); char* keyval = strtok(nullptr,"' \t\n\r\f"); - if (comm->me == 0) { - utils::logmesg(lmp, fmt::format("SNAP keyword {} {} \n", keywd, keyval)); - } + if (comm->me == 0) + utils::logmesg(lmp,"SNAP keyword {} {} \n", keywd, keyval); // check for keywords with one value per element diff --git a/src/PLUGIN/plugin.cpp b/src/PLUGIN/plugin.cpp index d311b64520..4434b28d16 100644 --- a/src/PLUGIN/plugin.cpp +++ b/src/PLUGIN/plugin.cpp @@ -69,8 +69,8 @@ namespace LAMMPS_NS utils::logmesg(lmp,"Currently loaded plugins\n"); for (int i=0; i < num; ++i) { auto entry = plugin_get_info(i); - utils::logmesg(lmp,fmt::format("{:4}: {} style plugin {}\n", - i+1,entry->style,entry->name)); + utils::logmesg(lmp,"{:4}: {} style plugin {}\n", + i+1,entry->style,entry->name); } } } else error->all(FLERR,"Illegal plugin command"); @@ -96,8 +96,7 @@ namespace LAMMPS_NS void *dso = dlopen(file,RTLD_NOW|RTLD_GLOBAL); if (dso == nullptr) { if (me == 0) - utils::logmesg(lmp,fmt::format("Open of file {} failed: {}\n", - file,dlerror())); + utils::logmesg(lmp,"Open of file {} failed: {}\n",file,dlerror()); return; } @@ -110,8 +109,8 @@ namespace LAMMPS_NS dlclose(dso); if (me == 0) - utils::logmesg(lmp,fmt::format("Plugin symbol lookup failure in " - "file {}: {}\n",file,dlerror())); + utils::logmesg(lmp,"Plugin symbol lookup failure in file {}: {}\n", + file,dlerror()); return; } @@ -144,20 +143,19 @@ namespace LAMMPS_NS int idx = plugin_find(plugin->style,plugin->name); if (idx >= 0) { if (me == 0) - utils::logmesg(lmp,fmt::format("Ignoring load of {} style {}: must " - "unload existing {} plugin first\n", - plugin->style,plugin->name,plugin->name)); + utils::logmesg(lmp,"Ignoring load of {} style {}: must " + "unload existing {} plugin first\n", + plugin->style,plugin->name,plugin->name); return; } if (me == 0) { - utils::logmesg(lmp,fmt::format("Loading plugin: {} by {}\n", - plugin->info,plugin->author)); + utils::logmesg(lmp,"Loading plugin: {} by {}\n", + plugin->info,plugin->author); // print version info only if the versions of host and plugin don't match if ((plugin->version) && (strcmp(plugin->version,lmp->version) != 0)) - utils::logmesg(lmp,fmt::format(" compiled for LAMMPS version {} " - "loaded into LAMMPS version {}\n", - plugin->version,lmp->version)); + utils::logmesg(lmp," compiled for LAMMPS version {}, loaded into " + "LAMMPS version {}\n",plugin->version,lmp->version); } pluginlist.push_back(*plugin); @@ -260,8 +258,8 @@ namespace LAMMPS_NS (*command_map)[plugin->name] = (Input::CommandCreator)plugin->creator.v1; } else { - utils::logmesg(lmp,fmt::format("Loading plugin for {} styles not " - "yet implemented\n",pstyle)); + utils::logmesg(lmp,"Loading plugins for {} styles not " + "yet implemented\n",pstyle); pluginlist.pop_back(); } #endif @@ -285,8 +283,8 @@ namespace LAMMPS_NS && (strcmp(style,"fix") != 0) && (strcmp(style,"region") != 0) && (strcmp(style,"command") != 0)) { if (me == 0) - utils::logmesg(lmp,fmt::format("Ignoring unload: {} is not a " - "supported plugin style\n",style)); + utils::logmesg(lmp,"Ignoring unload: {} is not a " + "supported plugin style\n",style); return; } @@ -294,8 +292,8 @@ namespace LAMMPS_NS int idx = plugin_find(style,name); if (idx < 0) { if (me == 0) - utils::logmesg(lmp,fmt::format("Ignoring unload of {} style {}: not " - "loaded from a plugin\n",style,name)); + utils::logmesg(lmp,"Ignoring unload of {} style {}: not " + "loaded from a plugin\n",style,name); return; } @@ -305,7 +303,7 @@ namespace LAMMPS_NS // remove selected plugin from list of plugins if (me == 0) - utils::logmesg(lmp,fmt::format("Unloading {} style {}\n",style,name)); + utils::logmesg(lmp,"Unloading {} style {}\n",style,name); plugin_erase(style,name); // remove style of given name from corresponding map diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index 3d5b3697f7..d185523537 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -277,8 +277,8 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) : nsum -= njoint; if (me == 0) - utils::logmesg(lmp,fmt::format("{} clusters, {} bodies, {} joints, {} atoms\n", - ncluster,nbody,njoint,nsum)); + utils::logmesg(lmp,"{} clusters, {} bodies, {} joints, {} atoms\n", + ncluster,nbody,njoint,nsum); } /* ---------------------------------------------------------------------- diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 3cd4f5dbc8..91cb0ce82c 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -602,8 +602,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : for (ibody = 0; ibody < nbody; ibody++) nsum += nrigid[ibody]; if (me == 0) - utils::logmesg(lmp,fmt::format(" {} rigid bodies with {} atoms\n", - nbody,nsum)); + utils::logmesg(lmp," {} rigid bodies with {} atoms\n",nbody,nsum); } /* ---------------------------------------------------------------------- */ diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 14bd9f7a55..c1c956f08e 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -401,8 +401,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : if (customflag) delete [] bodyID; if (comm->me == 0) - utils::logmesg(lmp,fmt::format(" create bodies CPU = {:.3f} seconds\n", - MPI_Wtime()-time1)); + utils::logmesg(lmp," create bodies CPU = {:.3f} seconds\n", + MPI_Wtime()-time1); // set nlocal_body and allocate bodies I own @@ -460,10 +460,9 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : MPI_Allreduce(&atomone,&atomall,1,MPI_LMP_BIGINT,MPI_SUM,world); if (me == 0) { - auto msg = fmt::format(" {} rigid bodies with {} atoms\n",nbody,atomall); - msg += fmt::format(" {:.8} = max distance from body owner to body atom\n", - maxextent); - utils::logmesg(lmp,msg); + utils::logmesg(lmp," {} rigid bodies with {} atoms\n" + " {:.8} = max distance from body owner to body atom\n", + nbody,atomall,maxextent); } // initialize Marsaglia RNG with processor-unique seed diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 5662e63c88..957898d361 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -226,8 +226,8 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) : find_clusters(); if (comm->me == 0) - utils::logmesg(lmp,fmt::format(" find clusters CPU = {:.3f} seconds\n", - MPI_Wtime()-time1)); + utils::logmesg(lmp," find clusters CPU = {:.3f} seconds\n", + MPI_Wtime()-time1); // initialize list of SHAKE clusters to constrain @@ -1007,11 +1007,11 @@ void FixShake::find_clusters() MPI_Allreduce(&tmp,&count4,1,MPI_INT,MPI_SUM,world); if (me == 0) { - auto mesg = fmt::format("{:>8} = # of size 2 clusters\n",count2/2); - mesg += fmt::format("{:>8} = # of size 3 clusters\n",count3/3); - mesg += fmt::format("{:>8} = # of size 4 clusters\n",count4/4); - mesg += fmt::format("{:>8} = # of frozen angles\n",count1/3); - utils::logmesg(lmp,mesg); + utils::logmesg(lmp,"{:>8} = # of size 2 clusters\n" + "{:>8} = # of size 3 clusters\n" + "{:>8} = # of size 4 clusters\n" + "{:>8} = # of frozen angles\n", + count2/2,count3/3,count4/4,count1/3); } } diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp index 7a1efa064f..9e6ef32f5a 100644 --- a/src/SHOCK/fix_msst.cpp +++ b/src/SHOCK/fix_msst.cpp @@ -327,7 +327,7 @@ void FixMSST::setup(int /*vflag*/) v0 = compute_vol(); v0_set = 1; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Fix MSST v0 = {:.8g}\n", v0)); + utils::logmesg(lmp,"Fix MSST v0 = {:.8g}\n", v0); } if (p0_set == 0) { @@ -335,7 +335,7 @@ void FixMSST::setup(int /*vflag*/) p0_set = 1; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Fix MSST p0 = {:.8g}\n", p0)); + utils::logmesg(lmp,"Fix MSST p0 = {:.8g}\n", p0); } if (e0_set == 0) { @@ -343,7 +343,7 @@ void FixMSST::setup(int /*vflag*/) e0_set = 1; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Fix MSST e0 = {:.8g}\n", e0)); + utils::logmesg(lmp,"Fix MSST e0 = {:.8g}\n", e0); } temperature->compute_vector(); @@ -364,10 +364,9 @@ void FixMSST::setup(int /*vflag*/) double fac2 = omega[direction]/v0; if ( comm->me == 0 && tscale != 1.0) - utils::logmesg(lmp,fmt::format("Fix MSST initial strain rate of " - "{:.8g} established by reducing " - "temperature by factor of {:.8g}\n", - fac2,tscale)); + utils::logmesg(lmp,"Fix MSST initial strain rate of {:.8g} " + "established by reducing temperature by factor " + "of {:.8g}\n",fac2,tscale); for (int i = 0; i < atom->nlocal; i++) { if (mask[i] & groupbit) { for (int k = 0; k < 3; k++) { diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index ae0023ddec..b4ee3c870a 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -565,8 +565,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) wjelem[jelem] = utils::numeric(FLERR,words[2].c_str(),false,lmp); if (comm->me == 0) - utils::logmesg(lmp,fmt::format("SNAP Element = {}, Radius {}, Weight {}\n", - elements[jelem], radelem[jelem], wjelem[jelem])); + utils::logmesg(lmp,"SNAP Element = {}, Radius {}, Weight {}\n", + elements[jelem], radelem[jelem], wjelem[jelem]); for (int icoeff = 0; icoeff < ncoeffall; icoeff++) { if (comm->me == 0) { @@ -660,7 +660,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) auto keyval = words[1]; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("SNAP keyword {} {}\n",keywd,keyval)); + utils::logmesg(lmp,"SNAP keyword {} {}\n",keywd,keyval); if (keywd == "rcutfac") { rcutfac = utils::numeric(FLERR,keyval.c_str(),false,lmp); diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp index 995f60ac85..26711026e8 100644 --- a/src/USER-COLVARS/group_ndx.cpp +++ b/src/USER-COLVARS/group_ndx.cpp @@ -58,7 +58,7 @@ void Group2Ndx::command(int narg, char **arg) if (fp == nullptr) error->one(FLERR,fmt::format("Cannot open index file for writing: {}", utils::getsyserror())); - utils::logmesg(lmp,fmt::format("Writing groups to index file {}:\n",arg[0])); + utils::logmesg(lmp,"Writing groups to index file {}:\n",arg[0]); } if (narg == 1) { // write out all groups @@ -86,7 +86,7 @@ void Group2Ndx::write_group(FILE *fp, int gid) int lnum, width, cols; if (comm->me == 0) { - utils::logmesg(lmp,fmt::format(" writing group {}...",group->names[gid])); + utils::logmesg(lmp," writing group {}...",group->names[gid]); // the "all" group in LAMMPS is called "System" in Gromacs if (gid == 0) { diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index d8d5632b06..6b9a69ccd3 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -88,7 +88,7 @@ void Ndx2Group::command(int narg, char **arg) if (fp == nullptr) error->one(FLERR,fmt::format("Cannot open index file for reading: {}", utils::getsyserror())); - utils::logmesg(lmp,fmt::format("Reading groups from index file {}:\n",arg[0])); + utils::logmesg(lmp,"Reading groups from index file {}:\n",arg[0]); } if (narg == 1) { // restore all groups @@ -103,7 +103,7 @@ void Ndx2Group::command(int narg, char **arg) continue; } - utils::logmesg(lmp,fmt::format(" Processing group '{}'\n",name)); + utils::logmesg(lmp," Processing group '{}'\n",name); len = name.size()+1; MPI_Bcast(&len,1,MPI_INT,0,world); if (len > 1) { @@ -147,8 +147,8 @@ void Ndx2Group::command(int narg, char **arg) // find named section, search from beginning of file rewind(fp); name = find_section(fp,arg[idx]); - utils::logmesg(lmp,fmt::format(" {} group '{}'\n", name.size() - ? "Processing" : "Skipping",arg[idx])); + utils::logmesg(lmp," {} group '{}'\n", name.size() + ? "Processing" : "Skipping",arg[idx]); len = name.size()+1; MPI_Bcast(&len,1,MPI_INT,0,world); if (len > 1) { diff --git a/src/USER-MISC/fix_orient_eco.cpp b/src/USER-MISC/fix_orient_eco.cpp index 56da3cd6a1..b8b3a00354 100644 --- a/src/USER-MISC/fix_orient_eco.cpp +++ b/src/USER-MISC/fix_orient_eco.cpp @@ -162,8 +162,8 @@ void FixOrientECO::init() { // compute normalization factor int neigh = get_norm(); if (me == 0) { - utils::logmesg(lmp,fmt::format(" fix orient/eco: cutoff={} norm_fac={} " - "neighbors={}\n", r_cut, norm_fac, neigh)); + utils::logmesg(lmp," fix orient/eco: cutoff={} norm_fac={} " + "neighbors={}\n", r_cut, norm_fac, neigh); } inv_norm_fac = 1.0 / norm_fac; diff --git a/src/USER-MISC/fix_pafi.cpp b/src/USER-MISC/fix_pafi.cpp index 7d5216f540..472bb8498f 100644 --- a/src/USER-MISC/fix_pafi.cpp +++ b/src/USER-MISC/fix_pafi.cpp @@ -86,7 +86,7 @@ FixPAFI::FixPAFI(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute for fix pafi must have 9 fields per atom"); if (comm->me==0) - utils::logmesg(lmp,fmt::format("fix pafi compute name,style: {},{}\n",computename,PathCompute->style)); + utils::logmesg(lmp,"fix pafi compute name,style: {},{}\n",computename,PathCompute->style); respa_level_support = 1; ilevel_respa = nlevels_respa = 0; diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index d6eda0f511..ae13859968 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -280,8 +280,8 @@ void PairPACE::settings(int narg, char **arg) { } if (comm->me == 0) { - utils::logmesg(lmp,fmt::format("ACE version: {}.{}.{}\n", - VERSION_YEAR, VERSION_MONTH, VERSION_DAY)); + utils::logmesg(lmp,"ACE version: {}.{}.{}\n", + VERSION_YEAR, VERSION_MONTH, VERSION_DAY); if (recursive) utils::logmesg(lmp,"Recursive evaluator is used\n"); else utils::logmesg(lmp,"Product evaluator is used\n"); } @@ -303,7 +303,7 @@ void PairPACE::coeff(int narg, char **arg) { //load potential file aceimpl->basis_set = new ACECTildeBasisSet(); if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Loading {}\n", potential_file_name)); + utils::logmesg(lmp,"Loading {}\n", potential_file_name); aceimpl->basis_set->load(potential_file_name); if (comm->me == 0) { @@ -312,7 +312,7 @@ void PairPACE::coeff(int narg, char **arg) { for (SPECIES_TYPE mu = 0; mu < aceimpl->basis_set->nelements; mu++) { int n_r1 = aceimpl->basis_set->total_basis_size_rank1[mu]; int n = aceimpl->basis_set->total_basis_size[mu]; - utils::logmesg(lmp,fmt::format("\t{}: {} (r=1) {} (r>1)\n", aceimpl->basis_set->elements_name[mu], n_r1, n)); + utils::logmesg(lmp,"\t{}: {} (r=1) {} (r>1)\n", aceimpl->basis_set->elements_name[mu], n_r1, n); } } @@ -334,8 +334,8 @@ void PairPACE::coeff(int narg, char **arg) { SPECIES_TYPE mu = aceimpl->basis_set->get_species_index_by_name(elemname); if (mu != -1) { if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Mapping LAMMPS atom type #{}({}) -> " - "ACE species type #{}\n", i, elemname, mu)); + utils::logmesg(lmp,"Mapping LAMMPS atom type #{}({}) -> " + "ACE species type #{}\n", i, elemname, mu); map[i] = mu; aceimpl->ace->element_type_mapping(i) = mu; // set up LAMMPS atom type to ACE species mapping for ace evaluator } else { diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp index a9dfb83f06..a21f5a59f0 100644 --- a/src/USER-QTB/fix_qbmsst.cpp +++ b/src/USER-QTB/fix_qbmsst.cpp @@ -415,7 +415,7 @@ void FixQBMSST::setup(int /*vflag*/) v0 = compute_vol(); v0_set = 1; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Fix QBMSST v0 = {:12.5e}\n", v0)); + utils::logmesg(lmp,"Fix QBMSST v0 = {:12.5e}\n", v0); } if (p0_set == 0) { @@ -423,7 +423,7 @@ void FixQBMSST::setup(int /*vflag*/) p0_set = 1; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Fix QBMSST p0 = {:12.5e}\n", p0)); + utils::logmesg(lmp,"Fix QBMSST p0 = {:12.5e}\n", p0); } if (e0_set == 0) { @@ -432,7 +432,7 @@ void FixQBMSST::setup(int /*vflag*/) old_eavg = e0; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Fix QBMSST e0 = to be {:12.5e}\n",e0)); + utils::logmesg(lmp,"Fix QBMSST e0 = to be {:12.5e}\n",e0); } temperature->compute_vector(); @@ -452,9 +452,9 @@ void FixQBMSST::setup(int /*vflag*/) double fac2 = omega[direction]/v0; if ( comm->me == 0 && tscale != 1.0) - utils::logmesg(lmp,fmt::format("Fix QBMSST initial strain rate of {:12.5e} " - "established by reducing temperature by " - "factor of {:12.5e}\n",fac2,tscale)); + utils::logmesg(lmp,"Fix QBMSST initial strain rate of {:12.5e} " + "established by reducing temperature by " + "factor of {:12.5e}\n",fac2,tscale); for (int i = 0; i < atom->nlocal; i++) { if (mask[i] & groupbit) { for (int k = 0; k < 3; k++) { diff --git a/src/bond.cpp b/src/bond.cpp index 1db4681c71..570d921abb 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -279,15 +279,15 @@ void Bond::write_file(int narg, char **arg) units, update->unit_style)); } std::string date = utils::get_potential_date(table_file,"table"); - utils::logmesg(lmp,fmt::format("Appending to table file {} with " - "DATE: {}\n", table_file, date)); + utils::logmesg(lmp,"Appending to table file {} with " + "DATE: {}\n", table_file, date); fp = fopen(table_file.c_str(),"a"); } else { char datebuf[16]; time_t tv = time(nullptr); strftime(datebuf,15,"%Y-%m-%d",localtime(&tv)); - utils::logmesg(lmp,fmt::format("Creating table file {} with " - "DATE: {}\n", table_file, datebuf)); + utils::logmesg(lmp,"Creating table file {} with " + "DATE: {}\n", table_file, datebuf); fp = fopen(table_file.c_str(),"w"); if (fp) fmt::print(fp,"# DATE: {} UNITS: {} Created by bond_write\n", datebuf, update->unit_style); diff --git a/src/comm.cpp b/src/comm.cpp index 6d3f72d9c0..85b6669d86 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -103,7 +103,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) if (!lmp->kokkos) omp_set_num_threads(nthreads); if (me == 0) - utils::logmesg(lmp,fmt::format(" using {} OpenMP thread(s) per MPI task\n",nthreads)); + utils::logmesg(lmp," using {} OpenMP thread(s) per MPI task\n",nthreads); #endif } diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 7591ae7587..0cec1eba33 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -596,10 +596,9 @@ void CreateAtoms::command(int narg, char **arg) MPI_Barrier(world); if (me == 0) - utils::logmesg(lmp, fmt::format("Created {} atoms\n" - " create_atoms CPU = {:.3f} seconds\n", - atom->natoms - natoms_previous, - MPI_Wtime() - time1)); + utils::logmesg(lmp,"Created {} atoms\n" + " create_atoms CPU = {:.3f} seconds\n", + atom->natoms - natoms_previous, MPI_Wtime() - time1); } /* ---------------------------------------------------------------------- diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index bedbe4b436..aba0178368 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -320,8 +320,8 @@ void CreateBonds::many() bigint nadd_bonds = atom->nbonds - nbonds_previous; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Added {} bonds, new total = {}\n", - nadd_bonds,atom->nbonds)); + utils::logmesg(lmp,"Added {} bonds, new total = {}\n", + nadd_bonds,atom->nbonds); } /* ---------------------------------------------------------------------- */ diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp index 2bb46e7564..74029c8d5b 100644 --- a/src/delete_bonds.cpp +++ b/src/delete_bonds.cpp @@ -535,24 +535,20 @@ void DeleteBonds::command(int narg, char **arg) if (comm->me == 0) { if (atom->avec->bonds_allow) - utils::logmesg(lmp,fmt::format(" {} total bonds, " - "{} turned on, {} turned off\n", - atom->nbonds,bond_on,bond_off)); + utils::logmesg(lmp," {} total bonds, {} turned on, {} turned off\n", + atom->nbonds,bond_on,bond_off); if (atom->avec->angles_allow) - utils::logmesg(lmp,fmt::format(" {} total angles, " - "{} turned on, {} turned off\n", - atom->nangles,angle_on,angle_off)); + utils::logmesg(lmp," {} total angles, {} turned on, {} turned off\n", + atom->nangles,angle_on,angle_off); if (atom->avec->dihedrals_allow) - utils::logmesg(lmp,fmt::format(" {} total dihedrals, " - "{} turned on, {} turned off\n", - atom->ndihedrals,dihedral_on,dihedral_off)); + utils::logmesg(lmp," {} total dihedrals, {} turned on, {} turned off\n", + atom->ndihedrals,dihedral_on,dihedral_off); if (atom->avec->impropers_allow) - utils::logmesg(lmp,fmt::format(" {} total impropers, " - "{} turned on, {} turned off\n", - atom->nimpropers,improper_on,improper_off)); + utils::logmesg(lmp," {} total impropers, {} turned on, {} turned off\n", + atom->nimpropers,improper_on,improper_off); } // re-compute special list if requested diff --git a/src/finish.cpp b/src/finish.cpp index 28596e3a72..42dc163e13 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -121,9 +121,9 @@ void Finish::end(int flag) if (me == 0) { int ntasks = nprocs * nthreads; - utils::logmesg(lmp,fmt::format("Loop time of {:.6g} on {} procs for " - "{} steps with {} atoms\n\n",time_loop, - ntasks,update->nsteps,atom->natoms)); + utils::logmesg(lmp,"Loop time of {:.6g} on {} procs for " + "{} steps with {} atoms\n\n",time_loop, + ntasks,update->nsteps,atom->natoms); // Gromacs/NAMD-style performance metric for suitable unit settings @@ -141,20 +141,18 @@ void Finish::end(int flag) if (strcmp(update->unit_style,"lj") == 0) { double tau_day = 24.0*3600.0 / t_step * update->dt / one_fs; - utils::logmesg(lmp,fmt::format("Performance: {:.3f} tau/day, {:.3f} " - "timesteps/s\n",tau_day,step_t)); + utils::logmesg(lmp,"Performance: {:.3f} tau/day, {:.3f} " + "timesteps/s\n",tau_day,step_t); } else if (strcmp(update->unit_style,"electron") == 0) { double hrs_fs = t_step / update->dt * one_fs / 3600.0; double fs_day = 24.0*3600.0 / t_step * update->dt / one_fs; - utils::logmesg(lmp,fmt::format("Performance: {:.3f} fs/day, {:.3f} " - "hours/fs, {:.3f} timesteps/s\n", - fs_day,hrs_fs,step_t)); + utils::logmesg(lmp,"Performance: {:.3f} fs/day, {:.3f} hours/fs, " + "{:.3f} timesteps/s\n",fs_day,hrs_fs,step_t); } else { double hrs_ns = t_step / update->dt * 1000000.0 * one_fs / 3600.0; double ns_day = 24.0*3600.0 / t_step * update->dt / one_fs/1000000.0; - utils::logmesg(lmp,fmt::format("Performance: {:.3f} ns/day, {:.3f} " - "hours/ns, {:.3f} timesteps/s\n", - ns_day,hrs_ns,step_t)); + utils::logmesg(lmp,"Performance: {:.3f} ns/day, {:.3f} hours/ns, " + "{:.3f} timesteps/s\n",ns_day,hrs_ns,step_t); } } @@ -162,17 +160,15 @@ void Finish::end(int flag) if (timeflag) { if (lmp->kokkos) { - utils::logmesg(lmp,fmt::format("{:.1f}% CPU use with {} MPI tasks " - "x {} OpenMP threads\n",cpu_loop,nprocs, - lmp->kokkos->nthreads)); + utils::logmesg(lmp,"{:.1f}% CPU use with {} MPI tasks x {} OpenMP " + "threads\n",cpu_loop,nprocs,lmp->kokkos->nthreads); } else { #if defined(_OPENMP) - utils::logmesg(lmp,fmt::format("{:.1f}% CPU use with {} MPI tasks " - "x {} OpenMP threads\n", - cpu_loop,nprocs,nthreads)); + utils::logmesg(lmp,"{:.1f}% CPU use with {} MPI tasks x {} OpenMP " + "threads\n",cpu_loop,nprocs,nthreads); #else - utils::logmesg(lmp,fmt::format("{:.1f}% CPU use with {} MPI tasks " - "x no OpenMP threads\n",cpu_loop,nprocs)); + utils::logmesg(lmp,"{:.1f}% CPU use with {} MPI tasks " + "x no OpenMP threads\n",cpu_loop,nprocs); #endif } } @@ -225,33 +221,33 @@ void Finish::end(int flag) time = timer->get_wall(Timer::DEPHASE); MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" Dephase time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," Dephase time (%) = {} ({})\n", + time,time/time_loop*100.0); time = timer->get_wall(Timer::DYNAMICS); MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" Dynamics time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," Dynamics time (%) = {} ({})\n", + time,time/time_loop*100.0); time = timer->get_wall(Timer::QUENCH); MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" Quench time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," Quench time (%) = {} ({})\n", + time,time/time_loop*100.0); time = timer->get_wall(Timer::REPCOMM); MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" Comm time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," Comm time (%) = {} ({})\n", + time,time/time_loop*100.0); time = timer->get_wall(Timer::REPOUT); MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" Output time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," Output time (%) = {} ({})\n", + time,time/time_loop*100.0); time = time_other; MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" Other time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," Other time (%) = {} ({})\n", + time,time/time_loop*100.0); } // TAD stats @@ -262,33 +258,33 @@ void Finish::end(int flag) time = timer->get_wall(Timer::NEB); MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" NEB time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," NEB time (%) = {} ({})\n", + time,time/time_loop*100.0); time = timer->get_wall(Timer::DYNAMICS); MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" Dynamics time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," Dynamics time (%) = {} ({})\n", + time,time/time_loop*100.0); time = timer->get_wall(Timer::QUENCH); MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" Quench time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," Quench time (%) = {} ({})\n", + time,time/time_loop*100.0); time = timer->get_wall(Timer::REPCOMM); MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" Comm time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," Comm time (%) = {} ({})\n", + time,time/time_loop*100.0); time = timer->get_wall(Timer::REPOUT); MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" Output time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," Output time (%) = {} ({})\n", + time,time/time_loop*100.0); time = time_other; MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" Other time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," Other time (%) = {} ({})\n", + time,time/time_loop*100.0); } // HYPER stats @@ -299,18 +295,18 @@ void Finish::end(int flag) time = timer->get_wall(Timer::DYNAMICS); MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" Dynamics time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," Dynamics time (%) = {} ({})\n", + time,time/time_loop*100.0); time = timer->get_wall(Timer::QUENCH); MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" Quench time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," Quench time (%) = {} ({})\n", + time,time/time_loop*100.0); time = time_other; MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world); time = tmp/nprocs; - if (me == 0) utils::logmesg(lmp,fmt::format(" Other time (%) = {} ({})\n", - time,time/time_loop*100.0)); + if (me == 0) utils::logmesg(lmp," Other time (%) = {} ({})\n", + time,time/time_loop*100.0); } // further timing breakdowns @@ -358,13 +354,11 @@ void Finish::end(int flag) if (me == 0) { if (timer->has_full()) - utils::logmesg(lmp,fmt::format("Other | | {:<10.4g} | " - " | | |{:6.2f}\n", - time,time/time_loop*100.0)); + utils::logmesg(lmp,"Other | | {:<10.4g} | | " + " | |{:6.2f}\n",time,time/time_loop*100.0); else - utils::logmesg(lmp,fmt::format("Other | | {:<10.4g} | " - " | |{:6.2f}\n", - time,time/time_loop*100.0)); + utils::logmesg(lmp,"Other | | {:<10.4g} | | " + " |{:6.2f}\n",time,time/time_loop*100.0); } } @@ -388,7 +382,7 @@ void Finish::end(int flag) "\nThread timing breakdown (MPI rank {}):\nTotal threaded time {:.4g} / {:.1f}%\n" "Section | min time | avg time | max time |%varavg| %total\n" "---------------------------------------------------------------\n"; - utils::logmesg(lmp,fmt::format(thr_fmt,me,thr_total,thr_total/time_loop*100.0)); + utils::logmesg(lmp,thr_fmt,me,thr_total,thr_total/time_loop*100.0); omp_times(fixomp,"Pair",Timer::PAIR,nthreads,screen,logfile); if (atom->molecular != Atom::ATOMIC) @@ -460,9 +454,9 @@ void Finish::end(int flag) } else fraction = flop3 = flop1 = 0.0; if (me == 0) - utils::logmesg(lmp,fmt::format("FFT time (% of Kspce) = {:.6} ({:.4})\n" - "FFT Gflps 3d (1d only) = {:.8} {:.8}\n", - time3d,fraction,flop3,flop1)); + utils::logmesg(lmp,"FFT time (% of Kspce) = {:.6} ({:.4})\n" + "FFT Gflps 3d (1d only) = {:.8} {:.8}\n", + time3d,fraction,flop3,flop1); } if (histoflag) { diff --git a/src/group.cpp b/src/group.cpp index 9e140779ef..997214cbc7 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -535,9 +535,9 @@ void Group::assign(int narg, char **arg) if (me == 0) { if (dynamic[igroup]) - utils::logmesg(lmp,fmt::format("dynamic group {} defined\n",names[igroup])); + utils::logmesg(lmp,"dynamic group {} defined\n",names[igroup]); else - utils::logmesg(lmp,fmt::format("{:.15g} atoms in group {}\n",all,names[igroup])); + utils::logmesg(lmp,"{:.15g} atoms in group {}\n",all,names[igroup]); } } diff --git a/src/lattice.cpp b/src/lattice.cpp index 3a0deb72db..bfc0b5b9ef 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -300,9 +300,8 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // print lattice spacings if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Lattice spacing in x,y,z = " - "{:.8} {:.8} {:.8}\n", - xlattice,ylattice,zlattice)); + utils::logmesg(lmp,"Lattice spacing in x,y,z = {:.8} {:.8} {:.8}\n", + xlattice,ylattice,zlattice); } /* ---------------------------------------------------------------------- */ diff --git a/src/modify.cpp b/src/modify.cpp index 246b855913..f8a75ca908 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -925,9 +925,9 @@ void Modify::add_fix(int narg, char **arg, int trysuffix) used_restart_global[i] = 1; fix[ifix]->restart_reset = 1; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Resetting global fix info from restart file:\n" - " fix style: {}, fix ID: {}\n", - fix[ifix]->style,fix[ifix]->id)); + utils::logmesg(lmp,"Resetting global fix info from restart file:\n" + " fix style: {}, fix ID: {}\n", + fix[ifix]->style,fix[ifix]->id); } // check if Fix is in restart_peratom list @@ -941,9 +941,9 @@ void Modify::add_fix(int narg, char **arg, int trysuffix) fix[ifix]->unpack_restart(j,index_restart_peratom[i]); fix[ifix]->restart_reset = 1; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Resetting peratom fix info from restart file:\n" - " fix style: {}, fix ID: {}\n", - fix[ifix]->style,fix[ifix]->id)); + utils::logmesg(lmp,"Resetting peratom fix info from restart file:\n" + " fix style: {}, fix ID: {}\n", + fix[ifix]->style,fix[ifix]->id); } // increment nfix (if new) @@ -1574,8 +1574,8 @@ void Modify::restart_deallocate(int flag) utils::logmesg(lmp,"Unused restart file global fix info:\n"); for (i = 0; i < nfix_restart_global; i++) { if (used_restart_global[i]) continue; - utils::logmesg(lmp,fmt::format(" fix style: {}, fix ID: {}\n", - style_restart_global[i],id_restart_global[i])); + utils::logmesg(lmp," fix style: {}, fix ID: {}\n", + style_restart_global[i],id_restart_global[i]); } } } @@ -1602,8 +1602,8 @@ void Modify::restart_deallocate(int flag) utils::logmesg(lmp,"Unused restart file peratom fix info:\n"); for (i = 0; i < nfix_restart_peratom; i++) { if (used_restart_peratom[i]) continue; - utils::logmesg(lmp,fmt::format(" fix style: {}, fix ID: {}\n", - style_restart_peratom[i],id_restart_peratom[i])); + utils::logmesg(lmp," fix style: {}, fix ID: {}\n", + style_restart_peratom[i],id_restart_peratom[i]); } } } diff --git a/src/molecule.cpp b/src/molecule.cpp index 644e3ff79c..9aca15820d 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -146,16 +146,14 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) : // stats if (me == 0) - utils::logmesg(lmp,fmt::format("Read molecule template {}:\n" - " {} molecules\n" - " {} atoms with max type {}\n" - " {} bonds with max type {}\n" - " {} angles with max type {}\n" - " {} dihedrals with max type {}\n" - " {} impropers with max type {}\n", - id,nmolecules,natoms,ntypes, - nbonds,nbondtypes,nangles,nangletypes, - ndihedrals,ndihedraltypes,nimpropers,nimpropertypes)); + utils::logmesg(lmp,"Read molecule template {}:\n {} molecules\n" + " {} atoms with max type {}\n" + " {} bonds with max type {}\n" + " {} angles with max type {}\n" + " {} dihedrals with max type {}\n" + " {} impropers with max type {}\n", id,nmolecules, + natoms,ntypes,nbonds,nbondtypes,nangles,nangletypes, + ndihedrals,ndihedraltypes,nimpropers,nimpropertypes); } /* ---------------------------------------------------------------------- */ diff --git a/src/output.cpp b/src/output.cpp index d7be9b8cd6..6f11079a75 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -817,7 +817,6 @@ void Output::memory_usage() mbavg /= comm->nprocs; if (comm->me == 0) - utils::logmesg(lmp,fmt::format("Per MPI rank memory allocation (min/avg/" - "max) = {:.4} | {:.4} | {:.4} Mbytes\n", - mbmin,mbavg,mbmax)); + utils::logmesg(lmp,"Per MPI rank memory allocation (min/avg/max) = " + "{:.4} | {:.4} | {:.4} Mbytes\n",mbmin,mbavg,mbmax); } diff --git a/src/pair.cpp b/src/pair.cpp index 0d90b0ce39..015129dc5d 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -1734,15 +1734,15 @@ void Pair::write_file(int narg, char **arg) units, update->unit_style)); } std::string date = utils::get_potential_date(table_file,"table"); - utils::logmesg(lmp,fmt::format("Appending to table file {} with " - "DATE: {}\n", table_file, date)); + utils::logmesg(lmp,"Appending to table file {} with DATE: {}\n", + table_file, date); fp = fopen(table_file.c_str(),"a"); } else { char datebuf[16]; time_t tv = time(nullptr); strftime(datebuf,15,"%Y-%m-%d",localtime(&tv)); - utils::logmesg(lmp,fmt::format("Creating table file {} with " - "DATE: {}\n", table_file, datebuf)); + utils::logmesg(lmp,"Creating table file {} with DATE: {}\n", + table_file, datebuf); fp = fopen(table_file.c_str(),"w"); if (fp) fmt::print(fp,"# DATE: {} UNITS: {} Created by pair_write\n", datebuf, update->unit_style); diff --git a/src/potential_file_reader.cpp b/src/potential_file_reader.cpp index bddfca9bce..ce369253cf 100644 --- a/src/potential_file_reader.cpp +++ b/src/potential_file_reader.cpp @@ -254,8 +254,8 @@ TextFileReader *PotentialFileReader::open_potential(const std::string &path) { std::string units = utils::get_potential_units(filepath, filetype); if (!date.empty()) - utils::logmesg(lmp, fmt::format("Reading {} file {} with DATE: {}\n", - filetype, filename, date)); + utils::logmesg(lmp,"Reading {} file {} with DATE: {}\n", + filetype, filename, date); if (units.empty()) { unit_convert = utils::NOCONVERT; diff --git a/src/read_data.cpp b/src/read_data.cpp index c0085f19d1..57d5d898a9 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -907,8 +907,7 @@ void ReadData::command(int narg, char **arg) MPI_Barrier(world); if (comm->me == 0) - utils::logmesg(lmp,fmt::format(" read_data CPU = {:.3f} seconds\n", - MPI_Wtime()-time1)); + utils::logmesg(lmp," read_data CPU = {:.3f} seconds\n",MPI_Wtime()-time1); } /* ---------------------------------------------------------------------- @@ -1239,7 +1238,7 @@ void ReadData::atoms() MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world); bigint nassign = sum - (atom->natoms - natoms); - if (me == 0) utils::logmesg(lmp,fmt::format(" {} atoms\n",nassign)); + if (me == 0) utils::logmesg(lmp," {} atoms\n",nassign); if (sum != atom->natoms) error->all(FLERR,"Did not assign all atoms correctly"); @@ -1293,7 +1292,7 @@ void ReadData::velocities() atom->map_style = Atom::MAP_NONE; } - if (me == 0) utils::logmesg(lmp,fmt::format(" {} velocities\n",natoms)); + if (me == 0) utils::logmesg(lmp," {} velocities\n",natoms); } /* ---------------------------------------------------------------------- @@ -1342,7 +1341,7 @@ void ReadData::bonds(int firstpass) if (addflag == NONE) maxall += atom->extra_bond_per_atom; if (me == 0) - utils::logmesg(lmp,fmt::format(" {} = max bonds/atom\n",maxall)); + utils::logmesg(lmp," {} = max bonds/atom\n",maxall); if (addflag != NONE) { if (maxall > atom->bond_per_atom) @@ -1364,7 +1363,7 @@ void ReadData::bonds(int firstpass) if (!force->newton_bond) factor = 2; if (me == 0) - utils::logmesg(lmp,fmt::format(" {} bonds\n",sum/factor)); + utils::logmesg(lmp," {} bonds\n",sum/factor); if (sum != factor*nbonds) error->all(FLERR,"Bonds assigned incorrectly"); @@ -1416,7 +1415,7 @@ void ReadData::angles(int firstpass) if (addflag == NONE) maxall += atom->extra_angle_per_atom; if (me == 0) - utils::logmesg(lmp,fmt::format(" {} = max angles/atom\n",maxall)); + utils::logmesg(lmp," {} = max angles/atom\n",maxall); if (addflag != NONE) { if (maxall > atom->angle_per_atom) @@ -1438,7 +1437,7 @@ void ReadData::angles(int firstpass) if (!force->newton_bond) factor = 3; if (me == 0) - utils::logmesg(lmp,fmt::format(" {} angles\n",sum/factor)); + utils::logmesg(lmp," {} angles\n",sum/factor); if (sum != factor*nangles) error->all(FLERR,"Angles assigned incorrectly"); @@ -1490,7 +1489,7 @@ void ReadData::dihedrals(int firstpass) if (addflag == NONE) maxall += atom->extra_dihedral_per_atom; if (me == 0) - utils::logmesg(lmp,fmt::format(" {} = max dihedrals/atom\n",maxall)); + utils::logmesg(lmp," {} = max dihedrals/atom\n",maxall); if (addflag != NONE) { if (maxall > atom->dihedral_per_atom) @@ -1512,7 +1511,7 @@ void ReadData::dihedrals(int firstpass) if (!force->newton_bond) factor = 4; if (me == 0) - utils::logmesg(lmp,fmt::format(" {} dihedrals\n",sum/factor)); + utils::logmesg(lmp," {} dihedrals\n",sum/factor); if (sum != factor*ndihedrals) error->all(FLERR,"Dihedrals assigned incorrectly"); @@ -1564,7 +1563,7 @@ void ReadData::impropers(int firstpass) if (addflag == NONE) maxall += atom->extra_improper_per_atom; if (me == 0) - utils::logmesg(lmp,fmt::format(" {} = max impropers/atom\n",maxall)); + utils::logmesg(lmp," {} = max impropers/atom\n",maxall); if (addflag != NONE) { if (maxall > atom->improper_per_atom) @@ -1586,7 +1585,7 @@ void ReadData::impropers(int firstpass) if (!force->newton_bond) factor = 4; if (me == 0) - utils::logmesg(lmp,fmt::format(" {} impropers\n",sum/factor)); + utils::logmesg(lmp," {} impropers\n",sum/factor); if (sum != factor*nimpropers) error->all(FLERR,"Impropers assigned incorrectly"); @@ -1625,7 +1624,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type) } if (me == 0) - utils::logmesg(lmp,fmt::format(" {} {}\n",natoms,type)); + utils::logmesg(lmp," {} {}\n",natoms,type); } /* ---------------------------------------------------------------------- @@ -1729,7 +1728,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr) } if (me == 0 && firstpass) - utils::logmesg(lmp,fmt::format(" {} bodies\n",natoms)); + utils::logmesg(lmp," {} bodies\n",natoms); } /* ---------------------------------------------------------------------- */ diff --git a/src/read_dump.cpp b/src/read_dump.cpp index ddb793c629..370752f698 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -157,13 +157,14 @@ void ReadDump::command(int narg, char **arg) domain->print_box(" "); if (me == 0) - utils::logmesg(lmp, fmt::format(" {} atoms before read\n",natoms_prev) - + fmt::format(" {} atoms in snapshot\n",nsnap_all) - + fmt::format(" {} atoms purged\n",npurge_all) - + fmt::format(" {} atoms replaced\n",nreplace_all) - + fmt::format(" {} atoms trimmed\n",ntrim_all) - + fmt::format(" {} atoms added\n",nadd_all) - + fmt::format(" {} atoms after read\n",atom->natoms)); + utils::logmesg(lmp," {} atoms before read\n" + " {} atoms in snapshot\n" + " {} atoms purged\n" + " {} atoms replaced\n" + " {} atoms trimmed\n" + " {} atoms added\n" + " {} atoms after read\n",natoms_prev,nsnap_all, + npurge_all,nreplace_all,ntrim_all,nadd_all,atom->natoms); } /* ---------------------------------------------------------------------- */ diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 2742dc5e4e..40e4414543 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -467,7 +467,7 @@ void ReadRestart::command(int narg, char **arg) MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); if (me == 0) - utils::logmesg(lmp,fmt::format(" {} atoms\n",natoms)); + utils::logmesg(lmp," {} atoms\n",natoms); if (natoms != atom->natoms) error->all(FLERR,"Did not assign all restart atoms correctly"); @@ -524,8 +524,8 @@ void ReadRestart::command(int narg, char **arg) MPI_Barrier(world); if (comm->me == 0) - utils::logmesg(lmp,fmt::format(" read_restart CPU = {:.3f} seconds\n", - MPI_Wtime()-time1)); + utils::logmesg(lmp," read_restart CPU = {:.3f} seconds\n", + MPI_Wtime()-time1); } /* ---------------------------------------------------------------------- @@ -634,8 +634,8 @@ void ReadRestart::header() if (flag == VERSION) { char *version = read_string(); if (me == 0) - utils::logmesg(lmp,fmt::format(" restart file = {}, LAMMPS = {}\n", - version,lmp->version)); + utils::logmesg(lmp," restart file = {}, LAMMPS = {}\n", + version,lmp->version); delete [] version; // we have no forward compatibility, thus exit with error @@ -809,7 +809,7 @@ void ReadRestart::header() argcopy[i] = read_string(); atom->create_avec(style,nargcopy,argcopy,1); if (comm->me ==0) - utils::logmesg(lmp,fmt::format(" restoring atom style {} from restart\n",style)); + utils::logmesg(lmp," restoring atom style {} from restart\n",style); for (int i = 0; i < nargcopy; i++) delete [] argcopy[i]; delete [] argcopy; delete [] style; @@ -950,15 +950,14 @@ void ReadRestart::force_fields() force->create_pair(style,1); delete [] style; if (comm->me ==0) - utils::logmesg(lmp,fmt::format(" restoring pair style {} from " - "restart\n", force->pair_style)); + utils::logmesg(lmp," restoring pair style {} from restart\n", + force->pair_style); force->pair->read_restart(fp); } else if (flag == NO_PAIR) { style = read_string(); if (comm->me ==0) - utils::logmesg(lmp,fmt::format(" pair style {} stores no " - "restart info\n", style)); + utils::logmesg(lmp," pair style {} stores no restart info\n", style); force->create_pair("none",0); force->pair_restart = style; @@ -967,8 +966,8 @@ void ReadRestart::force_fields() force->create_bond(style,1); delete [] style; if (comm->me ==0) - utils::logmesg(lmp,fmt::format(" restoring bond style {} from " - "restart\n", force->bond_style)); + utils::logmesg(lmp," restoring bond style {} from restart\n", + force->bond_style); force->bond->read_restart(fp); } else if (flag == ANGLE) { @@ -976,8 +975,8 @@ void ReadRestart::force_fields() force->create_angle(style,1); delete [] style; if (comm->me ==0) - utils::logmesg(lmp,fmt::format(" restoring angle style {} from " - "restart\n", force->angle_style)); + utils::logmesg(lmp," restoring angle style {} from restart\n", + force->angle_style); force->angle->read_restart(fp); } else if (flag == DIHEDRAL) { @@ -985,8 +984,8 @@ void ReadRestart::force_fields() force->create_dihedral(style,1); delete [] style; if (comm->me ==0) - utils::logmesg(lmp,fmt::format(" restoring dihedral style {} from " - "restart\n", force->dihedral_style)); + utils::logmesg(lmp," restoring dihedral style {} from restart\n", + force->dihedral_style); force->dihedral->read_restart(fp); } else if (flag == IMPROPER) { @@ -994,8 +993,8 @@ void ReadRestart::force_fields() force->create_improper(style,1); delete [] style; if (comm->me ==0) - utils::logmesg(lmp,fmt::format(" restoring improper style {} from " - "restart\n", force->improper_style)); + utils::logmesg(lmp," restoring improper style {} from restart\n", + force->improper_style); force->improper->read_restart(fp); } else error->all(FLERR, diff --git a/src/replicate.cpp b/src/replicate.cpp index 95bf615d04..5a596c524c 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -647,9 +647,8 @@ void Replicate::command(int narg, char **arg) MPI_Reduce(&num_replicas_added, &sum, 1, MPI_INT, MPI_SUM, 0, world); double avg = (double) sum / nprocs; if (me == 0) - utils::logmesg(lmp,fmt::format(" average # of replicas added to proc =" - " {:.2f} out of {} ({:.2f}%)\n", - avg,nx*ny*nz,avg/(nx*ny*nz)*100.0)); + utils::logmesg(lmp," average # of replicas added to proc = {:.2f} out " + "of {} ({:.2f}%)\n",avg,nx*ny*nz,avg/(nx*ny*nz)*100.0); } else { for (int iproc = 0; iproc < nprocs; iproc++) { @@ -753,7 +752,7 @@ void Replicate::command(int narg, char **arg) MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); if (me == 0) { - utils::logmesg(lmp,fmt::format(" {} atoms\n",natoms)); + utils::logmesg(lmp," {} atoms\n",natoms); } if (natoms != atom->natoms) @@ -763,16 +762,16 @@ void Replicate::command(int narg, char **arg) const char *molstyle = ""; if (atom->molecular == Atom::TEMPLATE) molstyle = "template "; if (atom->nbonds) { - utils::logmesg(lmp,fmt::format(" {} {}bonds\n",atom->nbonds,molstyle)); + utils::logmesg(lmp," {} {}bonds\n",atom->nbonds,molstyle); } if (atom->nangles) { - utils::logmesg(lmp,fmt::format(" {} {}angles\n",atom->nangles,molstyle)); + utils::logmesg(lmp," {} {}angles\n",atom->nangles,molstyle); } if (atom->ndihedrals) { - utils::logmesg(lmp,fmt::format(" {} {}dihedrals\n",atom->ndihedrals,molstyle)); + utils::logmesg(lmp," {} {}dihedrals\n",atom->ndihedrals,molstyle); } if (atom->nimpropers) { - utils::logmesg(lmp,fmt::format(" {} {}impropers\n",atom->nimpropers,molstyle)); + utils::logmesg(lmp," {} {}impropers\n",atom->nimpropers,molstyle); } } @@ -799,6 +798,5 @@ void Replicate::command(int narg, char **arg) MPI_Barrier(world); if (me == 0) - utils::logmesg(lmp,fmt::format(" replicate CPU = {:.3f} seconds\n", - MPI_Wtime()-time1)); + utils::logmesg(lmp," replicate CPU = {:.3f} seconds\n",MPI_Wtime()-time1); } diff --git a/src/reset_mol_ids.cpp b/src/reset_mol_ids.cpp index 39f7307ca1..9501c19861 100644 --- a/src/reset_mol_ids.cpp +++ b/src/reset_mol_ids.cpp @@ -131,11 +131,11 @@ void ResetMolIDs::command(int narg, char **arg) if (comm->me == 0) { if (nchunk < 0) - utils::logmesg(lmp,fmt::format(" number of new molecule IDs = unknown\n")); + utils::logmesg(lmp," number of new molecule IDs = unknown\n"); else - utils::logmesg(lmp,fmt::format(" number of new molecule IDs = {}\n",nchunk)); - utils::logmesg(lmp,fmt::format(" reset_mol_ids CPU = {:.3f} seconds\n", - MPI_Wtime()-time1)); + utils::logmesg(lmp," number of new molecule IDs = {}\n",nchunk); + utils::logmesg(lmp," reset_mol_ids CPU = {:.3f} seconds\n", + MPI_Wtime()-time1); } } diff --git a/src/set.cpp b/src/set.cpp index fdc0c37bfd..c36df7f1c7 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -600,11 +600,11 @@ void Set::command(int narg, char **arg) if (comm->me == 0) { if (strcmp(arg[origarg],"cc") == 0) - utils::logmesg(lmp,fmt::format(" {} settings made for {} index {}\n", - allcount,arg[origarg],arg[origarg+1])); + utils::logmesg(lmp," {} settings made for {} index {}\n", + allcount,arg[origarg],arg[origarg+1]); else - utils::logmesg(lmp,fmt::format(" {} settings made for {}\n", - allcount,arg[origarg])); + utils::logmesg(lmp," {} settings made for {}\n", + allcount,arg[origarg]); } } diff --git a/src/special.cpp b/src/special.cpp index d263112756..2d90f377a2 100644 --- a/src/special.cpp +++ b/src/special.cpp @@ -92,7 +92,7 @@ void Special::build() // print max # of 1-2 neighbors if (me == 0) - utils::logmesg(lmp,fmt::format("{:>6} = max # of 1-2 neighbors\n",maxall)); + utils::logmesg(lmp,"{:>6} = max # of 1-2 neighbors\n",maxall); // done if special_bond weights for 1-3, 1-4 are set to 1.0 @@ -115,7 +115,7 @@ void Special::build() // print max # of 1-3 neighbors if (me == 0) - utils::logmesg(lmp,fmt::format("{:>6} = max # of 1-3 neighbors\n",maxall)); + utils::logmesg(lmp,"{:>6} = max # of 1-3 neighbors\n",maxall); // done if special_bond weights for 1-4 are set to 1.0 @@ -138,7 +138,7 @@ void Special::build() // print max # of 1-4 neighbors if (me == 0) - utils::logmesg(lmp,fmt::format("{:>6} = max # of 1-4 neighbors\n",maxall)); + utils::logmesg(lmp,"{:>6} = max # of 1-4 neighbors\n",maxall); // finish processing the onetwo, onethree, onefour lists @@ -690,8 +690,7 @@ void Special::combine() force->special_extra = 0; if (me == 0) - utils::logmesg(lmp,fmt::format("{:>6} = max # of special " - "neighbors\n",atom->maxspecial)); + utils::logmesg(lmp,"{:>6} = max # of special neighbors\n",atom->maxspecial); if (lmp->kokkos) { AtomKokkos* atomKK = (AtomKokkos*) atom; @@ -793,8 +792,8 @@ void Special::angle_trim() MPI_Allreduce(&onethreecount,&allcount,1,MPI_DOUBLE,MPI_SUM,world); if (me == 0) - utils::logmesg(lmp,fmt::format(" {} = # of 1-3 neighbors " - "before angle trim\n",allcount)); + utils::logmesg(lmp," {} = # of 1-3 neighbors before angle trim\n", + allcount); // if angles or dihedrals are defined // rendezvous angle 1-3 and dihedral 1-3,2-4 pairs @@ -1023,8 +1022,8 @@ void Special::angle_trim() MPI_Allreduce(&onethreecount,&allcount,1,MPI_DOUBLE,MPI_SUM,world); if (me == 0) - utils::logmesg(lmp,fmt::format(" {} = # of 1-3 neighbors " - "after angle trim\n",allcount)); + utils::logmesg(lmp," {} = # of 1-3 neighbors after angle trim\n", + allcount); } /* ---------------------------------------------------------------------- @@ -1053,8 +1052,8 @@ void Special::dihedral_trim() MPI_Allreduce(&onefourcount,&allcount,1,MPI_DOUBLE,MPI_SUM,world); if (me == 0) - utils::logmesg(lmp,fmt::format(" {} = # of 1-4 neighbors " - "before dihedral trim\n",allcount)); + utils::logmesg(lmp," {} = # of 1-4 neighbors before dihedral trim\n", + allcount); // if dihedrals are defined, rendezvous the dihedral 1-4 pairs @@ -1197,8 +1196,8 @@ void Special::dihedral_trim() MPI_Allreduce(&onefourcount,&allcount,1,MPI_DOUBLE,MPI_SUM,world); if (me == 0) - utils::logmesg(lmp,fmt::format(" {} = # of 1-4 neighbors " - "after dihedral trim\n",allcount)); + utils::logmesg(lmp," {} = # of 1-4 neighbors after dihedral trim\n", + allcount); } /* ---------------------------------------------------------------------- @@ -1313,6 +1312,6 @@ void Special::fix_alteration() void Special::timer_output(double time1) { if (comm->me == 0) - utils::logmesg(lmp,fmt::format(" special bonds CPU = {:.3f} seconds\n", - MPI_Wtime()-time1)); + utils::logmesg(lmp," special bonds CPU = {:.3f} seconds\n", + MPI_Wtime()-time1); } diff --git a/src/timer.cpp b/src/timer.cpp index 9c8cf5db8c..79fb63e7b5 100644 --- a/src/timer.cpp +++ b/src/timer.cpp @@ -294,8 +294,7 @@ void Timer::modify_params(int narg, char **arg) strftime(timebuf,32,"%H:%M:%S",tm); } - utils::logmesg(lmp,fmt::format("New timer settings: style={} mode={} " - "timeout={}\n",timer_style[_level], - timer_mode[_sync],timebuf)); + utils::logmesg(lmp,"New timer settings: style={} mode={} timeout={}\n", + timer_style[_level],timer_mode[_sync],timebuf); } } diff --git a/src/utils.cpp b/src/utils.cpp index 4071b7b61b..fedf86149e 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -1099,10 +1099,8 @@ FILE *utils::open_potential(const std::string &name, LAMMPS *lmp, std::string date = get_potential_date(filepath, "potential"); std::string units = get_potential_units(filepath, "potential"); - if (!date.empty() && (me == 0)) { - logmesg(lmp, fmt::format("Reading potential file {} " - "with DATE: {}\n", name, date)); - } + if (!date.empty() && (me == 0)) + logmesg(lmp,"Reading potential file {} with DATE: {}\n", name, date); if (auto_convert == nullptr) { if (!units.empty() && (units != unit_style) && (me == 0)) { From 3aec5c64849ee925c20735dc71fa64899040c09e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 21 Apr 2021 23:50:13 -0400 Subject: [PATCH 0593/1217] tweak docs for logmesg() overload --- doc/src/Developer_utils.rst | 5 ++++- src/utils.h | 8 +++++--- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/doc/src/Developer_utils.rst b/doc/src/Developer_utils.rst index 17b4715dc7..7adaffa67c 100644 --- a/doc/src/Developer_utils.rst +++ b/doc/src/Developer_utils.rst @@ -164,7 +164,10 @@ Argument processing Convenience functions ^^^^^^^^^^^^^^^^^^^^^ -.. doxygenfunction:: logmesg +.. doxygenfunction:: logmesg(LAMMPS *lmp, const S &format, Args&&... args) + :project: progguide + +.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg) :project: progguide .. doxygenfunction:: getsyserror diff --git a/src/utils.h b/src/utils.h index 6eed8fd3bc..e0ab413e59 100644 --- a/src/utils.h +++ b/src/utils.h @@ -57,8 +57,7 @@ namespace LAMMPS_NS { * This function simplifies the repetitive task of outputting some * message to both the screen and/or the log file. The template * wrapper with fmtlib format and argument processing allows - * this function to work similar to fmt::print(). - * The specialization overload handles the case of no arguments. + * this function to work similar to ``fmt::print()``. * * \param lmp pointer to LAMMPS class instance * \param format format string of message to be printed @@ -70,7 +69,10 @@ namespace LAMMPS_NS { fmt::make_args_checked(format, args...)); } - /** \overload */ + /** \overload + * + * \param lmp pointer to LAMMPS class instance + * \param mesg string with message to be printed */ void logmesg(LAMMPS *lmp, const std::string &mesg); From e7cb20efeb0083631ca893699c6e4b11741ded24 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 21 Apr 2021 23:55:40 -0400 Subject: [PATCH 0594/1217] replace non-ASCII character in docs --- doc/src/fix_precession_spin.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst index 9bf9db24e1..6a563bc32f 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -197,6 +197,6 @@ Oxford University Press. .. _Chirac1: -**(Chirac)** Chirac, Théophile, et al. Ultrafast antiferromagnetic +**(Chirac)** Chirac, Theophile, et al. Ultrafast antiferromagnetic switching in NiO induced by spin transfer torques. Physical Review B 102.13 (2020): 134415. From c2579391c08204ab49d97f00d0d8ce031c65ae58 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 22 Apr 2021 00:03:57 -0400 Subject: [PATCH 0595/1217] silence compiler warnings --- src/KOKKOS/fix_eos_table_rx_kokkos.cpp | 6 +++--- src/KOKKOS/fix_rx_kokkos.cpp | 2 +- src/USER-PTM/compute_ptm_atom.cpp | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp index 4d181c2b41..095661a32b 100644 --- a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp +++ b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp @@ -531,11 +531,11 @@ void FixEOStableRXKokkos::create_kokkos_tables() h_table->hi[i] = tb->hi; h_table->invdelta[i] = tb->invdelta; - for (int j = 0; jr.extent(1); j++) + for (int j = 0; j < (int)h_table->r.extent(1); j++) h_table->r(i,j) = tb->r[j]; - for (int j = 0; je.extent(1); j++) + for (int j = 0; j < (int)h_table->e.extent(1); j++) h_table->e(i,j) = tb->e[j]; - for (int j = 0; jde.extent(1); j++) + for (int j = 0; j < (int)h_table->de.extent(1); j++) h_table->de(i,j) = tb->de[j]; } diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp index 036ecd1788..e512f19d1d 100644 --- a/src/KOKKOS/fix_rx_kokkos.cpp +++ b/src/KOKKOS/fix_rx_kokkos.cpp @@ -1451,7 +1451,7 @@ void FixRxKokkos::solve_reactions(const int /*vflag*/, const bool is { const int count = nlocal + (newton_pair ? nghost : 0); - if (count > k_dpdThetaLocal.template view().extent(0)) { + if (count > (int) k_dpdThetaLocal.template view().extent(0)) { memoryKK->destroy_kokkos (k_dpdThetaLocal, dpdThetaLocal); memoryKK->create_kokkos (k_dpdThetaLocal, dpdThetaLocal, count, "FixRxKokkos::dpdThetaLocal"); this->d_dpdThetaLocal = k_dpdThetaLocal.template view(); diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp index 0622b9dcc0..95f1cf5ad9 100644 --- a/src/USER-PTM/compute_ptm_atom.cpp +++ b/src/USER-PTM/compute_ptm_atom.cpp @@ -204,7 +204,7 @@ static int get_neighbours(void* vdata, size_t central_index, size_t atom_index, int *jlist = nullptr; int jnum = 0; - if (atom_index < data->nlocal) { + if ((int)atom_index < data->nlocal) { jlist = data->firstneigh[atom_index]; jnum = data->numneigh[atom_index]; } @@ -221,7 +221,7 @@ static int get_neighbours(void* vdata, size_t central_index, size_t atom_index, continue; j &= NEIGHMASK; - if (j == atom_index) + if (j == (int)atom_index) continue; double dx = pos[0] - x[j][0]; From eb85edfb3db3ddb8263eed15a3c3c711a7f2e965 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 22 Apr 2021 00:15:14 -0400 Subject: [PATCH 0596/1217] make naming of the compiled pace library consistent with those of other libs --- cmake/Modules/Packages/USER-PACE.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/USER-PACE.cmake index 66f228017c..2d88d3a313 100644 --- a/cmake/Modules/Packages/USER-PACE.cmake +++ b/cmake/Modules/Packages/USER-PACE.cmake @@ -20,7 +20,7 @@ file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PAC list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp) add_library(pace STATIC ${PACE_EVALUATOR_SOURCES}) -set_target_properties(pace PROPERTIES OUTPUT_NAME pace${LAMMPS_MACHINE}) +set_target_properties(pace PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE}) target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) target_link_libraries(lammps PRIVATE pace) From a49d783e16111172d75b2e3de265838d16634214 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 22 Apr 2021 05:44:35 -0400 Subject: [PATCH 0597/1217] check formatting and multiple arguments when using utils::logmesg() --- unittest/formats/test_file_operations.cpp | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/unittest/formats/test_file_operations.cpp b/unittest/formats/test_file_operations.cpp index 700990fb72..fe2bf2d2f6 100644 --- a/unittest/formats/test_file_operations.cpp +++ b/unittest/formats/test_file_operations.cpp @@ -126,7 +126,7 @@ TEST_F(FileOperationsTest, safe_fread) TEST_F(FileOperationsTest, logmesg) { - char buf[8]; + char buf[16]; BEGIN_HIDE_OUTPUT(); command("echo none"); END_HIDE_OUTPUT(); @@ -134,14 +134,15 @@ TEST_F(FileOperationsTest, logmesg) utils::logmesg(lmp, "one\n"); command("log test_logmesg.log"); utils::logmesg(lmp, "two\n"); + utils::logmesg(lmp, "three={}\n",3); command("log none"); std::string out = END_CAPTURE_OUTPUT(); - memset(buf, 0, 8); + memset(buf, 0, 16); FILE *fp = fopen("test_logmesg.log", "r"); - fread(buf, 1, 8, fp); + fread(buf, 1, 16, fp); fclose(fp); - ASSERT_THAT(out, StrEq("one\ntwo\n")); - ASSERT_THAT(buf, StrEq("two\n")); + ASSERT_THAT(out, StrEq("one\ntwo\nthree=3\n")); + ASSERT_THAT(buf, StrEq("two\nthree=3\n")); remove("test_logmesg.log"); } From d405f2ec4b5faa4db404132be08e09df4a0b0422 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 22 Apr 2021 09:16:37 -0400 Subject: [PATCH 0598/1217] Update defines to use old neighbor code for CUDA >= 11.2 --- lib/gpu/lal_neighbor.h | 4 ++-- lib/gpu/lal_neighbor_gpu.cu | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/lib/gpu/lal_neighbor.h b/lib/gpu/lal_neighbor.h index 5939567a41..fb854a706c 100644 --- a/lib/gpu/lal_neighbor.h +++ b/lib/gpu/lal_neighbor.h @@ -26,8 +26,8 @@ #if !defined(USE_OPENCL) && !defined(USE_HIP) #ifndef LAL_USE_OLD_NEIGHBOR -// Issue with incorrect results with CUDA 11.2 -#if (CUDA_VERSION > 11019) && (CUDA_VERSION < 11030) +// Issue with incorrect results with CUDA >= 11.2 +#if (CUDA_VERSION > 11019) #define LAL_USE_OLD_NEIGHBOR #endif #endif diff --git a/lib/gpu/lal_neighbor_gpu.cu b/lib/gpu/lal_neighbor_gpu.cu index 2aca505396..b6db97f68a 100644 --- a/lib/gpu/lal_neighbor_gpu.cu +++ b/lib/gpu/lal_neighbor_gpu.cu @@ -34,8 +34,8 @@ _texture_2d( pos_tex,int4); #endif #ifdef NV_KERNEL -#if (__CUDACC_VER_MAJOR__ == 11) && (__CUDACC_VER_MINOR__ == 2) -// Issue with incorrect results in CUDA 11.2 +#if (__CUDACC_VER_MAJOR__ == 11) && (__CUDACC_VER_MINOR__ >= 2) +// Issue with incorrect results in CUDA >= 11.2 #define LAL_USE_OLD_NEIGHBOR #endif #endif From ad02e9df69ae77cacea95424a9f6523479e18b67 Mon Sep 17 00:00:00 2001 From: Agilio Padua Date: Thu, 22 Apr 2021 18:40:45 +0200 Subject: [PATCH 0599/1217] Added example of SPCE hydration, LJ + q --- examples/USER/fep/README.md | 3 + examples/USER/fep/SPCEhyd/README.md | 45 + examples/USER/fep/SPCEhyd/fep01/fep01-lj.fep | 22 + examples/USER/fep/SPCEhyd/fep01/fep01-lj.out | 592 +++ examples/USER/fep/SPCEhyd/fep01/fep01-q.fep | 22 + examples/USER/fep/SPCEhyd/fep01/fep01-q.out | 561 +++ .../USER/fep/SPCEhyd/fep01/in-fep01-lj.lmp | 72 + .../USER/fep/SPCEhyd/fep01/in-fep01-q.lmp | 78 + examples/USER/fep/SPCEhyd/fep10/fep10-lj.fep | 22 + examples/USER/fep/SPCEhyd/fep10/fep10-lj.out | 592 +++ examples/USER/fep/SPCEhyd/fep10/fep10-q.fep | 22 + examples/USER/fep/SPCEhyd/fep10/fep10-q.out | 559 +++ .../USER/fep/SPCEhyd/fep10/in-fep10-lj.lmp | 72 + .../USER/fep/SPCEhyd/fep10/in-fep10-q.lmp | 76 + examples/USER/fep/SPCEhyd/mols/data.lmp | 3635 +++++++++++++++++ examples/USER/fep/SPCEhyd/mols/spce.ff | 14 + examples/USER/fep/SPCEhyd/mols/spce.zmat | 7 + examples/USER/fep/SPCEhyd/mols/spce_h.ff | 14 + examples/USER/fep/SPCEhyd/mols/spce_h.zmat | 7 + 19 files changed, 6415 insertions(+) create mode 100644 examples/USER/fep/SPCEhyd/README.md create mode 100644 examples/USER/fep/SPCEhyd/fep01/fep01-lj.fep create mode 100644 examples/USER/fep/SPCEhyd/fep01/fep01-lj.out create mode 100644 examples/USER/fep/SPCEhyd/fep01/fep01-q.fep create mode 100644 examples/USER/fep/SPCEhyd/fep01/fep01-q.out create mode 100644 examples/USER/fep/SPCEhyd/fep01/in-fep01-lj.lmp create mode 100644 examples/USER/fep/SPCEhyd/fep01/in-fep01-q.lmp create mode 100644 examples/USER/fep/SPCEhyd/fep10/fep10-lj.fep create mode 100644 examples/USER/fep/SPCEhyd/fep10/fep10-lj.out create mode 100644 examples/USER/fep/SPCEhyd/fep10/fep10-q.fep create mode 100644 examples/USER/fep/SPCEhyd/fep10/fep10-q.out create mode 100644 examples/USER/fep/SPCEhyd/fep10/in-fep10-lj.lmp create mode 100644 examples/USER/fep/SPCEhyd/fep10/in-fep10-q.lmp create mode 100644 examples/USER/fep/SPCEhyd/mols/data.lmp create mode 100644 examples/USER/fep/SPCEhyd/mols/spce.ff create mode 100644 examples/USER/fep/SPCEhyd/mols/spce.zmat create mode 100644 examples/USER/fep/SPCEhyd/mols/spce_h.ff create mode 100644 examples/USER/fep/SPCEhyd/mols/spce_h.zmat diff --git a/examples/USER/fep/README.md b/examples/USER/fep/README.md index 416af526e7..d8f0935115 100644 --- a/examples/USER/fep/README.md +++ b/examples/USER/fep/README.md @@ -9,6 +9,9 @@ to the final states. * `CH4hyd` -- free energy of hydration of methane (simple). FEP and FDTI methods. +* `SPCEhyd` -- free energy of hydration of SPCE water (simple). FEP + in separate steps for the LJ sites and the atomic charges. + * `CH4-CF4` -- free energy difference of transforming methane into perfluoromethane, in water (quite simple). FEP and BAR methods. diff --git a/examples/USER/fep/SPCEhyd/README.md b/examples/USER/fep/SPCEhyd/README.md new file mode 100644 index 0000000000..de30f0c19b --- /dev/null +++ b/examples/USER/fep/SPCEhyd/README.md @@ -0,0 +1,45 @@ +Free Energy of Hydration of SPCE Water +====================================== + +Example calculation of the free energy of hydration of water with +LAMMPS using *compute fep*, *fix adapt/fep* and *pair lj/cut/soft*. + +The Lennard-Jones sites and the electrostatic charges are +created/annihilated in separate runs, which simplifies the use of +*fix adapt/fep* and *compute fep*. The Lennard-Jones sites are handled +using soft core potentials (*pair lj/cut/soft*). Trajectories are at +constant NpT, so corrections for the fluctuating volume are included. + +The following directories contain input files and results for +calculations using free-energy perturbation (FEP): + +* `mols` -- molecule description files and force field database used + to create the initial configuration used for the simulations + `data.lmp` + +* `fep01` -- Calculation using FEP, multi-stage creation of one SPC/E + molecule, LJ and q. Results in `fep01-lj.fep` and `fep01-lj.fep` + +* `fep10` -- Calculation using FEP, multi-stage deletion of one SPC/E + molecule, q and LJ. Results in `fep10-q.fep` and `fep10-lj.fep` + +The Python script `fep.py` found in the +`tools` directory can be used to calculate the free-energy differences +corresponding to the transformations above: + + fep.py 300 < fep01-lj.fep + + fep.py 300 < fep01-q.fep + + fep.py 300 < fep10-q.fep + + fep.py 300 < fep10-lj.fep + +The outputs are in kcal/mol and can be compared with the experimental +value of -6.3 kcal/mol, or with a simulation value from the literature +of -6.7 kcal/mol +[Gonçalves, Stassen, Pure Appl Chem 76 (2004) 231](https://doi.org/10.1351/pac200476010231). + +These example calculations are for tutorial purposes only. The results +may not be of research quality (not enough sampling, size of the step +in lambda not optimized, etc.) diff --git a/examples/USER/fep/SPCEhyd/fep01/fep01-lj.fep b/examples/USER/fep/SPCEhyd/fep01/fep01-lj.fep new file mode 100644 index 0000000000..67dc4bfd8d --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep01/fep01-lj.fep @@ -0,0 +1,22 @@ +# Time-averaged data for fix FEP +# TimeStep c_FEP[1] c_FEP[2] c_FEP[3] +100000 0.00203701 17656.7 17717 +200000 0.0148799 17235.9 17669.1 +300000 0.0478517 16378 17736.4 +400000 0.100195 15034.8 17725.7 +500000 0.218866 12390.7 17698.7 +600000 0.371395 9907.37 17731.1 +700000 0.613593 7317.6 17750.5 +800000 0.895639 5984.39 17714.3 +900000 0.638838 8921.42 17726.2 +1000000 0.372214 11782.7 17728.6 +1100000 0.295555 12613 17730.3 +1200000 0.152975 15013.7 17792.5 +1300000 0.106403 15927.4 17737.2 +1400000 0.0570002 16875.1 17725.9 +1500000 0.0182185 17924.9 17790.8 +1600000 -0.0319612 19263.7 17775.1 +1700000 -0.0684472 20338.7 17786.9 +1800000 -0.0941487 21136.1 17764.8 +1900000 -0.132444 22374 17750.6 +2000000 -0.153928 23156.8 17744.8 diff --git a/examples/USER/fep/SPCEhyd/fep01/fep01-lj.out b/examples/USER/fep/SPCEhyd/fep01/fep01-lj.out new file mode 100644 index 0000000000..3eaf2fd98c --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep01/fep01-lj.out @@ -0,0 +1,592 @@ +LAMMPS (29 Oct 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (29.204526 29.204526 29.204526) + 2 by 2 by 3 MPI processor grid + reading atoms ... + 1800 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 1200 bonds + reading angles ... + 600 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.018 seconds +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 600 = # of size 3 clusters + 0 = # of size 4 clusters + 0 = # of frozen angles + find clusters CPU = 0.001 seconds +Setting atom values ... + 3 settings made for charge +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.25066829 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0030719151 + estimated relative force accuracy = 9.250981e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 3757 800 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut/coul/long, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/soft, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 9.477 | 9.489 | 9.507 Mbytes +Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density + 0 0 1344.7207 1251.046 93.67475 54.469999 30049.554 -30010.349 300 10284.691 24908.667 0.72058313 + 5000 28.694564 -5486.1043 1288.3881 -6774.4924 1379.4864 21688.643 -30296.277 308.95461 54.310852 17485.125 1.0265163 + 10000 60.154999 -5445.984 1289.4468 -6735.4308 1414.0583 21715.025 -30296.898 309.2085 479.66554 17890.87 1.003236 + 15000 93.146023 -5513.8313 1247.6759 -6761.5072 1299.4795 21790.371 -30301.687 299.19185 -508.0062 17325.35 1.0359828 + 20000 125.27418 -5449.2886 1284.4959 -6733.7844 1413.7763 21713.785 -30296.156 308.02126 590.93324 17813.863 1.0075729 + 25000 159.91521 -5488.9702 1263.558 -6752.5282 1419.1433 21691.575 -30298.164 303.00038 745.03072 17529.113 1.0239403 + 30000 192.99516 -5560.7692 1261.1821 -6821.9512 1417.204 21619.369 -30296.506 302.43062 247.03569 17579.175 1.0210243 + 35000 226.31455 -5475.9339 1217.5826 -6693.5164 1416.6051 21740.37 -30296.23 291.97549 585.78922 17897.211 1.0028805 + 40000 257.38113 -5547.1985 1242.3037 -6789.5022 1368.836 21696.099 -30299.114 297.90361 -308.25384 17644.122 1.017266 + 45000 290.1833 -5546.482 1247.5586 -6794.0405 1478.3456 21579.538 -30298.856 299.16372 1088.2882 17592.834 1.0202316 + 50000 323.27342 -5587.1305 1245.2866 -6832.4171 1494.5555 21518.708 -30301.175 298.6189 1294.6268 17477.389 1.0269707 + 55000 357.01676 -5579.512 1240.4584 -6819.9704 1395.6861 21642.898 -30295.857 297.46109 -99.93318 17770.807 1.0100141 + 60000 388.82447 -5489.9387 1234.3341 -6724.2728 1285.7293 21870.543 -30295.028 295.99251 -1147.8529 17885.706 1.0035257 + 65000 422.87575 -5552.7156 1212.0793 -6764.7949 1333.565 21754.173 -30298.11 290.65582 -712.18036 17669.638 1.015797 + 70000 457.6093 -5497.6045 1258.538 -6756.1425 1322.4574 21754.169 -30297.784 301.79659 -688.38797 17616.532 1.0188592 + 75000 491.97196 -5625.4891 1179.169 -6804.6581 1390.1744 21637.212 -30297.753 282.76395 42.978393 17500.681 1.0256038 + 80000 525.96216 -5522.0997 1232.6571 -6754.7568 1341.1534 21770.924 -30301.663 295.59035 -265.75148 17495.977 1.0258796 + 85000 559.772 -5429.8519 1249.9284 -6679.7803 1347.2093 21813.241 -30297.861 299.732 -111.81756 17957.604 0.9995078 + 90000 593.75975 -5560.9592 1265.0979 -6826.0571 1463.6326 21567.748 -30297.643 303.36965 599.30412 17830.144 1.0066528 + 95000 627.953 -5544.2442 1277.7084 -6821.9526 1407.1904 21633.729 -30299.133 306.39364 192.51289 17668.067 1.0158873 + 100000 662.08715 -5474.8467 1286.3434 -6761.1902 1377.3305 21690.898 -30299.316 308.46431 -161.00615 17888.012 1.0033963 +Loop time of 662.087 on 12 procs for 100000 steps with 1800 atoms + +Performance: 13.050 ns/day, 1.839 hours/ns, 151.038 timesteps/s +94.9% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 345.52 | 374.93 | 410.41 | 88.0 | 56.63 +Bond | 1.2655 | 1.3414 | 1.443 | 5.2 | 0.20 +Kspace | 99.52 | 135.77 | 165.42 | 148.0 | 20.51 +Neigh | 28.904 | 28.95 | 28.997 | 0.6 | 4.37 +Comm | 41.498 | 45.503 | 50.663 | 51.8 | 6.87 +Output | 0.0013665 | 0.0014183 | 0.0018614 | 0.4 | 0.00 +Modify | 49.685 | 64.033 | 72.601 | 117.1 | 9.67 +Other | | 11.56 | | | 1.75 + +Nlocal: 150.000 ave 169 max 133 min +Histogram: 1 2 1 1 2 1 0 3 0 1 +Nghost: 6036.17 ave 6092 max 5976 min +Histogram: 3 1 0 0 0 1 3 2 0 2 +Neighs: 86433.7 ave 96904 max 78425 min +Histogram: 3 1 1 0 2 1 1 0 1 2 + +Total # of neighbors = 1037204 +Ave neighs/atom = 576.22444 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 4498 +Dangerous builds = 9 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.25099061 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0035434233 + estimated relative force accuracy = 1.0670914e-05 + using double precision FFTW3 + 3d grid and FFT values/proc = 3328 648 +FEP settings ... + temperature = 300.000000 + tail no + lj/cut/soft lambda 1-2 3-4 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 4 4 4 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut/coul/long, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/soft, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 9.473 | 9.524 | 9.885 Mbytes +Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda + 0 -5474.8313 1286.3434 -6761.1748 1377.3305 21729.814 -30338.216 308.46431 -145.89091 1.0033963 0 + 5000 -5501.3742 1227.5839 -6728.9581 1383.6091 21832.227 -30338.792 294.37381 197.29783 1.0066092 0.0025 + 10000 -5464.6748 1299.6003 -6764.2751 1422.869 21700.714 -30339.338 311.64329 911.1393 1.0308533 0.005 + 15000 -5570.8381 1254.6639 -6825.502 1432.6295 21661.321 -30337.889 300.86757 606.08029 1.0232505 0.0075 + 20000 -5517.9977 1279.1 -6797.0976 1408.873 21713.571 -30334.986 306.72733 71.014518 1.00536 0.01 + 25000 -5502.8662 1256.1509 -6759.0171 1354.4185 21819.904 -30335.966 301.22416 -280.3804 1.0121715 0.0125 + 30000 -5479.0987 1247.8675 -6726.9662 1413.5362 21734.153 -30338.534 299.23779 347.7292 1.0037264 0.015 + 35000 -5507.6469 1301.4131 -6809.06 1460.033 21614.564 -30336.109 312.07801 771.56011 1.0011707 0.0175 + 40000 -5487.2955 1295.7159 -6783.0113 1321.8494 21814.192 -30340.297 310.71181 -399.68468 1.0295009 0.02 + 45000 -5582.7908 1203.9957 -6786.7865 1428.232 21690.272 -30335.2 288.71737 516.0938 1.0238261 0.0225 + 50000 -5543.0112 1239.5077 -6782.5189 1442.8695 21660.077 -30336.998 297.23314 966.89878 1.0234172 0.025 + 55000 -5590.3604 1232.4497 -6822.8101 1322.5893 21772.961 -30338.359 295.54062 -790.54432 1.0210518 0.0275 + 60000 -5479.6266 1218.6941 -6698.3207 1363.233 21839.328 -30336.264 292.24204 102.67075 1.0069364 0.03 + 65000 -5492.8433 1277.3976 -6770.2409 1361.2794 21754.915 -30335.072 306.31909 -345.94035 1.0111736 0.0325 + 70000 -5564.9632 1256.2689 -6821.2322 1418.089 21663.812 -30334.208 301.25246 -235.62062 1.0000081 0.035 + 75000 -5431.4667 1233.6963 -6665.163 1385.2972 21867.508 -30337.413 295.83957 605.68584 1.015264 0.0375 + 80000 -5560.6719 1236.9415 -6797.6134 1374.1241 21748.636 -30335.156 296.61776 -202.53528 1.015924 0.04 + 85000 -5636.8905 1233.835 -6870.7255 1480.1666 21576.608 -30340.174 295.87281 827.4631 1.0212177 0.0425 + 90000 -5551.2917 1222.5755 -6773.8672 1452.5674 21638.206 -30335.595 293.1728 661.99097 1.0090475 0.045 + 95000 -5543.8224 1249.9355 -6793.758 1396.082 21724.933 -30339.764 299.73372 201.87719 1.0163116 0.0475 + 100000 -5558.5664 1227.1814 -6785.7479 1463.1907 21666.038 -30337.879 294.2773 955.6758 1.0158894 0.05 + 105000 -5507.0698 1233.0098 -6740.0796 1356.1635 21774.574 -30334.594 295.67493 -359.01022 1.0056685 0.0525 + 110000 -5561.0676 1221.0774 -6782.145 1403.5966 21692.913 -30337.463 292.81355 -87.113696 1.0133037 0.055 + 115000 -5526.6141 1243.9541 -6770.5682 1475.7194 21626.703 -30337.179 298.29937 855.85038 1.0118327 0.0575 + 120000 -5555.6741 1253.3796 -6809.0538 1346.5604 21755.315 -30340.743 300.55961 -1079.5856 0.98312027 0.06 + 125000 -5620.4084 1221.0146 -6841.423 1406.8142 21677.116 -30335.053 292.7985 -61.600379 1.0173627 0.0625 + 130000 -5586.4001 1204.2423 -6790.6425 1352.9098 21770.892 -30339.505 288.77651 -460.92375 1.0164837 0.065 + 135000 -5568.5186 1239.2748 -6807.7934 1401.8615 21748.687 -30340.555 297.17728 371.66677 1.0241473 0.0675 + 140000 -5526.4808 1249.0145 -6775.4953 1424.2185 21664.576 -30340.16 299.51285 520.63161 1.0238118 0.07 + 145000 -5532.8733 1254.9515 -6787.8248 1379.0629 21737.241 -30337.358 300.93654 -64.517937 1.0105756 0.0725 + 150000 -5549.4332 1228.3832 -6777.8163 1428.5036 21702.196 -30337.055 294.56547 363.42307 1.0052127 0.075 + 155000 -5547.9284 1256.6973 -6804.6257 1379.9059 21727.03 -30338.382 301.35519 35.503942 1.0222903 0.0775 + 160000 -5481.1383 1320.4344 -6801.5727 1390.3369 21729.299 -30337.062 316.63929 50.667563 1.0171266 0.08 + 165000 -5560.7321 1247.5004 -6808.2325 1422.2771 21662.917 -30341.024 299.14978 56.116137 1.0020068 0.0825 + 170000 -5541.3469 1257.9624 -6799.3094 1381.0133 21739.612 -30336.303 301.65856 -176.83515 1.0084433 0.085 + 175000 -5481.784 1239.9656 -6721.7496 1366.9952 21834.266 -30335.454 297.34293 377.28019 1.0297034 0.0875 + 180000 -5609.1447 1180.414 -6789.5587 1410.9273 21683.391 -30338.821 283.06249 203.46781 1.013427 0.09 + 185000 -5508.6637 1237.4229 -6746.0866 1401.5929 21736.318 -30334.806 296.7332 287.44715 1.0114427 0.0925 + 190000 -5524.666 1249.3421 -6774.008 1414.6887 21711.574 -30338.223 299.5914 108.63857 0.99681381 0.095 + 195000 -5613.4475 1179.1603 -6792.6078 1415.5702 21704.669 -30335.058 282.76187 -4.252137 1.0025742 0.0975 + 200000 -5577.1744 1219.3392 -6796.5136 1358.774 21688.932 -30339.219 292.39674 -339.31655 1.0272643 0.1 + 205000 -5473.5241 1291.8332 -6765.3573 1364.0148 21747.958 -30335.578 309.78075 -140.98482 1.0134706 0.1025 + 210000 -5412.6987 1304.0334 -6716.7321 1399.175 21790.687 -30338.388 312.70635 475.62089 1.0077929 0.105 + 215000 -5498.5445 1272.4319 -6770.9765 1305.2038 21853.899 -30334.099 305.12834 -964.41064 1.0117303 0.1075 + 220000 -5552.46 1236.8433 -6789.3033 1413.5383 21633.766 -30337.007 296.59421 126.59413 1.0135386 0.11 + 225000 -5463.5199 1281.9539 -6745.4738 1391.2426 21760.978 -30337.489 307.41171 372.98508 1.0154691 0.1125 + 230000 -5556.2415 1213.9742 -6770.2157 1373.9439 21746.355 -30331.29 291.11021 310.03784 1.0411894 0.115 + 235000 -5468.6139 1256.2727 -6724.8866 1419.9068 21755.903 -30337.057 301.25335 446.80106 1.008653 0.1175 + 240000 -5505.2272 1297.8543 -6803.0815 1389.9299 21721.555 -30336.374 311.22461 -216.33356 1.0007317 0.12 + 245000 -5556.4175 1231.9791 -6788.3966 1385.1734 21697.589 -30334.804 295.42778 -115.65689 1.0127289 0.1225 + 250000 -5570.5583 1261.1376 -6831.6959 1404.3069 21667.366 -30337.205 302.41997 -90.154201 1.0161797 0.125 + 255000 -5581.0101 1222.6213 -6803.6314 1393.6905 21687.538 -30336.542 293.18377 -58.781363 1.013542 0.1275 + 260000 -5552.6506 1225.5794 -6778.2299 1446.9969 21648.822 -30336.275 293.89312 749.70391 1.0136121 0.13 + 265000 -5527.9133 1245.5123 -6773.4255 1328.166 21792.912 -30336.854 298.67302 -825.99884 1.0063806 0.1325 + 270000 -5565.2798 1266.7326 -6832.0124 1488.6605 21582.46 -30339.347 303.76165 1592.7435 1.0374567 0.135 + 275000 -5567.4599 1211.9673 -6779.4272 1306.1895 21846.2 -30334.296 290.62895 -1062.6911 1.0107451 0.1375 + 280000 -5456.1965 1291.476 -6747.6725 1324.4174 21839.645 -30339.854 309.69509 -531.26163 1.0140474 0.14 + 285000 -5561.638 1229.3427 -6790.9808 1353.7161 21794.932 -30334.258 294.79557 -269.97414 1.0110394 0.1425 + 290000 -5486.1623 1276.1413 -6762.3036 1380.4775 21777.115 -30336.678 306.01784 -56.691362 1.0105051 0.145 + 295000 -5531.2556 1253.1859 -6784.4415 1354.9857 21750.76 -30338.549 300.51314 -555.4993 1.0159961 0.1475 + 300000 -5583.1864 1250.0209 -6833.2073 1431.4702 21654.547 -30337.557 299.75419 360.48799 1.0226237 0.15 + 305000 -5492.9399 1263.2527 -6756.1925 1385.9115 21749.132 -30337.333 302.92716 -94.633279 1.0008411 0.1525 + 310000 -5583.9951 1217.2631 -6801.2582 1439.2175 21660.614 -30332.833 291.89889 575.48041 1.0264848 0.155 + 315000 -5554.3025 1247.1517 -6801.4542 1305.5379 21807.382 -30337.478 299.06616 -1206.257 1.0085908 0.1575 + 320000 -5596.1914 1233.0393 -6829.2307 1431.9073 21667.612 -30337.859 295.682 745.35002 1.0291 0.16 + 325000 -5532.0063 1245.6006 -6777.6069 1479.6102 21640.94 -30338.346 298.69419 1390.0859 1.0311996 0.1625 + 330000 -5511.0183 1236.8356 -6747.854 1332.4766 21826.148 -30335.853 296.59237 -346.80349 1.020578 0.165 + 335000 -5512.3188 1238.1769 -6750.4957 1324.5201 21836.682 -30338.607 296.91401 -457.67242 1.0274241 0.1675 + 340000 -5504.0924 1242.6354 -6746.7278 1432.7958 21708.299 -30333.659 297.98314 674.26615 1.0055018 0.17 + 345000 -5522.5796 1265.0266 -6787.6062 1382.0078 21743.218 -30338.398 303.35254 -151.81029 1.0067371 0.1725 + 350000 -5545.7535 1267.9089 -6813.6624 1404.8847 21674.34 -30337.099 304.04372 128.71982 1.0135501 0.175 + 355000 -5499.0073 1275.2358 -6774.2431 1484.721 21658.719 -30337.688 305.80071 1468.7411 1.0346991 0.1775 + 360000 -5540.4144 1242.034 -6782.4484 1440.0683 21684.985 -30338.578 297.83892 662.99982 1.0085045 0.18 + 365000 -5472.9692 1267.5044 -6740.4736 1350.7945 21806.742 -30338.576 303.94672 -303.53857 1.0149794 0.1825 + 370000 -5563.7998 1257.4972 -6821.297 1363.9578 21745.681 -30339.039 301.54699 -616.39894 1.0015708 0.185 + 375000 -5494.3434 1204.4931 -6698.8365 1308.4989 21883.359 -30336.609 288.83665 -1009.8181 0.99179087 0.1875 + 380000 -5516.3392 1223.7518 -6740.0911 1355.9449 21816.149 -30337.588 293.45488 36.407556 1.02042 0.19 + 385000 -5534.8879 1226.8136 -6761.7015 1433.131 21698.233 -30336.201 294.18909 1224.3283 1.0416014 0.1925 + 390000 -5506.0676 1262.1264 -6768.194 1449.4667 21692.815 -30334.182 302.65707 932.23514 1.0216439 0.195 + 395000 -5601.9693 1234.2373 -6836.2066 1425.5787 21658.64 -30337.816 295.96929 254.00155 1.0148905 0.1975 + 400000 -5523.9324 1254.811 -6778.7434 1371.5302 21763.333 -30334.914 300.90286 -41.512594 1.0129399 0.2 + 405000 -5615.7822 1209.5514 -6825.3336 1431.7105 21604.804 -30336.544 290.04963 385.86176 1.02069 0.2025 + 410000 -5564.9317 1238.9308 -6803.8625 1334.6011 21725.649 -30342.03 297.09479 -668.14712 1.0114204 0.205 + 415000 -5565.723 1201.4165 -6767.1395 1407.6153 21731.714 -30339.794 288.09888 284.39352 1.0181526 0.2075 + 420000 -5514.1574 1259.6967 -6773.8542 1397.8555 21765.77 -30335.098 302.07445 -93.583513 1.003494 0.21 + 425000 -5566.4826 1233.6609 -6800.1435 1354.6757 21745.391 -30337.658 295.83106 -543.91774 1.0113019 0.2125 + 430000 -5544.9786 1227.5367 -6772.5153 1391.971 21756.332 -30337.075 294.36248 -52.853646 1.0029339 0.215 + 435000 -5457.9703 1243.8289 -6701.7992 1355.8144 21842.63 -30336.263 298.26936 96.07031 1.0162599 0.2175 + 440000 -5444.1352 1261.5679 -6705.7031 1327.5589 21849.174 -30337.667 302.52315 -159.33457 1.0201548 0.22 + 445000 -5569.3089 1253.1592 -6822.4681 1450.3256 21615.072 -30333.867 300.50675 497.07257 1.0162108 0.2225 + 450000 -5499.4632 1276.3744 -6775.8376 1436.3419 21681.852 -30337.613 306.07374 416.13585 1.0087874 0.225 + 455000 -5527.7917 1199.0123 -6726.804 1371.2866 21773.376 -30335.146 287.52235 -330.60298 0.99153512 0.2275 + 460000 -5634.9316 1214.1147 -6849.0463 1471.6124 21618.634 -30339.723 291.14391 831.79551 1.0154836 0.23 + 465000 -5492.5994 1247.2074 -6739.8067 1425.1188 21720.998 -30333.086 299.0795 782.63379 1.0210767 0.2325 + 470000 -5528.6598 1242.3825 -6771.0422 1413.2305 21674.806 -30339.41 297.9225 371.75935 1.018354 0.235 + 475000 -5570.6679 1274.1035 -6844.7714 1423.8596 21624.648 -30335.904 305.52919 243.67178 1.0157084 0.2375 + 480000 -5487.1119 1241.0548 -6728.1667 1421.7563 21732.588 -30338.933 297.60413 814.07568 1.0255732 0.24 + 485000 -5575.4172 1242.9613 -6818.3785 1402.7921 21677.417 -30338.336 298.0613 20.597793 1.0229831 0.2425 + 490000 -5578.303 1221.4158 -6799.7188 1430.5395 21694.761 -30336.572 292.89469 430.02647 1.0131845 0.245 + 495000 -5573.1773 1222.1238 -6795.3011 1502.7203 21609.264 -30338.892 293.06448 1494.9905 1.0226527 0.2475 + 500000 -5470.7153 1208.6593 -6679.3745 1401.9799 21819.612 -30335.747 289.83569 552.82762 1.003873 0.25 + 505000 -5626.3096 1246.8303 -6873.1399 1504.3826 21517.763 -30336.928 298.98909 1008.6542 1.0255205 0.2525 + 510000 -5562.1313 1242.0291 -6804.1604 1360.6445 21745.689 -30334.283 297.83775 -300.55499 1.021938 0.255 + 515000 -5558.6681 1241.9812 -6800.6493 1399.186 21683.627 -30339.266 297.82628 -293.22181 1.0035268 0.2575 + 520000 -5450.6773 1276.8169 -6727.4943 1246.5956 21918.914 -30335.226 306.17986 -1527.0713 1.0017384 0.26 + 525000 -5495.0769 1260.1524 -6755.2294 1413.8065 21708.663 -30338.153 302.18372 193.49778 1.0090792 0.2625 + 530000 -5519.0236 1258.9944 -6778.018 1423.1288 21726.251 -30338.72 301.90602 402.81349 1.0058563 0.265 + 535000 -5523.3166 1265.8203 -6789.1369 1403.2616 21669.617 -30333.964 303.54286 -212.90176 1.0022662 0.2675 + 540000 -5469.6354 1267.2634 -6736.8988 1354.6136 21815.059 -30334.909 303.88893 -143.78705 1.0102562 0.27 + 545000 -5475.0926 1332.0416 -6807.1342 1362.668 21728.374 -30335.495 319.42269 -408.94813 1.008036 0.2725 + 550000 -5604.8235 1220.5785 -6825.4021 1466.9259 21609.628 -30340.185 292.69392 562.0671 0.99832249 0.275 + 555000 -5546.9498 1194.3285 -6741.2783 1324.6404 21805.776 -30334.506 286.39919 -831.67066 1.0068815 0.2775 + 560000 -5505.8852 1231.4127 -6737.2978 1403.1199 21743.566 -30336.518 295.29195 134.18023 1.0068652 0.28 + 565000 -5620.5688 1225.712 -6846.2808 1418.5638 21624.884 -30336.305 293.92493 -45.194557 1.0148173 0.2825 + 570000 -5522.2261 1265.1646 -6787.3907 1431.1348 21666.003 -30337.479 303.38564 470.11582 1.0164271 0.285 + 575000 -5586.7521 1277.3002 -6864.0523 1411.585 21610.013 -30338.867 306.29575 3.3115648 1.0213675 0.2875 + 580000 -5612.9476 1236.9792 -6849.9268 1385.7307 21698.533 -30334.246 296.62679 -180.75952 1.0145947 0.29 + 585000 -5564.6816 1225.6381 -6790.3197 1333.2129 21796.701 -30335.104 293.90721 -690.26993 1.0116307 0.2925 + 590000 -5505.6734 1225.965 -6731.6383 1388.9635 21758.959 -30333.889 293.98559 227.32836 1.0145465 0.295 + 595000 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296.67409 -143.30329 1.0091248 0.7325 + 1470000 -5531.193 1192.152 -6723.345 1469.0677 21691.379 -30335.647 285.87727 1394.3946 1.0169307 0.735 + 1475000 -5469.5125 1278.1335 -6747.6459 1374.8894 21790.652 -30336.291 306.49556 -320.76133 0.99923276 0.7375 + 1480000 -5569.7546 1225.3414 -6795.096 1369.5149 21704.23 -30339.752 293.83607 -295.5674 1.0086 0.74 + 1485000 -5570.7676 1229.0249 -6799.7924 1358.7067 21754.36 -30339.644 294.71935 -446.59245 1.0146734 0.7425 + 1490000 -5578.5093 1213.6038 -6792.1131 1361.3024 21746.493 -30339.324 291.0214 -279.50424 1.0188708 0.745 + 1495000 -5574.1959 1286.4102 -6860.6061 1391.1258 21669.913 -30338.466 308.48032 -404.60846 1.0074475 0.7475 + 1500000 -5499.0758 1257.807 -6756.8828 1293.9978 21854.746 -30334.433 301.62128 -995.33111 1.0061023 0.75 + 1505000 -5555.8386 1224.7451 -6780.5837 1398.2158 21721.994 -30333.807 293.69307 -108.77374 1.0017368 0.7525 + 1510000 -5516.6813 1232.9495 -6749.6308 1375.2615 21790.724 -30334.453 295.66048 -254.2256 0.99292399 0.755 + 1515000 -5506.9453 1232.1963 -6739.1416 1398.9195 21765.1 -30337.448 295.47987 280.5709 1.0059619 0.7575 + 1520000 -5572.2466 1203.9157 -6776.1623 1358.6224 21732.12 -30335.917 288.69819 -423.60315 1.013085 0.76 + 1525000 -5479.3423 1275.6547 -6754.997 1348.5224 21788.359 -30339.133 305.90116 -332.75562 1.0119609 0.7625 + 1530000 -5518.4409 1217.0162 -6735.4571 1369.8978 21790.403 -30338.036 291.83967 -211.5446 0.99823021 0.765 + 1535000 -5517.1315 1253.9634 -6771.0948 1424.4081 21690.09 -30337.668 300.69959 341.83304 1.0041481 0.7675 + 1540000 -5528.0888 1233.7041 -6761.7929 1405.9083 21710.981 -30336.39 295.84144 -32.35231 0.99593709 0.77 + 1545000 -5539.0412 1238.631 -6777.6723 1311.2439 21794.343 -30337.582 297.0229 -1311.3664 0.9961313 0.7725 + 1550000 -5595.0349 1240.5672 -6835.602 1441.0277 21670.814 -30338.678 297.48719 536.63002 1.015083 0.775 + 1555000 -5560.1434 1270.6028 -6830.7462 1443.7953 21637.472 -30333.488 304.68972 470.00368 1.0055598 0.7775 + 1560000 -5496.2344 1234.9637 -6731.1981 1330.1568 21821.108 -30335.645 296.14347 -757.48104 0.99041343 0.78 + 1565000 -5556.0238 1248.445 -6804.4688 1397.6434 21692.421 -30338.719 299.37629 -10.691405 1.0182037 0.7825 + 1570000 -5552.3079 1243.8513 -6796.1592 1397.511 21703.363 -30336.571 298.27472 32.033113 1.0089905 0.785 + 1575000 -5468.3273 1283.6822 -6752.0094 1361.1407 21787.216 -30336.574 307.82614 -164.38813 1.0083064 0.7875 + 1580000 -5488.0146 1232.0833 -6720.0979 1320.826 21829.873 -30335.918 295.45277 -417.97233 1.018807 0.79 + 1585000 -5535.136 1231.2656 -6766.4015 1440.3397 21691.223 -30338.944 295.25667 686.24285 1.0137355 0.7925 + 1590000 -5507.2274 1257.8264 -6765.0537 1388.9839 21718.772 -30335.685 301.62593 -138.69824 1.003965 0.795 + 1595000 -5493.0812 1223.4504 -6716.5316 1396.9927 21762.807 -30334.042 293.38261 250.04963 1.0085422 0.7975 + 1600000 -5542.7694 1256.563 -6799.3324 1383.1567 21709.773 -30338.003 301.32298 -51.465013 1.0131684 0.8 + 1605000 -5453.3692 1285.3523 -6738.7215 1362.5454 21803.391 -30335.547 308.22664 -321.46323 1.0029343 0.8025 + 1610000 -5503.9352 1259.2527 -6763.188 1421.5945 21696.436 -30334.944 301.96798 625.60637 1.0255178 0.805 + 1615000 -5476.5761 1246.0171 -6722.5932 1347.6694 21806.697 -30336.05 298.79408 -91.329161 1.0116498 0.8075 + 1620000 -5507.707 1237.031 -6744.738 1371.7693 21775.289 -30334.991 296.63921 -213.66643 1.0063229 0.81 + 1625000 -5456.168 1228.6159 -6684.7839 1372.1719 21806.244 -30336.186 294.62128 293.33707 1.0094967 0.8125 + 1630000 -5650.3002 1225.7447 -6876.0449 1465.0474 21543.498 -30336.757 293.93277 417.30626 1.0158098 0.815 + 1635000 -5450.49 1275.0111 -6725.5011 1481.2268 21684.726 -30337.105 305.74683 1426.6931 1.0094353 0.8175 + 1640000 -5617.7996 1227.1912 -6844.9908 1412.9007 21647.959 -30339.808 294.27965 -64.670241 1.0184979 0.82 + 1645000 -5479.4668 1286.8935 -6766.3603 1430.311 21716.402 -30338.791 308.59622 613.1652 1.002358 0.8225 + 1650000 -5500.2183 1280.3487 -6780.567 1385.4426 21748.104 -30337.348 307.02677 -65.179279 1.0098634 0.825 + 1655000 -5560.2962 1223.2516 -6783.5478 1311.1561 21783.296 -30335.262 293.33493 -1444.809 0.98862533 0.8275 + 1660000 -5560.1654 1221.3779 -6781.5433 1384.641 21766.196 -30337.4 292.88562 -30.809802 1.0055892 0.83 + 1665000 -5459.1135 1261.4358 -6720.5493 1334.6877 21855.177 -30336.221 302.49147 -691.93836 0.98631443 0.8325 + 1670000 -5426.4876 1277.2456 -6703.7331 1301.4361 21883.289 -30338.807 306.28264 -769.6473 1.0029395 0.835 + 1675000 -5560.3658 1228.1155 -6788.4813 1421.5285 21710.575 -30339.538 294.50128 134.14929 0.99950546 0.8375 + 1680000 -5533.0079 1239.2308 -6772.2386 1466.9684 21661.29 -30336.838 297.16672 1000.7926 1.0093582 0.84 + 1685000 -5532.7803 1282.6992 -6815.4795 1387.5896 21673.135 -30336.269 307.59043 -293.90054 1.0036548 0.8425 + 1690000 -5533.8573 1242.0398 -6775.8971 1295.4859 21813.204 -30335.918 297.84032 -1072.3783 1.0103958 0.845 + 1695000 -5569.1131 1236.3099 -6805.423 1391.4947 21734.459 -30337.665 296.46629 -42.852437 1.0020314 0.8475 + 1700000 -5514.6926 1236.9596 -6751.6522 1297.2083 21861.079 -30337.966 296.6221 -1035.3111 1.0148487 0.85 + 1705000 -5481.7854 1264.9348 -6746.7202 1394.4051 21765.618 -30334.989 303.33053 68.230386 0.99805471 0.8525 + 1710000 -5628.7652 1218.5732 -6847.3385 1424.8975 21629.726 -30339.018 292.21306 -18.822494 1.0061359 0.855 + 1715000 -5535.4768 1269.0696 -6804.5464 1310.4991 21778.662 -30338.107 304.32206 -1128.3429 1.0076215 0.8575 + 1720000 -5612.6083 1193.1968 -6805.8051 1383.4907 21742.438 -30339.657 286.12782 -186.2314 1.0077134 0.86 + 1725000 -5483.1527 1278.2192 -6761.3719 1414.7937 21718.362 -30332.789 306.51613 275.89425 0.99757317 0.8625 + 1730000 -5507.2292 1239.3969 -6746.626 1349.4125 21760.595 -30336.33 297.20655 -160.96278 1.0175868 0.865 + 1735000 -5471.6725 1274.6169 -6746.2893 1353.4867 21778.13 -30334.321 305.65228 -455.73375 0.99473861 0.8675 + 1740000 -5457.1173 1292.0777 -6749.195 1354.1425 21798.549 -30337.698 309.83938 105.28166 1.013856 0.87 + 1745000 -5526.7699 1217.2299 -6743.9998 1374.1349 21775.087 -30335.943 291.89093 21.249651 1.0097813 0.8725 + 1750000 -5558.9441 1238.0218 -6796.966 1398.6419 21742.403 -30337.165 296.87681 258.79723 1.0189989 0.875 + 1755000 -5510.581 1278.8181 -6789.3991 1388.2658 21710.876 -30337.981 306.65974 475.10366 1.0315721 0.8775 + 1760000 -5530.9869 1295.8685 -6826.8554 1479.5118 21573.341 -30338.944 310.74841 748.89788 1.0132734 0.88 + 1765000 -5533.3839 1317.0507 -6850.4347 1435.6808 21644.207 -30333.746 315.8279 594.0529 1.0192713 0.8825 + 1770000 -5465.8084 1240.5045 -6706.3129 1292.0385 21900.378 -30339.129 297.47215 -1025.2013 1.0024888 0.885 + 1775000 -5599.0359 1221.6792 -6820.7151 1462.1624 21619.581 -30339.425 292.95787 626.3862 1.0091902 0.8875 + 1780000 -5538.0385 1264.6729 -6802.7114 1372.7663 21730.471 -30338.894 303.26773 -192.55416 1.0065058 0.89 + 1785000 -5428.1822 1333.9892 -6762.1715 1389.1017 21728.7 -30336.27 319.88974 104.29655 1.0139352 0.8925 + 1790000 -5508.9545 1287.0739 -6796.0284 1445.185 21652.743 -30336.902 308.63947 391.87637 1.0000323 0.895 + 1795000 -5523.6516 1235.1646 -6758.8162 1418.1244 21721.296 -30337.575 296.19166 666.61502 1.0229146 0.8975 + 1800000 -5572.6377 1214.1205 -6786.7582 1392.4223 21722.483 -30335.66 291.14528 -97.658277 1.0013673 0.9 + 1805000 -5546.2419 1219.6808 -6765.9227 1366.9631 21762.107 -30337.944 292.47866 -57.351578 1.0188349 0.9025 + 1810000 -5570.7715 1247.1279 -6817.8994 1386.5773 21707.994 -30338.467 299.06045 128.40982 1.018309 0.905 + 1815000 -5527.1768 1236.8139 -6763.9907 1370.0226 21756.947 -30337.433 296.58716 -58.429002 1.0156077 0.9075 + 1820000 -5392.8702 1296.598 -6689.4682 1422.7107 21835.725 -30339.535 310.92334 1096.9698 1.0098001 0.91 + 1825000 -5403.1407 1273.2353 -6676.3761 1398.7473 21821.771 -30338.272 305.32099 575.09164 1.009625 0.9125 + 1830000 -5533.275 1223.962 -6757.237 1302.4782 21879.688 -30335.303 293.50528 -794.93635 1.0164392 0.915 + 1835000 -5537.9594 1230.3716 -6768.331 1359.2088 21780.105 -30337.746 295.04229 -301.96771 1.012533 0.9175 + 1840000 -5496.5607 1259.4196 -6755.9803 1392.4138 21810.816 -30335.129 302.00799 308.79809 1.0087261 0.92 + 1845000 -5516.8276 1233.6195 -6750.4471 1356.0628 21770.257 -30336.985 295.82114 -563.13925 0.99534053 0.9225 + 1850000 -5551.2862 1216.2779 -6767.5641 1315.4137 21779.186 -30338.525 291.66263 -1234.4928 0.9977088 0.925 + 1855000 -5514.4008 1278.8525 -6793.2533 1477.9866 21661.793 -30338.935 306.668 1192.9778 1.0126178 0.9275 + 1860000 -5445.2459 1262.0113 -6707.2573 1295.8277 21920.956 -30333.967 302.62948 -1093.2105 0.98876382 0.93 + 1865000 -5479.9894 1263.9698 -6743.9592 1342.5201 21812.688 -30335.4 303.09913 -141.70262 1.018338 0.9325 + 1870000 -5526.4829 1205.3702 -6731.8531 1376.0037 21811.821 -30332.663 289.04698 186.81383 1.0172778 0.935 + 1875000 -5566.9793 1221.657 -6788.6363 1352.419 21753.184 -30332.134 292.95254 -421.96475 1.0091425 0.9375 + 1880000 -5497.1676 1282.0374 -6779.205 1398.213 21722.715 -30339.838 307.43173 37.827778 1.0039977 0.94 + 1885000 -5557.4404 1233.9174 -6791.3578 1449.936 21642.09 -30339.056 295.89259 883.49759 1.0130214 0.9425 + 1890000 -5506.733 1295.1267 -6801.8597 1297.6178 21817.614 -30338.332 310.57052 -1073.8778 1.0180788 0.945 + 1895000 -5533.7516 1257.448 -6791.1996 1345.2106 21764.458 -30338.571 301.53521 -526.55649 1.0121615 0.9475 + 1900000 -5541.0051 1258.9341 -6799.9391 1381.6398 21733.321 -30338.593 301.89155 -252.04317 1.008764 0.95 + 1905000 -5609.2146 1182.6597 -6791.8743 1350.4308 21757.084 -30338.743 283.60101 -97.157492 1.0309631 0.9525 + 1910000 -5571.9982 1254.2855 -6826.2837 1389.361 21684.388 -30336.514 300.77683 -350.37238 1.0002085 0.955 + 1915000 -5504.046 1277.8838 -6781.9299 1392.3191 21732.799 -30339.549 306.43569 295.58866 1.0234965 0.9575 + 1920000 -5500.6241 1311.1129 -6811.737 1384.3734 21674.326 -30341.238 314.40401 84.788637 1.0209565 0.96 + 1925000 -5529.7992 1229.6795 -6759.4787 1408.9276 21763.324 -30339.966 294.87632 215.06361 1.0061547 0.9625 + 1930000 -5444.6302 1282.6892 -6727.3194 1334.5948 21864.664 -30333.059 307.58803 -76.344233 1.0195039 0.965 + 1935000 -5506.5314 1250.2755 -6756.8069 1346.0266 21804.791 -30335.384 299.81524 -400.10311 1.009444 0.9675 + 1940000 -5595.6735 1257.0187 -6852.6922 1445.275 21568.516 -30337.62 301.43225 543.8544 1.0288045 0.97 + 1945000 -5555.7495 1224.7877 -6780.5372 1333.6985 21795.754 -30338.445 293.70329 -560.62987 1.0145559 0.9725 + 1950000 -5481.8697 1239.3038 -6721.1735 1436.353 21745.545 -30335.269 297.18424 1090.0854 1.024844 0.975 + 1955000 -5586.7772 1263.8812 -6850.6584 1479.012 21594.084 -30335.219 303.07787 1031.8973 1.018222 0.9775 + 1960000 -5495.753 1254.4979 -6750.2508 1386.5525 21763.46 -30336.981 300.82776 72.271681 1.0073177 0.98 + 1965000 -5532.6074 1226.085 -6758.6924 1373.4537 21763.717 -30335.48 294.01437 49.27447 1.0207726 0.9825 + 1970000 -5592.2371 1226.5746 -6818.8117 1393.679 21701.959 -30338.233 294.13177 150.06013 1.0325882 0.985 + 1975000 -5564.1305 1237.5805 -6801.711 1398.2423 21736.76 -30338.459 296.77099 278.42773 1.0180523 0.9875 + 1980000 -5482.7493 1267.38 -6750.1292 1354.4265 21816.978 -30337.136 303.91688 -264.92549 1.0116111 0.99 + 1985000 -5486.0145 1244.3436 -6730.358 1338.1288 21844.074 -30336.86 298.39277 76.865939 1.0287137 0.9925 + 1990000 -5518.5592 1251.3748 -6769.9341 1251.2427 21885.87 -30337.966 300.07886 -1536.5189 1.0130877 0.995 + 1995000 -5487.626 1271.8163 -6759.4423 1356.5853 21769.656 -30337.831 304.9807 -374.70018 1.0071102 0.9975 + 2000000 -5510.6051 1219.5403 -6730.1454 1414.2091 21757.343 -30335.348 292.44495 576.54022 1.0102751 1 +Loop time of 13908.6 on 12 procs for 2000000 steps with 1800 atoms + +Performance: 12.424 ns/day, 1.932 hours/ns, 143.796 timesteps/s +95.4% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7652.9 | 8199.2 | 8886.6 | 354.2 | 58.95 +Bond | 25.21 | 26.012 | 27.096 | 14.0 | 0.19 +Kspace | 2159 | 2762 | 3232.9 | 533.0 | 19.86 +Neigh | 571.65 | 572.66 | 573.54 | 2.5 | 4.12 +Comm | 806.99 | 869.79 | 940.86 | 190.9 | 6.25 +Output | 0.032536 | 0.034245 | 0.041095 | 1.2 | 0.00 +Modify | 959.22 | 1140.3 | 1306.8 | 448.8 | 8.20 +Other | | 338.6 | | | 2.43 + +Nlocal: 150.000 ave 159 max 140 min +Histogram: 1 0 2 2 0 2 2 1 0 2 +Nghost: 6121.33 ave 6236 max 6003 min +Histogram: 2 0 0 3 0 2 2 2 0 1 +Neighs: 87038.7 ave 96826 max 77686 min +Histogram: 2 0 1 3 0 1 2 1 1 1 + +Total # of neighbors = 1044464 +Ave neighs/atom = 580.25778 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 89191 +Dangerous builds = 0 +Total wall time: 4:02:50 diff --git a/examples/USER/fep/SPCEhyd/fep01/fep01-q.fep b/examples/USER/fep/SPCEhyd/fep01/fep01-q.fep new file mode 100644 index 0000000000..553c231860 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep01/fep01-q.fep @@ -0,0 +1,22 @@ +# Time-averaged data for fix FEP +# TimeStep c_FEP[1] c_FEP[2] c_FEP[3] +100000 -0.00130466 18193.2 17742.3 +200000 -0.027526 18951.4 17742.7 +300000 -0.0459414 19629.2 17752.3 +400000 -0.0857092 21019.8 17772.6 +500000 -0.0982497 21457.5 17731.3 +600000 -0.137334 23057.4 17808.5 +700000 -0.170804 24395.7 17801 +800000 -0.223064 26797.3 17738.8 +900000 -0.261826 28800 17791.7 +1000000 -0.286374 30143.5 17783.4 +1100000 -0.349306 33728.2 17757.7 +1200000 -0.408164 37435.9 17787.7 +1300000 -0.496871 43896.5 17766.2 +1400000 -0.602917 53115.7 17749.9 +1500000 -0.72768 65474.3 17765 +1600000 -0.793802 73873.7 17785.7 +1700000 -0.912421 92487.7 17754.8 +1800000 -1.02249 109518 17762.7 +1900000 -1.12599 130115 17752.5 +2000000 -1.2899 174891 17768.3 diff --git a/examples/USER/fep/SPCEhyd/fep01/fep01-q.out b/examples/USER/fep/SPCEhyd/fep01/fep01-q.out new file mode 100644 index 0000000000..4d597f88b3 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep01/fep01-q.out @@ -0,0 +1,561 @@ +LAMMPS (29 Oct 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (29.204526 29.204526 29.204526) + 2 by 2 by 3 MPI processor grid + reading atoms ... + 1800 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 1200 bonds + reading angles ... + 600 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_data CPU = 0.019 seconds +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 600 = # of size 3 clusters + 0 = # of size 4 clusters + 0 = # of frozen angles + find clusters CPU = 0.001 seconds +Setting atom values ... + 3 settings made for charge +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.25066829 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0030719151 + estimated relative force accuracy = 9.250981e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 3757 800 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 8.214 | 8.226 | 8.244 Mbytes +Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density + 0 0 1344.0739 1251.046 93.027896 53.823145 30049.554 -30010.349 300 10284.878 24908.667 0.72058313 + 5000 26.813 -5450.5713 1282.0681 -6732.6394 1325.6489 21834.91 -30297.994 307.43909 -699.90679 18234.717 0.98431826 + 10000 55.604067 -5588.263 1217.9162 -6806.1792 1414.4085 21633.044 -30301.477 292.05551 23.383255 17964.154 0.99914336 + 15000 85.625894 -5502.4932 1306.1963 -6808.6896 1448.9698 21589.863 -30300.506 313.22502 674.44388 17764.828 1.010354 + 20000 119.30994 -5551.8753 1255.7906 -6807.6659 1438.0508 21600.534 -30296.631 301.13775 626.57778 17521.241 1.0244003 + 25000 153.36332 -5513.3214 1262.2974 -6775.6188 1448.1692 21624.738 -30300.649 302.69809 1082.1686 17539.064 1.0233594 + 30000 185.73754 -5517.07 1232.0851 -6749.1552 1351.1278 21743.778 -30297.746 295.45321 -345.74832 17641.782 1.0174009 + 35000 219.88466 -5461.9885 1261.1109 -6723.0993 1320.5321 21811.17 -30298.154 302.41356 -633.99545 17793.771 1.0087106 + 40000 250.59178 -5478.4688 1259.9078 -6738.3767 1361.0965 21772.195 -30298.632 302.12507 251.40827 17555.015 1.0224295 + 45000 284.497 -5586.9018 1253.0148 -6839.9166 1368.2811 21661.619 -30296.221 300.47212 -485.67054 17692.537 1.0144823 + 50000 318.07759 -5566.6473 1284.4686 -6851.116 1421.3632 21574.213 -30298.299 308.01473 123.81461 17666.827 1.0159586 + 55000 342.2475 -5571.8668 1241.516 -6813.3827 1320.1575 21745.617 -30297.514 297.71471 -757.9971 17553.891 1.0224949 + 60000 369.92714 -5405.9904 1244.2976 -6650.288 1321.6833 21864.494 -30297.613 298.38174 -252.7118 17729.038 1.0123936 + 65000 400.90471 -5536.8199 1222.3639 -6759.1838 1335.2142 21756.337 -30299.402 293.12205 -425.71516 17495.348 1.0259165 + 70000 421.35603 -5552.3284 1260.2509 -6812.5793 1340.624 21697.664 -30296.839 302.20732 -845.04229 17882.237 1.0037204 + 75000 441.98615 -5494.066 1286.3299 -6780.3959 1404.289 21683.326 -30293.835 308.46107 382.75947 17905.291 1.002428 + 80000 462.4957 -5550.6324 1269.8456 -6820.4779 1356.8274 21698.112 -30298.489 304.50813 -534.46185 17874.446 1.0041579 + 85000 483.079 -5656.6158 1200.4648 -6857.0807 1457.2846 21562.254 -30300.6 287.87068 686.28181 17521.518 1.0243841 + 90000 510.58296 -5480.2188 1242.2417 -6722.4605 1325.1999 21772.005 -30296.2 297.88874 -353.59603 17662.908 1.016184 + 95000 531.29699 -5537.8929 1265.7042 -6803.5971 1376.1449 21683.369 -30297.657 303.51504 -263.8525 17673.753 1.0155605 + 100000 563.33023 -5538.2683 1254.8684 -6793.1367 1343.4731 21751.843 -30299.503 300.91662 -623.47098 17857.853 1.0050909 +Loop time of 563.33 on 12 procs for 100000 steps with 1800 atoms + +Performance: 15.337 ns/day, 1.565 hours/ns, 177.516 timesteps/s +94.5% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 284.09 | 305.4 | 330.52 | 90.7 | 54.21 +Bond | 1.0744 | 1.1159 | 1.1633 | 3.1 | 0.20 +Kspace | 101.59 | 125.93 | 147.73 | 141.3 | 22.35 +Neigh | 22.44 | 22.466 | 22.486 | 0.3 | 3.99 +Comm | 39.278 | 41.789 | 46.639 | 43.5 | 7.42 +Output | 0.0012299 | 0.0012852 | 0.0017706 | 0.4 | 0.00 +Modify | 42.543 | 55.366 | 62.194 | 102.3 | 9.83 +Other | | 11.26 | | | 2.00 + +Nlocal: 150.000 ave 163 max 133 min +Histogram: 1 1 0 0 1 3 3 0 1 2 +Nghost: 6108.25 ave 6187 max 6048 min +Histogram: 3 0 2 1 1 1 1 1 1 1 +Neighs: 86944.1 ave 96258 max 75267 min +Histogram: 2 0 1 0 1 0 3 3 1 1 + +Total # of neighbors = 1043329 +Ave neighs/atom = 579.62722 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 4470 +Dangerous builds = 9 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.25102555 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0035374557 + estimated relative force accuracy = 1.0652943e-05 + using double precision FFTW3 + 3d grid and FFT values/proc = 3328 648 +FEP settings ... + temperature = 300.000000 + tail no + 1-1 charge + 2-2 charge +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 8.592 | 8.613 | 8.629 Mbytes +Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda v_qO v_qH + 0 -5538.2733 1254.8684 -6793.1417 1343.4731 21794.974 -30342.64 300.91662 -475.71492 1.0050909 0 -0 0 + 5000 -5579.9374 1246.75 -6826.6874 1443.8973 21614.133 -30343.039 298.96983 785.16037 1.0322471 0.0025 -0.002119 0.0010595 + 10000 -5528.9995 1276.273 -6805.2725 1375.6345 21734.24 -30343.779 306.04943 -41.209531 1.0207823 0.005 -0.004238 0.002119 + 15000 -5506.4227 1270.5724 -6776.9951 1356.298 21760.893 -30339.74 304.68242 -483.58254 1.0055775 0.0075 -0.006357 0.0031785 + 20000 -5520.1985 1271.766 -6791.9645 1413.5454 21705.741 -30340.672 304.96864 -25.849632 0.9997261 0.01 -0.008476 0.004238 + 25000 -5538.0793 1260.547 -6798.6264 1362.2032 21772.012 -30341.973 302.27834 -32.008776 1.0238659 0.0125 -0.010595 0.0052975 + 30000 -5519.1594 1267.066 -6786.2254 1327.6996 21784.187 -30341.191 303.84159 -919.77668 0.99978921 0.015 -0.012714 0.006357 + 35000 -5565.8849 1244.6201 -6810.505 1384.6297 21700.099 -30337.317 298.45908 -41.645325 1.0154185 0.0175 -0.014833 0.0074165 + 40000 -5610.4882 1225.8647 -6836.3529 1416.9133 21661.893 -30343.456 293.96154 86.229199 1.0091158 0.02 -0.016952 0.008476 + 45000 -5609.3562 1208.1008 -6817.457 1387.4135 21711.193 -30343.791 289.70178 -101.30213 1.0155204 0.0225 -0.019071 0.0095355 + 50000 -5512.9435 1272.9818 -6785.9253 1379.4084 21746.829 -30342.184 305.2602 -12.658236 1.0143328 0.025 -0.02119 0.010595 + 55000 -5568.845 1249.4227 -6818.2677 1397.4685 21704.581 -30340.419 299.61074 -409.12372 0.99849506 0.0275 -0.023309 0.0116545 + 60000 -5519.3972 1216.5292 -6735.9264 1369.8115 21830.467 -30342.642 291.72291 117.70437 1.0138535 0.03 -0.025428 0.012714 + 65000 -5525.0539 1229.5034 -6754.5573 1354.6275 21755.174 -30340.101 294.8341 -462.0909 1.0102225 0.0325 -0.027547 0.0137735 + 70000 -5472.0836 1237.9936 -6710.0772 1352.7747 21872.795 -30340.246 296.87006 -5.9707079 1.010185 0.035 -0.029666 0.014833 + 75000 -5514.8966 1241.7822 -6756.6788 1369.2902 21788.901 -30344.123 297.77855 -36.505421 1.0055449 0.0375 -0.031785 0.0158925 + 80000 -5501.5809 1244.4839 -6746.0648 1406.1414 21762.858 -30338.116 298.42642 356.6391 1.0044866 0.04 -0.033904 0.016952 + 85000 -5522.8846 1243.4435 -6766.3281 1277.631 21834.13 -30341.071 298.17693 -1501.0557 1.0030405 0.0425 -0.036023 0.0180115 + 90000 -5521.2512 1226.9606 -6748.2118 1426.6301 21707.584 -30342.842 294.22434 431.61937 1.0037325 0.045 -0.038142 0.019071 + 95000 -5606.4261 1239.7565 -6846.1826 1458.2919 21603.577 -30341.265 297.2928 452.3491 1.0064454 0.0475 -0.040261 0.0201305 + 100000 -5526.6029 1244.4811 -6771.084 1442.7891 21665.95 -30338.28 298.42575 499.20413 1.0045851 0.05 -0.04238 0.02119 + 105000 -5589.4951 1234.4407 -6823.9358 1418.2214 21663.025 -30341.483 296.01807 101.88725 1.0139383 0.0525 -0.044499 0.0222495 + 110000 -5511.859 1262.1425 -6774.0015 1353.5279 21783.245 -30339.283 302.66093 -199.18931 1.0257755 0.055 -0.046618 0.023309 + 115000 -5647.3449 1229.413 -6876.758 1408.5179 21641.362 -30341.598 294.81243 -298.02921 1.0020969 0.0575 -0.048737 0.0243685 + 120000 -5449.7674 1281.3875 -6731.155 1304.5518 21888.494 -30341.641 307.27589 -694.089 1.0046108 0.06 -0.050856 0.025428 + 125000 -5430.3553 1247.5854 -6677.9407 1342.5284 21899.097 -30343.376 299.17016 125.17161 1.0091105 0.0625 -0.052975 0.0264875 + 130000 -5604.2229 1198.864 -6803.0869 1343.9437 21741.913 -30342.105 287.4868 -1029.1103 0.99252488 0.065 -0.055094 0.027547 + 135000 -5550.2149 1233.8869 -6784.1018 1298.4466 21844.496 -30341.697 295.88527 -1083.9932 1.0128891 0.0675 -0.057213 0.0286065 + 140000 -5526.9114 1246.4353 -6773.3466 1346.6874 21790.011 -30343.164 298.89435 -384.65885 1.0089922 0.07 -0.059332 0.029666 + 145000 -5594.7954 1213.2963 -6808.0917 1391.4251 21671.653 -30341.641 290.94766 -59.474002 1.0195886 0.0725 -0.061451 0.0307255 + 150000 -5580.5229 1259.8574 -6840.3803 1384.5548 21703.974 -30342.483 302.11297 -91.974674 1.0257584 0.075 -0.06357 0.031785 + 155000 -5566.2712 1230.138 -6796.4093 1366.5696 21707.576 -30336.313 294.98629 -482.01244 1.0070735 0.0775 -0.065689 0.0328445 + 160000 -5491.8647 1293.2326 -6785.0974 1386.5259 21718.735 -30343.487 310.11633 -89.376893 1.0093767 0.08 -0.067808 0.033904 + 165000 -5531.3681 1279.7729 -6811.1409 1354.4198 21753.203 -30342.651 306.88869 -392.95774 1.0134907 0.0825 -0.069927 0.0349635 + 170000 -5594.2308 1213.4715 -6807.7023 1482.6412 21600.249 -30341.895 290.98966 928.50126 1.0132201 0.085 -0.072046 0.036023 + 175000 -5519.3482 1257.2925 -6776.6407 1420.4909 21726.753 -30340.213 301.49792 254.94623 0.98901793 0.0875 -0.074165 0.0370825 + 180000 -5426.929 1250.4297 -6677.3587 1356.866 21886.349 -30343.3 299.85221 -245.8457 0.98302571 0.09 -0.076284 0.038142 + 185000 -5512.2746 1245.7072 -6757.9817 1380.9844 21794.2 -30342.884 298.71976 149.05128 1.0150091 0.0925 -0.078403 0.0392015 + 190000 -5449.1514 1266.5892 -6715.7406 1324.6562 21889.348 -30342.468 303.72725 -620.02591 1.0004189 0.095 -0.080522 0.040261 + 195000 -5479.3945 1315.5655 -6794.96 1485.0588 21649.278 -30344.957 315.47174 1314.4492 1.0231026 0.0975 -0.082641 0.0413205 + 200000 -5563.7047 1217.2005 -6780.9051 1358.0191 21745.737 -30342.731 291.88386 -588.88047 1.0064764 0.1 -0.08476 0.04238 + 205000 -5580.3808 1230.1745 -6810.5553 1411.4424 21686.461 -30344.166 294.99504 214.77057 1.0029345 0.1025 -0.086879 0.0434395 + 210000 -5498.3534 1242.7043 -6741.0576 1370.6141 21796.013 -30341.015 297.99966 -26.716679 1.0117516 0.105 -0.088998 0.044499 + 215000 -5458.5956 1250.9454 -6709.541 1395.6557 21783.461 -30338.225 299.97588 406.41699 1.0137518 0.1075 -0.091117 0.0455585 + 220000 -5626.602 1214.9754 -6841.5774 1473.3289 21571.914 -30341.748 291.3503 599.47976 1.0096167 0.11 -0.093236 0.046618 + 225000 -5600.5356 1224.9039 -6825.4395 1342.4891 21754.804 -30341.025 293.73115 -626.27228 1.0198862 0.1125 -0.095355 0.0476775 + 230000 -5454.9477 1275.1464 -6730.0941 1372.8993 21798.515 -30340.963 305.77926 154.34847 1.0029435 0.115 -0.097474 0.048737 + 235000 -5481.9555 1227.4931 -6709.4486 1352.587 21840.233 -30343.313 294.35203 -208.20676 1.0008406 0.1175 -0.099593 0.0497965 + 240000 -5558.573 1218.8864 -6777.4595 1385.8452 21752.45 -30343.537 292.28816 162.10969 1.0215047 0.12 -0.101712 0.050856 + 245000 -5520.9207 1225.4691 -6746.3898 1338.4141 21841.905 -30342.557 293.86667 -587.07136 0.99909027 0.1225 -0.103831 0.0519155 + 250000 -5469.8293 1274.8021 -6744.6315 1384.4128 21775.904 -30342.629 305.69671 64.465989 1.0105027 0.125 -0.10595 0.052975 + 255000 -5583.4632 1209.565 -6793.0282 1426.1758 21667.168 -30342.466 290.0529 515.82984 1.0156235 0.1275 -0.108069 0.0540345 + 260000 -5536.1405 1237.073 -6773.2135 1357.8241 21771.52 -30340.823 296.64929 -438.57147 1.0071049 0.13 -0.110188 0.055094 + 265000 -5611.0013 1237.3831 -6848.3844 1417.6236 21598.469 -30339.452 296.72365 -367.70672 0.99925355 0.1325 -0.112307 0.0561535 + 270000 -5551.1345 1227.3483 -6778.4827 1430.3281 21692.104 -30340.818 294.31731 287.00159 1.0010721 0.135 -0.114426 0.057213 + 275000 -5602.2651 1241.1358 -6843.4009 1391.9031 21673.697 -30343.58 297.62355 -264.79926 1.014186 0.1375 -0.116545 0.0582725 + 280000 -5505.2292 1277.7478 -6782.9769 1380.5349 21747.333 -30343.992 306.40307 39.871379 1.0224709 0.14 -0.118664 0.059332 + 285000 -5527.7736 1230.4336 -6758.2072 1397.1892 21732.299 -30342.417 295.05716 276.95418 1.0126839 0.1425 -0.120783 0.0603915 + 290000 -5450.4061 1265.2269 -6715.6329 1360.3141 21842.086 -30344 303.40057 207.59349 1.0147077 0.145 -0.122902 0.061451 + 295000 -5617.5993 1217.4105 -6835.0098 1487.1573 21606.767 -30340.365 291.93424 808.20982 1.0058589 0.1475 -0.125021 0.0625105 + 300000 -5543.8664 1236.4411 -6780.3075 1377.4792 21755.298 -30344.078 296.49776 -182.45633 1.0097782 0.15 -0.12714 0.06357 + 305000 -5609.1426 1227.6292 -6836.7719 1437.6073 21603.923 -30343.337 294.38468 575.20852 1.0196556 0.1525 -0.129259 0.0646295 + 310000 -5549.1828 1228.5889 -6777.7717 1394.6395 21691.45 -30340.369 294.61482 348.39727 1.0352996 0.155 -0.131378 0.065689 + 315000 -5535.243 1248.2444 -6783.4874 1342.2366 21792.192 -30343.483 299.32819 -625.73677 1.0050826 0.1575 -0.133497 0.0667485 + 320000 -5534.3687 1255.4471 -6789.8158 1391.0816 21739.717 -30344.081 301.05539 302.16436 1.0216155 0.16 -0.135616 0.067808 + 325000 -5471.3922 1279.3669 -6750.759 1350.9981 21795.148 -30342.392 306.79133 -197.30703 1.0143436 0.1625 -0.137735 0.0688675 + 330000 -5598.8232 1226.4651 -6825.2883 1398.7718 21677.079 -30344.7 294.10553 -213.61646 1.0148836 0.165 -0.139854 0.069927 + 335000 -5551.2529 1259.6937 -6810.9465 1387.3662 21685.187 -30344.308 302.07371 138.36812 1.0229544 0.1675 -0.141973 0.0709865 + 340000 -5614.9057 1204.9401 -6819.8458 1400.0625 21668.036 -30343.31 288.94385 -386.78257 0.99685483 0.17 -0.144092 0.072046 + 345000 -5520.3252 1245.9691 -6766.2942 1428.7502 21696.415 -30345.482 298.78256 768.45616 1.0192108 0.1725 -0.146211 0.0731055 + 350000 -5513.6753 1249.7279 -6763.4032 1284.3535 21864.411 -30343.729 299.68392 -1040.9933 1.0093189 0.175 -0.14833 0.074165 + 355000 -5547.2549 1244.5392 -6791.7941 1428.3735 21662.08 -30340.69 298.43968 593.10891 1.0193921 0.1775 -0.150449 0.0752245 + 360000 -5589.7133 1245.8181 -6835.5314 1358.8909 21676.184 -30346.212 298.74637 -615.61801 1.0169406 0.18 -0.152568 0.076284 + 365000 -5487.1246 1223.3024 -6710.427 1333.6832 21894.405 -30339.2 293.34711 -385.63992 0.99614598 0.1825 -0.154687 0.0773435 + 370000 -5557.3434 1261.7301 -6819.0735 1430.6594 21657.49 -30341.935 302.56204 256.97472 1.0130616 0.185 -0.156806 0.078403 + 375000 -5453.0587 1250.9921 -6704.0508 1417.9533 21782.943 -30342.475 299.98708 759.88581 1.005535 0.1875 -0.158925 0.0794625 + 380000 -5556.3547 1222.266 -6778.6207 1358.5536 21812.006 -30343.775 293.09858 -190.9931 1.0101874 0.19 -0.161044 0.080522 + 385000 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0.336921 + 1595000 -5610.6145 1230.3441 -6840.9586 1511.4929 21579.699 -30370.822 295.0357 1400.7717 1.0243843 0.7975 -0.675961 0.3379805 + 1600000 -5491.408 1268.4415 -6759.8495 1321.4258 21860.885 -30367.203 304.17145 -684.17812 1.0109371 0.8 -0.67808 0.33904 + 1605000 -5605.9376 1229.4973 -6835.4349 1358.4846 21752.878 -30376.308 294.83264 -415.45398 1.0211259 0.8025 -0.680199 0.3400995 + 1610000 -5460.3646 1272.2569 -6732.6215 1287.6367 21919.033 -30377.556 305.08636 -1142.3466 1.0015738 0.805 -0.682318 0.341159 + 1615000 -5526.5568 1289.8001 -6816.3569 1429.3397 21650.996 -30374.701 309.29322 -24.570161 0.99788407 0.8075 -0.684437 0.3422185 + 1620000 -5535.2137 1227.5421 -6762.7558 1398.9652 21806.783 -30374.667 294.36379 27.416625 0.99409746 0.81 -0.686556 0.343278 + 1625000 -5561.6432 1218.8583 -6780.5015 1405.1751 21715.111 -30372.575 292.28141 18.274766 1.0106948 0.8125 -0.688675 0.3443375 + 1630000 -5489.0281 1289.6971 -6778.7251 1344.2314 21847.424 -30375.392 309.2685 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21842.338 -30371.235 284.34123 -1255.4953 0.98878939 0.835 -0.707746 0.353873 + 1675000 -5561.8847 1224.9469 -6786.8316 1430.0792 21692.395 -30375.915 293.74146 119.11524 0.99573454 0.8375 -0.709865 0.3549325 + 1680000 -5653.7552 1260.9531 -6914.7083 1519.8378 21487.885 -30376.356 302.37573 809.64185 1.015909 0.84 -0.711984 0.355992 + 1685000 -5512.3473 1274.3359 -6786.6832 1417.2785 21701.118 -30376.61 305.58491 445.91621 1.0312005 0.8425 -0.714103 0.3570515 + 1690000 -5508.29 1269.2138 -6777.5038 1366.728 21782.662 -30375.482 304.35663 14.172211 1.0249747 0.845 -0.716222 0.358111 + 1695000 -5591.9917 1161.3619 -6753.3536 1403.8396 21761.545 -30371.687 278.49382 339.64543 1.0133803 0.8475 -0.718341 0.3591705 + 1700000 -5466.9507 1266.1673 -6733.118 1372.2532 21825.493 -30372.223 303.62608 82.443385 1.0170363 0.85 -0.72046 0.36023 + 1705000 -5565.484 1255.6155 -6821.0995 1404.2864 21697.72 -30377.201 301.09577 115.4614 1.0224858 0.8525 -0.722579 0.3612895 + 1710000 -5468.4747 1242.5333 -6711.008 1261.827 21976.931 -30377.884 297.95866 -1282.3719 1.0025311 0.855 -0.724698 0.362349 + 1715000 -5506.6405 1286.9184 -6793.5589 1333.9602 21778.671 -30374.791 308.60219 -870.86182 0.99767742 0.8575 -0.726817 0.3634085 + 1720000 -5565.6601 1243.2447 -6808.9048 1453.7071 21688.169 -30376.668 298.12926 837.91968 1.0193803 0.86 -0.728936 0.364468 + 1725000 -5466.8293 1256.0749 -6722.9042 1322.9564 21895.211 -30378.325 301.20593 -717.52415 0.99658437 0.8625 -0.731055 0.3655275 + 1730000 -5558.3242 1213.4742 -6771.7984 1337.7732 21800.919 -30378.895 290.99031 -210.06727 1.0310242 0.865 -0.733174 0.366587 + 1735000 -5502.8243 1261.8071 -6764.6314 1382.0545 21775.488 -30375.951 302.58051 -0.31427925 1.0034826 0.8675 -0.735293 0.3676465 + 1740000 -5406.8705 1274.6358 -6681.5063 1334.7641 21893.52 -30376.72 305.65682 -231.76275 1.0050648 0.87 -0.737412 0.368706 + 1745000 -5469.6519 1259.7569 -6729.4088 1437.2403 21699.918 -30375.369 302.08887 487.94198 1.0000255 0.8725 -0.739531 0.3697655 + 1750000 -5510.7038 1273.4592 -6784.163 1346.9061 21834.988 -30377.095 305.37468 -381.44532 0.9990362 0.875 -0.74165 0.370825 + 1755000 -5498.5771 1291.9682 -6790.5453 1416.649 21698.465 -30377.922 309.81311 434.97184 1.020573 0.8775 -0.743769 0.3718845 + 1760000 -5518.5384 1277.985 -6796.5234 1361.2079 21765.884 -30377.646 306.45996 -37.746266 1.0246582 0.88 -0.745888 0.372944 + 1765000 -5507.052 1273.8365 -6780.8885 1421.9667 21726.518 -30377.959 305.46515 410.30385 1.0112394 0.8825 -0.748007 0.3740035 + 1770000 -5596.6543 1216.1185 -6812.7727 1416.069 21695.778 -30380.248 291.6244 1.5263758 1.0080966 0.885 -0.750126 0.375063 + 1775000 -5623.4083 1285.876 -6909.2843 1440.2387 21582.885 -30381.001 308.35222 -35.250138 1.0049289 0.8875 -0.752245 0.3761225 + 1780000 -5573.4547 1219.3235 -6792.7782 1442.9632 21676.665 -30377.304 292.39298 471.41075 1.0053462 0.89 -0.754364 0.377182 + 1785000 -5602.6194 1217.9746 -6820.594 1410.7105 21746.864 -30378.721 292.0695 188.14379 1.0190973 0.8925 -0.756483 0.3782415 + 1790000 -5545.0248 1232.4378 -6777.4626 1420.0285 21741.196 -30377.214 295.53778 756.19164 1.0274418 0.895 -0.758602 0.379301 + 1795000 -5518.8988 1253.2508 -6772.1496 1346.248 21846.81 -30376.809 300.52871 -133.93703 1.0242741 0.8975 -0.760721 0.3803605 + 1800000 -5440.5825 1267.2474 -6707.8299 1236.5895 21971.421 -30375.638 303.88509 -1636.0141 0.99063571 0.9 -0.76284 0.38142 + 1805000 -5447.8315 1288.0343 -6735.8658 1315.8015 21891.886 -30383.047 308.86977 -729.116 1.0031825 0.9025 -0.764959 0.3824795 + 1810000 -5612.711 1242.5543 -6855.2653 1383.4906 21692.082 -30384.343 297.96369 -319.45292 1.0215442 0.905 -0.767078 0.383539 + 1815000 -5557.273 1220.1604 -6777.4334 1421.1515 21742.938 -30384.256 292.59367 520.03095 1.0215411 0.9075 -0.769197 0.3845985 + 1820000 -5530.2316 1228.8432 -6759.0748 1332.6717 21862.178 -30382.059 294.67578 -655.51399 1.0042955 0.91 -0.771316 0.385658 + 1825000 -5602.3037 1229.7047 -6832.0084 1468.9012 21615.952 -30382.906 294.88237 421.71792 1.0045724 0.9125 -0.773435 0.3867175 + 1830000 -5547.6226 1200.4018 -6748.0244 1330.1166 21900.521 -30384.116 287.85555 -636.22865 1.0018051 0.915 -0.775554 0.387777 + 1835000 -5653.9568 1210.6899 -6864.6467 1386.2577 21734.456 -30383.944 290.32264 -127.89376 1.023499 0.9175 -0.777673 0.3888365 + 1840000 -5547.0916 1252.5655 -6799.6571 1419.6833 21720.231 -30379.345 300.36437 501.3533 1.0256074 0.92 -0.779792 0.389896 + 1845000 -5515.4901 1289.6285 -6805.1187 1364.8493 21767.014 -30383.713 309.25207 -436.33388 1.0012885 0.9225 -0.781911 0.3909555 + 1850000 -5486.8798 1292.9914 -6779.8712 1380.8937 21790.721 -30383.253 310.05848 22.6166 1.0096908 0.925 -0.78403 0.392015 + 1855000 -5533.7045 1263.0308 -6796.7353 1395.9678 21748.064 -30382.076 302.87396 -284.93741 0.9863725 0.9275 -0.786149 0.3930745 + 1860000 -5484.2708 1261.0621 -6745.3329 1439.0946 21765.649 -30381.058 302.40186 615.26529 0.9985027 0.93 -0.788268 0.394134 + 1865000 -5599.3124 1260.6731 -6859.9855 1381.0638 21741.092 -30385.213 302.30858 -582.58143 1.0024906 0.9325 -0.790387 0.3951935 + 1870000 -5529.7237 1260.0702 -6789.7939 1384.0683 21758.475 -30383.423 302.16399 53.835245 1.0113827 0.935 -0.792506 0.396253 + 1875000 -5455.8429 1269.0311 -6724.8739 1395.2702 21814.233 -30381.4 304.31281 191.35208 0.99331435 0.9375 -0.794625 0.3973125 + 1880000 -5522.3775 1257.2498 -6779.6273 1422.2951 21728.811 -30385.222 301.48766 210.15712 1.0034809 0.94 -0.796744 0.398372 + 1885000 -5581.928 1248.1059 -6830.0339 1353.7983 21777.194 -30384.398 299.29497 -685.33819 1.0064471 0.9425 -0.798863 0.3994315 + 1890000 -5504.863 1257.5766 -6762.4396 1382.3075 21802.301 -30382.745 301.56605 233.93301 1.0136359 0.945 -0.800982 0.400491 + 1895000 -5519.8568 1258.7721 -6778.629 1381.0637 21801.818 -30381.149 301.85273 157.33428 1.0106136 0.9475 -0.803101 0.4015505 + 1900000 -5415.1036 1245.1225 -6660.2261 1321.1611 21968.266 -30378.535 298.57955 -87.316091 1.0149157 0.95 -0.80522 0.40261 + 1905000 -5486.4216 1290.1083 -6776.5299 1344.556 21824.3 -30385.345 309.36712 -170.76911 1.0220988 0.9525 -0.807339 0.4036695 + 1910000 -5612.2769 1206.579 -6818.8559 1361.0857 21798.985 -30389.316 289.33686 -679.6889 1.0021422 0.955 -0.809458 0.404729 + 1915000 -5587.0108 1277.8116 -6864.8224 1390.9876 21720.193 -30387.546 306.41838 -88.421087 1.026429 0.9575 -0.811577 0.4057885 + 1920000 -5536.6115 1211.5465 -6748.1579 1346.0005 21869.713 -30386.249 290.52804 -614.6848 0.99432544 0.96 -0.813696 0.406848 + 1925000 -5475.7378 1270.4733 -6746.2111 1363.7746 21799.571 -30386.112 304.65867 263.14406 1.0338166 0.9625 -0.815815 0.4079075 + 1930000 -5509.1127 1248.2489 -6757.3616 1334.6571 21873.781 -30385.968 299.32926 -529.83539 1.0071671 0.965 -0.817934 0.408967 + 1935000 -5548.4157 1253.3639 -6801.7796 1361.0982 21797.539 -30389.563 300.55583 -390.63414 1.0119705 0.9675 -0.820053 0.4100265 + 1940000 -5585.3752 1257.0833 -6842.4584 1341.862 21777.004 -30390.791 301.44773 -588.69504 1.0234228 0.97 -0.822172 0.411086 + 1945000 -5553.1361 1239.7945 -6792.9307 1392.65 21775.612 -30388.808 297.30191 401.98554 1.0324973 0.9725 -0.824291 0.4121455 + 1950000 -5608.302 1257.6453 -6865.9473 1385.8155 21666.265 -30389.484 301.58252 -258.45732 1.0221941 0.975 -0.82641 0.413205 + 1955000 -5597.8019 1196.2504 -6794.0523 1368.6962 21798.614 -30384.841 286.86006 -187.46622 1.015951 0.9775 -0.828529 0.4142645 + 1960000 -5558.9543 1259.8231 -6818.7774 1402.0765 21687.027 -30386.699 302.10476 -130.60372 1.0087181 0.98 -0.830648 0.415324 + 1965000 -5522.1401 1225.1335 -6747.2736 1385.1221 21794.241 -30386.219 293.78621 59.455921 1.0156338 0.9825 -0.832767 0.4163835 + 1970000 -5460.8469 1294.812 -6755.6589 1403.377 21789.971 -30387.038 310.49507 67.767671 0.99695881 0.985 -0.834886 0.417443 + 1975000 -5562.7016 1276.5904 -6839.292 1381.4683 21781.499 -30385.8 306.12554 -104.19545 1.0255706 0.9875 -0.837005 0.4185025 + 1980000 -5519.6646 1253.4527 -6773.1173 1464.4023 21698.419 -30387.375 300.57712 1035.4507 1.0129337 0.99 -0.839124 0.419562 + 1985000 -5465.34 1288.7347 -6754.0747 1312.8409 21917.192 -30385.618 309.03772 -632.51392 1.0142034 0.9925 -0.841243 0.4206215 + 1990000 -5579.8472 1232.0079 -6811.8551 1325.3706 21848.546 -30387.507 295.43468 -736.79929 1.0087938 0.995 -0.843362 0.421681 + 1995000 -5474.4313 1277.8474 -6752.2787 1377.0964 21856.577 -30388.53 306.42697 -223.13166 0.99592342 0.9975 -0.845481 0.4227405 + 2000000 -5530.4657 1243.1127 -6773.5784 1448.1254 21758.477 -30388.792 298.09761 750.74861 1.0102049 1 -0.8476 0.4238 +Loop time of 13807.9 on 12 procs for 2000000 steps with 1800 atoms + +Performance: 12.515 ns/day, 1.918 hours/ns, 144.845 timesteps/s +95.3% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7308.6 | 8043.1 | 8855.3 | 457.7 | 58.25 +Bond | 24.229 | 25.717 | 27.246 | 21.9 | 0.19 +Kspace | 2227.1 | 3047.3 | 3772.6 | 744.0 | 22.07 +Neigh | 525.14 | 526.08 | 527.05 | 2.6 | 3.81 +Comm | 809.43 | 867.32 | 940.11 | 181.0 | 6.28 +Output | 0.033333 | 0.034507 | 0.043203 | 1.4 | 0.00 +Modify | 880.49 | 1047.6 | 1183.6 | 402.0 | 7.59 +Other | | 250.7 | | | 1.82 + +Nlocal: 150.000 ave 167 max 140 min +Histogram: 2 3 2 0 2 0 0 1 1 1 +Nghost: 6112.58 ave 6193 max 6037 min +Histogram: 3 0 2 0 0 3 1 1 0 2 +Neighs: 87266.4 ave 94192 max 79682 min +Histogram: 2 0 1 0 1 4 2 0 0 2 + +Total # of neighbors = 1047197 +Ave neighs/atom = 581.77611 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 89139 +Dangerous builds = 0 +Total wall time: 3:59:31 diff --git a/examples/USER/fep/SPCEhyd/fep01/in-fep01-lj.lmp b/examples/USER/fep/SPCEhyd/fep01/in-fep01-lj.lmp new file mode 100644 index 0000000000..2f9bdbb7c5 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep01/in-fep01-lj.lmp @@ -0,0 +1,72 @@ +# created by fftool + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic + +special_bonds lj/coul 0.0 0.0 0.5 + +# remove hybrid if not necessary +pair_style hybrid lj/cut/coul/long 12.0 12.0 lj/cut/soft 2 0.5 12.0 +pair_modify tail no +kspace_style pppm 1.0e-5 + +read_data data.lmp + +pair_coeff 1 1 lj/cut/soft 0.000000 1.000000 0.0 # Hwh Hwh +pair_coeff 1 2 lj/cut/soft 0.000000 1.000000 0.0 # Hwh Owh +pair_coeff 1 3 lj/cut/soft 0.000000 1.000000 0.0 # Hwh Hw +pair_coeff 1 4 lj/cut/soft 0.000000 1.000000 0.0 # Hwh Ow +pair_coeff 2 2 lj/cut/soft 0.155425 3.165500 0.0 # Owh Owh +pair_coeff 2 3 lj/cut/soft 0.000000 1.000000 0.0 # Owh Hw +pair_coeff 2 4 lj/cut/soft 0.155425 3.165500 0.0 # Owh Ow +pair_coeff 3 3 lj/cut/coul/long 0.000000 0.000000 # Hw Hw +pair_coeff 3 4 lj/cut/coul/long 0.000000 0.000000 # Hw Ow +pair_coeff 4 4 lj/cut/coul/long 0.155425 3.165500 # Ow Ow + +# minimize 1.0e-4 1.0e-6 100 1000 +# reset_timestep 0 + +fix SHAKE all shake 0.0001 20 0 b 1 + +neighbor 2.0 bin +# neigh_modify delay 0 every 1 check yes + +timestep 1.0 + +variable TK equal 300.0 +variable PBAR equal 1.0 + +velocity all create ${TK} 12345 + +fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000 + +thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density +thermo 5000 + +set type 1*2 charge 0.0 + +run 100000 + +reset_timestep 0 + +variable lambda equal ramp(0.0,1.0) + +fix ADAPT all adapt/fep 100000 & + pair lj/cut/soft lambda 1*2 3*4 v_lambda & + after yes + +thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda + +variable dlambda equal 0.05 + +compute FEP all fep ${TK} & + pair lj/cut/soft lambda 1*2 3*4 v_dlambda & + volume yes + +fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep01-lj.fep + +run 2000000 diff --git a/examples/USER/fep/SPCEhyd/fep01/in-fep01-q.lmp b/examples/USER/fep/SPCEhyd/fep01/in-fep01-q.lmp new file mode 100644 index 0000000000..19efe3a9b1 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep01/in-fep01-q.lmp @@ -0,0 +1,78 @@ +# created by fftool + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic + +special_bonds lj/coul 0.0 0.0 0.5 + +# remove hybrid if not necessary +pair_style lj/cut/coul/long 12.0 12.0 +pair_modify tail no +kspace_style pppm 1.0e-5 + +read_data data.lmp + +pair_coeff 1 1 0.000000 1.000000 # Hwh Hwh +pair_coeff 1 2 0.000000 1.000000 # Hwh Owh +pair_coeff 1 3 0.000000 1.000000 # Hwh Hw +pair_coeff 1 4 0.000000 1.000000 # Hwh Ow +pair_coeff 2 2 0.155425 3.165500 # Owh Owh +pair_coeff 2 3 0.000000 1.000000 # Owh Hw +pair_coeff 2 4 0.155425 3.165500 # Owh Ow +pair_coeff 3 3 0.000000 1.000000 # Hw Hw +pair_coeff 3 4 0.000000 1.000000 # Hw Ow +pair_coeff 4 4 0.155425 3.165500 # Ow Ow + +# minimize 1.0e-4 1.0e-6 100 1000 +# reset_timestep 0 + +fix SHAKE all shake 0.0001 20 0 b 1 + +neighbor 2.0 bin +# neigh_modify delay 0 every 1 check yes + +timestep 1.0 + +variable TK equal 300.0 +variable PBAR equal 1.0 + +velocity all create ${TK} 12345 + +fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000 + +thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density +thermo 5000 + +set type 1*2 charge 0.0 + +run 100000 + +reset_timestep 0 + +variable lambda equal ramp(0.0,1.0) +variable qH equal 0.4238*v_lambda +variable qO equal -0.8476*v_lambda + +fix ADAPT all adapt/fep 100000 & + atom charge 1 v_qH & + atom charge 2 v_qO & + after yes + +thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda v_qO v_qH + +variable dlambda equal 0.05 +variable dqH equal 0.4238*v_dlambda +variable dqO equal -0.8476*v_dlambda + +compute FEP all fep ${TK} & + atom charge 1 v_dqH & + atom charge 2 v_dqO & + volume yes + +fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep01-q.fep + +run 2000000 diff --git a/examples/USER/fep/SPCEhyd/fep10/fep10-lj.fep b/examples/USER/fep/SPCEhyd/fep10/fep10-lj.fep new file mode 100644 index 0000000000..e08c143542 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep10/fep10-lj.fep @@ -0,0 +1,22 @@ +# Time-averaged data for fix FEP +# TimeStep c_FEP[1] c_FEP[2] c_FEP[3] +100000 0.164332 13580.8 17770.4 +200000 0.129134 14470.4 17769.5 +300000 0.113694 14856.5 17741.9 +400000 0.0945078 15445.3 17780.8 +500000 0.0562545 16508.6 17735.1 +600000 0.0490523 16733.2 17757.8 +700000 -0.0236465 19372.6 17801.7 +800000 -0.0387399 19901 17785.3 +900000 -0.0718098 21703.2 17802.6 +1000000 -0.118193 24005.7 17774.1 +1100000 -0.170254 26527.3 17789.9 +1200000 -0.297445 41864.5 17773.6 +1300000 -0.431516 50576.8 17744 +1400000 -0.467669 44025.5 17719.1 +1500000 -0.317884 31440.4 17731.3 +1600000 -0.218939 25792.6 17718.6 +1700000 -0.107798 21322.2 17753.1 +1800000 -0.0458874 19135.5 17706.5 +1900000 -0.015392 18211.1 17744.9 +2000000 -0.00224303 17811.3 17744.3 diff --git a/examples/USER/fep/SPCEhyd/fep10/fep10-lj.out b/examples/USER/fep/SPCEhyd/fep10/fep10-lj.out new file mode 100644 index 0000000000..bc93b1637e --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep10/fep10-lj.out @@ -0,0 +1,592 @@ +LAMMPS (29 Oct 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (29.204526 29.204526 29.204526) + 2 by 2 by 3 MPI processor grid + reading atoms ... + 1800 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 1200 bonds + reading angles ... + 600 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.033 seconds +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 600 = # of size 3 clusters + 0 = # of size 4 clusters + 0 = # of frozen angles + find clusters CPU = 0.001 seconds +Setting atom values ... + 3 settings made for charge +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.25066829 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0030719151 + estimated relative force accuracy = 9.250981e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 3757 800 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut/coul/long, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/soft, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 9.477 | 9.489 | 9.507 Mbytes +Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density + 0 0 1344.0739 1251.046 93.027896 53.823145 30049.554 -30010.349 300 10284.878 24908.667 0.72058313 + 5000 26.829054 -5531.3966 1246.7673 -6778.164 1430.5662 21645.326 -30297.767 298.97398 343.00879 17939.671 1.0005069 + 10000 60.375331 -5491.2737 1280.0525 -6771.3262 1384.6297 21688.032 -30298.393 306.95574 -300.16806 18083.581 0.99254483 + 15000 94.076576 -5632.0108 1185.0761 -6817.0868 1373.1572 21657.834 -30299.165 284.18046 -509.30462 17853.507 1.0053356 + 20000 126.53271 -5557.9837 1273.3985 -6831.3822 1276.3348 21807.204 -30296.619 305.36012 -1423.8804 17810.87 1.0077422 + 25000 159.26926 -5561.3614 1271.5975 -6832.9588 1454.6816 21523.277 -30299.954 304.92823 245.53675 17839.133 1.0061456 + 30000 191.17362 -5569.1628 1224.4664 -6793.6292 1459.7735 21613.44 -30298.475 293.62623 1166.8411 17466.628 1.0276033 + 35000 225.54672 -5505.5765 1289.9333 -6795.5098 1374.8138 21675.444 -30297.568 309.32515 -277.00241 17845.641 1.0057787 + 40000 259.24748 -5529.8329 1222.5071 -6752.34 1368.482 21714.343 -30299.714 293.15639 -48.777351 17595.097 1.0201004 + 45000 292.69855 -5541.3772 1261.5499 -6802.9272 1371.5857 21681.912 -30295.814 302.51884 -335.65528 17817.714 1.0073551 + 50000 326.91392 -5573.7012 1222.2121 -6795.9133 1327.6979 21746.391 -30299.712 293.08565 -955.31142 17840.793 1.006052 + 55000 361.16613 -5449.164 1267.4384 -6716.6024 1412.1093 21720 -30299.63 303.9309 428.04385 18036.511 0.99513513 + 60000 393.91884 -5546.8912 1190.623 -6737.5143 1330.3252 21806.541 -30300.582 285.51061 -430.37809 17636.451 1.0177085 + 65000 428.22428 -5622.5584 1259.3301 -6881.8885 1509.1614 21478.163 -30299.496 301.98652 975.06072 17605.779 1.0194815 + 70000 462.45487 -5570.183 1218.0018 -6788.1847 1354.4694 21727.024 -30300.976 292.07602 -258.76822 17759.422 1.0106616 + 75000 496.90314 -5627.876 1230.7285 -6858.6045 1476.5693 21530.846 -30297.953 295.12788 553.50896 17749.215 1.0112428 + 80000 531.33879 -5494.2101 1259.607 -6753.8171 1380.283 21711.161 -30298.881 302.05292 211.62464 17627.074 1.0182499 + 85000 564.97941 -5519.5052 1245.7068 -6765.212 1413.8079 21662.496 -30297.084 298.71966 464.57065 17574.97 1.0212686 + 90000 597.70815 -5541.7394 1221.3799 -6763.1193 1438.245 21673.718 -30296.608 292.8861 594.92053 17785.328 1.0091894 + 95000 630.00979 -5506.2477 1292.8624 -6799.1101 1435.7457 21640.887 -30297.759 310.02754 746.74628 17535.628 1.0235599 + 100000 664.4401 -5517.294 1249.4101 -6766.7041 1435.9513 21681.832 -30299.249 299.60772 863.4493 17594.707 1.020123 +Loop time of 664.44 on 12 procs for 100000 steps with 1800 atoms + +Performance: 13.003 ns/day, 1.846 hours/ns, 150.503 timesteps/s +95.1% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 354.67 | 370.51 | 389.45 | 60.8 | 55.76 +Bond | 1.2832 | 1.3258 | 1.3684 | 2.3 | 0.20 +Kspace | 122.53 | 141.54 | 156.98 | 99.1 | 21.30 +Neigh | 28.973 | 29.038 | 29.092 | 0.6 | 4.37 +Comm | 42.452 | 45.845 | 51.532 | 54.0 | 6.90 +Output | 0.0013313 | 0.0013703 | 0.0017405 | 0.3 | 0.00 +Modify | 48.441 | 63.192 | 71.445 | 115.5 | 9.51 +Other | | 12.99 | | | 1.95 + +Nlocal: 150.000 ave 163 max 141 min +Histogram: 2 3 2 0 1 0 1 0 2 1 +Nghost: 6146.42 ave 6218 max 6094 min +Histogram: 3 3 0 0 0 0 4 0 1 1 +Neighs: 87791.7 ave 98973 max 80440 min +Histogram: 2 0 3 3 0 2 0 1 0 1 + +Total # of neighbors = 1053500 +Ave neighs/atom = 585.27778 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 4499 +Dangerous builds = 9 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.2513327 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0034853969 + estimated relative force accuracy = 1.0496169e-05 + using double precision FFTW3 + 3d grid and FFT values/proc = 3328 648 +FEP settings ... + temperature = 300.000000 + tail no + lj/cut/soft lambda 1-2 3-4 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 4 4 4 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut/coul/long, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/soft, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 9.472 | 9.556 | 10.27 Mbytes +Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda + 0 -5517.3031 1249.4101 -6766.7132 1435.9513 21762.036 -30379.462 299.60772 824.0149 1.020123 1 + 5000 -5558.3835 1278.7173 -6837.1007 1334.2641 21745.448 -30378.941 306.63556 -767.88312 1.0259151 0.9975 + 10000 -5536.0094 1281.998 -6818.0074 1400.7848 21722.638 -30382.662 307.42228 286.89597 1.0190965 0.995 + 15000 -5481.3474 1257.9731 -6739.3206 1399.5036 21761.099 -30377.92 301.66113 181.6173 1.0045157 0.9925 + 20000 -5576.3444 1286.5841 -6862.9285 1415.5303 21648.92 -30380.138 308.52201 -153.48635 1.0085717 0.99 + 25000 -5514.2625 1300.4887 -6814.7513 1407.9812 21728.21 -30379.084 311.85634 425.39113 1.018525 0.9875 + 30000 -5547.7134 1261.8317 -6809.5451 1380.2714 21733.843 -30375.593 302.58642 -17.777892 1.0150161 0.985 + 35000 -5477.5978 1281.4333 -6759.0311 1368.0059 21793.139 -30378.187 307.28686 -71.109919 1.0111779 0.9825 + 40000 -5508.6633 1240.2261 -6748.8893 1315.5039 21866.643 -30379.36 297.40539 -903.80351 1.0010855 0.98 + 45000 -5549.0382 1255.1907 -6804.2289 1427.4722 21710.804 -30378.942 300.9939 585.69847 1.0195923 0.9775 + 50000 -5475.0264 1312.3734 -6787.3998 1297.1559 21838.086 -30379.004 314.70627 -1273.035 1.0008054 0.975 + 55000 -5491.7123 1248.8257 -6740.538 1363.4371 21862.536 -30380.311 299.46758 99.128465 1.0180508 0.9725 + 60000 -5609.488 1190.986 -6800.474 1436.0545 21719.642 -30378.046 285.59765 701.33839 1.0113551 0.97 + 65000 -5518.7824 1259.5561 -6778.3385 1358.5984 21791.343 -30380.334 302.04072 -321.61092 1.023541 0.9675 + 70000 -5494.8931 1242.4517 -6737.3448 1305.9749 21912.178 -30379.338 297.9391 -630.02692 1.0139124 0.965 + 75000 -5546.698 1230.9889 -6777.6869 1335.3375 21837.661 -30375.416 295.19033 -852.37291 0.9905341 0.9625 + 80000 -5539.855 1242.8348 -6782.6898 1419.4903 21739.313 -30377.932 298.03096 412.87427 1.01156 0.96 + 85000 -5539.3458 1252.4243 -6791.7701 1324.7893 21793.186 -30381.357 300.33052 -863.18781 1.008687 0.9575 + 90000 -5481.581 1307.2598 -6788.8408 1346.6475 21844.712 -30381.327 313.48005 -408.54122 1.0084955 0.955 + 95000 -5529.9471 1250.3938 -6780.3409 1375.6186 21766.839 -30380.379 299.84361 -208.47283 1.0041284 0.9525 + 100000 -5611.8507 1205.3447 -6817.1954 1432.4671 21667.619 -30379.262 289.04087 575.38545 1.0196531 0.95 + 105000 -5516.1732 1249.0519 -6765.2251 1510.0799 21652.904 -30376.319 299.52182 1595.0527 1.0142387 0.9475 + 110000 -5465.4173 1258.6931 -6724.1103 1349.0925 21850.539 -30376.601 301.83377 -603.2308 0.98281583 0.945 + 115000 -5551.5788 1260.591 -6812.1698 1512.1661 21629.589 -30379.324 302.28889 1408.8013 1.0119216 0.9425 + 120000 -5507.219 1271.1602 -6778.3792 1287.9978 21860.629 -30381.307 304.82338 -1063.0529 1.0271704 0.94 + 125000 -5537.13 1258.8105 -6795.9405 1382.8613 21762.733 -30377.383 301.86193 -158.02523 1.0108426 0.9375 + 130000 -5549.0946 1266.6866 -6815.7812 1372.5433 21748.74 -30377.189 303.75061 -643.27667 0.99432531 0.935 + 135000 -5573.4448 1286.5394 -6859.9842 1446.9417 21606.202 -30379.095 308.51131 579.59371 1.0183103 0.9325 + 140000 -5486.2607 1218.2948 -6704.5555 1391.8317 21866.056 -30379.705 292.14629 239.66325 1.0017938 0.93 + 145000 -5528.1392 1237.3437 -6765.4829 1343.2831 21851.228 -30378.61 296.71421 -443.27605 1.0094072 0.9275 + 150000 -5524.9227 1258.9283 -6783.851 1371.8204 21782.513 -30377.396 301.89018 -100.72793 1.0162581 0.925 + 155000 -5559.5874 1249.0683 -6808.6557 1298.8221 21822.678 -30380.108 299.52576 -1283.9404 1.0098295 0.9225 + 160000 -5574.1599 1259.0423 -6833.2022 1386.5012 21768.271 -30378.898 301.91751 -274.81981 1.0036715 0.92 + 165000 -5558.2274 1268.7313 -6826.9587 1366.6284 21720.826 -30379.54 304.24093 -723.57468 1.0031713 0.9175 + 170000 -5558.0458 1243.1304 -6801.1762 1359.415 21794.026 -30377.538 298.10185 -284.08503 1.0125849 0.915 + 175000 -5557.9939 1250.5207 -6808.5146 1344.1211 21819.765 -30375.934 299.87403 -742.04372 1.008519 0.9125 + 180000 -5562.2438 1245.4126 -6807.6564 1442.5917 21688.098 -30381.444 298.64912 834.40431 1.0283372 0.91 + 185000 -5494.5329 1238.0904 -6732.6233 1374.4489 21815.526 -30379.394 296.89325 -127.96552 1.0129962 0.9075 + 190000 -5512.3632 1282.3603 -6794.7235 1331.0347 21826.906 -30381.177 307.50916 -975.48387 0.99030439 0.905 + 195000 -5555.5139 1268.6099 -6824.1238 1579.0357 21509.544 -30380.501 304.21181 2298.8088 1.0238224 0.9025 + 200000 -5561.6068 1235.0747 -6796.6815 1341.7814 21791.238 -30377.819 296.1701 -569.19717 1.0181737 0.9 + 205000 -5408.9255 1277.421 -6686.3465 1384.0288 21847.016 -30376.919 306.3247 306.84932 1.0058379 0.8975 + 210000 -5574.4209 1249.0534 -6823.4743 1390.0917 21708.289 -30375.252 299.52217 -137.92578 1.020659 0.895 + 215000 -5533.5343 1256.0469 -6789.5812 1397.7965 21759.307 -30379.639 301.19922 -167.33553 0.99448086 0.8925 + 220000 -5525.1497 1272.4337 -6797.5834 1349.1947 21798.064 -30375.86 305.12875 -636.29714 1.0040906 0.89 + 225000 -5504.1279 1280.7318 -6784.8598 1373.0777 21811.329 -30381.594 307.11864 -109.03674 1.0126578 0.8875 + 230000 -5556.0721 1227.0604 -6783.1325 1460.4513 21700.918 -30378.062 294.24828 1031.1913 1.0144785 0.885 + 235000 -5579.4548 1223.0151 -6802.47 1383.0244 21742.747 -30378.065 293.27823 -444.73244 0.99883895 0.8825 + 240000 -5478.8969 1256.3704 -6735.2673 1379.5164 21844.649 -30379.291 301.2768 134.8168 1.0086341 0.88 + 245000 -5473.7115 1247.7991 -6721.5106 1377.2785 21845.407 -30379.554 299.22139 152.12047 1.0028516 0.8775 + 250000 -5511.3331 1252.6671 -6764.0002 1391.242 21767.929 -30377.767 300.38874 42.815705 1.0071501 0.875 + 255000 -5527.2234 1305.1549 -6832.3783 1450.6004 21675.372 -30380.236 312.97529 568.31787 1.0194011 0.8725 + 260000 -5599.9408 1267.0163 -6866.9571 1414.5319 21681.001 -30380.447 303.82967 -296.86382 0.99844118 0.87 + 265000 -5609.1575 1202.8066 -6811.9641 1422.9683 21708.562 -30377.312 288.43224 396.28769 1.0282155 0.8675 + 270000 -5514.4973 1238.2917 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304.39806 -41.211787 1.0184863 0.13 + 1745000 -5601.6102 1211.6668 -6813.2769 1457.856 21646.431 -30379.268 290.55689 321.57165 1.0044935 0.1275 + 1750000 -5464.07 1262.7335 -6726.8035 1388.3238 21807.797 -30381.51 302.80266 347.94977 1.0199363 0.125 + 1755000 -5609.8158 1220.0117 -6829.8275 1449.8857 21660.858 -30381.398 292.55801 423.13734 1.0091913 0.1225 + 1760000 -5403.3906 1295.0506 -6698.4412 1376.6218 21890.749 -30379.696 310.55227 307.40852 1.0147058 0.12 + 1765000 -5516.242 1249.2409 -6765.4828 1382.647 21758.198 -30377.246 299.56714 167.93234 1.0231885 0.1175 + 1770000 -5582.0367 1264.8589 -6846.8955 1451.9857 21613.33 -30377.524 303.31232 595.73197 1.0185845 0.115 + 1775000 -5537.7575 1229.4186 -6767.1761 1369.0153 21805.496 -30381.159 294.81376 13.517698 1.0260482 0.1125 + 1780000 -5494.5434 1303.1737 -6797.7171 1436.2813 21746.59 -30380.854 312.50019 737.63948 1.019697 0.11 + 1785000 -5506.8968 1245.4135 -6752.3103 1381.9664 21814.635 -30377.185 298.64934 53.072035 1.0092991 0.1075 + 1790000 -5570.6629 1257.0357 -6827.6986 1389.5682 21752.819 -30378.813 301.43633 -254.1322 1.0049075 0.105 + 1795000 -5403.0983 1313.5161 -6716.6144 1299.9894 21921.198 -30378.568 314.98029 -534.90063 1.0142742 0.1025 + 1800000 -5571.5716 1221.6883 -6793.2599 1459.5581 21671.077 -30379.985 292.96006 1199.0646 1.0291174 0.1 + 1805000 -5576.3609 1224.1212 -6800.4821 1353.5425 21807.985 -30380.553 293.54345 -387.59054 1.0179841 0.0975 + 1810000 -5606.1276 1268.2463 -6874.3738 1461.2712 21629.806 -30377.587 304.12462 705.686 1.032963 0.095 + 1815000 -5528.0175 1213.0379 -6741.0554 1404.3111 21772.221 -30376.182 290.88569 360.59394 1.0146256 0.0925 + 1820000 -5519.9749 1246.5714 -6766.5463 1333.2785 21832.117 -30376.792 298.927 -490.34561 1.0222947 0.09 + 1825000 -5445.4758 1293.818 -6739.2938 1310.9077 21908.662 -30376.428 310.25669 -505.90791 1.0175154 0.0875 + 1830000 -5541.7133 1258.3353 -6800.0486 1342.3151 21835.187 -30378.672 301.74797 -431.49631 1.0112617 0.085 + 1835000 -5455.3051 1261.9795 -6717.2846 1352.0659 21888.34 -30378.24 302.62186 -278.9793 1.0005135 0.0825 + 1840000 -5550.1255 1264.0761 -6814.2015 1457.0559 21643.406 -30381.124 303.12461 732.70062 1.0158677 0.08 + 1845000 -5534.0588 1215.4174 -6749.4762 1393.3056 21800.212 -30376.843 291.45629 318.75691 1.0144019 0.0775 + 1850000 -5470.5935 1240.7072 -6711.3007 1398.1611 21825.075 -30377.387 297.52076 246.47011 0.99682722 0.075 + 1855000 -5562.2126 1269.9488 -6832.1614 1405.7155 21717.318 -30382.767 304.5329 158.21904 1.0206821 0.0725 + 1860000 -5593.1478 1212.5719 -6805.7197 1431.8435 21688.522 -30377.259 290.77394 490.69887 1.0155469 0.07 + 1865000 -5547.7314 1230.6551 -6778.3865 1415.4128 21748.348 -30378.118 295.11029 184.13907 0.99833163 0.0675 + 1870000 -5530.8677 1219.9933 -6750.861 1379.1571 21831.652 -30375.929 292.55359 34.766398 1.0094217 0.065 + 1875000 -5568.1541 1254.3638 -6822.5179 1355.1579 21740.634 -30379.983 300.7956 -705.50446 1.0143892 0.0625 + 1880000 -5653.4584 1235.3915 -6888.8499 1430.7173 21633.442 -30379.735 296.24606 102.70794 1.0154835 0.06 + 1885000 -5465.2275 1218.1694 -6683.3969 1239.8122 21974.299 -30378.879 292.11621 -1526.9501 1.00297 0.0575 + 1890000 -5596.8191 1179.0514 -6775.8705 1375.6822 21763.894 -30376.484 282.73574 -135.80694 1.0180663 0.055 + 1895000 -5465.5228 1216.5423 -6682.0651 1399.7408 21824.803 -30381.567 291.72604 189.86203 0.9918745 0.0525 + 1900000 -5525.4584 1268.983 -6794.4415 1386.5598 21763.346 -30379.48 304.30129 -147.74084 1.0101088 0.05 + 1905000 -5629.8529 1254.2275 -6884.0804 1455.3465 21571.828 -30380.574 300.76293 536.16177 1.0309795 0.0475 + 1910000 -5498.7043 1240.937 -6739.6413 1343.971 21867.501 -30378.531 297.57587 -307.05181 1.00532 0.045 + 1915000 -5489.6666 1266.2052 -6755.8718 1356.677 21815.921 -30373.873 303.63517 41.753289 1.0289101 0.0425 + 1920000 -5534.4011 1264.7423 -6799.1433 1414.4972 21675.646 -30381.358 303.28436 307.25885 1.030805 0.04 + 1925000 -5504.0398 1249.1105 -6753.1503 1407.4242 21780.765 -30377.439 299.53588 416.81022 1.0112989 0.0375 + 1930000 -5486.5931 1291.1596 -6777.7527 1380.6453 21793.976 -30378.396 309.61922 -167.68264 1.0083434 0.035 + 1935000 -5482.2055 1242.0698 -6724.2753 1296.2668 21881.772 -30378.102 297.84751 -1240.512 1.0083689 0.0325 + 1940000 -5413.7616 1287.0265 -6700.788 1300.618 21943.573 -30379.549 308.6281 -822.10018 0.9947525 0.03 + 1945000 -5618.7196 1214.3524 -6833.072 1410.8621 21689.242 -30381.323 291.2009 177.78285 1.0261522 0.0275 + 1950000 -5559.1869 1277.5888 -6836.7757 1384.1924 21715.907 -30380.281 306.36495 -269.07872 1.01053 0.025 + 1955000 -5556.8805 1290.1761 -6847.0566 1420.3306 21702.458 -30379.354 309.38338 63.181765 1.0037638 0.0225 + 1960000 -5536.3473 1288.352 -6824.6993 1333.2341 21766.427 -30380.118 308.94596 -956.94729 1.0098248 0.02 + 1965000 -5560.7629 1271.8239 -6832.5868 1394.6008 21745.026 -30375.628 304.98253 27.022116 1.014722 0.0175 + 1970000 -5571.8348 1246.9662 -6818.801 1368.7901 21728.521 -30376.246 299.02167 -642.85981 1.0038267 0.015 + 1975000 -5448.1873 1277.5391 -6725.7263 1376.1799 21855.417 -30379.445 306.35302 158.55616 1.010898 0.0125 + 1980000 -5569.4362 1227.1456 -6796.5818 1384.1163 21747.316 -30379.52 294.26871 -224.4952 1.0128917 0.01 + 1985000 -5490.1779 1256.3196 -6746.4975 1376.0987 21800.479 -30378.853 301.26461 -23.927186 1.0117616 0.0075 + 1990000 -5568.4743 1216.0821 -6784.5564 1365.6444 21804.572 -30380.078 291.61568 -40.531986 1.024747 0.005 + 1995000 -5623.9072 1244.7555 -6868.6627 1444.7105 21613.58 -30377.599 298.49155 401.54781 1.0221617 0.0025 + 2000000 -5564.5636 1253.8102 -6818.3738 1394.5734 21742.16 -30376.703 300.66286 -89.748646 1.0114229 0 +Loop time of 13852.8 on 12 procs for 2000000 steps with 1800 atoms + +Performance: 12.474 ns/day, 1.924 hours/ns, 144.375 timesteps/s +95.5% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7431.1 | 8143.6 | 8773.3 | 379.5 | 58.79 +Bond | 24.35 | 26.055 | 27.801 | 23.2 | 0.19 +Kspace | 2212.7 | 2764.8 | 3391.2 | 573.6 | 19.96 +Neigh | 568.42 | 569.87 | 570.75 | 2.7 | 4.11 +Comm | 806.14 | 866.5 | 930.63 | 180.1 | 6.26 +Output | 0.032719 | 0.034078 | 0.041882 | 1.3 | 0.00 +Modify | 964.98 | 1144.9 | 1300.5 | 428.3 | 8.26 +Other | | 337 | | | 2.43 + +Nlocal: 150.000 ave 166 max 139 min +Histogram: 3 0 2 0 2 3 0 0 1 1 +Nghost: 6125.92 ave 6158 max 6091 min +Histogram: 1 1 0 2 1 2 2 1 1 1 +Neighs: 87012.7 ave 102741 max 79216 min +Histogram: 2 1 2 3 3 0 0 0 0 1 + +Total # of neighbors = 1044152 +Ave neighs/atom = 580.08444 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 89145 +Dangerous builds = 0 +Total wall time: 4:01:57 diff --git a/examples/USER/fep/SPCEhyd/fep10/fep10-q.fep b/examples/USER/fep/SPCEhyd/fep10/fep10-q.fep new file mode 100644 index 0000000000..fd49769ec2 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep10/fep10-q.fep @@ -0,0 +1,22 @@ +# Time-averaged data for fix FEP +# TimeStep c_FEP[1] c_FEP[2] c_FEP[3] +100000 1.45025 1741.09 17759.6 +200000 1.34275 2079.09 17751.2 +300000 1.11463 3077.67 17744.5 +400000 1.05072 3418.61 17752.1 +500000 0.861524 4545.87 17736.9 +600000 0.752417 5411.55 17755.8 +700000 0.677848 6201.52 17715.7 +800000 0.594413 7014.15 17718.2 +900000 0.482601 8441.94 17738.8 +1000000 0.44748 8942.75 17761.6 +1100000 0.374076 9984.65 17731.4 +1200000 0.310756 11050 17774.3 +1300000 0.246639 12186.7 17783.6 +1400000 0.201753 13117.8 17825.2 +1500000 0.166052 13843.8 17784.7 +1600000 0.136584 14486.5 17742.2 +1700000 0.102778 15331.6 17778.7 +1800000 0.0716746 16103 17743.1 +1900000 0.0513218 16698.6 17801.1 +2000000 0.0250996 17424.1 17780.5 diff --git a/examples/USER/fep/SPCEhyd/fep10/fep10-q.out b/examples/USER/fep/SPCEhyd/fep10/fep10-q.out new file mode 100644 index 0000000000..36fc89e567 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep10/fep10-q.out @@ -0,0 +1,559 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (29.204526 29.204526 29.204526) + 2 by 2 by 3 MPI processor grid + reading atoms ... + 1800 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 1200 bonds + reading angles ... + 600 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_data CPU = 0.020 seconds +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 600 = # of size 3 clusters + 0 = # of size 4 clusters + 0 = # of frozen angles + find clusters CPU = 0.001 seconds +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.2506685 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0030770287 + estimated relative force accuracy = 9.2663804e-06 + using double precision FFTW3 + 3d grid and FFT values/proc = 3757 800 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 8.214 | 8.226 | 8.244 Mbytes +Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density + 0 0 1343.8082 1251.046 92.762256 53.823145 30098.377 -30059.438 300 10285.006 24908.667 0.72058313 + 5000 27.484029 -5481.5313 1291.2507 -6772.7821 1417.9265 21710.404 -30351.578 309.64107 573.94807 17792.658 1.0087737 + 10000 51.222479 -5557.9174 1247.8414 -6805.7588 1463.5652 21652.169 -30349.483 299.23155 1155.9001 17391.932 1.0320167 + 15000 81.534825 -5547.6429 1255.8047 -6803.4476 1434.9211 21679.801 -30351.564 301.14114 414.89266 17774.479 1.0098054 + 20000 108.19472 -5520.4365 1226.2567 -6746.6933 1363.6958 21763.102 -30350.115 294.05555 -159.5117 17640.377 1.017482 + 25000 139.47439 -5523.2547 1214.4617 -6737.7163 1403.2241 21727.256 -30347.421 291.2271 682.49951 17446.971 1.0287611 + 30000 173.52324 -5633.4887 1209.4695 -6842.9582 1384.9611 21696.903 -30350.921 290.02999 -439.40705 17870.41 1.0043846 + 35000 207.46148 -5609.1629 1202.7623 -6811.9252 1459.4041 21642.871 -30348.683 288.4216 870.04629 17620.845 1.0186098 + 40000 240.785 -5613.2727 1218.043 -6831.3157 1458.2338 21629.898 -30351.078 292.08591 578.74278 17728.011 1.0124523 + 45000 274.86574 -5567.9001 1234.3625 -6802.2626 1499.8464 21612.157 -30349.505 295.9993 1143.6708 17911.841 1.0020614 + 50000 308.33717 -5534.5804 1253.1529 -6787.7333 1383.4124 21740.111 -30349.237 300.50525 -236.43099 17808.85 1.0078565 + 55000 340.35767 -5558.5567 1237.2613 -6795.818 1472.1262 21640.69 -30349.9 296.69444 1169.6084 17518.859 1.0245396 + 60000 371.42788 -5620.3085 1217.3007 -6837.6091 1335.6617 21764.982 -30350.897 291.9079 -730.47206 17652.428 1.0167873 + 65000 400.4258 -5523.4332 1219.0927 -6742.5258 1377.9207 21790.846 -30351.438 292.33762 -67.377992 18008.535 0.99668103 + 70000 433.12056 -5549.9652 1278.9899 -6828.9551 1405.3901 21680.053 -30344.054 306.70094 -24.208971 17740.923 1.0117154 + 75000 465.43309 -5468.4134 1328.8758 -6797.2892 1404.3997 21721.55 -30346.155 318.66353 422.45424 17600.531 1.0197854 + 80000 498.33654 -5561.5506 1262.2191 -6823.7698 1375.8895 21728.477 -30350.941 302.67932 -480.08789 17936.63 1.0006765 + 85000 531.18843 -5561.7498 1243.7135 -6805.4633 1411.6336 21707.72 -30349.917 298.24169 31.756571 17844.951 1.0058176 + 90000 565.37172 -5548.2883 1305.5336 -6853.8219 1376.838 21698.95 -30345.634 313.06609 -580.39211 18032.442 0.99535964 + 95000 599.1335 -5491.6607 1249.0766 -6740.7373 1327.508 21805.341 -30346.173 299.52775 -747.34141 17928.72 1.001118 + 100000 632.97763 -5504.9781 1270.9776 -6775.9557 1348.4638 21759.337 -30349.51 304.7796 -112.23793 17469.352 1.0274431 +Loop time of 632.978 on 12 procs for 100000 steps with 1800 atoms + +Performance: 13.650 ns/day, 1.758 hours/ns, 157.983 timesteps/s +95.0% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 307.42 | 344.2 | 378.91 | 110.2 | 54.38 +Bond | 1.1476 | 1.2339 | 1.3345 | 6.3 | 0.19 +Kspace | 109.33 | 144.47 | 180.71 | 170.1 | 22.82 +Neigh | 25.619 | 25.671 | 25.708 | 0.6 | 4.06 +Comm | 41.234 | 45.135 | 50.464 | 52.8 | 7.13 +Output | 0.0012664 | 0.001324 | 0.0018066 | 0.4 | 0.00 +Modify | 46.059 | 59.064 | 69.016 | 114.7 | 9.33 +Other | | 13.2 | | | 2.09 + +Nlocal: 150.000 ave 160 max 138 min +Histogram: 2 0 0 2 1 1 3 0 0 3 +Nghost: 6169.08 ave 6215 max 6126 min +Histogram: 1 1 2 2 0 1 3 0 1 1 +Neighs: 88745.0 ave 98807 max 82382 min +Histogram: 3 0 1 3 0 3 1 0 0 1 + +Total # of neighbors = 1064940 +Ave neighs/atom = 591.63333 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 4480 +Dangerous builds = 8 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339) + G vector (1/distance) = 0.25148052 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0034663752 + estimated relative force accuracy = 1.0438886e-05 + using double precision FFTW3 + 3d grid and FFT values/proc = 3328 648 +FEP settings ... + temperature = 300.000000 + tail no + 1-1 charge + 2-2 charge +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 8.210 | 8.549 | 8.629 Mbytes +Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda v_qO v_qH + 0 -5504.9889 1270.9776 -6775.9665 1348.4638 21857.535 -30447.719 304.7796 -83.574867 1.0274431 1 -0.8476 0.4238 + 5000 -5524.9498 1270.0815 -6795.0313 1351.1305 21827.149 -30444.933 304.5647 -593.70775 1.005159 0.9975 -0.845481 0.4227405 + 10000 -5540.3394 1230.4582 -6770.7976 1419.9827 21833.217 -30447.512 295.06306 390.92433 1.0060179 0.995 -0.843362 0.421681 + 15000 -5552.7887 1238.4753 -6791.264 1335.4158 21841.316 -30448.525 296.98555 -977.57176 1.0018216 0.9925 -0.841243 0.4206215 + 20000 -5571.4362 1242.7492 -6814.1854 1430.7811 21758.542 -30446.37 298.01044 389.91739 1.0176182 0.99 -0.839124 0.419562 + 25000 -5460.6807 1271.7643 -6732.445 1445.8579 21824.91 -30444.435 304.96824 662.28347 0.99362968 0.9875 -0.837005 0.4185025 + 30000 -5454.6572 1289.2653 -6743.9226 1383.6837 21875.483 -30446.254 309.16498 76.696731 1.0117008 0.985 -0.834886 0.417443 + 35000 -5460.3689 1262.5044 -6722.8733 1424.7799 21854.486 -30444.887 302.74772 469.28759 0.99223648 0.9825 -0.832767 0.4163835 + 40000 -5617.7692 1259.5855 -6877.3547 1466.8238 21653.475 -30448.558 302.04777 518.56945 1.0149626 0.98 -0.830648 0.415324 + 45000 -5498.7892 1260.7599 -6759.5491 1354.8241 21911.823 -30445.433 302.32939 36.724958 1.0199193 0.9775 -0.828529 0.4142645 + 50000 -5556.2521 1276.3605 -6832.6126 1408.5453 21757.203 -30447.43 306.0704 38.976819 1.012915 0.975 -0.82641 0.413205 + 55000 -5513.8511 1239.4864 -6753.3375 1378.8961 21910.688 -30446.837 297.22802 -155.09229 0.99684598 0.9725 -0.824291 0.4121455 + 60000 -5482.86 1287.2484 -6770.1084 1383.4644 21876.85 -30446.035 308.68131 -23.984269 1.002056 0.97 -0.822172 0.411086 + 65000 -5556.4674 1243.4649 -6799.9323 1374.1364 21841.845 -30449.652 298.18207 13.80546 1.0185986 0.9675 -0.820053 0.4100265 + 70000 -5509.3689 1255.8787 -6765.2476 1342.6439 21905.378 -30448.437 301.15889 -636.57169 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-6769.6761 1309.8228 21913.235 -30398.337 298.02209 -850.35833 1.0059241 0.125 -0.10595 0.052975 + 1755000 -5508.0743 1308.7599 -6816.8341 1353.359 21760.125 -30400.191 313.83975 -749.9998 0.99685375 0.1225 -0.103831 0.0519155 + 1760000 -5542.8446 1265.3408 -6808.1854 1391.2186 21776.776 -30396.482 303.42789 117.90427 1.0236881 0.12 -0.101712 0.050856 + 1765000 -5526.6876 1268.5243 -6795.2119 1302.7664 21799.054 -30396.406 304.1913 -1161.5113 1.0216099 0.1175 -0.099593 0.0497965 + 1770000 -5579.5803 1246.8977 -6826.478 1486.5854 21651.454 -30399.954 299.00526 880.22447 1.0109541 0.115 -0.097474 0.048737 + 1775000 -5551.5053 1292.1271 -6843.6324 1405.0247 21688.07 -30398.863 309.85123 -251.03455 0.99873347 0.1125 -0.095355 0.0476775 + 1780000 -5515.8126 1282.9801 -6798.7927 1395.0164 21747.704 -30395.937 307.65779 333.80114 1.0239628 0.11 -0.093236 0.046618 + 1785000 -5510.7284 1208.8107 -6719.5391 1346.5399 21876.38 -30394.751 289.87201 -249.43776 1.0110945 0.1075 -0.091117 0.0455585 + 1790000 -5518.3081 1260.6355 -6778.9436 1399.7684 21796.94 -30397.3 302.29957 82.30008 1.0094344 0.105 -0.088998 0.044499 + 1795000 -5513.5389 1303.7533 -6817.2921 1421.97 21751.65 -30398.865 312.63917 500.03335 1.0096349 0.1025 -0.086879 0.0434395 + 1800000 -5572.7653 1214.8677 -6787.6331 1383.7533 21813.337 -30398.789 291.32448 -172.24736 1.0106323 0.1 -0.08476 0.04238 + 1805000 -5533.6069 1246.7853 -6780.3922 1412.9435 21800.334 -30394.707 298.97828 594.59696 1.0209456 0.0975 -0.082641 0.0413205 + 1810000 -5567.1324 1275.7954 -6842.9277 1442.9318 21676.766 -30398.215 305.93489 453.89649 1.0132054 0.095 -0.080522 0.040261 + 1815000 -5465.3294 1255.0662 -6720.3956 1341.0775 21912.58 -30394.54 300.96405 -302.59143 1.0016089 0.0925 -0.078403 0.0392015 + 1820000 -5588.4657 1233.5824 -6822.0481 1393.0967 21740.859 -30396.671 295.81224 -147.72631 1.0070758 0.09 -0.076284 0.038142 + 1825000 -5599.7235 1244.5645 -6844.288 1527.9294 21571.627 -30396.257 298.44576 1698.1117 1.0275341 0.0875 -0.074165 0.0370825 + 1830000 -5472.5833 1264.0019 -6736.5852 1327.0089 21908.977 -30394.568 303.10682 -394.05428 1.0135733 0.085 -0.072046 0.036023 + 1835000 -5559.5998 1243.4443 -6803.0442 1292.0778 21846.42 -30398.288 298.17713 -1254.4294 1.0141937 0.0825 -0.069927 0.0349635 + 1840000 -5498.5276 1283.2205 -6781.7481 1416.3308 21752.285 -30399.697 307.71542 317.53074 1.003693 0.08 -0.067808 0.033904 + 1845000 -5551.7395 1252.4882 -6804.2277 1374.7399 21772.215 -30396.489 300.34585 -263.50361 1.0114613 0.0775 -0.065689 0.0328445 + 1850000 -5525.5278 1240.7565 -6766.2843 1361.6208 21839.689 -30397.722 297.53259 -186.31575 1.0187838 0.075 -0.06357 0.031785 + 1855000 -5521.2867 1243.7856 -6765.0724 1347.4178 21874.625 -30396.108 298.25898 -284.75269 1.0228705 0.0725 -0.061451 0.0307255 + 1860000 -5640.4121 1146.9485 -6787.3606 1396.2408 21749.618 -30394.203 275.03749 -187.09544 1.006743 0.07 -0.059332 0.029666 + 1865000 -5525.2602 1260.9215 -6786.1817 1402.4348 21758.857 -30397.319 302.36813 -161.29785 0.99503244 0.0675 -0.057213 0.0286065 + 1870000 -5623.139 1216.967 -6840.1059 1413.5807 21703.495 -30397.576 291.82788 76.112007 1.0246491 0.065 -0.055094 0.027547 + 1875000 -5450.2615 1268.385 -6718.6465 1405.9759 21866.321 -30398.11 304.15789 307.93878 0.99773745 0.0625 -0.052975 0.0264875 + 1880000 -5539.8922 1245.1416 -6785.0337 1409.1823 21774.294 -30395.574 298.58413 82.127006 1.0058947 0.06 -0.050856 0.025428 + 1885000 -5514.3045 1240.5608 -6754.8653 1443.7995 21752.107 -30397.218 297.48566 611.17045 1.0085937 0.0575 -0.048737 0.0243685 + 1890000 -5438.3073 1258.3645 -6696.6718 1361.8049 21892.331 -30397.348 301.75497 -267.35927 0.9953092 0.055 -0.046618 0.023309 + 1895000 -5596.2731 1226.9718 -6823.2449 1402.9241 21732.185 -30395.165 294.22702 44.339776 1.0153331 0.0525 -0.044499 0.0222495 + 1900000 -5497.1413 1266.3676 -6763.5089 1373.9826 21832.991 -30399.356 303.67411 -27.290874 1.0132323 0.05 -0.04238 0.02119 + 1905000 -5517.4875 1236.6892 -6754.1767 1367.726 21857.698 -30393.874 296.55726 -499.76394 0.99284077 0.0475 -0.040261 0.0201305 + 1910000 -5552.0873 1269.7208 -6821.8081 1378.8021 21718.781 -30396.478 304.4782 -369.12045 1.0171861 0.045 -0.038142 0.019071 + 1915000 -5499.6451 1278.5051 -6778.1502 1430.6032 21725.761 -30396.795 306.58468 577.53122 1.01326 0.0425 -0.036023 0.0180115 + 1920000 -5487.2658 1251.9078 -6739.1736 1381.7635 21779.483 -30396.642 300.20666 -47.157489 1.0090288 0.04 -0.033904 0.016952 + 1925000 -5538.2174 1250.4348 -6788.6522 1378.1601 21776.002 -30397.01 299.85343 -635.20274 0.98963246 0.0375 -0.031785 0.0158925 + 1930000 -5539.4427 1260.8629 -6800.3057 1358.8021 21770.968 -30400.271 302.3541 -702.50699 0.99578271 0.035 -0.029666 0.014833 + 1935000 -5559.5408 1246.2889 -6805.8297 1426.6663 21737.226 -30396.429 298.85926 214.01347 1.0055051 0.0325 -0.027547 0.0137735 + 1940000 -5527.5821 1225.3364 -6752.9184 1378.8724 21850.255 -30395.169 293.83485 14.506752 1.0028753 0.03 -0.025428 0.012714 + 1945000 -5473.5551 1280.9318 -6754.4869 1425.106 21803.831 -30396.584 307.16659 506.19708 1.0032233 0.0275 -0.023309 0.0116545 + 1950000 -5567.2517 1222.2431 -6789.4948 1305.8232 21889.919 -30396.867 293.09308 -1294.1142 0.99788741 0.025 -0.02119 0.010595 + 1955000 -5484.5853 1260.6694 -6745.2547 1384.597 21831.404 -30392.929 302.30769 156.43697 1.0117059 0.0225 -0.019071 0.0095355 + 1960000 -5620.4544 1193.7438 -6814.1983 1383.8209 21783.257 -30401.598 286.25899 -66.845911 1.0220849 0.02 -0.016952 0.008476 + 1965000 -5545.5269 1233.4885 -6779.0154 1344.2005 21855.912 -30398.255 295.78973 -628.47314 1.0059777 0.0175 -0.014833 0.0074165 + 1970000 -5513.9042 1266.1527 -6780.057 1392.318 21762.753 -30395.542 303.62259 75.831811 1.0061881 0.015 -0.012714 0.006357 + 1975000 -5544.7648 1274.4083 -6819.1731 1391.4464 21746.624 -30396.103 305.60227 -75.461691 1.0034389 0.0125 -0.010595 0.0052975 + 1980000 -5538.5817 1248.0952 -6786.6769 1364.256 21830.009 -30395.903 299.2924 -83.978588 1.0205031 0.01 -0.008476 0.004238 + 1985000 -5595.8323 1230.885 -6826.7174 1357.6211 21780.506 -30393.427 295.16542 -709.11924 1.0035546 0.0075 -0.006357 0.0031785 + 1990000 -5482.4794 1286.6658 -6769.1452 1336.3899 21858.921 -30393.729 308.54161 -827.89365 1.0005728 0.005 -0.004238 0.002119 + 1995000 -5501.4886 1239.738 -6741.2266 1409.7478 21799.031 -30400.217 297.28836 653.89683 1.0202266 0.0025 -0.002119 0.0010595 + 2000000 -5611.4713 1229.0661 -6840.5373 1478.3644 21615.338 -30394.928 294.72923 480.97836 1.00402 0 -0 0 +Loop time of 13776.2 on 12 procs for 2000000 steps with 1800 atoms + +Performance: 12.543 ns/day, 1.913 hours/ns, 145.178 timesteps/s +95.3% CPU use with 12 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7579.8 | 8070.7 | 8564.2 | 287.6 | 58.58 +Bond | 24.942 | 25.514 | 26.056 | 6.9 | 0.19 +Kspace | 2484.3 | 2979.3 | 3459.7 | 467.2 | 21.63 +Neigh | 523.25 | 524.15 | 525.06 | 2.5 | 3.80 +Comm | 806.39 | 872.63 | 948.24 | 194.3 | 6.33 +Output | 0.033634 | 0.034536 | 0.042227 | 1.2 | 0.00 +Modify | 864.36 | 1044.2 | 1191.5 | 438.5 | 7.58 +Other | | 259.6 | | | 1.88 + +Nlocal: 150.000 ave 158 max 141 min +Histogram: 1 0 0 2 2 3 2 1 0 1 +Nghost: 6106.00 ave 6170 max 6046 min +Histogram: 2 1 1 1 0 1 2 2 1 1 +Neighs: 86710.6 ave 92374 max 78975 min +Histogram: 1 0 0 3 0 3 1 0 2 2 + +Total # of neighbors = 1040527 +Ave neighs/atom = 578.07056 +Ave special neighs/atom = 2.0000000 +Neighbor list builds = 89189 +Dangerous builds = 0 +Total wall time: 4:00:09 diff --git a/examples/USER/fep/SPCEhyd/fep10/in-fep10-lj.lmp b/examples/USER/fep/SPCEhyd/fep10/in-fep10-lj.lmp new file mode 100644 index 0000000000..56d2994ec2 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep10/in-fep10-lj.lmp @@ -0,0 +1,72 @@ +# created by fftool + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic + +special_bonds lj/coul 0.0 0.0 0.5 + +# remove hybrid if not necessary +pair_style hybrid lj/cut/coul/long 12.0 12.0 lj/cut/soft 2 0.5 12.0 +pair_modify tail no +kspace_style pppm 1.0e-5 + +read_data data.lmp + +pair_coeff 1 1 lj/cut/soft 0.000000 1.000000 1.0 # Hwh Hwh +pair_coeff 1 2 lj/cut/soft 0.000000 1.000000 1.0 # Hwh Owh +pair_coeff 1 3 lj/cut/soft 0.000000 1.000000 1.0 # Hwh Hw +pair_coeff 1 4 lj/cut/soft 0.000000 1.000000 1.0 # Hwh Ow +pair_coeff 2 2 lj/cut/soft 0.155425 3.165500 1.0 # Owh Owh +pair_coeff 2 3 lj/cut/soft 0.000000 1.000000 1.0 # Owh Hw +pair_coeff 2 4 lj/cut/soft 0.155425 3.165500 1.0 # Owh Ow +pair_coeff 3 3 lj/cut/coul/long 0.000000 0.000000 # Hw Hw +pair_coeff 3 4 lj/cut/coul/long 0.000000 0.000000 # Hw Ow +pair_coeff 4 4 lj/cut/coul/long 0.155425 3.165500 # Ow Ow + +# minimize 1.0e-4 1.0e-6 100 1000 +# reset_timestep 0 + +fix SHAKE all shake 0.0001 20 0 b 1 + +neighbor 2.0 bin +# neigh_modify delay 0 every 1 check yes + +timestep 1.0 + +variable TK equal 300.0 +variable PBAR equal 1.0 + +velocity all create ${TK} 12345 + +fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000 + +thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density +thermo 5000 + +set type 1*2 charge 0.0 + +run 100000 + +reset_timestep 0 + +variable lambda equal ramp(1.0,0.0) + +fix ADAPT all adapt/fep 100000 & + pair lj/cut/soft lambda 1*2 3*4 v_lambda & + after yes + +thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda + +variable dlambda equal -0.05 + +compute FEP all fep ${TK} & + pair lj/cut/soft lambda 1*2 3*4 v_dlambda & + volume yes + +fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep10-lj.fep + +run 2000000 diff --git a/examples/USER/fep/SPCEhyd/fep10/in-fep10-q.lmp b/examples/USER/fep/SPCEhyd/fep10/in-fep10-q.lmp new file mode 100644 index 0000000000..d9183f7f15 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/fep10/in-fep10-q.lmp @@ -0,0 +1,76 @@ +# created by fftool + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic + +special_bonds lj/coul 0.0 0.0 0.5 + +# remove hybrid if not necessary +pair_style lj/cut/coul/long 12.0 12.0 +pair_modify tail no +kspace_style pppm 1.0e-5 + +read_data data.lmp + +pair_coeff 1 1 0.000000 1.000000 # Hwh Hwh +pair_coeff 1 2 0.000000 1.000000 # Hwh Owh +pair_coeff 1 3 0.000000 1.000000 # Hwh Hw +pair_coeff 1 4 0.000000 1.000000 # Hwh Ow +pair_coeff 2 2 0.155425 3.165500 # Owh Owh +pair_coeff 2 3 0.000000 1.000000 # Owh Hw +pair_coeff 2 4 0.155425 3.165500 # Owh Ow +pair_coeff 3 3 0.000000 1.000000 # Hw Hw +pair_coeff 3 4 0.000000 1.000000 # Hw Ow +pair_coeff 4 4 0.155425 3.165500 # Ow Ow + +# minimize 1.0e-4 1.0e-6 100 1000 +# reset_timestep 0 + +fix SHAKE all shake 0.0001 20 0 b 1 + +neighbor 2.0 bin +# neigh_modify delay 0 every 1 check yes + +timestep 1.0 + +variable TK equal 300.0 +variable PBAR equal 1.0 + +velocity all create ${TK} 12345 + +fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000 + +thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density +thermo 5000 + +run 100000 + +reset_timestep 0 + +variable lambda equal ramp(1.0,0.0) +variable qH equal 0.4238*v_lambda +variable qO equal -0.8476*v_lambda + +fix ADAPT all adapt/fep 100000 & + atom charge 1 v_qH & + atom charge 2 v_qO & + after yes + +thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda v_qO v_qH + +variable dlambda equal -0.05 +variable dqH equal 0.4238*v_dlambda +variable dqO equal -0.8476*v_dlambda + +compute FEP all fep ${TK} & + atom charge 1 v_dqH & + atom charge 2 v_dqO & + volume yes + +fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep10-q.fep + +run 2000000 diff --git a/examples/USER/fep/SPCEhyd/mols/data.lmp b/examples/USER/fep/SPCEhyd/mols/data.lmp new file mode 100644 index 0000000000..b6ead1d442 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/mols/data.lmp @@ -0,0 +1,3635 @@ +created by fftool + +1800 atoms +1200 bonds +600 angles +4 atom types +1 bond types +1 angle types +0.000000 29.204526 xlo xhi +0.000000 29.204526 ylo yhi +0.000000 29.204526 zlo zhi + +Masses + + 1 1.008 # Hwh + 2 15.999 # Owh + 3 1.008 # Hw + 4 15.999 # Ow + +Bond Coeffs + + 1 517.630258 1.000000 # Ow-Hw + +Angle Coeffs + + 1 37.950526 109.470000 # Hw-Ow-Hw + +Atoms + + 1 1 1 0.423800 1.469233e+00 2.148142e+00 1.702038e+00 # Hwh SPCE + 2 1 2 -0.847600 1.979799e+00 1.409877e+00 2.142818e+00 # Owh SPCE + 3 1 1 0.423800 2.730865e+00 1.797090e+00 2.677576e+00 # Hwh SPCE + 4 2 3 0.423800 1.499900e+00 3.238303e+00 2.442531e+01 # Hw SPCE + 5 2 4 -0.847600 2.395752e+00 3.669948e+00 2.431980e+01 # Ow SPCE + 6 2 3 0.423800 2.296129e+00 4.663242e+00 2.437847e+01 # Hw SPCE + 7 3 3 0.423800 1.403661e+01 4.588770e+00 2.450878e+01 # Hw SPCE + 8 3 4 -0.847600 1.379951e+01 5.545591e+00 2.467695e+01 # Ow SPCE + 9 3 3 0.423800 1.402354e+01 6.091366e+00 2.386952e+01 # Hw SPCE + 10 4 3 0.423800 2.336049e+01 1.499786e+00 3.153124e+00 # Hw SPCE + 11 4 4 -0.847600 2.409385e+01 2.065977e+00 3.529439e+00 # Ow SPCE + 12 4 3 0.423800 2.490226e+01 1.500034e+00 3.691241e+00 # Hw SPCE + 13 5 3 0.423800 1.644196e+01 1.748367e+00 2.705436e+01 # Hw SPCE + 14 5 4 -0.847600 1.736546e+01 1.496062e+00 2.734329e+01 # Ow SPCE + 15 5 3 0.423800 1.783282e+01 2.301936e+00 2.770680e+01 # Hw SPCE + 16 6 3 0.423800 2.088933e+01 1.895579e+01 2.275309e+01 # Hw SPCE + 17 6 4 -0.847600 2.057929e+01 1.824793e+01 2.211841e+01 # Ow SPCE + 18 6 3 0.423800 1.984085e+01 1.772204e+01 2.254049e+01 # Hw SPCE + 19 7 3 0.423800 1.766189e+01 8.017800e+00 2.498964e+01 # Hw SPCE + 20 7 4 -0.847600 1.725196e+01 8.916174e+00 2.483189e+01 # Ow SPCE + 21 7 3 0.423800 1.625542e+01 8.836819e+00 2.485666e+01 # Hw SPCE + 22 8 3 0.423800 2.770687e+01 2.171554e+01 1.528009e+01 # Hw SPCE + 23 8 4 -0.847600 2.716811e+01 2.251048e+01 1.555905e+01 # Ow SPCE + 24 8 3 0.423800 2.770528e+01 2.307342e+01 1.618718e+01 # Hw SPCE + 25 9 3 0.423800 1.495385e+00 2.572800e+01 2.467279e+01 # Hw SPCE + 26 9 4 -0.847600 1.580382e+00 2.672428e+01 2.468743e+01 # Ow SPCE + 27 9 3 0.423800 1.767742e+00 2.702913e+01 2.562122e+01 # Hw SPCE + 28 10 3 0.423800 8.923646e+00 2.303176e+01 7.542360e+00 # Hw SPCE + 29 10 4 -0.847600 8.109007e+00 2.312152e+01 6.969379e+00 # Ow SPCE + 30 10 3 0.423800 7.298201e+00 2.288018e+01 7.502626e+00 # Hw SPCE + 31 11 3 0.423800 1.123659e+01 2.107791e+01 4.662100e+00 # Hw SPCE + 32 11 4 -0.847600 1.223538e+01 2.105512e+01 4.618509e+00 # Ow SPCE + 33 11 3 0.423800 1.259832e+01 2.069338e+01 5.477241e+00 # Hw SPCE + 34 12 3 0.423800 1.225298e+01 2.161218e+01 1.146502e+01 # Hw SPCE + 35 12 4 -0.847600 1.278626e+01 2.077538e+01 1.134100e+01 # Ow SPCE + 36 12 3 0.423800 1.216660e+01 1.999649e+01 1.124435e+01 # Hw SPCE + 37 13 3 0.423800 2.178085e+01 2.141393e+01 1.947311e+01 # Hw SPCE + 38 13 4 -0.847600 2.200950e+01 2.051108e+01 1.910897e+01 # Ow SPCE + 39 13 3 0.423800 2.190716e+01 1.982534e+01 1.982958e+01 # Hw SPCE + 40 14 3 0.423800 2.603847e+01 7.816317e+00 1.661274e+01 # Hw SPCE + 41 14 4 -0.847600 2.671903e+01 7.539282e+00 1.729103e+01 # Ow SPCE + 42 14 3 0.423800 2.712614e+01 6.667675e+00 1.701797e+01 # Hw SPCE + 43 15 3 0.423800 2.662104e+01 1.315276e+01 2.415551e+01 # Hw SPCE + 44 15 4 -0.847600 2.749092e+01 1.325361e+01 2.463837e+01 # Ow SPCE + 45 15 3 0.423800 2.770488e+01 1.422511e+01 2.474029e+01 # Hw SPCE + 46 16 3 0.423800 2.343696e+01 2.012869e+01 2.434140e+01 # Hw SPCE + 47 16 4 -0.847600 2.284311e+01 1.938463e+01 2.464753e+01 # Ow SPCE + 48 16 3 0.423800 2.328036e+01 1.889915e+01 2.540458e+01 # Hw SPCE + 49 17 3 0.423800 7.794521e+00 2.000989e+01 2.199182e+01 # Hw SPCE + 50 17 4 -0.847600 7.929378e+00 2.033080e+01 2.292928e+01 # Ow SPCE + 51 17 3 0.423800 8.857758e+00 2.010876e+01 2.322729e+01 # Hw SPCE + 52 18 3 0.423800 6.830410e+00 2.518010e+01 2.209866e+01 # Hw SPCE + 53 18 4 -0.847600 6.177519e+00 2.451264e+01 2.174056e+01 # Ow SPCE + 54 18 3 0.423800 6.309669e+00 2.363590e+01 2.220301e+01 # Hw SPCE + 55 19 3 0.423800 1.596377e+01 2.092461e+01 2.446023e+01 # Hw SPCE + 56 19 4 -0.847600 1.590738e+01 1.999342e+01 2.482037e+01 # Ow SPCE + 57 19 3 0.423800 1.681118e+01 1.956697e+01 2.478476e+01 # Hw SPCE + 58 20 3 0.423800 1.911326e+01 2.770546e+01 4.844631e+00 # Hw SPCE + 59 20 4 -0.847600 1.985915e+01 2.703939e+01 4.843586e+00 # Ow SPCE + 60 20 3 0.423800 2.073574e+01 2.752062e+01 4.840568e+00 # Hw SPCE + 61 21 3 0.423800 7.957677e+00 2.769262e+01 2.125162e+01 # Hw SPCE + 62 21 4 -0.847600 7.905132e+00 2.770650e+01 2.225015e+01 # Ow SPCE + 63 21 3 0.423800 8.829127e+00 2.770890e+01 2.263254e+01 # Hw SPCE + 64 22 3 0.423800 2.070265e+01 9.528473e+00 1.663276e+01 # Hw SPCE + 65 22 4 -0.847600 1.973165e+01 9.696078e+00 1.680328e+01 # Ow SPCE + 66 22 3 0.423800 1.934110e+01 8.919385e+00 1.729746e+01 # Hw SPCE + 67 23 3 0.423800 7.809959e+00 8.565464e+00 2.274346e+01 # Hw SPCE + 68 23 4 -0.847600 8.612896e+00 9.122442e+00 2.295575e+01 # Ow SPCE + 69 23 3 0.423800 9.372009e+00 8.852272e+00 2.236351e+01 # Hw SPCE + 70 24 3 0.423800 2.498899e+01 2.308095e+01 1.903531e+01 # Hw SPCE + 71 24 4 -0.847600 2.436019e+01 2.235497e+01 1.931382e+01 # Ow SPCE + 72 24 3 0.423800 2.484014e+01 2.170706e+01 1.990531e+01 # Hw SPCE + 73 25 3 0.423800 1.506895e+00 5.662694e+00 6.920599e+00 # Hw SPCE + 74 25 4 -0.847600 1.784503e+00 6.309796e+00 7.630665e+00 # Ow SPCE + 75 25 3 0.423800 2.707518e+00 6.641971e+00 7.436495e+00 # Hw SPCE + 76 26 3 0.423800 2.153403e+01 1.348159e+01 2.085837e+01 # Hw SPCE + 77 26 4 -0.847600 2.086248e+01 1.274077e+01 2.087218e+01 # Ow SPCE + 78 26 3 0.423800 2.067461e+01 1.247880e+01 2.181880e+01 # Hw SPCE + 79 27 3 0.423800 6.800685e+00 2.203104e+01 2.620499e+01 # Hw SPCE + 80 27 4 -0.847600 6.856841e+00 2.274258e+01 2.550459e+01 # Ow SPCE + 81 27 3 0.423800 6.369339e+00 2.244243e+01 2.468469e+01 # Hw SPCE + 82 28 3 0.423800 2.330650e+01 7.514481e+00 5.018724e+00 # Hw SPCE + 83 28 4 -0.847600 2.253073e+01 6.885276e+00 4.970822e+00 # Ow SPCE + 84 28 3 0.423800 2.286694e+01 5.944773e+00 4.921621e+00 # Hw SPCE + 85 29 3 0.423800 1.465322e+01 1.590735e+01 2.422856e+01 # Hw SPCE + 86 29 4 -0.847600 1.477140e+01 1.663018e+01 2.354771e+01 # Ow SPCE + 87 29 3 0.423800 1.453616e+01 1.751291e+01 2.395449e+01 # Hw SPCE + 88 30 3 0.423800 1.040291e+01 5.254847e+00 1.370622e+01 # Hw SPCE + 89 30 4 -0.847600 1.105724e+01 4.607844e+00 1.409768e+01 # Ow SPCE + 90 30 3 0.423800 1.077812e+01 3.674305e+00 1.387274e+01 # Hw SPCE + 91 31 3 0.423800 2.276938e+01 1.512055e+01 9.190561e+00 # Hw SPCE + 92 31 4 -0.847600 2.301556e+01 1.453653e+01 9.964062e+00 # Ow SPCE + 93 31 3 0.423800 2.340966e+01 1.368242e+01 9.624659e+00 # Hw SPCE + 94 32 3 0.423800 5.188719e+00 2.026958e+01 2.114125e+01 # Hw SPCE + 95 32 4 -0.847600 5.223057e+00 2.126505e+01 2.105256e+01 # Ow SPCE + 96 32 3 0.423800 4.292242e+00 2.162905e+01 2.101958e+01 # Hw SPCE + 97 33 3 0.423800 1.776246e+01 1.332125e+01 2.630655e+01 # Hw SPCE + 98 33 4 -0.847600 1.826497e+01 1.415453e+01 2.653702e+01 # Ow SPCE + 99 33 3 0.423800 1.924234e+01 1.400708e+01 2.638536e+01 # Hw SPCE + 100 34 3 0.423800 2.606566e+00 1.054762e+01 6.428992e+00 # Hw SPCE + 101 34 4 -0.847600 1.625220e+00 1.071787e+01 6.339693e+00 # Ow SPCE + 102 34 3 0.423800 1.425906e+00 1.104165e+01 5.414793e+00 # Hw SPCE + 103 35 3 0.423800 2.588493e+01 4.071742e+00 4.105367e+00 # Hw SPCE + 104 35 4 -0.847600 2.671121e+01 4.617835e+00 4.243387e+00 # Ow SPCE + 105 35 3 0.423800 2.741817e+01 4.051459e+00 4.666975e+00 # Hw SPCE + 106 36 3 0.423800 7.373843e+00 6.669901e+00 1.394201e+01 # Hw SPCE + 107 36 4 -0.847600 7.563042e+00 6.090000e+00 1.473442e+01 # Ow SPCE + 108 36 3 0.423800 7.053521e+00 6.429426e+00 1.552510e+01 # Hw SPCE + 109 37 3 0.423800 4.172482e+00 1.303888e+01 1.710824e+01 # Hw SPCE + 110 37 4 -0.847600 4.702018e+00 1.220690e+01 1.727375e+01 # Ow SPCE + 111 37 3 0.423800 4.203212e+00 1.141758e+01 1.691575e+01 # Hw SPCE + 112 38 3 0.423800 1.949787e+01 5.529973e+00 1.254239e+01 # Hw SPCE + 113 38 4 -0.847600 2.035077e+01 5.090120e+00 1.282362e+01 # Ow SPCE + 114 38 3 0.423800 2.089205e+01 4.864082e+00 1.201373e+01 # Hw SPCE + 115 39 3 0.423800 2.451616e+01 8.924670e+00 1.865568e+01 # Hw SPCE + 116 39 4 -0.847600 2.381451e+01 8.652982e+00 1.799699e+01 # Ow SPCE + 117 39 3 0.423800 2.311781e+01 9.367935e+00 1.793821e+01 # Hw SPCE + 118 40 3 0.423800 1.500065e+00 2.219167e+01 2.760505e+00 # Hw SPCE + 119 40 4 -0.847600 2.224501e+00 2.150236e+01 2.767217e+00 # Ow SPCE + 120 40 3 0.423800 1.817068e+00 2.059122e+01 2.829029e+00 # Hw SPCE + 121 41 3 0.423800 2.640554e+01 1.928714e+01 4.290644e+00 # Hw SPCE + 122 41 4 -0.847600 2.740415e+01 1.931798e+01 4.247967e+00 # Ow SPCE + 123 41 3 0.423800 2.770519e+01 2.026827e+01 4.168519e+00 # Hw SPCE + 124 42 3 0.423800 1.388747e+01 7.977813e+00 2.595555e+01 # Hw SPCE + 125 42 4 -0.847600 1.290644e+01 7.828209e+00 2.607882e+01 # Ow SPCE + 126 42 3 0.423800 1.244102e+01 8.710473e+00 2.614947e+01 # Hw SPCE + 127 43 3 0.423800 2.444541e+01 1.183745e+01 2.520365e+01 # Hw SPCE + 128 43 4 -0.847600 2.466934e+01 1.086365e+01 2.516413e+01 # Ow SPCE + 129 43 3 0.423800 2.566048e+01 1.075222e+01 2.509189e+01 # Hw SPCE + 130 44 3 0.423800 2.483417e+01 1.651695e+01 2.163120e+01 # Hw SPCE + 131 44 4 -0.847600 2.410271e+01 1.585943e+01 2.145058e+01 # Ow SPCE + 132 44 3 0.423800 2.445847e+01 1.492995e+01 2.154809e+01 # Hw SPCE + 133 45 3 0.423800 1.730263e+01 2.595540e+01 3.740298e+00 # Hw SPCE + 134 45 4 -0.847600 1.773679e+01 2.510003e+01 4.022883e+00 # Ow SPCE + 135 45 3 0.423800 1.770998e+01 2.444677e+01 3.266223e+00 # Hw SPCE + 136 46 3 0.423800 1.064666e+01 1.544703e+00 2.342635e+01 # Hw SPCE + 137 46 4 -0.847600 9.658303e+00 1.485990e+00 2.356670e+01 # Ow SPCE + 138 46 3 0.423800 9.290506e+00 2.400694e+00 2.373415e+01 # Hw SPCE + 139 47 3 0.423800 6.958351e+00 1.058272e+01 2.770522e+01 # Hw SPCE + 140 47 4 -0.847600 7.092574e+00 1.157367e+01 2.770263e+01 # Ow SPCE + 141 47 3 0.423800 6.203030e+00 1.203050e+01 2.769941e+01 # Hw SPCE + 142 48 3 0.423800 3.958262e+00 4.358392e+00 8.337038e+00 # Hw SPCE + 143 48 4 -0.847600 3.059091e+00 3.923448e+00 8.385147e+00 # Ow SPCE + 144 48 3 0.423800 3.110013e+00 3.117001e+00 8.974257e+00 # Hw SPCE + 145 49 3 0.423800 2.527221e+01 1.981465e+01 9.871580e+00 # Hw SPCE + 146 49 4 -0.847600 2.589272e+01 1.903608e+01 9.965427e+00 # Ow SPCE + 147 49 3 0.423800 2.675477e+01 1.934357e+01 1.036832e+01 # Hw SPCE + 148 50 3 0.423800 2.513678e+01 1.655111e+01 8.455263e+00 # Hw SPCE + 149 50 4 -0.847600 2.439311e+01 1.719386e+01 8.271354e+00 # Ow SPCE + 150 50 3 0.423800 2.390732e+01 1.691348e+01 7.443466e+00 # Hw SPCE + 151 51 3 0.423800 9.547080e+00 5.818685e+00 7.837619e+00 # Hw SPCE + 152 51 4 -0.847600 9.188230e+00 4.885428e+00 7.821533e+00 # Ow SPCE + 153 51 3 0.423800 9.947239e+00 4.237539e+00 7.757147e+00 # Hw SPCE + 154 52 3 0.423800 1.913212e+01 1.999545e+01 1.375657e+01 # Hw SPCE + 155 52 4 -0.847600 1.977845e+01 1.954444e+01 1.437208e+01 # Ow SPCE + 156 52 3 0.423800 2.009170e+01 1.868964e+01 1.395831e+01 # Hw SPCE + 157 53 3 0.423800 2.488521e+00 4.298268e+00 1.662022e+01 # Hw SPCE + 158 53 4 -0.847600 3.439105e+00 4.019650e+00 1.675720e+01 # Ow SPCE + 159 53 3 0.423800 3.840963e+00 4.558416e+00 1.749763e+01 # Hw SPCE + 160 54 3 0.423800 8.720856e+00 1.200478e+01 2.905857e+00 # Hw SPCE + 161 54 4 -0.847600 8.109727e+00 1.255626e+01 2.338060e+00 # Ow SPCE + 162 54 3 0.423800 7.159796e+00 1.233215e+01 2.555793e+00 # Hw SPCE + 163 55 3 0.423800 1.270857e+01 1.035303e+01 5.382569e+00 # Hw SPCE + 164 55 4 -0.847600 1.322488e+01 9.496640e+00 5.388255e+00 # Ow SPCE + 165 55 3 0.423800 1.305339e+01 9.009733e+00 6.244710e+00 # Hw SPCE + 166 56 3 0.423800 1.684898e+01 2.523462e+01 1.822162e+01 # Hw SPCE + 167 56 4 -0.847600 1.664347e+01 2.603725e+01 1.878158e+01 # Ow SPCE + 168 56 3 0.423800 1.648466e+01 2.575236e+01 1.972689e+01 # Hw SPCE + 169 57 3 0.423800 1.020796e+01 2.594114e+01 7.868994e+00 # Hw SPCE + 170 57 4 -0.847600 1.048594e+01 2.681088e+01 8.276773e+00 # Ow SPCE + 171 57 3 0.423800 1.003609e+01 2.692243e+01 9.162888e+00 # Hw SPCE + 172 58 3 0.423800 2.300209e+01 1.144525e+01 1.973611e+01 # Hw SPCE + 173 58 4 -0.847600 2.326720e+01 1.069841e+01 2.034599e+01 # Ow SPCE + 174 58 3 0.423800 2.274079e+01 1.075787e+01 2.119414e+01 # Hw SPCE + 175 59 3 0.423800 1.609161e+01 1.214359e+01 1.492237e+00 # Hw SPCE + 176 59 4 -0.847600 1.690824e+01 1.157531e+01 1.593113e+00 # Ow SPCE + 177 59 3 0.423800 1.664177e+01 1.065885e+01 1.891605e+00 # Hw SPCE + 178 60 3 0.423800 2.419902e+01 2.411706e+01 6.611761e+00 # Hw SPCE + 179 60 4 -0.847600 2.467864e+01 2.498895e+01 6.710596e+00 # Ow SPCE + 180 60 3 0.423800 2.544873e+01 2.487644e+01 7.338537e+00 # Hw SPCE + 181 61 3 0.423800 1.196568e+01 5.594696e+00 6.473038e+00 # Hw SPCE + 182 61 4 -0.847600 1.199305e+01 6.536579e+00 6.807864e+00 # Ow SPCE + 183 61 3 0.423800 1.267510e+01 6.612062e+00 7.535263e+00 # Hw SPCE + 184 62 3 0.423800 1.669021e+01 8.472310e+00 7.036663e+00 # Hw SPCE + 185 62 4 -0.847600 1.572284e+01 8.690729e+00 6.908251e+00 # Ow SPCE + 186 62 3 0.423800 1.554585e+01 9.621300e+00 7.228737e+00 # Hw SPCE + 187 63 3 0.423800 1.821528e+01 1.487703e+01 1.756524e+01 # Hw SPCE + 188 63 4 -0.847600 1.872911e+01 1.551055e+01 1.814370e+01 # Ow SPCE + 189 63 3 0.423800 1.854708e+01 1.644985e+01 1.785290e+01 # Hw SPCE + 190 64 3 0.423800 7.984302e+00 1.799893e+01 1.529353e+00 # Hw SPCE + 191 64 4 -0.847600 8.826448e+00 1.746123e+01 1.488465e+00 # Ow SPCE + 192 64 3 0.423800 9.462122e+00 1.778360e+01 2.189889e+00 # Hw SPCE + 193 65 3 0.423800 2.562243e+01 6.741416e+00 1.403530e+01 # Hw SPCE + 194 65 4 -0.847600 2.622983e+01 6.086036e+00 1.448423e+01 # Ow SPCE + 195 65 3 0.423800 2.717413e+01 6.262256e+00 1.420632e+01 # Hw SPCE + 196 66 3 0.423800 2.512713e+01 2.094793e+00 1.358574e+01 # Hw SPCE + 197 66 4 -0.847600 2.434949e+01 1.495442e+00 1.339585e+01 # Ow SPCE + 198 66 3 0.423800 2.355565e+01 1.803117e+00 1.392040e+01 # Hw SPCE + 199 67 3 0.423800 9.301908e+00 1.331503e+01 2.358584e+01 # Hw SPCE + 200 67 4 -0.847600 8.584183e+00 1.395669e+01 2.331540e+01 # Ow SPCE + 201 67 3 0.423800 8.271122e+00 1.373659e+01 2.239153e+01 # Hw SPCE + 202 68 3 0.423800 9.955846e+00 1.273829e+01 6.296276e+00 # Hw SPCE + 203 68 4 -0.847600 1.056341e+01 1.199023e+01 6.029323e+00 # Ow SPCE + 204 68 3 0.423800 1.029850e+01 1.165171e+01 5.126425e+00 # Hw SPCE + 205 69 3 0.423800 1.595831e+01 4.015404e+00 2.177868e+01 # Hw SPCE + 206 69 4 -0.847600 1.665439e+01 3.881186e+00 2.248398e+01 # Ow SPCE + 207 69 3 0.423800 1.647833e+01 4.501446e+00 2.324836e+01 # Hw SPCE + 208 70 3 0.423800 1.191249e+01 1.053961e+01 1.614692e+01 # Hw SPCE + 209 70 4 -0.847600 1.285965e+01 1.031522e+01 1.591770e+01 # Ow SPCE + 210 70 3 0.423800 1.326240e+01 1.106545e+01 1.539335e+01 # Hw SPCE + 211 71 3 0.423800 2.756106e+01 7.219592e+00 3.733621e+00 # Hw SPCE + 212 71 4 -0.847600 2.673030e+01 7.191784e+00 3.177694e+00 # Ow SPCE + 213 71 3 0.423800 2.592863e+01 7.212180e+00 3.775112e+00 # Hw SPCE + 214 72 3 0.423800 1.619051e+01 4.555961e+00 1.375257e+01 # Hw SPCE + 215 72 4 -0.847600 1.693660e+01 4.702954e+00 1.310315e+01 # Ow SPCE + 216 72 3 0.423800 1.692272e+01 3.981627e+00 1.241069e+01 # Hw SPCE + 217 73 3 0.423800 2.233085e+01 2.254376e+01 2.509491e+01 # Hw SPCE + 218 73 4 -0.847600 2.137546e+01 2.283349e+01 2.503760e+01 # Ow SPCE + 219 73 3 0.423800 2.132827e+01 2.383218e+01 2.505737e+01 # Hw SPCE + 220 74 3 0.423800 4.614385e+00 2.266996e+01 1.754496e+01 # Hw SPCE + 221 74 4 -0.847600 5.529231e+00 2.271822e+01 1.794587e+01 # Ow SPCE + 222 74 3 0.423800 6.044304e+00 2.345795e+01 1.751287e+01 # Hw SPCE + 223 75 3 0.423800 2.221903e+01 7.556525e+00 1.516871e+01 # Hw SPCE + 224 75 4 -0.847600 2.250349e+01 7.635346e+00 1.421326e+01 # Ow SPCE + 225 75 3 0.423800 2.176672e+01 7.313720e+00 1.361852e+01 # Hw SPCE + 226 76 3 0.423800 2.629759e+01 1.920638e+01 2.353714e+01 # Hw SPCE + 227 76 4 -0.847600 2.715395e+01 1.902228e+01 2.401958e+01 # Ow SPCE + 228 76 3 0.423800 2.770506e+01 1.837985e+01 2.348707e+01 # Hw SPCE + 229 77 3 0.423800 4.143809e+00 1.561555e+01 8.018737e+00 # Hw SPCE + 230 77 4 -0.847600 4.614959e+00 1.553180e+01 8.896805e+00 # Ow SPCE + 231 77 3 0.423800 4.199222e+00 1.615528e+01 9.558946e+00 # Hw SPCE + 232 78 3 0.423800 9.954198e+00 1.261788e+01 1.237010e+01 # Hw SPCE + 233 78 4 -0.847600 9.562880e+00 1.353598e+01 1.243307e+01 # Ow SPCE + 234 78 3 0.423800 8.569485e+00 1.346921e+01 1.252638e+01 # Hw SPCE + 235 79 3 0.423800 2.332846e+01 2.323923e+01 3.781581e+00 # Hw SPCE + 236 79 4 -0.847600 2.276687e+01 2.256928e+01 3.296002e+00 # Ow SPCE + 237 79 3 0.423800 2.333089e+01 2.178393e+01 3.040806e+00 # Hw SPCE + 238 80 3 0.423800 1.563376e+01 9.681389e+00 1.524542e+01 # Hw SPCE + 239 80 4 -0.847600 1.641808e+01 9.172361e+00 1.559999e+01 # Ow SPCE + 240 80 3 0.423800 1.655877e+01 9.404722e+00 1.656239e+01 # Hw SPCE + 241 81 3 0.423800 3.016047e+00 1.608090e+01 2.770691e+01 # Hw SPCE + 242 81 4 -0.847600 3.873141e+00 1.658768e+01 2.761432e+01 # Ow SPCE + 243 81 3 0.423800 4.041570e+00 1.678405e+01 2.664837e+01 # Hw SPCE + 244 82 3 0.423800 2.553862e+01 1.927894e+01 1.283389e+01 # Hw SPCE + 245 82 4 -0.847600 2.595825e+01 2.010455e+01 1.321108e+01 # Ow SPCE + 246 82 3 0.423800 2.694466e+01 1.996635e+01 1.329986e+01 # Hw SPCE + 247 83 3 0.423800 1.446078e+01 5.122478e+00 1.975466e+01 # Hw SPCE + 248 83 4 -0.847600 1.399157e+01 5.719286e+00 1.910377e+01 # Ow SPCE + 249 83 3 0.423800 1.387428e+01 6.626403e+00 1.950797e+01 # Hw SPCE + 250 84 3 0.423800 4.975267e+00 1.195188e+01 1.361200e+01 # Hw SPCE + 251 84 4 -0.847600 5.863360e+00 1.223599e+01 1.397335e+01 # Ow SPCE + 252 84 3 0.423800 6.001585e+00 1.182880e+01 1.487617e+01 # Hw SPCE + 253 85 3 0.423800 1.729394e+01 2.690297e+01 2.489413e+01 # Hw SPCE + 254 85 4 -0.847600 1.798622e+01 2.618717e+01 2.498570e+01 # Ow SPCE + 255 85 3 0.423800 1.753851e+01 2.531197e+01 2.516899e+01 # Hw SPCE + 256 86 3 0.423800 1.443295e+01 1.369845e+01 9.542794e+00 # Hw SPCE + 257 86 4 -0.847600 1.453225e+01 1.337010e+01 1.048212e+01 # Ow SPCE + 258 86 3 0.423800 1.407152e+01 1.248767e+01 1.057721e+01 # Hw SPCE + 259 87 3 0.423800 1.481041e+01 9.892914e+00 2.769929e+01 # Hw SPCE + 260 87 4 -0.847600 1.474545e+01 1.089078e+01 2.770556e+01 # Ow SPCE + 261 87 3 0.423800 1.566461e+01 1.128460e+01 2.771213e+01 # Hw SPCE + 262 88 3 0.423800 2.711944e+01 2.239741e+00 7.551846e+00 # Hw SPCE + 263 88 4 -0.847600 2.613715e+01 2.417616e+00 7.610794e+00 # Ow SPCE + 264 88 3 0.423800 2.588056e+01 2.557524e+00 8.567132e+00 # Hw SPCE + 265 89 3 0.423800 1.579109e+01 5.900382e+00 6.668995e+00 # Hw SPCE + 266 89 4 -0.847600 1.499190e+01 6.158630e+00 6.126217e+00 # Ow SPCE + 267 89 3 0.423800 1.487648e+01 5.510338e+00 5.373624e+00 # Hw SPCE + 268 90 3 0.423800 2.133610e+01 1.746297e+01 9.335501e+00 # Hw SPCE + 269 90 4 -0.847600 2.057506e+01 1.754198e+01 8.691632e+00 # Ow SPCE + 270 90 3 0.423800 2.092169e+01 1.747499e+01 7.756026e+00 # Hw SPCE + 271 91 3 0.423800 5.764508e+00 6.459756e+00 1.799860e+01 # Hw SPCE + 272 91 4 -0.847600 6.332363e+00 5.967190e+00 1.865808e+01 # Ow SPCE + 273 91 3 0.423800 6.766765e+00 6.620913e+00 1.927772e+01 # Hw SPCE + 274 92 3 0.423800 1.519730e+01 1.983322e+01 1.921450e+01 # Hw SPCE + 275 92 4 -0.847600 1.593017e+01 1.916543e+01 1.908429e+01 # Ow SPCE + 276 92 3 0.423800 1.663520e+01 1.955553e+01 1.849204e+01 # Hw SPCE + 277 93 3 0.423800 2.313253e+00 7.250692e+00 1.329362e+01 # Hw SPCE + 278 93 4 -0.847600 1.488319e+00 7.811762e+00 1.322518e+01 # Ow SPCE + 279 93 3 0.423800 1.540991e+00 8.563456e+00 1.388259e+01 # Hw SPCE + 280 94 3 0.423800 2.611731e+01 1.202552e+01 1.053768e+01 # Hw SPCE + 281 94 4 -0.847600 2.710862e+01 1.215596e+01 1.052099e+01 # Ow SPCE + 282 94 3 0.423800 2.756049e+01 1.126726e+01 1.044331e+01 # Hw SPCE + 283 95 3 0.423800 6.603696e+00 2.054040e+01 1.298798e+01 # Hw SPCE + 284 95 4 -0.847600 5.882293e+00 2.028304e+01 1.234506e+01 # Ow SPCE + 285 95 3 0.423800 6.172577e+00 2.050160e+01 1.141341e+01 # Hw SPCE + 286 96 3 0.423800 2.098737e+01 6.874062e+00 1.013861e+01 # Hw SPCE + 287 96 4 -0.847600 2.156028e+01 7.451122e+00 1.072066e+01 # Ow SPCE + 288 96 3 0.423800 2.195352e+01 8.190100e+00 1.017360e+01 # Hw SPCE + 289 97 3 0.423800 5.786826e+00 1.087307e+01 1.086502e+01 # Hw SPCE + 290 97 4 -0.847600 6.324427e+00 1.163284e+01 1.123071e+01 # Ow SPCE + 291 97 3 0.423800 7.142246e+00 1.127568e+01 1.168194e+01 # Hw SPCE + 292 98 3 0.423800 1.143842e+01 2.119323e+01 8.871945e+00 # Hw SPCE + 293 98 4 -0.847600 1.139221e+01 2.127877e+01 7.876682e+00 # Ow SPCE + 294 98 3 0.423800 1.071119e+01 2.064007e+01 7.518516e+00 # Hw SPCE + 295 99 3 0.423800 5.459585e+00 2.383383e+01 5.598160e+00 # Hw SPCE + 296 99 4 -0.847600 5.520099e+00 2.482379e+01 5.470403e+00 # Ow SPCE + 297 99 3 0.423800 5.586370e+00 2.503046e+01 4.494238e+00 # Hw SPCE + 298 100 3 0.423800 2.264458e+00 7.960990e+00 2.770952e+01 # Hw SPCE + 299 100 4 -0.847600 2.090525e+00 8.160734e+00 2.674523e+01 # Ow SPCE + 300 100 3 0.423800 1.495909e+00 7.454707e+00 2.636058e+01 # Hw SPCE + 301 101 3 0.423800 7.095393e+00 1.940453e+01 2.544132e+01 # Hw SPCE + 302 101 4 -0.847600 6.237306e+00 1.963392e+01 2.498190e+01 # Ow SPCE + 303 101 3 0.423800 5.644089e+00 1.882911e+01 2.496253e+01 # Hw SPCE + 304 102 3 0.423800 1.499078e+00 3.404424e+00 2.770580e+01 # Hw SPCE + 305 102 4 -0.847600 2.042815e+00 3.910224e+00 2.703609e+01 # Ow SPCE + 306 102 3 0.423800 1.977853e+00 4.889953e+00 2.722559e+01 # Hw SPCE + 307 103 3 0.423800 5.115452e+00 2.292057e+01 1.247440e+01 # Hw SPCE + 308 103 4 -0.847600 5.773141e+00 2.354653e+01 1.205533e+01 # Ow SPCE + 309 103 3 0.423800 6.680714e+00 2.312664e+01 1.205713e+01 # Hw SPCE + 310 104 3 0.423800 1.944181e+01 2.324594e+01 1.499570e+00 # Hw SPCE + 311 104 4 -0.847600 2.043993e+01 2.318469e+01 1.499022e+00 # Ow SPCE + 312 104 3 0.423800 2.071487e+01 2.222323e+01 1.498289e+00 # Hw SPCE + 313 105 3 0.423800 1.030626e+01 8.957281e+00 6.373247e+00 # Hw SPCE + 314 105 4 -0.847600 9.786014e+00 8.104555e+00 6.326252e+00 # Ow SPCE + 315 105 3 0.423800 8.880748e+00 8.243851e+00 6.727613e+00 # Hw SPCE + 316 106 3 0.423800 1.864859e+01 1.763094e+00 1.290621e+01 # Hw SPCE + 317 106 4 -0.847600 1.923656e+01 2.571543e+00 1.287976e+01 # Ow SPCE + 318 106 3 0.423800 2.017824e+01 2.292795e+00 1.269123e+01 # Hw SPCE + 319 107 3 0.423800 2.129031e+00 5.623946e+00 1.104896e+01 # Hw SPCE + 320 107 4 -0.847600 1.506474e+00 5.035776e+00 1.053275e+01 # Ow SPCE + 321 107 3 0.423800 1.486177e+00 4.126233e+00 1.094786e+01 # Hw SPCE + 322 108 3 0.423800 2.212734e+01 1.355457e+01 3.475366e+00 # Hw SPCE + 323 108 4 -0.847600 2.189942e+01 1.348653e+01 4.446665e+00 # Ow SPCE + 324 108 3 0.423800 2.141982e+01 1.431518e+01 4.735327e+00 # Hw SPCE + 325 109 3 0.423800 2.714041e+01 9.226233e+00 1.942138e+01 # Hw SPCE + 326 109 4 -0.847600 2.695029e+01 1.019981e+01 1.954785e+01 # Ow SPCE + 327 109 3 0.423800 2.770446e+01 1.073827e+01 1.917198e+01 # Hw SPCE + 328 110 3 0.423800 1.145913e+01 1.921390e+01 1.496917e+01 # Hw SPCE + 329 110 4 -0.847600 1.131470e+01 2.018773e+01 1.479367e+01 # Ow SPCE + 330 110 3 0.423800 1.033642e+01 2.036578e+01 1.468754e+01 # Hw SPCE + 331 111 3 0.423800 4.274133e+00 2.306189e+00 2.713568e+01 # Hw SPCE + 332 111 4 -0.847600 4.237246e+00 1.500039e+00 2.654512e+01 # Ow SPCE + 333 111 3 0.423800 3.652688e+00 1.690998e+00 2.575656e+01 # Hw SPCE + 334 112 3 0.423800 2.374365e+01 4.285483e+00 2.548838e+01 # Hw SPCE + 335 112 4 -0.847600 2.363447e+01 3.410101e+00 2.501744e+01 # Ow SPCE + 336 112 3 0.423800 2.453520e+01 3.022399e+00 2.482154e+01 # Hw SPCE + 337 113 3 0.423800 2.147633e+01 2.400029e+01 6.981339e+00 # Hw SPCE + 338 113 4 -0.847600 2.070482e+01 2.460854e+01 6.794782e+00 # Ow SPCE + 339 113 3 0.423800 2.100757e+01 2.555958e+01 6.856910e+00 # Hw SPCE + 340 114 3 0.423800 2.475952e+01 2.542350e+01 2.655084e+01 # Hw SPCE + 341 114 4 -0.847600 2.490466e+01 2.505812e+01 2.563137e+01 # Ow SPCE + 342 114 3 0.423800 2.404295e+01 2.469469e+01 2.527727e+01 # Hw SPCE + 343 115 3 0.423800 2.160335e+01 2.393199e+01 1.009846e+01 # Hw SPCE + 344 115 4 -0.847600 2.078275e+01 2.449002e+01 1.022179e+01 # Ow SPCE + 345 115 3 0.423800 2.003750e+01 2.411294e+01 9.671860e+00 # Hw SPCE + 346 116 3 0.423800 1.865506e+01 2.117845e+01 1.756982e+01 # Hw SPCE + 347 116 4 -0.847600 1.807847e+01 2.183151e+01 1.707884e+01 # Ow SPCE + 348 116 3 0.423800 1.837699e+01 2.276271e+01 1.728801e+01 # Hw SPCE + 349 117 3 0.423800 2.061645e+00 6.549304e+00 1.814025e+01 # Hw SPCE + 350 117 4 -0.847600 1.475173e+00 6.253958e+00 1.889446e+01 # Ow SPCE + 351 117 3 0.423800 1.571483e+00 5.267187e+00 1.902487e+01 # Hw SPCE + 352 118 3 0.423800 1.643494e+01 1.386321e+01 1.572937e+01 # Hw SPCE + 353 118 4 -0.847600 1.600041e+01 1.308756e+01 1.527161e+01 # Ow SPCE + 354 118 3 0.423800 1.500654e+01 1.318983e+01 1.531362e+01 # Hw SPCE + 355 119 3 0.423800 1.886154e+01 1.359977e+01 1.388201e+01 # Hw SPCE + 356 119 4 -0.847600 1.985547e+01 1.361236e+01 1.399129e+01 # Ow SPCE + 357 119 3 0.423800 2.020182e+01 1.267429e+01 1.399938e+01 # Hw SPCE + 358 120 3 0.423800 2.640146e+01 4.249195e+00 1.244508e+01 # Hw SPCE + 359 120 4 -0.847600 2.716791e+01 3.811578e+00 1.291523e+01 # Ow SPCE + 360 120 3 0.423800 2.770629e+01 3.285544e+00 1.225687e+01 # Hw SPCE + 361 121 3 0.423800 1.496812e+00 1.814687e+00 1.782668e+01 # Hw SPCE + 362 121 4 -0.847600 1.815569e+00 1.693357e+00 1.876672e+01 # Ow SPCE + 363 121 3 0.423800 1.625725e+00 2.522412e+00 1.929267e+01 # Hw SPCE + 364 122 3 0.423800 2.680988e+01 1.869516e+01 7.392907e+00 # Hw SPCE + 365 122 4 -0.847600 2.739577e+01 1.944655e+01 7.696489e+00 # Ow SPCE + 366 122 3 0.423800 2.770460e+01 1.997015e+01 6.902469e+00 # Hw SPCE + 367 123 3 0.423800 6.657051e+00 1.748551e+01 3.900748e+00 # Hw SPCE + 368 123 4 -0.847600 7.611764e+00 1.740782e+01 4.187954e+00 # Ow SPCE + 369 123 3 0.423800 7.719232e+00 1.780597e+01 5.098957e+00 # Hw SPCE + 370 124 3 0.423800 1.712795e+01 2.364901e+01 2.137752e+01 # Hw SPCE + 371 124 4 -0.847600 1.651270e+01 2.309626e+01 2.193960e+01 # Ow SPCE + 372 124 3 0.423800 1.702767e+01 2.235135e+01 2.236376e+01 # Hw SPCE + 373 125 3 0.423800 2.465960e+01 9.111990e+00 1.552092e+00 # Hw SPCE + 374 125 4 -0.847600 2.368347e+01 9.328956e+00 1.542385e+00 # Ow SPCE + 375 125 3 0.423800 2.356287e+01 1.032079e+01 1.500818e+00 # Hw SPCE + 376 126 3 0.423800 1.541633e+01 2.513037e+01 2.342964e+01 # Hw SPCE + 377 126 4 -0.847600 1.496712e+01 2.563480e+01 2.416705e+01 # Ow SPCE + 378 126 3 0.423800 1.407826e+01 2.521990e+01 2.436140e+01 # Hw SPCE + 379 127 3 0.423800 2.198927e+01 2.296037e+01 1.264179e+01 # Hw SPCE + 380 127 4 -0.847600 2.135361e+01 2.220618e+01 1.280650e+01 # Ow SPCE + 381 127 3 0.423800 2.142262e+01 2.154325e+01 1.206101e+01 # Hw SPCE + 382 128 3 0.423800 5.808379e+00 1.479597e+00 1.729754e+01 # Hw SPCE + 383 128 4 -0.847600 5.311955e+00 2.244876e+00 1.770731e+01 # Ow SPCE + 384 128 3 0.423800 4.490271e+00 1.903163e+00 1.816345e+01 # Hw SPCE + 385 129 3 0.423800 4.410407e+00 9.586919e+00 1.489573e+01 # Hw SPCE + 386 129 4 -0.847600 4.330005e+00 8.939478e+00 1.413786e+01 # Ow SPCE + 387 129 3 0.423800 5.226071e+00 8.810656e+00 1.371305e+01 # Hw SPCE + 388 130 3 0.423800 8.119198e+00 3.621439e+00 1.317752e+01 # Hw SPCE + 389 130 4 -0.847600 8.167483e+00 2.832111e+00 1.256545e+01 # Ow SPCE + 390 130 3 0.423800 7.317941e+00 2.308454e+00 1.262918e+01 # Hw SPCE + 391 131 3 0.423800 1.605369e+01 6.725170e+00 2.132125e+01 # Hw SPCE + 392 131 4 -0.847600 1.601692e+01 7.081523e+00 2.225488e+01 # Ow SPCE + 393 131 3 0.423800 1.677297e+01 7.720235e+00 2.239787e+01 # Hw SPCE + 394 132 3 0.423800 2.587812e+01 2.770384e+01 6.790070e+00 # Hw SPCE + 395 132 4 -0.847600 2.495789e+01 2.770683e+01 6.398688e+00 # Ow SPCE + 396 132 3 0.423800 2.428216e+01 2.770348e+01 7.135826e+00 # Hw SPCE + 397 133 3 0.423800 3.242275e+00 2.430164e+01 3.033818e+00 # Hw SPCE + 398 133 4 -0.847600 3.385077e+00 2.527679e+01 2.864385e+00 # Ow SPCE + 399 133 3 0.423800 4.115488e+00 2.539474e+01 2.191640e+00 # Hw SPCE + 400 134 3 0.423800 1.391872e+01 1.853150e+01 1.389147e+01 # Hw SPCE + 401 134 4 -0.847600 1.350915e+01 1.835748e+01 1.299594e+01 # Ow SPCE + 402 134 3 0.423800 1.277157e+01 1.768895e+01 1.309098e+01 # Hw SPCE + 403 135 3 0.423800 1.883256e+00 1.950562e+01 6.097187e+00 # Hw SPCE + 404 135 4 -0.847600 2.108048e+00 1.853214e+01 6.139671e+00 # Ow SPCE + 405 135 3 0.423800 1.664096e+00 1.805416e+01 5.381755e+00 # Hw SPCE + 406 136 3 0.423800 1.772073e+01 1.904358e+01 6.835467e+00 # Hw SPCE + 407 136 4 -0.847600 1.848360e+01 1.839868e+01 6.881595e+00 # Ow SPCE + 408 136 3 0.423800 1.815821e+01 1.748070e+01 6.654789e+00 # Hw SPCE + 409 137 3 0.423800 1.668142e+01 1.746799e+01 2.770692e+01 # Hw SPCE + 410 137 4 -0.847600 1.690378e+01 1.739205e+01 2.673492e+01 # Ow SPCE + 411 137 3 0.423800 1.607886e+01 1.715496e+01 2.622181e+01 # Hw SPCE + 412 138 3 0.423800 6.510214e+00 5.350768e+00 8.615350e+00 # Hw SPCE + 413 138 4 -0.847600 6.301757e+00 6.322395e+00 8.727089e+00 # Ow SPCE + 414 138 3 0.423800 7.064288e+00 6.868862e+00 8.380795e+00 # Hw SPCE + 415 139 3 0.423800 1.123604e+01 1.437475e+01 2.577805e+01 # Hw SPCE + 416 139 4 -0.847600 1.147623e+01 1.512029e+01 2.639973e+01 # Ow SPCE + 417 139 3 0.423800 1.064787e+01 1.561484e+01 2.666285e+01 # Hw SPCE + 418 140 3 0.423800 1.018251e+01 2.301900e+01 2.071248e+01 # Hw SPCE + 419 140 4 -0.847600 1.073103e+01 2.232837e+01 2.118382e+01 # Ow SPCE + 420 140 3 0.423800 1.020516e+01 2.148141e+01 2.126196e+01 # Hw SPCE + 421 141 3 0.423800 5.434060e+00 2.503928e+00 1.462372e+01 # Hw SPCE + 422 141 4 -0.847600 6.195222e+00 3.000981e+00 1.504034e+01 # Ow SPCE + 423 141 3 0.423800 5.916457e+00 3.943344e+00 1.522539e+01 # Hw SPCE + 424 142 3 0.423800 2.396703e+01 1.692595e+01 1.892427e+01 # Hw SPCE + 425 142 4 -0.847600 2.487591e+01 1.651107e+01 1.888188e+01 # Ow SPCE + 426 142 3 0.423800 2.528573e+01 1.669671e+01 1.798880e+01 # Hw SPCE + 427 143 3 0.423800 1.739023e+01 2.770535e+01 2.756282e+01 # Hw SPCE + 428 143 4 -0.847600 1.824208e+01 2.718404e+01 2.761360e+01 # Ow SPCE + 429 143 3 0.423800 1.803237e+01 2.621369e+01 2.773377e+01 # Hw SPCE + 430 144 3 0.423800 1.002054e+01 2.068443e+00 2.080057e+01 # Hw SPCE + 431 144 4 -0.847600 1.037196e+01 1.499358e+00 2.005717e+01 # Ow SPCE + 432 144 3 0.423800 1.137167e+01 1.499631e+00 2.008118e+01 # Hw SPCE + 433 145 3 0.423800 5.474756e+00 6.597903e+00 2.212606e+01 # Hw SPCE + 434 145 4 -0.847600 6.060290e+00 6.454103e+00 2.292385e+01 # Ow SPCE + 435 145 3 0.423800 5.607820e+00 5.830491e+00 2.356133e+01 # Hw SPCE + 436 146 3 0.423800 9.616079e+00 2.770577e+01 1.272301e+01 # Hw SPCE + 437 146 4 -0.847600 1.005389e+01 2.758118e+01 1.183261e+01 # Ow SPCE + 438 146 3 0.423800 1.104172e+01 2.770510e+01 1.192665e+01 # Hw SPCE + 439 147 3 0.423800 7.556371e+00 8.751423e+00 1.067315e+01 # Hw SPCE + 440 147 4 -0.847600 6.677067e+00 8.276682e+00 1.071118e+01 # Ow SPCE + 441 147 3 0.423800 6.692592e+00 7.605177e+00 1.145202e+01 # Hw SPCE + 442 148 3 0.423800 1.048902e+01 9.944021e+00 1.499856e+00 # Hw SPCE + 443 148 4 -0.847600 1.107788e+01 9.135791e+00 1.497048e+00 # Ow SPCE + 444 148 3 0.423800 1.051214e+01 8.311210e+00 1.495741e+00 # Hw SPCE + 445 149 3 0.423800 2.225224e+01 1.699334e+01 1.388572e+01 # Hw SPCE + 446 149 4 -0.847600 2.247601e+01 1.610910e+01 1.347578e+01 # Ow SPCE + 447 149 3 0.423800 2.332230e+01 1.619040e+01 1.294930e+01 # Hw SPCE + 448 150 3 0.423800 1.629210e+01 2.770573e+01 8.693261e+00 # Hw SPCE + 449 150 4 -0.847600 1.560110e+01 2.709673e+01 8.303856e+00 # Ow SPCE + 450 150 3 0.423800 1.580582e+01 2.615242e+01 8.561464e+00 # Hw SPCE + 451 151 3 0.423800 2.423080e+01 1.358698e+01 1.852585e+01 # Hw SPCE + 452 151 4 -0.847600 2.350560e+01 1.411138e+01 1.897204e+01 # Ow SPCE + 453 151 3 0.423800 2.267128e+01 1.406026e+01 1.842312e+01 # Hw SPCE + 454 152 3 0.423800 2.207406e+01 4.433705e+00 2.065867e+01 # Hw SPCE + 455 152 4 -0.847600 2.276959e+01 3.724600e+00 2.054287e+01 # Ow SPCE + 456 152 3 0.423800 2.359197e+01 4.126886e+00 2.014056e+01 # Hw SPCE + 457 153 3 0.423800 2.395702e+01 6.074153e+00 1.705293e+01 # Hw SPCE + 458 153 4 -0.847600 2.358426e+01 5.192507e+00 1.734233e+01 # Ow SPCE + 459 153 3 0.423800 2.433467e+01 4.558278e+00 1.752846e+01 # Hw SPCE + 460 154 3 0.423800 1.155557e+01 2.807646e+00 1.636444e+01 # Hw SPCE + 461 154 4 -0.847600 1.146110e+01 1.812305e+00 1.638374e+01 # Ow SPCE + 462 154 3 0.423800 1.138045e+01 1.503463e+00 1.733143e+01 # Hw SPCE + 463 155 3 0.423800 4.135912e+00 2.531900e+01 1.818837e+01 # Hw SPCE + 464 155 4 -0.847600 3.741676e+00 2.521934e+01 1.910196e+01 # Ow SPCE + 465 155 3 0.423800 4.213837e+00 2.448559e+01 1.959050e+01 # Hw SPCE + 466 156 3 0.423800 1.499258e+00 1.198985e+01 2.578979e+01 # Hw SPCE + 467 156 4 -0.847600 2.062832e+00 1.128002e+01 2.536727e+01 # Ow SPCE + 468 156 3 0.423800 1.537875e+00 1.043123e+01 2.530414e+01 # Hw SPCE + 469 157 3 0.423800 6.788951e+00 2.673524e+01 2.771333e+01 # Hw SPCE + 470 157 4 -0.847600 6.736475e+00 2.763375e+01 2.727752e+01 # Ow SPCE + 471 157 3 0.423800 5.853127e+00 2.773069e+01 2.681893e+01 # Hw SPCE + 472 158 3 0.423800 4.823100e+00 1.350860e+01 6.387855e+00 # Hw SPCE + 473 158 4 -0.847600 4.369663e+00 1.263897e+01 6.583146e+00 # Ow SPCE + 474 158 3 0.423800 4.571234e+00 1.236153e+01 7.522508e+00 # Hw SPCE + 475 159 3 0.423800 2.652742e+01 8.643512e+00 1.208390e+01 # Hw SPCE + 476 159 4 -0.847600 2.750728e+01 8.461636e+00 1.216639e+01 # Ow SPCE + 477 159 3 0.423800 2.770441e+01 7.539751e+00 1.183282e+01 # Hw SPCE + 478 160 3 0.423800 1.562548e+01 7.342341e+00 1.368183e+01 # Hw SPCE + 479 160 4 -0.847600 1.644892e+01 7.724632e+00 1.326255e+01 # Ow SPCE + 480 160 3 0.423800 1.657765e+01 7.324209e+00 1.235531e+01 # Hw SPCE + 481 161 3 0.423800 1.832876e+01 3.664241e+00 1.523424e+01 # Hw SPCE + 482 161 4 -0.847600 1.757342e+01 3.228540e+00 1.572376e+01 # Ow SPCE + 483 161 3 0.423800 1.723220e+01 2.455027e+00 1.518968e+01 # Hw SPCE + 484 162 3 0.423800 1.163979e+01 2.726442e+01 5.638394e+00 # Hw SPCE + 485 162 4 -0.847600 1.203117e+01 2.637033e+01 5.856191e+00 # Ow SPCE + 486 162 3 0.423800 1.265936e+01 2.646077e+01 6.628973e+00 # Hw SPCE + 487 163 3 0.423800 3.712836e+00 1.795600e+01 2.104265e+01 # Hw SPCE + 488 163 4 -0.847600 3.729339e+00 1.776723e+01 2.202453e+01 # Ow SPCE + 489 163 3 0.423800 2.793088e+00 1.774262e+01 2.237500e+01 # Hw SPCE + 490 164 3 0.423800 1.215495e+01 1.501989e+00 9.660698e+00 # Hw SPCE + 491 164 4 -0.847600 1.306022e+01 1.479590e+00 9.236442e+00 # Ow SPCE + 492 164 3 0.423800 1.376231e+01 1.546750e+00 9.945354e+00 # Hw SPCE + 493 165 3 0.423800 1.382068e+01 2.627313e+01 1.928618e+01 # Hw SPCE + 494 165 4 -0.847600 1.369118e+01 2.724037e+01 1.950452e+01 # Ow SPCE + 495 165 3 0.423800 1.457266e+01 2.771119e+01 1.946813e+01 # Hw SPCE + 496 166 3 0.423800 1.936570e+01 1.864386e+01 2.521456e+01 # Hw SPCE + 497 166 4 -0.847600 2.026756e+01 1.895792e+01 2.551126e+01 # Ow SPCE + 498 166 3 0.423800 2.023242e+01 1.993867e+01 2.570334e+01 # Hw SPCE + 499 167 3 0.423800 1.169885e+01 2.172581e+00 2.751632e+01 # Hw SPCE + 500 167 4 -0.847600 1.090011e+01 1.573456e+00 2.746098e+01 # Ow SPCE + 501 167 3 0.423800 1.061137e+01 1.490153e+00 2.650720e+01 # Hw SPCE + 502 168 3 0.423800 1.911213e+01 2.158443e+01 1.022983e+01 # Hw SPCE + 503 168 4 -0.847600 1.926141e+01 2.060202e+01 1.011766e+01 # Ow SPCE + 504 168 3 0.423800 1.928483e+01 2.016370e+01 1.101617e+01 # Hw SPCE + 505 169 3 0.423800 1.629210e+00 1.550801e+01 1.095958e+01 # Hw SPCE + 506 169 4 -0.847600 1.493041e+00 1.635194e+01 1.147846e+01 # Ow SPCE + 507 169 3 0.423800 2.168035e+00 1.703190e+01 1.119204e+01 # Hw SPCE + 508 170 3 0.423800 1.102279e+01 4.173853e+00 1.869068e+01 # Hw SPCE + 509 170 4 -0.847600 1.109242e+01 4.502781e+00 1.963246e+01 # Ow SPCE + 510 170 3 0.423800 1.122948e+01 5.493340e+00 1.963029e+01 # Hw SPCE + 511 171 3 0.423800 8.600246e+00 2.481675e+01 1.935975e+01 # Hw SPCE + 512 171 4 -0.847600 8.003650e+00 2.561907e+01 1.934092e+01 # Ow SPCE + 513 171 3 0.423800 7.051209e+00 2.532446e+01 1.926308e+01 # Hw SPCE + 514 172 3 0.423800 7.877713e+00 1.822785e+01 1.950056e+01 # Hw SPCE + 515 172 4 -0.847600 6.923133e+00 1.800620e+01 1.930144e+01 # Ow SPCE + 516 172 3 0.423800 6.847202e+00 1.767403e+01 1.836128e+01 # Hw SPCE + 517 173 3 0.423800 2.715931e+01 1.264839e+01 1.341405e+01 # Hw SPCE + 518 173 4 -0.847600 2.734880e+01 1.167554e+01 1.328112e+01 # Ow SPCE + 519 173 3 0.423800 2.648989e+01 1.118630e+01 1.312977e+01 # Hw SPCE + 520 174 3 0.423800 1.482572e+01 8.447714e+00 1.055548e+01 # Hw SPCE + 521 174 4 -0.847600 1.531227e+01 7.960482e+00 9.830314e+00 # Ow SPCE + 522 174 3 0.423800 1.465158e+01 7.577469e+00 9.184724e+00 # Hw SPCE + 523 175 3 0.423800 6.350160e+00 1.781671e+00 2.021119e+01 # Hw SPCE + 524 175 4 -0.847600 5.554766e+00 1.449580e+00 2.071820e+01 # Ow SPCE + 525 175 3 0.423800 4.990992e+00 2.226040e+00 2.099974e+01 # Hw SPCE + 526 176 3 0.423800 2.360588e+01 2.124534e+01 1.405838e+01 # Hw SPCE + 527 176 4 -0.847600 2.343533e+01 2.028764e+01 1.429017e+01 # Ow SPCE + 528 176 3 0.423800 2.247062e+01 2.007410e+01 1.413605e+01 # Hw SPCE + 529 177 3 0.423800 2.476177e+01 9.495265e+00 2.278084e+01 # Hw SPCE + 530 177 4 -0.847600 2.490594e+01 9.103976e+00 2.187194e+01 # Ow SPCE + 531 177 3 0.423800 2.584301e+01 8.762128e+00 2.180102e+01 # Hw SPCE + 532 178 3 0.423800 2.124801e+01 1.026202e+01 1.226324e+01 # Hw SPCE + 533 178 4 -0.847600 2.175978e+01 1.061858e+01 1.304488e+01 # Ow SPCE + 534 178 3 0.423800 2.143033e+01 1.018622e+01 1.388424e+01 # Hw SPCE + 535 179 3 0.423800 2.770461e+01 2.265303e+01 1.897481e+01 # Hw SPCE + 536 179 4 -0.847600 2.771622e+01 2.165817e+01 1.887413e+01 # Ow SPCE + 537 179 3 0.423800 2.699937e+01 2.137944e+01 1.823504e+01 # Hw SPCE + 538 180 3 0.423800 1.752412e+00 1.211560e+01 2.448378e+00 # Hw SPCE + 539 180 4 -0.847600 2.192876e+00 1.124630e+01 2.672646e+00 # Ow SPCE + 540 180 3 0.423800 1.502189e+00 1.052455e+01 2.717762e+00 # Hw SPCE + 541 181 3 0.423800 2.066796e+01 9.492666e+00 1.990433e+01 # Hw SPCE + 542 181 4 -0.847600 1.987345e+01 1.007578e+01 1.973481e+01 # Ow SPCE + 543 181 3 0.423800 1.945518e+01 1.033091e+01 2.060657e+01 # Hw SPCE + 544 182 3 0.423800 7.526139e+00 1.353553e+01 1.705107e+01 # Hw SPCE + 545 182 4 -0.847600 7.411920e+00 1.404119e+01 1.619593e+01 # Ow SPCE + 546 182 3 0.423800 7.814322e+00 1.495172e+01 1.629081e+01 # Hw SPCE + 547 183 3 0.423800 5.320834e+00 2.489018e+01 2.627333e+01 # Hw SPCE + 548 183 4 -0.847600 4.512268e+00 2.533586e+01 2.665751e+01 # Ow SPCE + 549 183 3 0.423800 3.697906e+00 2.503309e+01 2.616239e+01 # Hw SPCE + 550 184 3 0.423800 2.555518e+01 2.496555e+01 1.499745e+00 # Hw SPCE + 551 184 4 -0.847600 2.580931e+01 2.400607e+01 1.621410e+00 # Ow SPCE + 552 184 3 0.423800 2.498688e+01 2.343773e+01 1.596790e+00 # Hw SPCE + 553 185 3 0.423800 4.020936e+00 8.516876e+00 4.121746e+00 # Hw SPCE + 554 185 4 -0.847600 3.704058e+00 9.464727e+00 4.155894e+00 # Ow SPCE + 555 185 3 0.423800 4.491592e+00 1.008053e+01 4.131828e+00 # Hw SPCE + 556 186 3 0.423800 1.411577e+01 1.487915e+00 1.833251e+01 # Hw SPCE + 557 186 4 -0.847600 1.431943e+01 2.462252e+00 1.842837e+01 # Ow SPCE + 558 186 3 0.423800 1.347701e+01 2.990756e+00 1.832346e+01 # Hw SPCE + 559 187 3 0.423800 3.071401e+00 9.241825e+00 1.816214e+01 # Hw SPCE + 560 187 4 -0.847600 3.300129e+00 8.845865e+00 1.727282e+01 # Ow SPCE + 561 187 3 0.423800 2.487941e+00 8.845219e+00 1.668942e+01 # Hw SPCE + 562 188 3 0.423800 1.493937e+00 2.324979e+01 2.604098e+01 # Hw SPCE + 563 188 4 -0.847600 1.544148e+00 2.354108e+01 2.699630e+01 # Ow SPCE + 564 188 3 0.423800 1.493692e+00 2.273962e+01 2.759223e+01 # Hw SPCE + 565 189 3 0.423800 2.402950e+01 7.504644e+00 1.192867e+01 # Hw SPCE + 566 189 4 -0.847600 2.413727e+01 6.710938e+00 1.132999e+01 # Ow SPCE + 567 189 3 0.423800 2.508872e+01 6.403895e+00 1.135159e+01 # Hw SPCE + 568 190 3 0.423800 8.545646e+00 3.156383e+00 9.861230e+00 # Hw SPCE + 569 190 4 -0.847600 9.351073e+00 2.611171e+00 1.009367e+01 # Ow SPCE + 570 190 3 0.423800 1.011166e+01 3.219788e+00 1.031971e+01 # Hw SPCE + 571 191 3 0.423800 1.499645e+00 2.645193e+01 1.809386e+01 # Hw SPCE + 572 191 4 -0.847600 1.941124e+00 2.732475e+01 1.788582e+01 # Ow SPCE + 573 191 3 0.423800 2.336801e+00 2.770568e+01 1.872148e+01 # Hw SPCE + 574 192 3 0.423800 1.070874e+01 1.082303e+01 1.860632e+01 # Hw SPCE + 575 192 4 -0.847600 1.140325e+01 1.152845e+01 1.874785e+01 # Ow SPCE + 576 192 3 0.423800 1.230497e+01 1.110065e+01 1.881024e+01 # Hw SPCE + 577 193 3 0.423800 1.341290e+01 1.795517e+01 2.013626e+01 # Hw SPCE + 578 193 4 -0.847600 1.307952e+01 1.701238e+01 2.013931e+01 # Ow SPCE + 579 193 3 0.423800 1.309126e+01 1.665771e+01 2.107422e+01 # Hw SPCE + 580 194 3 0.423800 4.807785e+00 9.950438e+00 2.034530e+01 # Hw SPCE + 581 194 4 -0.847600 5.368387e+00 9.471078e+00 2.102053e+01 # Ow SPCE + 582 194 3 0.423800 6.091190e+00 8.962304e+00 2.055288e+01 # Hw SPCE + 583 195 3 0.423800 4.581666e+00 2.365989e+01 9.523923e+00 # Hw SPCE + 584 195 4 -0.847600 4.035775e+00 2.430184e+01 1.006236e+01 # Ow SPCE + 585 195 3 0.423800 3.083838e+00 2.426678e+01 9.758078e+00 # Hw SPCE + 586 196 3 0.423800 1.996454e+01 2.420988e+01 1.557209e+01 # Hw SPCE + 587 196 4 -0.847600 2.025724e+01 2.408856e+01 1.462361e+01 # Ow SPCE + 588 196 3 0.423800 2.091875e+01 2.479965e+01 1.438538e+01 # Hw SPCE + 589 197 3 0.423800 3.003372e+00 1.643713e+01 1.704879e+01 # Hw SPCE + 590 197 4 -0.847600 2.577322e+00 1.558424e+01 1.735056e+01 # Ow SPCE + 591 197 3 0.423800 1.583596e+00 1.569510e+01 1.736541e+01 # Hw SPCE + 592 198 3 0.423800 8.582183e+00 2.224273e+01 1.027837e+01 # Hw SPCE + 593 198 4 -0.847600 8.111157e+00 2.153125e+01 9.756897e+00 # Ow SPCE + 594 198 3 0.423800 8.773035e+00 2.084403e+01 9.457494e+00 # Hw SPCE + 595 199 3 0.423800 9.338267e+00 1.004752e+01 1.312920e+01 # Hw SPCE + 596 199 4 -0.847600 8.797900e+00 9.207329e+00 1.308363e+01 # Ow SPCE + 597 199 3 0.423800 7.916778e+00 9.352906e+00 1.353355e+01 # Hw SPCE + 598 200 3 0.423800 2.194779e+01 1.497417e+00 2.193037e+01 # Hw SPCE + 599 200 4 -0.847600 2.223387e+01 1.544058e+00 2.288744e+01 # Ow SPCE + 600 200 3 0.423800 2.323149e+01 1.499141e+00 2.293970e+01 # Hw SPCE + 601 201 3 0.423800 6.357928e+00 6.228009e+00 5.806627e+00 # Hw SPCE + 602 201 4 -0.847600 6.047437e+00 7.177648e+00 5.848827e+00 # Ow SPCE + 603 201 3 0.423800 6.617086e+00 7.741462e+00 5.250820e+00 # Hw SPCE + 604 202 3 0.423800 1.593029e+01 1.490608e+01 1.881990e+00 # Hw SPCE + 605 202 4 -0.847600 1.499401e+01 1.512044e+01 1.603720e+00 # Ow SPCE + 606 202 3 0.423800 1.441686e+01 1.431299e+01 1.725826e+00 # Hw SPCE + 607 203 3 0.423800 2.152874e+01 7.128493e+00 1.779600e+01 # Hw SPCE + 608 203 4 -0.847600 2.073272e+01 6.564299e+00 1.757685e+01 # Ow SPCE + 609 203 3 0.423800 2.013013e+01 6.514325e+00 1.837333e+01 # Hw SPCE + 610 204 3 0.423800 1.867722e+01 1.499875e+00 1.016897e+01 # Hw SPCE + 611 204 4 -0.847600 1.948249e+01 2.057017e+00 9.966143e+00 # Ow SPCE + 612 204 3 0.423800 2.030669e+01 1.498892e+00 1.006198e+01 # Hw SPCE + 613 205 3 0.423800 2.316922e+01 1.367353e+01 6.885430e+00 # Hw SPCE + 614 205 4 -0.847600 2.260716e+01 1.285895e+01 7.028829e+00 # Ow SPCE + 615 205 3 0.423800 2.319607e+01 1.205233e+01 7.079429e+00 # Hw SPCE + 616 206 3 0.423800 1.724802e+01 2.452784e+01 1.522277e+01 # Hw SPCE + 617 206 4 -0.847600 1.695269e+01 2.377047e+01 1.464039e+01 # Ow SPCE + 618 206 3 0.423800 1.764677e+01 2.305066e+01 1.465218e+01 # Hw SPCE + 619 207 3 0.423800 2.411268e+01 4.355955e+00 1.477705e+01 # Hw SPCE + 620 207 4 -0.847600 2.346927e+01 5.080864e+00 1.453102e+01 # Ow SPCE + 621 207 3 0.423800 2.313742e+01 4.930075e+00 1.359982e+01 # Hw SPCE + 622 208 3 0.423800 4.859519e+00 1.208976e+01 2.528815e+01 # Hw SPCE + 623 208 4 -0.847600 4.768744e+00 1.304357e+01 2.557451e+01 # Ow SPCE + 624 208 3 0.423800 3.968809e+00 1.313902e+01 2.616696e+01 # Hw SPCE + 625 209 3 0.423800 1.172825e+01 2.418010e+01 2.667409e+01 # Hw SPCE + 626 209 4 -0.847600 1.132283e+01 2.504940e+01 2.639133e+01 # Ow SPCE + 627 209 3 0.423800 1.154586e+01 2.522495e+01 2.543246e+01 # Hw SPCE + 628 210 3 0.423800 1.341122e+01 2.770513e+01 2.770549e+01 # Hw SPCE + 629 210 4 -0.847600 1.245960e+01 2.739875e+01 2.768238e+01 # Ow SPCE + 630 210 3 0.423800 1.204322e+01 2.766958e+01 2.681446e+01 # Hw SPCE + 631 211 3 0.423800 1.145241e+01 8.302455e+00 1.779676e+01 # Hw SPCE + 632 211 4 -0.847600 1.125478e+01 7.343016e+00 1.759571e+01 # Ow SPCE + 633 211 3 0.423800 1.210977e+01 6.857989e+00 1.741202e+01 # Hw SPCE + 634 212 3 0.423800 1.287925e+01 1.297774e+01 2.765935e+01 # Hw SPCE + 635 212 4 -0.847600 1.230585e+01 1.215930e+01 2.769630e+01 # Ow SPCE + 636 212 3 0.423800 1.134277e+01 1.242772e+01 2.771694e+01 # Hw SPCE + 637 213 3 0.423800 1.353894e+01 1.030050e+01 8.981176e+00 # Hw SPCE + 638 213 4 -0.847600 1.336051e+01 1.105021e+01 8.343917e+00 # Ow SPCE + 639 213 3 0.423800 1.239877e+01 1.103348e+01 8.070479e+00 # Hw SPCE + 640 214 3 0.423800 1.379608e+01 1.561648e+01 4.066143e+00 # Hw SPCE + 641 214 4 -0.847600 1.425485e+01 1.494262e+01 4.645317e+00 # Ow SPCE + 642 214 3 0.423800 1.500310e+01 1.538348e+01 5.141055e+00 # Hw SPCE + 643 215 3 0.423800 1.743267e+01 1.012996e+01 9.164174e+00 # Hw SPCE + 644 215 4 -0.847600 1.689952e+01 1.019764e+01 1.000748e+01 # Ow SPCE + 645 215 3 0.423800 1.610254e+01 1.078129e+01 9.852029e+00 # Hw SPCE + 646 216 3 0.423800 2.449752e+01 2.458848e+01 1.376845e+01 # Hw SPCE + 647 216 4 -0.847600 2.528553e+01 2.495639e+01 1.426210e+01 # Ow SPCE + 648 216 3 0.423800 2.534289e+01 2.452894e+01 1.516431e+01 # Hw SPCE + 649 217 3 0.423800 1.840558e+01 3.099439e+00 2.461987e+01 # Hw SPCE + 650 217 4 -0.847600 1.888190e+01 2.411523e+00 2.516749e+01 # Ow SPCE + 651 217 3 0.423800 1.859125e+01 1.498335e+00 2.488182e+01 # Hw SPCE + 652 218 3 0.423800 2.313333e+01 2.163166e+01 2.205864e+01 # Hw SPCE + 653 218 4 -0.847600 2.219594e+01 2.130927e+01 2.219041e+01 # Ow SPCE + 654 218 3 0.423800 2.158294e+01 2.209428e+01 2.227978e+01 # Hw SPCE + 655 219 3 0.423800 1.229832e+01 6.995752e+00 1.467363e+01 # Hw SPCE + 656 219 4 -0.847600 1.306529e+01 6.454869e+00 1.432837e+01 # Ow SPCE + 657 219 3 0.423800 1.350970e+01 5.982810e+00 1.508972e+01 # Hw SPCE + 658 220 3 0.423800 1.406803e+01 2.706445e+00 1.555541e+00 # Hw SPCE + 659 220 4 -0.847600 1.438807e+01 3.652120e+00 1.498299e+00 # Ow SPCE + 660 220 3 0.423800 1.360529e+01 4.272470e+00 1.547574e+00 # Hw SPCE + 661 221 3 0.423800 1.346094e+01 1.584618e+01 1.101422e+01 # Hw SPCE + 662 221 4 -0.847600 1.417123e+01 1.647755e+01 1.070299e+01 # Ow SPCE + 663 221 3 0.423800 1.506879e+01 1.605138e+01 1.081592e+01 # Hw SPCE + 664 222 3 0.423800 6.578749e+00 2.770463e+01 1.007095e+01 # Hw SPCE + 665 222 4 -0.847600 5.578913e+00 2.770497e+01 1.008903e+01 # Ow SPCE + 666 222 3 0.423800 5.245578e+00 2.676237e+01 1.010848e+01 # Hw SPCE + 667 223 3 0.423800 2.346524e+01 1.409205e+01 2.397168e+01 # Hw SPCE + 668 223 4 -0.847600 2.273539e+01 1.354071e+01 2.356753e+01 # Ow SPCE + 669 223 3 0.423800 2.313609e+01 1.282550e+01 2.299489e+01 # Hw SPCE + 670 224 3 0.423800 9.455855e+00 2.740531e+01 2.770496e+01 # Hw SPCE + 671 224 4 -0.847600 9.370999e+00 2.698567e+01 2.680125e+01 # Ow SPCE + 672 224 3 0.423800 9.379656e+00 2.769893e+01 2.610040e+01 # Hw SPCE + 673 225 3 0.423800 1.739219e+01 2.174463e+01 3.666550e+00 # Hw SPCE + 674 225 4 -0.847600 1.786402e+01 2.143690e+01 2.840303e+00 # Ow SPCE + 675 225 3 0.423800 1.877157e+01 2.109408e+01 3.082833e+00 # Hw SPCE + 676 226 3 0.423800 2.616571e+01 6.000875e+00 7.270531e+00 # Hw SPCE + 677 226 4 -0.847600 2.581662e+01 5.090419e+00 7.048703e+00 # Ow SPCE + 678 226 3 0.423800 2.500801e+01 5.176179e+00 6.466644e+00 # Hw SPCE + 679 227 3 0.423800 2.463564e+01 9.703885e+00 1.039308e+01 # Hw SPCE + 680 227 4 -0.847600 2.383949e+01 1.018568e+01 1.002699e+01 # Ow SPCE + 681 227 3 0.423800 2.359408e+01 1.093724e+01 1.063930e+01 # Hw SPCE + 682 228 3 0.423800 2.177044e+01 1.687390e+01 2.431866e+01 # Hw SPCE + 683 228 4 -0.847600 2.133664e+01 1.645723e+01 2.511753e+01 # Ow SPCE + 684 228 3 0.423800 2.195993e+01 1.578987e+01 2.552514e+01 # Hw SPCE + 685 229 3 0.423800 7.726348e+00 3.560323e+00 2.179374e+01 # Hw SPCE + 686 229 4 -0.847600 6.861868e+00 4.061639e+00 2.183058e+01 # Ow SPCE + 687 229 3 0.423800 6.645800e+00 4.420653e+00 2.092261e+01 # Hw SPCE + 688 230 3 0.423800 1.884037e+01 1.499599e+00 6.252581e+00 # Hw SPCE + 689 230 4 -0.847600 1.965401e+01 2.001138e+00 6.546590e+00 # Ow SPCE + 690 230 3 0.423800 2.008019e+01 1.523837e+00 7.315065e+00 # Hw SPCE + 691 231 3 0.423800 6.715548e+00 3.056808e+00 2.444232e+01 # Hw SPCE + 692 231 4 -0.847600 6.554914e+00 2.209760e+00 2.393566e+01 # Ow SPCE + 693 231 3 0.423800 6.112326e+00 1.542117e+00 2.453429e+01 # Hw SPCE + 694 232 3 0.423800 1.335233e+01 8.701900e+00 2.332491e+01 # Hw SPCE + 695 232 4 -0.847600 1.284324e+01 9.531573e+00 2.355397e+01 # Ow SPCE + 696 232 3 0.423800 1.192981e+01 9.484446e+00 2.314971e+01 # Hw SPCE + 697 233 3 0.423800 1.642811e+01 5.397368e+00 2.093058e+00 # Hw SPCE + 698 233 4 -0.847600 1.732324e+01 5.692575e+00 1.759011e+00 # Ow SPCE + 699 233 3 0.423800 1.732664e+01 6.686459e+00 1.648636e+00 # Hw SPCE + 700 234 3 0.423800 8.746384e+00 1.194555e+01 1.502826e+01 # Hw SPCE + 701 234 4 -0.847600 8.569902e+00 1.110875e+01 1.554655e+01 # Ow SPCE + 702 234 3 0.423800 9.214489e+00 1.104644e+01 1.630854e+01 # Hw SPCE + 703 235 3 0.423800 2.671040e+01 2.277390e+01 2.443136e+01 # Hw SPCE + 704 235 4 -0.847600 2.634248e+01 2.188483e+01 2.415900e+01 # Ow SPCE + 705 235 3 0.423800 2.540832e+01 2.199999e+01 2.382124e+01 # Hw SPCE + 706 236 3 0.423800 4.314700e+00 6.656624e+00 1.567087e+01 # Hw SPCE + 707 236 4 -0.847600 4.101082e+00 5.989344e+00 1.495735e+01 # Ow SPCE + 708 236 3 0.423800 4.681834e+00 6.155976e+00 1.416051e+01 # Hw SPCE + 709 237 3 0.423800 2.585970e+01 5.937546e+00 1.935423e+01 # Hw SPCE + 710 237 4 -0.847600 2.680819e+01 5.995046e+00 1.966578e+01 # Ow SPCE + 711 237 3 0.423800 2.685723e+01 6.574317e+00 2.047944e+01 # Hw SPCE + 712 238 3 0.423800 2.668626e+01 2.541072e+01 4.880638e+00 # Hw SPCE + 713 238 4 -0.847600 2.764667e+01 2.568864e+01 4.899778e+00 # Ow SPCE + 714 238 3 0.423800 2.770442e+01 2.668068e+01 5.011688e+00 # Hw SPCE + 715 239 3 0.423800 3.799348e+00 1.733873e+01 1.665944e+00 # Hw SPCE + 716 239 4 -0.847600 3.166531e+00 1.811195e+01 1.625052e+00 # Ow SPCE + 717 239 3 0.423800 2.227096e+00 1.777190e+01 1.582255e+00 # Hw SPCE + 718 240 3 0.423800 6.922100e+00 1.626292e+01 2.727964e+01 # Hw SPCE + 719 240 4 -0.847600 6.522882e+00 1.559908e+01 2.664724e+01 # Ow SPCE + 720 240 3 0.423800 6.008322e+00 1.491453e+01 2.716360e+01 # Hw SPCE + 721 241 3 0.423800 3.812524e+00 1.917142e+01 4.078941e+00 # Hw SPCE + 722 241 4 -0.847600 4.650408e+00 1.921783e+01 4.622812e+00 # Ow SPCE + 723 241 3 0.423800 5.291688e+00 1.985376e+01 4.193446e+00 # Hw SPCE + 724 242 3 0.423800 2.392996e+01 9.703159e+00 1.533263e+01 # Hw SPCE + 725 242 4 -0.847600 2.418034e+01 1.027088e+01 1.454841e+01 # Ow SPCE + 726 242 3 0.423800 2.425829e+01 9.697253e+00 1.373301e+01 # Hw SPCE + 727 243 3 0.423800 1.160740e+01 4.289690e+00 2.576183e+01 # Hw SPCE + 728 243 4 -0.847600 1.136615e+01 3.672164e+00 2.501319e+01 # Ow SPCE + 729 243 3 0.423800 1.134214e+01 4.183341e+00 2.415404e+01 # Hw SPCE + 730 244 3 0.423800 3.062271e+00 1.498880e+00 1.558829e+01 # Hw SPCE + 731 244 4 -0.847600 2.459085e+00 1.579929e+00 1.479482e+01 # Ow SPCE + 732 244 3 0.423800 1.507109e+00 1.499362e+00 1.509020e+01 # Hw SPCE + 733 245 3 0.423800 9.267839e+00 2.530564e+01 2.389467e+01 # Hw SPCE + 734 245 4 -0.847600 8.983831e+00 2.446671e+01 2.435894e+01 # Ow SPCE + 735 245 3 0.423800 8.616254e+00 2.382260e+01 2.368811e+01 # Hw SPCE + 736 246 3 0.423800 2.233187e+01 2.661754e+01 9.034738e+00 # Hw SPCE + 737 246 4 -0.847600 2.297202e+01 2.590388e+01 8.750298e+00 # Ow SPCE + 738 246 3 0.423800 2.361025e+01 2.571216e+01 9.495883e+00 # Hw SPCE + 739 247 3 0.423800 6.152311e+00 1.591896e+01 1.583244e+00 # Hw SPCE + 740 247 4 -0.847600 6.458131e+00 1.516173e+01 2.160380e+00 # Ow SPCE + 741 247 3 0.423800 7.447061e+00 1.522371e+01 2.295199e+00 # Hw SPCE + 742 248 3 0.423800 6.249483e+00 8.441998e+00 2.500313e+01 # Hw SPCE + 743 248 4 -0.847600 6.658605e+00 7.854146e+00 2.570102e+01 # Ow SPCE + 744 248 3 0.423800 7.286041e+00 7.207979e+00 2.526652e+01 # Hw SPCE + 745 249 3 0.423800 1.155584e+01 7.485508e+00 4.265325e+00 # Hw SPCE + 746 249 4 -0.847600 1.222371e+01 7.709122e+00 3.555440e+00 # Ow SPCE + 747 249 3 0.423800 1.307003e+01 7.203441e+00 3.722858e+00 # Hw SPCE + 748 250 3 0.423800 6.411808e+00 2.543586e+01 7.998512e+00 # Hw SPCE + 749 250 4 -0.847600 7.212358e+00 2.569130e+01 7.456414e+00 # Ow SPCE + 750 250 3 0.423800 7.538848e+00 2.659058e+01 7.747451e+00 # Hw SPCE + 751 251 3 0.423800 2.686488e+01 1.595570e+01 1.586290e+01 # Hw SPCE + 752 251 4 -0.847600 2.770669e+01 1.542553e+01 1.576147e+01 # Ow SPCE + 753 251 3 0.423800 2.766723e+01 1.489635e+01 1.491388e+01 # Hw SPCE + 754 252 3 0.423800 4.730891e+00 1.312809e+01 1.497769e+00 # Hw SPCE + 755 252 4 -0.847600 4.158177e+00 1.342867e+01 2.260428e+00 # Ow SPCE + 756 252 3 0.423800 3.624401e+00 1.422713e+01 1.981941e+00 # Hw SPCE + 757 253 3 0.423800 2.195203e+01 2.665489e+01 1.887230e+01 # Hw SPCE + 758 253 4 -0.847600 2.258974e+01 2.742501e+01 1.888802e+01 # Ow SPCE + 759 253 3 0.423800 2.352836e+01 2.708031e+01 1.890123e+01 # Hw SPCE + 760 254 3 0.423800 1.253712e+01 3.129762e+00 1.183063e+01 # Hw SPCE + 761 254 4 -0.847600 1.292118e+01 3.990106e+00 1.216575e+01 # Ow SPCE + 762 254 3 0.423800 1.383968e+01 3.827163e+00 1.252605e+01 # Hw SPCE + 763 255 3 0.423800 3.863000e+00 2.523218e+01 2.336537e+01 # Hw SPCE + 764 255 4 -0.847600 3.779878e+00 2.428180e+01 2.306556e+01 # Ow SPCE + 765 255 3 0.423800 4.073781e+00 2.367294e+01 2.380238e+01 # Hw SPCE + 766 256 3 0.423800 1.033123e+01 2.732718e+01 1.991221e+01 # Hw SPCE + 767 256 4 -0.847600 1.083128e+01 2.694936e+01 2.069145e+01 # Ow SPCE + 768 256 3 0.423800 1.037561e+01 2.611750e+01 2.100827e+01 # Hw SPCE + 769 257 3 0.423800 6.606032e+00 3.553686e+00 6.537013e+00 # Hw SPCE + 770 257 4 -0.847600 7.445947e+00 3.035012e+00 6.696762e+00 # Ow SPCE + 771 257 3 0.423800 7.233172e+00 2.208190e+00 7.217426e+00 # Hw SPCE + 772 258 3 0.423800 1.306905e+01 1.800714e+01 6.041763e+00 # Hw SPCE + 773 258 4 -0.847600 1.404572e+01 1.784783e+01 5.897769e+00 # Ow SPCE + 774 258 3 0.423800 1.446986e+01 1.867958e+01 5.539574e+00 # Hw SPCE + 775 259 3 0.423800 6.591547e+00 2.039778e+01 6.554188e+00 # Hw SPCE + 776 259 4 -0.847600 6.892178e+00 1.965746e+01 7.155484e+00 # Ow SPCE + 777 259 3 0.423800 7.891350e+00 1.961712e+01 7.160583e+00 # Hw SPCE + 778 260 3 0.423800 2.102357e+01 1.285810e+01 1.138197e+01 # Hw SPCE + 779 260 4 -0.847600 2.063601e+01 1.330654e+01 1.057655e+01 # Ow SPCE + 780 260 3 0.423800 2.040906e+01 1.425453e+01 1.079974e+01 # Hw SPCE + 781 261 3 0.423800 1.668139e+01 1.365676e+01 7.959222e+00 # Hw SPCE + 782 261 4 -0.847600 1.609109e+01 1.302602e+01 7.455519e+00 # Ow SPCE + 783 261 3 0.423800 1.657944e+01 1.216812e+01 7.295759e+00 # Hw SPCE + 784 262 3 0.423800 1.564369e+01 1.907066e+01 2.197727e+01 # Hw SPCE + 785 262 4 -0.847600 1.642857e+01 1.968608e+01 2.204959e+01 # Ow SPCE + 786 262 3 0.423800 1.726974e+01 1.914825e+01 2.210604e+01 # Hw SPCE + 787 263 3 0.423800 7.519411e+00 1.610097e+01 2.120584e+01 # Hw SPCE + 788 263 4 -0.847600 6.640364e+00 1.562428e+01 2.121221e+01 # Ow SPCE + 789 263 3 0.423800 5.897912e+00 1.629395e+01 2.119468e+01 # Hw SPCE + 790 264 3 0.423800 8.688944e+00 1.522738e+01 1.887923e+01 # Hw SPCE + 791 264 4 -0.847600 9.135790e+00 1.601512e+01 1.845520e+01 # Ow SPCE + 792 264 3 0.423800 1.009324e+01 1.579478e+01 1.826879e+01 # Hw SPCE + 793 265 3 0.423800 2.187599e+01 2.614658e+01 2.179133e+01 # Hw SPCE + 794 265 4 -0.847600 2.260916e+01 2.678722e+01 2.156320e+01 # Ow SPCE + 795 265 3 0.423800 2.235434e+01 2.770623e+01 2.186401e+01 # Hw SPCE + 796 266 3 0.423800 8.584848e+00 1.412426e+01 2.770388e+01 # Hw SPCE + 797 266 4 -0.847600 8.917922e+00 1.350413e+01 2.699360e+01 # Ow SPCE + 798 266 3 0.423800 8.385750e+00 1.363828e+01 2.615766e+01 # Hw SPCE + 799 267 3 0.423800 1.498403e+00 1.136667e+01 1.740482e+01 # Hw SPCE + 800 267 4 -0.847600 1.496704e+00 1.228079e+01 1.699937e+01 # Ow SPCE + 801 267 3 0.423800 1.493879e+00 1.296773e+01 1.772607e+01 # Hw SPCE + 802 268 3 0.423800 2.051142e+01 1.532290e+00 2.720074e+01 # Hw SPCE + 803 268 4 -0.847600 2.144152e+01 1.677620e+00 2.686340e+01 # Ow SPCE + 804 268 3 0.423800 2.143787e+01 1.673320e+00 2.586342e+01 # Hw SPCE + 805 269 3 0.423800 1.074975e+01 1.582297e+01 1.147179e+01 # Hw SPCE + 806 269 4 -0.847600 9.843024e+00 1.620321e+01 1.128940e+01 # Ow SPCE + 807 269 3 0.423800 9.486971e+00 1.582159e+01 1.043641e+01 # Hw SPCE + 808 270 3 0.423800 2.158512e+01 4.175374e+00 2.335242e+01 # Hw SPCE + 809 270 4 -0.847600 2.102097e+01 3.724302e+00 2.404399e+01 # Ow SPCE + 810 270 3 0.423800 2.100196e+01 4.281705e+00 2.487402e+01 # Hw SPCE + 811 271 3 0.423800 1.499420e+00 2.109325e+01 1.083546e+01 # Hw SPCE + 812 271 4 -0.847600 2.014482e+00 2.180659e+01 1.036021e+01 # Ow SPCE + 813 271 3 0.423800 2.990936e+00 2.159428e+01 1.039845e+01 # Hw SPCE + 814 272 3 0.423800 1.593017e+00 7.902730e+00 5.258905e+00 # Hw SPCE + 815 272 4 -0.847600 1.689156e+00 7.147133e+00 4.610962e+00 # Ow SPCE + 816 272 3 0.423800 1.505645e+00 7.476802e+00 3.684873e+00 # Hw SPCE + 817 273 3 0.423800 2.022395e+01 1.561529e+01 1.583840e+01 # Hw SPCE + 818 273 4 -0.847600 1.973203e+01 1.634844e+01 1.536883e+01 # Ow SPCE + 819 273 3 0.423800 1.880786e+01 1.603928e+01 1.514447e+01 # Hw SPCE + 820 274 3 0.423800 1.785576e+00 2.595467e+01 1.540470e+01 # Hw SPCE + 821 274 4 -0.847600 1.929174e+00 2.595737e+01 1.441507e+01 # Ow SPCE + 822 274 3 0.423800 1.499516e+00 2.676845e+01 1.401813e+01 # Hw SPCE + 823 275 3 0.423800 2.471608e+00 1.511177e+01 1.372759e+01 # Hw SPCE + 824 275 4 -0.847600 2.173815e+00 1.544011e+01 1.462398e+01 # Ow SPCE + 825 275 3 0.423800 1.499970e+00 1.616932e+01 1.450486e+01 # Hw SPCE + 826 276 3 0.423800 2.490164e+00 2.322823e+01 1.586321e+01 # Hw SPCE + 827 276 4 -0.847600 2.972830e+00 2.348324e+01 1.502535e+01 # Ow SPCE + 828 276 3 0.423800 3.763314e+00 2.405078e+01 1.525565e+01 # Hw SPCE + 829 277 3 0.423800 1.257057e+01 3.159471e+00 2.191679e+01 # Hw SPCE + 830 277 4 -0.847600 1.321241e+01 3.925963e+00 2.189377e+01 # Ow SPCE + 831 277 3 0.423800 1.270362e+01 4.785319e+00 2.184237e+01 # Hw SPCE + 832 278 3 0.423800 1.172696e+01 1.108398e+01 1.089481e+01 # Hw SPCE + 833 278 4 -0.847600 1.108144e+01 1.033095e+01 1.102229e+01 # Ow SPCE + 834 278 3 0.423800 1.021737e+01 1.055252e+01 1.057030e+01 # Hw SPCE + 835 279 3 0.423800 3.357999e+00 1.799692e+01 1.347523e+01 # Hw SPCE + 836 279 4 -0.847600 4.070804e+00 1.735174e+01 1.375027e+01 # Ow SPCE + 837 279 3 0.423800 4.175658e+00 1.737479e+01 1.474449e+01 # Hw SPCE + 838 280 3 0.423800 2.630102e+01 1.903409e+01 1.695517e+01 # Hw SPCE + 839 280 4 -0.847600 2.716892e+01 1.924741e+01 1.650657e+01 # Ow SPCE + 840 280 3 0.423800 2.727889e+01 1.866650e+01 1.570007e+01 # Hw SPCE + 841 281 3 0.423800 2.251004e+01 6.535603e+00 2.441833e+01 # Hw SPCE + 842 281 4 -0.847600 2.185183e+01 7.272694e+00 2.426517e+01 # Ow SPCE + 843 281 3 0.423800 2.104279e+01 7.120398e+00 2.483285e+01 # Hw SPCE + 844 282 3 0.423800 1.499087e+00 1.589499e+01 2.542090e+01 # Hw SPCE + 845 282 4 -0.847600 1.815620e+00 1.616034e+01 2.451019e+01 # Ow SPCE + 846 282 3 0.423800 2.765466e+00 1.587157e+01 2.439019e+01 # Hw SPCE + 847 283 3 0.423800 7.740973e+00 9.861514e+00 1.493066e+00 # Hw SPCE + 848 283 4 -0.847600 6.754170e+00 9.775212e+00 1.630077e+00 # Ow SPCE + 849 283 3 0.423800 6.577520e+00 9.309741e+00 2.497332e+00 # Hw SPCE + 850 284 3 0.423800 1.061617e+01 1.285220e+01 9.107683e+00 # Hw SPCE + 851 284 4 -0.847600 1.078537e+01 1.346180e+01 9.882119e+00 # Ow SPCE + 852 284 3 0.423800 1.170080e+01 1.385624e+01 9.802028e+00 # Hw SPCE + 853 285 3 0.423800 1.252982e+01 2.440492e+01 2.107781e+01 # Hw SPCE + 854 285 4 -0.847600 1.328350e+01 2.483431e+01 2.157539e+01 # Ow SPCE + 855 285 3 0.423800 1.301279e+01 2.575321e+01 2.186234e+01 # Hw SPCE + 856 286 3 0.423800 1.711392e+01 3.831843e+00 7.910876e+00 # Hw SPCE + 857 286 4 -0.847600 1.745648e+01 2.924441e+00 8.154342e+00 # Ow SPCE + 858 286 3 0.423800 1.668530e+01 2.317735e+00 8.347214e+00 # Hw SPCE + 859 287 3 0.423800 1.418372e+01 2.506933e+01 2.753477e+01 # Hw SPCE + 860 287 4 -0.847600 1.506448e+01 2.551120e+01 2.770510e+01 # Ow SPCE + 861 287 3 0.423800 1.537636e+01 2.596552e+01 2.687064e+01 # Hw SPCE + 862 288 3 0.423800 1.415443e+01 8.808654e+00 1.783263e+01 # Hw SPCE + 863 288 4 -0.847600 1.474094e+01 9.071980e+00 1.859858e+01 # Ow SPCE + 864 288 3 0.423800 1.484475e+01 1.006648e+01 1.861235e+01 # Hw SPCE + 865 289 3 0.423800 4.677556e+00 9.152557e+00 2.714451e+01 # Hw SPCE + 866 289 4 -0.847600 4.161429e+00 9.973113e+00 2.689895e+01 # Ow SPCE + 867 289 3 0.423800 3.680550e+00 1.031808e+01 2.770502e+01 # Hw SPCE + 868 290 3 0.423800 1.681375e+01 5.844343e+00 1.610055e+01 # Hw SPCE + 869 290 4 -0.847600 1.659584e+01 6.638638e+00 1.666766e+01 # Ow SPCE + 870 290 3 0.423800 1.560520e+01 6.774046e+00 1.668509e+01 # Hw SPCE + 871 291 3 0.423800 2.156748e+01 3.556166e+00 8.743084e+00 # Hw SPCE + 872 291 4 -0.847600 2.099885e+01 4.371413e+00 8.633380e+00 # Ow SPCE + 873 291 3 0.423800 2.011280e+01 4.110671e+00 8.250059e+00 # Hw SPCE + 874 292 3 0.423800 2.407964e+00 3.416603e+00 4.875553e+00 # Hw SPCE + 875 292 4 -0.847600 2.941172e+00 4.243659e+00 5.053503e+00 # Ow SPCE + 876 292 3 0.423800 3.734200e+00 4.013998e+00 5.617739e+00 # Hw SPCE + 877 293 3 0.423800 5.101947e+00 1.984796e+01 1.813229e+01 # Hw SPCE + 878 293 4 -0.847600 4.344155e+00 1.945528e+01 1.865340e+01 # Ow SPCE + 879 293 3 0.423800 4.223615e+00 1.849669e+01 1.839539e+01 # Hw SPCE + 880 294 3 0.423800 2.200936e+01 1.060534e+01 3.752114e+00 # Hw SPCE + 881 294 4 -0.847600 2.189049e+01 9.647989e+00 4.015453e+00 # Ow SPCE + 882 294 3 0.423800 2.092346e+01 9.401882e+00 3.949942e+00 # Hw SPCE + 883 295 3 0.423800 1.906823e+01 2.481498e+01 1.981312e+01 # Hw SPCE + 884 295 4 -0.847600 2.004704e+01 2.462769e+01 1.973036e+01 # Ow SPCE + 885 295 3 0.423800 2.020559e+01 2.364324e+01 1.980589e+01 # Hw SPCE + 886 296 3 0.423800 8.611320e+00 2.469462e+01 1.622672e+01 # Hw SPCE + 887 296 4 -0.847600 9.439002e+00 2.491431e+01 1.674313e+01 # Ow SPCE + 888 296 3 0.423800 9.564199e+00 2.590618e+01 1.676596e+01 # Hw SPCE + 889 297 3 0.423800 1.450721e+01 2.761357e+00 1.498414e+01 # Hw SPCE + 890 297 4 -0.847600 1.415911e+01 3.378652e+00 1.568967e+01 # Ow SPCE + 891 297 3 0.423800 1.492505e+01 3.846449e+00 1.613071e+01 # Hw SPCE + 892 298 3 0.423800 1.868170e+01 1.216338e+01 2.369258e+01 # Hw SPCE + 893 298 4 -0.847600 1.793724e+01 1.165537e+01 2.412583e+01 # Ow SPCE + 894 298 3 0.423800 1.733910e+01 1.127446e+01 2.342075e+01 # Hw SPCE + 895 299 3 0.423800 1.579916e+01 1.257851e+01 4.190722e+00 # Hw SPCE + 896 299 4 -0.847600 1.647864e+01 1.330728e+01 4.105902e+00 # Ow SPCE + 897 299 3 0.423800 1.738136e+01 1.290518e+01 3.952950e+00 # Hw SPCE + 898 300 3 0.423800 8.783834e+00 4.391999e+00 2.574931e+01 # Hw SPCE + 899 300 4 -0.847600 8.834362e+00 3.580977e+00 2.633214e+01 # Ow SPCE + 900 300 3 0.423800 9.303500e+00 3.811808e+00 2.718456e+01 # Hw SPCE + 901 301 3 0.423800 6.011865e+00 9.555313e+00 7.226940e+00 # Hw SPCE + 902 301 4 -0.847600 5.112292e+00 9.315952e+00 7.592283e+00 # Ow SPCE + 903 301 3 0.423800 5.076259e+00 9.543963e+00 8.565274e+00 # Hw SPCE + 904 302 3 0.423800 2.627737e+01 1.835769e+01 1.705721e+00 # Hw SPCE + 905 302 4 -0.847600 2.714217e+01 1.785579e+01 1.720783e+00 # Ow SPCE + 906 302 3 0.423800 2.696433e+01 1.689110e+01 1.915100e+00 # Hw SPCE + 907 303 3 0.423800 3.574592e+00 1.061416e+01 2.280540e+01 # Hw SPCE + 908 303 4 -0.847600 3.055829e+00 9.761396e+00 2.274473e+01 # Ow SPCE + 909 303 3 0.423800 2.083376e+00 9.969569e+00 2.263986e+01 # Hw SPCE + 910 304 3 0.423800 6.296561e+00 4.609936e+00 3.590033e+00 # Hw SPCE + 911 304 4 -0.847600 5.307980e+00 4.579235e+00 3.442501e+00 # Ow SPCE + 912 304 3 0.423800 4.921826e+00 5.491212e+00 3.581000e+00 # Hw SPCE + 913 305 3 0.423800 2.206674e+01 2.595682e+01 2.671382e+01 # Hw SPCE + 914 305 4 -0.847600 2.135678e+01 2.658763e+01 2.702694e+01 # Ow SPCE + 915 305 3 0.423800 2.078094e+01 2.613123e+01 2.770524e+01 # Hw SPCE + 916 306 3 0.423800 1.817609e+01 2.098444e+01 2.027086e+01 # Hw SPCE + 917 306 4 -0.847600 1.916371e+01 2.114133e+01 2.027198e+01 # Ow SPCE + 918 306 3 0.423800 1.957493e+01 2.067163e+01 2.105318e+01 # Hw SPCE + 919 307 3 0.423800 1.508206e+01 2.274541e+01 1.655332e+01 # Hw SPCE + 920 307 4 -0.847600 1.463912e+01 2.352206e+01 1.610542e+01 # Ow SPCE + 921 307 3 0.423800 1.476799e+01 2.434437e+01 1.665968e+01 # Hw SPCE + 922 308 3 0.423800 1.860141e+01 7.614679e+00 1.499272e+01 # Hw SPCE + 923 308 4 -0.847600 1.949309e+01 7.194380e+00 1.516084e+01 # Ow SPCE + 924 308 3 0.423800 1.938985e+01 6.200796e+00 1.520703e+01 # Hw SPCE + 925 309 3 0.423800 2.555072e+01 1.158947e+01 2.770860e+01 # Hw SPCE + 926 309 4 -0.847600 2.643932e+01 1.113079e+01 2.770565e+01 # Ow SPCE + 927 309 3 0.423800 2.716796e+01 1.181567e+01 2.770996e+01 # Hw SPCE + 928 310 3 0.423800 1.722971e+01 1.047192e+01 5.228288e+00 # Hw SPCE + 929 310 4 -0.847600 1.777259e+01 9.727661e+00 4.839246e+00 # Ow SPCE + 930 310 3 0.423800 1.859163e+01 9.586550e+00 5.395364e+00 # Hw SPCE + 931 311 3 0.423800 2.587903e+01 2.770480e+01 1.071070e+01 # Hw SPCE + 932 311 4 -0.847600 2.587408e+01 2.767484e+01 9.711163e+00 # Ow SPCE + 933 311 3 0.423800 2.681437e+01 2.762443e+01 9.374545e+00 # Hw SPCE + 934 312 3 0.423800 2.683452e+01 2.499904e+00 1.613606e+01 # Hw SPCE + 935 312 4 -0.847600 2.653269e+01 3.436233e+00 1.631547e+01 # Ow SPCE + 936 312 3 0.423800 2.724944e+01 3.928654e+00 1.680922e+01 # Hw SPCE + 937 313 3 0.423800 1.949268e+01 1.128367e+01 2.484942e+00 # Hw SPCE + 938 313 4 -0.847600 2.013505e+01 1.203650e+01 2.341412e+00 # Ow SPCE + 939 313 3 0.423800 1.964783e+01 1.290736e+01 2.406347e+00 # Hw SPCE + 940 314 3 0.423800 7.709374e+00 2.414404e+01 2.771162e+01 # Hw SPCE + 941 314 4 -0.847600 8.447079e+00 2.438436e+01 2.708072e+01 # Ow SPCE + 942 314 3 0.423800 9.057350e+00 2.360032e+01 2.696734e+01 # Hw SPCE + 943 315 3 0.423800 2.770494e+01 2.154717e+00 2.400702e+01 # Hw SPCE + 944 315 4 -0.847600 2.722867e+01 2.468793e+00 2.482831e+01 # Ow SPCE + 945 315 3 0.423800 2.767391e+01 2.087109e+00 2.563830e+01 # Hw SPCE + 946 316 3 0.423800 2.312652e+01 2.631054e+01 1.499737e+00 # Hw SPCE + 947 316 4 -0.847600 2.283269e+01 2.535561e+01 1.541925e+00 # Ow SPCE + 948 316 3 0.423800 2.209421e+01 2.526330e+01 2.209853e+00 # Hw SPCE + 949 317 3 0.423800 3.512223e+00 1.506331e+01 2.059379e+01 # Hw SPCE + 950 317 4 -0.847600 2.579657e+00 1.521266e+01 2.026513e+01 # Ow SPCE + 951 317 3 0.423800 1.995243e+00 1.548068e+01 2.103105e+01 # Hw SPCE + 952 318 3 0.423800 2.429693e+01 7.441439e+00 8.683691e+00 # Hw SPCE + 953 318 4 -0.847600 2.381138e+01 6.574628e+00 8.570202e+00 # Ow SPCE + 954 318 3 0.423800 2.314115e+01 6.662026e+00 7.833213e+00 # Hw SPCE + 955 319 3 0.423800 7.522703e+00 2.737277e+01 3.043788e+00 # Hw SPCE + 956 319 4 -0.847600 8.363778e+00 2.691935e+01 3.338753e+00 # Ow SPCE + 957 319 3 0.423800 9.106122e+00 2.758810e+01 3.380004e+00 # Hw SPCE + 958 320 3 0.423800 1.882098e+01 5.571858e+00 2.228557e+01 # Hw SPCE + 959 320 4 -0.847600 1.938648e+01 5.803385e+00 2.307715e+01 # Ow SPCE + 960 320 3 0.423800 1.882965e+01 5.766062e+00 2.390694e+01 # Hw SPCE + 961 321 3 0.423800 2.349594e+01 1.890656e+01 2.187820e+01 # Hw SPCE + 962 321 4 -0.847600 2.438719e+01 1.922899e+01 2.155931e+01 # Ow SPCE + 963 321 3 0.423800 2.446815e+01 1.906638e+01 2.057594e+01 # Hw SPCE + 964 322 3 0.423800 9.536260e+00 5.620589e+00 4.385983e+00 # Hw SPCE + 965 322 4 -0.847600 9.017970e+00 4.765629e+00 4.365479e+00 # Ow SPCE + 966 322 3 0.423800 9.365801e+00 4.147994e+00 5.070843e+00 # Hw SPCE + 967 323 3 0.423800 6.563604e+00 1.144852e+01 5.310816e+00 # Hw SPCE + 968 323 4 -0.847600 7.395750e+00 1.159137e+01 5.846659e+00 # Ow SPCE + 969 323 3 0.423800 7.176574e+00 1.211622e+01 6.669152e+00 # Hw SPCE + 970 324 3 0.423800 1.966990e+01 1.748868e+01 1.152281e+01 # Hw SPCE + 971 324 4 -0.847600 2.032778e+01 1.685289e+01 1.192649e+01 # Ow SPCE + 972 324 3 0.423800 1.986999e+01 1.629389e+01 1.261783e+01 # Hw SPCE + 973 325 3 0.423800 1.747869e+01 1.936643e+01 1.586861e+01 # Hw SPCE + 974 325 4 -0.847600 1.772310e+01 1.843509e+01 1.613854e+01 # Ow SPCE + 975 325 3 0.423800 1.692776e+01 1.783807e+01 1.603358e+01 # Hw SPCE + 976 326 3 0.423800 7.512513e+00 6.837798e+00 1.561602e+00 # Hw SPCE + 977 326 4 -0.847600 7.975365e+00 5.953103e+00 1.506077e+00 # Ow SPCE + 978 326 3 0.423800 8.941306e+00 6.067128e+00 1.738364e+00 # Hw SPCE + 979 327 3 0.423800 1.576153e+01 1.524842e+00 5.104682e+00 # Hw SPCE + 980 327 4 -0.847600 1.648750e+01 2.206265e+00 5.011799e+00 # Ow SPCE + 981 327 3 0.423800 1.619187e+01 3.066886e+00 5.426446e+00 # Hw SPCE + 982 328 3 0.423800 1.041282e+01 1.861899e+01 5.679153e+00 # Hw SPCE + 983 328 4 -0.847600 1.039014e+01 1.838326e+01 4.707600e+00 # Ow SPCE + 984 328 3 0.423800 1.080342e+01 1.748259e+01 4.573414e+00 # Hw SPCE + 985 329 3 0.423800 1.662912e+01 1.960472e+01 1.057467e+01 # Hw SPCE + 986 329 4 -0.847600 1.568158e+01 1.987224e+01 1.074964e+01 # Ow SPCE + 987 329 3 0.423800 1.512288e+01 1.905336e+01 1.088108e+01 # Hw SPCE + 988 330 3 0.423800 2.562112e+01 2.330374e+00 2.186263e+01 # Hw SPCE + 989 330 4 -0.847600 2.639694e+01 2.945170e+00 2.172070e+01 # Ow SPCE + 990 330 3 0.423800 2.613489e+01 3.671241e+00 2.108498e+01 # Hw SPCE + 991 331 3 0.423800 2.448963e+01 1.656753e+01 2.459110e+01 # Hw SPCE + 992 331 4 -0.847600 2.532168e+01 1.702758e+01 2.490103e+01 # Ow SPCE + 993 331 3 0.423800 2.611790e+01 1.646961e+01 2.466717e+01 # Hw SPCE + 994 332 3 0.423800 6.417758e+00 2.435520e+01 1.460340e+01 # Hw SPCE + 995 332 4 -0.847600 6.300358e+00 2.524145e+01 1.415532e+01 # Ow SPCE + 996 332 3 0.423800 7.192182e+00 2.558969e+01 1.386657e+01 # Hw SPCE + 997 333 3 0.423800 2.759772e+01 1.733045e+00 3.198930e+00 # Hw SPCE + 998 333 4 -0.847600 2.733255e+01 1.589050e+00 2.245541e+00 # Ow SPCE + 999 333 3 0.423800 2.681386e+01 2.379914e+00 1.920750e+00 # Hw SPCE + 1000 334 3 0.423800 2.588019e+01 1.500059e+00 1.857574e+01 # Hw SPCE + 1001 334 4 -0.847600 2.521085e+01 2.077152e+00 1.904366e+01 # Ow SPCE + 1002 334 3 0.423800 2.452203e+01 1.500061e+00 1.948240e+01 # Hw SPCE + 1003 335 3 0.423800 2.129430e+01 2.706783e+01 2.431980e+01 # Hw SPCE + 1004 335 4 -0.847600 2.048933e+01 2.761599e+01 2.454682e+01 # Ow SPCE + 1005 335 3 0.423800 1.990824e+01 2.770571e+01 2.373794e+01 # Hw SPCE + 1006 336 3 0.423800 7.846173e+00 1.094805e+01 9.044554e+00 # Hw SPCE + 1007 336 4 -0.847600 8.350386e+00 1.031715e+01 8.454855e+00 # Ow SPCE + 1008 336 3 0.423800 9.135128e+00 1.079028e+01 8.054438e+00 # Hw SPCE + 1009 337 3 0.423800 1.813806e+01 1.135820e+01 1.530019e+01 # Hw SPCE + 1010 337 4 -0.847600 1.803468e+01 1.102175e+01 1.436418e+01 # Ow SPCE + 1011 337 3 0.423800 1.870041e+01 1.029479e+01 1.419585e+01 # Hw SPCE + 1012 338 3 0.423800 1.930193e+01 1.912951e+00 3.422805e+00 # Hw SPCE + 1013 338 4 -0.847600 2.017995e+01 1.724286e+00 3.862672e+00 # Ow SPCE + 1014 338 3 0.423800 2.082751e+01 2.453171e+00 3.640448e+00 # Hw SPCE + 1015 339 3 0.423800 4.001940e+00 8.178245e+00 1.133370e+01 # Hw SPCE + 1016 339 4 -0.847600 3.264545e+00 8.098159e+00 1.066300e+01 # Ow SPCE + 1017 339 3 0.423800 3.600575e+00 7.615500e+00 9.854222e+00 # Hw SPCE + 1018 340 3 0.423800 1.659027e+01 2.182766e+01 6.306849e+00 # Hw SPCE + 1019 340 4 -0.847600 1.573368e+01 2.131770e+01 6.228114e+00 # Ow SPCE + 1020 340 3 0.423800 1.525717e+01 2.159339e+01 5.393290e+00 # Hw SPCE + 1021 341 3 0.423800 1.307614e+01 1.247914e+01 2.352415e+01 # Hw SPCE + 1022 341 4 -0.847600 1.282345e+01 1.342121e+01 2.374472e+01 # Ow SPCE + 1023 341 3 0.423800 1.200319e+01 1.367502e+01 2.323212e+01 # Hw SPCE + 1024 342 3 0.423800 1.497260e+00 1.394711e+01 5.663732e+00 # Hw SPCE + 1025 342 4 -0.847600 1.700412e+00 1.368341e+01 4.720762e+00 # Ow SPCE + 1026 342 3 0.423800 2.683724e+00 1.376262e+01 4.556984e+00 # Hw SPCE + 1027 343 3 0.423800 1.331392e+01 4.053633e+00 8.310192e+00 # Hw SPCE + 1028 343 4 -0.847600 1.396490e+01 4.044457e+00 7.551157e+00 # Ow SPCE + 1029 343 3 0.423800 1.422587e+01 3.100890e+00 7.347255e+00 # Hw SPCE + 1030 344 3 0.423800 1.981757e+01 1.143084e+01 8.740400e+00 # Hw SPCE + 1031 344 4 -0.847600 2.013820e+01 1.062139e+01 9.232317e+00 # Ow SPCE + 1032 344 3 0.423800 2.106600e+01 1.078181e+01 9.569139e+00 # Hw SPCE + 1033 345 3 0.423800 1.322045e+01 1.551728e+01 1.471662e+01 # Hw SPCE + 1034 345 4 -0.847600 1.356744e+01 1.622003e+01 1.533770e+01 # Ow SPCE + 1035 345 3 0.423800 1.280432e+01 1.676712e+01 1.568170e+01 # Hw SPCE + 1036 346 3 0.423800 2.397971e+01 1.596693e+01 4.479312e+00 # Hw SPCE + 1037 346 4 -0.847600 2.394370e+01 1.692386e+01 4.191220e+00 # Ow SPCE + 1038 346 3 0.423800 2.474897e+01 1.713577e+01 3.637489e+00 # Hw SPCE + 1039 347 3 0.423800 2.621039e+01 2.495880e+01 9.979554e+00 # Hw SPCE + 1040 347 4 -0.847600 2.717528e+01 2.491488e+01 9.720619e+00 # Ow SPCE + 1041 347 3 0.423800 2.770734e+01 2.453968e+01 1.047966e+01 # Hw SPCE + 1042 348 3 0.423800 1.496218e+01 1.063514e+01 2.219722e+01 # Hw SPCE + 1043 348 4 -0.847600 1.527717e+01 9.890283e+00 2.160902e+01 # Ow SPCE + 1044 348 3 0.423800 1.616433e+01 1.012956e+01 2.121444e+01 # Hw SPCE + 1045 349 3 0.423800 5.054437e+00 2.163300e+01 1.503551e+01 # Hw SPCE + 1046 349 4 -0.847600 4.322602e+00 2.106058e+01 1.466572e+01 # Ow SPCE + 1047 349 3 0.423800 4.564201e+00 2.009674e+01 1.477821e+01 # Hw SPCE + 1048 350 3 0.423800 1.707807e+01 2.164478e+01 1.236295e+01 # Hw SPCE + 1049 350 4 -0.847600 1.667106e+01 2.225955e+01 1.168739e+01 # Ow SPCE + 1050 350 3 0.423800 1.611709e+01 2.294854e+01 1.215474e+01 # Hw SPCE + 1051 351 3 0.423800 6.976035e+00 1.779520e+01 1.276337e+01 # Hw SPCE + 1052 351 4 -0.847600 6.523152e+00 1.699626e+01 1.236766e+01 # Ow SPCE + 1053 351 3 0.423800 7.208840e+00 1.630862e+01 1.212892e+01 # Hw SPCE + 1054 352 3 0.423800 2.164730e+01 2.694246e+01 1.255154e+01 # Hw SPCE + 1055 352 4 -0.847600 2.229751e+01 2.618901e+01 1.245390e+01 # Ow SPCE + 1056 352 3 0.423800 2.315706e+01 2.653692e+01 1.207954e+01 # Hw SPCE + 1057 353 3 0.423800 6.833277e+00 2.770802e+01 1.645841e+01 # Hw SPCE + 1058 353 4 -0.847600 7.004922e+00 2.688481e+01 1.699957e+01 # Ow SPCE + 1059 353 3 0.423800 6.350781e+00 2.617384e+01 1.674145e+01 # Hw SPCE + 1060 354 3 0.423800 1.839299e+01 2.770356e+01 2.009264e+01 # Hw SPCE + 1061 354 4 -0.847600 1.905118e+01 2.770991e+01 2.084546e+01 # Ow SPCE + 1062 354 3 0.423800 1.998036e+01 2.770478e+01 2.047586e+01 # Hw SPCE + 1063 355 3 0.423800 2.064587e+01 1.196502e+01 2.770409e+01 # Hw SPCE + 1064 355 4 -0.847600 2.115792e+01 1.209057e+01 2.685436e+01 # Ow SPCE + 1065 355 3 0.423800 2.178395e+01 1.286403e+01 2.695363e+01 # Hw SPCE + 1066 356 3 0.423800 2.679484e+01 2.239034e+01 1.193203e+01 # Hw SPCE + 1067 356 4 -0.847600 2.667630e+01 2.273676e+01 1.286259e+01 # Ow SPCE + 1068 356 3 0.423800 2.726684e+01 2.353199e+01 1.299996e+01 # Hw SPCE + 1069 357 3 0.423800 2.770507e+01 1.752615e+01 1.228536e+01 # Hw SPCE + 1070 357 4 -0.847600 2.749083e+01 1.721084e+01 1.320985e+01 # Ow SPCE + 1071 357 3 0.423800 2.659323e+01 1.677004e+01 1.321203e+01 # Hw SPCE + 1072 358 3 0.423800 7.054104e+00 1.410756e+01 4.776771e+00 # Hw SPCE + 1073 358 4 -0.847600 8.051952e+00 1.404602e+01 4.799402e+00 # Ow SPCE + 1074 358 3 0.423800 8.434858e+00 1.493321e+01 5.056846e+00 # Hw SPCE + 1075 359 3 0.423800 7.117855e+00 1.158648e+01 2.086169e+01 # Hw SPCE + 1076 359 4 -0.847600 7.039453e+00 1.242040e+01 2.031541e+01 # Ow SPCE + 1077 359 3 0.423800 7.832717e+00 1.249916e+01 1.971165e+01 # Hw SPCE + 1078 360 3 0.423800 2.261313e+01 1.962782e+01 4.727741e+00 # Hw SPCE + 1079 360 4 -0.847600 2.305377e+01 1.917276e+01 5.501535e+00 # Ow SPCE + 1080 360 3 0.423800 2.246091e+01 1.923188e+01 6.304662e+00 # Hw SPCE + 1081 361 3 0.423800 2.644084e+00 2.634256e+01 1.150517e+01 # Hw SPCE + 1082 361 4 -0.847600 2.636942e+00 2.733967e+01 1.158078e+01 # Ow SPCE + 1083 361 3 0.423800 1.836409e+00 2.770428e+01 1.110516e+01 # Hw SPCE + 1084 362 3 0.423800 8.040783e+00 1.358334e+01 9.796191e+00 # Hw SPCE + 1085 362 4 -0.847600 7.086989e+00 1.388373e+01 9.802364e+00 # Ow SPCE + 1086 362 3 0.423800 6.576055e+00 1.338543e+01 9.101906e+00 # Hw SPCE + 1087 363 3 0.423800 2.619651e+00 1.319647e+01 2.242900e+01 # Hw SPCE + 1088 363 4 -0.847600 1.972508e+00 1.282938e+01 2.309717e+01 # Ow SPCE + 1089 363 3 0.423800 1.494472e+00 1.358356e+01 2.354737e+01 # Hw SPCE + 1090 364 3 0.423800 4.287560e+00 6.326031e+00 2.681750e+01 # Hw SPCE + 1091 364 4 -0.847600 4.221751e+00 5.858179e+00 2.593615e+01 # Ow SPCE + 1092 364 3 0.423800 4.606223e+00 4.938624e+00 2.601739e+01 # Hw SPCE + 1093 365 3 0.423800 2.134184e+01 1.704290e+01 5.072956e+00 # Hw SPCE + 1094 365 4 -0.847600 2.040579e+01 1.710436e+01 4.726504e+00 # Ow SPCE + 1095 365 3 0.423800 2.037017e+01 1.673983e+01 3.795993e+00 # Hw SPCE + 1096 366 3 0.423800 1.898318e+01 2.671834e+01 1.475007e+01 # Hw SPCE + 1097 366 4 -0.847600 1.928304e+01 2.767034e+01 1.481164e+01 # Ow SPCE + 1098 366 3 0.423800 2.028241e+01 2.770555e+01 1.481376e+01 # Hw SPCE + 1099 367 3 0.423800 2.348205e+01 1.705352e+01 2.743345e+01 # Hw SPCE + 1100 367 4 -0.847600 2.446126e+01 1.722463e+01 2.754240e+01 # Ow SPCE + 1101 367 3 0.423800 2.461312e+01 1.819940e+01 2.770595e+01 # Hw SPCE + 1102 368 3 0.423800 2.430373e+01 1.513396e+01 1.529098e+01 # Hw SPCE + 1103 368 4 -0.847600 2.387002e+01 1.513478e+01 1.619203e+01 # Ow SPCE + 1104 368 3 0.423800 2.295803e+01 1.553908e+01 1.612260e+01 # Hw SPCE + 1105 369 3 0.423800 1.140164e+01 2.512691e+01 1.865711e+01 # Hw SPCE + 1106 369 4 -0.847600 1.159315e+01 2.415737e+01 1.850437e+01 # Ow SPCE + 1107 369 3 0.423800 1.256364e+01 2.403832e+01 1.829465e+01 # Hw SPCE + 1108 370 3 0.423800 1.903749e+01 1.236107e+01 6.079139e+00 # Hw SPCE + 1109 370 4 -0.847600 2.003143e+01 1.240506e+01 6.179850e+00 # Ow SPCE + 1110 370 3 0.423800 2.044270e+01 1.158083e+01 5.790615e+00 # Hw SPCE + 1111 371 3 0.423800 1.282548e+01 1.241244e+01 1.303471e+01 # Hw SPCE + 1112 371 4 -0.847600 1.310760e+01 1.337123e+01 1.300088e+01 # Ow SPCE + 1113 371 3 0.423800 1.235662e+01 1.392727e+01 1.264472e+01 # Hw SPCE + 1114 372 3 0.423800 1.455246e+01 1.713196e+01 1.777281e+01 # Hw SPCE + 1115 372 4 -0.847600 1.483389e+01 1.618051e+01 1.789743e+01 # Ow SPCE + 1116 372 3 0.423800 1.582185e+01 1.614204e+01 1.804727e+01 # Hw SPCE + 1117 373 3 0.423800 2.660254e+01 1.154715e+01 7.873309e+00 # Hw SPCE + 1118 373 4 -0.847600 2.566434e+01 1.120992e+01 7.951077e+00 # Ow SPCE + 1119 373 3 0.423800 2.566312e+01 1.021159e+01 7.893201e+00 # Hw SPCE + 1120 374 3 0.423800 8.706708e+00 9.237566e+00 1.972409e+01 # Hw SPCE + 1121 374 4 -0.847600 8.843305e+00 8.419627e+00 1.916524e+01 # Ow SPCE + 1122 374 3 0.423800 9.468501e+00 7.795949e+00 1.963445e+01 # Hw SPCE + 1123 375 3 0.423800 1.904385e+01 2.517573e+01 1.240879e+01 # Hw SPCE + 1124 375 4 -0.847600 1.846922e+01 2.435960e+01 1.234762e+01 # Ow SPCE + 1125 375 3 0.423800 1.904403e+01 2.355925e+01 1.217725e+01 # Hw SPCE + 1126 376 3 0.423800 1.112677e+01 1.997104e+01 2.147548e+00 # Hw SPCE + 1127 376 4 -0.847600 1.122781e+01 2.093546e+01 1.903215e+00 # Ow SPCE + 1128 376 3 0.423800 1.219941e+01 2.116740e+01 1.856343e+00 # Hw SPCE + 1129 377 3 0.423800 2.578920e+01 1.183896e+01 1.708350e+01 # Hw SPCE + 1130 377 4 -0.847600 2.566789e+01 1.208960e+01 1.612305e+01 # Ow SPCE + 1131 377 3 0.423800 2.594628e+01 1.304067e+01 1.598904e+01 # Hw SPCE + 1132 378 3 0.423800 1.394495e+01 2.009220e+01 8.623841e+00 # Hw SPCE + 1133 378 4 -0.847600 1.430818e+01 1.923404e+01 8.261025e+00 # Ow SPCE + 1134 378 3 0.423800 1.528668e+01 1.933569e+01 8.081558e+00 # Hw SPCE + 1135 379 3 0.423800 5.844676e+00 2.770452e+01 2.407135e+01 # Hw SPCE + 1136 379 4 -0.847600 6.002067e+00 2.672754e+01 2.421532e+01 # Ow SPCE + 1137 379 3 0.423800 6.928604e+00 2.658707e+01 2.456432e+01 # Hw SPCE + 1138 380 3 0.423800 1.960711e+01 1.884907e+01 1.867877e+01 # Hw SPCE + 1139 380 4 -0.847600 1.959153e+01 1.836640e+01 1.955444e+01 # Ow SPCE + 1140 380 3 0.423800 1.864928e+01 1.830285e+01 1.988328e+01 # Hw SPCE + 1141 381 3 0.423800 1.937001e+01 2.231144e+01 7.504950e+00 # Hw SPCE + 1142 381 4 -0.847600 1.903775e+01 2.136844e+01 7.486339e+00 # Ow SPCE + 1143 381 3 0.423800 1.981507e+01 2.074229e+01 7.425510e+00 # Hw SPCE + 1144 382 3 0.423800 1.186903e+01 7.804165e+00 2.097534e+01 # Hw SPCE + 1145 382 4 -0.847600 1.191707e+01 8.691479e+00 2.051668e+01 # Ow SPCE + 1146 382 3 0.423800 1.284539e+01 9.055616e+00 2.059166e+01 # Hw SPCE + 1147 383 3 0.423800 1.254816e+01 1.752163e+01 2.720322e+01 # Hw SPCE + 1148 383 4 -0.847600 1.171866e+01 1.807176e+01 2.729959e+01 # Ow SPCE + 1149 383 3 0.423800 1.195006e+01 1.895518e+01 2.770705e+01 # Hw SPCE + 1150 384 3 0.423800 2.457569e+01 2.221691e+01 1.644026e+01 # Hw SPCE + 1151 384 4 -0.847600 2.471053e+01 2.126493e+01 1.671514e+01 # Ow SPCE + 1152 384 3 0.423800 2.384588e+01 2.088835e+01 1.704767e+01 # Hw SPCE + 1153 385 3 0.423800 1.283404e+01 2.766561e+01 2.418101e+01 # Hw SPCE + 1154 385 4 -0.847600 1.206202e+01 2.770764e+01 2.354681e+01 # Ow SPCE + 1155 385 3 0.423800 1.120852e+01 2.757858e+01 2.405168e+01 # Hw SPCE + 1156 386 3 0.423800 1.749501e+01 9.243189e+00 2.770432e+01 # Hw SPCE + 1157 386 4 -0.847600 1.707406e+01 8.336104e+00 2.770498e+01 # Ow SPCE + 1158 386 3 0.423800 1.778896e+01 7.636892e+00 2.770954e+01 # Hw SPCE + 1159 387 3 0.423800 3.764698e+00 4.444911e+00 2.206397e+01 # Hw SPCE + 1160 387 4 -0.847600 3.228879e+00 4.580528e+00 2.123060e+01 # Ow SPCE + 1161 387 3 0.423800 3.845459e+00 4.663162e+00 2.044766e+01 # Hw SPCE + 1162 388 3 0.423800 1.825404e+01 5.005912e+00 1.014694e+01 # Hw SPCE + 1163 388 4 -0.847600 1.843498e+01 5.919465e+00 9.782683e+00 # Ow SPCE + 1164 388 3 0.423800 1.764323e+01 6.507321e+00 9.948697e+00 # Hw SPCE + 1165 389 3 0.423800 1.376578e+01 2.484946e+01 1.386117e+01 # Hw SPCE + 1166 389 4 -0.847600 1.385130e+01 2.411884e+01 1.318378e+01 # Ow SPCE + 1167 389 3 0.423800 1.295121e+01 2.391359e+01 1.279947e+01 # Hw SPCE + 1168 390 3 0.423800 6.083757e+00 4.915302e+00 1.185692e+01 # Hw SPCE + 1169 390 4 -0.847600 5.091254e+00 4.926633e+00 1.173522e+01 # Ow SPCE + 1170 390 3 0.423800 4.865042e+00 5.402990e+00 1.088557e+01 # Hw SPCE + 1171 391 3 0.423800 1.088455e+01 2.264855e+01 1.611957e+01 # Hw SPCE + 1172 391 4 -0.847600 1.184680e+01 2.283963e+01 1.592573e+01 # Ow SPCE + 1173 391 3 0.423800 1.194451e+01 2.378898e+01 1.562707e+01 # Hw SPCE + 1174 392 3 0.423800 2.206544e+01 9.962865e+00 2.373843e+01 # Hw SPCE + 1175 392 4 -0.847600 2.203099e+01 1.070683e+01 2.440575e+01 # Ow SPCE + 1176 392 3 0.423800 2.122829e+01 1.127638e+01 2.422883e+01 # Hw SPCE + 1177 393 3 0.423800 2.149681e+00 4.701448e+00 2.459932e+00 # Hw SPCE + 1178 393 4 -0.847600 2.971895e+00 4.426184e+00 1.961740e+00 # Ow SPCE + 1179 393 3 0.423800 3.296291e+00 5.191193e+00 1.405388e+00 # Hw SPCE + 1180 394 3 0.423800 2.234775e+01 2.162751e+01 2.770458e+01 # Hw SPCE + 1181 394 4 -0.847600 2.136405e+01 2.144770e+01 2.770458e+01 # Ow SPCE + 1182 394 3 0.423800 2.086664e+01 2.231522e+01 2.770463e+01 # Hw SPCE + 1183 395 3 0.423800 1.025105e+01 1.356885e+01 1.665922e+01 # Hw SPCE + 1184 395 4 -0.847600 1.035969e+01 1.403984e+01 1.578379e+01 # Ow SPCE + 1185 395 3 0.423800 1.099242e+01 1.352554e+01 1.520487e+01 # Hw SPCE + 1186 396 3 0.423800 1.072202e+01 2.377633e+01 9.484681e+00 # Hw SPCE + 1187 396 4 -0.847600 1.155152e+01 2.385537e+01 1.003758e+01 # Ow SPCE + 1188 396 3 0.423800 1.158705e+01 2.476225e+01 1.045747e+01 # Hw SPCE + 1189 397 3 0.423800 2.341205e+01 1.813661e+01 1.100851e+01 # Hw SPCE + 1190 397 4 -0.847600 2.312469e+01 1.893695e+01 1.153470e+01 # Ow SPCE + 1191 397 3 0.423800 2.213380e+01 1.891079e+01 1.166681e+01 # Hw SPCE + 1192 398 3 0.423800 1.500790e+01 2.394339e+01 3.351174e+00 # Hw SPCE + 1193 398 4 -0.847600 1.452101e+01 2.480831e+01 3.229359e+00 # Ow SPCE + 1194 398 3 0.423800 1.385157e+01 2.492026e+01 3.963743e+00 # Hw SPCE + 1195 399 3 0.423800 1.479502e+01 1.286237e+01 2.563621e+01 # Hw SPCE + 1196 399 4 -0.847600 1.547417e+01 1.230040e+01 2.516403e+01 # Ow SPCE + 1197 399 3 0.423800 1.510530e+01 1.138206e+01 2.502053e+01 # Hw SPCE + 1198 400 3 0.423800 8.068136e+00 1.885540e+01 1.505299e+01 # Hw SPCE + 1199 400 4 -0.847600 7.813925e+00 1.834922e+01 1.587711e+01 # Ow SPCE + 1200 400 3 0.423800 8.632664e+00 1.794760e+01 1.628743e+01 # Hw SPCE + 1201 401 3 0.423800 4.063418e+00 2.228502e+01 2.617453e+01 # Hw SPCE + 1202 401 4 -0.847600 4.103168e+00 2.200493e+01 2.713369e+01 # Ow SPCE + 1203 401 3 0.423800 4.240658e+00 2.281008e+01 2.771061e+01 # Hw SPCE + 1204 402 3 0.423800 1.495103e+00 1.280834e+01 9.475737e+00 # Hw SPCE + 1205 402 4 -0.847600 1.505699e+00 1.300445e+01 8.495213e+00 # Ow SPCE + 1206 402 3 0.423800 2.251321e+00 1.363848e+01 8.290148e+00 # Hw SPCE + 1207 403 3 0.423800 2.465760e+01 6.451081e+00 2.270306e+01 # Hw SPCE + 1208 403 4 -0.847600 2.409442e+01 5.715878e+00 2.232582e+01 # Ow SPCE + 1209 403 3 0.423800 2.432171e+01 4.854913e+00 2.278088e+01 # Hw SPCE + 1210 404 3 0.423800 1.999267e+01 7.260978e+00 2.497131e+00 # Hw SPCE + 1211 404 4 -0.847600 2.085928e+01 6.772162e+00 2.396875e+00 # Ow SPCE + 1212 404 3 0.423800 2.067784e+01 5.804151e+00 2.223575e+00 # Hw SPCE + 1213 405 3 0.423800 9.804016e+00 1.166498e+01 2.144260e+01 # Hw SPCE + 1214 405 4 -0.847600 1.060905e+01 1.108039e+01 2.134174e+01 # Ow SPCE + 1215 405 3 0.423800 1.143569e+01 1.162260e+01 2.149231e+01 # Hw SPCE + 1216 406 3 0.423800 3.092468e+00 1.075047e+01 1.184205e+01 # Hw SPCE + 1217 406 4 -0.847600 2.172613e+00 1.036170e+01 1.189426e+01 # Ow SPCE + 1218 406 3 0.423800 1.497139e+00 1.108044e+01 1.172948e+01 # Hw SPCE + 1219 407 3 0.423800 8.342000e+00 1.946949e+00 1.825736e+01 # Hw SPCE + 1220 407 4 -0.847600 7.967584e+00 2.874061e+00 1.827399e+01 # Ow SPCE + 1221 407 3 0.423800 8.362019e+00 3.379098e+00 1.904168e+01 # Hw SPCE + 1222 408 3 0.423800 1.182612e+01 2.367595e+01 5.346337e+00 # Hw SPCE + 1223 408 4 -0.847600 1.218656e+01 2.331296e+01 6.205591e+00 # Ow SPCE + 1224 408 3 0.423800 1.183999e+01 2.385789e+01 6.969091e+00 # Hw SPCE + 1225 409 3 0.423800 2.018572e+01 8.334075e+00 2.235069e+01 # Hw SPCE + 1226 409 4 -0.847600 1.935425e+01 8.544535e+00 2.286486e+01 # Ow SPCE + 1227 409 3 0.423800 1.940926e+01 9.477685e+00 2.322011e+01 # Hw SPCE + 1228 410 3 0.423800 1.150389e+01 1.904731e+01 2.337866e+01 # Hw SPCE + 1229 410 4 -0.847600 1.246144e+01 1.912402e+01 2.310078e+01 # Ow SPCE + 1230 410 3 0.423800 1.251260e+01 1.953763e+01 2.219177e+01 # Hw SPCE + 1231 411 3 0.423800 1.847815e+01 4.974998e+00 2.770084e+01 # Hw SPCE + 1232 411 4 -0.847600 1.940796e+01 5.342993e+00 2.770581e+01 # Ow SPCE + 1233 411 3 0.423800 2.006473e+01 4.589757e+00 2.767000e+01 # Hw SPCE + 1234 412 3 0.423800 1.580751e+01 1.573107e+01 1.381081e+01 # Hw SPCE + 1235 412 4 -0.847600 1.558902e+01 1.492275e+01 1.326411e+01 # Ow SPCE + 1236 412 3 0.423800 1.643597e+01 1.449518e+01 1.294811e+01 # Hw SPCE + 1237 413 3 0.423800 2.552671e+01 2.186200e+01 4.694186e+00 # Hw SPCE + 1238 413 4 -0.847600 2.590407e+01 2.278594e+01 4.631422e+00 # Ow SPCE + 1239 413 3 0.423800 2.664316e+01 2.279908e+01 3.957950e+00 # Hw SPCE + 1240 414 3 0.423800 1.035260e+01 1.601592e+01 2.375608e+01 # Hw SPCE + 1241 414 4 -0.847600 1.119407e+01 1.631619e+01 2.330691e+01 # Ow SPCE + 1242 414 3 0.423800 1.194221e+01 1.632219e+01 2.397043e+01 # Hw SPCE + 1243 415 3 0.423800 1.366476e+01 2.199974e+01 2.177637e+01 # Hw SPCE + 1244 415 4 -0.847600 1.412014e+01 2.188301e+01 2.265898e+01 # Ow SPCE + 1245 415 3 0.423800 1.408048e+01 2.274131e+01 2.317060e+01 # Hw SPCE + 1246 416 3 0.423800 2.364272e+01 2.771622e+01 1.585868e+01 # Hw SPCE + 1247 416 4 -0.847600 2.381273e+01 2.673639e+01 1.575366e+01 # Ow SPCE + 1248 416 3 0.423800 2.301817e+01 2.630404e+01 1.532735e+01 # Hw SPCE + 1249 417 3 0.423800 9.899911e+00 1.878785e+01 1.222479e+01 # Hw SPCE + 1250 417 4 -0.847600 9.152062e+00 1.943110e+01 1.238898e+01 # Ow SPCE + 1251 417 3 0.423800 9.422298e+00 2.034259e+01 1.207890e+01 # Hw SPCE + 1252 418 3 0.423800 1.878242e+01 4.765640e+00 5.930390e+00 # Hw SPCE + 1253 418 4 -0.847600 1.891751e+01 4.352003e+00 5.030026e+00 # Ow SPCE + 1254 418 3 0.423800 1.970449e+01 4.776921e+00 4.582694e+00 # Hw SPCE + 1255 419 3 0.423800 2.569329e+00 2.015592e+01 1.667337e+01 # Hw SPCE + 1256 419 4 -0.847600 1.639651e+00 1.989432e+01 1.641401e+01 # Ow SPCE + 1257 419 3 0.423800 1.669728e+00 1.906197e+01 1.586059e+01 # Hw SPCE + 1258 420 3 0.423800 1.419487e+01 1.526132e+01 2.687487e+01 # Hw SPCE + 1259 420 4 -0.847600 1.473359e+01 1.511839e+01 2.770514e+01 # Ow SPCE + 1260 420 3 0.423800 1.562750e+01 1.474196e+01 2.746177e+01 # Hw SPCE + 1261 421 3 0.423800 1.225934e+01 4.584227e+00 3.933375e+00 # Hw SPCE + 1262 421 4 -0.847600 1.246279e+01 3.746427e+00 4.440028e+00 # Ow SPCE + 1263 421 3 0.423800 1.333976e+01 3.376246e+00 4.133605e+00 # Hw SPCE + 1264 422 3 0.423800 1.620747e+01 1.499403e+00 1.137835e+01 # Hw SPCE + 1265 422 4 -0.847600 1.549499e+01 1.586802e+00 1.207458e+01 # Ow SPCE + 1266 422 3 0.423800 1.590320e+01 1.493891e+00 1.298273e+01 # Hw SPCE + 1267 423 3 0.423800 9.040061e+00 1.791814e+01 2.669513e+01 # Hw SPCE + 1268 423 4 -0.847600 9.361578e+00 1.786689e+01 2.574961e+01 # Ow SPCE + 1269 423 3 0.423800 9.763981e+00 1.874370e+01 2.548640e+01 # Hw SPCE + 1270 424 3 0.423800 4.419758e+00 1.589273e+01 4.038818e+00 # Hw SPCE + 1271 424 4 -0.847600 3.943488e+00 1.618125e+01 4.869433e+00 # Ow SPCE + 1272 424 3 0.423800 4.594864e+00 1.661046e+01 5.495121e+00 # Hw SPCE + 1273 425 3 0.423800 1.842571e+01 1.489983e+00 1.787524e+01 # Hw SPCE + 1274 425 4 -0.847600 1.758392e+01 1.950976e+00 1.815609e+01 # Ow SPCE + 1275 425 3 0.423800 1.679908e+01 1.499453e+00 1.773164e+01 # Hw SPCE + 1276 426 3 0.423800 9.617069e+00 1.503555e+01 7.768316e+00 # Hw SPCE + 1277 426 4 -0.847600 9.908997e+00 1.580937e+01 7.206183e+00 # Ow SPCE + 1278 426 3 0.423800 1.087713e+01 1.599609e+01 7.373049e+00 # Hw SPCE + 1279 427 3 0.423800 1.761915e+01 1.824001e+01 1.495841e+00 # Hw SPCE + 1280 427 4 -0.847600 1.707860e+01 1.740503e+01 1.598843e+00 # Ow SPCE + 1281 427 3 0.423800 1.610784e+01 1.764023e+01 1.646897e+00 # Hw SPCE + 1282 428 3 0.423800 2.926508e+00 1.529462e+00 2.267458e+01 # Hw SPCE + 1283 428 4 -0.847600 2.327395e+00 2.065396e+00 2.207974e+01 # Ow SPCE + 1284 428 3 0.423800 1.514758e+00 1.528181e+00 2.185386e+01 # Hw SPCE + 1285 429 3 0.423800 1.553029e+01 1.331892e+01 2.261128e+01 # Hw SPCE + 1286 429 4 -0.847600 1.550843e+01 1.423794e+01 2.221768e+01 # Ow SPCE + 1287 429 3 0.423800 1.458388e+01 1.444035e+01 2.189481e+01 # Hw SPCE + 1288 430 3 0.423800 4.535770e+00 7.778783e+00 1.481895e+00 # Hw SPCE + 1289 430 4 -0.847600 3.543503e+00 7.902817e+00 1.486495e+00 # Ow SPCE + 1290 430 3 0.423800 3.329718e+00 8.879692e+00 1.489737e+00 # Hw SPCE + 1291 431 3 0.423800 2.525719e+01 1.568518e+01 1.106507e+01 # Hw SPCE + 1292 431 4 -0.847600 2.557432e+01 1.474391e+01 1.094918e+01 # Ow SPCE + 1293 431 3 0.423800 2.628269e+01 1.454508e+01 1.162645e+01 # Hw SPCE + 1294 432 3 0.423800 1.664803e+01 1.910926e+01 3.917316e+00 # Hw SPCE + 1295 432 4 -0.847600 1.723132e+01 1.835477e+01 4.218178e+00 # Ow SPCE + 1296 432 3 0.423800 1.819067e+01 1.863032e+01 4.157108e+00 # Hw SPCE + 1297 433 3 0.423800 1.358310e+01 2.662050e+01 1.011150e+01 # Hw SPCE + 1298 433 4 -0.847600 1.300630e+01 2.743245e+01 1.002187e+01 # Ow SPCE + 1299 433 3 0.423800 1.296445e+01 2.770719e+01 9.061266e+00 # Hw SPCE + 1300 434 3 0.423800 1.435488e+01 2.080827e+01 2.772371e+01 # Hw SPCE + 1301 434 4 -0.847600 1.506496e+01 2.013414e+01 2.752040e+01 # Ow SPCE + 1302 434 3 0.423800 1.464175e+01 1.930210e+01 2.716177e+01 # Hw SPCE + 1303 435 3 0.423800 2.167525e+01 2.207461e+01 1.584656e+01 # Hw SPCE + 1304 435 4 -0.847600 2.087644e+01 2.148761e+01 1.597828e+01 # Ow SPCE + 1305 435 3 0.423800 2.114010e+01 2.067901e+01 1.650425e+01 # Hw SPCE + 1306 436 3 0.423800 1.336152e+01 8.766368e+00 1.286048e+01 # Hw SPCE + 1307 436 4 -0.847600 1.290502e+01 9.628651e+00 1.307975e+01 # Ow SPCE + 1308 436 3 0.423800 1.199822e+01 9.439351e+00 1.345642e+01 # Hw SPCE + 1309 437 3 0.423800 2.687223e+01 1.379076e+01 4.532287e+00 # Hw SPCE + 1310 437 4 -0.847600 2.610111e+01 1.321002e+01 4.793266e+00 # Ow SPCE + 1311 437 3 0.423800 2.541665e+01 1.376000e+01 5.271855e+00 # Hw SPCE + 1312 438 3 0.423800 2.387246e+01 1.507034e+00 1.669725e+01 # Hw SPCE + 1313 438 4 -0.847600 2.319211e+01 2.086236e+00 1.714629e+01 # Ow SPCE + 1314 438 3 0.423800 2.251393e+01 1.510750e+00 1.760333e+01 # Hw SPCE + 1315 439 3 0.423800 2.653441e+01 1.338040e+01 1.698890e+00 # Hw SPCE + 1316 439 4 -0.847600 2.568911e+01 1.287185e+01 1.862766e+00 # Ow SPCE + 1317 439 3 0.423800 2.578217e+01 1.194475e+01 1.499689e+00 # Hw SPCE + 1318 440 3 0.423800 1.654650e+01 7.351076e+00 4.198674e+00 # Hw SPCE + 1319 440 4 -0.847600 1.720204e+01 6.630419e+00 4.424346e+00 # Ow SPCE + 1320 440 3 0.423800 1.811991e+01 7.022369e+00 4.486733e+00 # Hw SPCE + 1321 441 3 0.423800 1.561748e+01 2.344616e+01 2.579500e+01 # Hw SPCE + 1322 441 4 -0.847600 1.584177e+01 2.276826e+01 2.649512e+01 # Ow SPCE + 1323 441 3 0.423800 1.643484e+01 2.318456e+01 2.718429e+01 # Hw SPCE + 1324 442 3 0.423800 6.712087e+00 1.647363e+01 2.402889e+01 # Hw SPCE + 1325 442 4 -0.847600 7.684457e+00 1.666294e+01 2.389230e+01 # Ow SPCE + 1326 442 3 0.423800 7.794810e+00 1.757954e+01 2.350803e+01 # Hw SPCE + 1327 443 3 0.423800 5.195124e+00 1.484833e+01 1.345621e+01 # Hw SPCE + 1328 443 4 -0.847600 5.562996e+00 1.495140e+01 1.438035e+01 # Ow SPCE + 1329 443 3 0.423800 4.853276e+00 1.472796e+01 1.504847e+01 # Hw SPCE + 1330 444 3 0.423800 8.810832e+00 8.170650e+00 3.650788e+00 # Hw SPCE + 1331 444 4 -0.847600 9.231504e+00 9.063820e+00 3.809800e+00 # Ow SPCE + 1332 444 3 0.423800 8.600516e+00 9.642123e+00 4.326925e+00 # Hw SPCE + 1333 445 3 0.423800 1.481433e+01 2.127865e+01 2.698847e+00 # Hw SPCE + 1334 445 4 -0.847600 1.527661e+01 2.130491e+01 1.812501e+00 # Ow SPCE + 1335 445 3 0.423800 1.564077e+01 2.039825e+01 1.599517e+00 # Hw SPCE + 1336 446 3 0.423800 2.770585e+01 9.745885e+00 6.112819e+00 # Hw SPCE + 1337 446 4 -0.847600 2.769138e+01 8.749499e+00 6.196517e+00 # Ow SPCE + 1338 446 3 0.423800 2.675145e+01 8.420868e+00 6.104123e+00 # Hw SPCE + 1339 447 3 0.423800 1.995729e+01 2.430246e+01 2.248412e+01 # Hw SPCE + 1340 447 4 -0.847600 1.958412e+01 2.507755e+01 2.299401e+01 # Ow SPCE + 1341 447 3 0.423800 1.884602e+01 2.549888e+01 2.246704e+01 # Hw SPCE + 1342 448 3 0.423800 1.497281e+00 1.817499e+01 1.855576e+01 # Hw SPCE + 1343 448 4 -0.847600 1.565131e+00 1.860877e+01 1.945422e+01 # Ow SPCE + 1344 448 3 0.423800 1.511007e+00 1.960184e+01 1.934984e+01 # Hw SPCE + 1345 449 3 0.423800 1.522308e+01 5.358237e+00 1.071042e+01 # Hw SPCE + 1346 449 4 -0.847600 1.552152e+01 4.758830e+00 9.967693e+00 # Ow SPCE + 1347 449 3 0.423800 1.530075e+01 3.810494e+00 1.019556e+01 # Hw SPCE + 1348 450 3 0.423800 2.551853e+01 2.712094e+01 2.391955e+01 # Hw SPCE + 1349 450 4 -0.847600 2.545744e+01 2.641384e+01 2.321508e+01 # Ow SPCE + 1350 450 3 0.423800 2.636236e+01 2.625938e+01 2.281851e+01 # Hw SPCE + 1351 451 3 0.423800 2.385946e+01 4.277050e+00 1.008061e+01 # Hw SPCE + 1352 451 4 -0.847600 2.334099e+01 3.853916e+00 1.082367e+01 # Ow SPCE + 1353 451 3 0.423800 2.397243e+01 3.414585e+00 1.146264e+01 # Hw SPCE + 1354 452 3 0.423800 1.024842e+01 2.543775e+01 1.414465e+01 # Hw SPCE + 1355 452 4 -0.847600 1.115630e+01 2.571591e+01 1.383099e+01 # Ow SPCE + 1356 452 3 0.423800 1.146598e+01 2.650375e+01 1.436336e+01 # Hw SPCE + 1357 453 3 0.423800 1.117636e+01 1.477962e+01 4.921439e+00 # Hw SPCE + 1358 453 4 -0.847600 1.106953e+01 1.411588e+01 4.181144e+00 # Ow SPCE + 1359 453 3 0.423800 1.192150e+01 1.360514e+01 4.065876e+00 # Hw SPCE + 1360 454 3 0.423800 1.155263e+01 2.419941e+01 2.638042e+00 # Hw SPCE + 1361 454 4 -0.847600 1.124181e+01 2.513186e+01 2.453834e+00 # Ow SPCE + 1362 454 3 0.423800 1.199737e+01 2.566636e+01 2.075120e+00 # Hw SPCE + 1363 455 3 0.423800 1.904382e+01 8.719465e+00 1.089114e+01 # Hw SPCE + 1364 455 4 -0.847600 1.879769e+01 8.867065e+00 1.184908e+01 # Ow SPCE + 1365 455 3 0.423800 1.935399e+01 8.274179e+00 1.243132e+01 # Hw SPCE + 1366 456 3 0.423800 2.055866e+01 2.186209e+01 5.026626e+00 # Hw SPCE + 1367 456 4 -0.847600 2.043424e+01 2.280967e+01 4.732347e+00 # Ow SPCE + 1368 456 3 0.423800 1.947974e+01 2.307708e+01 4.864316e+00 # Hw SPCE + 1369 457 3 0.423800 9.488490e+00 2.282360e+01 1.375688e+01 # Hw SPCE + 1370 457 4 -0.847600 1.031447e+01 2.268450e+01 1.321061e+01 # Ow SPCE + 1371 457 3 0.423800 1.029828e+01 2.329670e+01 1.242008e+01 # Hw SPCE + 1372 458 3 0.423800 2.759400e+01 1.561429e+01 1.901357e+01 # Hw SPCE + 1373 458 4 -0.847600 2.771901e+01 1.477632e+01 1.848237e+01 # Ow SPCE + 1374 458 3 0.423800 2.682701e+01 1.442853e+01 1.819361e+01 # Hw SPCE + 1375 459 3 0.423800 9.097112e+00 5.763777e+00 1.055170e+01 # Hw SPCE + 1376 459 4 -0.847600 8.930312e+00 6.009500e+00 1.150658e+01 # Ow SPCE + 1377 459 3 0.423800 9.350086e+00 6.896101e+00 1.170082e+01 # Hw SPCE + 1378 460 3 0.423800 5.431310e+00 2.264163e+01 3.120189e+00 # Hw SPCE + 1379 460 4 -0.847600 5.550080e+00 2.304881e+01 2.214596e+00 # Ow SPCE + 1380 460 3 0.423800 6.336473e+00 2.366641e+01 2.227360e+00 # Hw SPCE + 1381 461 3 0.423800 1.793842e+01 1.486923e+01 5.835118e+00 # Hw SPCE + 1382 461 4 -0.847600 1.846091e+01 1.518650e+01 5.043692e+00 # Ow SPCE + 1383 461 3 0.423800 1.785140e+01 1.566604e+01 4.412394e+00 # Hw SPCE + 1384 462 3 0.423800 2.184585e+00 1.115490e+01 1.453262e+01 # Hw SPCE + 1385 462 4 -0.847600 2.343389e+00 1.213111e+01 1.438500e+01 # Ow SPCE + 1386 462 3 0.423800 1.503737e+00 1.255845e+01 1.404979e+01 # Hw SPCE + 1387 463 3 0.423800 1.441481e+01 3.522791e+00 2.760204e+01 # Hw SPCE + 1388 463 4 -0.847600 1.362346e+01 4.133742e+00 2.762456e+01 # Ow SPCE + 1389 463 3 0.423800 1.393539e+01 5.080332e+00 2.770621e+01 # Hw SPCE + 1390 464 3 0.423800 1.499700e+00 2.188838e+01 2.362087e+01 # Hw SPCE + 1391 464 4 -0.847600 1.945099e+00 2.224829e+01 2.280106e+01 # Ow SPCE + 1392 464 3 0.423800 1.720463e+00 2.166848e+01 2.201789e+01 # Hw SPCE + 1393 465 3 0.423800 2.708400e+01 2.218371e+01 9.205305e+00 # Hw SPCE + 1394 465 4 -0.847600 2.770480e+01 2.226015e+01 8.425070e+00 # Ow SPCE + 1395 465 3 0.423800 2.735466e+01 2.294536e+01 7.786410e+00 # Hw SPCE + 1396 466 3 0.423800 1.333326e+01 1.012770e+01 2.714313e+00 # Hw SPCE + 1397 466 4 -0.847600 1.396010e+01 1.090684e+01 2.710577e+00 # Ow SPCE + 1398 466 3 0.423800 1.343444e+01 1.175750e+01 2.703131e+00 # Hw SPCE + 1399 467 3 0.423800 1.830816e+01 1.219159e+01 1.158591e+01 # Hw SPCE + 1400 467 4 -0.847600 1.755544e+01 1.270612e+01 1.117519e+01 # Ow SPCE + 1401 467 3 0.423800 1.789433e+01 1.322125e+01 1.038792e+01 # Hw SPCE + 1402 468 3 0.423800 2.172042e+01 6.831038e+00 2.770644e+01 # Hw SPCE + 1403 468 4 -0.847600 2.223302e+01 6.193086e+00 2.713176e+01 # Ow SPCE + 1404 468 3 0.423800 2.267323e+01 5.504849e+00 2.770842e+01 # Hw SPCE + 1405 469 3 0.423800 6.268257e+00 1.075389e+01 2.334065e+01 # Hw SPCE + 1406 469 4 -0.847600 7.056234e+00 1.126624e+01 2.368211e+01 # Ow SPCE + 1407 469 3 0.423800 7.274106e+00 1.096339e+01 2.460991e+01 # Hw SPCE + 1408 470 3 0.423800 3.714354e+00 2.000821e+00 1.146332e+01 # Hw SPCE + 1409 470 4 -0.847600 2.897249e+00 1.502381e+00 1.175297e+01 # Ow SPCE + 1410 470 3 0.423800 2.235593e+00 1.482765e+00 1.100342e+01 # Hw SPCE + 1411 471 3 0.423800 2.322907e+01 2.917361e+00 5.997148e+00 # Hw SPCE + 1412 471 4 -0.847600 2.223897e+01 2.777046e+00 5.995080e+00 # Ow SPCE + 1413 471 3 0.423800 2.177665e+01 3.663721e+00 6.003295e+00 # Hw SPCE + 1414 472 3 0.423800 1.763400e+01 1.243773e+01 2.094696e+01 # Hw SPCE + 1415 472 4 -0.847600 1.752266e+01 1.335506e+01 2.056472e+01 # Ow SPCE + 1416 472 3 0.423800 1.837391e+01 1.363744e+01 2.012242e+01 # Hw SPCE + 1417 473 3 0.423800 2.155614e+01 1.654986e+01 2.018860e+01 # Hw SPCE + 1418 473 4 -0.847600 2.107547e+01 1.603549e+01 1.947841e+01 # Ow SPCE + 1419 473 3 0.423800 2.128393e+01 1.642895e+01 1.858301e+01 # Hw SPCE + 1420 474 3 0.423800 1.728050e+01 2.423683e+01 9.871601e+00 # Hw SPCE + 1421 474 4 -0.847600 1.738375e+01 2.347556e+01 9.231428e+00 # Ow SPCE + 1422 474 3 0.423800 1.719527e+01 2.379354e+01 8.302252e+00 # Hw SPCE + 1423 475 3 0.423800 1.650810e+00 6.990915e+00 2.295043e+01 # Hw SPCE + 1424 475 4 -0.847600 2.208121e+00 7.329955e+00 2.370836e+01 # Ow SPCE + 1425 475 3 0.423800 3.171215e+00 7.128177e+00 2.353022e+01 # Hw SPCE + 1426 476 3 0.423800 1.499730e+00 8.992460e+00 8.752017e+00 # Hw SPCE + 1427 476 4 -0.847600 1.510449e+00 9.936633e+00 9.081292e+00 # Ow SPCE + 1428 476 3 0.423800 2.456253e+00 1.025222e+01 9.157852e+00 # Hw SPCE + 1429 477 3 0.423800 1.524357e+00 1.612612e+01 7.337394e+00 # Hw SPCE + 1430 477 4 -0.847600 1.499367e+00 1.628416e+01 8.324511e+00 # Ow SPCE + 1431 477 3 0.423800 1.500368e+00 1.726779e+01 8.504717e+00 # Hw SPCE + 1432 478 3 0.423800 4.508742e+00 2.060049e+01 1.519230e+00 # Hw SPCE + 1433 478 4 -0.847600 5.486779e+00 2.039253e+01 1.505170e+00 # Ow SPCE + 1434 478 3 0.423800 5.616682e+00 1.940102e+01 1.500039e+00 # Hw SPCE + 1435 479 3 0.423800 1.922274e+01 8.093379e+00 8.219502e+00 # Hw SPCE + 1436 479 4 -0.847600 1.916411e+01 7.383197e+00 7.517929e+00 # Ow SPCE + 1437 479 3 0.423800 1.995519e+01 6.775915e+00 7.591466e+00 # Hw SPCE + 1438 480 3 0.423800 1.943784e+01 1.013386e+01 2.597417e+01 # Hw SPCE + 1439 480 4 -0.847600 2.017081e+01 9.453976e+00 2.599674e+01 # Ow SPCE + 1440 480 3 0.423800 2.007103e+01 8.883198e+00 2.681176e+01 # Hw SPCE + 1441 481 3 0.423800 4.192983e+00 2.092863e+01 2.367681e+01 # Hw SPCE + 1442 481 4 -0.847600 3.622627e+00 2.015436e+01 2.340257e+01 # Ow SPCE + 1443 481 3 0.423800 3.162762e+00 1.977780e+01 2.420677e+01 # Hw SPCE + 1444 482 3 0.423800 2.075118e+01 1.717508e+01 2.770677e+01 # Hw SPCE + 1445 482 4 -0.847600 1.976142e+01 1.731709e+01 2.769234e+01 # Ow SPCE + 1446 482 3 0.423800 1.929769e+01 1.643117e+01 2.768228e+01 # Hw SPCE + 1447 483 3 0.423800 6.778056e+00 1.536002e+01 7.209241e+00 # Hw SPCE + 1448 483 4 -0.847600 7.198296e+00 1.626143e+01 7.313492e+00 # Ow SPCE + 1449 483 3 0.423800 6.485256e+00 1.694623e+01 7.463902e+00 # Hw SPCE + 1450 484 3 0.423800 2.425409e+01 5.401110e+00 1.659432e+00 # Hw SPCE + 1451 484 4 -0.847600 2.351087e+01 5.727686e+00 2.243365e+00 # Ow SPCE + 1452 484 3 0.423800 2.360826e+01 6.712456e+00 2.387383e+00 # Hw SPCE + 1453 485 3 0.423800 1.686252e+01 4.577775e+00 1.853409e+01 # Hw SPCE + 1454 485 4 -0.847600 1.717109e+01 5.331094e+00 1.911486e+01 # Ow SPCE + 1455 485 3 0.423800 1.782031e+01 4.985329e+00 1.979233e+01 # Hw SPCE + 1456 486 3 0.423800 2.559447e+01 6.830529e+00 2.554992e+01 # Hw SPCE + 1457 486 4 -0.847600 2.476010e+01 7.328675e+00 2.578589e+01 # Ow SPCE + 1458 486 3 0.423800 2.465753e+01 8.114730e+00 2.517630e+01 # Hw SPCE + 1459 487 3 0.423800 2.618329e+01 1.274776e+01 2.027220e+01 # Hw SPCE + 1460 487 4 -0.847600 2.536296e+01 1.243771e+01 2.075274e+01 # Ow SPCE + 1461 487 3 0.423800 2.554309e+01 1.241004e+01 2.173600e+01 # Hw SPCE + 1462 488 3 0.423800 1.919981e+01 2.661638e+00 2.030213e+01 # Hw SPCE + 1463 488 4 -0.847600 1.973061e+01 2.904574e+00 2.111406e+01 # Ow SPCE + 1464 488 3 0.423800 1.914388e+01 2.856844e+00 2.192244e+01 # Hw SPCE + 1465 489 3 0.423800 2.266744e+01 1.984307e+01 8.978618e+00 # Hw SPCE + 1466 489 4 -0.847600 2.185883e+01 2.037567e+01 9.228600e+00 # Ow SPCE + 1467 489 3 0.423800 2.212644e+01 2.132149e+01 9.412457e+00 # Hw SPCE + 1468 490 3 0.423800 4.817158e+00 1.523570e+00 6.050418e+00 # Hw SPCE + 1469 490 4 -0.847600 4.254228e+00 1.621274e+00 6.871127e+00 # Ow SPCE + 1470 490 3 0.423800 3.291277e+00 1.497598e+00 6.631484e+00 # Hw SPCE + 1471 491 3 0.423800 1.079473e+01 2.139909e+01 1.857674e+01 # Hw SPCE + 1472 491 4 -0.847600 1.177944e+01 2.140440e+01 1.840264e+01 # Ow SPCE + 1473 491 3 0.423800 1.226661e+01 2.114195e+01 1.923559e+01 # Hw SPCE + 1474 492 3 0.423800 2.471848e+01 2.047547e+01 7.260132e+00 # Hw SPCE + 1475 492 4 -0.847600 2.453164e+01 2.145726e+01 7.225866e+00 # Ow SPCE + 1476 492 3 0.423800 2.451936e+01 2.182685e+01 8.154981e+00 # Hw SPCE + 1477 493 3 0.423800 1.868210e+01 2.290815e+01 2.448807e+01 # Hw SPCE + 1478 493 4 -0.847600 1.872346e+01 2.190901e+01 2.448402e+01 # Ow SPCE + 1479 493 3 0.423800 1.929678e+01 2.160222e+01 2.372430e+01 # Hw SPCE + 1480 494 3 0.423800 9.843500e+00 1.140046e+01 2.548708e+01 # Hw SPCE + 1481 494 4 -0.847600 1.054880e+01 1.070283e+01 2.536110e+01 # Ow SPCE + 1482 494 3 0.423800 1.144375e+01 1.114300e+01 2.528825e+01 # Hw SPCE + 1483 495 3 0.423800 6.422993e+00 1.821276e+01 9.903863e+00 # Hw SPCE + 1484 495 4 -0.847600 7.333960e+00 1.850491e+01 9.612681e+00 # Ow SPCE + 1485 495 3 0.423800 8.018713e+00 1.813856e+01 1.024268e+01 # Hw SPCE + 1486 496 3 0.423800 2.471333e+01 2.384780e+01 2.166757e+01 # Hw SPCE + 1487 496 4 -0.847600 2.416185e+01 2.454566e+01 2.121055e+01 # Ow SPCE + 1488 496 3 0.423800 2.476291e+01 2.524546e+01 2.082453e+01 # Hw SPCE + 1489 497 3 0.423800 2.590620e+00 8.091003e+00 2.061080e+01 # Hw SPCE + 1490 497 4 -0.847600 3.231566e+00 7.330610e+00 2.071564e+01 # Ow SPCE + 1491 497 3 0.423800 3.920110e+00 7.372830e+00 1.999168e+01 # Hw SPCE + 1492 498 3 0.423800 8.949464e+00 2.425655e+01 3.695045e+00 # Hw SPCE + 1493 498 4 -0.847600 9.202844e+00 2.412128e+01 4.652907e+00 # Ow SPCE + 1494 498 3 0.423800 9.142579e+00 2.499262e+01 5.139877e+00 # Hw SPCE + 1495 499 3 0.423800 1.764683e+01 2.974023e+00 1.499949e+00 # Hw SPCE + 1496 499 4 -0.847600 1.685020e+01 2.477365e+00 1.844498e+00 # Ow SPCE + 1497 499 3 0.423800 1.705690e+01 1.499622e+00 1.880419e+00 # Hw SPCE + 1498 500 3 0.423800 2.126518e+01 3.913868e+00 1.808240e+01 # Hw SPCE + 1499 500 4 -0.847600 2.045368e+01 3.344904e+00 1.794915e+01 # Ow SPCE + 1500 500 3 0.423800 1.970398e+01 3.909289e+00 1.760359e+01 # Hw SPCE + 1501 501 3 0.423800 1.495876e+00 2.614890e+01 2.082634e+01 # Hw SPCE + 1502 501 4 -0.847600 2.060720e+00 2.545025e+01 2.126548e+01 # Ow SPCE + 1503 501 3 0.423800 1.496549e+00 2.465376e+01 2.148298e+01 # Hw SPCE + 1504 502 3 0.423800 2.279048e+01 9.290222e+00 2.681803e+01 # Hw SPCE + 1505 502 4 -0.847600 2.327017e+01 9.655579e+00 2.761579e+01 # Ow SPCE + 1506 502 3 0.423800 2.416046e+01 9.208611e+00 2.770297e+01 # Hw SPCE + 1507 503 3 0.423800 1.498663e+00 4.051791e+00 1.406843e+01 # Hw SPCE + 1508 503 4 -0.847600 2.227842e+00 4.516378e+00 1.356598e+01 # Ow SPCE + 1509 503 3 0.423800 2.947213e+00 3.859735e+00 1.333943e+01 # Hw SPCE + 1510 504 3 0.423800 4.121509e+00 1.297824e+01 1.026964e+01 # Hw SPCE + 1511 504 4 -0.847600 3.726321e+00 1.373934e+01 1.078398e+01 # Ow SPCE + 1512 504 3 0.423800 3.570218e+00 1.345664e+01 1.173040e+01 # Hw SPCE + 1513 505 3 0.423800 1.938062e+01 1.410367e+01 8.241157e+00 # Hw SPCE + 1514 505 4 -0.847600 1.995758e+01 1.491592e+01 8.155362e+00 # Ow SPCE + 1515 505 3 0.423800 2.066193e+01 1.475299e+01 7.464465e+00 # Hw SPCE + 1516 506 3 0.423800 1.635093e+01 4.629187e+00 2.599280e+01 # Hw SPCE + 1517 506 4 -0.847600 1.660343e+01 5.572751e+00 2.577847e+01 # Ow SPCE + 1518 506 3 0.423800 1.597027e+01 6.198813e+00 2.623361e+01 # Hw SPCE + 1519 507 3 0.423800 2.572095e+01 1.411800e+01 2.664163e+01 # Hw SPCE + 1520 507 4 -0.847600 2.489025e+01 1.466440e+01 2.653495e+01 # Ow SPCE + 1521 507 3 0.423800 2.417927e+01 1.431235e+01 2.714369e+01 # Hw SPCE + 1522 508 3 0.423800 2.106512e+01 3.934685e+00 1.521472e+01 # Hw SPCE + 1523 508 4 -0.847600 2.145982e+01 3.015920e+00 1.522367e+01 # Ow SPCE + 1524 508 3 0.423800 2.073659e+01 2.343985e+00 1.538314e+01 # Hw SPCE + 1525 509 3 0.423800 1.747101e+01 1.089516e+01 1.867742e+01 # Hw SPCE + 1526 509 4 -0.847600 1.750084e+01 1.180616e+01 1.826610e+01 # Ow SPCE + 1527 509 3 0.423800 1.671577e+01 1.192311e+01 1.765784e+01 # Hw SPCE + 1528 510 3 0.423800 2.149389e+01 8.833650e+00 6.611416e+00 # Hw SPCE + 1529 510 4 -0.847600 2.177394e+01 9.611791e+00 7.173615e+00 # Ow SPCE + 1530 510 3 0.423800 2.254669e+01 9.345700e+00 7.749852e+00 # Hw SPCE + 1531 511 3 0.423800 3.791408e+00 1.897825e+01 1.012530e+01 # Hw SPCE + 1532 511 4 -0.847600 3.851687e+00 1.885137e+01 9.135211e+00 # Ow SPCE + 1533 511 3 0.423800 3.179880e+00 1.943767e+01 8.682525e+00 # Hw SPCE + 1534 512 3 0.423800 1.252372e+01 2.047991e+01 2.549174e+01 # Hw SPCE + 1535 512 4 -0.847600 1.324747e+01 2.111712e+01 2.522688e+01 # Ow SPCE + 1536 512 3 0.423800 1.305955e+01 2.201712e+01 2.562020e+01 # Hw SPCE + 1537 513 3 0.423800 9.857980e+00 8.140566e+00 9.299584e+00 # Hw SPCE + 1538 513 4 -0.847600 1.080806e+01 7.847241e+00 9.193255e+00 # Ow SPCE + 1539 513 3 0.423800 1.136372e+01 8.620982e+00 8.889004e+00 # Hw SPCE + 1540 514 3 0.423800 2.468682e+01 1.540730e+01 1.499507e+00 # Hw SPCE + 1541 514 4 -0.847600 2.388089e+01 1.498355e+01 1.912937e+00 # Ow SPCE + 1542 514 3 0.423800 2.305466e+01 1.541498e+01 1.550717e+00 # Hw SPCE + 1543 515 3 0.423800 1.464646e+01 2.252692e+01 1.926250e+01 # Hw SPCE + 1544 515 4 -0.847600 1.547386e+01 2.308846e+01 1.925340e+01 # Ow SPCE + 1545 515 3 0.423800 1.626223e+01 2.251673e+01 1.902626e+01 # Hw SPCE + 1546 516 3 0.423800 2.767962e+01 2.118986e+01 2.645961e+01 # Hw SPCE + 1547 516 4 -0.847600 2.770572e+01 2.108694e+01 2.745396e+01 # Ow SPCE + 1548 516 3 0.423800 2.734198e+01 2.019016e+01 2.770589e+01 # Hw SPCE + 1549 517 3 0.423800 5.473025e+00 1.539565e+01 1.766372e+01 # Hw SPCE + 1550 517 4 -0.847600 5.457163e+00 1.532146e+01 1.866084e+01 # Ow SPCE + 1551 517 3 0.423800 5.719911e+00 1.439500e+01 1.893036e+01 # Hw SPCE + 1552 518 3 0.423800 1.355721e+01 1.609064e+01 7.981517e+00 # Hw SPCE + 1553 518 4 -0.847600 1.451195e+01 1.585086e+01 7.805517e+00 # Ow SPCE + 1554 518 3 0.423800 1.510515e+01 1.659197e+01 8.119965e+00 # Hw SPCE + 1555 519 3 0.423800 1.185686e+01 2.756045e+01 1.746044e+01 # Hw SPCE + 1556 519 4 -0.847600 1.271387e+01 2.750488e+01 1.694815e+01 # Ow SPCE + 1557 519 3 0.423800 1.289860e+01 2.655139e+01 1.670998e+01 # Hw SPCE + 1558 520 3 0.423800 2.770610e+01 1.433506e+01 2.192258e+01 # Hw SPCE + 1559 520 4 -0.847600 2.713948e+01 1.511976e+01 2.217392e+01 # Ow SPCE + 1560 520 3 0.423800 2.770524e+01 1.594383e+01 2.220271e+01 # Hw SPCE + 1561 521 3 0.423800 1.499493e+01 1.238797e+01 2.007948e+01 # Hw SPCE + 1562 521 4 -0.847600 1.464506e+01 1.280227e+01 1.923927e+01 # Ow SPCE + 1563 521 3 0.423800 1.485236e+01 1.378055e+01 1.923864e+01 # Hw SPCE + 1564 522 3 0.423800 1.136191e+01 6.926399e+00 2.399031e+01 # Hw SPCE + 1565 522 4 -0.847600 1.054592e+01 7.370139e+00 2.436079e+01 # Ow SPCE + 1566 522 3 0.423800 9.932311e+00 6.677061e+00 2.473911e+01 # Hw SPCE + 1567 523 3 0.423800 7.548290e+00 2.174968e+00 3.349358e+00 # Hw SPCE + 1568 523 4 -0.847600 6.864919e+00 1.475454e+00 3.558363e+00 # Ow SPCE + 1569 523 3 0.423800 5.952602e+00 1.884488e+00 3.539162e+00 # Hw SPCE + 1570 524 3 0.423800 2.257539e+01 7.886933e+00 2.106609e+01 # Hw SPCE + 1571 524 4 -0.847600 2.236455e+01 7.157236e+00 2.041564e+01 # Ow SPCE + 1572 524 3 0.423800 2.320865e+01 6.845285e+00 1.997954e+01 # Hw SPCE + 1573 525 3 0.423800 1.931716e+01 2.614213e+01 1.741829e+01 # Hw SPCE + 1574 525 4 -0.847600 1.896046e+01 2.707452e+01 1.747657e+01 # Ow SPCE + 1575 525 3 0.423800 1.970938e+01 2.770594e+01 1.767766e+01 # Hw SPCE + 1576 526 3 0.423800 1.293280e+01 1.317757e+01 1.712150e+01 # Hw SPCE + 1577 526 4 -0.847600 1.315759e+01 1.415177e+01 1.710169e+01 # Ow SPCE + 1578 526 3 0.423800 1.254740e+01 1.464728e+01 1.771987e+01 # Hw SPCE + 1579 527 3 0.423800 7.790007e+00 6.046852e+00 2.770758e+01 # Hw SPCE + 1580 527 4 -0.847600 6.829260e+00 5.769427e+00 2.770728e+01 # Ow SPCE + 1581 527 3 0.423800 6.770591e+00 4.771151e+00 2.770535e+01 # Hw SPCE + 1582 528 3 0.423800 1.123375e+01 2.298556e+01 2.380651e+01 # Hw SPCE + 1583 528 4 -0.847600 1.075845e+01 2.212317e+01 2.398080e+01 # Ow SPCE + 1584 528 3 0.423800 1.039779e+01 2.212396e+01 2.491350e+01 # Hw SPCE + 1585 529 3 0.423800 4.200882e+00 1.931622e+01 2.770757e+01 # Hw SPCE + 1586 529 4 -0.847600 5.175713e+00 1.953916e+01 2.770789e+01 # Ow SPCE + 1587 529 3 0.423800 5.710832e+00 1.869439e+01 2.770832e+01 # Hw SPCE + 1588 530 3 0.423800 2.770456e+01 1.697514e+01 9.342626e+00 # Hw SPCE + 1589 530 4 -0.847600 2.770706e+01 1.614854e+01 9.905419e+00 # Ow SPCE + 1590 530 3 0.423800 2.770253e+01 1.534242e+01 9.313697e+00 # Hw SPCE + 1591 531 3 0.423800 1.832884e+01 7.670320e+00 2.009972e+01 # Hw SPCE + 1592 531 4 -0.847600 1.770977e+01 8.379274e+00 1.976188e+01 # Ow SPCE + 1593 531 3 0.423800 1.728273e+01 8.071375e+00 1.891168e+01 # Hw SPCE + 1594 532 3 0.423800 1.164885e+01 2.369859e+00 6.675939e+00 # Hw SPCE + 1595 532 4 -0.847600 1.119973e+01 1.488536e+00 6.822766e+00 # Ow SPCE + 1596 532 3 0.423800 1.021557e+01 1.629733e+00 6.930003e+00 # Hw SPCE + 1597 533 3 0.423800 1.736192e+01 1.608261e+01 2.086977e+01 # Hw SPCE + 1598 533 4 -0.847600 1.663485e+01 1.658639e+01 2.133622e+01 # Ow SPCE + 1599 533 3 0.423800 1.582226e+01 1.661428e+01 2.075406e+01 # Hw SPCE + 1600 534 3 0.423800 2.770538e+01 1.618975e+01 6.697811e+00 # Hw SPCE + 1601 534 4 -0.847600 2.683077e+01 1.586285e+01 6.339763e+00 # Ow SPCE + 1602 534 3 0.423800 2.644970e+01 1.654559e+01 5.716346e+00 # Hw SPCE + 1603 535 3 0.423800 1.073071e+01 3.382764e+00 1.994761e+00 # Hw SPCE + 1604 535 4 -0.847600 1.068786e+01 2.506336e+00 2.474384e+00 # Ow SPCE + 1605 535 3 0.423800 1.061173e+01 1.764903e+00 1.807690e+00 # Hw SPCE + 1606 536 3 0.423800 5.975184e+00 9.418923e+00 1.756302e+01 # Hw SPCE + 1607 536 4 -0.847600 6.920951e+00 9.718084e+00 1.768962e+01 # Ow SPCE + 1608 536 3 0.423800 6.942337e+00 1.070925e+01 1.782049e+01 # Hw SPCE + 1609 537 3 0.423800 1.360924e+01 2.146817e+01 1.387145e+01 # Hw SPCE + 1610 537 4 -0.847600 1.450822e+01 2.119277e+01 1.353090e+01 # Ow SPCE + 1611 537 3 0.423800 1.516476e+01 2.119288e+01 1.428519e+01 # Hw SPCE + 1612 538 3 0.423800 8.874645e+00 2.735638e+00 1.567786e+01 # Hw SPCE + 1613 538 4 -0.847600 8.841213e+00 1.743745e+00 1.555526e+01 # Ow SPCE + 1614 538 3 0.423800 9.281324e+00 1.499682e+00 1.469112e+01 # Hw SPCE + 1615 539 3 0.423800 2.677837e+01 2.727822e+01 1.521683e+01 # Hw SPCE + 1616 539 4 -0.847600 2.716773e+01 2.651889e+01 1.573819e+01 # Ow SPCE + 1617 539 3 0.423800 2.770480e+01 2.593640e+01 1.512805e+01 # Hw SPCE + 1618 540 3 0.423800 1.348931e+01 2.050695e+01 1.644491e+01 # Hw SPCE + 1619 540 4 -0.847600 1.379303e+01 1.955419e+01 1.644174e+01 # Ow SPCE + 1620 540 3 0.423800 1.479253e+01 1.952299e+01 1.643578e+01 # Hw SPCE + 1621 541 3 0.423800 2.712765e+01 2.770458e+01 1.499784e+00 # Hw SPCE + 1622 541 4 -0.847600 2.710752e+01 2.724363e+01 2.386980e+00 # Ow SPCE + 1623 541 3 0.423800 2.619044e+01 2.731545e+01 2.779174e+00 # Hw SPCE + 1624 542 3 0.423800 9.946949e+00 2.110450e+01 2.770454e+01 # Hw SPCE + 1625 542 4 -0.847600 9.160696e+00 2.085784e+01 2.713800e+01 # Ow SPCE + 1626 542 3 0.423800 8.468408e+00 2.041129e+01 2.770486e+01 # Hw SPCE + 1627 543 3 0.423800 1.504399e+00 1.083302e+01 2.009960e+01 # Hw SPCE + 1628 543 4 -0.847600 1.816408e+00 1.177936e+01 2.018384e+01 # Ow SPCE + 1629 543 3 0.423800 2.807855e+00 1.181584e+01 2.005853e+01 # Hw SPCE + 1630 544 3 0.423800 2.543910e+01 2.947611e+00 2.768656e+01 # Hw SPCE + 1631 544 4 -0.847600 2.451490e+01 2.595735e+00 2.753807e+01 # Ow SPCE + 1632 544 3 0.423800 2.455905e+01 1.616936e+00 2.733806e+01 # Hw SPCE + 1633 545 3 0.423800 2.361457e+01 1.312219e+01 1.230861e+01 # Hw SPCE + 1634 545 4 -0.847600 2.413492e+01 1.356531e+01 1.303860e+01 # Ow SPCE + 1635 545 3 0.423800 2.440618e+01 1.288209e+01 1.371657e+01 # Hw SPCE + 1636 546 3 0.423800 1.870442e+01 2.642254e+01 9.001379e+00 # Hw SPCE + 1637 546 4 -0.847600 1.888946e+01 2.680197e+01 8.094851e+00 # Ow SPCE + 1638 546 3 0.423800 1.831281e+01 2.634447e+01 7.417974e+00 # Hw SPCE + 1639 547 3 0.423800 1.955187e+01 2.669861e+01 1.982066e+00 # Hw SPCE + 1640 547 4 -0.847600 1.983701e+01 2.765621e+01 2.023180e+00 # Ow SPCE + 1641 547 3 0.423800 2.083300e+01 2.770447e+01 2.098561e+00 # Hw SPCE + 1642 548 3 0.423800 5.421499e+00 2.757790e+01 1.294457e+01 # Hw SPCE + 1643 548 4 -0.847600 5.110506e+00 2.770464e+01 1.388649e+01 # Ow SPCE + 1644 548 3 0.423800 4.115657e+00 2.761068e+01 1.392453e+01 # Hw SPCE + 1645 549 3 0.423800 1.667681e+01 2.723516e+01 2.218951e+01 # Hw SPCE + 1646 549 4 -0.847600 1.593196e+01 2.771570e+01 2.265241e+01 # Ow SPCE + 1647 549 3 0.423800 1.507418e+01 2.754768e+01 2.216664e+01 # Hw SPCE + 1648 550 3 0.423800 2.433245e+01 2.342839e+01 1.128065e+01 # Hw SPCE + 1649 550 4 -0.847600 2.415467e+01 2.258524e+01 1.077321e+01 # Ow SPCE + 1650 550 3 0.423800 2.415864e+01 2.180938e+01 1.140410e+01 # Hw SPCE + 1651 551 3 0.423800 1.837587e+01 2.123822e+01 2.725995e+01 # Hw SPCE + 1652 551 4 -0.847600 1.779349e+01 2.043021e+01 2.734918e+01 # Ow SPCE + 1653 551 3 0.423800 1.833384e+01 1.966748e+01 2.770453e+01 # Hw SPCE + 1654 552 3 0.423800 1.592706e+01 1.936515e+00 2.435957e+01 # Hw SPCE + 1655 552 4 -0.847600 1.505896e+01 1.499035e+00 2.412505e+01 # Ow SPCE + 1656 552 3 0.423800 1.454993e+01 2.085140e+00 2.349467e+01 # Hw SPCE + 1657 553 3 0.423800 1.747565e+01 1.731294e+01 9.312832e+00 # Hw SPCE + 1658 553 4 -0.847600 1.766196e+01 1.635124e+01 9.111737e+00 # Ow SPCE + 1659 553 3 0.423800 1.809084e+01 1.592158e+01 9.906376e+00 # Hw SPCE + 1660 554 3 0.423800 8.312156e+00 2.203891e+01 1.687596e+01 # Hw SPCE + 1661 554 4 -0.847600 8.145446e+00 2.107334e+01 1.667629e+01 # Ow SPCE + 1662 554 3 0.423800 7.160271e+00 2.090436e+01 1.664666e+01 # Hw SPCE + 1663 555 3 0.423800 1.452310e+01 2.241336e+01 9.977204e+00 # Hw SPCE + 1664 555 4 -0.847600 1.467835e+01 2.336383e+01 9.707951e+00 # Ow SPCE + 1665 555 3 0.423800 1.427486e+01 2.397365e+01 1.039009e+01 # Hw SPCE + 1666 556 3 0.423800 2.770573e+01 9.991646e+00 1.639356e+01 # Hw SPCE + 1667 556 4 -0.847600 2.733485e+01 1.000499e+01 1.546498e+01 # Ow SPCE + 1668 556 3 0.423800 2.770500e+01 9.233753e+00 1.494711e+01 # Hw SPCE + 1669 557 3 0.423800 2.255789e+01 1.833507e+01 1.626641e+01 # Hw SPCE + 1670 557 4 -0.847600 2.351546e+01 1.820880e+01 1.652545e+01 # Ow SPCE + 1671 557 3 0.423800 2.406042e+01 1.802400e+01 1.570760e+01 # Hw SPCE + 1672 558 3 0.423800 1.525572e+01 2.770743e+01 1.200379e+01 # Hw SPCE + 1673 558 4 -0.847600 1.484040e+01 2.707735e+01 1.265992e+01 # Ow SPCE + 1674 558 3 0.423800 1.406834e+01 2.752601e+01 1.311006e+01 # Hw SPCE + 1675 559 3 0.423800 1.658932e+01 1.906188e+01 1.328318e+01 # Hw SPCE + 1676 559 4 -0.847600 1.675201e+01 1.815055e+01 1.290501e+01 # Ow SPCE + 1677 559 3 0.423800 1.758478e+01 1.776758e+01 1.330480e+01 # Hw SPCE + 1678 560 3 0.423800 1.004229e+01 1.712720e+01 2.079854e+01 # Hw SPCE + 1679 560 4 -0.847600 1.063564e+01 1.789587e+01 2.103746e+01 # Ow SPCE + 1680 560 3 0.423800 1.010311e+01 1.874227e+01 2.103197e+01 # Hw SPCE + 1681 561 3 0.423800 2.500505e+01 1.070351e+01 4.512067e+00 # Hw SPCE + 1682 561 4 -0.847600 2.573603e+01 1.010670e+01 4.181178e+00 # Ow SPCE + 1683 561 3 0.423800 2.648741e+01 1.066421e+01 3.828189e+00 # Hw SPCE + 1684 562 3 0.423800 1.210303e+01 1.800383e+01 9.349879e+00 # Hw SPCE + 1685 562 4 -0.847600 1.113080e+01 1.778888e+01 9.442458e+00 # Ow SPCE + 1686 562 3 0.423800 1.060025e+01 1.863653e+01 9.439283e+00 # Hw SPCE + 1687 563 3 0.423800 1.030762e+01 7.414060e+00 2.769564e+01 # Hw SPCE + 1688 563 4 -0.847600 1.049207e+01 6.470196e+00 2.742160e+01 # Ow SPCE + 1689 563 3 0.423800 1.141031e+01 6.209855e+00 2.772004e+01 # Hw SPCE + 1690 564 3 0.423800 4.398211e+00 2.689864e+01 2.124419e+01 # Hw SPCE + 1691 564 4 -0.847600 4.266022e+00 2.770576e+01 2.181959e+01 # Ow SPCE + 1692 564 3 0.423800 3.351717e+00 2.768078e+01 2.222384e+01 # Hw SPCE + 1693 565 3 0.423800 8.283521e+00 2.495708e+01 9.955134e+00 # Hw SPCE + 1694 565 4 -0.847600 7.965370e+00 2.543617e+01 1.077322e+01 # Ow SPCE + 1695 565 3 0.423800 8.600427e+00 2.526670e+01 1.152686e+01 # Hw SPCE + 1696 566 3 0.423800 2.718771e+01 5.401651e+00 2.294482e+01 # Hw SPCE + 1697 566 4 -0.847600 2.770619e+01 6.078594e+00 2.346725e+01 # Ow SPCE + 1698 566 3 0.423800 2.727173e+01 6.974594e+00 2.337542e+01 # Hw SPCE + 1699 567 3 0.423800 1.344671e+01 1.859690e+01 1.608430e+00 # Hw SPCE + 1700 567 4 -0.847600 1.362491e+01 1.880297e+01 2.570605e+00 # Ow SPCE + 1701 567 3 0.423800 1.316244e+01 1.812923e+01 3.146969e+00 # Hw SPCE + 1702 568 3 0.423800 1.583162e+01 2.444348e+01 5.926474e+00 # Hw SPCE + 1703 568 4 -0.847600 1.499075e+01 2.459672e+01 6.445563e+00 # Ow SPCE + 1704 568 3 0.423800 1.478045e+01 2.378288e+01 6.987262e+00 # Hw SPCE + 1705 569 3 0.423800 9.922789e+00 5.193782e+00 2.202243e+01 # Hw SPCE + 1706 569 4 -0.847600 9.563582e+00 6.125784e+00 2.207083e+01 # Ow SPCE + 1707 569 3 0.423800 8.644820e+00 6.149777e+00 2.167675e+01 # Hw SPCE + 1708 570 3 0.423800 8.914720e+00 8.315418e+00 1.641874e+01 # Hw SPCE + 1709 570 4 -0.847600 9.302874e+00 8.063947e+00 1.553212e+01 # Ow SPCE + 1710 570 3 0.423800 1.015658e+01 8.564357e+00 1.538800e+01 # Hw SPCE + 1711 571 3 0.423800 1.175235e+01 1.796050e+01 1.792472e+01 # Hw SPCE + 1712 571 4 -0.847600 1.132726e+01 1.866461e+01 1.849353e+01 # Ow SPCE + 1713 571 3 0.423800 1.034732e+01 1.870417e+01 1.829820e+01 # Hw SPCE + 1714 572 3 0.423800 2.334407e+01 2.469584e+01 1.753610e+01 # Hw SPCE + 1715 572 4 -0.847600 2.274051e+01 2.390140e+01 1.760386e+01 # Ow SPCE + 1716 572 3 0.423800 2.178874e+01 2.420714e+01 1.762968e+01 # Hw SPCE + 1717 573 3 0.423800 1.560477e+01 2.702754e+01 1.716266e+00 # Hw SPCE + 1718 573 4 -0.847600 1.525408e+01 2.737955e+01 2.584082e+00 # Ow SPCE + 1719 573 3 0.423800 1.428469e+01 2.760432e+01 2.485249e+00 # Hw SPCE + 1720 574 3 0.423800 7.381621e+00 2.092978e+01 1.938298e+01 # Hw SPCE + 1721 574 4 -0.847600 8.033211e+00 2.166093e+01 1.958511e+01 # Ow SPCE + 1722 574 3 0.423800 7.576710e+00 2.237804e+01 2.011176e+01 # Hw SPCE + 1723 575 3 0.423800 1.345344e+01 1.285413e+01 6.248165e+00 # Hw SPCE + 1724 575 4 -0.847600 1.335825e+01 1.348350e+01 7.019426e+00 # Ow SPCE + 1725 575 3 0.423800 1.239316e+01 1.371343e+01 7.144852e+00 # Hw SPCE + 1726 576 3 0.423800 1.684996e+01 1.496546e+00 2.112863e+01 # Hw SPCE + 1727 576 4 -0.847600 1.612315e+01 1.500121e+00 2.044180e+01 # Ow SPCE + 1728 576 3 0.423800 1.523334e+01 1.502605e+00 2.089813e+01 # Hw SPCE + 1729 577 3 0.423800 1.259795e+01 6.059961e+00 1.028903e+01 # Hw SPCE + 1730 577 4 -0.847600 1.265203e+01 6.809136e+00 1.094919e+01 # Ow SPCE + 1731 577 3 0.423800 1.210535e+01 6.583051e+00 1.175544e+01 # Hw SPCE + 1732 578 3 0.423800 1.175266e+01 1.642499e+01 1.504706e+00 # Hw SPCE + 1733 578 4 -0.847600 1.124046e+01 1.563939e+01 1.851816e+00 # Ow SPCE + 1734 578 3 0.423800 1.171187e+01 1.479512e+01 1.596895e+00 # Hw SPCE + 1735 579 3 0.423800 1.964008e+01 1.500636e+01 2.214316e+01 # Hw SPCE + 1736 579 4 -0.847600 2.038415e+01 1.503982e+01 2.281043e+01 # Ow SPCE + 1737 579 3 0.423800 2.013831e+01 1.449401e+01 2.361146e+01 # Hw SPCE + 1738 580 3 0.423800 6.359780e+00 1.494462e+00 9.725939e+00 # Hw SPCE + 1739 580 4 -0.847600 5.623160e+00 2.122431e+00 9.474851e+00 # Ow SPCE + 1740 580 3 0.423800 5.796855e+00 3.019459e+00 9.881263e+00 # Hw SPCE + 1741 581 3 0.423800 2.339449e+01 2.716322e+01 4.184562e+00 # Hw SPCE + 1742 581 4 -0.847600 2.365407e+01 2.624102e+01 4.471228e+00 # Ow SPCE + 1743 581 3 0.423800 2.284652e+01 2.575711e+01 4.808419e+00 # Hw SPCE + 1744 582 3 0.423800 2.817273e+00 2.461806e+01 5.932450e+00 # Hw SPCE + 1745 582 4 -0.847600 2.010189e+00 2.426140e+01 6.402994e+00 # Ow SPCE + 1746 582 3 0.423800 1.499435e+00 2.366530e+01 5.783477e+00 # Hw SPCE + 1747 583 3 0.423800 1.234255e+01 1.396176e+01 2.037507e+01 # Hw SPCE + 1748 583 4 -0.847600 1.153188e+01 1.453863e+01 2.027487e+01 # Ow SPCE + 1749 583 3 0.423800 1.071536e+01 1.396252e+01 2.023761e+01 # Hw SPCE + 1750 584 3 0.423800 2.810909e+00 2.179238e+01 7.310922e+00 # Hw SPCE + 1751 584 4 -0.847600 3.683406e+00 2.228090e+01 7.320812e+00 # Ow SPCE + 1752 584 3 0.423800 4.405822e+00 2.166653e+01 7.638090e+00 # Hw SPCE + 1753 585 3 0.423800 8.448996e+00 2.068506e+01 1.886024e+00 # Hw SPCE + 1754 585 4 -0.847600 8.120115e+00 2.158805e+01 1.609529e+00 # Ow SPCE + 1755 585 3 0.423800 8.825993e+00 2.227138e+01 1.796065e+00 # Hw SPCE + 1756 586 3 0.423800 1.552035e+01 1.189869e+01 1.283899e+01 # Hw SPCE + 1757 586 4 -0.847600 1.524184e+01 1.098045e+01 1.255745e+01 # Ow SPCE + 1758 586 3 0.423800 1.602690e+01 1.036326e+01 1.260993e+01 # Hw SPCE + 1759 587 3 0.423800 1.037404e+01 1.680250e+01 1.410571e+01 # Hw SPCE + 1760 587 4 -0.847600 9.390321e+00 1.671053e+01 1.395132e+01 # Ow SPCE + 1761 587 3 0.423800 9.132024e+00 1.574640e+01 1.401253e+01 # Hw SPCE + 1762 588 3 0.423800 1.925143e+01 2.771036e+01 1.136823e+01 # Hw SPCE + 1763 588 4 -0.847600 1.825753e+01 2.762221e+01 1.143454e+01 # Ow SPCE + 1764 588 3 0.423800 1.797827e+01 2.770904e+01 1.239082e+01 # Hw SPCE + 1765 589 3 0.423800 5.368954e+00 1.319885e+01 2.246010e+01 # Hw SPCE + 1766 589 4 -0.847600 5.623630e+00 1.391457e+01 2.311039e+01 # Ow SPCE + 1767 589 3 0.423800 4.872485e+00 1.456903e+01 2.319682e+01 # Hw SPCE + 1768 590 3 0.423800 2.502067e+01 2.248026e+01 2.658176e+01 # Hw SPCE + 1769 590 4 -0.847600 2.503552e+01 2.164180e+01 2.712652e+01 # Ow SPCE + 1770 590 3 0.423800 2.494862e+01 2.084997e+01 2.652199e+01 # Hw SPCE + 1771 591 3 0.423800 2.771210e+01 9.857496e+00 2.349471e+01 # Hw SPCE + 1772 591 4 -0.847600 2.758172e+01 1.077731e+01 2.312465e+01 # Ow SPCE + 1773 591 3 0.423800 2.770545e+01 1.075806e+01 2.213252e+01 # Hw SPCE + 1774 592 3 0.423800 2.236208e+01 1.289022e+01 1.568659e+01 # Hw SPCE + 1775 592 4 -0.847600 2.242230e+01 1.193201e+01 1.596625e+01 # Ow SPCE + 1776 592 3 0.423800 2.300802e+01 1.185651e+01 1.677324e+01 # Hw SPCE + 1777 593 3 0.423800 1.988201e+01 1.279194e+01 1.687017e+01 # Hw SPCE + 1778 593 4 -0.847600 2.021378e+01 1.300179e+01 1.778990e+01 # Ow SPCE + 1779 593 3 0.423800 2.066551e+01 1.219616e+01 1.817317e+01 # Hw SPCE + 1780 594 3 0.423800 1.468952e+01 2.770673e+01 5.255360e+00 # Hw SPCE + 1781 594 4 -0.847600 1.548366e+01 2.712680e+01 5.437112e+00 # Ow SPCE + 1782 594 3 0.423800 1.628119e+01 2.770158e+01 5.620343e+00 # Hw SPCE + 1783 595 3 0.423800 8.562539e+00 2.043599e+01 4.622579e+00 # Hw SPCE + 1784 595 4 -0.847600 8.510816e+00 2.140691e+01 4.856324e+00 # Ow SPCE + 1785 595 3 0.423800 7.721353e+00 2.181791e+01 4.400437e+00 # Hw SPCE + 1786 596 3 0.423800 2.770600e+01 1.600690e+01 2.686389e+01 # Hw SPCE + 1787 596 4 -0.847600 2.714850e+01 1.666860e+01 2.736525e+01 # Ow SPCE + 1788 596 3 0.423800 2.770517e+01 1.746675e+01 2.759565e+01 # Hw SPCE + 1789 597 3 0.423800 1.659849e+01 2.708928e+01 1.606821e+01 # Hw SPCE + 1790 597 4 -0.847600 1.561098e+01 2.693173e+01 1.606789e+01 # Ow SPCE + 1791 597 3 0.423800 1.515025e+01 2.770484e+01 1.563196e+01 # Hw SPCE + 1792 598 3 0.423800 2.769724e+01 2.030543e+01 2.142814e+01 # Hw SPCE + 1793 598 4 -0.847600 2.694008e+01 2.095316e+01 2.151277e+01 # Ow SPCE + 1794 598 3 0.423800 2.730269e+01 2.188246e+01 2.158290e+01 # Hw SPCE + 1795 599 3 0.423800 8.916687e+00 5.895426e+00 1.772221e+01 # Hw SPCE + 1796 599 4 -0.847600 9.042735e+00 5.158155e+00 1.705847e+01 # Ow SPCE + 1797 599 3 0.423800 9.690399e+00 5.450297e+00 1.635478e+01 # Hw SPCE + 1798 600 3 0.423800 1.753578e+01 1.707234e+01 2.389138e+01 # Hw SPCE + 1799 600 4 -0.847600 1.803190e+01 1.621348e+01 2.401877e+01 # Ow SPCE + 1800 600 3 0.423800 1.745017e+01 1.544840e+01 2.374267e+01 # Hw SPCE + +Bonds + + 1 1 2 1 # Ow-Hw + 2 1 3 2 # Ow-Hw + 3 1 5 4 # Ow-Hw + 4 1 6 5 # Ow-Hw + 5 1 8 7 # Ow-Hw + 6 1 9 8 # Ow-Hw + 7 1 11 10 # Ow-Hw + 8 1 12 11 # Ow-Hw + 9 1 14 13 # Ow-Hw + 10 1 15 14 # Ow-Hw + 11 1 17 16 # Ow-Hw + 12 1 18 17 # Ow-Hw + 13 1 20 19 # Ow-Hw + 14 1 21 20 # Ow-Hw + 15 1 23 22 # Ow-Hw + 16 1 24 23 # Ow-Hw + 17 1 26 25 # Ow-Hw + 18 1 27 26 # Ow-Hw + 19 1 29 28 # Ow-Hw + 20 1 30 29 # Ow-Hw + 21 1 32 31 # Ow-Hw + 22 1 33 32 # Ow-Hw + 23 1 35 34 # Ow-Hw + 24 1 36 35 # Ow-Hw + 25 1 38 37 # Ow-Hw + 26 1 39 38 # Ow-Hw + 27 1 41 40 # Ow-Hw + 28 1 42 41 # Ow-Hw + 29 1 44 43 # Ow-Hw + 30 1 45 44 # Ow-Hw + 31 1 47 46 # Ow-Hw + 32 1 48 47 # Ow-Hw + 33 1 50 49 # Ow-Hw + 34 1 51 50 # Ow-Hw + 35 1 53 52 # Ow-Hw + 36 1 54 53 # Ow-Hw + 37 1 56 55 # Ow-Hw + 38 1 57 56 # Ow-Hw + 39 1 59 58 # Ow-Hw + 40 1 60 59 # Ow-Hw + 41 1 62 61 # Ow-Hw + 42 1 63 62 # Ow-Hw + 43 1 65 64 # Ow-Hw + 44 1 66 65 # Ow-Hw + 45 1 68 67 # Ow-Hw + 46 1 69 68 # Ow-Hw + 47 1 71 70 # Ow-Hw + 48 1 72 71 # Ow-Hw + 49 1 74 73 # Ow-Hw + 50 1 75 74 # Ow-Hw + 51 1 77 76 # Ow-Hw + 52 1 78 77 # Ow-Hw + 53 1 80 79 # Ow-Hw + 54 1 81 80 # Ow-Hw + 55 1 83 82 # Ow-Hw + 56 1 84 83 # Ow-Hw + 57 1 86 85 # Ow-Hw + 58 1 87 86 # Ow-Hw + 59 1 89 88 # Ow-Hw + 60 1 90 89 # Ow-Hw + 61 1 92 91 # Ow-Hw + 62 1 93 92 # Ow-Hw + 63 1 95 94 # Ow-Hw + 64 1 96 95 # Ow-Hw + 65 1 98 97 # Ow-Hw + 66 1 99 98 # Ow-Hw + 67 1 101 100 # Ow-Hw + 68 1 102 101 # Ow-Hw + 69 1 104 103 # Ow-Hw + 70 1 105 104 # Ow-Hw + 71 1 107 106 # Ow-Hw + 72 1 108 107 # Ow-Hw + 73 1 110 109 # Ow-Hw + 74 1 111 110 # Ow-Hw + 75 1 113 112 # Ow-Hw + 76 1 114 113 # Ow-Hw + 77 1 116 115 # Ow-Hw + 78 1 117 116 # Ow-Hw + 79 1 119 118 # Ow-Hw + 80 1 120 119 # Ow-Hw + 81 1 122 121 # Ow-Hw + 82 1 123 122 # Ow-Hw + 83 1 125 124 # Ow-Hw + 84 1 126 125 # Ow-Hw + 85 1 128 127 # Ow-Hw + 86 1 129 128 # Ow-Hw + 87 1 131 130 # Ow-Hw + 88 1 132 131 # Ow-Hw + 89 1 134 133 # Ow-Hw + 90 1 135 134 # Ow-Hw + 91 1 137 136 # Ow-Hw + 92 1 138 137 # Ow-Hw + 93 1 140 139 # Ow-Hw + 94 1 141 140 # Ow-Hw + 95 1 143 142 # Ow-Hw + 96 1 144 143 # Ow-Hw + 97 1 146 145 # Ow-Hw + 98 1 147 146 # Ow-Hw + 99 1 149 148 # Ow-Hw + 100 1 150 149 # Ow-Hw + 101 1 152 151 # Ow-Hw + 102 1 153 152 # Ow-Hw + 103 1 155 154 # Ow-Hw + 104 1 156 155 # Ow-Hw + 105 1 158 157 # Ow-Hw + 106 1 159 158 # Ow-Hw + 107 1 161 160 # Ow-Hw + 108 1 162 161 # Ow-Hw + 109 1 164 163 # Ow-Hw + 110 1 165 164 # Ow-Hw + 111 1 167 166 # Ow-Hw + 112 1 168 167 # Ow-Hw + 113 1 170 169 # Ow-Hw + 114 1 171 170 # Ow-Hw + 115 1 173 172 # Ow-Hw + 116 1 174 173 # Ow-Hw + 117 1 176 175 # Ow-Hw + 118 1 177 176 # Ow-Hw + 119 1 179 178 # Ow-Hw + 120 1 180 179 # Ow-Hw + 121 1 182 181 # Ow-Hw + 122 1 183 182 # Ow-Hw + 123 1 185 184 # Ow-Hw + 124 1 186 185 # Ow-Hw + 125 1 188 187 # Ow-Hw + 126 1 189 188 # Ow-Hw + 127 1 191 190 # Ow-Hw + 128 1 192 191 # Ow-Hw + 129 1 194 193 # Ow-Hw + 130 1 195 194 # Ow-Hw + 131 1 197 196 # Ow-Hw + 132 1 198 197 # Ow-Hw + 133 1 200 199 # Ow-Hw + 134 1 201 200 # Ow-Hw + 135 1 203 202 # Ow-Hw + 136 1 204 203 # Ow-Hw + 137 1 206 205 # Ow-Hw + 138 1 207 206 # Ow-Hw + 139 1 209 208 # Ow-Hw + 140 1 210 209 # Ow-Hw + 141 1 212 211 # Ow-Hw + 142 1 213 212 # Ow-Hw + 143 1 215 214 # Ow-Hw + 144 1 216 215 # Ow-Hw + 145 1 218 217 # Ow-Hw + 146 1 219 218 # Ow-Hw + 147 1 221 220 # Ow-Hw + 148 1 222 221 # Ow-Hw + 149 1 224 223 # Ow-Hw + 150 1 225 224 # Ow-Hw + 151 1 227 226 # Ow-Hw + 152 1 228 227 # Ow-Hw + 153 1 230 229 # Ow-Hw + 154 1 231 230 # Ow-Hw + 155 1 233 232 # Ow-Hw + 156 1 234 233 # Ow-Hw + 157 1 236 235 # Ow-Hw + 158 1 237 236 # Ow-Hw + 159 1 239 238 # Ow-Hw + 160 1 240 239 # Ow-Hw + 161 1 242 241 # Ow-Hw + 162 1 243 242 # Ow-Hw + 163 1 245 244 # Ow-Hw + 164 1 246 245 # Ow-Hw + 165 1 248 247 # Ow-Hw + 166 1 249 248 # Ow-Hw + 167 1 251 250 # Ow-Hw + 168 1 252 251 # Ow-Hw + 169 1 254 253 # Ow-Hw + 170 1 255 254 # Ow-Hw + 171 1 257 256 # Ow-Hw + 172 1 258 257 # Ow-Hw + 173 1 260 259 # Ow-Hw + 174 1 261 260 # Ow-Hw + 175 1 263 262 # Ow-Hw + 176 1 264 263 # Ow-Hw + 177 1 266 265 # Ow-Hw + 178 1 267 266 # Ow-Hw + 179 1 269 268 # Ow-Hw + 180 1 270 269 # Ow-Hw + 181 1 272 271 # Ow-Hw + 182 1 273 272 # Ow-Hw + 183 1 275 274 # Ow-Hw + 184 1 276 275 # Ow-Hw + 185 1 278 277 # Ow-Hw + 186 1 279 278 # Ow-Hw + 187 1 281 280 # Ow-Hw + 188 1 282 281 # Ow-Hw + 189 1 284 283 # Ow-Hw + 190 1 285 284 # Ow-Hw + 191 1 287 286 # Ow-Hw + 192 1 288 287 # Ow-Hw + 193 1 290 289 # Ow-Hw + 194 1 291 290 # Ow-Hw + 195 1 293 292 # Ow-Hw + 196 1 294 293 # Ow-Hw + 197 1 296 295 # Ow-Hw + 198 1 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375 # Hw-Ow-Hw + 126 1 376 377 378 # Hw-Ow-Hw + 127 1 379 380 381 # Hw-Ow-Hw + 128 1 382 383 384 # Hw-Ow-Hw + 129 1 385 386 387 # Hw-Ow-Hw + 130 1 388 389 390 # Hw-Ow-Hw + 131 1 391 392 393 # Hw-Ow-Hw + 132 1 394 395 396 # Hw-Ow-Hw + 133 1 397 398 399 # Hw-Ow-Hw + 134 1 400 401 402 # Hw-Ow-Hw + 135 1 403 404 405 # Hw-Ow-Hw + 136 1 406 407 408 # Hw-Ow-Hw + 137 1 409 410 411 # Hw-Ow-Hw + 138 1 412 413 414 # Hw-Ow-Hw + 139 1 415 416 417 # Hw-Ow-Hw + 140 1 418 419 420 # Hw-Ow-Hw + 141 1 421 422 423 # Hw-Ow-Hw + 142 1 424 425 426 # Hw-Ow-Hw + 143 1 427 428 429 # Hw-Ow-Hw + 144 1 430 431 432 # Hw-Ow-Hw + 145 1 433 434 435 # Hw-Ow-Hw + 146 1 436 437 438 # Hw-Ow-Hw + 147 1 439 440 441 # Hw-Ow-Hw + 148 1 442 443 444 # Hw-Ow-Hw + 149 1 445 446 447 # Hw-Ow-Hw + 150 1 448 449 450 # Hw-Ow-Hw + 151 1 451 452 453 # Hw-Ow-Hw + 152 1 454 455 456 # Hw-Ow-Hw + 153 1 457 458 459 # Hw-Ow-Hw + 154 1 460 461 462 # Hw-Ow-Hw + 155 1 463 464 465 # Hw-Ow-Hw + 156 1 466 467 468 # Hw-Ow-Hw + 157 1 469 470 471 # Hw-Ow-Hw + 158 1 472 473 474 # Hw-Ow-Hw + 159 1 475 476 477 # Hw-Ow-Hw + 160 1 478 479 480 # Hw-Ow-Hw + 161 1 481 482 483 # Hw-Ow-Hw + 162 1 484 485 486 # Hw-Ow-Hw + 163 1 487 488 489 # Hw-Ow-Hw + 164 1 490 491 492 # Hw-Ow-Hw + 165 1 493 494 495 # Hw-Ow-Hw + 166 1 496 497 498 # Hw-Ow-Hw + 167 1 499 500 501 # Hw-Ow-Hw + 168 1 502 503 504 # Hw-Ow-Hw + 169 1 505 506 507 # Hw-Ow-Hw + 170 1 508 509 510 # Hw-Ow-Hw + 171 1 511 512 513 # Hw-Ow-Hw + 172 1 514 515 516 # Hw-Ow-Hw + 173 1 517 518 519 # Hw-Ow-Hw + 174 1 520 521 522 # Hw-Ow-Hw + 175 1 523 524 525 # Hw-Ow-Hw + 176 1 526 527 528 # Hw-Ow-Hw + 177 1 529 530 531 # Hw-Ow-Hw + 178 1 532 533 534 # Hw-Ow-Hw + 179 1 535 536 537 # Hw-Ow-Hw + 180 1 538 539 540 # Hw-Ow-Hw + 181 1 541 542 543 # Hw-Ow-Hw + 182 1 544 545 546 # Hw-Ow-Hw + 183 1 547 548 549 # Hw-Ow-Hw + 184 1 550 551 552 # Hw-Ow-Hw + 185 1 553 554 555 # Hw-Ow-Hw + 186 1 556 557 558 # Hw-Ow-Hw + 187 1 559 560 561 # Hw-Ow-Hw + 188 1 562 563 564 # Hw-Ow-Hw + 189 1 565 566 567 # Hw-Ow-Hw + 190 1 568 569 570 # Hw-Ow-Hw + 191 1 571 572 573 # Hw-Ow-Hw + 192 1 574 575 576 # Hw-Ow-Hw + 193 1 577 578 579 # Hw-Ow-Hw + 194 1 580 581 582 # Hw-Ow-Hw + 195 1 583 584 585 # Hw-Ow-Hw + 196 1 586 587 588 # Hw-Ow-Hw + 197 1 589 590 591 # Hw-Ow-Hw + 198 1 592 593 594 # Hw-Ow-Hw + 199 1 595 596 597 # Hw-Ow-Hw + 200 1 598 599 600 # Hw-Ow-Hw + 201 1 601 602 603 # Hw-Ow-Hw + 202 1 604 605 606 # Hw-Ow-Hw + 203 1 607 608 609 # Hw-Ow-Hw + 204 1 610 611 612 # Hw-Ow-Hw + 205 1 613 614 615 # Hw-Ow-Hw + 206 1 616 617 618 # Hw-Ow-Hw + 207 1 619 620 621 # Hw-Ow-Hw + 208 1 622 623 624 # Hw-Ow-Hw + 209 1 625 626 627 # Hw-Ow-Hw + 210 1 628 629 630 # Hw-Ow-Hw + 211 1 631 632 633 # Hw-Ow-Hw + 212 1 634 635 636 # Hw-Ow-Hw + 213 1 637 638 639 # Hw-Ow-Hw + 214 1 640 641 642 # Hw-Ow-Hw + 215 1 643 644 645 # Hw-Ow-Hw + 216 1 646 647 648 # Hw-Ow-Hw + 217 1 649 650 651 # Hw-Ow-Hw + 218 1 652 653 654 # Hw-Ow-Hw + 219 1 655 656 657 # Hw-Ow-Hw + 220 1 658 659 660 # Hw-Ow-Hw + 221 1 661 662 663 # Hw-Ow-Hw + 222 1 664 665 666 # Hw-Ow-Hw + 223 1 667 668 669 # Hw-Ow-Hw + 224 1 670 671 672 # Hw-Ow-Hw + 225 1 673 674 675 # Hw-Ow-Hw + 226 1 676 677 678 # Hw-Ow-Hw + 227 1 679 680 681 # Hw-Ow-Hw + 228 1 682 683 684 # Hw-Ow-Hw + 229 1 685 686 687 # Hw-Ow-Hw + 230 1 688 689 690 # Hw-Ow-Hw + 231 1 691 692 693 # Hw-Ow-Hw + 232 1 694 695 696 # Hw-Ow-Hw + 233 1 697 698 699 # Hw-Ow-Hw + 234 1 700 701 702 # Hw-Ow-Hw + 235 1 703 704 705 # Hw-Ow-Hw + 236 1 706 707 708 # Hw-Ow-Hw + 237 1 709 710 711 # Hw-Ow-Hw + 238 1 712 713 714 # Hw-Ow-Hw + 239 1 715 716 717 # Hw-Ow-Hw + 240 1 718 719 720 # Hw-Ow-Hw + 241 1 721 722 723 # Hw-Ow-Hw + 242 1 724 725 726 # Hw-Ow-Hw + 243 1 727 728 729 # Hw-Ow-Hw + 244 1 730 731 732 # Hw-Ow-Hw + 245 1 733 734 735 # Hw-Ow-Hw + 246 1 736 737 738 # Hw-Ow-Hw + 247 1 739 740 741 # Hw-Ow-Hw + 248 1 742 743 744 # Hw-Ow-Hw + 249 1 745 746 747 # Hw-Ow-Hw + 250 1 748 749 750 # Hw-Ow-Hw + 251 1 751 752 753 # Hw-Ow-Hw + 252 1 754 755 756 # Hw-Ow-Hw + 253 1 757 758 759 # Hw-Ow-Hw + 254 1 760 761 762 # Hw-Ow-Hw + 255 1 763 764 765 # Hw-Ow-Hw + 256 1 766 767 768 # Hw-Ow-Hw + 257 1 769 770 771 # Hw-Ow-Hw + 258 1 772 773 774 # Hw-Ow-Hw + 259 1 775 776 777 # Hw-Ow-Hw + 260 1 778 779 780 # Hw-Ow-Hw + 261 1 781 782 783 # Hw-Ow-Hw + 262 1 784 785 786 # Hw-Ow-Hw + 263 1 787 788 789 # Hw-Ow-Hw + 264 1 790 791 792 # Hw-Ow-Hw + 265 1 793 794 795 # Hw-Ow-Hw + 266 1 796 797 798 # Hw-Ow-Hw + 267 1 799 800 801 # Hw-Ow-Hw + 268 1 802 803 804 # Hw-Ow-Hw + 269 1 805 806 807 # Hw-Ow-Hw + 270 1 808 809 810 # Hw-Ow-Hw + 271 1 811 812 813 # Hw-Ow-Hw + 272 1 814 815 816 # Hw-Ow-Hw + 273 1 817 818 819 # Hw-Ow-Hw + 274 1 820 821 822 # Hw-Ow-Hw + 275 1 823 824 825 # Hw-Ow-Hw + 276 1 826 827 828 # Hw-Ow-Hw + 277 1 829 830 831 # Hw-Ow-Hw + 278 1 832 833 834 # Hw-Ow-Hw + 279 1 835 836 837 # Hw-Ow-Hw + 280 1 838 839 840 # Hw-Ow-Hw + 281 1 841 842 843 # Hw-Ow-Hw + 282 1 844 845 846 # Hw-Ow-Hw + 283 1 847 848 849 # Hw-Ow-Hw + 284 1 850 851 852 # Hw-Ow-Hw + 285 1 853 854 855 # Hw-Ow-Hw + 286 1 856 857 858 # Hw-Ow-Hw + 287 1 859 860 861 # Hw-Ow-Hw + 288 1 862 863 864 # Hw-Ow-Hw + 289 1 865 866 867 # Hw-Ow-Hw + 290 1 868 869 870 # Hw-Ow-Hw + 291 1 871 872 873 # Hw-Ow-Hw + 292 1 874 875 876 # Hw-Ow-Hw + 293 1 877 878 879 # Hw-Ow-Hw + 294 1 880 881 882 # Hw-Ow-Hw + 295 1 883 884 885 # Hw-Ow-Hw + 296 1 886 887 888 # Hw-Ow-Hw + 297 1 889 890 891 # Hw-Ow-Hw + 298 1 892 893 894 # Hw-Ow-Hw + 299 1 895 896 897 # Hw-Ow-Hw + 300 1 898 899 900 # Hw-Ow-Hw + 301 1 901 902 903 # Hw-Ow-Hw + 302 1 904 905 906 # Hw-Ow-Hw + 303 1 907 908 909 # Hw-Ow-Hw + 304 1 910 911 912 # Hw-Ow-Hw + 305 1 913 914 915 # Hw-Ow-Hw + 306 1 916 917 918 # Hw-Ow-Hw + 307 1 919 920 921 # Hw-Ow-Hw + 308 1 922 923 924 # Hw-Ow-Hw + 309 1 925 926 927 # Hw-Ow-Hw + 310 1 928 929 930 # Hw-Ow-Hw + 311 1 931 932 933 # Hw-Ow-Hw + 312 1 934 935 936 # Hw-Ow-Hw + 313 1 937 938 939 # Hw-Ow-Hw + 314 1 940 941 942 # Hw-Ow-Hw + 315 1 943 944 945 # Hw-Ow-Hw + 316 1 946 947 948 # Hw-Ow-Hw + 317 1 949 950 951 # Hw-Ow-Hw + 318 1 952 953 954 # Hw-Ow-Hw + 319 1 955 956 957 # Hw-Ow-Hw + 320 1 958 959 960 # Hw-Ow-Hw + 321 1 961 962 963 # Hw-Ow-Hw + 322 1 964 965 966 # Hw-Ow-Hw + 323 1 967 968 969 # Hw-Ow-Hw + 324 1 970 971 972 # Hw-Ow-Hw + 325 1 973 974 975 # Hw-Ow-Hw + 326 1 976 977 978 # Hw-Ow-Hw + 327 1 979 980 981 # Hw-Ow-Hw + 328 1 982 983 984 # Hw-Ow-Hw + 329 1 985 986 987 # Hw-Ow-Hw + 330 1 988 989 990 # Hw-Ow-Hw + 331 1 991 992 993 # Hw-Ow-Hw + 332 1 994 995 996 # Hw-Ow-Hw + 333 1 997 998 999 # Hw-Ow-Hw + 334 1 1000 1001 1002 # Hw-Ow-Hw + 335 1 1003 1004 1005 # Hw-Ow-Hw + 336 1 1006 1007 1008 # Hw-Ow-Hw + 337 1 1009 1010 1011 # Hw-Ow-Hw + 338 1 1012 1013 1014 # Hw-Ow-Hw + 339 1 1015 1016 1017 # Hw-Ow-Hw + 340 1 1018 1019 1020 # Hw-Ow-Hw + 341 1 1021 1022 1023 # Hw-Ow-Hw + 342 1 1024 1025 1026 # Hw-Ow-Hw + 343 1 1027 1028 1029 # Hw-Ow-Hw + 344 1 1030 1031 1032 # Hw-Ow-Hw + 345 1 1033 1034 1035 # Hw-Ow-Hw + 346 1 1036 1037 1038 # Hw-Ow-Hw + 347 1 1039 1040 1041 # Hw-Ow-Hw + 348 1 1042 1043 1044 # Hw-Ow-Hw + 349 1 1045 1046 1047 # Hw-Ow-Hw + 350 1 1048 1049 1050 # Hw-Ow-Hw + 351 1 1051 1052 1053 # Hw-Ow-Hw + 352 1 1054 1055 1056 # Hw-Ow-Hw + 353 1 1057 1058 1059 # Hw-Ow-Hw + 354 1 1060 1061 1062 # Hw-Ow-Hw + 355 1 1063 1064 1065 # Hw-Ow-Hw + 356 1 1066 1067 1068 # Hw-Ow-Hw + 357 1 1069 1070 1071 # Hw-Ow-Hw + 358 1 1072 1073 1074 # Hw-Ow-Hw + 359 1 1075 1076 1077 # Hw-Ow-Hw + 360 1 1078 1079 1080 # Hw-Ow-Hw + 361 1 1081 1082 1083 # Hw-Ow-Hw + 362 1 1084 1085 1086 # Hw-Ow-Hw + 363 1 1087 1088 1089 # Hw-Ow-Hw + 364 1 1090 1091 1092 # Hw-Ow-Hw + 365 1 1093 1094 1095 # Hw-Ow-Hw + 366 1 1096 1097 1098 # Hw-Ow-Hw + 367 1 1099 1100 1101 # Hw-Ow-Hw + 368 1 1102 1103 1104 # Hw-Ow-Hw + 369 1 1105 1106 1107 # Hw-Ow-Hw + 370 1 1108 1109 1110 # Hw-Ow-Hw + 371 1 1111 1112 1113 # Hw-Ow-Hw + 372 1 1114 1115 1116 # Hw-Ow-Hw + 373 1 1117 1118 1119 # Hw-Ow-Hw + 374 1 1120 1121 1122 # Hw-Ow-Hw + 375 1 1123 1124 1125 # Hw-Ow-Hw + 376 1 1126 1127 1128 # Hw-Ow-Hw + 377 1 1129 1130 1131 # Hw-Ow-Hw + 378 1 1132 1133 1134 # Hw-Ow-Hw + 379 1 1135 1136 1137 # Hw-Ow-Hw + 380 1 1138 1139 1140 # Hw-Ow-Hw + 381 1 1141 1142 1143 # Hw-Ow-Hw + 382 1 1144 1145 1146 # Hw-Ow-Hw + 383 1 1147 1148 1149 # Hw-Ow-Hw + 384 1 1150 1151 1152 # Hw-Ow-Hw + 385 1 1153 1154 1155 # Hw-Ow-Hw + 386 1 1156 1157 1158 # Hw-Ow-Hw + 387 1 1159 1160 1161 # Hw-Ow-Hw + 388 1 1162 1163 1164 # Hw-Ow-Hw + 389 1 1165 1166 1167 # Hw-Ow-Hw + 390 1 1168 1169 1170 # Hw-Ow-Hw + 391 1 1171 1172 1173 # Hw-Ow-Hw + 392 1 1174 1175 1176 # Hw-Ow-Hw + 393 1 1177 1178 1179 # Hw-Ow-Hw + 394 1 1180 1181 1182 # Hw-Ow-Hw + 395 1 1183 1184 1185 # Hw-Ow-Hw + 396 1 1186 1187 1188 # Hw-Ow-Hw + 397 1 1189 1190 1191 # Hw-Ow-Hw + 398 1 1192 1193 1194 # Hw-Ow-Hw + 399 1 1195 1196 1197 # Hw-Ow-Hw + 400 1 1198 1199 1200 # Hw-Ow-Hw + 401 1 1201 1202 1203 # Hw-Ow-Hw + 402 1 1204 1205 1206 # Hw-Ow-Hw + 403 1 1207 1208 1209 # Hw-Ow-Hw + 404 1 1210 1211 1212 # Hw-Ow-Hw + 405 1 1213 1214 1215 # Hw-Ow-Hw + 406 1 1216 1217 1218 # Hw-Ow-Hw + 407 1 1219 1220 1221 # Hw-Ow-Hw + 408 1 1222 1223 1224 # Hw-Ow-Hw + 409 1 1225 1226 1227 # Hw-Ow-Hw + 410 1 1228 1229 1230 # Hw-Ow-Hw + 411 1 1231 1232 1233 # Hw-Ow-Hw + 412 1 1234 1235 1236 # Hw-Ow-Hw + 413 1 1237 1238 1239 # Hw-Ow-Hw + 414 1 1240 1241 1242 # Hw-Ow-Hw + 415 1 1243 1244 1245 # Hw-Ow-Hw + 416 1 1246 1247 1248 # Hw-Ow-Hw + 417 1 1249 1250 1251 # Hw-Ow-Hw + 418 1 1252 1253 1254 # Hw-Ow-Hw + 419 1 1255 1256 1257 # Hw-Ow-Hw + 420 1 1258 1259 1260 # Hw-Ow-Hw + 421 1 1261 1262 1263 # Hw-Ow-Hw + 422 1 1264 1265 1266 # Hw-Ow-Hw + 423 1 1267 1268 1269 # Hw-Ow-Hw + 424 1 1270 1271 1272 # Hw-Ow-Hw + 425 1 1273 1274 1275 # Hw-Ow-Hw + 426 1 1276 1277 1278 # Hw-Ow-Hw + 427 1 1279 1280 1281 # Hw-Ow-Hw + 428 1 1282 1283 1284 # Hw-Ow-Hw + 429 1 1285 1286 1287 # Hw-Ow-Hw + 430 1 1288 1289 1290 # Hw-Ow-Hw + 431 1 1291 1292 1293 # Hw-Ow-Hw + 432 1 1294 1295 1296 # Hw-Ow-Hw + 433 1 1297 1298 1299 # Hw-Ow-Hw + 434 1 1300 1301 1302 # Hw-Ow-Hw + 435 1 1303 1304 1305 # Hw-Ow-Hw + 436 1 1306 1307 1308 # Hw-Ow-Hw + 437 1 1309 1310 1311 # Hw-Ow-Hw + 438 1 1312 1313 1314 # Hw-Ow-Hw + 439 1 1315 1316 1317 # Hw-Ow-Hw + 440 1 1318 1319 1320 # Hw-Ow-Hw + 441 1 1321 1322 1323 # Hw-Ow-Hw + 442 1 1324 1325 1326 # Hw-Ow-Hw + 443 1 1327 1328 1329 # Hw-Ow-Hw + 444 1 1330 1331 1332 # Hw-Ow-Hw + 445 1 1333 1334 1335 # Hw-Ow-Hw + 446 1 1336 1337 1338 # Hw-Ow-Hw + 447 1 1339 1340 1341 # Hw-Ow-Hw + 448 1 1342 1343 1344 # Hw-Ow-Hw + 449 1 1345 1346 1347 # Hw-Ow-Hw + 450 1 1348 1349 1350 # Hw-Ow-Hw + 451 1 1351 1352 1353 # Hw-Ow-Hw + 452 1 1354 1355 1356 # Hw-Ow-Hw + 453 1 1357 1358 1359 # Hw-Ow-Hw + 454 1 1360 1361 1362 # Hw-Ow-Hw + 455 1 1363 1364 1365 # Hw-Ow-Hw + 456 1 1366 1367 1368 # Hw-Ow-Hw + 457 1 1369 1370 1371 # Hw-Ow-Hw + 458 1 1372 1373 1374 # Hw-Ow-Hw + 459 1 1375 1376 1377 # Hw-Ow-Hw + 460 1 1378 1379 1380 # Hw-Ow-Hw + 461 1 1381 1382 1383 # Hw-Ow-Hw + 462 1 1384 1385 1386 # Hw-Ow-Hw + 463 1 1387 1388 1389 # Hw-Ow-Hw + 464 1 1390 1391 1392 # Hw-Ow-Hw + 465 1 1393 1394 1395 # Hw-Ow-Hw + 466 1 1396 1397 1398 # Hw-Ow-Hw + 467 1 1399 1400 1401 # Hw-Ow-Hw + 468 1 1402 1403 1404 # Hw-Ow-Hw + 469 1 1405 1406 1407 # Hw-Ow-Hw + 470 1 1408 1409 1410 # Hw-Ow-Hw + 471 1 1411 1412 1413 # Hw-Ow-Hw + 472 1 1414 1415 1416 # Hw-Ow-Hw + 473 1 1417 1418 1419 # Hw-Ow-Hw + 474 1 1420 1421 1422 # Hw-Ow-Hw + 475 1 1423 1424 1425 # Hw-Ow-Hw + 476 1 1426 1427 1428 # Hw-Ow-Hw + 477 1 1429 1430 1431 # Hw-Ow-Hw + 478 1 1432 1433 1434 # Hw-Ow-Hw + 479 1 1435 1436 1437 # Hw-Ow-Hw + 480 1 1438 1439 1440 # Hw-Ow-Hw + 481 1 1441 1442 1443 # Hw-Ow-Hw + 482 1 1444 1445 1446 # Hw-Ow-Hw + 483 1 1447 1448 1449 # Hw-Ow-Hw + 484 1 1450 1451 1452 # Hw-Ow-Hw + 485 1 1453 1454 1455 # Hw-Ow-Hw + 486 1 1456 1457 1458 # Hw-Ow-Hw + 487 1 1459 1460 1461 # Hw-Ow-Hw + 488 1 1462 1463 1464 # Hw-Ow-Hw + 489 1 1465 1466 1467 # Hw-Ow-Hw + 490 1 1468 1469 1470 # Hw-Ow-Hw + 491 1 1471 1472 1473 # Hw-Ow-Hw + 492 1 1474 1475 1476 # Hw-Ow-Hw + 493 1 1477 1478 1479 # Hw-Ow-Hw + 494 1 1480 1481 1482 # Hw-Ow-Hw + 495 1 1483 1484 1485 # Hw-Ow-Hw + 496 1 1486 1487 1488 # Hw-Ow-Hw + 497 1 1489 1490 1491 # Hw-Ow-Hw + 498 1 1492 1493 1494 # Hw-Ow-Hw + 499 1 1495 1496 1497 # Hw-Ow-Hw + 500 1 1498 1499 1500 # Hw-Ow-Hw + 501 1 1501 1502 1503 # Hw-Ow-Hw + 502 1 1504 1505 1506 # Hw-Ow-Hw + 503 1 1507 1508 1509 # Hw-Ow-Hw + 504 1 1510 1511 1512 # Hw-Ow-Hw + 505 1 1513 1514 1515 # Hw-Ow-Hw + 506 1 1516 1517 1518 # Hw-Ow-Hw + 507 1 1519 1520 1521 # Hw-Ow-Hw + 508 1 1522 1523 1524 # Hw-Ow-Hw + 509 1 1525 1526 1527 # Hw-Ow-Hw + 510 1 1528 1529 1530 # Hw-Ow-Hw + 511 1 1531 1532 1533 # Hw-Ow-Hw + 512 1 1534 1535 1536 # Hw-Ow-Hw + 513 1 1537 1538 1539 # Hw-Ow-Hw + 514 1 1540 1541 1542 # Hw-Ow-Hw + 515 1 1543 1544 1545 # Hw-Ow-Hw + 516 1 1546 1547 1548 # Hw-Ow-Hw + 517 1 1549 1550 1551 # Hw-Ow-Hw + 518 1 1552 1553 1554 # Hw-Ow-Hw + 519 1 1555 1556 1557 # Hw-Ow-Hw + 520 1 1558 1559 1560 # Hw-Ow-Hw + 521 1 1561 1562 1563 # Hw-Ow-Hw + 522 1 1564 1565 1566 # Hw-Ow-Hw + 523 1 1567 1568 1569 # Hw-Ow-Hw + 524 1 1570 1571 1572 # Hw-Ow-Hw + 525 1 1573 1574 1575 # Hw-Ow-Hw + 526 1 1576 1577 1578 # Hw-Ow-Hw + 527 1 1579 1580 1581 # Hw-Ow-Hw + 528 1 1582 1583 1584 # Hw-Ow-Hw + 529 1 1585 1586 1587 # Hw-Ow-Hw + 530 1 1588 1589 1590 # Hw-Ow-Hw + 531 1 1591 1592 1593 # Hw-Ow-Hw + 532 1 1594 1595 1596 # Hw-Ow-Hw + 533 1 1597 1598 1599 # Hw-Ow-Hw + 534 1 1600 1601 1602 # Hw-Ow-Hw + 535 1 1603 1604 1605 # Hw-Ow-Hw + 536 1 1606 1607 1608 # Hw-Ow-Hw + 537 1 1609 1610 1611 # Hw-Ow-Hw + 538 1 1612 1613 1614 # Hw-Ow-Hw + 539 1 1615 1616 1617 # Hw-Ow-Hw + 540 1 1618 1619 1620 # Hw-Ow-Hw + 541 1 1621 1622 1623 # Hw-Ow-Hw + 542 1 1624 1625 1626 # Hw-Ow-Hw + 543 1 1627 1628 1629 # Hw-Ow-Hw + 544 1 1630 1631 1632 # Hw-Ow-Hw + 545 1 1633 1634 1635 # Hw-Ow-Hw + 546 1 1636 1637 1638 # Hw-Ow-Hw + 547 1 1639 1640 1641 # Hw-Ow-Hw + 548 1 1642 1643 1644 # Hw-Ow-Hw + 549 1 1645 1646 1647 # Hw-Ow-Hw + 550 1 1648 1649 1650 # Hw-Ow-Hw + 551 1 1651 1652 1653 # Hw-Ow-Hw + 552 1 1654 1655 1656 # Hw-Ow-Hw + 553 1 1657 1658 1659 # Hw-Ow-Hw + 554 1 1660 1661 1662 # Hw-Ow-Hw + 555 1 1663 1664 1665 # Hw-Ow-Hw + 556 1 1666 1667 1668 # Hw-Ow-Hw + 557 1 1669 1670 1671 # Hw-Ow-Hw + 558 1 1672 1673 1674 # Hw-Ow-Hw + 559 1 1675 1676 1677 # Hw-Ow-Hw + 560 1 1678 1679 1680 # Hw-Ow-Hw + 561 1 1681 1682 1683 # Hw-Ow-Hw + 562 1 1684 1685 1686 # Hw-Ow-Hw + 563 1 1687 1688 1689 # Hw-Ow-Hw + 564 1 1690 1691 1692 # Hw-Ow-Hw + 565 1 1693 1694 1695 # Hw-Ow-Hw + 566 1 1696 1697 1698 # Hw-Ow-Hw + 567 1 1699 1700 1701 # Hw-Ow-Hw + 568 1 1702 1703 1704 # Hw-Ow-Hw + 569 1 1705 1706 1707 # Hw-Ow-Hw + 570 1 1708 1709 1710 # Hw-Ow-Hw + 571 1 1711 1712 1713 # Hw-Ow-Hw + 572 1 1714 1715 1716 # Hw-Ow-Hw + 573 1 1717 1718 1719 # Hw-Ow-Hw + 574 1 1720 1721 1722 # Hw-Ow-Hw + 575 1 1723 1724 1725 # Hw-Ow-Hw + 576 1 1726 1727 1728 # Hw-Ow-Hw + 577 1 1729 1730 1731 # Hw-Ow-Hw + 578 1 1732 1733 1734 # Hw-Ow-Hw + 579 1 1735 1736 1737 # Hw-Ow-Hw + 580 1 1738 1739 1740 # Hw-Ow-Hw + 581 1 1741 1742 1743 # Hw-Ow-Hw + 582 1 1744 1745 1746 # Hw-Ow-Hw + 583 1 1747 1748 1749 # Hw-Ow-Hw + 584 1 1750 1751 1752 # Hw-Ow-Hw + 585 1 1753 1754 1755 # Hw-Ow-Hw + 586 1 1756 1757 1758 # Hw-Ow-Hw + 587 1 1759 1760 1761 # Hw-Ow-Hw + 588 1 1762 1763 1764 # Hw-Ow-Hw + 589 1 1765 1766 1767 # Hw-Ow-Hw + 590 1 1768 1769 1770 # Hw-Ow-Hw + 591 1 1771 1772 1773 # Hw-Ow-Hw + 592 1 1774 1775 1776 # Hw-Ow-Hw + 593 1 1777 1778 1779 # Hw-Ow-Hw + 594 1 1780 1781 1782 # Hw-Ow-Hw + 595 1 1783 1784 1785 # Hw-Ow-Hw + 596 1 1786 1787 1788 # Hw-Ow-Hw + 597 1 1789 1790 1791 # Hw-Ow-Hw + 598 1 1792 1793 1794 # Hw-Ow-Hw + 599 1 1795 1796 1797 # Hw-Ow-Hw + 600 1 1798 1799 1800 # Hw-Ow-Hw diff --git a/examples/USER/fep/SPCEhyd/mols/spce.ff b/examples/USER/fep/SPCEhyd/mols/spce.ff new file mode 100644 index 0000000000..b9fd69f4fd --- /dev/null +++ b/examples/USER/fep/SPCEhyd/mols/spce.ff @@ -0,0 +1,14 @@ +# SPC/E water (kJ/mol, A, deg) + +ATOMS +# type m/uma q/e pot pars +Ow Ow 15.999 -0.8476 lj 3.1655 0.6503 +Hw Hw 1.008 0.4238 lj 0.0000 0.0000 + +BONDS +# i j pot re/A ka/kJmol-1 +Ow Hw cons 1.000 4331.53 + +ANGLES +# i j k pot th/deg ka/kjmol-1 +Hw Ow Hw harm 109.47 317.57 diff --git a/examples/USER/fep/SPCEhyd/mols/spce.zmat b/examples/USER/fep/SPCEhyd/mols/spce.zmat new file mode 100644 index 0000000000..e5e60c4f1b --- /dev/null +++ b/examples/USER/fep/SPCEhyd/mols/spce.zmat @@ -0,0 +1,7 @@ +SPCE + +Hw +Ow 1 1.000 +Hw 2 1.000 1 109.47 + +spce.ff diff --git a/examples/USER/fep/SPCEhyd/mols/spce_h.ff b/examples/USER/fep/SPCEhyd/mols/spce_h.ff new file mode 100644 index 0000000000..a1c6933404 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/mols/spce_h.ff @@ -0,0 +1,14 @@ +# SPC/E water (kJ/mol, A, deg) + +ATOMS +# type m/uma q/e pot pars +Owh Ow 15.999 -0.8476 lj 3.1655 0.6503 +Hwh Hw 1.008 0.4238 lj 0.0000 0.0000 + +BONDS +# i j pot re/A ka/kJmol-1 +Ow Hw cons 1.000 4331.53 + +ANGLES +# i j k pot th/deg ka/kjmol-1 +Hw Ow Hw harm 109.47 317.57 diff --git a/examples/USER/fep/SPCEhyd/mols/spce_h.zmat b/examples/USER/fep/SPCEhyd/mols/spce_h.zmat new file mode 100644 index 0000000000..54c4cf9107 --- /dev/null +++ b/examples/USER/fep/SPCEhyd/mols/spce_h.zmat @@ -0,0 +1,7 @@ +SPCE + +Hwh +Owh 1 1.000 +Hwh 2 1.000 1 109.47 + +spce_h.ff From 0f1f49afa786c9694bbcdaca5206c386c7e5d53d Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 22 Apr 2021 12:52:30 -0400 Subject: [PATCH 0600/1217] Add more output to ocl_get_devices --- lib/gpu/geryon/ocl_device.h | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/lib/gpu/geryon/ocl_device.h b/lib/gpu/geryon/ocl_device.h index 435ee24dd3..4e9e42a3cf 100644 --- a/lib/gpu/geryon/ocl_device.h +++ b/lib/gpu/geryon/ocl_device.h @@ -728,6 +728,9 @@ void UCL_Device::print_all(std::ostream &out) { out << "\nDevice " << i << ": \"" << name(i).c_str() << "\"\n"; out << " Type of device: " << device_type_name(i).c_str() << std::endl; + out << " Supported OpenCL Version: " + << _properties[i].cl_device_version / 100 << "." + << _properties[i].cl_device_version % 100 << std::endl; out << " Is a subdevice: "; if (is_subdevice(i)) out << "Yes\n"; @@ -796,6 +799,16 @@ void UCL_Device::print_all(std::ostream &out) { out << "Yes\n"; else out << "No\n"; + out << " Subgroup support: "; + if (_properties[i].has_subgroup_support) + out << "Yes\n"; + else + out << "No\n"; + out << " Shuffle support: "; + if (_properties[i].has_shuffle_support) + out << "Yes\n"; + else + out << "No\n"; } } } From 0632922a9bf93d71019017b4fde58cdd519e0891 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 22 Apr 2021 12:54:13 -0400 Subject: [PATCH 0601/1217] Explicitly check for subgroup support instead of CL version --- lib/gpu/lal_base_atomic.cpp | 2 +- lib/gpu/lal_base_charge.cpp | 2 +- lib/gpu/lal_base_dipole.cpp | 2 +- lib/gpu/lal_base_dpd.cpp | 2 +- lib/gpu/lal_base_ellipsoid.cpp | 2 +- lib/gpu/lal_base_three.cpp | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/lib/gpu/lal_base_atomic.cpp b/lib/gpu/lal_base_atomic.cpp index d35919105d..6aad138aa1 100644 --- a/lib/gpu/lal_base_atomic.cpp +++ b/lib/gpu/lal_base_atomic.cpp @@ -335,7 +335,7 @@ void BaseAtomicT::compile_kernels(UCL_Device &dev, const void *pair_str, _compiled=true; #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) - if (dev.cl_device_version() >= 210) { + if (dev.has_subgroup_support()) { size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size); #if defined(LAL_OCL_EV_JIT) mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); diff --git a/lib/gpu/lal_base_charge.cpp b/lib/gpu/lal_base_charge.cpp index b0d08e4df7..9045420425 100644 --- a/lib/gpu/lal_base_charge.cpp +++ b/lib/gpu/lal_base_charge.cpp @@ -348,7 +348,7 @@ void BaseChargeT::compile_kernels(UCL_Device &dev, const void *pair_str, _compiled=true; #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) - if (dev.cl_device_version() >= 210) { + if (dev.has_subgroup_support()) { size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size); #if defined(LAL_OCL_EV_JIT) mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); diff --git a/lib/gpu/lal_base_dipole.cpp b/lib/gpu/lal_base_dipole.cpp index 9781065b13..439637cbde 100644 --- a/lib/gpu/lal_base_dipole.cpp +++ b/lib/gpu/lal_base_dipole.cpp @@ -356,7 +356,7 @@ void BaseDipoleT::compile_kernels(UCL_Device &dev, const void *pair_str, _compiled=true; #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) - if (dev.cl_device_version() >= 210) { + if (dev.has_subgroup_support()) { size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size); #if defined(LAL_OCL_EV_JIT) mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); diff --git a/lib/gpu/lal_base_dpd.cpp b/lib/gpu/lal_base_dpd.cpp index 4b6a964bfb..d3c3353415 100644 --- a/lib/gpu/lal_base_dpd.cpp +++ b/lib/gpu/lal_base_dpd.cpp @@ -356,7 +356,7 @@ void BaseDPDT::compile_kernels(UCL_Device &dev, const void *pair_str, _compiled=true; #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) - if (dev.cl_device_version() >= 210) { + if (dev.has_subgroup_support()) { size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size); #if defined(LAL_OCL_EV_JIT) mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); diff --git a/lib/gpu/lal_base_ellipsoid.cpp b/lib/gpu/lal_base_ellipsoid.cpp index 98411a8033..2e22b2f602 100644 --- a/lib/gpu/lal_base_ellipsoid.cpp +++ b/lib/gpu/lal_base_ellipsoid.cpp @@ -554,7 +554,7 @@ void BaseEllipsoidT::compile_kernels(UCL_Device &dev, _compiled=true; #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) - if (dev.cl_device_version() >= 210) { + if (dev.has_subgroup_support()) { size_t mx_subgroup_sz = k_lj_fast.max_subgroup_size(_block_size); mx_subgroup_sz = std::min(mx_subgroup_sz, k_ellipsoid.max_subgroup_size(_block_size)); mx_subgroup_sz = std::min(mx_subgroup_sz, k_sphere_ellipsoid.max_subgroup_size(_block_size)); diff --git a/lib/gpu/lal_base_three.cpp b/lib/gpu/lal_base_three.cpp index 660385eb56..15ef20230d 100644 --- a/lib/gpu/lal_base_three.cpp +++ b/lib/gpu/lal_base_three.cpp @@ -461,7 +461,7 @@ void BaseThreeT::compile_kernels(UCL_Device &dev, const void *pair_str, _compiled=true; #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) - if (dev.cl_device_version() >= 210) { + if (dev.has_subgroup_support()) { size_t mx_subgroup_sz = k_pair.max_subgroup_size(_block_size); mx_subgroup_sz = std::min(mx_subgroup_sz, k_three_center.max_subgroup_size(_block_size)); mx_subgroup_sz = std::min(mx_subgroup_sz, k_three_end.max_subgroup_size(_block_size)); From 65cef12ae2fc441e99a9ea796308daa76416a3f3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 22 Apr 2021 16:10:51 -0400 Subject: [PATCH 0602/1217] print compiled in accelerator configuration with ./lmp -h --- src/info.cpp | 104 +++++++++++++++++++++++++------------------------ src/info.h | 1 + src/lammps.cpp | 3 ++ 3 files changed, 57 insertions(+), 51 deletions(-) diff --git a/src/info.cpp b/src/info.cpp index f1ee327191..18926ed49e 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -317,57 +317,8 @@ void Info::command(int narg, char **arg) } if (flags & ACCELERATOR) { - fputs("\nAccelerator configuration:\n\n",out); - std::string mesg; - if (has_package("GPU")) { - mesg = "GPU package API:"; - if (has_accelerator_feature("GPU","api","cuda")) mesg += " CUDA"; - if (has_accelerator_feature("GPU","api","hip")) mesg += " HIP"; - if (has_accelerator_feature("GPU","api","opencl")) mesg += " OpenCL"; - mesg += "\nGPU package precision:"; - if (has_accelerator_feature("GPU","precision","single")) mesg += " single"; - if (has_accelerator_feature("GPU","precision","mixed")) mesg += " mixed"; - if (has_accelerator_feature("GPU","precision","double")) mesg += " double"; - mesg += "\n"; - fputs(mesg.c_str(),out); - } - if (has_package("KOKKOS")) { - mesg = "KOKKOS package API:"; - if (has_accelerator_feature("KOKKOS","api","cuda")) mesg += " CUDA"; - if (has_accelerator_feature("KOKKOS","api","hip")) mesg += " HIP"; - if (has_accelerator_feature("KOKKOS","api","sycl")) mesg += " SYCL"; - if (has_accelerator_feature("KOKKOS","api","openmp")) mesg += " OpenMP"; - if (has_accelerator_feature("KOKKOS","api","serial")) mesg += " Serial"; - if (has_accelerator_feature("KOKKOS","api","pthreads")) mesg += " Pthreads"; - mesg += "\nKOKKOS package precision:"; - if (has_accelerator_feature("KOKKOS","precision","single")) mesg += " single"; - if (has_accelerator_feature("KOKKOS","precision","mixed")) mesg += " mixed"; - if (has_accelerator_feature("KOKKOS","precision","double")) mesg += " double"; - mesg += "\n"; - fputs(mesg.c_str(),out); - } - if (has_package("USER-OMP")) { - mesg = "USER-OMP package API:"; - if (has_accelerator_feature("USER-OMP","api","openmp")) mesg += " OpenMP"; - if (has_accelerator_feature("USER-OMP","api","serial")) mesg += " Serial"; - mesg += "\nUSER-OMP package precision:"; - if (has_accelerator_feature("USER-OMP","precision","single")) mesg += " single"; - if (has_accelerator_feature("USER-OMP","precision","mixed")) mesg += " mixed"; - if (has_accelerator_feature("USER-OMP","precision","double")) mesg += " double"; - mesg += "\n"; - fputs(mesg.c_str(),out); - } - if (has_package("USER-INTEL")) { - mesg = "USER-INTEL package API:"; - if (has_accelerator_feature("USER-INTEL","api","phi")) mesg += " Phi"; - if (has_accelerator_feature("USER-INTEL","api","openmp")) mesg += " OpenMP"; - mesg += "\nUSER-INTEL package precision:"; - if (has_accelerator_feature("USER-INTEL","precision","single")) mesg += " single"; - if (has_accelerator_feature("USER-INTEL","precision","mixed")) mesg += " mixed"; - if (has_accelerator_feature("USER-INTEL","precision","double")) mesg += " double"; - mesg += "\n"; - fputs(mesg.c_str(),out); - } + fmt::print(out,"\nAccelerator configuration:\n\n{}", + get_accelerator_info()); } if (flags & MEMORY) { @@ -1429,6 +1380,57 @@ std::string Info::get_cxx_info() #endif } +std::string Info::get_accelerator_info(const std::string &package) +{ + std::string mesg(""); + if ((package.empty() || (package == "GPU")) && has_package("GPU")) { + mesg += "GPU package API:"; + if (has_accelerator_feature("GPU","api","cuda")) mesg += " CUDA"; + if (has_accelerator_feature("GPU","api","hip")) mesg += " HIP"; + if (has_accelerator_feature("GPU","api","opencl")) mesg += " OpenCL"; + mesg += "\nGPU package precision:"; + if (has_accelerator_feature("GPU","precision","single")) mesg += " single"; + if (has_accelerator_feature("GPU","precision","mixed")) mesg += " mixed"; + if (has_accelerator_feature("GPU","precision","double")) mesg += " double"; + mesg += "\n"; + } + if ((package.empty() || (package == "KOKKOS")) && has_package("KOKKOS")) { + mesg += "KOKKOS package API:"; + if (has_accelerator_feature("KOKKOS","api","cuda")) mesg += " CUDA"; + if (has_accelerator_feature("KOKKOS","api","hip")) mesg += " HIP"; + if (has_accelerator_feature("KOKKOS","api","sycl")) mesg += " SYCL"; + if (has_accelerator_feature("KOKKOS","api","openmp")) mesg += " OpenMP"; + if (has_accelerator_feature("KOKKOS","api","serial")) mesg += " Serial"; + if (has_accelerator_feature("KOKKOS","api","pthreads")) mesg += " Pthreads"; + mesg += "\nKOKKOS package precision:"; + if (has_accelerator_feature("KOKKOS","precision","single")) mesg += " single"; + if (has_accelerator_feature("KOKKOS","precision","mixed")) mesg += " mixed"; + if (has_accelerator_feature("KOKKOS","precision","double")) mesg += " double"; + mesg += "\n"; + } + if ((package.empty() || (package == "USER-OMP")) && has_package("USER-OMP")) { + mesg += "USER-OMP package API:"; + if (has_accelerator_feature("USER-OMP","api","openmp")) mesg += " OpenMP"; + if (has_accelerator_feature("USER-OMP","api","serial")) mesg += " Serial"; + mesg += "\nUSER-OMP package precision:"; + if (has_accelerator_feature("USER-OMP","precision","single")) mesg += " single"; + if (has_accelerator_feature("USER-OMP","precision","mixed")) mesg += " mixed"; + if (has_accelerator_feature("USER-OMP","precision","double")) mesg += " double"; + mesg += "\n"; + } + if ((package.empty() || (package == "USER-INTEL")) && has_package("USER-INTEL")) { + mesg += "USER-INTEL package API:"; + if (has_accelerator_feature("USER-INTEL","api","phi")) mesg += " Phi"; + if (has_accelerator_feature("USER-INTEL","api","openmp")) mesg += " OpenMP"; + mesg += "\nUSER-INTEL package precision:"; + if (has_accelerator_feature("USER-INTEL","precision","single")) mesg += " single"; + if (has_accelerator_feature("USER-INTEL","precision","mixed")) mesg += " mixed"; + if (has_accelerator_feature("USER-INTEL","precision","double")) mesg += " double"; + mesg += "\n"; + } + return mesg; +} + /* ---------------------------------------------------------------------- */ void Info::get_memory_info(double *meminfo) diff --git a/src/info.h b/src/info.h index 386d38c39f..cc07327e9c 100644 --- a/src/info.h +++ b/src/info.h @@ -54,6 +54,7 @@ class Info : public Command { static std::string get_mpi_vendor(); static std::string get_mpi_info(int &, int &); static std::string get_cxx_info(); + static std::string get_accelerator_info(const std::string &pkg=""); void get_memory_info(double *); char **get_variable_names(int &num); diff --git a/src/lammps.cpp b/src/lammps.cpp index 277ec4414f..d6c63c1af8 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -1326,6 +1326,9 @@ void LAMMPS::print_config(FILE *fp) std::string infobuf = Info::get_mpi_info(major,minor); fmt::print(fp,"MPI v{}.{}: {}\n\n",major,minor,infobuf); + fmt::print(fp,"Accelerator configuration:\n\n{}\n", + Info::get_accelerator_info()); + fputs("Active compile time flags:\n\n",fp); if (Info::has_gzip_support()) fputs("-DLAMMPS_GZIP\n",fp); if (Info::has_png_support()) fputs("-DLAMMPS_PNG\n",fp); From a2e46c47e334af6974dff53ff32116ce005b87cd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 22 Apr 2021 16:20:34 -0400 Subject: [PATCH 0603/1217] download only a specific tag/version of MathJax when cloning --- doc/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/Makefile b/doc/Makefile index 7deaaf2a2e..a90b13e133 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -236,7 +236,7 @@ $(VENV): ) $(MATHJAX): - @git clone --depth 1 git://github.com/mathjax/MathJax.git $@ + @git clone -b 3.1.3 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@ $(TXT2RST) $(ANCHORCHECK): $(VENV) @( \ From 53a0ded240f89f0fc5d9da3e9047af214d116398 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 22 Apr 2021 16:26:49 -0400 Subject: [PATCH 0604/1217] update MathJax version for CMake based doc build --- cmake/Modules/Documentation.cmake | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Documentation.cmake b/cmake/Modules/Documentation.cmake index c0028676b7..b8f4c541e9 100644 --- a/cmake/Modules/Documentation.cmake +++ b/cmake/Modules/Documentation.cmake @@ -55,8 +55,8 @@ if(BUILD_DOC) COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade ) - set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" CACHE STRING "URL for MathJax tarball") - set(MATHJAX_MD5 "a4a6a093a89bc2ccab1452d766b98e53" CACHE STRING "MD5 checksum of MathJax tarball") + set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball") + set(MATHJAX_MD5 "b81661c6e6ba06278e6ae37b30b0c492" CACHE STRING "MD5 checksum of MathJax tarball") mark_as_advanced(MATHJAX_URL) # download mathjax distribution and unpack to folder "mathjax" From 2695495552959ce5df5099541f94710be04d4e23 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 22 Apr 2021 17:50:06 -0400 Subject: [PATCH 0605/1217] Avoid double free in Kokkos pair styles --- src/KOKKOS/pair_coul_cut_kokkos.cpp | 4 +++- src/KOKKOS/pair_coul_debye_kokkos.cpp | 4 +++- src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp | 1 + src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp | 3 +++ src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp | 3 +++ src/KOKKOS/pair_lj_expand_kokkos.cpp | 3 +++ 6 files changed, 16 insertions(+), 2 deletions(-) diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp index ff4028a792..2dcd8a5532 100644 --- a/src/KOKKOS/pair_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp @@ -46,8 +46,10 @@ PairCoulCutKokkos::PairCoulCutKokkos(LAMMPS *lmp) : PairCoulCut(lmp) template PairCoulCutKokkos::~PairCoulCutKokkos() { - if (allocated) + if (allocated) { memoryKK->destroy_kokkos(k_cutsq, cutsq); + cleanup_copy(); + } } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp index e380a874ff..280c447210 100644 --- a/src/KOKKOS/pair_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp @@ -56,8 +56,10 @@ PairCoulDebyeKokkos::PairCoulDebyeKokkos(LAMMPS *lmp):PairCoulDebye( template PairCoulDebyeKokkos::~PairCoulDebyeKokkos() { - if (allocated) + if (allocated) { memoryKK->destroy_kokkos(k_cutsq, cutsq); + cleanup_copy(); + } } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp index 636a72b5e1..9ffd42c1f3 100644 --- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp @@ -58,6 +58,7 @@ PairLJCutCoulCutKokkos::~PairLJCutCoulCutKokkos() memoryKK->destroy_kokkos(k_cutsq, cutsq); memoryKK->destroy_kokkos(k_cut_ljsq, cut_ljsq); memoryKK->destroy_kokkos(k_cut_coulsq, cut_coulsq); + cleanup_copy(); } } diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp index 8b4e189442..5c808e3eb9 100644 --- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp @@ -63,6 +63,9 @@ PairLJCutCoulDebyeKokkos::~PairLJCutCoulDebyeKokkos() memoryKK->destroy_kokkos(k_cut_ljsq, cut_ljsq); memoryKK->destroy_kokkos(k_cut_coulsq, cut_coulsq); } + if (allocated) { + cleanup_copy(); + } } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp index cbeb0ab70a..22412392e7 100644 --- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp @@ -73,6 +73,9 @@ PairLJCutCoulDSFKokkos::~PairLJCutCoulDSFKokkos() memoryKK->destroy_kokkos(k_cut_ljsq, cut_ljsq); //memoryKK->destroy_kokkos(k_cut_coulsq, cut_coulsq); } + if (allocated) { + cleanup_copy(); + } } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp index d351f2d5fc..5906096aa1 100644 --- a/src/KOKKOS/pair_lj_expand_kokkos.cpp +++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp @@ -60,6 +60,9 @@ PairLJExpandKokkos::~PairLJExpandKokkos() memory->sfree(cutsq); cutsq = nullptr; } + if (allocated) { + cleanup_copy(); + } } /* ---------------------------------------------------------------------- */ From 4ccb4c96038d9da6f05f0feac913d84fc2bc979c Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 22 Apr 2021 18:41:35 -0400 Subject: [PATCH 0606/1217] CMake: Add missing defines to GPU kernel compilation --- cmake/Modules/Packages/GPU.cmake | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index b706537825..fa1a493330 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -112,10 +112,10 @@ if(GPU_API STREQUAL "CUDA") endif() cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC} - -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING}) + -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES}) cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC} - -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING}) + -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES}) foreach(CU_OBJ ${GPU_GEN_OBJS}) get_filename_component(CU_NAME ${CU_OBJ} NAME_WE) @@ -289,18 +289,18 @@ elseif(GPU_API STREQUAL "HIP") if(HIP_COMPILER STREQUAL "clang") add_custom_command(OUTPUT ${CUBIN_FILE} - VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE} + VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE} DEPENDS ${CU_CPP_FILE} COMMENT "Generating ${CU_NAME}.cubin") else() add_custom_command(OUTPUT ${CUBIN_FILE} - VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE} + VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE} DEPENDS ${CU_CPP_FILE} COMMENT "Generating ${CU_NAME}.cubin") endif() elseif(HIP_PLATFORM STREQUAL "nvcc") add_custom_command(OUTPUT ${CUBIN_FILE} - VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE} + VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE} DEPENDS ${CU_FILE} COMMENT "Generating ${CU_NAME}.cubin") endif() From df7fe4431fe4ae4e9eeea4a6e86531c3bf18c879 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 22 Apr 2021 21:26:07 -0400 Subject: [PATCH 0607/1217] make LAMMPS homepage URL and C++ indicator comments consistent --- src/ASPHERE/compute_erotate_asphere.h | 2 +- src/ASPHERE/compute_temp_asphere.h | 2 +- src/ASPHERE/fix_nh_asphere.h | 2 +- src/ASPHERE/fix_nph_asphere.h | 2 +- src/ASPHERE/fix_npt_asphere.h | 2 +- src/ASPHERE/fix_nve_asphere.h | 2 +- src/ASPHERE/fix_nve_asphere_noforce.h | 2 +- src/ASPHERE/fix_nve_line.h | 2 +- src/ASPHERE/fix_nve_tri.h | 2 +- src/ASPHERE/fix_nvt_asphere.h | 2 +- src/ASPHERE/pair_gayberne.h | 2 +- src/ASPHERE/pair_line_lj.h | 2 +- src/ASPHERE/pair_resquared.h | 2 +- src/ASPHERE/pair_tri_lj.h | 2 +- src/BODY/body_nparticle.h | 2 +- src/BODY/body_rounded_polygon.h | 2 +- src/BODY/body_rounded_polyhedron.h | 2 +- src/BODY/compute_body_local.h | 2 +- src/BODY/compute_temp_body.h | 2 +- src/BODY/fix_nh_body.h | 2 +- src/BODY/fix_nph_body.h | 2 +- src/BODY/fix_npt_body.h | 2 +- src/BODY/fix_nve_body.h | 2 +- src/BODY/fix_nvt_body.h | 2 +- src/BODY/fix_wall_body_polygon.h | 2 +- src/BODY/fix_wall_body_polyhedron.h | 2 +- src/BODY/pair_body_nparticle.h | 2 +- src/BODY/pair_body_rounded_polygon.h | 2 +- src/BODY/pair_body_rounded_polyhedron.h | 2 +- src/CLASS2/angle_class2.h | 2 +- src/CLASS2/bond_class2.h | 2 +- src/CLASS2/dihedral_class2.h | 2 +- src/CLASS2/improper_class2.h | 2 +- src/CLASS2/pair_lj_class2.h | 2 +- src/CLASS2/pair_lj_class2_coul_cut.h | 2 +- src/CLASS2/pair_lj_class2_coul_long.h | 2 +- src/COLLOID/fix_wall_colloid.h | 2 +- src/COLLOID/pair_brownian.h | 2 +- src/COLLOID/pair_brownian_poly.h | 2 +- src/COLLOID/pair_colloid.h | 2 +- src/COLLOID/pair_lubricate.h | 2 +- src/COLLOID/pair_lubricateU.h | 2 +- src/COLLOID/pair_lubricateU_poly.h | 2 +- src/COLLOID/pair_lubricate_poly.h | 2 +- src/COLLOID/pair_yukawa_colloid.h | 2 +- src/COMPRESS/dump_atom_gz.h | 2 +- src/COMPRESS/dump_atom_zstd.h | 2 +- src/COMPRESS/dump_cfg_gz.h | 2 +- src/COMPRESS/dump_cfg_zstd.h | 2 +- src/COMPRESS/dump_custom_gz.h | 2 +- src/COMPRESS/dump_custom_zstd.h | 2 +- src/COMPRESS/dump_local_gz.h | 2 +- src/COMPRESS/dump_local_zstd.h | 2 +- src/COMPRESS/dump_xyz_gz.h | 2 +- src/COMPRESS/dump_xyz_zstd.h | 2 +- src/COMPRESS/gz_file_writer.h | 2 +- src/COMPRESS/zstd_file_writer.h | 2 +- src/CORESHELL/compute_temp_cs.h | 2 +- src/CORESHELL/pair_born_coul_dsf_cs.h | 2 +- src/CORESHELL/pair_born_coul_long_cs.h | 2 +- src/CORESHELL/pair_born_coul_wolf_cs.h | 4 ++-- src/CORESHELL/pair_buck_coul_long_cs.h | 2 +- src/CORESHELL/pair_coul_long_cs.h | 2 +- src/CORESHELL/pair_coul_wolf_cs.h | 2 +- src/CORESHELL/pair_lj_class2_coul_long_cs.h | 2 +- src/CORESHELL/pair_lj_cut_coul_long_cs.h | 2 +- src/DIPOLE/atom_vec_dipole.h | 2 +- src/DIPOLE/pair_lj_cut_dipole_cut.h | 2 +- src/DIPOLE/pair_lj_long_dipole_long.h | 2 +- src/GPU/fix_gpu.h | 2 +- src/GPU/fix_nh_gpu.h | 2 +- src/GPU/fix_npt_gpu.h | 2 +- src/GPU/fix_nve_asphere_gpu.h | 2 +- src/GPU/fix_nve_gpu.h | 2 +- src/GPU/fix_nvt_gpu.h | 2 +- src/GPU/gpu_extra.h | 2 +- src/GPU/pair_beck_gpu.h | 2 +- src/GPU/pair_born_coul_long_cs_gpu.h | 2 +- src/GPU/pair_born_coul_long_gpu.h | 2 +- src/GPU/pair_born_coul_wolf_cs_gpu.h | 2 +- src/GPU/pair_born_coul_wolf_gpu.h | 2 +- src/GPU/pair_born_gpu.h | 2 +- src/GPU/pair_buck_coul_cut_gpu.h | 2 +- src/GPU/pair_buck_coul_long_gpu.h | 2 +- src/GPU/pair_buck_gpu.h | 2 +- src/GPU/pair_colloid_gpu.h | 2 +- src/GPU/pair_coul_cut_gpu.h | 2 +- src/GPU/pair_coul_debye_gpu.h | 2 +- src/GPU/pair_coul_dsf_gpu.h | 2 +- src/GPU/pair_coul_long_cs_gpu.h | 2 +- src/GPU/pair_coul_long_gpu.h | 2 +- src/GPU/pair_dpd_gpu.h | 2 +- src/GPU/pair_dpd_tstat_gpu.h | 2 +- src/GPU/pair_eam_alloy_gpu.h | 2 +- src/GPU/pair_eam_fs_gpu.h | 2 +- src/GPU/pair_eam_gpu.h | 2 +- src/GPU/pair_gauss_gpu.h | 2 +- src/GPU/pair_gayberne_gpu.h | 2 +- src/GPU/pair_lj96_cut_gpu.h | 2 +- src/GPU/pair_lj_charmm_coul_charmm_gpu.h | 2 +- src/GPU/pair_lj_charmm_coul_long_gpu.h | 2 +- src/GPU/pair_lj_class2_coul_long_gpu.h | 2 +- src/GPU/pair_lj_class2_gpu.h | 2 +- src/GPU/pair_lj_cubic_gpu.h | 2 +- src/GPU/pair_lj_cut_coul_cut_gpu.h | 2 +- src/GPU/pair_lj_cut_coul_debye_gpu.h | 2 +- src/GPU/pair_lj_cut_coul_dsf_gpu.h | 2 +- src/GPU/pair_lj_cut_coul_long_gpu.h | 2 +- src/GPU/pair_lj_cut_coul_msm_gpu.h | 2 +- src/GPU/pair_lj_cut_dipole_cut_gpu.h | 2 +- src/GPU/pair_lj_cut_dipole_long_gpu.h | 2 +- src/GPU/pair_lj_cut_gpu.h | 2 +- src/GPU/pair_lj_cut_tip4p_long_gpu.h | 4 ++-- src/GPU/pair_lj_expand_coul_long_gpu.h | 2 +- src/GPU/pair_lj_expand_gpu.h | 2 +- src/GPU/pair_lj_gromacs_gpu.h | 2 +- src/GPU/pair_lj_sdk_coul_long_gpu.h | 2 +- src/GPU/pair_lj_sdk_gpu.h | 2 +- src/GPU/pair_lj_sf_dipole_sf_gpu.h | 2 +- src/GPU/pair_mie_cut_gpu.h | 2 +- src/GPU/pair_morse_gpu.h | 2 +- src/GPU/pair_resquared_gpu.h | 2 +- src/GPU/pair_soft_gpu.h | 2 +- src/GPU/pair_sw_gpu.h | 2 +- src/GPU/pair_table_gpu.h | 2 +- src/GPU/pair_tersoff_gpu.h | 2 +- src/GPU/pair_tersoff_mod_gpu.h | 2 +- src/GPU/pair_tersoff_zbl_gpu.h | 2 +- src/GPU/pair_ufm_gpu.h | 2 +- src/GPU/pair_vashishta_gpu.h | 2 +- src/GPU/pair_yukawa_colloid_gpu.h | 2 +- src/GPU/pair_yukawa_gpu.h | 2 +- src/GPU/pair_zbl_gpu.h | 2 +- src/GPU/pppm_gpu.h | 2 +- src/GRANULAR/fix_freeze.h | 2 +- src/GRANULAR/fix_pour.h | 2 +- src/GRANULAR/fix_wall_gran.h | 2 +- src/GRANULAR/fix_wall_gran_region.h | 2 +- src/GRANULAR/pair_gran_hertz_history.h | 2 +- src/GRANULAR/pair_gran_hooke.h | 2 +- src/GRANULAR/pair_gran_hooke_history.h | 2 +- src/GRANULAR/pair_granular.h | 4 ++-- src/KIM/fix_store_kim.h | 2 +- src/KIM/kim_command.h | 2 +- src/KIM/kim_init.h | 2 +- src/KIM/kim_interactions.h | 2 +- src/KIM/kim_param.h | 2 +- src/KIM/kim_property.h | 2 +- src/KIM/kim_query.h | 2 +- src/KIM/kim_units.h | 2 +- src/KIM/pair_kim.h | 2 +- src/KOKKOS/angle_charmm_kokkos.h | 2 +- src/KOKKOS/angle_class2_kokkos.h | 2 +- src/KOKKOS/angle_cosine_kokkos.h | 2 +- src/KOKKOS/angle_harmonic_kokkos.h | 2 +- src/KOKKOS/atom_kokkos.h | 2 +- src/KOKKOS/atom_vec_angle_kokkos.h | 2 +- src/KOKKOS/atom_vec_atomic_kokkos.h | 2 +- src/KOKKOS/atom_vec_bond_kokkos.h | 2 +- src/KOKKOS/atom_vec_charge_kokkos.h | 2 +- src/KOKKOS/atom_vec_dpd_kokkos.h | 2 +- src/KOKKOS/atom_vec_full_kokkos.h | 2 +- src/KOKKOS/atom_vec_hybrid_kokkos.h | 2 +- src/KOKKOS/atom_vec_kokkos.h | 2 +- src/KOKKOS/atom_vec_molecular_kokkos.h | 2 +- src/KOKKOS/atom_vec_sphere_kokkos.h | 2 +- src/KOKKOS/atom_vec_spin_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_spin_kokkos.h | 2 +- src/KOKKOS/bond_class2_kokkos.h | 2 +- src/KOKKOS/bond_fene_kokkos.h | 2 +- src/KOKKOS/bond_harmonic_kokkos.h | 2 +- src/KOKKOS/comm_kokkos.h | 2 +- src/KOKKOS/comm_tiled_kokkos.h | 2 +- src/KOKKOS/compute_coord_atom_kokkos.h | 2 +- src/KOKKOS/compute_orientorder_atom_kokkos.h | 2 +- src/KOKKOS/compute_temp_kokkos.h | 2 +- src/KOKKOS/dihedral_charmm_kokkos.h | 2 +- src/KOKKOS/dihedral_class2_kokkos.h | 2 +- src/KOKKOS/dihedral_harmonic_kokkos.h | 2 +- src/KOKKOS/dihedral_opls_kokkos.h | 2 +- src/KOKKOS/domain_kokkos.h | 2 +- src/KOKKOS/fft3d_kokkos.h | 4 ++-- src/KOKKOS/fftdata_kokkos.h | 4 ++-- src/KOKKOS/fix_deform_kokkos.h | 2 +- src/KOKKOS/fix_dpd_energy_kokkos.h | 4 ++-- src/KOKKOS/fix_enforce2d_kokkos.h | 2 +- src/KOKKOS/fix_eos_table_rx_kokkos.h | 2 +- src/KOKKOS/fix_freeze_kokkos.h | 2 +- src/KOKKOS/fix_gravity_kokkos.h | 2 +- src/KOKKOS/fix_langevin_kokkos.h | 2 +- src/KOKKOS/fix_minimize_kokkos.h | 2 +- src/KOKKOS/fix_momentum_kokkos.h | 2 +- src/KOKKOS/fix_neigh_history_kokkos.h | 2 +- src/KOKKOS/fix_nh_kokkos.h | 2 +- src/KOKKOS/fix_nph_kokkos.h | 2 +- src/KOKKOS/fix_npt_kokkos.h | 2 +- src/KOKKOS/fix_nve_kokkos.h | 2 +- src/KOKKOS/fix_nve_sphere_kokkos.h | 2 +- src/KOKKOS/fix_nvt_kokkos.h | 2 +- src/KOKKOS/fix_property_atom_kokkos.h | 2 +- src/KOKKOS/fix_qeq_reax_kokkos.h | 2 +- src/KOKKOS/fix_reaxc_bonds_kokkos.h | 2 +- src/KOKKOS/fix_reaxc_species_kokkos.h | 2 +- src/KOKKOS/fix_rx_kokkos.h | 4 ++-- src/KOKKOS/fix_setforce_kokkos.h | 2 +- src/KOKKOS/fix_shake_kokkos.cpp | 2 +- src/KOKKOS/fix_shake_kokkos.h | 2 +- src/KOKKOS/fix_shardlow_kokkos.h | 2 +- src/KOKKOS/fix_wall_lj93_kokkos.h | 2 +- src/KOKKOS/fix_wall_reflect_kokkos.h | 2 +- src/KOKKOS/gridcomm_kokkos.h | 2 +- src/KOKKOS/improper_class2_kokkos.h | 2 +- src/KOKKOS/improper_harmonic_kokkos.h | 2 +- src/KOKKOS/kissfft_kokkos.h | 4 ++-- src/KOKKOS/kokkos.h | 2 +- src/KOKKOS/kokkos_base.h | 4 ++-- src/KOKKOS/kokkos_base_fft.h | 4 ++-- src/KOKKOS/kokkos_type.h | 2 +- src/KOKKOS/math_special_kokkos.h | 2 +- src/KOKKOS/memory_kokkos.h | 2 +- src/KOKKOS/min_cg_kokkos.h | 2 +- src/KOKKOS/min_kokkos.h | 2 +- src/KOKKOS/min_linesearch_kokkos.h | 2 +- src/KOKKOS/modify_kokkos.h | 2 +- src/KOKKOS/nbin_kokkos.h | 2 +- src/KOKKOS/nbin_ssa_kokkos.h | 2 +- src/KOKKOS/neigh_bond_kokkos.h | 2 +- src/KOKKOS/neigh_list_kokkos.h | 2 +- src/KOKKOS/neighbor_kokkos.h | 2 +- src/KOKKOS/npair_copy_kokkos.h | 2 +- src/KOKKOS/npair_halffull_kokkos.h | 2 +- src/KOKKOS/npair_kokkos.h | 2 +- src/KOKKOS/npair_skip_kokkos.h | 2 +- src/KOKKOS/npair_ssa_kokkos.h | 2 +- src/KOKKOS/pack_kokkos.h | 2 +- src/KOKKOS/pair_buck_coul_cut_kokkos.h | 2 +- src/KOKKOS/pair_buck_coul_long_kokkos.h | 2 +- src/KOKKOS/pair_buck_kokkos.h | 2 +- src/KOKKOS/pair_coul_cut_kokkos.h | 2 +- src/KOKKOS/pair_coul_debye_kokkos.h | 2 +- src/KOKKOS/pair_coul_dsf_kokkos.h | 2 +- src/KOKKOS/pair_coul_long_kokkos.h | 2 +- src/KOKKOS/pair_coul_wolf_kokkos.h | 2 +- src/KOKKOS/pair_dpd_fdt_energy_kokkos.h | 2 +- src/KOKKOS/pair_eam_alloy_kokkos.h | 2 +- src/KOKKOS/pair_eam_fs_kokkos.h | 2 +- src/KOKKOS/pair_eam_kokkos.h | 2 +- src/KOKKOS/pair_exp6_rx_kokkos.h | 4 ++-- src/KOKKOS/pair_gran_hooke_history_kokkos.h | 2 +- src/KOKKOS/pair_hybrid_kokkos.h | 2 +- src/KOKKOS/pair_hybrid_overlay_kokkos.h | 2 +- src/KOKKOS/pair_kokkos.h | 2 +- src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h | 2 +- src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h | 2 +- src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h | 2 +- src/KOKKOS/pair_lj_class2_coul_cut_kokkos.h | 2 +- src/KOKKOS/pair_lj_class2_coul_long_kokkos.h | 2 +- src/KOKKOS/pair_lj_class2_kokkos.h | 2 +- src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h | 2 +- src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h | 2 +- src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h | 2 +- src/KOKKOS/pair_lj_cut_coul_long_kokkos.h | 2 +- src/KOKKOS/pair_lj_cut_kokkos.h | 2 +- src/KOKKOS/pair_lj_expand_kokkos.h | 2 +- src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h | 2 +- src/KOKKOS/pair_lj_gromacs_kokkos.h | 2 +- src/KOKKOS/pair_lj_sdk_kokkos.h | 2 +- src/KOKKOS/pair_morse_kokkos.h | 2 +- src/KOKKOS/pair_multi_lucy_rx_kokkos.h | 4 ++-- src/KOKKOS/pair_reaxc_kokkos.h | 2 +- src/KOKKOS/pair_snap_kokkos.h | 2 +- src/KOKKOS/pair_snap_kokkos_impl.h | 4 ++-- src/KOKKOS/pair_sw_kokkos.h | 2 +- src/KOKKOS/pair_table_kokkos.h | 2 +- src/KOKKOS/pair_table_rx_kokkos.h | 2 +- src/KOKKOS/pair_tersoff_kokkos.h | 2 +- src/KOKKOS/pair_tersoff_mod_kokkos.h | 2 +- src/KOKKOS/pair_tersoff_zbl_kokkos.h | 2 +- src/KOKKOS/pair_vashishta_kokkos.h | 2 +- src/KOKKOS/pair_yukawa_kokkos.h | 2 +- src/KOKKOS/pair_zbl_kokkos.h | 2 +- src/KOKKOS/pppm_kokkos.h | 2 +- src/KOKKOS/rand_pool_wrap_kokkos.h | 4 ++-- src/KOKKOS/region_block_kokkos.h | 2 +- src/KOKKOS/remap_kokkos.h | 2 +- src/KOKKOS/sna_kokkos.h | 2 +- src/KOKKOS/sna_kokkos_impl.h | 4 ++-- src/KOKKOS/verlet_kokkos.h | 2 +- src/KSPACE/ewald.h | 2 +- src/KSPACE/ewald_dipole.h | 2 +- src/KSPACE/ewald_dipole_spin.h | 2 +- src/KSPACE/ewald_disp.h | 2 +- src/KSPACE/fft3d.h | 2 +- src/KSPACE/fft3d_wrap.h | 2 +- src/KSPACE/fix_tune_kspace.h | 2 +- src/KSPACE/gridcomm.h | 2 +- src/KSPACE/kissfft.h | 2 +- src/KSPACE/msm.h | 2 +- src/KSPACE/msm_cg.h | 2 +- src/KSPACE/pair_born_coul_long.h | 2 +- src/KSPACE/pair_born_coul_msm.h | 2 +- src/KSPACE/pair_buck_coul_long.h | 2 +- src/KSPACE/pair_buck_coul_msm.h | 2 +- src/KSPACE/pair_buck_long_coul_long.h | 2 +- src/KSPACE/pair_coul_long.h | 2 +- src/KSPACE/pair_coul_msm.h | 2 +- src/KSPACE/pair_lj_charmm_coul_long.h | 2 +- src/KSPACE/pair_lj_charmm_coul_msm.h | 2 +- src/KSPACE/pair_lj_charmmfsw_coul_long.h | 2 +- src/KSPACE/pair_lj_cut_coul_long.h | 2 +- src/KSPACE/pair_lj_cut_coul_msm.h | 2 +- src/KSPACE/pair_lj_cut_tip4p_long.h | 2 +- src/KSPACE/pair_lj_long_coul_long.h | 2 +- src/KSPACE/pair_lj_long_tip4p_long.h | 2 +- src/KSPACE/pair_tip4p_long.h | 2 +- src/KSPACE/pppm.h | 2 +- src/KSPACE/pppm_cg.h | 2 +- src/KSPACE/pppm_dipole.h | 2 +- src/KSPACE/pppm_dipole_spin.h | 2 +- src/KSPACE/pppm_disp.h | 2 +- src/KSPACE/pppm_disp_tip4p.h | 2 +- src/KSPACE/pppm_stagger.h | 2 +- src/KSPACE/pppm_tip4p.h | 2 +- src/KSPACE/remap.h | 2 +- src/KSPACE/remap_wrap.h | 2 +- src/LATTE/fix_latte.h | 2 +- src/MANYBODY/fix_qeq_comb.h | 2 +- src/MANYBODY/pair_adp.h | 2 +- src/MANYBODY/pair_airebo.h | 2 +- src/MANYBODY/pair_airebo_morse.h | 2 +- src/MANYBODY/pair_atm.h | 2 +- src/MANYBODY/pair_bop.h | 2 +- src/MANYBODY/pair_comb.h | 2 +- src/MANYBODY/pair_comb3.h | 2 +- src/MANYBODY/pair_eam.h | 2 +- src/MANYBODY/pair_eam_alloy.h | 2 +- src/MANYBODY/pair_eam_cd.h | 2 +- src/MANYBODY/pair_eam_fs.h | 2 +- src/MANYBODY/pair_eam_he.h | 2 +- src/MANYBODY/pair_eim.h | 2 +- src/MANYBODY/pair_gw.h | 2 +- src/MANYBODY/pair_gw_zbl.h | 2 +- src/MANYBODY/pair_lcbop.h | 2 +- src/MANYBODY/pair_nb3b_harmonic.h | 4 ++-- src/MANYBODY/pair_polymorphic.h | 2 +- src/MANYBODY/pair_rebo.h | 2 +- src/MANYBODY/pair_sw.h | 2 +- src/MANYBODY/pair_tersoff.h | 2 +- src/MANYBODY/pair_tersoff_mod.h | 2 +- src/MANYBODY/pair_tersoff_mod_c.h | 2 +- src/MANYBODY/pair_tersoff_zbl.h | 2 +- src/MANYBODY/pair_vashishta.h | 2 +- src/MANYBODY/pair_vashishta_table.h | 2 +- src/MC/fix_atom_swap.h | 2 +- src/MC/fix_bond_break.h | 2 +- src/MC/fix_bond_create.h | 2 +- src/MC/fix_bond_create_angle.h | 2 +- src/MC/fix_bond_swap.h | 2 +- src/MC/fix_charge_regulation.cpp | 2 +- src/MC/fix_charge_regulation.h | 2 +- src/MC/fix_gcmc.h | 2 +- src/MC/fix_tfmc.h | 2 +- src/MC/fix_widom.h | 2 +- src/MC/pair_dsmc.h | 2 +- src/MESSAGE/fix_client_md.h | 2 +- src/MESSAGE/message.h | 2 +- src/MESSAGE/server.h | 2 +- src/MESSAGE/server_mc.h | 2 +- src/MESSAGE/server_md.h | 2 +- src/MISC/compute_msd_nongauss.h | 2 +- src/MISC/compute_ti.h | 2 +- src/MISC/dump_xtc.h | 2 +- src/MISC/fix_deposit.h | 2 +- src/MISC/fix_efield.h | 2 +- src/MISC/fix_evaporate.h | 2 +- src/MISC/fix_gld.h | 2 +- src/MISC/fix_oneway.h | 2 +- src/MISC/fix_orient_bcc.h | 2 +- src/MISC/fix_orient_fcc.h | 2 +- src/MISC/fix_thermal_conductivity.h | 2 +- src/MISC/fix_ttm.h | 2 +- src/MISC/fix_viscosity.h | 2 +- src/MISC/pair_nm_cut.h | 2 +- src/MISC/pair_nm_cut_coul_cut.h | 2 +- src/MISC/pair_nm_cut_coul_long.h | 2 +- src/MLIAP/compute_mliap.h | 2 +- src/MLIAP/mliap_data.h | 2 +- src/MLIAP/mliap_descriptor.h | 2 +- src/MLIAP/mliap_descriptor_snap.h | 2 +- src/MLIAP/mliap_model.h | 2 +- src/MLIAP/mliap_model_linear.h | 2 +- src/MLIAP/mliap_model_nn.h | 2 +- src/MLIAP/mliap_model_python.cpp | 2 +- src/MLIAP/mliap_model_python.h | 2 +- src/MLIAP/mliap_model_quadratic.h | 2 +- src/MLIAP/pair_mliap.h | 2 +- src/MOLECULE/angle_charmm.h | 2 +- src/MOLECULE/angle_cosine.h | 2 +- src/MOLECULE/angle_cosine_delta.h | 2 +- src/MOLECULE/angle_cosine_periodic.h | 2 +- src/MOLECULE/angle_cosine_squared.h | 2 +- src/MOLECULE/angle_harmonic.h | 2 +- src/MOLECULE/angle_table.h | 2 +- src/MOLECULE/atom_vec_angle.h | 2 +- src/MOLECULE/atom_vec_bond.h | 2 +- src/MOLECULE/atom_vec_full.h | 2 +- src/MOLECULE/atom_vec_molecular.h | 2 +- src/MOLECULE/atom_vec_template.h | 2 +- src/MOLECULE/bond_fene.h | 2 +- src/MOLECULE/bond_fene_expand.h | 2 +- src/MOLECULE/bond_gromos.h | 2 +- src/MOLECULE/bond_harmonic.h | 2 +- src/MOLECULE/bond_morse.h | 2 +- src/MOLECULE/bond_nonlinear.h | 2 +- src/MOLECULE/bond_quartic.h | 2 +- src/MOLECULE/bond_table.h | 2 +- src/MOLECULE/dihedral_charmm.h | 2 +- src/MOLECULE/dihedral_charmmfsw.h | 2 +- src/MOLECULE/dihedral_harmonic.h | 2 +- src/MOLECULE/dihedral_helix.h | 2 +- src/MOLECULE/dihedral_multi_harmonic.h | 2 +- src/MOLECULE/dihedral_opls.h | 2 +- src/MOLECULE/fix_cmap.h | 2 +- src/MOLECULE/improper_cvff.h | 2 +- src/MOLECULE/improper_harmonic.h | 2 +- src/MOLECULE/improper_umbrella.h | 2 +- src/MOLECULE/pair_hbond_dreiding_lj.h | 2 +- src/MOLECULE/pair_hbond_dreiding_morse.h | 2 +- src/MOLECULE/pair_lj_charmm_coul_charmm.h | 2 +- src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h | 2 +- src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.h | 2 +- src/MOLECULE/pair_lj_cut_tip4p_cut.h | 2 +- src/MOLECULE/pair_tip4p_cut.h | 2 +- src/MPIIO/dump_atom_mpiio.h | 2 +- src/MPIIO/dump_cfg_mpiio.h | 2 +- src/MPIIO/dump_custom_mpiio.h | 2 +- src/MPIIO/dump_xyz_mpiio.h | 2 +- src/MPIIO/restart_mpiio.h | 2 +- src/MSCG/fix_mscg.h | 2 +- src/OPT/pair_eam_alloy_opt.h | 2 +- src/OPT/pair_eam_fs_opt.h | 2 +- src/OPT/pair_eam_opt.h | 2 +- src/OPT/pair_lj_charmm_coul_long_opt.h | 2 +- src/OPT/pair_lj_cut_coul_long_opt.h | 2 +- src/OPT/pair_lj_cut_opt.h | 2 +- src/OPT/pair_lj_cut_tip4p_long_opt.h | 2 +- src/OPT/pair_lj_long_coul_long_opt.h | 2 +- src/OPT/pair_morse_opt.h | 2 +- src/OPT/pair_ufm_opt.h | 2 +- src/PERI/atom_vec_peri.h | 2 +- src/PERI/compute_damage_atom.h | 2 +- src/PERI/compute_dilatation_atom.h | 2 +- src/PERI/compute_plasticity_atom.h | 2 +- src/PERI/fix_peri_neigh.h | 2 +- src/PERI/pair_peri_eps.h | 2 +- src/PERI/pair_peri_lps.h | 2 +- src/PERI/pair_peri_pmb.h | 2 +- src/PERI/pair_peri_ves.h | 2 +- src/PLUGIN/plugin.h | 2 +- src/POEMS/fix_poems.h | 2 +- src/PYTHON/fix_python_invoke.h | 2 +- src/PYTHON/fix_python_move.h | 2 +- src/PYTHON/pair_python.h | 2 +- src/PYTHON/python_compat.h | 2 +- src/PYTHON/python_impl.h | 2 +- src/PYTHON/python_utils.h | 2 +- src/QEQ/fix_qeq.h | 2 +- src/QEQ/fix_qeq_dynamic.h | 2 +- src/QEQ/fix_qeq_fire.h | 2 +- src/QEQ/fix_qeq_point.h | 2 +- src/QEQ/fix_qeq_shielded.h | 2 +- src/QEQ/fix_qeq_slater.h | 2 +- src/REPLICA/compute_event_displace.h | 2 +- src/REPLICA/fix_event.h | 2 +- src/REPLICA/fix_event_hyper.h | 2 +- src/REPLICA/fix_event_prd.h | 2 +- src/REPLICA/fix_event_tad.h | 2 +- src/REPLICA/fix_hyper.h | 2 +- src/REPLICA/fix_hyper_global.h | 2 +- src/REPLICA/fix_hyper_local.h | 2 +- src/REPLICA/fix_neb.h | 2 +- src/REPLICA/hyper.h | 2 +- src/REPLICA/neb.h | 2 +- src/REPLICA/prd.h | 2 +- src/REPLICA/tad.h | 2 +- src/REPLICA/temper.h | 2 +- src/REPLICA/verlet_split.h | 2 +- src/RIGID/compute_erotate_rigid.h | 2 +- src/RIGID/compute_ke_rigid.h | 2 +- src/RIGID/compute_rigid_local.h | 2 +- src/RIGID/fix_ehex.h | 2 +- src/RIGID/fix_rattle.h | 2 +- src/RIGID/fix_rigid.h | 2 +- src/RIGID/fix_rigid_nh.h | 2 +- src/RIGID/fix_rigid_nh_small.h | 2 +- src/RIGID/fix_rigid_nph.h | 2 +- src/RIGID/fix_rigid_nph_small.h | 2 +- src/RIGID/fix_rigid_npt.h | 2 +- src/RIGID/fix_rigid_npt_small.h | 2 +- src/RIGID/fix_rigid_nve.h | 2 +- src/RIGID/fix_rigid_nve_small.h | 2 +- src/RIGID/fix_rigid_nvt.h | 2 +- src/RIGID/fix_rigid_nvt_small.h | 2 +- src/RIGID/fix_rigid_small.h | 2 +- src/RIGID/fix_shake.h | 2 +- src/RIGID/rigid_const.h | 2 +- src/SHOCK/fix_append_atoms.h | 2 +- src/SHOCK/fix_msst.h | 2 +- src/SHOCK/fix_nphug.h | 2 +- src/SHOCK/fix_wall_piston.h | 2 +- src/SNAP/compute_sna_atom.h | 2 +- src/SNAP/compute_snad_atom.h | 2 +- src/SNAP/compute_snap.h | 2 +- src/SNAP/compute_snav_atom.h | 2 +- src/SNAP/pair_snap.h | 2 +- src/SNAP/sna.h | 2 +- src/SPIN/atom_vec_spin.h | 2 +- src/SPIN/compute_spin.h | 2 +- src/SPIN/fix_langevin_spin.h | 2 +- src/SPIN/fix_neb_spin.h | 2 +- src/SPIN/fix_nve_spin.h | 2 +- src/SPIN/fix_precession_spin.h | 2 +- src/SPIN/fix_setforce_spin.h | 2 +- src/SPIN/min_spin.h | 2 +- src/SPIN/min_spin_cg.h | 2 +- src/SPIN/min_spin_lbfgs.h | 2 +- src/SPIN/neb_spin.h | 2 +- src/SPIN/pair_spin.h | 2 +- src/SPIN/pair_spin_dmi.h | 2 +- src/SPIN/pair_spin_exchange.h | 2 +- src/SPIN/pair_spin_exchange_biquadratic.cpp | 2 +- src/SPIN/pair_spin_exchange_biquadratic.h | 2 +- src/SPIN/pair_spin_magelec.h | 2 +- src/SPIN/pair_spin_neel.h | 2 +- src/SRD/fix_srd.h | 2 +- src/SRD/fix_wall_srd.h | 2 +- src/STUBS/mpi.h | 2 +- src/USER-ADIOS/dump_atom_adios.h | 2 +- src/USER-ADIOS/dump_custom_adios.h | 2 +- src/USER-ADIOS/reader_adios.h | 2 +- src/USER-AWPMD/atom_vec_wavepacket.h | 2 +- src/USER-AWPMD/fix_nve_awpmd.h | 2 +- src/USER-AWPMD/pair_awpmd_cut.h | 2 +- src/USER-BOCS/compute_pressure_bocs.h | 2 +- src/USER-BOCS/fix_bocs.h | 2 +- src/USER-CGDNA/bond_oxdna2_fene.h | 2 +- src/USER-CGDNA/bond_oxdna_fene.h | 2 +- src/USER-CGDNA/bond_oxrna2_fene.h | 2 +- src/USER-CGDNA/fix_nve_dot.h | 2 +- src/USER-CGDNA/fix_nve_dotc_langevin.h | 2 +- src/USER-CGDNA/mf_oxdna.h | 2 +- src/USER-CGDNA/pair_oxdna2_coaxstk.h | 2 +- src/USER-CGDNA/pair_oxdna2_dh.h | 2 +- src/USER-CGDNA/pair_oxdna2_excv.h | 2 +- src/USER-CGDNA/pair_oxdna_coaxstk.h | 2 +- src/USER-CGDNA/pair_oxdna_excv.h | 2 +- src/USER-CGDNA/pair_oxdna_hbond.h | 2 +- src/USER-CGDNA/pair_oxdna_stk.h | 2 +- src/USER-CGDNA/pair_oxdna_xstk.h | 2 +- src/USER-CGDNA/pair_oxrna2_dh.h | 2 +- src/USER-CGDNA/pair_oxrna2_excv.h | 2 +- src/USER-CGDNA/pair_oxrna2_hbond.h | 2 +- src/USER-CGDNA/pair_oxrna2_stk.h | 2 +- src/USER-CGDNA/pair_oxrna2_xstk.h | 2 +- src/USER-CGSDK/angle_sdk.h | 2 +- src/USER-CGSDK/lj_sdk_common.h | 2 +- src/USER-CGSDK/pair_lj_sdk.h | 2 +- src/USER-CGSDK/pair_lj_sdk_coul_long.h | 2 +- src/USER-CGSDK/pair_lj_sdk_coul_msm.h | 2 +- src/USER-COLVARS/fix_colvars.h | 2 +- src/USER-COLVARS/group_ndx.h | 2 +- src/USER-COLVARS/ndx_group.h | 2 +- src/USER-DIFFRACTION/compute_saed.h | 2 +- src/USER-DIFFRACTION/compute_saed_consts.h | 2 +- src/USER-DIFFRACTION/compute_xrd.h | 2 +- src/USER-DIFFRACTION/compute_xrd_consts.h | 2 +- src/USER-DIFFRACTION/fix_saed_vtk.h | 2 +- src/USER-DPD/atom_vec_dpd.h | 2 +- src/USER-DPD/compute_dpd.h | 2 +- src/USER-DPD/compute_dpd_atom.h | 2 +- src/USER-DPD/fix_dpd_energy.h | 2 +- src/USER-DPD/fix_eos_cv.h | 2 +- src/USER-DPD/fix_eos_table.h | 2 +- src/USER-DPD/fix_eos_table_rx.h | 2 +- src/USER-DPD/fix_rx.h | 2 +- src/USER-DPD/fix_shardlow.h | 2 +- src/USER-DPD/nbin_ssa.h | 2 +- src/USER-DPD/npair_half_bin_newton_ssa.h | 2 +- src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h | 2 +- src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h | 2 +- src/USER-DPD/nstencil_ssa.h | 2 +- src/USER-DPD/pair_dpd_fdt.h | 2 +- src/USER-DPD/pair_dpd_fdt_energy.h | 2 +- src/USER-DPD/pair_exp6_rx.h | 2 +- src/USER-DPD/pair_multi_lucy.h | 2 +- src/USER-DPD/pair_multi_lucy_rx.h | 2 +- src/USER-DPD/pair_table_rx.h | 2 +- src/USER-DPD/random_external_state.h | 2 +- src/USER-DRUDE/compute_temp_drude.h | 2 +- src/USER-DRUDE/fix_drude.h | 2 +- src/USER-DRUDE/fix_drude_transform.h | 2 +- src/USER-DRUDE/fix_langevin_drude.h | 2 +- src/USER-DRUDE/fix_tgnh_drude.h | 2 +- src/USER-DRUDE/fix_tgnpt_drude.h | 2 +- src/USER-DRUDE/fix_tgnvt_drude.h | 2 +- src/USER-DRUDE/pair_coul_tt.h | 2 +- src/USER-DRUDE/pair_lj_cut_thole_long.h | 2 +- src/USER-DRUDE/pair_thole.h | 2 +- src/USER-EFF/atom_vec_electron.h | 2 +- src/USER-EFF/compute_ke_atom_eff.h | 2 +- src/USER-EFF/compute_ke_eff.h | 2 +- src/USER-EFF/compute_temp_deform_eff.h | 2 +- src/USER-EFF/compute_temp_eff.h | 2 +- src/USER-EFF/compute_temp_region_eff.h | 2 +- src/USER-EFF/fix_langevin_eff.h | 2 +- src/USER-EFF/fix_nh_eff.h | 2 +- src/USER-EFF/fix_nph_eff.h | 2 +- src/USER-EFF/fix_npt_eff.h | 2 +- src/USER-EFF/fix_nve_eff.h | 2 +- src/USER-EFF/fix_nvt_eff.h | 2 +- src/USER-EFF/fix_nvt_sllod_eff.h | 2 +- src/USER-EFF/fix_temp_rescale_eff.h | 2 +- src/USER-EFF/pair_eff_cut.h | 2 +- src/USER-EFF/pair_eff_inline.h | 2 +- src/USER-FEP/compute_fep.h | 2 +- src/USER-FEP/fix_adapt_fep.h | 2 +- src/USER-FEP/pair_coul_cut_soft.h | 2 +- src/USER-FEP/pair_coul_long_soft.h | 2 +- src/USER-FEP/pair_lj_charmm_coul_long_soft.h | 2 +- src/USER-FEP/pair_lj_class2_coul_cut_soft.h | 2 +- src/USER-FEP/pair_lj_class2_coul_long_soft.h | 2 +- src/USER-FEP/pair_lj_class2_soft.h | 2 +- src/USER-FEP/pair_lj_cut_coul_cut_soft.h | 2 +- src/USER-FEP/pair_lj_cut_coul_long_soft.h | 2 +- src/USER-FEP/pair_lj_cut_soft.h | 2 +- src/USER-FEP/pair_lj_cut_tip4p_long_soft.h | 2 +- src/USER-FEP/pair_morse_soft.h | 2 +- src/USER-FEP/pair_tip4p_long_soft.h | 2 +- src/USER-H5MD/dump_h5md.h | 2 +- src/USER-INTEL/angle_charmm_intel.h | 2 +- src/USER-INTEL/angle_harmonic_intel.h | 2 +- src/USER-INTEL/bond_fene_intel.h | 2 +- src/USER-INTEL/bond_harmonic_intel.h | 2 +- src/USER-INTEL/dihedral_charmm_intel.h | 2 +- src/USER-INTEL/dihedral_fourier_intel.h | 2 +- src/USER-INTEL/dihedral_harmonic_intel.h | 2 +- src/USER-INTEL/dihedral_opls_intel.h | 2 +- src/USER-INTEL/fix_intel.h | 2 +- src/USER-INTEL/fix_nh_intel.h | 2 +- src/USER-INTEL/fix_npt_intel.h | 2 +- src/USER-INTEL/fix_nve_asphere_intel.h | 2 +- src/USER-INTEL/fix_nve_intel.h | 2 +- src/USER-INTEL/fix_nvt_intel.h | 2 +- src/USER-INTEL/fix_nvt_sllod_intel.h | 2 +- src/USER-INTEL/improper_cvff_intel.h | 2 +- src/USER-INTEL/improper_harmonic_intel.h | 2 +- src/USER-INTEL/intel_buffers.h | 2 +- src/USER-INTEL/intel_intrinsics.h | 2 +- src/USER-INTEL/intel_preprocess.h | 2 +- src/USER-INTEL/intel_simd.h | 2 +- src/USER-INTEL/math_extra_intel.h | 2 +- src/USER-INTEL/nbin_intel.h | 2 +- src/USER-INTEL/npair_full_bin_ghost_intel.h | 2 +- src/USER-INTEL/npair_full_bin_intel.h | 2 +- src/USER-INTEL/npair_half_bin_newton_intel.h | 2 +- src/USER-INTEL/npair_half_bin_newton_tri_intel.h | 2 +- src/USER-INTEL/npair_halffull_newtoff_intel.h | 2 +- src/USER-INTEL/npair_halffull_newton_intel.h | 2 +- src/USER-INTEL/npair_intel.h | 2 +- src/USER-INTEL/npair_skip_intel.h | 2 +- src/USER-INTEL/pair_airebo_intel.h | 2 +- src/USER-INTEL/pair_airebo_morse_intel.h | 2 +- src/USER-INTEL/pair_buck_coul_cut_intel.h | 2 +- src/USER-INTEL/pair_buck_coul_long_intel.h | 2 +- src/USER-INTEL/pair_buck_intel.h | 2 +- src/USER-INTEL/pair_dpd_intel.h | 2 +- src/USER-INTEL/pair_eam_alloy_intel.h | 2 +- src/USER-INTEL/pair_eam_fs_intel.h | 2 +- src/USER-INTEL/pair_eam_intel.h | 2 +- src/USER-INTEL/pair_gayberne_intel.h | 2 +- src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.h | 2 +- src/USER-INTEL/pair_lj_charmm_coul_long_intel.h | 2 +- src/USER-INTEL/pair_lj_cut_coul_long_intel.h | 2 +- src/USER-INTEL/pair_lj_cut_intel.h | 2 +- src/USER-INTEL/pair_lj_long_coul_long_intel.h | 2 +- src/USER-INTEL/pair_rebo_intel.h | 2 +- src/USER-INTEL/pair_sw_intel.h | 2 +- src/USER-INTEL/pair_tersoff_intel.h | 2 +- src/USER-INTEL/pppm_disp_intel.h | 2 +- src/USER-INTEL/pppm_intel.h | 2 +- src/USER-INTEL/verlet_lrt_intel.h | 2 +- src/USER-LB/fix_lb_momentum.h | 2 +- src/USER-LB/fix_lb_pc.h | 2 +- src/USER-LB/fix_lb_rigid_pc_sphere.h | 2 +- src/USER-LB/fix_lb_viscous.h | 2 +- src/USER-MANIFOLD/fix_manifoldforce.h | 2 +- src/USER-MANIFOLD/fix_nve_manifold_rattle.h | 2 +- src/USER-MANIFOLD/fix_nvt_manifold_rattle.h | 2 +- src/USER-MANIFOLD/manifold.h | 2 +- src/USER-MANIFOLD/manifold_factory.h | 2 +- src/USER-MANIFOLD/manifold_gaussian_bump.h | 4 ++-- src/USER-MEAMC/meam.h | 2 +- src/USER-MEAMC/pair_meamc.h | 2 +- src/USER-MESODPD/atom_vec_edpd.h | 2 +- src/USER-MESODPD/atom_vec_mdpd.h | 2 +- src/USER-MESODPD/atom_vec_tdpd.h | 2 +- src/USER-MESODPD/compute_edpd_temp_atom.h | 2 +- src/USER-MESODPD/compute_tdpd_cc_atom.h | 2 +- src/USER-MESODPD/fix_edpd_source.h | 2 +- src/USER-MESODPD/fix_mvv_dpd.h | 2 +- src/USER-MESODPD/fix_mvv_edpd.h | 2 +- src/USER-MESODPD/fix_mvv_tdpd.h | 2 +- src/USER-MESODPD/fix_tdpd_source.h | 2 +- src/USER-MESODPD/pair_edpd.h | 2 +- src/USER-MESODPD/pair_mdpd.h | 2 +- src/USER-MESODPD/pair_mdpd_rhosum.h | 2 +- src/USER-MESODPD/pair_tdpd.h | 2 +- src/USER-MESONT/atom_vec_mesont.h | 2 +- src/USER-MESONT/compute_mesont.h | 2 +- src/USER-MESONT/export_mesont.h | 2 +- src/USER-MESONT/pair_mesont_tpm.h | 2 +- src/USER-MGPT/mgpt_bgmul_7.c.h | 4 ++-- src/USER-MGPT/mgpt_linalg.h | 4 ++-- src/USER-MGPT/mgpt_mmul3_538.c.h | 4 ++-- src/USER-MGPT/mgpt_mmul3_748.c.h | 4 ++-- src/USER-MGPT/mgpt_mmul3d_526.c.h | 4 ++-- src/USER-MGPT/mgpt_mmul3d_744.c.h | 4 ++-- src/USER-MGPT/mgpt_mmul_bg_552.c.h | 4 ++-- src/USER-MGPT/mgpt_mmul_bg_722.c.h | 4 ++-- src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h | 4 ++-- src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h | 4 ++-- src/USER-MGPT/mgpt_readpot.h | 4 ++-- src/USER-MGPT/mgpt_splinetab.h | 4 ++-- src/USER-MGPT/mgpt_ttr_5022.c.h | 4 ++-- src/USER-MGPT/mgpt_ttr_5042.c.h | 4 ++-- src/USER-MGPT/mgpt_ttr_5123.c.h | 4 ++-- src/USER-MGPT/mgpt_ttr_5141.c.h | 4 ++-- src/USER-MGPT/mgpt_ttr_7022.c.h | 4 ++-- src/USER-MGPT/mgpt_ttr_7042.c.h | 4 ++-- src/USER-MGPT/mgpt_ttr_7123.c.h | 4 ++-- src/USER-MGPT/mgpt_ttr_7141.c.h | 4 ++-- src/USER-MGPT/pair_mgpt.h | 4 ++-- src/USER-MISC/angle_cosine_shift.h | 2 +- src/USER-MISC/angle_cosine_shift_exp.h | 2 +- src/USER-MISC/angle_dipole.h | 2 +- src/USER-MISC/angle_fourier.h | 2 +- src/USER-MISC/angle_fourier_simple.h | 2 +- src/USER-MISC/angle_gaussian.cpp | 2 +- src/USER-MISC/angle_gaussian.h | 2 +- src/USER-MISC/angle_quartic.h | 2 +- src/USER-MISC/bond_gaussian.cpp | 2 +- src/USER-MISC/bond_gaussian.h | 2 +- src/USER-MISC/bond_harmonic_shift.h | 2 +- src/USER-MISC/bond_harmonic_shift_cut.h | 2 +- src/USER-MISC/bond_special.h | 2 +- src/USER-MISC/compute_ackland_atom.h | 2 +- src/USER-MISC/compute_basal_atom.h | 2 +- src/USER-MISC/compute_cnp_atom.h | 2 +- src/USER-MISC/compute_entropy_atom.h | 2 +- src/USER-MISC/compute_gyration_shape.h | 2 +- src/USER-MISC/compute_gyration_shape_chunk.h | 2 +- src/USER-MISC/compute_hma.h | 2 +- src/USER-MISC/compute_pressure_cylinder.h | 2 +- src/USER-MISC/compute_pressure_grem.h | 2 +- src/USER-MISC/compute_stress_mop.h | 4 ++-- src/USER-MISC/compute_stress_mop_profile.h | 4 ++-- src/USER-MISC/compute_temp_rotate.h | 2 +- src/USER-MISC/compute_viscosity_cos.h | 2 +- src/USER-MISC/dihedral_cosine_shift_exp.h | 2 +- src/USER-MISC/dihedral_fourier.h | 2 +- src/USER-MISC/dihedral_nharmonic.h | 2 +- src/USER-MISC/dihedral_quadratic.h | 2 +- src/USER-MISC/dihedral_spherical.h | 2 +- src/USER-MISC/dihedral_table.h | 2 +- src/USER-MISC/dihedral_table_cut.h | 2 +- src/USER-MISC/fix_accelerate_cos.h | 2 +- src/USER-MISC/fix_addtorque.h | 2 +- src/USER-MISC/fix_ave_correlate_long.h | 2 +- src/USER-MISC/fix_electron_stopping.h | 2 +- src/USER-MISC/fix_electron_stopping_fit.cpp | 2 +- src/USER-MISC/fix_electron_stopping_fit.h | 4 ++-- src/USER-MISC/fix_ffl.h | 2 +- src/USER-MISC/fix_filter_corotate.h | 2 +- src/USER-MISC/fix_flow_gauss.h | 2 +- src/USER-MISC/fix_gle.h | 2 +- src/USER-MISC/fix_grem.h | 2 +- src/USER-MISC/fix_imd.h | 2 +- src/USER-MISC/fix_ipi.h | 2 +- src/USER-MISC/fix_momentum_chunk.h | 2 +- src/USER-MISC/fix_npt_cauchy.h | 2 +- src/USER-MISC/fix_nvk.h | 2 +- src/USER-MISC/fix_orient_eco.h | 4 ++-- src/USER-MISC/fix_pafi.h | 2 +- src/USER-MISC/fix_pimd.h | 2 +- src/USER-MISC/fix_propel_self.h | 2 +- src/USER-MISC/fix_rhok.h | 2 +- src/USER-MISC/fix_smd.h | 2 +- src/USER-MISC/fix_srp.h | 2 +- src/USER-MISC/fix_ti_spring.h | 2 +- src/USER-MISC/fix_ttm_mod.h | 2 +- src/USER-MISC/fix_wall_ees.h | 2 +- src/USER-MISC/fix_wall_reflect_stochastic.h | 2 +- src/USER-MISC/fix_wall_region_ees.h | 2 +- src/USER-MISC/improper_cossq.h | 2 +- src/USER-MISC/improper_distance.h | 2 +- src/USER-MISC/improper_fourier.h | 2 +- src/USER-MISC/improper_ring.h | 2 +- src/USER-MISC/pair_agni.h | 2 +- src/USER-MISC/pair_buck_mdf.h | 2 +- src/USER-MISC/pair_cosine_squared.h | 2 +- src/USER-MISC/pair_coul_diel.h | 2 +- src/USER-MISC/pair_coul_shield.h | 2 +- src/USER-MISC/pair_coul_slater_cut.h | 2 +- src/USER-MISC/pair_coul_slater_long.h | 2 +- src/USER-MISC/pair_drip.h | 4 ++-- src/USER-MISC/pair_e3b.h | 2 +- src/USER-MISC/pair_edip.h | 2 +- src/USER-MISC/pair_edip_multi.h | 2 +- src/USER-MISC/pair_extep.h | 2 +- src/USER-MISC/pair_gauss_cut.h | 2 +- src/USER-MISC/pair_ilp_graphene_hbn.h | 4 ++-- src/USER-MISC/pair_kolmogorov_crespi_full.h | 4 ++-- src/USER-MISC/pair_kolmogorov_crespi_z.h | 2 +- src/USER-MISC/pair_lebedeva_z.h | 2 +- src/USER-MISC/pair_lennard_mdf.h | 2 +- src/USER-MISC/pair_list.h | 2 +- src/USER-MISC/pair_lj_expand_coul_long.h | 2 +- src/USER-MISC/pair_lj_mdf.h | 2 +- src/USER-MISC/pair_lj_sf_dipole_sf.h | 2 +- src/USER-MISC/pair_local_density.h | 2 +- src/USER-MISC/pair_meam_spline.h | 2 +- src/USER-MISC/pair_meam_sw_spline.h | 2 +- src/USER-MISC/pair_momb.h | 2 +- src/USER-MISC/pair_morse_smooth_linear.h | 2 +- src/USER-MISC/pair_srp.h | 2 +- src/USER-MISC/pair_tersoff_table.h | 2 +- src/USER-MISC/pair_wf_cut.cpp | 2 +- src/USER-MISC/pair_wf_cut.h | 2 +- src/USER-MISC/temper_grem.h | 2 +- src/USER-MISC/temper_npt.h | 2 +- src/USER-MOFFF/angle_class2_p6.h | 2 +- src/USER-MOFFF/angle_cosine_buck6d.h | 2 +- src/USER-MOFFF/improper_inversion_harmonic.h | 2 +- src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.h | 2 +- src/USER-MOFFF/pair_buck6d_coul_gauss_long.h | 2 +- src/USER-MOLFILE/dump_molfile.h | 2 +- src/USER-MOLFILE/molfile_interface.h | 2 +- src/USER-MOLFILE/reader_molfile.h | 2 +- src/USER-NETCDF/dump_netcdf.h | 2 +- src/USER-NETCDF/dump_netcdf_mpiio.h | 2 +- src/USER-OMP/angle_charmm_omp.h | 2 +- src/USER-OMP/angle_class2_omp.h | 2 +- src/USER-OMP/angle_cosine_delta_omp.h | 2 +- src/USER-OMP/angle_cosine_omp.h | 2 +- src/USER-OMP/angle_cosine_periodic_omp.h | 2 +- src/USER-OMP/angle_cosine_shift_exp_omp.h | 2 +- src/USER-OMP/angle_cosine_shift_omp.h | 2 +- src/USER-OMP/angle_cosine_squared_omp.h | 2 +- src/USER-OMP/angle_dipole_omp.h | 2 +- src/USER-OMP/angle_fourier_omp.h | 2 +- src/USER-OMP/angle_fourier_simple_omp.h | 2 +- src/USER-OMP/angle_harmonic_omp.h | 2 +- src/USER-OMP/angle_quartic_omp.h | 2 +- src/USER-OMP/angle_sdk_omp.h | 2 +- src/USER-OMP/angle_table_omp.h | 2 +- src/USER-OMP/bond_class2_omp.h | 2 +- src/USER-OMP/bond_fene_expand_omp.h | 2 +- src/USER-OMP/bond_fene_omp.h | 2 +- src/USER-OMP/bond_gromos_omp.h | 2 +- src/USER-OMP/bond_harmonic_omp.h | 2 +- src/USER-OMP/bond_harmonic_shift_cut_omp.h | 2 +- src/USER-OMP/bond_harmonic_shift_omp.h | 2 +- src/USER-OMP/bond_morse_omp.h | 2 +- src/USER-OMP/bond_nonlinear_omp.h | 2 +- src/USER-OMP/bond_quartic_omp.h | 2 +- src/USER-OMP/bond_table_omp.h | 2 +- src/USER-OMP/dihedral_charmm_omp.h | 2 +- src/USER-OMP/dihedral_class2_omp.h | 2 +- src/USER-OMP/dihedral_cosine_shift_exp_omp.h | 2 +- src/USER-OMP/dihedral_fourier_omp.h | 2 +- src/USER-OMP/dihedral_harmonic_omp.h | 2 +- src/USER-OMP/dihedral_helix_omp.h | 2 +- src/USER-OMP/dihedral_multi_harmonic_omp.h | 2 +- src/USER-OMP/dihedral_nharmonic_omp.h | 2 +- src/USER-OMP/dihedral_opls_omp.h | 2 +- src/USER-OMP/dihedral_quadratic_omp.h | 2 +- src/USER-OMP/dihedral_table_omp.h | 2 +- src/USER-OMP/ewald_omp.h | 2 +- src/USER-OMP/fix_gravity_omp.h | 2 +- src/USER-OMP/fix_neigh_history_omp.h | 2 +- src/USER-OMP/fix_nh_asphere_omp.h | 2 +- src/USER-OMP/fix_nh_omp.h | 2 +- src/USER-OMP/fix_nh_sphere_omp.h | 2 +- src/USER-OMP/fix_nph_asphere_omp.h | 2 +- src/USER-OMP/fix_nph_omp.h | 2 +- src/USER-OMP/fix_nph_sphere_omp.h | 2 +- src/USER-OMP/fix_npt_asphere_omp.h | 2 +- src/USER-OMP/fix_npt_omp.h | 2 +- src/USER-OMP/fix_npt_sphere_omp.h | 2 +- src/USER-OMP/fix_nve_omp.h | 2 +- src/USER-OMP/fix_nve_sphere_omp.h | 2 +- src/USER-OMP/fix_nvt_asphere_omp.h | 2 +- src/USER-OMP/fix_nvt_omp.h | 2 +- src/USER-OMP/fix_nvt_sphere_omp.h | 2 +- src/USER-OMP/fix_omp.h | 2 +- src/USER-OMP/fix_peri_neigh_omp.h | 2 +- src/USER-OMP/fix_qeq_comb_omp.h | 2 +- src/USER-OMP/fix_qeq_reax_omp.h | 2 +- src/USER-OMP/fix_rigid_nh_omp.h | 2 +- src/USER-OMP/fix_rigid_nph_omp.h | 2 +- src/USER-OMP/fix_rigid_npt_omp.h | 2 +- src/USER-OMP/fix_rigid_nve_omp.h | 2 +- src/USER-OMP/fix_rigid_nvt_omp.h | 2 +- src/USER-OMP/fix_rigid_omp.h | 2 +- src/USER-OMP/fix_rigid_small_omp.h | 2 +- src/USER-OMP/improper_class2_omp.h | 2 +- src/USER-OMP/improper_cossq_omp.h | 2 +- src/USER-OMP/improper_cvff_omp.h | 2 +- src/USER-OMP/improper_fourier_omp.h | 2 +- src/USER-OMP/improper_harmonic_omp.h | 2 +- src/USER-OMP/improper_ring_omp.h | 2 +- src/USER-OMP/improper_umbrella_omp.h | 2 +- src/USER-OMP/msm_cg_omp.h | 2 +- src/USER-OMP/msm_omp.h | 2 +- src/USER-OMP/npair_full_bin_atomonly_omp.h | 2 +- src/USER-OMP/npair_full_bin_ghost_omp.h | 2 +- src/USER-OMP/npair_full_bin_omp.h | 2 +- src/USER-OMP/npair_full_multi_omp.h | 2 +- src/USER-OMP/npair_full_nsq_ghost_omp.h | 2 +- src/USER-OMP/npair_full_nsq_omp.h | 2 +- src/USER-OMP/npair_half_bin_atomonly_newton_omp.h | 2 +- src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h | 2 +- src/USER-OMP/npair_half_bin_newtoff_omp.h | 2 +- src/USER-OMP/npair_half_bin_newton_omp.h | 2 +- src/USER-OMP/npair_half_bin_newton_tri_omp.h | 2 +- src/USER-OMP/npair_half_multi_newtoff_omp.h | 2 +- src/USER-OMP/npair_half_multi_newton_omp.h | 2 +- src/USER-OMP/npair_half_multi_newton_tri_omp.h | 2 +- src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h | 2 +- src/USER-OMP/npair_half_nsq_newtoff_omp.h | 2 +- src/USER-OMP/npair_half_nsq_newton_omp.h | 2 +- src/USER-OMP/npair_half_respa_bin_newtoff_omp.h | 2 +- src/USER-OMP/npair_half_respa_bin_newton_omp.h | 2 +- src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h | 2 +- src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h | 2 +- src/USER-OMP/npair_half_respa_nsq_newton_omp.h | 2 +- src/USER-OMP/npair_half_size_bin_newtoff_omp.h | 2 +- src/USER-OMP/npair_half_size_bin_newton_omp.h | 2 +- src/USER-OMP/npair_half_size_bin_newton_tri_omp.h | 2 +- src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp | 2 +- src/USER-OMP/npair_half_size_multi_newtoff_omp.h | 2 +- src/USER-OMP/npair_half_size_multi_newton_omp.cpp | 2 +- src/USER-OMP/npair_half_size_multi_newton_omp.h | 2 +- src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp | 2 +- src/USER-OMP/npair_half_size_multi_newton_tri_omp.h | 2 +- src/USER-OMP/npair_half_size_nsq_newtoff_omp.h | 2 +- src/USER-OMP/npair_half_size_nsq_newton_omp.h | 2 +- src/USER-OMP/npair_halffull_newtoff_omp.h | 2 +- src/USER-OMP/npair_halffull_newton_omp.h | 2 +- src/USER-OMP/npair_omp.h | 2 +- src/USER-OMP/npair_skip_omp.h | 2 +- src/USER-OMP/pair_adp_omp.h | 2 +- src/USER-OMP/pair_agni_omp.h | 2 +- src/USER-OMP/pair_airebo_morse_omp.h | 2 +- src/USER-OMP/pair_airebo_omp.h | 2 +- src/USER-OMP/pair_beck_omp.h | 2 +- src/USER-OMP/pair_born_coul_long_omp.h | 2 +- src/USER-OMP/pair_born_coul_msm_omp.h | 2 +- src/USER-OMP/pair_born_coul_wolf_omp.h | 2 +- src/USER-OMP/pair_born_omp.h | 2 +- src/USER-OMP/pair_brownian_omp.h | 2 +- src/USER-OMP/pair_brownian_poly_omp.h | 2 +- src/USER-OMP/pair_buck_coul_cut_omp.h | 2 +- src/USER-OMP/pair_buck_coul_long_omp.h | 2 +- src/USER-OMP/pair_buck_coul_msm_omp.h | 2 +- src/USER-OMP/pair_buck_long_coul_long_omp.h | 2 +- src/USER-OMP/pair_buck_omp.h | 2 +- src/USER-OMP/pair_colloid_omp.h | 2 +- src/USER-OMP/pair_comb_omp.h | 2 +- src/USER-OMP/pair_coul_cut_global_omp.h | 2 +- src/USER-OMP/pair_coul_cut_omp.h | 2 +- src/USER-OMP/pair_coul_cut_soft_omp.h | 2 +- src/USER-OMP/pair_coul_debye_omp.h | 2 +- src/USER-OMP/pair_coul_diel_omp.h | 2 +- src/USER-OMP/pair_coul_dsf_omp.h | 2 +- src/USER-OMP/pair_coul_long_omp.h | 2 +- src/USER-OMP/pair_coul_long_soft_omp.h | 2 +- src/USER-OMP/pair_coul_msm_omp.h | 2 +- src/USER-OMP/pair_coul_wolf_omp.h | 2 +- src/USER-OMP/pair_dpd_omp.h | 2 +- src/USER-OMP/pair_dpd_tstat_omp.h | 2 +- src/USER-OMP/pair_eam_alloy_omp.h | 2 +- src/USER-OMP/pair_eam_fs_omp.h | 2 +- src/USER-OMP/pair_eam_omp.h | 2 +- src/USER-OMP/pair_edip_omp.h | 2 +- src/USER-OMP/pair_eim_omp.h | 2 +- src/USER-OMP/pair_gauss_cut_omp.h | 2 +- src/USER-OMP/pair_gauss_omp.h | 2 +- src/USER-OMP/pair_gayberne_omp.h | 2 +- src/USER-OMP/pair_gran_hertz_history_omp.h | 2 +- src/USER-OMP/pair_gran_hooke_history_omp.h | 2 +- src/USER-OMP/pair_gran_hooke_omp.h | 2 +- src/USER-OMP/pair_hbond_dreiding_lj_omp.h | 2 +- src/USER-OMP/pair_hbond_dreiding_morse_omp.h | 2 +- src/USER-OMP/pair_lj96_cut_omp.h | 2 +- src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h | 2 +- src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h | 2 +- src/USER-OMP/pair_lj_charmm_coul_long_omp.h | 2 +- src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.h | 2 +- src/USER-OMP/pair_lj_charmm_coul_msm_omp.h | 2 +- src/USER-OMP/pair_lj_class2_coul_cut_omp.h | 2 +- src/USER-OMP/pair_lj_class2_coul_long_omp.h | 2 +- src/USER-OMP/pair_lj_class2_omp.h | 2 +- src/USER-OMP/pair_lj_cubic_omp.h | 2 +- src/USER-OMP/pair_lj_cut_coul_cut_omp.h | 2 +- src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.h | 2 +- src/USER-OMP/pair_lj_cut_coul_debye_omp.h | 2 +- src/USER-OMP/pair_lj_cut_coul_dsf_omp.h | 2 +- src/USER-OMP/pair_lj_cut_coul_long_omp.h | 2 +- src/USER-OMP/pair_lj_cut_coul_long_soft_omp.h | 2 +- src/USER-OMP/pair_lj_cut_coul_msm_omp.h | 2 +- src/USER-OMP/pair_lj_cut_coul_wolf_omp.h | 2 +- src/USER-OMP/pair_lj_cut_dipole_cut_omp.h | 2 +- src/USER-OMP/pair_lj_cut_omp.h | 2 +- src/USER-OMP/pair_lj_cut_soft_omp.h | 2 +- src/USER-OMP/pair_lj_cut_thole_long_omp.h | 2 +- src/USER-OMP/pair_lj_cut_tip4p_cut_omp.h | 2 +- src/USER-OMP/pair_lj_cut_tip4p_long_omp.h | 2 +- src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.h | 2 +- src/USER-OMP/pair_lj_expand_omp.h | 2 +- src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h | 2 +- src/USER-OMP/pair_lj_gromacs_omp.h | 2 +- src/USER-OMP/pair_lj_long_coul_long_omp.h | 2 +- src/USER-OMP/pair_lj_long_tip4p_long_omp.h | 2 +- src/USER-OMP/pair_lj_relres_omp.h | 2 +- src/USER-OMP/pair_lj_sdk_coul_long_omp.h | 2 +- src/USER-OMP/pair_lj_sdk_coul_msm_omp.h | 2 +- src/USER-OMP/pair_lj_sdk_omp.h | 2 +- src/USER-OMP/pair_lj_sf_dipole_sf_omp.h | 2 +- src/USER-OMP/pair_lj_smooth_linear_omp.h | 2 +- src/USER-OMP/pair_lj_smooth_omp.h | 2 +- src/USER-OMP/pair_lubricate_omp.h | 2 +- src/USER-OMP/pair_lubricate_poly_omp.h | 2 +- src/USER-OMP/pair_meam_spline_omp.h | 2 +- src/USER-OMP/pair_morse_omp.h | 2 +- src/USER-OMP/pair_morse_smooth_linear_omp.h | 2 +- src/USER-OMP/pair_nm_cut_coul_cut_omp.h | 2 +- src/USER-OMP/pair_nm_cut_coul_long_omp.h | 2 +- src/USER-OMP/pair_nm_cut_omp.h | 2 +- src/USER-OMP/pair_peri_lps_omp.h | 2 +- src/USER-OMP/pair_peri_pmb_omp.h | 2 +- src/USER-OMP/pair_reaxc_omp.h | 2 +- src/USER-OMP/pair_rebo_omp.h | 2 +- src/USER-OMP/pair_resquared_omp.h | 2 +- src/USER-OMP/pair_soft_omp.h | 2 +- src/USER-OMP/pair_sw_omp.h | 2 +- src/USER-OMP/pair_table_omp.h | 2 +- src/USER-OMP/pair_tersoff_mod_c_omp.h | 2 +- src/USER-OMP/pair_tersoff_mod_omp.h | 2 +- src/USER-OMP/pair_tersoff_omp.h | 2 +- src/USER-OMP/pair_tersoff_table_omp.h | 2 +- src/USER-OMP/pair_tersoff_zbl_omp.h | 2 +- src/USER-OMP/pair_tip4p_cut_omp.h | 2 +- src/USER-OMP/pair_tip4p_long_omp.h | 2 +- src/USER-OMP/pair_tip4p_long_soft_omp.h | 2 +- src/USER-OMP/pair_ufm_omp.h | 2 +- src/USER-OMP/pair_vashishta_omp.h | 2 +- src/USER-OMP/pair_vashishta_table_omp.h | 2 +- src/USER-OMP/pair_yukawa_colloid_omp.h | 2 +- src/USER-OMP/pair_yukawa_omp.h | 2 +- src/USER-OMP/pair_zbl_omp.h | 2 +- src/USER-OMP/pppm_cg_omp.h | 2 +- src/USER-OMP/pppm_disp_omp.h | 2 +- src/USER-OMP/pppm_disp_tip4p_omp.h | 2 +- src/USER-OMP/pppm_omp.h | 2 +- src/USER-OMP/pppm_tip4p_omp.h | 2 +- src/USER-OMP/respa_omp.h | 2 +- src/USER-OMP/thr_data.h | 2 +- src/USER-OMP/thr_omp.h | 2 +- src/USER-PACE/pair_pace.h | 2 +- src/USER-PLUMED/fix_plumed.h | 2 +- src/USER-PTM/compute_ptm_atom.h | 2 +- src/USER-QMMM/fix_qmmm.h | 2 +- src/USER-QTB/fix_qbmsst.h | 2 +- src/USER-QTB/fix_qtb.h | 2 +- src/USER-QUIP/pair_quip.h | 2 +- src/USER-REACTION/fix_bond_react.h | 2 +- src/USER-REACTION/superpose3d.h | 2 +- src/USER-REAXC/compute_spec_atom.h | 2 +- src/USER-REAXC/fix_qeq_reax.h | 2 +- src/USER-REAXC/fix_reaxc.h | 2 +- src/USER-REAXC/fix_reaxc_bonds.h | 2 +- src/USER-REAXC/fix_reaxc_species.h | 2 +- src/USER-REAXC/pair_reaxc.h | 2 +- src/USER-SCAFACOS/scafacos.h | 2 +- src/USER-SDPD/fix_meso_move.h | 2 +- src/USER-SDPD/fix_rigid_meso.h | 2 +- src/USER-SDPD/pair_sdpd_taitwater_isothermal.h | 2 +- src/USER-SMD/atom_vec_smd.h | 2 +- src/USER-SMD/compute_smd_contact_radius.h | 2 +- src/USER-SMD/compute_smd_damage.h | 2 +- src/USER-SMD/compute_smd_hourglass_error.h | 2 +- src/USER-SMD/compute_smd_internal_energy.h | 2 +- src/USER-SMD/compute_smd_plastic_strain.h | 2 +- src/USER-SMD/compute_smd_plastic_strain_rate.h | 2 +- src/USER-SMD/compute_smd_rho.h | 2 +- src/USER-SMD/compute_smd_tlsph_defgrad.h | 2 +- src/USER-SMD/compute_smd_tlsph_dt.h | 2 +- src/USER-SMD/compute_smd_tlsph_num_neighs.h | 2 +- src/USER-SMD/compute_smd_tlsph_shape.h | 2 +- src/USER-SMD/compute_smd_tlsph_strain.h | 2 +- src/USER-SMD/compute_smd_tlsph_strain_rate.h | 2 +- src/USER-SMD/compute_smd_tlsph_stress.h | 2 +- src/USER-SMD/compute_smd_triangle_vertices.h | 2 +- src/USER-SMD/compute_smd_ulsph_effm.h | 2 +- src/USER-SMD/compute_smd_ulsph_num_neighs.h | 2 +- src/USER-SMD/compute_smd_ulsph_strain.h | 2 +- src/USER-SMD/compute_smd_ulsph_strain_rate.h | 2 +- src/USER-SMD/compute_smd_ulsph_stress.h | 2 +- src/USER-SMD/compute_smd_vol.h | 2 +- src/USER-SMD/fix_smd_adjust_dt.h | 2 +- src/USER-SMD/fix_smd_integrate_tlsph.h | 2 +- src/USER-SMD/fix_smd_integrate_ulsph.h | 2 +- src/USER-SMD/fix_smd_move_triangulated_surface.h | 2 +- src/USER-SMD/fix_smd_setvel.h | 2 +- src/USER-SMD/fix_smd_tlsph_reference_configuration.h | 2 +- src/USER-SMD/fix_smd_wall_surface.h | 2 +- src/USER-SMD/pair_smd_hertz.h | 2 +- src/USER-SMD/pair_smd_tlsph.h | 2 +- src/USER-SMD/pair_smd_triangulated_surface.h | 2 +- src/USER-SMD/pair_smd_ulsph.h | 2 +- src/USER-SMD/smd_material_models.h | 2 +- src/USER-SMTBQ/pair_smtbq.h | 2 +- src/USER-SPH/atom_vec_sph.h | 2 +- src/USER-SPH/compute_sph_e_atom.h | 2 +- src/USER-SPH/compute_sph_rho_atom.h | 2 +- src/USER-SPH/compute_sph_t_atom.h | 2 +- src/USER-SPH/fix_sph.h | 2 +- src/USER-SPH/fix_sph_stationary.h | 2 +- src/USER-SPH/pair_sph_heatconduction.h | 2 +- src/USER-SPH/pair_sph_idealgas.h | 2 +- src/USER-SPH/pair_sph_lj.h | 2 +- src/USER-SPH/pair_sph_rhosum.h | 2 +- src/USER-SPH/pair_sph_taitwater.h | 2 +- src/USER-SPH/pair_sph_taitwater_morris.h | 2 +- src/USER-TALLY/compute_force_tally.h | 2 +- src/USER-TALLY/compute_heat_flux_tally.h | 2 +- src/USER-TALLY/compute_pe_mol_tally.h | 2 +- src/USER-TALLY/compute_pe_tally.h | 2 +- src/USER-TALLY/compute_stress_tally.h | 2 +- src/USER-UEF/compute_pressure_uef.h | 2 +- src/USER-UEF/compute_temp_uef.h | 2 +- src/USER-UEF/dump_cfg_uef.h | 2 +- src/USER-UEF/fix_npt_uef.h | 2 +- src/USER-UEF/fix_nvt_uef.h | 2 +- src/USER-UEF/uef_utils.h | 2 +- src/USER-VTK/dump_vtk.h | 2 +- src/USER-YAFF/angle_cross.h | 2 +- src/USER-YAFF/angle_mm3.h | 2 +- src/USER-YAFF/bond_mm3.h | 2 +- src/USER-YAFF/improper_distharm.h | 2 +- src/USER-YAFF/improper_sqdistharm.h | 2 +- src/USER-YAFF/pair_lj_switch3_coulgauss_long.h | 2 +- src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h | 2 +- src/VORONOI/compute_voronoi_atom.h | 2 +- src/accelerator_kokkos.h | 2 +- src/accelerator_omp.h | 2 +- src/angle.h | 2 +- src/angle_deprecated.h | 2 +- src/angle_hybrid.h | 2 +- src/angle_zero.h | 2 +- src/arg_info.h | 2 +- src/atom.h | 2 +- src/atom_map.h | 2 +- src/atom_masks.h | 2 +- src/atom_vec.h | 2 +- src/atom_vec_atomic.h | 2 +- src/atom_vec_body.h | 2 +- src/atom_vec_charge.h | 2 +- src/atom_vec_ellipsoid.h | 2 +- src/atom_vec_hybrid.h | 2 +- src/atom_vec_line.h | 2 +- src/atom_vec_sphere.h | 2 +- src/atom_vec_tri.h | 2 +- src/balance.h | 2 +- src/body.h | 2 +- src/bond.h | 2 +- src/bond_deprecated.h | 2 +- src/bond_hybrid.h | 2 +- src/bond_zero.h | 2 +- src/change_box.h | 2 +- src/citeme.h | 2 +- src/comm.h | 2 +- src/comm_brick.h | 2 +- src/comm_tiled.h | 2 +- src/command.h | 2 +- src/compute.h | 2 +- src/compute_adf.h | 2 +- src/compute_aggregate_atom.h | 2 +- src/compute_angle.h | 2 +- src/compute_angle_local.h | 2 +- src/compute_angmom_chunk.h | 2 +- src/compute_bond.h | 2 +- src/compute_bond_local.h | 2 +- src/compute_centro_atom.h | 2 +- src/compute_centroid_stress_atom.h | 2 +- src/compute_chunk_atom.h | 2 +- src/compute_chunk_spread_atom.h | 2 +- src/compute_cluster_atom.h | 2 +- src/compute_cna_atom.h | 2 +- src/compute_com.h | 2 +- src/compute_com_chunk.h | 2 +- src/compute_contact_atom.h | 2 +- src/compute_coord_atom.h | 2 +- src/compute_deprecated.h | 2 +- src/compute_dihedral.h | 2 +- src/compute_dihedral_local.h | 2 +- src/compute_dipole_chunk.h | 2 +- src/compute_displace_atom.h | 2 +- src/compute_erotate_sphere.h | 2 +- src/compute_erotate_sphere_atom.h | 2 +- src/compute_fragment_atom.h | 2 +- src/compute_global_atom.h | 2 +- src/compute_group_group.h | 2 +- src/compute_gyration.h | 2 +- src/compute_gyration_chunk.h | 2 +- src/compute_heat_flux.h | 2 +- src/compute_hexorder_atom.h | 2 +- src/compute_improper.h | 2 +- src/compute_improper_local.h | 2 +- src/compute_inertia_chunk.h | 2 +- src/compute_ke.h | 2 +- src/compute_ke_atom.h | 2 +- src/compute_msd.h | 2 +- src/compute_msd_chunk.h | 2 +- src/compute_omega_chunk.h | 2 +- src/compute_orientorder_atom.h | 2 +- src/compute_pair.h | 2 +- src/compute_pair_local.h | 2 +- src/compute_pe.h | 2 +- src/compute_pe_atom.h | 2 +- src/compute_pressure.h | 2 +- src/compute_property_atom.h | 2 +- src/compute_property_chunk.h | 2 +- src/compute_property_local.h | 2 +- src/compute_rdf.h | 2 +- src/compute_reduce.h | 2 +- src/compute_reduce_chunk.h | 2 +- src/compute_reduce_region.h | 2 +- src/compute_slice.h | 2 +- src/compute_stress_atom.h | 2 +- src/compute_temp.h | 2 +- src/compute_temp_chunk.h | 2 +- src/compute_temp_com.h | 2 +- src/compute_temp_deform.h | 2 +- src/compute_temp_partial.h | 2 +- src/compute_temp_profile.h | 2 +- src/compute_temp_ramp.h | 2 +- src/compute_temp_region.h | 2 +- src/compute_temp_sphere.h | 2 +- src/compute_torque_chunk.h | 2 +- src/compute_vacf.h | 2 +- src/compute_vcm_chunk.h | 2 +- src/create_atoms.h | 2 +- src/create_bonds.h | 2 +- src/create_box.h | 2 +- src/delete_atoms.h | 2 +- src/delete_bonds.h | 2 +- src/deprecated.h | 2 +- src/dihedral.h | 2 +- src/dihedral_deprecated.h | 2 +- src/dihedral_hybrid.h | 2 +- src/dihedral_zero.h | 2 +- src/displace_atoms.h | 2 +- src/domain.h | 2 +- src/dump.h | 2 +- src/dump_atom.h | 2 +- src/dump_cfg.h | 2 +- src/dump_custom.h | 2 +- src/dump_dcd.h | 2 +- src/dump_deprecated.h | 2 +- src/dump_image.h | 2 +- src/dump_local.h | 2 +- src/dump_movie.h | 2 +- src/dump_xyz.h | 2 +- src/error.h | 2 +- src/exceptions.h | 2 +- src/file_writer.h | 2 +- src/finish.h | 2 +- src/fix.h | 2 +- src/fix_adapt.h | 2 +- src/fix_addforce.h | 2 +- src/fix_ave_atom.h | 2 +- src/fix_ave_chunk.h | 2 +- src/fix_ave_correlate.h | 2 +- src/fix_ave_histo.h | 2 +- src/fix_ave_histo_weight.h | 2 +- src/fix_ave_time.h | 2 +- src/fix_aveforce.h | 2 +- src/fix_balance.h | 2 +- src/fix_box_relax.h | 2 +- src/fix_controller.h | 2 +- src/fix_deform.h | 2 +- src/fix_deprecated.h | 2 +- src/fix_drag.h | 2 +- src/fix_dt_reset.h | 2 +- src/fix_dummy.h | 2 +- src/fix_enforce2d.h | 2 +- src/fix_external.h | 2 +- src/fix_gravity.h | 2 +- src/fix_group.h | 2 +- src/fix_halt.h | 2 +- src/fix_heat.h | 2 +- src/fix_indent.h | 2 +- src/fix_langevin.h | 2 +- src/fix_lineforce.h | 2 +- src/fix_minimize.h | 2 +- src/fix_momentum.h | 2 +- src/fix_move.h | 2 +- src/fix_neigh_history.h | 2 +- src/fix_nh.h | 2 +- src/fix_nh_sphere.h | 2 +- src/fix_nph.h | 2 +- src/fix_nph_sphere.h | 2 +- src/fix_npt.h | 2 +- src/fix_npt_sphere.h | 2 +- src/fix_numdiff.h | 2 +- src/fix_nve.h | 2 +- src/fix_nve_limit.h | 2 +- src/fix_nve_noforce.h | 2 +- src/fix_nve_sphere.h | 2 +- src/fix_nvt.h | 2 +- src/fix_nvt_sphere.h | 2 +- src/fix_planeforce.h | 2 +- src/fix_press_berendsen.h | 2 +- src/fix_print.h | 2 +- src/fix_property_atom.h | 2 +- src/fix_read_restart.h | 2 +- src/fix_recenter.h | 2 +- src/fix_respa.h | 2 +- src/fix_restrain.h | 2 +- src/fix_setforce.h | 2 +- src/fix_spring.h | 2 +- src/fix_spring_chunk.h | 2 +- src/fix_spring_rg.h | 2 +- src/fix_spring_self.h | 2 +- src/fix_store.h | 2 +- src/fix_store_force.h | 2 +- src/fix_store_state.h | 2 +- src/fix_temp_berendsen.h | 2 +- src/fix_temp_csld.h | 2 +- src/fix_temp_csvr.h | 2 +- src/fix_temp_rescale.h | 2 +- src/fix_tmd.h | 2 +- src/fix_vector.h | 2 +- src/fix_viscous.h | 2 +- src/fix_wall.h | 2 +- src/fix_wall_harmonic.h | 2 +- src/fix_wall_lj1043.h | 2 +- src/fix_wall_lj126.h | 2 +- src/fix_wall_lj93.h | 2 +- src/fix_wall_morse.h | 2 +- src/fix_wall_reflect.h | 2 +- src/fix_wall_region.h | 2 +- src/force.h | 2 +- src/group.h | 2 +- src/image.h | 2 +- src/imbalance.h | 2 +- src/imbalance_group.h | 2 +- src/imbalance_neigh.h | 2 +- src/imbalance_store.h | 2 +- src/imbalance_time.h | 2 +- src/imbalance_var.h | 2 +- src/improper.h | 2 +- src/improper_deprecated.h | 2 +- src/improper_hybrid.h | 2 +- src/improper_zero.h | 2 +- src/info.h | 2 +- src/input.h | 2 +- src/integrate.h | 2 +- src/irregular.h | 2 +- src/kspace.h | 2 +- src/kspace_deprecated.h | 2 +- src/lammps.h | 2 +- src/lammpsplugin.h | 2 +- src/lattice.h | 2 +- src/library.h | 2 +- src/lmppython.h | 2 +- src/lmprestart.h | 4 ++-- src/lmptype.h | 2 +- src/math_const.h | 2 +- src/math_eigen.h | 2 +- src/math_eigen_impl.h | 2 +- src/math_extra.h | 2 +- src/math_special.h | 2 +- src/memory.h | 2 +- src/min.h | 2 +- src/min_cg.h | 2 +- src/min_fire.h | 2 +- src/min_fire_old.h | 2 +- src/min_hftn.h | 2 +- src/min_linesearch.h | 2 +- src/min_quickmin.h | 2 +- src/min_sd.h | 2 +- src/minimize.h | 2 +- src/modify.h | 2 +- src/molecule.h | 2 +- src/mpiio.h | 2 +- src/my_page.h | 2 +- src/my_pool_chunk.h | 2 +- src/nbin.h | 2 +- src/nbin_standard.h | 2 +- src/neigh_list.h | 2 +- src/neigh_request.h | 2 +- src/neighbor.h | 2 +- src/npair.h | 2 +- src/npair_copy.h | 2 +- src/npair_full_bin.h | 2 +- src/npair_full_bin_atomonly.h | 2 +- src/npair_full_bin_ghost.h | 2 +- src/npair_full_multi.h | 2 +- src/npair_full_nsq.h | 2 +- src/npair_full_nsq_ghost.h | 2 +- src/npair_half_bin_atomonly_newton.h | 2 +- src/npair_half_bin_newtoff.h | 2 +- src/npair_half_bin_newtoff_ghost.h | 2 +- src/npair_half_bin_newton.h | 2 +- src/npair_half_bin_newton_tri.h | 2 +- src/npair_half_multi_newtoff.h | 2 +- src/npair_half_multi_newton.h | 2 +- src/npair_half_multi_newton_tri.h | 2 +- src/npair_half_nsq_newtoff.h | 2 +- src/npair_half_nsq_newtoff_ghost.h | 2 +- src/npair_half_nsq_newton.h | 2 +- src/npair_half_respa_bin_newtoff.h | 2 +- src/npair_half_respa_bin_newton.h | 2 +- src/npair_half_respa_bin_newton_tri.h | 2 +- src/npair_half_respa_nsq_newtoff.h | 2 +- src/npair_half_respa_nsq_newton.h | 2 +- src/npair_half_size_bin_newtoff.h | 2 +- src/npair_half_size_bin_newton.h | 2 +- src/npair_half_size_bin_newton_tri.h | 2 +- src/npair_half_size_multi_newtoff.cpp | 2 +- src/npair_half_size_multi_newtoff.h | 2 +- src/npair_half_size_multi_newton.cpp | 2 +- src/npair_half_size_multi_newton.h | 2 +- src/npair_half_size_multi_newton_tri.cpp | 2 +- src/npair_half_size_multi_newton_tri.h | 2 +- src/npair_half_size_nsq_newtoff.h | 2 +- src/npair_half_size_nsq_newton.h | 2 +- src/npair_halffull_newtoff.h | 2 +- src/npair_halffull_newton.h | 2 +- src/npair_skip.h | 2 +- src/npair_skip_respa.h | 2 +- src/npair_skip_size.h | 2 +- src/npair_skip_size_off2on.h | 2 +- src/npair_skip_size_off2on_oneside.h | 2 +- src/nstencil.h | 2 +- src/nstencil_full_bin_2d.h | 2 +- src/nstencil_full_bin_3d.h | 2 +- src/nstencil_full_ghost_bin_2d.h | 2 +- src/nstencil_full_ghost_bin_3d.h | 2 +- src/nstencil_full_multi_2d.h | 2 +- src/nstencil_full_multi_3d.h | 2 +- src/nstencil_half_bin_2d_newtoff.h | 2 +- src/nstencil_half_bin_2d_newton.h | 2 +- src/nstencil_half_bin_2d_newton_tri.h | 2 +- src/nstencil_half_bin_3d_newtoff.h | 2 +- src/nstencil_half_bin_3d_newton.h | 2 +- src/nstencil_half_bin_3d_newton_tri.h | 2 +- src/nstencil_half_ghost_bin_2d_newtoff.h | 2 +- src/nstencil_half_ghost_bin_3d_newtoff.h | 2 +- src/nstencil_half_multi_2d_newtoff.h | 2 +- src/nstencil_half_multi_2d_newton.h | 2 +- src/nstencil_half_multi_2d_newton_tri.h | 2 +- src/nstencil_half_multi_3d_newtoff.h | 2 +- src/nstencil_half_multi_3d_newton.h | 2 +- src/nstencil_half_multi_3d_newton_tri.h | 2 +- src/ntopo.h | 2 +- src/ntopo_angle_all.h | 2 +- src/ntopo_angle_partial.h | 2 +- src/ntopo_angle_template.h | 2 +- src/ntopo_bond_all.h | 2 +- src/ntopo_bond_partial.h | 2 +- src/ntopo_bond_template.h | 2 +- src/ntopo_dihedral_all.h | 2 +- src/ntopo_dihedral_partial.h | 2 +- src/ntopo_dihedral_template.h | 2 +- src/ntopo_improper_all.h | 2 +- src/ntopo_improper_partial.h | 2 +- src/ntopo_improper_template.h | 2 +- src/omp_compat.h | 2 +- src/output.h | 2 +- src/pack.h | 2 +- src/pair.h | 2 +- src/pair_beck.h | 2 +- src/pair_born.h | 2 +- src/pair_born_coul_dsf.h | 2 +- src/pair_born_coul_wolf.h | 2 +- src/pair_buck.h | 2 +- src/pair_buck_coul_cut.h | 2 +- src/pair_coul_cut.h | 2 +- src/pair_coul_cut_global.h | 2 +- src/pair_coul_debye.h | 2 +- src/pair_coul_dsf.h | 2 +- src/pair_coul_streitz.h | 2 +- src/pair_coul_wolf.h | 2 +- src/pair_deprecated.h | 2 +- src/pair_dpd.h | 2 +- src/pair_dpd_tstat.h | 2 +- src/pair_gauss.h | 2 +- src/pair_hybrid.h | 2 +- src/pair_hybrid_overlay.h | 2 +- src/pair_hybrid_scaled.h | 2 +- src/pair_lj96_cut.h | 2 +- src/pair_lj_cubic.h | 2 +- src/pair_lj_cubic_const.h | 2 +- src/pair_lj_cut.h | 2 +- src/pair_lj_cut_coul_cut.h | 2 +- src/pair_lj_cut_coul_debye.h | 2 +- src/pair_lj_cut_coul_dsf.h | 2 +- src/pair_lj_cut_coul_wolf.h | 2 +- src/pair_lj_expand.h | 2 +- src/pair_lj_gromacs.h | 2 +- src/pair_lj_gromacs_coul_gromacs.h | 2 +- src/pair_lj_relres.cpp | 2 +- src/pair_lj_relres.h | 2 +- src/pair_lj_smooth.h | 2 +- src/pair_lj_smooth_linear.h | 2 +- src/pair_mie_cut.h | 2 +- src/pair_morse.h | 2 +- src/pair_soft.h | 2 +- src/pair_table.h | 2 +- src/pair_ufm.h | 2 +- src/pair_yukawa.h | 2 +- src/pair_zbl.h | 2 +- src/pair_zbl_const.h | 2 +- src/pair_zero.h | 2 +- src/pointers.h | 2 +- src/potential_file_reader.h | 2 +- src/procmap.h | 2 +- src/random_mars.h | 2 +- src/random_park.h | 2 +- src/rcb.h | 2 +- src/read_data.h | 2 +- src/read_dump.h | 2 +- src/read_restart.h | 2 +- src/reader.h | 2 +- src/reader_native.h | 2 +- src/reader_xyz.h | 2 +- src/region.h | 2 +- src/region_block.h | 2 +- src/region_cone.h | 2 +- src/region_cylinder.h | 2 +- src/region_deprecated.h | 2 +- src/region_intersect.h | 2 +- src/region_plane.h | 2 +- src/region_prism.h | 2 +- src/region_sphere.h | 2 +- src/region_union.h | 2 +- src/replicate.h | 2 +- src/rerun.h | 2 +- src/reset_atom_ids.h | 2 +- src/reset_mol_ids.h | 2 +- src/respa.h | 2 +- src/run.h | 2 +- src/set.h | 2 +- src/special.h | 2 +- src/suffix.h | 2 +- src/table_file_reader.h | 2 +- src/text_file_reader.h | 2 +- src/thermo.h | 2 +- src/timer.h | 2 +- src/tokenizer.h | 2 +- src/universe.h | 2 +- src/update.h | 2 +- src/utils.h | 2 +- src/variable.h | 2 +- src/velocity.h | 2 +- src/verlet.h | 2 +- src/write_coeff.h | 2 +- src/write_data.h | 2 +- src/write_dump.h | 2 +- src/write_restart.h | 2 +- 1584 files changed, 1630 insertions(+), 1630 deletions(-) diff --git a/src/ASPHERE/compute_erotate_asphere.h b/src/ASPHERE/compute_erotate_asphere.h index 23e30d7c93..93244dd7e6 100644 --- a/src/ASPHERE/compute_erotate_asphere.h +++ b/src/ASPHERE/compute_erotate_asphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ASPHERE/compute_temp_asphere.h b/src/ASPHERE/compute_temp_asphere.h index 5ecbf8057a..61d3162d6c 100644 --- a/src/ASPHERE/compute_temp_asphere.h +++ b/src/ASPHERE/compute_temp_asphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ASPHERE/fix_nh_asphere.h b/src/ASPHERE/fix_nh_asphere.h index a5d8c3da6d..4c82a1b83c 100644 --- a/src/ASPHERE/fix_nh_asphere.h +++ b/src/ASPHERE/fix_nh_asphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ASPHERE/fix_nph_asphere.h b/src/ASPHERE/fix_nph_asphere.h index b0a5f19026..7e68e31048 100644 --- a/src/ASPHERE/fix_nph_asphere.h +++ b/src/ASPHERE/fix_nph_asphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ASPHERE/fix_npt_asphere.h b/src/ASPHERE/fix_npt_asphere.h index e8603e1395..5a3867e4eb 100644 --- a/src/ASPHERE/fix_npt_asphere.h +++ b/src/ASPHERE/fix_npt_asphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ASPHERE/fix_nve_asphere.h b/src/ASPHERE/fix_nve_asphere.h index 72442e9a62..f3b3e66429 100644 --- a/src/ASPHERE/fix_nve_asphere.h +++ b/src/ASPHERE/fix_nve_asphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ASPHERE/fix_nve_asphere_noforce.h b/src/ASPHERE/fix_nve_asphere_noforce.h index d15a88ffd6..eb65a928c8 100644 --- a/src/ASPHERE/fix_nve_asphere_noforce.h +++ b/src/ASPHERE/fix_nve_asphere_noforce.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ASPHERE/fix_nve_line.h b/src/ASPHERE/fix_nve_line.h index 2dc1a2961e..aa1711bbe7 100644 --- a/src/ASPHERE/fix_nve_line.h +++ b/src/ASPHERE/fix_nve_line.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ASPHERE/fix_nve_tri.h b/src/ASPHERE/fix_nve_tri.h index 57b7ad9918..b7f07755b5 100644 --- a/src/ASPHERE/fix_nve_tri.h +++ b/src/ASPHERE/fix_nve_tri.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ASPHERE/fix_nvt_asphere.h b/src/ASPHERE/fix_nvt_asphere.h index 63a4e487cc..cd03b3ff63 100644 --- a/src/ASPHERE/fix_nvt_asphere.h +++ b/src/ASPHERE/fix_nvt_asphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ASPHERE/pair_gayberne.h b/src/ASPHERE/pair_gayberne.h index 7ab8bf72ba..8e07156ce0 100644 --- a/src/ASPHERE/pair_gayberne.h +++ b/src/ASPHERE/pair_gayberne.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ASPHERE/pair_line_lj.h b/src/ASPHERE/pair_line_lj.h index 8722352e59..05e5a92cb1 100644 --- a/src/ASPHERE/pair_line_lj.h +++ b/src/ASPHERE/pair_line_lj.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ASPHERE/pair_resquared.h b/src/ASPHERE/pair_resquared.h index 9369208849..073c8b840a 100644 --- a/src/ASPHERE/pair_resquared.h +++ b/src/ASPHERE/pair_resquared.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ASPHERE/pair_tri_lj.h b/src/ASPHERE/pair_tri_lj.h index 287484887c..a92e0e1f89 100644 --- a/src/ASPHERE/pair_tri_lj.h +++ b/src/ASPHERE/pair_tri_lj.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/body_nparticle.h b/src/BODY/body_nparticle.h index c598fc8086..0853dfb341 100644 --- a/src/BODY/body_nparticle.h +++ b/src/BODY/body_nparticle.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/body_rounded_polygon.h b/src/BODY/body_rounded_polygon.h index f5129418c4..3bd5925069 100644 --- a/src/BODY/body_rounded_polygon.h +++ b/src/BODY/body_rounded_polygon.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/body_rounded_polyhedron.h b/src/BODY/body_rounded_polyhedron.h index 5aead799c3..ef4508180c 100644 --- a/src/BODY/body_rounded_polyhedron.h +++ b/src/BODY/body_rounded_polyhedron.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/compute_body_local.h b/src/BODY/compute_body_local.h index e2ff9a38bd..ddbaf3b797 100644 --- a/src/BODY/compute_body_local.h +++ b/src/BODY/compute_body_local.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/compute_temp_body.h b/src/BODY/compute_temp_body.h index 33fdb13ec8..1b272eefa7 100644 --- a/src/BODY/compute_temp_body.h +++ b/src/BODY/compute_temp_body.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/fix_nh_body.h b/src/BODY/fix_nh_body.h index 80fa9d53e0..8a80dd4148 100644 --- a/src/BODY/fix_nh_body.h +++ b/src/BODY/fix_nh_body.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/fix_nph_body.h b/src/BODY/fix_nph_body.h index a2e80caf38..6dcbb470ad 100644 --- a/src/BODY/fix_nph_body.h +++ b/src/BODY/fix_nph_body.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/fix_npt_body.h b/src/BODY/fix_npt_body.h index 24f6701dad..cd4eaff073 100644 --- a/src/BODY/fix_npt_body.h +++ b/src/BODY/fix_npt_body.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/fix_nve_body.h b/src/BODY/fix_nve_body.h index f33b5863fc..efb48df2ea 100644 --- a/src/BODY/fix_nve_body.h +++ b/src/BODY/fix_nve_body.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/fix_nvt_body.h b/src/BODY/fix_nvt_body.h index 26cc422baa..df27086222 100644 --- a/src/BODY/fix_nvt_body.h +++ b/src/BODY/fix_nvt_body.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/fix_wall_body_polygon.h b/src/BODY/fix_wall_body_polygon.h index b71dcb0683..e1b900bd7b 100644 --- a/src/BODY/fix_wall_body_polygon.h +++ b/src/BODY/fix_wall_body_polygon.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/fix_wall_body_polyhedron.h b/src/BODY/fix_wall_body_polyhedron.h index 7479f79e23..e3e7c64669 100644 --- a/src/BODY/fix_wall_body_polyhedron.h +++ b/src/BODY/fix_wall_body_polyhedron.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/pair_body_nparticle.h b/src/BODY/pair_body_nparticle.h index 9c7d832b64..d396291df2 100644 --- a/src/BODY/pair_body_nparticle.h +++ b/src/BODY/pair_body_nparticle.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/pair_body_rounded_polygon.h b/src/BODY/pair_body_rounded_polygon.h index aabe86270c..98eda90a88 100644 --- a/src/BODY/pair_body_rounded_polygon.h +++ b/src/BODY/pair_body_rounded_polygon.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/BODY/pair_body_rounded_polyhedron.h b/src/BODY/pair_body_rounded_polyhedron.h index 369f394c50..332432e533 100644 --- a/src/BODY/pair_body_rounded_polyhedron.h +++ b/src/BODY/pair_body_rounded_polyhedron.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CLASS2/angle_class2.h b/src/CLASS2/angle_class2.h index cc155747ac..cfefe507b7 100644 --- a/src/CLASS2/angle_class2.h +++ b/src/CLASS2/angle_class2.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CLASS2/bond_class2.h b/src/CLASS2/bond_class2.h index f83fecfce0..bf15f34cd4 100644 --- a/src/CLASS2/bond_class2.h +++ b/src/CLASS2/bond_class2.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CLASS2/dihedral_class2.h b/src/CLASS2/dihedral_class2.h index 32cd289137..4169b4a0f6 100644 --- a/src/CLASS2/dihedral_class2.h +++ b/src/CLASS2/dihedral_class2.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CLASS2/improper_class2.h b/src/CLASS2/improper_class2.h index cac805046a..4fb94f257f 100644 --- a/src/CLASS2/improper_class2.h +++ b/src/CLASS2/improper_class2.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CLASS2/pair_lj_class2.h b/src/CLASS2/pair_lj_class2.h index 7680498a07..a0402373c1 100644 --- a/src/CLASS2/pair_lj_class2.h +++ b/src/CLASS2/pair_lj_class2.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CLASS2/pair_lj_class2_coul_cut.h b/src/CLASS2/pair_lj_class2_coul_cut.h index f33502e23a..9fc8b57de7 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.h +++ b/src/CLASS2/pair_lj_class2_coul_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CLASS2/pair_lj_class2_coul_long.h b/src/CLASS2/pair_lj_class2_coul_long.h index 7b68382295..47e8077afe 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.h +++ b/src/CLASS2/pair_lj_class2_coul_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COLLOID/fix_wall_colloid.h b/src/COLLOID/fix_wall_colloid.h index 59b079f86e..92691a95e9 100644 --- a/src/COLLOID/fix_wall_colloid.h +++ b/src/COLLOID/fix_wall_colloid.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COLLOID/pair_brownian.h b/src/COLLOID/pair_brownian.h index 8745078522..8d3795c7fa 100644 --- a/src/COLLOID/pair_brownian.h +++ b/src/COLLOID/pair_brownian.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COLLOID/pair_brownian_poly.h b/src/COLLOID/pair_brownian_poly.h index 7808583876..875ce5b75d 100644 --- a/src/COLLOID/pair_brownian_poly.h +++ b/src/COLLOID/pair_brownian_poly.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COLLOID/pair_colloid.h b/src/COLLOID/pair_colloid.h index 24ebb9953c..6b52abe7db 100644 --- a/src/COLLOID/pair_colloid.h +++ b/src/COLLOID/pair_colloid.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COLLOID/pair_lubricate.h b/src/COLLOID/pair_lubricate.h index c2c4c6c417..2c66b7e324 100644 --- a/src/COLLOID/pair_lubricate.h +++ b/src/COLLOID/pair_lubricate.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COLLOID/pair_lubricateU.h b/src/COLLOID/pair_lubricateU.h index 4968c665a6..f588e21cda 100644 --- a/src/COLLOID/pair_lubricateU.h +++ b/src/COLLOID/pair_lubricateU.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COLLOID/pair_lubricateU_poly.h b/src/COLLOID/pair_lubricateU_poly.h index 0f22809cf2..35d5ad082a 100644 --- a/src/COLLOID/pair_lubricateU_poly.h +++ b/src/COLLOID/pair_lubricateU_poly.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COLLOID/pair_lubricate_poly.h b/src/COLLOID/pair_lubricate_poly.h index 5e58b24254..add7d2e3e3 100644 --- a/src/COLLOID/pair_lubricate_poly.h +++ b/src/COLLOID/pair_lubricate_poly.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COLLOID/pair_yukawa_colloid.h b/src/COLLOID/pair_yukawa_colloid.h index ac15d535b3..72ee88e7b6 100644 --- a/src/COLLOID/pair_yukawa_colloid.h +++ b/src/COLLOID/pair_yukawa_colloid.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COMPRESS/dump_atom_gz.h b/src/COMPRESS/dump_atom_gz.h index d540f5300a..7aa42ced5a 100644 --- a/src/COMPRESS/dump_atom_gz.h +++ b/src/COMPRESS/dump_atom_gz.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COMPRESS/dump_atom_zstd.h b/src/COMPRESS/dump_atom_zstd.h index 30108eeee9..a1ff05f040 100644 --- a/src/COMPRESS/dump_atom_zstd.h +++ b/src/COMPRESS/dump_atom_zstd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COMPRESS/dump_cfg_gz.h b/src/COMPRESS/dump_cfg_gz.h index 2844902a38..2294198340 100644 --- a/src/COMPRESS/dump_cfg_gz.h +++ b/src/COMPRESS/dump_cfg_gz.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COMPRESS/dump_cfg_zstd.h b/src/COMPRESS/dump_cfg_zstd.h index 6f4fe8face..1caf5ce657 100644 --- a/src/COMPRESS/dump_cfg_zstd.h +++ b/src/COMPRESS/dump_cfg_zstd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COMPRESS/dump_custom_gz.h b/src/COMPRESS/dump_custom_gz.h index db30b944ec..a8e499891c 100644 --- a/src/COMPRESS/dump_custom_gz.h +++ b/src/COMPRESS/dump_custom_gz.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COMPRESS/dump_custom_zstd.h b/src/COMPRESS/dump_custom_zstd.h index ce3f1325c5..679a908192 100644 --- a/src/COMPRESS/dump_custom_zstd.h +++ b/src/COMPRESS/dump_custom_zstd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COMPRESS/dump_local_gz.h b/src/COMPRESS/dump_local_gz.h index 7feb6a8945..93b605e0b9 100644 --- a/src/COMPRESS/dump_local_gz.h +++ b/src/COMPRESS/dump_local_gz.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COMPRESS/dump_local_zstd.h b/src/COMPRESS/dump_local_zstd.h index 398b1c3337..9d192679ee 100644 --- a/src/COMPRESS/dump_local_zstd.h +++ b/src/COMPRESS/dump_local_zstd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COMPRESS/dump_xyz_gz.h b/src/COMPRESS/dump_xyz_gz.h index 2fce0a3f5a..02903ddb8e 100644 --- a/src/COMPRESS/dump_xyz_gz.h +++ b/src/COMPRESS/dump_xyz_gz.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COMPRESS/dump_xyz_zstd.h b/src/COMPRESS/dump_xyz_zstd.h index 2422341557..56204c350b 100644 --- a/src/COMPRESS/dump_xyz_zstd.h +++ b/src/COMPRESS/dump_xyz_zstd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COMPRESS/gz_file_writer.h b/src/COMPRESS/gz_file_writer.h index 28473b1164..af91572d8e 100644 --- a/src/COMPRESS/gz_file_writer.h +++ b/src/COMPRESS/gz_file_writer.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/COMPRESS/zstd_file_writer.h b/src/COMPRESS/zstd_file_writer.h index a4dbbdff64..8980666856 100644 --- a/src/COMPRESS/zstd_file_writer.h +++ b/src/COMPRESS/zstd_file_writer.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CORESHELL/compute_temp_cs.h b/src/CORESHELL/compute_temp_cs.h index 3e93e4a68c..c05d96415b 100644 --- a/src/CORESHELL/compute_temp_cs.h +++ b/src/CORESHELL/compute_temp_cs.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.h b/src/CORESHELL/pair_born_coul_dsf_cs.h index a49df5971c..a3bd036fc6 100644 --- a/src/CORESHELL/pair_born_coul_dsf_cs.h +++ b/src/CORESHELL/pair_born_coul_dsf_cs.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CORESHELL/pair_born_coul_long_cs.h b/src/CORESHELL/pair_born_coul_long_cs.h index 68c29e4fc2..fdf50e0d88 100644 --- a/src/CORESHELL/pair_born_coul_long_cs.h +++ b/src/CORESHELL/pair_born_coul_long_cs.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.h b/src/CORESHELL/pair_born_coul_wolf_cs.h index 00bbd5874c..a6e2625942 100644 --- a/src/CORESHELL/pair_born_coul_wolf_cs.h +++ b/src/CORESHELL/pair_born_coul_wolf_cs.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CORESHELL/pair_buck_coul_long_cs.h b/src/CORESHELL/pair_buck_coul_long_cs.h index d6b117d677..bdca1fe5a8 100644 --- a/src/CORESHELL/pair_buck_coul_long_cs.h +++ b/src/CORESHELL/pair_buck_coul_long_cs.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CORESHELL/pair_coul_long_cs.h b/src/CORESHELL/pair_coul_long_cs.h index 48c1acb691..377c025000 100644 --- a/src/CORESHELL/pair_coul_long_cs.h +++ b/src/CORESHELL/pair_coul_long_cs.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CORESHELL/pair_coul_wolf_cs.h b/src/CORESHELL/pair_coul_wolf_cs.h index 8d98b1bbc6..b6369d4091 100644 --- a/src/CORESHELL/pair_coul_wolf_cs.h +++ b/src/CORESHELL/pair_coul_wolf_cs.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CORESHELL/pair_lj_class2_coul_long_cs.h b/src/CORESHELL/pair_lj_class2_coul_long_cs.h index b37685bda1..50833881ec 100644 --- a/src/CORESHELL/pair_lj_class2_coul_long_cs.h +++ b/src/CORESHELL/pair_lj_class2_coul_long_cs.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.h b/src/CORESHELL/pair_lj_cut_coul_long_cs.h index ba67e14978..e9fbc151d0 100644 --- a/src/CORESHELL/pair_lj_cut_coul_long_cs.h +++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/DIPOLE/atom_vec_dipole.h b/src/DIPOLE/atom_vec_dipole.h index 2030892a43..5239b8c13b 100644 --- a/src/DIPOLE/atom_vec_dipole.h +++ b/src/DIPOLE/atom_vec_dipole.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.h b/src/DIPOLE/pair_lj_cut_dipole_cut.h index 2cf38bb865..70e898f3eb 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.h +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/DIPOLE/pair_lj_long_dipole_long.h b/src/DIPOLE/pair_lj_long_dipole_long.h index 365ca3cf51..012b2b546e 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.h +++ b/src/DIPOLE/pair_lj_long_dipole_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/fix_gpu.h b/src/GPU/fix_gpu.h index 29a0907915..594a9fc144 100644 --- a/src/GPU/fix_gpu.h +++ b/src/GPU/fix_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/fix_nh_gpu.h b/src/GPU/fix_nh_gpu.h index edd210e813..6c764b7687 100644 --- a/src/GPU/fix_nh_gpu.h +++ b/src/GPU/fix_nh_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/fix_npt_gpu.h b/src/GPU/fix_npt_gpu.h index 2684935fe5..1b9f7066ac 100644 --- a/src/GPU/fix_npt_gpu.h +++ b/src/GPU/fix_npt_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/fix_nve_asphere_gpu.h b/src/GPU/fix_nve_asphere_gpu.h index 3c67e0e024..55b412c851 100644 --- a/src/GPU/fix_nve_asphere_gpu.h +++ b/src/GPU/fix_nve_asphere_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/fix_nve_gpu.h b/src/GPU/fix_nve_gpu.h index 1042d4eadd..671e3a1376 100644 --- a/src/GPU/fix_nve_gpu.h +++ b/src/GPU/fix_nve_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/fix_nvt_gpu.h b/src/GPU/fix_nvt_gpu.h index 7ccba97040..2623f92197 100644 --- a/src/GPU/fix_nvt_gpu.h +++ b/src/GPU/fix_nvt_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/gpu_extra.h b/src/GPU/gpu_extra.h index 1a957c9aef..81d2a6a511 100644 --- a/src/GPU/gpu_extra.h +++ b/src/GPU/gpu_extra.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_beck_gpu.h b/src/GPU/pair_beck_gpu.h index 8fd2cfad45..3500c7f765 100644 --- a/src/GPU/pair_beck_gpu.h +++ b/src/GPU/pair_beck_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_born_coul_long_cs_gpu.h b/src/GPU/pair_born_coul_long_cs_gpu.h index 65c80157f2..db8d015bce 100644 --- a/src/GPU/pair_born_coul_long_cs_gpu.h +++ b/src/GPU/pair_born_coul_long_cs_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_born_coul_long_gpu.h b/src/GPU/pair_born_coul_long_gpu.h index e929826a24..d9734fc401 100644 --- a/src/GPU/pair_born_coul_long_gpu.h +++ b/src/GPU/pair_born_coul_long_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.h b/src/GPU/pair_born_coul_wolf_cs_gpu.h index 5f4f4ea35c..92f6b163ab 100644 --- a/src/GPU/pair_born_coul_wolf_cs_gpu.h +++ b/src/GPU/pair_born_coul_wolf_cs_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_born_coul_wolf_gpu.h b/src/GPU/pair_born_coul_wolf_gpu.h index 6eb03f3e1a..6ca528c606 100644 --- a/src/GPU/pair_born_coul_wolf_gpu.h +++ b/src/GPU/pair_born_coul_wolf_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_born_gpu.h b/src/GPU/pair_born_gpu.h index d8ccbe0029..31aa978761 100644 --- a/src/GPU/pair_born_gpu.h +++ b/src/GPU/pair_born_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_buck_coul_cut_gpu.h b/src/GPU/pair_buck_coul_cut_gpu.h index d4e9a81d7b..9e81a88b19 100644 --- a/src/GPU/pair_buck_coul_cut_gpu.h +++ b/src/GPU/pair_buck_coul_cut_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_buck_coul_long_gpu.h b/src/GPU/pair_buck_coul_long_gpu.h index 3925209ae1..741aaeb641 100644 --- a/src/GPU/pair_buck_coul_long_gpu.h +++ b/src/GPU/pair_buck_coul_long_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_buck_gpu.h b/src/GPU/pair_buck_gpu.h index 4cd34db782..5b29bc7125 100644 --- a/src/GPU/pair_buck_gpu.h +++ b/src/GPU/pair_buck_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_colloid_gpu.h b/src/GPU/pair_colloid_gpu.h index 78ecfbc59a..6face4ea25 100644 --- a/src/GPU/pair_colloid_gpu.h +++ b/src/GPU/pair_colloid_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_coul_cut_gpu.h b/src/GPU/pair_coul_cut_gpu.h index 352147dbb9..10b1f4510e 100644 --- a/src/GPU/pair_coul_cut_gpu.h +++ b/src/GPU/pair_coul_cut_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_coul_debye_gpu.h b/src/GPU/pair_coul_debye_gpu.h index 9cc379d1ed..1fe4a05c8d 100644 --- a/src/GPU/pair_coul_debye_gpu.h +++ b/src/GPU/pair_coul_debye_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_coul_dsf_gpu.h b/src/GPU/pair_coul_dsf_gpu.h index 526b30a5c5..413ef2468e 100644 --- a/src/GPU/pair_coul_dsf_gpu.h +++ b/src/GPU/pair_coul_dsf_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_coul_long_cs_gpu.h b/src/GPU/pair_coul_long_cs_gpu.h index 95ed8d0182..8e712e384c 100644 --- a/src/GPU/pair_coul_long_cs_gpu.h +++ b/src/GPU/pair_coul_long_cs_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_coul_long_gpu.h b/src/GPU/pair_coul_long_gpu.h index 7cfb55cd9f..6e580302de 100644 --- a/src/GPU/pair_coul_long_gpu.h +++ b/src/GPU/pair_coul_long_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_dpd_gpu.h b/src/GPU/pair_dpd_gpu.h index e9d91b7ae0..a83d30101c 100644 --- a/src/GPU/pair_dpd_gpu.h +++ b/src/GPU/pair_dpd_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_dpd_tstat_gpu.h b/src/GPU/pair_dpd_tstat_gpu.h index f36944d6d6..e59e767f6a 100644 --- a/src/GPU/pair_dpd_tstat_gpu.h +++ b/src/GPU/pair_dpd_tstat_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_eam_alloy_gpu.h b/src/GPU/pair_eam_alloy_gpu.h index 3cd78ea511..250e1f5540 100644 --- a/src/GPU/pair_eam_alloy_gpu.h +++ b/src/GPU/pair_eam_alloy_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_eam_fs_gpu.h b/src/GPU/pair_eam_fs_gpu.h index 53825f2e8a..819f37e554 100644 --- a/src/GPU/pair_eam_fs_gpu.h +++ b/src/GPU/pair_eam_fs_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_eam_gpu.h b/src/GPU/pair_eam_gpu.h index 09566f7de9..857b5d59b1 100644 --- a/src/GPU/pair_eam_gpu.h +++ b/src/GPU/pair_eam_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_gauss_gpu.h b/src/GPU/pair_gauss_gpu.h index bda2e2644a..5fe30a68bd 100644 --- a/src/GPU/pair_gauss_gpu.h +++ b/src/GPU/pair_gauss_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_gayberne_gpu.h b/src/GPU/pair_gayberne_gpu.h index 88197f06bd..d86a9c2187 100644 --- a/src/GPU/pair_gayberne_gpu.h +++ b/src/GPU/pair_gayberne_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj96_cut_gpu.h b/src/GPU/pair_lj96_cut_gpu.h index d0acbfe350..2296e04212 100644 --- a/src/GPU/pair_lj96_cut_gpu.h +++ b/src/GPU/pair_lj96_cut_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_charmm_coul_charmm_gpu.h b/src/GPU/pair_lj_charmm_coul_charmm_gpu.h index d80730ca5c..3e84d9abaf 100644 --- a/src/GPU/pair_lj_charmm_coul_charmm_gpu.h +++ b/src/GPU/pair_lj_charmm_coul_charmm_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.h b/src/GPU/pair_lj_charmm_coul_long_gpu.h index 3c21ef4f37..910646a2c8 100644 --- a/src/GPU/pair_lj_charmm_coul_long_gpu.h +++ b/src/GPU/pair_lj_charmm_coul_long_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.h b/src/GPU/pair_lj_class2_coul_long_gpu.h index 8fe8a1c6db..6c171c0498 100644 --- a/src/GPU/pair_lj_class2_coul_long_gpu.h +++ b/src/GPU/pair_lj_class2_coul_long_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_class2_gpu.h b/src/GPU/pair_lj_class2_gpu.h index 470d15bc4a..46eda57f17 100644 --- a/src/GPU/pair_lj_class2_gpu.h +++ b/src/GPU/pair_lj_class2_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_cubic_gpu.h b/src/GPU/pair_lj_cubic_gpu.h index cdfc157e8e..855c1282e5 100644 --- a/src/GPU/pair_lj_cubic_gpu.h +++ b/src/GPU/pair_lj_cubic_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.h b/src/GPU/pair_lj_cut_coul_cut_gpu.h index 97d661c83f..7efe61f18a 100644 --- a/src/GPU/pair_lj_cut_coul_cut_gpu.h +++ b/src/GPU/pair_lj_cut_coul_cut_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.h b/src/GPU/pair_lj_cut_coul_debye_gpu.h index 6b0f2ed8d7..12ac8b64cc 100644 --- a/src/GPU/pair_lj_cut_coul_debye_gpu.h +++ b/src/GPU/pair_lj_cut_coul_debye_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.h b/src/GPU/pair_lj_cut_coul_dsf_gpu.h index 93cc5f6f3d..e86d008c29 100644 --- a/src/GPU/pair_lj_cut_coul_dsf_gpu.h +++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.h b/src/GPU/pair_lj_cut_coul_long_gpu.h index cea285fa04..eefb1c928d 100644 --- a/src/GPU/pair_lj_cut_coul_long_gpu.h +++ b/src/GPU/pair_lj_cut_coul_long_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.h b/src/GPU/pair_lj_cut_coul_msm_gpu.h index ca18ca89e4..b8d7382333 100644 --- a/src/GPU/pair_lj_cut_coul_msm_gpu.h +++ b/src/GPU/pair_lj_cut_coul_msm_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.h b/src/GPU/pair_lj_cut_dipole_cut_gpu.h index b665137955..6ddfff47f0 100644 --- a/src/GPU/pair_lj_cut_dipole_cut_gpu.h +++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.h b/src/GPU/pair_lj_cut_dipole_long_gpu.h index dc72921583..44695fcd28 100644 --- a/src/GPU/pair_lj_cut_dipole_long_gpu.h +++ b/src/GPU/pair_lj_cut_dipole_long_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_cut_gpu.h b/src/GPU/pair_lj_cut_gpu.h index d0587d0a46..b86946f149 100644 --- a/src/GPU/pair_lj_cut_gpu.h +++ b/src/GPU/pair_lj_cut_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.h b/src/GPU/pair_lj_cut_tip4p_long_gpu.h index e7ba93afb2..87ddce85bb 100644 --- a/src/GPU/pair_lj_cut_tip4p_long_gpu.h +++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.h b/src/GPU/pair_lj_expand_coul_long_gpu.h index 4b39d8679b..662da29786 100644 --- a/src/GPU/pair_lj_expand_coul_long_gpu.h +++ b/src/GPU/pair_lj_expand_coul_long_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_expand_gpu.h b/src/GPU/pair_lj_expand_gpu.h index f031fe5f6c..7e1536f366 100644 --- a/src/GPU/pair_lj_expand_gpu.h +++ b/src/GPU/pair_lj_expand_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_gromacs_gpu.h b/src/GPU/pair_lj_gromacs_gpu.h index 4f00662021..689abc0223 100644 --- a/src/GPU/pair_lj_gromacs_gpu.h +++ b/src/GPU/pair_lj_gromacs_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.h b/src/GPU/pair_lj_sdk_coul_long_gpu.h index 3248e94977..10a45c3c8d 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.h +++ b/src/GPU/pair_lj_sdk_coul_long_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_sdk_gpu.h b/src/GPU/pair_lj_sdk_gpu.h index 3865b34046..dcbb82bca6 100644 --- a/src/GPU/pair_lj_sdk_gpu.h +++ b/src/GPU/pair_lj_sdk_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.h b/src/GPU/pair_lj_sf_dipole_sf_gpu.h index 79df327293..050fa472fc 100644 --- a/src/GPU/pair_lj_sf_dipole_sf_gpu.h +++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_mie_cut_gpu.h b/src/GPU/pair_mie_cut_gpu.h index 2e9096e172..4520895ed5 100644 --- a/src/GPU/pair_mie_cut_gpu.h +++ b/src/GPU/pair_mie_cut_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_morse_gpu.h b/src/GPU/pair_morse_gpu.h index 23bfc431c0..663b4b8c6b 100644 --- a/src/GPU/pair_morse_gpu.h +++ b/src/GPU/pair_morse_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_resquared_gpu.h b/src/GPU/pair_resquared_gpu.h index ab87ff80b5..40bbee1f4f 100644 --- a/src/GPU/pair_resquared_gpu.h +++ b/src/GPU/pair_resquared_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_soft_gpu.h b/src/GPU/pair_soft_gpu.h index 61e8ee3db5..401d1035fd 100644 --- a/src/GPU/pair_soft_gpu.h +++ b/src/GPU/pair_soft_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_sw_gpu.h b/src/GPU/pair_sw_gpu.h index 95417386d8..a5eea58cf9 100644 --- a/src/GPU/pair_sw_gpu.h +++ b/src/GPU/pair_sw_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_table_gpu.h b/src/GPU/pair_table_gpu.h index 33cfa81268..255e7a9cce 100644 --- a/src/GPU/pair_table_gpu.h +++ b/src/GPU/pair_table_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_tersoff_gpu.h b/src/GPU/pair_tersoff_gpu.h index ed3dadef5d..c44ed5f5f2 100644 --- a/src/GPU/pair_tersoff_gpu.h +++ b/src/GPU/pair_tersoff_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_tersoff_mod_gpu.h b/src/GPU/pair_tersoff_mod_gpu.h index b3564afada..7a9ebb6a8a 100644 --- a/src/GPU/pair_tersoff_mod_gpu.h +++ b/src/GPU/pair_tersoff_mod_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_tersoff_zbl_gpu.h b/src/GPU/pair_tersoff_zbl_gpu.h index 6ee387aec4..9e0547b495 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.h +++ b/src/GPU/pair_tersoff_zbl_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_ufm_gpu.h b/src/GPU/pair_ufm_gpu.h index 59b883f3aa..766a0a1e75 100644 --- a/src/GPU/pair_ufm_gpu.h +++ b/src/GPU/pair_ufm_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_vashishta_gpu.h b/src/GPU/pair_vashishta_gpu.h index d54ede505b..540b7306ba 100644 --- a/src/GPU/pair_vashishta_gpu.h +++ b/src/GPU/pair_vashishta_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_yukawa_colloid_gpu.h b/src/GPU/pair_yukawa_colloid_gpu.h index 218cfa3320..d11a45af19 100644 --- a/src/GPU/pair_yukawa_colloid_gpu.h +++ b/src/GPU/pair_yukawa_colloid_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_yukawa_gpu.h b/src/GPU/pair_yukawa_gpu.h index 8210fe582e..d7bcccc9c1 100644 --- a/src/GPU/pair_yukawa_gpu.h +++ b/src/GPU/pair_yukawa_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pair_zbl_gpu.h b/src/GPU/pair_zbl_gpu.h index 3e6ac37394..ec1c3044f0 100644 --- a/src/GPU/pair_zbl_gpu.h +++ b/src/GPU/pair_zbl_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GPU/pppm_gpu.h b/src/GPU/pppm_gpu.h index 60b7e06d09..f6f4ab0ef2 100644 --- a/src/GPU/pppm_gpu.h +++ b/src/GPU/pppm_gpu.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GRANULAR/fix_freeze.h b/src/GRANULAR/fix_freeze.h index a249226aa7..4cf36ffc4e 100644 --- a/src/GRANULAR/fix_freeze.h +++ b/src/GRANULAR/fix_freeze.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GRANULAR/fix_pour.h b/src/GRANULAR/fix_pour.h index b56c1ca74f..8ea69a936a 100644 --- a/src/GRANULAR/fix_pour.h +++ b/src/GRANULAR/fix_pour.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GRANULAR/fix_wall_gran.h b/src/GRANULAR/fix_wall_gran.h index da48150fd0..560067aa11 100644 --- a/src/GRANULAR/fix_wall_gran.h +++ b/src/GRANULAR/fix_wall_gran.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GRANULAR/fix_wall_gran_region.h b/src/GRANULAR/fix_wall_gran_region.h index fd40e27e4c..2be9b1f693 100644 --- a/src/GRANULAR/fix_wall_gran_region.h +++ b/src/GRANULAR/fix_wall_gran_region.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GRANULAR/pair_gran_hertz_history.h b/src/GRANULAR/pair_gran_hertz_history.h index 6d6b7a1fed..b813149c7c 100644 --- a/src/GRANULAR/pair_gran_hertz_history.h +++ b/src/GRANULAR/pair_gran_hertz_history.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GRANULAR/pair_gran_hooke.h b/src/GRANULAR/pair_gran_hooke.h index 023438387c..a2d9cf4c3e 100644 --- a/src/GRANULAR/pair_gran_hooke.h +++ b/src/GRANULAR/pair_gran_hooke.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GRANULAR/pair_gran_hooke_history.h b/src/GRANULAR/pair_gran_hooke_history.h index f511d30237..70c8c469ca 100644 --- a/src/GRANULAR/pair_gran_hooke_history.h +++ b/src/GRANULAR/pair_gran_hooke_history.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/GRANULAR/pair_granular.h b/src/GRANULAR/pair_granular.h index 49eb457f0d..213d4d8c87 100644 --- a/src/GRANULAR/pair_granular.h +++ b/src/GRANULAR/pair_granular.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KIM/fix_store_kim.h b/src/KIM/fix_store_kim.h index 63a2edb74e..7244bd1b5f 100644 --- a/src/KIM/fix_store_kim.h +++ b/src/KIM/fix_store_kim.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KIM/kim_command.h b/src/KIM/kim_command.h index b27b0e0873..f54ce58c22 100644 --- a/src/KIM/kim_command.h +++ b/src/KIM/kim_command.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KIM/kim_init.h b/src/KIM/kim_init.h index a345340dc9..866744e236 100644 --- a/src/KIM/kim_init.h +++ b/src/KIM/kim_init.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KIM/kim_interactions.h b/src/KIM/kim_interactions.h index 8790f2df14..46fc95bff9 100644 --- a/src/KIM/kim_interactions.h +++ b/src/KIM/kim_interactions.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KIM/kim_param.h b/src/KIM/kim_param.h index 7988e494be..b19d2c507b 100644 --- a/src/KIM/kim_param.h +++ b/src/KIM/kim_param.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KIM/kim_property.h b/src/KIM/kim_property.h index a804ad573c..7b5c999c66 100644 --- a/src/KIM/kim_property.h +++ b/src/KIM/kim_property.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KIM/kim_query.h b/src/KIM/kim_query.h index ce59e2f67f..5d71856ee0 100644 --- a/src/KIM/kim_query.h +++ b/src/KIM/kim_query.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KIM/kim_units.h b/src/KIM/kim_units.h index 7130ce56d6..caf88d7c76 100644 --- a/src/KIM/kim_units.h +++ b/src/KIM/kim_units.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index cceecff14d..b769107b71 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/angle_charmm_kokkos.h b/src/KOKKOS/angle_charmm_kokkos.h index c7f64d4c22..7abb1d0ad2 100644 --- a/src/KOKKOS/angle_charmm_kokkos.h +++ b/src/KOKKOS/angle_charmm_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/angle_class2_kokkos.h b/src/KOKKOS/angle_class2_kokkos.h index 399ef3c47a..adc5ec7f4a 100644 --- a/src/KOKKOS/angle_class2_kokkos.h +++ b/src/KOKKOS/angle_class2_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/angle_cosine_kokkos.h b/src/KOKKOS/angle_cosine_kokkos.h index 8ea6719814..0d1eb863e1 100644 --- a/src/KOKKOS/angle_cosine_kokkos.h +++ b/src/KOKKOS/angle_cosine_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/angle_harmonic_kokkos.h b/src/KOKKOS/angle_harmonic_kokkos.h index 7fac902907..a826e28ff1 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.h +++ b/src/KOKKOS/angle_harmonic_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index f5cf4916cf..c4845173f2 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/atom_vec_angle_kokkos.h b/src/KOKKOS/atom_vec_angle_kokkos.h index 29b5ce8fc5..fcaaf5659e 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.h +++ b/src/KOKKOS/atom_vec_angle_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.h b/src/KOKKOS/atom_vec_atomic_kokkos.h index 2c682d4989..30a6c43b7e 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.h +++ b/src/KOKKOS/atom_vec_atomic_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale AtomicKokkos/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/atom_vec_bond_kokkos.h b/src/KOKKOS/atom_vec_bond_kokkos.h index 7f4d04c037..e73299dff0 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.h +++ b/src/KOKKOS/atom_vec_bond_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/atom_vec_charge_kokkos.h b/src/KOKKOS/atom_vec_charge_kokkos.h index 4d61b2a69c..00cf079039 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.h +++ b/src/KOKKOS/atom_vec_charge_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.h b/src/KOKKOS/atom_vec_dpd_kokkos.h index 71b0c85590..2ac6ff1c9b 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.h +++ b/src/KOKKOS/atom_vec_dpd_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale AtomicKokkos/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/atom_vec_full_kokkos.h b/src/KOKKOS/atom_vec_full_kokkos.h index 4a5a61e913..0a0f779884 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.h +++ b/src/KOKKOS/atom_vec_full_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.h b/src/KOKKOS/atom_vec_hybrid_kokkos.h index 3354735bf7..c70da508c8 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.h +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/atom_vec_kokkos.h b/src/KOKKOS/atom_vec_kokkos.h index f81b7715ad..55ebf3d960 100644 --- a/src/KOKKOS/atom_vec_kokkos.h +++ b/src/KOKKOS/atom_vec_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.h b/src/KOKKOS/atom_vec_molecular_kokkos.h index a356c6821c..7872dab52c 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.h +++ b/src/KOKKOS/atom_vec_molecular_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.h b/src/KOKKOS/atom_vec_sphere_kokkos.h index 676df431d1..6edda5dcdf 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.h +++ b/src/KOKKOS/atom_vec_sphere_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp index 399ab23a5f..afa1b6136a 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.cpp +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/atom_vec_spin_kokkos.h b/src/KOKKOS/atom_vec_spin_kokkos.h index bcb5ea3b45..c5f9a826ec 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.h +++ b/src/KOKKOS/atom_vec_spin_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/bond_class2_kokkos.h b/src/KOKKOS/bond_class2_kokkos.h index b3c1d5f682..15d3af7570 100644 --- a/src/KOKKOS/bond_class2_kokkos.h +++ b/src/KOKKOS/bond_class2_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/bond_fene_kokkos.h b/src/KOKKOS/bond_fene_kokkos.h index 83f21c5934..751c7f8312 100644 --- a/src/KOKKOS/bond_fene_kokkos.h +++ b/src/KOKKOS/bond_fene_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/bond_harmonic_kokkos.h b/src/KOKKOS/bond_harmonic_kokkos.h index cf716ec843..b337dff0db 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.h +++ b/src/KOKKOS/bond_harmonic_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/comm_kokkos.h b/src/KOKKOS/comm_kokkos.h index c5772bafe7..b66de5a0d0 100644 --- a/src/KOKKOS/comm_kokkos.h +++ b/src/KOKKOS/comm_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/comm_tiled_kokkos.h b/src/KOKKOS/comm_tiled_kokkos.h index 96944bc7d1..28f88de7b3 100644 --- a/src/KOKKOS/comm_tiled_kokkos.h +++ b/src/KOKKOS/comm_tiled_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/compute_coord_atom_kokkos.h b/src/KOKKOS/compute_coord_atom_kokkos.h index f292994a18..37b9d1f683 100644 --- a/src/KOKKOS/compute_coord_atom_kokkos.h +++ b/src/KOKKOS/compute_coord_atom_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/compute_orientorder_atom_kokkos.h b/src/KOKKOS/compute_orientorder_atom_kokkos.h index 7d8005f89b..80f2ddb221 100644 --- a/src/KOKKOS/compute_orientorder_atom_kokkos.h +++ b/src/KOKKOS/compute_orientorder_atom_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/compute_temp_kokkos.h b/src/KOKKOS/compute_temp_kokkos.h index 555881869d..61c7501784 100644 --- a/src/KOKKOS/compute_temp_kokkos.h +++ b/src/KOKKOS/compute_temp_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/dihedral_charmm_kokkos.h b/src/KOKKOS/dihedral_charmm_kokkos.h index 828abd2be7..dbd9986bf9 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.h +++ b/src/KOKKOS/dihedral_charmm_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/dihedral_class2_kokkos.h b/src/KOKKOS/dihedral_class2_kokkos.h index 0d0309928d..ef2b7f68ab 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.h +++ b/src/KOKKOS/dihedral_class2_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/dihedral_harmonic_kokkos.h b/src/KOKKOS/dihedral_harmonic_kokkos.h index f90e8944a4..1c50a9a4a5 100644 --- a/src/KOKKOS/dihedral_harmonic_kokkos.h +++ b/src/KOKKOS/dihedral_harmonic_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/dihedral_opls_kokkos.h b/src/KOKKOS/dihedral_opls_kokkos.h index b841193064..2ec2c4e4fa 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.h +++ b/src/KOKKOS/dihedral_opls_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/domain_kokkos.h b/src/KOKKOS/domain_kokkos.h index 3bfdeb708b..be0a036d06 100644 --- a/src/KOKKOS/domain_kokkos.h +++ b/src/KOKKOS/domain_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fft3d_kokkos.h b/src/KOKKOS/fft3d_kokkos.h index d78cd6d7c9..9a20580d4a 100644 --- a/src/KOKKOS/fft3d_kokkos.h +++ b/src/KOKKOS/fft3d_kokkos.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fftdata_kokkos.h b/src/KOKKOS/fftdata_kokkos.h index 51c444c2a3..ba62670bdf 100644 --- a/src/KOKKOS/fftdata_kokkos.h +++ b/src/KOKKOS/fftdata_kokkos.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_deform_kokkos.h b/src/KOKKOS/fix_deform_kokkos.h index 69f65fbcf4..4388030ec3 100644 --- a/src/KOKKOS/fix_deform_kokkos.h +++ b/src/KOKKOS/fix_deform_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_dpd_energy_kokkos.h b/src/KOKKOS/fix_dpd_energy_kokkos.h index 32066c1195..ddf33a5181 100644 --- a/src/KOKKOS/fix_dpd_energy_kokkos.h +++ b/src/KOKKOS/fix_dpd_energy_kokkos.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_enforce2d_kokkos.h b/src/KOKKOS/fix_enforce2d_kokkos.h index 520a58de04..df07a87f73 100644 --- a/src/KOKKOS/fix_enforce2d_kokkos.h +++ b/src/KOKKOS/fix_enforce2d_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.h b/src/KOKKOS/fix_eos_table_rx_kokkos.h index 21ec3d203b..4ca94f86cf 100644 --- a/src/KOKKOS/fix_eos_table_rx_kokkos.h +++ b/src/KOKKOS/fix_eos_table_rx_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_freeze_kokkos.h b/src/KOKKOS/fix_freeze_kokkos.h index 3b5bc8e437..4fdcb26c52 100644 --- a/src/KOKKOS/fix_freeze_kokkos.h +++ b/src/KOKKOS/fix_freeze_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_gravity_kokkos.h b/src/KOKKOS/fix_gravity_kokkos.h index 9aa9ef803f..1b9deaf247 100644 --- a/src/KOKKOS/fix_gravity_kokkos.h +++ b/src/KOKKOS/fix_gravity_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_langevin_kokkos.h b/src/KOKKOS/fix_langevin_kokkos.h index 411adc2219..f6e1c47a08 100644 --- a/src/KOKKOS/fix_langevin_kokkos.h +++ b/src/KOKKOS/fix_langevin_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_minimize_kokkos.h b/src/KOKKOS/fix_minimize_kokkos.h index 921cb2fc5d..0a6587c6da 100644 --- a/src/KOKKOS/fix_minimize_kokkos.h +++ b/src/KOKKOS/fix_minimize_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_momentum_kokkos.h b/src/KOKKOS/fix_momentum_kokkos.h index bc370fe674..4892f40aa4 100644 --- a/src/KOKKOS/fix_momentum_kokkos.h +++ b/src/KOKKOS/fix_momentum_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_neigh_history_kokkos.h b/src/KOKKOS/fix_neigh_history_kokkos.h index ba594a567f..513d29be2d 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.h +++ b/src/KOKKOS/fix_neigh_history_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_nh_kokkos.h b/src/KOKKOS/fix_nh_kokkos.h index ae18bd6dbd..06c4fecab1 100644 --- a/src/KOKKOS/fix_nh_kokkos.h +++ b/src/KOKKOS/fix_nh_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_nph_kokkos.h b/src/KOKKOS/fix_nph_kokkos.h index f555814a3a..c9feccba29 100644 --- a/src/KOKKOS/fix_nph_kokkos.h +++ b/src/KOKKOS/fix_nph_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_npt_kokkos.h b/src/KOKKOS/fix_npt_kokkos.h index 3d23fd9d8f..a04eb0ba92 100644 --- a/src/KOKKOS/fix_npt_kokkos.h +++ b/src/KOKKOS/fix_npt_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_nve_kokkos.h b/src/KOKKOS/fix_nve_kokkos.h index e5a551914b..5894b7c07e 100644 --- a/src/KOKKOS/fix_nve_kokkos.h +++ b/src/KOKKOS/fix_nve_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_nve_sphere_kokkos.h b/src/KOKKOS/fix_nve_sphere_kokkos.h index 87a1835eb7..41d5964f7f 100644 --- a/src/KOKKOS/fix_nve_sphere_kokkos.h +++ b/src/KOKKOS/fix_nve_sphere_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_nvt_kokkos.h b/src/KOKKOS/fix_nvt_kokkos.h index 4084b4f032..8ca680eb61 100644 --- a/src/KOKKOS/fix_nvt_kokkos.h +++ b/src/KOKKOS/fix_nvt_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_property_atom_kokkos.h b/src/KOKKOS/fix_property_atom_kokkos.h index ed1e4d7cfb..ade4375654 100644 --- a/src/KOKKOS/fix_property_atom_kokkos.h +++ b/src/KOKKOS/fix_property_atom_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.h b/src/KOKKOS/fix_qeq_reax_kokkos.h index bbfeb00266..e0205ce801 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.h +++ b/src/KOKKOS/fix_qeq_reax_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.h b/src/KOKKOS/fix_reaxc_bonds_kokkos.h index 55adb6f8d9..d8a5d3a1cc 100644 --- a/src/KOKKOS/fix_reaxc_bonds_kokkos.h +++ b/src/KOKKOS/fix_reaxc_bonds_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_reaxc_species_kokkos.h b/src/KOKKOS/fix_reaxc_species_kokkos.h index 7c163b23b5..8e5f961f17 100644 --- a/src/KOKKOS/fix_reaxc_species_kokkos.h +++ b/src/KOKKOS/fix_reaxc_species_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_rx_kokkos.h b/src/KOKKOS/fix_rx_kokkos.h index 0033e69649..1f7b66a18c 100644 --- a/src/KOKKOS/fix_rx_kokkos.h +++ b/src/KOKKOS/fix_rx_kokkos.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_setforce_kokkos.h b/src/KOKKOS/fix_setforce_kokkos.h index 709d31279b..5a8ba19d97 100644 --- a/src/KOKKOS/fix_setforce_kokkos.h +++ b/src/KOKKOS/fix_setforce_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_shake_kokkos.cpp b/src/KOKKOS/fix_shake_kokkos.cpp index 253c7ee7e0..245d4b5498 100644 --- a/src/KOKKOS/fix_shake_kokkos.cpp +++ b/src/KOKKOS/fix_shake_kokkos.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_shake_kokkos.h b/src/KOKKOS/fix_shake_kokkos.h index 82743573bd..ea3756856c 100644 --- a/src/KOKKOS/fix_shake_kokkos.h +++ b/src/KOKKOS/fix_shake_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_shardlow_kokkos.h b/src/KOKKOS/fix_shardlow_kokkos.h index 1d11de0fcb..1c5813bcfd 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.h +++ b/src/KOKKOS/fix_shardlow_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_wall_lj93_kokkos.h b/src/KOKKOS/fix_wall_lj93_kokkos.h index 15a853d820..ceaeb4d3bd 100644 --- a/src/KOKKOS/fix_wall_lj93_kokkos.h +++ b/src/KOKKOS/fix_wall_lj93_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.h b/src/KOKKOS/fix_wall_reflect_kokkos.h index d59088b592..e1f3f4f9b4 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.h +++ b/src/KOKKOS/fix_wall_reflect_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/gridcomm_kokkos.h b/src/KOKKOS/gridcomm_kokkos.h index 1f93c111ca..270ad98ad0 100644 --- a/src/KOKKOS/gridcomm_kokkos.h +++ b/src/KOKKOS/gridcomm_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/improper_class2_kokkos.h b/src/KOKKOS/improper_class2_kokkos.h index 11212249e7..b22b2361fa 100644 --- a/src/KOKKOS/improper_class2_kokkos.h +++ b/src/KOKKOS/improper_class2_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/improper_harmonic_kokkos.h b/src/KOKKOS/improper_harmonic_kokkos.h index e143e65adf..e15600dbf7 100644 --- a/src/KOKKOS/improper_harmonic_kokkos.h +++ b/src/KOKKOS/improper_harmonic_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/kissfft_kokkos.h b/src/KOKKOS/kissfft_kokkos.h index 9163366cb9..89e132e85a 100644 --- a/src/KOKKOS/kissfft_kokkos.h +++ b/src/KOKKOS/kissfft_kokkos.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h index b247d583a6..0994ff6e01 100644 --- a/src/KOKKOS/kokkos.h +++ b/src/KOKKOS/kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/kokkos_base.h b/src/KOKKOS/kokkos_base.h index adacaf6ad8..855ccf9108 100644 --- a/src/KOKKOS/kokkos_base.h +++ b/src/KOKKOS/kokkos_base.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/kokkos_base_fft.h b/src/KOKKOS/kokkos_base_fft.h index de3a293126..c087a4d3f6 100644 --- a/src/KOKKOS/kokkos_base_fft.h +++ b/src/KOKKOS/kokkos_base_fft.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index 8eb9744a94..a00c43bd2d 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/math_special_kokkos.h b/src/KOKKOS/math_special_kokkos.h index d10d164bcf..02b05739ee 100644 --- a/src/KOKKOS/math_special_kokkos.h +++ b/src/KOKKOS/math_special_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/memory_kokkos.h b/src/KOKKOS/memory_kokkos.h index 445ecd87f2..186168b9b1 100644 --- a/src/KOKKOS/memory_kokkos.h +++ b/src/KOKKOS/memory_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/min_cg_kokkos.h b/src/KOKKOS/min_cg_kokkos.h index 745bf702c7..1c51be7e72 100644 --- a/src/KOKKOS/min_cg_kokkos.h +++ b/src/KOKKOS/min_cg_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/min_kokkos.h b/src/KOKKOS/min_kokkos.h index da61d62d43..8cfb3c7c24 100644 --- a/src/KOKKOS/min_kokkos.h +++ b/src/KOKKOS/min_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/min_linesearch_kokkos.h b/src/KOKKOS/min_linesearch_kokkos.h index 5439a93932..6a82c43b93 100644 --- a/src/KOKKOS/min_linesearch_kokkos.h +++ b/src/KOKKOS/min_linesearch_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/modify_kokkos.h b/src/KOKKOS/modify_kokkos.h index 9ae1cfb5e2..99fbb26c5c 100644 --- a/src/KOKKOS/modify_kokkos.h +++ b/src/KOKKOS/modify_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/nbin_kokkos.h b/src/KOKKOS/nbin_kokkos.h index bf2ccc5908..5909dce4d3 100644 --- a/src/KOKKOS/nbin_kokkos.h +++ b/src/KOKKOS/nbin_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/nbin_ssa_kokkos.h b/src/KOKKOS/nbin_ssa_kokkos.h index c9a389bed4..e684a0eec0 100644 --- a/src/KOKKOS/nbin_ssa_kokkos.h +++ b/src/KOKKOS/nbin_ssa_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/neigh_bond_kokkos.h b/src/KOKKOS/neigh_bond_kokkos.h index 6acbb09c1f..ed62a5d859 100644 --- a/src/KOKKOS/neigh_bond_kokkos.h +++ b/src/KOKKOS/neigh_bond_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/neigh_list_kokkos.h b/src/KOKKOS/neigh_list_kokkos.h index 5de871166e..727295ead1 100644 --- a/src/KOKKOS/neigh_list_kokkos.h +++ b/src/KOKKOS/neigh_list_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/neighbor_kokkos.h b/src/KOKKOS/neighbor_kokkos.h index 304fe8f1da..74b82e88ce 100644 --- a/src/KOKKOS/neighbor_kokkos.h +++ b/src/KOKKOS/neighbor_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/npair_copy_kokkos.h b/src/KOKKOS/npair_copy_kokkos.h index 4bbb2749e5..eb330fb1ea 100644 --- a/src/KOKKOS/npair_copy_kokkos.h +++ b/src/KOKKOS/npair_copy_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/npair_halffull_kokkos.h b/src/KOKKOS/npair_halffull_kokkos.h index 15505a376c..cd7571b2c9 100644 --- a/src/KOKKOS/npair_halffull_kokkos.h +++ b/src/KOKKOS/npair_halffull_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/npair_kokkos.h b/src/KOKKOS/npair_kokkos.h index 0d96762432..2f5ee8f70a 100644 --- a/src/KOKKOS/npair_kokkos.h +++ b/src/KOKKOS/npair_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/npair_skip_kokkos.h b/src/KOKKOS/npair_skip_kokkos.h index a274c1738c..61ea2e57e1 100644 --- a/src/KOKKOS/npair_skip_kokkos.h +++ b/src/KOKKOS/npair_skip_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/npair_ssa_kokkos.h b/src/KOKKOS/npair_ssa_kokkos.h index 5bd0a67001..a1ccc21319 100644 --- a/src/KOKKOS/npair_ssa_kokkos.h +++ b/src/KOKKOS/npair_ssa_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pack_kokkos.h b/src/KOKKOS/pack_kokkos.h index 400048b1f0..3baad002b6 100644 --- a/src/KOKKOS/pack_kokkos.h +++ b/src/KOKKOS/pack_kokkos.h @@ -1,4 +1,4 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- SPARTA - Stochastic PArallel Rarefied-gas Time-accurate Analyzer http://sparta.sandia.gov Steve Plimpton, sjplimp@sandia.gov, Michael Gallis, magalli@sandia.gov diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.h b/src/KOKKOS/pair_buck_coul_cut_kokkos.h index 683cb37310..fd4594bdfb 100644 --- a/src/KOKKOS/pair_buck_coul_cut_kokkos.h +++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.h b/src/KOKKOS/pair_buck_coul_long_kokkos.h index c383a64081..1511035472 100644 --- a/src/KOKKOS/pair_buck_coul_long_kokkos.h +++ b/src/KOKKOS/pair_buck_coul_long_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_buck_kokkos.h b/src/KOKKOS/pair_buck_kokkos.h index 8bd8fc9ffe..370079973f 100644 --- a/src/KOKKOS/pair_buck_kokkos.h +++ b/src/KOKKOS/pair_buck_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_coul_cut_kokkos.h b/src/KOKKOS/pair_coul_cut_kokkos.h index 6fb5334cb4..947a133c7c 100644 --- a/src/KOKKOS/pair_coul_cut_kokkos.h +++ b/src/KOKKOS/pair_coul_cut_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_coul_debye_kokkos.h b/src/KOKKOS/pair_coul_debye_kokkos.h index b5dc2eaed4..c594ffe655 100644 --- a/src/KOKKOS/pair_coul_debye_kokkos.h +++ b/src/KOKKOS/pair_coul_debye_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.h b/src/KOKKOS/pair_coul_dsf_kokkos.h index 49b1806e3c..f42b99aa44 100644 --- a/src/KOKKOS/pair_coul_dsf_kokkos.h +++ b/src/KOKKOS/pair_coul_dsf_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_coul_long_kokkos.h b/src/KOKKOS/pair_coul_long_kokkos.h index 11847bc25c..358c4eed2e 100644 --- a/src/KOKKOS/pair_coul_long_kokkos.h +++ b/src/KOKKOS/pair_coul_long_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.h b/src/KOKKOS/pair_coul_wolf_kokkos.h index f6da745de3..0c06908eed 100644 --- a/src/KOKKOS/pair_coul_wolf_kokkos.h +++ b/src/KOKKOS/pair_coul_wolf_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h index 250a318568..778c117d81 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h index 71a30ec2b9..c0d4ffbc18 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.h +++ b/src/KOKKOS/pair_eam_alloy_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h index b216138c8b..ca0e64aa54 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.h +++ b/src/KOKKOS/pair_eam_fs_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h index 982b248af1..e4cc3f28ae 100644 --- a/src/KOKKOS/pair_eam_kokkos.h +++ b/src/KOKKOS/pair_eam_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.h b/src/KOKKOS/pair_exp6_rx_kokkos.h index 406353dd7c..640ea360db 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.h +++ b/src/KOKKOS/pair_exp6_rx_kokkos.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.h b/src/KOKKOS/pair_gran_hooke_history_kokkos.h index e40353d970..96997f45aa 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.h +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_hybrid_kokkos.h b/src/KOKKOS/pair_hybrid_kokkos.h index 799354cf01..618a3e76f2 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.h +++ b/src/KOKKOS/pair_hybrid_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.h b/src/KOKKOS/pair_hybrid_overlay_kokkos.h index 6bec57c453..c61c15fe52 100644 --- a/src/KOKKOS/pair_hybrid_overlay_kokkos.h +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index a3b31f54cc..08c33ca04c 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h index 1fb2c7724b..272cc2b491 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h index a7e3a80840..38caf1336e 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h index 6b76b00170..a4517c49d6 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h +++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.h b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.h index 96623a7b24..558719bd00 100644 --- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.h +++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.h b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.h index c5729697ee..392f3e217d 100644 --- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.h +++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_class2_kokkos.h b/src/KOKKOS/pair_lj_class2_kokkos.h index 4be6c40667..1931b196f3 100644 --- a/src/KOKKOS/pair_lj_class2_kokkos.h +++ b/src/KOKKOS/pair_lj_class2_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h index 6f2de779a6..644d3f164e 100644 --- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h +++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h index bfcf48aa98..1e367a6232 100644 --- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h +++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h index d45591c89e..222d873dba 100644 --- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h +++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h index 95210e06f7..6d04277851 100644 --- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h +++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_cut_kokkos.h b/src/KOKKOS/pair_lj_cut_kokkos.h index 557a28b698..d513bbff6c 100644 --- a/src/KOKKOS/pair_lj_cut_kokkos.h +++ b/src/KOKKOS/pair_lj_cut_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_expand_kokkos.h b/src/KOKKOS/pair_lj_expand_kokkos.h index ef288dcfe3..174711fefc 100644 --- a/src/KOKKOS/pair_lj_expand_kokkos.h +++ b/src/KOKKOS/pair_lj_expand_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h index 88dbf28699..8e29c00bfa 100644 --- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h +++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.h b/src/KOKKOS/pair_lj_gromacs_kokkos.h index 47804ffe0a..89a635df8a 100644 --- a/src/KOKKOS/pair_lj_gromacs_kokkos.h +++ b/src/KOKKOS/pair_lj_gromacs_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.h b/src/KOKKOS/pair_lj_sdk_kokkos.h index 470bda1f9f..7fe8ff18a3 100644 --- a/src/KOKKOS/pair_lj_sdk_kokkos.h +++ b/src/KOKKOS/pair_lj_sdk_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_morse_kokkos.h b/src/KOKKOS/pair_morse_kokkos.h index d747cc9e1e..e0205554ed 100644 --- a/src/KOKKOS/pair_morse_kokkos.h +++ b/src/KOKKOS/pair_morse_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_multi_lucy_rx_kokkos.h b/src/KOKKOS/pair_multi_lucy_rx_kokkos.h index aee1763b06..a112a79ff9 100644 --- a/src/KOKKOS/pair_multi_lucy_rx_kokkos.h +++ b/src/KOKKOS/pair_multi_lucy_rx_kokkos.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h index d54f275d6f..5f4ae68c42 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.h +++ b/src/KOKKOS/pair_reaxc_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h index b7208a577c..b0ed7d4703 100644 --- a/src/KOKKOS/pair_snap_kokkos.h +++ b/src/KOKKOS/pair_snap_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index f624131377..379140288f 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_sw_kokkos.h b/src/KOKKOS/pair_sw_kokkos.h index b9f4559bc2..755c2ce0e4 100644 --- a/src/KOKKOS/pair_sw_kokkos.h +++ b/src/KOKKOS/pair_sw_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_table_kokkos.h b/src/KOKKOS/pair_table_kokkos.h index ed4e73b095..b065d015bb 100644 --- a/src/KOKKOS/pair_table_kokkos.h +++ b/src/KOKKOS/pair_table_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_table_rx_kokkos.h b/src/KOKKOS/pair_table_rx_kokkos.h index 7aba307476..d05a7c582b 100644 --- a/src/KOKKOS/pair_table_rx_kokkos.h +++ b/src/KOKKOS/pair_table_rx_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_tersoff_kokkos.h b/src/KOKKOS/pair_tersoff_kokkos.h index dbc6dc7901..5f5d537ae7 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.h +++ b/src/KOKKOS/pair_tersoff_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.h b/src/KOKKOS/pair_tersoff_mod_kokkos.h index f6a03e1908..cdb1b578d5 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.h +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.h b/src/KOKKOS/pair_tersoff_zbl_kokkos.h index f82a69cc29..ed71aa5ec4 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.h +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_vashishta_kokkos.h b/src/KOKKOS/pair_vashishta_kokkos.h index aa8543e751..6bdd4b4fa1 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.h +++ b/src/KOKKOS/pair_vashishta_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_yukawa_kokkos.h b/src/KOKKOS/pair_yukawa_kokkos.h index a78f9d5f7c..11143248e1 100644 --- a/src/KOKKOS/pair_yukawa_kokkos.h +++ b/src/KOKKOS/pair_yukawa_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_zbl_kokkos.h b/src/KOKKOS/pair_zbl_kokkos.h index e5332af4a9..6109eceba4 100644 --- a/src/KOKKOS/pair_zbl_kokkos.h +++ b/src/KOKKOS/pair_zbl_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pppm_kokkos.h b/src/KOKKOS/pppm_kokkos.h index b2c7dbe852..2369bcc1a0 100644 --- a/src/KOKKOS/pppm_kokkos.h +++ b/src/KOKKOS/pppm_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/rand_pool_wrap_kokkos.h b/src/KOKKOS/rand_pool_wrap_kokkos.h index 8ae90011ab..fd7f773ca6 100644 --- a/src/KOKKOS/rand_pool_wrap_kokkos.h +++ b/src/KOKKOS/rand_pool_wrap_kokkos.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/region_block_kokkos.h b/src/KOKKOS/region_block_kokkos.h index 532bc588e2..2d11770470 100644 --- a/src/KOKKOS/region_block_kokkos.h +++ b/src/KOKKOS/region_block_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/remap_kokkos.h b/src/KOKKOS/remap_kokkos.h index d6e4ab828e..c77301503f 100644 --- a/src/KOKKOS/remap_kokkos.h +++ b/src/KOKKOS/remap_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/sna_kokkos.h b/src/KOKKOS/sna_kokkos.h index 33ef37ca98..72baa32c7c 100644 --- a/src/KOKKOS/sna_kokkos.h +++ b/src/KOKKOS/sna_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index 2b55f97c30..db710780ba 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/verlet_kokkos.h b/src/KOKKOS/verlet_kokkos.h index 1e36b1cf6e..ba5ee3464f 100644 --- a/src/KOKKOS/verlet_kokkos.h +++ b/src/KOKKOS/verlet_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/ewald.h b/src/KSPACE/ewald.h index ef7ff05675..81f6eb3237 100644 --- a/src/KSPACE/ewald.h +++ b/src/KSPACE/ewald.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/ewald_dipole.h b/src/KSPACE/ewald_dipole.h index c8dd18565c..105f1b7e3f 100644 --- a/src/KSPACE/ewald_dipole.h +++ b/src/KSPACE/ewald_dipole.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/ewald_dipole_spin.h b/src/KSPACE/ewald_dipole_spin.h index 32c7ddb5f1..13f9e79ae9 100644 --- a/src/KSPACE/ewald_dipole_spin.h +++ b/src/KSPACE/ewald_dipole_spin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/ewald_disp.h b/src/KSPACE/ewald_disp.h index ab880fd359..9bd7d1960b 100644 --- a/src/KSPACE/ewald_disp.h +++ b/src/KSPACE/ewald_disp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/fft3d.h b/src/KSPACE/fft3d.h index 4b5f36716f..478cbb05e5 100644 --- a/src/KSPACE/fft3d.h +++ b/src/KSPACE/fft3d.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/fft3d_wrap.h b/src/KSPACE/fft3d_wrap.h index 2809b0cd7e..6deb9baf03 100644 --- a/src/KSPACE/fft3d_wrap.h +++ b/src/KSPACE/fft3d_wrap.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/fix_tune_kspace.h b/src/KSPACE/fix_tune_kspace.h index 3e4db40344..1cd663c8cc 100644 --- a/src/KSPACE/fix_tune_kspace.h +++ b/src/KSPACE/fix_tune_kspace.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/gridcomm.h b/src/KSPACE/gridcomm.h index 97c914999f..4cadfdbf29 100644 --- a/src/KSPACE/gridcomm.h +++ b/src/KSPACE/gridcomm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/kissfft.h b/src/KSPACE/kissfft.h index 119dc17f66..8cb6dec820 100644 --- a/src/KSPACE/kissfft.h +++ b/src/KSPACE/kissfft.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov See the README file in the top-level LAMMPS directory. diff --git a/src/KSPACE/msm.h b/src/KSPACE/msm.h index a239e6f139..be28f19267 100644 --- a/src/KSPACE/msm.h +++ b/src/KSPACE/msm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/msm_cg.h b/src/KSPACE/msm_cg.h index 7a27e3b83a..b6c1a46b5f 100644 --- a/src/KSPACE/msm_cg.h +++ b/src/KSPACE/msm_cg.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_born_coul_long.h b/src/KSPACE/pair_born_coul_long.h index d9a9b8b085..2f7e31112b 100644 --- a/src/KSPACE/pair_born_coul_long.h +++ b/src/KSPACE/pair_born_coul_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_born_coul_msm.h b/src/KSPACE/pair_born_coul_msm.h index 477d2152e6..3435044dd2 100644 --- a/src/KSPACE/pair_born_coul_msm.h +++ b/src/KSPACE/pair_born_coul_msm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_buck_coul_long.h b/src/KSPACE/pair_buck_coul_long.h index c19c2d8a5a..22726cc4e1 100644 --- a/src/KSPACE/pair_buck_coul_long.h +++ b/src/KSPACE/pair_buck_coul_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_buck_coul_msm.h b/src/KSPACE/pair_buck_coul_msm.h index a6b4e878bf..e6147df108 100644 --- a/src/KSPACE/pair_buck_coul_msm.h +++ b/src/KSPACE/pair_buck_coul_msm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_buck_long_coul_long.h b/src/KSPACE/pair_buck_long_coul_long.h index 760ed5404a..6f4128f379 100644 --- a/src/KSPACE/pair_buck_long_coul_long.h +++ b/src/KSPACE/pair_buck_long_coul_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_coul_long.h b/src/KSPACE/pair_coul_long.h index a231127381..0864a45f29 100644 --- a/src/KSPACE/pair_coul_long.h +++ b/src/KSPACE/pair_coul_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_coul_msm.h b/src/KSPACE/pair_coul_msm.h index ed7b6864fd..575dd1ae14 100644 --- a/src/KSPACE/pair_coul_msm.h +++ b/src/KSPACE/pair_coul_msm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_lj_charmm_coul_long.h b/src/KSPACE/pair_lj_charmm_coul_long.h index 95c6d0d1c7..b232c46546 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.h +++ b/src/KSPACE/pair_lj_charmm_coul_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.h b/src/KSPACE/pair_lj_charmm_coul_msm.h index cda0fe2695..711d22687b 100644 --- a/src/KSPACE/pair_lj_charmm_coul_msm.h +++ b/src/KSPACE/pair_lj_charmm_coul_msm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.h b/src/KSPACE/pair_lj_charmmfsw_coul_long.h index b05c25790b..d541372ce2 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.h +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_lj_cut_coul_long.h b/src/KSPACE/pair_lj_cut_coul_long.h index e6f97c088d..2154382811 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.h +++ b/src/KSPACE/pair_lj_cut_coul_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_lj_cut_coul_msm.h b/src/KSPACE/pair_lj_cut_coul_msm.h index 75742d083d..aabb5dd120 100644 --- a/src/KSPACE/pair_lj_cut_coul_msm.h +++ b/src/KSPACE/pair_lj_cut_coul_msm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.h b/src/KSPACE/pair_lj_cut_tip4p_long.h index 42e40e041a..e5667a9a1d 100644 --- a/src/KSPACE/pair_lj_cut_tip4p_long.h +++ b/src/KSPACE/pair_lj_cut_tip4p_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_lj_long_coul_long.h b/src/KSPACE/pair_lj_long_coul_long.h index 3153fcb8a8..b3c780be37 100644 --- a/src/KSPACE/pair_lj_long_coul_long.h +++ b/src/KSPACE/pair_lj_long_coul_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_lj_long_tip4p_long.h b/src/KSPACE/pair_lj_long_tip4p_long.h index ef86e4ed80..7499fcb8b9 100644 --- a/src/KSPACE/pair_lj_long_tip4p_long.h +++ b/src/KSPACE/pair_lj_long_tip4p_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pair_tip4p_long.h b/src/KSPACE/pair_tip4p_long.h index d55859a1cb..bc52cd9456 100644 --- a/src/KSPACE/pair_tip4p_long.h +++ b/src/KSPACE/pair_tip4p_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pppm.h b/src/KSPACE/pppm.h index 7451af47b4..af105f129d 100644 --- a/src/KSPACE/pppm.h +++ b/src/KSPACE/pppm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pppm_cg.h b/src/KSPACE/pppm_cg.h index 8b5e26deca..6c7425b893 100644 --- a/src/KSPACE/pppm_cg.h +++ b/src/KSPACE/pppm_cg.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pppm_dipole.h b/src/KSPACE/pppm_dipole.h index eb49361842..93326262fe 100644 --- a/src/KSPACE/pppm_dipole.h +++ b/src/KSPACE/pppm_dipole.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pppm_dipole_spin.h b/src/KSPACE/pppm_dipole_spin.h index e50b342b19..2998278863 100644 --- a/src/KSPACE/pppm_dipole_spin.h +++ b/src/KSPACE/pppm_dipole_spin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pppm_disp.h b/src/KSPACE/pppm_disp.h index c250301d6e..3c952cb54d 100644 --- a/src/KSPACE/pppm_disp.h +++ b/src/KSPACE/pppm_disp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pppm_disp_tip4p.h b/src/KSPACE/pppm_disp_tip4p.h index 596be5f60b..1f6a92a4bf 100644 --- a/src/KSPACE/pppm_disp_tip4p.h +++ b/src/KSPACE/pppm_disp_tip4p.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pppm_stagger.h b/src/KSPACE/pppm_stagger.h index 2f4cf9fb9b..02f182fa68 100644 --- a/src/KSPACE/pppm_stagger.h +++ b/src/KSPACE/pppm_stagger.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/pppm_tip4p.h b/src/KSPACE/pppm_tip4p.h index 440bc46fa6..aba660253f 100644 --- a/src/KSPACE/pppm_tip4p.h +++ b/src/KSPACE/pppm_tip4p.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/remap.h b/src/KSPACE/remap.h index 90a327bb66..0d5a01e39a 100644 --- a/src/KSPACE/remap.h +++ b/src/KSPACE/remap.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/KSPACE/remap_wrap.h b/src/KSPACE/remap_wrap.h index 38b2ad5ad2..f2e69e995f 100644 --- a/src/KSPACE/remap_wrap.h +++ b/src/KSPACE/remap_wrap.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/LATTE/fix_latte.h b/src/LATTE/fix_latte.h index 6d30ced0a0..aba6f81ff6 100644 --- a/src/LATTE/fix_latte.h +++ b/src/LATTE/fix_latte.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/fix_qeq_comb.h b/src/MANYBODY/fix_qeq_comb.h index c3a0ac08f3..01163b7f90 100644 --- a/src/MANYBODY/fix_qeq_comb.h +++ b/src/MANYBODY/fix_qeq_comb.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_adp.h b/src/MANYBODY/pair_adp.h index 6a292dda14..b7a26affbf 100644 --- a/src/MANYBODY/pair_adp.h +++ b/src/MANYBODY/pair_adp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h index 7539cc5e7f..068f1afecf 100644 --- a/src/MANYBODY/pair_airebo.h +++ b/src/MANYBODY/pair_airebo.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_airebo_morse.h b/src/MANYBODY/pair_airebo_morse.h index c87cf160e1..b835e91d1b 100644 --- a/src/MANYBODY/pair_airebo_morse.h +++ b/src/MANYBODY/pair_airebo_morse.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h index 8a9d38ec3b..6f7fbc6d3d 100644 --- a/src/MANYBODY/pair_atm.h +++ b/src/MANYBODY/pair_atm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h index ba75d5c591..0acfb3c31b 100644 --- a/src/MANYBODY/pair_bop.h +++ b/src/MANYBODY/pair_bop.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_comb.h b/src/MANYBODY/pair_comb.h index 51b522badf..4e569dee00 100644 --- a/src/MANYBODY/pair_comb.h +++ b/src/MANYBODY/pair_comb.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_comb3.h b/src/MANYBODY/pair_comb3.h index d03ee0e474..19a0ef904a 100644 --- a/src/MANYBODY/pair_comb3.h +++ b/src/MANYBODY/pair_comb3.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index e9cbd15f34..8779042118 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_eam_alloy.h b/src/MANYBODY/pair_eam_alloy.h index 1a13af278c..d280a29da1 100644 --- a/src/MANYBODY/pair_eam_alloy.h +++ b/src/MANYBODY/pair_eam_alloy.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_eam_cd.h b/src/MANYBODY/pair_eam_cd.h index 4d938aad10..49daa78a35 100644 --- a/src/MANYBODY/pair_eam_cd.h +++ b/src/MANYBODY/pair_eam_cd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_eam_fs.h b/src/MANYBODY/pair_eam_fs.h index f10ccbab4a..137f25a048 100644 --- a/src/MANYBODY/pair_eam_fs.h +++ b/src/MANYBODY/pair_eam_fs.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_eam_he.h b/src/MANYBODY/pair_eam_he.h index eccd63857d..d69e0729c8 100644 --- a/src/MANYBODY/pair_eam_he.h +++ b/src/MANYBODY/pair_eam_he.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h index 7611898c45..52b94192c2 100644 --- a/src/MANYBODY/pair_eim.h +++ b/src/MANYBODY/pair_eim.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_gw.h b/src/MANYBODY/pair_gw.h index a1cbdb5c86..68fd366a79 100644 --- a/src/MANYBODY/pair_gw.h +++ b/src/MANYBODY/pair_gw.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_gw_zbl.h b/src/MANYBODY/pair_gw_zbl.h index de344e94f7..0c7c7e13e1 100644 --- a/src/MANYBODY/pair_gw_zbl.h +++ b/src/MANYBODY/pair_gw_zbl.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_lcbop.h b/src/MANYBODY/pair_lcbop.h index 4ee89b4148..92ebca1ed8 100644 --- a/src/MANYBODY/pair_lcbop.h +++ b/src/MANYBODY/pair_lcbop.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_nb3b_harmonic.h b/src/MANYBODY/pair_nb3b_harmonic.h index 38ec07c78b..ee32dfcaee 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.h +++ b/src/MANYBODY/pair_nb3b_harmonic.h @@ -1,6 +1,6 @@ -/* --*- c++ -*- --------------------------------------------------------- +/* -*- c++ -*- --------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h index a8a74267cd..98c4bc86f8 100644 --- a/src/MANYBODY/pair_polymorphic.h +++ b/src/MANYBODY/pair_polymorphic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_rebo.h b/src/MANYBODY/pair_rebo.h index 9c1a12d4de..42d50b47ac 100644 --- a/src/MANYBODY/pair_rebo.h +++ b/src/MANYBODY/pair_rebo.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_sw.h b/src/MANYBODY/pair_sw.h index 4e13caee85..21f9bb0819 100644 --- a/src/MANYBODY/pair_sw.h +++ b/src/MANYBODY/pair_sw.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_tersoff.h b/src/MANYBODY/pair_tersoff.h index a4612d03be..16bfcd7d57 100644 --- a/src/MANYBODY/pair_tersoff.h +++ b/src/MANYBODY/pair_tersoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_tersoff_mod.h b/src/MANYBODY/pair_tersoff_mod.h index 82631727cf..8d68e1c9bd 100644 --- a/src/MANYBODY/pair_tersoff_mod.h +++ b/src/MANYBODY/pair_tersoff_mod.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_tersoff_mod_c.h b/src/MANYBODY/pair_tersoff_mod_c.h index 4949cb76db..1491941a2c 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.h +++ b/src/MANYBODY/pair_tersoff_mod_c.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_tersoff_zbl.h b/src/MANYBODY/pair_tersoff_zbl.h index 42483b7d89..b489563928 100644 --- a/src/MANYBODY/pair_tersoff_zbl.h +++ b/src/MANYBODY/pair_tersoff_zbl.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_vashishta.h b/src/MANYBODY/pair_vashishta.h index 06c23b2384..468a33b4cc 100644 --- a/src/MANYBODY/pair_vashishta.h +++ b/src/MANYBODY/pair_vashishta.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MANYBODY/pair_vashishta_table.h b/src/MANYBODY/pair_vashishta_table.h index cf3bb19232..dade008fc8 100644 --- a/src/MANYBODY/pair_vashishta_table.h +++ b/src/MANYBODY/pair_vashishta_table.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MC/fix_atom_swap.h b/src/MC/fix_atom_swap.h index a5ce89b16b..7c56624ad1 100644 --- a/src/MC/fix_atom_swap.h +++ b/src/MC/fix_atom_swap.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MC/fix_bond_break.h b/src/MC/fix_bond_break.h index ba0e0f63b6..e3bdcb01fa 100644 --- a/src/MC/fix_bond_break.h +++ b/src/MC/fix_bond_break.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MC/fix_bond_create.h b/src/MC/fix_bond_create.h index 1c80be59df..333e98630e 100644 --- a/src/MC/fix_bond_create.h +++ b/src/MC/fix_bond_create.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MC/fix_bond_create_angle.h b/src/MC/fix_bond_create_angle.h index 41fe5909f8..320f3225f1 100644 --- a/src/MC/fix_bond_create_angle.h +++ b/src/MC/fix_bond_create_angle.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MC/fix_bond_swap.h b/src/MC/fix_bond_swap.h index d24159d807..ad72ac66aa 100644 --- a/src/MC/fix_bond_swap.h +++ b/src/MC/fix_bond_swap.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 4e7e5ab5a0..e369ab95e1 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MC/fix_charge_regulation.h b/src/MC/fix_charge_regulation.h index 3afaffddb7..4f7ae57f96 100644 --- a/src/MC/fix_charge_regulation.h +++ b/src/MC/fix_charge_regulation.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h index e111642548..99153865f2 100644 --- a/src/MC/fix_gcmc.h +++ b/src/MC/fix_gcmc.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MC/fix_tfmc.h b/src/MC/fix_tfmc.h index d4f121eb90..6b95704612 100644 --- a/src/MC/fix_tfmc.h +++ b/src/MC/fix_tfmc.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MC/fix_widom.h b/src/MC/fix_widom.h index 19102e4f4a..c12be4ad75 100644 --- a/src/MC/fix_widom.h +++ b/src/MC/fix_widom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MC/pair_dsmc.h b/src/MC/pair_dsmc.h index 1d24a7eeba..784ada286c 100644 --- a/src/MC/pair_dsmc.h +++ b/src/MC/pair_dsmc.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MESSAGE/fix_client_md.h b/src/MESSAGE/fix_client_md.h index 1c874c7278..f2e43717a9 100644 --- a/src/MESSAGE/fix_client_md.h +++ b/src/MESSAGE/fix_client_md.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MESSAGE/message.h b/src/MESSAGE/message.h index 88c658e44b..d4099737e6 100644 --- a/src/MESSAGE/message.h +++ b/src/MESSAGE/message.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MESSAGE/server.h b/src/MESSAGE/server.h index 7c93db8c64..dffecaf1c8 100644 --- a/src/MESSAGE/server.h +++ b/src/MESSAGE/server.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MESSAGE/server_mc.h b/src/MESSAGE/server_mc.h index d0fb489429..286a5ab465 100644 --- a/src/MESSAGE/server_mc.h +++ b/src/MESSAGE/server_mc.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MESSAGE/server_md.h b/src/MESSAGE/server_md.h index 289d70bdd8..1f15eccbec 100644 --- a/src/MESSAGE/server_md.h +++ b/src/MESSAGE/server_md.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/compute_msd_nongauss.h b/src/MISC/compute_msd_nongauss.h index aa029a7970..8931c50c09 100644 --- a/src/MISC/compute_msd_nongauss.h +++ b/src/MISC/compute_msd_nongauss.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/compute_ti.h b/src/MISC/compute_ti.h index d1557a436e..d82343f4eb 100644 --- a/src/MISC/compute_ti.h +++ b/src/MISC/compute_ti.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/dump_xtc.h b/src/MISC/dump_xtc.h index e242e7eef0..5ec9cee342 100644 --- a/src/MISC/dump_xtc.h +++ b/src/MISC/dump_xtc.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h index 12543fc2f3..9bb66930a1 100644 --- a/src/MISC/fix_deposit.h +++ b/src/MISC/fix_deposit.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/fix_efield.h b/src/MISC/fix_efield.h index 4a360b6464..d18629bdbc 100644 --- a/src/MISC/fix_efield.h +++ b/src/MISC/fix_efield.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/fix_evaporate.h b/src/MISC/fix_evaporate.h index d26e8dba84..d09875b5bd 100644 --- a/src/MISC/fix_evaporate.h +++ b/src/MISC/fix_evaporate.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/fix_gld.h b/src/MISC/fix_gld.h index abb3286544..d8fa7408a4 100644 --- a/src/MISC/fix_gld.h +++ b/src/MISC/fix_gld.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/fix_oneway.h b/src/MISC/fix_oneway.h index 75dcabda64..aeb0e9532f 100644 --- a/src/MISC/fix_oneway.h +++ b/src/MISC/fix_oneway.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/fix_orient_bcc.h b/src/MISC/fix_orient_bcc.h index 2035e85b15..ea6ee7a7a7 100644 --- a/src/MISC/fix_orient_bcc.h +++ b/src/MISC/fix_orient_bcc.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/fix_orient_fcc.h b/src/MISC/fix_orient_fcc.h index 8bdc098289..4819cd09c0 100644 --- a/src/MISC/fix_orient_fcc.h +++ b/src/MISC/fix_orient_fcc.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/fix_thermal_conductivity.h b/src/MISC/fix_thermal_conductivity.h index fa49a10bdf..0c59f29bd6 100644 --- a/src/MISC/fix_thermal_conductivity.h +++ b/src/MISC/fix_thermal_conductivity.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/fix_ttm.h b/src/MISC/fix_ttm.h index 76631dbf57..ddcebfe46a 100644 --- a/src/MISC/fix_ttm.h +++ b/src/MISC/fix_ttm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/fix_viscosity.h b/src/MISC/fix_viscosity.h index 547febfa60..519658a27f 100644 --- a/src/MISC/fix_viscosity.h +++ b/src/MISC/fix_viscosity.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/pair_nm_cut.h b/src/MISC/pair_nm_cut.h index 692c8559d7..83a0846321 100644 --- a/src/MISC/pair_nm_cut.h +++ b/src/MISC/pair_nm_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/pair_nm_cut_coul_cut.h b/src/MISC/pair_nm_cut_coul_cut.h index cefeb58ba9..0586f0a16f 100644 --- a/src/MISC/pair_nm_cut_coul_cut.h +++ b/src/MISC/pair_nm_cut_coul_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MISC/pair_nm_cut_coul_long.h b/src/MISC/pair_nm_cut_coul_long.h index 362474cffd..4a8e49e2b6 100644 --- a/src/MISC/pair_nm_cut_coul_long.h +++ b/src/MISC/pair_nm_cut_coul_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MLIAP/compute_mliap.h b/src/MLIAP/compute_mliap.h index 1172111247..01255fff6d 100644 --- a/src/MLIAP/compute_mliap.h +++ b/src/MLIAP/compute_mliap.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MLIAP/mliap_data.h b/src/MLIAP/mliap_data.h index a9ada7ebd7..bfefa53af0 100644 --- a/src/MLIAP/mliap_data.h +++ b/src/MLIAP/mliap_data.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MLIAP/mliap_descriptor.h b/src/MLIAP/mliap_descriptor.h index 44fe2f21ad..7f162d6ee4 100644 --- a/src/MLIAP/mliap_descriptor.h +++ b/src/MLIAP/mliap_descriptor.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MLIAP/mliap_descriptor_snap.h b/src/MLIAP/mliap_descriptor_snap.h index 40630e5131..09cb56f445 100644 --- a/src/MLIAP/mliap_descriptor_snap.h +++ b/src/MLIAP/mliap_descriptor_snap.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MLIAP/mliap_model.h b/src/MLIAP/mliap_model.h index 96cfff0a3d..98bae35d2f 100644 --- a/src/MLIAP/mliap_model.h +++ b/src/MLIAP/mliap_model.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MLIAP/mliap_model_linear.h b/src/MLIAP/mliap_model_linear.h index 89c69d3537..1603f0cb53 100644 --- a/src/MLIAP/mliap_model_linear.h +++ b/src/MLIAP/mliap_model_linear.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MLIAP/mliap_model_nn.h b/src/MLIAP/mliap_model_nn.h index abdb9dec0f..0f04b09f9a 100644 --- a/src/MLIAP/mliap_model_nn.h +++ b/src/MLIAP/mliap_model_nn.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MLIAP/mliap_model_python.cpp b/src/MLIAP/mliap_model_python.cpp index 4dda7df357..6f88c41bce 100644 --- a/src/MLIAP/mliap_model_python.cpp +++ b/src/MLIAP/mliap_model_python.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MLIAP/mliap_model_python.h b/src/MLIAP/mliap_model_python.h index 57110f36e2..f776b9a795 100644 --- a/src/MLIAP/mliap_model_python.h +++ b/src/MLIAP/mliap_model_python.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MLIAP/mliap_model_quadratic.h b/src/MLIAP/mliap_model_quadratic.h index 28f1732f9b..eabb8acfbe 100644 --- a/src/MLIAP/mliap_model_quadratic.h +++ b/src/MLIAP/mliap_model_quadratic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MLIAP/pair_mliap.h b/src/MLIAP/pair_mliap.h index c31634e923..d8fb82c8b7 100644 --- a/src/MLIAP/pair_mliap.h +++ b/src/MLIAP/pair_mliap.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/angle_charmm.h b/src/MOLECULE/angle_charmm.h index 444c833d37..28ed51e8ce 100644 --- a/src/MOLECULE/angle_charmm.h +++ b/src/MOLECULE/angle_charmm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/angle_cosine.h b/src/MOLECULE/angle_cosine.h index ca1f4178f8..915acab85e 100644 --- a/src/MOLECULE/angle_cosine.h +++ b/src/MOLECULE/angle_cosine.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/angle_cosine_delta.h b/src/MOLECULE/angle_cosine_delta.h index 70b574b234..28a14149f6 100644 --- a/src/MOLECULE/angle_cosine_delta.h +++ b/src/MOLECULE/angle_cosine_delta.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/angle_cosine_periodic.h b/src/MOLECULE/angle_cosine_periodic.h index f0188b6c17..2f25245dbe 100644 --- a/src/MOLECULE/angle_cosine_periodic.h +++ b/src/MOLECULE/angle_cosine_periodic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/angle_cosine_squared.h b/src/MOLECULE/angle_cosine_squared.h index a19a923850..d4539a3b23 100644 --- a/src/MOLECULE/angle_cosine_squared.h +++ b/src/MOLECULE/angle_cosine_squared.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/angle_harmonic.h b/src/MOLECULE/angle_harmonic.h index f371178d58..109da340c7 100644 --- a/src/MOLECULE/angle_harmonic.h +++ b/src/MOLECULE/angle_harmonic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/angle_table.h b/src/MOLECULE/angle_table.h index 8c854dc2e6..bbfa6d38b7 100644 --- a/src/MOLECULE/angle_table.h +++ b/src/MOLECULE/angle_table.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/atom_vec_angle.h b/src/MOLECULE/atom_vec_angle.h index 0ce0b4baab..6bff95af40 100644 --- a/src/MOLECULE/atom_vec_angle.h +++ b/src/MOLECULE/atom_vec_angle.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/atom_vec_bond.h b/src/MOLECULE/atom_vec_bond.h index 403167ac11..ba32265374 100644 --- a/src/MOLECULE/atom_vec_bond.h +++ b/src/MOLECULE/atom_vec_bond.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/atom_vec_full.h b/src/MOLECULE/atom_vec_full.h index 1abd3351d3..569ea4e11d 100644 --- a/src/MOLECULE/atom_vec_full.h +++ b/src/MOLECULE/atom_vec_full.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/atom_vec_molecular.h b/src/MOLECULE/atom_vec_molecular.h index bcfa13d9d3..9203e5d040 100644 --- a/src/MOLECULE/atom_vec_molecular.h +++ b/src/MOLECULE/atom_vec_molecular.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/atom_vec_template.h b/src/MOLECULE/atom_vec_template.h index 99acf5d855..efc178ad5a 100644 --- a/src/MOLECULE/atom_vec_template.h +++ b/src/MOLECULE/atom_vec_template.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/bond_fene.h b/src/MOLECULE/bond_fene.h index 78ce169870..915b5cf23b 100644 --- a/src/MOLECULE/bond_fene.h +++ b/src/MOLECULE/bond_fene.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/bond_fene_expand.h b/src/MOLECULE/bond_fene_expand.h index 8cfc17dc68..b2f62d49fc 100644 --- a/src/MOLECULE/bond_fene_expand.h +++ b/src/MOLECULE/bond_fene_expand.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/bond_gromos.h b/src/MOLECULE/bond_gromos.h index 95ecf8db10..54cfb19a92 100644 --- a/src/MOLECULE/bond_gromos.h +++ b/src/MOLECULE/bond_gromos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/bond_harmonic.h b/src/MOLECULE/bond_harmonic.h index 39b4f68af5..b335e23a97 100644 --- a/src/MOLECULE/bond_harmonic.h +++ b/src/MOLECULE/bond_harmonic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/bond_morse.h b/src/MOLECULE/bond_morse.h index 6d7ec8f8aa..6110eda171 100644 --- a/src/MOLECULE/bond_morse.h +++ b/src/MOLECULE/bond_morse.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/bond_nonlinear.h b/src/MOLECULE/bond_nonlinear.h index 29191698d3..8624e9bb14 100644 --- a/src/MOLECULE/bond_nonlinear.h +++ b/src/MOLECULE/bond_nonlinear.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/bond_quartic.h b/src/MOLECULE/bond_quartic.h index 60ccf307b9..0642b5e8d4 100644 --- a/src/MOLECULE/bond_quartic.h +++ b/src/MOLECULE/bond_quartic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/bond_table.h b/src/MOLECULE/bond_table.h index b08059415b..3c95069ee2 100644 --- a/src/MOLECULE/bond_table.h +++ b/src/MOLECULE/bond_table.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/dihedral_charmm.h b/src/MOLECULE/dihedral_charmm.h index 4be3925dad..54ff666e0b 100644 --- a/src/MOLECULE/dihedral_charmm.h +++ b/src/MOLECULE/dihedral_charmm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/dihedral_charmmfsw.h b/src/MOLECULE/dihedral_charmmfsw.h index b33250004b..89a0539a1d 100644 --- a/src/MOLECULE/dihedral_charmmfsw.h +++ b/src/MOLECULE/dihedral_charmmfsw.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/dihedral_harmonic.h b/src/MOLECULE/dihedral_harmonic.h index 6792d16a20..d1fe038c5e 100644 --- a/src/MOLECULE/dihedral_harmonic.h +++ b/src/MOLECULE/dihedral_harmonic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/dihedral_helix.h b/src/MOLECULE/dihedral_helix.h index 0213c59e8a..f8981dd34a 100644 --- a/src/MOLECULE/dihedral_helix.h +++ b/src/MOLECULE/dihedral_helix.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/dihedral_multi_harmonic.h b/src/MOLECULE/dihedral_multi_harmonic.h index bb3d7183f7..92e4d24723 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.h +++ b/src/MOLECULE/dihedral_multi_harmonic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/dihedral_opls.h b/src/MOLECULE/dihedral_opls.h index 01878173cd..c6f6ad7ad0 100644 --- a/src/MOLECULE/dihedral_opls.h +++ b/src/MOLECULE/dihedral_opls.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/fix_cmap.h b/src/MOLECULE/fix_cmap.h index cd0c01a921..d1dd3afbf2 100644 --- a/src/MOLECULE/fix_cmap.h +++ b/src/MOLECULE/fix_cmap.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/improper_cvff.h b/src/MOLECULE/improper_cvff.h index 055d2ca9b8..8edbe5144d 100644 --- a/src/MOLECULE/improper_cvff.h +++ b/src/MOLECULE/improper_cvff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/improper_harmonic.h b/src/MOLECULE/improper_harmonic.h index 5949c6911e..86b8bf34f6 100644 --- a/src/MOLECULE/improper_harmonic.h +++ b/src/MOLECULE/improper_harmonic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/improper_umbrella.h b/src/MOLECULE/improper_umbrella.h index da9d6c8f4b..7a89fc5331 100644 --- a/src/MOLECULE/improper_umbrella.h +++ b/src/MOLECULE/improper_umbrella.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.h b/src/MOLECULE/pair_hbond_dreiding_lj.h index 1f33e178c1..5cd745e6ae 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.h +++ b/src/MOLECULE/pair_hbond_dreiding_lj.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.h b/src/MOLECULE/pair_hbond_dreiding_morse.h index 77d0d43c86..dc4b9b8614 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.h +++ b/src/MOLECULE/pair_hbond_dreiding_morse.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.h b/src/MOLECULE/pair_lj_charmm_coul_charmm.h index 1c4ef00fc5..9a1e3cb1ea 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.h +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h index 7f0ab9d26e..ead7792c4f 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.h b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.h index 95272cd944..82dbd44e9e 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.h +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.h b/src/MOLECULE/pair_lj_cut_tip4p_cut.h index b69781b160..4852275030 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.h +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MOLECULE/pair_tip4p_cut.h b/src/MOLECULE/pair_tip4p_cut.h index ea801db685..d0ff796d39 100644 --- a/src/MOLECULE/pair_tip4p_cut.h +++ b/src/MOLECULE/pair_tip4p_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MPIIO/dump_atom_mpiio.h b/src/MPIIO/dump_atom_mpiio.h index 36b43e3f08..3486f20f53 100644 --- a/src/MPIIO/dump_atom_mpiio.h +++ b/src/MPIIO/dump_atom_mpiio.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MPIIO/dump_cfg_mpiio.h b/src/MPIIO/dump_cfg_mpiio.h index eec078e502..d0855f55fb 100644 --- a/src/MPIIO/dump_cfg_mpiio.h +++ b/src/MPIIO/dump_cfg_mpiio.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MPIIO/dump_custom_mpiio.h b/src/MPIIO/dump_custom_mpiio.h index 334b1377a5..8be38364b3 100644 --- a/src/MPIIO/dump_custom_mpiio.h +++ b/src/MPIIO/dump_custom_mpiio.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MPIIO/dump_xyz_mpiio.h b/src/MPIIO/dump_xyz_mpiio.h index 484d2a53db..b2fde6306a 100644 --- a/src/MPIIO/dump_xyz_mpiio.h +++ b/src/MPIIO/dump_xyz_mpiio.h @@ -1,6 +1,6 @@ /* -*- c++ -*- --------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MPIIO/restart_mpiio.h b/src/MPIIO/restart_mpiio.h index 4cc7558d46..f3594573be 100644 --- a/src/MPIIO/restart_mpiio.h +++ b/src/MPIIO/restart_mpiio.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/MSCG/fix_mscg.h b/src/MSCG/fix_mscg.h index bcc087f0dc..520a6b1ac3 100644 --- a/src/MSCG/fix_mscg.h +++ b/src/MSCG/fix_mscg.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/OPT/pair_eam_alloy_opt.h b/src/OPT/pair_eam_alloy_opt.h index 3fdfc449e9..6c56ca76dd 100644 --- a/src/OPT/pair_eam_alloy_opt.h +++ b/src/OPT/pair_eam_alloy_opt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/OPT/pair_eam_fs_opt.h b/src/OPT/pair_eam_fs_opt.h index f0288d5c57..63f0ea8499 100644 --- a/src/OPT/pair_eam_fs_opt.h +++ b/src/OPT/pair_eam_fs_opt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/OPT/pair_eam_opt.h b/src/OPT/pair_eam_opt.h index b9bc6a5a34..6805e2a1cb 100644 --- a/src/OPT/pair_eam_opt.h +++ b/src/OPT/pair_eam_opt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.h b/src/OPT/pair_lj_charmm_coul_long_opt.h index 39477fae99..3f1bf44a8f 100644 --- a/src/OPT/pair_lj_charmm_coul_long_opt.h +++ b/src/OPT/pair_lj_charmm_coul_long_opt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/OPT/pair_lj_cut_coul_long_opt.h b/src/OPT/pair_lj_cut_coul_long_opt.h index 435d27ff2f..b136dcb34d 100644 --- a/src/OPT/pair_lj_cut_coul_long_opt.h +++ b/src/OPT/pair_lj_cut_coul_long_opt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/OPT/pair_lj_cut_opt.h b/src/OPT/pair_lj_cut_opt.h index 4c145ab711..60afee870e 100644 --- a/src/OPT/pair_lj_cut_opt.h +++ b/src/OPT/pair_lj_cut_opt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/OPT/pair_lj_cut_tip4p_long_opt.h b/src/OPT/pair_lj_cut_tip4p_long_opt.h index 8aa3955c2b..79c1d1e001 100644 --- a/src/OPT/pair_lj_cut_tip4p_long_opt.h +++ b/src/OPT/pair_lj_cut_tip4p_long_opt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/OPT/pair_lj_long_coul_long_opt.h b/src/OPT/pair_lj_long_coul_long_opt.h index 0bed57cac2..39a8dabbfd 100644 --- a/src/OPT/pair_lj_long_coul_long_opt.h +++ b/src/OPT/pair_lj_long_coul_long_opt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/OPT/pair_morse_opt.h b/src/OPT/pair_morse_opt.h index 1415f6b789..bb870d6e6e 100644 --- a/src/OPT/pair_morse_opt.h +++ b/src/OPT/pair_morse_opt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/OPT/pair_ufm_opt.h b/src/OPT/pair_ufm_opt.h index edac708403..6df271edad 100644 --- a/src/OPT/pair_ufm_opt.h +++ b/src/OPT/pair_ufm_opt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PERI/atom_vec_peri.h b/src/PERI/atom_vec_peri.h index 5739ea55c1..66ef2d4230 100644 --- a/src/PERI/atom_vec_peri.h +++ b/src/PERI/atom_vec_peri.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PERI/compute_damage_atom.h b/src/PERI/compute_damage_atom.h index ae3886bc6c..ea0c4fd993 100644 --- a/src/PERI/compute_damage_atom.h +++ b/src/PERI/compute_damage_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PERI/compute_dilatation_atom.h b/src/PERI/compute_dilatation_atom.h index a247cc9291..ead6a68189 100644 --- a/src/PERI/compute_dilatation_atom.h +++ b/src/PERI/compute_dilatation_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PERI/compute_plasticity_atom.h b/src/PERI/compute_plasticity_atom.h index ccd6ef1e63..0022bf2215 100644 --- a/src/PERI/compute_plasticity_atom.h +++ b/src/PERI/compute_plasticity_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PERI/fix_peri_neigh.h b/src/PERI/fix_peri_neigh.h index 247ceaaa43..b72d666390 100644 --- a/src/PERI/fix_peri_neigh.h +++ b/src/PERI/fix_peri_neigh.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PERI/pair_peri_eps.h b/src/PERI/pair_peri_eps.h index c5d2cd2976..39e0a6c034 100644 --- a/src/PERI/pair_peri_eps.h +++ b/src/PERI/pair_peri_eps.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PERI/pair_peri_lps.h b/src/PERI/pair_peri_lps.h index caaac05185..0cdaa93656 100644 --- a/src/PERI/pair_peri_lps.h +++ b/src/PERI/pair_peri_lps.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PERI/pair_peri_pmb.h b/src/PERI/pair_peri_pmb.h index 25e7a8e83f..543d87424e 100644 --- a/src/PERI/pair_peri_pmb.h +++ b/src/PERI/pair_peri_pmb.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PERI/pair_peri_ves.h b/src/PERI/pair_peri_ves.h index 8aae426510..8e52027055 100644 --- a/src/PERI/pair_peri_ves.h +++ b/src/PERI/pair_peri_ves.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PLUGIN/plugin.h b/src/PLUGIN/plugin.h index 4b4bca9878..bc1d473c90 100644 --- a/src/PLUGIN/plugin.h +++ b/src/PLUGIN/plugin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/POEMS/fix_poems.h b/src/POEMS/fix_poems.h index 7c81889639..30f6c775d7 100644 --- a/src/POEMS/fix_poems.h +++ b/src/POEMS/fix_poems.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PYTHON/fix_python_invoke.h b/src/PYTHON/fix_python_invoke.h index 48fb0b404f..63cdaea8de 100644 --- a/src/PYTHON/fix_python_invoke.h +++ b/src/PYTHON/fix_python_invoke.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PYTHON/fix_python_move.h b/src/PYTHON/fix_python_move.h index 2220709970..e1257e8fe5 100644 --- a/src/PYTHON/fix_python_move.h +++ b/src/PYTHON/fix_python_move.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PYTHON/pair_python.h b/src/PYTHON/pair_python.h index 881bfe2835..1ca290f4a1 100644 --- a/src/PYTHON/pair_python.h +++ b/src/PYTHON/pair_python.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PYTHON/python_compat.h b/src/PYTHON/python_compat.h index 97946349b2..9263cd3e95 100644 --- a/src/PYTHON/python_compat.h +++ b/src/PYTHON/python_compat.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PYTHON/python_impl.h b/src/PYTHON/python_impl.h index f53694a00b..c031eb236c 100644 --- a/src/PYTHON/python_impl.h +++ b/src/PYTHON/python_impl.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/PYTHON/python_utils.h b/src/PYTHON/python_utils.h index 82422916ff..45dd58456c 100644 --- a/src/PYTHON/python_utils.h +++ b/src/PYTHON/python_utils.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/QEQ/fix_qeq.h b/src/QEQ/fix_qeq.h index 9a3087840b..1ec9df5932 100644 --- a/src/QEQ/fix_qeq.h +++ b/src/QEQ/fix_qeq.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/QEQ/fix_qeq_dynamic.h b/src/QEQ/fix_qeq_dynamic.h index dc885a6b1f..36bd448065 100644 --- a/src/QEQ/fix_qeq_dynamic.h +++ b/src/QEQ/fix_qeq_dynamic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/QEQ/fix_qeq_fire.h b/src/QEQ/fix_qeq_fire.h index 9fd81176e8..26663e5a45 100644 --- a/src/QEQ/fix_qeq_fire.h +++ b/src/QEQ/fix_qeq_fire.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/QEQ/fix_qeq_point.h b/src/QEQ/fix_qeq_point.h index eae9603bf5..323a2ba489 100644 --- a/src/QEQ/fix_qeq_point.h +++ b/src/QEQ/fix_qeq_point.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/QEQ/fix_qeq_shielded.h b/src/QEQ/fix_qeq_shielded.h index dfdea2b719..a9524fa382 100644 --- a/src/QEQ/fix_qeq_shielded.h +++ b/src/QEQ/fix_qeq_shielded.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/QEQ/fix_qeq_slater.h b/src/QEQ/fix_qeq_slater.h index bf1a98a6d5..9e9a9bbd67 100644 --- a/src/QEQ/fix_qeq_slater.h +++ b/src/QEQ/fix_qeq_slater.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/compute_event_displace.h b/src/REPLICA/compute_event_displace.h index 481df39b07..269eef438a 100644 --- a/src/REPLICA/compute_event_displace.h +++ b/src/REPLICA/compute_event_displace.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/fix_event.h b/src/REPLICA/fix_event.h index a8f6f93d5f..96a6626477 100644 --- a/src/REPLICA/fix_event.h +++ b/src/REPLICA/fix_event.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/fix_event_hyper.h b/src/REPLICA/fix_event_hyper.h index af685ee539..9a04a30bed 100644 --- a/src/REPLICA/fix_event_hyper.h +++ b/src/REPLICA/fix_event_hyper.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/fix_event_prd.h b/src/REPLICA/fix_event_prd.h index 363de31e9d..2f28c62dd4 100644 --- a/src/REPLICA/fix_event_prd.h +++ b/src/REPLICA/fix_event_prd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/fix_event_tad.h b/src/REPLICA/fix_event_tad.h index dcc8a67fe4..e1e976a0ba 100644 --- a/src/REPLICA/fix_event_tad.h +++ b/src/REPLICA/fix_event_tad.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/fix_hyper.h b/src/REPLICA/fix_hyper.h index 74acada4fe..e2ae205649 100644 --- a/src/REPLICA/fix_hyper.h +++ b/src/REPLICA/fix_hyper.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/fix_hyper_global.h b/src/REPLICA/fix_hyper_global.h index dd2c807ad3..8f7620ca66 100644 --- a/src/REPLICA/fix_hyper_global.h +++ b/src/REPLICA/fix_hyper_global.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/fix_hyper_local.h b/src/REPLICA/fix_hyper_local.h index aa3f050bb9..4085a82de4 100644 --- a/src/REPLICA/fix_hyper_local.h +++ b/src/REPLICA/fix_hyper_local.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/fix_neb.h b/src/REPLICA/fix_neb.h index 5324b06432..b686ef6d47 100644 --- a/src/REPLICA/fix_neb.h +++ b/src/REPLICA/fix_neb.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/hyper.h b/src/REPLICA/hyper.h index a96ccf3727..a6418c89a0 100644 --- a/src/REPLICA/hyper.h +++ b/src/REPLICA/hyper.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h index 8298766ccf..6c4071baa1 100644 --- a/src/REPLICA/neb.h +++ b/src/REPLICA/neb.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/prd.h b/src/REPLICA/prd.h index 0d8fde1bfe..c21ec4e319 100644 --- a/src/REPLICA/prd.h +++ b/src/REPLICA/prd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/tad.h b/src/REPLICA/tad.h index 91e570c707..cf2136f0d5 100644 --- a/src/REPLICA/tad.h +++ b/src/REPLICA/tad.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/temper.h b/src/REPLICA/temper.h index 3f7d813f2a..40293de483 100644 --- a/src/REPLICA/temper.h +++ b/src/REPLICA/temper.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/REPLICA/verlet_split.h b/src/REPLICA/verlet_split.h index f31ebdfa17..e2c9ac2900 100644 --- a/src/REPLICA/verlet_split.h +++ b/src/REPLICA/verlet_split.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/compute_erotate_rigid.h b/src/RIGID/compute_erotate_rigid.h index a08e8d51a0..fae6cf5a10 100644 --- a/src/RIGID/compute_erotate_rigid.h +++ b/src/RIGID/compute_erotate_rigid.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/compute_ke_rigid.h b/src/RIGID/compute_ke_rigid.h index 97ceb24cfd..2cbd059da3 100644 --- a/src/RIGID/compute_ke_rigid.h +++ b/src/RIGID/compute_ke_rigid.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/compute_rigid_local.h b/src/RIGID/compute_rigid_local.h index bedb8574d0..1fb7e93b5b 100644 --- a/src/RIGID/compute_rigid_local.h +++ b/src/RIGID/compute_rigid_local.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_ehex.h b/src/RIGID/fix_ehex.h index 860ed3d1f3..456b99320a 100644 --- a/src/RIGID/fix_ehex.h +++ b/src/RIGID/fix_ehex.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_rattle.h b/src/RIGID/fix_rattle.h index cab148f10c..7b541bac77 100644 --- a/src/RIGID/fix_rattle.h +++ b/src/RIGID/fix_rattle.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_rigid.h b/src/RIGID/fix_rigid.h index cd32d0ca72..e04b4cf143 100644 --- a/src/RIGID/fix_rigid.h +++ b/src/RIGID/fix_rigid.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_rigid_nh.h b/src/RIGID/fix_rigid_nh.h index 10ad9b24fb..86492e5531 100644 --- a/src/RIGID/fix_rigid_nh.h +++ b/src/RIGID/fix_rigid_nh.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_rigid_nh_small.h b/src/RIGID/fix_rigid_nh_small.h index 899cec1122..54d5421ceb 100644 --- a/src/RIGID/fix_rigid_nh_small.h +++ b/src/RIGID/fix_rigid_nh_small.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_rigid_nph.h b/src/RIGID/fix_rigid_nph.h index 836c357d8f..9f716286ae 100644 --- a/src/RIGID/fix_rigid_nph.h +++ b/src/RIGID/fix_rigid_nph.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_rigid_nph_small.h b/src/RIGID/fix_rigid_nph_small.h index 073fbee5eb..798d0b904b 100644 --- a/src/RIGID/fix_rigid_nph_small.h +++ b/src/RIGID/fix_rigid_nph_small.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_rigid_npt.h b/src/RIGID/fix_rigid_npt.h index 09efecdae8..6c10f44ac9 100644 --- a/src/RIGID/fix_rigid_npt.h +++ b/src/RIGID/fix_rigid_npt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_rigid_npt_small.h b/src/RIGID/fix_rigid_npt_small.h index 82bac2780e..2b3f0e3b5e 100644 --- a/src/RIGID/fix_rigid_npt_small.h +++ b/src/RIGID/fix_rigid_npt_small.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_rigid_nve.h b/src/RIGID/fix_rigid_nve.h index 22039eaf09..59ba184279 100644 --- a/src/RIGID/fix_rigid_nve.h +++ b/src/RIGID/fix_rigid_nve.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_rigid_nve_small.h b/src/RIGID/fix_rigid_nve_small.h index f534a3efa8..96de7f2bcd 100644 --- a/src/RIGID/fix_rigid_nve_small.h +++ b/src/RIGID/fix_rigid_nve_small.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_rigid_nvt.h b/src/RIGID/fix_rigid_nvt.h index 11091125ae..4c2c003d78 100644 --- a/src/RIGID/fix_rigid_nvt.h +++ b/src/RIGID/fix_rigid_nvt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_rigid_nvt_small.h b/src/RIGID/fix_rigid_nvt_small.h index 5fd0ce290a..4f83546b77 100644 --- a/src/RIGID/fix_rigid_nvt_small.h +++ b/src/RIGID/fix_rigid_nvt_small.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h index 6534017971..16a5e58da5 100644 --- a/src/RIGID/fix_rigid_small.h +++ b/src/RIGID/fix_rigid_small.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/fix_shake.h b/src/RIGID/fix_shake.h index f1be3e2d1d..d627986038 100644 --- a/src/RIGID/fix_shake.h +++ b/src/RIGID/fix_shake.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/RIGID/rigid_const.h b/src/RIGID/rigid_const.h index b345a6b9dc..b37bd9fad2 100644 --- a/src/RIGID/rigid_const.h +++ b/src/RIGID/rigid_const.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SHOCK/fix_append_atoms.h b/src/SHOCK/fix_append_atoms.h index cc26acc8b8..e2cf1cb025 100644 --- a/src/SHOCK/fix_append_atoms.h +++ b/src/SHOCK/fix_append_atoms.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SHOCK/fix_msst.h b/src/SHOCK/fix_msst.h index 43a4ca77a4..e253e1860f 100644 --- a/src/SHOCK/fix_msst.h +++ b/src/SHOCK/fix_msst.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SHOCK/fix_nphug.h b/src/SHOCK/fix_nphug.h index 9ad5e3ab00..bdf28d75d1 100644 --- a/src/SHOCK/fix_nphug.h +++ b/src/SHOCK/fix_nphug.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SHOCK/fix_wall_piston.h b/src/SHOCK/fix_wall_piston.h index 28135b2359..1801d5c86a 100644 --- a/src/SHOCK/fix_wall_piston.h +++ b/src/SHOCK/fix_wall_piston.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SNAP/compute_sna_atom.h b/src/SNAP/compute_sna_atom.h index 1ad325729d..c9ef46a2f5 100644 --- a/src/SNAP/compute_sna_atom.h +++ b/src/SNAP/compute_sna_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SNAP/compute_snad_atom.h b/src/SNAP/compute_snad_atom.h index 15609bdfdc..e5c54226e8 100644 --- a/src/SNAP/compute_snad_atom.h +++ b/src/SNAP/compute_snad_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SNAP/compute_snap.h b/src/SNAP/compute_snap.h index 7151839c8c..43fe4df882 100644 --- a/src/SNAP/compute_snap.h +++ b/src/SNAP/compute_snap.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SNAP/compute_snav_atom.h b/src/SNAP/compute_snav_atom.h index 857671388b..36a64239da 100644 --- a/src/SNAP/compute_snav_atom.h +++ b/src/SNAP/compute_snav_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SNAP/pair_snap.h b/src/SNAP/pair_snap.h index ee596d2ba7..3f8393b03c 100644 --- a/src/SNAP/pair_snap.h +++ b/src/SNAP/pair_snap.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SNAP/sna.h b/src/SNAP/sna.h index 746b55fb70..1444fecaf7 100644 --- a/src/SNAP/sna.h +++ b/src/SNAP/sna.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/atom_vec_spin.h b/src/SPIN/atom_vec_spin.h index f24791605d..6aa1cccee0 100644 --- a/src/SPIN/atom_vec_spin.h +++ b/src/SPIN/atom_vec_spin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/compute_spin.h b/src/SPIN/compute_spin.h index d98a61bb39..3b4c28674e 100644 --- a/src/SPIN/compute_spin.h +++ b/src/SPIN/compute_spin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/fix_langevin_spin.h b/src/SPIN/fix_langevin_spin.h index 090e5b666a..707ffa48a7 100644 --- a/src/SPIN/fix_langevin_spin.h +++ b/src/SPIN/fix_langevin_spin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/fix_neb_spin.h b/src/SPIN/fix_neb_spin.h index 9646684a3a..3c095ef3c2 100644 --- a/src/SPIN/fix_neb_spin.h +++ b/src/SPIN/fix_neb_spin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h index ac5bc57b25..b7992f61f9 100644 --- a/src/SPIN/fix_nve_spin.h +++ b/src/SPIN/fix_nve_spin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/fix_precession_spin.h b/src/SPIN/fix_precession_spin.h index d06a04f8f1..d3955cc822 100644 --- a/src/SPIN/fix_precession_spin.h +++ b/src/SPIN/fix_precession_spin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/fix_setforce_spin.h b/src/SPIN/fix_setforce_spin.h index 1c5ce54dd3..4809bb801b 100644 --- a/src/SPIN/fix_setforce_spin.h +++ b/src/SPIN/fix_setforce_spin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/min_spin.h b/src/SPIN/min_spin.h index f2df81e58c..ee4bfb20b4 100644 --- a/src/SPIN/min_spin.h +++ b/src/SPIN/min_spin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/min_spin_cg.h b/src/SPIN/min_spin_cg.h index 640721b8ef..5d87e05f4e 100644 --- a/src/SPIN/min_spin_cg.h +++ b/src/SPIN/min_spin_cg.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/min_spin_lbfgs.h b/src/SPIN/min_spin_lbfgs.h index 8b470b5d23..de21c8b3a5 100644 --- a/src/SPIN/min_spin_lbfgs.h +++ b/src/SPIN/min_spin_lbfgs.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/neb_spin.h b/src/SPIN/neb_spin.h index 54d85093a5..bdb7e34caf 100644 --- a/src/SPIN/neb_spin.h +++ b/src/SPIN/neb_spin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h index 9db2bd4177..2e115d69f1 100644 --- a/src/SPIN/pair_spin.h +++ b/src/SPIN/pair_spin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/pair_spin_dmi.h b/src/SPIN/pair_spin_dmi.h index 01022623ec..0d73a77dd5 100644 --- a/src/SPIN/pair_spin_dmi.h +++ b/src/SPIN/pair_spin_dmi.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/pair_spin_exchange.h b/src/SPIN/pair_spin_exchange.h index 2a31f9516e..d8e79b8775 100644 --- a/src/SPIN/pair_spin_exchange.h +++ b/src/SPIN/pair_spin_exchange.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/pair_spin_exchange_biquadratic.cpp b/src/SPIN/pair_spin_exchange_biquadratic.cpp index a00d1cc8b0..6d171cef16 100644 --- a/src/SPIN/pair_spin_exchange_biquadratic.cpp +++ b/src/SPIN/pair_spin_exchange_biquadratic.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/pair_spin_exchange_biquadratic.h b/src/SPIN/pair_spin_exchange_biquadratic.h index 9619416f2e..a4104edce3 100644 --- a/src/SPIN/pair_spin_exchange_biquadratic.h +++ b/src/SPIN/pair_spin_exchange_biquadratic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/pair_spin_magelec.h b/src/SPIN/pair_spin_magelec.h index 4df0078bea..1c3cf00b22 100644 --- a/src/SPIN/pair_spin_magelec.h +++ b/src/SPIN/pair_spin_magelec.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SPIN/pair_spin_neel.h b/src/SPIN/pair_spin_neel.h index a39cf839c9..03712b3ca3 100644 --- a/src/SPIN/pair_spin_neel.h +++ b/src/SPIN/pair_spin_neel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SRD/fix_srd.h b/src/SRD/fix_srd.h index b86b3d9f9b..923228f808 100644 --- a/src/SRD/fix_srd.h +++ b/src/SRD/fix_srd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/SRD/fix_wall_srd.h b/src/SRD/fix_wall_srd.h index b0f1560771..11ab8cc0bc 100644 --- a/src/SRD/fix_wall_srd.h +++ b/src/SRD/fix_wall_srd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/STUBS/mpi.h b/src/STUBS/mpi.h index 28e897960d..c4d8848f57 100644 --- a/src/STUBS/mpi.h +++ b/src/STUBS/mpi.h @@ -1,4 +1,4 @@ -/* ----------------------------------------------------------------------- +/* -*- c++ -*- ----------------------------------------------------------- LAMMPS 2003 (July 31) - Molecular Dynamics Simulator Sandia National Laboratories, www.cs.sandia.gov/~sjplimp/lammps.html Steve Plimpton, sjplimp@sandia.gov diff --git a/src/USER-ADIOS/dump_atom_adios.h b/src/USER-ADIOS/dump_atom_adios.h index dc6bc519bb..40ef386dc6 100644 --- a/src/USER-ADIOS/dump_atom_adios.h +++ b/src/USER-ADIOS/dump_atom_adios.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-ADIOS/dump_custom_adios.h b/src/USER-ADIOS/dump_custom_adios.h index d5d41eb8c7..6a2a2b84b2 100644 --- a/src/USER-ADIOS/dump_custom_adios.h +++ b/src/USER-ADIOS/dump_custom_adios.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-ADIOS/reader_adios.h b/src/USER-ADIOS/reader_adios.h index e9c59c502f..999375f2f5 100644 --- a/src/USER-ADIOS/reader_adios.h +++ b/src/USER-ADIOS/reader_adios.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-AWPMD/atom_vec_wavepacket.h b/src/USER-AWPMD/atom_vec_wavepacket.h index 123414eeb7..479bb267e4 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.h +++ b/src/USER-AWPMD/atom_vec_wavepacket.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-AWPMD/fix_nve_awpmd.h b/src/USER-AWPMD/fix_nve_awpmd.h index 832f5821a3..b3edfeb4e6 100644 --- a/src/USER-AWPMD/fix_nve_awpmd.h +++ b/src/USER-AWPMD/fix_nve_awpmd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-AWPMD/pair_awpmd_cut.h b/src/USER-AWPMD/pair_awpmd_cut.h index fb8b9c65dc..46f43c09cf 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.h +++ b/src/USER-AWPMD/pair_awpmd_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-BOCS/compute_pressure_bocs.h b/src/USER-BOCS/compute_pressure_bocs.h index 6592d5b35e..eccc43bf48 100644 --- a/src/USER-BOCS/compute_pressure_bocs.h +++ b/src/USER-BOCS/compute_pressure_bocs.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-BOCS/fix_bocs.h b/src/USER-BOCS/fix_bocs.h index a1a9f58d2b..da5eaac6d6 100644 --- a/src/USER-BOCS/fix_bocs.h +++ b/src/USER-BOCS/fix_bocs.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/bond_oxdna2_fene.h b/src/USER-CGDNA/bond_oxdna2_fene.h index 4bcce337ed..474692de67 100644 --- a/src/USER-CGDNA/bond_oxdna2_fene.h +++ b/src/USER-CGDNA/bond_oxdna2_fene.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/bond_oxdna_fene.h b/src/USER-CGDNA/bond_oxdna_fene.h index 0c702d719a..012aa35b0c 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.h +++ b/src/USER-CGDNA/bond_oxdna_fene.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/bond_oxrna2_fene.h b/src/USER-CGDNA/bond_oxrna2_fene.h index 585a253eb5..898202700c 100644 --- a/src/USER-CGDNA/bond_oxrna2_fene.h +++ b/src/USER-CGDNA/bond_oxrna2_fene.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/fix_nve_dot.h b/src/USER-CGDNA/fix_nve_dot.h index 2c2ff3be63..e87d856dda 100644 --- a/src/USER-CGDNA/fix_nve_dot.h +++ b/src/USER-CGDNA/fix_nve_dot.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.h b/src/USER-CGDNA/fix_nve_dotc_langevin.h index 7f011c0ff5..b2fe7d2eb0 100644 --- a/src/USER-CGDNA/fix_nve_dotc_langevin.h +++ b/src/USER-CGDNA/fix_nve_dotc_langevin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/mf_oxdna.h b/src/USER-CGDNA/mf_oxdna.h index 3c4e714f6b..05bf5eae8f 100644 --- a/src/USER-CGDNA/mf_oxdna.h +++ b/src/USER-CGDNA/mf_oxdna.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.h b/src/USER-CGDNA/pair_oxdna2_coaxstk.h index e20d1b3fdc..b397a8a60d 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.h +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/pair_oxdna2_dh.h b/src/USER-CGDNA/pair_oxdna2_dh.h index da72060927..6b6dbd6e50 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.h +++ b/src/USER-CGDNA/pair_oxdna2_dh.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/pair_oxdna2_excv.h b/src/USER-CGDNA/pair_oxdna2_excv.h index d61317009b..1faaca89ff 100644 --- a/src/USER-CGDNA/pair_oxdna2_excv.h +++ b/src/USER-CGDNA/pair_oxdna2_excv.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.h b/src/USER-CGDNA/pair_oxdna_coaxstk.h index 79c8fa24ed..c4095a2c21 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.h +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/pair_oxdna_excv.h b/src/USER-CGDNA/pair_oxdna_excv.h index 34fd323ec1..c9e51df46e 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.h +++ b/src/USER-CGDNA/pair_oxdna_excv.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/pair_oxdna_hbond.h b/src/USER-CGDNA/pair_oxdna_hbond.h index fe451480a8..0a0d99c998 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.h +++ b/src/USER-CGDNA/pair_oxdna_hbond.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/pair_oxdna_stk.h b/src/USER-CGDNA/pair_oxdna_stk.h index 29ed168ca3..f4ffe62dfa 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.h +++ b/src/USER-CGDNA/pair_oxdna_stk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/pair_oxdna_xstk.h b/src/USER-CGDNA/pair_oxdna_xstk.h index d2fc7fde89..5811ca3a76 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.h +++ b/src/USER-CGDNA/pair_oxdna_xstk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/pair_oxrna2_dh.h b/src/USER-CGDNA/pair_oxrna2_dh.h index 8ff4010113..a9f0640085 100644 --- a/src/USER-CGDNA/pair_oxrna2_dh.h +++ b/src/USER-CGDNA/pair_oxrna2_dh.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/pair_oxrna2_excv.h b/src/USER-CGDNA/pair_oxrna2_excv.h index 2dfb356203..e496db881e 100644 --- a/src/USER-CGDNA/pair_oxrna2_excv.h +++ b/src/USER-CGDNA/pair_oxrna2_excv.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.h b/src/USER-CGDNA/pair_oxrna2_hbond.h index 3386cc23ec..1122949110 100644 --- a/src/USER-CGDNA/pair_oxrna2_hbond.h +++ b/src/USER-CGDNA/pair_oxrna2_hbond.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/pair_oxrna2_stk.h b/src/USER-CGDNA/pair_oxrna2_stk.h index 519f7c0707..96ea2752ed 100644 --- a/src/USER-CGDNA/pair_oxrna2_stk.h +++ b/src/USER-CGDNA/pair_oxrna2_stk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.h b/src/USER-CGDNA/pair_oxrna2_xstk.h index 97e878c342..7b07f3fad4 100644 --- a/src/USER-CGDNA/pair_oxrna2_xstk.h +++ b/src/USER-CGDNA/pair_oxrna2_xstk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGSDK/angle_sdk.h b/src/USER-CGSDK/angle_sdk.h index 2e94b44470..8ff252f359 100644 --- a/src/USER-CGSDK/angle_sdk.h +++ b/src/USER-CGSDK/angle_sdk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGSDK/lj_sdk_common.h b/src/USER-CGSDK/lj_sdk_common.h index 51dcb4c2b7..d09fd9f439 100644 --- a/src/USER-CGSDK/lj_sdk_common.h +++ b/src/USER-CGSDK/lj_sdk_common.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGSDK/pair_lj_sdk.h b/src/USER-CGSDK/pair_lj_sdk.h index 11c123a72c..2d825d9a05 100644 --- a/src/USER-CGSDK/pair_lj_sdk.h +++ b/src/USER-CGSDK/pair_lj_sdk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.h b/src/USER-CGSDK/pair_lj_sdk_coul_long.h index 57779cc0b9..d505b4e161 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_long.h +++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.h b/src/USER-CGSDK/pair_lj_sdk_coul_msm.h index 8438ced66b..dc15b07820 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_msm.h +++ b/src/USER-CGSDK/pair_lj_sdk_coul_msm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-COLVARS/fix_colvars.h b/src/USER-COLVARS/fix_colvars.h index fff61ce218..21f7ca7d98 100644 --- a/src/USER-COLVARS/fix_colvars.h +++ b/src/USER-COLVARS/fix_colvars.h @@ -9,7 +9,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-COLVARS/group_ndx.h b/src/USER-COLVARS/group_ndx.h index 58b210937a..ec578a5b61 100644 --- a/src/USER-COLVARS/group_ndx.h +++ b/src/USER-COLVARS/group_ndx.h @@ -2,7 +2,7 @@ /* ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-COLVARS/ndx_group.h b/src/USER-COLVARS/ndx_group.h index 91b2e471ba..753d09ce82 100644 --- a/src/USER-COLVARS/ndx_group.h +++ b/src/USER-COLVARS/ndx_group.h @@ -2,7 +2,7 @@ /* ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DIFFRACTION/compute_saed.h b/src/USER-DIFFRACTION/compute_saed.h index 87785c4936..dc4268eee7 100644 --- a/src/USER-DIFFRACTION/compute_saed.h +++ b/src/USER-DIFFRACTION/compute_saed.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DIFFRACTION/compute_saed_consts.h b/src/USER-DIFFRACTION/compute_saed_consts.h index 0c07ae13ad..63743d0d9a 100644 --- a/src/USER-DIFFRACTION/compute_saed_consts.h +++ b/src/USER-DIFFRACTION/compute_saed_consts.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DIFFRACTION/compute_xrd.h b/src/USER-DIFFRACTION/compute_xrd.h index 61e1dae1bd..b0beca201c 100644 --- a/src/USER-DIFFRACTION/compute_xrd.h +++ b/src/USER-DIFFRACTION/compute_xrd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DIFFRACTION/compute_xrd_consts.h b/src/USER-DIFFRACTION/compute_xrd_consts.h index aeaddf7daa..945f0c51b7 100644 --- a/src/USER-DIFFRACTION/compute_xrd_consts.h +++ b/src/USER-DIFFRACTION/compute_xrd_consts.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.h b/src/USER-DIFFRACTION/fix_saed_vtk.h index 1f70bfd164..83c7161275 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.h +++ b/src/USER-DIFFRACTION/fix_saed_vtk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/atom_vec_dpd.h b/src/USER-DPD/atom_vec_dpd.h index 61abc658b8..ea3fb6abf0 100644 --- a/src/USER-DPD/atom_vec_dpd.h +++ b/src/USER-DPD/atom_vec_dpd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/compute_dpd.h b/src/USER-DPD/compute_dpd.h index 695048eef3..a77e19bee8 100644 --- a/src/USER-DPD/compute_dpd.h +++ b/src/USER-DPD/compute_dpd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/compute_dpd_atom.h b/src/USER-DPD/compute_dpd_atom.h index c77490be76..cbc913d628 100644 --- a/src/USER-DPD/compute_dpd_atom.h +++ b/src/USER-DPD/compute_dpd_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/fix_dpd_energy.h b/src/USER-DPD/fix_dpd_energy.h index 89ba84c08b..c7160596bf 100644 --- a/src/USER-DPD/fix_dpd_energy.h +++ b/src/USER-DPD/fix_dpd_energy.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/fix_eos_cv.h b/src/USER-DPD/fix_eos_cv.h index 8ae34dc6a9..1ca7fbad56 100644 --- a/src/USER-DPD/fix_eos_cv.h +++ b/src/USER-DPD/fix_eos_cv.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/fix_eos_table.h b/src/USER-DPD/fix_eos_table.h index 050e62d74b..4913250f90 100644 --- a/src/USER-DPD/fix_eos_table.h +++ b/src/USER-DPD/fix_eos_table.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/fix_eos_table_rx.h b/src/USER-DPD/fix_eos_table_rx.h index 9de7c5fbc7..07adb1ec41 100644 --- a/src/USER-DPD/fix_eos_table_rx.h +++ b/src/USER-DPD/fix_eos_table_rx.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/fix_rx.h b/src/USER-DPD/fix_rx.h index e2f9f5b88b..6113469274 100644 --- a/src/USER-DPD/fix_rx.h +++ b/src/USER-DPD/fix_rx.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/fix_shardlow.h b/src/USER-DPD/fix_shardlow.h index 67e4b8f32e..8762b67a23 100644 --- a/src/USER-DPD/fix_shardlow.h +++ b/src/USER-DPD/fix_shardlow.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/nbin_ssa.h b/src/USER-DPD/nbin_ssa.h index eb4b2db24c..41d94bf672 100644 --- a/src/USER-DPD/nbin_ssa.h +++ b/src/USER-DPD/nbin_ssa.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.h b/src/USER-DPD/npair_half_bin_newton_ssa.h index 584d87e3ad..7ed3574c4f 100644 --- a/src/USER-DPD/npair_half_bin_newton_ssa.h +++ b/src/USER-DPD/npair_half_bin_newton_ssa.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h b/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h index 1d5cc3f6b2..db6c687bfb 100644 --- a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h +++ b/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h b/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h index 450a696e46..e351faea80 100644 --- a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h +++ b/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/nstencil_ssa.h b/src/USER-DPD/nstencil_ssa.h index f6f91fefde..2e0de390f2 100644 --- a/src/USER-DPD/nstencil_ssa.h +++ b/src/USER-DPD/nstencil_ssa.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/pair_dpd_fdt.h b/src/USER-DPD/pair_dpd_fdt.h index 84b09b0fa2..768b264a40 100644 --- a/src/USER-DPD/pair_dpd_fdt.h +++ b/src/USER-DPD/pair_dpd_fdt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/pair_dpd_fdt_energy.h b/src/USER-DPD/pair_dpd_fdt_energy.h index e21b48f7bd..5692b5a836 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.h +++ b/src/USER-DPD/pair_dpd_fdt_energy.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/pair_exp6_rx.h b/src/USER-DPD/pair_exp6_rx.h index 45c046cc07..d306ac62c8 100644 --- a/src/USER-DPD/pair_exp6_rx.h +++ b/src/USER-DPD/pair_exp6_rx.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/pair_multi_lucy.h b/src/USER-DPD/pair_multi_lucy.h index 0a2d2f9885..e1440a12f2 100644 --- a/src/USER-DPD/pair_multi_lucy.h +++ b/src/USER-DPD/pair_multi_lucy.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/pair_multi_lucy_rx.h b/src/USER-DPD/pair_multi_lucy_rx.h index 2bfa5d20e3..005144173e 100644 --- a/src/USER-DPD/pair_multi_lucy_rx.h +++ b/src/USER-DPD/pair_multi_lucy_rx.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/pair_table_rx.h b/src/USER-DPD/pair_table_rx.h index da7889e99a..ac97b8af1e 100644 --- a/src/USER-DPD/pair_table_rx.h +++ b/src/USER-DPD/pair_table_rx.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DPD/random_external_state.h b/src/USER-DPD/random_external_state.h index e7d11a5926..037a5ee8b0 100644 --- a/src/USER-DPD/random_external_state.h +++ b/src/USER-DPD/random_external_state.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DRUDE/compute_temp_drude.h b/src/USER-DRUDE/compute_temp_drude.h index 530c84ce3d..b1ef758e23 100644 --- a/src/USER-DRUDE/compute_temp_drude.h +++ b/src/USER-DRUDE/compute_temp_drude.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DRUDE/fix_drude.h b/src/USER-DRUDE/fix_drude.h index 6775dcee6f..332ca837a9 100644 --- a/src/USER-DRUDE/fix_drude.h +++ b/src/USER-DRUDE/fix_drude.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DRUDE/fix_drude_transform.h b/src/USER-DRUDE/fix_drude_transform.h index b74a500c95..1b8e5fa46a 100644 --- a/src/USER-DRUDE/fix_drude_transform.h +++ b/src/USER-DRUDE/fix_drude_transform.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DRUDE/fix_langevin_drude.h b/src/USER-DRUDE/fix_langevin_drude.h index 9437883ba3..08e0ecd1a6 100644 --- a/src/USER-DRUDE/fix_langevin_drude.h +++ b/src/USER-DRUDE/fix_langevin_drude.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DRUDE/fix_tgnh_drude.h b/src/USER-DRUDE/fix_tgnh_drude.h index 4d29bb90e7..2063f0a97e 100644 --- a/src/USER-DRUDE/fix_tgnh_drude.h +++ b/src/USER-DRUDE/fix_tgnh_drude.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DRUDE/fix_tgnpt_drude.h b/src/USER-DRUDE/fix_tgnpt_drude.h index afb55ae0d7..f1cbb68f5a 100644 --- a/src/USER-DRUDE/fix_tgnpt_drude.h +++ b/src/USER-DRUDE/fix_tgnpt_drude.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DRUDE/fix_tgnvt_drude.h b/src/USER-DRUDE/fix_tgnvt_drude.h index 64f2e52e9c..eb73e8c918 100644 --- a/src/USER-DRUDE/fix_tgnvt_drude.h +++ b/src/USER-DRUDE/fix_tgnvt_drude.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DRUDE/pair_coul_tt.h b/src/USER-DRUDE/pair_coul_tt.h index f1c250f8b4..23ef827968 100644 --- a/src/USER-DRUDE/pair_coul_tt.h +++ b/src/USER-DRUDE/pair_coul_tt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.h b/src/USER-DRUDE/pair_lj_cut_thole_long.h index 8dbfe0240c..cd01db6f72 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.h +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-DRUDE/pair_thole.h b/src/USER-DRUDE/pair_thole.h index 88c00b6d20..ff93797f5e 100644 --- a/src/USER-DRUDE/pair_thole.h +++ b/src/USER-DRUDE/pair_thole.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/atom_vec_electron.h b/src/USER-EFF/atom_vec_electron.h index 9175ca52f7..3cdd218f55 100644 --- a/src/USER-EFF/atom_vec_electron.h +++ b/src/USER-EFF/atom_vec_electron.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/compute_ke_atom_eff.h b/src/USER-EFF/compute_ke_atom_eff.h index e5ef5e58d0..c1ea0ac8ce 100644 --- a/src/USER-EFF/compute_ke_atom_eff.h +++ b/src/USER-EFF/compute_ke_atom_eff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/compute_ke_eff.h b/src/USER-EFF/compute_ke_eff.h index c4752066bd..854c60f110 100644 --- a/src/USER-EFF/compute_ke_eff.h +++ b/src/USER-EFF/compute_ke_eff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/compute_temp_deform_eff.h b/src/USER-EFF/compute_temp_deform_eff.h index ef531d024b..880c436916 100644 --- a/src/USER-EFF/compute_temp_deform_eff.h +++ b/src/USER-EFF/compute_temp_deform_eff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/compute_temp_eff.h b/src/USER-EFF/compute_temp_eff.h index cb5af36ec1..d66b65e3a2 100644 --- a/src/USER-EFF/compute_temp_eff.h +++ b/src/USER-EFF/compute_temp_eff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/compute_temp_region_eff.h b/src/USER-EFF/compute_temp_region_eff.h index 682a415a42..064e0ae6de 100644 --- a/src/USER-EFF/compute_temp_region_eff.h +++ b/src/USER-EFF/compute_temp_region_eff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/fix_langevin_eff.h b/src/USER-EFF/fix_langevin_eff.h index 1ef9731395..3ba75b4fe0 100644 --- a/src/USER-EFF/fix_langevin_eff.h +++ b/src/USER-EFF/fix_langevin_eff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/fix_nh_eff.h b/src/USER-EFF/fix_nh_eff.h index 408286396e..b98a4fa481 100644 --- a/src/USER-EFF/fix_nh_eff.h +++ b/src/USER-EFF/fix_nh_eff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/fix_nph_eff.h b/src/USER-EFF/fix_nph_eff.h index 8178b121c3..04c28b0f66 100644 --- a/src/USER-EFF/fix_nph_eff.h +++ b/src/USER-EFF/fix_nph_eff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/fix_npt_eff.h b/src/USER-EFF/fix_npt_eff.h index 5dfb09ae92..e726a84668 100644 --- a/src/USER-EFF/fix_npt_eff.h +++ b/src/USER-EFF/fix_npt_eff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/fix_nve_eff.h b/src/USER-EFF/fix_nve_eff.h index b33546ce46..b8a31fb5e4 100644 --- a/src/USER-EFF/fix_nve_eff.h +++ b/src/USER-EFF/fix_nve_eff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/fix_nvt_eff.h b/src/USER-EFF/fix_nvt_eff.h index cff474f5ed..a333de126e 100644 --- a/src/USER-EFF/fix_nvt_eff.h +++ b/src/USER-EFF/fix_nvt_eff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/fix_nvt_sllod_eff.h b/src/USER-EFF/fix_nvt_sllod_eff.h index ef52541237..e1b6384c2d 100644 --- a/src/USER-EFF/fix_nvt_sllod_eff.h +++ b/src/USER-EFF/fix_nvt_sllod_eff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/fix_temp_rescale_eff.h b/src/USER-EFF/fix_temp_rescale_eff.h index f670a98808..c57230359b 100644 --- a/src/USER-EFF/fix_temp_rescale_eff.h +++ b/src/USER-EFF/fix_temp_rescale_eff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/pair_eff_cut.h b/src/USER-EFF/pair_eff_cut.h index bd04344373..0b3e4b3c13 100644 --- a/src/USER-EFF/pair_eff_cut.h +++ b/src/USER-EFF/pair_eff_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-EFF/pair_eff_inline.h b/src/USER-EFF/pair_eff_inline.h index f30a122265..4971b3d6ce 100644 --- a/src/USER-EFF/pair_eff_inline.h +++ b/src/USER-EFF/pair_eff_inline.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-FEP/compute_fep.h b/src/USER-FEP/compute_fep.h index 4a154b4685..947634f5a7 100644 --- a/src/USER-FEP/compute_fep.h +++ b/src/USER-FEP/compute_fep.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-FEP/fix_adapt_fep.h b/src/USER-FEP/fix_adapt_fep.h index cee19752e4..4846c6b7b9 100644 --- a/src/USER-FEP/fix_adapt_fep.h +++ b/src/USER-FEP/fix_adapt_fep.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-FEP/pair_coul_cut_soft.h b/src/USER-FEP/pair_coul_cut_soft.h index 2e9e1ac8d2..8aa6e2232e 100644 --- a/src/USER-FEP/pair_coul_cut_soft.h +++ b/src/USER-FEP/pair_coul_cut_soft.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-FEP/pair_coul_long_soft.h b/src/USER-FEP/pair_coul_long_soft.h index 013a94a2f4..7acbaaaffc 100644 --- a/src/USER-FEP/pair_coul_long_soft.h +++ b/src/USER-FEP/pair_coul_long_soft.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.h b/src/USER-FEP/pair_lj_charmm_coul_long_soft.h index 252c9f66f5..1061010bb9 100644 --- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.h +++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.h b/src/USER-FEP/pair_lj_class2_coul_cut_soft.h index d4d8c264b5..f35dd00a26 100644 --- a/src/USER-FEP/pair_lj_class2_coul_cut_soft.h +++ b/src/USER-FEP/pair_lj_class2_coul_cut_soft.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.h b/src/USER-FEP/pair_lj_class2_coul_long_soft.h index c334ef19df..2a38c1db7b 100644 --- a/src/USER-FEP/pair_lj_class2_coul_long_soft.h +++ b/src/USER-FEP/pair_lj_class2_coul_long_soft.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-FEP/pair_lj_class2_soft.h b/src/USER-FEP/pair_lj_class2_soft.h index ef031a1911..f107ae1fbc 100644 --- a/src/USER-FEP/pair_lj_class2_soft.h +++ b/src/USER-FEP/pair_lj_class2_soft.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.h b/src/USER-FEP/pair_lj_cut_coul_cut_soft.h index fa9e0ab71f..1a3f213c04 100644 --- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.h +++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.h b/src/USER-FEP/pair_lj_cut_coul_long_soft.h index d49d1c8641..0abd33b3e5 100644 --- a/src/USER-FEP/pair_lj_cut_coul_long_soft.h +++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-FEP/pair_lj_cut_soft.h b/src/USER-FEP/pair_lj_cut_soft.h index 46202d78a8..8795b4fb16 100644 --- a/src/USER-FEP/pair_lj_cut_soft.h +++ b/src/USER-FEP/pair_lj_cut_soft.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.h b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.h index 74a8ee742e..c95d7e162d 100644 --- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.h +++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-FEP/pair_morse_soft.h b/src/USER-FEP/pair_morse_soft.h index 3a8d5a777f..14cc51a90f 100644 --- a/src/USER-FEP/pair_morse_soft.h +++ b/src/USER-FEP/pair_morse_soft.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-FEP/pair_tip4p_long_soft.h b/src/USER-FEP/pair_tip4p_long_soft.h index ffd79d5f29..406a47a2ea 100644 --- a/src/USER-FEP/pair_tip4p_long_soft.h +++ b/src/USER-FEP/pair_tip4p_long_soft.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-H5MD/dump_h5md.h b/src/USER-H5MD/dump_h5md.h index 496c30441e..967bfed7fa 100644 --- a/src/USER-H5MD/dump_h5md.h +++ b/src/USER-H5MD/dump_h5md.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/angle_charmm_intel.h b/src/USER-INTEL/angle_charmm_intel.h index 798e3d1523..7ee04ba8d9 100644 --- a/src/USER-INTEL/angle_charmm_intel.h +++ b/src/USER-INTEL/angle_charmm_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/angle_harmonic_intel.h b/src/USER-INTEL/angle_harmonic_intel.h index 7df4a98877..5efd663cea 100644 --- a/src/USER-INTEL/angle_harmonic_intel.h +++ b/src/USER-INTEL/angle_harmonic_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/bond_fene_intel.h b/src/USER-INTEL/bond_fene_intel.h index 92ec4097c0..13bcc35e97 100644 --- a/src/USER-INTEL/bond_fene_intel.h +++ b/src/USER-INTEL/bond_fene_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/bond_harmonic_intel.h b/src/USER-INTEL/bond_harmonic_intel.h index 449df3b7a8..234d75bda4 100644 --- a/src/USER-INTEL/bond_harmonic_intel.h +++ b/src/USER-INTEL/bond_harmonic_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/dihedral_charmm_intel.h b/src/USER-INTEL/dihedral_charmm_intel.h index bb830b7292..1cca32468b 100644 --- a/src/USER-INTEL/dihedral_charmm_intel.h +++ b/src/USER-INTEL/dihedral_charmm_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/dihedral_fourier_intel.h b/src/USER-INTEL/dihedral_fourier_intel.h index f91d89f6bc..ce446eec0d 100644 --- a/src/USER-INTEL/dihedral_fourier_intel.h +++ b/src/USER-INTEL/dihedral_fourier_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/dihedral_harmonic_intel.h b/src/USER-INTEL/dihedral_harmonic_intel.h index cdbae365fd..75570f2444 100644 --- a/src/USER-INTEL/dihedral_harmonic_intel.h +++ b/src/USER-INTEL/dihedral_harmonic_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/dihedral_opls_intel.h b/src/USER-INTEL/dihedral_opls_intel.h index 77fd8c4b95..b34777748d 100644 --- a/src/USER-INTEL/dihedral_opls_intel.h +++ b/src/USER-INTEL/dihedral_opls_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h index df3aecbc81..46ebd95b6a 100644 --- a/src/USER-INTEL/fix_intel.h +++ b/src/USER-INTEL/fix_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/fix_nh_intel.h b/src/USER-INTEL/fix_nh_intel.h index cc6ba8c481..a2a53bb616 100644 --- a/src/USER-INTEL/fix_nh_intel.h +++ b/src/USER-INTEL/fix_nh_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/fix_npt_intel.h b/src/USER-INTEL/fix_npt_intel.h index bb0cbaf9e3..f383035050 100644 --- a/src/USER-INTEL/fix_npt_intel.h +++ b/src/USER-INTEL/fix_npt_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/fix_nve_asphere_intel.h b/src/USER-INTEL/fix_nve_asphere_intel.h index 0c9ce2cddd..91e4240369 100644 --- a/src/USER-INTEL/fix_nve_asphere_intel.h +++ b/src/USER-INTEL/fix_nve_asphere_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/fix_nve_intel.h b/src/USER-INTEL/fix_nve_intel.h index 182a12eb9f..1725f4266c 100644 --- a/src/USER-INTEL/fix_nve_intel.h +++ b/src/USER-INTEL/fix_nve_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/fix_nvt_intel.h b/src/USER-INTEL/fix_nvt_intel.h index 7e940191ca..839e561b0f 100644 --- a/src/USER-INTEL/fix_nvt_intel.h +++ b/src/USER-INTEL/fix_nvt_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.h b/src/USER-INTEL/fix_nvt_sllod_intel.h index 81552aa34a..f6cd9638f2 100644 --- a/src/USER-INTEL/fix_nvt_sllod_intel.h +++ b/src/USER-INTEL/fix_nvt_sllod_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/improper_cvff_intel.h b/src/USER-INTEL/improper_cvff_intel.h index 94aa29c55f..cc752e1501 100644 --- a/src/USER-INTEL/improper_cvff_intel.h +++ b/src/USER-INTEL/improper_cvff_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/improper_harmonic_intel.h b/src/USER-INTEL/improper_harmonic_intel.h index ce1da11a33..ccd1543c17 100644 --- a/src/USER-INTEL/improper_harmonic_intel.h +++ b/src/USER-INTEL/improper_harmonic_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/intel_buffers.h b/src/USER-INTEL/intel_buffers.h index 86fc921c9e..eafe3ad845 100644 --- a/src/USER-INTEL/intel_buffers.h +++ b/src/USER-INTEL/intel_buffers.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/intel_intrinsics.h b/src/USER-INTEL/intel_intrinsics.h index d1f019feea..34ba902a67 100644 --- a/src/USER-INTEL/intel_intrinsics.h +++ b/src/USER-INTEL/intel_intrinsics.h @@ -1,6 +1,6 @@ /* *- c++ -*- ----------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/intel_preprocess.h b/src/USER-INTEL/intel_preprocess.h index 3c285871cf..2e7101b42d 100644 --- a/src/USER-INTEL/intel_preprocess.h +++ b/src/USER-INTEL/intel_preprocess.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/intel_simd.h b/src/USER-INTEL/intel_simd.h index 9022f439c4..01fa1c0a45 100644 --- a/src/USER-INTEL/intel_simd.h +++ b/src/USER-INTEL/intel_simd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/math_extra_intel.h b/src/USER-INTEL/math_extra_intel.h index 547fadb6e9..679ca635e1 100644 --- a/src/USER-INTEL/math_extra_intel.h +++ b/src/USER-INTEL/math_extra_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/nbin_intel.h b/src/USER-INTEL/nbin_intel.h index a7a28010ba..2aa4013dd9 100644 --- a/src/USER-INTEL/nbin_intel.h +++ b/src/USER-INTEL/nbin_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.h b/src/USER-INTEL/npair_full_bin_ghost_intel.h index 94e6fc3928..a352f89f75 100644 --- a/src/USER-INTEL/npair_full_bin_ghost_intel.h +++ b/src/USER-INTEL/npair_full_bin_ghost_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/npair_full_bin_intel.h b/src/USER-INTEL/npair_full_bin_intel.h index 0f8a27b3b4..e5d8e0751e 100644 --- a/src/USER-INTEL/npair_full_bin_intel.h +++ b/src/USER-INTEL/npair_full_bin_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/npair_half_bin_newton_intel.h b/src/USER-INTEL/npair_half_bin_newton_intel.h index 54a8e24135..17a1785a94 100644 --- a/src/USER-INTEL/npair_half_bin_newton_intel.h +++ b/src/USER-INTEL/npair_half_bin_newton_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/npair_half_bin_newton_tri_intel.h b/src/USER-INTEL/npair_half_bin_newton_tri_intel.h index 7a7f4c8030..3e2ae2f25d 100644 --- a/src/USER-INTEL/npair_half_bin_newton_tri_intel.h +++ b/src/USER-INTEL/npair_half_bin_newton_tri_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/npair_halffull_newtoff_intel.h b/src/USER-INTEL/npair_halffull_newtoff_intel.h index c4c41a85a1..b606343cb5 100644 --- a/src/USER-INTEL/npair_halffull_newtoff_intel.h +++ b/src/USER-INTEL/npair_halffull_newtoff_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/npair_halffull_newton_intel.h b/src/USER-INTEL/npair_halffull_newton_intel.h index b3069d8074..5f727ac692 100644 --- a/src/USER-INTEL/npair_halffull_newton_intel.h +++ b/src/USER-INTEL/npair_halffull_newton_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/npair_intel.h b/src/USER-INTEL/npair_intel.h index e040a1d8f3..191c5385f5 100644 --- a/src/USER-INTEL/npair_intel.h +++ b/src/USER-INTEL/npair_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/npair_skip_intel.h b/src/USER-INTEL/npair_skip_intel.h index 6bb3dfa5d0..0e9494f941 100644 --- a/src/USER-INTEL/npair_skip_intel.h +++ b/src/USER-INTEL/npair_skip_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_airebo_intel.h b/src/USER-INTEL/pair_airebo_intel.h index 675fda8fe3..de90177939 100644 --- a/src/USER-INTEL/pair_airebo_intel.h +++ b/src/USER-INTEL/pair_airebo_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_airebo_morse_intel.h b/src/USER-INTEL/pair_airebo_morse_intel.h index 5210ea80ee..4a97fce38b 100644 --- a/src/USER-INTEL/pair_airebo_morse_intel.h +++ b/src/USER-INTEL/pair_airebo_morse_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.h b/src/USER-INTEL/pair_buck_coul_cut_intel.h index 4bc19ac157..020f8afff7 100644 --- a/src/USER-INTEL/pair_buck_coul_cut_intel.h +++ b/src/USER-INTEL/pair_buck_coul_cut_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.h b/src/USER-INTEL/pair_buck_coul_long_intel.h index 95492cd4e6..f05ebadeef 100644 --- a/src/USER-INTEL/pair_buck_coul_long_intel.h +++ b/src/USER-INTEL/pair_buck_coul_long_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_buck_intel.h b/src/USER-INTEL/pair_buck_intel.h index 0e473c7c3f..89702dd754 100644 --- a/src/USER-INTEL/pair_buck_intel.h +++ b/src/USER-INTEL/pair_buck_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_dpd_intel.h b/src/USER-INTEL/pair_dpd_intel.h index 409e123f29..94ef795ba5 100644 --- a/src/USER-INTEL/pair_dpd_intel.h +++ b/src/USER-INTEL/pair_dpd_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_eam_alloy_intel.h b/src/USER-INTEL/pair_eam_alloy_intel.h index 4967c3709d..82ba0c9f89 100644 --- a/src/USER-INTEL/pair_eam_alloy_intel.h +++ b/src/USER-INTEL/pair_eam_alloy_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_eam_fs_intel.h b/src/USER-INTEL/pair_eam_fs_intel.h index da2ab9d2d7..3614c5640e 100644 --- a/src/USER-INTEL/pair_eam_fs_intel.h +++ b/src/USER-INTEL/pair_eam_fs_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_eam_intel.h b/src/USER-INTEL/pair_eam_intel.h index b9ad11597a..a24b5e15dc 100644 --- a/src/USER-INTEL/pair_eam_intel.h +++ b/src/USER-INTEL/pair_eam_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_gayberne_intel.h b/src/USER-INTEL/pair_gayberne_intel.h index ecdd93d353..0374da4cb3 100644 --- a/src/USER-INTEL/pair_gayberne_intel.h +++ b/src/USER-INTEL/pair_gayberne_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.h b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.h index 006dbaade2..5bb6912363 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.h +++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.h b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.h index f5b46eaf76..fe743a9841 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.h +++ b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.h b/src/USER-INTEL/pair_lj_cut_coul_long_intel.h index 6172313639..5c3a4f38e2 100644 --- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.h +++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_lj_cut_intel.h b/src/USER-INTEL/pair_lj_cut_intel.h index b88d213211..710e4e39a0 100644 --- a/src/USER-INTEL/pair_lj_cut_intel.h +++ b/src/USER-INTEL/pair_lj_cut_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_lj_long_coul_long_intel.h b/src/USER-INTEL/pair_lj_long_coul_long_intel.h index b7d3504ecd..19adeda55e 100644 --- a/src/USER-INTEL/pair_lj_long_coul_long_intel.h +++ b/src/USER-INTEL/pair_lj_long_coul_long_intel.h @@ -1,6 +1,6 @@ /* *- c++ -*- ----------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_rebo_intel.h b/src/USER-INTEL/pair_rebo_intel.h index e76279a248..d4beebbaa7 100644 --- a/src/USER-INTEL/pair_rebo_intel.h +++ b/src/USER-INTEL/pair_rebo_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_sw_intel.h b/src/USER-INTEL/pair_sw_intel.h index f345b3d4ff..e8dfb00343 100644 --- a/src/USER-INTEL/pair_sw_intel.h +++ b/src/USER-INTEL/pair_sw_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pair_tersoff_intel.h b/src/USER-INTEL/pair_tersoff_intel.h index 195efa74de..48e1376110 100644 --- a/src/USER-INTEL/pair_tersoff_intel.h +++ b/src/USER-INTEL/pair_tersoff_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pppm_disp_intel.h b/src/USER-INTEL/pppm_disp_intel.h index 89f580aa08..0191bbcb81 100644 --- a/src/USER-INTEL/pppm_disp_intel.h +++ b/src/USER-INTEL/pppm_disp_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/pppm_intel.h b/src/USER-INTEL/pppm_intel.h index 0084301133..8dce1532ae 100644 --- a/src/USER-INTEL/pppm_intel.h +++ b/src/USER-INTEL/pppm_intel.h @@ -1,6 +1,6 @@ /* *- c++ -*- ----------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-INTEL/verlet_lrt_intel.h b/src/USER-INTEL/verlet_lrt_intel.h index 6c44ba7e57..02b24cae3f 100644 --- a/src/USER-INTEL/verlet_lrt_intel.h +++ b/src/USER-INTEL/verlet_lrt_intel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-LB/fix_lb_momentum.h b/src/USER-LB/fix_lb_momentum.h index 51c9f6f4a4..3f4fee5009 100644 --- a/src/USER-LB/fix_lb_momentum.h +++ b/src/USER-LB/fix_lb_momentum.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-LB/fix_lb_pc.h b/src/USER-LB/fix_lb_pc.h index 7d0be65e60..e088fab38f 100644 --- a/src/USER-LB/fix_lb_pc.h +++ b/src/USER-LB/fix_lb_pc.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.h b/src/USER-LB/fix_lb_rigid_pc_sphere.h index be7e9ee253..946889e1db 100644 --- a/src/USER-LB/fix_lb_rigid_pc_sphere.h +++ b/src/USER-LB/fix_lb_rigid_pc_sphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-LB/fix_lb_viscous.h b/src/USER-LB/fix_lb_viscous.h index 51cecc293b..2f4206fc31 100644 --- a/src/USER-LB/fix_lb_viscous.h +++ b/src/USER-LB/fix_lb_viscous.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MANIFOLD/fix_manifoldforce.h b/src/USER-MANIFOLD/fix_manifoldforce.h index 64a5011780..57dd2643d0 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.h +++ b/src/USER-MANIFOLD/fix_manifoldforce.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h index 9ec2b3c78c..587dd94896 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h index 69e4eb13e1..1d44192be9 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h +++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MANIFOLD/manifold.h b/src/USER-MANIFOLD/manifold.h index be9f2c9f65..c91647583f 100644 --- a/src/USER-MANIFOLD/manifold.h +++ b/src/USER-MANIFOLD/manifold.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MANIFOLD/manifold_factory.h b/src/USER-MANIFOLD/manifold_factory.h index c6533855ad..400929cef0 100644 --- a/src/USER-MANIFOLD/manifold_factory.h +++ b/src/USER-MANIFOLD/manifold_factory.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.h b/src/USER-MANIFOLD/manifold_gaussian_bump.h index d65979416b..30926f9815 100644 --- a/src/USER-MANIFOLD/manifold_gaussian_bump.h +++ b/src/USER-MANIFOLD/manifold_gaussian_bump.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h index e44e044d6e..f9440d9cbf 100644 --- a/src/USER-MEAMC/meam.h +++ b/src/USER-MEAMC/meam.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h index 24625c4076..de07d813b4 100644 --- a/src/USER-MEAMC/pair_meamc.h +++ b/src/USER-MEAMC/pair_meamc.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESODPD/atom_vec_edpd.h b/src/USER-MESODPD/atom_vec_edpd.h index a69c44a035..f44e16bc7b 100644 --- a/src/USER-MESODPD/atom_vec_edpd.h +++ b/src/USER-MESODPD/atom_vec_edpd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESODPD/atom_vec_mdpd.h b/src/USER-MESODPD/atom_vec_mdpd.h index 55f5e9bb2d..cac8437fa8 100644 --- a/src/USER-MESODPD/atom_vec_mdpd.h +++ b/src/USER-MESODPD/atom_vec_mdpd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESODPD/atom_vec_tdpd.h b/src/USER-MESODPD/atom_vec_tdpd.h index 971696cc5c..678e7ac62e 100644 --- a/src/USER-MESODPD/atom_vec_tdpd.h +++ b/src/USER-MESODPD/atom_vec_tdpd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESODPD/compute_edpd_temp_atom.h b/src/USER-MESODPD/compute_edpd_temp_atom.h index 4c61b664cc..e0899d4759 100644 --- a/src/USER-MESODPD/compute_edpd_temp_atom.h +++ b/src/USER-MESODPD/compute_edpd_temp_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESODPD/compute_tdpd_cc_atom.h b/src/USER-MESODPD/compute_tdpd_cc_atom.h index 324cb779a4..fe6278a16f 100644 --- a/src/USER-MESODPD/compute_tdpd_cc_atom.h +++ b/src/USER-MESODPD/compute_tdpd_cc_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESODPD/fix_edpd_source.h b/src/USER-MESODPD/fix_edpd_source.h index 1ea8610ce9..048fd55517 100644 --- a/src/USER-MESODPD/fix_edpd_source.h +++ b/src/USER-MESODPD/fix_edpd_source.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESODPD/fix_mvv_dpd.h b/src/USER-MESODPD/fix_mvv_dpd.h index 86cc79485f..ffaba67f92 100644 --- a/src/USER-MESODPD/fix_mvv_dpd.h +++ b/src/USER-MESODPD/fix_mvv_dpd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESODPD/fix_mvv_edpd.h b/src/USER-MESODPD/fix_mvv_edpd.h index 0d9c5f195a..d779780eee 100644 --- a/src/USER-MESODPD/fix_mvv_edpd.h +++ b/src/USER-MESODPD/fix_mvv_edpd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESODPD/fix_mvv_tdpd.h b/src/USER-MESODPD/fix_mvv_tdpd.h index 7adb23af69..37e725b68f 100644 --- a/src/USER-MESODPD/fix_mvv_tdpd.h +++ b/src/USER-MESODPD/fix_mvv_tdpd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESODPD/fix_tdpd_source.h b/src/USER-MESODPD/fix_tdpd_source.h index 302fe82090..451fa62e52 100644 --- a/src/USER-MESODPD/fix_tdpd_source.h +++ b/src/USER-MESODPD/fix_tdpd_source.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESODPD/pair_edpd.h b/src/USER-MESODPD/pair_edpd.h index 0670aa7754..c27a526225 100644 --- a/src/USER-MESODPD/pair_edpd.h +++ b/src/USER-MESODPD/pair_edpd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESODPD/pair_mdpd.h b/src/USER-MESODPD/pair_mdpd.h index ea0389c7fe..11977a32b3 100644 --- a/src/USER-MESODPD/pair_mdpd.h +++ b/src/USER-MESODPD/pair_mdpd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESODPD/pair_mdpd_rhosum.h b/src/USER-MESODPD/pair_mdpd_rhosum.h index a972ec7ccf..065bcc80b0 100644 --- a/src/USER-MESODPD/pair_mdpd_rhosum.h +++ b/src/USER-MESODPD/pair_mdpd_rhosum.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESODPD/pair_tdpd.h b/src/USER-MESODPD/pair_tdpd.h index bc0de79f8d..f141b3fe5b 100644 --- a/src/USER-MESODPD/pair_tdpd.h +++ b/src/USER-MESODPD/pair_tdpd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESONT/atom_vec_mesont.h b/src/USER-MESONT/atom_vec_mesont.h index e7de8c7d40..da6b7d2a09 100644 --- a/src/USER-MESONT/atom_vec_mesont.h +++ b/src/USER-MESONT/atom_vec_mesont.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESONT/compute_mesont.h b/src/USER-MESONT/compute_mesont.h index e7165230a4..e3ee9a53c8 100644 --- a/src/USER-MESONT/compute_mesont.h +++ b/src/USER-MESONT/compute_mesont.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESONT/export_mesont.h b/src/USER-MESONT/export_mesont.h index 08a5be21b5..517b445d54 100644 --- a/src/USER-MESONT/export_mesont.h +++ b/src/USER-MESONT/export_mesont.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MESONT/pair_mesont_tpm.h b/src/USER-MESONT/pair_mesont_tpm.h index a18e555349..f7e600b888 100644 --- a/src/USER-MESONT/pair_mesont_tpm.h +++ b/src/USER-MESONT/pair_mesont_tpm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_bgmul_7.c.h b/src/USER-MGPT/mgpt_bgmul_7.c.h index d4e87c9fe6..5719697759 100644 --- a/src/USER-MGPT/mgpt_bgmul_7.c.h +++ b/src/USER-MGPT/mgpt_bgmul_7.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_linalg.h b/src/USER-MGPT/mgpt_linalg.h index a22956a7f6..20993af68c 100644 --- a/src/USER-MGPT/mgpt_linalg.h +++ b/src/USER-MGPT/mgpt_linalg.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_mmul3_538.c.h b/src/USER-MGPT/mgpt_mmul3_538.c.h index f470590992..d615902214 100644 --- a/src/USER-MGPT/mgpt_mmul3_538.c.h +++ b/src/USER-MGPT/mgpt_mmul3_538.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_mmul3_748.c.h b/src/USER-MGPT/mgpt_mmul3_748.c.h index 298fe753c1..f6104c52a7 100644 --- a/src/USER-MGPT/mgpt_mmul3_748.c.h +++ b/src/USER-MGPT/mgpt_mmul3_748.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_mmul3d_526.c.h b/src/USER-MGPT/mgpt_mmul3d_526.c.h index 47a4c26a26..0a7e763f63 100644 --- a/src/USER-MGPT/mgpt_mmul3d_526.c.h +++ b/src/USER-MGPT/mgpt_mmul3d_526.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_mmul3d_744.c.h b/src/USER-MGPT/mgpt_mmul3d_744.c.h index 0f90438440..cfbe1236c6 100644 --- a/src/USER-MGPT/mgpt_mmul3d_744.c.h +++ b/src/USER-MGPT/mgpt_mmul3d_744.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_mmul_bg_552.c.h b/src/USER-MGPT/mgpt_mmul_bg_552.c.h index 16c6e9e4a8..069f96907f 100644 --- a/src/USER-MGPT/mgpt_mmul_bg_552.c.h +++ b/src/USER-MGPT/mgpt_mmul_bg_552.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_mmul_bg_722.c.h b/src/USER-MGPT/mgpt_mmul_bg_722.c.h index e9821436e3..732bb1319a 100644 --- a/src/USER-MGPT/mgpt_mmul_bg_722.c.h +++ b/src/USER-MGPT/mgpt_mmul_bg_722.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h b/src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h index 2e38b5b0cf..ce2fb5e159 100644 --- a/src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h +++ b/src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h b/src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h index 26f36c4844..da7e850cac 100644 --- a/src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h +++ b/src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_readpot.h b/src/USER-MGPT/mgpt_readpot.h index c2a6feabe0..11c2a1b4b0 100644 --- a/src/USER-MGPT/mgpt_readpot.h +++ b/src/USER-MGPT/mgpt_readpot.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_splinetab.h b/src/USER-MGPT/mgpt_splinetab.h index 05c9dbcafb..7458c1ecdd 100644 --- a/src/USER-MGPT/mgpt_splinetab.h +++ b/src/USER-MGPT/mgpt_splinetab.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_ttr_5022.c.h b/src/USER-MGPT/mgpt_ttr_5022.c.h index 2b697c6b84..c588d4925f 100644 --- a/src/USER-MGPT/mgpt_ttr_5022.c.h +++ b/src/USER-MGPT/mgpt_ttr_5022.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_ttr_5042.c.h b/src/USER-MGPT/mgpt_ttr_5042.c.h index 4d77a49c9d..f60ecb5fb1 100644 --- a/src/USER-MGPT/mgpt_ttr_5042.c.h +++ b/src/USER-MGPT/mgpt_ttr_5042.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_ttr_5123.c.h b/src/USER-MGPT/mgpt_ttr_5123.c.h index e8237f4eb2..ecab1d2c47 100644 --- a/src/USER-MGPT/mgpt_ttr_5123.c.h +++ b/src/USER-MGPT/mgpt_ttr_5123.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_ttr_5141.c.h b/src/USER-MGPT/mgpt_ttr_5141.c.h index d77c6935f3..0e3f04cdf4 100644 --- a/src/USER-MGPT/mgpt_ttr_5141.c.h +++ b/src/USER-MGPT/mgpt_ttr_5141.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_ttr_7022.c.h b/src/USER-MGPT/mgpt_ttr_7022.c.h index 99aeaec504..1e5e1cd94b 100644 --- a/src/USER-MGPT/mgpt_ttr_7022.c.h +++ b/src/USER-MGPT/mgpt_ttr_7022.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_ttr_7042.c.h b/src/USER-MGPT/mgpt_ttr_7042.c.h index 36ffe6714b..fb8cdb3123 100644 --- a/src/USER-MGPT/mgpt_ttr_7042.c.h +++ b/src/USER-MGPT/mgpt_ttr_7042.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_ttr_7123.c.h b/src/USER-MGPT/mgpt_ttr_7123.c.h index 39828ab481..60fa7eb5e3 100644 --- a/src/USER-MGPT/mgpt_ttr_7123.c.h +++ b/src/USER-MGPT/mgpt_ttr_7123.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/mgpt_ttr_7141.c.h b/src/USER-MGPT/mgpt_ttr_7141.c.h index 8309422333..2e61b34fe2 100644 --- a/src/USER-MGPT/mgpt_ttr_7141.c.h +++ b/src/USER-MGPT/mgpt_ttr_7141.c.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MGPT/pair_mgpt.h b/src/USER-MGPT/pair_mgpt.h index ff71edc9f3..f2f256ef80 100644 --- a/src/USER-MGPT/pair_mgpt.h +++ b/src/USER-MGPT/pair_mgpt.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/angle_cosine_shift.h b/src/USER-MISC/angle_cosine_shift.h index febabcc090..f4dc1b02e7 100644 --- a/src/USER-MISC/angle_cosine_shift.h +++ b/src/USER-MISC/angle_cosine_shift.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/angle_cosine_shift_exp.h b/src/USER-MISC/angle_cosine_shift_exp.h index 9614ddcc19..4a9ec15f95 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.h +++ b/src/USER-MISC/angle_cosine_shift_exp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/angle_dipole.h b/src/USER-MISC/angle_dipole.h index 187822d0d4..cc25c53b92 100644 --- a/src/USER-MISC/angle_dipole.h +++ b/src/USER-MISC/angle_dipole.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/angle_fourier.h b/src/USER-MISC/angle_fourier.h index 53eeea98da..ea4c8b2852 100644 --- a/src/USER-MISC/angle_fourier.h +++ b/src/USER-MISC/angle_fourier.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/angle_fourier_simple.h b/src/USER-MISC/angle_fourier_simple.h index df2253317f..734199939e 100644 --- a/src/USER-MISC/angle_fourier_simple.h +++ b/src/USER-MISC/angle_fourier_simple.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/angle_gaussian.cpp b/src/USER-MISC/angle_gaussian.cpp index ad311fdb5d..639d753afa 100644 --- a/src/USER-MISC/angle_gaussian.cpp +++ b/src/USER-MISC/angle_gaussian.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/angle_gaussian.h b/src/USER-MISC/angle_gaussian.h index cd97d62670..af2b097aee 100644 --- a/src/USER-MISC/angle_gaussian.h +++ b/src/USER-MISC/angle_gaussian.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/angle_quartic.h b/src/USER-MISC/angle_quartic.h index b916a5f89f..8b11b56488 100644 --- a/src/USER-MISC/angle_quartic.h +++ b/src/USER-MISC/angle_quartic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/bond_gaussian.cpp b/src/USER-MISC/bond_gaussian.cpp index e6460d808e..98c5086c2d 100644 --- a/src/USER-MISC/bond_gaussian.cpp +++ b/src/USER-MISC/bond_gaussian.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/bond_gaussian.h b/src/USER-MISC/bond_gaussian.h index 6fb587ff2b..98cbf171de 100644 --- a/src/USER-MISC/bond_gaussian.h +++ b/src/USER-MISC/bond_gaussian.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/bond_harmonic_shift.h b/src/USER-MISC/bond_harmonic_shift.h index b77cefb4af..4375e3787a 100644 --- a/src/USER-MISC/bond_harmonic_shift.h +++ b/src/USER-MISC/bond_harmonic_shift.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/bond_harmonic_shift_cut.h b/src/USER-MISC/bond_harmonic_shift_cut.h index ad2bcd61ad..0d13305f0b 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.h +++ b/src/USER-MISC/bond_harmonic_shift_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/bond_special.h b/src/USER-MISC/bond_special.h index d5e360ca53..e1807a29da 100644 --- a/src/USER-MISC/bond_special.h +++ b/src/USER-MISC/bond_special.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/compute_ackland_atom.h b/src/USER-MISC/compute_ackland_atom.h index dd70762627..0b2c0f98f1 100644 --- a/src/USER-MISC/compute_ackland_atom.h +++ b/src/USER-MISC/compute_ackland_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/compute_basal_atom.h b/src/USER-MISC/compute_basal_atom.h index 4d478cdd24..89e0ac739b 100644 --- a/src/USER-MISC/compute_basal_atom.h +++ b/src/USER-MISC/compute_basal_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/compute_cnp_atom.h b/src/USER-MISC/compute_cnp_atom.h index 4fdb3954f2..f90b09ff35 100644 --- a/src/USER-MISC/compute_cnp_atom.h +++ b/src/USER-MISC/compute_cnp_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/compute_entropy_atom.h b/src/USER-MISC/compute_entropy_atom.h index c09a6e791c..d11fcc850a 100644 --- a/src/USER-MISC/compute_entropy_atom.h +++ b/src/USER-MISC/compute_entropy_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/compute_gyration_shape.h b/src/USER-MISC/compute_gyration_shape.h index 1d58f000dd..92871a5827 100644 --- a/src/USER-MISC/compute_gyration_shape.h +++ b/src/USER-MISC/compute_gyration_shape.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/compute_gyration_shape_chunk.h b/src/USER-MISC/compute_gyration_shape_chunk.h index 1ce4b9f758..53800887f4 100644 --- a/src/USER-MISC/compute_gyration_shape_chunk.h +++ b/src/USER-MISC/compute_gyration_shape_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/compute_hma.h b/src/USER-MISC/compute_hma.h index 5fc1130c8b..bc504fd5f5 100644 --- a/src/USER-MISC/compute_hma.h +++ b/src/USER-MISC/compute_hma.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/compute_pressure_cylinder.h b/src/USER-MISC/compute_pressure_cylinder.h index 7151cca6ce..c633d196b1 100644 --- a/src/USER-MISC/compute_pressure_cylinder.h +++ b/src/USER-MISC/compute_pressure_cylinder.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/compute_pressure_grem.h b/src/USER-MISC/compute_pressure_grem.h index e6dc5e6839..11bcceb2a6 100644 --- a/src/USER-MISC/compute_pressure_grem.h +++ b/src/USER-MISC/compute_pressure_grem.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/compute_stress_mop.h b/src/USER-MISC/compute_stress_mop.h index 07bb774148..55e17b9e05 100644 --- a/src/USER-MISC/compute_stress_mop.h +++ b/src/USER-MISC/compute_stress_mop.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/compute_stress_mop_profile.h b/src/USER-MISC/compute_stress_mop_profile.h index d86237b0bd..809c60ea0a 100644 --- a/src/USER-MISC/compute_stress_mop_profile.h +++ b/src/USER-MISC/compute_stress_mop_profile.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/compute_temp_rotate.h b/src/USER-MISC/compute_temp_rotate.h index 9590366b15..b48374b81c 100644 --- a/src/USER-MISC/compute_temp_rotate.h +++ b/src/USER-MISC/compute_temp_rotate.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/compute_viscosity_cos.h b/src/USER-MISC/compute_viscosity_cos.h index 7bc27a9541..4a1a03425e 100644 --- a/src/USER-MISC/compute_viscosity_cos.h +++ b/src/USER-MISC/compute_viscosity_cos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.h b/src/USER-MISC/dihedral_cosine_shift_exp.h index 4d180f42de..6735624991 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.h +++ b/src/USER-MISC/dihedral_cosine_shift_exp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/dihedral_fourier.h b/src/USER-MISC/dihedral_fourier.h index 8b6291fc4c..93bb517568 100644 --- a/src/USER-MISC/dihedral_fourier.h +++ b/src/USER-MISC/dihedral_fourier.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/dihedral_nharmonic.h b/src/USER-MISC/dihedral_nharmonic.h index 6fd1da3b8b..91bcae3e50 100644 --- a/src/USER-MISC/dihedral_nharmonic.h +++ b/src/USER-MISC/dihedral_nharmonic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/dihedral_quadratic.h b/src/USER-MISC/dihedral_quadratic.h index 0b99cbc4f7..3bd8b0470f 100644 --- a/src/USER-MISC/dihedral_quadratic.h +++ b/src/USER-MISC/dihedral_quadratic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/dihedral_spherical.h b/src/USER-MISC/dihedral_spherical.h index 472db36f33..23f869f78c 100644 --- a/src/USER-MISC/dihedral_spherical.h +++ b/src/USER-MISC/dihedral_spherical.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/dihedral_table.h b/src/USER-MISC/dihedral_table.h index 9d5b03f5cc..0f63205fbc 100644 --- a/src/USER-MISC/dihedral_table.h +++ b/src/USER-MISC/dihedral_table.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/dihedral_table_cut.h b/src/USER-MISC/dihedral_table_cut.h index b956069e14..bff2472323 100644 --- a/src/USER-MISC/dihedral_table_cut.h +++ b/src/USER-MISC/dihedral_table_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_accelerate_cos.h b/src/USER-MISC/fix_accelerate_cos.h index e1e6c9f1b9..2f17eceded 100644 --- a/src/USER-MISC/fix_accelerate_cos.h +++ b/src/USER-MISC/fix_accelerate_cos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_addtorque.h b/src/USER-MISC/fix_addtorque.h index 49631ec916..62b77b52ae 100644 --- a/src/USER-MISC/fix_addtorque.h +++ b/src/USER-MISC/fix_addtorque.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_ave_correlate_long.h b/src/USER-MISC/fix_ave_correlate_long.h index a0c5863e99..bc7897cddd 100644 --- a/src/USER-MISC/fix_ave_correlate_long.h +++ b/src/USER-MISC/fix_ave_correlate_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_electron_stopping.h b/src/USER-MISC/fix_electron_stopping.h index f0f47698c6..968f7e6368 100644 --- a/src/USER-MISC/fix_electron_stopping.h +++ b/src/USER-MISC/fix_electron_stopping.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_electron_stopping_fit.cpp b/src/USER-MISC/fix_electron_stopping_fit.cpp index 8768ed5f3d..b36984f3df 100644 --- a/src/USER-MISC/fix_electron_stopping_fit.cpp +++ b/src/USER-MISC/fix_electron_stopping_fit.cpp @@ -1,6 +1,6 @@ /* --------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_electron_stopping_fit.h b/src/USER-MISC/fix_electron_stopping_fit.h index b40d6a3293..fa95c96483 100644 --- a/src/USER-MISC/fix_electron_stopping_fit.h +++ b/src/USER-MISC/fix_electron_stopping_fit.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_ffl.h b/src/USER-MISC/fix_ffl.h index 1225d25989..24f5405e3f 100644 --- a/src/USER-MISC/fix_ffl.h +++ b/src/USER-MISC/fix_ffl.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_filter_corotate.h b/src/USER-MISC/fix_filter_corotate.h index 7693feb94c..4819c00b8b 100644 --- a/src/USER-MISC/fix_filter_corotate.h +++ b/src/USER-MISC/fix_filter_corotate.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_flow_gauss.h b/src/USER-MISC/fix_flow_gauss.h index 75bdf8c1f9..84b647d484 100644 --- a/src/USER-MISC/fix_flow_gauss.h +++ b/src/USER-MISC/fix_flow_gauss.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_gle.h b/src/USER-MISC/fix_gle.h index 01f50f8925..39ea35a37b 100644 --- a/src/USER-MISC/fix_gle.h +++ b/src/USER-MISC/fix_gle.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_grem.h b/src/USER-MISC/fix_grem.h index 1899bf6fc2..0cd88477ea 100644 --- a/src/USER-MISC/fix_grem.h +++ b/src/USER-MISC/fix_grem.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_imd.h b/src/USER-MISC/fix_imd.h index a2f955b12d..3019c0908c 100644 --- a/src/USER-MISC/fix_imd.h +++ b/src/USER-MISC/fix_imd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_ipi.h b/src/USER-MISC/fix_ipi.h index 191b6c280d..32f81e596f 100644 --- a/src/USER-MISC/fix_ipi.h +++ b/src/USER-MISC/fix_ipi.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_momentum_chunk.h b/src/USER-MISC/fix_momentum_chunk.h index 5007e38c69..84ce3824c3 100644 --- a/src/USER-MISC/fix_momentum_chunk.h +++ b/src/USER-MISC/fix_momentum_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_npt_cauchy.h b/src/USER-MISC/fix_npt_cauchy.h index 052a5686ad..4842e59af8 100644 --- a/src/USER-MISC/fix_npt_cauchy.h +++ b/src/USER-MISC/fix_npt_cauchy.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_nvk.h b/src/USER-MISC/fix_nvk.h index 1d73e2f5df..63113342cd 100644 --- a/src/USER-MISC/fix_nvk.h +++ b/src/USER-MISC/fix_nvk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_orient_eco.h b/src/USER-MISC/fix_orient_eco.h index 9ae48be1f3..4c241fc8ea 100644 --- a/src/USER-MISC/fix_orient_eco.h +++ b/src/USER-MISC/fix_orient_eco.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_pafi.h b/src/USER-MISC/fix_pafi.h index dd272601e6..b71483f50e 100644 --- a/src/USER-MISC/fix_pafi.h +++ b/src/USER-MISC/fix_pafi.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_pimd.h b/src/USER-MISC/fix_pimd.h index bed5b0a256..5782246c76 100644 --- a/src/USER-MISC/fix_pimd.h +++ b/src/USER-MISC/fix_pimd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_propel_self.h b/src/USER-MISC/fix_propel_self.h index 47d1e1255b..968dd3af57 100644 --- a/src/USER-MISC/fix_propel_self.h +++ b/src/USER-MISC/fix_propel_self.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_rhok.h b/src/USER-MISC/fix_rhok.h index c950c08b1d..74e2f1031c 100644 --- a/src/USER-MISC/fix_rhok.h +++ b/src/USER-MISC/fix_rhok.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/USER-MISC/fix_smd.h b/src/USER-MISC/fix_smd.h index 4f86456f99..bb84d03f27 100644 --- a/src/USER-MISC/fix_smd.h +++ b/src/USER-MISC/fix_smd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_srp.h b/src/USER-MISC/fix_srp.h index f8343df8a6..f045f498c3 100644 --- a/src/USER-MISC/fix_srp.h +++ b/src/USER-MISC/fix_srp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_ti_spring.h b/src/USER-MISC/fix_ti_spring.h index 6379e9e039..96ed1bf042 100644 --- a/src/USER-MISC/fix_ti_spring.h +++ b/src/USER-MISC/fix_ti_spring.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_ttm_mod.h b/src/USER-MISC/fix_ttm_mod.h index 84d976ec07..e22e94ad49 100644 --- a/src/USER-MISC/fix_ttm_mod.h +++ b/src/USER-MISC/fix_ttm_mod.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_wall_ees.h b/src/USER-MISC/fix_wall_ees.h index 17246c094f..0e5050a53e 100644 --- a/src/USER-MISC/fix_wall_ees.h +++ b/src/USER-MISC/fix_wall_ees.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.h b/src/USER-MISC/fix_wall_reflect_stochastic.h index 558ad7d084..db818318af 100644 --- a/src/USER-MISC/fix_wall_reflect_stochastic.h +++ b/src/USER-MISC/fix_wall_reflect_stochastic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/fix_wall_region_ees.h b/src/USER-MISC/fix_wall_region_ees.h index 9da2cccce6..9c8e988937 100644 --- a/src/USER-MISC/fix_wall_region_ees.h +++ b/src/USER-MISC/fix_wall_region_ees.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/improper_cossq.h b/src/USER-MISC/improper_cossq.h index 9e430bfa1a..1245c6fc20 100644 --- a/src/USER-MISC/improper_cossq.h +++ b/src/USER-MISC/improper_cossq.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/improper_distance.h b/src/USER-MISC/improper_distance.h index d7575c3585..540671463b 100644 --- a/src/USER-MISC/improper_distance.h +++ b/src/USER-MISC/improper_distance.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/improper_fourier.h b/src/USER-MISC/improper_fourier.h index 91dfacfd8e..c9ed9ac406 100644 --- a/src/USER-MISC/improper_fourier.h +++ b/src/USER-MISC/improper_fourier.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/improper_ring.h b/src/USER-MISC/improper_ring.h index 7c53c6f59f..295a189066 100644 --- a/src/USER-MISC/improper_ring.h +++ b/src/USER-MISC/improper_ring.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_agni.h b/src/USER-MISC/pair_agni.h index 0a33c11b95..c687c5ad93 100644 --- a/src/USER-MISC/pair_agni.h +++ b/src/USER-MISC/pair_agni.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_buck_mdf.h b/src/USER-MISC/pair_buck_mdf.h index 4f9bac6341..7eda523999 100644 --- a/src/USER-MISC/pair_buck_mdf.h +++ b/src/USER-MISC/pair_buck_mdf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_cosine_squared.h b/src/USER-MISC/pair_cosine_squared.h index a638270e68..4a7470912c 100644 --- a/src/USER-MISC/pair_cosine_squared.h +++ b/src/USER-MISC/pair_cosine_squared.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_coul_diel.h b/src/USER-MISC/pair_coul_diel.h index 2113e45680..68804c7c90 100644 --- a/src/USER-MISC/pair_coul_diel.h +++ b/src/USER-MISC/pair_coul_diel.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_coul_shield.h b/src/USER-MISC/pair_coul_shield.h index d2cc3c3e84..066d670f25 100644 --- a/src/USER-MISC/pair_coul_shield.h +++ b/src/USER-MISC/pair_coul_shield.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_coul_slater_cut.h b/src/USER-MISC/pair_coul_slater_cut.h index fbf5f61f0f..c0854d47ed 100644 --- a/src/USER-MISC/pair_coul_slater_cut.h +++ b/src/USER-MISC/pair_coul_slater_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_coul_slater_long.h b/src/USER-MISC/pair_coul_slater_long.h index 267a10862e..5f71f6b1c2 100644 --- a/src/USER-MISC/pair_coul_slater_long.h +++ b/src/USER-MISC/pair_coul_slater_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_drip.h b/src/USER-MISC/pair_drip.h index 59dac076c8..ea783e3398 100644 --- a/src/USER-MISC/pair_drip.h +++ b/src/USER-MISC/pair_drip.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_e3b.h b/src/USER-MISC/pair_e3b.h index b37eee57f6..d8fa31b6b3 100644 --- a/src/USER-MISC/pair_e3b.h +++ b/src/USER-MISC/pair_e3b.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_edip.h b/src/USER-MISC/pair_edip.h index 006c124229..3588c609a8 100644 --- a/src/USER-MISC/pair_edip.h +++ b/src/USER-MISC/pair_edip.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_edip_multi.h b/src/USER-MISC/pair_edip_multi.h index 2aba064aa9..eebc174630 100644 --- a/src/USER-MISC/pair_edip_multi.h +++ b/src/USER-MISC/pair_edip_multi.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_extep.h b/src/USER-MISC/pair_extep.h index 08ee6d9a82..eb6ff8f025 100644 --- a/src/USER-MISC/pair_extep.h +++ b/src/USER-MISC/pair_extep.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_gauss_cut.h b/src/USER-MISC/pair_gauss_cut.h index 9173f83bc0..360a084945 100644 --- a/src/USER-MISC/pair_gauss_cut.h +++ b/src/USER-MISC/pair_gauss_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/USER-MISC/pair_ilp_graphene_hbn.h index 4f5e187782..8f62354fe1 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.h +++ b/src/USER-MISC/pair_ilp_graphene_hbn.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/USER-MISC/pair_kolmogorov_crespi_full.h index dd2721d37e..7e67f1460f 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.h +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.h b/src/USER-MISC/pair_kolmogorov_crespi_z.h index 7d242d67fd..e8574411bf 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.h +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_lebedeva_z.h b/src/USER-MISC/pair_lebedeva_z.h index 57cf445889..c7c99ef78c 100644 --- a/src/USER-MISC/pair_lebedeva_z.h +++ b/src/USER-MISC/pair_lebedeva_z.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_lennard_mdf.h b/src/USER-MISC/pair_lennard_mdf.h index 19325429ea..3a56ceb04a 100644 --- a/src/USER-MISC/pair_lennard_mdf.h +++ b/src/USER-MISC/pair_lennard_mdf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_list.h b/src/USER-MISC/pair_list.h index 4802194158..73284f5a36 100644 --- a/src/USER-MISC/pair_list.h +++ b/src/USER-MISC/pair_list.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_lj_expand_coul_long.h b/src/USER-MISC/pair_lj_expand_coul_long.h index d88acb99b7..41ccd4f357 100644 --- a/src/USER-MISC/pair_lj_expand_coul_long.h +++ b/src/USER-MISC/pair_lj_expand_coul_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_lj_mdf.h b/src/USER-MISC/pair_lj_mdf.h index 6ce6fdda2c..34e33e16d4 100644 --- a/src/USER-MISC/pair_lj_mdf.h +++ b/src/USER-MISC/pair_lj_mdf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.h b/src/USER-MISC/pair_lj_sf_dipole_sf.h index 76cc058e69..1c3ec982f9 100644 --- a/src/USER-MISC/pair_lj_sf_dipole_sf.h +++ b/src/USER-MISC/pair_lj_sf_dipole_sf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_local_density.h b/src/USER-MISC/pair_local_density.h index e999352680..339d04c963 100644 --- a/src/USER-MISC/pair_local_density.h +++ b/src/USER-MISC/pair_local_density.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_meam_spline.h b/src/USER-MISC/pair_meam_spline.h index b20454f18d..533db2e8ab 100644 --- a/src/USER-MISC/pair_meam_spline.h +++ b/src/USER-MISC/pair_meam_spline.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_meam_sw_spline.h b/src/USER-MISC/pair_meam_sw_spline.h index ecf56c7931..7046c504fe 100644 --- a/src/USER-MISC/pair_meam_sw_spline.h +++ b/src/USER-MISC/pair_meam_sw_spline.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_momb.h b/src/USER-MISC/pair_momb.h index 5c66ff7273..50962130be 100644 --- a/src/USER-MISC/pair_momb.h +++ b/src/USER-MISC/pair_momb.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_morse_smooth_linear.h b/src/USER-MISC/pair_morse_smooth_linear.h index cf47985479..83d2287421 100644 --- a/src/USER-MISC/pair_morse_smooth_linear.h +++ b/src/USER-MISC/pair_morse_smooth_linear.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_srp.h b/src/USER-MISC/pair_srp.h index 95cc5a5c94..1719dbed10 100644 --- a/src/USER-MISC/pair_srp.h +++ b/src/USER-MISC/pair_srp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_tersoff_table.h b/src/USER-MISC/pair_tersoff_table.h index 84e6f6fe50..cf1f44a745 100644 --- a/src/USER-MISC/pair_tersoff_table.h +++ b/src/USER-MISC/pair_tersoff_table.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_wf_cut.cpp b/src/USER-MISC/pair_wf_cut.cpp index e62217aad1..d421049cec 100644 --- a/src/USER-MISC/pair_wf_cut.cpp +++ b/src/USER-MISC/pair_wf_cut.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/pair_wf_cut.h b/src/USER-MISC/pair_wf_cut.h index d69efdf006..bbad8caf9c 100644 --- a/src/USER-MISC/pair_wf_cut.h +++ b/src/USER-MISC/pair_wf_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/temper_grem.h b/src/USER-MISC/temper_grem.h index 3c1891f22d..1bdd920233 100644 --- a/src/USER-MISC/temper_grem.h +++ b/src/USER-MISC/temper_grem.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MISC/temper_npt.h b/src/USER-MISC/temper_npt.h index a0eb1c1e9b..1c345cae12 100644 --- a/src/USER-MISC/temper_npt.h +++ b/src/USER-MISC/temper_npt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MOFFF/angle_class2_p6.h b/src/USER-MOFFF/angle_class2_p6.h index f2f324c0c6..caea234eeb 100644 --- a/src/USER-MOFFF/angle_class2_p6.h +++ b/src/USER-MOFFF/angle_class2_p6.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MOFFF/angle_cosine_buck6d.h b/src/USER-MOFFF/angle_cosine_buck6d.h index 1d0df10228..467abfb56a 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.h +++ b/src/USER-MOFFF/angle_cosine_buck6d.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MOFFF/improper_inversion_harmonic.h b/src/USER-MOFFF/improper_inversion_harmonic.h index 206b40aebf..cff0c14d92 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.h +++ b/src/USER-MOFFF/improper_inversion_harmonic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.h b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.h index 65acc400de..7fb22094d7 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.h +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.h b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.h index 0cfd45b69b..c814143cc4 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.h +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MOLFILE/dump_molfile.h b/src/USER-MOLFILE/dump_molfile.h index f07416cffa..f55c2f0762 100644 --- a/src/USER-MOLFILE/dump_molfile.h +++ b/src/USER-MOLFILE/dump_molfile.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MOLFILE/molfile_interface.h b/src/USER-MOLFILE/molfile_interface.h index 1146fb8251..8ac0f35bbf 100644 --- a/src/USER-MOLFILE/molfile_interface.h +++ b/src/USER-MOLFILE/molfile_interface.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-MOLFILE/reader_molfile.h b/src/USER-MOLFILE/reader_molfile.h index a56a4e0b96..d02f3e7986 100644 --- a/src/USER-MOLFILE/reader_molfile.h +++ b/src/USER-MOLFILE/reader_molfile.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-NETCDF/dump_netcdf.h b/src/USER-NETCDF/dump_netcdf.h index f74e95be38..a996ffc847 100644 --- a/src/USER-NETCDF/dump_netcdf.h +++ b/src/USER-NETCDF/dump_netcdf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.h b/src/USER-NETCDF/dump_netcdf_mpiio.h index 98ccb87927..2d1cd3ca2b 100644 --- a/src/USER-NETCDF/dump_netcdf_mpiio.h +++ b/src/USER-NETCDF/dump_netcdf_mpiio.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_charmm_omp.h b/src/USER-OMP/angle_charmm_omp.h index 8cbb992c3b..a96d62cad4 100644 --- a/src/USER-OMP/angle_charmm_omp.h +++ b/src/USER-OMP/angle_charmm_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_class2_omp.h b/src/USER-OMP/angle_class2_omp.h index fcfdae51a7..1f06e2bf06 100644 --- a/src/USER-OMP/angle_class2_omp.h +++ b/src/USER-OMP/angle_class2_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_cosine_delta_omp.h b/src/USER-OMP/angle_cosine_delta_omp.h index 57b1d9364d..3dbafe2682 100644 --- a/src/USER-OMP/angle_cosine_delta_omp.h +++ b/src/USER-OMP/angle_cosine_delta_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_cosine_omp.h b/src/USER-OMP/angle_cosine_omp.h index 16eb3ff944..cb7468a1f9 100644 --- a/src/USER-OMP/angle_cosine_omp.h +++ b/src/USER-OMP/angle_cosine_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_cosine_periodic_omp.h b/src/USER-OMP/angle_cosine_periodic_omp.h index 3c7da10ceb..db4a683141 100644 --- a/src/USER-OMP/angle_cosine_periodic_omp.h +++ b/src/USER-OMP/angle_cosine_periodic_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.h b/src/USER-OMP/angle_cosine_shift_exp_omp.h index aba70f8a3c..4a42872b1e 100644 --- a/src/USER-OMP/angle_cosine_shift_exp_omp.h +++ b/src/USER-OMP/angle_cosine_shift_exp_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_cosine_shift_omp.h b/src/USER-OMP/angle_cosine_shift_omp.h index 09402fb341..25b6234c52 100644 --- a/src/USER-OMP/angle_cosine_shift_omp.h +++ b/src/USER-OMP/angle_cosine_shift_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_cosine_squared_omp.h b/src/USER-OMP/angle_cosine_squared_omp.h index 758863e612..4fcd360125 100644 --- a/src/USER-OMP/angle_cosine_squared_omp.h +++ b/src/USER-OMP/angle_cosine_squared_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_dipole_omp.h b/src/USER-OMP/angle_dipole_omp.h index ab7133da34..b8c4067e0b 100644 --- a/src/USER-OMP/angle_dipole_omp.h +++ b/src/USER-OMP/angle_dipole_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_fourier_omp.h b/src/USER-OMP/angle_fourier_omp.h index 0185d09526..b273e01207 100644 --- a/src/USER-OMP/angle_fourier_omp.h +++ b/src/USER-OMP/angle_fourier_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_fourier_simple_omp.h b/src/USER-OMP/angle_fourier_simple_omp.h index 4ff0ce154f..68710a8b95 100644 --- a/src/USER-OMP/angle_fourier_simple_omp.h +++ b/src/USER-OMP/angle_fourier_simple_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_harmonic_omp.h b/src/USER-OMP/angle_harmonic_omp.h index 80c8f491aa..b617a0e5b6 100644 --- a/src/USER-OMP/angle_harmonic_omp.h +++ b/src/USER-OMP/angle_harmonic_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_quartic_omp.h b/src/USER-OMP/angle_quartic_omp.h index 72f8ffd821..7bb85d6277 100644 --- a/src/USER-OMP/angle_quartic_omp.h +++ b/src/USER-OMP/angle_quartic_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_sdk_omp.h b/src/USER-OMP/angle_sdk_omp.h index c041c2ecc2..7bed2d6878 100644 --- a/src/USER-OMP/angle_sdk_omp.h +++ b/src/USER-OMP/angle_sdk_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/angle_table_omp.h b/src/USER-OMP/angle_table_omp.h index 97c9bb65a7..84d5ded7d9 100644 --- a/src/USER-OMP/angle_table_omp.h +++ b/src/USER-OMP/angle_table_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/bond_class2_omp.h b/src/USER-OMP/bond_class2_omp.h index 845e28f592..e65d5006dd 100644 --- a/src/USER-OMP/bond_class2_omp.h +++ b/src/USER-OMP/bond_class2_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/bond_fene_expand_omp.h b/src/USER-OMP/bond_fene_expand_omp.h index 317b81e5de..4323dea61e 100644 --- a/src/USER-OMP/bond_fene_expand_omp.h +++ b/src/USER-OMP/bond_fene_expand_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/bond_fene_omp.h b/src/USER-OMP/bond_fene_omp.h index 13e843fe13..432321db9b 100644 --- a/src/USER-OMP/bond_fene_omp.h +++ b/src/USER-OMP/bond_fene_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/bond_gromos_omp.h b/src/USER-OMP/bond_gromos_omp.h index 69e92e4295..be7280d279 100644 --- a/src/USER-OMP/bond_gromos_omp.h +++ b/src/USER-OMP/bond_gromos_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/bond_harmonic_omp.h b/src/USER-OMP/bond_harmonic_omp.h index 0a81b52f41..77fa490e5f 100644 --- a/src/USER-OMP/bond_harmonic_omp.h +++ b/src/USER-OMP/bond_harmonic_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.h b/src/USER-OMP/bond_harmonic_shift_cut_omp.h index f465ff5b3a..2220b683fc 100644 --- a/src/USER-OMP/bond_harmonic_shift_cut_omp.h +++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/bond_harmonic_shift_omp.h b/src/USER-OMP/bond_harmonic_shift_omp.h index 58ee6ce23d..e614ebfbc0 100644 --- a/src/USER-OMP/bond_harmonic_shift_omp.h +++ b/src/USER-OMP/bond_harmonic_shift_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/bond_morse_omp.h b/src/USER-OMP/bond_morse_omp.h index 09d3a4458d..ac90359c7e 100644 --- a/src/USER-OMP/bond_morse_omp.h +++ b/src/USER-OMP/bond_morse_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/bond_nonlinear_omp.h b/src/USER-OMP/bond_nonlinear_omp.h index fcb0fa325d..0f27990729 100644 --- a/src/USER-OMP/bond_nonlinear_omp.h +++ b/src/USER-OMP/bond_nonlinear_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/bond_quartic_omp.h b/src/USER-OMP/bond_quartic_omp.h index 3a249a6cac..2d538b5a7b 100644 --- a/src/USER-OMP/bond_quartic_omp.h +++ b/src/USER-OMP/bond_quartic_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/bond_table_omp.h b/src/USER-OMP/bond_table_omp.h index 37e057ee26..4c9e7dc29f 100644 --- a/src/USER-OMP/bond_table_omp.h +++ b/src/USER-OMP/bond_table_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/dihedral_charmm_omp.h b/src/USER-OMP/dihedral_charmm_omp.h index cd0ae5f8ea..0164a00083 100644 --- a/src/USER-OMP/dihedral_charmm_omp.h +++ b/src/USER-OMP/dihedral_charmm_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/dihedral_class2_omp.h b/src/USER-OMP/dihedral_class2_omp.h index 889bbaf920..5f332ec372 100644 --- a/src/USER-OMP/dihedral_class2_omp.h +++ b/src/USER-OMP/dihedral_class2_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.h b/src/USER-OMP/dihedral_cosine_shift_exp_omp.h index 7e1accebf1..226a23c99f 100644 --- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.h +++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/dihedral_fourier_omp.h b/src/USER-OMP/dihedral_fourier_omp.h index 1ae49e0167..34d1a1ca53 100644 --- a/src/USER-OMP/dihedral_fourier_omp.h +++ b/src/USER-OMP/dihedral_fourier_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/dihedral_harmonic_omp.h b/src/USER-OMP/dihedral_harmonic_omp.h index b55bf015f2..7b8390352f 100644 --- a/src/USER-OMP/dihedral_harmonic_omp.h +++ b/src/USER-OMP/dihedral_harmonic_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/dihedral_helix_omp.h b/src/USER-OMP/dihedral_helix_omp.h index 24f16c4d7e..589971eed2 100644 --- a/src/USER-OMP/dihedral_helix_omp.h +++ b/src/USER-OMP/dihedral_helix_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.h b/src/USER-OMP/dihedral_multi_harmonic_omp.h index c6b80237a5..d4893c336c 100644 --- a/src/USER-OMP/dihedral_multi_harmonic_omp.h +++ b/src/USER-OMP/dihedral_multi_harmonic_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/dihedral_nharmonic_omp.h b/src/USER-OMP/dihedral_nharmonic_omp.h index 7d9daeab97..74c2d031cf 100644 --- a/src/USER-OMP/dihedral_nharmonic_omp.h +++ b/src/USER-OMP/dihedral_nharmonic_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/dihedral_opls_omp.h b/src/USER-OMP/dihedral_opls_omp.h index fbb5455f9c..4ac8efeb50 100644 --- a/src/USER-OMP/dihedral_opls_omp.h +++ b/src/USER-OMP/dihedral_opls_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/dihedral_quadratic_omp.h b/src/USER-OMP/dihedral_quadratic_omp.h index 7be6cbd8cb..73420ed7d2 100644 --- a/src/USER-OMP/dihedral_quadratic_omp.h +++ b/src/USER-OMP/dihedral_quadratic_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/dihedral_table_omp.h b/src/USER-OMP/dihedral_table_omp.h index fadb57ed1d..5c66e0f1c5 100644 --- a/src/USER-OMP/dihedral_table_omp.h +++ b/src/USER-OMP/dihedral_table_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/ewald_omp.h b/src/USER-OMP/ewald_omp.h index e3c779d786..1dcba93921 100644 --- a/src/USER-OMP/ewald_omp.h +++ b/src/USER-OMP/ewald_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_gravity_omp.h b/src/USER-OMP/fix_gravity_omp.h index 6bd1c64d99..d7a4db1211 100644 --- a/src/USER-OMP/fix_gravity_omp.h +++ b/src/USER-OMP/fix_gravity_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_neigh_history_omp.h b/src/USER-OMP/fix_neigh_history_omp.h index 9cd97ce3da..2bdb1b8dd1 100644 --- a/src/USER-OMP/fix_neigh_history_omp.h +++ b/src/USER-OMP/fix_neigh_history_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_nh_asphere_omp.h b/src/USER-OMP/fix_nh_asphere_omp.h index 0bfa72354e..3a6b40f334 100644 --- a/src/USER-OMP/fix_nh_asphere_omp.h +++ b/src/USER-OMP/fix_nh_asphere_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_nh_omp.h b/src/USER-OMP/fix_nh_omp.h index b3bdaa3683..bc5c748111 100644 --- a/src/USER-OMP/fix_nh_omp.h +++ b/src/USER-OMP/fix_nh_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_nh_sphere_omp.h b/src/USER-OMP/fix_nh_sphere_omp.h index bd12f9a174..f3f961e295 100644 --- a/src/USER-OMP/fix_nh_sphere_omp.h +++ b/src/USER-OMP/fix_nh_sphere_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_nph_asphere_omp.h b/src/USER-OMP/fix_nph_asphere_omp.h index 11de1948f4..874b15ff36 100644 --- a/src/USER-OMP/fix_nph_asphere_omp.h +++ b/src/USER-OMP/fix_nph_asphere_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_nph_omp.h b/src/USER-OMP/fix_nph_omp.h index 13f425c03b..3522ae831f 100644 --- a/src/USER-OMP/fix_nph_omp.h +++ b/src/USER-OMP/fix_nph_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_nph_sphere_omp.h b/src/USER-OMP/fix_nph_sphere_omp.h index 248423fd23..d3ada129c4 100644 --- a/src/USER-OMP/fix_nph_sphere_omp.h +++ b/src/USER-OMP/fix_nph_sphere_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_npt_asphere_omp.h b/src/USER-OMP/fix_npt_asphere_omp.h index 633c0b6d31..ca88944f2f 100644 --- a/src/USER-OMP/fix_npt_asphere_omp.h +++ b/src/USER-OMP/fix_npt_asphere_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_npt_omp.h b/src/USER-OMP/fix_npt_omp.h index 72c7662342..45a81282f1 100644 --- a/src/USER-OMP/fix_npt_omp.h +++ b/src/USER-OMP/fix_npt_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_npt_sphere_omp.h b/src/USER-OMP/fix_npt_sphere_omp.h index 074e55e46b..790e166993 100644 --- a/src/USER-OMP/fix_npt_sphere_omp.h +++ b/src/USER-OMP/fix_npt_sphere_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_nve_omp.h b/src/USER-OMP/fix_nve_omp.h index 5154116cac..6be58073b5 100644 --- a/src/USER-OMP/fix_nve_omp.h +++ b/src/USER-OMP/fix_nve_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_nve_sphere_omp.h b/src/USER-OMP/fix_nve_sphere_omp.h index 95cb4cf0af..a8454f7187 100644 --- a/src/USER-OMP/fix_nve_sphere_omp.h +++ b/src/USER-OMP/fix_nve_sphere_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_nvt_asphere_omp.h b/src/USER-OMP/fix_nvt_asphere_omp.h index e4062f6aff..55a36b2096 100644 --- a/src/USER-OMP/fix_nvt_asphere_omp.h +++ b/src/USER-OMP/fix_nvt_asphere_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_nvt_omp.h b/src/USER-OMP/fix_nvt_omp.h index 89d6f023ac..f931419459 100644 --- a/src/USER-OMP/fix_nvt_omp.h +++ b/src/USER-OMP/fix_nvt_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_nvt_sphere_omp.h b/src/USER-OMP/fix_nvt_sphere_omp.h index 9b5c4759e9..eb42ef1f8c 100644 --- a/src/USER-OMP/fix_nvt_sphere_omp.h +++ b/src/USER-OMP/fix_nvt_sphere_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_omp.h b/src/USER-OMP/fix_omp.h index 3020a927fd..3f8ea27ae9 100644 --- a/src/USER-OMP/fix_omp.h +++ b/src/USER-OMP/fix_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_peri_neigh_omp.h b/src/USER-OMP/fix_peri_neigh_omp.h index 77cc35777a..d0c144beb7 100644 --- a/src/USER-OMP/fix_peri_neigh_omp.h +++ b/src/USER-OMP/fix_peri_neigh_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_qeq_comb_omp.h b/src/USER-OMP/fix_qeq_comb_omp.h index 0febe6b0aa..707ce146c1 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.h +++ b/src/USER-OMP/fix_qeq_comb_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov See the README file in the top-level LAMMPS directory. diff --git a/src/USER-OMP/fix_qeq_reax_omp.h b/src/USER-OMP/fix_qeq_reax_omp.h index 46210647e5..323b1bdb09 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.h +++ b/src/USER-OMP/fix_qeq_reax_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_rigid_nh_omp.h b/src/USER-OMP/fix_rigid_nh_omp.h index 2f57b2723b..ceebccf620 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.h +++ b/src/USER-OMP/fix_rigid_nh_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_rigid_nph_omp.h b/src/USER-OMP/fix_rigid_nph_omp.h index f64a743fea..25f8cbe4f2 100644 --- a/src/USER-OMP/fix_rigid_nph_omp.h +++ b/src/USER-OMP/fix_rigid_nph_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_rigid_npt_omp.h b/src/USER-OMP/fix_rigid_npt_omp.h index 627b5a8c29..c68371cb87 100644 --- a/src/USER-OMP/fix_rigid_npt_omp.h +++ b/src/USER-OMP/fix_rigid_npt_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_rigid_nve_omp.h b/src/USER-OMP/fix_rigid_nve_omp.h index eea45ee358..3f5f21ed7a 100644 --- a/src/USER-OMP/fix_rigid_nve_omp.h +++ b/src/USER-OMP/fix_rigid_nve_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_rigid_nvt_omp.h b/src/USER-OMP/fix_rigid_nvt_omp.h index e1583aa4df..e6db85573c 100644 --- a/src/USER-OMP/fix_rigid_nvt_omp.h +++ b/src/USER-OMP/fix_rigid_nvt_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_rigid_omp.h b/src/USER-OMP/fix_rigid_omp.h index b666a173a8..40810bd04c 100644 --- a/src/USER-OMP/fix_rigid_omp.h +++ b/src/USER-OMP/fix_rigid_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/fix_rigid_small_omp.h b/src/USER-OMP/fix_rigid_small_omp.h index 298a1aa9de..dbb9e50421 100644 --- a/src/USER-OMP/fix_rigid_small_omp.h +++ b/src/USER-OMP/fix_rigid_small_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/improper_class2_omp.h b/src/USER-OMP/improper_class2_omp.h index 6f668a0078..f8f7e7b9f1 100644 --- a/src/USER-OMP/improper_class2_omp.h +++ b/src/USER-OMP/improper_class2_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/improper_cossq_omp.h b/src/USER-OMP/improper_cossq_omp.h index 8fd1bc09a0..929731f445 100644 --- a/src/USER-OMP/improper_cossq_omp.h +++ b/src/USER-OMP/improper_cossq_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/improper_cvff_omp.h b/src/USER-OMP/improper_cvff_omp.h index 8ab8f1615c..14f5bd7b7d 100644 --- a/src/USER-OMP/improper_cvff_omp.h +++ b/src/USER-OMP/improper_cvff_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/improper_fourier_omp.h b/src/USER-OMP/improper_fourier_omp.h index 8bd99cf4ca..b30694c424 100644 --- a/src/USER-OMP/improper_fourier_omp.h +++ b/src/USER-OMP/improper_fourier_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/improper_harmonic_omp.h b/src/USER-OMP/improper_harmonic_omp.h index d6325016a7..4a8000af53 100644 --- a/src/USER-OMP/improper_harmonic_omp.h +++ b/src/USER-OMP/improper_harmonic_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/improper_ring_omp.h b/src/USER-OMP/improper_ring_omp.h index 2b2616ab03..4378b8933e 100644 --- a/src/USER-OMP/improper_ring_omp.h +++ b/src/USER-OMP/improper_ring_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/improper_umbrella_omp.h b/src/USER-OMP/improper_umbrella_omp.h index 41bdfed4d5..190ea0ac72 100644 --- a/src/USER-OMP/improper_umbrella_omp.h +++ b/src/USER-OMP/improper_umbrella_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/msm_cg_omp.h b/src/USER-OMP/msm_cg_omp.h index e5842aaa28..c6ece318ca 100644 --- a/src/USER-OMP/msm_cg_omp.h +++ b/src/USER-OMP/msm_cg_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/msm_omp.h b/src/USER-OMP/msm_omp.h index 400772acf1..88cb16c157 100644 --- a/src/USER-OMP/msm_omp.h +++ b/src/USER-OMP/msm_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_full_bin_atomonly_omp.h b/src/USER-OMP/npair_full_bin_atomonly_omp.h index 643bf193a2..aa7bece0c2 100644 --- a/src/USER-OMP/npair_full_bin_atomonly_omp.h +++ b/src/USER-OMP/npair_full_bin_atomonly_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_full_bin_ghost_omp.h b/src/USER-OMP/npair_full_bin_ghost_omp.h index afc2eaef9d..a833ec36ad 100644 --- a/src/USER-OMP/npair_full_bin_ghost_omp.h +++ b/src/USER-OMP/npair_full_bin_ghost_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_full_bin_omp.h b/src/USER-OMP/npair_full_bin_omp.h index 832fb82c49..dcf8bd20a6 100644 --- a/src/USER-OMP/npair_full_bin_omp.h +++ b/src/USER-OMP/npair_full_bin_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_full_multi_omp.h b/src/USER-OMP/npair_full_multi_omp.h index 882e649183..71154e225e 100644 --- a/src/USER-OMP/npair_full_multi_omp.h +++ b/src/USER-OMP/npair_full_multi_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_full_nsq_ghost_omp.h b/src/USER-OMP/npair_full_nsq_ghost_omp.h index a080c17804..06cb73c393 100644 --- a/src/USER-OMP/npair_full_nsq_ghost_omp.h +++ b/src/USER-OMP/npair_full_nsq_ghost_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_full_nsq_omp.h b/src/USER-OMP/npair_full_nsq_omp.h index 251d059d1c..a2b6e884ad 100644 --- a/src/USER-OMP/npair_full_nsq_omp.h +++ b/src/USER-OMP/npair_full_nsq_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.h b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.h index 63223fd0bc..6ad9f3eee2 100644 --- a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.h +++ b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h index 9b75abbb8b..443caa01c6 100644 --- a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h +++ b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_bin_newtoff_omp.h b/src/USER-OMP/npair_half_bin_newtoff_omp.h index 06ef355f38..80d2c3a206 100644 --- a/src/USER-OMP/npair_half_bin_newtoff_omp.h +++ b/src/USER-OMP/npair_half_bin_newtoff_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_bin_newton_omp.h b/src/USER-OMP/npair_half_bin_newton_omp.h index f2468f04ad..f74aae6035 100644 --- a/src/USER-OMP/npair_half_bin_newton_omp.h +++ b/src/USER-OMP/npair_half_bin_newton_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_bin_newton_tri_omp.h b/src/USER-OMP/npair_half_bin_newton_tri_omp.h index f04f16f653..f430bbf098 100644 --- a/src/USER-OMP/npair_half_bin_newton_tri_omp.h +++ b/src/USER-OMP/npair_half_bin_newton_tri_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.h b/src/USER-OMP/npair_half_multi_newtoff_omp.h index a7aebf6579..a930ee8635 100644 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.h +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_multi_newton_omp.h b/src/USER-OMP/npair_half_multi_newton_omp.h index 85df36bb09..49657e8ee1 100644 --- a/src/USER-OMP/npair_half_multi_newton_omp.h +++ b/src/USER-OMP/npair_half_multi_newton_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.h b/src/USER-OMP/npair_half_multi_newton_tri_omp.h index 80faf8188f..3958bf5d22 100644 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.h +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h b/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h index 4294ab5f1f..5e66f8bee5 100644 --- a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h +++ b/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_nsq_newtoff_omp.h b/src/USER-OMP/npair_half_nsq_newtoff_omp.h index 23db92e10a..009abb4cf3 100644 --- a/src/USER-OMP/npair_half_nsq_newtoff_omp.h +++ b/src/USER-OMP/npair_half_nsq_newtoff_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_nsq_newton_omp.h b/src/USER-OMP/npair_half_nsq_newton_omp.h index cd40d4217d..3f45dc9a54 100644 --- a/src/USER-OMP/npair_half_nsq_newton_omp.h +++ b/src/USER-OMP/npair_half_nsq_newton_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.h b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.h index f4c7c69355..fc7d3d35f2 100644 --- a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.h +++ b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_respa_bin_newton_omp.h b/src/USER-OMP/npair_half_respa_bin_newton_omp.h index c4bad0aec8..6b3d9bd037 100644 --- a/src/USER-OMP/npair_half_respa_bin_newton_omp.h +++ b/src/USER-OMP/npair_half_respa_bin_newton_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h index ea913f5560..72e0ec077d 100644 --- a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h +++ b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h index c1d8fbc91a..7f53113b8a 100644 --- a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h +++ b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_respa_nsq_newton_omp.h b/src/USER-OMP/npair_half_respa_nsq_newton_omp.h index b3f06fb170..b8b9ccbac3 100644 --- a/src/USER-OMP/npair_half_respa_nsq_newton_omp.h +++ b/src/USER-OMP/npair_half_respa_nsq_newton_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.h b/src/USER-OMP/npair_half_size_bin_newtoff_omp.h index 891df55278..26b99cf834 100644 --- a/src/USER-OMP/npair_half_size_bin_newtoff_omp.h +++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.h b/src/USER-OMP/npair_half_size_bin_newton_omp.h index 4268ac36a1..62d0fcdbf7 100644 --- a/src/USER-OMP/npair_half_size_bin_newton_omp.h +++ b/src/USER-OMP/npair_half_size_bin_newton_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.h b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.h index 482ea4c36e..76e4512226 100644 --- a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.h +++ b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp index 415bfd3323..1e9b9369bd 100644 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.h b/src/USER-OMP/npair_half_size_multi_newtoff_omp.h index dd883d7f3c..bdcc217160 100644 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.h +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp index e4914fd9bd..0bf79ff77d 100644 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.h b/src/USER-OMP/npair_half_size_multi_newton_omp.h index 03d712145f..8f05bd908b 100644 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.h +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp index ce54c4135f..96b57cc7c6 100644 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h index 6e936c8da4..4a2043fbf2 100644 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h +++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.h b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.h index 95eb5d0d7a..0b018323a9 100644 --- a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.h +++ b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.h b/src/USER-OMP/npair_half_size_nsq_newton_omp.h index 6f8343d260..26d22e7cf4 100644 --- a/src/USER-OMP/npair_half_size_nsq_newton_omp.h +++ b/src/USER-OMP/npair_half_size_nsq_newton_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.h b/src/USER-OMP/npair_halffull_newtoff_omp.h index 961544a952..451ed801a2 100644 --- a/src/USER-OMP/npair_halffull_newtoff_omp.h +++ b/src/USER-OMP/npair_halffull_newtoff_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_halffull_newton_omp.h b/src/USER-OMP/npair_halffull_newton_omp.h index ef8be32a74..67a006b313 100644 --- a/src/USER-OMP/npair_halffull_newton_omp.h +++ b/src/USER-OMP/npair_halffull_newton_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_omp.h b/src/USER-OMP/npair_omp.h index 7f7d4d1cc2..bfcda382ed 100644 --- a/src/USER-OMP/npair_omp.h +++ b/src/USER-OMP/npair_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/npair_skip_omp.h b/src/USER-OMP/npair_skip_omp.h index a6ee1930d4..e3fa9624af 100644 --- a/src/USER-OMP/npair_skip_omp.h +++ b/src/USER-OMP/npair_skip_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_adp_omp.h b/src/USER-OMP/pair_adp_omp.h index e5c4c4af9f..de40ee2d5d 100644 --- a/src/USER-OMP/pair_adp_omp.h +++ b/src/USER-OMP/pair_adp_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_agni_omp.h b/src/USER-OMP/pair_agni_omp.h index 050696db28..506916467f 100644 --- a/src/USER-OMP/pair_agni_omp.h +++ b/src/USER-OMP/pair_agni_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_airebo_morse_omp.h b/src/USER-OMP/pair_airebo_morse_omp.h index 3e86f100b9..748ce991fa 100644 --- a/src/USER-OMP/pair_airebo_morse_omp.h +++ b/src/USER-OMP/pair_airebo_morse_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_airebo_omp.h b/src/USER-OMP/pair_airebo_omp.h index 5e7f4d4f58..75b86dae85 100644 --- a/src/USER-OMP/pair_airebo_omp.h +++ b/src/USER-OMP/pair_airebo_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov See the README file in the top-level LAMMPS directory. diff --git a/src/USER-OMP/pair_beck_omp.h b/src/USER-OMP/pair_beck_omp.h index 18a4401bbc..f1166c7c46 100644 --- a/src/USER-OMP/pair_beck_omp.h +++ b/src/USER-OMP/pair_beck_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_born_coul_long_omp.h b/src/USER-OMP/pair_born_coul_long_omp.h index bdf81e514e..403cc09658 100644 --- a/src/USER-OMP/pair_born_coul_long_omp.h +++ b/src/USER-OMP/pair_born_coul_long_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_born_coul_msm_omp.h b/src/USER-OMP/pair_born_coul_msm_omp.h index ab6c32b0e7..96262de856 100644 --- a/src/USER-OMP/pair_born_coul_msm_omp.h +++ b/src/USER-OMP/pair_born_coul_msm_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.h b/src/USER-OMP/pair_born_coul_wolf_omp.h index d714b32d29..e7e8194383 100644 --- a/src/USER-OMP/pair_born_coul_wolf_omp.h +++ b/src/USER-OMP/pair_born_coul_wolf_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_born_omp.h b/src/USER-OMP/pair_born_omp.h index db3c768f7a..e153178547 100644 --- a/src/USER-OMP/pair_born_omp.h +++ b/src/USER-OMP/pair_born_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_brownian_omp.h b/src/USER-OMP/pair_brownian_omp.h index c49560cbca..04c5185384 100644 --- a/src/USER-OMP/pair_brownian_omp.h +++ b/src/USER-OMP/pair_brownian_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_brownian_poly_omp.h b/src/USER-OMP/pair_brownian_poly_omp.h index df2c0b34bd..2e2fb2148e 100644 --- a/src/USER-OMP/pair_brownian_poly_omp.h +++ b/src/USER-OMP/pair_brownian_poly_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.h b/src/USER-OMP/pair_buck_coul_cut_omp.h index cf142b022a..eb3205d09b 100644 --- a/src/USER-OMP/pair_buck_coul_cut_omp.h +++ b/src/USER-OMP/pair_buck_coul_cut_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_buck_coul_long_omp.h b/src/USER-OMP/pair_buck_coul_long_omp.h index 1309bc4c4b..6792064aac 100644 --- a/src/USER-OMP/pair_buck_coul_long_omp.h +++ b/src/USER-OMP/pair_buck_coul_long_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_buck_coul_msm_omp.h b/src/USER-OMP/pair_buck_coul_msm_omp.h index 990a092911..56a89b8a23 100644 --- a/src/USER-OMP/pair_buck_coul_msm_omp.h +++ b/src/USER-OMP/pair_buck_coul_msm_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.h b/src/USER-OMP/pair_buck_long_coul_long_omp.h index f874dd9b68..7359bb0630 100644 --- a/src/USER-OMP/pair_buck_long_coul_long_omp.h +++ b/src/USER-OMP/pair_buck_long_coul_long_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_buck_omp.h b/src/USER-OMP/pair_buck_omp.h index 72e1178803..77c01bbc75 100644 --- a/src/USER-OMP/pair_buck_omp.h +++ b/src/USER-OMP/pair_buck_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_colloid_omp.h b/src/USER-OMP/pair_colloid_omp.h index 6605fbce00..bd35d153c9 100644 --- a/src/USER-OMP/pair_colloid_omp.h +++ b/src/USER-OMP/pair_colloid_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_comb_omp.h b/src/USER-OMP/pair_comb_omp.h index 85011064e7..ebd5ed0a97 100644 --- a/src/USER-OMP/pair_comb_omp.h +++ b/src/USER-OMP/pair_comb_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov See the README file in the top-level LAMMPS directory. diff --git a/src/USER-OMP/pair_coul_cut_global_omp.h b/src/USER-OMP/pair_coul_cut_global_omp.h index a2cb4a1dbe..7662dbbc9f 100644 --- a/src/USER-OMP/pair_coul_cut_global_omp.h +++ b/src/USER-OMP/pair_coul_cut_global_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_coul_cut_omp.h b/src/USER-OMP/pair_coul_cut_omp.h index 9e5fe81197..6708b3ff8c 100644 --- a/src/USER-OMP/pair_coul_cut_omp.h +++ b/src/USER-OMP/pair_coul_cut_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_coul_cut_soft_omp.h b/src/USER-OMP/pair_coul_cut_soft_omp.h index c4788bf25c..2c806170c0 100644 --- a/src/USER-OMP/pair_coul_cut_soft_omp.h +++ b/src/USER-OMP/pair_coul_cut_soft_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_coul_debye_omp.h b/src/USER-OMP/pair_coul_debye_omp.h index dc08647553..669e13b6a7 100644 --- a/src/USER-OMP/pair_coul_debye_omp.h +++ b/src/USER-OMP/pair_coul_debye_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_coul_diel_omp.h b/src/USER-OMP/pair_coul_diel_omp.h index 68206e4c28..53ab03d0e0 100644 --- a/src/USER-OMP/pair_coul_diel_omp.h +++ b/src/USER-OMP/pair_coul_diel_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_coul_dsf_omp.h b/src/USER-OMP/pair_coul_dsf_omp.h index 7897e2b29a..99b34ac6d3 100644 --- a/src/USER-OMP/pair_coul_dsf_omp.h +++ b/src/USER-OMP/pair_coul_dsf_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_coul_long_omp.h b/src/USER-OMP/pair_coul_long_omp.h index d628d22b60..7f0f08eca3 100644 --- a/src/USER-OMP/pair_coul_long_omp.h +++ b/src/USER-OMP/pair_coul_long_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_coul_long_soft_omp.h b/src/USER-OMP/pair_coul_long_soft_omp.h index 1454db23d7..07ae676805 100644 --- a/src/USER-OMP/pair_coul_long_soft_omp.h +++ b/src/USER-OMP/pair_coul_long_soft_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_coul_msm_omp.h b/src/USER-OMP/pair_coul_msm_omp.h index 41054cd661..acd369820e 100644 --- a/src/USER-OMP/pair_coul_msm_omp.h +++ b/src/USER-OMP/pair_coul_msm_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_coul_wolf_omp.h b/src/USER-OMP/pair_coul_wolf_omp.h index aef683d22c..2d5508eca4 100644 --- a/src/USER-OMP/pair_coul_wolf_omp.h +++ b/src/USER-OMP/pair_coul_wolf_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_dpd_omp.h b/src/USER-OMP/pair_dpd_omp.h index cacf4bd4bf..d39189eeec 100644 --- a/src/USER-OMP/pair_dpd_omp.h +++ b/src/USER-OMP/pair_dpd_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_dpd_tstat_omp.h b/src/USER-OMP/pair_dpd_tstat_omp.h index 48c5142038..5bea953378 100644 --- a/src/USER-OMP/pair_dpd_tstat_omp.h +++ b/src/USER-OMP/pair_dpd_tstat_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_eam_alloy_omp.h b/src/USER-OMP/pair_eam_alloy_omp.h index 6521d3e5a8..282c94878c 100644 --- a/src/USER-OMP/pair_eam_alloy_omp.h +++ b/src/USER-OMP/pair_eam_alloy_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_eam_fs_omp.h b/src/USER-OMP/pair_eam_fs_omp.h index c311f51cf3..5560c113dd 100644 --- a/src/USER-OMP/pair_eam_fs_omp.h +++ b/src/USER-OMP/pair_eam_fs_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_eam_omp.h b/src/USER-OMP/pair_eam_omp.h index 0f9d3cd51e..46630a82c9 100644 --- a/src/USER-OMP/pair_eam_omp.h +++ b/src/USER-OMP/pair_eam_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_edip_omp.h b/src/USER-OMP/pair_edip_omp.h index 55e10c83bb..512c0d33af 100644 --- a/src/USER-OMP/pair_edip_omp.h +++ b/src/USER-OMP/pair_edip_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov See the README file in the top-level LAMMPS directory. diff --git a/src/USER-OMP/pair_eim_omp.h b/src/USER-OMP/pair_eim_omp.h index c63222d7fb..737ac53cb7 100644 --- a/src/USER-OMP/pair_eim_omp.h +++ b/src/USER-OMP/pair_eim_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_gauss_cut_omp.h b/src/USER-OMP/pair_gauss_cut_omp.h index 2da2c14fdb..7bf96f4530 100644 --- a/src/USER-OMP/pair_gauss_cut_omp.h +++ b/src/USER-OMP/pair_gauss_cut_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_gauss_omp.h b/src/USER-OMP/pair_gauss_omp.h index a65a98730a..0b60e7f019 100644 --- a/src/USER-OMP/pair_gauss_omp.h +++ b/src/USER-OMP/pair_gauss_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_gayberne_omp.h b/src/USER-OMP/pair_gayberne_omp.h index 0e7b6708ff..ef6dfb1d8c 100644 --- a/src/USER-OMP/pair_gayberne_omp.h +++ b/src/USER-OMP/pair_gayberne_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.h b/src/USER-OMP/pair_gran_hertz_history_omp.h index cede3af206..dd3dd62114 100644 --- a/src/USER-OMP/pair_gran_hertz_history_omp.h +++ b/src/USER-OMP/pair_gran_hertz_history_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.h b/src/USER-OMP/pair_gran_hooke_history_omp.h index 32d2609ccc..9b114c3c1e 100644 --- a/src/USER-OMP/pair_gran_hooke_history_omp.h +++ b/src/USER-OMP/pair_gran_hooke_history_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_gran_hooke_omp.h b/src/USER-OMP/pair_gran_hooke_omp.h index 81f831fcea..6210314004 100644 --- a/src/USER-OMP/pair_gran_hooke_omp.h +++ b/src/USER-OMP/pair_gran_hooke_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.h b/src/USER-OMP/pair_hbond_dreiding_lj_omp.h index dc5108b3d7..47e73dd889 100644 --- a/src/USER-OMP/pair_hbond_dreiding_lj_omp.h +++ b/src/USER-OMP/pair_hbond_dreiding_lj_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.h b/src/USER-OMP/pair_hbond_dreiding_morse_omp.h index 5a8aaf2c5a..5db8419de5 100644 --- a/src/USER-OMP/pair_hbond_dreiding_morse_omp.h +++ b/src/USER-OMP/pair_hbond_dreiding_morse_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj96_cut_omp.h b/src/USER-OMP/pair_lj96_cut_omp.h index 037c68fc03..7061def774 100644 --- a/src/USER-OMP/pair_lj96_cut_omp.h +++ b/src/USER-OMP/pair_lj96_cut_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h index 9fb2835353..ce5eda3b24 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h +++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h index 9591d62c85..2e2275fa8c 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h +++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.h b/src/USER-OMP/pair_lj_charmm_coul_long_omp.h index ba28d05114..b0e09c55eb 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_long_omp.h +++ b/src/USER-OMP/pair_lj_charmm_coul_long_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.h b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.h index 961c41fdf7..b12e46d3a9 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.h +++ b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.h b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.h index 5a153f081e..e3ebf6c8fc 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.h +++ b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.h b/src/USER-OMP/pair_lj_class2_coul_cut_omp.h index f03da67a15..0beb5db2d1 100644 --- a/src/USER-OMP/pair_lj_class2_coul_cut_omp.h +++ b/src/USER-OMP/pair_lj_class2_coul_cut_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.h b/src/USER-OMP/pair_lj_class2_coul_long_omp.h index 973850c25c..87221ac58b 100644 --- a/src/USER-OMP/pair_lj_class2_coul_long_omp.h +++ b/src/USER-OMP/pair_lj_class2_coul_long_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_class2_omp.h b/src/USER-OMP/pair_lj_class2_omp.h index 5acd2cfb39..35b3c9529b 100644 --- a/src/USER-OMP/pair_lj_class2_omp.h +++ b/src/USER-OMP/pair_lj_class2_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cubic_omp.h b/src/USER-OMP/pair_lj_cubic_omp.h index 78b298bb35..f305869446 100644 --- a/src/USER-OMP/pair_lj_cubic_omp.h +++ b/src/USER-OMP/pair_lj_cubic_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.h b/src/USER-OMP/pair_lj_cut_coul_cut_omp.h index 0d5de5b7b7..9f4ccac03e 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_omp.h +++ b/src/USER-OMP/pair_lj_cut_coul_cut_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.h b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.h index 3716f548c5..8a6f443436 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.h +++ b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.h b/src/USER-OMP/pair_lj_cut_coul_debye_omp.h index b327fc665f..a2e9c5e426 100644 --- a/src/USER-OMP/pair_lj_cut_coul_debye_omp.h +++ b/src/USER-OMP/pair_lj_cut_coul_debye_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.h b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.h index bf1d74b017..d0c702962e 100644 --- a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.h +++ b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.h b/src/USER-OMP/pair_lj_cut_coul_long_omp.h index cea3271af0..abf7dbf755 100644 --- a/src/USER-OMP/pair_lj_cut_coul_long_omp.h +++ b/src/USER-OMP/pair_lj_cut_coul_long_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.h b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.h index 91ff8e0bab..636e050481 100644 --- a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.h +++ b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_coul_msm_omp.h b/src/USER-OMP/pair_lj_cut_coul_msm_omp.h index e496d133f6..cb49f14163 100644 --- a/src/USER-OMP/pair_lj_cut_coul_msm_omp.h +++ b/src/USER-OMP/pair_lj_cut_coul_msm_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.h b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.h index 4e56808c7b..744720c13a 100644 --- a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.h +++ b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.h b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.h index cebacac00f..96b01aa22d 100644 --- a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.h +++ b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_omp.h b/src/USER-OMP/pair_lj_cut_omp.h index 419b0693b1..6b5e4e168a 100644 --- a/src/USER-OMP/pair_lj_cut_omp.h +++ b/src/USER-OMP/pair_lj_cut_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_soft_omp.h b/src/USER-OMP/pair_lj_cut_soft_omp.h index e47262599d..2790bd106d 100644 --- a/src/USER-OMP/pair_lj_cut_soft_omp.h +++ b/src/USER-OMP/pair_lj_cut_soft_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.h b/src/USER-OMP/pair_lj_cut_thole_long_omp.h index 212f3c4e2e..844b1b3799 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.h +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.h b/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.h index f546d0dc3d..3fc7592e73 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.h +++ b/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.h b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.h index deb060ccbe..ba5556130c 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.h +++ b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.h b/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.h index 6759d346e7..208e9f3589 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.h +++ b/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_expand_omp.h b/src/USER-OMP/pair_lj_expand_omp.h index 8ca3bd41b0..d1723fabe2 100644 --- a/src/USER-OMP/pair_lj_expand_omp.h +++ b/src/USER-OMP/pair_lj_expand_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h index 353e4d673d..da014d73c1 100644 --- a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h +++ b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_gromacs_omp.h b/src/USER-OMP/pair_lj_gromacs_omp.h index 3669d1b219..7073f6de67 100644 --- a/src/USER-OMP/pair_lj_gromacs_omp.h +++ b/src/USER-OMP/pair_lj_gromacs_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.h b/src/USER-OMP/pair_lj_long_coul_long_omp.h index dd47231a9c..5e410ce3c7 100644 --- a/src/USER-OMP/pair_lj_long_coul_long_omp.h +++ b/src/USER-OMP/pair_lj_long_coul_long_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.h b/src/USER-OMP/pair_lj_long_tip4p_long_omp.h index 171edb6ddd..6c7eab6bc5 100644 --- a/src/USER-OMP/pair_lj_long_tip4p_long_omp.h +++ b/src/USER-OMP/pair_lj_long_tip4p_long_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_relres_omp.h b/src/USER-OMP/pair_lj_relres_omp.h index a367a1bc87..429e27b6ca 100644 --- a/src/USER-OMP/pair_lj_relres_omp.h +++ b/src/USER-OMP/pair_lj_relres_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.h b/src/USER-OMP/pair_lj_sdk_coul_long_omp.h index 1886d2c7b5..2ff3aa2025 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_long_omp.h +++ b/src/USER-OMP/pair_lj_sdk_coul_long_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.h b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.h index 9841408b8a..ad9e20d29c 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.h +++ b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_sdk_omp.h b/src/USER-OMP/pair_lj_sdk_omp.h index 36c913252a..b9186d3e78 100644 --- a/src/USER-OMP/pair_lj_sdk_omp.h +++ b/src/USER-OMP/pair_lj_sdk_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.h b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.h index b8f3e705a6..46bbafccd2 100644 --- a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.h +++ b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.h b/src/USER-OMP/pair_lj_smooth_linear_omp.h index 874e42eb9f..b63e4e5d8f 100644 --- a/src/USER-OMP/pair_lj_smooth_linear_omp.h +++ b/src/USER-OMP/pair_lj_smooth_linear_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lj_smooth_omp.h b/src/USER-OMP/pair_lj_smooth_omp.h index 0b47a792a4..c621fd60bc 100644 --- a/src/USER-OMP/pair_lj_smooth_omp.h +++ b/src/USER-OMP/pair_lj_smooth_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lubricate_omp.h b/src/USER-OMP/pair_lubricate_omp.h index b35dc5d563..203c1db03b 100644 --- a/src/USER-OMP/pair_lubricate_omp.h +++ b/src/USER-OMP/pair_lubricate_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_lubricate_poly_omp.h b/src/USER-OMP/pair_lubricate_poly_omp.h index e9984ce0d4..d72115fd46 100644 --- a/src/USER-OMP/pair_lubricate_poly_omp.h +++ b/src/USER-OMP/pair_lubricate_poly_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_meam_spline_omp.h b/src/USER-OMP/pair_meam_spline_omp.h index 2fd169609f..553b80320a 100644 --- a/src/USER-OMP/pair_meam_spline_omp.h +++ b/src/USER-OMP/pair_meam_spline_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_morse_omp.h b/src/USER-OMP/pair_morse_omp.h index 40797e2502..b73880dd8a 100644 --- a/src/USER-OMP/pair_morse_omp.h +++ b/src/USER-OMP/pair_morse_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_morse_smooth_linear_omp.h b/src/USER-OMP/pair_morse_smooth_linear_omp.h index 90109d2755..1753e69842 100644 --- a/src/USER-OMP/pair_morse_smooth_linear_omp.h +++ b/src/USER-OMP/pair_morse_smooth_linear_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_nm_cut_coul_cut_omp.h b/src/USER-OMP/pair_nm_cut_coul_cut_omp.h index 1892c80816..7a073ad3f6 100644 --- a/src/USER-OMP/pair_nm_cut_coul_cut_omp.h +++ b/src/USER-OMP/pair_nm_cut_coul_cut_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_nm_cut_coul_long_omp.h b/src/USER-OMP/pair_nm_cut_coul_long_omp.h index fe6317ce91..1457ef18eb 100644 --- a/src/USER-OMP/pair_nm_cut_coul_long_omp.h +++ b/src/USER-OMP/pair_nm_cut_coul_long_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_nm_cut_omp.h b/src/USER-OMP/pair_nm_cut_omp.h index 161804c783..5276708164 100644 --- a/src/USER-OMP/pair_nm_cut_omp.h +++ b/src/USER-OMP/pair_nm_cut_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_peri_lps_omp.h b/src/USER-OMP/pair_peri_lps_omp.h index aedb51472e..00322f95b1 100644 --- a/src/USER-OMP/pair_peri_lps_omp.h +++ b/src/USER-OMP/pair_peri_lps_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_peri_pmb_omp.h b/src/USER-OMP/pair_peri_pmb_omp.h index cb2d83250e..378926c830 100644 --- a/src/USER-OMP/pair_peri_pmb_omp.h +++ b/src/USER-OMP/pair_peri_pmb_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_reaxc_omp.h b/src/USER-OMP/pair_reaxc_omp.h index 38994c5264..08823489ef 100644 --- a/src/USER-OMP/pair_reaxc_omp.h +++ b/src/USER-OMP/pair_reaxc_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_rebo_omp.h b/src/USER-OMP/pair_rebo_omp.h index ef837f33df..0f256bb65b 100644 --- a/src/USER-OMP/pair_rebo_omp.h +++ b/src/USER-OMP/pair_rebo_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_resquared_omp.h b/src/USER-OMP/pair_resquared_omp.h index cc2a59d74a..d06747191b 100644 --- a/src/USER-OMP/pair_resquared_omp.h +++ b/src/USER-OMP/pair_resquared_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_soft_omp.h b/src/USER-OMP/pair_soft_omp.h index 74958208ed..c930cafc1e 100644 --- a/src/USER-OMP/pair_soft_omp.h +++ b/src/USER-OMP/pair_soft_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_sw_omp.h b/src/USER-OMP/pair_sw_omp.h index a99edba46e..546ff75bfa 100644 --- a/src/USER-OMP/pair_sw_omp.h +++ b/src/USER-OMP/pair_sw_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_table_omp.h b/src/USER-OMP/pair_table_omp.h index dbc0b8e5b9..d4a773b11f 100644 --- a/src/USER-OMP/pair_table_omp.h +++ b/src/USER-OMP/pair_table_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.h b/src/USER-OMP/pair_tersoff_mod_c_omp.h index 5cc669fa1a..9d613b502e 100644 --- a/src/USER-OMP/pair_tersoff_mod_c_omp.h +++ b/src/USER-OMP/pair_tersoff_mod_c_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov See the README file in the top-level LAMMPS directory. diff --git a/src/USER-OMP/pair_tersoff_mod_omp.h b/src/USER-OMP/pair_tersoff_mod_omp.h index 3eaf268073..2f4db53b3a 100644 --- a/src/USER-OMP/pair_tersoff_mod_omp.h +++ b/src/USER-OMP/pair_tersoff_mod_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov See the README file in the top-level LAMMPS directory. diff --git a/src/USER-OMP/pair_tersoff_omp.h b/src/USER-OMP/pair_tersoff_omp.h index 846b008921..b70bc3cf87 100644 --- a/src/USER-OMP/pair_tersoff_omp.h +++ b/src/USER-OMP/pair_tersoff_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov See the README file in the top-level LAMMPS directory. diff --git a/src/USER-OMP/pair_tersoff_table_omp.h b/src/USER-OMP/pair_tersoff_table_omp.h index e4f9f48abd..8f77e2316c 100644 --- a/src/USER-OMP/pair_tersoff_table_omp.h +++ b/src/USER-OMP/pair_tersoff_table_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov See the README file in the top-level LAMMPS directory. diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.h b/src/USER-OMP/pair_tersoff_zbl_omp.h index 32d7b6b4c4..1e76d04b76 100644 --- a/src/USER-OMP/pair_tersoff_zbl_omp.h +++ b/src/USER-OMP/pair_tersoff_zbl_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov See the README file in the top-level LAMMPS directory. diff --git a/src/USER-OMP/pair_tip4p_cut_omp.h b/src/USER-OMP/pair_tip4p_cut_omp.h index 952b3347e6..c546e7bdf9 100644 --- a/src/USER-OMP/pair_tip4p_cut_omp.h +++ b/src/USER-OMP/pair_tip4p_cut_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_tip4p_long_omp.h b/src/USER-OMP/pair_tip4p_long_omp.h index 6b6a2c4b61..489d68ee50 100644 --- a/src/USER-OMP/pair_tip4p_long_omp.h +++ b/src/USER-OMP/pair_tip4p_long_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_tip4p_long_soft_omp.h b/src/USER-OMP/pair_tip4p_long_soft_omp.h index 9142f156e9..89b1ecffc8 100644 --- a/src/USER-OMP/pair_tip4p_long_soft_omp.h +++ b/src/USER-OMP/pair_tip4p_long_soft_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_ufm_omp.h b/src/USER-OMP/pair_ufm_omp.h index 2a01da15d0..b17265a820 100644 --- a/src/USER-OMP/pair_ufm_omp.h +++ b/src/USER-OMP/pair_ufm_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_vashishta_omp.h b/src/USER-OMP/pair_vashishta_omp.h index 4c8efddb86..6ea60ea5ad 100644 --- a/src/USER-OMP/pair_vashishta_omp.h +++ b/src/USER-OMP/pair_vashishta_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_vashishta_table_omp.h b/src/USER-OMP/pair_vashishta_table_omp.h index eb892015ce..e19ff9662a 100644 --- a/src/USER-OMP/pair_vashishta_table_omp.h +++ b/src/USER-OMP/pair_vashishta_table_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.h b/src/USER-OMP/pair_yukawa_colloid_omp.h index b0ef483b5b..cec1e2977b 100644 --- a/src/USER-OMP/pair_yukawa_colloid_omp.h +++ b/src/USER-OMP/pair_yukawa_colloid_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_yukawa_omp.h b/src/USER-OMP/pair_yukawa_omp.h index d9db213474..943ea1dd8e 100644 --- a/src/USER-OMP/pair_yukawa_omp.h +++ b/src/USER-OMP/pair_yukawa_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pair_zbl_omp.h b/src/USER-OMP/pair_zbl_omp.h index a75d9dba53..ee40f2b1c7 100644 --- a/src/USER-OMP/pair_zbl_omp.h +++ b/src/USER-OMP/pair_zbl_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pppm_cg_omp.h b/src/USER-OMP/pppm_cg_omp.h index b421d6b525..1a965ce848 100644 --- a/src/USER-OMP/pppm_cg_omp.h +++ b/src/USER-OMP/pppm_cg_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pppm_disp_omp.h b/src/USER-OMP/pppm_disp_omp.h index 33dc9a308c..b6114e8b7a 100644 --- a/src/USER-OMP/pppm_disp_omp.h +++ b/src/USER-OMP/pppm_disp_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.h b/src/USER-OMP/pppm_disp_tip4p_omp.h index 442c36c31a..3351a056a9 100644 --- a/src/USER-OMP/pppm_disp_tip4p_omp.h +++ b/src/USER-OMP/pppm_disp_tip4p_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pppm_omp.h b/src/USER-OMP/pppm_omp.h index bbaaaa00ef..1df65d927e 100644 --- a/src/USER-OMP/pppm_omp.h +++ b/src/USER-OMP/pppm_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/pppm_tip4p_omp.h b/src/USER-OMP/pppm_tip4p_omp.h index de130030f9..7685bbbd6c 100644 --- a/src/USER-OMP/pppm_tip4p_omp.h +++ b/src/USER-OMP/pppm_tip4p_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/respa_omp.h b/src/USER-OMP/respa_omp.h index dc01e3dc5b..6c676328b2 100644 --- a/src/USER-OMP/respa_omp.h +++ b/src/USER-OMP/respa_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/thr_data.h b/src/USER-OMP/thr_data.h index 685040f0b8..1ec198c726 100644 --- a/src/USER-OMP/thr_data.h +++ b/src/USER-OMP/thr_data.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-OMP/thr_omp.h b/src/USER-OMP/thr_omp.h index 2db6e6f54f..966970eb4d 100644 --- a/src/USER-OMP/thr_omp.h +++ b/src/USER-OMP/thr_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-PACE/pair_pace.h b/src/USER-PACE/pair_pace.h index 4d5ddcb9e8..397b6dd1a9 100644 --- a/src/USER-PACE/pair_pace.h +++ b/src/USER-PACE/pair_pace.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov This software is distributed under the GNU General Public License. diff --git a/src/USER-PLUMED/fix_plumed.h b/src/USER-PLUMED/fix_plumed.h index e20633fadc..43096e8a26 100644 --- a/src/USER-PLUMED/fix_plumed.h +++ b/src/USER-PLUMED/fix_plumed.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-PTM/compute_ptm_atom.h b/src/USER-PTM/compute_ptm_atom.h index d7373a0763..2d6bfbb904 100644 --- a/src/USER-PTM/compute_ptm_atom.h +++ b/src/USER-PTM/compute_ptm_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-QMMM/fix_qmmm.h b/src/USER-QMMM/fix_qmmm.h index 9b1d3cf7bb..f7f599e8f1 100644 --- a/src/USER-QMMM/fix_qmmm.h +++ b/src/USER-QMMM/fix_qmmm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-QTB/fix_qbmsst.h b/src/USER-QTB/fix_qbmsst.h index cec54e40d8..31e9ae77cc 100644 --- a/src/USER-QTB/fix_qbmsst.h +++ b/src/USER-QTB/fix_qbmsst.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-QTB/fix_qtb.h b/src/USER-QTB/fix_qtb.h index 86a91bc9f6..88726e7253 100644 --- a/src/USER-QTB/fix_qtb.h +++ b/src/USER-QTB/fix_qtb.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-QUIP/pair_quip.h b/src/USER-QUIP/pair_quip.h index 216bf0dc28..b6029f0c40 100644 --- a/src/USER-QUIP/pair_quip.h +++ b/src/USER-QUIP/pair_quip.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-REACTION/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h index 67788df217..19852d93f7 100644 --- a/src/USER-REACTION/fix_bond_react.h +++ b/src/USER-REACTION/fix_bond_react.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-REACTION/superpose3d.h b/src/USER-REACTION/superpose3d.h index b0b290ddad..51de3ea739 100644 --- a/src/USER-REACTION/superpose3d.h +++ b/src/USER-REACTION/superpose3d.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-REAXC/compute_spec_atom.h b/src/USER-REAXC/compute_spec_atom.h index cf0aa0215d..a7411bbed3 100644 --- a/src/USER-REAXC/compute_spec_atom.h +++ b/src/USER-REAXC/compute_spec_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Labo0ratories + https://lammps.sandia.gov/, Sandia National Labo0ratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-REAXC/fix_qeq_reax.h b/src/USER-REAXC/fix_qeq_reax.h index 5658167aca..65e1643a0c 100644 --- a/src/USER-REAXC/fix_qeq_reax.h +++ b/src/USER-REAXC/fix_qeq_reax.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-REAXC/fix_reaxc.h b/src/USER-REAXC/fix_reaxc.h index 6a37002847..6fefb975fd 100644 --- a/src/USER-REAXC/fix_reaxc.h +++ b/src/USER-REAXC/fix_reaxc.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-REAXC/fix_reaxc_bonds.h b/src/USER-REAXC/fix_reaxc_bonds.h index e83e01f1d5..a19135f25a 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.h +++ b/src/USER-REAXC/fix_reaxc_bonds.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-REAXC/fix_reaxc_species.h b/src/USER-REAXC/fix_reaxc_species.h index 937af98527..35e3f31ab0 100644 --- a/src/USER-REAXC/fix_reaxc_species.h +++ b/src/USER-REAXC/fix_reaxc_species.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-REAXC/pair_reaxc.h b/src/USER-REAXC/pair_reaxc.h index 53b41ba9c8..d3fad7f63f 100644 --- a/src/USER-REAXC/pair_reaxc.h +++ b/src/USER-REAXC/pair_reaxc.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h index 33e714e136..62517561de 100644 --- a/src/USER-SCAFACOS/scafacos.h +++ b/src/USER-SCAFACOS/scafacos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SDPD/fix_meso_move.h b/src/USER-SDPD/fix_meso_move.h index a5e213ba81..27532fe5b6 100644 --- a/src/USER-SDPD/fix_meso_move.h +++ b/src/USER-SDPD/fix_meso_move.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SDPD/fix_rigid_meso.h b/src/USER-SDPD/fix_rigid_meso.h index 6945e3c144..fcec79e4c3 100644 --- a/src/USER-SDPD/fix_rigid_meso.h +++ b/src/USER-SDPD/fix_rigid_meso.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.h b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.h index 2d3d06297b..95f62bf166 100644 --- a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.h +++ b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/atom_vec_smd.h b/src/USER-SMD/atom_vec_smd.h index 055ad795c4..b5738d9b3f 100644 --- a/src/USER-SMD/atom_vec_smd.h +++ b/src/USER-SMD/atom_vec_smd.h @@ -11,7 +11,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_contact_radius.h b/src/USER-SMD/compute_smd_contact_radius.h index f22dce1bab..2c3098936f 100644 --- a/src/USER-SMD/compute_smd_contact_radius.h +++ b/src/USER-SMD/compute_smd_contact_radius.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_damage.h b/src/USER-SMD/compute_smd_damage.h index c8447872c7..5c3e96b339 100644 --- a/src/USER-SMD/compute_smd_damage.h +++ b/src/USER-SMD/compute_smd_damage.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_hourglass_error.h b/src/USER-SMD/compute_smd_hourglass_error.h index a6d1d1a1e2..4807164cb1 100644 --- a/src/USER-SMD/compute_smd_hourglass_error.h +++ b/src/USER-SMD/compute_smd_hourglass_error.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_internal_energy.h b/src/USER-SMD/compute_smd_internal_energy.h index fbccfbfb7e..0f11c2c9fe 100644 --- a/src/USER-SMD/compute_smd_internal_energy.h +++ b/src/USER-SMD/compute_smd_internal_energy.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_plastic_strain.h b/src/USER-SMD/compute_smd_plastic_strain.h index d2e64e31a1..fdc1f8af8d 100644 --- a/src/USER-SMD/compute_smd_plastic_strain.h +++ b/src/USER-SMD/compute_smd_plastic_strain.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.h b/src/USER-SMD/compute_smd_plastic_strain_rate.h index 03445e92f8..3311a5d28d 100644 --- a/src/USER-SMD/compute_smd_plastic_strain_rate.h +++ b/src/USER-SMD/compute_smd_plastic_strain_rate.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_rho.h b/src/USER-SMD/compute_smd_rho.h index 35dfdf8e91..9ee1ee11da 100644 --- a/src/USER-SMD/compute_smd_rho.h +++ b/src/USER-SMD/compute_smd_rho.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.h b/src/USER-SMD/compute_smd_tlsph_defgrad.h index 5dfa502991..2882d3bde6 100644 --- a/src/USER-SMD/compute_smd_tlsph_defgrad.h +++ b/src/USER-SMD/compute_smd_tlsph_defgrad.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_tlsph_dt.h b/src/USER-SMD/compute_smd_tlsph_dt.h index 09bf6c9727..6d0172f3f9 100644 --- a/src/USER-SMD/compute_smd_tlsph_dt.h +++ b/src/USER-SMD/compute_smd_tlsph_dt.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_tlsph_num_neighs.h b/src/USER-SMD/compute_smd_tlsph_num_neighs.h index da649fbce2..bd8bf80b90 100644 --- a/src/USER-SMD/compute_smd_tlsph_num_neighs.h +++ b/src/USER-SMD/compute_smd_tlsph_num_neighs.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_tlsph_shape.h b/src/USER-SMD/compute_smd_tlsph_shape.h index 193657870c..422073dffe 100644 --- a/src/USER-SMD/compute_smd_tlsph_shape.h +++ b/src/USER-SMD/compute_smd_tlsph_shape.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_tlsph_strain.h b/src/USER-SMD/compute_smd_tlsph_strain.h index 1294af2f45..1ebdfa5ba2 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain.h +++ b/src/USER-SMD/compute_smd_tlsph_strain.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.h b/src/USER-SMD/compute_smd_tlsph_strain_rate.h index cc4ed9f5ee..ccaec219a6 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain_rate.h +++ b/src/USER-SMD/compute_smd_tlsph_strain_rate.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_tlsph_stress.h b/src/USER-SMD/compute_smd_tlsph_stress.h index bf9079bb4f..97a01282d7 100644 --- a/src/USER-SMD/compute_smd_tlsph_stress.h +++ b/src/USER-SMD/compute_smd_tlsph_stress.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_triangle_vertices.h b/src/USER-SMD/compute_smd_triangle_vertices.h index 54c6055b98..5c6e178e14 100644 --- a/src/USER-SMD/compute_smd_triangle_vertices.h +++ b/src/USER-SMD/compute_smd_triangle_vertices.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_ulsph_effm.h b/src/USER-SMD/compute_smd_ulsph_effm.h index 68981fe76d..c4c5025a12 100644 --- a/src/USER-SMD/compute_smd_ulsph_effm.h +++ b/src/USER-SMD/compute_smd_ulsph_effm.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_ulsph_num_neighs.h b/src/USER-SMD/compute_smd_ulsph_num_neighs.h index 57340f01b6..cc3b56c0be 100644 --- a/src/USER-SMD/compute_smd_ulsph_num_neighs.h +++ b/src/USER-SMD/compute_smd_ulsph_num_neighs.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_ulsph_strain.h b/src/USER-SMD/compute_smd_ulsph_strain.h index a5796f34e2..37a33a8307 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain.h +++ b/src/USER-SMD/compute_smd_ulsph_strain.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_ulsph_strain_rate.h b/src/USER-SMD/compute_smd_ulsph_strain_rate.h index fc6df758e6..b306259aaf 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain_rate.h +++ b/src/USER-SMD/compute_smd_ulsph_strain_rate.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_ulsph_stress.h b/src/USER-SMD/compute_smd_ulsph_stress.h index 4e27a51723..17183d9f57 100644 --- a/src/USER-SMD/compute_smd_ulsph_stress.h +++ b/src/USER-SMD/compute_smd_ulsph_stress.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/compute_smd_vol.h b/src/USER-SMD/compute_smd_vol.h index 08ad150627..9b2b9e4728 100644 --- a/src/USER-SMD/compute_smd_vol.h +++ b/src/USER-SMD/compute_smd_vol.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/fix_smd_adjust_dt.h b/src/USER-SMD/fix_smd_adjust_dt.h index b89c136082..777519a35c 100644 --- a/src/USER-SMD/fix_smd_adjust_dt.h +++ b/src/USER-SMD/fix_smd_adjust_dt.h @@ -11,7 +11,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.h b/src/USER-SMD/fix_smd_integrate_tlsph.h index 6c152e6fe3..495bd65427 100644 --- a/src/USER-SMD/fix_smd_integrate_tlsph.h +++ b/src/USER-SMD/fix_smd_integrate_tlsph.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.h b/src/USER-SMD/fix_smd_integrate_ulsph.h index 9d954bf529..5339671ab1 100644 --- a/src/USER-SMD/fix_smd_integrate_ulsph.h +++ b/src/USER-SMD/fix_smd_integrate_ulsph.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.h b/src/USER-SMD/fix_smd_move_triangulated_surface.h index ec58a8bac1..9d0b3e6692 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.h +++ b/src/USER-SMD/fix_smd_move_triangulated_surface.h @@ -11,7 +11,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/fix_smd_setvel.h b/src/USER-SMD/fix_smd_setvel.h index f5fc34b4ea..af4f556942 100644 --- a/src/USER-SMD/fix_smd_setvel.h +++ b/src/USER-SMD/fix_smd_setvel.h @@ -11,7 +11,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h index 5f952bde93..29f759d3a3 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/fix_smd_wall_surface.h b/src/USER-SMD/fix_smd_wall_surface.h index 3ff2b49737..7f96222ff5 100644 --- a/src/USER-SMD/fix_smd_wall_surface.h +++ b/src/USER-SMD/fix_smd_wall_surface.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/pair_smd_hertz.h b/src/USER-SMD/pair_smd_hertz.h index 0866ef7486..2cdfaceb51 100644 --- a/src/USER-SMD/pair_smd_hertz.h +++ b/src/USER-SMD/pair_smd_hertz.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/pair_smd_tlsph.h b/src/USER-SMD/pair_smd_tlsph.h index 31a238d564..4a5d55c768 100644 --- a/src/USER-SMD/pair_smd_tlsph.h +++ b/src/USER-SMD/pair_smd_tlsph.h @@ -11,7 +11,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/pair_smd_triangulated_surface.h b/src/USER-SMD/pair_smd_triangulated_surface.h index f5772e0ead..6b4e83616c 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.h +++ b/src/USER-SMD/pair_smd_triangulated_surface.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/pair_smd_ulsph.h b/src/USER-SMD/pair_smd_ulsph.h index 435e0cb5a2..5313985bf7 100644 --- a/src/USER-SMD/pair_smd_ulsph.h +++ b/src/USER-SMD/pair_smd_ulsph.h @@ -11,7 +11,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMD/smd_material_models.h b/src/USER-SMD/smd_material_models.h index 557612bdf5..761ac4ec8a 100644 --- a/src/USER-SMD/smd_material_models.h +++ b/src/USER-SMD/smd_material_models.h @@ -11,7 +11,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SMTBQ/pair_smtbq.h b/src/USER-SMTBQ/pair_smtbq.h index 8bf1cba57c..b110b6aaae 100644 --- a/src/USER-SMTBQ/pair_smtbq.h +++ b/src/USER-SMTBQ/pair_smtbq.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SPH/atom_vec_sph.h b/src/USER-SPH/atom_vec_sph.h index 634c3c72f5..e6a8185760 100644 --- a/src/USER-SPH/atom_vec_sph.h +++ b/src/USER-SPH/atom_vec_sph.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SPH/compute_sph_e_atom.h b/src/USER-SPH/compute_sph_e_atom.h index 370fab148b..885a7bbcb6 100644 --- a/src/USER-SPH/compute_sph_e_atom.h +++ b/src/USER-SPH/compute_sph_e_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SPH/compute_sph_rho_atom.h b/src/USER-SPH/compute_sph_rho_atom.h index bd38f41199..37ba49a63f 100644 --- a/src/USER-SPH/compute_sph_rho_atom.h +++ b/src/USER-SPH/compute_sph_rho_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SPH/compute_sph_t_atom.h b/src/USER-SPH/compute_sph_t_atom.h index b3bf93a0eb..7489c00299 100644 --- a/src/USER-SPH/compute_sph_t_atom.h +++ b/src/USER-SPH/compute_sph_t_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SPH/fix_sph.h b/src/USER-SPH/fix_sph.h index 0a43997508..590612e2bd 100644 --- a/src/USER-SPH/fix_sph.h +++ b/src/USER-SPH/fix_sph.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SPH/fix_sph_stationary.h b/src/USER-SPH/fix_sph_stationary.h index f2bb6c39f2..90cc164ff1 100644 --- a/src/USER-SPH/fix_sph_stationary.h +++ b/src/USER-SPH/fix_sph_stationary.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SPH/pair_sph_heatconduction.h b/src/USER-SPH/pair_sph_heatconduction.h index c2c7f33d23..43ff122cf7 100644 --- a/src/USER-SPH/pair_sph_heatconduction.h +++ b/src/USER-SPH/pair_sph_heatconduction.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SPH/pair_sph_idealgas.h b/src/USER-SPH/pair_sph_idealgas.h index c47316865f..a0920aece2 100644 --- a/src/USER-SPH/pair_sph_idealgas.h +++ b/src/USER-SPH/pair_sph_idealgas.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SPH/pair_sph_lj.h b/src/USER-SPH/pair_sph_lj.h index f6a8f73b9f..2929e69783 100644 --- a/src/USER-SPH/pair_sph_lj.h +++ b/src/USER-SPH/pair_sph_lj.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SPH/pair_sph_rhosum.h b/src/USER-SPH/pair_sph_rhosum.h index ae6ee74eff..d7a168fbcb 100644 --- a/src/USER-SPH/pair_sph_rhosum.h +++ b/src/USER-SPH/pair_sph_rhosum.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SPH/pair_sph_taitwater.h b/src/USER-SPH/pair_sph_taitwater.h index ea4cfd8b26..41473da8d2 100644 --- a/src/USER-SPH/pair_sph_taitwater.h +++ b/src/USER-SPH/pair_sph_taitwater.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-SPH/pair_sph_taitwater_morris.h b/src/USER-SPH/pair_sph_taitwater_morris.h index 2736e347e1..8d98e7a0ed 100644 --- a/src/USER-SPH/pair_sph_taitwater_morris.h +++ b/src/USER-SPH/pair_sph_taitwater_morris.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-TALLY/compute_force_tally.h b/src/USER-TALLY/compute_force_tally.h index ae2f06a096..86703d1187 100644 --- a/src/USER-TALLY/compute_force_tally.h +++ b/src/USER-TALLY/compute_force_tally.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-TALLY/compute_heat_flux_tally.h b/src/USER-TALLY/compute_heat_flux_tally.h index 4158b2e29d..9f96946a19 100644 --- a/src/USER-TALLY/compute_heat_flux_tally.h +++ b/src/USER-TALLY/compute_heat_flux_tally.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-TALLY/compute_pe_mol_tally.h b/src/USER-TALLY/compute_pe_mol_tally.h index 1b022a9ef5..8c3bf3627d 100644 --- a/src/USER-TALLY/compute_pe_mol_tally.h +++ b/src/USER-TALLY/compute_pe_mol_tally.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-TALLY/compute_pe_tally.h b/src/USER-TALLY/compute_pe_tally.h index cd972e49db..f9d008f820 100644 --- a/src/USER-TALLY/compute_pe_tally.h +++ b/src/USER-TALLY/compute_pe_tally.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-TALLY/compute_stress_tally.h b/src/USER-TALLY/compute_stress_tally.h index 22f27a4a41..4236586822 100644 --- a/src/USER-TALLY/compute_stress_tally.h +++ b/src/USER-TALLY/compute_stress_tally.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-UEF/compute_pressure_uef.h b/src/USER-UEF/compute_pressure_uef.h index f5ce642a0e..9957ab4dd3 100644 --- a/src/USER-UEF/compute_pressure_uef.h +++ b/src/USER-UEF/compute_pressure_uef.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-UEF/compute_temp_uef.h b/src/USER-UEF/compute_temp_uef.h index 837e9c1c3e..638d87076a 100644 --- a/src/USER-UEF/compute_temp_uef.h +++ b/src/USER-UEF/compute_temp_uef.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-UEF/dump_cfg_uef.h b/src/USER-UEF/dump_cfg_uef.h index d8e7b15bcc..345d100721 100644 --- a/src/USER-UEF/dump_cfg_uef.h +++ b/src/USER-UEF/dump_cfg_uef.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-UEF/fix_npt_uef.h b/src/USER-UEF/fix_npt_uef.h index 4c0cd28ae0..74b4e55048 100644 --- a/src/USER-UEF/fix_npt_uef.h +++ b/src/USER-UEF/fix_npt_uef.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-UEF/fix_nvt_uef.h b/src/USER-UEF/fix_nvt_uef.h index b98da7963f..76ed7fd1ca 100644 --- a/src/USER-UEF/fix_nvt_uef.h +++ b/src/USER-UEF/fix_nvt_uef.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-UEF/uef_utils.h b/src/USER-UEF/uef_utils.h index 5936d4f6bd..13ee0dfa5a 100644 --- a/src/USER-UEF/uef_utils.h +++ b/src/USER-UEF/uef_utils.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-VTK/dump_vtk.h b/src/USER-VTK/dump_vtk.h index 9d46571d23..9ff57c642b 100644 --- a/src/USER-VTK/dump_vtk.h +++ b/src/USER-VTK/dump_vtk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-YAFF/angle_cross.h b/src/USER-YAFF/angle_cross.h index ba958f98ec..56b3579f50 100644 --- a/src/USER-YAFF/angle_cross.h +++ b/src/USER-YAFF/angle_cross.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-YAFF/angle_mm3.h b/src/USER-YAFF/angle_mm3.h index 985c4bb9b4..00d0a2a073 100644 --- a/src/USER-YAFF/angle_mm3.h +++ b/src/USER-YAFF/angle_mm3.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-YAFF/bond_mm3.h b/src/USER-YAFF/bond_mm3.h index 56f3136ea8..8b02ff0249 100644 --- a/src/USER-YAFF/bond_mm3.h +++ b/src/USER-YAFF/bond_mm3.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-YAFF/improper_distharm.h b/src/USER-YAFF/improper_distharm.h index 0a8d34ac44..1603e57194 100644 --- a/src/USER-YAFF/improper_distharm.h +++ b/src/USER-YAFF/improper_distharm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-YAFF/improper_sqdistharm.h b/src/USER-YAFF/improper_sqdistharm.h index 3aceb01a03..327f1683f6 100644 --- a/src/USER-YAFF/improper_sqdistharm.h +++ b/src/USER-YAFF/improper_sqdistharm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.h b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.h index 75686d55a2..1a8d34ea2c 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.h +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h index 35ae6c7995..f737481e35 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/VORONOI/compute_voronoi_atom.h b/src/VORONOI/compute_voronoi_atom.h index 5f2c36e67e..d38f2b5885 100644 --- a/src/VORONOI/compute_voronoi_atom.h +++ b/src/VORONOI/compute_voronoi_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h index 9fb9cf3690..5a510c77c3 100644 --- a/src/accelerator_kokkos.h +++ b/src/accelerator_kokkos.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/accelerator_omp.h b/src/accelerator_omp.h index 25910ae800..498f3dc417 100644 --- a/src/accelerator_omp.h +++ b/src/accelerator_omp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/angle.h b/src/angle.h index c8af8202f0..bd48a9ee83 100644 --- a/src/angle.h +++ b/src/angle.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/angle_deprecated.h b/src/angle_deprecated.h index 631df37da2..4882bc3ca9 100644 --- a/src/angle_deprecated.h +++ b/src/angle_deprecated.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/angle_hybrid.h b/src/angle_hybrid.h index 730d55b0e2..61193283e4 100644 --- a/src/angle_hybrid.h +++ b/src/angle_hybrid.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/angle_zero.h b/src/angle_zero.h index bc1ce0725f..843991f95d 100644 --- a/src/angle_zero.h +++ b/src/angle_zero.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/arg_info.h b/src/arg_info.h index f1328985a5..7b8865a1f7 100644 --- a/src/arg_info.h +++ b/src/arg_info.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/atom.h b/src/atom.h index bc69d3b27a..a8166bde65 100644 --- a/src/atom.h +++ b/src/atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/atom_map.h b/src/atom_map.h index 64e6e93689..1b98c69c26 100644 --- a/src/atom_map.h +++ b/src/atom_map.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/atom_masks.h b/src/atom_masks.h index daad323835..84faa492fb 100644 --- a/src/atom_masks.h +++ b/src/atom_masks.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/atom_vec.h b/src/atom_vec.h index a8f5f5ec22..ea2253d0c3 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/atom_vec_atomic.h b/src/atom_vec_atomic.h index 3caf1a5a94..61f8e8f37e 100644 --- a/src/atom_vec_atomic.h +++ b/src/atom_vec_atomic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h index 4a4c0d0e60..611f8485af 100644 --- a/src/atom_vec_body.h +++ b/src/atom_vec_body.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/atom_vec_charge.h b/src/atom_vec_charge.h index d52b4a068a..4f14d1027e 100644 --- a/src/atom_vec_charge.h +++ b/src/atom_vec_charge.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/atom_vec_ellipsoid.h b/src/atom_vec_ellipsoid.h index 57646522ec..2f9caffb18 100644 --- a/src/atom_vec_ellipsoid.h +++ b/src/atom_vec_ellipsoid.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h index 2d8d5dec29..9ff8ab643e 100644 --- a/src/atom_vec_hybrid.h +++ b/src/atom_vec_hybrid.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/atom_vec_line.h b/src/atom_vec_line.h index 449d8a1c04..726328a12c 100644 --- a/src/atom_vec_line.h +++ b/src/atom_vec_line.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/atom_vec_sphere.h b/src/atom_vec_sphere.h index bfd4e4241d..3a556c76f9 100644 --- a/src/atom_vec_sphere.h +++ b/src/atom_vec_sphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/atom_vec_tri.h b/src/atom_vec_tri.h index 06898f20f5..4f0151b2fd 100644 --- a/src/atom_vec_tri.h +++ b/src/atom_vec_tri.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/balance.h b/src/balance.h index 0642fe04f6..731dde9094 100644 --- a/src/balance.h +++ b/src/balance.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/body.h b/src/body.h index c9c289792e..72e66a3a15 100644 --- a/src/body.h +++ b/src/body.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/bond.h b/src/bond.h index 74f38ad455..e148113ea9 100644 --- a/src/bond.h +++ b/src/bond.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/bond_deprecated.h b/src/bond_deprecated.h index e81b7a5b27..64fb74e545 100644 --- a/src/bond_deprecated.h +++ b/src/bond_deprecated.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/bond_hybrid.h b/src/bond_hybrid.h index 19e4debfed..5a53ab47df 100644 --- a/src/bond_hybrid.h +++ b/src/bond_hybrid.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/bond_zero.h b/src/bond_zero.h index b31e89edf7..fdd16d3561 100644 --- a/src/bond_zero.h +++ b/src/bond_zero.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/change_box.h b/src/change_box.h index f48edb2d9f..9527260aa9 100644 --- a/src/change_box.h +++ b/src/change_box.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/citeme.h b/src/citeme.h index df87f1f9e5..4694b5b783 100644 --- a/src/citeme.h +++ b/src/citeme.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/comm.h b/src/comm.h index c8d7add79c..d283144501 100644 --- a/src/comm.h +++ b/src/comm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/comm_brick.h b/src/comm_brick.h index 6165f54de5..56fb833bab 100644 --- a/src/comm_brick.h +++ b/src/comm_brick.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/comm_tiled.h b/src/comm_tiled.h index fa2c76e6e9..45723a1d2d 100644 --- a/src/comm_tiled.h +++ b/src/comm_tiled.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/command.h b/src/command.h index 6abbc167ac..169fbc0c92 100644 --- a/src/command.h +++ b/src/command.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute.h b/src/compute.h index 71c07737d4..f0af428610 100644 --- a/src/compute.h +++ b/src/compute.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_adf.h b/src/compute_adf.h index f768013207..ab16c5b01d 100644 --- a/src/compute_adf.h +++ b/src/compute_adf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_aggregate_atom.h b/src/compute_aggregate_atom.h index 643c21e5fb..9b4d9312d0 100644 --- a/src/compute_aggregate_atom.h +++ b/src/compute_aggregate_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_angle.h b/src/compute_angle.h index b4240ff5db..6c84ace307 100644 --- a/src/compute_angle.h +++ b/src/compute_angle.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_angle_local.h b/src/compute_angle_local.h index a95e23206d..4338246cd2 100644 --- a/src/compute_angle_local.h +++ b/src/compute_angle_local.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_angmom_chunk.h b/src/compute_angmom_chunk.h index 66a57201d0..81f4988560 100644 --- a/src/compute_angmom_chunk.h +++ b/src/compute_angmom_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_bond.h b/src/compute_bond.h index f477b54fc5..f1e18e2bb4 100644 --- a/src/compute_bond.h +++ b/src/compute_bond.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_bond_local.h b/src/compute_bond_local.h index 17111a941c..b400456c53 100644 --- a/src/compute_bond_local.h +++ b/src/compute_bond_local.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_centro_atom.h b/src/compute_centro_atom.h index ffbf57a3ea..480919d4bf 100644 --- a/src/compute_centro_atom.h +++ b/src/compute_centro_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_centroid_stress_atom.h b/src/compute_centroid_stress_atom.h index 8d931c179c..88350262eb 100644 --- a/src/compute_centroid_stress_atom.h +++ b/src/compute_centroid_stress_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_chunk_atom.h b/src/compute_chunk_atom.h index 392179043a..da8e0db182 100644 --- a/src/compute_chunk_atom.h +++ b/src/compute_chunk_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_chunk_spread_atom.h b/src/compute_chunk_spread_atom.h index 80ee186450..fd5407e455 100644 --- a/src/compute_chunk_spread_atom.h +++ b/src/compute_chunk_spread_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_cluster_atom.h b/src/compute_cluster_atom.h index 253396b40e..4d6be634d1 100644 --- a/src/compute_cluster_atom.h +++ b/src/compute_cluster_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_cna_atom.h b/src/compute_cna_atom.h index 82cf8df608..e04ca3a41c 100644 --- a/src/compute_cna_atom.h +++ b/src/compute_cna_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_com.h b/src/compute_com.h index 5819b19650..d45f363749 100644 --- a/src/compute_com.h +++ b/src/compute_com.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_com_chunk.h b/src/compute_com_chunk.h index 610d6e39c3..c009f71ad2 100644 --- a/src/compute_com_chunk.h +++ b/src/compute_com_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_contact_atom.h b/src/compute_contact_atom.h index 2ce7678f56..67910ab340 100644 --- a/src/compute_contact_atom.h +++ b/src/compute_contact_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_coord_atom.h b/src/compute_coord_atom.h index 31bab18d87..dd1815dac2 100644 --- a/src/compute_coord_atom.h +++ b/src/compute_coord_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_deprecated.h b/src/compute_deprecated.h index 35c114c542..9082c72eae 100644 --- a/src/compute_deprecated.h +++ b/src/compute_deprecated.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_dihedral.h b/src/compute_dihedral.h index 2debd31e3c..8f59108735 100644 --- a/src/compute_dihedral.h +++ b/src/compute_dihedral.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_dihedral_local.h b/src/compute_dihedral_local.h index 5c50a66e96..fd084dbd19 100644 --- a/src/compute_dihedral_local.h +++ b/src/compute_dihedral_local.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_dipole_chunk.h b/src/compute_dipole_chunk.h index b0605b1c35..19c052367b 100644 --- a/src/compute_dipole_chunk.h +++ b/src/compute_dipole_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_displace_atom.h b/src/compute_displace_atom.h index 03ff838526..212619d3ce 100644 --- a/src/compute_displace_atom.h +++ b/src/compute_displace_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_erotate_sphere.h b/src/compute_erotate_sphere.h index 8a4f1f2def..ef75084859 100644 --- a/src/compute_erotate_sphere.h +++ b/src/compute_erotate_sphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_erotate_sphere_atom.h b/src/compute_erotate_sphere_atom.h index 820a75df8d..ee909c9151 100644 --- a/src/compute_erotate_sphere_atom.h +++ b/src/compute_erotate_sphere_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_fragment_atom.h b/src/compute_fragment_atom.h index e5cc2a5b6f..a8bc87c64e 100644 --- a/src/compute_fragment_atom.h +++ b/src/compute_fragment_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_global_atom.h b/src/compute_global_atom.h index e2da95fcce..b47c0cce22 100644 --- a/src/compute_global_atom.h +++ b/src/compute_global_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_group_group.h b/src/compute_group_group.h index c1231f07a7..b579863a55 100644 --- a/src/compute_group_group.h +++ b/src/compute_group_group.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_gyration.h b/src/compute_gyration.h index 0aa797ae00..ad31f7b382 100644 --- a/src/compute_gyration.h +++ b/src/compute_gyration.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_gyration_chunk.h b/src/compute_gyration_chunk.h index e489de5f77..7c1c15791a 100644 --- a/src/compute_gyration_chunk.h +++ b/src/compute_gyration_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_heat_flux.h b/src/compute_heat_flux.h index b74d02961f..e31989840b 100644 --- a/src/compute_heat_flux.h +++ b/src/compute_heat_flux.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_hexorder_atom.h b/src/compute_hexorder_atom.h index 39af576cb7..194ae35c4e 100644 --- a/src/compute_hexorder_atom.h +++ b/src/compute_hexorder_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_improper.h b/src/compute_improper.h index 34214f07a9..7b66bd9aca 100644 --- a/src/compute_improper.h +++ b/src/compute_improper.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_improper_local.h b/src/compute_improper_local.h index 29530d603d..1ff26b912e 100644 --- a/src/compute_improper_local.h +++ b/src/compute_improper_local.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_inertia_chunk.h b/src/compute_inertia_chunk.h index 8608b352b1..bf42bb66f3 100644 --- a/src/compute_inertia_chunk.h +++ b/src/compute_inertia_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_ke.h b/src/compute_ke.h index fb5bf427df..6561146d29 100644 --- a/src/compute_ke.h +++ b/src/compute_ke.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_ke_atom.h b/src/compute_ke_atom.h index a8fae9918d..9444aec7f6 100644 --- a/src/compute_ke_atom.h +++ b/src/compute_ke_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_msd.h b/src/compute_msd.h index 63abf4c4eb..3022369256 100644 --- a/src/compute_msd.h +++ b/src/compute_msd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_msd_chunk.h b/src/compute_msd_chunk.h index 216fde33bc..657cf45ab4 100644 --- a/src/compute_msd_chunk.h +++ b/src/compute_msd_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_omega_chunk.h b/src/compute_omega_chunk.h index 01fceb178e..ae4fb9d682 100644 --- a/src/compute_omega_chunk.h +++ b/src/compute_omega_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_orientorder_atom.h b/src/compute_orientorder_atom.h index 4fc122c5c8..7ddc45253a 100644 --- a/src/compute_orientorder_atom.h +++ b/src/compute_orientorder_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_pair.h b/src/compute_pair.h index 57d52a5bab..565b25c84d 100644 --- a/src/compute_pair.h +++ b/src/compute_pair.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_pair_local.h b/src/compute_pair_local.h index 3bd1dccd1a..e23cd2e67a 100644 --- a/src/compute_pair_local.h +++ b/src/compute_pair_local.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_pe.h b/src/compute_pe.h index 4048166939..21c0eaaebc 100644 --- a/src/compute_pe.h +++ b/src/compute_pe.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_pe_atom.h b/src/compute_pe_atom.h index 924399e867..781aeecc0f 100644 --- a/src/compute_pe_atom.h +++ b/src/compute_pe_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_pressure.h b/src/compute_pressure.h index 235ccbe1eb..fc67b1b699 100644 --- a/src/compute_pressure.h +++ b/src/compute_pressure.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_property_atom.h b/src/compute_property_atom.h index cab9d3ea1b..dc2bf92817 100644 --- a/src/compute_property_atom.h +++ b/src/compute_property_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_property_chunk.h b/src/compute_property_chunk.h index 48211ec91b..aef41ce719 100644 --- a/src/compute_property_chunk.h +++ b/src/compute_property_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_property_local.h b/src/compute_property_local.h index 855fb9d3e9..085e2e1f7a 100644 --- a/src/compute_property_local.h +++ b/src/compute_property_local.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_rdf.h b/src/compute_rdf.h index 85f6ce6ad2..f1cbc0e512 100644 --- a/src/compute_rdf.h +++ b/src/compute_rdf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_reduce.h b/src/compute_reduce.h index 53568ac942..09a83ace11 100644 --- a/src/compute_reduce.h +++ b/src/compute_reduce.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_reduce_chunk.h b/src/compute_reduce_chunk.h index 525bb0c7a7..886dc61542 100644 --- a/src/compute_reduce_chunk.h +++ b/src/compute_reduce_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_reduce_region.h b/src/compute_reduce_region.h index 2c86cfd782..02f58b7424 100644 --- a/src/compute_reduce_region.h +++ b/src/compute_reduce_region.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_slice.h b/src/compute_slice.h index 8cc0f9896d..3ffc5d52b5 100644 --- a/src/compute_slice.h +++ b/src/compute_slice.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_stress_atom.h b/src/compute_stress_atom.h index f470a59031..b22b021f69 100644 --- a/src/compute_stress_atom.h +++ b/src/compute_stress_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_temp.h b/src/compute_temp.h index 1550ae7a99..520c7e5027 100644 --- a/src/compute_temp.h +++ b/src/compute_temp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_temp_chunk.h b/src/compute_temp_chunk.h index d47d6d79ec..ac3c76b660 100644 --- a/src/compute_temp_chunk.h +++ b/src/compute_temp_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_temp_com.h b/src/compute_temp_com.h index 67bbdc39a9..95c3d41b7b 100644 --- a/src/compute_temp_com.h +++ b/src/compute_temp_com.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_temp_deform.h b/src/compute_temp_deform.h index 030294e1c8..836a858a70 100644 --- a/src/compute_temp_deform.h +++ b/src/compute_temp_deform.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_temp_partial.h b/src/compute_temp_partial.h index 62641d4799..d4a6e78352 100644 --- a/src/compute_temp_partial.h +++ b/src/compute_temp_partial.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_temp_profile.h b/src/compute_temp_profile.h index f0c07bbd48..d82fbd780e 100644 --- a/src/compute_temp_profile.h +++ b/src/compute_temp_profile.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_temp_ramp.h b/src/compute_temp_ramp.h index ab888ec31d..cebf73c001 100644 --- a/src/compute_temp_ramp.h +++ b/src/compute_temp_ramp.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_temp_region.h b/src/compute_temp_region.h index fd494ab8d1..a7cc343a91 100644 --- a/src/compute_temp_region.h +++ b/src/compute_temp_region.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_temp_sphere.h b/src/compute_temp_sphere.h index c15e02ffbb..2bd6553033 100644 --- a/src/compute_temp_sphere.h +++ b/src/compute_temp_sphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_torque_chunk.h b/src/compute_torque_chunk.h index 9e035570ee..e05be3b578 100644 --- a/src/compute_torque_chunk.h +++ b/src/compute_torque_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_vacf.h b/src/compute_vacf.h index 6fa013803c..4e1ed0c858 100644 --- a/src/compute_vacf.h +++ b/src/compute_vacf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/compute_vcm_chunk.h b/src/compute_vcm_chunk.h index 7096dec462..eeaf017502 100644 --- a/src/compute_vcm_chunk.h +++ b/src/compute_vcm_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/create_atoms.h b/src/create_atoms.h index deb155b96a..0d3ba58721 100644 --- a/src/create_atoms.h +++ b/src/create_atoms.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/create_bonds.h b/src/create_bonds.h index d2d50c86c6..b39ed00832 100644 --- a/src/create_bonds.h +++ b/src/create_bonds.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/create_box.h b/src/create_box.h index 26a2be6fe1..2d9eb10f26 100644 --- a/src/create_box.h +++ b/src/create_box.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/delete_atoms.h b/src/delete_atoms.h index 5ff1d12f65..f6e889fd80 100644 --- a/src/delete_atoms.h +++ b/src/delete_atoms.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/delete_bonds.h b/src/delete_bonds.h index 5c56a67f68..563da5057a 100644 --- a/src/delete_bonds.h +++ b/src/delete_bonds.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/deprecated.h b/src/deprecated.h index d5997d7199..42d8cca42f 100644 --- a/src/deprecated.h +++ b/src/deprecated.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/dihedral.h b/src/dihedral.h index c7fd459f1e..000fd2daba 100644 --- a/src/dihedral.h +++ b/src/dihedral.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/dihedral_deprecated.h b/src/dihedral_deprecated.h index 216791f623..8aa95d4525 100644 --- a/src/dihedral_deprecated.h +++ b/src/dihedral_deprecated.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/dihedral_hybrid.h b/src/dihedral_hybrid.h index 2804060af4..6904e8ecbe 100644 --- a/src/dihedral_hybrid.h +++ b/src/dihedral_hybrid.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/dihedral_zero.h b/src/dihedral_zero.h index e97f8f6641..4609ba60d9 100644 --- a/src/dihedral_zero.h +++ b/src/dihedral_zero.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/displace_atoms.h b/src/displace_atoms.h index c2c2e8306f..fecbc0ade3 100644 --- a/src/displace_atoms.h +++ b/src/displace_atoms.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/domain.h b/src/domain.h index 5009a67d28..89b326f83b 100644 --- a/src/domain.h +++ b/src/domain.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/dump.h b/src/dump.h index fb6627a2b3..351365fa0e 100644 --- a/src/dump.h +++ b/src/dump.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/dump_atom.h b/src/dump_atom.h index 47c2e0699b..5d95cff7b9 100644 --- a/src/dump_atom.h +++ b/src/dump_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/dump_cfg.h b/src/dump_cfg.h index 3a51bc8dd6..f42cbf4611 100644 --- a/src/dump_cfg.h +++ b/src/dump_cfg.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/dump_custom.h b/src/dump_custom.h index 2677f21dae..f8890c036a 100644 --- a/src/dump_custom.h +++ b/src/dump_custom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/dump_dcd.h b/src/dump_dcd.h index 3f59490b11..7b32b8f17c 100644 --- a/src/dump_dcd.h +++ b/src/dump_dcd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/dump_deprecated.h b/src/dump_deprecated.h index 51235ba4e4..7b2f35728f 100644 --- a/src/dump_deprecated.h +++ b/src/dump_deprecated.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/dump_image.h b/src/dump_image.h index fb560e252d..528aa9a8f7 100644 --- a/src/dump_image.h +++ b/src/dump_image.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/dump_local.h b/src/dump_local.h index 80f0692bb0..470f37a99c 100644 --- a/src/dump_local.h +++ b/src/dump_local.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/dump_movie.h b/src/dump_movie.h index 78c05bdef4..e65d11cbc4 100644 --- a/src/dump_movie.h +++ b/src/dump_movie.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/dump_xyz.h b/src/dump_xyz.h index 80719f6a84..1733ce3c48 100644 --- a/src/dump_xyz.h +++ b/src/dump_xyz.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/error.h b/src/error.h index dedebc4148..169ed4c6dd 100644 --- a/src/error.h +++ b/src/error.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/exceptions.h b/src/exceptions.h index db17a6526a..53d49b6fde 100644 --- a/src/exceptions.h +++ b/src/exceptions.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/file_writer.h b/src/file_writer.h index 02eef6ad70..0a18bbd1f7 100644 --- a/src/file_writer.h +++ b/src/file_writer.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/finish.h b/src/finish.h index dc69d41eb8..08ee4e571a 100644 --- a/src/finish.h +++ b/src/finish.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix.h b/src/fix.h index 31add74ee4..c8e5d0900e 100644 --- a/src/fix.h +++ b/src/fix.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_adapt.h b/src/fix_adapt.h index 1872e8b3a0..18e1837160 100644 --- a/src/fix_adapt.h +++ b/src/fix_adapt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_addforce.h b/src/fix_addforce.h index f06ed5ed4c..da7890bf6e 100644 --- a/src/fix_addforce.h +++ b/src/fix_addforce.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_ave_atom.h b/src/fix_ave_atom.h index 42aa282d53..a24da0878e 100644 --- a/src/fix_ave_atom.h +++ b/src/fix_ave_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_ave_chunk.h b/src/fix_ave_chunk.h index debab13165..09424f21c7 100644 --- a/src/fix_ave_chunk.h +++ b/src/fix_ave_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_ave_correlate.h b/src/fix_ave_correlate.h index 05fd6b6576..3a44ed141a 100644 --- a/src/fix_ave_correlate.h +++ b/src/fix_ave_correlate.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_ave_histo.h b/src/fix_ave_histo.h index 35bdfcfa7f..52c42a52e7 100644 --- a/src/fix_ave_histo.h +++ b/src/fix_ave_histo.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_ave_histo_weight.h b/src/fix_ave_histo_weight.h index 6ec3ba5721..f7b54204bb 100644 --- a/src/fix_ave_histo_weight.h +++ b/src/fix_ave_histo_weight.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h index 01228f9e55..a1658e0037 100644 --- a/src/fix_ave_time.h +++ b/src/fix_ave_time.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_aveforce.h b/src/fix_aveforce.h index a6228be7df..0c6c28224f 100644 --- a/src/fix_aveforce.h +++ b/src/fix_aveforce.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_balance.h b/src/fix_balance.h index 76cbea258a..588ce9892f 100644 --- a/src/fix_balance.h +++ b/src/fix_balance.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_box_relax.h b/src/fix_box_relax.h index 874fa169b0..19fa2f8db5 100644 --- a/src/fix_box_relax.h +++ b/src/fix_box_relax.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_controller.h b/src/fix_controller.h index 7431cb16d2..1c98b3bbf9 100644 --- a/src/fix_controller.h +++ b/src/fix_controller.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_deform.h b/src/fix_deform.h index 7f70c3a3d2..ebec11a57a 100644 --- a/src/fix_deform.h +++ b/src/fix_deform.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_deprecated.h b/src/fix_deprecated.h index a7267be04b..aa2bcad6c2 100644 --- a/src/fix_deprecated.h +++ b/src/fix_deprecated.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_drag.h b/src/fix_drag.h index fa444a4b35..ff4bae1a66 100644 --- a/src/fix_drag.h +++ b/src/fix_drag.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_dt_reset.h b/src/fix_dt_reset.h index 6df6913895..54638d32aa 100644 --- a/src/fix_dt_reset.h +++ b/src/fix_dt_reset.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_dummy.h b/src/fix_dummy.h index ea8ce97c3a..485d676bb5 100644 --- a/src/fix_dummy.h +++ b/src/fix_dummy.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_enforce2d.h b/src/fix_enforce2d.h index a3f79309dc..6cb0dada35 100644 --- a/src/fix_enforce2d.h +++ b/src/fix_enforce2d.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_external.h b/src/fix_external.h index 1485e0a60b..33da5ea526 100644 --- a/src/fix_external.h +++ b/src/fix_external.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_gravity.h b/src/fix_gravity.h index ba6a61ee0d..f1b1995ae4 100644 --- a/src/fix_gravity.h +++ b/src/fix_gravity.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_group.h b/src/fix_group.h index f3fecac316..9e2dd370bc 100644 --- a/src/fix_group.h +++ b/src/fix_group.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_halt.h b/src/fix_halt.h index ae1b8aeda7..67f8be6d3c 100644 --- a/src/fix_halt.h +++ b/src/fix_halt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_heat.h b/src/fix_heat.h index a5064c5947..31594e7de9 100644 --- a/src/fix_heat.h +++ b/src/fix_heat.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_indent.h b/src/fix_indent.h index c3a8882734..9cf833cb54 100644 --- a/src/fix_indent.h +++ b/src/fix_indent.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_langevin.h b/src/fix_langevin.h index 868b71a44d..8d787fcd86 100644 --- a/src/fix_langevin.h +++ b/src/fix_langevin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_lineforce.h b/src/fix_lineforce.h index 80e1cd2961..0d56743047 100644 --- a/src/fix_lineforce.h +++ b/src/fix_lineforce.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_minimize.h b/src/fix_minimize.h index 615eb6a095..6b9aaa7936 100644 --- a/src/fix_minimize.h +++ b/src/fix_minimize.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_momentum.h b/src/fix_momentum.h index 6e17f75a7f..1c0de195d4 100644 --- a/src/fix_momentum.h +++ b/src/fix_momentum.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_move.h b/src/fix_move.h index 740b051be0..67b50ec3fa 100644 --- a/src/fix_move.h +++ b/src/fix_move.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_neigh_history.h b/src/fix_neigh_history.h index 2cbdcef97a..57391cfa9a 100644 --- a/src/fix_neigh_history.h +++ b/src/fix_neigh_history.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_nh.h b/src/fix_nh.h index f137ecbe55..f784afefd8 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_nh_sphere.h b/src/fix_nh_sphere.h index 2e0394064e..a4710f2691 100644 --- a/src/fix_nh_sphere.h +++ b/src/fix_nh_sphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_nph.h b/src/fix_nph.h index 45b93c7422..eb20844a1b 100644 --- a/src/fix_nph.h +++ b/src/fix_nph.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_nph_sphere.h b/src/fix_nph_sphere.h index 50000446f2..5bfa68b2fc 100644 --- a/src/fix_nph_sphere.h +++ b/src/fix_nph_sphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_npt.h b/src/fix_npt.h index ea2db9dd26..137c44e8bc 100644 --- a/src/fix_npt.h +++ b/src/fix_npt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_npt_sphere.h b/src/fix_npt_sphere.h index 7481130afe..4d49399cff 100644 --- a/src/fix_npt_sphere.h +++ b/src/fix_npt_sphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_numdiff.h b/src/fix_numdiff.h index e4a2d06afd..e00edf3ee2 100644 --- a/src/fix_numdiff.h +++ b/src/fix_numdiff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_nve.h b/src/fix_nve.h index f4f3c4d4b7..b453c0d2b1 100644 --- a/src/fix_nve.h +++ b/src/fix_nve.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_nve_limit.h b/src/fix_nve_limit.h index aefececd72..5b69d1532c 100644 --- a/src/fix_nve_limit.h +++ b/src/fix_nve_limit.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_nve_noforce.h b/src/fix_nve_noforce.h index 1eacb2b1c2..da4e8c5246 100644 --- a/src/fix_nve_noforce.h +++ b/src/fix_nve_noforce.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_nve_sphere.h b/src/fix_nve_sphere.h index 777360081a..bbd2245b99 100644 --- a/src/fix_nve_sphere.h +++ b/src/fix_nve_sphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_nvt.h b/src/fix_nvt.h index 4903312f8d..ec5707e4ea 100644 --- a/src/fix_nvt.h +++ b/src/fix_nvt.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_nvt_sphere.h b/src/fix_nvt_sphere.h index f1fecc92bf..0c34f89186 100644 --- a/src/fix_nvt_sphere.h +++ b/src/fix_nvt_sphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_planeforce.h b/src/fix_planeforce.h index f507d8465a..f0c3fa3de6 100644 --- a/src/fix_planeforce.h +++ b/src/fix_planeforce.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_press_berendsen.h b/src/fix_press_berendsen.h index 79516ff6bc..1849957c6b 100644 --- a/src/fix_press_berendsen.h +++ b/src/fix_press_berendsen.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_print.h b/src/fix_print.h index 7b5eaa2b62..c806e50385 100644 --- a/src/fix_print.h +++ b/src/fix_print.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_property_atom.h b/src/fix_property_atom.h index 9e0236f61e..68ca40d41e 100644 --- a/src/fix_property_atom.h +++ b/src/fix_property_atom.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_read_restart.h b/src/fix_read_restart.h index 963cde9771..f33d08680a 100644 --- a/src/fix_read_restart.h +++ b/src/fix_read_restart.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_recenter.h b/src/fix_recenter.h index ff6c5e4212..6f0f3f9e13 100644 --- a/src/fix_recenter.h +++ b/src/fix_recenter.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_respa.h b/src/fix_respa.h index 96b5b5531b..62788ea187 100644 --- a/src/fix_respa.h +++ b/src/fix_respa.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_restrain.h b/src/fix_restrain.h index fa78f676e3..63f64ba4bf 100644 --- a/src/fix_restrain.h +++ b/src/fix_restrain.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_setforce.h b/src/fix_setforce.h index eefae562a3..9b479b6cf0 100644 --- a/src/fix_setforce.h +++ b/src/fix_setforce.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_spring.h b/src/fix_spring.h index 1bb551068b..8373dc80b4 100644 --- a/src/fix_spring.h +++ b/src/fix_spring.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_spring_chunk.h b/src/fix_spring_chunk.h index 2955d4b67d..87d798e7f9 100644 --- a/src/fix_spring_chunk.h +++ b/src/fix_spring_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_spring_rg.h b/src/fix_spring_rg.h index a46df0fa75..a19a852d80 100644 --- a/src/fix_spring_rg.h +++ b/src/fix_spring_rg.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_spring_self.h b/src/fix_spring_self.h index 0e5ddda127..a4ad306e8d 100644 --- a/src/fix_spring_self.h +++ b/src/fix_spring_self.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_store.h b/src/fix_store.h index 437c14f0f7..ce0055147a 100644 --- a/src/fix_store.h +++ b/src/fix_store.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_store_force.h b/src/fix_store_force.h index bcbb75a7c8..197fa19c2c 100644 --- a/src/fix_store_force.h +++ b/src/fix_store_force.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_store_state.h b/src/fix_store_state.h index 6397f16ef7..8deb407408 100644 --- a/src/fix_store_state.h +++ b/src/fix_store_state.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_temp_berendsen.h b/src/fix_temp_berendsen.h index 5657b0fd97..625408b1b9 100644 --- a/src/fix_temp_berendsen.h +++ b/src/fix_temp_berendsen.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_temp_csld.h b/src/fix_temp_csld.h index 8937ad43db..d4e5f206d7 100644 --- a/src/fix_temp_csld.h +++ b/src/fix_temp_csld.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_temp_csvr.h b/src/fix_temp_csvr.h index 44d6630525..da61789f6c 100644 --- a/src/fix_temp_csvr.h +++ b/src/fix_temp_csvr.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_temp_rescale.h b/src/fix_temp_rescale.h index b90ca905cb..3f2f0ac174 100644 --- a/src/fix_temp_rescale.h +++ b/src/fix_temp_rescale.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_tmd.h b/src/fix_tmd.h index f23a64a027..c1151734d7 100644 --- a/src/fix_tmd.h +++ b/src/fix_tmd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_vector.h b/src/fix_vector.h index ff962b235b..8859870b71 100644 --- a/src/fix_vector.h +++ b/src/fix_vector.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_viscous.h b/src/fix_viscous.h index 7d42a66cba..7ce58c1c86 100644 --- a/src/fix_viscous.h +++ b/src/fix_viscous.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_wall.h b/src/fix_wall.h index b2bdc2e27c..680fb50eb7 100644 --- a/src/fix_wall.h +++ b/src/fix_wall.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_wall_harmonic.h b/src/fix_wall_harmonic.h index b9efea7400..32a458c1ba 100644 --- a/src/fix_wall_harmonic.h +++ b/src/fix_wall_harmonic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_wall_lj1043.h b/src/fix_wall_lj1043.h index a7fdf5ae18..502fac293d 100644 --- a/src/fix_wall_lj1043.h +++ b/src/fix_wall_lj1043.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_wall_lj126.h b/src/fix_wall_lj126.h index a91ebf6f20..8f833fa077 100644 --- a/src/fix_wall_lj126.h +++ b/src/fix_wall_lj126.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_wall_lj93.h b/src/fix_wall_lj93.h index 3763a02910..1942464997 100644 --- a/src/fix_wall_lj93.h +++ b/src/fix_wall_lj93.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_wall_morse.h b/src/fix_wall_morse.h index a7359e9cde..1106ee85be 100644 --- a/src/fix_wall_morse.h +++ b/src/fix_wall_morse.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_wall_reflect.h b/src/fix_wall_reflect.h index 5abfb6afcf..409cc984ae 100644 --- a/src/fix_wall_reflect.h +++ b/src/fix_wall_reflect.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/fix_wall_region.h b/src/fix_wall_region.h index 663a12b257..36b19bb2ff 100644 --- a/src/fix_wall_region.h +++ b/src/fix_wall_region.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/force.h b/src/force.h index b087b8e187..e2ad12be97 100644 --- a/src/force.h +++ b/src/force.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/group.h b/src/group.h index 37199712c5..17f9b4d564 100644 --- a/src/group.h +++ b/src/group.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/image.h b/src/image.h index 1de455d4bd..5a08430fc9 100644 --- a/src/image.h +++ b/src/image.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/imbalance.h b/src/imbalance.h index 6e4971bf49..cd6ad81389 100644 --- a/src/imbalance.h +++ b/src/imbalance.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/imbalance_group.h b/src/imbalance_group.h index 605706bc55..2eec6eb494 100644 --- a/src/imbalance_group.h +++ b/src/imbalance_group.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/imbalance_neigh.h b/src/imbalance_neigh.h index c0bb35488e..40dc090030 100644 --- a/src/imbalance_neigh.h +++ b/src/imbalance_neigh.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/imbalance_store.h b/src/imbalance_store.h index 935b0aa0bc..2328c61966 100644 --- a/src/imbalance_store.h +++ b/src/imbalance_store.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/imbalance_time.h b/src/imbalance_time.h index 9190426965..3617bf1abd 100644 --- a/src/imbalance_time.h +++ b/src/imbalance_time.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/imbalance_var.h b/src/imbalance_var.h index 2db9a5f170..6c852f00d2 100644 --- a/src/imbalance_var.h +++ b/src/imbalance_var.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/improper.h b/src/improper.h index 1b3c9b6786..baaaee29e5 100644 --- a/src/improper.h +++ b/src/improper.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/improper_deprecated.h b/src/improper_deprecated.h index 04ecfeeb98..6f3e777dcb 100644 --- a/src/improper_deprecated.h +++ b/src/improper_deprecated.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/improper_hybrid.h b/src/improper_hybrid.h index 3e5423b173..f208a7055e 100644 --- a/src/improper_hybrid.h +++ b/src/improper_hybrid.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/improper_zero.h b/src/improper_zero.h index 1a70059070..78c560ba13 100644 --- a/src/improper_zero.h +++ b/src/improper_zero.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/info.h b/src/info.h index 386d38c39f..0aa61ac002 100644 --- a/src/info.h +++ b/src/info.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/input.h b/src/input.h index 59be026640..59369ac7cf 100644 --- a/src/input.h +++ b/src/input.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/integrate.h b/src/integrate.h index c9aa92e097..eb4e3107f9 100644 --- a/src/integrate.h +++ b/src/integrate.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/irregular.h b/src/irregular.h index c6ea7bc691..1a30cb05e7 100644 --- a/src/irregular.h +++ b/src/irregular.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/kspace.h b/src/kspace.h index 4777963d8a..8f081487a6 100644 --- a/src/kspace.h +++ b/src/kspace.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/kspace_deprecated.h b/src/kspace_deprecated.h index ca5205b9e3..ff127ea492 100644 --- a/src/kspace_deprecated.h +++ b/src/kspace_deprecated.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/lammps.h b/src/lammps.h index 553db6597e..b8e084edba 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/lammpsplugin.h b/src/lammpsplugin.h index e544e8bffe..0884ac8f84 100644 --- a/src/lammpsplugin.h +++ b/src/lammpsplugin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/lattice.h b/src/lattice.h index 65cba9f3ca..eae97c3506 100644 --- a/src/lattice.h +++ b/src/lattice.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/library.h b/src/library.h index 8db19f7eb2..4cfaf2ce44 100644 --- a/src/library.h +++ b/src/library.h @@ -1,6 +1,6 @@ /* -*- c -*- ------------------------------------------------------------ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/lmppython.h b/src/lmppython.h index 5254acb4e3..57a77628a7 100644 --- a/src/lmppython.h +++ b/src/lmppython.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/lmprestart.h b/src/lmprestart.h index ecdd272d81..745a1c45d1 100644 --- a/src/lmprestart.h +++ b/src/lmprestart.h @@ -1,6 +1,6 @@ -/* ---------------------------------------------------------------------- +/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/lmptype.h b/src/lmptype.h index 3e6f90f58e..3134624004 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/math_const.h b/src/math_const.h index 53a485bf99..6d24b63569 100644 --- a/src/math_const.h +++ b/src/math_const.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/math_eigen.h b/src/math_eigen.h index 7abf7eb539..4ecc0d6fc9 100644 --- a/src/math_eigen.h +++ b/src/math_eigen.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/math_eigen_impl.h b/src/math_eigen_impl.h index 98027812dd..26867083f7 100644 --- a/src/math_eigen_impl.h +++ b/src/math_eigen_impl.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/math_extra.h b/src/math_extra.h index 767ae3f531..90b8f8a686 100644 --- a/src/math_extra.h +++ b/src/math_extra.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/math_special.h b/src/math_special.h index 59517a2f76..cf435db281 100644 --- a/src/math_special.h +++ b/src/math_special.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/memory.h b/src/memory.h index d85eb64a36..b3ce1aa667 100644 --- a/src/memory.h +++ b/src/memory.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/min.h b/src/min.h index 438a775d16..5d94519e5a 100644 --- a/src/min.h +++ b/src/min.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/min_cg.h b/src/min_cg.h index bf199408e3..269726f803 100644 --- a/src/min_cg.h +++ b/src/min_cg.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/min_fire.h b/src/min_fire.h index 79e5cb7c14..18d64ff310 100644 --- a/src/min_fire.h +++ b/src/min_fire.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/min_fire_old.h b/src/min_fire_old.h index 5d7afaa627..f46ff463b5 100644 --- a/src/min_fire_old.h +++ b/src/min_fire_old.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/min_hftn.h b/src/min_hftn.h index 891639e2ac..afdfd005d4 100644 --- a/src/min_hftn.h +++ b/src/min_hftn.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/min_linesearch.h b/src/min_linesearch.h index 27e34fe6eb..ded5eb9871 100644 --- a/src/min_linesearch.h +++ b/src/min_linesearch.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/min_quickmin.h b/src/min_quickmin.h index a4766bbcdc..5697b9e5c9 100644 --- a/src/min_quickmin.h +++ b/src/min_quickmin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/min_sd.h b/src/min_sd.h index 705103b4d2..65fc3cfd8e 100644 --- a/src/min_sd.h +++ b/src/min_sd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/minimize.h b/src/minimize.h index 32d08c5f52..1ea4d3f5ff 100644 --- a/src/minimize.h +++ b/src/minimize.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/modify.h b/src/modify.h index 0f4f7e32d2..c756800b12 100644 --- a/src/modify.h +++ b/src/modify.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/molecule.h b/src/molecule.h index 00b2b123a0..2beab65b4a 100644 --- a/src/molecule.h +++ b/src/molecule.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/mpiio.h b/src/mpiio.h index 03c6ff6744..839d748f9f 100644 --- a/src/mpiio.h +++ b/src/mpiio.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/my_page.h b/src/my_page.h index 0e4375ed7f..d9617d5213 100644 --- a/src/my_page.h +++ b/src/my_page.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/my_pool_chunk.h b/src/my_pool_chunk.h index a9bcbd3e80..cfd4a9fa7b 100644 --- a/src/my_pool_chunk.h +++ b/src/my_pool_chunk.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nbin.h b/src/nbin.h index 4bfe579514..7bd5414315 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nbin_standard.h b/src/nbin_standard.h index 14b587c24c..1116653050 100644 --- a/src/nbin_standard.h +++ b/src/nbin_standard.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/neigh_list.h b/src/neigh_list.h index ad8e104f2a..88d86aaffd 100644 --- a/src/neigh_list.h +++ b/src/neigh_list.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/neigh_request.h b/src/neigh_request.h index 55fb533171..c58c17b4c5 100644 --- a/src/neigh_request.h +++ b/src/neigh_request.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/neighbor.h b/src/neighbor.h index 0babfae9ef..0dd809bcdb 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair.h b/src/npair.h index ec75042302..54132e6685 100644 --- a/src/npair.h +++ b/src/npair.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_copy.h b/src/npair_copy.h index 62467c2d20..2214ad754d 100644 --- a/src/npair_copy.h +++ b/src/npair_copy.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_full_bin.h b/src/npair_full_bin.h index 6dd9d2d94e..f744a9f227 100644 --- a/src/npair_full_bin.h +++ b/src/npair_full_bin.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_full_bin_atomonly.h b/src/npair_full_bin_atomonly.h index 804637b51e..6f4e7ce6e2 100644 --- a/src/npair_full_bin_atomonly.h +++ b/src/npair_full_bin_atomonly.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_full_bin_ghost.h b/src/npair_full_bin_ghost.h index c7ea139c23..f115875ae0 100644 --- a/src/npair_full_bin_ghost.h +++ b/src/npair_full_bin_ghost.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_full_multi.h b/src/npair_full_multi.h index 481a673060..0f5079f5e8 100644 --- a/src/npair_full_multi.h +++ b/src/npair_full_multi.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_full_nsq.h b/src/npair_full_nsq.h index 95623d65d4..c6b4fabc83 100644 --- a/src/npair_full_nsq.h +++ b/src/npair_full_nsq.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_full_nsq_ghost.h b/src/npair_full_nsq_ghost.h index 8489221f8c..16ecb4e0aa 100644 --- a/src/npair_full_nsq_ghost.h +++ b/src/npair_full_nsq_ghost.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_bin_atomonly_newton.h b/src/npair_half_bin_atomonly_newton.h index ad2e955dba..7388fc8674 100644 --- a/src/npair_half_bin_atomonly_newton.h +++ b/src/npair_half_bin_atomonly_newton.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_bin_newtoff.h b/src/npair_half_bin_newtoff.h index f6c14d9300..ba10094917 100644 --- a/src/npair_half_bin_newtoff.h +++ b/src/npair_half_bin_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_bin_newtoff_ghost.h b/src/npair_half_bin_newtoff_ghost.h index 02c19d469a..b0b1e2dd58 100644 --- a/src/npair_half_bin_newtoff_ghost.h +++ b/src/npair_half_bin_newtoff_ghost.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_bin_newton.h b/src/npair_half_bin_newton.h index 57b1267019..b1bec64e6b 100644 --- a/src/npair_half_bin_newton.h +++ b/src/npair_half_bin_newton.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_bin_newton_tri.h b/src/npair_half_bin_newton_tri.h index 56c5180cc7..f1fe9a47f7 100644 --- a/src/npair_half_bin_newton_tri.h +++ b/src/npair_half_bin_newton_tri.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_multi_newtoff.h b/src/npair_half_multi_newtoff.h index 593e2c1d9d..9341e69fb4 100644 --- a/src/npair_half_multi_newtoff.h +++ b/src/npair_half_multi_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_multi_newton.h b/src/npair_half_multi_newton.h index 427b771780..3186781357 100644 --- a/src/npair_half_multi_newton.h +++ b/src/npair_half_multi_newton.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_multi_newton_tri.h b/src/npair_half_multi_newton_tri.h index 6fe7577259..d0967af231 100644 --- a/src/npair_half_multi_newton_tri.h +++ b/src/npair_half_multi_newton_tri.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_nsq_newtoff.h b/src/npair_half_nsq_newtoff.h index 6904d602bd..09d177c503 100644 --- a/src/npair_half_nsq_newtoff.h +++ b/src/npair_half_nsq_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_nsq_newtoff_ghost.h b/src/npair_half_nsq_newtoff_ghost.h index 75afa9f7f5..2ccf23e586 100644 --- a/src/npair_half_nsq_newtoff_ghost.h +++ b/src/npair_half_nsq_newtoff_ghost.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_nsq_newton.h b/src/npair_half_nsq_newton.h index 60bd2f89d0..82a786b91e 100644 --- a/src/npair_half_nsq_newton.h +++ b/src/npair_half_nsq_newton.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_respa_bin_newtoff.h b/src/npair_half_respa_bin_newtoff.h index fa48f84ad7..afa528ec93 100644 --- a/src/npair_half_respa_bin_newtoff.h +++ b/src/npair_half_respa_bin_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_respa_bin_newton.h b/src/npair_half_respa_bin_newton.h index d74a653a24..43550d5ad6 100644 --- a/src/npair_half_respa_bin_newton.h +++ b/src/npair_half_respa_bin_newton.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_respa_bin_newton_tri.h b/src/npair_half_respa_bin_newton_tri.h index 44c8313609..0a1c6ec48e 100644 --- a/src/npair_half_respa_bin_newton_tri.h +++ b/src/npair_half_respa_bin_newton_tri.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_respa_nsq_newtoff.h b/src/npair_half_respa_nsq_newtoff.h index ffa7a5a6d5..b8667d0e8b 100644 --- a/src/npair_half_respa_nsq_newtoff.h +++ b/src/npair_half_respa_nsq_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_respa_nsq_newton.h b/src/npair_half_respa_nsq_newton.h index 45a9a9753f..80d038b565 100644 --- a/src/npair_half_respa_nsq_newton.h +++ b/src/npair_half_respa_nsq_newton.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_size_bin_newtoff.h b/src/npair_half_size_bin_newtoff.h index b874c6654c..02d021c4f8 100644 --- a/src/npair_half_size_bin_newtoff.h +++ b/src/npair_half_size_bin_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_size_bin_newton.h b/src/npair_half_size_bin_newton.h index 1e7665aa6b..641cb90d39 100644 --- a/src/npair_half_size_bin_newton.h +++ b/src/npair_half_size_bin_newton.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_size_bin_newton_tri.h b/src/npair_half_size_bin_newton_tri.h index ccf85e8f0d..e4203f5322 100644 --- a/src/npair_half_size_bin_newton_tri.h +++ b/src/npair_half_size_bin_newton_tri.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp index f1bc93de38..e419f59d2f 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_size_multi_newtoff.h b/src/npair_half_size_multi_newtoff.h index f255f9a17d..e8df7f1a1a 100644 --- a/src/npair_half_size_multi_newtoff.h +++ b/src/npair_half_size_multi_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index 22a02899ca..4e8bc267f7 100644 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_size_multi_newton.h b/src/npair_half_size_multi_newton.h index 3e3d6f4180..2bae728057 100644 --- a/src/npair_half_size_multi_newton.h +++ b/src/npair_half_size_multi_newton.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 268ca81f3d..785255f183 100644 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_size_multi_newton_tri.h b/src/npair_half_size_multi_newton_tri.h index 6afe8201a7..6d9be4955b 100644 --- a/src/npair_half_size_multi_newton_tri.h +++ b/src/npair_half_size_multi_newton_tri.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_size_nsq_newtoff.h b/src/npair_half_size_nsq_newtoff.h index 51349a8a5d..1c94c2d22a 100644 --- a/src/npair_half_size_nsq_newtoff.h +++ b/src/npair_half_size_nsq_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_half_size_nsq_newton.h b/src/npair_half_size_nsq_newton.h index 333ff94379..87869d976b 100644 --- a/src/npair_half_size_nsq_newton.h +++ b/src/npair_half_size_nsq_newton.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_halffull_newtoff.h b/src/npair_halffull_newtoff.h index 2f711629be..ec1d2dcdcc 100644 --- a/src/npair_halffull_newtoff.h +++ b/src/npair_halffull_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_halffull_newton.h b/src/npair_halffull_newton.h index dc82225216..7470d5491d 100644 --- a/src/npair_halffull_newton.h +++ b/src/npair_halffull_newton.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_skip.h b/src/npair_skip.h index 5fde8e7039..6e81286646 100644 --- a/src/npair_skip.h +++ b/src/npair_skip.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_skip_respa.h b/src/npair_skip_respa.h index a309d47124..2b04f2b0ee 100644 --- a/src/npair_skip_respa.h +++ b/src/npair_skip_respa.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_skip_size.h b/src/npair_skip_size.h index ae3f77d6ed..61eab9ba4f 100644 --- a/src/npair_skip_size.h +++ b/src/npair_skip_size.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_skip_size_off2on.h b/src/npair_skip_size_off2on.h index 59fc0878ef..4e9649496f 100644 --- a/src/npair_skip_size_off2on.h +++ b/src/npair_skip_size_off2on.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/npair_skip_size_off2on_oneside.h b/src/npair_skip_size_off2on_oneside.h index f7ae2338b7..1b83a97aa1 100644 --- a/src/npair_skip_size_off2on_oneside.h +++ b/src/npair_skip_size_off2on_oneside.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil.h b/src/nstencil.h index 75e678b483..d35035eb90 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_full_bin_2d.h b/src/nstencil_full_bin_2d.h index d85063596f..25fe7a450e 100644 --- a/src/nstencil_full_bin_2d.h +++ b/src/nstencil_full_bin_2d.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_full_bin_3d.h b/src/nstencil_full_bin_3d.h index facddd8ead..674333fc29 100644 --- a/src/nstencil_full_bin_3d.h +++ b/src/nstencil_full_bin_3d.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_full_ghost_bin_2d.h b/src/nstencil_full_ghost_bin_2d.h index 531c7d2eb1..6f6289d0a4 100644 --- a/src/nstencil_full_ghost_bin_2d.h +++ b/src/nstencil_full_ghost_bin_2d.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_full_ghost_bin_3d.h b/src/nstencil_full_ghost_bin_3d.h index ed4ca6c4d6..493c4f7c51 100644 --- a/src/nstencil_full_ghost_bin_3d.h +++ b/src/nstencil_full_ghost_bin_3d.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_full_multi_2d.h b/src/nstencil_full_multi_2d.h index f78eecc55f..4bef4f6349 100644 --- a/src/nstencil_full_multi_2d.h +++ b/src/nstencil_full_multi_2d.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_full_multi_3d.h b/src/nstencil_full_multi_3d.h index 9e3696f5d2..520e33389a 100644 --- a/src/nstencil_full_multi_3d.h +++ b/src/nstencil_full_multi_3d.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_half_bin_2d_newtoff.h b/src/nstencil_half_bin_2d_newtoff.h index 7a350df1bc..2c05a1ecc1 100644 --- a/src/nstencil_half_bin_2d_newtoff.h +++ b/src/nstencil_half_bin_2d_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_half_bin_2d_newton.h b/src/nstencil_half_bin_2d_newton.h index 64bbfc5fe4..4d45321281 100644 --- a/src/nstencil_half_bin_2d_newton.h +++ b/src/nstencil_half_bin_2d_newton.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_half_bin_2d_newton_tri.h b/src/nstencil_half_bin_2d_newton_tri.h index b9926608d7..2c5b13b990 100644 --- a/src/nstencil_half_bin_2d_newton_tri.h +++ b/src/nstencil_half_bin_2d_newton_tri.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_half_bin_3d_newtoff.h b/src/nstencil_half_bin_3d_newtoff.h index d1eac666cc..ea04199acd 100644 --- a/src/nstencil_half_bin_3d_newtoff.h +++ b/src/nstencil_half_bin_3d_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_half_bin_3d_newton.h b/src/nstencil_half_bin_3d_newton.h index 96f19adae1..cd854f6128 100644 --- a/src/nstencil_half_bin_3d_newton.h +++ b/src/nstencil_half_bin_3d_newton.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_half_bin_3d_newton_tri.h b/src/nstencil_half_bin_3d_newton_tri.h index 8c265acb46..9a2e7a31e0 100644 --- a/src/nstencil_half_bin_3d_newton_tri.h +++ b/src/nstencil_half_bin_3d_newton_tri.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_half_ghost_bin_2d_newtoff.h b/src/nstencil_half_ghost_bin_2d_newtoff.h index 3286810c1c..37aee019ba 100644 --- a/src/nstencil_half_ghost_bin_2d_newtoff.h +++ b/src/nstencil_half_ghost_bin_2d_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_half_ghost_bin_3d_newtoff.h b/src/nstencil_half_ghost_bin_3d_newtoff.h index ee58c29342..b22d397290 100644 --- a/src/nstencil_half_ghost_bin_3d_newtoff.h +++ b/src/nstencil_half_ghost_bin_3d_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_half_multi_2d_newtoff.h b/src/nstencil_half_multi_2d_newtoff.h index 5603f37beb..bba992725e 100644 --- a/src/nstencil_half_multi_2d_newtoff.h +++ b/src/nstencil_half_multi_2d_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_half_multi_2d_newton.h b/src/nstencil_half_multi_2d_newton.h index 9ecac4c696..4cba552cf3 100644 --- a/src/nstencil_half_multi_2d_newton.h +++ b/src/nstencil_half_multi_2d_newton.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_half_multi_2d_newton_tri.h b/src/nstencil_half_multi_2d_newton_tri.h index 62d7dfdebf..e129704ae8 100644 --- a/src/nstencil_half_multi_2d_newton_tri.h +++ b/src/nstencil_half_multi_2d_newton_tri.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_half_multi_3d_newtoff.h b/src/nstencil_half_multi_3d_newtoff.h index 99428deb6a..64c42f4e7a 100644 --- a/src/nstencil_half_multi_3d_newtoff.h +++ b/src/nstencil_half_multi_3d_newtoff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_half_multi_3d_newton.h b/src/nstencil_half_multi_3d_newton.h index bbdc7752c6..32642ca8ab 100644 --- a/src/nstencil_half_multi_3d_newton.h +++ b/src/nstencil_half_multi_3d_newton.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/nstencil_half_multi_3d_newton_tri.h b/src/nstencil_half_multi_3d_newton_tri.h index f6866489a4..fb8a957ce9 100644 --- a/src/nstencil_half_multi_3d_newton_tri.h +++ b/src/nstencil_half_multi_3d_newton_tri.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ntopo.h b/src/ntopo.h index 3e4204cead..8a1899d810 100644 --- a/src/ntopo.h +++ b/src/ntopo.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ntopo_angle_all.h b/src/ntopo_angle_all.h index 8b28f6c34c..6962e41c0c 100644 --- a/src/ntopo_angle_all.h +++ b/src/ntopo_angle_all.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ntopo_angle_partial.h b/src/ntopo_angle_partial.h index 03ee7587ca..5b5e3a8552 100644 --- a/src/ntopo_angle_partial.h +++ b/src/ntopo_angle_partial.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ntopo_angle_template.h b/src/ntopo_angle_template.h index 19fee41e80..52ea9ff429 100644 --- a/src/ntopo_angle_template.h +++ b/src/ntopo_angle_template.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ntopo_bond_all.h b/src/ntopo_bond_all.h index 6645cba7a1..73411b6d30 100644 --- a/src/ntopo_bond_all.h +++ b/src/ntopo_bond_all.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ntopo_bond_partial.h b/src/ntopo_bond_partial.h index ec377c76bd..0b4c0c8719 100644 --- a/src/ntopo_bond_partial.h +++ b/src/ntopo_bond_partial.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ntopo_bond_template.h b/src/ntopo_bond_template.h index 8cd02e6629..4b69f927f7 100644 --- a/src/ntopo_bond_template.h +++ b/src/ntopo_bond_template.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ntopo_dihedral_all.h b/src/ntopo_dihedral_all.h index 07dcaf8c9a..67e44ddb02 100644 --- a/src/ntopo_dihedral_all.h +++ b/src/ntopo_dihedral_all.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ntopo_dihedral_partial.h b/src/ntopo_dihedral_partial.h index 70625ed256..d2e47cc526 100644 --- a/src/ntopo_dihedral_partial.h +++ b/src/ntopo_dihedral_partial.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ntopo_dihedral_template.h b/src/ntopo_dihedral_template.h index 83a77f6b58..e3ebb7fa48 100644 --- a/src/ntopo_dihedral_template.h +++ b/src/ntopo_dihedral_template.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ntopo_improper_all.h b/src/ntopo_improper_all.h index 473ada8b53..558c3a190b 100644 --- a/src/ntopo_improper_all.h +++ b/src/ntopo_improper_all.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ntopo_improper_partial.h b/src/ntopo_improper_partial.h index 797dad36e4..417f7bb410 100644 --- a/src/ntopo_improper_partial.h +++ b/src/ntopo_improper_partial.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/ntopo_improper_template.h b/src/ntopo_improper_template.h index f9539c656e..8ddf22ba3b 100644 --- a/src/ntopo_improper_template.h +++ b/src/ntopo_improper_template.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/omp_compat.h b/src/omp_compat.h index 8587548615..5cb40a7c71 100644 --- a/src/omp_compat.h +++ b/src/omp_compat.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2020) Sandia Corporation. Under the terms of Contract diff --git a/src/output.h b/src/output.h index 1af03df228..2f00ff72f0 100644 --- a/src/output.h +++ b/src/output.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pack.h b/src/pack.h index 837c33d14b..d17a8dfa7c 100644 --- a/src/pack.h +++ b/src/pack.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair.h b/src/pair.h index b25ad448eb..aa89f316f6 100644 --- a/src/pair.h +++ b/src/pair.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_beck.h b/src/pair_beck.h index 922dac7507..4cc16c3a2b 100644 --- a/src/pair_beck.h +++ b/src/pair_beck.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_born.h b/src/pair_born.h index f32659817e..7d4c5d229c 100644 --- a/src/pair_born.h +++ b/src/pair_born.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_born_coul_dsf.h b/src/pair_born_coul_dsf.h index c7cfb26094..20f2298ca7 100644 --- a/src/pair_born_coul_dsf.h +++ b/src/pair_born_coul_dsf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_born_coul_wolf.h b/src/pair_born_coul_wolf.h index d097d33a0c..30aa59ec3e 100644 --- a/src/pair_born_coul_wolf.h +++ b/src/pair_born_coul_wolf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_buck.h b/src/pair_buck.h index d74934de82..d60368054d 100644 --- a/src/pair_buck.h +++ b/src/pair_buck.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_buck_coul_cut.h b/src/pair_buck_coul_cut.h index fef8396335..64341f48ab 100644 --- a/src/pair_buck_coul_cut.h +++ b/src/pair_buck_coul_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_coul_cut.h b/src/pair_coul_cut.h index fe44c0d8a4..732cd00f3b 100644 --- a/src/pair_coul_cut.h +++ b/src/pair_coul_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_coul_cut_global.h b/src/pair_coul_cut_global.h index 4b3a8ddbaa..f49700352e 100644 --- a/src/pair_coul_cut_global.h +++ b/src/pair_coul_cut_global.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_coul_debye.h b/src/pair_coul_debye.h index a83fbf3e82..36dd47b9bc 100644 --- a/src/pair_coul_debye.h +++ b/src/pair_coul_debye.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_coul_dsf.h b/src/pair_coul_dsf.h index c74c88ee16..62cdebbc46 100644 --- a/src/pair_coul_dsf.h +++ b/src/pair_coul_dsf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_coul_streitz.h b/src/pair_coul_streitz.h index 12da6afcfe..5da3a77e1d 100644 --- a/src/pair_coul_streitz.h +++ b/src/pair_coul_streitz.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_coul_wolf.h b/src/pair_coul_wolf.h index 89391ffc77..bf98332044 100644 --- a/src/pair_coul_wolf.h +++ b/src/pair_coul_wolf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_deprecated.h b/src/pair_deprecated.h index 029ec5e6d4..8a14e7424d 100644 --- a/src/pair_deprecated.h +++ b/src/pair_deprecated.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_dpd.h b/src/pair_dpd.h index 70deec33fe..755c92f91e 100644 --- a/src/pair_dpd.h +++ b/src/pair_dpd.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_dpd_tstat.h b/src/pair_dpd_tstat.h index 5232b367e3..b214304bc9 100644 --- a/src/pair_dpd_tstat.h +++ b/src/pair_dpd_tstat.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_gauss.h b/src/pair_gauss.h index 0380d1192a..b2802d46d6 100644 --- a/src/pair_gauss.h +++ b/src/pair_gauss.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index ca79163fc2..c9b6081be7 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_hybrid_overlay.h b/src/pair_hybrid_overlay.h index f1514ea079..33ec9dde34 100644 --- a/src/pair_hybrid_overlay.h +++ b/src/pair_hybrid_overlay.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_hybrid_scaled.h b/src/pair_hybrid_scaled.h index 38a031ad84..7a7293d34f 100644 --- a/src/pair_hybrid_scaled.h +++ b/src/pair_hybrid_scaled.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj96_cut.h b/src/pair_lj96_cut.h index 4d6df02127..782c71b85f 100644 --- a/src/pair_lj96_cut.h +++ b/src/pair_lj96_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj_cubic.h b/src/pair_lj_cubic.h index 4b5edf7e97..0ce6701b89 100644 --- a/src/pair_lj_cubic.h +++ b/src/pair_lj_cubic.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj_cubic_const.h b/src/pair_lj_cubic_const.h index 5fc773ac3c..3bf59d122d 100644 --- a/src/pair_lj_cubic_const.h +++ b/src/pair_lj_cubic_const.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj_cut.h b/src/pair_lj_cut.h index 3724685db6..d5d71ba717 100644 --- a/src/pair_lj_cut.h +++ b/src/pair_lj_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj_cut_coul_cut.h b/src/pair_lj_cut_coul_cut.h index dcf556cde7..7c3cef885e 100644 --- a/src/pair_lj_cut_coul_cut.h +++ b/src/pair_lj_cut_coul_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj_cut_coul_debye.h b/src/pair_lj_cut_coul_debye.h index 81a53a2556..04e3540c06 100644 --- a/src/pair_lj_cut_coul_debye.h +++ b/src/pair_lj_cut_coul_debye.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj_cut_coul_dsf.h b/src/pair_lj_cut_coul_dsf.h index 3dfe272777..c6391df692 100644 --- a/src/pair_lj_cut_coul_dsf.h +++ b/src/pair_lj_cut_coul_dsf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj_cut_coul_wolf.h b/src/pair_lj_cut_coul_wolf.h index 3264390ea5..2622a0c702 100644 --- a/src/pair_lj_cut_coul_wolf.h +++ b/src/pair_lj_cut_coul_wolf.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj_expand.h b/src/pair_lj_expand.h index 3a32716003..b42cfb5cef 100644 --- a/src/pair_lj_expand.h +++ b/src/pair_lj_expand.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj_gromacs.h b/src/pair_lj_gromacs.h index c58de220f8..c13f5bc4cc 100644 --- a/src/pair_lj_gromacs.h +++ b/src/pair_lj_gromacs.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj_gromacs_coul_gromacs.h b/src/pair_lj_gromacs_coul_gromacs.h index 85b3051b25..53be705181 100644 --- a/src/pair_lj_gromacs_coul_gromacs.h +++ b/src/pair_lj_gromacs_coul_gromacs.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj_relres.cpp b/src/pair_lj_relres.cpp index 2131907f3a..2f6bba80b5 100644 --- a/src/pair_lj_relres.cpp +++ b/src/pair_lj_relres.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj_relres.h b/src/pair_lj_relres.h index 6265c519fa..7df8275dfd 100644 --- a/src/pair_lj_relres.h +++ b/src/pair_lj_relres.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj_smooth.h b/src/pair_lj_smooth.h index 35d1374de0..dd06d85a85 100644 --- a/src/pair_lj_smooth.h +++ b/src/pair_lj_smooth.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_lj_smooth_linear.h b/src/pair_lj_smooth_linear.h index 7e26a7011e..74b591dbd1 100644 --- a/src/pair_lj_smooth_linear.h +++ b/src/pair_lj_smooth_linear.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_mie_cut.h b/src/pair_mie_cut.h index 9e12438d14..fd381b9beb 100644 --- a/src/pair_mie_cut.h +++ b/src/pair_mie_cut.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_morse.h b/src/pair_morse.h index 881fd6650e..c5cc2ca72a 100644 --- a/src/pair_morse.h +++ b/src/pair_morse.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_soft.h b/src/pair_soft.h index daa106204c..76e7028b03 100644 --- a/src/pair_soft.h +++ b/src/pair_soft.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_table.h b/src/pair_table.h index 4075fc5789..3def325303 100644 --- a/src/pair_table.h +++ b/src/pair_table.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_ufm.h b/src/pair_ufm.h index 492c0886e1..078fe4099e 100644 --- a/src/pair_ufm.h +++ b/src/pair_ufm.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_yukawa.h b/src/pair_yukawa.h index 3222019a0a..0641c6568b 100644 --- a/src/pair_yukawa.h +++ b/src/pair_yukawa.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_zbl.h b/src/pair_zbl.h index 6a16bc7419..98789e7050 100644 --- a/src/pair_zbl.h +++ b/src/pair_zbl.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_zbl_const.h b/src/pair_zbl_const.h index 385657693f..31f05a2e12 100644 --- a/src/pair_zbl_const.h +++ b/src/pair_zbl_const.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pair_zero.h b/src/pair_zero.h index 3af37aedb4..49a8f2bed0 100644 --- a/src/pair_zero.h +++ b/src/pair_zero.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/pointers.h b/src/pointers.h index 5dc1a63078..373d7a64a7 100644 --- a/src/pointers.h +++ b/src/pointers.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/potential_file_reader.h b/src/potential_file_reader.h index 4f69b8f757..ca403bb876 100644 --- a/src/potential_file_reader.h +++ b/src/potential_file_reader.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/procmap.h b/src/procmap.h index 9d83d359d3..f342b7d107 100644 --- a/src/procmap.h +++ b/src/procmap.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/random_mars.h b/src/random_mars.h index 1bcd16b051..e7862d19e4 100644 --- a/src/random_mars.h +++ b/src/random_mars.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/random_park.h b/src/random_park.h index dfa0b24312..e469491b35 100644 --- a/src/random_park.h +++ b/src/random_park.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/rcb.h b/src/rcb.h index a3dc37bb9b..0d7cf0eb4e 100644 --- a/src/rcb.h +++ b/src/rcb.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/read_data.h b/src/read_data.h index 7ccbeebd58..93f6e39feb 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/read_dump.h b/src/read_dump.h index 842b629fa4..df467db583 100644 --- a/src/read_dump.h +++ b/src/read_dump.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/read_restart.h b/src/read_restart.h index fc2a27fa67..51b154bb52 100644 --- a/src/read_restart.h +++ b/src/read_restart.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/reader.h b/src/reader.h index 7b31b666ba..a31fc99531 100644 --- a/src/reader.h +++ b/src/reader.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/reader_native.h b/src/reader_native.h index f34bd094ab..e2f5c04d7f 100644 --- a/src/reader_native.h +++ b/src/reader_native.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/reader_xyz.h b/src/reader_xyz.h index f8b0ebcea1..13cf069bd9 100644 --- a/src/reader_xyz.h +++ b/src/reader_xyz.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/region.h b/src/region.h index 0dce004a5b..54112283a9 100644 --- a/src/region.h +++ b/src/region.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/region_block.h b/src/region_block.h index 7989ddb8af..cfb37185ac 100644 --- a/src/region_block.h +++ b/src/region_block.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/region_cone.h b/src/region_cone.h index 4aa9e568ac..0976749d95 100644 --- a/src/region_cone.h +++ b/src/region_cone.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/region_cylinder.h b/src/region_cylinder.h index 55b4bf3142..332826a855 100644 --- a/src/region_cylinder.h +++ b/src/region_cylinder.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/region_deprecated.h b/src/region_deprecated.h index d7e0d20330..f26a79277c 100644 --- a/src/region_deprecated.h +++ b/src/region_deprecated.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/region_intersect.h b/src/region_intersect.h index 2c4a2f2a0b..dde7c3e1e2 100644 --- a/src/region_intersect.h +++ b/src/region_intersect.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/region_plane.h b/src/region_plane.h index 96b37133dc..67095248e8 100644 --- a/src/region_plane.h +++ b/src/region_plane.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/region_prism.h b/src/region_prism.h index 4b518def74..f5914ba06a 100644 --- a/src/region_prism.h +++ b/src/region_prism.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/region_sphere.h b/src/region_sphere.h index 82bac6a619..4ca385c4ae 100644 --- a/src/region_sphere.h +++ b/src/region_sphere.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/region_union.h b/src/region_union.h index cf481c324c..a87d236afb 100644 --- a/src/region_union.h +++ b/src/region_union.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/replicate.h b/src/replicate.h index b4be578b23..36d1c5ff32 100644 --- a/src/replicate.h +++ b/src/replicate.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/rerun.h b/src/rerun.h index c10ca8780e..46039a4360 100644 --- a/src/rerun.h +++ b/src/rerun.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/reset_atom_ids.h b/src/reset_atom_ids.h index 6c262f2bd8..f22b12b17f 100644 --- a/src/reset_atom_ids.h +++ b/src/reset_atom_ids.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/reset_mol_ids.h b/src/reset_mol_ids.h index 5759cf8b4e..8259acbf40 100644 --- a/src/reset_mol_ids.h +++ b/src/reset_mol_ids.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/respa.h b/src/respa.h index f910f0c666..1076a3602c 100644 --- a/src/respa.h +++ b/src/respa.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/run.h b/src/run.h index 747af6a61c..5557432d93 100644 --- a/src/run.h +++ b/src/run.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/set.h b/src/set.h index 330bd484a3..cc096bd3b0 100644 --- a/src/set.h +++ b/src/set.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/special.h b/src/special.h index 10d2609536..b98beace90 100644 --- a/src/special.h +++ b/src/special.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/suffix.h b/src/suffix.h index 177990eb68..32b2a3ce40 100644 --- a/src/suffix.h +++ b/src/suffix.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/table_file_reader.h b/src/table_file_reader.h index 962ddf4209..b6db23e6f8 100644 --- a/src/table_file_reader.h +++ b/src/table_file_reader.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/text_file_reader.h b/src/text_file_reader.h index 0da21e4581..1b7ca73fed 100644 --- a/src/text_file_reader.h +++ b/src/text_file_reader.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/thermo.h b/src/thermo.h index 90ce41c6e4..427266952b 100644 --- a/src/thermo.h +++ b/src/thermo.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/timer.h b/src/timer.h index a12d04311f..278ac1c65c 100644 --- a/src/timer.h +++ b/src/timer.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/tokenizer.h b/src/tokenizer.h index b3bbf05296..a17ab13d04 100644 --- a/src/tokenizer.h +++ b/src/tokenizer.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/universe.h b/src/universe.h index e37f07930b..aca644ea4c 100644 --- a/src/universe.h +++ b/src/universe.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/update.h b/src/update.h index f2a28619fb..86a9268536 100644 --- a/src/update.h +++ b/src/update.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/utils.h b/src/utils.h index ec4dd6ae85..c87f0b28a9 100644 --- a/src/utils.h +++ b/src/utils.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/variable.h b/src/variable.h index da759ecf6a..2c63790ea9 100644 --- a/src/variable.h +++ b/src/variable.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/velocity.h b/src/velocity.h index d7405f87fd..b86f7a8c32 100644 --- a/src/velocity.h +++ b/src/velocity.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/verlet.h b/src/verlet.h index e71932a861..91b69c2821 100644 --- a/src/verlet.h +++ b/src/verlet.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/write_coeff.h b/src/write_coeff.h index 8815162c48..ddbeb958a1 100644 --- a/src/write_coeff.h +++ b/src/write_coeff.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/write_data.h b/src/write_data.h index cecfaa4800..be13e03dc0 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/write_dump.h b/src/write_dump.h index 763fd12f60..75a8b57fd5 100644 --- a/src/write_dump.h +++ b/src/write_dump.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract diff --git a/src/write_restart.h b/src/write_restart.h index 05f5c45ec6..c04f18d50a 100644 --- a/src/write_restart.h +++ b/src/write_restart.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract From 1ac3991aad39dcd85503de4c273413230c384d61 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 22 Apr 2021 21:37:54 -0400 Subject: [PATCH 0608/1217] Lammps -> LAMMPS --- src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp | 2 +- src/USER-MANIFOLD/fix_nve_manifold_rattle.h | 2 +- src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp | 2 +- src/USER-MANIFOLD/fix_nvt_manifold_rattle.h | 2 +- src/USER-MANIFOLD/manifold_factory.cpp | 2 +- src/USER-MANIFOLD/manifold_factory.h | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index 4b141a3bd1..7c4d9cf942 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -1,5 +1,5 @@ /* ---------------------------------------------------------------------- - Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h index 587dd94896..30886434ec 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h @@ -1,5 +1,5 @@ /* -*- c++ -*- ---------------------------------------------------------- - Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp index 844f99b725..155d2b0842 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp @@ -1,5 +1,5 @@ /* ---------------------------------------------------------------------- - Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h index 1d44192be9..5ffc6af0c0 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h +++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h @@ -1,5 +1,5 @@ /* -*- c++ -*- ---------------------------------------------------------- - Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov diff --git a/src/USER-MANIFOLD/manifold_factory.cpp b/src/USER-MANIFOLD/manifold_factory.cpp index 9cc2c3d24d..43e0029b29 100644 --- a/src/USER-MANIFOLD/manifold_factory.cpp +++ b/src/USER-MANIFOLD/manifold_factory.cpp @@ -1,5 +1,5 @@ /* ---------------------------------------------------------------------- - Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov diff --git a/src/USER-MANIFOLD/manifold_factory.h b/src/USER-MANIFOLD/manifold_factory.h index 400929cef0..61d143feb6 100644 --- a/src/USER-MANIFOLD/manifold_factory.h +++ b/src/USER-MANIFOLD/manifold_factory.h @@ -1,5 +1,5 @@ /* -*- c++ -*- ---------------------------------------------------------- - Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov From 61e931ba31739dafadaf068f87a716246c69569f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 22 Apr 2021 21:38:29 -0400 Subject: [PATCH 0609/1217] add missing LAMMPS header comment --- src/USER-ATC/fix_atc.h | 13 +++++++++++++ src/USER-MANIFOLD/manifold_cylinder.h | 13 +++++++++++++ src/USER-MANIFOLD/manifold_cylinder_dent.h | 13 +++++++++++++ src/USER-MANIFOLD/manifold_dumbbell.h | 13 +++++++++++++ src/USER-MANIFOLD/manifold_ellipsoid.h | 13 +++++++++++++ src/USER-MANIFOLD/manifold_plane.h | 13 +++++++++++++ src/USER-MANIFOLD/manifold_plane_wiggle.h | 13 +++++++++++++ src/USER-MANIFOLD/manifold_sphere.h | 13 +++++++++++++ src/USER-MANIFOLD/manifold_spine.h | 13 +++++++++++++ src/USER-MANIFOLD/manifold_supersphere.h | 13 +++++++++++++ src/USER-MANIFOLD/manifold_thylakoid.h | 13 +++++++++++++ src/USER-MANIFOLD/manifold_thylakoid_shared.h | 13 +++++++++++++ src/USER-MANIFOLD/manifold_torus.h | 13 +++++++++++++ src/lmpwindows.h | 13 +++++++++++++ 14 files changed, 182 insertions(+) diff --git a/src/USER-ATC/fix_atc.h b/src/USER-ATC/fix_atc.h index 5bf26f6eaa..c98ac4b781 100644 --- a/src/USER-ATC/fix_atc.h +++ b/src/USER-ATC/fix_atc.h @@ -1,3 +1,16 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifdef FIX_CLASS FixStyle(atc,FixATC) diff --git a/src/USER-MANIFOLD/manifold_cylinder.h b/src/USER-MANIFOLD/manifold_cylinder.h index 78a1725e5e..10715b2683 100644 --- a/src/USER-MANIFOLD/manifold_cylinder.h +++ b/src/USER-MANIFOLD/manifold_cylinder.h @@ -1,3 +1,16 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef LMP_MANIFOLD_CYLINDER_H #define LMP_MANIFOLD_CYLINDER_H diff --git a/src/USER-MANIFOLD/manifold_cylinder_dent.h b/src/USER-MANIFOLD/manifold_cylinder_dent.h index 04c23d959d..770fa23aef 100644 --- a/src/USER-MANIFOLD/manifold_cylinder_dent.h +++ b/src/USER-MANIFOLD/manifold_cylinder_dent.h @@ -1,3 +1,16 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef LMP_MANIFOLD_CYLINDER_DENT_H #define LMP_MANIFOLD_CYLINDER_DENT_H diff --git a/src/USER-MANIFOLD/manifold_dumbbell.h b/src/USER-MANIFOLD/manifold_dumbbell.h index cb2a1f0d0e..ef6aec6271 100644 --- a/src/USER-MANIFOLD/manifold_dumbbell.h +++ b/src/USER-MANIFOLD/manifold_dumbbell.h @@ -1,3 +1,16 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef LMP_MANIFOLD_DUMBBELL_H #define LMP_MANIFOLD_DUMBBELL_H diff --git a/src/USER-MANIFOLD/manifold_ellipsoid.h b/src/USER-MANIFOLD/manifold_ellipsoid.h index 373bdc8e91..f728a95ff4 100644 --- a/src/USER-MANIFOLD/manifold_ellipsoid.h +++ b/src/USER-MANIFOLD/manifold_ellipsoid.h @@ -1,3 +1,16 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef LMP_MANIFOLD_ELLIPSOID_H #define LMP_MANIFOLD_ELLIPSOID_H diff --git a/src/USER-MANIFOLD/manifold_plane.h b/src/USER-MANIFOLD/manifold_plane.h index 2fa7d6829e..9a45b58c94 100644 --- a/src/USER-MANIFOLD/manifold_plane.h +++ b/src/USER-MANIFOLD/manifold_plane.h @@ -1,3 +1,16 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef LMP_MANIFOLD_PLANE_H #define LMP_MANIFOLD_PLANE_H diff --git a/src/USER-MANIFOLD/manifold_plane_wiggle.h b/src/USER-MANIFOLD/manifold_plane_wiggle.h index c1408d8900..06b55419ae 100644 --- a/src/USER-MANIFOLD/manifold_plane_wiggle.h +++ b/src/USER-MANIFOLD/manifold_plane_wiggle.h @@ -1,3 +1,16 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef LMP_MANIFOLD_PLANE_WIGGLE_H #define LMP_MANIFOLD_PLANE_WIGGLE_H diff --git a/src/USER-MANIFOLD/manifold_sphere.h b/src/USER-MANIFOLD/manifold_sphere.h index a0f7f48c5f..e0a80ab88b 100644 --- a/src/USER-MANIFOLD/manifold_sphere.h +++ b/src/USER-MANIFOLD/manifold_sphere.h @@ -1,3 +1,16 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef LMP_MANIFOLD_SPHERE_H #define LMP_MANIFOLD_SPHERE_H diff --git a/src/USER-MANIFOLD/manifold_spine.h b/src/USER-MANIFOLD/manifold_spine.h index 09b61b8300..1b54ceaa17 100644 --- a/src/USER-MANIFOLD/manifold_spine.h +++ b/src/USER-MANIFOLD/manifold_spine.h @@ -1,3 +1,16 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef LMP_MANIFOLD_SPINE_H #define LMP_MANIFOLD_SPINE_H diff --git a/src/USER-MANIFOLD/manifold_supersphere.h b/src/USER-MANIFOLD/manifold_supersphere.h index 031ec71932..7b9ad2e12c 100644 --- a/src/USER-MANIFOLD/manifold_supersphere.h +++ b/src/USER-MANIFOLD/manifold_supersphere.h @@ -1,3 +1,16 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef LMP_MANIFOLD_SUPERSPHERE_H #define LMP_MANIFOLD_SUPERSPHERE_H diff --git a/src/USER-MANIFOLD/manifold_thylakoid.h b/src/USER-MANIFOLD/manifold_thylakoid.h index 8044d13813..cdd69d05cc 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.h +++ b/src/USER-MANIFOLD/manifold_thylakoid.h @@ -1,3 +1,16 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef LMP_MANIFOLD_THYLAKOID_H #define LMP_MANIFOLD_THYLAKOID_H diff --git a/src/USER-MANIFOLD/manifold_thylakoid_shared.h b/src/USER-MANIFOLD/manifold_thylakoid_shared.h index 1af32cc206..a83603785b 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid_shared.h +++ b/src/USER-MANIFOLD/manifold_thylakoid_shared.h @@ -1,3 +1,16 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef MANIFOLD_THYLAKOID_SHARED_H #define MANIFOLD_THYLAKOID_SHARED_H diff --git a/src/USER-MANIFOLD/manifold_torus.h b/src/USER-MANIFOLD/manifold_torus.h index d7fbc7958b..15dd06c6bf 100644 --- a/src/USER-MANIFOLD/manifold_torus.h +++ b/src/USER-MANIFOLD/manifold_torus.h @@ -1,3 +1,16 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef LMP_MANIFOLD_TORUS_H #define LMP_MANIFOLD_TORUS_H diff --git a/src/lmpwindows.h b/src/lmpwindows.h index 5083f0cbb3..59210f35c3 100644 --- a/src/lmpwindows.h +++ b/src/lmpwindows.h @@ -1,3 +1,16 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #include #if !defined(__MINGW32__) #include "erf.h" From ac9f1fba864ad748a498ceb603c9abc5a372c582 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 22 Apr 2021 21:40:10 -0400 Subject: [PATCH 0610/1217] small fixes --- src/USER-ATC/fix_atc.h | 2 +- src/USER-PLUMED/fix_plumed.cpp | 2 +- src/file_writer.h | 1 - 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/src/USER-ATC/fix_atc.h b/src/USER-ATC/fix_atc.h index c98ac4b781..e810e6bf91 100644 --- a/src/USER-ATC/fix_atc.h +++ b/src/USER-ATC/fix_atc.h @@ -30,7 +30,7 @@ namespace LAMMPS_NS { /** * @class FixATC - * @brief Class for an atom-to-continuum (ATC) Lammps fix. + * @brief Class for an atom-to-continuum (ATC) LAMMPS fix. */ class FixATC : public Fix { diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/USER-PLUMED/fix_plumed.cpp index 8d3cdd5c34..293f4b0556 100644 --- a/src/USER-PLUMED/fix_plumed.cpp +++ b/src/USER-PLUMED/fix_plumed.cpp @@ -419,7 +419,7 @@ void FixPlumed::post_force(int /* vflag */) p->cmd("getBias",&bias); // Pass virial to plumed - // If energy is needed plmd_virial is equal to Lammps' virial + // If energy is needed plmd_virial is equal to LAMMPS' virial // If energy is not needed plmd_virial is initialized to zero // In the first case the virial will be rescaled and an extra term will be added // In the latter case only an extra term will be added diff --git a/src/file_writer.h b/src/file_writer.h index 0a18bbd1f7..f9b4abcb59 100644 --- a/src/file_writer.h +++ b/src/file_writer.h @@ -1,4 +1,3 @@ - /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://lammps.sandia.gov/, Sandia National Laboratories From 78d1c33bbedfb07af12d3c5ce909f1c61506fce6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 22 Apr 2021 21:42:34 -0400 Subject: [PATCH 0611/1217] a few more http://lammps.sandia.gov to https://lammps.sandia.gov updates --- src/MISC/fix_orient_bcc.h | 2 +- src/MISC/fix_orient_fcc.h | 2 +- src/USER-NETCDF/README | 2 +- src/USER-PTM/README | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/MISC/fix_orient_bcc.h b/src/MISC/fix_orient_bcc.h index ea6ee7a7a7..7059e4bbfd 100644 --- a/src/MISC/fix_orient_bcc.h +++ b/src/MISC/fix_orient_bcc.h @@ -110,6 +110,6 @@ E: Fix orient/bcc found self twice The neighbor lists used by fix orient/bcc are messed up. If this error occurs, it is likely a bug, so send an email to the -"developers"_http://lammps.sandia.gov/authors.html. +"developers"_https://lammps.sandia.gov/authors.html. */ diff --git a/src/MISC/fix_orient_fcc.h b/src/MISC/fix_orient_fcc.h index 4819cd09c0..a6ec2d1884 100644 --- a/src/MISC/fix_orient_fcc.h +++ b/src/MISC/fix_orient_fcc.h @@ -110,6 +110,6 @@ E: Fix orient/fcc found self twice The neighbor lists used by fix orient/fcc are messed up. If this error occurs, it is likely a bug, so send an email to the -"developers"_http://lammps.sandia.gov/authors.html. +"developers"_https://lammps.sandia.gov/authors.html. */ diff --git a/src/USER-NETCDF/README b/src/USER-NETCDF/README index 7d7874e5ac..fc2af83529 100644 --- a/src/USER-NETCDF/README +++ b/src/USER-NETCDF/README @@ -9,7 +9,7 @@ on your system. See lib/netcdf/README for additional details. PACKAGE DESCRIPTION ------------------- -This is a LAMMPS (http://lammps.sandia.gov/) dump style for output into a NetCDF +This is a LAMMPS (https://lammps.sandia.gov/) dump style for output into a NetCDF database. The database format follows the AMBER NetCDF trajectory convention (http://ambermd.org/netcdf/nctraj.xhtml), but includes extensions to this convention. These extension are: diff --git a/src/USER-PTM/README b/src/USER-PTM/README index d661fa5ac5..f6165a7881 100644 --- a/src/USER-PTM/README +++ b/src/USER-PTM/README @@ -6,7 +6,7 @@ The method is currently (Fall 2018) included in OVITO, LAMMPS, and ASAP. OVITO PTM documentation: http://www.ovito.org/manual/particles.modifiers.polyhedral_template_matching.html -LAMMPS PTM documentation: http://lammps.sandia.gov/doc/compute_ptm_atom.html +LAMMPS PTM documentation: https://lammps.sandia.gov/doc/compute_ptm_atom.html ASAP PTM documentation: http://wiki.fysik.dtu.dk/asap/Local%20crystalline%20order From ec7d3410f302a7ca9bf713b43310038887db1a76 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 22 Apr 2021 22:26:27 -0400 Subject: [PATCH 0612/1217] add or correct some more LAMMPS header comments --- src/KOKKOS/atom_vec_atomic_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_dpd_kokkos.cpp | 2 +- src/STUBS/mpi.cpp | 8 ++++---- src/USER-MANIFOLD/manifold_cylinder.cpp | 13 +++++++++++++ src/USER-MANIFOLD/manifold_cylinder_dent.cpp | 13 +++++++++++++ src/USER-MANIFOLD/manifold_dumbbell.cpp | 13 +++++++++++++ src/USER-MANIFOLD/manifold_ellipsoid.cpp | 13 +++++++++++++ src/USER-MANIFOLD/manifold_gaussian_bump.cpp | 13 +++++++++++++ src/USER-MANIFOLD/manifold_plane.cpp | 13 +++++++++++++ src/USER-MANIFOLD/manifold_plane_wiggle.cpp | 13 +++++++++++++ src/USER-MANIFOLD/manifold_spine.cpp | 13 +++++++++++++ src/USER-MANIFOLD/manifold_thylakoid.cpp | 13 +++++++++++++ src/USER-MANIFOLD/manifold_thylakoid_shared.cpp | 13 +++++++++++++ src/USER-MANIFOLD/manifold_torus.cpp | 13 +++++++++++++ src/USER-MISC/compute_momentum.cpp | 13 +++++++++++++ src/USER-PHONON/dynamical_matrix.cpp | 13 +++++++++++++ src/USER-PHONON/third_order.cpp | 13 +++++++++++++ src/ntopo_improper_template.cpp | 2 +- 18 files changed, 189 insertions(+), 7 deletions(-) diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index 71452e3634..d370aa1926 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -1,5 +1,5 @@ /* ---------------------------------------------------------------------- - LAMMPS - Large-scale AtomicKokkos/Molecular Massively Parallel Simulator + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 923f734d6e..504712ff0d 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -1,5 +1,5 @@ /* ---------------------------------------------------------------------- - LAMMPS - Large-scale AtomicKokkos/Molecular Massively Parallel Simulator + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov diff --git a/src/STUBS/mpi.cpp b/src/STUBS/mpi.cpp index 38fbbac3af..0e87492118 100644 --- a/src/STUBS/mpi.cpp +++ b/src/STUBS/mpi.cpp @@ -1,6 +1,6 @@ -/* ----------------------------------------------------------------------- - LAMMPS 2003 (July 31) - Molecular Dynamics Simulator - Sandia National Laboratories, www.cs.sandia.gov/~sjplimp/lammps.html +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -9,7 +9,7 @@ the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +------------------------------------------------------------------------- */ /* Single-processor "stub" versions of MPI routines */ diff --git a/src/USER-MANIFOLD/manifold_cylinder.cpp b/src/USER-MANIFOLD/manifold_cylinder.cpp index 28062d7a27..317934a34e 100644 --- a/src/USER-MANIFOLD/manifold_cylinder.cpp +++ b/src/USER-MANIFOLD/manifold_cylinder.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ----------------------------------------------------------------------- */ + #include "manifold_cylinder.h" using namespace LAMMPS_NS; diff --git a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp index 6fe8e3453c..9289fc93a5 100644 --- a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp +++ b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ----------------------------------------------------------------------- */ + #include "manifold_cylinder_dent.h" #include "math_const.h" diff --git a/src/USER-MANIFOLD/manifold_dumbbell.cpp b/src/USER-MANIFOLD/manifold_dumbbell.cpp index c40a5fff9f..af5fdc9edb 100644 --- a/src/USER-MANIFOLD/manifold_dumbbell.cpp +++ b/src/USER-MANIFOLD/manifold_dumbbell.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ----------------------------------------------------------------------- */ + #include "manifold_dumbbell.h" #include diff --git a/src/USER-MANIFOLD/manifold_ellipsoid.cpp b/src/USER-MANIFOLD/manifold_ellipsoid.cpp index d5e7bb146e..ea62b335ef 100644 --- a/src/USER-MANIFOLD/manifold_ellipsoid.cpp +++ b/src/USER-MANIFOLD/manifold_ellipsoid.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ----------------------------------------------------------------------- */ + #include "manifold_ellipsoid.h" using namespace LAMMPS_NS; diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp index 79d0185d1b..4893e86da2 100644 --- a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp +++ b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ----------------------------------------------------------------------- */ + #include "manifold_gaussian_bump.h" #include "comm.h" diff --git a/src/USER-MANIFOLD/manifold_plane.cpp b/src/USER-MANIFOLD/manifold_plane.cpp index 6c3f17393a..b533c27197 100644 --- a/src/USER-MANIFOLD/manifold_plane.cpp +++ b/src/USER-MANIFOLD/manifold_plane.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ----------------------------------------------------------------------- */ + #include "manifold_plane.h" using namespace LAMMPS_NS; diff --git a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp b/src/USER-MANIFOLD/manifold_plane_wiggle.cpp index 983702b6f3..f5e57d5f6f 100644 --- a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp +++ b/src/USER-MANIFOLD/manifold_plane_wiggle.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ----------------------------------------------------------------------- */ + #include "manifold_plane_wiggle.h" #include diff --git a/src/USER-MANIFOLD/manifold_spine.cpp b/src/USER-MANIFOLD/manifold_spine.cpp index 9641f53885..96e0418188 100644 --- a/src/USER-MANIFOLD/manifold_spine.cpp +++ b/src/USER-MANIFOLD/manifold_spine.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ----------------------------------------------------------------------- */ + #include "manifold_spine.h" #include diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp index b7eab17fe1..c8c9fe2721 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ----------------------------------------------------------------------- */ + #include "manifold_thylakoid.h" #include #include "manifold_thylakoid_shared.h" diff --git a/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp b/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp index 29e0ee82e9..fc49e3715e 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ----------------------------------------------------------------------- */ + #include "manifold_thylakoid_shared.h" #include diff --git a/src/USER-MANIFOLD/manifold_torus.cpp b/src/USER-MANIFOLD/manifold_torus.cpp index 4806af5213..1e25a3ffe2 100644 --- a/src/USER-MANIFOLD/manifold_torus.cpp +++ b/src/USER-MANIFOLD/manifold_torus.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ----------------------------------------------------------------------- */ + #include #include "manifold_torus.h" #include "error.h" diff --git a/src/USER-MISC/compute_momentum.cpp b/src/USER-MISC/compute_momentum.cpp index 3015cbe30e..c85457ad63 100644 --- a/src/USER-MISC/compute_momentum.cpp +++ b/src/USER-MISC/compute_momentum.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ----------------------------------------------------------------------- */ + #include "compute_momentum.h" diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp index 0476c734a5..aabf4adfab 100644 --- a/src/USER-PHONON/dynamical_matrix.cpp +++ b/src/USER-PHONON/dynamical_matrix.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ----------------------------------------------------------------------- */ + // // Created by charlie sievers on 6/21/18. // diff --git a/src/USER-PHONON/third_order.cpp b/src/USER-PHONON/third_order.cpp index ebcc682d7a..1cf52d83bb 100644 --- a/src/USER-PHONON/third_order.cpp +++ b/src/USER-PHONON/third_order.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ----------------------------------------------------------------------- */ + // // Created by charlie sievers on 7/5/18. // diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp index 43d8d2be38..5f586148cf 100644 --- a/src/ntopo_improper_template.cpp +++ b/src/ntopo_improper_template.cpp @@ -1,5 +1,5 @@ /* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Templatel Simulator + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov From 7bae94cb49bdc0e4ff6ac8fbeb8d16505ed620e6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 04:39:21 -0400 Subject: [PATCH 0613/1217] fix cut-n-paste bug detected by coverity scan --- src/SPIN/fix_nve_spin.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index c394b943b7..855b82c30e 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -266,7 +266,7 @@ void FixNVESpin::init() // init length of vector of ptrs to precession/spin styles if (nlangspin > 0) { - locklangevinspin = new FixLangevinSpin*[nprecspin]; + locklangevinspin = new FixLangevinSpin*[nlangspin]; } // loop 2: fill vector with ptrs to precession/spin styles From 92cc30e7ba42fd26bc0795626fa5dbf401ed0e0d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 05:13:36 -0400 Subject: [PATCH 0614/1217] correctly determine the number of active pair style instances --- src/SPIN/compute_spin.cpp | 17 ++++++++++------- src/SPIN/fix_nve_spin.cpp | 17 ++++++++++------- src/pair_hybrid.h | 4 +++- 3 files changed, 23 insertions(+), 15 deletions(-) diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp index 9108cd7dfa..26b02aa7c3 100644 --- a/src/SPIN/compute_spin.cpp +++ b/src/SPIN/compute_spin.cpp @@ -82,15 +82,18 @@ void ComputeSpin::init() // loop 1: obtain # of Pairs, and # of Pair/Spin styles - if (force->pair_match("spin",0,0)) { // only one Pair/Spin style - pair = force->pair_match("spin",0,0); - npairs = pair->instance_total; + PairHybrid *hybrid = (PairHybrid *)force->pair_match("^hybrid",0); + if (force->pair_match("^spin",0,0)) { // only one Pair/Spin style + pair = force->pair_match("^spin",0,0); + if (hybrid == nullptr) npairs = 1; + else npairs = hybrid->nstyles; npairspin = 1; - } else if (force->pair_match("spin",0,1)) { // more than one Pair/Spin style - pair = force->pair_match("spin",0,1); - npairs = pair->instance_total; + } else if (force->pair_match("^spin",0,1)) { // more than one Pair/Spin style + pair = force->pair_match("^spin",0,1); + if (hybrid == nullptr) npairs = 1; + else npairs = hybrid->nstyles; for (int i = 0; ipair_match("spin",0,i)) { + if (force->pair_match("^spin",0,i)) { npairspin ++; } } diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 855b82c30e..0c6a19b4ca 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -172,15 +172,18 @@ void FixNVESpin::init() // loop 1: obtain # of Pairs, and # of Pair/Spin styles - if (force->pair_match("spin",0,0)) { // only one Pair/Spin style - pair = force->pair_match("spin",0,0); - npairs = pair->instance_total; + PairHybrid *hybrid = (PairHybrid *)force->pair_match("^hybrid",0); + if (force->pair_match("^spin",0,0)) { // only one Pair/Spin style + pair = force->pair_match("^spin",0,0); + if (hybrid == nullptr) npairs = 1; + else npairs = hybrid->nstyles; npairspin = 1; - } else if (force->pair_match("spin",0,1)) { // more than one Pair/Spin style - pair = force->pair_match("spin",0,1); - npairs = pair->instance_total; + } else if (force->pair_match("^spin",0,1)) { // more than one Pair/Spin style + pair = force->pair_match("^spin",0,1); + if (hybrid == nullptr) npairs = 1; + else npairs = hybrid->nstyles; for (int i = 0; ipair_match("spin",0,i)) { + if (force->pair_match("^spin",0,i)) { npairspin ++; } } diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index ca79163fc2..1279bc04fa 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -25,13 +25,15 @@ PairStyle(hybrid,PairHybrid) namespace LAMMPS_NS { class PairHybrid : public Pair { + friend class ComputeSpin; friend class FixGPU; friend class FixIntel; friend class FixOMP; + friend class FixNVESpin; friend class Force; + friend class Info; friend class Neighbor; friend class Respa; - friend class Info; friend class PairDeprecated; public: PairHybrid(class LAMMPS *); From cbf81a5f9f7a40e6bcb44f0c35f18ad8823afc8f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 05:15:28 -0400 Subject: [PATCH 0615/1217] make detection of styles more specific and still support suffixed versions --- src/SPIN/compute_spin.cpp | 18 ++++++++++-------- src/SPIN/fix_nve_spin.cpp | 33 ++++++++++++++++++--------------- 2 files changed, 28 insertions(+), 23 deletions(-) diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp index 26b02aa7c3..c43e7784b4 100644 --- a/src/SPIN/compute_spin.cpp +++ b/src/SPIN/compute_spin.cpp @@ -23,8 +23,6 @@ #include "compute_spin.h" -#include -#include #include "atom.h" #include "error.h" #include "fix_precession_spin.h" @@ -32,9 +30,13 @@ #include "math_const.h" #include "memory.h" #include "modify.h" +#include "pair_hybrid.h" #include "pair_spin.h" #include "update.h" +#include +#include + using namespace LAMMPS_NS; using namespace MathConst; @@ -110,25 +112,25 @@ void ComputeSpin::init() int count = 0; if (npairspin == 1) { count = 1; - spin_pairs[0] = (PairSpin *) force->pair_match("spin",0,0); + spin_pairs[0] = (PairSpin *) force->pair_match("^spin",0,0); } else if (npairspin > 1) { for (int i = 0; ipair_match("spin",0,i)) { - spin_pairs[count] = (PairSpin *) force->pair_match("spin",0,i); + if (force->pair_match("^spin",0,i)) { + spin_pairs[count] = (PairSpin *) force->pair_match("^spin",0,i); count++; } } } if (count != npairspin) - error->all(FLERR,"Incorrect number of spin pairs"); + error->all(FLERR,"Incorrect number of spin pair styles"); // set pair/spin and long/spin flags if (npairspin >= 1) pair_spin_flag = 1; for (int i = 0; ipair_match("spin/long",0,i)) { + if (force->pair_match("^spin/long",0,i)) { long_spin_flag = 1; } } @@ -137,7 +139,7 @@ void ComputeSpin::init() int iforce; for (iforce = 0; iforce < modify->nfix; iforce++) { - if (strstr(modify->fix[iforce]->style,"precession/spin")) { + if (utils::strmatch(modify->fix[iforce]->style,"^precession/spin")) { precession_spin_flag = 1; lockprecessionspin = (FixPrecessionSpin *) modify->fix[iforce]; } diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 0c6a19b4ca..b340a08c65 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -22,21 +22,24 @@ ------------------------------------------------------------------------- */ #include "fix_nve_spin.h" -#include + #include "atom.h" #include "citeme.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "fix_precession_spin.h" #include "fix_langevin_spin.h" +#include "fix_precession_spin.h" #include "fix_setforce_spin.h" #include "force.h" #include "memory.h" #include "modify.h" +#include "pair_hybrid.h" #include "pair_spin.h" #include "update.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; @@ -200,18 +203,18 @@ void FixNVESpin::init() int count1 = 0; if (npairspin == 1) { count1 = 1; - spin_pairs[0] = (PairSpin *) force->pair_match("spin",0,0); + spin_pairs[0] = (PairSpin *) force->pair_match("^spin",0,0); } else if (npairspin > 1) { for (int i = 0; ipair_match("spin",0,i)) { - spin_pairs[count1] = (PairSpin *) force->pair_match("spin",0,i); + if (force->pair_match("^spin",0,i)) { + spin_pairs[count1] = (PairSpin *) force->pair_match("^spin",0,i); count1++; } } } if (count1 != npairspin) - error->all(FLERR,"Incorrect number of spin pairs"); + error->all(FLERR,"Incorrect number of spin pair styles"); // set pair/spin and long/spin flags @@ -229,7 +232,7 @@ void FixNVESpin::init() int iforce; for (iforce = 0; iforce < modify->nfix; iforce++) { - if (strstr(modify->fix[iforce]->style,"precession/spin")) { + if (utils::strmatch(modify->fix[iforce]->style,"^precession/spin")) { nprecspin++; } } @@ -245,7 +248,7 @@ void FixNVESpin::init() int count2 = 0; if (nprecspin > 0) { for (iforce = 0; iforce < modify->nfix; iforce++) { - if (strstr(modify->fix[iforce]->style,"precession/spin")) { + if (utils::strmatch(modify->fix[iforce]->style,"^precession/spin")) { precession_spin_flag = 1; lockprecessionspin[count2] = (FixPrecessionSpin *) modify->fix[iforce]; count2++; @@ -254,30 +257,30 @@ void FixNVESpin::init() } if (count2 != nprecspin) - error->all(FLERR,"Incorrect number of fix precession/spin"); + error->all(FLERR,"Incorrect number of precession/spin fixes"); // set ptrs for fix langevin/spin styles // loop 1: obtain # of fix langevin/spin styles for (iforce = 0; iforce < modify->nfix; iforce++) { - if (strstr(modify->fix[iforce]->style,"langevin/spin")) { + if (utils::strmatch(modify->fix[iforce]->style,"^langevin/spin")) { nlangspin++; } } - // init length of vector of ptrs to precession/spin styles + // init length of vector of ptrs to langevin/spin styles if (nlangspin > 0) { locklangevinspin = new FixLangevinSpin*[nlangspin]; } - // loop 2: fill vector with ptrs to precession/spin styles + // loop 2: fill vector with ptrs to langevin/spin styles count2 = 0; if (nlangspin > 0) { for (iforce = 0; iforce < modify->nfix; iforce++) { - if (strstr(modify->fix[iforce]->style,"langevin/spin")) { + if (utils::strmatch(modify->fix[iforce]->style,"^langevin/spin")) { maglangevin_flag = 1; locklangevinspin[count2] = (FixLangevinSpin *) modify->fix[iforce]; count2++; @@ -286,12 +289,12 @@ void FixNVESpin::init() } if (count2 != nlangspin) - error->all(FLERR,"Incorrect number of fix precession/spin"); + error->all(FLERR,"Incorrect number of langevin/spin fixes"); // ptrs FixSetForceSpin classes for (iforce = 0; iforce < modify->nfix; iforce++) { - if (strstr(modify->fix[iforce]->style,"setforce/spin")) { + if (utils::strmatch(modify->fix[iforce]->style,"^setforce/spin")) { setforce_spin_flag = 1; locksetforcespin = (FixSetForceSpin *) modify->fix[iforce]; } From a438c2bc7bf4d295b37861afc72c510bb49850a0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 05:43:03 -0400 Subject: [PATCH 0616/1217] tweak unit test YAML epsilon values for GPU mixed precision tests to pass --- unittest/force-styles/tests/atomic-pair-beck.yaml | 2 +- unittest/force-styles/tests/atomic-pair-table_bitmap.yaml | 2 +- unittest/force-styles/tests/atomic-pair-table_linear.yaml | 2 +- unittest/force-styles/tests/atomic-pair-table_spline.yaml | 2 +- unittest/force-styles/tests/manybody-pair-tersoff.yaml | 2 +- .../force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml | 2 +- unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml | 2 +- unittest/force-styles/tests/mol-pair-lj_cut_coul_cut.yaml | 2 +- unittest/force-styles/tests/mol-pair-lj_expand.yaml | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/unittest/force-styles/tests/atomic-pair-beck.yaml b/unittest/force-styles/tests/atomic-pair-beck.yaml index 3faebc561b..5416d2eb4f 100644 --- a/unittest/force-styles/tests/atomic-pair-beck.yaml +++ b/unittest/force-styles/tests/atomic-pair-beck.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:59 2021 -epsilon: 5e-13 +epsilon: 2e-12 prerequisites: ! | pair beck pre_commands: ! "" diff --git a/unittest/force-styles/tests/atomic-pair-table_bitmap.yaml b/unittest/force-styles/tests/atomic-pair-table_bitmap.yaml index c67ff58bf8..e9df0744c6 100644 --- a/unittest/force-styles/tests/atomic-pair-table_bitmap.yaml +++ b/unittest/force-styles/tests/atomic-pair-table_bitmap.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:09 2021 -epsilon: 5e-13 +epsilon: 2e-12 prerequisites: ! | pair table pre_commands: ! "" diff --git a/unittest/force-styles/tests/atomic-pair-table_linear.yaml b/unittest/force-styles/tests/atomic-pair-table_linear.yaml index bb7f3959e0..2a0e88e8ca 100644 --- a/unittest/force-styles/tests/atomic-pair-table_linear.yaml +++ b/unittest/force-styles/tests/atomic-pair-table_linear.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:10 2021 -epsilon: 5e-13 +epsilon: 2e-12 prerequisites: ! | pair table pre_commands: ! "" diff --git a/unittest/force-styles/tests/atomic-pair-table_spline.yaml b/unittest/force-styles/tests/atomic-pair-table_spline.yaml index 276dae27c2..9fce2192a5 100644 --- a/unittest/force-styles/tests/atomic-pair-table_spline.yaml +++ b/unittest/force-styles/tests/atomic-pair-table_spline.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:10 2021 -epsilon: 5e-13 +epsilon: 2e-12 prerequisites: ! | pair table pre_commands: ! "" diff --git a/unittest/force-styles/tests/manybody-pair-tersoff.yaml b/unittest/force-styles/tests/manybody-pair-tersoff.yaml index 366810b84e..8ebf41524e 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:20 2021 -epsilon: 5e-13 +epsilon: 1e-11 prerequisites: ! | pair tersoff pre_commands: ! | diff --git a/unittest/force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml b/unittest/force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml index a630f67ef8..2580778581 100644 --- a/unittest/force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml +++ b/unittest/force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:20 2021 -epsilon: 1e-12 +epsilon: 2e-11 skip_tests: intel prerequisites: ! | pair tersoff/mod/c diff --git a/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml b/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml index 4aeae6cd1b..c590c10dc7 100644 --- a/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml +++ b/unittest/force-styles/tests/mol-pair-hybrid-overlay.yaml @@ -1,7 +1,7 @@ --- lammps_version: 8 Apr 2021 date_generated: Mon Apr 19 08:49:07 2021 -epsilon: 7.5e-14 +epsilon: 1.5e-13 prerequisites: ! | atom full pair lj/cut diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_cut.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_cut.yaml index 23ee5a4b93..c08d9cf059 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_cut.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:48 2021 -epsilon: 1e-13 +epsilon: 2e-13 prerequisites: ! | atom full pair lj/cut/coul/cut diff --git a/unittest/force-styles/tests/mol-pair-lj_expand.yaml b/unittest/force-styles/tests/mol-pair-lj_expand.yaml index 7f7a73df55..fd0d04a6e2 100644 --- a/unittest/force-styles/tests/mol-pair-lj_expand.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_expand.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:08:50 2021 -epsilon: 1e-13 +epsilon: 5e-13 prerequisites: ! | atom full pair lj/expand From 62f7e9731690fcd7c0b5bf2b5d715a19cde917be Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 23 Apr 2021 14:39:55 +0200 Subject: [PATCH 0617/1217] rename pair_styles --- src/USER-DPDEXT/pair_dpd_ext.h | 2 +- ...d_tstat_ext.cpp => pair_dpd_ext_tstat.cpp} | 22 +++++++++---------- ...r_dpd_tstat_ext.h => pair_dpd_ext_tstat.h} | 12 +++++----- 3 files changed, 18 insertions(+), 18 deletions(-) rename src/USER-DPDEXT/{pair_dpd_tstat_ext.cpp => pair_dpd_ext_tstat.cpp} (95%) rename src/USER-DPDEXT/{pair_dpd_tstat_ext.h => pair_dpd_ext_tstat.h} (86%) diff --git a/src/USER-DPDEXT/pair_dpd_ext.h b/src/USER-DPDEXT/pair_dpd_ext.h index e85c3451c5..fabb95b773 100644 --- a/src/USER-DPDEXT/pair_dpd_ext.h +++ b/src/USER-DPDEXT/pair_dpd_ext.h @@ -13,7 +13,7 @@ #ifdef PAIR_CLASS -PairStyle(dpdext,PairDPDExt) +PairStyle(dpd/ext,PairDPDExt) #else diff --git a/src/USER-DPDEXT/pair_dpd_tstat_ext.cpp b/src/USER-DPDEXT/pair_dpd_ext_tstat.cpp similarity index 95% rename from src/USER-DPDEXT/pair_dpd_tstat_ext.cpp rename to src/USER-DPDEXT/pair_dpd_ext_tstat.cpp index bfd10c1374..5449ca7358 100644 --- a/src/USER-DPDEXT/pair_dpd_tstat_ext.cpp +++ b/src/USER-DPDEXT/pair_dpd_ext_tstat.cpp @@ -15,7 +15,7 @@ Contributing authors: Martin Svoboda (ICPF, UJEP), Martin Lísal (ICPF, UJEP) ------------------------------------------------------------------------- */ -#include "pair_dpd_tstat_ext.h" +#include "pair_dpd_ext_tstat.h" #include #include "atom.h" @@ -33,7 +33,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairDPDTstatExt::PairDPDTstatExt(LAMMPS *lmp) : PairDPDExt(lmp) +PairDPDExtTstat::PairDPDExtTstat(LAMMPS *lmp) : PairDPDExt(lmp) { single_enable = 0; writedata = 1; @@ -41,7 +41,7 @@ PairDPDTstatExt::PairDPDTstatExt(LAMMPS *lmp) : PairDPDExt(lmp) /* ---------------------------------------------------------------------- */ -void PairDPDTstatExt::compute(int eflag, int vflag) +void PairDPDExtTstat::compute(int eflag, int vflag) { int i,j,ii,jj,inum,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,fpairx,fpairy,fpairz,fpair; @@ -190,7 +190,7 @@ void PairDPDTstatExt::compute(int eflag, int vflag) global settings ------------------------------------------------------------------------- */ -void PairDPDTstatExt::settings(int narg, char **arg) +void PairDPDExtTstat::settings(int narg, char **arg) { if (narg != 4) error->all(FLERR,"Illegal pair_style command"); @@ -221,7 +221,7 @@ void PairDPDTstatExt::settings(int narg, char **arg) set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void PairDPDTstatExt::coeff(int narg, char **arg) +void PairDPDExtTstat::coeff(int narg, char **arg) { if (narg < 6 || narg > 7) error->all(FLERR,"Incorrect args for pair coefficients"); @@ -261,7 +261,7 @@ void PairDPDTstatExt::coeff(int narg, char **arg) proc 0 writes to restart file ------------------------------------------------------------------------- */ -void PairDPDTstatExt::write_restart(FILE *fp) +void PairDPDExtTstat::write_restart(FILE *fp) { write_restart_settings(fp); @@ -283,7 +283,7 @@ void PairDPDTstatExt::write_restart(FILE *fp) proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ -void PairDPDTstatExt::read_restart(FILE *fp) +void PairDPDExtTstat::read_restart(FILE *fp) { read_restart_settings(fp); @@ -316,7 +316,7 @@ void PairDPDTstatExt::read_restart(FILE *fp) proc 0 writes to restart file ------------------------------------------------------------------------- */ -void PairDPDTstatExt::write_restart_settings(FILE *fp) +void PairDPDExtTstat::write_restart_settings(FILE *fp) { fwrite(&t_start,sizeof(double),1,fp); fwrite(&t_stop,sizeof(double),1,fp); @@ -329,7 +329,7 @@ void PairDPDTstatExt::write_restart_settings(FILE *fp) proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ -void PairDPDTstatExt::read_restart_settings(FILE *fp) +void PairDPDExtTstat::read_restart_settings(FILE *fp) { if (comm->me == 0) { utils::sfread(FLERR,&t_start,sizeof(double),1,fp,nullptr,error); @@ -357,7 +357,7 @@ void PairDPDTstatExt::read_restart_settings(FILE *fp) proc 0 writes to data file ------------------------------------------------------------------------- */ -void PairDPDTstatExt::write_data(FILE *fp) +void PairDPDExtTstat::write_data(FILE *fp) { for (int i = 1; i <= atom->ntypes; i++) fprintf(fp,"%d %g %g %g %g\n",i,gamma[i][i],gammaT[i][i],ws[i][i],wsT[i][i]); @@ -367,7 +367,7 @@ void PairDPDTstatExt::write_data(FILE *fp) proc 0 writes all pairs to data file ------------------------------------------------------------------------- */ -void PairDPDTstatExt::write_data_all(FILE *fp) +void PairDPDExtTstat::write_data_all(FILE *fp) { for (int i = 1; i <= atom->ntypes; i++) for (int j = i; j <= atom->ntypes; j++) diff --git a/src/USER-DPDEXT/pair_dpd_tstat_ext.h b/src/USER-DPDEXT/pair_dpd_ext_tstat.h similarity index 86% rename from src/USER-DPDEXT/pair_dpd_tstat_ext.h rename to src/USER-DPDEXT/pair_dpd_ext_tstat.h index c8441f90bd..23cdd1d3c7 100644 --- a/src/USER-DPDEXT/pair_dpd_tstat_ext.h +++ b/src/USER-DPDEXT/pair_dpd_ext_tstat.h @@ -13,21 +13,21 @@ #ifdef PAIR_CLASS -PairStyle(dpdext/tstat,PairDPDTstatExt) +PairStyle(dpd/ext/tstat,PairDPDExtTstat) #else -#ifndef LMP_PAIR_DPD_TSTAT_EXT_H -#define LMP_PAIR_DPD_TSTAT_EXT_H +#ifndef LMP_PAIR_DPD_EXT_TSTAT_H +#define LMP_PAIR_DPD_EXT_TSTAT_H #include "pair_dpd_ext.h" namespace LAMMPS_NS { -class PairDPDTstatExt : public PairDPDExt { +class PairDPDExtTstat : public PairDPDExt { public: - PairDPDTstatExt(class LAMMPS *); - ~PairDPDTstatExt() {} + PairDPDExtTstat(class LAMMPS *); + ~PairDPDExtTstat() {} void compute(int, int); void settings(int, char **); void coeff(int, char **); From 2e63d126e3a2b2c5f966bd0abd46a72fe99c3831 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 23 Apr 2021 15:49:11 +0200 Subject: [PATCH 0618/1217] change dir to MISC --- examples/USER/{dpdext => misc/dpd_ext}/README | 0 .../dpd_ext}/dpdext/dpdext.data | 0 .../{dpdext => misc/dpd_ext}/dpdext/in.dpdext | 2 +- .../dpd_ext}/dpdext/log.10Mar21.dpdext.g++.1 | 28 +++++++------- .../dpd_ext}/dpdext/log.10Mar21.dpdext.g++.4 | 30 +++++++-------- .../dpd_ext}/dpdext_tstat/cg_spce.data | 0 .../dpd_ext}/dpdext_tstat/cg_spce_table.pot | 0 .../dpd_ext}/dpdext_tstat/in.cg_spce | 4 +- .../dpdext_tstat/log.10Mar21.dpdext.g++.1 | 38 +++++++++---------- .../dpdext_tstat/log.10Mar21.dpdext.g++.4 | 38 +++++++++---------- src/USER-DPDEXT/README | 10 ----- src/USER-MISC/README | 2 + .../pair_dpd_ext.cpp | 0 src/{USER-DPDEXT => USER-MISC}/pair_dpd_ext.h | 0 .../pair_dpd_ext_tstat.cpp | 0 .../pair_dpd_ext_tstat.h | 0 16 files changed, 72 insertions(+), 80 deletions(-) rename examples/USER/{dpdext => misc/dpd_ext}/README (100%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext/dpdext.data (100%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext/in.dpdext (95%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext/log.10Mar21.dpdext.g++.1 (91%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext/log.10Mar21.dpdext.g++.4 (90%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext_tstat/cg_spce.data (100%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext_tstat/cg_spce_table.pot (100%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext_tstat/in.cg_spce (76%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext_tstat/log.10Mar21.dpdext.g++.1 (91%) rename examples/USER/{dpdext => misc/dpd_ext}/dpdext_tstat/log.10Mar21.dpdext.g++.4 (91%) delete mode 100644 src/USER-DPDEXT/README rename src/{USER-DPDEXT => USER-MISC}/pair_dpd_ext.cpp (100%) rename src/{USER-DPDEXT => USER-MISC}/pair_dpd_ext.h (100%) rename src/{USER-DPDEXT => USER-MISC}/pair_dpd_ext_tstat.cpp (100%) rename src/{USER-DPDEXT => USER-MISC}/pair_dpd_ext_tstat.h (100%) diff --git a/examples/USER/dpdext/README b/examples/USER/misc/dpd_ext/README similarity index 100% rename from examples/USER/dpdext/README rename to examples/USER/misc/dpd_ext/README diff --git a/examples/USER/dpdext/dpdext/dpdext.data b/examples/USER/misc/dpd_ext/dpdext/dpdext.data similarity index 100% rename from examples/USER/dpdext/dpdext/dpdext.data rename to examples/USER/misc/dpd_ext/dpdext/dpdext.data diff --git a/examples/USER/dpdext/dpdext/in.dpdext b/examples/USER/misc/dpd_ext/dpdext/in.dpdext similarity index 95% rename from examples/USER/dpdext/dpdext/in.dpdext rename to examples/USER/misc/dpd_ext/dpdext/in.dpdext index 3101be9a1c..726f3a7b39 100755 --- a/examples/USER/dpdext/dpdext/in.dpdext +++ b/examples/USER/misc/dpd_ext/dpdext/in.dpdext @@ -23,7 +23,7 @@ mass 1 1.0 mass 2 2.0 ### -pair_style dpdext ${T} ${rc} 3854262 +pair_style dpd/ext ${T} ${rc} 3854262 pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD} pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD} diff --git a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 b/examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 similarity index 91% rename from examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 rename to examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 index ef61ed11b8..862aea77af 100644 --- a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 +++ b/examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (10 Mar 2021) +LAMMPS (8 Apr 2021) # DPD Fluid variable T equal 1.0 @@ -34,9 +34,9 @@ mass 1 1.0 mass 2 2.0 ### -pair_style dpdext ${T} ${rc} 3854262 -pair_style dpdext 1 ${rc} 3854262 -pair_style dpdext 1 1 3854262 +pair_style dpd/ext ${T} ${rc} 3854262 +pair_style dpd/ext 1 ${rc} 3854262 +pair_style dpd/ext 1 1 3854262 pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD} pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD} @@ -61,7 +61,7 @@ Neighbor list info ... ghost atom cutoff = 1.52 binsize = 0.76, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair dpdext, perpetual + (1) pair dpd/ext, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton @@ -169,20 +169,20 @@ Step Time Temp Press 49000 490 1.0337198 7.5777833 49500 495 0.94052507 7.3661443 50000 500 0.98527818 7.1746325 -Loop time of 10.2559 on 1 procs for 50000 steps with 200 atoms +Loop time of 9.88248 on 1 procs for 50000 steps with 200 atoms -Performance: 4212216.548 tau/day, 4875.251 timesteps/s -99.5% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 4371371.882 tau/day, 5059.458 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 8.9888 | 8.9888 | 8.9888 | 0.0 | 87.65 -Neigh | 0.832 | 0.832 | 0.832 | 0.0 | 8.11 -Comm | 0.30913 | 0.30913 | 0.30913 | 0.0 | 3.01 -Output | 0.0021966 | 0.0021966 | 0.0021966 | 0.0 | 0.02 -Modify | 0.084161 | 0.084161 | 0.084161 | 0.0 | 0.82 -Other | | 0.03957 | | | 0.39 +Pair | 8.7028 | 8.7028 | 8.7028 | 0.0 | 88.06 +Neigh | 0.73687 | 0.73687 | 0.73687 | 0.0 | 7.46 +Comm | 0.31881 | 0.31881 | 0.31881 | 0.0 | 3.23 +Output | 0.0013947 | 0.0013947 | 0.0013947 | 0.0 | 0.01 +Modify | 0.081394 | 0.081394 | 0.081394 | 0.0 | 0.82 +Other | | 0.04118 | | | 0.42 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 b/examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 similarity index 90% rename from examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 rename to examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 index bbbf47a46c..12b35ecf53 100644 --- a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 +++ b/examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (10 Mar 2021) +LAMMPS (8 Apr 2021) # DPD Fluid variable T equal 1.0 @@ -34,9 +34,9 @@ mass 1 1.0 mass 2 2.0 ### -pair_style dpdext ${T} ${rc} 3854262 -pair_style dpdext 1 ${rc} 3854262 -pair_style dpdext 1 1 3854262 +pair_style dpd/ext ${T} ${rc} 3854262 +pair_style dpd/ext 1 ${rc} 3854262 +pair_style dpd/ext 1 1 3854262 pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD} pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD} @@ -61,7 +61,7 @@ Neighbor list info ... ghost atom cutoff = 1.52 binsize = 0.76, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair dpdext, perpetual + (1) pair dpd/ext, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton @@ -169,20 +169,20 @@ Step Time Temp Press 49000 490 0.9759139 7.4839858 49500 495 0.91538068 7.1780491 50000 500 1.0310634 7.1522794 -Loop time of 9.14414 on 4 procs for 50000 steps with 200 atoms +Loop time of 8.5908 on 4 procs for 50000 steps with 200 atoms -Performance: 4724338.550 tau/day, 5467.984 timesteps/s -96.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 5028633.375 tau/day, 5820.178 timesteps/s +95.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.0824 | 5.212 | 5.3376 | 5.1 | 57.00 -Neigh | 0.49498 | 0.50029 | 0.505 | 0.6 | 5.47 -Comm | 3.1637 | 3.2822 | 3.4143 | 6.3 | 35.89 -Output | 0.0025831 | 0.003088 | 0.004569 | 1.5 | 0.03 -Modify | 0.067261 | 0.068927 | 0.070535 | 0.5 | 0.75 -Other | | 0.07762 | | | 0.85 +Pair | 4.9505 | 5.054 | 5.1885 | 4.1 | 58.83 +Neigh | 0.47025 | 0.47603 | 0.47954 | 0.5 | 5.54 +Comm | 2.7876 | 2.9237 | 3.0336 | 5.5 | 34.03 +Output | 0.0024114 | 0.0029766 | 0.0046443 | 1.8 | 0.03 +Modify | 0.062911 | 0.064188 | 0.065603 | 0.4 | 0.75 +Other | | 0.06992 | | | 0.81 Nlocal: 50.0000 ave 53 max 46 min Histogram: 1 0 0 0 1 0 0 0 1 1 @@ -198,4 +198,4 @@ Dangerous builds = 5000 write_data final.data pair ij System init for write_data ... -Total wall time: 0:00:09 +Total wall time: 0:00:08 diff --git a/examples/USER/dpdext/dpdext_tstat/cg_spce.data b/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data similarity index 100% rename from examples/USER/dpdext/dpdext_tstat/cg_spce.data rename to examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data diff --git a/examples/USER/dpdext/dpdext_tstat/cg_spce_table.pot b/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot similarity index 100% rename from examples/USER/dpdext/dpdext_tstat/cg_spce_table.pot rename to examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot diff --git a/examples/USER/dpdext/dpdext_tstat/in.cg_spce b/examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce similarity index 76% rename from examples/USER/dpdext/dpdext_tstat/in.cg_spce rename to examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce index ea1a3dfcba..b93dc3eec5 100755 --- a/examples/USER/dpdext/dpdext_tstat/in.cg_spce +++ b/examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce @@ -13,10 +13,10 @@ comm_modify vel yes read_data cg_spce.data -pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262 pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc} -pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD} +pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD} timestep 1.0 run_style verlet diff --git a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 b/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 similarity index 91% rename from examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 rename to examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 index 6916a5dd6e..8f75dfa917 100644 --- a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 +++ b/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (10 Mar 2021) +LAMMPS (8 Apr 2021) # Coarse-Grained SPC/E Water variable T equal 300.0 @@ -18,19 +18,19 @@ Reading data file ... 1 by 1 by 1 MPI processor grid reading atoms ... 2180 atoms - read_data CPU = 0.037 seconds + read_data CPU = 0.020 seconds -pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262 -pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 ${T} ${rc} 385262 -pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 ${rc} 385262 -pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 9 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 9 385262 pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc} pair_coeff 1 1 table cg_spce_table.pot VOTCA 9 WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr. Should only be flagged at inflection points (../pair_table.cpp:461) -pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD} -pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 10 +pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD} +pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10 timestep 1.0 run_style verlet @@ -56,7 +56,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard - (2) pair dpdext/tstat, perpetual, copy from (1) + (2) pair dpd/ext/tstat, perpetual, copy from (1) attributes: half, newton on pair build: copy stencil: none @@ -264,20 +264,20 @@ Step Time Temp Press 1980 1980 299.14574 5166.3501 1990 1990 300.07254 10019.769 2000 2000 301.78176 8789.7968 -Loop time of 79.8698 on 1 procs for 2000 steps with 2180 atoms +Loop time of 91.2059 on 1 procs for 2000 steps with 2180 atoms -Performance: 2.164 ns/day, 11.093 hours/ns, 25.041 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.895 ns/day, 12.667 hours/ns, 21.928 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 79.378 | 79.378 | 79.378 | 0.0 | 99.38 -Neigh | 0.22454 | 0.22454 | 0.22454 | 0.0 | 0.28 -Comm | 0.17969 | 0.17969 | 0.17969 | 0.0 | 0.22 -Output | 0.0063846 | 0.0063846 | 0.0063846 | 0.0 | 0.01 -Modify | 0.044496 | 0.044496 | 0.044496 | 0.0 | 0.06 -Other | | 0.03671 | | | 0.05 +Pair | 90.668 | 90.668 | 90.668 | 0.0 | 99.41 +Neigh | 0.23231 | 0.23231 | 0.23231 | 0.0 | 0.25 +Comm | 0.20819 | 0.20819 | 0.20819 | 0.0 | 0.23 +Output | 0.0049558 | 0.0049558 | 0.0049558 | 0.0 | 0.01 +Modify | 0.052906 | 0.052906 | 0.052906 | 0.0 | 0.06 +Other | | 0.03904 | | | 0.04 Nlocal: 2180.00 ave 2180 max 2180 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -290,4 +290,4 @@ Total # of neighbors = 261496 Ave neighs/atom = 119.95229 Neighbor list builds = 25 Dangerous builds = 0 -Total wall time: 0:01:20 +Total wall time: 0:01:31 diff --git a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 b/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4 similarity index 91% rename from examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 rename to examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4 index 890414d580..278aba0687 100644 --- a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 +++ b/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (10 Mar 2021) +LAMMPS (8 Apr 2021) # Coarse-Grained SPC/E Water variable T equal 300.0 @@ -18,19 +18,19 @@ Reading data file ... 1 by 2 by 2 MPI processor grid reading atoms ... 2180 atoms - read_data CPU = 0.012 seconds + read_data CPU = 0.005 seconds -pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262 -pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 ${T} ${rc} 385262 -pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 ${rc} 385262 -pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 9 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 ${T} ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 ${rc} 385262 +pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 9 385262 pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc} pair_coeff 1 1 table cg_spce_table.pot VOTCA 9 WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr. Should only be flagged at inflection points (../pair_table.cpp:461) -pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD} -pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 10 +pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD} +pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10 timestep 1.0 run_style verlet @@ -56,7 +56,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard - (2) pair dpdext/tstat, perpetual, copy from (1) + (2) pair dpd/ext/tstat, perpetual, copy from (1) attributes: half, newton on pair build: copy stencil: none @@ -264,20 +264,20 @@ Step Time Temp Press 1980 1980 297.94119 5615.6403 1990 1990 298.37687 9727.308 2000 2000 296.08394 6400.2746 -Loop time of 40.5503 on 4 procs for 2000 steps with 2180 atoms +Loop time of 41.5171 on 4 procs for 2000 steps with 2180 atoms -Performance: 4.261 ns/day, 5.632 hours/ns, 49.321 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 4.162 ns/day, 5.766 hours/ns, 48.173 timesteps/s +99.5% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 37.953 | 38.022 | 38.132 | 1.1 | 93.77 -Neigh | 0.10585 | 0.10835 | 0.10994 | 0.5 | 0.27 -Comm | 2.2287 | 2.3368 | 2.405 | 4.6 | 5.76 -Output | 0.0072037 | 0.0081832 | 0.011022 | 1.8 | 0.02 -Modify | 0.023132 | 0.024188 | 0.025948 | 0.7 | 0.06 -Other | | 0.05032 | | | 0.12 +Pair | 38.667 | 38.954 | 39.453 | 4.8 | 93.83 +Neigh | 0.10947 | 0.11039 | 0.11153 | 0.3 | 0.27 +Comm | 1.8661 | 2.3644 | 2.652 | 19.6 | 5.70 +Output | 0.0082644 | 0.0094232 | 0.01281 | 2.0 | 0.02 +Modify | 0.024678 | 0.025206 | 0.025888 | 0.3 | 0.06 +Other | | 0.05335 | | | 0.13 Nlocal: 545.000 ave 559 max 531 min Histogram: 1 0 0 0 1 1 0 0 0 1 @@ -290,4 +290,4 @@ Total # of neighbors = 261662 Ave neighs/atom = 120.02844 Neighbor list builds = 26 Dangerous builds = 0 -Total wall time: 0:00:40 +Total wall time: 0:00:41 diff --git a/src/USER-DPDEXT/README b/src/USER-DPDEXT/README deleted file mode 100644 index 73f8d047f8..0000000000 --- a/src/USER-DPDEXT/README +++ /dev/null @@ -1,10 +0,0 @@ -Martin Svoboda (ICPF, UJEP) - svobod.martin@gmail.com -Karel Sindelka (ICPF) - sindelka@icpf.cas.cz -Martin Lisal (ICPF, UJEP) - lisal@icpf.cas.cz - -This package implements a generalised force field for dissipative -particle dynamics (DPD). The extension divides contributions -of dissipative and random forces to parrallel and perpendicular parts. -See the doc pages for "pair_style dpdext" and "pair_style dpdext/tstat". - -There are example scripts for using this package in examples/USER/dpdext. diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 314fe6146e..3e2c8ed000 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -90,6 +90,8 @@ pair_style coul/slater/long, Evangelos Voyiatzis, evoyiatzis at gmail.com, 26 Fe pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11 pair_style e3b, Steven Strong (U Chicago), stevene.strong at gmail dot com, 16 Apr 19 pair_style drip, Mingjian Wen, University of Minnesota, wenxx151 at umn.edu, 17 Apr 19 +pair_style dpd/ext, Martin Svoboda, Karel Sindelka, Martin Lisal, ICPF and UJEP, svobod.martin at gmail dot com, 23 Apr 21 +pair_style dpd/ext/tstat, Martin Svoboda, Karel Sindelka, Martin Lisal, ICPF and UJEP , svobod.martin at gmail dot com, 23 Apr 21 pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11 pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17 pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 diff --git a/src/USER-DPDEXT/pair_dpd_ext.cpp b/src/USER-MISC/pair_dpd_ext.cpp similarity index 100% rename from src/USER-DPDEXT/pair_dpd_ext.cpp rename to src/USER-MISC/pair_dpd_ext.cpp diff --git a/src/USER-DPDEXT/pair_dpd_ext.h b/src/USER-MISC/pair_dpd_ext.h similarity index 100% rename from src/USER-DPDEXT/pair_dpd_ext.h rename to src/USER-MISC/pair_dpd_ext.h diff --git a/src/USER-DPDEXT/pair_dpd_ext_tstat.cpp b/src/USER-MISC/pair_dpd_ext_tstat.cpp similarity index 100% rename from src/USER-DPDEXT/pair_dpd_ext_tstat.cpp rename to src/USER-MISC/pair_dpd_ext_tstat.cpp diff --git a/src/USER-DPDEXT/pair_dpd_ext_tstat.h b/src/USER-MISC/pair_dpd_ext_tstat.h similarity index 100% rename from src/USER-DPDEXT/pair_dpd_ext_tstat.h rename to src/USER-MISC/pair_dpd_ext_tstat.h From 3ac2b369938e24c5dfc081a15bf374235db21d68 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 23 Apr 2021 16:10:00 +0200 Subject: [PATCH 0619/1217] add link to Commands_pair.rst --- doc/src/Commands_pair.rst | 2 ++ examples/USER/misc/dpd_ext/dpdext/dpdext.data | 0 examples/USER/misc/dpd_ext/dpdext/in.dpdext | 0 examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data | 0 examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot | 0 examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce | 0 6 files changed, 2 insertions(+) mode change 100755 => 100644 examples/USER/misc/dpd_ext/dpdext/dpdext.data mode change 100755 => 100644 examples/USER/misc/dpd_ext/dpdext/in.dpdext mode change 100755 => 100644 examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data mode change 100755 => 100644 examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot mode change 100755 => 100644 examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index b91a749364..15126d6d34 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -87,6 +87,8 @@ OPT. * :doc:`coul/wolf/cs ` * :doc:`dpd (gio) ` * :doc:`dpd/fdt ` + * :doc:`dpd/ext ` + * :doc:`dpd/ext/tstat ` * :doc:`dpd/fdt/energy (k) ` * :doc:`dpd/tstat (go) ` * :doc:`dsmc ` diff --git a/examples/USER/misc/dpd_ext/dpdext/dpdext.data b/examples/USER/misc/dpd_ext/dpdext/dpdext.data old mode 100755 new mode 100644 diff --git a/examples/USER/misc/dpd_ext/dpdext/in.dpdext b/examples/USER/misc/dpd_ext/dpdext/in.dpdext old mode 100755 new mode 100644 diff --git a/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data b/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data old mode 100755 new mode 100644 diff --git a/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot b/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot old mode 100755 new mode 100644 diff --git a/examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce b/examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce old mode 100755 new mode 100644 From 8ea5b8c41b76cfd9ad624132621eb21414cca9d5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 11:22:50 -0400 Subject: [PATCH 0620/1217] add false positives for recently added docs --- doc/utils/sphinx-config/false_positives.txt | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index da0617ce91..da69cc4edc 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -101,6 +101,7 @@ anisotropic anisotropies anisotropy ansi +antiferromagnetic antiquewhite Antisymmetrized antisymmetry @@ -2177,6 +2178,7 @@ nimpropers nimpropertypes Nimpropertype Ninteger +NiO Nissila nist nitride @@ -3163,6 +3165,7 @@ th thb thei Theodorou +Theophile Theor thermalization thermalize @@ -3315,6 +3318,7 @@ Uleft uloop Ulomek ulsph +Ultrafast uMech umin Umin @@ -3595,6 +3599,7 @@ ZBL Zc zcm Zeeman +zeeman Zemer Zepeda zflag From 9c21c8e3efc36466d096669056d445ad57659b41 Mon Sep 17 00:00:00 2001 From: kipbarrett Date: Fri, 23 Apr 2021 10:42:26 -0500 Subject: [PATCH 0621/1217] added upstream changes --- cmake/CMakeLists.txt | 862 +++++++++++++++++++++++++++++++++++++++++++ src/Makefile.txt | 443 ++++++++++++++++++++++ 2 files changed, 1305 insertions(+) create mode 100644 cmake/CMakeLists.txt create mode 100644 src/Makefile.txt diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt new file mode 100644 index 0000000000..426d2f76e0 --- /dev/null +++ b/cmake/CMakeLists.txt @@ -0,0 +1,862 @@ +######################################## +# CMake build system +# This file is part of LAMMPS +# Created by Christoph Junghans and Richard Berger +cmake_minimum_required(VERSION 3.10) +# set policy to silence warnings about ignoring _ROOT but use it +if(POLICY CMP0074) + cmake_policy(SET CMP0074 NEW) +endif() +######################################## + +project(lammps CXX) +set(SOVERSION 0) + +get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE) +get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE) + +set(LAMMPS_SOURCE_DIR ${LAMMPS_DIR}/src) +set(LAMMPS_LIB_SOURCE_DIR ${LAMMPS_DIR}/lib) +set(LAMMPS_DOC_DIR ${LAMMPS_DIR}/doc) +set(LAMMPS_TOOLS_DIR ${LAMMPS_DIR}/tools) +set(LAMMPS_PYTHON_DIR ${LAMMPS_DIR}/python) +set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials) + +set(LAMMPS_DOWNLOADS_URL "https://download.lammps.org" CACHE STRING "Base URL for LAMMPS downloads") +set(LAMMPS_POTENTIALS_URL "${LAMMPS_DOWNLOADS_URL}/potentials") +set(LAMMPS_THIRDPARTY_URL "${LAMMPS_DOWNLOADS_URL}/thirdparty") +mark_as_advanced(LAMMPS_DOWNLOADS_URL) + +find_package(Git) + +# by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed +if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) + set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE) +endif() + +# If enabled, no need to use LD_LIBRARY_PATH / DYLD_LIBRARY_PATH when installed +option(LAMMPS_INSTALL_RPATH "Set runtime path for shared libraries linked to LAMMPS binaries" OFF) +if(LAMMPS_INSTALL_RPATH) + set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR}) + set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON) +endif() + +# Cmake modules/macros are in a subdirectory to keep this file cleaner +set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules) + +# make sure LIBRARY_PATH is set if environment variable is set +if(DEFINED ENV{LIBRARY_PATH}) + list(APPEND CMAKE_LIBRARY_PATH "$ENV{LIBRARY_PATH}") + message(STATUS "Appending $ENV{LIBRARY_PATH} to CMAKE_LIBRARY_PATH: ${CMAKE_LIBRARY_PATH}") +endif() + +include(LAMMPSUtils) + +get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h PROJECT_VERSION) + +include(PreventInSourceBuilds) + +if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) + set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) +endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) +string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) + +# check for files auto-generated by make-based buildsystem +# this is fast, so check for it all the time +check_for_autogen_files(${LAMMPS_SOURCE_DIR}) + +###################################################################### +# compiler tests +# these need ot be done early (before further tests). +##################################################################### +include(CheckIncludeFileCXX) + +# set required compiler flags and compiler/CPU arch specific optimizations +if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") + if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4) + set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512") + else() + set(CMAKE_TUNE_DEFAULT "-xHost") + endif() +endif() + +# we require C++11 without extensions +set(CMAKE_CXX_STANDARD 11) +set(CMAKE_CXX_STANDARD_REQUIRED ON) +set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions") + +######################################################################## +# User input options # +######################################################################## +set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically") +mark_as_advanced(LAMMPS_MACHINE) +if(LAMMPS_MACHINE) + set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}") +endif() +set(LAMMPS_BINARY lmp${LAMMPS_MACHINE}) + +option(BUILD_SHARED_LIBS "Build shared library" OFF) +if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg + set(CMAKE_POSITION_INDEPENDENT_CODE ON) +endif() + +option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF) +option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF) + +include(GNUInstallDirs) +file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp) +file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp) +list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES}) +add_library(lammps ${ALL_SOURCES}) +add_executable(lmp ${MAIN_SOURCES}) +target_link_libraries(lmp PRIVATE lammps) +set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY}) +install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR}) + +option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF) + +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE + GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS + PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI + USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK + USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF + USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB + USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH + USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE) + +set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP) + +foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES}) + option(PKG_${PKG} "Build ${PKG} Package" OFF) +endforeach() + +###################################################### +# packages with special compiler needs or external libs +###################################################### +target_include_directories(lammps PUBLIC $) + +if(PKG_USER-ADIOS) + # The search for ADIOS2 must come before MPI because + # it includes its own MPI search with the latest FindMPI.cmake + # script that defines the MPI::MPI_C target + enable_language(C) + find_package(ADIOS2 REQUIRED) + target_link_libraries(lammps PRIVATE adios2::adios2) +endif() + +if(NOT CMAKE_CROSSCOMPILING) + set(MPI_CXX_SKIP_MPICXX TRUE) + find_package(MPI QUIET) + option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) +else() + option(BUILD_MPI "Build MPI version" OFF) +endif() + +if(BUILD_MPI) + # We use a non-standard procedure to cross-compile with MPI on Windows + if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING) + include(MPI4WIN) + target_link_libraries(lammps PUBLIC MPI::MPI_CXX) + else() + find_package(MPI REQUIRED) + target_link_libraries(lammps PUBLIC MPI::MPI_CXX) + option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF) + if(LAMMPS_LONGLONG_TO_LONG) + target_compile_definitions(lammps PRIVATE -DLAMMPS_LONGLONG_TO_LONG) + endif() + endif() +else() + file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.cpp) + add_library(mpi_stubs STATIC ${MPI_SOURCES}) + set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE}) + target_include_directories(mpi_stubs PUBLIC $) + if(BUILD_SHARED_LIBS) + target_link_libraries(lammps PRIVATE mpi_stubs) + target_include_directories(lammps INTERFACE $) + target_compile_definitions(lammps INTERFACE $) + else() + target_link_libraries(lammps PUBLIC mpi_stubs) + endif() + add_library(MPI::MPI_CXX ALIAS mpi_stubs) +endif() + +set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)") +set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall) +set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES}) +validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES) +string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES) +target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES}) + +# posix_memalign is not available on Windows +if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE) +else() + set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable") +endif() +if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0") + target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN}) +endif() + +option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" ${ENABLE_TESTING}) +if(LAMMPS_EXCEPTIONS) + target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS) +endif() + +# "hard" dependencies between packages resulting +# in an error instead of skipping over files +pkg_depends(MLIAP SNAP) +pkg_depends(MPIIO MPI) +pkg_depends(USER-ATC MANYBODY) +pkg_depends(USER-LB MPI) +pkg_depends(USER-PHONON KSPACE) +pkg_depends(USER-SCAFACOS MPI) + +# detect if we may enable OpenMP support by default +set(BUILD_OMP_DEFAULT OFF) +find_package(OpenMP QUIET) +if(OpenMP_FOUND) + check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE) + if(HAVE_OMP_H_INCLUDE) + set(BUILD_OMP_DEFAULT ON) + endif() +endif() + +option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT}) + +if(BUILD_OMP) + find_package(OpenMP REQUIRED) + check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE) + if(NOT HAVE_OMP_H_INCLUDE) + message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support") + endif() + + if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR + (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR + ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR + ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0))) + # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts. + # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe. + target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=4) + else() + target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=3) + endif() + target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX) +endif() + +# Compiler specific features for testing +if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") + option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF) + mark_as_advanced(ENABLE_COVERAGE) + if(ENABLE_COVERAGE) + if(CMAKE_VERSION VERSION_LESS 3.13) + if(CMAKE_CXX_FLAGS) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") + else() + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage") + endif() + else() + target_compile_options(lammps PUBLIC --coverage) + target_link_options(lammps PUBLIC --coverage) + endif() + endif() +endif() + +####################################### +# add custom target for IWYU analysis +####################################### +set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool") +mark_as_advanced(ENABLE_IWYU) +if(ENABLE_IWYU) + set(CMAKE_EXPORT_COMPILE_COMMANDS ON) + find_program(IWYU_EXE NAMES include-what-you-use iwyu) + find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py) + if (IWYU_EXE AND IWYU_TOOL) + add_custom_target( + iwyu + ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp + COMMENT "Running IWYU") + add_dependencies(iwyu lammps) + else() + message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable" + "and the iwyu-tool/iwyu_tool script installed in your PATH") + endif() +endif() + +set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)") +mark_as_advanced(ENABLE_SANITIZER) +set(ENABLE_SANITIZER_VALUES none address leak thread undefined) +set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES}) +validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES) +string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER) +if(NOT ENABLE_SANITIZER STREQUAL "none") + if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")) + if(CMAKE_VERSION VERSION_LESS 3.13) + if(CMAKE_CXX_FLAGS) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}") + else() + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}") + endif() + else() + target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER}) + target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER}) + endif() + else() + message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.") + set(ENABLE_SANITIZER "none") + endif() +endif() + +if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) + enable_language(C) + find_package(LAPACK) + find_package(BLAS) + if(NOT LAPACK_FOUND OR NOT BLAS_FOUND) + include(CheckGeneratorSupport) + if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN) + status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support") + endif() + enable_language(Fortran) + file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF]) + add_library(linalg STATIC ${LAPACK_SOURCES}) + set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE}) + set(BLAS_LIBRARIES "$") + set(LAPACK_LIBRARIES "$") + else() + list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES}) + endif() +endif() + +find_package(JPEG QUIET) +option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND}) +if(WITH_JPEG) + find_package(JPEG REQUIRED) + target_compile_definitions(lammps PRIVATE -DLAMMPS_JPEG) + if(CMAKE_VERSION VERSION_LESS 3.12) + target_include_directories(lammps PRIVATE ${JPEG_INCLUDE_DIRS}) + target_link_libraries(lammps PRIVATE ${JPEG_LIBRARIES}) + else() + target_link_libraries(lammps PRIVATE JPEG::JPEG) + endif() +endif() + +find_package(PNG QUIET) +find_package(ZLIB QUIET) +if(PNG_FOUND AND ZLIB_FOUND) + option(WITH_PNG "Enable PNG support" ON) +else() + option(WITH_PNG "Enable PNG support" OFF) +endif() +if(WITH_PNG) + find_package(PNG REQUIRED) + find_package(ZLIB REQUIRED) + target_link_libraries(lammps PRIVATE PNG::PNG ZLIB::ZLIB) + target_compile_definitions(lammps PRIVATE -DLAMMPS_PNG) +endif() + +find_program(GZIP_EXECUTABLE gzip) +find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE) +option(WITH_GZIP "Enable GZIP support" ${GZIP_FOUND}) +if(WITH_GZIP) + if(GZIP_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)) + target_compile_definitions(lammps PRIVATE -DLAMMPS_GZIP) + else() + message(FATAL_ERROR "gzip executable not found") + endif() +endif() + +find_program(FFMPEG_EXECUTABLE ffmpeg) +find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE) +option(WITH_FFMPEG "Enable FFMPEG support" ${FFMPEG_FOUND}) +if(WITH_FFMPEG) + if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)) + target_compile_definitions(lammps PRIVATE -DLAMMPS_FFMPEG) + else() + message(FATAL_ERROR "ffmpeg executable not found") + endif() +endif() + +if(BUILD_SHARED_LIBS) + set(CONFIGURE_REQUEST_PIC "--with-pic") + set(CMAKE_REQUEST_PIC "-DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}") + set(CUDA_REQUEST_PIC "-Xcompiler ${CMAKE_SHARED_LIBRARY_CXX_FLAGS}") +else() + set(CONFIGURE_REQUEST_PIC) + set(CMAKE_REQUEST_PIC) + set(CUDA_REQUEST_PIC) +endif() + +foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM + USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE) + if(PKG_${PKG_WITH_INCL}) + include(Packages/${PKG_WITH_INCL}) + endif() +endforeach() + +# optionally enable building script wrappers using swig +option(WITH_SWIG "Build scripting language wrappers with SWIG" OFF) +if(WITH_SWIG) + get_filename_component(LAMMPS_SWIG_DIR ${LAMMPS_SOURCE_DIR}/../tools/swig ABSOLUTE) + add_subdirectory(${LAMMPS_SWIG_DIR} swig) +endif() + +set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)") +separate_arguments(CMAKE_TUNE_FLAGS) +foreach(_FLAG ${CMAKE_TUNE_FLAGS}) + target_compile_options(lammps PRIVATE ${_FLAG}) +endforeach() +######################################################################## +# Basic system tests (standard libraries, headers, functions, types) # +######################################################################## +foreach(HEADER cmath) + check_include_file_cxx(${HEADER} FOUND_${HEADER}) + if(NOT FOUND_${HEADER}) + message(FATAL_ERROR "Could not find needed header - ${HEADER}") + endif(NOT FOUND_${HEADER}) +endforeach(HEADER) + +set(MATH_LIBRARIES "m" CACHE STRING "math library") +mark_as_advanced( MATH_LIBRARIES ) +target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES}) + +###################################### +# Generate Basic Style files +###################################### +include(StyleHeaderUtils) +RegisterStyles(${LAMMPS_SOURCE_DIR}) + +######################################################## +# Fetch missing external files and archives for packages +######################################################## +foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES}) + if(PKG_${PKG}) + FetchPotentials(${LAMMPS_SOURCE_DIR}/${PKG} ${LAMMPS_POTENTIALS_DIR}) + endif() +endforeach() + +############################################## +# add sources of enabled packages +############################################ +foreach(PKG ${STANDARD_PACKAGES}) + set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) + + file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp) + file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h) + + # check for package files in src directory due to old make system + DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS}) + + if(PKG_${PKG}) + # detects styles in package and adds them to global list + RegisterStyles(${${PKG}_SOURCES_DIR}) + + target_sources(lammps PRIVATE ${${PKG}_SOURCES}) + target_include_directories(lammps PRIVATE ${${PKG}_SOURCES_DIR}) + endif() + + RegisterPackages(${${PKG}_SOURCES_DIR}) +endforeach() + +# packages that need defines set +foreach(PKG MPIIO) + if(PKG_${PKG}) + target_compile_definitions(lammps PRIVATE -DLMP_${PKG}) + endif() +endforeach() + +# dedicated check for entire contents of accelerator packages +foreach(PKG ${SUFFIX_PACKAGES}) + set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) + + file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp) + file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h) + + # check for package files in src directory due to old make system + DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS}) + + RegisterPackages(${${PKG}_SOURCES_DIR}) +endforeach() + +############################################## +# add lib sources of (simple) enabled packages +############################################ +foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT) + if(PKG_${SIMPLE_LIB}) + string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}") + string(TOLOWER "${PKG_LIB}" PKG_LIB) + if(PKG_LIB STREQUAL mesont) + enable_language(Fortran) + file(GLOB_RECURSE ${PKG_LIB}_SOURCES + ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90) + else() + file(GLOB_RECURSE ${PKG_LIB}_SOURCES + ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c + ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp) + endif() + add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES}) + set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE}) + target_link_libraries(lammps PRIVATE ${PKG_LIB}) + if(PKG_LIB STREQUAL awpmd) + target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include) + elseif(PKG_LIB STREQUAL h5md) + target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS}) + else() + target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}) + endif() + endif() +endforeach() + +if(PKG_USER-AWPMD) + target_link_libraries(awpmd PRIVATE ${LAPACK_LIBRARIES}) +endif() + +if(PKG_USER-ATC) + if(LAMMPS_SIZES STREQUAL BIGBIG) + message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG") + endif() + target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES}) + if(BUILD_MPI) + target_link_libraries(atc PRIVATE MPI::MPI_CXX) + else() + target_link_libraries(atc PRIVATE mpi_stubs) + endif() + target_include_directories(atc PRIVATE ${LAMMPS_SOURCE_DIR}) + target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES}) +endif() + +if(PKG_USER-H5MD) + include(Packages/USER-H5MD) +endif() + +###################################################################### +# packages which selectively include variants based on enabled styles +# e.g. accelerator packages +###################################################################### +foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU) + if(PKG_${PKG_WITH_INCL}) + include(Packages/${PKG_WITH_INCL}) + endif() +endforeach() + +if(PKG_PLUGIN) + if(BUILD_SHARED_LIBS) + target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN) + else() + message(WARNING "Plugin loading will not work unless BUILD_SHARED_LIBS is enabled") + endif() + # link with -ldl or equivalent for plugin loading; except on Windows + if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS}) + endif() +endif() + +###################################################################### +# the windows version of LAMMPS requires a couple extra libraries +# and the MPI library - if use - has to be linked right before those +# and after everything else that is compiled locally +###################################################################### +if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi) +endif() + +###################################################### +# Generate style headers based on global list of +# styles registered during package selection +# Generate packages headers from all packages +###################################################### +set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles) + +GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR}) +GeneratePackagesHeaders(${LAMMPS_STYLE_HEADERS_DIR}) + +target_include_directories(lammps PRIVATE ${LAMMPS_STYLE_HEADERS_DIR}) + +###################################### +# Generate lmpinstalledpkgs.h +###################################### +set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n") +set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] = {\n") +set(temp_PKG_LIST ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES}) +list(SORT temp_PKG_LIST) +foreach(PKG ${temp_PKG_LIST}) + if(PKG_${PKG}) + set(temp "${temp} \"${PKG}\",\n") + endif() +endforeach() +set(temp "${temp} NULL\n};\n#endif\n\n") +message(STATUS "Generating lmpinstalledpkgs.h...") +file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${temp}" ) +execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h") + +###################################### +# Generate lmpgitversion.h +###################################### +add_custom_target(gitversion COMMAND ${CMAKE_COMMAND} + -DLAMMPS_DIR="${LAMMPS_DIR}" + -DGIT_EXECUTABLE="${GIT_EXECUTABLE}" + -DGIT_FOUND="${GIT_FOUND}" + -DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}" + -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/generate_lmpgitversion.cmake) +set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES ${LAMMPS_STYLE_HEADERS_DIR}/gitversion.h) +add_dependencies(lammps gitversion) + +########################################### +# Actually add executable and lib to build +############################################ +get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) +list (FIND LANGUAGES "Fortran" _index) +if(${_index} GREATER -1) + target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) +endif() +set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h + input.h info.h kspace.h lammps.h lattice.h library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h + pair.h pointers.h region.h timer.h universe.h update.h utils.h variable.h) +if(LAMMPS_EXCEPTIONS) + list(APPEND LAMMPS_CXX_HEADERS exceptions.h) +endif() + +set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE}) +set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION}) +target_include_directories(lammps PUBLIC $) +file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps) +foreach(_HEADER ${LAMMPS_CXX_HEADERS}) + add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER}) + add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER}) + add_dependencies(lammps ${_HEADER}) + if(BUILD_SHARED_LIBS) + install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) + endif() +endforeach() +target_include_directories(lammps INTERFACE $) +add_library(LAMMPS::lammps ALIAS lammps) +get_target_property(LAMMPS_DEFINES lammps INTERFACE_COMPILE_DEFINITIONS) +set(LAMMPS_API_DEFINES) +foreach(_DEF ${LAMMPS_DEFINES}) + set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}") +endforeach() +if(BUILD_SHARED_LIBS) + install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) + configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY) + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) + install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS) + include(CMakePackageConfigHelpers) + configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY) + write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion) + install(FILES "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake" "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfigVersion.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS) +endif() +install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1) + +include(Tools) +include(Documentation) + +############################################################################### +# Install potential and force field files in data directory +############################################################################### +set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps) +install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR}) +if(BUILD_TOOLS) + install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR}) +endif() + +configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY) +configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY) +install( + FILES ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh + ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh + DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d +) + +############################################################################### +# Install LAMMPS lib and python module into site-packages folder with +# "install-python" target. Behaves exactly like "make install-python" for +# conventional build. Only available, if a shared library is built. +# This is primarily for people that only want to use the Python wrapper. +############################################################################### +if(BUILD_SHARED_LIBS) + if(CMAKE_VERSION VERSION_LESS 3.12) + # adjust so we find Python 3 versions before Python 2 on old systems with old CMake + set(Python_ADDITIONAL_VERSIONS 3.9 3.8 3.7 3.6 3.5) + find_package(PythonInterp) # Deprecated since version 3.12 + if(PYTHONINTERP_FOUND) + set(Python_EXECUTABLE ${PYTHON_EXECUTABLE}) + endif() + else() + find_package(Python COMPONENTS Interpreter) + endif() + if (Python_EXECUTABLE) + add_custom_target( + install-python ${CMAKE_COMMAND} -E remove_directory build + COMMAND ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h + -p ${LAMMPS_PYTHON_DIR}/lammps + -l ${CMAKE_BINARY_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX} + WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR} + COMMENT "Installing LAMMPS Python module") + else() + add_custom_target( + install-python + ${CMAKE_COMMAND} -E echo "Must have Python installed to install the LAMMPS Python module") + endif() +else() + add_custom_target( + install-python + ${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module") +endif() + +############################################################################### +# Add LAMMPS python module to "install" target. This is taylored for building +# LAMMPS for package managers and with different prefix settings. +# This requires either a shared library or that the PYTHON package is included. +############################################################################### +if(BUILD_SHARED_LIBS OR PKG_PYTHON) + if(CMAKE_VERSION VERSION_LESS 3.12) + find_package(PythonInterp) # Deprecated since version 3.12 + if(PYTHONINTERP_FOUND) + set(Python_EXECUTABLE ${PYTHON_EXECUTABLE}) + endif() + else() + find_package(Python COMPONENTS Interpreter) + endif() + if (Python_EXECUTABLE) + file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python) + install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} setup.py build -b ${CMAKE_BINARY_DIR}/python install --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR}/ WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR})") + endif() +endif() + +include(Testing) +include(CodeCoverage) +include(CodingStandard) + +get_target_property(DEFINES lammps COMPILE_DEFINITIONS) +include(FeatureSummary) +feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND) +message(STATUS "<<< Build configuration >>> + Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION} + Build type: ${CMAKE_BUILD_TYPE} + Install path: ${CMAKE_INSTALL_PREFIX} + Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}") +############################################################################### +# Print package summary +############################################################################### +set(ENABLED_PACKAGES) +foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES}) + if(PKG_${PKG}) + list(APPEND ENABLED_PACKAGES ${PKG}) + endif() +endforeach() +if(ENABLED_PACKAGES) + list(SORT ENABLED_PACKAGES) +else() + set(ENABLED_PACKAGES "") +endif() +message(STATUS "Enabled packages: ${ENABLED_PACKAGES}") + +message(STATUS "<<< Compilers and Flags: >>> +-- C++ Compiler: ${CMAKE_CXX_COMPILER} + Type: ${CMAKE_CXX_COMPILER_ID} + Version: ${CMAKE_CXX_COMPILER_VERSION} + C++ Flags: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}} + Defines: ${DEFINES}") +get_target_property(OPTIONS lammps COMPILE_OPTIONS) +if(OPTIONS) + message(" Options: ${OPTIONS}") +endif() +get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) +list (FIND LANGUAGES "Fortran" _index) +if(${_index} GREATER -1) + message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER} + Type: ${CMAKE_Fortran_COMPILER_ID} + Version: ${CMAKE_Fortran_COMPILER_VERSION} + Fortran Flags:${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}") +endif() +list (FIND LANGUAGES "C" _index) +if(${_index} GREATER -1) + message(STATUS "C compiler: ${CMAKE_C_COMPILER} + Type: ${CMAKE_C_COMPILER_ID} + Version: ${CMAKE_C_COMPILER_VERSION} + C Flags: ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}") +endif() +message(STATUS "<<< Linker flags: >>>") +message(STATUS "Executable name: ${LAMMPS_BINARY}") +if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13) + get_target_property(OPTIONS lammps LINK_OPTIONS) + if(OPTIONS) + message(STATUS "Linker options: ${OPTIONS}") + endif() +endif() +if(CMAKE_EXE_LINKER_FLAGS) + message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}") +endif() +if(BUILD_SHARED_LIBS) + message(STATUS "Shared library flags: ${CMAKE_SHARED_LINKER_FLAGS}") +else() + message(STATUS "Static library flags: ${CMAKE_STATIC_LINKER_FLAGS}") +endif() +if(BUILD_MPI) + message(STATUS "<<< MPI flags >>> +-- MPI_defines: ${MPI_CXX_COMPILE_DEFINITIONS} +-- MPI includes: ${MPI_CXX_INCLUDE_PATH} +-- MPI libraries: ${MPI_CXX_LIBRARIES};${MPI_Fortran_LIBRARIES}") +endif() +if(PKG_GPU) + message(STATUS "<<< GPU package settings >>> +-- GPU API: ${GPU_API}") + if(GPU_API STREQUAL "CUDA") + message(STATUS "CUDA Compiler: ${CUDA_NVCC_EXECUTABLE}") + message(STATUS "GPU default architecture: ${GPU_ARCH}") + message(STATUS "GPU binning with CUDPP: ${CUDPP_OPT}") + message(STATUS "CUDA MPS support: ${CUDA_MPS_SUPPORT}") + elseif(GPU_API STREQUAL "HIP") + message(STATUS "HIP platform: ${HIP_PLATFORM}") + message(STATUS "HIP architecture: ${HIP_ARCH}") + if(HIP_USE_DEVICE_SORT) + message(STATUS "HIP GPU sorting: on") + else() + message(STATUS "HIP GPU sorting: off") + endif() + endif() + message(STATUS "GPU precision: ${GPU_PREC}") +endif() +if(PKG_KOKKOS) + message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}") +endif() +if(PKG_KSPACE) + message(STATUS "<<< FFT settings >>> +-- Primary FFT lib: ${FFT}") + if(FFT_SINGLE) + message(STATUS "Using single precision FFTs") + else() + message(STATUS "Using double precision FFTs") + endif() + if(FFT_FFTW_THREADS OR FFT_MKL_THREADS) + message(STATUS "Using threaded FFTs") + else() + message(STATUS "Using non-threaded FFTs") + endif() + if(PKG_KOKKOS) + if(Kokkos_ENABLE_CUDA) + if (${FFT} STREQUAL "KISS") + message(STATUS "Kokkos FFT: KISS") + else() + message(STATUS "Kokkos FFT: cuFFT") + endif() + else() + message(STATUS "Kokkos FFT: ${FFT}") + endif() + endif() +endif() +if(BUILD_DOC) + message(STATUS "<<< Building HTML Manual >>>") +endif() +if(BUILD_TOOLS) + message(STATUS "<<< Building Tools >>>") +endif() +if(BUILD_LAMMPS_SHELL) + message(STATUS "<<< Building LAMMPS Shell >>>") +endif() +if(ENABLE_TESTING) + message(STATUS "<<< Building Unit Tests >>>") + if(ENABLE_COVERAGE) + message(STATUS "Collecting code coverage data") + endif() +endif() diff --git a/src/Makefile.txt b/src/Makefile.txt new file mode 100644 index 0000000000..5542ed0cc5 --- /dev/null +++ b/src/Makefile.txt @@ -0,0 +1,443 @@ +# LAMMPS multiple-machine -*- Makefile -*- + +SHELL = /bin/bash +PYTHON = python + +#.IGNORE: + +# Definitions + +ROOT = lmp +EXE = lmp_$@ +ARLIB = liblammps_$@.a +SHLIB = liblammps_$@.so +ARLINK = liblammps.a +SHLINK = liblammps.so +TMPNAME= tmp_$@_name +LMPLINK= -L. -llammps_$@ + +OBJDIR = Obj_$@ +OBJSHDIR = Obj_shared_$@ + +SRC = $(wildcard *.cpp) +INC = $(filter-out lmpinstalledpkgs.h lmpgitversion.h,$(wildcard *.h)) +OBJ = $(SRC:.cpp=.o) + +SRCLIB = $(filter-out main.cpp,$(SRC)) +OBJLIB = $(filter-out main.o,$(OBJ)) + +# Command-line options for mode: static (default), shared, or print + +mode = static +objdir = $(OBJDIR) + +ifeq ($(mode),shared) +objdir = $(OBJSHDIR) +endif + +# Package variables + +# PACKAGE = standard packages +# PACKUSER = user packagse +# PACKLIB = all packages that require an additional lib +# should be PACKSYS + PACKINT + PACKEXT +# PACKSYS = subset that reqiure a common system library +# include MPIIO and LB b/c require full MPI, not just STUBS +# PACKINT = subset that require an internal (provided) library +# PACKEXT = subset that require an external (downloaded) library + +PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ + granular kim kokkos kspace latte manybody mc message misc \ + mliap molecule mpiio mscg opt peri plugin poems \ + python qeq replica rigid shock snap spin srd voronoi + +PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ + user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ + user-intel user-lb user-manifold user-meamc user-mesodpd user-mesont \ + user-mgpt user-misc user-mofff user-molfile \ + user-netcdf user-omp user-phonon user-pace user-plumed user-ptm user-qmmm \ + user-qtb user-quip user-rann user-reaction user-reaxc user-scafacos user-smd user-smtbq \ + user-sdpd user-sph user-tally user-uef user-vtk user-yaff + +PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \ + python voronoi \ + user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ + user-netcdf user-plumed user-qmmm user-quip user-scafacos \ + user-smd user-vtk user-mesont user-pace + +PACKSYS = compress mpiio python user-lb + +PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont + +PACKEXT = kim latte mscg voronoi \ + user-adios user-h5md user-molfile user-netcdf user-pace user-plumed \ + user-qmmm user-quip user-smd user-vtk + +PACKALL = $(PACKAGE) $(PACKUSER) + +# Helper GNU make function for conversion to upper case without using shell commands +uppercase_TABLE:=a,A b,B c,C d,D e,E f,F g,G h,H i,I j,J k,K l,L m,M n,N o,O p,P q,Q r,R s,S t,T u,U v,V w,W x,X y,Y z,Z +uppercase_internal=$(if $1,$$(subst $(firstword $1),$(call uppercase_internal,$(wordlist 2,$(words $1),$1),$2)),$2) +uppercase=$(eval uppercase_RESULT:=$(call uppercase_internal,$(uppercase_TABLE),$1))$(uppercase_RESULT) + +PACKAGEUC = $(call uppercase,$(PACKAGE)) +PACKUSERUC = $(call uppercase,$(PACKUSER)) + +YESDIR = $(call uppercase,$(@:yes-%=%)) +NODIR = $(call uppercase,$(@:no-%=%)) +LIBDIR = $(@:lib-%=%) +LIBUSERDIR = $(@:lib-user-%=%) + +# List of all targets + +help: + @echo '' + @echo 'make clean-all delete all object files' + @echo 'make clean-machine delete object files for one machine' + @echo 'make mpi-stubs build dummy MPI library in STUBS' + @echo 'make install-python install LAMMPS wrapper in Python' + @echo 'make tar create lmp_src.tar.gz for src dir and packages' + @echo '' + @echo 'make package list available packages and their dependencies' + @echo 'make package-status (ps) status of all packages' + @echo 'make package-installed (pi) list of installed packages' + @echo 'make yes-package install a single pgk in src dir' + @echo 'make no-package remove a single pkg from src dir' + @echo 'make yes-all install all pgks in src dir' + @echo 'make no-all remove all pkgs from src dir' + @echo 'make yes-standard (yes-std) install all standard pkgs' + @echo 'make no-standard (no-std) remove all standard pkgs' + @echo 'make yes-user install all user pkgs' + @echo 'make no-user remove all user pkgs' + @echo 'make yes-lib install all pkgs with libs (included or ext)' + @echo 'make no-lib remove all pkgs with libs (included or ext)' + @echo 'make yes-ext install all pkgs with external libs' + @echo 'make no-ext remove all pkgs with external libs' + @echo '' + @echo 'make package-update (pu) replace src files with updated package files' + @echo 'make package-overwrite replace package files with src files' + @echo 'make package-diff (pd) diff src files against package files' + @echo '' + @echo 'make lib-package help for download/build/install a package library' + @echo 'make lib-package args="..." download/build/install a package library' + @echo 'make purge purge obsolete copies of source files' + @echo '' + @echo 'make machine build LAMMPS for machine with static library' + @echo 'make mode=static machine same as above' + @echo 'make mode=shared machine build LAMMPS for machine with shared library' + @echo 'make mode=print machine print compiler/linker flags' + @echo '' + @echo 'machine is one of these from src/MAKE:' + @echo '' + @files="`ls MAKE/Makefile.*`"; \ + for file in $$files; do head -1 $$file; done + @echo '' + @echo '... or one of these from src/MAKE/OPTIONS:' + @echo '' + @files="`ls MAKE/OPTIONS/Makefile.*`"; \ + for file in $$files; do head -1 $$file; done + @echo '' + @echo '... or one of these from src/MAKE/MACHINES:' + @echo '' + @files="`ls MAKE/MACHINES/Makefile.*`"; \ + for file in $$files; do head -1 $$file; done + @echo '' + @echo '... or one of these from src/MAKE/MINE:' + @echo '' + @files="`ls MAKE/MINE/Makefile.* 2>/dev/null`"; \ + for file in $$files; do head -1 $$file; done + @echo '' + + +lmpinstalledpkgs.h: $(SRC) $(INC) + @echo '#ifndef LMP_INSTALLED_PKGS_H' > ${TMPNAME}.lmpinstalled + @echo '#define LMP_INSTALLED_PKGS_H' >> ${TMPNAME}.lmpinstalled + @echo 'const char * LAMMPS_NS::LAMMPS::installed_packages[] = {' >> ${TMPNAME}.lmpinstalled + @for p in $(PACKAGEUC) $(PACKUSERUC); do info=$$($(SHELL) Package.sh $$p installed); \ + [ -n "$$info" ] && echo "\"$$info\"" | sed -e 's/".*package \(.*\)"/"\1",/' >> ${TMPNAME}.lmpinstalled || :; done + @echo ' NULL };' >> ${TMPNAME}.lmpinstalled + @echo '#endif' >> ${TMPNAME}.lmpinstalled + @if [ -f lmpinstalledpkgs.h ]; \ + then test "`diff --brief ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h`" != "" && \ + mv ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h || rm ${TMPNAME}.lmpinstalled ; \ + else mv ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h ; fi + +gitversion: + @echo 'Gathering git version information' + @echo '#ifndef LMP_GIT_VERSION_H' > ${TMPNAME}.lmpgitversion + @echo '#define LMP_GIT_VERSION_H' >> ${TMPNAME}.lmpgitversion + @if (type git && test -e ../.git ) >> /dev/null 2>> /dev/null ; then \ + git='true'; \ + commit=$$(git rev-parse HEAD); \ + branch=$$(git rev-parse --abbrev-ref HEAD); \ + describe=$$(git describe --dirty=-modified); \ + else \ + git='false' ; \ + commit='(unknown)' ; \ + branch='(unknown)' ; \ + describe='(unknown)' ; \ + fi ; \ + echo "const bool LAMMPS_NS::LAMMPS::has_git_info = $${git};" >> ${TMPNAME}.lmpgitversion ; \ + echo "const char LAMMPS_NS::LAMMPS::git_commit[] = \"$${commit}\";" >> ${TMPNAME}.lmpgitversion ; \ + echo "const char LAMMPS_NS::LAMMPS::git_branch[] = \"$${branch}\";" >> ${TMPNAME}.lmpgitversion ; \ + echo "const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"$${describe}\";" >> ${TMPNAME}.lmpgitversion + @echo '#endif' >> ${TMPNAME}.lmpgitversion + @if [ -f lmpgitversion.h ]; \ + then test "`diff --brief ${TMPNAME}.lmpgitversion lmpgitversion.h`" != "" && \ + mv ${TMPNAME}.lmpgitversion lmpgitversion.h || rm ${TMPNAME}.lmpgitversion ; \ + else mv ${TMPNAME}.lmpgitversion lmpgitversion.h ; fi + +# Build LAMMPS in one of 2 modes +# static = static compile in Obj_machine (default) +# shared = shared compile in Obj_shared_machine + +.DEFAULT: + @if [ $@ = "serial" ]; \ + then cd STUBS; $(MAKE); cd ..; fi + @test -f MAKE/Makefile.$@ -o -f MAKE/OPTIONS/Makefile.$@ -o \ + -f MAKE/MACHINES/Makefile.$@ -o -f MAKE/MINE/Makefile.$@ + @if [ ! -d $(objdir) ]; then mkdir $(objdir); fi + @echo 'Gathering installed package information (may take a little while)' + @$(SHELL) Make.sh style + @$(SHELL) Make.sh packages + @$(MAKE) $(MFLAGS) lmpinstalledpkgs.h gitversion + @echo 'Compiling LAMMPS for machine $@' + @if [ -f MAKE/MACHINES/Makefile.$@ ]; \ + then cp MAKE/MACHINES/Makefile.$@ $(objdir)/Makefile; fi + @if [ -f MAKE/OPTIONS/Makefile.$@ ]; \ + then cp MAKE/OPTIONS/Makefile.$@ $(objdir)/Makefile; fi + @if [ -f MAKE/Makefile.$@ ]; \ + then cp MAKE/Makefile.$@ $(objdir)/Makefile; fi + @if [ -f MAKE/MINE/Makefile.$@ ]; \ + then cp MAKE/MINE/Makefile.$@ $(objdir)/Makefile; fi + @if [ ! -e Makefile.package ]; \ + then cp Makefile.package.empty Makefile.package; fi + @if [ ! -e Makefile.package.settings ]; \ + then cp Makefile.package.settings.empty Makefile.package.settings; fi + @cp Makefile.package Makefile.package.settings $(objdir) + @cd $(objdir); rm -f .depend; \ + $(MAKE) $(MFLAGS) "SRC = $(SRC)" "INC = $(INC)" depend || : + @rm -f $(ARLINK) $(SHLINK) $(EXE) +ifeq ($(mode),static) + @cd $(objdir); \ + $(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" "SHFLAGS =" \ + "LMPLIB = $(ARLIB)" "ARLIB = $(ARLIB)" "SHLIB = $(SHLIB)" \ + "LMPLINK = $(LMPLINK)" "EXE = ../$(EXE)" ../$(EXE) + @ln -s $(ARLIB) $(ARLINK) +endif +ifeq ($(mode),shared) + @cd $(objdir); \ + $(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" \ + "LMPLIB = $(SHLIB)" "ARLIB = $(ARLIB)" "SHLIB = $(SHLIB)" \ + "LMPLINK = $(LMPLINK)" "EXE = ../$(EXE)" ../$(EXE) + @ln -s $(SHLIB) $(SHLINK) +endif +# backward compatibility +ifeq ($(mode),exe) + $(MAKE) $(MFLAGS) mode=static $@ +endif +ifeq ($(mode),lib) + $(MAKE) $(MFLAGS) mode=static $@ +endif +ifeq ($(mode),shexe) + $(MAKE) $(MFLAGS) mode=shared $@ +endif +ifeq ($(mode),shlib) + $(MAKE) $(MFLAGS) mode=shared $@ +endif + +ifeq ($(mode),print) + @cd $(objdir); \ + $(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" \ + "EXE = ../$(ARLIB)" -f ../Makefile.print +endif + +# Remove machine-specific object files + +clean: + @echo 'make clean-all delete all object files' + @echo 'make clean-machine delete object files for one machine' + +clean-all: + rm -rf Obj_* + +clean-%: + @if [ $@ = "clean-serial" ]; \ + then cd STUBS; $(MAKE) clean; cd ..; fi + rm -rf Obj_$(@:clean-%=%) Obj_shared_$(@:clean-%=%) + +# Make MPI STUBS library + +mpi-stubs: + @cd STUBS; $(MAKE) clean; $(MAKE) + +# install LAMMPS shared lib and Python wrapper for Python usage +# include python package settings to automatically adapt name of +# the python interpreter. must purge build folder to not install +# unwanted outdated files. + +sinclude ../lib/python/Makefile.lammps +install-python: + @rm -rf ../python/build + @$(PYTHON) ../python/install.py -v ../src/version.h \ + -p ../python/lammps -l ../src/liblammps.so + +# Create a tarball of src dir and packages + +tar: + @cd STUBS; $(MAKE) clean + @cd ..; tar cvzf src/$(ROOT)_src.tar.gz \ + src/Make* src/Package.sh src/Depend.sh src/Install.sh src/Fetch.sh \ + src/MAKE src/DEPEND src/*.cpp src/*.h src/STUBS \ + $(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \ + --exclude=*/.svn + @cd STUBS; $(MAKE) + @echo "Created $(ROOT)_src.tar.gz" + +# Package management + +package: + @echo 'Standard packages:' $(PACKAGE) + @echo '' + @echo 'User-contributed packages:' $(PACKUSER) + @echo '' + @echo 'Packages that need system libraries:' $(PACKSYS) + @echo '' + @echo 'Packages that need provided libraries:' $(PACKINT) + @echo '' + @echo 'Packages that need external libraries:' $(PACKEXT) + @echo '' + @echo 'make package list available packages' + @echo 'make package list available packages' + @echo 'make package-status (ps) status of all packages' + @echo 'make package-installed (pi) list of installed packages' + @echo 'make yes-package install a single pgk in src dir' + @echo 'make no-package remove a single pkg from src dir' + @echo 'make yes-all install all pgks in src dir' + @echo 'make no-all remove all pkgs from src dir' + @echo 'make yes-standard (yes-std) install all standard pkgs' + @echo 'make no-standard (no-std) remove all standard pkgs' + @echo 'make yes-user install all user pkgs' + @echo 'make no-user remove all user pkgs' + @echo 'make yes-lib install all pkgs with libs (included or ext)' + @echo 'make no-lib remove all pkgs with libs (included or ext)' + @echo 'make yes-ext install all pkgs with external libs' + @echo 'make no-ext remove all pkgs with external libs' + @echo '' + @echo 'make package-update (pu) replace src files with package files' + @echo 'make package-overwrite replace package files with src files' + @echo 'make package-diff (pd) diff src files against package file' + @echo '' + @echo 'make lib-package build and/or download a package library' + +yes-all: + @for p in $(PACKALL); do $(MAKE) yes-$$p; done + +no-all: + @for p in $(PACKALL); do $(MAKE) no-$$p; done + +yes-standard yes-std: + @for p in $(PACKAGE); do $(MAKE) yes-$$p; done + +no-standard no-std: + @for p in $(PACKAGE); do $(MAKE) no-$$p; done + +yes-user: + @for p in $(PACKUSER); do $(MAKE) yes-$$p; done + +no-user: + @for p in $(PACKUSER); do $(MAKE) no-$$p; done + +yes-lib: + @for p in $(PACKLIB); do $(MAKE) yes-$$p; done + +no-lib: + @for p in $(PACKLIB); do $(MAKE) no-$$p; done + +yes-ext: + @for p in $(PACKEXT); do $(MAKE) yes-$$p; done + +no-ext: + @for p in $(PACKEXT); do $(MAKE) no-$$p; done + +yes-%: + @if [ ! -e Makefile.package ]; \ + then cp Makefile.package.empty Makefile.package; fi + @if [ ! -e Makefile.package.settings ]; \ + then cp Makefile.package.settings.empty Makefile.package.settings; fi + @if [ ! -e $(YESDIR) ]; then \ + echo "Package $(YESDIR) does not exist"; exit 1; \ + elif [ -e $(YESDIR)/Install.sh ]; then \ + echo "Installing package $(@:yes-%=%)"; \ + cd $(YESDIR); $(SHELL) Install.sh 1; cd ..; \ + $(SHELL) Depend.sh $(YESDIR) 1; \ + else \ + echo "Installing package $(@:yes-%=%)"; \ + cd $(YESDIR); $(SHELL) ../Install.sh 1; cd ..; \ + $(SHELL) Depend.sh $(YESDIR) 1; \ + fi; + @$(SHELL) Fetch.sh $(YESDIR) + +no-%: + @if [ ! -e $(NODIR) ]; then \ + echo "Package $(NODIR) does not exist"; exit 1; \ + elif [ -e $(NODIR)/Install.sh ]; then \ + echo "Uninstalling package $(@:no-%=%)"; \ + cd $(NODIR); $(SHELL) Install.sh 0; cd ..; \ + $(SHELL) Depend.sh $(NODIR) 0; \ + else \ + echo "Uninstalling package $(@:no-%=%)"; \ + cd $(NODIR); $(SHELL) ../Install.sh 0; cd ..; \ + $(SHELL) Depend.sh $(NODIR) 0; \ + fi; + +# download/build/install a package library +# update the timestamp on main.cpp to trigger a relink with "make machine" + +lib-%: + @if [ -e ../lib/$(LIBDIR)/Install.py ]; then \ + echo "Installing lib $(@:lib-%=%)"; \ + ( cd ../lib/$(LIBDIR); $(PYTHON) Install.py $(args) ); \ + elif [ -e ../lib/$(LIBUSERDIR)/Install.py ]; then \ + echo "Installing lib $(@:lib-user-%=%)"; \ + ( cd ../lib/$(LIBUSERDIR); $(PYTHON) Install.py $(args) ); \ + else \ + echo "Install script for lib $(@:lib-%=%) does not exist"; \ + fi; touch main.cpp + +# status = list src files that differ from package files +# installed = list of installed packages +# update = replace src files with newer package files +# overwrite = overwrite package files with newer src files +# diff = show differences between src and package files +# purge = delete obsolete and auto-generated package files + +package-status ps: + @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p status; done + @echo '' + @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p status; done + +package-installed pi: + @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p installed; done + @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p installed; done + +package-update pu: purge + @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p update; done + @echo '' + @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p update; done + +package-overwrite: purge + @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p overwrite; done + @echo '' + @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p overwrite; done + +package-diff pd: + @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p diff; done + @echo '' + @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p diff; done + +purge: Purge.list + @echo 'Purging obsolete and auto-generated source files' + @for f in `grep -v '#' Purge.list` ; \ + do test -f $$f && rm $$f && echo $$f || : ; \ + done From 6a1a58d7271aacd2013533733ed17816eee430e7 Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Fri, 23 Apr 2021 17:56:35 +0200 Subject: [PATCH 0622/1217] Added CMake imported target N2P2::N2P2 --- cmake/Modules/FindN2P2.cmake | 15 +++++++-- cmake/Modules/Packages/USER-HDNNP.cmake | 42 +++++++++++++++++++++++-- 2 files changed, 53 insertions(+), 4 deletions(-) diff --git a/cmake/Modules/FindN2P2.cmake b/cmake/Modules/FindN2P2.cmake index 95413edfb1..6bf4da5a79 100644 --- a/cmake/Modules/FindN2P2.cmake +++ b/cmake/Modules/FindN2P2.cmake @@ -33,8 +33,19 @@ find_package_handle_standard_args(N2P2 DEFAULT_MSG N2P2_CMAKE_EXTRA) if(N2P2_FOUND) - set(N2P2_INCLUDE_DIRS ${N2P2_INCLUDE_DIR}) - set(N2P2_LIBRARIES ${N2P2_LIBNNPIF} ${N2P2_LIBNNP}) + add_library(N2P2::LIBNNP UNKNOWN IMPORTED) + set_target_properties(N2P2::LIBNNP PROPERTIES + INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR} + IMPORTED_LOCATION ${N2P2_LIBNNP}) + add_library(N2P2::LIBNNPIF UNKNOWN IMPORTED) + set_target_properties(N2P2::LIBNNPIF PROPERTIES + INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR} + IMPORTED_LOCATION ${N2P2_LIBNNPIF}) + add_library(N2P2::N2P2 INTERFACE IMPORTED) + set_property(TARGET N2P2::N2P2 PROPERTY + INTERFACE_LINK_LIBRARIES N2P2::LIBNNPIF N2P2::LIBNNP) + #set(N2P2_INCLUDE_DIRS ${N2P2_INCLUDE_DIR}) + #set(N2P2_LIBRARIES ${N2P2_LIBNNPIF} ${N2P2_LIBNNP}) set(N2P2_CMAKE_EXTRAS ${N2P2_CMAKE_EXTRA}) mark_as_advanced( diff --git a/cmake/Modules/Packages/USER-HDNNP.cmake b/cmake/Modules/Packages/USER-HDNNP.cmake index 2ebc1f6e36..2d5fb406be 100644 --- a/cmake/Modules/Packages/USER-HDNNP.cmake +++ b/cmake/Modules/Packages/USER-HDNNP.cmake @@ -1,4 +1,42 @@ find_package(N2P2 REQUIRED) -target_include_directories(lammps PRIVATE ${N2P2_INCLUDE_DIRS}) -target_link_libraries(lammps PRIVATE ${N2P2_LIBRARIES}) +#target_include_directories(lammps PRIVATE ${N2P2_INCLUDE_DIRS}) +#target_link_libraries(lammps PRIVATE ${N2P2_LIBRARIES}) +target_link_libraries(lammps PRIVATE N2P2::N2P2) include(${N2P2_CMAKE_EXTRAS}) + +#find_package(N2P2 QUIET) +#if(N2P2_FOUND) +# set(DOWNLOAD_N2P2_DEFAULT OFF) +#else() +# set(DOWNLOAD_N2P2_DEFAULT ON) +#endif() +#option(DOWNLOAD_N2P2 "Download n2p2 library instead of using an already installed one)" ${DOWNLOAD_N2P2_DEFAULT}) +#if(DOWNLOAD_N2P2) +# set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.1.2.tar.gz" CACHE STRING "URL for n2p2 tarball") +# set(N2P2_MD5 "20cf194d14b1f1c72f38879bafda67e2" CACHE STRING "MD5 checksum of N2P2 tarball") +# mark_as_advanced(N2P2_URL) +# mark_as_advanced(N2P2_MD5) +# +# include(ExternalProject) +# ExternalProject_Add(n2p2_build +# URL ${N2P2_URL} +# URL_MD5 ${N2P2_MD5} +# SOURCE_SUBDIR src/ +# BUILD_COMMAND make libnnpif +# INSTALL_COMMAND "" +# BUILD_BYPRODUCTS /lib/libnnp.a /lib/libnnpif.a +# ) +# ExternalProject_get_property(n2p2_build INSTALL_DIR) +# add_library(LAMMPS::N2P2 UNKNOWN IMPORTED) +# set_target_properties(LAMMPS::N2P2 PROPERTIES +# IMPORTED_LOCATION "${INSTALL_DIR}/lib/libnnp.a" +# INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include") +# target_link_libraries(lammps PRIVATE LAMMPS::N2P2) +# add_dependencies(LAMMPS::N2P2 n2p2_build) +#else() +# find_package(N2P2) +# if(NOT N2P2_FOUND) +# message(FATAL_ERROR "n2p2 not found, help CMake to find it by setting N2P2_DIR, or set DOWNLOAD_N2P2=ON to download it") +# endif() +# target_link_libraries(lammps PRIVATE N2P2::N2P2) +#endif() From 792b411e46e03a6bf665ebd56dc02de16e0e90f6 Mon Sep 17 00:00:00 2001 From: kipbarrett Date: Fri, 23 Apr 2021 11:18:46 -0500 Subject: [PATCH 0623/1217] fix messed up merge --- src/Makefile | 443 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 443 insertions(+) create mode 100644 src/Makefile diff --git a/src/Makefile b/src/Makefile new file mode 100644 index 0000000000..5542ed0cc5 --- /dev/null +++ b/src/Makefile @@ -0,0 +1,443 @@ +# LAMMPS multiple-machine -*- Makefile -*- + +SHELL = /bin/bash +PYTHON = python + +#.IGNORE: + +# Definitions + +ROOT = lmp +EXE = lmp_$@ +ARLIB = liblammps_$@.a +SHLIB = liblammps_$@.so +ARLINK = liblammps.a +SHLINK = liblammps.so +TMPNAME= tmp_$@_name +LMPLINK= -L. -llammps_$@ + +OBJDIR = Obj_$@ +OBJSHDIR = Obj_shared_$@ + +SRC = $(wildcard *.cpp) +INC = $(filter-out lmpinstalledpkgs.h lmpgitversion.h,$(wildcard *.h)) +OBJ = $(SRC:.cpp=.o) + +SRCLIB = $(filter-out main.cpp,$(SRC)) +OBJLIB = $(filter-out main.o,$(OBJ)) + +# Command-line options for mode: static (default), shared, or print + +mode = static +objdir = $(OBJDIR) + +ifeq ($(mode),shared) +objdir = $(OBJSHDIR) +endif + +# Package variables + +# PACKAGE = standard packages +# PACKUSER = user packagse +# PACKLIB = all packages that require an additional lib +# should be PACKSYS + PACKINT + PACKEXT +# PACKSYS = subset that reqiure a common system library +# include MPIIO and LB b/c require full MPI, not just STUBS +# PACKINT = subset that require an internal (provided) library +# PACKEXT = subset that require an external (downloaded) library + +PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ + granular kim kokkos kspace latte manybody mc message misc \ + mliap molecule mpiio mscg opt peri plugin poems \ + python qeq replica rigid shock snap spin srd voronoi + +PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ + user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ + user-intel user-lb user-manifold user-meamc user-mesodpd user-mesont \ + user-mgpt user-misc user-mofff user-molfile \ + user-netcdf user-omp user-phonon user-pace user-plumed user-ptm user-qmmm \ + user-qtb user-quip user-rann user-reaction user-reaxc user-scafacos user-smd user-smtbq \ + user-sdpd user-sph user-tally user-uef user-vtk user-yaff + +PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \ + python voronoi \ + user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ + user-netcdf user-plumed user-qmmm user-quip user-scafacos \ + user-smd user-vtk user-mesont user-pace + +PACKSYS = compress mpiio python user-lb + +PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont + +PACKEXT = kim latte mscg voronoi \ + user-adios user-h5md user-molfile user-netcdf user-pace user-plumed \ + user-qmmm user-quip user-smd user-vtk + +PACKALL = $(PACKAGE) $(PACKUSER) + +# Helper GNU make function for conversion to upper case without using shell commands +uppercase_TABLE:=a,A b,B c,C d,D e,E f,F g,G h,H i,I j,J k,K l,L m,M n,N o,O p,P q,Q r,R s,S t,T u,U v,V w,W x,X y,Y z,Z +uppercase_internal=$(if $1,$$(subst $(firstword $1),$(call uppercase_internal,$(wordlist 2,$(words $1),$1),$2)),$2) +uppercase=$(eval uppercase_RESULT:=$(call uppercase_internal,$(uppercase_TABLE),$1))$(uppercase_RESULT) + +PACKAGEUC = $(call uppercase,$(PACKAGE)) +PACKUSERUC = $(call uppercase,$(PACKUSER)) + +YESDIR = $(call uppercase,$(@:yes-%=%)) +NODIR = $(call uppercase,$(@:no-%=%)) +LIBDIR = $(@:lib-%=%) +LIBUSERDIR = $(@:lib-user-%=%) + +# List of all targets + +help: + @echo '' + @echo 'make clean-all delete all object files' + @echo 'make clean-machine delete object files for one machine' + @echo 'make mpi-stubs build dummy MPI library in STUBS' + @echo 'make install-python install LAMMPS wrapper in Python' + @echo 'make tar create lmp_src.tar.gz for src dir and packages' + @echo '' + @echo 'make package list available packages and their dependencies' + @echo 'make package-status (ps) status of all packages' + @echo 'make package-installed (pi) list of installed packages' + @echo 'make yes-package install a single pgk in src dir' + @echo 'make no-package remove a single pkg from src dir' + @echo 'make yes-all install all pgks in src dir' + @echo 'make no-all remove all pkgs from src dir' + @echo 'make yes-standard (yes-std) install all standard pkgs' + @echo 'make no-standard (no-std) remove all standard pkgs' + @echo 'make yes-user install all user pkgs' + @echo 'make no-user remove all user pkgs' + @echo 'make yes-lib install all pkgs with libs (included or ext)' + @echo 'make no-lib remove all pkgs with libs (included or ext)' + @echo 'make yes-ext install all pkgs with external libs' + @echo 'make no-ext remove all pkgs with external libs' + @echo '' + @echo 'make package-update (pu) replace src files with updated package files' + @echo 'make package-overwrite replace package files with src files' + @echo 'make package-diff (pd) diff src files against package files' + @echo '' + @echo 'make lib-package help for download/build/install a package library' + @echo 'make lib-package args="..." download/build/install a package library' + @echo 'make purge purge obsolete copies of source files' + @echo '' + @echo 'make machine build LAMMPS for machine with static library' + @echo 'make mode=static machine same as above' + @echo 'make mode=shared machine build LAMMPS for machine with shared library' + @echo 'make mode=print machine print compiler/linker flags' + @echo '' + @echo 'machine is one of these from src/MAKE:' + @echo '' + @files="`ls MAKE/Makefile.*`"; \ + for file in $$files; do head -1 $$file; done + @echo '' + @echo '... or one of these from src/MAKE/OPTIONS:' + @echo '' + @files="`ls MAKE/OPTIONS/Makefile.*`"; \ + for file in $$files; do head -1 $$file; done + @echo '' + @echo '... or one of these from src/MAKE/MACHINES:' + @echo '' + @files="`ls MAKE/MACHINES/Makefile.*`"; \ + for file in $$files; do head -1 $$file; done + @echo '' + @echo '... or one of these from src/MAKE/MINE:' + @echo '' + @files="`ls MAKE/MINE/Makefile.* 2>/dev/null`"; \ + for file in $$files; do head -1 $$file; done + @echo '' + + +lmpinstalledpkgs.h: $(SRC) $(INC) + @echo '#ifndef LMP_INSTALLED_PKGS_H' > ${TMPNAME}.lmpinstalled + @echo '#define LMP_INSTALLED_PKGS_H' >> ${TMPNAME}.lmpinstalled + @echo 'const char * LAMMPS_NS::LAMMPS::installed_packages[] = {' >> ${TMPNAME}.lmpinstalled + @for p in $(PACKAGEUC) $(PACKUSERUC); do info=$$($(SHELL) Package.sh $$p installed); \ + [ -n "$$info" ] && echo "\"$$info\"" | sed -e 's/".*package \(.*\)"/"\1",/' >> ${TMPNAME}.lmpinstalled || :; done + @echo ' NULL };' >> ${TMPNAME}.lmpinstalled + @echo '#endif' >> ${TMPNAME}.lmpinstalled + @if [ -f lmpinstalledpkgs.h ]; \ + then test "`diff --brief ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h`" != "" && \ + mv ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h || rm ${TMPNAME}.lmpinstalled ; \ + else mv ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h ; fi + +gitversion: + @echo 'Gathering git version information' + @echo '#ifndef LMP_GIT_VERSION_H' > ${TMPNAME}.lmpgitversion + @echo '#define LMP_GIT_VERSION_H' >> ${TMPNAME}.lmpgitversion + @if (type git && test -e ../.git ) >> /dev/null 2>> /dev/null ; then \ + git='true'; \ + commit=$$(git rev-parse HEAD); \ + branch=$$(git rev-parse --abbrev-ref HEAD); \ + describe=$$(git describe --dirty=-modified); \ + else \ + git='false' ; \ + commit='(unknown)' ; \ + branch='(unknown)' ; \ + describe='(unknown)' ; \ + fi ; \ + echo "const bool LAMMPS_NS::LAMMPS::has_git_info = $${git};" >> ${TMPNAME}.lmpgitversion ; \ + echo "const char LAMMPS_NS::LAMMPS::git_commit[] = \"$${commit}\";" >> ${TMPNAME}.lmpgitversion ; \ + echo "const char LAMMPS_NS::LAMMPS::git_branch[] = \"$${branch}\";" >> ${TMPNAME}.lmpgitversion ; \ + echo "const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"$${describe}\";" >> ${TMPNAME}.lmpgitversion + @echo '#endif' >> ${TMPNAME}.lmpgitversion + @if [ -f lmpgitversion.h ]; \ + then test "`diff --brief ${TMPNAME}.lmpgitversion lmpgitversion.h`" != "" && \ + mv ${TMPNAME}.lmpgitversion lmpgitversion.h || rm ${TMPNAME}.lmpgitversion ; \ + else mv ${TMPNAME}.lmpgitversion lmpgitversion.h ; fi + +# Build LAMMPS in one of 2 modes +# static = static compile in Obj_machine (default) +# shared = shared compile in Obj_shared_machine + +.DEFAULT: + @if [ $@ = "serial" ]; \ + then cd STUBS; $(MAKE); cd ..; fi + @test -f MAKE/Makefile.$@ -o -f MAKE/OPTIONS/Makefile.$@ -o \ + -f MAKE/MACHINES/Makefile.$@ -o -f MAKE/MINE/Makefile.$@ + @if [ ! -d $(objdir) ]; then mkdir $(objdir); fi + @echo 'Gathering installed package information (may take a little while)' + @$(SHELL) Make.sh style + @$(SHELL) Make.sh packages + @$(MAKE) $(MFLAGS) lmpinstalledpkgs.h gitversion + @echo 'Compiling LAMMPS for machine $@' + @if [ -f MAKE/MACHINES/Makefile.$@ ]; \ + then cp MAKE/MACHINES/Makefile.$@ $(objdir)/Makefile; fi + @if [ -f MAKE/OPTIONS/Makefile.$@ ]; \ + then cp MAKE/OPTIONS/Makefile.$@ $(objdir)/Makefile; fi + @if [ -f MAKE/Makefile.$@ ]; \ + then cp MAKE/Makefile.$@ $(objdir)/Makefile; fi + @if [ -f MAKE/MINE/Makefile.$@ ]; \ + then cp MAKE/MINE/Makefile.$@ $(objdir)/Makefile; fi + @if [ ! -e Makefile.package ]; \ + then cp Makefile.package.empty Makefile.package; fi + @if [ ! -e Makefile.package.settings ]; \ + then cp Makefile.package.settings.empty Makefile.package.settings; fi + @cp Makefile.package Makefile.package.settings $(objdir) + @cd $(objdir); rm -f .depend; \ + $(MAKE) $(MFLAGS) "SRC = $(SRC)" "INC = $(INC)" depend || : + @rm -f $(ARLINK) $(SHLINK) $(EXE) +ifeq ($(mode),static) + @cd $(objdir); \ + $(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" "SHFLAGS =" \ + "LMPLIB = $(ARLIB)" "ARLIB = $(ARLIB)" "SHLIB = $(SHLIB)" \ + "LMPLINK = $(LMPLINK)" "EXE = ../$(EXE)" ../$(EXE) + @ln -s $(ARLIB) $(ARLINK) +endif +ifeq ($(mode),shared) + @cd $(objdir); \ + $(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" \ + "LMPLIB = $(SHLIB)" "ARLIB = $(ARLIB)" "SHLIB = $(SHLIB)" \ + "LMPLINK = $(LMPLINK)" "EXE = ../$(EXE)" ../$(EXE) + @ln -s $(SHLIB) $(SHLINK) +endif +# backward compatibility +ifeq ($(mode),exe) + $(MAKE) $(MFLAGS) mode=static $@ +endif +ifeq ($(mode),lib) + $(MAKE) $(MFLAGS) mode=static $@ +endif +ifeq ($(mode),shexe) + $(MAKE) $(MFLAGS) mode=shared $@ +endif +ifeq ($(mode),shlib) + $(MAKE) $(MFLAGS) mode=shared $@ +endif + +ifeq ($(mode),print) + @cd $(objdir); \ + $(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" \ + "EXE = ../$(ARLIB)" -f ../Makefile.print +endif + +# Remove machine-specific object files + +clean: + @echo 'make clean-all delete all object files' + @echo 'make clean-machine delete object files for one machine' + +clean-all: + rm -rf Obj_* + +clean-%: + @if [ $@ = "clean-serial" ]; \ + then cd STUBS; $(MAKE) clean; cd ..; fi + rm -rf Obj_$(@:clean-%=%) Obj_shared_$(@:clean-%=%) + +# Make MPI STUBS library + +mpi-stubs: + @cd STUBS; $(MAKE) clean; $(MAKE) + +# install LAMMPS shared lib and Python wrapper for Python usage +# include python package settings to automatically adapt name of +# the python interpreter. must purge build folder to not install +# unwanted outdated files. + +sinclude ../lib/python/Makefile.lammps +install-python: + @rm -rf ../python/build + @$(PYTHON) ../python/install.py -v ../src/version.h \ + -p ../python/lammps -l ../src/liblammps.so + +# Create a tarball of src dir and packages + +tar: + @cd STUBS; $(MAKE) clean + @cd ..; tar cvzf src/$(ROOT)_src.tar.gz \ + src/Make* src/Package.sh src/Depend.sh src/Install.sh src/Fetch.sh \ + src/MAKE src/DEPEND src/*.cpp src/*.h src/STUBS \ + $(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \ + --exclude=*/.svn + @cd STUBS; $(MAKE) + @echo "Created $(ROOT)_src.tar.gz" + +# Package management + +package: + @echo 'Standard packages:' $(PACKAGE) + @echo '' + @echo 'User-contributed packages:' $(PACKUSER) + @echo '' + @echo 'Packages that need system libraries:' $(PACKSYS) + @echo '' + @echo 'Packages that need provided libraries:' $(PACKINT) + @echo '' + @echo 'Packages that need external libraries:' $(PACKEXT) + @echo '' + @echo 'make package list available packages' + @echo 'make package list available packages' + @echo 'make package-status (ps) status of all packages' + @echo 'make package-installed (pi) list of installed packages' + @echo 'make yes-package install a single pgk in src dir' + @echo 'make no-package remove a single pkg from src dir' + @echo 'make yes-all install all pgks in src dir' + @echo 'make no-all remove all pkgs from src dir' + @echo 'make yes-standard (yes-std) install all standard pkgs' + @echo 'make no-standard (no-std) remove all standard pkgs' + @echo 'make yes-user install all user pkgs' + @echo 'make no-user remove all user pkgs' + @echo 'make yes-lib install all pkgs with libs (included or ext)' + @echo 'make no-lib remove all pkgs with libs (included or ext)' + @echo 'make yes-ext install all pkgs with external libs' + @echo 'make no-ext remove all pkgs with external libs' + @echo '' + @echo 'make package-update (pu) replace src files with package files' + @echo 'make package-overwrite replace package files with src files' + @echo 'make package-diff (pd) diff src files against package file' + @echo '' + @echo 'make lib-package build and/or download a package library' + +yes-all: + @for p in $(PACKALL); do $(MAKE) yes-$$p; done + +no-all: + @for p in $(PACKALL); do $(MAKE) no-$$p; done + +yes-standard yes-std: + @for p in $(PACKAGE); do $(MAKE) yes-$$p; done + +no-standard no-std: + @for p in $(PACKAGE); do $(MAKE) no-$$p; done + +yes-user: + @for p in $(PACKUSER); do $(MAKE) yes-$$p; done + +no-user: + @for p in $(PACKUSER); do $(MAKE) no-$$p; done + +yes-lib: + @for p in $(PACKLIB); do $(MAKE) yes-$$p; done + +no-lib: + @for p in $(PACKLIB); do $(MAKE) no-$$p; done + +yes-ext: + @for p in $(PACKEXT); do $(MAKE) yes-$$p; done + +no-ext: + @for p in $(PACKEXT); do $(MAKE) no-$$p; done + +yes-%: + @if [ ! -e Makefile.package ]; \ + then cp Makefile.package.empty Makefile.package; fi + @if [ ! -e Makefile.package.settings ]; \ + then cp Makefile.package.settings.empty Makefile.package.settings; fi + @if [ ! -e $(YESDIR) ]; then \ + echo "Package $(YESDIR) does not exist"; exit 1; \ + elif [ -e $(YESDIR)/Install.sh ]; then \ + echo "Installing package $(@:yes-%=%)"; \ + cd $(YESDIR); $(SHELL) Install.sh 1; cd ..; \ + $(SHELL) Depend.sh $(YESDIR) 1; \ + else \ + echo "Installing package $(@:yes-%=%)"; \ + cd $(YESDIR); $(SHELL) ../Install.sh 1; cd ..; \ + $(SHELL) Depend.sh $(YESDIR) 1; \ + fi; + @$(SHELL) Fetch.sh $(YESDIR) + +no-%: + @if [ ! -e $(NODIR) ]; then \ + echo "Package $(NODIR) does not exist"; exit 1; \ + elif [ -e $(NODIR)/Install.sh ]; then \ + echo "Uninstalling package $(@:no-%=%)"; \ + cd $(NODIR); $(SHELL) Install.sh 0; cd ..; \ + $(SHELL) Depend.sh $(NODIR) 0; \ + else \ + echo "Uninstalling package $(@:no-%=%)"; \ + cd $(NODIR); $(SHELL) ../Install.sh 0; cd ..; \ + $(SHELL) Depend.sh $(NODIR) 0; \ + fi; + +# download/build/install a package library +# update the timestamp on main.cpp to trigger a relink with "make machine" + +lib-%: + @if [ -e ../lib/$(LIBDIR)/Install.py ]; then \ + echo "Installing lib $(@:lib-%=%)"; \ + ( cd ../lib/$(LIBDIR); $(PYTHON) Install.py $(args) ); \ + elif [ -e ../lib/$(LIBUSERDIR)/Install.py ]; then \ + echo "Installing lib $(@:lib-user-%=%)"; \ + ( cd ../lib/$(LIBUSERDIR); $(PYTHON) Install.py $(args) ); \ + else \ + echo "Install script for lib $(@:lib-%=%) does not exist"; \ + fi; touch main.cpp + +# status = list src files that differ from package files +# installed = list of installed packages +# update = replace src files with newer package files +# overwrite = overwrite package files with newer src files +# diff = show differences between src and package files +# purge = delete obsolete and auto-generated package files + +package-status ps: + @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p status; done + @echo '' + @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p status; done + +package-installed pi: + @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p installed; done + @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p installed; done + +package-update pu: purge + @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p update; done + @echo '' + @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p update; done + +package-overwrite: purge + @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p overwrite; done + @echo '' + @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p overwrite; done + +package-diff pd: + @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p diff; done + @echo '' + @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p diff; done + +purge: Purge.list + @echo 'Purging obsolete and auto-generated source files' + @for f in `grep -v '#' Purge.list` ; \ + do test -f $$f && rm $$f && echo $$f || : ; \ + done From e28867eed0e440ac0e56f06fbd6948c2d74a23a2 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 23 Apr 2021 20:08:56 +0200 Subject: [PATCH 0624/1217] change doc --- doc/src/Commands_pair.rst | 4 ++-- doc/src/{pair_dpdext.rst => pair_dpd_ext.rst} | 0 doc/src/pair_style.rst | 2 ++ 3 files changed, 4 insertions(+), 2 deletions(-) rename doc/src/{pair_dpdext.rst => pair_dpd_ext.rst} (100%) diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 15126d6d34..40b81a2fd1 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -87,8 +87,8 @@ OPT. * :doc:`coul/wolf/cs ` * :doc:`dpd (gio) ` * :doc:`dpd/fdt ` - * :doc:`dpd/ext ` - * :doc:`dpd/ext/tstat ` + * :doc:`dpd/ext ` + * :doc:`dpd/ext/tstat ` * :doc:`dpd/fdt/energy (k) ` * :doc:`dpd/tstat (go) ` * :doc:`dsmc ` diff --git a/doc/src/pair_dpdext.rst b/doc/src/pair_dpd_ext.rst similarity index 100% rename from doc/src/pair_dpdext.rst rename to doc/src/pair_dpd_ext.rst diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 4990674973..94d4e07486 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -150,6 +150,8 @@ accelerated styles exist. * :doc:`coul/wolf ` - Coulomb via Wolf potential * :doc:`coul/wolf/cs ` - Coulomb via Wolf potential with core/shell adjustments * :doc:`dpd ` - dissipative particle dynamics (DPD) +* :doc:`dpd/ext ` - generalised force field for DPD +* :doc:`dpd/ext/tstat ` - pair-wise DPD thermostatting with generalised force field * :doc:`dpd/fdt ` - DPD for constant temperature and pressure * :doc:`dpd/fdt/energy ` - DPD for constant energy and enthalpy * :doc:`dpd/tstat ` - pair-wise DPD thermostatting From a9abcadc018ebbc49eb6c75f06d22133a7224bd6 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 23 Apr 2021 20:09:41 +0200 Subject: [PATCH 0625/1217] one more doc fix --- doc/src/pair_dpd_ext.rst | 43 ++++++++++++++++++++-------------------- 1 file changed, 22 insertions(+), 21 deletions(-) diff --git a/doc/src/pair_dpd_ext.rst b/doc/src/pair_dpd_ext.rst index 4b6855774d..cfc72fe84c 100644 --- a/doc/src/pair_dpd_ext.rst +++ b/doc/src/pair_dpd_ext.rst @@ -1,9 +1,10 @@ -.. index:: pair_style dpdext +.. index:: pair_style dpd/ext +.. index:: pair_style dpd/ext/tstat -pair_style dpdext command +pair_style dpd/ext command ========================== -pair_style dpdext/tstat command +pair_style dpd/ext/tstat command ================================ Syntax @@ -12,8 +13,8 @@ Syntax .. code-block:: LAMMPS - pair_style dpdext T cutoff seed - pair_style dpdext/tstat Tstart Tstop cutoff seed + pair_style dpd/ext T cutoff seed + pair_style dpd/ext/tstat Tstart Tstop cutoff seed * T = temperature (temperature units) * Tstart,Tstop = desired temperature at start/end of run (temperature units) @@ -26,22 +27,22 @@ Examples .. code-block:: LAMMPS - pair_style dpdext 1.0 2.5 34387 + pair_style dpd/ext 1.0 2.5 34387 pair_coeff 1 1 25.0 4.5 4.5 0.5 0.5 1.2 pair_coeff 1 2 40.0 4.5 4.5 0.5 0.5 1.2 - pair_style dpdext/tstat 1.0 1.0 2.5 34387 + pair_style dpd/ext/tstat 1.0 1.0 2.5 34387 pair_coeff 1 1 4.5 4.5 0.5 0.5 1.2 pair_coeff 1 2 4.5 4.5 0.5 0.5 1.2 Description """"""""""" -The style *dpdext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) `, :ref:`(Junghans) `. +The style *dpd/ext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) `, :ref:`(Junghans) `. -Style *dpdext/tstat* invokes an extended DPD thermostat on pairwise interactions, which is equivalent to the non-conservative portion of the extended DPD force field. To use *dpdext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay ` command to compute both the desired pair interaction and the thermostat for each pair of particles. +Style *dpd/ext/tstat* invokes an extended DPD thermostat on pairwise interactions, equivalent to the non-conservative portion of the extended DPD force field. To use *dpd/ext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay ` command to compute both the desired pair interaction and the thermostat for each pair of particles. -For the style *dpdext*\ , the force on atom I due to atom J is given as a sum +For the style *dpd/ext*\ , the force on atom I due to atom J is given as a sum of 3 terms .. math:: @@ -54,15 +55,15 @@ of 3 terms where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command. -For the style *dpdext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. +For the style *dpd/ext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. -For the style *dpdext*\ , the pairwise energy associated with style *dpdext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. For style *dpdext/tstat* there is no pairwise energy, but the last two terms of the formula make a contribution to the virial. +For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial. -For the style *dpdext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. +For the style *dpd/ext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. -For the style *dpdext*\ , the pairwise energy associated with style *dpdext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. For style *dpdext/tstat* there is no pairwise energy, but the last two terms of the formula make a contribution to the virial. +For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial. -For the style *dpdext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above: +For the style *dpd/ext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above: * A (force units) * :math:`\gamma_{\perp}` (force/velocity units) @@ -74,7 +75,7 @@ For the style *dpdext*, the following coefficients must be defined for each pair The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that :math:`\sigma`'s are set equal to :math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by the :doc:`pair_style ` command so it does not need to be specified. -For the style *dpdext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff ` command is the same, except that A is not included. +For the style *dpd/ext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff ` command is the same, except that A is not included. .. note:: @@ -89,17 +90,17 @@ For the style *dpdext/tstat*, the coefficients defined for each pair of atoms ty **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -The style *dpdext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. +The style *dpd/ext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. The pair styles do not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. Note that as discussed above, the energy due to the conservative :math:`\mathbf{f}^C` term is already shifted to be zero at the cutoff distance :math:`r_c`. -The :doc:`pair_modify ` table option is not relevant for the style *dpdext*. +The :doc:`pair_modify ` table option is not relevant for the style *dpd/ext*. -The style *dpdext* does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. +The style *dpd/ext* does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. The pair styles can only be used via the pair keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , and *outer*\ keywords. -The style *dpdext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. +The style *dpd/ext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. ---------- @@ -107,7 +108,7 @@ The style *dpdext/tstat* can ramp its target temperature over multiple runs, usi Restrictions """""""""""" -The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too infrequent for style *dpdext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. +The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too infrequent for style *dpd/ext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. The pair styles require to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. From 1f24a45ef7a32a7c62f28dd5a4043d9dddbe1d47 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 23 Apr 2021 20:09:51 +0200 Subject: [PATCH 0626/1217] fix Makefile --- src/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Makefile b/src/Makefile index 4fcc7402c9..d5f0e600d6 100644 --- a/src/Makefile +++ b/src/Makefile @@ -52,7 +52,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ python qeq replica rigid shock snap spin srd voronoi PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ - user-diffraction user-dpd user-dpdext user-drude user-eff user-fep user-h5md \ + user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ user-intel user-lb user-manifold user-meamc user-mesodpd user-mesont \ user-mgpt user-misc user-mofff user-molfile \ user-netcdf user-omp user-phonon user-pace user-plumed user-ptm user-qmmm \ From 628b06b7deb9b0b4824c397a00170b37e8ea2834 Mon Sep 17 00:00:00 2001 From: msvbd Date: Fri, 23 Apr 2021 20:15:11 +0200 Subject: [PATCH 0627/1217] fix CMakeLists.txt --- cmake/CMakeLists.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index d840dedf6c..f567a15d25 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -120,9 +120,9 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DPDEXT USER-DRUDE USER-EFF USER-FEP - USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC - USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB + USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF + USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE) From d60c630e56ef458929c5800020f2856fc078684d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 15:05:06 -0400 Subject: [PATCH 0628/1217] cosmetic changes: whitespace and include file order --- src/USER-MISC/pair_dpd_ext.cpp | 30 ++++++++++++++-------------- src/USER-MISC/pair_dpd_ext_tstat.cpp | 22 ++++++++++---------- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/src/USER-MISC/pair_dpd_ext.cpp b/src/USER-MISC/pair_dpd_ext.cpp index e5405cf071..ee03a6d1b9 100644 --- a/src/USER-MISC/pair_dpd_ext.cpp +++ b/src/USER-MISC/pair_dpd_ext.cpp @@ -20,17 +20,17 @@ ------------------------------------------------------------------------- */ #include "pair_dpd_ext.h" -#include #include "atom.h" #include "comm.h" -#include "update.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "random_mars.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "random_mars.h" +#include "update.h" +#include using namespace LAMMPS_NS; @@ -126,23 +126,23 @@ void PairDPDExt::compute(int eflag, int vflag) delvy = vytmp - v[j][1]; delvz = vztmp - v[j][2]; dot = delx*delvx + dely*delvy + delz*delvz; - + P[0][0] = 1.0 - delx*delx*rinv*rinv; P[0][1] = - delx*dely*rinv*rinv; P[0][2] = - delx*delz*rinv*rinv; - + P[1][0] = P[0][1]; P[1][1] = 1.0 - dely*dely*rinv*rinv; P[1][2] = - dely*delz*rinv*rinv; - + P[2][0] = P[0][2]; P[2][1] = P[1][2]; P[2][2] = 1.0 - delz*delz*rinv*rinv; - + wd = 1.0 - r/cut[itype][jtype]; wdPar = pow(wd,ws[itype][jtype]); wdPerp = pow(wd,wsT[itype][jtype]); - + randnum = random->gaussian(); randnumx = random->gaussian(); randnumy = random->gaussian(); @@ -156,7 +156,7 @@ void PairDPDExt::compute(int eflag, int vflag) // random force - parallel fpair += sigma[itype][jtype]*wdPar*randnum*dtinvsqrt; - + fpairx = fpair*rinv*delx; fpairy = fpair*rinv*dely; fpairz = fpair*rinv*delz; @@ -176,7 +176,7 @@ void PairDPDExt::compute(int eflag, int vflag) (P[1][0]*randnumx + P[1][1]*randnumy + P[1][2]*randnumz)*dtinvsqrt; fpairz += sigmaT[itype][jtype]*wdPerp* (P[2][0]*randnumx + P[2][1]*randnumy + P[2][2]*randnumz)*dtinvsqrt; - + fpairx *= factor_dpd; fpairy *= factor_dpd; fpairz *= factor_dpd; @@ -190,7 +190,7 @@ void PairDPDExt::compute(int eflag, int vflag) f[j][2] -= fpairz; } - if (eflag) { + if (eflag) { // unshifted eng of conservative term: // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]); // eng shifted to 0.0 at cutoff diff --git a/src/USER-MISC/pair_dpd_ext_tstat.cpp b/src/USER-MISC/pair_dpd_ext_tstat.cpp index 5449ca7358..a9f66fb38c 100644 --- a/src/USER-MISC/pair_dpd_ext_tstat.cpp +++ b/src/USER-MISC/pair_dpd_ext_tstat.cpp @@ -17,15 +17,15 @@ #include "pair_dpd_ext_tstat.h" -#include #include "atom.h" -#include "update.h" +#include "comm.h" +#include "error.h" #include "force.h" #include "neigh_list.h" -#include "comm.h" #include "random_mars.h" -#include "error.h" +#include "update.h" +#include using namespace LAMMPS_NS; @@ -114,23 +114,23 @@ void PairDPDExtTstat::compute(int eflag, int vflag) delvy = vytmp - v[j][1]; delvz = vztmp - v[j][2]; dot = delx*delvx + dely*delvy + delz*delvz; - + P[0][0] = 1.0 - delx*delx*rinv*rinv; P[0][1] = - delx*dely*rinv*rinv; P[0][2] = - delx*delz*rinv*rinv; - + P[1][0] = P[0][1]; P[1][1] = 1.0 - dely*dely*rinv*rinv; P[1][2] = - dely*delz*rinv*rinv; - + P[2][0] = P[0][2]; P[2][1] = P[1][2]; P[2][2] = 1.0 - delz*delz*rinv*rinv; - + wd = 1.0 - r/cut[itype][jtype]; wdPar = pow(wd,ws[itype][jtype]); wdPerp = pow(wd,wsT[itype][jtype]); - + randnum = random->gaussian(); randnumx = random->gaussian(); randnumy = random->gaussian(); @@ -141,7 +141,7 @@ void PairDPDExtTstat::compute(int eflag, int vflag) // random force - parallel fpair += sigma[itype][jtype]*wdPar*randnum*dtinvsqrt; - + fpairx = fpair*rinv*delx; fpairy = fpair*rinv*dely; fpairz = fpair*rinv*delz; @@ -161,7 +161,7 @@ void PairDPDExtTstat::compute(int eflag, int vflag) (P[1][0]*randnumx + P[1][1]*randnumy + P[1][2]*randnumz)*dtinvsqrt; fpairz += sigmaT[itype][jtype]*wdPerp* (P[2][0]*randnumx + P[2][1]*randnumy + P[2][2]*randnumz)*dtinvsqrt; - + fpairx *= factor_dpd; fpairy *= factor_dpd; fpairz *= factor_dpd; From 8fc9eb26bc6025b0849c4c64eef459d835feff58 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 15:08:20 -0400 Subject: [PATCH 0629/1217] address spell checker warnings --- doc/src/pair_style.rst | 4 ++-- doc/utils/sphinx-config/false_positives.txt | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 94d4e07486..ce74b0d873 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -150,8 +150,8 @@ accelerated styles exist. * :doc:`coul/wolf ` - Coulomb via Wolf potential * :doc:`coul/wolf/cs ` - Coulomb via Wolf potential with core/shell adjustments * :doc:`dpd ` - dissipative particle dynamics (DPD) -* :doc:`dpd/ext ` - generalised force field for DPD -* :doc:`dpd/ext/tstat ` - pair-wise DPD thermostatting with generalised force field +* :doc:`dpd/ext ` - generalized force field for DPD +* :doc:`dpd/ext/tstat ` - pair-wise DPD thermostatting with generalized force field * :doc:`dpd/fdt ` - DPD for constant temperature and pressure * :doc:`dpd/fdt/energy ` - DPD for constant energy and enthalpy * :doc:`dpd/tstat ` - pair-wise DPD thermostatting diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index da0617ce91..c29ff2b1d1 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2538,6 +2538,7 @@ ppn pppm prd Prakash +Praprotnik pre Pre prec From 5a12baeef9fe22679f89c0ef8146ff6895da7f84 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 15:14:01 -0400 Subject: [PATCH 0630/1217] remove dead code and silence compiler warnings --- src/SPIN/fix_langevin_spin.cpp | 8 ++------ src/SPIN/fix_langevin_spin.h | 2 +- src/SPIN/fix_nve_spin.h | 12 ++++++------ src/SPIN/fix_precession_spin.cpp | 5 ++--- src/SPIN/pair_spin_exchange_biquadratic.cpp | 7 ++----- 5 files changed, 13 insertions(+), 21 deletions(-) diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index 949833caa7..5c040da0f5 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -142,15 +142,11 @@ void FixLangevinSpin::add_tdamping(double spi[3], double fmi[3]) /* ---------------------------------------------------------------------- */ -void FixLangevinSpin::add_temperature(int i, double spi[3], double fmi[3]) +void FixLangevinSpin::add_temperature(double fmi[3]) { - // double rx = sigma*(2.0*random->uniform() - 1.0); - // double ry = sigma*(2.0*random->uniform() - 1.0); - // double rz = sigma*(2.0*random->uniform() - 1.0); double rx = sigma*random->gaussian(); double ry = sigma*random->gaussian(); double rz = sigma*random->gaussian(); - double hbar = force->hplanck/MY_2PI; // adding the random field @@ -172,6 +168,6 @@ void FixLangevinSpin::compute_single_langevin(int i, double spi[3], double fmi[3 int *mask = atom->mask; if (mask[i] & groupbit) { if (tdamp_flag) add_tdamping(spi,fmi); - if (temp_flag) add_temperature(i,spi,fmi); + if (temp_flag) add_temperature(fmi); } } diff --git a/src/SPIN/fix_langevin_spin.h b/src/SPIN/fix_langevin_spin.h index baa1cb1c84..b408e6ce2e 100644 --- a/src/SPIN/fix_langevin_spin.h +++ b/src/SPIN/fix_langevin_spin.h @@ -34,7 +34,7 @@ class FixLangevinSpin : public Fix { void init(); void setup(int); void add_tdamping(double *, double *); // add transverse damping - void add_temperature(int, double *, double *); + void add_temperature(double[3]); void compute_single_langevin(int, double *, double *); protected: diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h index 73716bac26..ec5917c7cf 100644 --- a/src/SPIN/fix_nve_spin.h +++ b/src/SPIN/fix_nve_spin.h @@ -61,6 +61,12 @@ friend class PairSpin; int tdamp_flag, temp_flag; int setforce_spin_flag; + // pointers to magnetic pair styles + + int npairs, npairspin; // # of pairs, and # of spin pairs + class Pair *pair; + class PairSpin **spin_pairs; // vector of spin pairs + // pointers to fix langevin/spin styles int nlangspin; @@ -76,12 +82,6 @@ friend class PairSpin; int nprecspin; class FixPrecessionSpin **lockprecessionspin; - // pointers to magnetic pair styles - - int npairs, npairspin; // # of pairs, and # of spin pairs - class Pair *pair; - class PairSpin **spin_pairs; // vector of spin pairs - // sectoring variables int nsectors; diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index c3f8a4d7df..e2ddccdd89 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -440,7 +440,7 @@ void FixPrecessionSpin::compute_stt(double spi[3], double fmi[3]) /* ---------------------------------------------------------------------- */ -double FixPrecessionSpin::compute_stt_energy(double spi[3]) +double FixPrecessionSpin::compute_stt_energy(double * /* spi */) { double energy = 0.0; // Non-conservative force return energy; @@ -530,14 +530,13 @@ double FixPrecessionSpin::compute_cubic_energy(double spi[3]) void FixPrecessionSpin::compute_hexaniso(double spi[3], double fmi[3]) { - double s_x,s_y,s_z; + double s_x,s_y; double pf, phi, ssint2; // changing to the axes' frame s_x = l6x*spi[0]+l6y*spi[1]+l6z*spi[2]; s_y = m6x*spi[0]+m6y*spi[1]+m6z*spi[2]; - s_z = n6x*spi[0]+n6y*spi[1]+n6z*spi[2]; // hexagonal anisotropy in the axes' frame diff --git a/src/SPIN/pair_spin_exchange_biquadratic.cpp b/src/SPIN/pair_spin_exchange_biquadratic.cpp index a00d1cc8b0..3c5a95e3dd 100644 --- a/src/SPIN/pair_spin_exchange_biquadratic.cpp +++ b/src/SPIN/pair_spin_exchange_biquadratic.cpp @@ -473,16 +473,13 @@ double PairSpinExchangeBiquadratic::compute_energy(int i, int j, double rsq, { int *type = atom->type; int itype,jtype; - double Jex,Kex,ra,sdots; - double rj,rk,r2j,r2k; + double Jex,Kex,sdots; + double r2j,r2k; double energy = 0.0; itype = type[i]; jtype = type[j]; - ra = sqrt(rsq); - rj = ra/J3[itype][jtype]; r2j = rsq/J3[itype][jtype]/J3[itype][jtype]; - rk = ra/K3[itype][jtype]; r2k = rsq/K3[itype][jtype]/K3[itype][jtype]; Jex = 4.0*J1_mech[itype][jtype]*r2j; From 8541b0da3e16f396112439500492476ea9351d38 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 15:35:45 -0400 Subject: [PATCH 0631/1217] reduce compiler warnings by avoiding to redeclare variables so they shadow others --- src/angle_hybrid.cpp | 8 ++++---- src/atom_vec_hybrid.cpp | 14 +++++++------- src/balance.cpp | 4 ++-- src/bond_hybrid.cpp | 6 +++--- src/change_box.cpp | 6 +++--- src/compute_angmom_chunk.cpp | 6 +++--- src/compute_centro_atom.cpp | 2 +- src/compute_chunk_atom.cpp | 9 +++------ src/compute_dipole_chunk.cpp | 6 +++--- src/compute_global_atom.cpp | 10 +++++----- src/compute_reduce_region.cpp | 21 +++++++-------------- src/compute_temp_sphere.cpp | 7 ++----- src/create_bonds.cpp | 2 +- src/dihedral_hybrid.cpp | 6 +++--- src/dump_custom.cpp | 12 +++++------- src/dump_image.cpp | 6 +++--- src/dump_local.cpp | 8 ++++---- src/fix_ave_chunk.cpp | 3 +-- 18 files changed, 60 insertions(+), 76 deletions(-) diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index d7e3051b90..1295776bef 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -183,16 +183,16 @@ void AngleHybrid::allocate() void AngleHybrid::settings(int narg, char **arg) { - int i,m,istyle; + int i, m,istyle; if (narg < 1) error->all(FLERR,"Illegal angle_style command"); // delete old lists, since cannot just change settings if (nstyles) { - for (int i = 0; i < nstyles; i++) delete styles[i]; + for (i = 0; i < nstyles; i++) delete styles[i]; delete [] styles; - for (int i = 0; i < nstyles; i++) delete [] keywords[i]; + for (i = 0; i < nstyles; i++) delete [] keywords[i]; delete [] keywords; } @@ -201,7 +201,7 @@ void AngleHybrid::settings(int narg, char **arg) memory->destroy(map); delete [] nanglelist; delete [] maxangle; - for (int i = 0; i < nstyles; i++) + for (i = 0; i < nstyles; i++) memory->destroy(anglelist[i]); delete [] anglelist; } diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 6ddb72a1bf..7faa5cc145 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -98,7 +98,7 @@ void AtomVecHybrid::process_args(int narg, char **arg) // call process_args() with set of args that are not atom style names // use known_style() to determine which args these are - int i,jarg,dummy; + int i,k,jarg,dummy; int iarg = 0; nstyles = 0; @@ -123,7 +123,7 @@ void AtomVecHybrid::process_args(int narg, char **arg) molecular = Atom::ATOMIC; maxexchange = 0; - for (int k = 0; k < nstyles; k++) { + for (k = 0; k < nstyles; k++) { if ((styles[k]->molecular == Atom::MOLECULAR && molecular == Atom::TEMPLATE) || (styles[k]->molecular == Atom::TEMPLATE && molecular == Atom::MOLECULAR)) error->all(FLERR, @@ -147,7 +147,7 @@ void AtomVecHybrid::process_args(int narg, char **arg) int mass_pertype = 0; int mass_peratom = 0; - for (int k = 0; k < nstyles; k++) { + for (k = 0; k < nstyles; k++) { if (styles[k]->mass_type == 0) mass_peratom = 1; if (styles[k]->mass_type == 1) mass_pertype = 1; } @@ -159,14 +159,14 @@ void AtomVecHybrid::process_args(int narg, char **arg) // free allstyles created by build_styles() - for (int i = 0; i < nallstyles; i++) delete [] allstyles[i]; + for (i = 0; i < nallstyles; i++) delete [] allstyles[i]; delete [] allstyles; // set field strings from all substyles fieldstrings = new FieldStrings[nstyles]; - for (int k = 0; k < nstyles; k++) { + for (k = 0; k < nstyles; k++) { fieldstrings[k].fstr = new char*[NFIELDSTRINGS]; fieldstrings[k].fstr[0] = styles[k]->fields_grow; fieldstrings[k].fstr[1] = styles[k]->fields_copy; @@ -226,7 +226,7 @@ void AtomVecHybrid::process_args(int narg, char **arg) // sum two sizes over contributions from each substyle with bonus data. nstyles_bonus = 0; - for (int k = 0; k < nstyles; k++) + for (k = 0; k < nstyles; k++) if (styles[k]->bonus_flag) nstyles_bonus++; if (nstyles_bonus) { @@ -235,7 +235,7 @@ void AtomVecHybrid::process_args(int narg, char **arg) nstyles_bonus = 0; size_forward_bonus = 0; size_border_bonus = 0; - for (int k = 0; k < nstyles; k++) { + for (k = 0; k < nstyles; k++) { if (styles[k]->bonus_flag) { styles_bonus[nstyles_bonus++] = styles[k]; size_forward_bonus += styles[k]->size_forward_bonus; diff --git a/src/balance.cpp b/src/balance.cpp index bf037e8f8f..0746ece1f0 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -919,7 +919,7 @@ int Balance::shift() // do this with minimal adjustment to splits double close = (1.0+EPSNEIGH) * neighbor->skin / boxsize; - double delta,midpt,start,stop,lbound,ubound,spacing; + double midpt,start,stop,lbound,ubound,spacing; i = 0; while (i < np) { @@ -1094,7 +1094,7 @@ int Balance::adjust(int n, double *split) } int change = 0; - for (int i = 1; i < n; i++) + for (i = 1; i < n; i++) if (sum[i] != target[i]) { change = 1; if (rho == 0) split[i] = 0.5 * (lo[i]+hi[i]); diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index f1debc0676..3a316d995d 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -182,9 +182,9 @@ void BondHybrid::settings(int narg, char **arg) // delete old lists, since cannot just change settings if (nstyles) { - for (int i = 0; i < nstyles; i++) delete styles[i]; + for (i = 0; i < nstyles; i++) delete styles[i]; delete [] styles; - for (int i = 0; i < nstyles; i++) delete [] keywords[i]; + for (i = 0; i < nstyles; i++) delete [] keywords[i]; delete [] keywords; has_quartic = -1; } @@ -194,7 +194,7 @@ void BondHybrid::settings(int narg, char **arg) memory->destroy(map); delete [] nbondlist; delete [] maxbond; - for (int i = 0; i < nstyles; i++) + for (i = 0; i < nstyles; i++) memory->destroy(bondlist[i]); delete [] bondlist; } diff --git a/src/change_box.cpp b/src/change_box.cpp index 4471d85132..78f1261caf 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -193,7 +193,7 @@ void ChangeBox::command(int narg, char **arg) // compute scale factors if FINAL,DELTA used since they have distance units int flag = 0; - for (int i = 0; i < nops; i++) + for (i = 0; i < nops; i++) if (ops[i].style == FINAL || ops[i].style == DELTA) flag = 1; if (flag && scaleflag) { @@ -295,7 +295,7 @@ void ChangeBox::command(int narg, char **arg) if (output->ndump) error->all(FLERR, "Cannot change box ortho/triclinic with dumps defined"); - for (int i = 0; i < modify->nfix; i++) + for (i = 0; i < modify->nfix; i++) if (modify->fix[i]->no_change_box) error->all(FLERR, "Cannot change box ortho/triclinic with " @@ -310,7 +310,7 @@ void ChangeBox::command(int narg, char **arg) if (output->ndump) error->all(FLERR, "Cannot change box ortho/triclinic with dumps defined"); - for (int i = 0; i < modify->nfix; i++) + for (i = 0; i < modify->nfix; i++) if (modify->fix[i]->no_change_box) error->all(FLERR, "Cannot change box ortho/triclinic with " diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp index 39cae07503..4fd2e14661 100644 --- a/src/compute_angmom_chunk.cpp +++ b/src/compute_angmom_chunk.cpp @@ -101,7 +101,7 @@ void ComputeAngmomChunk::compute_array() // zero local per-chunk values - for (int i = 0; i < nchunk; i++) { + for (i = 0; i < nchunk; i++) { massproc[i] = 0.0; com[i][0] = com[i][1] = com[i][2] = 0.0; angmom[i][0] = angmom[i][1] = angmom[i][2] = 0.0; @@ -117,7 +117,7 @@ void ComputeAngmomChunk::compute_array() double *rmass = atom->rmass; int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) + for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) { index = ichunk[i]-1; if (index < 0) continue; @@ -133,7 +133,7 @@ void ComputeAngmomChunk::compute_array() MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); - for (int i = 0; i < nchunk; i++) { + for (i = 0; i < nchunk; i++) { if (masstotal[i] > 0.0) { comall[i][0] /= masstotal[i]; comall[i][1] /= masstotal[i]; diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp index 9d40fa0fd5..8a9bb1fdf4 100644 --- a/src/compute_centro_atom.cpp +++ b/src/compute_centro_atom.cpp @@ -269,7 +269,7 @@ void ComputeCentroAtom::compute_peratom() delx = x[jj][0] + x[kk][0] - 2.0*xtmp; dely = x[jj][1] + x[kk][1] - 2.0*ytmp; delz = x[jj][2] + x[kk][2] - 2.0*ztmp; - double rsq = delx*delx + dely*dely + delz*delz; + rsq = delx*delx + dely*dely + delz*delz; pairs[n++] = rsq; if (rsq < rsq2) { diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index 5960e1fc6f..26967a1b12 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -687,6 +687,7 @@ void ComputeChunkAtom::compute_ichunk() // or if idsflag = NFREQ and lock is in place and are on later timestep // else proceed to recalculate per-atom chunk assignments + const int nlocal = atom->nlocal; int restore = 0; if (idsflag == ONCE && invoked_ichunk >= 0) restore = 1; if (idsflag == NFREQ && lockfix && update->ntimestep > lockstart) restore = 1; @@ -694,7 +695,6 @@ void ComputeChunkAtom::compute_ichunk() if (restore) { invoked_ichunk = update->ntimestep; double *vstore = fixstore->vstore; - int nlocal = atom->nlocal; for (i = 0; i < nlocal; i++) ichunk[i] = static_cast (vstore[i]); return; } @@ -711,8 +711,6 @@ void ComputeChunkAtom::compute_ichunk() // compress chunk IDs via hash of the original uncompressed IDs // also apply discard rule except for binning styles which already did - int nlocal = atom->nlocal; - if (compress) { if (binflag) { for (i = 0; i < nlocal; i++) { @@ -761,8 +759,7 @@ void ComputeChunkAtom::compute_ichunk() if (idsflag == ONCE || (idsflag == NFREQ && lockfix)) { double *vstore = fixstore->vstore; - int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) vstore[i] = ichunk[i]; + for (i = 0; i < nlocal; i++) vstore[i] = ichunk[i]; } // one-time check if which = MOLECULE and @@ -897,7 +894,7 @@ void ComputeChunkAtom::assign_chunk_ids() double **x = atom->x; int *mask = atom->mask; - int nlocal = atom->nlocal; + const int nlocal = atom->nlocal; if (regionflag) { for (i = 0; i < nlocal; i++) { diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp index 708ea3f755..5594229a97 100644 --- a/src/compute_dipole_chunk.cpp +++ b/src/compute_dipole_chunk.cpp @@ -119,7 +119,7 @@ void ComputeDipoleChunk::compute_array() // zero local per-chunk values - for (int i = 0; i < nchunk; i++) { + for (i = 0; i < nchunk; i++) { massproc[i] = chrgproc[i] = 0.0; com[i][0] = com[i][1] = com[i][2] = 0.0; dipole[i][0] = dipole[i][1] = dipole[i][2] = dipole[i][3] = 0.0; @@ -138,7 +138,7 @@ void ComputeDipoleChunk::compute_array() int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) + for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) { index = ichunk[i]-1; if (index < 0) continue; @@ -159,7 +159,7 @@ void ComputeDipoleChunk::compute_array() MPI_Allreduce(chrgproc,chrgtotal,nchunk,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); - for (int i = 0; i < nchunk; i++) { + for (i = 0; i < nchunk; i++) { if (masstotal[i] > 0.0) { comall[i][0] /= masstotal[i]; comall[i][1] /= masstotal[i]; diff --git a/src/compute_global_atom.cpp b/src/compute_global_atom.cpp index e49ee69b07..5097032708 100644 --- a/src/compute_global_atom.cpp +++ b/src/compute_global_atom.cpp @@ -74,14 +74,14 @@ ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) : nvalues = 0; for (iarg = 0; iarg < nargnew; iarg++) { - ArgInfo argi(arg[iarg]); + ArgInfo argi2(arg[iarg]); - which[nvalues] = argi.get_type(); - argindex[nvalues] = argi.get_index1(); - ids[nvalues] = argi.copy_name(); + which[nvalues] = argi2.get_type(); + argindex[nvalues] = argi2.get_index1(); + ids[nvalues] = argi2.copy_name(); if ((which[nvalues] == ArgInfo::UNKNOWN) || (which[nvalues] == ArgInfo::NONE) - || (argi.get_dim() > 1)) + || (argi2.get_dim() > 1)) error->all(FLERR,"Illegal compute slice command"); nvalues++; diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp index 626a681bbd..0a8526bb8f 100644 --- a/src/compute_reduce_region.cpp +++ b/src/compute_reduce_region.cpp @@ -109,18 +109,16 @@ double ComputeReduceRegion::compute_one(int m, int flag) if (j == 0) { double *compute_vector = compute->vector_atom; - int n = nlocal; if (flag < 0) { - for (i = 0; i < n; i++) + for (i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) combine(one,compute_vector[i],i); } else one = compute_vector[flag]; } else { double **compute_array = compute->array_atom; - int n = nlocal; int jm1 = j - 1; if (flag < 0) { - for (i = 0; i < n; i++) + for (i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) combine(one,compute_array[i][jm1],i); } else one = compute_array[flag][jm1]; @@ -134,17 +132,15 @@ double ComputeReduceRegion::compute_one(int m, int flag) if (j == 0) { double *compute_vector = compute->vector_local; - int n = compute->size_local_rows; if (flag < 0) - for (i = 0; i < n; i++) + for (i = 0; i < compute->size_local_rows; i++) combine(one,compute_vector[i],i); else one = compute_vector[flag]; } else { double **compute_array = compute->array_local; - int n = compute->size_local_rows; int jm1 = j - 1; if (flag < 0) - for (i = 0; i < n; i++) + for (i = 0; i < compute->size_local_rows; i++) combine(one,compute_array[i][jm1],i); else one = compute_array[flag][jm1]; } @@ -161,9 +157,8 @@ double ComputeReduceRegion::compute_one(int m, int flag) if (flavor[m] == PERATOM) { if (j == 0) { double *fix_vector = fix->vector_atom; - int n = nlocal; if (flag < 0) { - for (i = 0; i < n; i++) + for (i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) combine(one,fix_vector[i],i); } else one = fix_vector[flag]; @@ -180,17 +175,15 @@ double ComputeReduceRegion::compute_one(int m, int flag) } else if (flavor[m] == LOCAL) { if (j == 0) { double *fix_vector = fix->vector_local; - int n = fix->size_local_rows; if (flag < 0) - for (i = 0; i < n; i++) + for (i = 0; i < fix->size_local_rows; i++) combine(one,fix_vector[i],i); else one = fix_vector[flag]; } else { double **fix_array = fix->array_local; - int n = fix->size_local_rows; int jm1 = j - 1; if (flag < 0) - for (i = 0; i < n; i++) + for (i = 0; i < fix->size_local_rows; i++) combine(one,fix_array[i][jm1],i); else one = fix_array[flag][jm1]; } diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp index b8ac7cf566..5cd7dce43a 100644 --- a/src/compute_temp_sphere.cpp +++ b/src/compute_temp_sphere.cpp @@ -135,8 +135,8 @@ void ComputeTempSphere::dof_compute() // user should correct this via compute_modify if needed double *radius = atom->radius; - int *mask = atom->mask; - int nlocal = atom->nlocal; + const int *mask = atom->mask; + const int nlocal = atom->nlocal; count = 0; if (domain->dimension == 3) { @@ -170,9 +170,6 @@ void ComputeTempSphere::dof_compute() if (mode == ALL) dof -= tbias->dof_remove(-1) * natoms_temp; } else if (tempbias == 2) { - int *mask = atom->mask; - int nlocal = atom->nlocal; - tbias->dof_remove_pre(); count = 0; diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index bedbe4b436..d50fcbf3f7 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -310,7 +310,7 @@ void CreateBonds::many() // recount bonds bigint nbonds = 0; - for (int i = 0; i < nlocal; i++) nbonds += num_bond[i]; + for (i = 0; i < nlocal; i++) nbonds += num_bond[i]; MPI_Allreduce(&nbonds,&atom->nbonds,1,MPI_LMP_BIGINT,MPI_SUM,world); if (!force->newton_bond) atom->nbonds /= 2; diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index c30c0705f6..caebd2a079 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -177,9 +177,9 @@ void DihedralHybrid::settings(int narg, char **arg) // delete old lists, since cannot just change settings if (nstyles) { - for (int i = 0; i < nstyles; i++) delete styles[i]; + for (i = 0; i < nstyles; i++) delete styles[i]; delete [] styles; - for (int i = 0; i < nstyles; i++) delete [] keywords[i]; + for (i = 0; i < nstyles; i++) delete [] keywords[i]; delete [] keywords; } @@ -188,7 +188,7 @@ void DihedralHybrid::settings(int narg, char **arg) memory->destroy(map); delete [] ndihedrallist; delete [] maxdihedral; - for (int i = 0; i < nstyles; i++) + for (i = 0; i < nstyles; i++) memory->destroy(dihedrallist[i]); delete [] dihedrallist; } diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 53094849ac..40b3e6fc28 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -317,14 +317,14 @@ void DumpCustom::init_style() // check that fix frequency is acceptable int icompute; - for (int i = 0; i < ncompute; i++) { + for (i = 0; i < ncompute; i++) { icompute = modify->find_compute(id_compute[i]); if (icompute < 0) error->all(FLERR,"Could not find dump custom compute ID"); compute[i] = modify->compute[icompute]; } int ifix; - for (int i = 0; i < nfix; i++) { + for (i = 0; i < nfix; i++) { ifix = modify->find_fix(id_fix[i]); if (ifix < 0) error->all(FLERR,"Could not find dump custom fix ID"); fix[i] = modify->fix[ifix]; @@ -333,7 +333,7 @@ void DumpCustom::init_style() } int ivariable; - for (int i = 0; i < nvariable; i++) { + for (i = 0; i < nvariable; i++) { ivariable = input->variable->find(id_variable[i]); if (ivariable < 0) error->all(FLERR,"Could not find dump custom variable name"); @@ -341,7 +341,7 @@ void DumpCustom::init_style() } int icustom; - for (int i = 0; i < ncustom; i++) { + for (i = 0; i < ncustom; i++) { icustom = atom->find_custom(id_custom[i],flag_custom[i]); if (icustom < 0) error->all(FLERR,"Could not find custom per-atom property ID"); @@ -546,7 +546,7 @@ int DumpCustom::count() // grow choose and variable vbuf arrays if needed - int nlocal = atom->nlocal; + const int nlocal = atom->nlocal; if (atom->nmax > maxlocal) { maxlocal = atom->nmax; @@ -620,7 +620,6 @@ int DumpCustom::count() double *values; double value; int nstride,lastflag; - int nlocal = atom->nlocal; for (int ithresh = 0; ithresh < nthresh; ithresh++) { @@ -1536,7 +1535,6 @@ int DumpCustom::parse_fields(int narg, char **arg) default: return iarg; - break; } } } diff --git a/src/dump_image.cpp b/src/dump_image.cpp index 69ebad9c52..4b7c6e3cf8 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -1042,7 +1042,7 @@ void DumpImage::create_image() // render outline of my sub-box, orthogonal or triclinic if (subboxflag) { - double diameter = MIN(boxxhi-boxxlo,boxyhi-boxylo); + diameter = MIN(boxxhi-boxxlo,boxyhi-boxylo); if (domain->dimension == 3) diameter = MIN(diameter,boxzhi-boxzlo); diameter *= subboxdiam; @@ -1072,7 +1072,7 @@ void DumpImage::create_image() // render outline of simulation box, orthogonal or triclinic if (boxflag) { - double diameter = MIN(boxxhi-boxxlo,boxyhi-boxylo); + diameter = MIN(boxxhi-boxxlo,boxyhi-boxylo); if (domain->dimension == 3) diameter = MIN(diameter,boxzhi-boxzlo); diameter *= boxdiam; @@ -1100,7 +1100,7 @@ void DumpImage::create_image() // offset by 10% of box size and scale by axeslen if (axesflag) { - double diameter = MIN(boxxhi-boxxlo,boxyhi-boxylo); + diameter = MIN(boxxhi-boxxlo,boxyhi-boxylo); if (domain->dimension == 3) diameter = MIN(diameter,boxzhi-boxzlo); diameter *= axesdiam; diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 0f8d139f66..a354c6fbba 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -198,14 +198,14 @@ void DumpLocal::init_style() // check that fix frequency is acceptable int icompute; - for (int i = 0; i < ncompute; i++) { + for (i = 0; i < ncompute; i++) { icompute = modify->find_compute(id_compute[i]); if (icompute < 0) error->all(FLERR,"Could not find dump local compute ID"); compute[i] = modify->compute[icompute]; } int ifix; - for (int i = 0; i < nfix; i++) { + for (i = 0; i < nfix; i++) { ifix = modify->find_fix(id_fix[i]); if (ifix < 0) error->all(FLERR,"Could not find dump local fix ID"); fix[i] = modify->fix[ifix]; @@ -332,14 +332,14 @@ int DumpLocal::count() nmine = -1; - for (int i = 0; i < ncompute; i++) { + for (i = 0; i < ncompute; i++) { if (nmine < 0) nmine = compute[i]->size_local_rows; else if (nmine != compute[i]->size_local_rows) error->one(FLERR, "Dump local count is not consistent across input fields"); } - for (int i = 0; i < nfix; i++) { + for (i = 0; i < nfix; i++) { if (nmine < 0) nmine = fix[i]->size_local_rows; else if (nmine != fix[i]->size_local_rows) error->one(FLERR, diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index b0a99d332a..07064ded4c 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -488,7 +488,7 @@ void FixAveChunk::init() for (int m = 0; m < nvalues; m++) { if (which[m] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[m]); + icompute = modify->find_compute(ids[m]); if (icompute < 0) error->all(FLERR,"Compute ID for fix ave/chunk does not exist"); value2index[m] = icompute; @@ -984,7 +984,6 @@ void FixAveChunk::end_of_step() } } } else { - int j; if (ncoord == 0) { for (m = 0; m < nchunk; m++) { fprintf(fp," %d %d %g",m+1,chunkID[m],count_total[m]/normcount); From fe063b27c73d7b82c0b3993fe502d1d6608e2687 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 15:51:16 -0400 Subject: [PATCH 0632/1217] silence compiler warnings --- src/dump_image.cpp | 2 +- src/fix_adapt.cpp | 2 +- src/fix_ave_time.cpp | 1 - src/fix_deform.cpp | 2 +- src/fix_heat.cpp | 2 +- src/fix_momentum.cpp | 9 +++------ src/fix_nh.cpp | 12 ++++++------ src/group.cpp | 2 +- src/improper_hybrid.cpp | 6 +++--- src/input.cpp | 4 ++-- src/library.cpp | 5 ++--- 11 files changed, 21 insertions(+), 26 deletions(-) diff --git a/src/dump_image.cpp b/src/dump_image.cpp index 4b7c6e3cf8..c5dd7b455a 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -1244,7 +1244,7 @@ int DumpImage::modify_param(int narg, char **arg) else error->all(FLERR,"Illegal dump_modify command"); int nentry = utils::inumeric(FLERR,arg[5],false,lmp); if (nentry < 1) error->all(FLERR,"Illegal dump_modify command"); - int n = 6 + factor*nentry; + n = 6 + factor*nentry; if (narg < n) error->all(FLERR,"Illegal dump_modify command"); int flag = image->map_reset(0,n-1,&arg[1]); if (flag) error->all(FLERR,"Illegal dump_modify command"); diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index 51fdb16d5d..7db16badc9 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -302,7 +302,7 @@ void FixAdapt::init() // allow a dynamic group only if ATOM attribute not used if (group->dynamic[igroup]) - for (int i = 0; i < nadapt; i++) + for (i = 0; i < nadapt; i++) if (adapt[i].which == ATOM) error->all(FLERR,"Cannot use dynamic group with fix adapt atom"); diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index 7ecb88ddab..5e640aa37a 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -723,7 +723,6 @@ void FixAveTime::invoke_vector(bigint ntimestep) allocate_arrays(); } - bigint ntimestep = update->ntimestep; int lockforever_flag = 0; for (i = 0; i < nvalues; i++) { if (!varlen[i] || which[i] != ArgInfo::COMPUTE) continue; diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index b3e5722ee1..2624b30181 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -714,7 +714,7 @@ void FixDeform::end_of_step() // set new box size for VOLUME dims that are linked to other dims // NOTE: still need to set h_rate for these dims - for (int i = 0; i < 3; i++) { + for (i = 0; i < 3; i++) { if (set[i].style != VOLUME) continue; if (set[i].substyle == ONE_FROM_ONE) { diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp index 920d06dc49..14f2cceca2 100644 --- a/src/fix_heat.cpp +++ b/src/fix_heat.cpp @@ -213,7 +213,7 @@ void FixHeat::end_of_step() v[i][2] = scale*v[i][2] - vsub[2]; } } else { - for (int i = 0; i < nlocal; i++) + for (i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) { v[i][0] = scale*v[i][0] - vsub[0]; v[i][1] = scale*v[i][1] - vsub[1]; diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp index da86473e61..509da7d0fd 100644 --- a/src/fix_momentum.cpp +++ b/src/fix_momentum.cpp @@ -95,8 +95,11 @@ void FixMomentum::init() void FixMomentum::end_of_step() { + double **x = atom->x; double **v = atom->v; int *mask = atom->mask; + imageint *image = atom->image; + const int nlocal = atom->nlocal; double ekin_old,ekin_new; ekin_old = ekin_new = 0.0; @@ -157,12 +160,6 @@ void FixMomentum::end_of_step() // vnew_i = v_i - w x r_i // must use unwrapped coords to compute r_i correctly - double **x = atom->x; - double **v = atom->v; - int *mask = atom->mask; - imageint *image = atom->image; - int nlocal = atom->nlocal; - double dx,dy,dz; double unwrap[3]; diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index d95763f06b..e8b58a6152 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -1092,7 +1092,7 @@ void FixNH::remap() // omega is not used, except for book-keeping - for (int i = 0; i < 6; i++) omega[i] += dto*omega_dot[i]; + for (i = 0; i < 6; i++) omega[i] += dto*omega_dot[i]; // convert pertinent atoms and rigid bodies to lamda coords @@ -1781,7 +1781,7 @@ void FixNH::nhc_temp_integrate() if (eta_mass_flag) { eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq); - for (int ich = 1; ich < mtchain; ich++) + for (ich = 1; ich < mtchain; ich++) eta_mass[ich] = boltz * t_target / (t_freq*t_freq); } @@ -1853,12 +1853,12 @@ void FixNH::nhc_press_integrate() if (omega_mass_flag) { double nkt = (atom->natoms + 1) * kt; - for (int i = 0; i < 3; i++) + for (i = 0; i < 3; i++) if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]); if (pstyle == TRICLINIC) { - for (int i = 3; i < 6; i++) + for (i = 3; i < 6; i++) if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]); } } @@ -1866,9 +1866,9 @@ void FixNH::nhc_press_integrate() if (etap_mass_flag) { if (mpchain) { etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max); - for (int ich = 1; ich < mpchain; ich++) + for (ich = 1; ich < mpchain; ich++) etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max); - for (int ich = 1; ich < mpchain; ich++) + for (ich = 1; ich < mpchain; ich++) etap_dotdot[ich] = (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - boltz * t_target) / etap_mass[ich]; diff --git a/src/group.cpp b/src/group.cpp index 9e140779ef..0f46e17152 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -494,7 +494,7 @@ void Group::assign(int narg, char **arg) std::string fixcmd = "GROUP_"; fixcmd += fmt::format("{} {} GROUP",names[igroup],arg[2]); - for (int i = 3; i < narg; i++) fixcmd += std::string(" ") + arg[i]; + for (i = 3; i < narg; i++) fixcmd += std::string(" ") + arg[i]; modify->add_fix(fixcmd); // style = static diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index fd5d76049b..23f6633ef2 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -185,9 +185,9 @@ void ImproperHybrid::settings(int narg, char **arg) // delete old lists, since cannot just change settings if (nstyles) { - for (int i = 0; i < nstyles; i++) delete styles[i]; + for (i = 0; i < nstyles; i++) delete styles[i]; delete [] styles; - for (int i = 0; i < nstyles; i++) delete [] keywords[i]; + for (i = 0; i < nstyles; i++) delete [] keywords[i]; delete [] keywords; } @@ -196,7 +196,7 @@ void ImproperHybrid::settings(int narg, char **arg) memory->destroy(map); delete [] nimproperlist; delete [] maximproper; - for (int i = 0; i < nstyles; i++) + for (i = 0; i < nstyles; i++) memory->destroy(improperlist[i]); delete [] improperlist; } diff --git a/src/input.cpp b/src/input.cpp index d3352b380a..f71dffbf54 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -887,7 +887,7 @@ void Input::ifthenelse() char **commands = new char*[ncommands]; ncommands = 0; for (int i = first; i <= last; i++) { - int n = strlen(arg[i]) + 1; + n = strlen(arg[i]) + 1; if (n == 1) error->all(FLERR,"Illegal if command"); commands[ncommands] = new char[n]; strcpy(commands[ncommands],arg[i]); @@ -940,7 +940,7 @@ void Input::ifthenelse() char **commands = new char*[ncommands]; ncommands = 0; for (int i = first; i <= last; i++) { - int n = strlen(arg[i]) + 1; + n = strlen(arg[i]) + 1; if (n == 1) error->all(FLERR,"Illegal if command"); commands[ncommands] = new char[n]; strcpy(commands[ncommands],arg[i]); diff --git a/src/library.cpp b/src/library.cpp index c51006f8d8..b85abe6bad 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -1952,8 +1952,9 @@ void *lammps_extract_variable(void *handle, const char *name, const char *group) } } END_CAPTURE - +#if defined(LAMMPS_EXCEPTIONS) return nullptr; +#endif } /* ---------------------------------------------------------------------- */ @@ -2207,7 +2208,6 @@ void lammps_gather_atoms_concat(void *handle, char *name, int type, int count, v MPI_INT,lmp->world); } else if (imgunpack) { - int *copy; lmp->memory->create(copy,count*nlocal,"lib/gather:copy"); offset = 0; for (i = 0; i < nlocal; i++) { @@ -3057,7 +3057,6 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d MPI_INT,lmp->world); } else if (imgunpack) { - int *copy; lmp->memory->create(copy,count*nlocal,"lib/gather:copy"); offset = 0; for (i = 0; i < nlocal; i++) { From f759e6ffcf59942132964e8da080d1e765802882 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 15:51:43 -0400 Subject: [PATCH 0633/1217] don't implicitly assume an undefined define equals 0 --- src/info.cpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/info.cpp b/src/info.cpp index 18926ed49e..099a4582dc 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -1269,18 +1269,18 @@ std::string Info::get_os_info() std::string Info::get_compiler_info() { std::string buf; -#if __INTEL_LLVM_COMPILER +#if defined(__INTEL_LLVM_COMPILER) double version = static_cast(__INTEL_LLVM_COMPILER)*0.01; buf = fmt::format("Intel LLVM C++ {:.1f} / {}", version, __VERSION__); -#elif __clang__ +#elif defined(__clang__) buf = fmt::format("Clang C++ {}", __VERSION__); -#elif __PGI +#elif defined(__PGI) buf = fmt::format("PGI C++ {}.{}",__PGIC__,__PGIC_MINOR__); -#elif __INTEL_COMPILER +#elif defined(__INTEL_COMPILER) double version = static_cast(__INTEL_COMPILER)*0.01; buf = fmt::format("Intel Classic C++ {:.2f}.{} / {}", version, __INTEL_COMPILER_UPDATE, __VERSION__); -#elif __GNUC__ +#elif defined(__GNUC__) buf = fmt::format("GNU C++ {}", __VERSION__); #else buf = "(Unknown)"; From ef858ae70fc03752a16b49f670d50597fef61513 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 16:19:57 -0400 Subject: [PATCH 0634/1217] silence compiler warnings --- src/KSPACE/ewald_dipole.cpp | 1 - src/KSPACE/msm_cg.cpp | 4 +- src/KSPACE/pair_buck_coul_msm.cpp | 2 +- src/KSPACE/pair_buck_long_coul_long.cpp | 35 +++++++++-------- src/lmppython.cpp | 6 +-- src/math_extra.cpp | 4 +- src/neighbor.cpp | 4 +- src/read_dump.cpp | 6 +-- src/read_restart.cpp | 4 +- src/replicate.cpp | 2 +- src/text_file_reader.cpp | 2 +- src/utils.cpp | 4 +- src/variable.cpp | 50 ++++++++++++------------- 13 files changed, 61 insertions(+), 63 deletions(-) diff --git a/src/KSPACE/ewald_dipole.cpp b/src/KSPACE/ewald_dipole.cpp index 34c72dafc5..b918adede3 100644 --- a/src/KSPACE/ewald_dipole.cpp +++ b/src/KSPACE/ewald_dipole.cpp @@ -806,7 +806,6 @@ void EwaldDipole::slabcorr() if (atom->torque) { double ffact = qscale * (-4.0*MY_PI/volume); - double **mu = atom->mu; double **torque = atom->torque; for (int i = 0; i < nlocal; i++) { torque[i][0] += ffact * dipole_all * mu[i][1]; diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp index 4c9384f13e..6123aedfb8 100644 --- a/src/KSPACE/msm_cg.cpp +++ b/src/KSPACE/msm_cg.cpp @@ -166,7 +166,7 @@ void MSMCG::compute(int eflag, int vflag) // forward communicate charge density values to fill ghost grid points // compute direct sum interaction and then restrict to coarser grid - for (int n=0; n<=levels-2; n++) { + for (n=0; n<=levels-2; n++) { if (!active_flag[n]) continue; current_level = n; gc[n]->forward_comm_kspace(this,1,sizeof(double),FORWARD_RHO, @@ -209,7 +209,7 @@ void MSMCG::compute(int eflag, int vflag) // prolongate energy/virial from coarser grid to finer grid // reverse communicate from ghost grid points to get full sum - for (int n=levels-2; n>=0; n--) { + for (n=levels-2; n>=0; n--) { if (!active_flag[n]) continue; prolongation(n); diff --git a/src/KSPACE/pair_buck_coul_msm.cpp b/src/KSPACE/pair_buck_coul_msm.cpp index c7d237b161..c4ee5ce6f6 100644 --- a/src/KSPACE/pair_buck_coul_msm.cpp +++ b/src/KSPACE/pair_buck_coul_msm.cpp @@ -191,7 +191,7 @@ void PairBuckCoulMSM::compute(int eflag, int vflag) if (force->kspace->scalar_pressure_flag && vflag) { for (i = 0; i < 3; i++) virial[i] += force->pair->eng_coul/3.0; - for (int i = 0; i < nmax; i++) { + for (i = 0; i < nmax; i++) { f[i][0] += ftmp[i][0]; f[i][1] += ftmp[i][1]; f[i][2] += ftmp[i][2]; diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index f392179152..fa5b624462 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -506,40 +506,39 @@ void PairBuckLongCoulLong::compute(int eflag, int vflag) if (order1 && (rsq < cut_coulsq)) { // coulombic if (!ncoultablebits || rsq <= tabinnersq) { // series real space - double x = g_ewald*r; - double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x); + double x1 = g_ewald*r; + double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x1); if (ni == 0) { - s *= g_ewald*exp(-x*x); - force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s; + s *= g_ewald*exp(-x1*x1); + force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x1)+EWALD_F*s; if (eflag) ecoul = t; - } - else { // special case - double f = s*(1.0-special_coul[ni])/r; - s *= g_ewald*exp(-x*x); - force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-f; - if (eflag) ecoul = t-f; + } else { // special case + double fc = s*(1.0-special_coul[ni])/r; + s *= g_ewald*exp(-x1*x1); + force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x1)+EWALD_F*s-fc; + if (eflag) ecoul = t-fc; } } // table real space else { union_int_float_t t; t.f = rsq; const int k = (t.i & ncoulmask) >> ncoulshiftbits; - double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j]; + double fc = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j]; if (ni == 0) { - force_coul = qiqj*(ftable[k]+f*dftable[k]); - if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]); + force_coul = qiqj*(ftable[k]+fc*dftable[k]); + if (eflag) ecoul = qiqj*(etable[k]+fc*detable[k]); } else { // special case - t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]); - force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f); - if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]-t.f); + t.f = (1.0-special_coul[ni])*(ctable[k]+fc*dctable[k]); + force_coul = qiqj*(ftable[k]+fc*dftable[k]-t.f); + if (eflag) ecoul = qiqj*(etable[k]+fc*detable[k]-t.f); } } } else force_coul = ecoul = 0.0; if (rsq < cut_bucksqi[typej]) { // buckingham - double rn = r2inv*r2inv*r2inv, - expr = exp(-r*rhoinvi[typej]); + double rn = r2inv*r2inv*r2inv; + double expr = exp(-r*rhoinvi[typej]); if (order6) { // long-range if (!ndisptablebits || rsq <= tabinnerdispsq) { double x2 = g2*rsq, a2 = 1.0/x2; diff --git a/src/lmppython.cpp b/src/lmppython.cpp index 209cfc1e31..742e912411 100644 --- a/src/lmppython.cpp +++ b/src/lmppython.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "lmppython.h" -#if LMP_PYTHON +#if defined(LMP_PYTHON) #include "python_impl.h" #else #include "error.h" @@ -46,7 +46,7 @@ PythonInterface::~PythonInterface() void Python::init() { -#if LMP_PYTHON +#if defined(LMP_PYTHON) if (!impl) impl = new PythonImpl(lmp); #else error->all(FLERR,"Python support missing! Compile with PYTHON package installed!"); @@ -55,7 +55,7 @@ void Python::init() /* ---------------------------------------------------------------------- */ bool Python::is_enabled() const { -#if LMP_PYTHON +#if defined(LMP_PYTHON) return true; #else return false; diff --git a/src/math_extra.cpp b/src/math_extra.cpp index df74ad5be2..59e66242b3 100644 --- a/src/math_extra.cpp +++ b/src/math_extra.cpp @@ -71,8 +71,8 @@ int mldivide3(const double m[3][3], const double *v, double *ans) } for (unsigned j = i+1; j < 3; j++) { - double m = aug[j][i]/aug[i][i]; - for (unsigned k=i+1; k<4; k++) aug[j][k]-=m*aug[i][k]; + double n = aug[j][i]/aug[i][i]; + for (unsigned k=i+1; k<4; k++) aug[j][k]-=n*aug[i][k]; } } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index ee4226f43e..eb4e89e692 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -513,7 +513,7 @@ void Neighbor::init() // print_pairwise_info() made use of requests // set of NeighLists now stores all needed info - for (int i = 0; i < nrequest; i++) { + for (i = 0; i < nrequest; i++) { delete requests[i]; requests[i] = nullptr; } @@ -2079,7 +2079,7 @@ void Neighbor::build(int topoflag) if (style != Neighbor::NSQ) { if (last_setup_bins < 0) setup_bins(); - for (int i = 0; i < nbin; i++) { + for (i = 0; i < nbin; i++) { neigh_bin[i]->bin_atoms_setup(nall); neigh_bin[i]->bin_atoms(); } diff --git a/src/read_dump.cpp b/src/read_dump.cpp index ddb793c629..d30bec4d36 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -818,9 +818,9 @@ void ReadDump::process_atoms() int nlocal = atom->nlocal; memory->create(updateflag,nlocal,"read_dump:updateflag"); - for (int i = 0; i < nlocal; i++) updateflag[i] = 0; + for (i = 0; i < nlocal; i++) updateflag[i] = 0; memory->create(newflag,nnew,"read_dump:newflag"); - for (int i = 0; i < nnew; i++) newflag[i] = 1; + for (i = 0; i < nnew; i++) newflag[i] = 1; // loop over new atoms @@ -918,7 +918,7 @@ void ReadDump::process_atoms() if (trimflag) { AtomVec *avec = atom->avec; - int i = 0; + i = 0; while (i < nlocal) { if (!updateflag[i]) { avec->copy(nlocal-1,i,1); diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 2742dc5e4e..7d008b2518 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -339,7 +339,7 @@ void ReadRestart::command(int narg, char **arg) procfile, utils::getsyserror())); } - int flag,procsperfile; + int procsperfile; if (filereader) { utils::sfread(FLERR,&flag,sizeof(int),1,fp,nullptr,error); @@ -704,7 +704,7 @@ void ReadRestart::header() int procgrid[3]; read_int(); read_int_vec(3,procgrid); - int flag = 0; + flag = 0; if (comm->user_procgrid[0] != 0 && procgrid[0] != comm->user_procgrid[0]) flag = 1; if (comm->user_procgrid[1] != 0 && diff --git a/src/replicate.cpp b/src/replicate.cpp index 95bf615d04..12e3ad5cab 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -166,7 +166,7 @@ void Replicate::command(int narg, char **arg) atom->molecules = (Molecule **) memory->smalloc((old->nmolecule)*sizeof(Molecule *), "atom::molecules"); atom->nmolecule = old->nmolecule; - for (int i = 0; i < old->nmolecule; ++i) + for (i = 0; i < old->nmolecule; ++i) atom->molecules[i] = old->molecules[i]; memory->sfree(old->molecules); old->molecules = nullptr; diff --git a/src/text_file_reader.cpp b/src/text_file_reader.cpp index 7a6e914639..b0d5bef53e 100644 --- a/src/text_file_reader.cpp +++ b/src/text_file_reader.cpp @@ -100,7 +100,7 @@ char *TextFileReader::next_line(int nparams) { if (nwords > 0) n = strlen(line); while (nwords == 0 || nwords < nparams) { - char *ptr = fgets(&line[n], MAXLINE - n, fp); + ptr = fgets(&line[n], MAXLINE - n, fp); if (ptr == nullptr) { // EOF diff --git a/src/utils.cpp b/src/utils.cpp index e8f1c63606..0ff1d65633 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -1008,8 +1008,8 @@ std::string utils::get_potential_file_path(const std::string &path) { while (dirs.has_next()) { auto pot = utils::path_basename(filepath); - auto path = dirs.next(); - filepath = utils::path_join(path, pot); + auto dir = dirs.next(); + filepath = utils::path_join(dir, pot); if (utils::file_is_readable(filepath)) { return filepath; diff --git a/src/variable.cpp b/src/variable.cpp index 3e93a33797..dc9a2dbee5 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -1894,7 +1894,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) } else if (strncmp(word,"v_",2) == 0) { - int ivar = find(word+2); + ivar = find(word+2); if (ivar < 0) print_var_error(FLERR,fmt::format("Invalid variable reference " "{} in variable formula",word),ivar); @@ -2338,7 +2338,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) double Variable::collapse_tree(Tree *tree) { - double arg1,arg2; + double arg1,arg2,arg3; if (tree->type == VALUE) return tree->value; if (tree->type == ATOMARRAY) return 0.0; @@ -2805,19 +2805,19 @@ double Variable::collapse_tree(Tree *tree) error->one(FLERR,"Invalid math function in variable formula"); if (ivalue4 < ivalue1 || ivalue5 > ivalue2) error->one(FLERR,"Invalid math function in variable formula"); - bigint istep; + bigint istep, offset; if (update->ntimestep < ivalue1) istep = ivalue1; else if (update->ntimestep < ivalue2) { if (update->ntimestep < ivalue4 || update->ntimestep > ivalue5) { - bigint offset = update->ntimestep - ivalue1; + offset = update->ntimestep - ivalue1; istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3; if (update->ntimestep < ivalue2 && istep > ivalue4) tree->value = ivalue4; } else { - bigint offset = update->ntimestep - ivalue4; + offset = update->ntimestep - ivalue4; istep = ivalue4 + (offset/ivalue6)*ivalue6 + ivalue6; if (istep > ivalue5) { - bigint offset = ivalue5 - ivalue1; + offset = ivalue5 - ivalue1; istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3; if (istep > ivalue2) istep = MAXBIGINT; } @@ -2828,8 +2828,8 @@ double Variable::collapse_tree(Tree *tree) } if (tree->type == VDISPLACE) { - double arg1 = collapse_tree(tree->first); - double arg2 = collapse_tree(tree->second); + arg1 = collapse_tree(tree->first); + arg2 = collapse_tree(tree->second); if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0; tree->type = VALUE; double delta = update->ntimestep - update->beginstep; @@ -2838,9 +2838,9 @@ double Variable::collapse_tree(Tree *tree) } if (tree->type == SWIGGLE) { - double arg1 = collapse_tree(tree->first); - double arg2 = collapse_tree(tree->second); - double arg3 = collapse_tree(tree->extra[0]); + arg1 = collapse_tree(tree->first); + arg2 = collapse_tree(tree->second); + arg3 = collapse_tree(tree->extra[0]); if (tree->first->type != VALUE || tree->second->type != VALUE || tree->extra[0]->type != VALUE) return 0.0; tree->type = VALUE; @@ -2853,9 +2853,9 @@ double Variable::collapse_tree(Tree *tree) } if (tree->type == CWIGGLE) { - double arg1 = collapse_tree(tree->first); - double arg2 = collapse_tree(tree->second); - double arg3 = collapse_tree(tree->extra[0]); + arg1 = collapse_tree(tree->first); + arg2 = collapse_tree(tree->second); + arg3 = collapse_tree(tree->extra[0]); if (tree->first->type != VALUE || tree->second->type != VALUE || tree->extra[0]->type != VALUE) return 0.0; tree->type = VALUE; @@ -3134,19 +3134,19 @@ double Variable::eval_tree(Tree *tree, int i) error->one(FLERR,"Invalid math function in variable formula"); if (ivalue4 < ivalue1 || ivalue5 > ivalue2) error->one(FLERR,"Invalid math function in variable formula"); - bigint istep; + bigint istep, offset; if (update->ntimestep < ivalue1) istep = ivalue1; else if (update->ntimestep < ivalue2) { if (update->ntimestep < ivalue4 || update->ntimestep > ivalue5) { - bigint offset = update->ntimestep - ivalue1; + offset = update->ntimestep - ivalue1; istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3; if (update->ntimestep < ivalue2 && istep > ivalue4) tree->value = ivalue4; } else { - bigint offset = update->ntimestep - ivalue4; + offset = update->ntimestep - ivalue4; istep = ivalue4 + (offset/ivalue6)*ivalue6 + ivalue6; if (istep > ivalue5) { - bigint offset = ivalue5 - ivalue1; + offset = ivalue5 - ivalue1; istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3; if (istep > ivalue2) istep = MAXBIGINT; } @@ -3716,18 +3716,18 @@ int Variable::math_function(char *word, char *contents, Tree **tree, error->one(FLERR,"Invalid math function in variable formula"); if (ivalue4 < ivalue1 || ivalue5 > ivalue2) error->one(FLERR,"Invalid math function in variable formula"); - bigint istep; + bigint istep, offset; if (update->ntimestep < ivalue1) istep = ivalue1; else if (update->ntimestep < ivalue2) { if (update->ntimestep < ivalue4 || update->ntimestep > ivalue5) { - bigint offset = update->ntimestep - ivalue1; + offset = update->ntimestep - ivalue1; istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3; if (update->ntimestep < ivalue4 && istep > ivalue4) istep = ivalue4; } else { - bigint offset = update->ntimestep - ivalue4; + offset = update->ntimestep - ivalue4; istep = ivalue4 + (offset/ivalue6)*ivalue6 + ivalue6; if (istep > ivalue5) { - bigint offset = ivalue5 - ivalue1; + offset = ivalue5 - ivalue1; istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3; if (istep > ivalue2) istep = MAXBIGINT; } @@ -4107,9 +4107,9 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Compute *compute = nullptr; Fix *fix = nullptr; - int ivar = -1; int index,nvec,nstride; char *ptr1,*ptr2; + ivar = -1; // argument is compute @@ -4387,7 +4387,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, if (narg != 1) print_var_error(FLERR,"Invalid special function in variable formula",ivar); - int ivar = find(args[0]); + ivar = find(args[0]); if (ivar < 0) { std::string mesg = "Variable ID '"; mesg += args[0]; @@ -4399,7 +4399,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, // save value in tree or on argstack if (style[ivar] == SCALARFILE) { - double value = atof(data[ivar][0]); + value = atof(data[ivar][0]); int done = reader[ivar]->read_scalar(data[ivar][0]); if (done) remove(ivar); From 15ce976dbaf05de7e048e1dc7096ffbeb264e2ae Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 16:32:27 -0400 Subject: [PATCH 0635/1217] simplify --- src/velocity.cpp | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/src/velocity.cpp b/src/velocity.cpp index e0c80baa91..30d479b0eb 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -578,13 +578,9 @@ void Velocity::scale(int /*narg*/, char **arg) int tflag = 0; if (temperature == nullptr) { - char **arg = new char*[3]; - arg[0] = (char *) "velocity_temp"; - arg[1] = group->names[igroup]; - arg[2] = (char *) "temp"; - temperature = new ComputeTemp(lmp,3,arg); + modify->add_compute(fmt::format("velocity_temp {} temp")); + temperature = modify->compute[modify->ncompute-1]; tflag = 1; - delete [] arg; } // initialize temperature computation From 8ba1b59d8de62cde07e98e23359136e30d69d7c1 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 23 Apr 2021 16:34:12 -0400 Subject: [PATCH 0636/1217] Correct fprintf statement in debug code --- lib/gpu/geryon/nvd_kernel.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/gpu/geryon/nvd_kernel.h b/lib/gpu/geryon/nvd_kernel.h index c31b8cdf9b..8d73192de6 100644 --- a/lib/gpu/geryon/nvd_kernel.h +++ b/lib/gpu/geryon/nvd_kernel.h @@ -115,7 +115,7 @@ class UCL_Program { fprintf(foutput," UCL Error: Error compiling PTX Program...\n"); fprintf(foutput, "----------------------------------------------------------\n"); - fprintf(foutput,"%s\n",log); + fprintf(foutput,"%s\n",log->c_str()); fprintf(foutput, "----------------------------------------------------------\n"); fprintf(foutput,"\n\n"); From 24314b2316e2f73252a205307a6a3313daa0ca20 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 23 Apr 2021 16:36:01 -0400 Subject: [PATCH 0637/1217] Formatting --- lib/gpu/geryon/nvd_kernel.h | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/lib/gpu/geryon/nvd_kernel.h b/lib/gpu/geryon/nvd_kernel.h index 8d73192de6..798b12e53c 100644 --- a/lib/gpu/geryon/nvd_kernel.h +++ b/lib/gpu/geryon/nvd_kernel.h @@ -108,17 +108,14 @@ class UCL_Program { std::cerr << log << std::endl << "----------------------------------------------------------\n\n"; #endif - if (foutput != NULL) { - fprintf(foutput,"\n\n"); - fprintf(foutput, - "----------------------------------------------------------\n"); - fprintf(foutput," UCL Error: Error compiling PTX Program...\n"); - fprintf(foutput, - "----------------------------------------------------------\n"); - fprintf(foutput,"%s\n",log->c_str()); - fprintf(foutput, - "----------------------------------------------------------\n"); - fprintf(foutput,"\n\n"); + if (foutput != nullptr) { + fprintf(foutput,"\n\n"); + fprintf(foutput, "----------------------------------------------------------\n"); + fprintf(foutput, " UCL Error: Error compiling PTX Program...\n"); + fprintf(foutput, "----------------------------------------------------------\n"); + fprintf(foutput, "%s\n",log->c_str()); + fprintf(foutput, "----------------------------------------------------------\n"); + fprintf(foutput,"\n\n"); } return UCL_COMPILE_ERROR; } From b7272bbbf7bdfae3004a096cad7d0e8e1330e300 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 16:32:39 -0400 Subject: [PATCH 0638/1217] restore variable declaration --- src/KSPACE/pair_buck_long_coul_long.cpp | 6 +++--- src/variable.cpp | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index fa5b624462..8e8cf21da6 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -548,10 +548,10 @@ void PairBuckLongCoulLong::compute(int eflag, int vflag) r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq; if (eflag) evdwl = expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2; } else { // special case - double f = special_lj[ni], t = rn*(1.0-f); - force_buck = f*r*expr*buck1i[typej]- + double fc = special_lj[ni], t = rn*(1.0-fc); + force_buck = fc*r*expr*buck1i[typej]- g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*buck2i[typej]; - if (eflag) evdwl = f*expr*buckai[typej] - + if (eflag) evdwl = fc*expr*buckai[typej] - g6*((a2+1.0)*a2+0.5)*x2+t*buckci[typej]; } } else { //table real space diff --git a/src/variable.cpp b/src/variable.cpp index dc9a2dbee5..9fe3fdcd12 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -1894,7 +1894,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) } else if (strncmp(word,"v_",2) == 0) { - ivar = find(word+2); + int ivar = find(word+2); if (ivar < 0) print_var_error(FLERR,fmt::format("Invalid variable reference " "{} in variable formula",word),ivar); From f47333bebf1d95fdbe52044c65fe764e13687d60 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 16:38:54 -0400 Subject: [PATCH 0639/1217] Update MathJax to 3.1.4 hotfix version --- cmake/Modules/Documentation.cmake | 2 +- doc/Makefile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Documentation.cmake b/cmake/Modules/Documentation.cmake index b8f4c541e9..16dd5dd4fa 100644 --- a/cmake/Modules/Documentation.cmake +++ b/cmake/Modules/Documentation.cmake @@ -56,7 +56,7 @@ if(BUILD_DOC) ) set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball") - set(MATHJAX_MD5 "b81661c6e6ba06278e6ae37b30b0c492" CACHE STRING "MD5 checksum of MathJax tarball") + set(MATHJAX_MD5 "d1c98c746888bfd52ca8ebc10704f92f" CACHE STRING "MD5 checksum of MathJax tarball") mark_as_advanced(MATHJAX_URL) # download mathjax distribution and unpack to folder "mathjax" diff --git a/doc/Makefile b/doc/Makefile index a90b13e133..e49d42ca77 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -236,7 +236,7 @@ $(VENV): ) $(MATHJAX): - @git clone -b 3.1.3 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@ + @git clone -b 3.1.4 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@ $(TXT2RST) $(ANCHORCHECK): $(VENV) @( \ From 99fa6ed4b4fafa615cf85fba355288e62dd550c2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 16:50:35 -0400 Subject: [PATCH 0640/1217] delay part of the variable.cpp refactoring until we have better unit testing for it. --- src/KSPACE/pair_buck_long_coul_long.cpp | 20 ++++++++++---------- src/variable.cpp | 6 +++--- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index 8e8cf21da6..ca5a9ab3c2 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -563,9 +563,9 @@ void PairBuckLongCoulLong::compute(int eflag, int vflag) force_buck = r*expr*buck1i[typej]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*buckci[typej]; if (eflag) evdwl = expr*buckai[typej]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*buckci[typej]; } else { //special case - double f = special_lj[ni], t = rn*(1.0-f); - force_buck = f*r*expr*buck1i[typej] -(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*buckci[typej] +t*buck2i[typej]; - if (eflag) evdwl = f*expr*buckai[typej] -(edisptable[disp_k]+f_disp*dedisptable[disp_k])*buckci[typej]+t*buckci[typej]; + double fc = special_lj[ni], t = rn*(1.0-fc); + force_buck = fc*r*expr*buck1i[typej] -(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*buckci[typej] +t*buck2i[typej]; + if (eflag) evdwl = fc*expr*buckai[typej] -(edisptable[disp_k]+f_disp*dedisptable[disp_k])*buckci[typej]+t*buckci[typej]; } } } else { // cut @@ -574,10 +574,10 @@ void PairBuckLongCoulLong::compute(int eflag, int vflag) if (eflag) evdwl = expr*buckai[typej] - rn*buckci[typej]-offseti[typej]; } else { // special case - double f = special_lj[ni]; - force_buck = f*(r*expr*buck1i[typej]-rn*buck2i[typej]); + double fc = special_lj[ni]; + force_buck = fc*(r*expr*buck1i[typej]-rn*buck2i[typej]); if (eflag) - evdwl = f*(expr*buckai[typej]-rn*buckci[typej]-offseti[typej]); + evdwl = fc*(expr*buckai[typej]-rn*buckci[typej]-offseti[typej]); } } } @@ -586,10 +586,10 @@ void PairBuckLongCoulLong::compute(int eflag, int vflag) fpair = (force_coul+force_buck)*r2inv; if (newton_pair || j < nlocal) { - double *fj = f0+(j+(j<<1)), f; - fi[0] += f = d[0]*fpair; fj[0] -= f; - fi[1] += f = d[1]*fpair; fj[1] -= f; - fi[2] += f = d[2]*fpair; fj[2] -= f; + double *fj = f0+(j+(j<<1)), fp; + fi[0] += fp = d[0]*fpair; fj[0] -= fp; + fi[1] += fp = d[1]*fpair; fj[1] -= fp; + fi[2] += fp = d[2]*fpair; fj[2] -= fp; } else { fi[0] += d[0]*fpair; diff --git a/src/variable.cpp b/src/variable.cpp index 9fe3fdcd12..ac225230cf 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -4109,7 +4109,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Fix *fix = nullptr; int index,nvec,nstride; char *ptr1,*ptr2; - ivar = -1; + int ivar = -1; // argument is compute @@ -4387,7 +4387,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, if (narg != 1) print_var_error(FLERR,"Invalid special function in variable formula",ivar); - ivar = find(args[0]); + int ivar = find(args[0]); if (ivar < 0) { std::string mesg = "Variable ID '"; mesg += args[0]; @@ -4399,7 +4399,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, // save value in tree or on argstack if (style[ivar] == SCALARFILE) { - value = atof(data[ivar][0]); + double value = atof(data[ivar][0]); int done = reader[ivar]->read_scalar(data[ivar][0]); if (done) remove(ivar); From 917cd1b924f9f3044a099387b728b27e5de89700 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 16:57:39 -0400 Subject: [PATCH 0641/1217] silence more compiler warnings --- src/KSPACE/pair_born_coul_msm.cpp | 2 +- src/compute_coord_atom.cpp | 2 +- src/compute_gyration_chunk.cpp | 2 +- src/compute_inertia_chunk.cpp | 6 +++--- src/compute_omega_chunk.cpp | 6 +++--- src/compute_orientorder_atom.cpp | 2 +- src/compute_temp_chunk.cpp | 6 +++--- src/compute_temp_profile.cpp | 2 +- src/compute_torque_chunk.cpp | 6 +++--- src/irregular.cpp | 1 - 10 files changed, 17 insertions(+), 18 deletions(-) diff --git a/src/KSPACE/pair_born_coul_msm.cpp b/src/KSPACE/pair_born_coul_msm.cpp index c22e0e2ac6..a33e9d245b 100644 --- a/src/KSPACE/pair_born_coul_msm.cpp +++ b/src/KSPACE/pair_born_coul_msm.cpp @@ -195,7 +195,7 @@ void PairBornCoulMSM::compute(int eflag, int vflag) if (force->kspace->scalar_pressure_flag && vflag) { for (i = 0; i < 3; i++) virial[i] += force->pair->eng_coul/3.0; - for (int i = 0; i < nmax; i++) { + for (i = 0; i < nmax; i++) { f[i][0] += ftmp[i][0]; f[i][1] += ftmp[i][1]; f[i][2] += ftmp[i][2]; diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index 1c56466b36..aba22e3f60 100644 --- a/src/compute_coord_atom.cpp +++ b/src/compute_coord_atom.cpp @@ -305,7 +305,7 @@ void ComputeCoordAtom::compute_peratom() rsq = delx*delx + dely*dely + delz*delz; if (rsq < cutsq) { double dot_product = 0.0; - for (int m=0; m < 2*(2*l+1); m++) { + for (m=0; m < 2*(2*l+1); m++) { dot_product += normv[i][nqlist+m]*normv[j][nqlist+m]; } if (dot_product > threshold) n++; diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp index c2db9fa855..bedc815c34 100644 --- a/src/compute_gyration_chunk.cpp +++ b/src/compute_gyration_chunk.cpp @@ -139,7 +139,7 @@ void ComputeGyrationChunk::compute_vector() MPI_Allreduce(rg,rgall,nchunk,MPI_DOUBLE,MPI_SUM,world); - for (int i = 0; i < nchunk; i++) + for (i = 0; i < nchunk; i++) if (masstotal[i] > 0.0) rgall[i] = sqrt(rgall[i]/masstotal[i]); } diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp index 9e0084acfb..095a573e54 100644 --- a/src/compute_inertia_chunk.cpp +++ b/src/compute_inertia_chunk.cpp @@ -101,7 +101,7 @@ void ComputeInertiaChunk::compute_array() // zero local per-chunk values - for (int i = 0; i < nchunk; i++) { + for (i = 0; i < nchunk; i++) { massproc[i] = 0.0; com[i][0] = com[i][1] = com[i][2] = 0.0; for (j = 0; j < 6; j++) inertia[i][j] = 0.0; @@ -117,7 +117,7 @@ void ComputeInertiaChunk::compute_array() double *rmass = atom->rmass; int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) + for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) { index = ichunk[i]-1; if (index < 0) continue; @@ -133,7 +133,7 @@ void ComputeInertiaChunk::compute_array() MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); - for (int i = 0; i < nchunk; i++) { + for (i = 0; i < nchunk; i++) { if (masstotal[i] > 0.0) { comall[i][0] /= masstotal[i]; comall[i][1] /= masstotal[i]; diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp index da3b482341..9b81d1f19e 100644 --- a/src/compute_omega_chunk.cpp +++ b/src/compute_omega_chunk.cpp @@ -108,7 +108,7 @@ void ComputeOmegaChunk::compute_array() // zero local per-chunk values - for (int i = 0; i < nchunk; i++) { + for (i = 0; i < nchunk; i++) { massproc[i] = 0.0; com[i][0] = com[i][1] = com[i][2] = 0.0; for (j = 0; j < 6; j++) inertia[i][j] = 0.0; @@ -126,7 +126,7 @@ void ComputeOmegaChunk::compute_array() double *rmass = atom->rmass; int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) + for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) { index = ichunk[i]-1; if (index < 0) continue; @@ -142,7 +142,7 @@ void ComputeOmegaChunk::compute_array() MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); - for (int i = 0; i < nchunk; i++) { + for (i = 0; i < nchunk; i++) { if (masstotal[i] > 0.0) { comall[i][0] /= masstotal[i]; comall[i][1] /= masstotal[i]; diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index 8a836a97b8..98b8b7cb80 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -308,7 +308,7 @@ void ComputeOrientOrderAtom::compute_peratom() // if not nnn neighbors, order parameter = 0; if ((ncount == 0) || (ncount < nnn)) { - for (int jj = 0; jj < ncol; jj++) + for (jj = 0; jj < ncol; jj++) qn[jj] = 0.0; continue; } diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index 31f955fcb5..4ae0cc37c8 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -438,7 +438,7 @@ void ComputeTempChunk::vcm_compute() int *ichunk = cchunk->ichunk; - for (int i = 0; i < nchunk; i++) { + for (i = 0; i < nchunk; i++) { vcm[i][0] = vcm[i][1] = vcm[i][2] = 0.0; massproc[i] = 0.0; } @@ -487,7 +487,7 @@ void ComputeTempChunk::temperature(int icol) // zero local per-chunk values - for (int i = 0; i < nchunk; i++) { + for (i = 0; i < nchunk; i++) { count[i] = 0; sum[i] = 0.0; } @@ -560,7 +560,7 @@ void ComputeTempChunk::temperature(int icol) double mvv2e = force->mvv2e; double boltz = force->boltz; - for (int i = 0; i < nchunk; i++) { + for (i = 0; i < nchunk; i++) { dof = cdof + adof*countall[i]; if (dof > 0.0) tfactor = mvv2e / (dof * boltz); else tfactor = 0.0; diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp index 6938560359..11fe72440f 100644 --- a/src/compute_temp_profile.cpp +++ b/src/compute_temp_profile.cpp @@ -313,7 +313,7 @@ void ComputeTempProfile::compute_array() for (i = 0; i < nbins; i++) tbin[i] = 0.0; - for (int i = 0; i < nlocal; i++) + for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) { ibin = bin[i]; if (xflag) vthermal[0] = v[i][0] - binave[ibin][ivx]; diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp index 9aea024114..158bf178e8 100644 --- a/src/compute_torque_chunk.cpp +++ b/src/compute_torque_chunk.cpp @@ -100,7 +100,7 @@ void ComputeTorqueChunk::compute_array() // zero local per-chunk values - for (int i = 0; i < nchunk; i++) { + for (i = 0; i < nchunk; i++) { massproc[i] = 0.0; com[i][0] = com[i][1] = com[i][2] = 0.0; torque[i][0] = torque[i][1] = torque[i][2] = 0.0; @@ -116,7 +116,7 @@ void ComputeTorqueChunk::compute_array() double *rmass = atom->rmass; int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) + for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) { index = ichunk[i]-1; if (index < 0) continue; @@ -132,7 +132,7 @@ void ComputeTorqueChunk::compute_array() MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); - for (int i = 0; i < nchunk; i++) { + for (i = 0; i < nchunk; i++) { if (masstotal[i] > 0.0) { comall[i][0] /= masstotal[i]; comall[i][1] /= masstotal[i]; diff --git a/src/irregular.cpp b/src/irregular.cpp index c1c4ff44fb..072209af09 100644 --- a/src/irregular.cpp +++ b/src/irregular.cpp @@ -891,7 +891,6 @@ int Irregular::create_data_grouped(int n, int *procs, int sortflag) utils::merge_sort(order,nrecv_proc,(void *)proc_recv,compare_standalone); #endif - int j; for (i = 0; i < nrecv_proc; i++) { j = order[i]; proc_recv_ordered[i] = proc_recv[j]; From 8a49bf3a31c8b632787f1981b0c852df07c268e0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 18:07:24 -0400 Subject: [PATCH 0642/1217] fix missing argument bug in velocity code and simplify a second case --- src/dump_custom.cpp | 12 ++++-------- src/velocity.cpp | 18 +++++++----------- 2 files changed, 11 insertions(+), 19 deletions(-) diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 40b3e6fc28..2e752d7f31 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -316,33 +316,29 @@ void DumpCustom::init_style() // find current ptr for each compute,fix,variable // check that fix frequency is acceptable - int icompute; for (i = 0; i < ncompute; i++) { - icompute = modify->find_compute(id_compute[i]); + int icompute = modify->find_compute(id_compute[i]); if (icompute < 0) error->all(FLERR,"Could not find dump custom compute ID"); compute[i] = modify->compute[icompute]; } - int ifix; for (i = 0; i < nfix; i++) { - ifix = modify->find_fix(id_fix[i]); + int ifix = modify->find_fix(id_fix[i]); if (ifix < 0) error->all(FLERR,"Could not find dump custom fix ID"); fix[i] = modify->fix[ifix]; if (nevery % modify->fix[ifix]->peratom_freq) error->all(FLERR,"Dump custom and fix not computed at compatible times"); } - int ivariable; for (i = 0; i < nvariable; i++) { - ivariable = input->variable->find(id_variable[i]); + int ivariable = input->variable->find(id_variable[i]); if (ivariable < 0) error->all(FLERR,"Could not find dump custom variable name"); variable[i] = ivariable; } - int icustom; for (i = 0; i < ncustom; i++) { - icustom = atom->find_custom(id_custom[i],flag_custom[i]); + int icustom = atom->find_custom(id_custom[i],flag_custom[i]); if (icustom < 0) error->all(FLERR,"Could not find custom per-atom property ID"); } diff --git a/src/velocity.cpp b/src/velocity.cpp index 30d479b0eb..44d1556676 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -186,15 +186,11 @@ void Velocity::create(double t_desired, int seed) Compute *temperature_nobias = nullptr; if (temperature == nullptr || bias_flag) { - char **arg = new char*[3]; - arg[0] = (char *) "velocity_temp"; - arg[1] = group->names[igroup]; - arg[2] = (char *) "temp"; + modify->add_compute(fmt::format("velocity_temp {} temp",group->names[igroup])); if (temperature == nullptr) { - temperature = new ComputeTemp(lmp,3,arg); + temperature = modify->compute[modify->ncompute-1]; tcreate_flag = 1; - } else temperature_nobias = new ComputeTemp(lmp,3,arg); - delete [] arg; + } else temperature_nobias = modify->compute[modify->ncompute-1]; } // initialize temperature computation(s) @@ -401,8 +397,8 @@ void Velocity::create(double t_desired, int seed) // if temperature compute was created, delete it delete random; - if (tcreate_flag) delete temperature; - if (temperature_nobias) delete temperature_nobias; + if (tcreate_flag) modify->delete_compute("velocity_temp"); + if (temperature_nobias) modify->delete_compute("velocity_temp"); } /* ---------------------------------------------------------------------- */ @@ -578,7 +574,7 @@ void Velocity::scale(int /*narg*/, char **arg) int tflag = 0; if (temperature == nullptr) { - modify->add_compute(fmt::format("velocity_temp {} temp")); + modify->add_compute(fmt::format("velocity_temp {} temp",group->names[igroup])); temperature = modify->compute[modify->ncompute-1]; tflag = 1; } @@ -608,7 +604,7 @@ void Velocity::scale(int /*narg*/, char **arg) // if temperature was created, delete it - if (tflag) delete temperature; + if (tflag) modify->delete_compute("velocity_temp"); } /* ---------------------------------------------------------------------- From ed926812dc81bf880fff93a6a530b98e72cfe0a8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 18:47:57 -0400 Subject: [PATCH 0643/1217] simplify --- src/dump_local.cpp | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/dump_local.cpp b/src/dump_local.cpp index a354c6fbba..66f9bdb150 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -197,16 +197,14 @@ void DumpLocal::init_style() // find current ptr for each compute,fix,variable // check that fix frequency is acceptable - int icompute; for (i = 0; i < ncompute; i++) { - icompute = modify->find_compute(id_compute[i]); + int icompute = modify->find_compute(id_compute[i]); if (icompute < 0) error->all(FLERR,"Could not find dump local compute ID"); compute[i] = modify->compute[icompute]; } - int ifix; for (i = 0; i < nfix; i++) { - ifix = modify->find_fix(id_fix[i]); + int ifix = modify->find_fix(id_fix[i]); if (ifix < 0) error->all(FLERR,"Could not find dump local fix ID"); fix[i] = modify->fix[ifix]; if (nevery % modify->fix[ifix]->local_freq) From 9cdd926763ed176c6508246040604d762f4747f1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 19:19:41 -0400 Subject: [PATCH 0644/1217] remove excess quotes --- unittest/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/CMakeLists.txt b/unittest/CMakeLists.txt index 412cf8d3d6..addc8bc244 100644 --- a/unittest/CMakeLists.txt +++ b/unittest/CMakeLists.txt @@ -7,7 +7,7 @@ add_test(NAME RunLammps COMMAND $ -log none -echo none -in in.empty WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(RunLammps PROPERTIES - ENVIRONMENT "TSAN_OPTIONS='ignore_noninstrumented_modules=1'" + ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1" PASS_REGULAR_EXPRESSION "^LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]\\)") if(BUILD_MPI) From 8c50f56548da2b848451d9df2427271773747495 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Apr 2021 21:18:07 -0400 Subject: [PATCH 0645/1217] add unit test for TextFileReader class --- unittest/commands/test_variables.cpp | 2 +- unittest/formats/CMakeLists.txt | 5 + unittest/formats/test_text_file_reader.cpp | 148 +++++++++++++++++++++ 3 files changed, 154 insertions(+), 1 deletion(-) create mode 100644 unittest/formats/test_text_file_reader.cpp diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index f31959c3ff..663a2a78a1 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -105,8 +105,8 @@ protected: "# comments only\n five\n#END\n", fp); fclose(fp); - fp = fopen("test_variable.atomfile", "w"); + fp = fopen("test_variable.atomfile", "w"); fputs("# test file for atomfile style variable\n\n" "4 # four lines\n4 0.5 #with comment\n" "2 -0.5 \n3 1.5\n1 -1.5\n\n" diff --git a/unittest/formats/CMakeLists.txt b/unittest/formats/CMakeLists.txt index 4c6de98729..b4c637edfb 100644 --- a/unittest/formats/CMakeLists.txt +++ b/unittest/formats/CMakeLists.txt @@ -28,6 +28,11 @@ if(PKG_MANYBODY) set_tests_properties(EIMPotentialFileReader PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") endif() +add_executable(test_text_file_reader test_text_file_reader.cpp) +target_link_libraries(test_text_file_reader PRIVATE lammps GTest::GMock GTest::GTest) +add_test(NAME TextFileReader COMMAND test_text_file_reader WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) +set_tests_properties(TextFileReader PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") + add_executable(test_file_operations test_file_operations.cpp) target_link_libraries(test_file_operations PRIVATE lammps GTest::GMock GTest::GTest) add_test(NAME FileOperations COMMAND test_file_operations WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) diff --git a/unittest/formats/test_text_file_reader.cpp b/unittest/formats/test_text_file_reader.cpp new file mode 100644 index 0000000000..e0bb2d42b5 --- /dev/null +++ b/unittest/formats/test_text_file_reader.cpp @@ -0,0 +1,148 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "info.h" +#include "input.h" +#include "text_file_reader.h" +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include "../testing/core.h" + +#include +#include +#include +#include + +using namespace LAMMPS_NS; +using LAMMPS_NS::utils::split_words; + +// whether to print verbose output (i.e. not capturing LAMMPS screen output). +bool verbose = false; + +class TextFileReaderTest : public ::testing::Test { + +protected: + void TearDown() override + { + unlink("text_reader_one.file"); + unlink("text_reader_two.file"); + } + + void test_files() + { + FILE *fp = fopen("text_reader_one.file", "w"); + fputs("# test file 1 for text file reader\n\n\none\n two \n\n" + "three # with comment\nfour ! with non-comment\n" + "# comments only\n five\n#END\n", + fp); + fclose(fp); + + fp = fopen("text_reader_two.file", "w"); + fputs("# test file for atomfile style variable\n\n" + "4 # four lines\n4 0.5 #with comment\n" + "2 -0.5 \n3 1.5\n1 -1.5\n\n" + "2\n10 1.0 # test\n13 1.0\n\n######\n" + "4\n1 4.0 # test\n2 3.0\n3 2.0\n4 1.0\n#END\n", + fp); + fclose(fp); + } +}; + +TEST_F(TextFileReaderTest, nofile) +{ + ASSERT_THROW({ TextFileReader reader("text_reader_noexist.file", "test"); }, + FileReaderException); +} + +TEST_F(TextFileReaderTest, permissions) +{ + FILE *fp = fopen("text_reader_noperms.file", "w"); + fputs("word\n", fp); + fclose(fp); + chmod("text_reader_noperms.file", 0); + ASSERT_THROW({ TextFileReader reader("text_reader_noperms.file", "test"); }, + FileReaderException); + unlink("text_reader_noperms.file"); +} + +TEST_F(TextFileReaderTest, comments) +{ + test_files(); + TextFileReader reader("text_reader_two.file", "test"); + reader.ignore_comments = true; + auto line = reader.next_line(); + ASSERT_STREQ(line, "4 "); + line = reader.next_line(1); + ASSERT_STREQ(line, "4 0.5 "); + ASSERT_NO_THROW({ reader.skip_line(); }); + auto values = reader.next_values(1); + ASSERT_EQ(values.count(), 2); + ASSERT_EQ(values.next_int(), 3); + ASSERT_STREQ(values.next_string().c_str(), "1.5"); + ASSERT_NE(reader.next_line(), nullptr); + double data[20]; + ASSERT_THROW({ reader.next_dvector(data,20); }, FileReaderException); + ASSERT_THROW({ reader.skip_line(); }, EOFException); + ASSERT_EQ(reader.next_line(), nullptr); +} + +TEST_F(TextFileReaderTest, nocomments) +{ + test_files(); + TextFileReader reader("text_reader_one.file", "test"); + reader.ignore_comments = false; + auto line = reader.next_line(); + ASSERT_STREQ(line, "# test file 1 for text file reader\n"); + line = reader.next_line(1); + ASSERT_STREQ(line, "one\n"); + ASSERT_NO_THROW({ reader.skip_line(); }); + auto values = reader.next_values(4); + ASSERT_EQ(values.count(), 4); + ASSERT_STREQ(values.next_string().c_str(), "three"); + ASSERT_STREQ(values.next_string().c_str(), "#"); + ASSERT_STREQ(values.next_string().c_str(), "with"); + try { + reader.next_values(100); + FAIL() << "No exception thrown\n"; + } catch (EOFException &e) { + ASSERT_STREQ(e.what(), "Incorrect format in test file! 9/100 parameters"); + } + ASSERT_THROW({ reader.skip_line(); }, EOFException); + ASSERT_EQ(reader.next_line(), nullptr); +} + +int main(int argc, char **argv) +{ + MPI_Init(&argc, &argv); + ::testing::InitGoogleMock(&argc, argv); + + if (Info::get_mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) + std::cout << "Warning: using OpenMPI without exceptions. " + "Death tests will be skipped\n"; + + // handle arguments passed via environment variable + if (const char *var = getenv("TEST_ARGS")) { + std::vector env = split_words(var); + for (auto arg : env) { + if (arg == "-v") { + verbose = true; + } + } + } + if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; + + int rv = RUN_ALL_TESTS(); + MPI_Finalize(); + return rv; +} From cf81f72aadb68430ca34f73e302f086ad4cfdde9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 01:22:06 -0400 Subject: [PATCH 0646/1217] more tests for tokenizer classes --- unittest/utils/test_tokenizer.cpp | 44 ++++++++++++++++++++++++++++++- 1 file changed, 43 insertions(+), 1 deletion(-) diff --git a/unittest/utils/test_tokenizer.cpp b/unittest/utils/test_tokenizer.cpp index ec097abf62..7852abb632 100644 --- a/unittest/utils/test_tokenizer.cpp +++ b/unittest/utils/test_tokenizer.cpp @@ -53,6 +53,11 @@ TEST(Tokenizer, skip) ASSERT_FALSE(t.has_next()); ASSERT_EQ(t.count(), 2); ASSERT_THROW(t.skip(), TokenizerException); + try { + t.skip(); + } catch (TokenizerException &e) { + ASSERT_STREQ(e.what(), "No more tokens"); + } } TEST(Tokenizer, prefix_separators) @@ -87,6 +92,15 @@ TEST(Tokenizer, copy_constructor) ASSERT_EQ(u.count(), 2); } +TEST(Tokenizer, rvalue) +{ + auto u = Tokenizer(" test new word ", " "); + ASSERT_THAT(u.next(), Eq("test")); + ASSERT_THAT(u.next(), Eq("new")); + ASSERT_THAT(u.next(), Eq("word")); + ASSERT_EQ(u.count(), 3); +} + TEST(Tokenizer, no_separator_path) { Tokenizer t("one", ":"); @@ -181,12 +195,40 @@ TEST(ValueTokenizer, skip) ASSERT_FALSE(t.has_next()); ASSERT_EQ(t.count(), 2); ASSERT_THROW(t.skip(), TokenizerException); + try { + t.skip(); + } catch (TokenizerException &e) { + ASSERT_STREQ(e.what(), "No more tokens"); + } +} + +TEST(ValueTokenizer, copy_constructor) +{ + ValueTokenizer t(" test word ", " "); + ASSERT_THAT(t.next_string(), Eq("test")); + ASSERT_THAT(t.next_string(), Eq("word")); + ASSERT_EQ(t.count(), 2); + ValueTokenizer u(t); + ASSERT_THAT(u.next_string(), Eq("test")); + ASSERT_THAT(u.next_string(), Eq("word")); + ASSERT_EQ(u.count(), 2); +} + +TEST(ValueTokenizer, rvalue) +{ + auto u = ValueTokenizer(" test new word ", " "); + ASSERT_THAT(u.next_string(), Eq("test")); + ASSERT_THAT(u.next_string(), Eq("new")); + ASSERT_THAT(u.next_string(), Eq("word")); + ASSERT_EQ(u.count(), 3); } TEST(ValueTokenizer, bad_integer) { - ValueTokenizer values("f10"); + ValueTokenizer values("f10 f11 f12"); ASSERT_THROW(values.next_int(), InvalidIntegerException); + ASSERT_THROW(values.next_bigint(), InvalidIntegerException); + ASSERT_THROW(values.next_tagint(), InvalidIntegerException); } TEST(ValueTokenizer, bad_double) From 6a9b44133107f99b4b4999c3de5a6de4102f1443 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 01:22:23 -0400 Subject: [PATCH 0647/1217] add tests for writing restart files --- unittest/formats/test_file_operations.cpp | 109 +++++++++++++++++++++- 1 file changed, 107 insertions(+), 2 deletions(-) diff --git a/unittest/formats/test_file_operations.cpp b/unittest/formats/test_file_operations.cpp index 700990fb72..27f45b69fc 100644 --- a/unittest/formats/test_file_operations.cpp +++ b/unittest/formats/test_file_operations.cpp @@ -11,13 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "../testing/core.h" +#include "atom.h" +#include "domain.h" #include "info.h" #include "input.h" #include "lammps.h" -#include "utils.h" +#include "update.h" #include "gmock/gmock.h" #include "gtest/gtest.h" -#include "../testing/core.h" #include #include @@ -57,6 +59,13 @@ protected: LAMMPSTest::TearDown(); remove("safe_file_read_test.txt"); } + + bool file_exists(const char *file) + { + FILE *fp = fopen(file, "r"); + fclose(fp); + return fp ? true : false; + } }; #define MAX_BUF_SIZE 128 @@ -145,6 +154,102 @@ TEST_F(FileOperationsTest, logmesg) remove("test_logmesg.log"); } +TEST_F(FileOperationsTest, restart) +{ + BEGIN_HIDE_OUTPUT(); + command("echo none"); + END_HIDE_OUTPUT(); + TEST_FAILURE(".*ERROR: Write_restart command before simulation box is defined.*", + command("write_restart test.restart");); + + BEGIN_HIDE_OUTPUT(); + command("region box block -2 2 -2 2 -2 2"); + command("create_box 1 box"); + command("create_atoms 1 single 0.0 0.0 0.0"); + command("mass 1 1.0"); + command("reset_timestep 333"); + command("comm_modify cutoff 0.2"); + command("write_restart noinit.restart noinit"); + command("run 0 post no"); + command("write_restart test.restart"); + command("write_restart step*.restart"); + command("write_restart multi-%.restart"); + command("write_restart multi2-%.restart fileper 2"); + command("write_restart multi3-%.restart nfile 1"); + if (info->has_package("MPIIO")) command("write_restart test.restart.mpiio"); + END_HIDE_OUTPUT(); + + ASSERT_TRUE(file_exists("noinit.restart")); + ASSERT_TRUE(file_exists("test.restart")); + ASSERT_TRUE(file_exists("step333.restart")); + ASSERT_TRUE(file_exists("multi-base.restart")); + ASSERT_TRUE(file_exists("multi-0.restart")); + ASSERT_TRUE(file_exists("multi2-base.restart")); + ASSERT_TRUE(file_exists("multi2-0.restart")); + ASSERT_TRUE(file_exists("multi3-base.restart")); + ASSERT_TRUE(file_exists("multi3-0.restart")); + if (info->has_package("MPIIO")) ASSERT_TRUE(file_exists("test.restart.mpiio")); + + if (!info->has_package("MPIIO")) { + TEST_FAILURE(".*ERROR: Illegal write_restart command.*", + command("write_restart test.restart.mpiio");); + } else { + TEST_FAILURE(".*ERROR: Restart file MPI-IO output not allowed with % in filename.*", + command("write_restart test.restart-%.mpiio");); + } + + TEST_FAILURE(".*ERROR: Illegal write_restart command.*", command("write_restart");); + TEST_FAILURE(".*ERROR: Illegal write_restart command.*", + command("write_restart test.restart xxxx");); + TEST_FAILURE(".*ERROR on proc 0: Cannot open restart file some_crazy_dir/test.restart:" + " No such file or directory.*", + command("write_restart some_crazy_dir/test.restart");); + BEGIN_HIDE_OUTPUT(); + command("clear"); + END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->atom->natoms, 0); + ASSERT_EQ(lmp->update->ntimestep, 0); + ASSERT_EQ(lmp->domain->triclinic, 0); + + TEST_FAILURE( + ".*ERROR on proc 0: Cannot open restart file noexist.restart: No such file or directory.*", + command("read_restart noexist.restart");); + + BEGIN_HIDE_OUTPUT(); + command("read_restart step333.restart"); + command("change_box all triclinic"); + command("write_restart triclinic.restart"); + END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->atom->natoms, 1); + ASSERT_EQ(lmp->update->ntimestep, 333); + ASSERT_EQ(lmp->domain->triclinic, 1); + BEGIN_HIDE_OUTPUT(); + command("clear"); + END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->atom->natoms, 0); + ASSERT_EQ(lmp->update->ntimestep, 0); + ASSERT_EQ(lmp->domain->triclinic, 0); + BEGIN_HIDE_OUTPUT(); + command("read_restart triclinic.restart"); + END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->atom->natoms, 1); + ASSERT_EQ(lmp->update->ntimestep, 333); + ASSERT_EQ(lmp->domain->triclinic, 1); + + // clean up + unlink("noinit.restart"); + unlink("test.restart"); + unlink("step333.restart"); + unlink("multi-base.restart"); + unlink("multi-0.restart"); + unlink("multi2-base.restart"); + unlink("multi2-0.restart"); + unlink("multi3-base.restart"); + unlink("multi3-0.restart"); + unlink("triclinic.restart"); + if (info->has_package("MPIIO")) unlink("test.restart.mpiio"); +} + int main(int argc, char **argv) { MPI_Init(&argc, &argv); From 6943a3da354717404c7dfc6cf242c9e122a79656 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 07:12:45 -0400 Subject: [PATCH 0648/1217] must check if file is readable before changes to internal data --- src/read_data.cpp | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/read_data.cpp b/src/read_data.cpp index c0085f19d1..c8937cbfc9 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -304,6 +304,12 @@ void ReadData::command(int narg, char **arg) extra_dihedral_types || extra_improper_types)) error->all(FLERR,"Cannot use read_data extra with add flag"); + // check if data file is available and readable + + if (!utils::file_is_readable(arg[0])) + error->all(FLERR,fmt::format("Cannot open file {}: {}", + arg[0], utils::getsyserror())); + // first time system initialization if (addflag == NONE) { From 9e7d26351d68c7a2d8279a05961b6a1056cd153e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 07:13:06 -0400 Subject: [PATCH 0649/1217] tweak epsilon for GPU package tests --- unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml b/unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml index 1529cf51b9..1c5c24832d 100644 --- a/unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml +++ b/unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:10 2021 -epsilon: 5e-14 +epsilon: 2e-13 prerequisites: ! | atom sphere pair yukawa/colloid From 2c4017d3ace7317ea5e17cd435e2ca98ed021940 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 07:13:26 -0400 Subject: [PATCH 0650/1217] add test for write_dump cfg --- unittest/formats/test_dump_cfg.cpp | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/unittest/formats/test_dump_cfg.cpp b/unittest/formats/test_dump_cfg.cpp index b8f879de6f..fb404e07b5 100644 --- a/unittest/formats/test_dump_cfg.cpp +++ b/unittest/formats/test_dump_cfg.cpp @@ -75,6 +75,29 @@ TEST_F(DumpCfgTest, run0) delete_file("dump_cfg_run0.melt.cfg"); } +TEST_F(DumpCfgTest, write_dump) +{ + auto dump_file = "dump_cfg_run*.melt.cfg"; + auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; + + BEGIN_HIDE_OUTPUT(); + command(std::string("write_dump all cfg dump_cfg.melt.cfg ") + fields); + command(std::string("write_dump all cfg dump_cfg*.melt.cfg ") + fields); + END_HIDE_OUTPUT(); + + ASSERT_FILE_EXISTS("dump_cfg.melt.cfg"); + auto lines = read_lines("dump_cfg.melt.cfg"); + ASSERT_EQ(lines.size(), 124); + ASSERT_THAT(lines[0], Eq("Number of particles = 32")); + delete_file("dump_cfg.melt.cfg"); + + ASSERT_FILE_EXISTS("dump_cfg0.melt.cfg"); + lines = read_lines("dump_cfg0.melt.cfg"); + ASSERT_EQ(lines.size(), 124); + ASSERT_THAT(lines[0], Eq("Number of particles = 32")); + delete_file("dump_cfg0.melt.cfg"); +} + TEST_F(DumpCfgTest, unwrap_run0) { auto dump_file = "dump_cfg_unwrap_run*.melt.cfg"; From e980d178820e5ed642e08ca30a1562e7ead951bb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 07:14:04 -0400 Subject: [PATCH 0651/1217] reuse existing code. add tests for write_data --- unittest/formats/test_file_operations.cpp | 155 ++++++++++++++++------ 1 file changed, 117 insertions(+), 38 deletions(-) diff --git a/unittest/formats/test_file_operations.cpp b/unittest/formats/test_file_operations.cpp index 27f45b69fc..7683f712a7 100644 --- a/unittest/formats/test_file_operations.cpp +++ b/unittest/formats/test_file_operations.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "../testing/core.h" +#include "../testing/utils.h" #include "atom.h" #include "domain.h" #include "info.h" @@ -45,13 +46,10 @@ protected: LAMMPSTest::SetUp(); ASSERT_NE(lmp, nullptr); - FILE *fp = fopen("safe_file_read_test.txt", "wb"); - ASSERT_NE(fp, nullptr); - fputs("one line\n", fp); - fputs("two_lines\n", fp); - fputs("\n", fp); - fputs("no newline", fp); - fclose(fp); + std::ofstream out("safe_file_read_test.txt", std::ios_base::out | std::ios_base::binary); + ASSERT_TRUE(out.good()); + out << "one line\ntwo_lines\n\nno newline"; + out.close(); } void TearDown() override @@ -59,13 +57,6 @@ protected: LAMMPSTest::TearDown(); remove("safe_file_read_test.txt"); } - - bool file_exists(const char *file) - { - FILE *fp = fopen(file, "r"); - fclose(fp); - return fp ? true : false; - } }; #define MAX_BUF_SIZE 128 @@ -73,7 +64,7 @@ TEST_F(FileOperationsTest, safe_fgets) { char buf[MAX_BUF_SIZE]; - FILE *fp = fopen("safe_file_read_test.txt", "r"); + FILE *fp = fopen("safe_file_read_test.txt", "rb"); ASSERT_NE(fp, nullptr); memset(buf, 0, MAX_BUF_SIZE); @@ -109,7 +100,7 @@ TEST_F(FileOperationsTest, safe_fread) { char buf[MAX_BUF_SIZE]; - FILE *fp = fopen("safe_file_read_test.txt", "r"); + FILE *fp = fopen("safe_file_read_test.txt", "rb"); ASSERT_NE(fp, nullptr); memset(buf, 0, MAX_BUF_SIZE); @@ -154,7 +145,7 @@ TEST_F(FileOperationsTest, logmesg) remove("test_logmesg.log"); } -TEST_F(FileOperationsTest, restart) +TEST_F(FileOperationsTest, write_restart) { BEGIN_HIDE_OUTPUT(); command("echo none"); @@ -179,16 +170,16 @@ TEST_F(FileOperationsTest, restart) if (info->has_package("MPIIO")) command("write_restart test.restart.mpiio"); END_HIDE_OUTPUT(); - ASSERT_TRUE(file_exists("noinit.restart")); - ASSERT_TRUE(file_exists("test.restart")); - ASSERT_TRUE(file_exists("step333.restart")); - ASSERT_TRUE(file_exists("multi-base.restart")); - ASSERT_TRUE(file_exists("multi-0.restart")); - ASSERT_TRUE(file_exists("multi2-base.restart")); - ASSERT_TRUE(file_exists("multi2-0.restart")); - ASSERT_TRUE(file_exists("multi3-base.restart")); - ASSERT_TRUE(file_exists("multi3-0.restart")); - if (info->has_package("MPIIO")) ASSERT_TRUE(file_exists("test.restart.mpiio")); + ASSERT_FILE_EXISTS("noinit.restart"); + ASSERT_FILE_EXISTS("test.restart"); + ASSERT_FILE_EXISTS("step333.restart"); + ASSERT_FILE_EXISTS("multi-base.restart"); + ASSERT_FILE_EXISTS("multi-0.restart"); + ASSERT_FILE_EXISTS("multi2-base.restart"); + ASSERT_FILE_EXISTS("multi2-0.restart"); + ASSERT_FILE_EXISTS("multi3-base.restart"); + ASSERT_FILE_EXISTS("multi3-0.restart"); + if (info->has_package("MPIIO")) ASSERT_FILE_EXISTS("test.restart.mpiio"); if (!info->has_package("MPIIO")) { TEST_FAILURE(".*ERROR: Illegal write_restart command.*", @@ -237,17 +228,105 @@ TEST_F(FileOperationsTest, restart) ASSERT_EQ(lmp->domain->triclinic, 1); // clean up - unlink("noinit.restart"); - unlink("test.restart"); - unlink("step333.restart"); - unlink("multi-base.restart"); - unlink("multi-0.restart"); - unlink("multi2-base.restart"); - unlink("multi2-0.restart"); - unlink("multi3-base.restart"); - unlink("multi3-0.restart"); - unlink("triclinic.restart"); - if (info->has_package("MPIIO")) unlink("test.restart.mpiio"); + delete_file("noinit.restart"); + delete_file("test.restart"); + delete_file("step333.restart"); + delete_file("multi-base.restart"); + delete_file("multi-0.restart"); + delete_file("multi2-base.restart"); + delete_file("multi2-0.restart"); + delete_file("multi3-base.restart"); + delete_file("multi3-0.restart"); + delete_file("triclinic.restart"); + if (info->has_package("MPIIO")) delete_file("test.restart.mpiio"); +} + +TEST_F(FileOperationsTest, write_data) +{ + BEGIN_HIDE_OUTPUT(); + command("echo none"); + END_HIDE_OUTPUT(); + TEST_FAILURE(".*ERROR: Write_data command before simulation box is defined.*", + command("write_data test.data");); + + BEGIN_HIDE_OUTPUT(); + command("region box block -2 2 -2 2 -2 2"); + command("create_box 2 box"); + command("create_atoms 1 single 0.5 0.0 0.0"); + command("pair_style zero 1.0"); + command("pair_coeff * *"); + command("mass * 1.0"); + command("reset_timestep 333"); + command("write_data noinit.data"); + command("write_data nocoeff.data nocoeff"); + command("run 0 post no"); + command("write_data test.data"); + command("write_data step*.data pair ij"); + command("fix q all property/atom q"); + command("set type 1 charge -0.5"); + command("write_data charge.data"); + command("write_data nofix.data nofix"); + END_HIDE_OUTPUT(); + + ASSERT_FILE_EXISTS("noinit.data"); + ASSERT_EQ(count_lines("noinit.data"), 26); + ASSERT_FILE_EXISTS("test.data"); + ASSERT_EQ(count_lines("test.data"), 26); + ASSERT_FILE_EXISTS("step333.data"); + ASSERT_EQ(count_lines("step333.data"), 27); + ASSERT_FILE_EXISTS("nocoeff.data"); + ASSERT_EQ(count_lines("nocoeff.data"), 21); + ASSERT_FILE_EXISTS("nofix.data"); + ASSERT_EQ(count_lines("nofix.data"), 26); + ASSERT_FILE_EXISTS("charge.data"); + ASSERT_EQ(count_lines("charge.data"), 30); + + TEST_FAILURE(".*ERROR: Illegal write_data command.*", command("write_data");); + TEST_FAILURE(".*ERROR: Illegal write_data command.*", command("write_data test.data xxxx");); + TEST_FAILURE(".*ERROR on proc 0: Cannot open data file some_crazy_dir/test.data:" + " No such file or directory.*", + command("write_data some_crazy_dir/test.data");); + + BEGIN_HIDE_OUTPUT(); + command("clear"); + END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->domain->box_exist, 0); + ASSERT_EQ(lmp->atom->natoms, 0); + ASSERT_EQ(lmp->update->ntimestep, 0); + ASSERT_EQ(lmp->domain->triclinic, 0); + + TEST_FAILURE(".*ERROR: Cannot open file noexist.data: No such file or directory.*", + command("read_data noexist.data");); + + BEGIN_HIDE_OUTPUT(); + command("pair_style zero 1.0"); + command("read_data step333.data"); + command("change_box all triclinic"); + command("write_data triclinic.data"); + END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->atom->natoms, 1); + ASSERT_EQ(lmp->update->ntimestep, 0); + ASSERT_EQ(lmp->domain->triclinic, 1); + BEGIN_HIDE_OUTPUT(); + command("clear"); + END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->atom->natoms, 0); + ASSERT_EQ(lmp->domain->triclinic, 0); + BEGIN_HIDE_OUTPUT(); + command("pair_style zero 1.0"); + command("read_data triclinic.data"); + END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->atom->natoms, 1); + ASSERT_EQ(lmp->domain->triclinic, 1); + + // clean up + delete_file("charge.data"); + delete_file("nocoeff.data"); + delete_file("noinit.data"); + delete_file("nofix.data"); + delete_file("test.data"); + delete_file("step333.data"); + delete_file("triclinic.data"); } int main(int argc, char **argv) From 0aa64eaf14077343900351b1136e0e782857bb37 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 07:14:29 -0400 Subject: [PATCH 0652/1217] portability improvement. replace POSIX-only functionality. --- unittest/testing/utils.h | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/unittest/testing/utils.h b/unittest/testing/utils.h index c76b37872a..730c6fdb44 100644 --- a/unittest/testing/utils.h +++ b/unittest/testing/utils.h @@ -10,14 +10,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#ifndef TEST_EXTENSIONS__H -#define TEST_EXTENSIONS__H +#ifndef LMP_TESTING_UTILS_H +#define LMP_TESTING_UTILS_H #include #include #include -#include -#include #include static void delete_file(const std::string &filename) @@ -65,8 +63,8 @@ static std::vector read_lines(const std::string &filename) static bool file_exists(const std::string &filename) { - struct stat result; - return stat(filename.c_str(), &result) == 0; + std::ifstream infile(filename); + return infile.good(); } #define ASSERT_FILE_EXISTS(NAME) ASSERT_TRUE(file_exists(NAME)) From 66f690004d3ab2a7f55cdda5ac5b723935dfd9fc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 07:14:49 -0400 Subject: [PATCH 0653/1217] correctly test move constructors --- unittest/utils/test_tokenizer.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/unittest/utils/test_tokenizer.cpp b/unittest/utils/test_tokenizer.cpp index 7852abb632..5b20d24e7c 100644 --- a/unittest/utils/test_tokenizer.cpp +++ b/unittest/utils/test_tokenizer.cpp @@ -92,9 +92,9 @@ TEST(Tokenizer, copy_constructor) ASSERT_EQ(u.count(), 2); } -TEST(Tokenizer, rvalue) +TEST(Tokenizer, move_constructor) { - auto u = Tokenizer(" test new word ", " "); + Tokenizer u = std::move(Tokenizer("test new word ", " ")); ASSERT_THAT(u.next(), Eq("test")); ASSERT_THAT(u.next(), Eq("new")); ASSERT_THAT(u.next(), Eq("word")); @@ -214,9 +214,9 @@ TEST(ValueTokenizer, copy_constructor) ASSERT_EQ(u.count(), 2); } -TEST(ValueTokenizer, rvalue) +TEST(ValueTokenizer, move_constructor) { - auto u = ValueTokenizer(" test new word ", " "); + ValueTokenizer u = std::move(ValueTokenizer(" test new word ", " ")); ASSERT_THAT(u.next_string(), Eq("test")); ASSERT_THAT(u.next_string(), Eq("new")); ASSERT_THAT(u.next_string(), Eq("word")); From e6f57cdf2cb7ef9653c4b81d5dedde85fd834649 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 07:21:29 -0400 Subject: [PATCH 0654/1217] minor tweaks --- unittest/formats/test_dump_cfg.cpp | 2 ++ unittest/formats/test_file_operations.cpp | 3 ++- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/unittest/formats/test_dump_cfg.cpp b/unittest/formats/test_dump_cfg.cpp index fb404e07b5..64930c3ac6 100644 --- a/unittest/formats/test_dump_cfg.cpp +++ b/unittest/formats/test_dump_cfg.cpp @@ -96,6 +96,8 @@ TEST_F(DumpCfgTest, write_dump) ASSERT_EQ(lines.size(), 124); ASSERT_THAT(lines[0], Eq("Number of particles = 32")); delete_file("dump_cfg0.melt.cfg"); + + TEST_FAILURE(".*ERROR: Unrecognized dump style 'xxx'.*", command("write_dump all xxx test.xxx");); } TEST_F(DumpCfgTest, unwrap_run0) diff --git a/unittest/formats/test_file_operations.cpp b/unittest/formats/test_file_operations.cpp index 7683f712a7..dbbad03adf 100644 --- a/unittest/formats/test_file_operations.cpp +++ b/unittest/formats/test_file_operations.cpp @@ -257,7 +257,7 @@ TEST_F(FileOperationsTest, write_data) command("pair_coeff * *"); command("mass * 1.0"); command("reset_timestep 333"); - command("write_data noinit.data"); + command("write_data noinit.data noinit"); command("write_data nocoeff.data nocoeff"); command("run 0 post no"); command("write_data test.data"); @@ -283,6 +283,7 @@ TEST_F(FileOperationsTest, write_data) TEST_FAILURE(".*ERROR: Illegal write_data command.*", command("write_data");); TEST_FAILURE(".*ERROR: Illegal write_data command.*", command("write_data test.data xxxx");); + TEST_FAILURE(".*ERROR: Illegal write_data command.*", command("write_data test.data pair xx");); TEST_FAILURE(".*ERROR on proc 0: Cannot open data file some_crazy_dir/test.data:" " No such file or directory.*", command("write_data some_crazy_dir/test.data");); From e4c7c23843a098b714aef38a9ffb6b75905f7a64 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 11:09:09 -0400 Subject: [PATCH 0655/1217] move sanitizer and iwyu configuration to Testing module and update iwyu this changes the iwyu configuration so that it will check for using GNU or Clang only as supported compilers, enforces the necessary recording of compilation commands in a json file and tweaks the "iwyu" target to work around an issue with the current iwyu implementation by placing the "native" runtime of the chosen compiler first --- cmake/CMakeLists.txt | 63 -------------------------------- cmake/Modules/Testing.cmake | 73 +++++++++++++++++++++++++++++++++++++ 2 files changed, 73 insertions(+), 63 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 7f99b04cd6..dd4c3bcaba 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -245,69 +245,6 @@ if(BUILD_OMP) target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX) endif() -# Compiler specific features for testing -if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") - option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF) - mark_as_advanced(ENABLE_COVERAGE) - if(ENABLE_COVERAGE) - if(CMAKE_VERSION VERSION_LESS 3.13) - if(CMAKE_CXX_FLAGS) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") - else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage") - endif() - else() - target_compile_options(lammps PUBLIC --coverage) - target_link_options(lammps PUBLIC --coverage) - endif() - endif() -endif() - -####################################### -# add custom target for IWYU analysis -####################################### -set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool") -mark_as_advanced(ENABLE_IWYU) -if(ENABLE_IWYU) - set(CMAKE_EXPORT_COMPILE_COMMANDS ON) - find_program(IWYU_EXE NAMES include-what-you-use iwyu) - find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py) - if (IWYU_EXE AND IWYU_TOOL) - add_custom_target( - iwyu - ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp - COMMENT "Running IWYU") - add_dependencies(iwyu lammps) - else() - message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable" - "and the iwyu-tool/iwyu_tool script installed in your PATH") - endif() -endif() - -set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)") -mark_as_advanced(ENABLE_SANITIZER) -set(ENABLE_SANITIZER_VALUES none address leak thread undefined) -set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES}) -validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES) -string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER) -if(NOT ENABLE_SANITIZER STREQUAL "none") - if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")) - if(CMAKE_VERSION VERSION_LESS 3.13) - if(CMAKE_CXX_FLAGS) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}") - else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}") - endif() - else() - target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER}) - target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER}) - endif() - else() - message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.") - set(ENABLE_SANITIZER "none") - endif() -endif() - if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) enable_language(C) find_package(LAPACK) diff --git a/cmake/Modules/Testing.cmake b/cmake/Modules/Testing.cmake index 7fbd8212de..d1fa97a7a8 100644 --- a/cmake/Modules/Testing.cmake +++ b/cmake/Modules/Testing.cmake @@ -56,3 +56,76 @@ if(ENABLE_TESTING) get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE) add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN}) endif() + +# Compiler specific features for testing +if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") + option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF) + mark_as_advanced(ENABLE_COVERAGE) + if(ENABLE_COVERAGE) + if(CMAKE_VERSION VERSION_LESS 3.13) + if(CMAKE_CXX_FLAGS) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") + else() + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage") + endif() + else() + target_compile_options(lammps PUBLIC --coverage) + target_link_options(lammps PUBLIC --coverage) + endif() + endif() +endif() + +####################################### +# add custom target for IWYU analysis +####################################### +set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool") +mark_as_advanced(ENABLE_IWYU) +if(ENABLE_IWYU) + # enforce these settings + set(CMAKE_EXPORT_COMPILE_COMMANDS ON CACHE BOOL "Enable reporting compilation commands to compile_commands.json" FORCE) + if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU"))) + message(FATAL_ERROR "IWYU is only supported with Clang or GNU compilers") + endif() + # detect the "native" header folder so we can include them first + execute_process(COMMAND ${CMAKE_CXX_COMPILER} --print-search-dirs OUTPUT_VARIABLE IWYU_SEARCH_PATHS) + string(REGEX REPLACE ".*libraries: *=([^:]+):.*" "\\1/include" IWYU_EXTRA_INCLUDE_DIR ${IWYU_SEARCH_PATHS}) + find_program(IWYU_EXE NAMES include-what-you-use iwyu) + find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py) + if (IWYU_EXE AND IWYU_TOOL) + add_custom_target( + iwyu + ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -I${IWYU_EXTRA_INCLUDE_DIR} -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp + COMMENT "Running IWYU") + add_dependencies(iwyu lammps) + else() + message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable" + "and the iwyu-tool/iwyu_tool script installed in your PATH") + endif() +endif() + +####################################### +# select code sanitizer options +####################################### +set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)") +mark_as_advanced(ENABLE_SANITIZER) +set(ENABLE_SANITIZER_VALUES none address leak thread undefined) +set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES}) +validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES) +string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER) +if(NOT ENABLE_SANITIZER STREQUAL "none") + if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")) + if(CMAKE_VERSION VERSION_LESS 3.13) + if(CMAKE_CXX_FLAGS) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}") + else() + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}") + endif() + else() + target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER}) + target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER}) + endif() + else() + message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.") + set(ENABLE_SANITIZER "none") + endif() +endif() From 4738337e470980dbbf5ccd61d396a95425ec5cac Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 13:22:39 -0400 Subject: [PATCH 0656/1217] update/trim list of include files according to the IWYU principle --- src/BODY/fix_nph_body.cpp | 3 -- src/BODY/fix_npt_body.cpp | 3 -- src/BODY/fix_nvt_body.cpp | 2 -- src/BODY/fix_wall_body_polygon.cpp | 10 ++++--- src/BODY/pair_body_nparticle.cpp | 15 +++++----- src/COLLOID/pair_yukawa_colloid.cpp | 11 +++---- src/COMPRESS/gz_file_writer.h | 5 ++-- src/COMPRESS/zstd_file_writer.h | 4 +-- src/GPU/pair_born_coul_long_cs_gpu.cpp | 25 ++++++---------- src/GPU/pair_born_coul_long_gpu.cpp | 25 ++++++---------- src/GPU/pair_born_coul_wolf_cs_gpu.cpp | 23 +++++--------- src/GPU/pair_born_coul_wolf_gpu.cpp | 23 +++++--------- src/GPU/pair_born_gpu.cpp | 21 +++++-------- src/GPU/pair_buck_coul_cut_gpu.cpp | 21 +++++-------- src/GPU/pair_buck_coul_long_gpu.cpp | 23 +++++--------- src/GPU/pair_buck_gpu.cpp | 21 +++++-------- src/GPU/pair_colloid_gpu.cpp | 22 +++++--------- src/GPU/pair_coul_cut_gpu.cpp | 21 +++++-------- src/GPU/pair_coul_debye_gpu.cpp | 21 +++++-------- src/GPU/pair_coul_dsf_gpu.cpp | 21 +++++-------- src/GPU/pair_coul_long_cs_gpu.cpp | 23 +++++--------- src/GPU/pair_coul_long_gpu.cpp | 23 +++++--------- src/GPU/pair_dpd_gpu.cpp | 23 +++++--------- src/GPU/pair_dpd_tstat_gpu.cpp | 23 +++++--------- src/GPU/pair_eam_alloy_gpu.cpp | 24 +++++++-------- src/GPU/pair_eam_fs_gpu.cpp | 26 ++++++++-------- src/GPU/pair_eam_gpu.cpp | 14 ++++----- src/GPU/pair_gauss_gpu.cpp | 21 +++++-------- src/GPU/pair_gayberne_gpu.cpp | 24 ++++++--------- src/GPU/pair_lj96_cut_gpu.cpp | 21 +++++-------- src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp | 25 +++++++--------- src/GPU/pair_lj_charmm_coul_long_gpu.cpp | 23 +++++--------- src/GPU/pair_lj_class2_coul_long_gpu.cpp | 23 +++++--------- src/GPU/pair_lj_class2_gpu.cpp | 6 ---- src/GPU/pair_lj_cubic_gpu.cpp | 7 ----- src/GPU/pair_lj_cut_coul_cut_gpu.cpp | 21 +++++-------- src/GPU/pair_lj_cut_coul_debye_gpu.cpp | 21 +++++-------- src/GPU/pair_lj_cut_coul_dsf_gpu.cpp | 20 +++++-------- src/GPU/pair_lj_cut_coul_long_gpu.cpp | 23 +++++--------- src/GPU/pair_lj_cut_coul_msm_gpu.cpp | 23 +++++--------- src/GPU/pair_lj_cut_dipole_cut_gpu.cpp | 23 ++++++-------- src/GPU/pair_lj_cut_dipole_long_gpu.cpp | 27 +++++++---------- src/GPU/pair_lj_cut_gpu.cpp | 21 +++++-------- src/GPU/pair_lj_cut_tip4p_long_gpu.cpp | 30 ++++++++----------- src/GPU/pair_lj_expand_coul_long_gpu.cpp | 23 +++++--------- src/GPU/pair_lj_expand_gpu.cpp | 21 +++++-------- src/GPU/pair_lj_gromacs_gpu.cpp | 22 +++++--------- src/GPU/pair_lj_sdk_coul_long_gpu.cpp | 23 +++++--------- src/GPU/pair_lj_sdk_gpu.cpp | 21 +++++-------- src/GPU/pair_lj_sf_dipole_sf_gpu.cpp | 23 ++++++-------- src/GPU/pair_mie_cut_gpu.cpp | 21 +++++-------- src/GPU/pair_morse_gpu.cpp | 21 +++++-------- src/GPU/pair_resquared_gpu.cpp | 24 ++++++--------- src/GPU/pair_soft_gpu.cpp | 21 +++++-------- src/GPU/pair_sw_gpu.cpp | 17 ++++------- src/GPU/pair_table_gpu.cpp | 25 +++++----------- src/GPU/pair_tersoff_gpu.cpp | 15 ++++------ src/GPU/pair_tersoff_mod_gpu.cpp | 17 ++++------- src/GPU/pair_tersoff_zbl_gpu.cpp | 17 ++++------- src/GPU/pair_ufm_gpu.cpp | 21 +++++-------- src/GPU/pair_vashishta_gpu.cpp | 17 ++++------- src/GPU/pair_yukawa_colloid_gpu.cpp | 21 +++++-------- src/GPU/pair_yukawa_gpu.cpp | 21 +++++-------- src/GPU/pair_zbl_gpu.cpp | 22 +++++--------- src/KSPACE/fft3d.cpp | 7 +++-- src/KSPACE/msm_cg.cpp | 8 ++--- src/KSPACE/remap.cpp | 3 +- src/MANYBODY/pair_eam_he.cpp | 4 +-- src/MANYBODY/pair_eim.h | 1 + src/MANYBODY/pair_vashishta_table.cpp | 3 +- src/MC/fix_charge_regulation.cpp | 3 -- src/MC/fix_tfmc.cpp | 15 +++++----- src/MISC/fix_orient_bcc.cpp | 1 - src/MISC/fix_orient_fcc.cpp | 1 - src/MLIAP/pair_mliap.cpp | 1 - src/MOLECULE/dihedral_charmm.cpp | 13 ++++---- src/MOLECULE/dihedral_charmmfsw.cpp | 13 ++++---- src/QEQ/fix_qeq_point.cpp | 1 - src/QEQ/fix_qeq_shielded.cpp | 1 - src/RIGID/fix_rigid_nh_small.cpp | 1 - src/SNAP/pair_snap.cpp | 1 - src/SPIN/fix_langevin_spin.cpp | 9 +++--- src/SPIN/fix_neb_spin.cpp | 1 - src/SPIN/pair_spin.cpp | 9 +++--- src/USER-COLVARS/ndx_group.cpp | 3 -- src/USER-DRUDE/fix_tgnh_drude.cpp | 1 - src/USER-DRUDE/fix_tgnvt_drude.cpp | 2 -- src/USER-EFF/compute_temp_region_eff.cpp | 2 -- src/USER-EFF/fix_nve_eff.cpp | 11 ++++--- src/USER-EFF/fix_nvt_eff.cpp | 2 -- src/USER-MEAMC/pair_meamc.cpp | 15 +++++----- src/USER-MEAMC/pair_meamc.h | 2 +- src/USER-MESODPD/atom_vec_edpd.cpp | 1 - src/USER-MESODPD/pair_edpd.cpp | 30 +++++++++---------- src/USER-MISC/angle_gaussian.cpp | 9 +++--- src/USER-MISC/compute_gyration_shape.cpp | 1 - .../compute_gyration_shape_chunk.cpp | 1 - src/USER-MISC/compute_pressure_grem.cpp | 2 -- src/USER-MISC/dihedral_table_cut.cpp | 1 - src/USER-MISC/fix_addtorque.cpp | 2 -- src/USER-MISC/fix_electron_stopping_fit.cpp | 5 ---- src/USER-MISC/fix_nvk.cpp | 10 +++---- src/USER-MISC/fix_orient_eco.cpp | 1 - src/USER-MISC/fix_rhok.cpp | 1 - src/USER-MISC/fix_wall_region_ees.cpp | 1 - src/USER-MISC/pair_wf_cut.cpp | 2 -- src/USER-OMP/fix_nvt_asphere_omp.cpp | 4 +-- src/USER-OMP/fix_nvt_omp.cpp | 2 -- src/USER-OMP/fix_qeq_comb_omp.cpp | 8 ++--- src/USER-OMP/npair_full_bin_atomonly_omp.cpp | 11 +++---- .../npair_half_bin_atomonly_newton_omp.cpp | 10 ++++--- .../npair_half_size_bin_newtoff_omp.cpp | 11 +++---- .../npair_half_size_bin_newton_omp.cpp | 11 +++---- .../npair_half_size_bin_newton_tri_omp.cpp | 11 +++---- .../npair_half_size_multi_newtoff_omp.cpp | 11 +++---- .../npair_half_size_multi_newton_omp.cpp | 11 +++---- .../npair_half_size_multi_newton_tri_omp.cpp | 11 +++---- .../npair_half_size_nsq_newtoff_omp.cpp | 11 +++---- .../npair_half_size_nsq_newton_omp.cpp | 11 +++---- src/USER-OMP/npair_halffull_newtoff_omp.cpp | 11 +++---- src/USER-OMP/npair_halffull_newton_omp.cpp | 11 +++---- src/USER-OMP/pair_tersoff_mod_c_omp.cpp | 2 ++ src/USER-OMP/pair_tersoff_mod_omp.cpp | 4 +-- src/USER-OMP/pair_tersoff_omp.cpp | 4 +-- src/USER-OMP/pair_tersoff_zbl_omp.cpp | 9 +++--- src/USER-OMP/pair_vashishta_omp.cpp | 2 -- src/USER-PACE/pair_pace.cpp | 1 - src/USER-PTM/ptm_constants.cpp | 1 - src/USER-SMD/fix_smd_wall_surface.cpp | 1 - src/atom.cpp | 1 + src/atom_vec.h | 1 + tools/lammps-shell/lammps-shell.cpp | 9 +++--- 132 files changed, 618 insertions(+), 1011 deletions(-) diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp index a876ac9dc7..ca3923d278 100644 --- a/src/BODY/fix_nph_body.cpp +++ b/src/BODY/fix_nph_body.cpp @@ -18,11 +18,8 @@ #include "fix_nph_body.h" #include "error.h" -#include "group.h" #include "modify.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp index bc669fc971..3aacfe7f65 100644 --- a/src/BODY/fix_npt_body.cpp +++ b/src/BODY/fix_npt_body.cpp @@ -18,11 +18,8 @@ #include "fix_npt_body.h" #include "error.h" -#include "group.h" #include "modify.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp index 442aed2c94..6209e1db2f 100644 --- a/src/BODY/fix_nvt_body.cpp +++ b/src/BODY/fix_nvt_body.cpp @@ -21,8 +21,6 @@ #include "group.h" #include "modify.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp index 027c0dbd5a..25e3afb31d 100644 --- a/src/BODY/fix_wall_body_polygon.cpp +++ b/src/BODY/fix_wall_body_polygon.cpp @@ -16,18 +16,20 @@ ------------------------------------------------------------------------- */ #include "fix_wall_body_polygon.h" -#include -#include + #include "atom.h" #include "atom_vec_body.h" #include "body_rounded_polygon.h" #include "domain.h" -#include "update.h" +#include "error.h" #include "force.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" -#include "error.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/BODY/pair_body_nparticle.cpp b/src/BODY/pair_body_nparticle.cpp index 3ec0e4bbe6..68321f3b70 100644 --- a/src/BODY/pair_body_nparticle.cpp +++ b/src/BODY/pair_body_nparticle.cpp @@ -12,18 +12,19 @@ ------------------------------------------------------------------------- */ #include "pair_body_nparticle.h" -#include -#include -#include "math_extra.h" + #include "atom.h" #include "atom_vec_body.h" #include "body_nparticle.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "math_extra.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp index 36074a1a21..5b1a4e4e83 100644 --- a/src/COLLOID/pair_yukawa_colloid.cpp +++ b/src/COLLOID/pair_yukawa_colloid.cpp @@ -16,13 +16,14 @@ ------------------------------------------------------------------------- */ #include "pair_yukawa_colloid.h" -#include + #include "atom.h" -#include "atom_vec.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" #include "error.h" +#include "force.h" +#include "neigh_list.h" +#include "neighbor.h" + +#include using namespace LAMMPS_NS; diff --git a/src/COMPRESS/gz_file_writer.h b/src/COMPRESS/gz_file_writer.h index af91572d8e..669931399b 100644 --- a/src/COMPRESS/gz_file_writer.h +++ b/src/COMPRESS/gz_file_writer.h @@ -19,9 +19,10 @@ #define LMP_GZ_FILE_WRITER_H #include "file_writer.h" + +#include #include #include -#include namespace LAMMPS_NS { @@ -40,8 +41,6 @@ public: void setCompressionLevel(int level); }; - - } #endif diff --git a/src/COMPRESS/zstd_file_writer.h b/src/COMPRESS/zstd_file_writer.h index 8980666856..030a01690a 100644 --- a/src/COMPRESS/zstd_file_writer.h +++ b/src/COMPRESS/zstd_file_writer.h @@ -21,9 +21,9 @@ #define LMP_ZSTD_FILE_WRITER_H #include "file_writer.h" + #include #include -#include namespace LAMMPS_NS { @@ -47,8 +47,6 @@ public: void setCompressionLevel(int level); void setChecksum(bool enabled); }; - - } #endif diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp index 95c3df7b09..5782ff5969 100644 --- a/src/GPU/pair_born_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp @@ -16,28 +16,21 @@ ------------------------------------------------------------------------- */ #include "pair_born_coul_long_cs_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" -#include "kspace.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "kspace.h" +#include "math_const.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp index dbd55ef041..5b27e96cbd 100644 --- a/src/GPU/pair_born_coul_long_gpu.cpp +++ b/src/GPU/pair_born_coul_long_gpu.cpp @@ -16,28 +16,21 @@ ------------------------------------------------------------------------- */ #include "pair_born_coul_long_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" -#include "kspace.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "kspace.h" +#include "math_const.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + #define EWALD_F 1.12837917 #define EWALD_P 0.3275911 #define A1 0.254829592 diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp index 9663c4be51..0c3e36265f 100644 --- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp @@ -16,27 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_born_coul_wolf_cs_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "math_const.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp index 8db3761f1f..1cd91e2d61 100644 --- a/src/GPU/pair_born_coul_wolf_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_gpu.cpp @@ -16,27 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_born_coul_wolf_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "math_const.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp index 3454adda18..f7d383b528 100644 --- a/src/GPU/pair_born_gpu.cpp +++ b/src/GPU/pair_born_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_born_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp index ec002289f2..fe3e8f092c 100644 --- a/src/GPU/pair_buck_coul_cut_gpu.cpp +++ b/src/GPU/pair_buck_coul_cut_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_buck_coul_cut_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp index 913f68f4c4..0c23141060 100644 --- a/src/GPU/pair_buck_coul_long_gpu.cpp +++ b/src/GPU/pair_buck_coul_long_gpu.cpp @@ -16,27 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_buck_coul_long_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" -#include "kspace.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "kspace.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + #define EWALD_F 1.12837917 #define EWALD_P 0.3275911 #define A1 0.254829592 diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp index 4f091eede5..81bd987850 100644 --- a/src/GPU/pair_buck_gpu.cpp +++ b/src/GPU/pair_buck_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_buck_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp index 070b103ddf..d5391aeede 100644 --- a/src/GPU/pair_colloid_gpu.cpp +++ b/src/GPU/pair_colloid_gpu.cpp @@ -16,26 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_colloid_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp index fc4a44adc4..ef9b2dff4d 100644 --- a/src/GPU/pair_coul_cut_gpu.cpp +++ b/src/GPU/pair_coul_cut_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_coul_cut_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp index 1104175046..ca5cb7df9a 100644 --- a/src/GPU/pair_coul_debye_gpu.cpp +++ b/src/GPU/pair_coul_debye_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_coul_debye_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp index 85cd978f33..d988a47681 100644 --- a/src/GPU/pair_coul_dsf_gpu.cpp +++ b/src/GPU/pair_coul_dsf_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_coul_dsf_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + #define MY_PIS 1.77245385090551602729 #define EWALD_F 1.12837917 #define EWALD_P 0.3275911 diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp index 84b6a665db..f924f2c925 100644 --- a/src/GPU/pair_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_coul_long_cs_gpu.cpp @@ -16,27 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_coul_long_cs_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" -#include "kspace.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "kspace.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp index d27b4650ba..e1d51b1359 100644 --- a/src/GPU/pair_coul_long_gpu.cpp +++ b/src/GPU/pair_coul_long_gpu.cpp @@ -16,27 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_coul_long_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" -#include "kspace.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "kspace.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + #define EWALD_F 1.12837917 #define EWALD_P 0.3275911 #define A1 0.254829592 diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp index 884834d94a..f66fc6d594 100644 --- a/src/GPU/pair_dpd_gpu.cpp +++ b/src/GPU/pair_dpd_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_dpd_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "random_mars.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp index 507461fd23..957bb938f3 100644 --- a/src/GPU/pair_dpd_tstat_gpu.cpp +++ b/src/GPU/pair_dpd_tstat_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_dpd_tstat_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "random_mars.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index add3a3ca7a..fe2cc92450 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -16,23 +16,23 @@ ------------------------------------------------------------------------- */ #include "pair_eam_alloy_gpu.h" -#include -#include #include "atom.h" -#include "force.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "gpu_extra.h" #include "domain.h" - +#include "error.h" +#include "force.h" +#include "gpu_extra.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "potential_file_reader.h" #include "suffix.h" #include "tokenizer.h" -#include "potential_file_reader.h" + +#include +#include using namespace LAMMPS_NS; @@ -389,7 +389,7 @@ void PairEAMAlloyGPU::read_file(char *filename) ValueTokenizer values = reader.next_values(1); file->nelements = values.next_int(); - if (values.count() != file->nelements + 1) + if ((int)values.count() != file->nelements + 1) error->one(FLERR,"Incorrect element names in EAM potential file"); file->elements = new char*[file->nelements]; diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index 394b520a73..b92e348ddf 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -16,23 +16,23 @@ ------------------------------------------------------------------------- */ #include "pair_eam_fs_gpu.h" -#include -#include #include "atom.h" -#include "force.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "gpu_extra.h" #include "domain.h" -#include "suffix.h" - -#include "tokenizer.h" +#include "error.h" +#include "force.h" +#include "gpu_extra.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "suffix.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; @@ -388,7 +388,7 @@ void PairEAMFSGPU::read_file(char *filename) ValueTokenizer values = reader.next_values(1); file->nelements = values.next_int(); - if (values.count() != file->nelements + 1) + if ((int)values.count() != file->nelements + 1) error->one(FLERR,"Incorrect element names in EAM potential file"); file->elements = new char*[file->nelements]; diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp index fada4febb5..2ed72a3b08 100644 --- a/src/GPU/pair_eam_gpu.cpp +++ b/src/GPU/pair_eam_gpu.cpp @@ -16,22 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_eam_gpu.h" -#include -#include -#include #include "atom.h" -#include "force.h" #include "comm.h" #include "domain.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" -#include "neigh_request.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + #define MAXLINE 1024 using namespace LAMMPS_NS; diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp index 04fc65dd06..8431ce1b67 100644 --- a/src/GPU/pair_gauss_gpu.cpp +++ b/src/GPU/pair_gauss_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_gauss_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp index c5e0a1afb5..d7adb5c657 100644 --- a/src/GPU/pair_gayberne_gpu.cpp +++ b/src/GPU/pair_gayberne_gpu.cpp @@ -16,28 +16,22 @@ ------------------------------------------------------------------------- */ #include "pair_gayberne_gpu.h" -#include -#include -#include -#include "math_extra.h" #include "atom.h" -#include "atom_vec.h" #include "atom_vec_ellipsoid.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" #include "domain.h" -#include "update.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "math_extra.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp index 33774078d5..016147cb6e 100644 --- a/src/GPU/pair_lj96_cut_gpu.cpp +++ b/src/GPU/pair_lj96_cut_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_lj96_cut_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp b/src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp index 4d8d67cdca..a40da25da8 100644 --- a/src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp +++ b/src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp @@ -15,23 +15,18 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_charmm_coul_charmm_gpu.h" + #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" + +#include using namespace LAMMPS_NS; @@ -205,8 +200,8 @@ double PairLJCharmmCoulCharmmGPU::memory_usage() /* ---------------------------------------------------------------------- */ void PairLJCharmmCoulCharmmGPU::cpu_compute(int start, int inum, int eflag, - int vflag, int *ilist, - int *numneigh, int **firstneigh) + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp index 42e869207e..1fc8ba1c5f 100644 --- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp @@ -16,27 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_lj_charmm_coul_long_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" -#include "kspace.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "kspace.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + #define EWALD_F 1.12837917 #define EWALD_P 0.3275911 #define A1 0.254829592 diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp index ae5321bc4f..87dda4f190 100644 --- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp @@ -16,27 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_long_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" -#include "kspace.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "kspace.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + #define EWALD_F 1.12837917 #define EWALD_P 0.3275911 #define A1 0.254829592 diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp index e32561ab59..4e224cb2d3 100644 --- a/src/GPU/pair_lj_class2_gpu.cpp +++ b/src/GPU/pair_lj_class2_gpu.cpp @@ -18,20 +18,14 @@ #include "pair_lj_class2_gpu.h" #include "atom.h" -#include "atom_vec.h" -#include "comm.h" #include "domain.h" #include "error.h" #include "force.h" #include "gpu_extra.h" -#include "integrate.h" -#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" #include "neighbor.h" #include "suffix.h" -#include "universe.h" -#include "update.h" #include diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp index 73839bdbed..1c9b9a0820 100644 --- a/src/GPU/pair_lj_cubic_gpu.cpp +++ b/src/GPU/pair_lj_cubic_gpu.cpp @@ -18,23 +18,16 @@ #include "pair_lj_cubic_gpu.h" #include "atom.h" -#include "atom_vec.h" -#include "comm.h" #include "domain.h" #include "error.h" #include "force.h" #include "gpu_extra.h" -#include "integrate.h" -#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" #include "neighbor.h" #include "suffix.h" -#include "universe.h" -#include "update.h" #include -#include #include "pair_lj_cubic_const.h" diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp index 1583395f82..0a1076aef8 100644 --- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_cut_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp index d83678bd9f..75a16ae210 100644 --- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_debye_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp index 3a29d7e5a2..e3500ce60d 100644 --- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp @@ -17,25 +17,19 @@ #include "pair_lj_cut_coul_dsf_gpu.h" #include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + #define MY_PIS 1.77245385090551602729 #define EWALD_F 1.12837917 #define EWALD_P 0.3275911 diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp index 34e31fc044..3ac52c08c5 100644 --- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp @@ -16,27 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_long_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" -#include "kspace.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "kspace.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + #define EWALD_F 1.12837917 #define EWALD_P 0.3275911 #define A1 0.254829592 diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp index 2fd1d55b54..f92c83bcf7 100644 --- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp @@ -16,27 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_msm_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" -#include "kspace.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "kspace.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp index 93af562ed0..b15822bde9 100644 --- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp @@ -16,25 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_dipole_cut_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp index 9ec2bec258..d9d38d4cb0 100644 --- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp @@ -16,27 +16,22 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_dipole_long_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "kspace.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "kspace.h" +#include "math_const.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include "update.h" + +#include +#include #define EWALD_F 1.12837917 #define EWALD_P 0.3275911 diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp index 1de70701f0..65fed01321 100644 --- a/src/GPU/pair_lj_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp index c63d1a4e91..67dcd6d0b6 100644 --- a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp @@ -15,30 +15,24 @@ Contributing author: Vsevolod Nikolskiy (HSE) ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_lj_cut_tip4p_long_gpu.h" -#include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" -#include "domain.h" -#include "kspace.h" + #include "angle.h" +#include "atom.h" #include "bond.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "kspace.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + #define EWALD_F 1.12837917 #define EWALD_P 0.3275911 #define A1 0.254829592 diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp index af042bef42..d5a23507ae 100644 --- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp @@ -16,27 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_lj_expand_coul_long_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" -#include "kspace.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "kspace.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + #define EWALD_F 1.12837917 #define EWALD_P 0.3275911 #define A1 0.254829592 diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp index 87605af1a4..234173651d 100644 --- a/src/GPU/pair_lj_expand_gpu.cpp +++ b/src/GPU/pair_lj_expand_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_lj_expand_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp index b45d757ef4..df5d6aee89 100644 --- a/src/GPU/pair_lj_gromacs_gpu.cpp +++ b/src/GPU/pair_lj_gromacs_gpu.cpp @@ -16,27 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_lj_gromacs_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" -#include "kspace.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp index 97b53fec33..5b7cb1fa67 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp @@ -16,27 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_lj_sdk_coul_long_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" -#include "kspace.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "kspace.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + #define EWALD_F 1.12837917 #define EWALD_P 0.3275911 #define A1 0.254829592 diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp index cd6f4bc544..1cfacfde83 100644 --- a/src/GPU/pair_lj_sdk_gpu.cpp +++ b/src/GPU/pair_lj_sdk_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_lj_sdk_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp index cb7a889ed5..033c0c1d62 100644 --- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp +++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp @@ -16,25 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_lj_sf_dipole_sf_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp index e72c12da79..f2cfbc2637 100644 --- a/src/GPU/pair_mie_cut_gpu.cpp +++ b/src/GPU/pair_mie_cut_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_mie_cut_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp index 507edd33f4..024346afb2 100644 --- a/src/GPU/pair_morse_gpu.cpp +++ b/src/GPU/pair_morse_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_morse_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp index 90a7af1d0e..18817bf551 100644 --- a/src/GPU/pair_resquared_gpu.cpp +++ b/src/GPU/pair_resquared_gpu.cpp @@ -16,28 +16,22 @@ ------------------------------------------------------------------------- */ #include "pair_resquared_gpu.h" -#include -#include -#include -#include "math_extra.h" #include "atom.h" -#include "atom_vec.h" #include "atom_vec_ellipsoid.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" #include "domain.h" -#include "update.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "math_extra.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp index 66bd6deb8f..0c963e947c 100644 --- a/src/GPU/pair_soft_gpu.cpp +++ b/src/GPU/pair_soft_gpu.cpp @@ -16,27 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_soft_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" #include "math_const.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp index b819580488..1603704b9b 100644 --- a/src/GPU/pair_sw_gpu.cpp +++ b/src/GPU/pair_sw_gpu.cpp @@ -16,22 +16,17 @@ ------------------------------------------------------------------------- */ #include "pair_sw_gpu.h" -#include -#include -#include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" -#include "memory.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp index 6c5bb48e26..fb1a130398 100644 --- a/src/GPU/pair_table_gpu.cpp +++ b/src/GPU/pair_table_gpu.cpp @@ -16,30 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_table_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" -#define LOOKUP 0 -#define LINEAR 1 -#define SPLINE 2 -#define BITMAP 3 +#include using namespace LAMMPS_NS; diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp index c2f3413d3d..55576de4ec 100644 --- a/src/GPU/pair_tersoff_gpu.cpp +++ b/src/GPU/pair_tersoff_gpu.cpp @@ -16,22 +16,17 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_gpu.h" -#include -#include -#include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "gpu_extra.h" #include "memory.h" #include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" -#include "domain.h" -#include "gpu_extra.h" +#include "neigh_request.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp index 6a5e9892ec..5d79a68af4 100644 --- a/src/GPU/pair_tersoff_mod_gpu.cpp +++ b/src/GPU/pair_tersoff_mod_gpu.cpp @@ -16,22 +16,17 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_mod_gpu.h" -#include -#include -#include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" -#include "memory.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp index 0c56212fef..9594845fd0 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.cpp +++ b/src/GPU/pair_tersoff_zbl_gpu.cpp @@ -16,22 +16,17 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_zbl_gpu.h" -#include -#include -#include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" -#include "memory.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp index 47a32f7fc2..cdf53d6cc6 100644 --- a/src/GPU/pair_ufm_gpu.cpp +++ b/src/GPU/pair_ufm_gpu.cpp @@ -18,26 +18,19 @@ ------------------------------------------------------------------------- */ #include "pair_ufm_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp index b3c703952f..4c47b66b4a 100644 --- a/src/GPU/pair_vashishta_gpu.cpp +++ b/src/GPU/pair_vashishta_gpu.cpp @@ -16,22 +16,17 @@ ------------------------------------------------------------------------- */ #include "pair_vashishta_gpu.h" -#include -#include -#include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" -#include "memory.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp index 3ac5f6c693..4e4e555134 100644 --- a/src/GPU/pair_yukawa_colloid_gpu.cpp +++ b/src/GPU/pair_yukawa_colloid_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_yukawa_colloid_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp index 8558b57cd8..104adef8d5 100644 --- a/src/GPU/pair_yukawa_gpu.cpp +++ b/src/GPU/pair_yukawa_gpu.cpp @@ -16,26 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_yukawa_gpu.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp index 97a859a5bf..267b9252bd 100644 --- a/src/GPU/pair_zbl_gpu.cpp +++ b/src/GPU/pair_zbl_gpu.cpp @@ -16,27 +16,19 @@ ------------------------------------------------------------------------- */ #include "pair_zbl_gpu.h" -#include "lmptype.h" -#include -#include -#include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "integrate.h" -#include "memory.h" -#include "error.h" -#include "neigh_request.h" -#include "universe.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "gpu_extra.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "suffix.h" +#include + using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp index 6a05be4e6f..a21bbb0999 100644 --- a/src/KSPACE/fft3d.cpp +++ b/src/KSPACE/fft3d.cpp @@ -20,11 +20,12 @@ ------------------------------------------------------------------------- */ #include "fft3d.h" -#include -#include + +#include "remap.h" + #include #include -#include "remap.h" + #if defined(_OPENMP) #include #endif diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp index 6123aedfb8..d61db8db96 100644 --- a/src/KSPACE/msm_cg.cpp +++ b/src/KSPACE/msm_cg.cpp @@ -16,9 +16,7 @@ ------------------------------------------------------------------------- */ #include "msm_cg.h" -#include -#include -#include + #include "atom.h" #include "gridcomm.h" #include "domain.h" @@ -26,7 +24,9 @@ #include "force.h" #include "neighbor.h" #include "memory.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp index ab2ec687d7..c99bbb2562 100644 --- a/src/KSPACE/remap.cpp +++ b/src/KSPACE/remap.cpp @@ -12,8 +12,7 @@ ------------------------------------------------------------------------- */ #include "remap.h" -#include -#include + #include #define PACK_DATA FFT_SCALAR diff --git a/src/MANYBODY/pair_eam_he.cpp b/src/MANYBODY/pair_eam_he.cpp index 0018429862..b0c4b7c205 100644 --- a/src/MANYBODY/pair_eam_he.cpp +++ b/src/MANYBODY/pair_eam_he.cpp @@ -19,13 +19,13 @@ #include "atom.h" #include "comm.h" -#include "error.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" #include "update.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h index 52b94192c2..a68dcc2198 100644 --- a/src/MANYBODY/pair_eim.h +++ b/src/MANYBODY/pair_eim.h @@ -23,6 +23,7 @@ PairStyle(eim,PairEIM) #include "pair.h" #include +#include namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp index 14dacdae3f..05d9703443 100644 --- a/src/MANYBODY/pair_vashishta_table.cpp +++ b/src/MANYBODY/pair_vashishta_table.cpp @@ -16,11 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_vashishta_table.h" -#include + #include "atom.h" #include "error.h" #include "force.h" -#include "comm.h" #include "memory.h" #include "neigh_list.h" diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index e369ab95e1..6226dd5ba5 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -32,15 +32,12 @@ #include "improper.h" #include "kspace.h" #include "math_const.h" -#include "math_extra.h" #include "math_special.h" #include "memory.h" #include "modify.h" -#include "molecule.h" #include "neighbor.h" #include "pair.h" #include "random_park.h" -#include "region.h" #include "update.h" #include diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp index 4d481e7d68..ff49d84f6b 100644 --- a/src/MC/fix_tfmc.cpp +++ b/src/MC/fix_tfmc.cpp @@ -17,18 +17,19 @@ #include "fix_tfmc.h" -#include -#include -#include #include "atom.h" -#include "force.h" -#include "group.h" -#include "random_mars.h" #include "comm.h" #include "domain.h" +#include "error.h" +#include "force.h" +#include "group.h" #include "memory.h" #include "modify.h" -#include "error.h" +#include "random_mars.h" + +#include +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index 520940f2f0..d78a6bcb95 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -33,7 +33,6 @@ #include "update.h" #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index c94e91a0b5..559a56000e 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -30,7 +30,6 @@ #include "update.h" #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MLIAP/pair_mliap.cpp b/src/MLIAP/pair_mliap.cpp index 85374e9214..ab081f8462 100644 --- a/src/MLIAP/pair_mliap.cpp +++ b/src/MLIAP/pair_mliap.cpp @@ -35,7 +35,6 @@ #include #include -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index d56c875744..f8322fd9a1 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -17,19 +17,18 @@ #include "dihedral_charmm.h" -#include -#include #include "atom.h" #include "comm.h" -#include "neighbor.h" +#include "error.h" #include "force.h" -#include "pair.h" -#include "update.h" -#include "respa.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neighbor.h" +#include "pair.h" +#include "respa.h" +#include "update.h" +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index 09372f67ac..15e3aedc80 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -20,19 +20,18 @@ #include "dihedral_charmmfsw.h" -#include -#include #include "atom.h" #include "comm.h" -#include "neighbor.h" +#include "error.h" #include "force.h" -#include "pair.h" -#include "update.h" -#include "respa.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neighbor.h" +#include "pair.h" +#include "respa.h" +#include "update.h" +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index ac31f906e0..38deee696e 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -31,7 +31,6 @@ #include "update.h" #include -#include using namespace LAMMPS_NS; diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index ad6202abd8..7d8cfdb90d 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -32,7 +32,6 @@ #include "update.h" #include -#include using namespace LAMMPS_NS; diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 242c33eb3a..0f1e813234 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -31,7 +31,6 @@ #include "math_extra.h" #include "memory.h" #include "modify.h" -#include "molecule.h" #include "rigid_const.h" #include "update.h" diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index ae0023ddec..64dc5ee9c6 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -25,7 +25,6 @@ #include "tokenizer.h" #include -#include using namespace LAMMPS_NS; diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index 5c040da0f5..ae9d637180 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -22,21 +22,20 @@ ------------------------------------------------------------------------- */ #include "fix_langevin_spin.h" -#include -#include + #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" -#include "group.h" #include "math_const.h" -#include "memory.h" #include "modify.h" -// #include "random_park.h" #include "random_mars.h" #include "respa.h" #include "update.h" +#include +#include + using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; diff --git a/src/SPIN/fix_neb_spin.cpp b/src/SPIN/fix_neb_spin.cpp index 620d0a47bd..7bef18e9e7 100644 --- a/src/SPIN/fix_neb_spin.cpp +++ b/src/SPIN/fix_neb_spin.cpp @@ -27,7 +27,6 @@ #include "comm.h" #include "compute.h" #include "error.h" -#include "force.h" #include "group.h" #include "memory.h" #include "modify.h" diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp index c57feb8390..815ed2d290 100644 --- a/src/SPIN/pair_spin.cpp +++ b/src/SPIN/pair_spin.cpp @@ -22,20 +22,21 @@ ------------------------------------------------------------------------- */ #include "pair_spin.h" -#include + #include "atom.h" #include "comm.h" #include "error.h" -#include "fix.h" +#include "fix_nve_spin.h" #include "force.h" #include "math_const.h" #include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_request.h" +#include "neighbor.h" #include "pair.h" #include "update.h" -#include "fix_nve_spin.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index d8d5632b06..647cb1e125 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -22,11 +22,8 @@ #include "comm.h" #include "error.h" #include "group.h" -#include "memory.h" #include "tokenizer.h" -#include - using namespace LAMMPS_NS; #define BUFLEN 4096 #define DELTA 16384 diff --git a/src/USER-DRUDE/fix_tgnh_drude.cpp b/src/USER-DRUDE/fix_tgnh_drude.cpp index d8bf1d76f9..3cde93f1b5 100644 --- a/src/USER-DRUDE/fix_tgnh_drude.cpp +++ b/src/USER-DRUDE/fix_tgnh_drude.cpp @@ -24,7 +24,6 @@ #include "error.h" #include "fix_deform.h" #include "force.h" -#include "group.h" #include "irregular.h" #include "kspace.h" #include "memory.h" diff --git a/src/USER-DRUDE/fix_tgnvt_drude.cpp b/src/USER-DRUDE/fix_tgnvt_drude.cpp index 2339a6f9a7..ab566058d4 100644 --- a/src/USER-DRUDE/fix_tgnvt_drude.cpp +++ b/src/USER-DRUDE/fix_tgnvt_drude.cpp @@ -17,8 +17,6 @@ #include "group.h" #include "modify.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp index ca13aac06b..50ebf8abbe 100644 --- a/src/USER-EFF/compute_temp_region_eff.cpp +++ b/src/USER-EFF/compute_temp_region_eff.cpp @@ -27,8 +27,6 @@ #include "region.h" #include "update.h" -#include - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp index bfdd85df49..436f6f56da 100644 --- a/src/USER-EFF/fix_nve_eff.cpp +++ b/src/USER-EFF/fix_nve_eff.cpp @@ -15,15 +15,14 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include - #include "fix_nve_eff.h" + #include "atom.h" -#include "force.h" -#include "update.h" -#include "respa.h" -#include "error.h" #include "domain.h" +#include "error.h" +#include "force.h" +#include "respa.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/USER-EFF/fix_nvt_eff.cpp index f5358b5db1..1748530fba 100644 --- a/src/USER-EFF/fix_nvt_eff.cpp +++ b/src/USER-EFF/fix_nvt_eff.cpp @@ -17,8 +17,6 @@ #include "group.h" #include "modify.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index 67ab3522ad..f8cb2a3d91 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -17,20 +17,21 @@ #include "pair_meamc.h" -#include - -#include "meam.h" #include "atom.h" -#include "force.h" #include "comm.h" -#include "neighbor.h" +#include "error.h" +#include "force.h" +#include "meam.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" #include "potential_file_reader.h" #include "tokenizer.h" +#include +#include + using namespace LAMMPS_NS; #define MAXLINE 1024 diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h index de07d813b4..7672612c19 100644 --- a/src/USER-MEAMC/pair_meamc.h +++ b/src/USER-MEAMC/pair_meamc.h @@ -22,8 +22,8 @@ PairStyle(meam,PairMEAMC) #define LMP_PAIR_MEAMC_H #include "pair.h" + #include -#include namespace LAMMPS_NS { diff --git a/src/USER-MESODPD/atom_vec_edpd.cpp b/src/USER-MESODPD/atom_vec_edpd.cpp index ddeabd54db..4880b1303c 100644 --- a/src/USER-MESODPD/atom_vec_edpd.cpp +++ b/src/USER-MESODPD/atom_vec_edpd.cpp @@ -15,7 +15,6 @@ #include "atom.h" #include "error.h" -#include "modify.h" #include "update.h" #include diff --git a/src/USER-MESODPD/pair_edpd.cpp b/src/USER-MESODPD/pair_edpd.cpp index 04307429b4..147e5c322f 100644 --- a/src/USER-MESODPD/pair_edpd.cpp +++ b/src/USER-MESODPD/pair_edpd.cpp @@ -18,20 +18,20 @@ #include "pair_edpd.h" +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "random_mars.h" +#include "update.h" + #include #include #include -#include "atom.h" -#include "comm.h" -#include "update.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "random_mars.h" -#include "citeme.h" -#include "memory.h" -#include "error.h" - using namespace LAMMPS_NS; @@ -275,11 +275,9 @@ void PairEDPD::settings(int narg, char **arg) // initialize Marsaglia RNG with processor-unique seed - if (seed <= 0) { - struct timespec time; - clock_gettime( CLOCK_REALTIME, &time ); - seed = time.tv_nsec; // if seed is non-positive, get the current time as the seed - } + if (seed <= 0) + error->all(FLERR,"Invalid random number seed"); + delete random; random = new RanMars(lmp,(seed + comm->me) % 900000000); randomT = new RanMars(lmp,(2*seed + comm->me) % 900000000); diff --git a/src/USER-MISC/angle_gaussian.cpp b/src/USER-MISC/angle_gaussian.cpp index 639d753afa..b8bd68bd02 100644 --- a/src/USER-MISC/angle_gaussian.cpp +++ b/src/USER-MISC/angle_gaussian.cpp @@ -13,16 +13,17 @@ #include "angle_gaussian.h" -#include #include "atom.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/compute_gyration_shape.cpp b/src/USER-MISC/compute_gyration_shape.cpp index ac073d4cbc..12ccd84533 100644 --- a/src/USER-MISC/compute_gyration_shape.cpp +++ b/src/USER-MISC/compute_gyration_shape.cpp @@ -19,7 +19,6 @@ #include "error.h" #include "math_eigen.h" -#include "math_extra.h" #include "math_special.h" #include "modify.h" #include "update.h" diff --git a/src/USER-MISC/compute_gyration_shape_chunk.cpp b/src/USER-MISC/compute_gyration_shape_chunk.cpp index e66173d704..2adfa4d2c9 100644 --- a/src/USER-MISC/compute_gyration_shape_chunk.cpp +++ b/src/USER-MISC/compute_gyration_shape_chunk.cpp @@ -19,7 +19,6 @@ #include "error.h" #include "math_eigen.h" -#include "math_extra.h" #include "math_special.h" #include "memory.h" #include "modify.h" diff --git a/src/USER-MISC/compute_pressure_grem.cpp b/src/USER-MISC/compute_pressure_grem.cpp index 98f699491f..c3144c084c 100644 --- a/src/USER-MISC/compute_pressure_grem.cpp +++ b/src/USER-MISC/compute_pressure_grem.cpp @@ -21,8 +21,6 @@ #include "kspace.h" #include "error.h" -#include - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index 02e6d3e5da..eb90fd2dc4 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -29,7 +29,6 @@ #include "update.h" #include -#include #include // IWYU pragma: keep #include // IWYU pragma: keep diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp index 59f2560e0b..4bcc15933f 100644 --- a/src/USER-MISC/fix_addtorque.cpp +++ b/src/USER-MISC/fix_addtorque.cpp @@ -28,8 +28,6 @@ #include "update.h" #include "variable.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_electron_stopping_fit.cpp b/src/USER-MISC/fix_electron_stopping_fit.cpp index b36984f3df..b3dbfb3337 100644 --- a/src/USER-MISC/fix_electron_stopping_fit.cpp +++ b/src/USER-MISC/fix_electron_stopping_fit.cpp @@ -20,18 +20,13 @@ #include "atom.h" #include "citeme.h" -#include "compute.h" -#include "domain.h" #include "error.h" #include "force.h" #include "math_special.h" -#include "modify.h" -#include "region.h" #include "respa.h" #include "update.h" #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp index ef6c390f95..6426eee5cc 100644 --- a/src/USER-MISC/fix_nvk.cpp +++ b/src/USER-MISC/fix_nvk.cpp @@ -17,14 +17,14 @@ #include "fix_nvk.h" -#include -#include #include "atom.h" -#include "force.h" -#include "update.h" -#include "respa.h" #include "error.h" +#include "force.h" #include "math_extra.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_orient_eco.cpp b/src/USER-MISC/fix_orient_eco.cpp index 56da3cd6a1..ef68294fde 100644 --- a/src/USER-MISC/fix_orient_eco.cpp +++ b/src/USER-MISC/fix_orient_eco.cpp @@ -32,7 +32,6 @@ #include "update.h" #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp index 18e1ed195f..54c6a0a9aa 100644 --- a/src/USER-MISC/fix_rhok.cpp +++ b/src/USER-MISC/fix_rhok.cpp @@ -24,7 +24,6 @@ #include "update.h" #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index 8a79b73034..84514526b1 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -27,7 +27,6 @@ #include "update.h" #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/pair_wf_cut.cpp b/src/USER-MISC/pair_wf_cut.cpp index d421049cec..451b3f1e49 100644 --- a/src/USER-MISC/pair_wf_cut.cpp +++ b/src/USER-MISC/pair_wf_cut.cpp @@ -25,8 +25,6 @@ #include "memory.h" #include "neigh_list.h" -#include -#include #include using namespace LAMMPS_NS; diff --git a/src/USER-OMP/fix_nvt_asphere_omp.cpp b/src/USER-OMP/fix_nvt_asphere_omp.cpp index c8db9cc98d..2ed5632fad 100644 --- a/src/USER-OMP/fix_nvt_asphere_omp.cpp +++ b/src/USER-OMP/fix_nvt_asphere_omp.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_asphere_omp.h" + +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_nvt_omp.cpp b/src/USER-OMP/fix_nvt_omp.cpp index 240825b2c6..6dc59b2db6 100644 --- a/src/USER-OMP/fix_nvt_omp.cpp +++ b/src/USER-OMP/fix_nvt_omp.cpp @@ -17,8 +17,6 @@ #include "group.h" #include "modify.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp index 6844729e92..17b932baf0 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.cpp +++ b/src/USER-OMP/fix_qeq_comb_omp.cpp @@ -17,19 +17,19 @@ #include "fix_qeq_comb_omp.h" -#include -#include -#include "pair_comb.h" #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "group.h" #include "memory.h" -#include "error.h" #include "neigh_list.h" +#include "pair_comb.h" #include "respa.h" #include "update.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp index 9a08cd284c..1637805081 100644 --- a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp +++ b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp @@ -11,14 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "npair_full_bin_atomonly_omp.h" -#include "npair_omp.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" +#include "npair_omp.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp index 816ebcb693..2e4ab6509a 100644 --- a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp +++ b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp @@ -11,14 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "npair_half_bin_atomonly_newton_omp.h" -#include "npair_omp.h" -#include "neigh_list.h" + #include "atom.h" #include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" +#include "npair_omp.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp index 43b5e7e822..caea9e13d7 100644 --- a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp @@ -11,14 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "npair_half_size_bin_newtoff_omp.h" -#include "npair_omp.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" +#include "npair_omp.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp index 600348ca73..188e936cc4 100644 --- a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp @@ -11,14 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "npair_half_size_bin_newton_omp.h" -#include "npair_omp.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" +#include "npair_omp.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp index 88a72c4594..d0c6841c3e 100644 --- a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp @@ -11,14 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "npair_half_size_bin_newton_tri_omp.h" -#include "npair_omp.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" +#include "npair_omp.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp index 1e9b9369bd..a8d187d958 100644 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp @@ -11,14 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "npair_half_size_multi_newtoff_omp.h" -#include "npair_omp.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" +#include "npair_omp.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp index 0bf79ff77d..61031c553b 100644 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -11,14 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "npair_half_size_multi_newton_omp.h" -#include "npair_omp.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" +#include "npair_omp.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp index 96b57cc7c6..8acfc0e3bc 100644 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp @@ -11,14 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "npair_half_size_multi_newton_tri_omp.h" -#include "npair_omp.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" +#include "npair_omp.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp index 758eae2bd9..452a17fafe 100644 --- a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp @@ -11,15 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "npair_half_size_nsq_newtoff_omp.h" -#include "npair_omp.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" +#include "error.h" #include "group.h" #include "my_page.h" -#include "error.h" +#include "neigh_list.h" +#include "npair_omp.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp index 6f9a3fbbaa..e63c564a0e 100644 --- a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp @@ -11,15 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "npair_half_size_nsq_newton_omp.h" -#include "npair_omp.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" +#include "error.h" #include "group.h" #include "my_page.h" -#include "error.h" +#include "neigh_list.h" +#include "npair_omp.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.cpp b/src/USER-OMP/npair_halffull_newtoff_omp.cpp index 088e490384..378859beff 100644 --- a/src/USER-OMP/npair_halffull_newtoff_omp.cpp +++ b/src/USER-OMP/npair_halffull_newtoff_omp.cpp @@ -11,13 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "npair_halffull_newtoff_omp.h" -#include "npair_omp.h" -#include "neigh_list.h" -#include "atom_vec.h" -#include "my_page.h" + #include "error.h" +#include "my_page.h" +#include "neigh_list.h" +#include "npair_omp.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/npair_halffull_newton_omp.cpp b/src/USER-OMP/npair_halffull_newton_omp.cpp index 6ec75d2428..c9852b526f 100644 --- a/src/USER-OMP/npair_halffull_newton_omp.cpp +++ b/src/USER-OMP/npair_halffull_newton_omp.cpp @@ -11,14 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "npair_halffull_newton_omp.h" -#include "npair_omp.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" +#include "npair_omp.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp index 8f255ee1ba..9da74e36b1 100644 --- a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp @@ -20,6 +20,8 @@ #include "neigh_list.h" #include "suffix.h" +#include + #include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathExtra; diff --git a/src/USER-OMP/pair_tersoff_mod_omp.cpp b/src/USER-OMP/pair_tersoff_mod_omp.cpp index 454a387982..28d64ca19f 100644 --- a/src/USER-OMP/pair_tersoff_mod_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_omp.cpp @@ -16,12 +16,12 @@ #include "atom.h" #include "comm.h" -#include "force.h" #include "math_extra.h" #include "neigh_list.h" -#include "neighbor.h" #include "suffix.h" +#include + #include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathExtra; diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/USER-OMP/pair_tersoff_omp.cpp index c12e3b9859..55bb7791a4 100644 --- a/src/USER-OMP/pair_tersoff_omp.cpp +++ b/src/USER-OMP/pair_tersoff_omp.cpp @@ -16,13 +16,13 @@ #include "atom.h" #include "comm.h" -#include "force.h" #include "math_extra.h" #include "memory.h" #include "neigh_list.h" -#include "neighbor.h" #include "suffix.h" +#include + #include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathExtra; diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp index 2e433a12ee..c0fef02a23 100644 --- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp +++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp @@ -17,14 +17,15 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_zbl_omp.h" -#include "update.h" + #include "comm.h" -#include "memory.h" #include "error.h" -#include "tokenizer.h" -#include "potential_file_reader.h" #include "math_const.h" #include "math_special.h" +#include "memory.h" +#include "potential_file_reader.h" +#include "tokenizer.h" +#include "update.h" #include #include diff --git a/src/USER-OMP/pair_vashishta_omp.cpp b/src/USER-OMP/pair_vashishta_omp.cpp index 23d7235578..daac740dbf 100644 --- a/src/USER-OMP/pair_vashishta_omp.cpp +++ b/src/USER-OMP/pair_vashishta_omp.cpp @@ -16,10 +16,8 @@ #include "atom.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "neigh_list.h" -#include "neighbor.h" #include "suffix.h" #include "omp_compat.h" diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index d6eda0f511..cfa98cea54 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -40,7 +40,6 @@ Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, #include "neighbor.h" #include "update.h" -#include #include #include "ace_evaluator.h" diff --git a/src/USER-PTM/ptm_constants.cpp b/src/USER-PTM/ptm_constants.cpp index 82bead2101..47d6d010f0 100644 --- a/src/USER-PTM/ptm_constants.cpp +++ b/src/USER-PTM/ptm_constants.cpp @@ -8,7 +8,6 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI */ #include "ptm_constants.h" -#include const int ptm_num_nbrs[9] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS_BCC, PTM_NUM_NBRS_ICO, PTM_NUM_NBRS_SC, PTM_NUM_NBRS_DCUB, PTM_NUM_NBRS_DHEX, PTM_NUM_NBRS_GRAPHENE}; diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp index e9d32b5684..4c9c469bda 100644 --- a/src/USER-SMD/fix_smd_wall_surface.cpp +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -22,7 +22,6 @@ #include "comm.h" #include "domain.h" #include "error.h" -#include "memory.h" #include #include diff --git a/src/atom.cpp b/src/atom.cpp index ecb82993ce..70ed5a3836 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -34,6 +34,7 @@ #include "library.h" #include +#include #include #ifdef LMP_USER_INTEL diff --git a/src/atom_vec.h b/src/atom_vec.h index ea2253d0c3..a1bd8fd812 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -15,6 +15,7 @@ #define LMP_ATOM_VEC_H #include "pointers.h" // IWYU pragma: export +#include namespace LAMMPS_NS { diff --git a/tools/lammps-shell/lammps-shell.cpp b/tools/lammps-shell/lammps-shell.cpp index 6c8873093f..699062059a 100644 --- a/tools/lammps-shell/lammps-shell.cpp +++ b/tools/lammps-shell/lammps-shell.cpp @@ -11,7 +11,6 @@ #include #include #include -#include #include #include #include @@ -352,7 +351,7 @@ static char *plugin_generator(const char *text, int state) { const char *subcmd[] = {"load", "unload", "list", "clear", NULL}; const char *sub; - static std::size_t idx, len; + static std::size_t idx=0, len; if (!state) idx = 0; len = strlen(text); @@ -368,7 +367,7 @@ static char *plugin_style_generator(const char *text, int state) { const char *styles[] = {"pair", "fix", "command", NULL}; const char *s; - static std::size_t idx, len; + static std::size_t idx=0, len; if (!state) idx = 0; len = strlen(text); while ((s = styles[idx]) != NULL) { @@ -384,10 +383,10 @@ static char *plugin_name_generator(const char *text, int state) auto words = utils::split_words(text); if (words.size() < 4) return nullptr; - static std::size_t idx, len; + static std::size_t idx, len, nmax; if (!state) idx = 0; len = words[3].size(); - int nmax = lammps_plugin_count(); + nmax = lammps_plugin_count(); while (idx < nmax) { char style[buflen], name[buflen]; From 92a9994fd4a6998534b4fa0aee3bd199e54d5866 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 18:29:57 -0400 Subject: [PATCH 0657/1217] silence compiler warnings by avoiding to shadow variables --- src/KSPACE/remap.cpp | 40 +++++++++++++++---------------- src/MANYBODY/pair_eim.cpp | 6 ++--- src/RIGID/fix_rigid.cpp | 4 ++-- src/RIGID/fix_rigid_nh_small.cpp | 6 ++--- src/RIGID/fix_rigid_small.cpp | 20 ++++++++-------- src/USER-OMP/fix_rigid_nh_omp.cpp | 20 +++++++--------- 6 files changed, 46 insertions(+), 50 deletions(-) diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp index c99bbb2562..6caaa9fe2c 100644 --- a/src/KSPACE/remap.cpp +++ b/src/KSPACE/remap.cpp @@ -241,7 +241,7 @@ struct remap_plan_3d *remap_3d_create_plan( struct remap_plan_3d *plan; struct extent_3d *inarray, *outarray; struct extent_3d in,out,overlap; - int i,iproc,nsend,nrecv,ibuf,size,me,nprocs; + int i,j,iproc,nsend,nrecv,ibuf,size,me,nprocs; // query MPI info @@ -465,14 +465,14 @@ struct remap_plan_3d *remap_3d_create_plan( int *commringlist = (int *) malloc(maxcommsize*sizeof(int)); int commringlen = 0; - for (int i = 0; i < nrecv; i++) { + for (i = 0; i < nrecv; i++) { commringlist[i] = plan->recv_proc[i]; commringlen++; } - for (int i = 0; i < nsend; i++) { + for (i = 0; i < nsend; i++) { int foundentry = 0; - for (int j=0;jsend_proc[i]) foundentry = 1; if (!foundentry) { commringlist[commringlen] = plan->send_proc[i]; @@ -483,12 +483,12 @@ struct remap_plan_3d *remap_3d_create_plan( // sort initial commringlist int swap = 0; - for (int c = 0 ; c < (commringlen - 1); c++) { - for (int d = 0 ; d < commringlen - c - 1; d++) { - if (commringlist[d] > commringlist[d+1]) { - swap = commringlist[d]; - commringlist[d] = commringlist[d+1]; - commringlist[d+1] = swap; + for (i = 0 ; i < (commringlen - 1); i++) { + for (j = 0 ; j < commringlen - i - 1; j++) { + if (commringlist[j] > commringlist[j+1]) { + swap = commringlist[j]; + commringlist[j] = commringlist[j+1]; + commringlist[j+1] = swap; } } } @@ -502,12 +502,12 @@ struct remap_plan_3d *remap_3d_create_plan( while (commringappend) { int newcommringlen = commringlen; commringappend = 0; - for (int i=0;i commringlist[d+1]) { - swap = commringlist[d]; - commringlist[d] = commringlist[d+1]; - commringlist[d+1] = swap; + for (i = 0 ; i < ( commringlen - 1 ); i++) { + for (j = 0 ; j < commringlen - i - 1; j++) { + if (commringlist[j] > commringlist[j+1]) { + swap = commringlist[j]; + commringlist[j] = commringlist[j+1]; + commringlist[j+1] = swap; } } } diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index eda1838a5a..611f2a8ea8 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -1028,7 +1028,7 @@ std::pair EIMPotentialFileReader::get_pair(const std:: return std::make_pair(b, a); } -char * EIMPotentialFileReader::next_line(FILE * fp) { +char *EIMPotentialFileReader::next_line(FILE * fp) { // concatenate lines if they end with '&' // strip comments after '#' int n = 0; @@ -1058,7 +1058,7 @@ char * EIMPotentialFileReader::next_line(FILE * fp) { } while (n == 0 || concat) { - char *ptr = fgets(&line[n], MAXLINE - n, fp); + ptr = fgets(&line[n], MAXLINE - n, fp); if (ptr == nullptr) { // EOF @@ -1089,7 +1089,7 @@ char * EIMPotentialFileReader::next_line(FILE * fp) { void EIMPotentialFileReader::parse(FILE * fp) { - char * line = nullptr; + char *line = nullptr; bool found_global = false; while ((line = next_line(fp))) { diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 3cd4f5dbc8..da6785fc4a 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -329,7 +329,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : pstyle = ANISO; dimension = domain->dimension; - for (int i = 0; i < 3; i++) { + for (i = 0; i < 3; i++) { p_start[i] = p_stop[i] = p_period[i] = 0.0; p_flag[i] = 0; } @@ -551,7 +551,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : // set pstat_flag pstat_flag = 0; - for (int i = 0; i < 3; i++) + for (i = 0; i < 3; i++) if (p_flag[i]) pstat_flag = 1; if (pcouple == XYZ || (dimension == 2 && pcouple == XY)) pstyle = ISO; diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 0f1e813234..cc7ea24c34 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -705,7 +705,7 @@ void FixRigidNHSmall::final_integrate() if (pstat_flag) { akin_t = akin_r = 0.0; - for (int ibody = 0; ibody < nlocal_body; ibody++) { + for (ibody = 0; ibody < nlocal_body; ibody++) { Body *b = &body[ibody]; akin_t += b->mass*(b->vcm[0]*b->vcm[0] + b->vcm[1]*b->vcm[1] + b->vcm[2]*b->vcm[2]); @@ -856,7 +856,7 @@ void FixRigidNHSmall::nhc_press_integrate() double tb_mass = kt / (p_freq_max * p_freq_max); q_b[0] = dimension * dimension * tb_mass; - for (int i = 1; i < p_chain; i++) { + for (i = 1; i < p_chain; i++) { q_b[i] = tb_mass; f_eta_b[i] = q_b[i-1] * eta_dot_b[i-1] * eta_dot_b[i-1] - kt; f_eta_b[i] /= q_b[i]; @@ -941,7 +941,7 @@ double FixRigidNHSmall::compute_scalar() ke_t = 0.0; ke_q = 0.0; - for (int i = 0; i < nlocal_body; i++) { + for (i = 0; i < nlocal_body; i++) { vcm = body[i].vcm; quat = body[i].quat; ke_t += body[i].mass * (vcm[0]*vcm[0] + vcm[1]*vcm[1] + diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 14bd9f7a55..b7e9dd3902 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -192,7 +192,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : pcouple = NONE; pstyle = ANISO; - for (int i = 0; i < 3; i++) { + for (i = 0; i < 3; i++) { p_start[i] = p_stop[i] = p_period[i] = 0.0; p_flag[i] = 0; } @@ -367,7 +367,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : // error check and further setup for Molecule template if (onemols) { - for (int i = 0; i < nmol; i++) { + for (i = 0; i < nmol; i++) { if (onemols[i]->xflag == 0) error->all(FLERR,"Fix rigid/small molecule must have coordinates"); if (onemols[i]->typeflag == 0) @@ -385,7 +385,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : // set pstat_flag pstat_flag = 0; - for (int i = 0; i < 3; i++) + for (i = 0; i < 3; i++) if (p_flag[i]) pstat_flag = 1; if (pcouple == XYZ || (domain->dimension == 2 && pcouple == XY)) pstyle = ISO; @@ -451,7 +451,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : int one = 0; bigint atomone = 0; - for (int i = 0; i < nlocal; i++) { + for (i = 0; i < nlocal; i++) { if (bodyown[i] >= 0) one++; if (bodytag[i] > 0) atomone++; } @@ -978,7 +978,7 @@ void FixRigidSmall::compute_forces_and_torques() // include Langevin thermostat forces and torques if (langflag) { - for (int ibody = 0; ibody < nlocal_body; ibody++) { + for (ibody = 0; ibody < nlocal_body; ibody++) { fcm = body[ibody].fcm; fcm[0] += langextra[ibody][0]; fcm[1] += langextra[ibody][1]; @@ -1163,7 +1163,7 @@ int FixRigidSmall::dof(int tgroup) // 2 = # of particles in rigid body, disregarding temperature group memory->create(counts,nlocal_body+nghost_body,3,"rigid/small:counts"); - for (int i = 0; i < nlocal_body+nghost_body; i++) + for (i = 0; i < nlocal_body+nghost_body; i++) counts[i][0] = counts[i][1] = counts[i][2] = 0; // tally counts from my owned atoms @@ -1630,7 +1630,7 @@ void FixRigidSmall::create_bodies(tagint *bodyID) MPI_Allreduce(&rsqfar,&maxextent,1,MPI_DOUBLE,MPI_MAX,world); maxextent = sqrt(maxextent); if (onemols) { - for (int i = 0; i < nmol; i++) + for (i = 0; i < nmol; i++) maxextent = MAX(maxextent,onemols[i]->maxextent); } } @@ -1741,7 +1741,7 @@ int FixRigidSmall::rendezvous_body(int n, char *inbuf, double rsqfar = 0.0; - for (int i = 0; i < n; i++) { + for (i = 0; i < n; i++) { m = hash.find(in[i].bodyID)->second; xown = in[iclose[m]].x; x = in[i].x; @@ -1761,7 +1761,7 @@ int FixRigidSmall::rendezvous_body(int n, char *inbuf, OutRvous *out = (OutRvous *) memory->smalloc(nout*sizeof(OutRvous),"rigid/small:out"); - for (int i = 0; i < nout; i++) { + for (i = 0; i < nout; i++) { proclist[i] = in[i].me; out[i].ilocal = in[i].ilocal; m = hash.find(in[i].bodyID)->second; @@ -2493,7 +2493,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody) // for which = 0, store all but inertia directly in body struct // for which = 1, store inertia tensor array, invert 3,4,5 values to Voigt - for (int i = 0; i < nchunk; i++) { + for (i = 0; i < nchunk; i++) { next = strchr(buf,'\n'); values[0] = strtok(buf," \t\n\r\f"); diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index 5a1e6ca25e..ae6cb92cee 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -234,8 +234,6 @@ void FixRigidNHOMP::initial_integrate(int vflag) void FixRigidNHOMP::compute_forces_and_torques() { - int ibody; - double * const * _noalias const x = atom->x; const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0]; const double * const * const torque_one = atom->torque; @@ -373,9 +371,9 @@ void FixRigidNHOMP::compute_forces_and_torques() MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world); #if defined(_OPENMP) -#pragma omp parallel for LMP_DEFAULT_NONE private(ibody) schedule(static) +#pragma omp parallel for LMP_DEFAULT_NONE schedule(static) #endif - for (ibody = 0; ibody < nbody; ibody++) { + for (int ibody = 0; ibody < nbody; ibody++) { fcm[ibody][0] = all[ibody][0] + langextra[ibody][0]; fcm[ibody][1] = all[ibody][1] + langextra[ibody][1]; fcm[ibody][2] = all[ibody][2] + langextra[ibody][2]; @@ -388,9 +386,9 @@ void FixRigidNHOMP::compute_forces_and_torques() if (id_gravity) { #if defined(_OPENMP) -#pragma omp parallel for LMP_DEFAULT_NONE private(ibody) schedule(static) +#pragma omp parallel for LMP_DEFAULT_NONE schedule(static) #endif - for (ibody = 0; ibody < nbody; ibody++) { + for (int ibody = 0; ibody < nbody; ibody++) { fcm[ibody][0] += gvec[0]*masstotal[ibody]; fcm[ibody][1] += gvec[1]*masstotal[ibody]; fcm[ibody][2] += gvec[2]*masstotal[ibody]; @@ -628,12 +626,11 @@ void FixRigidNHOMP::set_xv_thr() // set x and v of each atom const int nlocal = atom->nlocal; - int i; #if defined(_OPENMP) -#pragma omp parallel for LMP_DEFAULT_NONE private(i) reduction(+:v0,v1,v2,v3,v4,v5) +#pragma omp parallel for LMP_DEFAULT_NONE reduction(+:v0,v1,v2,v3,v4,v5) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { const int ibody = body[i]; if (ibody < 0) continue; @@ -829,12 +826,11 @@ void FixRigidNHOMP::set_v_thr() // set v of each atom const int nlocal = atom->nlocal; - int i; #if defined(_OPENMP) -#pragma omp parallel for LMP_DEFAULT_NONE private(i) reduction(+:v0,v1,v2,v3,v4,v5) +#pragma omp parallel for LMP_DEFAULT_NONE reduction(+:v0,v1,v2,v3,v4,v5) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { const int ibody = body[i]; if (ibody < 0) continue; From 539ab023654bd9832e00b5cf7426cf2bff2a5884 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 21:05:11 -0400 Subject: [PATCH 0658/1217] provide more generic implementation of Comm::read_lines_from_file() in utils --- src/utils.cpp | 30 ++++++++++++++++++++ src/utils.h | 25 ++++++++++++++++- unittest/formats/test_file_operations.cpp | 34 ++++++++++++++++++++++- 3 files changed, 87 insertions(+), 2 deletions(-) diff --git a/src/utils.cpp b/src/utils.cpp index 0ff1d65633..9aa8e2f7ee 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -225,6 +225,36 @@ void utils::sfread(const char *srcname, int srcline, void *s, size_t size, /* ------------------------------------------------------------------ */ +/* read N lines and broadcast */ +int utils::read_lines_from_file(FILE *fp, int nlines, int maxline, + char *buffer, int me, MPI_Comm comm) +{ + char *ptr = buffer; + *ptr = '\0'; + + if (me == 0) { + if (fp) { + for (int i = 0; i < nlines; i++) { + ptr = fgets(ptr,maxline,fp); + if (!ptr) break; // EOF? + // advance ptr to end of string and append newline char if needed. + ptr += strlen(ptr); + if (*(--ptr) != '\n') *(++ptr) = '\n'; + // ensure buffer is null terminated. null char is start of next line. + *(++ptr) = '\0'; + } + } + } + + int n = strlen(buffer); + MPI_Bcast(&n,1,MPI_INT,0,comm); + if (n == 0) return 1; + MPI_Bcast(buffer,n+1,MPI_CHAR,0,comm); + return 0; +} + +/* ------------------------------------------------------------------ */ + std::string utils::check_packages_for_style(const std::string &style, const std::string &name, LAMMPS *lmp) diff --git a/src/utils.h b/src/utils.h index c87f0b28a9..b393f89ffa 100644 --- a/src/utils.h +++ b/src/utils.h @@ -17,9 +17,12 @@ /*! \file utils.h */ #include "lmptype.h" + +#include + +#include #include #include -#include namespace LAMMPS_NS { @@ -89,6 +92,26 @@ namespace LAMMPS_NS { void sfread(const char *srcname, int srcline, void *s, size_t size, size_t num, FILE *fp, const char *filename, Error *error); + /** Read N lines of text from file into buffer and broadcast them + * + * This function uses repeated calls to fread() to fill a buffer with + * newline terminated text. If a line does not end in a newline (e.g. + * at the end of a file), it is added. The caller has to allocate an + * nlines by maxline sized buffer for storing the text data. + * Reading is done by MPI rank 0 of the given communicator only, and + * thus only MPI rank 0 needs to provide a valid file pointer. + * + * \param fp file pointer used by fread + * \param nlines number of lines to be read + * \param maxline maximum length of a single line + * \param buffer buffer for storing the data. + * \param me MPI rank of calling process in MPI communicator + * \param comm MPI communicator for broadcast + * \return 1 if the read was short, 0 if read was succesful */ + + int read_lines_from_file(FILE *fp, int nlines, int maxline, + char *buffer, int me, MPI_Comm comm); + /** Report if a requested style is in a package or may have a typo * * \param style type of style that is to be checked for diff --git a/unittest/formats/test_file_operations.cpp b/unittest/formats/test_file_operations.cpp index 700990fb72..9209e67585 100644 --- a/unittest/formats/test_file_operations.cpp +++ b/unittest/formats/test_file_operations.cpp @@ -11,13 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "../testing/core.h" #include "info.h" #include "input.h" #include "lammps.h" #include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" -#include "../testing/core.h" #include #include @@ -28,6 +28,7 @@ using namespace LAMMPS_NS; using testing::MatchesRegex; using testing::StrEq; +using utils::read_lines_from_file; using utils::sfgets; using utils::sfread; using utils::split_words; @@ -124,6 +125,37 @@ TEST_F(FileOperationsTest, safe_fread) fclose(fp); } +TEST_F(FileOperationsTest, read_lines_from_file) +{ + char *buf = new char[MAX_BUF_SIZE]; + FILE *fp = nullptr; + MPI_Comm world = MPI_COMM_WORLD; + int me, rv; + memset(buf, 0, MAX_BUF_SIZE); + + rv = utils::read_lines_from_file(nullptr, 1, MAX_BUF_SIZE, buf, me, world); + ASSERT_EQ(rv, 1); + + MPI_Comm_rank(world, &me); + if (me == 0) { + fp = fopen("safe_file_read_test.txt", "r"); + ASSERT_NE(fp, nullptr); + } else + ASSERT_EQ(fp, nullptr); + + rv = utils::read_lines_from_file(fp, 2, MAX_BUF_SIZE / 2, buf, me, world); + ASSERT_EQ(rv, 0); + ASSERT_THAT(buf, StrEq("one line\ntwo_lines\n")); + + rv = utils::read_lines_from_file(fp, 2, MAX_BUF_SIZE / 2, buf, me, world); + ASSERT_EQ(rv, 0); + ASSERT_THAT(buf, StrEq("\nno newline\n")); + + rv = utils::read_lines_from_file(fp, 2, MAX_BUF_SIZE / 2, buf, me, world); + ASSERT_EQ(rv, 1); + delete[] buf; +} + TEST_F(FileOperationsTest, logmesg) { char buf[8]; From 8e5e9951886aabc927358d038d58018a2b384c61 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 21:31:01 -0400 Subject: [PATCH 0659/1217] add docs for new utility function --- doc/src/Developer_utils.rst | 18 +++++++++++++----- doc/utils/sphinx-config/false_positives.txt | 1 + src/utils.cpp | 4 ++-- src/utils.h | 8 ++++---- 4 files changed, 20 insertions(+), 11 deletions(-) diff --git a/doc/src/Developer_utils.rst b/doc/src/Developer_utils.rst index 17b4715dc7..00a8b43a24 100644 --- a/doc/src/Developer_utils.rst +++ b/doc/src/Developer_utils.rst @@ -12,11 +12,16 @@ reduces redundant implementations and encourages consistent behavior. I/O with status check ^^^^^^^^^^^^^^^^^^^^^ -These are wrappers around the corresponding C library calls like -``fgets()`` or ``fread()``. They will check if there were errors -on reading or an unexpected end-of-file state was reached. In that -case, the functions will stop the calculation with an error message, -indicating the name of the problematic file, if possible. +The the first two functions are wrappers around the corresponding C +library calls ``fgets()`` or ``fread()``. They will check if there +were errors on reading or an unexpected end-of-file state was reached. +In that case, the functions will stop the calculation with an error +message, indicating the name of the problematic file, if possible. +The :cpp:func:`read_lines_from_file` function will read the requested +number of lines of a maximum length into a buffer and will return 0 +if successful or 1 if not. It also guarantees that all lines are +terminated with a newline character and the entire buffer with a +NULL character. ---------- @@ -26,6 +31,9 @@ indicating the name of the problematic file, if possible. .. doxygenfunction:: sfread :project: progguide +.. doxygenfunction:: read_lines_from_file + :project: progguide + ---------- String to number conversions with validity check diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index da69cc4edc..c93685c221 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2190,6 +2190,7 @@ nl nlayers nlen Nlines +nlines nlo nlocal Nlocal diff --git a/src/utils.cpp b/src/utils.cpp index 9aa8e2f7ee..00510984fd 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -226,7 +226,7 @@ void utils::sfread(const char *srcname, int srcline, void *s, size_t size, /* ------------------------------------------------------------------ */ /* read N lines and broadcast */ -int utils::read_lines_from_file(FILE *fp, int nlines, int maxline, +int utils::read_lines_from_file(FILE *fp, int nlines, int nmax, char *buffer, int me, MPI_Comm comm) { char *ptr = buffer; @@ -235,7 +235,7 @@ int utils::read_lines_from_file(FILE *fp, int nlines, int maxline, if (me == 0) { if (fp) { for (int i = 0; i < nlines; i++) { - ptr = fgets(ptr,maxline,fp); + ptr = fgets(ptr,nmax,fp); if (!ptr) break; // EOF? // advance ptr to end of string and append newline char if needed. ptr += strlen(ptr); diff --git a/src/utils.h b/src/utils.h index b393f89ffa..770c0b527a 100644 --- a/src/utils.h +++ b/src/utils.h @@ -97,19 +97,19 @@ namespace LAMMPS_NS { * This function uses repeated calls to fread() to fill a buffer with * newline terminated text. If a line does not end in a newline (e.g. * at the end of a file), it is added. The caller has to allocate an - * nlines by maxline sized buffer for storing the text data. + * nlines by nmax sized buffer for storing the text data. * Reading is done by MPI rank 0 of the given communicator only, and * thus only MPI rank 0 needs to provide a valid file pointer. * * \param fp file pointer used by fread * \param nlines number of lines to be read - * \param maxline maximum length of a single line + * \param nmax maximum length of a single line * \param buffer buffer for storing the data. * \param me MPI rank of calling process in MPI communicator * \param comm MPI communicator for broadcast - * \return 1 if the read was short, 0 if read was succesful */ + * \return 1 if the read was short, 0 if read was successful */ - int read_lines_from_file(FILE *fp, int nlines, int maxline, + int read_lines_from_file(FILE *fp, int nlines, int nmax, char *buffer, int me, MPI_Comm comm); /** Report if a requested style is in a package or may have a typo From 7e7a448a08714a8a83bdb00f5c6f9b194905d1e6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 21:33:36 -0400 Subject: [PATCH 0660/1217] remove the old versions of the utility function and use the new --- lib/atc/LammpsInterface.cpp | 4 ++- src/REPLICA/neb.cpp | 5 +-- src/RIGID/fix_rigid.cpp | 2 +- src/RIGID/fix_rigid_small.cpp | 2 +- src/SPIN/neb_spin.cpp | 5 +-- src/comm.cpp | 68 ----------------------------------- src/comm.h | 3 -- src/read_data.cpp | 30 ++++++++-------- src/variable.cpp | 2 +- 9 files changed, 27 insertions(+), 94 deletions(-) diff --git a/lib/atc/LammpsInterface.cpp b/lib/atc/LammpsInterface.cpp index 5727af1904..b123331ee7 100644 --- a/lib/atc/LammpsInterface.cpp +++ b/lib/atc/LammpsInterface.cpp @@ -26,6 +26,7 @@ #include "bond.h" // bond potentials #include "comm.h" // #include "fix.h" +#include "utils.h" // ATC includes #include "ATC_Error.h" @@ -47,6 +48,7 @@ using std::pair; using std::string; using std::set; using LAMMPS_NS::bigint; +using LAMMPS_NS::utils::read_lines_from_file; namespace ATC { @@ -236,7 +238,7 @@ std::string LammpsInterface::read_file(std::string filename) const std::stringstream s; bool eof = false; while ( ! eof) { - eof = lammps_->comm->read_lines_from_file(fp,1,MAXLINE,buffer); + eof = read_lines_from_file(fp,1,MAXLINE,buffer,comm_rank(),lammps_->world); s << buffer; } fclose(fp); diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 7183bdd168..295e97dee8 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -436,9 +436,10 @@ void NEB::readfile(char *file, int flag) while (nread < nlines) { nchunk = MIN(nlines-nread,CHUNK); if (flag == 0) - eofflag = comm->read_lines_from_file_universe(fp,nchunk,MAXLINE,buffer); + eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer, + universe->me,universe->uworld); else - eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); + eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eofflag) error->all(FLERR,"Unexpected end of NEB file"); buf = buffer; diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 3cd4f5dbc8..2ec8821666 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -2302,7 +2302,7 @@ void FixRigid::readfile(int which, double *vec, int nread = 0; while (nread < nlines) { nchunk = MIN(nlines-nread,CHUNK); - eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); + eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eofflag) error->all(FLERR,"Unexpected end of fix rigid file"); buf = buffer; diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 14bd9f7a55..2cd87c45dc 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -2475,7 +2475,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody) int nread = 0; while (nread < nlines) { nchunk = MIN(nlines-nread,CHUNK); - eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); + eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eofflag) error->all(FLERR,"Unexpected end of fix rigid/small file"); buf = buffer; diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index 88a0ffc402..1761f73323 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -430,9 +430,10 @@ void NEBSpin::readfile(char *file, int flag) while (nread < nlines) { nchunk = MIN(nlines-nread,CHUNK); if (flag == 0) - eofflag = comm->read_lines_from_file_universe(fp,nchunk,MAXLINE,buffer); + eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer, + universe->me,universe->uworld); else - eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); + eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eofflag) error->all(FLERR,"Unexpected end of neb/spin file"); buf = buffer; diff --git a/src/comm.cpp b/src/comm.cpp index 6d3f72d9c0..aa51c0484f 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -1240,71 +1240,3 @@ void Comm::rendezvous_stats(int n, int nout, int nrvous, int nrvous_out, utils::logmesg(lmp,mesg); } } - -/* ---------------------------------------------------------------------- - proc 0 reads Nlines from file into buf and bcasts buf to all procs - caller allocates buf to max size needed - each line is terminated by newline, even if last line in file is not - return 0 if successful, 1 if get EOF error before read is complete -------------------------------------------------------------------------- */ - -int Comm::read_lines_from_file(FILE *fp, int nlines, int maxline, char *buf) -{ - int m; - - if (me == 0) { - m = 0; - for (int i = 0; i < nlines; i++) { - if (!fgets(&buf[m],maxline,fp)) { - m = 0; - break; - } - m += strlen(&buf[m]); - } - if (m) { - if (buf[m-1] != '\n') strcpy(&buf[m++],"\n"); - m++; - } - } - - MPI_Bcast(&m,1,MPI_INT,0,world); - if (m == 0) return 1; - MPI_Bcast(buf,m,MPI_CHAR,0,world); - return 0; -} - -/* ---------------------------------------------------------------------- - proc 0 reads Nlines from file into buf and bcasts buf to all procs - caller allocates buf to max size needed - each line is terminated by newline, even if last line in file is not - return 0 if successful, 1 if get EOF error before read is complete -------------------------------------------------------------------------- */ - -int Comm::read_lines_from_file_universe(FILE *fp, int nlines, int maxline, - char *buf) -{ - int m; - - int me_universe = universe->me; - MPI_Comm uworld = universe->uworld; - - if (me_universe == 0) { - m = 0; - for (int i = 0; i < nlines; i++) { - if (!fgets(&buf[m],maxline,fp)) { - m = 0; - break; - } - m += strlen(&buf[m]); - } - if (m) { - if (buf[m-1] != '\n') strcpy(&buf[m++],"\n"); - m++; - } - } - - MPI_Bcast(&m,1,MPI_INT,0,uworld); - if (m == 0) return 1; - MPI_Bcast(buf,m,MPI_CHAR,0,uworld); - return 0; -} diff --git a/src/comm.h b/src/comm.h index d283144501..0bcd23cd8a 100644 --- a/src/comm.h +++ b/src/comm.h @@ -114,9 +114,6 @@ class Comm : protected Pointers { int (*)(int, char *, int &, int *&, char *&, void *), int, char *&, int, void *, int statflag=0); - int read_lines_from_file(FILE *, int, int, char *); - int read_lines_from_file_universe(FILE *, int, int, char *); - // extract data useful to other classes virtual void *extract(const char *, int &) {return nullptr;} diff --git a/src/read_data.cpp b/src/read_data.cpp index c0085f19d1..6ea22264cd 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -1226,7 +1226,7 @@ void ReadData::atoms() while (nread < natoms) { nchunk = MIN(natoms-nread,CHUNK); - eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); + eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); atom->data_atoms(nchunk,buffer,id_offset,mol_offset,toffset,shiftflag,shift); nread += nchunk; @@ -1282,7 +1282,7 @@ void ReadData::velocities() while (nread < natoms) { nchunk = MIN(natoms-nread,CHUNK); - eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); + eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); atom->data_vels(nchunk,buffer,id_offset); nread += nchunk; @@ -1324,7 +1324,7 @@ void ReadData::bonds(int firstpass) while (nread < nbonds) { nchunk = MIN(nbonds-nread,CHUNK); - eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); + eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); atom->data_bonds(nchunk,buffer,count,id_offset,boffset); nread += nchunk; @@ -1398,7 +1398,7 @@ void ReadData::angles(int firstpass) while (nread < nangles) { nchunk = MIN(nangles-nread,CHUNK); - eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); + eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); atom->data_angles(nchunk,buffer,count,id_offset,aoffset); nread += nchunk; @@ -1472,7 +1472,7 @@ void ReadData::dihedrals(int firstpass) while (nread < ndihedrals) { nchunk = MIN(ndihedrals-nread,CHUNK); - eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); + eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); atom->data_dihedrals(nchunk,buffer,count,id_offset,doffset); nread += nchunk; @@ -1546,7 +1546,7 @@ void ReadData::impropers(int firstpass) while (nread < nimpropers) { nchunk = MIN(nimpropers-nread,CHUNK); - eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); + eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); atom->data_impropers(nchunk,buffer,count,id_offset,ioffset); nread += nchunk; @@ -1613,7 +1613,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type) while (nread < natoms) { nchunk = MIN(natoms-nread,CHUNK); - eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); + eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); atom->data_bonus(nchunk,buffer,ptr,id_offset); nread += nchunk; @@ -1739,7 +1739,7 @@ void ReadData::mass() char *next; char *buf = new char[ntypes*MAXLINE]; - int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf); + int eof = utils::read_lines_from_file(fp,ntypes,MAXLINE,buf,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); char *original = buf; @@ -1759,7 +1759,7 @@ void ReadData::paircoeffs() char *next; char *buf = new char[ntypes*MAXLINE]; - int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf); + int eof = utils::read_lines_from_file(fp,ntypes,MAXLINE,buf,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); char *original = buf; @@ -1785,7 +1785,7 @@ void ReadData::pairIJcoeffs() int nsq = ntypes * (ntypes+1) / 2; char *buf = new char[nsq * MAXLINE]; - int eof = comm->read_lines_from_file(fp,nsq,MAXLINE,buf); + int eof = utils::read_lines_from_file(fp,nsq,MAXLINE,buf,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); char *original = buf; @@ -1811,7 +1811,7 @@ void ReadData::bondcoeffs() char *next; char *buf = new char[nbondtypes*MAXLINE]; - int eof = comm->read_lines_from_file(fp,nbondtypes,MAXLINE,buf); + int eof = utils::read_lines_from_file(fp,nbondtypes,MAXLINE,buf,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); char *original = buf; @@ -1836,7 +1836,7 @@ void ReadData::anglecoeffs(int which) char *next; char *buf = new char[nangletypes*MAXLINE]; - int eof = comm->read_lines_from_file(fp,nangletypes,MAXLINE,buf); + int eof = utils::read_lines_from_file(fp,nangletypes,MAXLINE,buf,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); char *original = buf; @@ -1862,7 +1862,7 @@ void ReadData::dihedralcoeffs(int which) char *next; char *buf = new char[ndihedraltypes*MAXLINE]; - int eof = comm->read_lines_from_file(fp,ndihedraltypes,MAXLINE,buf); + int eof = utils::read_lines_from_file(fp,ndihedraltypes,MAXLINE,buf,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); char *original = buf; @@ -1892,7 +1892,7 @@ void ReadData::impropercoeffs(int which) char *next; char *buf = new char[nimpropertypes*MAXLINE]; - int eof = comm->read_lines_from_file(fp,nimpropertypes,MAXLINE,buf); + int eof = utils::read_lines_from_file(fp,nimpropertypes,MAXLINE,buf,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); char *original = buf; @@ -1922,7 +1922,7 @@ void ReadData::fix(int ifix, char *keyword) bigint nread = 0; while (nread < nline) { nchunk = MIN(nline-nread,CHUNK); - eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); + eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); modify->fix[ifix]->read_data_section(keyword,nchunk,buffer,id_offset); nread += nchunk; diff --git a/src/variable.cpp b/src/variable.cpp index ac225230cf..9cbbbc13d2 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -5176,7 +5176,7 @@ int VarReader::read_peratom() bigint nread = 0; while (nread < nlines) { nchunk = MIN(nlines-nread,CHUNK); - eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); + eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eof) return 1; char *buf = buffer; From b0cd6b3ef7fd34e6ce851230038b76aaf26edf2b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Apr 2021 22:08:28 -0400 Subject: [PATCH 0661/1217] improve docs also for related functions --- doc/src/Developer_utils.rst | 6 ++++-- doc/utils/sphinx-config/false_positives.txt | 1 + src/utils.h | 18 +++++++++++------- 3 files changed, 16 insertions(+), 9 deletions(-) diff --git a/doc/src/Developer_utils.rst b/doc/src/Developer_utils.rst index 00a8b43a24..3165aaae75 100644 --- a/doc/src/Developer_utils.rst +++ b/doc/src/Developer_utils.rst @@ -15,8 +15,10 @@ I/O with status check The the first two functions are wrappers around the corresponding C library calls ``fgets()`` or ``fread()``. They will check if there were errors on reading or an unexpected end-of-file state was reached. -In that case, the functions will stop the calculation with an error -message, indicating the name of the problematic file, if possible. +In that case, the functions will stop with an error message, indicating +the name of the problematic file, if possible unless the *error* argument +is a NULL pointer. + The :cpp:func:`read_lines_from_file` function will read the requested number of lines of a maximum length into a buffer and will return 0 if successful or 1 if not. It also guarantees that all lines are diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index c93685c221..cefed6949d 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2282,6 +2282,7 @@ Ntype ntypes Ntypes nucleotides +nullptr num numa numactl diff --git a/src/utils.h b/src/utils.h index 770c0b527a..21feef048b 100644 --- a/src/utils.h +++ b/src/utils.h @@ -55,7 +55,7 @@ namespace LAMMPS_NS { void logmesg(LAMMPS *lmp, const std::string &mesg); - /** return a string representing the current system error status + /** Return a string representing the current system error status * * This is a wrapper around calling strerror(errno). * @@ -63,8 +63,10 @@ namespace LAMMPS_NS { std::string getsyserror(); - /** safe wrapper around fgets() which aborts on errors - * or EOF and prints a suitable error message to help debugging + /** Safe wrapper around fgets() which aborts on errors + * or EOF and prints a suitable error message to help debugging. + * + * Use nullptr as the error parameter to avoid the abort on EOF or error. * * \param srcname name of the calling source file (from FLERR macro) * \param srcline line in the calling source file (from FLERR macro) @@ -72,13 +74,15 @@ namespace LAMMPS_NS { * \param size size of buffer s (max number of bytes read by fgets()) * \param fp file pointer used by fgets() * \param filename file name associated with fp (may be a null pointer; then LAMMPS will try to detect) - * \param error pointer to Error class instance (for abort) */ + * \param error pointer to Error class instance (for abort) or nullptr */ void sfgets(const char *srcname, int srcline, char *s, int size, FILE *fp, const char *filename, Error *error); - /** safe wrapper around fread() which aborts on errors - * or EOF and prints a suitable error message to help debugging + /** Safe wrapper around fread() which aborts on errors + * or EOF and prints a suitable error message to help debugging. + * + * Use nullptr as the error parameter to avoid the abort on EOF or error. * * \param srcname name of the calling source file (from FLERR macro) * \param srcline line in the calling source file (from FLERR macro) @@ -87,7 +91,7 @@ namespace LAMMPS_NS { * \param num number of data elements read by fread() * \param fp file pointer used by fread() * \param filename file name associated with fp (may be a null pointer; then LAMMPS will try to detect) - * \param error pointer to Error class instance (for abort) */ + * \param error pointer to Error class instance (for abort) or nullptr */ void sfread(const char *srcname, int srcline, void *s, size_t size, size_t num, FILE *fp, const char *filename, Error *error); From 43325dca82ac0d5dd4297697c0440e1b3737bfc2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 25 Apr 2021 00:19:22 -0400 Subject: [PATCH 0662/1217] update/add tests about starting up LAMMPS - move the test checking the help message from the c++ library to running the executable and checking the output - add a command line test for errors on invalid command line flags - add a c++ library test checking if ntreads is set to 1 without OMP_NUM_THREADS --- unittest/CMakeLists.txt | 16 +++++++ unittest/cplusplus/CMakeLists.txt | 1 + unittest/cplusplus/test_lammps_class.cpp | 59 ++++++++++++++++++++++-- 3 files changed, 71 insertions(+), 5 deletions(-) diff --git a/unittest/CMakeLists.txt b/unittest/CMakeLists.txt index addc8bc244..26db526b60 100644 --- a/unittest/CMakeLists.txt +++ b/unittest/CMakeLists.txt @@ -10,6 +10,22 @@ set_tests_properties(RunLammps PROPERTIES ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1" PASS_REGULAR_EXPRESSION "^LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]\\)") +# check if the compiled executable will print the help message +add_test(NAME HelpMessage + COMMAND $ -h + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) +set_tests_properties(HelpMessage PROPERTIES + ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1;PAGER=head" + PASS_REGULAR_EXPRESSION ".*Large-scale Atomic/Molecular Massively Parallel Simulator -.*Usage example:.*") + +# check if the compiled executable will error out on an invalid command line flag +add_test(NAME InvalidFlag + COMMAND $ -xxx + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) +set_tests_properties(InvalidFlag PROPERTIES + ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1" + PASS_REGULAR_EXPRESSION "ERROR: Invalid command-line argument.*") + if(BUILD_MPI) function(add_mpi_test) set(MPI_TEST_NUM_PROCS 1) diff --git a/unittest/cplusplus/CMakeLists.txt b/unittest/cplusplus/CMakeLists.txt index 90ef9a0282..aef69f3722 100644 --- a/unittest/cplusplus/CMakeLists.txt +++ b/unittest/cplusplus/CMakeLists.txt @@ -2,6 +2,7 @@ add_executable(test_lammps_class test_lammps_class.cpp) target_link_libraries(test_lammps_class PRIVATE lammps GTest::GMockMain GTest::GTest GTest::GMock) add_test(LammpsClass test_lammps_class) +set_tests_properties(LammpsClass PROPERTIES ENVIRONMENT "OMP_NUM_THREADS=1") add_executable(test_input_class test_input_class.cpp) target_link_libraries(test_input_class PRIVATE lammps GTest::GTest GTest::GTestMain) diff --git a/unittest/cplusplus/test_lammps_class.cpp b/unittest/cplusplus/test_lammps_class.cpp index c20cdf336a..6a0e6719cc 100644 --- a/unittest/cplusplus/test_lammps_class.cpp +++ b/unittest/cplusplus/test_lammps_class.cpp @@ -1,13 +1,17 @@ // unit tests for the LAMMPS base class +#include "comm.h" +#include "info.h" #include "lammps.h" -#include // for stdin, stdout +#include // for stdin, stdout +#include // for setenv #include #include #include "gmock/gmock.h" #include "gtest/gtest.h" +using ::testing::MatchesRegex; using ::testing::StartsWith; namespace LAMMPS_NS { @@ -95,6 +99,7 @@ TEST_F(LAMMPS_plain, InitMembers) EXPECT_STREQ(LAMMPS::git_branch, "(unknown)"); EXPECT_STREQ(LAMMPS::git_descriptor, "(unknown)"); } + EXPECT_EQ(lmp->comm->nthreads, 1); } TEST_F(LAMMPS_plain, TestStyles) @@ -229,6 +234,7 @@ TEST_F(LAMMPS_omp, InitMembers) EXPECT_STREQ(LAMMPS::git_branch, "(unknown)"); EXPECT_STREQ(LAMMPS::git_descriptor, "(unknown)"); } + EXPECT_EQ(lmp->comm->nthreads, 2); } // test fixture for Kokkos tests @@ -318,10 +324,49 @@ TEST_F(LAMMPS_kokkos, InitMembers) } } -// check help message printing -TEST(LAMMPS_help, HelpMessage) +// check if Comm::nthreads is initialized to either 1 or 2 (from the previous tests) +TEST(LAMMPS_init, OpenMP) { - const char *args[] = {"LAMMPS_test", "-h"}; + if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + + FILE *fp = fopen("in.lammps_empty", "w"); + fputs("\n", fp); + fclose(fp); + + const char *args[] = {"LAMMPS_init", "-in", "in.lammps_empty", "-log", "none", "-nocite"}; + char **argv = (char **)args; + int argc = sizeof(args) / sizeof(char *); + + ::testing::internal::CaptureStdout(); + LAMMPS *lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); + std::string output = ::testing::internal::GetCapturedStdout(); + EXPECT_THAT(output, MatchesRegex(".*using 2 OpenMP thread.*per MPI task.*")); + + if (LAMMPS_NS::Info::has_accelerator_feature("USER-OMP", "api", "openmp")) + EXPECT_EQ(lmp->comm->nthreads, 2); + else + EXPECT_EQ(lmp->comm->nthreads, 1); + ::testing::internal::CaptureStdout(); + delete lmp; + ::testing::internal::GetCapturedStdout(); + + remove("in.lammps_empty"); +} + +// check no OMP_NUM_THREADS warning message printing. this must be the +// last OpenMP related test as threads will be locked to 1 from here on. + +TEST(LAMMPS_init, NoOpenMP) +{ + if (!LAMMPS_NS::Info::has_accelerator_feature("USER-OMP", "api", "openmp")) + GTEST_SKIP() << "No threading enabled"; + + FILE *fp = fopen("in.lammps_class_noomp", "w"); + fputs("\n", fp); + fclose(fp); + unsetenv("OMP_NUM_THREADS"); + + const char *args[] = {"LAMMPS_init", "-in", "in.lammps_class_noomp", "-log", "none", "-nocite"}; char **argv = (char **)args; int argc = sizeof(args) / sizeof(char *); @@ -329,7 +374,11 @@ TEST(LAMMPS_help, HelpMessage) LAMMPS *lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); std::string output = ::testing::internal::GetCapturedStdout(); EXPECT_THAT(output, - StartsWith("\nLarge-scale Atomic/Molecular Massively Parallel Simulator -")); + MatchesRegex(".*OMP_NUM_THREADS environment is not set.*Defaulting to 1 thread.*")); + EXPECT_EQ(lmp->comm->nthreads, 1); + ::testing::internal::CaptureStdout(); delete lmp; + ::testing::internal::GetCapturedStdout(); } + } // namespace LAMMPS_NS From ba5f531619d0eba24ec82298c382085b0d5f7c8d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 25 Apr 2021 00:44:51 -0400 Subject: [PATCH 0663/1217] add some basic tests for the "processors" command --- unittest/commands/test_simple_commands.cpp | 34 ++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/unittest/commands/test_simple_commands.cpp b/unittest/commands/test_simple_commands.cpp index e8cebe98e2..ac8317b3da 100644 --- a/unittest/commands/test_simple_commands.cpp +++ b/unittest/commands/test_simple_commands.cpp @@ -14,6 +14,7 @@ #include "lammps.h" #include "citeme.h" +#include "comm.h" #include "force.h" #include "info.h" #include "input.h" @@ -25,6 +26,7 @@ #include "gmock/gmock.h" #include "gtest/gtest.h" #include "../testing/core.h" +#include "../testing/utils.h" #include #include @@ -174,6 +176,38 @@ TEST_F(SimpleCommandsTest, Partition) ASSERT_THAT(text, StrEq("")); } +TEST_F(SimpleCommandsTest, Processors) +{ + // default setting is "*" for all dimensions + ASSERT_EQ(lmp->comm->user_procgrid[0], 0); + ASSERT_EQ(lmp->comm->user_procgrid[1], 0); + ASSERT_EQ(lmp->comm->user_procgrid[2], 0); + + BEGIN_HIDE_OUTPUT(); + command("processors 1 1 1"); + END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->comm->user_procgrid[0], 1); + ASSERT_EQ(lmp->comm->user_procgrid[1], 1); + ASSERT_EQ(lmp->comm->user_procgrid[2], 1); + + BEGIN_HIDE_OUTPUT(); + command("processors * 1 *"); + END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->comm->user_procgrid[0], 0); + ASSERT_EQ(lmp->comm->user_procgrid[1], 1); + ASSERT_EQ(lmp->comm->user_procgrid[2], 0); + + BEGIN_HIDE_OUTPUT(); + command("processors 0 0 0"); + END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->comm->user_procgrid[0], 0); + ASSERT_EQ(lmp->comm->user_procgrid[1], 0); + ASSERT_EQ(lmp->comm->user_procgrid[2], 0); + + TEST_FAILURE(".*ERROR: Illegal processors command .*", command("processors -1 0 0");); + TEST_FAILURE(".*ERROR: Specified processors != physical processors.*", command("processors 100 100 100");); +} + TEST_F(SimpleCommandsTest, Quit) { BEGIN_HIDE_OUTPUT(); From b7088a14ae784fb1bd1b7c7171b3a2adee237286 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 25 Apr 2021 00:45:10 -0400 Subject: [PATCH 0664/1217] use alternate way to compare strings --- unittest/cplusplus/test_lammps_class.cpp | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/unittest/cplusplus/test_lammps_class.cpp b/unittest/cplusplus/test_lammps_class.cpp index 6a0e6719cc..8f12bd247b 100644 --- a/unittest/cplusplus/test_lammps_class.cpp +++ b/unittest/cplusplus/test_lammps_class.cpp @@ -13,6 +13,8 @@ using ::testing::MatchesRegex; using ::testing::StartsWith; +using ::testing::StrEq; +using ::testing::StrNe; namespace LAMMPS_NS { // test fixture for regular tests @@ -91,13 +93,13 @@ TEST_F(LAMMPS_plain, InitMembers) EXPECT_NE(lmp->python, nullptr); EXPECT_EQ(lmp->citeme, nullptr); if (LAMMPS::has_git_info) { - EXPECT_STRNE(LAMMPS::git_commit, ""); - EXPECT_STRNE(LAMMPS::git_branch, ""); - EXPECT_STRNE(LAMMPS::git_descriptor, ""); + EXPECT_THAT(LAMMPS::git_commit, StrNe("")); + EXPECT_THAT(LAMMPS::git_branch, StrNe("")); + EXPECT_THAT(LAMMPS::git_descriptor, StrNe("")); } else { - EXPECT_STREQ(LAMMPS::git_commit, "(unknown)"); - EXPECT_STREQ(LAMMPS::git_branch, "(unknown)"); - EXPECT_STREQ(LAMMPS::git_descriptor, "(unknown)"); + EXPECT_THAT(LAMMPS::git_commit, StrEq("(unknown)")); + EXPECT_THAT(LAMMPS::git_branch, StrEq("(unknown)")); + EXPECT_THAT(LAMMPS::git_descriptor, StrEq("(unknown)")); } EXPECT_EQ(lmp->comm->nthreads, 1); } From ba4781bd82228ac5aa386785b000a972e4aa4d3b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 25 Apr 2021 01:14:57 -0400 Subject: [PATCH 0665/1217] restore old string matching as it works just as well (on my machine) --- unittest/cplusplus/test_lammps_class.cpp | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/unittest/cplusplus/test_lammps_class.cpp b/unittest/cplusplus/test_lammps_class.cpp index 8f12bd247b..6a0e6719cc 100644 --- a/unittest/cplusplus/test_lammps_class.cpp +++ b/unittest/cplusplus/test_lammps_class.cpp @@ -13,8 +13,6 @@ using ::testing::MatchesRegex; using ::testing::StartsWith; -using ::testing::StrEq; -using ::testing::StrNe; namespace LAMMPS_NS { // test fixture for regular tests @@ -93,13 +91,13 @@ TEST_F(LAMMPS_plain, InitMembers) EXPECT_NE(lmp->python, nullptr); EXPECT_EQ(lmp->citeme, nullptr); if (LAMMPS::has_git_info) { - EXPECT_THAT(LAMMPS::git_commit, StrNe("")); - EXPECT_THAT(LAMMPS::git_branch, StrNe("")); - EXPECT_THAT(LAMMPS::git_descriptor, StrNe("")); + EXPECT_STRNE(LAMMPS::git_commit, ""); + EXPECT_STRNE(LAMMPS::git_branch, ""); + EXPECT_STRNE(LAMMPS::git_descriptor, ""); } else { - EXPECT_THAT(LAMMPS::git_commit, StrEq("(unknown)")); - EXPECT_THAT(LAMMPS::git_branch, StrEq("(unknown)")); - EXPECT_THAT(LAMMPS::git_descriptor, StrEq("(unknown)")); + EXPECT_STREQ(LAMMPS::git_commit, "(unknown)"); + EXPECT_STREQ(LAMMPS::git_branch, "(unknown)"); + EXPECT_STREQ(LAMMPS::git_descriptor, "(unknown)"); } EXPECT_EQ(lmp->comm->nthreads, 1); } From b4fa71857669bd5f9c27bae4461a8322c6c4935b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 25 Apr 2021 07:25:05 -0400 Subject: [PATCH 0666/1217] update the GitHub contributing guide to include the MatSci forum in addition to the mailing list. --- .github/CONTRIBUTING.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 62e7186360..31b9becc0c 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -26,11 +26,11 @@ __ ## I don't want to read this whole thing I just have a question! -> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. +> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to either the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html) or the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. The LAMMPS forum was recently created as part of a larger effort to build a materials science community and have discussions not just about using LAMMPS. Thus the forum may be also used for discussions that would be off-topic for the mailing list. Those will just have to be moved to a more general category. ## How Can I Contribute? -There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list), and you can contribute by submitting pull requests on GitHub or e-mail your code +There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list or posting in the LAMMPS Materials Science Discourse forum), and you can contribute by submitting pull requests on GitHub or e-mail your code to one of the [LAMMPS core developers](https://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers. ### Discussing How To Use LAMMPS @@ -42,6 +42,8 @@ Anyone can browse/search previous questions/answers in the archives. You do not If you post a message and you are a subscriber, your message will appear immediately. If you are not a subscriber, your message will be moderated, which typically takes one business day. Either way, when someone replies the reply will usually be sent to both, your personal email address and the mailing list. When replying to people, that responded to your post to the list, please always included the mailing list in your replies (i.e. use "Reply All" and **not** "Reply"). Responses will appear on the list in a few minutes, but it can take a few hours for postings and replies to show up in the SourceForge archive. Sending replies also to the mailing list is important, so that responses are archived and people with a similar issue can search for possible solutions in the mailing list archive. +The LAMMPS Materials Science Discourse forum was created recently to facilitate discussion not just about LAMMPS and as part of a larger effort towards building a materials science community. The forum contains a read-only sub-category with the continually updated mailing list archive, so you won't miss anything by joining only the forum and not the mailing list. + ### Reporting Bugs While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version. From a0b0681cc8d2c9c831fe8504ed2febdc0107ae8f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 25 Apr 2021 17:20:36 -0400 Subject: [PATCH 0667/1217] rename _internal_logmesg() to fmtargs_logmesg() vlogmesg() can be too easily confused with logmesg() --- src/utils.cpp | 4 ++-- src/utils.h | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/utils.cpp b/src/utils.cpp index fedf86149e..809e625a29 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -131,8 +131,8 @@ void utils::logmesg(LAMMPS *lmp, const std::string &mesg) if (lmp->logfile) fputs(mesg.c_str(), lmp->logfile); } -void utils::_internal_logmesg(LAMMPS *lmp, fmt::string_view format, - fmt::format_args args) +void utils::fmtargs_logmesg(LAMMPS *lmp, fmt::string_view format, + fmt::format_args args) { if (lmp->screen) fmt::vprint(lmp->screen, format, args); if (lmp->logfile) fmt::vprint(lmp->logfile, format, args); diff --git a/src/utils.h b/src/utils.h index e0ab413e59..5f3644b558 100644 --- a/src/utils.h +++ b/src/utils.h @@ -49,8 +49,8 @@ namespace LAMMPS_NS { /* Internal function handling the argument list for logmesg(). */ - void _internal_logmesg(LAMMPS *lmp, fmt::string_view format, - fmt::format_args args); + void fmtargs_logmesg(LAMMPS *lmp, fmt::string_view format, + fmt::format_args args); /** Send formatted message to screen and logfile, if available * @@ -65,8 +65,8 @@ namespace LAMMPS_NS { template void logmesg(LAMMPS *lmp, const S &format, Args&&... args) { - _internal_logmesg(lmp, format, - fmt::make_args_checked(format, args...)); + fmtargs_logmesg(lmp, format, + fmt::make_args_checked(format, args...)); } /** \overload From 07d4b09eb6661e2326b8a4cf949a2d20f8766c41 Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Mon, 26 Apr 2021 00:03:07 +0200 Subject: [PATCH 0668/1217] Updated CMake files, auto-download not yet working --- cmake/Modules/FindN2P2.cmake | 46 +++++++------- cmake/Modules/Packages/USER-HDNNP.cmake | 81 ++++++++++++------------- 2 files changed, 64 insertions(+), 63 deletions(-) diff --git a/cmake/Modules/FindN2P2.cmake b/cmake/Modules/FindN2P2.cmake index 6bf4da5a79..975f424a39 100644 --- a/cmake/Modules/FindN2P2.cmake +++ b/cmake/Modules/FindN2P2.cmake @@ -33,26 +33,28 @@ find_package_handle_standard_args(N2P2 DEFAULT_MSG N2P2_CMAKE_EXTRA) if(N2P2_FOUND) - add_library(N2P2::LIBNNP UNKNOWN IMPORTED) - set_target_properties(N2P2::LIBNNP PROPERTIES - INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR} - IMPORTED_LOCATION ${N2P2_LIBNNP}) - add_library(N2P2::LIBNNPIF UNKNOWN IMPORTED) - set_target_properties(N2P2::LIBNNPIF PROPERTIES - INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR} - IMPORTED_LOCATION ${N2P2_LIBNNPIF}) - add_library(N2P2::N2P2 INTERFACE IMPORTED) - set_property(TARGET N2P2::N2P2 PROPERTY - INTERFACE_LINK_LIBRARIES N2P2::LIBNNPIF N2P2::LIBNNP) - #set(N2P2_INCLUDE_DIRS ${N2P2_INCLUDE_DIR}) - #set(N2P2_LIBRARIES ${N2P2_LIBNNPIF} ${N2P2_LIBNNP}) - set(N2P2_CMAKE_EXTRAS ${N2P2_CMAKE_EXTRA}) - - mark_as_advanced( - N2P2_DIR - N2P2_INCLUDE_DIR - N2P2_LIBNNP - N2P2_LIBNNPIF - N2P2_CMAKE_EXTRA - ) + if (NOT TARGET N2P2::N2P2) + add_library(N2P2::LIBNNP UNKNOWN IMPORTED) + set_target_properties(N2P2::LIBNNP PROPERTIES + INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR} + IMPORTED_LOCATION ${N2P2_LIBNNP}) + add_library(N2P2::LIBNNPIF UNKNOWN IMPORTED) + set_target_properties(N2P2::LIBNNPIF PROPERTIES + INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR} + IMPORTED_LOCATION ${N2P2_LIBNNPIF}) + add_library(N2P2::N2P2 INTERFACE IMPORTED) + set_property(TARGET N2P2::N2P2 PROPERTY + INTERFACE_LINK_LIBRARIES N2P2::LIBNNPIF N2P2::LIBNNP) + #set(N2P2_INCLUDE_DIRS ${N2P2_INCLUDE_DIR}) + #set(N2P2_LIBRARIES ${N2P2_LIBNNPIF} ${N2P2_LIBNNP}) + set(N2P2_CMAKE_EXTRAS ${N2P2_CMAKE_EXTRA}) + endif() endif() + +mark_as_advanced( + N2P2_DIR + N2P2_INCLUDE_DIR + N2P2_LIBNNP + N2P2_LIBNNPIF + N2P2_CMAKE_EXTRA +) diff --git a/cmake/Modules/Packages/USER-HDNNP.cmake b/cmake/Modules/Packages/USER-HDNNP.cmake index 2d5fb406be..2517e3304d 100644 --- a/cmake/Modules/Packages/USER-HDNNP.cmake +++ b/cmake/Modules/Packages/USER-HDNNP.cmake @@ -1,42 +1,41 @@ -find_package(N2P2 REQUIRED) -#target_include_directories(lammps PRIVATE ${N2P2_INCLUDE_DIRS}) -#target_link_libraries(lammps PRIVATE ${N2P2_LIBRARIES}) -target_link_libraries(lammps PRIVATE N2P2::N2P2) -include(${N2P2_CMAKE_EXTRAS}) +find_package(N2P2 QUIET) +if(N2P2_FOUND) + set(DOWNLOAD_N2P2_DEFAULT OFF) +else() + set(DOWNLOAD_N2P2_DEFAULT ON) +endif() +option(DOWNLOAD_N2P2 "Download n2p2 library instead of using an already installed one)" ${DOWNLOAD_N2P2_DEFAULT}) +if(DOWNLOAD_N2P2) + set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.1.2.tar.gz" CACHE STRING "URL for n2p2 tarball") + set(N2P2_MD5 "20cf194d14b1f1c72f38879bafda67e2" CACHE STRING "MD5 checksum of N2P2 tarball") + mark_as_advanced(N2P2_URL) + mark_as_advanced(N2P2_MD5) -#find_package(N2P2 QUIET) -#if(N2P2_FOUND) -# set(DOWNLOAD_N2P2_DEFAULT OFF) -#else() -# set(DOWNLOAD_N2P2_DEFAULT ON) -#endif() -#option(DOWNLOAD_N2P2 "Download n2p2 library instead of using an already installed one)" ${DOWNLOAD_N2P2_DEFAULT}) -#if(DOWNLOAD_N2P2) -# set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.1.2.tar.gz" CACHE STRING "URL for n2p2 tarball") -# set(N2P2_MD5 "20cf194d14b1f1c72f38879bafda67e2" CACHE STRING "MD5 checksum of N2P2 tarball") -# mark_as_advanced(N2P2_URL) -# mark_as_advanced(N2P2_MD5) -# -# include(ExternalProject) -# ExternalProject_Add(n2p2_build -# URL ${N2P2_URL} -# URL_MD5 ${N2P2_MD5} -# SOURCE_SUBDIR src/ -# BUILD_COMMAND make libnnpif -# INSTALL_COMMAND "" -# BUILD_BYPRODUCTS /lib/libnnp.a /lib/libnnpif.a -# ) -# ExternalProject_get_property(n2p2_build INSTALL_DIR) -# add_library(LAMMPS::N2P2 UNKNOWN IMPORTED) -# set_target_properties(LAMMPS::N2P2 PROPERTIES -# IMPORTED_LOCATION "${INSTALL_DIR}/lib/libnnp.a" -# INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include") -# target_link_libraries(lammps PRIVATE LAMMPS::N2P2) -# add_dependencies(LAMMPS::N2P2 n2p2_build) -#else() -# find_package(N2P2) -# if(NOT N2P2_FOUND) -# message(FATAL_ERROR "n2p2 not found, help CMake to find it by setting N2P2_DIR, or set DOWNLOAD_N2P2=ON to download it") -# endif() -# target_link_libraries(lammps PRIVATE N2P2::N2P2) -#endif() + include(ExternalProject) + ExternalProject_Add(n2p2_build + DOWNLOAD_DIR ${CMAKE_CURRENT_BINARY_DIR} + URL ${N2P2_URL} + URL_MD5 ${N2P2_MD5} + UPDATE_COMMAND "" + SOURCE_SUBDIR src/ + BUILD_IN_SOURCE 1 + CONFIGURE_COMMAND "" + BUILD_COMMAND "make libnnpif" + INSTALL_COMMAND "" + #BUILD_BYPRODUCTS /lib/libnnp.a /lib/libnnpif.a + ) + ExternalProject_get_property(n2p2_build INSTALL_DIR) + add_library(LAMMPS::N2P2 STATIC IMPORTED GLOBAL) + set_target_properties(LAMMPS::N2P2 PROPERTIES + IMPORTED_LOCATION "${INSTALL_DIR}/lib/libnnp.a" + INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include") + target_link_libraries(lammps PRIVATE LAMMPS::N2P2) + add_dependencies(LAMMPS::N2P2 n2p2_build) +else() + find_package(N2P2) + if(NOT N2P2_FOUND) + message(FATAL_ERROR "n2p2 not found, help CMake to find it by setting N2P2_DIR, or set DOWNLOAD_N2P2=ON to download it") + endif() + target_link_libraries(lammps PRIVATE N2P2::N2P2) + include(${N2P2_CMAKE_EXTRAS}) +endif() From 60c2d8ea5bdf8d68aab9d1e8749e6ab28367f011 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 25 Apr 2021 18:33:37 -0400 Subject: [PATCH 0669/1217] rather than replicate code, expand format to string and call original function --- src/utils.cpp | 7 +++++-- unittest/formats/test_file_operations.cpp | 12 +++++++----- 2 files changed, 12 insertions(+), 7 deletions(-) diff --git a/src/utils.cpp b/src/utils.cpp index 809e625a29..2dcf77eacd 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -134,8 +134,11 @@ void utils::logmesg(LAMMPS *lmp, const std::string &mesg) void utils::fmtargs_logmesg(LAMMPS *lmp, fmt::string_view format, fmt::format_args args) { - if (lmp->screen) fmt::vprint(lmp->screen, format, args); - if (lmp->logfile) fmt::vprint(lmp->logfile, format, args); + try { + logmesg(lmp, fmt::vformat(format, args)); + } catch (fmt::format_error &e) { + logmesg(lmp, std::string(e.what())+"\n"); + } } /* define this here, so we won't have to include the headers diff --git a/unittest/formats/test_file_operations.cpp b/unittest/formats/test_file_operations.cpp index fe2bf2d2f6..392ca04656 100644 --- a/unittest/formats/test_file_operations.cpp +++ b/unittest/formats/test_file_operations.cpp @@ -126,7 +126,7 @@ TEST_F(FileOperationsTest, safe_fread) TEST_F(FileOperationsTest, logmesg) { - char buf[16]; + char buf[64]; BEGIN_HIDE_OUTPUT(); command("echo none"); END_HIDE_OUTPUT(); @@ -135,14 +135,16 @@ TEST_F(FileOperationsTest, logmesg) command("log test_logmesg.log"); utils::logmesg(lmp, "two\n"); utils::logmesg(lmp, "three={}\n",3); + utils::logmesg(lmp, "four {}\n"); + utils::logmesg(lmp, "five\n",5); command("log none"); std::string out = END_CAPTURE_OUTPUT(); - memset(buf, 0, 16); + memset(buf, 0, 64); FILE *fp = fopen("test_logmesg.log", "r"); - fread(buf, 1, 16, fp); + fread(buf, 1, 64, fp); fclose(fp); - ASSERT_THAT(out, StrEq("one\ntwo\nthree=3\n")); - ASSERT_THAT(buf, StrEq("two\nthree=3\n")); + ASSERT_THAT(out, StrEq("one\ntwo\nthree=3\nargument not found\nfive\n")); + ASSERT_THAT(buf, StrEq("two\nthree=3\nargument not found\nfive\n")); remove("test_logmesg.log"); } From 4e25204296ef4dbdd9c908965a544adc1e97167a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 25 Apr 2021 19:04:49 -0400 Subject: [PATCH 0670/1217] add vararg versions of Error::all() and Error::one() plus unit tests --- src/error.cpp | 24 +++++++++++ src/error.h | 17 ++++++++ unittest/formats/test_file_operations.cpp | 51 +++++++++++++++++++++-- 3 files changed, 89 insertions(+), 3 deletions(-) diff --git a/src/error.cpp b/src/error.cpp index 0cbfa4c4a1..a67a9e5865 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -213,6 +213,30 @@ void Error::one(const std::string &file, int line, const std::string &str) #endif } +/* ---------------------------------------------------------------------- + forward vararg version to single string version +------------------------------------------------------------------------- */ + +void Error::_all(const std::string &file, int line, fmt::string_view format, + fmt::format_args args) +{ + try { + all(file,line,fmt::vformat(format, args)); + } catch (fmt::format_error &e) { + all(file,line,e.what()); + } +} + +void Error::_one(const std::string &file, int line, fmt::string_view format, + fmt::format_args args) +{ + try { + one(file,line,fmt::vformat(format, args)); + } catch (fmt::format_error &e) { + one(file,line,e.what()); + } +} + /* ---------------------------------------------------------------------- called by one proc in world only write to screen if non-nullptr on this proc since could be file diff --git a/src/error.h b/src/error.h index dedebc4148..8b71974df5 100644 --- a/src/error.h +++ b/src/error.h @@ -32,6 +32,17 @@ class Error : protected Pointers { [[ noreturn ]] void all(const std::string &, int, const std::string &); [[ noreturn ]] void one(const std::string &, int, const std::string &); + template + [[ noreturn ]] void all(const std::string &file, int line, const S &format, + Args&&... args) { + _all(file, line, format, fmt::make_args_checked(format, args...)); + } + template + [[ noreturn ]] void one(const std::string &file, int line, const S &format, + Args&&... args) { + _one(file, line, format, fmt::make_args_checked(format, args...)); + } + void warning(const std::string &, int, const std::string &, int = 1); void message(const std::string &, int, const std::string &, int = 1); [[ noreturn ]] void done(int = 0); // 1 would be fully backwards compatible @@ -44,6 +55,12 @@ class Error : protected Pointers { private: std::string last_error_message; ErrorType last_error_type; + + // internal versions that accept explicit fmtlib arguments + [[ noreturn ]] void _all(const std::string &, int, fmt::string_view, + fmt::format_args args); + [[ noreturn ]] void _one(const std::string &, int, fmt::string_view, + fmt::format_args args); #endif }; diff --git a/unittest/formats/test_file_operations.cpp b/unittest/formats/test_file_operations.cpp index 392ca04656..414c2dba21 100644 --- a/unittest/formats/test_file_operations.cpp +++ b/unittest/formats/test_file_operations.cpp @@ -11,13 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "../testing/core.h" +#include "error.h" #include "info.h" #include "input.h" #include "lammps.h" #include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" -#include "../testing/core.h" #include #include @@ -134,9 +135,9 @@ TEST_F(FileOperationsTest, logmesg) utils::logmesg(lmp, "one\n"); command("log test_logmesg.log"); utils::logmesg(lmp, "two\n"); - utils::logmesg(lmp, "three={}\n",3); + utils::logmesg(lmp, "three={}\n", 3); utils::logmesg(lmp, "four {}\n"); - utils::logmesg(lmp, "five\n",5); + utils::logmesg(lmp, "five\n", 5); command("log none"); std::string out = END_CAPTURE_OUTPUT(); memset(buf, 0, 64); @@ -148,6 +149,50 @@ TEST_F(FileOperationsTest, logmesg) remove("test_logmesg.log"); } +TEST_F(FileOperationsTest, error_message_warn) +{ + char buf[64]; + BEGIN_HIDE_OUTPUT(); + command("echo none"); + command("log test_error_warn.log"); + END_HIDE_OUTPUT(); + BEGIN_CAPTURE_OUTPUT(); + lmp->error->message("testme.cpp", 10, "message me"); + lmp->error->warning("testme.cpp", 100, "warn me"); + command("log none"); + std::string out = END_CAPTURE_OUTPUT(); + memset(buf, 0, 64); + FILE *fp = fopen("test_error_warn.log", "r"); + fread(buf, 1, 64, fp); + fclose(fp); + auto msg = StrEq("message me (testme.cpp:10)\n" + "WARNING: warn me (testme.cpp:100)\n"); + ASSERT_THAT(out, msg); + ASSERT_THAT(buf, msg); + remove("test_error_warn.log"); +} + +TEST_F(FileOperationsTest, error_all_one) +{ + char buf[64]; + BEGIN_HIDE_OUTPUT(); + command("echo none"); + command("log none"); + END_HIDE_OUTPUT(); + TEST_FAILURE(".*ERROR: exit \\(testme.cpp:10\\).*", + lmp->error->all("testme.cpp", 10, "exit");); + TEST_FAILURE(".*ERROR: exit too \\(testme.cpp:10\\).*", + lmp->error->all("testme.cpp", 10, "exit {}", "too");); + TEST_FAILURE(".*ERROR: argument not found \\(testme.cpp:10\\).*", + lmp->error->all("testme.cpp", 10, "exit {} {}", "too");); + TEST_FAILURE(".*ERROR on proc 0: exit \\(testme.cpp:10\\).*", + lmp->error->one("testme.cpp", 10, "exit");); + TEST_FAILURE(".*ERROR on proc 0: exit too \\(testme.cpp:10\\).*", + lmp->error->one("testme.cpp", 10, "exit {}", "too");); + TEST_FAILURE(".*ERROR on proc 0: argument not found \\(testme.cpp:10\\).*", + lmp->error->one("testme.cpp", 10, "exit {} {}", "too");); +} + int main(int argc, char **argv) { MPI_Init(&argc, &argv); From 831b0fb70fe56919d56de5d28c5813e11db8540d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 25 Apr 2021 19:26:38 -0400 Subject: [PATCH 0671/1217] correct misplaced [[noreturn]] --- src/error.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/error.h b/src/error.h index 8b71974df5..cd42426501 100644 --- a/src/error.h +++ b/src/error.h @@ -33,12 +33,12 @@ class Error : protected Pointers { [[ noreturn ]] void all(const std::string &, int, const std::string &); [[ noreturn ]] void one(const std::string &, int, const std::string &); template - [[ noreturn ]] void all(const std::string &file, int line, const S &format, + void all(const std::string &file, int line, const S &format, Args&&... args) { _all(file, line, format, fmt::make_args_checked(format, args...)); } template - [[ noreturn ]] void one(const std::string &file, int line, const S &format, + void one(const std::string &file, int line, const S &format, Args&&... args) { _one(file, line, format, fmt::make_args_checked(format, args...)); } From 4cbe6200d61ec035b5be3baa1100111b050f86ea Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 25 Apr 2021 21:02:01 -0400 Subject: [PATCH 0672/1217] correct declaration --- src/error.cpp | 2 ++ src/error.h | 3 ++- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/src/error.cpp b/src/error.cpp index a67a9e5865..a6aaf5a360 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -225,6 +225,7 @@ void Error::_all(const std::string &file, int line, fmt::string_view format, } catch (fmt::format_error &e) { all(file,line,e.what()); } + exit(1); // to trick "smart" compilers into believing this does not return } void Error::_one(const std::string &file, int line, fmt::string_view format, @@ -235,6 +236,7 @@ void Error::_one(const std::string &file, int line, fmt::string_view format, } catch (fmt::format_error &e) { one(file,line,e.what()); } + exit(1); // to trick "smart" compilers into believing this does not return } /* ---------------------------------------------------------------------- diff --git a/src/error.h b/src/error.h index cd42426501..36b36669a4 100644 --- a/src/error.h +++ b/src/error.h @@ -56,12 +56,13 @@ class Error : protected Pointers { std::string last_error_message; ErrorType last_error_type; +#endif + private: // internal versions that accept explicit fmtlib arguments [[ noreturn ]] void _all(const std::string &, int, fmt::string_view, fmt::format_args args); [[ noreturn ]] void _one(const std::string &, int, fmt::string_view, fmt::format_args args); -#endif }; } From e9e0bb71b6aec7979af452ae8c5ceb755c9f1b11 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 25 Apr 2021 21:30:51 -0400 Subject: [PATCH 0673/1217] Use varargs version of Error:all() and Error::one() where applicable --- src/BODY/fix_wall_body_polygon.cpp | 2 +- src/BODY/fix_wall_body_polyhedron.cpp | 2 +- src/BODY/pair_body_rounded_polygon.cpp | 4 +- src/BODY/pair_body_rounded_polyhedron.cpp | 8 +- src/COMPRESS/dump_atom_gz.cpp | 2 +- src/COMPRESS/dump_atom_zstd.cpp | 2 +- src/COMPRESS/dump_cfg_gz.cpp | 2 +- src/COMPRESS/dump_custom_gz.cpp | 2 +- src/COMPRESS/dump_custom_zstd.cpp | 2 +- src/COMPRESS/dump_local_gz.cpp | 2 +- src/COMPRESS/dump_local_zstd.cpp | 2 +- src/COMPRESS/dump_xyz_gz.cpp | 2 +- src/COMPRESS/dump_xyz_zstd.cpp | 2 +- src/KIM/kim_command.cpp | 2 +- src/KIM/kim_init.cpp | 16 +- src/KIM/kim_interactions.cpp | 12 +- src/KIM/kim_param.cpp | 4 +- src/KIM/kim_query.cpp | 8 +- src/KIM/pair_kim.cpp | 28 +-- src/KOKKOS/fix_shake_kokkos.cpp | 4 +- src/KOKKOS/pppm_kokkos.cpp | 2 +- src/KSPACE/pppm.cpp | 2 +- src/KSPACE/pppm_dipole.cpp | 4 +- src/KSPACE/pppm_dipole_spin.cpp | 4 +- src/KSPACE/pppm_disp.cpp | 4 +- src/MANYBODY/pair_airebo.cpp | 4 +- src/MANYBODY/pair_bop.cpp | 4 +- src/MANYBODY/pair_eam_cd.cpp | 4 +- src/MANYBODY/pair_eim.cpp | 2 +- src/MISC/fix_ttm.cpp | 8 +- src/MLIAP/mliap_descriptor_snap.cpp | 4 +- src/MLIAP/mliap_model.cpp | 12 +- src/MLIAP/mliap_model_nn.cpp | 8 +- src/MOLECULE/fix_cmap.cpp | 10 +- src/PYTHON/pair_python.cpp | 4 +- src/PYTHON/python_impl.cpp | 8 +- src/QEQ/fix_qeq.cpp | 4 +- src/QEQ/fix_qeq_point.cpp | 4 +- src/QEQ/fix_qeq_shielded.cpp | 4 +- src/QEQ/fix_qeq_slater.cpp | 4 +- src/RIGID/fix_rigid.cpp | 8 +- src/RIGID/fix_rigid_small.cpp | 12 +- src/RIGID/fix_shake.cpp | 12 +- src/SNAP/pair_snap.cpp | 24 +-- src/USER-BOCS/compute_pressure_bocs.cpp | 2 +- src/USER-BOCS/fix_bocs.cpp | 4 +- src/USER-COLVARS/group_ndx.cpp | 4 +- src/USER-COLVARS/ndx_group.cpp | 4 +- src/USER-DIFFRACTION/fix_saed_vtk.cpp | 8 +- src/USER-DPD/pair_exp6_rx.cpp | 4 +- src/USER-MANIFOLD/fix_manifoldforce.cpp | 8 +- src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp | 6 +- src/USER-MEAMC/pair_meamc.cpp | 22 +-- src/USER-MESONT/pair_mesocnt.cpp | 14 +- src/USER-MISC/dihedral_table.cpp | 18 +- src/USER-MISC/dihedral_table_cut.cpp | 14 +- src/USER-MISC/fix_orient_eco.cpp | 4 +- src/USER-MISC/fix_ttm_mod.cpp | 8 +- src/USER-NETCDF/dump_netcdf.cpp | 4 +- src/USER-NETCDF/dump_netcdf_mpiio.cpp | 4 +- src/USER-OMP/reaxc_init_md_omp.cpp | 20 +- src/USER-PACE/pair_pace.cpp | 6 +- src/USER-PHONON/fix_phonon.cpp | 8 +- src/USER-QUIP/pair_quip.cpp | 4 +- src/USER-REAXC/reaxc_init_md.cpp | 20 +- src/atom_vec.cpp | 6 +- src/balance.cpp | 9 +- src/bond.cpp | 8 +- src/create_bonds.cpp | 4 +- src/dump_movie.cpp | 4 +- src/fix.cpp | 3 +- src/fix_ave_chunk.cpp | 4 +- src/fix_ave_correlate.cpp | 4 +- src/fix_ave_histo.cpp | 4 +- src/fix_ave_time.cpp | 4 +- src/fix_enforce2d.cpp | 4 +- src/fix_print.cpp | 4 +- src/fix_property_atom.cpp | 12 +- src/fix_restrain.cpp | 32 +-- src/fix_tmd.cpp | 8 +- src/force.cpp | 4 +- src/group.cpp | 4 +- src/input.cpp | 28 +-- src/lammps.cpp | 32 +-- src/library.cpp | 14 +- src/memory.cpp | 12 +- src/modify.cpp | 10 +- src/molecule.cpp | 182 +++++++++--------- src/ntopo_angle_all.cpp | 4 +- src/ntopo_angle_partial.cpp | 4 +- src/ntopo_angle_template.cpp | 4 +- src/ntopo_bond_all.cpp | 4 +- src/ntopo_bond_partial.cpp | 4 +- src/ntopo_bond_template.cpp | 4 +- src/ntopo_dihedral_all.cpp | 4 +- src/ntopo_dihedral_partial.cpp | 4 +- src/ntopo_dihedral_template.cpp | 4 +- src/ntopo_improper_all.cpp | 4 +- src/ntopo_improper_partial.cpp | 4 +- src/ntopo_improper_template.cpp | 4 +- src/pair.cpp | 8 +- src/pair_hybrid.cpp | 4 +- src/pair_hybrid_scaled.cpp | 12 +- src/pair_table.cpp | 18 +- src/potential_file_reader.cpp | 8 +- src/procmap.cpp | 8 +- src/read_data.cpp | 10 +- src/read_restart.cpp | 12 +- src/reader.cpp | 4 +- src/reset_atom_ids.cpp | 4 +- src/thermo.cpp | 4 +- src/universe.cpp | 8 +- src/utils.cpp | 8 +- src/variable.cpp | 24 +-- src/write_coeff.cpp | 8 +- src/write_data.cpp | 4 +- src/write_restart.cpp | 8 +- 117 files changed, 522 insertions(+), 524 deletions(-) diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp index 027c0dbd5a..574138fc67 100644 --- a/src/BODY/fix_wall_body_polygon.cpp +++ b/src/BODY/fix_wall_body_polygon.cpp @@ -97,7 +97,7 @@ FixWallBodyPolygon::FixWallBodyPolygon(LAMMPS *lmp, int narg, char **arg) : lo = hi = 0.0; cylradius = utils::numeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; - } else error->all(FLERR,fmt::format("Unknown wall style {}",arg[iarg])); + } else error->all(FLERR,"Unknown wall style {}",arg[iarg]); // check for trailing keyword/values diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp index acfafaefbe..2958a715ac 100644 --- a/src/BODY/fix_wall_body_polyhedron.cpp +++ b/src/BODY/fix_wall_body_polyhedron.cpp @@ -99,7 +99,7 @@ FixWallBodyPolyhedron::FixWallBodyPolyhedron(LAMMPS *lmp, int narg, char **arg) if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG; else hi = utils::numeric(FLERR,arg[iarg+2],false,lmp); iarg += 3; - } else error->all(FLERR,fmt::format("Unknown wall style {}",arg[iarg])); + } else error->all(FLERR,"Unknown wall style {}",arg[iarg]); // check for trailing keyword/values diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index fa8f7fed3e..7185dc2b54 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -570,8 +570,8 @@ void PairBodyRoundedPolygon::body2space(int i) } if ((body_num_edges > 0) && (edge_ends == nullptr)) - error->one(FLERR,fmt::format("Inconsistent edge data for body of atom {}", - atom->tag[i])); + error->one(FLERR,"Inconsistent edge data for body of atom {}", + atom->tag[i]); for (int m = 0; m < body_num_edges; m++) { edge[nedge][0] = static_cast(edge_ends[2*m+0]); diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index 3dbca5be7a..d9d1350329 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -557,8 +557,8 @@ void PairBodyRoundedPolyhedron::body2space(int i) } if ((body_num_edges > 0) && (edge_ends == nullptr)) - error->one(FLERR,fmt::format("Inconsistent edge data for body of atom {}", - atom->tag[i])); + error->one(FLERR,"Inconsistent edge data for body of atom {}", + atom->tag[i]); for (int m = 0; m < body_num_edges; m++) { edge[nedge][0] = static_cast(edge_ends[2*m+0]); @@ -584,8 +584,8 @@ void PairBodyRoundedPolyhedron::body2space(int i) } if ((body_num_faces > 0) && (face_pts == nullptr)) - error->one(FLERR,fmt::format("Inconsistent face data for body of atom {}", - atom->tag[i])); + error->one(FLERR,"Inconsistent face data for body of atom {}", + atom->tag[i]); for (int m = 0; m < body_num_faces; m++) { for (int k = 0; k < MAX_FACE_SIZE; k++) diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index 7b54fd8e62..73f1ddf5a2 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -194,7 +194,7 @@ int DumpAtomGZ::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); + error->one(FLERR,"Illegal dump_modify command: {}", e.what()); } } return consumed; diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index b53ebb2269..430deda177 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -208,7 +208,7 @@ int DumpAtomZstd::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); + error->one(FLERR,"Illegal dump_modify command: {}", e.what()); } } return consumed; diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp index c5942c1fc5..25328797dd 100644 --- a/src/COMPRESS/dump_cfg_gz.cpp +++ b/src/COMPRESS/dump_cfg_gz.cpp @@ -234,7 +234,7 @@ int DumpCFGGZ::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); + error->one(FLERR,"Illegal dump_modify command: {}", e.what()); } } return consumed; diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp index 9a3fc39d0a..9ed5a10b02 100644 --- a/src/COMPRESS/dump_custom_gz.cpp +++ b/src/COMPRESS/dump_custom_gz.cpp @@ -194,7 +194,7 @@ int DumpCustomGZ::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); + error->one(FLERR,"Illegal dump_modify command: {}", e.what()); } } return consumed; diff --git a/src/COMPRESS/dump_custom_zstd.cpp b/src/COMPRESS/dump_custom_zstd.cpp index b3f0971bf5..073e39a87e 100644 --- a/src/COMPRESS/dump_custom_zstd.cpp +++ b/src/COMPRESS/dump_custom_zstd.cpp @@ -213,7 +213,7 @@ int DumpCustomZstd::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); + error->one(FLERR,"Illegal dump_modify command: {}", e.what()); } } return consumed; diff --git a/src/COMPRESS/dump_local_gz.cpp b/src/COMPRESS/dump_local_gz.cpp index 7ffb8d80ff..9c6c06e65a 100644 --- a/src/COMPRESS/dump_local_gz.cpp +++ b/src/COMPRESS/dump_local_gz.cpp @@ -194,7 +194,7 @@ int DumpLocalGZ::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); + error->one(FLERR,"Illegal dump_modify command: {}", e.what()); } } return consumed; diff --git a/src/COMPRESS/dump_local_zstd.cpp b/src/COMPRESS/dump_local_zstd.cpp index 4d7fe9361b..f20dc5016c 100644 --- a/src/COMPRESS/dump_local_zstd.cpp +++ b/src/COMPRESS/dump_local_zstd.cpp @@ -211,7 +211,7 @@ int DumpLocalZstd::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); + error->one(FLERR,"Illegal dump_modify command: {}", e.what()); } } return consumed; diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index abd6e7fa78..1a51432d83 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -159,7 +159,7 @@ int DumpXYZGZ::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); + error->one(FLERR,"Illegal dump_modify command: {}", e.what()); } } return consumed; diff --git a/src/COMPRESS/dump_xyz_zstd.cpp b/src/COMPRESS/dump_xyz_zstd.cpp index 74e482717b..8866dcfffb 100644 --- a/src/COMPRESS/dump_xyz_zstd.cpp +++ b/src/COMPRESS/dump_xyz_zstd.cpp @@ -176,7 +176,7 @@ int DumpXYZZstd::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); + error->one(FLERR,"Illegal dump_modify command: {}", e.what()); } } return consumed; diff --git a/src/KIM/kim_command.cpp b/src/KIM/kim_command.cpp index 88072d1fda..2de86556b3 100644 --- a/src/KIM/kim_command.cpp +++ b/src/KIM/kim_command.cpp @@ -131,5 +131,5 @@ void KimCommand::command(int narg, char **arg) KimQuery *cmd = new KimQuery(lmp); cmd->command(narg, arg); delete cmd; - } else error->all(FLERR, fmt::format("Unknown kim subcommand {}", subcmd)); + } else error->all(FLERR,"Unknown kim subcommand {}", subcmd); } diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 2703ce24e0..f22335b411 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -93,10 +93,10 @@ void KimInit::command(int narg, char **arg) auto arg_str = std::string(arg[2]); if (arg_str == "unit_conversion_mode") unit_conversion_mode = true; else { - error->all(FLERR, fmt::format("Illegal 'kim init' command.\nThe argument " + error->all(FLERR, "Illegal 'kim init' command.\nThe argument " "followed by unit_style {} is an optional " "argument and when is used must " - "be unit_conversion_mode", user_units)); + "be unit_conversion_mode", user_units); } } else unit_conversion_mode = false; @@ -159,8 +159,8 @@ void get_kim_unit_names( } else if ((system_str == "lj") || (system_str == "micro") || (system_str == "nano")) { - error->all(FLERR, fmt::format("LAMMPS unit_style {} not supported " - "by KIM models", system_str)); + error->all(FLERR, "LAMMPS unit_style {} not supported " + "by KIM models", system_str); } else { error->all(FLERR, "Unknown unit_style"); } @@ -279,8 +279,8 @@ void KimInit::determine_model_type_and_units(char * model_name, const std::string model_units_str(*model_units); const std::string user_units_str(user_units); if ((!unit_conversion_mode) && (model_units_str != user_units_str)) { - error->all(FLERR, fmt::format("Incompatible units for KIM Simulator Model" - ", required units = {}", model_units_str)); + error->all(FLERR, "Incompatible units for KIM Simulator Model" + ", required units = {}", model_units_str); } } } @@ -475,9 +475,9 @@ void KimInit::do_variables(const std::string &from, const std::string &to) ier = lammps_unit_conversion(units[i], from, to, conversion_factor); if (ier != 0) - error->all(FLERR, fmt::format("Unable to obtain conversion factor: " + error->all(FLERR, "Unable to obtain conversion factor: " "unit = {}; from = {}; to = {}", - units[i], from, to)); + units[i], from, to); variable->internal_set(v_unit, conversion_factor); input->write_echo(fmt::format("variable {:<15s} internal {:<15.12e}\n", diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp index f12c1774d2..d1afd92a1f 100644 --- a/src/KIM/kim_interactions.cpp +++ b/src/KIM/kim_interactions.cpp @@ -102,11 +102,11 @@ void KimInteractions::do_setup(int narg, char **arg) if ((narg == 1) && (arg_str == "fixed_types")) { fixed_types = true; } else if (narg != atom->ntypes) { - error->all(FLERR, fmt::format("Illegal 'kim interactions' command.\nThe " + error->all(FLERR, "Illegal 'kim interactions' command.\nThe " "LAMMPS simulation has {} atom type(s), but " "{} chemical species passed to the " "'kim interactions' command", - atom->ntypes, narg)); + atom->ntypes, narg); } else { fixed_types = false; } @@ -164,8 +164,8 @@ void KimInteractions::do_setup(int narg, char **arg) if (atom_type_sym == sim_species) species_is_supported = true; } if (!species_is_supported) { - error->all(FLERR, fmt::format("Species '{}' is not supported by this " - "KIM Simulator Model", atom_type_sym)); + error->all(FLERR, "Species '{}' is not supported by this " + "KIM Simulator Model", atom_type_sym); } } } else { @@ -275,8 +275,8 @@ void KimInteractions::KIM_SET_TYPE_PARAMETERS(const std::string &input_line) con const std::string key = words[1]; if (key != "pair" && key != "charge") - error->one(FLERR, fmt::format("Unrecognized KEY {} for " - "KIM_SET_TYPE_PARAMETERS command", key)); + error->one(FLERR, "Unrecognized KEY {} for " + "KIM_SET_TYPE_PARAMETERS command", key); std::string filename = words[2]; std::vector species(words.begin() + 3, words.end()); diff --git a/src/KIM/kim_param.cpp b/src/KIM/kim_param.cpp index b7e3f4148e..8d3921f30c 100644 --- a/src/KIM/kim_param.cpp +++ b/src/KIM/kim_param.cpp @@ -124,8 +124,8 @@ void get_kim_unit_names( } else if ((system_str == "lj") || (system_str == "micro") || (system_str == "nano")) { - error->all(FLERR, fmt::format("LAMMPS unit_style {} not supported " - "by KIM models", system_str)); + error->all(FLERR, "LAMMPS unit_style {} not supported " + "by KIM models", system_str); } else { error->all(FLERR, "Unknown unit_style"); } diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index 74b0179302..05381b8fab 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -126,20 +126,20 @@ void KimQuery::command(int narg, char **arg) std::string query_function(arg[1]); if (query_function == "split" || query_function == "list" || query_function == "index") - error->all(FLERR, fmt::format("Illegal 'kim query' command.\nThe '{}' " + error->all(FLERR, "Illegal 'kim query' command.\nThe '{}' " "keyword can not be used after '{}'", - query_function, format_arg)); + query_function, format_arg); std::string model_name; // check the query_args format (a series of keyword=value pairs) for (int i = 2; i < narg; ++i) { if (!utils::strmatch(arg[i], "[=][\\[].*[\\]]")) - error->all(FLERR, fmt::format("Illegal query format.\nInput argument " + error->all(FLERR, "Illegal query format.\nInput argument " "of `{}` to 'kim query' is wrong. The " "query format is the keyword=[value], " "where value is always an array of one or " - "more comma-separated items", arg[i])); + "more comma-separated items", arg[i]); } if (query_function != "get_available_models") { diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index cf6374ab2d..aafc83aeaf 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -434,8 +434,8 @@ void PairKIM::coeff(int narg, char **arg) if (supported) { kim_particle_codes[i] = code; } else { - error->all(FLERR,fmt::format("GetSpeciesSupportAndCode: symbol not " - "found: {}",lmps_unique_elements[i])); + error->all(FLERR,"GetSpeciesSupportAndCode: symbol not " + "found: {}",lmps_unique_elements[i]); } } // Set the new values for PM parameters @@ -478,9 +478,9 @@ void PairKIM::coeff(int narg, char **arg) } if (param_index >= numberOfParameters) - error->all(FLERR,fmt::format("Wrong argument for pair coefficients.\n" + error->all(FLERR,"Wrong argument for pair coefficients.\n" "This Model does not have the requested " - "'{}' parameter", paramname)); + "'{}' parameter", paramname); // Get the index_range for the requested parameter int nlbound(0); @@ -491,9 +491,9 @@ void PairKIM::coeff(int narg, char **arg) // Check to see if the indices range contains only integer numbers & : if (argtostr.find_first_not_of("0123456789:") != std::string::npos) - error->all(FLERR,fmt::format("Illegal index_range.\nExpected integer" + error->all(FLERR,"Illegal index_range.\nExpected integer" " parameter(s) instead of '{}' in " - "index_range", argtostr)); + "index_range", argtostr); std::string::size_type npos = argtostr.find(':'); if (npos != std::string::npos) { @@ -504,16 +504,16 @@ void PairKIM::coeff(int narg, char **arg) if (nubound < 1 || nubound > extent || nlbound < 1 || nlbound > nubound) - error->all(FLERR,fmt::format("Illegal index_range '{}-{}' for '{}' " + error->all(FLERR,"Illegal index_range '{}-{}' for '{}' " "parameter with the extent of '{}'", - nlbound, nubound, paramname, extent)); + nlbound, nubound, paramname, extent); } else { nlbound = atoi(argtostr.c_str()); if (nlbound < 1 || nlbound > extent) - error->all(FLERR,fmt::format("Illegal index '{}' for '{}' parameter " + error->all(FLERR,"Illegal index '{}' for '{}' parameter " "with the extent of '{}'", nlbound, - paramname, extent)); + paramname, extent); nubound = nlbound; } @@ -543,10 +543,10 @@ void PairKIM::coeff(int narg, char **arg) } else error->all(FLERR,"Wrong parameter type to update"); } else { - error->all(FLERR,fmt::format("Wrong number of variable values for pair " + error->all(FLERR,"Wrong number of variable values for pair " "coefficients.\n'{}' values are requested " "for '{}' parameter", nubound - nlbound + 1, - paramname)); + paramname); } } @@ -1052,8 +1052,8 @@ void PairKIM::set_lmps_flags() } else if ((unit_style_str == "lj") || (unit_style_str == "micro") || (unit_style_str == "nano")) { - error->all(FLERR,fmt::format("LAMMPS unit_style {} not supported " - "by KIM models", unit_style_str)); + error->all(FLERR,"LAMMPS unit_style {} not supported " + "by KIM models", unit_style_str); } else { error->all(FLERR,"Unknown unit_style"); } diff --git a/src/KOKKOS/fix_shake_kokkos.cpp b/src/KOKKOS/fix_shake_kokkos.cpp index 253c7ee7e0..fced6297f6 100644 --- a/src/KOKKOS/fix_shake_kokkos.cpp +++ b/src/KOKKOS/fix_shake_kokkos.cpp @@ -285,8 +285,8 @@ void FixShakeKokkos::pre_neighbor() nlist = h_nlist(); if (h_error_flag() == 1) { - error->one(FLERR,fmt::format("Shake atoms missing on proc " - "{} at step {}",me,update->ntimestep)); + error->one(FLERR,"Shake atoms missing on proc " + "{} at step {}",me,update->ntimestep); } } diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 9dc2416dcc..e5bc3fa74b 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -199,7 +199,7 @@ void PPPMKokkos::init() } if (order < 2 || order > MAXORDER) - error->all(FLERR,fmt::format("PPPM order cannot be < 2 or > {}",MAXORDER)); + error->all(FLERR,"PPPM order cannot be < 2 or > {}",MAXORDER); // compute two charge force diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index 2419627642..3a96731be4 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -216,7 +216,7 @@ void PPPM::init() } if (order < 2 || order > MAXORDER) - error->all(FLERR,fmt::format("PPPM order cannot be < 2 or > {}",MAXORDER)); + error->all(FLERR,"PPPM order cannot be < 2 or > {}",MAXORDER); // compute two charge force diff --git a/src/KSPACE/pppm_dipole.cpp b/src/KSPACE/pppm_dipole.cpp index 44c3862b2f..8078c24f90 100644 --- a/src/KSPACE/pppm_dipole.cpp +++ b/src/KSPACE/pppm_dipole.cpp @@ -136,8 +136,8 @@ void PPPMDipole::init() } if (order < 2 || order > MAXORDER) - error->all(FLERR,fmt::format("PPPMDipole order cannot be < 2 or > {}", - MAXORDER)); + error->all(FLERR,"PPPMDipole order cannot be < 2 or > {}", + MAXORDER); // compute two charge force diff --git a/src/KSPACE/pppm_dipole_spin.cpp b/src/KSPACE/pppm_dipole_spin.cpp index 9b3d15fc76..daaacc6bd4 100644 --- a/src/KSPACE/pppm_dipole_spin.cpp +++ b/src/KSPACE/pppm_dipole_spin.cpp @@ -121,8 +121,8 @@ void PPPMDipoleSpin::init() } if (order < 2 || order > MAXORDER) - error->all(FLERR,fmt::format("PPPMDipoleSpin order cannot be < 2 or > {}", - MAXORDER)); + error->all(FLERR,"PPPMDipoleSpin order cannot be < 2 or > {}", + MAXORDER); // compute two charge force diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index 1844301ac5..eba653e7d7 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -278,8 +278,8 @@ void PPPMDisp::init() } if (order > MAXORDER || order_6 > MAXORDER) - error->all(FLERR,fmt::format("PPPMDisp coulomb or dispersion order cannot" - " be greater than {}",MAXORDER)); + error->all(FLERR,"PPPMDisp coulomb or dispersion order cannot" + " be greater than {}",MAXORDER); // compute two charge force diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 7d94ef7cec..058a769b14 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -3379,7 +3379,7 @@ void PairAIREBO::read_file(char *filename) break; default: - error->one(FLERR, fmt::format("Unknown REBO style variant {}",variant)); + error->one(FLERR,"Unknown REBO style variant {}",variant); } PotentialFileReader reader(lmp, filename, potential_name); @@ -3391,7 +3391,7 @@ void PairAIREBO::read_file(char *filename) char * line = reader.next_line(); if (std::string(line).find(header) == std::string::npos) { - error->one(FLERR, fmt::format("Potential file does not match AIREBO/REBO style variant: {}: {}", header, line)); + error->one(FLERR,"Potential file does not match AIREBO/REBO style variant: {}: {}", header, line); } // skip remaining comments diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index a8f64853bc..0802191c9f 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -685,8 +685,8 @@ void PairBOP::init_style() // check that user sets comm->cutghostuser to 3x the max BOP cutoff if (comm->cutghostuser < 3.0*cutmax - EPSILON) - error->all(FLERR,fmt::format("Pair style bop requires comm ghost cutoff " - "at least 3x larger than {}",cutmax)); + error->all(FLERR,"Pair style bop requires comm ghost cutoff " + "at least 3x larger than {}",cutmax); // need a full neighbor list and neighbors of ghosts diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp index b56166424c..da4d2b2c65 100644 --- a/src/MANYBODY/pair_eam_cd.cpp +++ b/src/MANYBODY/pair_eam_cd.cpp @@ -506,8 +506,8 @@ void PairEAMCD::read_h_coeff(char *filename) int convert_flag = unit_convert_flag; fptr = utils::open_potential(filename, lmp, &convert_flag); if (fptr == nullptr) - error->one(FLERR,fmt::format("Cannot open EAMCD potential file {}", - filename)); + error->one(FLERR,"Cannot open EAMCD potential file {}", + filename); // h coefficients are stored at the end of the file. // Skip to last line of file. diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index eda1838a5a..a868ac2fc0 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -1013,7 +1013,7 @@ EIMPotentialFileReader::EIMPotentialFileReader(LAMMPS *lmp, conversion_factor = utils::get_conversion_factor(utils::ENERGY,unit_convert); if (fp == nullptr) { - error->one(FLERR, fmt::format("cannot open eim potential file {}", filename)); + error->one(FLERR,"cannot open eim potential file {}", filename); } parse(fp); diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index da71d736c2..87832bd0f9 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -75,8 +75,8 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) : if (comm->me == 0) { fp = fopen(arg[15],"w"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open output file {}: {}", - arg[15], utils::getsyserror())); + error->one(FLERR,"Cannot open output file {}: {}", + arg[15], utils::getsyserror()); } } @@ -331,8 +331,8 @@ void FixTTM::read_initial_electron_temperatures(const char *filename) std::string name = utils::get_potential_file_path(filename); if (name.empty()) - error->one(FLERR,fmt::format("Cannot open input file: {}", - filename)); + error->one(FLERR,"Cannot open input file: {}", + filename); FILE *fpr = fopen(name.c_str(),"r"); // read initial electron temperature values from file diff --git a/src/MLIAP/mliap_descriptor_snap.cpp b/src/MLIAP/mliap_descriptor_snap.cpp index 5c73cb64df..098d9ccbba 100644 --- a/src/MLIAP/mliap_descriptor_snap.cpp +++ b/src/MLIAP/mliap_descriptor_snap.cpp @@ -379,8 +379,8 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename) if (comm->me == 0) { fpparam = utils::open_potential(paramfilename,lmp,nullptr); if (fpparam == nullptr) - error->one(FLERR,fmt::format("Cannot open SNAP parameter file {}: {}", - paramfilename, utils::getsyserror())); + error->one(FLERR,"Cannot open SNAP parameter file {}: {}", + paramfilename, utils::getsyserror()); } char line[MAXLINE],*ptr; diff --git a/src/MLIAP/mliap_model.cpp b/src/MLIAP/mliap_model.cpp index f993aeb725..214ac3358c 100644 --- a/src/MLIAP/mliap_model.cpp +++ b/src/MLIAP/mliap_model.cpp @@ -98,8 +98,8 @@ void MLIAPModelSimple::read_coeffs(char *coefffilename) if (comm->me == 0) { fpcoeff = utils::open_potential(coefffilename,lmp,nullptr); if (fpcoeff == nullptr) - error->one(FLERR,fmt::format("Cannot open MLIAPModel coeff file {}: {}", - coefffilename,utils::getsyserror())); + error->one(FLERR,"Cannot open MLIAPModel coeff file {}: {}", + coefffilename,utils::getsyserror()); } char line[MAXLINE],*ptr; @@ -136,8 +136,8 @@ void MLIAPModelSimple::read_coeffs(char *coefffilename) nelements = coeffs.next_int(); nparams = coeffs.next_int(); } catch (TokenizerException &e) { - error->all(FLERR,fmt::format("Incorrect format in MLIAPModel coefficient " - "file: {}",e.what())); + error->all(FLERR,"Incorrect format in MLIAPModel coefficient " + "file: {}",e.what()); } // set up coeff lists @@ -168,8 +168,8 @@ void MLIAPModelSimple::read_coeffs(char *coefffilename) throw TokenizerException("Wrong number of items",""); coeffelem[ielem][icoeff] = coeffs.next_double(); } catch (TokenizerException &e) { - error->all(FLERR,fmt::format("Incorrect format in MLIAPModel " - "coefficient file: {}",e.what())); + error->all(FLERR,"Incorrect format in MLIAPModel " + "coefficient file: {}",e.what()); } } } diff --git a/src/MLIAP/mliap_model_nn.cpp b/src/MLIAP/mliap_model_nn.cpp index 3805a5761b..fcc62c3059 100644 --- a/src/MLIAP/mliap_model_nn.cpp +++ b/src/MLIAP/mliap_model_nn.cpp @@ -73,8 +73,8 @@ void MLIAPModelNN::read_coeffs(char *coefffilename) if (comm->me == 0) { fpcoeff = utils::open_potential(coefffilename,lmp,nullptr); if (fpcoeff == nullptr) - error->one(FLERR,fmt::format("Cannot open MLIAPModel coeff file {}: {}", - coefffilename,utils::getsyserror())); + error->one(FLERR,"Cannot open MLIAPModel coeff file {}: {}", + coefffilename,utils::getsyserror()); } char line[MAXLINE], *ptr, *tstr; @@ -111,8 +111,8 @@ void MLIAPModelNN::read_coeffs(char *coefffilename) nelements = coeffs.next_int(); nparams = coeffs.next_int(); } catch (TokenizerException &e) { - error->all(FLERR,fmt::format("Incorrect format in MLIAPModel coefficient " - "file: {}",e.what())); + error->all(FLERR,"Incorrect format in MLIAPModel coefficient " + "file: {}",e.what()); } // set up coeff lists diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index 1b58037eb7..9400da3389 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -260,11 +260,11 @@ void FixCMAP::pre_neighbor() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1 || atom5 == -1) - error->one(FLERR,fmt::format("CMAP atoms {} {} {} {} {} missing on " + error->one(FLERR,"CMAP atoms {} {} {} {} {} missing on " "proc {} at step {}", crossterm_atom1[i][m],crossterm_atom2[i][m], crossterm_atom3[i][m],crossterm_atom4[i][m], - crossterm_atom5[i][m],me,update->ntimestep)); + crossterm_atom5[i][m],me,update->ntimestep); atom1 = domain->closest_image(i,atom1); atom2 = domain->closest_image(i,atom2); atom3 = domain->closest_image(i,atom3); @@ -640,8 +640,8 @@ void FixCMAP::read_grid_map(char *cmapfile) if (comm->me == 0) { fp = utils::open_potential(cmapfile,lmp,nullptr); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open fix cmap file {}: {}", - cmapfile, utils::getsyserror())); + error->one(FLERR,"Cannot open fix cmap file {}: {}", + cmapfile, utils::getsyserror()); } @@ -1071,7 +1071,7 @@ void FixCMAP::read_data_section(char *keyword, int n, char *buf, *next = '\n'; if (nwords != 7) - error->all(FLERR,fmt::format("Incorrect {} format in data file",keyword)); + error->all(FLERR,"Incorrect {} format in data file",keyword); // loop over lines of CMAP crossterms // tokenize the line into values diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index 5020119e0d..adf7e2bb49 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -382,11 +382,11 @@ void * PairPython::get_member_function(const char * name) PyObject * py_mfunc = PyObject_GetAttrString(py_pair_instance, name); if (!py_mfunc) { PyUtils::Print_Errors(); - error->all(FLERR, fmt::format("Could not find '{}' method'", name)); + error->all(FLERR,"Could not find '{}' method'", name); } if (!PyCallable_Check(py_mfunc)) { PyUtils::Print_Errors(); - error->all(FLERR, fmt::format("Python '{}' is not callable", name)); + error->all(FLERR,"Python '{}' is not callable", name); } return py_mfunc; } diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index c84d04b4b7..e2484f62f7 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -263,14 +263,14 @@ void PythonImpl::command(int narg, char **arg) if (!pFunc) { PyUtils::Print_Errors(); - error->all(FLERR,fmt::format("Could not find Python function {}", - pfuncs[ifunc].name)); + error->all(FLERR,"Could not find Python function {}", + pfuncs[ifunc].name); } if (!PyCallable_Check(pFunc)) { PyUtils::Print_Errors(); - error->all(FLERR,fmt::format("Python function {} is not callable", - pfuncs[ifunc].name)); + error->all(FLERR,"Python function {} is not callable", + pfuncs[ifunc].name); } pfuncs[ifunc].pFunc = (void *) pFunc; diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index e592ed2af4..fe6948c6a0 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -707,8 +707,8 @@ void FixQEq::read_file(char *file) if (comm->me == 0) { fp = utils::open_potential(file,lmp,nullptr); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open fix qeq parameter file {}: {}", - file,utils::getsyserror())); + error->one(FLERR,"Cannot open fix qeq parameter file {}: {}", + file,utils::getsyserror()); } // read each line out of file, skipping blank lines or leading '#' diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index ac31f906e0..9cea930de9 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -161,8 +161,8 @@ void FixQEqPoint::compute_H() } if (m_fill >= H.m) - error->all(FLERR,fmt::format("Fix qeq/point has insufficient H matrix " - "size: m_fill={} H.m={}\n",m_fill, H.m)); + error->all(FLERR,"Fix qeq/point has insufficient H matrix " + "size: m_fill={} H.m={}\n",m_fill, H.m); } /* ---------------------------------------------------------------------- */ diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index ad6202abd8..3c1cfb2919 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -226,8 +226,8 @@ void FixQEqShielded::compute_H() } if (m_fill >= H.m) - error->all(FLERR,fmt::format("Fix qeq/shielded has insufficient H matrix " - "size: m_fill={} H.m={}\n",m_fill,H.m)); + error->all(FLERR,"Fix qeq/shielded has insufficient H matrix " + "size: m_fill={} H.m={}\n",m_fill,H.m); } /* ---------------------------------------------------------------------- */ diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 326d71c93b..73f7cdf879 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -209,8 +209,8 @@ void FixQEqSlater::compute_H() } if (m_fill >= H.m) - error->all(FLERR,fmt::format(FLERR,"Fix qeq/slater has insufficient H " - "matrix size:m_fill={} H.m={}\n",m_fill,H.m)); + error->all(FLERR,FLERR,"Fix qeq/slater has insufficient H " + "matrix size:m_fill={} H.m={}\n",m_fill,H.m); } /* ---------------------------------------------------------------------- */ diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 91cb0ce82c..582d4ed3f5 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -2280,8 +2280,8 @@ void FixRigid::readfile(int which, double *vec, if (me == 0) { fp = fopen(inpfile,"r"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open fix rigid file {}: {}", - inpfile,utils::getsyserror())); + error->one(FLERR,"Cannot open fix rigid file {}: {}", + inpfile,utils::getsyserror()); while (1) { eof = fgets(line,MAXLINE,fp); if (eof == nullptr) error->one(FLERR,"Unexpected end of fix rigid file"); @@ -2389,8 +2389,8 @@ void FixRigid::write_restart_file(const char *file) auto outfile = std::string(file) + ".rigid"; FILE *fp = fopen(outfile.c_str(),"w"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open fix rigid restart file {}: {}", - outfile,utils::getsyserror())); + error->one(FLERR,"Cannot open fix rigid restart file {}: {}", + outfile,utils::getsyserror()); fmt::print(fp,"# fix rigid mass, COM, inertia tensor info for " "{} bodies on timestep {}\n\n",nbody,update->ntimestep); diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index c1c956f08e..8f2e855cea 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -2453,8 +2453,8 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody) if (me == 0) { fp = fopen(inpfile,"r"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open fix rigid/small file {}: {}", - inpfile,utils::getsyserror())); + error->one(FLERR,"Cannot open fix rigid/small file {}: {}", + inpfile,utils::getsyserror()); while (1) { eof = fgets(line,MAXLINE,fp); if (eof == nullptr) @@ -2567,8 +2567,8 @@ void FixRigidSmall::write_restart_file(const char *file) auto outfile = std::string(file) + ".rigid"; fp = fopen(outfile.c_str(),"w"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open fix rigid restart file {}: {}", - outfile,utils::getsyserror())); + error->one(FLERR,"Cannot open fix rigid restart file {}: {}", + outfile,utils::getsyserror()); fmt::print(fp,"# fix rigid mass, COM, inertia tensor info for " "{} bodies on timestep {}\n\n",nbody,update->ntimestep); @@ -3311,9 +3311,9 @@ void FixRigidSmall::reset_atom2body() if (bodytag[i]) { iowner = atom->map(bodytag[i]); if (iowner == -1) - error->one(FLERR,fmt::format("Rigid body atoms {} {} missing on " + error->one(FLERR,"Rigid body atoms {} {} missing on " "proc {} at step {}",atom->tag[i], - bodytag[i],comm->me,update->ntimestep)); + bodytag[i],comm->me,update->ntimestep); atom2body[i] = bodyown[iowner]; } diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 957898d361..f8c6b661b4 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -524,19 +524,19 @@ void FixShake::pre_neighbor() atom1 = atom->map(shake_atom[i][0]); atom2 = atom->map(shake_atom[i][1]); if (atom1 == -1 || atom2 == -1) - error->one(FLERR,fmt::format("Shake atoms {} {} missing on proc " + error->one(FLERR,"Shake atoms {} {} missing on proc " "{} at step {}",shake_atom[i][0], - shake_atom[i][1],me,update->ntimestep)); + shake_atom[i][1],me,update->ntimestep); if (i <= atom1 && i <= atom2) list[nlist++] = i; } else if (shake_flag[i] % 2 == 1) { atom1 = atom->map(shake_atom[i][0]); atom2 = atom->map(shake_atom[i][1]); atom3 = atom->map(shake_atom[i][2]); if (atom1 == -1 || atom2 == -1 || atom3 == -1) - error->one(FLERR,fmt::format("Shake atoms {} {} {} missing on proc " + error->one(FLERR,"Shake atoms {} {} {} missing on proc " "{} at step {}",shake_atom[i][0], shake_atom[i][1],shake_atom[i][2], - me,update->ntimestep)); + me,update->ntimestep); if (i <= atom1 && i <= atom2 && i <= atom3) list[nlist++] = i; } else { atom1 = atom->map(shake_atom[i][0]); @@ -544,10 +544,10 @@ void FixShake::pre_neighbor() atom3 = atom->map(shake_atom[i][2]); atom4 = atom->map(shake_atom[i][3]); if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) - error->one(FLERR,fmt::format("Shake atoms {} {} {} {} missing on " + error->one(FLERR,"Shake atoms {} {} {} {} missing on " "proc {} at step {}",shake_atom[i][0], shake_atom[i][1],shake_atom[i][2], - shake_atom[i][3],me,update->ntimestep)); + shake_atom[i][3],me,update->ntimestep); if (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4) list[nlist++] = i; } diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index b4ee3c870a..b307da4947 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -456,8 +456,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) if (comm->me == 0) { fpcoeff = utils::open_potential(coefffilename,lmp,nullptr); if (fpcoeff == nullptr) - error->one(FLERR,fmt::format("Cannot open SNAP coefficient file {}: ", - coefffilename, utils::getsyserror())); + error->one(FLERR,"Cannot open SNAP coefficient file {}: ", + coefffilename, utils::getsyserror()); } char line[MAXLINE],*ptr; @@ -490,8 +490,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) nelemtmp = words.next_int(); ncoeffall = words.next_int(); } catch (TokenizerException &e) { - error->all(FLERR,fmt::format("Incorrect format in SNAP coefficient " - "file: {}", e.what())); + error->all(FLERR,"Incorrect format in SNAP coefficient " + "file: {}", e.what()); } // clean out old arrays and set up element lists @@ -589,8 +589,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) coeffelem[jelem][icoeff] = coeff.next_double(); } catch (TokenizerException &e) { - error->all(FLERR,fmt::format("Incorrect format in SNAP coefficient " - "file: {}", e.what())); + error->all(FLERR,"Incorrect format in SNAP coefficient " + "file: {}", e.what()); } } } @@ -599,8 +599,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) for (int jelem = 0; jelem < nelements; jelem++) { if (elementflags[jelem] == 0) - error->all(FLERR,fmt::format("Element {} not found in SNAP coefficient " - "file", elements[jelem])); + error->all(FLERR,"Element {} not found in SNAP coefficient " + "file", elements[jelem]); } // set flags for required keywords @@ -626,8 +626,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) if (comm->me == 0) { fpparam = utils::open_potential(paramfilename,lmp,nullptr); if (fpparam == nullptr) - error->one(FLERR,fmt::format("Cannot open SNAP parameter file {}: {}", - paramfilename, utils::getsyserror())); + error->one(FLERR,"Cannot open SNAP parameter file {}: {}", + paramfilename, utils::getsyserror()); } eof = 0; @@ -687,8 +687,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) else if (keywd == "chunksize") chunksize = utils::inumeric(FLERR,keyval.c_str(),false,lmp); else - error->all(FLERR,fmt::format("Unknown parameter '{}' in SNAP " - "parameter file", keywd)); + error->all(FLERR,"Unknown parameter '{}' in SNAP " + "parameter file", keywd); } if (rcutfacflag == 0 || twojmaxflag == 0) diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp index 43cf7efb8f..49c644be71 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/USER-BOCS/compute_pressure_bocs.cpp @@ -215,7 +215,7 @@ double ComputePressureBocs::find_index(double * grid, double value) if (value >= grid[i] && value <= (grid[i] + spacing)) { return i; } - error->all(FLERR, fmt::format("find_index could not find value in grid for value: {}", value)); + error->all(FLERR,"find_index could not find value in grid for value: {}", value); for (int i = 0; i < gridsize; ++i) { fprintf(stderr, "grid %d: %f\n",i,grid[i]); diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index bd217e60a8..20c2a9dfe8 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -725,7 +725,7 @@ int FixBocs::read_F_table( char *filename, int p_basis_type ) } } else { - error->all(FLERR,fmt::format("ERROR: Unable to open file: {}", filename)); + error->all(FLERR,"ERROR: Unable to open file: {}", filename); } if (badInput && comm->me == 0) { @@ -744,7 +744,7 @@ int FixBocs::read_F_table( char *filename, int p_basis_type ) } else { - error->all(FLERR,fmt::format("ERROR: invalid p_basis_type value of {} in read_F_table", p_basis_type)); + error->all(FLERR,"ERROR: invalid p_basis_type value of {} in read_F_table", p_basis_type); } memory->destroy(data); diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp index 26711026e8..48d4157fc9 100644 --- a/src/USER-COLVARS/group_ndx.cpp +++ b/src/USER-COLVARS/group_ndx.cpp @@ -56,8 +56,8 @@ void Group2Ndx::command(int narg, char **arg) if (comm->me == 0) { fp = fopen(arg[0], "w"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open index file for writing: {}", - utils::getsyserror())); + error->one(FLERR,"Cannot open index file for writing: {}", + utils::getsyserror()); utils::logmesg(lmp,"Writing groups to index file {}:\n",arg[0]); } diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index 6b9a69ccd3..452bd681b1 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -86,8 +86,8 @@ void Ndx2Group::command(int narg, char **arg) if (comm->me == 0) { fp = fopen(arg[0], "r"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open index file for reading: {}", - utils::getsyserror())); + error->one(FLERR,"Cannot open index file for reading: {}", + utils::getsyserror()); utils::logmesg(lmp,"Reading groups from index file {}:\n",arg[0]); } diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index 90eedb1127..39c0ddc9d1 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -390,8 +390,8 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep) fp = fopen(nName.c_str(),"w"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open fix saed/vtk file {}: {}", - nName,utils::getsyserror())); + error->one(FLERR,"Cannot open fix saed/vtk file {}: {}", + nName,utils::getsyserror()); } fprintf(fp,"# vtk DataFile Version 3.0 c_%s\n",ids); @@ -512,8 +512,8 @@ void FixSAEDVTK::options(int narg, char **arg) fp = fopen(nName.c_str(),"w"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open fix saed/vtk file {}: {}", - nName,utils::getsyserror())); + error->one(FLERR,"Cannot open fix saed/vtk file {}: {}", + nName,utils::getsyserror()); } iarg += 2; } else if (strcmp(arg[iarg],"ave") == 0) { diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index 396047fca9..37013bcf48 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -832,8 +832,8 @@ void PairExp6rx::read_file2(char *file) if (comm->me == 0) { fp = fopen(file,"r"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open polynomial file {}: {}", - file,utils::getsyserror())); + error->one(FLERR,"Cannot open polynomial file {}: {}", + file,utils::getsyserror()); } // one set of params can span multiple lines diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index b48decddba..a5cc75f567 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -59,15 +59,15 @@ FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) : // Construct manifold from factory: if (!ptr_m) - error->all(FLERR,fmt::format("Manifold pointer for manifold '{}' " - "was NULL for some reason", arg[3])); + error->all(FLERR,"Manifold pointer for manifold '{}' " + "was NULL for some reason", arg[3]); // After constructing the manifold, you can safely make // room for the parameters nvars = ptr_m->nparams(); if (narg < nvars+4) - error->all(FLERR,fmt::format("Manifold {} needs at least {} " - "argument(s)!", m_name, nvars)); + error->all(FLERR,"Manifold {} needs at least {} " + "argument(s)!", m_name, nvars); ptr_m->params = new double[nvars]; if (ptr_m->params == nullptr) { diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index 4b141a3bd1..1e86fff77d 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -105,8 +105,8 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, // Check if you have enough args: if (6 + nvars > narg) - error->all(FLERR,fmt::format("Not enough args for manifold {}, {} expected " - "but got {}\n",ptr_m->id(),nvars, narg - 6)); + error->all(FLERR,"Not enough args for manifold {}, {} expected " + "but got {}\n",ptr_m->id(),nvars, narg - 6); // Loop over manifold args: for (int i = 0; i < nvars; ++i) { int len = 0, offset = 0; @@ -145,7 +145,7 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, } argi += 2; } else if (error_on_unknown_keyword) { - error->all(FLERR,fmt::format("Error parsing arg \"{}\".\n",arg[argi])); + error->all(FLERR,"Error parsing arg \"{}\".\n",arg[argi]); } else { argi += 1; } diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index 67ab3522ad..f8a7713d77 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -143,7 +143,7 @@ void PairMEAMC::compute(int eflag, int vflag) meam_inst->meam_dens_final(nlocal,eflag_either,eflag_global,eflag_atom, &eng_vdwl,eatom,ntype,type,map,scale,errorflag); if (errorflag) - error->one(FLERR,fmt::format("MEAM library error {}",errorflag)); + error->one(FLERR,"MEAM library error {}",errorflag); comm->forward_comm_pair(this); @@ -213,7 +213,7 @@ void PairMEAMC::coeff(int narg, char **arg) std::string lib_file = utils::get_potential_file_path(arg[2]); if (lib_file.empty()) - error->all(FLERR,fmt::format("Cannot open MEAM library file {}",lib_file)); + error->all(FLERR,"Cannot open MEAM library file {}",lib_file); // find meam parameter file in arguments: // first word that is a file or "NULL" after the MEAM library file @@ -249,9 +249,9 @@ void PairMEAMC::coeff(int narg, char **arg) nlibelements = paridx - 3; if (nlibelements < 1) error->all(FLERR,"Incorrect args for pair coefficients"); if (nlibelements > maxelt) - error->all(FLERR,fmt::format("Too many elements extracted from MEAM " + error->all(FLERR,"Too many elements extracted from MEAM " "library (current limit: {}). Increase " - "'maxelt' in meam.h and recompile.", maxelt)); + "'maxelt' in meam.h and recompile.", maxelt); for (int i = 0; i < nlibelements; i++) { libelements.push_back(arg[i+3]); @@ -413,8 +413,8 @@ void PairMEAMC::read_global_meamc_file(const std::string &globalfile) std::string lattice_type = values.next_string(); if (!MEAM::str_to_lat(lattice_type.c_str(), true, lat[index])) - error->one(FLERR,fmt::format("Unrecognized lattice type in MEAM " - "library file: {}", lattice_type)); + error->one(FLERR,"Unrecognized lattice type in MEAM " + "library file: {}", lattice_type); // store parameters @@ -541,8 +541,8 @@ void PairMEAMC::read_user_meamc_file(const std::string &userfile) for (which = 0; which < nkeywords; which++) if (keyword == keywords[which]) break; if (which == nkeywords) - error->all(FLERR,fmt::format("Keyword {} in MEAM parameter file not " - "recognized", keyword)); + error->all(FLERR,"Keyword {} in MEAM parameter file not " + "recognized", keyword); nindex = nparams - 2; for (int i = 0; i < nindex; i++) index[i] = values.next_int() - 1; @@ -552,8 +552,8 @@ void PairMEAMC::read_user_meamc_file(const std::string &userfile) std::string lattice_type = values.next_string(); lattice_t latt; if (!MEAM::str_to_lat(lattice_type, false, latt)) - error->all(FLERR, fmt::format("Unrecognized lattice type in MEAM " - "parameter file: {}", lattice_type)); + error->all(FLERR, "Unrecognized lattice type in MEAM " + "parameter file: {}", lattice_type); value = latt; } else value = values.next_double(); @@ -568,7 +568,7 @@ void PairMEAMC::read_user_meamc_file(const std::string &userfile) "expected more indices", "has out of range element index"}; if ((errorflag < 0) || (errorflag > 3)) errorflag = 0; - error->all(FLERR, fmt::format("Error in MEAM parameter file: keyword {} {}", keyword, descr[errorflag])); + error->all(FLERR,"Error in MEAM parameter file: keyword {} {}", keyword, descr[errorflag]); } } } diff --git a/src/USER-MESONT/pair_mesocnt.cpp b/src/USER-MESONT/pair_mesocnt.cpp index f460e3aebb..3a56c69d2d 100644 --- a/src/USER-MESONT/pair_mesocnt.cpp +++ b/src/USER-MESONT/pair_mesocnt.cpp @@ -758,7 +758,7 @@ void PairMesoCNT::read_file() fp = utils::open_potential(file,lmp,nullptr); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open mesocnt file: {}",file)); + error->one(FLERR,"Cannot open mesocnt file: {}",file); utils::sfgets(FLERR,line,MAXLINE,fp,file,error); @@ -768,14 +768,14 @@ void PairMesoCNT::read_file() num = sscanf(line,"%d %d %d %d", &uinf_points,&gamma_points,&phi_points,&usemi_points); if (num != 4) - error->one(FLERR,fmt::format("Could not correctly parse line 2 in " - "mesocnt file: {}",file)); + error->one(FLERR,"Could not correctly parse line 2 in " + "mesocnt file: {}",file); utils::sfgets(FLERR,line,MAXLINE,fp,file,error); num = sscanf(line,"%lg %lg %lg %lg",&r_ang,&sig_ang,&delta1,&delta2); if (num != 4) - error->one(FLERR,fmt::format("Could not correctly parse line 3 in " - "mesocnt file: {}",file)); + error->one(FLERR,"Could not correctly parse line 3 in " + "mesocnt file: {}",file); } MPI_Bcast(&uinf_points,1,MPI_INT,0,world); @@ -844,7 +844,7 @@ void PairMesoCNT::read_data(FILE *fp, double *data, for (int i = 0; i < ninput; i++) { if (nullptr == fgets(line,MAXLINE,fp)) - error->one(FLERR,fmt::format("Premature end of file in pair table: {}",file)); + error->one(FLERR,"Premature end of file in pair table: {}",file); if (i > 0) xtemp = x; if (2 != sscanf(line,"%lg %lg",&x,&data[i])) cerror++; @@ -897,7 +897,7 @@ void PairMesoCNT::read_data(FILE *fp, double **data, if (i > 0) xtemp = x; for (int j = 0; j < ninput; j++) { if (nullptr == fgets(line,MAXLINE,fp)) - error->one(FLERR,fmt::format("Premature end of file in pair table: {}",file)); + error->one(FLERR,"Premature end of file in pair table: {}",file); if (j > 0) ytemp = y; if (3 != sscanf(line,"%lg %lg %lg",&x,&y,&data[i][j])) cerror++; diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index ffbc9aad31..8ea5c7e21e 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -784,10 +784,10 @@ void DihedralTable::coeff(int narg, char **arg) // --- and resolve issues with periodicity --- if (tb->ninput < 2) - error->all(FLERR,fmt::format("Invalid dihedral table length: {}",arg[2])); + error->all(FLERR,"Invalid dihedral table length: {}",arg[2]); else if ((tb->ninput == 2) && (tabstyle == SPLINE)) - error->all(FLERR,fmt::format("Invalid dihedral spline table length: {} " - "(Try linear)",arg[2])); + error->all(FLERR,"Invalid dihedral spline table length: {} " + "(Try linear)",arg[2]); // check for monotonicity for (int i=0; i < tb->ninput-1; i++) { @@ -805,12 +805,12 @@ void DihedralTable::coeff(int narg, char **arg) double phihi = tb->phifile[tb->ninput-1]; if (tb->use_degrees) { if ((phihi - philo) >= 360) - error->all(FLERR,fmt::format("Dihedral table angle range must be < 360 " - "degrees ({}).",arg[2])); + error->all(FLERR,"Dihedral table angle range must be < 360 " + "degrees ({}).",arg[2]); } else { if ((phihi - philo) >= MY_2PI) - error->all(FLERR,fmt::format("Dihedral table angle range must be < 2*PI " - "radians ({}).",arg[2])); + error->all(FLERR,"Dihedral table angle range must be < 2*PI " + "radians ({}).",arg[2]); } // convert phi from degrees to radians @@ -1268,8 +1268,8 @@ void DihedralTable::param_extract(Table *tb, char *line) //else if (word == "EQ") { // tb->theta0 = values.next_double(); //} - else error->one(FLERR,fmt::format("Invalid keyword in dihedral angle " - "table parameters ({})", word)); + else error->one(FLERR,"Invalid keyword in dihedral angle " + "table parameters ({})", word); } } catch (TokenizerException &e) { error->one(FLERR, e.what()); diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index 02e6d3e5da..bae402145d 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -508,10 +508,10 @@ void DihedralTableCut::coeff(int narg, char **arg) // --- and resolve issues with periodicity --- if (tb->ninput < 2) - error->all(FLERR,fmt::format("Invalid dihedral table length: {}",arg[5])); + error->all(FLERR,"Invalid dihedral table length: {}",arg[5]); else if ((tb->ninput == 2) && (tabstyle == SPLINE)) - error->all(FLERR,fmt::format("Invalid dihedral spline table length: {} " - "(Try linear)",arg[5])); + error->all(FLERR,"Invalid dihedral spline table length: {} " + "(Try linear)",arg[5]); // check for monotonicity for (int i=0; i < tb->ninput-1; i++) { @@ -529,12 +529,12 @@ void DihedralTableCut::coeff(int narg, char **arg) double phihi = tb->phifile[tb->ninput-1]; if (tb->use_degrees) { if ((phihi - philo) >= 360) - error->all(FLERR,fmt::format("Dihedral table angle range must be < 360 " - "degrees ({})",arg[5])); + error->all(FLERR,"Dihedral table angle range must be < 360 " + "degrees ({})",arg[5]); } else { if ((phihi - philo) >= MY_2PI) - error->all(FLERR,fmt::format("Dihedral table angle range must be < 2*PI " - "radians ({})",arg[5])); + error->all(FLERR,"Dihedral table angle range must be < 2*PI " + "radians ({})",arg[5]); } // convert phi from degrees to radians diff --git a/src/USER-MISC/fix_orient_eco.cpp b/src/USER-MISC/fix_orient_eco.cpp index b8b3a00354..e247d8601e 100644 --- a/src/USER-MISC/fix_orient_eco.cpp +++ b/src/USER-MISC/fix_orient_eco.cpp @@ -95,8 +95,8 @@ FixOrientECO::FixOrientECO(LAMMPS *lmp, int narg, char **arg) : FILE *infile = utils::open_potential(dir_filename,lmp,nullptr); if (infile == nullptr) - error->one(FLERR,fmt::format("Cannot open fix orient/eco file {}: {}", - dir_filename, utils::getsyserror())); + error->one(FLERR,"Cannot open fix orient/eco file {}: {}", + dir_filename, utils::getsyserror()); for (int i = 0; i < 6; ++i) { result = fgets(line, IMGMAX, infile); if (!result) error->one(FLERR, "Fix orient/eco file read failed"); diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index d4023b6011..20f6853bf6 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -399,8 +399,8 @@ void FixTTMMod::read_parameters(const char *filename) char line[MAXLINE]; std::string name = utils::get_potential_file_path(filename); if (name.empty()) - error->one(FLERR,fmt::format("Cannot open input file: {}", - filename)); + error->one(FLERR,"Cannot open input file: {}", + filename); FILE *fpr = fopen(name.c_str(),"r"); // C0 (metal) @@ -550,8 +550,8 @@ void FixTTMMod::read_initial_electron_temperatures(const char *filename) std::string name = utils::get_potential_file_path(filename); if (name.empty()) - error->one(FLERR,fmt::format("Cannot open input file: {}", - filename)); + error->one(FLERR,"Cannot open input file: {}", + filename); FILE *fpr = fopen(name.c_str(),"r"); // read initial electron temperature values from file diff --git a/src/USER-NETCDF/dump_netcdf.cpp b/src/USER-NETCDF/dump_netcdf.cpp index 025fec3933..bdd79d0d05 100644 --- a/src/USER-NETCDF/dump_netcdf.cpp +++ b/src/USER-NETCDF/dump_netcdf.cpp @@ -288,8 +288,8 @@ void DumpNetCDF::openfile() // Fixme! Perform checks if dimensions and variables conform with // data structure standard. if (not utils::file_is_readable(filecurrent)) - error->all(FLERR, fmt::format("cannot append to non-existent file {}", - filecurrent)); + error->all(FLERR, "cannot append to non-existent file {}", + filecurrent); if (singlefile_opened) return; singlefile_opened = 1; diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.cpp b/src/USER-NETCDF/dump_netcdf_mpiio.cpp index 726b51ba3f..cd83d1cbff 100644 --- a/src/USER-NETCDF/dump_netcdf_mpiio.cpp +++ b/src/USER-NETCDF/dump_netcdf_mpiio.cpp @@ -284,8 +284,8 @@ void DumpNetCDFMPIIO::openfile() // Fixme! Perform checks if dimensions and variables conform with // data structure standard. if (not utils::file_is_readable(filecurrent)) - error->all(FLERR, fmt::format("cannot append to non-existent file {}", - filecurrent)); + error->all(FLERR, "cannot append to non-existent file {}", + filecurrent); MPI_Offset index[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS]; double d[1]; diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp index 1312953180..7450470095 100644 --- a/src/USER-OMP/reaxc_init_md_omp.cpp +++ b/src/USER-OMP/reaxc_init_md_omp.cpp @@ -129,29 +129,29 @@ void InitializeOMP(reax_system *system, control_params *control, "Mpi_data could not be initialized! Terminating."); if (Init_System(system,control,msg) == FAILURE) - error->one(FLERR,fmt::format("Error on: {}. System could not be " - "initialized! Terminating.",msg)); + error->one(FLERR,"Error on: {}. System could not be " + "initialized! Terminating.",msg); if (Init_Simulation_Data(system,control,data,msg) == FAILURE) - error->one(FLERR,fmt::format("Error on: {}. Sim_data could not be " - "initialized! Terminating.",msg)); + error->one(FLERR,"Error on: {}. Sim_data could not be " + "initialized! Terminating.",msg); if (Init_Workspace(system,control,workspace,msg) == FAILURE) error->one(FLERR,"init_workspace: not enough memory. " "Workspace could not be initialized. Terminating."); if (Init_ListsOMP(system,control,data,workspace,lists,mpi_data,msg) == FAILURE) - error->one(FLERR,fmt::format("Error on: {}. System could not be " - "initialized. Terminating.",msg)); + error->one(FLERR,"Error on: {}. System could not be " + "initialized. Terminating.",msg); if (Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) - error->one(FLERR,fmt::format("Error on: {}. Could not open output files! " - "Terminating.",msg)); + error->one(FLERR,"Error on: {}. Could not open output files! " + "Terminating.",msg); if (control->tabulate) if (Init_Lookup_Tables(system,control,workspace,mpi_data,msg) == FAILURE) - error->one(FLERR,fmt::format("Error on: {}. Could not create lookup " - "table. Terminating.",msg)); + error->one(FLERR,"Error on: {}. Could not create lookup " + "table. Terminating.",msg); Init_Force_FunctionsOMP(control); } diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index ae13859968..d146cb91bd 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -156,7 +156,7 @@ void PairPACE::compute(int eflag, int vflag) { firstneigh = list->firstneigh; if (inum != nlocal) - error->all(FLERR,fmt::format("inum: {} nlocal: {} are different",inum, nlocal)); + error->all(FLERR,"inum: {} nlocal: {} are different",inum, nlocal); // Aidan Thompson told RD (26 July 2019) that practically always holds: // inum = nlocal @@ -329,7 +329,7 @@ void PairPACE::coeff(int narg, char **arg) { char *elemname = elemtypes[i - 1]; int atomic_number = AtomicNumberByName_pace(elemname); if (atomic_number == -1) - error->all(FLERR,fmt::format("'{}' is not a valid element\n", elemname)); + error->all(FLERR,"'{}' is not a valid element\n", elemname); SPECIES_TYPE mu = aceimpl->basis_set->get_species_index_by_name(elemname); if (mu != -1) { @@ -339,7 +339,7 @@ void PairPACE::coeff(int narg, char **arg) { map[i] = mu; aceimpl->ace->element_type_mapping(i) = mu; // set up LAMMPS atom type to ACE species mapping for ace evaluator } else { - error->all(FLERR, fmt::format("Element {} is not supported by ACE-potential from file {}", elemname,potential_file_name)); + error->all(FLERR,"Element {} is not supported by ACE-potential from file {}", elemname,potential_file_name); } } diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp index 222f3fa1d2..1f8fe1c9cb 100644 --- a/src/USER-PHONON/fix_phonon.cpp +++ b/src/USER-PHONON/fix_phonon.cpp @@ -180,8 +180,8 @@ FixPhonon::FixPhonon(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) if (me == 0) { flog = fopen(logfile, "w"); if (flog == nullptr) - error->one(FLERR,fmt::format("Can not open output file {}: {}", - logfile,utils::getsyserror())); + error->one(FLERR,"Can not open output file {}: {}", + logfile,utils::getsyserror()); fprintf(flog,"############################################################\n"); fprintf(flog,"# group name of the atoms under study : %s\n", group->names[igroup]); fprintf(flog,"# total number of atoms in the group : %d\n", ngroup); @@ -555,8 +555,8 @@ void FixPhonon::readmap() char line[MAXLINE]; FILE *fp = fopen(mapfile, "r"); if (fp == nullptr) - error->all(FLERR,fmt::format("Cannot open input map file {}: {}", - mapfile, utils::getsyserror())); + error->all(FLERR,"Cannot open input map file {}: {}", + mapfile, utils::getsyserror()); if (fgets(line,MAXLINE,fp) == nullptr) error->all(FLERR,"Error while reading header of mapping file!"); diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp index 20a6c98cb8..365ab3b414 100644 --- a/src/USER-QUIP/pair_quip.cpp +++ b/src/USER-QUIP/pair_quip.cpp @@ -253,8 +253,8 @@ void PairQUIP::coeff(int narg, char **arg) int n = atom->ntypes; if (narg != (4+n)) - error->all(FLERR,fmt::format("Number of arguments {} is not correct, " - "it should be {}", narg, 4+n)); + error->all(FLERR,"Number of arguments {} is not correct, " + "it should be {}", narg, 4+n); // ensure I,J args are * * diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp index 9d10966d3b..7794a16ecd 100644 --- a/src/USER-REAXC/reaxc_init_md.cpp +++ b/src/USER-REAXC/reaxc_init_md.cpp @@ -231,29 +231,29 @@ void Initialize(reax_system *system, control_params *control, "Mpi_data could not be initialized! Terminating."); if (Init_System(system,control,msg) == FAILURE) - error->one(FLERR,fmt::format("Error on: {}. System could not be " - "initialized! Terminating.",msg)); + error->one(FLERR,"Error on: {}. System could not be " + "initialized! Terminating.",msg); if (Init_Simulation_Data( system,control,data,msg) == FAILURE) - error->one(FLERR,fmt::format("Error on: {}. Sim_data could not be " - "initialized! Terminating.",msg)); + error->one(FLERR,"Error on: {}. Sim_data could not be " + "initialized! Terminating.",msg); if (Init_Workspace( system,control,workspace,msg) == FAILURE) error->one(FLERR,"init_workspace: not enough memory. " "Workspace could not be initialized. Terminating."); if (Init_Lists(system, control, data, workspace, lists, mpi_data, msg) ==FAILURE) - error->one(FLERR,fmt::format("Error on: {}. System could not be " - "initialized. Terminating.",msg)); + error->one(FLERR,"Error on: {}. System could not be " + "initialized. Terminating.",msg); if (Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) - error->one(FLERR,fmt::format("Error on: {}. Could not open output files! " - "Terminating.",msg)); + error->one(FLERR,"Error on: {}. Could not open output files! " + "Terminating.",msg); if (control->tabulate) if (Init_Lookup_Tables(system,control,workspace,mpi_data,msg) == FAILURE) - error->one(FLERR,fmt::format("Error on: {}. Could not create lookup " - "table. Terminating.",msg)); + error->one(FLERR,"Error on: {}. Could not create lookup " + "table. Terminating.",msg); Init_Force_Functions(control); diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index eec09cf58a..9ae5a86039 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -2481,20 +2481,20 @@ int AtomVec::process_fields(char *str, const char *default_str, Method *method) for (match = 0; match < nperatom; match++) if (field == peratom[match].name) break; if (match == nperatom) - error->all(FLERR,fmt::format("Peratom field {} not recognized", field)); + error->all(FLERR,"Peratom field {} not recognized", field); index[i] = match; // error if field appears multiple times for (match = 0; match < i; match++) if (index[i] == index[match]) - error->all(FLERR,fmt::format("Peratom field {} is repeated", field)); + error->all(FLERR,"Peratom field {} is repeated", field); // error if field is in default str for (match = 0; match < ndef; match++) if (field == def_words[match]) - error->all(FLERR,fmt::format("Peratom field {} is a default", field)); + error->all(FLERR,"Peratom field {} is a default", field); } return nfield; diff --git a/src/balance.cpp b/src/balance.cpp index bf037e8f8f..8be98d4d19 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -371,9 +371,8 @@ void Balance::command(int narg, char **arg) bigint nblocal = atom->nlocal; MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); if (natoms != atom->natoms) - error->all(FLERR,fmt::format("Lost atoms via balance: " - "original {} current {}", - atom->natoms,natoms).c_str()); + error->all(FLERR,"Lost atoms via balance: original {} current {}", + atom->natoms,natoms); // imbfinal = final imbalance // set disable = 1, so weights no longer migrate with atoms @@ -478,8 +477,8 @@ void Balance::options(int iarg, int narg, char **arg) if (outflag && comm->me == 0) { fp = fopen(arg[outarg],"w"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open (fix) balance output file {}: {}", - arg[outarg], utils::getsyserror())); + error->one(FLERR,"Cannot open (fix) balance output file {}: {}", + arg[outarg], utils::getsyserror()); } } diff --git a/src/bond.cpp b/src/bond.cpp index 570d921abb..049d5da823 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -274,9 +274,9 @@ void Bond::write_file(int narg, char **arg) if (utils::file_is_readable(table_file)) { std::string units = utils::get_potential_units(table_file,"table"); if (!units.empty() && (units != update->unit_style)) { - error->one(FLERR,fmt::format("Trying to append to a table file " + error->one(FLERR,"Trying to append to a table file " "with UNITS: {} while units are {}", - units, update->unit_style)); + units, update->unit_style); } std::string date = utils::get_potential_date(table_file,"table"); utils::logmesg(lmp,"Appending to table file {} with " @@ -293,8 +293,8 @@ void Bond::write_file(int narg, char **arg) datebuf, update->unit_style); } if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open bond_write file {}: {}", - arg[4], utils::getsyserror())); + error->one(FLERR,"Cannot open bond_write file {}: {}", + arg[4], utils::getsyserror()); } // initialize potentials before evaluating bond potential diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index aba0178368..8598c1ca6e 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -298,8 +298,8 @@ void CreateBonds::many() if (!newton_bond || tag[i] < tag[j]) { if (num_bond[i] == atom->bond_per_atom) - error->one(FLERR,fmt::format("New bond exceeded bonds per atom limit " - " of {} in create_bonds",atom->bond_per_atom)); + error->one(FLERR,"New bond exceeded bonds per atom limit " + " of {} in create_bonds",atom->bond_per_atom); bond_type[i][num_bond[i]] = btype; bond_atom[i][num_bond[i]] = tag[j]; num_bond[i]++; diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp index 828c20af30..c224b9d292 100644 --- a/src/dump_movie.cpp +++ b/src/dump_movie.cpp @@ -60,8 +60,8 @@ void DumpMovie::openfile() #endif if (fp == nullptr) - error->one(FLERR,fmt::format("Failed to open FFmpeg pipeline to " - "file {}",filename)); + error->one(FLERR,"Failed to open FFmpeg pipeline to " + "file {}",filename); } } /* ---------------------------------------------------------------------- */ diff --git a/src/fix.cpp b/src/fix.cpp index 14c04bf4b5..e3e2b12ed2 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -175,8 +175,7 @@ void Fix::modify_params(int narg, char **arg) void::Fix::set_molecule(int, tagint, int, double *, double *, double *) { - error->all(FLERR,fmt::format("Molecule update not implemented for " - "fix {}", style)); + error->all(FLERR,"Molecule update not implemented for fix {}", style); } /* ---------------------------------------------------------------------- diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index b0a99d332a..87f1bf8b4c 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -206,8 +206,8 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) : if (comm->me == 0) { fp = fopen(arg[iarg+1],"w"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open fix ave/chunk file {}: {}", - arg[iarg+1], utils::getsyserror())); + error->one(FLERR,"Cannot open fix ave/chunk file {}: {}", + arg[iarg+1], utils::getsyserror()); } iarg += 2; } else if (strcmp(arg[iarg],"overwrite") == 0) { diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 81ca94cdc8..8793793682 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -129,8 +129,8 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg): if (me == 0) { fp = fopen(arg[iarg+1],"w"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open fix ave/correlate file {}:"" {}", - arg[iarg+1], utils::getsyserror())); + error->one(FLERR,"Cannot open fix ave/correlate file {}:"" {}", + arg[iarg+1], utils::getsyserror()); } iarg += 2; } else if (strcmp(arg[iarg],"overwrite") == 0) { diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index 0f6943ac31..7cacbda407 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -946,8 +946,8 @@ void FixAveHisto::options(int iarg, int narg, char **arg) if (me == 0) { fp = fopen(arg[iarg+1],"w"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open fix ave/histo file {}: {}", - arg[iarg+1], utils::getsyserror())); + error->one(FLERR,"Cannot open fix ave/histo file {}: {}", + arg[iarg+1], utils::getsyserror()); } iarg += 2; } else if (strcmp(arg[iarg],"kind") == 0) { diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index 7ecb88ddab..2a6e769799 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -1029,8 +1029,8 @@ void FixAveTime::options(int iarg, int narg, char **arg) if (me == 0) { fp = fopen(arg[iarg+1],"w"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open fix ave/time file {}: {}", - arg[iarg+1], utils::getsyserror())); + error->one(FLERR,"Cannot open fix ave/time file {}: {}", + arg[iarg+1], utils::getsyserror()); } iarg += 2; } else if (strcmp(arg[iarg],"ave") == 0) { diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index 11e041fcf4..c27e523efe 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -77,8 +77,8 @@ void FixEnforce2D::init() if (myindex < 0) flist[nfixlist++] = modify->fix[i]; else - error->all(FLERR,fmt::format("Fix enforce2d must be defined after fix {}", - modify->fix[i]->style)); + error->all(FLERR,"Fix enforce2d must be defined after fix {}", + modify->fix[i]->style); } if (modify->fix[i] == this) myindex = i; } diff --git a/src/fix_print.cpp b/src/fix_print.cpp index c6747ee1ee..43bab3f848 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -62,8 +62,8 @@ FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w"); else fp = fopen(arg[iarg+1],"a"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open fix print file {}: {}", - arg[iarg+1], utils::getsyserror())); + error->one(FLERR,"Cannot open fix print file {}: {}", + arg[iarg+1], utils::getsyserror()); } iarg += 2; } else if (strcmp(arg[iarg],"screen") == 0) { diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 6ce5b6360b..82c15eea1b 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -228,13 +228,13 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, try { ValueTokenizer values(buf); if ((int)values.count() != nvalue+1) - error->all(FLERR,fmt::format("Incorrect format in {} section " - "of data file: {}",keyword,buf)); + error->all(FLERR,"Incorrect format in {} section " + "of data file: {}",keyword,buf); itag = values.next_tagint() + id_offset; if (itag <= 0 || itag > map_tag_max) - error->all(FLERR,fmt::format("Invalid atom ID {} in {} section of " - "data file",itag, keyword)); + error->all(FLERR,"Invalid atom ID {} in {} section of " + "data file",itag, keyword); // assign words in line to per-atom vectors @@ -254,8 +254,8 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, } } } catch (TokenizerException &e) { - error->all(FLERR,fmt::format("Invalid format in {} section of data " - "file '{}': {}",keyword, buf,e.what())); + error->all(FLERR,"Invalid format in {} section of data " + "file '{}': {}",keyword, buf,e.what()); } buf = next + 1; } diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index ff61703c1a..b7321dd530 100644 --- a/src/fix_restrain.cpp +++ b/src/fix_restrain.cpp @@ -272,15 +272,15 @@ void FixRestrain::restrain_bond(int m) if (newton_bond) { if (i2 == -1 || i2 >= nlocal) return; if (i1 == -1) - error->one(FLERR,fmt::format("Restrain atoms {} {} missing on " + error->one(FLERR,"Restrain atoms {} {} missing on " "proc {} at step {}", ids[m][0],ids[m][1], - comm->me,update->ntimestep)); + comm->me,update->ntimestep); } else { if ((i1 == -1 || i1 >= nlocal) && (i2 == -1 || i2 >= nlocal)) return; if (i1 == -1 || i2 == -1) - error->one(FLERR,fmt::format("Restrain atoms {} {} missing on " + error->one(FLERR,"Restrain atoms {} {} missing on " "proc {} at step {}", ids[m][0],ids[m][1], - comm->me,update->ntimestep)); + comm->me,update->ntimestep); } delx = x[i1][0] - x[i2][0]; @@ -345,15 +345,15 @@ void FixRestrain::restrain_lbound(int m) if (newton_bond) { if (i2 == -1 || i2 >= nlocal) return; if (i1 == -1) - error->one(FLERR,fmt::format("Restrain atoms {} {} missing on " + error->one(FLERR,"Restrain atoms {} {} missing on " "proc {} at step {}",ids[m][0],ids[m][1], - comm->me,update->ntimestep)); + comm->me,update->ntimestep); } else { if ((i1 == -1 || i1 >= nlocal) && (i2 == -1 || i2 >= nlocal)) return; if (i1 == -1 || i2 == -1) - error->one(FLERR,fmt::format("Restrain atoms {} {} missing on " + error->one(FLERR,"Restrain atoms {} {} missing on " "proc {} at step {}",ids[m][0],ids[m][1], - comm->me,update->ntimestep)); + comm->me,update->ntimestep); } delx = x[i1][0] - x[i2][0]; @@ -427,16 +427,16 @@ void FixRestrain::restrain_angle(int m) if (newton_bond) { if (i2 == -1 || i2 >= nlocal) return; if (i1 == -1 || i3 == -1) - error->one(FLERR,fmt::format("Restrain atoms {} {} {} missing on " + error->one(FLERR,"Restrain atoms {} {} {} missing on " "proc {} at step {}",ids[m][0],ids[m][1], - ids[m][2],comm->me,update->ntimestep)); + ids[m][2],comm->me,update->ntimestep); } else { if ((i1 == -1 || i1 >= nlocal) && (i2 == -1 || i2 >= nlocal) && (i3 == -1 || i3 >= nlocal)) return; if (i1 == -1 || i2 == -1 || i3 == -1) - error->one(FLERR,fmt::format("Restrain atoms {} {} {} missing on " + error->one(FLERR,"Restrain atoms {} {} {} missing on " "proc {} at step {}",ids[m][0],ids[m][1], - ids[m][2],comm->me,update->ntimestep)); + ids[m][2],comm->me,update->ntimestep); } // 1st bond @@ -547,18 +547,18 @@ void FixRestrain::restrain_dihedral(int m) if (newton_bond) { if (i2 == -1 || i2 >= nlocal) return; if (i1 == -1 || i3 == -1 || i4 == -1) - error->one(FLERR,fmt::format("Restrain atoms {} {} {} {} missing on " + error->one(FLERR,"Restrain atoms {} {} {} {} missing on " "proc {} at step {}",ids[m][0],ids[m][1], ids[m][2],ids[m][3],comm->me, - update->ntimestep)); + update->ntimestep); } else { if ((i1 == -1 || i1 >= nlocal) && (i2 == -1 || i2 >= nlocal) && (i3 == -1 || i3 >= nlocal) && (i4 == -1 || i3 >= nlocal)) return; if (i1 == -1 || i2 == -1 || i3 == -1 || i4 == -1) - error->one(FLERR,fmt::format("Restrain atoms {} {} {} {} missing on " + error->one(FLERR,"Restrain atoms {} {} {} {} missing on " "proc {} at step {}",ids[m][0],ids[m][1], ids[m][2],ids[m][3],comm->me, - update->ntimestep)); + update->ntimestep); } // 1st bond diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index f462b0633b..ea76ca137b 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -74,8 +74,8 @@ nfileevery(0), fp(nullptr), xf(nullptr), xold(nullptr) if (me == 0) { fp = fopen(arg[6],"w"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open fix tmd file {}: {}", - arg[6], utils::getsyserror())); + error->one(FLERR,"Cannot open fix tmd file {}: {}", + arg[6], utils::getsyserror()); fprintf(fp,"%s %s\n","# Step rho_target rho_old gamma_back", "gamma_forward lambda work_lambda work_analytical"); } @@ -540,8 +540,8 @@ void FixTMD::open(char *file) } if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open file {}: {}", - file, utils::getsyserror())); + error->one(FLERR,"Cannot open file {}: {}", + file, utils::getsyserror()); } /* ---------------------------------------------------------------------- */ diff --git a/src/force.cpp b/src/force.cpp index 80f5ef22a7..aa93b0af7d 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -173,8 +173,8 @@ void Force::init() // check if pair style must be specified after restart if (pair_restart) { if (!pair) - error->all(FLERR,fmt::format("Must re-specify non-restarted pair style " - "({}) after read_restart", pair_restart)); + error->all(FLERR,"Must re-specify non-restarted pair style " + "({}) after read_restart", pair_restart); } if (kspace) kspace->init(); // kspace must come before pair diff --git a/src/group.cpp b/src/group.cpp index 997214cbc7..4a898106e5 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -321,8 +321,8 @@ void Group::assign(int narg, char **arg) delta = values.next_tagint(); } else throw TokenizerException("Syntax error",""); } catch (TokenizerException &e) { - error->all(FLERR,fmt::format("Incorrect range string " - "'{}': {}",arg[iarg],e.what())); + error->all(FLERR,"Incorrect range string " + "'{}': {}",arg[iarg],e.what()); } if (delta < 1) error->all(FLERR,"Illegal range increment value"); diff --git a/src/input.cpp b/src/input.cpp index d3352b380a..04ff4c70da 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -270,7 +270,7 @@ void Input::file() // execute the command if (execute_command() && line) - error->all(FLERR,fmt::format("Unknown command: {}",line)); + error->all(FLERR,"Unknown command: {}",line); } } @@ -302,8 +302,8 @@ void Input::file(const char *filename) infile = fopen(filename,"r"); if (infile == nullptr) - error->one(FLERR,fmt::format("Cannot open input script {}: {}", - filename, utils::getsyserror())); + error->one(FLERR,"Cannot open input script {}: {}", + filename, utils::getsyserror()); infiles[nfile++] = infile; } @@ -359,7 +359,7 @@ char *Input::one(const std::string &single) // execute the command and return its name if (execute_command()) - error->all(FLERR,fmt::format("Unknown command: {}",line)); + error->all(FLERR,"Unknown command: {}",line); return command; } @@ -613,8 +613,8 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag) } if (value == nullptr) - error->one(FLERR,fmt::format("Substitution for illegal " - "variable {}",var)); + error->one(FLERR,"Substitution for illegal " + "variable {}",var); // check if storage in str2 needs to be expanded // re-initialize ptr and ptr2 to the point beyond the variable. @@ -971,8 +971,8 @@ void Input::include() infile = fopen(arg[0],"r"); if (infile == nullptr) - error->one(FLERR,fmt::format("Cannot open input script {}: {}", - arg[0], utils::getsyserror())); + error->one(FLERR,"Cannot open input script {}: {}", + arg[0], utils::getsyserror()); infiles[nfile++] = infile; } @@ -1005,8 +1005,8 @@ void Input::jump() if (infile && infile != stdin) fclose(infile); infile = fopen(arg[0],"r"); if (infile == nullptr) - error->one(FLERR,fmt::format("Cannot open input script {}: {}", - arg[0], utils::getsyserror())); + error->one(FLERR,"Cannot open input script {}: {}", + arg[0], utils::getsyserror()); infiles[nfile-1] = infile; } @@ -1047,8 +1047,8 @@ void Input::log() else logfile = fopen(arg[0],"w"); if (logfile == nullptr) - error->one(FLERR,fmt::format("Cannot open logfile {}: {}", - arg[0], utils::getsyserror())); + error->one(FLERR,"Cannot open logfile {}: {}", + arg[0], utils::getsyserror()); } if (universe->nworlds == 1) universe->ulogfile = logfile; @@ -1123,8 +1123,8 @@ void Input::print() if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w"); else fp = fopen(arg[iarg+1],"a"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open print file {}: {}", - arg[iarg+1], utils::getsyserror())); + error->one(FLERR,"Cannot open print file {}: {}", + arg[iarg+1], utils::getsyserror()); } iarg += 2; } else if (strcmp(arg[iarg],"screen") == 0) { diff --git a/src/lammps.cpp b/src/lammps.cpp index 277ec4414f..cb7aaf9182 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -490,8 +490,8 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : else if (strcmp(arg[inflag], "none") == 0) infile = stdin; else infile = fopen(arg[inflag],"r"); if (infile == nullptr) - error->one(FLERR,fmt::format("Cannot open input script {}: {}", - arg[inflag], utils::getsyserror())); + error->one(FLERR,"Cannot open input script {}: {}", + arg[inflag], utils::getsyserror()); } if ((universe->me == 0) && !helpflag) @@ -515,16 +515,16 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : str = fmt::format("screen.{}",universe->iworld); screen = fopen(str.c_str(),"w"); if (screen == nullptr) - error->one(FLERR,fmt::format("Cannot open screen file {}: {}", - str,utils::getsyserror())); + error->one(FLERR,"Cannot open screen file {}: {}", + str,utils::getsyserror()); } else if (strcmp(arg[screenflag],"none") == 0) { screen = nullptr; } else { str = fmt::format("{}.{}",arg[screenflag],universe->iworld); screen = fopen(str.c_str(),"w"); if (screen == nullptr) - error->one(FLERR,fmt::format("Cannot open screen file {}: {}", - arg[screenflag],utils::getsyserror())); + error->one(FLERR,"Cannot open screen file {}: {}", + arg[screenflag],utils::getsyserror()); } } else if (strcmp(arg[partscreenflag],"none") == 0) { screen = nullptr; @@ -532,8 +532,8 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : str = fmt::format("{}.{}",arg[partscreenflag],universe->iworld); screen = fopen(str.c_str(),"w"); if (screen == nullptr) - error->one(FLERR,fmt::format("Cannot open screen file {}: {}", - str,utils::getsyserror())); + error->one(FLERR,"Cannot open screen file {}: {}", + str,utils::getsyserror()); } if (partlogflag == 0) { @@ -541,16 +541,16 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : str = fmt::format("log.lammps.{}",universe->iworld); logfile = fopen(str.c_str(),"w"); if (logfile == nullptr) - error->one(FLERR,fmt::format("Cannot open logfile {}: {}", - str, utils::getsyserror())); + error->one(FLERR,"Cannot open logfile {}: {}", + str, utils::getsyserror()); } else if (strcmp(arg[logflag],"none") == 0) { logfile = nullptr; } else { str = fmt::format("{}.{}",arg[logflag],universe->iworld); logfile = fopen(str.c_str(),"w"); if (logfile == nullptr) - error->one(FLERR,fmt::format("Cannot open logfile {}: {}", - str, utils::getsyserror())); + error->one(FLERR,"Cannot open logfile {}: {}", + str, utils::getsyserror()); } } else if (strcmp(arg[partlogflag],"none") == 0) { logfile = nullptr; @@ -558,15 +558,15 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : str = fmt::format("{}.{}",arg[partlogflag],universe->iworld); logfile = fopen(str.c_str(),"w"); if (logfile == nullptr) - error->one(FLERR,fmt::format("Cannot open logfile {}: {}", - str, utils::getsyserror())); + error->one(FLERR,"Cannot open logfile {}: {}", + str, utils::getsyserror()); } if (strcmp(arg[inflag], "none") != 0) { infile = fopen(arg[inflag],"r"); if (infile == nullptr) - error->one(FLERR,fmt::format("Cannot open input script {}: {}", - arg[inflag], utils::getsyserror())); + error->one(FLERR,"Cannot open input script {}: {}", + arg[inflag], utils::getsyserror()); } } diff --git a/src/library.cpp b/src/library.cpp index c51006f8d8..6565aa6630 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -4734,13 +4734,13 @@ void lammps_set_fix_external_callback(void *handle, char *id, FixExternalFnPtr c { int ifix = lmp->modify->find_fix(id); if (ifix < 0) - lmp->error->all(FLERR,fmt::format("Cannot find fix with ID '{}'!", id)); + lmp->error->all(FLERR,"Cannot find fix with ID '{}'!", id); Fix *fix = lmp->modify->fix[ifix]; if (strcmp("external",fix->style) != 0) - lmp->error->all(FLERR,fmt::format("Fix '{}' is not of style " - "external!", id)); + lmp->error->all(FLERR,"Fix '{}' is not of style " + "external!", id); FixExternal * fext = (FixExternal*) fix; fext->set_callback(callback, caller); @@ -4758,12 +4758,12 @@ void lammps_fix_external_set_energy_global(void *handle, char *id, { int ifix = lmp->modify->find_fix(id); if (ifix < 0) - lmp->error->all(FLERR,fmt::format("Can not find fix with ID '{}'!", id)); + lmp->error->all(FLERR,"Can not find fix with ID '{}'!", id); Fix *fix = lmp->modify->fix[ifix]; if (strcmp("external",fix->style) != 0) - lmp->error->all(FLERR,fmt::format("Fix '{}' is not of style external!", id)); + lmp->error->all(FLERR,"Fix '{}' is not of style external!", id); FixExternal * fext = (FixExternal*) fix; fext->set_energy_global(energy); @@ -4781,12 +4781,12 @@ void lammps_fix_external_set_virial_global(void *handle, char *id, { int ifix = lmp->modify->find_fix(id); if (ifix < 0) - lmp->error->all(FLERR,fmt::format("Can not find fix with ID '{}'!", id)); + lmp->error->all(FLERR,"Can not find fix with ID '{}'!", id); Fix *fix = lmp->modify->fix[ifix]; if (strcmp("external",fix->style) != 0) - lmp->error->all(FLERR,fmt::format("Fix '{}' is not of style external!", id)); + lmp->error->all(FLERR,"Fix '{}' is not of style external!", id); FixExternal * fext = (FixExternal*) fix; fext->set_virial_global(virial); diff --git a/src/memory.cpp b/src/memory.cpp index ef2d9c57a4..174932e35e 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -61,8 +61,8 @@ void *Memory::smalloc(bigint nbytes, const char *name) void *ptr = malloc(nbytes); #endif if (ptr == nullptr) - error->one(FLERR,fmt::format("Failed to allocate {} bytes for array {}", - nbytes,name)); + error->one(FLERR,"Failed to allocate {} bytes for array {}", + nbytes,name); return ptr; } @@ -100,8 +100,8 @@ void *Memory::srealloc(void *ptr, bigint nbytes, const char *name) ptr = realloc(ptr,nbytes); #endif if (ptr == nullptr) - error->one(FLERR,fmt::format("Failed to reallocate {} bytes for array {}", - nbytes,name)); + error->one(FLERR,"Failed to reallocate {} bytes for array {}", + nbytes,name); return ptr; } @@ -125,6 +125,6 @@ void Memory::sfree(void *ptr) void Memory::fail(const char *name) { - error->one(FLERR,fmt::format("Cannot create/grow a vector/array of " - "pointers for {}",name)); + error->one(FLERR,"Cannot create/grow a vector/array of " + "pointers for {}",name); } diff --git a/src/modify.cpp b/src/modify.cpp index f8a75ca908..1d6a3d7178 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -250,14 +250,14 @@ void Modify::init() for (i = 0; i < nfix; i++) if (!fix[i]->dynamic_group_allow && group->dynamic[fix[i]->igroup]) - error->all(FLERR,fmt::format("Fix {} does not allow use with a " - "dynamic group",fix[i]->id)); + error->all(FLERR,"Fix {} does not allow use with a " + "dynamic group",fix[i]->id); for (i = 0; i < ncompute; i++) if (!compute[i]->dynamic_group_allow && group->dynamic[compute[i]->igroup]) - error->all(FLERR,fmt::format("Compute {} does not allow use with a " - "dynamic group",compute[i]->id)); + error->all(FLERR,"Compute {} does not allow use with a " + "dynamic group",compute[i]->id); // warn if any particle is time integrated more than once @@ -1221,7 +1221,7 @@ void Modify::add_compute(int narg, char **arg, int trysuffix) for (int icompute = 0; icompute < ncompute; icompute++) if (strcmp(arg[0],compute[icompute]->id) == 0) - error->all(FLERR,fmt::format("Reuse of compute ID '{}'",arg[0])); + error->all(FLERR,"Reuse of compute ID '{}'",arg[0]); // extend Compute list if necessary diff --git a/src/molecule.cpp b/src/molecule.cpp index 9aca15820d..9961014a10 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -130,8 +130,8 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) : if (me == 0) { fp = fopen(arg[ifile],"r"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open molecule file {}: {}", - arg[ifile], utils::getsyserror())); + error->one(FLERR,"Cannot open molecule file {}: {}", + arg[ifile], utils::getsyserror()); } read(0); if (me == 0) fclose(fp); @@ -488,14 +488,14 @@ void Molecule::read(int flag) if (utils::strmatch(text,"^\\d+\\s+\\S+")) { values.next_int(); auto keyword = values.next_string(); - error->one(FLERR,fmt::format("Invalid header keyword: {}",keyword)); + error->one(FLERR,"Invalid header keyword: {}",keyword); } else break; } if (nmatch != nwant) error->one(FLERR,"Invalid header line format in molecule file"); } catch (TokenizerException &e) { - error->one(FLERR, fmt::format("Invalid header in molecule file\n" - "{}", e.what())); + error->one(FLERR, "Invalid header in molecule file\n" + "{}", e.what()); } } @@ -616,11 +616,11 @@ void Molecule::read(int flag) // Error: Either a too long/short section or a typo in the keyword if (utils::strmatch(keyword,"^[A-Za-z ]+$")) - error->one(FLERR,fmt::format("Unknown section '{}' in molecule " - "file\n",keyword)); - else error->one(FLERR,fmt::format("Unexpected line in molecule file " + error->one(FLERR,"Unknown section '{}' in molecule " + "file\n",keyword); + else error->one(FLERR,"Unexpected line in molecule file " "while looking for the next " - "section:\n{}",line)); + "section:\n{}",line); } keyword = parse_keyword(1,line); } @@ -689,8 +689,8 @@ void Molecule::coords(char *line) ValueTokenizer values(utils::trim_comment(line)); if (values.count() != 4) - error->all(FLERR,fmt::format("Invalid line in Coords section of " - "molecule file: {}",line)); + error->all(FLERR,"Invalid line in Coords section of " + "molecule file: {}",line); int iatom = values.next_int() - 1; if (iatom < 0 || iatom >= natoms) @@ -705,19 +705,19 @@ void Molecule::coords(char *line) x[iatom][2] *= sizescale; } } catch (TokenizerException &e) { - error->all(FLERR,fmt::format("Invalid line in Coords section of " - "molecule file: {}\n{}",e.what(),line)); + error->all(FLERR,"Invalid line in Coords section of " + "molecule file: {}\n{}",e.what(),line); } for (int i = 0; i < natoms; i++) - if (count[i] == 0) error->all(FLERR,fmt::format("Atom {} missing in Coords " - "section of molecule file",i+1)); + if (count[i] == 0) error->all(FLERR,"Atom {} missing in Coords " + "section of molecule file",i+1); if (domain->dimension == 2) { for (int i = 0; i < natoms; i++) if (x[i][2] != 0.0) - error->all(FLERR,fmt::format("Z coord in molecule file for atom {} " - "must be 0.0 for 2d-simulation.",i+1)); + error->all(FLERR,"Z coord in molecule file for atom {} " + "must be 0.0 for 2d-simulation.",i+1); } } @@ -735,8 +735,8 @@ void Molecule::types(char *line) ValueTokenizer values(utils::trim_comment(line)); if (values.count() != 2) - error->all(FLERR,fmt::format("Invalid line in Types section of " - "molecule file: {}",line)); + error->all(FLERR,"Invalid line in Types section of " + "molecule file: {}",line); int iatom = values.next_int() - 1; if (iatom < 0 || iatom >= natoms) @@ -746,17 +746,17 @@ void Molecule::types(char *line) type[iatom] += toffset; } } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid line in Types section of " - "molecule file: {}\n{}", e.what(),line)); + error->all(FLERR, "Invalid line in Types section of " + "molecule file: {}\n{}", e.what(),line); } for (int i = 0; i < natoms; i++) { - if (count[i] == 0) error->all(FLERR,fmt::format("Atom {} missing in Types " - "section of molecule file",i+1)); + if (count[i] == 0) error->all(FLERR,"Atom {} missing in Types " + "section of molecule file",i+1); if ((type[i] <= 0) || (domain->box_exist && (type[i] > atom->ntypes))) - error->all(FLERR,fmt::format("Invalid atom type {} for atom {} " - "in molecule file",type[i],i+1)); + error->all(FLERR,"Invalid atom type {} for atom {} " + "in molecule file",type[i],i+1); ntypes = MAX(ntypes,type[i]); } @@ -775,8 +775,8 @@ void Molecule::molecules(char *line) readline(line); ValueTokenizer values(utils::trim_comment(line)); if (values.count() != 2) - error->all(FLERR,fmt::format("Invalid line in Molecules section of " - "molecule file: {}",line)); + error->all(FLERR,"Invalid line in Molecules section of " + "molecule file: {}",line); int iatom = values.next_int() - 1; if (iatom < 0 || iatom >= natoms) @@ -786,18 +786,18 @@ void Molecule::molecules(char *line) // molecule[iatom] += moffset; // placeholder for possible molecule offset } } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid line in Molecules section of " - "molecule file: {}\n{}",e.what(),line)); + error->all(FLERR, "Invalid line in Molecules section of " + "molecule file: {}\n{}",e.what(),line); } for (int i = 0; i < natoms; i++) - if (count[i] == 0) error->all(FLERR,fmt::format("Atom {} missing in Molecules " - "section of molecule file",i+1)); + if (count[i] == 0) error->all(FLERR,"Atom {} missing in Molecules " + "section of molecule file",i+1); for (int i = 0; i < natoms; i++) if (molecule[i] < 0) - error->all(FLERR,fmt::format("Invalid molecule ID {} for atom {} " - "in molecule file",molecule[i],i+1)); + error->all(FLERR,"Invalid molecule ID {} for atom {} " + "in molecule file",molecule[i],i+1); for (int i = 0; i < natoms; i++) nmolecules = MAX(nmolecules,molecule[i]); @@ -824,15 +824,15 @@ void Molecule::fragments(char *line) while (values.has_next()) { int iatom = values.next_int()-1; if (iatom < 0 || iatom >= natoms) - error->all(FLERR,fmt::format("Invalid atom ID {} for fragment {} in " + error->all(FLERR,"Invalid atom ID {} for fragment {} in " "Fragments section of molecule file", - iatom+1, fragmentnames[i])); + iatom+1, fragmentnames[i]); fragmentmask[i][iatom] = 1; } } } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid atom ID in Fragments section of " - "molecule file: {}\n{}", e.what(),line)); + error->all(FLERR, "Invalid atom ID in Fragments section of " + "molecule file: {}\n{}", e.what(),line); } } @@ -849,8 +849,8 @@ void Molecule::charges(char *line) ValueTokenizer values(utils::trim_comment(line)); if ((int)values.count() != 2) - error->all(FLERR,fmt::format("Invalid line in Charges section of " - "molecule file: {}",line)); + error->all(FLERR,"Invalid line in Charges section of " + "molecule file: {}",line); int iatom = values.next_int() - 1; if (iatom < 0 || iatom >= natoms) @@ -860,13 +860,13 @@ void Molecule::charges(char *line) q[iatom] = values.next_double(); } } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid line in Charges section of " - "molecule file: {}.\n{}",e.what(),line)); + error->all(FLERR, "Invalid line in Charges section of " + "molecule file: {}.\n{}",e.what(),line); } for (int i = 0; i < natoms; i++) - if (count[i] == 0) error->all(FLERR,fmt::format("Atom {} missing in Charges " - "section of molecule file",i+1)); + if (count[i] == 0) error->all(FLERR,"Atom {} missing in Charges " + "section of molecule file",i+1); } /* ---------------------------------------------------------------------- @@ -883,8 +883,8 @@ void Molecule::diameters(char *line) ValueTokenizer values(utils::trim_comment(line)); if (values.count() != 2) - error->all(FLERR,fmt::format("Invalid line in Diameters section of " - "molecule file: {}",line)); + error->all(FLERR,"Invalid line in Diameters section of " + "molecule file: {}",line); int iatom = values.next_int() - 1; if (iatom < 0 || iatom >= natoms) error->all(FLERR,"Invalid atom index in Diameters section of molecule file"); @@ -895,16 +895,16 @@ void Molecule::diameters(char *line) maxradius = MAX(maxradius,radius[iatom]); } } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid line in Diameters section of " - "molecule file: {}\n{}",e.what(),line)); + error->all(FLERR, "Invalid line in Diameters section of " + "molecule file: {}\n{}",e.what(),line); } for (int i = 0; i < natoms; i++) { - if (count[i] == 0) error->all(FLERR,fmt::format("Atom {} missing in Diameters " - "section of molecule file",i+1)); + if (count[i] == 0) error->all(FLERR,"Atom {} missing in Diameters " + "section of molecule file",i+1); if (radius[i] < 0.0) - error->all(FLERR,fmt::format("Invalid atom diameter {} for atom {} " - "in molecule file", radius[i], i+1)); + error->all(FLERR,"Invalid atom diameter {} for atom {} " + "in molecule file", radius[i], i+1); } } @@ -921,8 +921,8 @@ void Molecule::masses(char *line) ValueTokenizer values(utils::trim_comment(line)); if (values.count() != 2) - error->all(FLERR,fmt::format("Invalid line in Masses section of " - "molecule file: {}",line)); + error->all(FLERR,"Invalid line in Masses section of " + "molecule file: {}",line); int iatom = values.next_int() - 1; if (iatom < 0 || iatom >= natoms) @@ -932,16 +932,16 @@ void Molecule::masses(char *line) rmass[iatom] *= sizescale*sizescale*sizescale; } } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid line in Masses section of " - "molecule file: {}\n{}",e.what(),line)); + error->all(FLERR, "Invalid line in Masses section of " + "molecule file: {}\n{}",e.what(),line); } for (int i = 0; i < natoms; i++) { - if (count[i] == 0) error->all(FLERR,fmt::format("Atom {} missing in Masses " - "section of molecule file",i+1)); + if (count[i] == 0) error->all(FLERR,"Atom {} missing in Masses " + "section of molecule file",i+1); if (rmass[i] <= 0.0) - error->all(FLERR,fmt::format("Invalid atom mass {} for atom {} " - "in molecule file", radius[i], i+1)); + error->all(FLERR,"Invalid atom mass {} for atom {} " + "in molecule file", radius[i], i+1); } } @@ -970,15 +970,15 @@ void Molecule::bonds(int flag, char *line) try { ValueTokenizer values(utils::trim_comment(line)); if (values.count() != 4) - error->all(FLERR,fmt::format("Invalid line in Bonds section of " - "molecule file: {}",line)); + error->all(FLERR,"Invalid line in Bonds section of " + "molecule file: {}",line); values.next_int(); itype = values.next_int(); atom1 = values.next_tagint(); atom2 = values.next_tagint(); } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid line in Bonds section of " - "molecule file: {}\n{}",e.what(),line)); + error->all(FLERR, "Invalid line in Bonds section of " + "molecule file: {}\n{}",e.what(),line); } itype += boffset; @@ -1040,16 +1040,16 @@ void Molecule::angles(int flag, char *line) try { ValueTokenizer values(utils::trim_comment(line)); if (values.count() != 5) - error->all(FLERR,fmt::format("Invalid line in Angles section of " - "molecule file: {}",line)); + error->all(FLERR,"Invalid line in Angles section of " + "molecule file: {}",line); values.next_int(); itype = values.next_int(); atom1 = values.next_tagint(); atom2 = values.next_tagint(); atom3 = values.next_tagint(); } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid line in Angles section of " - "molecule file: {}\n{}",e.what(),line)); + error->all(FLERR, "Invalid line in Angles section of " + "molecule file: {}\n{}",e.what(),line); } itype += aoffset; @@ -1126,8 +1126,8 @@ void Molecule::dihedrals(int flag, char *line) try { ValueTokenizer values(utils::trim_comment(line)); if (values.count() != 6) - error->all(FLERR,fmt::format("Invalid line in Dihedrals section of " - "molecule file: {}",line)); + error->all(FLERR,"Invalid line in Dihedrals section of " + "molecule file: {}",line); values.next_int(); itype = values.next_int(); @@ -1136,8 +1136,8 @@ void Molecule::dihedrals(int flag, char *line) atom3 = values.next_tagint(); atom4 = values.next_tagint(); } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid line in Dihedrals section of " - "molecule file: {}\n{}",e.what(),line)); + error->all(FLERR, "Invalid line in Dihedrals section of " + "molecule file: {}\n{}",e.what(),line); } itype += doffset; @@ -1228,8 +1228,8 @@ void Molecule::impropers(int flag, char *line) try { ValueTokenizer values(utils::trim_comment(line)); if (values.count() != 6) - error->all(FLERR,fmt::format("Invalid line in Impropers section of " - "molecule file: {}",line)); + error->all(FLERR,"Invalid line in Impropers section of " + "molecule file: {}",line); values.next_int(); itype = values.next_int(); atom1 = values.next_tagint(); @@ -1237,8 +1237,8 @@ void Molecule::impropers(int flag, char *line) atom3 = values.next_tagint(); atom4 = values.next_tagint(); } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid line in Impropers section of " - "molecule file: {}\n{}",e.what(),line)); + error->all(FLERR, "Invalid line in Impropers section of " + "molecule file: {}\n{}",e.what(),line); } itype += ioffset; @@ -1323,15 +1323,15 @@ void Molecule::nspecial_read(int flag, char *line) try { ValueTokenizer values(utils::trim_comment(line)); if (values.count() != 4) - error->all(FLERR,fmt::format("Invalid line in Special Bond Counts section of " - "molecule file: {}",line)); + error->all(FLERR,"Invalid line in Special Bond Counts section of " + "molecule file: {}",line); values.next_int(); c1 = values.next_tagint(); c2 = values.next_tagint(); c3 = values.next_tagint(); } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid line in Special Bond Counts section of " - "molecule file: {}\n{}",e.what(),line)); + error->all(FLERR, "Invalid line in Special Bond Counts section of " + "molecule file: {}\n{}",e.what(),line); } if (flag) { @@ -1370,8 +1370,8 @@ void Molecule::special_read(char *line) } } } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid line in Special Bonds section of " - "molecule file: {}\n{}",e.what(),line)); + error->all(FLERR, "Invalid line in Special Bonds section of " + "molecule file: {}\n{}",e.what(),line); } } @@ -1500,8 +1500,8 @@ void Molecule::shakeflag_read(char *line) shake_flag[i] = values.next_int(); } } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid Shake Flags section in molecule file\n" - "{}", e.what())); + error->all(FLERR, "Invalid Shake Flags section in molecule file\n" + "{}", e.what()); } for (int i = 0; i < natoms; i++) @@ -1570,8 +1570,8 @@ void Molecule::shakeatom_read(char *line) } } catch (TokenizerException &e) { - error->all(FLERR,fmt::format("Invalid shake atom in molecule file\n" - "{}", e.what())); + error->all(FLERR,"Invalid shake atom in molecule file\n" + "{}", e.what()); } for (int i = 0; i < natoms; i++) { @@ -1640,8 +1640,8 @@ void Molecule::shaketype_read(char *line) error->all(FLERR,"Invalid shake type data in molecule file"); } } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid shake type data in molecule file\n", - "{}", e.what())); + error->all(FLERR, "Invalid shake type data in molecule file\n", + "{}", e.what()); } for (int i = 0; i < natoms; i++) { @@ -1693,8 +1693,8 @@ void Molecule::body(int flag, int pflag, char *line) } else nword += ncount; } } catch (TokenizerException &e) { - error->all(FLERR, fmt::format("Invalid body params in molecule file\n", - "{}", e.what())); + error->all(FLERR, "Invalid body params in molecule file\n", + "{}", e.what()); } } @@ -2055,8 +2055,8 @@ void Molecule::skip_lines(int n, char *line, const std::string §ion) for (int i = 0; i < n; i++) { readline(line); if (utils::strmatch(utils::trim(utils::trim_comment(line)),"^[A-Za-z ]+$")) - error->one(FLERR,fmt::format("Unexpected line in molecule file while " - "skipping {} section:\n{}",section,line)); + error->one(FLERR,"Unexpected line in molecule file while " + "skipping {} section:\n{}",section,line); } } diff --git a/src/ntopo_angle_all.cpp b/src/ntopo_angle_all.cpp index b32d530a4c..b7811052df 100644 --- a/src/ntopo_angle_all.cpp +++ b/src/ntopo_angle_all.cpp @@ -60,10 +60,10 @@ void NTopoAngleAll::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR,fmt::format("Angle atoms {} {} {} missing on " + error->one(FLERR,"Angle atoms {} {} {} missing on " "proc {} at step {}",angle_atom1[i][m], angle_atom2[i][m],angle_atom3[i][m], - me,update->ntimestep)); + me,update->ntimestep); continue; } atom1 = domain->closest_image(i,atom1); diff --git a/src/ntopo_angle_partial.cpp b/src/ntopo_angle_partial.cpp index e793e0ee1d..543658f19f 100644 --- a/src/ntopo_angle_partial.cpp +++ b/src/ntopo_angle_partial.cpp @@ -61,10 +61,10 @@ void NTopoAnglePartial::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR,fmt::format("Angle atoms {} {} {} missing on " + error->one(FLERR,"Angle atoms {} {} {} missing on " "proc {} at step {}",angle_atom1[i][m], angle_atom2[i][m],angle_atom3[i][m], - me,update->ntimestep)); + me,update->ntimestep); continue; } atom1 = domain->closest_image(i,atom1); diff --git a/src/ntopo_angle_template.cpp b/src/ntopo_angle_template.cpp index d958f575b6..ad09979a7a 100644 --- a/src/ntopo_angle_template.cpp +++ b/src/ntopo_angle_template.cpp @@ -78,12 +78,12 @@ void NTopoAngleTemplate::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR,fmt::format("Angle atoms {} {} {} missing on " + error->one(FLERR,"Angle atoms {} {} {} missing on " "proc {} at step {}", angle_atom1[iatom][m]+tagprev, angle_atom2[iatom][m]+tagprev, angle_atom3[iatom][m]+tagprev, - me,update->ntimestep)); + me,update->ntimestep); continue; } atom1 = domain->closest_image(i,atom1); diff --git a/src/ntopo_bond_all.cpp b/src/ntopo_bond_all.cpp index 2ae9d35e59..578f98ec81 100644 --- a/src/ntopo_bond_all.cpp +++ b/src/ntopo_bond_all.cpp @@ -57,9 +57,9 @@ void NTopoBondAll::build() if (atom1 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR,fmt::format("Bond atoms {} {} missing on " + error->one(FLERR,"Bond atoms {} {} missing on " "proc {} at step {}",tag[i], - bond_atom[i][m],me,update->ntimestep)); + bond_atom[i][m],me,update->ntimestep); continue; } atom1 = domain->closest_image(i,atom1); diff --git a/src/ntopo_bond_partial.cpp b/src/ntopo_bond_partial.cpp index 2339db3afd..8d077106db 100644 --- a/src/ntopo_bond_partial.cpp +++ b/src/ntopo_bond_partial.cpp @@ -58,9 +58,9 @@ void NTopoBondPartial::build() if (atom1 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR,fmt::format("Bond atoms {} {} missing on " + error->one(FLERR,"Bond atoms {} {} missing on " "proc {} at step {}",tag[i], - bond_atom[i][m],me,update->ntimestep)); + bond_atom[i][m],me,update->ntimestep); continue; } atom1 = domain->closest_image(i,atom1); diff --git a/src/ntopo_bond_template.cpp b/src/ntopo_bond_template.cpp index 4a8ed6e069..887ac3aa81 100644 --- a/src/ntopo_bond_template.cpp +++ b/src/ntopo_bond_template.cpp @@ -74,10 +74,10 @@ void NTopoBondTemplate::build() if (atom1 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR,fmt::format("Bond atoms {} {} missing on " + error->one(FLERR,"Bond atoms {} {} missing on " "proc {} at step {}",tag[i], bond_atom[iatom][m]+tagprev, - me,update->ntimestep)); + me,update->ntimestep); continue; } atom1 = domain->closest_image(i,atom1); diff --git a/src/ntopo_dihedral_all.cpp b/src/ntopo_dihedral_all.cpp index 5cecad4f78..b77e0cc33f 100644 --- a/src/ntopo_dihedral_all.cpp +++ b/src/ntopo_dihedral_all.cpp @@ -62,11 +62,11 @@ void NTopoDihedralAll::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR,fmt::format("Dihedral atoms {} {} {} {} missing on " + error->one(FLERR,"Dihedral atoms {} {} {} {} missing on " "proc {} at step {}", dihedral_atom1[i][m],dihedral_atom2[i][m], dihedral_atom3[i][m],dihedral_atom4[i][m], - me,update->ntimestep)); + me,update->ntimestep); continue; } atom1 = domain->closest_image(i,atom1); diff --git a/src/ntopo_dihedral_partial.cpp b/src/ntopo_dihedral_partial.cpp index 9c7e1e0205..980f073b67 100644 --- a/src/ntopo_dihedral_partial.cpp +++ b/src/ntopo_dihedral_partial.cpp @@ -64,11 +64,11 @@ void NTopoDihedralPartial::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR,fmt::format("Dihedral atoms {} {} {} {} missing on " + error->one(FLERR,"Dihedral atoms {} {} {} {} missing on " "proc {} at step {}", dihedral_atom1[i][m],dihedral_atom2[i][m], dihedral_atom3[i][m],dihedral_atom4[i][m], - me,update->ntimestep)); + me,update->ntimestep); continue; } atom1 = domain->closest_image(i,atom1); diff --git a/src/ntopo_dihedral_template.cpp b/src/ntopo_dihedral_template.cpp index c30a3183b5..5c6f3d333f 100644 --- a/src/ntopo_dihedral_template.cpp +++ b/src/ntopo_dihedral_template.cpp @@ -80,13 +80,13 @@ void NTopoDihedralTemplate::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR,fmt::format("Dihedral atoms {} {} {} {} missing on " + error->one(FLERR,"Dihedral atoms {} {} {} {} missing on " "proc {} at step {}", dihedral_atom1[iatom][m]+tagprev, dihedral_atom2[iatom][m]+tagprev, dihedral_atom3[iatom][m]+tagprev, dihedral_atom4[iatom][m]+tagprev, - me,update->ntimestep)); + me,update->ntimestep); continue; } atom1 = domain->closest_image(i,atom1); diff --git a/src/ntopo_improper_all.cpp b/src/ntopo_improper_all.cpp index c36b02a300..936ed279d7 100644 --- a/src/ntopo_improper_all.cpp +++ b/src/ntopo_improper_all.cpp @@ -62,11 +62,11 @@ void NTopoImproperAll::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR,fmt::format("Improper atoms {} {} {} {} missing on " + error->one(FLERR,"Improper atoms {} {} {} {} missing on " "proc {} at step {}", improper_atom1[i][m],improper_atom2[i][m], improper_atom3[i][m],improper_atom4[i][m], - me,update->ntimestep)); + me,update->ntimestep); continue; } atom1 = domain->closest_image(i,atom1); diff --git a/src/ntopo_improper_partial.cpp b/src/ntopo_improper_partial.cpp index 7ff6cc864f..911e968326 100644 --- a/src/ntopo_improper_partial.cpp +++ b/src/ntopo_improper_partial.cpp @@ -64,13 +64,13 @@ void NTopoImproperPartial::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR,fmt::format("Improper atoms {} {} {} {}" + error->one(FLERR,"Improper atoms {} {} {} {}" " missing on proc {} at step {}", improper_atom1[i][m], improper_atom2[i][m], improper_atom3[i][m], improper_atom4[i][m], - me,update->ntimestep)); + me,update->ntimestep); continue; } atom1 = domain->closest_image(i,atom1); diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp index 43d8d2be38..d8294a7f23 100644 --- a/src/ntopo_improper_template.cpp +++ b/src/ntopo_improper_template.cpp @@ -80,13 +80,13 @@ void NTopoImproperTemplate::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR,fmt::format("Improper atoms {} {} {} {}" + error->one(FLERR,"Improper atoms {} {} {} {}" " missing on proc {} at step {}", improper_atom1[iatom][m]+tagprev, improper_atom2[iatom][m]+tagprev, improper_atom3[iatom][m]+tagprev, improper_atom4[iatom][m]+tagprev, - me,update->ntimestep)); + me,update->ntimestep); continue; } atom1 = domain->closest_image(i,atom1); diff --git a/src/pair.cpp b/src/pair.cpp index 015129dc5d..42ec13374b 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -1729,9 +1729,9 @@ void Pair::write_file(int narg, char **arg) if (utils::file_is_readable(table_file)) { std::string units = utils::get_potential_units(table_file,"table"); if (!units.empty() && (units != update->unit_style)) { - error->one(FLERR,fmt::format("Trying to append to a table file " + error->one(FLERR,"Trying to append to a table file " "with UNITS: {} while units are {}", - units, update->unit_style)); + units, update->unit_style); } std::string date = utils::get_potential_date(table_file,"table"); utils::logmesg(lmp,"Appending to table file {} with DATE: {}\n", @@ -1748,8 +1748,8 @@ void Pair::write_file(int narg, char **arg) datebuf, update->unit_style); } if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open pair_write file {}: {}", - table_file, utils::getsyserror())); + error->one(FLERR,"Cannot open pair_write file {}: {}", + table_file, utils::getsyserror()); fprintf(fp,"# Pair potential %s for atom types %d %d: i,r,energy,force\n", force->pair_style,itype,jtype); if (style == RLINEAR) diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 002429e7b3..c96859a6a5 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -265,8 +265,8 @@ void PairHybrid::settings(int narg, char **arg) { if (narg < 1) error->all(FLERR,"Illegal pair_style command"); if (lmp->kokkos && !utils::strmatch(force->pair_style,"^hybrid.*/kk$")) - error->all(FLERR,fmt::format("Must use pair_style {}/kk with Kokkos", - force->pair_style)); + error->all(FLERR,"Must use pair_style {}/kk with Kokkos", + force->pair_style); // delete old lists, since cannot just change settings diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index de8801fe24..b74515b083 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -72,8 +72,8 @@ void PairHybridScaled::compute(int eflag, int vflag) for (i = 0; i < nvars; ++i) { j = input->variable->find(scalevars[i].c_str()); if (j < 0) - error->all(FLERR,fmt::format("Variable '{}' not found when updating " - "scale factors",scalevars[i])); + error->all(FLERR,"Variable '{}' not found when updating " + "scale factors",scalevars[i]); vals[i] = input->variable->compute_equal(j); } for (i = 0; i < nstyles; ++i) { @@ -245,8 +245,8 @@ void PairHybridScaled::settings(int narg, char **arg) { if (narg < 1) error->all(FLERR,"Illegal pair_style command"); if (lmp->kokkos && !utils::strmatch(force->pair_style,"^hybrid.*/kk$")) - error->all(FLERR,fmt::format("Must use pair_style {}/kk with Kokkos", - force->pair_style)); + error->all(FLERR,"Must use pair_style {}/kk with Kokkos", + force->pair_style); if (atom->avec->forceclearflag) error->all(FLERR,"Atom style is not compatible with pair_style hybrid/scaled"); @@ -397,8 +397,8 @@ double PairHybridScaled::single(int i, int j, int itype, int jtype, double rsq, for (i = 0; i < nvars; ++i) { j = input->variable->find(scalevars[i].c_str()); if (j < 0) - error->all(FLERR,fmt::format("Variable '{}' not found when updating " - "scale factors",scalevars[i])); + error->all(FLERR,"Variable '{}' not found when updating " + "scale factors",scalevars[i]); vals[i] = input->variable->compute_equal(j); } for (i = 0; i < nstyles; ++i) { diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 7e331a16a4..3c9b51e3f2 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -116,27 +116,27 @@ void PairTable::compute(int eflag, int vflag) if (rsq < cutsq[itype][jtype]) { tb = &tables[tabindex[itype][jtype]]; if (rsq < tb->innersq) - error->one(FLERR,fmt::format("Pair distance < table inner cutoff: " - "ijtype {} {} dist {}",itype,jtype,sqrt(rsq))); + error->one(FLERR,"Pair distance < table inner cutoff: " + "ijtype {} {} dist {}",itype,jtype,sqrt(rsq)); if (tabstyle == LOOKUP) { itable = static_cast ((rsq - tb->innersq) * tb->invdelta); if (itable >= tlm1) - error->one(FLERR,fmt::format("Pair distance > table outer cutoff: " - "ijtype {} {} dist {}",itype,jtype,sqrt(rsq))); + error->one(FLERR,"Pair distance > table outer cutoff: " + "ijtype {} {} dist {}",itype,jtype,sqrt(rsq)); fpair = factor_lj * tb->f[itable]; } else if (tabstyle == LINEAR) { itable = static_cast ((rsq - tb->innersq) * tb->invdelta); if (itable >= tlm1) - error->one(FLERR,fmt::format("Pair distance > table outer cutoff: " - "ijtype {} {} dist {}",itype,jtype,sqrt(rsq))); + error->one(FLERR,"Pair distance > table outer cutoff: " + "ijtype {} {} dist {}",itype,jtype,sqrt(rsq)); fraction = (rsq - tb->rsq[itable]) * tb->invdelta; value = tb->f[itable] + fraction*tb->df[itable]; fpair = factor_lj * value; } else if (tabstyle == SPLINE) { itable = static_cast ((rsq - tb->innersq) * tb->invdelta); if (itable >= tlm1) - error->one(FLERR,fmt::format("Pair distance > table outer cutoff: " - "ijtype {} {} dist {}",itype,jtype,sqrt(rsq))); + error->one(FLERR,"Pair distance > table outer cutoff: " + "ijtype {} {} dist {}",itype,jtype,sqrt(rsq)); b = (rsq - tb->rsq[itable]) * tb->invdelta; a = 1.0 - b; value = a * tb->f[itable] + b * tb->f[itable+1] + @@ -568,7 +568,7 @@ void PairTable::param_extract(Table *tb, char *line) tb->fplo = values.next_double(); tb->fphi = values.next_double(); } else { - error->one(FLERR,fmt::format("Invalid keyword {} in pair table parameters", word).c_str()); + error->one(FLERR,"Invalid keyword {} in pair table parameters", word); } } } catch (TokenizerException &e) { diff --git a/src/potential_file_reader.cpp b/src/potential_file_reader.cpp index ce369253cf..3d357771c7 100644 --- a/src/potential_file_reader.cpp +++ b/src/potential_file_reader.cpp @@ -62,8 +62,8 @@ PotentialFileReader::PotentialFileReader(LAMMPS *lmp, try { reader = open_potential(filename); if (!reader) { - error->one(FLERR, fmt::format("cannot open {} potential file {}: {}", - potential_name, filename, utils::getsyserror())); + error->one(FLERR, "cannot open {} potential file {}: {}", + potential_name, filename, utils::getsyserror()); } } catch (FileReaderException &e) { error->one(FLERR, e.what()); @@ -268,9 +268,9 @@ TextFileReader *PotentialFileReader::open_potential(const std::string &path) { } else if ((units == "real") && (unit_style == "metal") && (unit_convert & utils::REAL2METAL)) { unit_convert = utils::REAL2METAL; } else { - lmp->error->one(FLERR, fmt::format("{} file {} requires {} units " + lmp->error->one(FLERR, "{} file {} requires {} units " "but {} units are in use", filetype, - filename, units, unit_style)); + filename, units, unit_style); } } } diff --git a/src/procmap.cpp b/src/procmap.cpp index 87ab415e5e..03a605c0d9 100644 --- a/src/procmap.cpp +++ b/src/procmap.cpp @@ -308,8 +308,8 @@ void ProcMap::custom_grid(char *cfile, int nprocs, procgrid[1] = procs.next_int(); procgrid[2] = procs.next_int(); } catch (TokenizerException &e) { - error->all(FLERR,fmt::format("Processors custom grid file " - "is inconsistent: {}", e.what())); + error->all(FLERR,"Processors custom grid file " + "is inconsistent: {}", e.what()); } int flag = 0; @@ -337,8 +337,8 @@ void ProcMap::custom_grid(char *cfile, int nprocs, cmap[i][2] = pmap.next_int(); cmap[i][3] = pmap.next_int(); } catch (TokenizerException &e) { - error->one(FLERR,fmt::format("Processors custom grid file is " - "inconsistent: {}", e.what())); + error->one(FLERR,"Processors custom grid file is " + "inconsistent: {}", e.what()); } } fclose(fp); diff --git a/src/read_data.cpp b/src/read_data.cpp index 57d5d898a9..01de7ab3a9 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -720,8 +720,8 @@ void ReadData::command(int narg, char **arg) if (firstpass) impropercoeffs(1); else skip_lines(nimpropertypes); - } else error->all(FLERR,fmt::format("Unknown identifier in data file: {}", - keyword)); + } else error->all(FLERR,"Unknown identifier in data file: {}", + keyword); parse_keyword(0); } @@ -1178,7 +1178,7 @@ void ReadData::header(int firstpass) for (n = 0; n < NSECTIONS; n++) if (strcmp(keyword,section_keywords[n]) == 0) break; if (n == NSECTIONS) - error->all(FLERR,fmt::format("Unknown identifier in data file: {}",keyword)); + error->all(FLERR,"Unknown identifier in data file: {}",keyword); // error checks on header values // must be consistent with atom style and other header values @@ -1970,8 +1970,8 @@ void ReadData::open(char *file) } if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open file {}: {}", - file, utils::getsyserror())); + error->one(FLERR,"Cannot open file {}: {}", + file, utils::getsyserror()); } /* ---------------------------------------------------------------------- diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 40e4414543..456839dc61 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -109,8 +109,8 @@ void ReadRestart::command(int narg, char **arg) } fp = fopen(hfile.c_str(),"rb"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open restart file {}: {}", - hfile, utils::getsyserror())); + error->one(FLERR,"Cannot open restart file {}: {}", + hfile, utils::getsyserror()); } // read magic string, endian flag, format revision @@ -271,8 +271,8 @@ void ReadRestart::command(int narg, char **arg) procfile.replace(procfile.find("%"),1,fmt::format("{}",iproc)); fp = fopen(procfile.c_str(),"rb"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open restart file {}: {}", - procfile, utils::getsyserror())); + error->one(FLERR,"Cannot open restart file {}: {}", + procfile, utils::getsyserror()); utils::sfread(FLERR,&flag,sizeof(int),1,fp,nullptr,error); if (flag != PROCSPERFILE) error->one(FLERR,"Invalid flag in peratom section of restart file"); @@ -335,8 +335,8 @@ void ReadRestart::command(int narg, char **arg) procfile.replace(procfile.find("%"),1,fmt::format("{}",icluster)); fp = fopen(procfile.c_str(),"rb"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open restart file {}: {}", - procfile, utils::getsyserror())); + error->one(FLERR,"Cannot open restart file {}: {}", + procfile, utils::getsyserror()); } int flag,procsperfile; diff --git a/src/reader.cpp b/src/reader.cpp index ba172f58ee..ae6f7f5329 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -56,8 +56,8 @@ void Reader::open_file(const char *file) } if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open file {}: {}", - file, utils::getsyserror())); + error->one(FLERR,"Cannot open file {}: {}", + file, utils::getsyserror()); } /* ---------------------------------------------------------------------- diff --git a/src/reset_atom_ids.cpp b/src/reset_atom_ids.cpp index 47dae3cb56..cc9a05d11e 100644 --- a/src/reset_atom_ids.cpp +++ b/src/reset_atom_ids.cpp @@ -253,8 +253,8 @@ void ResetIDs::command(int narg, char **arg) int all; MPI_Allreduce(&badcount,&all,1,MPI_INT,MPI_SUM,world); if (all) - error->all(FLERR,fmt::format("Reset_ids missing {} bond topology atom IDs - " - "use comm_modify cutoff",all)); + error->all(FLERR,"Reset_ids missing {} bond topology atom IDs - " + "use comm_modify cutoff",all); // reset IDs and atom map for owned atoms diff --git a/src/thermo.cpp b/src/thermo.cpp index 6cd5abd9de..2229b2efbd 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -422,8 +422,8 @@ bigint Thermo::lost_check() // error message if (lostflag == Thermo::ERROR) - error->all(FLERR,fmt::format("Lost atoms: original {} current {}", - atom->natoms,ntotal)); + error->all(FLERR,"Lost atoms: original {} current {}", + atom->natoms,ntotal); // warning message diff --git a/src/universe.cpp b/src/universe.cpp index 79de6948df..6dac83745c 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -111,8 +111,8 @@ void Universe::reorder(char *style, char *arg) rv = sscanf(line,"%d %d",&me_orig,&me_new); if (me_orig < 0 || me_orig >= nprocs || me_new < 0 || me_new >= nprocs || rv != 2) - error->one(FLERR,fmt::format("Invalid entry '{} {}' in -reorder " - "file", me_orig, me_new)); + error->one(FLERR,"Invalid entry '{} {}' in -reorder " + "file", me_orig, me_new); uni2orig[me_new] = me_orig; for (int i = 1; i < nprocs; i++) { @@ -121,8 +121,8 @@ void Universe::reorder(char *style, char *arg) rv = sscanf(line,"%d %d",&me_orig,&me_new); if (me_orig < 0 || me_orig >= nprocs || me_new < 0 || me_new >= nprocs || rv != 2) - error->one(FLERR,fmt::format("Invalid entry '{} {}' in -reorder " - "file", me_orig, me_new)); + error->one(FLERR,"Invalid entry '{} {}' in -reorder " + "file", me_orig, me_new); uni2orig[me_new] = me_orig; } fclose(fp); diff --git a/src/utils.cpp b/src/utils.cpp index 2dcf77eacd..aa13950620 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -1107,9 +1107,9 @@ FILE *utils::open_potential(const std::string &name, LAMMPS *lmp, if (auto_convert == nullptr) { if (!units.empty() && (units != unit_style) && (me == 0)) { - error->one(FLERR, fmt::format("Potential file {} requires {} units " + error->one(FLERR, "Potential file {} requires {} units " "but {} units are in use", name, units, - unit_style)); + unit_style); return nullptr; } } else { @@ -1123,9 +1123,9 @@ FILE *utils::open_potential(const std::string &name, LAMMPS *lmp, && (*auto_convert & REAL2METAL)) { *auto_convert = REAL2METAL; } else { - error->one(FLERR, fmt::format("Potential file {} requires {} units " + error->one(FLERR, "Potential file {} requires {} units " "but {} units are in use", name, - units, unit_style)); + units, unit_style); return nullptr; } } diff --git a/src/variable.cpp b/src/variable.cpp index 3e93a33797..dfe5494c3f 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -534,8 +534,8 @@ void Variable::set(int narg, char **arg) if (replaceflag) return; if (!utils::is_id(arg[0])) - error->all(FLERR,fmt::format("Variable name '{}' must have only alphanu" - "meric characters or underscores",arg[0])); + error->all(FLERR,"Variable name '{}' must have only alphanu" + "meric characters or underscores",arg[0]); names[nvar] = utils::strdup(arg[0]); nvar++; } @@ -606,8 +606,8 @@ int Variable::next(int narg, char **arg) for (int iarg = 0; iarg < narg; iarg++) { ivar = find(arg[iarg]); if (ivar < 0) - error->all(FLERR,fmt::format("Invalid variable '{}' in next command", - arg[iarg])); + error->all(FLERR,"Invalid variable '{}' in next command", + arg[iarg]); if (style[ivar] == ULOOP && style[find(arg[0])] == UNIVERSE) continue; else if (style[ivar] == UNIVERSE && style[find(arg[0])] == ULOOP) continue; else if (style[ivar] != style[find(arg[0])]) @@ -925,8 +925,8 @@ char *Variable::retrieve(const char *name) } else if (style[ivar] == PYTHON) { int ifunc = python->variable_match(data[ivar][0],name,0); if (ifunc < 0) - error->all(FLERR,fmt::format("Python variable {} does not match " - "Python function {}", name, data[ivar][0])); + error->all(FLERR,"Python variable {} does not match " + "Python function {}", name, data[ivar][0]); python->invoke_function(ifunc,data[ivar][1]); str = data[ivar][1]; // if Python func returns a string longer than VALUELENGTH @@ -5050,8 +5050,8 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) : if (me == 0) { fp = fopen(file,"r"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open file variable file {}: {}", - file, utils::getsyserror())); + error->one(FLERR,"Cannot open file variable file {}: {}", + file, utils::getsyserror()); } // if atomfile-style variable, must store per-atom values read from file @@ -5188,12 +5188,12 @@ int VarReader::read_peratom() tag = words.next_bigint(); value = words.next_double(); } catch (TokenizerException &e) { - error->all(FLERR,fmt::format("Invalid atomfile line '{}': {}", - buf,e.what())); + error->all(FLERR,"Invalid atomfile line '{}': {}", + buf,e.what()); } if ((tag <= 0) || (tag > map_tag_max)) - error->all(FLERR,fmt::format("Invalid atom ID {} in variable " - "file", tag)); + error->all(FLERR,"Invalid atom ID {} in variable " + "file", tag); if ((m = atom->map(tag)) >= 0) vstore[m] = value; buf = next + 1; } diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 79a99502a6..b0c547a7d6 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -52,8 +52,8 @@ void WriteCoeff::command(int narg, char **arg) FILE *one = fopen(file,"wb+"); if (one == nullptr) - error->one(FLERR,fmt::format("Cannot open coeff file {}: {}", - file, utils::getsyserror())); + error->one(FLERR,"Cannot open coeff file {}: {}", + file, utils::getsyserror()); if (force->pair && force->pair->writedata) { fprintf(one,"# pair_style %s\npair_coeff\n",force->pair_style); @@ -86,8 +86,8 @@ void WriteCoeff::command(int narg, char **arg) FILE *two = fopen(file+4,"w"); if (two == nullptr) - error->one(FLERR,fmt::format("Cannot open coeff file {}: {}", - file+4, utils::getsyserror())); + error->one(FLERR,"Cannot open coeff file {}: {}", + file+4, utils::getsyserror()); fprintf(two,"# LAMMPS coeff file via write_coeff, version %s\n", lmp->version); diff --git a/src/write_data.cpp b/src/write_data.cpp index 388fab1183..3db35190b5 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -175,8 +175,8 @@ void WriteData::write(const std::string &file) if (me == 0) { fp = fopen(file.c_str(),"w"); if (fp == nullptr) - error->one(FLERR,fmt::format("Cannot open data file {}: {}", - file, utils::getsyserror())); + error->one(FLERR,"Cannot open data file {}: {}", + file, utils::getsyserror()); } // proc 0 writes header, ntype-length arrays, force fields diff --git a/src/write_restart.cpp b/src/write_restart.cpp index 350f083be2..45a0267d19 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -231,8 +231,8 @@ void WriteRestart::write(std::string file) fp = fopen(base.c_str(),"wb"); if (fp == nullptr) - error->one(FLERR, fmt::format("Cannot open restart file {}: {}", - base, utils::getsyserror())); + error->one(FLERR, "Cannot open restart file {}: {}", + base, utils::getsyserror()); } // proc 0 writes magic string, endian flag, numeric version @@ -294,8 +294,8 @@ void WriteRestart::write(std::string file) if (filewriter) { fp = fopen(multiname.c_str(),"wb"); if (fp == nullptr) - error->one(FLERR, fmt::format("Cannot open restart file {}: {}", - multiname, utils::getsyserror())); + error->one(FLERR, "Cannot open restart file {}: {}", + multiname, utils::getsyserror()); write_int(PROCSPERFILE,nclusterprocs); } } From beca3e5f0dfab1b00d33043424cc97b43ead011c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 25 Apr 2021 22:27:36 -0400 Subject: [PATCH 0674/1217] collect the full help message --- unittest/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/CMakeLists.txt b/unittest/CMakeLists.txt index 26db526b60..2d86fa2663 100644 --- a/unittest/CMakeLists.txt +++ b/unittest/CMakeLists.txt @@ -15,7 +15,7 @@ add_test(NAME HelpMessage COMMAND $ -h WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(HelpMessage PROPERTIES - ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1;PAGER=head" + ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1" PASS_REGULAR_EXPRESSION ".*Large-scale Atomic/Molecular Massively Parallel Simulator -.*Usage example:.*") # check if the compiled executable will error out on an invalid command line flag From 792966a957e8afbfba3ccde9682de19da8468972 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 26 Apr 2021 11:02:15 -0400 Subject: [PATCH 0675/1217] always describe the git version, even when using a git clone without history --- cmake/Modules/generate_lmpgitversion.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/Modules/generate_lmpgitversion.cmake b/cmake/Modules/generate_lmpgitversion.cmake index 4ff01c7501..b19716d74b 100644 --- a/cmake/Modules/generate_lmpgitversion.cmake +++ b/cmake/Modules/generate_lmpgitversion.cmake @@ -17,7 +17,7 @@ if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git) ERROR_QUIET WORKING_DIRECTORY ${LAMMPS_DIR} OUTPUT_STRIP_TRAILING_WHITESPACE) - execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified + execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified --always OUTPUT_VARIABLE temp_git_describe ERROR_QUIET WORKING_DIRECTORY ${LAMMPS_DIR} From 4fa5840f136236d1eb47dda73471b37d6d9b9f6a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 26 Apr 2021 11:02:41 -0400 Subject: [PATCH 0676/1217] fix bug due to adding ArgInfo --- src/compute_chunk_atom.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index 26967a1b12..16090eb0ec 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -155,6 +155,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) : if ((which == ArgInfo::UNKNOWN) || (which == ArgInfo::NONE) || (argi.get_dim() > 1)) error->all(FLERR,"Illegal compute chunk/atom command"); + iarg = 4; } // optional args From ac60cfb0c32a0db720118ca09f158f6f943a6a97 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 17 Apr 2021 15:41:45 -0400 Subject: [PATCH 0677/1217] add custom constructor for TextFileReader that uses an already opened file descriptor --- src/text_file_reader.cpp | 14 +++++++++++++- src/text_file_reader.h | 3 ++- 2 files changed, 15 insertions(+), 2 deletions(-) diff --git a/src/text_file_reader.cpp b/src/text_file_reader.cpp index b0d5bef53e..e16edab4eb 100644 --- a/src/text_file_reader.cpp +++ b/src/text_file_reader.cpp @@ -41,7 +41,7 @@ using namespace LAMMPS_NS; * \param filetype Description of file type for error messages */ TextFileReader::TextFileReader(const std::string &filename, const std::string &filetype) - : filename(filename), filetype(filetype), ignore_comments(true) + : filetype(filetype), ignore_comments(true) { fp = fopen(filename.c_str(), "r"); @@ -51,6 +51,18 @@ TextFileReader::TextFileReader(const std::string &filename, const std::string &f } } +/** + * \overload + * + * \param fp File descriptor of the already opened file + * \param filetype Description of file type for error messages */ + +TextFileReader::TextFileReader(FILE *fp, const std::string &filetype) + : filetype(filetype), fp(fp), ignore_comments(true) +{ + if (fp == nullptr) throw FileReaderException("Invalid file descriptor"); +} + /** Closes the file */ TextFileReader::~TextFileReader() { diff --git a/src/text_file_reader.h b/src/text_file_reader.h index 1b7ca73fed..bfd6e558ff 100644 --- a/src/text_file_reader.h +++ b/src/text_file_reader.h @@ -25,7 +25,6 @@ namespace LAMMPS_NS { class TextFileReader { - std::string filename; std::string filetype; static constexpr int MAXLINE = 1024; char line[MAXLINE]; @@ -35,6 +34,8 @@ namespace LAMMPS_NS bool ignore_comments; //!< Controls whether comments are ignored TextFileReader(const std::string &filename, const std::string &filetype); + TextFileReader(FILE *fp, const std::string &filetype); + ~TextFileReader(); void skip_line(); From 8af1530e29ba3a726ffaf164c921e98507ae7319 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 18 Apr 2021 04:04:40 -0400 Subject: [PATCH 0678/1217] throw EOF exception in TextFileReader::next_values() if next_line() doesn't do it --- src/text_file_reader.cpp | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/text_file_reader.cpp b/src/text_file_reader.cpp index e16edab4eb..61bd803aa8 100644 --- a/src/text_file_reader.cpp +++ b/src/text_file_reader.cpp @@ -175,5 +175,8 @@ void TextFileReader::next_dvector(double * list, int n) { * \return ValueTokenizer object for read in text */ ValueTokenizer TextFileReader::next_values(int nparams, const std::string &separators) { - return ValueTokenizer(next_line(nparams), separators); + char *ptr = next_line(nparams); + if (ptr == nullptr) + throw EOFException(fmt::format("Missing line in {} file!", filetype)); + return ValueTokenizer(line, separators); } From dbd7d454b9b1226e9510771bc1b58c57e147e1b7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 26 Apr 2021 12:12:19 -0400 Subject: [PATCH 0679/1217] for consistent behavior we must not close the file pointer when it was passed as argument --- src/text_file_reader.cpp | 6 +++--- src/text_file_reader.h | 1 + 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/src/text_file_reader.cpp b/src/text_file_reader.cpp index 61bd803aa8..7344c6d5c3 100644 --- a/src/text_file_reader.cpp +++ b/src/text_file_reader.cpp @@ -41,7 +41,7 @@ using namespace LAMMPS_NS; * \param filetype Description of file type for error messages */ TextFileReader::TextFileReader(const std::string &filename, const std::string &filetype) - : filetype(filetype), ignore_comments(true) + : filetype(filetype), closefp(true), ignore_comments(true) { fp = fopen(filename.c_str(), "r"); @@ -58,7 +58,7 @@ TextFileReader::TextFileReader(const std::string &filename, const std::string &f * \param filetype Description of file type for error messages */ TextFileReader::TextFileReader(FILE *fp, const std::string &filetype) - : filetype(filetype), fp(fp), ignore_comments(true) + : filetype(filetype), closefp(false), fp(fp), ignore_comments(true) { if (fp == nullptr) throw FileReaderException("Invalid file descriptor"); } @@ -66,7 +66,7 @@ TextFileReader::TextFileReader(FILE *fp, const std::string &filetype) /** Closes the file */ TextFileReader::~TextFileReader() { - fclose(fp); + if (closefp) fclose(fp); } /** Read the next line and ignore it */ diff --git a/src/text_file_reader.h b/src/text_file_reader.h index bfd6e558ff..327d57c059 100644 --- a/src/text_file_reader.h +++ b/src/text_file_reader.h @@ -26,6 +26,7 @@ namespace LAMMPS_NS { class TextFileReader { std::string filetype; + bool closefp; static constexpr int MAXLINE = 1024; char line[MAXLINE]; FILE *fp; From 2c6fe2d0b546b63e226e1f29d06808f342f941c4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 26 Apr 2021 12:12:45 -0400 Subject: [PATCH 0680/1217] add tests for the overloaded constructor using a file pointer --- unittest/formats/test_text_file_reader.cpp | 34 ++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/unittest/formats/test_text_file_reader.cpp b/unittest/formats/test_text_file_reader.cpp index e0bb2d42b5..3294881352 100644 --- a/unittest/formats/test_text_file_reader.cpp +++ b/unittest/formats/test_text_file_reader.cpp @@ -76,6 +76,40 @@ TEST_F(TextFileReaderTest, permissions) unlink("text_reader_noperms.file"); } +TEST_F(TextFileReaderTest, nofp) +{ + ASSERT_THROW({ TextFileReader reader(nullptr, "test"); }, + FileReaderException); +} + +TEST_F(TextFileReaderTest, usefp) +{ + test_files(); + FILE *fp = fopen("text_reader_two.file","r"); + ASSERT_NE(fp,nullptr); + + auto reader = new TextFileReader(fp, "test"); + auto line = reader->next_line(); + ASSERT_STREQ(line, "4 "); + line = reader->next_line(1); + ASSERT_STREQ(line, "4 0.5 "); + ASSERT_NO_THROW({ reader->skip_line(); }); + auto values = reader->next_values(1); + ASSERT_EQ(values.count(), 2); + ASSERT_EQ(values.next_int(), 3); + ASSERT_STREQ(values.next_string().c_str(), "1.5"); + ASSERT_NE(reader->next_line(), nullptr); + double data[20]; + ASSERT_THROW({ reader->next_dvector(data,20); }, FileReaderException); + ASSERT_THROW({ reader->skip_line(); }, EOFException); + ASSERT_EQ(reader->next_line(), nullptr); + delete reader; + + // check that we reached EOF and the destructor didn't close the file. + ASSERT_EQ(feof(fp),1); + ASSERT_EQ(fclose(fp),0); +} + TEST_F(TextFileReaderTest, comments) { test_files(); From 0eee2d013d962cfc182772b2192c607affc5c9dd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 26 Apr 2021 12:15:03 -0400 Subject: [PATCH 0681/1217] add info to docs --- src/text_file_reader.cpp | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/text_file_reader.cpp b/src/text_file_reader.cpp index 7344c6d5c3..291d4348ea 100644 --- a/src/text_file_reader.cpp +++ b/src/text_file_reader.cpp @@ -54,6 +54,17 @@ TextFileReader::TextFileReader(const std::string &filename, const std::string &f /** * \overload * +\verbatim embed:rst + +This function is useful in combination with :cpp:func:`utils::open_potential`. + +.. note:: + + The FILE pointer is not closed in the destructor, but will be advanced + when reading from it. + +\endverbatim + * * \param fp File descriptor of the already opened file * \param filetype Description of file type for error messages */ From 462f27d661d924cab8c1a6b35645c94ee5f5d6d7 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 26 Apr 2021 14:28:13 -0400 Subject: [PATCH 0682/1217] Use copy-and-swap in Tokenizers Ensures that the classes behave consistently when copied, moved, copy assigned, and move assigned. --- src/tokenizer.cpp | 41 ++++++++++++++++++++ src/tokenizer.h | 10 +++-- unittest/utils/test_tokenizer.cpp | 64 +++++++++++++++++++++++++++++++ 3 files changed, 111 insertions(+), 4 deletions(-) diff --git a/src/tokenizer.cpp b/src/tokenizer.cpp index ea8ff2ce43..38cdfa73fb 100644 --- a/src/tokenizer.cpp +++ b/src/tokenizer.cpp @@ -68,6 +68,28 @@ Tokenizer::Tokenizer(Tokenizer && rhs) : reset(); } +Tokenizer& Tokenizer::operator=(const Tokenizer& other) +{ + Tokenizer tmp(other); + swap(tmp); + return *this; +} + +Tokenizer& Tokenizer::operator=(Tokenizer&& other) +{ + Tokenizer tmp(std::move(other)); + swap(tmp); + return *this; +} + +void Tokenizer::swap(Tokenizer& other) +{ + std::swap(text, other.text); + std::swap(separators, other.separators); + std::swap(start, other.start); + std::swap(ntokens, other.ntokens); +} + /*! Re-position the tokenizer state to the first word, * i.e. the first non-separator character */ void Tokenizer::reset() { @@ -181,6 +203,25 @@ ValueTokenizer::ValueTokenizer(const ValueTokenizer &rhs) : tokens(rhs.tokens) { ValueTokenizer::ValueTokenizer(ValueTokenizer &&rhs) : tokens(std::move(rhs.tokens)) { } +ValueTokenizer& ValueTokenizer::operator=(const ValueTokenizer& other) +{ + ValueTokenizer tmp(other); + swap(tmp); + return *this; +} + +ValueTokenizer& ValueTokenizer::operator=(ValueTokenizer&& other) +{ + ValueTokenizer tmp(std::move(other)); + swap(tmp); + return *this; +} + +void ValueTokenizer::swap(ValueTokenizer& other) +{ + std::swap(tokens, other.tokens); +} + /*! Indicate whether more tokens are available * * \return true if there are more tokens, false if not */ diff --git a/src/tokenizer.h b/src/tokenizer.h index a17ab13d04..8cc6d2d42b 100644 --- a/src/tokenizer.h +++ b/src/tokenizer.h @@ -37,8 +37,9 @@ public: Tokenizer(const std::string &str, const std::string &separators = TOKENIZER_DEFAULT_SEPARATORS); Tokenizer(Tokenizer &&); Tokenizer(const Tokenizer &); - Tokenizer& operator=(const Tokenizer&) = default; - Tokenizer& operator=(Tokenizer&&) = default; + Tokenizer& operator=(const Tokenizer&); + Tokenizer& operator=(Tokenizer&&); + void swap(Tokenizer &); void reset(); void skip(int n=1); @@ -93,8 +94,9 @@ public: ValueTokenizer(const std::string &str, const std::string &separators = TOKENIZER_DEFAULT_SEPARATORS); ValueTokenizer(const ValueTokenizer &); ValueTokenizer(ValueTokenizer &&); - ValueTokenizer& operator=(const ValueTokenizer&) = default; - ValueTokenizer& operator=(ValueTokenizer&&) = default; + ValueTokenizer& operator=(const ValueTokenizer&); + ValueTokenizer& operator=(ValueTokenizer&&); + void swap(ValueTokenizer &); std::string next_string(); tagint next_tagint(); diff --git a/unittest/utils/test_tokenizer.cpp b/unittest/utils/test_tokenizer.cpp index 5b20d24e7c..275a86a05f 100644 --- a/unittest/utils/test_tokenizer.cpp +++ b/unittest/utils/test_tokenizer.cpp @@ -101,6 +101,38 @@ TEST(Tokenizer, move_constructor) ASSERT_EQ(u.count(), 3); } +TEST(Tokenizer, copy_assignment) +{ + Tokenizer t(" test word ", " "); + Tokenizer u(" test2 word2 other2 ", " "); + ASSERT_THAT(t.next(), Eq("test")); + ASSERT_THAT(t.next(), Eq("word")); + ASSERT_EQ(t.count(), 2); + Tokenizer v = u; + u = t; + ASSERT_THAT(u.next(), Eq("test")); + ASSERT_THAT(u.next(), Eq("word")); + ASSERT_EQ(u.count(), 2); + + ASSERT_THAT(v.next(), Eq("test2")); + ASSERT_THAT(v.next(), Eq("word2")); + ASSERT_THAT(v.next(), Eq("other2")); + ASSERT_EQ(v.count(), 3); +} + +TEST(Tokenizer, move_assignment) +{ + Tokenizer t(" test word ", " "); + ASSERT_THAT(t.next(), Eq("test")); + ASSERT_THAT(t.next(), Eq("word")); + ASSERT_EQ(t.count(), 2); + t = Tokenizer("test new word ", " "); + ASSERT_THAT(t.next(), Eq("test")); + ASSERT_THAT(t.next(), Eq("new")); + ASSERT_THAT(t.next(), Eq("word")); + ASSERT_EQ(t.count(), 3); +} + TEST(Tokenizer, no_separator_path) { Tokenizer t("one", ":"); @@ -223,6 +255,38 @@ TEST(ValueTokenizer, move_constructor) ASSERT_EQ(u.count(), 3); } +TEST(ValueTokenizer, copy_assignment) +{ + ValueTokenizer t(" test word ", " "); + ValueTokenizer u(" test2 word2 other2 ", " "); + ASSERT_THAT(t.next_string(), Eq("test")); + ASSERT_THAT(t.next_string(), Eq("word")); + ASSERT_EQ(t.count(), 2); + ValueTokenizer v = u; + u = t; + ASSERT_THAT(u.next_string(), Eq("test")); + ASSERT_THAT(u.next_string(), Eq("word")); + ASSERT_EQ(u.count(), 2); + + ASSERT_THAT(v.next_string(), Eq("test2")); + ASSERT_THAT(v.next_string(), Eq("word2")); + ASSERT_THAT(v.next_string(), Eq("other2")); + ASSERT_EQ(v.count(), 3); +} + +TEST(ValueTokenizer, move_assignment) +{ + ValueTokenizer t(" test word ", " "); + ASSERT_THAT(t.next_string(), Eq("test")); + ASSERT_THAT(t.next_string(), Eq("word")); + ASSERT_EQ(t.count(), 2); + t = ValueTokenizer("test new word ", " "); + ASSERT_THAT(t.next_string(), Eq("test")); + ASSERT_THAT(t.next_string(), Eq("new")); + ASSERT_THAT(t.next_string(), Eq("word")); + ASSERT_EQ(t.count(), 3); +} + TEST(ValueTokenizer, bad_integer) { ValueTokenizer values("f10 f11 f12"); From ad843f977f3a80a8901f1466d37b226608d8f6ac Mon Sep 17 00:00:00 2001 From: Andreas Singraber Date: Mon, 26 Apr 2021 23:46:27 +0200 Subject: [PATCH 0683/1217] Auto-download works now for CMake build. --- cmake/Modules/FindN2P2.cmake | 5 ++-- cmake/Modules/Packages/USER-HDNNP.cmake | 32 ++++++++++++++++++------- 2 files changed, 26 insertions(+), 11 deletions(-) diff --git a/cmake/Modules/FindN2P2.cmake b/cmake/Modules/FindN2P2.cmake index 975f424a39..8a97b7dd81 100644 --- a/cmake/Modules/FindN2P2.cmake +++ b/cmake/Modules/FindN2P2.cmake @@ -34,19 +34,20 @@ find_package_handle_standard_args(N2P2 DEFAULT_MSG if(N2P2_FOUND) if (NOT TARGET N2P2::N2P2) + # n2p2 core library "libnnp" add_library(N2P2::LIBNNP UNKNOWN IMPORTED) set_target_properties(N2P2::LIBNNP PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR} IMPORTED_LOCATION ${N2P2_LIBNNP}) + # n2p2 interface library "libnnpif" add_library(N2P2::LIBNNPIF UNKNOWN IMPORTED) set_target_properties(N2P2::LIBNNPIF PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR} IMPORTED_LOCATION ${N2P2_LIBNNPIF}) + # Put libnnp, libnnpif and include directory together. add_library(N2P2::N2P2 INTERFACE IMPORTED) set_property(TARGET N2P2::N2P2 PROPERTY INTERFACE_LINK_LIBRARIES N2P2::LIBNNPIF N2P2::LIBNNP) - #set(N2P2_INCLUDE_DIRS ${N2P2_INCLUDE_DIR}) - #set(N2P2_LIBRARIES ${N2P2_LIBNNPIF} ${N2P2_LIBNNP}) set(N2P2_CMAKE_EXTRAS ${N2P2_CMAKE_EXTRA}) endif() endif() diff --git a/cmake/Modules/Packages/USER-HDNNP.cmake b/cmake/Modules/Packages/USER-HDNNP.cmake index 2517e3304d..1829585ea4 100644 --- a/cmake/Modules/Packages/USER-HDNNP.cmake +++ b/cmake/Modules/Packages/USER-HDNNP.cmake @@ -6,31 +6,45 @@ else() endif() option(DOWNLOAD_N2P2 "Download n2p2 library instead of using an already installed one)" ${DOWNLOAD_N2P2_DEFAULT}) if(DOWNLOAD_N2P2) - set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.1.2.tar.gz" CACHE STRING "URL for n2p2 tarball") - set(N2P2_MD5 "20cf194d14b1f1c72f38879bafda67e2" CACHE STRING "MD5 checksum of N2P2 tarball") + set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.1.3.tar.gz" CACHE STRING "URL for n2p2 tarball") + set(N2P2_MD5 "5cd30194701db198e4a72ee94fa6e0db" CACHE STRING "MD5 checksum of N2P2 tarball") mark_as_advanced(N2P2_URL) mark_as_advanced(N2P2_MD5) include(ExternalProject) ExternalProject_Add(n2p2_build - DOWNLOAD_DIR ${CMAKE_CURRENT_BINARY_DIR} URL ${N2P2_URL} URL_MD5 ${N2P2_MD5} UPDATE_COMMAND "" SOURCE_SUBDIR src/ BUILD_IN_SOURCE 1 CONFIGURE_COMMAND "" - BUILD_COMMAND "make libnnpif" + BUILD_COMMAND make libnnpif INSTALL_COMMAND "" #BUILD_BYPRODUCTS /lib/libnnp.a /lib/libnnpif.a ) - ExternalProject_get_property(n2p2_build INSTALL_DIR) - add_library(LAMMPS::N2P2 STATIC IMPORTED GLOBAL) - set_target_properties(LAMMPS::N2P2 PROPERTIES - IMPORTED_LOCATION "${INSTALL_DIR}/lib/libnnp.a" - INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include") + ExternalProject_get_property(n2p2_build SOURCE_DIR) + # n2p2 core library "libnnp" + add_library(LAMMPS::N2P2::LIBNNP UNKNOWN IMPORTED) + set_target_properties(LAMMPS::N2P2::LIBNNP PROPERTIES + IMPORTED_LOCATION "${SOURCE_DIR}/lib/libnnp.a" + INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include") + # n2p2 interface library "libnnpif" + add_library(LAMMPS::N2P2::LIBNNPIF UNKNOWN IMPORTED) + set_target_properties(LAMMPS::N2P2::LIBNNPIF PROPERTIES + IMPORTED_LOCATION "${SOURCE_DIR}/lib/libnnpif.a" + INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include") + # Put libnnp, libnnpif and include directory together. + add_library(LAMMPS::N2P2 INTERFACE IMPORTED) + set_property(TARGET LAMMPS::N2P2 PROPERTY + INTERFACE_LINK_LIBRARIES LAMMPS::N2P2::LIBNNPIF LAMMPS::N2P2::LIBNNP) target_link_libraries(lammps PRIVATE LAMMPS::N2P2) + add_dependencies(LAMMPS::N2P2 n2p2_build) + file(MAKE_DIRECTORY "${SOURCE_DIR}/include") + file(MAKE_DIRECTORY "${SOURCE_DIR}/lib") + file(TOUCH "${SOURCE_DIR}/lib/lammps-extra.cmake") + include("${SOURCE_DIR}/lib/lammps-extra.cmake") else() find_package(N2P2) if(NOT N2P2_FOUND) From 692da3bf88823da6e8cda09bc31d510577f298b3 Mon Sep 17 00:00:00 2001 From: Stan Gerald Moore Date: Mon, 26 Apr 2021 16:28:19 -0600 Subject: [PATCH 0684/1217] Update Kokkos library in LAMMPS to v3.4.0 --- lib/kokkos/CHANGELOG.md | 163 ++ lib/kokkos/CMakeLists.txt | 34 +- lib/kokkos/Makefile.kokkos | 87 +- lib/kokkos/Makefile.targets | 2 + lib/kokkos/algorithms/src/Kokkos_Random.hpp | 21 +- .../algorithms/unit_tests/CMakeLists.txt | 64 +- lib/kokkos/algorithms/unit_tests/Makefile | 12 +- .../unit_tests/TestOpenMP_Sort1D.cpp | 2 + .../algorithms/unit_tests/TestRandom.hpp | 28 + .../unit_tests/TestRandomCommon.hpp | 60 + .../unit_tests/TestSortCommon.hpp} | 12 +- lib/kokkos/appveyor.yml | 6 +- lib/kokkos/bin/kokkos_launch_compiler | 88 +- lib/kokkos/bin/nvcc_wrapper | 4 +- lib/kokkos/cmake/CTestConfig.cmake.in | 91 + lib/kokkos/cmake/KokkosCI.cmake | 350 +++ lib/kokkos/cmake/KokkosCTest.cmake.in | 261 ++ lib/kokkos/cmake/KokkosConfig.cmake.in | 45 +- lib/kokkos/cmake/KokkosConfigCommon.cmake.in | 219 +- lib/kokkos/cmake/KokkosCore_config.h.in | 4 + lib/kokkos/cmake/Modules/CudaToolkit.cmake | 86 +- lib/kokkos/cmake/Modules/FindTPLCUDA.cmake | 2 +- lib/kokkos/cmake/Modules/FindTPLPTHREAD.cmake | 2 +- lib/kokkos/cmake/Modules/FindTPLROCM.cmake | 11 + .../cmake/compile_tests/cplusplus14.cpp | 8 + .../compile_tests/cuda_compute_capability.cc | 1 + lib/kokkos/cmake/compile_tests/pthread.cpp | 2 +- lib/kokkos/cmake/fake_tribits.cmake | 81 +- lib/kokkos/cmake/kokkos_arch.cmake | 92 +- lib/kokkos/cmake/kokkos_compiler_id.cmake | 49 +- lib/kokkos/cmake/kokkos_corner_cases.cmake | 7 +- lib/kokkos/cmake/kokkos_enable_devices.cmake | 13 +- lib/kokkos/cmake/kokkos_enable_options.cmake | 18 +- lib/kokkos/cmake/kokkos_functions.cmake | 41 +- lib/kokkos/cmake/kokkos_test_cxx_std.cmake | 13 + lib/kokkos/cmake/kokkos_tpls.cmake | 8 + lib/kokkos/cmake/kokkos_tribits.cmake | 119 +- lib/kokkos/containers/src/CMakeLists.txt | 3 - lib/kokkos/containers/src/Kokkos_DualView.hpp | 170 +- .../containers/src/Kokkos_DynRankView.hpp | 36 +- .../containers/src/Kokkos_DynamicView.hpp | 6 + .../containers/src/Kokkos_OffsetView.hpp | 30 +- .../containers/src/Kokkos_ScatterView.hpp | 234 +- .../containers/src/Kokkos_UnorderedMap.hpp | 33 +- .../src/impl/Kokkos_Bitset_impl.hpp | 14 +- .../src/impl/Kokkos_UnorderedMap_impl.hpp | 4 +- .../containers/unit_tests/CMakeLists.txt | 6 +- lib/kokkos/containers/unit_tests/Makefile | 2 +- .../containers/unit_tests/TestDualView.hpp | 139 +- .../containers/unit_tests/TestDynamicView.hpp | 3 - .../unit_tests/TestHIP_Category.hpp | 51 - .../unit_tests/TestHPX_Category.hpp | 51 - .../containers/unit_tests/TestOffsetView.hpp | 18 - .../unit_tests/TestOpenMP_Category.hpp | 51 - .../unit_tests/TestSYCL_Category.hpp | 51 - .../containers/unit_tests/TestScatterView.hpp | 4 + .../unit_tests/TestSerial_Category.hpp | 51 - .../unit_tests/TestStaticCrsGraph.hpp | 3 - .../unit_tests/TestThreads_Category.hpp | 51 - .../unit_tests/TestUnorderedMap.hpp | 11 +- lib/kokkos/core/perf_test/CMakeLists.txt | 24 +- .../core/perf_test/PerfTestGramSchmidt.cpp | 6 +- lib/kokkos/core/src/CMakeLists.txt | 3 +- lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp | 469 +-- .../Cuda/Kokkos_Cuda_BlockSize_Deduction.hpp | 5 +- lib/kokkos/core/src/Cuda/Kokkos_Cuda_Half.hpp | 281 +- .../core/src/Cuda/Kokkos_Cuda_Instance.cpp | 156 +- .../core/src/Cuda/Kokkos_Cuda_Instance.hpp | 34 +- .../src/Cuda/Kokkos_Cuda_KernelLaunch.hpp | 14 +- .../src/Cuda/Kokkos_Cuda_MDRangePolicy.hpp | 37 + .../core/src/Cuda/Kokkos_Cuda_Parallel.hpp | 53 +- lib/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp | 97 +- lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp | 2 +- .../src/Cuda/Kokkos_Cuda_WorkGraphPolicy.hpp | 1 + .../HIP/Kokkos_HIP_BlockSize_Deduction.hpp | 226 -- .../core/src/HIP/Kokkos_HIP_Instance.cpp | 50 +- .../core/src/HIP/Kokkos_HIP_Instance.hpp | 74 +- .../core/src/HIP/Kokkos_HIP_KernelLaunch.hpp | 133 +- .../core/src/HIP/Kokkos_HIP_MDRangePolicy.hpp | 37 + .../src/HIP/Kokkos_HIP_Parallel_MDRange.hpp | 53 +- .../src/HIP/Kokkos_HIP_Parallel_Range.hpp | 27 +- .../core/src/HIP/Kokkos_HIP_Parallel_Team.hpp | 23 +- lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp | 363 +-- lib/kokkos/core/src/HIP/Kokkos_HIP_Team.hpp | 97 +- .../core/src/KokkosExp_MDRangePolicy.hpp | 193 +- lib/kokkos/core/src/Kokkos_AnonymousSpace.hpp | 14 - lib/kokkos/core/src/Kokkos_Complex.hpp | 250 +- lib/kokkos/core/src/Kokkos_Core.hpp | 9 + lib/kokkos/core/src/Kokkos_Core_fwd.hpp | 39 +- lib/kokkos/core/src/Kokkos_Crs.hpp | 2 +- lib/kokkos/core/src/Kokkos_Cuda.hpp | 46 +- lib/kokkos/core/src/Kokkos_CudaSpace.hpp | 237 +- lib/kokkos/core/src/Kokkos_ExecPolicy.hpp | 90 +- lib/kokkos/core/src/Kokkos_HBWSpace.hpp | 24 - lib/kokkos/core/src/Kokkos_HIP.hpp | 1 + lib/kokkos/core/src/Kokkos_HIP_Space.hpp | 220 +- lib/kokkos/core/src/Kokkos_HPX.hpp | 60 +- lib/kokkos/core/src/Kokkos_HostSpace.hpp | 27 +- lib/kokkos/core/src/Kokkos_LogicalSpaces.hpp | 4 +- lib/kokkos/core/src/Kokkos_Macros.hpp | 6 + .../core/src/Kokkos_MathematicalFunctions.hpp | 233 ++ lib/kokkos/core/src/Kokkos_MemoryPool.hpp | 7 +- lib/kokkos/core/src/Kokkos_NumericTraits.hpp | 191 +- lib/kokkos/core/src/Kokkos_OpenMP.hpp | 8 - lib/kokkos/core/src/Kokkos_OpenMPTarget.hpp | 18 - .../core/src/Kokkos_OpenMPTargetSpace.hpp | 74 +- lib/kokkos/core/src/Kokkos_Parallel.hpp | 83 +- .../core/src/Kokkos_Parallel_Reduce.hpp | 32 +- lib/kokkos/core/src/Kokkos_SYCL.hpp | 32 +- lib/kokkos/core/src/Kokkos_SYCL_Space.hpp | 167 +- lib/kokkos/core/src/Kokkos_ScratchSpace.hpp | 121 +- lib/kokkos/core/src/Kokkos_Serial.hpp | 39 +- lib/kokkos/core/src/Kokkos_TaskScheduler.hpp | 4 +- lib/kokkos/core/src/Kokkos_Threads.hpp | 8 - lib/kokkos/core/src/Kokkos_Tuners.hpp | 96 +- lib/kokkos/core/src/Kokkos_View.hpp | 86 +- .../core/src/OpenMP/Kokkos_OpenMP_Exec.hpp | 2 +- .../src/OpenMP/Kokkos_OpenMP_Parallel.hpp | 30 +- .../OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp | 106 +- .../Kokkos_OpenMPTarget_Error.hpp} | 36 +- .../OpenMPTarget/Kokkos_OpenMPTarget_Exec.cpp | 62 +- .../OpenMPTarget/Kokkos_OpenMPTarget_Exec.hpp | 489 +++- .../Kokkos_OpenMPTarget_Instance.cpp | 59 +- .../Kokkos_OpenMPTarget_Parallel.hpp | 733 +++-- .../Kokkos_OpenMPTarget_Parallel_MDRange.hpp | 118 +- .../Kokkos_OpenMPTarget_UniqueToken.hpp | 135 + lib/kokkos/core/src/SYCL/Kokkos_SYCL.cpp | 69 +- .../SYCL/Kokkos_SYCL_Abort.hpp} | 20 +- .../core/src/SYCL/Kokkos_SYCL_DeepCopy.hpp | 94 + .../core/src/SYCL/Kokkos_SYCL_Instance.cpp | 194 +- .../core/src/SYCL/Kokkos_SYCL_Instance.hpp | 273 +- .../src/SYCL/Kokkos_SYCL_MDRangePolicy.hpp | 37 + .../src/SYCL/Kokkos_SYCL_Parallel_Range.hpp | 224 +- .../src/SYCL/Kokkos_SYCL_Parallel_Reduce.hpp | 641 ++-- .../src/SYCL/Kokkos_SYCL_Parallel_Scan.hpp | 62 +- .../src/SYCL/Kokkos_SYCL_Parallel_Team.hpp | 835 ++++++ .../core/src/SYCL/Kokkos_SYCL_Space.cpp | 373 +-- lib/kokkos/core/src/SYCL/Kokkos_SYCL_Team.hpp | 816 ++++++ .../core/src/SYCL/Kokkos_SYCL_UniqueToken.hpp | 134 + .../core/src/Threads/Kokkos_ThreadsExec.cpp | 4 +- .../core/src/Threads/Kokkos_ThreadsTeam.hpp | 35 +- .../core/src/decl/Kokkos_Declare_CUDA.hpp | 9 + .../src/decl/Kokkos_Declare_OPENMPTARGET.hpp | 1 + .../core/src/decl/Kokkos_Declare_SYCL.hpp | 3 + lib/kokkos/core/src/fwd/Kokkos_Fwd_HIP.hpp | 5 +- lib/kokkos/core/src/fwd/Kokkos_Fwd_SYCL.hpp | 5 +- .../src/impl/KokkosExp_Host_IterateTile.hpp | 180 +- .../src/impl/KokkosExp_IterateTileGPU.hpp | 2580 ++--------------- .../core/src/impl/Kokkos_AnalyzePolicy.hpp | 396 +-- .../core/src/impl/Kokkos_Atomic_Exchange.hpp | 6 +- .../core/src/impl/Kokkos_Atomic_Generic.hpp | 2 +- .../core/src/impl/Kokkos_Atomic_MinMax.hpp | 96 + .../core/src/impl/Kokkos_Atomic_View.hpp | 12 +- lib/kokkos/core/src/impl/Kokkos_ClockTic.hpp | 14 +- .../core/src/impl/Kokkos_Combined_Reducer.hpp | 51 +- lib/kokkos/core/src/impl/Kokkos_Core.cpp | 505 ++-- lib/kokkos/core/src/impl/Kokkos_Error.cpp | 7 +- lib/kokkos/core/src/impl/Kokkos_Error.hpp | 17 +- .../src/impl/Kokkos_FixedBufferMemoryPool.hpp | 2 +- .../core/src/impl/Kokkos_FunctorAdapter.hpp | 141 +- lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp | 4 +- .../core/src/impl/Kokkos_HostBarrier.cpp | 27 +- .../core/src/impl/Kokkos_HostSharedPtr.hpp | 178 ++ lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp | 115 +- .../core/src/impl/Kokkos_HostThreadTeam.hpp | 29 +- .../core/src/impl/Kokkos_Memory_Fence.hpp | 3 + .../core/src/impl/Kokkos_NumericTraits.cpp | 73 + lib/kokkos/core/src/impl/Kokkos_Profiling.cpp | 582 ++-- lib/kokkos/core/src/impl/Kokkos_Profiling.hpp | 230 +- .../src/impl/Kokkos_Profiling_C_Interface.h | 53 +- .../src/impl/Kokkos_Profiling_Interface.hpp | 36 +- .../core/src/impl/Kokkos_SharedAlloc.hpp | 81 +- .../src/impl/Kokkos_SharedAlloc_timpl.hpp | 287 ++ .../src/impl/Kokkos_SimpleTaskScheduler.hpp | 6 +- lib/kokkos/core/src/impl/Kokkos_Spinwait.cpp | 24 +- lib/kokkos/core/src/impl/Kokkos_Traits.hpp | 7 - lib/kokkos/core/src/impl/Kokkos_Utilities.hpp | 358 +-- .../core/src/impl/Kokkos_ViewLayoutTiled.hpp | 185 +- .../core/src/impl/Kokkos_ViewMapping.hpp | 6 +- .../core/src/setup/Kokkos_Setup_SYCL.hpp | 73 + .../src/traits/Kokkos_ExecutionSpaceTrait.hpp | 95 + .../src/traits/Kokkos_GraphKernelTrait.hpp} | 73 +- .../core/src/traits/Kokkos_IndexTypeTrait.hpp | 107 + .../traits/Kokkos_IterationPatternTrait.hpp} | 68 +- .../src/traits/Kokkos_LaunchBoundsTrait.hpp} | 72 +- .../traits/Kokkos_OccupancyControlTrait.hpp | 208 ++ .../src/traits/Kokkos_PolicyTraitAdaptor.hpp | 156 + .../core/src/traits/Kokkos_ScheduleTrait.hpp | 112 + .../core/src/traits/Kokkos_Traits_fwd.hpp | 73 + .../traits/Kokkos_WorkItemPropertyTrait.hpp | 114 + .../core/src/traits/Kokkos_WorkTagTrait.hpp | 124 + lib/kokkos/core/unit_test/CMakeLists.txt | 382 ++- lib/kokkos/core/unit_test/Makefile | 12 +- lib/kokkos/core/unit_test/TestAtomics.hpp | 7 +- lib/kokkos/core/unit_test/TestComplex.hpp | 91 +- .../core/unit_test/TestDeepCopyAlignment.hpp | 46 +- .../core/unit_test/TestHalfOperators.hpp | 630 +++- lib/kokkos/core/unit_test/TestHostBarrier.cpp | 7 - .../core/unit_test/TestHostSharedPtr.hpp | 155 + .../TestHostSharedPtrAccessOnDevice.hpp | 156 + lib/kokkos/core/unit_test/TestMDRange.hpp | 101 +- lib/kokkos/core/unit_test/TestMDRange_a.hpp | 3 + lib/kokkos/core/unit_test/TestMDRange_b.hpp | 3 + lib/kokkos/core/unit_test/TestMDRange_c.hpp | 5 + lib/kokkos/core/unit_test/TestMDRange_d.hpp | 5 + lib/kokkos/core/unit_test/TestMDRange_e.hpp | 3 + lib/kokkos/core/unit_test/TestMDRange_f.hpp | 3 + .../unit_test/TestMathematicalFunctions.hpp | 871 ++++++ .../unit_test/TestNonTrivialScalarTypes.hpp | 6 +- .../core/unit_test/TestNumericTraits.hpp | 336 +++ .../core/unit_test/TestPolicyConstruction.hpp | 69 +- lib/kokkos/core/unit_test/TestRange.hpp | 22 +- .../core/unit_test/TestRangePolicyRequire.hpp | 24 +- lib/kokkos/core/unit_test/TestReduce.hpp | 79 +- .../unit_test/TestReduceCombinatorical.hpp | 21 - lib/kokkos/core/unit_test/TestReducers.hpp | 10 + lib/kokkos/core/unit_test/TestReducers_d.hpp | 8 +- .../unit_test/TestReductions_DeviceView.hpp | 14 + lib/kokkos/core/unit_test/TestResize.hpp | 6 - lib/kokkos/core/unit_test/TestScan.hpp | 10 +- lib/kokkos/core/unit_test/TestSharedAlloc.hpp | 3 + ...tCuda_Category.hpp => TestSubView_c14.hpp} | 15 +- lib/kokkos/core/unit_test/TestTeam.hpp | 206 +- lib/kokkos/core/unit_test/TestTeamBasic.hpp | 61 +- lib/kokkos/core/unit_test/TestTeamScratch.hpp | 5 + .../core/unit_test/TestTeamTeamSize.hpp | 12 +- lib/kokkos/core/unit_test/TestTeamVector.hpp | 243 +- .../core/unit_test/TestTeamVectorRange.hpp | 74 +- lib/kokkos/core/unit_test/TestUniqueToken.hpp | 14 +- lib/kokkos/core/unit_test/TestUtilities.hpp | 301 -- lib/kokkos/core/unit_test/TestViewAPI.hpp | 24 +- lib/kokkos/core/unit_test/TestViewAPI_c.hpp | 3 - lib/kokkos/core/unit_test/TestViewAPI_e.hpp | 3 - lib/kokkos/core/unit_test/TestViewCopy_a.hpp | 11 - .../TestViewLayoutStrideAssignment.hpp | 12 +- .../core/unit_test/TestViewMapping_a.hpp | 3 - lib/kokkos/core/unit_test/TestViewSubview.hpp | 51 +- lib/kokkos/core/unit_test/TestView_64bit.hpp | 7 +- .../core/unit_test/Test_InterOp_Streams.hpp | 2 + .../TestCudaHostPinned_Category.hpp | 0 .../TestCudaUVM_Category.hpp | 0 .../TestCuda_Category.hpp | 1 + .../TestDefaultDeviceType_Category.hpp | 0 .../TestHIPHostPinned_Category.hpp | 0 .../{ => category_files}/TestHIP_Category.hpp | 0 .../{ => category_files}/TestHPX_Category.hpp | 0 .../TestOpenMPTarget_Category.hpp | 0 .../TestOpenMP_Category.hpp | 0 .../TestSYCLSharedUSMSpace_Category.hpp} | 8 +- .../TestSYCL_Category.hpp | 1 + .../TestSerial_Category.hpp | 0 .../TestThreads_Category.hpp | 0 .../cuda/TestCudaHostPinned_SharedAlloc.cpp | 2 +- .../cuda/TestCudaHostPinned_ViewAPI_a.cpp | 2 +- .../cuda/TestCudaHostPinned_ViewAPI_b.cpp | 2 +- .../cuda/TestCudaHostPinned_ViewAPI_c.cpp | 2 +- .../cuda/TestCudaHostPinned_ViewAPI_d.cpp | 2 +- .../cuda/TestCudaHostPinned_ViewAPI_e.cpp | 2 +- .../cuda/TestCudaHostPinned_ViewCopy_a.cpp | 2 +- .../cuda/TestCudaHostPinned_ViewCopy_b.cpp | 2 +- .../cuda/TestCudaHostPinned_ViewMapping_a.cpp | 2 +- .../cuda/TestCudaHostPinned_ViewMapping_b.cpp | 2 +- ...TestCudaHostPinned_ViewMapping_subview.cpp | 2 +- .../cuda/TestCudaUVM_SharedAlloc.cpp | 2 +- .../unit_test/cuda/TestCudaUVM_ViewAPI_a.cpp | 2 +- .../unit_test/cuda/TestCudaUVM_ViewAPI_b.cpp | 2 +- .../unit_test/cuda/TestCudaUVM_ViewAPI_c.cpp | 2 +- .../unit_test/cuda/TestCudaUVM_ViewAPI_d.cpp | 2 +- .../unit_test/cuda/TestCudaUVM_ViewAPI_e.cpp | 2 +- .../unit_test/cuda/TestCudaUVM_ViewCopy_a.cpp | 2 +- .../unit_test/cuda/TestCudaUVM_ViewCopy_b.cpp | 2 +- .../cuda/TestCudaUVM_ViewMapping_a.cpp | 2 +- .../cuda/TestCudaUVM_ViewMapping_b.cpp | 2 +- .../cuda/TestCudaUVM_ViewMapping_subview.cpp | 2 +- .../cuda/TestCuda_DebugPinUVMSpace.cpp | 2 +- .../cuda/TestCuda_DebugSerialExecution.cpp | 2 +- .../core/unit_test/cuda/TestCuda_Graph.cpp | 2 +- .../unit_test/cuda/TestCuda_InterOp_Init.cpp | 11 +- .../cuda/TestCuda_InterOp_Streams.cpp | 2 +- .../core/unit_test/cuda/TestCuda_Spaces.cpp | 2 +- .../core/unit_test/cuda/TestCuda_Task.cpp | 2 +- .../cuda/TestCuda_TeamScratchStreams.cpp | 2 +- .../default/TestDefaultDeviceDevelop.cpp | 2 +- .../default/TestDefaultDeviceType.cpp | 2 +- .../default/TestDefaultDeviceTypeResize.cpp | 3 - .../default/TestDefaultDeviceType_a1.cpp | 10 +- .../default/TestDefaultDeviceType_a2.cpp | 10 +- .../default/TestDefaultDeviceType_a3.cpp | 5 +- .../default/TestDefaultDeviceType_b1.cpp | 10 +- .../default/TestDefaultDeviceType_b2.cpp | 10 +- .../default/TestDefaultDeviceType_b3.cpp | 5 +- .../default/TestDefaultDeviceType_c1.cpp | 10 +- .../default/TestDefaultDeviceType_c2.cpp | 10 +- .../default/TestDefaultDeviceType_c3.cpp | 5 +- .../default/TestDefaultDeviceType_d.cpp | 4 +- .../headers_self_contained/CMakeLists.txt | 38 +- .../hip/TestHIPHostPinned_Category.hpp | 53 - .../hip/TestHIPHostPinned_ViewAPI_a.cpp | 2 +- .../hip/TestHIPHostPinned_ViewAPI_b.cpp | 2 +- .../hip/TestHIPHostPinned_ViewAPI_c.cpp | 2 +- .../hip/TestHIPHostPinned_ViewAPI_d.cpp | 2 +- .../hip/TestHIPHostPinned_ViewAPI_e.cpp | 2 +- .../hip/TestHIPHostPinned_ViewCopy_a.cpp | 2 +- .../hip/TestHIPHostPinned_ViewCopy_b.cpp | 2 +- .../hip/TestHIPHostPinned_ViewMapping_a.cpp | 2 +- .../hip/TestHIPHostPinned_ViewMapping_b.cpp | 2 +- .../TestHIPHostPinned_ViewMapping_subview.cpp | 2 +- .../unit_test/hip/TestHIP_AsyncLauncher.cpp} | 67 +- .../unit_test/hip/TestHIP_InterOp_Init.cpp | 9 +- .../unit_test/hip/TestHIP_InterOp_Streams.cpp | 2 +- .../core/unit_test/hip/TestHIP_ScanUnit.cpp | 2 +- .../core/unit_test/hip/TestHIP_Spaces.cpp | 2 +- .../hip/TestHIP_TeamScratchStreams.cpp | 2 +- .../core/unit_test/hpx/TestHPX_Category.hpp | 54 - .../hpx/TestHPX_IndependentInstances.cpp | 2 +- ...X_IndependentInstancesDelayedExecution.cpp | 2 +- ...estHPX_IndependentInstancesInstanceIds.cpp | 2 +- ...estHPX_IndependentInstancesRefCounting.cpp | 2 +- .../core/unit_test/hpx/TestHPX_InterOp.cpp | 2 +- .../core/unit_test/hpx/TestHPX_Task.cpp | 2 +- .../incremental/Test12a_ThreadScratch.hpp | 22 +- .../incremental/Test12b_TeamScratch.hpp | 17 +- .../Test13a_ParallelRed_TeamThreadRange.hpp | 2 +- .../Test13b_ParallelRed_TeamVectorRange.hpp | 2 +- .../Test13c_ParallelRed_ThreadVectorRange.hpp | 2 +- .../unit_test/openmp/TestOpenMP_Category.hpp | 55 - .../unit_test/openmp/TestOpenMP_Graph.cpp | 2 +- .../unit_test/openmp/TestOpenMP_InterOp.cpp | 2 +- .../openmp/TestOpenMP_PartitionMaster.cpp | 2 +- .../core/unit_test/openmp/TestOpenMP_Task.cpp | 2 +- .../TestOpenMPTarget_Category.hpp | 54 - .../unit_test/serial/TestSerial_Category.hpp | 55 - .../unit_test/serial/TestSerial_Graph.cpp | 2 +- .../core/unit_test/serial/TestSerial_Task.cpp | 2 +- .../unit_test/standalone/UnitTestMainInit.cpp | 18 +- .../unit_test/sycl/TestSYCL_InterOp_Init.cpp} | 61 +- .../sycl/TestSYCL_InterOp_Init_Context.cpp | 120 + .../sycl/TestSYCL_InterOp_Streams.cpp | 118 + .../threads/TestThreads_Category.hpp | 54 - .../core/unit_test/tools/TestAllCalls.cpp | 8 +- .../core/unit_test/tools/printing-tool.cpp | 22 + .../CMakeLists.txt | 29 + .../bar.cpp | 7 + .../foo.cpp} | 78 +- .../tutorial/01_hello_world/hello_world.cpp | 9 +- .../hello_world_lambda.cpp | 5 + .../05_simple_atomics/simple_atomics.cpp | 2 +- .../06_simple_mdrangepolicy/CMakeLists.txt | 1 - .../01_data_layouts/data_layouts.cpp | 8 +- .../02_memory_traits/memory_traits.cpp | 3 +- .../Advanced_Views/03_subviews/subviews.cpp | 24 +- .../Advanced_Views/04_dualviews/dual_view.cpp | 3 +- .../01_thread_teams/thread_teams.cpp | 5 + .../thread_teams_lambda.cpp | 11 +- .../nested_parallel_for.cpp | 5 + lib/kokkos/generate_makefile.bash | 12 +- lib/kokkos/gnu_generate_makefile.bash | 6 +- lib/kokkos/master_history.txt | 1 + 358 files changed, 16375 insertions(+), 10003 deletions(-) create mode 100644 lib/kokkos/algorithms/unit_tests/TestRandomCommon.hpp rename lib/kokkos/{containers/unit_tests/TestCuda_Category.hpp => algorithms/unit_tests/TestSortCommon.hpp} (88%) create mode 100644 lib/kokkos/cmake/CTestConfig.cmake.in create mode 100644 lib/kokkos/cmake/KokkosCI.cmake create mode 100644 lib/kokkos/cmake/KokkosCTest.cmake.in create mode 100644 lib/kokkos/cmake/Modules/FindTPLROCM.cmake create mode 100644 lib/kokkos/cmake/compile_tests/cplusplus14.cpp delete mode 100644 lib/kokkos/containers/unit_tests/TestHIP_Category.hpp delete mode 100644 lib/kokkos/containers/unit_tests/TestHPX_Category.hpp delete mode 100644 lib/kokkos/containers/unit_tests/TestOpenMP_Category.hpp delete mode 100644 lib/kokkos/containers/unit_tests/TestSYCL_Category.hpp delete mode 100644 lib/kokkos/containers/unit_tests/TestSerial_Category.hpp delete mode 100644 lib/kokkos/containers/unit_tests/TestThreads_Category.hpp create mode 100644 lib/kokkos/core/src/Cuda/Kokkos_Cuda_MDRangePolicy.hpp create mode 100644 lib/kokkos/core/src/HIP/Kokkos_HIP_MDRangePolicy.hpp create mode 100644 lib/kokkos/core/src/Kokkos_MathematicalFunctions.hpp rename lib/kokkos/{algorithms/unit_tests/TestOpenMP.cpp => core/src/OpenMPTarget/Kokkos_OpenMPTarget_Error.hpp} (73%) create mode 100644 lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_UniqueToken.hpp rename lib/kokkos/core/{unit_test/cuda/TestCudaUVM_Category.hpp => src/SYCL/Kokkos_SYCL_Abort.hpp} (86%) create mode 100644 lib/kokkos/core/src/SYCL/Kokkos_SYCL_MDRangePolicy.hpp create mode 100644 lib/kokkos/core/src/SYCL/Kokkos_SYCL_Parallel_Team.hpp create mode 100644 lib/kokkos/core/src/SYCL/Kokkos_SYCL_Team.hpp create mode 100644 lib/kokkos/core/src/SYCL/Kokkos_SYCL_UniqueToken.hpp create mode 100644 lib/kokkos/core/src/impl/Kokkos_HostSharedPtr.hpp create mode 100644 lib/kokkos/core/src/impl/Kokkos_NumericTraits.cpp create mode 100644 lib/kokkos/core/src/impl/Kokkos_SharedAlloc_timpl.hpp create mode 100644 lib/kokkos/core/src/setup/Kokkos_Setup_SYCL.hpp create mode 100644 lib/kokkos/core/src/traits/Kokkos_ExecutionSpaceTrait.hpp rename lib/kokkos/{algorithms/unit_tests/TestCuda.cpp => core/src/traits/Kokkos_GraphKernelTrait.hpp} (58%) create mode 100644 lib/kokkos/core/src/traits/Kokkos_IndexTypeTrait.hpp rename lib/kokkos/{algorithms/unit_tests/TestSerial.cpp => core/src/traits/Kokkos_IterationPatternTrait.hpp} (54%) rename lib/kokkos/{algorithms/unit_tests/TestHPX.cpp => core/src/traits/Kokkos_LaunchBoundsTrait.hpp} (54%) create mode 100644 lib/kokkos/core/src/traits/Kokkos_OccupancyControlTrait.hpp create mode 100644 lib/kokkos/core/src/traits/Kokkos_PolicyTraitAdaptor.hpp create mode 100644 lib/kokkos/core/src/traits/Kokkos_ScheduleTrait.hpp create mode 100644 lib/kokkos/core/src/traits/Kokkos_Traits_fwd.hpp create mode 100644 lib/kokkos/core/src/traits/Kokkos_WorkItemPropertyTrait.hpp create mode 100644 lib/kokkos/core/src/traits/Kokkos_WorkTagTrait.hpp delete mode 100644 lib/kokkos/core/unit_test/TestHostBarrier.cpp create mode 100644 lib/kokkos/core/unit_test/TestHostSharedPtr.hpp create mode 100644 lib/kokkos/core/unit_test/TestHostSharedPtrAccessOnDevice.hpp create mode 100644 lib/kokkos/core/unit_test/TestMathematicalFunctions.hpp create mode 100644 lib/kokkos/core/unit_test/TestNumericTraits.hpp rename lib/kokkos/core/unit_test/{TestCuda_Category.hpp => TestSubView_c14.hpp} (88%) rename lib/kokkos/core/unit_test/{cuda => category_files}/TestCudaHostPinned_Category.hpp (100%) rename lib/kokkos/core/unit_test/{ => category_files}/TestCudaUVM_Category.hpp (100%) rename lib/kokkos/core/unit_test/{cuda => category_files}/TestCuda_Category.hpp (98%) rename lib/kokkos/core/unit_test/{default => category_files}/TestDefaultDeviceType_Category.hpp (100%) rename lib/kokkos/core/unit_test/{ => category_files}/TestHIPHostPinned_Category.hpp (100%) rename lib/kokkos/core/unit_test/{ => category_files}/TestHIP_Category.hpp (100%) rename lib/kokkos/core/unit_test/{ => category_files}/TestHPX_Category.hpp (100%) rename lib/kokkos/core/unit_test/{ => category_files}/TestOpenMPTarget_Category.hpp (100%) rename lib/kokkos/core/unit_test/{ => category_files}/TestOpenMP_Category.hpp (100%) rename lib/kokkos/core/unit_test/{hip/TestHIP_Category.hpp => category_files/TestSYCLSharedUSMSpace_Category.hpp} (91%) rename lib/kokkos/core/unit_test/{ => category_files}/TestSYCL_Category.hpp (98%) rename lib/kokkos/core/unit_test/{ => category_files}/TestSerial_Category.hpp (100%) rename lib/kokkos/core/unit_test/{ => category_files}/TestThreads_Category.hpp (100%) delete mode 100644 lib/kokkos/core/unit_test/hip/TestHIPHostPinned_Category.hpp rename lib/kokkos/{algorithms/unit_tests/TestThreads.cpp => core/unit_test/hip/TestHIP_AsyncLauncher.cpp} (61%) delete mode 100644 lib/kokkos/core/unit_test/hpx/TestHPX_Category.hpp delete mode 100644 lib/kokkos/core/unit_test/openmp/TestOpenMP_Category.hpp delete mode 100644 lib/kokkos/core/unit_test/openmptarget/TestOpenMPTarget_Category.hpp delete mode 100644 lib/kokkos/core/unit_test/serial/TestSerial_Category.hpp rename lib/kokkos/{algorithms/unit_tests/TestOpenMP_Random.cpp => core/unit_test/sycl/TestSYCL_InterOp_Init.cpp} (66%) create mode 100644 lib/kokkos/core/unit_test/sycl/TestSYCL_InterOp_Init_Context.cpp create mode 100644 lib/kokkos/core/unit_test/sycl/TestSYCL_InterOp_Streams.cpp delete mode 100644 lib/kokkos/core/unit_test/threads/TestThreads_Category.hpp create mode 100644 lib/kokkos/example/build_cmake_installed_different_compiler/CMakeLists.txt create mode 100644 lib/kokkos/example/build_cmake_installed_different_compiler/bar.cpp rename lib/kokkos/{algorithms/unit_tests/TestHIP.cpp => example/build_cmake_installed_different_compiler/foo.cpp} (63%) diff --git a/lib/kokkos/CHANGELOG.md b/lib/kokkos/CHANGELOG.md index c759181aa2..3ce38c37d8 100644 --- a/lib/kokkos/CHANGELOG.md +++ b/lib/kokkos/CHANGELOG.md @@ -1,5 +1,168 @@ # Change Log +## [3.4.00](https://github.com/kokkos/kokkos/tree/3.4.00) (2021-04-25) +[Full Changelog](https://github.com/kokkos/kokkos/compare/3.3.01...3.4.00) + +**Highlights:** +- SYCL Backend Almost Feature Complete +- OpenMPTarget Backend Almost Feature Complete +- Performance Improvements for HIP backend +- Require CMake 3.16 or newer +- Tool Callback Interface Enhancements +- cmath wrapper functions available now in Kokkos::Experimental + +**Features:** +- Implement parallel_scan with ThreadVectorRange and Reducer [\#3861](https://github.com/kokkos/kokkos/pull/3861) +- Implement SYCL Random [\#3849](https://github.com/kokkos/kokkos/pull/3849) +- OpenMPTarget: Adding Implementation for nested reducers [\#3845](https://github.com/kokkos/kokkos/pull/3845) +- Implement UniqueToken for SYCL [\#3833](https://github.com/kokkos/kokkos/pull/3833) +- OpenMPTarget: UniqueToken::Global implementation [\#3823](https://github.com/kokkos/kokkos/pull/3823) +- DualView sync's on ExecutionSpaces [\#3822](https://github.com/kokkos/kokkos/pull/3822) +- SYCL outer TeamPolicy parallel_reduce [\#3818](https://github.com/kokkos/kokkos/pull/3818) +- SYCL TeamPolicy::team_scan [\#3815](https://github.com/kokkos/kokkos/pull/3815) +- SYCL MDRangePolicy parallel_reduce [\#3801](https://github.com/kokkos/kokkos/pull/3801) +- Enable use of execution space instances in ScatterView [\#3786](https://github.com/kokkos/kokkos/pull/3786) +- SYCL TeamPolicy nested parallel_reduce [\#3783](https://github.com/kokkos/kokkos/pull/3783) +- OpenMPTarget: MDRange with TagType for parallel_for [\#3781](https://github.com/kokkos/kokkos/pull/3781) +- Adding OpenMPTarget parallel_scan [\#3655](https://github.com/kokkos/kokkos/pull/3655) +- SYCL basic TeamPolicy [\#3654](https://github.com/kokkos/kokkos/pull/3654) +- OpenMPTarget: scratch memory implementation [\#3611](https://github.com/kokkos/kokkos/pull/3611) + +**Implemented enhancements Backends and Archs:** +- SYCL choose a specific GPU [\#3918](https://github.com/kokkos/kokkos/pull/3918) +- [HIP] Lock access to scratch memory when using Teams [\#3916](https://github.com/kokkos/kokkos/pull/3916) +- [HIP] fix multithreaded access to get_next_driver [\#3908](https://github.com/kokkos/kokkos/pull/3908) +- Forward declare HIPHostPinnedSpace and SYCLSharedUSMSpace [\#3902](https://github.com/kokkos/kokkos/pull/3902) +- Let SYCL USMObjectMem use SharedAllocationRecord [\#3898](https://github.com/kokkos/kokkos/pull/3898) +- Implement clock_tic for SYCL [\#3893](https://github.com/kokkos/kokkos/pull/3893) +- Don't use a static variable in HIPInternal::scratch_space [\#3866](https://github.com/kokkos/kokkos/pull/3866)(https://github.com/kokkos/kokkos/pull/3866) +- Reuse memory for SYCL parallel_reduce [\#3873](https://github.com/kokkos/kokkos/pull/3873) +- Update SYCL compiler in CI [\#3826](https://github.com/kokkos/kokkos/pull/3826) +- Introduce HostSharedPtr to manage m_space_instance for Cuda/HIP/SYCL [\#3824](https://github.com/kokkos/kokkos/pull/3824) +- [HIP] Use shuffle for range reduction [\#3811](https://github.com/kokkos/kokkos/pull/3811) +- OpenMPTarget: Changes to the hierarchical parallelism [\#3808](https://github.com/kokkos/kokkos/pull/3808) +- Remove ExtendedReferenceWrapper for SYCL parallel_reduce [\#3802](https://github.com/kokkos/kokkos/pull/3802) +- Eliminate sycl_indirect_launch [\#3777](https://github.com/kokkos/kokkos/pull/3777) +- OpenMPTarget: scratch implementation for parallel_reduce [\#3776](https://github.com/kokkos/kokkos/pull/3776) +- Allow initializing SYCL execution space from sycl::queue and SYCL::impl_static_fence [\#3767](https://github.com/kokkos/kokkos/pull/3767) +- SYCL TeamPolicy scratch memory alternative [\#3763](https://github.com/kokkos/kokkos/pull/3763) +- Alternative implementation for SYCL TeamPolicy [\#3759](https://github.com/kokkos/kokkos/pull/3759) +- Unify handling of synchronous errors in SYCL [\#3754](https://github.com/kokkos/kokkos/pull/3754) +- core/Cuda: Half_t updates for cgsolve [\#3746](https://github.com/kokkos/kokkos/pull/3746) +- Unify HIPParallelLaunch structures [\#3733](https://github.com/kokkos/kokkos/pull/3733) +- Improve performance for SYCL parallel_reduce [\#3732](https://github.com/kokkos/kokkos/pull/3732) +- Use consistent types in Kokkos_OpenMPTarget_Parallel.hpp [\#3703](https://github.com/kokkos/kokkos/pull/3703) +- Implement non-blocking kernel launches for HIP backend [\#3697](https://github.com/kokkos/kokkos/pull/3697) +- Change SYCLInternal::m_queue std::unique_ptr -> std::optional [\#3677](https://github.com/kokkos/kokkos/pull/3677) +- Use alternative SYCL parallel_reduce implementation [\#3671](https://github.com/kokkos/kokkos/pull/3671) +- Use runtime values in KokkosExp_MDRangePolicy.hpp [\#3626](https://github.com/kokkos/kokkos/pull/3626) +- Clean up AnalyzePolicy [\#3564](https://github.com/kokkos/kokkos/pull/3564) +- Changes for indirect launch of SYCL parallel reduce [\#3511](https://github.com/kokkos/kokkos/pull/3511) + +**Implemented enhancements BuildSystem:** +- Also require C++14 when building gtest [\#3912](https://github.com/kokkos/kokkos/pull/3912) +- Fix compiling SYCL with OpenMP [\#3874](https://github.com/kokkos/kokkos/pull/3874) +- Require C++17 for SYCL (at configuration time) [\#3869](https://github.com/kokkos/kokkos/pull/3869) +- Add COMPILE_DEFINITIONS argument to kokkos_create_imported_tpl [\#3862](https://github.com/kokkos/kokkos/pull/3862) +- Do not pass arch flags to the linker with no rdc [\#3846](https://github.com/kokkos/kokkos/pull/3846) +- Try compiling C++14 check with C++14 support and print error message [\#3843](https://github.com/kokkos/kokkos/pull/3843) +- Enable HIP with Cray Clang [\#3842](https://github.com/kokkos/kokkos/pull/3842) +- Add an option to disable header self containment tests [\#3834](https://github.com/kokkos/kokkos/pull/3834) +- CMake check for C++14 [\#3809](https://github.com/kokkos/kokkos/pull/3809) +- Prefer -std=* over --std=* [\#3779](https://github.com/kokkos/kokkos/pull/3779) +- Kokkos launch compiler updates [\#3778](https://github.com/kokkos/kokkos/pull/3778) +- Updated comments and enabled no-op for kokkos_launch_compiler [\#3774](https://github.com/kokkos/kokkos/pull/3774) +- Apple's Clang not correctly recognised [\#3772](https://github.com/kokkos/kokkos/pull/3772) +- kokkos_launch_compiler + CUDA auto-detect arch [\#3770](https://github.com/kokkos/kokkos/pull/3770) +- Add Spack test support for Kokkos [\#3753](https://github.com/kokkos/kokkos/pull/3753) +- Split SYCL tests for aot compilation [\#3741](https://github.com/kokkos/kokkos/pull/3741) +- Use consistent OpenMP flag for IntelClang [\#3735](https://github.com/kokkos/kokkos/pull/3735) +- Add support for -Wno-deprecated-gpu-targets [\#3722](https://github.com/kokkos/kokkos/pull/3722) +- Add configuration to target CUDA compute capability 8.6 [\#3713](https://github.com/kokkos/kokkos/pull/3713) +- Added VERSION and SOVERSION to KOKKOS_INTERNAL_ADD_LIBRARY [\#3706](https://github.com/kokkos/kokkos/pull/3706) +- Add fast-math to known NVCC flags [\#3699](https://github.com/kokkos/kokkos/pull/3699) +- Add MI-100 arch string [\#3698](https://github.com/kokkos/kokkos/pull/3698) +- Require CMake >=3.16 [\#3679](https://github.com/kokkos/kokkos/pull/3679) +- KokkosCI.cmake, KokkosCTest.cmake.in, CTestConfig.cmake.in + CI updates [\#2844](https://github.com/kokkos/kokkos/pull/2844) + +**Implemented enhancements Tools:** +- Improve readability of the callback invocation in profiling [\#3860](https://github.com/kokkos/kokkos/pull/3860) +- V1.1 Tools Interface: incremental, action-based [\#3812](https://github.com/kokkos/kokkos/pull/3812) +- Enable launch latency simulations [\#3721](https://github.com/kokkos/kokkos/pull/3721) +- Added metadata callback to tools interface [\#3711](https://github.com/kokkos/kokkos/pull/3711) +- MDRange Tile Size Tuning [\#3688](https://github.com/kokkos/kokkos/pull/3688) +- Added support for command-line args for kokkos-tools [\#3627](https://github.com/kokkos/kokkos/pull/3627) +- Query max tile sizes for an MDRangePolicy, and set tile sizes on an existing policy [\#3481](https://github.com/kokkos/kokkos/pull/3481) + +**Implemented enhancements Other:** +- Try detecting ndevices in get_gpu [\#3921](https://github.com/kokkos/kokkos/pull/3921) +- Use strcmp to compare names() [\#3909](https://github.com/kokkos/kokkos/pull/3909) +- Add execution space arguments for constructor overloads that might allocate a new underlying View [\#3904](https://github.com/kokkos/kokkos/pull/3904) +- Prefix labels in internal use of kokkos_malloc [\#3891](https://github.com/kokkos/kokkos/pull/3891) +- Prefix labels for internal uses of SharedAllocationRecord [\#3890](https://github.com/kokkos/kokkos/pull/3890) +- Add missing hypot math function [\#3880](https://github.com/kokkos/kokkos/pull/3880) +- Unify algorithm unit tests to avoid code duplication [\#3851](https://github.com/kokkos/kokkos/pull/3851) +- DualView.template view() better matches for Devices in UVMSpace cases [\#3857](https://github.com/kokkos/kokkos/pull/3857) +- More extensive disentangling of Policy Traits [\#3829](https://github.com/kokkos/kokkos/pull/3829) +- Replaced nanosleep and sched_yield with STL routines [\#3825](https://github.com/kokkos/kokkos/pull/3825) +- Constructing Atomic Subviews [\#3810](https://github.com/kokkos/kokkos/pull/3810) +- Metadata Declaration in Core [\#3729](https://github.com/kokkos/kokkos/pull/3729) +- Allow using tagged final functor in parallel_reduce [\#3714](https://github.com/kokkos/kokkos/pull/3714) +- Major duplicate code removal in SharedAllocationRecord specializations [\#3658](https://github.com/kokkos/kokkos/pull/3658) + +**Fixed bugs:** +- Provide forward declarations in Kokkos_ViewLayoutTiled.hpp for XL [\#3911](https://github.com/kokkos/kokkos/pull/3911) +- Fixup absolute value of floating points in Kokkos complex [\#3882](https://github.com/kokkos/kokkos/pull/3882) +- Address intel 17 ICE [\#3881](https://github.com/kokkos/kokkos/pull/3881) +- Add missing pow(Kokkos::complex) overloads [\#3868](https://github.com/kokkos/kokkos/pull/3868) +- Fix bug {pow, log}(Kokkos::complex) [\#3866](https://github.com/kokkos/kokkos/pull/3866)(https://github.com/kokkos/kokkos/pull/3866) +- Cleanup writing to output streams in Cuda [\#3859](https://github.com/kokkos/kokkos/pull/3859) +- Fixup cache CUDA fallback execution space instance used by DualView::sync [\#3856](https://github.com/kokkos/kokkos/pull/3856) +- Fix cmake warning with pthread [\#3854](https://github.com/kokkos/kokkos/pull/3854) +- Fix typo FOUND_CUDA_{DRIVVER -> DRIVER} [\#3852](https://github.com/kokkos/kokkos/pull/3852) +- Fix bug in SYCL team_reduce [\#3848](https://github.com/kokkos/kokkos/pull/3848) +- Atrocious bug in MDRange tuning [\#3803](https://github.com/kokkos/kokkos/pull/3803) +- Fix compiling SYCL with Kokkos_ENABLE_TUNING=ON [\#3800](https://github.com/kokkos/kokkos/pull/3800) +- Fixed command line parsing bug [\#3797](https://github.com/kokkos/kokkos/pull/3797) +- Workaround race condition in SYCL parallel_reduce [\#3782](https://github.com/kokkos/kokkos/pull/3782) +- Fix Atomic{Min,Max} for Kepler30 [\#3780](https://github.com/kokkos/kokkos/pull/3780) +- Fix SYCL typo [\#3755](https://github.com/kokkos/kokkos/pull/3755) +- Fixed Kokkos_install_additional_files macro [\#3752](https://github.com/kokkos/kokkos/pull/3752) +- Fix a typo for Kokkos_ARCH_A64FX [\#3751](https://github.com/kokkos/kokkos/pull/3751) +- OpenMPTarget: fixes and workarounds to work with "Release" build type [\#3748](https://github.com/kokkos/kokkos/pull/3748) +- Fix parsing bug for number of devices command line argument [\#3724](https://github.com/kokkos/kokkos/pull/3724) +- Avoid more warnings with clang and C++20 [\#3719](https://github.com/kokkos/kokkos/pull/3719) +- Fix gcc-10.1 C++20 warnings [\#3718](https://github.com/kokkos/kokkos/pull/3718) +- Fix cuda cache config not being set correct [\#3712](https://github.com/kokkos/kokkos/pull/3712) +- Fix dualview deepcopy perftools [\#3701](https://github.com/kokkos/kokkos/pull/3701) +- use drand instead of frand in drand [\#3696](https://github.com/kokkos/kokkos/pull/3696) + +**Incompatibilities:** +- Remove unimplemented member functions of SYCLDevice [\#3919](https://github.com/kokkos/kokkos/pull/3919) +- Replace cl::sycl [\#3896](https://github.com/kokkos/kokkos/pull/3896) +- Get rid of SYCL workaround in Kokkos_Complex.hpp [\#3884](https://github.com/kokkos/kokkos/pull/3884) +- Replace most uses of if_c [\#3883](https://github.com/kokkos/kokkos/pull/3883) +- Remove Impl::enable_if_type [\#3863](https://github.com/kokkos/kokkos/pull/3863) +- Remove HostBarrier test [\#3847](https://github.com/kokkos/kokkos/pull/3847) +- Avoid (void) interface [\#3836](https://github.com/kokkos/kokkos/pull/3836) +- Remove VerifyExecutionCanAccessMemorySpace [\#3813](https://github.com/kokkos/kokkos/pull/3813) +- Avoid duplicated code in ScratchMemorySpace [\#3793](https://github.com/kokkos/kokkos/pull/3793) +- Remove superfluous FunctorFinal specialization [\#3788](https://github.com/kokkos/kokkos/pull/3788) +- Rename cl::sycl -> sycl in Kokkos_MathematicalFunctions.hpp [\#3678](https://github.com/kokkos/kokkos/pull/3678) +- Remove integer_sequence backward compatibility implementation [\#3533](https://github.com/kokkos/kokkos/pull/3533) + +**Enabled tests:** +- Fixup re-enable core performance tests [\#3903](https://github.com/kokkos/kokkos/pull/3903) +- Enable more SYCL tests [\#3900](https://github.com/kokkos/kokkos/pull/3900) +- Restrict MDRange Policy tests for Intel GPUs [\#3853](https://github.com/kokkos/kokkos/pull/3853) +- Disable death tests for rawhide [\#3844](https://github.com/kokkos/kokkos/pull/3844) +- OpenMPTarget: Block unit tests that do not pass with the nvidia compiler [\#3839](https://github.com/kokkos/kokkos/pull/3839) +- Enable Bitset container test for SYCL [\#3830](https://github.com/kokkos/kokkos/pull/3830) +- Enable some more SYCL tests [\#3744](https://github.com/kokkos/kokkos/pull/3744) +- Enable SYCL atomic tests [\#3742](https://github.com/kokkos/kokkos/pull/3742) +- Enable more SYCL perf_tests [\#3692](https://github.com/kokkos/kokkos/pull/3692) +- Enable examples for SYCL [\#3691](https://github.com/kokkos/kokkos/pull/3691) + ## [3.3.01](https://github.com/kokkos/kokkos/tree/3.3.01) (2021-01-06) [Full Changelog](https://github.com/kokkos/kokkos/compare/3.3.00...3.3.01) diff --git a/lib/kokkos/CMakeLists.txt b/lib/kokkos/CMakeLists.txt index 7bc3c77256..6fc1bf7d2f 100644 --- a/lib/kokkos/CMakeLists.txt +++ b/lib/kokkos/CMakeLists.txt @@ -72,7 +72,7 @@ ENDFUNCTION() LIST(APPEND CMAKE_MODULE_PATH cmake/Modules) IF(NOT KOKKOS_HAS_TRILINOS) - cmake_minimum_required(VERSION 3.10 FATAL_ERROR) + cmake_minimum_required(VERSION 3.16 FATAL_ERROR) set(CMAKE_DISABLE_SOURCE_CHANGES ON) set(CMAKE_DISABLE_IN_SOURCE_BUILD ON) IF (Spack_WORKAROUND) @@ -111,27 +111,25 @@ ENDIF() set(Kokkos_VERSION_MAJOR 3) -set(Kokkos_VERSION_MINOR 3) -set(Kokkos_VERSION_PATCH 1) +set(Kokkos_VERSION_MINOR 4) +set(Kokkos_VERSION_PATCH 00) set(Kokkos_VERSION "${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR}.${Kokkos_VERSION_PATCH}") math(EXPR KOKKOS_VERSION "${Kokkos_VERSION_MAJOR} * 10000 + ${Kokkos_VERSION_MINOR} * 100 + ${Kokkos_VERSION_PATCH}") -IF(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.12.0") - MESSAGE(STATUS "Setting policy CMP0074 to use _ROOT variables") - CMAKE_POLICY(SET CMP0074 NEW) -ENDIF() +MESSAGE(STATUS "Setting policy CMP0074 to use _ROOT variables") +CMAKE_POLICY(SET CMP0074 NEW) # Load either the real TriBITS or a TriBITS wrapper # for certain utility functions that are universal (like GLOBAL_SET) INCLUDE(${KOKKOS_SRC_PATH}/cmake/fake_tribits.cmake) -IF (Kokkos_ENABLE_CUDA AND ${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.14.0") - #If we are building CUDA, we have tricked CMake because we declare a CXX project - #If the default C++ standard for a given compiler matches the requested - #standard, then CMake just omits the -std flag in later versions of CMake - #This breaks CUDA compilation (CUDA compiler can have a different default - #-std then the underlying host compiler by itself). Setting this variable - #forces CMake to always add the -std flag even if it thinks it doesn't need it +IF (Kokkos_ENABLE_CUDA) + # If we are building CUDA, we have tricked CMake because we declare a CXX project + # If the default C++ standard for a given compiler matches the requested + # standard, then CMake just omits the -std flag in later versions of CMake + # This breaks CUDA compilation (CUDA compiler can have a different default + # -std then the underlying host compiler by itself). Setting this variable + # forces CMake to always add the -std flag even if it thinks it doesn't need it GLOBAL_SET(CMAKE_CXX_STANDARD_DEFAULT 98) ENDIF() @@ -139,15 +137,19 @@ ENDIF() # I really wish these were regular variables # but scoping issues can make it difficult GLOBAL_SET(KOKKOS_COMPILE_OPTIONS) -GLOBAL_SET(KOKKOS_LINK_OPTIONS -DKOKKOS_DEPENDENCE) +GLOBAL_SET(KOKKOS_LINK_OPTIONS) GLOBAL_SET(KOKKOS_CUDA_OPTIONS) GLOBAL_SET(KOKKOS_CUDAFE_OPTIONS) GLOBAL_SET(KOKKOS_XCOMPILER_OPTIONS) # We need to append text here for making sure TPLs # we import are available for an installed Kokkos GLOBAL_SET(KOKKOS_TPL_EXPORTS) -# this could probably be scoped to project +# KOKKOS_DEPENDENCE is used by kokkos_launch_compiler GLOBAL_SET(KOKKOS_COMPILE_DEFINITIONS KOKKOS_DEPENDENCE) +# MSVC never goes through kokkos_launch_compiler +IF(NOT MSVC) + GLOBAL_APPEND(KOKKOS_LINK_OPTIONS -DKOKKOS_DEPENDENCE) +ENDIF() # Include a set of Kokkos-specific wrapper functions that # will either call raw CMake or TriBITS diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos index 061b7a46ee..aa97f99b75 100644 --- a/lib/kokkos/Makefile.kokkos +++ b/lib/kokkos/Makefile.kokkos @@ -11,8 +11,8 @@ CXXFLAGS += $(SHFLAGS) endif KOKKOS_VERSION_MAJOR = 3 -KOKKOS_VERSION_MINOR = 3 -KOKKOS_VERSION_PATCH = 1 +KOKKOS_VERSION_MINOR = 4 +KOKKOS_VERSION_PATCH = 00 KOKKOS_VERSION = $(shell echo $(KOKKOS_VERSION_MAJOR)*10000+$(KOKKOS_VERSION_MINOR)*100+$(KOKKOS_VERSION_PATCH) | bc) # Options: Cuda,HIP,OpenMP,Pthread,Serial @@ -20,7 +20,7 @@ KOKKOS_DEVICES ?= "OpenMP" #KOKKOS_DEVICES ?= "Pthread" # Options: # Intel: KNC,KNL,SNB,HSW,BDW,SKX -# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75,Ampere80 +# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75,Ampere80,Ampere86 # ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2,A64FX # IBM: BGQ,Power7,Power8,Power9 # AMD-GPUS: Vega900,Vega906,Vega908 @@ -164,17 +164,17 @@ KOKKOS_INTERNAL_OS_DARWIN := $(call kokkos_has_string,$(KOKKOS_OS),Darwin) KOKKOS_CXX_VERSION := $(strip $(shell $(CXX) --version 2>&1)) KOKKOS_INTERNAL_COMPILER_INTEL := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),Intel Corporation) KOKKOS_INTERNAL_COMPILER_PGI := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),PGI) -KOKKOS_INTERNAL_COMPILER_XL := $(strip $(shell $(CXX) -qversion 2>&1 | grep XL | wc -l)) -KOKKOS_INTERNAL_COMPILER_CRAY := $(strip $(shell $(CXX) -craype-verbose 2>&1 | grep "CC-" | wc -l)) -KOKKOS_INTERNAL_COMPILER_NVCC := $(strip $(shell echo "$(shell export OMPI_CXX=$(OMPI_CXX); export MPICH_CXX=$(MPICH_CXX); $(CXX) --version 2>&1 | grep nvcc | wc -l)>0" | bc)) +KOKKOS_INTERNAL_COMPILER_XL := $(strip $(shell $(CXX) -qversion 2>&1 | grep -c XL)) +KOKKOS_INTERNAL_COMPILER_CRAY := $(strip $(shell $(CXX) -craype-verbose 2>&1 | grep -c "CC-")) +KOKKOS_INTERNAL_COMPILER_NVCC := $(strip $(shell echo "$(shell export OMPI_CXX=$(OMPI_CXX); export MPICH_CXX=$(MPICH_CXX); $(CXX) --version 2>&1 | grep -c nvcc)>0" | bc)) KOKKOS_INTERNAL_COMPILER_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),clang) -KOKKOS_INTERNAL_COMPILER_APPLE_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),Apple LLVM) +KOKKOS_INTERNAL_COMPILER_APPLE_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),Apple clang) KOKKOS_INTERNAL_COMPILER_HCC := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),HCC) KOKKOS_INTERNAL_COMPILER_GCC := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),GCC) # Check Host Compiler if using NVCC through nvcc_wrapper ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) - KOKKOS_INTERNAL_COMPILER_NVCC_WRAPPER := $(strip $(shell echo $(CXX) | grep nvcc_wrapper | wc -l)) + KOKKOS_INTERNAL_COMPILER_NVCC_WRAPPER := $(strip $(shell echo $(CXX) | grep -c nvcc_wrapper)) ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC_WRAPPER), 1) KOKKOS_CXX_HOST_VERSION := $(strip $(shell $(CXX) $(CXXFLAGS) --host-version 2>&1)) @@ -297,11 +297,11 @@ else #KOKKOS_INTERNAL_CXX1Z_FLAG := -hstd=c++1z #KOKKOS_INTERNAL_CXX2A_FLAG := -hstd=c++2a else - KOKKOS_INTERNAL_CXX14_FLAG := --std=c++14 - KOKKOS_INTERNAL_CXX1Y_FLAG := --std=c++1y - KOKKOS_INTERNAL_CXX17_FLAG := --std=c++17 - KOKKOS_INTERNAL_CXX1Z_FLAG := --std=c++1z - KOKKOS_INTERNAL_CXX2A_FLAG := --std=c++2a + KOKKOS_INTERNAL_CXX14_FLAG := -std=c++14 + KOKKOS_INTERNAL_CXX1Y_FLAG := -std=c++1y + KOKKOS_INTERNAL_CXX17_FLAG := -std=c++17 + KOKKOS_INTERNAL_CXX1Z_FLAG := -std=c++1z + KOKKOS_INTERNAL_CXX2A_FLAG := -std=c++2a endif endif endif @@ -332,6 +332,7 @@ KOKKOS_INTERNAL_USE_ARCH_VOLTA70 := $(call kokkos_has_string,$(KOKKOS_ARCH),Volt KOKKOS_INTERNAL_USE_ARCH_VOLTA72 := $(call kokkos_has_string,$(KOKKOS_ARCH),Volta72) KOKKOS_INTERNAL_USE_ARCH_TURING75 := $(call kokkos_has_string,$(KOKKOS_ARCH),Turing75) KOKKOS_INTERNAL_USE_ARCH_AMPERE80 := $(call kokkos_has_string,$(KOKKOS_ARCH),Ampere80) +KOKKOS_INTERNAL_USE_ARCH_AMPERE86 := $(call kokkos_has_string,$(KOKKOS_ARCH),Ampere86) KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KEPLER30) \ + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER32) \ + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER35) \ @@ -344,7 +345,8 @@ KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KEPLE + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA70) \ + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA72) \ + $(KOKKOS_INTERNAL_USE_ARCH_TURING75) \ - + $(KOKKOS_INTERNAL_USE_ARCH_AMPERE80)) + + $(KOKKOS_INTERNAL_USE_ARCH_AMPERE80) \ + + $(KOKKOS_INTERNAL_USE_ARCH_AMPERE86)) #SEK: This seems like a bug to me ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0) @@ -585,10 +587,10 @@ ifeq ($(KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT), 1) endif ifeq ($(KOKKOS_INTERNAL_ENABLE_TUNING), 1) - tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_TUNING") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_TUNING") endif -tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_LIBDL") +tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_LIBDL") ifeq ($(KOKKOS_INTERNAL_USE_HWLOC), 1) ifneq ($(KOKKOS_CMAKE), yes) @@ -752,6 +754,14 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_A64FX), 1) KOKKOS_CXXFLAGS += -march=armv8.2-a+sve KOKKOS_LDFLAGS += -march=armv8.2-a+sve + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + KOKKOS_CXXFLAGS += -msve-vector-bits=512 + KOKKOS_LDFLAGS += -msve-vector-bits=512 + endif + ifeq ($(KOKKOS_INTERNAL_COMPILER_GCC), 1) + KOKKOS_CXXFLAGS += -msve-vector-bits=512 + KOKKOS_LDFLAGS += -msve-vector-bits=512 + endif endif ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN), 1) @@ -1100,6 +1110,11 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA_ARCH), 1) tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMPERE80") KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_80 endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMPERE86), 1) + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMPERE") + tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMPERE86") + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_86 + endif ifneq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0) KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG) @@ -1159,7 +1174,7 @@ endif KOKKOS_INTERNAL_LS_CONFIG := $(shell ls KokkosCore_config.h 2>&1) ifeq ($(KOKKOS_INTERNAL_LS_CONFIG), KokkosCore_config.h) - KOKKOS_INTERNAL_NEW_CONFIG := $(strip $(shell diff KokkosCore_config.h KokkosCore_config.tmp | grep define | wc -l)) + KOKKOS_INTERNAL_NEW_CONFIG := $(strip $(shell diff KokkosCore_config.h KokkosCore_config.tmp | grep -c define)) else KOKKOS_INTERNAL_NEW_CONFIG := 1 endif @@ -1181,41 +1196,41 @@ tmp := $(call kokkos_update_config_header, KOKKOS_SETUP_HPP_, "KokkosCore_Config tmp := $(call kokkos_update_config_header, KOKKOS_DECLARE_HPP_, "KokkosCore_Config_DeclareBackend.tmp", "KokkosCore_Config_DeclareBackend.hpp") tmp := $(call kokkos_update_config_header, KOKKOS_POST_INCLUDE_HPP_, "KokkosCore_Config_PostInclude.tmp", "KokkosCore_Config_PostInclude.hpp") ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_SetupBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_SetupBackend.hpp") ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1) else endif endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") endif ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_SetupBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_SetupBackend.hpp") endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") endif ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") endif ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") endif ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") endif ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_FwdBackend.hpp") - tmp := $(call kokkos_append_config_header,"\#include ","KokkosCore_Config_DeclareBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_FwdBackend.hpp") + tmp := $(call kokkos_append_config_header,"$H""include ","KokkosCore_Config_DeclareBackend.hpp") endif KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/*.hpp) KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/impl/*.hpp) @@ -1334,7 +1349,7 @@ ifneq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) endif # With Cygwin functions such as fdopen and fileno are not defined -# when strict ansi is enabled. strict ansi gets enabled with --std=c++14 +# when strict ansi is enabled. strict ansi gets enabled with -std=c++14 # though. So we hard undefine it here. Not sure if that has any bad side effects # This is needed for gtest actually, not for Kokkos itself! ifeq ($(KOKKOS_INTERNAL_OS_CYGWIN), 1) diff --git a/lib/kokkos/Makefile.targets b/lib/kokkos/Makefile.targets index 5a03f7d17e..cf9fc24242 100644 --- a/lib/kokkos/Makefile.targets +++ b/lib/kokkos/Makefile.targets @@ -36,6 +36,8 @@ Kokkos_MemorySpace.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_ $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_MemorySpace.cpp Kokkos_HostSpace_deepcopy.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HostSpace_deepcopy.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HostSpace_deepcopy.cpp +Kokkos_NumericTraits.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_NumericTraits.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_NumericTraits.cpp ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) Kokkos_Cuda_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Instance.cpp diff --git a/lib/kokkos/algorithms/src/Kokkos_Random.hpp b/lib/kokkos/algorithms/src/Kokkos_Random.hpp index 69d6cf8f35..904cf5ccb9 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Random.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Random.hpp @@ -668,6 +668,25 @@ struct Random_UniqueIndex { }; #endif +#ifdef KOKKOS_ENABLE_SYCL +template <> +struct Random_UniqueIndex { + using locks_view_type = View; + KOKKOS_FUNCTION + static int get_state_idx(const locks_view_type& locks_) { +#ifdef KOKKOS_ARCH_INTEL_GEN + int i = Kokkos::Impl::clock_tic() % locks_.extent(0); +#else + int i = 0; +#endif + while (Kokkos::atomic_compare_exchange(&locks_(i), 0, 1)) { + i = (i + 1) % static_cast(locks_.extent(0)); + } + return i; + } +}; +#endif + } // namespace Impl template @@ -1028,7 +1047,7 @@ class Random_XorShift1024 { KOKKOS_INLINE_FUNCTION double drand(const double& start, const double& end) { - return frand(end - start) + start; + return drand(end - start) + start; } // Marsaglia polar method for drawing a standard normal distributed random diff --git a/lib/kokkos/algorithms/unit_tests/CMakeLists.txt b/lib/kokkos/algorithms/unit_tests/CMakeLists.txt index 819c9e54ba..9109837985 100644 --- a/lib/kokkos/algorithms/unit_tests/CMakeLists.txt +++ b/lib/kokkos/algorithms/unit_tests/CMakeLists.txt @@ -3,6 +3,7 @@ KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) KOKKOS_INCLUDE_DIRECTORIES(REQUIRED_DURING_INSTALLATION_TESTING ${CMAKE_CURRENT_SOURCE_DIR}) KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/../src ) +KOKKOS_INCLUDE_DIRECTORIES(${KOKKOS_SOURCE_DIR}/core/unit_test/category_files) SET(GTEST_SOURCE_DIR ${${PARENT_PACKAGE_NAME}_SOURCE_DIR}/tpls/gtest) @@ -25,7 +26,7 @@ KOKKOS_ADD_TEST_LIBRARY( TARGET_COMPILE_DEFINITIONS(kokkosalgorithms_gtest PUBLIC GTEST_HAS_TR1_TUPLE=0 GTEST_HAS_PTHREAD=0) IF((NOT (Kokkos_ENABLE_CUDA AND WIN32)) AND (NOT ("${KOKKOS_CXX_COMPILER_ID}" STREQUAL "Fujitsu"))) -TARGET_COMPILE_FEATURES(kokkosalgorithms_gtest PUBLIC cxx_std_11) + TARGET_COMPILE_FEATURES(kokkosalgorithms_gtest PUBLIC cxx_std_14) ENDIF() # Suppress clang-tidy diagnostics on code that we do not have control over @@ -33,51 +34,42 @@ IF(CMAKE_CXX_CLANG_TIDY) SET_TARGET_PROPERTIES(kokkosalgorithms_gtest PROPERTIES CXX_CLANG_TIDY "") ENDIF() -SET(SOURCES - UnitTestMain.cpp -) +SET(ALGORITHM UnitTestMain.cpp) IF(Kokkos_ENABLE_OPENMP) - LIST( APPEND SOURCES - TestOpenMP.cpp + LIST(APPEND ALGORITHM_SOURCES TestOpenMP_Sort1D.cpp TestOpenMP_Sort3D.cpp TestOpenMP_SortDynamicView.cpp - TestOpenMP_Random.cpp ) ENDIF() -IF(Kokkos_ENABLE_HIP) - LIST( APPEND SOURCES - TestHIP.cpp - ) -ENDIF() +foreach(Tag Threads;Serial;OpenMP;Cuda;HPX;HIP;SYCL) + # Because there is always an exception to the rule + if(Tag STREQUAL "Threads") + set(DEVICE "PTHREAD") + else() + string(TOUPPER ${Tag} DEVICE) + endif() -IF(Kokkos_ENABLE_CUDA) - LIST( APPEND SOURCES - TestCuda.cpp - ) -ENDIF() - -IF(Kokkos_ENABLE_HPX) - LIST( APPEND SOURCES - TestHPX.cpp - ) -ENDIF() - -IF(Kokkos_ENABLE_SERIAL) - LIST( APPEND SOURCES - TestSerial.cpp - ) -ENDIF() - -IF(Kokkos_ENABLE_PTHREAD) - LIST( APPEND SOURCES - TestThreads.cpp - ) -ENDIF() + if(Kokkos_ENABLE_${DEVICE}) + set(dir ${CMAKE_CURRENT_BINARY_DIR}) + set(file ${dir}/Test${Tag}.cpp) + # Write to a temporary intermediate file and call configure_file to avoid + # updating timestamps triggering unnecessary rebuilds on subsequent cmake runs. + file(WRITE ${dir}/dummy.cpp + "#include \n" + "#include \n" + "#include \n" + ) + configure_file(${dir}/dummy.cpp ${file}) + list(APPEND ALGORITHM_SOURCES ${file}) + endif() +endforeach() KOKKOS_ADD_EXECUTABLE_AND_TEST( UnitTest - SOURCES ${SOURCES} + SOURCES + UnitTestMain.cpp + ${ALGORITHM_SOURCES} ) diff --git a/lib/kokkos/algorithms/unit_tests/Makefile b/lib/kokkos/algorithms/unit_tests/Makefile index c112d7c6fc..dd0aa87de0 100644 --- a/lib/kokkos/algorithms/unit_tests/Makefile +++ b/lib/kokkos/algorithms/unit_tests/Makefile @@ -20,11 +20,19 @@ override LDFLAGS += -lpthread include $(KOKKOS_PATH)/Makefile.kokkos -KOKKOS_CXXFLAGS += -I$(GTEST_PATH) -I${KOKKOS_PATH}/algorithms/unit_tests +KOKKOS_CXXFLAGS += -I$(GTEST_PATH) -I${KOKKOS_PATH}/algorithms/unit_tests -I${KOKKOS_PATH}/core/unit_test/category_files TEST_TARGETS = TARGETS = +tmp := $(foreach device, $(KOKKOS_DEVICELIST), \ + $(if $(filter Test$(device).cpp, $(shell ls Test$(device).cpp 2>/dev/null)),,\ + $(shell echo "\#include " > Test$(device).cpp); \ + $(shell echo "\#include " >> Test$(device).cpp); \ + $(shell echo "\#include " >> Test$(device).cpp); \ + ) \ +) + ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) OBJ_CUDA = TestCuda.o UnitTestMain.o gtest-all.o TARGETS += KokkosAlgorithms_UnitTest_Cuda @@ -44,7 +52,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1) endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) - OBJ_OPENMP = TestOpenMP.o TestOpenMP_Random.o TestOpenMP_Sort1D.o TestOpenMP_Sort3D.o TestOpenMP_SortDynamicView.o UnitTestMain.o gtest-all.o + OBJ_OPENMP = TestOpenMP.o TestOpenMP_Sort1D.o TestOpenMP_Sort3D.o TestOpenMP_SortDynamicView.o UnitTestMain.o gtest-all.o TARGETS += KokkosAlgorithms_UnitTest_OpenMP TEST_TARGETS += test-openmp endif diff --git a/lib/kokkos/algorithms/unit_tests/TestOpenMP_Sort1D.cpp b/lib/kokkos/algorithms/unit_tests/TestOpenMP_Sort1D.cpp index a9b2010ad0..4a5839f0c8 100644 --- a/lib/kokkos/algorithms/unit_tests/TestOpenMP_Sort1D.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestOpenMP_Sort1D.cpp @@ -59,6 +59,8 @@ TEST(openmp, SortUnsigned1D) { Impl::test_1D_sort(171); } +TEST(openmp, SortIssue1160) { Impl::test_issue_1160_sort(); } + } // namespace Test #else void KOKKOS_ALGORITHMS_UNITTESTS_TESTOPENMP_PREVENT_LINK_ERROR() {} diff --git a/lib/kokkos/algorithms/unit_tests/TestRandom.hpp b/lib/kokkos/algorithms/unit_tests/TestRandom.hpp index caba92c152..1f14875096 100644 --- a/lib/kokkos/algorithms/unit_tests/TestRandom.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestRandom.hpp @@ -491,6 +491,34 @@ void test_random(unsigned int num_draws) { } } // namespace Impl +template +void test_random_xorshift64() { +#if defined(KOKKOS_ENABLE_SYCL) || defined(KOKKOS_ENABLE_CUDA) || \ + defined(KOKKOS_ENABLE_HIP) + const int num_draws = 132141141; +#else // SERIAL, HPX, OPENMP + const int num_draws = 10240000; +#endif + Impl::test_random>(num_draws); + Impl::test_random>>( + num_draws); +} + +template +void test_random_xorshift1024() { +#if defined(KOKKOS_ENABLE_SYCL) || defined(KOKKOS_ENABLE_CUDA) || \ + defined(KOKKOS_ENABLE_HIP) + const int num_draws = 52428813; +#else // SERIAL, HPX, OPENMP + const int num_draws = 10130144; +#endif + Impl::test_random>( + num_draws); + Impl::test_random>>( + num_draws); +} } // namespace Test #endif // KOKKOS_TEST_UNORDERED_MAP_HPP diff --git a/lib/kokkos/algorithms/unit_tests/TestRandomCommon.hpp b/lib/kokkos/algorithms/unit_tests/TestRandomCommon.hpp new file mode 100644 index 0000000000..c6d3b59ae1 --- /dev/null +++ b/lib/kokkos/algorithms/unit_tests/TestRandomCommon.hpp @@ -0,0 +1,60 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 3.0 +// Copyright (2020) National Technology & Engineering +// Solutions of Sandia, LLC (NTESS). +// +// Under the terms of Contract DE-NA0003525 with NTESS, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#ifndef KOKKOS_ALGORITHMS_UNITTESTS_TESTRANDOM_COMMON_HPP +#define KOKKOS_ALGORITHMS_UNITTESTS_TESTRANDOM_COMMON_HPP + +#include + +namespace Test { + +TEST(TEST_CATEGORY, Random_XorShift64) { + test_random_xorshift64(); +} +TEST(TEST_CATEGORY, Random_XorShift1024_0) { + test_random_xorshift1024(); +} +} // namespace Test + +#endif diff --git a/lib/kokkos/containers/unit_tests/TestCuda_Category.hpp b/lib/kokkos/algorithms/unit_tests/TestSortCommon.hpp similarity index 88% rename from lib/kokkos/containers/unit_tests/TestCuda_Category.hpp rename to lib/kokkos/algorithms/unit_tests/TestSortCommon.hpp index 50935d7a34..56657b6574 100644 --- a/lib/kokkos/containers/unit_tests/TestCuda_Category.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestSortCommon.hpp @@ -42,10 +42,14 @@ //@HEADER */ -#ifndef KOKKOS_TEST_CUDA_HPP -#define KOKKOS_TEST_CUDA_HPP +#ifndef KOKKOS_ALGORITHMS_UNITTESTS_TESTSORT_COMMON_HPP +#define KOKKOS_ALGORITHMS_UNITTESTS_TESTSORT_COMMON_HPP -#define TEST_CATEGORY cuda -#define TEST_EXECSPACE Kokkos::Cuda +#include +namespace Test { +TEST(TEST_CATEGORY, SortUnsigned) { + Impl::test_sort(171); +} +} // namespace Test #endif diff --git a/lib/kokkos/appveyor.yml b/lib/kokkos/appveyor.yml index c40bf066b7..e8763c0b66 100644 --- a/lib/kokkos/appveyor.yml +++ b/lib/kokkos/appveyor.yml @@ -3,8 +3,4 @@ image: clone_folder: c:\projects\source build_script: - cmd: >- - mkdir build && - cd build && - cmake c:\projects\source -DKokkos_ENABLE_TESTS=ON && - cmake --build . --target install && - ctest -C Debug -V + cmake c:\projects\source -DKokkos_ENABLE_TESTS=ON -DCMAKE_CXX_FLAGS="/W0 /EHsc /d1reportClassLayoutChanges" -DCTEST_ARGS="-C Debug -V --output-on-failure" -DBUILD_NAME=MSVC-2019 -DBUILD_TYPE=Debug -DSITE=AppVeyor -DTARGET=install -P cmake/KokkosCI.cmake diff --git a/lib/kokkos/bin/kokkos_launch_compiler b/lib/kokkos/bin/kokkos_launch_compiler index 1fbebf648f..d929d24f1d 100755 --- a/lib/kokkos/bin/kokkos_launch_compiler +++ b/lib/kokkos/bin/kokkos_launch_compiler @@ -13,6 +13,17 @@ # $1 are 'ar', 'cmake', etc. during the linking phase # +# emit a message about the underlying command executed +: ${DEBUG:=0} +: ${KOKKOS_DEBUG_LAUNCH_COMPILER:=${DEBUG}} + +debug-message() +{ + if [ "${KOKKOS_DEBUG_LAUNCH_COMPILER}" -ne 0 ]; then + echo -e "##### $(basename ${BASH_SOURCE[0]}) executing: \"$@\"... #####" + fi +} + # check the arguments for the KOKKOS_DEPENDENCE compiler definition KOKKOS_DEPENDENCE=0 for i in ${@} @@ -23,16 +34,30 @@ do fi done -# if C++ is not passed, someone is probably trying to invoke it directly +# if Kokkos compiler is not passed, someone is probably trying to invoke it directly if [ -z "${1}" ]; then - echo -e "\n${BASH_SOURCE[0]} was invoked without the C++ compiler as the first argument." + echo -e "\n${BASH_SOURCE[0]} was invoked without the Kokkos compiler as the first argument." echo "This script is not indended to be directly invoked by any mechanism other" - echo -e "than through a RULE_LAUNCH_COMPILE or RULE_LAUNCH_LINK property set in CMake\n" + echo -e "than through a RULE_LAUNCH_COMPILE or RULE_LAUNCH_LINK property set in CMake.\n" + exit 1 +fi + +# if Kokkos compiler is not passed, someone is probably trying to invoke it directly +if [ -z "${2}" ]; then + echo -e "\n${BASH_SOURCE[0]} was invoked without the C++ compiler as the second argument." + echo "This script is not indended to be directly invoked by any mechanism other" + echo -e "than through a RULE_LAUNCH_COMPILE or RULE_LAUNCH_LINK property set in CMake.\n" exit 1 fi # if there aren't two args, this isn't necessarily invalid, just a bit strange -if [ -z "${2}" ]; then exit 0; fi +if [ -z "${3}" ]; then exit 0; fi + +# store the Kokkos compiler +KOKKOS_COMPILER=${1} + +# remove the Kokkos compiler from the arguments +shift # store the expected C++ compiler CXX_COMPILER=${1} @@ -40,48 +65,57 @@ CXX_COMPILER=${1} # remove the expected C++ compiler from the arguments shift -# after the above shift, $1 is now the exe for the compile or link command, e.g. -# kokkos_launch_compiler g++ gcc -c file.c -o file.o +# NOTE: in below, ${KOKKOS_COMPILER} is usually nvcc_wrapper +# +# after the above shifts, $1 is now the exe for the compile or link command, e.g. +# kokkos_launch_compiler ${KOKKOS_COMPILER} g++ gcc -c file.c -o file.o # becomes: # kokkos_launch_compiler gcc -c file.c -o file.o -# Check to see if the executable is the C++ compiler and if it is not, then +# We check to see if the executable is the C++ compiler and if it is not, then # just execute the command. # # Summary: -# kokkos_launch_compiler g++ gcc -c file.c -o file.o +# kokkos_launch_compiler ${KOKKOS_COMPILER} g++ gcc -c file.c -o file.o # results in this command being executed: # gcc -c file.c -o file.o # and -# kokkos_launch_compiler g++ g++ -c file.cpp -o file.o +# kokkos_launch_compiler ${KOKKOS_COMPILER} g++ g++ -c file.cpp -o file.o # results in this command being executed: -# nvcc_wrapper -c file.cpp -o file.o +# ${KOKKOS_COMPILER} -c file.cpp -o file.o if [[ "${KOKKOS_DEPENDENCE}" -eq "0" || "${CXX_COMPILER}" != "${1}" ]]; then - # the command does not depend on Kokkos so just execute the command w/o re-directing to nvcc_wrapper + debug-message $@ + # the command does not depend on Kokkos so just execute the command w/o re-directing to ${KOKKOS_COMPILER} eval $@ else - # the executable is the C++ compiler, so we need to re-direct to nvcc_wrapper - - # find the nvcc_wrapper from the same build/install - NVCC_WRAPPER="$(dirname ${BASH_SOURCE[0]})/nvcc_wrapper" - - if [ -z "${NVCC_WRAPPER}" ]; then - echo -e "\nError: nvcc_wrapper not found in $(dirname ${BASH_SOURCE[0]}).\n" + # the executable is the C++ compiler, so we need to re-direct to ${KOKKOS_COMPILER} + if [ ! -f "${KOKKOS_COMPILER}" ]; then + echo -e "\nError: the compiler redirect for Kokkos was not found at ${KOKKOS_COMPILER}\n" exit 1 fi - # set default nvcc wrapper compiler if not specified - : ${NVCC_WRAPPER_DEFAULT_COMPILER:=${CXX_COMPILER}} - export NVCC_WRAPPER_DEFAULT_COMPILER + # find the nvcc_wrapper from the same build/install + NVCC_WRAPPER="$(dirname ${BASH_SOURCE[0]})/nvcc_wrapper" + if [ "${KOKKOS_COMPILER}" = "${NVCC_WRAPPER}" ]; then + # this should only be valid in the install tree -- it will be set to CMAKE_CXX_COMPILER used using Kokkos installation + if [ -z $(echo "@NVCC_WRAPPER_DEFAULT_COMPILER@" | grep 'NVCC_WRAPPER_DEFAULT_COMPILER') ]; then + : ${NVCC_WRAPPER_DEFAULT_COMPILER:="@NVCC_WRAPPER_DEFAULT_COMPILER@"} + fi - # calling itself will cause an infinitely long build - if [ "${NVCC_WRAPPER}" = "${NVCC_WRAPPER_DEFAULT_COMPILER}" ]; then - echo -e "\nError: NVCC_WRAPPER == NVCC_WRAPPER_DEFAULT_COMPILER. Terminating to avoid infinite loop!\n" - exit 1 + # set default nvcc wrapper compiler if not specified + : ${NVCC_WRAPPER_DEFAULT_COMPILER:=${CXX_COMPILER}} + export NVCC_WRAPPER_DEFAULT_COMPILER + + # nvcc_wrapper calling itself will cause an infinitely long build + if [ "${NVCC_WRAPPER}" = "${NVCC_WRAPPER_DEFAULT_COMPILER}" ]; then + echo -e "\nError: NVCC_WRAPPER == NVCC_WRAPPER_DEFAULT_COMPILER. Terminating to avoid infinite loop!\n" + exit 1 + fi fi # discard the compiler from the command shift - # execute nvcc_wrapper - ${NVCC_WRAPPER} $@ + debug-message ${KOKKOS_COMPILER} $@ + # execute ${KOKKOS_COMPILER} (again, usually nvcc_wrapper) + ${KOKKOS_COMPILER} $@ fi diff --git a/lib/kokkos/bin/nvcc_wrapper b/lib/kokkos/bin/nvcc_wrapper index 4ecf4c66d5..5556e888e3 100755 --- a/lib/kokkos/bin/nvcc_wrapper +++ b/lib/kokkos/bin/nvcc_wrapper @@ -191,11 +191,11 @@ do shift ;; #Handle known nvcc args - --dryrun|--verbose|--keep|--keep-dir*|-G|--relocatable-device-code*|-lineinfo|-expt-extended-lambda|-expt-relaxed-constexpr|--resource-usage|-Xptxas*|--fmad*|--Wext-lambda-captures-this|-Wext-lambda-captures-this) + --dryrun|--verbose|--keep|--keep-dir*|-G|--relocatable-device-code*|-lineinfo|-expt-extended-lambda|-expt-relaxed-constexpr|--resource-usage|-Xptxas*|--fmad*|--use_fast_math|--Wext-lambda-captures-this|-Wext-lambda-captures-this) cuda_args="$cuda_args $1" ;; #Handle more known nvcc args - --expt-extended-lambda|--expt-relaxed-constexpr) + --expt-extended-lambda|--expt-relaxed-constexpr|--Wno-deprecated-gpu-targets|-Wno-deprecated-gpu-targets) cuda_args="$cuda_args $1" ;; #Handle known nvcc args that have an argument diff --git a/lib/kokkos/cmake/CTestConfig.cmake.in b/lib/kokkos/cmake/CTestConfig.cmake.in new file mode 100644 index 0000000000..1f82c0d64d --- /dev/null +++ b/lib/kokkos/cmake/CTestConfig.cmake.in @@ -0,0 +1,91 @@ +#----------------------------------------------------------------------------------------# +# +# CTestConfig.cmake template for Kokkos +# +#----------------------------------------------------------------------------------------# + +# +# dash-board related +# +set(CTEST_PROJECT_NAME "Kokkos") +set(CTEST_NIGHTLY_START_TIME "01:00:00 UTC") +set(CTEST_DROP_METHOD "https") +set(CTEST_DROP_SITE "cdash.nersc.gov") +set(CTEST_DROP_LOCATION "/submit.php?project=${CTEST_PROJECT_NAME}") +set(CTEST_CDASH_VERSION "1.6") +set(CTEST_CDASH_QUERY_VERSION TRUE) +set(CTEST_SUBMIT_RETRY_COUNT "1") +set(CTEST_SUBMIT_RETRY_DELAY "30") + +# +# configure/build related +# +set(CTEST_BUILD_NAME "@BUILD_NAME@") +set(CTEST_MODEL "@MODEL@") +set(CTEST_SITE "@SITE@") +set(CTEST_CONFIGURATION_TYPE "@BUILD_TYPE@") +set(CTEST_SOURCE_DIRECTORY "@SOURCE_REALDIR@") +set(CTEST_BINARY_DIRECTORY "@BINARY_REALDIR@") + +# +# configure/build related +# +set(CTEST_UPDATE_TYPE "git") +set(CTEST_UPDATE_VERSION_ONLY ON) +# set(CTEST_GENERATOR "") +# set(CTEST_GENERATOR_PLATFORM "") + +# +# testing related +# +set(CTEST_TIMEOUT "7200") +set(CTEST_TEST_TIMEOUT "7200") +set(CTEST_CUSTOM_MAXIMUM_NUMBER_OF_ERRORS "100") +set(CTEST_CUSTOM_MAXIMUM_NUMBER_OF_WARNINGS "100") +set(CTEST_CUSTOM_MAXIMUM_PASSED_TEST_OUTPUT_SIZE "1048576") + +# +# coverage related +# +set(CTEST_CUSTOM_COVERAGE_EXCLUDE ".*tpls/.*;/usr/.*;.*unit_test/.*;.*unit_tests/.*;.*perf_test/.*") + +# +# commands +# +if(NOT "@CHECKOUT_COMMAND@" STREQUAL "") + set(CTEST_CHECKOUT_COMMAND "@CHECKOUT_COMMAND@") +endif() +set(CTEST_UPDATE_COMMAND "@GIT_EXECUTABLE@") +set(CTEST_CONFIGURE_COMMAND "@CMAKE_COMMAND@ -DCMAKE_BUILD_TYPE=@BUILD_TYPE@ -DKokkos_ENABLE_TESTS=ON @CONFIG_ARGS@ @SOURCE_REALDIR@") +set(CTEST_BUILD_COMMAND "@CMAKE_COMMAND@ --build @BINARY_REALDIR@ --target @TARGET@") +if(NOT WIN32) + set(CTEST_BUILD_COMMAND "${CTEST_BUILD_COMMAND} -- -j@BUILD_JOBS@") +endif() +set(CTEST_COVERAGE_COMMAND "gcov") +set(CTEST_MEMORYCHECK_COMMAND "valgrind") +set(CTEST_GIT_COMMAND "@GIT_EXECUTABLE@") + +# +# various configs +# +set(APPEND_VALUE @APPEND@) +if(APPEND_VALUE) + set(APPEND_CTEST APPEND) +endif() + +macro(SET_TEST_PROP VAR) + if(NOT "${ARGS}" STREQUAL "") + set(${VAR}_CTEST ${VAR} ${ARGN}) + endif() +endmacro() + +set_test_prop(START @START@) +set_test_prop(END @END@) +set_test_prop(STRIDE @STRIDE@) +set_test_prop(INCLUDE @INCLUDE@) +set_test_prop(EXCLUDE @EXCLUDE@) +set_test_prop(INCLUDE_LABEL @INCLUDE_LABEL@) +set_test_prop(EXCLUDE_LABEL @EXCLUDE_LABEL@) +set_test_prop(PARALLEL_LEVEL @PARALLEL_LEVEL@) +set_test_prop(STOP_TIME @STOP_TIME@) +set_test_prop(COVERAGE_LABELS @LABELS@) diff --git a/lib/kokkos/cmake/KokkosCI.cmake b/lib/kokkos/cmake/KokkosCI.cmake new file mode 100644 index 0000000000..e8c9af37ad --- /dev/null +++ b/lib/kokkos/cmake/KokkosCI.cmake @@ -0,0 +1,350 @@ +cmake_minimum_required(VERSION 3.16 FATAL_ERROR) + +message(STATUS "") + +get_cmake_property(_cached_vars CACHE_VARIABLES) +set(KOKKOS_CMAKE_ARGS) +set(EXCLUDED_VARIABLES "CMAKE_COMMAND" "CMAKE_CPACK_COMMAND" "CMAKE_CTEST_COMMAND" "CMAKE_ROOT" + "CTEST_ARGS" "BUILD_NAME" "CMAKE_CXX_FLAGS" "CMAKE_BUILD_TYPE") +list(SORT _cached_vars) +foreach(_var ${_cached_vars}) + if(NOT "${_var}" IN_LIST EXCLUDED_VARIABLES) + list(APPEND KOKKOS_CMAKE_ARGS ${_var}) + if("${_var}" STREQUAL "CMAKE_BUILD_TYPE") + set(BUILD_TYPE "${CMAKE_BUILD_TYPE}") + endif() + endif() +endforeach() + + +#----------------------------------------------------------------------------------------# +# +# Macros and variables +# +#----------------------------------------------------------------------------------------# + +macro(CHECK_REQUIRED VAR) + if(NOT DEFINED ${VAR}) + message(FATAL_ERROR "Error! Variable '${VAR}' must be defined") + endif() +endmacro() + +# require the build name variable +CHECK_REQUIRED(BUILD_NAME) + +# uses all args +macro(SET_DEFAULT VAR) + if(NOT DEFINED ${VAR}) + set(${VAR} ${ARGN}) + endif() + # remove these ctest configuration variables from the defines + # passed to the Kokkos configuration + if("${VAR}" IN_LIST KOKKOS_CMAKE_ARGS) + list(REMOVE_ITEM KOKKOS_CMAKE_ARGS "${VAR}") + endif() +endmacro() + +# uses first arg -- useful for selecting via priority from multiple +# potentially defined variables, e.g.: +# +# set_default_arg1(BUILD_NAME ${TRAVIS_BUILD_NAME} ${BUILD_NAME}) +# +macro(SET_DEFAULT_ARG1 VAR) + if(NOT DEFINED ${VAR}) + foreach(_ARG ${ARGN}) + if(NOT "${_ARG}" STREQUAL "") + set(${VAR} ${_ARG}) + break() + endif() + endforeach() + endif() + # remove these ctest configuration variables from the defines + # passed to the Kokkos configuration + if("${VAR}" IN_LIST KOKKOS_CMAKE_ARGS) + list(REMOVE_ITEM KOKKOS_CMAKE_ARGS "${VAR}") + endif() +endmacro() + +# determine the default working directory +if(NOT "$ENV{WORKSPACE}" STREQUAL "") + set(WORKING_DIR "$ENV{WORKSPACE}") +else() + get_filename_component(WORKING_DIR ${CMAKE_CURRENT_LIST_DIR} DIRECTORY) +endif() + +# determine the hostname +execute_process(COMMAND hostname + OUTPUT_VARIABLE HOSTNAME + OUTPUT_STRIP_TRAILING_WHITESPACE) + +SET_DEFAULT(HOSTNAME "$ENV{HOSTNAME}") + +# get the number of processors +include(ProcessorCount) +ProcessorCount(NUM_PROCESSORS) + +# find git +find_package(Git QUIET) +if(NOT GIT_EXECUTABLE) + unset(GIT_EXECUTABLE CACHE) + unset(GIT_EXECUTABLE) +endif() + +function(EXECUTE_GIT_COMMAND VAR) + set(${VAR} "" PARENT_SCOPE) + execute_process(COMMAND ${GIT_EXECUTABLE} ${ARGN} + OUTPUT_VARIABLE VAL + RESULT_VARIABLE RET + OUTPUT_STRIP_TRAILING_WHITESPACE + WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR} + ERROR_QUIET) + string(REPLACE ";" " " _CMD "${GIT_EXECUTABLE} ${ARGN}") + set(LAST_GIT_COMMAND "${_CMD}" PARENT_SCOPE) + if(RET EQUAL 0) + set(${VAR} "${VAL}" PARENT_SCOPE) + endif() +endfunction() + +# just gets the git branch name if available +function(GET_GIT_BRANCH_NAME VAR) + execute_git_command(GIT_BRANCH branch --show-current) + set(_INVALID "%D" "HEAD") + if(NOT GIT_BRANCH OR "${GIT_BRANCH}" IN_LIST _INVALID) + execute_git_command(GIT_BRANCH show -s --format=%D) + if(NOT GIT_BRANCH OR "${GIT_BRANCH}" IN_LIST _INVALID) + execute_git_command(GIT_BRANCH --describe all) + endif() + endif() + # + if(GIT_BRANCH) + string(REPLACE " " ";" _DESC "${GIT_BRANCH}") + # just set it to last one via loop instead of wonky cmake index manip + foreach(_ITR ${_DESC}) + set(GIT_BRANCH "${_ITR}") + endforeach() + set(${VAR} "${GIT_BRANCH}" PARENT_SCOPE) + message(STATUS "GIT BRANCH via '${LAST_GIT_COMMAND}': ${GIT_BRANCH}") + endif() +endfunction() + +# just gets the git branch name if available +function(GET_GIT_AUTHOR_NAME VAR) + execute_git_command(GIT_AUTHOR show -s --format=%an) + if(GIT_AUTHOR) + string(LENGTH "${GIT_AUTHOR}" STRLEN) + # if the build name gets too long, this can cause submission errors + if(STRLEN GREATER 24) + # remove middle initial + string(REGEX REPLACE " [A-Z]\. " " " GIT_AUTHOR "${GIT_AUTHOR}") + # get first and sur name + string(REGEX REPLACE "([A-Za-z]+) ([A-Za-z]+)" "\\1" F_NAME "${GIT_AUTHOR}") + string(REGEX REPLACE "([A-Za-z]+) ([A-Za-z]+)" "\\2" S_NAME "${GIT_AUTHOR}") + if(S_NAME) + set(GIT_AUTHOR "${S_NAME}") + elseif(F_NAME) + set(GIT_AUTHOR "${F_NAME}") + endif() + endif() + # remove any spaces, quotes, periods, etc. + string(REGEX REPLACE "[ ',;_\.\"]+" "" GIT_AUTHOR "${GIT_AUTHOR}") + set(${VAR} "${GIT_AUTHOR}" PARENT_SCOPE) + message(STATUS "GIT AUTHOR via '${LAST_GIT_COMMAND}': ${GIT_AUTHOR}") + endif() +endfunction() + +# get the name of the branch +GET_GIT_BRANCH_NAME(GIT_BRANCH) +# get the name of the author +GET_GIT_AUTHOR_NAME(GIT_AUTHOR) +# author, prefer git method for consistency +SET_DEFAULT_ARG1(AUTHOR ${GIT_AUTHOR} $ENV{GIT_AUTHOR} $ENV{AUTHOR}) +# SLUG == owner_name/repo_name +SET_DEFAULT_ARG1(SLUG $ENV{TRAVIS_PULL_REQUEST_SLUG} $ENV{TRAVIS_REPO_SLUG} $ENV{APPVEYOR_REPO_NAME} $ENV{PULL_REQUEST_SLUG} $ENV{REPO_SLUG}) +# branch name +SET_DEFAULT_ARG1(BRANCH $ENV{TRAVIS_PULL_REQUEST_BRANCH} $ENV{TRAVIS_BRANCH} $ENV{APPVEYOR_PULL_REQUEST_HEAD_REPO_BRANCH} $ENV{APPVEYOR_REPO_BRANCH} $ENV{GIT_BRANCH} $ENV{BRANCH_NAME} $ENV{BRANCH} ${GIT_BRANCH}) +# pull request number +SET_DEFAULT_ARG1(PULL_REQUEST_NUM $ENV{TRAVIS_PULL_REQUEST} $ENV{CHANGE_ID} $ENV{APPVEYOR_PULL_REQUEST_NUMBER} $ENV{PULL_REQUEST_NUM}) +# get the event type, e.g. push, pull_request, api, cron, etc. +SET_DEFAULT_ARG1(EVENT_TYPE $ENV{TRAVIS_EVENT_TYPE} ${EVENT_TYPE}) + +if("${BRANCH}" STREQUAL "") + message(STATUS "Checked: environment variables for Travis, Appveyor, Jenkins (git plugin), BRANCH_NAME, BRANCH and 'git branch --show-current'") + message(FATAL_ERROR "Error! Git branch could not be determined. Please provide -DBRANCH=") +endif() + +#----------------------------------------------------------------------------------------# +# +# Set default values if not provided on command-line +# +#----------------------------------------------------------------------------------------# + +SET_DEFAULT(SOURCE_DIR "${WORKING_DIR}") # source directory +SET_DEFAULT(BINARY_DIR "${WORKING_DIR}/build") # build directory +SET_DEFAULT(BUILD_TYPE "${CMAKE_BUILD_TYPE}") # Release, Debug, etc. +SET_DEFAULT(MODEL "Continuous") # Continuous, Nightly, or Experimental +SET_DEFAULT(JOBS 1) # number of parallel ctests +SET_DEFAULT(CTEST_COMMAND "${CMAKE_CTEST_COMMAND}") # just in case +SET_DEFAULT(CTEST_ARGS "-V --output-on-failure") # extra arguments when ctest is called +SET_DEFAULT(GIT_EXECUTABLE "git") # ctest_update +SET_DEFAULT(TARGET "all") # build target +SET_DEFAULT_ARG1(SITE "$ENV{SITE}" + "${HOSTNAME}") # update site +SET_DEFAULT_ARG1(BUILD_JOBS "$ENV{BUILD_JOBS}" + "${NUM_PROCESSORS}") # number of parallel compile jobs +# +# The variable below correspond to ctest arguments, i.e. START,END,STRIDE are +# '-I START,END,STRIDE' +# +SET_DEFAULT(START "") +SET_DEFAULT(END "") +SET_DEFAULT(STRIDE "") +SET_DEFAULT(INCLUDE "") +SET_DEFAULT(EXCLUDE "") +SET_DEFAULT(INCLUDE_LABEL "") +SET_DEFAULT(EXCLUDE_LABEL "") +SET_DEFAULT(PARALLEL_LEVEL "") +SET_DEFAULT(STOP_TIME "") +SET_DEFAULT(LABELS "") +SET_DEFAULT(NOTES "") + +# default static build tag for Nightly +set(BUILD_TAG "${BRANCH}") + +if(NOT BUILD_TYPE) + # default for kokkos if not specified + set(BUILD_TYPE "RelWithDebInfo") +endif() + +# generate dynamic name if continuous or experimental model +if(NOT "${MODEL}" STREQUAL "Nightly") + if(EVENT_TYPE AND PULL_REQUEST_NUM) + # e.g. pull_request/123 + if(AUTHOR) + set(BUILD_TAG "${AUTHOR}/${EVENT_TYPE}/${PULL_REQUEST_NUM}") + else() + set(BUILD_TAG "${EVENT_TYPE}/${PULL_REQUEST_NUM}") + endif() + elseif(SLUG) + # e.g. owner_name/repo_name + set(BUILD_TAG "${SLUG}") + elseif(AUTHOR) + set(BUILD_TAG "${AUTHOR}/${BRANCH}") + endif() + if(EVENT_TYPE AND NOT PULL_REQUEST_NUM) + set(BUILD_TAG "${BUILD_TAG}-${EVENT_TYPE}") + endif() +endif() + +# unnecessary +string(REPLACE "/remotes/" "/" BUILD_TAG "${BUILD_TAG}") +string(REPLACE "/origin/" "/" BUILD_TAG "${BUILD_TAG}") + +message(STATUS "BUILD_TAG: ${BUILD_TAG}") + +set(BUILD_NAME "[${BUILD_TAG}] [${BUILD_NAME}-${BUILD_TYPE}]") + +# colons in build name create extra (empty) entries in CDash +string(REPLACE ":" "-" BUILD_NAME "${BUILD_NAME}") +# unnecessary info +string(REPLACE "/merge]" "]" BUILD_NAME "${BUILD_NAME}") +# consistency +string(REPLACE "/pr/" "/pull/" BUILD_NAME "${BUILD_NAME}") +string(REPLACE "pull_request/" "pull/" BUILD_NAME "${BUILD_NAME}") +# miscellaneous from missing fields +string(REPLACE "--" "-" BUILD_NAME "${BUILD_NAME}") +string(REPLACE "-]" "]" BUILD_NAME "${BUILD_NAME}") + +# check binary directory +if(EXISTS ${BINARY_DIR}) + if(NOT IS_DIRECTORY "${BINARY_DIR}") + message(FATAL_ERROR "Error! '${BINARY_DIR}' already exists and is not a directory!") + endif() + file(GLOB BINARY_DIR_FILES "${BINARY_DIR}/*") + if(NOT "${BINARY_DIR_FILES}" STREQUAL "") + message(FATAL_ERROR "Error! '${BINARY_DIR}' already exists and is not empty!") + endif() +endif() + +get_filename_component(SOURCE_REALDIR ${SOURCE_DIR} REALPATH) +get_filename_component(BINARY_REALDIR ${BINARY_DIR} REALPATH) + +#----------------------------------------------------------------------------------------# +# +# Generate the CTestConfig.cmake +# +#----------------------------------------------------------------------------------------# + +set(CONFIG_ARGS) +foreach(_ARG ${KOKKOS_CMAKE_ARGS}) + if(NOT "${${_ARG}}" STREQUAL "") + get_property(_ARG_TYPE CACHE ${_ARG} PROPERTY TYPE) + if("${_ARG_TYPE}" STREQUAL "UNINITIALIZED") + if("${${_ARG}}" STREQUAL "ON" OR "${${_ARG}}" STREQUAL "OFF") + set(_ARG_TYPE "BOOL") + elseif(EXISTS "${${_ARG}}" AND NOT IS_DIRECTORY "${${_ARG}}") + set(_ARG_TYPE "FILEPATH") + elseif(EXISTS "${${_ARG}}" AND IS_DIRECTORY "${${_ARG}}") + set(_ARG_TYPE "PATH") + elseif(NOT "${${_ARG}}" STREQUAL "") + set(_ARG_TYPE "STRING") + endif() + endif() + set(CONFIG_ARGS "${CONFIG_ARGS}set(${_ARG} \"${${_ARG}}\" CACHE ${_ARG_TYPE} \"\")\n") + endif() +endforeach() + +file(WRITE ${BINARY_REALDIR}/initial-cache.cmake +" +set(CMAKE_CXX_FLAGS \"${CMAKE_CXX_FLAGS}\" CACHE STRING \"\") +${CONFIG_ARGS} +") + +file(READ ${BINARY_REALDIR}/initial-cache.cmake _CACHE_INFO) +message(STATUS "Initial cache:\n${_CACHE_INFO}") + +# initialize the cache +set(CONFIG_ARGS "-C ${BINARY_REALDIR}/initial-cache.cmake") + + +# generate the CTestConfig.cmake +configure_file( + ${CMAKE_CURRENT_LIST_DIR}/CTestConfig.cmake.in + ${BINARY_REALDIR}/CTestConfig.cmake + @ONLY) + +# copy/generate the dashboard script +configure_file( + ${CMAKE_CURRENT_LIST_DIR}/KokkosCTest.cmake.in + ${BINARY_REALDIR}/KokkosCTest.cmake + @ONLY) + +# custom CTest settings go in ${BINARY_DIR}/CTestCustom.cmake +execute_process( + COMMAND ${CMAKE_COMMAND} -E touch CTestCustom.cmake + WORKING_DIRECTORY ${BINARY_REALDIR} + ) + +#----------------------------------------------------------------------------------------# +# +# Execute CTest +# +#----------------------------------------------------------------------------------------# + +message(STATUS "") +message(STATUS "BUILD_NAME: ${BUILD_NAME}") +message(STATUS "Executing '${CTEST_COMMAND} -S KokkosCTest.cmake ${CTEST_ARGS}'...") +message(STATUS "") + +# e.g. -DCTEST_ARGS="--output-on-failure -VV" should really be -DCTEST_ARGS="--output-on-failure;-VV" +string(REPLACE " " ";" CTEST_ARGS "${CTEST_ARGS}") + +execute_process( + COMMAND ${CTEST_COMMAND} -S KokkosCTest.cmake ${CTEST_ARGS} + RESULT_VARIABLE RET + WORKING_DIRECTORY ${BINARY_REALDIR} + ) + +# ensure that any non-zero result variable gets propagated +if(NOT RET EQUAL 0) + message(FATAL_ERROR "CTest return non-zero exit code: ${RET}") +endif() diff --git a/lib/kokkos/cmake/KokkosCTest.cmake.in b/lib/kokkos/cmake/KokkosCTest.cmake.in new file mode 100644 index 0000000000..b6917f3cc1 --- /dev/null +++ b/lib/kokkos/cmake/KokkosCTest.cmake.in @@ -0,0 +1,261 @@ +cmake_minimum_required(VERSION 3.16 FATAL_ERROR) + +if(EXISTS "${CMAKE_CURRENT_LIST_DIR}/CTestConfig.cmake") + include("${CMAKE_CURRENT_LIST_DIR}/CTestConfig.cmake") +endif() + +include(ProcessorCount) +ProcessorCount(CTEST_PROCESSOR_COUNT) + +cmake_policy(SET CMP0009 NEW) +cmake_policy(SET CMP0011 NEW) + +# ---------------------------------------------------------------------------- # +# -- Commands +# ---------------------------------------------------------------------------- # +find_program(CTEST_CMAKE_COMMAND NAMES cmake) +find_program(CTEST_UNAME_COMMAND NAMES uname) + +find_program(CTEST_BZR_COMMAND NAMES bzr) +find_program(CTEST_CVS_COMMAND NAMES cvs) +find_program(CTEST_GIT_COMMAND NAMES git) +find_program(CTEST_HG_COMMAND NAMES hg) +find_program(CTEST_P4_COMMAND NAMES p4) +find_program(CTEST_SVN_COMMAND NAMES svn) + +find_program(VALGRIND_COMMAND NAMES valgrind) +find_program(GCOV_COMMAND NAMES gcov) +find_program(LCOV_COMMAND NAMES llvm-cov) +find_program(MEMORYCHECK_COMMAND NAMES valgrind ) + +set(MEMORYCHECK_TYPE Valgrind) +# set(MEMORYCHECK_TYPE Purify) +# set(MEMORYCHECK_TYPE BoundsChecker) +# set(MEMORYCHECK_TYPE ThreadSanitizer) +# set(MEMORYCHECK_TYPE AddressSanitizer) +# set(MEMORYCHECK_TYPE LeakSanitizer) +# set(MEMORYCHECK_TYPE MemorySanitizer) +# set(MEMORYCHECK_TYPE UndefinedBehaviorSanitizer) +set(MEMORYCHECK_COMMAND_OPTIONS "--trace-children=yes --leak-check=full") + +# ---------------------------------------------------------------------------- # +# -- Settings +# ---------------------------------------------------------------------------- # +## -- Process timeout in seconds +set(CTEST_TIMEOUT "7200") +## -- Set output to English +set(ENV{LC_MESSAGES} "en_EN" ) + + +# ---------------------------------------------------------------------------- # +# -- Copy ctest configuration file +# ---------------------------------------------------------------------------- # +macro(COPY_CTEST_CONFIG_FILES) + + foreach(_FILE CTestConfig.cmake CTestCustom.cmake) + + # if current directory is not binary or source directory + if(NOT "${CMAKE_CURRENT_LIST_DIR}" STREQUAL "${CTEST_BINARY_DIRECTORY}" AND + NOT "${CTEST_SOURCE_DIRECTORY}" STREQUAL "${CTEST_BINARY_DIRECTORY}") + + # if file exists in current directory + if(EXISTS ${CMAKE_CURRENT_LIST_DIR}/${_FILE}) + configure_file(${CMAKE_CURRENT_LIST_DIR}/${_FILE} + ${CTEST_BINARY_DIRECTORY}/${_FILE} COPYONLY) + endif() + + # if source and binary differ + elseif(NOT "${CTEST_SOURCE_DIRECTORY}" STREQUAL "${CTEST_BINARY_DIRECTORY}") + + # if file exists in source directory but not in binary directory + if(EXISTS ${CTEST_SOURCE_DIRECTORY}/${_FILE} AND + NOT EXISTS ${CTEST_BINARY_DIRECTORY}/${_FILE}) + configure_file(${CTEST_SOURCE_DIRECTORY}/${_FILE} + ${CTEST_BINARY_DIRECTORY}/${_FILE} COPYONLY) + endif() + + endif() + endforeach() + +endmacro() + +ctest_read_custom_files("${CMAKE_CURRENT_LIST_DIR}") + +message(STATUS "CTEST_MODEL: ${CTEST_MODEL}") + +#-------------------------------------------------------------------------# +# Start +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running START_CTEST stage...") +message(STATUS "") + +ctest_start(${CTEST_MODEL} TRACK ${CTEST_MODEL} ${APPEND_CTEST} + ${CTEST_SOURCE_DIRECTORY} ${CTEST_BINARY_DIRECTORY}) + + +#-------------------------------------------------------------------------# +# Config +# +copy_ctest_config_files() +ctest_read_custom_files("${CTEST_BINARY_DIRECTORY}") + + +#-------------------------------------------------------------------------# +# Update +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_UPDATE stage...") +message(STATUS "") + +ctest_update(SOURCE "${CTEST_SOURCE_DIRECTORY}" + RETURN_VALUE up_ret) + + +#-------------------------------------------------------------------------# +# Configure +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_CONFIGURE stage...") +message(STATUS "") + +ctest_configure(BUILD "${CTEST_BINARY_DIRECTORY}" + SOURCE ${CTEST_SOURCE_DIRECTORY} + ${APPEND_CTEST} + OPTIONS "${CTEST_CONFIGURE_OPTIONS}" + RETURN_VALUE config_ret) + + +#-------------------------------------------------------------------------# +# Echo configure log bc Damien wants to delay merging this PR for eternity +# +file(GLOB _configure_log "${CTEST_BINARY_DIRECTORY}/Testing/Temporary/LastConfigure*.log") +# should only have one but loop just for safety +foreach(_LOG ${_configure_log}) + file(READ ${_LOG} _LOG_MESSAGE) + message(STATUS "Configure Log: ${_LOG}") + message(STATUS "\n${_LOG_MESSAGE}\n") +endforeach() + + +#-------------------------------------------------------------------------# +# Build +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_BUILD stage...") +message(STATUS "") + +ctest_build(BUILD "${CTEST_BINARY_DIRECTORY}" + ${APPEND_CTEST} + RETURN_VALUE build_ret) + + +#-------------------------------------------------------------------------# +# Echo build log bc Damien wants to delay merging this PR for eternity +# +file(GLOB _build_log "${CTEST_BINARY_DIRECTORY}/Testing/Temporary/LastBuild*.log") +# should only have one but loop just for safety +foreach(_LOG ${_build_log}) + file(READ ${_LOG} _LOG_MESSAGE) + message(STATUS "Build Log: ${_LOG}") + message(STATUS "\n${_LOG_MESSAGE}\n") +endforeach() + + +#-------------------------------------------------------------------------# +# Test +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_TEST stage...") +message(STATUS "") + +ctest_test(RETURN_VALUE test_ret + ${APPEND_CTEST} + ${START_CTEST} + ${END_CTEST} + ${STRIDE_CTEST} + ${INCLUDE_CTEST} + ${EXCLUDE_CTEST} + ${INCLUDE_LABEL_CTEST} + ${EXCLUDE_LABEL_CTEST} + ${PARALLEL_LEVEL_CTEST} + ${STOP_TIME_CTEST} + SCHEDULE_RANDOM OFF) + + +#-------------------------------------------------------------------------# +# Coverage +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_COVERAGE stage...") +message(STATUS "") + +execute_process(COMMAND ${CTEST_COVERAGE_COMMAND} ${CTEST_COVERAGE_EXTRA_FLAGS} + WORKING_DIRECTORY ${CTEST_BINARY_DIRECTORY} + ERROR_QUIET) + +ctest_coverage(${APPEND_CTEST} + ${CTEST_COVERAGE_LABELS} + RETURN_VALUE cov_ret) + + +#-------------------------------------------------------------------------# +# MemCheck +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_MEMCHECK stage...") +message(STATUS "") + +ctest_memcheck(RETURN_VALUE mem_ret + ${APPEND_CTEST} + ${START_CTEST} + ${END_CTEST} + ${STRIDE_CTEST} + ${INCLUDE_CTEST} + ${EXCLUDE_CTEST} + ${INCLUDE_LABEL_CTEST} + ${EXCLUDE_LABEL_CTEST} + ${PARALLEL_LEVEL_CTEST}) + + +#-------------------------------------------------------------------------# +# Submit +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Running CTEST_SUBMIT stage...") +message(STATUS "") + +file(GLOB_RECURSE NOTE_FILES "${CTEST_BINARY_DIRECTORY}/*CTestNotes.cmake") +foreach(_FILE ${NOTE_FILES}) + message(STATUS "Including CTest notes files: \"${_FILE}\"...") + include("${_FILE}") +endforeach() + +# capture submit error so it doesn't fail because of a submission error +ctest_submit(RETURN_VALUE submit_ret + RETRY_COUNT 2 + RETRY_DELAY 10 + CAPTURE_CMAKE_ERROR submit_err) + +#-------------------------------------------------------------------------# +# Submit +# +message(STATUS "") +message(STATUS "[${CTEST_BUILD_NAME}] Finished ${CTEST_MODEL} Stages (${STAGES})") +message(STATUS "") + + +#-------------------------------------------------------------------------# +# Non-zero exit codes for important errors +# +if(NOT config_ret EQUAL 0) + message(FATAL_ERROR "Error during configuration! Exit code: ${config_ret}") +endif() + +if(NOT build_ret EQUAL 0) + message(FATAL_ERROR "Error during build! Exit code: ${build_ret}") +endif() + +if(NOT test_ret EQUAL 0) + message(FATAL_ERROR "Error during testing! Exit code: ${test_ret}") +endif() diff --git a/lib/kokkos/cmake/KokkosConfig.cmake.in b/lib/kokkos/cmake/KokkosConfig.cmake.in index 9fbd22ee5c..44a8fcd9c3 100644 --- a/lib/kokkos/cmake/KokkosConfig.cmake.in +++ b/lib/kokkos/cmake/KokkosConfig.cmake.in @@ -19,17 +19,44 @@ INCLUDE("${Kokkos_CMAKE_DIR}/KokkosTargets.cmake") INCLUDE("${Kokkos_CMAKE_DIR}/KokkosConfigCommon.cmake") UNSET(Kokkos_CMAKE_DIR) -# if CUDA was enabled and separable compilation was specified, e.g. -# find_package(Kokkos COMPONENTS separable_compilation) -# then we set the RULE_LAUNCH_COMPILE and RULE_LAUNCH_LINK -IF(@Kokkos_ENABLE_CUDA@ AND NOT "separable_compilation" IN_LIST Kokkos_FIND_COMPONENTS) +# check for conflicts +IF("launch_compiler" IN_LIST Kokkos_FIND_COMPONENTS AND + "separable_compilation" IN_LIST Kokkos_FIND_COMPONENTS) + MESSAGE(STATUS "'launch_compiler' implies global redirection of targets depending on Kokkos to appropriate compiler.") + MESSAGE(STATUS "'separable_compilation' implies explicitly defining where redirection occurs via 'kokkos_compilation(PROJECT|TARGET|SOURCE|DIRECTORY ...)'") + MESSAGE(FATAL_ERROR "Conflicting COMPONENTS: 'launch_compiler' and 'separable_compilation'") +ENDIF() + +IF("launch_compiler" IN_LIST Kokkos_FIND_COMPONENTS) + # + # if find_package(Kokkos COMPONENTS launch_compiler) then rely on the + # RULE_LAUNCH_COMPILE and RULE_LAUNCH_LINK to always redirect to the + # appropriate compiler for Kokkos + # + + MESSAGE(STATUS "kokkos_launch_compiler is enabled globally. C++ compiler commands with -DKOKKOS_DEPENDENCE will be redirected to the appropriate compiler for Kokkos") + kokkos_compilation( + GLOBAL + CHECK_CUDA_COMPILES) + +ELSEIF(@Kokkos_ENABLE_CUDA@ AND NOT "separable_compilation" IN_LIST Kokkos_FIND_COMPONENTS) + # + # if CUDA was enabled, separable compilation was not specified, and current compiler + # cannot compile CUDA, then set the RULE_LAUNCH_COMPILE and RULE_LAUNCH_LINK globally and + # kokkos_launch_compiler will re-direct to the compiler used to compile CUDA code during installation. + # kokkos_launch_compiler will re-direct if ${CMAKE_CXX_COMPILER} and -DKOKKOS_DEPENDENCE is present, + # otherwise, the original command will be executed + # + # run test to see if CMAKE_CXX_COMPILER=nvcc_wrapper kokkos_compiler_is_nvcc(IS_NVCC ${CMAKE_CXX_COMPILER}) - # if not nvcc_wrapper, use RULE_LAUNCH_COMPILE and RULE_LAUNCH_LINK - IF(NOT IS_NVCC AND NOT CMAKE_CXX_COMPILER_ID STREQUAL Clang AND - (NOT DEFINED Kokkos_LAUNCH_COMPILER OR Kokkos_LAUNCH_COMPILER)) - MESSAGE(STATUS "kokkos_launch_compiler is enabled globally. C++ compiler commands with -DKOKKOS_DEPENDENCE will be redirected to nvcc_wrapper") + + # if not nvcc_wrapper and Kokkos_LAUNCH_COMPILER was not set to OFF + IF(NOT IS_NVCC AND (NOT DEFINED Kokkos_LAUNCH_COMPILER OR Kokkos_LAUNCH_COMPILER)) + MESSAGE(STATUS "kokkos_launch_compiler is enabled globally. C++ compiler commands with -DKOKKOS_DEPENDENCE will be redirected to the appropriate compiler for Kokkos") kokkos_compilation(GLOBAL) ENDIF() - UNSET(IS_NVCC) # be mindful of the environment, pollution is bad + + # be mindful of the environment, pollution is bad + UNSET(IS_NVCC) ENDIF() diff --git a/lib/kokkos/cmake/KokkosConfigCommon.cmake.in b/lib/kokkos/cmake/KokkosConfigCommon.cmake.in index 42c755c215..ab93e65afe 100644 --- a/lib/kokkos/cmake/KokkosConfigCommon.cmake.in +++ b/lib/kokkos/cmake/KokkosConfigCommon.cmake.in @@ -3,6 +3,7 @@ SET(Kokkos_OPTIONS @KOKKOS_ENABLED_OPTIONS@) SET(Kokkos_TPLS @KOKKOS_ENABLED_TPLS@) SET(Kokkos_ARCH @KOKKOS_ENABLED_ARCH_LIST@) SET(Kokkos_CXX_COMPILER "@CMAKE_CXX_COMPILER@") +SET(Kokkos_CXX_COMPILER_ID "@KOKKOS_CXX_COMPILER_ID@") # These are needed by KokkosKernels FOREACH(DEV ${Kokkos_DEVICES}) @@ -13,13 +14,13 @@ IF(NOT Kokkos_FIND_QUIETLY) MESSAGE(STATUS "Enabled Kokkos devices: ${Kokkos_DEVICES}") ENDIF() -IF (Kokkos_ENABLE_CUDA AND ${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.14.0") - #If we are building CUDA, we have tricked CMake because we declare a CXX project - #If the default C++ standard for a given compiler matches the requested - #standard, then CMake just omits the -std flag in later versions of CMake - #This breaks CUDA compilation (CUDA compiler can have a different default - #-std then the underlying host compiler by itself). Setting this variable - #forces CMake to always add the -std flag even if it thinks it doesn't need it +IF (Kokkos_ENABLE_CUDA) + # If we are building CUDA, we have tricked CMake because we declare a CXX project + # If the default C++ standard for a given compiler matches the requested + # standard, then CMake just omits the -std flag in later versions of CMake + # This breaks CUDA compilation (CUDA compiler can have a different default + # -std then the underlying host compiler by itself). Setting this variable + # forces CMake to always add the -std flag even if it thinks it doesn't need it SET(CMAKE_CXX_STANDARD_DEFAULT 98 CACHE INTERNAL "" FORCE) ENDIF() @@ -90,52 +91,6 @@ function(kokkos_check) endif() endfunction() -# this function is provided to easily select which files use nvcc_wrapper: -# -# GLOBAL --> all files -# TARGET --> all files in a target -# SOURCE --> specific source files -# DIRECTORY --> all files in directory -# PROJECT --> all files/targets in a project/subproject -# -FUNCTION(kokkos_compilation) - CMAKE_PARSE_ARGUMENTS(COMP "GLOBAL;PROJECT" "" "DIRECTORY;TARGET;SOURCE" ${ARGN}) - - # search relative first and then absolute - SET(_HINTS "${CMAKE_CURRENT_LIST_DIR}/../.." "@CMAKE_INSTALL_PREFIX@") - - # find kokkos_launch_compiler - FIND_PROGRAM(Kokkos_COMPILE_LAUNCHER - NAMES kokkos_launch_compiler - HINTS ${_HINTS} - PATHS ${_HINTS} - PATH_SUFFIXES bin) - - IF(NOT Kokkos_COMPILE_LAUNCHER) - MESSAGE(FATAL_ERROR "Kokkos could not find 'kokkos_launch_compiler'. Please set '-DKokkos_COMPILE_LAUNCHER=/path/to/launcher'") - ENDIF() - - IF(COMP_GLOBAL) - # if global, don't bother setting others - SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") - SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") - ELSE() - FOREACH(_TYPE PROJECT DIRECTORY TARGET SOURCE) - # make project/subproject scoping easy, e.g. KokkosCompilation(PROJECT) after project(...) - IF("${_TYPE}" STREQUAL "PROJECT" AND COMP_${_TYPE}) - LIST(APPEND COMP_DIRECTORY ${PROJECT_SOURCE_DIR}) - UNSET(COMP_${_TYPE}) - ENDIF() - # set the properties if defined - IF(COMP_${_TYPE}) - # MESSAGE(STATUS "Using nvcc_wrapper :: ${_TYPE} :: ${COMP_${_TYPE}}") - SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") - SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") - ENDIF() - ENDFOREACH() - ENDIF() -ENDFUNCTION() - # A test to check whether a downstream project set the C++ compiler to NVCC or not # this is called only when Kokkos was installed with Kokkos_ENABLE_CUDA=ON FUNCTION(kokkos_compiler_is_nvcc VAR COMPILER) @@ -159,3 +114,161 @@ FUNCTION(kokkos_compiler_is_nvcc VAR COMPILER) ENDIF() ENDFUNCTION() +# this function checks whether the current CXX compiler supports building CUDA +FUNCTION(kokkos_cxx_compiler_cuda_test _VAR _COMPILER) + + FILE(WRITE ${PROJECT_BINARY_DIR}/compile_tests/compiles_cuda.cu +" +#include +#include + +__global__ +void kernel(int sz, double* data) +{ + int _beg = blockIdx.x * blockDim.x + threadIdx.x; + for(int i = _beg; i < sz; ++i) + data[i] += static_cast(i); +} + +int main() +{ + double* data = NULL; + int blocks = 64; + int grids = 64; + int ret = cudaMalloc(&data, blocks * grids * sizeof(double)); + if(ret != cudaSuccess) + return EXIT_FAILURE; + kernel<<>>(blocks * grids, data); + cudaDeviceSynchronize(); + return EXIT_SUCCESS; +} +") + + # save the command for debugging + SET(_COMMANDS "${_COMPILER} ${ARGN} -c ${PROJECT_BINARY_DIR}/compile_tests/compiles_cuda.cu") + + # use execute_process instead of try compile because we want to set custom compiler + EXECUTE_PROCESS(COMMAND ${_COMPILER} ${ARGN} -c ${PROJECT_BINARY_DIR}/compile_tests/compiles_cuda.cu + RESULT_VARIABLE _RET + WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/compile_tests + TIMEOUT 15 + OUTPUT_QUIET + ERROR_QUIET) + + IF(NOT _RET EQUAL 0) + # save the command for debugging + SET(_COMMANDS "${_COMMAND}\n${_COMPILER} --cuda-gpu-arch=sm_35 ${ARGN} -c ${PROJECT_BINARY_DIR}/compile_tests/compiles_cuda.cu") + # try the compile test again with clang arguments + EXECUTE_PROCESS(COMMAND ${_COMPILER} --cuda-gpu-arch=sm_35 -c ${PROJECT_BINARY_DIR}/compile_tests/compiles_cuda.cu + RESULT_VARIABLE _RET + WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/compile_tests + TIMEOUT 15 + OUTPUT_QUIET + ERROR_QUIET) + ENDIF() + + SET(${_VAR}_COMMANDS "${_COMMANDS}" PARENT_SCOPE) + SET(${_VAR} ${_RET} PARENT_SCOPE) +ENDFUNCTION() + +# this function is provided to easily select which files use the same compiler as Kokkos +# when it was installed (or nvcc_wrapper): +# +# GLOBAL --> all files +# TARGET --> all files in a target +# SOURCE --> specific source files +# DIRECTORY --> all files in directory +# PROJECT --> all files/targets in a project/subproject +# +# Use the COMPILER argument to specify a compiler, if needed. By default, it will +# set the values to ${Kokkos_CXX_COMPILER} unless Kokkos_ENABLE_CUDA=ON and +# Kokkos_CXX_COMPILER_ID is NVIDIA, then it will set it to nvcc_wrapper +# +# Use CHECK_CUDA_COMPILES to run a check when CUDA is enabled +# +FUNCTION(kokkos_compilation) + CMAKE_PARSE_ARGUMENTS(COMP + "GLOBAL;PROJECT;CHECK_CUDA_COMPILES" + "COMPILER" + "DIRECTORY;TARGET;SOURCE;COMMAND_PREFIX" + ${ARGN}) + + # if built w/o CUDA support, we want to basically make this a no-op + SET(_Kokkos_ENABLE_CUDA @Kokkos_ENABLE_CUDA@) + + # search relative first and then absolute + SET(_HINTS "${CMAKE_CURRENT_LIST_DIR}/../.." "@CMAKE_INSTALL_PREFIX@") + + # find kokkos_launch_compiler + FIND_PROGRAM(Kokkos_COMPILE_LAUNCHER + NAMES kokkos_launch_compiler + HINTS ${_HINTS} + PATHS ${_HINTS} + PATH_SUFFIXES bin) + + IF(NOT Kokkos_COMPILE_LAUNCHER) + MESSAGE(FATAL_ERROR "Kokkos could not find 'kokkos_launch_compiler'. Please set '-DKokkos_COMPILE_LAUNCHER=/path/to/launcher'") + ENDIF() + + # if COMPILER was not specified, assume Kokkos_CXX_COMPILER + IF(NOT COMP_COMPILER) + SET(COMP_COMPILER ${Kokkos_CXX_COMPILER}) + IF(_Kokkos_ENABLE_CUDA AND Kokkos_CXX_COMPILER_ID STREQUAL NVIDIA) + # find nvcc_wrapper + FIND_PROGRAM(Kokkos_NVCC_WRAPPER + NAMES nvcc_wrapper + HINTS ${_HINTS} + PATHS ${_HINTS} + PATH_SUFFIXES bin) + # fatal if we can't nvcc_wrapper + IF(NOT Kokkos_NVCC_WRAPPER) + MESSAGE(FATAL_ERROR "Kokkos could not find nvcc_wrapper. Please set '-DKokkos_NVCC_WRAPPER=/path/to/nvcc_wrapper'") + ENDIF() + SET(COMP_COMPILER ${Kokkos_NVCC_WRAPPER}) + ENDIF() + ENDIF() + + # check that the original compiler still exists! + IF(NOT EXISTS ${COMP_COMPILER}) + MESSAGE(FATAL_ERROR "Kokkos could not find original compiler: '${COMP_COMPILER}'") + ENDIF() + + # try to ensure that compiling cuda code works! + IF(_Kokkos_ENABLE_CUDA AND COMP_CHECK_CUDA_COMPILES) + + # this may fail if kokkos_compiler launcher was used during install + kokkos_cxx_compiler_cuda_test(_COMPILES_CUDA + ${Kokkos_COMPILE_LAUNCHER} ${COMP_COMPILER} ${CMAKE_CXX_COMPILER}) + + # if above failed, throw an error + IF(NOT _COMPILES_CUDA) + MESSAGE(FATAL_ERROR "kokkos_cxx_compiler_cuda_test failed! Test commands:\n${_COMPILES_CUDA_COMMANDS}") + ENDIF() + ENDIF() + + IF(COMP_COMMAND_PREFIX) + SET(_PREFIX "${COMP_COMMAND_PREFIX}") + STRING(REPLACE ";" " " _PREFIX "${COMP_COMMAND_PREFIX}") + SET(Kokkos_COMPILER_LAUNCHER "${_PREFIX} ${Kokkos_COMPILE_LAUNCHER}") + ENDIF() + + IF(COMP_GLOBAL) + # if global, don't bother setting others + SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${COMP_COMPILER} ${CMAKE_CXX_COMPILER}") + SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${COMP_COMPILER} ${CMAKE_CXX_COMPILER}") + ELSE() + FOREACH(_TYPE PROJECT DIRECTORY TARGET SOURCE) + # make project/subproject scoping easy, e.g. KokkosCompilation(PROJECT) after project(...) + IF("${_TYPE}" STREQUAL "PROJECT" AND COMP_${_TYPE}) + LIST(APPEND COMP_DIRECTORY ${PROJECT_SOURCE_DIR}) + UNSET(COMP_${_TYPE}) + ENDIF() + # set the properties if defined + IF(COMP_${_TYPE}) + # MESSAGE(STATUS "Using ${COMP_COMPILER} :: ${_TYPE} :: ${COMP_${_TYPE}}") + SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${COMP_COMPILER} ${CMAKE_CXX_COMPILER}") + SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${COMP_COMPILER} ${CMAKE_CXX_COMPILER}") + ENDIF() + ENDFOREACH() + ENDIF() +ENDFUNCTION() diff --git a/lib/kokkos/cmake/KokkosCore_config.h.in b/lib/kokkos/cmake/KokkosCore_config.h.in index 0259fe69d5..fbfae3711e 100644 --- a/lib/kokkos/cmake/KokkosCore_config.h.in +++ b/lib/kokkos/cmake/KokkosCore_config.h.in @@ -78,6 +78,7 @@ #cmakedefine KOKKOS_ARCH_POWER7 #cmakedefine KOKKOS_ARCH_POWER8 #cmakedefine KOKKOS_ARCH_POWER9 +#cmakedefine KOKKOS_ARCH_INTEL_GEN #cmakedefine KOKKOS_ARCH_KEPLER #cmakedefine KOKKOS_ARCH_KEPLER30 #cmakedefine KOKKOS_ARCH_KEPLER32 @@ -95,5 +96,8 @@ #cmakedefine KOKKOS_ARCH_VOLTA72 #cmakedefine KOKKOS_ARCH_TURING75 #cmakedefine KOKKOS_ARCH_AMPERE80 +#cmakedefine KOKKOS_ARCH_AMPERE86 #cmakedefine KOKKOS_ARCH_AMD_ZEN #cmakedefine KOKKOS_ARCH_AMD_ZEN2 + +#cmakedefine KOKKOS_IMPL_DISABLE_SYCL_DEVICE_PRINTF diff --git a/lib/kokkos/cmake/Modules/CudaToolkit.cmake b/lib/kokkos/cmake/Modules/CudaToolkit.cmake index d620a71d36..eda5541f7c 100644 --- a/lib/kokkos/cmake/Modules/CudaToolkit.cmake +++ b/lib/kokkos/cmake/Modules/CudaToolkit.cmake @@ -481,76 +481,6 @@ if(CMAKE_CUDA_COMPILER_LOADED AND NOT CUDAToolkit_BIN_DIR AND CMAKE_CUDA_COMPILE unset(cuda_dir) endif() -IF(CMAKE_VERSION VERSION_LESS "3.12.0") - function(import_target_link_libraries target) - cmake_parse_arguments(HACK - "SYSTEM;INTERFACE;PUBLIC" - "" - "" - ${ARGN} - ) - get_target_property(LIBS ${target} INTERFACE_LINK_LIBRARIES) - if (LIBS) - list(APPEND LIBS ${HACK_UNPARSED_ARGUMENTS}) - else() - set(LIBS ${HACK_UNPARSED_ARGUMENTS}) - endif() - set_target_properties(${target} PROPERTIES - INTERFACE_LINK_LIBRARIES "${LIBS}") - endfunction() -ELSE() - function(import_target_link_libraries) - target_link_libraries(${ARGN}) - endfunction() -ENDIF() - -IF(CMAKE_VERSION VERSION_LESS "3.13.0") - function(import_target_link_directories target) - cmake_parse_arguments(HACK - "SYSTEM;INTERFACE;PUBLIC" - "" - "" - ${ARGN} - ) - get_target_property(LINK_LIBS ${target} INTERFACE_LINK_LIBRARIES) - if (LINK_LIBS) #could be not-found - set(LINK_LIBS_LIST ${LINK_LIBS}) - endif() - foreach(LIB ${HACK_UNPARSED_ARGUMENTS}) - list(APPEND LINK_LIBS_LIST -L${LIB}) - endforeach() - set_target_properties(${target} PROPERTIES - INTERFACE_LINK_LIBRARIES "${LINK_LIBS_LIST}") - endfunction() -ELSE() - function(import_target_link_directories) - target_link_directories(${ARGN}) - endfunction() -ENDIF() - -IF(CMAKE_VERSION VERSION_LESS "3.12.0") - function(import_target_include_directories target) - cmake_parse_arguments(HACK - "SYSTEM;INTERFACE;PUBLIC" - "" - "" - ${ARGN} - ) - get_target_property(INLUDE_DIRS ${target} INTERFACE_INCLUDE_DIRECTORIES) - if (INCLUDE_DIRS) - list(APPEND INCLUDE_DIRS ${HACK_UNPARSED_ARGUMENTS}) - else() - set(INCLUDE_DIRS ${HACK_UNPARSED_ARGUMENTS}) - endif() - set_target_properties(${target} PROPERTIES - INTERFACE_INCLUDE_DIRECTORIES "${INCLUDE_DIRS}") - endfunction() -ELSE() - function(import_target_include_directories) - target_include_directories(${ARGN}) - endfunction() -ENDIF() - # Try language- or user-provided path first. if(CUDAToolkit_BIN_DIR) find_program(CUDAToolkit_NVCC_EXECUTABLE @@ -854,11 +784,11 @@ if(CUDAToolkit_FOUND) if (NOT TARGET CUDA::${lib_name} AND CUDA_${lib_name}_LIBRARY) add_library(CUDA::${lib_name} IMPORTED INTERFACE) - import_target_include_directories(CUDA::${lib_name} SYSTEM INTERFACE "${CUDAToolkit_INCLUDE_DIRS}") - import_target_link_libraries(CUDA::${lib_name} INTERFACE "${CUDA_${lib_name}_LIBRARY}") + target_include_directories(CUDA::${lib_name} SYSTEM INTERFACE "${CUDAToolkit_INCLUDE_DIRS}") + target_link_libraries(CUDA::${lib_name} INTERFACE "${CUDA_${lib_name}_LIBRARY}") foreach(dep ${arg_DEPS}) if(TARGET CUDA::${dep}) - import_target_link_libraries(CUDA::${lib_name} INTERFACE CUDA::${dep}) + target_link_libraries(CUDA::${lib_name} INTERFACE CUDA::${dep}) endif() endforeach() endif() @@ -866,8 +796,8 @@ if(CUDAToolkit_FOUND) if(NOT TARGET CUDA::toolkit) add_library(CUDA::toolkit IMPORTED INTERFACE) - import_target_include_directories(CUDA::toolkit SYSTEM INTERFACE "${CUDAToolkit_INCLUDE_DIRS}") - import_target_link_directories(CUDA::toolkit INTERFACE "${CUDAToolkit_LIBRARY_DIR}") + target_include_directories(CUDA::toolkit SYSTEM INTERFACE "${CUDAToolkit_INCLUDE_DIRS}") + target_link_directories(CUDA::toolkit INTERFACE "${CUDAToolkit_LIBRARY_DIR}") endif() _CUDAToolkit_find_and_add_import_lib(cuda_driver ALT cuda) @@ -882,11 +812,11 @@ if(CUDAToolkit_FOUND) AND TARGET CUDA::cudart_static) add_library(CUDA::cudart_static_deps IMPORTED INTERFACE) - import_target_link_libraries(CUDA::cudart_static INTERFACE CUDA::cudart_static_deps) + target_link_libraries(CUDA::cudart_static INTERFACE CUDA::cudart_static_deps) if(UNIX AND (CMAKE_C_COMPILER OR CMAKE_CXX_COMPILER)) find_package(Threads REQUIRED) - import_target_link_libraries(CUDA::cudart_static_deps INTERFACE Threads::Threads ${CMAKE_DL_LIBS}) + target_link_libraries(CUDA::cudart_static_deps INTERFACE Threads::Threads ${CMAKE_DL_LIBS}) endif() if(UNIX AND NOT APPLE) @@ -896,7 +826,7 @@ if(CUDAToolkit_FOUND) if(NOT CUDAToolkit_rt_LIBRARY) message(WARNING "Could not find librt library, needed by CUDA::cudart_static") else() - import_target_link_libraries(CUDA::cudart_static_deps INTERFACE ${CUDAToolkit_rt_LIBRARY}) + target_link_libraries(CUDA::cudart_static_deps INTERFACE ${CUDAToolkit_rt_LIBRARY}) endif() endif() endif() diff --git a/lib/kokkos/cmake/Modules/FindTPLCUDA.cmake b/lib/kokkos/cmake/Modules/FindTPLCUDA.cmake index a1072a60c6..8d58d96415 100644 --- a/lib/kokkos/cmake/Modules/FindTPLCUDA.cmake +++ b/lib/kokkos/cmake/Modules/FindTPLCUDA.cmake @@ -25,7 +25,7 @@ IF (TARGET CUDA::cuda_driver) SET(FOUND_CUDA_DRIVER TRUE) KOKKOS_EXPORT_IMPORTED_TPL(CUDA::cuda_driver) ELSE() - SET(FOUND_CUDA_DRIVVER FALSE) + SET(FOUND_CUDA_DRIVER FALSE) ENDIF() include(FindPackageHandleStandardArgs) diff --git a/lib/kokkos/cmake/Modules/FindTPLPTHREAD.cmake b/lib/kokkos/cmake/Modules/FindTPLPTHREAD.cmake index 1d154e29af..a743fca0e4 100644 --- a/lib/kokkos/cmake/Modules/FindTPLPTHREAD.cmake +++ b/lib/kokkos/cmake/Modules/FindTPLPTHREAD.cmake @@ -10,7 +10,7 @@ TRY_COMPILE(KOKKOS_HAS_PTHREAD_ARG # ${CMAKE_CXX${KOKKOS_CXX_STANDARD}_STANDARD_COMPILE_OPTION} INCLUDE(FindPackageHandleStandardArgs) -FIND_PACKAGE_HANDLE_STANDARD_ARGS(PTHREAD DEFAULT_MSG KOKKOS_HAS_PTHREAD_ARG) +FIND_PACKAGE_HANDLE_STANDARD_ARGS(TPLPTHREAD DEFAULT_MSG KOKKOS_HAS_PTHREAD_ARG) #Only create the TPL if we succeed IF (KOKKOS_HAS_PTHREAD_ARG) KOKKOS_CREATE_IMPORTED_TPL(PTHREAD diff --git a/lib/kokkos/cmake/Modules/FindTPLROCM.cmake b/lib/kokkos/cmake/Modules/FindTPLROCM.cmake new file mode 100644 index 0000000000..512ad6ceb2 --- /dev/null +++ b/lib/kokkos/cmake/Modules/FindTPLROCM.cmake @@ -0,0 +1,11 @@ +include(FindPackageHandleStandardArgs) + +FIND_LIBRARY(AMD_HIP_LIBRARY amdhip64 PATHS ENV ROCM_PATH PATH_SUFFIXES lib) +FIND_LIBRARY(HSA_RUNTIME_LIBRARY hsa-runtime64 PATHS ENV ROCM_PATH PATH_SUFFIXES lib) + +find_package_handle_standard_args(TPLROCM DEFAULT_MSG AMD_HIP_LIBRARY HSA_RUNTIME_LIBRARY) + +kokkos_create_imported_tpl(ROCM INTERFACE + LINK_LIBRARIES ${HSA_RUNTIME_LIBRARY} ${AMD_HIP_LIBRARY} + COMPILE_DEFINITIONS __HIP_ROCclr__ +) diff --git a/lib/kokkos/cmake/compile_tests/cplusplus14.cpp b/lib/kokkos/cmake/compile_tests/cplusplus14.cpp new file mode 100644 index 0000000000..52ec9885ec --- /dev/null +++ b/lib/kokkos/cmake/compile_tests/cplusplus14.cpp @@ -0,0 +1,8 @@ +#include + +int main() { + // _t versions of type traits were added in C++14 + std::remove_cv_t i = 0; + + return i; +} diff --git a/lib/kokkos/cmake/compile_tests/cuda_compute_capability.cc b/lib/kokkos/cmake/compile_tests/cuda_compute_capability.cc index 48c01c070c..a26ac5af4b 100644 --- a/lib/kokkos/cmake/compile_tests/cuda_compute_capability.cc +++ b/lib/kokkos/cmake/compile_tests/cuda_compute_capability.cc @@ -72,6 +72,7 @@ int main() { case 72: std::cout << "Set -DKokkos_ARCH_VOLTA72=ON ." << std::endl; break; case 75: std::cout << "Set -DKokkos_ARCH_TURING75=ON ." << std::endl; break; case 80: std::cout << "Set -DKokkos_ARCH_AMPERE80=ON ." << std::endl; break; + case 86: std::cout << "Set -DKokkos_ARCH_AMPERE86=ON ." << std::endl; break; default: std::cout << "Compute capability " << compute_capability << " is not supported" << std::endl; diff --git a/lib/kokkos/cmake/compile_tests/pthread.cpp b/lib/kokkos/cmake/compile_tests/pthread.cpp index 92310da029..3f83bf6a5f 100644 --- a/lib/kokkos/cmake/compile_tests/pthread.cpp +++ b/lib/kokkos/cmake/compile_tests/pthread.cpp @@ -2,7 +2,7 @@ void* kokkos_test(void* args) { return args; } -int main(void) { +int main() { pthread_t thread; /* Use NULL to avoid C++11. Some compilers do not have C++11 by default. Forcing C++11 diff --git a/lib/kokkos/cmake/fake_tribits.cmake b/lib/kokkos/cmake/fake_tribits.cmake index 2e82a46235..fbd6745a60 100644 --- a/lib/kokkos/cmake/fake_tribits.cmake +++ b/lib/kokkos/cmake/fake_tribits.cmake @@ -81,10 +81,16 @@ ENDMACRO() FUNCTION(KOKKOS_ADD_TEST) if (KOKKOS_HAS_TRILINOS) CMAKE_PARSE_ARGUMENTS(TEST - "" + "SKIP_TRIBITS" "EXE;NAME;TOOL" "ARGS" ${ARGN}) + + IF(TEST_SKIP_TRIBITS) + MESSAGE(STATUS "Skipping test ${TEST_NAME} in TriBits") + RETURN() + ENDIF() + IF(TEST_EXE) SET(EXE_ROOT ${TEST_EXE}) ELSE() @@ -119,11 +125,10 @@ FUNCTION(KOKKOS_ADD_TEST) endif() else() CMAKE_PARSE_ARGUMENTS(TEST - "WILL_FAIL" + "WILL_FAIL;SKIP_TRIBITS" "FAIL_REGULAR_EXPRESSION;PASS_REGULAR_EXPRESSION;EXE;NAME;TOOL" "CATEGORIES;ARGS" ${ARGN}) - SET(TESTS_ADDED) # To match Tribits, we should always be receiving # the root names of exes/libs IF(TEST_EXE) @@ -135,48 +140,27 @@ FUNCTION(KOKKOS_ADD_TEST) # These should be the full target name SET(TEST_NAME ${PACKAGE_NAME}_${TEST_NAME}) SET(EXE ${PACKAGE_NAME}_${EXE_ROOT}) - IF (TEST_ARGS) - SET(TEST_NUMBER 0) - FOREACH (ARG_STR ${TEST_ARGS}) - # This is passed as a single string blob to match TriBITS behavior - # We need this to be turned into a list - STRING(REPLACE " " ";" ARG_STR_LIST ${ARG_STR}) - IF(WIN32) - ADD_TEST(NAME ${TEST_NAME}${TEST_NUMBER} WORKING_DIRECTORY ${LIBRARY_OUTPUT_PATH} - COMMAND ${EXE}${CMAKE_EXECUTABLE_SUFFIX} ${ARG_STR_LIST}) - ELSE() - ADD_TEST(NAME ${TEST_NAME}${TEST_NUMBER} COMMAND ${EXE} ${ARG_STR_LIST}) - ENDIF() - LIST(APPEND TESTS_ADDED "${TEST_NAME}${TEST_NUMBER}") - MATH(EXPR TEST_NUMBER "${TEST_NUMBER} + 1") - ENDFOREACH() + IF(WIN32) + ADD_TEST(NAME ${TEST_NAME} WORKING_DIRECTORY ${LIBRARY_OUTPUT_PATH} + COMMAND ${EXE}${CMAKE_EXECUTABLE_SUFFIX} ${TEST_ARGS}) ELSE() - IF(WIN32) - ADD_TEST(NAME ${TEST_NAME} WORKING_DIRECTORY ${LIBRARY_OUTPUT_PATH} - COMMAND ${EXE}${CMAKE_EXECUTABLE_SUFFIX}) - ELSE() - ADD_TEST(NAME ${TEST_NAME} COMMAND ${EXE}) - ENDIF() - LIST(APPEND TESTS_ADDED "${TEST_NAME}") + ADD_TEST(NAME ${TEST_NAME} COMMAND ${EXE} ${TEST_ARGS}) + ENDIF() + IF(TEST_WILL_FAIL) + SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES WILL_FAIL ${TEST_WILL_FAIL}) + ENDIF() + IF(TEST_FAIL_REGULAR_EXPRESSION) + SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES FAIL_REGULAR_EXPRESSION ${TEST_FAIL_REGULAR_EXPRESSION}) + ENDIF() + IF(TEST_PASS_REGULAR_EXPRESSION) + SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES PASS_REGULAR_EXPRESSION ${TEST_PASS_REGULAR_EXPRESSION}) + ENDIF() + IF(TEST_TOOL) + ADD_DEPENDENCIES(${EXE} ${TEST_TOOL}) #make sure the exe has to build the tool + SET_PROPERTY(TEST ${TEST_NAME} APPEND_STRING PROPERTY ENVIRONMENT "KOKKOS_PROFILE_LIBRARY=$") ENDIF() - - FOREACH(TEST_NAME ${TESTS_ADDED}) - IF(TEST_WILL_FAIL) - SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES WILL_FAIL ${TEST_WILL_FAIL}) - ENDIF() - IF(TEST_FAIL_REGULAR_EXPRESSION) - SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES FAIL_REGULAR_EXPRESSION ${TEST_FAIL_REGULAR_EXPRESSION}) - ENDIF() - IF(TEST_PASS_REGULAR_EXPRESSION) - SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES PASS_REGULAR_EXPRESSION ${TEST_PASS_REGULAR_EXPRESSION}) - ENDIF() - if(TEST_TOOL) - add_dependencies(${EXE} ${TEST_TOOL}) #make sure the exe has to build the tool - set_property(TEST ${TEST_NAME} APPEND_STRING PROPERTY ENVIRONMENT "KOKKOS_PROFILE_LIBRARY=$") - endif() - ENDFOREACH() VERIFY_EMPTY(KOKKOS_ADD_TEST ${TEST_UNPARSED_ARGUMENTS}) - endif() + ENDIF() ENDFUNCTION() FUNCTION(KOKKOS_ADD_ADVANCED_TEST) @@ -326,14 +310,6 @@ ENDIF() ENDFUNCTION() -FUNCTION(KOKKOS_TARGET_COMPILE_DEFINITIONS) - IF (KOKKOS_HAS_TRILINOS) - TARGET_COMPILE_DEFINITIONS(${TARGET} ${ARGN}) - ELSE() - TARGET_COMPILE_DEFINITIONS(${TARGET} ${ARGN}) - ENDIF() -ENDFUNCTION() - FUNCTION(KOKKOS_INCLUDE_DIRECTORIES) IF(KOKKOS_HAS_TRILINOS) TRIBITS_INCLUDE_DIRECTORIES(${ARGN}) @@ -350,10 +326,6 @@ ENDIF() ENDFUNCTION() -MACRO(KOKKOS_ADD_COMPILE_OPTIONS) -ADD_COMPILE_OPTIONS(${ARGN}) -ENDMACRO() - MACRO(PRINTALL match) get_cmake_property(_variableNames VARIABLES) list (SORT _variableNames) @@ -376,4 +348,3 @@ FUNCTION(GLOBAL_APPEND VARNAME) LIST(APPEND TEMP ${ARGN}) GLOBAL_SET(${VARNAME} ${TEMP}) ENDFUNCTION() - diff --git a/lib/kokkos/cmake/kokkos_arch.cmake b/lib/kokkos/cmake/kokkos_arch.cmake index 53aaf7dccf..ec18e70a36 100644 --- a/lib/kokkos/cmake/kokkos_arch.cmake +++ b/lib/kokkos/cmake/kokkos_arch.cmake @@ -35,7 +35,7 @@ KOKKOS_ARCH_OPTION(ARMV80 HOST "ARMv8.0 Compatible CPU") KOKKOS_ARCH_OPTION(ARMV81 HOST "ARMv8.1 Compatible CPU") KOKKOS_ARCH_OPTION(ARMV8_THUNDERX HOST "ARMv8 Cavium ThunderX CPU") KOKKOS_ARCH_OPTION(ARMV8_THUNDERX2 HOST "ARMv8 Cavium ThunderX2 CPU") -KOKKOS_ARCH_OPTION(A64FX HOST "ARMv8.2 with SVE Suport") +KOKKOS_ARCH_OPTION(A64FX HOST "ARMv8.2 with SVE Support") KOKKOS_ARCH_OPTION(WSM HOST "Intel Westmere CPU") KOKKOS_ARCH_OPTION(SNB HOST "Intel Sandy/Ivy Bridge CPUs") KOKKOS_ARCH_OPTION(HSW HOST "Intel Haswell CPUs") @@ -60,11 +60,12 @@ KOKKOS_ARCH_OPTION(VOLTA70 GPU "NVIDIA Volta generation CC 7.0") KOKKOS_ARCH_OPTION(VOLTA72 GPU "NVIDIA Volta generation CC 7.2") KOKKOS_ARCH_OPTION(TURING75 GPU "NVIDIA Turing generation CC 7.5") KOKKOS_ARCH_OPTION(AMPERE80 GPU "NVIDIA Ampere generation CC 8.0") +KOKKOS_ARCH_OPTION(AMPERE86 GPU "NVIDIA Ampere generation CC 8.6") KOKKOS_ARCH_OPTION(ZEN HOST "AMD Zen architecture") KOKKOS_ARCH_OPTION(ZEN2 HOST "AMD Zen2 architecture") KOKKOS_ARCH_OPTION(VEGA900 GPU "AMD GPU MI25 GFX900") KOKKOS_ARCH_OPTION(VEGA906 GPU "AMD GPU MI50/MI60 GFX906") -KOKKOS_ARCH_OPTION(VEGA908 GPU "AMD GPU") +KOKKOS_ARCH_OPTION(VEGA908 GPU "AMD GPU MI100 GFX908") KOKKOS_ARCH_OPTION(INTEL_GEN GPU "Intel GPUs Gen9+") @@ -141,8 +142,16 @@ ENDIF() #------------------------------- KOKKOS_HIP_OPTIONS --------------------------- #clear anything that might be in the cache GLOBAL_SET(KOKKOS_AMDGPU_OPTIONS) -IF(KOKKOS_CXX_COMPILER_ID STREQUAL HIP) - SET(AMDGPU_ARCH_FLAG "--amdgpu-target") +IF(KOKKOS_ENABLE_HIP) + IF(KOKKOS_CXX_COMPILER_ID STREQUAL HIPCC) + SET(AMDGPU_ARCH_FLAG "--amdgpu-target") + ELSE() + SET(AMDGPU_ARCH_FLAG "--offload-arch") + GLOBAL_APPEND(KOKKOS_AMDGPU_OPTIONS -x hip) + IF(DEFINED ENV{ROCM_PATH}) + GLOBAL_APPEND(KOKKOS_AMDGPU_OPTIONS --rocm-path=$ENV{ROCM_PATH}) + ENDIF() + ENDIF() ENDIF() @@ -183,6 +192,8 @@ ENDIF() IF (KOKKOS_ARCH_A64FX) COMPILER_SPECIFIC_FLAGS( DEFAULT -march=armv8.2-a+sve + Clang -march=armv8.2-a+sve -msve-vector-bits=512 + GCC -march=armv8.2-a+sve -msve-vector-bits=512 ) ENDIF() @@ -309,7 +320,7 @@ IF (KOKKOS_ARCH_POWER8 OR KOKKOS_ARCH_POWER9) SET(KOKKOS_USE_ISA_POWERPCLE ON) ENDIF() -IF (Kokkos_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE) +IF (KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE) COMPILER_SPECIFIC_FLAGS( Clang -fcuda-rdc NVIDIA --relocatable-device-code=true @@ -333,8 +344,8 @@ ENDIF() #Right now we cannot get the compiler ID when cross-compiling, so just check #that HIP is enabled -IF (Kokkos_ENABLE_HIP) - IF (Kokkos_ENABLE_HIP_RELOCATABLE_DEVICE_CODE) +IF (KOKKOS_ENABLE_HIP) + IF (KOKKOS_ENABLE_HIP_RELOCATABLE_DEVICE_CODE) COMPILER_SPECIFIC_FLAGS( DEFAULT -fgpu-rdc ) @@ -345,8 +356,7 @@ IF (Kokkos_ENABLE_HIP) ENDIF() ENDIF() - -IF (Kokkos_ENABLE_SYCL) +IF (KOKKOS_ENABLE_SYCL) COMPILER_SPECIFIC_FLAGS( DEFAULT -fsycl ) @@ -363,7 +373,7 @@ FUNCTION(CHECK_CUDA_ARCH ARCH FLAG) MESSAGE(FATAL_ERROR "Multiple GPU architectures given! Already have ${CUDA_ARCH_ALREADY_SPECIFIED}, but trying to add ${ARCH}. If you are re-running CMake, try clearing the cache and running again.") ENDIF() SET(CUDA_ARCH_ALREADY_SPECIFIED ${ARCH} PARENT_SCOPE) - IF (NOT KOKKOS_ENABLE_CUDA AND NOT KOKKOS_ENABLE_OPENMPTARGET) + IF (NOT KOKKOS_ENABLE_CUDA AND NOT KOKKOS_ENABLE_OPENMPTARGET AND NOT KOKKOS_ENABLE_SYCL) MESSAGE(WARNING "Given CUDA arch ${ARCH}, but Kokkos_ENABLE_CUDA and Kokkos_ENABLE_OPENMPTARGET are OFF. Option will be ignored.") UNSET(KOKKOS_ARCH_${ARCH} PARENT_SCOPE) ELSE() @@ -396,6 +406,7 @@ CHECK_CUDA_ARCH(VOLTA70 sm_70) CHECK_CUDA_ARCH(VOLTA72 sm_72) CHECK_CUDA_ARCH(TURING75 sm_75) CHECK_CUDA_ARCH(AMPERE80 sm_80) +CHECK_CUDA_ARCH(AMPERE86 sm_86) SET(AMDGPU_ARCH_ALREADY_SPECIFIED "") FUNCTION(CHECK_AMDGPU_ARCH ARCH FLAG) @@ -405,12 +416,12 @@ FUNCTION(CHECK_AMDGPU_ARCH ARCH FLAG) ENDIF() SET(AMDGPU_ARCH_ALREADY_SPECIFIED ${ARCH} PARENT_SCOPE) IF (NOT KOKKOS_ENABLE_HIP AND NOT KOKKOS_ENABLE_OPENMPTARGET) - MESSAGE(WARNING "Given HIP arch ${ARCH}, but Kokkos_ENABLE_AMDGPU and Kokkos_ENABLE_OPENMPTARGET are OFF. Option will be ignored.") + MESSAGE(WARNING "Given AMD GPU architecture ${ARCH}, but Kokkos_ENABLE_HIP and Kokkos_ENABLE_OPENMPTARGET are OFF. Option will be ignored.") UNSET(KOKKOS_ARCH_${ARCH} PARENT_SCOPE) ELSE() SET(KOKKOS_AMDGPU_ARCH_FLAG ${FLAG} PARENT_SCOPE) GLOBAL_APPEND(KOKKOS_AMDGPU_OPTIONS "${AMDGPU_ARCH_FLAG}=${FLAG}") - IF(KOKKOS_ENABLE_HIP) + IF(KOKKOS_ENABLE_HIP_RELOCATABLE_DEVICE_CODE) GLOBAL_APPEND(KOKKOS_LINK_OPTIONS "${AMDGPU_ARCH_FLAG}=${FLAG}") ENDIF() ENDIF() @@ -451,6 +462,24 @@ IF (KOKKOS_ENABLE_OPENMPTARGET) ENDIF() ENDIF() +IF (KOKKOS_ENABLE_SYCL) + IF(CUDA_ARCH_ALREADY_SPECIFIED) + IF(KOKKOS_ENABLE_UNSUPPORTED_ARCHS) + COMPILER_SPECIFIC_FLAGS( + DEFAULT -fsycl-targets=nvptx64-nvidia-cuda-sycldevice + ) + # FIXME_SYCL The CUDA backend doesn't support printf yet. + GLOBAL_SET(KOKKOS_IMPL_DISABLE_SYCL_DEVICE_PRINTF ON) + ELSE() + MESSAGE(SEND_ERROR "Setting a CUDA architecture for SYCL is only allowed with Kokkos_ENABLE_UNSUPPORTED_ARCHS=ON!") + ENDIF() + ELSEIF(KOKKOS_ARCH_INTEL_GEN) + COMPILER_SPECIFIC_FLAGS( + DEFAULT -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device skl" + ) + ENDIF() +ENDIF() + IF(KOKKOS_ENABLE_CUDA AND NOT CUDA_ARCH_ALREADY_SPECIFIED) # Try to autodetect the CUDA Compute Capability by asking the device SET(_BINARY_TEST_DIR ${CMAKE_CURRENT_BINARY_DIR}/cmake/compile_tests/CUDAComputeCapabilityWorkdir) @@ -464,6 +493,43 @@ IF(KOKKOS_ENABLE_CUDA AND NOT CUDA_ARCH_ALREADY_SPECIFIED) ${CMAKE_CURRENT_SOURCE_DIR}/cmake/compile_tests/cuda_compute_capability.cc COMPILE_DEFINITIONS -DSM_ONLY RUN_OUTPUT_VARIABLE _CUDA_COMPUTE_CAPABILITY) + + # if user is using kokkos_compiler_launcher, above will fail. + IF(NOT _COMPILE_RESULT OR NOT _RESULT EQUAL 0) + # check to see if CUDA is not already enabled (may happen when Kokkos is subproject) + GET_PROPERTY(_ENABLED_LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) + # language has to be fully enabled, just checking for CMAKE_CUDA_COMPILER isn't enough + IF(NOT "CUDA" IN_LIST _ENABLED_LANGUAGES) + # make sure the user knows that we aren't using CUDA compiler for anything else + MESSAGE(STATUS "CUDA auto-detection of architecture failed with ${CMAKE_CXX_COMPILER}. Enabling CUDA language ONLY to auto-detect architecture...") + INCLUDE(CheckLanguage) + CHECK_LANGUAGE(CUDA) + IF(CMAKE_CUDA_COMPILER) + ENABLE_LANGUAGE(CUDA) + ELSE() + MESSAGE(STATUS "CUDA language could not be enabled") + ENDIF() + ENDIF() + + # if CUDA was enabled, this will be defined + IF(CMAKE_CUDA_COMPILER) + # copy our test to .cu so cmake compiles as CUDA + CONFIGURE_FILE( + ${PROJECT_SOURCE_DIR}/cmake/compile_tests/cuda_compute_capability.cc + ${PROJECT_BINARY_DIR}/compile_tests/cuda_compute_capability.cu + COPYONLY + ) + # run test again + TRY_RUN( + _RESULT + _COMPILE_RESULT + ${_BINARY_TEST_DIR} + ${PROJECT_BINARY_DIR}/compile_tests/cuda_compute_capability.cu + COMPILE_DEFINITIONS -DSM_ONLY + RUN_OUTPUT_VARIABLE _CUDA_COMPUTE_CAPABILITY) + ENDIF() + ENDIF() + LIST(FIND KOKKOS_CUDA_ARCH_FLAGS sm_${_CUDA_COMPUTE_CAPABILITY} FLAG_INDEX) IF(_COMPILE_RESULT AND _RESULT EQUAL 0 AND NOT FLAG_INDEX EQUAL -1) MESSAGE(STATUS "Detected CUDA Compute Capability ${_CUDA_COMPUTE_CAPABILITY}") @@ -500,7 +566,7 @@ IF (KOKKOS_ENABLE_CUDA) SET(KOKKOS_ARCH_VOLTA ON) ENDIF() - IF (KOKKOS_ARCH_AMPERE80) + IF (KOKKOS_ARCH_AMPERE80 OR KOKKOS_ARCH_AMPERE86) SET(KOKKOS_ARCH_AMPERE ON) ENDIF() ENDIF() diff --git a/lib/kokkos/cmake/kokkos_compiler_id.cmake b/lib/kokkos/cmake/kokkos_compiler_id.cmake index e6600161f9..4434d6928f 100644 --- a/lib/kokkos/cmake/kokkos_compiler_id.cmake +++ b/lib/kokkos/cmake/kokkos_compiler_id.cmake @@ -27,6 +27,12 @@ IF(Kokkos_ENABLE_CUDA) PATHS ${PROJECT_SOURCE_DIR} PATH_SUFFIXES bin) + FIND_PROGRAM(Kokkos_NVCC_WRAPPER + NAMES nvcc_wrapper + HINTS ${PROJECT_SOURCE_DIR} + PATHS ${PROJECT_SOURCE_DIR} + PATH_SUFFIXES bin) + # check if compiler was set to nvcc_wrapper kokkos_internal_have_compiler_nvcc(${CMAKE_CXX_COMPILER}) # if launcher was found and nvcc_wrapper was not specified as @@ -37,7 +43,7 @@ IF(Kokkos_ENABLE_CUDA) # if the second argument matches the C++ compiler, it forwards the rest of the # args to nvcc_wrapper kokkos_internal_have_compiler_nvcc( - ${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER} ${CMAKE_CXX_COMPILER} -DKOKKOS_DEPENDENCE) + ${Kokkos_COMPILE_LAUNCHER} ${Kokkos_NVCC_WRAPPER} ${CMAKE_CXX_COMPILER} ${CMAKE_CXX_COMPILER} -DKOKKOS_DEPENDENCE) SET(INTERNAL_USE_COMPILER_LAUNCHER true) ENDIF() ENDIF() @@ -55,32 +61,7 @@ IF(INTERNAL_HAVE_COMPILER_NVCC) SET(KOKKOS_CXX_COMPILER_VERSION ${TEMP_CXX_COMPILER_VERSION} CACHE STRING INTERNAL FORCE) MESSAGE(STATUS "Compiler Version: ${KOKKOS_CXX_COMPILER_VERSION}") IF(INTERNAL_USE_COMPILER_LAUNCHER) - IF(Kokkos_LAUNCH_COMPILER_INFO) - GET_FILENAME_COMPONENT(BASE_COMPILER_NAME ${CMAKE_CXX_COMPILER} NAME) - # does not have STATUS intentionally - MESSAGE("") - MESSAGE("Kokkos_LAUNCH_COMPILER_INFO (${Kokkos_COMPILE_LAUNCHER}):") - MESSAGE(" - Kokkos + CUDA backend requires the C++ files to be compiled as CUDA code.") - MESSAGE(" - kokkos_launch_compiler permits CMAKE_CXX_COMPILER to be set to a traditional C++ compiler when Kokkos_ENABLE_CUDA=ON") - MESSAGE(" by prefixing all the compile and link commands with the path to the script + CMAKE_CXX_COMPILER (${CMAKE_CXX_COMPILER}).") - MESSAGE(" - If any of the compile or link commands have CMAKE_CXX_COMPILER as the first argument, it replaces CMAKE_CXX_COMPILER with nvcc_wrapper.") - MESSAGE(" - If the compile or link command is not CMAKE_CXX_COMPILER, it just executes the command.") - MESSAGE(" - If using ccache, set CMAKE_CXX_COMPILER to nvcc_wrapper explicitly.") - MESSAGE(" - kokkos_compiler_launcher is available to downstream projects as well.") - MESSAGE(" - If CMAKE_CXX_COMPILER=nvcc_wrapper, all legacy behavior will be preserved during 'find_package(Kokkos)'") - MESSAGE(" - If CMAKE_CXX_COMPILER is not nvcc_wrapper, 'find_package(Kokkos)' will apply 'kokkos_compilation(GLOBAL)' unless separable compilation is enabled") - MESSAGE(" - This can be disabled via '-DKokkos_LAUNCH_COMPILER=OFF'") - MESSAGE(" - Use 'find_package(Kokkos COMPONENTS separable_compilation)' to enable separable compilation") - MESSAGE(" - Separable compilation allows you to control the scope of where the compiler transformation behavior (${BASE_COMPILER_NAME} -> nvcc_wrapper) is applied") - MESSAGE(" - The compiler transformation can be applied on a per-project, per-directory, per-target, and/or per-source-file basis") - MESSAGE(" - 'kokkos_compilation(PROJECT)' will apply the compiler transformation to all targets in a project/subproject") - MESSAGE(" - 'kokkos_compilation(TARGET [...])' will apply the compiler transformation to the specified target(s)") - MESSAGE(" - 'kokkos_compilation(SOURCE [...])' will apply the compiler transformation to the specified source file(s)") - MESSAGE(" - 'kokkos_compilation(DIRECTORY

[...])' will apply the compiler transformation to the specified directories") - MESSAGE("") - ELSE() - MESSAGE(STATUS "kokkos_launch_compiler (${Kokkos_COMPILE_LAUNCHER}) is enabled... Set Kokkos_LAUNCH_COMPILER_INFO=ON for more info.") - ENDIF() + MESSAGE(STATUS "kokkos_launch_compiler (${Kokkos_COMPILE_LAUNCHER}) is enabled...") kokkos_compilation(GLOBAL) ENDIF() ENDIF() @@ -92,7 +73,11 @@ IF(Kokkos_ENABLE_HIP) OUTPUT_STRIP_TRAILING_WHITESPACE) STRING(REPLACE "\n" " - " INTERNAL_COMPILER_VERSION_ONE_LINE ${INTERNAL_COMPILER_VERSION} ) - SET(KOKKOS_CXX_COMPILER_ID HIP CACHE STRING INTERNAL FORCE) + + STRING(FIND ${INTERNAL_COMPILER_VERSION_ONE_LINE} "HIP version" INTERNAL_COMPILER_VERSION_CONTAINS_HIP) + IF(INTERNAL_COMPILER_VERSION_CONTAINS_HIP GREATER -1) + SET(KOKKOS_CXX_COMPILER_ID HIPCC CACHE STRING INTERNAL FORCE) + ENDIF() STRING(REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" TEMP_CXX_COMPILER_VERSION ${INTERNAL_COMPILER_VERSION_ONE_LINE}) @@ -103,8 +88,7 @@ ENDIF() IF(KOKKOS_CXX_COMPILER_ID STREQUAL Clang) # The Cray compiler reports as Clang to most versions of CMake EXECUTE_PROCESS(COMMAND ${CMAKE_CXX_COMPILER} --version - COMMAND grep Cray - COMMAND wc -l + COMMAND grep -c Cray OUTPUT_VARIABLE INTERNAL_HAVE_CRAY_COMPILER OUTPUT_STRIP_TRAILING_WHITESPACE) IF (INTERNAL_HAVE_CRAY_COMPILER) #not actually Clang @@ -112,8 +96,7 @@ IF(KOKKOS_CXX_COMPILER_ID STREQUAL Clang) ENDIF() # The clang based Intel compiler reports as Clang to most versions of CMake EXECUTE_PROCESS(COMMAND ${CMAKE_CXX_COMPILER} --version - COMMAND grep icpx - COMMAND wc -l + COMMAND grep -c "DPC++\\|icpx" OUTPUT_VARIABLE INTERNAL_HAVE_INTEL_COMPILER OUTPUT_STRIP_TRAILING_WHITESPACE) IF (INTERNAL_HAVE_INTEL_COMPILER) #not actually Clang @@ -174,7 +157,7 @@ ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA) MESSAGE(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") ENDIF() SET(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Kokkos turns off CXX extensions" FORCE) -ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL HIP) +ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL HIPCC) IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 3.8.0) MESSAGE(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") ENDIF() diff --git a/lib/kokkos/cmake/kokkos_corner_cases.cmake b/lib/kokkos/cmake/kokkos_corner_cases.cmake index 3962c4b16e..a84ac2b630 100644 --- a/lib/kokkos/cmake/kokkos_corner_cases.cmake +++ b/lib/kokkos/cmake/kokkos_corner_cases.cmake @@ -49,11 +49,14 @@ ENDIF() IF (KOKKOS_CXX_STANDARD STREQUAL 17) IF (KOKKOS_CXX_COMPILER_ID STREQUAL GNU AND KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 7) - MESSAGE(FATAL_ERROR "You have requested c++17 support for GCC ${KOKKOS_CXX_COMPILER_VERSION}. Although CMake has allowed this and GCC accepts -std=c++1z/c++17, GCC <= 6 does not properly support *this capture. Please reduce the C++ standard to 14 or upgrade the compiler if you do need C++17 support.") + MESSAGE(FATAL_ERROR "You have requested C++17 support for GCC ${KOKKOS_CXX_COMPILER_VERSION}. Although CMake has allowed this and GCC accepts -std=c++1z/c++17, GCC < 7 does not properly support *this capture. Please reduce the C++ standard to 14 or upgrade the compiler if you do need C++17 support.") ENDIF() IF (KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA AND KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 11) - MESSAGE(FATAL_ERROR "You have requested c++17 support for NVCC ${KOKKOS_CXX_COMPILER_VERSION}. NVCC only supports C++17 from version 11 on. Please reduce the C++ standard to 14 or upgrade the compiler if you need C++17 support.") + MESSAGE(FATAL_ERROR "You have requested C++17 support for NVCC ${KOKKOS_CXX_COMPILER_VERSION}. NVCC only supports C++17 from version 11 on. Please reduce the C++ standard to 14 or upgrade the compiler if you need C++17 support.") + ENDIF() + IF (KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA AND KOKKOS_ENABLE_CUDA_CONSTEXPR) + MESSAGE(WARNING "You have requested -DKokkos_ENABLE_CUDA_CONSTEXPR=ON with C++17 support for NVCC ${KOKKOS_CXX_COMPILER_VERSION} which is known to trigger compiler bugs. See https://github.com/kokkos/kokkos/issues/3496") ENDIF() ENDIF() diff --git a/lib/kokkos/cmake/kokkos_enable_devices.cmake b/lib/kokkos/cmake/kokkos_enable_devices.cmake index 41ee10a8a0..445dad47ce 100644 --- a/lib/kokkos/cmake/kokkos_enable_devices.cmake +++ b/lib/kokkos/cmake/kokkos_enable_devices.cmake @@ -48,9 +48,6 @@ IF(KOKKOS_ENABLE_OPENMP) IF(KOKKOS_CLANG_IS_CRAY) SET(ClangOpenMPFlag -fopenmp) ENDIF() - IF(KOKKOS_CLANG_IS_INTEL) - SET(ClangOpenMPFlag -fiopenmp) - ENDIF() IF(KOKKOS_COMPILER_CLANG_MSVC) #for clang-cl expression /openmp yields an error, so directly add the specific Clang flag SET(ClangOpenMPFlag /clang:-fopenmp=libomp) @@ -64,6 +61,7 @@ IF(KOKKOS_ENABLE_OPENMP) COMPILER_SPECIFIC_FLAGS( COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID Clang -Xcompiler ${ClangOpenMPFlag} + IntelClang -Xcompiler -fiopenmp PGI -Xcompiler -mp Cray NO-VALUE-SPECIFIED XL -Xcompiler -qsmp=omp @@ -72,6 +70,7 @@ IF(KOKKOS_ENABLE_OPENMP) ELSE() COMPILER_SPECIFIC_FLAGS( Clang ${ClangOpenMPFlag} + IntelClang -fiopenmp AppleClang -Xpreprocessor -fopenmp PGI -mp Cray NO-VALUE-SPECIFIED @@ -152,3 +151,11 @@ IF (KOKKOS_ENABLE_HIP) ENDIF() KOKKOS_DEVICE_OPTION(SYCL OFF DEVICE "Whether to build SYCL backend") + +## SYCL has extra setup requirements, turn on Kokkos_Setup_SYCL.hpp in macros +IF (KOKKOS_ENABLE_SYCL) + IF(KOKKOS_CXX_STANDARD LESS 17) + MESSAGE(FATAL_ERROR "SYCL backend requires C++17 or newer!") + ENDIF() + LIST(APPEND DEVICE_SETUP_LIST SYCL) +ENDIF() diff --git a/lib/kokkos/cmake/kokkos_enable_options.cmake b/lib/kokkos/cmake/kokkos_enable_options.cmake index 5df498f373..95bce66c7b 100644 --- a/lib/kokkos/cmake/kokkos_enable_options.cmake +++ b/lib/kokkos/cmake/kokkos_enable_options.cmake @@ -48,6 +48,7 @@ KOKKOS_ENABLE_OPTION(COMPILER_WARNINGS OFF "Whether to print all compiler war KOKKOS_ENABLE_OPTION(PROFILING_LOAD_PRINT OFF "Whether to print information about which profiling tools got loaded") KOKKOS_ENABLE_OPTION(TUNING OFF "Whether to create bindings for tuning tools") KOKKOS_ENABLE_OPTION(AGGRESSIVE_VECTORIZATION OFF "Whether to aggressively vectorize loops") +KOKKOS_ENABLE_OPTION(LAUNCH_COMPILER ON "Whether to potentially use the launch compiler") IF (KOKKOS_ENABLE_CUDA) SET(KOKKOS_COMPILER_CUDA_VERSION "${KOKKOS_COMPILER_VERSION_MAJOR}${KOKKOS_COMPILER_VERSION_MINOR}") @@ -68,6 +69,15 @@ ELSE() ENDIF() KOKKOS_ENABLE_OPTION(COMPLEX_ALIGN ${COMPLEX_ALIGN_DEFAULT} "Whether to align Kokkos::complex to 2*alignof(RealType)") +IF (KOKKOS_ENABLE_TESTS) + SET(HEADER_SELF_CONTAINMENT_TESTS_DEFAULT ON) +ELSE() + SET(HEADER_SELF_CONTAINMENT_TESTS_DEFAULT OFF) +ENDIF() +KOKKOS_ENABLE_OPTION(HEADER_SELF_CONTAINMENT_TESTS ${HEADER_SELF_CONTAINMENT_TESTS_DEFAULT} "Enable header self-containment unit tests") +IF (NOT KOKKOS_ENABLE_TESTS AND KOKKOS_ENABLE_HEADER_SELF_CONTAINMENT_TESTS) + MESSAGE(WARNING "Kokkos_ENABLE_HEADER_SELF_CONTAINMENT_TESTS is ON but Kokkos_ENABLE_TESTS is OFF. Option will be ignored.") +ENDIF() IF (KOKKOS_ENABLE_CUDA AND (KOKKOS_CXX_COMPILER_ID STREQUAL Clang)) SET(CUDA_CONSTEXPR_DEFAULT ON) @@ -76,14 +86,14 @@ ELSE() ENDIF() KOKKOS_ENABLE_OPTION(CUDA_CONSTEXPR ${CUDA_CONSTEXPR_DEFAULT} "Whether to activate experimental relaxed constexpr functions") +Kokkos_ENABLE_OPTION(UNSUPPORTED_ARCHS OFF "Whether to allow architectures in backends Kokkos doesn't optimize for") + FUNCTION(check_device_specific_options) CMAKE_PARSE_ARGUMENTS(SOME "" "DEVICE" "OPTIONS" ${ARGN}) IF(NOT KOKKOS_ENABLE_${SOME_DEVICE}) FOREACH(OPTION ${SOME_OPTIONS}) - IF(CMAKE_VERSION VERSION_GREATER_EQUAL 3.14) - IF(NOT DEFINED CACHE{Kokkos_ENABLE_${OPTION}} OR NOT DEFINED CACHE{Kokkos_ENABLE_${SOME_DEVICE}}) - MESSAGE(FATAL_ERROR "Internal logic error: option '${OPTION}' or device '${SOME_DEVICE}' not recognized.") - ENDIF() + IF(NOT DEFINED CACHE{Kokkos_ENABLE_${OPTION}} OR NOT DEFINED CACHE{Kokkos_ENABLE_${SOME_DEVICE}}) + MESSAGE(FATAL_ERROR "Internal logic error: option '${OPTION}' or device '${SOME_DEVICE}' not recognized.") ENDIF() IF(KOKKOS_ENABLE_${OPTION}) MESSAGE(WARNING "Kokkos_ENABLE_${OPTION} is ON but ${SOME_DEVICE} backend is not enabled. Option will be ignored.") diff --git a/lib/kokkos/cmake/kokkos_functions.cmake b/lib/kokkos/cmake/kokkos_functions.cmake index 2b17d648b4..858322394d 100644 --- a/lib/kokkos/cmake/kokkos_functions.cmake +++ b/lib/kokkos/cmake/kokkos_functions.cmake @@ -169,9 +169,7 @@ MACRO(kokkos_export_imported_tpl NAME) ENDIF() SET(TPL_LINK_OPTIONS) - IF(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.13.0") - GET_TARGET_PROPERTY(TPL_LINK_OPTIONS ${NAME} INTERFACE_LINK_OPTIONS) - ENDIF() + GET_TARGET_PROPERTY(TPL_LINK_OPTIONS ${NAME} INTERFACE_LINK_OPTIONS) IF(TPL_LINK_OPTIONS) KOKKOS_APPEND_CONFIG_LINE("INTERFACE_LINK_OPTIONS ${TPL_LINK_OPTIONS}") ENDIF() @@ -230,9 +228,7 @@ MACRO(kokkos_import_tpl NAME) # I have still been getting errors about ROOT variables being ignored # I'm not sure if this is a scope issue - but make sure # the policy is set before we do any find_package calls - IF(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.12.0") - CMAKE_POLICY(SET CMP0074 NEW) - ENDIF() + CMAKE_POLICY(SET CMP0074 NEW) IF (KOKKOS_ENABLE_${NAME}) #Tack on a TPL here to make sure we avoid using anyone else's find @@ -314,7 +310,7 @@ MACRO(kokkos_create_imported_tpl NAME) CMAKE_PARSE_ARGUMENTS(TPL "INTERFACE" "LIBRARY" - "LINK_LIBRARIES;INCLUDES;COMPILE_OPTIONS;LINK_OPTIONS" + "LINK_LIBRARIES;INCLUDES;COMPILE_DEFINITIONS;COMPILE_OPTIONS;LINK_OPTIONS" ${ARGN}) @@ -334,6 +330,9 @@ MACRO(kokkos_create_imported_tpl NAME) IF(TPL_INCLUDES) TARGET_INCLUDE_DIRECTORIES(${NAME} INTERFACE ${TPL_INCLUDES}) ENDIF() + IF(TPL_COMPILE_DEFINITIONS) + TARGET_COMPILE_DEFINITIONS(${NAME} INTERFACE ${TPL_COMPILE_DEFINITIONS}) + ENDIF() IF(TPL_COMPILE_OPTIONS) TARGET_COMPILE_OPTIONS(${NAME} INTERFACE ${TPL_COMPILE_OPTIONS}) ENDIF() @@ -355,6 +354,10 @@ MACRO(kokkos_create_imported_tpl NAME) SET_TARGET_PROPERTIES(${NAME} PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${TPL_INCLUDES}") ENDIF() + IF(TPL_COMPILE_DEFINITIONS) + SET_TARGET_PROPERTIES(${NAME} PROPERTIES + INTERFACE_COMPILE_DEFINITIONS "${TPL_COMPILE_DEFINITIONS}") + ENDIF() IF(TPL_COMPILE_OPTIONS) SET_TARGET_PROPERTIES(${NAME} PROPERTIES INTERFACE_COMPILE_OPTIONS "${TPL_COMPILE_OPTIONS}") @@ -770,7 +773,7 @@ FUNCTION(kokkos_link_tpl TARGET) ENDFUNCTION() FUNCTION(COMPILER_SPECIFIC_OPTIONS_HELPER) - SET(COMPILERS NVIDIA PGI XL DEFAULT Cray Intel Clang AppleClang IntelClang GNU HIP Fujitsu) + SET(COMPILERS NVIDIA PGI XL DEFAULT Cray Intel Clang AppleClang IntelClang GNU HIPCC Fujitsu) CMAKE_PARSE_ARGUMENTS( PARSE "LINK_OPTIONS;COMPILE_OPTIONS;COMPILE_DEFINITIONS;LINK_LIBRARIES" @@ -926,6 +929,9 @@ ENDFUNCTION() # DIRECTORY --> all files in directory # PROJECT --> all files/targets in a project/subproject # +# NOTE: this is VERY DIFFERENT than the version in KokkosConfigCommon.cmake.in. +# This version explicitly uses nvcc_wrapper. +# FUNCTION(kokkos_compilation) # check whether the compiler already supports building CUDA KOKKOS_CXX_COMPILER_CUDA_TEST(Kokkos_CXX_COMPILER_COMPILES_CUDA) @@ -947,10 +953,21 @@ FUNCTION(kokkos_compilation) MESSAGE(FATAL_ERROR "Kokkos could not find 'kokkos_launch_compiler'. Please set '-DKokkos_COMPILE_LAUNCHER=/path/to/launcher'") ENDIF() + # find nvcc_wrapper + FIND_PROGRAM(Kokkos_NVCC_WRAPPER + NAMES nvcc_wrapper + HINTS ${PROJECT_SOURCE_DIR} + PATHS ${PROJECT_SOURCE_DIR} + PATH_SUFFIXES bin) + + IF(NOT Kokkos_COMPILE_LAUNCHER) + MESSAGE(FATAL_ERROR "Kokkos could not find 'nvcc_wrapper'. Please set '-DKokkos_COMPILE_LAUNCHER=/path/to/nvcc_wrapper'") + ENDIF() + IF(COMP_GLOBAL) # if global, don't bother setting others - SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") - SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") + SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${Kokkos_NVCC_WRAPPER} ${CMAKE_CXX_COMPILER}") + SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${Kokkos_NVCC_WRAPPER} ${CMAKE_CXX_COMPILER}") ELSE() FOREACH(_TYPE PROJECT DIRECTORY TARGET SOURCE) # make project/subproject scoping easy, e.g. KokkosCompilation(PROJECT) after project(...) @@ -961,8 +978,8 @@ FUNCTION(kokkos_compilation) # set the properties if defined IF(COMP_${_TYPE}) # MESSAGE(STATUS "Using nvcc_wrapper :: ${_TYPE} :: ${COMP_${_TYPE}}") - SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") - SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}") + SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${Kokkos_NVCC_WRAPPER} ${CMAKE_CXX_COMPILER}") + SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${Kokkos_NVCC_WRAPPER} ${CMAKE_CXX_COMPILER}") ENDIF() ENDFOREACH() ENDIF() diff --git a/lib/kokkos/cmake/kokkos_test_cxx_std.cmake b/lib/kokkos/cmake/kokkos_test_cxx_std.cmake index 1d7da922eb..707fb000af 100644 --- a/lib/kokkos/cmake/kokkos_test_cxx_std.cmake +++ b/lib/kokkos/cmake/kokkos_test_cxx_std.cmake @@ -86,6 +86,19 @@ ELSE() MESSAGE(FATAL_ERROR "Unknown C++ standard ${KOKKOS_CXX_STANDARD} - must be 14, 17, or 20") ENDIF() +# Enforce that we can compile a simple C++14 program + +TRY_COMPILE(CAN_COMPILE_CPP14 + ${KOKKOS_TOP_BUILD_DIR}/corner_cases + ${KOKKOS_SOURCE_DIR}/cmake/compile_tests/cplusplus14.cpp + OUTPUT_VARIABLE ERROR_MESSAGE + CXX_STANDARD 14 +) +if (NOT CAN_COMPILE_CPP14) + UNSET(CAN_COMPILE_CPP14 CACHE) #make sure CMake always re-runs this + MESSAGE(FATAL_ERROR "C++${KOKKOS_CXX_STANDARD}-compliant compiler detected, but unable to compile C++14 or later program. Verify that ${CMAKE_CXX_COMPILER_ID}:${CMAKE_CXX_COMPILER_VERSION} is set up correctly (e.g., check that correct library headers are being used).\nFailing output:\n ${ERROR_MESSAGE}") +ENDIF() +UNSET(CAN_COMPILE_CPP14 CACHE) #make sure CMake always re-runs this # Enforce that extensions are turned off for nvcc_wrapper. diff --git a/lib/kokkos/cmake/kokkos_tpls.cmake b/lib/kokkos/cmake/kokkos_tpls.cmake index b58d3696ea..d8d044c9d7 100644 --- a/lib/kokkos/cmake/kokkos_tpls.cmake +++ b/lib/kokkos/cmake/kokkos_tpls.cmake @@ -1,5 +1,6 @@ KOKKOS_CFG_DEPENDS(TPLS OPTIONS) KOKKOS_CFG_DEPENDS(TPLS DEVICES) +KOKKOS_CFG_DEPENDS(TPLS COMPILER_ID) FUNCTION(KOKKOS_TPL_OPTION PKG DEFAULT) CMAKE_PARSE_ARGUMENTS(PARSED @@ -38,6 +39,12 @@ IF(KOKKOS_ENABLE_MEMKIND) ENDIF() KOKKOS_TPL_OPTION(CUDA ${Kokkos_ENABLE_CUDA} TRIBITS CUDA) KOKKOS_TPL_OPTION(LIBRT Off) +IF(KOKKOS_ENABLE_HIP AND NOT KOKKOS_CXX_COMPILER_ID STREQUAL HIPCC) + SET(ROCM_DEFAULT ON) +ELSE() + SET(ROCM_DEFAULT OFF) +ENDIF() +KOKKOS_TPL_OPTION(ROCM ${ROCM_DEFAULT}) IF (WIN32) SET(LIBDL_DEFAULT Off) @@ -70,6 +77,7 @@ KOKKOS_IMPORT_TPL(LIBRT) KOKKOS_IMPORT_TPL(LIBDL) KOKKOS_IMPORT_TPL(MEMKIND) KOKKOS_IMPORT_TPL(PTHREAD INTERFACE) +KOKKOS_IMPORT_TPL(ROCM INTERFACE) #Convert list to newlines (which CMake doesn't always like in cache variables) STRING(REPLACE ";" "\n" KOKKOS_TPL_EXPORT_TEMP "${KOKKOS_TPL_EXPORTS}") diff --git a/lib/kokkos/cmake/kokkos_tribits.cmake b/lib/kokkos/cmake/kokkos_tribits.cmake index 059fb192f0..afa036066a 100644 --- a/lib/kokkos/cmake/kokkos_tribits.cmake +++ b/lib/kokkos/cmake/kokkos_tribits.cmake @@ -141,39 +141,54 @@ FUNCTION(KOKKOS_ADD_EXECUTABLE ROOT_NAME) ENDFUNCTION() FUNCTION(KOKKOS_ADD_EXECUTABLE_AND_TEST ROOT_NAME) -CMAKE_PARSE_ARGUMENTS(PARSE - "" - "" - "SOURCES;CATEGORIES;ARGS" - ${ARGN}) -VERIFY_EMPTY(KOKKOS_ADD_EXECUTABLE_AND_TEST ${PARSE_UNPARSED_ARGUMENTS}) + CMAKE_PARSE_ARGUMENTS(PARSE + "" + "" + "SOURCES;CATEGORIES;ARGS" + ${ARGN}) + VERIFY_EMPTY(KOKKOS_ADD_EXECUTABLE_AND_TEST ${PARSE_UNPARSED_ARGUMENTS}) -IF (KOKKOS_HAS_TRILINOS) - IF(DEFINED PARSE_ARGS) - STRING(REPLACE ";" " " PARSE_ARGS "${PARSE_ARGS}") - ENDIF() - TRIBITS_ADD_EXECUTABLE_AND_TEST( - ${ROOT_NAME} - SOURCES ${PARSE_SOURCES} - TESTONLYLIBS kokkos_gtest - NUM_MPI_PROCS 1 - COMM serial mpi - ARGS ${PARSE_ARGS} - CATEGORIES ${PARSE_CATEGORIES} - SOURCES ${PARSE_SOURCES} - FAIL_REGULAR_EXPRESSION " FAILED " - ARGS ${PARSE_ARGS} - ) -ELSE() - KOKKOS_ADD_TEST_EXECUTABLE(${ROOT_NAME} - SOURCES ${PARSE_SOURCES} - ) - KOKKOS_ADD_TEST(NAME ${ROOT_NAME} - EXE ${ROOT_NAME} - FAIL_REGULAR_EXPRESSION " FAILED " - ARGS ${PARSE_ARGS} - ) -ENDIF() + IF (KOKKOS_HAS_TRILINOS) + IF(DEFINED PARSE_ARGS) + STRING(REPLACE ";" " " PARSE_ARGS "${PARSE_ARGS}") + ENDIF() + TRIBITS_ADD_EXECUTABLE_AND_TEST( + ${ROOT_NAME} + SOURCES ${PARSE_SOURCES} + TESTONLYLIBS kokkos_gtest + NUM_MPI_PROCS 1 + COMM serial mpi + ARGS ${PARSE_ARGS} + CATEGORIES ${PARSE_CATEGORIES} + SOURCES ${PARSE_SOURCES} + FAIL_REGULAR_EXPRESSION " FAILED " + ARGS ${PARSE_ARGS} + ) + ELSE() + KOKKOS_ADD_TEST_EXECUTABLE(${ROOT_NAME} + SOURCES ${PARSE_SOURCES} + ) + IF (PARSE_ARGS) + SET(TEST_NUMBER 0) + FOREACH (ARG_STR ${PARSE_ARGS}) + # This is passed as a single string blob to match TriBITS behavior + # We need this to be turned into a list + STRING(REPLACE " " ";" ARG_STR_LIST ${ARG_STR}) + LIST(APPEND TEST_NAME "${ROOT_NAME}${TEST_NUMBER}") + MATH(EXPR TEST_NUMBER "${TEST_NUMBER} + 1") + KOKKOS_ADD_TEST(NAME ${TEST_NAME} + EXE ${ROOT_NAME} + FAIL_REGULAR_EXPRESSION " FAILED " + ARGS ${ARG_STR_LIST} + ) + ENDFOREACH() + ELSE() + KOKKOS_ADD_TEST(NAME ${ROOT_NAME} + EXE ${ROOT_NAME} + FAIL_REGULAR_EXPRESSION " FAILED " + ) + ENDIF() + ENDIF() ENDFUNCTION() FUNCTION(KOKKOS_SET_EXE_PROPERTY ROOT_NAME) @@ -301,11 +316,26 @@ ENDMACRO() ## Includes generated header files, scripts such as nvcc_wrapper and hpcbind, ## as well as other files provided through plugins. MACRO(KOKKOS_INSTALL_ADDITIONAL_FILES) - # kokkos_launch_compiler is used by Kokkos to prefix compiler commands so that they forward to nvcc_wrapper + + # kokkos_launch_compiler is used by Kokkos to prefix compiler commands so that they forward to original kokkos compiler + # if nvcc_wrapper was not used as CMAKE_CXX_COMPILER, configure the original compiler into kokkos_launch_compiler + IF(NOT "${CMAKE_CXX_COMPILER}" MATCHES "nvcc_wrapper") + SET(NVCC_WRAPPER_DEFAULT_COMPILER "${CMAKE_CXX_COMPILER}") + ELSE() + IF(NOT "$ENV{NVCC_WRAPPER_DEFAULT_COMPILER}" STREQUAL "") + SET(NVCC_WRAPPER_DEFAULT_COMPILER "$ENV{NVCC_WRAPPER_DEFAULT_COMPILER}") + ENDIF() + ENDIF() + + CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/bin/kokkos_launch_compiler + ${PROJECT_BINARY_DIR}/temp/kokkos_launch_compiler + @ONLY) + INSTALL(PROGRAMS "${CMAKE_CURRENT_SOURCE_DIR}/bin/nvcc_wrapper" "${CMAKE_CURRENT_SOURCE_DIR}/bin/hpcbind" "${CMAKE_CURRENT_SOURCE_DIR}/bin/kokkos_launch_compiler" + "${PROJECT_BINARY_DIR}/temp/kokkos_launch_compiler" DESTINATION ${CMAKE_INSTALL_BINDIR}) INSTALL(FILES "${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_config.h" @@ -313,7 +343,7 @@ MACRO(KOKKOS_INSTALL_ADDITIONAL_FILES) "${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_Config_SetupBackend.hpp" "${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_Config_DeclareBackend.hpp" "${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_Config_PostInclude.hpp" - DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) + DESTINATION ${KOKKOS_HEADER_DIR}) ENDMACRO() FUNCTION(KOKKOS_SET_LIBRARY_PROPERTIES LIBRARY_NAME) @@ -330,24 +360,12 @@ FUNCTION(KOKKOS_SET_LIBRARY_PROPERTIES LIBRARY_NAME) ${LIBRARY_NAME} PUBLIC $<$:${KOKKOS_LINK_OPTIONS}> ) - ELSEIF(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.13") + ELSE() #I can use link options #just assume CXX linkage TARGET_LINK_OPTIONS( ${LIBRARY_NAME} PUBLIC ${KOKKOS_LINK_OPTIONS} ) - ELSE() - #assume CXX linkage, we have no good way to check otherwise - IF (PARSE_PLAIN_STYLE) - TARGET_LINK_LIBRARIES( - ${LIBRARY_NAME} ${KOKKOS_LINK_OPTIONS} - ) - ELSE() - #well, have to do it the wrong way for now - TARGET_LINK_LIBRARIES( - ${LIBRARY_NAME} PUBLIC ${KOKKOS_LINK_OPTIONS} - ) - ENDIF() ENDIF() TARGET_COMPILE_OPTIONS( @@ -448,6 +466,13 @@ FUNCTION(KOKKOS_INTERNAL_ADD_LIBRARY LIBRARY_NAME) ${PARSE_SOURCES} ) + IF(PARSE_SHARED OR BUILD_SHARED_LIBS) + SET_TARGET_PROPERTIES(${LIBRARY_NAME} PROPERTIES + VERSION ${Kokkos_VERSION} + SOVERSION ${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR} + ) + ENDIF() + KOKKOS_INTERNAL_ADD_LIBRARY_INSTALL(${LIBRARY_NAME}) #In case we are building in-tree, add an alias name diff --git a/lib/kokkos/containers/src/CMakeLists.txt b/lib/kokkos/containers/src/CMakeLists.txt index 7000624b6b..98655896d4 100644 --- a/lib/kokkos/containers/src/CMakeLists.txt +++ b/lib/kokkos/containers/src/CMakeLists.txt @@ -26,8 +26,6 @@ KOKKOS_ADD_LIBRARY( HEADERS ${KOKKOS_CONTAINER_HEADERS} ) -SET_TARGET_PROPERTIES(kokkoscontainers PROPERTIES VERSION ${Kokkos_VERSION}) - KOKKOS_LIB_INCLUDE_DIRECTORIES(kokkoscontainers ${KOKKOS_TOP_BUILD_DIR} ${CMAKE_CURRENT_BINARY_DIR} @@ -36,4 +34,3 @@ KOKKOS_LIB_INCLUDE_DIRECTORIES(kokkoscontainers KOKKOS_LINK_INTERNAL_LIBRARY(kokkoscontainers kokkoscore) #----------------------------------------------------------------------------- - diff --git a/lib/kokkos/containers/src/Kokkos_DualView.hpp b/lib/kokkos/containers/src/Kokkos_DualView.hpp index 689f0eb2ed..45710d1f73 100644 --- a/lib/kokkos/containers/src/Kokkos_DualView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DualView.hpp @@ -91,6 +91,25 @@ namespace Kokkos { * behavior. Please see the documentation of Kokkos::View for * examples. The default suffices for most users. */ + +namespace Impl { + +#ifdef KOKKOS_ENABLE_CUDA + +inline const Kokkos::Cuda& get_cuda_space(const Kokkos::Cuda& in) { return in; } + +inline const Kokkos::Cuda& get_cuda_space() { + return *Kokkos::Impl::cuda_get_deep_copy_space(); +} + +template +inline const Kokkos::Cuda& get_cuda_space(const NonCudaExecSpace&) { + return get_cuda_space(); +} + +#endif // KOKKOS_ENABLE_CUDA + +} // namespace Impl template class DualView : public ViewTraits { @@ -295,6 +314,53 @@ class DualView : public ViewTraits { "DualView constructed with incompatible views"); } } + // does the DualView have only one device + struct impl_dualview_is_single_device { + enum : bool { + value = std::is_same::value + }; + }; + + // does the given device match the device of t_dev? + template + struct impl_device_matches_tdev_device { + enum : bool { + value = std::is_same::value + }; + }; + // does the given device match the device of t_host? + template + struct impl_device_matches_thost_device { + enum : bool { + value = std::is_same::value + }; + }; + + // does the given device match the execution space of t_host? + template + struct impl_device_matches_thost_exec { + enum : bool { + value = std::is_same::value + }; + }; + + // does the given device match the execution space of t_dev? + template + struct impl_device_matches_tdev_exec { + enum : bool { + value = std::is_same::value + }; + }; + + // does the given device's memory space match the memory space of t_dev? + template + struct impl_device_matches_tdev_memory_space { + enum : bool { + value = std::is_same::value + }; + }; //@} //! \name Methods for synchronizing, marking as modified, and getting Views. @@ -302,7 +368,7 @@ class DualView : public ViewTraits { /// \brief Return a View on a specific device \c Device. /// - /// Please don't be afraid of the if_c expression in the return + /// Please don't be afraid of the nested if_c expressions in the return /// value's type. That just tells the method what the return type /// should be: t_dev if the \c Device template parameter matches /// this DualView's device type, else t_host. @@ -323,10 +389,17 @@ class DualView : public ViewTraits { /// typename dual_view_type::t_host hostView = DV.view (); /// \endcode template - KOKKOS_INLINE_FUNCTION const typename Impl::if_c< - std::is_same::value, - t_dev, t_host>::type& + KOKKOS_INLINE_FUNCTION const typename std::conditional_t< + impl_device_matches_tdev_device::value, t_dev, + typename std::conditional_t< + impl_device_matches_thost_device::value, t_host, + typename std::conditional_t< + impl_device_matches_thost_exec::value, t_host, + typename std::conditional_t< + impl_device_matches_tdev_exec::value, t_dev, + typename std::conditional_t< + impl_device_matches_tdev_memory_space::value, + t_dev, t_host> > > > > view() const { constexpr bool device_is_memspace = std::is_same::value; @@ -463,6 +536,7 @@ class DualView : public ViewTraits { true); } } + /// \brief Update data on device or host only if data in the other /// space has been marked as modified. /// @@ -480,12 +554,9 @@ class DualView : public ViewTraits { /// the data in either View. You must manually mark modified data /// as modified, by calling the modify() method with the /// appropriate template parameter. - template - void sync(const typename std::enable_if< - (std::is_same::value) || - (std::is_same::value), - int>::type& = 0) { + // deliberately passing args by cref as they're used multiple times + template + void sync_impl(std::true_type, Args const&... args) { if (modified_flags.data() == nullptr) return; int dev = get_device_side(); @@ -497,12 +568,12 @@ class DualView : public ViewTraits { Kokkos::CudaUVMSpace>::value) { if (d_view.data() == h_view.data()) Kokkos::Impl::cuda_prefetch_pointer( - Kokkos::Cuda(), d_view.data(), + Impl::get_cuda_space(args...), d_view.data(), sizeof(typename t_dev::value_type) * d_view.span(), true); } #endif - deep_copy(d_view, h_view); + deep_copy(args..., d_view, h_view); modified_flags(0) = modified_flags(1) = 0; impl_report_device_sync(); } @@ -514,12 +585,12 @@ class DualView : public ViewTraits { Kokkos::CudaUVMSpace>::value) { if (d_view.data() == h_view.data()) Kokkos::Impl::cuda_prefetch_pointer( - Kokkos::Cuda(), d_view.data(), + Impl::get_cuda_space(args...), d_view.data(), sizeof(typename t_dev::value_type) * d_view.span(), false); } #endif - deep_copy(h_view, d_view); + deep_copy(args..., h_view, d_view); modified_flags(0) = modified_flags(1) = 0; impl_report_host_sync(); } @@ -533,10 +604,26 @@ class DualView : public ViewTraits { template void sync(const typename std::enable_if< - (!std::is_same::value) || + (std::is_same::value) || (std::is_same::value), int>::type& = 0) { + sync_impl(std::true_type{}); + } + + template + void sync(const ExecutionSpace& exec, + const typename std::enable_if< + (std::is_same::value) || + (std::is_same::value), + int>::type& = 0) { + sync_impl(std::true_type{}, exec); + } + + // deliberately passing args by cref as they're used multiple times + template + void sync_impl(std::false_type, Args const&...) { if (modified_flags.data() == nullptr) return; int dev = get_device_side(); @@ -557,7 +644,27 @@ class DualView : public ViewTraits { } } - void sync_host() { + template + void sync(const typename std::enable_if< + (!std::is_same::value) || + (std::is_same::value), + int>::type& = 0) { + sync_impl(std::false_type{}); + } + template + void sync(const ExecutionSpace& exec, + const typename std::enable_if< + (!std::is_same::value) || + (std::is_same::value), + int>::type& = 0) { + sync_impl(std::false_type{}, exec); + } + + // deliberately passing args by cref as they're used multiple times + template + void sync_host_impl(Args const&... args) { if (!std::is_same::value) Impl::throw_runtime_exception( @@ -569,18 +676,26 @@ class DualView : public ViewTraits { Kokkos::CudaUVMSpace>::value) { if (d_view.data() == h_view.data()) Kokkos::Impl::cuda_prefetch_pointer( - Kokkos::Cuda(), d_view.data(), + Impl::get_cuda_space(args...), d_view.data(), sizeof(typename t_dev::value_type) * d_view.span(), false); } #endif - deep_copy(h_view, d_view); + deep_copy(args..., h_view, d_view); modified_flags(1) = modified_flags(0) = 0; impl_report_host_sync(); } } - void sync_device() { + template + void sync_host(const ExecSpace& exec) { + sync_host_impl(exec); + } + void sync_host() { sync_host_impl(); } + + // deliberately passing args by cref as they're used multiple times + template + void sync_device_impl(Args const&... args) { if (!std::is_same::value) Impl::throw_runtime_exception( @@ -592,17 +707,23 @@ class DualView : public ViewTraits { Kokkos::CudaUVMSpace>::value) { if (d_view.data() == h_view.data()) Kokkos::Impl::cuda_prefetch_pointer( - Kokkos::Cuda(), d_view.data(), + Impl::get_cuda_space(args...), d_view.data(), sizeof(typename t_dev::value_type) * d_view.span(), true); } #endif - deep_copy(d_view, h_view); + deep_copy(args..., d_view, h_view); modified_flags(1) = modified_flags(0) = 0; impl_report_device_sync(); } } + template + void sync_device(const ExecSpace& exec) { + sync_device_impl(exec); + } + void sync_device() { sync_device_impl(); } + template bool need_sync() const { if (modified_flags.data() == nullptr) return false; @@ -658,6 +779,7 @@ class DualView : public ViewTraits { template void modify() { if (modified_flags.data() == nullptr) return; + if (impl_dualview_is_single_device::value) return; int dev = get_device_side(); if (dev == 1) { // if Device is the same as DualView's device type @@ -690,6 +812,7 @@ class DualView : public ViewTraits { } inline void modify_host() { + if (impl_dualview_is_single_device::value) return; if (modified_flags.data() != nullptr) { modified_flags(0) = (modified_flags(1) > modified_flags(0) ? modified_flags(1) @@ -710,6 +833,7 @@ class DualView : public ViewTraits { } inline void modify_device() { + if (impl_dualview_is_single_device::value) return; if (modified_flags.data() != nullptr) { modified_flags(1) = (modified_flags(1) > modified_flags(0) ? modified_flags(1) diff --git a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp index c66d7a5f36..c6323fef93 100644 --- a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp @@ -245,13 +245,10 @@ KOKKOS_INLINE_FUNCTION bool dyn_rank_view_verify_operator_bounds( return (size_t(i) < map.extent(R)) && dyn_rank_view_verify_operator_bounds(rank, map, args...); } else if (i != 0) { - // FIXME_SYCL SYCL doesn't allow printf in kernels -#ifndef KOKKOS_ENABLE_SYCL - printf( + KOKKOS_IMPL_DO_NOT_USE_PRINTF( "DynRankView Debug Bounds Checking Error: at rank %u\n Extra " "arguments beyond the rank must be zero \n", R); -#endif return (false) && dyn_rank_view_verify_operator_bounds(rank, map, args...); } else { @@ -575,37 +572,22 @@ class DynRankView : public ViewTraits { (is_layout_left || is_layout_right || is_layout_stride) }; - template ::accessible> - struct verify_space { - KOKKOS_FORCEINLINE_FUNCTION static void check() {} - }; - - template - struct verify_space { - KOKKOS_FORCEINLINE_FUNCTION static void check() { - Kokkos::abort( - "Kokkos::DynRankView ERROR: attempt to access inaccessible memory " - "space"); - }; - }; - // Bounds checking macros #if defined(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK) // rank of the calling operator - included as first argument in ARG -#define KOKKOS_IMPL_VIEW_OPERATOR_VERIFY(ARG) \ - DynRankView::template verify_space< \ - Kokkos::Impl::ActiveExecutionMemorySpace>::check(); \ - Kokkos::Impl::dyn_rank_view_verify_operator_bounds< \ - typename traits::memory_space> \ +#define KOKKOS_IMPL_VIEW_OPERATOR_VERIFY(ARG) \ + Kokkos::Impl::verify_space::check(); \ + Kokkos::Impl::dyn_rank_view_verify_operator_bounds< \ + typename traits::memory_space> \ ARG; #else -#define KOKKOS_IMPL_VIEW_OPERATOR_VERIFY(ARG) \ - DynRankView::template verify_space< \ - Kokkos::Impl::ActiveExecutionMemorySpace>::check(); +#define KOKKOS_IMPL_VIEW_OPERATOR_VERIFY(ARG) \ + Kokkos::Impl::verify_space::check(); #endif diff --git a/lib/kokkos/containers/src/Kokkos_DynamicView.hpp b/lib/kokkos/containers/src/Kokkos_DynamicView.hpp index 06bd556661..cc949d4c55 100644 --- a/lib/kokkos/containers/src/Kokkos_DynamicView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DynamicView.hpp @@ -76,6 +76,12 @@ struct ChunkArraySpace { using memory_space = typename Kokkos::Experimental::HIPHostPinnedSpace; }; #endif +#ifdef KOKKOS_ENABLE_SYCL +template <> +struct ChunkArraySpace { + using memory_space = typename Kokkos::Experimental::SYCLSharedUSMSpace; +}; +#endif } // end namespace Impl /** \brief Dynamic views are restricted to rank-one and no layout. diff --git a/lib/kokkos/containers/src/Kokkos_OffsetView.hpp b/lib/kokkos/containers/src/Kokkos_OffsetView.hpp index 4fd084338e..0f21a08ba3 100644 --- a/lib/kokkos/containers/src/Kokkos_OffsetView.hpp +++ b/lib/kokkos/containers/src/Kokkos_OffsetView.hpp @@ -377,34 +377,20 @@ class OffsetView : public ViewTraits { std::is_same::value && (is_layout_left || is_layout_right || is_layout_stride); - template ::accessible> - struct verify_space { - KOKKOS_FORCEINLINE_FUNCTION static void check() {} - }; - - template - struct verify_space { - KOKKOS_FORCEINLINE_FUNCTION static void check() { - Kokkos::abort( - "Kokkos::View ERROR: attempt to access inaccessible memory space"); - }; - }; - #if defined(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK) -#define KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY(ARG) \ - OffsetView::template verify_space< \ - Kokkos::Impl::ActiveExecutionMemorySpace>::check(); \ - Kokkos::Experimental::Impl::offsetview_verify_operator_bounds< \ - typename traits::memory_space> \ +#define KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY(ARG) \ + Kokkos::Impl::verify_space::check(); \ + Kokkos::Experimental::Impl::offsetview_verify_operator_bounds< \ + typename traits::memory_space> \ ARG; #else -#define KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY(ARG) \ - OffsetView::template verify_space< \ - Kokkos::Impl::ActiveExecutionMemorySpace>::check(); +#define KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY(ARG) \ + Kokkos::Impl::verify_space::check(); #endif public: diff --git a/lib/kokkos/containers/src/Kokkos_ScatterView.hpp b/lib/kokkos/containers/src/Kokkos_ScatterView.hpp index 5e18f5a80e..dcd4cf73e5 100644 --- a/lib/kokkos/containers/src/Kokkos_ScatterView.hpp +++ b/lib/kokkos/containers/src/Kokkos_ScatterView.hpp @@ -649,13 +649,13 @@ struct ReduceDuplicatesBase { size_t stride; size_t start; size_t n; - ReduceDuplicatesBase(ValueType const* src_in, ValueType* dest_in, - size_t stride_in, size_t start_in, size_t n_in, - std::string const& name) + ReduceDuplicatesBase(ExecSpace const& exec_space, ValueType const* src_in, + ValueType* dest_in, size_t stride_in, size_t start_in, + size_t n_in, std::string const& name) : src(src_in), dst(dest_in), stride(stride_in), start(start_in), n(n_in) { parallel_for( std::string("Kokkos::ScatterView::ReduceDuplicates [") + name + "]", - RangePolicy(0, stride), + RangePolicy(exec_space, 0, stride), static_cast(*this)); } }; @@ -667,9 +667,10 @@ template struct ReduceDuplicates : public ReduceDuplicatesBase { using Base = ReduceDuplicatesBase; - ReduceDuplicates(ValueType const* src_in, ValueType* dst_in, size_t stride_in, - size_t start_in, size_t n_in, std::string const& name) - : Base(src_in, dst_in, stride_in, start_in, n_in, name) {} + ReduceDuplicates(ExecSpace const& exec_space, ValueType const* src_in, + ValueType* dst_in, size_t stride_in, size_t start_in, + size_t n_in, std::string const& name) + : Base(exec_space, src_in, dst_in, stride_in, start_in, n_in, name) {} KOKKOS_FORCEINLINE_FUNCTION void operator()(size_t i) const { for (size_t j = Base::start; j < Base::n; ++j) { ScatterValue struct ResetDuplicatesBase { using Derived = ResetDuplicates; ValueType* data; - ResetDuplicatesBase(ValueType* data_in, size_t size_in, - std::string const& name) + ResetDuplicatesBase(ExecSpace const& exec_space, ValueType* data_in, + size_t size_in, std::string const& name) : data(data_in) { parallel_for( std::string("Kokkos::ScatterView::ResetDuplicates [") + name + "]", - RangePolicy(0, size_in), + RangePolicy(exec_space, 0, size_in), static_cast(*this)); } }; @@ -703,8 +704,9 @@ struct ResetDuplicatesBase { template struct ResetDuplicates : public ResetDuplicatesBase { using Base = ResetDuplicatesBase; - ResetDuplicates(ValueType* data_in, size_t size_in, std::string const& name) - : Base(data_in, size_in, name) {} + ResetDuplicates(ExecSpace const& exec_space, ValueType* data_in, + size_t size_in, std::string const& name) + : Base(exec_space, data_in, size_in, name) {} KOKKOS_FORCEINLINE_FUNCTION void operator()(size_t i) const { ScatterValue @@ -713,6 +715,16 @@ struct ResetDuplicates : public ResetDuplicatesBase { } }; +template +void check_scatter_view_allocation_properties_argument( + ViewCtorProp const&) { + static_assert(ViewCtorProp::has_execution_space && + ViewCtorProp::has_label && + ViewCtorProp::initialize, + "Allocation property must have an execution name as well as a " + "label, and must perform the view initialization"); +} + } // namespace Experimental } // namespace Impl } // namespace Kokkos @@ -762,10 +774,26 @@ class ScatterView const& original_view) : internal_view(original_view) {} + template + ScatterView(execution_space const& /* exec_space */, + View const& original_view) + : internal_view(original_view) {} + template ScatterView(std::string const& name, Dims... dims) : internal_view(name, dims...) {} + // This overload allows specifying an execution space instance to be + // used by passing, e.g., Kokkos::view_alloc(exec_space, "label") as + // first argument. + template + ScatterView(::Kokkos::Impl::ViewCtorProp const& arg_prop, Dims... dims) + : internal_view(arg_prop, dims...) { + using ::Kokkos::Impl::Experimental:: + check_scatter_view_allocation_properties_argument; + check_scatter_view_allocation_properties_argument(arg_prop); + } + template KOKKOS_FUNCTION ScatterView( const ScatterView void contribute_into(View const& dest) const { + contribute_into(execution_space(), dest); + } + + template + void contribute_into(execution_space const& exec_space, + View const& dest) const { using dest_type = View; static_assert(std::is_same::value, "ScatterView contribute destination has different layout"); static_assert( - Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< - memory_space, typename dest_type::memory_space>::value, + Kokkos::Impl::SpaceAccessibility< + execution_space, typename dest_type::memory_space>::accessible, "ScatterView contribute destination memory space not accessible"); if (dest.data() == internal_view.data()) return; Kokkos::Impl::Experimental::ReduceDuplicates( - internal_view.data(), dest.data(), 0, 0, 1, internal_view.label()); + exec_space, internal_view.data(), dest.data(), 0, 0, 1, + internal_view.label()); } - void reset() { + void reset(execution_space const& exec_space = execution_space()) { Kokkos::Impl::Experimental::ResetDuplicates( - internal_view.data(), internal_view.size(), internal_view.label()); + exec_space, internal_view.data(), internal_view.size(), + internal_view.label()); } template void reset_except(View const& view) { - if (view.data() != internal_view.data()) reset(); + reset_except(execution_space(), view); + } + + template + void reset_except(const execution_space& exec_space, + View const& view) { + if (view.data() != internal_view.data()) reset(exec_space); } void resize(const size_t n0 = 0, const size_t n1 = 0, const size_t n2 = 0, @@ -928,10 +970,16 @@ class ScatterView ScatterView(View const& original_view) + : ScatterView(execution_space(), original_view) {} + + template + ScatterView(execution_space const& exec_space, + View const& original_view) : unique_token(), internal_view( view_alloc(WithoutInitializing, - std::string("duplicated_") + original_view.label()), + std::string("duplicated_") + original_view.label(), + exec_space), unique_token.size(), original_view.rank_dynamic > 0 ? original_view.extent(0) : KOKKOS_IMPL_CTOR_DEFAULT_ARG, @@ -949,14 +997,32 @@ class ScatterView ScatterView(std::string const& name, Dims... dims) - : internal_view(view_alloc(WithoutInitializing, name), + : ScatterView(view_alloc(execution_space(), name), dims...) {} + + // This overload allows specifying an execution space instance to be + // used by passing, e.g., Kokkos::view_alloc(exec_space, "label") as + // first argument. + template + ScatterView(::Kokkos::Impl::ViewCtorProp const& arg_prop, Dims... dims) + : internal_view(view_alloc(WithoutInitializing, + static_cast<::Kokkos::Impl::ViewCtorProp< + void, std::string> const&>(arg_prop) + .value), unique_token.size(), dims...) { - reset(); + using ::Kokkos::Impl::Experimental:: + check_scatter_view_allocation_properties_argument; + check_scatter_view_allocation_properties_argument(arg_prop); + + auto const exec_space = + static_cast<::Kokkos::Impl::ViewCtorProp const&>( + arg_prop) + .value; + reset(exec_space); } template @@ -984,37 +1050,51 @@ class ScatterView void contribute_into(View const& dest) const { + contribute_into(execution_space(), dest); + } + + template + void contribute_into(execution_space const& exec_space, + View const& dest) const { using dest_type = View; static_assert(std::is_same::value, "ScatterView deep_copy destination has different layout"); static_assert( - Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< - memory_space, typename dest_type::memory_space>::value, + Kokkos::Impl::SpaceAccessibility< + execution_space, typename dest_type::memory_space>::accessible, "ScatterView deep_copy destination memory space not accessible"); bool is_equal = (dest.data() == internal_view.data()); size_t start = is_equal ? 1 : 0; Kokkos::Impl::Experimental::ReduceDuplicates( - internal_view.data(), dest.data(), internal_view.stride(0), start, - internal_view.extent(0), internal_view.label()); + exec_space, internal_view.data(), dest.data(), internal_view.stride(0), + start, internal_view.extent(0), internal_view.label()); } - void reset() { + void reset(execution_space const& exec_space = execution_space()) { Kokkos::Impl::Experimental::ResetDuplicates( - internal_view.data(), internal_view.size(), internal_view.label()); + exec_space, internal_view.data(), internal_view.size(), + internal_view.label()); } + template void reset_except(View const& view) { + reset_except(execution_space(), view); + } + + template + void reset_except(execution_space const& exec_space, + View const& view) { if (view.data() != internal_view.data()) { - reset(); + reset(exec_space); return; } Kokkos::Impl::Experimental::ResetDuplicates( - internal_view.data() + view.size(), internal_view.size() - view.size(), - internal_view.label()); + exec_space, internal_view.data() + view.size(), + internal_view.size() - view.size(), internal_view.label()); } void resize(const size_t n0 = 0, const size_t n1 = 0, const size_t n2 = 0, @@ -1075,7 +1155,13 @@ class ScatterView - ScatterView(View const& original_view) : unique_token() { + ScatterView(View const& original_view) + : ScatterView(execution_space(), original_view) {} + + template + ScatterView(execution_space const& exec_space, + View const& original_view) + : unique_token() { size_t arg_N[8] = {original_view.rank > 0 ? original_view.extent(0) : KOKKOS_IMPL_CTOR_DEFAULT_ARG, original_view.rank > 1 ? original_view.extent(1) @@ -1094,14 +1180,27 @@ class ScatterView - ScatterView(std::string const& name, Dims... dims) { + ScatterView(std::string const& name, Dims... dims) + : ScatterView(view_alloc(execution_space(), name), dims...) {} + + // This overload allows specifying an execution space instance to be + // used by passing, e.g., Kokkos::view_alloc(exec_space, "label") as + // first argument. + template + ScatterView(::Kokkos::Impl::ViewCtorProp const& arg_prop, + Dims... dims) { + using ::Kokkos::Impl::Experimental:: + check_scatter_view_allocation_properties_argument; + check_scatter_view_allocation_properties_argument(arg_prop); + original_view_type original_view; size_t arg_N[8] = {original_view.rank > 0 ? original_view.static_extent(0) : KOKKOS_IMPL_CTOR_DEFAULT_ARG, @@ -1120,10 +1219,20 @@ class ScatterView const&>( + arg_prop) + .value; internal_view = internal_view_type(view_alloc(WithoutInitializing, name), arg_N[0], arg_N[1], arg_N[2], arg_N[3], arg_N[4], arg_N[5], arg_N[6], arg_N[7]); - reset(); + + auto const exec_space = + static_cast<::Kokkos::Impl::ViewCtorProp const&>( + arg_prop) + .value; + reset(exec_space); } template @@ -1166,6 +1275,12 @@ class ScatterView void contribute_into(View const& dest) const { + contribute_into(execution_space(), dest); + } + + template + void contribute_into(execution_space const& exec_space, + View const& dest) const { using dest_type = View; static_assert( std::is_same::value, "ScatterView deep_copy destination has different layout"); static_assert( - Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< - memory_space, typename dest_type::memory_space>::value, + Kokkos::Impl::SpaceAccessibility< + execution_space, typename dest_type::memory_space>::accessible, "ScatterView deep_copy destination memory space not accessible"); auto extent = internal_view.extent(internal_view_type::rank - 1); bool is_equal = (dest.data() == internal_view.data()); size_t start = is_equal ? 1 : 0; Kokkos::Impl::Experimental::ReduceDuplicates( - internal_view.data(), dest.data(), + exec_space, internal_view.data(), dest.data(), internal_view.stride(internal_view_type::rank - 1), start, extent, internal_view.label()); } - void reset() { + void reset(execution_space const& exec_space = execution_space()) { Kokkos::Impl::Experimental::ResetDuplicates( - internal_view.data(), internal_view.size(), internal_view.label()); + exec_space, internal_view.data(), internal_view.size(), + internal_view.label()); } + template void reset_except(View const& view) { + reset_except(execution_space(), view); + } + + template + void reset_except(execution_space const& exec_space, + View const& view) { if (view.data() != internal_view.data()) { - reset(); + reset(exec_space); return; } Kokkos::Impl::Experimental::ResetDuplicates( - internal_view.data() + view.size(), internal_view.size() - view.size(), - internal_view.label()); + exec_space, internal_view.data() + view.size(), + internal_view.size() - view.size(), internal_view.label()); } void resize(const size_t n0 = 0, const size_t n1 = 0, const size_t n2 = 0, @@ -1316,21 +1439,21 @@ template ::array_layout, typename ViewTraits::device_type, Op, - typename Kokkos::Impl::if_c< + std::conditional_t< std::is_same::value, typename Kokkos::Impl::Experimental::DefaultDuplication< typename ViewTraits::execution_space>::type, - Duplication>::type, - typename Kokkos::Impl::if_c< + Duplication>, + std::conditional_t< std::is_same::value, typename Kokkos::Impl::Experimental::DefaultContribution< typename ViewTraits::execution_space, - typename Kokkos::Impl::if_c< + typename std::conditional_t< std::is_same::value, typename Kokkos::Impl::Experimental::DefaultDuplication< typename ViewTraits::execution_space>::type, - Duplication>::type>::type, - Contribution>::type> + Duplication>>::type, + Contribution>> create_scatter_view(View const& original_view) { return original_view; // implicit ScatterView constructor call } @@ -1365,12 +1488,21 @@ create_scatter_view(Op, Duplication, Contribution, namespace Kokkos { namespace Experimental { +template +void contribute( + typename ES::execution_space const& exec_space, View& dest, + Kokkos::Experimental::ScatterView const& src) { + src.contribute_into(exec_space, dest); +} + template void contribute( View& dest, Kokkos::Experimental::ScatterView const& src) { - src.contribute_into(dest); + using execution_space = typename ES::execution_space; + contribute(execution_space{}, dest, src); } } // namespace Experimental diff --git a/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp b/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp index d2affda93a..edb0e7261d 100644 --- a/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp +++ b/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp @@ -264,26 +264,24 @@ class UnorderedMap { private: enum : size_type { invalid_index = ~static_cast(0) }; - using impl_value_type = - typename Impl::if_c::type; + using impl_value_type = std::conditional_t; - using key_type_view = typename Impl::if_c< + using key_type_view = std::conditional_t< is_insertable_map, View, - View > >::type; + View > >; - using value_type_view = - typename Impl::if_c, - View > >::type; + using value_type_view = std::conditional_t< + is_insertable_map || is_modifiable_map, + View, + View > >; - using size_type_view = typename Impl::if_c< + using size_type_view = std::conditional_t< is_insertable_map, View, - View > >::type; + View > >; using bitset_type = - typename Impl::if_c, - ConstBitset >::type; + std::conditional_t, + ConstBitset >; enum { modified_idx = 0, erasable_idx = 1, failed_insert_idx = 2 }; enum { num_scalars = 3 }; @@ -540,10 +538,7 @@ class UnorderedMap { // Previously claimed an unused entry that was not inserted. // Release this unused entry immediately. if (!m_available_indexes.reset(new_index)) { - // FIXME_SYCL SYCL doesn't allow printf in kernels -#ifndef KOKKOS_ENABLE_SYCL - printf("Unable to free existing\n"); -#endif + KOKKOS_IMPL_DO_NOT_USE_PRINTF("Unable to free existing\n"); } } @@ -659,8 +654,8 @@ class UnorderedMap { /// /// 'const value_type' via Cuda texture fetch must return by value. KOKKOS_FORCEINLINE_FUNCTION - typename Impl::if_c<(is_set || has_const_value), impl_value_type, - impl_value_type &>::type + std::conditional_t<(is_set || has_const_value), impl_value_type, + impl_value_type &> value_at(size_type i) const { return m_values[is_set ? 0 : (i < capacity() ? i : capacity())]; } diff --git a/lib/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp b/lib/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp index 6e450598d1..6047e60f3d 100644 --- a/lib/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp +++ b/lib/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp @@ -57,10 +57,22 @@ namespace Kokkos { namespace Impl { +KOKKOS_FORCEINLINE_FUNCTION +unsigned rotate_left(unsigned i, int r) { + constexpr int size = static_cast(sizeof(unsigned) * CHAR_BIT); + return r ? ((i << r) | (i >> (size - r))) : i; +} + KOKKOS_FORCEINLINE_FUNCTION unsigned rotate_right(unsigned i, int r) { - enum { size = static_cast(sizeof(unsigned) * CHAR_BIT) }; + constexpr int size = static_cast(sizeof(unsigned) * CHAR_BIT); + // FIXME_SYCL llvm.fshr.i32 missing + // (https://github.com/intel/llvm/issues/3308) +#ifdef __SYCL_DEVICE_ONLY__ + return rotate_left(i, size - r); +#else return r ? ((i >> r) | (i << (size - r))) : i; +#endif } template diff --git a/lib/kokkos/containers/src/impl/Kokkos_UnorderedMap_impl.hpp b/lib/kokkos/containers/src/impl/Kokkos_UnorderedMap_impl.hpp index b06ab0846c..d7c4a5d1ff 100644 --- a/lib/kokkos/containers/src/impl/Kokkos_UnorderedMap_impl.hpp +++ b/lib/kokkos/containers/src/impl/Kokkos_UnorderedMap_impl.hpp @@ -250,8 +250,8 @@ struct UnorderedMapPrint { uint32_t list = m_map.m_hash_lists(i); for (size_type curr = list, ii = 0; curr != invalid_index; curr = m_map.m_next_index[curr], ++ii) { - printf("%d[%d]: %d->%d\n", list, ii, m_map.key_at(curr), - m_map.value_at(curr)); + KOKKOS_IMPL_DO_NOT_USE_PRINTF("%d[%d]: %d->%d\n", list, ii, + m_map.key_at(curr), m_map.value_at(curr)); } } }; diff --git a/lib/kokkos/containers/unit_tests/CMakeLists.txt b/lib/kokkos/containers/unit_tests/CMakeLists.txt index c84c5f6d5e..947d222c27 100644 --- a/lib/kokkos/containers/unit_tests/CMakeLists.txt +++ b/lib/kokkos/containers/unit_tests/CMakeLists.txt @@ -2,6 +2,7 @@ KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) KOKKOS_INCLUDE_DIRECTORIES(REQUIRED_DURING_INSTALLATION_TESTING ${CMAKE_CURRENT_SOURCE_DIR}) KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/../src ) +KOKKOS_INCLUDE_DIRECTORIES(${KOKKOS_SOURCE_DIR}/core/unit_test/category_files) foreach(Tag Threads;Serial;OpenMP;HPX;Cuda;HIP;SYCL) # Because there is always an exception to the rule @@ -41,11 +42,6 @@ foreach(Tag Threads;Serial;OpenMP;HPX;Cuda;HIP;SYCL) configure_file(${dir}/dummy.cpp ${file}) list(APPEND UnitTestSources ${file}) endforeach() - list(REMOVE_ITEM UnitTestSources - ${CMAKE_CURRENT_BINARY_DIR}/sycl/TestSYCL_Bitset.cpp - ${CMAKE_CURRENT_BINARY_DIR}/sycl/TestSYCL_ScatterView.cpp - ${CMAKE_CURRENT_BINARY_DIR}/sycl/TestSYCL_UnorderedMap.cpp - ) KOKKOS_ADD_EXECUTABLE_AND_TEST(UnitTest_${Tag} SOURCES ${UnitTestSources}) endif() endforeach() diff --git a/lib/kokkos/containers/unit_tests/Makefile b/lib/kokkos/containers/unit_tests/Makefile index f42b9b7519..82669fe1ab 100644 --- a/lib/kokkos/containers/unit_tests/Makefile +++ b/lib/kokkos/containers/unit_tests/Makefile @@ -26,7 +26,7 @@ override LDFLAGS += -lpthread include $(KOKKOS_PATH)/Makefile.kokkos -KOKKOS_CXXFLAGS += -I$(GTEST_PATH) -I${KOKKOS_PATH}/containers/unit_tests +KOKKOS_CXXFLAGS += -I$(GTEST_PATH) -I${KOKKOS_PATH}/containers/unit_tests -I${KOKKOS_PATH}/core/unit_test/category_files TEST_TARGETS = TARGETS = diff --git a/lib/kokkos/containers/unit_tests/TestDualView.hpp b/lib/kokkos/containers/unit_tests/TestDualView.hpp index 531caf0f85..3eee85ed10 100644 --- a/lib/kokkos/containers/unit_tests/TestDualView.hpp +++ b/lib/kokkos/containers/unit_tests/TestDualView.hpp @@ -114,6 +114,8 @@ struct test_dualview_combinations { a.template modify(); a.template sync(); + a.template sync( + Kokkos::DefaultExecutionSpace{}); a.h_view(5, 1) = 3; a.h_view(6, 1) = 4; @@ -122,11 +124,15 @@ struct test_dualview_combinations { ViewType b = Kokkos::subview(a, std::pair(6, 9), std::pair(0, 1)); a.template sync(); + a.template sync( + Kokkos::DefaultExecutionSpace{}); b.template modify(); Kokkos::deep_copy(b.d_view, 2); a.template sync(); + a.template sync( + Kokkos::DefaultExecutionSpace{}); Scalar count = 0; for (unsigned int i = 0; i < a.d_view.extent(0); i++) for (unsigned int j = 0; j < a.d_view.extent(1); j++) @@ -180,6 +186,7 @@ struct test_dual_view_deep_copy { } else { a.modify_device(); a.sync_host(); + a.sync_host(Kokkos::DefaultExecutionSpace{}); } // Check device view is initialized as expected @@ -208,6 +215,7 @@ struct test_dual_view_deep_copy { b.template sync(); } else { b.sync_host(); + b.sync_host(Kokkos::DefaultExecutionSpace{}); } // Perform same checks on b as done on a @@ -302,6 +310,7 @@ struct test_dualview_resize { ASSERT_EQ(a.extent(1), m / factor); a.sync_device(); + a.sync_device(Kokkos::DefaultExecutionSpace{}); // Check device view is initialized as expected a_d_sum = 0; @@ -404,19 +413,14 @@ void test_dualview_resize() { Impl::test_dualview_resize(); } -// FIXME_SYCL requires MDRange policy -#ifndef KOKKOS_ENABLE_SYCL TEST(TEST_CATEGORY, dualview_combination) { test_dualview_combinations(10, true); } -#endif TEST(TEST_CATEGORY, dualview_alloc) { test_dualview_alloc(10); } -// FIXME_SYCL requires MDRange policy -#ifndef KOKKOS_ENABLE_SYCL TEST(TEST_CATEGORY, dualview_combinations_without_init) { test_dualview_combinations(10, false); } @@ -433,8 +437,133 @@ TEST(TEST_CATEGORY, dualview_realloc) { TEST(TEST_CATEGORY, dualview_resize) { test_dualview_resize(); } + +namespace { +/** + * + * The following tests are a response to + * https://github.com/kokkos/kokkos/issues/3850 + * and + * https://github.com/kokkos/kokkos/pull/3857 + * + * DualViews were returning incorrect view types and taking + * inappropriate actions based on the templated view methods. + * + * Specifically, template view methods were always returning + * a device view if the memory space was UVM and a Kokkos::Device was passed. + * Sync/modify methods completely broke down So these tests exist to make sure + * that we keep the semantics of UVM DualViews intact. + */ +// modify if we have other UVM enabled backends +#ifdef KOKKOS_ENABLE_CUDA // OR other UVM builds +#define UVM_ENABLED_BUILD #endif +#ifdef UVM_ENABLED_BUILD +template +struct UVMSpaceFor; +#endif + +#ifdef KOKKOS_ENABLE_CUDA // specific to CUDA +template <> +struct UVMSpaceFor { + using type = Kokkos::CudaUVMSpace; +}; +#endif + +#ifdef UVM_ENABLED_BUILD +template <> +struct UVMSpaceFor { + using type = typename UVMSpaceFor::type; +}; +#else +template +struct UVMSpaceFor { + using type = typename ExecSpace::memory_space; +}; +#endif + +using ExecSpace = Kokkos::DefaultExecutionSpace; +using MemSpace = typename UVMSpaceFor::type; +using DeviceType = Kokkos::Device; + +using DualViewType = Kokkos::DualView; +using d_device = DeviceType; +using h_device = Kokkos::Device< + Kokkos::DefaultHostExecutionSpace, + typename UVMSpaceFor::type>; + +TEST(TEST_CATEGORY, dualview_device_correct_kokkos_device) { + DualViewType dv("myView", 100); + dv.clear_sync_state(); + auto v_d = dv.template view(); + using vdt = decltype(v_d); + using vdt_d = vdt::device_type; + using vdt_d_e = vdt_d::execution_space; + ASSERT_STREQ(vdt_d_e::name(), Kokkos::DefaultExecutionSpace::name()); +} +TEST(TEST_CATEGORY, dualview_host_correct_kokkos_device) { + DualViewType dv("myView", 100); + dv.clear_sync_state(); + auto v_h = dv.template view(); + using vht = decltype(v_h); + using vht_d = vht::device_type; + using vht_d_e = vht_d::execution_space; + ASSERT_STREQ(vht_d_e::name(), Kokkos::DefaultHostExecutionSpace::name()); +} + +TEST(TEST_CATEGORY, dualview_host_modify_template_device_sync) { + DualViewType dv("myView", 100); + dv.clear_sync_state(); + dv.modify_host(); + dv.template sync(); + EXPECT_TRUE(!dv.need_sync_device()); + EXPECT_TRUE(!dv.need_sync_host()); + dv.clear_sync_state(); +} + +TEST(TEST_CATEGORY, dualview_host_modify_template_device_execspace_sync) { + DualViewType dv("myView", 100); + dv.clear_sync_state(); + dv.modify_host(); + dv.template sync(); + EXPECT_TRUE(!dv.need_sync_device()); + EXPECT_TRUE(!dv.need_sync_host()); + dv.clear_sync_state(); +} + +TEST(TEST_CATEGORY, dualview_device_modify_template_host_sync) { + DualViewType dv("myView", 100); + dv.clear_sync_state(); + dv.modify_device(); + dv.template sync(); + EXPECT_TRUE(!dv.need_sync_device()); + EXPECT_TRUE(!dv.need_sync_host()); + dv.clear_sync_state(); +} +TEST(TEST_CATEGORY, dualview_device_modify_template_host_execspace_sync) { + DualViewType dv("myView", 100); + dv.clear_sync_state(); + dv.modify_device(); + dv.template sync(); + EXPECT_TRUE(!dv.need_sync_device()); + EXPECT_TRUE(!dv.need_sync_host()); + dv.clear_sync_state(); +} + +TEST(TEST_CATEGORY, + dualview_template_views_return_correct_executionspace_views) { + DualViewType dv("myView", 100); + dv.clear_sync_state(); + using hvt = decltype(dv.view()); + using dvt = decltype(dv.view()); + ASSERT_STREQ(Kokkos::DefaultExecutionSpace::name(), + dvt::device_type::execution_space::name()); + ASSERT_STREQ(Kokkos::DefaultHostExecutionSpace::name(), + hvt::device_type::execution_space::name()); +} + +} // anonymous namespace } // namespace Test #endif // KOKKOS_TEST_DUALVIEW_HPP diff --git a/lib/kokkos/containers/unit_tests/TestDynamicView.hpp b/lib/kokkos/containers/unit_tests/TestDynamicView.hpp index 4b9f994417..f018793dd6 100644 --- a/lib/kokkos/containers/unit_tests/TestDynamicView.hpp +++ b/lib/kokkos/containers/unit_tests/TestDynamicView.hpp @@ -243,8 +243,6 @@ struct TestDynamicView { } }; -// FIXME_SYCL needs resize_serial -#ifndef KOKKOS_ENABLE_SYCL TEST(TEST_CATEGORY, dynamic_view) { using TestDynView = TestDynamicView; @@ -252,7 +250,6 @@ TEST(TEST_CATEGORY, dynamic_view) { TestDynView::run(100000 + 100 * i); } } -#endif } // namespace Test diff --git a/lib/kokkos/containers/unit_tests/TestHIP_Category.hpp b/lib/kokkos/containers/unit_tests/TestHIP_Category.hpp deleted file mode 100644 index c2d60d1814..0000000000 --- a/lib/kokkos/containers/unit_tests/TestHIP_Category.hpp +++ /dev/null @@ -1,51 +0,0 @@ -/* -//@HEADER -// ************************************************************************ -// -// Kokkos v. 3.0 -// Copyright (2020) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// 1. Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// 2. Redistributions in binary form must reproduce the above copyright -// notice, this list of conditions and the following disclaimer in the -// documentation and/or other materials provided with the distribution. -// -// 3. Neither the name of the Corporation nor the names of the -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY -// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE -// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// -// Questions? Contact Christian R. Trott (crtrott@sandia.gov) -// -// ************************************************************************ -//@HEADER -*/ - -#ifndef KOKKOS_TEST_HIP_HPP -#define KOKKOS_TEST_HIP_HPP - -#define TEST_CATEGORY hip -#define TEST_EXECSPACE Kokkos::Experimental::HIP - -#endif diff --git a/lib/kokkos/containers/unit_tests/TestHPX_Category.hpp b/lib/kokkos/containers/unit_tests/TestHPX_Category.hpp deleted file mode 100644 index 64fc7c0757..0000000000 --- a/lib/kokkos/containers/unit_tests/TestHPX_Category.hpp +++ /dev/null @@ -1,51 +0,0 @@ -/* -//@HEADER -// ************************************************************************ -// -// Kokkos v. 3.0 -// Copyright (2020) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// 1. Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// 2. Redistributions in binary form must reproduce the above copyright -// notice, this list of conditions and the following disclaimer in the -// documentation and/or other materials provided with the distribution. -// -// 3. Neither the name of the Corporation nor the names of the -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY -// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE -// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// -// Questions? Contact Christian R. Trott (crtrott@sandia.gov) -// -// ************************************************************************ -//@HEADER -*/ - -#ifndef KOKKOS_TEST_HPX_HPP -#define KOKKOS_TEST_HPX_HPP - -#define TEST_CATEGORY hpx -#define TEST_EXECSPACE Kokkos::Experimental::HPX - -#endif diff --git a/lib/kokkos/containers/unit_tests/TestOffsetView.hpp b/lib/kokkos/containers/unit_tests/TestOffsetView.hpp index 802813b13b..9ddc226e29 100644 --- a/lib/kokkos/containers/unit_tests/TestOffsetView.hpp +++ b/lib/kokkos/containers/unit_tests/TestOffsetView.hpp @@ -130,8 +130,6 @@ void test_offsetview_construction() { } } - // FIXME_SYCL requires MDRange policy -#ifndef KOKKOS_ENABLE_SYCL const int ovmin0 = ov.begin(0); const int ovend0 = ov.end(0); const int ovmin1 = ov.begin(1); @@ -178,7 +176,6 @@ void test_offsetview_construction() { } ASSERT_EQ(OVResult, answer) << "Bad data found in OffsetView"; -#endif #endif { @@ -215,8 +212,6 @@ void test_offsetview_construction() { point3_type{{extent0, extent1, extent2}}); #if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA) - // FIXME_SYCL requires MDRange policy -#ifdef KOKKOS_ENABLE_SYCL int view3DSum = 0; Kokkos::parallel_reduce( rangePolicy3DZero, @@ -239,7 +234,6 @@ void test_offsetview_construction() { ASSERT_EQ(view3DSum, offsetView3DSum) << "construction of OffsetView from View and begins array broken."; -#endif #endif } view_type viewFromOV = ov.view(); @@ -266,8 +260,6 @@ void test_offsetview_construction() { Kokkos::deep_copy(aView, ov); #if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA) - // FIXME_SYCL requires MDRange policy -#ifndef KOKKOS_ENABLE_SYCL int sum = 0; Kokkos::parallel_reduce( rangePolicy2D, @@ -277,7 +269,6 @@ void test_offsetview_construction() { sum); ASSERT_EQ(sum, 0) << "deep_copy(view, offsetView) broken."; -#endif #endif } @@ -288,8 +279,6 @@ void test_offsetview_construction() { Kokkos::deep_copy(ov, aView); #if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA) - // FIXME_SYCL requires MDRange policy -#ifndef KOKKOS_ENABLE_SYCL int sum = 0; Kokkos::parallel_reduce( rangePolicy2D, @@ -299,7 +288,6 @@ void test_offsetview_construction() { sum); ASSERT_EQ(sum, 0) << "deep_copy(offsetView, view) broken."; -#endif #endif } } @@ -471,8 +459,6 @@ void test_offsetview_subview() { ASSERT_EQ(offsetSubview.end(1), 9); #if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA) - // FIXME_SYCL requires MDRange policy -#ifndef KOKKOS_ENABLE_SYCL using range_type = Kokkos::MDRangePolicy, Kokkos::IndexType >; using point_type = typename range_type::point_type; @@ -498,7 +484,6 @@ void test_offsetview_subview() { sum); ASSERT_EQ(sum, 6 * (e0 - b0) * (e1 - b1)); -#endif #endif } @@ -701,12 +686,9 @@ void test_offsetview_offsets_rank3() { } #endif -// FIXME_SYCL needs MDRangePolicy -#ifndef KOKKOS_ENABLE_SYCL TEST(TEST_CATEGORY, offsetview_construction) { test_offsetview_construction(); } -#endif TEST(TEST_CATEGORY, offsetview_unmanaged_construction) { test_offsetview_unmanaged_construction(); diff --git a/lib/kokkos/containers/unit_tests/TestOpenMP_Category.hpp b/lib/kokkos/containers/unit_tests/TestOpenMP_Category.hpp deleted file mode 100644 index a0169d1702..0000000000 --- a/lib/kokkos/containers/unit_tests/TestOpenMP_Category.hpp +++ /dev/null @@ -1,51 +0,0 @@ -/* -//@HEADER -// ************************************************************************ -// -// Kokkos v. 3.0 -// Copyright (2020) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// 1. Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// 2. Redistributions in binary form must reproduce the above copyright -// notice, this list of conditions and the following disclaimer in the -// documentation and/or other materials provided with the distribution. -// -// 3. Neither the name of the Corporation nor the names of the -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY -// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE -// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// -// Questions? Contact Christian R. Trott (crtrott@sandia.gov) -// -// ************************************************************************ -//@HEADER -*/ - -#ifndef KOKKOS_TEST_OPENMP_HPP -#define KOKKOS_TEST_OPENMP_HPP - -#define TEST_CATEGORY openmp -#define TEST_EXECSPACE Kokkos::OpenMP - -#endif diff --git a/lib/kokkos/containers/unit_tests/TestSYCL_Category.hpp b/lib/kokkos/containers/unit_tests/TestSYCL_Category.hpp deleted file mode 100644 index 51fd3fc911..0000000000 --- a/lib/kokkos/containers/unit_tests/TestSYCL_Category.hpp +++ /dev/null @@ -1,51 +0,0 @@ -/* -//@HEADER -// ************************************************************************ -// -// Kokkos v. 3.0 -// Copyright (2020) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// 1. Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// 2. Redistributions in binary form must reproduce the above copyright -// notice, this list of conditions and the following disclaimer in the -// documentation and/or other materials provided with the distribution. -// -// 3. Neither the name of the Corporation nor the names of the -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY -// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE -// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// -// Questions? Contact Christian R. Trott (crtrott@sandia.gov) -// -// ************************************************************************ -//@HEADER -*/ - -#ifndef KOKKOS_TEST_SYCL_HPP -#define KOKKOS_TEST_SYCL_HPP - -#define TEST_CATEGORY sycl -#define TEST_EXECSPACE Kokkos::Experimental::SYCL - -#endif diff --git a/lib/kokkos/containers/unit_tests/TestScatterView.hpp b/lib/kokkos/containers/unit_tests/TestScatterView.hpp index 3a3cb607a6..fdbce2d492 100644 --- a/lib/kokkos/containers/unit_tests/TestScatterView.hpp +++ b/lib/kokkos/containers/unit_tests/TestScatterView.hpp @@ -437,6 +437,10 @@ struct test_scatter_view_config { Contribution, Op, NumberType>::orig_view_type; + void compile_constructor() { + auto sv = scatter_view_def(Kokkos::view_alloc(DeviceType{}, "label"), 10); + } + void run_test(int n) { // test allocation { diff --git a/lib/kokkos/containers/unit_tests/TestSerial_Category.hpp b/lib/kokkos/containers/unit_tests/TestSerial_Category.hpp deleted file mode 100644 index 2aa09a315a..0000000000 --- a/lib/kokkos/containers/unit_tests/TestSerial_Category.hpp +++ /dev/null @@ -1,51 +0,0 @@ -/* -//@HEADER -// ************************************************************************ -// -// Kokkos v. 3.0 -// Copyright (2020) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// 1. Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// 2. Redistributions in binary form must reproduce the above copyright -// notice, this list of conditions and the following disclaimer in the -// documentation and/or other materials provided with the distribution. -// -// 3. Neither the name of the Corporation nor the names of the -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY -// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE -// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// -// Questions? Contact Christian R. Trott (crtrott@sandia.gov) -// -// ************************************************************************ -//@HEADER -*/ - -#ifndef KOKKOS_TEST_SERIAL_HPP -#define KOKKOS_TEST_SERIAL_HPP - -#define TEST_CATEGORY serial -#define TEST_EXECSPACE Kokkos::Serial - -#endif diff --git a/lib/kokkos/containers/unit_tests/TestStaticCrsGraph.hpp b/lib/kokkos/containers/unit_tests/TestStaticCrsGraph.hpp index 8bb267ce5d..a9a178f95e 100644 --- a/lib/kokkos/containers/unit_tests/TestStaticCrsGraph.hpp +++ b/lib/kokkos/containers/unit_tests/TestStaticCrsGraph.hpp @@ -285,10 +285,7 @@ void run_test_graph4() { TEST(TEST_CATEGORY, staticcrsgraph) { TestStaticCrsGraph::run_test_graph(); - // FIXME_SYCL requires MDRangePolicy -#ifndef KOKKOS_ENABLE_SYCL TestStaticCrsGraph::run_test_graph2(); -#endif TestStaticCrsGraph::run_test_graph3(1, 0); TestStaticCrsGraph::run_test_graph3(1, 1000); TestStaticCrsGraph::run_test_graph3(1, 10000); diff --git a/lib/kokkos/containers/unit_tests/TestThreads_Category.hpp b/lib/kokkos/containers/unit_tests/TestThreads_Category.hpp deleted file mode 100644 index 74a2b0da36..0000000000 --- a/lib/kokkos/containers/unit_tests/TestThreads_Category.hpp +++ /dev/null @@ -1,51 +0,0 @@ -/* -//@HEADER -// ************************************************************************ -// -// Kokkos v. 3.0 -// Copyright (2020) National Technology & Engineering -// Solutions of Sandia, LLC (NTESS). -// -// Under the terms of Contract DE-NA0003525 with NTESS, -// the U.S. Government retains certain rights in this software. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// 1. Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// -// 2. Redistributions in binary form must reproduce the above copyright -// notice, this list of conditions and the following disclaimer in the -// documentation and/or other materials provided with the distribution. -// -// 3. Neither the name of the Corporation nor the names of the -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY -// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE -// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// -// Questions? Contact Christian R. Trott (crtrott@sandia.gov) -// -// ************************************************************************ -//@HEADER -*/ - -#ifndef KOKKOS_TEST_THREADS_HPP -#define KOKKOS_TEST_THREADS_HPP - -#define TEST_CATEGORY threads -#define TEST_EXECSPACE Kokkos::Threads - -#endif diff --git a/lib/kokkos/containers/unit_tests/TestUnorderedMap.hpp b/lib/kokkos/containers/unit_tests/TestUnorderedMap.hpp index d39e0061c7..4413cfbc80 100644 --- a/lib/kokkos/containers/unit_tests/TestUnorderedMap.hpp +++ b/lib/kokkos/containers/unit_tests/TestUnorderedMap.hpp @@ -163,7 +163,8 @@ struct TestFind { KOKKOS_INLINE_FUNCTION void operator()(typename execution_space::size_type i, value_type &errors) const { - const bool expect_to_find_i = (i < m_max_key); + const bool expect_to_find_i = + (i < typename execution_space::size_type(m_max_key)); const bool exists = m_map.exists(i); @@ -293,10 +294,11 @@ void test_deep_copy(uint32_t num_nodes) { } } -// FIXME_HIP wrong result in CI but works locally -#ifndef KOKKOS_ENABLE_HIP +// FIXME_SYCL wrong results on Nvidia GPUs but correct on Host and Intel GPUs +// FIXME_HIP // WORKAROUND MSVC -#ifndef _WIN32 +#if !(defined(KOKKOS_ENABLE_HIP) && (HIP_VERSION < 401)) && \ + !defined(_WIN32) && !defined(KOKKOS_ENABLE_SYCL) TEST(TEST_CATEGORY, UnorderedMap_insert) { for (int i = 0; i < 500; ++i) { test_insert(100000, 90000, 100, true); @@ -304,7 +306,6 @@ TEST(TEST_CATEGORY, UnorderedMap_insert) { } } #endif -#endif TEST(TEST_CATEGORY, UnorderedMap_failed_insert) { for (int i = 0; i < 1000; ++i) test_failed_insert(10000); diff --git a/lib/kokkos/core/perf_test/CMakeLists.txt b/lib/kokkos/core/perf_test/CMakeLists.txt index b7b817c910..9ff4b6006d 100644 --- a/lib/kokkos/core/perf_test/CMakeLists.txt +++ b/lib/kokkos/core/perf_test/CMakeLists.txt @@ -9,6 +9,14 @@ # that in TriBITS KokkosAlgorithms can be disabled... #INCLUDE_DIRECTORIES("${CMAKE_CURRENT_SOURCE_DIR}/../../algorithms/src") +# FIXME_OPENMPTARGET - the NVIDIA HPC compiler nvc++ in the OpenMPTarget backend does not pass the perf_tests. +IF (KOKKOS_ENABLE_OPENMPTARGET + AND (KOKKOS_CXX_COMPILER_ID STREQUAL PGI + OR KOKKOS_CXX_COMPILER_ID STREQUAL NVHPC)) + RETURN() +ENDIF() + + SET(SOURCES PerfTestMain.cpp PerfTestGramSchmidt.cpp @@ -68,8 +76,7 @@ KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) KOKKOS_INCLUDE_DIRECTORIES(REQUIRED_DURING_INSTALLATION_TESTING ${CMAKE_CURRENT_SOURCE_DIR}) # This test currently times out for MSVC -# FIXME_SYCL these tests don't compile yet (require parallel_for). -IF(NOT KOKKOS_CXX_COMPILER_ID STREQUAL "MSVC" AND NOT Kokkos_ENABLE_SYCL) +IF(NOT KOKKOS_CXX_COMPILER_ID STREQUAL "MSVC") KOKKOS_ADD_EXECUTABLE_AND_TEST( PerfTestExec SOURCES ${SOURCES} @@ -77,13 +84,11 @@ IF(NOT KOKKOS_CXX_COMPILER_ID STREQUAL "MSVC" AND NOT Kokkos_ENABLE_SYCL) ) ENDIF() -# FIXME_SYCL -IF(NOT Kokkos_ENABLE_SYCL) - KOKKOS_ADD_EXECUTABLE_AND_TEST( - PerformanceTest_Atomic - SOURCES test_atomic.cpp - CATEGORIES PERFORMANCE - ) +KOKKOS_ADD_EXECUTABLE_AND_TEST( + PerformanceTest_Atomic + SOURCES test_atomic.cpp + CATEGORIES PERFORMANCE +) IF(NOT KOKKOS_ENABLE_CUDA OR KOKKOS_ENABLE_CUDA_LAMBDA) KOKKOS_ADD_EXECUTABLE_AND_TEST( @@ -98,7 +103,6 @@ KOKKOS_ADD_EXECUTABLE_AND_TEST( SOURCES test_mempool.cpp CATEGORIES PERFORMANCE ) -ENDIF() IF(NOT Kokkos_ENABLE_OPENMPTARGET) # FIXME OPENMPTARGET needs tasking diff --git a/lib/kokkos/core/perf_test/PerfTestGramSchmidt.cpp b/lib/kokkos/core/perf_test/PerfTestGramSchmidt.cpp index 70186283c1..dee21fd7a5 100644 --- a/lib/kokkos/core/perf_test/PerfTestGramSchmidt.cpp +++ b/lib/kokkos/core/perf_test/PerfTestGramSchmidt.cpp @@ -69,7 +69,7 @@ struct InvNorm2 : public Kokkos::DotSingle { KOKKOS_INLINE_FUNCTION void final(value_type& result) const { - result = std::sqrt(result); + result = Kokkos::Experimental::sqrt(result); Rjj() = result; inv() = (0 < result) ? 1.0 / result : 0; } @@ -145,7 +145,7 @@ struct ModifiedGramSchmidt { // Q(:,j) *= ( 1 / R(j,j) ); => Q(:,j) *= tmp ; Kokkos::scale(tmp, Qj); - for (size_t k = j + 1; k < count; ++k) { + for (size_type k = j + 1; k < count; ++k) { const vector_type Qk = Kokkos::subview(Q_, Kokkos::ALL(), k); const value_view Rjk = Kokkos::subview(R_, j, k); @@ -165,7 +165,7 @@ struct ModifiedGramSchmidt { //-------------------------------------------------------------------------- - static double test(const size_t length, const size_t count, + static double test(const size_type length, const size_type count, const size_t iter = 1) { multivector_type Q_("Q", length, count); multivector_type R_("R", count, count); diff --git a/lib/kokkos/core/src/CMakeLists.txt b/lib/kokkos/core/src/CMakeLists.txt index e0590a78a4..2ab0989805 100644 --- a/lib/kokkos/core/src/CMakeLists.txt +++ b/lib/kokkos/core/src/CMakeLists.txt @@ -72,8 +72,6 @@ KOKKOS_ADD_LIBRARY( ADD_BUILD_OPTIONS # core should be given all the necessary compiler/linker flags ) -SET_TARGET_PROPERTIES(kokkoscore PROPERTIES VERSION ${Kokkos_VERSION}) - KOKKOS_LIB_INCLUDE_DIRECTORIES(kokkoscore ${KOKKOS_TOP_BUILD_DIR} ${CMAKE_CURRENT_BINARY_DIR} @@ -87,3 +85,4 @@ KOKKOS_LINK_TPL(kokkoscore PUBLIC HPX) KOKKOS_LINK_TPL(kokkoscore PUBLIC LIBDL) KOKKOS_LINK_TPL(kokkoscore PUBLIC LIBRT) KOKKOS_LINK_TPL(kokkoscore PUBLIC PTHREAD) +KOKKOS_LINK_TPL(kokkoscore PUBLIC ROCM) diff --git a/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp b/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp index 4a30c914f0..916f109758 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp @@ -45,6 +45,10 @@ #include #ifdef KOKKOS_ENABLE_CUDA +#include +#include +#include + #include #include #include @@ -52,10 +56,6 @@ #include #include -#include -#include -#include - //#include #include #include @@ -65,6 +65,22 @@ /*--------------------------------------------------------------------------*/ /*--------------------------------------------------------------------------*/ +cudaStream_t Kokkos::Impl::cuda_get_deep_copy_stream() { + static cudaStream_t s = nullptr; + if (s == nullptr) { + cudaStreamCreate(&s); + } + return s; +} + +const std::unique_ptr &Kokkos::Impl::cuda_get_deep_copy_space( + bool initialize) { + static std::unique_ptr space = nullptr; + if (!space && initialize) + space = std::make_unique(Kokkos::Impl::cuda_get_deep_copy_stream()); + return space; +} + namespace Kokkos { namespace Impl { @@ -72,13 +88,6 @@ namespace { static std::atomic num_uvm_allocations(0); -cudaStream_t get_deep_copy_stream() { - static cudaStream_t s = nullptr; - if (s == nullptr) { - cudaStreamCreate(&s); - } - return s; -} } // namespace DeepCopy::DeepCopy(void *dst, const void *src, @@ -115,7 +124,7 @@ DeepCopy::DeepCopy(const Cuda &instance, void *dst, } void DeepCopyAsyncCuda(void *dst, const void *src, size_t n) { - cudaStream_t s = get_deep_copy_stream(); + cudaStream_t s = cuda_get_deep_copy_stream(); CUDA_SAFE_CALL(cudaMemcpyAsync(dst, src, n, cudaMemcpyDefault, s)); cudaStreamSynchronize(s); } @@ -128,14 +137,14 @@ void DeepCopyAsyncCuda(void *dst, const void *src, size_t n) { namespace Kokkos { -void CudaSpace::access_error() { +KOKKOS_DEPRECATED void CudaSpace::access_error() { const std::string msg( "Kokkos::CudaSpace::access_error attempt to execute Cuda function from " "non-Cuda space"); Kokkos::Impl::throw_runtime_exception(msg); } -void CudaSpace::access_error(const void *const) { +KOKKOS_DEPRECATED void CudaSpace::access_error(const void *const) { const std::string msg( "Kokkos::CudaSpace::access_error attempt to execute Cuda function from " "non-Cuda space"); @@ -459,79 +468,6 @@ SharedAllocationRecord::attach_texture_object( return tex_obj; } -//============================================================================== -// {{{1 - -std::string SharedAllocationRecord::get_label() const { - SharedAllocationHeader header; - - Kokkos::Impl::DeepCopy( - &header, RecordBase::head(), sizeof(SharedAllocationHeader)); - - return std::string(header.m_label); -} - -std::string SharedAllocationRecord::get_label() - const { - return std::string(RecordBase::head()->m_label); -} - -std::string -SharedAllocationRecord::get_label() const { - return std::string(RecordBase::head()->m_label); -} - -// end SharedAllocationRecord::get_label() }}}1 -//============================================================================== - -//============================================================================== -// {{{1 - -SharedAllocationRecord - *SharedAllocationRecord::allocate( - const Kokkos::CudaSpace &arg_space, const std::string &arg_label, - const size_t arg_alloc_size) { - return new SharedAllocationRecord(arg_space, arg_label, arg_alloc_size); -} - -SharedAllocationRecord - *SharedAllocationRecord::allocate( - const Kokkos::CudaUVMSpace &arg_space, const std::string &arg_label, - const size_t arg_alloc_size) { - return new SharedAllocationRecord(arg_space, arg_label, arg_alloc_size); -} - -SharedAllocationRecord - *SharedAllocationRecord::allocate( - const Kokkos::CudaHostPinnedSpace &arg_space, - const std::string &arg_label, const size_t arg_alloc_size) { - return new SharedAllocationRecord(arg_space, arg_label, arg_alloc_size); -} - -// end SharedAllocationRecord allocate() }}}1 -//============================================================================== - -//============================================================================== -// {{{1 - -void SharedAllocationRecord::deallocate( - SharedAllocationRecord *arg_rec) { - delete static_cast(arg_rec); -} - -void SharedAllocationRecord::deallocate( - SharedAllocationRecord *arg_rec) { - delete static_cast(arg_rec); -} - -void SharedAllocationRecord::deallocate( - SharedAllocationRecord *arg_rec) { - delete static_cast(arg_rec); -} - -// end SharedAllocationRecord deallocate }}}1 -//============================================================================== - //============================================================================== // {{{1 @@ -580,7 +516,7 @@ SharedAllocationRecord::SharedAllocationRecord( const SharedAllocationRecord::function_type arg_dealloc) // Pass through allocated [ SharedAllocationHeader , user_memory ] // Pass through deallocation function - : SharedAllocationRecord( + : base_t( #ifdef KOKKOS_ENABLE_DEBUG &SharedAllocationRecord::s_root_record, #endif @@ -592,13 +528,7 @@ SharedAllocationRecord::SharedAllocationRecord( SharedAllocationHeader header; - // Fill in the Header information - header.m_record = static_cast *>(this); - - strncpy(header.m_label, arg_label.c_str(), - SharedAllocationHeader::maximum_label_length); - // Set last element zero, in case c_str is too long - header.m_label[SharedAllocationHeader::maximum_label_length - 1] = (char)0; + this->base_t::_fill_host_accessible_header_info(header, arg_label); // Copy to device memory Kokkos::Impl::DeepCopy(RecordBase::m_alloc_ptr, &header, @@ -611,7 +541,7 @@ SharedAllocationRecord::SharedAllocationRecord( const SharedAllocationRecord::function_type arg_dealloc) // Pass through allocated [ SharedAllocationHeader , user_memory ] // Pass through deallocation function - : SharedAllocationRecord( + : base_t( #ifdef KOKKOS_ENABLE_DEBUG &SharedAllocationRecord::s_root_record, #endif @@ -620,16 +550,8 @@ SharedAllocationRecord::SharedAllocationRecord( sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc), m_tex_obj(0), m_space(arg_space) { - // Fill in the Header information, directly accessible via UVM - - RecordBase::m_alloc_ptr->m_record = this; - - strncpy(RecordBase::m_alloc_ptr->m_label, arg_label.c_str(), - SharedAllocationHeader::maximum_label_length); - - // Set last element zero, in case c_str is too long - RecordBase::m_alloc_ptr - ->m_label[SharedAllocationHeader::maximum_label_length - 1] = (char)0; + this->base_t::_fill_host_accessible_header_info(*base_t::m_alloc_ptr, + arg_label); } SharedAllocationRecord:: @@ -639,7 +561,7 @@ SharedAllocationRecord:: const SharedAllocationRecord::function_type arg_dealloc) // Pass through allocated [ SharedAllocationHeader , user_memory ] // Pass through deallocation function - : SharedAllocationRecord( + : base_t( #ifdef KOKKOS_ENABLE_DEBUG &SharedAllocationRecord::s_root_record, @@ -648,319 +570,13 @@ SharedAllocationRecord:: arg_alloc_size), sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc), m_space(arg_space) { - // Fill in the Header information, directly accessible on the host - - RecordBase::m_alloc_ptr->m_record = this; - - strncpy(RecordBase::m_alloc_ptr->m_label, arg_label.c_str(), - SharedAllocationHeader::maximum_label_length); - // Set last element zero, in case c_str is too long - RecordBase::m_alloc_ptr - ->m_label[SharedAllocationHeader::maximum_label_length - 1] = (char)0; + this->base_t::_fill_host_accessible_header_info(*base_t::m_alloc_ptr, + arg_label); } // end SharedAllocationRecord constructors }}}1 //============================================================================== -//============================================================================== -// {{{1 - -void *SharedAllocationRecord::allocate_tracked( - const Kokkos::CudaSpace &arg_space, const std::string &arg_alloc_label, - const size_t arg_alloc_size) { - if (!arg_alloc_size) return nullptr; - - SharedAllocationRecord *const r = - allocate(arg_space, arg_alloc_label, arg_alloc_size); - - RecordBase::increment(r); - - return r->data(); -} - -void SharedAllocationRecord::deallocate_tracked( - void *const arg_alloc_ptr) { - if (arg_alloc_ptr != nullptr) { - SharedAllocationRecord *const r = get_record(arg_alloc_ptr); - - RecordBase::decrement(r); - } -} - -void *SharedAllocationRecord::reallocate_tracked( - void *const arg_alloc_ptr, const size_t arg_alloc_size) { - SharedAllocationRecord *const r_old = get_record(arg_alloc_ptr); - SharedAllocationRecord *const r_new = - allocate(r_old->m_space, r_old->get_label(), arg_alloc_size); - - Kokkos::Impl::DeepCopy( - r_new->data(), r_old->data(), std::min(r_old->size(), r_new->size())); - - RecordBase::increment(r_new); - RecordBase::decrement(r_old); - - return r_new->data(); -} - -void *SharedAllocationRecord::allocate_tracked( - const Kokkos::CudaUVMSpace &arg_space, const std::string &arg_alloc_label, - const size_t arg_alloc_size) { - if (!arg_alloc_size) return nullptr; - - SharedAllocationRecord *const r = - allocate(arg_space, arg_alloc_label, arg_alloc_size); - - RecordBase::increment(r); - - return r->data(); -} - -void SharedAllocationRecord::deallocate_tracked( - void *const arg_alloc_ptr) { - if (arg_alloc_ptr != nullptr) { - SharedAllocationRecord *const r = get_record(arg_alloc_ptr); - - RecordBase::decrement(r); - } -} - -void *SharedAllocationRecord::reallocate_tracked( - void *const arg_alloc_ptr, const size_t arg_alloc_size) { - SharedAllocationRecord *const r_old = get_record(arg_alloc_ptr); - SharedAllocationRecord *const r_new = - allocate(r_old->m_space, r_old->get_label(), arg_alloc_size); - - Kokkos::Impl::DeepCopy( - r_new->data(), r_old->data(), std::min(r_old->size(), r_new->size())); - - RecordBase::increment(r_new); - RecordBase::decrement(r_old); - - return r_new->data(); -} - -void * -SharedAllocationRecord::allocate_tracked( - const Kokkos::CudaHostPinnedSpace &arg_space, - const std::string &arg_alloc_label, const size_t arg_alloc_size) { - if (!arg_alloc_size) return nullptr; - - SharedAllocationRecord *const r = - allocate(arg_space, arg_alloc_label, arg_alloc_size); - - RecordBase::increment(r); - - return r->data(); -} - -void SharedAllocationRecord::deallocate_tracked(void *const - arg_alloc_ptr) { - if (arg_alloc_ptr != nullptr) { - SharedAllocationRecord *const r = get_record(arg_alloc_ptr); - - RecordBase::decrement(r); - } -} - -void * -SharedAllocationRecord::reallocate_tracked( - void *const arg_alloc_ptr, const size_t arg_alloc_size) { - SharedAllocationRecord *const r_old = get_record(arg_alloc_ptr); - SharedAllocationRecord *const r_new = - allocate(r_old->m_space, r_old->get_label(), arg_alloc_size); - - Kokkos::Impl::DeepCopy( - r_new->data(), r_old->data(), std::min(r_old->size(), r_new->size())); - - RecordBase::increment(r_new); - RecordBase::decrement(r_old); - - return r_new->data(); -} - -// end SharedAllocationRecored::(re|de|)allocate_tracked }}}1 -//============================================================================== - -//============================================================================== -// {{{1 - -SharedAllocationRecord * -SharedAllocationRecord::get_record(void *alloc_ptr) { - using RecordCuda = SharedAllocationRecord; - - using Header = SharedAllocationHeader; - - // Copy the header from the allocation - Header head; - - Header const *const head_cuda = - alloc_ptr ? Header::get_header(alloc_ptr) : nullptr; - - if (alloc_ptr) { - Kokkos::Impl::DeepCopy( - &head, head_cuda, sizeof(SharedAllocationHeader)); - } - - RecordCuda *const record = - alloc_ptr ? static_cast(head.m_record) : nullptr; - - if (!alloc_ptr || record->m_alloc_ptr != head_cuda) { - Kokkos::Impl::throw_runtime_exception( - std::string("Kokkos::Impl::SharedAllocationRecord< Kokkos::CudaSpace , " - "void >::get_record ERROR")); - } - - return record; -} - -SharedAllocationRecord *SharedAllocationRecord< - Kokkos::CudaUVMSpace, void>::get_record(void *alloc_ptr) { - using Header = SharedAllocationHeader; - using RecordCuda = SharedAllocationRecord; - - Header *const h = - alloc_ptr ? reinterpret_cast
(alloc_ptr) - 1 : nullptr; - - if (!alloc_ptr || h->m_record->m_alloc_ptr != h) { - Kokkos::Impl::throw_runtime_exception( - std::string("Kokkos::Impl::SharedAllocationRecord< " - "Kokkos::CudaUVMSpace , void >::get_record ERROR")); - } - - return static_cast(h->m_record); -} - -SharedAllocationRecord - *SharedAllocationRecord::get_record( - void *alloc_ptr) { - using Header = SharedAllocationHeader; - using RecordCuda = SharedAllocationRecord; - - Header *const h = - alloc_ptr ? reinterpret_cast
(alloc_ptr) - 1 : nullptr; - - if (!alloc_ptr || h->m_record->m_alloc_ptr != h) { - Kokkos::Impl::throw_runtime_exception( - std::string("Kokkos::Impl::SharedAllocationRecord< " - "Kokkos::CudaHostPinnedSpace , void >::get_record ERROR")); - } - - return static_cast(h->m_record); -} - -// end SharedAllocationRecord::get_record() }}}1 -//============================================================================== - -//============================================================================== -// {{{1 - -// Iterate records to print orphaned memory ... -void SharedAllocationRecord::print_records( - std::ostream &s, const Kokkos::CudaSpace &, bool detail) { - (void)s; - (void)detail; -#ifdef KOKKOS_ENABLE_DEBUG - SharedAllocationRecord *r = &s_root_record; - - char buffer[256]; - - SharedAllocationHeader head; - - if (detail) { - do { - if (r->m_alloc_ptr) { - Kokkos::Impl::DeepCopy( - &head, r->m_alloc_ptr, sizeof(SharedAllocationHeader)); - } else { - head.m_label[0] = 0; - } - - // Formatting dependent on sizeof(uintptr_t) - const char *format_string; - - if (sizeof(uintptr_t) == sizeof(unsigned long)) { - format_string = - "Cuda addr( 0x%.12lx ) list( 0x%.12lx 0x%.12lx ) extent[ 0x%.12lx " - "+ %.8ld ] count(%d) dealloc(0x%.12lx) %s\n"; - } else if (sizeof(uintptr_t) == sizeof(unsigned long long)) { - format_string = - "Cuda addr( 0x%.12llx ) list( 0x%.12llx 0x%.12llx ) extent[ " - "0x%.12llx + %.8ld ] count(%d) dealloc(0x%.12llx) %s\n"; - } - - snprintf(buffer, 256, format_string, reinterpret_cast(r), - reinterpret_cast(r->m_prev), - reinterpret_cast(r->m_next), - reinterpret_cast(r->m_alloc_ptr), r->m_alloc_size, - r->m_count, reinterpret_cast(r->m_dealloc), - head.m_label); - s << buffer; - r = r->m_next; - } while (r != &s_root_record); - } else { - do { - if (r->m_alloc_ptr) { - Kokkos::Impl::DeepCopy( - &head, r->m_alloc_ptr, sizeof(SharedAllocationHeader)); - - // Formatting dependent on sizeof(uintptr_t) - const char *format_string; - - if (sizeof(uintptr_t) == sizeof(unsigned long)) { - format_string = "Cuda [ 0x%.12lx + %ld ] %s\n"; - } else if (sizeof(uintptr_t) == sizeof(unsigned long long)) { - format_string = "Cuda [ 0x%.12llx + %ld ] %s\n"; - } - - snprintf(buffer, 256, format_string, - reinterpret_cast(r->data()), r->size(), - head.m_label); - } else { - snprintf(buffer, 256, "Cuda [ 0 + 0 ]\n"); - } - s << buffer; - r = r->m_next; - } while (r != &s_root_record); - } -#else - Kokkos::Impl::throw_runtime_exception( - "SharedAllocationHeader::print_records only works with " - "KOKKOS_ENABLE_DEBUG enabled"); -#endif -} - -void SharedAllocationRecord::print_records( - std::ostream &s, const Kokkos::CudaUVMSpace &, bool detail) { - (void)s; - (void)detail; -#ifdef KOKKOS_ENABLE_DEBUG - SharedAllocationRecord::print_host_accessible_records( - s, "CudaUVM", &s_root_record, detail); -#else - Kokkos::Impl::throw_runtime_exception( - "SharedAllocationHeader::print_records only works with " - "KOKKOS_ENABLE_DEBUG enabled"); -#endif -} - -void SharedAllocationRecord::print_records( - std::ostream &s, const Kokkos::CudaHostPinnedSpace &, bool detail) { - (void)s; - (void)detail; -#ifdef KOKKOS_ENABLE_DEBUG - SharedAllocationRecord::print_host_accessible_records( - s, "CudaHostPinned", &s_root_record, detail); -#else - Kokkos::Impl::throw_runtime_exception( - "SharedAllocationHeader::print_records only works with " - "KOKKOS_ENABLE_DEBUG enabled"); -#endif -} - -// end SharedAllocationRecord::print_records() }}}1 -//============================================================================== - void cuda_prefetch_pointer(const Cuda &space, const void *ptr, size_t bytes, bool to_device) { if ((ptr == nullptr) || (bytes == 0)) return; @@ -984,6 +600,29 @@ void cuda_prefetch_pointer(const Cuda &space, const void *ptr, size_t bytes, } // namespace Impl } // namespace Kokkos + +//============================================================================== +// {{{1 + +#include + +namespace Kokkos { +namespace Impl { + +// To avoid additional compilation cost for something that's (mostly?) not +// performance sensitive, we explicity instantiate these CRTP base classes here, +// where we have access to the associated *_timpl.hpp header files. +template class SharedAllocationRecordCommon; +template class HostInaccessibleSharedAllocationRecordCommon; +template class SharedAllocationRecordCommon; +template class SharedAllocationRecordCommon; + +} // end namespace Impl +} // end namespace Kokkos + +// end Explicit instantiations of CRTP Base classes }}}1 +//============================================================================== + #else void KOKKOS_CORE_SRC_CUDA_CUDASPACE_PREVENT_LINK_ERROR() {} #endif // KOKKOS_ENABLE_CUDA diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_BlockSize_Deduction.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_BlockSize_Deduction.hpp index 0d6d3bdb3a..0f4259072d 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_BlockSize_Deduction.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_BlockSize_Deduction.hpp @@ -140,7 +140,7 @@ inline int cuda_deduce_block_size(bool early_termination, } } - if (early_termination && blocks_per_sm != 0) break; + if (early_termination && opt_block_size != 0) break; } return opt_block_size; @@ -222,7 +222,8 @@ inline size_t get_shmem_per_sm_prefer_l1(cudaDeviceProp const& properties) { case 52: case 61: return 96; case 70: - case 80: return 8; + case 80: + case 86: return 8; case 75: return 32; default: Kokkos::Impl::throw_runtime_exception( diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Half.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Half.hpp index a9a62380e5..ec9c434fe6 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Half.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Half.hpp @@ -175,30 +175,42 @@ class half_t { return cast_from_half(*this); } + /** + * Conversion constructors. + * + * Support implicit conversions from impl_type, float, double -> half_t + * Mixed precision expressions require upcasting which is done in the + * "// Binary Arithmetic" operator overloads below. + * + * Support implicit conversions from integral types -> half_t. + * Expressions involving half_t with integral types require downcasting + * the integral types to half_t. Existing operator overloads can handle this + * with the addition of the below implicit conversion constructors. + */ KOKKOS_FUNCTION half_t(impl_type rhs) : val(rhs) {} KOKKOS_FUNCTION - explicit half_t(float rhs) : val(cast_to_half(rhs).val) {} + half_t(float rhs) : val(cast_to_half(rhs).val) {} + KOKKOS_FUNCTION + half_t(double rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION explicit half_t(bool rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(double rhs) : val(cast_to_half(rhs).val) {} + half_t(short rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(short rhs) : val(cast_to_half(rhs).val) {} + half_t(int rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(int rhs) : val(cast_to_half(rhs).val) {} + half_t(long rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(long rhs) : val(cast_to_half(rhs).val) {} + half_t(long long rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(long long rhs) : val(cast_to_half(rhs).val) {} + half_t(unsigned short rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(unsigned short rhs) : val(cast_to_half(rhs).val) {} + half_t(unsigned int rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(unsigned int rhs) : val(cast_to_half(rhs).val) {} + half_t(unsigned long rhs) : val(cast_to_half(rhs).val) {} KOKKOS_FUNCTION - explicit half_t(unsigned long rhs) : val(cast_to_half(rhs).val) {} - KOKKOS_FUNCTION - explicit half_t(unsigned long long rhs) : val(cast_to_half(rhs).val) {} + half_t(unsigned long long rhs) : val(cast_to_half(rhs).val) {} // Unary operators KOKKOS_FUNCTION @@ -243,7 +255,7 @@ class half_t { #else float tmp = __half2float(val); --tmp; - val = __float2half(tmp); + val = __float2half(tmp); #endif return *this; } @@ -276,88 +288,317 @@ class half_t { return *this; } + template + KOKKOS_FUNCTION void operator=(T rhs) volatile { + val = cast_to_half(rhs).val; + } + // Compound operators KOKKOS_FUNCTION half_t& operator+=(half_t rhs) { #ifdef __CUDA_ARCH__ val += rhs.val; #else - val = __float2half(__half2float(val) + __half2float(rhs.val)); + val = __float2half(__half2float(val) + __half2float(rhs.val)); #endif return *this; } + KOKKOS_FUNCTION + volatile half_t& operator+=(half_t rhs) volatile { +#ifdef __CUDA_ARCH__ + // Cuda 10 supports __half volatile stores but not volatile arithmetic + // operands. Cast away volatile-ness of val for arithmetic but not for store + // location. + val = const_cast(val) + rhs.val; +#else + // Use non-volatile val_ref to suppress: + // "warning: implicit dereference will not access object of type ‘volatile + // __half’ in statement" + auto val_ref = const_cast(val); + val_ref = __float2half(__half2float(const_cast(val)) + + __half2float(rhs.val)); +#endif + return *this; + } + + // Compund operators: upcast overloads for += + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator+=(T& lhs, half_t rhs) { + lhs += static_cast(rhs); + return lhs; + } + + KOKKOS_FUNCTION + half_t& operator+=(float rhs) { + float result = static_cast(val) + rhs; + val = static_cast(result); + return *this; + } + + KOKKOS_FUNCTION + half_t& operator+=(double rhs) { + double result = static_cast(val) + rhs; + val = static_cast(result); + return *this; + } + KOKKOS_FUNCTION half_t& operator-=(half_t rhs) { #ifdef __CUDA_ARCH__ val -= rhs.val; #else - val = __float2half(__half2float(val) - __half2float(rhs.val)); + val = __float2half(__half2float(val) - __half2float(rhs.val)); #endif return *this; } + KOKKOS_FUNCTION + volatile half_t& operator-=(half_t rhs) volatile { +#ifdef __CUDA_ARCH__ + // Cuda 10 supports __half volatile stores but not volatile arithmetic + // operands. Cast away volatile-ness of val for arithmetic but not for store + // location. + val = const_cast(val) - rhs.val; +#else + // Use non-volatile val_ref to suppress: + // "warning: implicit dereference will not access object of type ‘volatile + // __half’ in statement" + auto val_ref = const_cast(val); + val_ref = __float2half(__half2float(const_cast(val)) - + __half2float(rhs.val)); +#endif + return *this; + } + + // Compund operators: upcast overloads for -= + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator-=(T& lhs, half_t rhs) { + lhs -= static_cast(rhs); + return lhs; + } + + KOKKOS_FUNCTION + half_t& operator-=(float rhs) { + float result = static_cast(val) - rhs; + val = static_cast(result); + return *this; + } + + KOKKOS_FUNCTION + half_t& operator-=(double rhs) { + double result = static_cast(val) - rhs; + val = static_cast(result); + return *this; + } + KOKKOS_FUNCTION half_t& operator*=(half_t rhs) { #ifdef __CUDA_ARCH__ val *= rhs.val; #else - val = __float2half(__half2float(val) * __half2float(rhs.val)); + val = __float2half(__half2float(val) * __half2float(rhs.val)); #endif return *this; } + KOKKOS_FUNCTION + volatile half_t& operator*=(half_t rhs) volatile { +#ifdef __CUDA_ARCH__ + // Cuda 10 supports __half volatile stores but not volatile arithmetic + // operands. Cast away volatile-ness of val for arithmetic but not for store + // location. + val = const_cast(val) * rhs.val; +#else + // Use non-volatile val_ref to suppress: + // "warning: implicit dereference will not access object of type ‘volatile + // __half’ in statement" + auto val_ref = const_cast(val); + val_ref = __float2half(__half2float(const_cast(val)) * + __half2float(rhs.val)); +#endif + return *this; + } + + // Compund operators: upcast overloads for *= + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator*=(T& lhs, half_t rhs) { + lhs *= static_cast(rhs); + return lhs; + } + + KOKKOS_FUNCTION + half_t& operator*=(float rhs) { + float result = static_cast(val) * rhs; + val = static_cast(result); + return *this; + } + + KOKKOS_FUNCTION + half_t& operator*=(double rhs) { + double result = static_cast(val) * rhs; + val = static_cast(result); + return *this; + } + KOKKOS_FUNCTION half_t& operator/=(half_t rhs) { #ifdef __CUDA_ARCH__ val /= rhs.val; #else - val = __float2half(__half2float(val) / __half2float(rhs.val)); + val = __float2half(__half2float(val) / __half2float(rhs.val)); #endif return *this; } + KOKKOS_FUNCTION + volatile half_t& operator/=(half_t rhs) volatile { +#ifdef __CUDA_ARCH__ + // Cuda 10 supports __half volatile stores but not volatile arithmetic + // operands. Cast away volatile-ness of val for arithmetic but not for store + // location. + val = const_cast(val) / rhs.val; +#else + // Use non-volatile val_ref to suppress: + // "warning: implicit dereference will not access object of type ‘volatile + // __half’ in statement" + auto val_ref = const_cast(val); + val_ref = __float2half(__half2float(const_cast(val)) / + __half2float(rhs.val)); +#endif + return *this; + } + + // Compund operators: upcast overloads for /= + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator/=(T& lhs, half_t rhs) { + lhs /= static_cast(rhs); + return lhs; + } + + KOKKOS_FUNCTION + half_t& operator/=(float rhs) { + float result = static_cast(val) / rhs; + val = static_cast(result); + return *this; + } + + KOKKOS_FUNCTION + half_t& operator/=(double rhs) { + double result = static_cast(val) / rhs; + val = static_cast(result); + return *this; + } + // Binary Arithmetic KOKKOS_FUNCTION half_t friend operator+(half_t lhs, half_t rhs) { #ifdef __CUDA_ARCH__ lhs.val += rhs.val; #else - lhs.val = __float2half(__half2float(lhs.val) + __half2float(rhs.val)); + lhs.val = __float2half(__half2float(lhs.val) + __half2float(rhs.val)); #endif return lhs; } + // Binary Arithmetic upcast operators for + + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator+(half_t lhs, T rhs) { + return T(lhs) + rhs; + } + + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator+(T lhs, half_t rhs) { + return lhs + T(rhs); + } + KOKKOS_FUNCTION half_t friend operator-(half_t lhs, half_t rhs) { #ifdef __CUDA_ARCH__ lhs.val -= rhs.val; #else - lhs.val = __float2half(__half2float(lhs.val) - __half2float(rhs.val)); + lhs.val = __float2half(__half2float(lhs.val) - __half2float(rhs.val)); #endif return lhs; } + // Binary Arithmetic upcast operators for - + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator-(half_t lhs, T rhs) { + return T(lhs) - rhs; + } + + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator-(T lhs, half_t rhs) { + return lhs - T(rhs); + } + KOKKOS_FUNCTION half_t friend operator*(half_t lhs, half_t rhs) { #ifdef __CUDA_ARCH__ lhs.val *= rhs.val; #else - lhs.val = __float2half(__half2float(lhs.val) * __half2float(rhs.val)); + lhs.val = __float2half(__half2float(lhs.val) * __half2float(rhs.val)); #endif return lhs; } + // Binary Arithmetic upcast operators for * + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator*(half_t lhs, T rhs) { + return T(lhs) * rhs; + } + + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator*(T lhs, half_t rhs) { + return lhs * T(rhs); + } + KOKKOS_FUNCTION half_t friend operator/(half_t lhs, half_t rhs) { #ifdef __CUDA_ARCH__ lhs.val /= rhs.val; #else - lhs.val = __float2half(__half2float(lhs.val) / __half2float(rhs.val)); + lhs.val = __float2half(__half2float(lhs.val) / __half2float(rhs.val)); #endif return lhs; } + // Binary Arithmetic upcast operators for / + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator/(half_t lhs, T rhs) { + return T(lhs) / rhs; + } + + template + KOKKOS_FUNCTION std::enable_if_t< + std::is_same::value || std::is_same::value, T> friend + operator/(T lhs, half_t rhs) { + return lhs / T(rhs); + } + // Logical operators KOKKOS_FUNCTION bool operator!() const { diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp index b8e8163458..016cb6cdcb 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp @@ -54,6 +54,7 @@ #include #include #include +#include #include #include @@ -248,11 +249,11 @@ void CudaInternal::print_configuration(std::ostream &s) const { const CudaInternalDevices &dev_info = CudaInternalDevices::singleton(); #if defined(KOKKOS_ENABLE_CUDA) - s << "macro KOKKOS_ENABLE_CUDA : defined" << std::endl; + s << "macro KOKKOS_ENABLE_CUDA : defined\n"; #endif #if defined(CUDA_VERSION) s << "macro CUDA_VERSION = " << CUDA_VERSION << " = version " - << CUDA_VERSION / 1000 << "." << (CUDA_VERSION % 1000) / 10 << std::endl; + << CUDA_VERSION / 1000 << "." << (CUDA_VERSION % 1000) / 10 << '\n'; #endif for (int i = 0; i < dev_info.m_cudaDevCount; ++i) { @@ -274,7 +275,6 @@ CudaInternal::~CudaInternal() { m_scratchConcurrentBitset) { std::cerr << "Kokkos::Cuda ERROR: Failed to call Kokkos::Cuda::finalize()" << std::endl; - std::cerr.flush(); } m_cudaDev = -1; @@ -358,8 +358,7 @@ void CudaInternal::initialize(int cuda_device_id, cudaStream_t stream) { if (m_cudaArch == 0) { std::stringstream ss; - ss << "Kokkos::Cuda::initialize ERROR: likely mismatch of architecture" - << std::endl; + ss << "Kokkos::Cuda::initialize ERROR: likely mismatch of architecture\n"; std::string msg = ss.str(); Kokkos::abort(msg.c_str()); } @@ -373,7 +372,7 @@ void CudaInternal::initialize(int cuda_device_id, cudaStream_t stream) { "compute capability " << compiled_major << "." << compiled_minor << " on device with compute capability " << cudaProp.major << "." - << cudaProp.minor << " is not supported by CUDA!" << std::endl; + << cudaProp.minor << " is not supported by CUDA!\n"; std::string msg = ss.str(); Kokkos::abort(msg.c_str()); } @@ -458,7 +457,7 @@ void CudaInternal::initialize(int cuda_device_id, cudaStream_t stream) { Kokkos::Impl::SharedAllocationRecord; Record *const r = - Record::allocate(Kokkos::CudaSpace(), "InternalScratchBitset", + Record::allocate(Kokkos::CudaSpace(), "Kokkos::InternalScratchBitset", sizeof(uint32_t) * buffer_bound); Record::increment(r); @@ -492,17 +491,11 @@ void CudaInternal::initialize(int cuda_device_id, cudaStream_t stream) { #ifdef KOKKOS_ENABLE_CUDA_UVM if (Kokkos::show_warnings() && !cuda_launch_blocking()) { - std::cerr << "Kokkos::Cuda::initialize WARNING: Cuda is allocating into " - "UVMSpace by default" - << std::endl; - std::cerr << " without setting " - "CUDA_LAUNCH_BLOCKING=1." - << std::endl; - std::cerr << " The code must call " - "Cuda().fence() after each kernel" - << std::endl; - std::cerr << " or will likely crash when " - "accessing data on the host." + std::cerr << R"warning( +Kokkos::Cuda::initialize WARNING: Cuda is allocating into UVMSpace by default + without setting CUDA_LAUNCH_BLOCKING=1. + The code must call Cuda().fence() after each kernel + or will likely crash when accessing data on the host.)warning" << std::endl; } @@ -520,19 +513,13 @@ void CudaInternal::initialize(int cuda_device_id, cudaStream_t stream) { if (Kokkos::show_warnings() && (!visible_devices_one && !force_device_alloc)) { - std::cerr << "Kokkos::Cuda::initialize WARNING: Cuda is allocating into " - "UVMSpace by default" + std::cerr << R"warning( +Kokkos::Cuda::initialize WARNING: Cuda is allocating into UVMSpace by default + without setting CUDA_MANAGED_FORCE_DEVICE_ALLOC=1 or + setting CUDA_VISIBLE_DEVICES. + This could on multi GPU systems lead to severe performance" + penalties.)warning" << std::endl; - std::cerr << " without setting " - "CUDA_MANAGED_FORCE_DEVICE_ALLOC=1 or " - << std::endl; - std::cerr - << " setting CUDA_VISIBLE_DEVICES." - << std::endl; - std::cerr << " This could on multi GPU " - "systems lead to severe performance" - << std::endl; - std::cerr << " penalties." << std::endl; } #endif @@ -575,7 +562,7 @@ Cuda::size_type *CudaInternal::scratch_flags(const Cuda::size_type size) const { if (m_scratchFlags) Record::decrement(Record::get_record(m_scratchFlags)); Record *const r = - Record::allocate(Kokkos::CudaSpace(), "InternalScratchFlags", + Record::allocate(Kokkos::CudaSpace(), "Kokkos::InternalScratchFlags", (sizeof(ScratchGrain) * m_scratchFlagsCount)); Record::increment(r); @@ -600,7 +587,7 @@ Cuda::size_type *CudaInternal::scratch_space(const Cuda::size_type size) const { if (m_scratchSpace) Record::decrement(Record::get_record(m_scratchSpace)); Record *const r = - Record::allocate(Kokkos::CudaSpace(), "InternalScratchSpace", + Record::allocate(Kokkos::CudaSpace(), "Kokkos::InternalScratchSpace", (sizeof(ScratchGrain) * m_scratchSpaceCount)); Record::increment(r); @@ -624,7 +611,7 @@ Cuda::size_type *CudaInternal::scratch_unified( Record::decrement(Record::get_record(m_scratchUnified)); Record *const r = Record::allocate( - Kokkos::CudaHostPinnedSpace(), "InternalScratchUnified", + Kokkos::CudaHostPinnedSpace(), "Kokkos::InternalScratchUnified", (sizeof(ScratchGrain) * m_scratchUnifiedCount)); Record::increment(r); @@ -646,8 +633,9 @@ Cuda::size_type *CudaInternal::scratch_functor( if (m_scratchFunctor) Record::decrement(Record::get_record(m_scratchFunctor)); - Record *const r = Record::allocate( - Kokkos::CudaSpace(), "InternalScratchFunctor", m_scratchFunctorSize); + Record *const r = + Record::allocate(Kokkos::CudaSpace(), "Kokkos::InternalScratchFunctor", + m_scratchFunctorSize); Record::increment(r); @@ -662,7 +650,7 @@ void *CudaInternal::resize_team_scratch_space(std::int64_t bytes, if (m_team_scratch_current_size == 0) { m_team_scratch_current_size = bytes; m_team_scratch_ptr = Kokkos::kokkos_malloc( - "CudaSpace::ScratchMemory", m_team_scratch_current_size); + "Kokkos::CudaSpace::TeamScratchMemory", m_team_scratch_current_size); } if ((bytes > m_team_scratch_current_size) || ((bytes < m_team_scratch_current_size) && (force_shrink))) { @@ -676,6 +664,9 @@ void *CudaInternal::resize_team_scratch_space(std::int64_t bytes, //---------------------------------------------------------------------------- void CudaInternal::finalize() { + // skip if finalize() has already been called + if (was_finalized) return; + was_finalized = true; if (nullptr != m_scratchSpace || nullptr != m_scratchFlags) { // Only finalize this if we're the singleton @@ -719,6 +710,11 @@ void CudaInternal::finalize() { if (this == &singleton()) { cudaFreeHost(constantMemHostStaging); cudaEventDestroy(constantMemReusable); + auto &deep_copy_space = + Kokkos::Impl::cuda_get_deep_copy_space(/*initialize*/ false); + if (deep_copy_space) + deep_copy_space->impl_internal_space_instance()->finalize(); + cudaStreamDestroy(cuda_get_deep_copy_stream()); } } @@ -821,62 +817,23 @@ Cuda::size_type Cuda::device_arch() { void Cuda::impl_finalize() { Impl::CudaInternal::singleton().finalize(); } Cuda::Cuda() - : m_space_instance(&Impl::CudaInternal::singleton()), m_counter(nullptr) { + : m_space_instance(&Impl::CudaInternal::singleton(), + [](Impl::CudaInternal *) {}) { Impl::CudaInternal::singleton().verify_is_initialized( "Cuda instance constructor"); } Cuda::Cuda(cudaStream_t stream) - : m_space_instance(new Impl::CudaInternal), m_counter(new int(1)) { + : m_space_instance(new Impl::CudaInternal, [](Impl::CudaInternal *ptr) { + ptr->finalize(); + delete ptr; + }) { Impl::CudaInternal::singleton().verify_is_initialized( "Cuda instance constructor"); m_space_instance->initialize(Impl::CudaInternal::singleton().m_cudaDev, stream); } -KOKKOS_FUNCTION Cuda::Cuda(Cuda &&other) noexcept { - m_space_instance = other.m_space_instance; - other.m_space_instance = nullptr; - m_counter = other.m_counter; - other.m_counter = nullptr; -} - -KOKKOS_FUNCTION Cuda::Cuda(const Cuda &other) - : m_space_instance(other.m_space_instance), m_counter(other.m_counter) { -#ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_CUDA - if (m_counter) Kokkos::atomic_add(m_counter, 1); -#endif -} - -KOKKOS_FUNCTION Cuda &Cuda::operator=(Cuda &&other) noexcept { - m_space_instance = other.m_space_instance; - other.m_space_instance = nullptr; - m_counter = other.m_counter; - other.m_counter = nullptr; - return *this; -} - -KOKKOS_FUNCTION Cuda &Cuda::operator=(const Cuda &other) { - m_space_instance = other.m_space_instance; - m_counter = other.m_counter; -#ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_CUDA - if (m_counter) Kokkos::atomic_add(m_counter, 1); -#endif - return *this; -} - -KOKKOS_FUNCTION Cuda::~Cuda() noexcept { -#ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_CUDA - if (m_counter == nullptr) return; - int const count = Kokkos::atomic_fetch_sub(m_counter, 1); - if (count == 1) { - delete m_counter; - m_space_instance->finalize(); - delete m_space_instance; - } -#endif -} - void Cuda::print_configuration(std::ostream &s, const bool) { Impl::CudaInternal::singleton().print_configuration(s); } @@ -924,54 +881,53 @@ void CudaSpaceInitializer::fence() { Kokkos::Cuda::impl_static_fence(); } void CudaSpaceInitializer::print_configuration(std::ostream &msg, const bool detail) { - msg << "Device Execution Space:" << std::endl; - msg << " KOKKOS_ENABLE_CUDA: "; - msg << "yes" << std::endl; + msg << "Device Execution Space:\n"; + msg << " KOKKOS_ENABLE_CUDA: yes\n"; - msg << "Cuda Atomics:" << std::endl; + msg << "Cuda Atomics:\n"; msg << " KOKKOS_ENABLE_CUDA_ATOMICS: "; #ifdef KOKKOS_ENABLE_CUDA_ATOMICS - msg << "yes" << std::endl; + msg << "yes\n"; #else - msg << "no" << std::endl; + msg << "no\n"; #endif - msg << "Cuda Options:" << std::endl; + msg << "Cuda Options:\n"; msg << " KOKKOS_ENABLE_CUDA_LAMBDA: "; #ifdef KOKKOS_ENABLE_CUDA_LAMBDA - msg << "yes" << std::endl; + msg << "yes\n"; #else - msg << "no" << std::endl; + msg << "no\n"; #endif msg << " KOKKOS_ENABLE_CUDA_LDG_INTRINSIC: "; #ifdef KOKKOS_ENABLE_CUDA_LDG_INTRINSIC - msg << "yes" << std::endl; + msg << "yes\n"; #else - msg << "no" << std::endl; + msg << "no\n"; #endif msg << " KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE: "; #ifdef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE - msg << "yes" << std::endl; + msg << "yes\n"; #else - msg << "no" << std::endl; + msg << "no\n"; #endif msg << " KOKKOS_ENABLE_CUDA_UVM: "; #ifdef KOKKOS_ENABLE_CUDA_UVM - msg << "yes" << std::endl; + msg << "yes\n"; #else - msg << "no" << std::endl; + msg << "no\n"; #endif msg << " KOKKOS_ENABLE_CUSPARSE: "; #ifdef KOKKOS_ENABLE_CUSPARSE - msg << "yes" << std::endl; + msg << "yes\n"; #else - msg << "no" << std::endl; + msg << "no\n"; #endif msg << " KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA: "; #ifdef KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA - msg << "yes" << std::endl; + msg << "yes\n"; #else - msg << "no" << std::endl; + msg << "no\n"; #endif msg << "\nCuda Runtime Configuration:" << std::endl; diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp index 13773d70c5..aaec2c2926 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.hpp @@ -17,30 +17,24 @@ namespace Kokkos { namespace Impl { struct CudaTraits { - enum : CudaSpace::size_type { WarpSize = 32 /* 0x0020 */ }; - enum : CudaSpace::size_type { - WarpIndexMask = 0x001f /* Mask for warpindex */ - }; - enum : CudaSpace::size_type { - WarpIndexShift = 5 /* WarpSize == 1 << WarpShift */ - }; + static constexpr CudaSpace::size_type WarpSize = 32 /* 0x0020 */; + static constexpr CudaSpace::size_type WarpIndexMask = + 0x001f; /* Mask for warpindex */ + static constexpr CudaSpace::size_type WarpIndexShift = + 5; /* WarpSize == 1 << WarpShift */ - enum : CudaSpace::size_type { - ConstantMemoryUsage = 0x008000 /* 32k bytes */ - }; - enum : CudaSpace::size_type { - ConstantMemoryCache = 0x002000 /* 8k bytes */ - }; - enum : CudaSpace::size_type { - KernelArgumentLimit = 0x001000 /* 4k bytes */ - }; - enum : CudaSpace::size_type { - MaxHierarchicalParallelism = 1024 /* team_size * vector_length */ - }; + static constexpr CudaSpace::size_type ConstantMemoryUsage = + 0x008000; /* 32k bytes */ + static constexpr CudaSpace::size_type ConstantMemoryCache = + 0x002000; /* 8k bytes */ + static constexpr CudaSpace::size_type KernelArgumentLimit = + 0x001000; /* 4k bytes */ + static constexpr CudaSpace::size_type MaxHierarchicalParallelism = + 1024; /* team_size * vector_length */ using ConstantGlobalBufferType = unsigned long[ConstantMemoryUsage / sizeof(unsigned long)]; - enum { ConstantMemoryUseThreshold = 0x000200 /* 512 bytes */ }; + static constexpr int ConstantMemoryUseThreshold = 0x000200 /* 512 bytes */; KOKKOS_INLINE_FUNCTION static CudaSpace::size_type warp_count( CudaSpace::size_type i) { diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp index 39404e0bf3..d892a893b3 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp @@ -158,6 +158,9 @@ inline void check_shmem_request(CudaInternal const* cuda_instance, int shmem) { } } +// This function needs to be template on DriverType and LaunchBounds +// so that the static bool is unique for each type combo +// KernelFuncPtr does not necessarily contain that type information. template inline void configure_shmem_preference(KernelFuncPtr const& func, bool prefer_shmem) { @@ -355,8 +358,7 @@ struct CudaParallelLaunchKernelInvoker< if (!Impl::is_empty_launch(grid, block)) { Impl::check_shmem_request(cuda_instance, shmem); - Impl::configure_shmem_preference( + Impl::configure_shmem_preference( base_t::get_kernel_func(), prefer_shmem); void const* args[] = {&driver}; @@ -449,8 +451,7 @@ struct CudaParallelLaunchKernelInvoker< if (!Impl::is_empty_launch(grid, block)) { Impl::check_shmem_request(cuda_instance, shmem); - Impl::configure_shmem_preference( + Impl::configure_shmem_preference( base_t::get_kernel_func(), prefer_shmem); auto* driver_ptr = Impl::allocate_driver_storage_for_kernel(driver); @@ -627,9 +628,8 @@ struct CudaParallelLaunchImpl< get_cuda_func_attributes(), block, shmem, prefer_shmem); Impl::configure_shmem_preference< - DriverType, Kokkos::LaunchBounds, - decltype(base_t::get_kernel_func())>(base_t::get_kernel_func(), - prefer_shmem); + DriverType, Kokkos::LaunchBounds>( + base_t::get_kernel_func(), prefer_shmem); KOKKOS_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE(); diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_MDRangePolicy.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_MDRangePolicy.hpp new file mode 100644 index 0000000000..12b7f70a97 --- /dev/null +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_MDRangePolicy.hpp @@ -0,0 +1,37 @@ +#ifndef KOKKOS_CUDA_MDRANGEPOLICY_HPP_ +#define KOKKOS_CUDA_MDRANGEPOLICY_HPP_ + +#include + +namespace Kokkos { + +template <> +struct default_outer_direction { + using type = Iterate; + static constexpr Iterate value = Iterate::Left; +}; + +template <> +struct default_inner_direction { + using type = Iterate; + static constexpr Iterate value = Iterate::Left; +}; + +namespace Impl { + +// Settings for MDRangePolicy +template <> +inline TileSizeProperties get_tile_size_properties( + const Kokkos::Cuda& space) { + TileSizeProperties properties; + properties.max_threads = + space.impl_internal_space_instance()->m_maxThreadsPerSM; + properties.default_largest_tile_size = 16; + properties.default_tile_size = 2; + properties.max_total_tile_size = 512; + return properties; +} + +} // Namespace Impl +} // Namespace Kokkos +#endif diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp index 131d180980..2834e6f3de 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp @@ -60,6 +60,7 @@ #include #include #include +#include #include #include @@ -67,6 +68,7 @@ #include #include +#include //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- @@ -474,7 +476,7 @@ class ParallelFor, Kokkos::Cuda> { Policy const& get_policy() const { return m_policy; } - inline __device__ void operator()(void) const { + inline __device__ void operator()() const { const Member work_stride = blockDim.y * gridDim.x; const Member work_end = m_policy.end(); @@ -537,9 +539,23 @@ class ParallelFor, Kokkos::Cuda> { const Policy m_rp; public: + template + static int max_tile_size_product(const Policy& pol, const Functor&) { + cudaFuncAttributes attr = + CudaParallelLaunch::get_cuda_func_attributes(); + auto const& prop = pol.space().cuda_device_prop(); + // Limits due to registers/SM, MDRange doesn't have + // shared memory constraints + int const regs_per_sm = prop.regsPerMultiprocessor; + int const regs_per_thread = attr.numRegs; + int const max_threads_per_sm = regs_per_sm / regs_per_thread; + return std::min( + max_threads_per_sm, + static_cast(Kokkos::Impl::CudaTraits::MaxHierarchicalParallelism)); + } Policy const& get_policy() const { return m_rp; } - - inline __device__ void operator()(void) const { + inline __device__ void operator()() const { Kokkos::Impl::DeviceIterateTile(m_rp, m_functor) .exec_range(); @@ -689,7 +705,7 @@ class ParallelFor, public: Policy const& get_policy() const { return m_policy; } - __device__ inline void operator()(void) const { + __device__ inline void operator()() const { // Iterate this block through the league int64_t threadid = 0; if (m_scratch_size[1] > 0) { @@ -1248,8 +1264,21 @@ class ParallelReduce, ReducerType, using DummySHMEMReductionType = int; public: + template + static int max_tile_size_product(const Policy& pol, const Functor&) { + cudaFuncAttributes attr = + CudaParallelLaunch::get_cuda_func_attributes(); + auto const& prop = pol.space().cuda_device_prop(); + // Limits due do registers/SM + int const regs_per_sm = prop.regsPerMultiprocessor; + int const regs_per_thread = attr.numRegs; + int const max_threads_per_sm = regs_per_sm / regs_per_thread; + return std::min( + max_threads_per_sm, + static_cast(Kokkos::Impl::CudaTraits::MaxHierarchicalParallelism)); + } Policy const& get_policy() const { return m_policy; } - inline __device__ void exec_range(reference_type update) const { Kokkos::Impl::Reduce::DeviceIterateTile, ReducerType, .exec_range(); } - inline __device__ void operator()(void) const { + inline __device__ void operator()() const { /* run(Kokkos::Impl::if_c::select(1,1.0) ); } @@ -2074,7 +2103,7 @@ class ParallelScan, Kokkos::Cuda> { //---------------------------------------- - __device__ inline void initial(void) const { + __device__ inline void initial() const { const integral_nonzero_constant word_count(ValueTraits::value_size(m_functor) / sizeof(size_type)); @@ -2110,7 +2139,7 @@ class ParallelScan, Kokkos::Cuda> { //---------------------------------------- - __device__ inline void final(void) const { + __device__ inline void final() const { const integral_nonzero_constant word_count(ValueTraits::value_size(m_functor) / sizeof(size_type)); @@ -2195,7 +2224,7 @@ class ParallelScan, Kokkos::Cuda> { //---------------------------------------- - __device__ inline void operator()(void) const { + __device__ inline void operator()() const { #ifdef KOKKOS_IMPL_DEBUG_CUDA_SERIAL_EXECUTION if (m_run_serial) { typename ValueTraits::value_type value; @@ -2364,7 +2393,7 @@ class ParallelScanWithTotal, //---------------------------------------- - __device__ inline void initial(void) const { + __device__ inline void initial() const { const integral_nonzero_constant word_count(ValueTraits::value_size(m_functor) / sizeof(size_type)); @@ -2400,7 +2429,7 @@ class ParallelScanWithTotal, //---------------------------------------- - __device__ inline void final(void) const { + __device__ inline void final() const { const integral_nonzero_constant word_count(ValueTraits::value_size(m_functor) / sizeof(size_type)); @@ -2487,7 +2516,7 @@ class ParallelScanWithTotal, //---------------------------------------- - __device__ inline void operator()(void) const { + __device__ inline void operator()() const { #ifdef KOKKOS_IMPL_DEBUG_CUDA_SERIAL_EXECUTION if (m_run_serial) { typename ValueTraits::value_type value; diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp index 4b472f5d4f..e780639015 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp @@ -661,13 +661,14 @@ KOKKOS_INLINE_FUNCTION thread, count); } -template -KOKKOS_INLINE_FUNCTION - Impl::ThreadVectorRangeBoundariesStruct - ThreadVectorRange(const Impl::CudaTeamMember& thread, iType arg_begin, - iType arg_end) { +template +KOKKOS_INLINE_FUNCTION Impl::ThreadVectorRangeBoundariesStruct< + typename std::common_type::type, Impl::CudaTeamMember> +ThreadVectorRange(const Impl::CudaTeamMember& thread, iType1 arg_begin, + iType2 arg_end) { + using iType = typename std::common_type::type; return Impl::ThreadVectorRangeBoundariesStruct( - thread, arg_begin, arg_end); + thread, iType(arg_begin), iType(arg_end)); } KOKKOS_INLINE_FUNCTION @@ -983,7 +984,7 @@ KOKKOS_INLINE_FUNCTION void parallel_scan( //---------------------------------------------------------------------------- -/** \brief Intra-thread vector parallel exclusive prefix sum. +/** \brief Intra-thread vector parallel scan with reducer. * * Executes closure(iType i, ValueType & val, bool final) for each i=[0..N) * @@ -991,25 +992,25 @@ KOKKOS_INLINE_FUNCTION void parallel_scan( * thread and a scan operation is performed. * The last call to closure has final == true. */ -template -KOKKOS_INLINE_FUNCTION void parallel_scan( - const Impl::ThreadVectorRangeBoundariesStruct& - loop_boundaries, - const Closure& closure) { +template +KOKKOS_INLINE_FUNCTION + typename std::enable_if::value>::type + parallel_scan(const Impl::ThreadVectorRangeBoundariesStruct< + iType, Impl::CudaTeamMember>& loop_boundaries, + const Closure& closure, const ReducerType& reducer) { (void)loop_boundaries; (void)closure; + (void)reducer; #ifdef __CUDA_ARCH__ - // Extract value_type from closure - - using value_type = typename Kokkos::Impl::FunctorAnalysis< - Kokkos::Impl::FunctorPatternInterface::SCAN, void, Closure>::value_type; + using value_type = typename ReducerType::value_type; + value_type accum; + reducer.init(accum); + const value_type identity = accum; // Loop through boundaries by vector-length chunks // must scan at each iteration - value_type accum = 0; - // All thread "lanes" must loop the same number of times. // Determine an loop end for all thread "lanes." // Requires: @@ -1026,44 +1027,68 @@ KOKKOS_INLINE_FUNCTION void parallel_scan( const int end = loop_boundaries.end + (rem ? blockDim.x - rem : 0); for (int i = threadIdx.x; i < end; i += blockDim.x) { - value_type val = 0; + value_type val = identity; - // First acquire per-lane contributions: - if (i < loop_boundaries.end) closure(i, val, false); + // First acquire per-lane contributions. + // This sets i's val to i-1's contribution + // to make the latter in_place_shfl_up an + // exclusive scan -- the final accumulation + // of i's val will be included in the second + // closure call later. + if (i < loop_boundaries.end && threadIdx.x > 0) closure(i - 1, val, false); - value_type sval = val; - - // Bottom up inclusive scan in triangular pattern + // Bottom up exclusive scan in triangular pattern // where each CUDA thread is the root of a reduction tree // from the zeroth "lane" to itself. // [t] += [t-1] if t >= 1 // [t] += [t-2] if t >= 2 // [t] += [t-4] if t >= 4 // ... - + // This differs from the non-reducer overload, where an inclusive scan was + // implemented, because in general the binary operator cannot be inverted + // and we would not be able to remove the inclusive contribution by + // inversion. for (int j = 1; j < (int)blockDim.x; j <<= 1) { - value_type tmp = 0; - Impl::in_place_shfl_up(tmp, sval, j, blockDim.x, active_mask); + value_type tmp = identity; + Impl::in_place_shfl_up(tmp, val, j, blockDim.x, active_mask); if (j <= (int)threadIdx.x) { - sval += tmp; + reducer.join(val, tmp); } } - // Include accumulation and remove value for exclusive scan: - val = accum + sval - val; + // Include accumulation + reducer.join(val, accum); - // Provide exclusive scan value: + // Update i's contribution into the val + // and add it to accum for next round if (i < loop_boundaries.end) closure(i, val, true); - - // Accumulate the last value in the inclusive scan: - Impl::in_place_shfl(sval, sval, mask, blockDim.x, active_mask); - - accum += sval; + Impl::in_place_shfl(accum, val, mask, blockDim.x, active_mask); } #endif } +//---------------------------------------------------------------------------- + +/** \brief Intra-thread vector parallel exclusive prefix sum. + * + * Executes closure(iType i, ValueType & val, bool final) for each i=[0..N) + * + * The range [0..N) is mapped to all vector lanes in the + * thread and a scan operation is performed. + * The last call to closure has final == true. + */ +template +KOKKOS_INLINE_FUNCTION void parallel_scan( + const Impl::ThreadVectorRangeBoundariesStruct& + loop_boundaries, + const Closure& closure) { + using value_type = typename Kokkos::Impl::FunctorAnalysis< + Kokkos::Impl::FunctorPatternInterface::SCAN, void, Closure>::value_type; + value_type dummy; + parallel_scan(loop_boundaries, closure, Kokkos::Sum(dummy)); +} + } // namespace Kokkos namespace Kokkos { diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp index f24abb377d..c55956ede9 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp @@ -139,7 +139,7 @@ struct CudaLDGFetch { template KOKKOS_INLINE_FUNCTION ValueType operator[](const iType& i) const { -#ifdef __CUDA_ARCH__ +#if defined(__CUDA_ARCH__) && (350 <= _CUDA_ARCH__) AliasType v = __ldg(reinterpret_cast(&m_ptr[i])); return *(reinterpret_cast(&v)); #else diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_WorkGraphPolicy.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_WorkGraphPolicy.hpp index 05876a9f02..fc52e41514 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_WorkGraphPolicy.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_WorkGraphPolicy.hpp @@ -46,6 +46,7 @@ #define KOKKOS_CUDA_WORKGRAPHPOLICY_HPP #include +#include namespace Kokkos { namespace Impl { diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_BlockSize_Deduction.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_BlockSize_Deduction.hpp index 89135b6c45..9278d1bdc9 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_BlockSize_Deduction.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_BlockSize_Deduction.hpp @@ -75,17 +75,6 @@ void hipOccupancy(int *numBlocks, int blockSize, int sharedmem) { hipOccupancy( numBlocks, blockSize, sharedmem); } -template -struct HIPGetMaxBlockSize; - -template -int hip_get_max_block_size(typename DriverType::functor_type const &f, - size_t const vector_length, - size_t const shmem_extra_block, - size_t const shmem_extra_thread) { - return HIPGetMaxBlockSize::get_block_size( - f, vector_length, shmem_extra_block, shmem_extra_thread); -} template int hip_internal_get_block_size(const F &condition_check, @@ -131,10 +120,6 @@ int hip_internal_get_block_size(const F &condition_check, int opt_block_size = (blocks_per_sm >= min_blocks_per_sm) ? block_size : min_blocks_per_sm; int opt_threads_per_sm = threads_per_sm; - // printf("BlockSizeMax: %i Shmem: %i %i %i %i Regs: %i %i Blocks: %i %i - // Achieved: %i %i Opt: %i %i\n",block_size, - // shmem_per_sm,max_shmem_per_block,functor_shmem,total_shmem, - // regs_per_sm,regs_per_wavefront,max_blocks_shmem,max_blocks_regs,blocks_per_sm,threads_per_sm,opt_block_size,opt_threads_per_sm); block_size -= HIPTraits::WarpSize; while (condition_check(blocks_per_sm) && (block_size >= HIPTraits::WarpSize)) { @@ -160,10 +145,6 @@ int hip_internal_get_block_size(const F &condition_check, opt_threads_per_sm = threads_per_sm; } } - // printf("BlockSizeMax: %i Shmem: %i %i %i %i Regs: %i %i Blocks: %i %i - // Achieved: %i %i Opt: %i %i\n",block_size, - // shmem_per_sm,max_shmem_per_block,functor_shmem,total_shmem, - // regs_per_sm,regs_per_wavefront,max_blocks_shmem,max_blocks_regs,blocks_per_sm,threads_per_sm,opt_block_size,opt_threads_per_sm); block_size -= HIPTraits::WarpSize; } return opt_block_size; @@ -178,62 +159,6 @@ int hip_get_max_block_size(const HIPInternal *hip_instance, [](int x) { return x == 0; }, hip_instance, attr, f, vector_length, shmem_block, shmem_thread); } -template -struct HIPGetMaxBlockSize { - static int get_block_size(typename DriverType::functor_type const &f, - size_t const vector_length, - size_t const shmem_extra_block, - size_t const shmem_extra_thread) { - int numBlocks = 0; - int blockSize = LaunchBounds::maxTperB == 0 ? 1024 : LaunchBounds::maxTperB; - int sharedmem = - shmem_extra_block + shmem_extra_thread * (blockSize / vector_length) + - ::Kokkos::Impl::FunctorTeamShmemSize< - typename DriverType::functor_type>::value(f, blockSize / - vector_length); - - hipOccupancy(&numBlocks, blockSize, sharedmem); - - if (numBlocks > 0) return blockSize; - while (blockSize > HIPTraits::WarpSize && numBlocks == 0) { - blockSize /= 2; - sharedmem = - shmem_extra_block + shmem_extra_thread * (blockSize / vector_length) + - ::Kokkos::Impl::FunctorTeamShmemSize< - typename DriverType::functor_type>::value(f, blockSize / - vector_length); - - hipOccupancy(&numBlocks, blockSize, sharedmem); - } - int blockSizeUpperBound = blockSize * 2; - while (blockSize < blockSizeUpperBound && numBlocks > 0) { - blockSize += HIPTraits::WarpSize; - sharedmem = - shmem_extra_block + shmem_extra_thread * (blockSize / vector_length) + - ::Kokkos::Impl::FunctorTeamShmemSize< - typename DriverType::functor_type>::value(f, blockSize / - vector_length); - - hipOccupancy(&numBlocks, blockSize, sharedmem); - } - return blockSize - HIPTraits::WarpSize; - } -}; - -template -struct HIPGetOptBlockSize; - -template -int hip_get_opt_block_size(typename DriverType::functor_type const &f, - size_t const vector_length, - size_t const shmem_extra_block, - size_t const shmem_extra_thread) { - return HIPGetOptBlockSize< - DriverType, LaunchBounds, - (HIPTraits::ConstantMemoryUseThreshold < - sizeof(DriverType))>::get_block_size(f, vector_length, shmem_extra_block, - shmem_extra_thread); -} template int hip_get_opt_block_size(HIPInternal const *hip_instance, @@ -245,157 +170,6 @@ int hip_get_opt_block_size(HIPInternal const *hip_instance, shmem_block, shmem_thread); } -// FIXME_HIP the code is identical to the false struct except for -// hip_parallel_launch_constant_memory -template -struct HIPGetOptBlockSize, true> { - static int get_block_size(typename DriverType::functor_type const &f, - size_t const vector_length, - size_t const shmem_extra_block, - size_t const shmem_extra_thread) { - int blockSize = HIPTraits::WarpSize / 2; - int numBlocks; - int sharedmem; - int maxOccupancy = 0; - int bestBlockSize = 0; - - while (blockSize < HIPTraits::MaxThreadsPerBlock) { - blockSize *= 2; - - // calculate the occupancy with that optBlockSize and check whether its - // larger than the largest one found so far - sharedmem = - shmem_extra_block + shmem_extra_thread * (blockSize / vector_length) + - ::Kokkos::Impl::FunctorTeamShmemSize< - typename DriverType::functor_type>::value(f, blockSize / - vector_length); - hipOccupancy(&numBlocks, blockSize, sharedmem); - if (maxOccupancy < numBlocks * blockSize) { - maxOccupancy = numBlocks * blockSize; - bestBlockSize = blockSize; - } - } - return bestBlockSize; - } -}; - -template -struct HIPGetOptBlockSize, false> { - static int get_block_size(const typename DriverType::functor_type &f, - const size_t vector_length, - const size_t shmem_extra_block, - const size_t shmem_extra_thread) { - int blockSize = HIPTraits::WarpSize / 2; - int numBlocks; - int sharedmem; - int maxOccupancy = 0; - int bestBlockSize = 0; - - while (blockSize < HIPTraits::MaxThreadsPerBlock) { - blockSize *= 2; - sharedmem = - shmem_extra_block + shmem_extra_thread * (blockSize / vector_length) + - ::Kokkos::Impl::FunctorTeamShmemSize< - typename DriverType::functor_type>::value(f, blockSize / - vector_length); - - hipOccupancy(&numBlocks, blockSize, sharedmem); - - if (maxOccupancy < numBlocks * blockSize) { - maxOccupancy = numBlocks * blockSize; - bestBlockSize = blockSize; - } - } - return bestBlockSize; - } -}; - -// FIXME_HIP the code is identical to the false struct except for -// hip_parallel_launch_constant_memory -template -struct HIPGetOptBlockSize< - DriverType, Kokkos::LaunchBounds, - true> { - static int get_block_size(const typename DriverType::functor_type &f, - const size_t vector_length, - const size_t shmem_extra_block, - const size_t shmem_extra_thread) { - int blockSize = HIPTraits::WarpSize / 2; - int numBlocks; - int sharedmem; - int maxOccupancy = 0; - int bestBlockSize = 0; - int max_threads_per_block = - std::min(MaxThreadsPerBlock, - hip_internal_maximum_warp_count() * HIPTraits::WarpSize); - - while (blockSize < max_threads_per_block) { - blockSize *= 2; - - // calculate the occupancy with that optBlockSize and check whether its - // larger than the largest one found so far - sharedmem = - shmem_extra_block + shmem_extra_thread * (blockSize / vector_length) + - ::Kokkos::Impl::FunctorTeamShmemSize< - typename DriverType::functor_type>::value(f, blockSize / - vector_length); - hipOccupancy( - &numBlocks, blockSize, sharedmem); - if (numBlocks >= static_cast(MinBlocksPerSM) && - blockSize <= static_cast(MaxThreadsPerBlock)) { - if (maxOccupancy < numBlocks * blockSize) { - maxOccupancy = numBlocks * blockSize; - bestBlockSize = blockSize; - } - } - } - if (maxOccupancy > 0) return bestBlockSize; - return -1; - } -}; - -template -struct HIPGetOptBlockSize< - DriverType, Kokkos::LaunchBounds, - false> { - static int get_block_size(const typename DriverType::functor_type &f, - const size_t vector_length, - const size_t shmem_extra_block, - const size_t shmem_extra_thread) { - int blockSize = HIPTraits::WarpSize / 2; - int numBlocks; - int sharedmem; - int maxOccupancy = 0; - int bestBlockSize = 0; - int max_threads_per_block = - std::min(MaxThreadsPerBlock, - hip_internal_maximum_warp_count() * HIPTraits::WarpSize); - - while (blockSize < max_threads_per_block) { - blockSize *= 2; - sharedmem = - shmem_extra_block + shmem_extra_thread * (blockSize / vector_length) + - ::Kokkos::Impl::FunctorTeamShmemSize< - typename DriverType::functor_type>::value(f, blockSize / - vector_length); - - hipOccupancy( - &numBlocks, blockSize, sharedmem); - if (numBlocks >= int(MinBlocksPerSM) && - blockSize <= int(MaxThreadsPerBlock)) { - if (maxOccupancy < numBlocks * blockSize) { - maxOccupancy = numBlocks * blockSize; - bestBlockSize = blockSize; - } - } - } - if (maxOccupancy > 0) return bestBlockSize; - return -1; - } -}; - } // namespace Impl } // namespace Experimental } // namespace Kokkos diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp index 45512038ac..18ef10e22c 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp @@ -164,6 +164,8 @@ HIPInternal &HIPInternal::singleton() { void HIPInternal::fence() const { HIP_SAFE_CALL(hipStreamSynchronize(m_stream)); + // can reset our cycle id now as well + m_cycleId = 0; } void HIPInternal::initialize(int hip_device_id, hipStream_t stream) { @@ -256,7 +258,7 @@ void HIPInternal::initialize(int hip_device_id, hipStream_t stream) { void>; Record *const r = Record::allocate(Kokkos::Experimental::HIPSpace(), - "InternalScratchBitset", + "Kokkos::InternalScratchBitset", sizeof(uint32_t) * buffer_bound); Record::increment(r); @@ -303,8 +305,10 @@ Kokkos::Experimental::HIP::size_type *HIPInternal::scratch_space( Kokkos::Impl::SharedAllocationRecord; - static Record *const r = Record::allocate( - Kokkos::Experimental::HIPSpace(), "InternalScratchSpace", + if (m_scratchSpace) Record::decrement(Record::get_record(m_scratchSpace)); + + Record *const r = Record::allocate( + Kokkos::Experimental::HIPSpace(), "Kokkos::InternalScratchSpace", (sizeScratchGrain * m_scratchSpaceCount)); Record::increment(r); @@ -325,8 +329,10 @@ Kokkos::Experimental::HIP::size_type *HIPInternal::scratch_flags( Kokkos::Impl::SharedAllocationRecord; + if (m_scratchFlags) Record::decrement(Record::get_record(m_scratchFlags)); + Record *const r = Record::allocate( - Kokkos::Experimental::HIPSpace(), "InternalScratchFlags", + Kokkos::Experimental::HIPSpace(), "Kokkos::InternalScratchFlags", (sizeScratchGrain * m_scratchFlagsCount)); Record::increment(r); @@ -345,7 +351,7 @@ void *HIPInternal::resize_team_scratch_space(std::int64_t bytes, if (m_team_scratch_current_size == 0) { m_team_scratch_current_size = bytes; m_team_scratch_ptr = Kokkos::kokkos_malloc( - "HIPSpace::ScratchMemory", m_team_scratch_current_size); + "Kokkos::HIPSpace::TeamScratchMemory", m_team_scratch_current_size); } if ((bytes > m_team_scratch_current_size) || ((bytes < m_team_scratch_current_size) && (force_shrink))) { @@ -388,6 +394,40 @@ void HIPInternal::finalize() { m_team_scratch_current_size = 0; m_team_scratch_ptr = nullptr; } + if (nullptr != d_driverWorkArray) { + HIP_SAFE_CALL(hipHostFree(d_driverWorkArray)); + d_driverWorkArray = nullptr; + } +} + +char *HIPInternal::get_next_driver(size_t driverTypeSize) const { + std::lock_guard const lock(m_mutexWorkArray); + if (d_driverWorkArray == nullptr) { + HIP_SAFE_CALL( + hipHostMalloc(&d_driverWorkArray, + m_maxDriverCycles * m_maxDriverTypeSize * sizeof(char), + hipHostMallocNonCoherent)); + } + if (driverTypeSize > m_maxDriverTypeSize) { + // fence handles the cycle id reset for us + fence(); + HIP_SAFE_CALL(hipHostFree(d_driverWorkArray)); + m_maxDriverTypeSize = driverTypeSize; + if (m_maxDriverTypeSize % 128 != 0) + m_maxDriverTypeSize = + m_maxDriverTypeSize + 128 - m_maxDriverTypeSize % 128; + HIP_SAFE_CALL( + hipHostMalloc(&d_driverWorkArray, + m_maxDriverCycles * m_maxDriverTypeSize * sizeof(char), + hipHostMallocNonCoherent)); + } else { + m_cycleId = (m_cycleId + 1) % m_maxDriverCycles; + if (m_cycleId == 0) { + // ensure any outstanding kernels are completed before we wrap around + fence(); + } + } + return &d_driverWorkArray[m_maxDriverTypeSize * m_cycleId]; } //---------------------------------------------------------------------------- diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp index 07ec8625e6..f4f88628e3 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp @@ -49,6 +49,8 @@ #include +#include + namespace Kokkos { namespace Experimental { namespace Impl { @@ -83,33 +85,46 @@ class HIPInternal { public: using size_type = ::Kokkos::Experimental::HIP::size_type; - int m_hipDev; - int m_hipArch; - unsigned m_multiProcCount; - unsigned m_maxWarpCount; - unsigned m_maxBlock; - unsigned m_maxBlocksPerSM; - unsigned m_maxSharedWords; + int m_hipDev = -1; + int m_hipArch = -1; + unsigned m_multiProcCount = 0; + unsigned m_maxWarpCount = 0; + unsigned m_maxBlock = 0; + unsigned m_maxBlocksPerSM = 0; + unsigned m_maxSharedWords = 0; int m_regsPerSM; - int m_shmemPerSM; - int m_maxShmemPerBlock; - int m_maxThreadsPerSM; + int m_shmemPerSM = 0; + int m_maxShmemPerBlock = 0; + int m_maxThreadsPerSM = 0; + + // array of DriverTypes to be allocated in host-pinned memory for async + // kernel launches + mutable char *d_driverWorkArray = nullptr; + // number of kernel launches that can be in-flight w/o synchronization + const int m_maxDriverCycles = 100; + // max size of a DriverType [bytes] + mutable size_t m_maxDriverTypeSize = 1024 * 10; + // the current index in the driverWorkArray + mutable int m_cycleId = 0; + // mutex to access d_driverWorkArray + mutable std::mutex m_mutexWorkArray; // Scratch Spaces for Reductions - size_type m_scratchSpaceCount; - size_type m_scratchFlagsCount; + size_type m_scratchSpaceCount = 0; + size_type m_scratchFlagsCount = 0; - size_type *m_scratchSpace; - size_type *m_scratchFlags; + size_type *m_scratchSpace = nullptr; + size_type *m_scratchFlags = nullptr; uint32_t *m_scratchConcurrentBitset = nullptr; hipDeviceProp_t m_deviceProp; - hipStream_t m_stream; + hipStream_t m_stream = nullptr; // Team Scratch Level 1 Space - mutable int64_t m_team_scratch_current_size; - mutable void *m_team_scratch_ptr; + mutable int64_t m_team_scratch_current_size = 0; + mutable void *m_team_scratch_ptr = nullptr; + mutable std::mutex m_team_scratch_mutex; bool was_finalized = false; @@ -117,9 +132,7 @@ class HIPInternal { int verify_is_initialized(const char *const label) const; - int is_initialized() const { - return m_hipDev >= 0; - } // 0 != m_scratchSpace && 0 != m_scratchFlags ; } + int is_initialized() const { return m_hipDev >= 0; } void initialize(int hip_device_id, hipStream_t stream = nullptr); void finalize(); @@ -128,25 +141,12 @@ class HIPInternal { void fence() const; + // returns the next driver type pointer in our work array + char *get_next_driver(size_t driverTypeSize) const; + ~HIPInternal(); - HIPInternal() - : m_hipDev(-1), - m_hipArch(-1), - m_multiProcCount(0), - m_maxWarpCount(0), - m_maxBlock(0), - m_maxSharedWords(0), - m_shmemPerSM(0), - m_maxShmemPerBlock(0), - m_maxThreadsPerSM(0), - m_scratchSpaceCount(0), - m_scratchFlagsCount(0), - m_scratchSpace(nullptr), - m_scratchFlags(nullptr), - m_stream(nullptr), - m_team_scratch_current_size(0), - m_team_scratch_ptr(nullptr) {} + HIPInternal() = default; // Resizing of reduction related scratch spaces size_type *scratch_space(const size_type size); diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp index 3e972c7346..f774423b37 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_KernelLaunch.hpp @@ -49,9 +49,9 @@ #if defined(__HIPCC__) -#include #include #include +#include // Must use global variable on the device with HIP-Clang #ifdef __HIP__ @@ -127,19 +127,69 @@ struct HIPDispatchProperties { HIPLaunchMechanism launch_mechanism = l; }; -template , +template +struct HIPParallelLaunchKernelFunc; + +template +struct HIPParallelLaunchKernelFunc< + DriverType, Kokkos::LaunchBounds, + HIPLaunchMechanism::LocalMemory> { + static auto get_kernel_func() { + return hip_parallel_launch_local_memory; + } +}; + +template +struct HIPParallelLaunchKernelFunc, + HIPLaunchMechanism::LocalMemory> { + static auto get_kernel_func() { + return hip_parallel_launch_local_memory; + } +}; + +template +struct HIPParallelLaunchKernelInvoker; + +template +struct HIPParallelLaunchKernelInvoker + : HIPParallelLaunchKernelFunc { + using base_t = HIPParallelLaunchKernelFunc; + + static void invoke_kernel(DriverType const *driver, dim3 const &grid, + dim3 const &block, int shmem, + HIPInternal const *hip_instance) { + (base_t::get_kernel_func())<<m_stream>>>( + driver); + } +}; + +template , HIPLaunchMechanism LaunchMechanism = HIPLaunchMechanism::LocalMemory> struct HIPParallelLaunch; -template struct HIPParallelLaunch< DriverType, Kokkos::LaunchBounds, - HIPLaunchMechanism::LocalMemory> { - inline HIPParallelLaunch(const DriverType &driver, const dim3 &grid, - const dim3 &block, const int shmem, - const HIPInternal *hip_instance, - const bool /*prefer_shmem*/) { + HIPLaunchMechanism::LocalMemory> + : HIPParallelLaunchKernelInvoker< + DriverType, Kokkos::LaunchBounds, + HIPLaunchMechanism::LocalMemory> { + using base_t = HIPParallelLaunchKernelInvoker< + DriverType, Kokkos::LaunchBounds, + HIPLaunchMechanism::LocalMemory>; + + HIPParallelLaunch(const DriverType &driver, const dim3 &grid, + const dim3 &block, const int shmem, + const HIPInternal *hip_instance, + const bool /*prefer_shmem*/) { if ((grid.x != 0) && ((block.x * block.y * block.z) != 0)) { if (hip_instance->m_maxShmemPerBlock < shmem) { Kokkos::Impl::throw_runtime_exception( @@ -148,72 +198,16 @@ struct HIPParallelLaunch< KOKKOS_ENSURE_HIP_LOCK_ARRAYS_ON_DEVICE(); - // FIXME_HIP -- there is currently an error copying (some) structs - // by value to the device in HIP-Clang / VDI - // As a workaround, we can malloc the DriverType and explictly copy over. - // To remove once solved in HIP - DriverType *d_driver; - HIP_SAFE_CALL(hipMalloc(&d_driver, sizeof(DriverType))); - HIP_SAFE_CALL(hipMemcpyAsync(d_driver, &driver, sizeof(DriverType), - hipMemcpyHostToDevice, - hip_instance->m_stream)); - hip_parallel_launch_local_memory - <<m_stream>>>(d_driver); - -#if defined(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK) - HIP_SAFE_CALL(hipGetLastError()); - hip_instance->fence(); -#endif - HIP_SAFE_CALL(hipFree(d_driver)); - } - } - - static hipFuncAttributes get_hip_func_attributes() { - static hipFuncAttributes attr = []() { - hipFuncAttributes attr; - HIP_SAFE_CALL(hipFuncGetAttributes( - &attr, - reinterpret_cast( - hip_parallel_launch_local_memory))); - return attr; - }(); - return attr; - } -}; - -template -struct HIPParallelLaunch, - HIPLaunchMechanism::LocalMemory> { - inline HIPParallelLaunch(const DriverType &driver, const dim3 &grid, - const dim3 &block, const int shmem, - const HIPInternal *hip_instance, - const bool /*prefer_shmem*/) { - if ((grid.x != 0) && ((block.x * block.y * block.z) != 0)) { - if (hip_instance->m_maxShmemPerBlock < shmem) { - Kokkos::Impl::throw_runtime_exception(std::string( - "HIPParallelLaunch FAILED: shared memory request is too large")); - } - - KOKKOS_ENSURE_HIP_LOCK_ARRAYS_ON_DEVICE(); - // Invoke the driver function on the device - - // FIXME_HIP -- see note about struct copy by value above - DriverType *d_driver; - HIP_SAFE_CALL(hipMalloc(&d_driver, sizeof(DriverType))); - HIP_SAFE_CALL(hipMemcpyAsync(d_driver, &driver, sizeof(DriverType), - hipMemcpyHostToDevice, - hip_instance->m_stream)); - hip_parallel_launch_local_memory - <<m_stream>>>(d_driver); + DriverType *d_driver = reinterpret_cast( + hip_instance->get_next_driver(sizeof(DriverType))); + std::memcpy((void *)d_driver, (void *)&driver, sizeof(DriverType)); + base_t::invoke_kernel(d_driver, grid, block, shmem, hip_instance); #if defined(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK) HIP_SAFE_CALL(hipGetLastError()); hip_instance->fence(); #endif - HIP_SAFE_CALL(hipFree(d_driver)); } } @@ -221,8 +215,7 @@ struct HIPParallelLaunch, static hipFuncAttributes attr = []() { hipFuncAttributes attr; HIP_SAFE_CALL(hipFuncGetAttributes( - &attr, reinterpret_cast( - hip_parallel_launch_local_memory))); + &attr, reinterpret_cast(base_t::get_kernel_func()))); return attr; }(); return attr; diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_MDRangePolicy.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_MDRangePolicy.hpp new file mode 100644 index 0000000000..ce1aff9586 --- /dev/null +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_MDRangePolicy.hpp @@ -0,0 +1,37 @@ +#ifndef KOKKOS_HIP_MDRANGEPOLICY_HPP_ +#define KOKKOS_HIP_MDRANGEPOLICY_HPP_ + +#include + +namespace Kokkos { + +template <> +struct default_outer_direction { + using type = Iterate; + static constexpr Iterate value = Iterate::Left; +}; + +template <> +struct default_inner_direction { + using type = Iterate; + static constexpr Iterate value = Iterate::Left; +}; + +namespace Impl { + +// Settings for MDRangePolicy +template <> +inline TileSizeProperties get_tile_size_properties( + const Kokkos::Experimental::HIP& space) { + TileSizeProperties properties; + properties.max_threads = + space.impl_internal_space_instance()->m_maxThreadsPerSM; + properties.default_largest_tile_size = 16; + properties.default_tile_size = 4; + properties.max_total_tile_size = 1024; + return properties; +} + +} // Namespace Impl +} // Namespace Kokkos +#endif diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp index 6b831ff7a3..35e7d6fb85 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_MDRange.hpp @@ -49,6 +49,7 @@ #include #include #include +#include #include namespace Kokkos { @@ -72,7 +73,7 @@ class ParallelFor, ParallelFor& operator=(ParallelFor const&) = delete; public: - inline __device__ void operator()(void) const { + inline __device__ void operator()() const { Kokkos::Impl::DeviceIterateTile(m_policy, m_functor) @@ -175,6 +176,25 @@ class ParallelFor, ParallelFor(FunctorType const& arg_functor, Policy const& arg_policy) : m_functor(arg_functor), m_policy(arg_policy) {} + + template + static int max_tile_size_product(const Policy& pol, const Functor&) { + using closure_type = + ParallelFor, + Kokkos::Experimental::HIP>; + hipFuncAttributes attr = Kokkos::Experimental::Impl::HIPParallelLaunch< + closure_type, LaunchBounds>::get_hip_func_attributes(); + auto const& prop = pol.space().hip_device_prop(); + // Limits due to registers/SM, MDRange doesn't have + // shared memory constraints + int const regs_per_sm = prop.regsPerMultiprocessor; + int const regs_per_thread = attr.numRegs; + int const max_threads_per_sm = regs_per_sm / regs_per_thread; + return std::min( + max_threads_per_sm, + static_cast( + Kokkos::Experimental::Impl::HIPTraits::MaxThreadsPerBlock)); + } }; // ParallelReduce @@ -231,7 +251,7 @@ class ParallelReduce, ReducerType, DeviceIteratePattern(m_policy, m_functor, update).exec_range(); } - inline __device__ void operator()(void) const { + inline __device__ void operator()() const { const integral_nonzero_constant word_count(ValueTraits::value_size( @@ -291,13 +311,19 @@ class ParallelReduce, ReducerType, ::Kokkos::Experimental::Impl::HIPTraits::MaxThreadsPerBlock; int shmem_size = ::Kokkos::Impl::hip_single_inter_block_reduce_scan_shmem< false, FunctorType, WorkTag>(f, n); + using closure_type = Impl::ParallelReduce; + hipFuncAttributes attr = ::Kokkos::Experimental::Impl::HIPParallelLaunch< + closure_type, LaunchBounds>::get_hip_func_attributes(); while ( (n && (m_policy.space().impl_internal_space_instance()->m_maxShmemPerBlock < shmem_size)) || - (n > static_cast( - ::Kokkos::Experimental::Impl::hip_get_max_block_size< - ParallelReduce, LaunchBounds>(f, 1, shmem_size, 0)))) { + (n > + static_cast( + ::Kokkos::Experimental::Impl::hip_get_max_block_size( + m_policy.space().impl_internal_space_instance(), attr, f, 1, + shmem_size, 0)))) { n >>= 1; shmem_size = ::Kokkos::Impl::hip_single_inter_block_reduce_scan_shmem< false, FunctorType, WorkTag>(f, n); @@ -391,6 +417,23 @@ class ParallelReduce, ReducerType, memory_space>::accessible), m_scratch_space(nullptr), m_scratch_flags(nullptr) {} + template + static int max_tile_size_product(const Policy& pol, const Functor&) { + using closure_type = + ParallelReduce, + ReducerType, Kokkos::Experimental::HIP>; + hipFuncAttributes attr = Kokkos::Experimental::Impl::HIPParallelLaunch< + closure_type, LaunchBounds>::get_hip_func_attributes(); + auto const& prop = pol.space().hip_device_prop(); + // Limits due do registers/SM + int const regs_per_sm = prop.regsPerMultiprocessor; + int const regs_per_thread = attr.numRegs; + int const max_threads_per_sm = regs_per_sm / regs_per_thread; + return std::min( + max_threads_per_sm, + static_cast( + Kokkos::Experimental::Impl::HIPTraits::MaxThreadsPerBlock)); + } }; } // namespace Impl } // namespace Kokkos diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp index 5607f1c91a..7d2825eeb4 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Range.hpp @@ -92,7 +92,7 @@ class ParallelFor, public: using functor_type = FunctorType; - inline __device__ void operator()(void) const { + inline __device__ void operator()() const { const Member work_stride = blockDim.y * gridDim.x; const Member work_end = m_policy.end(); @@ -174,11 +174,14 @@ class ParallelReduce, ReducerType, size_type* m_scratch_space = nullptr; size_type* m_scratch_flags = nullptr; - // FIXME_HIP_PERFORMANCE Need a rule to choose when to use shared memory and - // when to use shuffle +#if HIP_VERSION < 401 static bool constexpr UseShflReduction = ((sizeof(value_type) > 2 * sizeof(double)) && static_cast(ValueTraits::StaticValueSize)); +#else + static bool constexpr UseShflReduction = + static_cast(ValueTraits::StaticValueSize); +#endif private: struct ShflReductionTag {}; @@ -330,13 +333,19 @@ class ParallelReduce, ReducerType, int shmem_size = hip_single_inter_block_reduce_scan_shmem( f, n); + using closure_type = Impl::ParallelReduce; + hipFuncAttributes attr = ::Kokkos::Experimental::Impl::HIPParallelLaunch< + closure_type, LaunchBounds>::get_hip_func_attributes(); while ( (n && (m_policy.space().impl_internal_space_instance()->m_maxShmemPerBlock < shmem_size)) || - (n > static_cast( - Kokkos::Experimental::Impl::hip_get_max_block_size< - ParallelReduce, LaunchBounds>(f, 1, shmem_size, 0)))) { + (n > + static_cast( + ::Kokkos::Experimental::Impl::hip_get_max_block_size( + m_policy.space().impl_internal_space_instance(), attr, f, 1, + shmem_size, 0)))) { n >>= 1; shmem_size = hip_single_inter_block_reduce_scan_shmem( @@ -493,7 +502,7 @@ class ParallelScanHIPBase { //---------------------------------------- - __device__ inline void initial(void) const { + __device__ inline void initial() const { const integral_nonzero_constant word_count(ValueTraits::value_size(m_functor) / sizeof(size_type)); @@ -529,7 +538,7 @@ class ParallelScanHIPBase { //---------------------------------------- - __device__ inline void final(void) const { + __device__ inline void final() const { const integral_nonzero_constant word_count(ValueTraits::value_size(m_functor) / sizeof(size_type)); @@ -606,7 +615,7 @@ class ParallelScanHIPBase { public: //---------------------------------------- - __device__ inline void operator()(void) const { + __device__ inline void operator()() const { if (!m_final) { initial(); } else { diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp index 5da83d289e..96c3ff2a75 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Parallel_Team.hpp @@ -433,6 +433,9 @@ class ParallelFor, int m_shmem_size; void* m_scratch_ptr[2]; int m_scratch_size[2]; + // Only let one ParallelFor/Reduce modify the team scratch memory. The + // constructor acquires the mutex which is released in the destructor. + std::unique_lock m_scratch_lock; template __device__ inline @@ -449,7 +452,7 @@ class ParallelFor, } public: - __device__ inline void operator()(void) const { + __device__ inline void operator()() const { // Iterate this block through the league int64_t threadid = 0; if (m_scratch_size[1] > 0) { @@ -513,7 +516,10 @@ class ParallelFor, m_policy(arg_policy), m_league_size(arg_policy.league_size()), m_team_size(arg_policy.team_size()), - m_vector_size(arg_policy.impl_vector_length()) { + m_vector_size(arg_policy.impl_vector_length()), + m_scratch_lock(m_policy.space() + .impl_internal_space_instance() + ->m_team_scratch_mutex) { hipFuncAttributes attr = ::Kokkos::Experimental::Impl::HIPParallelLaunch< ParallelFor, launch_bounds>::get_hip_func_attributes(); m_team_size = @@ -640,6 +646,9 @@ class ParallelReduce, const size_type m_league_size; int m_team_size; const size_type m_vector_size; + // Only let one ParallelFor/Reduce modify the team scratch memory. The + // constructor acquires the mutex which is released in the destructor. + std::unique_lock m_scratch_lock; template __device__ inline @@ -877,7 +886,10 @@ class ParallelReduce, m_scratch_ptr{nullptr, nullptr}, m_league_size(arg_policy.league_size()), m_team_size(arg_policy.team_size()), - m_vector_size(arg_policy.impl_vector_length()) { + m_vector_size(arg_policy.impl_vector_length()), + m_scratch_lock(m_policy.space() + .impl_internal_space_instance() + ->m_team_scratch_mutex) { hipFuncAttributes attr = Kokkos::Experimental::Impl::HIPParallelLaunch< ParallelReduce, launch_bounds>::get_hip_func_attributes(); m_team_size = @@ -976,7 +988,10 @@ class ParallelReduce, m_scratch_ptr{nullptr, nullptr}, m_league_size(arg_policy.league_size()), m_team_size(arg_policy.team_size()), - m_vector_size(arg_policy.impl_vector_length()) { + m_vector_size(arg_policy.impl_vector_length()), + m_scratch_lock(m_policy.space() + .impl_internal_space_instance() + ->m_team_scratch_mutex) { hipFuncAttributes attr = Kokkos::Experimental::Impl::HIPParallelLaunch< ParallelReduce, launch_bounds>::get_hip_func_attributes(); m_team_size = diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp index 00cef28f82..15ca089d14 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Space.cpp @@ -42,12 +42,6 @@ //@HEADER */ -#include -#include -#include -#include -#include -#include #include #include @@ -57,6 +51,13 @@ #include #include +#include +#include +#include +#include +#include +#include + /*--------------------------------------------------------------------------*/ /*--------------------------------------------------------------------------*/ namespace Kokkos { @@ -172,14 +173,14 @@ void DeepCopyAsyncHIP(void* dst, void const* src, size_t n) { namespace Kokkos { -void Experimental::HIPSpace::access_error() { +KOKKOS_DEPRECATED void Experimental::HIPSpace::access_error() { const std::string msg( "Kokkos::Experimental::HIPSpace::access_error attempt to execute " "Experimental::HIP function from non-HIP space"); Kokkos::Impl::throw_runtime_exception(msg); } -void Experimental::HIPSpace::access_error(const void* const) { +KOKKOS_DEPRECATED void Experimental::HIPSpace::access_error(const void* const) { const std::string msg( "Kokkos::Experimental::HIPSpace::access_error attempt to execute " "Experimental::HIP function from non-HIP space"); @@ -326,45 +327,6 @@ SharedAllocationRecord SharedAllocationRecord< Kokkos::Experimental::HIPHostPinnedSpace, void>::s_root_record; #endif -std::string SharedAllocationRecord::get_label() const { - SharedAllocationHeader header; - - Kokkos::Impl::DeepCopy( - &header, RecordBase::head(), sizeof(SharedAllocationHeader)); - - return std::string(header.m_label); -} - -std::string SharedAllocationRecord::get_label() const { - return std::string(RecordBase::head()->m_label); -} - -SharedAllocationRecord* -SharedAllocationRecord::allocate( - const Kokkos::Experimental::HIPSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size) { - return new SharedAllocationRecord(arg_space, arg_label, arg_alloc_size); -} - -SharedAllocationRecord* -SharedAllocationRecord:: - allocate(const Kokkos::Experimental::HIPHostPinnedSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size) { - return new SharedAllocationRecord(arg_space, arg_label, arg_alloc_size); -} - -void SharedAllocationRecord::deallocate( - SharedAllocationRecord* arg_rec) { - delete static_cast(arg_rec); -} - -void SharedAllocationRecord:: - deallocate(SharedAllocationRecord* arg_rec) { - delete static_cast(arg_rec); -} - SharedAllocationRecord::~SharedAllocationRecord() { const char* label = nullptr; @@ -393,7 +355,7 @@ SharedAllocationRecord:: const SharedAllocationRecord::function_type arg_dealloc) // Pass through allocated [ SharedAllocationHeader , user_memory ] // Pass through deallocation function - : SharedAllocationRecord( + : base_t( #ifdef KOKKOS_ENABLE_DEBUG &SharedAllocationRecord::s_root_record, @@ -405,13 +367,7 @@ SharedAllocationRecord:: SharedAllocationHeader header; - // Fill in the Header information - header.m_record = static_cast*>(this); - - strncpy(header.m_label, arg_label.c_str(), - SharedAllocationHeader::maximum_label_length); - // Set last element zero, in case c_str is too long - header.m_label[SharedAllocationHeader::maximum_label_length - 1] = (char)0; + this->base_t::_fill_host_accessible_header_info(header, arg_label); // Copy to device memory Kokkos::Impl::DeepCopy( @@ -425,7 +381,7 @@ SharedAllocationRecord:: const SharedAllocationRecord::function_type arg_dealloc) // Pass through allocated [ SharedAllocationHeader , user_memory ] // Pass through deallocation function - : SharedAllocationRecord( + : base_t( #ifdef KOKKOS_ENABLE_DEBUG &SharedAllocationRecord::s_root_record, @@ -435,223 +391,8 @@ SharedAllocationRecord:: sizeof(SharedAllocationHeader) + arg_alloc_size, arg_dealloc), m_space(arg_space) { // Fill in the Header information, directly accessible via host pinned memory - - RecordBase::m_alloc_ptr->m_record = this; - - strncpy(RecordBase::m_alloc_ptr->m_label, arg_label.c_str(), - SharedAllocationHeader::maximum_label_length); - // Set last element zero, in case c_str is too long - RecordBase::m_alloc_ptr - ->m_label[SharedAllocationHeader::maximum_label_length - 1] = (char)0; -} - -//---------------------------------------------------------------------------- - -void* SharedAllocationRecord:: - allocate_tracked(const Kokkos::Experimental::HIPSpace& arg_space, - const std::string& arg_alloc_label, - const size_t arg_alloc_size) { - if (!arg_alloc_size) return nullptr; - - SharedAllocationRecord* const r = - allocate(arg_space, arg_alloc_label, arg_alloc_size); - - RecordBase::increment(r); - - return r->data(); -} - -void SharedAllocationRecord::deallocate_tracked(void* const - arg_alloc_ptr) { - if (arg_alloc_ptr != nullptr) { - SharedAllocationRecord* const r = get_record(arg_alloc_ptr); - - RecordBase::decrement(r); - } -} - -void* SharedAllocationRecord:: - reallocate_tracked(void* const arg_alloc_ptr, const size_t arg_alloc_size) { - SharedAllocationRecord* const r_old = get_record(arg_alloc_ptr); - SharedAllocationRecord* const r_new = - allocate(r_old->m_space, r_old->get_label(), arg_alloc_size); - - Kokkos::Impl::DeepCopy( - r_new->data(), r_old->data(), std::min(r_old->size(), r_new->size())); - - RecordBase::increment(r_new); - RecordBase::decrement(r_old); - - return r_new->data(); -} - -void* SharedAllocationRecord:: - allocate_tracked(const Kokkos::Experimental::HIPHostPinnedSpace& arg_space, - const std::string& arg_alloc_label, - const size_t arg_alloc_size) { - if (!arg_alloc_size) return nullptr; - - SharedAllocationRecord* const r = - allocate(arg_space, arg_alloc_label, arg_alloc_size); - - RecordBase::increment(r); - - return r->data(); -} - -void SharedAllocationRecord::deallocate_tracked(void* const - arg_alloc_ptr) { - if (arg_alloc_ptr) { - SharedAllocationRecord* const r = get_record(arg_alloc_ptr); - - RecordBase::decrement(r); - } -} - -void* SharedAllocationRecord:: - reallocate_tracked(void* const arg_alloc_ptr, const size_t arg_alloc_size) { - SharedAllocationRecord* const r_old = get_record(arg_alloc_ptr); - SharedAllocationRecord* const r_new = - allocate(r_old->m_space, r_old->get_label(), arg_alloc_size); - - using HIPHostPinnedSpace = Kokkos::Experimental::HIPHostPinnedSpace; - Kokkos::Impl::DeepCopy( - r_new->data(), r_old->data(), std::min(r_old->size(), r_new->size())); - - RecordBase::increment(r_new); - RecordBase::decrement(r_old); - - return r_new->data(); -} - -//---------------------------------------------------------------------------- - -SharedAllocationRecord* -SharedAllocationRecord::get_record( - void* alloc_ptr) { - using Header = SharedAllocationHeader; - using RecordHIP = - SharedAllocationRecord; - - // Copy the header from the allocation - Header head; - - Header const* const head_hip = - alloc_ptr ? Header::get_header(alloc_ptr) : nullptr; - - if (alloc_ptr) { - Kokkos::Impl::DeepCopy( - &head, head_hip, sizeof(SharedAllocationHeader)); - } - - RecordHIP* const record = - alloc_ptr ? static_cast(head.m_record) : nullptr; - - if (!alloc_ptr || record->m_alloc_ptr != head_hip) { - Kokkos::Impl::throw_runtime_exception(std::string( - "Kokkos::Impl::SharedAllocationRecord< Kokkos::Experimental::HIPSpace " - ", void >::get_record ERROR")); - } - - return record; -} - -SharedAllocationRecord* -SharedAllocationRecord::get_record(void* alloc_ptr) { - using Header = SharedAllocationHeader; - using RecordHIP = - SharedAllocationRecord; - - Header* const h = - alloc_ptr ? reinterpret_cast(alloc_ptr) - 1 : nullptr; - - if (!alloc_ptr || h->m_record->m_alloc_ptr != h) { - Kokkos::Impl::throw_runtime_exception(std::string( - "Kokkos::Impl::SharedAllocationRecord< " - "Kokkos::Experimental::HIPHostPinnedSpace , void >::get_record ERROR")); - } - - return static_cast(h->m_record); -} - -// Iterate records to print orphaned memory ... -void SharedAllocationRecord:: - print_records(std::ostream& s, const Kokkos::Experimental::HIPSpace&, - bool detail) { -#ifdef KOKKOS_ENABLE_DEBUG - SharedAllocationRecord* r = &s_root_record; - - char buffer[256]; - - SharedAllocationHeader head; - - if (detail) { - do { - if (r->m_alloc_ptr) { - Kokkos::Impl::DeepCopy( - &head, r->m_alloc_ptr, sizeof(SharedAllocationHeader)); - } else { - head.m_label[0] = 0; - } - - // Formatting dependent on sizeof(uintptr_t) - const char* format_string; - - if (sizeof(uintptr_t) == sizeof(unsigned long)) { - format_string = - "HIP addr( 0x%.12lx ) list( 0x%.12lx 0x%.12lx ) extent[ 0x%.12lx + " - "%.8ld ] count(%d) dealloc(0x%.12lx) %s\n"; - } else if (sizeof(uintptr_t) == sizeof(unsigned long long)) { - format_string = - "HIP addr( 0x%.12llx ) list( 0x%.12llx 0x%.12llx ) extent[ " - "0x%.12llx + %.8ld ] count(%d) dealloc(0x%.12llx) %s\n"; - } - - snprintf(buffer, 256, format_string, reinterpret_cast(r), - reinterpret_cast(r->m_prev), - reinterpret_cast(r->m_next), - reinterpret_cast(r->m_alloc_ptr), r->m_alloc_size, - r->m_count, reinterpret_cast(r->m_dealloc), - head.m_label); - s << buffer; - r = r->m_next; - } while (r != &s_root_record); - } else { - do { - if (r->m_alloc_ptr) { - Kokkos::Impl::DeepCopy( - &head, r->m_alloc_ptr, sizeof(SharedAllocationHeader)); - - // Formatting dependent on sizeof(uintptr_t) - const char* format_string; - - if (sizeof(uintptr_t) == sizeof(unsigned long)) { - format_string = "HIP [ 0x%.12lx + %ld ] %s\n"; - } else if (sizeof(uintptr_t) == sizeof(unsigned long long)) { - format_string = "HIP [ 0x%.12llx + %ld ] %s\n"; - } - - snprintf(buffer, 256, format_string, - reinterpret_cast(r->data()), r->size(), - head.m_label); - } else { - snprintf(buffer, 256, "HIP [ 0 + 0 ]\n"); - } - s << buffer; - r = r->m_next; - } while (r != &s_root_record); - } -#else - (void)s; - (void)detail; - throw_runtime_exception( - "Kokkos::Impl::SharedAllocationRecord::print_records" - " only works with KOKKOS_ENABLE_DEBUG enabled"); -#endif + this->base_t::_fill_host_accessible_header_info(*RecordBase::m_alloc_ptr, + arg_label); } } // namespace Impl @@ -680,63 +421,22 @@ void HIP::impl_initialize(const HIP::SelectDevice config) { void HIP::impl_finalize() { Impl::HIPInternal::singleton().finalize(); } HIP::HIP() - : m_space_instance(&Impl::HIPInternal::singleton()), m_counter(nullptr) { + : m_space_instance(&Impl::HIPInternal::singleton(), + [](Impl::HIPInternal*) {}) { Impl::HIPInternal::singleton().verify_is_initialized( "HIP instance constructor"); } HIP::HIP(hipStream_t const stream) - : m_space_instance(new Impl::HIPInternal), m_counter(new int(1)) { + : m_space_instance(new Impl::HIPInternal, [](Impl::HIPInternal* ptr) { + ptr->finalize(); + delete ptr; + }) { Impl::HIPInternal::singleton().verify_is_initialized( "HIP instance constructor"); m_space_instance->initialize(Impl::HIPInternal::singleton().m_hipDev, stream); } -KOKKOS_FUNCTION HIP::HIP(HIP&& other) noexcept { - m_space_instance = other.m_space_instance; - other.m_space_instance = nullptr; - m_counter = other.m_counter; - other.m_counter = nullptr; -} - -KOKKOS_FUNCTION HIP::HIP(HIP const& other) - : m_space_instance(other.m_space_instance), m_counter(other.m_counter) { -#ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HIP_GPU - if (m_counter) Kokkos::atomic_add(m_counter, 1); -#endif -} - -KOKKOS_FUNCTION HIP& HIP::operator=(HIP&& other) noexcept { - m_space_instance = other.m_space_instance; - other.m_space_instance = nullptr; - m_counter = other.m_counter; - other.m_counter = nullptr; - - return *this; -} - -KOKKOS_FUNCTION HIP& HIP::operator=(HIP const& other) { - m_space_instance = other.m_space_instance; - m_counter = other.m_counter; -#ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HIP_GPU - if (m_counter) Kokkos::atomic_add(m_counter, 1); -#endif - - return *this; -} - -KOKKOS_FUNCTION HIP::~HIP() noexcept { -#ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HIP_GPU - if (m_counter == nullptr) return; - int const count = Kokkos::atomic_fetch_sub(m_counter, 1); - if (count == 1) { - delete m_counter; - m_space_instance->finalize(); - delete m_space_instance; - } -#endif -} - void HIP::print_configuration(std::ostream& s, const bool) { Impl::HIPInternal::singleton().print_configuration(s); } @@ -810,3 +510,26 @@ void HIPSpaceInitializer::print_configuration(std::ostream& msg, } // namespace Impl } // namespace Kokkos + +//============================================================================== +// {{{1 + +#include + +namespace Kokkos { +namespace Impl { + +// To avoid additional compilation cost for something that's (mostly?) not +// performance sensitive, we explicity instantiate these CRTP base classes here, +// where we have access to the associated *_timpl.hpp header files. +template class HostInaccessibleSharedAllocationRecordCommon< + Kokkos::Experimental::HIPSpace>; +template class SharedAllocationRecordCommon; +template class SharedAllocationRecordCommon< + Kokkos::Experimental::HIPHostPinnedSpace>; + +} // end namespace Impl +} // end namespace Kokkos + +// end Explicit instantiations of CRTP Base classes }}}1 +//============================================================================== diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Team.hpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Team.hpp index 7571510c31..fe52886ced 100644 --- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Team.hpp +++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Team.hpp @@ -644,13 +644,14 @@ KOKKOS_INLINE_FUNCTION thread, count); } -template -KOKKOS_INLINE_FUNCTION - Impl::ThreadVectorRangeBoundariesStruct - ThreadVectorRange(const Impl::HIPTeamMember& thread, iType arg_begin, - iType arg_end) { +template +KOKKOS_INLINE_FUNCTION Impl::ThreadVectorRangeBoundariesStruct< + typename std::common_type::type, Impl::HIPTeamMember> +ThreadVectorRange(const Impl::HIPTeamMember& thread, iType1 arg_begin, + iType2 arg_end) { + using iType = typename std::common_type::type; return Impl::ThreadVectorRangeBoundariesStruct( - thread, arg_begin, arg_end); + thread, iType(arg_begin), iType(arg_end)); } KOKKOS_INLINE_FUNCTION @@ -961,7 +962,7 @@ KOKKOS_INLINE_FUNCTION //---------------------------------------------------------------------------- -/** \brief Intra-thread vector parallel exclusive prefix sum. +/** \brief Intra-thread vector parallel scan with reducer. * * Executes closure(iType i, ValueType & val, bool final) for each i=[0..N) * @@ -969,22 +970,21 @@ KOKKOS_INLINE_FUNCTION * thread and a scan operation is performed. * The last call to closure has final == true. */ -template -KOKKOS_INLINE_FUNCTION void parallel_scan( - const Impl::ThreadVectorRangeBoundariesStruct& - loop_boundaries, - const Closure& closure) { +template +KOKKOS_INLINE_FUNCTION + typename std::enable_if::value>::type + parallel_scan(const Impl::ThreadVectorRangeBoundariesStruct< + iType, Impl::HIPTeamMember>& loop_boundaries, + const Closure& closure, const ReducerType& reducer) { #ifdef __HIP_DEVICE_COMPILE__ - // Extract value_type from closure - - using value_type = typename Kokkos::Impl::FunctorAnalysis< - Kokkos::Impl::FunctorPatternInterface::SCAN, void, Closure>::value_type; + using value_type = typename ReducerType::value_type; + value_type accum; + reducer.init(accum); + const value_type identity = accum; // Loop through boundaries by vector-length chunks // must scan at each iteration - value_type accum = 0; - // All thread "lanes" must loop the same number of times. // Determine an loop end for all thread "lanes." // Requires: @@ -997,47 +997,72 @@ KOKKOS_INLINE_FUNCTION void parallel_scan( const int end = loop_boundaries.end + (rem ? blockDim.x - rem : 0); for (int i = threadIdx.x; i < end; i += blockDim.x) { - value_type val = 0; + value_type val = identity; - // First acquire per-lane contributions: - if (i < loop_boundaries.end) closure(i, val, false); + // First acquire per-lane contributions. + // This sets i's val to i-1's contribution + // to make the latter in_place_shfl_up an + // exclusive scan -- the final accumulation + // of i's val will be included in the second + // closure call later. + if (i < loop_boundaries.end && threadIdx.x > 0) closure(i - 1, val, false); - value_type sval = val; - - // Bottom up inclusive scan in triangular pattern + // Bottom up exclusive scan in triangular pattern // where each HIP thread is the root of a reduction tree // from the zeroth "lane" to itself. // [t] += [t-1] if t >= 1 // [t] += [t-2] if t >= 2 // [t] += [t-4] if t >= 4 // ... - + // This differs from the non-reducer overload, where an inclusive scan was + // implemented, because in general the binary operator cannot be inverted + // and we would not be able to remove the inclusive contribution by + // inversion. for (int j = 1; j < static_cast(blockDim.x); j <<= 1) { - value_type tmp = 0; - ::Kokkos::Experimental::Impl::in_place_shfl_up(tmp, sval, j, blockDim.x); + value_type tmp = identity; + ::Kokkos::Experimental::Impl::in_place_shfl_up(tmp, val, j, blockDim.x); if (j <= static_cast(threadIdx.x)) { - sval += tmp; + reducer.join(val, tmp); } } - // Include accumulation and remove value for exclusive scan: - val = accum + sval - val; + // Include accumulation + reducer.join(val, accum); - // Provide exclusive scan value: + // Update i's contribution into the val + // and add it to accum for next round if (i < loop_boundaries.end) closure(i, val, true); - - // Accumulate the last value in the inclusive scan: - ::Kokkos::Experimental::Impl::in_place_shfl(sval, sval, blockDim.x - 1, + ::Kokkos::Experimental::Impl::in_place_shfl(accum, val, blockDim.x - 1, blockDim.x); - - accum += sval; } #else (void)loop_boundaries; (void)closure; + (void)reducer; #endif } +//---------------------------------------------------------------------------- + +/** \brief Intra-thread vector parallel exclusive prefix sum. + * + * Executes closure(iType i, ValueType & val, bool final) for each i=[0..N) + * + * The range [0..N) is mapped to all vector lanes in the + * thread and a scan operation is performed. + * The last call to closure has final == true. + */ +template +KOKKOS_INLINE_FUNCTION void parallel_scan( + const Impl::ThreadVectorRangeBoundariesStruct& + loop_boundaries, + const Closure& closure) { + using value_type = typename Kokkos::Impl::FunctorAnalysis< + Kokkos::Impl::FunctorPatternInterface::SCAN, void, Closure>::value_type; + value_type dummy; + parallel_scan(loop_boundaries, closure, Kokkos::Sum(dummy)); +} + } // namespace Kokkos namespace Kokkos { diff --git a/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp b/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp index 140376425c..b7d8e62f69 100644 --- a/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp +++ b/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp @@ -48,17 +48,11 @@ #include #include - +#include #include #include -#include #include -#if defined(KOKKOS_ENABLE_CUDA) || \ - (defined(__HIPCC__) && defined(KOKKOS_ENABLE_HIP)) -#include -#endif - namespace Kokkos { // ------------------------------------------------------------------ // @@ -74,22 +68,14 @@ enum class Iterate template struct default_outer_direction { - using type = Iterate; -#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP) - static constexpr Iterate value = Iterate::Left; -#else + using type = Iterate; static constexpr Iterate value = Iterate::Right; -#endif }; template struct default_inner_direction { - using type = Iterate; -#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP) - static constexpr Iterate value = Iterate::Left; -#else + using type = Iterate; static constexpr Iterate value = Iterate::Right; -#endif }; // Iteration Pattern @@ -179,6 +165,25 @@ constexpr NVCC_WONT_LET_ME_CALL_YOU_Array to_array_potentially_narrowing( } return a; } + +struct TileSizeProperties { + int max_threads; + int default_largest_tile_size; + int default_tile_size; + int max_total_tile_size; +}; + +template +TileSizeProperties get_tile_size_properties(const ExecutionSpace&) { + // Host settings + TileSizeProperties properties; + properties.max_threads = std::numeric_limits::max(); + properties.default_largest_tile_size = 0; + properties.default_tile_size = 2; + properties.max_total_tile_size = std::numeric_limits::max(); + return properties; +} + } // namespace Impl // multi-dimensional iteration pattern @@ -208,7 +213,7 @@ struct MDRangePolicy : public Kokkos::Impl::PolicyTraits { using launch_bounds = typename traits::launch_bounds; using member_type = typename range_policy::member_type; - enum { rank = static_cast(iteration_pattern::rank) }; + static constexpr int rank = iteration_pattern::rank; using index_type = typename traits::index_type; using array_index_type = std::int64_t; @@ -231,37 +236,20 @@ struct MDRangePolicy : public Kokkos::Impl::PolicyTraits { point_type m_tile_end = {}; index_type m_num_tiles = 1; index_type m_prod_tile_dims = 1; + bool m_tune_tile_size = false; - /* - // NDE enum impl definition alternative - replace static constexpr int ? - enum { outer_direction = static_cast ( - (iteration_pattern::outer_direction != Iterate::Default) - ? iteration_pattern::outer_direction - : default_outer_direction< typename traits::execution_space>::value ) }; - - enum { inner_direction = static_cast ( - iteration_pattern::inner_direction != Iterate::Default - ? iteration_pattern::inner_direction - : default_inner_direction< typename traits::execution_space>::value ) }; - - enum { Right = static_cast( Iterate::Right ) }; - enum { Left = static_cast( Iterate::Left ) }; - */ - // static constexpr int rank = iteration_pattern::rank; - - static constexpr int outer_direction = static_cast( + static constexpr auto outer_direction = (iteration_pattern::outer_direction != Iterate::Default) ? iteration_pattern::outer_direction - : default_outer_direction::value); + : default_outer_direction::value; - static constexpr int inner_direction = static_cast( + static constexpr auto inner_direction = iteration_pattern::inner_direction != Iterate::Default ? iteration_pattern::inner_direction - : default_inner_direction::value); + : default_inner_direction::value; - // Ugly ugly workaround intel 14 not handling scoped enum correctly - static constexpr int Right = static_cast(Iterate::Right); - static constexpr int Left = static_cast(Iterate::Left); + static constexpr auto Right = Iterate::Right; + static constexpr auto Left = Iterate::Left; KOKKOS_INLINE_FUNCTION const typename traits::execution_space& space() const { return m_space; @@ -320,7 +308,7 @@ struct MDRangePolicy : public Kokkos::Impl::PolicyTraits { point_type const& lower, point_type const& upper, tile_type const& tile = tile_type{}) : m_space(work_space), m_lower(lower), m_upper(upper), m_tile(tile) { - init(); + init_helper(Impl::get_tile_size_properties(work_space)); } template { m_tile(p.m_tile), m_tile_end(p.m_tile_end), m_num_tiles(p.m_num_tiles), - m_prod_tile_dims(p.m_prod_tile_dims) {} + m_prod_tile_dims(p.m_prod_tile_dims), + m_tune_tile_size(p.m_tune_tile_size) {} + + void impl_change_tile_size(const point_type& tile) { + m_tile = tile; + init_helper(Impl::get_tile_size_properties(m_space)); + } + bool impl_tune_tile_size() const { return m_tune_tile_size; } private: - void init() { - // Host - if (true -#if defined(KOKKOS_ENABLE_CUDA) - && !std::is_same::value -#endif -#if defined(KOKKOS_ENABLE_HIP) - && !std::is_same::value -#endif - ) { - index_type span; - for (int i = 0; i < rank; ++i) { - span = m_upper[i] - m_lower[i]; - if (m_tile[i] <= 0) { - if (((int)inner_direction == (int)Right && (i < rank - 1)) || - ((int)inner_direction == (int)Left && (i > 0))) { - m_tile[i] = 2; - } else { - m_tile[i] = (span == 0 ? 1 : span); - } - } - m_tile_end[i] = - static_cast((span + m_tile[i] - 1) / m_tile[i]); - m_num_tiles *= m_tile_end[i]; - m_prod_tile_dims *= m_tile[i]; - } + void init_helper(Impl::TileSizeProperties properties) { + m_prod_tile_dims = 1; + int increment = 1; + int rank_start = 0; + int rank_end = rank; + if (inner_direction == Iterate::Right) { + increment = -1; + rank_start = rank - 1; + rank_end = -1; } -#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP) - else // Cuda or HIP - { - index_type span; - int increment = 1; - int rank_start = 0; - int rank_end = rank; - if ((int)inner_direction == (int)Right) { - increment = -1; - rank_start = rank - 1; - rank_end = -1; - } - bool is_cuda_exec_space = -#if defined(KOKKOS_ENABLE_CUDA) - std::is_same::value; -#else - false; -#endif - for (int i = rank_start; i != rank_end; i += increment) { - span = m_upper[i] - m_lower[i]; - if (m_tile[i] <= 0) { - // TODO: determine what is a good default tile size for Cuda and HIP - // may be rank dependent - if (((int)inner_direction == (int)Right && (i < rank - 1)) || - ((int)inner_direction == (int)Left && (i > 0))) { - if (m_prod_tile_dims < 256) { - m_tile[i] = (is_cuda_exec_space) ? 2 : 4; - } else { - m_tile[i] = 1; - } + for (int i = rank_start; i != rank_end; i += increment) { + const index_type length = m_upper[i] - m_lower[i]; + if (m_tile[i] <= 0) { + m_tune_tile_size = true; + if ((inner_direction == Iterate::Right && (i < rank - 1)) || + (inner_direction == Iterate::Left && (i > 0))) { + if (m_prod_tile_dims * properties.default_tile_size < + static_cast(properties.max_total_tile_size)) { + m_tile[i] = properties.default_tile_size; } else { - m_tile[i] = 16; + m_tile[i] = 1; } - } - m_tile_end[i] = - static_cast((span + m_tile[i] - 1) / m_tile[i]); - m_num_tiles *= m_tile_end[i]; - m_prod_tile_dims *= m_tile[i]; - } - if (m_prod_tile_dims > - 1024) { // Match Cuda restriction for ParallelReduce; 1024,1024,64 - // max per dim (Kepler), but product num_threads < 1024 - if (is_cuda_exec_space) { - printf(" Tile dimensions exceed Cuda limits\n"); - Kokkos::abort( - "Cuda ExecSpace Error: MDRange tile dims exceed maximum number " - "of threads per block - choose smaller tile dims"); } else { - printf(" Tile dimensions exceed HIP limits\n"); - Kokkos::abort( - "HIP ExecSpace Error: MDRange tile dims exceed maximum number of " - "threads per block - choose smaller tile dims"); + m_tile[i] = properties.default_largest_tile_size == 0 + ? std::max(length, 1) + : properties.default_largest_tile_size; } } + m_tile_end[i] = + static_cast((length + m_tile[i] - 1) / m_tile[i]); + m_num_tiles *= m_tile_end[i]; + m_prod_tile_dims *= m_tile[i]; + } + if (m_prod_tile_dims > static_cast(properties.max_threads)) { + printf(" Product of tile dimensions exceed maximum limit: %d\n", + static_cast(properties.max_threads)); + Kokkos::abort( + "ExecSpace Error: MDRange tile dims exceed maximum number " + "of threads per block - choose smaller tile dims"); } -#endif } }; diff --git a/lib/kokkos/core/src/Kokkos_AnonymousSpace.hpp b/lib/kokkos/core/src/Kokkos_AnonymousSpace.hpp index 8e226a078d..fb94049d7a 100644 --- a/lib/kokkos/core/src/Kokkos_AnonymousSpace.hpp +++ b/lib/kokkos/core/src/Kokkos_AnonymousSpace.hpp @@ -104,20 +104,6 @@ struct MemorySpaceAccess { enum : bool { deepcopy = true }; }; -template -struct VerifyExecutionCanAccessMemorySpace { - enum { value = 1 }; - KOKKOS_INLINE_FUNCTION static void verify(void) {} - KOKKOS_INLINE_FUNCTION static void verify(const void *) {} -}; - -template -struct VerifyExecutionCanAccessMemorySpace { - enum { value = 1 }; - KOKKOS_INLINE_FUNCTION static void verify(void) {} - KOKKOS_INLINE_FUNCTION static void verify(const void *) {} -}; - } // namespace Impl } // namespace Kokkos diff --git a/lib/kokkos/core/src/Kokkos_Complex.hpp b/lib/kokkos/core/src/Kokkos_Complex.hpp index fb2925a066..6578723fc8 100644 --- a/lib/kokkos/core/src/Kokkos_Complex.hpp +++ b/lib/kokkos/core/src/Kokkos_Complex.hpp @@ -45,14 +45,13 @@ #define KOKKOS_COMPLEX_HPP #include +#include #include +#include #include +#include #include -#ifdef KOKKOS_ENABLE_SYCL -#include -#endif - namespace Kokkos { /// \class complex @@ -220,10 +219,11 @@ class // Conditional noexcept, just in case RType throws on divide-by-zero KOKKOS_CONSTEXPR_14 KOKKOS_INLINE_FUNCTION complex& operator/=( const complex& y) noexcept(noexcept(RealType{} / RealType{})) { + using Kokkos::Experimental::fabs; // Scale (by the "1-norm" of y) to avoid unwarranted overflow. // If the real part is +/-Inf and the imaginary part is -/+Inf, // this won't change the result. - const RealType s = std::fabs(y.real()) + std::fabs(y.imag()); + const RealType s = fabs(y.real()) + fabs(y.imag()); // If s is 0, then y is zero, so x/y == real(x)/0 + i*imag(x)/0. // In that case, the relation x/y == (x/s) / (y/s) doesn't hold, @@ -248,10 +248,11 @@ class KOKKOS_INLINE_FUNCTION complex& operator/=( const std::complex& y) noexcept(noexcept(RealType{} / RealType{})) { + using Kokkos::Experimental::fabs; // Scale (by the "1-norm" of y) to avoid unwarranted overflow. // If the real part is +/-Inf and the imaginary part is -/+Inf, // this won't change the result. - const RealType s = std::fabs(y.real()) + std::fabs(y.imag()); + const RealType s = fabs(y.real()) + fabs(y.imag()); // If s is 0, then y is zero, so x/y == real(x)/0 + i*imag(x)/0. // In that case, the relation x/y == (x/s) / (y/s) doesn't hold, @@ -693,35 +694,96 @@ KOKKOS_INLINE_FUNCTION RealType real(const complex& x) noexcept { return x.real(); } +//! Constructs a complex number from magnitude and phase angle +template +KOKKOS_INLINE_FUNCTION complex polar(const T& r, const T& theta = T()) { + using Kokkos::Experimental::cos; + using Kokkos::Experimental::sin; + KOKKOS_EXPECTS(r >= 0); + return complex(r * cos(theta), r * sin(theta)); +} + //! Absolute value (magnitude) of a complex number. template KOKKOS_INLINE_FUNCTION RealType abs(const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::hypot; -#else - using std::hypot; -#endif + using Kokkos::Experimental::hypot; return hypot(x.real(), x.imag()); } //! Power of a complex number -template -KOKKOS_INLINE_FUNCTION Kokkos::complex pow(const complex& x, - const RealType& e) { - RealType r = abs(x); -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::atan; - using cl::sycl::cos; - using cl::sycl::pow; - using cl::sycl::sin; -#else - using std::atan; - using std::cos; - using std::pow; - using std::sin; -#endif - RealType phi = atan(x.imag() / x.real()); - return pow(r, e) * Kokkos::complex(cos(phi * e), sin(phi * e)); +template +KOKKOS_INLINE_FUNCTION complex pow(const complex& x, const T& y) { + using Kokkos::Experimental::atan2; + using Kokkos::Experimental::pow; + T r = abs(x); + T theta = atan2(x.imag(), x.real()); + return polar(pow(r, y), y * theta); +} + +template +KOKKOS_INLINE_FUNCTION complex pow(const T& x, const complex& y) { + return pow(complex(x), y); +} + +template +KOKKOS_INLINE_FUNCTION complex pow(const complex& x, + const complex& y) { + using Kokkos::Experimental::log; + + return x == T() ? T() : exp(y * log(x)); +} + +namespace Impl { +// NOTE promote would also be useful for math functions +template ::value> +struct promote { + using type = double; +}; +template +struct promote {}; +template <> +struct promote { + using type = long double; +}; +template <> +struct promote { + using type = double; +}; +template <> +struct promote { + using type = float; +}; +template +using promote_t = typename promote::type; +template +struct promote_2 { + using type = decltype(promote_t() + promote_t()); +}; +template +using promote_2_t = typename promote_2::type; +} // namespace Impl + +template ::value>> +KOKKOS_INLINE_FUNCTION complex> pow( + const T& x, const complex& y) { + using type = Impl::promote_2_t; + return pow(type(x), complex(y)); +} + +template ::value>> +KOKKOS_INLINE_FUNCTION complex> pow(const complex& x, + const U& y) { + using type = Impl::promote_2_t; + return pow(complex(x), type(y)); +} + +template +KOKKOS_INLINE_FUNCTION complex> pow( + const complex& x, const complex& y) { + using type = Impl::promote_2_t; + return pow(complex(x), complex(y)); } //! Square root of a complex number. This is intended to match the stdc++ @@ -729,26 +791,21 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex pow(const complex& x, template KOKKOS_INLINE_FUNCTION Kokkos::complex sqrt( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::abs; - using cl::sycl::sqrt; -#else - using std::abs; - using std::sqrt; -#endif + using Kokkos::Experimental::fabs; + using Kokkos::Experimental::sqrt; RealType r = x.real(); RealType i = x.imag(); if (r == RealType()) { - RealType t = sqrt(abs(i) / 2); + RealType t = sqrt(fabs(i) / 2); return Kokkos::complex(t, i < RealType() ? -t : t); } else { - RealType t = sqrt(2 * (abs(x) + abs(r))); + RealType t = sqrt(2 * (abs(x) + fabs(r))); RealType u = t / 2; - return r > RealType() - ? Kokkos::complex(u, i / t) - : Kokkos::complex(abs(i) / t, i < RealType() ? -u : u); + return r > RealType() ? Kokkos::complex(u, i / t) + : Kokkos::complex(fabs(i) / t, + i < RealType() ? -u : u); } } @@ -762,15 +819,9 @@ KOKKOS_INLINE_FUNCTION complex conj( //! Exponential of a complex number. template KOKKOS_INLINE_FUNCTION complex exp(const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::cos; - using cl::sycl::exp; - using cl::sycl::sin; -#else - using std::cos; - using std::exp; - using std::sin; -#endif + using Kokkos::Experimental::cos; + using Kokkos::Experimental::exp; + using Kokkos::Experimental::sin; return exp(x.real()) * complex(cos(x.imag()), sin(x.imag())); } @@ -778,14 +829,9 @@ KOKKOS_INLINE_FUNCTION complex exp(const complex& x) { template KOKKOS_INLINE_FUNCTION Kokkos::complex log( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::atan; - using cl::sycl::log; -#else - using std::atan; - using std::log; -#endif - RealType phi = atan(x.imag() / x.real()); + using Kokkos::Experimental::atan2; + using Kokkos::Experimental::log; + RealType phi = atan2(x.imag(), x.real()); return Kokkos::complex(log(abs(x)), phi); } @@ -793,17 +839,10 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex log( template KOKKOS_INLINE_FUNCTION Kokkos::complex sin( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::cos; - using cl::sycl::cosh; - using cl::sycl::sin; - using cl::sycl::sinh; -#else - using std::cos; - using std::cosh; - using std::sin; - using std::sinh; -#endif + using Kokkos::Experimental::cos; + using Kokkos::Experimental::cosh; + using Kokkos::Experimental::sin; + using Kokkos::Experimental::sinh; return Kokkos::complex(sin(x.real()) * cosh(x.imag()), cos(x.real()) * sinh(x.imag())); } @@ -812,17 +851,10 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex sin( template KOKKOS_INLINE_FUNCTION Kokkos::complex cos( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::cos; - using cl::sycl::cosh; - using cl::sycl::sin; - using cl::sycl::sinh; -#else - using std::cos; - using std::cosh; - using std::sin; - using std::sinh; -#endif + using Kokkos::Experimental::cos; + using Kokkos::Experimental::cosh; + using Kokkos::Experimental::sin; + using Kokkos::Experimental::sinh; return Kokkos::complex(cos(x.real()) * cosh(x.imag()), -sin(x.real()) * sinh(x.imag())); } @@ -838,17 +870,10 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex tan( template KOKKOS_INLINE_FUNCTION Kokkos::complex sinh( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::cos; - using cl::sycl::cosh; - using cl::sycl::sin; - using cl::sycl::sinh; -#else - using std::cos; - using std::cosh; - using std::sin; - using std::sinh; -#endif + using Kokkos::Experimental::cos; + using Kokkos::Experimental::cosh; + using Kokkos::Experimental::sin; + using Kokkos::Experimental::sinh; return Kokkos::complex(sinh(x.real()) * cos(x.imag()), cosh(x.real()) * sin(x.imag())); } @@ -857,17 +882,10 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex sinh( template KOKKOS_INLINE_FUNCTION Kokkos::complex cosh( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::cos; - using cl::sycl::cosh; - using cl::sycl::sin; - using cl::sycl::sinh; -#else - using std::cos; - using std::cosh; - using std::sin; - using std::sinh; -#endif + using Kokkos::Experimental::cos; + using Kokkos::Experimental::cosh; + using Kokkos::Experimental::sin; + using Kokkos::Experimental::sinh; return Kokkos::complex(cosh(x.real()) * cos(x.imag()), sinh(x.real()) * sin(x.imag())); } @@ -898,13 +916,8 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex acosh( template KOKKOS_INLINE_FUNCTION Kokkos::complex atanh( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::atan2; - using cl::sycl::log; -#else - using std::atan2; - using std::log; -#endif + using Kokkos::Experimental::atan2; + using Kokkos::Experimental::log; const RealType i2 = x.imag() * x.imag(); const RealType r = RealType(1.0) - i2 - x.real() * x.real(); @@ -933,12 +946,7 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex asin( template KOKKOS_INLINE_FUNCTION Kokkos::complex acos( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::acos; - -#else - using std::acos; -#endif + using Kokkos::Experimental::acos; Kokkos::complex t = asin(x); RealType pi_2 = acos(RealType(0.0)); return Kokkos::complex(pi_2 - t.real(), -t.imag()); @@ -948,13 +956,8 @@ KOKKOS_INLINE_FUNCTION Kokkos::complex acos( template KOKKOS_INLINE_FUNCTION Kokkos::complex atan( const complex& x) { -#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_SYCL - using cl::sycl::atan2; - using cl::sycl::log; -#else - using std::atan2; - using std::log; -#endif + using Kokkos::Experimental::atan2; + using Kokkos::Experimental::log; const RealType r2 = x.real() * x.real(); const RealType i = RealType(1.0) - r2 - x.imag() * x.imag(); @@ -996,12 +999,13 @@ KOKKOS_INLINE_FUNCTION operator/(const complex& x, const complex& y) noexcept(noexcept(RealType1{} / RealType2{})) { + using Kokkos::Experimental::fabs; // Scale (by the "1-norm" of y) to avoid unwarranted overflow. // If the real part is +/-Inf and the imaginary part is -/+Inf, // this won't change the result. using common_real_type = typename std::common_type::type; - const common_real_type s = std::fabs(real(y)) + std::fabs(imag(y)); + const common_real_type s = fabs(real(y)) + fabs(imag(y)); // If s is 0, then y is zero, so x/y == real(x)/0 + i*imag(x)/0. // In that case, the relation x/y == (x/s) / (y/s) doesn't hold, @@ -1046,7 +1050,7 @@ std::istream& operator>>(std::istream& is, complex& x) { } template -struct reduction_identity > { +struct reduction_identity> { using t_red_ident = reduction_identity; KOKKOS_FORCEINLINE_FUNCTION constexpr static Kokkos::complex sum() noexcept { diff --git a/lib/kokkos/core/src/Kokkos_Core.hpp b/lib/kokkos/core/src/Kokkos_Core.hpp index 4dac463a66..c3771ab393 100644 --- a/lib/kokkos/core/src/Kokkos_Core.hpp +++ b/lib/kokkos/core/src/Kokkos_Core.hpp @@ -58,6 +58,7 @@ #include #include #include +#include #include #include #include @@ -86,6 +87,10 @@ struct InitArguments { int skip_device; bool disable_warnings; bool tune_internals; + bool tool_help = false; + std::string tool_lib = {}; + std::string tool_args = {}; + InitArguments(int nt = -1, int nn = -1, int dv = -1, bool dw = false, bool ti = false) : num_threads{nt}, @@ -139,6 +144,10 @@ void pre_initialize(const InitArguments& args); void post_initialize(const InitArguments& args); +void declare_configuration_metadata(const std::string& category, + const std::string& key, + const std::string& value); + } // namespace Impl bool is_initialized() noexcept; diff --git a/lib/kokkos/core/src/Kokkos_Core_fwd.hpp b/lib/kokkos/core/src/Kokkos_Core_fwd.hpp index 7502719c73..fe7eba3f6e 100644 --- a/lib/kokkos/core/src/Kokkos_Core_fwd.hpp +++ b/lib/kokkos/core/src/Kokkos_Core_fwd.hpp @@ -50,6 +50,7 @@ // and compiler environment then sets a collection of #define macros. #include +#include #include #include @@ -180,7 +181,6 @@ using DefaultHostExecutionSpace KOKKOS_IMPL_DEFAULT_HOST_EXEC_SPACE_ANNOTATION = // a given memory space. namespace Kokkos { - namespace Impl { #if defined(KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_CUDA) && \ @@ -196,16 +196,22 @@ using ActiveExecutionMemorySpace = Kokkos::HostSpace; using ActiveExecutionMemorySpace = void; #endif -template -struct VerifyExecutionCanAccessMemorySpace { - enum { value = 0 }; +template +struct MemorySpaceAccess; + +template ::accessible> +struct verify_space { + KOKKOS_FUNCTION static void check() {} }; -template -struct VerifyExecutionCanAccessMemorySpace { - enum { value = 1 }; - KOKKOS_INLINE_FUNCTION static void verify(void) {} - KOKKOS_INLINE_FUNCTION static void verify(const void *) {} +template +struct verify_space { + KOKKOS_FUNCTION static void check() { + Kokkos::abort( + "Kokkos::View ERROR: attempt to access inaccessible memory space"); + }; }; // Base class for exec space initializer factories @@ -220,13 +226,13 @@ class LogicalMemorySpace; } // namespace Kokkos -#define KOKKOS_RESTRICT_EXECUTION_TO_DATA(DATA_SPACE, DATA_PTR) \ - Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< \ - Kokkos::Impl::ActiveExecutionMemorySpace, DATA_SPACE>::verify(DATA_PTR) +#define KOKKOS_RESTRICT_EXECUTION_TO_DATA(DATA_SPACE, DATA_PTR) \ + Kokkos::Impl::verify_space::check(); -#define KOKKOS_RESTRICT_EXECUTION_TO_(DATA_SPACE) \ - Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< \ - Kokkos::Impl::ActiveExecutionMemorySpace, DATA_SPACE>::verify() +#define KOKKOS_RESTRICT_EXECUTION_TO_(DATA_SPACE) \ + Kokkos::Impl::verify_space::check(); //---------------------------------------------------------------------------- @@ -256,8 +262,7 @@ template struct ViewCopy; -template +template struct FunctorPolicyExecutionSpace; //---------------------------------------------------------------------------- diff --git a/lib/kokkos/core/src/Kokkos_Crs.hpp b/lib/kokkos/core/src/Kokkos_Crs.hpp index 4a573d82c0..1a10500b19 100644 --- a/lib/kokkos/core/src/Kokkos_Crs.hpp +++ b/lib/kokkos/core/src/Kokkos_Crs.hpp @@ -199,7 +199,7 @@ class CrsRowMapFromCounts { public: KOKKOS_INLINE_FUNCTION void operator()(index_type i, value_type& update, bool final_pass) const { - if (i < m_in.size()) { + if (i < static_cast(m_in.size())) { update += m_in(i); if (final_pass) m_out(i + 1) = update; } else if (final_pass) { diff --git a/lib/kokkos/core/src/Kokkos_Cuda.hpp b/lib/kokkos/core/src/Kokkos_Cuda.hpp index 81e11f3f12..7a218120bb 100644 --- a/lib/kokkos/core/src/Kokkos_Cuda.hpp +++ b/lib/kokkos/core/src/Kokkos_Cuda.hpp @@ -63,6 +63,7 @@ #include #include #include +#include /*--------------------------------------------------------------------------*/ @@ -198,16 +199,6 @@ class Cuda { Cuda(); - KOKKOS_FUNCTION Cuda(Cuda&& other) noexcept; - - KOKKOS_FUNCTION Cuda(const Cuda& other); - - KOKKOS_FUNCTION Cuda& operator=(Cuda&& other) noexcept; - - KOKKOS_FUNCTION Cuda& operator=(const Cuda& other); - - KOKKOS_FUNCTION ~Cuda() noexcept; - Cuda(cudaStream_t stream); //-------------------------------------------------------------------------- @@ -253,13 +244,12 @@ class Cuda { static const char* name(); inline Impl::CudaInternal* impl_internal_space_instance() const { - return m_space_instance; + return m_space_instance.get(); } uint32_t impl_instance_id() const noexcept { return 0; } private: - Impl::CudaInternal* m_space_instance; - int* m_counter; + Kokkos::Impl::HostSharedPtr m_space_instance; }; namespace Tools { @@ -319,38 +309,8 @@ struct MemorySpaceAccess -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = true }; - KOKKOS_INLINE_FUNCTION static void verify(void) {} - KOKKOS_INLINE_FUNCTION static void verify(const void*) {} -}; - -template <> -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = false }; - inline static void verify(void) { CudaSpace::access_error(); } - inline static void verify(const void* p) { CudaSpace::access_error(p); } -}; - } // namespace Impl } // namespace Kokkos -/*--------------------------------------------------------------------------*/ -/*--------------------------------------------------------------------------*/ - -#include -#include -#include -#include -#include -#include -#include - -#include -//---------------------------------------------------------------------------- - #endif /* #if defined( KOKKOS_ENABLE_CUDA ) */ #endif /* #ifndef KOKKOS_CUDA_HPP */ diff --git a/lib/kokkos/core/src/Kokkos_CudaSpace.hpp b/lib/kokkos/core/src/Kokkos_CudaSpace.hpp index fc1c0e2f8a..e10fae93c7 100644 --- a/lib/kokkos/core/src/Kokkos_CudaSpace.hpp +++ b/lib/kokkos/core/src/Kokkos_CudaSpace.hpp @@ -53,8 +53,10 @@ #include #include #include +#include #include +#include #include @@ -119,8 +121,8 @@ class CudaSpace { /*--------------------------------*/ /** \brief Error reporting for HostSpace attempt to access CudaSpace */ - static void access_error(); - static void access_error(const void* const); + KOKKOS_DEPRECATED static void access_error(); + KOKKOS_DEPRECATED static void access_error(const void* const); private: int m_device; ///< Which Cuda device @@ -128,42 +130,6 @@ class CudaSpace { static constexpr const char* m_name = "Cuda"; friend class Kokkos::Impl::SharedAllocationRecord; }; - -namespace Impl { -/// \brief Initialize lock array for arbitrary size atomics. -/// -/// Arbitrary atomics are implemented using a hash table of locks -/// where the hash value is derived from the address of the -/// object for which an atomic operation is performed. -/// This function initializes the locks to zero (unset). -void init_lock_arrays_cuda_space(); - -/// \brief Retrieve the pointer to the lock array for arbitrary size atomics. -/// -/// Arbitrary atomics are implemented using a hash table of locks -/// where the hash value is derived from the address of the -/// object for which an atomic operation is performed. -/// This function retrieves the lock array pointer. -/// If the array is not yet allocated it will do so. -int* atomic_lock_array_cuda_space_ptr(bool deallocate = false); - -/// \brief Retrieve the pointer to the scratch array for team and thread private -/// global memory. -/// -/// Team and Thread private scratch allocations in -/// global memory are acquired via locks. -/// This function retrieves the lock array pointer. -/// If the array is not yet allocated it will do so. -int* scratch_lock_array_cuda_space_ptr(bool deallocate = false); - -/// \brief Retrieve the pointer to the scratch array for unique identifiers. -/// -/// Unique identifiers in the range 0-Cuda::concurrency -/// are provided via locks. -/// This function retrieves the lock array pointer. -/// If the array is not yet allocated it will do so. -int* threadid_lock_array_cuda_space_ptr(bool deallocate = false); -} // namespace Impl } // namespace Kokkos /*--------------------------------------------------------------------------*/ @@ -313,6 +279,11 @@ class CudaHostPinnedSpace { namespace Kokkos { namespace Impl { +cudaStream_t cuda_get_deep_copy_stream(); + +const std::unique_ptr& cuda_get_deep_copy_space( + bool initialize = true); + static_assert(Kokkos::Impl::MemorySpaceAccess::assignable, ""); @@ -784,104 +755,21 @@ struct DeepCopy { namespace Kokkos { namespace Impl { -/** Running in CudaSpace attempting to access HostSpace: error */ -template <> -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = false }; - KOKKOS_INLINE_FUNCTION static void verify(void) { - Kokkos::abort("Cuda code attempted to access HostSpace memory"); - } - - KOKKOS_INLINE_FUNCTION static void verify(const void*) { - Kokkos::abort("Cuda code attempted to access HostSpace memory"); - } -}; - -/** Running in CudaSpace accessing CudaUVMSpace: ok */ -template <> -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = true }; - KOKKOS_INLINE_FUNCTION static void verify(void) {} - KOKKOS_INLINE_FUNCTION static void verify(const void*) {} -}; - -/** Running in CudaSpace accessing CudaHostPinnedSpace: ok */ -template <> -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = true }; - KOKKOS_INLINE_FUNCTION static void verify(void) {} - KOKKOS_INLINE_FUNCTION static void verify(const void*) {} -}; - -/** Running in CudaSpace attempting to access an unknown space: error */ -template -struct VerifyExecutionCanAccessMemorySpace< - typename std::enable_if::value, - Kokkos::CudaSpace>::type, - OtherSpace> { - enum : bool { value = false }; - KOKKOS_INLINE_FUNCTION static void verify(void) { - Kokkos::abort("Cuda code attempted to access unknown Space memory"); - } - - KOKKOS_INLINE_FUNCTION static void verify(const void*) { - Kokkos::abort("Cuda code attempted to access unknown Space memory"); - } -}; - -//---------------------------------------------------------------------------- -/** Running in HostSpace attempting to access CudaSpace */ -template <> -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = false }; - inline static void verify(void) { CudaSpace::access_error(); } - inline static void verify(const void* p) { CudaSpace::access_error(p); } -}; - -/** Running in HostSpace accessing CudaUVMSpace is OK */ -template <> -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = true }; - inline static void verify(void) {} - inline static void verify(const void*) {} -}; - -/** Running in HostSpace accessing CudaHostPinnedSpace is OK */ -template <> -struct VerifyExecutionCanAccessMemorySpace { - enum : bool { value = true }; - KOKKOS_INLINE_FUNCTION static void verify(void) {} - KOKKOS_INLINE_FUNCTION static void verify(const void*) {} -}; - -} // namespace Impl -} // namespace Kokkos - -//---------------------------------------------------------------------------- -//---------------------------------------------------------------------------- - -namespace Kokkos { -namespace Impl { - template <> class SharedAllocationRecord - : public SharedAllocationRecord { + : public HostInaccessibleSharedAllocationRecordCommon { private: friend class SharedAllocationRecord; + friend class SharedAllocationRecordCommon; + friend class HostInaccessibleSharedAllocationRecordCommon; using RecordBase = SharedAllocationRecord; + using base_t = + HostInaccessibleSharedAllocationRecordCommon; SharedAllocationRecord(const SharedAllocationRecord&) = delete; SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - static void deallocate(RecordBase*); - static ::cudaTextureObject_t attach_texture_object( const unsigned sizeof_alias, void* const alloc_ptr, const size_t alloc_size); @@ -890,39 +778,19 @@ class SharedAllocationRecord static RecordBase s_root_record; #endif - ::cudaTextureObject_t m_tex_obj; + ::cudaTextureObject_t m_tex_obj = 0; const Kokkos::CudaSpace m_space; protected: ~SharedAllocationRecord(); - SharedAllocationRecord() : RecordBase(), m_tex_obj(0), m_space() {} + SharedAllocationRecord() = default; SharedAllocationRecord( const Kokkos::CudaSpace& arg_space, const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &deallocate); + const RecordBase::function_type arg_dealloc = &base_t::deallocate); public: - std::string get_label() const; - - static SharedAllocationRecord* allocate(const Kokkos::CudaSpace& arg_space, - const std::string& arg_label, - const size_t arg_alloc_size); - - /**\brief Allocate tracked memory in the space */ - static void* allocate_tracked(const Kokkos::CudaSpace& arg_space, - const std::string& arg_label, - const size_t arg_alloc_size); - - /**\brief Reallocate tracked memory in the space */ - static void* reallocate_tracked(void* const arg_alloc_ptr, - const size_t arg_alloc_size); - - /**\brief Deallocate tracked memory in the space */ - static void deallocate_tracked(void* const arg_alloc_ptr); - - static SharedAllocationRecord* get_record(void* arg_alloc_ptr); - template inline ::cudaTextureObject_t attach_texture_object() { static_assert((std::is_same::value || @@ -945,57 +813,35 @@ class SharedAllocationRecord // Texture object is attached to the entire allocation range return ptr - reinterpret_cast(RecordBase::m_alloc_ptr); } - - static void print_records(std::ostream&, const Kokkos::CudaSpace&, - bool detail = false); }; template <> class SharedAllocationRecord - : public SharedAllocationRecord { + : public SharedAllocationRecordCommon { private: + friend class SharedAllocationRecordCommon; + + using base_t = SharedAllocationRecordCommon; using RecordBase = SharedAllocationRecord; SharedAllocationRecord(const SharedAllocationRecord&) = delete; SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - static void deallocate(RecordBase*); - static RecordBase s_root_record; - ::cudaTextureObject_t m_tex_obj; + ::cudaTextureObject_t m_tex_obj = 0; const Kokkos::CudaUVMSpace m_space; protected: ~SharedAllocationRecord(); - SharedAllocationRecord() : RecordBase(), m_tex_obj(0), m_space() {} + SharedAllocationRecord() = default; SharedAllocationRecord( const Kokkos::CudaUVMSpace& arg_space, const std::string& arg_label, const size_t arg_alloc_size, - const RecordBase::function_type arg_dealloc = &deallocate); + const RecordBase::function_type arg_dealloc = &base_t::deallocate); public: - std::string get_label() const; - - static SharedAllocationRecord* allocate(const Kokkos::CudaUVMSpace& arg_space, - const std::string& arg_label, - const size_t arg_alloc_size); - - /**\brief Allocate tracked memory in the space */ - static void* allocate_tracked(const Kokkos::CudaUVMSpace& arg_space, - const std::string& arg_label, - const size_t arg_alloc_size); - - /**\brief Reallocate tracked memory in the space */ - static void* reallocate_tracked(void* const arg_alloc_ptr, - const size_t arg_alloc_size); - - /**\brief Deallocate tracked memory in the space */ - static void deallocate_tracked(void* const arg_alloc_ptr); - - static SharedAllocationRecord* get_record(void* arg_alloc_ptr); - template inline ::cudaTextureObject_t attach_texture_object() { static_assert((std::is_same::value || @@ -1019,57 +865,32 @@ class SharedAllocationRecord // Texture object is attached to the entire allocation range return ptr - reinterpret_cast(RecordBase::m_alloc_ptr); } - - static void print_records(std::ostream&, const Kokkos::CudaUVMSpace&, - bool detail = false); }; template <> class SharedAllocationRecord - : public SharedAllocationRecord { + : public SharedAllocationRecordCommon { private: + friend class SharedAllocationRecordCommon; + using RecordBase = SharedAllocationRecord; + using base_t = SharedAllocationRecordCommon; SharedAllocationRecord(const SharedAllocationRecord&) = delete; SharedAllocationRecord& operator=(const SharedAllocationRecord&) = delete; - static void deallocate(RecordBase*); - static RecordBase s_root_record; const Kokkos::CudaHostPinnedSpace m_space; protected: ~SharedAllocationRecord(); - SharedAllocationRecord() : RecordBase(), m_space() {} + SharedAllocationRecord() = default; SharedAllocationRecord( const Kokkos::CudaHostPinnedSpace& arg_space, const std::string& arg_label, const size_t arg_alloc_size, const RecordBase::function_type arg_dealloc = &deallocate); - - public: - std::string get_label() const; - - static SharedAllocationRecord* allocate( - const Kokkos::CudaHostPinnedSpace& arg_space, - const std::string& arg_label, const size_t arg_alloc_size); - /**\brief Allocate tracked memory in the space */ - static void* allocate_tracked(const Kokkos::CudaHostPinnedSpace& arg_space, - const std::string& arg_label, - const size_t arg_alloc_size); - - /**\brief Reallocate tracked memory in the space */ - static void* reallocate_tracked(void* const arg_alloc_ptr, - const size_t arg_alloc_size); - - /**\brief Deallocate tracked memory in the space */ - static void deallocate_tracked(void* const arg_alloc_ptr); - - static SharedAllocationRecord* get_record(void* arg_alloc_ptr); - - static void print_records(std::ostream&, const Kokkos::CudaHostPinnedSpace&, - bool detail = false); }; } // namespace Impl diff --git a/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp b/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp index 3afe081701..55aed13670 100644 --- a/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp +++ b/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp @@ -856,11 +856,12 @@ KOKKOS_INLINE_FUNCTION_DELETED Impl::ThreadVectorRangeBoundariesStruct ThreadVectorRange(const TeamMemberType&, const iType& count) = delete; -template -KOKKOS_INLINE_FUNCTION_DELETED - Impl::ThreadVectorRangeBoundariesStruct - ThreadVectorRange(const TeamMemberType&, const iType& arg_begin, - const iType& arg_end) = delete; +template +KOKKOS_INLINE_FUNCTION_DELETED Impl::ThreadVectorRangeBoundariesStruct< + typename std::common_type::type, TeamMemberType> +ThreadVectorRange(const TeamMemberType&, const iType1& arg_begin, + const iType2& arg_end) = delete; namespace Impl { @@ -902,85 +903,6 @@ struct ParallelConstructName { } // namespace Kokkos namespace Kokkos { -namespace Experimental { - -namespace Impl { -template -struct PolicyPropertyAdaptor; - -template class Policy, - class... Properties> -struct PolicyPropertyAdaptor, - Policy> { - using policy_in_t = Policy; - static_assert(is_execution_policy::value, ""); - using policy_out_t = Policy, - typename policy_in_t::traits::occupancy_control>; -}; - -template

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